February 9, 2010

PhenX Newsletter - Information and Updates Issue 11. February 9, 2010




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 21 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 January 21-22, 2010 the PhenX Steering Committee (SC) held its ninth in-person meeting in Washington DC. The meeting included updates from nine Working Groups (WGs). Three WGs (Respiratory, Ocular and Reproductive Health) made presentations and received approval of their measures for inclusion in the Toolkit. Two WG Chairs made their final presentations to the SC as their measures were added to the Toolkit in December. Another four WGs are identifying measures for Community Outreach; these include Diabetes, Psychiatric, Neurology, and Physical Fitness and Physical Activity.

The SC discussed the status of the remaining WGs, which are Infectious Diseases and Immunity (Jonathan Haines), Skin, Bone, Muscle and Joint (Lindsay Farrer), Psychosocial (Carlos Pato), Social Environments (Peter Kraft), Gastrointestinal (Bill Harlan) and Speech and Hearing (Mary Marazita).


PhenX Toolkit Release


On January 29, 2010, Version 2.9 of the PhenX Toolkit was released. The release included the following additions, changes and improvements:
  • The Respiratory measures were added to the Toolkit
  • The complete list of PhenX Domains were added as place markers for future measures (links to these are grayed out, remaining Domains are continually being loaded as they become available)
  • Domains and Measures are now listed alphabetically on display pages
  • A convenient reminder was added to remind registered users to update their profiles (users can easily decline the option when the reminder appears)
  • Improvements were made to the instructions for citing the PhenX Toolkit

Measures from the Reproductive Health and Ocular WGs will be added to the Toolkit in upcoming releases. We encourage you to visit the PhenX Toolkit website and register.


Register for the PhenX Toolkit


The PhenX team urges you to become a registered user of the PhenX Toolkit and take full advantage of the array of features the Toolkit offers. As a registered user, you can:
  1. Save and load carts - you can return to the Toolkit and view your saved measures at any time
  2. Share your cart with colleagues
  3. Make notes about measures and include them in your report

Currently, the PhenX Toolkit contains 125 measures from the following 9 domains:

  1. Demographics
  2. Anthropometrics
  3. Alcohol, Tobacco and Other Substances
  4. Cardiovascular
  5. Nutrition and Dietary Supplements
  6. Environmental Exposures
  7. Cancer
  8. Oral Health
  9. Respiratory

To see details about the measures please visit the toolkit: https://www.phenxtoolkit.org/


Working Group (WG) Updates


The Cancer WG, Co-chaired by Dr. Christine Ambrosone and Dr. Neil Caporaso, shared the proposed Cancer research measures with the research community between November 5 and November 18, 2009. Twelve measures have been included in the PhenX Toolkit under the Cancer domain.

Oral Health
The Oral Health WG, Co-chaired by Drs. Jim Beck and Bryan Michalowicz, shared the proposed Oral Health research measures with the research community between October 22 and November 4, 2009. Fifteen measures have been included in the PhenX Toolkit. Two measures were included as supplemental measures.

The Respiratory WG, chaired by Dr. Edwin Silverman, shared the proposed Respiratory research measures with the research community between November 12 and November 25, 2009. Fourteen measures have been included in the PhenX Toolkit. Two measures were included as supplemental measures.


Current Outreach Efforts


Currently, the Physical Activity and Physical Fitness WG is presenting their measures to the scientific community for review and comment. Upcoming outreach efforts will include the Diabetes, Neurology and Psychiatric WGs. If you would like to provide feedback on one or all of the mentioned WG’s proposed measures, send an e-mail to feedback@phenx.org.


Featured Working Group Chairs


In each newsletter, we highlight a Working Group chair. Here, we present Dr. Ambrosone and Dr. Caporaso, the Cancer WG Co-Chairs.


Dr. Christine B. Ambrosone, Professor of Oncology, joined the faculty of Roswell Park Cancer Institute (RPCI) in 2002 and now serves as Chair of the Department of Cancer Prevention and Control. She also serves as a Research Professor in the Department of Social and Preventive Medicine at the University at Buffalo.

Dr. Ambrosone earned her doctoral degree in Epidemiology from the RPCI Graduate Division of the University at Buffalo (UB) in 1994; and completed postdoctoral training in breast cancer research at UB in 1995. She was a Research Epidemiologist at the National Center for Toxicological Research, Food & Drug Administration, Jefferson, AR (1996-2000) before becoming Director of Cancer Epidemiology in the Derald H. Ruttenberg Cancer Center at Mount Sinai School of Medicine, New York, NY (2000-2002).

Dr. Ambrosone’s research focuses on molecular epidemiology and the role of genetic factors in modifying relationships between reproductive, dietary and environmental exposures and cancer risk. She is also interested in genetic and non-genetic factors that impact prognosis after a diagnosis of cancer.
Dr. Ambrosone is a member of many professional organizations and is currently the past year chair (2006) of the Molecular Epidemiology Group of the American Association for Cancer Research (AACR) as well as co-chair of the Molecular Epidemiology Subcommittee of the Southwest Oncology Group. She has received numerous honors and awards including the Thomas B. Tomasi Achievement Award, Roswell Park Cancer Institute a Service Award from the AACR (2000); a Special Recognition Award, AACR (1999); and the Outstanding Achievement award, US Food & Drug Administration (1997).

Dr. Ambrosone has authored or co-authored more than 140 publications and she is past senior editor for Cancer Research as well as acting as a reviewer for numerous scientific journals, including Journal of the American Medical Association, Journal of the National Cancer Institute, The Lancet and the British Journal of Cancer. She is past member of the NCI EPIC Study Section and the ACS Study Section on Carcinogenesis, Nutrition and the Environment and is on the Board of Scientific Advisors to the Director of the National Cancer Institute.


Dr. Neil Caporaso received his undergraduate degree from Rutgers University and his M.D. from the University of Medicine and Dentistry of New Jersey. In 1983 he came to the National Cancer Institute (NCI) as an Oncology fellow in the Medicine Branch. He served as a research fellow and biotechnology fellow in the Environmental Epidemiology Branch of NCI.

Since 1996, he has been the Chief of the Pharmacogenetics Section, Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics. He is a currently a member of the Prostate, Lung, Colorectal and Ovarian (PLCO) steering committee, the DCEG Lung Cancer Interest Group, the NCI Program Review Group for Lung Cancer, and the National Lung Screening Trial (NLST) Biomarkers and Research Evaluation Subcommittees. He helps guide NCI Tobacco priorities and implementation of tobacco-related research as Co-Chair of the Tobacco Research Opportunity Team. He is the Chair of the Phenotype Harmonization Committee for GENEVA (GeneEnvironment Association Studies) and Co-Chair of the PhenX Cancer group, creating standard questionnaire modules for studies of cancer in populations.

He is PI of a Grant funded by GENEVA under the Gene-Environment initiative to conduct a GWAS on lung cancer and smoking and co-PI on a UO1 supporting the Genetic Epidemiology of CLL Consortium. During the last year his group has published a large GWAS of lung cancer implicating a specific genetic locus in the most common histology involved in lung cancer. Also, his group reported that the precursor condition they identified in 2005 named Monoclonal B-Cell Lymphocytosis (MBL) precedes virtually every case of the most common leukemia (CLL) occurring in adults.


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


Upcoming In-Person Meetings


  • Infectious Diseases WG in-person meeting: March 5, 2010
  • Skin, Bone, Muscle and Joint WG in-person meeting: March 10, 2010




On December 30 2009, Version 2.8 of the PhenX Toolkit was released. This release included:
  • Cancer Measures (12)
  • Oral Health Measures (15)


Link to Previous PhenX Newsletters




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