April 30, 2009

PhenX Newsletter - Information and Updates Issue 8. April 30, 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 high priority measures for 20 research domains that are recommended for use in genome-wide association studies (GWAS) and other large-scale genomic studies. Active input from the scientific community is critically important to the process so we solicit feedback through web-based surveys and through the use of the PhenX Toolkit. Your expertise and insight are extremely valuable in the process to achieve effective consensus.




Toolkit Use Statistics


The PhenX Toolkit is already being used by the scientific community. In just the first few months, the Toolkit has had more than 1,000 visits, with the total number of visitors doubling roughly every month (see the graph below).

Toolkit Users by Month

On April 20, 2009, NHGRI and RTI announced, via press releases, the official launch of the PhenX Toolkit. These announcements led to a distinct spike in the number of Toolkit visitors. Following the releases, views jumped from an average of 10 visits per day to 535! Visits to the Toolkit have since leveled out to approximately 50 distinct visits per day.

The majority of Toolkit users have come from the United States. However, Toolkit users have also come from 10 other countries, including Canada, the United Kingdom, Spain and France. This indicates that PhenX is being noticed by the international scientific community.

Additionally, most PhenX Toolkit users examined more than one page on the site. Beyond the home page, the most visited pages include:

  • The page displaying all Domains currently in the Toolkit
  • The Demographics Domain page
  • The Alcohol, Tobacco, and Other Substances Domain page

The most viewed measures (in order) were:

  • Annual Family Income
  • Current Age
  • Ethnicity from the Demographics Domain
  • Birth Weight from the Anthropometrics Domain


Nutrition and Dietary Supplements Working Group


The Chair of the Nutrition and Dietary Supplements Working Group is Dr. Patrick Stover, a molecular biophysicist who is Director of the Division of Nutritional Sciences at Cornell University. The Steering Committee liaison is Dr. Jose Ordovas from Tufts University. The WG has been actively evaluating measures that cover the range of nutrition and dietary supplements. They plan to present the proposed measures and measurement protocols in late spring 2009 in an Internet-based survey available at (www.phenx.org). Because of the broad implications of these measures for many genome-wide association studies, the WG is interested in having input on the proposed measures from the scientific community - both nutrition and disease-specific researchers. The current list of measures includes:
    Breastfeeding     Fruit and Vegetables  
    Caffeine     Percentage Energy from Fat and Saturated Fat  
    Calcium - Adults     Selenium  
    Calcium - Children     Sugar (Added)  
    Dairy     Total Dietary Intake  
    Dietary Supplements     Vitamin D  


Next Steps for the Environmental Exposures Working Group


The Environmental Exposures Working Group (WG) held its sixth meeting on April 14, 2009. The WG is chaired by Dr. Lynn Goldman, a pediatrician and environmental epidemiologist from the Johns Hopkins Bloomberg School of Public Health. The Steering Committee liaison is Dr. Diane Wagener from RTI International. During the last meeting, the WG discussed the measures being proposed for the web-based survey. The proposed measurement protocols will include specific sample collection methods, as well as questionnaires. The current list of measures includes:
    Current Residence Characteristics     Previous ETS Exposure  
    Residence History     ETS- Cotinine in Serum, Urine or Saliva  
    Water Source     Blood Sample- Lead  
    Water Sample- Nitrates     Lived on a Farm  
    Current Occupation     Sibship/Birth Order  
    Longest Held Job     Daycare  
    Personal Protective Equipment and Exposures at Work     History of Being Breast Fed  
    Occupational Checklist     Hobbies  
    Paraoccupational     Dust Sample-Vacuum Bag  
    Occupational History     Dust Sample- Electrostatic Dust Fall Collector (EDC)  
    Air Contaminants in Home Environments     Time Activity and Location  
    Current Environmental Tobacco Smoke (ETS) Exposure     Ultraviolet Light Exposure  


Featured Working Group Chairs


In each newsletter, we highlight two Working Group (WG) members. Here, we present Dr. Forman and Dr. Pearson.


Michele Forman, PhD, MS - Professor in the Department of Epidemiology, University of Texas M.D. Anderson Cancer Center; adjunct Professor at the Department of Pediatrics, Baylor College of Medicine, UT School of Public Health and the Department of Nutrition, Texas Women's University - Anthropometrics WG Chair

Dr. Forman is a Professor and Director of the Nutritional Epidemiology Working group who joined the Department of Epidemiology at the University of Texas M. D. Anderson Cancer Center in January 2006. Dr. Forman is also an adjoint Professor of Epidemiology at the U.T. School of Public Health, adjunct at the Texas Women’s University, and adjunct senior investigator in the Laboratory of Human Carcinogenesis at the Intramural Program of the National Cancer Institute. Dr. Forman has experience in field and analytical epidemiology with an emphasis on nutritional assessment, diet-biochemical validation studies, and etiologic and preventive research in nutrition and cancer. Her interests range from early life exposures and cancer through dietary intervention studies.


Thomas Pearson, MD, MPH, PhD - Cardiovascular WG Chair

Dr. Pearson is Albert D. Kaiser Professor in the Department of Community and Preventive Medicine and Professor of Medicine at the University of Rochester School of Medicine. Dr. Pearson is also Senior Associate Dean for Clinical Research at the University of Rochester Medical Center and directs the Rochester Prevention Research Center. He is Co-Principal Investigator of the Rochester Clinical and Translational Science Institute. Dr. Pearson’s major research interests are in the epidemiology and prevention of atherosclerotic cardiovascular disease, with a special interest in the international trends of coronary heart disease and stroke. Dr. Pearson received his Doctor of Medicine, Master in Public Health, and Doctor of Philosophy in cardiovascular epidemiology, all from The Johns Hopkins University, where he also completed residencies in preventive medicine and internal medicine and a fellowship in cardiology. Dr. Pearson is a Fellow of the American Heart Association, American College of Cardiology, the American College of Preventive Medicine, and the American College of Physicians. Dr. Pearson has served as a member and chair of important committees of the National Heart, Lung, and Blood Institute, the Institute of Medicine, the American Heart Association, and the American College of Cardiology. He has lectured and published extensively in the prevention of cardiovascular disease, including research at the patient, healthcare system, community, and public policy levels.


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
Lisa C. Strader, MPH     PhenX Co-Investigator, RTI International
Richard Kwok, PhD     PhenX Investigator, RTI International
Jane Hammond, PhD     PhenX Investigator, RTI International
Tabitha Hendershot     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


  • Reproductive WG in-person meeting - June 3, 2009
  • Steering Committee in-person meeting - June 4-5, 2009
  • Ocular WG in-person meeting - June 9, 2009
  • Cancer WG in-person meeting - June 17, 2009


Link to Previous PhenX Newsletters




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