Figure 2 from Clinical Validation of a Cell-Free DNA Fragmentome Assay for Augmentation of Lung Cancer Early Detection

Genome-wide fragmentation profiles are altered in patients with cancer and reflect underlying chromatin structure. A, The fragmentation profile (ratio of short to long cfDNA fragments in 5 Mb bins) across the genome was evaluated in the classifier training plasma samples of lung cancer (n = 181) and noncancer individuals (n = 395). The noncancer individuals had similar fragmentation profiles, whereas patients with lung cancer exhibited significant variation. B, Comparison of cfDNA profiles with Hi-C A/B chromatin compartment reference data from lung cancer tissue or peripheral blood cells. Track 1 shows A/B compartments extracted from LUSC cancer tissue (48). Track 2 shows a median lung cancer component extracted from the LUSC plasma samples of 7 patients with lung cancer from the classifier training set with high tumor fraction by ichorCNA (49). The 7 LUSC cases with high ichorCNA have values of 0.051, 0.439, 0.230, 0.259 0.439, 0.167, and 0.057. Track 3 shows the median profile for 10 noncancer plasma samples from the training set. Track 4 shows A/B compartments for lymphoblast cells (48). These four tracks show chromosome 22 as an example, with darker shading indicating informative regions of the genome where the two reference tracks differ in domain (open/closed). C, 100-kb regions were selected using the reference LUSC and lymphoblast A/B tracks as having the same chromatin state or opposite chromatin state. Within these regions, the deviation of the fragmentation value from a noncancer cfDNA reference (n = 10) was plotted per region per individual (noncancer n = 20, LUSC n = 7). Values around 0 have little variation from the noncancer reference. Negative values indicate a region has a more open chromatin state than the reference and positive values indicate a region has a more closed chromatin state than the reference. These data suggest that although cfDNA profiles of healthy individuals reflect the chromatin structure of blood cells, those of patients with lung cancer represent a mixture of cfDNA patterns of chromatin compartments from lung cancer as well as blood cells.