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Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions

Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four com...

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Autores principales: Lee, Eun Young, Lee, Eun-Ju, Yoon, Hana, Lee, Dong Hyeon, Kim, Kwang Hyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236016/
https://www.ncbi.nlm.nih.gov/pubmed/32325682
http://dx.doi.org/10.3390/diagnostics10040234
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author Lee, Eun Young
Lee, Eun-Ju
Yoon, Hana
Lee, Dong Hyeon
Kim, Kwang Hyun
author_facet Lee, Eun Young
Lee, Eun-Ju
Yoon, Hana
Lee, Dong Hyeon
Kim, Kwang Hyun
author_sort Lee, Eun Young
collection PubMed
description Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection.
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spelling pubmed-72360162020-05-28 Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions Lee, Eun Young Lee, Eun-Ju Yoon, Hana Lee, Dong Hyeon Kim, Kwang Hyun Diagnostics (Basel) Article Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection. MDPI 2020-04-18 /pmc/articles/PMC7236016/ /pubmed/32325682 http://dx.doi.org/10.3390/diagnostics10040234 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lee, Eun Young
Lee, Eun-Ju
Yoon, Hana
Lee, Dong Hyeon
Kim, Kwang Hyun
Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions
title Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions
title_full Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions
title_fullStr Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions
title_full_unstemmed Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions
title_short Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions
title_sort comparison of four commercial kits for isolation of urinary cell-free dna and sample storage conditions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236016/
https://www.ncbi.nlm.nih.gov/pubmed/32325682
http://dx.doi.org/10.3390/diagnostics10040234
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