HL7 v3 Clinical Genomics – Overview

HL7 v3 Clinical Genomics –

Overview

The HL7 Clinical Genomics Work Group

Prepared by Amnon Shabo (Shvo), PhD

HL7 Clinical Genomics WGCo-chair and Modeling Facilitator

HL7 Structured Documents WGCDA Co-editorCCD Implementation Guide Co-editorGTR Implementation Guide prime editor

HL7 RIMBAA WG, Co-chair

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The Mission of HL7 Clinical Genomics Work Group

The HL7 Clinical Genomics Work Group (CGWG) supports the HL7 mission to create and promote its standards by enabling the communication between interested parties of clinical and genomic data related to an individual. The focus of the CGWG efforts is the personalization of the genomic data – the so-call ’omics differences in an individual’s genomic – and its association with relevant phenotypic and clinical information. Associations to interpretive/expected phenotypes will be modeled as knowledge that can be utilized to transform an individual's data into meaningful information.

CGWG will facilitate the development of common standards for clinical research information management across a variety of organizations -- including national and international government agencies and regulatory bodies, private research efforts, and sponsored research -- and thus the availability of safe and effective therapies by improving the processes and efficiencies associated with regulated clinical research.

CGWG will strive to achieve common semantics across the clinical and research environments. Consequently, the group will start each standardization effort in Universal specifications that later on can be refined to specific realms.

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Overview of Activities

v3:

Family History (Pedigree) Topic

Genetic Variations Topic

Gene Expression Topic

CMETs defined by the Domain

v2:

v2 Implementation Guides

* The IG “Genetic Test Result Reporting to EHR” is modeled after the HL7 Version 2.5.1 Implementation Guide: Orders And Observations; Interoperable Laboratory Result Reporting To EHR (US Realm), Release 1

CDA:

A CDA Implementation Guide for Genetic Testing Reports

Common:

Domain Analysis Models for the various topics

A Domain Information Model (v3) describing the common semantics

Semantic alignment among the various specs

Three Tracks:

Normative

DSTU

Informative

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HL7 Clinical Genomics v3 Static Models

Family

History

Genetic

Loci

Utilize

Genetic

Locus

Constrained GeneticVariation

Phenotype(utilizing the HL7

Clinical Statement)

Utilize

Utilize

Utilize

Implementation Topic

Normative

DSTU

Constrained Gene Expression

Implementation Topic

Comments

RCRIM LAB

Other domains

Utilize

Utilize

CDA IG

Re

fere

nc

e

Reference

Domain Information

Model: Genome

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To achieve semantic interoperability…

ClinicalTrials

Imaging

EHR

Orders& Observations

Pharmacy

ClinicalGuidelines

Health RIM

ClinicalDocuments

ClinicalGenomics

Central Health RIM (e.g., an extended HL7 V3 Reference Information Model):Bio & medical-informatics standard specs are derived from the same RIM

…we need standard specs derived from a Central Health RIM:

Bioinformatics

Data Models

encapsulate

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0..* associatedObservation

typeCode*: <= COMP

component

0..* associatedProperty

typeCode*: <= DRIV

derivedFrom2

0..* polypeptide

typeCode*: <= DRIV

derivedFrom5

SEQUENCES & PROTEOMICS

0..* expression

typeCode*: <= COMPcomponent1

0..* sequenceVariation

typeCode*: <= COMP

component3

IndividualAlleleclassCode*: <= OBSmoodCode*: <= EVNid: II [0..1]negationInd: BL [0..1]text: ED [0..1]effectiveTime: GTS [0..1]value: CD [0..1] (allele code, drawn from HUGO-HGVS or OMIM)methodCode: SET<CE> CWE [0..*]

GeneticLocusclassCode*: <= OBSmoodCode*: <= EVNid: II [0..1]code: CE CWE [0..1] (e.g., ALLELIC, NON_ALLELIC)text: ED [0..1]effectiveTime: IVL<TS> [0..1]confidentialityCode: SET<CE> CWE [0..*] <= ConfidentialityuncertaintyCode: CE CNE [0..1] <= Uncertaintyvalue: CD [0..1] (identifying a gene through GenBank GeneID with an optional translation to HUGO name.)methodCode: SET<CE> CWE [0..*]

0..* individualAllele

typeCode*: <= COMP

component1

SequenceclassCode*: <= OBSmoodCode*: <= EVNid: II [0..1]code: CD CWE [1..1] (the sequence standard code, e.g. BSML)text: ED [0..1] (sequence's annotations)effectiveTime: GTS [0..1]uncertaintyCode: CE CNE [0..1] <= Uncertaintyvalue: ED [1..1] (the actual sequence)interpretationCode: SET<CE> CWE [0..*] <= ObservationInterpretationmethodCode: SET<CE> CWE [0..*] (the sequencing method)

ExpressionclassCode*: <= OBSmoodCode*: <= EVNid: II [0..1]code: CE CWE [1..1] (the standard's code (e.g., MAGE-ML identifier)negationInd: BL [0..1]text: ED [0..1]effectiveTime: GTS [0..1]uncertaintyCode: CE CNE [0..1] <= Uncertaintyvalue: ED [1..1] (the actual gene or protein expression levels)interpretationCode: SET<CE> CWE [0..*] <= ObservationInterpretationmethodCode: SET<CE> CWE [0..*]

PolypeptideclassCode*: <= OBSmoodCode*: <= EVNid: II [0..1]text: ED [0..1]effectiveTime: GTS [0..1]value: CD [0..1] (protein code, drawn from SwissProt, PDB, PIR,HUPO, etc.)methodCode: SET<CE> CWE [0..*]

DeterminantPeptidesclassCode*: <= OBSmoodCode*: <= EVNid: II [0..1]text: ED [0..1]effectiveTime: GTS [0..1]value: CD [0..1] (peptide code, drawn from referencedatabases like those used in the Polypeptide class)methodCode: SET<CE> CWE [0..*]

Constrained to a restrictedMAGE-ML constrained schema,specified separately.

Constraint: GeneExpression.value

Note:A related allele that is ona different locus, and hasinterrelation with thesource allele, e.g.,translocated duplicatesof the gene.

0..* clinicalPhenotype

typeCode*: <= PERTpertinentInformation

ExternalObservedClinicalPhenotypeclassCode*: <= OBSmoodCode*: <= EVNid*: II [1..1] (The unique id of an external observation residing outside of the instance)code: CD CWE [0..1]text: ED [0..1]effectiveTime: GTS [0..1]

Note:An external observation is preferably a valid observationinstance existing in any other HL7-compliant instance,e.g., a document or a message.Use the id attribute of this class to point to the uniqueinstance identifier of that observation.

Note:A phenotype which has been actuallyobserved in the patient representedinternally in this model.

Note:This is a computed outcome, i.e.,the lab does not test for the actualprotein, but secondary processespopulate this class with thetranslational protein.

SequenceVariationclassCode*: <= OBSmoodCode*: <= EVNid: II [0..1]code: CD CWE [0..1]negationInd: BL [0..1]text: ED [0..1]effectiveTime: GTS [0..1]value: ANY [0..1] (The variation itself expressed with recognized notation like 269T>C or markup like BSML or drawn from an external reference like OMIM or dbSNP.)interpretationCode: SET<CE> CWE [0..*] <= ObservationInterpretationmethodCode: SET<CE> CWE [0..*]

KnownClinicalPhenotypeclassCode*: <= OBSmoodCode*: <= DEFcode: CD CWE [0..1]text: ED [0..1]effectiveTime: GTS [0..1]uncertaintyCode: CE CNE [0..1] <= ActUncertaintyvalue: ANY [0..1]

Note:These phenotypes are not the actual (observed)phenotypes for the patient, rather they are thescientifically known phenotypes of the sourcegenomic observation (e.g., known risks of amutation or know responsiveness to a medication).

Note:Code: COPY_NUMBER, ZYGOSITY, DOMINANCY, GENE_FAMILY,etc. For example, if code = COPY_NUMBER, then the value is oftype INT and is holding the no. of copies of this gene or allele.


typeCode*: <= PERT

pertinentInformation

EXPRESSION DATA

SEQUENCE VARIATIONS

Polypeptide

Note:The Expression class refers to both gene and proteinexpression levels. It is an encapsulating class that allowsthe encapsulation of raw expression data in its value attribute.

0..* sequence

typeCode*: <= COMPcomponent2

0..* clinicalPhenotypetypeCode*: <= PERT



typeCode*: <= PERT


Note:The code attribute indicates inwhat molecule the variation occurs,i.e., DNA, RNA or Protein.

0..* expression

typeCode*: <= COMP

component5

Note:Use the associations to the shadowclasses when the data set type (e.g.,expression) is not at deeper levels(e.g., allelic level) and needs to beassociated directly with the locus(e.g., the expression level is thetranslational result of both alleles).

0..* associatedObservationtypeCode*: <= COMP

component2

0..1 associatedObservation

typeCode*: <= COMP

component4 Note:This recursive associationenables the association of anRNA sequence derived froma DNA sequence and apolypeptide sequence derivedfrom the RNA sequence.


typeCode*: <= PERT


Note:

This class is a placeholder for a specific locus on the genome - that is - a position of a particulargiven sequence in the subject’s genome or linkage map.Note that the semantics of the locus (e.g., gene, marker, variation, etc.) is defined by data assignedin the code & value attributes of this class, and also by placing additional data relating to thislocus into the classes associated with this class like Sequence, Expression, etc..

Note:The term 'Individual Allele' doesn't refer necessarily to aknown variant of the gene/locus, rather it refers to theindividual patient data regarding the gene/locus and mightwell contain personal variations w/unknown significance.

AssociatedObservationclassCode*: <= OBSmoodCode*: <= EVNid: SET<II> [0..*]code: CD CWE [0..1]text: ED [0..1]effectiveTime: GTS [0..1]value: ANY [0..1]methodCode: SET<CE> CWE [0..*]

Note:The code attribute could hold codes likeNORMALIZED_INTENSITY, P_VALUE, etc.The value attribute is populated based on theselected code and its data type is then setupaccordingly during instance creation.

Note:The code attribute could hold codes like TYPE,POSITION.GENOME, LENGTH, REFERENCE, REGION, etc..The value attribute is populated based on the selected codeand its data type is then setup accordingly during instancecreation. Here are a few examples:If code = TYPE, then the value is of type CV and holds one of thefollowing: SNP (tagSNP), INSERTION, DELETION,TRANSLOCATION, etc.

if code = POSITION, then value is of type INT and holdsthe actual numeric value representing the variation positionalong the gene.

if code = LENGTH, then value is of type INT and holdsthe actual numeric value representing the variation length.

If code = POSITION.GENE, then value is of type CV and is oneof the following codes:INTRON, EXON, UTR, PROMOTER, etc.

If code = POSITION.GENOME, then value is of type CV and is oneof the following codes:NORMAL_LOCUS, ECTOPIC, TRANSLOCATION, etc.

If the code = REFERENCE, then value istype CD and holds the reference gene identifier drawn from areference database like GenBank.

The full description of the allowed vocabularies for codes and itsrespective values could be found in the specification.

AssociatedObservation

Note:Code: CLASSIFICATION, etc.For example, if code =CLASSIFICATION, then the valueis of type CV and is holding eitherKNOWN or NOVEL.

reference

0..* geneticLocus

typeCode*: <= REFR

Note:A related gene that is on adifferent locus, and stillhas significant interrelationwith the source gene (similarto the recursive associationof an IndividualAllele).

ClinicalPhenotypeclassCode*: <= ORGANIZERmoodCode*: <= EVN

0..* observedClinicalPhenotype

typeCode*: <= COMP

component1

0..* knownClinicalPhenotype

typeCode*: <= COMP

component2

0..* externalObservedClinicalPhenotype

typeCode*: <= COMP

component3

At least one of the target acts ofthe three component act relationshipsshould be populated, since this isjust a wrapper class.

Constraint: ClinicalPhenotype

Note:- code should indicate the type of source, e.g., OMIM- text could contain pieces from research papers- value could contain a phenotype code if known (e.g., if it’s a disease, then the disease code)

ClinicalPhenotype

ClinicalPhenotype

ClinicalPhenotype

ClinicalPhenotype

ClinicalPhenotype

ClinicalPhenotype

0..1 identifiedEntity

typeCode*: <= SBJcontextControlCode: CS CNE [0..1] <= ContextControl "OP"

subject

reference

0..* individualAllele

typeCode*: <= REFR

ObservedClinicalPhenotype

Note:This CMET might be replacedwith the Clinical Statement SharedModel for richer expressivity, whenthe that mode is approved(currently in ballot).

Constrained to a restricted BSMLcontent model, specified in aseparate schema.

Constraint: Sequence.value

0..* sequence

typeCode*: <= COMP

component4

0..* sequenceVariation

typeCode*: <= COMP

component3

AssociatedPropertyclassCode*: <= OBSmoodCode*: <= EVNcode: CD CWE [0..1]text: ED [0..1]value: ANY [0..1]


typeCode*: <= DRIVderivedFrom1

AssociatedObservation

0..* associatedObservation

typeCode*: <= COMP

component

AssociatedPropertyAssociatedObservation


typeCode*: <= DRIV

derivedFrom

AssociatedProperty0..* associatedProperty


AssociatedObservation0..* associatedObservation

typeCode*: <= COMPcomponent

0..* sequenceVariationtypeCode*: <= DRIV

derivedFrom3derivedFrom2

0..* sequence

typeCode*: <= DRIV

0..* determinantPeptides

typeCode*: <= DRIV

derivedFrom4

0..* determinantPeptides

typeCode*: <= DRIVderivedFrom


typeCode*: <= PERT

pertinentInformation 0..* clinicalPhenotype

typeCode*: <= PERT


AssociatedProperty


typeCode*: <= DRIV

derivedFrom

AssociatedProperty

GeneticLociclassCode*: <= OBSmoodCode*: <= EVNid: SET<II> [0..*]code: CD CWE [0..1]effectiveTime: GTS [0..1]value: ANY [0..1]

0..* geneticLocitypeCode*: <= COMPcomponentOf


typeCode*: <= PERTpertinentInformation

GeneticLoci

0..* geneticLoci

typeCode*: <= COMP

componentOf

GeneticLoci

0..* geneticLoci

typeCode*: <= COMP

componentOf

0..* polypeptide


Polypeptide

0..* polypeptide

typeCode*: <= DRIV

derivedFrom2

Note:Use this class to indicate a set of genetic locito which this locus belongs. The loci set couldbe a haplotype, a genetic profile and so forth.Use the id attribute to point to the GeneticLociinstance if available. The other attributesserve as a minimal data set about the loci group.

PHENOTYPES

Note:Any observation related to the variation and is notan inherent part of the variation observation (the lattershould be represented in the AssociatedProperty class).For example, the zygosity of the variation.

Note:Use this class to point to a variationgroup to which this variation belongs.For example, a SNP haplotype.

Note:Any observation related to the sequence and is notan inherent part of the sequence observation (the lattershould be represented in the AssociatedProperty class).For example, splicing alternatives.

Note:Key peptides in the proteinthat determine its function.

Note:There could be zero to manyIndividualAllele objects in aspecific instance. A typicalcase would be an allele pair,one on the paternalchromosome and one on thematernal chromosome.

Note:Use this class toshow an allelehaplotype like in HLA.

Note:Any observationrelated to theexpression assayand is not aninherent part ofthe expressionobservation.

Note:Use this class forinherent dataabout the locus, e.g.chromosome no.

IdentifiedEntityclassCode*: <= IDENTid: SET<II> [0..*]code: CE CWE [0..1] <= RoleCode

Note:Use this role to identify a different subject(e.g., healthy tissue, virus, etc.) than theone propagated from the wrappingmessage or payload (e.g., GeneticLoci).

ScopingEntityclassCode*: <= LIVdeterminerCode*: <= INSTANCEid: SET<II> [0..*]code: CE CWE [0..1] <= EntityCode

0..* assignedEntity

typeCode*: <= PRFcontextControlCode: CS CNE [0..1] <= ContextControl "OP"

performer

0..*

performer

0..*

performer1

0..*

performer2

0..*

performer1

0..*

performer2

Genetic Locus(POCG_RM000010)

The entry point tothe GeneticLocus modelis any locus on the genome.

Constrained to a restricted MAGE-MLcontent model, specified in aseparate schema.

Constraint: Expression.value

Expression

Sequence

SequenceVariation

SequenceVariation

0..* clinicalPhenotypetypeCode*: <= PERT


ClinicalPhenotype

CMET: (ASSIGNED) R_AssignedEntity

[universal](COCT_MT090000)

0..1 scopedRoleName

CMET: (ACT) A_SupportingClinicalInformation

[universal](COCT_MT200000)

The Locus and its Alleles

SequenceVariations

ExpressionData

Sequenceand

Proteomics

(Clinical)Phenotypes

The DSTU GeneticLocus Model (deprecated) Focal Areas:

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The Underlying Paradigm: Encapsulate & Bubble-up

Clinical PracticesGenomic Data Sources

EHR System

HL7 CG Messages with m

ainly

Encapsulating HL7 Objects HL7 C

G M

essa

ges

with

enca

psul

ated

dat

a as

soci

ated

with

HL7 c

linic

al o

bjec

ts (p

heno

type

s)

Bubble up the most clinically-significant raw

genomic data into specialized HL7 objects and

link them with clinical data from the patient EHR

Decision Support Applications

Knowledge(KBs, Ontologies, registries,

reference DBs, Papers, etc.)

Bridging is the challenge…

Encapsulation by predefined & constrained

bioinformatics schemas

Bubbling-up is done continuously by specialized DS

applications

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Decision Support Applications

Encapsulate & Bubble-up Example

Genetic CounselingDNA Lab

HL7 CG Messages with a Sequence

HL7 Object encapsulating the raw

sequencing results

HL7 C

G M

essa

ges

with

enca

psul

ated

seq

uenc

ing

data

asso

ciat

ed w

ith c

linic

al p

heno

type

s

Bubble up the most clinically-significant SNP data into

HL7 SNP and Mutation objects and

link them with clinical data from the patient EHR

Sequencing Example…

Encapsulation by a constrained BSML schema

Bubbling-up is done dynamically

by specialized applications, e.g.,

sequence analyzing programs

EHR System

Knowledge Sources

on genetic variants

(e.g., OMIM)

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Omics in the LS DAM - Molecular Biologyclass Molecular Biology Core

Chromosome

+ name: ST

NucleicAcidPhysicalLocation

+ endCoordinate: INT+ startCoordinate: INT

NucleicAcidSequence

NucleicAcidSequenceFeature

+ orientation: ST+ typeCode: CD

Protein

+ name: DSET<SC>+ symbol: DSET<SC>

Gene

+ name: DSET<SC>+ symbol: DSET<SC>

SingleNucleotidePolymorphism

AminoAcidSequenceFeature

+ typeCode: CD

ExonIntron

MolecularSequence

+ value: SC

AminoAcidSequence

Genome

+ assemblySource: ST+ assemblyVersion: ST

CytobandRange

+ endBand: ST+ endChromosomeArm: ST+ startBand: ST+ startChromosomeArm: ST

AminoAcidPhysicalLocation

+ endCoordinate: INT+ startCoordinate: INT

GeneticVariation

MessengerRNA

DNASequence

RNASequence

MolecularSequenceAnnotation

+ date: TS

Name: Molecular Biology CoreAuthor: lschickVersion: 1.0Created: 6/17/2011 2:49:18 PMUpdated: 1/9/2012 1:43:45 PM

BRIDG-aligned

LS DAM

Legend0..*

includes / isincluded in

1

1..*

contains / is partof

1

1

is included in /includes

0..*

1..*is for /has 0..1

0..*


1..*

1

is located on /has

1..*

1..*

is translated to /is translated from

0..1

0..*

is representedby / represents

0..*

1..*is included in/ includes 1

0..*is located in /has

0..*

0..*

is located in /has

0..*

0..*


1..*0..*

encodes / is encodedby

0..*

0..*

is transcribed to /is transcribed from

0..*

0..*

reports / isreported by 0..*

0..*

reports / isreported by 0..*

0..*is representedby / represents 0..*

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Omics in the LS DAM - Experimentclass Experiment Core

Experiment

+ activeDateRange: IVL<TS>+ description: ST+ designType: DSET<SC>+ name: ST+ typeCode: CD

ExperimentalFactor

+ name: ST+ typeCode: SC+ value: DSET<ANY>

ExperimentalParameter

+ description: ST+ name: ST+ statusCode: CD+ typeCode: CD

ExperimentalStudy

+ activeDateRange: IVL<TS>+ description: ST+ name: ST+ typeCode: DSET<CD>

PointOfContact

+ effectiveDateRange: IVL<TS.DATETIME>+ postalAddress: AD+ primaryIndicator: BL+ telecomAddress: BAG<TEL>+ typeCode: CD

constraints{ExclusiveOr}

Protocol

+ name: ST

Data

+ creationDate: TS.DATETIME

ExperimentalParameterValue

StringParameterValue

+ value: ST

QuantitativeParameterValue

+ range: IVL<PQ>+ single: PQ

Activity

+ comment: ST+ identifier: II+ reasonCode: DSET<CD>

Software

+ buildDate: TS.DATE+ buildNumber: ST+ content: ED+ effectiveDateRange: IVL<TS>+ identifier: DSET<II>+ licenseEffectiveDateRange: IVL<TS.DATE>+ licenseKey: ST+ licenseTypeCode: CD+ name: ST+ typeCode: CD+ version: ST

Product

Equipment

+ manufactureDate: TS.DATETIME+ reprocessedDeviceCode: CD+ validationDate: DSET<TS.DATETIME>

Material

+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD+ functionTypeCode: DSET<CD>+ nameCode: CD+ subTypeCode: CD+ typeCode: CDExperimentalItem

+ typeCode: CD


DefinedActiv ity

+ categoryCode: CD+ description: ST+ nameCode: CD+ statusCode: CD+ statusDate: TS.DATETIME

PlannedActivity

+ description: ST+ name: ST+ plannedDuration: PQ.TIME+ purpose: ST+ targetAccrualNumberRange:

URG<INT.NONNEG>

PerformedActiv ity

+ actualDateRange: IVL<TS.DATETIME>+ /actualDuration: PQ.TIME+ /delayDuration: PQ.TIME+ missedIndicator: BL+ missedReason: DSET<SC>+ /repetitionNumber: INT.POS+ statusCode: CD+ statusDate: TS.DATETIME

Name: Experiment CoreAuthor: lschickVersion: 1.0Created: 11/16/2011 9:30:18 AMUpdated: 12/22/2011 8:02:53 AM

Specimen no attributes

BRIDG-aligned

LS DAM

Legend

Organization

+ actualIndicator: BL+ description: ST+ name: DSET<ON>+ postalAddress: AD+ telecomAddress:

BAG<TEL>+ typeCode: CD

BiologicEntity

Person

+ deathIndicator: BL+ educationLevelCode: CD+ ethnicGroupCode: DSET<CD>+ initials: ST+ maritalStatusCode: CD+ name: DSET<PN>+ occupationDateRange:

IVL<TS.DATE>+ postalAddress: AD+ primaryOccupationCode: CD+ raceCode: DSET<CD>+ telecomAddress: BAG<TEL>

0..*

is used by / uses

0..*

0..*

is performed as per /describes the stepsto conduct

0..*

0..*

instantiates

0..1

specializesspecializes specializes

0..*supports / issupported by

0..*

0..*

instantiates

0..1

0..*

supports / issupported by

0..*

0..*

is processed into /is processed from1

0..*

is played by / plays

0..1

specializes

0..1is a collection of /isconducted as part of

0..*

0..*supports / issupported by

0..*

0..*


0..*

0..1

results in / is the result of

0..*

0..1


0..*

0..*

participates in /is performedon

1

1

has value /is value for

0..*

0..*

is a part of / is a collection of

0..*

0..*

uses / defines use of

0..*

1

has value / is value for

0..*

0..*


0..*

0..*is played by / plays

0..1

0..*

is played by / plays

0..1

0..*


0..*

0..*

is part of / is a collection of0..*

0..*uses / defines use of

0..*

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Haifa Research Lab

Omics in the LS DAM - Specimenclass Specimen Core

SpecimenCollectionProtocolSubject

BiologicEntity

+ actualIndicator: BL+ administrativeGenderCode: CD+ birthCountryCode: CD+ birthDate: TS.DATETIME+ birthOrder: INT.POS+ deathDate: TS.DATETIME+ sexGenotypeCode: CD+ subSpeciesRank: SC

Animal

+ breedCode: CD+ description: ED+ reproductiveOrgansPresentIndicator: BL+ strain: ST

Person

+ deathIndicator: BL+ educationLevelCode: CD+ ethnicGroupCode: DSET<CD>+ initials: ST+ maritalStatusCode: CD+ name: DSET<PN>+ occupationDateRange: IVL<TS.DATE>+ postalAddress: AD+ primaryOccupationCode: CD+ raceCode: DSET<CD>+ telecomAddress: BAG<TEL>

Subject Activity

+ comment: ST+ identifier: II+ reasonCode: DSET<CD>

PerformedActiv ity

+ actualDateRange: IVL<TS.DATETIME>+ /actualDuration: PQ.TIME+ /delayDuration: PQ.TIME+ missedIndicator: BL+ missedReason: DSET<SC>+ /repetitionNumber: INT.POS+ statusCode: CD+ statusDate: TS.DATETIME

PerformedProcedure

+ approachAnatomicSiteCode: CD+ approachAnatomicSiteLateralityCode: CD+ methodCode: CD+ targetAnatomicSiteCode: CD+ targetAnatomicSiteConditionCode: CD+ targetAnatomicSiteLateralityCode: CD

PerformedSpecimenCollection

+ fastingStatusIndicator: BL

PerformedObserv ation

+ bodyPositionCode: CD+ /focalDateRange: IVL<TS.DATETIME>+ /focalDuration: PQ.TIME+ methodCode: DSET<CD>+ targetAnatomicSiteCode: CD+ targetAnatomicSiteLateralityCode: CD

PerformedObserv ationResult

+ baselineIndicator: BL+ bodySystemCode: CD+ comment: ST+ confidentialityCode: CD+ identifier: II+ reportedDate: TS.DATETIME+ result: ANY+ resultCodeModifiedText: ST+ targetAnatomicSiteCode: CD+ targetAnatomicSiteLateralityCode: CD+ typeCode: CD+ uncertaintyCode: CD

PerformedMedicalHistoryResult

+ ageAtDiagnosis: PQ+ endRelativeToReferenceCode: CD+ occurrenceDateRange: IVL<TS.DATETIME>

PerformedClinicalResult

+ asCollectedIndicator: BL+ biomarkerIndicator: BL+ /infectiousAgent: ST+ /normalRangeComparisonCode: CD+ reportedResultStatusCode: CD

PerformedDiagnosis

+ diseaseStatusCode: CD+ recurrenceIndicator: BL

PerformedHistopathology

+ cellTypeCode: DSET<CD>+ differentiationGradeCode: DSET<CD>+ involvedSurgicalMarginIndicator: BL

PerformedLesionDescription

+ appearanceTypeCode: CD+ contactAnatomicSiteCode: CD+ /dimensionProduct: PQ+ lesionNumber: INT.NONNEG+ lymphaticInvasion: CD+ measurableIndicator: BL+ perineuralInvasion: CD+ venousInvasion: CD+ xDimension: PQ+ yDimension: PQ+ zDimension: PQ

PerformedSpecimenQualityRev iew

PerformedPathologicalStaging

+ distantMetastasisStage: CD+ lymphNodeStage: CD+ metastasisSite: CD+ numberLymphNodesExamined: INT+ numberLymphNodesInvolved: INT+ primaryTumorStage: CD

PerformedSpecimenRev iewResult

+ nameCode: CD

PerformedMaterialProcessStep

PerformedSpecimenEmbedded

+ embeddingMediumType: CD

PerformedSpecimenFixed

+ fixationType: CD

PerformedSpecimenFrozen PerformedSpecimenReturn

PerformedSpecimenSpun

+ gravityForce: PQ

PerformedSpecimenThaw

PerformedSpecimenCheckInCheckOut

+ storageStatus: CD

Material

+ description: ST+ effectiveDateRange: IVL<TS.DATETIME>+ formCode: CD+ functionTypeCode: DSET<CD>+ nameCode: CD+ subTypeCode: CD+ typeCode: CD

Specimen no attributesCellCulture

+ biosafetyLevel: CD

ExperimentalItem

+ typeCode: CD


Product

+ expirationDate: TS.DATE.FULL+ lotNumberText: ST.SIMPLE+ typeCode: CD

Equipment

+ manufactureDate: TS.DATETIME+ reprocessedDeviceCode: CD+ validationDate: DSET<TS.DATETIME>

MaterialRelationship

+ subTypeCode: CD+ typeCode: CD

Name: Specimen CoreAuthor: lschickVersion: 1.0Created: 2/7/2011 9:02:28 AMUpdated: 1/10/2012 12:56:05 PM

Container

+ containerType: CD+ description: ST+ dimensionOneCapacity: INT+ dimensionOneLabel: ST+ dimensionPointOfOrigin: ST+ dimensionThreeCapacity: INT+ dimensionThreeLabel: ST+ dimensionTwoCapacity: INT+ dimensionTwoLabel: ST+ name: ST

Place

+ identifier: DSET<II>+ locatorTypeCode: CD+ locatorValue: ST+ physicalAddress: AD+ typeCode: CD

StorageEquipment

+ dimensionOneCapacity: INT+ dimensionOneLabel: ST+ dimensionPointOfOrigin: ST+ dimensionThreeCapacity: INT+ dimensionThreeLabel: ST+ dimensionTwoCapacity: INT+ dimensionTwoLabel: ST

PerformedSpecimenPlacement

+ fromPositionDimensionOne: INT+ fromPositionDimensionThree: INT+ fromPositionDimensionTwo: INT+ toPositionDimensionOne: INT+ toPositionDimensionThree: INT+ toPositionDimensionTwo: INT

BiologicEntityIdentifier

+ effectiveDateRange: IVL<TS.DATETIME>+ identifier: II+ typeCode: CD

Organization

+ actualIndicator: BL+ description: ST+ name: DSET<ON>+ postalAddress: AD+ telecomAddress: BAG<TEL>+ typeCode: CD

SubjectIdentifier

+ effectiveDateRange: IVL<TS.DATETIME>

+ identifier: II+ primaryIndicator: BL+ typeCode: CD

Manufacturer

Processor

Reprocessor

MaterialName

+ name: EN.TN+ typeCode: CD

MaterialIdentifier

+ identifier: II+ typeCode: CD

SpecimenCollectionGroup

+ name: ST

SpecimenCollectionProtocol

+ activeDateRange: IVL<TS>+ aliquotInSameContainer: BL+ consentsWaived: BL+ enrollment: INT+ irbIdentifier: ST+ shortTitle: ST

Protocol

+ name: ST

Laboratory

+ identifier: II

CollectingLaboratory

BRIDG-aligned LS DAM

LS DAM

Legend

DefinedActiv ity

DefinedCompositionRelationship

CellLine

+ originCellName: ST+ passageNumber: INT+ sourceAge: PQ+ sourceAnatomicSiteCode: CD+ sourceDevelopmentalStage: SC+ sourceTissueType: CD

MicrobiologicalCulture

0..1

plays / is played by

0..*

0..*

is the parent of 1

specializes

specializes

0..*

identifies

1

1..*

names/ isnamedby

1

0..*

is assigned by

0..1

specializes

0..1

plays / is played by

0..*

0..*

is a function performed by

{functions as}0..1

specializes

0..*

iscontainedin

0..1

0..*

instantiates

0..1

specializes

1

is the product of / produces

1

1

is the subject of / is performed on

0..*

specializes0..*

is a function performed by

{functions as}1

0..1

is a functionperformed by

{functions as}

1

0..*

is assigned by{assigns}

1

0..*

identifies / isidentified by

{is identified by} 1

0..1

is a function performed by{functions as}

1

0..*

produces

1..*

0..*

executes/ is executed at 1..*

0..*is the component of

1

0..*

is located at/is the location of

1

0..*

is enclosed by / encloses

1

0..*is converted into

0..1

1

is assigner of/is assigned to

0..*

0..*

is assessed via / is an assessment of

0..*

0..*

is part of / includes

0..1

0..1is takenfrom/ takes

0..*

1

has / is a part of

0..*

0..*

is assignedby / assigns

1

0..*

produces / is produced by

0..*

0..*

is derived from / is source of

1

0..*

is performed on / is the subject of

1..*

0..*participates in / is performed on

1

1

functions as / is afunction performed by

0..*

0..*

is a result of

1

specializes

specializes

specializes specializes

specializes

1

isplacedat/places 0..*

0..1


0..*

1..*is collected during / results in

0..1

0..1

produces / is the product of

0..1

0..* is part of / iscomposed of

1

0..*

is an assessment of / is assessed via

0..*

0..1

performs / is performed at

1..*

0..*

is participated inby / participatesin0..1

1

is identifiedby /identifies

0..*

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Haifa Research Lab

Gene Expression Topic (outdated)

Domain Analysis Model (DAM) Passed informative

ballot Based on several

models for geneexpression dataalong with extensions

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Haifa Research Lab

The Domain Information Model - Genome

Individual Allele

Bio Sequenc

e

Sequence Variation

(SNP, Mutation,

Polymorphism, etc.)

Polypeptide

Expression Data

Phenotype

Entry Point: Geneome

Expression

Attributes

Variation

Attributes

Encapsulating Obj.

Bubbled-up Obj.

genotypephenotype

Genetic Loci

Genetic Locus

Non-locus specific

data

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Haifa Research Lab

Example: Family History XML Encoding

Point

back…

Bubble

up… To

phenotype

and beyond….

Taken from a patient pedigree, the

portion related to patient’s daughter

(in collaboration with Partners HealthCare

& other HL7 CG SIG members)

Point back to the raw data of this relative providing “personal evidence”

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Haifa Research Lab

XML Fusion: Encapsulation of Raw Genomic DataR

aw g

eno

mic

dat

a re

pre

sen

ted

in

Bio

info

rmat

ics

mar

kup

HL

7 v3

XM

L

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Haifa Research Lab

The Phenotype Model

Observed Phenotype

Interpretive

Phenotype

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Haifa Research Lab

The Genetic Variation CMET (passed normative in Jan. 2010)

Genetic Loci

Genetic

Locus

Individual Allele

Sequence

Variation

Sequence

(observed or reference)

Participants

(including specimen)

Associated data (vocab. Controlled)

Observed or Interpretive phenotypes

Genetic Report (CDA)

Genetic Testing Order

Timing issues: collecting specimen, extracting genetic material, identifying genomic observations, interpretation

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Haifa Research Lab

The HL7 RCRIM CT Laboratory Model- The Pharmacogenomics Extension

Utilizes the Clinical Genomics

CMET

Genetic Lab

Clinical

Trial

Enrolled Subject

Specimen

Consent to Genotype

Pharmacogenomics Test

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Haifa Research Lab

The Gene Expression CMET Draft

Genetic Loci

Genetic Locus

Gene Expression

Associated observations

GTR Report

Participants

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Haifa Research Lab

The CG V3 Query Model: Query by Parameter

QueryByParameterPayload(QueryByParameter)queryId: II [0..1]statusCode: CS CNE [0..1] <= QueryStatusCoderesponseElementGroupId: SET<II> [0..*]responseModalityCode: CS CNE [0..1] <= ResponseModalityresponsePriorityCode: CS CNE [0..1] <= QueryPriorityinitialQuantity: INT [0..1]initialQuantityCode: CE CWE [0..1] <= QueryRequestLimit

ControlActProcessclassCode*: <= CACTmoodCode*: <= ActMoodCompletionTrack

0..1queryByParameterPayload

GeneticLocus.value(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (GeneticLocus.value)

0..*geneticLocus.value

Query(POCG_RM000090)

Entry point for Clinical Genomics query message

GeneticLocus.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (GeneticLocus.ID)

0..*geneticLocus.id

IndividualAllele.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (IndividualAllele.id)

IndividualAllele.value(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (IndividualAllele.value)

0..1individualAllele.value

0..*individualAllele.id

SequenceVariation.value(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (SequenceVariation.value)

SequenceVariation.id(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (SequenceVariation.id)

0..1sequenceVariation.value

0..1sequenceVariation.id

Expression.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Expression.id)

Sequence.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Sequence.id)

0..*sequence.id

0..*expression.id

Polypeptide.value(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Polypeptide.value)

Polypeptide.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Polypeptide.id)

0..*polypeptide.value

0..*polypeptide.id

DeterminantPeptide.value(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (DeterminantPeptide.value)

DeterminantPeptide.id(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (DeterminantPeptide.value)

0..*determinantPeptide.value

0..*determinantPeptide.id

GeneticLoci.id(ParameterItem)value: II CWE [0..1]semanticsText: ST [0..1] (GeneticLoci.id)

GeneticLoci.value(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (GeneticLoci.value)

0..*geneticLoci.value

0..*geneticLoci.id

GeneticLoci.code(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (GeneticLoci.code)

0..*geneticLoci.code

ClinicalPhenotype.id(ParameterItem)value: II CWE [0..1]semanticsText: ST [0..1] (ClinicalPhenotype.id)

ClinicalPhenotype.code(ParameterItem)value: CD CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (ClinicalPhenotype.code)

ClinicalPhenotype.value(ParameterItem)value: ANY CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (ClinicalPhenotype.value)

0..*clinicalPhenotype.id

0..*clinicalPhenotype.code

0..*clinicalPhenotype.value

RecordTarget.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (RecordTarget.id)

0..*recordTarget.id

Subject.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Subject.id)

0..*subject.id

Performer.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Performer.id)

0..*performer.id

Author.id(ParameterItem)value: II CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Author.id)

0..*author.id

Method.code(ParameterItem)value: CE CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Method.code)

Interpretation.code(ParameterItem)value: CE CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (Interpretation.code)

effectiveTime(ParameterItem)value: GTS CWE [0..1] <= QueryParameterValuesemanticsText: ST [0..1] (effectiveTime)

0..*method.code

0..*interpretation.code

0..*effectiveTime

GeneticLocus parameters

Starting point with query

identifiers and attributes

Miscellaneous parameters

GeneticLoci parameters

participants parameters

Phenotype parameters

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Haifa Research Lab

V2 Implementation Guides

The IG “Genetic Test Result Reporting to EHR” passed informative ballot

It is modeled after the HL7 Version 2.5.1 Implementation Guide: Orders And Observations; Interoperable Laboratory Result Reporting To EHR (US Realm), Release 1

Is used in a pilot of information exchange between Partners Healthcare and Intermountain Health Care

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Haifa Research Lab

V2 update for January 2012

Genetic variations

Cytogenetics

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Haifa Research Lab

The v2 Message Structure

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Haifa Research Lab

V2 Sample Message OBR|1||PM-08-J00094^HPCGG-LMM^2.16.840.1.113883.3.167.1ÎSO|

lm_DCM-pnlB_L^Dilated Cardiomyopathy Panel B (5 genes)^99LMM-ORDER-TEST-ID||20080702000000|20080702100909|||||||||234567891^Pump^Patrick^^^^^^NPI^L||||||20080703000000|||F||||||00000009^Cardiovascular^99HPCGG-GVIE-INDICATION^^^^^^Clinical Diagnosis and Family History of DCM|&Geneticist&Gene&&&&&NPI^^^^^^^HPCGG-LMM&2.16.840.1.113883.3.167.1&ISO|||||||||||||||55233-1^Genetic analysis master panel ^LN

SPM|1|||119273009&Peripheral blood&SNM3&&&&0707Intl&&Blood, Peripheral|||||||||||||20080702000000

OBR|2||PM-08-J00094-1^HPCGG-LMM^2.16.840.1.113883.3.167.1ÎSO|55232-3^Genetic analysis summary panel^LN|||20080702000000|||||||||||||||20080703000000|||F||||^PM-08-J00094&HPCGG-LMM&2.16.840.1.113883.3.167.1&ISO

OBX|1|CWE|51967-8^Genetic disease assessed^LN||399020009^DCM-Dilated Cardiomyopathy^SNM3^^^0707Intl||||||F|20080702100909|||||||||||Laboratory for Molecular Medicine^L^22D1005307^^^CLIA&2.16.840.1.113883.4.7&ISO|1000 Laboratory Lane^Ste. 123^Cambridge^MA^99999ÛSA^B

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Haifa Research Lab

CDA IG: Genetic Testing Report (GTR)

Define an implementation guide for a genetic testing report that is both human readable and machine-processable Target at all types of GTR producers, e.g., genetic labs, clin. geneticists Readable content is larger in scope E.g., detailed description of the tests performed along with references Machine-processable should be limited, e.g., exclude raw data

Ballot a Universal IG; then derive specific types of GTR: Healthcare & Research Realm-specific guides Omic-specific guides

Developed using the MDHT open source tool (OHT)

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Haifa Research Lab

GTR - Design Principles

Follow existing report formats commonly used in healthcare & research

Emphasize interpretations & recommendations

Provide general background information on tests performed

Reference HL7 Clinical Genomics instances (e.g., v3 or v2 GeneticVariation and Pedigree) as the place holders of full-blown raw genomic data and fully-structured family history data

Utilize patterns of ‘genotype-phenotype’ associations in the HL7 v3 Clinical Genomics Domain Implement them as ‘clinical genomic statement’ entry-level templates

(see next slide), enabling meaningful use of the data

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Haifa Research Lab

The Clinical Genomic Statement

An abstract Clinical Genomic Statement (CGS) template that Has at its core a genomic observation (e.g., a DNA sequence variation) If it’s a reportable finding, then it should be associated with indications and interpretations,

specimen and genomic source class The major finding can be associated with associated observation (e.g., amino acid change) Optionally, performers may be specified (overriding header performers)

The CGS abstract template is instantiated by specialized CGS’s, e.g., for genetic variations or cytogenetics

Indications InterpretationsGenomicObservation

Performers

SpecimenGenomic Source

Clin

ical

Gen

om

ic S

tate

men

t

Associated Observations

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Haifa Research Lab

Narrative and Structured Data

All CGS structured data items shall be part of clinical genomic statement (CGS) instances so that parsing applications can find the full semantics explicitly represented in one coherent structure In the case of the overall interpretation, it is part of CGS that has references to

the various testing interpretations

Sub-sections such as Indications, Interpretations and Specimen are mainly for presenting narrative, but they may also contain structured data In this way, it is possible to have less redundant documents, e.g., in the case

where all tests reported in a GTR document have the same indication, an Indications section in the Summary section consists of a full-blown indication observation which all CGS indication observations reference

CGS structured data may point to the respective narrative in sub-sections (by means of XML ID)

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Haifa Research Lab

GTR Overall Layout

Sections order

constraint

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Haifa Research Lab

GTR Rendered – The Header

Draft that has not been clinically validated

31

Haifa Research Lab

GTR Rendered – Summary Section


32

Haifa Research Lab

GTR Rendered – Genetic Variation Sections


33

Haifa Research Lab

GTR Rendered – Test Information Section


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Haifa Research Lab

GTR Main Hierarchies

Test Details Section

• specimen

• indications

• interpretations

• test performed

• findings

• test information

Genetic Variations Section

• Genetic variations CGS

Cytogenetic Section

• Genetic variations CGS

Gene Expression Section

• Gene Expression CGS

Clinical Genomic Statement (CGS)

Genetic Variations CGS

• GV Associated Observations

• GV Interpretive Phenotypes

Cytogenetic CGS

• Cyt Associated Observations

• Cyt Interpretive Phenotypes

Gene Expression CGS

• GE Associated Observations

• GE Interpretive Phenotypes

Abstract section template w/common

sub-sections:

Extended by specialized

sections

Abstract CGS template:

Extended by specialized CGS’s

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Haifa Research Lab

GTR UML Model - Section Outline

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Haifa Research Lab

GTR UML Model - Summary Section

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Haifa Research Lab

GTR Genetic Variation Section

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Haifa Research Lab

Clinical Genomic Statement

Extended by specialized Clinical Genomic Statements

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Haifa Research Lab

Interpretive Phenotype Observation

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Haifa Research Lab

GTR XML Snippets – Indications Section

Indication’s narrative

Indication’s structured

data

Summary Section

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Haifa Research Lab

GTR XML Snippets – Specimen Section

Specimen’s narrative

Specimen’s structured data

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Haifa Research Lab

GTR XML Snippets – Overall Interpretation Section

Interpretation’s narrative

Structured Interpretation

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Haifa Research Lab

GTR XML Snippets – Genetic Variation Section

Genetic Variation

Genetic Variation

associated observations

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Haifa Research Lab

GTR XML Snippets – Genetic Variation Section (cont.)

Genetic Variation indication

Genetic Variation

interpretation

45

Haifa Research Lab

CDA GTR Ballot Status

Balloted as DSTU and passed in October 2010 Still under ballot to refine & reconcile ballot comments Main issues:

Vocabulary: Universal spec vs. Realm (e.g. mandate the use of LOINC code?) Binding syntax (align with new vocabulary spec and the respective

SDWG guidance for CDA IGs) Layout:

Semantics – compare to recommended layouts in the literature Syntactic – works closely with MDHT developers to adhere to SDWG

guidelines Sections specific to every type of genetic test (derived from abstract) Section and Entry level template ids registration (when layout agreed) Suggestion to add drug safety template (considered for future use)

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Haifa Research Lab

Alignment Among the Various Specs

v3 specs and CDA are all based the RIM CDA GTR-IG will be based on CDA R3 Depending on the “right side” of R3, if it allows RIM-based domain

models, then alignment is trivial

v3-v2 alignment: Proposal: represent semantics with v3 and implement it in various

ways, one of which is v2; develop an “v2 ITS” for the v3 models See proposal made by Amnon in a separate presentation

(click here to see that presentation)

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Haifa Research Lab

Utilizations in HL7

Clinical Trials:HL7 RCRIM Work Group (clinical trials specs) utilized the CG DSTU model (Genetic Locus) in their Pharmacogenomics message, which was an extension of the CTLab message (an approved but expired DSTU)

Laboratory:The Lab Work Group might utilize a constrained version of the Genetic Variation model in their next release if the Lab Result message

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Haifa Research Lab

Selected Implementation

v2 Exchange of genetic testing results between Intermountain and Harvard

v3 The Family History spec is used in Mass General Hospital Expanding to other family history applications including the

US Surgeon General Family History tool

The Genetic Variation model is used in Hypergenes (a European project on essential hypertension, http://www.hypergenes.eu/)

The Pedigree and Genetic Variation models are used in Italy, the Rizzoli institute in Bologna

CDA GTR has been used in uHealth – a PHR/EHR system in Korea

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Haifa Research Lab

HL7 WG Health Check – Need to Improve!

Active projects SWOT current 3 year plan current Mission and charter current Co-chair post-WGM survey participation Ballot presence Minutes posted since last WGM Last listserv activity Wiki presence WG conference calls schedules Steering division conference call participation Steering division co-chair (TSC representation) election participation WG rep at steering division WGM WG meetings at WGM scheduled WG has an approved DMP based on review of the updated template

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Haifa Research Lab

Planning ahead

May 2012 WGM (Vancouver) Schedule (from Tuesday Q3 to Thursday Q2) Joint meetings

AP – Wed Q4 CDS - informal OO+AP – Wed Q1

Weekly conf. calls Continue Tuesday’s 11EST

Submit ‘renewed’ PSSs for GTR and Omics

Prepare to ballot GTR, Omics & Sequencing storyboards in May 2012

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Haifa Research Lab

Summary

Small group coping with Various HL7 formats: v3, v2 and CDA Clinical & Research environments

Developing a DAM and component models (CMETs) to be used in other HL7 domains Genetic Variation Gene Expression

CDA Genetic Testing Report (GTR) Bridge from raw data to human readable reports and bubbled-up data Model-driven development of standards (use of MDHT CDA Editor)

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Haifa Research Lab

The End

• Thank you for your attention…

• Questions? Contact Amnon at [email protected]

• Comments of general interest should be posted to the CG mailing list at [email protected]