Hl7 clinical genomics and structured documents work groups
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HL7 Clinical Genomics and Structured Documents Work Groups. CDA Implementation Guide: Genetic Testing Report DRAFT PROPOSAL Amnon Shabo (Shvo), PhD [email protected] HL7 Clinical Genomics WG Co-chair and Modeling Facilitator HL7 Structured Documents WG CDA R2 Co-editor

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Hl7 clinical genomics and structured documents work groups

HL7 Clinical Genomics and Structured Documents Work Groups

CDA Implementation Guide:

Genetic Testing Report

DRAFT PROPOSAL

Amnon Shabo (Shvo), PhD

[email protected]

HL7 Clinical Genomics WG

Co-chair and Modeling Facilitator

HL7 Structured Documents WG

CDA R2 Co-editor

CCD Implementation Guide Co-editor


The hl7 clinical genomics sig

HL7 Clinical Genomics -

A bridge standard…

MAGE

HL7

DICOM

X12

BSML

PSI

GenBank

ICD

HUGO

SNOMED

SwissProt

LOINC

The HL7 Clinical Genomics SIG

  • 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

Genomic Data

Clinical Data


How to handle raw and mass data

How to Handle Raw and Mass Data

  • Could we learn from the imaging integration effort?


Hl7 clinical genomics v3 static models

HL7 Clinical Genomics v3 Static Models

Family

History

CDA IG

Normative

RCRIM

LAB

Reference

DSTU

Utilize

Utilize

Utilize

Utilize

Reference

Comments

Genetic

Loci

Other domains

Constrained

GeneticVariation

Utilize

Implementation Topic

Genetic

Locus

Constrained

Gene Expression

Implementation Topic

Utilize

Phenotype

(utilizing the HL7

Clinical Statement)


Hl7 clinical genomics and structured documents work groups

The GeneticLocus Model - Focal Areas:

Expression

Data

The Locus

and its Alleles

Sequence

and

Proteomics

Sequence

Variations

Clinical

Phenotypes


The underlying paradigm encapsulate bubble up

The Underlying Paradigm:Encapsulate & Bubble-up

Genomic Data Sources

Clinical Practices

the challenge…

HL7 CG Messages with encapsulated data associated with

HL7 clinical objects (phenotypes)

Knowledge

(KBs, Ontologies, registries,

reference DBs, Papers, etc.)

HL7 CG Messages with mainly

Encapsulating HL7 Objects

Encapsulation by predefined & constrained bioinformatics schemas

EHR System

Bubbling-up is done continuously by specialized DS applications

Decision Support Applications

Bubble up the most clinically-significant raw

genomic data into specialized HL7 objects and

link them with clinical data from the patient EHR


The geneticlocus model

Entry Point: GeneticLocus

The GeneticLocus Model

Encapsulating Obj.

Individual Allele

Determinant

Polypeptide

Bubbled-up Obj.

Bio Sequence

Expression

Attributes

Expression Data

Related

Allele

Polypeptide

genotypephenotype

Clinical Phenotype

Variation

Attributes

Sequence Variation

(SNP, Mutation,

Polymorphism, etc.)


The geneticvariation model

Genetic Loci

Genetic Locus

The GeneticVariation Model

Associated data (vocab. Controlled)

participants

Individual Allele

Point to CDA Documents

Sequence

(observed or reference)

Sequence Variation


Cda ig for genetic testing report

CDA IG for Genetic Testing Report

  • Design principles:

    • Follow existing report formats commonly used in healthcare & research

      • Emphasis on interpretations & recommendations

      • Provide inline & detailed (generic) information on tests performed

    • Interpretation: Utilize patterns of ‘genotype-phenotype’ associations in the HL7 v3 Clinical Genomics and implement them as templates in this IG

    • Reference HL7 Clinical Genomics instances (most likely constrained)

      • Place holders of raw data (evidences) and for structured family history

  • Section outline:

    • Content sections: Genetic Variations, Gene Expression, others

    • Sub-sections in each content section:

      • Specimen

      • Findings

      • Interpretations

      • Recommendations

      • Test Information

      • Family History

Open the draft outline


Technical issues

Technical Issues

  • Design & register genotype-phenotype templates

    • Similar a bit to the CCD templates for “Allergies, Adverse Reactions, Alerts” where ‘agent’ is the genomic entity/observation and the reaction is the phenotypic information

    • Note that in CCD the relationship is fixed to “MFST” while in genomics we’ll have a variety of codes representing various ‘genotype-phenotype’ relationships

  • Enable associating a genotype to phenotypes in several places across the document (reference an observation)

  • Links to HL7 v3 Clinical Genomics instances

    • Similar to referencing images in CDA Diagnostic Report IG


Hl7 clinical genomics and structured documents work groups

Cause of allergy

Allergen is manifested by…

Manifestation of the allergy


Referencing a dicom object

Referencing a DICOM Object


The end

The End

  • Thank you for your attention… 

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