This article is part of the supplement: Genetic Analysis Workshop 14: Microsatellite and single-nucleotide polymorphism

Open Access Proceedings

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

Priya Duggal1*, Elizabeth M Gillanders1, Rasika A Mathias1, Grace P Ibay1, Alison P Klein1, Agnes B Baffoe-Bonnie2, Liang Ou2, Ian P Dusenberry1, Ya-Yu Tsai3, Peter S Chines4, Betty Q Doan1 and Joan E Bailey-Wilson1

Author Affiliations

1 Inherited Disease Research Branch, NHGRI/NIH, Baltimore, MD, USA

2 Fox Chase Cancer Center, Division of Population Science, Philadelphia, PA, USA

3 CIDR, Johns Hopkins Medical School, Baltimore, MD, USA

4 Genome Technology Branch, NHGRI/NIH, Bethesda, MD, USA

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BMC Genetics 2005, 6(Suppl 1):S73  doi:10.1186/1471-2156-6-S1-S73

Published: 30 December 2005


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.