The overall objective of Dr. O'Donnell's Genomic Epidemiology of Cardiovascular Disease research program during FY 2013 is to define specific functional genetic variation underlying our Cardiovascular Genomic Epidemiology projects (studies of the genomic epidemiology of subclinical and clinical atherosclerotic cardiovascular disease (CVD) and its risk factors, including hemostatic and thrombotic risk). Next generation DNA sequencing is being targeted to specific gene regions, the whole exome and the whole genome (low pass) to define functional genetic variants underlying findings from GWAS/genomic epidemiology studies. The longer term goal is to translate these results to prediction, prevention and personalization of CVD medicine for human populations. The major projects have emanated from the SNP Health Association Resource (SHARe), the Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) Consortium, and collaborative DNA and RNA sequencing projects. Dr. O'Donnell is the Associate Director of the NHLBI's Framingham Heart Study (FHS), Scientific Director and Steering Committee Chair of the NHLBI's Framingham Heart Study (FHS) SHARe Program, co-founder and Steering Committee Co-chair of the CHARGE Consortium, and Co-Director of the HeartGO Consortium of the NHLBI GO Exome Sequencing Project (ESP). Research Subjects: The research subjects consist primarily of participants of the Framingham Heart Study FHS original cohort, Offspring cohort and Generation 3, and secondarily of participants of several collaborating cohort studies. Phenotyping: Phenotyping consisted of: (a) risk factor measures from usual clinical exams (lipids, blood pressure, anthropometric and physical examination);(b) biomarkers from peripheral blood (eg, C-reactive protein, fibrinogen, and von Willebrand factor);(c) imaging measures of subclinical atherosclerosis (coronary artery calcium (CAC) and abdominal and thoracic aortic calcific atherosclerosis by multidetector CT imaging (MDCT) in 3500 Offspring and Generation 3 subjects;carotid intimal medial thickness (CIMT) and carotid plaque by B-mode ultrasonography in 3800 Offspring: aortic plaque, LV mass by cardiovascular magnetic resonance imaging (CMRI) in 1800);(d) clinical CVD outcomes (myocardial infarction;coronary heart disease;CVD) adjudicated by a physician endpoint validation committee;(e) gene expression of lymphocyte- and platelet-derived RNA using rtPCR, whole genome RNA profiling (Affymetrix Exon Array), and next-generation RNA sequencing. Genotyping in SHARe and resequencing: Genotyping derived from two dense genomewide SNP scans, a 100K SNP scan (Affymetrix platform) in 1400 FHS Offspring and original cohort subjects and a 550K SNP scan (Affymetrix platform, 250K Nsp and 250K Sty and 50K gene-focussed MIP) in 9,400 FHS subjects from all three generations. Imputation of the 550K SNPs was conducted to 2.4 million HapMap SNPs using MACH and to 40 million SNPs from the 1000 Genomes Project. Additional SNP genotyping is being conducted using various platforms including 250K functional exon variants on the exome chip (Illumina). Next-Generation sequencing including targeted gene region sequencing, whole exome sequencing (high pass), and whole genome sequencing (low pass), is being conducted in several US genome centers. Statistical association and linkage methods: Statistical association analyses of genomewide association (GWA) of genotypes with phenotypes were conducted using mixed linear and/or logistic regression, generalized estimating equations, and survival analyses, when appropriate;additionally, family based association testing. Testing for association of low frequency variants and burden of rare variants was conducted using various tests. Replication Collaboration with the Cohorts for Heart andd Aging Research in Genome Epidemiology (CHARGE) Consortium: To seek strong evidence for replication, we combbbined data within a consortium of prospective, observational cohort studies with genomewide SNP scans and a large, common set of phenotypes. In silico replication meta-analysis is performed. Research Accomplishments for Major Projects Directed by Dr. O'Donnell in FY 2014: 1. Exome chip genotype associations: Exome chip association analysis was completed in the CHARGE Consortium, to identify functional genetic variants underlying lipid subfractions (published), coronary artery calcium and carotid IMT (in preparation), circulating hemostatic factors (in preparation), red blood cell and white blood cell counts (in preparation), and coronary artery disease/myocardial infarction (in preparation). 2. Targeted sequencing of SLC174A (6p22.2) and PIK3CG (7q22.3) region for CIMT: Within the CHARGE Consortium, we have completed analysis of targeted sequencing of two regions previously implicated from our GWAS for high CIMT. 3. Whole exome sequencing in FHS and collaborating cohorts for high levels of CAC: We have completed whole exome-sequencing of >400 participants with high levels of CAC and data cleaning and data analysis using up to 1800 participants with whole exome sequencing is underway. 4. Whole exome sequencing and whole genome sequencing projects: We are collaborating in analysis of whole exome sequencing data from the CHARGE Consortium and Exome Sequencing Project whole genome sequencing from the CHARGE Consortium, leading to our collaboration in the largest study of exome sequencing for early MI (submitted) as well as a large study of whole exome sequencing and lipids (published) and hemostatic/thrombotic factors (submitted). 5. Personalized Genomics of CVD: We collaborated in a published study on notifiable genetic variants and we are leading an analysis of the prevalence and implications of functional exomic variants in >50 CVD genes, in a collaboration within the Exome Sequencing Program. We are also leading an analysis of notifiable gene variants in exome chip in >50000 persons. Selected references (out of >50 publications published/in press in PubMed September 2013 to September 15 2014): 1: Tabor HK, ..., O'Donnell CJ, Rich SS, Nickerson DA;Bamshad MJ. Pathogenic variants for mendelian and complex traits in exomes of 6,517 European and african americans: implications for the return of incidental results. Am J Hum Genet 2014;95:183-193. 2: Mkinen VP, ..., O'Donnell CJ, ..., Assimes TL. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS Genet 2014;10:e1004502. 3: Sen SK, ..., O'Donnell CJ, ..., Biesecker LG. Integrative DNA, RNA, and protein evidence connects TREML4 to coronary artery calcification. Am J Hum Genet 2014;95:66-76. 4: Zhang X, ..., O'Donnell CJ, Emilsson V, Johnson AD. Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics 2014;15:532. 5: TG and HDL Working Group of the Exome Sequencing Project, National Heart, Lung, and Blood Institute, Crosby J, ..., O'Donnell CJ, ..., Kathiresan S. Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N Engl J Med 2014;371:22-31. 6: Ramos EM, ..., O'Donnell C, ..., Williams MS. Characterizing genetic variants for clinical action. Am J Med Genet C Semin Med Genet 2014;166C(1):93-104. 7: Lange LA, ..., O'Donnell CJ, ..., Willer CJ. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet 2014;94:233-245. 8: Peloso GM, ..., O'Donnell CJ, Rice K, Boerwinkle E, Kathiresan S, Cupples LA. Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. Am J Hum Genet 2014;94:223-232.
Showing the most recent 10 out of 112 publications
