1. INTRODUCTION

OJPsych

Open Journal of Psychiatry

2161-7325

Scientific Research Publishing

10.4236/ojpsych.2013.31008

OJPsych-27404

Articles

Biomedical&Life Sciences

Genomics of schizophrenia and pharmacogenomics of antipsychotic drugs

amón

Cacabelos

¹^*Pablo

Cacabelos

¹Gjumrakch

Aliev

¹²

EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, Corunna, Spain

EuroEspes Biomedical Research Center, Institute for CNS Disorders and Genomic Medicine, EuroEspes Chair of Biotechnology and Genomics, Camilo José Cela University, Corunna, Spain&Gally International Biomedical Research Consulting LLC, San Antonio, USA

* E-mail:rcacabelos@euroespes.com(AC);

29012013

03014613913 October 201215 November 2012 24 November 2012

2014

This work is licensed under the Creative Commons Attribution International License (CC BY). http://creativecommons.org/licenses/by/4.0/

Antipsychotic drugs are the neuroleptics currently used in the treatment of schizophrenia (SCZ) and psychotic disorders. SCZ has a heritability estimated at 70% - 90%; and pharmacogenomics accounts for 60% - 90% variability in the pharmacokinetics and pharmacodynamics of psychotropic drugs. Personalized therapeutics based on individual genomic profiles in SCZ entails the characterization of 5 types of gene clusters and their related metabolomic profiles: 1) genes associated with disease pathogenesis; 2) genes associated with the mechanism of action of drugs; 3) genes associated with drug metabolism (phase I and II reactions); 4) genes associated with drug transporters; and 5) pleiotropic genes involved in multifaceted cascades and metabolic reactions. Genetic studies in SCZ have revealed the presence of chromosome anomalies, copy number variants, multiple single-nucleotide polymorphisms of susceptibility distributed across the human genome, aberrant single-nucleotide polymorphisms in microRNA genes, mitochondrial DNA mutations, and epigenetic phenomena. Pharmacogenetic studies of psychotropic drug response have focused on determining the relationship between variation in specific candidate genes and the positive and adverse effects of drug treatment. Approximately 18% of neuroleptics are major substrates of CYP1A2 enzymes, 40% of CYP2D6, and 23% of CYP3A4. About 10% - 20% of Western populations are defective in genes of the CYP superfamily. Only 26% of Southern Europeans are pure extensive metabolizers for the trigenic cluster integrated by the CYP2D6 + CYP2C19 + CYP2C9 genes. Efficacy and safety issues in the pharmacological treatment of SCZ are directly linked to genetic clusters involved in the pharmacogenomics of antipsychotic drugs and also to environmental factors. Consequently, the incorporation of pharmacogenomic procedures both to drugs under development and drugs on the market would help to optimize therapeutics in SCZ and other central nervous system disorders.

Genomics; Antipsychotic Drugs; Schizophrenia

1. INTRODUCTION

Central nervous system (CNS) disorders are the third greatest problem of health in developed countries, representing 10% - 15% of deaths after cardiovascular disorders (25%) and cancer (20%). CNS disorders pose several challenges to our society and the scientific community: 1) they represent an epidemiological problem and a socio-economic, psychological and family burden; 2) most of them have an obscure/complex pathogenesis; 3) their diagnosis is not easy and lacks specific biomarkers; and 4) their treatment is difficult and inefficient. In terms of economic burden, approximately 10% - 20% of direct costs are associated with their pharmacological treatment, with a gradual increase in parallel with the severity of the disease [1,2].

Approximately 127 million Europeans suffer brain disorders. The total annual cost of brain disorders in Europe is about EUR386 billion, with EUR135 billion in direct medical expenditures (EUR78 billion, inpatients; EUR45 billion, outpatients; EUR13 billion, pharmacological treatment), EUR179 billion in indirect costs (lost workdays, loss of productivity, permanent disability), and EUR72 billion in direct non-medical costs. Mental disorders represent EUR240 billion (62% of the total cost, excluding dementia), followed by neurological diseases (EUR84 billion, 22%) [3].

Common features in CNS disorders include the following: 1) polygenic/complex disorders in which genetic, epigenetic and environmental factors are involved; 2) deterioration of higher activities of the CNS; 3) multifactorial dysfunctions in several metabolomic networks leading to functional damage to specific brain circuits; and 4) accumulation of toxic proteins in the nervous tissue in cases of neurodegeneration [1,2].

Our understanding of the pathophysiology of CNS disorders has advanced dramatically during the last 30 years, especially in terms of their molecular pathogenesis and genetics. Drug treatment has also made remarkable strides, with the introduction of many new drugs; however, improvement in terms of clinical outcome has fallen short of expectations, with up to one third of patients continuing to experience clinical relapse or unacceptable medication-related side-effects in spite of efforts to identify optimal treatment regimens. Potential reasons to explain this historical setback might be that: 1) the molecular pathology of brain disorders is still poorly understood; 2) drug targets are inappropriate, not fitting into the real etiology of the disease; 3) most treatments are symptomatic, but not anti-pathogenic; 4) the genetic component of CNS disorders is poorly defined; and 5) the understanding of genome-drug interactions is very limited [2,4-6].

The pharmacological management of CNS disorders is an issue of special concern due to the polymedication required to modulate the symptomatic complexity of brain disorders. The introduction of novel procedures into an integral genomic medicine protocol in CNS disorders is an imperative requirement for clinical practice and drug development in order to improve diagnostic accuracy (disease-specific biomarkers) and to optimize therapeutics (pharmacogenomics) [7-12]. A growing body of fresh knowledge on the pathogenesis of CNS disorders, together with data on neurogenomics and pharmacogenomics, is emerging in recent times. The incorporation of this new armamentarium of molecular pathology and genomic medicine to daily medical practice, together with educational programs for the correct use of drugs, must help to: 1) understand brain pathogenesis, 2) establish an early diagnosis, and 3) optimize therapeutics either as a preventive strategy or as a formal symptomatic treatment [2,5,6,13,14].

Schizophrenia (SCZ) is a typical paradigm of mental disorder with a prevalence of 1% and a high socioeconomic impact in our society. SCZ and related disorders are highly heritable but cannot be explained by currently known genetic risk factors. SCZ has a heritability estimated at 70% - 90% [1,15-17]. Several neurobiological hypotheses have been postulated as responsible for SCZ pathogenesis: polygenic/multifactorial genomic defects, intrauterine and perinatal environment-genome interactions, neurodevelopmental defects, dopaminergic, cholinergic, serotonergic, GABAergic, neuropeptidergic and glutamatergic/NMDA dysfunctions, seasonal infection, neuroimmune dysfunction, and epigenetic dysregulation.The dopamine hypothesis of SCZ has been one of the most enduring ideas in psychiatry. Initially, the emphasis was on the role of hyperdopaminergia in the etiology of SCZ, but it was subsequently reconceptualized to specify subcortical hyperdopaminergia with prefrontal hypodopaminergia [18]. Carlsson’s hypothesis postulates that the positive and negative symptoms of SCZ are due to failure of mesolimbic and mesocortical projections consequent on hypofunction of the glutamate N-methylD-aspartate (NMDA) receptor. The emergence of positive symptoms (hallucinations), and synapse regression involves molecules such as neuregulin and its receptor ErbB4, which have been implicated in SCZ [19]. While multiple theories have been put forth regarding the origin of SCZ, by far the vast majority of evidence points to the neurodevelopmental model in which developmental insults as early as late first or early second trimester lead to the activation of pathologic neural circuits during adolescence or young adulthood, leading to the emergence of positive or negative symptoms. There is evidence from brain pathology (enlargement of the cerebroventricular system, changes in gray and white matters, and abnormal laminar organization), genetics (changes in the normal expression of proteins involved in early migration of neurons and glia, cell proliferation, axonal outgrowth, synaptogenesis, and apoptosis), environmental factors (increased frequency of obstetric complications and increased rates of schizophrenic births due to prenatal viral or bacterial infections), and gene-environmental interactions (a disproportionate number of SCZ candidate genes are regulated by hypoxia, microdeletions and microduplications, the overrepresentation of pathogenrelated genes among SCZ candidate genes) in support of the neurodevelopmental model [20]. Dean [21] reviewed evidence to assess the hypothesis that SCZ is a human-specific disorder associated with the need for highly complex CNS development. Changes in the size of the frontal lobe, increases in numbers of specific cell types, changes in gene expression and changes in genome sequence all seem to be involved in the evolution of the human CNS. Human-specific changes in CNS development are wide-ranging. The modification in CNS structure and function that has resulted from these changes affects many pathways and behaviors that also appear to be affected in subjects with SCZ. Therefore, there is evidence to support the hypothesis that SCZ is a disease that develops due to derangements to human-specific CNS functions that have emerged since our species diverged from non-human primates.

Antipsychotic drugs (neuroleptics) represent the primary pharmacological treatment for schizophrenia and psychotic disorders worldwide. The proportion of treatment-resistant patients is estimated to be 20 to 40%, and the treatment of patients with schizophrenia who fail to respond to antipsychotics is a major challenge in psychiatry [22]. Studies reported during the past 20 years have demonstrated that the efficacy and safety of antipsychotics are closely related to the pharmacogenomic profiles of schizophrenic patients [1,17,22].

2. GENES INVOLVED IN PHARMACOGENOMICS

The genes involved in the pharmacogenomic response to drugs in CNS disorders may fall into five major categories: 1) genes associated with CNS pathogenesis (disease-specific genes); 2) genes associated with the mechanism of action of drugs; 3) genes associated with drug metabolism; 4) genes associated with drug transporters; and 5) pleiotropic genes involved in multifaceted cascades and metabolic reactions [2]. The therapeutic outcome (efficacy and safety) is the result of the interplay of drugs with these different categories of gene products and epigenetic factors to reverse or modify the phenotypic expression of a given disease [23]. Pharmacogenomics accounts for 30% - 90% variability in pharmacokinetics and pharmacodynamics.

2.1. Pathogenic Genes

Over 6000 genes distributed across the human genome have been screened for associations with CNS disorders during the past 30 years [1,24]. Studies of many candidate genes potentially associated with a particular CNS disorder could not be replicated in different settings, cohorts, and geographical contexts due to methodological problems, sample selection and multi-ethnic genetic variation. In the case of SCZ and related disorders, over 200 genes have been associated with psychotic disorders [1,7] (Figure 1; Table 1).

2.2. Genes Associated with the Mechanism of Action of Drugs

Most genes associated with the mechanism of action of CNS drugs encode receptors, enzymes, and neurotransmitters (Tables 1 and 2) on which psychotropic drugs act as ligands (agonists, antagonists), enzyme modulators (substrates, inhibitors, inducers) or neurotransmitter regulators (releasers, reuptake inhibitors) [25].

2.3. Genes Involved in Drug Metabolism

Drug metabolism includes phase I reactions (i.e. oxidation, reduction, hydrolysis) and phase II conjugation reactions (i.e. acetylation, glucuronidation, sulphation, methylation). The principal enzymes with polymorphic variants involved in phase I reactions are the following: Cytochrome P450 monooxygenases (CYP3A4/5/7, CYP2E1, CYP2D6, CYP2C19, CYP2C9, CYP2C8, CYP2B6, CYP2A6, CYP1B1, CYP1A1/2), epoxide hydrolase, esterases, NQO1 (NADPH-quinone oxidoreductase), DPD (dihydropyrimidine dehydrogenase), ADH (alcohol dehydrogenase), and ALDH (aldehyde dehydrogenase); and major enzymes involved in phase II reactions include UGTs (uridine 5’-triphosphate glucuronosyl transferases), TPMT (thiopurine methyltransferase), COMT (catechol-O-methyltransferase), HMT (histamine methyl-transferase), STs (sulfotransferases), GST-A (glutathione S-transferase A), GST-P, GST-T, GST-M, NAT1 (N-acetyl transferase 1), NAT2, and others. Among these enzymes, CYP2D6, CYP2C9, CYP2C19, and CYP3A4/5 are the most relevant in the pharmacogenetics of CNS drugs [14,25] (Table 2). Approximately, 18% of neuroleptics are major substrates of

Table 1. Genes potentially associated with schizophrenia and psychotic disorders.

Symbol

Name

Locus

SZC-Related SNPs

Other Diseases

ABCA7

ATP-binding cassette, sub-family A (ABC1), member 7

19p13.3

ABCA13

ATP-binding cassette, sub-family A (ABC1), member 13

7p12.3

ABCB1

ATP-binding cassette, sub-family A (ABC1), member 1

9q31.1

rs3858075

Atherosclerosis; Cerebral amyloid angiopathy; Colorectal cancer; Colorectal neoplasms; Coronary artery disease; Coronary disease; Dyslipidemias; Familial hypercholesterolemia; High density lipoprotein deficiency (type 1); High density lipoprotein deficiency (type 2); Hyperalphalipoproteinemia; Hypercholesterolemia; Hyperlipidemia; Kidney diseases; Tangier disease

ACE

Angiotensin I converting enzyme (peptidyl-dipeptidase A) 1

17q23.3

Alzheimer disease; Anxiety disorders; Cardiovascular diseases; Hemorrhagic stroke; Dementia; Depression; Diabetes mellitus; Diabetic nephropathy; Hyperlipidemias; Hypertension; Hypotension; IgA glomerulonephritis; IgA nephropathy; Ischemic stroke; Major depressive disorder; Meningococcal disease; Myocardial infarction; Myophosphorylase deficiency; Preterm cardiorespiratory disease; Renal tubular dysgenesis; Severe acute respiratory syndrome; Stroke; Susceptibility to microvascular complications of diabetes I; Vascular dementia

ACSL6

Acyl-CoA synthetase long-chain family member 6

5q31

rs11743803

Acute eosinophilic leukemia; Acute myelogenous leukemia; Acute myelogenous leukemia; Myelodysplastic syndrome

ADRA1A

Adrenergic, alpha-1A-, receptor

8p21.2

ADRA2A

Adrenergic alpha-2A, receptor

10q24-q26

rs1800544

Attention-deficit hyperactivity disorder; Hypertension

Diarrhea-predominant irritable bowel syndrome; Response to methylphenidate treatment in Korean subjects with attention- deficit hyperactivity disorder; Obesity; Predisposition to tobacco smoking

ADSS

Adenylosuccinate synthase

1cen-q12

rs227061;

rs3102460

AHI1

Abelson helper integration site 1

6q23.3

rs7750586; rs911507

Joubert syndrome-3

AKT1

v-akt murine thymoma viral oncogene homolog 1

14q32.32

rs3803300

Breast cancer, somatic; Colorectal cancer, somatic; Ovarian cancer, somatic

ALDH1A2

Aldehyde dehydrogenase 1 family, member A2

15q21.3

rs4646642-rs4646580

ALDH3B1

Aldehyde dehydrogenase 3 family, member B1

11q13

AP3M1

Adaptor-related protein complex 3, mu 1 subunit

10q22.2

rs6688

APOE

Apolipoprotein E

19q13.2

Age-related macular degeneration; Age-related macular degeneration 1; Alzheimer disease; Amyloidosis; APOE5-associated hyperlipoproteinemia and atherosclerosis; APOE7-associated type III hyperlipoproteinemia; Apolipoproteinemia E1; Arteriosclerosis; Asthma; Atherosclerosis; Autosomal dominant type III hyperlipoproteinemia; Autosomal recessive hyperlipoproteinemia; Autosomal recessive type III hyperlipoproteinemia associated with APOE deficiency; Cardiovascular disease; Carotid stenosis; Cerebrovascular disease; Coronary arteriosclerosis; Craniocerebral trauma; Drug-induced liver injury; Dysbetalipoproteinemia; Dysbetalipoproteinemia due to APOE2; Dyslipidemias; Familial dysbetalipoproteinemias; Macular degeneration; Hypertriglyceridemia; Ischemic cerebrovascular disease; Ischemic heart disease; Ischemic stroke; Lipoprotein glomerulopathy; Lung neoplasms; Hyperlipoproteinemia (type II); Hyperlipoproteinemia (type III);

Continued

Hyperlipoproteinemias; Metabolic syndrome; Multiple sclerosis; Myocardial infarction; Myocardial ischemia; Neurodegenerative diseases; Psoriasis; Sea-blue histiocyte syndrome; Type III hypercholesterolemia and hypertriglyceridemia; Type III hyperlipoproteinemia; Type III hyperlipoproteinemia associated with APOE deficiency; Type III hyperlipoproteinemia associated with APOE Leiden; Type III hyperlipoproteinemia associated with APOE2; Type III hyperlipoproteinemia associated with APOE2-Fukuoka; Type III hyperlipoproteinemia associated with APOE4; Type III hyperlipoproteinemia due to APOE1-Harrisburg; Type III hyperlipoproteinemia due to APOE4-Philadelphia; Type III hyperliporpoteinemia due to APOE2-Christchurch; Type V hyperlipoproteinemia; Vascular dementia; Vascular disease

APOL1

Apolipoprotein L, 1

22q13.1

APOL2

Apolipoprotein l, 2

22q12

APOL4

Apolipoprotein l, 4

22q11.2-q13.2

ARRB2

Arrestin, beta 2

17p13

rs1045280 Ser280Ser

ARVCF

Armadillo repeat gene deleted in velocardiofacial syndrome

22q11.21

ATM

Ataxia telangiectasia Mutated

11q22-q23

rs664143 rs227061

AVPR1A

Arginine vasopressin receptor 1A

12q14-q15

AVPR1B

Arginine vasopressin receptor 1B

1q32

BDNF

Brain-derived neurotrophic factor

11p13

rs6265 Val66Met C270T

Aniridia; Anorexia nervosa; Bipolar disorder; Bulimia nervosa; Congenital central hypoventilation syndrome; Depressive disorder; Genitourinary anomalies, Lithium response; Major depressive disorder; Memory impairment; Mental retardation; Methadone response; Obesity; Obsessive-compulsive disorder; Parkinson’s disease; Protection against obsessive-compulsive disorder; Tardive dyskinesia; WAGR syndrome; Wilms’ tumor

BIK

BCL2-interacting killer (apoptosis-inducing)

22q13.31

rs926328; rs2235316

BLOC1S3

Biogenesis of lysosomal organelles complex-1, subunit 3

19q13.32

BRD1

Bromodomain containing 1

22q13.33

Complement component 3

19p13.3-p13.2

Age-related macular degeneration 9; C3 deficiency; Susceptibility to atypical hemolytic uremic syndrome 5

C4B

Complement component 4B (Chido blood group)

6p21.3

C4 deficiency

C6orf217

Chromosome 6 open reading frame 217

6q23.3

rs1475069

C10orf26, OPAL1

Chromosome 10 open reading frame 26

10q24.32

C22DDELS

Chromosome 22q11.2 deletion syndrome, distal

22q11.2

CACNA1C

Calcium channel, voltage-dependent, L type, alpha 1C subunit

12p13.3

rs1006737; rs22512119

CALR

Calreticulin

19p13.3-p13.2

CCKAR

Cholecystokinin A receptor

4p15.1-p15.2

rs1800857; 779T/C

Continued

CDC42SE2

CDC42 small effector 2

5q31.1

CFB

Complement factor B

6p21.3

Reduced risk of age-related macular degeneration; Susceptibility to atypical hemolytic uremic syndrome 4

CHAT

Choline O-acetyltransferase

10q11.2

Alzheimer disease; Congenital myasthenic syndrome associated with episodic apnea; Myasthenic syndrome; Neurodegenerative diseases; Neurotoxicity syndromes; Parkinson’s disease (secondary); Peripheral nervous system diseases

CHGA

Chromogranin A (parathyroid secretory protein 1)

14q32

CHGB

Chromogranin B (secretogranin 1)

20pter-p12

CHI3L1

Chitinase 3-like 1 (cartilage glycoprotein-39)

1q32.1

Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function; Susceptibility to asthma-related traits 7

CHRFAM7A

CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5 - 10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion

15q13.1

CHRNA2

Cholinergic receptor, nicotinic, alpha 2 (neuronal)

8p21

Nocturnal frontal lobe epilepsy type 4

CHRNA6

Cholinergic receptor, nicotinic, alpha 6

8p11.21

CHRNA7

Cholinergic receptor, nicotinic, alpha 7

15q14

rs3087454

CHRNB3

Cholinergic receptor, nicotinic, beta 3

8p11.2

CLDN5

Claudin 5

22q11.21

CLINT1

Clathrin interactor 1

5q33.3

CLOCK

Clock homolog (mouse)

4q12

CLU

Clusterin

8p21-p12

rs11136000

CMYA5

Cardiomyopathy associated 5

5q14.1

rs10043986; rs4704591

CNP

2’,3’-cyclic nucleotide 3’ phosphodiesterase

17q21

CNR1

Cannabinoid receptor 1 (brain)

6q14-q15

Alzheimer disease; Central nervous system diseases; Cocaine-related disorders; Muscle spasticity; Neurodegenerative diseases; Neurotoxicity syndromes; Substance withdrawal syndrome

CNR2

Cannabinoid receptor 2 (macrophage)

1p36.11

CNTNAP2

Contactin associated protein-like 2

7q35

Cortical dysplasia focal epilepsy syndrome; Autism (susceptibility); Pitt-Hopkins-like syndrome

COMT

Catechol-O-methyltransferase

22q11.21

rs4680; rs6267; rs737865 rs7378-rs4680- rs165599 rs2075507 rs362204

Anxiety disorders; Autistic disorder; Bipolar disorder; Depressive disorder; DiGeorge syndrome; Migraine; Mood disorders; Nervous system diseases; Panic disorder; Obsessive-compulsive disorder; Parkinson’s disease; Prostatic neoplasms

Susceptibility to panic disorder

CPLX2

Complexin 2

5q35.2

rs3822674

CRP

C-reactive protein, pentraxin-related

1q21-q23

Atherosclerosis; Cardiovascular disease; Cerebrovascular disease; Coronary disease; Diabetes mellitus (type 2); Heart diseases; Heart failure; Heart injuries; Hepatocellular carcinoma; Inflammation; Lung neoplasms; Lupus erythematosus; Malaria; Pasteurellaceae infections; Stroke; Systemic lupus erythematosus; Thrombosis

CSF2RA

Colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)

Xp22.32 and Yp11.3

Acute M2 type myeloid leukemia; Pulmonary alveolar proteinosis

Continued

CSF2RB

Colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)

22q13.1

Pulmonary alveolar proteinosis

CSMD1

KIAA1890 Cub and Sushi multiple domains 1

8p23.2

CTL4

cytotoxic T-lymphocyte-associated protein 4

2q33

rs231779;

rs16840252

CTSK

cathepsin K

1q21

Pycnodysostosis

CYBB

Cytochrome b-245, beta polypeptide

Xp21.1

CYP1A2

Cytochrome P450, family 1, subfamily A, polypeptide 2

15q24.1

Experimental liver cirrhosis; Experimental liver neoplasms; Experimental neoplasms; Gastric adenocarcinoma; Gastrointestinal neoplasms; Hepatocellular carcinoma; Leflunomide-induced toxicity; Methemoglobinemia; Myocardial infarction; Liver diseases; Neoplasms; Susceptibility to tobacco addiction; Tardive dyskinesia; Tobacco use disorder

CYP3A4/5

Cytochrome P450, family 3, subfamily A, polypeptide 4/5

7q21.1

Acute hypoxia; Acute lymphoblastic leukemia; Acute myeloid leukemia; Age-related metabolism variation; Alcoholism; Allergic rhinitis; Alveolar echinococcosis; Antiplatelet drug resistance; Antiretroviral-antineoplastic drug interactions; Atherosclerosis; Azoospermia; Balkan endemic nephropathy; Barrett’s metaplasia; Benign prostate hyperplasia; Bile acid metabolism; Bladder cancer; Blood pressure; Brain tumors; Breast cancer; Breast neoplasms; Cancer; Celiac disease; Cerebrotendinous xanthomatosis; Cholestasis; Cholesterol homeostasis; Chronic hepatitis C; Cirrhosis; Colon adenoma; Colorectal cancer; Colorectal liver metastases; Crohn’s disease; Cushing’s syndrome; Cystic fibrosis; Depression; Depressive disorder; Diabetes mellitus (type 2); Diffuse panbronchiolitis; Drug-induced liver injury; Drug-virus interaction; Ehrlichiosis; Endometrial cancer; Epilepsy; Erectile dysfunction; Esophageal squamous cell carcinoma; Food-drug interactions; Gastric tumors; Gingival hyperplasia; Glucocorticoid-induced hypertension in children with acute lymphoblastic leukemia; Headache; Helicobacter pylori; Hepatic steatosis; Hepatitis; Hepatitis B infection; Hepatocellular tumors; Hodgkin’s disease; Hodgkin’s lymphoma; Hypertension; Hypothermia; Inflammatory bowel diseases; Lactobacillus rhamnosus; Leukemia; Liver cancer; Liver diseases; Liver neoplasms; Lung cancer; Lung neoplasms; Lymphocytes; Malaria; Menopause; Menstruation; Metabolic syndrome; Metabolic syndrome X; Migraine; Multiple myeloma; Myocardial infarction; Myocardial ischemia; Nasopharyngeal carcinoma; Neuropathic pain; Non-alcoholic fatty liver disease; Non-small cell lung cancer; Non-small cell lung carcinoma; Onychomycosis; Osteomalacia; Osteonecrosis; Osteosarcoma; Ovarian cancer; Ovarian neoplasms; Oxidative stress; Parkinson’s disease; Porphyrias; Precocious puberty; Pregnancy; Pregnancy complications; Primary biliary cirrhosis; Proctitis; Prostate cancer; Prostatic hyperplasia; Prostatic neoplasms; QT interval prolongation; Renal cancer; Renal cell carcinoma; Rhabdomyolysis; Schizophrenia; Squamous cell carcinoma of the larynx and hypopharynx; Stroke; T-cell lymphomas; Testicular germ cell cancer; Thalassemia; Torsades de pointes; Tuberculosis; Veno-occlusive disease; Venous thromboembolism; Venous thrombosis

DAAM2

Dishevelled associated activator of morphogenesis 2

6p21.2

Continued

DAO

D-amino-acid oxidase

12q24

rs2111902;

rs3741775;

rs3918346;

rs4623951;

rs3918347-rs4964770;

rs3825251-rs3918347-; rs4964770

DAOA

D-amino acid oxidase activator

13q34

rs3916971;

rs778293;

rs2391191 (M15);

rs778293;

rs3918342

DBH

Dopamine beta-hydroxylase (dopamine beta-monooxygenase)

9q34

rs1108580

DDR1

Discoidin domain receptor tyrosine kinase 1

6p21.3

rs4532

Attention-deficit hyperactivity disorder; Autistic disorder; Bipolar disorder; Mental disorders; Nicotine dependence

DGCR2

DiGeorge syndrome critical region gene 2

22q11.21

rs2073776

DGCR6

DiGeorge syndrome critical region gene 6

22q11

DISC1

Disrupted in schizophrenia 1

1q42.1

rs3737597;

rs821616;

rs6675281;

rs821597

Susceptibility to schizoaffective disorder

DISC2

Disrupted in schizophrenia 2 (non-protein coding)

1q42.1

Association of lipid-lowering response to statins in combined study populations

DKK4

Dickkopf homolog 4 (Xenopus laevis)

8p11.2-p11.1

DNMT3B

DNA (cytosine-5-)-methyltransferase 3 beta

20q11.2

rs6119954;

rs2424908

DPYSL2

Dihydropyrimidinase-like 2

8p22-p21

DRD1

Dopamine receptor D1

5q35.1

DRD2

Dopamine receptor D2

11q23

rs1799732;

rs2283265;

rs12364283;

rs1076560;

rs1079597 (Taql-B);

rs6277;

rs1801028;

rs6275; rs6277;

rs11608185

Alcoholism; Myoclonic dystonia; Myoclonus-dystonia syndrome; Obesity; Parkinson’s disease; Substance withdrawal syndrome; Tardive dyskinesia

DRD3

Dopamine receptor D3

3q13.3

rs6280

Autistic disorder; Hereditary essential tremor 1; Nicotine addiction; Parkinson’s disease; Susceptibility to essential tremor; Tardive dyskinesia

DRD4

Dopamine receptor D4

11p15.5

rs1805186;

120-bp TR;

rs1800955;

rs4646983;

rs4646984

Attention-deficit hyperactivity disorder; Autonomic nervous system dysfunction; Novelty-seeking personality trait; Parkinson’s disease; Personality disorders; Protection against Parkinson’s disease; Psychotic disorders; Tobacco use disorder

DRD5

Dopamine receptor D5

4p16.1

(CT/GT/GA)_n

(CA)_n

Primary benign blepharospasm; Primary cervical dystonia; Susceptibility to attention-deficit hyperactivity disorder

Continued

DTNBP1

Dystrobrevin binding protein 1

6p22.3

rs104893945;

rs2619522;

rs7758659;

rs1047631;

rs1474605;

rs2005976;

rs2619539;

rs760666;

rs2619528;

rs2619538;

rs875462;

rs3213207;

rs760761;

rs1011313;

rs1018381;

rs2619538 (SNPA);

rs3213207 (P1635)

Bipolar disorder; Major depressive disorder; Hermansky-Pudlak syndrome; Hermansky-Pudlak syndrome 7

EGF

Epidermal growth factor

4q25

Renal hypomagnesemia 4

ERBB3

v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)

12q13

rs773123

Lethal congenital contractural syndrome 2

ERBB4

v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)

2q33.3-q34

ESR1

Estrogen receptor 1

6q25.1

FABP7

Fatty acid binding protein 7, brain

6q22-q23

FADS2

Fatty acid desaturase 2

11q12.2

FAS

Fas (TNF receptor superfamily, member 6)

10q24.1

Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency; Autoimmune lymphoproliferative syndrome; Autoimmune lymphoproliferative syndrome, type IA; Burn scar-related somatic squamous cell carcinoma

FGF1

Fibroblast growth factor 1 (acidic)

5q31

FGF17

Fibroblast growth factor 17

8p21

FGFR1

Fibroblast growth factor receptor 1

8p12

FMO3

Flavin containing monooxygenase 3

1q24.3

Familial adenomatous polyposis; Trimethylaminuria

FOLH1

Folate hydrolase (prostate-specific membrane antigen) 1

11p11.2

FOXP2

Forkhead box P2

7q31

Speech-language disorder-1

FTO

Fat mass and obesity associated

16q12.2

rs9939609

FXYD2

FXYD domain containing ion transport regulator 2

11q23

Renal hypomagnesemia-2

FXYD6

FXYD domain containing ion transport regulator 6

11q23.3

rs11544201 rs10790212- rs11544201

FYN

FYN oncogene related to SRC, FGR, YES

6q21

rs6916861; rs3730353

FZD3

Frizzled homolog 3 (Drosophila)

8p21

Continued

GABBR1

Gamma-aminobutyric acid (GABA) B receptor, 1

6p21.31

GABRB1

Gamma-aminobutyric acid (GABA) A receptor, beta 1

4p12

GABRB2

Gamma-aminobutyric acid (GABA) A receptor, beta 2

5q34

rs1816072

GABRG2

Gamma-aminobutyric acid (GABA) A receptor, gamma 2

5q34

Childhood absence epilepsy; Childhood absence epilepsy 2; Familial febrile convulsions 8; Generalized epilepsy with febrile seizures plus; Generalized epilepsy with febrile seizures plus, type 3; Severe myoclonic epilepsy of infancy; Susceptibility to childhood absence epilepsy 2

GAD1

Glutamate decarboxylase 1 (brain, 67 kDa)

2q31

Autosomal recessive symmetric spastic cerebral palsy

GAD2

Glutamate decarboxylase 2 (pancreatic islets and brain, 65 kDa)

10p11.23

Group-specific component (vitamin D binding protein)

4q12-q13

Susceptibility to Graves’ disease 3

GCLM

Glutamate-cysteine ligase, modifier subunit

1p22.1

Susceptibility to myocardial infarction

GJA8

Gap junction protein, alpha 8, 50 kDa

1q21.1

Cataract-microcornea syndrome; Nuclear progressive cataract; Nuclear pulverulent cataract; Zonular pulverulent cataract 1

GLS

Glutaminase

2q32-q34

GLUL

Glutamate-ammonia ligase

1q31

GNB1L

Guanine nucleotide binding protein (G protein), beta polypeptide 1-like

22q11.2

GRIA1

Glutamate receptor, ionotropic, AMPA 1

5q31.1

GRIA4

Glutamate receptor, ionotrophic, AMPA 4

11q22

GRID1

Glutamate receptor, ionotropic, delta 1

10q22

rs3814614; rs10749535; rs11201985

GRIK3

Glutamate receptor, ionotropic, kainate 3

1p34-p33

rs6691840

GRIK4

Glutamate receptor, ionotropic, kainate 4

11q22.3

rs4935752;

rs6589846;

rs4430518

Bipolar disorder; Depression

GRIK5

Glutamate receptor, ionotropic, kainate 5

19q13.2

GRIN1

Glutamate receptor, ionotropic, N-methyl D-aspartate 1

9q34.3

GRIN2B

Glutamate receptor, ionotropic, N-methyl D-aspartate 2B

12p12

rs1019385

rs7301328

GRIN2D

Glutamate receptor, ionotropic, N-methyl D-aspartate 2D

19q13.1-qter

GRM3

Glutamate receptor, metabotropic 3

7q21.1-q21.2

GRM4

Glutamate receptor, metabotropic 4

6p21.3

Continued

GRM7

Glutamate receptor, metabotropic 7

3p26.1-p25.1

rs12491620; rs1450099

GPR109A

G protein-coupled receptor 109A

12q24.31

GPR109B

G protein-coupled receptor 109B

12q24.31

GSK3B

Glycogen synthase kinase 3 beta

3q13.3

(CAA)_nrepeat polymorphisms;

-1727 A/T

Alzheimer disease; Bipolar disorder; Cancer; Colonic neoplasms; Colorectal neoplasms; Diabetes (type 2); Diabetes mellitus; Depression; Insulin resistance; Lithium sensitivity; Major depression; Myeloid/lymphoid or mixed lineage leukemia; Neurodegenerative diseases; Parkinsonian disorders; Tauopathy

GSTM1

Glutathione S-transferase mu 1

1p13.3

GSTM1*0

Acute lymphoblastic leukemia; Acute myeloid leukemia; Acute promyelocytic leukemia; Adverse drug reactions to azathioprine; Aflatoxin-related hepatocarcinogenesis; Aplastic anemia; Autism; Autistic disorder; Azathioprine adverse effects; Benzene toxicity; Basal cell nervous syndrome; Basal cell carcinoma; Bladder cancer; Bleomycin moderate toxicity; Breast cancer; Busulfan pharmacokinetics; Carbamazepine-induced mild hepatotoxicity; Carcinogen toxicity; Colorectal cancer; Colorectal neoplasms; Coronary artery disease; Cytochrome P450 1A1 gene transcription; Diabetes mellitus (type 2); DNA damage after exposure to hydroquinone; Diabetic nephropathy; GSTM1 methylation; Head and neck neoplasms; Hepatocellular carcinoma; Leukemia; Hydroquinone-induced DNA damage; High inducibility of cytochrome P450 1A1 gene transcription; Liver cancer; Liver neoplasms; Lung cancer; Lung neoplasms; Lymphoblastic leukemia; Mesothelioma; Methotrexate toxicity; Myelodisplastic syndrome; Myeloid leukemia; Prostate cancer; Prostatic neoplasms; Raynaud’s disease; Responses to environmental and industrial carcinogens; Second primary neoplasms; Skin diseases; Systemic lupus erythematosus; Tacrine-induced hepatotoxicity; Testicular neoplasms; Thimerosal sensitization; Urinary bladder neoplasms; Troglitazone-induced liver failure

GSTP1

Glutathione S-transferase pi 1

11q13

GSTT1

Glutathione S-transferase theta 1

22q11.23

GULP1

GULP, engulfment adaptor PTB domain containing 1

2q32.3-q33

rs2004888

GWA 10q2613

rs17101921

GWA 11p141

rs1602565

GWA 16p1312

rs71992086

GWA_10q26.13

rs17101921

GWA_11p14.1

rs1602565

GWA_16p13.12

rs7192086

HINT1

Histidine triad nucleotide binding protein 1

5q31.2

HLA-A

Major histocompatibility complex, class I, A

6p21.3

HLA-B

Major histocompatibility complex, class I, B

6p21.3

HLA-C

Major histocompatibility complex, class I, C

6p21.3

Continued

HLA-DQA1

Major histocompatibility complex, class II, DQ alpha 1

6p21.3

Asthma; Celiac disease; Diabetes (type 1); Gluten-sensitive enteropathy; HLA-DQA1 differential expression; Lung adenocarcinoma; Metamizol-related agranulocytosis; Oligoarticular juvenile idiopathic arthritis; Rheumatoid arthritis; Susceptibility to onchocerciasis; Toxoplasmic encephalitis; Ximelagratan sensitivity

HLA-DQB

Major histocompatibility complex, class II, DQ beta 1

6p21.3

HLA-DRB1

Major histocompatibility complex, class II, DR beta 1

6p21.3

HLA-E

Major histocompatibility complex, class I,

6p21.3

Bipolar disorder

HIST1H2BJ

Histone cluster 1, H2bj

6p22.1

rs6913660

HOMER

Homer homolog 2 (Drosophila)

15q24.3

rs17158184; rs2306428

Haptoglobin

16q22.1

Hp1/2

Anemia; Atherosclerosis; Autoimmune diseases; Breast neoplasms; Cardiovascular disease; Chronic hepatitis B; Chronic hepatitis C; Coronary atherosclerosis; Crohn’s disease; Diabetic vascular disease; Dyslipidemias; Diabetes mellitus (type 1); Diabetes mellitus (type 2); Diabetic angiopathy; Diabetic nephropathy; Female genital neoplasms; Hemochromatosis; Hepatitis B; HIV infections; Hypersensitivity; Hypertension; Leukemia; Malaria; Myocardial infarction; Nasopharingeal carcinoma; Parkinson’s disease; Pasteurellaceae infections; Pregnancy-induced hypertension; Primary sclerosis cholangitis; Retinal detachment; Sickle cell anemia; Tuberculosis; Trachoma

HRH1

Histamine receptor H1

3p25

Allergy; Allergic contact dermatitis; Angioedema; Asthma; Atopic dermatitis; Bronchial hyperreactivity; Hypersensitivity; Inflammation; Learning disorders; Long QT syndrome; Memory disorders; Mental disorders; Perennial allergic rhinitis; Pruritus; Pulmonary eosinophilia; Respiratory hypersensitivity; Respiratory tract diseases; Rhinitis; Urticaria; Sinusitis; Skin disorders; Sneezing; Seasonal allergic rhinitis; Seizures

HSPA1B

Heat shock 70kDa protein 1B

6q21.3

rs539689

HTR1A

5-Hydroxytryptamine (serotonin) receptor 1A

5q11.2-q13

Alzheimer disease; Antidepressant sensitivity; Anxiety disorders; Depression; Macular degeneration; Major depression; Mental disorders; Neuroleptic-related weight gain in schizophrenia; Panic disorder; Personality disorders; Psychotic disorders; Schizophrenia-related weight gain; Sudden infant death

HTR2A

5-Hydroxytryptamine (serotonin) receptor 2A

13q14-q21

rs6313;

rs6314;

rs6311

Alcohol dependence; Alzheimer disease; Anorexia nervosa; Antidepressant-related response; Antipsychotic-related response; Asperger’s syndrome; Attention-deficit hyperactivity disorder; Autistic disorder; Bipolar disorder; Clozapine-induced weight gain; Depression; Depressive disorder; Major depression; Major depressive disorder; Memory performance; Mental disorders; Mental retardation; Migraine; Mood disorders; Neuroleptic-induced weight gain; Neuroleptic-related response; Neurotoxicity syndromes; Obsessive-compulsive disorder; Personality disorders; Pervasive child development disorders; Psychotic disorders; Substance abuse; Response to citalopram therapy in major depressive disorder; Tardive dyskinesia

HTR3A

5-Hydroxytryptamine (serotonin) receptor 3A

11q23.1

HTR4

5-Hydroxytryptamine (serotonin) receptor 4

5q31-q33

IDE

Insulin-degrading enzyme

10q23-q25

Continued

IFNG

Interferon, gamma

12q14

rs62559044

AIDS; Allergic contact dermatitis; Aortic aneurysm; Aplastic anemia; Appendicitis; Asthma; Atherosclerosis; Autistic disorder; Crohn’s disease; Drug-induced liver injury; Entamebiasis; Hepatitis; Hepatitis C; Hepatocellular carcinoma; Hepatomegaly; Inflammation; Job’s syndrome; Kidney angiomyolipoma; Kidney failure; Myocardial infarction; Liver neoplasms; Lupus nephritis; Multiple sclerosis; Liver cirrhosis; Liver diseases; Oral submucous fibrosis; Renal cell carcinoma; Tuberculosis; Tuberous sclerosis; Susceptibility to human immunodeficiency virus type 1

IGHA1

Immunoglobulin heavy constant alpha 1

14q32.33

IL1A

Interleukin 1, alpha

2q14

IL1B

Interleukin 1, beta

Alzheimer disease; Ankylosing spondylitis; Arsenic poisoning; Body fat mass; Breast neoplasms; Bronchopulmonary dysplasia; Colon cancer; Colonic neoplasms; Diabetic nephropathy; Distal interphalangeal joint osteoarthritis; Entamebiasis; Experimental liver cirrhosis; Fever; Gastric cancer; Gastric cancer and Helicobacter pylori; Glioblastoma; IgA nephropathy; Inflammation; Inflammatory bowel disease; Lung diseases; Major depression; Major depressive disorder; Osteoporosis; Microvascular complications of diabetes; Multiple sclerosis; Nervous system diseases; Non-small cell lung cancer; Parkinson’s disease; Postmenopausal osteoporosis; Primary open-angle glaucoma; Pulmonary fibrosis; Skin diseases; Stomach neoplasms; Ulcerative colitis

2q14

rs1143634 rs16944

IL1RN

Interleukin 1 receptor antagonist

2q14.2

Arsenic poisoning; Autistic disorder; Colonic neoplams; Chagas’ disease; Diabetes; Gastric cancer susceptibility after H. pylori infection; Generalized aggressive periodontitis; Inflammatory bowel disease; Interleukin 1 receptor antagonist deficiency; Memory disorders; Metabolic syndrome; Multiple sclerosis; Osteoarthritis; Osteoporosis; Prostatic neoplasms; Skin diseases; Stroke; Susceptibility to microvascular complications of diabetes 4; Tourette’s syndrome; Ulcer

IL3

Interleukin 3 (colony-stimulating factor, multiple)

5q31.1

IL3RA

Interleukin 3 receptor, alpha (low affinity)

Xp22.3 or Yp11.3

rs6603272

IL4

Interleukin 4

5q31.1

Allergic contact dermatitis; Arthritis; Asthma; Atopic dermatitis; Autistic disorder; Autoimmune hypothyroidism; Bladder cancer; Chronic periodontitis; Common variable immunodeficiency; Graves’ disease; Glioblastoma; Hypersensitivity; Psoriasis; Subacute sclerosing panencephalitis; Systemic lupus erythematosus; Thromboembolic stroke

IL10

Interleukin 10

1q31-q32

rs1800896; rs1800872

Acquired immunodeficiency syndrome; Alcoholic liver disease; Alzheimer disease; Appendicitis; Autistic disorder; Colitis; Coronary heart disease; Crohn’s disease; Diabetes mellitus (type 1); Enterocolitis; Entamebiasis; Experimental mammary neoplasms; Graft vs host disease (acute); Hepatitis B; Hepatocellular carcinoma; HIV infections; Inflammatory bowel disease; Irritable bowel syndrome; Kawasaki disease; Leprosy; Lung neoplasms; Malaria; Prostate cancer; Prostatic neoplasms; Psoriasis; Rheumatoid arthritis; Severe malaria anemia; Skin carcinomas; Skin neoplasms; Squamous cell carcinoma; Sudden infant death syndrome; Systemic lupus erythematosus; Trachoma; Ulcerative colitis

IL12B

Interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)

5q31.1-q33.1

Asthma; Atopic dermatitis; Bacillus Calmette-Guérin and Salmonella infection; Colorectal cancer; Crohn’s disease; Diabetes mellitus (type 1); Familial atypical mycobacteriosis; Gastric cancer; Hypothermia; Leprosy; Malaria; Psoriasis; Psoriasis vulgaris; Psoriatic arthritis; Salmonella infection; Tuberculosis; Ulcerative colitis

IL18

Interleukin 18 (interferon-gamma-inducing factor)

11q22.2-q22.3

Continued

IL18R1

Interleukin 18 receptor 1

2q12

IL18RAP

Interleukin 18 receptor accessory protein

2q12

IPO5

Importin 5

13q32.2

ITIH3/4

Inter-alpha (globulin) inhibitor, H3/4 polypeptides

3p21.1

JARID2

Jumonji, AT rich interactive domain 2

6p24-p23

rs9654600; rs2235258

KCNH2

Potassium voltage-gated channel, subfamily H (eag-related), member 2

7q36.1

Arrhythmia; Bradycardia-induced long QT syndrome; Drug-associated torsades de pointes; Long QT syndrome; Long QT syndrome 1/2; Long QT syndrome 2; Long QT syndrome 2/3; Long QT syndrome 2/5; Long QT syndrome 2/9; Nonfamiliar atrial fibrillation (AF); Schizophrenia; Short QT syndrome 1; Torsades de pointes

LEPR

Leptin receptor

1p31

Acute lymphoblastic leukemia; Diabetes; Diabetes mellitus (type 2); Glucocorticoid-induced hypertension; Hypogonadism; Impaired glucose tolerance; Low bone mineral content; Morbid obesity; Obesity; Osteoporosis; Risk of metabolic syndrome, diabetes or vascular disease

LGR4

Leucine-rich repeat containing G protein-coupled receptor 4

11p14-p13

LTA

Lymphotoxin alpha (TNF superfamily, member 1)

6p21.3

Susceptibility to leprosy 4; Susceptibility to myocardial infarction; Susceptibility to psoriatic arthritis

MAGI1

Membrane associated guanylate kinase, WW and PDZ domain containing 1

3p14.1

MAGI2

Membrane associated guanylate kinase, WW and PDZ domain containing 2

7q21

MAGI3

Membrane associated guanylate kinase, WW and PDZ domain containing 3

1p12-p11.2

MBP

Myelin basic protein

18q23

MC5R

Melanocortin 5 receptor

18p11.2

MCHR1

Melanin-concentrating hormone receptor 1

22q13.2

MCHR2

Melanin-concentrating hormone receptor 2

6q16

MCTP2

Multiple C2 domains, transmembrane 2

15q26.2

MDGA1

MAM domain containing glycosylphosphatidylinositol anchor 1

6p21

rs11759115

ME2

Malic enzyme 2, NAD(+)-dependent, mitochondrial

18q21

MED12

Mediator complex subunit 12

Xq13

FG syndrome 1; Lujan-Fryns syndrome; Opitz-Kaveggia syndrome

MEGF10

Multiple EGF-like-domains 10

5q33

MICB

MHC class I polypeptide-related sequence B

6p21.3

MLC1

Megalencephalic leukoencephalopathy with subcortical cysts 1

22q13.33

Megalencephalic leukoencephalopathy with subcortical cysts

Continued

MMP3

Matrix metallopeptidase 3 (stromelysin 1, progelatinase)

11q22.3

Abdominal aortic aneurysm; Breast neoplasms; Coronary arteriosclerosis; Coronary disease; Coronary heart disease; Rheumatoid arthritis; Schizophrenia

MMP9

Matrix metallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase)

20q11.2-q13.1

MOG

Myelin oligodendrocyte glycoprotein

6p22.1

MTHFR

Methylenetetrahydrofolate reductase (NAD(P)H)

1p36.3

rs1801131;

rs1801133

Abnormal spermatogenesis; Acute lymphocytic leukemia (ALL); Alzheimer disease; Autistic disorder; B-cell chronic lymphocytic leukemia; Bipolar disorder; Breast neoplasms; Budd-Chiari syndrome; Cancer; Cardiovascular diseases; Cervical intraepithelial neoplasia; Cleft lip; Cleft lip/palate; Clubfoot; Cognition disorders; Colonic neoplasms; Colorectal neoplasms; Congenital cardiac disease; Congenital heart defects; Coronary artery disease; Coronary heart disease; Coronary restenosis; Decreased viability among fetuses; Depression; Depressive disorder; Diabetic angiopathy; Down’s syndrome; Endometrial neoplasms; Female infertility; Folate-sensitive neural tube defects; Follicular lymphoma; Gastric cancer; Glaucoma; Graft vs host disease; Homocystinuria; Homocystinuria due to deficiency of N(5,10)-methylenetetrahydrofolate reductase activity; Hyperhomocysteinemia; Hypersensitivity; Hypertension; Ischemic stroke; Liver diseases; Lower toxicity in 5-FU treatment; Lung neoplasms; Lymphoma; Major depressive disorder; Male infertility; Malnutrition; Maxillofacial abnormalities; Meningomyelocele; Metabolic diseases; Microsatellite instability; Microvascular angina; Migraine; Migraine with aura; MTHFR deficiency; Mucositis; Neoplasm metastasis; Neural tube defects; Nitrous oxide sensitivity in MTHFR deficiency; Non-Hodgkin lymphoma; Orofacial cleft 1; Precursor cell lymphoblastic leukemia-lymphoma; Pre-eclampsia; Primary open-angle glaucoma; Prostatic neoplasms; Retinal artery occlusion; Rheumatoid arthritis; Smallpox vaccine; Spinal cord diseases; Stomach neoplasms; Stroke; Sudden hearing loss; Thrombophilia; Thrombosis; Uterine cervical neoplasms

MUTED

Muted homolog (mouse)

6p25.1-p24.3

NALCN

Sodium leak channel, nonselective

13q33.1

rs2152324

NCAM1

Neural cell adhesion molecule 1

11q23.1

NDEL1

NudE nuclear distribution gene E homolog (A. nidulans)-like 1

17p13.1

rs17806986

NEFM

Neurofilament, medium polypeptide

8p21

NEUROG1

Neurogenin 1

5q23-q31

NOS1

Nitric oxide synthase 1 (neuronal)

12q24.2-q24.31

Susceptibility to infantile hypertrophic pyloric stenosis 1

NOS1AP

Nitric oxide synthase 1 (neuronal) adaptor protein

1q23.3

rs12742393

NOTCH4

Notch 4

6p21.3

rs3131296

HIV-1 in humans

NPHP1

Nephronophthisis 1 (juvenile)

2q13

Joubert syndrome 4; Juvenile nephronophthisis 1; Juvenile nephronophthisis; Senior-Loken syndrome-1

NPY

Neuropeptide Y

7p15.1

Alcoholism; Anorexia nervosa; Anxiety disorders; Anxious depression; Appetite disorders; Birth weight; Cachexia; Carotid atherosclerosis; Cerebral infarction; Diabetes mellitus (type 2); Essential hypertension; Hypercholesterolemia; Hyperlipidemias; Hypertriglyceridemia; Ischemic stroke; Left ventricular hypertrophy; Myocardial infarction; Obesity; Stress

NQO2

NAD(P)H dehydrogenase, quinone 2

6pter-q12

Breast cancer susceptibility

Continued

NR4A2

Nuclear receptor subfamily 4, group A, member 2

2q22-q23

Parkinson’s disease

NRG1

Neuregulin 1

8p12

rs2439272;

rs35753505;

rs473376;

rs10503929;

rs7825588;

rs6994992;

rs4623364

NRG2

Neuregulin 2

5q23-q33

NRG3

Neuregulin 3

10q22-q23

rs7825588;

rs10883866;

rs10748842;

rs6584400

NRGN

Neurogranin (protein kinase C substrate, RC3)

11q24

rs12807809; rs7113041

NRXN1

Neurexin 1

2p16.3

NTF3

Neurotrophin 3

12p13

NTNG1

Netrin G1

1p13.3

NTRK3

Neurotrophic tyrosine kinase, receptor, type 3

15q25

rs999905 rs4887348

NUMBL

Numb homolog (Drosophila)-like

19q13.13-q13.2

OLIG2

Oligodendrocyte lineage transcription factor 2

21q22.11

rs762237; rs2834072

OPCML

Opioid binding protein/cell adhesion molecule-like

11q25

rs3016384

Somatic epithelial ovarian cancer; Somatic ovarian cancer

OXSR1

Oxidative-stress responsive 1

3p22.2

PALB2

Partner and localizer of BRCA2

16p12.2

PCM1

Pericentriolar material 1

8p22-p21.3

Papillary thyroid carcinoma

PCNT

Pericentrin

21q22.3

PDE4B

Phosphodiesterase 4B, cAMP-specific

1p31

rs910694;

rs741271

PDE4D

Phosphodiesterase 4D, cAMP-specific

5q12

rs1120303

PDILM5

PDZ and LIM domain 5

4q22

PDE7B

Phosphodiesterase 7B

6q23-q24

rs9389370

PGBD1

PiggyBac transposable element derived 1

6p22.1

rs13211507

PICALM

Phosphatidylinositol binding clathrin assembly protein

11q14

rs3851179

PICK1

Protein interacting with PRKCA 1

22q13.1

PIK3C3

Phosphoinositide-3-kinase, class 3

18q12.3

PI4K2B

Phosphatidylinositol 4-kinase type 2 beta

4p15.2

PLA2G4A

Phospholipase A2, group IVA (cytosolic, calcium-dependent)

1q25

rs10798059

Deficiency of phospholipase A2, group IV A

PLAT

Plasminogen activator, tissue

8p12

Familial hyperfibrinolysis, due to increased release of PLAT; Plasminogen activator deficiency

Continued

PLXNA2

plexin A2

1q32.2

rs1327175;

rs841865

PPP1R1B

Protein phosphatase 1, regulatory (inhibitor) subunit 1B

17q12

rs907094

PPP3CC

Protein phosphatase 3, catalytic subunit, gamma isozyme

8p21.3

rs10108011

PRDX6

Peroxiredoxin 6

1q25.1

rs1295645;

rs11405;

rs6759;

rs1046240;

rs8383

PRODH

Proline dehydrogenase (oxidase) 1

22q11.21

PRSS16

Protease, serine, 16 (thymus)

6p21

rs6932590

PSEN2

Presenilin 2 (Alzheimer disease 4)

1q31-q42

rs1295645

Alzheimer disease; Central nervous system diseases; Dilated cardiomyopathy; Frontotemporal dementia; Ischemic stroke; Left ventricular dysfunction; Left ventricular hypertrophy; Peripartum cardiomyopathy; Schizophrenia

PTGS2

Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase

1q25.2-q25.3

rs2745557

Acute pancreatitis; Adenocarcinoma; Adenoma; Adenomatous polyposis coli; Amyotrophic lateral sclerosis; Cholangiocarcinoma; Basal cell carcinoma; B-cell chronic lymphocytic leukemia; B-cell lymphoma; Asthma; Breast neoplasms; Carcinoma; Carcinoma in situ; Autistic disorder; Esophageal neoplasms; Coronary artery disease; Diabetes mellitus (type 2); Drug-induced abnormalities; Duodenal ulcer; Colonic neoplasms; Colorectal neoplasms; Experimental liver cirrhosis; Glioma; Hepatocellular carcinoma; Inflammation; Intestinal polyps; Ischemic stroke; Ischemic proliferative retinopathy; Leiomyosarcoma; Kidney neoplasms; Myocardial infarction; Myocardial ischemia; Non-small cell lung carcinoma; Oral submucous fibrosis; Pancreatic neoplasms; Pituitary neoplasms; Renal cell carcinoma; Prostatic neoplasms; Inflammation; Intestinal polyps; Ischemic stroke; Ischemic proliferative retinopathy; Leiomyosarcoma; Kidney neoplasms; Myocardial infarction; Myocardial ischemia; Non-small cell lung carcinoma; Oral submucous fibrosis; Pancreatic neoplasms; Pituitary neoplasms; Renal cell carcinoma; Prostatic neoplasms; Skin diseases; Squamous cell carcinoma; Stomach neoplasms; Stomach ulcer; Tongue neoplasms; Urinary bladder neoplasms; Transitional cell carcinoma

PTPRZ1

Protein tyrosine phosphatase, receptor-type, Z polypeptide 1

7q31.3

Susceptibility to H. pylori infection

QKI

Quaking homolog, KH domain RNA binding (mouse)

6q26

RNABP1

RAN binding protein 1

22q11.21

rs2238798;

rs175162

RAPGEF6

Rap guanine nucleotide exchange factor (GEF) 6

5q31.1

RELN

Reelin

7q22

rs7341475

Lissencephaly syndrome, Norman-Roberts type

RGS4

Regulator of G-protein signaling 4

1q23.3

rs2661319 (SNP16)

RPGRIP1L

RPGRIP1-like

16q12.2

rs9922369

COACH syndrome; Joubert syndrome 7; Meckel syndrome, type 5

RPP21

Ribonuclease P/MRP 21kDa subunit

6p22.1

rs3130375

RTN4

Reticulon 4

2p16.3

RTN4R

Reticulon 4 receptor

22q11.21

SAT1

Spermidine/spermine N1-acetyltransferase 1

Xp22.1

Continued

SCNB

Synuclein, beta

5q35

Lewy body dementia

SCZD1

Schizophrenia disorder 1

5q11.2-q13.3

SCZD2

Schizophrenia disorder 2

11q14-q21

SCZD3

Schizophrenia disorder 3

6p24-p22

SCZD6

Schizophrenia disorder 6

8p21

SCZD7

Schizophrenia disorder 7

13q32

SCZD8

Schizophrenia disorder 8

18p

SCZD10

Schizophrenia disorder 10

15q15

SCZD11

Schizophrenia susceptibility locus, chromosome 10q-related

10q22.3

SCZD12

Schizophrenia 12

SDCCAG8

CCCAP SLSN7 Serologically defined colon cancer antigen 8

1q43

SELENBP1

Selenium binding protein 1

1q21.3

SFRP1

Secreted frizzled-related protein 1

8p11.21

SH2B1

SH2B adaptor protein 1

16p11.2

SHANK3

SH3 and multiple ankyrin repeat domains 3

22q13.3

Chromosome 22q13.3 deletion syndrome-related autism; Chromosome 22q13.3 deletion syndrome

SHMT1

Serine hydroxymethyltransferase 1 (soluble)

17p11.2

SIGMAR1

Sigma non-opioid intracellular receptor 1

9p13.3

SLC1A1

Solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1

9p24

SLC1A2

Solute carrier family 1 (glial high affinity glutamate transporter), member 2

11p13-p12

SLC1A3

Solute carrier family 1 (glial high affinity glutamate transporter), member 3

5p13

SLC1A6

Solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6

19p13.12

SLC6A1

Solute carrier family 6 (neurotransmitter transporter, GABA), member 1

3p25-p24

SLC6A3

Solute carrier family 6 (neurotransmitter transporter, dopamine), member 3

5p15.3

rs6347

Anxiety disorders; Attention-deficit hyperactivity disorder; Bipolar affective disorder; Bipolar disorder; Brain diseases; Cocaine dependence; Cocaine-induced paranoia; Major depressive disorder; Parkinson’s disease; Parkinsonian disorders; Pervasive development disorders; Protection against nicotine dependence; Susceptibility to tobacco addiction; Tic disorders; Tourette’s syndrome

Continued

SLC6A4

Solute carrier family 6 (neurotransmitter transporter, serotonin), member 4

17q11.2

Alcoholism; Alzheimer disease; Anorexia nervosa; Anxiety disorders; Anxiety-related personality traits; Attention-deficit hyperactivity disorder; Autistic disorder; Bipolar affective disorder and personality traits; Bipolar affective disorders; Bipolar disorder; Brain diseases; Chronobiology disorders; Diabetes mellitus type 2; Frontotemporal lobar degeneration; Irritable bowel syndrome; Major depressive disorder; Migraine with aura; Mood disorders; Obsessive-compulsive disorder; Pain threshold; Primary insomnia; Pulmonary hypertension; Seasonal affective disorder; Sleep disorders; Susceptibility to major depression, to attention-deficit hyperactivity disorder, to autism and rigid-compulsive behaviors; Susceptibility to obsessive-compulsive disorder; Sudden infant death; Tinnitus

SLC6A9

Solute carrier family 6 (neurotransmitter transporter, glycine), member 9

1p33

SLC12A2

Solute carrier family 12 (sodium/potassium/chloride transporters), member 2

5q23.3

SLC12A5

Solute carrier family 12 (potassium/chloride transporter), member 5

20q13.12

SLC17A7

Solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7

19q13

SLC18A1

Solute carrier family 18 (vesicular monoamine), member 1

8p21.3

rs2270641

SMARCA2

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2

9p22.3

rs2296212;

rs3793490;

rs3763627

SNAP25

Synaptosomal-associated protein, 25 kDa

20p12-p11.2

SNAP29

Synaptosomal-associated protein, 29 kDa

22q11.21

Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome

SOX10

SRY (sex determining region Y)-box 10

22q13.1

rs139887

PCWH; PCWH syndrome; Waardenburg syndrome, type 2E, with or without neurologic involvement; Waardenburg syndrome, type 4C; Waardenburg syndrome, type IIE; Waardenburg-Shah syndrome; Yemenite deaf-blind hypopigmentation syndrome

SP4

Sp4 transcription factor

7p15.3

rs12673091;

rs12668354;

rs12673091;

rs3735440;

rs11974306;

rs1018954

SRR

Serine racemase

17p13

rs408067

ST8SIA2

ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2

15q26

rs4586379;

rs2168351

STX1A

Syntaxin 1A (brain)

7q11.23

STX7

Syntaxin 7

6q23.1

SYNGAP1

Synaptic Ras GTPase activating protein 1

6p21.3

Autosomal dominant mental retardation 5

SULT4A1

Sulfotransferase family 4A, member1

22q13.2

SYN2

Synapsin II

3p25

Continued

SYN3

Synapsin III

22q12.3

SYNGR1

Synaptogyrin 1

22q13.1

rs715505

SYT11

Synaptotagmin XI

1q21.2

TAAR6

Trace amine associated receptor 6

6q23.2

TAP1

Transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)

6p21.3

Allergic rhinitis; Bare lymphocyte syndrome (type I); Cervical neoplasia; Dengue viral infection; Hypersensitivity pneumonitis

TARDBP

TAR DNA binding protein

1p36.22

TBP

TATA box binding protein

6q27

Huntington disease-like-4; Parkinson’s disease

TCF4

Transcription factor 4

18q21.1

rs9960767

Pitt-Hopkins syndrome; Risk of bipolar disorder

TDO2

Tryptophan 2,3-dioxygenase

4q31-q32

Tyrosine hydroxylase

11p15.5

rs6356

Segawa syndrome, recessive

TNF

Tumor necrosis factor

6p21.3

rs1800629

Acute kidney failure; Alzheimer disease; Anemia; Arsenic poisoning; Asthma; Behçet’s disease; Bipolar affective disorder; Breast neoplasms; Bronchiectasis; Cerebral malaria; Chronic allograft nephropathy; Coronary artery disease; Coronary restenosis; Diaphragmatic hernia; Experimental diabetes mellitus; Experimental liver cirrhosis; Fever; Hemochromatosis; Hyperalgesia; Hypersensitivity; Hypothermia; Infection; Inflammation; Irritable bowel syndrome; Listeria infections; Lung diseases; Lung neoplasms; Major depressive disorder; Malaria; Microchimerism and diminished immune responsiveness; Migraine; Multiple organ failure; Oral submucous fibrosis; Pain; Plasmodium falciparum blood infection; Postmenopausal osteoporosis; Psoriasis; Pulmonary fibrosis; Pulmonary tuberculosis; Reperfusion injury; Respiratory hypersensitivity; Respiratory tract diseases; Rheumatic heart disease; Rheumatoid arthritis; Sepsis; Septic shock; Skin diseases; Stomach neoplasms; Stomach ulcer; Systemic lupus erythematosus; Ulcerative colitis; Vascular dementia

TP53

Tumor protein p53

17p13.1

rs1042522

Adrenal cortical carcinoma; Alzheimer disease; Bladder neoplasms; Breast neoplasms; Cervical intraepithelial neoplasia; Choroid plexus papilloma; Colonic neoplasms; Colorectal neoplasms; Esophageal cancer; Gastric cancer; Glioblastoma; Head and neck neoplasms; Hepatocellular carcinoma; Histiocytoma; Li-Fraumeni syndrome 1; Lung neoplasms; Lymphocytic leukemia; Multiple malignancy syndrome; Nasopharyngeal carcinoma; Neoplasms; Osteosarcoma; Ovarian neoplasms; Pancreatic cancer; Pancreatic carcinoma; Pancreatic neoplasms; Prostatic neoplasms; Rhabdomyosarcoma; Rheumatoid arthritis; Skin neoplasms; Telangiectasia; Thyroid carcinoma

TPH1

Tryptophan hydroxylase 1

11p15.3-p14

rs1800532

Bulimia; Cardiovascular diseases; Major depression; Obsessive-compulsive disorder; Pulmonary hypertension; Risk for suicidal behavior; Slower response to fluvoxamine

TRIM32

Tripartite motif containing 32

9q33.1

TSNAX

Translin-associated factor X

1q42.1

UFD1L

Ubiquitin fusion degradation 1 like (yeast)

22q11.21

VEGFA

Vascular endothelial growth factor A

6p12

Acute myocardial infarction; Alzheimer disease; Asthma; Atherosclerosis; Biliary atresia; Bladder cancer; Bladder neoplasms; Colon cancer; Colonic neoplasms; Diabetes mellitus (type 2); Diabetic nephropathy; Diabetic retinopathy; Endometriosis; Esophageal cancer; Experimental liver cirrhosis; Gastric cancer; Glioblastoma; Liver neoplasms; Macular degeneration; Neoplasms; Non-small cell lung carcinoma; Ovarian cancer; Psoriasis; Retinopathy; Rhabdomyosarcoma; Rheumatoid arthritis; Squamous cell carcinoma

Continued

VIPR2

Vasoactive intestinal peptide receptor 2

7q36.3

WNK3

WNK lysine deficient protein kinase 3

Xp11.22

XBP1

X-box binding protein 1

22q12

Susceptibility to bipolar disorder; Susceptibility to major affective disorder-7

XRCC1

X-ray repair complementing defective repair In Chinese hamster cells 4

19q13.2

rs6452536 rs35260

Acute lymphoblastic leukemia; Bladder neoplasms; Breast cancer; Breast neoplasms; Gastric cancer; Mesothelioma; Non-small cell lung cancer; Occupational diseases; Prostatic neoplasms; Squamous cell carcinoma of the head and neck

XRCC4

X-ray repair complementing defective repair in Chinese hamster cells 4

5q14.2

YWHAE

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide

17p13.3

YWHAH

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide

22q12.3

ZBED4

Zinc finger, BED-type containing 4

22q13.33

ZDHHC8

Zinc finger, DHHC-type containing 8

22q11.21

ZNF804A

ZInc finger protein 804A

2q32.1

rs1344706;

rs7597593;

rs1344706;

rs4667000;

rs1366842;

rs3731834

(Updated from Cacabelos and Martínez-Bouza [17], and Cacabelos et al. [1]).

Table 2. Pharmacogenomics of Neuroleptics.

Drug

Features

Aripiprazole

Category: Atypical antipsychotic; Arilpiperazine Mechanism: Full agonist: 5-HT_1A, 5-HT_1B, 5-HT_1D, 5-HT₆, 5-HT receptors; partial agonist: D₂ and 5-HT_1A receptors; antagonist: 5-HT_2A receptor Genes: ABCB1, ADRA1A, CYP2D6, CYP3A4, DRD2, DRD3, HRH1, HTR1A, HTR1B, HTR1D, HTR2A, HTR2C, HTR7 Substrate: CYP2D6 (major), CYP3A4 (major)

Benperidol

Category: Antipsychotic, Neuroleptic; Butyrophenone Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors

Genes: DRD1, DRD2

Bromperidol

Category: Antipsychotic, Neuroleptic; Butyrophenone Mechanism: D₂ receptor antagonist; moderate serotonin 5-HT₂receptor antagonist

Genes: ABCB1, ADRA1A, CYP2D6, DRD2, HTR2A Substrate: CYP2D6 (minor), CYP3A4 (major), UGTs Inhibitor: CYP2D6 (moderate)

Chlorpromazine

Category: Phenothiazine antipsychotic; Aliphatic phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors; has a strong anticholinergic effect; weakly blocks ganglionic, antihistaminic and antiserotonergic receptors; blocks α-adrenergic receptors (strong); inverse agonist: 5-HT₆, 5-HT₇; antagonist: 5-HT_1A, 5-HT_2c

Genes: ABCB1, ACACA, ADRA1A, ADRA2A, ADRA2B, ADRA2C, BDNF, CYP1A2, CYP2D6, CYP3A4, CYP2E1, DAO, DRD1, DRD2, DRD3, FABP1, FMO1, HRH1, HTR1A, HTR1E, HTR2A, HTR2C, HTR6, HTR7, KCNE2, LEP, NPY, SCN5A, UGT1A3, UGT1A4 Substrate: CYP1A2 (minor), CYP2D6 (major), CYP3A4 (minor), UGT1A3, UGT1A4 Inhibitor: CYP2D6 (strong), CYP2E1 (weak), DAO

Continued

Clozapine

Category: Atypical antipsychotic; Dibenzodiazepine Mechanism: Antagonist of histamine H₁, cholinergic and α₁-adrenergic receptors; antagonist: 5-HT_1A, 5-HT_2B; full agonist: 5-HT_1A, 5-HT_1B, 5-HT_1D, 5-HT_1F; inverse agonist: 5-HT₆, 5-HT₇

Genes: ABCB1, ADRA1A, ADRA1B, ADRA1D, ADRB3, APOA5, APOC3, APOD, CNR1, CYP1A2, CYP2A6, CYP2C8/9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, DRD1, DRD2, DRD3, DRD4, DTNBP1, FABP1, GNAS1, GNB3, GSK3B, HLAA, HRH1, HRH2, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR3A, HTR6, HTR7, LPL, RGS2, SLC6A2, SLC6A4, TNF, UGT1A3, UGT1A4 Substrate: ABCB1, CYP1A2 (major), CYP2A6 (minor), CYP2C8/9 (minor), CYP2C19 (minor), CYP2D6 (minor), CYP3A4 (major), FMO3, UGT1A3, UGT1A4 Inhibitor: CYP1A2 (weak), CYP2C8/9 (moderate), CYP2C19 (moderate), CYP2D6 (moderate), CYP2E1 (weak), CYP3A4 (weak)

Droperidol

Category: Atypical antipsychotic; Butyrophenone Mechanism: Blocks dopaminergic and α-adrenergic receptors Genes: ABCC8, ADRA1A, ADRAB1, ADRA2A, DRD2, CHRM2, CYP2C9, CYP2C19, CYP3D6, CYP3A4, KCNE1, KCNE2, KCNH2, KCNJ11, KCNQ1, SCN5A Substrate: CYP2C9 (major), CYP2C19 (major), CYP2D6 (major), CYP3A4 (major)

Fluphenazine

Category: Typical antipsychotic; Piperazine phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁ and D₂ receptors; inverse agonist: 5-HT₇; antagonist: 5-HT_2A

Genes: ABCB1, CYP1A2, CYP2A6, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, DRD1, DRD2, HRH1, HTR2A, HTR7 Substrate: CYP2D6 (major)

Inhibitor: CYP1A2 (weak), CYP2C9 (weak), CYP2D6 (strong), CYP2E1 (weak)

Flupenthixol

Category: Typical antipsychotic; Thioxanthene Mechanism: Blocks postsynaptic dopaminergic receptors Genes: DRD1, DRD2

Haloperidol

Category: Typical antipsychotic; Butyrophenone Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors; antagonist: 5-HT_2A, 5-HT_2B

Genes: ABCB1, ABCC1, ADRA1A, ADRA2A, BDNF, CHRM2, CYP1A2, CYP2C9, CYP2D6, CYP3A4, DRD1, DRD2, DRD4, DTNBP1, FOS, GRIN2B, GSK3B, GSTP1, HRH1, HTR2A, HTR2B, HTT, IL1RN, KCNE1, KCNE2, KCNH2, KCNJ11, KCNQ1, SCN5A, UGTs Substrate: CBR, CYP1A1 (minor), CYP1A2 (minor), CYP2C8/9 (minor), CYP2C19 (minor), CYP2D6 (major), CYP3A4 (major), UGTs Inhibitor: CYP2D6 (moderate), CYP3A4 (moderate)

Loxapine

Category: Typical antipsychotic; Dibenzoxazepine Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors; blocks serotonin 5-HT₂receptors; inverse agonist: 5-HT_2c, 5-HT₆

Genes: ADRA1A, DRD1, DRD2, HRH1, HTR2A, HTR2C, HTR6, KCNE2, SCN5A, UGT1A4 Substrate: UGT1A4

Mesoridazine

Category: Typical antipsychotic; Phenothiazine Mechanism: Putative dopaminergic, cholinergic, and adrenergic inhibition Genes: ADRA1A, DRD2, CHRM2, CYP2J2, KCNE1, KCNE2, KCNH2, KCNJ11, KCNQ1, SCN5A Substrate: CYP2J2

Molindone

Category: Typical antipsychotic; Dihydroindolone Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors; has a strong anticholinergic effect; weak ganglionic, antihistaminic and antiserotonergic block; strong α-adrenergic block; antagonist: 5-HT_2A

Genes: ADRA1A, CYPs, DRD2,DRD3, HRH1, HTR1A, HTR1E, HTR2A, HTR2C

Olanzapine

Category: Atypical antipsychotic; Thienobenzodiazepine Mechanism: Strong antagonist of serotonin 5-HT_2A and 5-HT_2C, 5-HT₇, dopaminergic D_1-4, histamine H₁ and α₁-adrenergic receptors; antagonist: 5-HT_2A, 5-HT₃ and muscarinic M_1-5; full agonist: 5-HT_1A, 5-HT_1B, 5-HT_1D, 5-HT_1F; inverse agonist: 5-HT_2c, 5-HT₆

Genes: ABCB1, ADRA1A, ADRB3, APOA5, APOC3, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, COMT, CYP1A2, CYP2C8/9, CYP2C19, CYP2D6, CYP3A4, DRD1, DRD2, DRD3, DRD4, FMO1, GNB3, GRM3, HRH1, HRH2, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2C, HTR3A, HTR6, HTR7, KCNH2, LEP, LEPR, LPL, RGS2, SLC6A2, TNF, UGT1A4 Substrate: CYP1A2 (major), CYP2D6 (major), UGT1A4 Inhibitor: CYP1A2 (weak), CYP2C8/9 (weak), CYP2C19 (weak), CYP2D6 (weak), CYP3A4 (weak)

Continued

Paliperidone

Category: Atypical antipsychotic; Benzisoxazole Mechanism: Serotonin and dopamine receptor antagonist; has high affinity for α₁, D₂, H₁, and 5-HT_2C receptors; low affinity for muscarinic and 5-HT_1A receptors Genes: ABCB1, ADRA1A, ADRA1B, ADRA1D, CHRMs, CYP2D6, CYP3A4, DRD2, HRH1, HTR1A, HTR2A, UGTs Substrate: ABCB1, ADH, CYP2D6 (major), CYP3A4 (major), UGTs Inhibitor: ABCB1, CYP2D6 (moderate), CYP3A4 (moderate)

Periciazine

Category: Typical antipsychotic; Piperidine phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors; blocks α-adrenergic receptors; inverse agonist: 5-HT₆, 5-HT₇; antagonist: 5-HT_2A_, 5-HT_2c

Genes: ADRA1A, CYP2D6, CYP3A4/5, DRD1, DRD2, DRD3, HTR2A, HTR2C, HTR6, HTR7 Substrate: CYP2D6, CYP3A4

Perphenazine

Category: Typical antipsychotic; Piperazine phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors Genes: ABCB1, CYP1A2, CYP2C8/9, CYP2C19, CYP2D6, CYP3A4, DRD1, DRD2, RGS4 Substrate: CYP1A2 (major), CYP2C8/9 (major), CYP2C18/19 (major), CYP2D6 (major), CYP3A4/5 (major)

Inhibitor: CYP1A2 (weak), CYP2D6 (weak)

Pimozide

Category: Typical antipsychotic; Difenylbutylpiperidine Mechanism: Dopaminergic antagonist; antagonist: 5-HT_1A, 5-HT_2A,5-HT₇

Genes: ABCB1, ADRA1A, CHRM2, CYP1A2, CYP2C19, CYP2D6, CYP2E1, CYP3A4, DRD2, HRH1, HTR1A, HTR2A, HTR7, KCNE1, KCNE2, KCNH2, KCNQ1, SCN5A Substrate: CYP1A2 (minor), CYP3A4 (major)

Inhibitor: CYP2C19 (weak), CYP2D6 (strong), CYP2E1 (weak), CYP3A4 (moderate)

Pipotiazine

Category: Typical antipsychotic; Piperidine phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors Genes: CYP2D6, CYP3A4, DRDs Substrate: CYP2D6, CYP3A4

Prochlorperazine

Category: Typical antipsychotic; Piperazine phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors; strong α-adrenergic and anticholinergic block Genes: ABCB1, ADRA1A, CYPs, DRD1, DRD2

Quetiapine

Category: Atypical antipsychotic; Dibenzothiazepine Mechanism: Serotonergic (5-HT_1A, 5-HT_2A_, 5-HT₂), dopaminergic (D₁ and D₂), histaminergic H₁, and adrenergic (α₁- and α₂-) receptor antagonist; full agonist: 5-HT_1A, 5-HT_1D, 5-HT_1F, 5-HT_2A

Genes: ABCB1, ADRA1A, ADRA2A, CYP3A4, CYP2D6, DRD1, DRD2, DRD4, HRH1, HTR1A, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, KCNE1, KCNE2, KCNH2, KCNQ1, RGS4, SCN5A Substrate: CYP3A4 (major), CYP2D6 (minor)

Risperidone

Category: Atypical antipsychotic; Benzisoxazole Mechanism: Serotonergic, dopaminergic, α₁-, α₂-adrenergic and histaminergic receptor antagonist; low-moderate affinity for 5-HT_1C, 5-HT_1D, and 5-HT_1A receptors, low affinity for D₁; inverse agonist: 5-HT_2c, 5-HT₆, 5-HT₇

Genes: ABCB1, ADRA1A, ADRA1B, ADRA1D, APOA5, COMT, CYP2D6, CYP2A4, CYP3A4, DRD1, DRD2, DRD3, DRD4, FOS, GRM3, HRH1, HTR1A, HTR1B, HTR1C, HTR1D, HTR1E, HTR1F, HTR2A, HTR2C, HTR3A, HTR6, HTR7, KCNE2, KCNH2, PON1, RGS2, RGS4, SCN5A, SLC6A2, SLC6A4 Substrate: ABCB1, CYP2D6 (major), CYP3A4 (minor)

Inhibitor: ABCB1, CYP2D6 (weak), CYP3A4 (weak)

Sulpiride

Category: Atypical antipsychotic; Benzamide Mechanism: Postsynaptic D₂ antagonist Genes: CYP2D6, CYP3A4, DRD2 Substrate: CYP2D6

Thioridazine

Category: Typical antipsychotic; Phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic receptors; blocks α-adrenergic receptors (strong); inverse agonist: 5-HT₆, 5-HT₇; antagonist: 5-HT_2c

Genes: ABCB1, ADRA1A, CHRM2, CYP1A2, CYP2C8/9, CYP2D6, CYP2C19, CYP2E1, CYP2J2, DRD2, FABP1, HRH1, HTR6, HTR7, HTR2C, KCNE1, KCNE2, KCNH2, KCNJ11, KCNQ1, SCN5A Substrate: CYP1A2 (major), CYP2C19 (minor), CYP2D6 (major), CYP2J2 (major), CYP3A4 (major)

Inhibitor: ADRA1, ADRA2, ADRBs, CYP1A2 (weak), CYP2C8/9 (weak), CYP2D6 (moderate), CYP2E1 (weak), DRD1

Thiothixene

Category: Typical antipsychotic; Thioxanthene Mechanism: Inhibits dopamine receptors; blocks α-adrenergic receptors; antagonist: 5-HT_2a

Genes: ADRA1A, CYP1A2, CYP2D6, DRD2, HRH1, HTR2A, KCNE1, KCNE2, KCNQ1, KCNH6, SCN5A Substrate: CYP1A2 (major)

Inhibitor: CYP2D6 (weak)

Continued

Trifluoperazine

Category: Typical antipsychotic; Phenothiazine Mechanism: Blocks postsynaptic mesolimbic dopaminergic receptors; blocks α-adrenergic receptors Genes: ABCB1, ADRA1A, CYP1A2, DRD2, IL12B, UGT1A4 Substrate: CYP1A2 (major), UGT1A4

Ziprasidone

Category: Atypical antipsychotic; Benzylisothiazolylpiperazine Mechanism: High affinity for: D₂, D₃, 5-HT_2A, 5-HT_1A, 5-HT_2C, 5-HT_1D and α₁-adrenergic receptors; moderate affinity for histamine H₁ receptors; antagonist: D₂, 5-HT_1A, 5-HT_2A, and 5-HT_1D; full agonist: 5-HT_1B, 5-HT_1D; partial agonist: 5-HT_1A; inverse agonist: 5-HT_2c, 5-HT₇

Genes: ADRA1A, AOX1, CYP1A2, CYP2D6, CYP3A4, DRD2, DRD3, DRD4, HRH1, HTR1A, HTR1B, HTR1D, HTR1E, HTR2A, HTR2C, HTR7, KCNE2, KCNH2, RGS4, SCN5A Substrate: AOXs, CYP1A2 (minor), CYP3A4 (major), HTR1A Inhibitor: CYP2D6 (moderate), CYP3A4 (moderate), HTR2A, DRD2

Zuclopenthixol

Category: Typical antipsychotic; Thioxanthene Mechanism: Blocks postsynaptic mesolimbic dopaminergic receptors Genes: CYP2D6, DRD1, DRD2 Substrate: CYP2D6 (major)

Symbols: ABCB1: ATP-binding cassette, sub-family B (MDR/TAP), member 1, ACACA: Acetyl-Coenzyme A carboxylase alpha, ADRA1A: Adrenergic, alpha-1A-, receptor, ADRA1B: Adrenergic, alpha-1B-, receptor, ADRB3: Adrenergic, beta-3-, receptor, ADRA1D: Adrenergic, alpha-1D-, receptor, AOX1: Aldehyde oxidase 1, APOA5: Apolipoprotein A-V, APOC3: Apolipoprotein C-III, APOD: Apolipoprotein D, BDNF: Brain-derived neurotrophic factor, CFTR: Cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7), CHRMs: Muscarinic receptors, CHRM1: Cholinergic receptor, muscarinic 1, CHRM2: Cholinergic receptor, muscarinic 2, CHRM3: Cholinergic receptor, muscarinic 3, CHRM4: Cholinergic receptor, muscarinic 4, CHRM5: Cholinergic receptor, muscarinic 5, CNR1: Cannabinoid receptor 1 (brain), COMT: Catechol-O-methyltransferase, CYP1A2: Cytochrome P450, family 1, subfamily A, polypeptide 2, CYP2A6: Cytochrome P450, family 2, subfamily A, polypeptide 6, CYP2C19: Cytochrome P450, family 2, subfamily C, polypeptide 19, CYP2C8: Cytochrome P450, family 2, subfamily C, polypeptide 8, CYP2C9: Cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2D6: Cytochrome P450, family 2, subfamily D, polypeptide 6, CYP2J2: Cytochrome P450, family 2, subfamily J, polypeptide 2, CYP2E1: Cytochrome P450, family 2, subfamily E, polypeptide 1, CYP3A4: Cytochrome P450, family 3, subfamily A, polypeptide 4, DRDs: Dopamine receptors, DRD1: Dopamine receptor D1, DRD2: Dopamine receptor D2, DRD3: Dopamine receptor D3, DRD4: Dopamine receptor D4, DTNBP1: Dystrobrevin binding protein 1, FABP1: Fatty acid binding protein 1, liver, FMO1: Flavin containing monooxygenase 1, FOS: FBJ murine osteosarcoma viral oncogene homolog, GNAS: GNAS complex locus, GNB3: Guanine nucleotide binding protein (G protein), beta polypeptide 3, GRIN2B: Glutamate receptor, ionotropic, N-methyl D-aspartate 2B, GRM3: Glutamate receptor, metabotropic 3, GSK3B: Glycogen synthase kinase 3 beta, HLA: Major histocompatibility complex, HLA-A: Major histocompatibility complex, class I, A, HRH1: Histamine receptor H1, HRH2: Histamine receptor H2, HRH3: Histamine receptor H3, HRH4: Histamine receptor H4, HTR1A: 5-Hydroxytryptamine (serotonin) receptor 1A, HTR1B: 5-Hydroxytryptamine (serotonin) receptor 1B, HTR1D: 5-Hydroxytryptamine (serotonin) receptor 1D, HTR1E: 5-Hydroxytryptamine (serotonin) receptor 1E, HTR1F: 5-Hydroxytryptamine (serotonin) receptor 1F, HTR2A: 5-Hydroxytryptamine (serotonin) receptor 2A, HTR2B: 5-Hydroxytryptamine (serotonin) receptor 2B, HTR2C: 5-Hydroxytryptamine (serotonin) receptor 2C, HTR3A: 5-Hydroxytryptamine (serotonin) receptor 3A, HTR6: 5-Hydroxytryptamine (serotonin) receptor 6, HTR7:5-Hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled), HTT: Huntingtin, IL12B: Interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40), IL1RN: Interleukin 1 receptor antagonist, KCNE1: Potassium voltage-gated channel, Isk-related family, member 1, KCNE2: Potassium voltage-gated channel, Isk-related family, member 2, KCNH: Potassium voltage-gated channel, subfamily H (eag-related), member 1-8, KCNH2: Potassium voltage-gated channel, subfamily H (eag-related), member 2, KCNH6: Potassium voltage-gated channel, subfamily H (eag-related), member 6, KCNJ11: Potassium inwardly-rectifying channel, subfamily J, member 11, KCNQ1: Potassium voltage-gated channel, KQT-like subfamily, member 1, LEP: Leptin, LEPR: Leptin receptor, LPL: Lipoprotein lipase, NPY: Neuropeptide Y, PON1: Paraoxonase 1, RGS2: Regulator of G-protein signaling 2, 24kDa, RGS4: Regulator of G-protein signaling 4, SCN5A: Sodium channel, voltage-gated, type V, alpha subunit, SLC6A2: Solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2, SLC6A4: Solute carrier family 6 (neurotransmitter transporter, serotonin), member 4, TNF: Tumor necrosis factor (TNF superfamily, member 2), UGT1A3: UDP glucuronosyltransferase 1 family, polypeptide A3, UGT1A4: UDP glucuronosyltransferase 1 family, polypeptide A4. (Generated with data from Cacabelos [25]).

CYP1A2 enzymes, 40% of CYP2D6, and 23% of CYP3A4; 24% of antidepressants are major substrates of CYP1A2 enzymes, 5% of CYP2B6, 38% of CYP2C19, 85% of CYP2D6, and 38% of CYP3A4; 7% of benzodiazepines are major substrates of CYP2C19 enzymes, 20% of CYP2D6, and 95% of CYP3A4 [14]. Most CYP enzymes exhibit ontogenic-, age-, sex-, circadian-, and ethnic-related differences [26]. The practical consequence of this genetic variation is that the same drug can be differentially metabolized according to the genetic profile/expression during each subject’s lifespan, and that knowing the pharmacogenomic profile of an individual, his/her pharmacodynamic response is potentially predictable to some extent.

Among genes of the CYP superfamily with relevance in the metabolism of psychotropic drugs, the CYP2D6, CYP2C19, CYP2C9, and CYP3A4/5 genes deserve special attention.

CYP2D6. CYP2D6 is a 4.38 kb gene with 9 exons mapped on 22q13.2. Four RNA transcripts of 1190 - 1684 bp are expressed in the brain, liver, spleen and reproductive system, where 4 major proteins of 48 - 55 kDa (439 - 494 aa) are identified. This protein is a transport enzyme of the cytochrome P450 subfamily IID or multigenic cytochrome P450 superfamily of mixedfunction monooxygenases which localizes to the endoplasmic reticulum and is known to metabolize as many as 25% of commonly-prescribed drugs and over 60% of current psychotropics. The gene is highly polymorphic in the population. There are 141 CYP2D6 allelic variants, of which −100C > T, −1023C > T, −1659G > A, −1707delT, −1846G > A, −2549delA, −2613 − 2615delAGA, −2850C > T, −2988G > A, and −3183G > A represent the 10 most important variants. Different alleles result in the extensive, intermediate, poor, and ultra-rapid metabolizer phenotypes, characterized by normal, intermediate, decreased, and multiplied ability to metabolize the enzyme’s substrates, respectively. P450 enzymes convert xenobiotics into electrophilic intermediates which are then conjugated by phase II enzymes to hydrophilic derivatives that can be excreted. According to the database of the World Guide for Drug Use and Pharmacogenomics [25], 982 drugs are CYP2D6-related: 371 drugs are substrates, over 300 drugs are inhibitors, and 18 drugs are CYP2D6 inducers.

Among healthy individuals, extensive metabolizers (EMs) account for 55.71% of the population, whereas intermediate metabolizers (IMs) are 34.7%, poor metabolizers (PMs) 2.28%, and ultra-rapid metabolizers (UMs) 7.31%. Remarkable interethnic differences exist in the frequency of the PM and UM phenotypes among different societies all over the world [4,27-29]. On average, approximately 6.28% of the world population belongs to the PM category. Europeans (7.86%), Polynesians (7.27%), and Africans (6.73%) exhibit the highest rate of PMs, whereas Orientals (0.94%) show the lowest rate [27]. The frequency of PMs among Middle Eastern populations, Asians, and Americans is in the range of 2% - 3%. CYP2D6 gene duplications are relatively infrequent among Northern Europeans, but in East Africa the frequency of alleles with duplication of CYP2D6 is as high as 29% [30]. In Europe, there is a North-South gradient in the frequency of PMs (6% - 12% of PMs in Southern European countries, and 2% - 3% PMs in Northern latitudes) [25]. In SCZ, EMs, IMs, PMs, and UMs are 58.42%, 27.72%, 3.96%, and 9.9%, respectively, with a 3% increase in the frequency of EMs, and a 7% decrease in the frequency of IMs with respect to controls in the Iberian population. In Alzheimer disease (AD), EMs, IMs, PMs, and UMs are 56.38%, 27.66%, 7.45%, and 8.51%, respectively, and in vascular dementia, 52.81%, 34.83%, 6.74%, and 5.62%, respectively (Figures 2 and 3). There is an accumulation of AD-related genes of risk in PMs and UMs. EMs and IMs are the best responders, and PMs and UMs are the worst responders to pharmacological treatment. Patients with depression show significant differences in the genotypic and phenotypic profiles as compared to controls and also with respect to patients with psychosis, Parkinson’s disease, or brain tumors. Patients with stroke show differences as compared to patients with brain tumors, and both patients with brain tumors or with cranial nerve neuropathies differ in their CYP2D6 phenotype with regard to controls. These geno-phenotypic profiles might be important in

the pathogenesis of some CNS disorders and in the therapeutic response to conventional psychotropic drugs as well [2] (Figures 2 - 3).

CYP2C9. CYP2C9 is a gene (50.71 kb) with 9 exons mapped on 10q24. An RNA transcript of 1860 bp is mainly expressed in hepatocytes, where a protein of 55.63 kDa (490 aa) can be identified. Over 600 drugs are CYP2C9-related, 311 acting as substrates (177 are major substrates, 134 are minor substrates), 375 as inhibitors (92 weak, 181 moderate, and 102 strong inhibitors), and 41 as inducers of the CYP2C9 enzyme [25]. There are 481 CYP2C9 SNPs. CYP2C9-*1/*1 EMs represent 60.56% of the healthy population; *1/*2 and *1/*3 IMs 18.78% and 13.62%, respectively (32.39% IMs); and *2/*2, *2/*3, and *3/*3 PMs, 3.76%, 3.28%, and 0%, respectively (7.04% PMs). No CYP2C9-*3/*3 cases have been found in the control population; however, in patients with depression, psychosis, and mental retardation the frequency of this genotype is 0.91%, 1.03%, and 1.37%, respectively (Figure 4). The frequency of PMs, IMs, and PMs in the control population are 60.56%, 32.39%, and 7.04%, respectively, and in SCZ are 61.86%, 32.99%, and 5.15% (Figure 5). Significant variation has been found in CYP2C9 genotypes among diverse brain diseases [2] (Figures 4 - 5).The plethora of metabolizing profiles in CNS disorders suggest a potential pathogenic role of CYP2C9 in brain pathology and a very strong role of the CYP2C9 enzyme on drugs with deleterious effects on cerebrovascular function (e.g. NSAIDs) and thromboembolic phenomena and/or bleeding (e.g. warfarin, coumarinics).

CYP2C19. CYP2C19 is a gene (90.21 kb) with 9 exons mapped on 10q24.1q24.3. RNA transcripts of 1901 bp, 2395 bp, and 1417 bp are expressed in liver cells where a protein of 55.93 kDa (490 aa) is identified. Nearly 500 drugs are CYP2C19-related, 281 acting as substrates (151 are major substrates, 130 are minor substrates), 263 as inhibitors (72 weak, 127 moderate, and 64 strong inhibitors), and 23 as inducers of the CYP2C19 enzyme [25]. About 541 SNPs have been detected in the CYP2C19 gene. The frequencies of the 3 major CYP2C19 geno-phenotypes in the control population are CYP2C19-*1/*1-EMs 68.54%, CYP2C19-*1/*2-IMs 30.05%, and CYP2C19-*2/*2-PMs 1.41%. In SCZ, EMs, IMs, and PMs represent 76.29%, 22.68%, and 1.03%, respectively (Figure 6). Minor variation has been reported in different brain disorders [2].

CYP3A4/5. CYP3A4 is a gene (27.2 kb) with 13 exons mapped on 7q21.1. RNA transcripts of 2153 bp, 651 bp, 564 bp, 2318 bp and 2519 bp are expressed in intestine, liver, prostate and other tissues where 4 protein variants of 57.34 kDa (503 aa), 17.29 kDa (153 aa), 40.39 kDa (353 aa), and 47.99 kDa (420 aa) are identified. The human CYP3A locus contains the three CYP3A genes (CYP3A4, CYP3A5 and CYP3A7), three pseudogenes as well as a novel CYP3A gene termed CYP3A43. The gene encodes a putative protein with between 71.5% and 75.8% identity to the other CYP3A proteins. The predominant hepatic form is CYP3A4, but CYP3A5 contributes significantly to the total liver CYP3A activity. This enzyme metabolizes over 1900 drugs, 1033 acting as substrates (897 are major substrates, 136 are minor substrates), 696 as inhibitors (118 weak, 437 moderate, and 141 strong inhibitors), and 241 as

inducers of the CYP3A4 enzyme [25]. About 347 SNPs have been identified in the CYP3A4 gene (CYP3A4*1A: Wild-type), 25 of which are of clinical relevance; in a Caucasian population, 82.75% are EMs (CYP3A5*3/*3), 15.88% are IMs (CYP3A5*1/*3), and 1.37% are UMs (CYP3A5*1/*1). Unlike other human P450s (CYP2D6, CYP2C19) there is no evidence of a “null” allele for CYP3A4 [2].

CYP Clustering. The construction of a genetic map integrating the most prevalent CYP2D6 + CYP2C19 + CYP2C9 polymorphic variants in a trigenic cluster yields 82 different haplotype-like profiles. The most frequent trigenic genotypes are *1*1-*1*1-*1*1 (25.70%), *1*1-*1*2-*1*2 (10.66%), *1*1-*1*1-*1*1 (10.45%), *1*4-*1*1-*1*1 (8.09%), *1*4-*1*2-*1*1 (4.91%), *1*4-*1*1-*1*2 (4.65%), and *1*1-*1*3-*1*3 (4.33%). These 82 trigenic genotypes represent 36 different pharmacogenetic phenotypes. According to these trigenic

clusters, only 26.51% of the population show a pure 3EM phenotype, 15.29% are 2EM1IM, 2.04% are pure 3IM, 0% are pure 3PM, and 0% are 1UM2PM (the worst possible phenotype). This implies that only one-quarter of the population processes normally the drugs which are metabolized via CYP2D6, CYP2C9 and CYP2C19 (approximately 60% of the drugs of current use) [2,5,10,12].

2.4. Genes Encoding Drug Transporters

ABC genes, especially ABCB1 (ATP-binding cassette, subfamily B, member 1; P-glycoprotein-1, P-gp1; Multidrug Resistance 1, MDR1) (7q21.12), ABCC1 (9q31.1), ABCG2 (White1) (21q22.3), and other genes of this family encode proteins which are essential for drug metabolism and transport. The multidrug efflux transporters P-gp, multidrug-resistance associated protein 4 (MRP4) and breast cancer resistance protein (BCRP), located on endothelial cells lining brain vasculature, play important roles in limiting movement of substances into and enhancing their efflux from the brain. Transporters also cooperate with Phase I/Phase II metabolism enzymes by eliminating drug metabolites. Their major features are their capacity to recognize drugs belonging to unrelated pharmacological classes, and their redundancy, by which a single molecule can act as a substrate for different transporters. This ensures an efficient neuroprotection against xenobiotic invasions. The pharmacological induction of ABC gene expression is a mechanism of drug interaction, which may affect substrates of the up-regulated transporter, and overexpression of MDR transporters confers resistance to anticancer agents and CNS drugs [31,32]. Also of importance for CNS pharmacogenomics are transporters encoded by genes of the solute carrier superfamily (SLC) and solute carrier organic (SLCO) transporter family, responsible for the transport of multiple endogenous and exogenous compounds, including folate (SLC19A1), urea (SLC14A1, SLC14A2), monoamines (SLC29A4, SLC22A3), aminoacids (SLC1A5, SLC3A1, SLC7A3, SLC7A9, SLC38A1, SLC38A4, SLC38A5, SLC38A7, SLC43A2, SLC45A1), nucleotides (SLC29A2, SLC29A3), fatty acids (SLC27A1-6), neurotransmitters (SLC6A2 (noradrenaline transporter), SLC6A3 (dopamine transporter), SLC6A4 (serotonin transporter, SERT), SLC6A5, SLC6A6, SLC6A9, SLC6A11, SLC6A12, SLC6A14, SLC6A15, SLC6A16, SLC6A17, SLC6A18, SLC6A19), glutamate (SLC1A6, SLC1A7), and others [24]. Some organic anion transporters (OAT), which belong to the solute carrier (SLC) 22A family, are also expressed at the BBB, and regulate the excretion of endogenous and exogenous organic anions and cations [33]. The transport of amino acids and diand tripeptides is mediated by a number of different transporter families, and the bulk of oligopeptide transport is attributable to the activity of members of the SLC15A superfamily (Peptide Transporters 1 and 2 [SLC15A1 (PepT1) and SLC15A2 (PepT2), and Peptide/Histidine Transporters 1 and 2 [SLC15A4 (PHT1) and SLC15A3 (PHT2)]. ABC and SLC transporters expressed at the BBB may cooperate to regulate the passage of different molecules into the brain [34]. Polymorphic variants in ABC and SLC genes may also be associated with pathogenic events in CNS disorders and drug-related safety and efficacy complications [25].

2.5. Pleiotropic Genes

Apolipoprotein E (APOE) is a pathogenic gene in dementia and the prototypical paradigm of a pleiotropic gene with multifaceted activities in physiological and pathological conditions, including cardiovascular disease, dyslipidemia, atherosclerosis, stroke, and AD [2,6,14]. ApoE is consistently associated with the amyloid plaque marker for AD. APOE-4 may influence AD pathology interacting with APP metabolism and Aβ accumulation, enhancing hyperphosphorylation of tau protein and NFT formation, reducing choline acetyltransferase activity, increasing oxidative processes, modifying inflammationrelated neuroimmunotrophic activity and glial activation, altering lipid metabolism, lipid transport and membrane biosynthesis in sprouting and synaptic remodeling, and inducing neuronal apoptosis [35].

The distribution of APOE genotypes in the Iberian Peninsula is as follows: APOE-2/2 0.32%, APOE-2/3 7.3%, APOE-2/4 1.27%, APOE-3/3 71.11%, APOE-3/4 18.41%, and APOE-4/4 1.59% (Figure 3). These frequencies are very similar in Europe and in other Western societies. There is a clear accumulation of APOE-4 carriers among patients with AD (APOE-3/4 30.30%; APOE-4/4 6.06%) and vascular dementia (APOE-3/4 35.85%, APOE-4/4 6.57%) as compared to controls (Figure 7). The distribution and frequencies of APOE genotypes in AD also differ from those of patients with anxiety, depression, psychosis, migraine, vascular encephalopathy, and post-traumatic brain injury syndrome [2,6,14] (Figure 3). Different APOE genotypes confer specific phenotypic profiles to AD patients. Some of these profiles may add risk or benefit when the patients are treated with conventional drugs, and in many instances the clinical phenotype demands the administration of additional drugs which increase the complexity of therapeutic protocols. From studies designed to define APOE-related AD phenotypes, several conclusions can be drawn: 1) the age-at-onset is 5 - 10 years earlier in approximately 80% of AD cases harboring the APOE-4/4 genotype; 2) the serum levels of ApoE are lowest in APOE-4/4, intermediate in APOE-3/3 and APOE-3/4, and highest in APOE-2/3 and APOE-2/4; 3) serum cholesterol levels are higher in APOE-4/4 than in the other genotypes; 4) HDL-cholesterol levels tend to be lower in APOE-3 homozygotes than in APOE-4 allele carriers; 5) LDL-cholesterol levels are systematically higher in APOE-4/4 than in any other genotype; 6) triglyceride levels are significantly lower in APOE-4/4; 7) nitric oxide levels are slightly lower in APOE-4/4; 8) serum and cerebrospinal fluid Aβ levels tend to differ between APOE-4/4 and the other most frequent genotypes (APOE-3/3, APOE-3/4); 9) blood histamine levels are dramatically reduced in APOE-4/4 as compared with the other genotypes; 10) brain atrophy is markedly increased in APOE-4/4 > APOE-3/4 > APOE-3/3; 11) brain mapping activity shows a significant increase in slow wave activity in APOE-4/4 from early stages of the disease; 12) brain hemodynamics, as reflected by reduced brain blood flow velocity and increased pulsatility and resistance indices, is significantly worse in APOE-4/4 (and in APOE-4 carriers in general, as compared with APOE-3 carriers); brain hypoperfusion and neocortical oxygenation is also more deficient in APOE-4 carriers; 13) lymphocyte apoptosis is markedly enhanced in APOE-4 carriers; 14) cognitive deterioration is faster in APOE-4/4

patients than in carriers of any other APOE genotype; 15) in approximately 3% - 8% of the AD cases, the presence of some dementia-related metabolic dysfunctions accumulates more in APOE-4 carriers than in APOE-3 carriers; 16) some behavioral disturbances, alterations in circadian rhythm patterns, and mood disorders are slightly more frequent in APOE-4 carriers; 17) aortic and systemic atherosclerosis is also more frequent in APOE-4 carriers; 18) liver metabolism and transaminase activity also differ in APOE-4/4 with respect to other genotypes; 19) hypertension and other cardiovascular risk factors also accumulate in APOE-4; and 20) APOE-4/4 carriers are the poorest responders to conventional drugs. These 20 major phenotypic features clearly illustrate the biological disadvantage of APOE-4 homozygotes and the potential consequences that these patients may experience when they receive pharmacological treatment for AD and/or concomitant pathologies [2,4-6,9-12,35].

When APOE and CYP2D6 genotypes are integrated in bigenic clusters and the APOE + CYP2D6-related therapeutic response to a combination therapy is analyzed in AD patients, it becomes clear that the presence of the APOE-4/4 genotype is able to convert pure CYP2D6*1/*1 extensive metabolizers into full poor responders to conventional treatments, indicating the existence of a powerful influence of the APOE-4 homozygous genotype on the drug-metabolizing capacity of pure CYP2D6 extensive metabolizers. In addition, a clear accumulation of APOE-4/4 genotypes is observed among CYP2D6 poor and ultra-rapid metabolizers [4,11].

3. GENOMICS OF SCHIZOPHRENIA AND PSYCHOTIC DISORDERS3.1. Structural Genomics

Genetic studies in SCZ have revealed the presence of cytogenetic changes, chromosome anomalies and multiple candidate genes potentially associated with psychosis and related traits; and neurocognitive impairment was found to be heritable in individuals with SCZ and their relatives [36]. First-degree relatives of probands with SCZ or bipolar disorder (BD) are at increased risk of these disorders. Half-siblings have a significantly increased risk, but substantially lower than that of fullsiblings. Heritability for SCZ and BD is 64% and 59%, respectively. Shared environmental effects are small but substantial (SCZ: 4.5%, 4.4% - 7.4%; BD: 3.4%, 2.3% - 6.2%) for both disorders. SCZ and BD partly share common genetic determinants [37]. Linkage analysis of SCZ in African-American families revealed that several regions show a decrease in the evidence for linkage as the definition broadens: 8q22.1 (rs911, 99.26 cM), 16q24.3 (rs1006547, 130.48 cM), and 20q13.2 (rs1022689, 81.73 cM). One region shows a substantial increase in evidence for linkage, 11p15.2 (rs722317, 24.27 cM). These linkage results overlap two broad, previously-reported linkage regions: 8p23.3-p12, found in studies sampling largely families of European ancestry; and 11p11.2-q22.3, reported by a study of AfricanAmerican families [38].

The genome-wide linkage scan analysis of 707 European-ancestry families identified suggestive evidence for linkage on chromosomes 8p21, 8q24.1, 9q34 and 12q24.1. Genome-wide significant evidence for linkage was observed on chromosome 10p12. Significant heterogeneity was also observed on chromosome 22q11.1. Evidence for linkage across family sets and analyses was most consistent on chromosome 8p21, with a one-LOD support interval that does not include the candidate gene NRG1, suggesting that one or more other susceptibility loci might exist in the region [39]. Genome-wide significant evidence for linkage for SCZ or schizoaffective disorder was found in a region on chromosome 17q21 in families of Mexican and Central American ancestry. A region on chromosome 15q22-23 showed suggestive evidence of linkage with this same phenotype [40].

The human genome is enriched in interspersed segmental duplications that sensitize approximately 10% of our genome to recurrent microdeletions and microduplications as a result of unequal crossing-over. Studies of common complex genetic disease show that a subset of these recurrent events plays an important role in autism, SCZ, and epilepsy [41]. The advent of genome-wide SNP and copy number variant (CNV) microarray technologies heralds identification of additional SCZ loci. Over 200 genes, reported in about 2400 studies, have been associated with SCZ during the past two decades; however, it is likely that over 1000 genes might be involved in SCZ pathogenesis through epistatic interaction and epigenetic phenomena. Many of these associations could not be replicated in different populations, as happens with many other multifactorial/complex disorders [42]. Data suggest that these susceptibility genes influence the cortical information processing which characterizes the schizophrenic phenotype. Aberrant postnatal brain maturation is an essential mechanism underlying the disease. Several candidate genes have been suggested, with the strongest evidence for genes encoding dystrobrevin binding protein 1 (DTNBP1), neuregulin 1 (NRG1), neuregulin 1 receptor (ERBB4) and disrupted in SCZ1 (DISC1), as well as several neurotrophic factors. These genes are involved in neuronal plasticity and also play a role in adult neurogenesis [43].

Several studies of the dystrobrevin-binding protein 1 gene (DTNBP1), neuregulin 1 (NRG1), D-amino-acid oxidase (DAO), DAO activator (DAOA, G72), and metabotropic glutamate receptor 3 (GRM3) genes have suggested an association between variants of these genes and SCZ; however, several studies did not replicate associations of DTNBP1, NRG1, DAO, DAOA, and GRM3 gene polymorphisms and SCZ [44]. Within the last 2 years, a number of genome-wide association studies (GWAS) of SCZ and BD have been published [45-48]. These have produced stronger evidence for association to specific risk loci than had earlier studies, specifically for the zinc finger binding protein 804A (ZNF804A) locus in SCZ and for the calcium channel, voltage-dependent, L type, alpha 1C subunit (CACNA1C) and ankyrin 3, node of Ranvier (ANK3) loci in BD. The ZNF804A and CACNA1C loci appear to influence risk for both disorders, a finding that supports the hypothesis that SCZ and BD are not etiologically distinct. In the case of SCZ, a number of rare copy number variants have also been detected that have fairly large effect sizes on disease risk, and that additionally influence risk of autism, mental retardation, and other neurodevelopmental disorders. The existing findings point to some likely pathophysiological mechanisms but also challenge current concepts of disease classification [49]. A genome scan meta-analysis (GSMA) was carried out on 32 independent genomewide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with SCZ or related disorders. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142 - 168 Mb) and 2q (103 - 134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119 - 152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for ‘aggregate’ genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16 - 33 Mb) [50]. In another GWAS, evidence was found for association to genes reported in other GWAS data sets (CACNA1C) or to closely-related family members of those genes, including CSF2RB, CACNA1B and DGKI [51].

A summary of genes (or pathological pathways) with potential effect in SCZ pathogenesis is the major goal of the present review in order to understand the complex molecular mechanisms which might be responsible for the clinical manifestations of one of the oldest diseases in the constellation of mental illness.

3.2. Genes Potentially Associated with Schizophrenia and Psychotic Disorders

ABCA13 (ATP-binding cassette, sub-family A (ABC1), member 13). The lipid transporter gene ABCA13 is a susceptibility factor for both SCZ and BD. SCZ and BD are leading causes of morbidity across all populations, with heritability estimates of approximately 80%, indicating a substantial genetic component. Population genetics and GWAS suggest an overlap of genetic risk factors between these illnesses. Knight et al. [52] resequenced ABCA13 exons in cases with SCZ and controls. Multiple rare coding variants were identified, including one nonsense and nine missense mutations and compound heterozygosity/homozygosity in 6% of cases. Variants were genotyped in additional SCZ, bipolar, depression and control cohorts, and the frequency of all rare variants combined was greater than controls in SCZ and BD. The population-attributable risk of these mutations was 2.2% for SCZ and 4.0% for BD [52].

Abelson helper integration site 1 (AHI1). The Abelson helper integration site 1 (AHI1) gene locus on chromosome 6q23.3 is among a group of candidate loci for SCZ susceptibility that were initially identified by linkage followed by linkage disequilibrium (LD) mapping, and subsequent replication of the association in an independent sample. The region contains two genes, AHI1 and C6orf217. Both genes and the neighboring phosphodiesterase 7B (PDE7B) may be considered candidates for involvement in the genetic etiology of SCZ [53]. Of 14 SNPs tested (ATP2B2, HS3ST2, UNC5C, BAG3, PDE7B, PAICS, PTGFRN, NR3C2, ZBTB20, ST6GAL2, PIP5K1B, EPHA6, KCNH5, and AJAP1), only one (rs9389370) in PDE7B (high-affinity cAMP-specific phosphodiesterase 7B) showed significant evidence for association with SCZ in a Japanese sample [54].

The AHI1 gene is required for both cerebellar and cortical development in humans. According to Rivero et al. [55], while the accelerated evolution of AHI1 in the human lineage indicates a role in cognitive function, a linkage scan in large pedigrees identified AHI1 as a positional candidate for SCZ. These authors evaluated the effect of AHI1 variation on the vulnerability to psychosis in two samples from Spain and Germany. 29 SNPs located in a genomic region including the AHI1 gene were genotyped in the Ibero-German sample. rs7750586 and rs911507, both located upstream of the AHI1 coding region, were found to be associated with SCZ in the analysis of genotypic and allelic frequencies. Several other risk and protective haplotypes were also detected. Joint analysis of both ethnic samples supported the association of rs7750586 and rs911507 with the risk for SCZ.

Adenylosuccinate synthase (ADSS) and ataxia telangiectasia (ATM) genes. The blood-derived RNA levels of the adenylosuccinate synthase (ADSS) and ataxia telangiectasia mutated (ATM) genes were found to be downand up-regulated, respectively, in schizophrenics compared with controls, and ADSS and ATM were among eight biomarker genes to discriminate schizophrenics from normal controls. ADSS catalyzes the first committed step of AMP synthesis, while ATM kinase serves as a key signal transducer in the DNA double-strand breaks response pathway. Studies with 6 SNPs in the ADSS gene and 3 SNPs in the ATM gene did not show significant difference in the genotype, allele, or haplotype distributions in a Chinese population of SCZ patients. Using the Multifactor Dimensionality Reduction (MDR) method, interactions among rs3102460 in the ADSS gene and rs227061 and rs664143 in the ATM gene revealed a significant association with SCZ with a maximum testing accuracy of 60.4%, suggesting that the combined effects of the polymorphisms in the ADSS and ATM genes may confer susceptibility to the development of SCZ in a Chinese population [56].

Adrenergic alpha-2A, receptor (ADRA2A). Several lines of studies have shown the existence of an important inhibitory mechanism for the control of water intake involving adrenergic alpha-2A receptors. A human study using patients with SCZ demonstrated an exacerbation of polydipsia by the administration of clonidine, an ADRA2A-agonist, and a relief of polydipsia by mianserin, an ADRA2A-antagonist, suggesting the involvement of the central adrenergic system in the drinking behavior of patients with SCZ. Based on these findings Yamaguchi et al. [57] examined a possible association between the C-1291G polymorphism in the promoter region of the ADRA2A gene and polydipsia in SCZ using a Japanese case-control sample. No significant association between the ADRA2A C-1291G polymorphism and polydipsia was found [57].

ALDHs and retinoic acid-related genes. Vitamin A (retinol), the biologically active form of retinoic acid, has been proposed as being involved in the pathogenesis of SCZ. 18 SNPs in the regulatory and coding sequences of 7 genes involved in the synthesis, degradation and transportation of retinoic acid, ALDH1A1, ALDH1A2, ALDH1A3, CYP26A1, CYP26B1, CYP26C1 and transthyretin (TTR) have been studied in SCZ. Association analyses using both allelic and genotypic single-locus tests revealed no significant association between the risk for each of these genes and SCZ; however, analyses of multiple-locus haplotypes indicated that the overall frequency of rs4646642-rs4646580 of the ALDH1A2 gene showed a significant difference between patients and control subjects in the Chinese population [58].

Alphaand beta-synuclein (SNCA, SNCB). Alpha-synuclein is expressed in the CNS. A high concentration of alpha-synuclein in presynaptic terminals can mimic the normal function of endogenous alpha-synuclein in regulating synaptic vesicle mobilization at nerve terminals. Beta-synuclein protein is seen primarily in brain tissue. Beta-synuclein may act as an inhibitor of alpha-synuclein aggregation, which occurs in neurodegenerative diseases, such as Parkinson’s disease. NooriDaloii et al. [59] studied the changes of alphaand beta-synucleins in SCZ patients in relation to a control group. The relative expression of alphaand beta-synucleins showed downregulation in patients in comparison to the control group. Beta-synuclein mRNA expression in the control group was significantly higher than that in the patient group, but downregulation of alpha-synuclein gene was not significant.

Angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 (ACE). ACE variants are currently associated with cardiovascular and cerebrovascular risk factors [5,10,11,35]. ACE insertion/deletion polymorphism was also associated with SCZ and BD. DD genotype and D allele distributions in bipolar patients and their first-degree relatives were significantly higher than those of SCZ patients, their relatives, and controls. In contrast, II genotype and I allele were reduced in both the patient groups and their relatives as compared with controls [60].

AP-3 complex genes. Dysbindin is a component of BLOC-1, which interacts with the adaptor protein (AP)-3 complex. Hashimoto et al. [61] examined a possible association between 16 SNPs in the AP3 complex genes and SCZ in Japanese patients. Nominal association between rs6688 in the AP3M1 gene and SCZ was initially found, but this association was no longer positive after correction for multiple testing, suggesting that AP3 complex genes might not play a major role in the pathogenesis of SCZ in this population [61].

APOE and cholesterol transport genes. Several studies suggest an accumulation of APOE-4 allele in SCZ [35]. Disturbances in lipid homeostasis and myelination have been proposed in the pathophysiology of SCZ and BD. Several antipsychotic and antidepressant drugs increase lipid biosynthesis through activation of the Sterol Regulatory Element-Binding Protein (SREBP) transcription factors, which control the expression of numerous genes involved in fatty acid and cholesterol biosynthesis. Quantitative PCR and immunoblotting were used to determine the level of lipid transport genes in human glioblastoma (GaMg) exposed to clozapine, olanzapine, haloperidol or imipramine. The effect of some of these drugs was also investigated in human astrocytoma (CCF-STTG1), neuroblastoma (SH-SY5Y) and hepatocellular carcinoma (HepG2) cells. Significant transcriptional changes of cholesterol transport genes (APOE, ABCA1, NPC1, NPC2, NPC1L1), which are predominantly controlled by the liver X receptor (LXR; NR1H2) transcription factor, have been detected. Stimulation of cellular lipid biosynthesis by amphiphilic psychotropic drugs is followed by a transcriptional activation of cholesterol transport and efflux pathways. Such effects may be relevant for both therapeutic effects and metabolic adverse effects of psychotropic drugs [62].

Apoptotic engulfment pathway. Apoptosis has been speculated to be involved in SCZ. The apoptotic engulfment pathway involving the MEGF10, GULP1, ABCA1 and ABCA7 genes has been investigated in SCZ. Nominally significant associations were found in GULP1 (rs2004888), ABCA1 (rs3858075) and ABCA7 genes. A significant 2-marker (rs2242436*rs3858075) interaction between the ABCA1 and ABCA7 genes and a 3-marker interaction (rs246896*rs4522565*rs3858075) amongst the MEGF10, GULP1 and ABCA1 genes were found in different samples. The GULP1 gene and the apoptotic engulfment pathway may be involved in SCZ in subjects of European ancestry and multiple genes in the pathway may interactively increase the risk of the disease [63].

Arginine vasopressin receptor 1A (AVPR1A). Arginine vasopressin (AVP) and the arginine vasopressin receptor 1A gene contribute to memory function and a range of social behaviors both in lower vertebrates and in humans. Human promoter-region microsatellite repeat regions (RS1 and RS3) in the AVPR1a gene region have been associated with autism spectrum disorders, prosocial behavior and social cognition. Prepulse inhibition (PPI) of the startle response to auditory stimuli is a largely autonomic response that resonates with social cognition in both animal models and humans. Reduced PPI has been observed in disorders, including SCZ, which are distinguished by deficits in social skills. Association studies between PPI and the AVPR1a RS1 and RS repeat regions detected association between AVPR1a promoter-region repeat length (especially RS3) and PPI. Longer RS3 alleles were associated with greater levels of prepulse inhibition. Using a short/long classification scheme for the repeat regions, significant association was also observed between all three PPI intervals (30, 60 and 120 ms) and both RS1 and RS3 polymorphisms. Longer alleles, especially in male subjects, are associated with significantly higher PPI response, consistent with a role for the promoter repeat region in partially molding social behavior in both animals and humans [64]. Molecular genetic studies of AVPR1a and oxytocin (OXTR) receptors have strengthened the evidence regarding the role of these two neuropeptides in a range of normal and pathological behaviors. Significant association has been shown between both AVPR1a repeat regions and OXTR SNPs with risk for autism. AVPR1a has also been linked to eating behavior in both clinical and non-clinical groups. Evidence also suggests that repeat variations in AVPR1a are associated with two other social domains in Homo sapiens: music and altruism. AVPR1a was associated with dance and musical cognition, probably reflecting the ancient role of this hormone in social interactions executed by vocalization, ritual movement and dyadic (mother-offspring) and group communication. Individual differences have been observed in allocation of funds in the dictator game, a laboratory game of pure altruism, associated with length of the AVPR1a RS3 promoterregion repeat [65]. Although molecular data are very limited, it might be possible that dysfunctions in these primitive neuropeptides involved in higher activities of the CNS may influence autism/SCZ pathogenesis [66].

Arrestin, beta 2 (ARRB2). Tardive dyskinesia (TD) may be associated with mediators or signaling complexes behind DRD2, such as beta-arrestin-2 (ARRB2), an important mediator between DRD2 and serine-threonine protein kinase (AKT) signal cascade. There is a significant difference in the genotype distribution of ARRB2- rs1045280 (Ser280Ser) between TD and non-TD SCZ groups; and patients with the T allele have increased risk of tardive dyskinesia [67].

BCL2-interacting killer (apoptosis-inducing) (BIK). The Bcl2-interacting killer (BIK) gene interacts with cellular and viral survival-promoting proteins, such as Bcl-2, to enhance apoptosis. The BIK protein promotes cell death in a manner analogous to Bcl-2-related deathpromoting proteins, Bax and Bak. Low Bcl-2 levels and increased Bax/Bcl-2 ratio have been found in the temporal cortex of patients with SCZ. The BIK protein is suggested to be a likely target for antiapoptotic proteins. Nominal evidence for association of alleles rs926328 and rs2235316 with SCZ was found in Japanese patients; however, these associations were no longer positive after correction for multiple testing [68].

Biogenesis of lysosome-related organelles complex 1 (BLOC-1). Biogenesis of lysosome-related organelles complex 1 (BLOC-1) is a protein complex formed by the products of eight distinct genes. Loss-of-function mutations in two of these genes, DTNBP1 and BLOC1S3, cause Hermansky-Pudlak syndrome, a human disorder characterized by defective biogenesis of lysosome-related organelles. Haplotype variants within the same two genes have been postulated to increase the risk of developing SCZ. In a fly model of BLOC-1 deficiency, mutant flies lacking the conserved Blos1 subunit displayed eye pigmentation defects due to abnormal pigment granules, which are lysosome-related organelles, as well as abnormal glutamatergic transmission and behavior [69].

Brain-derived neurotrophic factor (BDNF). A variety of evidence suggests brain-derived neurotrophic factor (BDNF) as a candidate gene for SCZ. Several genetic studies have shown a significant association between the disease and certain SNPs within BDNF (specifically, Val66Met and C270T). The functional microsatellite marker BDNF-LCPR (BDNF-linked complex polymorphic region), which affects the expression level of BDNF, is associated with BD. A meta-analysis of the two most extensively studied polymorphisms (Val66Met and C270T) revealed no association in single-marker or multimarker analysis and no association of the Val66Met polymorphism with SCZ, whereas C270T showed a trend for association in a fixed model, but not in a random model. These findings suggest that if BDNF is indeed associated with SCZ, the A1 allele in BDNF-LCPR would be the most promising candidate [70]. In a Taiwanese population no association was found between the BDNF Val66Met polymorphism and SCZ; however, this polymorphism may reduce psychopathology, in particular negative symptoms [71]. Allelic variation in the BDNF gene has been associated with affective disorders, but generally not SCZ. BDNF variants may help clarify the status of schizoaffective disorder. Patients with schizoaffective disorder and other affective disorders are significantly more likely to carry two copies of the most common BDNF haplotype (containing the valine allele of the Val66Met polymorphism) compared with healthy volunteers. When compared with SCZ patients, individuals with schizoaffective disorder are significantly more likely to carry two copies of the common haplotype [72].

Defective BDNF has been proposed as a candidate pathogenic mechanism in SCZ and dementia. BDNF transcription is regulated during the protracted period of human frontal cortex development. Expression of the four most abundant alternative 5’ exons of the BDNF gene (exons I, II, IV, and VI) has been studied in RNA extracted from the prefrontal cortex. Expression of transcripts I-IX and VI-IX was highest during infancy, whereas that of transcript II-IX was lowest just after birth, slowly increasing to reach a peak in toddlers. Transcript IV-IX was significantly upregulated within the first year of life, and was maintained at this level until school age. Quantification of BDNF protein revealed that levels followed a similar developmental pattern as transcript IV-IX. In situ hybridization of mRNA in cortical sections showed the highest expression in layers V and VI for all four BDNF transcripts, whereas moderate expression was observed in layers II and III. Although low expression of BDNF was observed in cortical layer IV, this BDNF mRNA low-zone decreased in prominence with age and showed an increase in neuronal mRNA localization. These findings reported by Wong et al. [73] show that dynamic regulation of BDNF expression occurs through differential use of alternative promoters during the development of the human prefrontal cortex, particularly in the younger age groups, when the prefrontal cortex is more plastic. Alterations in BDNF processing during brain maturation cannot be neglected as a potential mechanism for prefrontal cortex dysfunction in SCZ. The levels of (pro)BDNF and receptor proteins, TrkB and p75, are altered in the hippocampus in SCZ and mood disorder and polymorphisms in each gene influence protein expression [74].

Neurodegenerative processes may be involved in the pathogenesis of tardive dyskinesia (TD), and a growing body of evidence suggests that BDNF plays a role in both the antipsychotic effects and the pathogenesis of TD. BDNF and glycogen synthase kinase (GSK)-3beta are important in neuronal survival, and thus abnormal regulation of BDNF and GSK-3beta may contribute to TD pathophysiology. Park et al. [75] studied the relationship between two polymorphisms, Val66Met in the BDNF coding region and −50T/C in the GSK-3beta promoter, and susceptibility to TD among a matched sample of patients having SCZ with TD, patients with SCZ without TD, and normal control subjects. PCR analysis revealed no significant difference in the occurrence of the polymorphisms among the TD, non-TD, and control subjects, but a significant interaction was observed among the groups possessing BDNF Val allele in compound genotypes. The schizophrenic subjects with the C/C GSK-3beta genotype, who carry the Val allele of the BDNF gene, are expected to have a decreased risk of developing neuroleptic-induced tardive dyskinesia [75].

Bromodomain containing 1 (BRD1). The bromodomain-containing protein 1 (BRD1) gene located at chromosome 22q13.33 has been associated with SCZ and BD susceptibility [76].

Calcium channel, voltage-dependent, L type, alpha 1C subunit (CACNA1C). Strong evidence of association at the polymorphism rs1006737 (within CACNA1C, the gene encoding the alpha-1C subunit of the L-type voltage-gated calcium channel) with the risk of BD has recently been reported in a meta-analysis of three genome-wide association studies of BD. The risk allele also conferred increased risk for SCZ and recurrent major depression with similar effect sizes to those previously observed in BD. These findings are evidence of some degree of overlap in the biological underpinnings of susceptibility to mental illness across the clinical spectrum of mood and psychotic disorders [77]. A recent meta-analysis of five case-control cohorts for major mood disorder, including over 13600 individuals genotyped on high-density SNP arrays performed by the Bipolar Disorder Genome Study (BiGS) Consortium [78] identified SNPs at 3p21.1 associated with major mood disorders (rs2251219), with supportive evidence for association observed in two out of three independent replication cohorts. These results provide another example of a shared genetic susceptibility locus for BD and major depressive disorder [78].

To identify the neural system mechanism that explains the genetic association between the CACNA1C gene and psychiatric illness, Bigos et al. [79] used blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) to measure brain activation in circuitries related to bipolar disorder and schizophrenia by comparing CACNA1C genotype groups among healthy subjects. The risk-associated SNP rs1006737 in CACNA1C predicted increased hippocampal activity during emotional processing and increased prefrontal activity during executive cognition. The risk-associated SNP also predicted increased expression of CACNA1C mRNA in the human brain. The risk-associated SNP in CACNA1C maps to circuitries implicated in genetic risk for bipolar disorder and schizophrenia. According to Bigos and coworkers [79], its effects in human brain expression implicate a molecular and neural system mechanism for the clinical genetic association.

Calreticulin (CALR). Tissue-specific expression of the calreticulin (CALR) gene in the gray matter is development-dependent and coincides with the expression of psychosis phenotypes. Farokhashtiani et al. [80] reported instances of mutations within the core promoter sequence of the gene in schizoaffective disorder. A unique mutation at nucleotide −220 from the transcription start site, located at a conserved genomic block in the promoter region of the gene, co-occurs with the spectrum of psychoses. This mutation reverts the human promoter sequence to the ancestral type observed in chimpanzee, mouse, and several other species, implying that the genomic block harboring nucleotide −220 may be involved in the evolution of human-specific higherorder functions of the brain that are ubiquitously impaired in psychoses.

Cannabinoid receptors. Two endocannabinoid receptors, CB1 and CB2 (CNR1, CNR2), are found in the brain. The R63 allele of rs2501432 (R63Q), the C allele of rs12744386 and the haplotype of the R63-C allele of CB2 were significantly increased among patients with SCZ. A significantly lower response to CB2 ligands in cultured CHO cells transfected with the R63 allele compared with those with Q63, and significantly lower CB2 receptor mRNA and protein levels found in human brain with the CC and CT genotypes of rs12744386 compared with TT genotype were observed. Endocannabinoid function appears to be involved in SCZ. An increased risk of SCZ might be present in people with low CB2 receptor function [81].

Cathepsin K (CTSK). Recent studies associate cathepsin K with SCZ. Cathepsin K is capable of liberating Met-enkephalin from beta-endorphin (beta-EP) in vitro. To verify if this process might possibly contribute to the pathogenesis of SCZ, post-mortem brains were analyzed immunohistochemically for the presence and co-localization of cathepsin K and beta-EP. In support of a functional role of the observed formation of Met-enkephalin on the expense of beta-EP, increased numbers of cathepsin K immunoreactive cells, but diminished numbers of both beta-EP-positive cells and double-positive (cathepsin K/beta-EP) cells, were found in left and right arcuate nucleus of schizophrenics. A reduced density of beta-EP-immunoreactive neuropil (fibers, nerve terminals) was estimated in the left and right paraventricular nucleus (PVN) of individuals with SCZ. Cathepsin K, which becomes up-regulated in its cerebral expression by neuroleptic treatment, might significantly contribute to altered opioid levels in brains of schizophrenics [82].

Cholecystokinin A receptor gene. Cholecystokinin A receptor (CCKAR) has been implicated in the pathophysiology of SCZ through its mediation of dopamine-release in the CNS. Association between the CCKAR gene and SCZ has been observed, especially between the 779T/C polymorphism and auditory hallucinations or positive symptoms of SCZ. In the Japanese population, no significant difference was observed in genotypic distributions or allelic frequencies between SCZ and controls, although there was a trend for the association between the C allele of the polymorphism and hallucination or hallucinatory-paranoid state [83].

Cholinergic receptor, nicotinic, alpha 7 (CHRNA7). Multiple genetic linkage studies support the hypothesis that the 15q14 chromosomal region contributes to the etiology of SCZ. Among the putative candidate genes in this area are the alpha7 nicotinic acetylcholine receptor gene (CHRNA7) and its partial duplication, CHRFAM7A. A large chromosomal segment including the CHRFAM7A gene locus, but not the CHRNA7 locus, is deleted in some individuals. The CHRFAM7A gene contains a polymorphism consisting of a 2 base pair (2 bp) deletion at position 497 - 498 bp of exon 6. The 2 bp polymorphism was associated with SCZ in African-Americans and in Caucasians [84]. The rs3087454 SNP, located at position −1831 bp in the upstream regulatory region of CHRNA7, was significantly associated with SCZ in African-American and non-Hispanic Caucasian case-control samples [85].

CLOCK. The clock genes have been reported to play some roles in neural transmitter systems, including the dopamine system, as well as to regulate circadian rhythms. Abnormalities in both of these mechanisms are thought to be involved in the pathophysiology of major mental illness such as SCZ and mood disorders including BP and major depressive disorder (MDD). Recent genetic studies have reported that CLOCK, one of the clock genes, might be associated with these psychiatric disorders; however, association of CLOCK with SCZ might be weak [86].

Clusterin (CLU). Clusterin (CLU) and clathrin assembly lymphoid myeloid (CALM; PICALM) protein are implicated in the function of neuronal synapses. Zhou et al. [87] examined whether SNPs rs11136000 within the CLU gene and rs3851179 within the CALM gene, were associated with SCZ in the Chinese population. Patients with SCZ and with family history showed a significant increase of allele C frequency in rs11136000 in comparison to normal controls. The C allele frequency was also higher in patients with negative symptoms. In contrast, allele and genotype frequencies of rs3851179 did not show significant differences between patients and normal subjects or between patients with different symptoms.

CMYA5 (Cardiomyopathy-associated protein 5; myosprym; tripartite motif-containing protein 76, TRIM76). Chen et al. [88] found that in the CMYA5 gene, there were two non-synonymous markers, rs3828611 and rs10043986, showing nominal significance in both the CATIE (Clinical Antipsychotic Trials of Intervention Effectiveness) and MGS-GAIN (molecular genetics of schizophrenia genome-wide association study supported by the genetic association information network) samples. In a combined analysis of both the CATIE and MGS-GAIN samples, rs4704591 was identified as the most significant marker in the gene. Linkage disequilibrium analyses indicated that these markers were in low LD. CMYA5 was reported to be physically interacting with the DTNBP1 gene, a promising candidate for schizophrenia, suggesting that CMYA5 may be involved in the same biological pathway and process. In a meta-analysis of all 23 replication samples (family samples, 912 families with 4160 subjects; case-control samples, 11380 cases and 15021 controls), the authors found that the rs10043986 and rs4704591 markers are significantly associated with SCZ. Haplotype conditioned analyses indicated that the association signals observed at these two markers are independent.

CNP. 2’,3’-Cyclic nucleotide 3’-phosphodiesterase (CNP), another candidate gene for SCZ, participates in oligodendrocyte function and in myelination. Five CNP SNPs were investigated in a Chinese Han SCZ casecontrol sample set with negative results. Factors including gender, genotype, sub-diagnosis and antipsychotic treatment were found not to contribute to the expression regulation of the CNP gene in SCZ [89].

CNTNAP2, NRXN1, and the neurexin superfamily. Heterozygous copy-number variants and SNPs of CNTNAP2 and NRXN1, two distantly related members of the neurexin superfamily, have been repeatedly associated with a wide spectrum of neuropsychiatric disorders, such as developmental language disorders, autism spectrum disorders, epilepsy, and SCZ. Homozygous and compound-heterozygous deletions and mutations via molecular karyotyping and mutational screening in CNTNAP2 and NRXN1 were identified in four patients with severe mental retardation and variable features, such as autistic behavior, epilepsy, and breathing anomalies, phenotypically overlapping with Pitt-Hopkins syndrome. With a frequency of at least 1%, recessive defects in CNTNAP2 appear to contribute significantly to severe mental retardation. As known for fly Nrx-1, the CASPR2 ortholog Nrx-IV might also localize to synapses. Overexpression of either protein can reorganize synaptic morphology and induce increased density of active zones, the synaptic domains of neurotransmitter release. Both Nrx-I and Nrx-IV determine the level of the presynaptic active-zone protein bruchpilot, indicating a possible common molecular mechanism in Nrx-1 and Nrx-IV mutant conditions [90].

Complexin-2. Because synaptic dysfunction plays a key role in SCZ, the complexin 2 gene (CPLX2) was examined by Begemann et al. [91] in the first phenotypebased genetic association study (PGAS) of GRAS (Göttingen Research Association for Schizophrenia). Six SNPs, distributed over the whole CPLX2 gene, were found to be highly associated with current cognition of schizophrenic subjects but only marginally with premorbid intelligence. Correspondingly, in CPLX2-null mutant mice, prominent cognitive loss of function was obtained only in combination with a minor brain lesion applied during puberty. In the human CPLX2 gene, 1 of the identified 6 cognition-relevant SNPs, rs3822674 in the 3’ untranslated region, was detected to influence microRNA-498 binding and gene expression. The same marker was associated with differential expression of CPLX2 in peripheral blood mononuclear cells. Results extracted from this study suggest that cognitive performance in schizophrenic patients may be modified by CPLX2 variants modulating post-transcriptional gene expression.

COMT. The catechol-O-methyltransferase (COMT) gene, which is located in the 22q11.21 microdeletion, has been considered as a candidate gene for SCZ due to its ability to degrade catecholamines, including dopamine. Human COMT contains three common polymorphisms (A22S, A52T, and V108M), two of which (A22S and V108M) render the protein susceptible to deactivation by temperature or oxidation. The A52T mutation had no significant effect on COMT structure. Residues 22 (alpha2) and 108 (alpha5) interact with each other and are located in a polymorphic hotspot approximately 20 Ǻ from the active site. Introduction of either the larger Ser (22) or Met (108) tightens this interaction, pulling alpha2 and alpha5 toward each other and away from the protein core. The V108M polymorphism rearranges active-site residues in alpha5, beta3, and alpha6, increasing the S-adenosylmethionine site solvent exposure. The A22S mutation reorients alpha2, moving critical catecholbinding residues away from the substrate-binding pocket. The A22S and V108M polymorphisms evolved independently in Northern European and Asian populations. While the decreased activities of both A22S and V108M COMT are associated with an increased risk for SCZ, the V108M-induced destabilization is also linked with improved cognitive function. Polymorphisms within this hotspot may have evolved to regulate COMT activity, and heterozygosity for either mutation may be advantageous [92].

A common functional polymorphism (Val/Met) in COMT that markedly affects enzyme activity has been shown to affect executive cognition and the physiology of the prefrontal cortex in humans. The high activity Val allele slightly increases risk for SCZ through its effect on dopamine-mediated prefrontal information processing. The Val/Met polymorphism has become the most widely studied polymorphism in psychiatry [93]. No statistically significant differences were found in allele or genotype frequencies between patient and normal control subjects, although a nonsignificant over-representation of the Val allele has been detected in Han Chinese patients with SCZ. The meta-analysis of all published populationbased association studies showed statistically significant evidence for heterogeneity among the group of studies. Stratification of the studies by ethnicity of the samples yielded no significant evidence for an association with the Val allele in the Asian population [94,95].

The functional SNP Val108/158Met (rs4680) and haplotypes rs737865-rs4680-rs165599 in COMT have been extensively examined for association to SCZ; however, results of replication studies have been inconsistent. Okochi et al. [96] performed a mutation scan to detect the existence of potent functional variants in the 5’-flanking and exon regions, and conducted a genebased case-control study between tagging SNPs in COMT [19 SNPs including six possible functional SNPs (rs2075507, rs737865, rs4680, rs165599, rs165849)] and SCZ in the Japanese population. A meta-analysis of 5 functional SNPs and haplotypes (rs737865-rs4680- rs165599) was also carried out. No novel functional variant was detected in the mutation scan and no association was found between these tagging SNPs in COMT and Japanese SCZ. No evidence was found for an association between Val108/158Met polymorphisms, rs6267, rs165599, and haplotypes (rs7378655-rs4680-rs165599) and SCZ, although rs2075507 and rs737865 showed trends for significance in allele-wise analyses [96].

COMT impacts the regulation of dopamine neuronal activity in the brainstem, which is associated with psychosis [97]. The rs362204 polymorphism shows association with SCZ in different populations [97,98] and rs6267 showed an association with reduced risk of SCZ [99]. There is an association between the COMT gene and violent behavior in Chinese schizophrenics. The haplotypes A-A-G and G-G-A may be used to predict violent behavior in schizophrenics [100]. COMT genotype contributes to cognitive flexibility, a fundamental cognitive ability that potentially influences an individual’s performance in a variety of other neurocognitive tasks. COMT genotype was significantly associated with signal discrimination index d’ in SCZ. The Val/Val genotype was associated with the highest and the Met/Met genotype with the lowest scores; heterozygous individuals displayed an intermediate performance [101]. The [oxy-Hb] increase in the Met carriers during the verbal fluency task was significantly greater than that in the Val/Val individuals in the frontopolar prefrontal cortex of patients with SCZ, although neither medication nor clinical symptoms differed significantly between the two subgroups [102].

The Val108/158Met (rs4680) SNP in the COMT gene is specifically related to impairments in executive functioning. A different genomic region composed of three SNPs (rs737865, rs4680, rs165599) within the COMT gene has been reported to be significantly associated with SCZ in Ashkenazi Jews, but not in other populations. In the Taiwanese population, the A allele of rs165599 was transmitted preferentially to the affected individuals, and significantly associated with a later age of onset, more severe delusion/hallucination symptom dimension, and poorer performance in the CPT. The triple SNP haplotypes did not reveal any significant association with SCZ or neurocognitive function [103]. According to these results, the SNP rs165599, which has been mapped to the 3’-UTR region of the COMT gene, was significantly associated with SCZ, and possibly associated with the age of onset, delusion/hallucination symptom dimension, and CPT performance. Therefore, COMT may contribute to the genetic risk for SCZ not through the Val108/158Met polymorphism, but through other variants that are situated 3’ to this region [103].

Liao et al. [104] examined the relations of genetic variants in COMT, including rs737865 in intron 1, rs4680 in exon 4 (Val158Met) and downstream rs165599, to SCZ and its related neurocognitive functions in families of patients with SCZ. The genotypes of rs4680 were associated with both the Wisconsin Card Sorting Test (WCST) and Continuous Performance Test (CPT) performance scores in these families, but not with SCZ per se in either whole sample or subgroup analyses. The other two SNPs were differentially associated with the two tasks. For WCST indexes, only rs737865 exhibited moderate associations. For CPT indexes, rs737865 exhibited association for the subgroup with deficit on CPT reaction time, whereas rs165599 exhibited association for the subgroup with deficit on CPT d’ as well as quantitative undegraded d’. These results suggest that COMT variants might be involved in modulation of neurocognitive functions, conferring increased risk for SCZ [104].

Some studies revealed potential epistatic effects of two intronic SNPs located in the COMT and aldehyde dehydrogenase 3B1 (ALDH3B1) genes, which conferred genetic risk to paranoid SCZ. Among the individuals carrying the rs3751082 A allele in the ALDH3B1 gene, the rs4633 T allele in the COMT gene was associated with susceptibility to paranoid SCZ, development of hallucination, delay of P300 latency, and increased expression of the COMT gene; however, the rs4633 T allele did not show any association in the rs3751082 G/G genotype carriers [105].

CSF2RB (Colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)). CSF2RB encodes the protein which is the common β chain of the high affinity receptor for IL-3, IL-5 and CSF. It locates in the linkage region 22q13.1 of both bipolar disorder and SCZ, and is expressed in most cells. Chen et al. [106] carried out a large-scale case-control study to test the association between CSF2RB and three major mental disorders in the Chinese Han population. Seven SNPs were genotyped in 1140 bipolar affective disorder patients (including 645 type I bipolar affective disorder patients), 1140 schizophrenia patients, 1139 major depressive disorder patients and 1140 healthy controls. Three SNPs were found to be associated with both SCZ and major depressive disorder. Haplotype association analysis revealed one protective haplotype for SCZ and for MDD and one risk haplotype for SCZ and for MDD. These results support CSF2RB as a risk factor common to both SCZ and major depression in the Chinese Han population.

CTLA4 (Cytotoxic T-lymphocyte-associated protein 4). Some studies have reported that the cytotoxic T lymphocyte antigen-4 (CTLA-4) gene, which is related to immunological functions such as T-cell regulation, is associated with psychiatric disorders. Liu et al. [107] studied the relationship between CTLA-4 and three major psychiatric disorders, SCZ, major depressive disorder and bipolar disorder in the Chinese Han population. They screened 6 tag SNPs (rs231777, rs231775, rs231779, rs3087243, rs5742909, rs16840252) in the CTLA-4 gene, and found that rs231779 conferred a risk for SCZ, major depressive disorder, and bipolar disorder. rs231777 and rs16840252 had a significant association with SCZ, and rs231777 had significant association with bipolar disorder; however, after 10000 permutations, only rs231779 remained significant. These results led the Chinese authors to conclude that shared common risk factors for SCZ, major depressive disorder and bipolar disorder exist in the CTLA-4 gene in the Chinese Han population.

CYP3A4 and CYP3A5. Two-marker haplotypes covering components CYP3A41G and CYP3A53 were observed to be significantly associated with SCZ in Chinese patients [108].

D-Amino acid oxidase activator (DAOA, G72). The DAOA gene locus on chromosome 13q34 has been implicated in the etiology of SCZ. 3 SNPs (rs778294, rs779293 and rs3918342) have been identified in this region, and two of them (rs778293, rs3918342) have shown significant transmission disequilibrium and a highly significant under-transmission between haplotype CAT and SCZ. G72 is one of the most widely tested genes for association with SCZ. As G72 activates the D-amino acid oxidase (DAO), G72 is termed D-amino acid oxidase activator (DAOA). Ohi et al. [109] found nominal evidence for association of alleles M22/rs778293, M23/rs3918342 and M24/rs1421292, and the genotype of M22/rs778293 with SCZ, although there was no association of allele or genotype in the other five SNPs. They also found nominal haplotypic association, including M15/rs2391191 and M19/rs778294, with SCZ; however, these associations were no longer positive after correction for multiple testing, which suggests that G72 might not play a major role in the risk for SCZ in the Japanese population [109]. Association of the G72/G30 locus with SCZ and BD has been reported in several studies. The G72/G30 locus spans a broad region of chromosome 13q. One meta-analysis of published association studies shows highly significant evidence of association between nucleotide variations in the G72/ G30 region and SCZ, along with compelling evidence of association with BD [110]. This locus has been associated with panic disorder, SCZ, and BD, especially the 3 SNPs rs2391191, rs3918341, and rs1935062, with controversial results [111]. G72 is an activator of D-amino acid oxidase (DAO), supporting the glutamate dysfunction hypothesis of SCZ. G72 mRNA is poorly expressed in a variety of human tissues (e.g. adult brain, amygdala, caudate nucleus, fetal brain, spinal cord and testis) from human cell lines or SCZ/control post-mortem BA10 samples. The lack of demonstrable G72 expression in relevant brain regions does not support a role for G72 in modulation of DAO activity and the pathology of SCZ via a DAO-mediated mechanism. In silico analysis suggests that G72 is not robustly expressed and that the transcript is potentially labile [112].

Disrupted-in-schizophrenia-1 (DISC1). The disrupted-in-schizophrenia-1 (DISC1) locus is located at the breakpoint of a balanced t(1;11) (q42.1; q14.3) chromosomal translocation in a large and unique Scottish family. This translocation segregates in a highly statistically significant manner with a broad diagnosis of psychiatric illness, including SCZ, BD and major depression, as well as with a narrow diagnosis of SCZ alone. Two novel genes were identified at this locus and due to the high prevalence of SCZ in this family, they were named disrupted-in-schizophrenia-1 (DISC1) and disrupted-inschizophrenia-2 (DISC2). DISC1 encodes a novel multifunctional scaffold protein, whereas DISC2 is a putative noncoding RNA gene antisense to DISC1. A number of independent genetic linkage and association studies in diverse populations support the original linkage findings in the Scottish family and genetic evidence now implicates the DISC locus in susceptibility to SCZ, schizoaffective disorder, BD and major depression as well as various cognitive traits. DISC1 is a hub protein in a multidimensional risk pathway for major mental illness [113]. Many alternatively spliced transcripts were identified, including groups lacking exon 3 (Delta3), exons 7 and 8 (Delta7Delta8), an exon 3 insertion variant (extra short variant-1, Esv1), and intergenic splicing between TSNAX and DISC1. Isoforms Delta7Delta8, Esv1, and Delta3, which encode truncated DISC1 proteins, were expressed more abundantly during fetal development than during postnatal ages, and their expression was higher in the hippocampus of patients with SCZ. SCZ risk-associated polymorphisms [non-synonymous SNPs rs821616 (Cys704Ser) and rs6675281 (Leu607Phe), and rs821597] were associated with the expression of Delta3 and Delta7Delta8 [114]. An inherited 2.07 Mb microduplication in 1q42.2 was identified in two brothers with autism and mild mental retardation in Belgium. The duplication contains seven genes, including the DISC1 gene which has been associated to SCZ, BD, autism and Asperger syndrome [115]. DISC1 regulates neuronal migration and differentiation during mammalian brain development. Enomoto et al. [116] reported that DISC1 interacts with the actin-binding protein girdin to regulate axonal development. Dentate granule cells (DGCs) in girdin-deficient neonatal mice exhibit deficits in axonal sprouting in the cornu ammonis 3 region of the hippocampus. Girdin deficiency, RNA interference-mediated knockdown, and inhibition of the DISC1/girdin interaction lead to overextended migration and mispositioning of the DGCs resulting in profound cytoarchitectural disorganization of the DG. These findings identify girdin as an intrinsic factor in postnatal development of the DG and provide insights into the critical role of the DISC1/girdin interaction in postnatal neurogenesis in the DG. DISC1 suppression in newborn neurons of the adult hippocampus leads to overactivated signaling of AKT, another SCZ susceptibility gene. Mechanistically, DISC1 directly interacts with KIAA1212, an AKT-binding partner that enhances AKT signaling in the absence of DISC1, and DISC1 binding to KIAA1212 prevents AKT activation in vitro. Multiple genetic manipulations to enhance AKT signaling in adult-born neurons in vivo exhibit similar defects to DISC1 suppression in neuronal development, which can be rescued by pharmacological inhibition of mammalian target of rapamycin (mTOR), an AKT downstream effector. The AKT-mTOR signaling pathway acts as a critical DISC1 target in regulating neuronal development [117].

To elucidate how DISC1 confers susceptibility to psychiatric disorders, identification of the molecules, which bind to the domain close to the translocation breakpoint in the DISC1 gene, was performed and fasciculation and elongation protein zeta-1 (Fez1), a novel DISC1-interacting protein, termed DISC1-binding zinc-finger protein (DBZ), and Kendrin were identified. The DISC1-Fez1 interaction is up-regulated by nerve growth factor (NGF) and involved in neurite extension. Transient dissociation of the DISC1-DBZ interaction by pituitary adenylate cyclase-activating polypeptide (PACAP) causes neurite extension. SNP association studies have shown the relation of the Fez1, PACAP and PACAP receptor (PAC1) genes to SCZ. In SCZ with DISC1 translocation carrier, the DISC1-Fez1 and DISC1-DBZ interaction is disrupted, and it is likely that neural circuit formation remains immature, suggesting that SCZ is a neurodevelopmental disease. The DISC1-Kendrin interaction is suggested to be involved in microtubule network formation and an association between SNPs of the Kendrin gene and bipolar disease has also been suggested in a Japanese population [118].

DISC1 interacts directly with phosphodiesterase 4B (PDE4B), an independently identified risk factor for SCZ. DISC1-PDE4B complexes are therefore likely to be involved in molecular mechanisms underlying psychiatric illness. PDE4B hydrolyzes cAMP, and DISC1 may regulate cAMP signaling through modulating PDE4B activity. There is evidence that expression of both genes is altered in some psychiatric patients. DISC1 missense mutations that give rise to phenotypes related to SCZ and depression in mice are located within binding sites for PDE4B. These mutations reduce the association between DISC1 and PDE4B, and one results in reduced brain PDE4B activity. Altered DISC1-PDE4B interaction may thus underlie the symptoms of some cases of SCZ and depression [119]. DISC1 protein binding partners include the nuclear distribution factor E homologs (NDE1 and NDEL1), LIS1, and phosphodiesterases 4B and 4D (PDE4B and PDE4D). NDE1, NDEL1 and LIS1, together with their binding partner dynein, associate with DISC1, PDE4B and PDE4D within the cell, and provide evidence that this complex is present at the centrosome. LIS1, NDEL1, DISC1, NDE1, and PDE4B are localized at synapses in cultured neurons. NDE1 is phosphorylated by cAMP-dependent protein kinase A (PKA), whose activity is, in turn, regulated by the cAMP hydrolysis activity of phosphodiesterases, including PDE4. DISC1 might act as an assembly scaffold for all of these proteins and the NDE1/NDEL1/LIS1/dynein complex might be modulated by cAMP levels via PKA and PDE4 [120].

A DISC1 haplotype, HEP3, and an NDE1 spanning tag haplotype are associated with SCZ in Finnish families. Tomppo et al. [121] identified three SNPs as being associated with SCZ in PDE4D (rs1120303), PDE4B (rs7412571), and NDEL1 (rs17806986). Greater significance was observed with allelic haplotypes of PDE4D, PDE4B, and NDEL1 that increased or decreased SCZ susceptibility, highlighting the potential importance of DISC1-related molecular pathways in the etiology of SCZ and other major mental illnesses [121].

DISC1 is expressed in cranial neural crest (CNC) cells. Loss of Disc1 resulted in persistent CNC cell medial migration, dorsal to the developing neural epithelium, and hindered migration away from the region dorsal to the neural rod. The failure of CNC cells to migrate away from the neural rod correlated with the enhanced expression of two transcription factors, foxd3 and sox10. These transcription factors have many functions in CNC cells, including the maintenance of precursor pools, timing of migration onset, and the induction of cell differentiation. DISC1 functions in the transcriptional repression of foxd3 and sox10, thus mediating CNC cell migration and differentiation [122].

DISC1 is widely expressed in cortical and limbic regions. Association between the DISC1 Ser704Cys polymorphism and volumetric measurements for a broad range of fronto-parietal, temporal, and limbic-paralimbic regions was studied in Japanese patients with SCZ using magnetic resonance imaging. The Cys carriers had significantly larger volumes of the medial superior frontal gyrus and shorter insular cortex than the Ser homozygotes, but only in healthy comparison subjects. The Cys carriers tended to have a smaller supramarginal gyrus than the Ser homozygotes in SCZ patients, but not in healthy comparison subjects. The right medial superior frontal gyrus volume was significantly correlated with daily dosage of antipsychotic medication in Ser homozygote SCZ patients. These different genotype effects of the DISC1 Ser704Cys polymorphism on the brain morphology in SCZ suggest that variation in the DISC1 gene might be involved in the neurobiology of SCZ [123]. Schumacher et al. [124] found evidence for a common SCZ risk interval within DISC1 intron 4 - 6.

DNA methyltransferases (DNMTs). Aberrant DNA methylation may be involved in the development of SCZ. DNA methyltransferase 3B (DNMT3B) is the key methyltransferase in DNA methylation regulations. Casecontrol and family-based studies were performed through genotyping two tag SNPs (rs2424908 and rs6119954) covering the whole DNMT3B gene. The frequency of G allele of rs6119954 was significantly higher in SCZ. Genotype distribution of rs6119954 was significantly different between patients and controls. A haplotype-wise analysis revealed a higher frequency of the T-G (rs2424908-rs6119954) haplotype in SCZ. In the transmission disequilibrium test analysis, the G allele of rs6119954 was preferentially transmitted in the trios. According to these findings reported by Zhang et al. [125] in Chinese patients, DNMT3B may be a candidate gene for susceptibility to early onset SCZ. In SCZ, a functional downregulation of the prefrontal cortex GABAergic neuronal system is mediated by a promoter hypermethylation, presumably catalyzed by an increase in DNA-methyltransferase-1 (DNMT-1) expression. This promoter hypermethylation may be mediated not only by DNMT-1 but also by an entire family of de novo DNA-methyltransferases, such as DNA-methyltransferase-3a (DNMT-3a) and -3b (DNMT-3b). There is an overexpression of DNMT-3a and DNMT-3b in Brodmann’s area 10 (BA10) and in the caudate nucleus and putamen of SCZ brains. DNMT-3a and DNMT-1 are expressed and co-localize in distinct GABAergic neuron populations whereas DNMT-3b mRNA is virtually undetectable. Unlike DNMT-1, which is frequently overexpressed in telencephalic GABAergic neurons of SCZ, DNMT-3a mRNA is overexpressed only in layer I and II GABAergic interneurons of BA10. DNMT-1 and DNMT-3a mRNAs are also overexpressed in peripheral blood lymphocytes of SCZ patients. The upregulation of DNMT-1 and to a lesser extent that of DNMT-3a mRNA in lymphocytes of SCZ supports the concept that this readily available peripheral cell type can express an epigenetic variation of specific biomarkers relevant to SCZ morbidity [126].

Dopamine-Related Genes

DARPP-32 (PPP1R1B). Recent findings have highlighted the importance of DARPP-32 (dopamineand cAMP-regulated phosphoprotein, 32 kDa), a key regulatory molecule in the dopaminergic signaling pathway for dopamine-related phenoltypes such as antisocial behavior, drug addiction and SCZ. Reuter et al. [127] reported the first study investigating the role of the DARPP-32 gene for personality. In a sample of healthy German Caucasian subjects they found a significant association between rs907094 and anger. Carriers of the T-allele showed significantly higher anger scores than participants without a T-allele. A negative association between ANGER scores and the volume of the left amygdala was also detected [127].

Dopamine beta-hydroxylase. The SNP rs1108580 A/G in DBH has been associated with SCZ [98].

Dopamine transporter (DAT; SLC6A3) 3’ UTR VNTR. Dopamine has a crucial role in the modulation of neurocognitive function, and synaptic dopamine activity is normally regulated by the dopamine transporter (DAT) and catechol-O-methyltransferase (COMT). Altered dopamine function is a key pathophysiological feature of SCZ. Prata et al. [128] examined epistasis between the DAT 3’ UTR variable number of tandem repeats (VNTR) and COMT Val158Met polymorphisms on brain activation during executive function in SCZ. There was a significant COMT × DAT non-additive interaction effect on activation in the left supramarginal gyrus. In this region, relatively increased activation was detected only when COMT Met-158/Met-158 subjects also carried the 9-repeat DAT allele, or when, reversely, Val-158/Val-158 subjects carried the 10/10-repeat genotype. There was also a significant diagnosis × COMT × DAT non-additive interaction in the right orbital gyrus. Greater activation was only associated with a 9-repeat allele and Val-158 conjunction, and with a 10-repeat and Met-158 conjunction. COMT and DAT genes interact nonadditively to modulate cortical function during executive processing, and this effect is significantly altered in SCZ, which may reflect abnormal dopamine function in the disorder [128]. The dopamine transporter plays a key role in the regulation of central dopaminergic transmission, which modulates cognitive processing. The effect of a polymorphism in the dopamine transporter gene (the variable number of tandem repeats in the 3’ untranslated region) (3’UTR VNTR) on brain function during executive processing has been studied in healthy volunteers and patients with SCZ. The 10-repeat allele was associated with greater activation than the 9-repeat allele in the left anterior insula and right caudate nucleus. Insular, cingulate, and striatal function during an executive task is normally modulated by variation in the dopamine transporter gene. Its effect on activation in the dorsolateral prefrontal cortex and ventral striatum is altered in patients with SCZ. This may reflect altered dopamine function in these regions in SCZ [129].

Dopamine receptor D₂ (DRD2). 16 Polymorphisms from three genes, dopamine receptor D₂ (DRD2), COMT and BDNF, which are involved in the dopaminergic pathways, and which have been reported to be associated with susceptibility to SCZ and response to antipsychotic therapy, were investigated in SCZ. Initial significant associations of two SNPs for DRD2 (rs11608185, rs6275), and one SNP in the COMT gene (rs4680) were found, but not after correction for multiple comparisons, indicating a weak association of individual markers of DRD2 and COMT with SCZ. Multifactor-dimensionality reduction analysis suggested a two-loci model (rs6275/DRD2 and rs4680/COMT) as the best model for gene-gene interaction with 90% cross-validation consistency and 42.42% prediction error in predicting disease risk among SCZ patients [130].

Dopamine D₄ receptor (DRD4). Associations have been reported between the variable number of tandem repeat (VNTR) polymorphisms in exon 3 of the dopamine D₄ receptor (DRD4) gene and multiple psychiatric illnesses/traits. The size of allele “7R” is less frequent (0.5%) in Japanese than in Caucasian populations (20%). The most common 4R variant is considered to be the ancestral haplotype. In a gene tree of VNTR constructed on the basis of this inferred ancestral haplotype, the allele 7R has five descendent haplotypes in relatively long lineage, where genetic drift can have major influence. No evidence of association between the allele 7R and SCZ was found in the Japanese population [131]. Tardive dyskinesia (TD) is a side-effect of chronic antipsychotic medication exposure. Abnormalities in dopaminergic activity in the nigro-striatal system have most often been suggested to be involved because the agents that cause TD share in common potent antagonism of dopamine D₂ receptors (DRD2). A number of studies have focused on the association of dopamine system gene polymorphisms and TD, with the most consistent findings being an association between TD and the Ser9Gly polymorphism of the DRD3 gene and the TaqIA site 3’ of the DRD2 gene. A haplotype containing rs3732782, rs905568, and rs7620754 in the 5’ region of DRD3 was associated with TD diagnosis [132]. The DRD4 gene codes for the third member of the D₂-like dopamine receptor family, and the VNTR polymorphism in exon 3 of DRD4 has been associated with TD. Although the exon 3 variable number tandem repeat was not associated with TD, haplotypes consisting of four tag polymorphisms were associated with TD in males, suggesting DRD4 may be involved in TD in the Caucasian population [133].

Tyrosine hydroxylase (TH). Tyrosine hydroxylase (EC 1.14.16.2) is involved in the conversion of phenylalanine to dopamine. As the rate-limiting enzyme in the synthesis of catecholamines, tyrosine hydroxylase has a key role in the physiology of adrenergic neurons. The TH variant rs6356 A/G has been associated with SCZ [98].

Dystrobrevin binding protein 1 (DTNBP1) and dysbindin. Dystrobrevin binding protein 1, a gene encoding dysbindin protein, is a susceptibility gene for SCZ identified by family-based association analysis. A large number of independent studies have reported evidence for association between the dysbindin gene (DTNBP1) and SCZ. Up to 14 SNPs spanning the DTNBP1 locus may show association with SCZ in different studies [134]; however, a high-resolution melting analysis (HRMA) to screen the 11 DTNBP1 exons with their corresponding DNA variants in a sample from the UK revealed no significant associations with SCZ [135]. DTNBP1 and MUTED encode proteins that belong to the endosome-localized biogenesis of lysosome-related organelles complex-1 (BLOC-1). BLOC-1 plays a key role in endosomal trafficking and as such has been found to regulate cell-surface abundance of the D₂ dopamine receptor, the biogenesis and fusion of synaptic vesicles, and neurite outgrowth. These functions are pertinent to both neurodevelopment and synaptic transmission, processes tightly regulated by selective cell-surface delivery of membrane proteins to and from endosomes. It has been proposed that cellular processes, such as endosomal trafficking, act as convergence points in which multiple small effects from polygenic genetic polymorphisms accumulate to promote the development of SCZ [136]. BLOC-1 physically interacts with the adaptor protein AP-3 complex, which is essential for vesicle or protein sorting. Dysbindin forms a complex with the AP-3 complex through the direct binding to its µ subunit. Dysbindin partially co-localized with the AP-3 complex in CA1 and CA3 of mouse hippocampus, and at presynaptic terminals and axonal growth cones of cultured hippocampal neurons. Suppression of dysbindin results in the reduction of presynaptic protein expression and glutamate release. Thus, dysbindin appears to participate in the exocytosis or sorting of the synaptic vesicle via direct interaction with the AP-3 complex [137]. Dysbindin is involved in the exocytosis and/or formation of synaptic vesicles. Proteins involved in protein localization process, including Munc18-1, were identified as dysbindin-interacting proteins [138]. A three-marker C-A-T dysbindin haplotype is associated with increased risk for SCZ, decreased mRNA expression, reduced gray matter volume in both the right dorsolateral prefrontal and left occipital cortex, poorer cognitive performance, and early sensory processing deficits [139]. 4 SNPs (rs3213207, rs1011313, rs760761, and rs2619522) have been genotyped in a large Korean SCZ sample. Haplotype analyses revealed a significant association with SCZ with the haplotypes A-C-C-C and A-C-T-A having an eminent protective effect toward SCZ. The major contribution to the difference in the haplotype distribution between patients and the controls was the rs760761 (C/T) and rs2619522 (A/C) haplotypes. No association of DTNBP1 with other clinical variables was found. This study suggests a possible protective effect of rare DTNBP1 variants in SCZ [140]. Recent studies suggest a degree of overlap in genetic susceptibility across the traditional categories of SCZ and BD. DTNBP1 has also become a focus of investigation in BD. Seven DTNBP1 SNPs: rs2743852 (SNP C), rs760761 (P1320), rs1011313 (P1325), rs3213207 (P1635), rs2619539 (P1655), rs16876571 and rs17470454, were investigated using the SNPlex genotyping system. Significant differences in genotypic and allelic frequencies of rs3213207 and rs760761 of DTNBP1 were found between bipolar patients and controls, as well as a global haplotypic association and an association of a particular haplotype with BD [141].

ErbB4 (v-Erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)). ErbB4 is a growth factor receptor tyrosine kinase essential for neurodevelopment. Genetic variation in ErbB4 is associated with SCZ. Risk-associated polymorphisms predict overexpression of ErbB4 CYT-1 isoforms in the brain of schizophrenic patients. The molecular mechanism of association is unclear because the polymorphisms flank exon 3 of the gene and reside 700 kb distal to the CYT-1 defining exon. Tan et al. [142] hypothesized that the polymorphisms are indirectly associated with ErbB4 CYT-1 via splicing of exon 3 on the CYT-1 background. They identified novel splice isoforms of ErbB4, whereby exon 3 is skipped (del.3). ErbB4 del.3 transcripts exist as CYT-2 isoforms and are predicted to produce truncated proteins. Juxtamembrane (JM) splice variants of ErbB4, JM-a and JM-b respectively, are characterized by the replacement of a 75 nucleotide (nt) sequence with a 45-nt insertion, and represent four alternative exons in the gene. Novel splice variants of ErbB4 exist in the developing and adult human brain and, given the failure to identify ErbB4 del3 CYT-1 transcripts, suggest that the association of risk polymorphisms in the ErbB4 gene with CYT-1 transcript levels is not mediated via an exon 3 splicing event, according to Tan and coworkers [142].

Estrogen signaling. Estrogen signaling may be altered in the brains of people with SCZ. DNA sequence variation in the estrogen receptor (ER) alpha gene (ESR1), lower ERalpha mRNA levels, and/or blunted ERalpha signaling is associated with SCZ. The naturally-occurring truncated ERalpha isoform, Delta7, which acts as a dominant negative, can attenuate gene expression induced by the wild-type (WT) receptor in an estrogen-dependent manner in neuronal (SHSY5Y) and non-neuronal (CHOK1 and HeLa) cells. ERalpha may also interact with NRG1-ErbB4, a leading SCZ susceptibility pathway. Reductions in the transcriptionally active form of ErbB4 comprising the intracytoplasmic domain (ErbB4-ICD) have been found in SCZ, and ERalpha and ErbB4 may converge to control gene expression. ErbB4-ICD can potentiate the transcriptional activity of WT-ERalpha at EREs in two cell lines and this potentiation effect is abolished by the presence of Delta7-ERalpha. Convergence between ERalpha and ErbB4-ICD in the transcriptional control of ERalpha-target gene expression may represent a convergent pathway that may be disrupted in SCZ [143]. Studies in Japan reported no association between ERBB3 and SCZ in the Japanese population. Li et al. [144] investigated the ERBB3 gene given the putative functional nature of the gene and population heterogeneity between Asian and Caucasian. A Scottish case and control samples were sequenced with four SNPs (rs705708 at intron 15, rs2271189, rs773123, rs2271188 at exon 27), and association of rs773123, which is a nonsynonymous Ser/Cys polymorphism located seven bases downstream of rs2271189, with SCZ was detected in the Caucasian population [144].

FADS2 (Fatty acid desaturase 2). Emerging evidence suggests that SCZ might be associated with peripheral and central polyunsaturated fatty acid (PUFA) deficits. Abnormalities in fatty acid composition have been reported in peripheral tissues from drug-naïve first-episode schizophrenic patients, including deficits in ω-3 and ω-6 PUFAs, which are partially normalized following chronic antipsychotic treatment. Post-mortem cortical tissue from patients with SCZ also exhibits deficits in cortical docosahexaenoic acid (DHA, 22:6n − 3) and arachidonic acid (AA; 20:4n − 6) relative to normal controls, and these deficits tend to be greater in drug-free SCZ patients. Lower DHA (−20%) concentrations, and significantly greater vaccenic acid (VA) (+12.5%) concentrations, were found in the orbitofrontal cortex (OFC) (Brodmann’s area 10) of SCZ patients relative to normal controls. Relative to age-matched same-gender controls, OFC DHA deficits, and elevated AA:DHA, oleic acid:DHA and docosapentaenoic acid (22:5n − 6):DHA ratios, were found in male but not female SCZ patients. SCZ patients that died of cardiovascular-related disease exhibited lower DHA (−31%) and AA (−19%) concentrations, and greater OA (+20%) and VA (+17%) concentrations, relative to normal controls that also died of cardiovascular-related disease. OFC DHA and AA deficits, and elevations in oleic acid and vaccenic acid, were numerically greater in drug-free SCZ patients and were partially normalized in SCZ patients treated with antipsychotic medications (atypical > typical) [145]. Delta-5 desaturase (FADS1), delta-6 desaturase (FADS2), elongase (HELO1 [ELOVL5]), peroxisomal (PEX19), and delta-9 desaturase (stearoyl-CoA desaturase, SCD) mRNA expression has been studied in the post-mortem prefrontal cortex (PFC) of patients with SCZ. FADS2 mRNA expression was significantly greater in SCZ patients relative to controls (+36%), and there was a positive trend found for FADS1 (+26%). No differences were found for HELO1 (+10%), PEX19 (+12%), or SCD (−6%). Both male (+34%) and female (+42%) SCZ patients exhibited greater FADS2 mRNA expression relative to same-gender controls. Drug-free SCZ patients (+37%), and SCZ patients treated with typical (+40%) or atypical (+31%) antipsychotics, exhibited greater FADS2 mRNA expression relative to controls. Consistent with increased delta6 desaturase activity, SCZ patients exhibited a greater PUFA (product:precursor) 20:3/18:2 ratio (+20%), and a positive trend was found for 20:4/18:2 (+13%). Abnormal elevations in delta-6 desaturase (FADS2) expression in the PFC of SCZ patients are independent of gender and antipsychotic medications, and might influence SCZ pathogenesis [146].

Fat massand obesity-associated gene (FTO). Weight gain is one of the major adverse effects of antipsychotics. Pérez-Iglesias et al. [147] studied whether the fat mass and obesity-associated gene (FTO) rs9939609 variant, the SNP that has shown the strongest association with common obesity in different populations, and 3 other strong candidate genes involved in the leptinsignaling pathway including leptin, leptin receptor, and Src homology 2, influence weight gain during the first year of antipsychotic treatment. Before antipsychotic treatment, the homozygous subjects for the risk allele A of the FTO rs9939609 variant had a higher body mass index at baseline (24.2 T 3.8 kg/m²) than the AT/TT group (22.82 T 3.3 kg/m²); however, after 1 year of treatment with antipsychotics, the magnitude of weight increase was similar in the 3 genotypes defined by the rs9939609 variant. These results suggest that the pharmacological intervention accompanied by changes in energy intake and expenditure could suppress the genetic susceptibility conferred by the FTO genotype, with no major impact of other SNPs associated with weight gain.

FXYD6 (FXYD domain-containing ion transport regulator 6). The FXYD6 gene is located in chromosome region 11q23.3, where previous studies have shown an association with SCZ; but subsequent studies failed to replicate this finding. Zhong et al. [148] investigated the relationship between FXYD6 locus and SCZ in the Chinese population. Significant associations with SCZ and the marker rs11544201 and the haplotype rs10790212-rs11544201 were found, supporting that FXYD6 might be a susceptibility gene of SCZ.

Fyn (FYN oncogene related to SRC, FGR, YES). Fyn, a Src-family kinase, is highly expressed in brain tissue and blood cells. FYN participates in brain development, synaptic transmission through the phosphorylation of N-methyl-D-aspartate (NMDA) receptor subunits, and the regulation of emotional behavior. Fyn is required for the signal transduction in striatal neurons that is initiated by haloperidol. FYN abnormalities are present in patients with SCZ. A Western blot analysis revealed significantly lower levels of Fyn protein among the patients with SCZ and their relatives, compared with the level in the control group. At the mRNA level, the splicing patterns of FYN were altered in the patients and their relatives; specifically, the ratio of fynDelta7, in which exon 7 is absent, was elevated. An expression study in HEK293T cells revealed that FynDelta7 had a dominantnegative effect on the phosphorylation of Fyn’s substrate. Downregulation of Fyn protein or altered transcription of the FYN gene might influence SCZ pathogenesis [149]. The Src family tyrosine kinase FYN plays a key role in the interaction between BDNF and glutamatergic receptor N-methyl-D-aspartate. An association was found between FYN polymorphisms and cognitive test performance in schizophrenic patients. rs706895 (-93A/G in the 5’-flanking region), rs6916861 (Ex12 + 894T/G in the 3’-UTR) and rs3730353 (IVS10 + 37T/C in intron 10) were investigated, and a significant association was found between rs6916861 T/G and rs3730353 T/C polymorphisms of the FYN gene and BD [150].

GABAergic gene expression. Prefrontal deficits in gamma-aminobutyric acid (GABA) and GABAergic gene expression, including neuropeptide Y (NPY), somatostatin (SST), and parvalbumin (PV) messenger RNAs (mRNAs), have been reported for multiple SCZ cohorts. Preclinical models suggest that a subset of these GABAergic markers (NPY/SST) is regulated by BDNF, which in turn is under the inhibitory influence of small noncoding RNAs. Subjects with SCZ show deficits in NPY and PV mRNAs. Within-pair differences in BDNF protein levels exhibit strong positive correlations with NPY and SST and a robust inverse association with miR-195 levels, which in turn are not affected by antipsychotic treatment or genetic ablation of BDNF. Prefrontal deficits in a subset of GABAergic mRNAs, including NPY, are dependent on the regional supply of BDNF, which in turn is fine-tuned through a microRNA (miRNA)-mediated mechanism [151].

Another important player in GABAergic neurotransmission is the sodium-dependent and chloride-dependent gamma-aminobutyric acid (GABA) transporter 1 (SLC6A1), the target of a number of drugs of clinical importance and a major determinant of synaptic GABA concentrations. A novel 21 bp insertion in the predicted promoter region of SLC6A1 was identified. This mutation creates a second tandem copy of the sequence. Reporter assays showed that the insertion allele significantly increases promoter activity in multiple cell lines. The zinc finger transcription factor ZNF148 was found to significantly transactivate the promoter and increase expression when overexpressed but could not account for the differences in activity between the two alleles of the promoter. Copy number of the insertion sequence was associated with exponentially increasing activity of a downstream promoter, suggesting that the insertion sequence has enhanced activity when present in multiple copies. The SLC6A1 promoter genotype was found to predict SLC6A1 RNA expression in human post-mortem hippocampal samples. The genotyping of individuals from Tanzania suggested that the insertion allele has its origin in Africa. This relatively common polymorphism, of African origin, may prove useful in predicting clinical response to pharmacological modulators of SLC6A1 as well as GABAergic function in individuals of African descent [152].

Glutamatergic Neurotransmission

Glutamate cysteine ligase modifier (GCLM) gene. Experimental evidence shows that glutathione and its rate-limiting synthesizing enzyme, glutamate-cysteine ligase (GCL), are involved in the pathogenesis of SCZ. Genetic association was reported between two SNPs lying in noncoding regions of the glutamate cysteine ligase modifier (GCLM) gene, which specifies for the modifier subunit of GCL and SCZ. Ten sequence variations were identified, five of which were not previously described, but none of these DNA changes was within the GCLM coding sequence, and in silico analysis failed to indicate functional impairment induced by these variations. It is unlikely that functional mutations in the GCLM gene could play a major role in genetic predisposition to SCZ [153].

Glutamate transporter genes. Glutamatergic neurotransmission is involved in the pathogenesis of schizophrenic psychosis, in particular regarding cognitive and negative symptoms. The reported molecular mechanisms include increased glutamate transporter expression, and antipsychotic agents such as clozapine were found able to suppress the expression of these genes. The astroglial excitatory amino acid transporter genes EAAT1 (SLC1A3) and EAAT2 (SLC1A2) as well as the neuronal transporter EAAT3 (SLC1A1) were suppressed by aripiprazole, while the presynaptic vesicular glutamate transporter vGluT1 (SLC17A7) was transiently induced in hippocampal subregions and EAAT4 (SLC1A6) was transiently suppressed in frontocortical areas. These transcriptional effects exerted by aripiprazole may counteract a glutamatergic deficit state and strengthen the neurotransmission of glutamate with positive consequences on cognitive and negative symptoms of SCZ [154].

Glutamic acid decarboxylase 2 and the glutamine synthetase genes (GAD2, GLUL). Two genes encoding glutamate metabolic enzymes, the glutamic acid decarboxylase 2 gene (GAD2) and the glutamine synthetase gene (GLUL) have been studied in Japanese patients with SCZ, including 14 SNPs in GAD2 (approximately 91 kb in size) and 6 SNPs in GLUL (approximately 14 kb in size). No significant ‘single-point’ associations with the disease were found in any of the 20 SNPs after correction for multiple testing. Gene-gene interactions with 6 glutamate receptor genes (GRIA4, GRIN2D, GRIK3, GRIK4, GRIK5, GRM3) did not reveal significant association, indicating that GAD2 and GLUL do not play a major role in SCZ pathogenesis and that there is no gene-gene interaction between the eight genes in the Japanese population [155]. The frequencies of GRIK3 (T928G) genotype distributions in patients with SCZ is similar to those of their relatives. The frequency of the GG genotype is significantly higher in patients than in healthy controls. GG genotype distribution in relatives is elevated compared with that in controls [156].

Glutaminase (GLS1). Genetic knockdown of glutaminase (GLS1) to reduce glutamatergic transmission presynaptically by slowing the recycling of glutamine to glutamate can produce a phenotype relevant to SCZ. GLS1 heterozygous (GLS1 het) mice showed about a 50% global reduction in glutaminase activity, and a modest reduction in glutamate levels in brain regions relevant to SCZ pathophysiology. GLS1 het mice were less sensitive to the behavioral stimulating effects of amphetamine, showed a reduction in amphetamine-induced striatal dopamine release and in ketamine-induced frontal cortical activation, suggesting that GLS1 het mice are resistant to the effects of these pro-psychotic challenges. GLS1 het mice showed clozapine-like potentiation of latent inhibition, suggesting that reduction in glutaminase has antipsychotic-like properties. These observations suggest that presynaptic modulation of the glutamine-glutamate pathway through glutaminase inhibition may provide a new direction for the pharmacotherapy of SCZ [157].

Glutamate receptor, ionotropic, delta 1 (GRID1). Recent linkage and association data have implicated the glutamate receptor delta 1 (GRID1) locus in the etiology of SCZ. The distribution of CpG islands, which are known to be relevant for transcriptional regulation, was computationally determined at the GRID1 locus, and the putative transcriptional regulatory region at the 5’-terminus was systematically tagged using HapMap data. Genotype analyses were performed with 22 haplotype-tagging SNPs (htSNPs) and two SNPs in intron 2 and one in intron 3 which have been found to be significantly associated with SCZ. Association was obtained with rs3814614, rs10749535, and rs11201985. Genetic variants in the GRID1 transcriptional regulatory region may play a role in the etiology of SCZ [158].

Glutamate carboxypeptidase II (GCPII; FOLH1). N-Acetyl aspartyl glutamate (NAAG) is an endogenous agonist at the metabotropic glutamate receptor 3 (mGluR3, GRM3) receptor and antagonist at the N-methyl D-aspartate (NMDA) receptor, both receptors important to the pathophysiology of SCZ. Glutamate carboxypeptidase II (GCPII), an enzyme that metabolizes NAAG, is also implicated in psychosis. In situ hybridization experiments to examine expression of mGluR3 and GCPII transcripts along the rostrocaudal axis of the human post-mortem hippocampus show a significant reduction of GCPII mRNA level in the anterior hippocampus in SCZ. There is a positive correlation between GCPII and mGluR3 mRNA in the CA3 of the control anterior hippocampus which is not present in SCZ, probably reflecting a disrupted functional interaction between NAAG and mGluR3 in CA3 in SCZ [159].

Group III metabotropic glutamate receptor genes, GRM4 and GRM7. Since a glutamatergic dysfunction is involved in the pathophysiology of SCZ, systematic studies on the association between glutamate receptor genes and SCZ have been performed in different populations. Shibata et al. [160] reported association studies of SCZ with 8 and 43 common SNPs in group III metabotropic glutamate receptor genes, GRM4 and GRM7, distributed in the entire gene regions of GRM4 (>111 kb) and GRM7 (>900 kb), respectively. Two neighboring SNPs (rs12491620 and rs1450099) in GRM7 showed highly significant haplotype association with SCZ. At least one susceptibility locus for SCZ might be located within or nearby GRM7, whereas GRM4 is unlikely to be a major susceptibility gene for SCZ in the Japanese population [160].

Glycine-and serine-related genes. Differences in the levels of the glutamate-related amino acids glycine and serine in brain/plasma between schizophrenic patients and normal subjects and changes in the plasma concentrations of these amino acids according to the clinical course have been reported. Glycine and serine metabolism may be altered in SCZ, and some genes related to the metabolism of these amino acids have been suggested to be candidate genes for SCZ. Case-control genetic association analysis of PHGDH, SHMT1, SRR, and DAO was performed, showing no association with SCZ. Only the two (rs3918347-rs4964770) and three (rs3825251-rs3918347-rs4964770) SNP-based haplotype analysis of the DAO gene showed an association with SCZ. None of the genotypes studied was associated with changes in the plasma glycine and Land D-serine levels in SCZ [161].

NMDAR (N-Methyl D-aspartate (NMDA) receptor; GRIN1). Early postnatal inhibition of NMDAR activity in corticolimbic GABAergic interneurons contributes to the pathophysiology of SCZ-related disorders [162]. Consistent with the NMDAR hypofunction theory of SCZ, in animal models in which the essential NR1 subunit of the NMDA receptor (NMDAR) was selectively eliminated in 40% - 50% of cortical and hippocampal interneurons in early postnatal development, distinct SCZ-related symptoms emerged after adolescence, including novelty-induced hyperlocomotion, mating and nest-building deficits, as well as anhedonia-like and anxiety-like behaviors. Social memory, spatial working memory and prepulse inhibition were also impaired. Reduced expression of glutamic acid decarboxylase 67 and parvalbumin was accompanied by disinhibition of cortical excitatory neurons and reduced neuronal synchrony [162]. Phosphorylation of the NR1 subunit of NMDA receptors (NMDARs) at serine (S) 897 is markedly reduced in SCZ patients. Knock-in mutations (mice in which the NR1 S897 is replaced with alanine) cause severe impairment in NMDAR synaptic incorporation and NMDAR-mediated synaptic transmission. Phosphomutant animals have reduced AMPA receptor (AMPAR)-mediated synaptic transmission, decreased AMPARGluR1 subunit in the synapse, impaired long-term potentiation, and behavioral deficits in social interaction and sensorimotor gating, suggesting that an impairment in NR1 phosphorylation leads to glutamatergic hypofunction that can contribute to behavioral deficits associated with psychiatric disorders [163].

Glutathione S-transferase GST-M1, GST-T1, and GST-P1. Data from several studies suggest that oxidative stress may play a role in the pathophysiology of tardive dyskinesia (TD). Glutathione S-transferase (GST) enzymes exert a protecting effect on cells against oxidative stress. The GST-M1, GST-T1, and GST-P1 loci were analyzed in SCZ patients with TD and without TD. There were no significant differences in the distributions of the GST-M1, GST-T1, and GST-P1 genotypes between the TD and non-TD groups. The Ile/Ile genotype of GST-P1 had higher AIMS score compared to Ile/Val + Val/Val genotype, and MDR analysis did not show a significant interaction between the three GST gene variants and susceptibility to TD. These results suggest that GST gene polymorphisms do not confer increased susceptibility to TD in patients with SCZ but TD severity might be related with GST-P1 variants [164].

Glycogen synthase kinase-3 (GSK3). Adult neurogenesis augments neuronal plasticity, and deficient neurogenesis might contribute to mood disorders and SCZ and impede treatment responses. These diseases might be associated with inadequately controlled glycogen synthase kinase-3 (GSK3). There is a drastic 40% impairment in neurogenesis in vivo in GSK3 alpha/beta (21A/21A/9A/9A) knockin mice compared with wildtype mice. Impaired neurogenesis could be due to effects of GSK3 in neural precursor cells (NPCs) or in surrounding cells that modulate NPCs. In vitro proliferation was equivalent for NPCs from GSK3 knockin and wild-type mice, suggesting an in vivo deficiency in GSK3 knockin mice of external support for NPC proliferation. Measurements of two neurotrophins that promote neurogenesis demonstrated less hippocampal vascular endothelial growth factor but not BDNF in GSK3 knockin mice than wild-type mice, reinforcing the possibility that insufficient environmental support in GSK3 knockin mice might contribute to impaired neurogenesis [165]. Accumulating evidence implicates deregulation of GSK3ss as a converging pathological event in AD and in neuropsychiatric disorders, including BD and SCZ. These neurological disorders share cognitive dysfunction as a hallmark. In rodents, increased phosphorylation of GSK3ss at serine-9 has been reported following cognitive training in two different hippocampus dependent cognitive tasks, i.e. inhibitory avoidance and novel object recognition task. Transgenic mice expressing the phosphorylation defective mutant GSK3ss [S9A] show impaired memory in these tasks. GSK3ss [S9A] mice displayed impaired hippocampal L-LTP and facilitated LTD. Application of actinomycin, but not anisomycin, mimicked GSK3ss [S9A]-induced defects in L-LTP, suggesting that transcriptional activation is affected. This was further supported by decreased expression of the immediate early gene c-Fos, a target gene of CREB. These data suggest a role for GSK3ss in long-term memory formation, by inhibitory phosphorylation at serine-9 [166].

Golli-MBP. Multiple studies have reported oligodendrocyte and myelin abnormalities, as well as dysregulation of their related genes, in brains of SCZ patients. One of these genes is the myelin-basic-protein (MBP) gene, which encodes two families of proteins: classic-MBPs and golli-MBPs. While the classic-MBPs are predominantly located in the myelin sheaths of the nervous system, the golli proteins are more widely expressed and are found in both the immune and the nervous systems. Association between six (out of 26 genotyped) SNPs has been found in Jewish Ashkenazi cohorts. Of these, three (rs12458282, rs2008323, rs721286) are from one linkage disequilibrium (LD) block which contains a CTCF binding region. Haplotype analysis revealed significant “risk”/“protective” haplotypes for SCZ, suggesting that golli-MBP is a possible susceptibility gene for SCZ [167].

Growth factor signaling pathways. Evidence has accumulated that the activity of the signaling cascades of neuregulin-1, Wnt, TGF-beta, BDNF-p75 and DISC1 is different between control subjects and patients with SCZ. These pathways are involved in embryonic and adult neurogenesis and neuronal maturation. Clinical data indicate that in SCZ the Wnt pathway is most likely hypoactive, whereas the Nrg1-ErbB4, the TGF-betaand the BDNF-p75-pathways are hyperactive. Haplo-insuffiency of the DISC1 gene is currently the best-established SCZ risk factor. Preclinical experiments indicate that suppression of DISC1 signaling leads to accelerated dendrite development in neuronal stem cells, accelerated migration and aberrant integration into the neuronal network. Increasing NRG1-, BDNFand TGF-beta signaling and decreasing Wnt signaling also promotes adult neuronal differentiation and migration. Deviations in these pathways detected in SCZ might contribute to premature neuronal differentiation, accelerated migration and inappropriate insertion into the neuronal network. Neuronal stem cells isolated from nasal biopsies from SCZ patients display signs of accelerated development, whilst increased erosion of telomeres and bone age provide further support for accelerated cell maturation in SCZ [168].

The role of fibroblast growth factor receptors (FGFR) in normal brain development has been welldocumented in transgenic and knock-out mouse models. Changes in FGF and its receptors have also been observed in SCZ and related developmental disorders. A transgenic th(tk-)/th(tk-) mouse model with FGF receptor signaling disruption targeted to dopamine (DA) neurons, results in neurodevelopmental, anatomical, and biochemical alterations similar to those observed in human SCZ. In th(tk-)/th(tk-) mice hypoplastic development of DA systems induces serotonergic hyperinnervation of midbrain DA nuclei, demonstrating the co-developmental relationship between DA and 5-HT systems. Behaviorally, th(tk-)/th(tk-) mice displayed impaired sensory gaiting and reduced social interactions correctable by atypical antipsychotics and a specific 5-HT_2A antagonist, M100907. The adult onset of neurochemical and behavioral deficits was consistent with the postpubertal time course of psychotic symptoms in SCZ and related disorders. The spectrum of abnormalities observed in th(tk-)/th(tk-) mice and the ability of atypical neuroleptics to correct the behavioral deficits consistent with human psychosis suggests that midbrain 5-HT_2A-controlling systems are important loci of therapeutic action [169].

Heat shock proteins (HSPA1B). Pae et al. [170] investigated a group of SNPs of a set of genes coding for heat shock proteins (HSPA1A, HSPA1B and HSPA1L) and found a significant association between one HSPA1B variation and SCZ. An association between a set of variations (rs2227956, rs2075799, rs1043618, rs562047 and rs539689) within the same genes and a larger sample of schizophrenic inpatients was studied. A single variation, rs539689 (HSPA1B), was found to be marginally associated with Positive and Negative Syndrome Scale (PANSS) positive scores at discharge, and haplotype analysis revealed a significant association between improvement in PANSS scores with both A-C-G-G and A-C-G-G haplotypes. These findings support a role of heat shock proteins in the pathophysiology of SZ [170].

HOMER2. SNPs rs2306428 and rs17158184 of HOMER2 were significantly associated with SCZ in Irish samples. The protective allele at rs2306428 removes a predicted splice-enhancer binding site where HOMER2 is naturally truncated. No allelic effect of rs2306428 on neuropsychological function or on HOMER2 splicing was found [171].

IFNG (Interferon gamma). Dysregulation of the cytokine network in schizophrenia has been well documented. Such changes may occur due to disturbances in cytokine levels that are linked to polymorphisms of cytokine genes. Paul-Samojedny et al. [172] performed the first study to examine the association between the IFN-γ gene polymorphism and psychopathological symptoms in Polish patients with paranoid SCZ. A SNP in the IFN-γ gene (+874T/A, rs 62559044) was found to be associated with paranoid SCZ in males, but not in females. The presence of allele A at position +874 in the IFN-γ gene correlates with 1.66-fold higher risk of paranoid SCZ development in males.

3’ Ig heavy chain locus enhancer HS1,2*A (IGHA1). Infectious and autoimmune pathogenic hypotheses of SCZ have been proposed, prompting searches for antibodies against viruses or brain structures, and for altered levels of immunoglobulins. Allele frequencies of the Ig heavy chain 3’ enhancer HS1,2*A are associated with several autoimmune diseases, suggesting a possible correlation between HS1,2 alleles and Ig production. Levels of serum Igs and HS1,2*A genotypes have been studied in SCZ. Serum concentrations of Ig classes and IgG subclasses are higher in SCZ (80%) as compared to controls (68%). An increased frequency of the HS1,2*2A allele corresponded to increased Ig plasma levels, while an increased frequency of the HS1,2*1A allele corresponded to decreased Ig plasma levels. The transcription factor SP1 bound to the polymorphic region of both HS1,2*1A and HS1,2*2A while NF-kB bound only to the HS1,2*2A. Differences in transcription factor binding sites in the two allelic variants of the 3’ IgH enhancer HS1,2 may provide a mechanism by which differences in Ig expression are affected [173].

Insulin-degrading enzyme (IDE). Insulin-degrading enzyme (IDE) is a neutral thiol metalloprotease, which cleaves insulin with high specificity. IDE also hydrolyzes Aβ, glucagon, IGF I and II, and beta-endorphin. The gene encoding IDE is located on chromosome 10q23-q25, a gene locus linked to SCZ. Insulin resistance with brain insulin receptor deficits/receptor dysfunction was reported in SCZ. IDE cleaves IGF-I and IGF-II, which are implicated in the pathophysiology of SCZ, although polymorphic CA repeat in IGF1 did not show association with SCZ [174]. Brain gamma-endorphin levels, liberated from beta-endorphin exclusively by IDE, have been reported to be altered in SCZ. Studies on the expression of IDE protein in post-mortem brains of patients with SCZ and controls revealed a reduced number of IDE-expressing neurons and IDE protein content in the left and right dorsolateral prefrontal cortex in SCZ compared with controls, but not in other brain areas. Haloperidol might exert some effect on IDE, through changes of the expression levels of its substrates IGF-I and II, insulin and beta-endorphin. Reduced cortical IDE expression might be part of the disturbed insulin signaling cascades found in SCZ and it might contribute to the altered metabolism of certain neuropeptides (IGF-I and IGF-II, beta-endorphin) in SCZ [175].

Interleukins. SCZ has been associated with abnormalities in cytokines and cytokine receptors potentially linked to a defective immunological function in psychotic disorders. Some reports have shown that IL-3, colony stimulating factor 2 receptor alpha (CSF2RA) and IL-3 receptor alpha (IL3RA) are associated with SCZ. A significant association for IL3RA-rs6603272, but not for rs6645249, and a genotypic association of both polymorphisms with SCZ was found in a Chinese population. Haplotype TDT was statistically significant, with the rs6603272 (T) - rs6645249 (G) haplotype significantly associated with SCZ [176]. Interleukin-10 (IL-10), an important immunoregulatory cytokine, is located on chromosome 1q31-32, a region previously reported to be linked to SCZ in genetic studies. Polymorphisms at positions −1082, −819 and −592 in the IL-10 promoter region were determined in Turkish SCZ patients, and significant differences were observed in both allelic and genotypic frequencies of the -592A/C polymorphism. GTA homozygotes (the high IL-10-producing haplotype) were more prevalent among schizophrenic patients than in controls, suggesting that the IL-10 gene promoter polymorphism may be one of the susceptibility factors to develop SCZ in the Turkish population [177].

ITIH3/4 (Inter-alpha-tryptin inhibitor, heavy chain 4), CACNA1C (Calcium channel, voltage-dependent, L type, alpha-1C subunit), and SDCCAG8 (Serologically defined colon cancer antigen 8). The Schizophrenia Psychiatric Genome-Wide Association Study Consortium (PGC) highlighted 81 single-nucleotide polymorphisms (SNPs) with moderate evidence for association to schizophrenia. After follow-up in independent samples, seven loci attained genome-wide significance (GWS), but multi-locus tests suggested some SNPs that did not do so represented true associations. Hamshere et al. [47] found that variants at three loci (ITIH3/4, CACNA1C and SDCCAG8) are associated with SCZ.

JARID2 (Jumonji (JMJ), at-rich interactive domain 2). An association was found of D6S289, a dinucleotide repeat polymorphism in the JARID2 gene, with SCZ and was confirmed by individual genotyping after a genome screen with 400 microsatellite markers spaced at approximately 10 cM in two DNA pools consisting of 119 SCZ patients and 119 controls recruited from a homogenous population in the Chang Le area of the Shandong peninsula of China. rs2235258 and rs9654600 in JARID2 showed association in allelic, genotypic and haplotypic tests with SCZ patients [178].

KCNH2 (Potassium voltage-gated channel, subfamily h (eag-related), member 2). Organized neuronal firing is crucial for cortical processing and this is disrupted in SCZ. A primate-specific isoform (3.1) of the ether-a-go-go-related K⁺ channel KCNH2 that modulates neuronal firing has been identified. KCNH2-3.1 messenger RNA levels are comparable to full-length KCNH2-1A levels in brain but three orders of magnitude lower in heart. In hippocampus from individuals with SCZ, KCNH2-3.1 expression is 2.5-fold greater than KCNH2-1A expression. A meta-analysis of five clinical data sets shows association of SNPs in KCNH2 with SCZ. Risk-associated alleles predict lower intelligence quotient scores and speed of cognitive processing, altered memory-linked functional magnetic resonance imaging signals and increased KCNH2-3.1 mRNA levels in post-mortem hippocampus. KCNH2-3.1 lacks a domain that is crucial for slow channel deactivation. Overexpression of KCNH2-3.1 in primary cortical neurons induces a rapidly deactivating K⁺ current and a high-frequency, nonadapting firing pattern [179].

The potassium channels are thought to have a role in modulating electrical excitability in neurons, regulating calcium signaling in oligodendrocytes and regulating action potential duration in presynaptic terminals and GABA release. Shen et al. [180] chose three potassium channel genes, KCNH1, KCNJ10 and KCNN3, to investigate the role of potassium channels in SCZ by genotyping 23 SNPs (9 in KCNH1, 5 in KCNJ10 and 9 in KCNN3) in a Han Chinese sample consisting of 893 SCZ patients and 611 healthy controls. No significant difference in allelic or genotypic frequency was revealed between SCZ patients and healthy individuals. According to these results, it appears that the 23 SNPs within the three potassium genes examined by Shen et al. do not play a major role in SCZ in the Han Chinese population.

Kynurenine pathway. Some studies of mRNA expression, protein expression, and pathway metabolite levels have implicated dysregulation of the kynurenine pathway in the etiology of SCZ and BD. A SNP in each of six genes, TDO2 (tryptophan 2,3-dioxygenase), HM74 (chemokine receptor HM74/ G protein-coupled receptor 109B; GRP109B), HM74A (G protein-coupled receptor 109A; GRP109A), MCHR1 (melaninconcentrating hormone receptor 1/G protein-coupled receptor 24; GPR24), MCHR2 (melanin-concentrating hormone receptor 2), and MC5R (melanocortin 5 receptor), was tested for association with SCZ. An A allele in HM74 was significantly associated with SCZ and with SCZ plus BD combined. Augmentation of disease risk was found for the complex genotype HM74[A, any] + MCHR1[T, any] + MCHR2[C, any] which conferred an OR maximal for the combined diagnostic category of SCZ plus BD, carried by 30% of the cases. TDO2[CC] + MC5R[G, any] + MCHR2[GC] conferred an OR maximal for SCZ alone, carried by 8% of SCZ cases. The combined risk posed by these related, complex genotypes is greater than any identified single locus and may derive from co-regulation of the kynurenine pathway by interacting genes, a lack of adequate melanotropin-controlled sequestration of the kynureninederived pigments, or the production of melanotropin receptor ligands through kynurenine metabolism [181].

MAGI2 (Membrane-associated guanylate kinase, WW and PDZ domains-containing, 2). MAGI2, a large gene (∼1.5 Mbps) that maps to chromosome 7q21, is involved in recruitment of neurotransmitter receptors such as AMPAand NMDA-type glutamate receptors. Koide et al. [182] examined the relationship of SNP variations in MAGI2 and risk for SCZ in a large Japanese sample and explored the potential relationships between variations in MAGI2 and aspects of human cognitive function related to glutamate activity. They found suggestive evidence for genetic association of common SNPs within MAGI2 locus and SCZ.

Major histocompatibility complex (MHC). The International Schizophrenia Consortium [183] and the European SGENE-plus [184] found significant association with several markers spanning the major histocompatibility complex (MHC) region on chromosome 6p21.3- 22.1. In the MHC region, the five genome-wide significant markers (MHC/HIST1H2BJ: rs6913660-C; MHC/ PRSS16: rs13219354-T; MHC/PRSS16: rs6932590-T; MHC/PGBD1: rs13211507-T; MHC/NOTCH4: rs3131296- G) have risk alleles with average control frequencies between 78% and 92%. The five chromosome 6p markers, spanning about 5 Mb, cover 1.4 cM and exhibit substantial linkage disequilibrium. rs3131296 shows correlation with classical HLA alleles (HLA-A*0101, HLA-B*0801, HLA-C*0701, HLA-DRB*0301, HLA-DQA* 0501, HLA-DQB*0201) [183,184]. This finding might give support to the infective-neuroimmune hypothesis of SCZ. Bergen et al. [48] reported a genome-wide significant association in the MHC region (rs886424). Singleton deletions were more frequent in both case groups compared with controls, whereas the largest CNVs (>500 kb) were significantly enriched only in SCZ cases. Two CNVs (16p11.2 duplications and 22q11 deletions) associated with SCZ were also overrepresented in the SCZ sample.

Malic enzyme 2. Some studies have identified a putative gene locus for both SCZ and BD in the chromosome 18q21 region. Microsatellite analyses showed evidence of association at two contiguous markers, both located at the same genetic distance and spanning approximately 11 known genes. In a corollary gene expression study, one of these genes, malic enzyme 2 (ME2), showed levels of gene expression 5.6-fold lower in anterior cingulate tissue from post-mortem bipolar brains. Subsequent analysis of individual SNPs in strong linkage disequilibrium with the ME2 gene revealed one SNP and one haplotype associated with the phenotype of psychosis. ME2 interacts directly with the malate shuttle system, which has been shown to be altered in SCZ and BD, and has roles in neuronal synthesis of glutamate and gamma-amino butyric acid. Genetic variation in or near the ME2 gene might be associated with both psychotic and manic disorders, including SCZ and BD [185].

Matrix metaloproteinases. Recent studies have demonstrated that matrix metalloproteinase 3 (MMP3) is a key event in associative memory formation, learning and synaptic plasticity, which are important in psychiatric disorders. Genetic variations in the MMP3 -1171 5A/6A have been studied in patients with SCZ. The frequencies of the 6A6A genotype and 6A allele distributions of MMP3 in patients with SCZ were significantly decreased when compared with controls. In contrast, in patients with SCZ, the distribution of the 5A5A genotype and 5A allele were significantly increased as compared with healthy controls. When the frequencies of genotypes or alleles in schizophrenic patients and bipolar patients were compared, 6A6A genotype and 6A allele in patients with BD-I were significantly higher than in patients with SCZ. A potential link between MMP3-1171 5A/6A variants and SCZ might be possible [186].

Matrix metallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase) (MMP9). This gene plays a role in many pathological conditions such as cancer and heart disease and brain functions. It has been hypothesized that the MMP-9 gene may be associated with bipolar mood disorder. A functional −1562C/T polymorphism of the MMP-9 gene was genotyped. Patients with bipolar mood disorder had significant preponderance of T allele vs C allele of 1562C/T polymorphism of the MMP-9 gene, compared to healthy control subjects. The higher frequency of T allele compared to healthy subjects was especially evident in a subgroup of patients with BD, type II. The results may provide the first evidence for an involvement of the MMP-9 gene in the pathogenesis of bipolar mood disorder. They may also contribute to explaining genetic connection between bipolar mood disorder and some somatic illnesses. MMP-9 may be a common susceptibility gene to major psychoses with different allelic variants occurring in bipolar illness and SCZ [187].

MCTP2 (Multiple C2 domains, transmembrane 2). The MCTP2 gene is involved in intercellular signal transduction and synapse function. Djurovic et al. [188] genotyped 37 tagging SNPs across the MCTP2 gene to study a possible association with SCZ in three independent Scandinavian samples, and found a possible involvement of MCTP2 as a potential novel susceptibility gene for SCZ.

Methylenetetrahydrofolate reductase (MTHFR). The frequency of homozygosity for the 677T allele of the MTHFR gene was found higher in Chinese patients with SCZ than in controls. A significant difference was observed in the plasma homocysteine levels among the different genotypes in the patient and control groups. Both elevated plasma homocysteine levels and variation in the MTHFR 677C > T gene are related to increased rates of SCZ and are risk factors for psychosis [189]. The methylenetetrahydrofolate reductase gene (MTHFR) functional polymorphism A1298C may be a risk factor for schizophrenia. Zhang et al. [190] found a genetic association between the MTHFR A1298C polymorphism and SCZ in the Chinese Han population.

MDGA1 (MAM domain-containing glycosylphosphatidylinositol anchor 1; glycosylphosphatidylinositol-MAM; GPIM). The structural, cytoarchitectural and functional brain abnormalities reported in patients with mental disorders may be due to aberrant neuronal migration influenced by cell adhesion molecules. MDGA1, like Ig-containing cell adhesion molecules, has several cell adhesion molecule-like domains. Kahler et al. [191] reported that the MDGA1 gene was a SCZ susceptibility gene in the Scandinavian population. Li et al. [192] investigated the association of MDGA1 with SCZ in the Chinese Han population and found that the genotype frequency of rs11759115 differed significantly between patients and controls. The C-C haplotype of rs11759115- rs7769372 was also positively associated with SCZ. rs1883901 was found to be positively associated with bipolar disorder, and the A-G-G haplotype of rs1883901- rs10807187-rs9462343 was also positively associated with bipolar disorder.

NADPH oxidase NOX2. Sorce et al. [193] investigated the role of NOX2 in acute responses to subanesthetic doses of ketamine. In wild-type mice, ketamine caused rapid behavioral alterations, release of neurotransmitters, and brain oxidative stress, whereas NOX2- deficient mice did not display such alterations. Decreased expression of the subunit 2A of the NMDA receptor after repetitive ketamine exposure was also precluded by NOX2 deficiency. Neurotransmitter release and behavioral changes in response to amphetamine were not altered in NOX2-deficient mice. NOX2 is a major source of ROS production in the prefrontal cortex controlling glutamate release and associated behavioral alterations after acute ketamine exposure. Prolonged NOX2-dependent glutamate release may lead to neuroadaptative downregulation of NMDA receptor subunits. Subanesthetic doses of NMDA receptor antagonist ketamine induce schizophrenia-like symptoms in humans and behavioral changes in rodents. Subchronic administration of ketamine leads to loss of parvalbumin-positive interneurons through reactive oxygen species (ROS), generated by the NADPH oxidase NOX2. However, ketamine induces very rapid alterations, in both mice and humans.

NALCN (Sodium leak channel, nonselective). Teo et al. [22] screened markers for nominal significance and for statistical significance after multiple-testing correction in treatment-resistant schizophrenia and found that the most significant single nucleotide polymorphism was the rs2152324 marker in the NALCN gene (13q33.1).

Neural cell adhesion molecule 1 (NCAM1). Neural cell adhesion molecule 1 (NCAM1) is involved in several neurodevelopmental processes and abnormal expression of this gene has been associated in the pathology of SCZ and, thus, altered NCAM1 expression may be characteristic of the early stages of the illness. NCAM is a membrane-bound cell recognition molecule that exerts important functions in normal neurodevelopment including cell migration, neurite outgrowth, axon fasciculation, and synaptic plasticity. Alternative splicing of NCAM mRNA generates three main protein isoforms: NCAM-180, −140, and −120. Ectodomain shedding of NCAM isoforms can produce an extracellular 105 - 115 kDa soluble neural cell adhesion molecule fragment (NCAM-EC) and a smaller intracellular cytoplasmic fragment (NCAM-IC). NCAM also undergoes a unique post-translational modification in brain by the addition of polysialic acid (PSA)-NCAM. Both PSA-NCAM and NCAM-EC have been implicated in the pathophysiology of SCZ. mRNA expression of one of these isoforms, the 180 kDa isoform of NCAM1 (NCAM-180), was studied in the Brodmann Area (BA) 46, BA10 and BA17, of post-mortem samples from patients with SCZ. NCAM-180 mRNA expression was increased in BA46 from subjects with SCZ compared to controls. No differences in the expression of NCAM-180 mRNA were observed in BA10 or BA17. NCAM-180 mRNA expression is altered in a regionally-specific manner in early stages of SCZ [194]. The developmental expression patterns of the main NCAM isoforms and PSA-NCAM have been described in rodent brain and across human cortical development. Each NCAM isoform (NCAM-180, −140, and −120), post-translational modification (PSA-NCAM) and cleavage fragment (NCAM-EC and NCAM-IC) shows developmental regulation in frontal cortex. NCAM-180, −140, and −120, as well as PSA-NCAM, and NCAM-IC all showed strong developmental regulation during fetal and early postnatal ages, consistent with their identified roles in axon growth and plasticity. NCAM-EC demonstrated a more gradual increase from the early postnatal period to reach a plateau by early adolescence, potentially implicating involvement in later developmental processes. Altered NCAM signaling during specific developmental intervals might affect synaptic connectivity and circuit formation, and thereby contribute to neurodevelopmental disorders [195].

Neuregulin (NRG1, NRG3). Chromosome 8p12 has been identified as a locus for SCZ in several genomewide scans and confirmed by meta-analysis of published linkage data. Systematic fine mapping using extended Icelandic pedigrees identified an associated haplotype in the gene neuregulin 1 (NRG1), also known as heuregulin, glial growth factor, NDF43 and ARIA. A 290 kb core at risk haplotype at the 5’ end of the gene (HAP_ICE), defined by five SNPs and two microsatellite polymorphisms, was found to be associated with SCZ in the Icelandic and Scottish populations. Analysis of the HAP_ICE markers showed the association of a 7-marker and 2-microsatellite haplotype, different from the haplotypes associated in the Icelandic population, and overrepresented in northern Swedish control individuals. Significant association was found with 5 SNPs located in the second intron of NRG1. Furthermore, 2-, 3-, and 4-SNP windows that comprise these SNPs were also associated. One protective haplotype (0% vs 1.8%) and 1 disease risk-causing haplotype (40.4% vs 34.9%) were defined [196]. Li et al. [197] analyzed data from the SNP markers SNP8NRG241930, SNP8NRG243177, SNP8NRG- 221132 and SNP8NRG221533, and the microsatellite markers 478B14-848, 420M9-1395. Across these studies, a strong positive association was found for all six polymorphisms. The haplotype analysis also showed significant association in the pooled international populations. In Asian populations, the risk haplotype was focused around the two microsatellite markers, 478B14- 848, 420M9-1395 (haplotype block B), and in Caucasian populations with the remaining four SNP markers (haplotype block A). This meta-analysis supports the involvement of NRG1 in the pathogenesis of SCZ, but with association between two different but adjacent haplotype blocks in the Caucasian and Asian populations [197]. The promoter for the NRG1 isoform, SMDF, maps to the 3’ end of the gene complex. Analysis of the SNP data-base revealed several polymorphisms within the approximate borders of the region immunoprecipitated in ChIP-chip experiments, one of which is rs7825588. This SNP was analyzed in patients with SCZ and BD and its effect on promoter function was assessed by electromobility gel shift assays and luciferase reporter constructs. A significant increase in homozygosity for the minor allele was found in patients with SCZ, but not in BD. Molecular studies demonstrated modest, but statistically significant, allele-specific differences in protein binding and promoter function. The findings suggest that homozygosity for rs725588 could be a risk genotype for SCZ [198]. Prata et al. [199] tested 4 SNPs, SNP8NRG221533 (rs35753505), SNP8NRG241930, SNP8NRG243177 (rs6994992) and SNPNRG222662 (rs4623364) for allelic and haplotypic association with BD and the presence of psychotic or mood-incongruent psychotic features. Nominal allele-wise significant association for SNP8NRG- 221533 was found, with the T allele being overrepresented in SCZ. This is the opposite allelic association to the original association study where the C allele was associated with SCZ. Subphenotypes were significantly associated with the SNP8NRG221533(T)-SNP8NRG241930- (G) haplotype and with the SNP8NRG221533 (T)-SNP8- NRG222662-(C)-SNP8NRG241930(G) haplotype in the case of the broader subphenotype of psychotic bipolar. This study supports the hypothesis that NRG1 may play a role in the development of BD, especially in psychotic subtypes, albeit with different alleles to previous association reports in SCZ and BD [199]. NRG1 influences the development of white matter connectivity. The cingulum bundle is a white matter structure implicated in SCZ. Abnormalities in the structural integrity of the anterior cingulum in patients with SCZ have been reported. Fractional anisotropy is reduced in the anterior cingulum in SCZ. There is interaction between genetic variation in NRG1 and diagnosis of SCZ, and patients with the T allele for SNP8NRG221533: rs35753505 have decreased anterior cingulum fractional anisotropy compared with patients homozygous for the C allele and healthy controls who were T-carriers [200]. NRG1 is one of the most researched genes associated with SCZ. Although three meta-analyses in this area have been published, the results have been inconclusive and even conflicting. Gong et al. [201] performed a meta-analysis of 26 published case-control and family-based association studies up to September 2008 covering 8049 cases, 8869 controls and 1515 families. Across these studies, the conclusions are as follows: 1) only SNP8NRG- 221132, 420M9-1395(0) and 478B14-848(0) showed significant association in the relatively small sample size; 2) the association analysis of case-control studies was statistically consistent with that of family studies; and 3) the matrix of coancestry coefficient suggested obvious population stratification. The study reveals that one SNP of the NRG1 gene does not contribute significantly to SCZ and that population stratification is evident [201]. Quantitative real-time PCR was used to check the genotypes of four SNPsrs221533 (C/T), rs7820838 (C/T), 433E1006 (A/G) and rs3924999 (C/T), located at the 510 terminus of the NRG1 gene, in 258 Chinese Han schizophrenic parent-proband trios. There was significant transmission disequilibrium in allelic transmission of C, A, T from rs221533, 433E1006, rs3924999 loci, respectively. Haplotype was analyzed at a frequency exceeding 1%. In three-marker-haplotype, C/C/G and C/C/A (rs221533, rs7820838, 433E1006) transmitted predominantly. In four-marker-haplotype (rs221533, rs7820838, 433E1006, rs3924999), C/C/G/T, C/C/A/C and C/C/A/T showed transmission disequilibrium. According to these studies, the NRG1 gene polymorphism is significantly associated with SCZ in Chinese Han, especially in the positive subtype of SCZ [202].

NRG1 is a pleiotropic growth factor involved in diverse aspects of brain development and function. In SCZ, expression of the NRG1 type I isoform is selectively increased [203]. NRG1 and ERBB4 have emerged as some of the most reproducible SCZ risk genes. The Neuregulin (NRG)/ErbB4 signaling pathway has been implicated in dendritic spine morphogenesis, glutamatergic synaptic plasticity, and neural network control. ErbB4-expressing interneurons, but not pyramidal neurons, are primary targets of NRG signaling in the hippocampus and implicate ErbB4 as a selective marker for glutamatergic synapses on inhibitory interneurons [204].

Structural brain abnormalities are present at early phases of psychosis and might be the consequence of neurodevelopmental derailment. The SNP8NRG243177 risk T allele was significantly associated, in an allele copy number-dependent fashion, with increased lateral ventricle volume in psychosis. Genotype explained 7% of the variance of lateral ventricle volume. Genetic variations of the NRG1 gene can contribute to the enlargement of the lateral ventricles described in early phases of SCZ [205].

Linkage studies have implicated 10q22-q23 as a SCZ susceptibility locus in Ashkenazi Jewish (AJ) and Han Chinese from Taiwan populations. Chen et al. [206] performed a peakwide association fine mapping study by using 1414 SNPs across approximately 12.5 Mb in 10q22-q23 of Ashkenazi Jews, and found strong evidence of association by using the “delusion” factor as the quantitative trait at three SNPs (rs10883866, rs10748842, and rs6584400) located in a 13 kb interval in intron 1 of NRG3. NRG3 is primarily expressed in the CNS and is one of three paralogs of NRG1 [206]. Zhang et al. [207] genotyped 13 SNPs within NRG3 to investigate the association between NRG3 and schizophrenia in 488 patients and 506 compared controls in Northwest China and no association was detected either in SNPs or in haplotypes.

Neurogranin (NRGN). A marker located 3457 bases upstream of the neurogranin gene (NRGN) on 11q24 (rs128078009-T) has been associated with SCZ [208]. This marker has an average risk allele control frequency of 83%. Another NRGN SNP (rs7113041) has been reported to be associated with SCZ in Portuguese patients [209]. NRGN is expressed exclusively in brain under control of thyroid hormones, and is reduced in the prefrontal cortex of patients with SCZ. NRGN encodes a postsynaptic protein kinase substrate that binds calmodulin in the absence of calcium. NRGN is abundant in dendritic spines of hippocampal CA1 pyramidal neurons, probably acting as a calmodulin reservoir. Altered NRGN activity might mediate the effects of NMDA hypofunction implicated in SCZ pathogenesis [208].

Neuropeptide Y. It has been suggested that hypoactivity of neuropeptide Y (NPY) may be involved in the pathophysiology of SCZ. A post-mortem study revealed a decreased level of NPY in the brain of patients with SCZ. An increased level of NPY after antipsychotic treatment was also reported in animal brain and cerebrospinal fluid of patients. A positive association between the functional -485C > T polymorphism in the NPY gene and SCZ was reported in the Japanese population; however, more recent studies suggest that the NPY −485C > T polymorphism may not confer susceptibility to SCZ [210].

Neurotrophin receptor (NTRK-3). Based on the important role of neurotrophic factors in brain development and plasticity as well as their extensive expression in hippocampal areas, it has been hypothesized that a variation in the neurotrophin receptor 3 gene (NTRK-3) is associated with hippocampal function and SCZ. rs999905 was significantly associated with SCZ and the haplotype block that includes markers rs999905 and rs4887348 remained significant after permutation tests. The NTRK-3 gene influences hippocampal function and may modify the risk for SCZ [211].

Nitric oxide synthase (NOS). The neuronal nitric oxide synthase gene (NOS1) is located on 12q24.2-q24.31, in a susceptibility region for SCZ, and produces nitric oxide (NO) in the brain. NO plays a role in neurotransmitter release and is the second messenger of the N-methyl-D-aspartate (NMDA) receptor. It is also connected to the dopaminergic and serotonergic neural transmission systems. Therefore, abnormalities in the NO pathway are thought to be involved in the pathophysiology of SCZ. NOS1-G/G is associated with clinically significant variation in cognition. Whether this is a mechanism by which SCZ risk is increased is yet to be confirmed [212]. Several genetic studies showed an association of NOS1 with SCZ; however, results of replication studies have been inconsistent. In a replication study of NOS1 with SCZ in a Japanese sample, Okumura et al. [213] selected seven SNPs (rs41279104, rs3782221, rs3782219, rs561712, rs3782206, rs2682826, and rs6490121) in NOS1 that were positively associated with SCZ in previous studies. Two SNPs showed an association with Japanese schizophrenic patients (rs3782219, rs3782206); however, these associations might have resulted from type I error on account of multiple testing [213]. In other studies no evidence was found of association with rs6490121 in NOS1 [214].

Association between markers within a region on chromosome 1q23.3, including the NOS1AP (nitric oxide synthese 1 (neuronal) adaptor protein) gene and SCZ has been found in a set of Canadian families of European descent, as well as significantly increased expression in SCZ of NOS1AP in unrelated post-mortem samples from the dorsolateral prefrontal cortex. Using the posterior probability of linkage disequilibrium (PPLD) to measure the probability that a SNP is in linkage disequilibrium with SCZ, Wratten et al. [215] evaluated 60 SNPs from NOS1AP in 24 Canadian families demonstrating linkage and association to this region. Two human neural cell lines (SK-N-MC and PFSK-1) were transfected with a vector containing each allelic variant of the NOS1AP promoter and a luciferase gene. Three SNPs produced PPLDs > 40%. One of them, rs12742393, demonstrated significant allelic expression differences in both cell lines tested. The allelic variation at this SNP altered the affinity of nuclear protein binding to this region of DNA, indicating that the A allele of rs12742393 appears to be a risk allele associated with SCZ that acts by enhancing transcription factor binding and increasing gene expression [215]. Findings of another study in the South American population are also consistent with a role for NOS1AP in susceptibility to SCZ, especially for the “negative syndrome” of the disorder [216].

NKCC1 and KCC2 (SLC12A2; SLC12A5). The nature of γ-aminobutyric acid neurotransmission depends on the local intracellular chloride concentration. In the CNS, the intracellular chloride level is determined by the activity of 2 cation-chloride transporters, NKCC1 and KCC2. The activities of these transporters are in turn regulated by a network of serine-threonine kinases that includes OXSR1, STK39, and the WNK kinases WNK1, WNK3, and WNK4. Arion and Lewis [217] compared the levels of NKCC1, KCC2, OXSR1, STK39, WNK1, WNK3, and WNK4 transcripts in prefrontal cortex area 9 between subjects with SCZ and healthy subjects. OXSR1 and WNK3 transcripts were substantially overexpressed in subjects with schizophrenia relative to comparison subjects. In contrast, NKCC1, KCC2, STK39, WNK1, and WNK4 transcript levels did not differ between subject groups. OXSR1 and WNK3 transcript expression levels were not changed in antipsychotic-exposed monkeys and were not affected by potential confounding factors in the subjects with schizophrenia. According to Arion and Lewis, in schizophrenia, increased expression levels, and possibly increased kinase activities, of OXSR1 and WNK3 may shift the balance of chloride transport by NKCC1 and KCC2 and alter the nature of γ-aminobutyric acid neurotransmission in the prefrontal cortex.

NOGO-66 receptor 1 (RTN4R). SCZ or schizoaffective disorders are quite common features in patients with DiGeorge/velo-cardio-facial syndrome (DGS/VCFS) as a result of chromosome 22q11.21 haploinsufficiency. In SCZ, genetic predisposition has been linked to chromosome 22q11, and myelin-specific genes are misexpressed in SCZ. Nogo-66 receptor 1 (NGR or RTN4R) has been considered to be a 22q11 candidate gene for SCZ susceptibility because it encodes an axonal protein that mediates myelin inhibition of axonal sprouting. The RTN4R gene encodes a subunit of the receptor complex (RTN4R-p75NTR) which results in neuronal growth inhibitory signals in response to Nogo-66, MAG or OMG signaling. RTN4R regulates axonal growth, as well as axon regeneration after injury. The gene maps to the 22q11.21 SCZ susceptibility locus and is thus a strong functional and positional candidate gene. RTN4R encodes for a functional cell surface receptor, a glycosylphosphatidylinositol (GPI)-linked protein, with multiple leucine-rich repeats (LRR), which is implicated in axonal growth inhibition. Three mutant alleles were detected, including two missense changes (c.355C > T; R119W and c.587G > A; R196H), and one synonymous codon variant (c.54G > A; L18L). Schizophrenic patients with the missense changes were strongly resistant to the neuroleptic treatment at any dosage. Both missense changes were absent in 300 control subjects. Molecular modeling revealed that both changes lead to putative structural alterations of the native protein [218]. RTN4R deficiency can modulate the long-term behavioral effects of transient postnatal N-methyl-D-aspartate (NMDA) receptor hypofunction. Results reported by Meng et al. [219] and Hsu et al. [220] do not support a major role of RTN4R in susceptibility to SCZ or the cognitive and behavioral deficits observed in individuals with 22q11 microdeletions; however, they suggest that RTN4R may modulate the genetic risk or clinical expression of SCZ in a subset of patients.

Neuronal cultures demonstrate that four different SCZderived NgR1 variants fail to transduce myelin signals into axon inhibition, and function as dominant negatives to disrupt endogenous NgR1. Mice lacking NgR1 protein exhibit reduced working memory function, consistent with a potential endophenotype of SCZ. For a restricted subset of individuals diagnosed with SCZ, the expression of dysfunctional NGR variants may contribute to increased disease risk [221].

NOTCH4. The NOTCH4 gene is located within the major histocompatability complex region on chromosome 6p21.3 and sequence variants have shown association with SCZ. McDonald et al. [222] examined the methylation status of a region surrounding the NOTCH4 −25C/T site in leukocyte genomic DNA and human brain regions. They also studied the polymorphism status of NOTCH4 −25C/T. −25C was the only cytosine which showed methylation in any of the blood or brain samples analyzed. −25C was always fully or partially methylated in blood, was methylated in a similar pattern between SCZ and controls in the blood and was variably methylated in the brain, including completely methylated, partially methylated, subtly methylated or not methylated. –25C/T polymorphism was not associated to schizophrenia. The polymorphism and methylation analysis of NOTCH4 established that the −25C/T polymorphism and methylation status is not associated with schizophrenia, and that −25C is variably methylated in a regionspecific manner in the brain.

NRXN1 (Neurexin 1). Copy number variants (CNVs) and intragenic rearrangements of the NRXN1 (neurexin 1) gene are associated with a wide spectrum of developmental and neuropsychiatric disorders, including intellectual disability, speech delay, autism spectrum disorders (ASDs), hypotonia and schizophrenia. Schaaf et al. [223] performed a clinical and molecular characterization of 24 patients who underwent clinical microarray analysis and had intragenic deletions of NRXN1. 17 of these deletions involved exons of NRXN1, whereas 7 deleted intronic sequences only. The patients with exonic deletions manifested developmental delay/intellectual disability (93%), infantile hypotonia (59%) and ASDs (56%). The more C-terminal deletions, including those affecting the β isoform of neurexin 1, manifested increased head size and a high frequency of seizure disorder (88%) when compared with N-terminal deletions of NRXN1.

OLIG2 (Oligodendrocyte lineage transcription factor 2). Psychotic symptoms are common in more than 10% of patients with AD and define a phenotype with more rapid cognitive and functional decline. Oligodendrocyte lineage transcription factor 2 (OLIG2) is a regulator of white matter development and a candidate gene for SCZ [224], which may also be associated with psychotic symptoms in AD. 11 SNPs in OLIG2 previously tested for association with SCZ were tested for association with AD. Significant evidence for association of psychotic symptoms within cases was identified for the SNPs rs762237 and rs2834072 [225]. Deficits in the expression of oligodendrocyte and myelin genes have been described in numerous cortical regions in SCZ and affective disorders. mRNA expression of 17 genes expressed by oligodendrocyte precursors (OLPs) and their derivatives, including astrocytes, have been studied in four subcortical regions (the anteroventral (AV) and mediodorsal thalamic nuclei (MDN), internal capsule (IC) and putamen (Put)). Genes expressed after the terminal differentiation of oligodendrocytes tended to have lower levels of mRNA expression in subjects with SCZ compared to controls. These differences were statistically significant across regions for four genes (CNP, GALC, MAG and MOG) and approached significance for TF. Two astrocyte-associated genes (GFAP and ALDH1L1) had higher mean expression levels across regions in SCZ. Significant positive correlations were also observed in some regions between cumulative neuroleptic exposure and the expression of genes associated with mature oligodendrocytes as well as with bipotential OLPs [226].

PALB2 (Partner and localizer of BRCA2). A genome-wide association study (GWAS) found significant association between the PALB2 SNP rs420259 and bipolar disorder (BD). The intracellular functions of the expressed proteins from the breast cancer risk genes PALB2 and BRCA2 are closely related. Tesli et al. [227] investigated the relation between genetic variants in PALB2 and BRCA2 and BD/SCZ in a Scandinavian case-control sample and found the BRCA2 SNP rs9567552 to be significantly associated with BD. When they combined their sample with another Nordic case-control sample from Iceland, and added results from the Wellcome Trust Case Control Consortium (WTCCC) and the STEP-UCL/EDDUB-STEP2 study in a metaanalysis, an association between PALB2 SNP rs420259 and BD was observed. Neither the PALB2 SNP rs420259 nor the BRCA2 SNP rs9567552 were nominally significantly associated with the SCZ phenotype in the Scandinavian sample.

Pericentrin (PCNT). Pericentrin (PCNT) interacts with DISC1, BD and major depressive disorder (MDD). A significant allelic association has been found between 3 SNPs (rs3788265, rs2073376 and rs2073380) of the PCNT gene and MDD. After correction for multiple testing, 2 SNPs (rs3788265 and rs2073376) retained significant allelic associations with MDD. A significant association has also been detected between the 2 marker haplotypes (r3788265 and rs2073376) and MDD. According to these results reported by Numata et al. [228], genetic variations in the PCNT gene may play a role in the etiology of MDD in the Japanese population.

Peroxisome proliferator-activated receptor gamma (PPARG), PLAG2G4A, and PTGS2. Patients with SCZ have an increased risk of type-2 diabetes. The combined effects of the PLA2G4A, PTGS2 and PPARG genes were tested among 221 British nuclear families consisting of fathers, mothers and affected offspring with SCZ. A total of 10 SNPs were tested and the likelihood-based association analysis for nuclear families was used to analyze the genotyping data. Eight SNPs detected across the PPARG gene did not show allelic association with SCZ; a weak association was detected at rs2745557 in the PTGS2 locus and rs10798059 in the PLA2G4A locus. The gene-gene interaction test did not show any evidence of either cis-phase interactions for the PLA2G4A and PTGS2 combinations or a trans-phase interaction for the PLA2G4A and PPARG combinations. The PPARG gene has been reported to be strongly associated with type-2 diabetes, but the results reported by Mathur et al. [229] did not support the hypothesis that the PPARG gene may play a role in the development of SCZ.

Phosphatidylinositol 4-kinase type-II beta (PI4K2B). Linkage of BD and recurrent major depression with markers on chromosome 4p15.2 has been identified in a large Scottish family and three smaller families. Analysis of haplotypes in the four chromosome 4p-linked families, identified two regions, each shared by three of the four families, which are also supported by a case-control association study. The candidate gene phosphatidylinositol 4-kinase type-II beta (PI4K2B) lies within one of these regions. PI4K2B is a strong functional candidate as it is a member of the phosphatidylinositol pathway, which is targeted by lithium for therapeutic effect in BD. A casecontrol association study, using tagging SNPs from the PI4K2B genomic region, in BD, SCZ and controls showed association with a two-marker haplotype in SCZ but not in BD (rs10939038 and rs17408391). Expression studies at the allele-specific mRNA and protein level using lymphoblastoid cell lines from members of the large Scottish family, which showed linkage to 4p15.2 in BD and recurrent major depression, showed no difference in expression differences between affected and non-affected family members. There is no evidence to suggest that PI4K2B is contributing to BD in this family but a role for this gene in SCZ has not been excluded [230].

Presenilin 2 (PSEN2). Mutations in the presenilin 1 (PSEN1) and PSEN2 genes are major causative factors for AD [35]. Presenilins are a group of proteins playing an important role in the Notch, ErbB4 and Wnt signaling pathways which might also be associated with SCZ and/or psychotic symptoms in dementia. The gene coding for presenilin 2 (PSEN2) is located on 1q31-q42 and adjacent to a balanced translocation t (1; 11) (q42; q14.3) that was found to co-segregate within family members of patients with SCZ. Five functional SNPs (rs1295645, rs11405, rs6759, rs1046240 and rs8383) present in the coding regions of the PSEN2 gene were tested in 410 patients with SCZ and 355 controls in a Chinese Han population. Association analysis showed a weak association for rs1295645, and the rs1295645-T allele was involved in increased risk of SCZ. The T-C-T-T-T haplotype also showed association with increased risk of SCZ. Analysis of gene expression demonstrated that PSEN2 mRNA levels in peripheral leukocytes were significantly lower in SCZ than in controls and that expression levels of the PSEN2 gene were significantly correlated to its genotypes. Analysis of clinical profiles showed an association between the PSEN2 gene and some clinical phenotypes scored using the PANSS. The PSEN2 gene may be a novel candidate involved in the development of certain psychotic symptoms in SCZ [231].

Proline dehydrogenase/proline oxidase (PRODH). Significant associations have been shown for haplotypes comprising three PRODH SNPs: 1945T/C, 1766A/G, and 1852G/A, located in the 3’ region of the gene, suggesting a role of these variants in the pathogenesis of SCZ. Studies on prepulse inhibition (PPI), verbal and working memory, trait anxiety and schizotypy indicate that CGA carriers exhibit attenuated PPI and verbal memory together with higher anxiety and schizotypy compared with noncarriers [232].

Quaking homolog, KH domain RNA binding (QKI). Chromosome 6q26 includes a susceptibility locus for SCZ in a large pedigree from northern Sweden. Aberg et al. [233] fine-mapped a 10.7 Mb region, included in this locus, using 42 microsatellites or SNP markers, and found a 0.5 Mb haplotype, within the large family that is shared among the majority of the patients (69%). A gamete competition test of this haplotype in 176 unrelated nuclear families from the same geographical area as the large family showed association to SCZ. The only gene located in the region, the quaking homolog, KH domain RNA binding (mouse) (QKI), was investigated in human brain autopsies. Relative mRNA expression levels of two QKI splice variants were clearly downregulated in schizophrenic patients. The mouse homolog is involved in neural development and myelination [233]. Disturbed QKI mRNA expression is observed in the prefrontal cortex of patients, and some of these changes correlate to treatment with antipsychotic drugs. In human astrocytoma (U343) and oligodendroglioma (HOG) cell lines treated with five different antipsychotic drugs including haloperidol, aripiprazole, clozapine, olanzapine and risperidone, haloperidol treatment doubled QKI-7 mRNA levels in U343 cells after 6 hours. The effect was dose-dependent, and cells treated with ten times higher concentration responded with a five-fold and three-fold increase in QKI-7, 6 and 24 hours after treatment, respectively. QKI-7 mRNA expression in human astrocytes is induced by haloperidol, at concentrations similar to plasma levels relevant to clinical treatment of SCZ [234].

RANBP1 (RAN-binding protein 1). Smooth pursuit eye movement (SPEM) disturbance is proposed as one of the most consistent neurophysiological endophenotypes in SCZ. Cheong et al. [235] examined the genetic association of RANBP1 polymorphisms (22q11.21) with the risk of SCZ and with the risk of SPEM abnormality in schizophrenic patients in a Korean population. No RANBP1 polymorphisms were associated with the risk of schizophrenia; however, a common haplotype, RANBP1-ht2 (rs2238798G-rs175162T), showed significant association with the risk of SPEM abnormality among schizophrenic patients.

Reelin (RELN). Reelin is a large secreted protein of the extracellular matrix that has been proposed to participate to the etiology of SCZ. The reelin gene (RELN) encodes a secretory glycoprotein critical for brain development and synaptic plasticity. Post-mortem studies have shown lower reelin protein levels in the brains of patients with SCZ and BP compared with controls. In a genome-wide association study of SCZ, the strongest association was found in a marker within RELN, although this association was seen only in women. RELN is also associated with BP in women [236]. Several authors successfully replicated SCZ linkage on chromosome 7q22 in different populations and demonstrated that an intragenic short tandem repeat (STR) allele of the regional RELN gene is associated with multiple cognitive traits representing central cognitive functions regarded as valid endophenotypes for SCZ. There is association between RELN intragenic STR allele and working memory, impaired cognitive functioning and more severe positive and negative symptoms of SCZ [237]. Reelin plays a pivotal role in neurodevelopment. Excessive RELN promoter methylation and/or decreased RELN gene expression have been described in SCZ and autism. Temporocortical tissue (Brodmann’s area 41/42) of postpuberal individuals is heavily methylated, especially at CpG positions located between −131 and −98 bp. Sex hormones thus seemingly boost DNA methylation at the RELN promoter. This physiological mechanism might contribute to the onset of SCZ and the worsening of autistic behaviors during the puberal period [238]. During development, reelin is crucial for the correct cytoarchitecture of laminated brain structures and is produced by a subset of neurons named Cajal-Retzius. After birth, most of these cells degenerate and reelin expression persists in postnatal and adult brain. In hippocampal cultures, reelin is secreted by GABAergic neurons displaying an intense reelin immunoreactivity (IR). Secreted reelin binds to receptors of the lipoprotein family on neurons with punctate reelin IR. Blocking protein secretion rapidly and reversibly changes the subunit composition of N-methyl-D-aspartate glutamate receptors (NMDARs) to a predominance of NR2B-containing NMDARs. Addition of recombinant or endogenously secreted reelin rescues the effects of protein secretion blockade and reverts the fraction of NR2B-containing NMDARs to control levels. The continuous secretion of reelin is necessary to control the subunit composition of NMDARs in hippocampal neurons. Defects in reelin secretion could play a major role in the development of neuropsychiatric disorders, particularly those associated with deregulation of NMDARs such as SCZ [239]. Reelin is down-regulated in the brain of schizophrenic patients and of heterozygous reeler mice (rl/+). The behavioral phenotype of rl/− mice, however, matches only partially the SCZ hallmarks. Homozygous reeler mutants (rl/rl) exhibit reduced density of parvalbumin-positive (PV+) GABAergic interneurons in anatomically circumscribed regions of the neostriatum. The striatal regions in which rl/rl mice exhibited decreased density of PV+ interneurons are either unaltered (rostral striatum) or equally altered (dorsomedial and ventromedial intermediate striatum, caudal striatum) in rl/+ mice. Reelin haploinsufficiency alters the density of PV+ neurons in circumscribed regions of the striatum and selectively disrupts behaviors sensitive to dysfunction of these targeted regions [240]. Brain abnormalities in +/rl are similar to the psychotic brain and include a reduction in glutamic acid decarboxylase 67 (GAD67), dendritic arbors and spine density in cortex and hippocampus, and abnormalities in synaptic function including long-term potentiation (LTP). RELN and GAD67 promoters are hypermethylated in GABAergic neurons of psychotic post-mortem brain and DNA methyltransferase 1 (DNMT1) is up-regulated. Hypermethlyation of RELN and GAD67 promoters can be induced by treating mice with methionine, and these mice display brain and behavioral abnormalities similar to +/rl [241,242].

Selenium binding protein 1 (SELENBP1). The SELENBP1 gene was found to be up-regulated in both peripheral blood cell and brain tissue samples from SCZ patients. One of four haplotype-tagging SNPs and two different two-marker haplotypes showed nominally significant evidence for association with SCZ in Han Chinese patients living in Taiwan [243].

Serine racemase. D-Serine is an important NMDAR modulator. The D-serine synthesis enzyme serine racemase (SRR) has been found to be defective in SCZ. Mice with an ENU-induced mutation that results in a complete loss of SRR activity exhibit dramatically reduced D-serine levels. Mutant mice displayed behaviors relevant to SCZ, including impairments in prepulse inhibition, sociability and spatial discrimination. Behavioral deficits were exacerbated by an NMDAR antagonist and ameliorated by D-serine or the atypical antipsychotic clozapine. Expression profiling revealed that the SRR mutation influenced several genes that have been linked to SCZ and cognitive ability. Transcript levels altered by the SRR mutation were also normalized by D-serine or clozapine treatment. Analysis of SRR genetic variants in humans identified a potential association with SCZ. Aberrant Srr function and diminished D-serine may contribute to SCZ pathogenesis [244].

Serotonin 6 (5-HT6) receptors (HTR6). Genetic alterations in serotonin 6 (5-HT6) receptors might be associated with the pathophysiology of SCZ. Kishi et al. [245] conducted an association study of the HTR6 gene (rs1805054 (C267T)) in Japanese patients and found no significant associations between the tagging SNPs in HTR6 and SCZ. In a meta-analysis of rs1805054, drawing data from five studies, rs1805054 was not associated with SCZ.

Serotonin (5-Hydroxytryptamine (5-HT)) transporter (SLC6A4). Serotonin (5-hydroxytryptamine (5-HT)) transporter (SLC6A4) is known to influence mood, emotion, cognition and efficacy of antidepressants, particularly that of selective serotonin reuptake inhibitors. Atypical antipsychotics exert their effects partially through serotonergic systems, and hence, variation in 5-HT uptake may affect antipsychotic action mediated through the serotonergic system. The genetic roles of five polymorphisms of SLC6A4, including those of the widely studied 44 base pair variable number of tandem repeat (VNTR) in the promoter region of SLC6A4 (the serotonin transporter gene-linked polymorphic region: 5HTTLPR) and a VNTR polymorphism (STin2) in the second intron, have been studied in SCZ. Significant allelic and genotypic associations with rs2066713, 5HTTLPR and STin2 polymorphisms have been detected. A haplotype linking these three risk alleles, 5HTTLPR/ S-rs2066713/C-STin2/12-repeat, was also significantly associated with SCZ in a South Indian population [246]. A common polymorphism STin2 VNTR in the 5-HTT gene has been extensively investigated in genetic association studies. Lin et al. [247] conducted a case-control study of the association between STin2 VNTR and three tagging SNPs in 5-HTT and SCZ in the Han Chinese population and no association was found in the single locus, but haplotype-based analyses revealed significant association between two haplotypes with SCZ [247]. A 44 base pair insertion (“l”)/deletion (“s”) polymorphism (called 5-HTTLPR) in the 5’ promoter region of the human serotonin transporter gene modulates expression and has been associated to anxiety and depressive traits in otherwise healthy individuals. In individuals with SCZ it seems to modulate symptom severity, acting as a disease modifying gene. In dominant models, the 5-HTTLPR genotype accounted for a significant portion of the variance in SCID depression and SANS negative symptoms (about 5%). The l allele was associated with greater psychopathology and the s allele was associated with greater anxiety and depression levels. Allelic variation may have different consequences for personality traits or psychiatric symptoms depending on epistasis or epigenetic context [248]. The serotonin transporter-linked polymorphic region (5-HTTLPR) short allele confers a general sensitivity to environmental stimuli, and anger is suspected to have a direct influence on aggressive behavior in SCZ. The 5-HTTLPR gene was associated with aggression and/or anger-related traits in SCZ; however, there was no significant difference in the distribution of the 5-HTTLPR genotype/alleles between the aggressive and nonaggressive patients. Aggressive patients carrying the s allele exhibited more anger-related traits than those with the l/l homozygotes, but this difference was not significant after correction for multiple testing. 5-HTTLPR predisposes aggressive patients to exhibit more anger-related traits, but there is no association between 5-HTTLPR and aggressive behavior in SCZ [249].

SH2B1 (SH2B adaptor protein 1). The short arm of chromosome 16 is rich in segmental duplications, predisposing this region of the genome to a number of recurrent rearrangements. Genomic imbalances of an approximately 600-kb region in 16p11.2 (29.5 - 30.1 Mb) have been associated with autism, intellectual disability, congenital anomalies, and SCZ. A separate, distal 200-kb region in 16p11.2 (28.7 - 28.9 Mb) that includes the SH2B1 gene has been associated with isolated obesity. Bachmann-Gagescu et al. [250] studied the phenotype of this recurrent SH2B1-containing microdeletion in a cohort of phenotypically abnormal patients with developmental delay. Deletions of the SH2B1-containing region were identified in 31 patients. The deletion is enriched in the patient population when compared with controls, with both inherited and de novo events. Body mass index was ≥ 95^th percentile in four of six patients, supporting the previously described association with obesity. Accordingly, it appears that deletions of the 16p11.2 SH2B1-containing region are pathogenic and are associated with developmental delay in addition to obesity.

SHMT1 (Serine hydroxymethyltransferase, cytosolic). NMDA receptor function affects PPI integrity and D-serine and glycine are endogenous co-agonists for the receptor. A quantitative trait loci analysis using C57BL/6 (B6) mice with better PPI performance and C3H/He (C3) with lower PPI score has been reported. Genes for both D-serine synthesizing enzyme and enzyme for reversible conversion between glycine and L-serine (SRR and SHMT1, respectively) are located in the same PPI-quantitative trait loci peak. Maekawa et al. [251] analyzed expression levels and genetic polymorphisms of the two genes. There were promoter polymorphisms in SHMT1, which elicit lower transcriptional activity in B6 compared to C3 conforming to the results of brain expression levels, but no functional genetic variants in SRR. SHMT1 levels were higher in schizophrenic brains compared to controls, with no changes in SRR levels. A nominal association between SHMT1 and SCZ has been suggested. Shmt1 (SHMT1), but not Srr, is likely to be one of the genetic components regulating PPI in mice and possibly relevant to SCZ.

Sialyltransferase 8B (ST8SIA2). McAuley et al. [252] identified a significant bipolar spectrum disorder linkage peak on 15q25-26 using 35 extended families with a broad clinical phenotype, including bipolar disorder (types I and II), recurrent unipolar depression and schizoaffective disorder. By a fine mapping association study in an Australian case-control cohort, they found that the sialyltransferase 8B (ST8SIA2) gene, coding for an enzyme that glycosylates proteins involved in neuronal plasticity which has previously shown association to both schizophrenia and autism, is associated with increased risk to bipolar spectrum disorder. Nominal single point association was observed with SNPs in ST8SIA2 (rs4586379, rs2168351), and a specific risk haplotype was identified. Using GWAS data from the NIMH bipolar disorder and NIMH schizophrenia cohorts, the equivalent haplotype was significantly over-represented in bipolar disorder, with the same direction of effect in SCZ. Variation in the ST8SIA2 gene is associated with increased risk to mental illness, acting to restrict neuronal plasticity and disrupt early neuronal network formation, rendering the developing and adult brain more vulnerable to secondary genetic or environmental insults, according to the Australian authors [252].

Sigma non-opioid intracellular receptor 1 (Sig-1R; SIGMAR1). The sigma-1 receptor (Sig-1R) is engaged in modulating NMDA and dopamine receptors which are involved in the pathophysiology of SCZ and the mechanism of psychotropic drug efficacy. Signals, detected from prefrontal regions by 52-channel near-infrared spectroscopy (NIRS) during cognitive activation, were compared between two Sig1-R genotype subgroups (Gln/Gln individuals and Pro carriers) matched for age, gender, premorbid IQ and task performance. The prefrontal hemodynamic response of healthy controls during the verbal fluency task was higher than that of patients with SCZ. For the patients with SCZ, even after controlling the effect of medication, the [oxy-Hb] increase in the prefrontal cortex of the Gln/Gln genotype group was significantly greater than that of the Pro carriers. Clinical symptoms were not significantly different between the two Sig-1R genotype subgroups. This was the first functional imaging genetics study to implicate the association between the Sig-1R genotype and prefrontal cortical function in SCZ in vivo [253].

SLC6A3 (Solute carrier family 6 (neurotransmitter transporter, Dopamine), member 3; Dopamine transporter; DAT). Cordeiro et al. [254] reported an association between a novel SNP (rs6347) located in exon 9 of the dopamine transporter (SLC6A3) and SCZ.

SMARCA2/BRM and the SWI/SNF chromatinremodeling complex. Chromatin remodeling may play a role in the neurobiology of SCZ. The SMARCA2 gene encodes BRM in the SWI/SNF chromatin-remodeling complex, and associations of SNPs with SCZ were found in two linkage disequilibrium blocks in the SMARCA2 gene after screening of 11883 SNPs (rs2296212) and subsequent screening of 22 genes involved in chromatin remodeling (rs3793490) in a Japanese population. A risk allele of a missense polymorphism (rs2296212) induced a lower nuclear localization efficiency of BRM, and risk alleles of intronic polymorphisms (rs3763627 and rs3793490) were associated with low SMARCA2 expression levels in the post-mortem prefrontal cortex. A significant correlation in the fold changes of gene expression from schizophrenic prefrontal cortex was seen with suppression of SMARCA2 in transfected human cells by specific siRNA, and of orthologous genes in the prefrontal cortex of SMARCA2 knockout mice. SMARCA2 knockout mice showed impaired social interaction and prepulse inhibition. Psychotogenic drugs lowered SMARCA2 expression while antipsychotic drugs increased it in the mouse brain. According to Koga et al. [255] these findings support the role of BRM in the pathophysiology of SCZ.

SOX10 (SRY-BOX 10). A SNP (rs139887) in the sexdetermining region Y-box 10 (SOX10) gene, was suggested to be associated with SCZ although inconsistent results had been reported. Yuan et al. [256] evaluated the association between SOX10 rs139887 polymorphism and SCZ and three studies were selected for meta-analysis to determine the effect of rs139887 on SCZ. The allele and genotype frequencies were significantly different between schizophrenic patients and controls, and a significant association in allele and genotype frequencies were found in male patients, but not female patients. The C/C genotype had a significant association with an earlier age of onset in male schizophrenic patients, but not in female patients. The meta-analysis showed that the same C allele was significantly associated with SCZ.

SP4 transcription factor. The Sp4 transcription factor plays a critical role for both development and function of mouse hippocampus. Reduced expression of the mouse Sp4 gene results in a variety of behavioral abnormalities relevant to human psychiatric disorders. The human SP4 gene was examined for its association with both BD and SCZ in European Caucasian and Chinese populations respectively. Out of ten SNPs selected from human SP4 genomic locus, four displayed significant association with BD in European Caucasian families (rs12668354; rs12673091; rs3735440; rs11974306). Four SNPs displayed significant association (rs40245; rs12673091; rs1018954; rs3735440) in the Chinese population and two of them (rs12673091, rs3735440) were shared with positive SNPs from European Caucasian families. Considering the genetic overlap between BD and SCZ, extended studies in Chinese trio families for SCZ revealed that SNP7 (rs12673091) also displayed a significant association. SNP7 (rs12673091) was therefore significantly associated in all three samples, and shared the same susceptibility allele (A) across all three samples. A gene dosage effect for mouse Sp4 gene in the modulation of sensorimotor gating, a putative endophenotype for both SCZ and BD, was also found. The deficient sensorimotor gating in Sp4 hypomorphic mice was partially reversed by the administration of a dopamine D₂ antagonist or mood stabilizers. Both human genetic and mouse pharmacogenetic studies support the Sp4 gene as a susceptibility gene for BD or SCZ [257].

Spermidine/Spermine N1-acetyltransferase (SSAT1; SAT1). Psychotic patients tend to show increased blood and fibroblast total polyamine levels. Spermidine/spermine N1-acetyltransferase (SSAT-1) and its coding gene (SAT-1) are the main factors regulating polyamine catabolism. No association between the SAT-1 −1415T/C SNP and SCZ was found in Spanish patients; however, a mild association between allele C and psychopathology was found in the female group [258].

Sulfotransferase 4A1 (SULT4A1). Sulfotransferase 4A1 (SULT4A1) is a novel sulfotransferase expressed almost exclusively in the brain. The gene is located on chromosome 22q13.2, a region implicated in predisposition to SCZ. A variable microsatellite region located upstream of SULT4A1 was found to be associated with an increase in SCZ risk. If functional dysregulation of SULT4A1 was involved in the etiology of SCZ, then genetic variants in the coding sequence of SULT4A1 might be identified in cases compared with controls. A mutation analysis of the coding region (exons 2 - 7) in 71 Australian SCZ cases found no mutations, either synonymous or nonsynonymous. However, intronic variants (IVS5 + 12 C > T and IVS5 + 28 G > C) were identified, the frequency of which was not statistically different between cases and controls. The lack of polymorphisms in the coding region of the SULT4A1 gene is highly unusual and, along with its high conservation between species, suggests that SULT4A1 may have an important function in vivo, but recent findings do not support the hypothesis that germline mutations in the coding region of SULT4A1 contribute to susceptibility to SCZ [259].

Synapsin 2-3 (SYN2, SYN3). The synapsin III gene (SYN3), which belongs to the family of synaptic vesicle-associated proteins, has been implicated in the modulation of neurotransmitter release and in synaptogenesis, suggesting a potential role in several neuropsychiatric diseases. The human SYN3 gene is located on chromosome 22q12-13, a candidate region implicated in previous linkage studies of SCZ. Four SYN3 SNPs (rs133945 (−631C > G), rs133946 (−196G > A), rs9862 and rs1056484) did not show association with SCZ in either Irish or Chinese case-control samples [260]. Studies of SYN3 mRNA expression in human brain regions as well as the methylation specificity in the closest CpG island of this gene indicate that the cytosine methylation in this genomic region is restricted to cytosines in CpG dinucleotides, and is similar in brain regions and blood, and appears conserved in primate evolution. Two cytosines (cytosine 8 and 20) localized as the CpG dinucleotide are partially methylated in all brain regions. The methylation of these sites in SCZ and control blood samples is variable. The variation in SYN3 methylation is not related to SCZ or a monozygotic twin pair discordant for SCZ and is not related to the mRNA level of SYN3a in different human brain regions [261].

Synaptogyrin 1 (SYNGR1). Synaptogyrin 1 (SYNGR1) is a transmembrane protein of neurotransmitter-containing vesicle. Suggestive association between SYNGR1 intragenic polymorphisms and SCZ has been reported in the Indian population. Rare nucleotide changes with a potential pathogenic effect have been found in Indian and Chinese SCZ patients. Evidence of association has been found for rs715505 in the Italian population [262]. Polymorphisms of the synaptogyrin 1 (SYNGR1) and synasin II (SYNII) genes have been shown to be a risk factor for BD or SCZ. A case-control study with these two genes was conducted in 506 BD patients and 507 healthy individuals from the Han Chinese population. No association was found in this study [263].

Synaptosomal-associated protein 25 kDa (SNAP- 25). SNAP-25 (synaptosomal-associated protein of 25 kDa) is a plasma membrane protein that, together with syntaxin and the synaptic vesicle protein VAMP/synaptobrevin, forms the SNARE (soluble N-ethylmaleimidesensitive factor attachment protein receptor) docking complex for regulated exocytosis. SNAP-25 also modulates different voltage-gated calcium channels, representing therefore a multifunctional protein that plays essential roles in neurotransmitter release at different steps. Recent genetic studies of human populations and of some mouse models implicate alterations in SNAP-25 gene structure, expression, and/or function in contributing directly to these distinct neuropsychiatric and neurological disorders [264]. Both reduced and excessive SNAP-25 activity has been implicated in various disease states that involve cognitive dysfunctions such as ADHD, SCZ and AD. Long-term memory is formed by alterations in glutamate-dependent excitatory synaptic transmission, which is in turn regulated by SNAP-25, a key component of the SNARE complex essential for exocytosis of neurotransmitter-filled synaptic vesicles. Excess SNAP-25 activity, restricted to the adult period, is sufficient to mediate significant deficits in the memory formation process [265].

TAPASIN. Chlamydiaceae species has been identified as a major factor in the pathogenesis of SCZ, suggesting defective immune responses of schizophrenic patients against this environmental factor. Immune responses against Chlamydiaceae species are controlled by immunogenetic factors. Successful responses against microbes depend on the presentation of immunogenic peptides by HLA molecules, which are encoded by a highly polymorphic gene system. Several HLA alleles or HLA antigens have been found to be associated with SCZ in some studies. It has been proposed that variants of these genes, which control transportation and loading of microbial peptides onto HLA molecules, could prevent clearing of immune cell infection by selection of non-immunogenic peptides for HLA presentation. To generate support for this hypothesis, Fellerhoff and Wank [266] determined in a small group of schizophrenic patients and control individuals allele frequencies of the transporter proteins TAP1/TAP2, which select the immunoproteasome-tailored peptides for transportation. Frequencies of TAPASIN alleles, which encode chaperons and may also select peptides for loading on MHC molecules, have also been studied and significant associations between SCZ and TAP1 allele frequencies as well as TAPASIN allele frequencies were found, suggesting that variants of these two genetic systems could influence SCZ. These genes belong to the family of ABC transporter proteins and may also influence the efficiency of drugs [266].

TATA box-binding protein gene (TBP). Spinocerebellar ataxia type 17 (SCA17) is a rare autosomal dominant neurodegenerative disorder with ataxia and psychotic symptoms. SCA17 is caused by an expanded polyglutamine tract in the TATA box-binding protein (TBP) gene. Ohi et al. [267] investigated the association between SCZ and CAG repeat length in common TBP alleles with fewer than 42 CAG repeats in a Japanese population. A higher frequency of alleles with greater than 35 CAG repeats was found in patients with SCZ compared with that in controls. A negative correlation between the number of CAG repeats in the chromosome with longer CAG repeats out of two chromosomes and age at onset of SCZ was also observed. TBP genotypes with greater than 35 CAG repeats, which were enriched in patients with SCZ, were significantly associated with hypoactivation of the prefrontal cortex measured by near-infrared spectroscopy during the tower of Hanoi, a task of executive function. These findings suggest possible associations of the genetic variations of the TBP gene with risk for SCZ, age at onset and prefrontal function [267].

TDP-43 (TAR DNA-binding protein; TARDBP). Clinical features of SCZ and BD overlap with some aspects of the behavioral variant of frontotemporal lobar degeneration. The significance of pathological 43-kDa (transactivation response) DNA-binding protein (TDP-43) for frontotemporal lobar degeneration was recently suggested. Geser et al. [268] studied patients with chronic psychiatric diseases, mainly SCZ, for evidence of neurodegenerative TDP-43 pathology in comparison with controls. Significant TDP-43 pathology in the amygdala/periamygdaloid region or the hippocampus/transentorhinal cortex was absent in both groups in subjects younger than 65 years but present in elderly subjects (29%) of the psychiatric patients and 29% of control subjects. Twenty-three percent of the positive cases showed significant TDP-43 pathology in extended brain scans. There were no evident differences between the 2 groups in the frequency, degree, or morphological pattern of TDP-43 pathology. The latter included subpial and subependymal, focal, or diffuse lesions in deep brain parenchyma and perivascular pathology. A new GRN variant of unknown significance (c.620T > C, p.Met207Thr) was found in one patient with SCZ with TDP-43 pathology. No known TARDBP mutations or other variants were found in any of the subjects studied. The similar findings of TDP-43 pathology in elderly patients with severe mental illness and controls suggest common age-dependent TDP-43 changes in limbic brain areas that may signify that these regions are affected early in the course of a cerebral TDP-43 multisystem proteinopathy.

Transcription factor 4 (TCF4). A marker in intron 4 of the transcription factor 4 (TCF4) on 18q21.1 (rs9960767-C) has been associated with SCZ [269]. The risk allele control frequency of this marker is about 6%. TCF4 is essential for normal brain development. Mutations in this gene were found to be responsible for Pitt-Hopkins syndrome, an autosomal-dominant neurodevelopmental disorder characterized by mental and psychomotor retardation, microcephaly, epilepsy and facial dysmorphism.

Tripartite motif protein 32 (TRIM32). Mutations in the gene encoding tripartite motif protein 32 (TRIM32) cause two seemingly diverse diseases: limb-girdle muscular dystrophy type 2H (LGMD2H) or sarcotubular myopathy (STM) and Bardet-Biedl syndrome type 11 (BBS11). TRIM32 is involved in protein ubiquitination, acting as a widely-expressed ubiquitin ligase, localized to the Z-line in skeletal muscle. TRIM32 binds and ubiquitinates dysbindin, a protein implicated in the genetic etiology of SCZ, augmenting its degradation. Small-interfering RNA-mediated knockdown of TRIM32 in myoblasts resulted in elevated levels of dysbindin. The LGMD2H/STM-associated TRIM32 mutations, D487N and R394H, impair ubiquitin ligase activity towards dysbindin and were mislocalized in heterologous cells. These mutants were able to self-associate and also co-immunoprecipitated with wild-type TRIM32 in transfected cells. D487N mutant could bind to both dysbindin and its E2 enzyme but was defective in monoubiquitination. The BBS11 mutant P130S did not show any biochemical differences compared with the wild-type protein. TRIM32 is a regulator of dysbindin and LGMD2H/ STM mutations may impair substrate ubiquitination [270].

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase Activation Protein, Eta Isoform (YWHAH). Brain protein 14-3-3, eta isoform, or tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein 1 (YWHAH; 14-3-3-ETA) is a protein kinase-dependent activator of tyrosine and tryptophan hydroxyllases and an endogenous inhibitor of protein kinase C. The 14-3-3 protein exists in several distinct forms: beta (YWHAB), gamma (YWHAG), epsilon (YWHAE), zeta (YWHAZ), theta (YWHAQ), sigma (SFN), and eta (YWHAH). YWHAH is a positional and functional candidate gene for both SCZ and BP. This gene has previously been shown to be associated with both disorders, and the chromosome location (22q12.3) has been repeatedly implicated in linkage studies for these disorders. It codes for the eta subtype of the 14-3-3 protein family, is expressed mainly in brain, and is involved in HPA axis regulation. Five tag SNPs and the (GCCTGCA)_n polymorphic locus present in this gene have been genotyped and the rs2246704 SNP was associated with BP and psychotic BP. The polymorphic repeat and two other SNPs were also modestly associated with psychotic BP [271].

Vitamin D-related genes. According to Amato et al. [272], many natural phenomena are directly or indirectly related to latitude. Living at different latitudes, indeed, has its consequences with being exposed to different climates, diets, or light/dark cycles. In humans, one of the best known examples of genetic traits following a latitudinal gradient is skin pigmentation. The authors investigated latitude-driven adaptation phenomena, for the first time on a wide genomic scale. They selected a set of genes showing signs of latitude-dependent population differentiation and studied whether genes associated with neuropsychiatric diseases were enriched by Latitude-Related Genes (LRGs). With this strategy, they found a strong enrichment of LRGs in the set of genes associated to SCZ, especially a set of vitamin D-related genes.

X-ray repair complementing defective repair in Chinese hamster cells 1 (XRCC1) and 4 (XRCC4). Human cells fused with Chinese hamster ovary (CHO) mutant lines, defective at different genes for excision repair of DNA following ultraviolet (UV) irradiation or defective in repair following X-irradiation, produce hybrids that retain the human gene that complements the defect in the CHO line when selected under conditions that require repair. The 1893-bp open reading frame of this gene encodes a protein of 631 amino acids, compared with the 633-amino acid polypeptide of human XRCC1, which shares 86% sequence identity with mouse proteins. An association between genetic polymorphism of XRCC1 Arg194Trp and risk of SCZ has been reported [273].

Genetic factors related to the regulation of apoptosis in schizophrenic patients may be involved in a reduced vulnerability to cancer. XRCC4 is one of the potential candidate genes associated with SCZ which might induce colorectal cancer resistance. To examine the genetic association between colorectal cancer and schizophrenia, Wang et al. [274] analyzed five SNPs (rs6452526, rs2662238, rs963248, rs35268, rs2386275) covering ~205.7 kb in the region of XRCC4. Two of the five genetic polymorphisms (rs6452536, rs35268) showed statistically significant differences between 312 colorectal cancer subjects without SCZ and 270 schizophrenic subjects. The haplotype which combined all five markers was the most significant. XRCC4 may be a potential protective gene towards SCZ, conferring reduced susceptibility to colorectal cancer in the Han Chinese population.

YWHAE (Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon isoform; 14-3-3 epsilon protein). YWHAE is a gene encoding 14-3-3 epsilon, which is highly conserved across species, from bacteria to humans, and binds to phosphoserine/phosphothreonine motifs in a sequence-specific manner. YWHAE has been reported to be associated with SCZ in a study based on the Japanese population. Liu et al. [275] conducted a genetic association analysis between common SNPs in the YWHAE gene and psychiatric diseases including SCZ, major depressive disorder and bipolar disorder in Han Chinese samples (1140 schizophrenia cases, 1140 major depressive disorder cases, 1140 bipolar disorder cases and 1140 normal controls). Of the 11 SNPs studied, 7 had previously been reported as significant in YWHAE. No association was found with SCZ, major depressive disorder or bipolar disorder. Considering the size of this sample set, these results suggest that YWHAE does not play a major role in SCZ, major depressive disorder or bipolar disorder in the Han Chinese population.

Zinc finger protein 804A (ZNF804A). Two recent genome-wide association studies reported association between SCZ and the ZNF804A gene on chromosome 2q32.1 (rs1344706, rs7597593, rs1344706) [214]. The associated SNP rs1344706 lies in approximately 30 bp of conserved mammalian sequence, and the associated A allele is predicted to maintain binding sites for the brain-expressed transcription factors MYT1l and POU3F1/OCT-6. In controls, expression is significantly increased from the A allele of rs1344706 compared with the C allele. Expression is increased in schizophrenic cases compared with controls, but this difference does not achieve statistical significance. This study replicates the original reported association of ZNF804A with SCZ and suggests that there is a consistent link between the A allele of rs1344706, increased expression of ZNF804A and risk for SCZ [276].

ZNF804A rs1344706 is the first genetic risk variant to achieve genome-wide significance for psychosis. Following earlier evidence that patients carrying the ZNF804A risk allele had relatively spared memory function compared to patient non-carriers, Donohoe et al. [277] investigated whether ZNF804A was also associated with variation in brain volume. In a sample of 70 patients and 38 healthy participants they used voxelbased morphometry to compare homozygous (AA) carriers of the ZNF804A risk allele to heterozygous and homozygous (AC/CC) non-carriers for both whole brain volume and specific regions implicated in earlier ZNF804A studies (the dorsolateral pre-frontal cortex, the hippocampus, and the amygdala). Homozygous SCZ “AA” risk carriers had relatively larger gray matter volumes than heterozygous/homozygous non-carriers (AC/CC), particularly for hippocampal volumes. ZNF804A might be delineating a SCZ subtype characterized by relatively intact brain volume.

Dwyer et al. [278] undertook a study to identify whether rare (frequency ~0.001%) coding variants in the SCZ susceptibility gene ZNF804A are involved in this psychotic disorder. No single rare variant was associated with SCZ, nor was the burden of rare, or even fairly common, non-synonymous variants. These results do not support the hypothesis that moderately rare non-synonymous variants at the ZNF804A locus are involved in schizophrenia susceptibility.

As the first gene to have achieved genome-wide significance for psychosis, ZNF804A has predictably been a subject of intense research activity. Donohoe et al. [279] reviewed the evidence to date for the association between SCZ and the original risk variant rs1344706, as well as additional common and rare variants at this locus, and concluded that ZNF804A is robustly, if modestly, associated with SCZ risk.

For markers rs4667000 and rs1366842, significant differences in allele frequencies were found between cases and controls in the Chinese Han population. Analysis of haplotype rs61739290-rs1366842 showed significant association with SCZ. A meta-analysis comprised of studies that utilized sample sets of either European and/or Han Chinese origin revealed statistically significant associations for two SNPs (rs1366842, rs3731834) and SCZ.

MicroRNAs (miRNAs) are small non-coding RNAs that mainly function as negative regulators of gene expression and have been shown to be involved in schizophrenia etiology through genetic and expression studies. A polymorphism (rs1625579) located in the primary transcript of a miRNA gene, hsa-miR-137, was reported to be strongly associated with SCZ. Four SCZ loci (CACNA1C, TCF4, CSMD1, C10orf26) were predicted as hsa-miR-137 targets, and Kim et al. [280] showed that ZNF804A is also a target for hsa-miR-137.

3.3. Copy Number Variants and Cytogenetic Anomalies

The mechanisms underlying generation of neuronal variability and complexity still remain enigmatic, and represent the central challenge for neuroscience. Structural variation in the neuronal genome is likely to be a relevant feature of neuronal diversity and brain dysfunction. Large-scale genomic variations due to loss or gain of whole chromosomes (aneuploidy) have been described in cells of the normal and diseased human brain, which are generated from neural stem cells during the intrauterine period of life. In studies with more than 600,000 neural cells, it has been found that the average aneuploidy frequency is 1.25% - 1.45% per chromosome, with the overall percentage of aneuploidy tending to approach 30% - 35%, and that mosaic aneuploidy may be exclusively confined to the brain. These findings might indicate that 1) aneuploidization could be an additional pathological mechanism for neuronal genome diversification; 2) aneuploidy is involved in brain development; and 3) a link between developmental chromosomal instability and intercellular/intertissular genome diversity might be associated with pathogenic mechanisms underlying specific CNS disorders [281].

Using DNA probes for chromosomes 1, 7, 11, 13, 14, 17, 18, 21, X and Y, the mean rate of stochastic aneuploidy per chromosome is 0.5% in the normal human brain. The overall proportion of aneuploid cells in the normal brain has been estimated at approximately 10%. The overall proportion of aneuploid cells in the brain of patients with ataxia-telangiectasia was estimated at approximately 20% - 50%. A dramatic 10-fold increase of chromosome 21-specific aneuploidy (both hypoploidy and hyperploidy) was detected in the AD cerebral cortex (6% - 15% vs 0.8% - 1.8% in control). It appears that somatic mosaic aneuploidy differentially contributes to intercellular genomic variation in the brain, probably influencing brain dysfunction and neurodegeneration [282].

Brain aneuploidy was hypothesized to be involved in the pathogenesis of SCZ. In normal brains, average frequencies of stochastic chromosome 1 loss and gain were 0.3% and 0.3%, respectively, with a threshold level for stochastic chromosome gain and loss of 0.7%. Average rate of aneuploidy in SCZ brains is 0.9% for chromosome 1 loss and 0.9% for chromosome 1 gain. Significantly increased level of mosaic aneuploidy involving chromosome 1 was revealed in brains (3.6% and 4.7% of cells with chromosome 1 loss and gain, respectively). Stochastic aneuploidy rate for chromosome 1 in SCZ brains reached 0.6% for loss and 0.5% for gain and was higher than in controls, suggesting that subtle genomic imbalances manifesting as low-level mosaic aneuploidy may contribute to SCZ pathogenesis [283].

Copy number variants (CNVs) have been identified in individual patients with SCZ and also in neurodevelopmental disorders [284]. A genome-wide survey of rare CNVs in 3391 patients with SCZ and 3181 ancestrally matched controls, using high-density microarrays, detected CNVs in less than 1% of the sample with 100 kb in length. The total burden was increased 1.15-fold in patients with SCZ in comparison with controls. Deletions were found within the region critical for velo-cardiofacial syndrome, which includes psychotic symptoms in 30% of patients. Associations with SCZ were also found for large deletions on chromosome 15q13.3 and 1q21.1 [184]. CNVs have been shown to increase the risk to develop SCZ. The best supported findings are at 1q21.1, 15q11.2, 15q13.3, 16p13.1, 16p13.11 and 22q11.2, and deletions at the gene neurexin 1 (NRXN1). In the Japanese population, as in other Western populations, there is a trend for excess of rare CNVs in SCZ; however, previously implicated association for very large CNVs (>500 kb) could not be confirmed in this population [285]. In a genome-wide search for CNVs associating with SCZ, 66 de novo CNVs were identified in a sample of 1433 SCZ cases and 33250 controls. Three deletions at 1q21.1, 15q11.2 and 15q13.3 showing nominal association with SCZ in the first sample (phase I) were followed up in a second sample of 3285 cases and 7951 controls (phase II). All three deletions significantly associate with SCZ and related psychoses in the combined sample [208].

There are 484 annotated genes located on 8p; many are most likely oncogenes and tumor-suppressor genes. Molecular genetics and developmental studies have identified 21 genes in this region (ADRA1A, ARHGEF10, CHRNA2, CHRNA6, CHRNB3, DKK4, DPYSL2, EGR3, FGF17, FGF20, FGFR1, FZD3, LDL, NAT2, NEF3, NRG1, PCM1, PLAT, PPP3CC, SFRP1 and VMAT1/SLC18A1) that are most likely to contribute to neuropsychiatric disorders (SCZ, autism, BD and depression), neurodegenerative disorders (Parkinson’s and Alzheimer diseases) and cancer. At least seven nonprotein-coding RNAs (microRNAs) are located at 8p. Structural variants on 8p, such as copy number variants, microdeletions or microduplications, might also contribute to autism, SCZ and other human diseases including cancer [286]. A genome-wide assessment of SNPs and CNVs in 1460 patients with SCZ and 12,995 controls of European ancestry identified 8 cases and zero controls with deletions greater than 2 Mb, of which two, at 8p22 and 16p13.11-p12.4, were novel. A further evaluation of 1378 controls identified no deletions greater than 2 Mb, suggesting a high prior probability of disease involvement when such deletions are observed in cases. Further evidence for some smaller SCZ-associated CNVs, such as those in NRXN1 and APBA2, was confirmed; however, this study could not provide strong support for the hypothesis that SCZ patients have a significantly greater “load” of large (>100 kb), rare CNVs, nor could it find common CNVs that associate with SCZ or SCZ-associated CNVs that disrupt genes in neurodevelopmental pathways [287].

Kirov et al. [288] investigated the involvement of rare (<1%) copy number variants (CNVs) in 471 cases of SCZ and 2792 controls that had been genotyped using the Affymetrix GeneChip 500K Mapping Array. Large CNVs >1 Mb were 2.26 times more common in cases, with the effect coming mostly from deletions, although duplications were also more common. Two large deletions were found in two cases each, but in no controls: a deletion at 22q11.2 known to be a susceptibility factor for SCZ and a deletion on 17p12, at 14.0 - 15.4 Mb. The latter is known to cause hereditary neuropathy with liability to pressure palsies. The same deletion was found in 6 of 4618 (0.13%) cases and 6 of 36,092 (0.017%) controls in the re-analyzed data of two recent large CNV studies of SCZ. One large duplication on 16p13.1, which has been previously implicated as a susceptibility factor for autism, was found in three cases and six controls (0.6% vs 0.2%). This study also provided the first support for a recently reported association between deletions at 15q11.2 and SCZ [288]. A susceptibility locus in 13q13-q14 is shared by SCZ and mood disorder, and that locus would be additional to another well-documented and more distal 13q locus where the G72/G30 gene is mapped [289].

Idiopathic generalized epilepsies account for 30% of all epilepsies. Microdeletions at 15q13.3 have recently been shown to constitute a strong genetic risk factor for common idiopathic generalized epilepsy syndromes, implicating that other recurrent microdeletions may also be involved in epileptogenesis. Five microdeletions at the genomic hotspot regions 1q21.1, 15q11.2, 16p11.2, 16p13.11 and 22q11.2 represent genetic risk to common idiopathic generalized epilepsy syndromes and other neuropsychiatric disorders [290]. Microdeletion at chromosomal position 15q13.3 has been described in intellectual disability, autism spectrum disorders, SCZ and in idiopathic generalized epilepsy [291]. The phenotypic profile of children with microdeletions of 15q13.3 includes developmental delay, mental retardation, or borderline IQ, autistic spectrum disorder, speech delay, aggressiveness, attention-deficit hyperactivity disorder, and other behavioral problems [292]. Positive genetic linkage to the 15q13-q14 region has been found in many studies, and several association reports support this locus as a candidate region for SCZ. A candidate gene in the region, the alpha7 nicotinic receptor CHRNA7, plays a seminal role in the linked endophenotype, and is decreased in expression in the patient population. The 15q13-q14 region contains a partial duplication of the CHRNA7 gene that includes exons 5 - 10 and considerable sequence downstream. Evidence from multiple studies supports a broad region of genetic linkage around the marker D15S1360 [293].

Autism and mental retardation show high rates of comorbidity and potentially share genetic risk factors. A rare approximately 2 Mb microdeletion involving chromosome band 15q13.3 was detected in a multiplex autism family. This genomic loss lies between distal break points of the Prader-Willi/Angelman syndrome locus and was first described in association with mental retardation and epilepsy. Together with recent studies that have also implicated this genomic imbalance in SCZ, this CNV shows considerable phenotypic variability [294].

Deletions and reciprocal duplications of the chromosome 16p13.1 region have been reported in several cases of autism, mental retardation and SCZ. Ingason et al. [295] found a threefold excess of duplications and deletions in SCZ cases compared with controls, with duplications present in 0.30% of cases vs 0.09% of controls and deletions in 0.12% of cases and 0.04% of controls. The region can be divided into three intervals defined by flanking low copy repeats. Duplications spanning intervals I and II showed the most significant association with SCZ. The age of onset in duplication and deletion carriers among cases ranged from 12 to 35 years, and the majority were males with a family history of psychiatric disorders. Candidate genes in the region include NTAN1 and NDE1.

Velocardiofacial syndrome, now known as 22q11.2 deletion syndrome (22qDS), is estimated to affect more than 700 children born in the United States each year. Some clinical studies have found increased rates of SCZ in adults with 22qDS. The psychiatric disorders most commonly reported in children and adolescents with 22qDS have been attention-deficit hyperactivity disorder, oppositional defiant disorder, anxiety disorders, and major depression. Psychotic symptoms have been observed in 14% to 28% of children with 22qDS [296]. Chromosome 22q11.2 deletion syndrome (22q11DS) is associated with cognitive deficits and morphometric brain abnormalities in childhood and a markedly elevated risk of SCZ in adolescence/early adulthood. Children with 22q11DS demonstrate gray matter reductions in multiple brain regions that are thought to be relevant to SCZ. The correlation of these volumetric reductions with poor neurocognition indicates that these brain regions may mediate higher neurocognitive functions implicated in SCZ [297]. Recurrent or overlapping CNVs were found in cases at 39.3% of selected loci. The collective frequency of CNVs at these loci is significantly increased in cases with autism, in cases with SCZ, and in cases with mental retardation compared with controls in France. Individual significance was reached for the association between autism and a 350-kilobase deletion located at 22q11 and spanning the PRODH and DGCR6 genes [298]. The 22q11 deletion (or DiGeorge) syndrome (22q11DS), the result of a 1.5- to 3-megabase hemizygous deletion on human chromosome 22, results in dramatically increased susceptibility for “diseases of cortical connectivity” thought to arise during development, including SCZ and autism. Diminished dosage of the genes deleted in the 1.5-megabase 22q11 minimal critical deleted region in a mouse model of 22q11DS specifically compromises neurogenesis and subsequent differentiation in the cerebral cortex [299]. There is overwhelming evidence that children and adults with 22q11.2 deletion syndrome (22q11.2DS) have a characteristic behavioral phenotype. In particular, there is a growing body of evidence that indicates an unequivocal association between 22q11.2DS and SCZ, especially in adulthood. Deletion of 22q11.2 is the third highest risk for the development of SCZ, with a greater risk only conferred by being the child of two parents with SCZ or the monozygotic co-twin of an affected individual. Both linkage and association studies of people with SCZ have implicated several susceptibility genes, of which three are in the 22q11.2 region: catechol-o-methyltransferase (COMT), proline dehydrogenase (PRODH), and Gnb1L. In addition, variation in Gnb1L is associated with the presence of psychosis in males with 22q11.2DS. In mouse models of 22q11.2DS, haploinsufficiency of Tbx1 and Gnb1L is associated with reduced prepulse inhibition, a SCZ endophenotype [300].

Initial studies of genome-wide trinucleotide repeats using the repeat expansion detection technique suggested possible association of large CAG/CTG repeat tracts with SCZ and bipolar affective disorder [301]. Tandem repeats, particularly with long (>50 bp) repeat units, are a relatively common yet underexplored type of CNV that may significantly contribute to human genomic variation and disease risk. A bacterial artificial chromosome-based array comparative genomic hybridization (aCGH) platform screen detected an apparent deletion on 5p15.1 in two probands, caused by the presence in each proband of two low copy number (short) alleles of a tandem repeat that ranges in length from fewer than 10 to greater than 50 3.4 kb units in the population examined. Short alleles partially segregate with SCZ in a small number of families [302].

Significant familiality of incongruent psychosis was observed in patients with bipolar I disorder or schizoaffective disorder, bipolar type. Covariate linkage analysis provided three regions with genome-wide suggestive evidence for linkage on chromosomes 1q32.3, 7p13 and 20q13.31 in a European sample [303].

The advent of molecular cytogenetic technologies has altered the means by which new microdeletion syndromes are identified. Whereas the cytogenetic basis of microdeletion syndromes has traditionally depended on the serendipitous ascertainment of a patient with established clinical features and a chromosomal rearrangement visible by G-banding, comparative genomic hybridization using microarrays has enabled the identification of novel, recurrent imbalances in patients with mental retardation and apparently nonspecific features. Compared with the “phenotype-first” approach of traditional cytogenetics, array-based comparative genomic hybridization has enabled the detection of novel genomic disorders using a “genotype-first” approach. An illustrative example was the characterization of a novel microdeletion syndrome of 1q41q42. In a sample of over 10,000 patients with developmental disabilities, 7 cases were found with de novo deletions of 1q41q42. The smallest region of overlap is 1.17 Mb and encompasses five genes, including DISP1, a gene involved in the sonic hedgehog signaling pathway, the deletion of which has been implicated in holoprosencephaly in mice. Although none of these patients showed frank holoprosencephaly, many had other midline defects (cleft palate, diaphragmatic hernia), seizures, and mental retardation or developmental delay. Dysmorphic features are present in all patients at varying degrees. This new microdeletion syndrome with its variable clinical presentation may be responsible for a proportion of Fryns syndrome patients and adds to the increasing number of new syndromes identified with array-based comparative genomic hybridization [304].

Some other novel microdeletion syndromes have been detected with array-comparative genomic hybridization (array CGH), including the 17q21.31 deletion and 17q21.31 duplication syndromes, 15q13.3 deletion syndrome, 16p11.2 deletion syndrome, 15q24 deletion syndrome, 1q41q42 deletion syndrome, 2p15p16.1 deletion syndrome and 9q22.3 deletion syndrome [305].

Autism spectrum disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies focusing on candidate genes or genomic regions have identified several CNVs associated with an increased risk of ASDs. A whole-genome CNV study on a cohort of 859 ASD cases and 1409 healthy children of European ancestry genotyped with approximately 550000 SNP markers, besides previously reported ASD candidate genes such as NRXN1 and CNTN4, several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls. CNVs within or surrounding genes involved in the ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40, were affected by CNVs not observed in controls. Duplications 55 kb upstream of complementary DNA AK123120 were also identified. Genes involved in neuronal cell-adhesion or ubiquitin degradation that belong to important gene networks expressed within the CNS may contribute to the genetic susceptibility of ASD [306].

In another genome-wide CNVs study, through prioritization of exonic deletions (eDels), exonic duplications (eDups), and whole gene duplication events (gDups), over 150 loci harboring rare variants in multiple unrelated probands, but no controls, were identified in ASDs. Rare variants at known loci, including exonic deletions at NRXN1 and whole gene duplications encompassing UBE3A and several other genes in the 15q11-q13 region, were observed in these analyses. Strong support was likewise observed for previously unreported genes such as BZRAP1, an adaptor molecule known to regulate synaptic transmission, with eDels or eDups observed in twelve unrelated cases but no controls. MDGA2 was observed to be case-specific, and the encoded protein showed an unexpectedly high similarity to Contactin 4, which has also been linked to disease [307].

Linkage studies have identified several replicated susceptibility loci for ASDs, including 2q24-2q31, 7q, and 17q11-17q21. Association studies and mutation analysis of candidate genes have implicated the synaptic genes NRXN1, NLGN3, NLGN4, SHANK3, and CNTNAP2 in ASDs. Traditional cytogenetic approaches highlight the high frequency of large chromosomal abnormalities (3% - 7% of patients), including the most frequentlyobserved maternal 15q11-13 duplications (1% - 3% of patients) [308].

Cornelia de Lange syndrome (CdLS) is a multisystem congenital anomaly disorder. Heterozygous point mutations in three genes (NIPBL, SMC3 and SMC1A), encoding components of the sister chromatid cohesion apparatus, are responsible for approximately 50% - 60% of CdLS cases. Recent studies have revealed a high degree of genomic rearrangements (deletions and duplications) in the human genome, which result in gene CNVs. Duplications on chromosomes 5 or X have been identified in CdLS using genome-wide array comparative genomic hybridization. The duplicated regions contain either the NIPBL or the SMC1A genes. Junction sequence analyses revealed the involvement of three genomic rearrangement mechanisms. The patients share some common features including mental retardation, developmental delay, sleep abnormalities, and craniofacial and limb defects. The systems affected are the same as in CdLS, but clinical manifestations are distinct from CdLS; particularly the absence of the CdLS facial gestalt. The results confirm the notion that duplication CNV of genes can be a common mechanism for human genetic diseases [309].

The rate of de novo mutations is of relevance to evolution and disease. Kong et al. [310] conducted a study of genome-wide mutation rates by sequencing the entire genomes of 78 Icelandic parent-offspring trios at high coverage, and showed that with an average father’s age of 29.7, the average de novo mutation rate is 1.20 × 10⁻⁸ per nucleotide per generation. The diversity in mutation rate of single nucleotide polymorphisms is dominated by the age of the father at conception of the child. The effect is an increase of about two mutations per year with paternal mutations doubling every 16.5 years. According to Steffanson’s group [310], father’s age is estimated to explain nearly all of the remaining variation in the de novo mutation counts with potential repercussion on the risk of diseases such as SCZ and autism.

3.4. SNPs in Human miRNA Genes

MicroRNAs (miRNAs) are 21 - 25-nucleotide-long, noncoding RNAs involved in translational regulation. Most miRNAs derive from a two-step sequential processing: the generation of pre-miRNA from pri-miRNA by the Drosha/DGCR8 complex in the nucleus, and the generation of mature miRNAs from pre-miRNAs by the Dicer/TRBP complex in the cytoplasm. Sequence variation around the processing sites, and sequence variations in the mature miRNA, especially the seed sequence, may have profound effects on miRNA biogenesis and function. Naturally occurring SNPs can impair or enhance miRNA processing as well as alter the sites of processing. Since miRNAs are small functional units, single base changes in both the precursor elements as well as the mature miRNA sequence may drive the evolution of new microRNAs by altering their biological function. At least 24 human X-linked miRNA variants with potential influence in SCZ have been identified [311]. Individual microRNAs (miRNAs) affect moderate downregulation of gene expression. Components required for miRNA processing and/or function have also been implicated in X-linked mental retardation, neurological and neoplastic diseases, pointing to the wide-ranging involvement of miRNAs in disease. To explore the role of miRNAs in SCZ, 59 microRNA genes on the X-chromosome were amplified and sequenced in males with and without SCZ spectrum disorders to test the hypothesis that ultra-rare mutations in microRNA collectively contribute to the risk of SCZ. Feng et al. [312] provided the first association of microRNA gene dysfunction with SCZ. Eight ultra-rare variants in the precursor or mature miRNA were identified in eight distinct miRNA genes in 4% of analyzed males with SCZ. One ultra-rare variant was identified in a control sample. These variants were not found in an additional 7197 control X-chromosomes. Functional analyses of ectopically expressed copies of the variant miRNA precursors demonstrate loss of function, gain of function or altered expression levels. These findings suggest that microRNA mutations can contribute to SCZ [312].

At least one third of known miRNA genes are expressed in the brain. Mutations disrupting MECP2 protein lead to abnormal development of the brain and resulting behavior. MiR-130b expressed in the brain and potentially targeting MECP2 is located in the susceptibility locus for SCZ (22q11). Screening for mutations has identified a population polymorphism in the 5-upstream miR-130b gene region containing DNA elements for putative transcription factors. Genetic association analysis of 300 schizophrenics and 316 controls revealed no statistically significant association of any of the miR-130b allelic variants with SCZ [313].

For posttranscriptional gene silencing, one strand of the miRNA is used to guide components of the RNA interference machinery, including Argonaute 2, to messenger RNAs (mRNAs) with complementary sequences. Targeted mRNAs are either cleaved by the endonuclease Argonaute 2, or protein synthesis is blocked by a specific mechanism. Genes encoding miRNAs are transcribed as long primary miRNAs (pri-miRNAs) that are sequentially processed by components of the nucleus and cytoplasm to yield a mature, approx 22-nucleotide (nt)-long miRNA. Two members of the ribonuclease (RNase) III endonuclease protein family, Drosha and Dicer, have been implicated in this two-step processing. Several proteins are required for the initial nuclear processing of pri-miRNAs to the approx 60- to 70-nt stem-loop intermediates known as precursor miRNAs (pre-miRNAs). A protein complex, termed Microprocessor by Gregory et al. [314], is necessary and sufficient for processing pri-miRNA to premiRNAs. The Microprocessor complex comprises Drosha and the double-stranded RNA-binding protein DiGeorge syndrome critical region 8 gene (DGCR8), which is deleted in DiGeorge syndrome [314].

Identification of known miRNA targets on all human genes indicates that miRNA-346 targets SCZ susceptibility genes listed in the Schizophrenia Gene database twice as frequently as expected, relative to other genes in the genome. The gene encoding this miRNA, miR-346, is located in intron 2 of the glutamate receptor ionotropic delta 1 (GRID1) gene, which has been previously implicated in SCZ susceptibility. Expression of both miR-346 and GRID1 is lower in SCZ patients than in normal controls; however, the expression of miR-346 and GRID1 is less correlated in SCZ patients than in bipolar patients or in normal controls [315]. Cummings et al. [316] genotyped 821 patients with confirmed DSM-IV diagnoses of SCZ, bipolar affective disorder I and schizoaffective disorder for the risk SNP (rs1625579) of a micro-RNA, MIR-137, and found that carriers of the risk allele had lower scores for an OPCRIT-derived positive symptom factor and lower scores on a lifetime measure of psychosis incongruity. Risk allele carriers also had more cognitive deficits involving episodic memory and attentional control. The MIR-137 risk variant may be associated with a specific subgroup of psychosis patients.

3.5. Epigenetics

Despite the promising results obtained with structural and functional genomic procedures to identify associations with disease pathogenesis and potential drug targets in CNS disorders, it must be kept in mind that allelic mRNA expression is affected by genetic and epigenetic events, both with the potential to modulate neurotransmitter tone in the CNS [317]. Epigenetics is the study of how the environment can affect the genome of the individual during its development as well as the development of its descendants, all without changing the DNA sequence, but inducing modifications in gene expression through DNA methylation-demethylation or through modification of histones by processes of methylation, deacetylation, and phosphorylation [318]. DNA methylation is an epigenetic mechanism in which the methyl group is covalently coupled to the C5 position of the cytosine residue of CpG dinucleotides, generally leading to gene silencing. DNA methylation is catalyzed by a group of enzymes known as DNA methyltransferases (DNMT). DNA methylation changes only happen during DNA replication to maintain methylation patterns on hemimethylated DNA or establish new methylation. DNMT expression generally decreases after cell division, but significant levels of DNMTs are present in postmitotic neurons. There is evidence that DNA methylation correlates with some neuropsychiatric disorders, influences neural development, plasticity, learning, and memory, and is potentially reversible at certain genomic loci. This epigenetic mechanism of gene regulation gives support to a maintenance role of DNMT to prevent active demethylation in postmitotic neurons [319]. Genomic and epigenetic changes can affect complex cognitive functions, including learning and memory, and are causative in several developmental and psychiatric disorders affecting language, social functioning and IQ [320]. DNA methylation and histone deacetylation are two major epigenetic modifications that contribute to the stability of gene expression states. Perturbing DNA methylation, or disrupting the downstream response to DNA methylation-methyl-CpG-binding domain proteins (MBDs) and histone deacetylases (HDACs) by genetic or pharmacological means, has revealed a critical requirement for epigenetic regulation in brain development, learning, and mature nervous system stability, and has identified the first distinct gene sets that are epigenetically regulated within the nervous system [321].

Epigenetic mechanisms such as DNA methylation and modifications to histone proteins regulate high-order DNA structure and gene expression. Aberrant epigenetic mechanisms are involved in different CNS disorders (Rett syndrome, mental retardation disorders, alpha-thalassemia/mental retardation X-linked syndrome, Rubinstein-Taybi syndrome, Coffin-Lowry syndrome, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, multiple sclerosis, epilepsy, amyotrophic lateral sclerosis) and also probably in mental disorders [322].

More than 150 post-translation modifications of histones have been reported, including methylations, acetylations, ubiquitinations, SUMOylations and phosphorylations. A macro-molecular complex, called ECREM for “Epigenetic Code REplication Machinery”, has been proposed as a potential mechanism involved in the inheritance of the epigenetic code. The composition of ECREM may vary in a spatio-temporal manner according to the chromatin state, the cell phenotype and the development stage. Members of ECREM, responsible for the epigenetic code inheritance, include enzymes involved in DNA methylation and histone post-translational modifications. Some of them, such as DNA methyltransferases (DNMTs), histone acetyltransferases (HATs) and histone deacetylases (HDACS, including sirtuins), have been found to be deregulated in several types of pathologies and are already targeted by inhibitors [323].

Epigenetic phenomena cannot be neglected in the pathogenesis and pharmacogenomics of CNS disorders. Studies in cancer research have demonstrated the antineoplastic effects of the DNA methylation inhibitor hydralazine and the histone deacetylase inhibitor valproic acid, of current use in epilepsy [324]. Novel effects of some pleiotropic drugs with activity on the CNS have to be explored to understand in full their mechanisms of action and adjust their dosages for new indications. Both hyperand hypo-DNA methylation changes of the regulatory regions play critical roles in defining the altered functionality of genes (MB-COMT, MAOA, DAT1, TH, DRD1, DRD2, RELN, BDNF) in major psychiatric disorders, such as SCZ and BD [325].

Histone deacetylases (HDACs), enzymes that affect the acetylation status of histones and other important cellular proteins, have been recognized as potentially useful therapeutic targets for a broad range of human disorders. Pharmacological manipulations using smallmolecule HDAC inhibitors, which may restore transcriptional balance to neurons, modulate cytoskeletal function, affect immune responses and enhance protein degradation pathways, have been beneficial in various experimental models of brain diseases [326].

Recent advances in SCZ research indicate that the telencephalic gamma-aminobutyric acid (GABA)ergic neurotransmission deficit associated with this psychiatric disorder is probably mediated by the hypermethylation of the glutamic acid decarboxylase 67 (GAD67), reelin and other GABAergic promoters. A pharmacological strategy to reduce the hypermethylation of GABAergic promoters is to induce a DNA-cytosine demethylation by altering the chromatin remodeling with valproate (VPA). When co-administered with VPA, the clinical efficacy of atypical antipsychotics is enhanced. VPA facilitates chromatin remodeling when it is associated with clozapine or sulpiride but not with haloperidol or olanzapine [327]. This remodeling might contribute to reelinand GAD67- promoter demethylation and might reverse the GABAergic gene-expression downregulation associated with SCZ morbidity [328,329].

Reduction of prefrontal cortex glutamic acid decarboxylase (GAD67) and reelin (mRNAs and proteins) expression is the most consistent finding reported by several studies of post-mortem SCZ brains. The reduced GAD67 and reelin expression in cortical GABAergic interneurons of SCZ brains is the consequence of an epigenetic hypermethylation of RELN and GAD67 promoters very likely mediated by the overexpression of DNA methyltransferase 1 in cortical GABAergic interneurons. RELN and GAD67 promoters express an increased recruitment of methyl-CpG binding domain proteins. The histone deacetylase inhibitor valproate, which increases acetylated histone content in cortical GABAergic interneurons, also prevents MET-induced RELN promoter hypermethylation and reduces the methyl-CpG binding domain protein binding to RELN and GAD67 promoters. DNA hypermethylation and the associated chromatin remodeling may be critically important in mediating the epigenetic down-regulation of reelin and GAD67 expression detected in cortical GABAergic interneurons of SCZ patients [330,331].

Novel strategies in psychiatric epigenetics have been developed. With two novel approaches, it has been observed that valproic acid induced a 383% increase in GAD67 mRNA, an 89% increase in total acetylated histone 3 (H3K9, K14ac) levels, and a 482% increase in H3K9,K14ac attachment to the GAD67 promoter. Trichostatin A (TSA) induced comparable changes on all measures. Bipolar patients had significantly higher baseline levels of H3K9, K14ac compared to patients with SCZ. Subjects with clinically relevant serum levels of valproic acid (>65 μg/mL) showed a significant increase in mRNA expression. Separate approaches for examining chromatin remodeling in real clinical time provide evidence for differential epigenetic events in cultured lymphocytes isolated from patients with SCZ and bipolar depression [332].

Li et al. [333] examined associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Methylation deserts, the ~1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR-mediated NAHR. Rare CNVs occurring in the genomes of individuals diagnosed with SCZ, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions.

3.6. Mitochondrial DNA Mutations

Mitochondria provide most of the energy for brain cells by the process of oxidative phosphorylation. Mitochondrial oxidative phosphorylation is the major ATPproducing pathway, which supplies more than 95% of the total energy requirement in the cells. Damage to the mitochondrial electron transport chain has been suggested to be an important factor in the pathogenesis of a range of psychiatric disorders. Tissues with high energy demands, such as the brain, contain a large number of mitochondria, being therefore more susceptible to reduction of the aerobic metabolism. Mitochondrial abnormalities and deficiencies in oxidative phosphorylation have been reported in individuals with SCZ, BD, and major depressive disorder (MDD) in transcriptomic, proteomic, and metabolomic studies. The evidence includes impaired energy metabolism in the brain, detected using results of magnetic resonance spectroscopy, electron microscopy, co-morbidity with mitochondrial diseases, the effects of psychotropics on mitochondria, increased mitochondrial DNA (mtDNA) deletion in the brain, and association with mtDNA mutations/polymorphisms or nuclear-encoded mitochondrial genes. Alterations of mitochondrial oxidative phosphorylation in SCZ have been reported in several brain regions and also in platelets. Abnormal mitochondrial morphology, size and density have all been reported in the brains of schizophrenic individuals [334,335]. Several mutations in mtDNA sequence have been reported in SCZ and BD patients. The rate of synonymous base pair substitutions in the coding regions of the mtDNA genome is 22% higher in the dorsolateral prefrontal cortex of individuals with SCZ compared to controls [336].

Analyses of mitochondria-related genes using DNA microarray showed significantly increased LARS2 (mitochondrial leucyl-tRNA synthetase) in the post-mortem prefrontal cortices of patients with BD. LARS2 is a nuclear gene encoding the enzyme catalyzing the aminoacylation of mitochondrial tRNA-Leu. A well-studied mitochondrial DNA point mutation, 3243A > G, in the region of tRNA-Leu^UUR, related with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes), is known to decrease the efficiency of aminoacylation of tRNA-Leu^UUR. The steady state level of LARS2 was examined in the transmitochondrial cybrids carrying 3243A > G. LARS2 was upregulated in the transmitochrondrial cybrids carrying 3243A > G. The 3243A > G was detected in the post-mortem brains of patients with BD and SCZ, who also showed higher levels of the mutation in their livers and significantly higher gene expression of LARS2. Upregulation of LARS2 is a hallmark of 324A > G mutation. The accumulation of 3243A > G mutation in the brain may have a pathophysiologic role in BD and SCZ [337].

A decreased expression of mitochondrial complex I subunit gene, NDUFV2 at 18p11, in lymphoblastoid cell lines (LCLs) from Japanese patients with BD, has been reported. No differences were found in NDUFV2 mRNA levels in LCLs of Caucasian BD patients compared with controls [338].

Park et al. [339] characterized Mitofilin, a mitochondrial inner membrane protein, as a mediator of the mitochondrial function of DISC1. A fraction of DISC1 was localized to the inside of mitochondria and directly interacts with Mitofilin. A reduction in DISC1 function induced mitochondrial dysfunction, evidenced by decreased mitochondrial NADH dehydrogenase activities, reduced cellular ATP contents, and perturbed mitochondrial Ca²⁺ dynamics. Deficiencies in DISC1 and Mitofilin induced a reduction in mitochondrial monoamine oxidase-A activity. The mitochondrial dysfunctions evoked by the deficiency of DISC1 were partially phenocopied by an overexpression of truncated DISC1 that is associated with SCZ in humans. DISC1 deficiencies induced the ubiquitination of Mitofilin, suggesting that DISC1 is critical for the stability of Mitofilin. The mitochondrial dysfunction induced by DISC1 deficiency was partially reversed by coexpression of Mitofilin, confirming a functional link between DISC1 and Mitofilin for the normal mitochondrial function. DISC1 may play essential roles for mitochondrial function in collaboration with the mitochondrial interacting partner Mitofilin.

3.7. Genotype-Phenotype Correlations, Transcriptomics, Proteomics, and Metabolomics

Genotype-phenotype correlations represent a central issue in functional genomics to validate the impact of genomic factors on disease pathogenesis and phenotypic expression of disease-related genes as well as in pharmacogenetics and pharmacogenomics [4]. Phenomics, the systematic study of phenotypes on a genome-wide scale, comprises a rate-limiting step on the road to genomic discovery [340]. Novel strategies to assess genotype-phenotype correlates have been developed. For instance, by using the parallel independent component analysis (para-ICA) of Liu to analyze a multimodal data set in which each subject was characterized on 24 different SNP markers spanning multiple risk genes previously associated with SCZ, Meda et al. [341] detected three fMRI components significantly correlated with two distinct gene components. The fMRI components, along with their significant genetic profile (dominant SNP) correlations were as follows: 1) Inferior frontal-anterior/ posterior cingulate-thalamus-caudate with SNPs from BDNF and DAT, 2) superior/middle temporal gyruscingulate-premotor with SLC6A4_PR and SLC6A4_PR_ AG (serotonin transporter promoter; 5HTTLPR), and 3) default mode-fronto-temporal gyrus with BDNF and DAT. These results reveal the effect/influence of specific interactions, between SCZ risk genes on imaging endophenotypes representing attention/working memory and goal-directed related brain function, thus establishing a useful methodology to probe multivariate genotypephenotype relationships [341].

Bergen et al. [342] tested four genes [phenylalanine hydroxylase (PAH), the serotonin transporter (SLC6A4), monoamine oxidase B (MAOB), and the gamma-aminobutyric acid A receptor beta-3 subunit (GABRB3)] for their impact on five SCZ symptom factors: delusions, hallucinations, mania, depression, and negative symptoms. The PAH 232 bp microsatellite allele demonstrated significant association with the delusions factor, and a significant association between the GABRB3 191 bp allele and the hallucinations factor was also detected [342].

Transcriptomics and gene expression studies are also helping to elucidate the role of the prefrontal cortex in SCZ and affective disorders. Owing to reciprocal connectivity, the thalamic nuclei and their cortical fields act as functional units. Chu et al. [343] screened the expression of the entire human genome of neurons harvested by laser-capture microdissection (LCM) from the thalamic primary relay to dorsolateral prefrontal cortex in three psychiatric disease states as compared with controls. Microarray analysis of gene expression showed the largest number of dysregulated genes in SCZ, followed by major depression and D8, respectively. Significantly, IGF1-mTOR-, AKT-, RAS-, VEGF-, Wntand immunerelated signaling, eIF2- and proteasome-related genes were unique to SCZ. Vitamin D receptor and calcium signaling pathway were unique to BD. AKAP95 pathway and pantothenate and CoA biosynthesis were unique to major depression [343].

Studies on the human CNS transcriptome suggest changes in pro-inflammatory pathways and myelination in SCZ, whereas changes in the proteome suggest that pathways involved in energy and metabolism may be particularly stressed. There appear to be complex changes in the expression of proposed candidate genes for SCZ such as NRG1, DISC1, RGS4 and DTNB1, and there are continued reports of alterations in central gamma-aminobutyric acidergic, dopaminergic, glutamatergic and cholinergic pathways in patients with the disorder. Data on epigenetic mechanisms and transcriptome regulation suggest that at least some changes in gene expression may be due to changes in levels of gene promoter methylation or microRNAs in the CNS of patients with SCZ [344].

SCZ is likely to be a consequence of DNA alterations that, together with environmental factors, will lead to protein expression differences and the ultimate establishment of the illness. The superior temporal gyrus is implicated in SCZ and executes functions such as the processing of speech, language skills and sound processing. Proteomics studies in the left posterior superior temporal gyrus (Wernicke’s area - BA22p) revealed 11 downregulated and 14 upregulated proteins, most of them related to energy metabolism. Whereas many of the identified proteins have been previously implicated in SCZ, such as fructose-bisphosphate aldolase C, creatine kinase and neuron-specific enolase, new putative disease markers were also identified such as dihydrolipoyl dehydrogenase, tropomyosin 3, breast cancer metastasis-suppressor 1, heterogeneous nuclear ribonucleoproteins C1/C2 and phosphate carrier protein, mitochondrial precursor [345].

Genome-wide expression analysis of peripheral blood identified candidate biomarkers for SCZ. Using Affymetrix micoarrays, Kuzman et al. [346] identified significantly altered expression of 180 gene probes in psychotic patients compared to controls. The following genes were significantly altered in patients: glucose transporter, SLC2A3 and actin assembly factor DAAM2 were increased, whereas translation, zinc metallopeptidase, neurolysin 1 and myosin C were significantly decreased. DAAM2 polymorphic variants have been found significantly associated with SCZ [346].

The repertoire of biochemicals present in cells, tissue, and body fluids is known as the metabolome. State of the art metabolomic analytical platforms and informatics tools are being used to map potential biomarkers for CNS disorders. Early findings from metabolomic studies may help to identify promising biomarkers for SCZ and many other neuropsychiatric disorders [347].

4. PHARMACOGENOMICS OF ANTIPSYCHOTIC DRUGS4.1. Aripiprazole

Aripiprazole is an arylpiperazine atypical antipsychotic with full agonist activity for 5-HT_1A, 5-HT_1B, 5-HT_1D, 5-HT₆, 5-HT receptors, acting also as a partial agonist of D₂ and 5-HT_1A receptors and antagonist of the 5-HT_2A receptor. Aripiprazole is a major substrate of CYP2D6 and CYP3A4. Caution and personalized dose adjustment should be made in patients with the following genotypes: ADRA1A (Arg347Cys), CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17, CYP2D6*1xN), CYP3A4 and CYP3A5 (CYP3A4*1, CYP3A4*1B, CYP3A4*2, CYP3A4*3, CYP3A4*4, CYP3A4*5, CYP3A4*6, CYP3A4*8, CYP3A4*11, CYP3A4*12, CYP3A4*13, CYP3A4*15, CYP3A4*17, CYP3A4*18, CYP3A4*19, CYP3A5*3), DRD2 (TaqIA RFLP (rs1800497, ANKK1), TaqIB (rs1079597), rs6277), DRD3 (Ser9Gly), HTR2A (His452Tyr, His368Tyr, Ile197Val, Ile113Val, Ala447Val, Ala363Val, Thr25Asn, A-1438G (rs6311), T102C (rs6313)), HTR2C (Cys23Ser, −759C/T), and also in ABCB1 and HTR1A mutants [25] (Table 2).

4.2. Benperidol

Benperidol is a butyrophenone antipsychotic which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors. Genes potentially involved in efficacy and safety might be DRD1 and DRD2 [25] (Table 2).

4.3. Bromperidol

Bromperidol is a butyrophenone with antagonistic activity on D₂ receptors and a moderate antagonistic activity on serotonin 5-HT₂receptors. Bromperidol is a major substrate of CYP3A4, a minor substrate of CYP2D6, a substrate of several UGTs, and a moderate inhibitor of CYP2D6. ABCB1 (C3435T and G2677T/A), DRD2 (Taq IA RFLP and rs1800497, ANKK1), and HTR2 variants may influence its pharmacokinetics and pharmacodynamics [25] (Table 2).

4.4. Chlorpromazine

Chlorpromazine is an aliphatic phenothiazine antipsychotic which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors, has a strong anticholinergic effect, weakly blocks ganglionic, antihistaminic and antiserotonergic receptors, strongly blocks α-adrenergic receptors, and behaves as an inverse agonist of 5-HT₆ and 5-HT₇ receptors and as an antagonist of 5-HT_1A and 5-HT_2c receptors. Chlorpromazine is a major substrate of CYP2D6, a minor substrate of CYP1A2 and CYP3A4, and a substrate of UGT1A3 and UGT1A4. This neuroleptic strongly inhibits CYP2D6 and weakly CYP2E1 and DAO. Caution and personalized dose adjustment should be made in patients with the following genotypes: ACACA (rs4072032,rs2229416 (Gln526His), rs1266175, rs12453407, rs9906543), BDNF ((GT)_n), CYP1A2 (C734A, G-2964A), CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8,

CYP2D6*10, CYP2D6*17, CYP2D6*1xN), DRD2 (−141C Ins/Del) (rs1799732) TaqIA RFLP (rs1800497, ANKK1), TaqIB (rs1079597), TaqID (rs1800498), (Ser311Cys, rs6276 and rs6277), DRD3 (Ser9Gly), HTR2C (−759C/T in the promoter region), LEP (–2548G/A), and NPY (rs1468271). ABCB1, CFTR, CYP2A6, CYP2C9, CYP2C19, CYP2E1, CYP3A4, DAO, FABP1, FMO1, UGT1A3, and UGT1A4 variants may also influence its pharmacokinetics and pharmacodynamics [25] (Table 2).

4.5. Clozapine

Clozapine is a dibenzodiazepine atypical antipsychotic which acts as an antagonist of histamine H₁, cholinergic and α₁-adrenergic receptors, an antagonist of 5-HT_1A and 5-HT_2B receptors, a full agonist of 5-HT_1A, 5-HT_1B, 5-HT_1D, and 5-HT_1F receptors, and an inverse agonist of 5-HT₆ and 5-HT₇ receptors. Clozapine is a major substrate of ABCB1, CYP1A2 and CYP3A4, a minor substrate of CYP2A6, CYP2C8, CYP2C9, CYP2C19 and CYP2D6, and also substrate of FMO3, UGT1A3 and UGT1A4. This atypical antipsychotic moderately inhibits CYP2C9, CYP2C19 and CYP2D6, and weakly inhibits CYP1A2, CYP2E1 and CYP3A4. Caution and personalized dose adjustment should be made in patients with the following genotypes: APOA5 (−1131C > T, Ser19Trp), APOC3 (C1100T), APOD (rs7659), CYP1A2 (C734A, G-2964A, C1545T), DRD1 (rs4532, rs265976), DRD2 (TaqIA RFLP (rs1800497, ANKK1), Taq1B (rs1079597), rs1125394), DRD3 (Ser9Gly), DTNBP1 (rs1018381, rs760761, rs2619539, rs742105, Diplotype ACCCTC/ GTTGCC, rs742106), GNB3 (Ser275Ser), HTR1F (C267T), HTR2A (His452Tyr, His368Tyr, Ile197Val, Ile113Val, Ala447Val, Ala363Val, Thr25Asn), HTR2C (Cys23Ser), TNF (−308G > A), and UGT1A4 (Leu48Val, Leu150Leu, 43fcX22). Other polymorphic variants in the ABCB1, CNR1, CYP2A6, CYP2D6, CYP2C8, CYP2C9, CYP2C19, CYP2E1, CYP3A4, DRD4, FABP1, FMO3, GSK3B, HTR3A, HRH1, HTR6, LPL, NRXN1, RGS2, and UGT1A3 genes may also influence its pharmacokinetics and pharmacodynamics [25] (Table 2).

4.6. Droperidol

Droperidol is a butyrophenone which blocks dopaminergic and α-adrenergic receptors. This atypical antipsychotic is a major substrate of CYP2C9, CYP2C19, CYP2D6, and CYP3A4. ABCC8, ADRA2A, ADRB1, CHRM2, CYP2C9, CYP2C19, CYP2D6, CYP3A4, KCNE1, KCNE2, KCNQ1, KCNJ11, and KCNH2 variants influence its efficacy and safety [25] (Table 2).

4.7. Fluphenazine

Fluphenazine is a piperazine phenothiazine which blocks postsynaptic mesolimbic dopaminergic D₁ and D₂ receptors and is an inverse agonist of 5-HT₇receptors, and an antagonist of 5-HT_2A receptors. This typical antipsychotic is a major substrate of CYP2D6; weakly inhibits CYP1A2, CYP2C9, and CYP2E1; and strongly inhibits CYP2D6. Caution and personalized dose adjustment should be made in patients with the following CYP2D6 genotypes: CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17, CYP2D6*1xN. ABCB1, CYP1A2, CYP2A6, CYP2B6, CYP2C9, CYP2C19, CYP2E1, CYP3A4, DRD1, DRD2, HRH1, HTR2A, and HTR7 variants may also affect its pharmacokinetic and pharmacodynamic properties [25] (Table 2).

4.8. Flupenthixol

Flupenthixol is a thioxanthene with typical antipsychotic activity by blocking postsynaptic dopaminergic receptors. DRD1 (Ala229Thr, Arg50Ser, Ser199Ala, Thr37Arg, Thr37Pro) and DRD2 variants may affect its biopharmaceutical properties [25] (Table 2).

4.9. Haloperidol

Haloperidol is a butyrophenone which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors, acting also as an antagonist of 5-HT_2A and 5-HT_2B receptors. This typical antipsychotic is a major substrate of CYP2D6 and CYP3A4/5, a minor substrate of CYP1A1, CYP1A2, CYP2C8, CYP2C9, and CYP2C19, a substrate of CBR and several UGTs, and a moderate inhibitor of CYP2D6 and CYP3A4. Caution and personalized dose adjustment should be made in patients with the following genotypes: CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17, CYP2D6*1xN), CYP3A4 and CYP3A5 (CYP3A4*1, CYP3A4*1B, CYP3A4*2, CYP3A4*3, CYP3A4*4, CYP3A4*5, CYP3A4*6, CYP3A4*8, CYP3A4*11, CYP3A4*12, CYP3A4*13, CYP3A4*15, CYP3A4*17, CYP3A4*18, CYP3A4*19, CYP3A5*3), DRD2 (TaqIA RFLP (rs1800497, ANKK1)), DTNBP1 (rs909706, diplotype ACCCTC/GCCGCC), HTR2A (A-1438G (rs6311)), and IL1RN (VNTR (IL1RN*1 and IL1RN*2). ABCB1, ABCC1, ADRA2A, BDNF, CHRM2, CYP1A2, CYP2A6, CYP2C9, CYP2C19, DRD1, DRD4, FOS, GRIN2B, GSK3B, GSTP1, HRH1, HTT, KCNE1, KCNE2, KCNH2, KCNJ11, and KCNQ1 variants also affect its neuroleptic properties and side-effects [25] (Table 2).

4.10. Loxapine

Loxapine is a dibenzoxazepine which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors and serotonin 5-HT₂receptors, also acting as an inverse agonist of 5-HT_2c and 5-HT₆ receptors. This typical antipsychotic is a substrate of UGT1A4, and DRD1, DRD2, HTR2A, and UGT1A4 variants might be able to modify its biopharmaceutical properties [25] (Table 2).

4.11. Mesoridazine

Mesoridazine is a phenothiazine with putative dopaminergic, cholinergic and adrenergic inhibition. This typical antipsychotic is a substrate of CYP2J2, and ADRA1A, DRD2, CHRM2, CYP2J2, KCNE1, KCNE2, KCNH2, KCNJ11, KCNQ1, SCN5A variants may affect its pharmacokinetic and pharmacodynamic properties [25] (Table 2).

4.12. Molindone

Molindone is a dihydroindolone which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors, has a strong anticholinergic effect, a weak ganglionic, antihistaminic and antiserotonergic blocking capacity, and a strong α-adrenergic blocking activity, also acting as an antagonist of 5-HT_2A receptors. Polymorphic variants in the ADRA1A, DRD2, DRD3, HRH1, HTR1A, HTR1E, HTR2A, and HTR2C genes may induce changes in proteomic byproducts leading to modifications in the biopharmaceutical properties of this typical antipsychotic [25] (Table 2).

4.13. Olanzapine

Olanzapine is a thienobenzodiazepine which acts as a strong antagonist of serotonergic 5-HT_2A, 5-HT_2C, and 5-HT₇ receptors, dopaminergic D_1-4 receptors, histaminergic H₁ receptors, and α₁-adrenergic receptors. This atypical antipsychotic is also an antagonist of 5-HT_2A,

5-HT₃ and muscarinic M_1-5 receptors, a full agonist of 5-HT_1A, 5-HT_1B, 5-HT_1D, and 5-HT_1F receptors, and an inverse agonist of 5-HT_2c and 5-HT₆ receptors. Olanzapine is a major substrate of CYP1A2, CYP2D6 and UGT1A4, and a weak inhibitor of CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4. Caution and personalized dose adjustment should be made in patients with the following genotypes: ABCB1 (C1236T, G2677T/A, C3435T), ADRB3 (Arg64Trp), APOA5 (−1131T > C, Ser19Trp), APOC3 (C1100T), COMT (Val(108/158) Met), CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17, CYP2D6*1xN), DRD2 (TaqIA RFLP (rs1800497, ANKK1), −141C Ins/Del (rs1799732), −241 A > G, Ser311Cys), DRD3 (Ser9Gly), GNB3 (Ser275Ser), GRM3 (rs6465084, rs274622), HTR2A (His452Tyr, His368Tyr, Ile197Val, Ile113Val, Ala447Val, Ala363Val, Thr25Asn, T102C (rs6313)), HTR2C (Cys23Ser, −759C > T), LEP (rs4731426, −1548G > A), LEPR (Gln223Arg), RGS2 (rs4606, rs1152746, rs1819741, rs1933695, rs2179652, rs2746073), SLC6A2 (G1287A, T-182C), and UGT1A4 (Leu48Val). These genotypes and other polymorphic variants in the CYP1A2, CYP2C9, CYP2C19, CYP3A4, DRD4, FMO1, KCNH2, and LPL genes are determinant for olanzapine-related pharmacological properties and/or side-effects [25] (Table 2).

4.14. Paliperidone

Paliperidone is a benzisoxazole which acts as a serotonin and dopamine receptor antagonist, with high affinity for α₁, D₂, H₁, and 5-HT_2C receptors and low affinity for muscarinic and 5-HT_1A receptors. This atypical antipsychotic is a major substrate of ABCB1, ADH, CYP2D6, CYP3A4, and several UGTs, and inhibits ABCB1, CYP2D6, and CYP3A4. Polymorphic variants in the ABCB1, ADRA1A, ADRA1B, ADRA1D, CYP2D6, CYP3A4, DRD2, HRH1, and HTR2A genes may affect its biopharmaceutical properties and also the manifestation of potential adverse drug reactions [25] (Table 2).

4.15. Periciazine

Periciazine is a piperidine phenothiazine which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors, and α-adrenergic receptors, also acting as an inverse agonist of 5-HT₆ and 5-HT₇ receptors, and an antagonist of 5-HT_2A and 5-HT_2c receptors. This typical antipsychotic is a substrate of CYP2D6 and CYP3A4. Caution and personalized dose adjustment should be made in patients with the following genotypes: CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17, CYP2D6*1xN), and CYP3A4 (CYP3A4*3). ADRA1A, DRD1, DRD2, DRD3, HTR2A, HTR2C, HTR6, HTR7 variants may influence its pharmacokinetic and pharmacodynamic properties [25] (Table 2).

4.16. Perphenazine

Perphenazine is a piperazine phenothiazine which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors. This typical antipsychotic is a major substrate of CYP1A2, CYP2C8, CYP2C9, CYP2C18, CYP2C19, CYP2D6, and CYP3A4/5, and a weak inhibitor of CYP1A2 and CYP2D6. Caution and personalized dose adjustment should be made in patients with the following genotypes: ADRA1A (Arg347Cys), CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17), and DRD2 (−141C Ins/Del (rs1799732), TaqlA (rs1800497), TaqIB (rs1079597), rs1125394). ABCB1, CYP1A2, CYP2C9, CYP2C19, CYP3A4, DRD1, and RGS4 variants may affect its biopharmaceutical properties [25] (Table 2).

4.17. Pimozide

Pimozide is a diphenylbutylpiperidine with antagonistic activity on dopaminergic receptors and 5-HT_1A, 5-HT_2A and 5-HT₇ receptors. This typical antipsychotic is a major substrate of CYP3A4, a minor substrate of CYP1A2, a weak inhibitor of CYP2C19 and CYP2E1, a moderate inhibitor of CYP3A4, and a strong inhibitor of CYP2D6. Caution and personalized dose adjustment should be made in patients with the following genotypes: ADRA1A (Arg347Cys), CYP1A2 (C734A, G-2964A), CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17, CYP2D6*1xN), CYP3A4 (CYP3A4*3), KCNE2 (Gln9Glu, Met54Thr,Thr8Ala), KCNH2 (Arg784Trp), KCNQ1 (Arg583Cys), and SCN5A (Gly615Glu, Leu618Phe, Phe1250Leu, Leu1825Pro). Other genes potentially involved in its metabolism and pharmacological properties are ABCB1, CHRM2, CYP2C19, CYP2E1, DRD2, KCNE1, and KCNJ11 [25] (Table 2).

4.18. Pipotiazine

Pipotiazine is a piperidine phenothiazine which blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors. This typical antipsychotic is a substrate of CYP2D6 and CYP3A4. Different polymorphic variants in the CYP2D6, CYP3A4, and DRD genes may affect its metabolism and pharmacological properties [25] (Table 2).

4.19. Prochlorperazine

Prochlorperazine is a piperazine phenothiazine which strongly blocks postsynaptic mesolimbic dopaminergic D₁and D₂ receptors, α-adrenergic receptors and cholinergic receptors. The metabolism and pharmacological properties of this typical antipsychotic may be affected by polymorphic variants in the ABCB1, ADRA1A, CYPs, DRD1, and DRD2 genes, as well as other genes associated with histaminergic and cholinergic neurotransmission [25] (Table 2).

4.20. Quetiapine

Quetiapine is a dibenzothiazepine which acts as a serotonergic (5-HT_1A, 5-HT_2A_, 5-HT₂), dopaminergic (D₁ and D₂), histaminergic H₁, and adrenergic (α₁- and α₂-) receptor antagonist, and a full agonist of 5-HT_1A, 5-HT_1D, 5-HT_1F, and 5-HT_2Areceptors. This atypical antipsychotic is a minor substrate of CYP2D6 and a major substrate of CYP3A4/5. Caution and personalized dose adjustment should be made in patients with the following genotypes: ADRA1A (Arg347Cys), CYP3A4 (CYP3A4*3), HTR2A (His452Tyr, His368Tyr, Ile197Val, Ile113Val, Ala447Val, Ala363Val, Thr25Asn), KCNE2 (Gln9Glu, Met54Thr, Thr8Ala), KCNH2 (Arg784Trp), KCNQ1 (Arg583Cys), and SCN5A (Gly615Glu, Leu618Phe, Phe1250Leu, Leu1825Pro). These genotypes and other polymorphisms in the ABCB1, CYP2D6, DRD1, DRD2, DRD4, HRH1, HTR1A, HTR2B, KCNE1, and RGS4 genes are responsible for the metabolism and biopharmaceutical properties of quetiapine [25] (Table 2).

4.21. Risperidone

Risperidone is a benzisoxazole with serotonergic, dopaminergic, α₁-, α₂-adrenergic and histaminergic receptor antagonist activity, low-moderate affinity for 5-HT_1C, 5-HT_1D, and 5-HT_1A receptors, low affinity for D₁ receptors, and inverse agonist activity on 5-HT_2c, 5-HT₆, and 5-HT₇ receptors. This atypical antipsychotic is a major substrate of ABCB1 and CYP2D6, a minor substrate of CYP3A4/5, and weakly inhibits ABCB1, CYP2D6, and CYP3A4. Caution and personalized dose adjustment should be made in patients with the following genotypes: ABCB1 (C1236T, G2677T, C3435T), COMT (rs4633, rs4680, rs737865, rs6269, rs4818, rs165599), CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17), DRD2 (TaqIA (rs1800497), −141C Ins/Del (rs1799732), A-241G), DRD3 (Gly9Ser (rs6280), rs167771), GRM3 (rs724226), HTR2A (His452Tyr, His368Tyr, Ile197Val, Ala447Val, Ala363Val, Thr25Asn, 102-T/C (rs6313)), HTR3A (rs1176713), and HTR6 (T267C). These genotypes and other variants in the ADRA1A, ADRA1B, APOA5, CYP3A4/5, DRD1, DRD4, FOS, HTR2C, KCNH2, RGS4, and SLC6A4 genes are responsible for the metabolism, pharmacological effects, and adverse drug events associated with risperidone administration to psychotic patients [25] (Table 2).

4.22. Sulpiride

Sulpiride is a benzamide with postsynaptic D₂ antagonist activity. This atypical antipsychotic is a substrate of CYP2D6, and polymorphisms in the CYP2D6 and DRD2 genes influence its metabolism and pharmacological properties [25] (Table 2).

4.23. Thioridazine

Thioridazine is a phenothiazine which blocks postsynaptic mesolimbic dopaminergic receptors and α-adrenergic receptors, also acting as an inverse agonist of 5-HT₆ and 5-HT₇ receptors, and as an antagonist of 5-HT_2c receptors. This typical antipsychotic is a major substrate of CYP1A2, CYP2D6, CYP2J2, and CYP3A4, a minor substrate of CYP2C19, a weak inhibitor of CYP1A2, CYP2C9, CYP2E1, and DRD1, a moderate inhibitor of CYP2D6, and a strong blocker of ADRA1s, ADRA2s, and ADRBs. Caution and personalized dose adjustment should be made in patients with the following genotypes: ADRA1A (Arg347Cys), CYP2D6 (CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17), and KCNE2 (Gln9Glu, Met54Thr, Thr8Ala). Other genes that may be involved in thioridazine metabolism and pharmacological effects include ABCB1, CHRM2, CYP1A2, CYP2A6, CYP2C9, CYP2C19, CYP2E1, CYP2J2, CYP3A4, DRD2, FABP1, HRH1, KCNE1, KCNH2, KCNQ1, and KCNJ11 [25] (Table 2).

4.24. Thiothixene

Thiothixene is a thioxanthene which inhibits dopamine receptors, blocks α-adrenergic receptors, and is an antagonist of 5-HT_2a receptors. This typical antipsychotic is a major substrate of CYP1A2 and a weak inhibitor of CYP2D6. Caution and personalized dose adjustment should be made in patients with the following genotypes: ADRA1A (Arg347Cys), CYP1A2 (C734A, G-2964A), KCNE2 (Gln9Glu, Met54Thr, Thr8Ala), KCNQ1 (Arg583Cys), KCNH6 (Arg784Trp), and SCN5A (Gly615Glu, Leu618Phe, Phe1250Leu, Leu1825Pro). Other genes potentially involved in thiothixene metabolism and pharmacological effects are CYP2D6, DRD2, and KCNE1 [25] (Table 2).

4.25. Trifluoperazine

Trifluoperazine is a phenothiazine which blocks postsynaptic mesolimbic dopaminergic receptors and α-adrenergic receptors. This typical antipsychotic is a major substrate of CYP1A2 and UGT1A4. Caution and personalized dose adjustment should be made in patients with the following genotypes: ADRA1A (Arg347Cys), and CYP1A2 (C734A, G-2964A). Some other genes (ABCB1, DRD2, IL12B, UGT1A4) may affect trifluoperazine pharmacokinetics and pharmacodynamics [25] (Table 2).

4.26. Ziprasidone

Ziprasidone is a benzylisothiazolylpiperazine with high affinity for D₂, D₃, 5-HT_2A, 5-HT_1A, 5-HT_2C, 5-HT_1D and α₁-adrenergic receptors; moderate affinity for histamine H₁ receptors; antagonist of D₂, 5-HT_1A, 5-HT_2A, and 5-HT_1D receptors; full agonist of 5-HT_1B and 5-HT_1D receptors; partial agonist of 5-HT_1A receptors; and inverse agonist of 5-HT_2c and 5-HT₇ receptors. This atypical antipsychotic is a major substrate of CYP3A4, a minor substrate of CYP1A2, a substrate of AOXs and HTR1A, and an inhibitor of CYP2D6, CYP3A4, HTR2A, and DRD2. Caution and personalized dose adjustment should be made in in patients with the following genotypes: CYP3A4 (CYP3A4*1, CYP3A4*1B, CYP3A4*2, CYP3A4*3, CYP3A4*4, CYP3A4*5, CYP3A4*6, CYP3A4*8, CYP3A4*11, CYP3A4*12, CYP3A4*13, CYP3A4*15, CYP3A4*17, CYP3A4*18, CYP3A4*19), HTR2A (His452Tyr, His368Tyr, Ile197Val, Ile113Val, Ala447Val, Ala363Val, Thr25Asn), KCNH2 (Tyr652Ala, Phe656Ala), and RGS4 (rs951439, rs2661319, rs2842030). Other genes involved in ziprasidone pharmacokinetics and pharmacodynamics include AOX1, CYP1A2, CYP2D6, DRD2, DRD4, HTR1A, HTR2A, HRH1, and KCNH2 [25] (Table 2).

4.27. Zuclopenthixol

Zuclopenthixol is a thioxanthene which blocks postsynaptic mesolimbic dopaminergic receptors. This typical antipsychotic is a major substrate of CYP2D6; consequently, caution and personalized dose adjustment should be made in patients with the following CYP2D6 variants: CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*7, CYP2D6*8, CYP2D6*10, CYP2D6*17, CYP2D6*1xN. Other genes to take into account in the pharmacokinetics and pharmacodynamics of zuclopenthixol are ADRA1A, DRD1, DRD2, KCNE2, and SCN5A [25] (Table 2).

5. FUTURE DIRECTIONS

Historically, the vast majority of pharmacogenetic studies of CNS disorders have been addressed to evaluate the impact of cytochrome P450 enzymes on drug metabolism, and conventional targets for psychotropic drugs were dopamine, serotonin, noradrenaline, GABA, ion channels, acetylcholine and their respective biosynthetic and catalyzing enzymes, receptors and transporters; however, in the past few years many different genes have been associated with both pathogenesis and pharmacogenomics of neuropsychiatric disorders [1,2,5,6,17]. Some of these genes and their products constitute potential targets for future treatments. New developments in genomics, including whole genome genotyping approaches and comprehensive information on genomic variation across populations, coupled with large-scale clinical trials in which DNA collection is routine, now provide the impetus for a next generation of pharmacogenetic studies and identification of novel candidate drugs.

Priority areas for pharmacogenetic research are predicting serious adverse reactions (ADRs) and establishing variation in efficacy [348]. Both requirements are necessary in CNS disorders to cope with efficacy and safety issues associated with both current psychotropic drugs and new drugs. Since drug response is a complex trait, genome-wide approaches may provide new insights into drug metabolism and drug response. Of paramount importance is the identification of polymorphisms affecting gene regulation and mRNA processing in genes encoding cytochrome P450s and other drug-metabolizing enzymes, drug transporters, and drug targets and receptors, with broad implication in pharmacogenetics since functional polymorphisms which alter gene expression and mRNA processing appear to play a critical role in shaping human phenotypic variability [349]. It is also most relevant, from a practical point of view, to understand the pharmacogenomics of drug transporters, especially ABCB1 (P-glycoprotein/MDR1) variants, due to the pleiotropic activity of this gene on a large number of drugs [350]. It is necessary to have a better documentation related to the pharmacogenetic roles of the enormous number (>170) of human solute carrier transporters which transport a variety of substrates, including amino acids, lipids, inorganic ions, peptides, saccharides, metals, drugs, toxic xenobiotics, chemical compounds, and proteins [351]. RNAi pharmacogenomics will also bring new insights into the nature and therapeutic value of gene silencing in CNS disorders [352-356].

The optimization of CNS therapeutics, in general, and the pharmacological treatment of SCZ and psychotic disorders, in particular, requires the establishment of new postulates regarding 1) the costs of medicines, 2) the assessment of protocols for multifactorial treatment in chronic disorders, 3) the implementation of novel therapeutics addressing causative factors, and 4) the setting-up of pharmacogenomic strategies for drug development and drugs on the market [2,6,14].

By knowing the pharmacogenomic profiles of patients who require treatments with psychotropic drugs of current use, it might be possible to obtain some of the following benefits: 1) to identify candidate patients with the ideal genomic profile to receive a particular drug; 2) to adapt the dose in over 60% - 90% of the cases according to the condition of EM, IM, PM or UM (diminishing the occurrence of direct side-effects in 30% - 50% of the cases); 3) to reduce drug interactions by 30% - 50% (avoiding the administration of inhibitors or inducers able to modify the normal enzymatic activity on a particular substrate); 4) to enhance efficacy and pharmacodynamic specificity; and 5) to eliminate unnecessary costs (>30% of pharmaceutical costs) derived from the consequences of an inappropriate drug selection and the overmedication administered to mitigate ADRs.

6. ACKNOWLEDGEMENTS

We thank Carmen Fraile and Adam McKay for technical support.

Most studies on pharmacogenomics of CNS disorders in our institution are funded by the International Agency for Brain Research and Aging (IABRA).

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