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TruSight™ Oncology 500 (TSO500) Plasma Assay

The TSO500 plasma assay employs a hybrid capture-based approach targeting 523 clinically relevant genes and leverages unique molecular indices to enable ultra-low frequency detection of SNVs, Indels, and CNVs

This comprehensive cancer panel interrogates relevant cancer biomarkers with as little as 20-30 ng of cfDNA and demonstrates robust analytical performance. In addition to variant calls, the assay reports a tumor mutational burden (TMB) score and microsatellite instability (MSI) status. Available now as an RUO offering at our genomics center of excellence in North Carolina, USA.

Highlights

  • Reportable biomarkers: SNVs, Indels, CNVs, MSI, and TMB
  • Sample types: Streck whole blood, Streck & EDTA plasma, cfDNA
  • Pre-analytical QC incudes Fragment Analysis Quantification
  • Detection of variants down to 0.5% VAF
  • Sensitivity of SNVs at 92.87% and Indels at 96.34%
  • PPV of SNVs at 99.84% and Indels at 99.99%

Reproducible Variant Calling



TMB Methodology

Enhanced algorithm to robustly call TMB from cfDNA. Reports include a synonymous and non- synonymous score using eligible variants that meet the following criteria:
  • Variants in the coding region (RefSeq Cds)
  • Variants not in low confidence regions (black list)
  • Variant Frequency ≥ Minimum reporting TMB threshold
  • Coverage ≥ 1000
  • SNVs and Indels (MNVs excluded)
  • Nonsynonymous and synonymous variants
  • Variants with cosmic count > 50 excluded
  • Exclude clonal hematopoiesis driver genes
  • Exclude variants with VAF > 40%

TSO500-plasma Specifications

Sample Types
Plasma (EDTA, Streck or purified circulating-free nucleic acids)
Sample Recommendations
> 3 mL plasma (minimum 2 mL plasma)
Double-spun EDTA within 4 hr of collection
OR
Streck cfDNA BCT extends stability window to 6 days @ RT
Input Requirements
20-30 ng cfDNA (as quantified using Fragment Analyzer)
Sequencing Platform
NovaSeq 6000
Read Depth
> 400 M PE Reads; 150bp PE
Software Analysis
Illumina’s Early Access TSO500 Plasma pipeline for ctDNA analysis
Deliverables QC Report, VCFs (SNVs and Indels), CNVs, MSI and TMB scores BAMs can be made available
upon request for additional fee