Post on 22-Feb-2016
description
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 ResourcesGenetic Analysis • Implemented as an extension to Observation resource
• Summary of genetic test
• Documentation of phenotype-genotype association
• Clinical decision support
Extension to Observation resourceAdded 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 ResourcesRaw 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 ResourcesAbstract 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 ResourcesSequencing 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