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.
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 (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 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
Cell3™ Target: Whole Exome
Exome enrichment that delivers 33Mb of content focused on what matters allowing you reduce sequencing costs and improve throughput.
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 Panels, please contact fill in the support request form here and one of our team will get back to you as soon as possible.