MDR 2.0 alpha

An alpha version of MDR 2.0 will be ready next week for testing. If you would like to try it out send me an email. Feedback is required!

This new version will load and analyze a genome-wide association study (GWAS) using stochastic search algorithms. The key to a successfull GWAS using MDR is expert or domain-specific knowledge. This can be in the form of LOD scores from a linkage analysis, ReliefF score on the SNPs or any other number you can assign to each SNP such as that derived from biochemical pathways or Gene Ontology, for example. I am a firm believer that expert knowledge of this type is the only thing that will make a GWAS of epistasis technically feasible.

The first stochastic search algroithm provided in MDR is a simple estimation of distribution algorithm (EDA) that assigns and updates probabilities to SNPs from the quality of the models the SNPs find themselves in and/or the expert knowledge you provide. These probabilities are used to pick SNPs for MDR models. Our recent paper at the ANTS conference describes this algorithm. See my June 19, 2008 post for a short description of the paper. Email me for a preprint. The final version of the paper will be available soon.