February 27, 2009

PhenX Newsletter - Information and Updates Issue 7. February 27, 2009




The project PhenX, consensus measures for Phenotypes and eXposures, is funded by the National Institutes of Health, National Human Genome Research Institute. The goal of the project is to select 15 measures for 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 use of web-based surveys and the PhenX Toolkit. Your expertise and insight will be extremely valuable while developing an effective consensus process.




Toolkit Release


The PhenX Toolkit (https://www.phenxtoolkit.org) was released on February 6, 2009. The Toolkit is a web-based catalog of high priority measures for use in genome-wide association studies (GWAS) and other large-scale genomic research efforts. Because PhenX measures are selected by an expert panel that considers input from the larger scientific community, researchers can have confidence in the measures included in the PhenX Toolkit. The initial version of the Toolkit contains measures selected by the Demographics Working Group (WG) and the Alcohol, Tobacco and Other Substances WG. Measures from the Anthropometric WG will be added soon. Additional measures will be added to the Toolkit as they are finalized by upcoming WGs and approved by the Steering Committee.
  • Researchers will visit the Toolkit to:
    • Add high priority measures to ongoing studies
    • Consider PhenX measures when planning new studies
    • Obtain high-quality measures outside of their primary research area

  • By selecting some of the PhenX standard measures:
    • Researchers ensure that their study will be compatible with other studies that incorporate the same PhenX measures-thus facilitating cross-study analysis
    • Researchers will be able to combine studies-thus increasing statistical power and the ability to identify genes associated with complex diseases and traits, gene-gene, and gene-environment interactions

For each PhenX measure, the Toolkit provides: a brief description of the measure, protocol(s) for collecting the measure, the rationale for selecting the protocol(s) and additional information about the measure. The Toolkit provides a glossary, FAQs and a basic guidance document.

     Please check out the PhenX Toolkit at https://www.phenxtoolkit.org.     

Researchers are invited to provide feedback on the Toolkit - we welcome your input!

Adding Measures to the Toolkit:

    Research Area (Domain)     Status     WG Chair     SC Liaison  
    Demographics     In Toolkit     Dr. Myles Cockburn     Dr. Peter Kraft  
    ATOS     In Toolkit     Dr. Deborah Hasin     Dr. Erin Ramos  
    Anthropometrics     Coming Soon to the Toolkit     Dr. Michele Forman     Dr. Michelle Williams  
    Cardiovascular     Survey Launch in March     Dr. Tom Pearson     Dr. William Harlan  
    Nutrition and Dietary
    In Progress     Dr. Patrick Stover     Dr. Jose Ordovas  
    Environmental Exposures     In Progress     Dr. Lynn Goldman     Dr. Diane Wagener  
    Cancer     In Progress     Drs. Neil Caporaso and
  Christine Ambrosone
    Dr. Margaret Spitz  
    Oral Health     In Progress     Drs. James Beck and
  Bryan Michalowicz
    Dr. Mary Marazita  
    Ocular     Assembling WG     TBD     Dr. Jonathan Haines  
    Lung Function     Assembling WG     TBD     Dr. Terri Beaty  
    Reproduction     Assembling WG     TBD     Dr. Michelle Williams  


Steering Committee


On January 6-7, 2009 the PhenX Steering Committee (SC) held its fourth in-person meeting in Washington DC. All twelve members of the SC attended, along with five liaisons from NIH Institutes and Centers (ICs). The meeting began with the RTI development team presenting an interactive look at the PhenX Toolkit. Using the Demographic measures, the features and functionality of the Toolkit were demonstrated.

The meeting also included updates from the Chairs of four WGs: Anthropometrics, Alcohol, Tobacco and Other Substances (ATOS), Cardiovascular (CV) and Nutrition and Dietary Supplements. As part of the consensus process, each WG selects 25 preliminary measures that are vetted with the scientific community via a web-based survey. The WG considers this input as they select the final measures for the Toolkit. Having considered input from the web-based PhenX Survey, the Anthropometrics WG Chair, Dr. Michele Forman, presented the final measures for inclusion in the Toolkit and the SC voiced their approval subject to a review of the datasheets once they are complete. The ATOS Chair, Dr. Deborah Hasin, presented the results of their survey as well as the final measures, which the SC approved. The Cardiovascular WG Chair, Dr. Tom Pearson, discussed a list of preliminary measures and plans for adding personal and family history and medication usage measures to go to survey. The Nutrition and Dietary Supplements WG Chair, Dr. Patrick Stover, presented the current scope of the domain and discussed their approach for collecting information about dietary intake.

The SC Liaisons gave updates on other WGs that are in the beginning stages of the consensus process. The SC Liaison for the Environmental Exposures WG, Dr. Diane Wagener, discussed the scope of the domain. Dr. Margaret Spitz, SC Liaison for the Cancer WG, discussed WG membership and scope of the domain. According to SC Liaison Dr. Mary Marazita, the Oral Health WG is currently being organized.

The SC deliberated about the scope of the upcoming domains and refined the list of 20 domains.


Environmental Exposures


On January 8, 2009, the Environmental Exposures Working Group (WG) gathered for an in-person meeting with the goal of identifying a set of measures and protocols to cover the broad range of environmental and occupational exposures. During this meeting, the WG members presented information on several key topics and identified potential measures that addressed elements within residential history, occupational history, hobbies, early life exposures, environmental sample collection, environmental tobacco smoke, and time spent outdoors. The WG Chair is Dr. Lynn Goldman, a pediatrician and environmental epidemiologist from the Johns Hopkins Bloomberg School of Public Health. The WG consists of eight experts in the fields of environmental epidemiology, occupational health, and exposure science.


Next Steps from the Cardiovascular Working Group


The Cardiovascular Working Group (WG) held its fifth meeting on December 19th, 2008. The WG is chaired by Dr. Thomas Pearson from the University of Rochester Medical Center and the Steering Committee liaison is Dr. William Harlan from the National Institutes of Health. During their meeting, they discussed the measures and protocols that will be included in the web-based survey circulated to the scientific community. The survey presents the proposed measures and measurement protocols and asks the research community to rank the measures and provide feedback on the utility of the proposed measures. The survey will be posted on the PhenX website in March 2009.


Featured Working Group Chairs


We have highlighted two Working Group (WG) chairs in this newsletter. Here, we present Drs. Cockburn and Hasin.


Myles Cockburn, PhD - Associate Professor, Department of Preventive Medicine and Department of Geography, University of Southern California

Dr. Myles Cockburn has a PhD in Epidemiology from the University of Otago, New Zealand. His research interests are cancer epidemiology and applications of geographic information systems (GIS) in epidemiology. He is particularly interested in how race and ethnicity may influence cancer incidence. Dr. Cockburn has led many NIH-funded grants and has co-authored books on cancer epidemiology. Current studies focus on gene-environment interaction in melanoma and prostate cancer, and cancer control among distinct racial/ethnic groups (particularly Hispanics and Pacific Islanders).


Deborah S. Hasin, PhD - Professor of Clinical Epidemiology (in Psychiatry) at Columbia University, College of Physicians & Surgeons and the Mailman School of Public Health

Dr. Deborah Hasin is an epidemiologist whose research focuses on alcohol and drug disorders and related psychiatric comorbidity. Dr. Hasin's work has been published in over 200 publications. Her current projects include a study in Israel on gene-environment interaction in the etiology of alcohol, analyses of national data and longitudinal cohorts for risk factors affecting the occurrence and course of alcohol and drug disorders, and a clinical trial of a technologically enhanced brief drinking-reduction intervention in HIV primary care patients. Dr. Hasin's diagnostic research interview, the PRISM, is in use in numerous studies of the relationship of substance and psychiatric disorders in the U.S. and internationally.


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 School of Public Health and Community Medicine


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


Upcoming In-Person Meetings


The Oral Health Working Group will hold an in-person meeting on April 6, 2009
The Steering Committee will hold an in-person meeting on June 4-5, 2009 in Washington, DC


Link to Previous PhenX Newsletters




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