Imputation disparities driven by recent selection and their impact on disease risk estimation in East and Southeast Asian populations.

ABSTRACT: Accurate genotype imputation is essential for large-scale genetic studies and precision medicine. While East Asian (EAS)-specific reference panels like ChinaMAP and CHN100k have been developed, most studies still rely on multi-ancestry panels like TOPMed due to the large sample size. However, their performance in underrepresented groups like Southeast Asians remains unclear. Using high-coverage whole-genome sequencing and SNP-array data from 8,316 Chinese and Thai individuals, we systematically evaluate six state-of-the-art reference panels for genotype imputation. Our results show that EAS-specific panels outperformed multi-ancestry panels for East and Southeast Asian populations. For example, ChinaMAP achieves a mean heterozygosity concordance rate above 0.90 without R² filter

SUBMITTER: Li D 

PROVIDER: S-EPMC12749855 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature