The new Ion Hi-Q™ View chemistry for research using the Ion PGM™ , Ion Chef™, and Ion OneTouch™ 2 systems takes everything that made the previous Hi-Q chemistry robust and reliable, and advances it to a new level. In addition to high sequencing accuracy, Ion Hi-Q View chemistry enables enhanced experimental reproducibility and sequence coverage uniformity, helping you to answer questions with even greater confidence.
Our most advanced sequencing chemistry for the Ion PGM System
Experience the superior speed of the Ion PGM System, now with our most accurate and robust sequencing chemistry. The original Ion Hi-Q chemistry reduced variant false positives and indel errors and increased read lengths and throughput, helping to improve sequencing performance (see the data). The new Ion Hi-Q View kit is designed to deliver powerful enhancements to the previous Ion Hi-Q chemistry for improved variant detection accuracy, to help you achieve even greater confidence in your results at no additional cost. With this latest sequencing chemistry, we observed significant improvement in the total number of quality bases for targeted sequencing (total AQ20 bases) when compared to the original Hi-Q chemistry (Figure 1). The improved total quality bases per targeted sequencing run were due to better end-to-end amplicon coverage, uniformity, and the number of amplicons with no strand bias (Figure 2).
The new Ion Hi-Q View kit also helps to enhance reproducibility by minimizing user error in manual chip-loading, with visible Ion Sphere™ Particles (ISPs) that can be easily visualized during sequencing template preparation using the Ion OneTouch 2 System.
Figure 1.Significant improvement in total AQ20 bases with Ion Hi-Q View chemistry. Comparison of total quality bases using a custom Ion AmpliSeq™ panel targeting ~48,000 human exonic amplicons. A 32% increase in the median AQ20 bases was observed using the new Ion Hi-Q View Chef sequencing kit (**N=11) versus the Ion Hi-Q Chef sequencing kit (*N=8). N=number of sequencing run
Figure 2.Improvements to targeted sequencing. Comparison of end-to-end amplicon coverage, uniformity, and number of amplicons with reduced strand bias using a custom Ion AmpliSeq panel targeting ~48,000 human exonic amplicons. Amplicons were more efficiently sequenced using the new Ion Hi-Q View Chef sequencing kit (**N=11) when compared to the previous Ion Hi-Q Chef sequencing kit (*N=8). N=number of sequencing run
Accurate sequencing for robust variant detection
Ion Hi-Q View chemistry was designed to deliver sequencing accuracy that is equivalent to or better than that of the previous Ion Hi-Q chemistry for the Ion PGM System, while maintaining the same high-quality variant calling. Ion Hi-Q View Chef chemistry, when used for targeted sequencing of a custom ~48,000-amplicon Ion AmpliSeq panel, demonstrated improved single nucleotide variant (SNV) sensitivity (Figure 3A) compared to the previous Ion Hi-Q chemistry, while decreasing the false positive rate for indel variants (Figure 3B).
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Figure 3. Variant calling is improved using Ion Hi-Q View Chef chemistry for a custom ~48,000-amplicon Ion AmpliSeq panel. A) Single nucleotide variant (SNV) sensitivity was improved using the new Ion Hi-Q View Chef sequencing kit (**N=11) when compared to the Ion Hi-Q Chef sequencing kit (*N=8). B) A 22% increase in the median false positive rate per megabase was observed using the new Ion Hi-Q View Chef sequencing kit (**N=11) versus the Ion Hi-Q Chef sequencing kit (*N=8). N=number of sequencing run
Improved sequencing accuracy
Hi-Q chemistry and Hi-Q View chemistry improve sequencing accuracy for the Ion PGM System (Figure 4), resulting in high-quality variant calling accuracy using just 10 ng of DNA input compared to the 150 ng recommended for the competitor. It also helps improve de novo assembly with up to a 90% decrease in indel error rates compared to previous Ion PGM System sequencing chemistries (Figure 5), making it ideal for microbial sequencing applications.
+ click to enlarge Figure 4. Comparison of somatic variant calling accuracy for targeted resequencing panels. The Ion PGM System with Ion Hi-Q chemistry and 10 ng of DNA input outperforms the competitor using 150 ng of DNA input.
+ click to enlarge Figure 5. Decrease in indel false positives for microbial de novo assembly, using the Ion PGM™ Hi-Q™ Sequencing Kit instead of the Ion PGM™ Sequencing 200 Kit v2. Template preparation for 200-base read fragment libraries was performed using the Ion PGM™ Template OT2 200 Kit. Indel error rate per 100 kb analysis performed with SPADE 3.1 delta-score filter.
Advantages of Hi-Q View chemistry for Ion PGM System
The Ion PI™ Hi-Q™ kit is available for use with the Ion Proton™ System to enable improved variant calling performance compared to our previous chemistries. The Hi-Q chemistry helps reduce variant false positive rates by up to 71% for exome sequencing (Figure 6), using the Ion Proton System.
Advantages of Hi-Q chemistry for the Ion Proton System include:
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Figure 6. Improved variant calling accuracy. Up to 71% reduction in variant false positives detected for Ion AmpliSeq™ Exome sequencing.
Improved variant calling accuracy
Up to 71% reduction in false positive rates for exome sequencing using the Ion AmpliSeq™ Exome Kit.
Improved coverage of GC-rich amplicons
Up to 80% increase in relative coverage improvement for amplicons with >85% GC content.
Reduced burden of orthogonal confirmation
Improved variant calling accuracy helps reduce the volume of confirmatory testing, alleviating a substantial amount of labor and cost burden.
“We’ve always been happy with the Ion AmpliSeq™ Exome data but with the new Ion PI™ Hi-Q™ 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