Combined Variant Output

File name: {Pair_ID}_CombinedVariantOutput.tsv

The combined variant output file contains the variants and biomarkers in a single file that is based on a single sample. If using pair ID, the file is based on paired DNA and RNA samples from the same individual. The output contains the following variant types and biomarkers:

• Small variants
• Gene amplifications
• TMB
• MSI
• Fusions
• Splice variants
• [HRD] GIS
• Exon-level CNVs

The combined variant output file also contains Analysis Details and Sequencing Run Details sections. The details of each are is listed in the following table:

Analysis Details

Sequencing Run Details
• Pair ID
• DNA Sample ID (if DNA is run)
• RNA Sample ID (if RNA is run)
• Output Date
• Output Time
• Module Version
• Pipeline Version (Docker Image Version #)
• Run Name
• Run Date
• DNA Sample Index ID (if DNA is run)
• RNA Sample Index ID (if RNA is run)
• [HRD] Sample Feature ([HRD])
• Instrument ID
• Instrument Control Software Version
• Instrument Type
• RTA Version
• Reagent Cartridge Lot Number

Combined variant output produces small variants with blank fields in the following situations:

• The variant has been matched to a canonical RefSeq transcript on an overlapping gene not targeted by TruSight Oncology 500.
• The variant is located in a region designated iSNP, iIndel, or Flanking in the TST500_Manifest.bed file located in the Resources folder.
• Small Variants—All variants with the FILTER field marked as PASS in the hard-filtered genome VCF are present in the combined variant output.
– Gene information is only present for variants belonging to canonical transcripts that are within the Gene Allow List–Small Variants.
– Transcript information is only present for variants belonging to canonical transcripts that are within the Gene Allow List–Small Variants.
• Copy Number Variants—Copy number variants must meet the following conditions:
– FILTER field marked as PASS.
– ALT field is <DUP>.
• Fusion Variants—Fusion variants must meet the following conditions:
– Passing variant call (KeepFusion field is true).
– Contains at least one gene on the fusion allow list.
– Genes separated by a dash (-) indicate that the fusion directionality could be determined. Genes separated by a slash (/) indicate that the fusion directionality could not be determined.
• Biomarkers TMB/MSI—Always present when DNA sample is processed.
• Splice Variants—Passing splice variants that are contained on genes EGFR, MET, and AR.
• Biomarker GIS—Present only when TruSight Oncology 500 HRD is run.
• Exon-Level CNV—Exon-level CNVs must meet the following conditions:
– BRCA1 or BRCA2 contains at least one affected exon.
– ALT field is <DUP> or <LOSS>.