CG WG Call Notes leading to 2012 May WGM

Back to Agendas and Minutes.

February 21, 2012

Agenda

• Final Decisions on Intent to Ballot

February 16, 2012 -- Clinical Sequencing

Agenda

• Final Decisions on Intent to Ballot

Attendees

• Daryl Thomas; Life Technologies
• Mollie Ullman-Cullere; Partners & DFCI
• Scott Bolte; GE Healthcare
• Amnon Shabo; IBM
• Grant Wood; Intermountain
• Larry Babb; Partners
• Jesse Tennenbaum; Duke
• Don Benson; DNAnexus

Draft Minutes

• Reviewed group progress for Don Benson
• Reviewed the current workflows
• Discussed some extensions to support primary data repositories
• Discussed support for secondary uses -- research and clinical trials

February 14, 2012

Agenda

• Next steps in terms of the BRIDG Model and the LS-DAM. Discuss how to ensure alignment of genomics-related modeling activities between BRIDG, LS-DAM and the modeling work of the CDISC HL7 CG Workgroup. (Becky Kush)
• Family History Release 2
• V2 Ballot Reconciliation

February 9, 2012 -- Clinical Sequencing

Agenda

• Reconcile Workflow versions from February 2 with notes from February 7
• Extend Workflow to include steps from Lynn Bry's use cases

February 7, 2012

Agenda

• Clinical Sequencing

Attendees

• Amnon Shabo, Mollie Ullman-Cullere, Grant Wood, Lynn Bry, Mukesh Sharma, Scott Bolte, Michael Miller, Mark Whitsitt, Joyce Hernandez, Don Rule, Larry Babb

Draft Minutes

• Reviewed Historical context for HL7 Clinical Genomic Standards (from US Realm perspective)
  • Current published HL7 Clinical Genomics standards align with the ONC/HHS Personalized Healthcare Use Case (http://healthit.hhs.gov/portal/server.pt/community/use_cases_and_requirements_documents/1202/personalized_healthcare/15671) and HL7 standards listed in HHS' Final Rule: http://www.hl7.org/implement/standards/product_matrix.cfm?Category=HHSFR
• Described approach for Clinical Sequencing Project
  • Develop high-level workflow by starting with HHS Use Case and extending with leasons learned and modern technologies
• Reviewed Germline workflow
  • Positive feedback with recommendation to further define bioinformatic and computational aspects of bioinformatic pipeline and transcoding and interpretation stages
  • Add COSMIC and LSDB's to reference databases
  • Extend bioinformatic processes with information detailed in Lynn Bry's use case specifically 5 tiers of the pipeline
• Reviewed Updated Project Scope Statement for Clinical Squencing

January 31, 2012

Agenda

• Ballot Reconciliation
  • Cytogenetics
  • Genetic Variation
  • GTR - including CAP and ACMG harmonization
• Group Health
  • DMP - Amnon to edit and circulate for review
• Product guide
• Approval of 2012 January WGM minutes
• Group Health Issues (Status and Descriptions)
  • Mission and Charter
  • Decision Making Practices
  • 3 year plan
  • Post WGM Survey
  • SD participation at WGM -- Mollie to correct September 2011 bookkeeping
  • SD participation on weekly calls -- plan for co-chair involvement
  • Project review (Project Insight)
    • 844 Family Health History and Pedigree standard, Release 2; On Track; SD Approval 12/16/2012
    • 841 Clinical Sequencing; On Track; SD Approval 12/16/2012
    • 752 Publish CDA IGs from Tooling; Sponsored by Structured Documents Work Group; past deadline: 2011 May WGM
    • 729 Canonical Pedigree (Family History) Interoperability Implementation Guide; On Hold
    • 705 HL7 CG- omics Domain Analysis Model; past deadline - 2011 September WGM
    • 693 Clinical Genomics - Genetic Variation (CMET); past deadline - 2011 September WGM
    • 692 Clinical Genomics - Genetic Variation (Fully LOINC- Qualified Genetic Variation Model); On Track
    • 663 Cytogenetic Lab Results; On Track? Adjust project end date
    • 565 Specimen Handling CMET; Move to O&O
    • 564 Connection with Decision Support; Place on hold
    • 479 Health Informatics: Clinical Genomics Pedigree Topic (ISO Ballot Project); past deadline - 2011 September WGM; Approved 3/30/2009 - Place on hold
    • 460 CDA Implementation Guide for Genetic Testing Reports; Approved 2/24/2009 - re-submit PSS
    • 333 Gene Expression; past deadline - 2011 September WGM; Approved 1/27/2009 - re-submit PSS
• Approval of updated Project Scope Statements (These need to be approved and submitted by January 29, which is before our next call.)
  • 460 CDA Implementation Guide for Genetic Testing Reports; Approved 2/24/2009
  • 333 Gene Expression; past deadline - 2011 September WGM; Approved 1/27/2009
• Planning Clinical Sequencing work for May 2012 Informative ballot (Due February 26)
  • Use Cases
  • Class Models
  • Activity Diagrams
• Vancouver WGM agenda / joint sessions / room reservations
• Other new business

Attendees

• John David Nolen; Cerner
• Mollie Ullman-Cullere; DFCI
• Amnon Shabo; IBM
• Grant Wood; Intermountain
• Larry Bibb; Partners Healthcare
• Don Rule; Translational Software
• Daryl Thomas; Life Technologies
• Jessie Tennenbaum; Duke
• Scott Bolte; GE Healthcare
• Mukesh Sharma; WUSTL
• Costa Makrodimitris; ONC/S&I

Draft Minutes

• Informational: Initial content deadlines
  • Intent to ballot February 26
  • V3 is March 4
  • GTR is March 25
• Postponed: Ballot Reconciliation - Mollie and Grant to work on comments and share in a later meeting (February 14, 2012)
  • Cytogenetics - one substantive comment (needs ~15 minutes)
  • Genetic Variation - minimal (needs ~10 minutes)
  • GTR - including CAP and ACMG harmonization (Mollie to work with Amnon next week and to circulate before the February 28 meeting)
• May 2012 Ballot Planning
  • CMET: March 4 initial submission, complete on March 25
  • Reaffirmation of Pedigree: nothing to submit
  • GTR: March 25
  • Clinical Sequencing (preparation for DAM, not necessarily storyboards): March 25
  • Omics DAM: March 25
• Group Health
  • DMP - Reviewed Mollie and Amnon's comments. Amnon will update and re-circulate. We intend to complete this next week.
• 2012 Jan WGM Minutes
  • Continued discussion on the Omics DAM perspective.

January 26, 2012 -- Clinical Sequencing

Agenda

• Develop initial draft workflow for clinical sequencing

Attendees

• Mollie Ullman-Cullere
• Grant Wood
• Larry Babb
• Daryl Thomas

Draft Minutes

• Discussed plan to prepare for May ballot
  • Generalized workflow with connection points to other stakeholders (HL7 work groups)
  • Detailed versions for two use cases described at WGM
    • Somatic variant detection
    • Inherited disease (cardiomyopathy or hearing loss)
• Wrote draft workflow in Visio

January 24, 2012

Agenda

• Introduction of Illumina stakeholders
• Approval of 2012 January WGM minutes
• Group Health Issues (Status and Descriptions)
  • Mission and Charter
  • Decision Making Practices
  • 3 year plan
  • Post WGM Survey
  • SD participation at WGM -- Mollie to correct September 2011 bookkeeping
  • SD participation on weekly calls -- plan for co-chair involvement
  • Project review (Project Insight)
    • 844 Family Health History and Pedigree standard, Release 2; On Track; SD Approval 12/16/2012
    • 841 Clinical Sequencing; On Track; SD Approval 12/16/2012
    • 752 Publish CDA IGs from Tooling; Sponsored by Structured Documents Work Group; past deadline: 2011 May WGM
    • 729 Canonical Pedigree (Family History) Interoperability Implementation Guide; On Hold
    • 705 HL7 CG- omics Domain Analysis Model; past deadline - 2011 September WGM
    • 693 Clinical Genomics - Genetic Variation (CMET); past deadline - 2011 September WGM
    • 692 Clinical Genomics - Genetic Variation (Fully LOINC- Qualified Genetic Variation Model); On Track
    • 663 Cytogenetic Lab Results; On Track? Adjust project end date
    • 565 Specimen Handling CMET; Move to O&O
    • 564 Connection with Decision Support; Place on hold
    • 479 Health Informatics: Clinical Genomics Pedigree Topic (ISO Ballot Project); past deadline - 2011 September WGM; Approved 3/30/2009 - Place on hold
    • 460 CDA Implementation Guide for Genetic Testing Reports; Approved 2/24/2009 - re-submit PSS
    • 333 Gene Expression; past deadline - 2011 September WGM; Approved 1/27/2009 - re-submit PSS
• Approval of updated Project Scope Statements (These need to be approved and submitted by January 29, which is before our next call.)
  • 460 CDA Implementation Guide for Genetic Testing Reports; Approved 2/24/2009
  • 333 Gene Expression; past deadline - 2011 September WGM; Approved 1/27/2009
• Planning Clinical Sequencing work for May 2012 Informative ballot (Due February 26)
  • Use Cases
  • Class Models
  • Activity Diagrams
• Vancouver WGM agenda / joint sessions / room reservations
• Other new business

Attendees

• Amnon Shabo. IBM
• Mollie Ullman-Cullere
• Daryl Thomas. Life Technologies
• Dipesh Risal. Illumnina
• Steve Burgett. Illumina Dir SW Dev
• Mukesh Sharma. WUSTL
• Larry Babb. Parnters. SW Developer
• Grant Wood. Intermountain
• Costa Makrodimitris. ONC/S&I
• Scott Bolte. GE Healthcare
• Joyce Hernandez. Merck

Approved Minutes (approved Jan 31)

• Approved Pedigree R1 Reaffirmation PSS (Risal and Burgett abstained; all others approved). Thomas to submit to DESD for approval.
• Amended and approved Gene Expression PSS (Burgett and Makodimitris had left; Babb and Risal abstained; all others approved). Hernandez to submit to DESD for approval.
• CDA Implementation Guide for Genetic Testing Reports PSS to be amended by Amnon and circulated for review and approval by email. Voted to extend DMP to allow email voting for this specific PSS.
• Amnon will amend DMP to include email approval process and will circulate to the group for review at the next call.
• Postponed approval of the 2012 WGM draft minutes to next call.
• Initiated clinical sequencing focus group to meet on Thursday mornings at 8 AM PST. First meeting January 26. Contact daryl.thomas@lifetech.com for details now (will be documented later). Initial group is Thomas, Ullman-Cullere, Shabo, Hernandez, Babb, Risal, Wood, Bolte and Hambuch.
• postponed other items to next call