Rheumatoid arthritis-associated gene-gene interaction network for rheumatoid arthritis candidate genesReport as inadecuate

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BMC Proceedings

, 3:S75

First Online: 15 December 2009DOI: 10.1186-1753-6561-3-S7-S75

Cite this article as: Huang, CH., Cong, L., Xie, J. et al. BMC Proc 2009 3Suppl 7: S75. doi:10.1186-1753-6561-3-S7-S75


Rheumatoid arthritis RA, MIM 180300 is a chronic and complex autoimmune disease. Using the North American Rheumatoid Arthritis Consortium NARAC data set provided in Genetic Analysis Workshop 16 GAW16, we used the genotype-trait distortion GTD scores and proposed analysis procedures to capture the gene-gene interaction effects of multiple susceptibility gene regions on RA. In this paper, we focused on 27 RA candidate gene regions 531 SNPs based on a literature search. Statistical significance was evaluated using 1000 permutations. HLADRB1 was found to have strong marginal association with RA. We identified 14 significant interactions p < 0.01, which were aggregated into an association network among 12 selected candidate genes PADI4, FCGR3, TNFRSF1B, ITGAV, BTLA, SLC22A4, IL3, VEGF, TNF, NFKBIL1, TRAF1-C5, and MIF. Based on our and other contributors- findings during the GAW16 conference, we further studied 24 candidate regions with 336 SNPs. We found 23 significant interactions p-value < 0.01, nine interactions in addition to our initial findings, and the association network was extended to include candidate genes HLA-A, HLA-B, HLA-C, CTLA4, and IL6. As we will discuss in this paper, the reported possible interactions between genes may suggest potential biological activities of RA.

List of abbreviations usedCGEMSCancer Genetic Markers of Susceptibility

GAW16Genetic Analysis Workshop 16

GTDGenotype-trait distortion

NARACNorth American Rheumatoid Arthritis Consortium

RARheumatoid arthritis

SNPSingle-nucleotide polymorphism

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Author: Chien-Hsun Huang - Lei Cong - Jun Xie - Bo Qiao - Shaw-Hwa Lo - Tian Zheng

Source: https://link.springer.com/

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