Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

## Example Bundle: bundle-cgexample

Bundle bundle-cgexample of type collection

Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/report

Resource DiagnosticReport:

> Profile: Genomic Report

> ## Genetic analysis report (Genetics)

> Subject | Anonymous Patient (no stated gender), DoB Unknown
> When For | 2016
> Reported | 2016-09-06 00:00:00-0500
> Performer | Organization Some lab

> Report Details

> Code | Value | Flags
> Genetic variant assessment | Present | Final
> Diagnostic Implication |  | Final
> Genetic variant assessment | Present | Final
> Diagnostic Implication |  | Final
> Haplotype name | *2 | Final
> Genotype display name | CYP2C9 *2/*5 | Final
> Therapeutic Implication |  | Final
> Therapeutic Implication |  | Final

> Coded Conclusions:

> - Positive
> - Positive

Entry 2 - fullUrl = http://example.org/fhir/Patient/ExamplePatient

Resource Patient:

> This would contain patient identifiers, demographics, etc.

Entry 3 - fullUrl = http://example.org/fhir/Specimen/ExampleSpecimen

Resource Specimen:

> subject: Anonymous Patient (no stated gender), DoB Unknown

Entry 4 - fullUrl = http://example.org/fhir/Organization/ExampleLab

Resource Organization:

> name: Some lab

Entry 5 - fullUrl = http://example.org/fhir/ServiceRequest/ExampleServiceRequest

Resource ServiceRequest:

> status: Active

> intent: Original Order

> code: No display for ServiceRequest.code (concept: Genetic analysis report)

> subject: Anonymous Patient (no stated gender), DoB Unknown

Entry 6 - fullUrl = http://example.org/fhir/Observation/discrete-variant

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> value: Present

> specimen: Specimen

> > component

> > code: Discrete genetic variant

> > value: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)

> > component

> > code: Gene studied [ID]

> > value: ACAD9

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_014049.4

> > component

> > code: Genomic reference sequence [ID]

> > value: NG_017064.1

> > component

> > code: Genomic DNA change (gHGVS)

> > value: NC_000003.11:g.128625063C>T

> > component

> > code: Discrete genetic variant

> > value: rs368949613

> > component

> > code: DNA change (c.HGVS)

> > value: NM_014049.4:c.1249C>T

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_054768.2:p.Arg417Cys

> > component

> > code: DNA change type

> > value: Substitution

> > component

> > code: Genomic ref allele [ID]

> > value: C

> > component

> > code: Genomic allele start-end

> > value: 31731-31731

> > component

> > code: Genomic alt allele [ID]

> > value: T

> > component

> > code: Cytogenetic (chromosome) location

> > value: 3q21

> > component

> > code: Genomic source class [Type]

> > value: Germline

> > component

> > code: Allelic state

> > value: Heterozygous

> > component

> > code: Sample variant allelic frequency [NFr]

> > value: 47 % (Details: UCUM code% = '%')

> > component

> > code: Allelic read depth

> > value: 208 1 (Details: UCUM code1 = '1')

> > component

> > code: Genomic structural variant copy number

> > value: 1 1 (Details: UCUM code1 = '1')

> > component

> > code: Structural variant reported arrCGH [Ratio]

> > value: 0.48

> > component

> > code: Structural variant [Length]

> > value: 1396929 1 (Details: UCUM code1 = '1')

> > component

> > code: Structural variant outer start and end

> > value: 13200589-15592000

> > component

> > code: Structural variant inner start and end

> > value: 14184616-15581544

Entry 7 - fullUrl = http://example.org/fhir/Observation/dis-path

Resource Observation:

> Profile: Diagnostic Implication

> status: Final

> category: Laboratory, Genetics

> code: Diagnostic Implication

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> derivedFrom: Observation Genetic variant assessment

> > component

> > code: Genetic variation clinical significance [Imp]

> > value: Pathogenic

> > component

> > code: Associated phenotype

> > value: acyl-CoA dehydrogenase 9 deficiency

Entry 8 - fullUrl = http://example.org/fhir/Observation/complex-variant

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> value: Present

> specimen: Specimen

> hasMember:

> - Observation Genetic variant assessment
> - Observation Genetic variant assessment

Entry 9 - fullUrl = http://example.org/fhir/Observation/complex-dis-path

Resource Observation:

> Profile: Diagnostic Implication

> status: Final

> category: Laboratory, Genetics

> code: Diagnostic Implication

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> derivedFrom: Observation Genetic variant assessment

> > component

> > code: Genetic variation clinical significance [Imp]

> > value: Pathogenic

> > component

> > code: Associated phenotype

> > value: Debrisoquine adverse reaction (disorder)

Entry 10 - fullUrl = http://example.org/fhir/Observation/complex-component-D

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> value: Present

> specimen: Specimen

> > component

> > code: Discrete genetic variant

> > value: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_000106.5

> > component

> > code: DNA change (c.HGVS)

> > value: NM_000106.5:c.886C>T

> > component

> > code: Amino acid change (pHGVS)

> > value: NP_000097.3:p.Arg296Cys

> > component

> > code: DNA change type

> > value: Substitution

Entry 11 - fullUrl = http://example.org/fhir/Observation/complex-component-E

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> value: Present

> specimen: Specimen

> > component

> > code: Discrete genetic variant

> > value: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)

> > component

> > code: Transcript reference sequence [ID]

> > value: NM_000106.5

> > component

> > code: DNA change (c.HGVS)

> > value: NM_000106.5:c.1457G>C

Entry 12 - fullUrl = http://example.org/fhir/Observation/haplotype

Resource Observation:

> Profile: Haplotype

> status: Final

> category: Laboratory, Genetics

> code: Haplotype name

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> value: *2

> specimen: Specimen

> derivedFrom: Observation Genetic variant assessment

Entry 13 - fullUrl = http://example.org/fhir/Observation/genotype

Resource Observation:

> Profile: Genotype

> status: Final

> category: Laboratory, Genetics

> code: Genotype display name

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> value: CYP2C9 *2/*5

> specimen: Specimen

> derivedFrom: Observation Haplotype name

> > component

> > code: Gene studied [ID]

> > value: CYP2C9

> > component

> > code: Gene studied [ID]

> > value: VKORC1

Entry 14 - fullUrl = http://example.org/fhir/Observation/metab

Resource Observation:

> Profile: Therapeutic Implication

> status: Final

> category: Laboratory, Genetics

> code: Therapeutic Implication

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> derivedFrom: Observation Genotype display name

> > component

> > code: Medication assessed [ID]

> > value: Warfarin

> > component

> > code: Therapeutic Implication

> > value: Rapid metabolizer

Entry 15 - fullUrl = http://example.org/fhir/Observation/efficacy

Resource Observation:

> Profile: Therapeutic Implication

> status: Final

> category: Laboratory, Genetics

> code: Therapeutic Implication

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> derivedFrom: Observation Genotype display name

> > component

> > code: Therapeutic Implication

> > value: Resistant

> > component

> > code: Medication assessed [ID]

> > value: Warfarin

Entry 16 - fullUrl = http://example.org/fhir/Observation/highrisk

Resource Observation:

> Profile: Therapeutic Implication

> status: Final

> category: Laboratory, Genetics

> code: Therapeutic Implication

> subject: Anonymous Patient (no stated gender), DoB Unknown

> effective: 2016

> issued: 2016-09-06 00:00:00-0500

> performer: Organization Some lab

> derivedFrom: Observation Genotype display name

> > component

> > code: Therapeutic Implication

> > value: Low risk

> > component

> > code: Medication assessed [ID]

> > value: Warfarin

Entry 17 - fullUrl = http://example.org/fhir/Task/usage

Resource Task:

> Profile: Medication Recommendation

> status: Requested

> intent: Proposal

> code: May need higher dosage than usual.

> focus: MedicationStatement: status = unknown; medication[x] = Warfarin

> for: Anonymous Patient (no stated gender), DoB Unknown

> requester: Organization Some lab