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Evaluation of imputation performance of multiple reference panels in a Pakistani population.


ABSTRACT: Genotype imputation is crucial for GWAS, 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 1814 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 despite its 30-fold smaller sample size, supporting efforts to create future panels with diverse populations.

SUBMITTER: Xu J 

PROVIDER: S-EPMC10793543 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Evaluation of imputation performance of multiple reference panels in a Pakistani population.

Xu Jiayi J   Liu Dongjing D   Hassan Arsalan A   Genovese Giulio G   Cote Alanna C AC   Fennessy Brian B   Cheng Esther E   Charney Alexander W AW   Knowles James A JA   Ayub Muhammad M   Peterson Roseann E RE   Bigdeli Tim B TB   Huckins Laura M LM  

medRxiv : the preprint server for health sciences 20231226


Genotype imputation is crucial for GWAS, 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 1814 Pakistani individuals, finding the best performance balancing accuracy and coverage  ...[more]

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