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Comparison of SNP tagging methods using empirical data: association study of 713 SNPs on chromosome 12q14.3–12q24.21 for asthma and total serum IgE in an African Caribbean population
Author(s) -
Chi Peter B.,
Duggal Priya,
Kao W.H. Linda,
Mathias Rasika A.,
Grant Audrey V.,
Stockton Maria L.,
Garcia Joe G.N.,
Ingersoll Roxann G.,
Scott Alan F.,
Beaty Terri H.,
Barnes Kathleen C.,
Fallin M. Daniele
Publication year - 2006
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.20172
Subject(s) - single nucleotide polymorphism , snp , genetics , proband , biology , genetic association , asthma , genome wide association study , chromosome , population , tag snp , genotype , medicine , gene , immunology , mutation , environmental health
Few comparison studies have been performed on single nucleotide polymorphism (SNP) tagging methods to examine their consistency and effectiveness in terms of inferences about association with disease. We applied several SNP tagging methods to SNPs on chromosome 12q ( n =713) and compared the utility of these methods to detect association for asthma and serum IgE levels among a sample of African Caribbean families from Barbados selected through asthmatic probands. We found that a high level of information regarding association is retained in Clayton's htSNP, Stram's TagSNP, and de Bakker's Tagger. We also found a high degree of consistency between TagSNP and Tagger. Using this set of 713 SNPs on chromosome 12q, our study provides insight towards analytic strategies for future studies of complex traits. Genet. Epidemiol. 2006. © 2006 Wiley‐Liss, Inc.