CNSistent integration and feature extraction from somatic copy number profiles.

ABSTRACT:

Background

Most cancers exhibit somatic copy number alterations (SCNAs)-gains and losses of variable regions of DNA. SCNAs play a key role in cancer adaptation through modulation of gene expression, deletion of tumor suppressor genes, or amplification of oncogenes. Systematic analysis of SCNAs is now a routine task in both the clinic and research and can help identify novel cancer genes, improve our understanding of cancer gene regulation, and enable us to accurately reconstruct cancer phylogenies. However, to conduct such analyses, SCNA profiles have to be integrated between samples, patients, and cohorts-often a nontrivial task, for which dedicated toolkits are lacking.

Results

To fill this gap, we developed CNSistent, a Python package for imputation, filtering, consistent

SUBMITTER: Streck A 

PROVIDER: S-EPMC12448185 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature