TruSight RNA Pan-Cancer Panel

Target 1385 cancer genes for gene expression, variant, and fusion detection studies in many RNA sample types, including blood, bone marrow, and FFPE tissue.

2.5 days

Assay time

11 hr

Hands-on time

10 ng total RNA, 20–100 ng FFPE RNA

Input quantity

See full details in the specifications table

Reagent and library prep kit bundles available for the MiniSeq System

Order MiniSeq reagents and library prep kits together for additional savings and convenience (Catalog no. 20005611).

Overview

The TruSight RNA Pan-Cancer Panel offers in-depth and cost-effective assessment of cancer-related RNA transcripts in limited and degraded samples on a benchtop sequencing system.

  • Industry-validated content for a comprehensive view of 1385 genes implicated in cancer pathways

  • Comprehensive view of cancer pathways enabling interrogation of gene expression levels, variants, and gene fusions

  • Low-input protocol for most sample types, including formalin-fixed, paraffin-embedded (FFPE) samples

Efficient analysis of difficult samples

Libraries can be prepared from as little as 10 ng of total RNA input (or 20 ng from FFPE samples). The focus on a subset of relevant genes enables RNA-Seq with high sensitivity.

Intuitive cloud-based data analysis

Analysis can be performed using the BaseSpace RNA-Seq Alignment App, which provides gene expression profiles, identifies gene fusions, and reports single nucleotide variants and small indels, offering a comprehensive, intuitive solution to cancer researchers.

Sample data sets

Register or sign in to BaseSpace Sequence Hub to access MiSeq System data and MiniSeq System data (view run or view project).


Specifications


Required products

Requires purchase of TruSight RNA Pan-Cancer Panel Set A and/or B. Each set includes library preparation reagents and oligos for 48 samples with 12 indexes. Each index is sufficient for 4 individual samples. Both sets may be used together to pool up to 24 samples.

If using the MiniSeq System, reagents and library prep kits can be ordered together in the TruSight Pan-Cancer Set A MiniSeq kit.

/ Results

Applications

The TruSight RNA Pan-Cancer Panel provides comprehensive assessment of cancer-related RNA transcripts and fusion detection in FFPE tissue and other oncology samples for research.

Example workflow


Project recommendations

Instrument Recommended number of samples Read length
MiniSeq System

Samples per run: mid output: 2-3, high output: 8 (based on 3 million reads per sample)

2 × 75 bp (max recommended)

MiSeq System

8 samples per run with v3 reagents (based on 3 million reads per sample)

2 × 75 bp (max recommended)


Related applications and methods

Compare

TruSight RNA Pan-Cancer Panel TruSight RNA Fusion Panel
Assay time 2.5 days 2.5 days
Automation details Explore available automation methods Explore available automation methods
Cancer type Pan-Cancer, Hematologic, Solid Tumor Pan-Cancer, Hematologic, Solid Tumor
Content specifications Pan-cancer panel with 1,385 targeted genes and 21,043 targeted exonic regions. Includes 507 genes involved in cancer gene fusions.
Description Comprehensive assessment of cancer-related RNA transcripts that enables research on gene fusions, variants, and gene expression changes in multiple cancer types.

Provides a cost-effective NGS solution for cancer research, offering deep coverage of 507 genes implicated in multiple cancer types, including solid tumors, sarcomas, and hematological malignancies. 

Hands-on time 11 hr 11 hr
Input quantity 10 ng total RNA, 20–100 ng FFPE RNA 10 ng total RNA, 20–100 ng FFPE RNA
Instruments MiSeq System, NextSeq 550 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 500 System MiSeq System, NextSeq 550 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 500 System
Method Targeted RNA sequencing, Target enrichment, Custom sequencing Targeted RNA sequencing, Target enrichment
Nucleic acid type RNA RNA
Specialized sample types Low-Input Samples, FFPE Tissue Low-Input Samples, FFPE Tissue
Species category Human Human
Technology Sequencing Sequencing
Variant class Gene fusions, Somatic variants, Novel transcripts, Transcript variants Gene fusions

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Figures

TruSight Pan-Cancer capture chemistry

The TruSight RNA PanCancer Panel provides a simple, streamlined method for isolating targeted regions of interest from total RNA.

Identification of novel gene fusion partners

(A) The size distribution of total RNA from 3 different FFPE samples derived from melanoma are shown on a Bioanalyzer. (B) Table shows the detection of the gene fusion partner in FFPE samples when only one gene (highlighted) of the fusion pair is targeted.

TruSight RNA Pan-Cancer Panel Set A

RS-303-1002

Includes library preparation reagents and oligos for 48 samples with 12 indexes; each index is sufficient for 4 individual samples. May be used with TruSight RNA Pan-Cancer Panel Set B to allow for pooling up to 24 samples.

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TruSight RNA Pan-Cancer Panel Set B

RS-303-1003

Includes library preparation reagents and oligos for 48 samples with 12 indexes; each index is sufficient for 4 individual samples. May be used with TruSight RNA Pan-Cancer Panel Set A to allow for pooling up to 24 samples.

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TruSight RNA Pan-Cancer Set A MiniSeq Kit

20005611

Includes library preparation reagents and oligos for 48 samples with 12 indexes, plus 6 MiniSeq High Output Kits (150 Cycles).

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Trusight RNA Pan-Cancer Oligo Panel

20046104

Trusight RNA Pan-Cancer Oligo Panel includes oligos sufficient for 96 total RNA samples for sequencing if using 1-plex enrichment or 288 total RNA samples for sequencing if using 3-plex* enrichment. No library prep is included with this panel. *Only applicable to library prep workflows that permit multiplexed enrichment.

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Selection summary

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FAQs

The TruSight RNA Pan-Cancer workflow involves six major steps:

  • Generating stranded RNA-Seq libraries
  • Hybridizing biotinylated probes to targeted regions
  • Capturing targets using streptavidin beads
  • Eluting captured fragments from beads
  • Generating clusters and sequencing
  • Analyzing data and calling gene fusions with BaseSpace RNA Alignment App

Learn more.

The probes are designed to target 1385 cancer genes and detect fusions by spanning all exons of every gene.

Run the RNA-Seq workflow (FASTQ only) on the MiSeq System and stream the data to BaseSpace Sequence Hub. The BaseSpace RNA-Seq Alignment App analyzes data from the TruSight RNA Pan-Cancer Panel, providing a simple results summary that includes a fusion table, variant table, and gene expression table. You may also use your own pipeline for analysis.

/ Results

Order the NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

TruSight Oncology 500

Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

Speak with a specialist

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