Methods for the selection of tagging SNPs: A comparison of tagging efficiency and performance

Keyue Ding, Iftikhar J. Kullo

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


There is great interest in the use of tagging single nucleotide polymorphisms (tSNPs) to facilitate association studies of complex diseases. This is based on the premise that a minimum set of tSNPs may be sufficient to capture most of the variation in certain regions of the human genome. Several methods have been described to select tSNPs, based on either haplotype-block structure or independent of the underlying block structure. In this paper, we compare eight methods for choosing tSNPs in 10 representative resequenced candidate genes (a total of 194.2kb) with different levels of linkage disequilibrium (LD) in a sample of European-Americans. We compared tagging efficiency (TE) and prediction accuracy of tSNPs identified by these methods, as a function of several factors, including LD level, minor allele frequency, and tagging criteria. We also assessed tagging consistency between each method. We found that tSNPs selected based on the methods Haplotype Diversity and Haplotype r2 provided the highest TE, whereas the prediction accuracy was comparable among different methods. Tagging consistency between different methods of tSNPs selection was poor. This work demonstrates that when tSNPs-based association studies are undertaken, the choice of method for selecting tSNPs requires careful consideration.

Original languageEnglish (US)
Pages (from-to)228-236
Number of pages9
JournalEuropean Journal of Human Genetics
Issue number2
StatePublished - Feb 2007

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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