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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

Association mapping of susceptibility loci for rheumatoid arthritis

Tai-Yue Kuo12, Winston Lau1, Cheng Hu3 and Weihua Zhang45*

Author Affiliations

1 Human Genetics Division, Duthie Building (Mailpoint 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK

2 National Cheng Kung University Hospital, No. 138, Shengli Road, Tainan City, Taiwan

3 Shanghai Diabetes Institute, Shanghai Jiaotong University, 600 Yishan Road, Shanghai 200233, People's Republic of China

4 Section of Cancer Genetics, The Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton Surrey SM2 5NG, UK

5 Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UB1 3HW, UK

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BMC Proceedings 2007, 1(Suppl 1):S15  doi:

Published: 18 December 2007


We analyzed a case-control data set for chromosome 18q from the Genetic Analysis Workshop 15 to detect susceptibility loci for rheumatoid arthritis (RA). A total number of 460 cases and 460 unaffected controls were genotyped on 2300 single-nucleotide polymorphisms (SNPs) by the North American Rheumatoid Arthritis Consortium. Using a multimarker approach for association mapping under the framework of the Malecot model and composite likelihood, we identified a region showing significant association with RA (p < 0.002) and the predicted disease locus was at a genomic location of 53,306 kb with a 95% confidence interval (CI) of 53,295–53,331 kb. A common haplotype in this region was protective against RA (p = 0.002). In another region showing nominal significant association (51,585 kb, 95% CI: 51,541–51,628 kb, p = 0.037), a haplotype was also protective (p = 0.002). We further demonstrated that reducing SNP density decreased power and accuracy of association mapping. SNP selection based on equal linkage disequilibrium (LD) distance generally produced higher accuracy than that based on equal kilobase distance or tagging.