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

• 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 variantgenotype : Resource(Sequence) // 1..1 reference to genotypeinterpretation : CodeableConcept // 0..1 interpretation of genotypecomment : 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 resourceAdded 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 labsource : 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