PhenX Toolkit

The PhenX Toolkit
PhenX: consensus measures for Phenotypes and eXposures
Screenshot
Screenshot of the website as of August 2012.
Type of site
 Content Site
Available in English
Owner NHGRI
Created by RTI International
Website www.phenxtoolkit.org
Commercial no
Registration Optional
Users 2700+ Registered, 1M+ visits
Launched 6 February 2009 (2009-02-06)
Current status Active
Content license
 Public Domain

PhenX (consensus measures for Phenotypes and eXposures) is a community-driven effort to provide standard measures for use in biomedical research. The goals are to help investigators identify opportunities for collaborative biomedical research and improve the consistency of data collection. The PhenX Toolkit is a web-based catalog of high-priority measures related to complex diseases, phenotypic traits and environmental exposures. These measures were selected by working groups of experts using a consensus process.[1] Use of PhenX measures facilitates combining data from a variety of studies, and makes it easy for investigators to expand a study design beyond the primary research focus.[2][3] The Toolkit is funded by the National Institute of Health's National Human Genome Research Institute (NHGRI) with co-funding by the Office of Behavioral and Social Sciences Research (OBSSR) and the National Institute on Drug Abuse (NIDA).[4] Supplemental funding is provided by the National Heart, Lung, and Blood Institute (NHLBI) and the National Institute on Minority Health and Health Disparities (NIMHD).[5] The PhenX Toolkit is available to the scientific community at no cost.

Objectives

For genome-wide association studies (GWAS) and other studies involving human subjects, the use of standard measures can facilitate cross-study analyses.[6][7] Such analyses compare independent findings to validate results or combine studies to increase sample size and statistical power. This increased power makes it possible to identify more subtle and complex associations such as gene-gene and gene-environment interactions.[8][9][10][11]

PhenX Measures

The Toolkit has a broad scope and currently provides assessments for 24 research domains.[12]

Specialty collections

In addition, the Toolkit includes more focused add-on collections for specialists in 4 areas.[12]

Substance Abuse and Addiction (SAA) Research[13]
Substance Use, including substance use disorders and substance-specific intermediate phenotypes
Risk Factors: neurobehavioral, cognitive, and psychosocial
Community, Comorbidities, and Outcomes
Tobacco Regulatory Research[14]
Social/Cognitive
Biobehavioral
Agent
Vector
Environment
Mental Health Research[15]
Suicide
Post-traumatic Stress Psychopathology (including PTSD)
Eating Disorders
Early Psychosis
Sickle Cell Disease[16]
Cardiovascular, Pulmonary, and Renal
Neurology, Quality of Life, and Health Services

The Toolkit

The PhenX Toolkit is a catalog of measures recommended by domain experts, with browse and search capabilities and bioinformatics support.[2] PhenX measures and protocols are included in the Cancer Data Standards Repository (caDSR) Common Data Elements (CDE) Dictionary and the National Center for Biomedical Ontology (NCBO) BioPortal. PhenX protocols are available as REDCap Instrument Zip files, and work is underway to map PhenX variables to all studies in dbGaP. PhenX provides easy access to standard measures with the potential to increase the overall impact of individual studies via cross-study analyses. For each measure, the PhenX Toolkit provides a brief description, the protocol for measurement with supporting images and tables, the reasons for selecting the protocol, details about training and equipment, translations available and selected references.[17] Users can browse research domains, measures, or collections, search using a “Smart Search” or a full text search, collect measures of interest in “My Toolkit”, and request custom data dictionaries and custom data collection worksheets.

The Toolkit can be particularly helpful when an investigator wants to expand a study to include measures that are outside his or her primary area of expertise. Whereas study specific measures are needed to address the primary research goal, common measures are needed to increase the overall impact of the study; both types of measures are important to overall study design.

The "Link Your Study" feature allows registered users to share their study with other registered users or find other studies using the same protocols and identify opportunities for cross-study analysis.

Protocols

In addition to measures, PhenX also defines protocols. There may be multiple protocols defined for a measure. For example, for smoking cessation, there is an adult protocol (id: 030901) and adolescent protocol (id:030902).[17]

Variables

PhenX also provides a datatype (e.g., integer, string, date, enumerated, or encoded values) for each PhenX variable. For example, variable 'PX070501_Pregnancy_Outcome_1' for 'Outcome of Pregnancy?' is of type enumerated with value set of four possible values (Live birth,Still born,Miscarriage,Induced abortion).

See also

References

  1. ↑ Maiese DR, Hendershot TP, Strader LC, et al. (2013). PhenX—Establishing a consensus process to select common measures for collaborative research (Technical report). Research Triangle Park, NC: RTI Press. doi:10.3768/rtipress.2013.mr.0027.1310. MR-0027-1310.
  2. 1 2 Hamilton CM, Strader LC, Pratt JG, et al. (1 August 2011). "The PhenX Toolkit: Get the Most From Your Measures". American Journal of Epidemiology. 174 (3): 253–260. doi:10.1093/aje/kwr193. PMC 3141081. PMID 21749974.
  3. ↑ Hendershot T, Pan H, Haines J, et al. (October 2011). "Using the PhenX Toolkit to Add Standard Measures to Your Study". Current Protocols in Human Genetics. 1 (21). Unit 1.21. doi:10.1002/0471142905.hg0121s71. PMID 21975939. (Subscription required (help)).
  4. ↑ "A research toolkit of standard measures to be expanded to further support the biomedical community". RTI International. September 28, 2017. Retrieved 9 May 2018.
  5. ↑ Eckman, JR; et al. (December 26, 2017). "Standard measures for sickle cell disease research: the PhenX Toolkit sickle cell disease collections" (PDF). Blood Advances. 1 (27): 2703–2711. doi:10.1182/bloodadvances.2017010702. Retrieved 9 May 2018.
  6. ↑ Pan H, Tryka KA, Vreeman DJ, et al. (May 2012). "Using PhenX Measures to Identify Opportunities for Cross-Study Analysis". Human Mutation. 33 (5): 849–857. doi:10.1002/humu.22074. PMC 3780790. PMID 22415805.
  7. ↑ Manolio TA (February 2009). "Collaborative Genome-wide Association Studies of Diverse Diseases: Programs of the NHGRI's Office of Population Genomics". Pharmacogenomics. 10 (3): 235–241. doi:10.2217/14622416.10.2.235. PMC 2714942. PMID 19207024.
  8. ↑ Barrett JC, Hansoul S, Nicolae DL, et al. (August 2008). "Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease". Nature Genetics. 40 (8): 955–962. doi:10.1038/ng.175. PMC 2574810. PMID 18587394.
  9. ↑ Barrett JC, Clayton DG, Concannon P, et al. (June 2009). "Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes". Nature Genetics. 41 (6): 703–707. doi:10.1038/ng.381. PMC 2889014. PMID 19430480.
  10. ↑ Cooper JD, Smyth DJ, Smiles AM, et al. (December 2008). "Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci". Nature Genetics. 40 (12): 1399–1401. doi:10.1038/ng.249. PMC 2635556. PMID 18978792.
  11. ↑ Hunter DJ (April 2005). "Gene-environment Interactions in Human Diseases". Nature Reviews Genetics. 6 (4): 287–298. doi:10.1038/nrg1578. PMID 15803198. (Subscription required (help)).
  12. 1 2 "Browse Domains". PhenX Toolkit, ver 22.2. RTI International. 14 March 2018.
  13. ↑ "Browse Collections: Substance Abuse and Addiction". PhenX Toolkit, ver 19.0. RTI International. 17 January 2017.
  14. ↑ "Browse Collections: Tobacco Regulatory Research". PhenX Toolkit, ver 19.0. RTI International. 17 January 2017.
  15. ↑ "Browse Collections: Mental Health Research". PhenX Toolkit, ver 19.0. RTI International. 17 January 2017.
  16. ↑ "Browse Collections: Sickle Cell Disease". PhenX Toolkit, ver 19.0. RTI International. 17 January 2017.
  17. 1 2 "PhenX Example Measure".

Further reading

  • dbGaP
  • NIH Common Data Elements (CDE) Resource Portal
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