December 16, 2011

PhenX Newsletter - Information and Updates Issue 17. December 16, 2011


The PhenX project (consensus measures for Phenotypes and eXposures) is funded by the National Institutes of Health, The National Human Genome Research Institute. The initial phase of the project is complete, and the PhenX Toolkit now includes measures for each of the 21 domains selected by the PhenX Steering Committee. A Working Group of experts was convened for each domain, and a consensus-based process was used to select high priority, relatively low burden and well-established measures. Preliminary measures were vetted with the broader scientific community before final selections were made, resulting in the set of measures that were included in the Toolkit.

The Toolkit includes detailed protocols to ensure that the data collected will be 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 meets the needs of the scientific community.


PhenX Toolkit Update

On November 29, 2011, Version 4.6 of the PhenX Toolkit was released. This release included the following updates and enhancements to the Toolkit site:
  • Data Collection Worksheet (DCW) and Data Dictionary (DD) diagrams were added to the homepage with descriptions and definitions.
  • New DCW/DD buttons were added at the top of My Toolkit for better visibility.
  • DD is now in Rich Text Format (RTF) to enhance downloading performance.
  • The DD.csv files were updated to include types and values fields for compatibility with dbGaP submissions.
  • The PhenX variable definition and Toolkit Bibliography were updated.

Top Domains and Top Measures

Top domains and measures are those found most often in the reports generated from user “My Toolkits.” They are listed on the home page of the PhenX Toolkit: These 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. These lists are recalculated and updated with each new release. Toolkit release notes and dates can be found at the following link:

Top 5 domains in the PhenX Toolkit

Following are the top 5 domains as of the November 29, 2011 PhenX Toolkit release.

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

Top 20 measures in the PhenX Toolkit

Following are the top 20 measures chosen by toolkit users as of the November 29, 2011 PhenX Toolkit release.

  1.  Current Age   11.  Annual Family Income
  2.  Gender   12.  Birthplace
  3.  Ethnicity   13.  Current Employment Status
  4.  Race   14.  Current Marital Status
  5.  Weight   15.  Household Roster - Relationships
  6.  Alcohol - 30-Day Quantity and Frequency   16.  Lipid Profile
  7.  Height   17.  Current Address
  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.  Tobacco - 30-Day Quantity and Frequency

Substance Abuse and Addiction (SAA)

Measures pertaining to SAA are found in seven domains, including the Alcohol, Tobacco and Other Substances domain. To expand the breadth and depth of SAA measures in the Toolkit, a project was launched in March 2011 to create six “Specialty” Collections and one “Core” Collection of measures. It is envisioned that the Core Collection of measures will be appropriate for all SAA and other researchers, and that use of the Specialty Collections will be study specific.

Substance Abuse and Addiction Scientific Panel (SSP)

Having previously selected and defined the scope of the six Specialty Collections to be addressed by the three SAA Working Groups (WGs), the PhenX Substance Abuse and Addiction Scientific Panel (SSP) met three times by teleconference over recent months to review the extent to which the measures selected by the WGs cover the scopes of the Specialty Collections. For a list of the six Specialty Collections, see Newsletter dated June 29 2011.
The SSP approved the measures that were then shared with the scientific community for review and comment in October and November. The WGs are now in the process of selecting their final measures and obtaining approval from the SSP. The release of the final measures in the Toolkit is anticipated for February 2012.

The SSP also reviewed the process for drafting and further refining a set of Core Collection measures and deliberated the specific content of the draft Core Collection, which may consist of currently existing PhenX Toolkit measures as well as newly proposed SAA measures. Prioritization of the Core Collection is being balanced with the time required to administer the protocols. The goal is to have a set of measures that will be widely utilized and will make cross study analysis possible.

WG 1 (Substance Use)

The first Substance Abuse and Addiction WG was tasked with identifying measures for two specialty area topics, Assessment of Substance Use and Substance Use Disorders and Substance-specific Intermediate Phenotypes. The SAA WG 1, co-chaired by Drs. Harriet de Wit from the University of Chicago and Stephanie O’Malley from Yale University, held their in-person meeting on July 20-21, 2011 to identify the measures and appropriate protocols for community outreach, which took place October 4-13, 2011. The SAA WG 1 met via teleconference on November 2, 2011 to review the community outreach report and to further refine their set of proposed measures based on responses from the scientific community. SAA WG 1 is working to finalize their Specialty Collection measures for inclusion in the Toolkit.

WG 2 (Risk Factors)

The second Substance Abuse and Addiction WG was tasked with identifying measures for two specialty area topics, Substance use-related Neurobehavioral and Cognitive Risk Factors and Substance use-related Psychosocial Risk Factors. The SAA WG 2, chaired by Dr. Matt McGue from the University of Minnesota, met in person and via phone and Web conferencing on August 29-30, 2011 to determine the measures and protocols for community outreach, which took place November 3-13, 2011. The WG met via teleconference on December 2, 2011 to review the community outreach report and to further refine their set of proposed measures based on responses from the scientific community. WG 2 is currently working to finalize their measures for inclusion in the Toolkit.

WG 3 (Community, Comorbidities and Outcomes)

The third Substance Abuse and Addiction WG was tasked with identifying measures for two specialty area topics, Substance use-related Community Factors and Substance use-related Comorbidities and Health-related Outcomes. Drs. Frank Chaloupka and Patrick Flynn, Co-chairs for the WG, lead the group in proposing research measures, for consideration by the scientific community and inclusion in the Toolkit. The WG met in-person on August 25–26, 2011 and several times by teleconference to identify measures. Between October 17 and October 26, 2011, researchers in the scientific community provided input and indicated which measures they felt were most valuable for human subjects research. Following the community outreach, the WG selected the final eight measures for each of the two specialty areas. The final set of measures include measures of perceived availability, treatment quality, and health quality and treatment participation, among others. In addition, two measures that went to outreach will be placed in Supplemental Information.


PhenX RISING (Real world, Implementation, SharingING) is a group of seven investigators funded by NHGRI to include PhenX measures in existing population-based genomic studies. In total, these seven groups are incorporating 81 PhenX measures, representing a quarter of the 295 measures in the Toolkit. The measures encompass demographics, psychosocial risk factors, psychiatric assessments, and a variety of exposures. Each group is adding between 4 and 37 measures with five groups adding more than 20 measures. In all, 55 of these 81 measures are shared by two or more groups providing common ground for future cross-study analysis.

PhenX RISING provides a cross-section of different study designs, populations, and topics. For example, these seven groups include single site studies, multi-center studies, members of genetics consortia, and biobanks. These studies are collecting data from children as young as three years through adolescence and adults. One study has a large population of centenarians. The projects address the role of genes and environment in psychopathology and behavior, neuro-imaging and genomics; the determinants of longevity; and the genetics of conditions such as diabetes, cataracts, and high cholesterol.

The seven studies that have been funded under PhenX RISING 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
    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 the SAA WG chairs: Dr. Harriet de Wit and Dr. Stephanie O’Malley from WG 1; Dr. Matt McGue from WG 2; and Dr. Frank Chaloupka and Dr. Patrick Flynn from WG 3.

Harriet de Wit, PhD, WG 1 Co-ChairHarriet de Wit, PhD, WG 1 Co-Chair
Professor and Director, Human Behavioral Pharmacology Laboratory, Department of Psychiatry and Behavioral Neuroscience, University of Chicago

Dr. de Wit is Professor in the Department of Psychiatry and Behavioral Neuroscience at the University of Chicago. She obtained her PhD in Experimental Psychology from Concordia University in Montreal, Canada, in 1981. She is Principal Investigator for several NIH-funded research projects studying the acute effects of drugs of abuse in human volunteers. In addition, Dr. de Wit serves as Field Editor for the journal Psychopharmacology and Deputy Editor for Alcoholism: Clinical and Experimental Research. She is a consultant to the Food and Drug Administration and serves on several scientific advisory boards at other institutions. In 1999 she received the Solvay Award for Outstanding Basic Psychopharmacological Research in Affective Disorders, and in 2009 she received the Marian W. Fischman Memorial Lectureship Award. Dr. de Wit's research focuses on the physiological, subjective (i.e., mood-altering) and behavioral effects of drugs in healthy human volunteers. Current projects in her laboratory include: i) investigating individual differences in responses to drugs, including genetic factors that influence drug responses, ii) examining interactions between acute stress and responses to drugs, and iii) studying the effects of drugs on impulsive behavior and risk-taking. The studies are designed to improve our understanding of the mechanisms underlying motivated behavior and of the processes underlying drug and alcohol use. Ultimately, it is hoped that studies such as these will lead to better approaches to preventing and treating drug abuse.

Stephanie O’Malley, PhD, WG 1 Co-ChairStephanie O’Malley, PhD, WG 1 Co-Chair
Professor of Psychiatry; Director, Division of Substance Abuse Research; Assistant Chair for Clinical Research in Psychiatry, Yale School of Medicine

Dr. O’Malley’s research focuses on alcohol and smoking. The goal of her laboratory is the development of efficacious treatments for alcohol use disorders and nicotine dependence. Toward this end, she and her colleagues are conducting clinical trials to determine efficacy of medications and behavioral interventions, and laboratory studies to understand addictive behaviors and to screen and evaluate mechanisms of new treatments. She is the Co-Director of the NIAAA Center for the Translational Neuroscience of Alcoholism and previously directed the Yale Transdisciplinary Tobacco Use Research Center funded by NIDA, NIAAA and NCI. This center incorporated tools from epidemiology, genetics, economics, psychology, behavioral pharmacology, brain imaging, and clinical trials to address questions related to smoking and smoking cessation. Dr. O’Malley Co-Directs a Clinician Scientist Training Program funded by NIDA and has other ongoing NIH supported research. She received her PhD in Clinical Psychology from Vanderbilt University in 1983.

>Matt McGue, PhD, WG 2 ChairMatt McGue, PhD, WG 2 Chair
Regents Professor, Department of Psychology, University of Minnesota

Dr. Matt McGue is a Regents Professor in the Department of Psychology at the University of Minnesota, where he is also a member of the Institute of Human Genetics. He received his undergraduate degree in Psychology and Mathematics at the University of California at Berkeley and his PhD in Psychology at the University of Minnesota. He is a behavioral geneticist with two primary areas of research focus. The first concerns the development of substance use disorders from adolescence to adulthood. The second concerns genetic contributions to normative aging processes and mortality. His research on substance use disorders is based primarily on several ongoing longitudinal studies of adolescents and their parents that he co-directs at the University of Minnesota. His research on aging is based primarily in Denmark, where he holds a position of Guest Professor in the Department of Epidemiology at the University of Southern Denmark. He has produced numerous publications, as well as serving as an editorial consultant for various journals and national institutes.

>Frank Chaloupka, PhD, WG 3 Co-ChairFrank Chaloupka, PhD, WG 3 Co-Chair
Professor, Department of Economics
University of Illinois at Chicago

Dr. Chaloupka received his PhD from the City University of New York, specializing in health economics, industrial organization, labor economics, and applied econometrics. His research focuses on the impact of economic, policy, and other environmental influences on health behaviors, including tobacco, alcohol and illicit drug use, physical activity, diet, and related outcomes and the economics of tobacco and tobacco control, particularly in developing countries. Dr. Chaloupka is distinguished professor of economics at the University of Illinois at Chicago and directs the Institute for Health Research and Policy’s (IHRP's) Health Policy Center. He is also a research associate at the National Bureau of Economic Research's Health Economics Program and Program on Children. Since 1997, Dr. Chaloupka has co-directed, with Lloyd Johnston of the University of Michigan, Bridging the Gap, an interdisciplinary research collaborative funded by the Robert Wood Johnson Foundation to improve understanding of the influences of policy, programs, and environment on youth health behavior. He is currently the director of ImpacTeen: A Policy Research Partnership to Reduce Substance Use at IHRP at the University of Illinois at Chicago (UIC). He has been the Principal Investigator on many tobacco-related research projects that have led to numerous publications. Since 2000, he has served as the chair of the Tobacco Policy Advisory Committee at the American Legacy Foundation. Dr. Chaloupka is also a member of many research and consulting groups, such as the Tobacco Control Resource Centre, the World Health Organization, the Society for Research on Nicotine and Tobacco, the National Center for Tobacco-Free Kids, and the U.S. Government Accountability Office.

>Patrick Flynn, PhD, WG 3 Co-ChairPatrick Flynn, PhD, WG 3 Co-Chair
Director, Institute of Behavioral Research, and Professor and Saul B. Sells Chair in Psychology
Texas Christian University

Dr. Flynn received his PhD in counseling psychology from the University of Miami in 1982 and was appointed Director of the Institute of Behavioral Research (IBR) at Texas Christian University in 2009. His research has focused on the effectiveness and benefits of treatment and has included clinical assessment; questionnaire development; multisite clinical trials; dissemination and implementation in community-based programs in the United States, United Kingdom, and Italy; studies of organizational functioning and costs in outpatient treatments; and treatment services and outcomes research in correctional settings. He is a Fellow in the American Educational Research Association and in several divisions of the American Psychological Association, is a frequent member of federal grant review panels, serves on journal editorial boards, is a regular reviewer for professional journals, and has served as chairperson of a National Institutes of Health (NIH) Health Services Research Study Section. He served on the NIH/National Institute on Drug Abuse (NIDA) Health Services Research Initial Review Group for the term of 2004–07. Since 1990, when he returned to the research environs, he has been the Principal Investigator (PI)/Project Director and Co-Director of national studies and a Co-PI and key investigator for a number of other treatment studies. He recently completed a 5-year, NIDA-funded project designed to develop and implement a treatment cost and organizational monitoring system. Currently, he is PI on a major 5-year NIDA project that is adapting, adopting, and implementing an intervention in therapeutic communities for adolescents. He is also PI on a recently awarded multiple PI project titled “A Randomized Clinical Trial of an Augmented Test, Treat, Link, and Retain Model for North Carolina and Texas Prisoners.” Prior to his return to full-time research, Dr. Flynn worked in therapeutic community, methadone, and outpatient drug-free treatment programs in several capacities and served in upper-level management positions in higher education.

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
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


  • On July 29, 2011 Version 4.5 of the PhenX Toolkit was released:
  • On May 20, 2011 Version 4.4 of the PhenX Toolkit was released:
  • PhenX presented at the following meetings in 2011:
    • Society for Epidemiologic Research (SER) Annual Meeting – Montreal, Quebec, Canada - June 21-24, 2011
    • NIDA and NIAAA Genetics Satellite Miniconvention to World Congress on Psychiatric Genetics - September 9-10, 2011 - Washington, DC
    • International Congress of Human Genetics (ICHG) - Montreal, Canada - October 11-15, 2011
    • NIDA Frontiers in Addiction Research Mini-Convention to the Society for Neuroscience Annual Meeting - Washington, DC - November 11, 2011
    • American Society of Criminology Annual Meeting - Washington, DC - November 16-19, 2011
  • PhenX will present at the following meetings in 2012:
    • Society for Research on Nicotine and Tobacco – Houston, TX – March 13-16, 2012

Link to Previous PhenX Newsletters

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