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SMART/FHIR Genomic Resources

SMART/FHIR Genomic Resources. An overview. List of Genomic Resources. Genetic Observation Implemented as an extension to Observation resource Summary of genetic test Documentation of phenotype-genotype association Clinical decision support. Extension to Observation resource.

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SMART/FHIR Genomic Resources

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

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

  3. Extension to Observation resource • Added fields below to establish genotype-phenotype association • traitAssesed: Target of the observation; reason why the observation is performed • variantIdentifier: HGVS nomenclature of the variant • variant : reference to genotype

  4. List of Genomic Resources • Abstract representation - Sequence • Enables developer to view genotypes without being constrained by file formats • References raw data

  5. List of Genomic Resources • Sequencing Lab • “Folders” containing files of genetic data • Facilitates collaboration in research (files can be shared via the API between various labs) • Implemented as an extension to Observation resource

  6. Extension to Observation Observation • Extended fields • Species : e.g. Homo sapiens • sampleType: e.g. germline • sampleSource: e.g. saliva • assembly: assembly used for alignment • readSets: readset

  7. Use Case – Breast Cancer Testing • Developer A has access to database for variants associated with breast cancer • Query Sequence resource with regions within BRCA1 and BRCA2 • Map the result against database and find out potential risk factor of patient • Profile discovery of such risk factors with GeneticObservation • With the reported risk factors and family history, physicians order further testing to confirm diagnosis

  8. 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

  9. Use Case – Prenatal Testing • Users need to analyze sequencing data from infant • Query Sequence resource by specifying sample type • GET Sequence?sampleType=prenatal&coordinates=...

  10. Use Case – Finding Drug Resistant TB • API Supports capturing microbial sequencing data – GET /Sequence?species={SNOMED coding of species}&coordinates=... • Developer can query by species (default is homo sapien – i.e. sequences directly from patients) • Source of the sample captured in Sequence resource can also be useful – allows developer to find out where the bacteria are from (i.e. lung)

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