Stream: genomics
Topic: Simplifying Variant Guidance
Jamie Jones (Nov 23 2021 at 14:52):
Hi all, preview of the new Variant guidance is up on https://build.fhir.org/ig/HL7/genomics-reporting/branches/variant-component-groups/sequencing.html, please review and comment here or on https://docs.google.com/document/d/15g1rngmgFoE8_i7UGpXRpISkOCrd1QCoQBg9REY80EI/edit#heading=h.66b6emu5lnph
Kevin Power (Nov 23 2021 at 15:25):
@Jamie Jones - The google doc still has 3 ways of defining a variant, but the sequencing page only shows 2? Did you decide to remove 'by providing a specific code in a variant database' ?
Jamie Jones (Nov 23 2021 at 15:26):
Yes, @Bob Dolin suggested on call last week that we don't reinforce that pattern, especially since we aren't binding the component to a particular database
Jamie Jones (Nov 23 2021 at 15:27):
I'll make the change in the doc as well
Kevin Power (Nov 23 2021 at 15:32):
Did we also discuss leaving off the compound het section?
Jamie Jones (Nov 23 2021 at 15:40):
I'd like to go over that section and review our current examples: https://build.fhir.org/ig/HL7/genomics-reporting/branches/variant-component-groups/Bundle-compound-heterozygote.html and https://build.fhir.org/ig/HL7/genomics-reporting/branches/variant-component-groups/Bundle-complexVariant-nonHGVS.html
Bob Dolin (Nov 23 2021 at 15:43):
@Jamie Jones I really like what you've done with the page. Thanks. Minor question, did you mean to leave out "Outer and/or inner end should be populated"?
Jamie Jones (Nov 23 2021 at 15:44):
Bob Dolin good catch I'll clean that up
Jamie Jones (Nov 23 2021 at 15:48):
@Bob Dolin wondering if we can revert to https://loinc.org/81301-4/ and https://loinc.org/81302-2/ for inner and outer start-end now that we are clearly treating variants with those populated as structural
Bob Dolin (Nov 23 2021 at 15:50):
I kinda remember the history - we had quit using those codes because they had 'structural' in the name? If so, yes, I'd agree with you.
Bret H (Nov 23 2021 at 17:07):
To clarify, the variant guidance branch is to change the main IG not create a second IG? so the LOINC code changes will be part of the main IG. Are these breaking changes?
Kevin Power (Nov 23 2021 at 17:08):
Not a new IG, no. So any code changes would be breaking. However, STU2 will have numerous other breaking changes.
Last updated: Apr 12 2022 at 19:14 UTC
