A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA

Abstract Low yields of extracted cell-free DNA (cfDNA) from plasma limit continued development of liquid biopsy in cancer, especially in early-stage cancer diagnostics and cancer screening applications. We investigate a novel liquid-phase-based DNA isolation method that utilizes aqueous two-phase sy...

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Autores principales:	Filip Janku, Helen J. Huang, David Y. Pereira, Masae Kobayashi, Chung Hei Chiu, S. Greg Call, Kristen T. Woodbury, Felix Chao, Daniel R. Marshak, Ricky Y. T. Chiu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5b8e5b31d9594c7e8e04f5fa388234cc
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spelling	oai:doaj.org-article:5b8e5b31d9594c7e8e04f5fa388234cc2021-12-02T18:07:52ZA novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA10.1038/s41598-021-98815-x2045-2322https://doaj.org/article/5b8e5b31d9594c7e8e04f5fa388234cc2021-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98815-xhttps://doaj.org/toc/2045-2322Abstract Low yields of extracted cell-free DNA (cfDNA) from plasma limit continued development of liquid biopsy in cancer, especially in early-stage cancer diagnostics and cancer screening applications. We investigate a novel liquid-phase-based DNA isolation method that utilizes aqueous two-phase systems to purify and concentrate circulating cfDNA. The PHASIFY MAX and PHASIFY ENRICH kits were compared to a commonly employed solid-phase extraction method on their ability to extract cfDNA from a set of 91 frozen plasma samples from cancer patients. Droplet digital PCR (ddPCR) was used as the downstream diagnostic to detect mutant copies. Compared to the QIAamp Circulating Nucleic Acid (QCNA) kit, the PHASIFY MAX method demonstrated 60% increase in DNA yield and 171% increase in mutant copy recovery, and the PHASIFY ENRICH kit demonstrated a 35% decrease in DNA yield with a 153% increase in mutant copy recovery. A follow-up study with PHASIFY ENRICH resulted in the positive conversion of 9 out of 47 plasma samples previously determined negative with QCNA extraction (all with known positive tissue genotyping). Our results indicate that this novel extraction technique offers higher cfDNA recovery resulting in better sensitivity for detection of cfDNA mutations compared to a commonly used solid-phase extraction method.Filip JankuHelen J. HuangDavid Y. PereiraMasae KobayashiChung Hei ChiuS. Greg CallKristen T. WoodburyFelix ChaoDaniel R. MarshakRicky Y. T. ChiuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Filip Janku Helen J. Huang David Y. Pereira Masae Kobayashi Chung Hei Chiu S. Greg Call Kristen T. Woodbury Felix Chao Daniel R. Marshak Ricky Y. T. Chiu A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA
description	Abstract Low yields of extracted cell-free DNA (cfDNA) from plasma limit continued development of liquid biopsy in cancer, especially in early-stage cancer diagnostics and cancer screening applications. We investigate a novel liquid-phase-based DNA isolation method that utilizes aqueous two-phase systems to purify and concentrate circulating cfDNA. The PHASIFY MAX and PHASIFY ENRICH kits were compared to a commonly employed solid-phase extraction method on their ability to extract cfDNA from a set of 91 frozen plasma samples from cancer patients. Droplet digital PCR (ddPCR) was used as the downstream diagnostic to detect mutant copies. Compared to the QIAamp Circulating Nucleic Acid (QCNA) kit, the PHASIFY MAX method demonstrated 60% increase in DNA yield and 171% increase in mutant copy recovery, and the PHASIFY ENRICH kit demonstrated a 35% decrease in DNA yield with a 153% increase in mutant copy recovery. A follow-up study with PHASIFY ENRICH resulted in the positive conversion of 9 out of 47 plasma samples previously determined negative with QCNA extraction (all with known positive tissue genotyping). Our results indicate that this novel extraction technique offers higher cfDNA recovery resulting in better sensitivity for detection of cfDNA mutations compared to a commonly used solid-phase extraction method.
format	article
author	Filip Janku Helen J. Huang David Y. Pereira Masae Kobayashi Chung Hei Chiu S. Greg Call Kristen T. Woodbury Felix Chao Daniel R. Marshak Ricky Y. T. Chiu
author_facet	Filip Janku Helen J. Huang David Y. Pereira Masae Kobayashi Chung Hei Chiu S. Greg Call Kristen T. Woodbury Felix Chao Daniel R. Marshak Ricky Y. T. Chiu
author_sort	Filip Janku
title	A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA
title_short	A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA
title_full	A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA
title_fullStr	A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA
title_full_unstemmed	A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA
title_sort	novel method for liquid-phase extraction of cell-free dna for detection of circulating tumor dna
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5b8e5b31d9594c7e8e04f5fa388234cc
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A novel method for liquid-phase extraction of cell-free DNA for detection of circulating tumor DNA

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