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Updated: Jan 27, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
DEFOR: depth- and frequency-based somatic copy number alteration detector
He Zhang1, Xiaowei Zhan1, James Brugarolas2
1Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Motivation:
Detection of somatic copy number alterations (SCNAs) using high-throughput sequencing has become popular because of rapid developments in sequencing technology. Existing methods do not perform well in calling SCNAs for the unstable tumor genomes.
Results:
We developed a new method, DEFOR, to detect SCNAs in tumor samples from exome-sequencing data. The evaluation showed that DEFOR has a higher accuracy for SCNA detection from exome sequencing compared with the five existing tools. This advantage is especially apparent in unstable tumor genomes with a large proportion of SCNAs.
Availability And Implementation:
DEFOR is available at https://github.com/drzh/defor.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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