HCLSIG/TranslationalMedicine/pharmacogenomics

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Overview

Pharmacogenomics aims to understand how genetic variation affects the drug response. One key aspect is that this variation leads to a reduced or augmented capacity to metabolize the drug which consequently leads to toxic accumulation or is so rapidly transformed and eliminated that it has no impact.

Biomarkers

Biomarkers include chromosomal abnormalities, haplotypes, gene copy numbers, gene variants, and changes in gene expression.

Drugs for which genetic testing is required, recommended, or mentioned

@FDA @pharmgkb

Examples

Pharmacogenomic-related Tests

  • list at PharmGKB
  • ADmark® Alzheimer's Evaluation Detects ApoE2, E3, E4 alleles using Restriction Fragment Length Polymorphism (RFLP)
  • Drug metabolizing enzyme tests e.g. Cytochrome P450 tests


Databases

Supporting Databases

  • SIDER

Phenotype projects

Formal representations


Coding Systems

  • ICD - (michel)
  • CDISC - Clinical Data Interchange Standard
  • SNOMED-CT - (bob)
    • SNOMED CT is probably the most important clinical coding system. The terms are all concepts, with loose meaning and little modeling. There is vocabulary for describing genetic and genomic data of various kinds, but there appears to be no formal constraint on how one would specify, e.g., a particular SNP.
    • Wikipedia has a good description of the semantics in SNOMED, including a brief example of post-coordinated terms. SNOMED logic is restricted to EL++. The 370,000 pre-coordinated codes are atomic, in that, unlike LOINC codes (below), there is no structure to the code itself.
    • SNOMED CT User Guide describes the nature of the few relations in SNOMED, in particular the 'isA' hierarchy and the 'interprets' relation.
    • Browsing resources include:
    • SNOMED CT has a hierarchy of 'isA' terms under 'Clinical finding':
   Clinical finding
       Evaluation finding
           Genetic finding
               Gene expression
               Genetic polymorphism
               Molecular sequence data
               and a host of other genetic terms for states, processes, abnormalities, etc.
    • Browsing the NCI Metathesaurus, 'Gene expression' has no children. 'Genetic polymorphism' has just one child, a specific polymorphism. There is no actual code for a SNP there.
    • Under 'Molecular sequence data' there is a list of possible sequences types, including:
   Abnormal amino acid sequence
   Abnormal carbohydrate sequence...
   Abnormal nucleotide base sequence...
   Base sequence...
   Nucleotide base deletion
   Nucleotide base sequence...
   Transcriptional RNA splicing
    • Terms like 'Gene expression' and 'Abnormal nucleotide base sequence' bear an 'interprets' relation to 'Genetic test (procedure)'. Note that there are no special codes for concepts like 'abnormal' or 'missing', etc., that can be post-coordinated with other concepts. 'Nucleotide base sequence' appears as a sibling with its 'abnormal' version.


-> bosse astrazeneca -> lodd offering (elgar)


EHRs and support for reporting genetic results

  • I2B2

Further reading

  • Description of dbSNP in the NCBI handbook
  • Information from/about the HGVS nomenclature for the description of sequence variants
    • Contains interesting insight into nomenclature, such as "In some disciplines the term "mutation" is used to indicate "a change" while in other disciplines it is used to indicate "a disease-causing change". Similarly, the term "polymorphism" is used both to indicate "a non disease-causing change" or "a change found at a frequency of 1% or higher in the population". To prevent this confusion we do not use the terms mutation and polymorphism (including SNP or Single Nucleotide Polymorphism) but use neutral terms like "sequence variant", "alteration" and "allelic variant"."