September 21, 2012

PhenX Newsletter - Information and Updates Issue 19. September 21, 2012




The PhenX (Phenotypes and eXposures) Toolkit ( is a catalogue of well-established, standard measures of phenotypes and exposures recommended for research studies with human subjects. The PhenX Toolkit includes 21 research domains (fields of research) and 295 measures. An additional 43 measures in support of Substance Abuse and Addiction research are also available. The Toolkit is funded by the National Human Genome Research Institute (NHGRI) through a cooperative agreement with RTI International. Additional support was provided by the Office of Behavioral and Social Sciences Research (OBSSR) and the National Institute on Drug Abuse (NIDA).

The Toolkit includes detailed 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 high quality, having been validated in previous studies. This is particularly helpful for investigators who want to expand their study’s data collection beyond the primary research focus. We encourage you to provide feedback when you use the Toolkit, so we can ensure that the Toolkit continues to meet the needs of the scientific community.




PhenX Toolkit Update
On May 15, 2012, Version 5.2 of the PhenX Toolkit was released. This release included the following updates and enhancements to the Toolkit site:
  • A new page describing the categories of substances covered by the Substance Abuse and Addiction (SAA) Collections that can be accessed by clicking on the SAA logo (feature)
  • Updates of the following resource pages: Publication and Presentations, Press Releases, and News and Views (resource)

On June 13, 2012, Version 5.3 of the PhenX Toolkit was released. This release included the following updates and enhancements to the Toolkit site:
  • Addition of "Substance Abuse and Dependence - Past Year" (data)
  • Hyperlinks to the "Cognitive Atlas" to help better conceptualize the intent and associated concepts of seven Neurocognitive Measures (data)
  • Enhanced "Add to My Toolkit" image (feature)
  • Separation of self-administered and interview-administered questionnaires on the Data Collection Worksheet page (feature)
  • Resource update - new "Acronyms" page, updated glossary (resource)

Top Domains and Top Measures

Top domains and measures are calculated based on the number of times they are present in reports generated from user Toolkits, cumulatively. The measures and domains with the highest inclusion in reports are those listed as Top Measures and Top Domains. The top domains and measures are listed on the home page of the PhenX Toolkit: and are recalculated and updated with each new release.


Top 5 domains in the PhenX Toolkit

June 13, 2012

  • Demographics
  • Anthropometrics
  • Alcohol, Tobacco and Other Substances
  • Cardiovascular
  • Environmental Exposures

Top 20 measures in the PhenX Toolkit

June 13, 2012


  1.  Current Age   11.  Birthplace
  2.  Gender   12.  Annual Family Income
  3.  Ethnicity   13.  Current Marital Status
  4.  Race   14.  Current Address
  5.  Weight   15.  Current Employment Status
  6.  Alcohol - 30-Day Quantity and Frequency   16.  Household Roster-Relationships
  7.  Height   17.  Tobacco - 30-Day Quantity and Frequency
  8.  Tobacco - Smoking Status   18.  Tobacco - Age of Initiation of Use
  9.  Alcohol - Lifetime Use   19.  Alcohol - Lifetime Abuse and Dependence
  10.  Current Educational Attainment   20.  Alcohol - Age of First Use


Visit us at ASHG 2012!
The PhenX team will be in San Francisco at the American Society of Human Genetics (ASHG) annual meeting from November 6-10, 2012. The PhenX booth is #125. We look forward to seeing you there!
Want to increase the impact of your study? Test-drive the PhenX Toolkit at ASHG 2012! The PhenX team will host a free workshop on Wednesday, November 7 from 12:45 PM to 2:15 PM PST. The workshop will be held at the Marriott Marquis Hotel in the Pacific conference room. Lunch and internet access will be provided at no charge but seating is limited. Please register here.


Duke/UNC Health Informatics Seminar
Dr. Carol M. Hamilton is presenting the PhenX Toolkit as an invited speaker on September 26, 2012 from 4:00 - 5:00 PM EDT hosted by the Duke/UNC Joint Health Informatics Seminar Series. This series, sponsored by Duke Center for Health Informatics (DCHI) and UNC-Chapel Hill, explores key areas in Health Informatics and includes research results, overview of programs of research, basic, applied, and evaluative projects, as well as research from varied epistemological stances. To view the seminar live by streaming video conference, please click on this link after the conference has started:
Username: guest
Password: guest


PhenX Rising
PhenX RISING (Real world, Implementation, SharingING) is now on the homepage at! PhenX RISING is comprised of seven groups of investigators funded by National Human Genome Research Institute (NHGRI) and the Office of Behavioral and Social Sciences Research (OBSSR) to incorporate PhenX measures into existing population-based genomic studies.


The PhenX RISING group held an in-person meeting on July 30, 2012 in the Washington DC area. During the all-day event, each of the seven groups provided updates on their progress including status of data collection, status of dbGaP submission, sample size and summary demographics characteristics, and preliminary results. The groups also provided extensive feedback on their experience implementing Toolkit measures. These recommendations, which will be summarized and presented to council in September, will be used to improve the PhenX Toolkit. The groups also provided updates on the progress of on-going internal and external cross-study collaborations. Although this meeting marked the unofficial end of the one year administrative supplements, several monthly teleconferences will be held through the fall.

The seven studies that have been funded under PhenX RISING (NOT-HG-11-009) are:

  • Ecologic Stressors, Post-Traumatic Stress Disorder, and Drug Use in Detroit
    University of Michigan, Ann Arbor, Allison Aiello, PhD
    National Institute on Drug Abuse
  • Human Translational Applications Core
    University of California, Los Angeles, Robert Bilder, PhD (Chair)
    National Institute of Mental Health
  • Creating a Pediatric Imaging-Genomics Data Resource
    University of California, San Diego, Terry Jernigan, PhD
    National Institute on Drug Abuse
  • Genome-Wide Study of Cataract and Low HDL in Personalized Medicine Research Project
    Essentia Institute of Rural Health, Duluth, Minn., Catherine McCarty, PhD
    National Human Genome Research Institute
  • Genome-Wide Association Scan to Identify Risk Genes for Type 2 Diabetes in Asian Indians
    University of Oklahoma, Oklahoma City, Dharambir Sanghera, PhD
    National Institute of Diabetes and Digestive and Kidney Diseases
  • Self-Regulation Failure: Identifying and Modifying a Risk Phenotype
    Duke University, Durham, NC, Timothy Strauman, PhD, and Ahmad Hariri, PhD
    National Institute on Drug Abuse
  • Determinants of Healthy Longevity in China
    Duke University, Durham, NC, Zeng Yi, PhD
    National Institute on Aging


Featured PhenX Contributors


In this newsletter, we highlight Jun (Jim) Zhang, MD, Ph.D. who served as a Working Group member on the Reproductive Health domain and is working to translate PhenX measures into Chinese.


Jun (Jim) Zhang, MD, Ph.D.Jun (Jim) Zhang, MD, Ph.D.
Executive Director of the MOE-Shanghai Key Laboratory of Children’s Environmental Health, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Jun Jim ZHANG, Professor. Graduated from Shanghai Medical University in 1988; obtained PhD degree in epidemiology from the University of North Carolina at Chapel Hill, U.S. in 1993. He was an Assistant Professor at the Mount Sinai School of Medicine, New York; and an Investigator and, then, a Senior Investigator at the National Institute of Child Health and Human Development, National Institutes of Health (NIH) from 1997 to 2011. He was granted NIH tenure in 2005. He served as a member of Advisory Boards of the NIH Reproductive Medicine Research Network and Neonatal Research Network, the World Health Organization (WHO) Consultant on Reproductive Health; received NIH Merit Award twice. His research focuses on reproductive and perinatal epidemiology. Currently, he is the Director of Shanghai Key Laboratory of Children’s Environmental Health, Shanghai Jiao Tong University School of Medicine, Professor of the Shanghai Jiao Tong University School of Public Health; and WHO Consultant. He has conducted a number of observational studies and clinical trials and published over 150 papers in prestigious journals such as New England Journal of Medicine, Lancet and JAMA.


Kimberly A. Tryka, Ph.D.Kimberly A. Tryka, Ph.D.
National Center for Biotechnology Information, National Library of Medicine

Dr. Tryka earned her Ph.D. in Planetary Science from Caltech in 1995. After post-doctoral work, she enrolled in a Library Science program at the University of Pittsburgh, receiving her MLIS with a concentration in Archival Science in 2000. She was Associate Director at the Virginia Center for Digital History at the University of Virginia, where she worked with historians to create digital projects based on primary records, such as census data, newspapers and manuscripts, until 2005. In 2006, after working with the University of Virginia Library on a project related to digital video, she moved to the National Center for Biotechnology Information at the National Library of Medicine in Bethesda, MD, where she is currently employed. Her primary responsibility is with Database of Genotypes of Phenotypes (dbGaP) where she created a workflow to create electronic versions of the documentation (such as protocols and questionnaires) that accompany data submitted to dbGaP; these electronic documents are then annotated to create links between them and phenotype data in the database. She began working with the PhenX project in 2008 because of her familiarity with the documentation of dbGaP studies. Since then, she has participated in many Working Group meetings and conference calls, as well as working on the project to map dbGaP variables to PhenX variables.


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     Baylor College of Medicine, Duncan Cancer Center
Diane Wagener, PhD     RTI International
Michelle Williams, ScD     Harvard School of Public Health


SAA Scientific Panel Members


Kenneth Sher, PhD, Chair     University of Missouri
Arpana Agrawal, PhD     Washington University in St. Louis
Erik Augustson, PhD     National Cancer Institute
Warren Bickel, PhD     Virginia Tech Carilion Research Institute
James Bjork, PhD     National Institute on Drug Abuse
Kevin Conway, PhD     National Institute on Drug Abuse
Lindsay Farrer, PhD, SC Liaison     Boston University
Andrea Hussong, PhD     University of North Carolina at Chapel Hill
Marcia Scott, PhD     National Institute on Alcohol Abuse and Alcoholism
Paul Wakim, PhD     National Institute on Drug Abuse


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
Dana Hancock     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     Health Science Analyst, NHGRI
Teri Manolio, MD, PhD     Director, Office of Population Genomics;
  Senior Advisor to the Director, NHGRI, for Population Genomics





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