Cell3™ Target: Custom NGS Panels - Prenatal

Non-invasive prenatal genetic testing

Reliable targeted enrichment developed for prenatal testing and diagnosis using cell-free fetal DNA (cffDNA) or genomic DNA (gDNA).

Validated for cell-free and genomic DNA

NGS enrichment developed for and validated on cell-free DNA as well as gDNA for prenatal applications like non-invasive prenatal diagnosis

Confidently detect fetal fraction in maternal blood

QC validation guarantees uniformity of coverage which combined with error suppression technology ensures confident detection of even the lowest fetal fraction

 

Simple and rapid design process

Our online panel design tool means you can design and optimise a panel in minutes and our novel rapid manufacture process means minimal time between design and delivery

Optimised for large and small panels

Cell3™ Target enrichment has been optimised to deliver efficient target capture and unrivalled on-target performance regardless of panel size from 1 gene to 1,000.

Non-invasive prenatal testing

Cell-free DNA (cfDNA) are degraded DNA fragments released into the bloodstream through a natural process of cell death. During pregnancy, the mother’s blood contains cfDNA from her own tissue and from the fetus (cell-free fetal DNA (cffDNA)) via the placenta.  Sequence analysis of cfDNA from a sample of maternal blood can therefore provide genetic information about the fetus and inform clinical decisions without the need for invasive techniques like amniocentesis. However, as only between 2 and 20% of the total cell-free DNA in maternal blood is fetal1,2 (the fetal fraction), its analysis requires ultra-sensitive sequencing methods capable of accurately detecting genetic variants in samples with even the lowest of fetal fractions.

Targeted NGS/resequencing panels for NIPD or prenatal testing

Targeted sequencing, through the use of custom designed NGS panels, offers a cost-effective method for the ultra-sensitive sequencing required for non-invasive prenatal genetics. Without the data burden of whole-genome sequencing (WGS) or whole-exome sequencing (WES) it allows researchers to achieve very high depths of coverage providing the increased sensitivity and accuracy needed for the analysis of low abundance cell free fetal DNA (cffDNA).

Cell3™ Target is a novel target enrichment system developed by Nonacus for converting cell-free DNA or genomic DNA into libraries for next generation sequencing that has been validated to ensure confident detection and analysis for even the lowest of fetal fractions.

Reliable target enrichment for cffDNA and gDNA

We understand that our customers have different questions to answer so Cell3™ Target has been developed for and validated on cffDNA and gDNA for a range of prenatal applications. Whether you are using amniocentesis or non-invasive prenatal testing (NIPT), you know you will be able to use the same method and panel design.

Liquid biopsy sample, DNA from a blood sample
automated testing service

Quick and convenient workflow for cfDNA

Cell3™ Target offers quick, Covaris-free, enzymatic shearing for genomic DNA samples and is available without enzymatic fragmentation reagents for cfDNA.

  • Quick and easy workflow takes less than 10 hours, with less than 2 hours hands-on time.
  • Supports manual or automated preparation of 1 – 96 samples in a single batch
  • 384 patient/sample indexes ensure that customer can use Cell3™ Target on the smallest to the largest output sequencers.
  • Suitable for use from 1ng cfDNA or genomic DNA.

Ultra-sensitive NGS enrichment for NIPD

Cell3™ Target enrichments incorporate error suppression technology including unique molecular indexes (UMIs) and unique dual indexes (UDI’s) which remove of both PCR and sequencing errors and index hopping events. This error suppression technique, combined with our excellent uniformity of coverage, allows you to confidently and accurately call variants in even the lowest of fetal fractions. (and from as little as 1ng cfDNA or gDNA input). We provide advice and provision of ready to go analysis scripts for error removal using UMI’s.

Diagram demonstrating Using UMI’s to identify and quantify individual DNA molecules during library preparation increases sensitivity

Figure 1. Using UMI’s to identify and quantify individual DNA molecules during library preparation increases sensitivity

Screenshot of Nonacus Probe design tool homepage

Successful custom panel design for targeted NGS

Good design is key to a successful NGS panel ensuring adequate coverage and robust variant calling.  It’s not always easy to achieve, especially first time, but our Panel Design tool, makes it simple and easy allowing you to optimise panels in minutes. Create designs instantly from scratch using uploaded BED files, gene lists or genomic coordinates, customise catalogue products or add your own content onto one of our fixed panels.

• Easily merge, compare and share panels

• Get coverage data instantly and request a quote

• Our rapid manufacturing process means minimal time between design and delivery

 

Log into the Panel Design Tool at My Nonacus  to start on a design and get a quote.

 

Optimised sequencing performance for NIPD

The baits used in Cell3™ Target are designed to deliver excellent uniformity of coverage. By improving uniformity of coverage and reducing the number of low coverage exons, our Cell3™ Target enrichment optimises sequencing efficiency and sample capacity per sequencing run ultimately reducing your sequencing costs.

Nonacus-Uniformity-of-coverage-ST1
Figure 2. showing Coverage uniformity and % target capture for a 40 Kb panel designed using Cell3™ Target technology and Company (A) High Sensitivity enrichment kit. Targeted enrichment performed on genomic DNA samples and sequenced on the Illumina MiSeq

Figure 2. Coverage uniformity and % target capture for a 40 Kb panel designed using Cell3™ Target technology and Company (A) High Sensitivity enrichment kit. Targeted enrichment performed on genomic DNA samples and sequenced on the Illumina MiSeq

Improved on-target for small and large panels

Most capture target enrichment technologies suffer from a significant percentage of off target sequencing reads when targeting small regions of the genome. Cell3™ Target has been developed so that whether you wish to sequence 1 or 1,000 genes you will find lower off target and more uniform coverage when compared with alternative capture technologies.

 

Product Resources

Detailed product information available to download.





                                                                                                                                         

References

  1. Barrett, A, Zimmerman BG, Wang D, Holloway A, Chitty L. Implementing prenatal diagnosis based on cell-free fetal DNA: Accurate identification of factors affecting fetal DNA yield. PLoS One. 2011;6(10):e25202.
  2. Nigam A, Saxena P, Prakash A, Acharya A.Detection of fetal nucleic acid in maternal plasma: A novel noninvasive prenatal diagnostic technique. J Interntl Med Sci Acad. 2012; 25(3): 119-120.

Publications

van Campen, J., Silcock, L., Yau, S., Daniel, Y., Ahn, J.W., Ogilvie, C., Mann, K. and Oteng‐Ntim, E. (2020), A novel non‐invasive prenatal sickle cell disease test for all at‐risk pregnancies Br J Haematol, 190: 119-124. https://doi.org/10.1111/bjh.16529

Product Support

If you have a query relating to any of our products, including the Fetal RhD Blood Group Genotyping, Nexome, or ExomeCG, please take a look at our FAQs or complete our contact me form and one of our team will get back to you as soon as possible.

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 Custom Panel Extra Small (50-500 probes) Frag 48 Samples NGS_C3C_XS_FR_48
Cell3™ Target Custom Panel Extra Small (50-500 probes) Non Frag 48 Samples NGS_C3C_XS_NF_48
Cell3™ Target Custom Panel Extra Small (50-500 probes) Frag 96 Samples NGS_C3C_XS_FR_96_A/B/C/D*
Cell3™ Target Custom Panel Extra Small (50-500 probes) Non Frag 96 Samples NGS_C3C_XS_NF_96_A/B/C/D*
Cell3™ Target Custom Panel Small (501-1000 probes) Frag 48 Samples NGS_C3C_S_FR_48
Cell3™ Target Custom Panel Small (501-1000 probes) Non Frag 48 Samples NGS_C3C_S_NF_48
Cell3™ Target Custom Panel Small (501-1000 probes) Frag 96 Samples NGS_C3C_S_FR_96_A/B/C/D*
Cell3™ Target Custom Panel Small (501-1000 probes) Non Frag 96 Samples NGS_C3C_S_NF_96_A/B/C/D*
Cell3™ Target Custom Panel Medium (1001-5000 probes) Frag 48 Samples NGS_C3C_M_FR_48
Cell3™ Target Custom Panel Medium (1001-5000 probes) Non Frag 48 Samples NGS_C3C_M_NF_48
Cell3™ Target Custom Panel Medium (1001-5000 probes) Frag 96 samples NGS_C3C_M_FR_96_A/B/C/D*
Cell3™ Target Custom Panel Medium (1001-5000 probes) Non Frag 96 samples NGS_C3C_M_NF_96_A/B/C/D*
Cell3™ Target Custom Panel Large (5001-7500 probes) Frag 48 Samples NGS_C3C_L_FR_48
Cell3™ Target Custom Panel Large (5001-7500 probes) Non Frag 48 Samples NGS_C3C_L_NF_48
Cell3™ Target Custom Panel Large (5001-7500 probes) Frag 96 Samples NGS_C3C_L_FR_96_A/B/C/D*
Cell3™ Target Custom Panel Large (5001-7500 probes) Non Frag 96 Samples NGS_C3C_L_NF_96_A/B/C/D*
Cell3™ Target Custom Panel Extra Large (7501-10000 probes) Frag 48 Samples NGS_C3C_XL_FR_48
Cell3™ Target Custom Panel Extra Large (7501-10000 probes) Non Frag 48 Samples NGS_C3C_XL_NF_48
Cell3™ Target Custom Panel Extra Large (7501-10000 probes) Frag 96 Samples NGS_C3C_XL_FR_96_A/B/C/D*
Cell3™ Target Custom Panel Extra Large (7501-10000 probes) Non Frag 96 Samples NGS_C3C_XL_NF_96_A/B/C/D*
Cell3™ Target Custom Panel Extra Extra Large (10001-25000 probes) Frag 48 Samples NGS_C3C_XXL_FR_48
Cell3™ Target Custom Panel Extra Extra Large (10001-25000 probes) Non Frag 48 Samples NGS_C3C_XXL_NF_48
Cell3™ Target Custom Panel Extra Extra Large (10001-25000 probes) Frag 96 Samples NGS_C3C_XXL_FR_96_A/B/C/D*
Cell3™ Target Custom Panel Extra Extra Large (10001-25000 probes) Non Frag 96 Samples NGS_C3C_XXL_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

Learn more about our products for prenatal testing

Woman having Non-invasive prenatal testing done

Fetal RhD Genotyping kit

The first direct from plasma prenatal diagnosis kit for fetal RhD genotyping.

Exome enrichment for cytogenetics

ExomeCG

Clinically enhanced exome capture for whole exome sequencing and copy number analysis in a single test.

Blue and Green gem in the bottom of test tube

Cell3™ Preserver

A whole blood stabilisation tube for the collection of blood in cell free DNA applications.

cell free DNA extraction, Gloved hand placing test tubes in a centrifuge machine

Cell3™ Extract

A cell free DNA extraction kit that is a fast, accurate and flexible solution to obtain cfDNA directly from plasma.