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Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer

Next‐generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole‐exome sequencin...

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Autores principales: Olmedillas‐López, Susana, García‐Olmo, Dolores C., García‐Arranz, Mariano, Peiró‐Pastor, Ramón, Aguado, Begoña, García‐Olmo, Damián
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943476/
https://www.ncbi.nlm.nih.gov/pubmed/29573240
http://dx.doi.org/10.1002/cam4.1399
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author Olmedillas‐López, Susana
García‐Olmo, Dolores C.
García‐Arranz, Mariano
Peiró‐Pastor, Ramón
Aguado, Begoña
García‐Olmo, Damián
author_facet Olmedillas‐López, Susana
García‐Olmo, Dolores C.
García‐Arranz, Mariano
Peiró‐Pastor, Ramón
Aguado, Begoña
García‐Olmo, Damián
author_sort Olmedillas‐López, Susana
collection PubMed
description Next‐generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole‐exome sequencing (WES) of cell‐free DNA (cfDNA) circulating in plasma, with the goal of identifying differential clinical profiles in patients with CRC. To this end, we applied an original concept, “differential presence of exons” (DPE). We determined differences in levels of 379 exons in plasma cfDNA and used DPE analysis to cluster and classify patients with disseminated and localized disease. The resultant bioinformatics analysis pipeline allowed us to design a predictive DPE algorithm in a small subset of patients that could not be initially classified based on the selection criteria. This DPE suggests that these nucleic acids could be actively released by both tumor and nontumor cells as a means of intercellular communication and might thus play a role in the process of malignant transformation. DPE is a new technique for the study of plasma cfDNA by WES that might have predictive and prognostic value in patients with CRC.
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spelling pubmed-59434762018-05-14 Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer Olmedillas‐López, Susana García‐Olmo, Dolores C. García‐Arranz, Mariano Peiró‐Pastor, Ramón Aguado, Begoña García‐Olmo, Damián Cancer Med Clinical Cancer Research Next‐generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole‐exome sequencing (WES) of cell‐free DNA (cfDNA) circulating in plasma, with the goal of identifying differential clinical profiles in patients with CRC. To this end, we applied an original concept, “differential presence of exons” (DPE). We determined differences in levels of 379 exons in plasma cfDNA and used DPE analysis to cluster and classify patients with disseminated and localized disease. The resultant bioinformatics analysis pipeline allowed us to design a predictive DPE algorithm in a small subset of patients that could not be initially classified based on the selection criteria. This DPE suggests that these nucleic acids could be actively released by both tumor and nontumor cells as a means of intercellular communication and might thus play a role in the process of malignant transformation. DPE is a new technique for the study of plasma cfDNA by WES that might have predictive and prognostic value in patients with CRC. John Wiley and Sons Inc. 2018-03-23 /pmc/articles/PMC5943476/ /pubmed/29573240 http://dx.doi.org/10.1002/cam4.1399 Text en © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Clinical Cancer Research
Olmedillas‐López, Susana
García‐Olmo, Dolores C.
García‐Arranz, Mariano
Peiró‐Pastor, Ramón
Aguado, Begoña
García‐Olmo, Damián
Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer
title Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer
title_full Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer
title_fullStr Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer
title_full_unstemmed Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer
title_short Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer
title_sort liquid biopsy by ngs: differential presence of exons (dpe) in cell‐free dna reveals different patterns in metastatic and nonmetastatic colorectal cancer
topic Clinical Cancer Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943476/
https://www.ncbi.nlm.nih.gov/pubmed/29573240
http://dx.doi.org/10.1002/cam4.1399
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