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PhenX Toolkit

February 19, 2024

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] PhenX Toolkit's mission is to provide investigators with standard measurement protocols for use in genomic, epidemiologic, clinical and translational research. 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][4] The Toolkit is funded by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) with co-funding by the Office of the Director (OD), the National Institute of Neurological Disorders and Stroke (NINDS), and the National Heart, Lung, and Blood Institute (NHLBI).[5][6] Continuously funded since 2007, PhenX has received funding from a variety of NIH institutes, including the National Institute on Drug Abuse (NIDA), the National Institute on Mental Health (NIMH), the National Cancer Institute (NCI) and the National Institute on Minority Health and Health Disparities (NIMHD).[7][8] The PhenX Toolkit is available to the scientific community at no cost.

The PhenX Toolkit
Type of site
Content Site
Available inEnglish
OwnerNHGRI
Created byRTI International
URLwww.phenxtoolkit.org
Commercialno
RegistrationOptional
Users3700+ Registered, 1.6M+ visits
Launched6 February 2009 (2009-02-06)
Current statusActive
Content license
Public Domain

For genome-wide association studies (GWAS) and other studies involving human subjects, the use of standard measures can facilitate cross-study analyses.[9][10][11] Such analyses compare independent findings to validate results or combine studies to increase sample size and statistical power.[12][13] This increased power makes it possible to identify more subtle and complex associations such as gene-gene and gene-environment interactions.[14][15][16][17] PhenX is an NIH Common Data Element (CDE) Repository project and supports the NIH Strategic Plan for Data Science, which promotes FAIR principles (i.e., Findable, Accessible, Interoperable, Reusable) to facilitate data sharing.[18]

In 2020, PhenX collaborated with the U.S. NIH's Public Health Emergency and Disaster Research Response Program (DR2) to collect and review research protocols for epidemiologists, clinicians and other scientists studying COVID-19.[19] The Toolkit released six specialty collections of protocols to promote the use of CDEs for research on COVID-19 in October 2020.[20]

See also edit

References edit

  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. ^ 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. S2CID 7273784.
  4. ^ Fortier, Isabel; Doiron, Dany; Burton, Paul; Raina, Parminder (2011-08-01). "Invited Commentary: Consolidating Data Harmonization—How to Obtain Quality and Applicability?". American Journal of Epidemiology. 174 (3): 261–264. doi:10.1093/aje/kwr194. ISSN 0002-9262. PMID 21749975.
  5. ^ RTI (January 30, 2023). "RTI's PhenX Toolkit to be established as biomedical knowledgebase with latest award". RTI International. Retrieved 10 February 2023.
  6. ^ "Resource Summaries". wayback.archive-it.org. Retrieved 2021-05-21.
  7. ^ 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. PMC 5745137. PMID 29296922. Retrieved 9 May 2018.
  8. ^ "The PhenX Toolkit". RTI. 2021-12-15. Retrieved 2023-02-10.
  9. ^ 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.
  10. ^ 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.
  11. ^ Sheehan, Jerry; Hirschfeld, Steven; Foster, Erin; Ghitza, Udi; Goetz, Kerry; Karpinski, Joanna; Lang, Lisa; Moser, Richard P.; Odenkirchen, Joanne; Reeves, Dianne; Rubinstein, Yaffa (December 2016). "Improving the value of clinical research through the use of Common Data Elements (CDEs)". Clinical Trials (London, England). 13 (6): 671–676. doi:10.1177/1740774516653238. ISSN 1740-7745. PMC 5133155. PMID 27311638.
  12. ^ Sheehan, Jerry; Hirschfeld, Steven; Foster, Erin; Ghitza, Udi; Goetz, Kerry; Karpinski, Joanna; Lang, Lisa; Moser, Richard P.; Odenkirchen, Joanne; Reeves, Dianne; Rubinstein, Yaffa (December 2016). "Improving the value of clinical research through the use of Common Data Elements (CDEs)". Clinical Trials (London, England). 13 (6): 671–676. doi:10.1177/1740774516653238. ISSN 1740-7745. PMC 5133155. PMID 27311638.
  13. ^ Fortier, Isabel; Dragieva, Nataliya; Saliba, Matilda; Craig, Camille; Robson, Paula J. (2019-04-16). "Harmonization of the Health and Risk Factor Questionnaire data of the Canadian Partnership for Tomorrow Project: a descriptive analysis". CMAJ Open. 7 (2): E272–E282. doi:10.9778/cmajo.20180062. ISSN 2291-0026. PMC 6498449. PMID 31018973.
  14. ^ 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.
  15. ^ 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" (PDF). Nature Genetics. 41 (6): 703–707. doi:10.1038/ng.381. PMC 2889014. PMID 19430480.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  16. ^ 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.
  17. ^ Hunter DJ (April 2005). "Gene-environment Interactions in Human Diseases". Nature Reviews Genetics. 6 (4): 287–298. doi:10.1038/nrg1578. PMID 15803198. S2CID 27052260.
  18. ^ "NIH Common Data Elements (CDE) Repository". cde.nlm.nih.gov. Retrieved 2021-05-21.
  19. ^ "Covid-19 researchers gain quick access to surveys, protocols (Environmental Factor, May 2020)". National Institute of Environmental Health Sciences. Retrieved 2021-05-20.
  20. ^ Krzyzanowski, Michelle C.; Terry, Ian; Williams, David; West, Pat; Gridley, Lauren N.; Hamilton, Carol M. (2021). "The PhenX Toolkit: Establishing Standard Measures for COVID-19 Research". Current Protocols. 1 (4): e111. doi:10.1002/cpz1.111. ISSN 2691-1299. PMC 8206667. PMID 33905618.

External links edit

  • [1] dbGaP
  • [2] NIH Common Data Elements (CDE) Repository

February 19, 2024
phenx, toolkit, based, catalog, high, priority, measures, related, complex, diseases, phenotypic, traits, environmental, exposures, these, measures, were, selected, working, groups, experts, using, consensus, process, mission, provide, investigators, with, sta. 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 PhenX Toolkit s mission is to provide investigators with standard measurement protocols for use in genomic epidemiologic clinical and translational research 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 4 The Toolkit is funded by the National Human Genome Research Institute NHGRI of the National Institutes of Health NIH with co funding by the Office of the Director OD the National Institute of Neurological Disorders and Stroke NINDS and the National Heart Lung and Blood Institute NHLBI 5 6 Continuously funded since 2007 PhenX has received funding from a variety of NIH institutes including the National Institute on Drug Abuse NIDA the National Institute on Mental Health NIMH the National Cancer Institute NCI and the National Institute on Minority Health and Health Disparities NIMHD 7 8 The PhenX Toolkit is available to the scientific community at no cost The PhenX ToolkitType of siteContent SiteAvailable inEnglishOwnerNHGRICreated byRTI InternationalURLwww wbr phenxtoolkit wbr orgCommercialnoRegistrationOptionalUsers3700 Registered 1 6M visitsLaunched6 February 2009 2009 02 06 Current statusActiveContent licensePublic DomainFor genome wide association studies GWAS and other studies involving human subjects the use of standard measures can facilitate cross study analyses 9 10 11 Such analyses compare independent findings to validate results or combine studies to increase sample size and statistical power 12 13 This increased power makes it possible to identify more subtle and complex associations such as gene gene and gene environment interactions 14 15 16 17 PhenX is an NIH Common Data Element CDE Repository project and supports the NIH Strategic Plan for Data Science which promotes FAIR principles i e Findable Accessible Interoperable Reusable to facilitate data sharing 18 In 2020 PhenX collaborated with the U S NIH s Public Health Emergency and Disaster Research Response Program DR2 to collect and review research protocols for epidemiologists clinicians and other scientists studying COVID 19 19 The Toolkit released six specialty collections of protocols to promote the use of CDEs for research on COVID 19 in October 2020 20 See also editPatient Reported Outcomes Measurement Information System Health informatics REDCap Research Electronic Data Capture LOINCReferences edit 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 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 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 S2CID 7273784 Fortier Isabel Doiron Dany Burton Paul Raina Parminder 2011 08 01 Invited Commentary Consolidating Data Harmonization How to Obtain Quality and Applicability American Journal of Epidemiology 174 3 261 264 doi 10 1093 aje kwr194 ISSN 0002 9262 PMID 21749975 RTI January 30 2023 RTI s PhenX Toolkit to be established as biomedical knowledgebase with latest award RTI International Retrieved 10 February 2023 Resource Summaries wayback archive it org Retrieved 2021 05 21 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 PMC 5745137 PMID 29296922 Retrieved 9 May 2018 The PhenX Toolkit RTI 2021 12 15 Retrieved 2023 02 10 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 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 Sheehan Jerry Hirschfeld Steven Foster Erin Ghitza Udi Goetz Kerry Karpinski Joanna Lang Lisa Moser Richard P Odenkirchen Joanne Reeves Dianne Rubinstein Yaffa December 2016 Improving the value of clinical research through the use of Common Data Elements CDEs Clinical Trials London England 13 6 671 676 doi 10 1177 1740774516653238 ISSN 1740 7745 PMC 5133155 PMID 27311638 Sheehan Jerry Hirschfeld Steven Foster Erin Ghitza Udi Goetz Kerry Karpinski Joanna Lang Lisa Moser Richard P Odenkirchen Joanne Reeves Dianne Rubinstein Yaffa December 2016 Improving the value of clinical research through the use of Common Data Elements CDEs Clinical Trials London England 13 6 671 676 doi 10 1177 1740774516653238 ISSN 1740 7745 PMC 5133155 PMID 27311638 Fortier Isabel Dragieva Nataliya Saliba Matilda Craig Camille Robson Paula J 2019 04 16 Harmonization of the Health and Risk Factor Questionnaire data of the Canadian Partnership for Tomorrow Project a descriptive analysis CMAJ Open 7 2 E272 E282 doi 10 9778 cmajo 20180062 ISSN 2291 0026 PMC 6498449 PMID 31018973 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 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 PDF Nature Genetics 41 6 703 707 doi 10 1038 ng 381 PMC 2889014 PMID 19430480 a href Template Cite journal html title Template Cite journal cite journal a CS1 maint numeric names authors list link 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 Hunter DJ April 2005 Gene environment Interactions in Human Diseases Nature Reviews Genetics 6 4 287 298 doi 10 1038 nrg1578 PMID 15803198 S2CID 27052260 NIH Common Data Elements CDE Repository cde nlm nih gov Retrieved 2021 05 21 Covid 19 researchers gain quick access to surveys protocols Environmental Factor May 2020 National Institute of Environmental Health Sciences Retrieved 2021 05 20 Krzyzanowski Michelle C Terry Ian Williams David West Pat Gridley Lauren N Hamilton Carol M 2021 The PhenX Toolkit Establishing Standard Measures for COVID 19 Research Current Protocols 1 4 e111 doi 10 1002 cpz1 111 ISSN 2691 1299 PMC 8206667 PMID 33905618 External links edit 1 dbGaP 2 NIH Common Data Elements CDE Repository Retrieved from https en wikipedia org w index php title PhenX Toolkit amp oldid 1207026221, wikipedia, wiki, book, books, library,

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