Fig. 6

SCNA landscape in grade II and III gliomas. WHO-grade, histological class, and molecular subtype classification are shown by color as indicated. The thirty-eight samples are divided into 4 distinct subtypes based on the occurrence of a mutation in IDH1/2, co-deletion of chromosomes 1p and 19q and the presence of 17p cnLOH. Deletions and amplifications are visualized by boxes with different shades of blue and red, respectively. White regions are either normal or cnLOH regions. The bar charts below each box represent the mirrored and smoothed BAF values. Large mirrored and smoothed BAF values (close to 0.5) point to heterozygous SNP allelic imbalance. In the second subtype (from the top), at chromosome 17p, recurring cnLOH is apparent where the bar charts point to large mirrored and smoothed BAF values, though no deletion or amplification is detected at that region (Additional file 1: Table S5 for TCGA LGG sample barcode names)