Apostle MiniMax® High Efficiency Cell-Free DNA Isolation Kit

  • Extracts cell-free DNA (cfDNA) ≥80 bp from plasma, serum or urine samples in manual or automated mode
  • Uses Apostle MiniMax® magnetic nanoparticle technology (no phenol or chloroform needed)
  • Supports various blood collection tubes
  • Yields cfDNA suitable for a broad range of subsequent methods, including sequencing and PCR
  • Enables applications in liquid biopsy research, cancer research and biomarker discovery
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C40605, Apostle MiniMax® High Efficiency Cell-Free DNA Isolation Kit, 5 ml x 50 preps
C40603, Apostle MiniMax® High Efficiency cfDNA Isolation Kit, 1 mL x 50 preps
C40604, Apostle MiniMax® High Efficiency cfDNA Isolation Kit, 1 mL x 10 preps
C43459, Apostle MiniMax® High Efficiency cfDNA Isolation Kit, 4 mL x 384 preps

Apostle MiniMax® cfDNA Extraction Workflow

Apostle MiniMax® cfDNA Extraction Workflow
  1. Lyse the sample
  2. Bind cfDNA to Apostle MiniMax® magnetic nanoparticles
  3. Separate the nanoparticles from contaminants and wash them
  4. Elute cfDNA from the nanoparticles and transfer to a new tube or plate

Data and Performance

Charts demonstrating reproducibility of cfDNA extraction with Apostle MiniMax® High Efficiency cfDNA Isolation Kit

Figure 1. DNA was extracted from 1 mL of plasma collected in cfDNA Tube 1 using the Apostle MiniMax® High Efficiency cfDNA Isolation Kit and Kit A. The extractions represent technical replicates, and both replicates extracted using the Apostle MiniMax® cfDNA Kit were nearly identical. In contrast, the replicates extracted using Kit A had two distinct traces. Isolated cfDNA was characterized using an Agilent Bioanalyzer 2100; the peaks at 35 bp and 10,380 bp are internal markers. Most cfDNA fragments cluster around the 165‑170 bp mononucleosome peak, with additional dinucleosome and trinucleosome peaks near 320‑350 bp and 480‑550 bp, respectively.

Charts demonstrating DNA Ladder recovery from serum with the Apostle Apostle MiniMax® High Efficiency Cell-Free DNA Isolation Kit

Figure 2. Left: DNA ladder was spiked in serum, followed by isolation with the Apostle MiniMax® High Efficiency cfDNA Isolation Kit. The isolated DNA was characterized using an Agilent Bioanalyzer 2100 (red curve), and compared with the original DNA ladder (blue curve). The Apostle MiniMax® Kit offers superior DNA recovery efficiency of >95% across the range of 80‑3,000 bp. Right: DNA ladder was spiked in serum, followed by isolation with the Apostle MiniMax® cfDNA Kit (red curve) and a major alternative product (blue curve). The isolated DNA was characterized using an Agilent Bioanalyzer 2100. The Apostle MiniMax® cfDNA Kit offers superior DNA enrichment efficiency of 2x‑10x.

Charts demonstrating cfDNA extraction efficiency when collecting blood in 3 different tubes an isolating cfDNA with the Apostle MiniMax® High Efficiency Cell-Free DNA Isolation Kit

Figure 3. Apostle MiniMax® High Efficiency cfDNA Isolation Kit was used to extract DNA from 1 mL of plasma collected in three types of stabilization containers, referred to here as cfDNA Tube 1, EDTA Collection Tube, and cfDNA Tube 2. A market-leading column-based kit (Kit A) was also used to extract DNA from 1 mL of plasma from cfDNA Tube 1, EDTA Collection Tube, and cfDNA Tube 2. A second bead-based kit (Kit B) was used to extract DNA from the EDTA Collection Tube. DNA yield was quantified using the Quant‑iT PicoGreen dsDNA assay kit (Thermo Fisher Scientific). The error bars represent the standard deviation of three technical replicates. For each tube type, the Apostle MiniMax® cfDNA Kit extracted a higher total yield of DNA. DNA size was analyzed on an Agilent Bioanalyzer 2100. For all three tube types, the Bioanalyzer traces indicate the DNA extracted correlates with the expected sizes of cfDNA (~170 bp).

qPCR amplification plots demonstrating high efficiency of cfDNA extraction with Apostle MiniMax® High Efficiency Cell-Free DNA Isolation Kit

Figure 4. Left: 20 μL of a 170 bp synthetic DNA fragment containing the EGFR C2573T>G L858R mutation was spiked into 1 mL of TE buffer (blue) or serum (red) at concentrations ranging from 1 ng/μL to 0.001 ng/μL. The Apostle MiniMax® High Efficiency cfDNA Isolation Kit was used to isolate the DNA fragments. A) The qPCR amplification plot shows highly overlapping curves for the isolated DNA fragments and the original synthetic DNA solution at the different concentrations. B) To quantify the amount of DNA that the Apostle MiniMax® cfDNA Kit can recover, a qPCR standard curve was generated using the original synthetic DNA solution. The DNA isolation recovery rate was calculated to be >90% for the Apostle MiniMax® cfDNA Kit. Right: qPCR performance was compared between the Apostle MiniMax® cfDNA Kit and one other market-leading column-based kit (Kit A). The Apostle MiniMax® cfDNA Kit outperformed Kit A for DNA extracted from all three collection tubes presented.

Diagrams demonstrating high yield of cfDNA extraction with Apostle MiniMax® High Efficiency Cell-Free DNA Isolation Kit

Figure 5. Left: DNA isolation from varying volumes of plasma. Nucleosomes were spiked into plasma to ensure enough DNA was present for quality control. The Apostle MiniMax® High Efficiency cfDNA Isolation Kit isolated nearly all the input DNA, while Kit 2 isolated less DNA from larger plasma volumes. Right: Isolation of DNA from 1–5 mL of EDTA plasma. Yields were highest with the Apostle MiniMax® Kit for 3–5 mL, and yields were similar across all kits at 1 mL.

Frequently Asked Questions

cfDNA concentration varies significantly, ranging from 1–100 ng per mL of plasma. In healthy donors, cfDNA concentrations are typically between 1 to 15 ng/mL of plasma.

No. NanoDrop spectrophotometers are not suitable for cfDNA characterization. Due to the low concentration of cfDNA in human plasma, the concentration of isolated cfDNA can be less than 1 ng/µL. The detection limit of a NanoDrop spectrophotometer is 2 ng/µL, which is not suitable for cfDNA measurement in most cases.

The Agilent 2100 Bioanalyzer with the high-sensitivity DNA kit (detection limit 5 pg/μL), or quantitative PCR (detection limit 1%-0.1% copy sensitivity) are sensitive and accurate methods for cfDNA quantification. Fluorometric methods, like Qubit™ or PicoGreen®, can be used for a rough estimation of cfDNA concentration.

Yes, the kit has been demonstrated to work for cfDNA isolation from these fluids. A centrifugation step is required to remove cellular components before cfDNA isolation.

No, the kit can't be used for gDNA isolation from blood. The chemistry of this kit is specifically designed for circulating cell-free DNA isolation from body fluids.

Yes, the kit is a bead-based kit and is automation-agnostic. We have demonstrated it on Biomek i-Series Workstations and KingFisher platforms.

Yes, this is normal. cfDNA concentration varies significantly between different samples, ranging from 1 to 100 ng/mL of plasma. For samples containing low levels of cfDNA, you can increase the starting sample volume. This kit is scalable for flexible input and elution volumes.

This kit has a scalable format for flexible input volumes, from 0.2 mL to 5 mL, or even higher if the container volume capacity allows. The standard protocol included with this kit provides instruction for cfDNA isolation from 1 mL, 2 mL and 5 mL plasma. A supplemental protocol for processing 10 mL plasma is also available.

To prevent gDNA contamination in the eluate, it is important to handle blood samples properly. Delays in processing blood collected in EDTA tubes can lead to cell lysis, which releases gDNA into the plasma. Additionally, ensuring the complete removal of cellular components during the isolation process is crucial to avoid contamination. Be cautious with the storage of whole blood; freezing can lead to significant cell breakage and result in gDNA contamination. Following these best practices can help minimize the risk of gDNA contamination.

Yes. We suggest using 20 μL of elution solution per 1 mL of the initial sample. You can adjust the elution volume when needed.

Still have questions? We’re here to help—reach out anytime.

Specifications

Application Extraction of cfDNA ≥80 bp
Technology Apostle MiniMax® magnetic nanoparticle technology
Recovery > 95%
Sample Amount 1–5 mL (scalable)
Sample types Plasma, serum, urine
Processing mode Automated or manual
Kit Sizes
  • 1 mL x 10 preps
  • 1 mL x 50 preps
  • 5 mL x 50 preps
  • 4 mL x 384 preps
Kit Components and Storage Conditions Magnetic Nanoparticles (2 to 30°C), Proteinase K (2 to 30°C), Sample Lysis Buffer (15 to 30°C, in dark), Lysis Binding Solution (15 to 30°C, in dark), Wash Solution (15 to 30°C, in dark), 2nd Wash Solution (15 to 30°C), Elution Buffer (15 to 30°C)

Citations

These data establish that tumor and cfDNA methylation can be used to identify small cell lung cancer (SCLC) subtypes and might guide precision SCLC therapy... cfDNA was extracted using the Apostle MiniMax High Efficiency Cell-Free DNA Isolation Kit."

Heeke S., Gay C.M., Estecio M.R. et al. Cancer Cell 2024, 42(2):225-237.e5. doi: 10.1016/j.ccell.2024.01.001

Our integrative model detects early-stage cancers, including those of pancreatic origin, with high sensitivity that is comparable to that of late-stage detection... (Methods section) cfDNA was extracted from 0.4 mL plasma ... and eluted in a final volume of 22 μL, using an Apostle MiniMax High Efficiency cfDNA Isolation Kit."

Bae M., Kim G., Lee T.R. et al. Nat Commun 2023, 14(1):2017. doi: 10.1038/s41467-023-37768-3

Exploratory biomarker analyses showed decreased circulating tumor DNA (ctDNA) in patients with prolonged overall survival... cfDNA was extracted from the entire plasma volume of a single draw using the Apostle MiniMax cfDNA Isolation kit."

Palmer C.D., Rappaport A.R., Davis M.J. et al. Nat Med 2022, 28(8):1619-1629. doi: 10.1038/s41591-022-01937-6

The model detected four of the five hepatocellular carcinoma (HCC) cases in the cohort, showing 80% sensitivity and 94% specificity. These findings demonstrate that the MCP technology has potential for the discovery and validation of multiomics biomarkers for the noninvasive detection of cancer. This study also provides a comprehensive database of genetic and epigenetic alterations in the cfDNA of a large cohort of HCC cases and high-risk non-HCC individuals." "cfDNA was extracted from the plasma samples using the Apostle MiniMax cfDNA isolation kit."

Wang P., Song Q., Ren J. et al. Sci Transl Med 2022, 14(672):eabp8704. doi: 10.1126/scitranslmed.abp8704

In this study, we administered a recombinant bicistronic adeno-associated virus (AAV8) vector coding for both the light and heavy chains of the potent broadly neutralizing HIV-1 antibody VRC07 (AAV8-VRC07) to eight adults living with HIV... Plasma AAV8-VRC07 plasmid DNA was measured by extracting DNA from plasma... DNA was extracted from serum using an Apostle MiniMax High Efficiency cfDNA Isolation Kit, following the manufacturer’s protocol with slight modification."

Casazza J.P., Cale E.M., Narpala S. et al. Nat Med 2022, 28(5):1022-1030. doi: 10.1038/s41591-022-01762-x

This data suggests that liquid biopsy combining analysis of cfRNA with cfDNA is practical and may provide helpful information in predicting genomic abnormalities, diagnosis of neoplasms and evaluating both the tumor biology and the host response... We used Apostle MiniMax High Efficiency cfRNA/cfDNA isolation kit and followed the recommended protocol. After extraction, half of the cfDNA was treated with DNase to obtain cfRNA and the other half was used for DNA studies."

Albitar M., Zhang H., Charifa A.et al. Heliyon 2023, 9(5):e16261. doi: 10.1016/j.heliyon.2023.e16261

The methylation-specific quantitative PCR (mqMSP) assay is cost-effective and easily implementable for routine clinical monitoring of colorectal cancer recurrence, which can lead to better patient management after surgery... Plasma DNA extraction was performed using 2 to 5 mL of plasma with the Apostle MiniMax High-Efficiency cfDNA Isolation Kit, according to the product manual."

Jin S., Zhu D., Shao F. et al. Proc Natl Acad Sci U S A 2021, 118(5):e2017421118. doi: 10.1073/pnas.2017421118

Most notably, the Apostle particles outperformed all others, achieving almost 2-fold higher recovery yields than the particles supplied in the X kit."

Stark A., Pisanic T.R., Herman J.G. et al. SLAS Technology 2022, 27(3):172-179. doi: 10.1016/j.slast.2021.12.002

We used single-molecule sequencing-based (SMS-based) noninvasive prenatal screening (NIPS) to screen for common fetal aneuploidies in 477 pregnant women... Compared with NGS, SMS (without PCR) had less GC bias, a better distinction between T21 or T18 and euploidies, and better diagnostic performance... cfDNA was extracted from 0.6 mL of maternal plasma using Apostle MiniMax High-Efficiency cfDNA Isolation Kit according to the manufacturer’s instructions."

Qian Y., Liu Y., Yan Y. et al. Lab Invest 2023, 103(4):100043. doi: 10.1016/j.labinv.2022.100043

H3K36me3 cfChIP-seq demonstrated increased enrichment of mutated alleles compared to normal alleles in plasma from patients with known somatic cancer mutations... Findings here expand the utility of cfDNA in liquid biopsies to characterize treatment resistance, cancer subtyping, and disease progression... Both the input as well as the cfChIP samples were purified using Apostle MiniMax High Efficiency cfDNA Isolation Kit according to manufacturer’s instructions."

Maansson C.T., Meldgaard P., Stougaard M. et al. Mol Oncol 2023, 17(5):722-736. doi: 10.1002/1878-0261.13394

Plasma cell-free DNA (cfDNA) from 2821 myeloid or lymphoid neoplasm patients were collected. cfDNA was sequenced using a 275 gene panel... This data shows that liquid biopsy using targeted NGS is reliable in detecting chromosomal structural abnormalities in myeloid neoplasms... Overall, this study supports the use of liquid biopsy for early diagnosis and monitoring of patients with myeloid neoplasms... We extracted cfDNA from 2821 peripheral blood samples using the Apostle MiniMax High Efficiency cfDNA Isolation Kit."

Ip A., Della Pia A., Kim G.Y.G. et al. Front Oncol 2022, 14:12:923809. doi: 10.3389/fonc.2022.923809

Elucidating the relationship between these pathways and the increased circulating mitochondrial DNA observed here will provide further insight into the cell-damaging effects of prolonged inhalation of e-cigarette aerosols... For measurement of in vivo plasma mtDNA/nDNA ratio, mice plasma was first subjected to cell-free DNA (cfDNA) extraction using Apostle MiniMax cfDNA extraction kit."

Peng G., Xi Y., Bellini C. et al. Am J Cancer Res 2022, 12(8):3679–3692

As a proof-of-concept, we developed a 222-plex Ultra-dPCR assay and demonstrated its potential use as a rapid, low-cost screening assay for non-invasive prenatal testing (NIPT) for as low as 4% trisomy fraction samples with high precision, accuracy, and reproducibility... Cell-free plasma DNA was isolated using the Apostle MiniMax kit according to the manufacturer’s protocol with an elution volume of 60 μL."

Shum E.Y., Lai J.H., Li S.. et al. Anal Chem 2022, 94(51):17868-17876. doi: 10.1021/acs.analchem.2c03649/p>

Our study confirmed that SD regions are preferred biomarkers for aneuploidy detection and in particular SD-based digital PCR could find potential use for NIPT of trisomy... The cfDNA was isolated from 1 mL of each plasma sample by the Apostle MiniMax High Efficiency cfDNA Isolation Kit."

Jin S., Ye Q., Hong Y. et al. Clin Chem Lab Med 2020, 59(1):91-99. doi: 10.1515/cclm-2020-0300

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Products and demonstrated applications are not intended or validated for use in diagnostic procedures.