Professor, Department of Human Genetics
Member: Computation Institute; Committee on Genetics, Genomics, and Systems Biology; Committee on Molecular Medicine; Committee on Cancer Biology
B.S. in biology from the University of Notre Dame, 1978
Fax: (773) 702-2567
The Cox Lab conducts research to identify and characterize the genetic component to common diseases and complex human traits. Our lab is computational and “dry” rather than a traditional molecular genetics (“wet”) laboratory. We develop methods to analyze and integrate a wide variety of data types and then apply these methods to analyze data from many different diseases and phenotypes. For example, we are currently funded to analyze RNAseq data generated through the GTEx (Genotype-Tissue Expression) project (http://commonfund.nih.gov/GTEx/), as well as sequence data generated through the 1000 Genomes Project. Our lab was the first to show that the genetic variation associated with complex human phenotypes is much more likely than expected to be variation that is also associated with mRNA levels for human transcripts1 – i.e. that SNPs associated with human diseases are also likely to be eQTLs (expression quantitative trait loci). More recently, we have also shown that SNPs associated with microRNA levels2 and alternative splicing are over-represented among SNPs associated with human diseases3. We are utilizing this information to develop new gene-based methods for genome association analysis that allow us to place more weight on genetic variation for which we have prior evidence of function.
We work extensively in pharmacogenomics on research projects designed to identify the genetic basis of response to chemotherapeutic agents and adverse events4. We also have a long history of conducting research on the genetics of type 2 diabetes5, and are currently analyzing sequence data generated for the T2DGENES project – more than 10,000 exomes, and 600 whole genomes (60X coverage). We are also part of the University of Chicago Conte Center, focused on applying new approaches to understand the genetic basis of autism, bipolar disorder and schizophrenia.6,7 I lead the analytic group for the International Tourette Syndrome Consortium, where we are conducting analyses for both GWAS (genome-wide association studies)8, and sequencing studies. We are also working on breast cancer using both GWAS and sequence data, and have had recent success in characterizing genetic risk factors for mesothelioma9.
Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.
Genetic architecture of microRNA expression: implications for the transcriptome and complex traits.
Variants affecting exon skipping contribute to complex traits.
(2012) PLoS genetics (in press)
A genome-wide association study of overall survival in pancreatic cancer patients treated with gemcitabine in CALGB 80303.
Genome-wide association and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility loci and enrichment for expression quantitative trait loci in top signals.
(Aug 2011) Diabetologia 54(8):2047-55 PMID:21647700
Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants.
(Jan 2012) Molecular psychiatry PMID:22212596
Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci.
(May 2012) Molecular autism 3(1):3 PMID:22591576
Genome-wide association study of Tourette's syndrome.
(Aug 2012) Molecular psychiatry PMID:22889924
Germline BAP1 mutations predispose to malignant mesothelioma.