OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data.

ABSTRACT: Open chromatin regions (OCRs) are special regions of the human genome that can be accessed by DNA regulatory elements. Several studies have reported that a series of OCRs are associated with mechanisms involved in human diseases, such as cancers. Identifying OCRs using ATAC-seq or DNase-seq is often expensive. It has become popular to detect OCRs from plasma cell-free DNA (cfDNA) sequencing data, because both the fragmentation modes of cfDNA and the sequencing coverage in OCRs are significantly different from those in other regions. However, it is a challenging computational problem to accurately detect OCRs from plasma cfDNA-seq data, as multiple factors-e.g., sequencing and mapping bias, insufficient read depth, etc.-often mislead the computational model. In this paper, we propose a nove

SUBMITTER: Wang J 

PROVIDER: S-EPMC8198695 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature