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

2. List of Genomic Resources
Genetic Observation
Implemented as an extension to Observation resource
Summary of genetic test
Documentation of phenotype-genotype association
Clinical decision support

3. Extension to Observation resource
Added fields below to establish genotype-phenotype association
traitAssesed : Target of the observation; reason why the observation is performed
variantIdentifier : HGVS nomenclature of the variant
variant : reference to genotype

4. List of Genomic Resources
Abstract representation - Sequence
Enables developer to view genotypes without being constrained by file formats
References raw data

5. List of Genomic Resources
Sequencing Lab
“Folders” containing files of genetic data
Facilitates collaboration in research (files can be shared via the API between various labs)
Implemented as an extension to Observation resource

6. Extension to Observation Observation
Extended fields
Species : e.g. Homo sapiens
sampleType : e.g. germline
sampleSource : e.g. saliva
assembly : assembly used for alignment
readSets : readset

8. Use Case – Breast Cancer Testing
Developer A has access to database for variants associated with breast cancer
Query Sequence resource with regions within BRCA1 and BRCA2
Map the result against database and find out potential risk factor of patient
Profile discovery of such risk factors with GeneticObservation
With the reported risk factors and family history, physicians order further testing to confirm diagnosis

10. 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

11. Use Case – Prenatal Testing
Users need to analyze sequencing data from infant
Query Sequence resource by specifying sample type
GET Sequence?sampleType=prenatal&coordinates=...

12. Finding Drug Resistant TB
Use Case –
Finding Drug Resistant TB
API Supports capturing microbial sequencing data – GET /Sequence?species={SNOMED coding of species}&coordinates=...
Developer can query by species (default is homo sapien – i.e. sequences directly from patients)
Source of the sample captured in Sequence resource can also be useful – allows developer to find out where the bacteria are from (i.e. lung)