Work

DEFOR: depth- and frequency-based somatic copy number alteration detector

Year: 2019

Type: article

Abstract: 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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btz170

Authors: He Zhang, Xiaowei Zhan, James Brugarolas, Yang Xie

Institutions: The University of Texas Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center

Language: English

Topic: Cancer Genomics and Diagnostics

Subfield: Cancer Research

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: green

Funders: Cancer Prevention and Research Institute of Texas, National Institutes of Health, National Cancer Institute