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  1. FHIR Specification Feedback
  2. FHIR-25296

Uncallable subregions in a region studied

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    • Type: Change Request
    • Status: Triaged (View Workflow)
    • Priority: Medium
    • Resolution: Persuasive with Modification
    • Specification:
      Genomics Reporting (FHIR)
    • Raised in Version:
      1.0
    • Work Group:
      Clinical Genomics
    • Related URL:
    • Related Page(s):
      genomics
    • Grouping:
    • Resolution Description:
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      To allow full use of the current profile's components, add in a required [1..1] value for region-studied (currently 0..0) with an extensible binding to a local answer list with the 2 LOINC answer codes:

      (callable/not-callable)

      Add in textual guidance for this value, along the lines of:

      'When reporting regions of study, the value field is used to filter regions by callability. A value of "Present" shall accompany components describing a region fully called by the lab, so that omission of variant results within that region implies wildtype calls in the sample, compared to a specified reference. A value of "No Call" shall accompany components describing a region explicitly deemed uncallable by the lab. A value of "Unknown" shall accompany components describing a region where callability varies, for example the full list of genes studied in a panel. Omission of variants within a "No Call" or "Unknown" region shall not be used to imply wildtype calls in the sample.'

      Show
      To allow full use of the current profile's components, add in a required [1..1] value for region-studied (currently 0..0) with an extensible binding to a local answer list with the 2 LOINC answer codes: ( callable/not-callable ) Add in textual guidance for this value, along the lines of: 'When reporting regions of study, the value field is used to filter regions by callability. A value of "Present" shall accompany components describing a region fully called by the lab, so that omission of variant results within that region implies wildtype calls in the sample, compared to a specified reference. A value of "No Call" shall accompany components describing a region explicitly deemed uncallable by the lab. A value of "Unknown" shall accompany components describing a region where callability varies, for example the full list of genes studied in a panel. Omission of variants within a "No Call" or "Unknown" region shall not be used to imply wildtype calls in the sample.'

      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
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              Created:
              Updated:
              Resolved: