Stream: genomics/committers
Topic: Variant component groups
Kevin Power (Nov 23 2021 at 21:44):
We need to take more advantage of the committers stream to discuss more technical detail, so starting a thread to talk about 'Variant Component Groups' branch work.
CC: @Bret H @Jamie Jones
Kevin Power (Nov 23 2021 at 21:56):
I will make a pass through the component names in this branch and commit some corrections.
Jamie Jones (Nov 23 2021 at 22:35):
i responded to a couple comments in the doc
Kevin Power (Nov 23 2021 at 22:44):
Pushed up some changes and they have built.
Kevin Power (Nov 23 2021 at 23:49):
Pushed up one last change for today (improved the look of the JSON snippets)
Kevin Power (Nov 24 2021 at 15:54):
@Jamie Jones - I remember that @ Bob Milius asked something like 'can HLA Alleles be a Variant?' At first I was thinking no, but if we are going to list ISCN as a way to identify a 'variant', it seems like HLA Nomenclature should be OK as well? What do you all think?
Kevin Power (Nov 24 2021 at 16:15):
Also, if we are going to allow ISCN, we probably need to define it as a CodeSystem? Yes/No? If Yes, any suggestions on a URI? The LRI V2 Implementation Guide did point me at an OID, so I suppose we could use "system": "urn:oid:2.16.840.1.113883.6.299"
Jamie Jones (Nov 24 2021 at 17:00):
Good question about ISCN code system, that should be in there. Updating codes for the positions per FHIR#32424 now. Recent IM discussion have me thinking there's little reason not to use Variant for Bob M's case.
Kevin Power (Nov 24 2021 at 17:04):
So for ISCN code system, use the OID for now, or do we (at least tentatively) agree on a URI?
Kevin Power (Nov 24 2021 at 17:31):
For my last thing of the day, I pushed up a change for ISCN example using OID as the system.
Jamie Jones (Nov 24 2021 at 19:03):
minor updates to https://build.fhir.org/ig/HL7/genomics-reporting/branches/variant-component-groups/sequencing.html are live
Bret H (Nov 25 2021 at 00:50):
Jamie Jones said:
Good question about ISCN code system, that should be in there. Updating codes for the positions per FHIR#32424 now. Recent IM discussion have me thinking there's little reason not to use Variant for Bob M's case.
What do you mean Jaime? His use case is for Alleles these are haplotypes with underlying variants.
Kevin Power (Nov 25 2021 at 03:58):
If we are allowing the ISCN string on Variant, it is probably worth discussing if the HLA Allele fits better here versus Haplotype.
Joel Schneider (Nov 29 2021 at 16:14):
To obtain an official "system" uri for ISCN, we should start by creating a JIRA ticket for HTA. A lookup on https://hl7.org/oid indicates the 2.16.840.1.113883.6.299 oid was registered in 2011.
Kevin Power (Nov 29 2021 at 16:16):
Thanks @Joel Schneider - Do you mind logging it?
Bret H (Nov 29 2021 at 16:27):
Kevin Power said:
If we are allowing the ISCN string on Variant, it is probably worth discussing if the HLA Allele fits better here versus Haplotype.
So, what would you do with a complex Star Allele that had multiple locations involved? Here Haplotype allows each underlying site-specific locus to have a variant profile, with the Star Allele appearing as the Haplotype. To me this would be similar to HLA Allele. But I see the desire to simplify as one could think about ISCN strings similarly.
So, that would bring up what to do with a complex HGVS that involves multiple, discrete, loci. Perhaps leave both options available? That would, of course, mean that implementers need to look at genotypes, haplotypes and variant observations to find the Allele. It is a tough call. I lean towards not having alleles as Variant observations but in a higher level construct, but it would be technically doable to use the Variant observation. If we're not in a position to dictate one (use of Haplotype and Genotype for alleles) over the other (using GL-strings, complex HGVS strings in Variant), then maybe the community could be given both and use in practice will dictate?
Bret H (Nov 29 2021 at 16:29):
ISCN is a way to try to address chromosomal rearrangements - I thought the component for ISCN was limited to that use and not open for Allele nomenclatures like GL-strings?
Kevin Power (Nov 29 2021 at 16:32):
If we are going to add gl-string as an option on Variant, we would likely need a new component.
Kevin Power (Nov 29 2021 at 16:35):
I think Star Allele should still be a haplotype with corresponding variants that make up the star allele. I say that since we don't have a widely accepted definition of Star Alleles which everyone agrees with (though I hope that PharmVar will get there). I get the sense that ISCN and gl-strings are accepted enough as a description of the 'variation' that we can express them via the expression.
At least that is my thinking.
Joel Schneider (Nov 29 2021 at 19:06):
To obtain an official "system" uri for ISCN, we should start by creating a JIRA ticket for HTA. A lookup on https://hl7.org/oid indicates the 2.16.840.1.113883.6.299 oid was registered in 2011.
Kevin Power (Dec 08 2021 at 15:18):
@Jamie Jones - So, where are we with this branch? Any pending changes? Ay other feedback?
Jamie Jones (Dec 10 2021 at 18:46):
i do have unsaved work here I will push this weekend - realigning some examples and adding in the last of the content from the google doc :)
Kevin Power (Dec 14 2021 at 23:11):
@Jamie Jones - I just reviewed the JIRAs for this, and I am afraid none of them have a resolution or resolution description:
https://jira.hl7.org/issues/?jql=cf%5B11402%5D%20%3D%20IG-Lite
Kevin Power (Dec 15 2021 at 17:56):
@Jamie Jones - any chance you can propose some resolutions on these today so I can send around for a block vote next Tuesday?
Jamie Jones (Dec 15 2021 at 19:55):
consider them disposed
Jamie Jones (Dec 21 2021 at 15:44):
made the minor tweaks we went over last monday, branch should be good for final review & vote
Kevin Power (Dec 21 2021 at 15:49):
We have the block vote today (just in time :wink: )
Jamie Jones (Dec 21 2021 at 22:04):
Do we really want to keep component[copy-number] as a Count datatype instead of a Quantity? It means we have to add code = #1 and system = UCUM to instances using it and can't just send value=1 or value=3, etc http://hl7.org/fhir/R4/datatypes.html#QuantityVariations
Bret H (Dec 29 2021 at 16:26):
change to quantity seems fine to me.
Bret H (Dec 29 2021 at 16:26):
It should always be a whole number
Bret H (Dec 29 2021 at 16:26):
(positive whole number)
Kevin Power (Dec 30 2021 at 21:28):
I merged latest QA changes from master into this branch, so if there is more to do, you should pull down changes first before making additional change.
Kevin Power (Jan 07 2022 at 19:02):
@Jamie Jones -- Is this branch ready to merge to master?
Jamie Jones (Jan 07 2022 at 19:55):
i'll pull down latest and review
Jamie Jones (Jan 11 2022 at 15:53):
merged with master, let me know if you spot any additional QA. Otherwise will sunset the branch
Bret H (Jan 20 2022 at 13:29):
@Jamie Jones I missed it before. Is there a link to the Variant profile page on http://build.fhir.org/ig/HL7/genomics-reporting/sequencing.html . I would suggest a hyper-link in section 1.3 Variant reporting in the sentence "Currently, there is one profile used to model most variant information" on the word variant. Or be more explicit and add a sentence like 'the Variant profile can be found here'
Joel Schneider (Jan 20 2022 at 16:19):
Joel Schneider said:
To obtain an official "system" uri for ISCN, we should start by creating a JIRA ticket for HTA. A lookup on https://hl7.org/oid indicates the 2.16.840.1.113883.6.299 oid was registered in 2011.
HTA has now published draft content for the ISCN external code system here:
International System for Human Cytogenomic Nomenclature (ISCN)
Joel Schneider (Jan 20 2022 at 16:22):
Please review and add any comments to HTA-65
Last updated: Apr 12 2022 at 19:14 UTC
