Fig. 4: Molecular Profiles in LGDIT, SMARCB1-mutant, and Atypical teratoid/rhabdoid tumor (AT/RT).

a Analysis of genes with non-synonymous somatic mutations that have damaging effects in AT/RT. The top panel shows allele fractions of DNA mutations, with mutations in LGDIT, SMARCB1-mutant, (yellow) and AT/RT (green), with corresponding RNA expression and DNA methylation status of the genes in LGDIT, SMARCB1-mutant, and AT/RT. b Somatic variants and molecular profiles specific to AT/RT. Somatic variants unique to AT/RT were identified across intergenic, intronic, and exonic regions, with 167 genes showing significant RNA expression changes ( | log2FC | > 5). The top panel illustrates the allele fraction of variants categorized as intronic/intergenic (yellow) or exonic (green). The middle panel displays RNA expression levels (log-transformed counts per million, log(CPM + 1)) for LGDIT, SMARCB1-mutant, and AT/RT. The bottom panel shows methylation beta values stratified by genomic features, including promoters, enhancers, and gene bodies, comparing LGDIT, SMARCB1-mutant, and AT/RT. Gene names with red color indicate known oncogenes. blue gene names indicate known tumor suppressor genes.