CG WG Call Notes leading to 2016 January WGM

October 27, 2015 -- Weekly call

Agenda

• None

Attendees

• Amnon Shabo (Shvo), Siew Lam, Jonathan Holt, Anwar, Bret, Perry Mar, M'Lynda Owens, David Kreda, Bob Freimuth

Draft Minutes

• Amnon commented on the FHIR development that if we can introduce a base resource to next FHIR DSTU, it should be the current Genetic Observation Profile (with possible refinements) and then Sequence can be a profile over the base Genetic Observation Resource. The rationale is that Sequence is a type of genetic observation so that's the natural hierarchy. We can then introduce more profiles like structural variations, expression data, etc.

October 20, 2015 -- Weekly call

Agenda

• 5 min Updates from
  • ClinGen
  • GA4GH
  • IOM
  • other?

• Atlanta WGM review
  • minutes

• "HL7 v2 genomics report lite"

• Orlando WGM - room reservation
• Oct 23 deadline

• FHIR review (Gil)

• Upcoming deadlines:
  • 2015-10-23: Deadline to complete the Post-WGM Evaluation (WG Health metric)
  • 2015-10-23: Deadline to complete WGM Room Request form for the January WGM (WG Health metric)
  • 2015-10-23: Deadline to post your October WGM minutes on the website or wiki (WG Health metric)
  • 2015-10-23: Deadline to notify HQ of additions/changes/corrections to Co-Chair openings
  • 2015-10-25: Notification of Intent to Ballot (NIB) Deadline
  • 2015-10-26: Initial Harmonization proposals due
  • 2015-10-28: Co-Chair Nominations Open

Attendees

• Amnon Shabo (Shvo), Siew Lam, Jon Holt, Gil Alterovitz, Grant Wood, Anwar, Bob Freimuth, Bret, Heale, Clem Mcdonald, David Kreda, Eric Whitebay, JD Nolen, Kevin Power, Mollie (joined after 30 minutes)

Draft Minutes

• ClinGen
  • Bob F gave an update on structured variants (opy number, large indels, etc) in ClinGen
  • Jon asked if using ISCN syntax would help (Cytogenetics)
  • Bob F - good question, issue about fuzzy borders that need to be considered. Need more info about what ISCN can do.
  • question about whether anyone has looked at CYDAS - a system for parsing ISCN. This is an open source project that hasn't been updated in a long time.
• GA4GH
  • Grant gave an update on GA4GH, in particular on the effort related to family health history, and how FHH can be incorporated to the EHR. There is a short document (about 4-5 pages) that is being developed. It includes as section on HL7 standards on family history (Grant wrote this). The document is not a history of the domain, but it captures how family history is used today. It hasn't been published it yet, but expect it to be published in a couple weeks.
  • Gil - GA4GH is looking at different use cases. Gil will present to GA4GH use cases based on the DAM in December. Gil will share the date/time.
• IOM
  • Grant and JD gave an update on the EHR and genomics group
  • Grant - Sandy Aronson, and JD Nolan, asked Grant to co-chair another workgroup for moving to pilot phase.
  • JD - also working with PMI
• Gil gave an update on FHIR activities
• CPIC
  • Bob F. - CPIC informatics workgroup met yesterday, terminolgy/semantics work, proposed observation codes to use, they are slightly different from IOMs codes. Will work on harmonizing and send to Clem for LOINC. Analagous to v2 gentetic report LOINC codes. Harmonized with Delphi method of harmonizing phenotypic terms using experts digesting many rounds of surveys.
• Atlanta WGM review
  • Bob Milius gave an overview of the Atlanta WGM discussions
  • Amnon commented on the FHIR discussion that if we can introduce a base resource to FHIR it should be the Genetic Observation Profile (with possible refinements) and then Sequence becomes a profile over the base Genetic Observation Resource. The rationale is that Sequence is a type of genetic observation so that's the natural hierarchy.
• Gil gave an update on FHIR activities
  • FHIR is asking each Work Group to designate a single point of contact that will act as group lead for FHIR communications.
  • Mollie made a motion to have Gil designated as the CG rep. to FHIR ('group lead')
  • Jon asked about the exact role of FHIR rep.
  • Bob M. suggested we should have full transparency in the relations with FHIR, and that in any case the group can designate others and it's not an election process
  • Bob F. suggested that an update from the FHIR group lead be put in the agenda for every weekly call.
  • Amnon said we need to get it to the DMP
  • Motion passed (0 abstains, 0 nays)