Scaling Comprehensive Genomic Profiling and other Clinical Research Applications with the Ion 560 Chip

Sequencing demands continue to evolve across both clinical research and translational research applications. Comprehensive genomic profiling workflows are expanding in oncology research, while transcriptome studies and custom targeted sequencing projects increasingly require greater sequencing depth and larger sample batches.

As projects scale, laboratories often seek ways to increase sequencing output without introducing additional workflow complexity, adding instrumentation, or changing established processes. Greater throughput can help laboratories process more samples per run, support larger studies, and improve overall instrument utilization while maintaining operational consistency.

The Ion 560 Chip was developed to address these needs by expanding the sequencing capacity within the existing GeneStudio S5 workflow.

The Ion 560 Chip was developed with particular emphasis on supporting laboratories running the Oncomine Comprehensive Assay Plus, a targeted sequencing solution that combines DNA and RNA biomarker analysis within a single workflow. The additional sequencing capacity provided by the Ion 560 Chip enables larger sample batches and supports increasing project volumes while preserving established workflows.

For laboratories conducting large-scale oncology research projects, the ability to process more samples per run can help support growing sequencing demand and facilitate broader adoption of routine comprehensive genomic profiling strategies.

The benefits of the Ion 560 Chip extend beyond oncology research applications.

Transcriptome studies often require substantial sequencing output, particularly when researchers are analyzing large cohorts or seeking comprehensive gene expression data. The Ion AmpliSeq Transcriptome Human Gene Expression Kit enables expression analysis across more than 20,000 RefSeq genes from low-input RNA samples, including FFPE-derived material.

By providing significantly greater sequencing capacity than previous GeneStudio chip options, the Ion 560 Chip enables laboratories to increase throughput for transcriptome projects while continuing to leverage existing Ion Torrent workflows and automation solutions.

For core laboratories, translational researchers, and biopharmaceutical organizations running large transcriptomic studies, the expanded capacity supports larger projects without requiring a platform transition.

Many laboratories require targeted sequencing solutions tailored to specific research questions, disease areas, or biomarker strategies.

Custom AmpliSeq panels and AmpliSeq HD workflows are used for applications that require broader gene coverage, higher sequencing depth, or greater analytical sensitivity. The Ion 560 Chip was designed to support these workflows by providing additional sequencing capacity that can be allocated toward increased sample throughput, deeper sequencing, or larger panel designs.

This flexibility is particularly relevant for laboratories developing custom oncology research assays, translational genomics applications, and high-sensitivity targeted sequencing workflows. The additional sequencing output available on the Ion 560 Chip can support evolving project requirements while maintaining a familiar workflow environment.

A central objective of the Ion 560 Chip is to preserve workflow continuity while expanding sequencing capacity.

The GeneStudio ecosystem integrates with Ion Chef automation for templating and chip loading and supports streamlined progression from sequencing through analysis. The Ion 560 Chip extends throughput within this established workflow, allowing laboratories to increase sequencing output without introducing new workflow steps or additional operational complexity.

This approach provides a practical path for laboratories seeking greater sequencing capacity while maintaining familiar processes, infrastructure, and analytical workflows.

The Ion 560 Chip represents an expansion of the GeneStudio S5 platform, extending sequencing capacity to support larger projects and higher sample volumes across oncology research, transcriptomics, and custom targeted sequencing applications.

For laboratories performing comprehensive genomic profiling, transcriptome analysis, custom targeted sequencing, or AmpliSeq HD workflows, the Ion 560 Chip enables greater throughput across both the GeneStudio platform and workflow.

By supporting more samples per run and increasing overall sequencing capacity, laboratories can scale research operations while continuing to leverage the automation, flexibility, and workflow simplicity of the GeneStudio ecosystem.

What is the Ion 560 Chip?

The Ion 560 Chip is a next-generation sequencing chip designed for the Ion GeneStudio S5 Plus and Ion GeneStudio S5 Prime platforms, providing approximately 240–280 million reads per run.

Which GeneStudio systems support the Ion 560 Chip?

The Ion 560 Chip is designed for use with the Ion GeneStudio S5 Plus and Ion GeneStudio S5 Prime systems.

How does the Ion 560 Chip compare with the Ion 550 Chip?

The Ion 560 Chip approximately doubles sequencing capacity relative to the Ion 550 Chip, increasing throughput from approximately 130 million reads to approximately 240–280 million reads per run.

Which assays are supported on the Ion 560 Chip?

Supported applications include Oncomine Comprehensive Assay Plus, Ion AmpliSeq Transcriptome Human Gene Expression workflows, Custom AmpliSeq panels, and Custom AmpliSeq HD panels.

Why is throughput important for comprehensive genomic profiling workflows?

Higher throughput enables laboratories to process larger sample volumes, support growing project demand, and increase utilization of existing sequencing infrastructure.

Does the Ion 560 Chip require a new workflow?

No. Laboratories continue to use familiar GeneStudio S5 workflows, Ion Chef automation, and existing analysis infrastructure.

How does the Ion 560 Chip support transcriptome sequencing?

The increased sequencing capacity supports larger transcriptome studies and enables higher-throughput use of the Ion AmpliSeq Transcriptome Human Gene Expression workflow.

What types of laboratories benefit most from the Ion 560 Chip?

Core laboratories, translational research groups, oncology research laboratories, biopharmaceutical organizations, and laboratories running large custom targeted sequencing projects are among the primary users that can benefit from expanded sequencing throughput.