PhenX Newsletter - Information and Updates | Issue 16. June 29, 2011 |
Overview
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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. |
Highlights
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PhenX Toolkit Update
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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:
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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.
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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. |
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PhenX In Focus
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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:
- Assessment of substance use and substance use disorders,
- Substance-specific intermediate phenotypes,
- Substance-use related neurobehavioral and cognitive risk factors,
- Substance-use related psychosocial risk factors,
- Substance-use related community factors, and
- Substance-use related co-morbidities and health-related outcomes.
Steering Committee Web Conference
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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:
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WG #1
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WG #2
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WG #3
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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.
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Featured PhenX Contributors
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Steering Committee Members
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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
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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 |
Announcements
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Link to Previous PhenX Newsletters
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https://www.phenx.org/Default.aspx?tabid=146 |