Table 1 Frequency of genetic abnormalities by tumour type
| Â | Tumour grade | |||||||
|---|---|---|---|---|---|---|---|---|
AOA | AA | GB | Total | |||||
N | % | N | % | N | % | N | % | |
Chromosome 1 status | ||||||||
 Normal copy number | 3 | 50% | 26 | 72% | 127 | 56% | 156 | 58% |
 Trisomy | 0 | 0% | 0 | 0% | 4 | 2% | 4 | 1% |
 Monosomy | 0 | 0% | 0 | 0% | 0 | 0% | 0 | 0% |
 Any other abnormality | 3 | 50% | 10 | 28% | 94 | 42% | 107 | 40% |
1p status | ||||||||
 Normal copy number | 4 | 67% | 28 | 78% | 150 | 67% | 182 | 68% |
 Loss of 1 copy | 1 | 17% | 1 | 3% | 2 | 1% | 4 | 1% |
 Any other abnormality | 1 | 17% | 7 | 19% | 73 | 32% | 81 | 30% |
1p36 status | ||||||||
 Normal copy number | 4 | 67% | 31 | 86% | 161 | 72% | 196 | 73% |
 Loss of 1 copy | 1 | 17% | 4 | 11% | 49 | 22% | 54 | 20% |
 Loss of both regions | 0 | 0% | 0 | 0% | 6 | 3% | 6 | 2% |
 Any other abnormality | 1 | 17% | 1 | 3% | 9 | 4% | 11 | 4% |
Other abnormality | ||||||||
 No | 4 | 67% | 28 | 78% | 160 | 71% | 192 | 72% |
 Yes | 2 | 33% | 8 | 22% | 65 | 29% | 75 | 28% |
Chromosome 10 status | ||||||||
 Normal copy number | 4 | 67% | 14 | 39% | 24 | 11% | 42 | 16% |
 Monosomy | 0 | 0% | 4 | 11% | 146 | 65% | 150 | 56% |
 10q partial deletion | 2 | 33% | 14 | 39% | 45 | 20% | 61 | 23% |
 Any other abnormality | 0 | 0% | 4 | 11% | 10 | 4% | 14 | 5% |
PTEN | ||||||||
 Normal copy number | 6 | 100% | 26 | 72% | 54 | 24% | 86 | 32% |
 Hemizygous deletion | 0 | 0% | 10 | 28% | 162 | 72% | 172 | 64% |
 Homozygous deletion | 0 | 0% | 0 | 0% | 9 | 4% | 9 | 3% |
MGMT | ||||||||
 Normal copy number | 4 | 67% | 15 | 42% | 28 | 12% | 47 | 18% |
 Hemizygous deletion | 2 | 33% | 21 | 58% | 196 | 87% | 219 | 82% |
 Homozygous deletion | 0 | 0% | 0 | 0% | 1 | 0% | 1 | 0% |
| Â | 6 | 100% | 36 | 100% | 225 | 100% | 267 | 100% |
Chromosome 7 status | ||||||||
 Normal copy number | 3 | 50% | 22 | 61% | 36 | 16% | 61 | 23% |
 Trisomy/polysomy | 0 | 0% | 2 | 6% | 143 | 64% | 145 | 54% |
 Monosomy | 0 | 0% | 0 | 0% | 1 | 0% | 1 | 0% |
 Any other abnormality | 3 | 50% | 12 | 33% | 45 | 20% | 60 | 22% |
Chromosome 19 status | ||||||||
 Normal copy number | 4 | 67% | 26 | 72% | 135 | 60% | 165 | 62% |
 Trisomy | 0 | 0% | 4 | 11% | 48 | 21% | 52 | 19% |
 Monosomy | 0 | 0% | 0 | 0% | 4 | 2% | 4 | 1% |
 Any other abnormality | 2 | 33% | 6 | 17% | 38 | 17% | 46 | 17% |
19q status | ||||||||
 Normal copy number | 4 | 67% | 27 | 75% | 139 | 62% | 170 | 64% |
 Loss of 1 copy | 1 | 17% | 1 | 3% | 2 | 1% | 4 | 1% |
 Any other abnormality | 1 | 17% | 8 | 22% | 84 | 37% | 93 | 35% |
19q13 status | ||||||||
 Normal copy number | 4 | 67% | 27 | 75% | 139 | 62% | 170 | 64% |
 Loss of 1 copy | 0 | 0% | 3 | 8% | 20 | 9% | 23 | 9% |
 Any other abnormality | 2 | 33% | 6 | 17% | 66 | 29% | 74 | 28% |
EGFR Amplification | ||||||||
 No | 6 | 100% | 32 | 89% | 125 | 56% | 163 | 61% |
 Yes (>4 copies) | 0 | 0% | 4 | 11% | 100 | 44% | 104 | 39% |
CDKN2A/p14 ARF | ||||||||
 Normal copy number | 4 | 67% | 24 | 67% | 87 | 39% | 115 | 43% |
 Hemizygous deletion | 2 | 33% | 11 | 31% | 67 | 30% | 80 | 30% |
 Homozygous deletion | 0 | 0% | 1 | 3% | 71 | 32% | 72 | 27% |
MDM2 Amplification | ||||||||
 No | 6 | 100% | 34 | 94% | 205 | 91% | 245 | 92% |
 Yes (>4 copies) | 0 | 0% | 2 | 6% | 20 | 9% | 22 | 8% |
CDK4 amplification | ||||||||
 No | 6 | 100% | 33 | 92% | 200 | 89% | 239 | 90% |
 Yes (>4 copies) | 0 | 0% | 3 | 8% | 25 | 11% | 28 | 10% |
PDGFRA amplification | ||||||||
 No | 6 | 100% | 33 | 92% | 211 | 94% | 250 | 94% |
 Yes (>4 copies) | 0 | 0% | 3 | 8% | 14 | 6% | 17 | 6% |
RB1 copy number | ||||||||
 Normal | 5 | 100% | 31 | 86% | 164 | 73% | 200 | 75% |
 Hemizygous deletion | 0 | 0% | 5 | 14% | 60 | 27% | 65 | 24% |
 3 copies | 0 | 0% | 0 | 0% | 1 | 0% | 1 | 0% |
TP53 mutation cases with complete dataset only | ||||||||
 No | 2 | 40% | 4 | 40% | 43 | 64% | 49 | 60% |
 Yes | 3 | 60% | 6 | 60% | 24 | 36% | 33 | 40% |
IDH1/IDH2 mutation | ||||||||
 No | 1 | 17% | 7 | 16% | 191 | 82% | 199 | 71% |
 Yes | 5 | 83% | 36 | 84% | 41 | 18% | 82 | 29% |
RB1 pathway | ||||||||
 Normal | 3 | 60% | 19 | 53% | 52 | 23% | 74 | 28% |
 Abnormal | 2 | 40% | 17 | 47% | 173 | 77% | 192 | 72% |
p53 pathway | ||||||||
 Normal | 2 | 33% | 2 | 7% | 10 | 5% | 14 | 6% |
 Abnormal | 4 | 67% | 26 | 93% | 181 | 95% | 211 | 94% |
MGMT Methylation | ||||||||
 <10% | 0 | 0% | 5 | 12% | 66 | 28% | 71 | 25% |
 ≥10% | 6 | 100% | 36 | 88% | 168 | 72% | 210 | 75% |