Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease.
Sara Ballouz, Jason Y Liu, Martin Oti, Bruno Gaeta, Diane Fatkin, Melanie Bahlo, Merridee A Wouters
Molecular Genetics and Genomic Medicine | Published : 2014
Current single-locus-based analyses and candidate disease gene prediction methodologies used in genome-wide association studies (GWAS) do not capitalize on the wealth of the underlying genetic data, nor functional data available from molecular biology. Here, we analyzed GWAS data from the Wellcome Trust Case Control Consortium (WTCCC) on coronary artery disease (CAD). Gentrepid uses a multiple-locus-based approach, drawing on protein pathway- or domain-based data to make predictions. Known disease genes may be used as additional information (seeded method) or predictions can be based entirely on GWAS single nucleotide polymorphisms (SNPs) (ab initio method). We looked in detail at specific p..View full abstract