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 genetic code, but contains ~85% of known disease-related variants,1 making whole-exome sequencing a cost-effective alternative to whole-genome sequencing.

Exome sequencing 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 seamless 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.

Recommended Workflow for Whole-Exome Sequencing

1 2 3
1 Library Prep

Your Library with

TruSeq Exome Library Prep Kit

Cost-effective library preparation and exome enrichment solution with industry-leading accuracy.

2 Sequence Efficently

Efficiently with

HiSeq 3000/HiSeq 4000

Production power to sequence up to 180 human exomes per run.

3 Analyze and Store Data

Analyze and
Store Data with BaseSpace Apps

Isaac Enrichment

Push-button alignment and variant calling of Illumina exomes to rapidly identify disease-associated variants.

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 data quality, Illumina offers integrated exome sequencing 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 Exome Kit

Cost-effective library preparation and exome enrichment solution with industry-leading accuracy.

TruSeq Rapid Exome Kit

Fast library preparation and exome enrichment kit accommodating low input amounts.

Nextera Rapid Capture Custom Enrichment Kit

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

TruSight One Sequencing Panel

Targets exons in 4,813 genes with known disease associations, providing one workflow for multiple assays.

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 Series

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

HiSeq Series
Production power to sequence up to 180 human exomes 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/or buffers tailored to each Illumina sequencing system.

BWA Enrichment App

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

Isaac Enrichment App

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

VariantStudio App

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

The Broad’s IGV

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.

BaseSpace Correlation Engine

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

Cancer Exome Sequencing
Cancer Exome Sequencing

Sequencing the cancer exome provides useful information about the coding mutations that contribute to 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 Discovery
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. Genetic association and linkage studies provide insights into complex diseases through common genetic variants shared between many individuals. 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.

Recent Publications
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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.

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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.

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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.

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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.

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Exome Sequencing Data Analysis
DNA Sequencing Data Analysis

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

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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.

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  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