The PhenX (Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) 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: https://www.phenxtoolkit.org/ and are recalculated and updated with each new release.
Top 5 domains in the PhenX Toolkit
June 13, 2012
Alcohol, Tobacco and Other Substances
Top 20 measures in the PhenX Toolkit
June 13, 2012
Annual Family Income
Current Marital Status
Current Employment Status
Alcohol - 30-Day Quantity and Frequency
Tobacco - 30-Day Quantity and Frequency
Tobacco - Smoking Status
Tobacco - Age of Initiation of Use
Alcohol - Lifetime Use
Alcohol - Lifetime Abuse and Dependence
Current Educational Attainment
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.
PhenX RISING (Real world, Implementation, SharingING) is now on the homepage at www.phenxtoolkit.org! 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.
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.
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
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