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Evaluation of methodologies for microRNA biomarker detection by next generation sequencing

In recent years, microRNAs (miRNAs) in tissues and biofluids have emerged as a new class of promising biomarkers for numerous diseases. Blood-based biomarkers are particularly desirable since serum or plasma is easily accessible and can be sampled repeatedly. To comprehensively explore the biomarker...

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Autores principales: Coenen-Stass, Anna M.L., Magen, Iddo, Brooks, Tony, Ben-Dov, Iddo Z., Greensmith, Linda, Hornstein, Eran, Fratta, Pietro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161688/
https://www.ncbi.nlm.nih.gov/pubmed/30223713
http://dx.doi.org/10.1080/15476286.2018.1514236
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author Coenen-Stass, Anna M.L.
Magen, Iddo
Brooks, Tony
Ben-Dov, Iddo Z.
Greensmith, Linda
Hornstein, Eran
Fratta, Pietro
author_facet Coenen-Stass, Anna M.L.
Magen, Iddo
Brooks, Tony
Ben-Dov, Iddo Z.
Greensmith, Linda
Hornstein, Eran
Fratta, Pietro
author_sort Coenen-Stass, Anna M.L.
collection PubMed
description In recent years, microRNAs (miRNAs) in tissues and biofluids have emerged as a new class of promising biomarkers for numerous diseases. Blood-based biomarkers are particularly desirable since serum or plasma is easily accessible and can be sampled repeatedly. To comprehensively explore the biomarker potential of miRNAs, sensitive, accurate and cost-efficient miRNA profiling techniques are required. Next generation sequencing (NGS) is emerging as the preferred method for miRNA profiling; offering high sensitivity, single-nucleotide resolution and the possibility to profile a considerable number of samples in parallel. Despite the excitement about miRNA biomarkers, challenges associated with insufficient characterization of the sequencing library preparation efficacy, precision and method-related quantification bias have not been addressed in detail and are generally underappreciated in the wider research community. Here, we have tested in parallel four commercially available small RNA sequencing kits against a cohort of samples comprised of human plasma, human serum, murine brain tissue and a reference library containing ~ 950 synthetic miRNAs. We discuss the advantages and limits of these methodologies for massive parallel microRNAs profiling. This work can serve as guideline for choosing an adequate library preparation method, based on sensitivity, specificity and accuracy of miRNA quantification, workflow convenience and potential for automation.
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spelling pubmed-61616882018-10-01 Evaluation of methodologies for microRNA biomarker detection by next generation sequencing Coenen-Stass, Anna M.L. Magen, Iddo Brooks, Tony Ben-Dov, Iddo Z. Greensmith, Linda Hornstein, Eran Fratta, Pietro RNA Biol Research Paper In recent years, microRNAs (miRNAs) in tissues and biofluids have emerged as a new class of promising biomarkers for numerous diseases. Blood-based biomarkers are particularly desirable since serum or plasma is easily accessible and can be sampled repeatedly. To comprehensively explore the biomarker potential of miRNAs, sensitive, accurate and cost-efficient miRNA profiling techniques are required. Next generation sequencing (NGS) is emerging as the preferred method for miRNA profiling; offering high sensitivity, single-nucleotide resolution and the possibility to profile a considerable number of samples in parallel. Despite the excitement about miRNA biomarkers, challenges associated with insufficient characterization of the sequencing library preparation efficacy, precision and method-related quantification bias have not been addressed in detail and are generally underappreciated in the wider research community. Here, we have tested in parallel four commercially available small RNA sequencing kits against a cohort of samples comprised of human plasma, human serum, murine brain tissue and a reference library containing ~ 950 synthetic miRNAs. We discuss the advantages and limits of these methodologies for massive parallel microRNAs profiling. This work can serve as guideline for choosing an adequate library preparation method, based on sensitivity, specificity and accuracy of miRNA quantification, workflow convenience and potential for automation. Taylor & Francis 2018-09-18 /pmc/articles/PMC6161688/ /pubmed/30223713 http://dx.doi.org/10.1080/15476286.2018.1514236 Text en © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Paper
Coenen-Stass, Anna M.L.
Magen, Iddo
Brooks, Tony
Ben-Dov, Iddo Z.
Greensmith, Linda
Hornstein, Eran
Fratta, Pietro
Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
title Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
title_full Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
title_fullStr Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
title_full_unstemmed Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
title_short Evaluation of methodologies for microRNA biomarker detection by next generation sequencing
title_sort evaluation of methodologies for microrna biomarker detection by next generation sequencing
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161688/
https://www.ncbi.nlm.nih.gov/pubmed/30223713
http://dx.doi.org/10.1080/15476286.2018.1514236
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