Genomic Study Somatic Study Example - Clinical Genomics Resource Incubator v0.1.0-ci-build

Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

Example GenomicStudy: Genomic Study Somatic Study Example

Page standards status: Informative

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:somatic-study-0001 (use: temp, )

status: Available

type: My Test Cancer 700 Gene Panel

subject: Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --> (ongoing)))

startDate: 2023-02-02

basedOn: ServiceRequest

interpreter: Practitioner Jane Doel

Reasons

Concept

Adenocarcinoma of lung, stage IV (disorder)

note:

I. Assay Overview: The Genomic Cancer Testing Assay is a comprehensive molecular examination designed to detect and quantify specific DNA and RNA alterations associated with malignancies. The test incorporates Next Generation Sequencing (NGS) technology to profile tumor samples. II. Target Genes and Biomarkers: This assay evaluates an extensive panel of cancer-related genes. Sample Type: Formalin-fixed, paraffin-embedded (FFPE) tumor tissue. Sequencing Platform: Illumina-based NGS technology. Sensitivity: Detects variants with a mutant allele frequency (MAF) as low as 5%. Results are delivered within 10-14 working days from sample receipt.

description:

Comprehensive somatic genomic profiling of lung adenocarcinoma (stage IV) using a 700-gene panel. Includes paired tumor/normal DNA sequencing for SNV, MNV, InDel and CNV detection, and RNA sequencing for gene fusion and transcript variant detection.

analysis
identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:somatic-analysis-dna-0001 (use: temp, )
methodType: Sequence analysis of the entire coding region, Deletion/duplication analysis
changeType: SNV, MNV, delins, copy_number_variation
genomeBuild: GRCh38
genomicSourceClass: Somatic
title: Tumor/Normal Paired DNA Sequencing - SNV, MNV, InDel, CNV
focus: Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --> (ongoing)))
specimen:
Specimen: identifier = http://example.org/identifiers/specimens#222333; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2023-01-23 01:01:01+0000; note = FFPE tumor tissue. Tumor cellularity: 20%.
Specimen: identifier = http://example.org/identifiers/specimens#444555; status = available; type = Blood specimen (specimen); receivedTime = 2023-01-23 01:01:01+0000; note = Matched normal blood specimen for tumor/normal paired sequencing.
date: 2023-02-02 01:01:10-0600
note:
For technical reasons, BCR gene was deemed uncallable.

Metrics
- ReadDepth SequencingCoverage Description
* 500 x (Details: UCUM code1 = '1') 97 % (Details: UCUM code% = '%') 500x average tumor read depth, 97% target region coverage. Minimum allele frequency threshold 5%.
genomicRegion
type: Studied
Locus
- Reference
* DocumentReference: identifier = http://example.org/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.
genomicRegion
type: Called
Locus
- Reference
* DocumentReference: identifier = http://example.org/identifiers/files#somatic-called-001; status = current; docStatus = preliminary; description = BED file describing regions that passed coverage and quality thresholds in the tumor/normal DNA analysis; securityLabel = Restricted
genomicRegion
type: Uncalled
Locus
- Concept
* BCR
description: BCR was not callable due to low sequencing coverage in this tumor sample.
Outputs
- File Type
* DocumentReference: identifier = http://example.org/identifiers/files#1134121; status = current; docStatus = preliminary; description = VCF file containing somatic variants identified from tumor/normal paired DNA sequencing; securityLabel = Restricted VCF
Performers
- Actor Role
* Practitioner Jane Doel Performer
Devices
- Device Function
* Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object) Sequencing

analysis
identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:somatic-analysis-rna-0001 (use: temp, )
methodType: RNA analysis
changeType: gene_fusion, transcript_variant
genomicSourceClass: Somatic
title: Tumor RNA Sequencing - Gene Fusions and Transcript Variants
focus: Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --> (ongoing)))
specimen: Specimen: identifier = http://example.org/identifiers/specimens#222333; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2023-01-23 01:01:01+0000; note = FFPE tumor tissue. Tumor cellularity: 20%.
date: 2023-02-02 01:01:10-0600
genomicRegion
type: Studied
Locus
- Reference
* DocumentReference: identifier = http://example.org/identifiers/files#1076146520; status = current; docStatus = preliminary; description = BED file describing studied regions for RNA sequencing (fusion and transcript variant detection); securityLabel = Restricted
Outputs
- File Type
* DocumentReference: identifier = http://example.org/identifiers/files#somatic-fusion-001; status = current; docStatus = preliminary; description = VCF file containing gene fusions and transcript variants identified from tumor RNA sequencing; securityLabel = Restricted VCF
Performers
- Actor Role
* Practitioner Jane Doel Performer
Devices
- Device Function
* Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object) Sequencing

IG © 2026+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.cg-incubator#0.1.0-ci-build based on FHIR 6.0.0-ballot3. Generated 2026-03-24
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