Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
作者： Qing Duan , Eric Yi Liu , Paul L. Auer , Guosheng Zhang , Ethan M. Lange
DOI: 10.1093/BIOINFORMATICS/BTT477
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摘要: Summary: Although the 1000 Genomes haplotypes are most commonly used reference panel for imputation, medical sequencing projects generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 from Exome Sequencing Project, compared with 2184 increased effective sample size by 8.3–11.4% coding variants minor allele frequency 51%. No loss imputation quality was observed a built phenotypic extremes. We recommend Project alone or concatenation two panels over score-based post-imputation selection IMPUTE2’s twopanel combination.
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James G. Wilson, Cheryl Nelson, Daniel F. Sarpong, Herman A. Taylor, Sharon B. Wyatt, Robert J Garrison, Daniel W Jones, Asoka Srinivasan, Toward resolution of cardiovascular health disparities in African Americans: design and methods of the Jackson Heart Study. Ethnicity & Disease. ,vol. 15, ,(2005)
Brian L. Browning, Zhaoxia Yu, Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies American Journal of Human Genetics. ,vol. 85, pp. 847- 861 ,(2009) , 10.1016/J.AJHG.2009.11.004
Gary D. Friedman, Gary R. Cutter, Richard P. Donahue, Glenn H. Hughes, Stephen B. Hulley, David R. Jacobs, Kiang Liu, Peter J. Savage, Cardia: study design, recruitment, and some characteristics of the examined subjects Journal of Clinical Epidemiology. ,vol. 41, pp. 1105- 1116 ,(1988) , 10.1016/0895-4356(88)90080-7
Michael J. Bamshad, Joshua M. Akey, , , , Jacob A. Tennessen, Abigail W. Bigham, Timothy D. O’Connor, Wenqing Fu, Eimear E. Kenny, Simon Gravel, Sean McGee, Ron Do, Xiaoming Liu, Goo Jun, Hyun Min Kang, Daniel Jordan, Suzanne M. Leal, Stacey Gabriel, Mark J. Rieder, Goncalo Abecasis, David Altshuler, Deborah A. Nickerson, Eric Boerwinkle, Shamil Sunyaev, Carlos D. Bustamante, Evolution and functional impact of rare coding variation from deep sequencing of human exomes Science. ,vol. 337, pp. 64- 69 ,(2012) , 10.1126/SCIENCE.1219240
Jonathan K. Pritchard, Molly Przeworski, Linkage Disequilibrium in Humans: Models and Data American Journal of Human Genetics. ,vol. 69, pp. 1- 14 ,(2001) , 10.1086/321275
Paul L Auer, Jill M Johnsen, Andrew D Johnson, Benjamin A Logsdon, Leslie A Lange, Michael A Nalls, Guosheng Zhang, Nora Franceschini, Keolu Fox, Ethan M Lange, Stephen S Rich, Christopher J O’Donnell, Rebecca D Jackson, Robert B Wallace, Zhao Chen, Timothy A Graubert, James G Wilson, Hua Tang, Guillaume Lettre, Alex P Reiner, Santhi K Ganesh, Yun Li, None, Imputation of Exome Sequence Variants into Population- Based Samples and Blood-Cell-Trait-Associated Loci in African Americans: NHLBI GO Exome Sequencing Project American Journal of Human Genetics. ,vol. 91, pp. 794- 808 ,(2012) , 10.1016/J.AJHG.2012.08.031
Ian J. Barnett, Seunggeun Lee, Xihong Lin, Detecting Rare Variant Effects Using Extreme Phenotype Sampling in Sequencing Association Studies Genetic Epidemiology. ,vol. 37, pp. 142- 151 ,(2013) , 10.1002/GEPI.21699
G. V. Kryukov, A. Shpunt, J. A. Stamatoyannopoulos, S. R. Sunyaev, Power of deep, all-exon resequencing for discovery of human trait genes. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 106, pp. 3871- 3876 ,(2009) , 10.1073/PNAS.0812824106
Carles Muntaner, F.Javier Nieto, Lawton Cooper, John Meyer, Moyses Szklo, Herman A. Tyroler, Work organization and atherosclerosis: Findings from the ARIC study American Journal of Preventive Medicine. ,vol. 14, pp. 9- 18 ,(1998) , 10.1016/S0749-3797(97)00018-4
Alexander P Reiner, Guillaume Lettre, Michael A Nalls, Santhi K Ganesh, Rasika Mathias, Melissa A Austin, Eric Dean, Sampath Arepalli, Angela Britton, Zhao Chen, David Couper, J David Curb, Charles B Eaton, Myriam Fornage, Struan FA Grant, Tamara B Harris, Dena Hernandez, Naoyuki Kamatini, Brendan J Keating, Michiaki Kubo, Andrea LaCroix, Leslie A Lange, Simin Liu, Kurt Lohman, Yan Meng, Emile R Mohler III, Solomon Musani, Yusuke Nakamura, Christopher J O'Donnell, Yukinori Okada, Cameron D Palmer, George J Papanicolaou, Kushang V Patel, Andrew B Singleton, Atsushi Takahashi, Hua Tang, Herman A Taylor Jr, Kent Taylor, Cynthia Thomson, Lisa R Yanek, Lingyao Yang, Elad Ziv, Alan B Zonderman, Aaron R Folsom, Michele K Evans, Yongmei Liu, Diane M Becker, Beverly M Snively, James G Wilson, None, Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT) PLOS Genetics. ,vol. 7, ,(2011) , 10.1371/JOURNAL.PGEN.1002108