Fig. 4

Cancer-associated fragmentation features of cfNano vs. Illumina WGS. A Fragment length density plot for each cfNano sample, with cancer samples divided into low tumor fraction (TF < 0.15) and high tumor fraction (TF > 0.15) based on ichorCNA. Short mononucleosomes are defined as 100–150 bp [15, 35], and short dinucleosomes are defined at 275–325 bp. B The ratio (fraction) of short mononucleosome fragments (100–150 bp) to all mononucleosome fragments (100–220 bp). C Short mononucleosome ratios based on cfNano are compared to short mononucleosome ratios based on matched Illumina WGS libraries for four LuAd cases. cfNano samples were processed with either the 2019 Oxford Nanopore Real-time base calling model (2019) or the 2022 Oxford Nanopore High Accuracy model (HAC), as indicated by color. D The ratio (fraction) of short dinucleosome fragments (275–325 bp) to all dinucleosome fragments (275–400 bp). E Short dinucleosome ratios based on cfNano vs. Illumina WGS ratios for matched LuAd samples. F Frequency of 4-mer sequences occurring at fragment ends, for cfNano vs. matched Illumina samples. The 25 most frequent 4-mers are shown in ranked order based on frequencies in healthy plasma from [36]. G End-motif frequencies for all 256 possible 4-mers, comparing the average frequency in four cfNano samples vs. four matched Illumina WGS samples. H End-motif frequencies, comparing the average frequency in four healthy HU Italy cfNano samples vs. three healthy HU Israel cfNano samples. I Frequency of CCCA 4-mer in all cfNano samples. J CCCA 4-mer frequencies from cfNano samples vs. frequencies calculated from Illumina WGS for four matched LuAd samples. Statistical significance levels for B, D, and I were determined by a two-tailed t-test