Aneuploidy Detection by Ion Torrent Next-Generation Sequencing
The Ion ReproSeq PGS kits for the Ion S5 Systems
The Ion ReproSeq PGS kits for the Ion S5 System enable a simple and scalable next-generation sequencing (NGS) workflow for reliable and rapid aneuploidy detection across all 24 chromosomes (22 autosomes plus X/Y chromosomes) when studying biopsy samples from preimplantation embryos. These kits take advantage of automated template preparation using the Ion Chef System and can be used to analyze 16-96 samples.
Aneuploidy detection via NGS is also available using the Ion PGM System for rapid analysis of 2–24 samples. The information below includes a comparison of the Ion ReproSeq kits for the Ion PGM System and Ion S5 Systems.
Simple and scalable on-demand aneuploidy detection on the Ion S5 System
Leveraging the speed of Ion Torrent NGS, the Ion ReproSeq PGS kits for the Ion S5 System enable detection of whole-chromosome and down to 17 Mbp copy number events* in less than 10 hours** from just 6 pg of DNA from a single or multiple cells.
The simple cartridge-loaded reagents and straightforward user interface of the Ion S5 System, along with automated template preparation on the Ion Chef System, minimize user errors and facilitate rapid implementation of preimplantation genetic screening (PGS) research in your lab. Three Ion sequencing chips—the Ion 510 Chip, Ion 520 Chip, and Ion 530 Chip—provide throughput flexibility to match your needs and enable cost-effective analysis of 16, 24, or 96 samples in a single sequencing run.
The Ion ReproSeq PGS kits for the Ion S5 System offer:
- Sample throughput flexibility—three kit configurations enable analysis of 16, 24, or 96 samples in a single run on a single platform
- Rapid NGS workflow for aneuploidy analysis—cells to results in less than 10 hours on the Ion S5 XL System**
- Simple, end-to-end workflow—reduce hands on time to less than 2 hours** and minimize user error
- Enhanced interpretation of results with Ion Reporter v5.4—mosaicism detection, gender masking, and improved data plotting (for easier data interpretation)
Figure 1. Aneuploidy detection from a single cell using the Ion ReproSeq PGS Kit for the Ion S5 System. Data shown in the top panel illustrate a deviation (in blue) from baseline, indicating 45 Mbp duplication of chromosome 9 (male). Data shown on bottom panel indicate a deletion (in red) of 48 Mbp on chromosome 13 (female).
Ion ReproSeq PGS kits for the Ion S5 System workflow
The workflow below illustrates a simple and rapid workflow from a single cell to aneuploidy detection. The Ion ReproSeq PGS kits for the Ion S5 System include all materials for library construction, template preparation, and sequencing for the Ion S5 System workflow.
Whole-genome amplification and fragment library construction with Ion SingleSeq kits
Isothermal amplification with Ion Chef System
Ion S5 System
Sequence up to 96 preimplantation embryo biopsy samples with Ion 530 Chip
Ion Reporter Software v5.4
Data analysis and storage with Torrent Suite Software and Ion Reporter Software and server
Ion S5 and Ion S5 XL NGS systems
Adopting NGS in your lab is now simpler than ever. The Ion S5 and Ion S5 XL Systems enable the simplest targeted sequencing workflow for your lab with industry-leading speed and affordability.
Simple and automated data analysis solution
Torrent Suite Software coordinates all the experiment planning and data processing steps necessary to complete your targeted sequencing workflow. Its intuitive, web-based interface through the Torrent Browser enables users to plan, monitor, and view sequencing run results quickly and simply. Data generated on an Ion S5 System are transferred to the Ion S5 Torrent Server for base calling and automatically uploaded to Ion Reporter Software for further analysis.
Aneuploidy analysis workflow on Ion Reporter Software makes analyzing and reporting aneuploidy results simple and fast. This low-pass coverage analysis workflow processes samples by comparing to a built-in bioinformatics control baseline to deliver the DNA ploidy status of each sample. Users can visualize aneuploidy profiles using the customized IGV Karyotype View and create their own interpretive report.
Results obtained from the Ion ReproSeq PGS kits run on either an Ion S5 System or the Ion PGM System benefit from new functionalities such as mosaicism detection, gender masking, and improved analysis time using Ion Reporter Software v5.4.
Comparison of the Ion ReproSeq PGS View kits for the Ion PGM System to the Ion ReproSeq PGS kits for the Ion S5 System
The figure below compares the number of samples and turnaround times for PGS research using different configurations of the Ion ReproSeq PGS View kits for the Ion PGM System (using Ion 314 Chip, Ion 316 Chip and Ion 318 Chip) and the Ion ReproSeq PGS kits for the Ion S5 System (using Ion 510 Chip, Ion 520 Chip, and Ion 530 Chip). Compared to the Ion PGM kits, the Ion ReproSeq PGS kits for the Ion S5 System are a more scalable PGS solution that enables analysis of 16 to 96 samples while decreasing hands-on time with similar total turnaround time due, in part, to the advantage of automated template preparation using the Ion Chef System.
Click to enlarge
Ion ReproSeq PGS View kits for the Ion PGM System
Aneuploidy detection via NGS is also available using the Ion PGM System for cost-effective and rapid analysis of 2–24 samples. This solution is ideal for low-throughput research labs interested in rapidly and reliably assessing preimplantation embryos for aneuploidy.
The Ion ReproSeq PGS View Kit, when used with the Ion PGM System, Ion OneTouch ES, and Ion PGM Enrichment Beads, provides all reagents and materials required to detect aneuploidies starting from single or multiple cells. The entire workflow takes as little as 8 hours*** from cells to analyzed data.
Watch the on-demand webinar featuring Dr. Luis A. Alcaraz of Bioarray, Spain.
Download the application note to see how the aneuploidy results compared to aCGH data.
Download the flyer to discover data generated from a single cell using the Ion PGM System.
* Detecting copy number events <48 Mbp using the Ion ReproSeq PGS Kit with Ion 530 Chips (96 samples/run) requires running ≤24 samples on an Ion 530 Chip
** Turnaround time for the Ion ReproSeq PGS Kit with Ion 510 Chips (16 samples/run) is less than 10 hours with less than 2 hours of hands on time
*** Turnaround time is 8 hours with the Ion 314 Chip for up to 2 samples, or 10 hours with the Ion 318 Chip for up to 24 samples.