Table 1.
Amplificators1,2 versus non-amplificators in both the TCGA and UCSD datasets.
| Information for TCGA and for UCSD Cancer Cohort | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Total samples N (% total) |
TP53-mutated samples N (% total) |
Number of WGS amplifications per sample, mean [CI95%] |
Number of FM-panel amplifications per sample, mean [CI95%] |
||||||
| TCGA Data* | |||||||||
| All samples | 7246 (100) | 2897 (40) | 344 [331–357] | 5.1 [4.9–5.3] | |||||
| Non-amplificators (WGS) | 6519 (100) | 2448 (38) | 190 [184–197] | 3.2 [3.1–3.3] | |||||
| WGS amplificators1 | 727 (100) | 449 (62) | 1720 [1662–1778] | 22.4 [21.5–23.2] | |||||
| Non-amplificators (FM) | 6514 (100) | 2416 (37) | 207 [199–215] | 3.0 [2.9–3.1] | |||||
| FM-panel amplificators2 |
732 (100) |
481 (66) |
1562 [1503–1621] |
24.0 [23.2–24.7] |
|||||
| UCSD** | |||||||||
| All samples | 1891 (100) | 824 (44) | - | 2.5 [2.2–2.7] | |||||
| Non-amplificators (FM) | 1706 (100) | 707 (41) | - | 1.2 [1.1–1.3] | |||||
| FM-panel amplificators2 |
185 (100) |
117 (63) |
- |
14.2 [13.4–15.0] |
|||||
| Amplifications in TP53 mutated vs. wild-type samples in the TCGA and UCSD datasets | |||||||||
| |
Total samples N (% total) |
Number of WGS amplifications per sample1 Mean [CI95%] Median [range] |
p-value |
Number of FM panel amplifications per sample2 Mean [CI95%] Median [range] |
p-value |
||||
| TCGA Data* | |||||||||
| TP53 mutated samples | 2897 (40%) | 516 [491–542] 289 [0–9658] |
6.58E-83 | 7.7 [7.3–8.0] 5 [0–93] |
9.28E-96 | ||||
|
TP53 wild-type samples |
4349 (60%) |
229 [215–243] 7 [0–6981] |
|
3.4 [3.2–3.6] 0 [0–73] |
|
||||
| UCSD** | |||||||||
| TP53 mutated samples | 824 (44%) | - | - | 3.3 [3.0–3.7] 1 [0–32] |
3.39E-13 | ||||
| TP53 wild-type samples | 1067 (56%) | - | 1.8 [1.5–2.0] 0 [0–38] |
||||||
*In the TCGA data, a total of 7,246 samples that had copy number variation (CNV) and mutation data were curated from 11,245 possible TCGA samples across all cancer cohorts.
1The phenotype “WGS amplificator” corresponds to tumors presenting a high number of amplifications considering the whole genome (top 10% amplification burden, within the whole genome): All p < 0.0001.
2The phenotype “FM-panel amplificator” corresponds to tumors presenting a high number of amplifications considering only genes included in the Foundation One panel (top 10% amplification burden, within the 315 genes of the Foundation One panel manufactured by Foundation Medicine). All p < 0.0001.
**In the UCSD data, a total of 1,891 samples sequenced from patients treated at Moores Cancer Center in La Jolla, CA, were analyzed across all cancer types.
Abbreviations: CI95% = 95% confidence interval; FM = Foundation Medicine; N = number; TCGA = The Cancer Genome Atlas; UCSD = University of California San Diego; WGS = whole genome sequencing.