We propose to create a """"""""Center for GEI Association Studies"""""""" in support of the NIH's Genes by Environment Initiative (GEI) at the Broad Institute, within the Genetic Analysis Platform.
Our aim i s to enable whole genome association scans to succeed by supplying high quality large-scale genotyping in an environment that has proven ability in industrial process, commitment to scientific rigor and a depth of analytic expertise. Specifically, according to the stated goals of the RFA, we will genotype at least 7200 samples in year one, and at least 12,000 in total over the first three years of the award. We will receive and qualify DNA samples from external investigators. Once qualified we will use the Affymetrix whole genome genotyping platform to carry out genotyping of 1M SNPs on a single array. We will also make available three other platforms for genotyping (Illumina Infinium, Illumina Golden Gate and Sequenom MassArray) as options for whole genome studies, or critically, to be used in rapid validation and follow up of putative associations. We will apply rigorous QC metrics and filters to supply """"""""clean"""""""" data sets to users. Finally, we will work with the NCBI to deposit data according to the NIH's guidelines on data sharing in a timely and efficient manner. Given the fast pace of development of genetic analysis tools, we will continue to improve upon existing products in terms of content and quality and will drive forward the adoption of new technologies as they become available.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project--Cooperative Agreements (U01)
Project #
Application #
Study Section
Special Emphasis Panel (ZHG1-HGR-P (M2))
Program Officer
Wise, Anastasia Leigh
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Broad Institute, Inc.
United States
Zip Code
Loomis, Stephanie J; Li, Man; Maruthur, Nisa M et al. (2018) Genome-Wide Association Study of Serum Fructosamine and Glycated Albumin in Adults Without Diagnosed Diabetes: Results From the Atherosclerosis Risk in Communities Study. Diabetes 67:1684-1696
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
Bailey, Jessica N Cooke; Gharahkhani, Puya; Kang, Jae H et al. (2018) Testosterone Pathway Genetic Polymorphisms in Relation to Primary Open-Angle Glaucoma: An Analysis in Two Large Datasets. Invest Ophthalmol Vis Sci 59:629-636
Goto, Atsushi; Chen, Brian H; Chan, Kei-Hang K et al. (2018) Genetic variants in sex hormone pathways and the risk of type 2 diabetes among African American, Hispanic American, and European American postmenopausal women in the US. J Diabetes 10:524-533
Bray, Michael J; Wellons, Melissa F; Jones, Sarah H et al. (2018) Transethnic and race-stratified genome-wide association study of fibroid characteristics in African American and European American women. Fertil Steril 110:737-745.e34
Keaton, Jacob M; Gao, Chuan; Guan, Meijian et al. (2018) Genome-wide interaction with the insulin secretion locus MTNR1B reveals CMIP as a novel type 2 diabetes susceptibility gene in African Americans. Genet Epidemiol 42:559-570
Bhagwandin, Candida; Ashbeck, Erin L; Whalen, Michael et al. (2018) The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific manner. PLoS One 13:e0204898
Khawaja, Anthony P; Cooke Bailey, Jessica N; Wareham, Nicholas J et al. (2018) Genome-wide analyses identify 68 new loci associated with intraocular pressure and improve risk prediction for primary open-angle glaucoma. Nat Genet 50:778-782
Wang, Liuyang; Pittman, Kelly J; Barker, Jeffrey R et al. (2018) An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host Microbe 24:308-323.e6
Ochs-Balcom, Heather M; Preus, Leah; Nie, Jing et al. (2018) Physical activity modifies genetic susceptibility to obesity in postmenopausal women. Menopause 25:1131-1137

Showing the most recent 10 out of 99 publications