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HL7 Clinical Genomics Weekly Call - 03 Mar 2020 11:00 AM (US Eastern)

Minutes

http://tinyurl.com/HL7CGGroupCall 

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit

Archive of minutes: https://confluence.hl7.org/pages/viewpage.action?pageId=25559917&src=contextnavpagetreemode

Attending the meeting

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Agenda

Attendees Sign-in

Presiding Co-Chair (Kevin Power - Cerner): 

  1. Liz Amos - NLM - liz.amos@nih.gov 
  2. Jamie Jones - BCH - james.jones.bch@gmail.com
  3. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  4. Alex Mankovich - Philips - alex.mankovich@philips.com 
  5. Scott Bauer - Mayo Clinic - bauer.scott@mayo.edu
  6. Bret Heale - Intermountain HealthCare - bheale@gmail.com  
  7. Stephen Schwartz - Epic - sschwart@epic.com 
  8. Clem McDonald - NLM - clemmcdonald@mail.nih.gov
  9. Patrick Werner - MOLIT Institut - pw@molit.eu
  10.  Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  11. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  12.  Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  13.  Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com 
  14. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org 
  15. Ling teng - BWH -tenglingling@gmai.com

Standing Informational Items

Agendas and Important Dates 

CG Call Date

Co-Chair

Agenda https://confluence.hl7.org/display/CGW/Future+Topics+for+Weekly+Meetings

Important Dates

2/18/20

Patrick



2/25/20

Kevin

Topic 1: ‘find-variant’ operation - outstanding questions (Bob D / Patrick)

Topic 2: Update/Discussion on Implication Profiles (Jamie)


3/3/20

Kevin

CG IG Lite: Liz & Clem
Attachments from 1/28 email


3/10/20

Bob M



3/17/20




3/24/20




3/31/20

Patrick



4/7/20

Bob M



4/14/20

Patrick



4/21/20




4/28/20




5/5/20

Bob M



5/12/20




Working Group Meeting

May 16-22, 2020   • San Antonio, Texas

Register Today!

CG WG will be meeting Monday Q3 & Q4, and all-day Tuesday and Wednesday

External efforts

Subgroup reports

  • FHIR (Jamie, Gil)
    • Minutes:

https://docs.google.com/document/d/1FGCQRtxJKyHhnC1uB_t4sJZ9yXbLMGOqPXHPr5tSLLQ/

WG projects and outreach

  • MOLIT will start a inter-institutional virtual tumor board project with 5 hospitals 2020/04/01 the whole persistence layer is FHIR with extensive usage of our IG. Our lab partner CEGAT (https://www.cegat.de/en/) will send the Diagnostic Reports using our profiles.

Topic 0: Approval of Minutes from Last Meeting

Feb 25 

Topic 1: “Lite” IG

Clem

"Focus is on the variant.  Pharmacogenomics and HLA type stuff is out. They add a lot of complexity and tend to be reported on their own and already have a pretty good start.

 

I treated all variants (big/little 0 the same). Did not model either genotype or haplotype. They get in the way of simplicity (but I may get fired because of that).

 

I focused on the 5 ways of specifying a variant.  Some of our fields are convenience fields – don’t add real information, but people like them-so segregated them"

Attachments from 1/28 email

https://docs.google.com/document/d/1eVBvUsezw69qlylWnPAz5bVQpATJ3g_F-gm4dD1ENsU/edit 

https://docs.google.com/spreadsheets/d/1UAphpeYuyiQ1ANwusaculVt2vFmSvmaju1TfMv67RU8/edit#gid=1509314707 

New 3/3/20 :  Genomics Reporting Implementation Guide- Variant structure with suggesteds simplification (002).pdf 



Clem: where are allelic frequency? We have a component:sample-allelic-frequency, population frequency is in the backlog. 

Bret. Population frequency needs a description of the population looked at.

Clem: last four components should be grouped together.

Bob D.: how do we use arrCGH ratio?

Clem: we can remove the last four components? Of the UML (in the pdf). Wants to carve out pharmacogenomics out of the IG, or make it a distinct IG.

Bob M.: is this about modifying the CG IG? Or should this be a “simple” CG IG.

Jamie: The idea is to have a structured way of using only some parts of the IG.

Bob M.: Could do this by example and guidance

Jamie: all Components are optional

Bob D.: could see this as a review of our current variant profile.

Kevin: focus on improving the current variant (and other profiles) then we can think about a simpler version

Bret: we have redundancies as there are several ways to transport variants

Clem: wants to have a simpler way to show labs how to implement.

Bob D.: we can start with cleaning up our variant profile.

Kevin.: two approaches: get rid of a lot of stuff. Or focus on the variant level. Can do derived profiles from variant.

Patrick: i understand the need of better guidance for implementers. We should give better guidance (text, uml diagrams, graphics) how to implement a Genomics Diagnostic Report with Variants.
Kevin: Let’s start with a spreadsheet representation of Variant and Clem can mark all components he thinks aren’t necessary anymore.

Bob M.: I support Kevin's approach, but I've found the best way to show labs how to send Genomics Report bundle is with many examples with lots of comments.These examples should be showing different kinds of reports


Chat

[Mar 3, 2020 at 10:06:51 AM] Kevin Power: Minutes

http://tinyurl.com/HL7CGGroupCall

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit

[Mar 3, 2020 at 10:10:40 AM] Patrick: +1 for voting and merging to master branch

[Mar 3, 2020 at 10:16:25 AM] Liz Amos: I'm trying to add the PDF to the meeting notes but am stuck

[Mar 3, 2020 at 10:16:34 AM] Kevin Power: While I am sharing, can someone take notes?  @Jamie / @Patrick / @Bob M / @Bob F ?

[Mar 3, 2020 at 10:16:40 AM] Patrick: will do

[Mar 3, 2020 at 10:16:44 AM] Bret Heale: It IS very hard to find our current IG. The one that is most visible is the old implementation guidance created during dstu3. We really should do more to expose our published IG better. +100 to Clem

[Mar 3, 2020 at 10:18:13 AM] Liz Amos: Try this one: https://drive.google.com/file/d/1PMVRyh0MRrCIzCHgvdftvRocgYQuSvLX/view?usp=sharing

[Mar 3, 2020 at 10:23:30 AM] Patrick:  component:sample-allelic-frequency

[Mar 3, 2020 at 10:31:39 AM] Bret Heale: I recall that folks were not negative but asking that you use profiling to create an implementation guide as a more constrained version with less fields.

[Mar 3, 2020 at 10:32:02 AM] Jamie Jones: +1 to simplified "view" of functional ways to use variant

[Mar 3, 2020 at 10:32:02 AM] Jamie Jones: either as additional profiles or through examples

[Mar 3, 2020 at 10:33:25 AM] Jamie Jones: quick notes I drafted to help group the components based on these comments: https://docs.google.com/spreadsheets/d/1hnoaWjdNZbGkIzl4gZugzANnulQXF6ky7aWCjzbAiks/edit#gid=0

[Mar 3, 2020 at 10:38:48 AM] Jamie Jones: +1 for considering the direction, Bret

[Mar 3, 2020 at 10:39:04 AM] Bret Heale: I do not see that we have the right consortium of stakeholders in our meetings to really move the ball forward

[Mar 3, 2020 at 10:39:18 AM] Jamie Jones: I don't want us to consider removing components from Variant right now

[Mar 3, 2020 at 10:39:22 AM] Bret Heale: through implementation the field will move better

[Mar 3, 2020 at 10:39:41 AM] Jamie Jones: just don't add include them in sub-profiles and/or examples

[Mar 3, 2020 at 10:39:47 AM] Bret Heale: pardon closer to a specific normalized version of sending genetic data

[Mar 3, 2020 at 10:42:50 AM] Patrick: +100 to all of jamies statements

[Mar 3, 2020 at 10:44:11 AM] Bob Freimuth: Adoption lags for a lot of reasons, not just because the spec is complex. A big reason is that it is not yet stable.

[Mar 3, 2020 at 10:45:13 AM] Bret Heale: don't call it my principals. it was the historic perspective and guidance from the group, including specific members of this conversation.

[Mar 3, 2020 at 10:48:31 AM] Jamie Jones: "improvable" is very diplomatic

[Mar 3, 2020 at 10:49:20 AM] Bob Milius: I support Kevin's approach, but I

[Mar 3, 2020 at 10:50:20 AM] Bob Milius: I support Kevin's approach, but I've found the best way to show labs how to send Genomics Report bundle is with many examples with lots of comments.

[Mar 3, 2020 at 10:50:20 AM] Bob Milius: These examples should be showing different kinds of reports

[Mar 3, 2020 at 10:52:13 AM] Jamie Jones: https://docs.google.com/spreadsheets/d/1hnoaWjdNZbGkIzl4gZugzANnulQXF6ky7aWCjzbAiks/edit#gid=0

[Mar 3, 2020 at 10:53:15 AM] Bob Milius: This work should be based on example  use cases (high level narrative on what is being reported), and then examples can be created from them.

[Mar 3, 2020 at 10:53:46 AM] Bret Heale: regards examples, you'll see that all is possible

[Mar 3, 2020 at 10:53:46 AM] Bret Heale: it depends on what the lab is willing to do bioinformatically

[Mar 3, 2020 at 10:59:03 AM] Jamie Jones: exactly, Bret

[Mar 3, 2020 at 10:59:03 AM] Jamie Jones: If we can outline common or suggested breakpoints in workflows those will drive the examples

Future Topics

LOINC changes for Level of Evidence / Clinical Significance

See these notes from Swapna: LOINC Significance vs Evidence and TMB code proposal.pdf

Level of evidence 

https://loinc.org/93044-6/

https://loinc.org/LL5356-2/

See these previous call notes for earlier discussion:  CG-2019-08-27

Need to consider the following two new motions:

    • Motion A: Use 53037-8 for both germline and somatic variant clinical significance reporting, and add information to the Term description about the different guidelines for somatic and germline variants;  Keep the Answer list the same, but update the type from Preferred to Example



       o  1st/2nd -

       o  Discussion -

       o  Abstain/Nay/Yea -  / /

       o  Result -

(Notes from Jamie:)

Want to separate clinical significance from level of evidence.

Sites want to continue to use the tier system as well.

Ask: a therapeutic somatic variant: 

E.g. from http://build.fhir.org/ig/HL7/genomics-reporting/Bundle-oncologyexamples-r4.xml

(note, this example uses placeholder value “AMP Guidelines” instead of a tier)

Profile: http://build.fhir.org/ig/HL7/genomics-reporting/somatic-predictive.html

Code: somatic-predictive (TBD LOINC)

Value: E.g. Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response

Component: Level of evidence - 

Code: 93044-6, 

Value: from LOINC Answer List LL5356-2 (preferred) CAN USE TIER SYSTEM HERE

Component: medication

Component: cancer

  • Motion B: Consider creating new codes for diagnostic, therapeutic, and prognostic significance (see Quest screenshot, LabCorp report) and/or type of evidence (see Baylor report)

       o  1st/2nd -

       o  Discussion -

       o  Abstain/Nay/Yea -  / /

       Result - 

Need to create an example to understand the meaning of this change/concepts.
Need a caretaker for this topic.

FHIR-25296 Uncallable subregions in a region studied

FHIR-24598 How to reference a region studied observation from genotype, haplotype, variant observations

FHIR-19844 PGx High Risk Allele Medication Impact is confusing

Clinical Genomics Reference Docs



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