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Updated: Jan 24, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs
Yongzhuang Liu1, Jian Liu1, Yadong Wang1
1School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
Motivation:
Whole-genome sequencing (WGS) of tumor-normal sample pairs is a powerful approach for comprehensively characterizing germline copy number variations (CNVs) and somatic copy number alterations (SCNAs) in cancer research and clinical practice. Existing computational approaches for detecting copy number events cannot detect germline CNVs and SCNAs simultaneously, and yield low accuracy for SCNAs.
Results:
In this study, we developed TumorCNV, a novel approach for jointly detecting germline CNVs and SCNAs 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 And Implementation:
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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