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 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 in 3 Simple Steps

Deep sequence PCR amplicons with this seamless workflow solution.

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  • Offers efficiency for discovering, validating, and screening genetic variants using a highly targeted approach
  • Multiplexes hundreds to over a thousand 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
Advantages of Amplicon Sequencing

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.

Highly Targeted, Multiplexed Analysis

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.

TruSeq Custom Amplicon Low Input Library Prep Kit

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.

TruSight Tumor 15

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.

MiniSeq System

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.

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.

TruSeq Amplicon App

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.

The Broad’s IGV

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.

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.

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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 Condition Research
Condition Screening

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 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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NextSeq Series Amplicon Sequencing Solution
NextSeq Series Amplicon Sequencing Solution

The NextSeq Series of systems offers a fast, easy, and accurate way for researchers to detect variants in genes of interest.

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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.

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Custom Amplicon Sequencing for Cancer Research
Amplicon Sequencing for Cancer Research

Dr. Robert Daber uses Illumina NGS technology to study molecular changes and genomic signatures in tumor DNA.

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Genotyping by Sequencing
Genotyping by Sequencing

NGS-based genotyping is a genetic screening method for discovering plant and animal SNPs and performing genotyping studies.

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NGS Technologies Fuel Cancer Research
NGS Technologies Fuel Cancer Research

Endocrinologists use MiSeq System and TruSeq Custom Amplicon Assay to discover causative variants of heritable endocrine cancer.

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High-Throughput Detection of Somatic Mosaicism
High-Throughput Detection of Somatic Mosaicism

Targeted resequencing is enabling a high-throughput approach to identify rare mosaic mutations in brain malformations.

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