Segmentum: a tool for copy number analysis of cancer genomes.

ABSTRACT:

Background

Somatic alterations, including loss of heterozygosity, can affect the expression of oncogenes and tumor suppressor genes. Whole genome sequencing enables detailed characterization of such aberrations. However, due to the limitations of current high throughput sequencing technologies, this task remains challenging. Hence, accurate and reliable detection of such events is crucial for the identification of cancer-related alterations.

Results

We introduce a new tool called Segmentum for determining somatic copy numbers using whole genome sequencing from paired tumor/normal samples. In our approach, read depth and B-allele fraction signals are smoothed, and double sliding windows are used to detect breakpoints, which makes our approach fast and straightforward. Because

SUBMITTER: Afyounian E 

PROVIDER: S-EPMC5390478 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature