Cancer Genomics Research
Cancer Genomics Research Clinical Cancer Research Cancer Companion Diagnostics NGS in Oncology
Cancer Genomics Research
Cancer Genomics Research Clinical Cancer Research Cancer Companion Diagnostics NGS in Oncology

Cancer RNA sequencing for transcriptome insights

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

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
Profile view of a female scientist interacting with the load consumables touch screen on the monitor of a NextSeq 550 in front of a window; green status bar

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

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
Side view of a female scientist using a single pipette; pipetting clear liquid in a sample tube; male scientist sitting next to the female working separately on the lab bench; also on the lab bench are six library tubes filled with clear liquid and and two larger tubes filled dark liquid; library prep box blurry in the background

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

Featured cancer RNA-Seq methods

Bulk RNA-Seq

Bulk 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.

mRNA-Seq

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.

Spatial transcriptomics

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

See more cancer sequencing methods

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.

Cancer RNA sequencing workflow

1
Library prep

Illumina Stranded mRNA Prep

Illumina Stranded mRNA Prep is a high-performance, fast, and complete whole-exome sequencing kit that includes library prep and hybridization reagents, a comprehensive exome probe panel, clean up/size selection beads, and indexes.

Illumina Stranded Total RNA Prep with Ribo-Zero Plus

Illumina Total RNA Prep with Ribo-Zero Plus provides exceptional performance for the analysis of coding and multiple forms of noncoding RNA.

Illumina RNA Prep for Enrichment

Illumina RNA Prep with Enrichment uses on-bead tagmentation followed by a simplified, single hybridization step to provide an exceptionally fast workflow for RNA-based library prep and enrichment.

2
Sequencing or arrays

NextSeq 1000 and 2000 Systems

The NextSeq 1000 and 2000 Systems are cost-efficient, user-friendly, mid-throughput benchtop sequencers that offer extreme flexibility to support new and emerging applications.

NovaSeq X Series

The NovaSeq X Series offers vast application breadth, enabling data-intensive methods at production scale.

3
Data analysis

DRAGEN RNA and DRAGEN RNA Differential Expression apps

DRAGEN RNA and DRAGEN RNA Differential Expression apps offer accurate, comprehensive, and efficient analysis of NGS data, including alignment, quantification, fusion detection, and differential gene expression analysis.

Correlation Engine (for mRNA)

Correlation Engine is an interactive omics knowledgebase that puts private omics data in biological context with highly curated public data.

Keep exploring

Targeted RNA-Seq

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

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