Table 1.

Significant sample type effects on copy number alterations in GBM

(A)
	206 TCGA primary tumors	12 primary tumors	10 primary cultures	15 xenografts	21 cell lines	50 Sanger CGP cell lines
High-level amplifications
EGFR	43%	83%	10%	40%	5%	2%
CDK4/6	16%	8%	0%	13%	5%	4%
MDM2/4	15%	17%	10%	13%	10%	4%
PDGFRA	11%	17%	0%	7%	0%	2%
CCND1/D2/D3	4%	8%	0%	7%	5%	2%
Genomic deletions
CDKN2A/B	55%	58%	60%	87%	81%	70%
PTEN	8%	8%	10%	7%	14%	18%
CDKN2C	3%	0%	10%	27%	19%	20%
NF1	2%	0%	0%	7%	5%	8%
(B)
Genomic deletions
CDKN2A	1.0 ± 0.3	0.6 ± 0.1	0.3 ± 0.2	0.2 ± 0.1	0.3 ± 0.1
PTEN	1.0 ± 0.3	0.7*	0.2*	0.2*	0.5 ± 0.4
CDKN2C	1.1 ± 0.3	—	0.4*	1.1 ± 0.2	0.5 ± 0.3
NF1	1.4 ± 0.2	—	—	0.3*	0.3*

NOTE: A, percentage of tumor samples with focal (<10 Mb) genomic deletion and high-level (copy number >7) focal amplification of the indicated gene loci. B, mean copy number and SD at the indicated gene loci in those tumor samples with focal genomic deletion. Two-tailed unpaired t test analysis was used to compare the statistical significance of any difference in frequency of copy number alteration (A) and mean copy number (B) between the TCGA primary tumors and other GBM tumor samples. Statistically significant differences (P < 0.05) in frequency (A) and copy number means (B) are highlighted in boldface. —, no samples with focal genomic deletion at the indicated gene loci.

^*, less than three samples with genomic deletion, no SD calculation or t test analysis possible.