Genome-Wide Association Studies and Deep-Learning Functional Annotation of Opioid Use Disorder across Three Ancestries in the All of Us Research Program

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Abstract
Background: Opioid use disorder (OUD) is heritable, yet most genome-wide association studies (GWAS) have focused on European populations, leaving the genetic architecture of OUD in non- European populations underexplored. Methods: We conducted GWAS of OUD across three ancestries using electronic health records and genomic data from 52,357 All of Us Research Program participants (8,912 cases; 43,445 matched opioid-exposed controls; 48.5% female). Participants were stratified into European (EUR), African (AFR), and Admixed American (AMR) ancestry groups for logistic regression GWAS, with independent replication in the Million Veteran Program. We then applied the deep- learning model AlphaGenome to predict the tissue-specific transcriptomic and splicing consequences of top risk variants across 13 reward-pathway brain regions. Results: We identified and replicated a novel DDX6 risk locus, alongside established OPRM1 and FURIN signals. AlphaGenome predicted the DDX6 regulatory allele downregulates the stress-resistance gene FOXR1 in the nucleus accumbens, while the protective OPRM1 variant (rs1799971) upregulates OPRM1 expression across reward networks. Other signals of interest included IL6R and SHISA9 (EUR); GHR (AFR); and ASTN2 (AMR). Conclusions: This study identifies DDX6 as a novel OUD risk locus, replicates associations with OPRM1 and FURIN , and highlights biologically plausible ancestry-specific signals in AFR and AMR populations. We also replicated top variants in an independent population. Finally, integrating GWAS with deep-learning annotations provides specific, localized biological hypotheses to guide future experimental validation and targeted therapeutics.
Funding Information
  • Ohio Attorney General's Office (15974)
  • National Institutes of Health, Office of the Director: Regional Medical Centers (1 OT2 OD026549; 1 OT2 OD026550; 1 OT2 OD026551; 1 OT2 OD026552; 1 OT2 OD026553; 1 OT2 OD026554; 1 OT2 OD026555; 1 OT2 OD026556; 1 OT2 OD026557; 1 OT2 OD026558; 1 OT2 OD026615; 1 OT2 OD025277; 1 OT2 OD025300; 1 OT2 OD025315; 1 OT2 OD025332; and 1 OT2 OD025276)

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