June 18, 2014

PhenX Newsletter - Information and Updates Issue 22. June 18, 2014


PhenX Steering Committee Update

In April, the PhenX Steering Committee (SC) met in Washington, DC for a 2-day meeting. Project updates were presented and emerging issues discussed. The SC decided to move forward with Obesity as the second domain and to use the REDCap (Research Electronic Data Capture) tool to create web-based protocols for all PhenX measures. SC members saw a live demonstration of the REDCap pilot work completed by the PhenX Toolkit Team, making 14 PhenX protocols web-based.

Guest speakers Jennie Larkin, from the National Heart Lung and Blood Institute (NHLBI), and Jerry Sheehan, from the National Library of Medicine (NLM) presented on two important initiatives within the National Institutes of Health (NIH). Jennie Larkin presented the Big Data to Knowledge (BD2K) initiative, whose mission is to enable biomedical scientists to capitalize more fully on the Big Data being generated by those research communities (http://bd2k.nih.gov/). Jerry Sheehan highlighted NIH's work to improve coordination among similar efforts across NIH on identifying common data elements (CDEs).

The SC will meet again via web conference this summer and in-person on September 29-30.

PhenX Measures for Tobacco Regulatory Research (TRR)

To expand the breadth and depth of tobacco measures already in the Toolkit, the NIH Tobacco Regulatory Science Program (TRSP) and the Food and Drug Administration, Center for Tobacco Products, launched the PhenX Measures for Tobacco Regulatory Research Project.
The Tobacco Regulatory Research Panel (TRRP) consists of 9 experts in the field of TRR and has met 3 times since the group first convened in November 2013. The Panel defined the scopes of the 4 Working Groups (WG), which are based on a HAVE (Host, Agent, Vector, and Environment) framework and listed below. To read more about the TRRP and WGs, refer to the PhenX portal, PhenX TRRP WGs.
  • WG 1 -Social/Cognitive
  • WG 2 -Biobehavioral
  • WG 3 -Agent
  • WG 4 -Vector & Environment
WG 1 - Social/Cognitive

The TRR’s Social/Cognitive Working Group (WG) met April 1-2 in Washington, DC to determine measures for proposal to the research community. Co-chaired by Drs. Thomas Brandon and Stephen Tiffany, the WG features 5 academic researchers and 5 liaisons with expertise in the intrapersonal factors that influence product use, including cognitive, affective, motivational, and perceptive factors such as risk perceptions, perceived norms, stress, and motivation to quit.

The Social/Cognitive WG members include:
  • Thomas Brandon, PhD (Co-Chair), Moffitt Cancer Center
  • Stephen Tiffany, PhD (Co-Chair), University at Buffalo, The State University of New York
  • Laurie Chassin, PhD, Arizona State University
  • Pebbles Fagan, PhD, MPH, University of Hawaii Cancer Center
  • Megan Piper, PhD, University of Wisconsin, Madison
Tobacco Regulatory Research Panel Liaisons:
  • Judith Prochaska, PhD, MPH, Stanford University
  • Kay Wanke, PhD, MPH, National Institutes of Health, Office of Disease Prevention
Tobacco Centers of Regulatory Science (TCORS) Liaison:
  • Bonnie Halpern-Felsher, PhD, MA, Stanford University
Additional Liaisons:
  • Sarah Johnson, PhD, Food and Drug Administration, Center for Tobacco Products
  • Annette Kaufman, PhD, National Cancer Institute
Presentations by WG members at the in-person meeting covered the scope of the specialty area and informed the discussion of which measures to propose for inclusion in the Toolkit. Currently, we are soliciting feedback on these pre-selected measures and protocols and invite you to participate until June 25!

we want your feedback

PhenX Measures for Mental Health Research

The National Institute of Mental Health has initiated the PhenX Measures for Mental Health Research Project. The Mental Health Research Panel (MHRP) provides direction and guidance to the PhenX Measures for Mental Health Research Project and consists of 8 mental health researchers. The Panel has met 2 times to refine the scope of the 2 Working Groups and help identify their members.
The WGs for Suicidality and Post Traumatic Stress Disorder (PTSD) will select high-quality measures for inclusion in the PhenX Toolkit. These measures will help establish a common currency to better understand the etiology, progression, and treatment of these two high-priority mental health conditions.

During subsequent MHRP meetings, updates on current WG activities for Suicide and PTSD such as Core Tier 1 and 2 measures have been defined.

WG 1 - Suicide

The Mental Health Research (MHR) Suicide Working Group convened in Rockville, MD on April 30, 2014. Chaired by Dr. Greg Brown, the WG consists of 5 academic researchers and 9 liaisons with expertise in Suicidal areas.

The Suicide WG members include:
  • Greg K Brown, PhD (Chair), University of Pennsylvania
  • David A. Brent, MD, University at Pittsburgh
  • Matthew K. Nock, PhD, Harvard University
  • Sean Joe, PhD, University of Michigan
  • Lauren Weinstock, PhD, Brown University
Mental Health Research Panel Liaisons:
  • Danny Pine, MD, National Institute of Mental Health
  • Charles Hendricks Brown, PhD, Northwestern University
National Institute of Mental Health Liaison:
  • Jane Pearson, PhD
Centers for Disease Control and Prevention Liaison:
  • Asha Ivey-Stephenson, PhD
Department of Defense Liaisons:
  • LTC Dennis McGurk, PhD, Walter Reed Army Institute of Research
  • Katharine W. Nassauer, PhD, U.S Army Medical Research and Material Command (USAMRMC)
Veteran's Affairs Liaisons:
  • Theresa Gleason, PhD, Department of Veterans Affairs
  • Peter Gutierrez, PhD, Denver VA Medical Center, MIRECC
  • Samantha Smith, PhD, Department of Veterans Affairs
During the meeting, WG members made presentations on the scope of the specialty area, which included suicidal ideation, suicidal behaviors, lethality, and risk and protective factors across epidemiology studies and clinical trials. The 12 measures and protocols selected by the WG for community outreach cover Suicidal Ideation, Suicidal Behaviors, Lethality of Suicide Attempts, Hopelessness, and Deterrents Towards Suicide. (To read more about the MHR WGs, refer to the PhenX portal PhenX MHR WGs).

PhenX Expert Review Panels

Expert Review Panels (ERP) provide a comprehensive review of the measures in the PhenX Toolkit to ensure that the Toolkit measures remain highly relevant. Each ERP reviews one or more domains and will make recommendations to update, retire or add new measures. An ERP is composed of at least one former PhenX WG Member and one or more experts with relevant experience for each domain. The ERP Lead(s) drive the consensus process and present their recommendations to the Steering Committee. The ERP clusters as defined by the SC are shown below:
  1. Anthropometrics, Physical Activity and Physical Fitness, Nutrition and Dietary Supplements, Diabetes
  2. Psychiatric, Neurology, Psychosocial, Social Environments
  3. Demographics, Environmental Exposures, Infectious Diseases and Immunity
  4. Alcohol, Tobacco and Other Substances, Cancer
  5. Respiratory, Cardiovascular
  6. Skin, Bone, Muscle and Joint
  7. Speech and Hearing, Ocular
  8. Oral Health, Gastrointestinal
  9. Reproductive Health

Explore the PhenX Toolkit

Top Domains and Top Measures

Top Domains and Measures are calculated based on the number of times they are included in reports generated by user Toolkits, cumulatively. The top Domains and Measures are listed on the PhenX Toolkit home page and are recalculated and updated with each new release. The top 5 domains and measures for June 2014 are listed below.

Top 5 Domains in the PhenX Toolkit
  1. Demographics
  2. Anthropometrics
  3. Alcohol, Tobacco and Other Substances
  4. Cardiovascular
  5. Environmental Exposures

Top 5 Measures in the PhenX Toolkit
  1. Current Age
  2. Gender
  3. Race
  4. Ethnicity
  5. Weight

Featured Measure

The new Featured Measure, Personal History of Type 1 and Type 2 Diabetes, comes from the Diabetes domain. WG members selected this measure to provide researchers the ability to ascertain whether an individual has ever been told by a doctor or health care professional that they have diabetes. It captures age of diagnosis, whether the respondent is taking medication for diabetes, and whether the diagnosis was made only during pregnancy.
PhenX Featured Measure button

PhenX in the News

PhenX RISING Investigators published a research article entitled "PhenX RISING: real world implementation and sharing of PhenX measures" in the BMC Medical Genomics Journal in March 2014.

Recently, members of the PhenX Substance Abuse and Addiction Scientific Panel along with other PhenX scientists published the following manuscript "Data compatibility in the addiction sciences: An examination of measure commonality" in the Drug and Alcohol Dependence Journal in May 2014.

To date, PhenX has been cited in 59 publications and mentioned in 27 articles. In addition, 88 Funding Opportunity Announcements have recommended the use of PhenX measures. For a full list of PhenX publications and presentations, be sure to visit the Resources Page on the Toolkit, and the news articles and funding opportunities can be found on the Toolkit's News and Views Page.

PhenX on the Move

2014 ASHG Logo
The PhenX Toolkit Booth will be featured in San Diego, CA, October 18-22 at the American Society of Human Genetics Annual Conference. By visiting us in Booth #1719, you can demo the Toolkit, meet PhenX Investigators, and take home some Toolkit souvenirs.

PhenX Investigators presented at the following conferences in the United States and abroad in 2014:

PhenX Project Scientist, Dr. Erin Ramos, presented the poster entitled, The PhenX Toolkit: An online resource of standard protocols for collecting phenotypic and environmental exposure data at the 2014 American College of Genetics and Genomics (ACMG) Annual Clinical Genetics Meeting in Nashville, TN, March 25-29.

Dr. Carol Hamilton, PhenX Principal Investigator, was invited to give a Podium Presentation on April 8 on The PhenX Toolkit: Promoting Data Sharing and Translational Research, at the American Medical Informatics Association (AMIA): Joint Summits on Translational Science in San Francisco, CA.

PhenX Co-Investigator, Tabitha Hendershot, presented on the Tobacco Regulatory Research Measures in the PhenX Toolkit at the NIH Tobacco Regulatory Science Conference in Bethesda, MD on April 29.

Abroad, Dr. Carol Hamilton presented the poster, The PhenX Toolkit: Phenotype and Exposure Measures for Collaborative Research in Paris France, at the 5th Biennial Meeting of the Human Variome Project Consortium (HVP) the week of May 19.

Featured PhenX TRRP and MHRP Working Group Chairs

Meet the Social/Cognitive WG Co-Chairs

Thomas Brandon, PhD, Moffitt Cancer Center

Thomas H. Brandon, PhD, is Department Chair and Program Leader of Health Outcomes and Behavior at the H. Lee Moffitt Cancer Center & Research Institute in Tampa, Florida, where he also directs the Tobacco Research & Intervention Program. He is also Professor of Psychology and Oncologic Sciences at the University of South Florida. He received his bachelor’s degree from the University of California, Berkeley, and his doctorate in clinical psychology from the University of Wisconsin-Madison. He held assistant and associate professor positions at the State University of New York at Binghamton for seven years before moving to Moffitt and the University of South Florida in 1997. He is a Fellow of the Society for Behavioral Medicine and the American Psychological Association’s Divisions on Addiction; Psychopharmacology and Substance Abuse; and Clinical Psychology. Dr. Brandon has been working in the area of tobacco dependence for over 30 years. He conducts basic human behavioral research on factors that influence the maintenance and cessation of smoking (e.g., mood management, conditioned responding, outcome expectancies) as well as applied research in which those factors are targeted in smoking cessation interventions. Lately he has also been developing cost-effective minimal interventions designed to reduce the rate of smoking relapse. From 2000 to 2004, Dr. Brandon served as Editor of the peer-reviewed journal, Psychology of Addictive Behaviors, published by the American Psychological Association. He is a past president of the Society of Addiction Psychology (Division 50 of the American Psychological Association). He has been principal investigator on research grants funded by the National Cancer Institute, the National Institute on Drug Abuse, as well as foundations including the American Cancer Society, the American Heart Association, the American Lung Association, and the Prevent Cancer Foundation.

Stephen T. Tiffany, PhD, University at Buffalo, The State University of New York

Dr. Tiffany received his PhD in 1984 from the University of Wisconsin - Madison in Clinical Psychology from the Department of Psychology. In 1984, he took a faculty position as an assistant professor in the Department of Psychological Sciences at Purdue University. In 1990, he was appointed as an associate professor and, in 1994, achieved the rank of full professor at Purdue. In 2002, Dr. Tiffany joined the faculty as a professor in the Department of Psychiatry in the University of Utah School of Medicine. He also had a joint appointment in the Department of Psychology at the University of Utah and was a member of the Utah Addiction Center. In 2006, Dr. Tiffany was appointed the Director of the Mental Illness Research, Education and Clinical Center at the VA Salt Lake City Health Care System. Dr. Tiffany joined the faculty of the Department of Psychology, University at Buffalo, SUNY in 2007. He is also an Affiliated Research Scientist at the University at Buffalo's Research Institute on Addiction. From 2008 to 2011, he was the Director of Clinical Training and Head of the Clinical Psychology Program in the Department of Psychology at the University at Buffalo. In 2011, Dr. Tiffany became the Chair of the Department of Psychology at the University at Buffalo. Dr. Tiffany was awarded the American Psychological Association Distinguished Scientific Award for Early Career Contribution to Psychology in 1993. Purdue named him a Purdue University Faculty Scholar in 1999 in recognition of his outstanding contributions to scientific research. At the University at Buffalo Dr. Tiffany holds the position of Empire Innovation Professor. He has been on the editorial boards of several journals and was a Deputy Editor for Nicotine and Tobacco Research. He has also served as a member of several NIH scientific review panels and was a member of the Scientific Core Group of the Robert Wood Johnson Foundation’s Tobacco Etiology Research Network (TERN). At present, Dr. Tiffany is a regular member of the NIH study section Risk, Prevention and Intervention for Addictions (RPIA). Dr. Tiffany has also served as Principal Investigator on 14 major research grants from the federal government and private foundations. He has also been the major professor for 15 students who have received their Ph.D. in clinical psychology. Dr. Tiffany has published over 100 peer-reviewed articles, numerous book chapters, and books on the processes of drug craving, the etiology of drug dependence, adolescent drug use, and the interaction of biological and psychological factors in the control of addictive behaviors.

Meet the Suicide WG Chair

Gregory K. Brown, PhD, University of Pennsylvania

Dr. Brown is a Research Associate Professor of Clinical Psychology in the Department of Psychiatry at the University of Pennsylvania and a VISN 4 MIRECC Investigator and Clinical Psychologist at the Philadelphia VA Medical Center. He is the Director of the Center for the Prevention of Suicide at the University of Pennsylvania. His research has focused on developing, evaluating, and disseminating targeted, psychotherapy interventions, such as cognitive therapy and safety planning, for individuals who are indicated as being at high risk for suicide. His expertise also includes suicide risk assessment. He has previously served as a consultant to NIMH for review of suicide risk assessment measures for intervention research and for an analysis of NIH suicide research portfolio. He is currently a member of the Scientific Council for the American Foundation for Suicide Prevention.

Research Team Members

RTI International NHGRI
Carol M. Hamilton, PhD Principal Investigator Erin Ramos, PhD, MPH Project Scientist
Tabitha Hendershot Co-Investigator Teri Manolio, MD, PhD Director,
Joe Pratt, MPM Project Manager   Division of Genomic Medicine
Deborah Maiese, MPA Consensus Coordinator    
Darigg Brown, PhD Investigator    
Wayne Huggins, PhD Investigator    
Destiney Nettles, MPM Investigator    
Michael Phillips, MS Investigator    
Helen Pan, PhD Toolkit Lead    
Elizabeth Bullard Communications Lead    

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