Exome Sequencing by Ion Torrent Next-Generation Sequencing
Discover disease-causing variants in your research with exome sequencing
Exome sequencing is a targeted sequencing approach that is restricted to the protein-coding regions of genomes. The exome is estimated to encompass approximately 1% of the genome, yet contains approximately 85% of disease-causing mutations . For genetic researchers trying to identify the genes implicated in over 6,800 rare diseases , exome sequencing enables rapid, cost-effective identification of common single nucleotide variants (SNVs), copy number variations (CNVs), and small insertions or deletions (indels), as well as rare de novo mutations that may explain the heritability of Mendelian and complex disorders .
Sequencing 8 or more exomes in one day
“Speed is important for our service. But so is processing of 8–12 exomes a day without batching. Ion S5 XL offers us both.”
Dr. Sara Alvarez, Medical Director
Rapid, accurate exome sequencing with the Ion AmpliSeq Exome workflow
Leveraging the ultrahigh-multiplex PCR approach of Ion AmpliSeq™ technology and the superior accuracy of the new Ion S5™ Sequencing Solution, the Ion AmpliSeq™ Exome RDY S5 Kit allows for rapid, accurate sequencing of key exonic regions of the genome, going from DNA to variants in just 2 days.
Exome sequencing workflow
Exome sequencing services: Ion Torrent Certified Service Providers
The Ion Torrent™ Certified Service Provider program is a global network of validated service providers that enable researchers in small- and medium-sized laboratories to get high-quality exome and transcriptome sequencing data generated on the Ion Proton™ System from small amounts of input material with very fast turnaround.
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 compared to other exome enrichment technologies (Figure 1), and as little as 50 ng of DNA can be used.
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 RDY Kit provides high efficiency of enrichment with >90% on-target bases and >90% coverage uniformity (Figure 2).
Alternative bench-top sequencing platforms are not as flexible, and running a small number of samples may be costly or researchers may have to wait for large batches of samples to fill each run. With the Ion AmpliSeq exome research solution, researchers have the flexibility to sequence 1 or 2 exomes per run and up to 40 exomes per work week* on the Ion S5™ XL System. The combination of the Ion 540™ Chip, platform pricing, and an integrated and simplified analysis workflow makes Ion AmpliSeq exome sequencing a highly cost-effective solution for small- and mid-sized laboratories.
*Assuming a 24 hour work day and 5-day work week
The Ion AmpliSeq exome research solution integrates software and a bioinformatics pipeline to deliver a focused list of annotated exome variants, which helps to minimize the necessity for expensive bioinformatics resources.
Torrent Suite Software: Available as part of the Ion S5 Systems, Torrent Suite™ Software is preconfigured to support Ion AmpliSeq exome sequencing including optimized variant calling parameters, enabling you to discover relevant variants with confidence. 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.
Ion Reporter Software: Data is easily uploaded via a small, efficient file directly from Torrent Suite Software into Ion Reporter™ Software 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.
Commercial analysis solutions: 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.
Find out how researchers are utilizing exome sequencing to accelerate their clinical research studies.
Case study: Whole-exome sequencing for research in complex pediatric-onset disorders
“With whole-exome sequencing there is less data to transfer, analyze, and interpret, which is an important consideration, and it’s more cost-effective with a faster turnaround time.”
– Dr. Christian Marshall, Research Associate, The Hospital for Sick Children, Toronto, Canada
“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.”
– Richard Allcock, Director, Lotterywest State Biomedical Facility, Genomics School of Pathology and Laboratory Medicine, The University of Western Australia
“This new [Ion PI™ Hi-Q™] chemistry has greatly reduced the amount of orthogonal confirmation of variants we need to perform in our lab.”
– John Thompson, Sr. Director, Research and Development, Claritas Genomics
“We’ve always been happy with the [Ion] AmpliSeq Exome data but with the new [Ion PI] HiQ chemistry we get even better data. We’ve noticed a 50% reduction in indel false positives which will give us a shorter candidate list, making it ideal for de novo or trio experiments.”
– Adam Ameur, Bioinformatician, Genome Center, Uppsala University
“The new [Ion] PIv3 chips are great, the time savings is a major improvement”
– Inger Jonasson, Laboratory Manager, Genome Center, Uppsala University
- Liu, Qi et al. (2012) Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing. BMC Genomics 13:692.
- National Institutes of Health, Office of Rare Diseases Research.
- Marth GT, Yu F, Indap AR et al. (2011) The functional spectrum of low-frequency coding variation. Genome Biol 12(9):R84.