Ion Torrent Technology with S5 + Ion Chef: Fast, Flexible and Accessible NGS

Semiconductor-based NGS sequencing

At Biomol, we work to make next-generation sequencing (NGS) easier to implement and simpler to scale. Ion Torrent technology is based on direct detection using a semiconductor chip, resulting in an agile, robust workflow that is particularly practical for research and clinical research laboratories.

Ion Torrent performs sequencing by detecting the pH changes that occur in each well of the chip when the polymerase incorporates a nucleotide and releases a hydrogen ion (H⁺). This pH change is measured by ion-sensitive sensors and converted into an electrical signal, enabling direct detection without cameras, scanners, or optics. Nucleotide incorporation is recorded within seconds, and the process occurs in parallel across millions of wells.

The Ion GeneStudio™ S5 systems are designed for flexible and scalable targeted sequencing, enabling laboratories to move — within the same workflow — from small to large projects without changing platforms, simply by selecting a different chip. Five chip options are available, offering a throughput ranging from 2–3 million reads up to 100–130 million reads. This allows optimization of cost per sample and improved responsiveness to varying demands (from small panels to larger panels), while maintaining the same workflow.

Automation and integrated analysis

The Ion Chef™ system automates template preparation and chip loading using cartridge-based consumables, minimizing user intervention. Full traceability of samples and reagents is ensured through network integration with Torrent Suite™ software.

Ion Reporter™ Software automates bioinformatics analysis, integrating, annotating, and interpreting identified variants. By selecting the appropriate analysis workflow, analysis can be automatically launched after sequencing, accelerating the transition from raw data to actionable results.

Thanks to Ion AmpliSeq™ technology used for library preparation, Ion GeneStudio™ S5 instruments can work with very low DNA or RNA input amounts (down to 1 ng), even with complex samples such as FFPE or cfDNA. Combined with the broad range of validated Oncomine™ panels and dedicated analysis workflows for solid tumors and oncohematology, this technology is particularly well suited for pathology and hematology laboratories.

Applications in reproductive health and customized research

For reproductive health and translational research laboratories, Ion ReproSeq™ (PGS/PGT-A, RUO) enables the analysis of aneuploidies from very low-input samples (e.g., embryo biopsy). With Ion GeneStudio™ S5, laboratories can adjust run output using different chips (510/520/530), optimizing time and cost according to sample volume. Automation with Ion Chef™ simplifies preparation and chip loading, reducing handling and variability. To complete the workflow, Ion Reporter™ provides automated bioinformatics analysis with application-specific workflows, standardizing output and accelerating result generation.

In academic research, a “catalog” panel rarely fits perfectly. With Ion AmpliSeq™ Designer, it is possible to create custom amplicon-level panels: designs can be based on preloaded reference genomes or on any organism by uploading a FASTA reference. This enables precise adaptation of the panel to the research hypothesis (genes, exons, UTRs, or specific regions), optimizing cost and sequencing depth according to project objectives. When creating custom panels, laboratories may start from On-Demand panels (covering common research areas) and personalize them by adding Spike-in genes outside the catalog, facilitating rapid iterations as projects evolve.