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This article is part of the supplement: Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci

Open Access Proceedings

Multilocus analysis of GAW15 NARAC chromosome 18 case-control data

Sharon R Browning* and Jessica Thomas

Author Affiliations

Department of Statistics, The University of Auckland, Private Bag 92019, Auckland, New Zealand

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BMC Proceedings 2007, 1(Suppl 1):S11  doi:

Published: 18 December 2007


The Genetic Analysis Workshop 15 rheumatoid arthritis data included a set of 460 cases and 460 controls genotyped at 2300 closely spaced markers on a 10 megabase region of chromosome 18q. We conducted a multilocus analysis of these data using a localized haplotype clustering method that adapts to linkage disequilibrium structure and can be applied to large, densely genotyped data sets such as this one. We found a protective haplotype carried by 33 individuals that was significantly associated with rheumatoid arthritis in these data after adjusting for multiple testing. This haplotype was located less than 500 base pairs upstream of the CCBE1 gene. The association was not detected using single-marker tests, but could be found using a variety of multilocus tests.