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This article is part of the supplement: Genetic Analysis Workshop 16

Open Access Proceedings

A search for non-chromosome 6 susceptibility loci contributing to rheumatoid arthritis

Brian K Suarez12*, Robert Culverhouse3, Carol H Jin1 and Anthony L Hinrichs1

Author Affiliations

1 Department of Psychiatry, Washington University School of Medicine, 660 South Euclid, Campus Box 8134, St. Louis, Missouri 63110, USA

2 Department of Genetics, Washington University School of Medicine, 660 South Euclid, St. Louis, Missouri 63110, USA

3 Department of Medicine, Washington University School of Medicine, 660 South Euclid, St. Louis, Missouri 63110, USA

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BMC Proceedings 2009, 3(Suppl 7):S15  doi:

Published: 15 December 2009

Abstract

We conducted a search for non-chromosome 6 genes that may increase risk for rheumatoid arthritis (RA). Our approach was to retrospectively ascertain three "extreme" subsamples from the North American Rheumatoid Arthritis Consortium. The three subsamples are: 1) RA cases who have two low-risk HLA-DRB1 alleles (N = 18), 2) RA cases who have two high-risk HLA-DRB1 alleles (N = 163), and 3) controls who have two low-risk HLA-DRB1 alleles (N = 652). We hypothesized that since Group 1's RA was likely due to non-HLA related risk factors, and because Group 3, by definition, is unaffected, comparing Group 1 with Group 2 and Group 1 with Group 3 would result in the identification of candidate susceptibility loci located outside of the MHC region. Accordingly, we restricted our search to the 21 non-chromosome 6 autosomes. The case-case comparison of Groups 1 and 2 resulted in the identification of 17 SNPs with allele frequencies that differed at p < 0.0001. The case-control comparison of Groups 1 and 3 identified 23 SNPs that differed in allele frequency at p < 0.0001. Eight of these SNPs (rs10498105, rs2398966, rs7664880, rs7447161, rs2793471, rs2611279, rs7967594, and rs742605) were common to both lists.