Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome

被引：22

作者：

Lau, Winston

Kuo, Tai-Yue

Tapper, William

Cox, Simon

Collins, Andrew

机构：

[1] Southampton Gen Hosp, Human Genet Div, Southampton SO16 6YD, Hants, England

[2] Univ Southampton, Sch Engn Sci, Southampton Reg E Sci Ctr, Southampton SO17 1BJ, Hants, England

来源：

BIOINFORMATICS | 2007年 / 23卷 / 04期

关键词：

D O I：

10.1093/bioinformatics/btl615

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Linkage disequilibrium (LD) maps increase power and precision in association mapping, define optimal marker spacing and identify recombination hot-spots and regions influenced by natural selection. Phase II of HapMap provides similar to 2.8-fold more single nucleotide polymorphisms (SNPs) than phase I for constructing higher resolution maps. LDMAP-cluster, is a parallel program for rapid map construction in a Linux environment used here to construct genome-wide LD maps with > 8.2 million SNPs from the phase II data.

引用

页码：517 / 519

页数：3

共 8 条

[1] A haplotype map of the human genome [J].

Altshuler, D ;

Brooks, LD ;

Chakravarti, A ;

Collins, FS ;

Daly, MJ ;

Donnelly, P ;

Gibbs, RA ;

Belmont, JW ;

Boudreau, A ;

Leal, SM ;

Hardenbol, P ;

Pasternak, S ;

Wheeler, DA ;

Willis, TD ;

Yu, FL ;

Yang, HM ;

Zeng, CQ ;

Gao, Y ;

Hu, HR ;

Hu, WT ;

Li, CH ;

Lin, W ;

Liu, SQ ;

Pan, H ;

Tang, XL ;

Wang, J ;

Wang, W ;

Yu, J ;

Zhang, B ;

Zhang, QR ;

Zhao, HB ;

Zhao, H ;

Zhou, J ;

Gabriel, SB ;

Barry, R ;

Blumenstiel, B ;

Camargo, A ;

Defelice, M ;

Faggart, M ;

Goyette, M ;

Gupta, S ;

Moore, J ;

Nguyen, H ;

Onofrio, RC ;

Parkin, M ;

Roy, J ;

Stahl, E ;

Winchester, E ;

Ziaugra, L ;

Shen, Y .

NATURE, 2005, 437 (7063) :1299-1320

[2] The impact of SNP density on fine-scale patterns of linkage disequilibrium [J].

Ke, XY ;

Hunt, S ;

Tapper, W ;

Lawrence, R ;

Stavrides, G ;

Ghori, J ;

Whittaker, P ;

Collins, A ;

Morris, AP ;

Bentley, D ;

Cardon, LR ;

Deloukas, P .

HUMAN MOLECULAR GENETICS, 2004, 13 (06) :577-588

[3] A first-generation metric linkage disequilibrium map of bovine chromosome 6 [J].

Khatkar, Mehar S. ;

Collins, Andrew ;

Cavanagh, Julie A. L. ;

Hawken, Rachel J. ;

Hobbs, Matthew ;

Zenger, Kyall R. ;

Barris, Wes ;

McClintock, Alexander E. ;

Thomson, Peter C. ;

Nicholas, Frank W. ;

Raadsma, Herman W. .

GENETICS, 2006, 174 (01) :79-85

[4] The optimal measure of linkage disequilibrium reduces error in association mapping of affection status [J].

Maniatis, N ;

Morton, NE ;

Xu, CF ;

Hosking, LK ;

Collins, A .

HUMAN MOLECULAR GENETICS, 2005, 14 (01) :145-153

[5] The first linkage disequilibrium (LD) maps: Delineation of hot and cold blocks by diplotype analysis [J].

Maniatis, N ;

Collins, A ;

Xu, CF ;

McCarthy, LC ;

Hewett, DR ;

Tapper, W ;

Ennis, S ;

Ke, X ;

Morton, NE .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (04) :2228-2233

[6] Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies [J].

Service, S ;

DeYoung, J ;

Karayiorgou, M ;

Roos, JL ;

Pretorious, H ;

Bedoya, G ;

Ospina, J ;

Ruiz-Linares, A ;

Macedo, A ;

Palha, JA ;

Heutink, P ;

Aulchenko, Y ;

Oostra, B ;

van Duijn, C ;

Jarvelin, MR ;

Varilo, T ;

Peddle, L ;

Rahman, P ;

Piras, G ;

Monne, M ;

Murray, S ;

Galver, L ;

Peltonen, L ;

Sabatti, C ;

Collins, A ;

Freimer, N .

NATURE GENETICS, 2006, 38 (05) :556-560

[7] A map of the human genome in linkage disequilibrium units [J].

Tapper, W ;

Collins, A ;

Gibson, J ;

Maniatis, N ;

Ennis, S ;

Morton, NE .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (33) :11835-11839

[8] Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps [J].

Zhang, WH ;

Collins, A ;

Gibson, J ;

Tapper, WJ ;

Hunt, S ;

Deloukas, P ;

Bentley, DR ;

Morton, NE .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (52) :18075-18080

← 1 →