LIQUORICE

LIQUORICE extracts bias-corrected coverage signatures from aligned whole-genome sequencing (WGS) data of cell-free DNA (cfDNA) by leveraging nucleosome-protected fragmentation patterns to infer chromatin accessibility and cell-of-origin from liquid biopsies.

Key Features:

• Bias-correction: Computes coverage signatures with corrections for biases introduced by nucleosome positioning and chromatin structure.
• Input data: Operates on aligned whole-genome sequencing (WGS) data derived from cfDNA.
• Predefined and application-specific genomic regions: Produces coverage signatures across user-defined genomic region sets specific to tissues or diseases.
• cfDNA fragmentation analysis: Leverages cfDNA fragmentation patterns caused by nucleosome protection, including decreased sequencing coverage in open chromatin regions.
• Detection, classification, and quantification: Enables detection, classification, and quantification tasks based on bias-corrected coverage signatures from liquid biopsies.

Scientific Applications:

• Tumor chromatin state assessment: Infers tumor chromatin accessibility and cell-of-origin from blood-derived cfDNA to support oncology studies.
• Cell death monitoring: Uses cfDNA fragmentation patterns to monitor cell death processes across tissues.
• Disease- and tissue-specific studies: Targets tissue-specific or disease-specific open chromatin regions for focused diagnostic or research analyses.

Methodology:

Processes aligned WGS cfDNA data to compute coverage signatures across predefined genomic regions and corrects for biases arising from nucleosome positioning and chromatin structure.