New Day in Next Generation Sequencing – Introducing the IonTorrent™ Genexus™ System
The promise of 1 day in-house NGS in every Cancer centre
The advancements in Cancer Research and Technology helps us progressing Cancer Diagnostics and Therapy. The ultimate goal of every improvement made is to provide timely and accurate patient diagnoses that enables clinicians to start appropriate therapy as early as possible.
The evolving Next Generation Sequencing technologies in the past decade have made a huge step forward in achieving these goals. Thermo Fisher Scientific offer an extensive portfolio for Oncology solutions, ranging from Real Time PCR based TaqMan Assays, Sanger Sequencing and Microarrays to IonTorrent™ NGS solutions. The Ion Torrent Gene Studio NGS Systems in combination with the IonChef™ System Automation offers fully automated Ampliseq NGS library preparation, templating and Sequencing. The content of the Oncomine™ libraries are based on relevant and actionable targeted mutations including hotspot variants, copy number variants or RNA fusions. Because of the improving patient care and the development of less invasive biopsy techniques there is a need for more and more sensitive technologies enabling mutation detection in small and often degraded DNA. The introduction of AmpliseqHD technology has improved the limit of detection. The Ion Reporter™ Data Analysis workflow together with the Oncomine Reporter™ offers an easy solution to interpret the NGS data. The Oncomine Knowledgebase Reporter translates the data into a clinical context based on the actionable targets. The Database is regularly curated and contains available Therapy or Clinical trial information.
ThermoFisher Scientific’s oncology solutions keep the patient in mind to help early and actionable diagnosis and continues to work on addressing challenges.
As a result of these efforts Thermo Fisher Scientific have announced a New Day in NGS and launched the IonTorrent™ Genexus™ Integrated Sequencer on November 6th 2019.
The new IonTorrent™ Genexus™ System
The IonTorrent™ Genexus™ Integrated Sequencer is the first NGS solution that automates the entire specimen to report workflow within a single day.
This solution answers the previous challenges such as the complicated NGS workflow. Turnaround time can be lengthy in situations where pooling samples is necessary to make the tests cost efficient.
The new system offers a fully automated workflow, including NGS library preparation, templating, sequencing and data analysis on a single platform. As part of the IonTorrent™ Genexus™ System an additional Genexus™ Purification System will be released in 2020 to complete the specimen-to-report workflow (Figure1.). It will offer automated nucleic acid extraction from FFPE and tissue lysate or plasma sample types.
Outsourcing samples to sequencing facilities can take weeks for results and can delay answers in a clinical setting. With the IonTorrent™ Genexus™ Integrated Sequencer users can get up and running with very little training making NGS accessible to every lab without previous experience. The system consumables and instrument software are designed for easy operation. The setup requires only two touchpoints with 10 minutes hands-on time from the user (Figure 2.) and delivers report within a single day.
Introducing the new Ion Torrent™ GX5™ Chip
The well-known Ion Semiconductor Chip is now divided into 4 separate lanes. Users can run up to 4 compatible assays on the same chip, giving further flexibility to users. It is also possible to run libraries in a single lane for up to 15 million reads and use the additional 3 lanes later. This feature enables a more cost efficient sample processing for smaller throughput laboratories and also allows for faster sample to report turnaround time by eliminating the need for pooling samples for cost-efficiency. The total capacity of the new Ion Torrent GX5 Chip is 60 million reads. Please see specifications below:
Introducing the Oncomine™ Precision Assay on the Ion Torrent™ Genexus™ System
The Ion Torrent™ Genexus™ System is launched with the Oncomine™ Precision Assay to complete the NGS Oncology workflow. The Assay utilises AmpliSeq HD chemistry and requires only 10 ng DNA/RNA or 20ng cell free TNA for successful sequencing results of more than 95% of samples. The Oncomine Precision Assay analyses 50 key genes and 78 variants. Among the variants there are 48 hotspot mutations, 14 copy number variants and 18 fusion variants. The content has been carefully curated to include all relevant targets and targets of emerging importance in precision oncology clinical research.
The Ion Torrent™ Genexus™ System offers unmatched ease of use makes NGS accessible to every lab who are new to the technology. The system and its single software ecosystem integrates and automates the full NGS oncology workflow from nucleic acid extraction and purification, library preparation and sequencing to analysis reporting. When compared to current technologies, the Genexus System can help improve every lab’s productivity.
There are additional Oncomine solutions available on the Genexus system that previously existed on The Ion Torrent Gene Studio Platform. The Oncomine TCR Beta-LR Assay GX is designed to efficiently capture all three complementary-determining regions of the TCR beta chain (CDR1, CDR2, CDR3) with high accuracy. Immunologists and Immuno-Oncologists are interested in T cell repertoire sequencing to characterise diversity and monitor features of T lymphocytes in blood and infiltrated tumours. T-cell repertoire sequencing helps identifying variable gene polymorphisms implicated in immune-mediated adverse events or in autoimmune diseases.
Sequencing of the TCR beta chain is also used to optimize the manufacture and function of therapeutic or engineered T cells. The use of the Oncomine TCR Beta-LR Assay allows for the identification of rare and abundant clones with a flexible RNA input amount of 10 ng (minimum) up to 1 µg. The use of RNA template allows sequencing of productive and relevant variable (V), diversity (D), and joining (J) rearrangements—which enables the identification of rare clones.
The Oncomine™ Comprehensive Assay v3 GX enables the detection of SNVs, CNVs, Indels and Gene Fusions from 161 unique genes from FFPE samples including fine-needle biopsies. Oncomine informatics with Oncomine Reporter Software variant results can be filtered from hundreds to a few key driver variants. The filtering and the annotations from on-market labels, established guidelines (US-NCCN, US-FDA, EMSO, EMA), and global clinical trials, helps contextualse and interpret findings. Users can create reports that align labels, guidelines, and clinical trials.
The New Genexus system is available not only for the above mentioned Oncomine™ Solutions but can be used in other research areas combined with Custom Ion Ampliseq™, Ampliseq On-Demand™ and Ion Ampliseq HD™ panels. Users can benefit from the flexibility, ease-of-use and the single day turnaround time of their Ampliseq™ Workflow.
The applications and the repertoire of compatible Assays will further expand in 2020 and beyond.
Gyongyi Lukacs, PhD, Field Application Specialist