AmpliSeq™ Technology

Targeted Genotyping with Ion Torrent DNA sequencing

Since dideoxy (Sanger) sequencing was developed over 30 years ago, amplicon sequencing has been a mainstay of genome analysis. Now, with AmpliSeq™, it is possible to simultaneously amplify, sequence and genotype hundreds of genomic regions in a single project.

By focusing next-generation DNA sequencing (NGS) technologies on specific targets, tens to hundreds of genetic markers can be quickly and cost effectively identified or genotyped in large populations. 

After sequencing, NGS data from each sample is analyzed independently and scored for genotypes based on sequencing quality and depth of coverage. 

Genotyping Applications

Phylogenetic Analysis

Linkage and QTL Mapping

Population Structure

Genome Wide Association


Ion AmpliSeq™ Training Workshops


Have you ever wanted to re-sequence a particular region of a genome? Or perhaps completed a sequencing project and now want to begin genotyping studies using select loci of interest? From June through August 2016 Floragenex will be hosting a series of training workshops to educate researchers on best practices for configuring, designing and preparing targeted sequencing and genotyping applications using the Ion Torrent AmpliSeq system. 


Research scientists working on molecular genomics applications that want to sequence targeted regions or targeted SNPs.


  • Introduction to AmpliSeqTM
  • AmpliSeq Applications
    • Multi-Amplicon Sequencing Studies 
    • Targeted Gene Resequencing
  • Best Practices for AmpliSeqTM Oligo Design
    • Starting Genomic Resources
    • Amplicon Design / Sequence Pre-Filtering / Bioinformatics
    • Navigating the Ion AmpliSeqTM Web Designer Ordering Panels
  • Library Preparation and NGS
  • General Q/A
  • Supplemental Tools and Hands on Teaching 

AmpliSeq™ is an ideal solution for a range of molecular genetic applications

  • Target specific variants for genotyping
  • Survey from 96 to 384 SNP variants
  • DNA to genotypes in 20-30 days
  • Flexible project architectures: sequence from 192 to 768 samples each week
  • Rapid and streamlined bioinformatics and analysis
  • Economical pricing competitive with leading genotyping systems

How AmpliSeq Works

    Ion AmpliSeq™ technology enables scalable, multiplex PCR reactions from 12- to 3,072-plex in a single tube using just 10 ng of starting DNA. Pre-existing or customized primer pools allow highly multiplexed PCR amplification of thousands of genomic target regions, with superior coverage uniformity and specificity.

    Each primer contains modifications that enable removal of primer sequences during library preparation, for efficient target assessment during sequencing. 

    Barcoded libraries from multiple samples can be combined and loaded onto a single Ion Torrent™ sequencing chip to minimize the sequencing run time and cost and allow for accurate sample-to-sample comparisons.


    Ion Torrent™ and AmpliSeq™ are registered trademarks of ThermoFisher Scientific and Life Technologies Corporation