HL7 WGM
HL7 Clinical Genomics
Meeting Minutes
May 17-20, 2010
For more information on the Clinical Genomics Work Group, please contact one of the co-chairs
listed below:
First Name
Last Name
Organization
IBM Research Lab in
Haifa
Massachusetts
General Hospital,
Partners HealthCare
e-mail
Amnon
Shabo (Shvo)
Kevin
Hughes
Mollie
Ullman-Cullere
Dana Farber
-
Phil
Pochon
Covance
phil.pochon@covance.com
shabo@il.ibm.com
KSHUGHES@PARTNERS.ORG
Attendance
First Name
Hans
Last Name
Buitendijk
Organization
Siemens Health
Mayo
Clinic/Foundation
Intermountain
Healthcare
e-mail
hans.buitendijk@siemens.com
Participation
Rick
Haddorff
haddorff.richard@mayo.edu
Wed Q1, Wed Q2
Stanley
Huff
stan.huff@ihc.com
Wed Q2
Marta
Jaremek
Austin
Kreisler
SAIC
austin.j.kreisler@saic.com
Thu Q1
Clem
McDonald
NIH
clemmcdonald@mail.nih.gov
Wed Q2
Amnon
Shabo
IBM Research Lab in
Haifa
shabo@il.ibm.com
Grant
Wood
Intermountain
Healthcare
grant.wood@imail.org
Isabelle
Davias
Sanofi-Aventis
Isabelle.davias@sanofiaventis.com
Thu Q1
David
Fallas
Sysmex
-
Thu Q1
Patrick
Loyd
Gordon Point
Informatics
-
Thu Q1
Wed Q1, Wed
Siemens Healthcare marta.jaremek@siemens.com Q2,Thu Q1, Thu
Q2
HL7 CG WG meeting minutes
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Wed Q1, Wed
Q2, Thu Q1, Thu
Q2
Wed Q1, Wed
Q2, Thu Q1, Thu
Q2
for more information contact
marta.jaremek@siemens.com
Monday Q3/Q4 , 17 May, 2010
Agenda
Joint session Structured Documents/Tooling/CG
- Resolution to have the CG genetic test reports (GTR) developed through the MDHT (= model
driven health tools), a new tool for creating templates
- MDHT : a project under OHT (open source)
- The Static Model Designer (SMD) is another option to develop CDA Templates, however, the
Templates features in SMD have not been released to OHT and in addition the SMD has a
broader scope in general (any static model in v3) and is targeted to any template on top of v3
specs while the MDHT is focused on CDA
- Clinical Genomics (CG) will be the first test case to develop and publish a CDA template using
MDHT
- The development of a Genetic Testing Report CDA Template can be done from scratch and or
by resuing lower-level templates (e.g., entry level templates) from approved templates such CCD,
Lab results, etc.
Next steps :
CG needs to decide on the outline of the genetic report and then start modeling using the MDHT
CG to find section and entry-level templates to reuse or constrain for its GTR template
Tuesday Q3, 18 May, 2010
Agenda
Joint session RCRIM/CG
- Amnon gave a status report on CG work
- renew the effort of CTLab message with genetic content with the goal of developing a third
release to the R2 that already utilized our models
Next steps :
- RCRIM needs to update the CTLab message (ask Phil Pochon if he can/wants to continue to
lead this effort)
- the current CTLab uses the GeneticLocus DSTU model
- in terms of modeling, it was proposed CTLab will be updated with a choice box, so that different
genetic CMETS can be plugged-in
Specimen
Topic
- RCRIM agreed to get involved in the requirement process of changing the current Specimen
Topic model to accommodate genetic data
Future collaboration with RCRIM :
- joint meeting was scheduled on Tuesday Q2 during the next HL7 WGM in Cambridge
Wednesday Q1, 19 May 2010
Agenda
Review of the HL7 WGM Agenda
Review of the ballot results on the Gene Expression DAM
- CG received 16 Negatives and 30 Affirmative votes
HL7 CG WG meeting minutes
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marta.jaremek@siemens.com
- Negatives coming from : CDISC, NCI, FDA and Siemens
HL7 CG SWOT analysis (May 2010)
- Intention of the SWOT analysis is to comprehensively assess progress of HL7 working groups
- CG did a revision of the HL7 CG SWOT document
- main concerns with the SWOT (Threats) : conflicting standards
- Example : Clinical Statement model vs Pedigree Model
- Amnon reported that recent JAMIA paper was published comparing Clinical Statement Model
and Pedigree Mode Clinical Statement covers 70% of and Pedigree Model covers >90% of
the family history statements representing typical information found in clinicians narratives
- Motion was made to approve the updated SWOT document
For :4
Against :0
Abstain :0
=> SWOT document approved
- updated SWOT will be made available on the CG wiki (link to to be provided by Rick Haddorff)
- this is a living document that could (and should) be changed at any time by the group when new
SWOT issues are identified
Wednesday Q2, 19 May 2010
Agenda
HL7 V2.5.1 – Pilot Project Updates
- Grant Wood gave a status report on the HL7 V2.5.1 project
- HL7 2.5.1 is making good progress :
 Work on including cytogenetic testing data
- Yan Heras (Intermountain Healthcare) is working on creating HL7 V2.5.1 cytogenetic lab results,
that will be included in the next version of the HL7 V2.5.1 CG standard on reporting laboratory
results into EHR
- due to different structure of cytogenetic data that could not be harmonized with current HL7 2.x
terminology, new cytogenetic panels had to be created
 Work on including Test definitions
- Test definitions were piloted already, but were not included in the previous Implementation
Guide (IG)
 Test order definition
- In genetic testing there is a difference between what test was ordered and what part of the
genetic sequence was analyzed (due to different definitions of test requests, genetic loci and
genetic sequence annotations).
- Currently there is no agreement on the definition what is ordered and what is tested
- Approach : target this item for the next ballot cycle (October 2010).
 Handling of large datasets
- sending large amount of clinical trial data in a batch mode
- Large datasets can be : either many patients at time or many SNPs at a time
- Approach : ask Mollie on the priority for this project
 Alignment on CG´s HL7 V2 and HL7 V3 work
HL7 CG WG meeting minutes
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marta.jaremek@siemens.com
- Current status : Alignment was done manually by Amnon
- Challenges : Structure is the toughest issue. There are no tools available to match V2 to V3
(something like an „V2 ITS“)
- Main difference between the current HL7 V2 and V3 models are :
- V3 : is GeneticLocus oriented,
order and result are combined around the tested locus,
phenotypic data : Clinical Statement is used to represent complex phenotypes,
more difficult to represent it in V2
- V2 : clear definition between order and result
phenotypic data : more difficult to represent it in V2, as necessary data structures
are not present
- Approach: start with vocabulary first and make sure the same vocabularies are used by v2 and
v3
- per Clem reuest, Amnon will send v3 samples on the same data sets that serve the v2 samples
 Future pilots
- TBD
 Varian knowledge base (Partner´s PGE)
-TBD
 Expression, targeted micro array genetic results
- Can our current HL7 V2 model handle microarray data
 LOINC codes for family history
- Clem McDonald reported of existing LOINC codes to represent family history. There is a
program available that takes LOINC codes and converts it in a particular tree structure.
 What will we ballot next and when?
- TBD
Genetic Variation CMET – modeling of the timing attributes
- Genetic Variation CMET passed the ballot
- Amnon presented the modeling work of timing issues in the Genetic Variation CMET
- Discussion about time attributes :
effectiveTime vs activityTime vs availablityTime
- action item: to produce a model with all timing attributes documented within the model (not only
in the walk-through) and send it to key modelers for preview before reconciling the negative
comments and re-ballot (this action item is pending on the availability of the new modeling tool
SMD which is not yet approved for publishing)
Thursday Q1, 20 May 2010
Agenda
Joint meeting with O&O; hosted by O&O
V3 Specimen CMET
- Amnon and Austin explored the efforts made by OO and CG to propose a project that will
modify the existing Specimen model to accommodate genetic data
HL7 CG WG meeting minutes
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- Status of Specimen topic :
- Specimen CMETs only
- Normative
- Project around specimen messages (dynamic model) is probably not relevant to the CG needs
- Discussion on timing attributes :
- CG decided to take out the interpretation code in the Specimen
- Probably take out the effectiveTime from the „Intrepretative Phenotype class“ class in the
Phenotype model
Next steps :
- Joint O&O/CG telcos will be scheduled for discussing the timing attributes for the Specimen
- O&O and CG to make changes and vote on the Specimen Project Scope Statement in the
regular telcos next Thursday for O&O and Tuesday for CG
- by June 8/9 CG to articulate changes requests
- after that, O&O joint session to finalize and agree to that
- any change request by june 9th will be discussed by June 17th
- Next week Thursday : O&O to articulate general purpose project statement
- Disposition of change requests by June 24th, start review on Thursday O&O meeting
- target : next ballot cycle (October 2010)
O&O action items :
- O&O to work on the generic purpose Project Scope Statement
- project will be owned by O&O
CG Action items : :
- Update DMIM , review existing CMETS, and create new CG CMETs if necessary
- CG to make change requests
- assign who is going to work on it
- O&O will update the changes
- goal : develop a new release of the Specimen CMET
- key resource : modeling facilitator to update the model
- party with the biggest interest shall provide the resources
CDA IG for Genetic Testing Reports
- CG and Structured Documents to develop a joint CDA IG for genetic testing reports
- A new tool has been developed for creating templates from HL7 messages (MDHT – Model
Driven Health Tool – an OHT open source project))
- Current status of MDHT: currently mature enough to create templates
- The genetic test reports were the chosen to be the first pilot using MDHT
Next steps :
- Amnon will make the modeling by using the MDHT as soon as the model is agreed upon by the
CG group (need to go through the draft outline published in the Jan. 2010 ballot cycle,)
V2 Implementation Guide
- Grant Wood gave a status report on CG´s V2 project
- addition of Cytogenetics into HL7 V2
- a new Implementation Guide will be written for Cytogenetics
- CG will likely collaborate with O&O on Test definition and Test ordering with O&O, as O&O is
also working on test definitions and test ordering
Thursday Q2, 20 May 2010
HL7 CG WG meeting minutes
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Wrap up
Revision : joint session Structured Documents/Tooling/CG (Amnon)
Meeting minutes
Motion was made to upload the draft minutes in the CG wiki for review
After approval, final minutes will be moved to the HL7 site based on ANSI requirements
In favour: 4
Abstain : 0
Negatives :0
=>approved
Revision : joint meeting with RCRIM
- does CG want and RCRIM to move with CTLAB
- CTLab DSTU that used the CG components already expired
Action item :
- check with Phil Pochon whether he would like to proceed with the CT Lab work
- CG additions to CTLab : create a choice box in the CTlab model accommodate CG
components
Other
- CG is looking for volunteers for facilitating the WIKI
- There is an issue with the tooling to develop our static models (including CMETs)
(1) Continue with Visio and the old suite of tools
(2) Move to SMD which is not yet approved for publishing
Planning the Next HL7 WGM in Cambridge
- Meetings on Wednesday Q1, Q2 and Q4
- Thursday Q1 : joint meting in O&O
- Thursday Q2 : tentative joint session with RCRIM was scheduled
- Thursday Q3 : joint meeting with Clinical Decision Support
Planning the Cambridge campus visit/field trip
- Tuesday afternoon or Friday morning?
- Possible Family History tutorial or field trip to Mass. General on Wed. Q4
Future Conference Calls:
Tuesday, 12:00 p.m. ET.
HL7 CG WG meeting minutes
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for more information contact
marta.jaremek@siemens.com