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  1. FHIR Specification Feedback
  2. FHIR-25296

Uncallable subregions in a region studied

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    Details

    • Type: Change Request
    • Status: Applied (View Workflow)
    • Priority: Medium
    • Resolution: Persuasive with Modification
    • Specification:
      Genomics Reporting (FHIR)
    • Raised in Version:
      1.0
    • Work Group:
      Clinical Genomics
    • Related Page(s):
      genomics
    • Resolution Description:
      Hide

      New Component:

      0..* uncallable-region (TBDCode=uncallable-region) (Data type=Range)

      Guidance:

      Subset of the 'ranges-examined', should include 'reference-sequence' and 'coordinate-system'

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      New Component : 0..* uncallable-region (TBDCode=uncallable-region) (Data type=Range) Guidance: Subset of the 'ranges-examined', should include 'reference-sequence' and 'coordinate-system'
    • Resolution Vote:
      Bob Dolin / Patrick Werner : 14 - 0 - 0
    • Change Category:
      Enhancement
    • Change Impact:
      Compatible, substantive

      Description

       Would like to consider a new 'no call region' component for the region-studied profile. With this component, in response to a query for variants in a given region, a server can provide a report that also enumerates non-callable subregions, potentially enabling one to differentiate non-callable vs. true negatives.
       
      (The main use case we based this on was the need to include wildtype variant calls for PharmGKB's PharmCAT (https://github.com/PharmGKB/PharmCAT) software).
       

      The attached example is a set of variants found for 1000 Genomes patient HG00403 in range chr1:1000000-1100000 that includes non-callable subregions. (It's based on a slightly outdated pre-publication version of the IG).

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              Assignee:
              Unassigned Unassigned
              Reporter:
              bob.dolin Bob Dolin
              Watchers:
              4 Start watching this issue

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