Detect SNVs, INDELs and CNVs in a single, clinical-grade assay
Cell3™ Target: Nexome
Capture more variants and increase your diagnostic yield.
Features
Empower informed prenatal decisions
Nexome's enhanced prenatal testing capabilities provide a more thorough assessment of fetal health. This empowers expectant parents and healthcare providers to make informed decisions regarding pregnancy management and future healthcare planning for the child.
High precision CNV calling with minimal DNA input
Confidently call SNVs, INDELs and CNVs with high recall and precision from as little as 1 ng of DNA, unlocking prenatal or limited samples, without compromising on quality or robustness.
Optimize treatment decisions with personalized pharmacogenomics
Nexome incorporates pharmacogenomic (PGx) testing, enabling physicians to tailor medication plans based on an individual's unique genetic makeup. By analyzing variations in drug response, Nexome helps optimize treatment efficacy while minimizing the risk of side effects.
Unifying variant analysis workflows with confidence
Validate and run one workflow for all variants including SNVs, INDELs and CNVs in a single, clinical-grade assay giving you the confidence to replace your array and Multiplex Ligation-dependent Probe Amplification (MLPA) based CNV analysis.
Nexome vs. traditional workflows
Nexome streamlines the diagnostic process by eliminating the need for multiple tests like chromosomal microarrays (CMA), Multiplex ligation-dependent probe amplification (MLPA), and Fluorescence in situ hybridization (FISH). This translates to:
Reduced cost:
Upgrade to a cost-effective solution compared to traditional workflows that require multiple assays.
Faster turn-around time:
Consolidate your testing and achieve to quicker results, allowing for prompt and informed clinical decisions.
Minimal sample requirements:
Nexome requires a smaller sample volume, making it ideal for situations with limited sample availability.
Comprehensive coverage of unrivaled clinically relevant regions, and enhanced content
Cell3 Target:Nexome is designed so excellent data coverage across the wider exome is easily attainable:
- Protein coding regions of the human genome with additional clinically relevant non-coding regions
- CCDS, ClinVar, GENCODE, RefSeq and ACMG73 databases (Figure 1) with enhanced probes to enable CNV detection at loci with known gene and exon level rearrangements
Figure 1: Coverage of different databases by Cell3 Target: Nexome compared to other commercially available kits.
Increased diagnostic yield for exomes
Optimizing diagnostic yield from a genomics test is important so our Cell3 Target: Nexome panel has been designed to cover clinically relevant coding, and noncoding, regions to achieve outstanding coverage across the wider exome.
Boosted regions of the panel include:
- Additional RefSeq transcripts across the Online Mendelian Inheritance in Man (OMIM) morbid set of genes1
- Genes associated with pre and postnatal phenotypes (fetal anomalies)
- Transcripts and extra exons associated with Early Infant Epileptic Encephalopathy (EIEE) genes for enhanced epilepsy diagnosis
- Promoter, 5’ and 3’ UTR sequences for current OMIM morbid genes
- Non-coding, disease-causing variants as reported by Smedley et al2,3
Figure 2: Percentage coverage of gene transcripts and variants by Nexome compared to other commercially available kits.
Pharmacogenomic (PGx) marker inclusion
Our Cell3 Target: Nexome panel contains PGx markers for drug response prediction in accordance with the Clinical Pharmacogenetics Implementation Consortium (CPIG), which outperforms current market leaders, as illustrated in Figure 3.
Figure 3a: Nonacus
Figure 3b: Company T
Figure 3c: Company I
Precision and recall of SNVs and INDELs
Cell3 Target: Nexome detects significantly more truth variants present in the HG001 human genome reference standard than other exome captures, whilst maintaining superior precision and comparable recall for both SNVs and INDELs.
Figure 4a: Precision and recall of SNVs detected by Cell3 Target: Nexome and other commercially available exome panels.
Figure 4b: Total number of truth variants (SNVs) detected by Cell3 Target: Nexome and other commercially available exome panels.
Figure 5a: Precision and recall of Indels detected by Cell3 Target: Nexome and other commercially available exome panels.
Figure 5b: Total number of truth variants (Indels) detected by Cell3 Target: Nexome and other commercially available exome panels.
Precision CNV calling from exome sequencing using Cell3
Copy number variants account for ~10% of curated disease associated variants and are identified in ~10–20% of individuals with neurodevelopmental disorders.
- Designed for superior CNV detection at loci known to have both gene and exon level rearrangements
- Capable of detecting CNVs with sizes spanning from just a few exons up to multiple contiguous genes (~100 bp–40 Mb)
- Evaluated using samples with known CNV events tested by either MLPA or CMA and confidently recalled CNV mutations from 50 bp (a single exon) up to 42 Mb
- Detection of clinically relevant events is achieved with superior precision and recall and provides an exome alternative to CMA and MLPA based CNV analysis. (Table 1a and 1b)
Table 1a: Detection of MLPA-confirmed CNVs
| Affected gene | |||||
|---|---|---|---|---|---|
| CNV region | |||||
| CNV size (bp) | |||||
| CNV exons | |||||
| CNV type | |||||
| Bayes factor | FBN1 | exons 29-65 | 74632 | 37 | deletion | 320.0 |
| BRCA1 | exons 1-23 | 77841 | 24 | deletion | 190.0 |
| FBN1 | exons 1-17 | 142063 | 18 | deletion | 300.0 |
| BRCA1 | exons 1-17 | 57876 | 18 | deletion | 200.0 |
| BRCA1 | exons 8-13 | 17956 | 6 | deletion | 40.4 |
| BRCA1 | exons 8-13 | 17956 | 6 | deletion | 82.4 |
| BRCA2 | exons 5-7 | 513 | 3 | deletion | 22.1 |
| NSD1 | exons 7-9 | 6034 | 3 | deletion | 34.5 |
| FBN1 | exons 60-62 | 3934 | 3 | deletion | 32.8 |
| NSD1 | exons 1-3 | 58095 | 3 | deletion | 54.8 |
| BRCA2 | exons 1-2 | 1054 | 2 | deletion | 28.3 |
| BRCA1 | exons 7-8 | 311 | 2 | deletion | 4.7 |
| BRCA1 | exons 8-9 | 1444 | 2 | deletion | 7.5 |
| BRCA1 | exon 16 | 211 | 1 | deletion | 14.5 |
| BRCA1 | exon 20 | 84 | 1 | deletion | 9.4 |
Table 1b: Detection of CMA-confirmed multi-gene CNVs.
| CNV region | ||||
|---|---|---|---|---|
| CNV size | ||||
| CNV genes | ||||
| CNV type | ||||
| Bayes factor | 13q14.2q32.1 | 42.0 | 367.0 | deletion | 2410.0 |
| 4p16.3p15.2 | 22.9 | 339.0 | deletion | 4620.0 |
| 20q11.22q13.12 | 11.3 | 244.0 | deletion | 7000.0 |
| 7p14.1p11.2 | 15.9 | 182.0 | deletion | 5040.0 |
| 1p36.32 | 3.7 | 140.0 | deletion | 2710.0 |
| 22q11.21 | 2.0 | 83.0 | deletion | 2890.0 |
| 8q23.1q24.12 | 11.8 | 71.0 | deletion | 1330.0 |
| 22q.11.21 | 2.2 | 64.0 | duplication | 1430.0 |
| 11p12p11.2 | 2.3 | 54.0 | deletion | 1240.0 |
| 7q11.23 | 1.4 | 38.0 | deletion | 2080.0 |
| 15q11.2 | 0.9 | 31.0 | deletion | 494.0 |
| 17p12 | 1.3 | 24.0 | deletion | 275.0 |
| 14q22.1 | 0.7 | 20.0 | deletion | 508.0 |
| 15q11.2 | 0.5 | 4.0 | duplication | 370.0 |
| 13q12.11 | 0.2 | 2.0 | deletion | 75.0 |
Delivers more content without increasing sequencing costs and additional assay testing
Detect more clinically relevant variants without increasing your sequencing costs.
- Cell3 Target: Nexome panel targets just over 51 Mb of the human genome
- Ensures that you can call up to 30% more variants than other commercially available exome panels and detect a wide range of CNVs
- Probe design and superior performance (Table 2) means that, when compared to smaller commercially available exome panels, Nexome requires a similar, or less amount, of sequencing to achieve a mean coverage of 100× with 6.63 Gb
Combine workflows into one
- Cell3 Target: Nexome panel presents an advanced alternative to MLPA by offering:
- Increased coverage and improved targeting of classic MLPA regions
- Surpasses Sanger sequencing
- Cell3 Target: Nexome seamlessly delivers PMS2 sequencing, avoiding the need of additional analysis via PCR or MLPA
Table 2: Gb of sequence required to achieve mean coverage of 100x for Cell3 Target: Nexome and other commercially available exome products. Data was down sampled to 100x per sample for each exome panel.
| Exome product | ||||
|---|---|---|---|---|
| Panel size (Mb) | ||||
| Percentage target covered at 1x | ||||
| Gb required for mean 100x coverage | ||||
| Percentage of bases on or near bait | Nexome | 51.90 | 98.78% | 6.63 | 94.18% |
| ExomeCG | 51.60 | 98.78% | 6.57 | 94.07% |
| CompanyT | 36.70 | 97.42% | 6.85 | 85.89% |
| Company I | 45.20 | 98.15% | 7.16 | 86.18% |
| CompanyI.D | 34.10 | 98.49% | 6.04 | 93.09% |
Benefits from straight forward, automatable protocols
- The Cell3 Target: Nexome kit contains all reagents for both library preparation and hybridization and capture.
- The Cell3 Target workflow is simple and easy, requires as little as 1 ng of DNA and takes less than 10 hours, with less than two 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 facilitate high throughput laboratories, allow for flexible batch sizes and provide scalability across all Illumina sequencers.
For Research Use Only. Not for use in diagnostic procedures.
References
1.McKusick V. Online Mendelian Inheritance in Man, OMIM™. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 2000. Accessed October 10, 2023. https://omim. org. 2009. Full article
2.Smedley D, Schubach M, Jacobsen JO, Köhler S, Zemojtel T, Spielmann M, et al. A whole-genome analysis framework for effective identification of pathogenic regulatory variants in Mendelian disease. The American Journal of Human Genetics. 2016; 99(3):595-606. Full article
3. Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Research. 2018;46(D1):D1062-7.. Full article
See our customer publications
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.
| Enrichment method | Hybridisation and capture |
| Capture panel Size | 51.9 Mb |
| Sequencing platform | Illumina |
| Targets | Clinically relevant genes |
| Variant types | SNVs, indels and CNVs |
| Sample type | gDNA from blood, saliva, amniotic fluid, tissue or FFPE, cfDNA |
| Input DNA requirements | 1-1000 ng |
| Expected percentage duplication | ~5-6% |
| Expected percentage on target (150 bp padding) | ~95% |
| Gb required for mean 100× coverage | 6.63 |
| Multiplex capability | 384 |
Cell3™ Target panels are available with one of two versions of our library preparation kits:
- Fragmentation: for use with DNA (genomic, FF, FFPE)
- Non-fragmentation: for use with cell-free DNA
| Product | Catalog No. |
| Cell3™ Target: Nexome, Frag 16 samples | NGS_C3T_NEX_FR_16 |
| Cell3™ Target: Nexome, Frag 96 samples | NGS_C3T_NEX_FR_96_A/B/C/D* |
| Cell3™ Target: Nexome, Non Frag 16 samples | NGS_C3T_NEX_NF_16 |
| Cell3™ Target: Nexome, Non Frag 96 samples | NGS_C3T_NEX_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
What is meant by ‘clinically enhanced’ when referring to the Nexome panel?
The term ‘clinically enhanced’ refers to the addition of probes, to the human whole exome panel, with clinical relevance increasing the diagnostic potential of the assay. These fall into several categories including:
- Additional RefSeq transcripts across the Online Mendelian Inheritance in Man (OMIM) morbid set of genes
- Genes associated with pre and postnatal phenotypes (fetal anomalies)
- Transcripts and extra exons associated with Early Infant Epileptic Encephalopathy (EIEE) genes for enhanced epilepsy diagnosis
- Promoter, 5’ and 3’ UTR sequences for current OMIM morbid genes
- Non-coding, disease-causing variants
- Pharmacogenomic (PGx) marker inclusion for drug response prediction
Has the Cell3 Target:Nexome panel been designed with copy number variation in mind?
Yes. The panel has been designed for CNV detection at both gene and exon level rearrangements. This was evaluated with known CNV events tested by either MLPA, or CMA, showing confident calling of CNV mutations from as small as 50 bp, up to 42 Mb.
What depth of coverage should we aim for when planning our sequencing runs?
To capture CNV events with the Cell3 Target: Nexome panel, especially those covering small regions, we recommend sequencing to a depth of 200-250x.
What sample types can be used with the Cell3 Target: Nexome panel?
The <a href=“https://nonacus.com/wp-content/uploads/2023/08/Nonacus-Cell3-Target-V2-Protocol-v1.5.pdf” target=“_blank”>Cell3 Target library preparation</a> protocol accommodates a broad range of sample types; cell-free (cfDNA), cell-free fetal (cffDNA), and DNA from fresh frozen as well as formalin fixed paraffin embedded (FFPE) tissue.
