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HL7 Clinical Genomics – Implementation Roadmap

HL7 Clinical Genomics – Implementation Roadmap

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HL7 Clinical Genomics – Implementation Roadmap

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  1. HL7 Clinical Genomics – Implementation Roadmap The HL7 Clinical Genomics SIG Amnon Shabo (Shvo), PhD HL7 Clinical Genomics SIG Co-chair and Modeling Facilitator HL7 Structured Documents TC CDA R2 Co-editor CCD Implementation Guide Co-editor

  2. V2 :||: V3 Challenges • What should be the position of the HL7 community towards independent modeling attempts of v2 messages applied to new domains that have been solely modeled in v3? • What’s the long term vision? • Gradual conversion to v3 until v2 is deprecated? Or - • V2/V3 Co-existent? If so - how? • Divergence is the current situation: • V3 and V2 ‘languages’ have different semantics • V2 - V3 ‘attribute mapping’ does NOT help when semantics at the source level is different, e.g., different structures, dynamics, etc.

  3. Proposed Approach • Recognize V3 models as a single source of semantics • Refer to V2 messages is a partial v3 implementation • Automatically generate v2 messages from v3 models, much like the V3 XML ITS • Acknowledge the incompleteness of the v2 implementation, but • Address specific requirements of use cases • Let the operator of the v3v2 generator make domain choices • Document the gaps • Imply missing semantics from the v3 models

  4. A Proposed Roadmap for CG Implementations The Clinical Genomics semantics: represented by normative HL7 V3 Models CDISC SDTM V2 message generation V3 XML ITS Implementation Technologies: Family History Implementation Pharmacogemomics Implementation Genetic testing Implementation Balloted informative implementation specifications

  5. Genetic Loci Genetic Locus Example: The GeneticVariation Model Associated data (vocab. Controlled) participants Individual Allele Genetic Document Sequence (observed or reference) Sequence Variation

  6. New ITS Tool: Domain-Specific V3V2 Generator Subject Associated data PID OBR OBX OBX OBX Sequence Variation Individual Allele Genetic Locus Genetic Loci User-defined preferences OBR OBR OBR OBR OBX OBX OBX OBX OBX OBX OBX OBX OBX OBX OBX OBX

  7. GeneticVariation in V2 (with V3 similarities) V3 GeneticLoci overall ‘summary’ e.g., GeneticLoci.interpretationCode V3 GeneticLocus & SequenceVariation e.g., GeneticLocus.value

  8. What Should the V3V2 ITS Tool Facilitate? • Consistently capture v3 structural codes & clone names in v2 fields (is it doable?) • The choice of v2 ‘common patterns’, e.g.: • Patterns of implementing v3 nesting clones (Sub-ID? Parent id?) • Document common gaps like v3 associations • Transform v3 XML schemas to v2 XML-encoded and on to v2 ASCII