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Selective capture of plasma cell-free tumor DNA on magnetic beads: a sensitive and versatile tool for liquid biopsy

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Abstract

Purpose

Recently, ‘solid tumor biopsies’ have been challenged by the emergence of ‘liquid biopsies’, which are aimed at the isolation and detection of circulating cell-free tumor DNA (ctDNA) in body fluids. Here, we developed and optimized a method for selective capture of ctDNA on magnetic beads (SCC-MAG) for mutation detection in plasma of patients with colorectal cancer (CRC).

Methods

Blood and tissue samples from 28 CRC patients were included for the detection of KRAS mutations. For the tissue samples, mutation analysis was conducted by high resolution melting (HRM) analysis and sequencing. For the SCC-MAG method, ctDNA was isolated from 200 µl plasma from patients with a mutant KRAS gene. For comparison, ctDNA extraction was carried out using a silica membrane-based method, after which mutations were detected using Intplex allele-specific PCR.

Results

The mean ctDNA integrity index in plasma samples of cancer patients was 1.03, comparable with that of silica membrane-derived ctDNA (1.011). Notably, the limit of detection for the SCC-MAG approach was lower than that of the silica membrane method and measured 2.25 pg/ml ctDNA in plasma. Our analyses showed that while the silica membrane-based approach was capable of collecting ctDNA from two out of six CRC patient samples (average Cq 34.23), the SCC-MAG captured ctDNA from all samples with an average Cq of 29.76.

Conclusions

We present a robust, reproducible, and highly sensitive method for the analysis of mutation statuses in liquid biopsies. The SCC-MAG method can readily be applied to any nucleic acid target for diagnostic purposes upon careful design of the specific capture probes, and can be multiplexed by several probes to identify multiple targets.

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Acknowledgements

We would like to thank Ehsan Shams Davodly for designing and preparing the figures, and the charity of Reza Radiotherapy and Oncology Center for supporting this study. This work is in memorial of Mrs Robabeh Aminian for her contribution to cancer research studies.

Funding

This study was supported financially by the Reza Radiotherapy and Oncology Center; Mashhad University of Medical Sciences (Grant number: 961467) and the Iran National Science Foundation (INSF) (Grant number: 93048371).

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Correspondence to Mohammad Amin Kerachian or Sina Mozaffari-Jovin.

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The authors declare that there is no conflict of interest.

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The current study was approved by the Mashhad University of Medical Sciences (MUMS) ethics committee (approval number: 961467) and all analyses were performed in accordance with the relevant guidelines and regulations of MUMS.

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Kerachian, M., Azghandi, M., Javadmanesh, A. et al. Selective capture of plasma cell-free tumor DNA on magnetic beads: a sensitive and versatile tool for liquid biopsy. Cell Oncol. 43, 949–956 (2020). https://doi.org/10.1007/s13402-020-00536-2

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  • DOI: https://doi.org/10.1007/s13402-020-00536-2

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