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 from blood, plasma, serum, not gDNA, 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

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Liquid Biopsy workflow

Use this kit with KingFisher instruments and Oncomine Assays to optimize the liquid biopsy workflow from extraction and purification to analysis.

Liquid Biopsy workflow

Optimized for Cell-free DNA

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

We chose the industry’s best beads for our MagMAX kit. 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
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
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.
Reproducibility of cfDNA recovery
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.
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. Four 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.
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).
Protein carryover

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.

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 DNA & RNA from the FFPE tissue sample
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
  • 50 samples for 2mL plasma input
  • 25 samples for 4mL plasma input
  • 48 samples for sequential DNA and RNA
  • 96 samples for DNA or RNA only
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.

Liquid Biopsy workflow

Optimized for Cell-free DNA

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

We chose the industry’s best beads for our MagMAX kit. 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
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
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.
Reproducibility of cfDNA recovery
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.
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. Four 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.
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).
Protein carryover

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.

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 DNA & RNA from the FFPE tissue sample
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
  • 50 samples for 2mL plasma input
  • 25 samples for 4mL plasma input
  • 48 samples for sequential DNA and RNA
  • 96 samples for DNA or RNA only
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.