Unraveling cfDNA Fragmentation Patterns: Linking Chromatin Architecture to Cancer Diagnostic Sensitivity

Circulating cell-free DNA (cfDNA) liquid biopsies offer a powerful, non-invasive approach for cancer diagnostics, leveraging DNA fragments primarily released during apoptosis. Using droplet digital PCR on cfDNA samples from 88 breast and colorectal cancer patients, we uncovered highly consistent nucleosome breakpoints across individuals. Proximity to these cfDNA breakpoints diminishes the sensitivity of somatic mutation assays, including those targeting IDH1 and NRAS hotspot mutations, underscoring the importance of precise nucleosome positioning data. We introduce a probabilistic nucleosome protection scoring method that enables high-resolution mapping of nucleosome positions and cfDNA breakpoints. These maps reveal distinct nucleosome spacing patterns between heterochromatin and euchromatin, corresponding to different chromatin fiber topologies. Analysis of X-chromosome inactivation further supports the topoisomer model: heterochromatins 187 bp nucleosome repeat length differs from euchromatins 182 bp, generating wave interference patterns in nucleosome signals. Our findings suggest that loop-mediated transitions from T2 to T1 topoisomers shape chromatin accessibility and cfDNA fragmentation, advancing the diagnostic potential of liquid biopsy assays. HighlightsO_LINucleosome breakpoint conservation impacts somatic mutation assay sensitivity C_LIO_LIProbabilistic protection scoring enhances cfDNA nucleosome peak resolution C_LIO_LIChromatin states exhibit unique nucleosome spacing linked to distinct topologies, influencing cfDNA fragmentation C_LIO_LIChromosome X-inactivation phasing analyses reveal waveform interference in nucleosome positioning signals C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/623159v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@65893corg.highwire.dtl.DTLVardef@14c986org.highwire.dtl.DTLVardef@ba9306org.highwire.dtl.DTLVardef@10a7364_HPS_FORMAT_FIGEXP M_FIG C_FIG