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Fig. 2 | Genome Biology

Fig. 2

From: Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

Fig. 2

Genomic context of DNA methylation changes detected using cfNano. A Plasma cfDNA methylation levels were averaged from − 1 to + 1 kb at 5974 pneumocyte-specific NKX2-1 transcription factor binding sites (TFBS) taken from [25]. All methylation values are fold change relative to the flanking region (region from 0.8 to 1 kb from the TFBS). From left to right, plots show 23 healthy plasma samples from [13], 32 healthy plasma samples from [30], 3 healthy and 18 LuAd WGBS samples from [20], and 7 healthy and 6 LuAd cfNano samples from this study. B Average DNA methylation across chr16p, comparing lung tissue WGBS (top) to plasma cfNano samples from this study (bottom). Reference partially methylated domains (PMDs) are taken from [29]. C Methylation delta is shown for all 10-Mbp bins overlapping a reference PMD (methylation delta defined as the average methylation of the bin minus the average methylation genome-wide). Each cancer sample was compared to the group of healthy samples using a one-tailed t-test, and statistical significance is shown using asterisks. D 10-Mbp PMD bins were stratified by copy number status for each cancer sample, and statistically significant differences were calculated by performing one-tailed Wilcoxon tests within each sample.*p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001

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