CG WG Call Notes leading to 2014 September WGM

Proposed Agenda

• Discussed FHIR efforts at Vanderbilt

Attendees

• Amnon Shabo, Grant Wood, Bob Milius, Mollie Ullman-Cullere, Scot Bolte, Siew Lam, Gil Alterovitz, Perry Mar, Vanderbilt team: Jonathan, Ann, Marc Beller,

Draft Minutes

• Mollie reviewed the draft proposal for a genomics FHIR observation
• Discussed issues of common interest with the Vanderbilt team
• Discussed differences in the use of terms such as germline, constitutional, mosaic (e.g., in use cases after bone-marrow transplant), etc.

Proposed Agenda

• Continue work for FHIR extension of Observation
• Administrative topics
• Sept ballot

Proposed Agenda

• Review draft of FHIR extension of Observation

Attendees

• Mollie Ullman-Cullere, Bob Milius, Grant Wood, Bob Freimuth

Draft Minutes

• Notes from today's call were posted to the HL7 CG main site under file name: CG_FHIR_Obs_v1

http://www.hl7.org/Special/committees/clingenomics/docs.cfm?wg_id=7&wg_docs_subfolder_name=docs

Proposed Agenda

• Review a Clinical genomics WG to-do list (in an Excel spreadsheet)

Attendees

• Amnon Shabo, Mollie Ullman-Cullere, Scott Bolte, Bob Milius,

Draft Minutes

• A team to review the BRIDG ballot from CG view point
• The coming FHIR DSTU ballot was discussed
• Mollie is going to draft extensions to the LOINC codes for genomic coordinates
• Amnon will try to clarify to newcomers and occasional visitors the location and organization of our minutes in the HL7 main site and wiki
• Lam will hold the to-do list as a working document and send it out to the list
• in the beginning of the weekly calls we should be reviewing the to-do list for ~5 minutes

Proposed Agenda

• Review ballot documents (DAM and DIM)

Attendees

• Amnon Shabo, Mollie Ullman-Cullere, Scott Bolte, Bob Milius, Siew Lam, Grant Wood, Brian Pech, Lloyd McKenzie, Larry Babb

Draft Minutes

• Mollie reviewed recent changes made to the DAM document
• Discussed the challenges in aligning the various HL7 Clinical Genomics specs with the DAM / DIM work
• Lam - need at least to agree on terminology such as traits, phenotype
• Amnon - top-down and bottom-up iterative effort between the DAM/DIM documents and the various development/implementation efforts
• Discussed green-field work and how/if it can align with the main stream work
• Green-field is ok but could hinder interoperability
• Voted affirmatively on motion to submit the DAM and DIM documents to 9/2014 ballot

Proposed Agenda

• Review ballot documents (DAM and DIM)

Attendees

• Amnon Shabo, Mollie Ullman-Cullere, Scott Bolte, Bob Milius, Bob Freimuth, Brian Pech, Lloyd McKenzie, Larry Babb

Draft Minutes

• Motion passed on adding Gil to the FHIR PSS as a facilitator
• Mollie reviewed the latest revision of the DAM document
• Discussed the figure of depicting the various types of genetic / genomic data
• Recommended to switch the figure graphics to a Venn Diagram, showing overlaps between variations, cytogenetics and NGS
• Ballot the DAM and DIM documents at informative level and then terminate the two projects (Clinical Sequencing DAM and the CG DIM)
• For the January cycle, consolidate the CS DAM and CG DIM into a single CG DAM, where we can introduce high level changes

Proposed Agenda

• Discuss comments on the Clinical Genomics DIM

Attendees

• Amnon Shabo, Bob Freimuth, Mollie Ullman-Cullere, Larry Babb, Scott Bolte

Draft Minutes

• Results of the discussion are reflected in the CGS DIM revision sent out to the CG listserv on July 29th
• Revisions are uploaded to the CG DIM project page on this wiki

Proposed Agenda

• Review of CGS DIM ballot document in light of Bob's comments and Amnon's reply
• Review of FHH DIM walk-through

Attendees

• Amnon Shabo, Bob Milius, Lloyd McKenzie, Gil Alterovitz, Grant Wood, Mollie Ullman-Cullere, Siew Lam,

Draft Minutes

• Voted affirmative on motion to have Siew Lam as a fifth co-chair (will be interim in this cycle and be up to formal vote in the January Cycle)
• Continued to review the comments on the Clinical Genomics Statement DIM
  • Discussed the way core genomic observation and its associated observations should be modeled (star schema based on generic type-vale pair mechanism versus more specialized classes
  • Have DNA data only in the core observation (the Genetic Variation class)?
• Ballot submission deadline is August 3rd so we need more time to discuss the DAM/DIM documents by then

Proposed Agenda

• Review of CGS DIM ballot document in light of Bob's comments and Amnon's reply
• Request from HL7 Hq. following cleanup of materials:
  • Need to vote on Notice of Withdrawal of the changes proposed to Clinical Genomics CMETs Release 10, which apparently were never reconciled (no package posted)

Attendees

• Amnon Shabo, Siew Lam, Grant Wood, Mollie Ullman-Cullere, Bob Milius, Larry Babb, Lloyd McKenzie, JD Nolen, Bob Freimuth

Draft Minutes

• Vote affirmative on the CG CMET withdrawal request from HL7 Hq.
• Voted affirmative to add age attribute to the Family History base FHIR resource
• JD reported on the "IOM Roundtable on Translating Genomic-Based Research for Health" Developing Guiding Principles for Integrating Genomic Information

Into the Electronic Health Record Ecosystem: Meeting that took place on June 26, 2014

• Amnon started reviewing Bob Freimuth comments on the Clinical Genomics Statement DIM
  • How to represent such a diversity of omics data and avoiding having the AssociatedOmicsData class becoming 'other' and eventually holding non standardized data
  • Decided to set up a call devoted just to this discussion

Proposed Agenda

• Review of DAM and DIM ballot documents for this cycle (see CGS DIM Walk-through document in the project page in this wiki)
• Agenda for Chicago WGM

Attendees

• Amnon Shabo, Mollie Ullman-Cullere, Scott Bolte, Siew Lam, Grant Wood, Bob Freimuth, Kathleen Rossello,

Draft Minutes

• Mollie reviewed sections of the DAM relating to raw genomic data and repositories
• Decided that the draft agenda for Chicago WGM can be published, thought it may be refined
• Members are encouraged to provide feedback to the DAM and DIM documents prior to their submission to ballot (around end of July)

Proposed Agenda

• Review of DAM and DIM
• Agenda for Chicago WGM

Attendees

• Amnon Shabo, Grant Wood, Mollie Ullman-Cullere, Scott Bolte, Bob Milius, Kathleen Rossello, Larry Babb

Draft Minutes

• Mollie Reviewed the latest DAM document
  • Suggested to split the editing of the DAM chapters among various members of the group
• Amnon mentioned the issues of Phenotype status attribute that needs still to be worked out
• FHIR
  • Scott is working on FHIR for family history but this will not be ready for this ballot cycle
  • Mollie said it's important to have a genetic profile over the FHIR Observation Resource
  • Mollie will drive the Observation profile and might try to do the modeling work or ask from help from the FHIR group
  • Discussed whether we could work together with Gil's team where there is already expertise in FHIR modeling
• Briefly discussed the agenda for the Chicago WGM (Amnon sent out a draft to the active members)

Proposed Agenda

• Review and approve Notice of Intent to Ballot(s) for Sept
• Review and approve SAIF addition to Mission and Charter
• Host PHER members sponsoring the PSS CDA Implementation Guide for Ambulatory Healthcare Provider Reporting to Central Cancer Registries - This work includes genetics and family history, and the data is used downstream for genomic discovery. We've asked to be a co-sponsor; however looking at their time line, it looks like the work is already complete. This may mean the only way to contribute is through the ballot in Sept.
• FHIR for genetic observation
• DAM and DIM
• Family History

Attendees

• Amnon Shabo, Siew Lam, Bob Freimuth, Mollie Ullman-Cullere, Austin Kreisler, Hector Cintron, Scott Bolte, Mark Roche, Wendy Scharber, Atanu Sen

Draft Minutes

• Voted affirmative to submit NIBs for the Clinical Sequencing DAM and CG DIM
• Mollie went through the current DAM document
• Amnon commented that the v2 message structure should appear in a chapter that reviews existing CG specs, rather as a domain information model

Proposed Agenda

• Voting on the mission & charter document

Attendees

• Amnon Shabo, Grant Wood, Siew Lam, Bob Milius, Bob Freimuth, Larry Babb, Kathleen Rossello

Draft Minutes

• Discussed family health history in the context of privacy of the family members
  • Kathleen thought security, privacy, consent of family members must be included in the standards
• Discussed mission & charter
  • Kathleen thought this document should include explicit mentioning of security, privacy, consent and ethics in general
• Voted and approved the mission & charter
• Decided to schedule a separate call on privacy of the family members
• Based on that discussion, a revision of the mission & charter might be discussed
• Decided to devote the next calls to developing the DAM and DIM towards its submission to ballot

Proposed Agenda

• Updating mission & charter and DMP documents

Attendees

• Amnon Shabo, Scott Bolte, Grant Wood, Siew Lam, Mollie Ullman-Cullere, Lloyd McKenzie

Draft Minutes

• Discussed and revised the the mission & charter document
• Decided to the mission & charter document to the group mailing list and vote on it during next week call
• Discussed and revised the SWOT document

Proposed Agenda

• DAM, DIMs

Attendees

• Amnon Shabo, Scott Bolte, Siew Lam, Mollie Ullman-Cullere, Larry Babb, Bob Milius, Bob Freimuth

Draft Minutes

• Approved the draft minutes of the Phoenix WGM, May 2014
• Family Health History DIM discussion
  • consider having a proband class
  • change Relative to Relationship
  • Add causeOfDeath attribute to the Family Member
  • Double check against the core minimal data set
  • Consider having clinical observations represented separately and not through the Clinical Genomics Statement
    • The current modeling of the CGS allows having phenotype observations not associated with genomic observations
  • Consider representing the Risk Assessed using a Clinical Genomics Statement instance
    • Could create confusion
    • a tension between a simpler model and clarity to the model reviewer/implementer

Proposed Agenda

• FHIR PSS

Attendees

• Amnon Shabo, Scott Bolte, Grant Wood, Bob Milius, Bob Freimuth, Mollie Ullman-Cullere, Lloyd McKenzie

Draft Minutes

• Mollie went through the genetic observation resource proposal
• Amnon asked that CDA GTR will be added to the proposal, along with the v2
• Scott went through the genetic family history profile proposal
• Lloyd went through the change proposals for the current family history profile
• Change proposals were approved except for the addition of a pointer to medical records of a patient's relative, which needs further discussion
  • Amnon: should we prepare a consent placeholder along with that pointer?
• Next week - DAM and DIM

Proposed Agenda

• FHIR PSS

Attendees

• Amnon Shabo, Scott Bolte, Siew Lam, Bob Milius, Grant Wood, Mollie Ullman-Cullere, Ruby

Draft Minutes

• FHIR PSS was discussed, revised and approved
• Lam will contact Laura Heermann Langford with regard to the suggested joint meetings in Chicago