In the TCGA dataset where both copy number and expression data were available, MYCN copy number gain was highly enriched in the C5 subtype (p<0.0001, two sided Mann-Whitney test; Figure 3B).
Also of note was the fact that multiple genes associated with the complement cascade (C1S, C1R, C1RL, F13A1, and CFI) were within the set of genes showing both copy number and expression changes between PN-OA and PN-GBM samples.
Our analysis also highlights 19 regions with both copy number and expression imbalances in greater than 40% of cases.
We have defined a number of chromosome regions with a high frequency of both copy number and expression change in TGCT.
In addition to genes exhibiting changes in both copy number and expression, the remaining 79% of the CNVs in homozygotes or 89% of the CNVs in heterozygotes in our study were not responsive to gene copy-number changes (dosage insensitive).
Although this may seem in contradiction with our previous results [ 35] it must be noticed that the expression of the molecule was evaluated, in that study, using a score obtained by evaluating both number and intensity of expression.
Among the primary samples also, heterogeneity in both number and level of expression of ABC transporters was observed.
A number of recent comprehensive studies have reported differences at both the copy number and expression levels that distinguish pediatric DIPG from both their adult and pediatric supratentorial GBM counterparts, indicating that they may be separate biologic entities [ 1, 17, 26].
Further, by integrating the genomic and transcriptional datasets, we could define a set of candidate cancer genes residing at these loci and exhibiting both altered copy number and expression.
First, we integrated both miRNA copy number and expression into a single matrix.
