Abstract
UltraPrep is an open-source, two-step method for purification of cell-free DNA that entails extraction of total DNA followed by size-selective enrichment of the smaller fragments that are characteristic of DNA originating from fragmentation between nucleosome. The advantages of the two related protocols that are described are that they can easily accommodate a wide range of sample input volumes, they rely on simple, magnetic bead-based technology, the yields of cfDNA are directly comparable to the most popular methods for cfDNA purification, and they dramatically reduce the cost of cfDNA isolation relative to currently available commercial methods. We provide a framework for physical and molecular quality analysis of purified cfDNA and demonstrate that the cfDNA generated by UltraPrep meets or exceeds the quality metrics of the most commonly used procedure. In addition, our method removes high molecular weight genomic DNA (hmwgDNA) that can interfere with downstream assay results, thereby addressing one of the primary concerns for preanalytical collection of blood samples.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Cell-Free Nucleic Acids / blood
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Cell-Free Nucleic Acids / isolation & purification*
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Humans
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Liquid Biopsy
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Magnetics
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Nucleosomes / genetics
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Silicon Dioxide / chemistry
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Solid Phase Extraction / economics
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Solid Phase Extraction / methods*
Substances
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Cell-Free Nucleic Acids
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Nucleosomes
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Silicon Dioxide
Grants and funding
Funding for this study was provided jointly by Ripple Biosolutions and by PlasmaLab International. These entities provided the resources necessary to conduct this study in the form of materials, supplies and salaries. All of the authors are employees and/or owners of these entities, as detailed below. CKR and FCR are co-founders and employees of Ripple Biosolutions, and both have an ownership stake in RB. KH is an owner and director of Plasma Lab International and has an ownership stake in PLI. The funder provided support in the form of salaries for authors, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.