Journal article
A New Method for Improving Extraction Efficiency and Purity of Urine and Plasma Cell-Free DNA
Diagnostics (Basel), v 11(4), p650
03 Apr 2021
PMID: 33916811
Featured in Collection : UN Sustainable Development Goals @ Drexel
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 than did kits 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 demonstrate that DNApure can provide an efficient means of improving the yield and purity of cfDNA and minimize the effects of pre-analytical biospecimen variability on liquid biopsy assay performance.
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Details
- Title
- A New Method for Improving Extraction Efficiency and Purity of Urine and Plasma Cell-Free DNA
- Creators
- Selena Y. Lin - JBS Science (United States)Yue Luo - Baruch S. Blumberg InstituteMatthew M. Marshall - JBS Sci Inc, Doylestown, PA 18902 USABarbara J. Johnson - JBS Science (United States)Sung R. Park - Baruch S. Blumberg InstituteZhili Wang - JBS Science (United States)Ying-Hsiu Su - Baruch S. Blumberg Institute
- Publication Details
- Diagnostics (Basel), v 11(4), p650
- Publisher
- Mdpi
- Number of pages
- 9
- Grant note
- R44 CA165312-06; R44 R44HG008700 / NCI; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000642982600001
- Scopus ID
- 2-s2.0-85109071815
- Other Identifier
- 991021463318804721
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- Web of Science research areas
- Medical Laboratory Technology