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. 2010 Nov;42(11):969-72.
doi: 10.1038/ng.680. Epub 2010 Oct 3.

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

Yingrui Li  1 , Nicolas Vinckenbosch, Geng Tian, Emilia Huerta-Sanchez, Tao Jiang, Hui Jiang, Anders Albrechtsen, Gitte Andersen, Hongzhi Cao, Thorfinn Korneliussen, Niels Grarup, Yiran Guo, Ines Hellman, Xin Jin, Qibin Li, Jiangtao Liu, Xiao Liu, Thomas Sparsø, Meifang Tang, Honglong Wu, Renhua Wu, Chang Yu, Hancheng Zheng, Arne Astrup, Lars Bolund, Johan Holmkvist, Torben Jørgensen, Karsten Kristiansen, Ole Schmitz, Thue W Schwartz, Xiuqing Zhang, Ruiqiang Li, Huanming Yang, Jian Wang, Torben Hansen, Oluf Pedersen, Rasmus Nielsen, Jun Wang
Affiliations

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

Yingrui Li et al. Nat Genet. 2010 Nov.

Abstract

Targeted capture combined with massively parallel exome sequencing is a promising approach to identify genetic variants implicated in human traits. We report exome sequencing of 200 individuals from Denmark with targeted capture of 18,654 coding genes and sequence coverage of each individual exome at an average depth of 12-fold. On average, about 95% of the target regions were covered by at least one read. We identified 121,870 SNPs in the sample population, including 53,081 coding SNPs (cSNPs). Using a statistical method for SNP calling and an estimation of allelic frequencies based on our population data, we derived the allele frequency spectrum of cSNPs with a minor allele frequency greater than 0.02. We identified a 1.8-fold excess of deleterious, non-syonomyous cSNPs over synonymous cSNPs in the low-frequency range (minor allele frequencies between 2% and 5%). This excess was more pronounced for X-linked SNPs, suggesting that deleterious substitutions are primarily recessive.

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