Targeted sequencing to detect exonic variants

Investigate the protein-coding regions of the genome to uncover genetic influences on disease and population health

Exome Sequencing

Perhaps the most widely used targeted sequencing method is exome sequencing. The exome (the protein-coding region of the human genome) represents less than 2% of the genome, but contains ~85% of known disease-related variants,1 making whole-exome sequencing a cost-effective alternative to whole-genome sequencing.

Exome sequencing using exome enrichment can efficiently identify coding variants across a wide range of applications, including population genetics, genetic disease, and cancer studies.

Whole-Exome Sequencing in 3 Simple Steps

Investigate the protein-coding regions of the genome with this comprehensive workflow solution.

View Recommended Workflow  

  • Identifies variants across a wide range of applications
  • Achieves comprehensive coverage of coding regions
  • Provides a cost-effective alternative to whole-genome sequencing (4–5 Gb of sequencing per exome compared to ~90 Gb per whole human genome)
  • Produces a smaller, more manageable data set for faster, easier analysis compared to whole-genome approaches

Exome sequencing is a cost-effective approach when whole-genome sequencing is not practical or necessary. Sequencing only the coding regions of the genome enables researchers to focus their resources on the genes most likely to affect phenotype, and offers an accessible combination of turnaround time and price.

Exome sequencing detects variants in coding exons, with the capability to expand targeted content to include untranslated regions (UTRs) and microRNA for a more comprehensive view of gene regulation. DNA libraries can be prepared in as little as 1 day and require only 4–5 Gb of sequencing per exome.

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

Illumina offers integrated exome sequencing workflows like whole exome enrichment 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.

Nextera Flex for Enrichment

Nextera Flex for Enrichment uses a fast, user-friendly workflow. On-bead tagmentation chemistry is combined with a simplified, single hybridization protocol to reduce total workflow time.

TruSeq DNA Exome

Cost-effective library preparation and exome enrichment solution that delivers exceptional target coverage over a broad range of read depths.

Nextera DNA Exome

Fast library preparation and exome enrichment that accommodates low input amounts.

Nextera Rapid Capture Custom Enrichment Kit

Custom assay for enriching genomic regions of interest, with add-on functionality.

AmpliSeq for Illumina Exome Panel

Targeted research panel for sequencing the protein-coding regions of the genome.

TruSight One Sequencing Panels

Comprehensive panels targeting disease-associated regions of the exome with high analytical sensitivity and specificity.

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.

Exome Comparative Table

Find the right Illumina library preparation kit for your exome sequencing project and application.

MiSeq Series

Focused power to sequence targeted regions or 1 human exome per run.

NextSeq 550 System

Flexible power to sequence up to 9 human exomes per run.

HiSeq 4000 System

Production power to sequence up to 96 human exomes per run.

NovaSeq 6000 System

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

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/or buffers tailored to each Illumina sequencing system.

BaseSpace BWA Enrichment App

Performs targeted resequencing using BWA, the community’s most popular algorithm for alignment, and GATK for variant calling.

BaseSpace Enrichment App

Performs targeted resequencing using fast and accurate Isaac algorithms for alignment and variant calling.

BaseSpace Variant Interpreter

Leverages leading annotation databases and a powerful filtering interface for rapid identification of disease-associated variants.

BaseSpace Integrative Genomics Viewer App

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

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

Local Run Manager

An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.

BaseSpace Correlation Engine

A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.

Partnering with IDT to Enhance Exome Sequencing

Illumina and IDT have joined forces to deliver high-quality, efficient exome library preparation. TruSeq and Nextera library prep workflows featuring XGen Exome Research Panel and Enrichment Reagents from IDT will be available soon.

Learn More
Partnering with IDT to Enhance Exome Sequencing
Cancer Exome Sequencing Studies
Cancer Exome Sequencing

This method provides useful information about coding mutations associated with tumor progression. By sequencing less than 2% of the genome, it is possible to sequence to higher depth more economically. Learn more about cancer exome sequencing.

Causal Variant Studies
Causal Variant Discovery

Whole-exome sequencing of individuals or trios is a common approach to finding causal variants in cases of rare, complex, or Mendelian disorders. Learn more about causal variant discovery.

Translational Research
Translational Research

Exome sequencing is increasingly being applied in translational and clinical settings to understand the role of genetics in human disease. Learn more about translational research.

Interested in receiving newsletters, case studies, and information on genomic analysis techniques? Enter your email address.
Exome Sequencing With the NextSeq Series
Exome Sequencing With the NextSeq Series

The NextSeq Series of systems offers a cost-effective, high-coverage workflow solution for exome analysis.

Access PDF
How to Improve Exome Sequencing Data
How to Improve Exome Sequencing Data

This technical note provides guidance about how to optimize experimental parameters for exome sequencing.

Access PDF
Exome Sequencing of FFPE Samples
Whole-Exome Sequencing of FFPE Samples

Researchers in Italy developed a quality check method that enables them to sequence formalin-fixed, paraffin-embedded tissues.

Access PDF
Analyzing Challenging Cancer Samples
Analyzing Challenging Cancer Samples

Yasser Riazalhosseini uses Illumina exome sequencing to preserve the integrity of low-input DNA from low-quality samples.

Access PDF
Exome Sequencing Data Analysis
DNA Sequencing Data Analysis

Illumina offers BaseSpace Apps for intuitive analysis of DNA sequencing data, including exome data.

Learn More
NGS to Study Genetics of Brain Development
NGS to Study Genetics of Brain Development

Researchers apply functional genomic methods to identify the role of gene variants in intellectual disability.

Read Interview
Whole Genome and Exome Sequencing Infographic
Whole Genome and Exome Sequencing Infographic

Explore the benefits of Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES).

Access PDF
High-Throughput Flipbook
High-Throughput Flipbook

Explore how researchers are using a range of high-throughput, next-generation sequencing (NGS) methods to drive their discoveries.

Access PDF
  1. van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014;30:418-426.

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