Admixture mapping identifies complex trait associations with local ancestry in the All of Us Research Program

Genetic studies have largely focused on homogeneous populations, limiting our understanding of the genetic architecture of complex traits in admixed individuals. The advent of diverse biobanks like the All of Us Research Program (AoU) and computationally efficient local ancestry inference (LAI) methods now enable admixture mapping (ADM) at biobank scale. Here, we used two orthogonal LAI methods (GNOMIX and FLARE) to characterize local ancestry in the entire AoU v7.1 cohort (n=230,019). We then used GNOMIX labels to identify associations between African (AFR) and Native American (NAT) local ancestry with 29 quantitative traits. We first analyzed All of Us v7.1 data across African (n=49,797) and Admixed American (n=40,327) cohorts, which identified 97 significant local ancestry associations (65 AFR, 32 NAT). These include strong known signals, such as an association between AFR ancestry at the DARC locus and white blood cell traits and between NAT ancestry at the BUD13/APOE5/ZPR1 locus and triglycerides, as well as additional signals not previously associated with local ancestry. We observed that trait associations with AFR local ancestry are largely consistent across the African and Admixed American cohorts, but that several AFR signals reach genome-wide significance exclusively in Admixed Americans. Grouping associations by trait category revealed distinct ancestral patterns: all endocrine, renal, and 75.0% of liver signals were driven by associations with NAT ancestry, whereas white blood cell (90.9%), red blood cell (65.1%), and lipid (66.7%) signals were largely associated with AFR ancestry, possibly reflecting different population-driven environmental exposures throughout history. Finally, we performed a second round of analysis, comprising the largest ADM study to date, on the entire AoU v7.1 cohort in which we pooled individuals from all ancestries. Despite evidence of confounding due to population structure, summary statistics for pooled results showed strong correlation (r>0.98) with those from single ancestry analysis and detected 2.7x fold more signals, most of which passed at least nominal significance and all of which showed consistent effect directions in the single ancestry cohorts. Overall, these results demonstrate the power of using large, admixed cohorts to gain new insights into the relationship between local ancestry and the genetic architecture of medically relevant complex traits.