biostudies-literatureMa YNational Natural Science Foundation of ChinaNational Research Foundation of KoreaClinical Medicine Plus X - Young Scholars ProjectInnovation Fund for Outstanding Doctoral Candidates of Peking University Health Science Center356https://www.ebi.ac.uk/biostudies/studies/S-EPMC12533355biostudies-literatureUnknown26(1)<h4>Background</h4>Inclusion of individuals with diverse or admixed genetic ancestries is crucial to discover novel findings that may be missed by genomics analyses rooted solely in European population.<h4>Results</h4>Here, we present an analysis framework, SPAmix, which is scalable to a large-scale biobank data analysis including hundreds of thousands of admixed individuals and is universally applicable to various types of complex traits including quantitative traits, time-to-event traits, ordinal traits, and longitudinal traits. Since no alternative model is fitted, SPAmix primarily focuses on association p values. For each genetic variant, SPAmix uses genotype data and genetic principal components to estimate individual-specific allele frequency, which is subsequently used to calibrate Genome biologySPAmix: a scalable, accurate, and universal analysis framework for large-scale genetic association studies in admixed populations.PMC12533355624115402398244100462273010PKU2023LCXQ043BMU2025BSS001324712022024K2A9A2A0601368311Lee SBi WXu PZhou XJKim HZhang JFMa YZhou WMao FXu HMiao LXu LLZhang PLi YfalseSPAmix: a scalable, accurate, and universal analysis framework for large-scale genetic association studies in admixed populations.<h4>Background</h4>Inclusion of individuals with diverse or admixed genetic ancestries is crucial to discover novel findings that may be missed by genomics analyses rooted solely in European population.<h4>Results</h4>Here, we present an analysis framework, SPAmix, which is scalable to a large-scale biobank data analysis including hundreds of thousands of admixed individuals and is universally applicable to various types of complex traits including quantitative traits, time-to-event traits, ordinal traits, and longitudinal traits. Since no alternative model is fitted, SPAmix primarily focuses on association p values. For each genetic variant, SPAmix uses genotype data and genetic principal components to estimate individual-specific allele frequency, which is subsequently used to calibrate 2025-01-01T00:00:00Z2025 Oct2026-07-15T11:56:06.441Z2026-07-04T03:12:17.056ZS-EPMC125333554110281910.1186/s13059-025-03827-9