Biomarker variants not in Pathogenic/Likely Pathogenic section of report

[AidanGCr]

Hello,

I have run CPSR on some germline samples, and am looking at the biomarker section now. I see that class 4 and 5 variants overlapping the CIViC markers are considered, however, the biomarkers found in my reports (exact matches) are not reported in the class 4/5 section of the report, and variants noted in the biomarker section seem to be classified by CPSR as benign/likely benign in the output TSV. Furthermore, the benign/likely benign variants noted as biomarkers and as benign/likely benign in the TSV, are not reported in their corresponding (class 1/2) section of the HTML report. Is this expected behaviour, or am I missing something?

Thanks, Aidan

[sigven]

Hi Aidan, Untuitively this sounds very much like unexpected behaviour, ideally i'd like to have your test data to debug, if that's possible at all? Just for clarification, is it so that some of the biomarker variants reported are not shown among the classified variants at all (i.e. for which genes)? I believe the present version only considers ClinVar-classified variants for the biomarker mapping, since these are most confident classifications, that might be parts of the explanation, but I'd really like to understand more what's going on.

best, Sigve