Loading...

XML

Word

Printable

JSON

Details

Type: Change Request
Resolution: Persuasive with Modification
Priority: Medium

Specification:

Genomics Reporting (FHIR)
Raised in Version:

2.0.0
Work Group:

Clinical Genomics
Related URL:
http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition-variant.html
Related Artifact(s):

Variant
Resolution Description:

Hide

Further refine how the Genomic Study Analysis profile represents regions:

The Genomic Study profile page, where it gives some highlights of the new complex extensions I introduced:
https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study.html

The Genomic Study Analysis with new extensions for Metrics and Regions:
https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study-analysis.html

The new 'Metrics' extension:
https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study-analysis-metrics.html

The new 'Regions' extension:
https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study-analysis-regions.html

A new section on 'Variant Assessment' on the 'sequencing' page (most important is the guidance for 'Pertinent Negatives' and 'No Call' and how it can have additional context from other attributes (like the new complex extension introduced here)
https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/sequencing.html#variantassessment

The GitHub PR:
https://github.com/HL7/genomics-reporting/pull/84

Show
Further refine how the Genomic Study Analysis profile represents regions: The Genomic Study profile page, where it gives some highlights of the new complex extensions I introduced: https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study.html The Genomic Study Analysis with new extensions for Metrics and Regions: https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study-analysis.html The new 'Metrics' extension: https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study-analysis-metrics.html The new 'Regions' extension: https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/StructureDefinition-genomic-study-analysis-regions.html A new section on 'Variant Assessment' on the 'sequencing' page (most important is the guidance for 'Pertinent Negatives' and 'No Call' and how it can have additional context from other attributes (like the new complex extension introduced here) https://build.fhir.org/ig/HL7/genomics-reporting/branches/kp-coverage-and-negatives/sequencing.html#variantassessment The GitHub PR: https://github.com/HL7/genomics-reporting/pull/84
Resolution Vote:
May Terry/Srikar Chamala : 11 - 0 - 0
Change Category:
Enhancement
Change Impact:
Non-compatible

Description

The genomics reporting IG needs further guidance on how to represent genes for which there were no alterations determined because of low coverage.

This would be coming from a generated report where the user reading the report might have expected a definite present or absent finding for a given gene variant, but in return the lab is reporting that could not be reported due to low coverage. See attachments for examples of the limited data set which only has the name of the gene and the reason that it could not determine any alterations.