Detecting changes in the cancer transcriptome

RNA-Seq provides functional information about cancer gene expression and the gene fusions that drive tumor progression


Monitoring gene expression and transcriptome changes with cancer RNA sequencing (RNA-Seq) can aid in understanding tumor classification and progression. Cancers accumulate numerous genetic changes, but typically only a few drive tumor progression. Cancer RNA-Seq can help to determine which variants are expressed in cancer samples.


Sequencing the coding regions or the whole cancer transcriptome can provide valuable information about gene expression changes in tumors. Cancer RNA-Seq enables detection of strand-specific information, an important component of gene regulation. Cancer transcriptome sequencing captures both coding and noncoding RNA and provides strand orientation for a complete view of expression dynamics.

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Targeted RNA amplicon sequencing analyzes the expression of specific cancer genes. Predesigned cancer gene expression panels focus on relevant pathways, such as p53 and NFκB. Researchers can add custom content to broaden the scope of an experiment.

Learn About Targeted Amplicon RNA-Seq

Genomic regions containing deleted or amplified miRNA loci have been linked to multiple forms of cancer. Small RNA-Seq enables the discovery and profiling of miRNAs and other small, noncoding RNAs present in the cancer transcriptome.

Learn More About Small RNA-Seq

Formalin-fixed, paraffin-embedded (FFPE) tumor samples potentially contain valuable information about cancer pathogenesis and outcomes. Because FFPE samples generally contain partially degraded RNA, cancer RNA-Seq can pose challenges. Next-generation RNA-Seq methods enable researchers to access this important data, yielding high-quality results from degraded and FFPE-derived RNA.

Learn More About FFPE Sample RNA-Seq

Illumina offers several library preparation, sequencing, and data analysis options for cancer RNA sequencing. Streamlined library prep workflows and flexible kit configurations accommodate multiple study designs. Illumina systems deliver industry-leading data quality—in fact, approximately 90% of the world’s sequencing data are generated using Illumina sequencing by synthesis (SBS) chemistry.

Push-button apps in BaseSpace Sequence Hub simplify data analysis, so you can spend less time analyzing data and more time focusing on the next breakthrough.

Click on the below to view products for each workflow step.

TruSight RNA Pan-Cancer

Targeting 1385 oncology genes for gene expression, variant and fusion detection in all RNA sample types including FFPE.

TruSeq RNA Access Library Prep Kit

A reproducible, economical method for sequencing coding RNA from FFPE and other low-quality samples.

TruSeq Targeted RNA Expression Kit

Predesigned or custom panels for cancer gene expression profiling.

TruSeq Small RNA Library Prep Kit

Sensitive kit for microRNA analysis.

TruSeq Stranded mRNA Library Prep Kit

Precise measurement of mRNA strand orientation for detection of antisense transcription and discovery of alternative transcripts, gene fusions, and allele-specific expression.

TruSeq Stranded Total RNA Library Prep Kit

Scalable solution for whole-transcriptome analysis that delivers accurate strand information for a complete view of the transcriptome.

NeoPrep System

An easy-to-use system for preparing high-quality NGS libraries compatible with all Illumina sequencing platforms.

TruSeq Stranded mRNA Library Prep Kit for NeoPrep

Compatible with the NeoPrep System, delivering high-quality, reproducible libraries from low RNA input.

MiniSeq System

Simplest and most affordable solution for low-throughput targeted gene expression profiling.

MiSeq System

Desktop sequencer featuring a simple NGS workflow, integrated data analysis software, and unmatched accuracy.

MiSeqDx Instrument

FDA-cleared in vitro diagnostic NGS system that also operates in research mode to generate accurate, reliable data.

NextSeq Series

Flexible desktop sequencing systems to perform various cancer RNA-Seq applications, including whole-transcriptome analysis and cancer gene expression profiling.

HiSeq 2500 System

High-throughput system for large-scale cancer RNA-Seq experiments.

HiSeq 3000/HiSeq 4000 Systems

Ultra-high-throughput systems for production-scale cancer RNA-Seq experiments.

RNA Express App

Aligns RNA reads with the STAR aligner, followed by differential expression with DESeq2.

TopHat Alignment App

Performs spliced alignment, variant calling, and reference quantification for RNA samples.

Cufflinks Assembly & DE App

Performs novel transcript assembly and differential expression analysis on RNA samples.

MiSeq Reporter

Easy-to-use software for analysis and variant calling on the MiSeq System.

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

BaseSpace Correlation Engine

A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and prognostic or predictive biomarkers.

Cancer RNA-Seq for Transcriptome Analysis

Learn about RNA-Seq for cancer transcriptome analysis of single cells.

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High-Throughput Genomic Technologies for Cancer Research

Learn how cancer RNA-Seq can provide detailed information about gene expression in tumors.

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