Cell3™ Target: ExomeCG

Exome capture for cytogenomic analysis

Clinically enhanced human exome capture enabling detection of SNVs, indels and CNVs in a single assay.

Streamline your workflow

ExomeCG lets you detect all variants (SNVs, indels and CNVs) in a single, clinical-grade assay, suitable for constitutional postnatal and prenatal analysis. Less handling. Less time. More results first time.

Clinically relevant genes

The best coverage of clinical targets thanks to superior CNV detection at loci known to have both gene and exon-level rearrangements. Giving you the option to replace your array and MLPA-based CNV analysis.

Save time. Save resources

Use as little as 1ng of DNA unlocking prenatal or limited samples and get results days earlier. ExomeCG saves you time and sample, without compromising on quality or robustness.

Software to support you

ExomeCG fully integrates with the Congenica® clinical decision support platform for data visualisation and analysis. Combined with the Cell3™ Target range, we have your research needs covered, from start to finish.

Exome sequencing for cytogenetics

Your standard workflow as a cytogeneticist probably involves multiple steps and assays, such as chromosomal microarrays (CMA), multiplex ligation probe amplification (MLPA), FISH and often this will be followed by NGS (exome sequencing). This not only increases the time you need to reach a final test report but uses up valuable sample and increases cost to result.

The ExomeCG is a clinically enhanced human exome capture kit that streamlines this workflow allowing you to carry out robust whole-exome sequencing and targeted copy number analysis in one single test.

CNV detection using exome sequencing

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

The design of the ExomeCG kit is formulated to give superior CNV detection at loci known to have both gene and exon level rearrangements, allowing unparalleled coverage of clinical targets and providing an exome alternative to CMA and MLPA based CNV analysis. Optimized for use with the Congenica® clinical decision support platform, ExomeCG is a complete solution for calling and analysis of SNVs, indels and CNVs in a single test.

Nonacus ExomeCG clinically enhanced human exome capture kit
Figure 1. showing Design coverage of targeted gene panels and variants sets by ExomeCG compared to other comercially available kits.

Figure 1. Design coverage of targeted gene panels and variants sets by ExomeCG compared to other commercially available kits.

Increased diagnostic yield for exomes

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

• OMIM morbid genes (Online Mendelian Inheritance in Man 2018),

• Genes associated with pre and postnatal phenotypes (fetal anomalies).

• Epilepsy genes.

• Pharmacogenomic markers and sample tracking variants

• Non-coding RNA’s.


These give ExomeCG the most comprehensive coverage of these genes than any other commercially available exome product.

Superior read depth across key genes

ExomeCG gives superior read depth across clinically relevant gene panels, while having fewer low-coverage exons, compared with alternative exome products.


Precision CNV calling from exome sequencing

ExomeCG generates data you can rely on. A key requirement for any NGS CNV assay is the ability to detect variants previously identified using CMA or MLPA technologies. As part of our validation, we evaluated samples with known CNV tested by either MLPA or CMA and confidently recall the CNV mutations from 50bp (a single exon) up to 42Mb.

Using simulated data to provide truth sets we have shown that exceptional precision recall is possible with the Exome CG assay.

Affected Gene CNV region CNV size
CNV exons CNV type Bayes
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 1. Detection of MLPA-confirmed CNVs by the ExomeCG assay. The Bayes factor is the log10 of the likelihood ratio, which quantifies the eveidence for the CNV call divided by that for normal copy number. *FBN1 exons 60-62 deletion.

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

Table 2. Detection of CMA-confirmed multi-gene CNVs by the ExomeCG assay. *22q11.21 CNV gain as visualised in Figure 4.

Ordering Information

Cell3 Target panels are available with one of two versions of our library preparation kits:

-Fragmentation: for use with gDNA (FF or FFPE)

-Non-Fragmentation: for use with cell free DNA

Cell3™ Target: Exome CG, Frag 16 samples NGS_C3T_CEX_FR_16
Cell3™ Target: Exome CG, Frag 96 samples NGS_C3T_CEX_FR_96_A/B/C/D*
Cell3™ Target: Exome CG, Non Frag 16 samples NGS_C3T_CEX_NF_16
Cell3™ Target: Exome CG, Non Frag 96 samples NGS_C3T_CEX_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

Product Resources

Detailed product information available to download.



Clinically relevant CNV detection via WGS and WES – a single assay approach, Listen to Dominic McMullan, Birmingham Women’s and Children’s NHS Foundation Trust talk about the use of ExomeCG to analyse clinically relevant CNV's, live at ESHG.


Interested in evaluating the ExomeCG data within the Congenica clinical decision support platform, please find out more information and request a demo here


Learn more

Green Exome

Cell3™ Target: Whole Exome

Exome enrichment that delivers 33Mb of content focused on what matters allowing you reduce sequencing costs and improve throughput.

DNA sequencing for genetic screening

Cell3™ Target: Carrier Screening

A comprehensive panel covering variants for 488 severe recessive childhood disorders in one NGS workflow. No arrays. No MLPA.


Product Support

If you have a query relating to any of our prenatal products, including Nexome, Fetal RhD Genotyping, Whole Exome Enrichment, and Custom NGS Panelsplease contact fill in the support request form here and one of our team will get back to you as soon as possible.