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

Pan cancer
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


Validated on 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 has been validated on 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 tumour 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. showing Pan-Cancer (524) TMB/MSI Panel gene content

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, delivers accurate TMB estimation, cost effectively.

Validated on 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 has been validated on 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 tumour origin– in a single, simple workflow.

Gloved hand holding Microscope ffpe slide with liquid onDiagram 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

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.

SequencerFlow CellSamples/Flow CellAverage 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*


** Liquid Biopsy ctDNA

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.

Screenshot of Nonacus Probe design tool homepage

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 Probe Design Tool makes this a simple and easy process to implement. And our rapid production turnaround means you will receive a fully NGS-validated custom exome within 4 weeks.

  • 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 Probe Design Tool at MyNonacus to start the design process and get a quote or drop us an email at 


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