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
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.
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.
Figure 1. Nonacus Hereditary Cancer Panel delivers a mean recall of 99.78% for SNVs across four replicates outperforming Company I and Company P.
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%|
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|
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.
|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||1-1000 ng|
|Expected percent duplication||3%|
|Expected coverage uniformity (Percentage of targets covered >30x)||98%|
|Expected percentage on target (150bp padding)||91%|
|Mb required for mean 100x coverage||78.1|
Detailed product information available to download.
For access to the BED files for this panel design, please visit MyNonacus
FASTQ files for example data sets are available on request, please email firstname.lastname@example.org 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.
|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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