Ioncopy：一个用于在靶向 NGS 数据中调用拷贝数改变的 R Shiny 应用程序。
Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data.
机构信息
Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.
German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany.
出版信息
BMC Bioinformatics. 2018 Apr 24;19(1):157. doi: 10.1186/s12859-018-2159-5.
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.
背景
体细胞拷贝数改变（CNAs）导致肿瘤基因组中可临床靶向的异常。对于常规诊断和生物标志物研究，非常希望在单一检测中同时分析 CNA 和体细胞突变。
结果
Ioncopy 是一种经过验证的方法，也是一种用于从靶向 NGS 数据中调用 CNA 的易用软件。对每个样本中的每个基因进行拷贝数和 CNA 显著性的估计。在使用或不使用正常（种系）DNA 对照的情况下，对 CNA 的拷贝数增益和丢失进行多次测试校正控制 FWER 或 FDR 后调用。
结论
Ioncopy 方便了在肿瘤组织样本中调用 CNA，无论是否使用正常（种系）DNA 对照。
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