cfDNA Extraction Simplified: An Automated Workflow on Omega Bio-tek’s Cutting-Edge Platform

Brandon Easparro¹, Claire McClain¹, Sara Amirahmadi¹, Tesfaye Kemsi¹, Jeff Roeder¹, and Travis Butts¹

  1. Omega Bio-tek, Inc., Norcross, GA 30071

As presented at SLAS 2024

Abstract

Plasma is a well-known sample type used in the isolation of cell-free DNA (cfDNA) for disease detection, diagnosis, and monitoring. cfDNA consists of small fragments of DNA released by cells as a result of processes such as apoptosis, damage to cells, and the shedding of DNA by normal cells. Leveraging the information stored in cfDNA can revolutionize diagnostics, enabling tests to track cancer progression, assess treatment responses, and customize personalized therapies. Omega Bio-tek has developed a semi-automated solution to extract cfDNA from 4 mL of human-derived plasma with minimal manual intervention. This revolutionary high-volume nucleic acid purification system used together with prefilled reagent cartridges can extract DNA from up to 24 samples in a single run. Here, we demonstrate this workflow’s capability of extracting cfDNA from human-derived plasma compared to Company T’s extraction workflow on their magnetic processor. cfDNA size, quality, and qPCR analyses were performed.

Materials and Methods

Streamlined Workflow from Sample Collection to Downstream Applications 
Figure 1. Illustration of the workflow from sample collection to DNA extraction with Omega Bio-tek's MagBinder® Fit24 to implementation in downstream applications.
cfDNA Extraction Solution from 4 mL Plasma with the MagBinder® Fit24 and MB Fit24™ cfDNA Kit
Figure 2. cfDNA extraction was performed on 4 mL plasma (n=3) using the MB Fit24™ cfDNA Kit on the MagBinder® Fit24 and Company T's cfDNA extraction kit on their equivalent magnetic processor. Pooled human-derived plasma was obtained from two different manufacturers: Innovative Research (Lot #42552) and Lampire Biological Laboratories (Lot #HMN1095120).
Size and Integrity Analysis

Size and quality of extracted cfDNA were evaluated using Agilent’s TapeStation® 4200.

Quantitative PCR

cfDNA extracted from both lots of plasma using the MB Fit24™ cfDNA Kit was subjected to real-time PCR using primers for the reference gene RPI13a to evaluate the suitability of the purified DNA for downstream applications. Average Ct values were determined.

Results

TapeStation Analysis of Purified cfDNA from 4 mL Plasma Samples
Figure 3. cfDNA was extracted from human-derived pooled plasma using MB Fit24™ cfDNA Kit implemented on the MagBinder® Fit24 and Company T's equivalent cfDNA extraction kit implemented on their equivalent magnetic processor with 4 mL sample volume input. cfDNA peaks are evident at 200 bp.
TapeStation Analysis of Purified cfDNA from 4 mL Plasma Samples
Figure 4. cfDNA was analyzed on the TapeStation® 4200 after extraction from human-derived pooled plasma using the MB Fit24™ cfDNA Kit implemented on the MagBinder® Fit24 and Company T's equivalent cfDNA extraction kit implemented on their equivalent magnetic processor with 4 mL sample volume input. cfDNA peaks are evident at 200 bp, with additional cfDNA multimers above.
Average Ct Values from Purified cfDNA
Figure 5. Average Ct values obtained using the MB Fit24™ cfDNA Kit on the MagBinder® Fit24 are in the 3-3.5 range, indicating positive amplification and efficiency, with little inhibition.

Conclusions

  • Minimal genomic DNA contamination and inhibition with MB Fit24™ cfDNA Kit
  • Size and integrity of extracted cfDNA appropriate for downstream applications
  • 24 samples can be extracted in approximately 90 minutes using the MB Fit24™ cfDNA Kit on the MagBinder® Fit24

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