Stream: genomics
Topic: Updates to all key documents based on latest version of IG
Arthur Hermann (May 04 2020 at 15:15):
Updates needed to all WG Documents with our most current version (I am not sure if the version we published at end of year is the current version or if the changes/discussions since then are considered current.
Update all implementation guides and all information listed on the HL7 website to reflect the newly "published" version of the STU. If necessary, form a subcommittee to work on this effort. Many of the current documents reflect HL7v2 and need to be updated to reflect FHIR. It is possible that by working with some leading laboratories, a rough Laboratory Reference Implementation guide can be developed.********
Examples of documentation which must be review and updated include (this is not meant to be an exhaustive list):
Genomics on this page:
Same page has link to existing DAM from January 2013
Do these need to be updated?
10.1.7.4 Genomics
The following Observations show examples of genomics observations:
• Genetics example 1
• Genetics example 2
• Genetics example 3
• Genetics example 4
• Genetics example 5
• Example of diplotype data (with haplotypes observation as reference)
• Example of haplotype data that is basis of a diplotype data
• Example of another haplotype data that is basis of a diplotype data
• Example of phenotype data
• Example of a TPMT diplotype that link to two TPMT haplotype observations
• Example of a TPMT haplotype observation
• Example of another TPMT haplotype observation
A few other examples from DAM
11.3 HL7 CDA Implementation Guide for Genetic testing reports
The Clinical Genomics Work Group developed a CDA Implementation Guide (IG) for genetic testing reports, with the support of the Structured Documents Work Group. The main purpose of this IG is to specify a Universal document standard for a Genetic Testing Report (GTR) typically sent out from a genetic laboratory to recipients who ordered the report. The GTR IG targets both human viewing and machine processing by representing the data in a renderable format along with structured entries; these entries are associated by 'clinical genomic statement' templates defined by this guide, which could empower clinical decision support by conveying clinical genomics semantics in an explicit way. This guide is defined as ‘Universal’ as it is flexible enough to accommodate various use cases, e.g. in translational medicine and clinical environments or of different genetic testing types.
For more information see:
http://www.hl7.org/implement/standards/product_brief.cfm?product_id=292
GAPS
14.1 Laboratory order entry
One significant gap is the need to develop a laboratory order implementation guide for clinical sequencing/molecular diagnostics, which is capable of including relevant clinical history and a fully structured family history with familial mutations and risk assessment. While many laboratories currently use electronic ordering, some laboratory orders are still paper- or PDF-based. However, as genetic analysis becomes a standards part of clinical care, paper-based order entry will not scale.
Please schedule time at an upcoming meeting to discuss or if the WG will meet virtually in May - then provide time for the discussion at that time
Arthur Hermann (May 04 2020 at 15:51):
Sorry to Clarify all of these should have been URL's .. the come from this page: Which is the Observations Examples Page - there is a section on Genomics with all of the info below, each one of which is a URL... having trouble getting Zulip to take my text as URL's even when I am pasting as test with URLs :)
http://hl7.org/fhir/observation-examples.html
• Genetics example 1
• Genetics example 2
• Genetics example 3
• Genetics example 4
• Genetics example 5
• Example of diplotype data (with haplotypes observation as reference)
• Example of haplotype data that is basis of a diplotype data
• Example of another haplotype data that is basis of a diplotype data
• Example of phenotype data
• Example of a TPMT diplotype that link to two TPMT haplotype observations
• Example of a TPMT haplotype observation
• Example of another TPMT haplotype observation
Bret H (May 05 2020 at 12:22):
@ Bob Milius Back in September, or maybe in Jan 2019, I thought the group was requesting that OandO remove some of these examples: such as http://hl7.org/fhir/observation-example-genetics-3.json.html
Bret H (May 06 2020 at 04:21):
@Arthur Hermann a tracker is here GF#19965
Bret H (May 06 2020 at 04:22):
@Kevin Power looks like OandO did not fulfill our tracker or is the change in R5?
Patrick Werner (May 06 2020 at 11:11):
no it still isn't voted on. I poked O&O about this several times already. (Tried to get it into the last R4.0.1 TC release.
Patrick Werner (May 06 2020 at 11:14):
O&O tracker is here: GF#20165
Kevin Power (May 06 2020 at 11:27):
Do we need O&O to do it? I suppose we can do it ourselves if they are ok with it.
Patrick Werner (May 06 2020 at 12:16):
Yes. We could just prepare a PR to the FHIR CI R5 branch, but normally only after O&O voted on this.
Patrick Werner (May 06 2020 at 12:17):
Patrick Werner (May 06 2020 at 12:18):
Was the thread. Just saw that i got an answer to my last question. I would suggest to create a PR and point O&O to it.
Kevin Power (May 06 2020 at 13:08):
Any takers to create the PR? :slight_smile: I can do it, but it will probably be next week before I can take the time.
Kevin Power (May 06 2020 at 13:16):
Also - those trackers from above (GF#19965 and GF#20165) are basically the same request, and are actually both in the Clinical Genomics 'queue' (Work Group = Clinical Genomics). Anyone object to canceling one as a duplicate?
Bob Milius (May 06 2020 at 16:17):
Bret H said:
Bob Milius Back in September, or maybe in Jan 2019, I thought the group was requesting that OandO remove some of these examples: such as http://hl7.org/fhir/observation-example-genetics-3.json.html
We discussed it in our joint meeting at the WGM last Sept (Wed, Q2) - https://confluence.hl7.org/display/OO/OO+WGM+Meeting+Minutes%3A+September+16-20
From their minutes:
Clinical Genomics
- close to publishing Genomics reporting Implementation guide
- Changes to observation in R5:
- will replace current extensions in R4 that will result in R5 deprecations
- technical correction on examples
- questions about searching and computational observations
Kevin Power (May 10 2020 at 00:23):
@Bret H ^^^ Regarding your question about O & O in the committers stream, we need to make a PR to remove our CG artifacts.
Bret H (May 10 2020 at 13:53):
wasn't that done?
Kevin Power (May 10 2020 at 13:58):
Nope, afraid not
Bret H (May 10 2020 at 13:59):
why not?
Bret H (May 10 2020 at 14:00):
I thought having Grahame Grieve bless the effort, and tracker that was logged was enough to get things moving @Patrick Werner logged the tracker.
Kevin Power (May 10 2020 at 14:02):
The best excuse I can give you is that we have been focused on the IG and no one has taken the time to do it. Anyone can put together the PR if you are interested?
Bret H (May 10 2020 at 14:02):
Yes. point me to the documentation
Kevin Power (May 10 2020 at 14:06):
Documentation on how to make a PR?
Kevin Power (May 15 2020 at 16:30):
Hey all - Just for awareness, I am currently hacking away at removing our out dated artifacts from FHIR Core.
Wanted to ask @ Bob Milius -- Is it OK to remove all of the HLA specific stuff some FHIR Core, or do you you need it there?
Bob Milius (May 15 2020 at 16:49):
Kevin Power said:
Wanted to ask Bob Milius -- Is it OK to remove all of the HLA specific stuff some FHIR Core, or do you you need it there?
I don't see any HLA profiles/extensions/example under Observation
I found these under DiagnosticReport
Profile
Extension
- hla-genotyping-results-allele-database
- hla-genotyping-results-glstring
- hla-genotyping-results-haploid
- hla-genotyping-results-method
Example
You can delete these.
I don't think there are any others, but let me know if you find some.
Kevin Power (May 15 2020 at 16:52):
Yup, it was the stuff under DiagReport I was wondering about. Thanks sir.
Kevin Power (May 15 2020 at 19:46):
I created a branch and pushed up a commit, welcome everyone to take a look:
https://github.com/HL7/fhir/commit/3cfe12f1b403
Kevin Power (May 15 2020 at 19:54):
And the PR:
https://github.com/HL7/fhir/pull/877
Kevin Power (May 15 2020 at 19:58):
Just so everyone knows - on the main FHIR branch, a 'build' doesn't happen until you create a pull request. Once this completes, I can share a link to the built version and everyone can do a better review of the new 'genomics implementation guidance' page as well as poke around Observation, DiagnosticReport and Service request to make sure things still look OK before we share with O&O.
https://dev.azure.com/fhir-build/build.fhir.org/_build/results?buildId=3017&view=results
Kevin Power (May 15 2020 at 21:06):
You can see the full build here: http://build.fhir.org/branches/kpower_cg_outdated_artifacts/index.html
Kevin Power (May 15 2020 at 22:05):
@John David Larkin Nolen -- It might be good to have this on the agenda for our joint meeting next week?
Last updated: Apr 12 2022 at 19:14 UTC
