In 2011, Ion AmpliSeq™
technology enabled targeted
sequencing from 10 ng of DNA
or less. And the world responded.

Sequencing success

Find out about Ion AmpliSeq™ sequencing with samples of low quality and low input amount

Content for all

Find out about both fixed panel and custom content options for your genome

Walk away freedom

Find out about automated library workflows on the Ion Chef™ System

Sequencing success with AmpliSeq technology

Since its launch in 2012, Ion AmpliSeq targeted sequencing technology has seen broad global adoption and resulted in the publication of greater than 140 peer-reviewed publications. Applications span such studies as investigating phenovariance in mice1, assessing gene copy number alterations2, and defining genetic changes associated with lung cancer3 research.

Researchers are not only using Ion AmpliSeq technology for less challenging research samples where available sample quantity and quality are not limiting, such as cell culture or fresh-frozen tissues, but also seeing tremendous success with challenging sample types, such as formalin-fixed paraffin-embedded (FFPE) tissue, achieved samples from fine needle aspirates, and cell-free DNA extracted from blood (cfDNA).

Video: Analysis of FFPE Tumor Samples

Formalin-fixed paraffin-embedded (FFPE) samples are challenging to work with. Dr. Nicole Pfarr discusses her experience with Ion AmpliSeq Panels on the Ion PGM™ System. (They currently use eight panels, both standard and custom).

“The Ion PGM System coupled with Ion AmpliSeq technology has allowed us to substantially improve the turnaround time and cost of sequencing these important genes - BRCA 1 and 2. The methodology proved robust enough to call even difficult mutations, including homopolymers of 7 to 9 bases in BRCA 1 and 2 genes.”

- Dr. José Luis Costa, Postdoctoral Fellow, Institute of Molecular Pathology and Immunology, Porto, Portugal
  1. Wang et al. (2015) Proc. Natl. Acad. Sci. 112: E440-E449.
  2. Grasso et al. (2014) J. Mol. Diagn. 17: 53-63.
  3. de Bruin et al. (2014) Science 346: 251-256.
Content for all—Ion AmpliSeq Panels

From off-the-shelf pre-designed panels to fully customized panels of your own design, Ion AmpliSeq Panels is designed to meet the needs of any targeted sequencing research application. Not working with human samples? Not a problem. Our Ion AmpliSeq™ Designer tool offers the ability to design custom panels from 12 predefined genomes, or your own reference genome by uploading a reference file. 

All Ion AmpliSeq Panels offer the following: 

  • High coverage uniformity and high specificity 
  • Starting input amounts as small as 10 ng of gDNA or cDNA 
  • Compatibility with degraded research samples such as FFPE samples or cfDNA 
  • Automated analysis solutions through Ion Reporter™ software 
  • Single-day sequencing workflows from sample to result 
Cancer research

Genomics plays an essential role in the field of oncology research since both inherited genetic variations and acquired somatic mutations are integral to cancer tumorgenesis. Ion AmpliSeq technology enables robust targeted sequencing from as little as 10 ng of FFPE DNA or RNA to simultaneously target tens to hundreds of genes simultaneously. Additionally, targeted sequencing with Ion AmpliSeq Panels enables the detection of various mutation types including SNPs, indels, gene fusions, and copy number variants with a single technology.

Learn more about cancer panels using the Ion AmpliSeq technology

Mendelian disease research

Whether your research is focused on a single gene or more complex Mendelian disorders, Ion AmpliSeq technology offers a solution that fits your needs. 

For mutations associated with known disorders, consider the Ion AmpliSeq™ Inherited Disease Panel, offering full exon coverage for genes reported in the NCBI ClinVar database to be mutated in over 700 unique inherited disorders, or consider community panels that have been created by key opinion leaders.

If de novo mutations are suspected, or for study of rare phenotypes, exome sequencing using the Ion AmpliSeq™ Exome RDY Panel offers full coverage of >97% of coding sequence.

Should none of these options fit your needs, customize your own panel content in minutes using the online AmpliSeq Designer tool.

Interested in detecting RNA expression changes? The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit provides coverage across more than 20,000 RefSeq genes, enabling the surveying of samples with as little as 10 ng of input RNA.

Plant and animal biology

For research in non-human model species and other non-model organisms the online Ion AmpliSeq Designer tool enables custom Ion AmpliSeq Panel designs for 11 non-human species using the latest reference genomes. 

Should you not find your particular species of interest, upload your own custom reference genome to design a custom panel. Custom Ion AmpliSeq panels can be designed for any genome using this simple-to-use online tool. 

Not sure where to start? Use our Ion AmpliSeq™ Assist Service to receive personalized project consultation from Thermo Fisher Scientific bioinfomatics professionals. 

Fast Turn-Around Genotyping without a Reference Genome PAGXXIII

Dr. James Schnable from the University of Nebraska-Lincoln has developed a technology called "tunable genotyping by sequencing" (tGBS) that provides much better read-depth compared to conventional genotyping-by-sequencing approaches. 

Human identification

Whether you are looking to crack tough cases with DNA mixture samples, generate more leads for investigations, or analyze highly degraded or trace DNA, Ion AmpliSeq technology enables rapid and accurate answers in a simple and cost effective manner. 

Learn more

Ion AmpliSeq targeted sequencing workflow

1 Construct Library
ampliseq primer pool
2 Prepare Template
Ion OneTouch 2 System
3 Run
5 Annotate Results
Product literature
Ion PGM™ Hi-Q™ Sequencing Kit
Targeted sequencing available for any genome

*The content provided herein may relate to products that have not been officially released and is subject to change without notice.