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| − | == | + | =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 | ||
| + | ==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= | =August 2, 2011= | ||
==Agenda== | ==Agenda== | ||
* HL7 WGM September 2011 in San Diego: mini-symposium W Q1/Q2 to encourage community engagement | * HL7 WGM September 2011 in San Diego: mini-symposium W Q1/Q2 to encourage community engagement | ||
| − | |||
==Attendees== | ==Attendees== | ||
* Mollie Ullman-Cullere – Dana Farber | * Mollie Ullman-Cullere – Dana Farber | ||
| Line 17: | Line 26: | ||
* Don Rule – Translational Software | * Don Rule – Translational Software | ||
* Grant Wood - Intermountain Healthcare | * Grant Wood - Intermountain Healthcare | ||
| − | * Lynn Bry - CAP & | + | * Lynn Bry - CAP & BWH |
| − | |||
==Draft Minutes== | ==Draft Minutes== | ||
* Grant discussed issues with securing a room for the event | * Grant discussed issues with securing a room for the event | ||
* Lynn described four use cases and will circulate after CAP approval | * Lynn described four use cases and will circulate after CAP approval | ||
| − | |||
| − | |||
==Actions== | ==Actions== | ||
* Daryl to circulate NIST workshop proposal | * Daryl to circulate NIST workshop proposal | ||
* Daryl to prepare list of institutions / contacts | * Daryl to prepare list of institutions / contacts | ||
* Don to prepare letter describing the event | * Don to prepare letter describing the event | ||
| − | |||
| − | |||
=July 26, 2011= | =July 26, 2011= | ||
| − | |||
| − | |||
| − | |||
==Attendees== | ==Attendees== | ||
* Mollie Ullman-Cullere – Dana Farber | * Mollie Ullman-Cullere – Dana Farber | ||
| Line 42: | Line 43: | ||
* Mukesh Sharma - WUSTL | * Mukesh Sharma - WUSTL | ||
* Joyce Hernandez - Merck | * Joyce Hernandez - Merck | ||
| − | |||
==Draft Minutes== | ==Draft Minutes== | ||
* Agreed to ballot GTR for Comment Only | * Agreed to ballot GTR for Comment Only | ||
| Line 52: | Line 52: | ||
** Aimed at unifying the nomenclature among domains to make data sharing easier | ** Aimed at unifying the nomenclature among domains to make data sharing easier | ||
** They will circulate an outline to recruit collaborators | ** They will circulate an outline to recruit collaborators | ||
| − | |||
| − | |||
=July 19, 2011= | =July 19, 2011= | ||
==Agenda== | ==Agenda== | ||
* GTR ballot | * GTR ballot | ||
* Tumor profiling | * Tumor profiling | ||
| − | |||
==Attendees== | ==Attendees== | ||
* Amnon Shabo - IBM | * Amnon Shabo - IBM | ||
| Line 67: | Line 64: | ||
* Grant Wood - Intermountain Healthcare | * Grant Wood - Intermountain Healthcare | ||
* Mukesh Sharma - WUSTL | * Mukesh Sharma - WUSTL | ||
| − | |||
==Draft Minutes== | ==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. | * 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. | ||
| Line 81: | Line 77: | ||
** 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 | ** 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… | * 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= | =July 12, 2011= | ||
==Agenda== | ==Agenda== | ||
* GTR ballot | * GTR ballot | ||
| − | |||
==Attendees== | ==Attendees== | ||
* Amnon Shabo - IBM | * Amnon Shabo - IBM | ||
| Line 93: | Line 86: | ||
* Daryl Thomas – Life Technologies | * Daryl Thomas – Life Technologies | ||
* Don Rule – Translational Software | * Don Rule – Translational Software | ||
| − | |||
==Draft Minutes== | ==Draft Minutes== | ||
* A large part of the discussion was about what to ballot in September. | * A large part of the discussion was about what to ballot in September. | ||
| Line 104: | Line 96: | ||
** Create a summarized communication channel so that all members do not have to attend all meetings | ** 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 | ** 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= | =July 5, 2011= | ||
==Agenda== | ==Agenda== | ||
* GTR ballot | * GTR ballot | ||
| − | |||
==Attendees== | ==Attendees== | ||
* Phil Pochon, Grant Wood, Amnon Shabo, Mollie Ullman, Clyde Ulmer | * Phil Pochon, Grant Wood, Amnon Shabo, Mollie Ullman, Clyde Ulmer | ||
==Draft Minutes== | ==Draft Minutes== | ||
* Discussed GTR harmonization with recommendations in the litrature. | * Discussed GTR harmonization with recommendations in the litrature. | ||
| − | |||
| − | |||
=June 28, 2011= | =June 28, 2011= | ||
==Agenda== | ==Agenda== | ||
* GTR ballot: section codes and vocab binding | * GTR ballot: section codes and vocab binding | ||
* Review of Mollie's ballot comments | * Review of Mollie's ballot comments | ||
| − | |||
==Attendees== | ==Attendees== | ||
* Phil Pochon, Don Rule, Scott Bolte, Grant Wood, Daryl Thomas, Amnon Shabo, Mollie Ullman, Dr. Christopher Burrow | * Phil Pochon, Don Rule, Scott Bolte, Grant Wood, Daryl Thomas, Amnon Shabo, Mollie Ullman, Dr. Christopher Burrow | ||
| − | |||
==Draft Minutes== | ==Draft Minutes== | ||
* BALLOT COMMENTS submitted by Mollie Ullman on the GTR | * BALLOT COMMENTS submitted by Mollie Ullman on the GTR | ||
| Line 130: | Line 115: | ||
**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). | **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. | **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. | |
**REFERENCES | **REFERENCES | ||
| − | *** Gulley ML, Braziel RM, Halling KC, et al. Clinical laboratory reports in molecular pathology. Arch. Pathol. Lab. Med. 2007;131(6):852-863. | + | *** Gulley ML, Braziel RM, Halling KC, et al. Clinical laboratory reports in molecular pathology. Arch. Pathol. Lab. Med. 2007;131(6):852-863. http://www.ncbi.nlm.nih.gov/pubmed/17550311 |
| − | + | *** Lubin IM, McGovern MM, Gibson Z, et al. Clinician perspectives about molecular genetic testing for heritable conditions and development of a clinician-friendly laboratory report. J Mol Diagn. 2009;11(2):162-171 http://www.ncbi.nlm.nih.gov/pubmed/19197001 | |
| − | *** Lubin IM, McGovern MM, Gibson Z, et al. Clinician perspectives about molecular genetic testing for heritable conditions and development of a clinician-friendly laboratory report. J Mol Diagn. 2009;11(2):162-171 | ||
| − | |||
*** Up-to-date guidelines from American College of Medical Genetics is available here (starting at section G17, page 29): http://www.acmg.net/StaticContent/SGs/Section_G_2010.pdf | *** Up-to-date guidelines from American College of Medical Genetics is available here (starting at section G17, page 29): http://www.acmg.net/StaticContent/SGs/Section_G_2010.pdf | ||
* 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. | * 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. | ||
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=June 21, 2011= | =June 21, 2011= | ||
==Agenda== | ==Agenda== | ||
| Line 148: | Line 129: | ||
==Approved Minutes== | ==Approved Minutes== | ||
* Discussion of family history and workflow from generalist to specialist, potential release 2, ISO ballot, CPP | * 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. | + | * Amnon is looking for feedback on GTR sections. - recommendation came for comparing recommendations to published recommendations for the field. |
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Revision as of 16:51, 9 August 2011
Contents
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
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.
- REFERENCES
- Gulley ML, Braziel RM, Halling KC, et al. Clinical laboratory reports in molecular pathology. Arch. Pathol. Lab. Med. 2007;131(6):852-863. http://www.ncbi.nlm.nih.gov/pubmed/17550311
- Lubin IM, McGovern MM, Gibson Z, et al. Clinician perspectives about molecular genetic testing for heritable conditions and development of a clinician-friendly laboratory report. J Mol Diagn. 2009;11(2):162-171 http://www.ncbi.nlm.nih.gov/pubmed/19197001
- Up-to-date guidelines from American College of Medical Genetics is available here (starting at section G17, page 29): http://www.acmg.net/StaticContent/SGs/Section_G_2010.pdf
- REFERENCES
- 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.
