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BMC Proceedings

, 3:S81

First Online: 15 December 2009DOI: 10.1186-1753-6561-3-S7-S81

Cite this article as: Manning, A.K., Ngwa, J.S., Hendricks, A.E. et al. BMC Proc 2009 3Suppl 7: S81. doi:10.1186-1753-6561-3-S7-S81


We sought to find significant gene × gene interaction in a genome-wide association analysis of rheumatoid arthritis RA by performing pair-wise tests of interaction among collections of single-nucleotide polymorphisms SNPs obtained by one of two methods. The first method involved screening the results of the genome-wide association analysis for main effects p-values < 1 × 10. The second method used biological databases such as the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes to define gene collections that each contained one of four genes with known associations with RA: PTPN22, STAT4, TRAF1, and C5. We used a permutation approach to determine whether any of these SNP sets had empirical enrichment of significant interaction effects. We found that the SNP set obtained by the first method was significantly enriched with significant interaction effects empirical p = 0.003. Additionally, we found that the -protein complex assembly- collection of genes from the Gene Ontology collection containing the TRAF1 gene was significantly enriched with interaction effects with p-values < 1 × 10 empirical p = 0.012.

List of abbreviations usedGAW16Genetic Analysis Workshop 16

GWASGenome-wide association studies

RARheumatoid arthritis

GOGene ontology

KEGGKyoto Encyclopedia of Genes and Genomes

SNPSingle-nucleotide polymorphism

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Autor: Alisa K Manning - Julius Suh Ngwa - Audrey E Hendricks - Ching-Ti Liu - Andrew D Johnson - Josée Dupuis - L Adrienne 


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