【摘 要】
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Dear Editor,rnThe genotype imputation is an efficient and pivotal approach to estimate the unobserved genotypes in the genomic data from the single nucleotide polymorphism (SNP) genotyping arrays or whole-genome sequencing (WGS).The fine mapping of varian
【机 构】
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Department of Endocrine and Metabolic Diseases,Shanghai Institute of Endocrine and Metabolic Disease
论文部分内容阅读
Dear Editor,rnThe genotype imputation is an efficient and pivotal approach to estimate the unobserved genotypes in the genomic data from the single nucleotide polymorphism (SNP) genotyping arrays or whole-genome sequencing (WGS).The fine mapping of variants in the genome-wide association study (GWAS) could be critically improved by the imputation with an optimal reference panel based on the population-specific haplotypes.1 The significant progresses of imputation were recently achieved by large high-resolution reference panels,such as the 1KGP3 (1000 Genomes Project Phase 3,n=2504),2 the UK10K (10,000 UK Genome Sequences,n =3781),3 the HRC (Haplotype Reference Consortium,n =32,470),4 TOPMed (Trans-Omics for Precision Medicine,n =97,256)5 and the GAsP (The GenomeAsia 100 K Project,n =1654)6(Supplementary information,Table S1).The multi-ethnic 1KGP3 reference panel is most commonly used for the genetic studies of Asian populations.However,the European ancestry-dominant reference panels exhibited poor performance in the genotype imputation for Chinese and other East Asian populations.7-9 The number of well-imputed variants and imputation accuracy depend on the characteristics of the reference panel dataset,including the sample size,sequencing data quality and population composition.
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