Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA

Abstract The use of blood-circulating cell-free DNA (cfDNA) as ‘liquid-biopsy’ is explored worldwide, with hopes for its potential in providing prognostic or predictive information in cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, ho...

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Autores principales:	Marjolein J. A. Weerts, Ronald van Marion, Jean C. A. Helmijr, Corine M. Beaufort, Niels M. G. Krol, Anita M. A. C. Trapman-Jansen, Winand N. M. Dinjens, Stefan Sleijfer, Maurice P. H. M. Jansen, John W. M. Martens
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/569193aba5394563865fe2f9224685ca
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spelling	oai:doaj.org-article:569193aba5394563865fe2f9224685ca2021-12-02T12:30:46ZSomatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA10.1038/s41598-017-02388-72045-2322https://doaj.org/article/569193aba5394563865fe2f9224685ca2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02388-7https://doaj.org/toc/2045-2322Abstract The use of blood-circulating cell-free DNA (cfDNA) as ‘liquid-biopsy’ is explored worldwide, with hopes for its potential in providing prognostic or predictive information in cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, however these retrospective cohorts have restrictive resources. In this study, we aimed to detect tumor-specific mutations in only minute amounts of serum-derived cfDNA by using a targeted next generation sequencing (NGS) approach. In a retrospective cohort of ten metastatic breast cancer patients, we profiled DNA from primary tumor tissue (frozen), tumor-adjacent normal tissue (formalin-fixed paraffin embedded), and three consecutive serum samples (frozen). Our presented workflow includes comparisons with matched normal DNA or in silico reference DNA to discriminate germline from somatic variants, validation of variants through the detection in at least two DNA samples of an individual, and the use of public databases on variants. By our workflow, we were able to detect a total of four variants traceable as circulating tumor DNA (ctDNA) in the sera of three of the ten patients.Marjolein J. A. WeertsRonald van MarionJean C. A. HelmijrCorine M. BeaufortNiels M. G. KrolAnita M. A. C. Trapman-JansenWinand N. M. DinjensStefan SleijferMaurice P. H. M. JansenJohn W. M. MartensNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Marjolein J. A. Weerts Ronald van Marion Jean C. A. Helmijr Corine M. Beaufort Niels M. G. Krol Anita M. A. C. Trapman-Jansen Winand N. M. Dinjens Stefan Sleijfer Maurice P. H. M. Jansen John W. M. Martens Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA
description	Abstract The use of blood-circulating cell-free DNA (cfDNA) as ‘liquid-biopsy’ is explored worldwide, with hopes for its potential in providing prognostic or predictive information in cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, however these retrospective cohorts have restrictive resources. In this study, we aimed to detect tumor-specific mutations in only minute amounts of serum-derived cfDNA by using a targeted next generation sequencing (NGS) approach. In a retrospective cohort of ten metastatic breast cancer patients, we profiled DNA from primary tumor tissue (frozen), tumor-adjacent normal tissue (formalin-fixed paraffin embedded), and three consecutive serum samples (frozen). Our presented workflow includes comparisons with matched normal DNA or in silico reference DNA to discriminate germline from somatic variants, validation of variants through the detection in at least two DNA samples of an individual, and the use of public databases on variants. By our workflow, we were able to detect a total of four variants traceable as circulating tumor DNA (ctDNA) in the sera of three of the ten patients.
format	article
author	Marjolein J. A. Weerts Ronald van Marion Jean C. A. Helmijr Corine M. Beaufort Niels M. G. Krol Anita M. A. C. Trapman-Jansen Winand N. M. Dinjens Stefan Sleijfer Maurice P. H. M. Jansen John W. M. Martens
author_facet	Marjolein J. A. Weerts Ronald van Marion Jean C. A. Helmijr Corine M. Beaufort Niels M. G. Krol Anita M. A. C. Trapman-Jansen Winand N. M. Dinjens Stefan Sleijfer Maurice P. H. M. Jansen John W. M. Martens
author_sort	Marjolein J. A. Weerts
title	Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA
title_short	Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA
title_full	Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA
title_fullStr	Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA
title_full_unstemmed	Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA
title_sort	somatic tumor mutations detected by targeted next generation sequencing in minute amounts of serum-derived cell-free dna
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/569193aba5394563865fe2f9224685ca
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Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA

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