Cell3™ Target: Nexome - a clinically enhanced exome panel

Detect SNVs, indels and CNVs in a single, clinical-grade assay

Capture more variants and increase your diagnostic yield without increasing your sequencing costs.

Clinically relevant content

Maximise your diagnostic yield with coverage of important clinical targets from the major genetic databases including CNVs and non-coding regions associated with prenatal and postnatal disease.

Streamlined workflow

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 MLPA-based CNV analysis.

Robust calling of variants

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.

Maximise content, minimise sequencing costs

Superior hybridization capture performance delivers significantly more content without increasing the amount of sequencing per sample or your sequencing costs.

Exome sequencing for clinical genetics

Current clinical genetic workflows often involve undertaking multiple tests with different technologies such as chromosomal microarrays (CMA), multiplex ligation probe amplification (MLPA), fluorescent in situ hybridization (FISH) all often followed by NGS (exome sequencing). This increases associated test cost, time to result and has negative implications for the required amount of sample input and the cost to process a given sample.

Cell3™ Target: Nexome has been developed combining our experience of exome panel design and input from experts in the field. As well as maximising coverage of clinically relevant targets for SNVs and indels, Nexome is designed to cover exon level deletions and duplications providing an exome alternative to CMA and MLPA based CNV analysis. It is a clinically enhanced human exome capture kit that allows you to carry out robust whole-exome sequencing and targeted copy number analysis in one single test.

Comprehensive coverage of clinically relevant regions

Larger than most exome products, Cell3™ Target: Nexome targets not only the protein coding regions of the human genome but clinically relevant non-coding regions. It is designed to offer excellent coverage of 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. showing Coverage of different databases by Nexome compared to other commercially available kits.

Figure 1. Coverage of different databases by Nexome compared to other commercially available kits.

Figure 2. showing Percentage coverage of gene transcripts and variants by Nexome compared to other commercially available kits.

Figure 2. Percentage coverage of gene transcripts and variants by Nexome compared to other commercially available kits.

Increased diagnostic yield for exomes

Optimising diagnostic yield from a genomics test is important so our Nexome panel has been designed to cover clinically relevant coding and noncoding regions with no loss of coverage across the wider exome. Boosted regions of the Nexome panel include:

  • Additional RefSeq transcripts across the Online Mendelian Inheritance in Man (OMIM) morbid set of genes.1
  • 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 al. 2,3
  • Pharmacogenomic (PGx) markers for drug response prediction.

Precision and recall of SNVs and indels

Nexome detects significantly more truth variants present in the HG001 human genome reference standard than other exome captures, and maintains superior precision and comparable recall for both SNVs and indels (Figures 3 and 4).

Figure 3a: Precision and recall of SNVs detected by Nexome and other commercially available exome panels.

Figure 3b: Total number of truth variants (SNVs) detected by Nexome and other commercially available exome panels.

Figure 4a: Precision and recall of Indels detected by Nexome and other commercially available exome panels.

Figure 4b: Total number of truth variants (Indels) detected by Nexome and other commercially available exome panels.

Precision CNV calling from exome sequencing

Copy number variants account for ~10% of curated disease associated variants and are identified in ~10–20% of individuals with neurodevelopmental disorders.

Enhanced coverage across loci with known gene and exon level rearrangements means that Cell3™ Target: Nexome is capable of detecting CNVs with sizes spanning from just a few exons up to multiple contiguous genes (~100 bp–40 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)

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 1a. Detection of MLPA-confirmed CNVs

CNV region CNV size CNV genes CNV type Bayes factor
13q14.2q32.1 42.0 367 deletion 2410
4p16.3p15.2 22.9 339 deletion 4620
20q11.22q13.12 11.3 244 deletion 7000
7p14.1p11.2 15.9 182 deletion 5040
1p36.32 3.7 140 deletion 2710
22q11.21 2.0 83 deletion 2890
8q23.1q24.12 11.8 71 deletion 1330
22q.11.21 2.2 64 duplication 1430
11p12p11.2 2.3 54 deletion 1240
7q11.23 1.4 38 deletion 2080
15q11.2 0.9 31 deletion 494
17p12 1.3 24 deletion 275
14q22.1 0.7 20 deletion 508
15q11.2 0.5 4 duplication 370
13q12.11 0.2 2 deletion 75

Table 1b. Detection of CMA-confirmed multi-gene CNVs.

Deliver more content without increasing sequencing costs

Our Nexome panel targets just over 51Mb of the human genome. This large capture size ensures that you can call up to 30% more variants than other commercially available exome panels and detect a wide range of CNVs, but our probe design and superior performance (Table 2) mean that despite being larger, Nexome requires a similar amount or less sequencing to achieve a mean coverage of 100x.

That means you can detect more clinically relevant variants without increasing your sequencing costs.

Panel Size (Mb) Percentage target covered at 1x Gb Required for mean 100x coverage Percent Bases on or near bait
Nexome 51.90 98.78% 6.63 94.18%
Exome CG 51.60 98.78% 6.57 94.07%
Company T 36.70 97.42% 6.85 85.89%
Company I 45.20 98.15% 7.16 86.18%
Company I.D 34.10% 98.49% 6.04 93.09%

Table 2. Gb of sequence required to achieve mean coverage of 100x for Nexome and other commercially available exome products. Data was down sampled to 100x per sample for each exome panel.

Automated NGS library preparation

Simple, 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 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 facilitate high through put laboratories, allow for flexible batch sizes and provide scalability across all Illumina sequencers.

References

  1. Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), 2018.
  2. Smedley D et al. (2016). A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Hum Genet. 99(3): 595-606 (2016).
  3. Landrum, MJ et al. (2018) ClinVar: improving access to variant interpretations and supporting evidenceNucleic Acids Research, Volume 46, Issue D1, D1062–D1067 (2018).

Product Specifications

Product Specifications.
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 (150bp padding) ~95%
Gb required for mean 100x coverage 6.63
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: Nexome, 16 samples C3230NX (options A/B*)
Cell3™ Target: Nexome, 96 samples C3231NX (options A/B/C*)

* Cell3™ Target panels are available in the following options:

A = non-fragmentation e.g. cffDNA/ctDNA,
B = fragmentation e.g. gDNA (cell-pellet DNA) or FFPE,
C = Both Fragmentation and Non-Fragmentation (half of each)

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