Figure 2

Identification of differentially methylated probes in fusion-positive and fusion-negative rhabdomyosarcoma. (a) Volcano plot displaying significant, differentially methylated CpG sites. The β-value difference in DNA methylation between 20 fusion-positive and 17 fusion-negative rhabdomyosarcoma cases is plotted on the x axis, and the P-value for FDR-corrected Limma test of differences between fusion-positive and fusion-negative rhabdomyosarcoma (−1 × log₁₀ scale) is plotted on the y axis. Probes that are significantly different between fusion-positive and fusion-negative rhabdomyosarcoma are colored in red (hypermethylated in fusion-positive rhabdomyosarcoma) or blue (hypomethylated in fusion-positive rhabdomyosarcoma). (b) Heat map comparing DNA methylation profiles of normal skeletal muscle and bone marrow with fusion-positive and fusion-negative rhabdomyosarcoma. The clustering analysis was performed using the differentially methylated genes/probes identified in the comparison of fusion-positive vs fusion-negative rhabdomyosarcoma. Pearson correlation distance and Ward linkage were applied. Each individual sample is shown in one column with the 20 fusion-positive rhabdomyosarcoma cases, 17 fusion-negative rhabdomyosarcoma cases, 4 normal muscle cases, and 4 normal bone marrow cases labeled as red, blue, green, and purple rectangles, respectively, above the heat map. The four numbered rectangles on the left side highlight groups of differentially methylated genes, as described in the text. (c and d) Comparison of methylation of differentially methylated probes (in fusion-positive vs fusion-negative rhabdomyosarcoma) to methylation in normal muscle (c) or bone marrow (d). B&H, Benjamini and Hochberg; BM, normal bone marrow; FN, fusion-negative rhabdomyosarcoma; FP, fusion-positive rhabdomyosarcoma; Hyper, hypermethylated; Hypo, hypomethylated; MUS, normal skeletal muscle.