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Implementing CDISC Using SAS, 2nd Edition

Author Jack Shostak , Chris Holland
Release Date: 2019/05/01
ISBN: 9781642952414
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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, Revised 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 edition include an implementation of the Define-XML 2.0 standard, new SDTM domains, validation with Pinnacle 21 software, event narratives in JMP Clinical, STDM and ADAM metadata spreadsheets, and of course new versions of SAS and JMP software. The second edition was revised to add the latest C-Codes from the most recent release as well as update the make_define macro that accompanies this book in order to add the capability to handle C-Codes. The metadata spreadsheets were updated accordingly.

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
    2. Define File Creation SAS Program
  14. Chapter Summary
  15. Chapter 3: Implementing the CDISC SDTM with Base SAS
  16. 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
  17. 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
  18. Chapter Summary
  19. Chapter 4: Implementing CDISC SDTM with the SAS Clinical Standards Toolkit and Base SAS
  20. SAS Clinical Standards Toolkit Background
  21. Clinical Standards Setup for Study XYZ123
  22. Building SDTM Datasets
    1. Base SAS Macros and Tools for SDTM Conversions
    2. Building the Special-Purpose DM and SUPPDM Domains
  23. Building Define.xml
  24. Chapter Summary
  25. Chapter 5: Implementing the CDISC SDTM with SAS Clinical Data Integration
  26. SAS Clinical Data Integration Introduction
  27. SAS Clinical Data Integration Metadata
    1. Classifications of SAS Clinical Data Integration Metadata
    2. Setup of SAS Clinical Data Integration Metadata
  28. 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
  29. 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
  30. Using SAS Clinical Data Integration to Create Define.xml
  31. Chapter Summary
  32. Chapter 6: ADaM Metadata and ADaM Define.xml
  33. Metadata Spreadsheets
    1. Variable Metadata in ADaM
    2. Analysis Parameter Value-Level Metadata
    3. Analysis Results Metadata
    4. Building Define.xml
  34. Define.xml Navigation and Rendering
  35. Chapter Summary
  36. Chapter 7: Implementing ADaM with Base SAS
  37. ADaM Tools
    1. ISO 8601 Date and DateTime Conversions
    2. Merging in Supplemental Qualifiers
  38. ADSL – The Subject-Level Dataset
  39. The ADaM Basic Data Structure (BDS)
  40. ADAE – Adverse Event Analysis Datasets
  41. ADTTE – The Time-to-Event Analysis Dataset
  42. Chapter Summary
  43. Chapter 8: CDISC Validation Using SAS
  44. SAS Clinical Standards Toolkit SDTM Validation
    1. SAS Clinical Standards Toolkit Setup
    2. SAS Clinical Standards Toolkit SDTM Validation Program
  45. SAS Clinical Data Integration SDTM Validation
    1. SAS Clinical Standards Toolkit Define.xml Validation Program
    2. SAS Clinical Data Integration Define.xml Validation
  46. Chapter Summary
  47. Chapter 9: CDISC Validation Using Pinnacle 21 Community
  48. 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)
  49. ADaM Validation with Pinnacle 21 Community
  50. ADaM Traceability Checks with SAS
  51. Define.xml Validation with Pinnacle 21 Community
  52. Chapter Summary
  53. Chapter 10: CDISC Data Review and Analysis
  54. Safety Evaluations with JMP Clinical
    1. Getting Started with JMP Clinical
    2. Safety Analyses
    3. Patient Profiles
    4. Event Narratives
  55. One PROC Away with ADaM Data Sets
  56. Transposing the Basic Data Structure for Data Review
    1. Progression Free Survival with Investigator and Central Assessment
  57. Chapter Summary
  58. Chapter 11: Integrated Data and Regulatory Submissions
  59. Regulatory Guidance
  60. Data Integration Challenges
  61. 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
  62. 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
  63. Getting Submission Ready
  64. Chapter Summary
  65. Chapter 12: Other Topics
  66. Standard for Exchange of Non-Clinical Data
  67. Dataset-XML
  68. BRIDG Model
  69. Protocol Representation Model
  70. FDA Janus Clinical Trials Repository
  71. CDISC Model Versioning
  72. Future CDISC Directions
  73. Chapter Summary
  74. Appendix A: Source Data Programs
  75. adverse Dataset
  76. demographics Dataset
  77. dosing Dataset
  78. laboratory Dataset
  79. pain scores Dataset
  80. Appendix B: SDTM Metadata
  81. Appendix B.1 - Define Header Metadata
  82. Appendix B.2 - Table of Contents Metadata
  83. Appendix B.3 - Variable-Level Metadata
  84. Appendix B.4 - Value-Level Metadata
  85. Appendix B.5 - Computational Method Metadata
  86. Appendix B.6 - Codelist Metadata
  87. Appendix B.7 - Where Clause Metadata
  88. Appendix B.8 - Comment Metadata
  89. Appendix B.6 - External Links Metadata
  90. Appendix C: ADaM Metadata
  91. Appendix C.1 - Define Header Metadata
  92. Appendix C.2 - Table of Contents Metadata
  93. Appendix C.3 - Variable-Level Metadata
  94. Appendix C.4 - Parameter-Level Metadata
  95. Appendix C.5 - Computational Method Metadata
  96. Appendix C.6 - Where Clause Metadata
  97. Appendix C.7 - Comments Metadata
  98. Appendix C.8 - Codelist Metadata
  99. Appendix C.9 - Analysis Results Metadata
  100. Appendix C.10 - External Links Metadata
  101. Appendix D: %run_p21v.SAS macro
  102. %run_p21v.SAS Macro
  103. Additional SAS Code Comments
  104. Index