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.
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.
Chi
Peter B
PB
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Duggal
Priya
P
Kao
W H Linda
WH
Mathias
Rasika A
RA
Grant
Audrey V
AV
Stockton
Maria L
ML
Garcia
Joe G N
JG
Ingersoll
Roxann G
RG
Scott
Alan F
AF
Beaty
Terri H
TH
Barnes
Kathleen C
KC
Fallin
M Daniele
MD
D001249:Asthma / Q000235:genetics*; D001460:Barbados; D044383:Black People / Q000235:genetics*; D002881:Chromosomes, Human, Pair 12 / Q000235:genetics*; D006801:Humans; D007073:Immunoglobulin E / Q000097:blood*; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
D007073:Immunoglobulin E