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PhenX Project

PhenX Toolkit


Genome-wide association (GWA) studies have identified hundreds of associations between genetic variants and complex human diseases, and for some diseases, such as diabetes and Crohn's disease, pooling of multiple GWA studies by meta-analysis has led to the discovery of new gene associations. However, most GWA studies have had relatively few phenotypic and exposure measures in common. Harmonizing data across studies that have used disparate measures to collect similar information is difficult and time consuming. Development and adoption of standard phenotypic and exposure measures could facilitate the creation of larger, more comprehensive datasets with a variety of phenotype and exposure data for cross-study analysis, thus increasing statistical power and the ability to detect associations of modest effect sizes and gene-gene and gene-environment interactions.

Recognizing the need for standard phenotypic and exposure measures, particularly as related to GWA studies, NHGRI initiated the PhenX Toolkit in 2006 through RFA-HG-07-006, "High-Priority Phenotype and Exposure Measures for Cross-Study Analysis in Genome-Wide Association Studies." The goal of this program is to identify and catalogue 15 high-quality, well-established, and broadly applicable measures for each of 21 research domains for use in GWA studies and other large-scale genomic research. A PhenX domain is a topic area with a unifying theme such as Demographics, Anthropometrics, Neurology, Cancer, or Social Environments. PhenX measures are selected by Working Groups of domain experts using a consensus process and are made available to the scientific community via the PhenX Toolkit (

Project Structure

    PhenX structure

  • The Steering Committee is the governing body for the PhenX program and includes the PhenX Principal Investigator (Carol Hamilton, Ph.D., RTI International), the NIH Project Scientist, and members of the extramural community with expertise in genomics, epidemiology, and biostatistics.

    • Steering Committee Chair: Jonathan Haines, Vanderbilt University (Chair) and William Harlan, National Institutes of Health (Co-Chair, retired)

  • The External Science Panel provides input to the NHGRI Director about the progress and direction of the PhenX Program.

  • The NIH IC Liaisons are scientists from the various NIH Institute and Centers (IC) that participate in shaping PhenX by providing content-specific input and overall guidance for the program.

  • PhenX Working Groups were assembled for each PhenX Domain (e.g., Demographics, Neurology, Social Environments) to select and prioritize the measures included in the PhenX Toolkit. Members of the Working Groups have expertise in phenotyping, epidemiology, and genomics.

Number of Measures and Toolkit Release Date for Each PhenX Domain

    Domain Release Date Number of Measures
    in PhenX Toolkit
    Demographics Feb 2009 15
    Alcohol, Tobacco, & Other Substances Feb 2009 14
    Anthropometrics Mar 2009 16
    Cardiovascular Sep 2009 14
    Nutrition & Dietary Supplements Oct 2009 12
    Environmental Exposures Oct 2009 14
    Cancer Dec 2009 12
    Oral Health Dec 2009 15
    Respiratory Jan 2010 14
    Ocular Feb 2010 15
    Reproductive Health Feb 2010 14
    Diabetes May 2010 15
    Physical Activity & Physical Fitness May 2010 14
    Psychiatric May 2010 14
    Neurology May 2010 13
    Infectious Diseases & Immunity Oct 2010 15
    Skin, Bone, Muscle & Joint Oct 2010 10
    Speech & Hearing Nov 2010 15
    Psychosocial Nov 2010 15
    Social Environments Dec 2010 15
    Gastrointestinal Dec 2010 12


Pan, H., Tryka, K., Vreeman, D., Huggins, W., Phillips, M., Mehta, J., Phillips, J., McDonald, C., Junkins, H., Ramos, E. & Hamilton, C. M. (2012) Using PhenX Measures to Identify Opportunities for Cross-Study Analysis. Human Mutation, 33(5):849-857. 2012. [PubMed]

Hendershot, T., Pan, H., Haines, J., Harlan, W., Junkins, H., Ramos, E., & Hamilton, C. M. Using the PhenX Toolkit to Add Standard Measures to Your Study. Current Protocols in Human Genetics, Chapter 1:Unit1.21. 2011. [PubMed]

Hamilton, C. M., Strader, L. C., Pratt, J., Maiese, D., Hendershot, T., Kwok, R., Hammond, J., Huggins, W., Jackman, D., Pan, H., Nettles, D., Beaty, T., Farrer, L., Kraft, P., Marazita, M., Ordovas, J., Pato, C., Spitz, M., Wagener, D., Williams, M., Junkins, H., Harlan, W., Ramos, E & Haines, J. Response to Invited Commentary: Consolidating Data Harmonization. American Journal of Epidemiology, 174 (3), 265-266. 2011. [Response in AJE]

Schad, P. A., L. R. Mobley, et al. Building a biomedical cyberinfrastructure for collaborative research. Am J Prev Med, 40(5 Suppl 2): S144-150. 2011. [PubMed]

Pathak J., Pan H., Wang, J., Kashyap, S., Schad, P., Hamilton, C. M., Masys, D. & Chute. Evaluating Phenotypic Data Elements for Genetics and Epidemiological Research: Experiences from the eMERGE and PhenX Network Projects. American Medical Informatics Association (AMIA) Clinical Research Informatics (CRI) Summit Proceedings, 2011:41-5. 2011. [PubMed]

Hamilton CM, Strader LC, Pratt JG, Maiese D, Hendershot T, Kwok R, Hammond JA, Huggins W, Jackman D, Pan H, Nettles DS, Beaty TH, Farrer LA, Kraft P, Marazita M, Ordovas JM, Pato CN, Spitz MR, Wagener D, Williams M, Junkins HA, Harlan WR, Ramos EM, Haines J. The PhenX Toolkit: Get the Most From Your Measures. American Journal of Epidemiology, 2010. [PubMed]

Stover PJ, Harlan W, Hammond J, Hendershot T, Hamilton CM. PhenX: a toolkit for interdisciplinary genetics research. Current Opinion in Lipidology, 21(2):136-40. 2010. [PubMed]


PhenX Real World Sharing and Implementation of the PhenX Toolkit (PhenX RISING) New


Erin M. Ramos, Ph.D., M.P.H.
Epidemiologist, Project Scientist

Heather A. Junkins, M.S.
Health Science Analyst

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Last Updated: June 20, 2012