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Targeted RNA Sequencing

Introduction to Targeted RNA Sequencing

Targeted RNA-sequencing (RNA-Seq) is a highly accurate method for selecting and sequencing specific transcripts of interest. It 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. Enrichment assays also provide the ability to detect both known and novel gene fusion partners in many sample types, including formalin-fixed paraffin-embedded (FFPE) tissue.

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Advantages of Targeted Enrichment RNA-Seq

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 FFPE tissue
  • Low input (requires 10 ng of total RNA or 20 – 100 ng of FFPE RNA)
  • Detects both known and novel fusion gene partners
  • Profiles gene expression with a broad dynamic range

Advantages of Targeted Amplicon RNA-Seq

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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Targeted RNA Sequencing and Schizophrenia

Dr. Frank Middleton from 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-Seq Workflow

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

We offer integrated targeted RNA-Seq workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.

Gene Panel and Array Finder

Identify sequencing panels or microarrays that target your genes of interest. Search panels by gene, or find genotyping arrays by genomic location, variant ID, or species.

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Gene Panel and Array Finder

Related Solutions

Cancer Research: Variant Detection

Monitor gene expression and transcriptome changes with targeted RNA-Seq to better understand which variants are expressed and which may affect tumorigenesis and progression. Learn more about RNA-Seq in cancer research.

Drug Development Research

Explore 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.

Neurobiology Research

Gain insight into neurological disorders such as Alzheimer's and Parkinson's disease with specifically designed targeted RNA expression panels and arrays. Learn more about neuroscience research.

Immunology Research

See how NGS enables research into autoimmune disease mechanisms, the immune repertoire, and the functional consequences of immune-related genetic variation. Learn more about immunology research.

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Additional Resources

RNA-Seq Methods Review
RNA-Seq Methods Review

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

Push-Button Informatics
Push-Button Informatics

Illumina bioinformatics tools make it easier to manage, analyze, and interpret large amounts of complex genomic data.

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.

FFPE RNA-Seq Tips
FFPE RNA-Seq Tips

RNA-Seq analysis of FFPE and other low-quality samples offers valuable insights for disease research.

RNA-Seq with the NextSeq Series
RNA-Seq with the NextSeq Series

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

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.

Removing Cancer's Veil: TruSight Tumor 170
Removing Cancer's Veil: TruSight Tumor 170

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

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