THEME DATA SHARING
WP CDISC
Presented by Mary Thiongo & Harry van Loen 4th ADMIT workshop, ITM Belgium, 30 NOV-4 DEC 2015
1
1 THEME DATA SHARING WP CDISC Presented by Mary Thiongo & - - PowerPoint PPT Presentation
1 THEME DATA SHARING WP CDISC Presented by Mary Thiongo & Harry van Loen 4th ADMIT workshop, ITM Belgium, 30 NOV-4 DEC 2015 Contents 2 CDISC Introduction SDTM 1. Introduction 2. Background 3. Objective 4. SDTM
Presented by Mary Thiongo & Harry van Loen 4th ADMIT workshop, ITM Belgium, 30 NOV-4 DEC 2015
1
Introduction
1. Introduction 2. Background 3. Objective 4. SDTM concept
2
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
1. Introduction 2. Value of CDASH 3. CDASH Model 4. CDASH Metadata Tables 5. CDASH Implementation
3
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
CDISC
Clinical Data Interchange Standards Consortium Introductional VIDEO WEBSITE: http://www.cdisc.org
4
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Study Data Tabulation Model : organize data
improve regulatory review and approval
5
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
6
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
1999 2001 2002 2004 Submission Data Model (SDM) focus only ‘safety’ Submission Data Domain Model Study Data submission Model v1.0 (SDTM) focus ‘all study’ 2015 SDTM v 1.4 FDA recognizes SDTM
7
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Data submission SDTM datasets
and
SDTM metadata
4.1 SDTM documentation:
8
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Study Tabulation Data Model SDTM Implementation Guide Controlled Terminology Case Report Tabulation Data Definition Specification (‘define.’)
SDTM dataset(s) SDTM metadata
4.2 SDTM basics :
correspond to column in dataset
9
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
10
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Example data set (AE):
Domain: Adverse Events (AE) Variables Observation (s)
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
11
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS EVENTS CLASS
Adverse Events AE Medical History MH Demo graphics DM
FINDINGS CLASS
Vital Signs VS Phyical Exam PE Con Med CM Substance use SU
GENERAL OBSERVATION CLASSES SPECIAL PURPOSE DOMAINS
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- - Subject Visits SV
two character domain code: AE, DM…
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
12
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS EVENTS CLASS
Adverse Events AE Medical History MH Demo graphics DM
FINDINGS CLASS
Vital Signs VS Phyical Exam PE Con Med CM Substance use SU
GENERAL OBSERVATION CLASSES SPECIAL PURPOSE DOMAINS
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- - Subject Visits SV
two character domain code: AE, DM…
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
13
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS
Con Med CM Substance use SU
two character domain code: AE, DM…
study
affecting efficay & safety
investigational products Following domains/SDTM datasets:
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
14
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS EVENTS CLASS
Adverse Events AE Medical History MH Demo graphics DM
FINDINGS CLASS
Vital Signs VS Phyical Exam PE Con Med CM Substance use SU
GENERAL OBSERVATION CLASSES SPECIAL PURPOSE DOMAINS
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- - Subject Visits SV
two character domain code: AE, DM…
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
15
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
two character domain code: AE, DM…
completion status & reason discontinuation
EVENTS CLASS
Adverse Events AE Medical History MH
classified as AEs e.g. efficacy endpoints like malaria in study
Following domains/SDTM datasets:
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
16
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS EVENTS CLASS
Adverse Events AE Medical History MH Demo graphics DM
FINDINGS CLASS
Vital Signs VS Phyical Exam PE Con Med CM Substance use SU
GENERAL OBSERVATION CLASSES SPECIAL PURPOSE DOMAINS
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- - Subject Visits SV
two character domain code: AE, DM…
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
17
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
two character domain code: AE, DM…
not met
LAB or CRO)
FINDINGS CLASS
Vital Signs VS Phyical Exam PE
Following domains/SDTM datasets:
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
(cont.)
18
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
two character domain code: AE, DM…
Pulse,Body temperature & BMI
receipt, dispensing, return, packaging
data, growth status
FINDINGS CLASS
Vital Signs VS Phyical Exam PE
Following domains/SDTM datasets:
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
(cont.)
19
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
two character domain code: AE, DM…
(serum, blood) – concentrations of study drug & metabolites
time~concentration curve
FINDINGS CLASS
Vital Signs VS Phyical Exam PE
Following domains/SDTM datasets:
Interventions not represented within Events/Interventions (e.g. AE severity changing over time)
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
20
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS EVENTS CLASS
Adverse Events AE Medical History MH Demo graphics DM
FINDINGS CLASS
Vital Signs VS Phyical Exam PE Con Med CM Substance use SU
GENERAL OBSERVATION CLASSES SPECIAL PURPOSE DOMAINS
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- - Subject Visits SV
two character domain code: AE, DM…
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
21
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
two character domain code: AE, DM…
& values of ARM (study treatment)
CRF comments pages
elements (screening, randomization, Follow up...)
Following domains/SDTM datasets:
Demo graphics DM
SPECIAL PURPOSE DOMAINS
Subject Visits SV
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
22
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS EVENTS CLASS
Adverse Events AE Medical History MH Demo graphics DM
FINDINGS CLASS
Vital Signs VS Phyical Exam PE Con Med CM Substance use SU
GENERAL OBSERVATION CLASSES SPECIAL PURPOSE DOMAINS
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- - Subject Visits SV
two character domain code: AE, DM…
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
23
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
two character domain code: AE, DM…
(screening, randomization, Follow up...)
criteria for the trial Following domains/SDTM datasets:
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV
phase, protocol title, design objectives
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
24
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015 INTER VENTIONS CLASS EVENTS CLASS
Adverse Events AE Medical History MH Demo graphics DM
FINDINGS CLASS
Vital Signs VS Phyical Exam PE Con Med CM Substance use SU
GENERAL OBSERVATION CLASSES SPECIAL PURPOSE DOMAINS
Trial Summary TS
TRIAL DESIGN DOMAINS
Trial Visits TV Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- - Subject Visits SV
two character domain code: AE, DM…
4.2.1 Domains & Classes listed in SDTM IG doc v3.1.2 p. 13
25
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
two character domain code: AE, DM…
between datasets
standard data from the other domains Following domains/SDTM datasets:
Related Records RELREC
RELATIONSHIP
Supplemental qualifierss SUPP- -
26
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
4.2.2 Variable(s) listed in SDTM doc v1.4 p. 9-35
Variable(s)
3 core categories:
presence can be null Required: always no
Expected:
always yes Permissible: if collected yes 27
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Identifier
Topic Qualifier Timing
To identify the
To specify the focus e.g.
To specify results
To specify the timing e.g.
eg.
(Note: 5th variable ‘Rule’ referring to algoritm/method to define start/end and looping conditions, only in Trial Design model)
28
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Example data set (AE):
Identifiers Topic Qualifier
Variable
29
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Variable(s) list metadata per domain
(1)Variable (2)Label (3)Type (4)Contro lled terms/ (5)Origin (6)Role (7)Comment STUDYID Study identifier Char CRF page Identifier DOMAIN Domain Abbreviat ion (=AE) Char AE CRF page Identifier USUBJID Unique Subject number Char CRF page Identifier AESEQ Sequence number Num Derived Identifier AETERM Reported term f or AE Char CRF page Topic AEDECOD Char Derived Qualifier (1) Field name (code) (2) Description variable (3)Variable type (4)Controlled teminology if applicable (5)Origin (6)Which role in dataset: identifier, topic, timing , qualifier (7)Comment: other relevant information
4. 2.3 Some rules/assumptions
USUBJID, --SEQ)
30
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
4. 2.3 Some rules/assumptions (cont.)
e.g. - -TRT AETRT; MHTRT
31
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Clinical Data Acquisition Standards Harmonization (CDASH)
agnostic
32
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
33
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
34
Streamline the processes
You don’t reinvent the wheel every time when
conducting a study:
reuse of CRFs, edit checks and output programs Reuse of analysis programs i.e. do files.
Makes data more usable
Data aggregation Data mining Data usability
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
35
Sharing research data with your research partners
Integrates the SDTM requirements into CRF Provides traceability and more transparency to
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
36
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
ID GENDER A1 Male A2 Male A3 Female A4 Female A5 Male SUBJID SEX 0001 M 0002 F 0003 F 0004 M 0005 F USUBID SEX 00011 00012 1 00013 1 00014 00015 1 PTID GENDER 0001 1 0002 1 0003 2 0004 2 0005 1
Study #2 – dmg.xpt Study #3 – axd222.xpt Study #4 – dmgph.xpt
Name for Subject ID is never the same Name for demography dataset is variable??? Is Sex Male or Female, M or F, 1 or 2? Gender or Sex, what will this study use? Adapted from slide courtesy of Armando Oliva, M.D. and Amy Malla, FDA
Study #1 – demo.xpt
38
data monitoring at the sites.
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
39 Harmonize process across standards
Ensure Harmonization with other CDISC standards Uses an SDTM concept (domain variable) if available and possible. When data collected can be placed directly into SDTM variable Standardize a CDASH variable if there is not an appropriate SDTM one CDASH variable is used that can map to SDTM
Use existing controlled terminology
That supports:
3.0 CDASH Model
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
40
CDASH standards are presented in metadata tables
4.0 . CDASH Metadata Tables
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
Full question text for the data collection field. Short prompt for the data collection field; could be used as the CRF label SDTMIG Variable Name OR CDASH Variable Name BRIDG Mapping Defines the purpose of Data collection field Contains standard Instructions for the clinical site
enter data
Includes controlled terminolog y Information/ratio nale and instructions on how to implement the CRF data collection fields Contains CDASH core designations for basic data collection fields
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
42
Following :
Highly recommended(H R), Recommended/co nditional (R/C) Optional(O)
Using Question test or prompt
Using controlled
terminology Following Best practice recommendation in the specifications
Conformance to CDASH
4.1 . Conformance
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
43
4.2 . Domain Names
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
44
Creating new variables Creating new domain
Custom domains are created when they are no published
domains
The rules for creating custom domains are described in
STDMIG
5.0. CDASH Implementation
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
45
Created to address the specific needs of data collection and
management.
Not possible to collect data using same data type, controlled
terminology or format with SDTM.
More than one variable is needed for data collection & data
management, but will be mapped into a single SDTM variable.
When a single variable can map into more than one place in
SDTM.
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
46
Process of creating new variables
SDTM and not in CDASH
variable naming fragments to create with similar conventions
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
47
Using the SDTMIG V 3.1 or higher & CDASH
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
48
Confirm there is no published domain
Determine the one General Observation class for your custom domain
Create an appropriate 2 character domain code
from: class, common identifier and timing fields
Create the variables Create a standard mapping into SDTM from your output
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
49
Using the SDTMIG V 3.1 or higher as a
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
50
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015
51
Http://www.cdisc.org/standard/cdash/downloads/
CDISC SDTM Implementation Guide version 3.2,
Mary Thiongo & Harry van Loen, 4th ADMIT Workshop, ITM BELGIUM, 30 NOV-4DEC2015