The Center for Public Health Genomics (CPHG) was established January, 2007, with the recruitment of Stephen Rich, PhD, from Wake Forest University as its founding Director and Board of Visitors Distinguished Faculty Scholar and Harrison Teaching Chair in Public Health Sciences. Simultaneously, Pat Concannon, PhD, was recruited from the Benaroya Research Institute in Seattle to serve as the Associate Director of the Center and Harrison Teaching Chair in Biochemistry and Molecular Genetics. By March 2007, four additional faculty (Drs. Mychaleckyj, Onengut-Gumuscu, Sale and Teraoka) arrived at the University of Virginia and together initiated a focused program of research in human genomics. The past 3 years has seen expansion of the research portfolio, continued renovation of space and recruitment of new faculty (Chen, Farber, Keene, Mackey, Manichaikul, Quinlan and Nayak).
The focus of the CPHG has been developing a foundation for genomics research both within the Center and through collaborations with faculty across the University of Virginia. The research has targeted areas of existing expertise at UVA including endocrine (type 1 diabetes, type 2 diabetes, diabetic complications, bone diseases), cardiovascular (atherosclerosis and coronary heart disease), cancer (breast) and cerebrovascular (ischemic stroke) diseases. The CPHG faculty has developed independent research projects through investigator-initiated grants and subcontracts. In FY 2008-09, there were 22 awards, totalling $25,856,365. The faculty average 79% of salary coverage by extramural funding. Three examples of research, one within the CPHG and two collaborative, are:
- Genomic architecture of type 1 diabetes
The Type 1 Diabetes Genetics Consortium (S Rich, PI) has become the cornerstone of the NIDDK’s efforts in diabetes genetics research. The T1DGC is at the forefront in genome-wide linkage and association scans for type 1 diabetes, and has now identified nearly 50 loci that contribute to disease risk. Using the resources of the CPHG, the T1DGC is performing fine mapping of these loci using the ImmunoChip, a genotyping array containing 200,000 SNPs covering over 180 loci identified from genome-wide association scans for autoimmune diseases (including type 1 diabetes). Importantly, these resources have been leveraged to support two newly funded grants on the role of structural variation in the genome (Rich) and functional characteristics of known loci (Concannon) on type 1 diabetes risk.
- Genome and microbiome effects on malnutrition.
Through efforts pioneered by Drs. Dick Guerrant and Bill Petri, several populations across the world have been the focus of investigations of malnutrition, growth retardation and impact of health care and nutritional intervention on recovery from infectious diseases. The CPHG has established collaborations with these and other investigators in the Center for Global Health on studies of specific genes (ApoE and leptin) and genome-wide evaluations as they relate to clinical outcome. This collaboration has evolved into a major scientific discovery project supported by the Gates Foundation on the roles of the host genome and the microbiome on recovery from malnutrition. The CPHG provides two critical components to this project – data analysis/bioinformatics and molecular genetics. These collaborations are now being expanded to target new infectious disease genomics and funding opportunities.
- Exome Sequencing in Cardiovascular Disease
Accumulating evidence suggests that common human diseases have both genetic and environmental components to risk. Cardiovascular (e.g., myocardial infarction) and cerebrovascular (e.g., stroke) have strong genetic risk, yet results of genome-wide association and linkage scans have found limited effects of common genetic variants on susceptibility. In order to interrogate genes for variation that may be functionally significant, next-generation sequencing approaches are being used to target the exons of the entire human genome (the human exome). The CPHG is leading a consortium of six well-phenotyped NHLBI cohorts (ARIC, CARDIA, CHS, Framingham Heart Study, Jackson Heart Study, MESA) that account for over 40,000 participants with longitudinal risk factor data and DNA. These participants are contributing their DNA for exome sequencing to examine genes involved in diseases and risk factors related to heart, lung and blood disorders. The Exome Sequencing Project is examining genomic features related to risk of early-onset myocardial infarction, extremes of low-density lipoprotein (LDL), type 2 diabetes, obesity, ischemic stroke and blood pressure.
For more information about the activities of the CPHG and its faculty, please explore the web site, the individual sites of faculty laboratories, and the educational and outreach opportunities of our Center.