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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

Constructing gene association networks for rheumatoid arthritis using the backward genotype-trait association (BGTA) algorithm

Yuejing Ding1, Lei Cong1, Iuliana Ionita-Laza2, Shaw-Hwa Lo1 and Tian Zheng1*

Author Affiliations

1 Department of Statistics, Columbia University, New York, New York 10027, USA

2 Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA

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BMC Proceedings 2007, 1(Suppl 1):S13  doi:

Published: 18 December 2007

Abstract

Background

Rheumatoid arthritis (RA, MIM 180300) is a common and complex inflammatory disorder. The North American Rheumatoid Arthritis Consortium (NARAC) data, as part of the Genetic Analysis Workshop 15 data, consists of both genome scan and candidate gene studies on RA patients.

Results

We applied the backward genotype-trait association (BGTA) algorithm to capture marginal and gene × gene interaction effects of multiple susceptibility loci on RA disease status. A two-stage screening approach was used for the genome scan, whereas a comprehensive study of all possible subsets was conducted for the candidate genes. For the genome scan, we constructed an association network among 39 genetic loci that demonstrated strong signals, 19 of which have been reported in the RA literature. For the candidate genes, we found strong signals for PTPN22 and SUMO4. Based on significant association evidence, we built an association network among the loci of PTPN22, PADI4, DLG5, SLC22A4, SUMO4, and CARD15. To control for false positives, we used permutation tests to constrain the family-wise type I error rate to 1%.

Conclusion

Using the BGTA algorithm, we identified genetic loci and candidate genes that were associated with RA susceptibility and association networks among them. For the first time, we report possible interactions between single-nucleotide polymorphisms/genes, which may be useful for biological interpretation.