Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits.
- Authors
- Zhou, Hang; Sealock, Julia M; Sanchez-Roige, Sandra; Clarke, Toni-Kim; Levey, Daniel F; Cheng, Zhongshan; Li, Boyang; Polimanti, Renato; Kember, Rachel L; Smith, Rachel Vickers; Thygesen, Johan H; Morgan, Marsha Y; Atkinson, Stephen R; Thursz, Mark R; Nyegaard, Mette; Mattheisen, Manuel; BΓΈrglum, Anders D; Johnson, Emma C; Justice, Amy C; Palmer, Abraham A; McQuillin, Andrew; Davis, Lea K; Edenberg, Howard J; Agrawal, Arpana; Kranzler, Henry R; Gelernter, Joel
- Year
- 2020
- Journal
- Nature neuroscience
- PMID
- 32451486
- DOI
- 10.1038/s41593-020-0643-5
- PMCID
- PMC7485556
Problematic alcohol use (PAU) is a leading cause of death and disability worldwide. Although genome-wide association studies have identified PAU risk genes, the genetic architecture of this trait is not fully understood. We conducted a proxy-phenotype meta-analysis of PAU, combining alcohol use disorder and problematic drinking, in 435,563βEuropean-ancestry individuals. We identified 29βindependent risk variants, 19 of them novel. PAU was genetically correlated with 138βphenotypes, including substance use and psychiatric traits. Phenome-wide polygenic risk score analysis in an independent biobank sample (BioVU, nβ=β67,589) confirmed the genetic correlations between PAU and substance use and psychiatric disorders. Genetic heritability of PAU was enriched in brain and in conserved and regulatory genomic regions. Mendelian randomization suggested causal effects on liability to PAU of substance use, psychiatric status, risk-taking behavior and cognitive performance. In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other traits.
Overview of the analysis.The four datasets that were meta-analyzed as the discovery sample for problematic alcohol use (PAU) included MVP phase1, MVP phase2, PGC, and UK Biobank (UKB). MVP phase1 and phase2 were meta-analyzed, and the result was used to test the genetic correlation with PGC alcohol dependence. An intermediary meta-analysis (AUD meta) combining MVP phase1, phase2, and PGC was then conducted to measure the genetic correlation with UKB AUDIT-P. Due to the sample overlap between UKB and GSCAN, we used the AUD (intermediary) meta-analysis for Mendelian Randomization (MR) analysis rather than the PAU (i.e., from the final) meta-analysis. MTAG, which used the summary data from PAU and DrnkWk (drinks per week) in GSCAN (without 23andMe samples, as those data were not available) as input to increase the power for each trait without introducing bias from sample overlap, returned summary results for PAU and DrnkWk separately.
Association results for AUD and PAU meta-analyses.a. Manhattan and QQ plots for AUD (MVP+PGC), ncase=57,564, ncontrol=256,395, neffective=179,185; b. Manhattan and QQ plots for PAU, n=435,563, neffective=300,789. Effective sample size weighted meta-analyses were performed using METAL. Red lines indicate GWS after correction for multiple testing (p < 5Γ10β8).
Estimated SNP-based h2.h2 results for single datasets or meta-analysis between datasets, from published studies or analyzed here. MVP is the phase1-phase2 MVP metaanalysis, PAU is the discovery meta-analysis. Effective sample sizes (nE) were used in LDSC. Center values are the estimated h2 and error bars indicate 95% confidence intervals.
Genetic correlations with published traits.LDSC was applied to test genetic correlation between PAU and 715 traits. Of 228 published traits, 26 were genetically correlated with PAU after Bonferroni correction (p < 6.99Γ10β5). MDD, major depressive disorder; ADHD, attention deficit hyperactivity disorder. Center values are the estimated genetic correlation and error bars indicate 95% confidence intervals.
| Name | Type |
|---|---|
| 1000 Genomes Project | cohort |
| 1000 Genomes Project Phase 3 European sample local | cohort |
| 23andMe | cohort |
| 27 cohorts local | cohort |
| 715 traits local | phenotype |
| absence of mental illness and harmful substance use local | phenotype |
| ADH1A | gene |
| ADH1B | gene |
| ADH1C | gene |
| ADH4 | gene |
| ADH5 | gene |
| ADH7 | gene |
| ADH gene cluster | gene |
| ADH gene locus local | gene |
| adipose tissue | phenotype |
| adrenal local | anatomy |
| Affymetrix Biobank Array local | drug |
| African American | cohort |
| alcohol | phenotype |
| alcohol dependence | phenotype |
| alcoholic liver disease | phenotype |
| alcoholism | phenotype |
| alcohol-related phenotypes | phenotype |
| Alcohol Use | phenotype |
| Alcohol Use Disorder | phenotype |
| alcohol use disorders | phenotype |
| ALDH2 | gene |
| Alzheimer's disease | phenotype |
| ARID4A | gene |
| Asian | cohort |
| AUD | phenotype |
| AUDIT | phenotype |
| AUDIT-C | phenotype |
| AUDIT-P | phenotype |
| AUD (MVP+PGC) local | phenotype |
| AUD PRS | drug |
| Bdnf | gene |
| BioVU | cohort |
| brain | anatomy |
| brain germinal matrix local | anatomy |
| C14orf2 local | gene |
| C1QTNF4 local | gene |
| Cadm2 | gene |
| cardiovascular disease | phenotype |
| central nervous system | anatomy |
| cerebellum | anatomy |
| cognition | phenotype |
| CognitivePerformance local | phenotype |
| cognitive traits | phenotype |
| common SNPs (MAF > 0.05) local | variant |
| conditionally independent variant local | variant |
| conserved regions local | drug |
| conserved regions with 500bp extended local | drug |
| cortex | anatomy |
| CRHR1 | gene |
| CYP2A6 | gene |
| CYP2A6 activity local | phenotype |
| DGN | anatomy |
| DHS | drug |
| DPIM study AD arm local | cohort |
| Dpp6 | gene |
| DRD2 | gene |
| drinks per week | phenotype |
| drugs | drug |
| DSM-IV alcohol dependence | phenotype |
| Eagle2 | drug |
| educational attainment | phenotype |
| ethanol consumption | phenotype |
| ethanol metabolic processes local | phenotype |
| European ancestry | cohort |
| European ancestry (EA) subjects local | cohort |
| European population | cohort |
| European population (EUR) local | cohort |
| Europeans | cohort |
| ever smoked regularly local | phenotype |
| EverSmokedRegularly local | phenotype |
| F10.2 local | phenotype |
| FastPCA | drug |
| fetal brain | anatomy |
| fetal DHS local | drug |
| FTO | gene |
| FUT2 | gene |
| gastrointestinal local | anatomy |
| GCKR | gene |
| gene-based associations local | gene |
| GeneralRiskTolerance local | phenotype |
| GSCAN | cohort |
| GTEx | cohort |
| H3K27ac | drug |
| H3K36me3 | drug |
| H3K3me3 local | drug |
| H3K4me1 | drug |
| H3K4me3 | drug |
| H3K9ac | drug |
| Haplotype Reference Consortium panel local | drug |
| HapMap3 | cohort |
| heart | anatomy |
| heritability enrichment local | phenotype |
| histone mark H3K4me1 local | drug |
| HRC panel local | drug |
| Illumina | drug |
| Illumina Human Core Exome Array local | drug |
| immune and hematopoietic local | anatomy |
| independent variant local | variant |
| index variant | variant |
| insomnia | phenotype |
| iPSYCH | cohort |
| iPSYCH group local | cohort |
| Klb | gene |
| LD Hub | cohort |
| lifetime cannabis use | phenotype |
| liver | anatomy |
| major depressive disorder | phenotype |
| Million Veteran Program | cohort |
| minimac3 | drug |
| mood disorders | phenotype |
| MVP | cohort |
| MVP meta-analysis | cohort |
| MVP+PGC local | cohort |
| MVP phase1 local | cohort |
| MVP phase1 AUD local | phenotype |
| MVP phase1 sample local | cohort |
| MVP phase2 local | cohort |
| MVP phase2 dataset local | cohort |
| newborn bloodspots local | cohort |
| novel variant | cohort |
| number of sexual partners | phenotype |
| NumberSexualPartners local | phenotype |
| pancreas | anatomy |
| parentsβ age at death local | phenotype |
| PAU | phenotype |
| PAU liability local | phenotype |
| PAU polygenic score local | drug |
| PAU PRS | phenotype |
| Pde4b | gene |
| PGC | cohort |
| PGC AD | cohort |
| PGC AD local | phenotype |
| PGC AD GWAS local | cohort |
| Phase1 local | cohort |
| Phase2 local | cohort |
| phase2 EAs local | cohort |
| phs001672.v3.p1 local | cohort |
| Plink1.9 local | drug |
| population registry data local | cohort |
| problematic alcohol use | phenotype |
| PRS of AUD local | drug |
| Psych Array local | drug |
| psychiatric disorders | phenotype |
| Psychiatric Genomics Consortium | cohort |
| psychiatric traits | phenotype |
| published traits local | phenotype |
| Respiratory conditions local | phenotype |
| risk allele | cohort |
| risk loci | cohort |
| risk-taking behavior | phenotype |
| Roadmap Epigenomics consortium | cohort |
| rs10717830 local | variant |
| rs12296477 local | variant |
| rs1229984 | variant |
| rs13125415 local | variant |
| rs1402398 local | variant |
| rs1612735 local | variant |
| rs1783835 local | variant |
| rs2066702 | variant |
| rs2533200 local | variant |
| rs2683616 local | variant |
| rs492602 local | variant |
| rs61974485 local | variant |
| rs62250713 local | variant |
| rs6421482 local | variant |
| rs72768626 local | variant |
| rs75967634 | variant |
| Sanger Imputation server local | drug |
| schizophrenia | phenotype |
| SIX3 | gene |
| SLC39A13 | gene |
| SLC39A8 | gene |
| smoking phenotypes | phenotype |
| S-MultiXcan | drug |
| SNP | cohort |
| STOPAH trial local | cohort |
| study cohort | cohort |
| substance use | phenotype |
| SYNGAP1 | gene |
| THSD7B | gene |
| thyroid local | anatomy |
| TMX2 | gene |
| TNRC6A local | gene |
| tobacco dependence | phenotype |
| TSS local | drug |
| UCL Core Exome Array local | cohort |
| UCL Psych Array local | cohort |
| UKB | cohort |
| UKB AUDIT-P local | phenotype |
| UK Biobank | cohort |
| UK Household Longitudinal Study local | cohort |
| UK subjects local | cohort |
| U.S. Department of Veterans Affairs | cohort |
| variant | cohort |
| VRK2 | gene |
| weak enhancers local | drug |
| White-British local | cohort |
| WorryNeuroticism local | phenotype |
| worry sub-cluster local | phenotype |
| Worry sub-cluster of neuroticism local | phenotype |
No uploaded files.
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In this knowledge base
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