January 28, 2014

PhenX Newsletter - Information and Updates Issue 21. January 28, 2014




The PhenX Toolkit - Register your Study!


The Toolkit provides 339 measures across 21 research domains with content specific protocols to ensure that the data collected are comparable across studies. Investigators who come to the Toolkit when designing or expanding a study can be confident that PhenX measures are well-established, high quality, and low-burden. Thus, Investigators who want to expand their study beyond the primary research focus can select additional measures and be confident that they are high quality measures.
The Toolkit offers a Register Your Study feature. This feature allows Investigators who are using PhenX measures in their studies to share information with other Registered Users of the PhenX Toolkit. For example, Investigators who are planning new studies can identify other studies using PhenX measures and propose/plan ahead for future cross-study analysis. To access the Register Your Study feature, you must become a Registered Toolkit User. Registered Users can save multiple "Toolkits" for different studies and share them with colleagues.


Genomic Resource Grant for PhenX Toolkit (U41)


On July 1, 2013, the National Human Genome Research Institute (NHGRI) awarded RTI a 4-year cooperative agreement for $5.3 million to continue to expand and improve the PhenX Toolkit. The goals of the proposed work are to:
  • Add four new research domains;
  • Review and update measures in the Toolkit;
  • Extend Toolkit capabilities (e.g. integrating Chinese and Spanish translations of PhenX protocols and providing some PhenX protocols as web-based protocols);
  • Map PhenX measure variables to additional studies in the database of Genotypes and Phenotypes (dbGaP);
  • Expand and nurture existing collaborations;
  • Build new collaborations across the National Institutes of Health (NIH) and with other government agencies, and continue to engage and inform the scientific community.

Widespread adoption of PhenX measures will increase the overall impact of individual studies by making it easier to compare and combine data from different studies. With continued support, PhenX will promote and advance collaborative research across the biomedical research community.


PhenX Steering Committee


Under the leadership of PhenX Co-Chairs, Drs. Mary Marazita and Cathy McCarty, the newly formed PhenX Steering Committee (SC) held their first in-person meeting, November 18 - 19, 2013, in Washington, DC. New and former SC members make up the current SC and during the two-day meeting were able to accomplish the following meeting goals:
  • Identifying, prioritizing and defining the scope of 4 new domains;
  • Establishing the expert review panel (ERP) process for updating the Toolkit content with new policies, procedures and panel composition;
  • Identifying SC liaisons to the Tobacco Regulatory Research Panel (TRRP) and Mental Health Research Panel (MHRP).

Dr. Teri Manolio, Director of the Division of Genomic Medicine at NHGRI, presented the current and future genomic medicine efforts at NHGRI and across the NIH. Dr. Erin Ramos, the PhenX Project Scientist, shared perspectives on what has been accomplished with the PhenX Toolkit and described some of its uses.

At the end of the two-day meeting, the SC identified obesity, geriatrics, rare conditions, and pediatrics as the potential new domains for the Toolkit and decided to start with rare conditions. The Rare Conditions Working Group (WG) members will be tasked with identifying up to 15 new measures under a scope that includes dysmorphology, conditions identified through newborn screening, blood disorders, exema, and skin conditions. They will also do a thorough review of current PhenX Toolkit measures and add notations to measures that may be relevant to rare conditions.

The SC also provided guidance for the ERP process and decided to cluster the existing domains into related groups. The first of these clustered ERPs will include the Anthropometrics, Physical Activity and Physical Fitness, Nutrition and Dietary Supplements, and Diabetes domains. The SC will reach out to the scientific community and current and past project affiliates to assist in this endeavor to ensure successful completion.

SC meetings for 2014 have been scheduled for February 7 (Conference Call), April 28-29 (In-Person Meeting), and September 29-30 (In-Person Meeting). Stay tuned for more details on SC activities as the project year progresses.

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. Over the next several months, Working Groups (WGs) will convene to identify high-priority measures in specialty areas related to Tobacco Regulatory Research for inclusion in the PhenX Toolkit.


Tobacco Regulatory Research Panel

The Tobacco Regulatory Research Panel (TRRP) convened in Washington, DC for its first in-person meeting December 9-10, 2013. Co-chaired by Drs. Gary Swan and Jodi Prochaska, the TRRP consists of nine experts in the field of TRR from various academic institutions, independent research organizations, and NIH Institutes. The TRRP includes:

  • Jodi Prochaska, PhD, MPH (Co-Chair), Stanford University
  • Gary Swan, PhD (Co-Chair), SRI International
  • Neal Benowitz, MD, University of California - San Francisco
  • Kevin Conway, PhD, National Institute on Drug Abuse
  • Andrew Hyland, PhD, Roswell Park Cancer Institute
  • Robin Mermelstein, PhD, University of Illinois at Chicago
  • Dana van Bemmel, PhD, MPH, Food and Drug Administration
  • Kay Wanke, PhD, MPH, National Institutes of Health
  • Gordon Willis, PhD, National Cancer Institute
  • Lynn Goldman, MD, George Washington University, Steering Committee Liaison

During the meeting, the TRRP scoped out the work into 4 WGs based on the HAVE models (Host, Agent, Vector, Environment) framework:

  • WG1 - Tobacco Regulatory Social/Cognitive
  • WG2 - Tobacco Regulatory Biobehavioral
  • WG3 - Tobacco Regulatory Agent
  • WG4 - Tobacco Regulatory Vector/Environment

The TRRP began a discussion of a Core Collection of TRR-related measures, similar to the Core Collection for addiction research, which was created by the Substance Abuse and Addiction Scientific Panel.

PhenX Measures for Research in Mental Health


On August 10, 2013, President Obama announced a National Research Action Plan (NRAP) designed to improve access to mental health services for veterans, service members, and military families. Focused on traumatic brain injury (TBI), post-traumatic stress disorders (PTSD), and suicide prevention, the NRAP calls for the National Institute of Mental Health (NIMH), the Department of Defense (DoD) and the Veterans Affairs (VA) to identify common data elements that facilitate sharing of research data. To achieve this goal, NIMH has initiated the PhenX Measures for Mental Health Research Project. During the coming months, Working Groups (WGs) for PTSD and Suicidality, consisting of recognized experts in each field, will be convened to 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.

Mental Health Research Panel (MHRP)

The Mental Health Research Panel (MHRP) provides the overall direction and guidance to the PhenX Measures for Mental Health Research Project. This includes defining the scope to be addressed by the Mental Health Research (MHR) WGs, serving as liaisons to the MHR WGs, and providing guidance during MHR WG deliberations. The MHRP is also tasked with identifying a core set of measures that are broadly applicable across mental health research. Co-chaired by Drs. Deanna Barch and Ian Gotlib, the MHRP consists of eight mental health researchers from academic and government institutions. The MHRP includes:

  • Deanna Barch, PhD (Co-Chair), Washington University
  • Ian Gotlib, PhD (Co-Chair), Stanford University
  • Robert Bilder, PhD, University of California - Los Angeles
  • Hendricks Brown, PhD, Northwestern University
  • Gregory Farber, PhD, National Institute of Mental Health
  • Adam Haim, PhD, National Institute of Mental Health
  • Daniel Pine, MD, National Institute of Mental Health
  • Jordan Smoller, MD, Harvard University
  • William R. Harlan, MD, Retired - National Institutes of Health, Steering Committee Liaison

The MHRP held a day-long teleconference on January 8, 2014. During this meeting, the MHRP reviewed the scope of the PTSD and Suicidality WGs and discussed potential mental health core measures.


PhenX Outreach


Featured Measure


The current Featured Measure is Cancer: Personal and Family History, which was selected by the Cancer Working Group to assess the presence and age of onset cancer in all first-degree, biological relatives. A positive family history of cancer in a first-degree relative (parent, siblings, or children) is a cancer-specific risk factor. By obtaining the vital status and age at first cancer diagnosis, this measure can assist with assessing cancer risk in a person. You can find the Featured Measure in the lower left corner of the PhenX Toolkit homepage.
PhenX Featured Measure button


PhenX Toolkit News and Views


PhenX scientists authored a process paper entitled "PhenX -- Establishing a Consensus Process to Select Common Measures for Collaborative Research." This methods report was published by RTI Press in October 2013 and is available via PubMed and RTI Press.


NIH-funded data repositories are incorporating the Toolkit into their own web portal as a helpful link for Investigators to peruse. Check out the National Addiction & HIV Data Archive Program (NAHDAP), funded by the National Institute on Drug Abuse (NIDA) and the Office of Behavioral and Social Sciences Research (OBSSR) that provides a direct link to the PhenX Toolkit and recommends it as a 'Quick Link for Data Producers.'


To date, PhenX has been cited in 55 publications and has been mentioned in 27 articles. In addition, 62 Funding Opportunity Announcements have recommended the use of PhenX measures. This list of scientific articles and funding opportunities can be found on the News and Views Page along with other media announcements and sources that mention PhenX.


PhenX Conference News


The PhenX Toolkit was exhibited in Boston, MA this past October for attendees to visit at the American Society of Human Genetics (ASHG). PhenX Investigator, Dr. Wayne Huggins, presented a Poster entitled, The PhenX Toolkit: Discovering and Promoting Opportunities for Cross-study Analyses.

Looking forward into 2014:


Featured PhenX Steering Committee and Research Panel Co-Chairs


PhenX Steering Committee Co-Chairs


Mary L. Marazita, PHD, FACMG, University of Pittsburgh

Dr. Mary Marazita has been on the faculty of the University of Pittsburgh since 1993, currently serving as the Director of the Center for Craniofacial and Dental Genetics, Professor and Vice Chair of the Department of Oral Biology (School of Dental Medicine). She has secondary faculty appointments in the Department of Human Genetics, the Clinical and Translational Science Institute, and the Department of Psychiatry. Her PhD in Genetics was received from the University of North Carolina, Chapel Hill; postdoctoral training in Craniofacial Biology from the University of Southern California; and board certification in Medical Genetics. Prior to coming to Pittsburgh, she was on the faculty of UCLA and then the Medical College of Virginia. She has served on a variety of NIH advisory groups, and is the co-director of the FaceBase Hub: an online resource funded by NIDCR to integrate human and animal model genetic data related to facial development. She was a member of the first PhenX Steering Committee, and is serving as the co-chair of the current PhenX Steering Committee. Currently, Dr. Marazita’s research focuses on the human genetics of complex traits, primarily facial birth defects (primarily cleft lip, cleft palate and other craniofacial anomalies), and oral disease (such as caries, malocclusion, and periodontal disease). She has more than 270 peer-reviewed publications, and substantial grant support, mostly from NIDCR.


Cathy McCarty, PhD, Essentia Institute of Rural Health

Cathy McCarty, PhD, MPH, is a genetic epidemiologist. She earned her BS and MPH degrees in nutrition from the University of Minnesota and her PhD in Epidemiology from the University of Pittsburgh. After her completing her PhD, she was the Head of the Epidemiology Research Unit in the Department of Ophthalmology at the University of Melbourne for 8 years. Upon her return to the US, she was the Director of the Center for Human Genetics and the PI for the Personalized Medicine Research Project at Marshfield Clinic Research Foundation. She commenced her current position as Principal Research Scientist at Essentia Institute of Rural Health in Duluth, MN in 2011. She was one of the original PIs in the eMERGE network and had an administrative supplement to her eMERGE grant to collect PhenX measures for research subjects for whom GWAS data were available.


PhenX Tobacco Regulatory Research Panel Co-Chairs


Judith (Jodi) Prochaska, PhD, MPH, Stanford University

Judith (Jodi) Prochaska, PhD, MPH, is an Associate Professor in the Department of Medicine at Stanford University with the Stanford Prevention Research Center. Dr. Prochaska conducts measurement development studies and clinical trials research with youth and adults with attention to leading health behaviors including tobacco and other substance use, physical activity and diet, stress and distress. Her behavioral assessment tools have been translated into over 20 different languages. Her research combines social media, interactive expert system interventions, and mHealth interventions with biomarker validation. Communities of interest center on complex and disenfranchised groups including people with serious mental illness, alcohol and drug problems, heart disease, the unemployed, and individuals who are homeless. She has also helped develop, evaluate, and disseminate tobacco treatment curricula in cardiology and psychiatry as part of the Rx for Change curriculum suite with over 8000 registrants and 170,000 file downloads (http:rxforchange.ucsf.edu).

Dr. Prochaska has authored over 100 peer-reviewed articles. Her current research funding includes NIDA, NIMH, the State of California TRDRP, and an investigator initiated research award from Pfizer. She co-founded the Society of Behavioral Medicine’s Special Interest Group on Multiple Health Behavior Change (MHBC), is on the editorial board of JAMA Internal Medicine, and in 2013 was elected Member Delegate-North America for the Society for Research on Nicotine and Tobacco (SRNT). In 2007, Dr. Prochaska received the SRNT Jarvik-Russell Young Investigator Award, in 2010 NIDA’s Division of Clinical Neuroscience & Behavioral Research Outstanding Early Career Investigator Award, and in 2011 the Bay Area Clinical Research Mentor of the Year Award.


Gary Swan, PhD, SRI International

Gary E. Swan has conducted research at SRI International (formerly Stanford Research Institute) for the past 35 years, and served as the Director of the Center for Health Sciences from 1987 through 2013. His research areas of interest include treatment of nicotine dependence, genetic and environmental determinants of addiction and disease, brain aging, and pharmacogenetics. He has been Principal Investigator or Co-Investigator on over 20 NIH-funded grants and has published over 230 manuscripts in peer-reviewed journals. Dr. Swan was a National Consultant to the Transdisciplinary Tobacco Use Research Centers, is a member of the NIDA Genetics Consortium, served on the Steering Committee for NCI’s Women, Tobacco, & Cancer Meeting, participated in the 2005 review of NIH's portfolio of grants on the genetic epidemiology of drug abuse, is the senior editor of a recently published NCI Monograph, and was elected as the 2012-2013 President of the Society for Research on Nicotine and Tobacco, a professional organization consisting of 1000 scientists from more than 20 countries. Dr. Swan reviews grants for a number of institutes at the NIH, reviews manuscripts for over 20 peer-reviewed journals, and is a member of the American Psychological Association, Society of Behavioral Medicine (Fellow, 1993), and the Society for Research on Nicotine and Tobacco. Dr. Swan served as the founding Editor-in-Chief of Nicotine & Tobacco Research for 8 years – from its inception in 1998 through 2006. The journal is now published by Oxford University Press and is in its 16th year of operation. At SRI International, Dr. Swan has twice received Professional Excellence Awards in addition to the Fellowship Award, SRI’s highest honor for scientists.


PhenX Mental Health Research Panel Co-Chairs


Deanna Barch, PhD, Washington University in St. Louis

Deanna M. Barch, Ph.D. is the Gregory B. Couch Professor of Psychology, Psychiatry and Radiology at Washington University in Saint Louis, MO. After receiving her undergraduate degree from Northwestern University, Dr. Barch completed graduate school at the University of Illinois in Champaign-Urbana and an NIMH sponsored postdoctoral fellowship at Western Psychiatric Institute and Clinic at the University of Pittsburgh Medical School. Dr. Barch is the Editor of Cognitive, Affective and Behavioral Neuroscience, and is on the Editorial Boards of Schizophrenia Bulletin, Current Directions in Psychological Science, Journal of Abnormal Psychology, and Clinical Psychological Science. Dr. Barch is President of the Society for Research in Psychopathology, was on the DSM-V Psychosis Committee, is on the Steering committee for the NIMH Research Domain Criteria initiative, and is a member of the NIMH Scientific Council. Dr. Barch’s research has been funded by the NIMH, NARSAD, NSF, the Dana Foundation and the McDonnell Center for Systems Neuroscience. Dr. Barch is the recipient of several awards, including the American Psychological Association’s Distinguished Scientific Award for Early Career Contribution to Psychology in the area of Psychopathology, and the Joseph Zubin Memorial Fund Award. She is a Fellow of the Association for Psychological Science.


Ian Gotlib, PhD, Stanford University

Ian H. Gotlib is the David Starr Jordan Professor and Director of the Stanford Mood and Anxiety Disorders Laboratory at Stanford University. Dr. Gotlib has served as Senior Associate Dean for the Social Sciences, and is Chair of the Department of Psychology at Stanford. In his research, Dr. Gotlib is broadly examining psychological and biological factors that place individuals at increased risk for depression, as well as processes that are involved in recovery from this disorder. Dr. Gotlib is conducting research examining cognitive, social, endocrinological, and neural factors and genetics in depressed individuals, as well as predictors of depression in children at familial risk for developing this disorder. He is also examining the impact of innovative procedures to reduce young children’s risk for depression. Dr. Gotlib’s research is supported largely by grants from the NIMH. He has also been funded by the NHRDP, the MRC of Canada, and the Hope for Depression Research Foundation. He has received the Distinguished Investigator Award from NARSAD, the Joseph Zubin Award for lifetime research contributions to the understanding of psychopathology, the APA Award for Distinguished Scientific Contribution, and the APS Distinguished Scientist Award. Dr. Gotlib has published over 450 scientific articles and has written or edited several books in the areas of depression and stress, including the Handbook of Depression with Constance Hammen. He is a Fellow of the American Psychological Association, the Association for Psychological Science, and the American Psychopathological Association.


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    
Helen Pan, PhD Toolkit Lead    
Elizabeth Eubanks Communications Lead    


Link to Previous PhenX Newsletters




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