Genome‐wide association study of facial emotion recognition in children and association with polygenic risk for mental health disorders

Emotion recognition is disrupted in many mental health disorders, which may reflect shared genetic aetiology between this trait and these disorders. We explored genetic influences on emotion recognition and the relationship between these influences and mental health phenotypes. Eight‐year‐old participants (n = 4,097) from the Avon Longitudinal Study of Parents and Children (ALSPAC) completed the Diagnostic Analysis of Non‐Verbal Accuracy (DANVA) faces test. Genome‐wide genotype data was available from the Illumina HumanHap550 Quad microarray. Genome‐wide association studies were performed to assess associations with recognition of individual emotions and emotion in general. Exploratory polygenic risk scoring was performed using published genomic data for schizophrenia, bipolar disorder, depression, autism spectrum disorder, anorexia, and anxiety disorders. No individual genetic variants were identified at conventional levels of significance in any analysis although several loci were associated at a level suggestive of significance. SNP‐chip heritability analyses did not identify a heritable component of variance for any phenotype. Polygenic scores were not associated with any phenotype. The effect sizes of variants influencing emotion recognition are likely to be small. Previous studies of emotion identification have yielded non‐zero estimates of SNP‐heritability. This discrepancy is likely due to differences in the measurement and analysis of the phenotype.     

Genome‐wide association study of cognitive performance in U.S. veterans with schizophrenia or bipolar disorder

Cognitive impairment is a frequent and serious problem in patients with various forms of severe mental illnesses (SMI), including schizophrenia (SZ) and bipolar disorder (BP). Recent research suggests genetic links to several cognitive phenotypes in both SMI and in the general population. Our goal in this study was to identify potential genomic signatures of cognitive functioning in veterans with severe mental illness and compare them to previous findings for cognition across different populations. Veterans Affairs (VA) Cooperative Studies Program (CSP) Study #572 evaluated cognitive and functional capacity measures among SZ and BP patients. In conjunction with the VA Million Veteran Program, 3,959 European American (1,095 SZ, 2,864 BP) and 2,601 African American (1,095 SZ, 2,864 BP) patients were genotyped using a custom Affymetrix Axiom Biobank array. We performed a genome‐wide association study of global cognitive functioning, constructed polygenic scores for SZ and cognition in the general population, and examined genetic correlations with 2,626 UK Biobank traits. Although no single locus attained genome‐wide significance, observed allelic effects were strongly consistent with previous studies. We observed robust associations between global cognitive functioning and polygenic scores for cognitive performance, intelligence, and SZ risk. We also identified significant genetic correlations with several cognition‐related traits in UK Biobank. In a diverse cohort of U.S. veterans with SZ or BP, we demonstrate broad overlap of common genetic effects on cognition in the general population, and find that greater polygenic loading for SZ risk is associated with poorer cognitive performance.     

Association study of schizophrenia with dopamine D3 receptor gene polymorphisms: Probable effects of family history of schizophrenia?

Using a case-control design, a reported association of schizophrenia with homozygosity at the dopamine D3 receptor gene locus was investigated in a group of patients (n = 53), with schizophrenia (DSM-III-R), and psychiatrically normal controls (n = 61), matched for ethnicity and area of residence. No significant differences in the distribution of alleles or genotypes between the two groups could be deteched. However, among patients with a family history of schizophrenia, as compared to controls without such family history, an association with allele 1 at this locus was noted (Odds ratio 12.4, C.I. 1.61, 96.35). © 1993 Wiley-Liss, Inc.     

Genome‐wide analysis of adolescent psychotic‐like experiences shows genetic overlap with psychiatric disorders

This study aimed to test for overlap in genetic influences between psychotic‐like experience traits shown by adolescents in the community, and clinically‐recognized psychiatric disorders in adulthood, specifically schizophrenia, bipolar disorder, and major depression. The full spectra of psychotic‐like experience domains, both in terms of their severity and type (positive, cognitive, and negative), were assessed using self‐ and parent‐ratings in three European community samples aged 15–19 years (Final N incl. siblings = 6,297–10,098). A mega‐genome‐wide association study (mega‐GWAS) for each psychotic‐like experience domain was performed. Single nucleotide polymorphism (SNP)‐heritability of each psychotic‐like experience domain was estimated using genomic‐relatedness‐based restricted maximum‐likelihood (GREML) and linkage disequilibrium‐ (LD‐) score regression. Genetic overlap between specific psychotic‐like experience domains and schizophrenia, bipolar disorder, and major depression was assessed using polygenic risk score (PRS) and LD‐score regression. GREML returned SNP‐heritability estimates of 3–9% for psychotic‐like experience trait domains, with higher estimates for less skewed traits (Anhedonia, Cognitive Disorganization) than for more skewed traits (Paranoia and Hallucinations, Parent‐rated Negative Symptoms). Mega‐GWAS analysis identified one genome‐wide significant association for Anhedonia within IDO2 but which did not replicate in an independent sample. PRS analysis revealed that the schizophrenia PRS significantly predicted all adolescent psychotic‐like experience trait domains (Paranoia and Hallucinations only in non‐zero scorers). The major depression PRS significantly predicted Anhedonia and Parent‐rated Negative Symptoms in adolescence. Psychotic‐like experiences during adolescence in the community show additive genetic effects and partly share genetic influences with clinically‐recognized psychiatric disorders, specifically schizophrenia and major depression.     

Genome‐wide association analysis of age at onset in schizophrenia in a European‐American sample

We performed a genome‐wide association analysis to identify genetic variants influencing age at onset (AAO) and examine gene × gender interactions for AAO in schizophrenia (SCZ) using a European‐American sample (1,162 cases). Linear regression model in PLINK was used to test for associations with AAO while the GxE option was chosen to test for the influence of gene × gender interactions. The most significant association with AAO was observed with SNP rs7819815 (P = 3.10 × 10^?7) at 8q24.22. The next best signal was at 4q25 in COL25A1 gene (rs17039583, P = 4.30 × 10^?6) and the third region was at 4p16.1 (rs17407555, P = 4.56 × 10^?6, near RAF1P1, and rs4697924, P = 1.23 × 10^?5 within WDR1 gene). Conditional analysis on chromosome 4 indicated that 4p16.1 and 4q25 loci were independent. Furthermore, 2 SNPs (rs16834822 and rs16834824) at 1q43 in RYR2 showed strong associations in the female sample (P = 2.10 × 10^?6 and 2.33 × 10^?6, respectively) and strong gene × gender interactions in influencing AAO (P = 9.23 × 10^?7 and 1.15 × 10^?6, respectively) while the second best region showing gene × gender interaction was at 7q22.3 (rs179863, P = 2.33 × 10^?6). Using an independent sample of 1,068 cases, we could not replicate the associations for above top SNPs; however, we found nominal significance associations for their flanking SNPs (P < 0.05). These findings provide evidence of several genetic variants influencing AAO of SCZ. © 2011 Wiley‐Liss, Inc.     

Genome‐wide scan for linkage to schizophrenia in a Spanish‐origin cohort from Costa Rica

Genetic isolates have been useful cohorts in which to search for genes underlying disorders of unknown pathology. One such cohort is thought to exist in the Central Valley of Costa Rica surrounding the city of San Jose. Previous investigators identified a rare dominant gene for hereditary deafness in this population, and a suggestive linkage of severe bipolar psychosis has been reported in another study. Ninety‐nine families with at least one pair of siblings affected with schizophrenia or a schizophrenia‐spectrum diagnosis had clinical evaluations and DNA collected for genotyping. The Marshfield Medical Research Foundation (NHLBI) Mammalian Genotyping Service performed all genotyping using 404 short‐tandem repeat polymorphic markers (STRPs) spaced on average 10 cM apart. Data were analyzed using the nonparametric program, GeneHunterPlus. The population structure was investigated using the STRUCT program. No region was found with genome‐wide significance for linkage. Using a phenotype of schizophrenia plus schizoaffective disorder, the highest maximum likelihood score (MLS) observed was 1.78 (P < 0.004) at 176.6 cM from pter on chromosome 5q, an area previously implicated by some other groups. In addition, five regions on chromosomes 1p, 2p, 2q, 14p, and 8p had MLSs above 1.0. All other regions produced scores below 1.0. Population genetic analysis reveals no evidence for population substructure, for admixture with other populations, such as Amerindians, or for inbreeding in the parental generation. The latter casts some doubt on this population being an isolate, although there was evidence of inbreeding among the offspring. © 2002 Wiley‐Liss, Inc.     

Genome‐wide association study of cognitive flexibility assessed by the Wisconsin Card Sorting Test

Cognitive flexibility is a critical component of executive function and is strongly influenced by genetic factors. We conducted a genome‐wide association study of cognitive flexibility (as measured by perseverative errors on the Wisconsin Card Sorting Test) in two sets of African American (AA) and European American (EA) subjects (Yale‐Penn‐1: 1,411 AAs/949 EAs; Yale‐Penn‐2: 1,178 AAs/1,335 EAs). We examined the association of cognitive flexibility with genotyped or imputed SNPs across the genome. In AAs, two correlated common single nucleotide polymorphisms (SNPs) (rs7165213/rs35633795) in the downstream region of the noncoding gene LOC101927286 on chromosome 15 showed genome‐wide significant (GWS) associations with cognitive flexibility (Yale‐Penn‐1: p = 6.0 × 10^?9/1.3 × 10^?8; Yale‐Penn‐2: p = .029/.010; meta‐analysis: p = 4.2 × 10^?7/1.0 × 10^?7) in the same effect direction. In EAs, no GWS associations were observed. Enriched gene sets identified by Data‐driven Expression‐Prioritized Integration for Complex Traits (DEPICT) analysis of the top SNPs (p_{meta‐analysis} < 10^?5) included the signalosome and ubiquitin‐specific peptidase 9, X‐linked (USP9X) subnetwork in AAs, and abnormal frontal and occipital bone morphology in EAs. We also performed polygenic risk score (PRS) analysis to examine the genetic correlation of cognition‐proxy phenotypes (general cognitive function, education attainment, childhood intelligence, and infant head circumference) and cognitive flexibility in EAs. The PRS derived from general cognitive function‐associated SNPs was significantly associated with cognitive flexibility. Nongenetic factors (age, education, sex, and tobacco recency) also exerted significant effects on cognitive flexibility. Our study demonstrates that both genetic and nongenetic factors impact cognitive flexibility, and variants in genes involved in protein degradation and brain development may contribute to population variation in cognitive function.     

A molecule‐based genetic association approach implicates a range of voltage‐gated calcium channels associated with schizophrenia

Traditional genome‐wide association studies (GWAS) have successfully detected genetic variants associated with schizophrenia. However, only a small fraction of heritability can be explained. Gene‐set/pathway‐based methods can overcome limitations arising from single nucleotide polymorphism (SNP)‐based analysis, but most of them place constraints on size which may exclude highly specific and functional sets, like macromolecules. Voltage‐gated calcium (Ca_v) channels, belonging to macromolecules, are composed of several subunits whose encoding genes are located far away or even on different chromosomes. We combined information about such molecules with GWAS data to investigate how functional channels associated with schizophrenia. We defined a biologically meaningful SNP‐set based on channel structure and performed an association study by using a validated method: SNP‐set (sequence) kernel association test. We identified eight subtypes of Ca_v channels significantly associated with schizophrenia from a subsample of published data (N = 56,605), including the L‐type channels (Ca_v1.1, Ca_v1.2, Ca_v1.3), P‐/Q‐type Ca_v2.1, N‐type Ca_v2.2, R‐type Ca_v2.3, T‐type Ca_v3.1, and Ca_v3.3. Only genes from Ca_v1.2 and Ca_v3.3 have been implicated by the largest GWAS (N = 82,315). Each subtype of Ca_v channels showed relatively high chip heritability, proportional to the size of its constituent gene regions. The results suggest that abnormalities of Ca_v channels may play an important role in the pathophysiology of schizophrenia and these channels may represent appropriate drug targets for therapeutics. Analyzing subunit‐encoding genes of a macromolecule in aggregate is a complementary way to identify more genetic variants of polygenic diseases. This study offers the potential of power for discovery the biological mechanisms of schizophrenia.     

Polygenic transmission and complex neuro developmental network for attention deficit hyperactivity disorder: Genome‐wide association study of both common and rare variants

Attention‐deficit hyperactivity disorder (ADHD) is a complex polygenic disorder. This study aimed to discover common and rare DNA variants associated with ADHD in a large homogeneous Han Chinese ADHD case–control sample. The sample comprised 1,040 cases and 963 controls. All cases met DSM‐IV ADHD diagnostic criteria. We used the Affymetrix6.0 array to assay both single nucleotide polymorphisms (SNPs) and copy number variants (CNVs). Genome‐wide association analyses were performed using PLINK. SNP‐heritability and SNP‐genetic correlations with ADHD in Caucasians were estimated with genome‐wide complex trait analysis (GCTA). Pathway analyses were performed using the Interval enRICHment Test (INRICH), the Disease Association Protein–Protein Link Evaluator (DAPPLE), and the Genomic Regions Enrichment of Annotations Tool (GREAT). We did not find genome‐wide significance for single SNPs but did find an increased burden of large, rare CNVs in the ADHD sample (P = 0.038). SNP‐heritability was estimated to be 0.42 (standard error, 0.13, P = 0.0017) and the SNP‐genetic correlation with European Ancestry ADHD samples was 0.39 (SE 0.15, P = 0.0072). The INRICH, DAPPLE, and GREAT analyses implicated several gene ontology cellular components, including neuron projections and synaptic components, which are consistent with a neurodevelopmental pathophysiology for ADHD. This study suggested the genetic architecture of ADHD comprises both common and rare variants. Some common causal variants are likely to be shared between Han Chinese and Caucasians. Complex neurodevelopmental networks may underlie ADHD's etiology. © 2013 Wiley Periodicals, Inc.     

Genome‐wide association study of lncRNA polymorphisms with bone mineral density

Recent studies suggested that long noncoding RNAs (lncRNAs) were widely transcribed in the genome, but their potential roles in the genetic complexity of human disorders required further exploration. The purpose of the present study was to explore genetic polymorphisms of lncRNAs associated with bone mineral density (BMD) and its potential value. Based on the lncRNASNP database, 55,906 lncSNPs were selected to conduct a genome‐wide association study meta‐analysis among 11,140 individuals of seven independent studies for BMDs at femoral neck (FN), lumbar spine, and total hip (HIP). Promising results were replicated in Genetic Factors for Osteoporosis Consortium (GEFOS Sequencing, n = 32,965). We found two lncRNA loci that were significantly associated with BMD. MEF2C antisense RNA 1 (MEF2C‐AS1) located at 5q14.3 was significantly associated with FN‐BMD after Bonferroni correction, and the strongest association signal was detected at rs6894139 (P = 3.03 × 10^?9). LOC100506136 rs6465531 located at 7q21.3 showed significant association with HIP‐BMD (P = 7.43 × 10^?7). MEF2C‐AS1 rs6894139 was replicated in GEFOS Sequencing with P‐value of 1.43 × 10^?23. Our results illustrated the important role of polymorphisms in lncRNAs in determining variations of BMD and provided justification and evidence for subsequent functional studies.     

Predictive modeling of schizophrenia from genomic data: Comparison of polygenic risk score with kernel support vector machines approach

A major controversy in psychiatric genetics is whether nonadditive genetic interaction effects contribute to the risk of highly polygenic disorders. We applied a support vector machines (SVMs) approach, which is capable of building linear and nonlinear models using kernel methods, to classify cases from controls in a large schizophrenia case–control sample of 11,853 subjects (5,554 cases and 6,299 controls) and compared its prediction accuracy with the polygenic risk score (PRS) approach. We also investigated whether SVMs are a suitable approach to detecting nonlinear genetic effects, that is, interactions. We found that PRS provided more accurate case/control classification than either linear or nonlinear SVMs, and give a tentative explanation why PRS outperforms both multivariate regression and linear kernel SVMs. In addition, we observe that nonlinear kernel SVMs showed higher classification accuracy than linear SVMs when a large number of SNPs are entered into the model. We conclude that SVMs are a potential tool for assessing the presence of interactions, prior to searching for them explicitly.     

Evaluation of risk loci for schizophrenia derived from genome‐wide association studies in a German population

In the genome‐wide association study (GWAS) on schizophrenia [O'Donovan et al. (2008); Nat Genet 40:1053–1055] a UK‐sample of 479 cases with DSM‐IV schizophrenia was genotyped in comparison to control subjects with follow up of 12 putative loci in international replication sets of approximately 15,000 cases and controls. In these cohorts and a combined bipolar and schizophrenia UK‐sample, six single nucleotide polymorphisms (SNPs) supported association, with the strongest evidence for SNP‐marker rs1344706 at the zinc finger ZNF804A locus on chromosome 2q32.1 (P = 1.61 × 10^?7). We attempted replication of these findings in a German population of 2,154 individuals (632 with affective disorders, 937 with schizophrenia, and 585 controls), but found none of the GWAS risk alleles significantly associated with psychosis. Particularly rs1344706, initially surpassing the genome‐wide significance level in an extended phenotype of schizophrenia and affective disorder, produced consistently negative results. At the ZNF804A locus estimated Odds ratios reached 1.08 (0.93–1.26 95% CI) for the schizophrenia sample and 1.04 (0.90–1.20 95% CI) for the combined set of cases with schizophrenia and affective disorder. The main limitation of our study may be the reduced power of the sample size, but our data may be useful for future meta‐analysis of GWA data sets. Although GWAS have proven extraordinary successful in identifying susceptibility genes for complex genetic disorders, the hypothesis of common genetic variants in the complex group of the schizophrenic psychoses with small effect size but relatively high frequency is still put to further scrutiny. © 2011 Wiley‐Liss, Inc.