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MagMAX Cell-Free DNA (cfDNA) Isolation
Scalable extraction of circulating cfDNA with magnetic bead technology
- Isolate 6 to 24 samples of cell-free DNA in 45-60 minutes when used with KingFisher instrument
- Designed for enrichment of small (<300 bp) circulating DNA, not gDNA, from blood, plasma, and serum, which means increased recovery and lower starting volumes
- Wide range of sample input volumes (500 µL to 10 mL) of plasma, serum, or urine
- Elution volumes ranging from 15 µL to 50 µL, compatible with Ion Torrent Oncomine assays, or other real-time PCR, digital PCR, and NGS platforms
Liquid biopsy workflow
Use this kit with KingFisher instruments and Oncomine assays to optimize the liquid biopsy workflow from extraction and purification to analysis.
Optimized for cell-free DNA
Cell-free DNA (cfDNA) refers to all non-encapsulated DNA within the blood stream or sample. Magnetic beads and optimized chemistry means a more efficient nucleic acid isolation that specifically recovers the circulating cfDNA while leaving the larger DNA molecules behind. This aspect of enrichment for the cfDNA portion of the nucleic acid ensures that the shorter, fragmented DNA is concentrated and ready for downstream analysis using real-time PCR, digital PCR, or next-generation sequencing.
Beads are better
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.
Dynabeads inside
MagMAX kits leverage Dynabeadsfor sample extraction, the best beads in the industry. The Dynabeads MyOne Silane contained in the MagMAX Cell-Free DNA Isolation Kit have an optimized silica-like surface chemistry with high specific surface area that allows efficient kinetics and high sensitivity in nucleic acid capture. These aspects make Dynabeads MyOne Silane ideal for the recovery of circulating cfDNA targets present at low concentrations in cell-free body fluids. Once captured, these rare DNA fragments can then be eluted in small elution volumes of 15 µL to 50 µL and are ready for downstream applications.
 Applied Biosystems MagMAX Cell-Free DNA Isolation Kit Order now | |
| Sample type | Serum, plasma, and urine |
| Sample input volume | 0.5–10 mL plasma, 0.1–10 mL serum, 10 mL of urine |
| Yield | 40–50 ng from 4 mL plasma |
| Elution volume | 15–50 μL |
| Total processing time | 45–55 min total (10–15 min hands-on time) |
| Reactions (rxn) | 50 rxn for 2 mL plasma input 25 rxn for 4 mL plasma input |
| Shipping conditions | Room temperature |
| Kit contents | 1.5 mL MagMAX Cell Free DNA Magnetic Beads 125 mL MagMAX Cell Free DNA Lysis/Binding Solution 100 mL MagMAX Cell Free DNA Wash Solution 5 mL MagMAX Cell Free DNA Elution Solution |
| Cat. No. | A29319 |
Read our application notes
Click image to enlarge
Figure 1. Efficiency of short DNA recovery. cfDNA is highly fragmented with the major fraction around 170 bp. To examine DNA size-dependent recovery, 50 bp DNA Ladder was spiked into 4 mL of commercially available plasma that was depleted of endogenous cfDNA. 50 µL of 2 ng/µL DNA Ladder was spiked in and 60 µL Dynabeads MyOne SILANE was added into the cfDNA-depleted plasma. DNA was eluted in 50 µL after the binding and washing steps. 1 µL of ladder and 1 µL of the extracted DNA sample were run on the Agilent Bioanalyzer 2100 with HS dsDNA chip to assess recovery efficiency of the MagMAX cfDNA Isolation Kit. Approximately 100% of cfDNA ranging from 100 to 750 bp was recovered, while less efficient elution of DNA ≥800 bp is observed. This efficient recovery of dsDNA <800 bp yields eluted DNA samples specifically enriched for cfDNA.
Figure 2. Reproducibility of cfDNA recovery. To examine reproducibility, cfDNA was extracted from 4 mL plasma and eluted in 50 µL. Plasma samples from 4 samples were processed in duplicate. 20 µL of extracted DNA was analyzed with 2% E-Gel EX Agarose Gel. Each replicate set showed the same yield of cfDNA with the ~170 bp ribosomal monomer unit clearly visible.
Click image to enlarge
Figure 3. Automation friendly. Processing up to 5 mL of plasma input can be automated with the KingFisher Flex (24 samples per run) or the KingFisher Duo Prime (6 samples per run) systems. Enriched cfDNA samples are ready in ~40 minutes after reagents and plasma samples are loaded into the KingFisher plates. Using the MagMAX cfDNA kit, both KingFisher automated enrichment systems and manual processing demonstrate similar enrichment performance. 4 mL per sample was processed from 4 samples, and the eluted DNA was loaded onto a DNA HS chip and run on the Agilent Bioanalyzer 2100. The overlapping traces of the KingFisher Flex (red) and KingFisher Duo (blue) indicate similar recovery performance. The yield and size profile are approximately equivalent for all 4 samples.
Click image to enlarge
Figure 4. Scalability. Sample volume processed and DNA recovered are highly scalable using the MagMAX cfDNA kit. Double-stranded DNA (dsDNA) of 120 bp and 170 bp in length were spiked into plasma samples at varying input amounts ranging from 10 ng to 200 ng. Consistent, efficient recovery of both DNA spikes is observed over the input range (Panel A). To demonstrate sample volume scalability, cfDNA from 4 mL and 10 mL plasma samples from the same sample were isolated. As expected, DNA yield from 10 mL plasma was ~2.5X greater than that from the 4 mL plasma sample (Panel B & C), while total protein carryover only marginally increased (Panel D).
Figure 5. Protein carryover. Protein contamination in DNA extracted with the two isolation methods was quantified with Qubit Protein Assay. The MagMAX samples show considerably less protein carryover as compared to Kit Q even though the MagMAX protocol does not use Proteinase K, while Kit Q starts with a 30 minute Proteinase K digestion at 60°C.
Protocols for cfDNA extraction
Download protocols for cfDNA extraction on KingFisher Flex and Duo instruments.
| Protocol type | KingFisher Duo | KingFisher Flex |
|---|---|---|
| 2 mL script | MagMAX cfDNA-2mL-DUO.bdz | MagMAX cfDNA-2mL-Flex.bdz |
| 4 mL script | MagMAX cfDNA-4mL-DUO.bdz | MagMAX cfDNA-4mL-Flex.bdz |
| 600 μL script | - | KingFisher File: MagMAX-cfDNA-600ul-Flex96R-V1.bdz |
| Standard | KingFisher Duo Protocol MagMAX cfDNA | KingFisher Flex Protocol MagMAX cfDNA |
Related products for cancer research
MagMAX kits purify high-quality nucleic acids from cell-free samples suitable for a range of research applications, including next-generation sequencing (NGS), qPCR, and digital PCR.
 MagMAX Cell-Free Total Nucleic Acid Isolation Kit Purify free-circulating DNA, RNA, and miRNA Order now |  MagMAX FFPE DNA/RNA Ultra Kit Sequential isolation of Order now | |
| Sample volumes | 1.0–6 mL plasma | 5–40 µm standard input of slides or curls |
| Elution volumes | 15–60 μL | 20–50 µL |
| Time per run | 90 minutes total, 10–15 min hands-on time with KingFisher instruments | 20 min for DNA, 48 min for RNA |
| Automation/HT |
|
|
| Cat. No. | A36716 | A31881 |
Liquid biopsy workflow
Use this kit with KingFisher instruments and Oncomine assays to optimize the liquid biopsy workflow from extraction and purification to analysis.
Optimized for cell-free DNA
Cell-free DNA (cfDNA) refers to all non-encapsulated DNA within the blood stream or sample. Magnetic beads and optimized chemistry means a more efficient nucleic acid isolation that specifically recovers the circulating cfDNA while leaving the larger DNA molecules behind. This aspect of enrichment for the cfDNA portion of the nucleic acid ensures that the shorter, fragmented DNA is concentrated and ready for downstream analysis using real-time PCR, digital PCR, or next-generation sequencing.
Beads are better
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.
Dynabeads inside
MagMAX kits leverage Dynabeadsfor sample extraction, the best beads in the industry. The Dynabeads MyOne Silane contained in the MagMAX Cell-Free DNA Isolation Kit have an optimized silica-like surface chemistry with high specific surface area that allows efficient kinetics and high sensitivity in nucleic acid capture. These aspects make Dynabeads MyOne Silane ideal for the recovery of circulating cfDNA targets present at low concentrations in cell-free body fluids. Once captured, these rare DNA fragments can then be eluted in small elution volumes of 15 µL to 50 µL and are ready for downstream applications.
Applied Biosystems MagMAX Cell-Free DNA Isolation Kit Order now | |
| Sample type | Serum, plasma, and urine |
| Sample input volume | 0.5–10 mL plasma, 0.1–10 mL serum, 10 mL of urine |
| Yield | 40–50 ng from 4 mL plasma |
| Elution volume | 15–50 μL |
| Total processing time | 45–55 min total (10–15 min hands-on time) |
| Reactions (rxn) | 50 rxn for 2 mL plasma input 25 rxn for 4 mL plasma input |
| Shipping conditions | Room temperature |
| Kit contents | 1.5 mL MagMAX Cell Free DNA Magnetic Beads 125 mL MagMAX Cell Free DNA Lysis/Binding Solution 100 mL MagMAX Cell Free DNA Wash Solution 5 mL MagMAX Cell Free DNA Elution Solution |
| Cat. No. | A29319 |
Read our application notes
Click image to enlarge
Figure 1. Efficiency of short DNA recovery. cfDNA is highly fragmented with the major fraction around 170 bp. To examine DNA size-dependent recovery, 50 bp DNA Ladder was spiked into 4 mL of commercially available plasma that was depleted of endogenous cfDNA. 50 µL of 2 ng/µL DNA Ladder was spiked in and 60 µL Dynabeads MyOne SILANE was added into the cfDNA-depleted plasma. DNA was eluted in 50 µL after the binding and washing steps. 1 µL of ladder and 1 µL of the extracted DNA sample were run on the Agilent Bioanalyzer 2100 with HS dsDNA chip to assess recovery efficiency of the MagMAX cfDNA Isolation Kit. Approximately 100% of cfDNA ranging from 100 to 750 bp was recovered, while less efficient elution of DNA ≥800 bp is observed. This efficient recovery of dsDNA <800 bp yields eluted DNA samples specifically enriched for cfDNA.
Figure 2. Reproducibility of cfDNA recovery. To examine reproducibility, cfDNA was extracted from 4 mL plasma and eluted in 50 µL. Plasma samples from 4 samples were processed in duplicate. 20 µL of extracted DNA was analyzed with 2% E-Gel EX Agarose Gel. Each replicate set showed the same yield of cfDNA with the ~170 bp ribosomal monomer unit clearly visible.
Click image to enlarge
Figure 3. Automation friendly. Processing up to 5 mL of plasma input can be automated with the KingFisher Flex (24 samples per run) or the KingFisher Duo Prime (6 samples per run) systems. Enriched cfDNA samples are ready in ~40 minutes after reagents and plasma samples are loaded into the KingFisher plates. Using the MagMAX cfDNA kit, both KingFisher automated enrichment systems and manual processing demonstrate similar enrichment performance. 4 mL per sample was processed from 4 samples, and the eluted DNA was loaded onto a DNA HS chip and run on the Agilent Bioanalyzer 2100. The overlapping traces of the KingFisher Flex (red) and KingFisher Duo (blue) indicate similar recovery performance. The yield and size profile are approximately equivalent for all 4 samples.
Click image to enlarge
Figure 4. Scalability. Sample volume processed and DNA recovered are highly scalable using the MagMAX cfDNA kit. Double-stranded DNA (dsDNA) of 120 bp and 170 bp in length were spiked into plasma samples at varying input amounts ranging from 10 ng to 200 ng. Consistent, efficient recovery of both DNA spikes is observed over the input range (Panel A). To demonstrate sample volume scalability, cfDNA from 4 mL and 10 mL plasma samples from the same sample were isolated. As expected, DNA yield from 10 mL plasma was ~2.5X greater than that from the 4 mL plasma sample (Panel B & C), while total protein carryover only marginally increased (Panel D).
Figure 5. Protein carryover. Protein contamination in DNA extracted with the two isolation methods was quantified with Qubit Protein Assay. The MagMAX samples show considerably less protein carryover as compared to Kit Q even though the MagMAX protocol does not use Proteinase K, while Kit Q starts with a 30 minute Proteinase K digestion at 60°C.
Protocols for cfDNA extraction
Download protocols for cfDNA extraction on KingFisher Flex and Duo instruments.
| Protocol type | KingFisher Duo | KingFisher Flex |
|---|---|---|
| 2 mL script | MagMAX cfDNA-2mL-DUO.bdz | MagMAX cfDNA-2mL-Flex.bdz |
| 4 mL script | MagMAX cfDNA-4mL-DUO.bdz | MagMAX cfDNA-4mL-Flex.bdz |
| 600 μL script | - | KingFisher File: MagMAX-cfDNA-600ul-Flex96R-V1.bdz |
| Standard | KingFisher Duo Protocol MagMAX cfDNA | KingFisher Flex Protocol MagMAX cfDNA |
Related products for cancer research
MagMAX kits purify high-quality nucleic acids from cell-free samples suitable for a range of research applications, including next-generation sequencing (NGS), qPCR, and digital PCR.
MagMAX Cell-Free Total Nucleic Acid Isolation Kit Purify free-circulating DNA, RNA, and miRNA Order now | MagMAX FFPE DNA/RNA Ultra Kit Sequential isolation of Order now | |
| Sample volumes | 1.0–6 mL plasma | 5–40 µm standard input of slides or curls |
| Elution volumes | 15–60 μL | 20–50 µL |
| Time per run | 90 minutes total, 10–15 min hands-on time with KingFisher instruments | 20 min for DNA, 48 min for RNA |
| Automation/HT |
|
|
| Cat. No. | A36716 | A31881 |
How to purify circulating cell-free DNA (cfDNA)
Learn how to perform manual and automated purification of circulating cell-free DNA from plasma samples.
MagMAX Cell-Free DNA Isolation Kit
The magnetic bead-based purification format of this kit allows you to easily process a wide range of sample input volumes (500 µL to 10 mL). When used with the Thermo Scientific KingFisher Duo Prime or KingFisher Flex Magnetic Particle Processor, 6 to 24 plasma/serum samples of 2 mL input volume can be isolated at once. Alternatively, samples can be processed manually with the use of a magnetic stand.
The MagMAX Cell-Free DNA Isolation Kit offers you:
- Automation-ready, phenol-free extraction
- Fast procedure that allows 6 to 24 samples to be processed in 40 minutes or less when used with the KingFisher Duo Prime or KingFisher Flex with a 24 Deep-Well Head
- Flexible protocol that accommodates sample volume inputs ranging from 500 µL to 10 mL of plasma, serum, or urine
- Advantage of MagMAX technology based on Invitrogen Dynabeads MyOne Silane for consistent isolation of cell-free DNA
- Elution volumes ranging from 15 µL to 50 µL
Unlock a wealth of information with the enrichment of cell-free DNA
Isolating and analyzing circulating cell-free DNA (cfDNA) from plasma, serum, or urine has the potential to serve as a non-invasive approach to detect and monitor targets associated with certain disease states such as cancer.
The first step in attaining this valuable information is efficient nucleic acid isolation that specifically recovers the circulating cfDNA while leaving the larger DNA molecules behind. This aspect of enrichment for the cfDNA portion of the nucleic acid ensures that the shorter, fragmented DNA is concentrated and ready for downstream analysis using real-time PCR, digital PCR, or next-generation sequencing.
The MagMAX Cell-Free DNA Isolation Kit is designed for both manual and automated isolation of cfDNA from a wide sample volume input range (0.5 mL to 10 mL). The phenol-free, magnetic bead format makes the kit fully amenable to automated isolation.
Thanks to the scalable format that allows for various sample inputs, it is possible to vary the number of samples processed with a single kit. For example, sufficient reagents are provided in each kit to process 50 samples of 2 mL plasma or serum each. Alternatively, one can process 25 samples of 4 mL plasma or serum each. Input volumes can be scaled up or down as desired, with the only effect being to change the total number of samples that can be processed. This feature of the kit empowers scientists to tailor the procedure to their specific needs.
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