UltraPrep is a scalable, cost-effective, bead-based method for purifying cell-free DNA
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 proto...
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| Veröffentlicht in: | PloS one 2020-06, Vol.15 (6), p.e0231854-e0231854 |
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| creator | Raymond, Christopher K Raymond, Fenella C Hill, Kay |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0231854 |
| format | Article |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0231854</identifier><identifier>PMID: 32479545</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biology and Life Sciences ; Cell-Free Nucleic Acids - blood ; Cell-Free Nucleic Acids - isolation & purification ; Computer and Information Sciences ; Deoxyribonucleic acid ; DNA ; DNA fragmentation ; EDTA ; Genetic research ; Genetic testing ; Humans ; Isolation ; Laboratories ; Liquid Biopsy ; Magnetics ; Medicine and Health Sciences ; Methods ; Molecular weight ; Nucleic acid isolation ; Nucleosomes - genetics ; Plasma ; Purification ; Research and analysis methods ; Silicon Dioxide - chemistry ; Solid Phase Extraction - economics ; Solid Phase Extraction - methods ; Technology</subject><ispartof>PloS one, 2020-06, Vol.15 (6), p.e0231854-e0231854</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Raymond et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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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. 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| subjects | Biology and Life Sciences Cell-Free Nucleic Acids - blood Cell-Free Nucleic Acids - isolation & purification Computer and Information Sciences Deoxyribonucleic acid DNA DNA fragmentation EDTA Genetic research Genetic testing Humans Isolation Laboratories Liquid Biopsy Magnetics Medicine and Health Sciences Methods Molecular weight Nucleic acid isolation Nucleosomes - genetics Plasma Purification Research and analysis methods Silicon Dioxide - chemistry Solid Phase Extraction - economics Solid Phase Extraction - methods Technology |
| title | UltraPrep is a scalable, cost-effective, bead-based method for purifying cell-free DNA |
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