The purpose of this briefing note is to introduce a proposed structure for the representation of human gene names and their associated chromosomal locations in the context of body structures, specifically as subcellular structures. This shift from the current location of genes within SNOMED CT reflects the biological reality of genes as physical, organized, and functional units within chromosomes, aligns SNOMED CT with contemporary clinical practice, and future-proofs the terminology for the era of precision medicine.
It does not intend to replicate all of the genomic relationships that might be represented in a gene ontology such as the HUGO Gene Nomenclature Committee (HGNC), but only those necessary to associate clinically relevant genes with their representative chromosomes. This proposal provides non-normative examples of how gene names may be used in modeling other content (Appendix 1) such as Observable entities, Clinical findings, or Diseases.
This proposal also does not address the notion of a gene as an informational artifact (an alternative representation supported by organizations such as NCBI), but focuses on the structural relationship of a gene to its associated chromosome.
I am unable to access the previous Briefing Note from: Representation of Human Genes in SNOMED CT - Member Forum - SNOMED Forums. There were a number of comments made by Members to that Briefing Note (including responses from SNOMED International) which are not currently visible on the new platform. Having visibility of the previous BN and comments/responses will help us with our review.
Hi @paul.wright39 , thank you for pointing that out. The link on the related MF topic has now been updated and you will be able to get to the old discussion in Spaces.
Hi Jim, I forwarded the briefing note to DHD, the Dutch organisation that maintains thesauri (linked to SNOMED) for diagnoses and procedures for hospital registration. One of the medical specialities included is clinical genetics.
They think any negative impact on their thesauri would be small and they do see advantages for clinical genetics. They would like to be able to code the gene and the disorder separately, yet establish equivalency with the precoordinated concept.
Personally, I see the value of an attribute to link disorder with gene, but I have my reservations about the addition of all those genes as separate SNOMED concepts. I think scope creep is a highly likely consequence.
I would prefer to find a way to use HGNC without replicating its content in SNOMED. Do these genes have a hierarchy themselves? If not, could we treat them as datatype properties, with the HGNC name as its String value?
We have discussed alternatives to adding genes to SNOMED vs. developing a mechanism to link directly to HGNC. If I am understanding your suggestion correctly, the issue with adding the HGNC name as a data property (i.e. concrete string) is that it would require more work to maintain than adding the gene names as concepts in SNOMED. This is because gene names and symbols change over time and adding them as data properties would require updating all of the associated concepts that use the string as opposed to just updating the gene concept.
As for the scope expansion, our plan is to only add those genes necessary to define existing content (i.e. Disorders, Observables, etc.). There is already a recognized need for gene names in the LOINC and NPU extension work.
The other issue with using concrete values as string values is it eliminates the benefit of linking the genes to their resident chromosomes and any analytical benefits coming from that hierarchy.
Adding gene names based on modeling need seems to be tractable as we are not adding variants or any other element from HUGO.
Happy to discduss further.
The briefing ´note has been sent to the Head/Chair for Genomic Medicine Sweden, who then distributed it to all his academic and clinical associates who are experts in genetics. It was also sent to National Advisory Group for rare Diseases, the National Group for Diagnostic Medicine, the Swedish Society for Pathologists. Members in the pilot project for NPU also received the briefing note.
Comments and a concern was received from the National Advisory Group for Rare Diseases, where in their opinion, it sound logical and the argument put forth by SNOMED International is sound and well balanced. However, they, too, have concerns about concepts representing genomic /chromosomal aberrations, annotations, and the disease (disorder) that are associated with the aberrations, as earlier expressed by Feikje. They would like to know how SNOMED International intend to resolve the issue, more from a curious point of view. They are in favor if the HGNC ID be retained and be connected to the respective SNOMED concept, than to have the description (string) that is associated with the genetic concept as disease/disorder names changed over time.
The Regional National Quality Register for Cancer had other comments regarding representation of human genes in SNOMED CT.
The National Quality Registry for Cancer uses a national plattform called INCA (Information network for Cancer Care) where all data from cancer care plans are gathered for improving patient care and research purposes. They have a model that depicts the data being collected, for eg. Gene: BRAC1 (HGNC:1100), Changes: Mutation (the type of mutation is then specified separately) and the Status: Detected/Present.
They wondered if concepts such as 412734009 |BRCA1 gene mutation detected (finding)| are created that would mean a huge explosion of such concepts be created to represent all the finding related to all genetic associated disorders, and that would not be practical for maintenance. Their recommendation is that the modelling of such concepts be represented with distinct concepts separation Gene structure (the entity), Observable entity (the entity being observed or measured) and Clinical finding (results) to represent the mutation detected to improve granularity in documentation for precision medicine.
The committee for Genomic Medicine Sweden will have their strategic meeting on the 9th of Dec. They will discuss further their insights and questions amongst themselves pertaining to the briefing note and they will also respond if they should have a call with Jim Case.
The working group for the NPU pilot study, though we did not discuss the issue in depth, they was a mention by one of the NPU experts that it seem logical to have concepts on genes be under body structure.