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

Peter B. Chi, Priya Duggal, W. H.Linda Kao, Rasika A. Mathias, Audrey V. Grant, Maria L. Stockton, Joe G.N. Garcia, Roxann G. Ingersoll, Alan F. Scott, Terri H. Beaty, Kathleen C. Barnes, M. Daniele Fallin

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)609-619
Number of pages11
JournalGenetic Epidemiology
Volume30
Issue number7
DOIs
StatePublished - Nov 2006
Externally publishedYes

Keywords

  • Association
  • FBAT
  • LD blocks
  • SNP tags

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

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