Fast & Flexible Cell-Free DNA Extraction Kit
Our cfDNA extraction kit is a fast, accurate and flexible solution designed to optimise cell-free DNA extraction from plasma.
Fast and flexible
Cell3™ Xtract has a simple and flexible protocol that requires no specialist equipment and with just 90 minutes of processing time will speed up your extractions.
Maximise sample input
Whether you are working with 1ml or 10ml you can extract all cfDNA in one extraction. With a small elution volume of just 35ul you can avoid the need for a DNA concentration step.
Supports multiple uses
Isolate cfDNA from a wide range of samples types: plasma, cerebrospinal fluid (CSF), saliva and amniotic fluid.
Efficient cfDNA extraction without carrier RNA ensures accurate quantification of your extracted cfDNA for sensitive downstream applications like NGS.
Optimsing cell-free DNA extraction from plasma
The utility of cell-free DNA (cfDNA) in both translational research and diagnostic settings has increased dramatically since its discovery. CfDNA is typically found in short fragment sizes of ~160 bp and low quantities of 1 to 100 ng/ml in plasma. It is therefore critical that sufficient cfDNA of good quality can be extracted for downstream applications like NGS and qPCR.
To address this need Nonacus has developed a fast, accurate and flexible cfDNA extraction protocol designed to optimise cfDNA extraction from plasma and maximise yield.
Large volume cell-free DNA extraction
Cell3™ Xtract has a simple and flexible workflow which allows 1-10 ml of biological sample to be processed within 90 minutes.
Obtain higher concentration cfDNA
With a small elution volume of just 35ul, regardless of your starting volume, you can avoid the need for a DNA vacuum concentration step. This means you can add more cfDNA to your downstream applications including ddPCR and NGS enabling more sensitive detection of variants.
Accurate quantification of cfDNA
Accurate quantification of extracted cfDNA is important for downstream applications, particularly Next Generation Sequencing (NGS) where input amounts for assays can be critical. Many companies use carrier RNA to improve cfDNA extraction which can lead to an overestimate of cfDNA quantification and compromise the effectiveness of NGS library preparation.
The Cell3™ Xtract kit does not require carrier RNA to optimise cfDNA isolation enabling accurate quantification of cfDNA and efficient library preparation.
Superior technical performance
We compared Cell3™ Xtract to spin column and bead-based cfDNA extraction kits from four other companies (companies Q, A, O, M).
Using cfDNA extracted from 1ml plasma from a pregnant woman carrying a male fetus, qPCR, DNA concentration and fragment size analysis showed that, in the majority of cases, Cell3™ Xtract outperformed other manufacturers.
Figure 1. Column-based extraction kits: qPCR data revealed that the Cell3™ Xtract kit performed on par with the Company Q kit and outperformed the Company A kit. However, the use of carrier RNA in the Company Q kit resulted in a 50-fold higher DNA concentration measurement and the appearance of a high molecular weight peak in the fragment analysis electropherogram.
Figure 2. Bead-based extraction kits: qPCR and DNA concentration data showed that the Cell3™ Xtract kit performed better than the Company M kit and on par with the Company O kit.
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Our own lab validated protocol uses a different sample "spin-down" protocol than the Nonacus recommendation. In our lab the second spin is 3000 g for 20 minutes, however the Nonacus protocol suggests a minimum of 10000 g for 10 minutes. We would like to run all samples together using the same protocol. Do you have any experience using different plasma isolation parameters and is the one we use still suitable for use with Cell3™ Xtract?
The protocol you are using would still work fine to remove excess intact cells in the 2nd spin however, it may not remove cell debris which usually floats around in plasma and requires higher speeds to pellet. In order to get a cleaner plasma sample, we recommend you perform the second spin at 10,000g or higher. Nevertheless, the Cell3 Xtract kit will still work with either isolation protocol.
We regularly see a slight pink colouration to plasma that is extracted from our Cell3 Preserver tubes. This is nothing to worry about. Our tubes protect and prevent white blood cells (containing DNA) from breaking down, however they do not prevent completely the red cells with thinner walls (not containing DNA) from breaking down. The pink colour is due to some of the red blood cells breaking open and this does not affect or create any gDNA contamination.