Table 2.
Copy number alterations correlate with GBM subtype
| ROI | Proneural (n=54) |
Neural (n=24) |
Classical (n=37) |
Mesenchymal (n=55) |
Total # Samples Altered |
Known Cancer Gene in Region |
|---|---|---|---|---|---|---|
| A. Low and High Level Amplified Events | ||||||
| 7p11.2 | 29 (54%)* | 23 (96%) | 37 (100%) | 52 (95%) | 141 | EGFR |
| 7q21.2 | 25 (46%)* | 23 (96%) | 34 (92%) | 49 (89%) | 131 | CDK6 |
| 7q31.2 | 29 (54%)* | 22 (92%) | 32 (86%) | 50 (91%) | 131 | MET |
| 7q34 | 28 (52%)* | 22 (92%) | 32 (86%) | 50 (91%) | 132 | - |
| B. High Level Amplification Events | ||||||
| 7p11.2 | 9 (17%)* | 16 (67%) | 35 (95%)* | 16 (29%) | 76 | EGFR |
| 4q12 | 19 (35%)* | 3 (13%) | 2 (5%) | 5 (9%) | 29 | PDGFRA‡ |
| C. Homozygous and Hemizygous Deletion Events | ||||||
| 17q11.2 | 3 (6%) | 4 (17%) | 2 (5%) | 21 (38%)* | 28 | NF1 |
| 10q23 | 37 (69%) | 23 (96%) | 37 (100%) | 48 (87%) | 145 | PTEN |
| 9p21.3 | 30 (56%) | 17 (71%) | 35 (95%) | 37 (67%) | 119 | CDKN2A/CDKN2B |
| 13q14 | 28 (52%) | 11 (46%) | 6 (16%) | 29 (53%) | 74 | RB1 |
| D. Homozygous Deletion Events | ||||||
| 9p21.3 | 22 (40%) | 13 (54%) | 34 (92%)* | 29 (53%) | 98 | CDKN2A/CDKN2B |
Abbreviations: ROI, region of interest;
‡
The peak of the amplification is adjacent to PDGFRA; Significance of the difference in number of events between subtypes and remainder of the subtypes was tested using a two sided Fisher’s exact test, corrected for multiple testing using a Family Wise Error Rate. Bolded entries indicate p-values significant at 0.1 level. An asterisk indicates p-values significant at 0.01 level. Also see Figure S4 and Table S1.