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Pharmacogenomics Update RCRIM TC Philip M. Pochon Covance Enterprise Architecture. History. HL7 Models Single Gene (Genetic Locus) common message element Draft Standard for Trial Use – May 2005 (Revised May 2006) Multiple Gene (Genetic Loci) model common message element

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slide1
Pharmacogenomics Update

RCRIM TC

Philip M. Pochon

Covance Enterprise Architecture

history
History
  • HL7 Models
    • Single Gene (Genetic Locus) common message element
      • Draft Standard for Trial Use – May 2005 (Revised May 2006)
    • Multiple Gene (Genetic Loci) model common message element
      • Draft Standard for Trial Use – Jan 2007
    • Pharmacogenomics Clinical Research Message
      • Extension of the CDISC/HL7 LAB message
      • Draft Standard for Trial Use – May 2006
    • Clinical Genomics Clinical Practice Message
      • Piloted in pre-ballot form, June 2006
  • CDISC SDTM
    • Pharmacogenomics domains
      • Under development
genetic locus cmet structure
Genetic Locus CMET Structure

Expression

Data

The Genotype

and its Alleles

Sequence

Data

Significant

Variations

Clinical

Phenotypes

sdtm domain assumptions
SDTM Domain Assumptions
  • CDISC PG Domain Content
    • Specimen Data
    • Specimen Preparation Results
    • Testing Methods
    • Mainly Derived from RCRIM/CTLAB
  • CDISC PR Domain
    • Genetic Results
    • Interpretation of Results
    • Links to Scientific databases
    • Mainly Derived from CG CMETs
ctlabr2 changes needed
CTLABR2 Changes Needed
  • Inclusion of new genetic LOCI CMET to handle multiple gene tests
fda use issues
FDA Use Issues
  • Need to Handle Animal and Human Genetic Data
    • SDTM domains can easily be converted to CDISC SEND domains
    • No format/message available for the animal observation data
  • FDA Pilot to include National Center for Toxicology Research (NCTR), which has used Array Track with animal data
current state
Current State
  • SDTM and HL7 message work well with SNP Probe, Sequence, Electrophoresis and PCR methods (Classic Genetic Method)
  • Some model fitting work with Gene Expression Array data
    • Need to continue/expand this work
next steps
Next Steps
  • Vocabulary development
    • At least for Genetic Methodologies
  • Implementation Guide for pilot participants
    • CMET guide updated in draft model
    • CTLAB Release 1 guide available to be updated
  • End-to-end pilot projects
    • Use of
      • HL7 Pharmacogenomics Message
      • CDISC SDTM Pharmacogenomics Domains
      • Pre-Clinical data with CDISC SEND?
time lines for 2007
Time Lines for 2007
  • Q1
    • Complete Gene Expression Array Work
    • Informal Vocabularies Completed
    • HL7 XML to SDTM mapping completed
  • Q2-Q3
    • Complete Implementation Guide
    • Execute pilot projects (4+)
      • Submission and Lab to Sponsor
  • Q4
    • Lessons Learned and Recommendations
contact information
Contact Information

Philip M. Pochon

Covance CLS

8211 SciCor Drive

Indianapolis, IN 46214

phil.pochon@covance.com