Email Address

info@shivascientific.in

Phone Number

+91 -11- 61340405

Our Location

Sector 14, Dwarka, New Delhi

Send Query

Cell3™ Target: Nexome

  • Products
  • Cancer Genetics
  • Cell3™ Target: Nexome

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

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.

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.

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.

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.

Increased diagnostic yield for exomes

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 Indels detected by Cell3 Target: Nexome and other commercially available exome panels.

Figure 4b Total number of truth variants (Indels) 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

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.

  • 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.

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

Product Description

Pack Size

Catalogue Number
GALEAS HereditaryPlus 16 samples NGS_GAL_HCP_FR_16
(with enzymatic fragmentation for gDNA) 96 samples NGS_GAL_HCP_FR_96_A/B/C/D*

Get in Touch

For any queries or detailed requirements, get in touch with our team of experts at Shiva Scientific.

Contact Us

Our Partners

About

the company embarked on a journey into the realm of Genomics. Since then, it has continuously evolved, presenting forward-looking and ingenious solutions in this field.

Social Media

Facebook Linkedin Pinterest Youtube

Quick Links

Support Links

Locations

  • 140, SFS, Pocket 1 & 2, Sector-3, Dwarka, New Delhi -110078 India
  • info@shivascientific.in
  • +91 9810764834
  • Mon-Sat : 8:00 AM to 07:00 PM

Shiva Scientific

Copyright © 2024. All rights reserved.