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November 21, 2025Communications BiologyOpen Access

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

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Authors

DLDingyang LiPTPattarin TangtanatakulYLYao, Lei

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Implication

Genetic studies reveal improved disease prediction in East and Southeast Asians, indicating the need for precise reference panels.

Key Points

  • This research aims to evaluate the impact of genotype imputation methods on disease risk estimation in East and Southeast Asian populations.
  • Evaluated six reference panels for genotype imputation using high-coverage whole-genome sequencing and SNP-array data.
  • Analyzed data from 8,316 individuals from China and Thailand.
  • Compared performance metrics such as heterozygosity concordance rate and R2 thresholds.
  • EAS-specific panels outperformed multi-ancestry panels in imputation accuracy.
  • ChinaMAP showed a mean heterozygosity concordance rate above 0.90 without R2 filtering.
  • Recent positive selection was linked to disparities in imputation accuracy across populations.

Cite This Study

Li et al. (2025) studied this question.

synapsesocial.com/papers/6924e3f8c0ce034ddc34f30ahttps://doi.org/10.1038/s42003-025-09214-1
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Also Consider

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  1. 1A reanalysis of a genome-wide association study on breast cancer in Asian populations using the SG10K_Health reference panel for imputation: a multi-Centre case–control analysis2026
  2. 2Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context2024 · 2 citations
  3. 3Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts2024
  4. 4A population-specific genomic reference panel for Taiwan: NHRI-RP-12026
  5. 5Bioinformatic insights into five Chinese population substructures inferred from the East Asian-specific AISNP panel2025 · 3 citations