Haploview: analysis and visualization of LD and haplotype maps

被引:12633
作者
Barrett, JC
Fry, B
Maller, J
Daly, MJ
机构
[1] Whitehead Inst Biomed Res, Cambridge, MA 02142 USA
[2] MIT, Media Lab, Cambridge, MA 02139 USA
[3] Harvard Univ, Broad Inst, Cambridge, MA 02138 USA
[4] MIT, Broad Inst, Cambridge, MA 02139 USA
关键词
D O I
10.1093/bioinformatics/bth457
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface.
引用
收藏
页码:263 / 265
页数:3
相关论文
共 10 条
[1]   High-resolution haplotype structure in the human genome [J].
Daly, MJ ;
Rioux, JD ;
Schaffner, SE ;
Hudson, TJ ;
Lander, ES .
NATURE GENETICS, 2001, 29 (02) :229-232
[2]   The structure of haplotype blocks in the human genome [J].
Gabriel, SB ;
Schaffner, SF ;
Nguyen, H ;
Moore, JM ;
Roy, J ;
Blumenstiel, B ;
Higgins, J ;
DeFelice, M ;
Lochner, A ;
Faggart, M ;
Liu-Cordero, SN ;
Rotimi, C ;
Adeyemo, A ;
Cooper, R ;
Ward, R ;
Lander, ES ;
Daly, MJ ;
Altshuler, D .
SCIENCE, 2002, 296 (5576) :2225-2229
[3]   Haplotype-based identification of a microsomal transfer protein marker associated with the human lifespan [J].
Geesaman, BJ ;
Benson, E ;
Brewster, SJ ;
Kunkel, LM ;
Blanché, H ;
Thomas, G ;
Perls, TT ;
Daly, MJ ;
Puca, AA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (24) :14115-14120
[4]   The International HapMap Project [J].
Gibbs, RA ;
Belmont, JW ;
Hardenbol, P ;
Willis, TD ;
Yu, FL ;
Yang, HM ;
Ch'ang, LY ;
Huang, W ;
Liu, B ;
Shen, Y ;
Tam, PKH ;
Tsui, LC ;
Waye, MMY ;
Wong, JTF ;
Zeng, CQ ;
Zhang, QR ;
Chee, MS ;
Galver, LM ;
Kruglyak, S ;
Murray, SS ;
Oliphant, AR ;
Montpetit, A ;
Hudson, TJ ;
Chagnon, F ;
Ferretti, V ;
Leboeuf, M ;
Phillips, MS ;
Verner, A ;
Kwok, PY ;
Duan, SH ;
Lind, DL ;
Miller, RD ;
Rice, JP ;
Saccone, NL ;
Taillon-Miller, P ;
Xiao, M ;
Nakamura, Y ;
Sekine, A ;
Sorimachi, K ;
Tanaka, T ;
Tanaka, Y ;
Tsunoda, T ;
Yoshino, E ;
Bentley, DR ;
Deloukas, P ;
Hunt, S ;
Powell, D ;
Altshuler, D ;
Gabriel, SB ;
Qiu, RZ .
NATURE, 2003, 426 (6968) :789-796
[5]   The fine-scale structure of recombination rate variation in the human genome [J].
McVean, GAT ;
Myers, SR ;
Hunt, S ;
Deloukas, P ;
Bentley, DR ;
Donnelly, P .
SCIENCE, 2004, 304 (5670) :581-584
[6]   Linkage disequilibrium in the human genome [J].
Reich, DE ;
Cargill, M ;
Bolk, S ;
Ireland, J ;
Sabeti, PC ;
Richter, DJ ;
Lavery, T ;
Kouyoumjian, R ;
Farhadian, SF ;
Ward, R ;
Lander, ES .
NATURE, 2001, 411 (6834) :199-204
[7]   Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease [J].
Rioux, JD ;
Daly, MJ ;
Silverberg, MS ;
Lindblad, K ;
Steinhart, H ;
Cohen, Z ;
Delmonte, T ;
Kocher, K ;
Miller, K ;
Guschwan, S ;
Kulbokas, EJ ;
O'Leary, S ;
Winchester, E ;
Dewar, K ;
Green, T ;
Stone, V ;
Chow, C ;
Cohen, A ;
Langelier, D ;
Lapointe, G ;
Gaudet, D ;
Faith, J ;
Branco, N ;
Bull, SB ;
McLeod, RS ;
Griffiths, AM ;
Bitton, A ;
Greenberg, GR ;
Lander, ES ;
Siminovitch, KA ;
Hudson, TJ .
NATURE GENETICS, 2001, 29 (02) :223-228
[8]   Genetic variation in DLG5 is associated with inflammatory bowel disease [J].
Stoll, M ;
Corneliussen, B ;
Costello, CM ;
Waetzig, GH ;
Mellgard, B ;
Koch, WA ;
Rosenstiel, P ;
Albrecht, M ;
Croucher, PJP ;
Seegert, D ;
Nikolaus, S ;
Hampe, J ;
Lengauer, T ;
Pierrou, S ;
Foelsch, UR ;
Mathew, CG ;
Lagerstrom-Fermer, M ;
Schreiber, S .
NATURE GENETICS, 2004, 36 (05) :476-480
[9]   Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness [J].
Van Eerdewegh, P ;
Little, RD ;
Dupuis, J ;
Del Mastro, RG ;
Falls, K ;
Simon, J ;
Torrey, D ;
Pandit, S ;
McKenny, J ;
Braunschweiger, K ;
Walsh, A ;
Liu, ZY ;
Hayward, B ;
Folz, C ;
Manning, SP ;
Bawa, A ;
Saracino, L ;
Thackston, M ;
Benchekroun, Y ;
Capparell, N ;
Wang, M ;
Adair, R ;
Feng, Y ;
Dubois, J ;
FitzGerald, MG ;
Huang, H ;
Gibson, R ;
Allen, KM ;
Pedan, A ;
Danzig, MR ;
Umland, SP ;
Egan, RW ;
Cuss, FM ;
Rorke, S ;
Clough, JB ;
Holloway, JW ;
Holgate, ST ;
Keith, TP .
NATURE, 2002, 418 (6896) :426-430
[10]   Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation [J].
Wang, N ;
Akey, JM ;
Zhang, K ;
Chakraborty, R ;
Jin, L .
AMERICAN JOURNAL OF HUMAN GENETICS, 2002, 71 (05) :1227-1234