Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data.
Ontology highlight
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.
SUBMITTER: Budczies J
PROVIDER: S-EPMC5921540 | biostudies-literature | 2018 Apr
REPOSITORIES: biostudies-literature
Publications
Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data.
Budczies Jan J Budczies Jan J Pfarr Nicole N Romanovsky Eva E Endris Volker V Stenzinger Albrecht A Denkert Carsten C
BMC bioinformatics 20180424 1
<h4>Background</h4>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.<h4>Results</h4>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 a ...[more]
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