Cell3™ Target: Hereditary Cancer Panel

Target 129 genes associated with hereditary cancer

A comprehensive NGS sequencing panel for analysing germline mutations including SNVs, indels and CNVs across a range of cancer types

Comprehensive content

Target germline mutations in 129 genes associated with an increased risk of developing hereditary cancer

High quality data

Confidently call all variants including SNVs, indels and CNVs with high precision and recall

 

Streamlined workflow

Validate and run one workflow for profiling known genetic associations for hereditary cancers regardless of cancer type or input amount

Lower sequencing costs

Generate more sequence per sample with high on-target rates, superior uniformity of coverage and low levels of duplication

Genetic testing to identify inherited variants associated with cancer

Hereditary cancers account for around 5-10% of all cancers1 and include cancers of the breast, ovary, uterus, prostate, and gastrointestinal system, which includes the stomach, colon, rectum, small bowel, and pancreas.

Genetic testing to identify an inherited variant associated with cancer can provide a cancer risk assessment for an individual and guide the implementation of additional screening and surveillance if necessary. This in turn may result in an early diagnosis and help guide treatment.

As well as helping improve outcomes for patients diagnosed with hereditary cancer, testing for inherited variants associated with cancer may also help guide additional screening and early diagnosis of at-risk relatives.

By using a multi-cancer panel to screen for germline mutations, researchers can profile known genetic associations for hereditary cancer regardless of cancer type. This maximises diagnostic yield for individuals with a personal or family history of mixed cancers affecting multiple organ systems or those with an unknown family history.

Cell3™ Target: Hereditary Cancer Panel

The Cell3™ Target Hereditary Cancer Panel is a hybridisation and capture NGS panel designed to target germline mutations in 129 genes associated with an increased risk of developing hereditary cancer. These genes have been selected to cover not only the common hereditary cancers listed above but also some of the rarer hereditary cancers like Phaeochromocytoma and paediatric cancers like Wilms tumor.

 

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Table 1. Nonacus Hereditary Cancer Panel gene content

Superior precision and recall ensure confident calling of SNV, indel and CNV variants

The precision and recall for single nucleotide variants (SNVs) and insertion-deletion mutations (indels) for the Nonacus Cell3™ Target Hereditary Cancer panel were tested alongside two competitor panels on commercially available reference standards (Genome in a Bottle HG002; Seracare Seraseq® Inherited Cancer DNA Mix v1) containing multiple variants. The Nonacus panel showed excellent recall for SNVs (Figure 1), and indels (Figure 2) with both higher than either of the competitors’ products.

 

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Figure 1. Nonacus Hereditary Cancer Panel delivers a mean recall of 99.78% for SNVs across four replicates outperforming Company I and Company P.

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Figure 2. Nonacus Hereditary Cancer Panel delivers a mean indel recall of 100% across four replicates outperforming Company I and Company P.

CNV Genotypic Sex CNV Type Detected Recall Position
Copy normal male copy neutral YES 100% 100%
MSH2 deletion exons 1-6, heterozygous male multi-exon deletion YES 100% 100%
MSH2 deletion exon 7, heterozygous male single exon deletion YES 100% 100%
MSH2 deletion exons 1-2, heterozygous female multi-exon deletion YES 100% 100%
MSH2 deletion exon 1, heterozygous male single exon deletion YES 100% 100%
MLH1 exon 13 amplification
(3 or more copies)
female multi-exon deletion YES 100% 100%

Table 2. Nonacus Cell3 Target Hereditary Cancer Panel confidently calls CNVs with 100% recall and precision.

Table 2 shows the precision and recall for a range of CNVs in the MLH1/MSH2 Exon Copy Number Reference Panel (NIBSC) detected with the Nonacus Cell3™ Target: Hereditary Cancer panel and Nonacus analysis pipeline. All CNVs were detected with 100% recall and precision.

 

 

High on-target rates and uniform coverage deliver more efficient sequencing...

The Cell3™ Target Hereditary Cancer panel design delivers a higher percentage of on-target reads (with padding at 150bp) when compared with a leading competitors panel.  Even more importantly, the Nonacus panel also resulted in lower duplication rates and more consistent vertical coverage with 98% of targets covered with 30 reads of more (Table 3).  This 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.

Nonacus Company I
Panel size (kb) 644 403
Mb required for mean 100x coverage 78.1 116.6
Percentage coverage >30x 98% 96%
Percentage on target (150bp padding) 90.99% 61.51%
Percentage duplication 3.00% 8.99%

Table 3. Performance data for the Nonacus Cell3 Target Hereditary Cancer Panel compared with a leading competitor panel.

Sequencer Flow Cell Hereditary Cancer Panel Samples/Flow Cell
MiSeq V3.0 Nonacus 96
Company I 64
V2.0
Nonacus 58
Company I 39
V2 Micro Nonacus 15
Company I 10
V2 Nano Nonacus 4
Company I 3

Table 4. Estimated maximum number of samples per flow cell to achieve 100x mean depth of coverage based on 2 x 150bp PE sequencing calculated based on data obtained in Table 3. 

...and lower sequencing costs

The impact of effective hybridisation and capture on sequencing efficiency can be seen in Table 4. Laboratories can run 50% more samples per flow cell or generate more sequencing data per sample than the leading competitors product.

 

Validate and run one workflow

Rather than running multiple panels to cover different cancer syndromes, the Cell3™ Target Hereditary Cancer panel enables laboratories to validate and run just one workflow for profiling all hereditary cancer types. In addition to maximising diagnostic yield, this simplifies laboratory workflows reducing laboratory validation and operating costs.

The Cell3™ Target workflow is simple and easy. Taking less than 10 hours, with less than 2 hours hands-on time, it is designed with multiple stop points to provide flexibility within laboratory processing. Library preparation can be run manually or automated (up to 96 samples in a single batch).

Indexes are available for up to 384 samples to allow for flexible batch sizes and scalability across all Illumina benchtop sequencers.

 

COVID-19 Whole Genome Sequencing Service

Product Specifications

Product Specifications.
Enrichment method Hybridisation and capture
Number of genes 129 (all exons)
Capture Panel Size 644 Kb
Sequencing platform Compatible with all current Illumina Sequencers
Targets Genes associated with hereditary cancers
Variant types SNVs, indels and CNVs
Sample type gDNA from blood, saliva, tissue or FFPE
Input DNA requirements 10-200 ng
Expected percent duplication 3%
Expected coverage uniformity (Percentage of targets covered >30x) 98%
Expected percentage on target (150bp padding) 91%
Multiplex capability 384

Product Support

For access to the BED files for this panel design, please visit My Nonacus

FASTQ files for example data sets are available on request, please email support@nonacus.com or complete our support request form.

If you have any other questions about this panel or any of our products, please fill in the support request form here and we will get back to you as soon as possible.

Ordering Information

Cell3™ Target: Hereditary Cancer Panel, 16 samples C3228HC*
Cell3™ Target: Hereditary Cancer Panel, 96 samples C3229HC*

*Includes fragmentation library prep kit for gDNA (blood or saliva) or FFPE DNA

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