Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
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DOI：
10.1093/bioinformatics/btt477
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发表时间：
2013-11-01
期刊：
影响因子：
5.8
通讯作者：
Li, Yun
中科院分区：
文献类型：
--
作者：
Duan, Qing;Liu, Eric Yi;Li, Yun
虽然1000个基因组单倍型是最常用的推论参考板，但医学测序项目正在产生大量替代的测序样本集。使用Exome测序计划的3384个单倍型对非裔美国人进行归因，与1000个基因组计划的2184个单倍型相比，编码微小等位基因频率51%的变异的有效样本量增加了8.3-11.4%。使用由表型极端建立的小组，没有观察到归因质量的损失。我们建议单独使用Exome测序项目的单倍型，或将两个小组串联起来，而不是基于质量分数的后归责选择或IMPUTE2‘S双小组组合。
Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3-11.4% for coding variants with minor allele frequency 51%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2' s two-panel combination.