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!
Xiaoyan