TruSight Oncology 500 Assays and Analysis Options

The TruSight Oncology 500 product family enables comprehensive genomic profiling of tumor samples, measuring key current and emerging variants and biomarkers. Illumina currently offers three TruSight Oncology 500 (TSO500) products, each with different instrument compatibility and analysis options. If needed, interpretation and reporting solutions for the TruSight Oncology portfolio are available from Illumina Connected Insights*, Velsera (formerly Pierian) Clinical Genomics Workspace, and other commercial providers. This bulletin outlines the key differences between each product and the available analysis options.

* Not available in all countries. Illumina Connected Insights supports user-defined tertiary analysis through API calls to third-party knowledge sources.

The three released TruSight Oncology 500 assays are:

• TruSight Oncology 500 (TSO500)

  • HRD content is available in all regions except Japan.

• Solid tumor assay for FFPE samples with DNA and RNA content. Compatible with NextSeq 500/550 and NextSeq 550Dx (in research mode) instruments only. This is the original release from the TruSight Oncology 500 product family.

• TruSight Oncology 500 High-Throughput (TSO500 HT)

• Solid tumor assay for FFPE samples with DNA and RNA content. Compatible with NovaSeq 6000, NovaSeq X, NextSeq 500/550, NextSeq 550Dx (in research mode), and NextSeq 1000/2000 instruments.

• TruSight Oncology 500 ctDNA (TSO500 ctDNA), v1 and v2 assays

• Liquid biopsy assay for cell-free DNA with no RNA content. Compatible with NovaSeq 6000 and NovaSeq X instruments only.

The following table provides more details on usage of each assay on each instrument and compatibility with available software analysis pipelines.

Links to documentation For the following documentation for TruSight Oncology 500 and TruSight Oncology 500 High-Throughput, see the TruSight Oncology 500 Documentation page.

• TruSight Oncology 500 Local App (v1.0 to v2.2) Documentation

• DRAGEN TruSight Oncology 500 Analysis Software (v1.1 to v2.5.3) on-premise Documentation

• DRAGEN TruSight Oncology 500 Analysis Software (v1.1 to v2.5.3) on ICA Documentation

• Local Run Manager TruSight Oncology 500 Analysis Module Workflow Guide

For the following documentation for TruSight Oncology 500 ctDNA v1 assay, see the TruSight Oncology 500 ctDNA v1 Documentation page.

• DRAGEN TruSight Oncology 500 ctDNA Local Analysis Software (v1.1 to v2.6) on-premise Documentation

• DRAGEN TruSight Oncology 500 ctDNA Analysis Software (v1.2 to v2.6) on ICA

• DRAGEN Analysis Workflows Product Documentation

For the following documentation for TruSight Oncology 500 ctDNA v2 assay, see the TruSight Oncology 500 ctDNA v2 Documentation page.

• DRAGEN TruSight Oncology 500 ctDNA Local Analysis Software (v2.1 to v2.6) on-premise Documentation

• DRAGEN TruSight Oncology 500 ctDNA Analysis Software (v2.1.1 to v2.6) on ICA

• DRAGEN Analysis Workflows Product Documentation

For DRAGEN v3 and v4 Server information, see the Illumina DRAGEN Bio-IT Platform product page.

For Illumina Connected Insights, see the Illumina Connected Insights Product Documentation page.

Important Notes:

• The current software versions are:

• DRAGEN TSO500 v2.5.3

• DRAGEN TSO500 ctDNA v2.6.0

• Read length and index length for each assay must be exact to ensure correct processing by the analysis pipelines.

• Sample sheets can be generated for DRAGEN TSO500 and DRAGEN TSO500 ctDNA in BaseSpace Run Planning.

• Editable sample sheet templates are available for download from the Illumina support site. The sample sheet must be saved as a comma-separated text (CSV) file. Illumina recommends setting the system language of the computer used to edit the sample sheet to US English to preserve the correct formatting.

• TSO500 and TSO500 with HRD sample sheet templates

• TSO500 HT sample sheet templates

• TSO500 ctDNA v1 assay sample sheet templates

• TSO500 ctDNA v2 assay sample sheet templates

• The Local Run Manager TSO500 analysis module is compatible only with the on-instrument version of Local Run Manager for the NextSeq 550 that is bundled with NextSeq Control Software version ≥4.0.1; the module is not compatible with any other version of Local Run Manager.

• TSO500 HT libraries cannot be analyzed with the Local Run Manager TSO500 module.

• Only the TSO500 analysis module for Local Run Manager will generate FASTQs that are compatible as input for the TSO500 analysis pipeline. The Generate FASTQ module for Local Run Manager cannot be used to generate FASTQs for downstream TSO500 analysis as the necessary UMI handling options for the TSO500 libraries are not supported in the Generate FASTQ module.

Compatibility with Illumina Connected Insights

Users of Illumina Connected Insights can interpret results and produce reports from all assays in the TSO500 product family by uploading VCF files from local storage or importing from Illumina Connected Analytics (ICA).

Compatibility with Velsera CGWUsers of Velsera CGW can interpret results and produce reports from TSO500 data for all assays in the TSO500 product family. Different file types can be uploaded for analysis depending on the assay type. * BCL Convert is the preferred software for FASTQ generation compared to bcl2fastq. ** FASTQs created with the Local Run Manager Generate FASTQ analysis module are not compatible with TSO500 analysis and cannot be uploaded to Pierian CGW.

For any feedback or questions regarding this article (Illumina Knowledge Article #3812), contact Illumina Technical Support [e-mail].