Fig. 20
From: Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing
a–d Accuracy result of the MinION detection of cytosine methylation variants found in the synthetic oligonucleotides. Outputs from the classification of 6,966 C, 294 5mC, and 467 5hmC strands were sequenced in similar MinION flow cells. a Pre-read accuracy distribution results expressed by comparing normal distributions as Maximum-likelihood estimates (MLE) and HDP model distributions. Distributions are shown by triangles. b Across all cite three-way classification (C, mC, and hmC) of the template and co-template reads. c Confusion matrix showing the performance of HMM-HDP three-way cytosine classification on template reads of synthetic oligonucleotides. d Correlation between the log-odds of correct classification and the mean pairwise Hellinger distance between the methylation statuses of the 6-mer distributions overlapping a cytosine. e–h Variation between the ionic current distribution and effect of reading quality for left (6 mA in GATC) and right (5mC in CC(A/T) GG) motifs. The ionic current distribution between A and 6-mA (e) and C and 5mC (f) has shown a difference. Ionic current levels from 100 alignments are shown as a histogram g for A and 6-mA and h for C and mC. Learned probability densities of HDP are shown as curves. Image is Reprinted from [348] with permission of the publisher (Request ID 600061677, 27 Nov 2021)