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

Open Access Proceedings

Characteristics of replicated single-nucleotide polymorphism genotypes from COGA: Affymetrix and Center for Inherited Disease Research

Nathan L Tintle1*, Kwangmi Ahn1, Nancy Role Mendell1, Derek Gordon2 and Stephen J Finch1

Author Affiliations

1 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794 USA

2 Laboratory of Statistical Genetics, Rockefeller University, New York, New York, 10021 USA

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BMC Genetics 2005, 6(Suppl 1):S154  doi:10.1186/1471-2156-6-S1-S154

Published: 30 December 2005

Abstract

Genetic Analysis Workshop 14 provided re-genotyped single-nucleotide polymorphism (SNP) data. Specifically, both Center for Inherited Disease Research (CIDR) and Affymetrix genotyped the same 11,560 SNPs from the Affymetrix GeneChip Mapping 10K Array marker set on the same 184 individuals from the Collaborative Study on the Genetics of Alcoholism database. While the inconsistency rate between CIDR and Affymetrix (two different genotypes for the same subject) was low (0.2%), the non-replication rate (two different genotypes for the same subject or one identified genotype and one missing genotype) was substantial (9.5%). The missing data could be from no-call regions, which is inconsistent with recent recommendations about the use of no-call regions in association tests. In addition, no-call regions would suggest that the actual inconsistency rate is higher than reported. A high inconsistency rate has significant impact on power in related hypothesis tests. In addition, the data are consistent with assumptions made in a recently proposed likelihood ratio test of association for re-genotyped data.