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Separation, Purification, and Detection of cfDNA in a Microfluidic Device

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Abstract

Cell free DNA (cfDNA) is degraded DNA fragments found in the blood plasma of cancer patients. While cfDNA is a good marker for early diagnostics and cancer prognosis, the extraction of cfDNA from whole blood and sample preparation for later sequencing is still challenging. Here, we presented a microfluidic device for the removal of cells from a cfDNA sample in a first step. In a second step, carboxylated magnetic beads were used for cfDNA extraction and purification. Lastly, cfDNA was amplified using a low-power, plasmonic polymerase chain reaction (PCR) system. Using fluorescent-labeled beads, we demonstrated that the separation efficiency for cells was 99% and the mixing efficiency for purification of cfDNA was 94%. Captured cfDNA could be successfully amplified by PCR, as demonstrated by gel electrophoresis. We confirmed that the limit of detection of our microfluidic system was 10 ng/mL.

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Acknowledgements

This research was supported by the National Research Foundation funded by the Ministry of Science and ICT of Korea (Grant number 2015M3A9D7030461, 2016M3A7B4910652, 2017R 1C1B3012221, 2015M3D3A1A01064926, 2019M3A 9H2032547).

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  1. These authors contributed equally.

Authors and Affiliations

  1. Department of Mechanical Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, 04107, Korea

    Hyeon Gi Kye, Christian D. Ahrberg, Byeong Seon Park, Jong Min Lee & Bong Geun Chung

Authors
  1. Hyeon Gi Kye
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  2. Christian D. Ahrberg
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  3. Byeong Seon Park
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  4. Jong Min Lee
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  5. Bong Geun Chung
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Correspondence to Bong Geun Chung.

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Conflict of Interests The authors declare no competing financial interests.

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Kye, H.G., Ahrberg, C.D., Park, B.S. et al. Separation, Purification, and Detection of cfDNA in a Microfluidic Device. BioChip J 14, 195–203 (2020). https://doi.org/10.1007/s13206-020-4208-1

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  • DOI: https://doi.org/10.1007/s13206-020-4208-1

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