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SMART/FHIR Genomic Resources. An overview. Change Log. Made a few changes to Sequence resource Added data support for alignment data (e.g. SAM or BAM file) - PowerPoint PPT Presentation
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SMART/FHIR Genomic Resources
An overview...
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