Complete Guide to Ion Ampliseq Technology - How Does Ion Ampliseq Technology Work?

Next Generation Sequencing (NGS) is now producing more sequencing data, faster than anyone had ever envisioned even just 10 years ago, making it now possible to sequence a genome in days rather than months or years. However, for many clinical research applications this large amount of data can be overwhelming, creating processing and informatics headaches, and additional cost with potentially little to no benefit. For such applications, a focused approach, or targeted next-generation sequencing method, that zeroes in on specific genomic regions of interest, can result in significant savings in terms of time, cost, and data analysis.

So how does targeted NGS work? Simply put, using current genomic knowledge, a targeted NGS approach introduces a sequence enrichment step focusing in on genes or genomic regions of interest. Unlike broader approaches like exome or whole-genome sequencing, targeted panels generate a smaller and more manageable data set which reduces the data analysis burden for researchers studying variants known to cause diseases¹. With targeted next-generation sequencing, researchers can sequence few to hundreds of gene targets in as little as 24 hours at half the cost of analysis, making this approach attractive to clinical and translational researchers.

Six years ago, Thermo Fisher Scientific launched the first ever amplicon-based enrichment method for preparing libraries for targeted next-generation sequencing – Ion AmpliSeq™ technology. The Ion AmpliSeq targeted sequencing panels have empowered researchers by enabling them to capture and study biomarkers from as little as 1ng of low-quality DNA and RNA and simultaneously detect single nucleotide variants, indels, copy number variants and fusions using a single assay. AmpliSeq technology has seen broad global adoption and resulted in over 700 peer reviewed publications across a broad range of applications from cancer² and inherited disease research ³ to microbial research⁴.

How Does Ion AmpliSeq Technology Work?

At its most basic level, an Ion AmpliSeq™ panel consists of a pool of oligonucleotide primer pairs, each pair designed to amplify a specified genomic region. Unique to this approach is the ability to multiplex up to 24,000 primer pairs in a single PCR reaction, meaning one can target from just a few to hundreds of genes in one run. Following simple PCR amplification of the selected genomic regions, remaining primers are digested and a library containing the remaining amplicons is prepared for sequencing.

The AmpliSeq technology can accommodate two different approaches depending on the research need. In the first “gene design” approach, which relies on the tiling of overlapping amplicons to study the continuous sequence of interest, overlapping primer pair must be separated into independent, multiplexed PCR reactions to achieve full coverage. As a result, this approach will require two separate PCR multiplexed reactions per sample to achieve full coverage. In contrast, a “mutation hotspot design” typically results in non-overlapping amplicons whose primers can be accommodated in a single multiplexed reaction.

Gene Design

Mutation Hotspot Design

In addition, researchers using Ion Ampliseq technology report successful library preparation from challenging sample types⁵, such as formalin-fixed, paraffin-embedded (FFPE) tissue, retrospective samples from fine needle aspirates, and cell-free DNA (cfDNA) extracted from blood. Consideration of the sample source is important to final design performance. Shorter amplicons with a maximum length of 175bp work best with degraded sample sources such as FFPE but come with a trade-off of coverage within the design⁶.

If you’d like to explore designing your gene panel, the Ion Torrent™ AmpliSeq Designer tool is what you need. You can also get started with predesigned panels including content curated for inherited disease, cancer, and infectious disease research applications.

Simplifying the Next-Generation Sequencing Workflow

Many have the perception that next-generation sequencing is highly complex and we understand that data analysis can often be perceived as a daunting task. To help you with your sequencing experiments, we provide software tools and instruments that streamline the NGS workflow for targeted panels.

Ion Torrent Targeted Sequencing Workflow

Ion Torrent AmpliSeq Designer is an online assay design tool that enables you to design and order custom or pre-designed gene panels. You can design panels by uploading your own reference genes or build from a pre-designed panel by adding or removing specific genes. Panels are delivered in tubes of pre-pooled, multiplexed primers in ready-to-use concentrations. The Ion Chef™ System automates library preparation for Ion AmpliSeq 1- and 2-pool designs using pre-packaged library reagents and primers for up to 8 samples in a single run. It also automates template preparation and chip loading. Sequencing can then be run on the Ion S5™ System and is typically completed in less than 4 hours. That’s less than 24 hours from DNA to data (with overnight Ion Chef System run) with about 45 mins of hands-on time.

Finally, the pre-configured workflows for Ion AmpliSeq panels in the Ion Reporter™ Software enables variant annotation and reporting for a variety of research applications in the areas on oncology, inherited diseases, reproductive health, and infectious diseases. The Ion Reporter Software is available in a local server system or the Thermo Fisher Cloud.

Examples of Application of targeted NGS panels

The human opioid system plays a crucial role in pain processing and therefore has been a key subject of interest for research and development of analgesics. However, little information has been established about opioid-related variants⁷. Kringel et al. demonstrated that NGS panels can be used to uncover important genetic information to better understand the genetics of human opioid receptors⁷. The authors developed a custom Ion AmpliSeq panel to analyze genes associated with human opioid receptor group consisting of OPRM1, OPRD1, OPRK1, SIGMA1, OPRL1 ⁷. Such research can open avenues for evaluating the effects of opioid analgesics or understanding the epidemiology of substance abuse⁷.

To guide biomarker discovery, tuberculosis vaccine development, and to better predict individual response, researchers at The Ohio State University (OSU) used next-gen RNA sequencing, and DNA genotyping to identify candidate genes and gene networks and reveal operative genetic variants and address genotype-RNA-cellular phenotype relationships in M.tb-infected human alveolar macrophage cultures on a genome-wide scale. RNA seq transcriptome, or targeted RNA-Seq, using the Ion AmpliSeq Human Transcriptome Gene Expression panel enabled the team at OSU to conduct highly-sensitive and reproducible measurement of differential gene expression, facilitating downstream network and component analysis. (Learn more about transcriptome sequencing, then watch a webinar by the OSU team detailing their research.)

In 2013, West Africa was affected by the largest known Ebola outbreak to date⁸. Shortly after, we followed Dr. Ian Goodfellow on his journey to study this deadly virus in real time in Sierra Leone, the epicenter of the outbreak. When this devastating outbreak recurred in Sierra Leon in 2016, Arias et al. set out to obtain important information based on phylogenetic analysis to better understand possible transmission pathways and sources of this new outbreak using the Ion AmpliSeq workflow on Ion PGM System⁸. The team generated sequence data that contributed to more than a third of known Ebola virus Makona genomes which enabled identification of viral transmission chains in other countries and across borders⁸.

To date, most DNA profiles in forensics genetics have been generated via STR (short tandem repeat) analysis using capillary electrophoresis (CE). However, for analysis of highly degraded samples, one can benefit greatly from targeted sequencing of SNP (single nucleotide polymorphism) markers using next-generation sequencing. Zhang et al designed a custom SNP panel and report results of their performance evaluation using the Ion PGM™ System. The team has found that SNPs make up important markers for individual identification including paternity testing⁹. Read the full story here.

When to use Sanger Sequencing vs NGS?

Clinical researchers can now choose from multiple technologies for targeted sequencing to study human genetic diseases based on the levels of phenotypic heterogeneity observed. Sanger sequencing with 99.99% accuracy is the “gold standard” for clinical research sequencing. However, newer NGS-based technologies such as targeted panels are becoming common in clinical research labs due to their higher throughput capabilities and lower costs per sample¹⁰. Here are a few things to consider when choosing the technology that best fits your project needs:

It’s also important note that these two technologies can complement each other to provide an end-to-end genetic analysis workflow that makes it easier to scale up to analyze more targets using NGS or confirm sequenced NGS variants with Sanger sequencing. Learn about the complete workflow here.

For more information:

Learn about Ion AmpliSeq technology here
Learn about our menu of gene panels for cancer research, inherited disease, infectious disease research and more here
Learn about our latest next-generation sequencing instrument here
Learn about our bioinformatics solutions here
To help get you started with you NGS experiments visit us here

For Research Use Only. Not for use in diagnostic procedures.

References:

1] Saudi Mendeliome Group Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases, Genome Biology 2015 16:134

2] Won-Suk Lee et al. Genomic Profiling of Patient-Derived Colon Cancer Xenograft Models, Medicine (Baltimore), 93(28): e298

3] Chen Chen et al. A Novel Splicing Mutation Identified in a Chinese Family with X-linked Alport Syndrome Using Targeted Next-Generation Sequencing, Genetic Testing and Molecular Biomarkers. April 2016, 20(4): 203-207

4] Shea N. Gardner et al. Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing, BMC Research Notes 2015 8:682

5] Chad M. McCall et al. False Positives in Multiplex PCR-Based Next-Generation Sequencing Have Unique Signatures, Elsevier (2014) Volume 16, Issue 5

6] Suhua Zhang et al. Massively parallel sequencing of 231 autosomal SNPs with a custom panel: a SNP typing assay developed for human identification with Ion Torrent PGM, Forensic Sciences Research (2017)

7] Dario Kringel et al. Next-generation sequencing of human opioid receptor genes based on a custom AmpliSeq™ library and ion torrent personal genome machine, Clinica Chimica Acta, Volume 463, 32-38

8] Armando Arias et al. Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases, Virus Evol (2016) 2 (1): vew016

9] Suhua Zhang et al. Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM. Forensic Science International: Genetics, Volume 27, 50 – 57

10] Jie Gao et al. Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR. BMJ Open (2016), 6(1): e009532.