The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival

We obtained processed RNA-seq data for CBTN tumors from the CBTN Cavatica site on March 7, 2023, from both “CBTN” and “CBTN-X01” folders. As we observed extensive batch effects between the CBTN and CBTN-X01 RNA-seq datasets (due to the data for the CBTN dataset being generated much earlier than the CBTN-X01 dataset), we generated a batch effect-corrected RNA-seq dataset using the SVA package and ComBat algorithm in R Bioconductor, using histology as the experimental group (with histologies of <20 tumors consolidated into an “other” group), and removing genes with non-zero values in <20 tumors from the batch-correction.