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2009 Annual Conference
New Orleans, LA

           Considerations for an SDTM
           Compliant Study Definition
                      Steven Rifkin
               Sr. Director of Consulting
                   BioPharm Systems
Topics

•   History of the SDTM
•   Horizontal Collection vs. Vertical Reporting
•   Variable Names
•   Date Formats




                  Oracle Clinical and the SDTM
CDISC Organization

• Clinical Data Interchange Standards
  Consortium
    –   CDISC started in 1999
    –   Is a non-profit organization
    –   Data models are created by industry volunteers
    –   Mission: to develop & support global, platform-
        independent data standards that enable
        information system interoperability to improve
        medical research & related areas of healthcare
http://www.cdisc.org




                       Oracle Clinical and the SDTM
CDISC Models

     Acronym                    Title                         Use
                                Clinical Data Acquisition     Data
B    CDASH
                                Standards Harmonization       Collection
R
                                Study Data Tabulation Model   Content
 I   SDTM
D
                                Analysis Dataset Model        Content
G    ADaM
 /                              Case Report Tabulation Data   Metadata
H    Define.xml
     CRT-DDS                    Definition Specification
L
7*   ODM                        Operational Data Model        Format
     LAB                        Clinical Laboratory Model     Content

     PRG*                       Protocol Representation       Content
        * under development     Group


                              Oracle Clinical and the SDTM
SDTM

• Study Data Tabulation Model
• Goal:
    – Define a global standard for study data
      tabulations
    – Standardize regulatory submissions
    – Currently, de facto standard between the CROs
      and sponsors
• Focus on study data tabulation content
• Requested by FDA for all submissions
http://www.cdisc.org/models/sds/v3.1/index.html




                                      Oracle Clinical and the SDTM
SDTM IG 3.1.2




 http://www.cdisc.org/standards/index.html




                                 Oracle Clinical and the SDTM
SDTM Model History

• 2001: Submission Data Domain Models Version 1.0
• 2002: Submission Data Domain Models Version 2.0
   – Well received by industry
   – Major shortcomings (focus on safety domains only)
• 2003: Submission Data Domain Models Version 3.0
   – Standard for all clinical trial data
   – Based on data modeling (e.g. events, interventions and findings)
• 2004: SDTM 1.0 - SDTM IG 3.1
   – First version intended for implementation
• 2005: SDTM 1.1 - SDTM IG 3.1.1
   – Enhancements resulting from FDA/industry pilot testing
• 2009: SDTM 1.2 - SDTM IG 3.1.2
   – Major enhancements, expanded model




                        Oracle Clinical and the SDTM
Horizontal Collection vs
Vertical Reporting
• SDTM Domains are modeled (and reported)
  in a vertical manner
  – In many cases, this structure can be easily
    modeled using OC Repeating Question groups
     • CM, AE and PE domains are examples
  – In other cases, this vertical reporting structure
    leads to difficulties if OC repeating Question
    groups are used
     • VS Domain is an example to be discussed here




                    Oracle Clinical and the SDTM
VS Domain in the SDTM

  USUBJID VSTESTCD           VSPOS          VSORRES   VSORRESU
    100      SYSBP           STANDING           120    mmHg
    100      DIASBP          STANDING            80    mmHg
    100      PULSE                               55    BEATS/MIN
    100      HEIGHT                             210    LB
    100      WEIGHT                              69    IN


• Simplified VS Domain Structure
• Indicates individual records for each VS finding
  even though two findings may be related




                      Oracle Clinical and the SDTM
Modeling the VS Domain in OC

• Could create a “vertical” structure in OC
   – Questions for VSTESTCD, VSPOS, VSORRES etc
   – Put these questions in a Question Group
   – Make the Question Group repeat
      • Supply repeating defaults
• Similar to LPARM, LVALUE model for normalized lab
  data
• Default extract view mimics the way the SDTM
  reports

                 So what’s the problem?


                       Oracle Clinical and the SDTM
Vertical OC as Model for SDTM
VS Domain: Difficulties
• Awkward Data Entry
   – Physicians used to entering 120/80 as one measurement
     not two
      • Can be somewhat minimized in RDC Graphic Data Entry and
        training DE for Paper Studies
• Limit utility of OC Univariate Discrepancies
   – The univariate checks can not vary with each repeat – e.g.
     different high/low limits for sysbp and diasbp
      • May be able to write a complex multivariate to accomplish
        this however
• Validation checks between repeats are more
  difficult to create


                       Oracle Clinical and the SDTM
Solutions

• Model Horizontal and reformat in extract
  view definitions
• Model Horizontal and post-process in SAS
• Create a Collection QG (horizontal) and a
  Reporting QG (vertical) for the vital signs
  – Entry into the Collection QG all normal univariate
    checks and “easy” multivariate
  – Use a derivation routine to derive data from the
    collection QG to the reporting QG
  – Place both in a single DCM

                  Oracle Clinical and the SDTM
Two Question Groups for Vital Signs

• Horizontal
  – Typical non-repeating QG with Normal OC
    functionality and layouts
• Vertical
  – Create a repeating question group with the
    SDTM questions like VSTESTCD, VSORRES, etc.
  – Use protected repeating defaults for VSTESTCD
    and VSTEST (cannot make these fields not
    displayed)
  – Make other questions in this question group
    “non-displayed”


                 Oracle Clinical and the SDTM
Collection to Reporting Derivation
Procedure
• Could create a procedure for a standard VS
  domain
  – Assumes the names of the fields in the collection
    DCM and the repeat number into which this field
    will be derived
• Could create a more general routine with a
  database package and assumptions
  – E.g. assumptions like collection question name
    will be the same as the TESTCD in the reporting
    QG, names of subsidiary questions in HELP text


                  Oracle Clinical and the SDTM
Extract Views for Two QG Solution

• Will get two default extract views
  – The non-repeating “collection” view can be
    dropped or ignored
  – The repeating “reporting” view can be used for
    the submission




                 Oracle Clinical and the SDTM
SAS Names …

• Many SDTM Variables have an 8 character length
• OC supports using 8 characters, but, usually, it is
  not recommended to use 8
   – Extended attributes could add one character at end and
     multiple occurrences of a question will add another
   – If name is 8 (or at eight because of additional extended
     attribute character) will not be able to create multiple
     occurrences
• SDTM uses multiple occurrences only in the CO
  Domain, so not usually a problem
• Extended Attributes could cause problems


                      Oracle Clinical and the SDTM
SAS Names …

• The Extended attributes are created when
  the Global Library Question is created.
  – If length of SAS Name is 8, the last character of
    the name is truncated and the extended
    attribute character is added to name the
    extended attribute
• Problems occur when the extended attribute
  character added is the same as the last
  character removed
• Problem doesn’t appear until the views are
  actually generated

                  Oracle Clinical and the SDTM
SAS Names:
Solutions
• Make sure the extended attributes are not
  part of the view definition
  – Usually not part of the SDTM submission
    anyway, although may be useful for analysis
• Change the name of the extended attribute
  in the view definition
  – Can run a SQL statement to indicate where there
    are duplicate column names and change just
    these names
• Change the Extended Attribute names in the
  GLib

                 Oracle Clinical and the SDTM
Date Formats …

• Oracle Clinical stores and reports dates in
  the YYYYMMDD format
  – Time is collected as separate variable in
    HHMMSS format (Military)
  – Partial dates and times are possible
• SDTM requires dates in the ISO 8601
  format YYYY-MM-DDThh:mm:ss and
  reported as __DTC variables in the domains
• Differences in how “missing significant” data
  is recorded
  – Unknown year is possible in SDTM but not in OC

                  Oracle Clinical and the SDTM
Date Formats: Solution

• Use a database package to convert from 2
  OC fields to a single __DTC field for the
  SDTM
• Package can include use of a third input
  AM/PM so that military time need not be
  used in OC




               Oracle Clinical and the SDTM
Some good things

• Copy Groups
  – Make its easy to create all Domain objects in a
    single group and copy “standard” to target study
• RDC
  – Might make some entry considerations for
    Horizontal vs Vertical easier to handle




                 Oracle Clinical and the SDTM
Summary

• SDTM and other CDISC Standards are
  evolving
• Modeling a completely compliant submission
  in OC can be problematic
• Workarounds exist for some of the common
  problems to reduce amount of post
  processing




               Oracle Clinical and the SDTM
Acknowledgements



     Prof. Dr. Jerry Welkenhuysen-Gybels
     jerry.welkenhuysen@businessdecision.com

     Nico De Leeuw
     nico.deleeuw@businessdecision.com




                Oracle Clinical and the SDTM
Contact Information

      Steve Rifkin
      Biopharm Systems
      908 822 0553
      srifkin@biopharm.com




               Oracle Clinical and the SDTM
?



Oracle Clinical and the SDTM
Steve Rifkin has almost 14 years of experience working with the
OLS Product Suite. As an Functional Consultant, and then as a
Practice Manager with Oracle Consulting in the Oracle Clinical
Group, Steve has assisted over 60 companies with implementation
of Oracle Clinical, RDC and TMS. He has led the implementation
process and has provided training and performed custom coding.
Since joining Biopharm Systems in 2000, Steve has been
responsible for developing Oracle Clinical training courses, and
providing training and implementation services for Biopharm
clients.




                      Oracle Clinical and the SDTM

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Considerations for an SDTM Compliant Study Definition

  • 1. 2009 Annual Conference New Orleans, LA Considerations for an SDTM Compliant Study Definition Steven Rifkin Sr. Director of Consulting BioPharm Systems
  • 2. Topics • History of the SDTM • Horizontal Collection vs. Vertical Reporting • Variable Names • Date Formats Oracle Clinical and the SDTM
  • 3. CDISC Organization • Clinical Data Interchange Standards Consortium – CDISC started in 1999 – Is a non-profit organization – Data models are created by industry volunteers – Mission: to develop & support global, platform- independent data standards that enable information system interoperability to improve medical research & related areas of healthcare http://www.cdisc.org Oracle Clinical and the SDTM
  • 4. CDISC Models Acronym Title Use Clinical Data Acquisition Data B CDASH Standards Harmonization Collection R Study Data Tabulation Model Content I SDTM D Analysis Dataset Model Content G ADaM / Case Report Tabulation Data Metadata H Define.xml CRT-DDS Definition Specification L 7* ODM Operational Data Model Format LAB Clinical Laboratory Model Content PRG* Protocol Representation Content * under development Group Oracle Clinical and the SDTM
  • 5. SDTM • Study Data Tabulation Model • Goal: – Define a global standard for study data tabulations – Standardize regulatory submissions – Currently, de facto standard between the CROs and sponsors • Focus on study data tabulation content • Requested by FDA for all submissions http://www.cdisc.org/models/sds/v3.1/index.html Oracle Clinical and the SDTM
  • 6. SDTM IG 3.1.2 http://www.cdisc.org/standards/index.html Oracle Clinical and the SDTM
  • 7. SDTM Model History • 2001: Submission Data Domain Models Version 1.0 • 2002: Submission Data Domain Models Version 2.0 – Well received by industry – Major shortcomings (focus on safety domains only) • 2003: Submission Data Domain Models Version 3.0 – Standard for all clinical trial data – Based on data modeling (e.g. events, interventions and findings) • 2004: SDTM 1.0 - SDTM IG 3.1 – First version intended for implementation • 2005: SDTM 1.1 - SDTM IG 3.1.1 – Enhancements resulting from FDA/industry pilot testing • 2009: SDTM 1.2 - SDTM IG 3.1.2 – Major enhancements, expanded model Oracle Clinical and the SDTM
  • 8. Horizontal Collection vs Vertical Reporting • SDTM Domains are modeled (and reported) in a vertical manner – In many cases, this structure can be easily modeled using OC Repeating Question groups • CM, AE and PE domains are examples – In other cases, this vertical reporting structure leads to difficulties if OC repeating Question groups are used • VS Domain is an example to be discussed here Oracle Clinical and the SDTM
  • 9. VS Domain in the SDTM USUBJID VSTESTCD VSPOS VSORRES VSORRESU 100 SYSBP STANDING 120 mmHg 100 DIASBP STANDING 80 mmHg 100 PULSE 55 BEATS/MIN 100 HEIGHT 210 LB 100 WEIGHT 69 IN • Simplified VS Domain Structure • Indicates individual records for each VS finding even though two findings may be related Oracle Clinical and the SDTM
  • 10. Modeling the VS Domain in OC • Could create a “vertical” structure in OC – Questions for VSTESTCD, VSPOS, VSORRES etc – Put these questions in a Question Group – Make the Question Group repeat • Supply repeating defaults • Similar to LPARM, LVALUE model for normalized lab data • Default extract view mimics the way the SDTM reports So what’s the problem? Oracle Clinical and the SDTM
  • 11. Vertical OC as Model for SDTM VS Domain: Difficulties • Awkward Data Entry – Physicians used to entering 120/80 as one measurement not two • Can be somewhat minimized in RDC Graphic Data Entry and training DE for Paper Studies • Limit utility of OC Univariate Discrepancies – The univariate checks can not vary with each repeat – e.g. different high/low limits for sysbp and diasbp • May be able to write a complex multivariate to accomplish this however • Validation checks between repeats are more difficult to create Oracle Clinical and the SDTM
  • 12. Solutions • Model Horizontal and reformat in extract view definitions • Model Horizontal and post-process in SAS • Create a Collection QG (horizontal) and a Reporting QG (vertical) for the vital signs – Entry into the Collection QG all normal univariate checks and “easy” multivariate – Use a derivation routine to derive data from the collection QG to the reporting QG – Place both in a single DCM Oracle Clinical and the SDTM
  • 13. Two Question Groups for Vital Signs • Horizontal – Typical non-repeating QG with Normal OC functionality and layouts • Vertical – Create a repeating question group with the SDTM questions like VSTESTCD, VSORRES, etc. – Use protected repeating defaults for VSTESTCD and VSTEST (cannot make these fields not displayed) – Make other questions in this question group “non-displayed” Oracle Clinical and the SDTM
  • 14. Collection to Reporting Derivation Procedure • Could create a procedure for a standard VS domain – Assumes the names of the fields in the collection DCM and the repeat number into which this field will be derived • Could create a more general routine with a database package and assumptions – E.g. assumptions like collection question name will be the same as the TESTCD in the reporting QG, names of subsidiary questions in HELP text Oracle Clinical and the SDTM
  • 15. Extract Views for Two QG Solution • Will get two default extract views – The non-repeating “collection” view can be dropped or ignored – The repeating “reporting” view can be used for the submission Oracle Clinical and the SDTM
  • 16. SAS Names … • Many SDTM Variables have an 8 character length • OC supports using 8 characters, but, usually, it is not recommended to use 8 – Extended attributes could add one character at end and multiple occurrences of a question will add another – If name is 8 (or at eight because of additional extended attribute character) will not be able to create multiple occurrences • SDTM uses multiple occurrences only in the CO Domain, so not usually a problem • Extended Attributes could cause problems Oracle Clinical and the SDTM
  • 17. SAS Names … • The Extended attributes are created when the Global Library Question is created. – If length of SAS Name is 8, the last character of the name is truncated and the extended attribute character is added to name the extended attribute • Problems occur when the extended attribute character added is the same as the last character removed • Problem doesn’t appear until the views are actually generated Oracle Clinical and the SDTM
  • 18. SAS Names: Solutions • Make sure the extended attributes are not part of the view definition – Usually not part of the SDTM submission anyway, although may be useful for analysis • Change the name of the extended attribute in the view definition – Can run a SQL statement to indicate where there are duplicate column names and change just these names • Change the Extended Attribute names in the GLib Oracle Clinical and the SDTM
  • 19. Date Formats … • Oracle Clinical stores and reports dates in the YYYYMMDD format – Time is collected as separate variable in HHMMSS format (Military) – Partial dates and times are possible • SDTM requires dates in the ISO 8601 format YYYY-MM-DDThh:mm:ss and reported as __DTC variables in the domains • Differences in how “missing significant” data is recorded – Unknown year is possible in SDTM but not in OC Oracle Clinical and the SDTM
  • 20. Date Formats: Solution • Use a database package to convert from 2 OC fields to a single __DTC field for the SDTM • Package can include use of a third input AM/PM so that military time need not be used in OC Oracle Clinical and the SDTM
  • 21. Some good things • Copy Groups – Make its easy to create all Domain objects in a single group and copy “standard” to target study • RDC – Might make some entry considerations for Horizontal vs Vertical easier to handle Oracle Clinical and the SDTM
  • 22. Summary • SDTM and other CDISC Standards are evolving • Modeling a completely compliant submission in OC can be problematic • Workarounds exist for some of the common problems to reduce amount of post processing Oracle Clinical and the SDTM
  • 23. Acknowledgements Prof. Dr. Jerry Welkenhuysen-Gybels jerry.welkenhuysen@businessdecision.com Nico De Leeuw nico.deleeuw@businessdecision.com Oracle Clinical and the SDTM
  • 24. Contact Information Steve Rifkin Biopharm Systems 908 822 0553 srifkin@biopharm.com Oracle Clinical and the SDTM
  • 26. Steve Rifkin has almost 14 years of experience working with the OLS Product Suite. As an Functional Consultant, and then as a Practice Manager with Oracle Consulting in the Oracle Clinical Group, Steve has assisted over 60 companies with implementation of Oracle Clinical, RDC and TMS. He has led the implementation process and has provided training and performed custom coding. Since joining Biopharm Systems in 2000, Steve has been responsible for developing Oracle Clinical training courses, and providing training and implementation services for Biopharm clients. Oracle Clinical and the SDTM