Fig. 3 Contact maps of breast cancer cell line HCC1954 and standard cell line NA12878
Using the bioinformatics pipeline outlined in Fig. 2 we constructed contact maps at a 1 Mb resolution by mapping against human reference hg37, with each cell in the matrix representing the number of Pore-C reads that map to both parts of the genome. For both cell lines the chromosome boundaries are clearly visible, indicating that most of the interactions are intra-chromosomal (Fig. 3a). In the case of the cancer cell line (HCC1954, below the diagonal),amplifications of the underlying genome are visible as higher density horizontal and vertical bands, while regions of higher intensity off the diagonal indicate either genomic rearrangement or changes in the spatial organisation of the chromatin associated with cancer (Fig. 3b).