Detecting changes in the cancer transcriptome

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

Cancer RNA Sequencing

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.


Cancer RNA-Seq Research Stories

Cancer RNA-Seq for Precision Oncology Research
Cancer RNA-Seq for Precision Oncology Research

Clinical researchers at Avera Health rely on next-generation sequencing to uncover multiple drug-susceptible tumorigenic pathways.

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Deciphering the Role of Long Non-Coding RNA in Cancer
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.

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Library Prep Comparison for Cancer RNA-Seq
Library Prep Comparison for Cancer RNA-Seq

Researchers compared two TruSeq RNA kits to identify the optimal library prep method for their cancer gene expression studies.

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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.

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Analyze Gene Expression in Single Cells

Highly sensitive RNA-Seq methods enable gene expression analysis of very low-input samples, even single cells.

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Analyze Gene Expression in Single Cells

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.

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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.

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Illumina offers several library preparation, sequencing, and data analysis options for cancer RNA-Seq. 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.

TruSight Tumor 170

Comprehensive panel detects single-nucleotide variants (SNVs), amplifications, and fusions that contribute to solid tumor progression.

TruSeq RNA Exome

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

AmpliSeq for Illumina Custom RNA Fusion Panel

A customizable targeted panel for detecting fusion genes and measuring gene expression.

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.

TruSeq Small RNA Library Prep Kit

Sensitive kit for microRNA analysis.

AmpliSeq for Illumina Custom RNA Panel

Targeted custom RNA research panels optimized for sequencing up to 1200 targets of interest.

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 550 System

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

NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

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.

RNA Biomarkers for Drug Response

RNA sequencing (RNA-Seq) is increasingly being used to discover and profile RNA-based drug response biomarkers. Find resources designed to help you adopt RNA-Seq for biomarker analysis, including a workflow introduction, experimental considerations, and start-up advice.

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RNA Biomarkers for Drug Response
RNA-Seq for Cancer Transcriptome Analysis 

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

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Genomic Technologies for Cancer Research

Explore various genomic approaches to cancer research. Learn how cancer RNA-Seq can provide detailed information about gene expression in tumors.

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Removing Cancer's Veil: TruSight Tumor 170

An enrichment-based cancer research assay interrogates both DNA and RNA, detecting small variants, gene amplifications, gene fusions, and splice variants.

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Cancer Research Review

An overview of peer-reviewed cancer research publications featuring Illumina technology.

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Integrative Genomics to Inform Cancer Prognosis
Integrative Genomics to Inform Cancer Prognosis

Molecular profiling that combines DNA- and RNA-level data can more easily identify genes that may be driving cancer.

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