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Please use this identifier to cite or link to this item: http://hdl.handle.net/10481/28445

Title: PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS
Authors: Arnedo, Javier
Val, Coral del
Erausquin, Gabriel Alejandro de
Romero-Zaliz, Rocío
Swrakic, Dragan
Cloninger, Claude Robert
Zwir, Igor
Issue Date: 2013
Abstract: It has been proposed that single nucleotide polymorphisms (SNPs) discovered by genome-wide association studies (GWAS) account for only a small fraction of the genetic variation of complex traits in human population. The remaining unexplained variance or missing heritability is thought to be due to marginal effects of many loci with small effects and has eluded attempts to identify its sources. Combination of different studies appears to resolve in part this problem. However, neither individual GWAS nor meta-analytic combinations thereof are helpful for disclosing which genetic variants contribute to explain a particular phenotype. Here, we propose that most of the missing heritability is latent in the GWAS data, which conceals intermediate phenotypes. To uncover such latent information, we propose the PGMRA server that introduces phenomics—the full set of phenotype features of an individual—to identify SNP-set structures in a broader sense, i.e. causally cohesive genotype–phenotype relations. These relations are agnostically identified (without considering disease status of the subjects) and organized in an interpretable fashion. Then, by incorporating a posteriori the subject status within each relation, we can establish the risk surface of a disease in an unbiased mode. This approach complements—instead of replaces—current analysis methods. The server is publically available at http://phop.ugr.es/fenogeno.
Sponsorship: Funding for open access charge: Spanish Ministry of Science and Technology under projects [TIN2009-13950] and [TIN2012-38805]; Consejería de Innovación, Investigación y Ciencia, Junta de Andalucía, under project [TIC-02788]; UGR, under project [GREIB 2011]; R. L. Kirschstein National Research Award at Washington University School of Medicine.
Publisher: Oxford University Press (OUP)
Keywords: Single nucleotide polymorphisms (SNPs)
Genome-wide association studies (GWAS)
Regulatory network
URI: http://hdl.handle.net/10481/28445
ISSN: 0305-1048
Citation: Arnedo, J.; et al. PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS. Nucleic Acids Research, 41(W1): W142-W149 (2013). [http://hdl.handle.net/10481/28445]
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