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Fig. 1 | Genome Biology

Fig. 1

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

Fig. 1

Estimating cell type fractions from cfNano. A Non-negative least squares regression based on [5] was used to deconvolute cell types in healthy plasma cfDNA samples from three whole-genome DNA methylation studies. Two representative samples are shown for each study (FF8 and FF23 for the Fox-Fisher et al. study, N1 and N8 for the Nguyen et al. study, and BC03 and HU11 for our cfNano samples). Each sample is downsampled from full read depth down to an average genome coverage of 0.001 (corresponding to approximately 13,000 fragments). All samples are shown in Additional file 1: Figs. S1-S3. B Deconvolution of all samples at full depth, with samples ordered within each group by epithelial cell fraction. Healthy vs. lung adenocarcinoma (LuAd) is shown as an annotation bar, as is the source site (HU Israel vs. BC for ISPRO Italy) for the cfNano samples. Asterisks mark the two HU samples with coverage less than 0.2× sequence depth. Statistical significance (p-value = 0.004) is shown for percent epithelial in healthy cfNano samples vs. LuAd cfNano samples. C The same samples downsampled to 0.2× sequence depth. D ichorCNA CNA plots for 4 representative cfNano samples, two healthy and two LuAds. Plots for all samples are included in Additional file 5. E Tumor fraction (TF) estimates from four LuAd samples based on ichorCNA from cfNano and matched Illumina WGS. F Two-component DNA methylation deconvolution of lung fraction using CpGs from MethAtlas-purified lung epithelia samples, showing scatter plot of ichorCNA estimates vs. deconvolution estimates for all cfNano samples. Statistical significance is shown for the DNA methylation estimate of healthy cfNano vs. LuAd cfNano samples (p-value = 0.003). G Two-component DNA methylation deconvolution of lung cancer fraction using CpGs from TCGA LuAd tumor samples, showing scatter plot of ichorCNA estimates vs. deconvolution estimates for all cfNano samples (healthy vs. LuAd p-value = 0.004). Statistical significance for B, C, F, and G was determined by a one-tailed t-test

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