1 / 19

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)

agnes
Download Presentation

SMART/FHIR Genomic Resources

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related