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SMART/FHIR Genomic Resources

SMART/FHIR Genomic Resources. An overview. Change Log. Made a few changes to Sequence resource Added data support for alignment data (e.g. SAM or BAM file)

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SMART/FHIR Genomic Resources

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  1. SMART/FHIR Genomic Resources An overview...

  2. Change Log • Madea few changes to Sequence resource • Added data support for alignment data (e.g. SAM or BAM file) • VCFMeta, VCFVariant, GVFMeta, GVFVariant, AlignmentMeta, AlignmentRead are exchanged using REST path /binary, recognized as a Binary resource • SequencingLab replaced with an extension to Procedure resource • GeneticAnalysis replaced with an extension to Observation resource

  3. List of Genomic Resources Genetic Analysis • Implemented as an extension to Observation resource • Summary of genetic test • Documentation of phenotype-genotype association • Clinical decision support

  4. Extension to Observation resource Added fields below to establish genotype-phenotype association • phenotype : CodeableConcept // 0..1 Target phenotype in the observation; reason why the observation is performed • variantObservation : { identifier : string // 0..1 HGVS nomenclature of the variant genotype : Resource(Sequence) // 1..1 reference to genotype interpretation : CodeableConcept // 0..1 interpretation of genotype comment : string // 0..1 comment... } // 0..*

  5. List of Genomic Resources Raw data encapsulation (e.g. VCF Variant) • Encapsulates a row of raw genetic data (VCF, GVF, SAM, BAM) • With reference to original file • Change note: We now support encapsulation of alignment files SAM/BAM

  6. List of Genomic Resources Abstract representation - Sequence • An abstract of VCFVariant/GVFVariant • Enables developer to view genotypes without being constrained by file formats • References raw data (e.g. reference to VCFVariant)

  7. List of Genomic Resources Sequencing Lab • “Folders” containing files of genetic data • Facilitatescollaboration in research (bulks of data can be shared via the API between variouslabs) • Implemented as an extension to Procedure resource

  8. Extension to Procedure resource Added fields below to document sequencing labs • species : CodeableConcept // 1..1 species of the sample used in the sequencing lab • sample : { type: code // 1..1 type of the sample used in the sequencing lab source : CodeableConcept // 0..1 specific sample used } // 1..1 • assembly : code // 0..1 assembly used in for alignment for analysis • file : attachment // 0..* File generated from the lab for analysis

  9. Use Case – Clinical Decision Support • Developer A has access to database documenting genotype-phenotype association • Query Sequence resource with region of interest • Map the result against database and find out potential risk factor of patient • Profile discovery of such risk factors with GeneticObservation

  10. Use Case – File Analysis • Developer B found some VCF files attached in /procedure/123 as result generated from sequencing lab • User can query for regions that he/she is interested in using the API • VCFVariant – variant (genotypic) information • VCFMeta – legends that help user understand some of the user-defined data within the variant info

  11. Sequence

  12. VCF Meta

  13. VCF Variant

  14. GVF Meta

  15. GVF Variant

  16. Alignment Meta

  17. Alignment Read

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