Genexus™ Integrated Sequencer (Ion Torrent™)

The Ion Torrent Genexus Integrated Sequencer is part of the Ion Torrent Genexus System, the first turnkey next-generation sequencing (NGS) solution that automates the specimen-to-report workflow and can deliver results in a single day.

The Genexus Integrated Sequencer automates all steps of the targeted NGS workflow starting from purified and quantified nucleic acid. With a single touchpoint and five minutes of hands-on time, the Genexus sequencer automates NGS library preparation (including cDNA synthesis), template preparation, sequencing, primary data analysis, and variant reporting for DNA, RNA, and cfTNA applications. Sequencing on the Genexus sequencer is done on a four-lane semiconductor chip: the Ion Torrent GX5 Chip. Each of the four lanes of the GX5 Chip supports the output of 12–15 million reads, and they can be used individually or all at once depending on throughput needs. Ion Torrent Genexus Software streamlines the NGS workflow by integrating the setup-to-report workflow within a single software ecosystem.

• Rapidly go from nucleic acid to report in a single day
• Simplify the NGS workflow with a single instrument that can automate library prep, sequencing, and analysis, including variant calling
• Modulate run setup as samples come in with the flexibility of multiplexing up to 32 library reactions per run in increments of four
• Simultaneously create libraries and sequence up to four different assays using the four-lane GX5 Chip
• Reduce NGS operating costs with simplified setup using pre-filled reagents, a single touchpoint, and five minutes of total hands-on time
• Prevent user error by allowing the Genexus sequencer’s onboard vision system to verify reagent placement and detect errors in real time
• Ease the burden of assay adoption and test new software versions while retaining previous versions with Genexus Software

Experience in-house NGS refined
Many labs performing NGS in-house today or considering the adoption of in-house NGS in the future face significant challenges and barriers. Existing NGS workflows can be slow, complex, and costly for many clinical research labs. These workflows, as well as the outsourcing of samples to external laboratories, can take weeks to get results, which may delay answers. The complexity of the workflows, high operating costs, and lengthy turnaround times are roadblocks for labs considering in-house NGS and limit the way labs can utilize the power of next-generation sequencing.

The Genexus Integrated Sequencer helps create a paradigm shift in the way labs implement NGS in-house. Library preparation using Ion AmpliSeq and Ion AmpliSeq HD technologies, template preparation via isothermal amplification, and semiconductor sequencing are all automated on the Genexus Integrated Sequencer, enabling a hands-off nucleic acid-to-report workflow in a single day. Users of the Genexus sequencer have the power to generate and deliver a comprehensive molecular profile for sequenced samples every day of the week.

Complexity reduction is accomplished through several key innovations of the Genexus Integrated Sequencer. The hands-off, automated workflow from nucleic acid to variant report begins with run planning using Genexus Software. During run planning the user can select their desired sample(s) and assay(s) and use the setup wizard to create a run plan for the sequencer. During sequencer setup, which takes five minutes of hands-on time, the onboard vision system verifies consumable installation in real-time using barcode and RFID detection, ensuring proper setup before the run begins. After the run is completed, the user can view an integrated variant report for each sample, sample-level quality control metrics, and a list of reagents that were used.

A new way to think about assay adoption
In addition to streamlining the NGS workflow by integrating all steps from run planning to variant reporting into a single software ecosystem, Genexus Software helps reduce the burden of assay implementation by containerizing assay design files, algorithms, and UI features into a self-sufficient package. Multiple assays can be supported simultaneously by the same version of the software, allowing users to retain previously implemented workflows while optimizing new assay workflows. Software updates will be less frequent since new assays can be installed as a self-contained app. Genexus Software provides users the flexibility of optimizing a new assay while running an already implemented assay on a single Genexus Integrated Sequencer, eliminating the need for multiple instruments in a testing environment.