Figure 4

Chromosomal copy number profiles for sample 240 demonstrating intratumoral copy number heterogeneity. (A) CNA profile of initial tumor, clonal 1p/19q co-deletion, loss of chromosome 4 and intermediate level of loss of chromosome 10. (B) Hematoxylin and eosin stained slide showing regions used for DNA isolation: the red dotted line corresponds to the region used for chromosomal profile of 4A and regions outlined with a solid black line (labeled i to iv) were used for the chromosomal profiles of 4C. (C) CNA profiles from four non-overlapping regions. Insets at the top right corner of each profile show histological features representative for individual regions. In all regions the histopathological diagnosis was LGG, although within a tumor the regions analyzed for spatial heterogeneity often showed some variation in microscopic features, such as cellularity and nuclear size and shape. (i) Clonal 1p/19q co-deletion and loss of chromosome 4; (ii) clonal 1p/19q co-deletion, loss of chromosome 4 and intermediate loss of chromosome 10; (iii) clonal 1p/19q co-deletion, loss of chromosome 4, intermediate loss of chromosome 10 and intermediate gain of chromosome 11; (iv) clonal 1p/19q co-deletion, intermediate loss of chromosomes 4, 10q, 13, 15 and 18. The y-axis represents normalized log2 sequence read counts per bin, and the x-axis represents 15 kb bins ordered by genomic position from chromosomes 1 to 22.