High Yield Cell-Free DNA (cfDNA) Extraction from Plasma for Liquid Biopsy

cfDNA in plasma

Learn more basics about Cell-free DNA (cfDNA) Extraction.

MagVigen™ Plasma cfDNA Extraction Kit Cat# K61003

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MagVigen™ – Plasma cfDNA Extraction Kit For DNA extraction from plasma samples. Proteinase K and buffer included.
Product Sheet
K61003-
Sizes (Plasma)

MagVigen™ Plasma cfDNA Extraction Kit (Cat# K61003) is specially designed to capture, extract cell-free DNA (cfDNA), also called as circulating free DNA, from Plasma or Serum with no need of column or centrifugation.

Citations:

  1. Giant Magnetoresistive Nanosensor Analysis of Circulating Tumor DNA for Therapy Response Monitoring and Early Detection of Cancer
  2. Giant Magnetoresistive Nanosensor Analysis of Circulating Tumor DNA Epidermal Growth Factor Receptor Mutations for Diagnosis and Therapy Response Monitoring
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How to extract cell-free DNA (cfDNA)?

nvigen cfdna extration workflow (kit 61003)

Figure 1. cfDNA Extraction workflow.

  1. Lyse: Lyse plasma sample.
  2. Bind & Capture: Mix MagVigen™ nanoparticles with sample. Nanoparticles bind to the cfDNA fragments.
  3. Pellet & Re-disperse 1: Magnetic pellet the beads until the solution is clear. The beads respond to a magnetic force (by use of a magnet, e.g. magnetic separation rack), allowing bound material to be rapidly and efficiently separated from the rest of the sample. Remove supernatant (unbound materials) by aspiration, what remains is the nanoparticle-bound targets. Then re-disperse beads pellet in Wash 1 Buffer.
  4. Transfer: Transfer Wash 1 Solution to 1.5 or 2ml tube.
  5. Pellet & Re-disperse 2: Magnetic pelleting, remove supernatant as in step 3. This time re-disperse the beads pellet in 75% Ethanol.
  6. Wash & Pellet 2,3: Wash the beads pellet using 75% Ethanol. Pellet the beads and remove all supernatant. Re-disperse the beads pellet in 75% Ethanol. Do this step twice.
  7. Elute: Final elution of high quality cfDNA. Ready for downstream NGS, PCR or other Applications.
    2 times of elution can help improve cfDNA yield.

Please refer to the K61003 Product Sheet for further detailed steps.

MagVigen™ cfDNA Extraction workflow can be scaled up linearly from 100 µl to 10 ml of plasma input samples. cfDNA isolated with MagVigen™ cfDNA Extraction kit presents high quality for downstream PCR or sequencing assays. The yield and quality of extracted cfDNA can be significantly better than other methods on market.



And MagVigen™ allows simple and efficient DNA extraction ideal for automation. Learn more about cfDNA/ctDNA in Cancer Detection, Surveillance and Treatment.
nvigen-cfdna-kit-higher-yield-higher-quality-for-pcr-ngs
Figure 2. NVIGEN cfDNA Extraction kit presents higher yield and higher quality for PCR and NGS library.
Higher Yield of cfDNA Extracted with NVIGEN Extraction Kit vs. Q-ccf Extraction Kit
Higher Yield and Quality NGS Library from cfDNA Extracted with  NVIGEN Extraction Kit vs. Q-ccf Extraction Kit.
Figure 3. Clean bioanalyzer profiles showing higher yield and higher quality NGS library from cfDNA extracted with NVIGEN Extraction Kit vs. Q-ccf Extraction Kit.
high-yield-4ml-plasma-input-nvigen-vs-qiagen
Figure 4. Higher yield with 4 ml plasma input.
Efficiency of MagVigen DNA recovery
Figure 5. Efficiency of DNA recovery. Bioanalyzer files of original ladder DNA (red line) and recovered spiked-in ladder DNA after extraction (blue line).
cfDNA extraction yield & size from 1.5 ml plasma samples
Figure 6. cfDNA extraction yield and size from 1.5 ml plasma samples with (blue) and without (red) spiking in DNA. Calculated yield of spiking in DNA by subtraction of endogenous cfDNA from total DNA were 80% using picogreen assay and 91% with bioanalyzer quantification.
Higher capture rate for smaller sizes of cfDNA
Figure 7. Higher capture rate for smaller sizes of cfDNA is possible with NVIGEN MagVigen cfDNA Extraction kit.
magvigen-cfdna-extraction-kit-scalability
Figure 8. The yield of cfDNA increases in proporation to the volume of plasma input. Captured cfDNA was quantified by pico-green analysis.
cfDNA extraction yield quantification MagVigen Plasma DNA Capture Kit vs kit C
Figure 9. cfDNA extraction yield was quantified by pico-green analysis following DNA isolation with the MagVigen™ Plasma cfDNA Extraction Kit and kit C.
PCR analysis Beta-globin level & GAPDH levels
Figure 10. Beta-globin level and GAPDH levels were estimated by PCR analysis.
NIPT Sequencing library construction NIPT Sequencing library construction NIPT Sequencing library construction NIPT Sequencing library construction NIPT Sequencing library construction
Figure 11. NIPT Sequencing library constructed with NVIGEN cfDNA and DNA sizing kits in genomic diagnostic company using real clinical samples.
cfDNA extraction, MagVigen CT=25.4 vs MyOne 28.1

Figure 12. Much better differentiation between patient plasma and normal plasma was achieved using MagVigen cfDNA extraction followed by sequence specific target capture with MagVigen-Streptavidin nanobeads vs. MyOne-Streptavidin beads. The qPCR Ct differences between patient and normal plasma samples were over 9 when using MagVigen-Streptavidin Nanobeads (Cat# K61002) and less than 2 when using MyOne-Streptavidin beads, corresponding to over 100x better differentiation power when referring to ctDNA copy numbers of the original plasma samples of 2^9 vs. 2^2.

 
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