Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1 deficient cases

Genome wide DNA methylation profiling of ATRTs and extracranial malignant rhabdoid tumors (eMRTs) samples harboring mutations in SMARCA4 and of small cell carcinoma of the ovary hypercalcemic type (SCCOHT) was performed . The Illumina Infinium HumanMethylation450 BeadChip and the Illumina Infinium MethylationEPIC arrays were used to obtain DNA methylation profiles across approximately 450,000 CpGs and 850,000 CpGs, respectively, in FFPE derived tumor samples. In total n=14 ATRT, n=6 eMRTs and n=28 SCCOHT samples were analyzed. Bisulphite converted DNA from the 14 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip and the Illumina Infinium MethylationEPIC BeadChip Array.