Hl7 and the Clinical Genomics Work

Group

Mukesh Sharma

Washington University in St. Louis

Agenda

• HL7 introduction

• Reference Information Model

• Clinical Genomics Work Group

• Clinical Genomics Work Group Accomplishments

• Gene Expression DAM

• Upcoming Activities

• Useful Links

Health Level 7

• HL7 was founded in 1987 and accredited in 1994 by the American National Standards Institute (ANSI).

• Health Level Seven (HL7), is an all-volunteer, not-for-profit organization involved in development of international healthcare standards.

• HL7 is also used to refer to some of the specific standards created by the organization (e.g., HL7 v2.x, v3.0, HL7 RIM) standards

What does the name mean?

Source: http://www.hl7.com.au/FAQ.htm

Health Level 7

• HL7 and its members provide a framework (and related standards) for the exchange, integration, sharing, and retrieval of electronic health information.

• v2.x of the standards, which support clinical practice and the management, delivery, and evaluation of health services, are the most commonly used in the world

• Work Group Meetings/Balloting Cycles

• 3 times annually

• January, May, September

• >700 members attend the meetings.

Health Level 7

• HL7 is one of several American National Standards Institute (ANSI) -accredited Standards Developing Organizations (SDOs) operating in the healthcare arena.

• HL7 has been adopted by several national SDOs outside the U.S.

• 36 countries

• These SDOs are not accredited by ANSI.

• ISO adopted HL7 as a centre of gravity in international standardization and accredited HL7 as a partnering organization for mutual issuing of standards.

• The first mutually published standard was ISO/HL7 21731:2006 Health informatics—HL7 version 3—Reference information model—Release 1

What is the Reference Information Model (RIM)?

• The Reference Information Model (RIM) is the cornerstone of the HL7 Version 3 development process.

• It is a shared model between all the domains (clinical data) from which all domains create their messages.

• The RIM and the vocabulary domains are the bases for the semantic specification of message elements.

• Current version 2.3.1

• Available at http://www.hl7.org/implement/standards/rim.cfm

• Graphics in folder rim0231g

RIM v2.3.1

Entities

Roles

Acts

Infrastructure (communications)

Partic-ipation

The HL7 Clinical Genomics (CG) Work Group

• Established as a SIG in 2003

• Mission To enable the standard use of patient-related genetic data such as DNA sequence variations and gene expression levels, for healthcare purposes (‘personalized medicine’) as well as for clinical trials & research

• Work Products and Contributions to HL7 ProcessesThe Work Group will collect, review, develop and document clinical genomics use cases in order to determine what data needs to be exchanged. The WG will review existing genomics standards formats such as BSML (Bioinformatics Sequence Markup Language), MAGE-ML (Microarray and Gene Expression Markup Language), LSID (Life Science Identifier) and other. This group will recommend enhancements to and/or extensions of HL7's normative standards for exchange of information about clinical genomic orders and observations.

In addition, Clinical Genomics will seek to assure that related or supportive standards produced by other HL7 groups are robust enough to accommodate their use in both research and clinical care use. The group will also monitor information interchange standards developed outside HL7, and attempt harmonization of information content and representation of such standards with the HL7 content and representation.

CG Work Group Leadership (Co-Chairs)

• Joyce Hernandez

Merck & Co. Inc.

• Kevin Hughes MD   Partners HealthCare System, Inc.

• Amnon Shabo, PhD

IBM

• Mollie Ullman-Cullere   Partners HealthCare System, Inc.

Formal Relationships with Other HL7 Groups

CG Work Group coordinates with a large number of other Work Groups in order to accomplish its mission. Strongest relationships are with

•Orders and Observation

•Clinical Statement

•Clinical Decision Support

•Regulated Clinical Research Information Management

•Patient Care

•Electronic Health Records

•Modeling and Methodology

•Structured Documents

Accomplishments

Focus on V2 and V3 genetic and genomics data models

• V3 Genetic Models

•Single Gene (Genetic Locus) Common Message Elements (CMET)• Draft Standard for Trial Use – May 2005 (Revised May 2006)

•Multiple Gene (Genetic Loci) CMET• Draft Standard for Trial Use – Jan 2007

•Unified Full Genetic Variation CMET• Draft Standard for Trial Use – Jan 2008• Normative – Jan 2010

•V3 Pedigree Topic - Family History • Normative – May, 2007

Accomplishments

• Genetic Variation V2 message• Developed for clinical practice to carry findings from a lab to a

physician, genetic councilor, etc.• Subset of full V3 model, focus on interpretive, not raw (sequence)

data

• Genetic Variation V3 Reduced CMET• Companion to V2 message

• Gene Expression Model• Intended for V2 and V3 implementation• Domain Analysis Model balloted Sept 2009, currently in Ballot May

2010

CG Gene Expression Domain Analysis Model-Diagram

CG Gene Expression Domain Analysis Model-Details

• Subpackages

• Array Design• Classes e.g Array, ArrayDesign, ArrayGroup, Reporter etc.

• Common Classes• Identifiable, OntologySource, OntologyTerm etc.

• Data• DataFile, DataMatrix, Image, ImageAcquistion etc.

• Design Element• DesignElement, DimensionElement etc.

• Experiement Definition• GenomicProtocol, LabExperiment, NormalizationTypes, ProtocolParameter etc.

• Relationship• Relationships between: Samples, Arrays and Data

• Bio-Specimen Diagrams• Classes e.g BioSpecimen, Bio-Specimen-Characteristics, Specimen Handling

etc.

Clinical Genomics Domain Analysis Model-Terminology

• Terminology: definitions from NCI EVS team for a number of terms needed for genetic sample type entries

• nDNA (Nuclear DNA)

• pDNA (plasmid DNA)

• RNA (Ribonucleic acid)

• RNAP (RNA polymerase)

• mRNA (Messenger Ribonucleic Acid)

• snRNA (Small nuclear RNA)

• miRNA (microRNA)

• ssRNA (single-stranded RNA)

• dsRNA (double-stranded RNA)

• snoRNA (small nucleolar RNA)

• tRNA (Transfer RNA)

• hnRNA (heterogeneous nuclear RNA)

• RNP (Ribonucleoprotein)

• snRNP (small nuclear ribonucleoproteins)

CG Gene Expression Domain Analysis Model-Ballot

• Model available at http://www.hl7.org/v3ballot/html/domains/uvcg/uvcg_GeneExpressionDAM.htm#POCG_DO000000UV-GeneExpressionDam-ic

• Comments due May 9, 2010

• Under review by IRWG (ICR WS)

• Model will be expanded in future to include Genetic Variations

Upcoming Activities

• Cytogenetic Lab Results

• Project Scope statement being prepared

• Model would consider classes from caBIO

• Gene Expression Domain Analysis Model

• Ballot reconciliation

Useful links

• HL7.org

http://www.hl7.org/

• HL 7 Wiki

http://wiki.hl7.org/index.php?title=Main_Page

• Clinical Genomics Wiki

http://wiki.hl7.org/index.php?title=CG

• HL7 Standards

http://www.hl7.org/implement/standards/index.cfm

• HL7v3 Ballot Site http://www.hl7.org/v3ballot/html/welcome/environment/index.htm

Questions?

Additional slides

What does the name mean?

Health Level 7 symbolizes the seventh layer of the International Standards Organization (ISO) Communications Model:

1. Physical: Connects the entity to the transmission media

2. Data Link: Provides error control between adjacent nodes

3. Network: Routes the information in the network

4. Transport: Provides end-to-end communication control

5. Session: Handles problems that are not communication issues

6. Presentation: Converts the information

7. Application: Provides different services to the applications

HL7 v3.0

• HL7 V3, like V2.x, is a standard for exchanging messages among information systems that implement healthcare applications. However, V3 strives to improve the V2 process and its outcomes. The original process for defining HL7 messages was established in 1987 and has served well. The development principles behind HL7 V3 lead to a more robust, fully specified standard.

• New capabilities offered in Version 3 include:

• Top-down message development emphasizing reuse across multiple contexts and semantic interoperability

• Representation of complex relationships

• Formalisms for vocabulary support

• Support for large scale integration

• Solving re-use and interoperability across multiple domain contexts

• A uniform set of models

• Expanded scope to include community medicine, epidemiology, veterinary medicine, clinical genomics, security, etc.

HL7 Development Framework: HDF

• The basis for the specification of a messaging standard is a Reference Information Model (RIM) that completely covers the domain being addressed. The RIM and the vocabulary domains are the bases for the semantic specification of message elements. The Domain Information Model (DIM ) defines the information content for a specific area of expertise or interest. The DIM represents one group’s view of the world.

• A proper subset of the RIM, called Refined Message Information Model (R-MIM) is used to express the information content for one or more related messages. The R-MIM provides one method of controlling optionality.

• The Hierarchical Message Description (HMD) specifies a set of messages based of one R-MIM. A message type is specified in one HMD.