lungMass-analysis1 - Genomics Reporting Implementation Guide v3.0.0

Genomics Reporting Implementation Guide
3.0.0 - STU3 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 3.0.0 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 Procedure: lungMass-analysis1

Generated Narrative: Procedure lungMass-analysis1

Genomic Study Analysis Method Type: Sequence analysis of the entire coding region

Genomic Study Analysis Source Class: Somatic

Genomic Study Analysis Change Type: SNV

Genomic Study Analysis Change Type: MNV

Genomic Study Analysis Change Type: delins

Genomic Study Analysis Genome Build: GRCh38

Genomic Study Analysis Specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000

Genomic Study Analysis Focus: John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))

Genomic Study Analysis Device
device: Device: identifier = http://www.somesystemabc.net/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)

Genomic Study Analysis Regions
studied: DocumentReference: identifier = http://www.somesystemabc.net/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.; securityLabel = Restricted
uncalled: DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11125; status = current; docStatus = preliminary; description = Representing a BED file that represents uncallable regions; securityLabel = Restricted
called: DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted

Genomic Study Analysis Output
type: VCF
file: DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11119; status = current; docStatus = preliminary; description = genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted

instantiatesUri: https://pubmed.ncbi.nlm.nih.gov/33927380/

status: Completed

category: Laboratory

subject: John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))

performed: 2019-03-01 01:01:10-0600