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Apostle MiniMax Technology


Overview

The ability to isolate and analyze circulating cell free DNA (cfDNA) at very low concentrations is becoming increasingly important, particularly in non-invasive prenatal test (NIPT), early cancer detection, and infectious disease diagnosis. Highly efficient isolation of cfDNA from complexed biological medium is a crucial step for subsequent cfDNA analysis. 

Apostle MiniMax® technology offers a best-in-class efficiency and purity compared with conventional technologies to capture and isolate the circulating cell-free genetic materials.

What our community say

Individualized, heterologous chimpanzee adenovirus and self-amplifying mRNA neoantigen vaccine for advanced metastatic solid tumors: phase 1 trial interim results
"Exploratory biomarker analyses showed decreased circulating tumor DNA (ctDNA) in patients with prolonged OS... cfDNA was extracted from the entire plasma volume of a single draw using the Apostle MiniMax cfDNA Isolation kit (ApostleBio) "
- An independent clinical study published in Nature Medicine by a joint clinical team from Gritstone, Columbia University Medical Center, Mayo Clinic, MSKCC, MD Anderson, etc.
Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection
"The model detected four of the five 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 (C43468, Apostle). "
- An independent clinical study published in Science Translational Medicine from the National Cancer Center of China
"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."
- An independent clinical study published in Nature Medicine by NIH, Medical University of South Carolina, MIT and Harvard, Caltech, Duke, Vaxart, and ModeX
"The mqMSP assay is cost-effective and easily implementable for routine clinical monitoring of CRC 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. "
- An independent clinical study published in PNAS
"This illustrates a 34.3% higher yield when using the Apostle kit as compared to the X kit." "This data demonstrates an average of 14.8% higher yield using the Apostle kit." "The Apostle mononucleosomal cfDNA yield was 70.0% higher than the yield for the X samples." "A summary provided in Table 2 shows the consistently higher yield achieved by the Apostle MiniMax High Efficiency cfDNA Isolation Kit as compared to the X circulating nucleic acid kit. The average 40% improvement in yield underscores the importance of extraction kit selection in cfDNA assay development and highlights the potential impact of cfDNA isolation efficiency in ctDNA detection."
- An independent study by scientists at Beckman Coulter Life Sciences (read Technical Note)
(Figure 4) "Most notably, the Apostle particles outperformed all others, achieving almost 2-fold higher recovery yields than the particles supplied in the X kit".
- An independent study by scientists at Johns Hopkins University and University of Pittsburgh (read article)
"We used SMS-based 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 (ref. number: A17622-50; Apostle) according to the manufacturer’s instructions."
- An independent study by scientists at Women’s Hospital, School of Medicine; Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, China (read article)
"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 (Beckman Coulter, Indianapolis, IN, USA) according to manufacturer’s instructions."
- An independent clinical study published in Molecular Oncology by Department of Clinical Biochemistry, Aarhus University Hospital, and Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
"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 (San Jose, CA). "
- An independent clinical study published in Frontiers in Oncology by Hackensack University Medical Center, Ernest Mario School of Pharmacy at Rutgers University, Englewood Health Internal Medicine Residency Program, and Genomic Testing Cooperative
"...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 (ApostleBio, CA, US). "
- An independent research study published in American Journal of Cancer Research from Yale University
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 was isolated using the Apostle MiniMax kit (Beckman Coulter) according to the manufacturer’s protocol with an elution volume of 60 μL.
- An dependent study published in Analytical Chemistry by Enumerix
"Magnetic beads-based DNA extraction using the supernatant from the homogenized stool was chosen for further analysis due to better reproducibility, higher hgDNA yield, lower non-hgDNA background, and the potential for automation. With this protocol, a combination of SDC2 and NDRG4 methylation signals with a linear regression model achieved a sensitivity and specificity of 81.82 and 93.75%, respectively...Through the systematic evaluation of different stool processing and DNA extraction methods, we established a reproducible protocol for analyzing tumor DNA methylation markers in stool samples for colorectal cancer screening...Apostle Stool gDNA Isolation Kit (APOSTLE) was used according to the manufacturer’s instructions. Either 0.2 g pellets or 0.2 mL supernatant from homogenized stool was mixed with 1 mL lysis buffer (APOSTLE) for DNA extractions. "
- An independent clinical study published in Clinical Chemistry and Laboratory Medicine (CCLM)
"We developed a ddPCR assay to quantify the T790M mutation in plasma. Quantification of longitudinal plasma T790M mutation may allow noninvasive assessment of drug resistance and guide follow-up treatment in TKI-treated patients with NSCLC....cfDNA was extracted from 2–6 ml of plasma using an Apostle MiniMax High Efficiency cfDNA Isolation Kit (standard edition) (Apostle, Silicon Valley, CA, USA) according to the manufacturer’s instructions. "
- An independent clinical study published in Targeted Oncology
"The combination of mutation profiling and CNA profiling can improve the detection of MRD, which may help optimize the treatment strategies for patients with locally advanced rectal cancer (LARC)...cfDNA was extracted from 1.5-4.5 mL of plasma with the Apostle MiniMax cfDNA isolation kit (C40605, Apostle; San Jose, CA, USA). "
- An independent clinical study published in EBioMedicine from Peking Union Medical College, Sun Yat-sen University Cancer Center, Jinchenjunchuang Clinical Laboratory, China
"...This includes recognizing that an innovative product from Apostle is the best technology to address these needs."
- Steve Wowk, Director of Genomics, Beckman Coulter Life Sciences
(Figure 1) "For each tube the Apostle MiniMax extracted higher total yield of DNA".
- An independent study by scientists at Beckman Coulter Life Sciences (read data sheet)
"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 (Apostle Inc, San Jose, CA). "
- An independent clinical study published in EBioMedicine from State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, China
"BGI Genomics announces that its Stool Sample Collection Kit, DNA Isolation Kit together with Sample Pretreatment Kit for Methylation Detection have been CE marked. " (Note by Apostle: Apostle is the Original Equipment Manufacturer or OEM for the Stool DNA Isolation Kit mentioned in this news. )
- BGI

Performance Assessment

Apostle MiniMax technology offers a best-in-class efficiency and purity compared with conventional technologies to capture and isolate the circulating cell-free genetic materials. It is trusted by many of the world's most prestigious leaders in life sciences.  Its superior performance has been independently validated and verified by many academic and industrial groups.

For a complete list of publications, visit here.

Independent Validation Data Set 1

High-throughput sample processing for methylation analysis in an automated, enclosed environment. Alejandro Stark, Thomas R. Pisanic, James G. Herman, Tza-Huei Wang. SLAS Technology Volume 27, Issue 3, June 2022, Pages 172-179. 

(Note: Apostle MiniMax technology is compared and discussed in this study.) 



(Figure 4) - "Most notably, the Apostle particles outperformed all others, achieving almost 2-fold higher recovery yields than the particles supplied in the X kit. "


Abstract

Variation in methylcytosine is perhaps the most well-studied epigenetic mechanism of gene regulation. Methods that have been developed and implemented for assessing DNA methylation require sample DNA to be extracted, purified and chemically-processed through bisulfite conversion before downstream analysis. While some automated solutions exist for each of these individual process steps, a fully integrated solution for accomplishing the entire process in a high-throughput manner has yet to be demonstrated. Thus, sample processing methods still require numerous manual steps that may reduce sample throughput and precision, while increasing the risk of contamination and human error. In this work, we present an integrated, automated solution for performing the entire sample preparation process, including DNA extraction, purification, bisulfite conversion and PCR plate preparation within in an enclosed environment. The method employs silica-coated magnetic particles that eliminate the need for a centrifuge or vacuum manifold, thereby reducing the complexity and cost of the required automation platform. Toward this end, we also compare commercial DNA extraction and bisulfite conversion kits to identify a protocol suitable for automation to significantly improve genomic and bisulfite-treated DNA yields over manufacturer protocols. Overall, this research demonstrated development of an automated protocol that offers the ability to generate high-quality, bisulfite-treated DNA samples in a high-throughput and clean environment with minimal user intervention and comparable yields to manual processing.


Independent Validation Data Set 2

Comparative analysis of cell-free DNA extraction efficiency from plasma.  Beckman Coulter Life Sciences. Indianapolis, IN. Technical Note 2022.

(Note: Apostle MiniMax technology is compared and discussed in this study.) 



Results and discussion

Mean cfDNA concentrations in the eluates were determined to be 8.30 ng/μL for samples extracted with the QIAamp kit and 11.15 ng/μL for samples extracted with the Apostle kit when measured with the Qubit assay (Figure 1A). This illustrates a 34.3% higher yield when using the Apostle kit as compared to the QIAamp kit.

When evaluating the contents of specific genes in the eluate, the Apostle purification displayed a higher yield than QIAamp (Figure 1B). 8358 DNAJC5G positive droplets were detected in the Apostle samples compared to 7269 droplets in the QIAamp samples. Similarly, 10849 ACTG1 droplets were detected in the Apostle-extracted samples versus 9463 droplets detected in the QIAamp-extracted samples. This data demonstrates an average of 14.8% higher yield using the Apostle kit.

Finally, when evaluating cfDNA fragments via the Agilent bioanalyzer instrument, the Apostle kit demonstrated the highest yield (Figure 1C and D). Mononucleosomal cfDNA concentration in the eluate of Apostle samples was estimated to be 10.64 ng/μL versus 6.26 ng/μL in the eluate of QIAamp samples. The dinucleosomal cfDNA concentration was low for both kits, with 0.13 ng/μL recorded for Apostle samples and 0.24 ng/μL for QIAamp samples. This indicates a slightly better purification of dinucleosomal cfDNA using QIAamp; however, this could also be an artifact given the low concentrations. The Apostle mononucleosomal cfDNA yield was 70.0% higher than the yield for the QIAamp samples.



A summary provided in Table 2 shows the consistently higher yield achieved by the Apostle MiniMax High Efficiency cfDNA Isolation Kit as compared to the QIAamp® circulating nucleic acid kit. The average 40% improvement in yield underscores the importance of extraction kit selection in cfDNA assay development and highlights the potential impact of cfDNA isolation efficiency in ctDNA detection.

Independent Validation Data Set 3

cfDNA Extraction Efficiency Affects NGS Data.  Han Wei, Ph.D., Beckman Coulter Life Sciences. Indianapolis, IN. Technical Note 2020.

Figure 1. cfDNA extraction method affects allele frequency (AF%). EGFR L858R standards with AF% of 0.3%, 1.0%, and 3.0% were spiked into plasma and isolated using Product A (red) or Apostle MiniMax cfDNA isolation kit (blue and green). The eluates were analyzed by NGS (performed by the Institute B) following standard protocol and AF% calculated using their established workflow. cfDNA isolated by Apostle MiniMax cfDNA isolation kit shows higher concordance between detected AF% and expected AF%.


In order to understand how cfDNA extraction efficiency affects NGS data, we present Institute B titration data. EGFR L858R standards with an allele frequency (AF%) of 0.3%, 1.0%, and 3.0% were spiked into plasma and isolated using either Apostle MiniMaxTM High Efficiency cfDNA Isolation or Product A. The cfDNA was analyzed via NGS and AF% was calculated by Institute B. cfDNA isolated by Apostle MiniMax cfDNA isolation kit shows concordance between detected AF% and expected AF%.

For cancer samples, the allele frequency represents the percentage of sequence reads carrying a mutant allele of an individual patient’s cancer. Researchers often set thresholds for defining the variant allele frequency as mutation; therefore, low cfDNA recovery efficiency can decrease sensitivity and lead to an increase in false negatives for mutation calling.

Independent Validation Data Set 4

cfDNA Extraction from Plasma for Liquid Biopsy: Apostle MiniMaxTM High Efficiency cfDNA Isolation Kit. Beckman Coulter Life Sciences, Data Sheet. 2019. 


(Figure 1) "For each tube the Apostle MiniMax extracted higher total yield of DNA. "


Apostle MiniMax High Efficiency cfDNA Isolation Kit, Apostle MiniMax is a cell–free DNA (cfDNA) isolation reagent kit, built on magnetic bead–based technology. Apostle MiniMax has been demonstrated to purify cfDNA from human plasma in both manual and automated workflows. 

• Data representative of results of cfDNA extracted from 1–5mL of plasma 

• Demonstrated compatibility with a variety of collection tubes 

• cfDNA purity shown to be suitable for downstream PCR based assays

Applications

Apostle MiniMax technology has been applied in world-class research and development projects of novel liquid biopsy technologies.  

For a more detailed discussion, visit here. Some examples include:

Apostle MiniMax Technology in Clinical Research on Metastatic Solid Tumors

Apostle MiniMax Technology in Hepatocellular Carcinoma Detection

Apostle MiniMax Technology in HIV Research & Clinical Trial

Apostle MiniMax Technology in Colon Cancer Detection and Post-Surgical Monitoring

Apostle MiniMax Technology in Detecting Chromosomal Structural Abnormalities in Patients with Myeloid Neoplasms

Apostle MiniMax Technology in Rectal Cancer Response Prediction and Risk Stratification

Apostle MiniMax Technology in Non-Invasive Prenatal Testing

Apostle MiniMax Technology in Prenatal Diagnostics using ddPCR

Apostle MiniMax Technology in Early Gender Prediction

Apostle MiniMax Technology in Cardiovascular Research

Apostle MiniMax Technology in Next Generation Digital PCR

Significance

A recent paper published in JAMA Oncology by Torga & Pienta revealed that, strikingly, 2 major commercial liquid biopsy tests show significant and clinically unacceptable discordance. 

Why do liquid biopsy tests differ so significantly? Are they reliable? 

Among other impact factors, the extraction method of circulating free DNA (cfDNA) plays a major role here. Data show that different cfDNA extraction methods yield significantly different amounts of cfDNA by 10% to 10 folds, and consequently result in discordant conclusions. When we study genomic DNA isolated from the nucleus of cells, this level of difference may not matter much – because the amount of genetic material commonly reaches hundreds of micrograms (ug), so the downstream testing methods have enough genetic material to work with anyway. However, when we study cfDNA, this level of difference may result in a fundamental discordance, because the amount of cfDNA is commonly less than 100 nanograms (ng). Slight difference of cfDNA yields may result in critical impact on the testable copies of cancer mutations and the signal-to-noise ratio. 

We illustrate how the accuracy of a liquid biopsy is impacted by the cfDNA sample preparation in a figure below. To have a reliable liquid biopsy testing, a highly efficient cfDNA extraction must be achieved.

Exhibit 1. Sample preparation is a critical yet unaddressed challenge in liquid biopsy.

Uniqueness

Apostle MiniMax technology ensures precise capture and separation of circulating genetic materials for liquid biopsy analysis. This is achieved through Apostle’s novel proprietary MiniMax magnetic nanoparticles (Exhibit 2-8) with innovative features:

  • Novel material composition and surface chemistry - completely distinct from the conventional paramagnetic or superparamagnetic technologies
  • Exceptionally large surface area
  • Minimized variation
  • Best-in-class suspension property
  • Superb magnetic power
  • Superb resistance to particle clustering
  •  Superior cfDNA isolation efficiency
  • Superior performance of DNA mutation detection 

Exhibit 2. Apostle’s proprietary MiniMax magnetic nanoparticles under scanning electron microscope.

The Apostle MiniMax nanoparticles have an increased magnetic strength and a decreased particle size compared to other leading technologies in the market, which ensures excellent suspension in solution and rapid mobility. The optimized surface chemistry allows efficient enrichment of genetic materials from complex biological materials.

Exhibit 3. Apostle’s proprietary MiniMax nanoparticles have uniform sizes.

Apostle’s MiniMax magnetic nanoparticles generated from our proprietary technology have a uniform size distribution with minimized doublets, distinct from the particles from five current technological providers showing random sizes and significant doublets. Highly consistent size distribution of Apostle’s nanoparticles ensure reproducible results.

Exhibit 4. The Apostle MiniMax nanoparticles have a best-in-class suspension property.

Excellent suspension is one of the critical properties of nanoparticles to excel in cfDNA isolation. In this simple but quite visual experiment, we compare Apostle MiniMax with the nanoparticles from other two technologies on the market. The three tubes contain equal weight of different types of nanoparticles. By 1 minute, the other technology #2 is almost completely sedimented. By 15 minute, the other technology #1 is almost completely sedimented. However, Apostle MiniMax has kept the suspension status, showing a superb suspension property.  


https://www.youtube.com/watch?v=ym63t4oLnkQ

Exhibit 5. The Apostle MiniMax nanoparticles have a best-in-class magnetic power.

A strong magnetic power is another critical property of nanoparticles to achieve a good cfDNA isolation performance. In this simple experiment, we compare the magnatic power of Apostle MiniMax with the nanoparticles from other two technologies on the market. The three tubes contain equal weight of different types of nanoparticles. A magnetic plate slowly approaches the three tubes at equal distances. Whichever tube having the strongest magnetic power makes the first move. 
The tube containing Apostle MiniMax makes the first move, while the other two technologies stay still. Apostle MiniMax shows a superb magnetic power.

https://www.youtube.com/watch?v=6SDVUoYzD9Y

Exhibit 7. Superior cfDNA isolation efficiency in human plasma and urine.

A) Cell-free plasma was separated from blood samples by centrifugation for 10 minutes at 2000g at 4oC, then centrifuged for 10 minutes at 16000g at 4oC. cfDNA was isolated from 4mL plasma with Apostle MiniMax High Efficiency cfDNA Isolation Kit (red curve) and major alternative product (blue curve). The isolated cfDNA was characterized by Bioanalyzer 2100. 

B) Cell-free urine was prepared by centrifugation for 10 minutes at 16000g at 4oC. cfDNA was isolated from 20mL urine with Apostle MiniMax High Efficiency cfDNA Isolation Kit (red curve) and major alternative product (blue curve). The isolated cfDNA was characterized by Bioanalyzer 2100. Apostle MiniMaxTM High Efficiency cfDNA Isolation Kit offers superior cfDNA isolation efficiency for both plasma and urine samples.

Exhibit 6. The Apostle MiniMax nanoparticles have a superb resistance to particle clustering.

The unwanted clustering of particles reduces the performance of the cfDNA isolation, and sometimes even interferes with the normal lab procedures. In this experiment, we compare MiniMax's ability to resist clustering with another leading technology on the market. After adding isopropyl alcohol, the other technology shows particle clustering visible to naked eye, while Apostle MiniMax does not. The Apostle MiniMax nanoparticles show a superb resistance to particle clustering. 

Large Image

Exhibit 8. Superior performance of DNA mutation detection isolated with Apostle MiniMax High Efficiency Cell-Free DNA Isolation Kit

20 uL of DNA fragment containing the EGFR c.2573T>G L858R mutation (synthetic, ~170 bp), with concentration of 1 ng/uL, 0.1 ng/uL, 0.01 ng/uL, 0.001 ng/uL, was spiked into 1mL TE buffer (blue) or Serum (red) respectively. The mutated DNA fragment was isolated with Apostle MiniMax High Efficiency Cell-Free DNA Isolation Kit (Standard Edition), with a final elution volume of 20 uL. qPCR was performed using 1 uL of the isolated DNA, and compared with 1 uL of the corresponding original mutated DNA solution at 1 ng/uL, 0.1 ng/uL, 0.01 ng/uL, 0.001 ng/uL. 

A) Amplification plot showing highly overlapping curves for mutated DNA fragment isolated with Apostle MiniMaxTM High Efficiency Cell-Free DNA Isolation Kit and original DNA solution at different concentrations. 

B) qPCR standard curve generated using original mutated DNA solution, in order to quantify the recovery of DNA isolated with Apostle MiniMax High Efficiency Cell-Free DNA Isolation Kit. DNA isolation recovery rate was calculated to be >90%. 

Note: Displayed DNA concentration series at 1, 0.1, 0.01, 0.001 ng/ul are the concentrations of the original DNA dilution series before spiking into 1mL of serum. The corresponding DNA isolation working concentrations are 20 pg/ul, 2 pg/ul, 0.2 pg/ul, 0.02 pg/ul, respectively.

Other Information

Apostle also partners with Beckman Coulter to offer the Apostle MiniMaxTM High Efficiency Isolation Kit. If you wish to order the kit through Beckman Coulter, please visit Beckman Coulter's website:

Apostle image 
https://www.beckman.com/reagents/genomic/dna-isolation/from-plasma

For more information about this partnership: https://www.beckman.com/news/liquid-biopsy-partnership-with-apostle

ProductsCat#
Apostle MiniMaxTM High Efficiency Cell-Free DNA Isolation Kit (Standard Edition) (1mL X 10 preps)A17622-10
Apostle MiniMaxTM High Efficiency Cell-Free DNA Isolation Kit (Standard Edition) (1mL X 50 preps)A17622-50
Apostle MiniMaxTM High Efficiency Cell-Free DNA Isolation Kit (Standard Edition) (5mL X 50 preps)A17622-250
For research use only. Not for use in diagnostic procedures.
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About Us
With the help of Apostle MiniMax cfDNA Isolation Technology, a recent clinical study demonstrated the clinical validity of the circulating cell-free DNA for hepatocellular carcinoma (HCC) detection with high sensitivity and specificity, published in Science Translational Medicine.