The overall purpose 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, von Willebrand factor, platelet aggregation, circulating bilirubin);(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 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. Research Accomplishments for Major Projects Directed by Dr. O'Donnell in FY 2013: 1. Common calling of exome chip genotyping: Within the CHARGE Consortium, our collaborative group conducted common genotyping calling of exome chip genotypes across more than 10 large population cohort studies to allow exome chip meta-analyses for clinical CVD, subclinical atherosclerosis, CVD risk factors, and many other quantitative traits. The common calling was reported in a manuscript. 2. Targeted sequencing of 9p21 region for coronary heart disease and CAC: We completed analysis of sequencing of the chromosome 9p21 region: Our published 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 ("Anril") and the CDKN2B transcript. We have identified sequence-discovered 9p21 variants that show strong associations with clinical CVD, high CAC levels, increased aortic diameters and altered levels of CDKN2BAS ("Anril"). 3. 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. 4. Collaboration in Targeted Sequencing Projects: Our group collaborates in analysis of targeted sequencing of FHS participants for several CVD traits including increased LV mass (published) and increased duration of PR, QRS and QT intervals on electrocardiography (submitted). 5. Whole exome sequencing in FHS 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 is underway. 6. 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) and a first published study of whole genome sequence analysis of 1000 persons for a quantitative disease trait (HDL cholesterol). 7. Personalized Genomics of CVD: 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. Selected references (out of >50 publications published/in press in PubMed October 2012 to September 15 2013): 1. Grove ML, ..., O'Donnell CJ, Rotter JI, Boerwinkle E. Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. PLoS One 2013 Jul 12;8(7):e68095. 2. Cohorts for Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium, Morrison AC, ..., O'Donnell CJ, Psaty BM, Cupples LA, Gibbs R, Boerwinkle E. Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet 2013 Aug;45(8):899-901. 3. Johnson AD, ..., O'Donnell CJ. Resequencing and clinical associations of the 9p21.3 region: a comprehensive investigation in the Framingham heart study. Circulation 2013 Feb 19;127(7):799-810. 4. Auer PL,...,O'Donnell CJ,..., Ganesh SK, Li Y. Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. Am J Hum Genet. 2012 Nov 2;91(5):794-808. 5. Bick AG,...O'Donnell CJ, Wilson JG, Altshuler DM, Hirschhorn JN, Seidman JG, Seidman C. Burden of rare sarcomere gene variants in the Framingham and Jackson Heart Study cohorts. Am J Hum Genet. 2012 Sep 7;91(3):513-9.
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|Rosenquist, Klara J; Massaro, Joseph M; Pencina, Karol M et al. (2013) Neck circumference, carotid wall intima-media thickness, and incident stroke. Diabetes Care 36:e153-4|
|Morrison, Alanna C; Voorman, Arend; Johnson, Andrew D et al. (2013) Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet 45:899-901|
|Tsao, Connie W; O'Donnell, Christopher J (2013) Lipid profiles and coronary artery plaque by CT angiography: Promise for translation of biology to imaging. J Cardiovasc Comput Tomogr 7:91-3|
|Thanassoulis, George; Peloso, Gina M; O'Donnell, Christopher J (2013) Genomic medicine for improved prediction and primordial prevention of cardiovascular disease. Arterioscler Thromb Vasc Biol 33:2049-50|
|Ho, Jennifer E; Chen, Wei-Yu; Chen, Ming-Huei et al. (2013) Common genetic variation at the IL1RL1 locus regulates IL-33/ST2 signaling. J Clin Invest 123:4208-18|
|Markus, Hugh S; Mäkelä, Kari-Matti; Bevan, Steve et al. (2013) Evidence HDAC9 genetic variant associated with ischemic stroke increases risk via promoting carotid atherosclerosis. Stroke 44:1220-5|