Cell3™ Target: Pan-Cancer (524) TMB/MSI Panel

Comprehensive cancer mutation, TMB and MSI analysis

Comprehensive cancer mutation analysis providing robust calling of SNVs, indels and CNVs, as well as TMB and MSI across 524 oncogenes using a single NGS enrichment workflow.

One workflow for multiple biomarkers

Detect all variant types including SNVs, CNVs and indels as well as TMB and MSI across 524 oncogenes in a single NGS enrichment.

Run cfDNA and FFPE samples

Compatible with cfDNA and FFPE samples, as well as gDNA, giving you the option of profiling either primary, metastatic or liquid biopsies.

Measure tumor genomic instability

Confidently extrapolate tumor mutation burden (TMB) from panel sequencing data for immunotherapy response prediction.

An alternative to whole exome sequencing

Simplified analysis and reduced costs make this targeted panel an attractive alternative to tumor whole exome sequencing (WES) for routine use.

Profile solid tumors with Cell3™ Target Pan-Cancer Panel

If you have limited time and limited sample, targeted sequencing offers the best approach to profile common cancer genes via a comprehensive set of biomarkers in a single panel.

The Cell3™ Target: Pan-Cancer (524) TMB/MSI panel is a next generation sequencing (NGS) panel that covers common driver mutations including SNVs, CNVs and indels in 524 oncogenes and supports the analysis of immuno-oncology biomarkers like tumor mutation burden (TMB) and microsatellite instability (MSI).

This targeted enrichment panel is compatible with a range of sample types from cell free circulating tumor DNA (ctDNA) to formalin-fixed paraffin-embedded (FFPE) DNA meaning you can process all of your oncology samples – regardless of sample type or tumor origin – in a single, simple workflow.

Comprehensive content for clinical cancer research

The Pan-Cancer (524) TMB/MSI panel covers 63 genes from NCCN/FDA cancer treatment guidelines, 116 cancer driver genes and 345 genes in vital cancer signalling pathways. The design, whilst exon focused, covers key intronic and promoter regions and contains a selection of CNV probes to support copy number calling across the genome. It is a comprehensive panel that allows you to accurately identify and profile variants associated with cancer and stratify all common cancers in a single workflow.

Table 1. Pan-Cancer (524) TMB/MSI Panel gene content.

Profiling cancer to predict response to immunotherapy

Analysis of TMB and MSI using NGS panels

Immune checkpoint inhibitors have shown great potential as treatments across a number of cancers. However, as not all patients will respond to immunotherapies, positive biomarkers are needed to help match patients with the appropriate treatment.  Tumor genomic instability has been shown to correlate positively with immunotherapy response for which there are two known biomarkers: TMB and MSI.

Targeted NGS sequencing offers a cost-effective way to measure TMB and MSI, but the size of a panel can influence the precision of TMB measurement1. Too small and the measurement is imprecise (and therefore clinically suboptimal for patient stratification and response prediction) but too large and it is not cost effective for routine use. At 1.58Mb, the Nonacus Pan-Cancer (524) TMB/MSI panel, allows for accurate TMB estimation, cost effectively.

Compatible with FFPE and cfDNA samples

Running a clinical cancer laboratory can require the analysis of a range of sample types from blood samples (liquid biopsies) to solid tumors (fresh or frozen).

Our Pan-Cancer TMB/MSI Panel is compatible with a broad range of samples including formalin-fixed, paraffin-embedded (FFPE), fresh frozen, genomic and cell-free circulating tumor DNA (ctDNA).

That means you can process all of your oncology samples – regardless of sample type or tumor origin– in a single, simple workflow.

Gloved hand holding Microscope ffpe slide with liquid on
Diagram demonstrating Using UMI’s to identify and quantify individual DNA molecules during library preparation increases sensitivity

Figure 1. Using UMI’s to identify and quantify individual DNA molecules during library preparation increases sensitivity when working with cfDNA

Detect low-level variants with pan-cancer panels

The Cell3™ Target technology behind the Pan-Cancer panel incorporates error suppression technology, which includes unique molecular indexes (UMIs) and unique dual indexes (UDIs), to remove both PCR and sequencing errors and index hopping events. This allows confident and sensitive calling of mutations down to 0.1% VAF and enables generation of sequencing libraries from as little as 1 ng of cfDNA input.

Maximise sequencing efficiency

High uniformity of coverage combined with a low duplication rate and high percentage of on-target reads delivers exceptional performance resulting in less wasted sequencing. Cell3™ Target libraries allow you to run more samples per flow cell, which increases your efficiency and reduces your cost per sample.

Sequencer Flow Cell Samples/Flow Cell Average Depth (expected)
NextSeq 300 cycle mid output 21 500x*
NextSeq 300 cycle high output 64 500x*
NovaSeq SP 300 cycle 144 500x*
NovaSeq S1 200 cycle 288 500x*
NovaSeq S2 200 cycle >600 500x*
NovaSeq S4 200 cycle >1,600 500x*


Table 2. Number of samples per flow cell to achieve 500x mean depth of coverage based on 2 x 100bp PE sequencing and maximum quoted sequencer output for Nonacus Cell3™ Target Pan-Cancer (524) TMB/MSI Panel. Based on in-silico calculations.

Panel Design Tool

Customise content for NGS cancer panels

Designed to be flexible, our Cell3™ Target Pan-Cancer panel allows you to add extra content specific to your project. Whether this is additional content or increased coverage of existing content, our Panel Design Tool makes this a simple and easy process to implement. And our rapid production turnaround means you will quickly receive a fully NGS-validated custom exome.

  • Additional content with high enrichment uniformity
  • Increased coverage of specific genes covered by Cell3™ Target Pan Cancer Panel
  • Optimization of spike-in ratio

Log into the Panel Design Tool at MyNonacus to start the design process and get a quote or drop us an email at info@nonacus.com

Ordering Information

Cell3 Target panels are available with one of two versions of our library preparation kits:

-Fragmentation: for use with gDNA (FF or FFPE)

-Non-Fragmentation: for use with cell free DNA

Cell3™ Target: Pan-Cancer (524) TMB/MSI Panel, Frag 16 samples NGS_C3T_TMB_FR_16
Cell3™ Target: Pan-Cancer (524) TMB/MSI Panel, Frag 96 samples NGS_C3T_TMB_FR_96_A/B/C/D*
Cell3™ Target: Pan-Cancer (524) TMB/MSI Panel, Non Frag 16 samples NGS_C3T_TMB_NF_16
Cell3™ Target: Pan-Cancer (524) TMB/MSI Panel, Non Frag 96 samples NGS_C3T_TMB_NF_96_A/B/C/D*

* To provide flexibility in multiplexing samples, our 96-sample kits offer a choice in adapter plate:

A = Adapter plate with indexes 1-96
B = Adapter plate with indexes 97-192
C = Adapter plate with indexes 193-288
D = Adapter plate with indexes 289-384

Product Resources

Detailed product information available to download.



For Research Use Only. Not for use in diagnostic procedures.

Product Support

If you have any questions about any of our products, including access to the BED files and example data sets, please fill in the support request form here and we will get back to you as soon as possible.

We offer several NGS cancer panels including the Hereditary Cancer PanelBladder Cancer Panel, Tumor Exome, Actionable Mutation Panel (EGFR), Whole Exome, and Custom NGS panels.

Learn more about our products for oncology

Cell3™ Target: Hereditary Cancer Panel

A comprehensive NGS sequencing panel for analysing germline mutations associated with hereditary cancers

Gloved hand holding Microscope slide with liquid on

Cell3™ Target: Tumor Exome

Whole exome capture with improved, clinically relevant content for comprehensive primary tumor sequencing

DNA sequencing for cancer diagnostics

Cell3™ Target: Actionable Mutation Panel (EGFR)

A highly focused panel covering actionable mutations in the EGFR pathway.

Scientist in lab coat pointing at DNA molecule

Cell3™ Target: Custom NGS Panels

Target the genes and variants important to you by creating your own NGS panel using our ultra-sensitive Cell3™ Target technology