CG WG Call Notes leading to 2014 September WGM

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September 9, 2014 -- Weekly call

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/chimera (e.g., in use cases after bone-marrow transplant), etc.
  • Somatic mutations were derived from the self genome while in post-transplant patients there are two genomes

September 2, 2014 -- Weekly call

Proposed Agenda

  • Continued discussion of FHIR extension for CG

Attendees

  • Grant Wood, Bob Milius, Scott Bolte, Mollie Ullman-Cullere, Larry Babb, and Siew Lam

Draft Minutes

  • Conversation centered on the use of 'derived' tag
  • Primary data vs. interpretation
  • --> what the physician gets it the primary data (within the EHR), downstream is the interpretive data
  • --> However, the lab will have different primary data, more upstream . Primary data is the level at which the stakeholder would revert to for a recalculation. If genomic, cDNA, Amino Acid and Allele/Common name are reported from the laboratory, uses should not use one of these elements to recalculate another, because the laboratory likely detected the mutation at one level (genomic) and made decisions at another level (amino acid change). Therefore, the mutation definition should be used in its entirety. If something is inaccurate, the test should be rerun or re-reported.
  • Derived
  • --> should not be used to tag the translation to cDNA/AA change or calculation of genomic coordinates (from cDNA). Derived should be used when the presence of a variant is assumed due to presence of another which was measured e.g. * alleles

If desire is to denote the initial context of testing, should we use ‘testing platform’ and add ‘providence’ (of the test). providence = source of the information (who e.g. ) (when) what and how

  • --> LMM’s NGS pipeline 1.0 see how it works here with link to website (e.g. BI pipeline details etc...) In the future this might be held in NCBI’s genetic test registry
  • --> Look for definition of providence and derived in FHIR

August 26, 2014 -- Weekly call

Proposed Agenda

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

Attendees

Draft Minutes

August 19, 2014 -- Weekly call

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


August 12, 2014 -- Weekly call

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


August 5, 2014 -- Weekly call

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


July 29, 2014 -- Weekly call

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


July 28, 2014 -- Special call

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


July 22, 2014 -- Weekly call

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


July 15, 2014 -- Weekly call

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

July 8, 2014 -- Weekly call

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)


July 1, 2014 -- Weekly call

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)


June 24, 2014 -- Weekly call

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


June 17, 2014 -- Weekly call

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

June 10, 2014 -- Weekly call

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


May 27, 2014 -- Weekly call

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


May 20, 2014 -- Weekly call

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


May 13, 2014 -- Weekly call

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