SMART/FHIR Genomic Resources

SMART/FHIR Genomic Resources

An overview...

Tom Chen

Possible names: geneticSummaryAnalysis

Tom Chen

TODO: change PhenotypeAnalysis to something less confusing

Tom Chen

The "report" field sort of overlaps with the "text" field (narrative) of generic FHIR resources. Don't know if we should leave this here -- as this is important for emphasizing the "summary" aspect of the resource, we don't want to make it redundant

Tom Chen

TODO: finish this

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..*


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


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)


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

SMART/FHIR Genomic Resources

Documents

alignment data

vcf files

procedure resource extension

row of raw genetic data

userdefined data

vcf variantencapsulates

research bulks of data

observation reason