Fig. 2

Differential global chromatin (5 Mb windows) and sub-compartments in cfDNA of between pCR and non-pCR patients. a Genome-wide fragmentation profiles shown in 5 Mb bins in cfDNA of pCR and non-pCR patients. b Sub-compartments in cfDNA of pCR patients. c. Sub-compartments annotated in cfDNA of non-pCR patients. d The fold change and P-value of sub-compartments in cfDNA of pCR versus non-pCR patients. Sub-compartments of the human genome were annotated by the Hi-C data of GM12878. A1 and A2 regions are enriched regions. B1 consists of facultative heterochromatic regions. B2 is enriched at the nuclear lamina and NADs. B3 is also enriched at the nuclear lamina but not at NADs. cfDNA, cell-free DNA; pCR, pathological complete response; non-pCR, non-pathological complete response; cfDNA, cell-free DNA; NADs, nucleolus-associated domains