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About the PhenX Toolkit

The PhenX Toolkit offers well-established, broadly validated measures of phenotypes and exposures relevant to investigators in human genomics, epidemiology, and biomedical research. The measures in the Toolkit are selected by Working Groups of domain experts using a consensus process. The Toolkit provides detailed protocols, information about the measures, and tools to help investigators incorporate PhenX measures into their studies. Inclusion of PhenX measures facilitates cross-study analysis downstream, thus increasing the scientific impact of each individual study.

PhenX Toolkit Contents

The Toolkit includes all the necessary information to administer the protocol and record the data, including:
  • A brief description of the measure
  • Recommended protocol(s) for collecting the measure
  • The rationale for selecting the protocol
  • Details about personnel and equipment needed to collect the protocol
  • A description of special requirements for collecting the protocol
  • A data dictionary and data collection worksheet for each protocol
  • References

PhenX Toolkit Features

  • Quick Start and Tutorial help new users become familiar with the Toolkit.
  • Data Collection Worksheet (DCW): A prototype data collection tool (in MS Word) that identifies each data item required and collected by the protocol.
  • Data Dictionary (DD): Lists each variable in the DCW and its attributes.
  • REDCap™ Instrument Zip Files: PhenX protocols can be uploaded directly to REDCap to facilitate Web-based data collection.
  • Standards: cancer Data Standards Registry and Repository (caDSR) Common Data Elements (CDEs) and Logical Observation Identifiers Names and Codes (LOINC).
  • My Toolkit: Add measures and protocols useful to your study to your personal Toolkit.
  • Annotation Tool: Annotate the PhenX protocols used to assess rare genetic diseases and conditions.
  • Smart Query Tool provides two search options: a Smart Search based on keywords (and synonyms) and a Text Search that searches all text.
  • Browse options: Domains, Measures, Protocols, Collections, Supplemental Information, and hierarchical tree view.
  • Register as a Toolkit user to access more features and functionality, such as the ability to save and share more than one “My Toolkit”.
  • Link Your Study to find other researchers using the same measures and explore opportunities for cross-study analysis.

PhenX Project Background

PhenX Phase 1: Consensus Measures for Phenotypes and Exposures (U01)

PhenX was established in September 2007 by a cooperative agreement from the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH), with Dr. Erin Ramos as NHGRI Project Scientist. Supplemental funding was provided by the NIH Office of Behavioral and Social Sciences Research (OBSSR).

The goal of the PhenX project was to provide the scientific community with recommended, standard high-priority measures of phenotypes and exposures for use in Genome-wide Association Studies (GWAS) and more generally, epidemiological and biomedical research.

Under the guidance of the PhenX Steering Committee (SC), policies and guidelines were adopted to aid in the selection of 21 research domains and their respective domain experts. Working Groups (WG) were established for each domain, each with a chair or co-chairs and four to six scientists with relevant expertise, a liaison from the SC, and an RTI WG supervisor and manager. Using a consensus process with guidance from the SC, the WGs chose up to 15 measures for each domain for inclusion in the PhenX Toolkit. With support from the National Institute on Drug Abuse (NIDA), a Substance Abuse and Addiction administrative supplement was launched in 2011to expand the depth and breadth of SAA-related measures in the PhenX Toolkit. The first 21 domains and the SAA project added 339 measures in the Toolkit.

PhenX Phase 2: Genomic Resource for PhenX Toolkit (U41)

In July 2013, a Genomic Resource Grant (U41) was awarded by the NHGRI to RTI International, with co-funding from NIDA, to:
  • Enhance and update the PhenX Toolkit content;
  • Implement new Toolkit capabilities and features;
  • Map PhenX variables to completed studies in dbGaP; and
  • Continue to extend collaborations.
The PhenX Steering Committee (SC) continues to support and guide this consensus based process. Liaisons from the NIH and other Federal organizations continue to be key stakeholders in the PhenX Toolkit.

New WGs are being established for each of four new domains. They follow the established consensus process, identifying up to 15 measures for their domain and delivering a set of high-priority measures for inclusion in the PhenX Toolkit.

Expert Review Panels (ERPs) composed of scientists with relevant expertise are being established to review existing content in the Toolkit. The ERPs enhance the Toolkit content (e.g. adding keywords and new references) and recommend archiving or adding new measures to the domains they review. An RTI manager and supervisor provide support for each ERP.

Funding

PhenX is funded by the National Human Genome Research Institute (cooperative agreement number U41 HG007050) with co-funding from the National Institute on Drug Abuse.

Management

Project Scientist, NHGRI: Erin Ramos, PhD MPH
Principal Investigator, RTI International: Carol Hamilton, PhD
Co-Investigator, RTI International: Tabitha P. Hendershot, BA
Participants: Project Participants

More information about the PhenX Project is available on the Project Portal.

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