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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  1. DRAGEN TSO 500 Guides
  2. DRAGEN TSO 500 v2.5
  3. Analysis Output
  4. Metrics Output

HRD Metrics Report

The Illumina DRAGEN TruSight Oncology 500 Analysis Software allows for analysis of sequencing data generated from the TruSight Oncology 500 HRD assay. When HRD samples are analyzed new results and metrics are included in the CombinedVariantOutput and MetricsOutput files respectively. The following tables detail how these scores and QC metrics are derived.

Metric
Description

GIS Score*

Proprietary Genomic Instability Score (GIS) indicating level of genomic instability in sample genome. Combination of Loss of Heterozygosity (LOH), Telomeric allelic imbalance and Large-scale State Transitions (LST) scores. The GIS scores provided by TruSight Oncology 500 HRD show good correlation (R2= 0.98) with Myriad Genetics GIS however they are not identical (Refer to TruSight Oncology 500 HRD Product Data Sheet Doc# M-GL-00748 for more details). GIS from alternative HRD assays should be not be considered equivalent to Illumina/Myriad GIS.

*The GIS algorithm within the TSO500 pipeline (which does not have a cell line mode due to the TSO500 pipeline being non-configurable) is only intended for FFPE samples. Cell line samples will not accurately report GIS results as the tumor fraction (>90%) is too high to reliably distinguish tumor vs germline variants.

HRD Metrics Added to Metrics Output File

Metric
Description
Section in Metrics Output

PCT_TARGET_HRD_50X

Percent of HRD probe SNP panel covered by at least 50X coverage

DNA Library QC Metrics for GIS

EXCESSIVE_TF

EXCESSIVE TF indicates if there is excessive tumor content in sample. Troubleshooting: Samples with pure tumor fraction >90% are outside the design for GIS estimation (this includes pure tumor cell lines)

DNA Library QC Metrics for GIS

ALLELE_DOSAGE_RATIO

Proprietary Myriad Genetics estimate of b-allele dosage based on b-allele noise/signal ratio. B-Allele noise is correlated with coverage; lower coverage samples will have higher noise. B-allele signal is also correlated with tumor fraction; a higher tumor fraction produces a higher signal for b-allele sites. Samples with lower tumor fraction and higher amount of noise (or lower coverage) will have higher Allele Dosage Ratio. The upper limit of the score is 50, therefore any sample with 50 Allele Dosage Ratio can be assumed to have tumor fraction close to zero and typically has a GIS = 0.

DNA Expanded Metrics

MEDIAN_TARGET_HRD_COVERAGE

Median target fragment coverage across all target positions in the genome. Coverage is the total number of non-duplicate pair alignments that overlap.

DNA Expanded Metrics

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Last updated 3 months ago

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