Genomic Data in the CDM

CDM Builders
88

Got it. Just want to make sure you are not confused:

  1. The G-CDM is a model proposed by the original Genomics WG. It is an Open World model, meaning, it doesn’t use pre-specified OMOP Vocabulary Concepts, but introduced new tables and fields. It is more similar to a generic NGS pipeline representation.

  2. The Oncology WG created a Closed World (hence OMOP CDM type) model, using predefined Genetic Variant concepts, but no new structure. Those concepts live in the MEASUREMENT table. Those Concepts define somatic mutations found in cancers.

  3. If you want to use predefined Genetic variants for germ line mutations in syndromic conditions or pharmacogenetics we don’t have that today.

Makes sense?

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