November 7, 2008

PhenX Newsletter - Information and Updates Issue 6. November 7, 2008


The project PhenX, for Phenotypes and eXposures, is funded by National Institutes of Health's, National Human Genome Research Institute. The goal of the project is to select 15 measures for up to 20 research domains that will be recommended for use in genome-wide association studies (GWAS) and other large-scale genomic studies. The active input from researchers is critically important for this consensus effort. We seek input from the research community through web-based surveys. Your expertise and insight will be extremely valuable while developing an effective consensus process.


Call for Survey Response on Alcohol, Tobacco, and Other Substances Measures

RTI International is currently seeking comments on measuring quantity and frequency of consumption, age of initiation and offset of use, and other alcohol, tobacco, and substance use measures. Feedback is being gathered via an anonymous web-based survey. The initial comment period for this survey is November 3rd through December 1st and may be accessed at The survey features two sections. The first section allows you to provide your feedback on proposed measures such as Lifetime use, 30-day consumption: quantity and frequency, Age of initiation of use, and also welcomes suggestions for additional measures and/or alternative protocols. In the second section of the survey, you can prioritize measures to be included in the Toolkit. Your expertise and insight will be extremely valuable to developing consensus on a set of measures.

These measures are being proposed by the PhenX Alcohol, Tobacco and Other Substances Working Group chaired by Deborah Hasin, with representatives from academia and government. Your input will help the PhenX Working Group prioritize the 15 measures that will be recommended for genome wide research studies.

Posters to be presented at ASHG Conference

Two posters representing the PhenX consensus project will be presented at the 2008 American Society for Human Genetics (ASHG) conference. One poster provides an Overview of PhenX processes and the Toolkit. The second poster focuses on the Demographics Domain and highlights the measures that will be included in the PhenX Toolkit. The conference will be held in Philadelphia, PA from November 11 – 15. Presenters are the PhenX PI, Carol Hamilton, and the PhenX Co-Investigator and Steering Committee member, Diane Wagener.

Steering Committee

On September 22-23, 2008, the PhenX Steering Committee (SC) held its third in-person meeting in Washington DC. All twelve members of the SC attended, along with six liaisons from NIH Institutes and Centers (ICs). Discussions during the two-day meeting covered a wide range of topics, including updates from the Chairs of the four active Working Groups (WGs): Demographics, Anthropometrics, Alcohol, Tobacco and Other Substances (ATOS) and Cardiovascular (CV). The Demographics and Anthropometrics WGs had already collected and considered input from the web-based surveys on their preliminary measures. The Demographics WG Chair (Myles Cockburn) presented the final 15 measures for inclusion in the Toolkit, and the SC voiced their approval. In the absence of the Anthropometrics WG Chair (Michelle Forman), the SC Liaison, Michelle Williams, discussed some of the issues that the WG faces as they narrow down the measures to the final 15. The ATOS Chair (Deborah Hasin) reported that the WG was on track and was in the process of finalizing the measures that would be included in the survey. Finally, as work begins on the first disease-based domain, the SC and Cardiovascular WG Chair (Tom Pearson) discussed ways to refine the scope of that domain.

A highlight of the meeting was getting the first glimpse of the Toolkit. The development team presented an interactive prototype for the Toolkit to illustrate the functionality and show how researchers will use the Toolkit. Some features include:

  • Browse and Search functions will help the user view and select measures
  • A 'shopping cart' will include selected measures and protocols
  • Custom reports will include detailed protocols and information about the selected measures
  • The SC deliberated about the scope of the upcoming domains and refined the list of 20 domains. The upcoming domains and the SC Liaison to each WG are as follows:

      Nutrition and Dietary Supplements   Jose Ordovas
      Cancer   Margaret Spitz
      Exposures   Diane Wagener
      Oral Health   Mary Marazita
      Reproduction   Michelle Williams
      Lung Function   Terry Beaty
      Diabetes   Bill Harlan
      Neurological   Lindsay Farrer
      Psychiatric   Carlos Pato
      Physical Activity and Physical Fitness   Jose Ordovas
      Ocular   Jonathan Haines
      Psychosocial   Carlos Pato

    Featuring Steering Committee Members

    We have highlighted the newest member of the Steering Committee (SC) in this newsletter. Here, we present Dr. Carlos Neves Pato.

    Carlos Neves Pato, M.D., Ph.D.

    Dr. Carlos Pato has an ongoing interest in the genetics of complex phenotypes such as psychotic disorders, schizophrenia and bipolar disorder, as well as obsessive-compulsive disorder. Trying to understand the genetics of these complex diseases has been extremely difficult, given inherent genetic variability and variability in the disorders themselves. Dr. Pato’s other interests include pioneering techniques for using microarray gene expression studies to pursue potential diagnostic and screening tests for these mental-health disorders and looking at whole-genome linkage studies and family-based association studies to better understand the genetics of schizophrenia and bipolar disorder. Dr. Pato has had over 70 publications.

    Steering Committee Members

    Jonathan Haines, PhD, Chair   Vanderbilt University, Center for Human Genetics Research
    William R. Harlan, MD, Vice Chair   National Library of Medicine Consultant
    Terri H. Beaty, PhD   Johns Hopkins School of Public Health
    Lindsay A. Farrer, PhD   Boston University
    Peter Kraft, PhD   Harvard School of Public Health
    Mary L. Marazita, PhD   University of Pittsburgh, Center for Craniofacial and Dental Genetics
    Jose M. Ordovas, PhD   Tufts University, Human Nutrition Research Center on Aging
    Carlos Neves Pato, M.D., Ph.D.   University of Southern California, Zilkha Neurogenetic Institute
    Erin Ramos, PhD, MPH   National Human Genome Research Institute
    Margaret R. Spitz, MD, MPH   University of Texas, MD Anderson Cancer Center
    Diane Wagener, PhD   RTI International
    Michelle Williams, ScD   University of Washington

    Research Team Members

    Carol M. Hamilton, PhD   PhenX Principal Investigator, RTI International
    Diane Wagener, PhD   PhenX co-Investigator, RTI International
    Richard Kwok, PhD   PhenX Investigator, RTI International
    Deborah Maiese, MPA   Consensus Coordinator, RTI International
    Joe Pratt, MPM   PhenX Project Manager, RTI International
    Erin Ramos, PhD, MPH   Project Scientist, NHGRI
    Teri Manolio, MD, PhD   Director, Office of Population Genomics;
      Senior Advisor to the Director, NHGRI, for Population Genomics
    Heather Junkins, MS   Scientific Program Analyst, NHGRI


  • The Anthropometrics Survey was closed on September 8, 2008
  • The Steering Committee had an in-person meeting on September 22-23, 2008
  • The Cardiovascular WG had an Introductory call on October 1, 2008
  • The Nutrition and Dietary Supplements WG had an Introductory call on November 3, 2008

  • More...

    Upcoming In-Person Meetings

    Cardiovascular in-person meeting November 24, 2008
    Nutrition and Dietary Supplements in-person meeting December 17, 2008
    Steering Committee in-person meeting January 6-7, 2008

    Link to Previous PhenX Newsletters

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