PERMORY-MPI: a program for high-speed parallel permutation testing in genome-wide association studies

被引：12

作者：

Steiss, Volker ^{[1
,2
]}

Letschert, Thomas ^{[2
]}

Schaefer, Helmut ^{[1
]}

Pahl, Roman ^{[1
]}

机构：

[1] Univ Marburg, Inst Med Biometry & Epidemiol, D-35037 Marburg, Germany

[2] Tech Hsch Mittelhessen, Inst Software Architecture, D-35390 Giessen, Germany

来源：

BIOINFORMATICS | 2012年 / 28卷 / 08期

关键词：

GENETIC ASSOCIATION; MULTIPLE;

D O I：

10.1093/bioinformatics/bts086

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

PERMORY is software for accelerated permutation testing of genome-wide association studies (GWAS). We have parallelized PERMORY using the Message-Passing Interface resulting in a nearly linear speedup. Furthermore, we added accelerated analysis of GWAS using quantitative phenotypes, and an accurate estimation of the effective number of independent

引用

页码：1168 / 1169

页数：2

共 12 条

[1] PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies [J].

Browning, Brian L. .

BMC BIOINFORMATICS, 2008, 9 (1)

[2] Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls [J].

Burton, Paul R. ;

Clayton, David G. ;

Cardon, Lon R. ;

Craddock, Nick ;

Deloukas, Panos ;

Duncanson, Audrey ;

Kwiatkowski, Dominic P. ;

McCarthy, Mark I. ;

Ouwehand, Willem H. ;

Samani, Nilesh J. ;

Todd, John A. ;

Donnelly, Peter ;

Barrett, Jeffrey C. ;

Davison, Dan ;

Easton, Doug ;

Evans, David ;

Leung, Hin-Tak ;

Marchini, Jonathan L. ;

Morris, Andrew P. ;

Spencer, Chris C. A. ;

Tobin, Martin D. ;

Attwood, Antony P. ;

Boorman, James P. ;

Cant, Barbara ;

Everson, Ursula ;

Hussey, Judith M. ;

Jolley, Jennifer D. ;

Knight, Alexandra S. ;

Koch, Kerstin ;

Meech, Elizabeth ;

Nutland, Sarah ;

Prowse, Christopher V. ;

Stevens, Helen E. ;

Taylor, Niall C. ;

Walters, Graham R. ;

Walker, Neil M. ;

Watkins, Nicholas A. ;

Winzer, Thilo ;

Jones, Richard W. ;

McArdle, Wendy L. ;

Ring, Susan M. ;

Strachan, David P. ;

Pembrey, Marcus ;

Breen, Gerome ;

St Clair, David ;

Caesar, Sian ;

Gordon-Smith, Katherine ;

Jones, Lisa ;

Fraser, Christine ;

Green, Elain K. .

NATURE, 2007, 447 (7145) :661-678

[3] A simple correction for multiple comparisons in interval mapping genome scans [J].

Cheverud, JM .

HEREDITY, 2001, 87 (1) :52-58

[4] A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms [J].

Gao, Xiaoyi ;

Stamier, Joshua ;

Martin, Eden R. .

GENETIC EPIDEMIOLOGY, 2008, 32 (04) :361-369

[5] Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers [J].

Han, Buhm ;

Kang, Hyun Min ;

Eskin, Eleazar .

PLOS GENETICS, 2009, 5 (04)

[6] Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix [J].

Li, J ;

Ji, L .

HEREDITY, 2005, 95 (03) :221-227

[7] Evaluating statistical significance in two-stage genomewide association studies [J].

Lin, DY .

AMERICAN JOURNAL OF HUMAN GENETICS, 2006, 78 (03) :505-509

[8]

Message Passing Interface Forum, 2009, MPI MESS PASS INT ST

[9] PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing [J].

Pahl, Roman ;

Schaefer, Helmut .

BIOINFORMATICS, 2010, 26 (17) :2093-2100

[10] PLINK: A tool set for whole-genome association and population-based linkage analyses [J].

Purcell, Shaun ;

Neale, Benjamin ;

Todd-Brown, Kathe ;

Thomas, Lori ;

Ferreira, Manuel A. R. ;

Bender, David ;

Maller, Julian ;

Sklar, Pamela ;

de Bakker, Paul I. W. ;

Daly, Mark J. ;

Sham, Pak C. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (03) :559-575

← 1 2 →