Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data

BACKGROUND: Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together with somatic mutations is highly desirable. RESULTS: Ioncopy is a validated method...

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Autores principales: Budczies, Jan, Pfarr, Nicole, Romanovsky, Eva, Endris, Volker, Stenzinger, Albrecht, Denkert, Carsten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5921540/
https://www.ncbi.nlm.nih.gov/pubmed/29699497
http://dx.doi.org/10.1186/s12859-018-2159-5
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author Budczies, Jan
Pfarr, Nicole
Romanovsky, Eva
Endris, Volker
Stenzinger, Albrecht
Denkert, Carsten
author_facet Budczies, Jan
Pfarr, Nicole
Romanovsky, Eva
Endris, Volker
Stenzinger, Albrecht
Denkert, Carsten
author_sort Budczies, Jan
collection PubMed
description BACKGROUND: Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together with somatic mutations is highly desirable. RESULTS: Ioncopy is a validated method and easy-to-use software for CNA calling from targeted NGS data. Copy number and significance of CNA are estimated for each gene in each sample. Copy number gains and losses are called after multiple testing corrections controlling FWER or FDR. CONCLUSIONS: Ioncopy facilitates calling of CNAs in a cohort of tumors tissues with or without using normal (germline) DNA controls. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2159-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-59215402018-05-01 Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data Budczies, Jan Pfarr, Nicole Romanovsky, Eva Endris, Volker Stenzinger, Albrecht Denkert, Carsten BMC Bioinformatics Software BACKGROUND: Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together with somatic mutations is highly desirable. RESULTS: Ioncopy is a validated method and easy-to-use software for CNA calling from targeted NGS data. Copy number and significance of CNA are estimated for each gene in each sample. Copy number gains and losses are called after multiple testing corrections controlling FWER or FDR. CONCLUSIONS: Ioncopy facilitates calling of CNAs in a cohort of tumors tissues with or without using normal (germline) DNA controls. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2159-5) contains supplementary material, which is available to authorized users. BioMed Central 2018-04-24 /pmc/articles/PMC5921540/ /pubmed/29699497 http://dx.doi.org/10.1186/s12859-018-2159-5 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Budczies, Jan
Pfarr, Nicole
Romanovsky, Eva
Endris, Volker
Stenzinger, Albrecht
Denkert, Carsten
Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
title Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
title_full Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
title_fullStr Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
title_full_unstemmed Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
title_short Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
title_sort ioncopy: an r shiny app to call copy number alterations in targeted ngs data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5921540/
https://www.ncbi.nlm.nih.gov/pubmed/29699497
http://dx.doi.org/10.1186/s12859-018-2159-5
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