The overall purpose of Dr. O'Donnell's research during FY 2012 is to investigate the epidemiology and genetic/genomic epidemiology of subclinical and clinical atherosclerotic cardiovascular disease (CVD) and its risk factors. The longer term goal is to translate these results to prediction, prevention and personalization of CVD medicine. 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 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, von Willebrand factor, platelet aggregation, circulating bilirubin);(c) imaging measures of subclinical atherosclerosis (coronary and abdominal and thoracic aortic 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 10 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, and whole genome sequencing, 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. Statistical linkage analyses were conducted using SOLAR. Testing for association of low frequency variants and burden of rare variants was conducted using various tests. Replication Collaboration with the Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) Consortium: To seek strong evidence for replication, we combined 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. New Projects Underway: These new projects include (a) profiling of metabolites in collaboration with the SABRe project and separately with MGH PIs;(b) gene expression profiling and targeted gene expression in Offspring subjects;(c) pilot study of RNA sequencing through the NHLBI DNA Sequencing Core lab;(d) collection of cells for eventual conversion to induced pluripotential stem cells (iPSC), reprogramming iPSC into specific tissues and comprehensive assay of the reprogrammed tissues;(e) collaborations with labs that can dissect the function of discovered genes and variants in tissue culture, mouse models, etc. Research Accomplishments for Major Projects Directed by Dr. O'Donnell in FY 2011: 1. Bioinformatics Databases and Tools: Our group conducted comprehensive studies of a large database we compiled of >1400 GWA studies through August 2012. We have used this catalogue to conduct and publish an survey of the reporting of results across GWA studies. 2. Genetic determinants of subclinical atherosclerosis and risk factors: In conjunction with the CHARGE Consortium, we completed and reported further GWA analysis of coronary artery calcification (published), ankle brachial index (published), and aortic valve calcium by MDCT (submitted). Multiple genomewide significant associations have been discovered, many that are also associated with myocardial infarction. In addition, Dr. O'Donnell has contributed to multiple other large, published GWA studies of liver function tests, electrocardiographic measures, and . 3. Sequencing projects: We completed analysis of sequencing of the chromosome 9p21 region: A manuscript describes phenotype-genotype associations of variants identified in the CDKN2A and CDKN2B and non-coding region of 9p21 and transcription characteristics of the non-coding RNA CDKN2BAS and CDKN2B in 7000 FHS subjects has been submitted. Numerous other projects are underway to explore loci implicated in GWA studies using targeted and exomewide DNA sequencing. We have contributed to manuscripts in preparation that identified exome sequence variants in loci implicated by GWAS underlying carotid intimal medial thickness, LDL cholesterol and myocardial infarction. 4. Genetic determinants of myocardial infarction/coronary heart disease: We contributed to the largest meta-analysis of coronary artery disease to date, CARDIOGRAM Plus C4D, reporting over 40 total loci. 5. Genetic determinants of hemostatic factors and other biomarkers: The largest ever GWAS meta-analysis in the CHARGE Consortium were completed and submitted for publication for various hemostatic factors including fibrinogen, plasminogen activator inhibitor 1, and tissue plasminogen activator, and by collaboration, we have extended some of these studies to African American populations. 6. Epidemiology of the risk of subclinical disease, metabolomics and genetics: We reported the increased risk for myocardial infarction/cardiovascular disease and for coronary artery calcium of a myocardial infarction genetic risk score. In the CHARGE Consortium, we have completed a GWAS for incident MI. We are developing an updated Framingham CHD risk score that includes family history in the model. Selected references (out of >40 publications published/in press in PubMed October 2011 to September 15 2012): 1: Bick AG et al. Am J Hum Genet. 2012 Sep 7;91(3):513-9. 2: Lucas G et al PLoS One. 2012;7(8):e41730. 3: Raghavachari N et al. BMC Med Genomics. 2012 Jun 29;5:28. 4: Sinner MF et al. Heart Rhythm. 2012 Jun 6. 5: Voight BF et al. Lancet. 2012 Aug 11;380(9841):572-80. 6: Cheng S et al. Circulation. 2012 May 8;125(18):2222-31. 7: Dastani Z et al. PLoS Genet. 2012;8(3):e1002607. 8: Sarwar N et al. Lancet. 2012 Mar 31;379(9822):1205-13. 9: Demirkan A et al. PLoS Genet. 2012 Feb;8(2):e1002490. 10: Thanassoulis G et al. Circ Cardiovasc Genet. 2012 Feb 1;5(1):113-21. 11. Murabito JM et al. Circ Cardiovasc Genet. 2012 Feb 1;5(1):100-12. 12: O'Donnell CJ et al. Circulation. 2011 Dec 20;124(25):2855-64. 13: O'Donnell CJ, Nabel EG. N Engl J Med. 2011 Dec 1;365(22):2098-109. 14: Chambers JC et al. Nat Genet. 2011 Oct 16;43(11):1131-8.
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