Exome Sequencing by Ion Torrent™ Next-Generation Sequencing
Easy exome sequencing
New Ion AmpliSeq™ RDY Exome Kit
• Simplified workflows
• High uniformity
The simplicity, specificity, and speed of PCR, with less than 50 minutes of hands-on time when using dried-down primers
Flexible throughput of 1 to 3 exomes per run, or up to 24 exomes per week
Integrated software and pipeline deliver a focused list of annotated variants
Easy Exome Sequencing
The Ion AmpliSeq™ Exome RDY Kit enables the fastest and simplest method of exome enrichment, making it even easier to use with oligo pools for ultrahigh multiplex PCR exome enrichment on a dried-down plate. With half as many target amplification pipetting steps compared to the original protocol, and the elimination of small pipetting volumes, exome libraries can now be produced with unparalleled ease in under 6 hours and with less than 50 minutes of hands-on time.
In addition, the Ion AmpliSeq™ Exome RDY Kit is compatible with the Ion Library Equalizer™ Kit for ultimate ease in library normalization. Leveraging the ultrahigh multiplex PCR approach of Ion AmpliSeq™ technology along with the Ion Proton™ Sequencer, the Ion AmpliSeq™ Exome RDY Kit allows for rapid sequencing of key exonic regions of the genome, going from DNA to variants in just 2 days.
Ion AmpliSeq™ Exome RDY Kit provides the simplest exome enrichment. The dried-down primers reduce the number of pipetting steps and allow preparation of reproducible libraries that sequence with high uniformity. The straightforward workflow–similar to PCR–allows someone with little to no next-generation sequencing experience to successfully perform the protocol.
Director, Lotterywest State Biomedical Facility
Genomics School of Pathology and Laboratory Medicine
The University of Western Australia
Simple exome enrichment
The Ion AmpliSeq™ Exome RDY Kit provides enhanced simplicity and speed for exome enrichment. With a workflow requiring less than 50 minutes of hands-on time, the Ion AmpliSeq™ Exome RDY Kit enables enrichment and library construction for 1 to 8 samples in less than 6 hours. The kit requires less 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 ultrahigh multiplex PCR approach of Ion AmpliSeq™ technology with the Ion Proton™ System, the Ion AmpliSeq™ Exome RDY 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 high efficiency of enrichment with >90% on-target bases and >90% coverage uniformity (Figure 2).
Figure 2. Ion AmpliSeq™ Exome RDY results are based on 36 exomes across 18 sequencing runs. Data from a MiSeq® System running a Nextera® Rapid Capture Exome Kit is shown for comparison (http://blog.basespace.illumina.com/2013/03/14/nextera-rapid-capture-exome-data-sets-2/). Uniformity value obtained from the Illumina® Nextera®Rapid Capture Exome Kit data sheet.
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 next-generation sequencing (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 uses 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 to 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 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® Variant Analysis™ Software which combines analytical tools and integrated content to help users rapidly prioritize variants down to a small targeted subset.
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.