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Faculty Investigator

Greg Cooper, Ph.D., completed his graduate work at Stanford in 2006 in the area of comparative genomics. His post-doctoral studies focused on using SNP genotyping to identify copy number variants. Cooper became a faculty investigator at HudsonAlpha in 2010.

The Cooper lab is interested in the broad goal of identifying genetic variants that causally influence human traits. The pursuit of this goal by Cooper and others has included genome-wide association studies and the application of next-generation sequencing for discovery of common and rare variants associated with human phenotypes. Despite the promise for these technologies, several analytical challenges exist for understanding the data. The Cooper lab is focused on developing computational and statistical strategies to understand structure, function and evolutionary history of human genomes with the long-term goal of predicting how genomic variation shapes phenotypic variation. 
Current research areas in the Cooper Lab include :
• Using exome and whole-genome sequencing to identify the genetic basis for Mendelian disorders using comparative genomics and functional annotations.
• Identifying expression QTLs in liver. The Cooper lab is working to incorporate functional and comparative genomic annotations into eQTL prediction to evaluate the quality of prediction and identify and test putative causative variants.
• Characterizing genetic alterations, with a focus on copy number variation, found in children with intellectual disability. Previous work by Cooper revealed new copy number variants found in affected children. Future plans include using capture and sequencing of known disease associated regions to determine whether they have new mutations in previously characterized regions.
Selected recent publications
Patwardhan, R. P. et al. (2012). Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol. 30: 265–270.
Cooper, G. M. and Mefford, H. C. (2011). Detection of copy number variation using SNP genotyping. Methods Mol. Biol. 767: 243–252.
Cooper, G. M. and Shendure, J. (2011). Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 12: 628–640.
Cooper, G. M. et al. (2010). Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat. Methods. 7: 250–251.
Cooper, G. M. et al. (2011). A copy number variation morbidity map of developmental delay. Nat. Genet. 43: 838–846.