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

In: BMC Bioinformatics, 19 (2018), Nr. 157. pp. 1-4. ISSN 1471-2105

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DOI: 10.1186/s12859-018-2159-5
URN: urn:nbn:de:bsz:16-heidok-244215
URL: http://www.ub.uni-heidelberg.de/archiv/24421

Abstract

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.

Document type:	Article
Journal or Publication Title:	BMC Bioinformatics
Volume:	19
Number:	157
Publisher:	BioMed Central ; Springer
Place of Publication:	London ; Berlin ; Heidelberg
Date Deposited:	02 May 2018 09:29
Date:	2018
ISSN:	1471-2105
Page Range:	pp. 1-4
Faculties / Institutes:	Medizinische Fakultät Heidelberg > Pathologisches Institut
DDC-classification:	610 Medical sciences Medicine