Principal Investigator: Prof Nathan Pankratz
Department: Laboratory Medicine and Pathyology
University of Minnesota, Laboratory Medicine and Pathyology. 515 Delaware Street E, Minneapolis MN 55455, United StatesTags: 17731, cancer, cardiovascular_disease, Copy_number_variation, deletions, duplications
Funding body: Internally funded by University of Minnesota
1a: To identify changes in the DNA, particularly large deletions and duplications of the genome, that are related to complex diseases and intermediate biomarkers
1b: The identification of genetic risk factors that are related to disease will help reveal the underlying biology and thereby expose targets for environmental modification and/or novel drug development.
1c: We will use the raw Affymetrix Axiom data (.CEL files) and apply a principal components analysis on these intensities to correct for DNA quality and batch effects. We will then perform a joint calling across all samples to determine potential deletions and duplications using our soon to be open-source Genvisis software package, which will also assess the quality of these calls and filter them down to a set of high quality calls (~1 year to complete). We will then associate the high quality calls with the phenotypes available, and replicate any findings using external data sources (~1 additional year).
1d: Full cohort; all samples with high quality intensity data will be analysed