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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Jan Budczies, Nicole Pfarr, Eva Romanovsky, Volker Endris, Albrecht Stenzinger, Carsten Denkert

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. More... »

PAGES

157

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12859-018-2159-5

DOI

http://dx.doi.org/10.1186/s12859-018-2159-5

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1103659326

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/29699497


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