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Genomic CDM

We are in the process of transforming our genomics data into G-CDM V2.0, and wondering how the current G-CDM schema store the following data elements:

  • zygosity → I(sample values: HET or HOM), should it go for the “variant_annotation” table?
  • aatype → indicates pathogenicity, which should go in variant_annotation (sample values: VLP = very likely pathogenic, PAT = pathogenic, VUS = variant of unknown significance, etc.)?
  • refseq → variant_occurrence.reference_sequence (sample value: NM_000091.4)
    chrpos → chrmosome position (sample value: 2:228176554)
  • exon → (indicates whether exonic or intronic mutation; sample value: exonic, intronic), which table we could store the data elements

Also, should we just have a generic “Genetic Test Occurrence” procedure concept? Or should we have one for each Genomic Test? it Looks like [OHDSI implementation] recommends using [46257601]-(Genomic Sequencing Procedures and Other Molecular Multianalyte Assays), and procedure_type_concept_id: Follow OHDSI implementation recommendation ([here] Lab (32856)

It will be great if we have could get you vice on this. thanks the community for the wonderful work in the area!