February 24, 2011

PhenX Newsletter - Information and Updates Issue 15. February 24, 2011




The PhenX project, consensus measures for Phenotypes and eXposures, is funded by the National Institutes of Health, National Human Genome Research Institute. The initial phase of the project is complete and the PhenX Toolkit now includes measures for each of the 21 domains selected by the PhenX Steering Committee. A Working Group of experts was convened for each domain, and a consensus-based process was used to select high priority, relatively low burden and well-established measures. Preliminary measures were vetted with the broader scientific community before final selections were made, leading to the set of measures that were loaded in the Toolkit.

The Toolkit includes detailed protocols for collecting the measures, to ensure that the data collected will be comparable between studies. Investigators who come to the Toolkit when designing or expanding a study can be confident that PhenX measures are high quality, having been validated in previous studies. This is particularly helpful for investigators who want to expand their study's data collection beyond their primary research focus. We encourage you to provide feedback when you use the Toolkit, so we can ensure that the Toolkit meets the needs of the scientific community.




PhenX Toolkit Update
All 21 research domains have been added to the Toolkit. The nearly 300 measures were selected over the past three years by working groups of more than 200 scientists from diverse disciplines and backgrounds, including scientists from across the 27 National Institutes of Health (NIH) Institutes and Centers, using a consensus-based process. In a December 20, 2010 RTI press release, Carol M. Hamilton, Ph.D., PhenX Principal Investigator (PI) and Director of Bioinformatics at RTI, said, "We all hope that the PhenX Toolkit will usher in a new era of collaborative research that will have a positive impact on biomedical science and the human condition."
Please visit the Toolkit to see measures for all 21 research domains!


Top 20 measures in the PhenX Toolkit

Following are the top 20 measures chosen by toolkit users as of the February 4 PhenX Toolkit release.


  1.  Current Age   11.  Lipid Profile
  2.  Gender   12.  Current Educational Attainment
  3.  Ethnicity   13.  Annual Family Income
  4.  Race   14.  Current Employment Status
  5.  Weight   15.  Substances - Lifetime Abuse and Dependence
  6.  Alcohol - 30-Day Quantity and Frequency   16.  Birthplace of Grandparents
  7.  Tobacco - Smoking Status   17.  Air Contaminants in the Home Environment
  8.  Height   18.  Tobacco - 30-Day Quantity and Frequency
  9.  Alcohol - Lifetime Use   19.  Tobacco - Age of Initiation of Use
  10.  Birthplace   20.  Current Address


PhenX In Focus
The Toolkit in Focus
In the upcoming year there are plans to evaluate the usability of the PhenX Toolkit website, continue to raise awareness of the Toolkit in the scientific community, and consider adding new measures and features.

Browse Tree
The Toolkit incorporates a Dynamic Browse Tree feature that allows users to easily browse pages and Collections of measures. The Browse Tree is hidden unless you open it up. To see the Tree, click on the Show Tree/Hide Tree option found in the upper left corner of the Browse page; the Tree can be toggled on or off. Collections of measures, organized by shared characteristics, target population or topics, can be found under the Tree. Examples of Collections include measures grouped by risk factors, the top 5 measures within a domain, and the top 20 measures under the latest Toolkit release (currently 4.2). Collections of measures can be downloaded as a group or the user can select individual measures within the Collection.


Steering Committee Update
The in-person PhenX Steering Committee (SC) meeting scheduled for January 27-28, 2011 was held instead as a web-conference due to winter weather in Washington DC. During the two 2-hour web-sessions, the PI reported that all 21 domains were in the Toolkit and highlighted some new Toolkit features. The SC discussed the External Scientific Panel's recommendations and future directions for PhenX. The SC heard reports from two Working Group Chairs: Dr. Richard Kaslow for Infectious Diseases and Immunity and Dr. Doug Kiel for Skin, Bone, Muscle and Joint.


PhenX Press Release
On Dec. 27, 2010 the Toolkit was featured on localtechwire.com. This press release can be found at: http://wraltechwire.com/business/tech_wire/news/blogpost/8837782/


Featured Working Group Chairs


In each newsletter, we highlight some of the PhenX Working Group chairs. Here, we present Drs. Richard Kaslow (Infectious Diseases and Immunity), Bernice Pescosolido (Psychosocial) and David Whitcomb (Gastrointestinal).


Dr. Richard Kaslow
Richard A. Kaslow attended Harvard Medical School. He received his clinical training at Mount Sinai Hospital in New York, University of California at San Francisco, and Children's Hospital-Beth Israel Hospital in Boston. He is board certified in internal medicine, infectious diseases, and preventive medicine. He spent 23 years at CDC and NIH, during which time he held concurrent adjunct faculty appointments at George Washington University and the Uniformed Services University. Dr. Kaslow joined the University of Alabama at Birmingham in the Schools of Public Health and Medicine 16 years ago and holds current appointments as Professor of Epidemiology, Medicine, Microbiology and Genetics, and Director of the Program in Epidemiology of Infection and Immunity. Largely through NIH support mechanisms, he has concentrated on the role of human genetic variation in modulating the risk of infection, disease progression, and vaccine response. He has long experience in cohort studies of human populations, particularly on many facets of HIV/AIDS infection. His team has recently concentrated on investigating the host genetic determinants of transmission and control of HIV infection in HIV-discordant couples. His program has focused more broadly on the role of genetic variation in such conditions as non-Hodgkin's lymphoma, Kawasaki syndrome, and Chlamydia infection as well as in the control of the immune response to HBV and anthrax vaccines. Besides producing more than 200 scholarly publications as a lead, contributing or senior author, he has co-edited texts on HIV/AIDS and on viral diseases and is primary editor of a recently published textbook on genetic susceptibility to infectious diseases. Dr. Kaslow has also served as a mentor and as the Director of the Training Academy for the UAB Center for Clinical and Translational Science. He continues to lead the training of clinicians and other translational scientists in design, conduct and analysis of studies covering a wide range of clinical conditions.


Dr. Bernice Pescosolido
Bernice A. Pescosolido (Ph.D., Yale, Sociology) is Distinguished and Chancellor's Professor of Sociology at Indiana University and Director of the Indiana Consortium for Mental Health Services Research. She has focused her research and teaching on social issues in health, illness, and healing. Specifically, Pescosolido's research agenda addresses how social networks connect individuals to their communities and to institutional structures, providing the "wires" through which people's attitudes and actions are influenced.

In the early 1990s, Pescosolido developed the Network Episode Model which has provided new insights to understanding the patterns and pathways to care, adherence to treatment and the outcomes of health care. With a team of medical and socio-behavioral scientists, she has recently published a multidisciplinary frame and analysis of the gene x environment interaction on the likelihood of being diagnosed with alcohol dependence, receiving the 2009 Eliot Freidson Outstanding Publication Award.

Pescosolido is a leading researcher on the stigma of mental illness. In 1996, she initiated the first national study of MI stigma in the U.S. in over 40 years and, with colleagues, developed a model on the underlying roots of stigma, and recently completed a series of papers based on the first national study of stigma towards children with mental health problems. She also led a team of researchers in the first international stigma study and is currently expanding this 16-country effort to examine MI stigma in China.

Pescosolido's research also focuses on suicide. Her work has examined claims and evaluated the utility of official suicide statistics, and looked at the way that religion and family ties can protect individuals or push them to suicide. With Arthur Kleinman, she helped to shape and write the chapter on social and cultural influences in the 2002 IOM report, Reducing Suicide: A National Imperative.

In 2005, Pescosolido was presented with the American Sociological Association's Leo G. Reeder Award for a career of distinguished scholarship in medical sociology. She has received numerous grants from federal and private sources including two NIMH Scientist Awards, and currently has a Career Development Award from NIDA for epigenetic research on substance abuse and comorbidities. Pescosolido has published widely in sociology, social science, public health and medical journals; served on the editorial board of a dozen national and international journals; and been elected to a variety of leadership positions in professional associations.


Dr. David Whitcomb
Dr. Whitcomb serves as the administrative director of the combined Divisions of Gastroenterology, Hepatology and Nutrition at the University of Pittsburgh, Director of the Cancer Genetics Program at the University of Pittsburgh Cancer Institute and Medical Director of the Comprehensive Pancreas Program, Liver-Pancreas Institute. Cutting edge research is being conducted in genetics, neurobiology (including visceral pain), immunology, epidemiology, early cancer detection and advanced technologies.

Dr. Whitcomb's research group is organized to determine the mechanism of complex disorders including acute pancreatitis, chronic pancreatitis and pancreatic cancer. This has led to the publication of over one hundred peer reviewed manuscripts, multiple reviews, book chapters and the editing of 6 books.

With a background in physiology and medicine, Dr Whitcomb's work has been truly translational - integrating key techniques and perspectives from multiple disciplines with the goal of revolutionizing patient care. His major contributions include discovery of the gene responsible for hereditary pancreatitis, which became the "Rosetta Stone" of pancreatitis. A gene for pancreatic cancer was identified in collaboration with Dr. Brentnall's group.

He co-founded and directed the Center for Genomic Sciences at the University of Pittsburgh, which formed the foundation for the current multi-million dollar Genomic and Proteomic Core Laboratories. This facility makes cutting edge genetic and genomic technologies available to laboratories and investigators throughout the University of Pittsburgh and other institutions. Dr Whitcomb also co-founded the Midwest Multicenter Study Group, which has become the North American Pancreatic Study Group, an organization of academic medical centers dedicated to performing multi-center studies on pancreatic diseases.

Dr. Whitcomb served as a member of the American Gastroenterology Association (AGA) Committee on Gastroenterology Research, AGA nominating committee, Elected as a Counselor for the AGA, and Chairman of the AGA Pancreatic Disorders Section. He served as Counselor, followed by President of the American Pancreatic Association (2003). He has served as counselor of the International Association of Pancreatology since 2000. He also serves as Associate Editor or Pancreatology, and is on the editorial board of Pancreas, Journal of the Pancreas, the American Journal of Physiology and other scientific journals. He is a member of the Board of the National Pancreas Foundation, Director of the NPF Fellow's Symposium, and is honored as the first NPF "Courage at the Corner" awardee. Dr. Whitcomb initiated and has directed six International Hereditary Diseases of the Pancreas symposium, as well as serving as director of over a dozen other continuous medical education-certified (CME) programs. He remains a popular mentor, teacher, lecturer and professor - all linked to diseases of the pancreas.


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
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
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





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