Cancer RNA Sequencing


Understanding the Cancer Transcriptome

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 scientists:

  • Determine which variants are expressed in cancer samples
  • Identify gene expression signatures and mutational profiles associated with individual tumors, single cells, and tumor types
  • Focus on somatic mutations that have a clear functional effect, and identify key cancer driver mutations
  • Find novel small RNAs that regulate gene expression
  • Identify gene fusions arising from chromosomal translocations
connections bring meaning to cancer testing

Key benefits of cancer RNA sequencing

  • Provides sensitive and accurate measurement of gene expression at the transcript level
  • Provides both qualitative and quantitative data
  • Sequences with high specificity and accuracy
  • Maintains and tracks strand-specific information for both mRNA and total RNA workflows
  • Provides excellent performance with degraded RNA from samples such as FFPE and tissue
Potential applications of RNA-seq in cancer research

Potential applications of RNA-seq in cancer research

Take advantage of bulk RNA-Seq with its exceptionally well-defined workflows backed by thousands of peer-reviewed scientific publications. Ease of use and the low cost of implementation make RNA-Seq an ideal method to obtain high-quality transcriptomic data for those new to NGS.

Learn more about NGS for beginners

RNA-Seq enables you to:

Differentiate driver mutations from passenger mutations

Although cancer cells contain many mutations, only a few contribute to cancer initiation and progression. Researchers can use bulk RNA-Seq to examine the complete set of RNA transcripts produced by a genome. Data from the RNA-Seq experiment can reveal whether mutations result in transcriptomic changes that either drive cancer or act as passenger mutations.

Identify potentially druggable pathways

RNA-Seq can reveal pathways that are up- or down-regulated in cancer. This functional information is crucial for identification of molecular targets for precision therapeutics. Targeting upregulated pathways, for example, is a common method for suppressing tumor growth.

Discover pathways associated with disease

Studies into the transcriptomic differences between cancer samples and non-cancerous tissue have been shown to be useful in differentiating cancer subtypes, assessing the impact of mutations, identifying biomarkers, and other variables.

Assess biological responses

Bulk RNA-Seq can identify genes and pathways associated with biological responses to novel cancer therapies, such as immunotherapeutics in model systems or retrospective studies using past tissue samples.

Learn more about RNA-Seq

View more cancer research applications

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Featured cancer RNA-Seq methods

Bulk RNA-Seq

RNA-Seq allows researchers to detect known and novel features in a single assay, enabling the identification of transcript isoforms, gene fusions, single nucleotide variants, and other features without the limitation of prior knowledge.

Single-cell RNA-Seq

Learn more about single-cell RNA sequencing to examine the transcriptomes of individual cells for a high-resolution view of cell-to-cell variation.


See how mRNA-Seq can identify both known and novel transcript isoforms, gene fusions, and other features, as well as allele-specific expression for a complete view of the coding transcriptome.

Total RNA-Seq

Learn how total RNA-Seq can accurately measure gene and transcript abundance and identify known and novel transcriptome features.


Explore the unique advantages of this method that simultaneously quantifies cell surface protein and transcriptomic data within a single cell readout.

Spatial transcriptomics

Explore how this method can provide a topographical arrangement of gene expression patterns mapped onto tissue sections to link structure and activity.

cancer research methods guide

Cancer Research Methods Guide

The Cancer Research Methods Guide is a 40+ page comprehensive resource with simple, comprehensive workflows for a broad range of cancer research applications. This guide includes single-cell sequencing, spatial sequencing, methylation profiling, multiomics, cell-free RNA sequencing, and more.

Download free guide

Keep exploring

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A diverse country with younger-than-average cancer patients launches a national initiative to understand the genetics of oncology.

Deciphering the role of long non-coding RNA in cancer

Researchers are using RNA-Seq to reveal how lncRNAs could be used to identify, measure, and treat cancer.

Targeted RNA-Seq

Targeted RNA sequencing analyzes the expression of specific cancer genes and transcripts of interest.

Genomics and transcriptomics basics

Download the infographic to learn the basics of genome and transcriptome sequencing at a glance.

Sequencing DNA and RNA from the same sample

Watch the new in-lab quick start video to learn how to prepare high quality DNA and RNA samples for multiomic sequencing.

Advancing cancer research with multiomics

Learn how to link the causes and consequences of complex phenotypes through multiomics to enable discoveries that weren’t possible before.