1. SMART/FHIR Genomic Resources An overview...

2. Change Log Added 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

3. 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

4. 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..*

5. 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 supports encapsulation of alignment files SAM/BAM

6. 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)

7. List of Genomic Resources “Folder resource” -- Sequencing Lab “Folders” containing files of genetic data Facilitate collaboration in research (bulks of data can be shared via the API among difference labs) Implemented as an extension to Procedure resource

8. 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

10. Sequence

11. VCF Meta

12. VCF Variant

13. GVF Meta

14. GVF Variant

15. Alignment Meta

16. Alignment Read