NextPrep-Mag cfDNA Automated Isolation Kit

  • Ideal for extracting cfDNA from up to 5 mL human plasma and serum for cell-free DNA sequencing and other downstream applications
  • Automation friendly, magnetic bead-based format without compromising purity or  yields
  • Supported on the chemagic 360 instrument
  • Fast, 15 – 30 minute hands-on-time and approximately 1.5 hour turnaround for 24 samples using a 24-rod head or 96 samples using a 96-rod head

Independent Analysis of cfDNA Isolation Solutions

An independent study was published in which four commercial cfDNA extraction kits were evaluated for liquid biopsies based on yield, scalability, turnaround time for processing, and cost effectiveness. Based on these criteria, the NEXTPrep-Mag™ cfDNA isolation kit was chosen.

Sisson, B. A., et al (2019) Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitor™ Assay. Biomarker Insights, 14, 117727191982654. doi:10.1177/1177271919826545.

Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitorTM Assay

Download 24 Rod Head Automation Manual
Download 96 Rod Head Automation Manual
NextPrep-Mag cfDNA Isolation Kit <1 mL-3 mL manual
NextPrep-Mag cfDNA Isolation Kit 3 mL-5 mL manual
For research use only. Not for use in diagnostic procedures. This product should be used in accordance with all applicable laws and regulations, including without limitation, any consumption and disposal requirements under the European REACH regulations (EC 1907/2006).

  • NOVA-3825-01


    1-3 mL | 16-50 ISOLATIONS

  • NOVA-3825-03


    3-5 mL | 50 ISOLATIONS

  • NOVA-3825-05


    5 mL | 240 ISOLATIONS

  • NOVA-3825-06


    5 mL | 48 ISOLATIONS

  • NOVA-3825-10


    1.5 mL | 960 ISOLATIONS

Complete Solution for Isolation of Circulating DNA from Plasma
for Downstream Applications

The NextPrep-Mag cfDNA Automated Isolation Kit is a complete solution for automated cell-free DNA extraction from human blood plasma or serum using the PerkinElmer chemagic 360 instrument.

The challenges of extraction of cfDNA from plasma or serum are rooted in the fact that the circulating DNA is highly fragmented and present at low concentrations, especially in healthy individuals. The NextPrep-Mag cfDNA automated isolation kit was developed to facilitate the workflow demands for high throughput labs while delivering optimal results.

The NextPrep-Mag cfDNA automated isolation kit allows for the extraction of cell-free DNA from human blood plasma or serum  using the chemagic 360 instrument. The kit is all-inclusive and contains ready-to-use reagents and disposable plastics for 240 automated cfDNA isolations from up to 5 mL of starting plasma/serum on a 24-rod head system and 960 isolations from up to 1.5 mL on a 96-rod head system. The cfDNA recovered can be used in a wide variety of downstream applications including next-gen sequencing and PCR analysis.

The cfDNA isolated with the NextPrep-Mag cfDNA kits have been verified to be compatible with manual and automated NGS library construction on the Sciclone® G3 NGSx workstation and the Zephyr® NGS workstation using the NEXTFLEX® Cell-Free DNA-Seq kit 2.0 for Illumina® sequencing.

Automated cfDNA Isolation Protocol

The automated process allows for a significant decrease in total turnaround time and hands on time compared to current manual and partially automated solutions on-market.


workflow protocol separator


workflow protocol separator


workflow protocol separator


NextPrep-Mag cfDNA Automated Isolation Kit Design Highlights

The kit offers a number of key advantages over other commercially available cfDNA extraction kits, including speed of cfDNA extraction while delivering robust yields and high concentration NGS libraries.

* For compatibility information for the chemagic Prime® instrument, please contact [email protected].

Attributes NextPrep-Mag cfDNA Automated Isolation Kit
Approximate Turnaround Time
(24 samples)
1 hr 15 min
Approximate Hands-on Time ~15 mins for 24 samples
Isolation Method Magnetic beads
Temperature Consideration Reagents shipped & all steps performed at room temperature
Automated Extraction Platforms chemagic 360 instrument*
Automated Prep Platform Sciclone® and Zephyr® G3 NGSx Workstations
Number of Heating Steps None
Number of Steps on Ice None
Carrier RNA Requirement No
User Supplied Alcohol Requirement No, included in kit
Plasma Input chemagic™ 360 instrument – 5 mL on a 24-rod head system and 1.5 mL on a 96-rod head system

NextPrep-Mag cfDNA Automated Isolation Kit Performance

The kit generated robust cfDNA recovery from both plasma and serum on the chemagic 360 and chemagic MSM I platforms as analyzed with electropherogram traces and Qubit® spectrophotometer.

cfDNA Fig1

Figure 1: Performance on the chemagic 360 Instrument. cfDNA was extracted from plasma (PL) or serum (SER) from 5 donors. (A) Yields were quantified electropherogram traces (for mononucleosome peak) and Qubit® spectrophotometer (for total DNA yield). (B) Overlay traces of triplicate 4 mL extractions.

cfDNA Fig2

Figure 2: The NextPrep-Mag cfDNA Automated Isolation Kit is robust on the chemagic MSM I instrument. Blood from different donors was collected in either (A) SST tubes or (B) Streck BCT tubes and extracted for serum. Serum was pooled from each collection method and 5 mLs were extracted using the automated protocol.

cfdna figure 3

Figure 3: cfDNA extraction yields and profiles. cfDNA was extracted in triplicate on 2 separate days from 1 mL of plasma in 2 K2EDTA and 2 Streck® BCT® tubes using NextPrep-Mag chemistry.  Yields were quantified using the Thermo Fisher® Scientific Qubit® HS DNA assay (left).  DNA profiles were observed using the PerkinElmer NGS3K assay on a LabChip® GXII Touch instrument (right).

Downstream sequencing application of cfDNA extracted using the NextPrep-Mag chemistry

cfDNA Fig3

Figure 4: Sequencing results from cfDNA extracted using NextPrep-Mag chemistry shows good concordance with expected mutation frequencies (A, B).

NextPrep-Mag cfDNA Automated Isolation Kit Citations

Sisson, B. A., Uvalic, J., Kelly, K., Selvam, P., Hesse, A. N., Ananda, G., . . . Reddi, H. V. (2019). Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitorTM Assay. Biomarker Insights,14, 117727191982654. doi:10.1177/1177271919826545


    • cfDNA Lysis/Binding Solution
    • cfDNA Proteinase K
    • cfDNA Magnetic Beads
    • cfDNA Wash 1 Solution
    • cfDNA Wash 2 Solution
    • cfDNA Elution Solution (10 mM Tris/0.1 mM EDTA, pH 8)
  • chemagic 360 PLATFORM PLASTICS
    • Disposable tips
    • Rod-head specific plates, tubes, and elution tubes/plates
    • Please refer to respective protocol guides for details on plastics


  • Distilled deionized water used to dissolve Proteinase K
  • Vortex mixer
  • Pipettors
  • 5 mL disposable pipets


  • Please refer to respective protocol guides for details for each rod-head configuration
Do we need special equipment to process large volumes of plasma?

No, the same kind of clinical centrifuges are used. For Input volumes less than or above 5 mL, slight modifications to the protocol may be required. Please inquire directly to [email protected]

What is the size distribution of cell free DNA recovered from human plasma?

The cell free DNA isolated from plasma of healthy donors, typically runs as a single small “hump” of ~ 150 bp when analyzed directly on an Agilent 2100 high sensitivity DNA chip. When the cell free DNA is converted into a library using the ligation-based format in the NEXTflex® Cell Free DNA-Seq Library Prep Kit, a greater range of sizes of library products is observed, from ~ 300 bp – 5,000 bp. The 5’ and 3’ adapters used to make the library add a total of ~150 bp. This indicates that cell free DNA fragments present at concentrations too low to be visualized directly are detectable after the amplification step used to create cell free DNA libraries.

Is it necessary to add carrier nucleic acid or glycogen when processing plasma to recover cell free DNA?

No. Addition of nucleic acid carrier compromises quantification and use of the cell free DNA as input for NGS libraries.

How many PCR cycles are needed to make cell free DNA libraries?

We typically use 9 – 12 PCR cycles for making cell free DNA libraries.

The NextPrep-Mag™ cfDNA Automated Isolation Kit is all-inclusive and contains ready-to-use reagents and disposable plastics for 240 automated cfDNA isolations from up to 5 mL of starting plasma/serum on a 24-rod head system, and 960 isolations from up to 1.5 mL on a 96-rod head system. The kit components are stable for at least 12 months from time of receipt, when properly stored.

Contact an cfDNA Expert