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Amplicon sequencing


Amplicon sequencing is a type of targeted next generation sequencing that uses PCR to create sequences of DNA called amplicons. It is simple and fast and has a variety of applications.

What is amplicon sequencing?

Amplicon sequencing is a method of targeted next generation sequencing that enables you to analyze genetic variation in specific genomic regions. This method uses PCR to create sequences of DNA called amplicons. Amplicons from different samples can be multiplexed, also called indexed or pooled, which involves adding a barcode (index) to samples so they can be identified. Before multiplexing, individual samples used for amplicon sequencing must be transformed into libraries by adding adapters and enriching target regions via PCR amplification. The adapters allows formation of indexed amplicons and allow the amplicons to adhere to the flow cell for sequencing. Amplicon sequencing is typically used for variant detection.

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Targeted sequencing application guide

This detailed overview walks you through major advances in capture and enrichment technology, types of targeted next generation sequencing, their applications, and more.

Simple and fast with high on-target rates

Amplicon sequencing is a quick and easy method of targeted sequencing with a simple workflow and fast turnaround time. Amplicon sequencing has naturally higher on-target rates than other targeted sequencing methods due to the specificity of primer design.

This method is appropriate for genotyping by sequencing, detection of germline single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and known fusions. Amplicon sequencing should be used for experiments that require less sensitivity, meaning they can tolerate more false positive variant calls, since bias that might be created during the PCR amplification step cannot be removed.

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Combining NGS technologies for biomarker identification and confirmation research application note

IDT has developed 2 unique, high-performing targeted NGS approaches to maximize researchers’ ability to confidently identify and confirm biomarkers in germline and somatic mutations. Here, we describe the benefits and caveats of using either hybridization capture or amplicon sequencing to identify mutations in normal tissue, formalin-fixed, paraffin-embedded (FFPE) tumor, and cell-free DNA (cfDNA).

Uses of amplicon sequencing

  • Genotyping by sequencing
  • CRISPR edit validation
  • Disease-associated variant detection
  • Detecting germline inherited SNPs and indels

Get started with amplicon sequencing

Working in one of these applications? Just starting? See how you can easily improve your workflows and results.

rhAmpSeq amplicon sequencing system

The rhAmpSeq™ system enables highly accurate amplicon sequencing on Illumina® next generation sequencing (NGS) platforms. Whether you are investigating thousands of targets or a few, the fast and easy rhAmpSeq workflow generates NGS-ready amplicon libraries for deep, targeted resequencing.

Learn more

Explore amplicon sequencing applications