Conversion of Company Standard Trial Data to SDTMcdiscportal.digitalinfuzion.com/CDISC User...

Conversion of Company Standard Trial Data to SDTM

CDISC Italian-Speaking User Group MeetingMilan, Italy

March 6, 2009

Jennifer Lin, Niki MolnarNovartis Vaccines

Agenda

• Our Clinical Data Management Environment

• Major Transformation Decisions

• SDTM Conversion Tool

• Mapping of Non-Standard Data

• Validation

• Trial Metadata

• Resources Used

Novartis Vaccines division

• separate from Pharma and Diagnostics

• relatively small group (e.g., 17 statistical programmers)

• existed for many years as Chiron

Our Clinical Data Management (CDM) Environment

Vaccines studies are characterized by:

• relatively small number of data domains

• similar data collection profiles from study to study


Our Clinical Data Management (CDM) Environment: Data Flow

Inform or Clintrial

DatabaseTFLs

NVS Datasets

In our favor:

• strong standard developed over 10 years (NVS) • only approximately 12 panels to convert• not too much non-standard per study• most of the decision-makers located at the same site


Challenges:• few people • lean budget • lots of applications relying on NVS format • too many other urgent priorities

= changing a wheel on a moving express train!


1. Focus on generic transformation tool first

• can produce SDTM datasets without requiring change to any other applications

• can transform legacy data for eventual data warehouse

Major Transformation Decisions

2. Use in-house SAS programmer

• develop in-house CDISC expertise• application can be completely customized to our needs• skilled SAS programmer had time • budget was lean

Major Transformation Decisions

Major Transformation Decisions: Data Flow

Inform or Clintrial

Database

SDTM Datasets TFLsNVS

Datasets

Major Transformation Decisions: Data Flow

Inform or Clintrial

Database

SDTM Datasets TFLsNVS

Datasets

SDTM Conversion Tool


• Web application

• Converts 12 NVS panels into 17 CDISC domainsADVERSE CMED COMMENTS DEATH DEMOG IMMUN LABSEDT MEDHX POSTINJ PREGRPT PREGFU STUDYTER

AE, SUPPAECM, SUPPCMCODS, SUPPDSDM, SUPPDM, DS, SCEX, SUPPEXLB, SUPPLBMH, SUPPMHAE, SUPPAE, VSSUPPDMSUPPDMDS, SUPPDS

SDTM Conversion Tool: Prerequisites

• Input datasets must be located in development study folder (i.e., “\DEVEL\SSD” in the folder path)


Leverages the fact that every study has a standard folder structure in Windows:

E:\PROJNAME\STUDYNAME\PURPOSE\VALIDATION_LEVEL\FILETYPE

PURPOSE: e.g., 03MAY09_Analysis

VALIDATION_LEVEL: DEVEL, QA, PROD

FILETYPE: e.g., SSD, SAS, SDTM

SDTM Conversion Tool: User Input

SDTM Conversion Tool: Output

#1. DEVEL\SDTM output


#2. SAS code for generating SDTM in DEVEL\SAS





#3. Metadata Listing




#3. Metadata Listing

#4. Discrepancy Listing

#2. SAS code for generating SDTM in DEVEL\SAS#3. Metadata Listing


#1. DEVEL\SDTM Output




#2. SAS code for generating SDTM in DEVEL\SAS#3. Metadata listing





#3. Metadata listing






• Run cdisc_run_all_sdtm.sas after promotion to generate all sdtm datasets in PROD\SDTM

• Promote all programs to PROD after validation



A listing of the standard mappings conducted by the SDTM Conversion Tool.






A listing of the discrepancies, i.e., the non-standard panels or variables that could not be mapped by the SDTM Transformation Tool.




SDTM Conversion Tool: Process

• Mapping of non-standard data


• Validation

• Trial Design Data (e.g., number of visits, phase, milestones)

Not handled by the SDTM Conversion Tool:

Ø Specs to be written by the Statistical Programmer, and signed off by the Study Statistician

Ø Identified by discrepancy listing

Mapping of Non-Standard Data

Ø Write the code! Ø New panel: cdisc_mk_sdtm_surghx.sasØ Preproc: cdisc_preproc_demog.sasØ Postproc:cdisc_postproc_demog.sas

• Validate all SDTM Datasets against NVS datasets

Validation

• Budget extra validation time

• OQ / Peer Review

Trial Design Data

• Plan to automate this

• Part of SDTM submission

• Trial Specific Data, e.g., protocol title, trial phase, trial blinding schema

• Initially to be manually collected

• Programmed using SAS 9.1 Windows and SAS/INTRNET

• Specifications completed in 3 mos. with 4 people meeting 2x per week for 1 hour

• Programming completed by 1 programmer in 1 year working in between many other projects

• Validation has not started

SDTM Conversion Tool Resources

Questions?

Conversion of Company Standard Trial Data to SDTMcdiscportal.digitalinfuzion.com/CDISC User...

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