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

Autor: Janku F; Department of Investigational Cancer Therapeutics (Phase1 Clinical Trials Program)-Unit 455, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA. fjanku@me.com., Huang HJ; Department of Investigational Cancer Therapeutics (Phase1 Clinical Trials Program)-Unit 455, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA., Pereira DY; Phase Scientific International Ltd, Garden Grove, CA, USA., Kobayashi M; Phase Scientific International Ltd, Garden Grove, CA, USA., Chiu CH; Phase Scientific International Ltd, Kwun Tong, Hong Kong., Call SG; Department of Investigational Cancer Therapeutics (Phase1 Clinical Trials Program)-Unit 455, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA., Woodbury KT; Department of Investigational Cancer Therapeutics (Phase1 Clinical Trials Program)-Unit 455, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA., Chao F; Phase Scientific International Ltd, Garden Grove, CA, USA.; Phase Scientific International Ltd, Kwun Tong, Hong Kong., Marshak DR; Phase Scientific International Ltd, Garden Grove, CA, USA.; Phase Scientific International Ltd, Kwun Tong, Hong Kong., Chiu RYT; Phase Scientific International Ltd, Garden Grove, CA, USA.; Phase Scientific International Ltd, Kwun Tong, Hong Kong.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2021 Oct 04; Vol. 11 (1), pp. 19653. Date of Electronic Publication: 2021 Oct 04.
DOI: 10.1038/s41598-021-98815-x
Abstrakt: 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.
(© 2021. The Author(s).)
Databáze: MEDLINE
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