Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
- Authors
- Cross-Disorder Group of the Psychiatric Genomics Consortium
- Year
- 2013
- Journal
- Lancet (London, England)
- PMID
- 23453885
- DOI
- 10.1016/S0140-6736(12)62129-1
- PMCID
- PMC3714010
BACKGROUND: Findings from family and twin studies suggest that genetic contributions to psychiatric disorders do not in all cases map to present diagnostic categories. We aimed to identify specific variants underlying genetic effects shared between the five disorders in the Psychiatric Genomics Consortium: autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia. METHODS: We analysed genome-wide single-nucleotide polymorphism (SNP) data for the five disorders in 33,332 cases and 27,888 controls of European ancestory. To characterise allelic effects on each disorder, we applied a multinomial logistic regression procedure with model selection to identify the best-fitting model of relations between genotype and phenotype. We examined cross-disorder effects of genome-wide significant loci previously identified for bipolar disorder and schizophrenia, and used polygenic risk-score analysis to examine such effects from a broader set of common variants. We undertook pathway analyses to establish the biological associations underlying genetic overlap for the five disorders. We used enrichment analysis of expression quantitative trait loci (eQTL) data to assess whether SNPs with cross-disorder association were enriched for regulatory SNPs in post-mortem brain-tissue samples. FINDINGS: SNPs at four loci surpassed the cutoff for genome-wide significance (p<5Γ10(-8)) in the primary analysis: regions on chromosomes 3p21 and 10q24, and SNPs within two L-type voltage-gated calcium channel subunits, CACNA1C and CACNB2. Model selection analysis supported effects of these loci for several disorders. Loci previously associated with bipolar disorder or schizophrenia had variable diagnostic specificity. Polygenic risk scores showed cross-disorder associations, notably between adult-onset disorders. Pathway analysis supported a role for calcium channel signalling genes for all five disorders. Finally, SNPs with evidence of cross-disorder association were enriched for brain eQTL markers. INTERPRETATION: Our findings show that specific SNPs are associated with a range of psychiatric disorders of childhood onset or adult onset. In particular, variation in calcium-channel activity genes seems to have pleiotropic effects on psychopathology. These results provide evidence relevant to the goal of moving beyond descriptive syndromes in psychiatry, and towards a nosology informed by disease cause. FUNDING: National Institute of Mental Health.
Manhattan plot of primary fixed-effects meta-analysisHorizontal line shows threshold for genome-wide significance (p<5Γ10β8).
LLM interpretation
This is a Manhattan plot showing the results of a primary fixed-effects meta-analysis across 22 chromosomes. The y-axis represents the $-\log_{10}(p\text{-value})$, with a red horizontal line indicating the genome-wide significance threshold of $p < 5 \times 10^{-8}$. Several genomic loci, including *ITIH3*, *MHC*, and *CACNB2*, are labeled as they exceed or approach this significance threshold.
Association results and forest plots showing effect size for genome-wide significant loci by disorderData in parentheses are numbers of cases or controls. Het_p=p value for the heterogeneity test. Het_I=heterogeneity test statistic. IQS=imputation quality score (INFO). ln(OR)=log of the odds ratio (OR). F=frequency. SE=standard error of the log OR. ADHD=attention deficit-hyperactivity disorder. ASD=autism spectrum disorders. BPD=bipolar disorder. MDD=major depressive disorder. *Number of studies in which the variant was directly genotyped.
LLM interpretation
This figure consists of four forest plots (labeled A-D) showing the association of specific genetic variants (rs2535629, rs1191454, rs1024582, and rs2799573) with five psychiatric disorders (ADHD, ASD, BPD, MDD, and Schizophrenia). Each panel displays a table of statisticsβincluding p-values, case/control frequencies, and log odds ratios (ln(OR))βalongside a plot of effect sizes and 95% confidence intervals. The "All" row at the bottom of each panel provides a pooled effect size represented by a diamond, indicating the overall association across the studied groups.
Pair-wise cross-disorder polygene analysisWe derived polygene risk scores for each disorder (discovery sets) and applied them sequentially to the remaining disorders (target sets). Results are grouped by each discovery set. Each pair is shown on the x-axis and the proportion of variance explained for the target disorder (estimated via Nagelkerkeβs pseudo R2) on the y-axis. For purposes of illustration, three pT cutoffs are shown, but appendix p 62 shows the proportion of variance results for a broader range of cutoffs. pT=training-set p value (used to select training set SNPs). Significance of results: a=p<0Β·05; b=p<10β4; c=p<10β8; d=p<1012; e=p<10β16; f=p<10β50. ADHD=attention deficit-hyperactivity disorder. ASD=autism spectrum disorders. BPD=bipolar disorder. MDD=major depressive disorder.
LLM interpretation
This grouped bar chart shows the proportion of variance explained ($R^2$) for target psychiatric disorders using polygene risk scores derived from different discovery sets. The x-axis lists pairs of disorders grouped by discovery set (ADHD, ASD, BPD, MDD, and Schizophrenia), while the y-axis measures $R^2$. The highest variance is explained when Schizophrenia is the discovery set for BPD and when BPD is the discovery set for Schizophrenia, with significance markers (a-f) indicating varying p-value thresholds.
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