SMART/FHIR Genomic Resources

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Presentation transcript:

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 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

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

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

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

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

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

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

Finding Drug Resistant TB 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)