PhenX Phase I: Consensus Measures for Phenotypes and Exposures
Supported by a cooperative agreement from the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH), PhenX was launched in September 2007 with the goal 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 aide in the selection of 21 research domains and their respective domain experts. 21 WGs were established, each with a chair or co-chairs and four to six scientists with relevant expertise, a liaison from the SC, and an RTI WG manager and supervisor.
Following a consensus process model, these WGs chose up to 15 measures for each domain and identified a total of 339 measures for inclusion in the PhenX Toolkit, along with the addition of Substance Abuse and Addiction Collections of measures.
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 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 our collaborations.
The PhenX Steering Committee (SC) has been re-established to support and guide this consensus based process with the scientific community regarding standard measures for collaborative research. Liaisons from the NIH Institutes and Centers (IC liaisons) will continue to be key stakeholders in the PhenX Toolkit.
Following the same WG composition, new WGs will be established for each of four new domains. They will follow the consensus process described above, each identifying up to 15 measures for their domain and delivering a set of high-priority measures for inclusion in the PhenX Toolkit. It is anticipated that two WGs will be formed in FY 2014; one in FY 2015; and one in FY 2016.
Expert Review Panels (ERPs) composed of up to three scientists with relevant expertise will also be established to review existing domain-specific content in the Toolkit. Each ERP will be supported by an RTI review panel manager and a domain expert. It is anticipated that each ERP will address four domains in FY 2014; six in FY 2015; six in FY 2016 and five in FY 2017.
The PhenX Toolkit
The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) is an online catalog of standard measures of phenotypes and exposures for use in biomedical research. PhenX measures cover a broad scope of research domains (e.g., Demographics, Cardiovascular, Diet and Nutrition) and provide depth in Substance Abuse and Addiction (SAA).
PhenX Toolkit Contents
The measures in the Toolkit are well established protocols that were identified by experts in the field. 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
PhenX Toolkit Features
- Search options: Smart Query Tool (ontology based) and Text (full-text) Query
- Browse options: Domains, Measures, Collections, Supplemental Information, and hierarchical tree view
- Standards: cancer Data Standards Registry and Repository (caDSR), Common Data Elements (CDEs), National Center for Biomedical Ontologies (NCBO), and Logical Observation Identifiers Names and Codes (LOINC)
- Data Dictionary and Data Collection Worksheets
- Featured Measure and Top Measures
- Register Your Study: allowing users to find other studies using the same measures and to identify opportunities for cross-study analysis
- Registered Users have access to additional features and functionality, including Register Your Study.
- Quick Start and Tutorial resources help new users become familiar with the Toolkit
Collaboration with the Database of Genotypes and Phenotypes (dbGaP)
The PhenX Data Dictionary is formatted for dbGaP data submission, allowing investigators to easily submit PhenX variables.