March 11, 2015

PhenX Newsletter - Information and Updates Issue 23. March 11, 2015





PhenX Measures for Mental Health Research—Special Release December 5, 2014



This project, “PhenX Measures for Mental Health Research,” is funded by the National Institute of Mental Health (NIMH) as an Administrative Supplement to the PhenX Genomic Resource award. The goal is to use the PhenX consensus process to select Core and Specialty collections of measures and make them available to the scientific community via the PhenX Toolkit. Guidance is provided by the Mental Health Research Panel, which is co-chaired by Drs. Deanna Barch and Ian Gotlib. The NIMH Project Scientist is Dr. Greg Farber.

Mental Health Research Collections

– Core Collection

                Tier 1: Relevant and essential to all areas of mental health research and  NIMH grantees/applicants conducting human-subject studies are very strongly  encouraged to use the Core: Tier 1 measures. (10 measures)

                Tier 2: Relevant to many areas mental health research, but more specialized than Core: Tier 1. NIMH grantees and applicants conducting human-subject studies are encouraged to incorporate the Core: Tier 2 whenever possible and appropriate. (11 measures)

– Suicide Specialty Collection (10 measures)

– Post-traumatic Stress Psychopathology (including PTSD) Specialty Collection (10 measures)

 National Institute of Mental Health–National Institutes of Health Guide Notice, January 16, 2015


Tobacco Regulatory Research Measures—Special Release February 20, 2015


This project, “PhenX Measures for Tobacco Regulatory Research,” is funded by the Tobacco Regulatory Science Program (TRSP) as an Administrative Supplement to the PhenX Genomic Resource award. The goal is to use the PhenX consensus process to select Core and Specialty collections of measures to support TRR, and make them available to the scientific community via the PhenX Toolkit. Guidance is provided by the TRRP, which is co-chaired by Drs. Gary Swan and Jodi Prochaska. The TRSP Project Scientist is Dr. Kay Wanke.

Tobacco Regulatory Research Collections

– Social/Cognitive Specialty Collection (10 measures)

– Biobehavioral Specialty Collection (9 measures)



Introducing PhenX Measures for Sickle Cell Disease Research



This project, “PhenX Measures for Sickle Cell Disease Research,” is funded by the National Heart, Lung, and Blood Institute (NHLBI) as an Administrative Supplement to the PhenX Genomic Research award. The goal is to use the PhenX consensus process to select Core and Specialty Collections of measures to support Sickle Cell Disease (SCD) Research and to make them available to the scientific community via the PhenX Toolkit. Guidance is provided by the Sickle Cell Disease Research and Scientific Panel (SRSP), co-chaired by Dr. James Eckman and Dr. Kathryn Hassell. The NHLBI Project Scientist is Dr. Ellen Werner. Consistent use of the standard measures from this project will establish a common currency to help researchers better understand the etiology, progression, and treatment of SCD.



Sickle Cell Disease Research and Scientific Panel



The SRSP held an in-person meeting in September 2014 to define the scope of two Working Groups (WGs) and begin discussions of a Core Collection of measures for use by all SCD researchers. The panel consists of nine SCD researchers from various academic and government institutions. The co-chairs also serve as the SRSP liaisons to two WGs:                        
  • James R. Eckman, MD (Co-chair), Emory University School of Medicine
  • Kathryn Hassell, MD (Co-chair), University of Colorado, Denver
  • Kenneth Ataga, MD, University of North Carolina at Chapel Hill
  • Zora Rogers, MD, University of Texas, Southwestern
  • Kim Smith-Whitley, MD, Children’s Hospital of Philadelphia
  • Jon A. Detterich, MD, Children’s Hospital Los Angeles
  • Marilyn Telen, MD, Duke University School of Medicine
  • Jeffrey Glassberg, MD, Mount Sinai Hospital, New York
  • J. J. Strouse, MD, PhD, Johns Hopkins University
  • Ellen Werner, PhD, NHLBI



PhenX Measures in REDCap



The first three PhenX domains were released in REDCap™ (Research Electronic Data Capture) in November 2014. Demographics; Anthropometrics; and Alcohol, Tobacco and Other Substances are now available in REDCap, a secure web application for building and managing online surveys and databases. The REDCap Consortium includes 1,347 active institutional partners in 88 countries. The application allows users to build and manage online surveys and databases quickly and securely. It is in production use or development-build status for more than 156,000 projects with more than 215,000 users spanning numerous research focus areas across the consortium, including the Clinical and Translational Science Awards (CTSA) Centers. You can find 55 PhenX protocols at the REDCap public website by clicking on the “Library” tab and using “PhenX” in “Keyword search” box. The next release will include the Cardiovascular, Environmental Exposures, Nutrition and Dietary Supplements, Oral Health, and Cancer domains. Our thanks to REDCap collaborators, Dr. Paul Harris and Brenda Minor.



PhenX on the Move



On February 25, Kay L. Wanke, PhD, MPH, Deputy Director of the National Institutes of Health (NIH), Office of Disease Prevention, and a member of PhenX Tobacco Regulatory Research (TRR) Panel (TRRP), was session chair for “Building Toward Evidence and Consensus in Tobacco Control Measurement: PROMIS and PhenX” at the 2015 Society for Research on Nicotine and Tobacco (SRNT) meeting in Philadelphia, PA. Presenters for the workshop included Ray Niaura, PhD, American Legacy Foundation; Gary Swan, PhD, Stanford Prevention Research Center; Maria Orlando Edelen, PhD, RAND Corporation; and Tabitha Hendershot, RTI International. Dr. Wanke also presented an abstract as an oral paper, “Tobacco Regulatory Research Measures in the PhenX Toolkit,” at SRNT, on February 28.

The PhenX team presented the PhenX Toolkit booth, and Dr. Wayne Huggins (RTI) presented a poster, “The PhenX Toolkit: A Genomic Resource for Standard Measures of Phenotypes and Exposures,” at the American Society of Human Genetics Annual Conference in San Diego, CA, October 18–22, 2014.

PhenX Project Scientist Dr. Erin Ramos presented a poster, “The PhenX Toolkit: An Online Resource of Standard Protocols for Collecting Phenotypic and Environmental Exposure Data,” at the Genomics of Common Diseases conference in Potomac, MD, September 17–20, 2014.

Dr. Hamilton was invited to participate in the National Institute of Environmental Health Sciences (NIEHS) Workshop for the Development of a Framework for an Environmental Health Science Language at Research Triangle Park, NC, September 15, 2014. Dr. Hamilton gave a talk, “PhenX: Consensus-based Process and Community Engagement.”




Explore the PhenX Toolkit




To date, the PhenX Toolkit has been cited in more than 70 professional publications and mentioned in 27 articles. In addition, 95 Funding Opportunity Announcements have recommended the use of PhenX measures. For a full list of PhenX publications and presentations, visit the Resources page on the Toolkit. News articles and funding opportunities can be found on the Toolkit's News and Views page .

Since the last Newsletter, 41 new measures have been added to the Toolkit, bringing the total number of measures available to 380. Recent releases are summarized below.



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 March 2015 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. Ethnicity
  4. Race
  5. Weight




Featured Measure




The current Featured Measure is impairment, selected by the Mental Health Research Core Collection Working Group. Protocols for measuring impairment for both Adolescent and Adult individuals are available for this measure. The Youth protocol employs the Columbia Impairment Scale (CIS), Youth Version, and is a parent- or self-reporting instrument that measures interpersonal relations, broad psychological domains, functioning in job or school work, and use of leisure time. The Adult protocol employs the World Health Organization (WHO) Disability Assessment Schedule 2.0, which measures impairment due to health conditions. The measures have the advantages of requiring no special personnel training or equipment needs.
PhenX Featured Measure button



Featured Steering Committee Members and PTSD Working Group Chairs



Meet the New Steering Committee Members



Rosalind J. Wright, PhD

Dr. Wright is an adult pulmonary and critical care physician and a developmental epidemiologist with transdisciplinary training in environmental health, multilevel modeling, and stress mechanisms. She has a primary interest in early life (prenatal and early childhood) predictors of developmental and chronic diseases, including asthma, obesity, neurobehavioral development, and lung growth and development. A particular focus is on the implementation of studies considering the role of both social (e.g., individual- and community-level psychosocial stress and other socioeconomic risk factors) and physical (e.g., air pollution, chemicals, dietary factors, allergens) environmental factors in explaining health disparities among lower-income urban populations. Dr. Wright is the Principal Investigator and Director of the Asthma Coalition on Community, Environment, and Social Stress project as well as the Programming of Intergenerational Stress Mechanisms study funded by NHLBI. This research program also explores underlying mechanisms by incorporating biomarkers of physiological pathways through which psychological stress as well as chemical stressors may influence health (e.g., altered hypothalamic-pituitary-adrenal axis functioning, altered maturation of the immune system, disruption of the autonomic nervous system, and epigenetics).


Elaine M. Faustman, PhD

Dr. Faustman is a professor of environmental and occupational health sciences at the University of Washington School of Public Health and directs the Institute for Risk Analysis and Risk Communication. Her research interests include understanding molecular mechanisms of developmental and reproductive toxicants, characterizing in vitro techniques, and developing biologically based dose-response models for noncancer risk assessment. Her research expertise includes the development of tools for incorporating new scientific findings into risk assessment decisions. Dr. Faustman is an elected fellow of the American Association for the Advancement of Science and the Society for Risk Analysis. She is the Secretary General for the International Union of Toxicology. She has served on numerous committees for NIEHS, including the National Toxicology Program Board of Scientific Counselors and for WHO (including Environmental Health Criteria Document Committees for modeling dose-response and children’s risk assessment). She has also been involved in National Research Council committees, including the Committee on Spacecraft Exposure Guidelines, the Subcommittee on Zinc-Cadmium Sulfide, the Subcommittee on Upper Reference Levels of Nutrients for the Food and Nutrition Board (Institute of Medicine), and the Committee on Toxicology. She chaired the National Academy of Sciences Committee on Developmental Toxicology. She currently serves on the U.S. Environmental Protection Agency (EPA) Scientific Advisory Panel. From 2001–08, Dr. Faustman was an adjunct professor for the Department of Engineering and Public Policy, Carnegie-Mellon University, Pittsburgh, PA. Dr. Faustman is a Principal Investigator of an EPA/NIEHS-funded Center for Child Environmental Health Risks Research; of an NIEHS/National Science Foundation–funded Pacific Northwest Center for Human Health and Ocean Studies; and of the Pacific Northwest Center for the National Children’s Study. She is the elected Sigma Xi Lecturer for the Society for Risk Analysis (SRA) for 2012–14. Dr. Faustman received a PhD in toxicology from Michigan State University. She is the 2104 SRA Distinguished Achievement Awardee. Dr. Faustman has authored over 200 peer-reviewed articles and book chapters.



Meet the PTSD WG Co-Chairs



Danny G. Kaloupek, PhD

Dr. Kaloupek is a clinical psychologist with interests in measurement and health-related aspects of psychological trauma and PTSD. He currently is Deputy Director of the Behavioral Science Division of the National Center for PTSD at the U.S. Department of Veterans Affairs Boston Healthcare System, and he holds academic appointments in both psychiatry and behavioral neuroscience at the Boston University School of Medicine.



Tanja Jovanovic, PhD

Dr. Jovanovic’s research focuses on fear conditioning paradigms in patients with stress-related disorders, using startle response as well as other psychophysiological and neuroimaging measures. She has extensive expertise using fear-potentiated startle with different PTSD populations, including combat veterans and civilians suffering from trauma. Her research interests are in the association between genetic risk factors and psychopathology, with a focus on intermediate phenotypes. As a co-investigator at the Grady Trauma Project, she directs the Neurophysiological Laboratory. She has been collecting startle data for several years on adults with stress-related disorders and has significant expertise in this field. She is the principal investigator on two NIMH R21 grants to examine the effects of cortisol suppression on fear-potentiated startle in PTSD and neuroimaging correlates of fear inhibition in PTSD. In addition, she was awarded a National Alliance for Research in Schizophrenia and Affective Disorders Young Investigator Grant from the Brain and Behavior Foundation to investigate biomarkers of anxiety in children, and she is the Principal Investigator on an NIMH R01 investigating psychophysiological markers of development in children with trauma exposure.



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,
Amanda Riley, PMP Project Manager   Division of Genomic Medicine
Deborah Maiese, MPA Consensus Coordinator Brenda Iglesias Scientific Program Analyst
Darigg Brown, PhD Investigator    
Wayne Huggins, PhD Investigator    
Destiney Nettles, MPM Investigator    
Michael Phillips, MS Investigator    
Helen Pan, PhD Toolkit Lead    
Pat West Communications Lead    



Link to Previous PhenX Newsletters






PhenX is supported by a Genomic Resource award (U41) funded by National Human Genome Research Institute (NHGRI) with co-funding by National Institute on Drug Abuse (NIDA).




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