Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations

Abstract

Summary: Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic studies of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations.

Availability and implementation: Admix-kit package is open-source and available at https://github.com/KangchengHou/admix-kit. Additionally, users can use the pipeline designed for admixed genotype simulation available at https://github.com/UW-GAC/admix-kit_workflow.

Figure 1.

Overview of admix-kit’s data structure, functionality, and illustrative analyses using a simulated dataset. (a) Local ancestry and phased genotypes are stored in matrix format. Individual-specific and SNP-specific covariates are stored as two tables with matching orders. (b) Analysis based on ancestry-specific genotype dosage. Starting with a phased genotype for an individual (0/1 denotes presence of minor allele), genotypes are separated into ancestry-specific dosages. Local ancestry-informed downstream analyses can be subsequently performed. (c) visualization of local ancestry tracts. (d) Consistency of genome-wide genetic ancestry of simulated dataset using YRI and CEU in 1000 Genomes as reference populations. (e) Consistency of allele frequencies from the simulated admixed genotypes.