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

Autor: Budczies J; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany. jan.budczies@charite.de.; German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany. jan.budczies@charite.de., Pfarr N; Institute of Pathology, Technical University Munich (TUM), Munich, Germany.; German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany., Romanovsky E; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany., Endris V; Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany., Stenzinger A; Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.; German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany., Denkert C; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.; German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany.
Jazyk: angličtina
Zdroj: BMC bioinformatics [BMC Bioinformatics] 2018 Apr 24; Vol. 19 (1), pp. 157. Date of Electronic Publication: 2018 Apr 24.
DOI: 10.1186/s12859-018-2159-5
Abstrakt: 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.
Databáze: MEDLINE
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