Multivariate genome-wide association meta-analysis of over 1 million subjects identifies loci underlying multiple substance use disorders.
- Authors
- Hatoum, Alexander S; Colbert, Sarah M C; Johnson, Emma C; Huggett, Spencer B; Deak, Joseph D; Pathak, Gita; Jennings, Mariela V; Paul, Sarah E; Karcher, Nicole R; Hansen, Isabella; Baranger, David A A; Edwards, Alexis; Grotzinger, Andrew; Substance Use Disorder Working Group of the Psychiatric Genomics Consortium; Tucker-Drob, Elliot M; Kranzler, Henry R; Davis, Lea K; Sanchez-Roige, Sandra; Polimanti, Renato; Gelernter, Joel; Edenberg, Howard J; Bogdan, Ryan; Agrawal, Arpana
- Year
- 2023
- Journal
- Nature. Mental health
- PMID
- 37250466
- DOI
- 10.1038/s44220-023-00034-y
- PMCID
- PMC10217792
Genetic liability to substance use disorders can be parsed into loci that confer general or substance-specific addiction risk. We report a multivariate genome-wide association meta-analysis that disaggregates general and substance-specific loci for published summary statistics of problematic alcohol use, problematic tobacco use, cannabis use disorder, and opioid use disorder in a sample of individuals of European descent and African descent. Nineteen independent SNPs were genome-wide significant ( < 5e-8) for the general addiction risk factor (), which showed high polygenicity. Across ancestries, was significant (among other genes), suggesting dopamine regulation as a cross-substance vulnerability. An polygenic risk score was associated with substance use disorders, psychopathologies, somatic conditions, and environments associated with the onset of addictions. Substance-specific loci (9 for alcohol, 32 for tobacco, 5 for cannabis, 1 for opioids) included metabolic and receptor genes. These findings provide insight into genetic risk loci for substance use disorders that could be leveraged as treatment targets.
Manhattan Plot of Addiction-rf Genome-Wide Significant Results.The dotted line represents genome-wide significance at 5e-8. Each SNP peak is annotated with the closest mapped gene from FUMA (Table 1). We have not included all SNPs in the credible set in Table 1, but they are shown in Supplementary Table 4. Significance is set at genome-wide significance Bonferroni correction in a two-sided test (P < 5e-8).
LLM interpretation
This is a Manhattan plot showing genome-wide significant results for addiction risk across 22 chromosomes. The x-axis represents the chromosomes and the y-axis represents the $-\log_{10}(P\text{-value})$, with a dotted horizontal line indicating the genome-wide significance threshold of $5 \times 10^{-8}$. Several significant SNP peaks are highlighted with yellow dots and labeled with their closest mapped genes, including *BANK1*, *DRD2*, *FTO*, and *GCKR*.
Manhattan Plot of TWAS Results for Addiction-rf.A Transcriptome-Wide Association Study (TWAS) of the addiction-rf, plotted as a Manhattan plot. In Panel A, Analyses were conducted in S-MultiXcan with GTeX v8 data. In Panel B, the analysis was run using S-PredixCan with weights trained from PsychEncode. The y-axis is presented as βlog10(p), the color of the data point represents the tissue in which correlation between gene expression and outcome was the highest. The dotted black line represents Bonferroni corrected TWAS significance of a two-sided test (Plot A has 9,944 genes, Bonferroni = 5Γ10^-6 and the line is at 5.3, Plot B has 13,850 genes, Bonferroni = 3.6Γ10^-6, line is at 5.4)
LLM interpretation
This figure consists of two Manhattan plots (Panels A and B) showing Transcriptome-Wide Association Study (TWAS) results for addiction-rf, with the y-axis representing $-\log_{10}(p)$ and the x-axis representing genes. Panel A uses S-MultiXcan with GTeX v8 data, and Panel B uses S-PredixCan with PsychEncode weights, with data points colored by the tissue showing the highest correlation. Both panels include a dotted black line indicating the Bonferroni corrected significance threshold (5.3 for A, 5.4 for B), with several labeled genes exceeding these thresholds.
PheWAS of Genetic Correlations using MASSIVE.Genetic correlations between 1,547 traits and the addiction-rf, calculated in MASSIVE, mapped by their statistical significance (-log10(p) on the y-axis), and broad category. The top 20 correlations are annotated. The black dashed line represents Bonferroni significance for association of a two-sided test (pbon= .05/1,574 = 3.232e-05).
LLM interpretation
This is a Manhattan-style scatter plot showing genetic correlations between 1,547 traits and "addiction-rf," with the y-axis representing $-\log_{10}(p) \times \text{Direction of effect}$. Data points are color-coded by broad category (e.g., behavior, psychiatric disease, substance use), with the top 20 most significant correlations annotated by trait name. A black dashed line indicates the Bonferroni significance threshold, with several traitsβmost notably "Smoking status: Current" and "Smoking status: Never"βshowing high statistical significance.
Polygenic Risk Score Prediction in Yale-Penn.(A) Polygenic risk score (PRS) of the addiction-rf predicts lifetime alcohol (AUD), cannabis (CUD), opioid (OUD), tobacco (TD), and cocaine (CoUD) use disorders, and variables representing more than one lifetime substance use disorder diagnosis vs no SUDs diagnosis (Polysubstance Use Disorder, 2 level), more than one lifetime diagnosis vs. one lifetime diagnosis (polysubstance vs. unitary), as well as any substance use disorder diagnosis (Any Addiction) in an independent sample (Yale Penn 3; N=1,986 individuals of European genetic ancestry). (B) The addiction-rf PRS was associated with a comparable phenotypic substance use disorders (SUD) common factor in the Yale-Penn sample. Controlling for age, sex and 10 genetic principal components of ancestry, all path estimates are fully standardized. Estimates were significant at p < .001 of a two-sided test (LAVAAN does not report P-values lower than .001).
LLM interpretation
Figure A is a horizontal bar chart showing the Nagelkerke's $R^2$ values for the addiction-rf PRS in predicting various substance use disorders (SUDs) and polysubstance categories, with the highest predictive value seen for "Polysubstance, 2 level." Figure B is a structural equation model diagram illustrating the standardized path estimates between the addiction-rf PRS, a common SUD factor, and five specific disorders (AUD, CUD, OUD, TD, CoUD). All paths in Figure B are marked with asterisks, indicating statistical significance at $p < .001$.
| # | Section | Preview |
|---|---|---|
| 40 | METHODS β Post-hoc analyses of European ancestry GWAS results β Drug Repurposing | Our signature matching technique used data from the Library of Integrated Network-based Cellularβ¦ |
| 41 | METHODS β Post-hoc analyses of European ancestry GWAS results β Drug Repurposing | In vitro medication signatures were matched with addiction-rf signatures from the transcriptome-wideβ¦ |
| 42 | METHODS β Post-hoc analyses of European ancestry GWAS results β Polygenic Risk Score Analyses in Yale-Penn β Yale-Penn. | The Yale-Penn16,66 sample includes 11,332 genotyped and phenotyped individuals recruited acrossβ¦ |
| 43 | METHODS β Post-hoc analyses of European ancestry GWAS results β Polygenic Risk Score Analyses in Yale-Penn β Yale-Penn. | For the present analysis, only Yale-Penn 3 EUR subjects (N=1,986) were included. DSM-IV29 substanceβ¦ |
| 44 | METHODS β Post-hoc analyses of European ancestry GWAS results β Polygenic Risk Score Analyses in Yale-Penn β Yale-Penn. | We calculated the addiction-rf PRS using the PRS-cs auto approach70. This method assumes a generalβ¦ |
| 45 | METHODS β Genetic Correlations and Latent Causal Variable modeling | To examine phenotypes that were genetically correlated with the addiction-rf, we calculated geneticβ¦ |
| 46 | METHODS β Phenome-wide Association Studies (PheWAS) β PheWAS in adult samples. | As MASSIVE includes a fairly sparse set of diagnoses (not all ICD codes are available) for geneticβ¦ |
| 47 | METHODS β Phenome-wide Association Studies (PheWAS) β ABCD PheWAS of phenotypes collected in childhood. | To identify phenotypes that were associated with the addiction-rf before the onset of regularβ¦ |
| 48 | METHODS β Phenome-wide Association Studies (PheWAS) β ABCD PheWAS of phenotypes collected in childhood. | PRS were generated using the PRS-cs software package70 consistent with our other (i.e., Yale-Penn 4,β¦ |
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