SMART/FHIR Genomic Resources

SMART/FHIR Genomic Resources

An overview...For latest see

http://smartgenomics.wikispaces.com/Clinical+Genomics+Presentation

Change Log

•Made a 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•GeneticObservation replaced with an extension to Observation resource

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 : CodeableConcept // 0..1 Target phenotype in the observation; reason why the observation is performed●variantIdentifier: 1..1 HGVS nomenclature of the variant●variant : Resource(Sequence) // 1..1 reference to genotype

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

List of Genomic Resources

Abstract representation - Sequence•An abstraction of VCFVariant/GVFVariant

•Enables developer to view genotypes without being constrained by file formats

•References raw data (e.g. reference to VCFVariant)

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 ObservationAdded fields below to document sequencing labs●species : CodeableConcept // 1..1 species of the sample used in a sequencing lab●sampleType: code // 1..1 type of the sample used in a sequencing lab●sampleSource : CodeableConcept // 0..1 specific sample used●assembly : code // 0..1 assembly used in for alignment for analysis●file: Attachment // 0..* files generated from a sequencing lab

Use Case – Clinical Decision Support

•Developer A has access to database for 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

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

Sequence

VCF Meta

VCF Variant

GVF Meta

GVF Variant

Alignment Meta

Alignment Read