June 29, 2011

PhenX Newsletter - Information and Updates Issue 16. June 29, 2011


The PhenX project, consensus measures for Phenotypes and eXposures, is funded by the National Institutes of Health, 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, leading to the set of measures that were loaded in the Toolkit.

The Toolkit includes detailed protocols for collecting the measures, to ensure that the data collected will be comparable between 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 their 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 May 20, 2011 Version 4.4 of the PhenX Toolkit was released. This release included the following updates and enhancements to the Toolkit site:
  • A "Cart Overload" message was added to indicate when a Cart is too large, directing the user to go to the Data Collection Worksheet (DCW)/Data Dictionary (DD) Support page.
  • A Smart Query Tool (SQT) filter was added at the Protocol Level.
  • User login and password support features were added.
  • A DCW/DD Support page was added under the Help heading.
  • PhenX Working Group flyers were added under the Resource heading.
  • A PhenX Early Adopters section was added to the News & Views page under the Resource heading.

Top Domains and Top Measures

Top domains and measures are those found the most often in the reports generated from user “Carts”. They are listed on the home page of the PhenX Toolkit: https://www.phenxtoolkit.org/. They are calculated by the number of times they are present in reports generated from user Carts, cumulatively. The measures and domains with the highest inclusion in reports are those listed as Top Measures and Top Domains. This list is recalculated and updated with each new release. Toolkit release notes and dates can be found at the following link: https://www.phenxtoolkit.org/index.php?pageLink=about.releases.

Top 5 domains in the PhenX Toolkit

Following are the top 5 domains as of the May 20, 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 May 20, 2011 PhenX Toolkit release.

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

PhenX In Focus

Substance Abuse and Addiction
The PhenX Toolkit currently contains 295 measures spanning 21 research domains and 16 collections (sets of related measures). The Alcohol, Tobacco and Other Substances (ATOS) domain includes 14 measures of substance abuse and addiction (SAA). There are also measures related to SAA in 6 other domains: Cancer, Environmental Exposures, Infectious Diseases and Immunity, Oral Health, Reproductive Health, and Respiratory. Using key words in the Toolkit Search function will enable you to see the current SAA protocols that are recommended. To expand the breadth and depth of SAA-related measures, a project to identify additional PhenX measures was launched in March 2011, with funding and logistic support of NIDA, NIAAA, and NHGRI. The goal is to create six “specialty” collections and one “core” collection of measures for use by SAA and other investigators. Working Groups composed of SAA experts will select up to eight high-priority measures for each of the six specialty areas for inclusion in the Toolkit. It is expected that these SAA measures will be added to the Toolkit by spring 2012.

To provide guidance, a SAA Scientific Panel (SSP) of 10 academic and federal governmental scientists was assembled. Its members include:

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

The SSP has selected and defined the scope of the six specialty areas to be addressed:

  1. Assessment of substance use and substance use disorders,
  2. Substance-specific intermediate phenotypes,
  3. Substance-use related neurobehavioral and cognitive risk factors,
  4. Substance-use related psychosocial risk factors,
  5. Substance-use related community factors, and
  6. Substance-use related co-morbidities and health-related outcomes.

Steering Committee Web Conference

The PhenX Steering Committee (SC) met by teleconference on May 31, 2011. During the 1 hour webcast, the project PI provided updates on active collaborations with dbGaP, LOINC and eMERGE. She also gave an update on publications, with 1 recently published journal article and 3 in press. The SC then heard about the progress that has been made on the PhenX measures for Substance Abuse and Addiction Administrative Supplement funded by NIDA. Dr. Kevin Conway (NIDA) discussed data harmonizing in NIDA-funded clinical research. After which Dr. Kenneth Sher (SSP Chair) reported on the progress of the SSP. This includes identification of 3 Working Groups that will cover the 6 specialty areas:

WG #1
  1. Assessment of substance use and substance use disorders
  2. Substance-specific intermediate phenotypes

WG #2
  1. Substance use-related neurobehavioral and cognitive risk factors
  2. Substance use-related psychosocial risk factors

WG #3
  1. Substance use-related community factors
  2. Substance use-related co-morbidities and health-related outcomes

The PI then discussed the results of the Toolkit usability testing and what changes would be implemented as a result of the feedback received. Finally, the PI sought and discussed input from the SC on how the new SAA measures would appear in the Toolkit.

Usability Testing

In March and April of 2011, usability testing was conducted for the PhenX Toolkit. Nine volunteers local to the Research Triangle Park, NC area viewed the Toolkit website with one of RTI’s survey methodologists. No special skills or knowledge were required to participate, but we recruited from a base of research scientists and screened in favor of participants with research and GWAS experience. An effort was made to have a diverse group of participants. These volunteers provided feedback on the appearance of the site, as well as information on how easy or difficult it was to navigate. After exploring the website independently, participants were given research scenarios and asked how they would utilize the PhenX Toolkit if they were in each situation. These tests provide insight into how investigators use the Toolkit and the results suggest ways to potentially improve Toolkit usability. After reviewing the Usability Testing report, the PhenX Steering Committee will make their recommendations to the Toolkit development team.

Featured PhenX Contributors

In this newsletter, we highlight two of the SSP members, Dr. Kenneth Sher (SSP chair) and Dr. Kevin Conway.

Dr. Kenneth Sher
Curators’ Distinguished Professor of Psychological Sciences, University of Missouri.

Dr. Sher’s research interests are broad but primarily focus on the diagnosis, etiology, and course of substance use disorders (particularly alcohol dependence) across the life span. He’s been the principal investigator on two large prospective studies of alcohol use and associated problems in young adults targeted at understanding individual susceptibility and environmental effects on substance use and associated problems. In addition to ongoing analyses of data collected at the University of Missouri (MU) and new data collections, he currently has a research grant to conduct secondary data analyses on a large, nationally representative data set with a goal of characterizing developmental aspects of alcohol use disorders and related comorbidities. He also collaborates with colleagues in studying the behavioral effects of alcohol consumption in laboratory studies and the effects of extreme drinking events (e.g., 21st birthday celebrations) on neurological functioning. He is a co-director of the Midwest Alcoholism Research Center (MARC), a P60 based in the Department of Psychiatry of Washington University School of Medicine (WUSM) and the Department of Psychological Sciences at MU. Current MARC research projects focus on the behavioral pharmacology of alcohol, event-based analysis of drinking using electronic diaries, and the genetics of alcoholism and Dr. Sher is involved in each of these efforts. He is the Director of a predoctoral and postdoctoral training grant (T32) at MU, and his research is currently supported by a K05, a R01, and a P60 from NIAAA.

Dr. Kevin Conway
Deputy Director, Division of Epidemiology, Services and Prevention Research, National Institute on Drug Abuse

Dr. Conway is the Deputy Director of the Division of Epidemiology, Services and Prevention Research at the National Institute on Drug Abuse (NIDA). Before assuming this position in 2007, he served as Associate Director of the Division of Clinical Neuroscience and Behavioral Research at NIDA, and Deputy Branch Chief and Program Director for the Epidemiology Research Branch at NIDA. Prior to joining NIDA in 2001, Dr. Conway was an Associate Research Scientist in the Genetic Epidemiology Research Unit in the Department of Epidemiology and Public Health at the Yale University School of Medicine. Dr. Conway earned the PhD in Experimental Psychology from Temple University in 1998. Dr. Conway has authored numerous peer-reviewed articles and book chapters focusing on the epidemiology of drug abuse, co-occurring psychiatric disorders, and violence.

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   University of Texas, MD Anderson Cancer Center
Diane Wagener, PhD   RTI International
Michelle Williams, ScD   University of Washington School of Public Health and Community Medicine

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   Scientific Program Analyst, NHGRI
Teri Manolio, MD, PhD   Director, Office of Population Genomics;
  Senior Advisor to the Director, NHGRI, for Population Genomics


  • On April 15, 2011 Version 4.3 of the PhenX Toolkit was released: https://www.phenxtoolkit.org/index.php?pageLink=about.releasedetails&id=27
  • On February 4, 2011 Version 4.2 of the PhenX Toolkit was released: https://www.phenxtoolkit.org/index.php?pageLink=about.releasedetails&id=26
  • PhenX plans to present 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

Link to Previous PhenX Newsletters


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