Model-based inference of haplotype block variation

被引:44
作者
Greenspan, G [1 ]
Geiger, D [1 ]
机构
[1] Technion Israel Inst Technol, Dept Comp Sci, IL-32000 Haifa, Israel
关键词
haplotype blocks; haplotype resolution; Bayesian networks; recombination hotspots; linkage disequilibrium mapping;
D O I
10.1089/1066527041410300
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The haplotype block structure of SNP variation in human DNA has been demonstrated by several recent studies. The presence of haplotype blocks can be used to dramatically increase the statistical power of genetic mapping. Several criteria have already been proposed for identifying these blocks, all of which require haplotypes as input. We propose a comprehensive statistical model of haplotype block variation and show how the parameters of this model can be learned from haplotypes and/or unphased genotype data. Using real-world SNP data, we demonstrate that our approach can be used to resolve genotypes into their constituent haplotypes with greater accuracy than previously known methods.
引用
收藏
页码:495 / 506
页数:12
相关论文
共 35 条
[1]   Patterns of linkage disequilibrium in the human genome [J].
Ardlie, KG ;
Kruglyak, L ;
Seielstad, M .
NATURE REVIEWS GENETICS, 2002, 3 (04) :299-309
[2]  
Bafna V., 2003, P 7 INT C COMP MOL B, P19
[3]  
CLARK AG, 1990, MOL BIOL EVOL, V7, P111
[4]   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
[5]  
Dechter R, 1996, UNCERTAINTY IN ARTIFICIAL INTELLIGENCE, P211
[6]   Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies [J].
Douglas, JA ;
Boehnke, M ;
Gillanders, E ;
Trent, JA ;
Gruber, SB .
NATURE GENETICS, 2001, 28 (04) :361-364
[7]  
EXCOFFIER L, 1995, MOL BIOL EVOL, V12, P921
[8]   Apolipoprotein E variation at the sequence haplotype level:: Implications for the origin and maintenance of a major human polymorphism [J].
Fullerton, SM ;
Clark, AG ;
Weiss, KM ;
Nickerson, DA ;
Taylor, SL ;
Stengård, JH ;
Salomaa, V ;
Vartiainen, E ;
Perola, M ;
Boerwinkle, E ;
Sing, CF .
AMERICAN JOURNAL OF HUMAN GENETICS, 2000, 67 (04) :881-900
[9]   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
[10]   Islands of linkage disequilibrium [J].
Goldstein, DB .
NATURE GENETICS, 2001, 29 (02) :109-111