Description

BioChain’s cfPure® Cell Free DNA Extraction Kit is designed for rapid and efficient purification of circulating cell free DNA (cfDNA). The system utilizes silica-coated paramagnetic particles to purify cell free DNA from less than 1 mL to greater than 10 mL of serum or plasma. The buffers were developed to ensure efficient recovery of 100 bp – 500 bp DNA fragments in order to maximize recovery of cell free DNA. The recovered DNA is suitable for a wide range of down-stream applications, such as bisulfite sequencing, NGS, and qPCR.

Applications:

Extract high quality cell free DNA from plasma, serum, and urine for Next Generation Sequencing (NGS), Bisulfite Sequencing, PCR, qPCR, ddPCR and other demanding applications

Advantages and Features:

• Versatile: Extraction from <1mL to >10 mL serum or plasma – in single tubes or 24 to 96-well plates

• Automation Friendly: On both the KingFisher™ and liquid handling instruments, with extractions taking approximately 50 minutes

• Time Efficient: Manual extraction protocol takes less than 75 minutes

• Cost Effective: Competitive price <$3 per extraction from 1 mL plasma (List price for 250 mL kit)

• Elution volumes: Range from 15 µL to 50 µL

Rapid and Efficient Magnetic Bead-Based Protocol

The cfPure® protocol is rapid and easy, allowing users to process several samples in an hour or less and making it ideal for biomarker screening. BioChain has developed its own silica-coated magnetic bead technology, which is designed to efficiently recover low molecular weight cell free DNA during isolation. In addition to being easy to perform, and easy to automate, you can use less magnetic bead solution if you are purifying small amounts of plasma – saving you money. The key to successful analysis of cfDNA is to ensure efficient purification of smaller DNA fragments (100-500 bp). As Figure 1 shows, the cfPure® Cell Free DNA Extraction Kit does efficiently recover these important small fragments.

cfPure – A Scalable Cell Free DNA Extraction Kit:

Cfpure is designed to be a scalable kit (Fig. 2.).  This means that you can use just the amount of beads and reagents that you need for your cfDNA extraction.  This also means that the number of extractions per kit is dependent on the amount of sample you wish to purify DNA from.  For example, if you are working with 1mL samples, our 100mL kit (Catalog # K5011610) can process up to 100 samples, and our 250 mL kit (Catalog # K5011610) can process 250 samples.  If you are working with 10mL samples, our 100mL kit (Catalog # K5011610) can process up to 10 samples, and our 250 mL cell free DNA Extraction kit (Catalog # K5011625) can process 25 samples.

Benefits of cfPure® Magnetic Bead-Based Purification

Magnetic beads offer many benefits compared to other technologies for isolating cfDNA. Beads bind the DNA more efficiently than glass fiber filters, resulting in higher and more consistent yields. Additionally, because filters and vacuum manifolds are not used, there is no risk of cellular particulates clogging these items during the extraction process. This clogging issue is of particular concern with protein-rich, large-volume samples such as plasma that are commonly used in cfDNA studies.

cfDNA Validated with NGS by End Users

cfDNA extracted by cfPure® cfDNA Extraction kit is excellent for downstream applications such as NGS. In a third party study cfDNA was extracted from 10 ml’s of human plasma from 4 donors using BioChain’s cfPure® (B), Competitor T’s(T), and Competitor Q’s (Q, column-based) cfDNA extraction kits. Libraries were then constructed for each sample , and whole genome sequencing was performed . From the data analysis, three extraction methods did not show significant performance difference across the board: Insert size (Fig. 3.), Mapping rate, Whole genome coverage, Substitution rates and GC bias (Fig. 4.).

Reproducible and Efficient Recovery of cfDNA

Our optimized magnetic bead based protocol enables the user to scale the protocol for use with any sample volume from 100 µl to 10 ml with highly reproducible results and efficient cfDNA recovery rate (Table 1 & 2).

cfPure® Cell Free DNA extraction kit is applicable on both the KingFisher™  (Fig. 5. ) and liquid handling instruments. With the KingFisher™ Flex and BioChain’s cfPure® Cell Free DNA Extraction kit can extract up to 96 one ml samples in 50 minutes, or 24 five ml samples in one hour.

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