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May 2014 Work Group Meeting Clinical Genomics Minutes. Pheonix , AZ. HL7 Clinical Genomics workgroup HL7 May 2014 Workgroup meeting. Q1 Notes

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hl7 clinical genomics workgroup hl7 may 2014 workgroup meeting
HL7 Clinical Genomics workgroup HL7 May 2014 Workgroup meeting

Q1 Notes

  • Q1 Attendance: Siew Lam (Intermountain Healthcare), Christina Knotts (First Databank), Amnon Shabo (Haifa University), Grant Wood (Intermountain Healthcare), Bob Milius (NNDP), Scott Bolte (GE Healthcare), Mollie Ullman-Cullere (Partners Healthcare)
  • Bob Milius – voted liaison to the BRIDG working group
  • Yan Heras has withdrawn as co-chair. Grant will inform the office, so this position can be formally filled
  • Bob Milius was unanimously voted as interim co-chair of clinical genomics
  • Reminder to vote to fill the open position – Amnon running
  • Genomics England 100,000 whole genome sequencing by 2017

Q2 Notes

  • Q2 Attendance: Clem McDonald added to Q1 attendance
  • Unanimous vote - Genotype is replaced by Genetic Variation in the DIM
  • Clem recommended  define minimal dataset of structured content, with option for remaining details included in the narrative text. People are requesting LOINC codes to do this today (Lab Core).

Q3 Notes

  • Joint with AP – hosting workgroup
  • See AP minutes
slide3

Wed – Q1: Topic Family History

  • Q1 Attendance: Siew Lam (Intermountain Healthcare), Christina Knotts (First Databank), Amnon Shabo (Haifa University), Grant Wood (Intermountain Healthcare), Scott Bolte (GE Healthcare), Mollie Ullman-Cullere (Partners Healthcare)
  • Grant Wood
    • NHGRI demonstration project: Grant that Intermountain has with Duke and other organizations (informational links below). IHC will be creating a data store for HL7 compliant Pedigree/Family History data and develop an guide to inform other organizations on how to do this.
      • Dukes family history tool MeTree, which will be publically available in the future.
      • http://www.genome.gov/27554264
      • http://rt5.cceb.med.upenn.edu/public/ignite_duke.html
    • Intel: Intel is a partner with ICH’s transformation lab. This partnership will be result in the development of a data warehouse for CDS which contains clinical genetic, family history and other clinical data.

Amnon Shabo - Suggested roadmap for extension of FHIR base resource for a profile to support current Normative Pedigree/Family History model

  • Problem: Base FHIR resource is a weaker representation of family history than the CCD and Pedigree/family history and will not support personalized medicine or risk assessment
  • Solution:
    • Create a family history DIM (hopefully using FHIR tooling) which is compatible with the normative family history model
    • Build the FHIR profile compatible with normative standard and DIM
    • Amnon will lead DIM work and Scott and Lam will help with the FHIR work
  • Outstanding question:
    • Inclusion of clinical data and genetic data was accomplished through pointers to the clinical statement and genetic cmet. How should this be accomplished in FHIR??
wed q3 joint with ap ii cg and oo
Wed Q3 – Joint with AP, II, CG and OO
  • See OO minutes – hosting workgroup
  • FMG critical for id of scope for Sept deliverables
  • Definition scope move in parallel with lab
  • Reach out to John Quin regarding Gil’s work to develop baseline genetic reporting FHIR profile.
slide7

Steve Bleyl of IHC – participating in NHGRI’s Genomic Medicine Centers Meeting VI: Global Leaders in Genomic Medicine

    • For minutes presentations etc.. Go here

https://www.genome.gov/27555775

In follow-up Steve will be leading an bioinformatics IT workgroup and Grant Wood and Lam will be assisting

One of the goals will be to identify what data should be stored within the EHR.

slide8

DAM, DIM, FHIR,

    • Extend support for Genomics & BioMarkers
clingen org updates
ClinGen Org Updates
  • Project Insight Review
    • Please close the following projects:
    • Proj ID: 867
    • Name: Gene Expression
    • 752 delete
    • 729 - complete and close
    • 693 - remove
    • 663 - close successful completion
    • Amnon to investigate FH R2 PSS
      • mod or delete
    • 479 - close
    • 460 - successful completion – close
wed q4
Wed Q4

Attendance: Scott Bolte, Mollie Ullman, Grant Wood, Lloyd McKenzie, Grahame Grieve, Amnon Shabo, Siew Lam, Bob Milius, David Hay, John Carter

ToDo’s

Family History: http://www.hl7.org/implement/standards/fhir/familyhistory.html

  • PSS needed for FH- genetics pedigree profile extensions
    • Maintenance of the pedigree profile
    • Include for creation of new resources and new profiles – one PSS for each

Genetic Variation (and other genetic/genomic data)

Diagnostic Report: http://www.hl7.org/implement/standards/fhir/diagnosticreport.html

    • data/data and results/ or results
  • PSS profiles on observations for genetic variation and phenotype
  • All work done including QA guidelines - ready by Sept WGM
  • DSTU by Jan 2015 ballot – DSTU publication end March 2015
  • Send sources to Graham for prep work add EBI, Sanger
  • Get sources and panel information from Bob
  • Also profile with encapsulated sequence data for HLA
  • Get OID’s for Bob’s stuff

FH need to be able to capture civil relationships and their duration to capture marage & context of a 3rd profile

  • Resource proposals and profile proposals – FHIR management group
  • Sept meeting – Wed Q4 for Lloyd and Graham