Exome Sequencing by Ion Torrent Next-Generation Sequencing
Experience the simplicity of PCR-based enrichment, flexible throughput and integrated analysis in your research.
Whole exome enrichment with the simplicity, specificity, and speed of PCR, and less than 60 minutes of hands-on time
Lowest cost per exome on a benchtop sequencer, with flexible throughput of 1 to 3 exomes per run or up to 24 exomes per week
Integrated software and pipeline delivers a focused list of annotated variants
Ion semiconductor sequencing makes high-quality exome sequencing accessible to all.Now, more research laboratories can adopt powerful exome sequencing to identify disease-causing variants in rare and complex disease research faster—with increased throughput, high accuracy, and the simplest workflow from sample preparation to data analysis. The exome is estimated to encompass approximately 1% of the genome, yet contains approximately 85% of disease-causing mutations. For genetic researchers trying to unravel the disease-causing genes of over 6,800 rare diseases , exome sequencing enables the identification of the single-nucleotide variants (SNVs) and small insertions or deletions (indels) responsible for Mendelian diseases, as well as rare de novo mutations that explain the heritability of complex diseases . The Ion AmpliSeq™ exome research solution offers the simplest exome enrichment approach with less than 60 minutes of hands-on time, and the lowest cost per sample on a benchtop sequencer—with flexible throughput from 1 to 3 exomes per run or up to 24 exomes per week. The Ion Proton™ System combined with Ion AmpliSeq™ technology and an integrated data analysis solution offers fast and high-quality exome sequencing that scales with your research needs.
As a service provider this system gives us a huge amount of flexibility. We can take on multiple projects of various sizes and turn them around in just two days, without the need to batch in order to keep our costs down. This is especially important when dealing with urgent samples that require fast turnaround time, such as clinical research specimens.
This workflow is simple and straightforward to follow, it’s similar to PCR, and anyone with basic molecular biology skills, even someone with no NGS experience, could successfully perform the protocol. This is going to enable exome sequencing in more labs and accelerate human disease research.
Vice President of Genomic Services
Greenville, South Carolina
Simple exome enrichment
The Ion AmpliSeq™ Exome Kit provides unmatched simplicity and speed for exome enrichment. With a workflow requiring less than 60 minutes of hands-on time, the Ion AmpliSeq™ Exome Kit enables enrichment and library construction for 1 to 8 samples in less than 6 hours. The kit requires the least amount of hands-on time when compared with other exome enrichment technologies (Figure 1), and as low as 50 ng of DNA can be used. Leveraging the ultra-high multiplex PCR approach of Ion AmpliSeq™ technology with the Ion Proton™ System, the Ion AmpliSeq™ Exome Kit allows for rapid exome sequencing, going from DNA to annotated variants in 2 days.
Figure 1. Comparison of hands-on and total turnaround time for a single exome enrichment workflow.
The efficiency of exome enrichment is measured by specificity, defined as the percent of on-target bases, and coverage uniformity, defined as the percent of bases covered at a certain sequencing depth. High uniformity in sequence coverage is important for exome sequencing since this minimizes the amount of sequencing needed to achieve a desired coverage threshold (e.g., 20x). Coverage depth is critical for accurate variant calling. The Ion AmpliSeq™ Exome Kit provides the highest efficiency of enrichment with >90% on-target bases and >92% coverage uniformity. Additionally, a high percentage of bases are covered at 10x and 20x sequencing depth (Figure 2). Other exome enrichment technologies provide lower specificity and a lower percentage of bases covered at 10x, resulting in less efficient exome sequencing.
Figure 2. The Ion PI™ Chip accommodates 1, 2, or 3 exomes per run, yielding a high percentage of bases covered at 10x and 20x sequencing depth. Results above are based on 54 exomes across 30 sequencing runs. The MiSeq™ System running Nextera® Rapid Exome Capture Kit can produce a single exome per run and covers only 80% of bases at 10x.
On-demand exome sequencing
The Ion Proton™ System coupled with Ion AmpliSeq™ technology makes exome sequencing accessible to research laboratories of every size.
The alternative NGS benchtop platform is designed for 12 barcoded samples to be pooled for exome enrichment, and then requires 12 sequencing runs to generate enough data for analysis. Data from each run must be separated into 12 barcodes. Data across 12 runs with the same barcode is then merged and finally ready for exome analysis. The alternative NGS high-throughput platform use the same 12 pooled-sample enrichment method and is designed to produce 23 exomes per sequencing run. These alternative platforms are not flexible, and require researchers to either pay a price penalty when running fewer samples or wait for large batches of samples to fill each run.
With the Ion AmpliSeq™ exome research solution, researchers have flexibility to sequence 1-3 exomes per run and up to 24 exomes per week per instrument. The combination of the Ion PI™ Chip, platform pricing, and an integrated and simplified analysis workflow makes Ion AmpliSeq™ exome sequencing the most cost-effective solution in the market.
The upcoming Ion Chef™ System* for fully automated template preparation, combined with Ion AmpliSeq™ target technology, and the Ion Proton™ System, will further enhance the simplicity and speed of the exome sequencing workflow.
The Ion AmpliSeq™ exome research solution integrates software and a bioinformatics pipeline to deliver a focused list of annotated exome variants, so additional bioinformatics resources are not required. Torrent Suite™ Software, part of the Ion Proton™ System, is preconfigured to support Ion AmpliSeq™ exome sequencing including optimized variant calling parameters. Torrent Suite™ Software provides a simple run quality report, access to coverage metrics, and full variant calling - all without the need for any command line skills.
Data is easily uploaded via a small, efficient file directly from Torrent Suite™ Software into Ion Reporter™ workflows—allowing researchers access to public annotations of called variants and simple, intuitive filters of only the most relevant variants. For more complicated experiments, like pairs or trios, more sophisticated Ion Reporter™ workflows are available to find variants unique to one sample in either a pair or a trio analysis. For researchers who want to leverage annotation information within the public domain, variant lists can be exported directly into Ingenuity®’s Variant Analysis™ Software that combines analytical tools and integrated content to help users rapidly prioritize variants down to a small targeted subset.
Torrent Suite™ Software, part of the Ion Proton™ System, is preconfigured to support Ion AmpliSeq™ exome sequencing including optimized variant calling parameters. The Ion AmpliSeq™ exome research solution integrates free software and a bioinformatics pipeline, so additional resources are not required. Data is easily uploaded directly from Torrent Suite™ Software into Ion Reporter™ workflows—allowing researchers access to public annotations of called variants and simple, intuitive filters of only the most relevant variants.Use Torrent Suite Software 3.6.2 for optimal Ion AmpliSeq Exome results >
- National Institute of Health, Office of Rare Diseases Research.
- Marth GT et al. (2011) The functional spectrum of low-frequency coding variation. Genome Biol. 12(9):R84.
*The content provided herein may relate to products that have not been officially released and is subject to change without notice.
For Research Use Only. Not for use in diagnostic procedures.
Ion AmpliSeq™ Exome Kit provides unmatched simplicity and speed for exome enrichment. With a workflow requiring less than 60 minutes of hands-on time, the Ion AmpliSeq™ Exome Kit enables enrichment and library construction for 1 to 8 samples in less than 6 hours.
The Ion Chef™ System*† will provide high-throughput automated template preparation and chip loading for users of all expertise. Lower-throughput users can choose the Ion OneTouch™ 2 System, available now, for fully automated template preparation.
The Ion Proton™ System is ideal for sequencing exomes and transcriptomes. The sequencing run time is only 3 hours. Torrent Suite™ Software, part of the Ion Proton™ System, is preconfigured to support Ion AmpliSeq™ exome sequencing including optimized variant calling parameters.
The Ion AmpliSeq™ exome solution integrates software and bioinformatics pipeline to deliver a focused list of annotated exome variants, so additional bioinformatics resources are not required. Data is easily uploaded via a small, efficient file directly from Torrent Suite™ Software into Ion Reporter™ workflows – allowing researchers access to public annotations of called variants and simple, intuitive filters of only the most relevant variants.