Analysis of cell-free DNA for cancer diagnostics using liquid biopsies

Chromatin organisation influences gene regulation and genome stability, yet its dysregulation in cancer remains incompletely understood. This has become particularly important for patient diagnostics using cell-free DNA (cfDNA) from body fluids, based on computational analyses of nucleosome occupancy landscapes reconstructed from cfDNA. This thesis establishes the first comprehensive atlas of nucleosome positioning signatures across repetitive elements in tumour tissues and cfDNA. Using original approaches to cfDNA analysis, I demonstrate that genomic repetitive elements, including satellite repeats, LINEs, SINEs, and LTRs, undergo reproducible family-, subfamily-, and tissue-specific nucleosome repositioning in cancer. Integration with DNA methylation profiling reveals coordinated changes in methylation and nucleosome positioning at specific genomic repeats, underscoring the epigenetic interplay that drives chromatin instability. Quantifying cfDNA profiles at DNA sequence repeats, including unmappable genomic regions, identified highly informative cfDNA signatures. Machine learning models trained on these cfDNA repeat features successfully discriminated healthy individuals from patients with colorectal, pancreatic, bile lung, and gastric cancer, achieving robust performance even when minimal sets of repeated elements were used as top features. My analyses showed that nucleosome signatures at genomic repeats vary substantially across cfDNA fragment-size fractions, offering both pan-cancer and tissue-specific diagnostic insights. Additional nucleosomics-based approaches were benchmarked in glioblastoma (GBM). Using differential nucleosome occupancy in paired GBM and normal brain tissues, repeat-based cfDNA profiling achieved high accuracy and clearly distinguished patients from healthy controls. Combined analyses revealed that nucleosome organisation of repetitive elements in cfDNA mirrors tumour-specific chromatin reprogramming, providing a non-invasive readout of disease state. Together, these findings highlight the repetitive genome as a structured, regulatory, and clinically tractable layer of cancer epigenetics, establishing a conceptual and methodological foundation for repeat-based cfDNA diagnostics for early cancer detection and patient stratification.