Application Note

Read the latest peer-reviewed publications and application notes using Ion AmpliSeq™ DNA technology

Data Set

Download several targeted DNA datasets generated on the Ion PGM™ System and see the results for yourself

Informatics Solutions

Empower your data analysis with push-button variant detection and annotation.

Targeted DNA Workflow for the Ion PGM™ System

1 Create
gene panels

Select from our wide offering of gene panels or simply select a subset of the...Read more

2 Construct
Ion AmpliSeq™Library Kit 2.0 for rapid preparation of amplicon libraries

Use the Ion AmpliSeq™Library Kit 2.0 for rapid preparation of amplicon libraries using...Read more

3 Prepare
Ion OneTouch 2 system, prepare template

Ion OneTouch™ 2 System, available now, provides fully automated template preparation...Read more

4 Run

Ideal for sequencing targeted regions, the Ion PGM™ System and the Ion PGM™...Read more

5 Analyze
torrent suite software

Torrent Suite™ Software automatically aligns the sequence reads and...Read more

Design your own Ion AmpliSeq™ DNA Custom Panel

Creating and ordering custom panels is easy with the Ion AmpliSeq™ Designer—a free, online assay design tool that connects you directly to our assay design pipeline. Create and order custom DNA panels by simply selecting your targets of interest or simply enter your specific genomic content online and we will design and create customized Ion AmpliSeq™ Panel just for you. Leveraging more than a decade of expertise powering the TaqMan® Custom Assay design pipeline, Ion AmpliSeq™ Designer produces optimized primer designs in just hours.

Targeted sequencing for any genome

You now have full flexibility to analyze hundreds of genes of your choice, such as those implicated in a particular disease state or representing specific biochemical pathways. Ion AmpliSeq™ DNA custom designs target selection of 12 to 6,144 amplicons per pool, leveraging the experience from a community of &gt;1000 DNA-based AmpliSeq™ registered users with &gt;5,000 panels submitted. Custom panels are delivered in ready-to-use concentrations of pre-pooled multiplexed primers and concentrated 384-well plate format in which each well contains individual primer pairs.

Ready-to-use Panels

In addition to custom panels, there are several Ion AmpliSeq™ Ready-to-use Panels that were designed and validated by Life Technologies:

Ion AmpliSeq™ Cancer Hotspot Panel v2
This focused cancer panel is now expanded to target "hot spot" regions of 50 oncogenes and tumor suppressor genes, with wide coverage of KRAS, BRAF, and EGFR genes

Ion AmpliSeq™ Comprehensive Cancer Panel
Broad oncology panel targeting exons within >400 oncogenes and tumor suppressor genes

Ion AmpliSeq™ Inherited Disease Panel
Broad inherited disease panel targeting exons of over 300 genes associated with over 700 inherited diseases including neuromuscular, cardiovascular, developmental, and metabolic diseases

Ion AmpliSeq™ Sample ID Panel
Human SNP genotyping panel that allows generation of unique identification code for research samples in sequencing runs providing increased confidence during data analysis

Community Panels

Designed with leading disease researchers, Ion AmpliSeq™ Community Panels provide the ability to selectively analyze gene content with the aim of transforming cancer and inherited disease research. The following Ion AmpliSeq™ Community Panels have been designed with input from leading researchers and available for any lab to order via

Ion AmpliSeq™ Community Panels Flyer
Ion AmpliSeq™ Colon and Lung Cancer Research Panel v2 and RNA Fusion Lung Cancer Research Panel Flyer
Ion AmpliSeq™ BRCA1 and BRCA2 Panel Flyer

Targeted DNA Sequencing Informatics Solutions

Torrent Suite™ Software coordinates all the experiment planning and data processing steps necessary to complete your targeted sequencing workflow. New product templates enable users to plan targeted runs simply and quickly. Raw data are processed on the Ion PGM™ Sequencer and transferred to the PGM™ Torrent Server for base calling and variant calling. This entire process takes just a few hours, and further analysis can be performed using Ion Reporter™ Software, or third-party software solutions such as the Ingenuity® Variant Analysis™ Knowledge Module for Ion Reporter™ Software.

Ion Reporter™ Software comprises a suite of bioinformatics tools that streamline and simplify analysis of semiconductor sequencing data. Data generated on the Ion PGM™ System are automatically uploaded from the Torrent Browser to the hosted Ion Reporter™ Software environment for read mapping, annotation and reporting of common and rare variants, and multi-sample analysis—all with version control and audit traceability.

Ingenuity® Variant Analysis™ Knowledge Module for Ion Reporter™ Software helps researchers identify causal variants from targeted DNA data. Ingenuity® Variant Analysis™ Software can be accessed from within Ion Reporter™ Software to help identify, prioritize, and report the most biologically interesting variants for follow-up. Variant Analysis™ Software features a series of filters that users can apply to quickly exclude common variants (based on the 1000 Genomes Project) and non-deleterious variants, and then relate the remaining variants to relevant biology. The biological filtering in Variant Analysis™ Software is made possible by the rich biological content in the Ingenuity® Knowledge Base. Published findings about each variant of interest can be reviewed to assess the likely strength of its effect. Also, regulatory diagrams depicting how each variant may impact disease progression, with supporting literature, are readily accessible.

Cancer Research Solutions To Identify Your Driver Mutations

Ion Torrent™ systems provides an end-to-end solution that simplifies all of your sequencing and analysis needs for cancer research. Identify driver mutations using Ion Reporter™ Software, a suite of bioinformatics tools that streamlines your data analysis by mapping, calling variants, annotating those variants, and providing simple tools that allow you to identify and report on biologically relevant mutations. Ingenuity® Variant Analysis™ Knowledge Module for Ion Reporter™ Software, provides simple and secure access to a web-based application that helps you rapidly identify cancer driver variants from human DNA sequencing datasets and interpret their impact on signaling pathways and drug response. Ingenuity provides cancer disease models that streamline the identification of causally-consistent cancer driver variants. Both single tumors and tumor-normal pairs can be analyzed to assess the impact of SNP, Indel, gene fusion, and copy number variants on gain or loss of function of gene activity. The consequences of deleterious mutations can be visualized on cancer pathway diagrams to understand synergistic effects and to identify commonalities across tumor type or time series. Curated pharmacogenetic and drug target/treatment information relevant to driver mutations can also be readily reviewed.

Targeted DNA Sequencing Basics

Researchers employ targeted sequencing as a rapid and cost-effective alternative to whole genome sequencing and focus on detection of known and novel variants in selected sets of genes or genomic regions. The ability to efficiently and evenly amplify just the genomic regions of interest and to keep the DNA input amount low are critical factors, especially in human disease research applications. Ion AmpliSeq™ technology transforms this application by enabling researchers to rapidly and simply amplify thousands of targets using just 10 ng of DNA. This technology, coupled with the Ion PGM™ System and easy-to-use Ion Reporter™ Software, enables researchers to go from precious FFPE samples to variants in a single day.

Researchers can select from Ion AmpliSeq™ ready-to-use gene panels designed for important targeted genes implicated in cancer or inherited diseases. Additionally, leading researchers have made available Ion AmpliSeq ™ community panel designs that were verified for their specific research such as BRCA1 and BRCA2. If the array of panels available does not meet your research needs, join over 1,000 researchers and submit your genes for the creation of Ion AmpliSeq™ Custom Panels. Traditional sequencing technology offers single-gene sequencing that consumes prohibitive amounts of DNA and is slow and labor intensive. Using this technology, researchers often sequence only a few genes, though their research would benefit from having information from tens to hundreds of genes. Other next-generation sequencing (NGS) technologies do offer targeted sequencing; however, these systems target fewer genes and require 25x more DNA input. Targeted sequencing allows researchers to interrogate specific regions in the genome with high specificity and sensitivity, increase the cost-effectiveness of studies, and improve the depth of coverage, all of which leads to better detection of both rare and common variants.

Ion PGM™ Hi-Q™ Sequencing Kit
Targeted sequencing available for any genome