Amplicon sequencing is a highly targeted approach for analyzing genetic variation in specific genomic regions. The ultra-deep sequencing of PCR products (amplicons) allows efficient variant identification and characterization. Illumina amplicon technology uses a pair of oligonucleotide probes designed to target and capture regions of interest, followed by next-generation sequencing (NGS).
Amplicon sequencing is useful for the discovery of rare somatic mutations in complex samples (such as tumors mixed with germline DNA). Another common application is sequencing the bacterial 16S rRNA gene across multiple species, a widely used method for phylogeny and taxonomy studies, particularly in diverse metagenomics samples.
Amplicon sequencing allows researchers to sequence 16–1536 targets at a time, spanning 150 bp–1.5 kb per target, depending on the library preparation method used. This highly multiplexed approach expedites research by assessing multiple genes simultaneously at approximately the same cost as a single-gene assay. DNA libraries can be prepared in 6.5 hours and sequenced in 5–56 hours.
Amplicon sequencing enables a wide range of applications for the discovery, validation, or screening of genetic variants.
Fully customizable, amplicon-based assay for targeted resequencing of low DNA input and/or FFPE samples.
Focused power for sequencing 1536 amplicons or more in a single run.
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 amplicon 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.
Fully customizable, amplicon-based assay for targeted resequencing of low DNA input and/or FFPE samples.TruSeq Custom Amplicon v1.5 Library Prep Kit
Fully customizable, amplicon-based assay for targeted resequencing.TruSeq Amplicon – Cancer Panel
Highly multiplexed targeted resequencing assay for detecting somatic mutations in 48 genes of interest.TruSight Myeloid Sequencing Panel
Predesigned panel targeting 54 genes frequently mutated in hematological cancers.Nextera DNA Flex Library Prep Kit
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
Focused panel to assess relevant solid tumor somatic variants in a simple, sample-to-data workflow.Nextera XT DNA Library Prep Kit
Library preparation for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.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.DesignStudio Assay Design Tool
An easy-to-use online software tool that provides dynamic feedback to optimize probe designs.
Targeted power for sequencing up to 96 samples and 1536 amplicons or more in a single run.MiSeq Series
Focused power for sequencing up to 96 samples and 1536 amplicons or more in a single run.NextSeq Series
Flexible power for sequencing up to 96 samples and 1536 amplicons or more per run.
Streamlined analysis of NGS data enriched for particular target sequences using TruSeq Amplicon reads.16S Metagenomics App
Analyzes DNA from amplicon sequencing of prokaryotic 16S small subunit rRNA genes and provides visuals of taxonomic classification.BaseSpace Variant Interpreter
Leverages leading annotation databases and a powerful filtering interface for rapid identification of disease-associated variants.
A genome browser developed by the Broad Institute of MIT and Harvard that displays NGS data for complex variant analysis.BaseSpace Sequence Hub
Differential gene expression, drug interaction, and disease analysis.BaseSpace Correlation Engine
A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.
Access the proven power of Illumina NGS for low-throughput applications with the small and robust MiniSeq System. Study single genes or entire pathways with a sequencing solution that fits your benchtop, your budget, and your workflow.View System
Targeted sequencing enables researchers to focus on select genes or amplicons that have known associations with cancer. Both predesigned and custom panels are available. Learn more about targeted cancer sequencing.
NGS technology can help researchers discover causative variants of inherited disorders by assessing many genes at the same time, in contrast to traditional methods, which are often costly and require extensive testing. Learn more about genetic disease research.
16S ribosomal RNA (rRNA) sequencing is a common amplicon sequencing method used to identify and compare bacteria within a given sample. It can identify strains that might not be found using other methods. Learn more about 16S rRNA sequencing.
Targeted resequencing can uncover genetic variation in animals and plants. These variants may represent beneficial mutations that can help inform breeding decisions, or mutations linked to disease susceptibility. Learn more about plant and animal sequencing.
*Data calculations on file. Illumina, Inc., 2015