LYCEUM: learning to call copy number variants on low-coverage ancient genomes.

ABSTRACT:

Motivation

Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduces additional noise into sequencing data; and finally, (iii) the typically low-coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high-coverage read-depth signals, underperform under such condition

SUBMITTER: Yılmaz MA 

PROVIDER: S-EPMC12261418 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature