Focused sequencing of specific transcripts of interest

Gene expression and fusion detection in RNA samples

Targeted RNA Sequencing

Targeted RNA-sequencing (RNA-Seq) is a highly accurate method for selecting and sequencing specific transcripts of interest and offers both quantitative and qualitative information. Targeted RNA-Seq can be achieved via either enrichment or amplicon-based approaches, both of which enable gene expression analysis in a focused set of genes of interest, with enrichment assays also providing the ability to detect both known and novel gene fusion partners in many sample types including formalin fixed paraffin embedded (FFPE) tissue.

RNA-enrichment provides quantitative expression information as well as the detection of small variants and gene fusions. RNA enrichment offers the following features:

  • Compatible with difficult samples such as formalin fixed paraffin embedded (FFPE) tissue
  • Low input requiring 10ng of total RNA or 20 – 100ng of FFPE RNA
  • Detection of known and novel fusion gene partners
  • Gene expression profiles with a broad dynamic range
Advantages of Targeted Enrichment RNA Sequencing

RNA expression panels can be designed to focus on RNA sequences of interest or custom content can be added to fully optimized and experimentally validated panels.

  • Offers a highly accurate and specific method for measuring transcripts of interest
  • Provides qualitative and quantitative information for differential expression analysis, allele-specific expression measurement, and gene fusion verification
  • Measures dozens to thousands of targets simultaneously
  • Is compatible with low-quality or FFPE-derived RNA samples
New Views of Cancer Pathways in Pediatric Leukemia

Researchers are using the TruSight RNA Pan-Cancer Panel to understand the role of fusion genes in pediatric leukemia.

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Frank Middleton, Ph.D., at SUNY Upstate Medical University (UMU) developed a focused gene panel to screen for expression alterations caused by a newly discovered CNV in schizophrenia. See why Dr. Middleton used targeted RNA-Seq rather than PCR or arrays to analyze several hundred genes associated with schizophrenia, bipolar disorder, and autism.

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Targeted RNA Sequencing and Schizophrenia

Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*

In addition to our industry-leading sequencing, Illumina offers integrated targeted RNA-Seq workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.

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

TruSeq Targeted RNA Expression Kits

Highly customizable panels for mid- to high-plex gene expression profiling starting with as little as 50 ng RNA. FFPE RNA compatible.

TruSight RNA Pan-Cancer

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

TruSight Tumor 170

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

TruSight RNA Fusion

A gene fusion detection panel targeting fusion associated genes in many cancer types with the ability to detect known and novel fusion gene partners.


Easy-to-use, web-based assay design tool. Customize sequencing content to fit the needs of your study.

Library Prep Kit Selector Library Prep Kit Selector

Determine the best kit for your needs based on project type, starting material, and method or application.

MiniSeq System

Targeted Power. Access proven Illumina quality with this small, robust NGS system. Up to 384 targeted RNA samples per run.**

MiSeq Series

Focused Power. Speed and simplicity for targeted and small genome sequencing. Up to 384 targeted RNA samples per run.**

NextSeq Series

Flexible power. Speed and simplicity for everyday genomics. Up to 384 targeted RNA samples per run.**

HiSeq Series

Production power. Max throughput and lowest cost for production-scale genomics. Up to 6144 targeted RNA samples per run.**

Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and buffers tailored to each Illumina sequencing system.

The TruSeq Targeted RNA App is available on MiSeq Reporter and BaseSpace.

Local Run Manager

Easy-to-use software for automated on-instrument data analysis.

The Broad’s IGV

A genome browser developed by the Broad Institute of MIT and Harvard that displays NGS data for complex variant analysis.

Genomatix Pathway System (GePS)

Associates single gene or list of genes with annotation data for pathways, diseases, tissues, and small molecules.

iPathway Guide

Differential gene expression, drug interaction, and disease analysis.

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 biomarkers.

Local Run Manager

Easy-to-use software for automated on-instrument data analysis.

Gene Panel and Array Finder

Next-generation sequencing (NGS) offers the scalability, speed, and resolution for targeted resequencing. Our Gene Panel and Array Finder will help you identify predesigned Illumina sequencing panels to match your genes of interest.

Find the Right Panel
Gene Panel and Array Finder
Cancer Research: Variant Detection
Cancer Research: Variant Detection

Monitoring gene expression and transcriptome changes with targeted RNA-Seq can help researchers understand which variants are expressed and which may affect tumorigenesis and progression. Learn more about targeted RNA-Seq in cancer research.

Drug Development and RNA Sequencing
Drug Development and RNA Sequencing

Illumina provides an innovative portfolio of genomic sequencing solutions for all phases of the drug development pipeline. Characterize gene expression profiles from a custom panel with a few defined targets to the whole transcriptome. Learn more about NGS in drug development.

Complex Disease: Neural Disorders
Complex Disease: Neural Disorders

With specifically designed targeted RNA expression panels, neuroscientists can gain insights into whether neurodegenerative and neurotoxic pathways are compromised within study populations. Learn more about neuroscience research.

RNA Drug Response Biomarker Profiling
RNA Drug Response Biomarker Profiling

Find out how to utilize RNA-Seq to profile or discover RNA-based drug response biomarkers. Access resources designed to help new users adopt this application. Learn more about drug response RNA biomarker analysis.

TruSeq Targeted RNA Expression fixed panels (including neurodegeneration, p53, apoptosis, stem cells, and others) have been discontinued. We recommend using TruSeq Targeted RNA Expression custom panels as a replacement. Illumina remains committed to providing you with high-quality support and service.

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Design a Targeted RNA-Seq Experiment
Design a Targeted RNA-Seq Experiment

Learn about normalization, multiplexing, sample pooling, and how to work with your “read budget.”

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Push-Button Informatics
Push-Button Informatics

Access user-friendly tools that enable researchers to easily analyze, store, and share NGS data.

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Targeted RNA-Seq and Circadian Rhythms
Targeted RNA-Seq and Circadian Rhythms

Dr. Hughes at University of Missouri-St. Louis uses targeted RNA-Seq to uncover the genetic mechanisms of circadian rhythms.

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Key Targeted RNA-Seq Publications
RNA-Seq Methods Review

This overview discusses recent RNA-Seq research publications featuring Illumina technology.

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RNA-Seq on the NextSeq 500 System

A flexible, cost-effective solution for RNA sequencing provides a deeper understanding of biology.

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Paired-End RNA-Seq
Paired-End RNA-Seq

All Illumina sequencing systems are capable of paired-end sequencing, which facilitates detection of novel RNA transcripts, gene fusions, and more.

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Webinar: FFPE RNA-Seq
Webinar: FFPE RNA-Seq

Learn how to overcome hurdles in FFPE RNA sequencing.

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Removing Cancer's Veil: TruSight Tumor 170

A new cancer research assay targets both DNA and RNA, detecting small variants, gene amplifications, gene fusions, and splice variants.

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*Data calculations on file. Illumina, Inc., 2015

**Based on TruSeq indexing and up to 65 targets for MiniSeq or MiSeq, 1041 targets for NextSeq 500, and 651 targets/lane for HiSeq.