A new method for improving extraction efficiency and purity of urine and plasma cell-free DNA

Abstract This study assessed three commercially available cell-free DNA (cfDNA) extraction kits and the impact of a PEG-based DNA cleanup procedure (DNApure) on cfDNA quality and yield. Six normal donor urine and plasma samples, and specimens from four pregnant (PG) women carrying male fetuses under...

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Published inbioRxiv
Main Authors Lin, Selena Y, Luo, Yue, Marshall, Matthew M, Johnson, Barbara J, Park, Sung R, Wang, Zhili, Su, Ying-Hsiu
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 03.01.2021
Subjects
Biopsy
Deoxyribonucleic acid
DNA
Fetuses
Plasma
Urine
Y chromosomes
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Summary:Abstract This study assessed three commercially available cell-free DNA (cfDNA) extraction kits and the impact of a PEG-based DNA cleanup procedure (DNApure) on cfDNA quality and yield. Six normal donor urine and plasma samples, and specimens from four pregnant (PG) women carrying male fetuses underwent extractions with the JBS cfDNA extraction kit (kit J), MagMAX Cell-Free DNA Extraction kit (kit M), and QIAamp Circulating Nucleic Acid Kit (kit Q). Recovery of a PCR product spike-in, endogenous TP53, and Y-chromosome DNA was used to assess kit performance. Nucleosomal-sized DNA profiles varied among the kits, with prominent multi-nucleosomal-sized peaks present in urine and plasma DNA isolated by kits J and M only. Kit J recovered significantly more spike-in DNA compared with kit M or Q (p<0.001) from urine, and similar amounts from plasma (p=0.12). Applying DNApure to kit M- and Q-isolated DNA significantly improved the amplification efficiency of spike-in DNA from urine (p<0.001) and plasma (p≤0.013). Furthermore, kit J isolated significantly more Y-chromosome DNA from PG urine compared to kit Q (p=0.05). We conclude that DNApure provides an efficient means of improving the yield and purity of cfDNA and minimizing effects of pre-analytical biospecimen variability on liquid biopsy assay performance. Competing Interest Statement Selena Lin, Matthew Marshall, and Barbara Johnson are employees of JBS Science, Inc. Selena Lin is a stock-holder of JBS Science, Inc. Ying-Hsiu Su has received funding from JBS Science, Inc. All other authors has no conflicts to declare.
DOI:10.1101/2020.12.31.425003