Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs

MOTIVATION Whole genome sequencing (WGS) of tumor-normal sample pairs is a powerful approach for comprehensively characterizing germline copy number variations and somatic copy number alterations in cancer research and clinical practice. Existing computational approaches for detecting copy number events cannot detect germline copy number variations and somatic copy number alterations simultaneously, and yield low accuracy for somatic copy number alterations. RESULTS In this study, we developed TumorCNV, a novel approach for jointly detecting germline copy number variations and somatic copy number alterations from WGS data of the matched tumor-normal sample pair. We compared TumorCNV with existing copy number event detection approaches using the simulated data and real data for the COLO-829 melanoma cell line. The experimental results showed that TumorCNV achieved superior performance than existing approaches. AVAILABILITY The software TumorCNV is implemented using a combination of Java and R, and it is freely available from the website at https://github.com/yongzhuang/TumorCNV. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

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