Evaluation of imputation performance of multiple reference panels in a Pakistani population.
Evaluation of imputation performance of multiple reference panels in a Pakistani population.
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巴基斯坦人口中多个参考小组的插补性能评估。
DOI：
10.1101/2023.12.22.23300448
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Huckins,LauraM
中科院分区：
文献类型：
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作者：
Xu,Jiayi;Liu,Dongjing;Hassan,Arsalan;Genovese,Giulio;Cote,AlannaC;Fennessy,Brian;Cheng,Esther;Charney,AlexanderW;Knowles,JamesA;Ayub,Muhammad;Peterson,RoseannE;Bigdeli,TimB;Huckins,LauraM
基因型归责对于全基因组关联研究（GWAS）至关重要，但参考小组和现有的基准研究优先考虑欧洲个体。因此，目前尚不清楚哪个公开可用的参考小组应用于巴基斯坦个人，以及小组的祖先组成或样本量是否对插补准确性更重要。我们的研究比较了不同的参考面板，以估算1，814名巴基斯坦人的基因型数据，发现使用TOPMed和扩展的1000个基因组（ex1KG）参考的元估算的准确性和覆盖率的最佳性能平衡。ex1KG的插补准确性优于常见变异的TOPMed，尽管其样本量小30倍，支持创建具有不同人群的未来面板的努力。
Genotype imputation is crucial for genome-wide association studies (GWASs), but reference panels and existing benchmarking studies prioritize European individuals. Consequently, it is unclear which publicly available reference panel should be used for Pakistani individuals, and whether ancestry composition or sample size of the panel matters more for imputation accuracy. Our study compared different reference panels to impute genotype data in 1,814 Pakistani individuals, finding the best performance balancing accuracy and coverage with meta-imputation with TOPMed and the expanded 1000 Genomes (ex1KG) reference. Imputation accuracy of ex1KG outperformed TOPMed for common variants despite its 30-fold smaller sample size, supporting efforts to create future panels with diverse populations.