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CDISC Pharmacogenomics Standards

CDISC Pharmacogenomics Standards. Joyce Hernandez (Joyce Hernandez Consulting, LLC). Agenda. Project background Domains, Relationships & Molecular Concepts Variables Specimen Genealogy Specimen Hierarchy Pharmacogenomics (PGx) Examples: Biospecimen events and findings

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CDISC Pharmacogenomics Standards

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  1. CDISC Pharmacogenomics Standards Joyce Hernandez (Joyce Hernandez Consulting, LLC)

  2. Agenda • Project background • Domains, Relationships & Molecular Concepts • Variables • Specimen Genealogy • Specimen Hierarchy • Pharmacogenomics (PGx) Examples: • Biospecimen events and findings • Genetic Variation • Gene Expression • Next steps and team

  3. Background • Initial Data Focus for Version 1.0 • Specimen Collection and Handling • Specimen Hierarchy • Genetic Variation utilizing well-known standards (HGVS) • Genotyping data (common formats currently used) • Viral Genetics (includes some viral classification variables) • Special sections to enhance understanding • Glossary of genetic and genomic terms • Nomenclatures (HGVS, HLA) • CMAPS to document common processes

  4. New Domains to support PGx

  5. DomainRelationshipswithin a STUDYID

  6. 1 Molecular concepts represented in the domains 2 3 4 4c 5 4a 4b

  7. PGx Specific Variables - Specimen RELSPEC

  8. List of IG Use Cases • BE/BS – BiospecimenDomains • Specimen handling such as freeze/thaw cycles and transportation. • Steps in obtaining cell-free RNA from blood plasma. • Types of quality evaluation. • RELSPEC – Related Specimens • Specimen genealogy and hierarchy. • PF – Pharmacogenomics Findings • Protein variation in viral genetics. • Protein and nucleic variation in viral genetics. • Frame shifts, both viral and subject. • Nucleotide reads. • Zygosity. • Single-nucleotide polymorphisms (SNP) reads. • HLA allelic records • Observed somatic vs. gremlins variations. • Observed levels of somatic variations in a biopsy sample. • Gene expression measured via qRT-PCR. • Gene expression measured via microarray. • PG – PGx Methods and Supporting Information • Run parameters for PCR. • Details of SNP probe assays. • PB/SB – PGx Marker Domains • Simple and complex genetic markers for drug resistance. • Relating PGx Domains • A somatic variation and its related medical diagnosis. • Germline variations and related inherited risk of cancer. • Genetic variations relating to drug metabolism.

  9. Specimen Genealogy RELSPEC

  10. Biospecimen Events and Findings

  11. Variables – (Pathogens) *** SDTMIG omits --SPCIES because all subjects in most human clinical trials must be homo sapiens; the nature of the study obviates the need for this information to be included in SDTM datasets. The exception is Virology when a viral species must be identified.

  12. Variables – (Genetics/Genomics Test related)

  13. Variables – (Genetics/Genomics Result related)

  14. Genetic Variation Example

  15. Gene Expression Example – Arrays

  16. Next Steps • Currently under CDISC internal review • Public Review Posting – 2nd Quarter • Final Posting – 3rd Quarter • Next Project – 4th Quarter - Cytogenetics

  17. Contact Information and Team Anyone that wishes to join the team please contact Joyce: Joyce.hernandez_0029@yahoo.com

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