November 10, 2009

PhenX Newsletter - Information and Updates Issue 10. November 10, 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, low burden, 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 regarding proposed measures through a consensus building process meant to access subject matter experts and research professionals and through the use of the PhenX Toolkit. Your expertise and insight are extremely valuable in the process to achieve effective consensus.




Steering Committee (SC) In-Person Meeting


On September 10-11, 2009 the PhenX Steering Committee (SC) held its eighth in-person meeting in Washington DC. The meeting included updates from the seven active Working Groups (WGs). Two of the WGs, Nutrition and Dietary Supplements and Environmental Exposures, received approval to place their final measures into the Toolkit. Five of the other active WGs are identifying measures for community consensus, including Oral Health, Reproductive Health, Ocular, Cancer, and Respiratory.

The Nutrition and Dietary Supplements WG Chair, Dr. Patrick Stover, and the Environmental Exposures WG Chair, Dr. Lynn Goldman, reported on the respective proposed measures for Toolkit. WG Co-Chairs Drs. James Beck and Bryan Michalowicz for Oral Health, Dr. Carol Hogue for Reproductive Health, Dr. Janey Wiggs for Ocular, and Dr. Neil Caporaso for Cancer participated in the meeting to share their proposed measures for consensus outreach. SC Liaison Terri Beaty updated the SC on proposed measures for the Respiratory WG. The Cardiovascular WG Chair, Dr. Tom Pearson, made his final presentation to the SC on the Cardiovascular measures, which are now available in the Toolkit.

SC Liaisons provided updates on other WGs that are in the initial stages of the consensus process, including Physical Activity and Physical Fitness, Psychiatric, Neurology and Diabetes. The SC approved a proposal to add a domain on Social Environment, which has funding from Office of Behavioral and Social Sciences Research (OBSSR).


Changes to the Outreach and Consensus Process


During the September 10-11 PhenX SC in-person meeting, the SC concluded that the Survey portion of the current outreach and consensus process should be replaced with a more streamlined approach.

The revised outreach and consensus process will consist of e-mail blasts to PhenX participants and members of the professional research community, including subject matter experts identified by WG members. To reduce the burden on respondents, members of the scientific community will be asked to answer four questions about the WG’s proposed measures:

  • Which measures do you think are most valuable for population based genomic studies?
  • Which measures do you think are least valuable?
  • Would you like to recommend other measures for inclusion in the Toolkit? If so, please comment.
  • Is this WG domain your primary research focus?

Responses can be sent via e-mail or fax and will be collated, organized and then presented to the WG. We anticipate that this focused outreach plan will lead to an increase in community input.


Current Outreach Efforts


Current outreach efforts include the Oral Health and Cancer WGs. Please be on the lookout for an email invitation to review and comment on measures from the following WGs:
  • Ocular
  • Respiratory
  • Reproductive Health


Working Group (WG) In-Person Meetings


Physical Activity

On September 23, 2009, the Physical Activity and Physical Fitness WG gathered for an in-person meeting with the goal of revising the current list of domain elements and proposed measures and identifying the most appropriate protocols. Dr. Bill Haskell and Dr. Rick Troiano are the WG Co-Chairs. Dr. Haskell is an Emeritus Professor at Stanford University’s School of Medicine Prevention Research Center. Dr. Rick Troiano is an epidemiologist in the Risk Factor Monitoring and Methods Branch of the Applied Research Program in the Division of Cancer Control and Population Sciences at the National Cancer Institute (NCI). The SC Liaison is Dr. Jose Ordovas. The WG consists of four additional physical activity experts and one expert on the genetics of obesity. During the in-person meeting, the experts discussed many aspects of physical activity and physical fitness including the use of subjective and objective measures to determine total physical activity, fitness, and mediators and moderators that influence a person’s physical activity.


On October 7, 2009, the Diabetes Working Group gathered for an in-person meeting and considered key topics in diabetes health research including risk factors such as family history of diabetes, biological assessments such as fasting blood glucose and serum insulin and associated complications including retinopathy, nephropathy and neuropathy. The Chair of the Diabetes Working Group is Dr. Craig Hanis, Professor of Genetics and Epidemiology at the Human Genetics Center at University of Texas, Houston. The SC liaison is Dr. William Harlan.


On October 9, 2009, the Neurology WG gathered for an in-person meeting. During this meeting, the WG members presented information on several key topics and identified potential measures that address elements within the neurology domain. The Neurology Working Group Chair is Dr. Jeffery Vance, Chair of Dr. John T. Macdonald Foundation Department of Human Genetics and Director, Center for Genomic Medicine, Hussman Institute for Human Genomics at the University Of Miami Miller School Of Medicine. The SC liaison is Dr. Lindsay Farrer from Boston University School of Medicine.


Conferences and Presentations at Professional Meetings


PhenX presented 2 posters in October 2009; the first was presented by SC Member Peter Kraft at the International Genetic Epidemiology Society (IGES) meeting and the second was presented by WG Supervisor and SC Coordinator Tabitha Hendershot at the American Society of Human Genetics (ASHG) meeting. These posters, titled "The PhenX Toolkit - Get the Most from Your Measures", presented the progress that PhenX has made to a wide variety of meeting attendees in the field of genetics.

In November, Michael Phillips from RTI made an oral presentation titled "Consensus of Environmental Exposure Measures for Genome-wide Association Studies" at the 2009 International Society of Exposure Science (ISES) Conference in Minneapolis, Minnesota.


Featured Working Group Chairs


In each newsletter, we highlight a Working Group chair. Here, we present Dr. Vance, the Neurology WG Chair.


Jeffery M. Vance, MD, PhD, is Chair of the Dr. John T. Macdonald Foundation Department of Human Genetics and Director of the Center for Genomic Medicine in the John P. Hussman Institute for Human Genomics at the University of Miami Miller School of Medicine. Dr. Vance is boarded in both the American Board of Psychiatry and Neurology and the American College of Medical Genetics as a board-certified PhD Medical Geneticist.

Dr. Vance’s primary areas of expertise and national recognition are in Neurogenetics, especially in Parkinson’s disease and Charcot-Marie-Tooth Disease. His research has focused on the application of clinical, molecular, and mathematical genetic techniques to identify genes leading to human disease. He has identified five loci for Charcot-Marie-Tooth disease(CMT) (CMT1A, CMT2A, CMT4A, CMT4B, CMT4C), the gene defects for CMT4A (GDAP-1), CMT2A (Mitofusin 2), dominant intermediate (Dynamin-2) CMTB, collaborated on CMT2D/ Distal Spinal Muscular Atrophy Type V gene discovery (Glycyl tRNA Synthetase), spastic paraparesis (REEP1) 31 and gene mutations for three different muscular dystrophies (including a-sarcoglycan), as well as identified the gene defect in the Haw River Syndrome.

Dr. Vance has also been a leader in applying genetics to common medical diseases to identify susceptibility genes. He serves as the director (primary principle investigator) of a NIH Morris K. Udall Parkinson Disease (PD) Research Center of Excellence. This Udall group has demonstrated that Parkinson Disease (PD) has significant genetic contributions, having identified a large number of the confirmed susceptibility genes in PD to date. He served as one of the principle investigators of the Guilford Genomic Medicine Initiative (GGMI) now known as the Genomedical Connection, a genomic medicine project funded by the Department of Defense.

He has published over 200 publications including more than 180 peer-reviewed. His work has been cited more than 6,000 times.


Steering Committee Members


Jonathan Haines, PhD, Chair     Vanderbilt University, Center for Human Genetics Research
William R. Harlan, MD, Vice Chair     Retired, National Institutes of Health
Terri H. Beaty, PhD     Johns Hopkins School of Public Health
Lindsay A. Farrer, PhD     Boston University
Peter Kraft, PhD     Harvard University 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
Wayne Huggins, 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
Heather Junkins, MS     Scientific Program Analyst, NHGRI
Teri Manolio, MD, PhD     Director, Office of Population Genomics;
  Senior Advisor to the Director, NHGRI, for Population Genomics




On October 30, 2009, Version 2.7 was released to the Toolkit. This release included:
      1.   Addition of the Nutrition and Dietary Supplements measures.
      2.   Addition of the Environmental Exposures measures.


Upcoming In-Person Meetings


  • SC in-person meeting: January 21-22, 2010


Link to Previous PhenX Newsletters


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