De novo Characterization of Cell-free DNA Fragmentation Hotspots in Plasma Whole-genome Sequencing.

The raw sequencing data deposited here are low-coverage (~1X) whole-genome sequencing (WGS) of plasma cell-free DNA (cfDNA). The purpose is to validate the performance of early-stage cancer diagnosis in the Zhou et al. 2020 BioRxiv paper, mainly for two types of cancer: early-stage liver cancer and breast cancer. The cases and controls are matched with age, gender, smoking history, and alcohol usage. We developed a computational method to identify the cfDNA fragmentation hotspots from pooled low-coverage cfDNA WGS data. We found the cfDNA fragmentation hotspots are highly enriched in regulatory regions, such as open chromatin regions. The signals from these regions can help the diagnosis of early-stage cancers and their tissues-of-origin.