Cell3™ Target: Custom Panel for cfDNA

Custom NGS Panels for Cell-Free DNA (cfDNA) Analysis

Custom Panels for Cell-Free DNA (cfDNA) with High Sensitivity and Precision

Cell3™ Target delivers highly customizable Next-Generation Sequencing (NGS) panels, optimized for cfDNA analysis. Using hybridization capture and Illumina technology, it detects low-frequency variants with exceptional accuracy. This makes it ideal for applications like cancer diagnostics, liquid biopsy, and non-invasive prenatal testing (NIPT).

With a streamlined workflow under two hours, Cell3™ Target provides rapid and reliable results tailored to your needs.

The table of contents

Why Choose Cell3™ Target for cfDNA Analysis?

Accurate Detection of Diverse Variants

Our technology ensures precise identification of a wide range of genetic alterations, including:

SNVs (Single Nucleotide Variants)
InDels (Insertions and Deletions)
CNVs (Copy Number Variants)
SVs (Structural Variants)

This comprehensive coverage enhances the reliability of genomic profiling for research and diagnostic applications

Ultra-sensitive Variant
Detection

Cell3™ Target achieves high sensitivity with:

Dual indexing and Unique Molecular Identifiers (UMIs) to reduce errors
Variant Allele Frequency (VAF) detection down to 0.1%
Critical applications in cancer diagnostics and monitoring

This level of precision supports early disease detection and treatment monitoring

Broad Sample Compatibility

Our technology demonstrates a proven track record for cfDNA analysis from multiple sample types, including:

Blood
Urine
Saliva
Rectal mucosa

This versatility allows for comprehensive, non-invasive genomic testing across various clinical and research settings

Extensive Applications

Cell3™ Target supports a wide range of applications:

Cancer diagnostics
Minimal Residual Disease (MRD) detection
Non-Invasive Prenatal Testing (NIPT)
Liquid biopsy research

This broad applicability ensures enhanced diagnostic accuracy and better patient management

User Story: Early Detection of OSCC Using Salivary cfDNA

Dr. Ahmed, a researcher at King’s College London, faced the challenge of early detection of oral squamous cell carcinoma (OSCC). Traditional imaging diagnostics made it difficult to identify recurrences at an early and treatable stage. To address this issue, Dr. Ahmed’s team utilized Nonacus’s custom panel to analyze cfDNA from saliva samples of OSCC patients.

By employing Nonacus’s custom panel specifically designed for OSCC, Dr. Ahmed’s team successfully detected somatic mutations in the saliva samples. This innovative approach allowed for sequencing a 12-gene panel at a depth of 20,000-fold, enabling high sensitivity and specificity in detection. The allele frequencies of the mutations detected in saliva ranged from 0.004 to 0.061.

The use of Nonacus’s custom panel significantly improved the early detection of OSCC recurrences. This study confirmed that cfDNA derived from saliva is a reliable means of detecting tumor-derived mutations, demonstrating an 82% detection rate. This non-invasive method enhances patient prognosis and streamlines the management of OSCC.

Ahmed, Ahmed A., et al. “Mutation detection in saliva from oral cancer patients.”
Oral Oncology 151 (2024).

Design Your Own Custom NGS Panel

Complete Customization
Modify panel elements to fit your clinical or research needs
Flexible Input Options
Upload BED files, gene lists, or genomic coordinates
Advanced Algorithms
Ensure uniform target coverage and efficiency, even with small panels
Instant Feedback
Get real-time insights into target coverage and probe details

Start Designing Now

Whether you are creating a new panel or customizing an existing one, our panel design tool makes it easy to design NGS panel effortlessly.

Read Our Partner’s Testimony

Advanced Genomics APAC

Tried, Tested, and Proven: Why a Head of Oncology Service Chose Nonacus? | Advanced Genomics APAC Dr. Danny, Hon Fai So, Head of Oncology Service at Pangenia Inc., shares his experience with Nonacus and explains why he

Optimized Sequencing Performance & Cost Efficiency

Cell3™ Target is designed to maximize efficiency while maintaining high sensitivity:

Uniform coverage, even with small panels (<500 probes)
Detect variants from just 25 ng of cfDNA at 0.1% VAF
Lower sequencing costs without compromising accuracy

Enhanced On-Target Efficiency & Reliable Detection

Compared to standard capture methods, Cell3™ Target delivers:

Higher on-target rates
Reduced off-target sequencing noise
Consistent performance across panels (single-gene to 1,000-gene panels)

In tests using SeraCare’s standard reference, Cell3™ Target accurately detected variants even at a low VAF of 0.6%

**Figure 1** Sequencing metrics summary showing equivalent coverage uniformity and increased on target capture between Nonacus and competitor A.

**Figure 2** Expected vs. observed VAF using the HBB gene capture panel with artifical gDNA at known VAF of 0.0%, 1.0% and 2.5%.

Order Information

The Cell3™ Target panels are available with two types of library preparation kits:

Fragmentation-Compatible Kit: Designed for use with DNA samples (Genomic, FF, FFPE).
Non-Fragmentation-Compatible Kit: Specifically intended for use with cfDNA samples.

Panel Size	Panel Size from XS(50 probe)-XXL(25000 probe)
Panel size based on probe number	Frag	Non-Frag
48 Sample	NGS_C3C_(size)_FR_48	NGS_C3C_(size)_NF_48
96 Sample	NGS_C3C_(size)_FR_96_A/B/C/D	NGS_C3C_(size)_NF_96_A/B/C/D

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

*To provide flexibility for multiplexing samples, the kit for 96 samples includes an adapter plate.

Product Resources

Data Sheet

Cell3™ Target: Custom Panel for cfDNA

Protocols

Cell3™ Target V2 Reagents Protocol

User Manual for My Nonacus

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