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CGI biomarker match issue #59

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HomoPolyethylen opened this issue Oct 17, 2024 · 0 comments
Open

CGI biomarker match issue #59

HomoPolyethylen opened this issue Oct 17, 2024 · 0 comments
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@HomoPolyethylen
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Description of the bug

CGI biomarkers.tsv contains two columns Match and BioM.

  • we used to filter biomarkers for BioM == "complete", now we filter for Match == "YES", but we need both!
  • BioM describes a match between query and alteration of the biomarker
  • Match only refers to the cancer type!
  • To include off-label use (level A evidences for different tumor), filter hard by Match == "YES" and then adjust Evidence level from A->C for evidences where Match == "NO" and level == "A"

Best: refactor, do not change evidence levels, but gather evidence (cgi and civic) and check for different tumor type only in tier assignment

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@HomoPolyethylen HomoPolyethylen added the bug Something isn't working label Oct 17, 2024
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