Table Of ContentClinical Data Quality Checks
for CDISC Compliance
Using SAS
Clinical Data Quality
Checks for CDISC
Compliance Using SAS
Sunil Gupta
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2020 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business
No claim to original U.S. Government works
Printed on acid-free paper
International Standard Book Number-13: 9 78-0-367-36278-2 (Hardback)
978-0-367-36277-5 (Paperback)
This book contains information obtained from authentic and highly regarded sources. Reasonable efforts
have been made to publish reliable data and information, but the author and publisher cannot assume
responsibility for the validity of all materials or the consequences of their use. The authors and publishers
have attempted to trace the copyright holders of all material reproduced in this publication and apologize to
copyright holders if permission to publish in this form has not been obtained. If any copyright material has
not been acknowledged please write and let us know so we may rectify in any future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted,
or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented,
including photocopying, microfilming, and recording, or in any information storage or retrieval system,
without written permission from the publishers.
For permission to photocopy or use material electronically from this work, please access www.copyright.
com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood
Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and
registration for a variety of users. For organizations that have been granted a photocopy license by the CCC,
a separate system of payment has been arranged.
Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used
only for identification and explanation without intent to infringe.
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
Visit the Taylor & Francis Web site at
http://www.taylorandfrancis.com
and the CRC Press Web site at
http://www.crcpress.com
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2020 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business Contents
No claim to original U.S. Government works
Printed on acid-free paper
International Standard Book Number-13: 9 78-0-367-36278-2 (Hardback)
978-0-367-36277-5 (Paperback)
This book contains information obtained from authentic and highly regarded sources. Reasonable efforts
have been made to publish reliable data and information, but the author and publisher cannot assume
Preface, ix
responsibility for the validity of all materials or the consequences of their use. The authors and publishers
have attempted to trace the copyright holders of all material reproduced in this publication and apologize to
copyright holders if permission to publish in this form has not been obtained. If any copyright material has Acknowledgments, xiii
not been acknowledged please write and let us know so we may rectify in any future reprint.
Author, xv
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted,
or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented,
including photocopying, microfilming, and recording, or in any information storage or retrieval system,
without written permission from the publishers. Chapter 1 ◾ Overview of Data Quality and Compliance
Checks 1
For permission to photocopy or use material electronically from this work, please access www.copyright.
com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood INTRODUCTION 1
Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and
registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, 1.1 LEVEL OF CHECKS TO APPLY 3
a separate system of payment has been arranged.
1.1.1 SDTMs and ADaMs Vitals 4
Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used
only for identification and explanation without intent to infringe. 1.1.2 SDTMs and ADaM Data 5
1.1.3 CDISC Specifications Compliance 9
Library of Congress Cataloging‑in‑Publication Data
1.1.4 CDISC Data Compliance 9
Names: Gupta, Sunil, 1963- author.
Title: Clinical data quality checks for CDISC compliance using SAS / by
1.1.5 Protocol Compliance 10
Sunil Gupta.
Description: Boca Raton, FL : Taylor & Francis, [2020] | Includes bibliographical references and
1.1.6 Codelist Dictionary Compliance 10
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 1.2 WHEN TO APPLY CHECKS 12
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 1.2.1 Database Acceptance and Lock 12
monitor these and more complex data and CDISC compliance issues. With increased
standardization in SDTM and ADaM specifications and data values, codelist dictionaries can 1.2.2 SDTMs and ADaMs Refresh 12
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 1.2.3 Snapshot Analysis 12
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 1.3 CUSTOMIZED CHECKS FOR EACH CLIENT 13
saves time from doing it manually”-- Provided by publisher.
Identifiers: LCCN 2019023651 (print) | LCCN 2019023652 (ebook) | ISBN 9780367362775 1.3.1 Site Management 13
(paperback) | ISBN 9780367362782 (hardback) | ISBN 9780429345043 (ebook)
1.3.2 Data Management 13
Subjects: LCSH: SAS (Computer file) | Medical care--Standards--United
States. | Medical care--United States--Quality control.
1.3.3 SAS Programmers 14
Classification: LCC QA276.45.S27 G87 2020 (print) | LCC QA276.45.S27
(ebook) | DDC 005.5/5--dc23
1.3.4 Statisticians 14
LC record available at https://lccn.loc.gov/2019023651
LC ebook record available at https://lccn.loc.gov/2019023652 SUMMARY 14
Visit the Taylor & Francis Web site at
http://www.taylorandfrancis.com v
and the CRC Press Web site at
http://www.crcpress.com
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
Clinical 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
