October 12, 2016

PhenX Newsletter - Information and Updates Issue 26, October 12, 2016




PhenX Measures for Tobacco Regulatory Research - Released August 30, 2016


The PhenX Tobacco Regulatory Research Panel (TRRP) released the Tobacco Regulatory Research (TRR) Core Collection. Tier 1 and Tier 2 include 20 measures from the PhenX Toolkit and four new measures. (Note that one new measure will be released soon.) Core Tier 1 measures are relevant and essential to all areas of TRR and are recommended for use by all National Institutes of Health (NIH)-funded investigators performing human subjects TRR. Core Tier 2 measures are relevant to many areas of TRR but are more specialized, require a greater time commitment, and complement the Core Tier 1 measures.

This project is funded by U.S. the Food and Drug Administration's Center for Tobacco Products (FDA-CTP) and the NIH Tobacco Regulatory Science Program (TRSP) as an administrative supplement to the PhenX Genomic Resource Grant. Dr. Gary Swan and Dr. Jodi Prochaska, both of Stanford University, served as co-chairs of the TRRP.

The TRR Core Collections of measures represent a collaborative effort by the extramural scientific community along with staff members at FDA, TRSP, National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and RTI International. In addition to the TRR Core Collections are the measures added by of the five TRR Working Groups (WGs), which follow the HAVE model (Preventive Medicine, 48, 2009, S4-S43): Host - Social/Cognitive, Host - Biobehavioral, Agent, Vector, and Environment.

The Core Collection of measures can be found at the link below:

TRR Core Collection:
Core Tier 1 (10 measures)
Core Tier 2 (15 measures)




PhenX Toolkit Introduces Spanish Translations of Protocols


To increase utility, the PhenX Toolkit began providing Spanish translations on May 20, 2016, adding 35 Spanish protocol translations. Spanish translations are obtained from the protocol source.

When a translation is available in the Toolkit, it can be found on the Measure page. You can also search for measures that have Spanish translations using the "Available Translation" filters, selecting Spanish, and clicking either "Smart Search" or "Text Search."

New translations will be added to the Toolkit as they become available.


Expert Review Panels Update Four Toolkit Domains and One Collection


Two PhenX Expert Review Panels (ERPs) recently completed work on updates to four domains and one collection in the PhenX Toolkit.

ERP 2 reviewed 44 measures in the Demographics, Social Environments, and Environmental Exposures domains and 21 in Supplemental Information. The ERP’s recommendations were available via the PhenX Community Outreach process in late January and early February 2016. All of the ERP 2 recommendations were approved by the Steering Committee during their April in-person meeting, and the changes to the three domains were released May 31, 2016.

The three domains released by ERP 2 are linked below:
Demographics (15 measures)
Environmental Exposures (14 measures)
Social Environments (15 measures)

ERP 3 reviewed 56 measures in the Alcohol, Tobacco, and Other Substances (ATOS) domain and the Substance Abuse and Addiction (SAA) collection and 19 measures in Supplemental information. The ERP received comments on its recommendations during Community Outreach in June, and its recommendations were approved by the PhenX Steering Committee August 16 during a teleconference. ERP 3 changes to the Toolkit are scheduled for release in October.

Each ERP identifies protocols that do not need modification, that need to be replaced or updated, and any new measures to be added. In the PhenX Toolkit, the "Process and Review" section of each measure provides a summary of any ERP changes. Protocols that have been updated, replaced or retired are available on the Archived Measures and Protocols page.


PhenX Steering Committee In-Person Meeting—April 21–22, 2016


The PhenX Steering Committee (SC) met in-person in Chevy Chase, MD. During the two-day meeting, the SC heard from representatives of the Precision Medicine Initiative, the Trans-NIH CDE (Common Data Element) Working Group, and the Adolescent Brain Cognitive Development Study.

The SC provided guidance on several emerging issues related to the Expert Review Panel (ERP) process, proprietary protocols, creating a core collection of Demographics measures, and identifying protocols for sexual identity, sexual orientation, and gender identity.

The SC chose the Geriatrics domain for the next Working Group (WG) and developed the scope of this new domain. The SC set the order for assembling remaining ERPs. The next two ERPs will be:

ERP 5: Reproductive Health
ERP 6: Respiratory

In addition, the SC received updates from the current ERPs, the Pregnancy WG, and two Supplements: PhenX Measures for Tobacco Regulatory Research and PhenX Measures for Mental Health Research.


PhenX on the Move


PhenX will be at the American Society of Human Genetics (ASHG) 2016 annual meeting Oct. 18-22 in Vancouver, Canada. PhenX Co-Investigator Tabitha Hendershot will present a poster, "The PhenX Toolkit: Standard Measures and Bioinformatics for Collaborative Research," at 2 p.m. Wednesday, Oct. 19. Members of our team will also be on hand in the PhenX Toolkit booth, No. 735 in the exhibit hall. We hope to see you there! We will help you "Link Your Study" if it includes PhenX measures.

PhenX Principal Investigator Dr. Carol Hamilton presented "The PhenX Toolkit: Standard Measures for Collaborative Research" at the National Heart, Lung, and Blood Institute’s annual Sickle Cell Disease Clinical Research Meetings in Bethesda, MD, August 16, 2016. Co-Investigator Tabitha Hendershot gave a workshop on how to use the PhenX Toolkit.

PhenX Investigator Dr. Wayne Huggins presented "The PhenX Toolkit: Standard Measures for Collaborative Research" at the Human Variome Project conference in Paris, France, June 2, 2016.

Tabitha Hendershot presented information about PhenX measures for tobacco regulatory research at a booth at the Tobacco Regulatory Science Conference at the National Institutes of Health in Bethesda, MD, May 16–18, 2016.

Dr. Hamilton and PhenX Investigator Rebecca Boyles presented a poster, "The PhenX Toolkit: Consensus Measures for e-Cigarettes Research," at the Society of Toxicology 55th Annual Meeting and ToxExpo in New Orleans, LA, March 13–17, 2016.

PhenX Investigator Michael Phillips presented a poster, "The PhenX Toolkit: Standard Measures to Assess Rare Genetic Conditions and Sickle Cell Disease," at the Annual Clinical Genetics Meeting (ACMG), hosted by the American College of Medical Genetics and Genomics in Tampa, FL, March 10, 2016. The ACMG poster committee awarded the poster a blue ribbon.

The PhenX team presented a poster, "The PhenX Toolkit: Standard Phenotype and Exposure Measures for Epidemiological Studies," at the NC Chapter of the Society of Toxicology meeting in Research Triangle Park, NC, March 2, 2016.

Dr. Hamilton presented "PhenX Measures for Sickle Cell Disease Research" at the Sickle Cell Disease Ontology Workshop hosted by H3Africa (Human Heredity and Health in Africa) in Cape Town, South Africa, February 8–10, 2016.

Dr. Kathy Hassell presented an abstract at the American Society of Hematology conference in Orlando, FL, on December 6, 2015. Dr. Hassell, professor of medicine in the Hematology Division at the University of Colorado, is co-chair of the PhenX Sickle Cell Disease Research and Scientific Panel.

Explore the PhenX Toolkit


Top Domains and Top Measures


The Top 5 Domains and Top 5 Measures as of August 2016 are listed below. The top domains and measures are listed on the Toolkit Use Statistics Page and are recalculated and updated with each new release.


Top 5 Domains in the PhenX Toolkit Top 5 Measures in the PhenX Toolkit
1. Demographics
2. Anthropometrics
3. Alcohol, Tobacco and Other Substances
4. Environmental Exposures
5. Cardiovascular
1. Current Age
2. Gender
3. Ethnicity
4. Race
5. Weight


Featured: Expert Review Panel (ERP) Co-Leads

Demographics, Social Environments, and Environmental Exposures Co-Leads


Barbara Entwisle, PhD

Dr. Entwisle is Vice Chancellor for Research, Kenan Distinguished Professor of Sociology, Adjunct Professor of Geography, Faculty in the Ecology Curriculum, and Fellow of the Carolina Population Center. She is a social demographer whose research focuses broadly on the study of the social, natural, and built environment and consequences for a range of demographic and health outcomes. Dr. Entwisle served as Principal Investigator (PI) of the North Carolina components of the National Children Study from 2005–2013. In that role, she developed innovative approaches to sample design, recruitment, and measurement of neighborhood characteristic in diverse settings. In 2010, she chaired the PhenX Social Environment WG. Dr. Entwisle is currently engaged in the design of 21st-century social science data infrastructure. Earlier in her career, she was part of the team that developed statistical methods for multilevel analysis that are in common use today. She chaired the Board of Overseers for the U.S. General Social Survey and contributed innovations to major longitudinal surveys in China, Russia, and Thailand. Dr. Entwisle’s research contributions have been recognized by her election as President of the Sociological Research Association (2015), President of the Population Association of America (2007), the award of a distinguished chair (2007), and election as Fellow of the American Association for the Advancement of Science (2003).


Myles Cockburn, MD

Dr. Cockburn is the Director of the Division of Disease Prevention and Global Health at the University of Southern California’s Keck School of Medicine, in the Department of Preventive Medicine, with joint appointments in Dermatology and Spatial Sciences. His research focuses on environmental causes of cancer, particularly those with directly translatable prevention opportunities in the diverse populations of Los Angeles County’s 10 million residents. He studies prevention interventions for skin cancer; the role of pesticides in hormone-related cancers and childhood cancer and in other chronic diseases; and methods of improving cancer control through screening and outreach activities targeted to underserved populations identified by the Los Angeles Cancer Surveillance program, where he is the Scientific Director. Dr. Cockburn maintains active research programs that engage graduate and doctoral students in research, and he trains dermatology residents in population-based prevention approaches. Most of the above work requires development of new methods in spatially derived exposure assessment, and he is the co-leader of a new doctoral program in Health and Place that aims to train the next generation of spatially aware health researchers.


Alcohol, Tobacco, and Other Substances, and Substance Abuse and Addiction Co-Leads


James Bjork, MD

Dr. Bjork is Associate Professor of Psychiatry, Pharmacology and Toxicology at the Virginia Commonwealth University (VCU) Institute for Drug and Alcohol Studies. He conducts behavioral and neuroimaging research on substance-dependent individuals, neurotypical adolescents, and adolescents at risk for addiction, with a focus on brain mechanisms of impulsivity and incentive processing. He is a co-PI of the signature Adolescent Brain and Cognitive Development longitudinal neuroimaging study of 10,000 American youth recently launched by NIH. Other research interests include psychopharmacology and traumatic brain injury and drug abuse in military and other populations. Prior to joining the VCU faculty, Dr. Bjork was a Program Official in the Division of Clinical Neuroscience and Behavioral Research of the National Institute on Drug Abuse (NIDA), where he maintained a grant portfolio centered on neuroimaging of addicted populations and cognitive processes germane to addiction. While in the NIH program, Dr. Bjork also served as the Scientific Officer on the landmark NIH Blueprint Human Connectome Project. Dr. Bjork did his postdoctoral fellowship in the Laboratory of Clinical and Translational Studies at the National Institute on Alcohol Abuse and Alcoholism in Bethesda, MD, where he conducted laboratory research on the psychotropic effects of alcohol and monoamine manipulation on human aggression and impulsivity. Dr. Bjork has authored dozens of peer-reviewed behavioral and neuroimaging papers on human impulsivity and aggression, and he is a frequent speaker to community and professional audiences about the motivational neurocircuitry of addiction and the at-risk brain. When not writing grant applications or analyzing brain images, Dr. Bjork moonlights as a professional saxophonist.


Kevin Conway, PhD

Dr. Conway is the Deputy Director of the Division of Epidemiology, Services, and Prevention Research at NIDA. Before joining NIDA in 2001, Dr. Conway was a faculty member in the Department of Epidemiology and Public Health at the Yale University School of Medicine. Dr. Conway’s research and publications focus on the epidemiology of substance use, mental health, and violence. He is the recipient of many awards for leadership in research, and is a Fellow of the American Psychopathological Association. Dr. Conway earned a PhD in Experimental Psychology from Temple University in 1998.


Research Team Members



RTI International National Human Genome Research Institute
Carol M. Hamilton, PhD Principal Investigator Erin Ramos, PhD, MPH Project Scientist
Tabitha Hendershot Co-Investigator Teri Manolio, MD, PhD Director, Division of Genomic Medicine
Amanda Riley, PMP Project Manager Margaret Ginoza Scientific Program Analyst
Deborah Maiese, MPA Consensus Coordinator    
Rebecca Boyles, MSPH Investigator    
Darigg Brown, PhD, MPH Investigator    
Wayne Huggins, PhD Investigator    
Destiney Nettles, MPM Investigator    
Michael Phillips, MS Investigator    
Helen Pan, PhD Toolkit Lead    
Pat West Communications Lead    

Previous PhenX Newsletters         Phenx Steering Committee

PhenX is supported by Genomic Resource for PhenX Toolkit (U41) funded by the National Institutes of Health (NIH) National Human Genome Research Institute (NHGRI) with co-funding by the National Institute on Drug Abuse (NIDA). Supplemental funding was provided by the Tobacco Regulatory Science Program (TRSP), the Food and Drug Administration (FDA), the National Institute of Mental Health (NIMH) and the National Heart, Lung, and Blood Institute (NHLBI).


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