precisionFDA

precisionFDA
Developer(s)
Status Active
License Open-source

PrecisionFDA (stylized precisionFDA)[1][2] is a cloud-based next-generation DNA sequencing (NGS) data platform developed by the United States Food and Drug Administration (FDA).[3][4] It was designed as part of President Barack Obama's Precision Medicine Initiative in 2015.[5] The platform allows researchers to upload and compare data against reference genomes, bioinformatics pipelines, and genomic data.[6] Users may also use the service to verify their genetic tests against reference genomes.[7] The platform's code is open source and available on GitHub.[8]

History

President Barack Obama announced the formation of the Precision Medicine Initiative during the State of the Union Address in January 2015.[6] In August 2015, the FDA announced the launch of precisionFDA as a part of the initiative.[9][10] The FDA's Office of Health Informatics (previously responsible for the creation of OpenFDA) and DNAnexus (a California-based company specializing in cloud-based data analysis and management) were tasked with the development of the web platform.[11][12] Taha Kass-Hout, the FDA's chief health informatics officer and the director of the office of health informatics, created and oversees the development of the project.[5][11]

In November 2015, the FDA launched a "closed beta" version of the platform, giving select groups and individuals access to the portal.[5][6][13] An open beta version of the platform was released in December 2015.[14][15] In February 2016, the FDA announced that its first "consistency challenge," which tasked users with testing the reliability and reproducibility of standard gene mapping and variant calling tools like BWA, the Genome Analysis Toolkit, and Bowtie. By March 2016, the platform maintained 1,000 community members representing around 500 public and private organizations including the National Institutes of Health, the Centers for Disease Control and Prevention, 23andMe, Illumina, and the Broad Institute.[16][17]

In April 2016, precisionFDA was awarded the top prize in the Informatics category at the Bio IT World Best Practices Awards.[18]

Functionality

The precisionFDA portal is an open-source, cloud-based platform for collaborating and testing bioinformatics pipelines and data related to next-generation sequencing.[3][4] Its code can be found on GitHub. The platform allows researchers to upload data from their own studies and analyze data uploaded by other researchers.[5][8][19] The platform supports files such as reference genomes or genomic data, comparisons (quantification of similarities between sets of genomic variants), and apps (bioinformatics pipelines) that scientists and researchers can upload and work with.[6][20] The long-term goal of the platform is to streamline the process of evaluating tests leading to medical patients being able to get precise care based on their own individual genomic data.[11]

References

  1. ↑ Blair Wyckoff, Whitney (11 February 2016). "Five tech projects buried in the budget". FedScoop. Retrieved 15 April 2016.
  2. ↑ Kern, Christine (1 January 2016). "precisionFDA Launched By FDA". Health IT Outcomes. Retrieved 15 April 2016.
  3. 1 2 Taylor, Nick Paul (16 November 2015). "FDA starts beta-testing 'the most advanced bioinformatics platform in the world'". FierceBiotechIT. Retrieved 15 April 2016.
  4. 1 2 Taylor, Nick Paul (26 February 2016). "FDA challenges industry to improve reproducibility and accuracy of informatics pipelines". FierceBiotechIT. Retrieved 15 April 2016.
  5. 1 2 3 4 Blair Wyckoff, Whitney (13 November 2015). "FDA debuts 'closed beta' of precisionFDA platform". FedScoop. Retrieved 15 April 2016.
  6. 1 2 3 4 Hall, Susan D. (16 November 2015). "PrecisionFDA cloud platform unveiled". FierceHealthIT. Retrieved 15 April 2016.
  7. ↑ Allen, Arthur (13 November 2015). "Our microscope on teladoc, King of telemedicine". Politico. Retrieved 15 April 2016.
  8. 1 2 Downing Peck, Andrea (28 March 2016). "FDA's New Next-Generation DNA Sequencing Platform Intended to Increase Collaboration among Scientists, Pathologists, and Clinical Laboratory Experts". Dark Daily. Retrieved 15 April 2016.
  9. ↑ Kass-Hout, Taha A.; Litwack, David (5 August 2015). "Advancing precision medicine by enabling a collaborative informatics community". FDA. Retrieved 25 April 2016.
  10. ↑ Kass-Hout, Taha A.; Johanson, Elaine (15 December 2015). "FDA Launches precisionFDA to Harness the Power of Scientific Collaboration". FDA. Retrieved 25 April 2016.
  11. 1 2 3 Fidler, Ben (5 August 2015). "FDA Taps DNAnexus to Build Platform for Crowdsourcing Diagnostics". Xconomy. Retrieved 15 April 2016.
  12. ↑ Mezher, Michael (6 August 2015). "precisionFDA: A Crowd-Sourced, Cloud-Based Platform for Precision Medicine". Regulatory Affairs Professional Society. Retrieved 15 April 2016.
  13. ↑ Harley, Liz (16 November 2015). "FDA launch "closed beta" of PrecisionFDA platform". Front Line Genomics. Retrieved 15 April 2016.
  14. ↑ Blair Wyckoff, Whitney (15 December 2015). "FDA unveils open beta of precisionFDA". FedScoop. Retrieved 15 April 2016.
  15. ↑ Hall, Susan D. (15 December 2015). "PrecisionFDA platform opens to the public". FierceHealthIT. Retrieved 15 April 2016.
  16. ↑ Krol, Aaron (4 March 2016). "PrecisionFDA Consistency Challenge Will Benchmark the Basic Software Tools of Genetic Research". Bio IT World. Retrieved 15 April 2016.
  17. ↑ "Launch of the First precisionFDA Consistency Challenge on DNAnexus-Built Cloud-Based Community Platform". Business Wire. 3 March 2016. Retrieved 15 April 2016.
  18. ↑ Krol, Aaron (15 April 2016). "Odds and Ends from the 2016 Bio-IT World Conference and Expo". Bio IT World. Retrieved 16 April 2016.
  19. ↑ Golden, Hallie (25 November 2015). "FDA Crowdsourcing its Way to Precision Medicine. But What About Security?". Nextgov. Retrieved 16 April 2016.
  20. ↑ Anderson, Angela (15 December 2015). "FDA Advancing Innovation Through Deep Collaboration". DNA Nexus. Retrieved 9 May 2016.
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