Table 2. Aberrant methylation and mutation rates in oncogenes, tumor suppressor genes, and all other genes.

For three pediatric tumor types, we identified aberrant methylation events (either hypomethylation or hypermethylation) that had occurred in a given tumor and gene. For the same tumor/gene combinations, we identified somatic single-nucleotide variants, indels, and structural variants that had occurred. These numbers indicate overall rates of aberrant methylation or mutation across all tumors of a given type. Methylation rates and mutation rates were typically similar across all three gene categories, but mutation rates for oncogenes and tumor suppressor genes were always higher than for other genes.

Tumor type	Aberration type	Oncogene	TSG	Other
Neuroblastoma	Hypermethylation	0.348	0.256	0.176
Neuroblastoma	Hypomethylation	0.158	0.145	0.203
Neuroblastoma	Mutation	0.052	0.058	0.035
Osteosarcoma	Hypermethylation	0.402	0.199	0.179
Osteosarcoma	Hypomethylation	0.089	0.110	0.203
Osteosarcoma	Mutation	0.027	0.036	0.021
Wilms tumor	Hypermethylation	0.477	0.194	0.171
Wilms tumor	Hypomethylation	0.048	0.152	0.197
Wilms tumor	Mutation	0.011	0.012	0.006