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Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma

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Abstract

Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnostics, and prediction and monitoring of treatment response, but its amount is usually limited. Therefore, the choice of methods to extract and characterize ccfDNA is crucial. In the current study, we performed the most comprehensive comparison of methods for ccfDNA extraction (11 methods), quantification (3 methods), and estimation of the integrity index (2 methods) from small quantities of different kinds of plasma. The QIAamp® Circulating Nucleic Acid Kit and the Norgen Plasma/Serum Circulating DNA Purification Mini Kit showed the best accuracy and reproducibility, but the Norgen kit allowed to extract a higher amount of ccfDNA. This workflow provides a reliable protocol for the multiple applications of ccfDNA in biomedicine.

Workflow for the evaluation of methods to isolate, quantify and characterize circulating cell-free DNA from small volumes of plasma

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Acknowledgments

The authors would like to thank Chao Feng (CNG) for his help with the statistical analysis and Steven McGinn (CNG) for the critical reading of the manuscript. This work was partly supported by the EU FP7 under grant agreement number 241669 (the CAGEKID project, http://www.cng.fr/cagekid).

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Authors and Affiliations

  1. Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, 2 rue Gaston Crémieux, CP 5721, 91000, Evry, France

    Florence Mauger, Cécile Dulary, Christian Daviaud, Jean-François Deleuze & Jorg Tost

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  1. Florence Mauger
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  2. Cécile Dulary
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  3. Christian Daviaud
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  4. Jean-François Deleuze
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  5. Jorg Tost
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Correspondence to Jorg Tost.

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Mauger, F., Dulary, C., Daviaud, C. et al. Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma. Anal Bioanal Chem 407, 6873–6878 (2015). https://doi.org/10.1007/s00216-015-8846-4

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  • DOI: https://doi.org/10.1007/s00216-015-8846-4

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