Effectiveness of in silico tagSNP selection methods: virtual analysis of the genotypes of pharmacogenetic genes.
BACKGROUND
SNP tagging has been recently introduced, and the use of this strategy reduces the dimension of disease association studies and eventually saves on genotyping costs. There is no single set of tagging SNPs (tagSNPs) that will satisfy every association study design; thus, many different methods have been introduced. We evaluated various tagSNP selection methods using known haplotype data of pharmacogenetic genes. We also compared the selected tagSNPs among different ethnic groups.


METHODS
We collected genotype data for the NAT2 and CYP2D6 genes from the previously published literature where the linkage phase was resolved directly through molecular haplotyping. Three computational tagSNP selection methods (ldSelect, Tagger and TagIT software) were evaluated with these data sets.


RESULTS
Tagging effectiveness and efficiency were variable in all three tagSNP selection methods. No tagSNP sets were identical among the different ethnic groups. The haplotype r(2)-based method was more effective in determining genotype-phenotype correlation than the other methods employed.


CONCLUSIONS
All of the three computational tagSNP selection methods showed acceptable efficiency and effectiveness. The selected tagSNPs were different from each other among the different ethnic groups.
Nam
Myung-Hyun
MH
College of Medicine, Korea University, Department of Laboratory Medicine, Seoul 136-705, South Korea. yuret@dreamwiz.com
Won
Hong-Hee
HH
Lee
Kyung-A
KA
Kim
Jong-Won
JW
D000465:Algorithms; D001191:Arylamine N-Acetyltransferase / Q000235:genetics; D019389:Cytochrome P-450 CYP2D6 / Q000235:genetics; D020224:Expressed Sequence Tags; D005838:Genotype; D006801:Humans; D010597:Pharmacogenetics / Q000379:methods*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012984:Software
D019389:Cytochrome P-450 CYP2D6; D001191:Arylamine N-Acetyltransferase; C478900:NAT2 protein, human