Clinical Data Quality Checks for CDISC Compliance Using

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 Clinical Data Quality
Checks for CDISC
Compliance Using SAS

Sunil Gupta
CRC Press
Taylor & Francis Group
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Library of Congress Cataloging‑in‑Publication Data

Names: Gupta, Sunil, 1963- author.

Title: Clinical data quality checks for CDISC compliance using SAS / by
Sunil Gupta.
Description: Boca Raton, FL : Taylor & Francis, [2020] | Includes bibliographical references and
index. | Summary: “This book helps you create a system of SDTM and ADaM checks that can
be tracked for continuous improvement. How often have you encountered issues such as
missing required variables, duplicate records, invalid derived variables and invalid sequence
of two dates? With the SAS programming techniques introduced in this book, you can start to
monitor these and more complex data and CDISC compliance issues. With increased
standardization in SDTM and ADaM specifications and data values, codelist dictionaries can
be created for better organization, planning and maintenance. This book includes a SAS
program to create excel files containing unique values from all SDTM and ADaM variables as
columns. In addition, another SAS program compares SDTM and ADaM codelist dictionaries
with codelists from define.xml specifications. Having tools to automate this process greatly
saves time from doing it manually”-- Provided by publisher.
Identifiers: LCCN 2019023651 (print) | LCCN 2019023652 (ebook) | ISBN 9780367362775
(paperback) | ISBN 9780367362782 (hardback) | ISBN 9780429345043 (ebook)
Subjects: LCSH: SAS (Computer file) | Medical care--Standards--United
States. | Medical care--United States--Quality control.
Classification: LCC QA276.45.S27 G87 2020 (print) | LCC QA276.45.S27
(ebook) | DDC 005.5/5--dc23
LC record available at https://lccn.loc.gov/2019023651
LC ebook record available at https://lccn.loc.gov/2019023652

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Contents

Preface, ix
Acknowledgments, xiii
Author, xv

Chapter 1 ◾ Overview of Data Quality and Compliance

Checks 1
INTRODUCTION 1
1.1 LEVEL OF CHECKS TO APPLY 3
1.1.1 SDTMs and ADaMs Vitals 4
1.1.2 SDTMs and ADaM Data 5
1.1.3 CDISC Specifications Compliance 9
1.1.4 CDISC Data Compliance 9
1.1.5 Protocol Compliance 10
1.1.6 Codelist Dictionary Compliance 10
1.2 WHEN TO APPLY CHECKS 12
1.2.1 Database Acceptance and Lock 12
1.2.2 SDTMs and ADaMs Refresh 12
1.2.3 Snapshot Analysis 12
1.3 CUSTOMIZED CHECKS FOR EACH CLIENT 13
1.3.1 Site Management 13
1.3.2 Data Management 13
1.3.3 SAS Programmers 14
1.3.4 Statisticians 14
SUMMARY 14

v
vi ◾ Contents

Chapter 2 ◾ SDTMs and ADaMs Vital Checks 17

INTRODUCTION 17
2.1 DATASET VITALS 17
2.2 DATA TRANSFERS 23
2.3 GROUP DESCRIPTIVE STATISTICS 30
2.4 ZERO DATASET RECORDS 34
2.5 DISPOSITION POPULATION TREES (SAFFL, ITTFL) 35
2.6 SDTM ONCOLOGY DOMAIN 37
SUMMARY 37

Chapter 3 ◾ SDTMs and ADaMs Data Checks 39

INTRODUCTION 39
3.1 DUPLICATE RECORDS 39
3.2 MISSING VALUES IN REQUIRED VARIABLES 43
3.3 VARIABLE UNIQUE COUNTS 47
3.4 ISO8601 DATETIME AND TIME 48
3.5 DURATION 52
3.6 DATA RANGE 54
3.7 NEGATIVE VALUES 55
3.8 NUMERIC OUTLIERS 56
3.9 COMPARE RELATED VARIABLES 59
3.10 CALCULATIONS AND DERIVED VARIABLE 72
3.11 LAB DATA 75
SUMMARY 78

Chapter 4 ◾ CDISC Specification Compliance Checks 79

INTRODUCTION 79
4.1 CONSISTENCY BETWEEN DM SPECIFICATIONS
AND ATTRIBUTES (TYPE, NAME, LENGTH, LABEL) 80
4.2 NON-MISSING DATASET LABEL 85
 Contents ◾ vii

4.3 NO PERMANENT FORMAT IN DM 86

4.4 DM CORRECT ORDER OF VARIABLES 87
4.5 VARIABLE LENGTH IS MAXIMUM OF VALUES OR 200 89
SUMMARY 92

Chapter 5 ◾ CDISC Data Compliance Checks 93

INTRODUCTION 93
5.1 SDTM CONSISTENCY 93
5.1.1 AENUM and CENUM 93
5.1.2 AE.AESEQ and SUPPAE.IDVARVAL 94
5.1.3 Orphan Records in SUPPXX 95
5.1.4 DOMAIN Variable and Name 97
5.1.5 Required SDTM Domains (TA, DM, EX and DS)
Do Not Exist 97
5.1.6 Required ADaMs (ADSL) Do Not Exist 99
5.1.7 SE Start and End Dates Sequence Requirement 99
5.2 ADaM CONSISTENCY 100
SUMMARY 102

Chapter 6 ◾ Protocol Compliance Checks 103

INTRODUCTION 103
6.1 USUBJID MISSING IN DM/ADSL 103
6.2 MISSING EXPOSURE RECORD IN EX FOR DM
USUBJID 105
6.3 LAB DATA BASELINE 108
6.3.1 Incorrect ADBLFL Baseline Flag Record 108
6.3.2 No Baseline Result for VS, LB, EG, DA 109
6.4 DISPOSITION TREE CHECK – ONE-PROC AWAY 112
SUMMARY 113
viii ◾ Contents

Chapter 7 ◾ Codelist Dictionary Compliance Checks 115

INTRODUCTION 115
7.1 CODELIST, VALUE-LEVEL CHECKS AND LOOKUP
TABLES 116
7.2 CODELIST AND VALUE-LEVEL UPPERCASE 125
SUMMARY 126

APPENDIX, 127

REFERENCES, 141

INDEX, 145
Preface

C linical data quality checks for CDISC compliance using SAS

is a concise guide to help you apply innovative SAS programming
techniques for improving data quality and CDISC compliance. The book
capitalizes on these topics for more effective management.

• Manage controlled terminology dictionaries

• Monitor and better understand Pinnacle 21 issues
• Control and customize CDISC compliance checks
• Leverage metadata for automation
• QA checklists for better FDA submissions

Managing controlled terminology dictionaries involves automatically

creating SDTM and ADaM codelist dictionaries without manually run-
ning Proc FREQ on each SDTM and ADaM variable. In addition, tools
to automatically compare SDTM and ADaM codelist dictionaries with
define.xml specification codelists help to quickly identify differences in
codelists so that define.xml files are correctly represented.
Monitoring and understanding Pinnacle 21 issues are essential for SAS
programmers in the pharmaceutical industry. Most SAS programmers
use Pinnacle 21 Community or Enterprise versions to check for CDISC
compliance. This book reviews the main components of the Pinnacle 21
Enterprise version – SDTM/ADaM compliance, SDTM/ADaM repository,
define.xml and control terms and value-level metadata. This book also
shows examples of the five channels of CDISC compliance issues – unit
level, multiple variables and datasets, new variables, protocol compliance
and metadata and data transfer metrics.

ix
x ◾ Preface

This book has tools to jumpstart controlling and customizing CDISC

compliance checks. Below are key features:

• Level of checks to apply

• SDTMs and ADaMs vitals
• SDTMs and ADaMs data
• CDISC specifications compliance
• CDISC data compliance
• Protocol compliance
• Codelist dictionary compliance
• When to apply checks
• Database acceptance lock
• SDTMs and ADaMs refresh
• Snapshot analysis
• Different checks for different customers
• Site management
• Data management
• SAS programmers
• Statisticians

Leveraging metadata for automation requires advanced SAS program-

ming skills to dynamically access and process a directory of files, such as
SAS datasets or SAS programs, so that no hard coding is required. SAS
tools include LIBNAME, DATA step, SAS macro programming, SAS and
dataset functions, Proc SQL, Proc COMPARE and Proc MEANS. Many
standard and custom metadata such as # and type variables, maximum
variable length and descriptive statistics on categorical and continuous
variables can be created to manage the quality of data.
With each FDA submission, QA checklists assure all items are com-
pleted and validated. The book includes four practical QA checklists for
SDTM and ADaM mapping, clinical study milestones, Pinnacle 21 issues
 Preface ◾ xi

and Pinnacle 21 define specifications to define.XML. The SDTM and

ADaM mapping checklist includes examples of macros that many organi-
zations have to perform common functions. The clinical study milestones
checklist includes items in the database lock process. Both Pinnacle 21
checklists confirm key compliance levels.
Acknowledgments

A s I complete the final review of clinical data quality Checks

for CDISC Compliance using the SAS book, I am reminded of fond
memories of being in the pharmaceutical and medical device industries
for over 25 years and the passion I have had to improve data quality and
strive for higher standards. For each project I have supported, data qual-
ity checks were just as important as primary and secondary safety and
efficacy analysis. This book is a result of all my long hours to push the
SAS envelope for more robust and data-driven processes. The unique SAS
programming techniques I developed along the way have enabled me to
reach my goals as well as enable me to mentor other SAS programmers.
In addition, my clients have benefited from the comprehensive checklists
I have created to assure all proper steps were followed in FDA submis-
sion preparation and execution. I hope you too will find the book and
SASSavvy.com invaluable resources. I look forward to hearing your com-
ments about the book.
I would like to thank my wife, Bindiya, and daughters, Aarti and
Anupama, for their support, commitment and excitement. I would also
like to thank my book reviewers, Linfeng Xu, Paul Gill, Roger DeAngelis
and Chris Weiner, for their valuable suggestions to improve the book.
Their experience in the industry has helped make the book more practical.
This book along with my other four SAS books, Quick Results with the
Output Delivery System, Data Management Using the SAS Learning
Edition, Sharpening Your SAS Skills, and Sharpening Your Advanced SAS
Skills has been a dream come true.

xiii
Author

Sunil Guptais an international speaker, bestselling SAS author and a

global corporate CDISC trainer. Mr. Gupta is a principal SAS/CDISC con-
sultant and mentor. Most recently, he taught both of his CDISC online
classes in conjunction with the University of California at San Diego and
SAS ® Institute India. New in 2019, he is developing a new class on data sci-
ence using SAS class. In 2011, he launched his unique SAS resource blog,
SASSavvy.com, for smarter SAS searches. Currently, SAS Savvy’s mem-
bership consists mostly of SAS programmers, university students and
pharmaceutical corporate accounts.
In 2018, Mr. Gupta was the Quick Tips section chair at the first PhUSE
conference in Raleigh, and in 2016, he was a CDISC oncology ADaM
reviewer. In 2013, he was recognized by SAS Institute’s Circle of Excellence
for 20 years of service. In 2008, he was chosen as one of the ‘100 Notable
People in the Medical Device Industry’ for his contributions. Two of his
popular pharmaceutical industry leadership articles include ‘How Cloud-
Based Tools Can Help with FDA Compliance’ in the Life Science Leadership
magazine and ‘Standards for Clinical Data Quality and Compliance
Checks’ in the Society for Clinical Data Management and Pharmaceutical
Programming journals.
Each year, Mr. Gupta has been an invited presenter at many SAS confer-
ences for his ‘highly acclaimed’ Proc SQL hands-on workshops. In 2018,
he was the keynote speaker at the PhUSE SDE International Meeting
in Hyderabad, India. He has been using SAS software for over 20 years
and is a SAS-based certified professional. He is also the author of Quick
Results with the Output Delivery System, Sharpening Your SAS Skills, and
Sharpening Your Advanced SAS Skills.

xv