CNTNAP2 gene dosage variation is associated with schizophrenia and epilepsy

Persistence criteria for susceptibility genes for schizophrenia: a discussion from an evolutionary viewpoint

BACKGROUND

The central paradox of schizophrenia genetics is that susceptibility genes are preserved in the human gene-pool against a strong negative selection pressure. Substantial evidence of epidemiology suggests that nuclear susceptibility genes, if present, should be sustained by mutation-selection balance without heterozygote advantage. Therefore, putative nuclear susceptibility genes for schizophrenia should meet special conditions for the persistence of the disease as well as the condition of bearing a positive association with the disease.

METHODOLOGY/PRINCIPAL FINDINGS

We deduced two criteria that every nuclear susceptibility gene for schizophrenia should fulfill for the persistence of the disease under general assumptions of the multifactorial threshold model. The first criterion demands an upper limit of the case-control difference of the allele frequencies, which is determined by the mutation rate at the locus, and the prevalence and the selection coefficient of the disease. The second criterion demands an upper limit of odds ratio for a given allele frequency in the unaffected population. When we examined the top 30 genes at SZGene and the recently reported common variants on chromosome 6p with the criteria using the epidemiological data in a large-sampled Finnish cohort study, it was suggested that most of these are unlikely to confer susceptibility to schizophrenia. The criteria predict that the common disease/common variant hypothesis is unlikely to fit schizophrenia and that nuclear susceptibility genes of moderate effects for schizophrenia, if present, are limited to 'rare variants', 'very common variants', or variants with exceptionally high mutation rates.

CONCLUSIONS/SIGNIFICANCE

If we assume the nuclear DNA model for schizophrenia, it should have many susceptibility genes of exceptionally high mutation rates; alternatively, it should have many disease-associated resistance genes of standard mutation rates on different chromosomes. On the other hand, the epidemiological data show that pathogenic genes, if located in the mitochondrial DNA, could persist through sex-related mechanisms.

Microduplications of 16p11.2 are associated with schizophrenia

Recurrent microdeletions and microduplications of a 600-kb genomic region of chromosome 16p11.2 have been implicated in childhood-onset developmental disorders. We report the association of 16p11.2 microduplications with schizophrenia in two large cohorts. The microduplication was detected in 12/1,906 (0.63%) cases and 1/3,971 (0.03%) controls (P = 1.2 x 10(-5), OR = 25.8) from the initial cohort, and in 9/2,645 (0.34%) cases and 1/2,420 (0.04%) controls (P = 0.022, OR = 8.3) of the replication cohort. The 16p11.2 microduplication was associated with a 14.5-fold increased risk of schizophrenia (95% CI (3.3, 62)) in the combined sample. A meta-analysis of datasets for multiple psychiatric disorders showed a significant association of the microduplication with schizophrenia (P = 4.8 x 10(-7)), bipolar disorder (P = 0.017) and autism (P = 1.9 x 10(-7)). In contrast, the reciprocal microdeletion was associated only with autism and developmental disorders (P = 2.3 x 10(-13)). Head circumference was larger in patients with the microdeletion than in patients with the microduplication (P = 0.0007).

CNTNAP2 and NRXN1 are mutated in autosomal-recessive Pitt-Hopkins-like mental retardation and determine the level of a common synaptic protein in Drosophila

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 schizophrenia. We now identified homozygous and compound-heterozygous deletions and mutations via molecular karyotyping and mutational screening in CNTNAP2 and NRXN1 in four patients with severe mental retardation (MR) and variable features, such as autistic behavior, epilepsy, and breathing anomalies, phenotypically overlapping with Pitt-Hopkins syndrome. With a frequency of at least 1% in our cohort of 179 patients, recessive defects in CNTNAP2 appear to significantly contribute to severe MR. Whereas the established synaptic role of NRXN1 suggests that synaptic defects contribute to the associated neuropsychiatric disorders and to severe MR as reported here, evidence for a synaptic role of the CNTNAP2-encoded protein CASPR2 has so far been lacking. Using Drosophila as a model, we now show that, as known for fly Nrx-I, 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. Moreover, both Nrx-I and Nrx-IV determine the level of the presynaptic active-zone protein bruchpilot, indicating a possible common molecular mechanism in Nrx-I and Nrx-IV mutant conditions. We therefore propose that an analogous shared synaptic mechanism contributes to the similar clinical phenotypes resulting from defects in human NRXN1 and CNTNAP2.

Genetic overlap between autism, schizophrenia and bipolar disorder

There is strong evidence that genetic factors make substantial contributions to the etiology of autism, schizophrenia and bipolar disorders, with heritability estimates being at least 80% for each. These illnesses have complex inheritance, with multiple genetic and environmental factors influencing disease risk; however, in psychiatry, complex genetics is further compounded by phenotypic complexity. Autism, schizophrenia and bipolar disorder are effectively syndromic constellations of symptoms that define groups of patients with broadly similar outcomes and responses to treatment. As such the diagnostic categories are likely to be heterogeneous and the boundaries between them somewhat arbitrary. Recent applications of whole-genome technologies have discovered rare copy number variants and common single-nucleotide polymorphisms that are associated with risk of developing these disorders. Furthermore, these studies have shown an overlap between the genetic loci and even alleles that predispose to the different phenotypes. The findings have several implications. First, they show that copy number variations are likely to be important risk factors for autism and schizophrenia, whereas common single-nucleotide polymorphism alleles have a role in all disorders. Second, they imply that there are specific genetic loci and alleles that increase an individual's risk of developing any of these disorders. Finally, the findings suggest that some of the specific genetic loci implicated so far encode proteins, such as neurexins and neuroligins, that function in synaptic development and plasticity, and therefore may represent a common biological pathway for these disorders.

Genetics, medicine, and the Plain people

The Old Order Amish and Old Order Mennonite populations of Pennsylvania are descended from Swiss Anabaptist immigrants who came to the New World in the early eighteenth century. Today they live in many small endogamous demes across North America. Genetically, these demes have dissimilar allele frequencies and disease spectra owing to unique founders. Biological and social aspects of Old Order communities make them ideal for studies in population genetics and genomic medicine, and over the last 40 years, advances in genomic science coincided with investigational studies in Plain populations. Newer molecular genetic technologies are sufficiently informative, rapid, and flexible to use in a clinical setting, and we have successfully integrated these tools into a rural pediatric practice. Our studies with the Pennsylvania Plain communities show that population-specific genetic knowledge provides a powerful framework in which to prevent disease, reduce medical costs, and create new insights into human biology.

Recurrent rearrangements in synaptic and neurodevelopmental genes and shared biologic pathways in schizophrenia, autism, and mental retardation

CONTEXT

Results of comparative genomic hybridization studies have suggested that rare copy number variations (CNVs) at numerous loci are involved in the cause of mental retardation, autism spectrum disorders, and schizophrenia.

OBJECTIVES

To provide an estimate of the collective frequency of a set of recurrent or overlapping CNVs in 3 different groups of cases compared with healthy control subjects and to assess whether each CNV is present in more than 1 clinical category.

DESIGN

Case-control study.

SETTING

Academic research.

PARTICIPANTS

We investigated 28 candidate loci previously identified by comparative genomic hybridization studies for gene dosage alteration in 247 cases with mental retardation, in 260 cases with autism spectrum disorders, in 236 cases with schizophrenia or schizoaffective disorder, and in 236 controls.

MAIN OUTCOME MEASURES

Collective and individual frequencies of the analyzed CNVs in cases compared with controls.

RESULTS

Recurrent or overlapping CNVs were found in cases at 39.3% of the selected loci. The collective frequency of CNVs at these loci is significantly increased in cases with autism, in cases with schizophrenia, and in cases with mental retardation compared with controls (P < .001, P = .01, and P = .001, respectively, Fisher exact test). Individual significance (P = .02 without correction for multiple testing) was reached for the association between autism and a 350-kilobase deletion located at 22q11 and spanning the PRODH and DGCR6 genes.

CONCLUSIONS

Weakly to moderately recurrent CNVs (transmitted or occurring de novo) seem to be causative or contributory factors for these diseases. Most of these CNVs (which contain genes involved in neurotransmission or in synapse formation and maintenance) are present in the 3 pathologic conditions (schizophrenia, autism, and mental retardation), supporting the existence of shared biologic pathways in these neurodevelopmental disorders.

A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB

Psychiatric disorders such as schizophrenia are commonly accompanied by cognitive impairments that are treatment resistant and crucial to functional outcome. There has been great interest in studying cognitive measures as endophenotypes for psychiatric disorders, with the hope that their genetic basis will be clearer. To investigate this, we performed a genome-wide association study involving 11 cognitive phenotypes from the Cambridge Neuropsychological Test Automated Battery. We showed these measures to be heritable by comparing the correlation in 100 monozygotic and 100 dizygotic twin pairs. The full battery was tested in approximately 750 subjects, and for spatial and verbal recognition memory, we investigated a further 500 individuals to search for smaller genetic effects. We were unable to find any genome-wide significant associations with either SNPs or common copy number variants. Nor could we formally replicate any polymorphism that has been previously associated with cognition, although we found a weak signal of lower than expected P-values for variants in a set of 10 candidate genes. We additionally investigated SNPs in genomic loci that have been shown to harbor rare variants that associate with neuropsychiatric disorders, to see if they showed any suggestion of association when considered as a separate set. Only NRXN1 showed evidence of significant association with cognition. These results suggest that common genetic variation does not strongly influence cognition in healthy subjects and that cognitive measures do not represent a more tractable genetic trait than clinical endpoints such as schizophrenia. We discuss a possible role for rare variation in cognitive genomics.

Aneuploidy: from a physiological mechanism of variance to Down syndrome

Quantitative differences in gene expression emerge as a significant source of variation in natural populations, representing an important substrate for evolution and accounting for a considerable fraction of phenotypic diversity. However, perturbation of gene expression is also the main factor in determining the molecular pathogenesis of numerous aneuploid disorders. In this review, we focus on Down syndrome (DS) as the prototype of "genomic disorder" induced by copy number change. The understanding of the pathogenicity of the extra genomic material in trisomy 21 has accelerated in the last years due to the recent advances in genome sequencing, comparative genome analysis, functional genome exploration, and the use of model organisms. We present recent data on the role of genome-altering processes in the generation of diversity in DS neural phenotypes focusing on the impact of trisomy on brain structure and mental retardation and on biological pathways and cell types in target brain regions (including prefrontal cortex, hippocampus, cerebellum, and basal ganglia). We also review the potential that genetically engineered mouse models of DS bring into the understanding of the molecular biology of human learning disorders.

The emerging role of synaptic cell-adhesion pathways in the pathogenesis of autism spectrum disorders

Recent advances in genetics and genomics have unveiled numerous cases of autism spectrum disorders (ASDs) associated with rare, causal genetic variations. These findings support a novel view of ASDs in which many independent, individually rare genetic variants, each associated with a very high relative risk, together explain a large proportion of ASDs. Although these rare variants impact diverse pathways, there is accumulating evidence that synaptic pathways, including those involving synaptic cell adhesion, are disrupted in some subjects with ASD. These findings provide insights into the pathogenesis of ASDs and enable the development of model systems with construct validity for specific causes of ASDs. In several neurodevelopmental disorders frequently associated with ASD, including fragile X syndrome, Rett syndrome and tuberous sclerosis, animal models have led to the development of new therapeutic approaches, giving rise to optimism with other causes of ASDs.

Genetics of Schizophrenia Spectrum Disorders: Looking Back and Peering Ahead

The genetics of schizophrenia spectrum disorders have come a long way since the early demonstration of a substantial genetic component by family, twin and adoption studies. After over a decade of intensive molecular genetic studies, initially by linkage scans and candidate gene association studies, and more recently genome-wide association studies, a picture is now emerging that susceptibility to schizophrenia spectrum disorders is determined by many genetic variants of different types, ranging from single nucleotide polymorphisms to copy number variants, including rare and de novo variants, of pleiotropic effects on multiple diagnoses and traits. Further large-scale genome-wide association studies, and the forthcoming availability of affordable whole-genome sequencing technology, will further characterise the genetic variants involved, which in turn will be translated to improved clinical practice. Key words: Copy number variation, Genome-wide association, Linkage

Singleton deletions throughout the genome increase risk of bipolar disorder

An overall burden of rare structural genomic variants has not been reported in bipolar disorder (BD), although there have been reports of cases with microduplication and microdeletion. Here, we present a genome-wide copy number variant (CNV) survey of 1001 cases and 1034 controls using the Affymetrix single nucleotide polymorphism (SNP) 6.0 SNP and CNV platform. Singleton deletions (deletions that appear only once in the dataset) more than 100 kb in length are present in 16.2% of BD cases in contrast to 12.3% of controls (permutation P=0.007). This effect was more pronounced for age at onset of mania <or=18 years old. Our results strongly suggest that BD can result from the effects of multiple rare structural variants.

Copy variations in schizophrenia and bipolar disorder

The analysis of copy number variations (CNVs) is an emerging tool for identifying genetic factors underlying complex traits. In this chapter I will review studies that have been carried out showing that CNVs play a role in the development of two such complex traits; schizophrenia (SZ) and bipolar disorder (BD). There are two aspects to consider regarding the role of copy variations in these conditions. One is gene discovery in which DNA from patients is analyzed for the purpose of identifying rare, patient-specific CNVs that may be informative to a larger population of affected individuals. The model for this concept is based on the emergence of DISC1 as a SZ candidate gene, which was discovered in a single informative family with a rare chromosomal translocation. Another aspect revolves around the idea that polymorphic CNVs found in the general population, many of which appear to disrupt previously identified SZ and BD candidate genes, contribute to disease pathogenesis. Here, gene-disrupting CNVs are viewed in the same manner as functional SNPs and analyzed for involvement in disease susceptibility using genetic association. Although the analysis of CNVs in patients with psychiatric disorders is in its infancy, informative new findings have already been made, suggesting that this is a very promising line of research.

Genes, cognition, and communication: insights from neurodevelopmental disorders

Twin and family studies have demonstrated that most cognitive traits are moderately to highly heritable. Neurodevelopmental disorders such as dyslexia, autism, and specific language impairment (SLI) also show strong genetic influence. Nevertheless, it has proved difficult for researchers to identify genes that would explain substantial amounts of variance in cognitive traits or disorders. Although this observation may seem paradoxical, it fits with a multifactorial model of how complex human traits are influenced by numerous genes that interact with one another, and with the environment, to produce a specific phenotype. Such a model can also explain why genetic influences on cognition have not vanished in the course of human evolution. Recent linkage and association studies of SLI and dyslexia are reviewed to illustrate these points. The role of nonheritable genetic mutations (sporadic copy number variants) in causing autism is also discussed. Finally, research on phenotypic correlates of allelic variation in the genes ASPM and microcephalin is considered; initial interest in these as genes for brain size or intelligence has been dampened by a failure to find phenotypic differences in people with different versions of these genes. There is a current vogue for investigators to include measures of allelic variants in studies of cognition and cognitive disorders. It is important to be aware that the effect sizes associated with these variants are typically small and hard to detect without extremely large sample sizes.

New applications and developments in the use of multiplex ligation-dependent probe amplification

Multiplex ligation-dependent probe amplification (MLPA) is a commonly used technique for determining relative DNA sequence dosage (or copy number) in a complex DNA sample. Originally MLPA was designed as a copy number analysis tool for detecting disease-causing genomic mutations and has been successfully applied in the testing and identification of hundreds of genomic mutations in numerous genes including DMD, BRCA1, NF1, and TSC2. More recently, several modifications of the original technique have been implemented. Arguably the most important enhancement of MLPA has been probe generation by chemical synthesis, enabling the facile creation of novel probe sets for any desired application. Other newer applications of MLPA include methylation status determination, copy number analysis in segmentally duplicated regions, expression profiling, and transgene genotyping. MLPA has a potential major role in the analysis of common copy number variation in genome-wide association analyses, which may be enhanced by future improvements to increase throughput and lower costs, such as array-MLPA.

Nuclear and mitochondrial genome defects in autisms

In this review we will evaluate evidence that altered gene dosage and structure impacts neurodevelopment and neural connectivity through deleterious effects on synaptic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrix SNP 6.0 microarray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Collectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chromosome. Precise analyses of Y located genes are often difficult because of the high degree of homology of X- and Y-related genes. However, continued efforts to analyze the latter are important, given the consistent evidence for a 4:1 ratio of males to females affected by autism. It is also important to consider whether environmental factors play a role in generating the nuclear and mitochondrial genomic instability we have observed. The study of autism will benefit from a move to analysis of pathways and multigene clusters for identification of subtypes that share a specific genetic etiology.

Jean PL, Giegling I, Hartmann AM, Möller HJ, Ruppert A, Fraser G, Crombie C, Middleton LT, St. Clair D, Roses AD, Muglia P, Francks C, Rujescu D, Meltzer HY, Goldstein DB. A genome-wide investigation of SNPs and CNVs in schizophrenia

We report a genome-wide assessment of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) in schizophrenia. We investigated SNPs using 871 patients and 863 controls, following up the top hits in four independent cohorts comprising 1,460 patients and 12,995 controls, all of European origin. We found no genome-wide significant associations, nor could we provide support for any previously reported candidate gene or genome-wide associations. We went on to examine CNVs using a subset of 1,013 cases and 1,084 controls of European ancestry, and a further set of 60 cases and 64 controls of African ancestry. We found that eight cases and zero controls carried deletions greater than 2 Mb, of which two, at 8p22 and 16p13.11-p12.4, are newly reported here. A further evaluation of 1,378 controls identified no deletions greater than 2 Mb, suggesting a high prior probability of disease involvement when such deletions are observed in cases. We also provide further evidence for some smaller, previously reported, schizophrenia-associated CNVs, such as those in NRXN1 and APBA2. We could not provide strong support for the hypothesis that schizophrenia patients have a significantly greater "load" of large (>100 kb), rare CNVs, nor could we find common CNVs that associate with schizophrenia. Finally, we did not provide support for the suggestion that schizophrenia-associated CNVs may preferentially disrupt genes in neurodevelopmental pathways. Collectively, these analyses provide the first integrated study of SNPs and CNVs in schizophrenia and support the emerging view that rare deleterious variants may be more important in schizophrenia predisposition than common polymorphisms. While our analyses do not suggest that implicated CNVs impinge on particular key pathways, we do support the contribution of specific genomic regions in schizophrenia, presumably due to recurrent mutation. On balance, these data suggest that very few schizophrenia patients share identical genomic causation, potentially complicating efforts to personalize treatment regimens.

Contact in the genetics of autism and schizophrenia

Although autism and schizophrenia are considered to be distinct neuropsychiatric developmental disorders, recent studies indicate that they share genetic factors. The same chromosomal rearrangements and several single genes have emerged as genetic risks in both disorders. One such gene is contactin-associated protein-2 (CNTNAP2). These findings raise the possibility that these neuropsychiatric disorders share pathogenic mechanisms and that similar defects in biological pathways of brain development might underlie the phenotypic spectrum of these disorders.

Contactins: emerging key roles in the development and function of the nervous system

Contactins are a subgroup of molecules belonging to the immunoglobulin superfamily that are expressed exclusively in the nervous system. The subgroup consists of six members: contactin, TAG-1, BIG-1, BIG-2, NB-2 and NB-3. Since their identification in the late 1980s, contactin and TAG-1 have been studied extensively. Axonal expression and the neurite extension activity of contactin and TAG-1 attracted researchers to study the function of these molecules in axon guidance during development. After the exciting discovery of the molecular function of contactin and TAG-1 in myelination earlier this decade, these two molecules have come to be known as the principal molecules in the function and maintenance of myelinated neurons. In contrast, the function of the other four members of this subgroup remained unknown until recently. Here, we will give an overview of contactin function, including recent progress on BIG-2, NB-2 and NB-3.

Autism spectrum disorders and childhood-onset schizophrenia: clinical and biological contributions to a relation revisited

OBJECTIVE

To highlight emerging evidence for clinical and biological links between autism/pervasive developmental disorder (PDD) and schizophrenia, with particular attention to childhood-onset schizophrenia (COS).

METHOD

Clinical, demographic, and brain developmental data from the National Institute of Mental Health (and other) COS studies and selected family, imaging, and genetic data from studies of autism, PDD, and schizophrenia were reviewed.

RESULTS

In the two large studies that have examined this systematically, COS is preceded by and comorbid with PDD in 30% to 50% of cases. Epidemiological and family studies find association between the disorders. Both disorders have evidence of accelerated trajectories of anatomic brain development at ages near disorder onset. A growing number of risk genes and/or rare small chromosomal variants (microdeletions or duplications) are shared by schizophrenia and autism.

CONCLUSIONS

Biological risk does not closely follow DSM phenotypes, and core neurobiological processes are likely common for subsets of these two heterogeneous clinical groups. Long-term prospective follow-up of autistic populations and greater diagnostic distinction between schizophrenia spectrum and autism spectrum disorders in adult relatives are needed.

Recurrent CNVs disrupt three candidate genes in schizophrenia patients

Schizophrenia is a severe psychiatric disease with complex etiology, affecting approximately 1% of the general population. Most genetics studies so far have focused on disease association with common genetic variation, such as single-nucleotide polymorphisms (SNPs), but it has recently become apparent that large-scale genomic copy-number variants (CNVs) are involved in disease development as well. To assess the role of rare CNVs in schizophrenia, we screened 54 patients with deficit schizophrenia using Affymetrix's GeneChip 250K SNP arrays. We identified 90 CNVs in total, 77 of which have been reported previously in unaffected control cohorts. Among the genes disrupted by the remaining rare CNVs are MYT1L, CTNND2, NRXN1, and ASTN2, genes that play an important role in neuronal functioning but--except for NRXN1--have not been associated with schizophrenia before. We studied the occurrence of CNVs at these four loci in an additional cohort of 752 patients and 706 normal controls from The Netherlands. We identified eight additional CNVs, of which the four that affect coding sequences were found only in the patient cohort. Our study supports a role for rare CNVs in schizophrenia susceptibility and identifies at least three candidate genes for this complex disorder.

Genomic imprinting in the development and evolution of psychotic spectrum conditions

I review and evaluate genetic and genomic evidence salient to the hypothesis that the development and evolution of psychotic spectrum conditions have been mediated in part by alterations of imprinted genes expressed in the brain. Evidence from the genetics and genomics of schizophrenia, bipolar disorder, major depression, Prader-Willi syndrome, Klinefelter syndrome, and other neurogenetic conditions support the hypothesis that the etiologies of psychotic spectrum conditions commonly involve genetic and epigenetic imbalances in the effects of imprinted genes, with a bias towards increased relative effects from imprinted genes with maternal expression or other genes favouring maternal interests. By contrast, autistic spectrum conditions, including Kanner autism, Asperger syndrome, Rett syndrome, Turner syndrome, Angelman syndrome, and Beckwith-Wiedemann syndrome, commonly engender increased relative effects from paternally expressed imprinted genes, or reduced effects from genes favouring maternal interests. Imprinted-gene effects on the etiologies of autistic and psychotic spectrum conditions parallel the diametric effects of imprinted genes in placental and foetal development, in that psychotic spectrum conditions tend to be associated with undergrowth and relatively-slow brain development, whereas some autistic spectrum conditions involve brain and body overgrowth, especially in foetal development and early childhood. An important role for imprinted genes in the etiologies of psychotic and autistic spectrum conditions is consistent with neurodevelopmental models of these disorders, and with predictions from the conflict theory of genomic imprinting.

Rare chromosomal deletions and duplications increase risk of schizophrenia

Schizophrenia is a severe mental disorder marked by hallucinations, delusions, cognitive deficits and apathy, with a heritability estimated at 73-90% (ref. 1). Inheritance patterns are complex, and the number and type of genetic variants involved are not understood. Copy number variants (CNVs) have been identified in individual patients with schizophrenia and also in neurodevelopmental disorders, but large-scale genome-wide surveys have not been performed. Here we report a genome-wide survey of rare CNVs in 3,391 patients with schizophrenia and 3,181 ancestrally matched controls, using high-density microarrays. For CNVs that were observed in less than 1% of the sample and were more than 100 kilobases in length, the total burden is increased 1.15-fold in patients with schizophrenia in comparison with controls. This effect was more pronounced for rarer, single-occurrence CNVs and for those that involved genes as opposed to those that did not. As expected, deletions were found within the region critical for velo-cardio-facial syndrome, which includes psychotic symptoms in 30% of patients. Associations with schizophrenia were also found for large deletions on chromosome 15q13.3 and 1q21.1. These associations have not previously been reported, and they remained significant after genome-wide correction. Our results provide strong support for a model of schizophrenia pathogenesis that includes the effects of multiple rare structural variants, both genome-wide and at specific loci.

The evolutionary social brain: From genes to psychiatric conditions

The commentaries on our target article, “Psychosis and Autism as Diametrical Disorders of the Social Brain,” reflect the multidisciplinary yet highly fragmented state of current studies of human social cognition. Progress in our understanding of the human social brain must come from studies that integrate across diverse analytic levels, using conceptual frameworks grounded in evolutionary biology.

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia

Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications >100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia.