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CG WG Call Notes leading to 2011 September WGM

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August 23, 2011

Web meeting information

If the default WebEx is not available, please use the follwoing site: https://www.lotuslive.com/join?schedid=1136358 (no need for user name or password)

Agenda

  • Finalize the NGS program for the Wednesday morning sessions

Attendees

Draft Minutes

Actions

August 16, 2011

Web meeting information

https://www.lotuslive.com/join?schedid=1136358 (no need for user name or password)

Agenda

  • Finalize the NGS program for the Wednesday morning sessions
  • Discuss Lynn Bry's use case slides
  • CPP

Attendees

  • Amnon Shabo (IBM)
  • Daryl Thomas (Life Technologies)
  • Grant Wood (Intermountain)
  • Mukesh Sharma (WUSTL)
  • Sandy Jones (CDC)
  • Scott Bolte (GE Healthcare)
  • Don Rule (Translational Software)
  • Lynn Bry (CAP & BWH)
  • Joyce Hernandez (Merck)

Draft Minutes

  • Discussed agenda
  • Lynn reviewed slides

Actions

August 9, 2011

Agenda

  • HL7 WGM September 2011 in San Diego: mini-symposium W Q1/Q2 to encourage community engagement
  • Discussion of Clinical Sequencing Use Cases

Attendees

  • Mollie Ullman-Cullere – Dana Farber
  • Daryl Thomas – Life Technologies
  • Don Rule – Translational Software
  • Grant Wood - Intermountain Healthcare
  • Lynn Bry - CAP & BWH
  • Scott Bolte - GE

Draft Minutes

  • Lynn reviewed document of five use cases


Challenges of NGS in Clinical

  • New data and formats complicates the use of genomics for some installations
  • New bioinformatics are necessary to make the data useful
  • Some labs that provide NGS are not CLIA

Standards

  • Leverage what is in place whenever possible
  • The system that receives the data is an EHR so focus on their capabilities
  • Call variants and process data upstream of the clinic
  • Provide sufficient and consistent metadata to enable use of the data
  • As the specific variations are more stable and well known less metadata will be needed
  • Quality of calls – likely that quality metrics will be controlled at the lab and only data that meets a threshold will be released.
  • Most clinics want the lab to be a “black box”

Cancer

  • Currently 6% or fewer cancers have a Whole Genome Analysis (experience at Partners)
  • Up front still doing gross pathology
  • Reimbursement is a hurdle for WGA
  • When it is done, usually under a pharma or NIH grant
  • Most common for soft tissue – e.g. myeloma

Linkage – what are the data links between pathology report and specimen. How to link pathology IHC with genetic result

  • IDs
    • Sample
    • Accession
    • Patient Medical Record ID
    • Case ID associated with procedure
  • May be more than one specimen per accession
  • Path accessioned by assistant pathologist evaluates gross description and documents sample prep
  • Often will create FFPE samples - each has sample ID
  • Each Block has slides with barcode labels
  • Slides are read and special stains may be ordered
  • May send for IHC if there are questions about subtype
  • May be frozen

Genetic analysis

  • Genetic report it will be separate from pathology report
  • Pathology and genetic report may be separate - Genetic may be an addendum
  • Both are needed together in the clinic
  • Links between them
    • Patient Medical Record
    • Case id
    • Accession #
    • Sample

Representing the data

  • Can currently represent Translocation, Inversions, Deletions (methelation unsure)
  • Often called against reference sequence
  • How many variants
  • Commonly version 19 in US or EU2 sequence in europe
  • Far east or Africa may require other reference sequences
  • Clinical grade reference seq per
  • Infectious agents may be de novo and represented as just sequence
  • Human testing is almost always against reference sequence

What is stored for how long and what report

  • Not raw sequences
  • Sometimes calls but rarely
  • Most sites want significant variants
  • Some may want assembled genome separate from EHR for re-interrogation
  • Accession ID
  • Daryl working on specimen types and harmonizing definition of specimens
    • Tissue DNA RNA
    • Germline or somatic
  • HGVS for carrier type, Cytogenetics uses ISCN
  • Seq variant HGVS
  • HGNC gene name is being extended to cover copy number

Needs

  • Need messaging standards both within the lab and to transfer to clinical
  • Oncomap uses 12 probes out of 200-300. Keep all the probes for reference or only those that are immediately clinically useful?
  • May be seeing significant increase in factors with WGS
  • Growing examples with EGFR receptors
  • Need additional statistical and computational tools
  • Genomics must have GMP, GLP, and GCP standards
  • Need to figure out how to verify
  • Work with FDA for verification protocols
  • Regulatory agencies are adding more scientists to move standards forward

Actions

  • Daryl to prepare list of institutions / contacts
  • Daryl to extend research use cases to include RNA-Seq and Methyl-Seq
  • All to comment via email on Don's invitation letter for the sequencing symposium by end of Wednesday, August 10.
  • Invitations to go out later this week??

August 2, 2011

Agenda

  • HL7 WGM September 2011 in San Diego: mini-symposium W Q1/Q2 to encourage community engagement

Attendees

  • Mollie Ullman-Cullere – Dana Farber
  • Daryl Thomas – Life Technologies
  • Don Rule – Translational Software
  • Grant Wood - Intermountain Healthcare
  • Lynn Bry - CAP & BWH

Draft Minutes

  • Grant discussed issues with securing a room for the event
  • Lynn described four use cases and will circulate after CAP approval

Actions

  • Daryl to circulate NIST workshop proposal
  • Daryl to prepare list of institutions / contacts
  • Don to prepare letter describing the event

July 26, 2011

Attendees

  • Mollie Ullman-Cullere – Dana Farber
  • Clyde Ulmer – FDA
  • Daryl Thomas – Life Technologies
  • Don Rule – Translational Software
  • Grant Wood - Intermountain Healthcare
  • Mukesh Sharma - WUSTL
  • Joyce Hernandez - Merck

Draft Minutes

  • Agreed to ballot GTR for Comment Only
  • Mollie will incorporate feedback for V2 implementation guide for balloting and receive further feedback via email
  • Joyce and Mukesh will be collaborating with NCI on a Domain Analysis Model for all ‘omics. We need to update the scope statement to reflect the presence of NCI.
  • Joyce and Mukesh discussed the DAM
    • It is intended as a high level structure for all ‘omics
    • Meant to cover Research, Clinical Trials, and Healthcare domains
    • Aimed at unifying the nomenclature among domains to make data sharing easier
    • They will circulate an outline to recruit collaborators

July 19, 2011

Agenda

  • GTR ballot
  • Tumor profiling

Attendees

  • Amnon Shabo - IBM
  • Mollie Ullman-Cullere – Dana Farber & Partners
  • Clyde Ulmer – FDA
  • Daryl Thomas – Life Technologies
  • Don Rule – Translational Software
  • Grant Wood - Intermountain Healthcare
  • Mukesh Sharma - WUSTL

Draft Minutes

  • Decision on how to proceed on the GTR – Amnon presented three options including i) proceed to Draft Standard for Trial Use (DSTU), ii) proceed for comments only, or iii) withdraw. The consensus was that we would like to move the specification forward and encourage further feedback but there is not enough time to obtain feedback and resolve outstanding issues. It was agreed to proceed for comments only with the document modified to clarify that it is not finalized, and to focus reviewers on specific parts of the document for which we need specific input.
  • Motion to approve minutes passed with one minor update
  • Review of modifications to Version 2 Implementation Guide to address tumor profiling including
    • Incorporation of large genetic profiling result sets that do not include interpretation
    • Inclusion of OMIM and COSMIC identifiers to provide further information about genetic mutations
    • Linking references to PubMed, PharmGKB, or ClinicalTrials.gov
    • Providing and Overall Interpretation for the results of a genetic test
    • Updates to the LOINC answer lists based upon experience using the existing specification
    • Extensions to the Genomic Source Class that are motivated by Tumor Profiling (e.g. a mutation may be labeled “likely somatic” if it is unlikely to be a germline mutation but no confirmatory test has been done)
    • Addition of a Genetic Knowledge Reference Type
    • Definitions for Genetic Testing Kits and Genetic Tests that include the registry where the test is defined and data from the manufacturer of the test. The genetic test definition includes the region of the genome that is covered by the test
  • Agreed that next week (7/26) we will complete discussion about updates to the V2 Implementation Guide and then Grant will begin the discussion of…

July 12, 2011

Agenda

  • GTR ballot

Attendees

  • Amnon Shabo - IBM
  • Mollie Ullman-Cullere – Dana Farber & Partners
  • Clyde Ulmer – FDA
  • Daryl Thomas – Life Technologies
  • Don Rule – Translational Software

Draft Minutes

  • A large part of the discussion was about what to ballot in September.
  • There are mixed feelings about the Genetic Test Results (GTR) specification - on one hand it would be good to provide some guidance to the people that are actively developing solutions for exchanging genetic test results, on the other there is a concern that there has not been sufficient engagement on the clinical side to give it the rigor that is required, particularly for a clinical specification.
  • Of particular concern is LOINC coding. The issue is that the coding affects the entire ecosystem including lab, physician, genetic counselor, and especially decision support systems. Further work needs to be done on the GTR so that it will work for clinical workflows. For instance, coded message structure should model practice standards for clinical reporting of genetics, if scope includes the clinical reporting.
  • In addition concern was raised regarding ballot level of the current GTR document. The document is targeted at DSTU ballot level (as indicated in its project scope statement) but the final ballot level in each cycle is voted by the group prior to the submission deadline and the ballot level is corrected accordingly. It is important to note that the GTR passed DSTU ballot and in these cycles, with negatives which are still being addressed. we are reconciling negative comments and refining its structure and supplemental samples. Therefore, it is not yet in final DSTU status.
  • There is a concern that some topics take unexpectedly long in working group discussions and that as a result we don’t get to all topics that are important (e.g. tumor profiling). A number of suggestions were made:
    • Create parallel tracks that will discuss sub-topics and then coalesce into periodic meetings of the full working group
    • Spend some time in each meeting discussing the logistics of the working group to strategize and prioritize the discussion
    • Create a summarized communication channel so that all members do not have to attend all meetings
    • It was decided that next week’s meeting (7/19) will include a brief prioritization session and a full discussion of the Tumor Profiling work

July 5, 2011

Agenda

  • GTR ballot

Attendees

  • Phil Pochon, Grant Wood, Amnon Shabo, Mollie Ullman, Clyde Ulmer

Draft Minutes

  • Discussed GTR harmonization with recommendations in the litrature.

June 28, 2011

Agenda

  • GTR ballot: section codes and vocab binding
  • Review of Mollie's ballot comments

Attendees

  • Phil Pochon, Don Rule, Scott Bolte, Grant Wood, Daryl Thomas, Amnon Shabo, Mollie Ullman, Dr. Christopher Burrow

Draft Minutes

  • BALLOT COMMENTS submitted by Mollie Ullman on the GTR
    • The importance of this guide to emerging standard for transmission and EHR documentation warrant the need to perform a GAP analysis, between recommended standards for report formatting (published in literature) and format of the GTR, and make revision accordingly. This analysis should be documented within the guide and references provided to the reader/implementer.
    • Many systems will likely need to receive a mixture of messages; therefore, a GAP analysis between codes used in the v2 guides and GTR and make revisions accordingly. This analysis should be documented within the guide. Not all messages need to look exactly alike, but the elements do need to logically come together for patient care and discovery research. - Should change specific laboratories (e.g. HPCGG) to generic laboratories, if not a lab generated sample message.
    • Should change mutations used in DCM example to pathogenic and benign mutations of the same gene listed in dbSNP and thereby change the internal lab mutation identifier to an external standard. (Note the internal identifier can be retained if generalized).
    • Review of message is a bit difficult. Harmonization with recommended genetic report format may help; however, analysis should be preformed to ensure both narrative and machine readable logic is completely captured in each section.
  • Discussion of GTR organization following published recommendations on the formatting of genetic test reports. General consensus of the group was to create a table capturing recommended formats from each of the three references with CTR in a fourth column.
  • Dr. Burrow emphasized the importance of using current published clinical recommendations, for formatting genetic test reports. In addition, discussion/analysis of how the GTR incorporates the Analytic Result vs. Clinical Interpretation (of the result) should be done.

June 21, 2011

Agenda

  • Future agenda items: Daryl Thomas presenting on clinical sequencing workflow, my interactions with NIST (6/14), and the FDA meeting (6/23) on next week's call (6.28).
  • Future agenda items: Continued work on GTR and review of Mollie's ballot comments

Attendees

  • Grant Wood, Clyder Ulmer, Amnon Shabo, Phil Pochon, and Mollie Ullman-Cullere

Approved Minutes

  • Discussion of family history and workflow from generalist to specialist, potential release 2, ISO ballot, CPP
  • Amnon is looking for feedback on GTR sections. - recommendation came for comparing recommendations to published recommendations for the field.
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