Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes.

ABSTRACT:

Background

Detection of DNA copy number alterations (CNAs) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales, and distinct biological origins and functions. Although several computational tools are available to identify CNAs using read depth (RD) signal, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. Additionally, RD signal is affected by overdispersion-driven biases at low coverage, which significantly inflate false detection of CNA regions.

Results

We have developed CNAtra framewor

SUBMITTER: Khalil AIS 

PROVIDER: S-EPMC7160937 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature