ATACAmp: a tool for detecting ecDNA/HSRs from bulk and single-cell ATAC-seq data.

ABSTRACT:

Background

High oncogene expression in cancer cells is a major cause of rapid tumor progression and drug resistance. Recent cancer genome research has shown that oncogenes as well as regulatory elements can be amplified in the form of extrachromosomal DNA (ecDNA) or subsequently integrated into chromosomes as homogeneously staining regions (HSRs). These genome-level variants lead to the overexpression of the corresponding oncogenes, resulting in poor prognosis. Most existing detection methods identify ecDNA using whole genome sequencing (WGS) data. However, these techniques usually detect many false positive regions owing to chromosomal DNA interference.

Results

In the present study, an algorithm called "ATACAmp" that can identify ecDNA/HSRs in tumor genomes using ATAC-seq d

SUBMITTER: Cheng H 

PROVIDER: S-EPMC10638764 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature