Dr Gyongyi Lukacs , our Field Application Specialist tells us more .

Ion GeneStudio™ S5 series and the new Ion550™ chip

The new line of benchtop NGS systems offers flexible solution for the sample throughput required. As an addition to the automated Ion Ampliseq™ library-, template preparation, and chip loading IonChef™ System there are three new sequencing systems to choose from. The Ion GeneStudio ™ S5, the Ion GeneStudio ™ S5 Plus and the Ion GeneStudio ™ S5 Prime are only different in their computing power and storage capacity. When using the larger sequencing capacity Ion540™ and Ion 550™ chips the Ion GeneStudio ™ S5 Plus and the Ion GeneStudio ™ S5 Prime provides faster turnaround and analysis time (see Table below). All three systems offers scalable workflow within a single platform, by chosing from the IonChip kits available in five sequencing throughput. New introduction is the Ion550™ chip using the same sequencing chemistry and smaller Ion Sphere Particles as Ion540™ chip. The new Ion550™ chip is offering 100-130 million reads. With the new Ion550™ chip Ion Torrent offers 2-130 million reads per run (or 2-260 million reads per day) on any Ion GeneStudio S5 series instrument in a single sequencing platform.

Ion Torrent Oncomine Portfolio Updates

There are new products available in the Oncomine™ product groups expanding the NGS Oncology Solutions. These products are available in both Manual Library preparation and automated IonChef™ format.

• Oncomine™ Myeloid Research Assay

The Ion Torrent™ Oncomine™ Myeloid Research Assay covers the most relevant targets in major myeloid disorders: acute myeloid leukemia (AML), myeloid dysplastic syndrome (MDS), myeloproliferative neoplasms (MPN), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML). Three primer pools of Ampliseq oligonucleotide primers target 40 key DNA genes and a broad fusion panel of 29 driver genes associated with myeloid disorders. The panel size allows for multiplexing up to 4 samples per Ion 318 chip on PGM instrument and up to 12 samples on Ion530 chip on an Ion GeneStudio S5 instrument. The kit uniquely provides excellent coverage of challenging targets such as CEBPA and FLT3-ITDs and validated to detect somatic variants down to 5% allele frequency.

• Oncomine™ Tumor Mutation Load Assay

The Ion Torrent™ Oncomine™ Tumor Mutation Load Assay provides clinical researchers with accurate quantitation of somatic mutations to assess tumour mutation load from limited FFPE samples (as little as 20 ng of DNA). The assay covers a large genomic footprint of 1.7 Mb in two primer pools, replacing the need for whole-exome sequencing. The kit is interrogating 409 key cancer genes and counts single nucleotid variants. It is possible to sequence up to 8 samples per Ion™ 540 chip. This Assay is to provide additional research opportunity to evaluate biomarkers associated with responses to immuno-oncology (I-O) therapies.

• Oncomine™ Pan-Cancer Cell-free Assay

The newest member of the cell-free DNA assays is the Oncomine™ Pan-Cancer Cell-free Assay. The assay provides the reagents and a single pool of multiplex PCR primers for preparation of an amplicon library from cell-free total nucleic acid (cfTNA) obtained from the plasma fraction of a single 10-mL tube of whole blood with a detection limit of 0.1% for SNVs. The panel includes 52 frequently mutated genes in multiple cancer types, including: bladder, brain and CNS, breast, cervical, colorectal, endometrial, esophageal, gastric, head and neck, kidney, liver, lung, melanoma, ovarian, pancreatic, prostate, sarcoma, and thyroid. The panel also detects TP53 whole-target SNVs/indels: 0.5% allele frequency (looking at all bases within amplicons).

For isolation of both DNA and RNA from the plasma fraction of whole blood the MagMAX Cell-Free Total Nucleic Acid Isolation Kit (A36716) is highly recommended.

The Ion Ampliseq™ On-Demand Research Panels were introduced last year offering a flexible targeted solution for inherited disease research. An on-line available catalogue of over 5000 pretested genes supported with empirical data offers a solution for customisable panel configuration. The content of the catalogue is increasing as more and more optimised and pre-tested gene targets are added.

Coming soon – Ion Ampliseq™ HD Technology

A new, customisable next generation core chemistry will be released in 2018 providing sensitivity down to 0.1% of the mutant allele fractions for FFPE and cell-free assay. Beyond improvements in assay sensitivity the new chemistry will have shorter library preparation time.

The Oncomine™ oncology portfolio including the highly sensitive cell-free nucleic acid (cfNA) research assays together with the new improved Ion Ampliseq HD Technology continues to provide unique and proprietary multi-biomarker next generation sequencing solutions that enable molecular insight into tumour evolution and detection of primary driver and resistance mutations.

If you have questions or require any additional information please let me know

Dr Gyongyi Lukacs, Field Application Specialist, NGS