Conversion of Company Standard Trial Data to SDTM CDISC Italian-Speaking User Group Meeting Milan, Italy March 6, 2009 Jennifer Lin, Niki Molnar Novartis Vaccines
Agenda Our Clinical Data Management Environment Major Transformation Decisions SDTM Conversion Tool Mapping of Non-Standard Data Validation Trial Metadata Resources Used
Our Clinical Data Management (CDM) Environment 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 Database NVS Datasets TFLs
Our Clinical Data Management (CDM) Environment 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
Our Clinical Data Management (CDM) Environment 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!
Major Transformation Decisions 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: Data Flow Inform or Clintrial Database NVS Datasets SDTM Datasets TFLs
Major Transformation Decisions: Data Flow Inform or Clintrial Database NVS Datasets SDTM Datasets TFLs SDTM Conversion Tool
SDTM Conversion Tool Web application Converts 12 NVS panels into 17 CDISC domains ADVERSE CMED COMMENTS DEATH DEMOG IMMUN LABSEDT MEDHX POSTINJ PREGRPT PREGFU STUDYTER AE, SUPPAE CM, SUPPCM CO DS, SUPPDS DM, SUPPDM, DS, SC EX, SUPPEX LB, SUPPLB MH, SUPPMH AE, SUPPAE, VS SUPPDM SUPPDM DS, SUPPDS
SDTM Conversion Tool: Prerequisites Input datasets must be located in development study folder (i.e., \DEVEL\SSD in the folder path)
SDTM Conversion Tool Leverages the fact that every study has a standard folder structure in Windows: E:\PROJNAME\STUDYNAME\PURPOSE\VALIDATION_LE VEL\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: User Input
SDTM Conversion Tool: User Input
SDTM Conversion Tool: User Input
SDTM Conversion Tool: Output #1. DEVEL\SDTM output
SDTM Conversion Tool: Output #1. DEVEL\SDTM output #2. SAS code for generating SDTM in DEVEL\SAS
SDTM Conversion Tool: Output #1. DEVEL\SDTM output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata Listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata Listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing Promote all programs to PROD after validation Run cdisc_run_all_sdtm.sas after promotion to generate all sdtm datasets in PROD\SDTM
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing A listing of the standard mappings conducted by the SDTM Conversion Tool.
SDTM Conversion Tool: Output
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing
SDTM Conversion Tool: Output #1. DEVEL\SDTM Output #2. SAS code for generating SDTM in DEVEL\SAS #3. Metadata listing #4. Discrepancy Listing 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: Output
SDTM Conversion Tool: Output
SDTM Conversion Tool: Output
SDTM Conversion Tool: Process
SDTM Conversion Tool Not handled by the SDTM Conversion Tool: Mapping of non-standard data Validation Trial Design Data (e.g., number of visits, phase, milestones)
Mapping of Non-Standard Data Identified by discrepancy listing Specs to be written by the Statistical Programmer, and signed off by the Study Statistician Write the code! New panel: cdisc_mk_sdtm_surghx.sas Preproc: cdisc_preproc_demog.sas Postproc:cdisc_postproc_demog.sas
Validation Validate all SDTM Datasets against NVS datasets OQ / Peer Review Budget extra validation time
Trial Design Data Part of SDTM submission Trial Specific Data, e.g., protocol title, trial phase, trial blinding schema Initially to be manually collected Plan to automate this
SDTM Conversion Tool Resources 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
Questions?