American Statistical Association
Genome wide association studies (GWAS) measure hundreds of thousands of genetic markers (single nucleotide polymorphsisms, SNPs) on large numbers of diseased cases and non-diseased controls, with analyses tending to focus on the association of single SNPs with disease status. Although many GWAS find that the associations of SNPs with disease status tend to be small, with odds ratios 1.25 1.5, and that modeling of multiple SNPs has limited ability to accurately predict disease status, the greatest benefit of GWAS might be new leads towards complex genetic pathways. This benefit can be enhanced by using prior information about how genes work together in biological pathways in order to form groups of genes a group of genes with modest effect might be more powerful than individual genes or single SNPs. This presentation will discuss general strategies for analyzing sets of SNPs, or sets of genes, as well as newly developed computational and statistical methods that use information from the publically available Gene Ontology (GO). The GO provides standardized representations of gene and gene product attributes across species and databases, and achieves this by a controlled vocabulary. Specifically, GO structures details about genes in a directed acyclic graph, such that specific details are linked to more general details. This provides a natural way to recursively create gene sets, from highly-specific small sets of genes to very general large sets of genes. By mapping SNPs from a GWAS to genes, and then mapping genes to the GO structure, we are able to scan the entire GO structure in terms of gene sets, to seek the set with the most extreme statistic for the association of the gene set with disease. Computational and statistical methods will be emphasized in this presentation, along with applications to several GWAS data sets. Strengths and limitations of our approach will be discussed, as well as future research directions.
|Date:||Wednesday, December 7, 2011|
|Time:||4:00 - 5:00 P.M.|
Memorial Sloan-Kettering Cancer Center
Department of Epidemiology and Biostatistics
307 East 63rd Street
(between First and Second Avenues)
Third Floor Conference Room
New York, New York
Note: To gain access to the building, please follow the directions by the telephone in the foyer.