The recent tremendous progress in genomics provides biomedical science with a remarkable opportunity to unravel the complex interactions between genetic variation and environmental variables (Gene and Environment Interactions or GEI) responsible for common complex human disease. Some of the advances contributing to this opportunity include availability of high quality whole genome sequence from >30 vertebrate species including our own plus a growing catalog of human genetic variation provided by HapMap and the fledgling projects aimed at understanding common structural variation. This opportunity is accompanied by a host of challenges including optimal study design, selection and utilization of a genotyping platform appropriate for each study, generation of high quality genotypic data and efficient and comprehensive downstream data analysis for genome wide association studies. The Johns Hopkins University Center for Inherited Disease Research (JH/CIDR) proposes to provide state-of- the-art whole genome association SNP genotyping for 12,000 samples over 3 years that will capture at least 80% of the genetic variation in the relevant study population as well as flexible regional genotyping that will enable custom fine mapping of genomic regions shown to harbor genes contributing risk for complex traits. We will also provide ancillary services as needed for individual projects including DNA isolation, whole genome amplification, assistance in study design and data analysis and provision of genotypic data in study-specific formats to the investigators and to the specified central database. Finally, we will work with the GEI Coordinating Committee in the planning and performance of this project. To achieve these aims we will build on the ten-year experience of JH/CIDR releasing more than 30 million high quality STRP and 1.2 billion high quality SNP genotypes for 128 projects and ~165,000 DNA samples. In this effort, we have interacted with >125 investigators providing genetic epidemiology expertise to assist with study design and analysis. Additionally, we will continue our commitment to evaluation of the rapidly evolving technological environment to provide the genetics community with the most robust, reliable and cost-effective genotyping platforms available. We will also take advantage of the rich scientific environment provided by the Johns Hopkins McKusick-Nathans Institute of Genetic Medicine and the greater Johns Hopkins School of Medicine and School of Public Health environment to maximize the broad expertise we bring to bear on this project.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project--Cooperative Agreements (U01)
Project #
3U01HG004438-04S1
Application #
8140051
Study Section
Special Emphasis Panel (ZHG1-HGR-P (M2))
Program Officer
Wise, Anastasia Leigh
Project Start
2007-08-06
Project End
2013-05-31
Budget Start
2010-06-01
Budget End
2013-05-31
Support Year
4
Fiscal Year
2010
Total Cost
$911,147
Indirect Cost
Name
Johns Hopkins University
Department
Type
Schools of Medicine
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Wang, Kesheng; Chen, Xue; Ward, Stephen C et al. (2018) CYP2A6 is associated with obesity: studies in human samples and a high fat diet mouse model. Int J Obes (Lond) :
Feng, Yun; Wang, Yanru; Liu, Hongliang et al. (2018) Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer. Mol Carcinog 57:216-224
Mosley, Jonathan D; Feng, QiPing; Wells, Quinn S et al. (2018) A study paradigm integrating prospective epidemiologic cohorts and electronic health records to identify disease biomarkers. Nat Commun 9:3522
Neumeyer, Sonja; Banbury, Barbara L; Arndt, Volker et al. (2018) Mendelian randomisation study of age at menarche and age at menopause and the risk of colorectal cancer. Br J Cancer 118:1639-1647
van der Vaart, Andrew; Meng, Xianfang; Bowers, M Scott et al. (2018) Glycogen synthase kinase 3 beta regulates ethanol consumption and is a risk factor for alcohol dependence. Neuropsychopharmacology 43:2521-2531
Agrawal, A; Chou, Y-L; Carey, C E et al. (2018) Genome-wide association study identifies a novel locus for cannabis dependence. Mol Psychiatry 23:1293-1302
Liu, Dungang; Zhang, Heping (2018) Residuals and Diagnostics for Ordinal Regression Models: A Surrogate Approach. J Am Stat Assoc 113:845-854
Jeon, Jihyoun; Du, Mengmeng; Schoen, Robert E et al. (2018) Determining Risk of Colorectal Cancer and Starting Age of Screening Based on Lifestyle, Environmental, and Genetic Factors. Gastroenterology 154:2152-2164.e19
Teitelbaum, A M; Murphy, S E; Akk, G et al. (2018) Nicotine dependence is associated with functional variation in FMO3, an enzyme that metabolizes nicotine in the brain. Pharmacogenomics J 18:136-143
Montalvo-Ortiz, Janitza L; Zhou, Hang; D'Andrea, Ivana et al. (2018) Translational studies support a role for serotonin 2B receptor (HTR2B) gene in aggression-related cannabis response. Mol Psychiatry 23:2277-2286

Showing the most recent 10 out of 277 publications