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Implementing CDISC Using SAS

Book Description

For decades researchers and programmers have used SAS to analyze, summarize, and report clinical trial data. Now Chris Holland and Jack Shostak have updated their popular Implementing CDISC Using SAS, the first comprehensive book on applying clinical research data and metadata to the Clinical Data Interchange Standards Consortium (CDISC) standards. Implementing CDISC Using SAS: An End-to-End Guide, Second Edition, is an all-inclusive guide on how to implement and analyze the Study Data Tabulation Model (SDTM) and the Analysis Data Model (ADaM) data and prepare clinical trial data for regulatory submission. Updated to reflect the 2017 FDA mandate for adherence to CDISC standards, this new edition covers creating and using metadata, developing conversion specifications, implementing and validating SDTM and ADaM data, determining solutions for legacy data conversions, and preparing data for regulatory submission. The book covers products such as Base SAS, SAS Clinical Data Integration, and the SAS Clinical Standards Toolkit, as well as JMP Clinical. Topics included in this new edition include an implementation of the Define-XML 2.0 standard, new SDTM domains, validation with Pinnacle 21 software, event narratives in JMP Clinical, and of course new versions of SAS and JMP software. Any manager or user of clinical trial data in this day and age is likely to benefit from knowing how to either put data into a CDISC standard or analyzing and finding data once it is in a CDISC format. If you are one such person--a data manager, clinical and/or statistical programmer, biostatistician, or even a clinician--then this book is for you.

Table of Contents

  1. About the Book
  2. About the Authors
  3. Chapter 1: Implementation Strategies
  4. The Case for Standards
  5. Which Models to Use and Where
  6. Starting with the Clinical Data Acquisition Standards Harmonization (CDASH) Standard
  7. Implementation Plans and the Need for Governance
  8. SDTM Considerations
  9. ADaM Considerations
  10. Chapter Summary
  11. Chapter 2: SDTM Metadata and Define.xml for Base SAS Implementation
  12. SDTM Metadata
    1. Table of Contents Metadata
    2. Variable-Level Metadata
    3. Codelist Metadata
    4. Value-Level Metadata
    5. Where Clause Metadata
    6. Computational Method Metadata
    7. Comments Metadata
    8. External Links
  13. Building Define.xml
    1. Define File Header Metadata
  14. Chapter 3: Implementing the CDISC SDTM with Base SAS
  15. Base SAS Macros and Tools for SDTM Conversions
    1. Creating an SDTM Codelist SAS Format Catalog
    2. Creating an Empty SDTM Domain Dataset
    3. Creating an SDTM --DTC Date Variable
    4. Creating an SDTM Study Day Variable
    5. Sorting the Final SDTM Domain Dataset
  16. Building SDTM Datasets
    1. Building the Special-Purpose DM and SUPPDM Domains
    2. Building the LB Findings Domain
    3. Building a Custom XP Findings Domain
    4. Building the AE Events Domain
    5. Building the EX Exposure Interventions Domain
    6. Building Trial Design Model (TDM) Domains
  17. Chapter Summary
  18. Chapter 4: Implementing CDISC SDTM with the SAS Clinical Standards Toolkit and Base SAS
  19. SAS Clinical Standards Toolkit Background
  20. Clinical Standards Setup for Study XYZ123
  21. Building SDTM Datasets
    1. Base SAS Macros and Tools for SDTM Conversions
    2. Building the Special-Purpose DM and SUPPDM Domains
  22. Building Define.xml
  23. Chapter Summary
  24. Chapter 5: Implementing the CDISC SDTM with SAS Clinical Data Integration
  25. SAS Clinical Data Integration Introduction
  26. SAS Clinical Data Integration Metadata
    1. Classifications of SAS Clinical Data Integration Metadata
    2. Setup of SAS Clinical Data Integration Metadata
  27. SAS Clinical Data Integration Study Setup
    1. Define the Clinical Study and Subfolders
    2. Register Source Datasets and Define Target SDTM Datasets
    3. Setting SAS Clinical Data Integration Defaults
  28. Creating SDTM Domains
    1. Creating the Special-Purpose DM and SUPPDM Domain
    2. Creating the AE (Adverse Events) Events Domain
    3. Creating the XP Pain Scale Customized Findings Domain
    4. Creating the EX Exposure Interventions Domain
    5. Creating the LB Laboratory Findings Domain
    6. Creating the Trial Design Model Domains
    7. Using Customized Code in SDTM Production
    8. Templating Your SDTM Conversion Jobs for Reuse
  29. Using SAS Clinical Data Integration to Create Define.xml
  30. Chapter Summary
  31. Chapter 6: ADaM Metadata and ADaM Define.xml
  32. Metadata Spreadsheets
    1. Variable Metadata in ADaM
    2. Analysis Parameter Value-Level Metadata
    3. Analysis Results Metadata
    4. Building Define.xml
  33. Define.xml Navigation and Rendering
  34. Chapter Summary
  35. Chapter 7: Implementing ADaM with Base SAS
  36. ADaM Tools
    1. ISO 8601 Date and DateTime Conversions
    2. Merging in Supplemental Qualifiers
  37. ADSL – The Subject-Level Dataset
  38. The ADaM Basic Data Structure (BDS)
  39. ADAE – Adverse Event Analysis Datasets
  40. ADTTE – The Time-to-Event Analysis Dataset
  41. Chapter Summary
  42. Chapter 8: CDISC Validation Using SAS
  43. SAS Clinical Standards Toolkit SDTM Validation
    1. SAS Clinical Standards Toolkit Setup
    2. SAS Clinical Standards Toolkit SDTM Validation Program
  44. SAS Clinical Data Integration SDTM Validation
    1. SAS Clinical Standards Toolkit Define.xml Validation Program
    2. SAS Clinical Data Integration Define.xml Validation
  45. Chapter Summary
  46. Chapter 9: CDISC Validation Using Pinnacle 21 Community
  47. Getting Started with Pinnacle 21 Community
    1. Running Pinnacle 21 Community (Graphical User Interface)
    2. Evaluating the Report
    3. Modifying the Configuration Files
    4. A Note about Controlled Terminology
    5. Running Pinnacle 21 Community (Command-Line Mode)
  48. ADaM Validation with Pinnacle 21 Community
  49. ADaM Traceability Checks with SAS
  50. Define.xml Validation with Pinnacle 21 Community
  51. Chapter Summary
  52. Chapter 10: CDISC Data Review and Analysis
  53. Safety Evaluations with JMP Clinical
    1. Getting Started with JMP Clinical
    2. Safety Analyses
    3. Patient Profiles
    4. Event Narratives
  54. One PROC Away with ADaM Data Sets
  55. Transposing the Basic Data Structure for Data Review
    1. Progression Free Survival with Investigator and Central Assessment
  56. Chapter Summary
  57. Chapter 11: Integrated Data and Regulatory Submissions
  58. Regulatory Guidance
  59. Data Integration Challenges
  60. Data Integration Strategies
    1. Representing Subjects Who Appear in Multiple Studies in Subject-Level Data Sets
    2. Deciding Which Data to Integrate
    3. Coding Dictionary Issues
    4. Summary of Data Integration Strategies
  61. Data Integration and Submission Tools
    1. Setting Variable Lengths Based on the Longest Observed Value
    2. Converting from Native SAS to Version 5.0 Transport Files
    3. Converting from Version 5.0 Transport Files to Native SAS
  62. Getting Submission Ready
  63. Chapter Summary
  64. Chapter 12: Other Topics
  65. Standard for Exchange of Non-Clinical Data
  66. Dataset-XML
  67. BRIDG Model
  68. Protocol Representation Model
  69. FDA Janus Clinical Trials Repository
  70. CDISC Model Versioning
  71. Future CDISC Directions
  72. Chapter Summary
  73. Appendix A: Source Data Programs
  74. adverse Dataset
  75. demographics Dataset
  76. dosing Dataset
  77. laboratory Dataset
  78. pain scores Dataset
  79. Appendix B: SDTM Metadata
  80. Appendix B.1 - Table of Contents Metadata
  81. Appendix B.2 - Variable-Level Metadata
  82. Appendix B.3 - Codelist Metadata
  83. Appendix B.4 - Value-Level Metadata
  84. Appendix B.5 - Computational Method Metadata
  85. Appendix B.6 - Define Header Metadata
  86. Appendix C: ADaM Metadata
  87. Appendix C.1 - Define Header Metadata
  88. Appendix C.2 - Table of Contents Metadata
  89. Appendix C.3 - Variable-Level Metadata
  90. Appendix C.4 - Parameter-Level Metadata
  91. Appendix C.5 - Computational Method Metadata
  92. Appendix C.6 - Codelist Metadata
  93. Appendix C.7 - Analysis Results Metadata
  94. Appendix C.8 - External Links Metadata
  95. Appendix D: %run_p21v.SAS macro
  96. %run_p21v.SAS Macro
  97. Index