Entropy-based SNP selection for genetic association studies

被引:61
作者
Hampe, J
Schreiber, S
Krawczak, M
机构
[1] Univ Kiel, Klin Allgemeine Innere Med, D-24105 Kiel, Germany
[2] Univ Kiel, Inst Med Informat & Stat, D-24105 Kiel, Germany
关键词
D O I
10.1007/s00439-003-1017-2
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Because of their abundance, density, and ease of practical use, single-nucleotide polymorphisms (SNPs) have become the major source of information for association gene mapping in humans. Sensible strategies for selecting practically useful SNPs are therefore required. Among the factors influencing the mapping utility of a given set of SNPs are (1) their individual diversity, (2) their haplotype structure in the population of interest, and (3) their physical distribution. We propose a strategy integrating these aspects into a single mapping utility measure, which is based upon Shannon entropy, and which maximizes the amount of information extracted from a genomic region under a Malecot model of linkage disequilibrium (LD) decay. The same utility measure has also been used to define a criterion guiding SNP discovery and rational decision-making about the continuation or termination of a mapping study. The proposed strategy performs consistently well in a data set comprising 549 German control individuals, genotyped for 136 SNPs from four genomic regions of different LD structure. Adoption of the method in practice is estimated to save up to 30% of genotyping load when compared with equidistant SNP localization or pair-wise LD minimization alone.
引用
收藏
页码:36 / 43
页数:8
相关论文
共 23 条
[11]   A NONORGANIC AND NONENZYMATIC EXTRACTION METHOD GIVES HIGHER YIELDS OF GENOMIC DNA FROM WHOLE-BLOOD SAMPLES THAN DO 9 OTHER METHODS TESTED [J].
LAHIRI, DK ;
BYE, S ;
NURNBERGER, JI ;
HODES, ME ;
CRISP, M .
JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS, 1992, 25 (04) :193-205
[12]   Efficiency of estimation of haplotype frequencies: Use of marker phenotypes of unrelated individuals versus counting of phase-known gametes [J].
McKeigue, PM .
AMERICAN JOURNAL OF HUMAN GENETICS, 2000, 67 (06) :1626-1627
[13]   The optimal measure of allelic association [J].
Morton, NE ;
Zhang, W ;
Taillon-Miller, P ;
Ennis, S ;
Kwok, PY ;
Collins, A .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (09) :5217-5221
[14]   Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21 [J].
Patil, N ;
Berno, AJ ;
Hinds, DA ;
Barrett, WA ;
Doshi, JM ;
Hacker, CR ;
Kautzer, CR ;
Lee, DH ;
Marjoribanks, C ;
McDonough, DP ;
Nguyen, BTN ;
Norris, MC ;
Sheehan, JB ;
Shen, NP ;
Stern, D ;
Stokowski, RP ;
Thomas, DJ ;
Trulson, MO ;
Vyas, KR ;
Frazer, KA ;
Fodor, SPA ;
Cox, DR .
SCIENCE, 2001, 294 (5547) :1719-1723
[15]   The allelic architecture of human disease genes: common disease - common variant ... or not? [J].
Pritchard, JK ;
Cox, NJ .
HUMAN MOLECULAR GENETICS, 2002, 11 (20) :2417-2423
[16]   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
[17]   The future of genetic studies of complex human diseases [J].
Risch, N ;
Merikangas, K .
SCIENCE, 1996, 273 (5281) :1516-1517
[18]   Detecting recent positive selection in the human genome from haplotype structure [J].
Sabeti, PC ;
Reich, DE ;
Higgins, JM ;
Levine, HZP ;
Richter, DJ ;
Schaffner, SF ;
Gabriel, SB ;
Platko, JV ;
Patterson, NJ ;
McDonald, GJ ;
Ackerman, HC ;
Campbell, SJ ;
Altshuler, D ;
Cooper, R ;
Kwiatkowski, D ;
Ward, R ;
Lander, ES .
NATURE, 2002, 419 (6909) :832-837
[19]   Relative efficiency of ambiguous vs. directly measured haplotype frequencies [J].
Schaid, DJ .
GENETIC EPIDEMIOLOGY, 2002, 23 (04) :426-443
[20]   A MATHEMATICAL THEORY OF COMMUNICATION [J].
SHANNON, CE .
BELL SYSTEM TECHNICAL JOURNAL, 1948, 27 (03) :379-423