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

Open Access Proceedings

A comparison in association and linkage genome-wide scans for alcoholism susceptibility genes using single-nucleotide polymorphisms

Yen-Feng Chiu1*, Su-Yun Liu1 and Ya-Yu Tsai2

Author Affiliations

1 Division of Biostatistics and Bioinformatics, National Health Research Institutes, Miaoli, Taiwan, ROC

2 Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA

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BMC Genetics 2005, 6(Suppl 1):S89  doi:10.1186/1471-2156-6-S1-S89

Published: 30 December 2005

Abstract

We conducted genome-wide linkage scans using both microsatellite and single-nucleotide polymorphism (SNP) markers. Regions showing the strongest evidence of linkage to alcoholism susceptibility genes were identified. Haplotype analyses using a sliding-window approach for SNPs in these regions were performed. In addition, we performed a genome-wide association scan using SNP data. SNPs in these regions with evidence of association (P ≦ 0.0001) were identified. We found that the general patterns for nonparametric linkage (NPL) scores from SNP and microsatellite genome scans are fairly consistent; however, the peaks of the NPL scores are mostly higher in the SNP-based scan than those using microsatellite markers, which might be located at different regions. Furthermore, SNPs identified from linkage screens were not so strongly associated with alcoholism (the most significant SNP had a p-value of 0.030) as those identified from association genomic screening (the most significant SNP had a p-value of 2.0 × 10-8).