cfPure® Cell Free DNA Extraction Kit is a magnetic bead-based DNA extraction kit designed to isolate circulating cell free DNA (cfDNA) from human plasma and serum. The kit has a quick, simple, and automation friendly protocol that allows users to quickly extract high quality cfDNA that is ready for use in downstream applications including real-time PCR, digital PCR, and next-generation sequencing.
| Catalog # | Product Name | Sample Volume | Quantity | Manuals | COA | SDS | List Price | Buy Now |
|---|---|---|---|---|---|---|---|---|
| K5011610 | cfPure™ Cell Free DNA Extraction Kit (100 ml) | <1ml - 10ml | 10 - 100 isolations |  | | | $407.00 | Buy Now |
| K5011625 | cfPure™ Cell Free DNA Extraction Kit (250 ml) | <1ml - 10ml | 25 - 250 isolations | | | | $713.00 | Buy Now |
| K5011625MA | cfPure™ MAX Cell Free DNA Extraction Kit (250 ml) | 5ml - 10ml | 25 - 50 isolations | | | | $458.00 | Buy Now |
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 >10mL 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 250mL kit)
- Elution volumes: Range from 15 µL to 50 µL
High cfDNA Quality, Purity and Yield
cfPure® Cell-Free DNA Extraction Kit is BioChain’s new magnetic bead based DNA extraction kit designed to isolate circulating Cell-Free DNA(cfDNA) from plasma, serum, and urine. This kit touts a simple and automation friendly protocol that allows users to quickly extract from range of sample volumes, high quality downstream ready cfDNA.
| Plasma ID | Total DNA Recovered (ng) |
|---|---|
| A | 7.00 |
| A | 7.05 |
| B | 32.45 |
| B | 33.50 |
| C | 26.80 |
| C | 27.70 |
| D | 10.90 |
| D | 10.90 |
cfDNA Kit Yields Reproducible Results
Table 1. To assess reproducibility, DNA was extracted from 1 mL of plasma from 4 different human donors in duplicate using the cfPure® cell free DNA extraction kit.
| Extraction Kit | Sample ID | cfDNA recovered per ml of plasma (ng) |
115 nt ALU sequence cfDNA per ml of plasma (ng) (by PCR) |
|---|---|---|---|
| Competitor T | 1 | 4.99 | 1.97 |
| BioChain’s cfPure | 1 | 6.35 | 2.53 |
| Competitor T | 2 | 6.18 | 3.21 |
| BioChain’s cfPure | 2 | 8.28 | 3.93 |
| Competitor T | 3 | 6.93 | 3.79 |
| BioChain’s cfPure | 3 | 7.50 | 3.87 |
Efficient Recovery of cfDNA Relative to Competition
Table 2. cfDNA was purified from 2 mL of plasma from three different donors by either the cfPure® Cell Free DNA Extraction Kit or by a competitor’s magnetic bead-based cell free DNA extraction kit. DNA recovery was assessed either by a fluorescent method or by qPCR using primers complimentary to ALU sequence DNA.
Figure 1. cfPure® Cell Free DNA Kit was used to isolate DNA from 5 ml of healthy human plasma. 62 ng of cfDNA (150-200 bp fragments) were recovered with low amounts of gDNA contamination.
Figure 2. cfDNA was extracted from the plasma of two human donors using various sample volumes(.2, .5, 1, 5, 10ml). The cfDNA yield was then quantitated by Qubit High Sensitivity DNA assay. The yields were plotted against the starting sample volumes and the R2 values of their trend lines were calculated.
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, Mapping rate, Whole genome coverage, Substitution rates and GC bias.
Figure 3. Number of reads against the length of the inserts. Each curve represents average of 4 samples from the same extraction method.
Figure 4. The percentage of coverage or depth in a GC bin is calculated by dividing the number of reads of a particular GC content by the mean number of reads of all GC bins. A number of 1 represents mean coverage, a number less than 1 represents lower than mean coverage while a number greater than 1 represents higher than mean coverage.
Automation Ready
cfPure® Cell Free DNA extraction kit is applicable on both the KingFisher™ 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.
Figure 5. cfDNA was purified from 4 mLs of EDTA plasma, using the KingFisher Flex automated purification system and either BioChain’s cfPure® system (cfPure KingFisher), or a competitor’s kit (Competitor T KingFisher). Both automated extraction methods were compared with extractions done manually with cfPure® (cfPure Manual). cfDNA recovery was assessed by qPCR, using primers complementary to ALU repeat sequences.
Specifications
| Sample Type (General): | Liquid Samples (e.g. Serum), dsDNA |
| High Throughput Compatibility: | Automated Protocols |
| Downstream Application: | Next-Generation Sequencing, PCR, Real-Time PCR |
| Product Line: | cfPure® |
| Product Size: | 1 kit |
| Shipping Condition: | Room Temperature |
Kit Contents
| K5011610 | K5011625 | K5011625MA |
|---|---|---|
| 2 x 1.33 mL cfPure Cell Free DNA Magnetic Beads | 5 x 1.33 mL cfPure Cell Free DNA Magnetic Beads | 5 x 1.33 mL cfPure Cell Free DNA Magnetic Beads |
| 1 x 115 mL cfPure Cell Free DNA Lysis/Binding Solution | 3 x 95 mL cfPure Cell Free DNA Lysis/Binding Solution | 1 x 95 mL cfPure Cell Free DNA Lysis/Binding Solution |
| 2 x 55 mL cfPure Cell Free DNA Wash Solution | 5 x 55 mL cfPure Cell Free DNA Wash Solution | 1 x 65 mL cfPure Cell Free DNA Wash Solution |
| 1 x 6 mL cfPure Cell Free DNA Elution Solution | 1 x 15 mL cfPure Cell Free DNA Elution Solution | 1 x 15 mL cfPure Cell Free DNA Elution Solution |
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.
First Step to Non-Invasive Disease State Detection
Cell free DNA offers a library of information for the non-invasive detection of cancer and prenatal genetic testing, find out more. cfDNA is present in the human blood at varying levels, from 1 to 100 ng per ml of plasma. The size of cell free DNA is typically 100 bp to 500 bp in length (with most fragments being about 160-180 bp long), making traditional DNA extraction difficult. 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. Lastly, while cfPure® employs a magnetic bead-based DNA extraction method, the recovered cell free DNA performs identically in sensitive applications, such as Next Generation Sequencing, to current spin column based cfDNA kits on the market.