What is Ion AmpliSeq technology?


Ion AmpliSeq is a targeted next-generation sequencing (NGS) technology developed by Thermo Fisher Scientific. It is designed to simplify and streamline the NGS workflow by enabling the amplification of specific genomic regions of interest. Ion AmpliSeq utilizes an ultrahigh multiplex polymerase chain reaction (PCR) approach to selectively amplify targeted regions, allowing for highly efficient and sensitive sequencing of specific gene panels or custom targets. This technology has been widely adopted in various translational research and clinical research applications, including cancer research, inherited disease research, infectious disease research, and pharmacogenomics research.

Design your custom NGS panel

Ion AmpliSeq Designer is a free online tool that makes it easy to design customized Ion AmpliSeq panels to meet your unique targeted NGS testing needs.

Ion AmpliSeq panels flyer

Learn more about custom Ion AmpliSeq panels for focused clinical NGS research and amplicon-based targeted NGS testing.

What are the advantages of Ion Ampliseq technology?

Ion AmpliSeq technology is widely recognized as a trusted amplicon-based enrichment method for targeted NGS. For a fast, easy, and scalable NGS solution, many researchers choose Ion AmpliSeq technology.


Ion AmpliSeq technology offers several advantages that contribute to its widespread adoption in translational and clinical research applications:

 Targeted and specific amplification  

Ion AmpliSeq technology allows for the selective amplification of specific genomic regions of interest, enabling focused sequencing of targeted gene panels or custom targets. This targeted amplification reduces the complexity of the sequencing library and improves the depth of coverage, increasing the sensitivity for detecting variants in the targeted regions.

High multiplexing capability

Ion AmpliSeq PCR reactions can amplify hundreds to thousands of targets in a single reaction, allowing for efficient and cost-effective sequencing of multiple samples simultaneously. This high multiplexing capability minimizes the amount of input DNA required and maximizes sequencing throughput.

  Easy, streamlined workflow

The Ion AmpliSeq workflow is designed to be simple and user-friendly, with optimized primer custom design and a standardized library preparation protocol. This streamlined workflow reduces the hands-on time and reduces the potential for errors, making it accessible to users with varying levels of expertise.


Ion AmpliSeq technology allows for the design of custom gene panels or targets, enabling researchers to focus on specific regions of interest relevant to their clinical research needs. This customizability facilitates targeted sequencing in diverse fields, including cancer research, inherited disease research, and infectious disease research.

  Data analysis and interpretation

Thermo Fisher Scientific provides comprehensive bioinformatics tools and resources to support data analysis and interpretation of Ion AmpliSeq sequencing results. These tools assist in variant calling, annotation, and downstream analysis, facilitating the extraction of meaningful insights from the sequencing data.

Gene panels on demand, how and when you want them

Ion AmpliSeq On-Demand panels bring smaller pack sizes and an optimized catalog of pre-tested genes to custom NGS panels, so you can iterate panel design for human disease research with efficiency and convenience.

Applications for Ion AmpliSeq technology

When navigating through the complexities of genetic diseases, you need a discovery and testing tool that is both flexible and rapid for analyzing variants of interest. Ion AmpliSeq technology can help.


Ion AmpliSeq technology can be used for a wide range of applications in translational research and clinical research settings. Some of the key applications include:

  Cancer research

Ion AmpliSeq technology enables targeted sequencing of cancer-related genes and biomarkers, allowing for the identification of somatic mutations, copy number variations, and gene fusions. It is used for studying tumor heterogeneity, identifying potential relevant targets in a clinical research setting, and genetic testing on research samples.

 Inherited disease research

Ion AmpliSeq technology facilitates the identification of genetic variants associated with inherited diseases. It can be used for gene panel sequencing to test biomarkers for genetic disorders, assess carrier status, and perform pre-implantation genetic testing.

  Infectious disease research

Ion AmpliSeq technology can be used to study infectious diseases by targeting specific pathogens or regions of interest in their genomes. It enables the identification and characterization of microbial strains, tracking of outbreaks, and study of drug resistance mechanisms.

 Pharmacogenomics research

Ion AmpliSeq technology is ideally suited to clinical research studies investigating how genomic variations in drug metabolizing enzymes (DMEs) impact drug efficacy and safety.

 Forensic genetics

Ion AmpliSeq technology is employed in forensic investigations to analyze specific genetic markers for individual identification, kinship determination, and analysis of biological evidence.

One NGS test for CNV, SNP, indel, and fusion detection


Simple, versatile technology based on highly multiplexed PCR helps you target tens to hundreds of genes across mutation types including SNPs, indels, fusions, and copy number variants.

What can you do with NGS using Ion AmpliSeq panels? Get results.


After more than 25,000 custom designs and numerous publications, custom Ion AmpliSeq panels have a track record of exceptional coverage uniformity, reproducibility, and specificity to help you get results.

Ion AmpliSeq panels

Available in ready-to-use, made-to-order, and on-demand formats, Ion AmpliSeq panels consist of one or more pools of oligonucleotide primer pairs, with each pair designed to amplify a specified genomic region. Each panel can be designed to interrogate all bases across a gene, or can be focused on specific mutation hotspots.

On-Demand panels

Ion AmpliSeq On-Demand panels enable custom panel design in smaller pack sizes from pre-tested genes for practical customization that helps reduce upfront cost and risk.


Oncomine tumor-specific panels

Oncomine tumor-specific panels are 12 pre-designed yet customizable panels created from a curated inventory of pre-tested genes relevant to cancer research and sized to be economical (15–30 genes).

Community panels

Ion AmpliSeq community panels are designed with input from leading disease researchers and verified for performance to provide targeted sequencing for your research in cancer, inherited disease, and microbial and infectious disease. Most community panels can be customized to add or remove genes or regions of interest.

Made-to-order panels

For maximum flexibility, simply select a subset of targets and enter your specific genomic content online using the Ion AmpliSeq Designer tool, and we will design and create customized Ion AmpliSeq panels just for you. Choose from a number of reference genomes or upload your own reference sequence.

Ready-to-use panels

The convenient predesigned Ion AmpliSeq ready-to-use panels allow researchers to focus on data generation and analysis, not on the labor-intensive primer design and target selection steps.

Exome panel

The Ion AmpliSeq Exome RDY S5 Kit allows for rapid, accurate sequencing of key exonic regions of the genome, going from DNA to variants in just 2 days.

Transcriptome panels

The Ion AmpliSeq Transcriptome Human Gene Expression Kit is ideal for traditional gene expression analysis of known transcripts from the RefSeq database.

RNA-seq panels

Choose from over 20,000 genes to survey gene expression fold changes starting with as little as 500 pg of unfixed RNA or 5 ng of FFPE RNA.

Need even higher sensitivity?

To design your own panels and find variants with a very low limit of detection (down to 0.1%), try Ion AmpliSeq HD technology. This novel library amplification technology enables researchers to get answers when ultrahigh sensitivity is required, such as when detecting low-frequency alleles in circulating tumor DNA or trace pathogenic microbial species in blood.

Not working with human research samples? No problem.


Design a custom panel from 13 predefined genomes, or from your own reference genome after uploading a reference file.

Ion Torrent next-generation sequencing systems

Ion AmpliSeq panels are compatible with both the Ion GeneStudio S5 System and the Ion Torrent Genexus System to deliver ease of use, automation capabilities, and rapid NGS test results in as little as 24 hours.

Ion GeneStudio SS System

Scalable targeted NGS to support small and large projects

The Ion GeneStudio S5 system is a scalable, targeted NGS workhorse with wide application breadth and throughput capability.

Ion Torrent Genexus System

Specimen to report in a single day with an end-to-end automated workflow

The Genexus System is a turnkey NGS solution that automates the specimen-to-report workflow and delivers results in as little as 24 hours with just two user touchpoints.

Ion AmpliSeq resources

Video: How does Ion AmpliSeq technology work?

Video: Transitioning from Sanger sequencing? It 's easy to get started.

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