Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium

Priya Duggal, Elizabeth M. Gillanders, Rasika A. Mathias, Grace P. Ibay, Alison P. Klein, Agnes B. Baffoe-Bonnie, Liang Ou, Ian P. Dusenberry, Ya Yu Tsai, Peter S. Chines, Betty Q. Doan, Joan E. Bailey-Wilson

Research output: Contribution to journalArticlepeer-review

Abstract

We compared seven different tagging single-nucleotide polymorphism (SNP) programs in 10 regions with varied amounts of linkage disequilibrium (LD) and physical distance. We used the Collaborative Studies on the Genetics of Alcoholism dataset, part of the Genetic Analysis Workshop 14. We show that in regions with moderate to strong LD these programs are relatively consistent, despite different parameters and methods. In addition, we compared the selected SNPs in a multipoint linkage analysis for one region with strong LD. As the number of selected SNPs increased, the LOD score, mean information content, and type I error also increased.

Original languageEnglish (US)
Article numberS73
JournalBMC genetics
Volume6
Issue numberSUPPL.1
DOIs
StatePublished - Dec 30 2005
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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