James Tynan Rhys Walters

Analysis of copy number variations at 15 schizophrenia-associated loci

Background A number of copy number variants (CNVs) have been suggested as susceptibility factors for schizophrenia. For some of these the data remain equivocal, and the frequency in individuals with schizophrenia is uncertain. Aims To determine the contribution of CNVs at 15 schizophrenia-associated loci (a) using a large new data-set of patients with schizophrenia (n = 6882) and controls (n = 6316), and (b) combining our results with those from previous studies. Method We used Illumina microarrays to analyse our data. Analyses were restricted to 520 766 probes common to all arrays used in the different data-sets. Results We found higher rates in participants with schizophrenia than in controls for 13 of the 15 previously implicated CNVs. Six were nominally significantly associated (P<0.05) in this new data-set: deletions at 1q21.1, NRXN1, 15q11.2 and 22q11.2 and duplications at 16p11.2 and the Angelman/Prader-Willi Syndrome (AS/PWS) region. All eight AS/PWS duplications in patients were of maternal origin. When combined with published data, 11 of the 15 loci showed highly significant evidence for association with schizophrenia (P<4.1×10–4). Conclusions We strengthen the support for the majority of the previously implicated CNVs in schizophrenia. About 2.5% of patients with schizophrenia and 0.9% of controls carry a large, detectable CNV at one of these loci. Routine CNV screening may be clinically appropriate given the high rate of known deleterious mutations in the disorder and the comorbidity associated with these heritable mutations.

Genome wide significant associations in schizophrenia to ITIH3/4, CACNA1C and SDCCAG8, and extensive replication of associations reported by the Schizophrenia PGC

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. We tested 78 of the 81 SNPs in 2640 individuals with a clinical diagnosis of schizophrenia attending a clozapine clinic (CLOZUK), 2504 cases with a research diagnosis of bipolar disorder, and 2878 controls. In CLOZUK, we obtained significant replication to the PGC-associated allele for no fewer than 37 (47%) of the SNPs, including many prior GWS major histocompatibility complex (MHC) SNPs as well as 3/6 non-MHC SNPs for which we had data that were reported as GWS by the PGC. After combining the new schizophrenia data with those of the PGC, variants at three loci (ITIH3/4, CACNA1C and SDCCAG8) that had not previously been GWS in schizophrenia attained that level of support. In bipolar disorder, we also obtained significant evidence for association for 21% of the alleles that had been associated with schizophrenia in the PGC. Our study independently confirms association to three loci previously reported to be GWS in schizophrenia, and identifies the first GWS evidence in schizophrenia for a further three loci. Given the number of independent replications and the power of our sample, we estimate 98% (confidence interval (CI) 78–100%) of the original set of 78 SNPs represent true associations. We also provide strong evidence for overlap in genetic risk between schizophrenia and bipolar disorder.

Endophenotypes in psychiatric genetics

There has been a recent surge in interest in the use of endophenotypes in psychiatric research, although the concept was introduced to psychiatry by Gottesman and Shields as long as 35 years ago. This has been driven by concerns about the limited success and poor reproducibility of existing approaches as well as the fact that current diagnostic systems in psychiatry by and large lack aetiological justification. In addition, the identification of disease endophenotypes offers the prospect of creating animal models relevant to human psychopathology, which will be suitable for experimental approaches and greatly facilitate the development and screening of novel therapeutics. Gottesman and Shields, who adapted the term from insect biology, described endophenotypes as internal phenotypes that lie on the pathway between genes and disease. Fundamental to the concept is the assumption that variation in an endophenotype will depend upon variation in fewer genes than the more complex disease phenotype and therefore be more tractable to genetic analysis. There has been a number of attempts to devise criteria to define the optimal characteristics of an endophenotype. There is a general agreement that an endophenotype should occur at a higher frequency in individuals with the disease than the general population; moreover, this association should derive from shared genes. It therefore follows that an endophenotype should be heritable, tend to co-segregate with the illness in multiply affected families, be found in unaffected relatives of cases at a higher rate than in the general population and ideally show evidence for common genetic risk factors from twin studies. In addition, if an endophenotype truly lies on the causal pathway between genes and disease, it should be stateindependent, in that it manifests in an individual whether or not illness is active (although it may require challenge or provocation) and to an extent that is not critically dependent upon the degree of activity of the illness. However, it is important to note that even if a putative endophenotype satisfies all these criteria, this does not exclude the possibility that it is epiphenomenal with respect to the disease. In other words, it might occur as a pleiotropic consequence of the risk gene or genes and not lie on the disease pathway (see Figure 1 and Table 1). A further widely supported criterion is that an endophenotype should have good psychometric properties, especially reliability and validity, and be sufficiently sensitive to detect individual differences. Whilst there is widespread acceptance of the importance of these criteria, it is disconcerting how few endophenotypes used in psychiatric research actually fulfil them. For example, there is limited evidence for co-segregation with illness, let alone heritability for many neurophysiological and neurocognitive measures that have been suggested as schizophrenia endophenotypes. The extent to which this matters depends upon the use to which an endophenotype is being put and it is helpful to consider the possibilities in some detail. Broadly speaking, endophenotypes are used under two circumstances. First, as originally proposed, they are used to aid in the discovery of novel genes. The critical assumption here as we have seen is that the genetic architecture of the endophenotype is simpler than that of the disease phenotype and this, together with the opportunity to study clinically unaffected relatives, who display the endophenotype by virtue of their increased risk of disorder, should increase power. However there are a number of concerns that need to be addressed before the wholesale adoption of endophenotype approaches in genefinding studies. First, it is often not clear how stateindependent many of the measures proposed really are, with the potential for contamination not just by fluctuations in course of illness and drug treatment, but also by factors such as smoking and menstrual cycle phase. Second, there are uncertainties about reliability and particularly inter-laboratory variation for many of the methods espoused. For example, there are no generally agreed protocols for reliably eliciting electrophysiological deficits in pre-pulse inhibition (PPI) and P50 sensory gating, which have been proposed as endophenotypes in schizophrenia, as well as concerns regarding test–retest reliability. The neuroimaging community is still struggling with issues of reliability as well as in developing methods to allow data obtained from different scanners to be meaningfully combined. The neurocognition literature continues to be overwhelmed by the use of multiple variations of tests for the same cognitive domains and poor examination of reliability issues, although consensus approaches and computer-delivered batteries should help. Fortunately, many of these issues are being addressed by the development of multisite initiatives such as the Consortium on the Genetics of Endophenotypes in Schizophrenia. Such projects represent an advance in this field in aiming to address reliability concerns by standardizing methodologies for electrophysiological and neurocognitive measures with regular monitoring of procedures, training and reliability. Molecular Psychiatry (2007) 12, 886–890 & 2007 Nature Publishing Group All rights reserved 1359-4184/07

The penetrance of copy number variations for schizophrenia and developmental delay.

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Copy number variation in schizophrenia in Sweden

BACKGROUND Several recurrent copy number variants (CNVs) have been shown to increase the risk of developing schizophrenia (SCZ), developmental delay (DD), autism spectrum disorders (ASD), and various congenital malformations (CM). Their penetrance for SCZ has been estimated to be modest. However, comparisons between their penetrance for SCZ or DD/ASD/CM, or estimates of the total penetrance for any of these disorders have not yet been made. METHODS We use data from the largest available studies on SCZ and DD/ASD/CM, including a new sample of 6882 cases and 6316 controls, to estimate the frequencies of 70 implicated CNVs in carriers with these disorders, healthy control subjects, and the general population. On the basis of these frequencies, we estimate their penetrance. We also estimate the strength of the selection pressure against CNVs and correlate this against their overall penetrance. RESULTS The rates of nearly all CNVs are higher in DD/ASD/CM compared with SCZ. The penetrance of CNVs is at least several times higher for the development of a disorder from the group of DD/ASD/CM. The overall penetrance of SCZ-associated CNVs for developing any disorder is high, ranging between 10.6% and 100%. CONCLUSIONS CNVs associated with SCZ have high pathogenicity. The majority of the increased risk conferred by CNVs is toward the development of an earlier-onset disorder, such as DD/ASD/CM, rather than SCZ. The penetrance of CNVs correlates strongly with their selection coefficients. The improved estimates of penetrance will provide crucial information for genetic counselling.

Psychosis susceptibility gene ZNF804A and cognitive performance in schizophrenia.

Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500 kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ genome-wide association studies and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry—genome-wide screens for CNVs, common variation and exonic variation—are converging on similar sets of pathways and/or genes.

Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders

CONTEXT The Zinc Finger Protein 804A gene (ZNF804A) has been implicated in schizophrenia susceptibility by several genome-wide association studies. ZNF804A is brain expressed but of unknown function. OBJECTIVE To investigate whether the identified risk allele at the disease-associated single nucleotide polymorphism rs1344706 is associated with variation in neuropsychological performance in patients and controls. DESIGN Comparison of cases and controls grouped according to ZNF804A genotype (AA vs AC vs CC) on selected measures of cognition in 2 independent samples. SETTING Unrelated patients from general adult psychiatric inpatient and outpatient services and unrelated healthy participants from the general population were ascertained. PARTICIPANTS Patients with DSM-IV-diagnosed schizophrenia and healthy participants from independent samples of Irish (297 cases and 165 controls) and German (251 cases and 1472 controls) nationality. MAIN OUTCOME MEASURES In this 2-stage study, we tested for an association between ZNF804A rs1344706 and cognitive functions known to be impaired in schizophrenia (IQ, episodic memory, working memory, and attention) in an Irish discovery sample. We then tested significant results in a German replication sample. RESULTS In the Irish samples, the ZNF804A genotype was associated with differences in episodic and working memory in patients but not in controls. These findings replicated in the same direction in the German samples. Furthermore, in both samples, when patients with a lower IQ were excluded, the association between ZNF804A and schizophrenia strengthened. CONCLUSIONS In a disorder characterized by heterogeneity, a risk variant at ZNF804A seems to delineate a patient subgroup characterized by relatively spared cognitive ability. Further work is required to establish whether this represents a discrete molecular pathogenesis that differs from that of other patient groups and whether this also has consequences for nosologic classification, illness course, or treatment.

Genome-wide association study implicates HLA-C*01:02 as a risk factor at the major histocompatibility complex locus in schizophrenia

By analyzing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls and 1,077 trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in SETD1A and risk for schizophrenia (P = 3.3 × 10−9). We found only two heterozygous LoF variants in 45,376 exomes from individuals without a neuropsychiatric diagnosis, indicating that SETD1A is substantially depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying SETD1A LoF variants also had learning difficulties. We further identified four SETD1A LoF carriers among 4,281 children with severe developmental disorders and two more carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations indicate that LoF variants in SETD1A cause a range of neurodevelopmental disorders, including schizophrenia. Combining these data with previous common variant evidence, we suggest that epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, is an important mechanism in the pathogenesis of schizophrenia.

Treatment-Resistant Schizophrenia: Treatment Response and Resistance in Psychosis (TRRIP) Working Group Consensus Guidelines on Diagnosis and Terminology

BACKGROUND We performed a genome-wide association study (GWAS) to identify common risk variants for schizophrenia. METHODS The discovery scan included 1606 patients and 1794 controls from Ireland, using 6,212,339 directly genotyped or imputed single nucleotide polymorphisms (SNPs). A subset of this sample (270 cases and 860 controls) was subsequently included in the Psychiatric GWAS Consortium-schizophrenia GWAS meta-analysis. RESULTS One hundred eight SNPs were taken forward for replication in an independent sample of 13,195 cases and 31,021 control subjects. The most significant associations in discovery, corrected for genomic inflation, were (rs204999, p combined = 1.34 × 10(-9) and in combined samples (rs2523722 p combined = 2.88 × 10(-16)) mapped to the major histocompatibility complex (MHC) region. We imputed classical human leukocyte antigen (HLA) alleles at the locus; the most significant finding was with HLA-C*01:02. This association was distinct from the top SNP signal. The HLA alleles DRB1*03:01 and B*08:01 were protective, replicating a previous study. CONCLUSIONS This study provides further support for involvement of MHC class I molecules in schizophrenia. We found evidence of association with previously reported risk alleles at the TCF4, VRK2, and ZNF804A loci.

Evidence that duplications of 22q11.2 protect against schizophrenia

OBJECTIVE Research and clinical translation in schizophrenia is limited by inconsistent definitions of treatment resistance and response. To address this issue, the authors evaluated current approaches and then developed consensus criteria and guidelines. METHOD A systematic review of randomized antipsychotic clinical trials in treatment-resistant schizophrenia was performed, and definitions of treatment resistance were extracted. Subsequently, consensus operationalized criteria were developed through 1) a multiphase, mixed methods approach, 2) identification of key criteria via an online survey, and 3) meetings to achieve consensus. RESULTS Of 2,808 studies identified, 42 met inclusion criteria. Of these, 21 studies (50%) did not provide operationalized criteria. In the remaining studies, criteria varied considerably, particularly regarding symptom severity, prior treatment duration, and antipsychotic dosage thresholds; only two studies (5%) utilized the same criteria. The consensus group identified minimum and optimal criteria, employing the following principles: 1) current symptoms of a minimum duration and severity determined by a standardized rating scale; 2) moderate or worse functional impairment; 3) prior treatment consisting of at least two different antipsychotic trials, each for a minimum duration and dosage; 4) systematic monitoring of adherence and meeting of minimum adherence criteria; 5) ideally at least one prospective treatment trial; and 6) criteria that clearly separate responsive from treatment-resistant patients. CONCLUSIONS There is considerable variation in current approaches to defining treatment resistance in schizophrenia. The authors present consensus guidelines that operationalize criteria for determining and reporting treatment resistance, adequate treatment, and treatment response, providing a benchmark for research and clinical translation.