Genetic association analysis with FAMHAP: a major program update

被引：60

作者：

Herold, Christine ^{[1
]}

Becker, Tim ^{[1
]}

机构：

[1] Univ Bonn, Inst Med Biometry Informat & Epidemiol, D-53105 Bonn, Germany

来源：

BIOINFORMATICS | 2009年 / 25卷 / 01期

关键词：

HAPLOTYPE ANALYSIS; FREQUENCIES; CONTEXT;

D O I：

10.1093/bioinformatics/btn581

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

FAMHAP is an established software for haplotype association analysis of nuclear families. We have released a major update that comprises various new features for case-control data. Furthermore, we provide an additional program runFamhap that allows users to start the same method repeatedly for varying sets of genetic markers. In addition, a platform-independent graphical user interface (GUI) was developed to simplify the usage of both FAMHAP and runFamhap. The runFamhap program greatly facilitates the application of FAMHAP to genome-wide association studies (GWAS) and supports flexible genome-wide haplotype analysis. As an example, we describe application to HapMap data.

引用

页码：134 / 136

页数：3

共 11 条

[1] TESTS FOR LINEAR TRENDS IN PROPORTIONS AND FREQUENCIES [J].

ARMITAGE, P .

BIOMETRICS, 1955, 11 (03) :375-386

[2] Multiple testing in the context of haplotype analysis revisited:: Application to case-control data [J].

Becker, T ;

Cichon, S ;

Jönson, E ;

Knapp, M .

ANNALS OF HUMAN GENETICS, 2005, 69 :747-756

[3] A powerful strategy to account for multiple testing in the context of haplotype analysis [J].

Becker, T ;

Knapp, M .

AMERICAN JOURNAL OF HUMAN GENETICS, 2004, 75 (04) :561-570

[4] Maximum-likelihood estimation of haplotype frequencies in nuclear families [J].

Becker, T ;

Knapp, M .

GENETIC EPIDEMIOLOGY, 2004, 27 (01) :21-32

[5] The role of haplotypes in candidate gene studies [J].

Clark, AG .

GENETIC EPIDEMIOLOGY, 2004, 27 (04) :321-333

[6] A second generation human haplotype map of over 3.1 million SNPs [J].

Frazer, Kelly A. ;

Ballinger, Dennis G. ;

Cox, David R. ;

Hinds, David A. ;

Stuve, Laura L. ;

Gibbs, Richard A. ;

Belmont, John W. ;

Boudreau, Andrew ;

Hardenbol, Paul ;

Leal, Suzanne M. ;

Pasternak, Shiran ;

Wheeler, David A. ;

Willis, Thomas D. ;

Yu, Fuli ;

Yang, Huanming ;

Zeng, Changqing ;

Gao, Yang ;

Hu, Haoran ;

Hu, Weitao ;

Li, Chaohua ;

Lin, Wei ;

Liu, Siqi ;

Pan, Hao ;

Tang, Xiaoli ;

Wang, Jian ;

Wang, Wei ;

Yu, Jun ;

Zhang, Bo ;

Zhang, Qingrun ;

Zhao, Hongbin ;

Zhao, Hui ;

Zhou, Jun ;

Gabriel, Stacey B. ;

Barry, Rachel ;

Blumenstiel, Brendan ;

Camargo, Amy ;

Defelice, Matthew ;

Faggart, Maura ;

Goyette, Mary ;

Gupta, Supriya ;

Moore, Jamie ;

Nguyen, Huy ;

Onofrio, Robert C. ;

Parkin, Melissa ;

Roy, Jessica ;

Stahl, Erich ;

Winchester, Ellen ;

Ziaugra, Liuda ;

Altshuler, David ;

Shen, Yan .

NATURE, 2007, 449 (7164) :851-U3

[7]

HILLMER AM, 2008, NAT GENET IN PRESS

[8] The new genomics: Global views of biology [J].

Lander, ES .

SCIENCE, 1996, 274 (5287) :536-539

[9] Principal components analysis corrects for stratification in genome-wide association studies [J].

Price, Alkes L. ;

Patterson, Nick J. ;

Plenge, Robert M. ;

Weinblatt, Michael E. ;

Shadick, Nancy A. ;

Reich, David .

NATURE GENETICS, 2006, 38 (08) :904-909

[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

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