The overall purpose of Dr. O'Donnell's research during FY 2011 is to investigate the epidemiology and genetic 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 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 and whole genome RNA profiling (Affymetrix Exon Array). 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. Candidate SNP genotyping is conducted using various platforms including bead array assays (Illumina). Next-Generation targeted and whole exome 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 also conducted using SOLAR. 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 1100 GWA studies to September 30, 2011. We have used this catalogue to conduct and publish initial analyses (1) and to develop new tools for study of pleiotropy across GWA studies (2). 2. Genetic determinants of subclinical atherosclerosis and risk factors: In conjunction with the CHARGE Consortium, we have completed further GWA analysis of coronary artery calcification and aortic valve calcium by MDCT (submitted);and carotid intimal medial thickness by carotid ultrasonography (3). Multiple genomewide significant associations have been discovered, many that are also associated with myocardial infarction. Several manuscripts are published or in press. In addition, Dr. O'Donnell has contributed to large, published GWA studies of hypertension (4), obesity/BMI (5), and height (6). 3. Sequencing projects: We completed analysis of sequencing of the chromosome 9p21 region: During FY11, analysis of follow-up genotyping was completed and targeted gene expression profiling to follow-up resequencing completed in 282 FHS subjects in a 200,000 bp in the region of chromosome 9p21 implicated in MI as well as nearby genes, CDKN2A and CDKN2B and the non-coding RNA CDKN2BAS. A manuscript describes phenotype-genotype associations and transcription characteristics of these variants in 7000 FHS subjects. Additionally, we contributed to a manuscript that identified sequence variants in loci implicated by GWAS underlying hypertriglyceridemia (7). Numerous other projects are underway to explore loci implicated in GWA studies using targeted and exomewide DNA sequencing. 4. Genetic determinants of myocardial infarction/coronary heart disease: We contributed to the largest meta-analysis of coronary artery disease to date, CARDIOGRAM (8), reporting over 30 loci. 5. Genetic determinants of white blood cell indices, hemostatic factors, platelet aggregability and biomarkers: A GWAS meta-analysis in the CHARGE Consortium was published for circulating white blood cells and their indices (9), and by collaboration, we helped confirm these findings in African Americans and Japanese. Further research is underway for expression of genes implicated in GWAS for hemostatic and platelet traits. A GWAS of metabolomic measures reported many new and known genes and pathways (10). 6. Epidemiology of the risk of subclinical disease, metabolomics and genetics: We reported the clear incresased risk for cardiovascular disease of internal carotid intimal medial thickness (11). We also reported novel association of metabolite profiles with increased risk for diseases including diabetes (12). We are developing an updated Framingham CHD risk score that includes CRP and family history of CHD in the model and we have submitted a manuscript examining the role of a genetic risk score to predict incident cardiovascular disease. Selected references (out of 64 publications that are published or in press in PubMed from October 2009 through September 15 2010): 1: Johnson AD, et al. PLoS Genet 2011;7:e1002269. 2: Huang J, et al. Bioinformatics 2011;27:1201-6. 3: Bis JC, et al. Nat Genet 2011 Sep 11. 4: Ehret GB, et al. Nature 2011 Sep 11. 5: Speliotes EK, et al. Nat Genet 2010;42:937-48. 6: Lango Allen H, et al. Nature 2010;467:832-8. 7: Johansen CT, et al. Arterioscler Thromb Vasc Biol 2011;31:1916-26. 8: Schunkert H, et al. Nat Genet 2011;43:333-8. 9: Nalls MA, et al. PLoS Genet 2011;7:e1002113. 10: Suhre K, et al. Nature 2011;477:54-60. 11: Polak JF, et al. N Engl J Med 2011;365:213-21. 12: Wang TJ, et al. Nat Med 2011;17:448-53.
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