Incorporating Biological Knowledge in the Search for Gene × Gene Interaction in Genome-Wide Association Studies


Show simple item record Manning, Alisa K en_US Ngwa, Julius Suh en_US Hendricks, Audrey E en_US Liu, Ching-Ti en_US Johnson, Andrew D en_US Dupuis, Josée en_US Cupples, L Adrienne en_US 2012-01-11T15:51:14Z 2012-01-11T15:51:14Z 2009 en_US 2009-12-15 en_US
dc.identifier.citation Manning, Alisa K, Julius Suh Ngwa, Audrey E Hendricks, Ching-Ti Liu, Andrew D Johnson, Josée Dupuis, L Adrienne Cupples. "Incorporating biological knowledge in the search for gene × gene interaction in genome-wide association studies" BMC Proceedings 3(Suppl 7):S81. (2009) en_US
dc.identifier.issn 1753-6561 en_US
dc.description.abstract 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 × 10-4. 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 × 10-8 (empirical p = 0.012). en_US
dc.description.sponsorship National Institutes of Health (National Institute of General Medical Sciences R01 GM031575); Boston University School of Medicine & Boston Medical Center (Robert Dawson Evans Endowment of the Department of Medicine) en_US
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights Copyright 2009 Manning et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. en_US
dc.rights.uri en_US
dc.title Incorporating Biological Knowledge in the Search for Gene × Gene Interaction in Genome-Wide Association Studies en_US
dc.type article en_US
dc.identifier.pubmedid 20018077 en_US
dc.identifier.pmcid 2795984 en_US

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