<i>CNAdjust</i>: enhancing CNA calling accuracy through systematic baseline adjustment.

ABSTRACT: Accurate determination of the genomic copy number baseline is crucial for identifying copy number alterations (CNAs) in cancer, yet it remains a significant challenge in tumors with complex karyotypes. To address this, we present CNAdjust, an integrated method to systematically detect and correct baseline inaccuracies in CNA data. CNAdjust employs a Bayesian framework that integrates cohort-specific CNA frequency priors with a data-driven plausibility score, ensuring that adjusted calls align with both biological cohort patterns and study-specific data. Performance validation using the TCGA pan-cancer dataset demonstrated improved alignment with absolute copy number estimates and enhanced CNA pattern interpretation. Furthermore, we revealed a strong correlation between chromo

SUBMITTER: Zhao H 

PROVIDER: S-EPMC12510678 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature