CG Working Group Meeting Minutes

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Contents

2017

HL7 WGM San Diego Sep 2017

link to PDF file

File:Clinical Genomics WGM - Sep 2017 San Diego.pdf

HL7 WGM Madrid Spain May 2017

Return to: WGM Minutes > 2017 > May Madrid

link to minutes

HL7CG_WGM_May2017_Madrid_Minutes

HL7 WGM San Antonio January 2017

Return to: WGM Minutes > 2017 > January San Antonio

link to PDF file

HL7CG_WGM_January2017_SanAntonio_Minutes.pdf


2016

HL7 WGM Baltimore September 2016

Return to: WGM Minutes > 2016 > September Baltimore

link to PDF file

HL7CG_WGM_September2016_Baltimore_Minutes.pdf


HL7 WGM Montreal May 2016

Return to: WGM Minutes > 2016 > May Montreal

link to PDF file

HL7CG_WGM_May2016_Montreal_Minutes.pdf


HL7 WGM Orlando January 2016

Return to: WGM Minutes > 2016 > January Orlando

Tuesday, Q1: Introductions, Planning, Preparation

Attendees:

  • Gil Alterovitz, Boston Children's Hospital (co-chair)
  • Bret Heale, University of Utah
  • Mary Kennedy, College of American Pathologists
  • Carolyn Knapik, College of American Pathologists
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Clem McDonald, NLM
  • Terry McDonnel, Syapse
  • Bob Milius, NMDP (presiding co-chair)
  • Elizabeth, Newton Kaiser
  • Viet Nguyen, Systems Made Simple
  • Jared Nichols, Wolters Kluwer Health
  • Kevin Power, Cerner
  • Amnon Shabo (Shvo), Philips (co-chair)
  • Jeremy Warner, Vanderbilt/ASCO
  • Jiawyun Yang, HFUT
  • Heming Yao, Boston Children's Hospital
  • Xiaojia Yu, Boston Children's Hospital

Discussion:

  • Introductions
  • Review Agenda
  • Review of Clinical Genomics activities for newcomers
  • Review of external efforts
    • ClinGen/NCBI Allele Registry - neither Larry nor Bob F were available to give an update
    • GA4GH - nothing new to report
    • IOM - Grant will give update later this week
    • CAP - biomarkers committee,
    • Structured data capture - SDC had a FHIR connectathon track
    • ASCO - Jeremy will send update - article/video, now officially supporting FHIR
  • Review and Planning of Roadmap for CG Workgroup
    • open discussion of balancing all the things we want/need to do vs resources
    • limited number of members who have time/expertise to work on projects.
    • continue this conversation throughout the meeting

Tuesday, Q2: BRIDG, DAM, DIM, GTR Roadmap

Attendees:

  • Gil Alterovitz, Boston Children's Hospital (co-chair)
  • Bret Heale, University of Utah
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Terry McDonnel, Syapse
  • Bob Milius, NMDP (presiding co-chair)
  • Elizabeth Newton, Kaiser
  • Kevin Power, Cerner
  • Amnon Shabo (Shvo), Philips (co-chair)
  • Jeremy Warner, Vanderbilt/ASCO
  • Jiawyun Yang, HFUT
  • Heming Yao, Boston Children's Hospital
  • Xiaojia Yu, Boston Children's Hospital
  • Robert Freimuth, Mayo Clinic
  • Grant Wood, Intermountain

Discussion:

  • BRIDG - http://wiki.hl7.org/index.php?title=BRIDG
    • Bob M. reported BRIDG activities
    • comments relating to genetics from last BRIDG ballot are posted on the BRIDG wiki
    • BRIDG WG is asking CG to read and make comments
    • This is for preparation for their next ballot in May
      • Note from Bob M. after meeting: Molecular Biology subdomain will be out of scope for next BRIDG ballot, but they still want comments from CG
  • DAM -
    • Bob showed how to find DAM doc on the HL7 site. Opened for review.
    • Gil and Mollie have been working to include new material.
    • discussed different DAMs that are in our project page
    • we need to prune and or consolidate, incorporate new work
    • should we consolidate DAM and DIM?
      • reconsider this after evaluation & consolidation
  • DIM - Amnon
    • Goal is to have a conceptual information model with which all standard specifications could be semantically aligned
    • The DIM reflects the information requirements in the DAM and show the relations between the various data items
    • Briefly presented the principles reflected in the current DIM, as described in the model walk-through (e.g., explicit many-to-many association of genomic observations and phenotype, distinguishing between observed phenotypes and others that are used for interpretation, prediction, etc., the semantics in the association class, the approach to raw data, etc.)
    • Overview of modeling approach was provided, following the OMG Model-driven methods (which HL7 follows and are described in the SAIF spec), that is, developing conceptual models that can be derived to logical models and possibly to specifications of data sent across the wire
    • presented DIM, and focused on the Clinical Genomics Statement model, which is one of a few models included in the DIM; therefore - the DIM is not necessarily one monolithic model, and in addition it is developed as top-down effort, but at the same time it is informed from lessons learned in trial implementations of standard specifications
    • use of DIM is to check implementations (eg FHIR) against the larger view; decide which to include and exclude
  • GTR roadmap
    • we could take published GTR implementation guide and port it into a FHIR Profile over the Composition Resource (possibly with extensions if needed)
  • Action
    • Gil will lead group effort to evaluate current DAM products and work to consolidate new material into a single DAM
    • Amnon will work on broadening DIM into a more general model with fewer if any attributes, or with less technical specifications of the attributes than it is now, in order for it to be flexible enough as a focal point of semantic alignment.
    • Glossaries (at a minimum) will be created for DAM (use cases) and DIM with concepts defined and used as a foundation for harmonization. Bob F. will lead this effort.
    • After the above actions are taken, we will decide whether or not we should merge the DAM and DIM.

Tuesday, Q3: FHIR Connectathon Review; Family History

Attendees:

  • Gil Alterovitz, Boston Children's Hospital (co-chair)
  • Huangin Dai, Boston Children's Hospital
  • Robert Freimuth, Mayo Clinic
  • Bret Heale, University of Utah
  • Jocelyn Keegan, Navinet
  • Mary Kennedy, College of American Pathologists
  • Carolyn Knapik, College of American Pathologists
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Clem McDonald, NLM
  • Terry McDonnel, Syapse
  • Bob Milius, NMDP (presiding co-chair)
  • Elizabeth Newton, Kaiser
  • Viet Nguyen, Systems Made Simple
  • Jared Nichols, Wolters Kluwer Health
  • Kevin Power, Cerner
  • Amnon Shabo (Shvo), Philips (co-chair)
  • Yunuri Wang, Intellegent Medical Objects
  • Jeremy Warner, Vanderbilt/ASCO
  • Grant Wood, Intermountain
  • Jiawyun Yang, HFUT
  • Heming Yao, Boston Children's Hospital
  • Xiaojia Yu, Boston Children's Hospital

Discussion:

  • FHIR Connectathon Review
    • presentation update
    • 9 attendees
    • fhirgenomics.com
    • 100+ attendees at webinar
    • downloadable virtual machine, had app creation feature
    • did before/after surveys (results in presentation)
    • send Gil info about any pilots so they can be included in ONC report
    • connectathon growth may be a problem in the future - changes likely
  • Family History
    • Viet gave recap of Clinical Connectathon in Atlanta, worked with Scott B on family history use case.
    • Grant - https://genomicsandhealth.org/working-groups/clinical-working-group,
      • Family History Tool Inventory - excel spreadsheet;
      • Statement of best practices - living document, review of current practices about family history in clinical practice; about 5 pages right now
      • available in GA4GH website
      • will map to FHIR profile and send to Kevin Hughes as pilot

Tuesday, Q4: V2 & LOINC; Concurrent Joint with Patient Care (PC is hosting)

Attendees:

  • Gil Alterovitz, Boston Children's Hospital (co-chair)
  • Lorraine Constable, Constable Consulting
  • Huangin Dai, Boston Children's Hospital
  • Robert Freimuth, Mayo Clinic
  • Bret Heale, University of Utah
  • Yan Heras,
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Clem McDonald, NLM
  • Terry McDonnel, Syapse
  • Bob Milius, NMDP (presiding co-chair)
  • Elizabeth Newton, Kaiser
  • Andrea Pitkus, Intelligen Medical Objects
  • Kevin Power, Cerner
  • Dan Rutz, Epic
  • Daniel Vreeman, Regenstrief
  • Grant Wood, Intermountain
  • Jiawyun Yang, HFUT
  • Heming Yao, Boston Children's Hospital
  • Xiaojia Yu, Boston Children's Hospital

Discussion:

  • V2 & LOINC
    • Clem sent out updated documents
    • Presented slide deck (Bob sent slides to listserv)
    • Dan Rutz(EPIC) is working on similar but orthogonal effort.
    • Motion - CG will accept primary stakeholder role for this PSS, if offered from OO
      • Abstain: David Kreda, Dan Rutz
      • Nays: 0
      • Yeas: rest (to be filled)
      • Motion passed
  • Joint Meeting with Patient Care
    • There was also a joint meeting hosted by Patient Care that some of the CG members (not listed) above attended
    • focused on negation modeling
    • triggered by long-standing problems under negation
    • no specific CG discussion/problem
    • collective agreement about problem space.
    • current implementations that describe negation are not consistent
    • set aside goal (implementation) - too much disagreement
    • identify categories
    • voted and agreed to develop PSS to initiate analysis of problem space
    • explicit vs implicit negatives
    • AMIAs NLP work group has done a lot of work in this area

Wednesday, Q1: Test Script by Aegis.net; FHIR - future work

Attendees:

  • Gil Alterovitz, Boston Children's Hospital (co-chair)
  • Huangin Dai, Boston Children's Hospital
  • Richard Ettema, Aegis.net
  • Robert Freimuth, Mayo Clinic
  • Bret Heale, University of Utah
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Clem McDonald, NLM
  • Terry McDonnel, Syapse
  • Bob Milius, NMDP (presiding co-chair)
  • Elizabeth Newton, Kaiser
  • Andrea Pitkus, Intelligent Medical Objects
  • Kevin Power, Cerner
  • Amnon Shabo (Shvo), Philips (co-chair)
  • Heming Yao, Boston Children's Hospital
  • Xiaojia Yu, Boston Children's Hospital

Discussion:

  • Test scripts, Richard Ettema (Aegis.net)
    • presentation will be uploaded to the HL7 site
    • free
    • scripts are in XML
    • evaluatie servers for conformance and function
    • Steps:
      • register
      • create organization or become a member of a current one
      • define a test system
      • test setup
    • Amnon commented that no data requirements were tested and that should have the highest priority, e.g., the fact that Sequence.type is required (has cardinality of [1..1]) and has a value set should first be tested
  • FHIR – future work, e.g., sequence resource
    • Gil presented current state and potential future work
    • Bob M. reminded that the WG vote to include the new work (sequence resource and other profiles) was just for the purpose of the connectathon for evaluation.
    • We must decide as a group whether or not the current specification is sufficient for inclusion into the next STU and what changes if any need to be included.
    • Bob M. suggested forming a separate sub-group focused on FHIR
      • motion made by Bret, seconded by Lam, no abstains, no nays, motion passed
      • Bob recommended that Gil lead this sub-group. Goal is to gather evaluation of the specification vetted in the connecthon, suggest changes if any, prepare for next STU.
  • Reference sequences
    • we did not have time to get to this

Wednesday, Q2: Joint with CDS (CG Hosting); concurrent with Joint with OO (OO Hosting)

Attendees:

  • Muhammad Asim, Philips
  • Huangin Dai, Boston Children's Hospital
  • Guilherme Del Fiol, University of Utah
  • Robert Freimuth, Mayo Clinic
  • Peter Haug, Intermountain
  • Bret Heale, University of Utah
  • Robert Jenders, UCLA
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Clem McDonald, NLM
  • Terry McDonnel, Syapse
  • Elizabeth Newton, Kaiser
  • Kevin Power, Cerner
  • Amnon Shabo (Shvo), Philips (co-chair)
  • Howard Strasberg, Wolters Kluwer Health
  • Grant Wood, Intermountain
  • Heming Yao, Boston Children's Hospital
  • Xiaojia Yu, Boston Children's Hospital

Discussion:

  • CG hosting Clinical Decision Support to discuss Infobutton
    • main action item: decision to move forward with ad hoc calls between CDS and CG to determine the level of action required.
    • further specification of gaps and roadmap requested.
    • Siew Lam, Guilherme Del Fiol and Bret Heale will work together to refine simple case of Problem list and document prior to ad hoc calls.
  • There was also a concurrent Q2 joint meeting hosted by OO
    • Bob M. and Gil Alterovitz attended as CG representatives
    • Bob M. presented V2 lite background and relayed CG’s agreement to accept primary stakeholder role for PSS
    • OO voted to transfer to CG
    • need to harmonize V2 IG with OO updated guides
    • we will invite OO to join in future call(s) to work on V2
    • need to send Clem’s slides to OO
    • Gil presented FHIR work
    • CG will invite OO to new FHIR subgroup meetings

Wednesday, Q3: Leftover topics; WB business & planning; Deadlines

Attendees:

  • Gil Alterovitz, Boston Children's Hospital (co-chair)
  • Huangin Dai, Boston Children's Hospital
  • Robert Freimuth, Mayo Clinic
  • Bret Heale, University of Utah
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Clem McDonald, NLM
  • Terry McDonnel, Syapse
  • Bob Milius, NMDP (presiding co-chair)
  • Viet Nguyen, Systems Made Simple
  • Kevin Power, Cerner
  • Amnon Shabo (Shvo), Philips (co-chair)
  • Grant Wood, Intermountain
  • Xiaojia Yu, Boston Children's Hospital

Discussion:

  • Leftover topics
    • IOM report from Grant
      • DIGITizE - minimum participation requirements/elements for pilot teams
      • how to include genomic information into the EMR
      • developed implementation guide
        • developed in large part by Larry Babb;
        • pharmacogenomics use cases
        • HL-B*57:01 testing, abacavir hyoersensitivity;
        • TPMT metabolizer
        • V2 message, based on CG IG for V2
      • Team includes reps from EHR vendor, health care provider, & lab
      • Self-organizing
      • does not include electronic test ordering
      • guide includes pre-pilot checklist; high-level expectations, etc
      • shared with IOM WG on monday - very fresh
      • uses CPIC codes
      • Clem asked if the results can be generalizable - Yes
    • Variation nomenclature/syntax WG position document
      • HL7 product and/or published manuscript
      • It should at least be a standalone HL7 artifact that reflects the opinion of the CG workgroup and so we need to create a PSS.
      • Bob F will lead this


  • Report back from joint meetings (PC & OO)
    • see joint reports from Tue Q4 and Wed Q2 above.


  • WG business and planning
    • WG health - we are green, but have been lacking in three areas
      • WG not partcipated nor sent notice of review to Harmonization list
      • Work Group had < 50% representation at SD calls or e-votes) since last WGM
      • Work Group did not cast a vote for their Steering Division co-chair in annual election
    • SWOT (<2yrs), Mission & Charter (<3yrs), DMP (<3yrs)
      • The last time these were approved was Sep 2014
      • We need to review these so that they are ready when needed. Next one is SWOT due in Sep of this year.


  • Deadlines
    • May WGM Room Requests - Due Friday, January 22, 2016
    • we will request same room slots, plus Mon Q4 and Thu Q1
    • WGM Minutes must be posted by January 29, 2016
    • Must submit PSS to PMO and Steering Division - February 1, 2016
      • must obtain Steering Divisions and TSC approval before the ballot opening date of April 3rd
      • Please use the latest version of the Project Scope Statement template (i.e. v2015.1), available at:
      • www.HL7.org > Resources > Templates > Project Scope Statement and Project Approval Process
      • (http://www.hl7.org/permalink/?ProjectScopeStatement)
    • Submit Notice of Intent to Ballot - February 21, 2015
    • FHIR deadlines - TBD
    • Co-chair election in May
      • Fri 2/12 - Deadline to notify HQ of additions/changes/corrections to co-chair openings - Amnon’s term is up in may
      • Wed 2/17 - Call for nominations
      • Fri 3/18 - Nominations close at 5:00 p.m. ET
      • Fri 4/01 - Co-chair statements due by 5:00 p.m. ET
      • Wed 4/06 - Co-chair statements e-mailed to membership

Wednesday, Q4: Joint with FHIR (CG is hosting)

Attendees:

  • Gil Alterovitz, Boston Children's Hospital (co-chair)
  • Sung Chun Bae, IHIS Research Center
  • Huangin Dai, Boston Children's Hospital
  • Robert Freimuth, Mayo Clinic
  • Grahame Grieve, Health Intersections
  • Bret Heale, University of Utah
  • Il Kon Kim, KNU
  • David Kreda, HMS Consultant
  • Siew Lam, Intermountain (co-chair)
  • Joshua Mandel, Boston Children's Hospital
  • Terry McDonnel, Syapse
  • Lloyd McKenzie, Grevity
  • Bob Milius, NMDP (presiding co-chair)
  • Elizabeth Newton, Kaiser
  • Viet Nguyen, Systems Made Simple
  • Dennis Patterson, Cerner
  • Vadim Peretokin, NEHTA
  • Kevin Power, Cerner
  • Amnon Shabo (Shvo), Philips (co-chair)
  • Joon Hyun Song, IHIS Research Center
  • Grant Wood, Intermountain
  • Xiaojia Yu, Boston Children's Hospital

Discussion:

  • FHIR joint meeting (CG is hosting FHIR)
    • Connectathon Review
      • Gil gave overview of the connectathon - slides to be made available
    • FHIR and genomics
      • discussed mataturity levels of resources
      • The motion that was passed in the Nov 3, 2015 CG call is "The Orlando FHIR connectathon in Jan 2016 will include a FHIR resource and/or profile that will include the Sequence Resource being developed by Gil."
        • There was a question about what this means for including the sequence resource in the next STU.
        • New FHIR subgroup will go through technical evaluation of sequence resource and associated profiles based on experiences in the Connectathon and other testing.
        • Questions of whether sequence resource should be renamed (it's really more than a sequence) or refactored (perhaps variation should be a profile of sequence?), or both, and whether the semantics are aligned with our DIM/DAM. Being aligned to one doesn't necessarily mean it's aligned to both.
        • Gil showed the Medication Resource as an example of the kind of metatdata that is associated with other resources.
      • Amnon argued that the current FHIR Sequence Resource as a 'mixed bag' because it has a mixture of the following: pointers to individual and reference sequences persisted in some repositories, variants found, allele frequencies, copy number, etc. To the meet the criteria of adding a new resource to FHIR, it's better if its scope is solely a wrapper to individual's sequence. Reference sequences and variants found by comparing to those references should be handled separably. Amnon reiterated his general comment that Sequence is too specialized to be a Resource and some base genomic observation should have been the resource, having properties/attributes common to all genomic observation (e.g., location).
    • FHIR and family history
      • we did not have time for this discussion

2015

HL7 WGM Atlanta October 2015

Tuesday, Q1: Introductions, Planning, Preparation

Attendees:

  • Bob Milius, NMDP
  • Siew Lam, Intermountain
  • Scott Bolte, GE Healthcare
  • Bob Freimuth, Mayo Clinic
  • Grant Wood, Intermountain
  • Bret Heale, U of Utah
  • Amnon Shabo (Shvo), Philips
  • Elizabeth Newton, Kaiser
  • Gil Alterovitz, BCH-HMS
  • Lauralee Barret, Duke School of Nursing

Discussion:

  • Introductions
  • Review Agenda for this WGM
  • Bret Heale spoke about Infobutton
    • www.openinfobutton.org
    • lite.bmi.utah.edu/OpenInfobuttonDemo.html

Tuesday, Q2: Infobutton, DIM/DAM

Attendees:

  • Bob Milius, NMDP
  • Siew Lam, Intermountain
  • Scott Bolte, GE Healthcare
  • Bob Freimuth, Mayo Clinic
  • Grant Wood, Intermountain
  • Bret Heale, U of Utah
  • Amnon Shabo, Philips
  • Elizabeth Newton, Kaiser
  • Gil Alterovitz, BCH-HMS
  • Lauralee Barret, Duke School of Nursing
  • Brian Pech, Kaiser Permanete
  • Viet Nguyen, Systems Made Simple

Discussion:

  • Brett continued with Infobutton presentation
  • DIM/DAM
    • Amnon reviewed the DIM
    • Clinical Genomic Statement - Core principles
      • explicit representation of a ‘genotype-phenotype’ association
      • many-to-many relationship; one genotype may have many phenotypes; one phenotype may be associated with many genotypes
    • Brett — Can the infobutton be used to inform the Clinical Genomic Statement?
    • Amnon - not the CGS itself, but an instantiation of it.
    • Genotype-Phenotype association similar to assertions/provenance in ClinGen data model
      • For a future CG weekly call; invite Larry to talk about ClinGen model and discuss how it relates to the DIM

should include Method of how association was created.

      • We should do this for the GA4GH model as well (determine how it relates to the DIM)
    • Lam - we need to talk about terminology binding
      • Amnon - look into terminfo (based snomed, which is based on cononical forms)
      • Saying we want to do post-coordination is good, how we do it is not clear
      • SNOMED and LOINC don’t provide a framework for this.
      • Should we give guidance to SNOMED to support this?
      • Bob F - difficult question, ClinGen is exploring this, can we push this down the road? Can we start developing FHIR resources without this?

Tuesday, Q3: IOM discussion

Attendees:

  • Bob Milius, NMDP
  • Siew Lam, Intermountain
  • Scott Bolte, GE Healthcare
  • Bob Freimuth, Mayo Clinic
  • Grant Wood, Intermountain
  • Bret Heale, U of Utah
  • Amnon Shabo (Shvo), Philips
  • Elizabeth Newton, Kaiser
  • Gil Alterovitz, BCH-HMS
  • Viet Nguyen, Systems Made Simple
  • M'Lynda Owens, Cognosante


Discussion:

  • Joint with AP - cancelled
  • FHIR & Family History - Grant/Gil

Tuesday, Q4: FHIR Sequence Resource

Attendees:

  • Bob Milius, NMDP
  • Siew Lam, Intermountain
  • Scott Bolte, GE Healthcare
  • Bob Freimuth, Mayo Clinic
  • Grant Wood, Intermountain
  • Bret Heale, U of Utah
  • Amnon Shabo (Shvo), Philips
  • Gil Alterovitz, BCH-HMS
  • Viet Nguyen, Systems Made Simple
  • M'Lynda Owens, Cognosante
  • Daniel Vreeman, Regenstrief
  • Martin Madera, AJCC
  • Yan Heras, Independent

Discussion:

  • FHIR – future work, e.g., sequence resource - Gil
    • Gil presented a proposed Sequence resource that would replace the Standard Profile for Genetics
    • Includes not only sequence information, but also other info as well.
    • Some thought we were trying to fit too much into this single resource and that a sequence resource should be smaller in scope. Maybe it's name should be changed.
    • Next FHIR connectathon may have a Genetics component

Wednesday, Q1: Joint with BRIDG WG

Attendees:

  • Bob Milius, NMDP
  • Siew Lam, Intermountain
  • Scott Bolte, GE Healthcare
  • Bob Freimuth, Mayo Clinic
  • Grant Wood, Intermountain
  • Bret Heale, U of Utah
  • Amnon Shabo (Shvo), Philips
  • Gil Alterovitz, BCH-HMS
  • Diane Wold, CDISC
  • Ulrike Wagner, FNLCR
  • Smita Hastak, Samvit Solutions
  • Edward Helton, NCI
  • Bill Friggle, Sanofi
  • Wendy Ver Hoef, Samvit/NCI
  • John Kiser, ABBVIE
  • Panagiotis Telonis, EMA
  • Lise Stevens, FDA
  • Clem McDonald, NLM

Discusion

  • Bob - intro to BRIDG
    • bridgmodel.org
  • Smita - summary of BRIDG Comments
  • BRIDG was focused on protocol driven research, with the integration of LSDAM the scope was expanded, but we can’t boil the ocean

There is a need to reign it in.

  • Modeling by reference: e.g., DICOM/Imaging, for molecular biology may refer to CG DIM/DAM, ClinGen model, GA4GH, etc
  • Amnon - what is the long term goals of BRIDG?
  • CG DIM is not implementable, it informs the implementation
  • BRIDG has both layers, includes semantics; mostly a conceptual model, but has many logical features.
  • Question about controlled vocabularies
    • how to design a model so that once a vocabulary is bound, it doesn’t change the model.
    • Bob F: binding to vocabularies is essentially modeling by reference.
  • ToDo for BRIDG: Set up HL7 wiki for addressing ballot comments, even though negative comment were withdrawn, they still need to be addressed.

Wednesday, Q2: Joint with OO

Attendees:

  • recorded by OO

Discusion

  • hosted by OO, minutes recorded by them.
  • Bob reported
    • the publication of Standar Profile for Genetic (profile of Observation) which was published in FHIR DSTU2
    • first draft of Sequence Resource developed by Gil
      • OO wants to be included in the modeling of the resource. Asked if they should set up a modeling call, or if we'll inform them. Bob said CG will arrange it once CG has taken a close look at the first draft.

Wednesday, Q3: LOINC, General Business

Attendees:

  • Bob Milius, NMDP
  • Siew Lam, Intermountain
  • Bob Freimuth, Mayo Clinic
  • Grant Wood, Intermountain
  • Bret Heale, U of Utah
  • Amnon Shabo (Shvo), Philips
  • Elizabeth Newton, Kaiser
  • Gil Alterovitz, BCH-HMS
  • Clem McDonald, NLM

Discusion

  • Clem McDonald
    • getting info from instrument vendors.
    • Need position statement from CG on what gets sent. Not only the narrative, but also minimal structured data.
    • Asked if he was looking for a "HL7 v2 genomics report lite." Clem replied that would be great.
    • Clem said he would write something up for possible endorsement by CG.
  • Business meeting - discussed deadlines coming up.

Wednesday, Q4: Joint with FHIR

Attendees:

  • Bob Milius, NMDP
  • Siew Lam, Intermountain
  • Scott Bolte, GE Healthcare
  • Bob Freimuth, Mayo Clinic
  • Grant Wood, Intermountain
  • Bret Heale, U of Utah
  • Amnon Shabo (Shvo), Philips
  • Elizabeth Newton, Kaiser
  • Gil Alterovitz, BCH-HMS
  • Clem McDonald, NLM
  • Viet Nguyen, Systems Made Simple
  • Daniel Vreeman, Regenstrief
  • Dennis Patterson, Cerner
  • Michelle Miller, Cerner
  • Grahame Grieve, Health Intersections
  • Josh Mandel, BCH
  • Senthil Nachimuthu, 3M

Discusion

  • Joint with FHIR
  • We may want to schedule our joint meeting earlier in Orlando - connect with lloyd
  • Orlando FHIR Connectathon
    • CG was just introduce to Gil's draft of a Sequence Resource and the group still has questions about it
      • Can we have "bake off" during the Connectathon - Gil's Sequence resource vs Genetic profile vs alternative?
      • Yes, we can do that.
    • Logistics
      • 100 members at capacity at Connectathon
      • we need to be looking for upcoming deadlines
      • need to have materials and use cases ready
  • Bob M questioned Sequence Resource structure
    • thought it tried to do too much and that it was much more than a sequence.
    • described an "80/20" rule for the CG group as it tries to fit what it does with the whole of Clinical Genomics outside of HL7.
    • what are our "80" that we can help standardize on?
    • Showed the kind of information that NMDP sends in HML.
    • Gil added HLA specific data structures to Sequence Resource, Bob M will evaluate it.

2014

HL7 WGM San Antonio January 2014

Tuesday, Q1: Introductions, Planning, Preparation

Attendees:

  • Scott Bolte, GE Healthcare
  • Howard Strasberg, Wolters Klewer
  • Bob Milius, National Marrow Donor Program
  • Grant Wood, Intermountain Healthcare
  • Siew Lam, Intermountain Healthcare
  • Clem McDonald, National Library of Medicine
  • Remote attendance:
    • Amnon Shabo (Shvo), IBM Haifa Research Lab
    • Mollie Ullman-Cullere, Dana Farber

Discussion:

  • Mollie will lead discussion with A/P in Q4.
    • Will include work shes doing on cancer biomarkers and work being done with CAP (College of Anatomical Pathologists)
    • Looking to LOINC for NextGen sequencing codes
  • Marrow donor needs
    • HLM - Histoimmunogenetics Markup Language
    • Need to accommodate existing HML user base conventions
    • Looking to incorporate into CDA narrative parts
    • Might translate or encapsulate into structured data part of CDA

Tuesday, Q2: FHIR Knowledge Sharing

Attendees:

  • Scott Bolte, GE Healthcare
  • Howard Strasberg, Wolters Klewer
  • Bob Milius, National Marrow Donor Program
  • Chuck Swegle, GE Healthcare
  • Phil Pochon, Covance
  • Siew Lam, Intermountain Healthcare
  • Clem McDonald, National Library of Medicine

Discussion:

  • Much discussion about the FHIR tutorials (available at GForge) and the FHIR connectathon
  • Grahame's test server is at http://hl7connect.healthintersections.com.au/open. It is both a FHIR endpoint and a web server. As such, it is a great learning resource to explore the resources, searches, and sample RESTful URLs.
  • FHIR profiles can both constrain and extend a resource.
  • Constraints are implemented using XPath. Can enforce complex criteria such as maternal cousins being invalid when the mother is an only child.
  • Not clear if HL7, or HL7 working groups, will take on the role of endorsing or approving profiles. If so, could end up with multiple tiers of profiles: HL7 core, HL7 approved, 3rd party.
  • Providers, vendors, or even governmental bodies could have their own FHIR servers with their own FHIR profiles that their constituents could use.
  • Clem demonstrated a JavaScript package, developed by the NLM (National Library of Medicine), that allows exploration of coding systems. Could complement the pedigree work provided by the Surgeon General's My Family Health Portrait web site.

Tuesday, Q3: GTR, New, merged CG Domain Analysis Model

Attendees:

  • Scott Bolte, GE Healthcare
  • Bob Milius, National Marrow Donor Program
  • Grant Wood, Intermountain Healthcare
  • Siew Lam, Intermountain Healthcare
  • Amnon Shabo, IBM (remote)


Discussion:

  • Free form discussion about the Clinical Genomics Clinical Statement; an evolving document circulated multiple times by Amnon to the CG distribution list over the last month, aimed at be part of a standards-independent Domain Information Model (suggested as a new project to DESD).
  • Discussed how the CG Clinical Statement could/would map to FHIR. Since both use UML style cardinality, external code sets, aggregation & reference, it was thought to be feasible.

Tuesday, Q4: Joint with A/P

Attendees:

  • John David Nolen, Cerner
  • Victor Brodsky, Weill Cornell Medical College
  • Joe Birsa, GE Healthcare
  • Scott Bolte, GE Healthcare
  • Bob Milius, National Marrow Donor Program
  • Grant Wood, Intermountain Healthcare
  • Siew Lam, Intermountain Healthcare
  • Phil Pochon, Covance
  • Amnon Shabo, IBM (remote)
  • Mollie Ullman-Cullere, Dana-Farber Cancer Institute (remote)
  • Jeff Knapp (remote)

Wednesday, Q1: Family History

Attendees:

  • Scott Bolte, GE Healthcare
  • Bob Milius, National Marrow Donor Program
  • Robert Worden,
  • Grant Wood, Intermountain Healthcare
  • Phil Pochon, Covance
  • Mollie Ullman-Cullere, Dana-Farber Cancer Institute (remote)

Discussion:

  • Talked about FH (Family History) and upcoming Q4 meeting with Lloyd.
    • Need to identify sources of sample data, covering diverse clinical situations.
    • CAP, NMDP were both identified as potential sources.
    • Hughes Risk Apps, as the leading commercial adopter of the V3 FH, should also be consulted.
    • The approved | V3 Implementation Guide clearly should be used.
  • Intermountain is working with Cerner on their family history and genomic capabilities.
    • Meetings are slated for February. Not sure if they will be open to external, interested parties.
    • Mark Hoffman, who has worked with the HL7 CG work group in the past, is still involved in Cerner's genomic efforts.

Wednesday, Q2: Joint w/O&O, AP, II

Wednesday, Q3: Project Planning and CG Roadmap

Wednesday, Q4: Joint w/FHIR

Attendees:

  • Scott Bolte, GE Healthcare
  • Bob Milius, National Marrow Donor Program
  • Lloyd McKenzie, HL7 Canada
  • Jeffery Ting, Systems Made Simple
  • Lee Unangst, Academy of Nutrition and Dietetics
  • Kay Howarter, Academy of Nutrition and Dietetics
  • Grant Wood, Intermountain Healthcare
  • Steve Fine, Cerner

Discussion:

  • The FHIR Management Group has decided, after ballot reconciliation, to proceed to DSTU. That said, they are already looking to the next revisions.
    • If the CG work group wants to propose any new resources, extensions, or profiles, there is a tight schedule in order to make next January's ballot for second DSTU:
      • Notify the FHIR Management Group of intent in the next month or two.
      • Complete new resources/profiles, with examples, by August.
      • The FHIR Quality Assessment review will be done in September.
      • Ballot will be prepared and submitted by November.
    • There is a Wiki page and submission form that needs to be completed to propose any new, core resources.
    • The quality criteria for FHIR encourages at least five examples of each resource.
    • Need to clearly document why a new resource, as opposed to profiling an existing one, is necessary.
    • Breadth and depth of DSTU implementations will dictate what FHIR resources go normative.
  • Three levels of FHIR profiles:
  1. ad hoc: developed by one person or group on their own
  2. vetted: profile submitted to workgroup for modification and subsequently receives HL7 stamp of approval (whatever that means).
  3. balloted: profile is taken forward by HL7 to formal ballot for approval. Lays the groundwork for ISO et al standardization.
  • The GeneticPedigree Profile, part of the Family History FHIR Resource documentation, was developed by Lloyd using the standard V3 Family History model. It has not yet be exercises using sample data, but it's great start.
  • The FHIR build process -- taking the source code from GForge and building the documentation -- involves validating the examples against the profiles. Therefore there is high confidence that any example that is provided is well formed and valid.
    • While not in the final documentation, the build process also captures which resource elements were used when validating the examples.
    • The need for V3 style implementation guides, created independently of the V3 structure, should be reduced. The aforementioned validation of examples, and the insistence that at least five examples be provided, implies that more documentation will be available as a profile/resource is developed.
Observations, Interpretations, and Diagnostic Reports
  • The observation resource has no support for genetics at this time.
  • O&O provided persuasive feedback wrt the Observation resource at the San Antonio WGM. As a result, it's expected that it will be modified during the DSTU rev 1 period.
  • Distinction between observation and interpretation: an observation documents that someone has a specific genetic sequence (e.g., an allele of a Cytochrome P450 drug metabolizing gene). An interpretation documents expected implications of the observation (e.g., that someone will rapidly metabolize Warfarin (aka Coumadin)).
  • It is TBD if capturing sequence information, either current or Next Gen, might be an Observation resource, a DiagnosticReport resource, or something new.
V3 Family History
  • Lloyd found it odd that there would ever be an approximate date of death for the patient. It was explained that when traversing a family tree, and conducting risk assessments for each individual, one whose date of death was not known could be treated as the patient of interest. Such an undertaking is done to determine the most likely carrier for a shared family mutation.

2013

Meeting Minutes - HL7 WGM Phoenix January 2013

 Media:HL7_Clinical_Genomics_-_WGM_Phoenix_2013_Minutes.doc

2012

Meeting Minutes - HL7 WGM in Vancouver - May 2012

  • CG Monday Q3 Joint with CIC
    • Attendance: CG - Joyce and Amnon, CIC - Anita and Ed
    • M&M is in the process of coming up with some DAM guidance for HL7. It is our understanding they will be starting with the document CIC created on the subject.
    • Lloyd McKenzie is spear-heading this effort. The DAM guidance will be based on the document produced by CIC on Feb. 2011.
    • Spoke about the different projects with a focus on how the disease projects in HL7 are interfacing with the CDISC therapeutic area standards. The modeling effort in HL7 is focused on clinical and administration domains
    • Example interaction for cardiovascular standards:
    • CDISC ACS (Acute Coronary Syndrome), HL7, FDA working through C-PATH (funded by Gates Foundation) work on identifying disease data end points and DAMs.
    • Subsequently these end-points are presented to the CDISC SDS team for inclusion into the standard.
    • HL7 WGM Vancouver May 2012


  • Tues Q3
    • Attendance: Amnon Shabo, Bob Milius, Jill Kaufman, Joyce Hernandez, Phil Pochon, Grant Wood
    • Jill suggests that the CG WG consider doing a CME tutorial at the next WGM in Baltimore.
    • Amnon reviews the agenda.
    • Joyce suggests we get AP more involved in Omics DAM development.
    • Amnon gives a quick description of the new HL7 initiative called FHIR.
    • A deeper discussion is scheduled for Wed Q2.
    • Amnon also gives a quick description of an outside effort called iPOP. A deeper discussion is scheduled for Thurs Q2.
    • He then went through a review of CG activities.
    • Joyce had a question about O&O Lab 3.0 and genetic variation. Phil shared related efforts with CDISC and RCRIM.
    • Lab V3 no research or genomics – also need to upgrade specimen semantics
    • Research labs could use V2.5.1 message
    • Sponsors might be more interested in a V3 XML solution – add clinical research concepts – study, visits, subject id etc. into O&O Lab V3 message. Unclear what is going to be used on the Research side.
    • Can we use FHIR?


  • Tues Q4
    • Attendance: Amnon Shabo, Bob Milius, Joyce Hernandez, Phil Pochon, Lisa Schick, Grant Wood
    • Amnon continued his slides on CG activities, reviewing CG CMETs and the Pedigree specification.
    • Genetic Variation - Take out specimen handling and identifiers that will be revised in the current Specimen project
    • The Phenotype CEMT model is okay since we are pointing to a separate model
    • Associated Observations are used through controlled vocabulary
    • The Pedigree model was successfully reaffirmed in HL7 balloting, with Release 2 and a US-specific Implementation Guide under development; Exchange of pedigrees in CCD was discussed; Pilots: Hughes Risk Apps and Surgeon General.
    • The V2 Implementation Guides publishing status was given by Grant. Official HL7 publishing forms have been completed, and the TSC will (likely) approve the guides at their next meeting.
    • Amnon reviewed the CG DAMs (Clinical genomics including gene expression, and clinical sequencing). Amnon concluded with a review of CG work on clinical sequencing workflows and use cases - from summary slides written by Mollie.
    • Bob presented his work on HLA tissue typing. This comes from the NMDP matching program, and interest in adopting HL7 standards (CDA GTR) to transmit and receive electronic data with transplant sites. He gave an explanation of the NMDP HLA tissue typing nomenclature version 3. Their Allele types cover up to 6 exons and 800 SNPs. Bob reviewed the NMDP gold and silver standards for reporting data. He showed how he is attempting to put this data into a CDA GTR and Genetic Variation message. They have 150,000 allele codes, but are looking for a different code format. They are looking to use GL Strings for the report, and QR codes that can take you back to the original sequence.


  • Wed Q1
    • Attendance: Amnon Shabo, Joyce Hernandez, Phil Pochon, Lisa Schick, Grant Wood
    • This was a joint meeting with O&O, II (Imaging Integration) and AP (Anatomic Pathology). AP is discussing using the same unique identifier throughout the sample collection, sample prep, lab accession, and result reporting process. They are discussing using a dumb (random number) or smart identifier (meta data, code that describes the specimen). Either way, the container is what is labeled.
    • APSR – Anatomic Pathology Structure Report is a joint IHE-HL7 AP initiative and includes 21 CDA templates (Document Content Modules) and 490 observations and procedure templates
    • The discussion then switched to some of the molecular biology work based on CAP protocols and AJCC (American Joint Committee on Cancer)
    • They are working on a design to implement "value sets" a constrained set of terminology.
    • Based on high-level requirements it seemed they wanted to have a unique identifier that corresponds to the status of the samples as it is processed: bio-specimen collection, resection, and glass slide.
    • Various techniques of associating an id to a specimen were discussed – affixing a barcode on a specimen to bar-coding the container.
    • Two current ideas regarding the specimen ids were mentioned:
      • Use of a pseudo random number
      • Building intelligence in the key. The ramification is that the key would need to appropriately be sized to handle the required built-in intelligence.
      • Specimen process is current documented in DICOM 5.17 specs which are currently informative.
      • DICOM is using OIDS to provide unique identifiers for specimens and containers.


  • Wed Q2
    • Attendance: Amnon Shabo, Joyce Hernandez, Lisa Schick, Grant Wood
    • Amnon reviewed the status of CDA GTR
      • Joyce suggested separating human and viral genomics in the Genetic Variation section.
      • Amnon describes the concept of clinical genetic statements. He suggests we consider doing dynamic binding of answer lists.
      • Amnon then reviewed what he calls the Layout Challenge (see slides in the overview presentation at our page in the HL7 main site), the question of the separation of CDA rendering and logic which CDA R2 core model cannot accommodate but style-sheets could work around this limit.
      • A motion was made to adopt GTR sections, get LOINC codes for those sections, then offer style sheets (CAP, ACMG, JMD); the motion received no objections.
      • Amnon plans to do tissue typing pilot with Bob and two transplant centers.
      • Grant plans to do a pilot with Pathology group at Intermountain, and hopefully Myriad and ARUP.
      • It was mentioned that Don Rule has also talked about doing a CDA GTR pilot on previous CG calls.
    • Family history:
      • FH in Meaningful Use Stage 2 was discussed.
      • Amnon continued slides that reviewed the Pedigree Release 2 Implementation Guide work (*** For more details, see slides in the overview presentation at our page in the HL7 main site).
      • The question of Pedigree and the new HL7 FHIR was discussed.
      • Joyce commented that the IG should show how to move from CCD to full Pedigree.
      • Stage 2 proposed rule does not require pedigree and it talks about family history for the first time.
      • EHR system structured data for the person's first degree relatives mother, father, siblings and children.
      • Meaningful Use Final rule not released and won’t be for months – expectation is that it will be available for the fall time-frame.
      • HITSP recommended use HL7 CCD to exchange data between EHR and PHR and Pedigree to exchange family history information between EHR/PHR systems and decision support applications, and portions of these recommendations are utilized in the new US guide


  • Wed Q3
    • Attendance: Amnon Shabo, Joyce Hernandez, Phil Pochon, Lisa Schick, Grant Wood, Elaine Ayers (NIH)
    • Omics DAM ballot reconciliation and comments were addressed. There was not enough time to complete this process.
    • Since the Analytic phase includes quality control information we need to expand on the data examples to ensure complete coverage.
    • Some QC areas briefly discussed:
      • Hydra well – distilled water hot plant DNA – ensure it is not corrupted.
      • Controls used in fluorescent to detect contamination. Readings are not about the subject (i.e. patient) but quality/purity of material.
      • Mechanical failure
      • need to have a complete quality profile
    • The items above were deemed part of the analytic phase.
    • Post analytic phase would focus on reporting what genes were over and under expressed and tie these readings to a medical statement about the patient.
    • Examples: classify cancer and it phenotypic effect. Correlate this disease/effect to the gene expression profile.
    • One question that came up in the discussion was whether we need a direct association from findings to "updater".


  • Wed Q4
    • Joint meeting with AP.
    • Amnon presented the collaboration with AP to harmonize the GTR and APSR.
    • Discussion centered on the specimen process.
    • The point was made that taking an image of a specimen would result in that being a specimen too in terms of tracking.
    • Requirements would include specimen attributes (e.g. role, collection date/time) and container attributes.
  • Thur Q1
    • Joint with CIC
    • The team provided updates on the various projects around disease models. They have assigned a team member to act as Project Manager or liaison (for external projects).
      • EMS - Jay
      • Cardio - Brian
      • Schizophrenia - Meredith
      • TB - Anita
      • Anesthesiology - Anita
      • Trauma - Jay
      • CG - TBD
    • CIC is focused on disease analysis models – the main exception is emergency services.
    • Abdul-Malik Shakir is the project manager for the Max Tool – a tool developed by City of Hope. It is hoped that this tool will help in exchanging UML models between modeling tools.


2010

HL7 WGM Rio May 2010

 Media:HL7_WGM_Rio_2010_as.doc

HL7 WGM Phoenix Jan 2010

 Media:HL7 CG WGM Phoenix 2010_latest.doc

2009

HL7 WGM Orlando Jan 2009

 Media:HL7_WGM_Orlando_2009_Jan15.doc

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