Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets.

ABSTRACT: Copy number alterations (CNAs) are an important type of genomic variation which play a crucial role in the initiation and progression of cancer. With the explosion of single-cell RNA sequencing (scRNA-seq), several computational methods have been developed to infer CNAs from scRNA-seq studies. However, to date, no independent studies have comprehensively benchmarked their performance. Herein, we evaluated five state-of-the-art methods based on their performance in tumor versus normal cell classification; CNAs profile accuracy, tumor subclone inference, and aneuploidy identification in non-malignant cells. Our results showed that Numbat outperformed others across most evaluation criteria, while CopyKAT excelled in scenarios when expression matrix alone was used as input. In specific tasks,

SUBMITTER: Song M 

PROVIDER: S-EPMC11879432 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature