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Gene Environment Association Studies (GENEVA)

GENEVA - Gene Environment Association Studies 

Background

The Genes, Environment and Health Initiative (GEI) is a National Institutes of Health (NIH)-wide initiative that aims to accelerate understanding of genetic and environmental contributions to health and disease. There are two components to GEI: genetics and exposure biology. The genetics component currently consists of eight programs including the Gene Environment Association Studies (GENEVA) consortium. GENEVA was initiated to: identify genetic variants related to complex diseases; identify variations in gene-trait associations related to environmental exposures; and ensure rapid sharing of data through the Database of Genotypes and Phenotypes (dbGaP). GENEVA is led by NHGRI, and consists of multiple academic institutions, including a coordinating center, two genotyping centers and 16 studies of various phenotypes, as well as several Institutes and Centers of the NIH. GENEVA was funded in two rounds: the first round of GENEVA was funded in 2007 in response to RFA-HG-06-033 and the second in 2008 in response to RFA-HG-07-012. In 2009, existing GWAS studies joined the GENEVA consortium to take advantage of the consortium expertise and participate in the collaborative aspect of the network.

Coordinating Center

The coordinating center for GENEVA is headed by Bruce Weir of the University of Washington. The Coordinating Center assists with genotypic data cleaning and analysis, phenotype data organization and coordination of the logistics and administration of the study. The Coordinating Center serves as an internal data repository for GENEVA and also assists in phenotypic data harmonization across multiple studies.

Study Investigators

Principal Investigator (PI) Institution Title Sample Size Study Population Description
Chris Amos, Ph.D. University of Texas High Density SNP Association Analysis of Melanoma 3,035 European Ancestry
Kathleen Barnes, Ph.D. Johns Hopkins University Genome-Wide Associations Environmental Interactions in the Lung Health Study 4,397 European Ancestry
Terri Beaty, Ph.D. Johns Hopkins University International Consortium to Identify Genes and Interactions Controlling Oral Clefts 7,089 European Ancestry, Asian/Pacific Islander, African Ancestry, Other
Laura Bierut, M.D. Washington University Study of Addiction: Genetics and Environment 4,121 European Ancestry, Asian/Pacific Islander, African Ancestry, Other
Eric Boerwinkle, Ph.D. University of Texas GWA for Gene-Environment Interaction Effects Influencing CHD 12,771 European and African Ancestry
Neil Caporaso, M.D. National Cancer Institute Population-based Lung Cancer Study 5,588 European Ancestry
Myriam Fornage, Ph..D University of Texas GWAS of longitudinal blood pressure profiles from young adulthood to middle-age 1,725 European Ancestry
David Ginsburg, M.D. University of Michigan Genes and Blood Clotting 1,115 European Ancestry, Asian Ancestry, Other
Christopher Haiman, Sc.D. University of Southern California A Multiethnic Genome-Wide Scan of Prostate Cancer 9,253 Asian Ancestry, African Ancestry, Hispanic/Latino
John Heit, M.D. Mayo Clinic GWAS of Venous Thrombosis 2,594 European Ancestry, Other
Frank Hu, M.D., Ph.D. Harvard University Genes and Environment Initiatives in Type 2 Diabetes 5,961 European Ancestry, African Ancestry, Asian Ancestry, Hispanic, Other
William Lowe, M.D. Northwestern University GWA Mapping: Maternal Metabolism-Birth Weight Interactions 6,513 African Ancestry, European Ancestry, Hispanic
Mary Marazita, Ph.D. University of Pittsburgh Dental Caries: Whole Genome Association and Gene x Environment Studies 4,020 European Ancestry, African Ancestry, Other
Braxton Mitchell, Ph.D. University of Maryland Genetic Risk to Stroke in Smokers and Nonsmokers in Two Ethnic Groups 1,818 European Ancestry, African Ancestry, Hispanic, Asian Ancestry, Other
Jeffrey Murray, M.D. University of Iowa Genome-wide association studies of prematurity and its complications 7,472 European Ancestry, African Ancestry
Louis Pasquale, M.D. Harvard University Genes and Environment Initiative in Glaucoma 2,188 European Ancestry, Other

 

Genotyping Centers

There are two laboratories that conduct the genotyping for GENEVA studies: the Center for Inherited Disease Research (CIDR) at Johns Hopkins University and the Broad Institute of MIT and Harvard.

Center for Inherited Disease Research (CIDR) at Johns Hopkins University

PI: David Valle, M.D.
Co-PI: Kimberly F. Doheny, Ph.D.
Co-PI: Elizabeth Pugh, Ph.D.

Broad Institute of MIT and Harvard

PI: Stacey Gabriel, Ph.D.
Co-PI: Daniel Mirel, Ph.D.

NIH Participants

National Human Genome Research Institute (NHGRI)

The GENEVA program officials at the NHGRI Office of Population Genomics facilitate the achievement of scientific goals and provide institutional oversight and guidance to the project.

National Center for Biotechnology Information (NCBI)

The data from each individual study will be deposited in the Database of Genotypes and Phenotypes (dbGaP), which is housed at NCBI.

Expert Scientific Panel and Steering Committee

The Expert Scientific Panel provides input to the NHGRI director about the progress and direction of the network.

The Steering Committee is responsible for the coordination of all activities conducted by the network.

Steering Committee Chair: Bill Lowe, Northwestern University

Subcommittees

  • Analysis Subcommittee
    Chairs: Jun Li and Mariza de Andrade. Provide guidance on the analysis of GENEVA data, including cut-offs for significant associations and analysis methods for G x G and G x E interactions. The group will also identify common methods and strategies among each of the sixteen studies.
     
  • Cross-Study Integration Subcommittee
    Chairs: Myriam Fornage and Jeff Murray. Help bring the phenotype data together as well as harmonize and review the genotype data; discuss statistical methods; draft GENEVA-wide policies, including authorship guidelines and standardized methods and data-cleaning sections; form alliances with other NIH GWAS.
     
  • Genotyping Subcommittee
    Chairs: Eric Boerwinkle and Julie Cunningham. Advise the Steering Committee on issues related to genotyping data quality, data flow, dataset preparation and posting data on dbGaP.
     
  • Phenotype Harmonization Subcommittee
    Chairs: Neil Caporaso and Siiri Bennett. Identify phenotypes that are present across studies and encourage investigators to share data; identify, define and code key variables and covariates; be engaged in the broader data process with the Coordinating Center, including cleaning, validating and coding to create a usable end result; coordinate with other subcommittees on the use of harmonized phenotypic data.
     

Phenotype Working Groups

For each phenotype category of interest, the Phenotype Harmonization Subcommittee has convened a Working Group, led by an investigator from one of the studies, to identify and define specific variables to be shared in cross-study analyses.

  • Alcohol use
  • Anthropometrics
  • Caffeine use
  • Hypertension
  • Oral health
  • Physical activity and exercise
  • Protective effects
  • Reproductive history
  • Sleep
  • Tobacco use
     

Published Manuscripts

Contacts

GENEVA Website [genevastudy.org]

Last updated: September 30, 2013