Effectiveness of in silico tagSNP selection methods: Virtual analysis of the genotypes of pharmacogenetic genes

Myung Hyun Nam, Hong Hee Won, Kyung A. Lee, Jong Won Kim

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Introduction: 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 (IdSelect, 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 r2-based method was more effective in determining genotype-phenotype correlation than the other methods employed. Conclusion: 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.

Original languageEnglish
Pages (from-to)1347-1357
Number of pages11
JournalPharmacogenomics
Volume8
Issue number10
DOIs
Publication statusPublished - 2007 Oct 1

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Computer Simulation
Genotype
Genes
Single Nucleotide Polymorphism
Ethnic Groups
Haplotypes
Cytochrome P-450 CYP2D6
Pharmacogenomic Testing
Pharmacogenetics
Genetic Association Studies
Software
Costs and Cost Analysis

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Genetics
  • Pharmacology

Cite this

Nam, Myung Hyun ; Won, Hong Hee ; Lee, Kyung A. ; Kim, Jong Won. / Effectiveness of in silico tagSNP selection methods : Virtual analysis of the genotypes of pharmacogenetic genes. In: Pharmacogenomics. 2007 ; Vol. 8, No. 10. pp. 1347-1357.
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Effectiveness of in silico tagSNP selection methods : Virtual analysis of the genotypes of pharmacogenetic genes. / Nam, Myung Hyun; Won, Hong Hee; Lee, Kyung A.; Kim, Jong Won.

In: Pharmacogenomics, Vol. 8, No. 10, 01.10.2007, p. 1347-1357.

Research output: Contribution to journalArticle

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