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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Detalles Bibliográficos
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
Descripción
Sumario: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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