DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • DRAGEN TSO 500 Guides
    • DRAGEN TSO 500 v2.6
      • Introduction to DRAGEN TSO 500 Analysis Software v2.6.x
      • Getting Started
        • Installation of 2.6.0 on Standalone DRAGEN Server
        • Installation of 2.6.1 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • RNA Analysis Methods
        • Quality Control
        • Performance Testing
      • Troubleshooting
    • DRAGEN TSO 500 v2.5
      • Introduction to DRAGEN TSO 500 Analysis Software v2.5.x
      • Getting Started
        • Installation of 2.5.3 on Standalone DRAGEN Server
        • Installation of v2.5.4 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
          • Block List
        • Analysis Methods
          • FASTQ Generation
          • DNA Analysis Methods
          • RNA Analysis Methods
          • Quality Control
          • Performance Testing
      • Troubleshooting
  • DRAGEN TSO 500 ctDNA Guides
    • DRAGEN TSO 500 ctDNA v2.6
      • Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6
      • Getting Started
        • Installation of TSO 500 ctDNA v2.6.0 on Standalone DRAGEN Server
        • Installation of TSO 500 ctDNA v2.6.2 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 ctDNA Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
      • Analysis Output
        • DNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • Quality Control
      • Troubleshooting
  • Reference
    • Revision History
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  • Analytical Performance Testing
  • In Silico Testing Methods
  • Beta Features

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  1. DRAGEN TSO 500 Guides
  2. DRAGEN TSO 500 v2.6
  3. Analysis Methods

Performance Testing

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Last updated 3 months ago

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The following sections describe performance testing methods.

Analytical Performance Testing

Illumina tests the analytical performance of variant calling using an approach that covers the entire workflow including library preparation, sequencing, and secondary analysis. This approach is used to test a diverse selection of variants. When the variant calling pipeline is expanded to call a new variant class, this approach is always used.

This version of the software includes results generated by features tested in silico and by beta features. Beta features have not been fully evaluated for performance, see .

In Silico Testing Methods

Illumina uses in silico testing to the test the ability of the software to call an expanded scope of clinically relevant variants, including rare variants. In silico testing is used as a complementary method to analytical performance testing with wet lab step to expand the scope of testing. For example, while Illumina has analytically verified the performance of the software for calling complex variants in EGFR, the in silico testing approach characterizes the ability of the software to call complex variants in other genes.

For in silico testing, variants of interest are extracted from public databases like Cosmic and ClinVar. Each variant is simulated at different VAF levels by, depending on the variant class, spiking in mutant reads into a normal FFPE background (for sequence variants) or by increasing or decreasing the coverage of exons in the normal FFPE sample (for CNVs, for example, exon-level CNVs. The simulated reads match the expected quality of typical FFPE samples, such as fragment length, error rate, and family size. After the simulation, the software processes samples with spiked-in variants and determines the results. This approach does not include library prep and sequencing of tumor FFPE samples that include the rare variants of interest. The software reports these variants, but analytical verification was not performed.

DRAGEN TruSight Oncology 500 Analysis Software includes the following features that were tested in silico for both TruSight Oncology 500 and TruSight Oncology 500 HT:

  • Complex variants in genes beyond EGFR

  • Insertions and deletions > 25 bp

  • CNV amplifications

  • CNV deletions

  • Variants in intron-exon junctions (2 bp – 10 bp into introns)

In addition, the following features were tested in silico for TruSight Oncology 500 HT:

  • Exon-level CNVs in BRCA1 and BRCA2

Beta Features

This version of DRAGEN TruSight Oncology 500 Analysis Software includes beta features which have not been verified by Illumina due to limited access to samples or lack of an appropriate orthogonal method to perform testing, and, the use of in silico testing alone is not sufficient for verification purposes.

Customers are responsible for evaluating and demonstrating performance of any beta features they choose to implement. Beta features are indicated as such in the CombinedVariantOutput.tsv file. Illumina will continue to evaluate beta features with intent to fully release upon completion of verification for each feature.

This version includes the following beta features that may be used with the TruSight Oncology 500 HRD Assay:

  • Tumor fraction (beta)

  • Ploidy (beta)

  • Absolute copy numbers (ACN) (beta)

  • Gene-level loss of heterozygosity (LOH) events (beta)

Beta feature results are included in the Combined Variant Output file and other files. However, disclaimers that the results are generated by beta features are only provided in the Combined Variant Output file.

Beta Features