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

Open Access Proceedings

Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses

Ayse Ulgen12* and Wentian Li3

Author Affiliations

1 G.H. Sergievsky Center, Columbia University, New York, NY, 10032, USA

2 EMI-0006 INSERM-Université d'Evry, Méthodologie Statistique et Epidémiologie Génétique des Maladies Mulitfactorielles, Evry, 91034, France

3 The Robert S Boas Center for Genomics and Human Genetics, North Shore LIJ, Institute for Medical Research, Manhasset, NY, 11030, USA

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BMC Genetics 2005, 6(Suppl 1):S13  doi:10.1186/1471-2156-6-S1-S13

Published: 30 December 2005


We compared linkage analysis results for an alcoholism trait, ALDX1 (DSM-III-R and Feigner criteria) using a nonparametric linkage analysis method, which takes into account allele sharing among several affected persons, for both microsatellite and single-nucleotide polymorphism (SNP) markers (Affymetrix and Illumina) in the Collaborative Study on the Genetics of Alcoholism (COGA) dataset provided to participants at the Genetic Analysis Workshop 14 (GAW14). The two sets of linkage results from the dense Affymetrix SNP markers and less densely spaced Illumina SNP markers are very similar. The linkage analysis results from microsatellite and SNP markers are generally similar, but the match is not perfect. Strong linkage peaks were found on chromosome 7 in three sets of linkage analyses using both SNP and microsatellite marker data. We also observed that for SNP markers, using the given genetic map and using the map by converting 1 megabase pair (1 Mb) to 1 centimorgan (cM), did not change the linkage results. We recommend the use of the 1 Mb-to-1 cM converted map in a first round of linkage analysis with SNP markers in which map integration is an issue.