Implementing CDISC Using SAS. Full book available for purchase here.

Transcription

1 Implementing CDISC Using SAS. Full book available for purchase here. Contents About the Book... ix About the Authors... xv Chapter 1: Implementation Strategies... 1 The Case for Standards... 1 Which Models to Use and Where... 4 Starting with the Clinical Data Acquisition Standards Harmonization (CDASH) Standard... 4 Implementation Plans and the Need for Governance... 5 SDTM Considerations... 6 ADaM Considerations... 7 Chapter Summary... 8 Chapter 2: SDTM Metadata and Define.xml for Base SAS Implementation... 9 SDTM Metadata Table of Contents Metadata Variable-Level Metadata Codelist Metadata Value-Level Metadata Where Clause Metadata Computational Method Metadata Comments Metadata External Links Building Define.xml Define File Header Metadata Chapter 3: Implementing the CDISC SDTM with Base SAS Base SAS Macros and Tools for SDTM Conversions Creating an SDTM Codelist SAS Format Catalog Creating an Empty SDTM Domain Dataset Creating an SDTM --DTC Date Variable Creating an SDTM Study Day Variable... 36

2 iv Sorting the Final SDTM Domain Dataset Building SDTM Datasets Building the Special-Purpose DM and SUPPDM Domains Building the LB Findings Domain Building a Custom XP Findings Domain Building the AE Events Domain Building the EX Exposure Interventions Domain Building Trial Design Model (TDM) Domains Chapter Summary Chapter 4: Implementing CDISC SDTM with the SAS Clinical Standards Toolkit and Base SAS SAS Clinical Standards Toolkit Background Clinical Standards Setup for Study XYZ Building SDTM Datasets Base SAS Macros and Tools for SDTM Conversions Building the Special-Purpose DM and SUPPDM Domains Building Define.xml Chapter Summary Chapter 5: Implementing the CDISC SDTM with SAS Clinical Data Integration SAS Clinical Data Integration Introduction SAS Clinical Data Integration Metadata Classifications of SAS Clinical Data Integration Metadata Setup of SAS Clinical Data Integration Metadata SAS Clinical Data Integration Study Setup Define the Clinical Study and Subfolders Register Source Datasets and Define Target SDTM Datasets Setting SAS Clinical Data Integration Defaults Creating SDTM Domains Creating the Special-Purpose DM and SUPPDM Domain Creating the AE (Adverse Events) Events Domain Creating the XP Pain Scale Customized Findings Domain Creating the EX Exposure Interventions Domain Creating the LB Laboratory Findings Domain Creating the Trial Design Model Domains Using Customized Code in SDTM Production Templating Your SDTM Conversion Jobs for Reuse

3 v Using SAS Clinical Data Integration to Create Define.xml Chapter Summary Chapter 6: ADaM Metadata and ADaM Define.xml Metadata Spreadsheets Variable Metadata in ADaM Analysis Parameter Value-Level Metadata Analysis Results Metadata Building Define.xml Define.xml Navigation and Rendering Chapter Summary Chapter 7: Implementing ADaM with Base SAS ADaM Tools ISO 8601 Date and DateTime Conversions Merging in Supplemental Qualifiers ADSL The Subject-Level Dataset The ADaM Basic Data Structure (BDS) ADAE Adverse Event Analysis Datasets ADTTE The Time-to-Event Analysis Dataset Chapter Summary Chapter 8: CDISC Validation Using SAS SAS Clinical Standards Toolkit SDTM Validation SAS Clinical Standards Toolkit Setup SAS Clinical Standards Toolkit SDTM Validation Program SAS Clinical Data Integration SDTM Validation SAS Clinical Standards Toolkit Define.xml Validation Program SAS Clinical Data Integration Define.xml Validation Chapter Summary Chapter 9: CDISC Validation Using Pinnacle 21 Community Getting Started with Pinnacle 21 Community Running Pinnacle 21 Community (Graphical User Interface) Evaluating the Report Modifying the Configuration Files A Note about Controlled Terminology Running Pinnacle 21 Community (Command-Line Mode) ADaM Validation with Pinnacle 21 Community ADaM Traceability Checks with SAS Define.xml Validation with Pinnacle 21 Community Chapter Summary

4 vi Chapter 10: CDISC Data Review and Analysis Safety Evaluations with JMP Clinical Getting Started with JMP Clinical Safety Analyses Patient Profiles Event Narratives One PROC Away with ADaM Data Sets Transposing the Basic Data Structure for Data Review Progression Free Survival with Investigator and Central Assessment Chapter Summary Chapter 11: Integrated Data and Regulatory Submissions Regulatory Guidance Data Integration Challenges Data Integration Strategies Representing Subjects Who Appear in Multiple Studies in Subject-Level Data Sets Deciding Which Data to Integrate Coding Dictionary Issues Summary of Data Integration Strategies Data Integration and Submission Tools Setting Variable Lengths Based on the Longest Observed Value Converting from Native SAS to Version 5.0 Transport Files Converting from Version 5.0 Transport Files to Native SAS Getting Submission Ready Chapter Summary Chapter 12: Other Topics Standard for Exchange of Non-Clinical Data Dataset-XML BRIDG Model Protocol Representation Model FDA Janus Clinical Trials Repository CDISC Model Versioning Future CDISC Directions Chapter Summary

5 Appendix A: Source Data Programs adverse Dataset demographics Dataset dosing Dataset laboratory Dataset pain scores Dataset Appendix B: SDTM Metadata Appendix B.1 - Table of Contents Metadata Appendix B.2 - Variable-Level Metadata Appendix B.3 - Codelist Metadata Appendix B.4 - Value-Level Metadata Appendix B.5 - Computational Method Metadata Appendix B.6 - Define Header Metadata Appendix C: ADaM Metadata Appendix C.1 - Define Header Metadata Appendix C.2 - Table of Contents Metadata Appendix C.3 - Variable-Level Metadata Appendix C.4 - Parameter-Level Metadata Appendix C.5 - Computational Method Metadata Appendix C.6 - Codelist Metadata Appendix C.7 - Analysis Results Metadata Appendix C.8 - External Links Metadata Appendix D: %run_p21v.sas macro %run_p21v.sas Macro Additional SAS Code Comments Index vii From Implementing CDISC Using SAS, by Chris Holland and Jack Shostak. Copyright 2016, SAS Institute Inc., Cary, North Carolina, USA. ALL RIGHTS RESERVED.