CG WG Call Notes leading to 2015 May WGM

May 5, 2015 -- Weekly call

Agenda

• FHIR PSS for work to support precision medicine, including potential sequence resource

Attendees

• Scott Bolte (serving as interim co-chair), Mollie Ullman-Cullere (co-chair), Grant Wood, Lori Dieterle, Perry Mar, Jonathan Holt, Bob Freimuth, Jami, Larry Babb

Draft Minutes

• Approval of FHIR PSS - 8 approved, 1 abstain, 0 negative
• Discussion of negative comments submitted on May ballot for FHIR family history and BRIDG molecular biology

April 28, 2015 -- Weekly call

Proposed Agenda

• Miscellaneous

Attendees

• Amnon Shabo (Shvo), Bob Milius, Mollie Ullman-Cullere, Gil Alterovitz, Jeremy Warner, Grant Wood, Lori Dieterle, Perry Mar, Jonathan Holt, Travis

Draft Minutes

• Discussion of CG view on BRIDG and the concerns Mollie had on LS-DAM, a model which has partially propagated to the BRIDG model
• PSS for a core Sequence Resource
• Genetic Observation could point to a Sequence it came from

April 21, 2015 -- Weekly call

Proposed Agenda

• Miscellaneous

Attendees

• Amnon Shabo (Shvo), Bob Milius, Johnathan Holt, Grant Wood

Draft Minutes

• Agenda for Paris

April 14, 2015 -- Weekly call

Proposed Agenda

• Miscellaneous

Attendees

• Amnon Shabo (Shvo), Mollie Ullman-Cullere, Larry Babb, Gil Alterovitz, Jeremy Warner, Mamatha Shekar (Illumina), John Holt, Jami

Draft Minutes

• Agenda for Paris
• Intros of new members
• Gil discussed a possible PSS for a FHIR Sequence Resource
• Discussed the intention behind a Sequence Resource and how it differs from the genetic observation resource
• Discussed the idea of having a generic FHIR Sequence Data Type, which can be leveraged for DNA Sequence

March 24, 2015 -- Weekly call

Proposed Agenda

• Discussion of FHIR profiles to Observation Resource

Attendees

• Amnon Shabo (Shvo), Mollie Ullman-Cullere, Bob Milius, Scott Botle, Larry Babb, Gil Alterovitz, Bob Milius, Jami, Jeremy Warner, Siew Lam

Draft Minutes

• Larry asked what if we don’t submit to this ballot cycle
• Mollie: FHIR is about the 80:20 rule
• Scott and Mollie said it’s mainly for getting broader feedback, beyond our group
• Amnon:
  • not sure if 80:20 rule applies to profiles
  • if we submit, we have to add comments, disclaimers, indication that this attribute is just a stub to be evolving to structures in future releases
• Bob: my understanding is that a core resource follows the 80:20 rule. The 20 goes into an extension. A bundle of resources and extensions is used to develop a use case (e.g., HLA typing report) is called a profile. Am I wrong? Why is the Genetic Observation extension listed as a profile? Basically, I'm not comfortable with my understanding of all this.
• Larry: we need develop a bundle of resources like the bundles already on the FHIR ballot
• Mollie walked us through the proposed genetic profile over Observation and showed a few samples
• Larry walked us through his comments on the sample Mollie showed:
  • dbSNP id is problematic, for example the id used in the sample points to 4 different alleles
  • in ClinGen, they use Sequence Ontology to identify DNA changes
  • separate the first 19 attributes that describe the variant / allele from the rest of the attributes that describe other issues like indications, condition assessed, interpretations, etc.
  • Amnon: fully agreed with the separation Larry proposed
• Mollie: interpretation was removed in the sample following Amnon's recommendation, but it is inherited from the base Observation Resource
• Motion was made by Mollie to vote on the profile as it was presented today
• Amnon suggested to put the rest of attributes beyond attribute 19 as future work
• Motion was seconded by Jeremy
• Vote: Bob, Jami: abstain; Amnon and Larry: negative; Mollie, Gil, Jeremy: affirmative

March 3, 2015 -- Weekly call

Proposed Agenda

• Open discussion

Attendees

• Amnon Shabo (Shvo), Perry Mar, Mollie Ullman-Cullere, JD Nolen, Bob Freimuth, Bob Milius, Scott Botle, John Holt

Draft Minutes

• Discussed the bio-marker standardization effort
• how to get to 'common names' for mutations
• differences in testing platforms
• nomenclatures are problematic and it's better to get to the sequence level

February 24, 2015 -- Weekly call

Proposed Agenda

• Ballot reconciliation of the CG DIM 9/2014 ballot

Attendees

• Amnon Shabo (Shvo), Jonathan Holt, Grant Wood, Bob Milius, Perry Mar, Sue Lam, Mollie Ullman-Cullere, [the seventh participant - could you please add your name?]

Draft Minutes

• Amnon walked through his proposed dispositions & comments to the 9/2014 CG DIM ballot
• discussion was held and votes were recorded
• Perry Mar's comments on the Family Health History DIM were briefly discussed towards the end of the call but not concluded, so it was agreed to continue the discussion at a future call
• a few of the ballot comments on the relation between the DAM and the DIM triggered discussion on the best way forward in this regard
  • Mollie suggested the DAM and the DIM will be maintained and balloted separately since they might be developed in different paces
    • e.g. DAM will drive the DIM content and evolve at an earlier and faster pace particularly with rapidly evolving use cases
  • Amnon said that it was already decided to merge the two documents, and while the DAM could exist without the DIM, the latter has to have the context that is provided by the DAM
  • a possible way to handle the two documents is to have them reference each other, but that could lead to editorial integrity issues
  • Mollie suggested the two documents be maintained and balloted separately, with more mature use cases and story boards needed to support the DIM content be created in summary fashion from the DAM. For instance the DAM may have 25 to 50 use cases showing the breadth of clinical paradigms (including very stable and emerging) to be considered by implementers, but the DIM would contain 3-4 stable use cases to support the information model.
  • need to continue the DAM/DIM discussion but in any case the DIM will not be balloted in 5/2015; however, project database, ballot resolution, and publication of the clinical sequencing DAM are influenced by this decision.
• Porting the DIM to a web-based tool
  • Amnon briefly mentioned the porting of the DIM to a web-based UML editing tool that allows collaborative development of the model (it's available to everybody to view at https://repository.genmymodel.com/amnon.shvo/Clinical-Genomics-DIM)
  • click on a class name on the right side bar to see the comment
  • if you're interested to join the editing of the DIM, please drop a message to Amnon

January 27, 2015 -- Weekly call

Proposed Agenda

• Briefing on the San Antonio WGM meetings

Attendees

• Amnon Shabo (Shvo), Jonathan Holt, Grant Wood, Scott Bolte, Bob Milius, Larry Babb, Sue Lam

Draft Minutes

• Scott briefed on the San Antonio WGM meetings
• John:
  • Genetic family history: gender vs. sex
  • Modelling "Sequence"
• Larry: HGVS is not computable and quite ambiguous, and that's why it's important to pursue the "Sequence"modeling effort
• John: HGVS is actually interpretation and it's hard to get back to the raw data, based on which that HGVS expression was created
• Bob: rendering for the human viewing is case-specific (e.g., HLA) but the underlying structure should be unambiguous and common to all types of rendering