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

作者: Yingrui Li , Nicolas Vinckenbosch , Geng Tian , Emilia Huerta-Sanchez , Tao Jiang

DOI: 10.1038/NG.680

关键词: AlleleBiologySingle-nucleotide polymorphismMinor allele frequencyPopulationGenetic variationGeneticsAllele frequencyExomeExome sequencing

摘要: 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 …

参考文章(27)
Thomas J Albert, Michael N Molla, Donna M Muzny, Lynne Nazareth, David Wheeler, Xingzhi Song, Todd A Richmond, Chris M Middle, Matthew J Rodesch, Charles J Packard, George M Weinstock, Richard A Gibbs, Direct selection of human genomic loci by microarray hybridization. Nature Methods. ,vol. 4, pp. 903- 905 ,(2007) , 10.1038/NMETH1111
Carlos D Bustamante, Adi Fledel-Alon, Scott Williamson, Rasmus Nielsen, Melissa Todd Hubisz, Stephen Glanowski, David M Tanenbaum, Thomas J White, John J Sninsky, Ryan D Hernandez, Daniel Civello, Mark D Adams, Michele Cargill, Andrew G Clark, None, Natural selection on protein-coding genes in the human genome Nature. ,vol. 437, pp. 1153- 1157 ,(2005) , 10.1038/NATURE04240
P. L. F. Johnson, M. Slatkin, Accounting for Bias from Sequencing Error in Population Genetic Estimates Molecular Biology and Evolution. ,vol. 25, pp. 199- 206 ,(2007) , 10.1093/MOLBEV/MSM239
Sarah B. Ng, Emily H. Turner, Peggy D. Robertson, Steven D. Flygare, Abigail W. Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E. Eichler, Michael Bamshad, Deborah A. Nickerson, Jay Shendure, Targeted capture and massively parallel sequencing of 12 human exomes Nature. ,vol. 461, pp. 272- 276 ,(2009) , 10.1038/NATURE08250
Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, Geng Tian, Laurie Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, Xiaodong Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie Hu, Zhenzhen Yang, Hancheng Zheng, Ines Hellmann, Michael Inouye, John Pool, Xin Yi, Jing Zhao, Jinjie Duan, Yan Zhou, Junjie Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wenjie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hongmei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, Jianguo Zhang, Jia Ye, Lin Fang, Qin Hao, Quan Chen, Yu Liang, Yeyang Su, A San, Cuo Ping, Shuang Yang, Fang Chen, Li Li, Ke Zhou, Hongkun Zheng, Yuanyuan Ren, Ling Yang, Yang Gao, Guohua Yang, Zhuo Li, Xiaoli Feng, Karsten Kristiansen, Gane Ka-Shu Wong, Rasmus Nielsen, Richard Durbin, Lars Bolund, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang, None, The diploid genome sequence of an Asian individual. Nature. ,vol. 456, pp. 60- 65 ,(2008) , 10.1038/NATURE07484
Adam R. Boyko, Scott H. Williamson, Amit R. Indap, Jeremiah D. Degenhardt, Ryan D. Hernandez, Kirk E. Lohmueller, Mark D. Adams, Steffen Schmidt, John J. Sninsky, Shamil R. Sunyaev, Thomas J. White, Rasmus Nielsen, Andrew G. Clark, Carlos D. Bustamante, Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome PLoS Genetics. ,vol. 4, pp. e1000083- ,(2008) , 10.1371/JOURNAL.PGEN.1000083
Mark I McCarthy, Gonçalo R Abecasis, Lon R Cardon, David B Goldstein, Julian Little, John PA Ioannidis, Joel N Hirschhorn, None, Genome-wide association studies for complex traits: consensus, uncertainty and challenges Nature Reviews Genetics. ,vol. 9, pp. 356- 369 ,(2008) , 10.1038/NRG2344
Shamil R. Sunyaev, Warren C. Lathe III, Vasily E. Ramensky, Peer Bork, SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends in Genetics. ,vol. 16, pp. 335- 337 ,(2000) , 10.1016/S0168-9525(00)02058-8
S. H. Williamson, R. Hernandez, A. Fledel-Alon, L. Zhu, R. Nielsen, C. D. Bustamante, Simultaneous inference of selection and population growth from patterns of variation in the human genome Proceedings of the National Academy of Sciences of the United States of America. ,vol. 102, pp. 7882- 7887 ,(2005) , 10.1073/PNAS.0502300102
Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang, None, SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. ,vol. 25, pp. 1966- 1967 ,(2009) , 10.1093/BIOINFORMATICS/BTP336