Challenges in Clinical DataAnalysis with RIan CookRaleigh-Durham-Chapel Hill R Users GroupJanuary 24, 2013
Background• R is a full-featured and mature environment for  clinical data analysis• Significant use of R by industry in n...
FDA Regulatory Guidance• 21 CFR Part 11 - Electronic Records; Electronic Signatures   • Validation of systems to ensure ac...
JSM : Use of R in Regulated Environment• FDA talk with Sue Bell at JSM 2006:  “Times „R‟ A Changing: FDA Perspectives on  ...
useR! : Use of R in RegulatedEnvironment• useR! 2007 session hosted by Marc Schwartz  • Perception of SAS as the gold stan...
useR! : Use of R in RegulatedEnvironment (continued)• useR! 2007 Mat Soukup (FDA) talk  • FDA Reviewer Expectations/Reques...
useR! : Use of R in RegulatedEnvironment (continued)• Announcement of document from the R  Foundation at useR! 2007:  “R: ...
useR! : Use of R in RegulatedEnvironment (continued)• useR! 2011 Ian Cook and Michael O’Connell  (TIBCO) talk  • Framework...
Learning More“Clinical Trial DataAnalysis Using R”(2010)• Presents methods for  analysis of clinical trial  data• Shows st...
Challenges in Clinical Data Analysis with R
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Challenges in Clinical Data Analysis with R

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R is a full-featured and mature environment for clinical data analysis. However, a common misperception exists that R cannot support the various regulatory requirements for clinical data analysis. This presentation provides an overview of proceedings at useR! conferences and elsewhere regarding the acceptability of use of R in regulated environments, e.g., clinical trials for pharmaceuticals and medical devices.

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Challenges in Clinical Data Analysis with R

  1. 1. Challenges in Clinical DataAnalysis with RIan CookRaleigh-Durham-Chapel Hill R Users GroupJanuary 24, 2013
  2. 2. Background• R is a full-featured and mature environment for clinical data analysis• Significant use of R by industry in non-regulated environments, but R has been slower to penetrate regulated environments, e.g. clinical trials, financial services• Common misperception exists that R cannot support the various regulatory requirements for validation/qualification
  3. 3. FDA Regulatory Guidance• 21 CFR Part 11 - Electronic Records; Electronic Signatures • Validation of systems to ensure accuracy, reliability and consistent intended performance • Paper equivalence in deployed environment• 21 CFR Part 58 - Good Laboratory Practice (GLP)• 21 CFR Part 312 - Good Clinical Practice (GCP)• 21 CFR Part 210 - Current Good Manufacturing Practice (cGMP)• Guidance for Industry - Computerized Systems Used in Clinical Investigations (2007)• General Principles of Software Validation; Final Guidance for Industry and FDA Staff (2002)
  4. 4. JSM : Use of R in Regulated Environment• FDA talk with Sue Bell at JSM 2006: “Times „R‟ A Changing: FDA Perspectives on Use of „Open Source‟”• No regulation prohibiting open source• FDA narrowly interprets and enforces 21 CFR 11 • Software installation, operation and performance must be “qualified” to be reproducibly installed and tested to ensure accuracy, reliability and consistent intended performance in regulated company’s environment (IQ/OQ/PQ) • FDA expects to be able to reconstruct a clinical study submitted to the agency • FDA may ask to see the regulated company’s documentation that demonstrates software qualification
  5. 5. useR! : Use of R in RegulatedEnvironment• useR! 2007 session hosted by Marc Schwartz • Perception of SAS as the gold standard, but reasons to be optimistic about future of R in regulated environments• useR! 2007 Frank Harrell talk • Validation should encompass practices to prevent user error • R includes tools to eliminate tedious low-level commands and manual actions, resulting in fewer sources of error• useR! 2007 Anthony Rossini and David A. James (Novartis) talk • R presents risks in regulated environments, but manageable given proper validation and qualification procedures
  6. 6. useR! : Use of R in RegulatedEnvironment (continued)• useR! 2007 Mat Soukup (FDA) talk • FDA Reviewer Expectations/Requests for submissions generated with R • What R functions are used and where do they reside (base vs. user-contributed packages)? • Have the R functions been properly validated in user environment? • Can the validation tests be reproduced? • Is there any certification of the validation test? • Are there any known data structures which can potentially alter results?
  7. 7. useR! : Use of R in RegulatedEnvironment (continued)• Announcement of document from the R Foundation at useR! 2007: “R: Regulatory Compliance and Validation Issues: A Guidance Document for the Use of R in Regulated Clinical Trial Environments”• Document addresses significant hurdles, but burden of implementation on usershttp://www.r-project.org/doc/R-FDA.pdf
  8. 8. useR! : Use of R in RegulatedEnvironment (continued)• useR! 2011 Ian Cook and Michael O’Connell (TIBCO) talk • Framework for successfully complying with regulatory software validation requirements when using R• useR! 2012 Jae Brodsky (FDA) talk • Drug developers may use R in their FDA submissions. • "R use at the FDA is completely acceptable and has not caused any problems."
  9. 9. Learning More“Clinical Trial DataAnalysis Using R”(2010)• Presents methods for analysis of clinical trial data• Shows step by step how to implement the statistical methods using Rhttp://www.crcpress.com/product/isbn/9781439840207

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