Implementing CDISC Using SAS®: An End-to-End Guide, Revised Second Edition

Contents
About This Book
	Background
	What’s New in This Edition?
	Is This Book for You?
	Prerequisites
	Purpose
	Organization and Scope of This Book
	Software Used to Develop This Book’s Content
		Data and Programs Used in This Book
		Author Pages
		Example Code and Data
	Additional Help
	Keep in Touch
		Contact the Author through SAS Press
		Purchase SAS Books
		Subscribe to the SAS Learning Report
		Publish with SAS
	Acknowledgments
About These Authors
Implementation Strategies
	The Case for Standards
		Table 1.1: FDA Documents and Events in Support of Data Standards
	Which Models to Use and Where
	Starting with the Clinical Data Acquisition Standards Harmonization (CDASH) Standard
	Implementation Plans and the Need for Governance
	SDTM Considerations
	ADaM Considerations
	Chapter Summary
SDTM Metadata and Define.xml for Base SAS Implementation
	More Information
	See Also
	SDTM Metadata
		Table of Contents Metadata
			Table 2.1: Table of Contents Metadata
		Variable-Level Metadata
			Table 2.2: Variable-Level Metadata
		Codelist Metadata
			Table 2.3: Codelist Metadata
		Value-Level Metadata
			Table 2.4: Value-Level Metadata
		Where Clause Metadata
			Table 2.5: Where Clause Metadata
		Computational Method Metadata
			Table 2.6: Computational Method Metadata
		Comments Metadata
			Table 2.7: Comments Metadata
		External Links
			Table 2.8: External Links Metadata
	Building Define.xml
		Define File Header Metadata
			Table 2.9: Metadata File for Define.xml
		Define File Creation SAS Program
	Chapter Summary
Implementing the CDISC SDTM with Base SAS
	More Information
	See Also
	Base SAS Macros and Tools for SDTM Conversions
		Table 3.1: Base SAS Programs 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
		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
Implementing CDISC SDTM with the SAS Clinical Standards Toolkit and Base SAS
	More Information
	SAS Clinical Standards Toolkit Background
	Clinical Standards Setup for Study XYZ123
		Copy SDTM 3.2 Standard to XYZ123
		Edit Study XYZ123 Metadata
		Edit the XYZ123 SAS Clinical Standards Toolkit Control Files
		Register the XYZ123 Standard
	Building SDTM Datasets
		Base SAS Macros and Tools for SDTM Conversions
			Empty Dataset Creator via the SAS Clinical Standards Toolkit
			Domain Sorter via the SAS Clinical Standards Toolkit
		Building the Special-Purpose DM and SUPPDM Domains
	Building Define.xml
		Create the Study Level Metadata Dataset
		Create the Table and Column-Level Metadata Datasets
		Create the Value-Level Metadata Dataset
		Create the Codelists Metadata Dataset
		Create the Document Reference Metadata Dataset
		Create Define File Generation Programs
	Chapter Summary
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
			CDISC-Published Metadata
			Company-Specific 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
			Register Source Datasets
			Define Target SDTM Datasets
		Setting SAS Clinical Data Integration Defaults
	Creating SDTM Domains
		Creating the Special-Purpose DM and SUPPDM Domain
			Extract Transformation
			SQL Join Transformation
			Lookup Transformation
			Transpose Transformation
		Creating the AE (Adverse Events) Events Domain
			Subject Sequence Generator Transformation
		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
			Figure 5.1: General SAS Clinical Data Integration Job Flow to Create an SDTM File
	Using SAS Clinical Data Integration to Create Define.xml
	Chapter Summary
ADaM Metadata and ADaM Define.xml
	More Information
	See Also
	Metadata Spreadsheets
		Variable Metadata in ADaM
		Analysis Parameter Value-Level Metadata
			Table 6.1: Selected Analysis Parameter Value-Level Metadata for ADEF
		Analysis Results Metadata
			Table 6.2: Description of Metadata Captured in the ANALYSIS_RESULTS Worksheet
		Building Define.xml
	Define.xml Navigation and Rendering
	Chapter Summary
Implementing ADaM with Base SAS
	See Also
	ADaM Tools
		ISO 8601 Date and DateTime Conversions
			Log 7.1:  Use of ISO 8601 Informats
		Merging in Supplemental Qualifiers
			Table 7.1:  Supplemental Qualifiers to DM
	ADSL – The Subject-Level Dataset
	The ADaM Basic Data Structure (BDS)
		Table 7.2:  Snippet of XP SDTM Data
	ADAE – Adverse Event Analysis Datasets
	ADTTE – The Time-to-Event Analysis Dataset
		Table 7.3:  CNSR and EVNTDESC Values
	Chapter Summary
CDISC Validation Using SAS
	SAS Clinical Standards Toolkit SDTM Validation
		SAS Clinical Standards Toolkit Setup
			Validation Control Data Set
			Study-Based Custom Codelist Format Catalog
			Reference and Source Data Set Metadata
			Properties Files
			SDTM Data Sets
		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
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)
			Table 9.1: Selected Pinnacle 21 Community  Command-Line Parameters
	ADaM Validation with Pinnacle 21 Community
	ADaM Traceability Checks with SAS
	Define.xml Validation with Pinnacle 21 Community
	Chapter Summary
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
Integrated Data and Regulatory Submissions
	See Also
	Regulatory Guidance
	Data Integration Challenges
	Data Integration Strategies
		Representing Subjects Who Appear in Multiple Studies in Subject-Level Data Sets
			Table 11.1: DM Data for a Double-Blind Study and Open-Label Extension Study
			Table 11.2: Integration Option 1(IADSL Data for a Double-Blind Study and Open-Label Extension Study (One Record per Subject per Study)
			Table 11.3: Integration Option 2(ADSL Data for a Double-Blind Study and Open-Label Extension Study Combined (One Record per Subject)
		Deciding Which Data to Integrate
		Coding Dictionary Issues
			Table 11.4: Historic Coding Variables Recommended by ADAE
		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
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
Source Data Programs
	adverse Dataset
	demographics Dataset
	dosing Dataset
	laboratory Dataset
	pain scores Dataset
SDTM Metadata
	Appendix B.1 – Define Header Metadata
	Appendix B.2 – Table of Contents Metadata
	Appendix B.3 – Variable-Level Metadata
	Appendix B.4 – Value-Level Metadata
	Appendix B.5 – Computational Method Metadata
	Appendix B.6 – Codelist Metadata
	Appendix B.7 – Where Clause Metadata
	Appendix B.8 – Comment Metadata
	Appendix B.9 – External Links Metadata
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 – Where Clause Metadata
	Appendix C.7 – Comments Metadata
	Appendix C.8 – Codelist Metadata
	Appendix C.9 – Analysis Results Metadata
	Appendix C.10 – External Links Metadata
%run_p21v SAS macro
	%run_p21v SAS Macro
	Additional SAS Code Comments
Index
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