Extended Data Fig. 5: Methylation-based subtyping of T-ALL patients.
From: Acute lymphoblastic leukemia displays a distinct highly methylated genome
a) Hierarchical clustering with Euclidean distance of T-ALL patients based on commonly covered variable CGIs (n = 8,863, top). Violin plots (bottom) show the distribution of variable CGIs in the three main clusters compared to healthy precursor T cells. White dots denote the median, edges denote the IQR and whiskers denote either 1.5 × IQR or minima/maxima (if no point exceeded 1.5 × IQR; minima/maxima are indicated by the violin plot range). b) Heatmap of standardized, log2-transformed expression for T-ALL patients and a selection of T-ALL marker genes. c) Event-free and overall survival for T-ALL patients of different methylation-based groups (information not available for all samples with WGBS data). No significant difference in outcome was detected (log-rank test). d) Boxplots of DNA methylation entropy across commonly covered variable CGIs (n = 8,863) for every healthy T-cell and T-ALL patient sample. Lines denote the median, edges denote the IQR and whiskers denote either 1.5 × IQR or minima/maxima (if no point exceeded 1.5 × IQR; outliers were omitted). The entropy is highest for samples of T-ALLLM and T-ALLIM. The line indicates the median variable CGI methylation per sample (right y-axis).
