SMART/FHIR Genomic Resources An overview... For latest see

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 GeneticAnalysis replaced with an extension to Observation resource

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

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..*

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 abstract 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 (bulks of data can be shared via the API between various labs) Implemented as an extension to Procedure resource

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

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

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