title: Effectiveness of in silico tagSNP selection methods: virtual analysis of the genotypes of pharmacogenetic genes.
abstract: 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.
authors.affiliation: College of Medicine, Korea University, Department of Laboratory Medicine, Seoul 136-705, South Korea. yuret@dreamwiz.com
authors.forename: Myung-Hyun
authors.initials: MH
authors.lastname: Nam
authors.forename: Hong-Hee
authors.initials: HH
authors.lastname: Won
authors.forename: Kyung-A
authors.initials: KA
authors.lastname: Lee
authors.forename: Jong-Won
authors.initials: JW
authors.lastname: Kim
mesh_terms: 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
chemical_list: D019389:Cytochrome P-450 CYP2D6; D001191:Arylamine N-Acetyltransferase; C478900:NAT2 protein, human