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
Copy number variants (CNV) (with absolute copy number when HRD Assay is run)
TMB
MSI
Fusions
Splice variants
GIS (when HRD Assay is run)
Gene-level Loss of Heterozygosity (when HRD Assay is run)
Exon-level CNVs
The combined variant output file also contains Analysis Details and Sequencing Run Details sections. The details of each are listed in the following table:
- 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 - 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, indel, 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 or <DEL> .
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 if TruSight Oncology 500 HRD analysis is performed
Loss of Heterozygosity - Present only when TruSight Oncology 500 HRD is run. Loss of heterozygosity (LOH) must meet the following condition:
MCN field is equal to 0
Exon-level CNVs - Exon-levels CNVs must meet the following conditions:
BRCA1 or BRCA2 contains at least one affected exon.
ALT field is <DUP> or <LOSS> .