Highly targeted resequencing of regions of interest

Deep sequencing of PCR amplicons allows for efficient characterization of gene targets

Amplicon Sequencing

Amplicon sequencing is a highly targeted approach that enables researchers to analyze genetic variation in specific genomic regions. The ultra-deep sequencing of PCR products (amplicons) allows efficient variant identification and characterization. This method uses 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 in 3 Simple Steps

Deep sequence PCR amplicons with this comprehensive workflow solution.

View Recommended Workflow  

  • Enables researchers to efficiently discover, validate, and screen genetic variants using a highly targeted approach
  • Supports multiplexing of hundreds to thousands of amplicons per reaction to achieve high coverage
  • Delivers highly targeted resequencing even in difficult-to-sequence areas, such as GC-rich regions
  • Allows flexibility for a wide range of experimental designs
  • Reduces sequencing costs and turnaround time compared to broader approaches such as whole-genome sequencing
Advantages of Amplicon Sequencing

Amplicon sequencing allows researchers to sequence targets ranging from a few to hundreds of genes in a single run. This ultra-high multiplexed PCR approach expedites research by assessing multiple genes simultaneously. Libraries can be prepared in as little as 5–7.5 hours and sequenced in 17–32 hours.

Amplicon sequencing enables a wide range of research applications for the discovery, validation, or screening of genetic variants.

Highly Targeted, Multiplexed Analysis
COVID-19 Sequencing

NGS is uniquely positioned in an infectious disease surveillance and outbreak model. Compare amplicon sequencing with other pathogen NGS methods such as shotgun metagenomics and target enrichment. Find solutions to detect SARS-CoV2, track transmission routes, study co-infection, and investigate viral evolution. 

Explore Coronavirus Sequencing Solutions
COVID-19 Solutions

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

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.

AmpliSeq for Illumina Sequencing Solution

Delivers a range of ready-to-use and custom panels for simple, flexible targeted resequencing that provides high-quality data you can trust.

Illumina DNA Prep

A fast, integrated workflow for a variety of applications, from human whole-genome sequencing to amplicons, plasmids, and microbes.

TruSight Tumor 15

Focused sequencing research panel to assess 15 genes commonly mutated in solid tumors in a single assay, with a simple, rapid workflow.

Nextera XT DNA Library Prep Kit

Library preparation for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.

Cancer Research Panel Portfolio

Illumina targeted sequencing panels facilitate clinical cancer research by providing expert-defined gene content plus simple data analysis and reporting options.

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.

iSeq 100 System

Affordable, fast, and accessible sequencing power for targeted or small genome sequencing in any lab.

MiniSeq System

Supports a broad range of targeted DNA and RNA applications for examining single genes or entire pathways.

MiSeq System

Enables focused applications, from targeted resequencing to metagenomics, small genome sequencing, and more.

NextSeq 550 System

Provides the flexible power you need for whole-genome, transcriptome, and targeted resequencing.

Illumina sequencing platform

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 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.

DNA Amplicon App

Streamlined analysis of NGS data enriched for particular target sequences using amplicon reads.

16S Metagenomics App

Analyzes DNA from amplicon sequencing of prokaryotic 16S small subunit rRNA genes and provides visuals of taxonomic classification.

Integrative Genomics Viewer App

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

BaseSpace Variant Interpreter

Leverages leading annotation databases and a powerful filtering interface, enabling researchers to rapidly identify disease-associated variants.

BaseSpace Correlation Engine

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

Targeted Sequencing Power with the MiniSeq Benchtop Sequencer

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
MiniSeq Desktop Sequencer
Cancer Gene Sequencing
Cancer Gene Sequencing

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.

Genetic and Rare Diseases
Condition Screening

NGS technology can help rapidly identify causative variants associated with rare and inherited genetic disorders. In contrast, traditional methods are often costly and require extensive testing. Learn more about NGS for genetic diseases.

16S rRNA Sequencing
16S rRNA Sequencing

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.

Plant and Animal Sequencing
Plant and Animal 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.

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Demonstrated 16S rRNA Amplicon Sequencing Protocol
Demonstrated 16S rRNA Sequencing Protocol

Illumina offers a demonstrated amplicon-based library prep protocol for 16S metagenomic sequencing.

Download Protocol
AmpliSeq for Illumina on the iSeq 100 System
AmpliSeq for Illumina on the iSeq 100 System

Find step-by-step guidance designed to help you transition your workflows to AmpliSeq for Illumina panels on the iSeq 100 System.

View Guide
Transitioning from TruSeq Custom Amplicon
Transitioning from TruSeq Custom Amplicon

Our detailed guide is designed to help you transfer projects from TruSeq Custom Amplicon to AmpliSeq for Illumina panels.

View Guide

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