Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build International flag

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-prequel-prenatal-trisomy13

Bundle bundle-prequel-prenatal-trisomy13 of type transaction

Entry 1 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000001

Resource Patient:

Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

Request:

POST Patient

Entry 2 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000002

Resource Practitioner:

identifier: United States National Provider Identifier/4253506008

name: Paul Smith

Request:

POST Practitioner

Entry 3 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000003

Resource Organization:

name: University Medical Center

Contacts

-TelecomAddress
*ph: (800) 555-1212, fax: (800) 555-1212123 Main Street City CA 10231

Request:

POST Organization

Entry 4 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000004

Resource Organization:

identifier: Clinical Laboratory Improvement Amendments/05D1102604

name: Myriad Women's Health, Inc.

Contacts

-TelecomAddress
*ph: (888) 268-6795, http://www.myriadwomenshealth.com180 Kimball Way South San Francisco CA 94080

Request:

POST Organization

Entry 5 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000005

Resource ServiceRequest:

status: Completed

intent: Order

Codes

-Concept
*Myriad Prequel Prenatal Screen with AMPLIFY technology — Chromosomes 13, 18, 21 aneuploidy screening (NIPS v4.0)

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

authoredOn: 2024-06-06

requester: Practitioner Paul Smith

performer: Organization Myriad Women's Health, Inc.

specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09

note:

Singleton pregnancy; gestational age 8 weeks 0 days; ovum donor: N/A; patient height 5ft 6in; patient weight 120lbs; NT 1mm (ultrasound 2024-06-06); CRL 10cm; expected due date 2025-01-16

Request:

POST ServiceRequest

Entry 6 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000006

Resource Specimen:

identifier: http://example.org/barcode/31200020477415

status: Available

type: Streck Cell-Free DNA Blood Tube (cell-free DNA)

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

receivedTime: 2024-06-09

Collections

-CollectorCollected[x]
*Practitioner Paul Smith 2024-06-06

Request:

POST Specimen

Entry 7 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000007

Resource Observation:

status: Final

category: Laboratory, Biomarker Category, Genetics

code: Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

effective: 2024-06-16

performer: Organization Myriad Women's Health, Inc.

value: 25 % (Details: UCUM code% = '%')

note:

Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result.

specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09

Components

-CodeValue[x]
*Biomarker CategoryCell-free fetal DNA fraction

Request:

POST Observation

Entry 8 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000008

Resource Observation:

Profile: Variant

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

effective: 2024-06-16

performer: Organization Myriad Women's Health, Inc.

value: Present

method: Sequencing with fetal chromosome analysis (NIPS v4.0); Genome Reference Consortium Human Build 37 (GRCh37)/hg19

specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09

component

code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method

value: Chromosome 13

component

code: Human reference sequence assembly version

value: GRCh37

component

code: Genomic source class [Type]

value: Fetal

component

code: Genomic structural variant copy number

value: 3 1 (Details: UCUM code1 = '1')

component

code: DNA change type

value: copy_number_gain

component

code: Conclusion Text

value: Results suggestive of trisomy for chromosome 13. Positive predictive value (PPV): 34.07% (34.07 in 100). Test performance: Sensitivity 99.0% (95% CI: 65.8-100.0); Specificity 99.96% (95% CI: 99.93-99.98).

Request:

POST Observation

Entry 9 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000009

Resource Observation:

Profile: Variant

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

effective: 2024-06-16

performer: Organization Myriad Women's Health, Inc.

value: Absent

method: Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19

specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09

component

code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method

value: Chromosome 18

component

code: Human reference sequence assembly version

value: GRCh37

component

code: Genomic source class [Type]

value: Fetal

component

code: Genomic structural variant copy number

value: 2 1 (Details: UCUM code1 = '1')

component

code: Conclusion Text

value: Results consistent with two copies of chromosome 18. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 97.9% (95% CI: 94.9-99.1); Specificity 99.96% (95% CI: 99.93-99.97).

Request:

POST Observation

Entry 10 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000010

Resource Observation:

Profile: Variant

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

effective: 2024-06-16

performer: Organization Myriad Women's Health, Inc.

value: Absent

method: Sequencing with fetal chromosome analysis (NIPS v4.0); GRCh37/hg19

specimen: Specimen: identifier = http://example.org/barcode#31200020477415; status = available; type = Blood venous; receivedTime = 2024-06-09

component

code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method

value: Chromosome 21

component

code: Human reference sequence assembly version

value: GRCh37

component

code: Genomic source class [Type]

value: Fetal

component

code: Genomic structural variant copy number

value: 2 1 (Details: UCUM code1 = '1')

component

code: Conclusion Text

value: Results consistent with two copies of chromosome 21. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 99.7% (95% CI: 99.1-99.9); Specificity 99.96% (95% CI: 99.93-99.98).

Request:

POST Observation

Entry 11 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000011

Resource Observation:

status: Final

category: Laboratory, Genetics

code: Diagnostic Implication

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

effective: 2024-06-16

performer: Organization Myriad Women's Health, Inc.

derivedFrom: Observation Genetic variant assessment

component

code: Genetic variation clinical significance [Imp]

value: Pathogenic

component

code: Associated phenotype

value: Trisomy 13 (Patau Syndrome)

component

code: Condition Inheritance

value: Contiguous gene syndrome (chromosomal aneuploidy; typically sporadic)

component

code: Conclusion Text

value: POSITIVE: Aneuploidy suspected (borderline value). Results suggestive of trisomy for chromosome 13. Positive predictive value (PPV): 34.07% (34.07 in 100). Trisomy 13 (Patau syndrome) is a life-limiting condition caused by an extra copy of chromosome 13. Common features include heart defects, brain and spine abnormalities, polydactyly, micropthalmia, hypotonia, kidney problems, and cleft lip/palate. Most infants die within the first few weeks of life. This is a screening test — false positives can occur. Definitive diagnosis requires CVS or amniocentesis.

Request:

POST Observation

Entry 12 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000014

Resource Observation:

status: Final

category: Laboratory, Genetics

code: Diagnostic Implication

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

effective: 2024-06-16

performer: Organization Myriad Women's Health, Inc.

derivedFrom: Observation Genetic variant assessment

component

code: Genetic variation clinical significance [Imp]

value: Likely benign

component

code: Associated phenotype

value: Trisomy 18 (Edwards Syndrome)

component

code: Conclusion Text

value: NEGATIVE: Results consistent with two copies of chromosome 18. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 97.9% (95% CI: 94.9-99.1); Specificity 99.96% (95% CI: 99.93-99.97).

Request:

POST Observation

Entry 13 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000015

Resource Observation:

status: Final

category: Laboratory, Genetics

code: Diagnostic Implication

subject: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

effective: 2024-06-16

performer: Organization Myriad Women's Health, Inc.

derivedFrom: Observation Genetic variant assessment

component

code: Genetic variation clinical significance [Imp]

value: Likely benign

component

code: Associated phenotype

value: Trisomy 21 (Down Syndrome)

component

code: Conclusion Text

value: NEGATIVE: Results consistent with two copies of chromosome 21. Residual risk < 0.01% (1 in 10,000). Test performance: Sensitivity 99.7% (95% CI: 99.1-99.9); Specificity 99.96% (95% CI: 99.93-99.98).

Request:

POST Observation

Entry 14 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000012

Resource Task:

status: Requested

intent: Proposal

code: Genetic counseling recommended

description: Genetic counseling is recommended in view of a positive NIPS result for Trisomy 13 (PPV 34.07%). No irreversible decision should be made based on this screening result alone. If definitive diagnosis is desired, chorionic villus sampling (CVS) or amniocentesis is necessary. Clinical correlation with ultrasound findings and history is indicated.

for: Jane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)

Reasons

-Reference
*Observation Diagnostic Implication

Request:

POST Task

Entry 15 - fullUrl = urn:uuid:2c9e6be3-1b0e-4e3a-9d9e-000000000013

Resource DiagnosticReport:

Genetic analysis report (Genetics)

SubjectJane Miller Female, DoB: 1997-11-11 ( http://example.org/mrn#FAKERQIHPT13S)
When For2024-06-17
Reported2024-06-17 00:00:00+0000
Performer Organization Myriad Women's Health, Inc.

Report Details

CodeValueFlagsNoteWhen For
Cell-free DNA.fetal/Cell-free DNA.total in Plasma cell-free DNA by Dosage of chromosome-specific cfDNA25 % (Details: UCUM code% = '%')Final

Fetal fraction is one component of the algorithm used and is combined with other quality metrics to determine the aneuploidy screening result.

2024-06-16
Genetic variant assessmentPresentFinal2024-06-16
Genetic variant assessmentAbsentFinal2024-06-16
Genetic variant assessmentAbsentFinal2024-06-16
Diagnostic ImplicationFinal2024-06-16
Diagnostic ImplicationFinal2024-06-16
Diagnostic ImplicationFinal2024-06-16

POSITIVE: PREGNANCY AT INCREASED RISK. Chromosome 13 aneuploidy detected — results suggestive of Trisomy 13 (Patau Syndrome). Positive predictive value (PPV): 34.07% (34.07 in 100). Chromosomes 18 (Edwards Syndrome) and 21 (Down Syndrome) are NEGATIVE with residual risk < 0.01% (1 in 10,000) each. Fetal fraction: 25.0%. Method: sequencing with fetal chromosome analysis (NIPS v4.0; GRCh37/hg19). This is a screening test — false positive and false negative results can occur. Genetic counseling is recommended. If definitive diagnosis is desired, chorionic villus sampling or amniocentesis is necessary.

Coded Conclusions:

Request:

POST DiagnosticReport