HL7 Clinical Genomics SIG Meeting May 2-4, 2005



HL7 Clinical Genomics SIG

The Netherlands

Meeting Minutes

HL7 Clinical Genomics SIG Meeting May 2-4, 2005, the Netherlands

For more information on the Clinical Genomics Special Interest Group, please contact one of the co-chairs listed below:

|Peter Elkin, MD |Jill Kaufman, PhD |Scott Whyte |Amnon Shabo |

|Mayo Clinic |IBM Life Sciences |Catholic Healthcare West |IBM Research, Haiffa, Israel |

| |Phone: (201) 447-0227 |Phone: (602) 307-21778 |shabo@il. |

|Elkin.peter@mayo.edu |jillkauf@us. |scott.whyte@chw.edu | |

Attendance

|First Name |Last Name |Organization |Representing |Email |Attendance |

|Joyce |Hernandez |IBM Life Sciences |RCRIM |jhernan@us. |M, T, W |

|Peter |Elkin |Mayo Clinic |CG |elkin.peter@mayo.edu | |

|Hiro |Hoshimoto |Kobe University |CG |hhoshi@med.kobe-u.ac.jp |M, T, W |

|Jill |Kaufman |IBM Life Sciences |CG |jillkauf@us. |M, T, W |

|Jun |Nakaya |Kobe University Medical|CG |junnaka@med.kobe-u.ac.jp |M, T, W |

| | |School | | | |

|Usha |Reddy |IBM Life Sciences |CG |ushareddy@us. |M, T, W |

|Amnon |Shabo |IBM Research, Haiffa, |CG |shabo@il. |M, T, W |

| | |Israel | | | |

|Scott |Whyte |Catholic Healthcare |CG |Scott.whyte@chw.edu |M, T, W |

| | |West | | | |

|Philip |Pochon |Covance |CG |Phil.pochon@ |M, T, W |

|Anita |Walden |Duke Medical Center/ | |Anita.Walden@duke.edu |M |

| | |Clinical Research | | | |

| | |Institute | | | |

|Philippe |Rocca-Serra |EBI |Guest | |M |

|Nori |Sakamoto |Kobe University |CG |nori@med.kobe-u.ac.jp |T |

Monday, May 2

Q1 Agenda and Elections: co-chair elections HL7 Hq.

Welcome, Review Agenda Jill Kaufman

Education topic:

Overview of the Clinical Genomics ballot package (V3 May 2005)

Overview of the Clinical Genomics Model Specifications: Amnon Shabo

The Genotype R-MIM and the new Genetic Profile model Amnon Shabo

We welcome all new participntsparticipants

Note: For HIV alone, Phil Pochon has 37 different genomic data formats. Next, have opportunity for Hepatitis, viral and bateria genotyping.

Co-chair elections: Karen and John Quinn conducted the election. Amnon Shabo was elected to a 2 year co-chair term starting May, 2005 and ending May, 2007.

Medra vocabulary used by Duke for Pharma-related work.

Overview of the Clinical Genomics ballot package (V3 May 2005)

Overview of the Clinical Genomics Specifications:

The Genotype R-MIM and the new Genetic Profile model Amnon Shabo

Amnon – Presented HL7 v3

Note: The CG balloted proposal does not change the RIM. CG has not yet added Observation specialization.

Q2: Education topic:

Overview of the Clinical Genomics Vocabularies Usha Reddy

See the HL7-Clinical –Genomics-Genotype-0.15.doc

Genotype – vocabulary now called ‘GenotypeLocus’

If have expression data that is not specific to an allele, the use the “NON-ALLELIC” code. Then, may go to the gene expression portion of the model.

If ‘NON-ALLELIC’, then IndividualAllele = NULL. Then traverse to Expression (e.g., for MAGE).

If tables will continue to grow (scientifically), then point to external terminologies (e.g., sequence ontologies, NCI, MeSH…).

LOINC – Want one code for ordering test. Probably want to specify method when ordering (for time, resolution, cost …reasons).

Action Item – put ‘zygosity’ into LOINC. (homo, hetero, loh – loss of heterozygosity)

Action Item – Add column for maintenance source – e.g., NCI Thesaurus or LOINC

Action items – Go to major equipment manufacturers and reagent kit manufacturers. Roche (now provides LOINC codes) And Roche has an Affy-chip based set, Behr …

Central lab doesn’t want to send a LOINC code different than what equipment vendor might send.

Q3: Selecting Subset of MAGE/MIAME Philippe

Rocca-Serra

Use of MAGE in real life: Good Practices, Constraints and Future

Presentation developed with Susanna-Assunta Sansone

MIAMI – defines the content

MAGE – provides the container

CEL files – the raw, binary file, proprietary generated by Affymetrix. Interesting only if you want to recomputed data.

Goal – Produce/suppport public repositories of microarray data.

MGED Ontology (MO)

Needs to be expanded – FuGO (SMRS, PSI …)

Cube vs. Tuple

Depends on number of genes – 1 – 2000 genes, tuple is ok. Size of file too large if sending 20,000 genes.

FuGE – Functional Genomics Object Model

Action Item – Phil will take on message Use Case for Clinical Trials and will share with Phillipe. Phil will try to get an Alsheimers data set and Usha

Q3Q4: Ballot items comments discussionreconciliation All

The use of the Genotype model in the CDC NHANES project Tom Savel

(a presentation will be made through a teleconference at 4PM)

See PowerPoint

Public Health Example

Q4: ?

Potential Joint with LAB SIG to join CMET with LAB order and results

Tuesday, May 3

Q1: Ballot comments reconciliation and planning of next steps All

Response to Negatives:

Austin Kreisler –

• 3.4.1 – Response – Technical glitch that Amnon will correct matching of labels.

• 3.5.1 – Response – There is inconsistency between CMET and DMIM. CG SIG would prefer to leave the model as a DMIM that will behave as a CMET. There is an issue with the hierarchy of the Genotype RMIM and Pedigree. There were constraints with the publication tool – Amnon to follow-up with publications team.

• 3.6.1 – Genotype model is supposed to be a CMET – there aren’t any interactions around the model.

Virginia Lorenzi –

• 3.6.1 – Original Pedigree section – Response - Negative comment not understood. Amnon to follow-up via email. Genotype model is supposed to be a CMET – there aren’t any interactions around the model.

• Clinical Statement Comment – Response - When CG CMET is rendered into an Orders and Observation message, the Clinical Statement will be developed then.

• Interaction diagrams missing – Diagrams will be added.

• 3.5 – Neg. - Attribute level narrative is missing. Response – Persuasive – Amnon to add attributes.

Once Genotype is moved to CMET, documentation will be more clear.

Clinical Statement

Q2a: Clinical Genomics work session – ISO, Jun Nakaya & Nori Sakamoto

Clinical Genome Informatics Center

For ISO TC215 WG2

See PowerPoint

Polymorphism Markup Language (PML)

For SNP and STRP – not other polymorphisms

For services oriented messaging related to the E.H.R., OMG is defining the format

The Clinical Genomics SIG is supportive of the development of the PML and the Clinical Genomics SIG recommends using the HL7 Genotype model as the foundation for the PML.

Q2b – Workplan

Next Steps:

• Publish DSTU – editing in order to send to ANSI.

o CG to demonstrate that we’ve addressed negatives

o Gain Board approval

o Editing diagrams, vocabulary and text

o Karen Van Hetenryck

• Vocabulary Steps

o Propose New HL7 vocabulary – work with NCI

o Open vocabulary documents to those outside HL7

o Propose Clinical Genomics changes to the HL7 Vocabulary (e.g.,. Orders & Observations) – work with HL7 Harmonization process

o Use “C1410 – Nucleic acid Sequence Based Analysis” as parent – develop clinical genomics methods as children beneath this code.

• Develop an implementation guide for each Use Case

o Rick Haddord – for Cystic Fibrosis or Web Genetic testing

o Phil Pochon (Covance) & Tom Savel (CDC)

Target date for conference call, June 22, 2005, 11am EST

Q31: Clinical Genomics Family historyHistory Specifications - Cancelled

Kevin Hughes &

Amnon Shabo

Q42: RCRIM / Patient Safety / Clinical Genomics work Joint session – hosted by RCRIM

RCRIM has formal notes and attendee list.

Susan Bassion presented Terminology Activities.

Evaluated EVS (Enterprise Vocabulary Services) of NCI, caDSR, NCI Thesaurus, CHI recommendations

Q3: Ballot comments reconciliation and Pplanning of next steps All

Q4: joint Joint meeting with RCRIM on vocabulary and Genotype utilization

Wednesday, May 4

Q1: Joint meeting – hosted by with RCRIM on (cont.) – attendee list recorded by RCRIM

Amnon Shabo update

Purpose of Draft Standard – use and feedback. Partners Healthcare & CDC. Note that the CDC will be presenting the CG pilot message use at the PHIN conference.

RCRIM would like to include

Pharmacogenomics – ready for committee ballot in December, 2005. Membership ballot earliest, May 2006. RCRIM would like approved (but not normative?) Clinical Genomics CMET included as part of the Pharmacogenomics ballot.

Action Item – Target Draft Standard usage for 6 months after board approval.

Clinical Trial genomics message

Phil Pochon update

Additions – initial model focuses on one gene. Some clinical trials now deal with multiple genes. Alzheimer’s disease biomarkers.

Decision to leave subject identifier in the constrained MAGE model.

Goal is to develop an end-to-end pharmacogenomic model. As such, portions of the model will not be used at different steps in the clinical trials life cycle.

Model must eventually accommodate all types of genomic data – Human, Animal and Viral/bacterial.

Differences - Viral/bacterial may not be in initial model. Note – Viral doesn’t have alleles. Human – look at SNPs, where viral focus on codon triplets… Codons and Amino acids need to be modeled.

Recommendation – for near term, focus on Human/animal allele based genotype model.

Q3: Joint meeting with Orders & Observations on potential use

of the Genotype model in the LAB specifications

Next Agenda – Draft

Target date for conference call, June 22, 2005, 11am EST

Plan to meet Wed, Thurs in San Diego

Target joint CG/ RCRIM meeting – Wed, Q4, hosted by RCRIM

Vocabulary – Stan Huff, including support for version 2.

“Every question is LOINC and every answer is SNOMED”. NCI is metathesaurus – references vocabularies beyond LOINC and SNOMED.

Interest in molecular imaging – Covance interested in molecular imaging for HIV (envelope folding) for the research and discovery phase (1 and 2).

2006 Action Item – Clinical Statement Shared Model

Q1 & Q2 – Clinical Genomics – Tutorial Session hosted by Amnon

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