minimac2: faster genotype imputation

被引：407

作者：

Fuchsberger, Christian ^{[1
]}

Abecasis, Goncalo R. ^{[1
]}

Hinds, David A. ^{[2
]}

机构：

[1] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA

[2] 23andMe Inc, Mountain View, CA USA

来源：

BIOINFORMATICS | 2015年 / 31卷 / 05期

基金：

美国国家卫生研究院;

关键词：

GENOME-WIDE ASSOCIATION;

D O I：

10.1093/bioinformatics/btu704

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Genotype imputation is a key step in the analysis of genome-wide association studies. Upcoming very large reference panels, such as those from The 1000 Genomes Project and the Haplotype Consortium, will improve imputation quality of rare and less common variants, but will also increase the computational burden. Here, we demonstrate how the application of software engineering techniques can help to keep imputation broadly accessible. Overall, these improvements speed up imputation by an order of magnitude compared with our previous implementation.

引用

页码：782 / 784

页数：3

共 14 条

[1] An integrated map of genetic variation from 1,092 human genomes [J].

Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Schmidt, Jeanette P. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Dinh, Huyen ;

Kovar, Christie ;

Lee, Sandra ;

Lewis, Lora ;

Muzny, Donna ;

Reid, Jeff ;

Wang, Min ;

Wang, Jun ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Li, Zhuo ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Su, Zhe ;

Tai, Shuaishuai ;

Tang, Meifang .

NATURE, 2012, 491 (7422) :56-65

[2] A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals [J].

Browning, Brian L. ;

Browning, Sharon R. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 84 (02) :210-223

[3]

COTTINGHAM RW, 1993, AM J HUM GENET, V53, P252

[4] Whole-genome sequence variation, population structure and demographic history of the Dutch population [J].

Francioli, Laurent C. ;

Menelaou, Andronild ;

Pulit, Sara L. ;

Van Dijk, Freerk ;

Palamara, Pier Francesco ;

Elbers, Clara C. ;

Neerincx, Pieter B. T. ;

Ye, Kai ;

Guryev, Victor ;

Kloosterman, Wigard P. ;

Deelen, Patrick ;

Abdellaoui, Abdel ;

Van Leeuwen, Elisabeth M. ;

Van Oven, Mannis ;

Vermaat, Martijn ;

Li, Mingkun ;

Laros, Jeroen F. J. ;

Karssen, Lennart C. ;

Kanterakis, Alexandros ;

Amin, Najaf ;

Hottenga, Jouke Jan ;

Lameijer, Eric-Wubbo ;

Kattenberg, Mathijs ;

Dijkstra, Martijn ;

Byelas, Heorhiy ;

Van Settenl, Jessica ;

Van Schaik, Barbera D. C. ;

Bot, Jan ;

Nijman, Isaac J. ;

Renkens, Ivo ;

Marscha, Tobias ;

Schonhuth, Alexander ;

Hehir-Kwa, Jayne Y. ;

Handsaker, Robert E. ;

Polak, Paz ;

Sohail, Mashaal ;

Vuzman, Dana ;

Hormozdiari, Fereydoun ;

Van Enckevort, David ;

Mei, Hailiang ;

Koval, Vyacheslav ;

Moed, Ma-Tthijs H. ;

Van der Velde, K. Joeri ;

Rivadeneira, Fernando ;

Estrada, Karol ;

Medina-Gomez, Carolina ;

Isaacs, Aaron ;

McCarroll, Steven A. ;

Beekrnan, Marian ;

De Craen, Anton J. M. .

NATURE GENETICS, 2014, 46 (08) :818-825

[5] Allegro, a new computer program for multipoint linkage analysis [J].

Gudbjartsson, DF ;

Jonasson, K ;

Frigge, ML ;

Kong, A .

NATURE GENETICS, 2000, 25 (01) :12-13

[6] Fast and accurate genotype imputation in genome-wide association studies through pre-phasing [J].

Howie, Bryan ;

Fuchsberger, Christian ;

Stephens, Matthew ;

Marchini, Jonathan ;

Abecasis, Goncalo R. .

NATURE GENETICS, 2012, 44 (08) :955-+

[7] Generating samples under a Wright-Fisher neutral model of genetic variation [J].

Hudson, RR .

BIOINFORMATICS, 2002, 18 (02) :337-338

[8] Genotype Imputation [J].

Li, Yun ;

Willer, Cristen ;

Sanna, Serena ;

Abecasis, Goncalo .

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2009, 10 :387-406

[9] A new multipoint method for genome-wide association studies by imputation of genotypes [J].

Marchini, Jonathan ;

Howie, Bryan ;

Myers, Simon ;

McVean, Gil ;

Donnelly, Peter .

NATURE GENETICS, 2007, 39 (07) :906-913

[10] Whole-genome sequence-based analysis of high-density lipoprotein cholesterol [J].

Morrison, Alanna C. ;

Voorman, Arend ;

Johnson, Andrew D. ;

Liu, Xiaoming ;

Yu, Jin ;

Li, Alexander ;

Muzny, Donna ;

Yu, Fuli ;

Rice, Kenneth ;

Zhu, Chengsong ;

Bis, Joshua ;

Heiss, Gerardo ;

O'Donnell, Christopher J. ;

Psaty, Bruce M. ;

Cupples, L. Adrienne ;

Gibbs, Richard ;

Boerwinkle, Eric .

NATURE GENETICS, 2013, 45 (08) :899-U29

← 1 2 →