This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level events and 8 clinical features across 472 patients, 93 significant findings detected with Q value < 0.25.
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1p gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
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1q gain cnv correlated to 'YEARS_TO_BIRTH'.
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3p gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
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3q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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4p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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7p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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7q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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9q gain cnv correlated to 'GENDER'.
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10p gain cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'ETHNICITY'.
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11p gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
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12q gain cnv correlated to 'Time to Death'.
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16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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17p gain cnv correlated to 'Time to Death'.
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17q gain cnv correlated to 'Time to Death'.
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19p gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
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19q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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20p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.
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20q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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21q gain cnv correlated to 'YEARS_TO_BIRTH'.
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22q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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xp gain cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
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xq gain cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.
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1p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
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1q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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3p loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
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3q loss cnv correlated to 'Time to Death'.
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4p loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
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4q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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5p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
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5q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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6p loss cnv correlated to 'Time to Death'.
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6q loss cnv correlated to 'Time to Death', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
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8p loss cnv correlated to 'Time to Death'.
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8q loss cnv correlated to 'Time to Death'.
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9p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
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9q loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
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10p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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10q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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11p loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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11q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
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12q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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13q loss cnv correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.
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14q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
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16p loss cnv correlated to 'YEARS_TO_BIRTH'.
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16q loss cnv correlated to 'YEARS_TO_BIRTH'.
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17p loss cnv correlated to 'Time to Death' and 'KARNOFSKY_PERFORMANCE_SCORE'.
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17q loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
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18p loss cnv correlated to 'YEARS_TO_BIRTH'.
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18q loss cnv correlated to 'YEARS_TO_BIRTH'.
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19q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
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21q loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'HISTOLOGICAL_TYPE'.
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22q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.
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xq loss cnv correlated to 'Time to Death'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 93 significant findings detected.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
10p loss | 74 (16%) | 398 |
0 (0) |
3.96e-17 (8.46e-15) |
0.703 (1.00) |
0.00324 (0.0493) |
0.00019 (0.00486) |
0.524 (0.934) |
0.0132 (0.136) |
0.751 (1.00) |
10q loss | 87 (18%) | 385 |
0 (0) |
1.05e-14 (1.69e-12) |
0.475 (0.895) |
0.0166 (0.161) |
5e-05 (0.00139) |
0.654 (1.00) |
0.0344 (0.241) |
0.546 (0.948) |
10p gain | 53 (11%) | 419 |
0.742 (1.00) |
0.0236 (0.199) |
0.243 (0.688) |
0.0695 (0.367) |
0.00072 (0.0132) |
0.0255 (0.204) |
1 (1.00) |
0.034 (0.241) |
1p loss | 171 (36%) | 301 |
0.00267 (0.0438) |
0.000263 (0.00625) |
0.847 (1.00) |
0.751 (1.00) |
1e-05 (0.000427) |
0.0153 (0.153) |
0.314 (0.736) |
1 (1.00) |
20p gain | 38 (8%) | 434 |
1.14e-07 (9.12e-06) |
3.59e-07 (2.56e-05) |
0.733 (1.00) |
0.0317 (0.241) |
0.252 (0.688) |
1 (1.00) |
0.366 (0.797) |
1 (1.00) |
6q loss | 55 (12%) | 417 |
3.39e-05 (0.00114) |
0.0878 (0.422) |
0.567 (0.962) |
0.0032 (0.0493) |
0.00051 (0.0105) |
0.146 (0.559) |
0.111 (0.475) |
1 (1.00) |
9p loss | 104 (22%) | 368 |
0.000495 (0.0105) |
0.0322 (0.241) |
0.823 (1.00) |
0.0813 (0.406) |
0.176 (0.593) |
0.0356 (0.245) |
0.939 (1.00) |
1 (1.00) |
19q loss | 193 (41%) | 279 |
0.0191 (0.18) |
0.0258 (0.204) |
0.925 (1.00) |
0.618 (0.987) |
1e-05 (0.000427) |
0.126 (0.506) |
0.904 (1.00) |
0.467 (0.894) |
22q loss | 50 (11%) | 422 |
1.93e-05 (0.000688) |
1.87e-05 (0.000688) |
0.548 (0.948) |
0.0284 (0.221) |
0.253 (0.688) |
0.853 (1.00) |
0.168 (0.585) |
1 (1.00) |
1p gain | 11 (2%) | 461 |
0.0116 (0.126) |
0.0456 (0.286) |
0.223 (0.664) |
0.975 (1.00) |
0.00822 (0.0939) |
0.455 (0.875) |
1 (1.00) |
1 (1.00) |
3p gain | 11 (2%) | 461 |
0.00348 (0.0518) |
0.0888 (0.424) |
0.545 (0.948) |
0.753 (1.00) |
0.0258 (0.204) |
0.455 (0.875) |
1 (1.00) |
1 (1.00) |
3q gain | 8 (2%) | 464 |
0.000903 (0.0161) |
0.0347 (0.241) |
0.305 (0.734) |
0.293 (0.728) |
0.0805 (0.406) |
0.191 (0.622) |
1 (1.00) |
1 (1.00) |
7p gain | 110 (23%) | 362 |
9.45e-06 (0.000427) |
3.39e-08 (3.1e-06) |
0.19 (0.622) |
0.106 (0.464) |
0.214 (0.648) |
0.681 (1.00) |
0.041 (0.269) |
0.778 (1.00) |
7q gain | 141 (30%) | 331 |
5e-05 (0.00139) |
1e-08 (1.28e-06) |
0.417 (0.84) |
0.308 (0.734) |
0.0597 (0.338) |
0.377 (0.806) |
0.0659 (0.358) |
0.8 (1.00) |
11p gain | 30 (6%) | 442 |
0.517 (0.928) |
0.0244 (0.201) |
0.182 (0.608) |
0.936 (1.00) |
0.0121 (0.129) |
1 (1.00) |
1 (1.00) |
0.339 (0.766) |
19p gain | 91 (19%) | 381 |
0.641 (1) |
0.0155 (0.153) |
0.412 (0.834) |
0.0986 (0.454) |
1e-05 (0.000427) |
0.661 (1.00) |
0.692 (1.00) |
0.764 (1.00) |
19q gain | 22 (5%) | 450 |
1.49e-05 (0.000597) |
4.07e-05 (0.00124) |
0.83 (1.00) |
0.234 (0.681) |
0.257 (0.688) |
0.782 (1.00) |
0.155 (0.574) |
0.595 (0.978) |
20q gain | 38 (8%) | 434 |
2.28e-08 (2.43e-06) |
4.76e-07 (3.05e-05) |
0.306 (0.734) |
0.0562 (0.324) |
0.442 (0.862) |
0.831 (1.00) |
0.698 (1.00) |
1 (1.00) |
xq gain | 34 (7%) | 438 |
0.515 (0.928) |
0.196 (0.625) |
0.00394 (0.0549) |
0.147 (0.561) |
0.0218 (0.191) |
0.506 (0.928) |
0.308 (0.734) |
0.118 (0.497) |
4p loss | 63 (13%) | 409 |
0.67 (1.00) |
0.00371 (0.054) |
0.101 (0.461) |
0.615 (0.987) |
0.00054 (0.0108) |
0.231 (0.681) |
0.273 (0.709) |
0.489 (0.91) |
5p loss | 33 (7%) | 439 |
0.925 (1.00) |
0.3 (0.731) |
1 (1.00) |
0.0749 (0.387) |
0.0138 (0.14) |
0.0201 (0.181) |
0.803 (1.00) |
0.629 (0.992) |
11q loss | 20 (4%) | 452 |
0.00213 (0.0359) |
0.173 (0.585) |
1 (1.00) |
0.0401 (0.267) |
0.0169 (0.161) |
0.391 (0.81) |
1 (1.00) |
0.577 (0.969) |
14q loss | 70 (15%) | 402 |
3.62e-05 (0.00116) |
0.00031 (0.00685) |
0.897 (1.00) |
0.14 (0.544) |
0.172 (0.585) |
0.513 (0.928) |
0.249 (0.688) |
0.489 (0.91) |
17p loss | 12 (3%) | 460 |
0.00732 (0.0867) |
0.0513 (0.301) |
0.38 (0.806) |
0.00311 (0.0493) |
0.71 (1.00) |
0.476 (0.895) |
1 (1.00) |
0.0828 (0.411) |
21q loss | 29 (6%) | 443 |
0.89 (1.00) |
0.653 (1.00) |
0.7 (1.00) |
0.000655 (0.0123) |
0.0218 (0.191) |
0.628 (0.992) |
0.779 (1.00) |
1 (1.00) |
1q gain | 20 (4%) | 452 |
0.428 (0.852) |
0.000188 (0.00486) |
0.647 (1.00) |
0.246 (0.688) |
0.16 (0.585) |
0.563 (0.96) |
0.407 (0.826) |
1 (1.00) |
4p gain | 11 (2%) | 461 |
0.238 (0.684) |
0.847 (1.00) |
1 (1.00) |
0.98 (1.00) |
0.0245 (0.201) |
0.7 (1.00) |
0.449 (0.873) |
1 (1.00) |
9q gain | 22 (5%) | 450 |
0.165 (0.585) |
0.0419 (0.269) |
0.00706 (0.0867) |
0.281 (0.726) |
0.0692 (0.367) |
0.592 (0.978) |
0.336 (0.765) |
0.595 (0.978) |
12q gain | 14 (3%) | 458 |
0.0236 (0.199) |
0.314 (0.736) |
0.286 (0.727) |
0.122 (0.497) |
1 (1.00) |
1 (1.00) |
0.301 (0.731) |
1 (1.00) |
16q gain | 18 (4%) | 454 |
0.421 (0.844) |
0.801 (1.00) |
0.338 (0.766) |
0.849 (1.00) |
0.0229 (0.198) |
0.365 (0.797) |
0.603 (0.978) |
1 (1.00) |
17p gain | 18 (4%) | 454 |
0.0324 (0.241) |
0.07 (0.367) |
0.226 (0.671) |
0.634 (0.998) |
0.0862 (0.421) |
0.763 (1.00) |
0.363 (0.797) |
0.518 (0.928) |
17q gain | 20 (4%) | 452 |
0.00649 (0.0815) |
0.189 (0.622) |
0.253 (0.688) |
0.986 (1.00) |
0.161 (0.585) |
1 (1.00) |
0.384 (0.809) |
0.518 (0.928) |
21q gain | 23 (5%) | 449 |
0.181 (0.606) |
0.011 (0.124) |
0.4 (0.821) |
0.237 (0.684) |
0.963 (1.00) |
0.788 (1.00) |
0.478 (0.895) |
0.614 (0.987) |
22q gain | 17 (4%) | 455 |
0.533 (0.943) |
0.0426 (0.27) |
1 (1.00) |
0.206 (0.635) |
0.00478 (0.0624) |
1 (1.00) |
1 (1.00) |
0.45 (0.873) |
xp gain | 18 (4%) | 454 |
0.987 (1.00) |
0.674 (1.00) |
0.149 (0.566) |
0.033 (0.241) |
0.127 (0.509) |
0.365 (0.797) |
0.258 (0.688) |
1 (1.00) |
1q loss | 24 (5%) | 448 |
0.883 (1.00) |
0.049 (0.295) |
0.836 (1.00) |
0.838 (1.00) |
0.0124 (0.13) |
0.438 (0.86) |
0.169 (0.585) |
1 (1.00) |
3p loss | 26 (6%) | 446 |
0.0369 (0.251) |
0.79 (1.00) |
0.223 (0.664) |
0.000594 (0.0115) |
0.935 (1.00) |
0.799 (1.00) |
0.516 (0.928) |
0.0763 (0.391) |
3q loss | 25 (5%) | 447 |
0.00785 (0.0913) |
0.564 (0.96) |
0.301 (0.731) |
0.203 (0.634) |
1 (1.00) |
0.603 (0.978) |
0.395 (0.815) |
0.259 (0.688) |
4q loss | 82 (17%) | 390 |
0.495 (0.913) |
0.211 (0.645) |
0.271 (0.708) |
0.89 (1.00) |
0.00415 (0.0565) |
0.36 (0.797) |
0.545 (0.948) |
0.335 (0.765) |
5q loss | 33 (7%) | 439 |
0.11 (0.474) |
0.267 (0.701) |
0.367 (0.797) |
0.357 (0.797) |
0.0201 (0.181) |
0.0645 (0.353) |
0.804 (1.00) |
1 (1.00) |
6p loss | 26 (6%) | 446 |
8.82e-06 (0.000427) |
0.0912 (0.433) |
0.84 (1.00) |
0.156 (0.574) |
0.199 (0.625) |
1 (1.00) |
0.0927 (0.436) |
1 (1.00) |
8p loss | 15 (3%) | 457 |
0.0287 (0.222) |
0.234 (0.681) |
1 (1.00) |
0.185 (0.612) |
0.173 (0.585) |
0.506 (0.928) |
0.197 (0.625) |
0.473 (0.895) |
8q loss | 9 (2%) | 463 |
0.0199 (0.181) |
0.151 (0.567) |
0.513 (0.928) |
0.345 (0.777) |
0.435 (0.857) |
0.69 (1.00) |
0.192 (0.624) |
0.318 (0.736) |
9q loss | 44 (9%) | 428 |
0.0511 (0.301) |
0.0526 (0.306) |
1 (1.00) |
0.00135 (0.0234) |
0.959 (1.00) |
1 (1.00) |
0.306 (0.734) |
0.688 (1.00) |
11p loss | 57 (12%) | 415 |
0.206 (0.635) |
0.26 (0.688) |
0.257 (0.688) |
0.156 (0.574) |
0.00387 (0.0549) |
0.29 (0.728) |
0.71 (1.00) |
1 (1.00) |
12q loss | 46 (10%) | 426 |
0.722 (1.00) |
0.0708 (0.368) |
1 (1.00) |
0.259 (0.688) |
0.00562 (0.0719) |
0.696 (1.00) |
0.54 (0.948) |
0.238 (0.684) |
13q loss | 105 (22%) | 367 |
0.642 (1) |
0.853 (1.00) |
0.0941 (0.44) |
0.172 (0.585) |
0.544 (0.948) |
0.0115 (0.126) |
0.389 (0.81) |
0.774 (1.00) |
16p loss | 11 (2%) | 461 |
0.115 (0.487) |
0.000239 (0.00588) |
0.362 (0.797) |
0.156 (0.574) |
0.545 (0.948) |
1 (1.00) |
1 (1.00) |
0.374 (0.803) |
16q loss | 19 (4%) | 453 |
0.123 (0.497) |
0.000301 (0.00685) |
1 (1.00) |
0.387 (0.809) |
0.365 (0.797) |
0.39 (0.81) |
0.645 (1.00) |
0.558 (0.956) |
17q loss | 8 (2%) | 464 |
0.38 (0.806) |
0.165 (0.585) |
0.733 (1.00) |
0.0344 (0.241) |
0.826 (1.00) |
1 (1.00) |
1 (1.00) |
0.0388 (0.261) |
18p loss | 63 (13%) | 409 |
0.862 (1.00) |
0.00447 (0.0596) |
0.172 (0.585) |
0.511 (0.928) |
0.284 (0.727) |
0.735 (1.00) |
0.0631 (0.348) |
0.715 (1.00) |
18q loss | 58 (12%) | 414 |
0.477 (0.895) |
0.0346 (0.241) |
0.573 (0.967) |
0.884 (1.00) |
0.106 (0.464) |
1 (1.00) |
0.0475 (0.295) |
0.469 (0.895) |
xq loss | 65 (14%) | 407 |
0.00725 (0.0867) |
0.249 (0.688) |
0.591 (0.978) |
0.196 (0.625) |
0.729 (1.00) |
0.868 (1.00) |
0.403 (0.822) |
0.73 (1.00) |
2p gain | 13 (3%) | 459 |
0.301 (0.731) |
0.133 (0.52) |
0.573 (0.967) |
0.291 (0.728) |
0.677 (1.00) |
1 (1.00) |
1 (1.00) |
0.4 (0.821) |
2q gain | 12 (3%) | 460 |
0.598 (0.978) |
0.279 (0.724) |
0.38 (0.806) |
0.291 (0.728) |
0.709 (1.00) |
1 (1.00) |
1 (1.00) |
0.374 (0.803) |
4q gain | 5 (1%) | 467 |
0.241 (0.688) |
0.318 (0.736) |
1 (1.00) |
0.223 (0.664) |
0.588 (0.978) |
1 (1.00) |
1 (1.00) |
|
5p gain | 9 (2%) | 463 |
0.256 (0.688) |
0.112 (0.477) |
1 (1.00) |
0.902 (1.00) |
0.133 (0.52) |
1 (1.00) |
0.168 (0.585) |
1 (1.00) |
5q gain | 6 (1%) | 466 |
0.696 (1.00) |
0.264 (0.695) |
1 (1.00) |
0.984 (1.00) |
0.587 (0.978) |
0.602 (0.978) |
0.104 (0.464) |
1 (1.00) |
6p gain | 7 (1%) | 465 |
0.698 (1.00) |
0.122 (0.497) |
0.248 (0.688) |
0.984 (1.00) |
0.206 (0.635) |
0.627 (0.992) |
1 (1.00) |
1 (1.00) |
8p gain | 43 (9%) | 429 |
0.913 (1.00) |
0.894 (1.00) |
0.422 (0.844) |
0.618 (0.987) |
0.325 (0.746) |
0.689 (1.00) |
1 (1.00) |
0.682 (1.00) |
8q gain | 51 (11%) | 421 |
0.823 (1.00) |
0.285 (0.727) |
0.372 (0.803) |
0.943 (1.00) |
0.078 (0.396) |
1 (1.00) |
0.76 (1.00) |
0.433 (0.856) |
9p gain | 15 (3%) | 457 |
0.123 (0.497) |
0.0487 (0.295) |
0.109 (0.474) |
0.315 (0.736) |
0.3 (0.731) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
10q gain | 9 (2%) | 463 |
0.948 (1.00) |
0.492 (0.912) |
0.738 (1.00) |
0.218 (0.658) |
0.0413 (0.269) |
0.387 (0.809) |
0.0868 (0.421) |
0.288 (0.728) |
11q gain | 56 (12%) | 416 |
0.234 (0.681) |
0.0608 (0.34) |
0.199 (0.625) |
0.574 (0.967) |
0.359 (0.797) |
1 (1.00) |
0.688 (1.00) |
1 (1.00) |
12p gain | 30 (6%) | 442 |
0.677 (1.00) |
0.402 (0.822) |
0.26 (0.688) |
0.973 (1.00) |
0.311 (0.736) |
1 (1.00) |
0.597 (0.978) |
1 (1.00) |
13q gain | 6 (1%) | 466 |
0.431 (0.853) |
0.935 (1.00) |
1 (1.00) |
0.042 (0.269) |
0.888 (1.00) |
0.602 (0.978) |
1 (1.00) |
1 (1.00) |
14q gain | 3 (1%) | 469 |
0.385 (0.809) |
0.212 (0.645) |
1 (1.00) |
1 (1.00) |
0.0986 (0.454) |
1 (1.00) |
1 (1.00) |
|
15q gain | 9 (2%) | 463 |
0.048 (0.295) |
0.0494 (0.295) |
0.738 (1.00) |
0.325 (0.746) |
0.243 (0.688) |
0.69 (1.00) |
1 (1.00) |
1 (1.00) |
16p gain | 16 (3%) | 456 |
0.693 (1.00) |
0.119 (0.497) |
0.317 (0.736) |
0.524 (0.934) |
0.122 (0.497) |
0.528 (0.939) |
0.559 (0.956) |
1 (1.00) |
18p gain | 15 (3%) | 457 |
0.0685 (0.367) |
0.925 (1.00) |
0.799 (1.00) |
0.493 (0.912) |
0.295 (0.73) |
0.746 (1.00) |
0.557 (0.956) |
1 (1.00) |
18q gain | 10 (2%) | 462 |
0.0597 (0.338) |
0.923 (1.00) |
1 (1.00) |
0.964 (1.00) |
0.477 (0.895) |
0.695 (1.00) |
0.417 (0.84) |
1 (1.00) |
2p loss | 19 (4%) | 453 |
0.199 (0.625) |
0.722 (1.00) |
0.64 (1) |
0.321 (0.742) |
0.363 (0.797) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
2q loss | 16 (3%) | 456 |
0.907 (1.00) |
0.285 (0.727) |
0.799 (1.00) |
0.145 (0.558) |
0.105 (0.464) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
7p loss | 3 (1%) | 469 |
0.601 (0.978) |
0.637 (0.999) |
0.583 (0.977) |
0.629 (0.992) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
7q loss | 3 (1%) | 469 |
0.782 (1.00) |
0.936 (1.00) |
1 (1.00) |
0.931 (1.00) |
0.629 (0.992) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
12p loss | 24 (5%) | 448 |
0.771 (1.00) |
0.0611 (0.34) |
0.534 (0.943) |
0.293 (0.728) |
0.0849 (0.418) |
0.795 (1.00) |
1 (1.00) |
0.614 (0.987) |
15q loss | 46 (10%) | 426 |
0.44 (0.861) |
0.428 (0.852) |
0.757 (1.00) |
0.618 (0.987) |
0.547 (0.948) |
0.845 (1.00) |
0.453 (0.875) |
1 (1.00) |
19p loss | 22 (5%) | 450 |
0.697 (1.00) |
0.84 (1.00) |
1 (1.00) |
0.103 (0.464) |
1 (1.00) |
0.164 (0.585) |
0.132 (0.52) |
0.166 (0.585) |
20p loss | 5 (1%) | 467 |
0.766 (1.00) |
0.993 (1.00) |
0.657 (1.00) |
0.551 (0.951) |
0.252 (0.688) |
0.105 (0.464) |
1 (1.00) |
|
xp loss | 89 (19%) | 383 |
0.199 (0.625) |
0.836 (1.00) |
0.478 (0.895) |
0.171 (0.585) |
0.775 (1.00) |
1 (1.00) |
0.692 (1.00) |
0.13 (0.516) |
P value = 0.0116 (logrank test), Q value = 0.13
Table S1. Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
1P GAIN MUTATED | 11 | 4 | 0.2 - 42.7 (15.0) |
1P GAIN WILD-TYPE | 459 | 90 | 0.0 - 211.2 (18.7) |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'
![](D1V1.png)
P value = 0.00822 (Fisher's exact test), Q value = 0.094
Table S2. Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
1P GAIN MUTATED | 9 | 0 | 2 |
1P GAIN WILD-TYPE | 167 | 118 | 176 |
Figure S2. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D1V5.png)
P value = 0.000188 (Wilcoxon-test), Q value = 0.0049
Table S3. Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
1Q GAIN MUTATED | 20 | 54.1 (11.6) |
1Q GAIN WILD-TYPE | 451 | 42.6 (13.3) |
Figure S3. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D2V2.png)
P value = 0.00348 (logrank test), Q value = 0.052
Table S4. Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
3P GAIN MUTATED | 11 | 4 | 0.2 - 47.8 (8.8) |
3P GAIN WILD-TYPE | 459 | 90 | 0.0 - 211.2 (18.8) |
Figure S4. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'
![](D5V1.png)
P value = 0.0258 (Fisher's exact test), Q value = 0.2
Table S5. Gene #5: '3p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
3P GAIN MUTATED | 8 | 0 | 3 |
3P GAIN WILD-TYPE | 168 | 118 | 175 |
Figure S5. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D5V5.png)
P value = 0.000903 (logrank test), Q value = 0.016
Table S6. Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
3Q GAIN MUTATED | 8 | 4 | 0.2 - 47.8 (13.1) |
3Q GAIN WILD-TYPE | 462 | 90 | 0.0 - 211.2 (18.7) |
Figure S6. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'
![](D6V1.png)
P value = 0.0347 (Wilcoxon-test), Q value = 0.24
Table S7. Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
3Q GAIN MUTATED | 8 | 52.8 (11.4) |
3Q GAIN WILD-TYPE | 463 | 42.9 (13.4) |
Figure S7. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D6V2.png)
P value = 0.0245 (Fisher's exact test), Q value = 0.2
Table S8. Gene #7: '4p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
4P GAIN MUTATED | 8 | 0 | 3 |
4P GAIN WILD-TYPE | 168 | 118 | 175 |
Figure S8. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D7V5.png)
P value = 9.45e-06 (logrank test), Q value = 0.00043
Table S9. Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
7P GAIN MUTATED | 110 | 37 | 0.1 - 211.2 (16.7) |
7P GAIN WILD-TYPE | 360 | 57 | 0.0 - 182.3 (19.2) |
Figure S9. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'
![](D12V1.png)
P value = 3.39e-08 (Wilcoxon-test), Q value = 3.1e-06
Table S10. Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
7P GAIN MUTATED | 110 | 49.3 (13.1) |
7P GAIN WILD-TYPE | 361 | 41.1 (13.0) |
Figure S10. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D12V2.png)
P value = 5e-05 (logrank test), Q value = 0.0014
Table S11. Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
7Q GAIN MUTATED | 141 | 43 | 0.1 - 211.2 (17.4) |
7Q GAIN WILD-TYPE | 329 | 51 | 0.0 - 182.3 (19.6) |
Figure S11. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'
![](D13V1.png)
P value = 1e-08 (Wilcoxon-test), Q value = 1.3e-06
Table S12. Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
7Q GAIN MUTATED | 141 | 48.5 (13.2) |
7Q GAIN WILD-TYPE | 330 | 40.7 (12.9) |
Figure S12. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D13V2.png)
P value = 0.00706 (Fisher's exact test), Q value = 0.087
Table S13. Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 206 | 266 |
9Q GAIN MUTATED | 16 | 6 |
9Q GAIN WILD-TYPE | 190 | 260 |
Figure S13. Get High-res Image Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'
![](D17V3.png)
P value = 0.0236 (Wilcoxon-test), Q value = 0.2
Table S14. Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
10P GAIN MUTATED | 53 | 38.4 (10.9) |
10P GAIN WILD-TYPE | 418 | 43.6 (13.6) |
Figure S14. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D18V2.png)
P value = 0.00072 (Fisher's exact test), Q value = 0.013
Table S15. Gene #18: '10p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
10P GAIN MUTATED | 28 | 17 | 8 |
10P GAIN WILD-TYPE | 148 | 101 | 170 |
Figure S15. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D18V5.png)
P value = 0.0255 (Fisher's exact test), Q value = 0.2
Table S16. Gene #18: '10p gain' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 92 | 380 |
10P GAIN MUTATED | 17 | 36 |
10P GAIN WILD-TYPE | 75 | 344 |
Figure S16. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
![](D18V6.png)
P value = 0.034 (Fisher's exact test), Q value = 0.24
Table S17. Gene #18: '10p gain' versus Clinical Feature #8: 'ETHNICITY'
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 18 | 419 |
10P GAIN MUTATED | 5 | 42 |
10P GAIN WILD-TYPE | 13 | 377 |
Figure S17. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #8: 'ETHNICITY'
![](D18V8.png)
P value = 0.0244 (Wilcoxon-test), Q value = 0.2
Table S18. Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
11P GAIN MUTATED | 30 | 48.9 (14.7) |
11P GAIN WILD-TYPE | 441 | 42.7 (13.3) |
Figure S18. Get High-res Image Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D20V2.png)
P value = 0.0121 (Fisher's exact test), Q value = 0.13
Table S19. Gene #20: '11p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
11P GAIN MUTATED | 4 | 10 | 16 |
11P GAIN WILD-TYPE | 172 | 108 | 162 |
Figure S19. Get High-res Image Gene #20: '11p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D20V5.png)
P value = 0.0236 (logrank test), Q value = 0.2
Table S20. Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
12Q GAIN MUTATED | 14 | 6 | 1.2 - 77.9 (17.2) |
12Q GAIN WILD-TYPE | 456 | 88 | 0.0 - 211.2 (18.7) |
Figure S20. Get High-res Image Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'
![](D23V1.png)
P value = 0.0229 (Fisher's exact test), Q value = 0.2
Table S21. Gene #28: '16q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
16Q GAIN MUTATED | 12 | 1 | 5 |
16Q GAIN WILD-TYPE | 164 | 117 | 173 |
Figure S21. Get High-res Image Gene #28: '16q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D28V5.png)
P value = 0.0324 (logrank test), Q value = 0.24
Table S22. Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
17P GAIN MUTATED | 18 | 6 | 7.2 - 62.2 (18.3) |
17P GAIN WILD-TYPE | 452 | 88 | 0.0 - 211.2 (18.7) |
Figure S22. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'
![](D29V1.png)
P value = 0.00649 (logrank test), Q value = 0.081
Table S23. Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
17Q GAIN MUTATED | 20 | 7 | 5.8 - 62.2 (17.4) |
17Q GAIN WILD-TYPE | 450 | 87 | 0.0 - 211.2 (18.7) |
Figure S23. Get High-res Image Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'
![](D30V1.png)
P value = 0.0155 (Wilcoxon-test), Q value = 0.15
Table S24. Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
19P GAIN MUTATED | 90 | 46.3 (14.2) |
19P GAIN WILD-TYPE | 381 | 42.3 (13.2) |
Figure S24. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D33V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S25. Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
19P GAIN MUTATED | 18 | 17 | 56 |
19P GAIN WILD-TYPE | 158 | 101 | 122 |
Figure S25. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D33V5.png)
P value = 1.49e-05 (logrank test), Q value = 6e-04
Table S26. Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
19Q GAIN MUTATED | 22 | 8 | 0.2 - 49.5 (15.7) |
19Q GAIN WILD-TYPE | 448 | 86 | 0.0 - 211.2 (18.8) |
Figure S26. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'
![](D34V1.png)
P value = 4.07e-05 (Wilcoxon-test), Q value = 0.0012
Table S27. Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
19Q GAIN MUTATED | 22 | 55.1 (12.1) |
19Q GAIN WILD-TYPE | 449 | 42.5 (13.2) |
Figure S27. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D34V2.png)
P value = 1.14e-07 (logrank test), Q value = 9.1e-06
Table S28. Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
20P GAIN MUTATED | 38 | 14 | 0.5 - 49.5 (14.0) |
20P GAIN WILD-TYPE | 432 | 80 | 0.0 - 211.2 (18.8) |
Figure S28. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'
![](D35V1.png)
P value = 3.59e-07 (Wilcoxon-test), Q value = 2.6e-05
Table S29. Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
20P GAIN MUTATED | 38 | 54.4 (12.8) |
20P GAIN WILD-TYPE | 433 | 42.1 (13.0) |
Figure S29. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D35V2.png)
P value = 0.0317 (Wilcoxon-test), Q value = 0.24
Table S30. Gene #35: '20p gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
20P GAIN MUTATED | 22 | 83.6 (12.2) |
20P GAIN WILD-TYPE | 247 | 88.1 (11.9) |
Figure S30. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D35V4.png)
P value = 2.28e-08 (logrank test), Q value = 2.4e-06
Table S31. Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
20Q GAIN MUTATED | 38 | 14 | 0.5 - 49.5 (14.0) |
20Q GAIN WILD-TYPE | 432 | 80 | 0.0 - 211.2 (19.0) |
Figure S31. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'
![](D36V1.png)
P value = 4.76e-07 (Wilcoxon-test), Q value = 3e-05
Table S32. Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
20Q GAIN MUTATED | 38 | 54.3 (13.0) |
20Q GAIN WILD-TYPE | 433 | 42.1 (13.0) |
Figure S32. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D36V2.png)
P value = 0.011 (Wilcoxon-test), Q value = 0.12
Table S33. Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
21Q GAIN MUTATED | 23 | 51.8 (17.3) |
21Q GAIN WILD-TYPE | 448 | 42.6 (13.1) |
Figure S33. Get High-res Image Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D37V2.png)
P value = 0.00478 (Fisher's exact test), Q value = 0.062
Table S34. Gene #38: '22q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
22Q GAIN MUTATED | 2 | 2 | 13 |
22Q GAIN WILD-TYPE | 174 | 116 | 165 |
Figure S34. Get High-res Image Gene #38: '22q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D38V5.png)
P value = 0.033 (Wilcoxon-test), Q value = 0.24
Table S35. Gene #39: 'xp gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
XP GAIN MUTATED | 10 | 95.0 (5.3) |
XP GAIN WILD-TYPE | 259 | 87.5 (12.1) |
Figure S35. Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D39V4.png)
P value = 0.00394 (Fisher's exact test), Q value = 0.055
Table S36. Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 206 | 266 |
XQ GAIN MUTATED | 23 | 11 |
XQ GAIN WILD-TYPE | 183 | 255 |
Figure S36. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'
![](D40V3.png)
P value = 0.0218 (Fisher's exact test), Q value = 0.19
Table S37. Gene #40: 'xq gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
XQ GAIN MUTATED | 15 | 13 | 6 |
XQ GAIN WILD-TYPE | 161 | 105 | 172 |
Figure S37. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D40V5.png)
P value = 0.00267 (logrank test), Q value = 0.044
Table S38. Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
1P LOSS MUTATED | 170 | 23 | 0.1 - 182.3 (20.2) |
1P LOSS WILD-TYPE | 300 | 71 | 0.0 - 211.2 (18.5) |
Figure S38. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'
![](D41V1.png)
P value = 0.000263 (Wilcoxon-test), Q value = 0.0062
Table S39. Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
1P LOSS MUTATED | 170 | 45.8 (12.7) |
1P LOSS WILD-TYPE | 301 | 41.5 (13.6) |
Figure S39. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D41V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S40. Gene #41: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
1P LOSS MUTATED | 9 | 34 | 128 |
1P LOSS WILD-TYPE | 167 | 84 | 50 |
Figure S40. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D41V5.png)
P value = 0.0153 (Fisher's exact test), Q value = 0.15
Table S41. Gene #41: '1p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 92 | 380 |
1P LOSS MUTATED | 23 | 148 |
1P LOSS WILD-TYPE | 69 | 232 |
Figure S41. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
![](D41V6.png)
P value = 0.0124 (Fisher's exact test), Q value = 0.13
Table S42. Gene #42: '1q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
1Q LOSS MUTATED | 4 | 4 | 16 |
1Q LOSS WILD-TYPE | 172 | 114 | 162 |
Figure S42. Get High-res Image Gene #42: '1q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D42V5.png)
P value = 0.000594 (Wilcoxon-test), Q value = 0.012
Table S43. Gene #45: '3p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
3P LOSS MUTATED | 19 | 78.9 (13.3) |
3P LOSS WILD-TYPE | 250 | 88.4 (11.6) |
Figure S43. Get High-res Image Gene #45: '3p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D45V4.png)
P value = 0.00785 (logrank test), Q value = 0.091
Table S44. Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
3Q LOSS MUTATED | 25 | 12 | 0.0 - 117.4 (21.4) |
3Q LOSS WILD-TYPE | 445 | 82 | 0.1 - 211.2 (18.4) |
Figure S44. Get High-res Image Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'
![](D46V1.png)
P value = 0.00371 (Wilcoxon-test), Q value = 0.054
Table S45. Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
4P LOSS MUTATED | 63 | 47.4 (12.5) |
4P LOSS WILD-TYPE | 408 | 42.4 (13.5) |
Figure S45. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D47V2.png)
P value = 0.00054 (Fisher's exact test), Q value = 0.011
Table S46. Gene #47: '4p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
4P LOSS MUTATED | 12 | 14 | 37 |
4P LOSS WILD-TYPE | 164 | 104 | 141 |
Figure S46. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D47V5.png)
P value = 0.00415 (Fisher's exact test), Q value = 0.057
Table S47. Gene #48: '4q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
4Q LOSS MUTATED | 20 | 18 | 44 |
4Q LOSS WILD-TYPE | 156 | 100 | 134 |
Figure S47. Get High-res Image Gene #48: '4q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D48V5.png)
P value = 0.0138 (Fisher's exact test), Q value = 0.14
Table S48. Gene #49: '5p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
5P LOSS MUTATED | 17 | 11 | 5 |
5P LOSS WILD-TYPE | 159 | 107 | 173 |
Figure S48. Get High-res Image Gene #49: '5p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D49V5.png)
P value = 0.0201 (Fisher's exact test), Q value = 0.18
Table S49. Gene #49: '5p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 92 | 380 |
5P LOSS MUTATED | 12 | 21 |
5P LOSS WILD-TYPE | 80 | 359 |
Figure S49. Get High-res Image Gene #49: '5p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
![](D49V6.png)
P value = 0.0201 (Fisher's exact test), Q value = 0.18
Table S50. Gene #50: '5q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
5Q LOSS MUTATED | 20 | 6 | 7 |
5Q LOSS WILD-TYPE | 156 | 112 | 171 |
Figure S50. Get High-res Image Gene #50: '5q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D50V5.png)
P value = 8.82e-06 (logrank test), Q value = 0.00043
Table S51. Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
6P LOSS MUTATED | 26 | 11 | 0.2 - 50.9 (18.6) |
6P LOSS WILD-TYPE | 444 | 83 | 0.0 - 211.2 (18.7) |
Figure S51. Get High-res Image Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'
![](D51V1.png)
P value = 3.39e-05 (logrank test), Q value = 0.0011
Table S52. Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
6Q LOSS MUTATED | 54 | 16 | 0.1 - 57.9 (17.7) |
6Q LOSS WILD-TYPE | 416 | 78 | 0.0 - 211.2 (18.8) |
Figure S52. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'
![](D52V1.png)
P value = 0.0032 (Wilcoxon-test), Q value = 0.049
Table S53. Gene #52: '6q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
6Q LOSS MUTATED | 34 | 82.4 (12.8) |
6Q LOSS WILD-TYPE | 235 | 88.5 (11.7) |
Figure S53. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D52V4.png)
P value = 0.00051 (Fisher's exact test), Q value = 0.011
Table S54. Gene #52: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
6Q LOSS MUTATED | 34 | 10 | 11 |
6Q LOSS WILD-TYPE | 142 | 108 | 167 |
Figure S54. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D52V5.png)
P value = 0.0287 (logrank test), Q value = 0.22
Table S55. Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
8P LOSS MUTATED | 14 | 5 | 0.2 - 50.9 (19.5) |
8P LOSS WILD-TYPE | 456 | 89 | 0.0 - 211.2 (18.6) |
Figure S55. Get High-res Image Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'
![](D55V1.png)
P value = 0.0199 (logrank test), Q value = 0.18
Table S56. Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
8Q LOSS MUTATED | 9 | 3 | 0.2 - 41.1 (15.7) |
8Q LOSS WILD-TYPE | 461 | 91 | 0.0 - 211.2 (18.7) |
Figure S56. Get High-res Image Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'
![](D56V1.png)
P value = 0.000495 (logrank test), Q value = 0.011
Table S57. Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
9P LOSS MUTATED | 103 | 32 | 0.1 - 169.8 (18.4) |
9P LOSS WILD-TYPE | 367 | 62 | 0.0 - 211.2 (18.7) |
Figure S57. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'
![](D57V1.png)
P value = 0.0322 (Wilcoxon-test), Q value = 0.24
Table S58. Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
9P LOSS MUTATED | 103 | 45.4 (13.1) |
9P LOSS WILD-TYPE | 368 | 42.4 (13.5) |
Figure S58. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D57V2.png)
P value = 0.0356 (Fisher's exact test), Q value = 0.24
Table S59. Gene #57: '9p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 92 | 380 |
9P LOSS MUTATED | 28 | 76 |
9P LOSS WILD-TYPE | 64 | 304 |
Figure S59. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
![](D57V6.png)
P value = 0.00135 (Wilcoxon-test), Q value = 0.023
Table S60. Gene #58: '9q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
9Q LOSS MUTATED | 27 | 81.5 (12.0) |
9Q LOSS WILD-TYPE | 242 | 88.4 (11.8) |
Figure S60. Get High-res Image Gene #58: '9q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D58V4.png)
P value = 0 (logrank test), Q value = 0
Table S61. Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
10P LOSS MUTATED | 74 | 37 | 0.1 - 134.3 (15.0) |
10P LOSS WILD-TYPE | 396 | 57 | 0.0 - 211.2 (20.0) |
Figure S61. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'
![](D59V1.png)
P value = 3.96e-17 (Wilcoxon-test), Q value = 8.5e-15
Table S62. Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
10P LOSS MUTATED | 74 | 55.5 (11.3) |
10P LOSS WILD-TYPE | 397 | 40.7 (12.5) |
Figure S62. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D59V2.png)
P value = 0.00324 (Wilcoxon-test), Q value = 0.049
Table S63. Gene #59: '10p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
10P LOSS MUTATED | 44 | 83.0 (13.7) |
10P LOSS WILD-TYPE | 225 | 88.7 (11.4) |
Figure S63. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D59V4.png)
P value = 0.00019 (Fisher's exact test), Q value = 0.0049
Table S64. Gene #59: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
10P LOSS MUTATED | 44 | 14 | 16 |
10P LOSS WILD-TYPE | 132 | 104 | 162 |
Figure S64. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D59V5.png)
P value = 0.0132 (Fisher's exact test), Q value = 0.14
Table S65. Gene #59: '10p loss' versus Clinical Feature #7: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 8 | 15 | 437 |
10P LOSS MUTATED | 1 | 1 | 6 | 65 |
10P LOSS WILD-TYPE | 0 | 7 | 9 | 372 |
Figure S65. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #7: 'RACE'
![](D59V7.png)
P value = 0 (logrank test), Q value = 0
Table S66. Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
10Q LOSS MUTATED | 87 | 43 | 0.1 - 172.8 (15.7) |
10Q LOSS WILD-TYPE | 383 | 51 | 0.0 - 211.2 (19.6) |
Figure S66. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'
![](D60V1.png)
P value = 1.05e-14 (Wilcoxon-test), Q value = 1.7e-12
Table S67. Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
10Q LOSS MUTATED | 87 | 53.3 (12.7) |
10Q LOSS WILD-TYPE | 384 | 40.7 (12.5) |
Figure S67. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D60V2.png)
P value = 0.0166 (Wilcoxon-test), Q value = 0.16
Table S68. Gene #60: '10q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
10Q LOSS MUTATED | 51 | 84.3 (13.2) |
10Q LOSS WILD-TYPE | 218 | 88.5 (11.6) |
Figure S68. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D60V4.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.0014
Table S69. Gene #60: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
10Q LOSS MUTATED | 51 | 17 | 19 |
10Q LOSS WILD-TYPE | 125 | 101 | 159 |
Figure S69. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D60V5.png)
P value = 0.0344 (Fisher's exact test), Q value = 0.24
Table S70. Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 8 | 15 | 437 |
10Q LOSS MUTATED | 1 | 1 | 6 | 78 |
10Q LOSS WILD-TYPE | 0 | 7 | 9 | 359 |
Figure S70. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'
![](D60V7.png)
P value = 0.00387 (Fisher's exact test), Q value = 0.055
Table S71. Gene #61: '11p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
11P LOSS MUTATED | 32 | 13 | 12 |
11P LOSS WILD-TYPE | 144 | 105 | 166 |
Figure S71. Get High-res Image Gene #61: '11p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D61V5.png)
P value = 0.00213 (logrank test), Q value = 0.036
Table S72. Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
11Q LOSS MUTATED | 20 | 7 | 0.2 - 49.5 (18.7) |
11Q LOSS WILD-TYPE | 450 | 87 | 0.0 - 211.2 (18.6) |
Figure S72. Get High-res Image Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'
![](D62V1.png)
P value = 0.0169 (Fisher's exact test), Q value = 0.16
Table S73. Gene #62: '11q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
11Q LOSS MUTATED | 12 | 6 | 2 |
11Q LOSS WILD-TYPE | 164 | 112 | 176 |
Figure S73. Get High-res Image Gene #62: '11q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D62V5.png)
P value = 0.00562 (Fisher's exact test), Q value = 0.072
Table S74. Gene #64: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
12Q LOSS MUTATED | 25 | 13 | 8 |
12Q LOSS WILD-TYPE | 151 | 105 | 170 |
Figure S74. Get High-res Image Gene #64: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D64V5.png)
P value = 0.0115 (Fisher's exact test), Q value = 0.13
Table S75. Gene #65: '13q loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 92 | 380 |
13Q LOSS MUTATED | 30 | 75 |
13Q LOSS WILD-TYPE | 62 | 305 |
Figure S75. Get High-res Image Gene #65: '13q loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'
![](D65V6.png)
P value = 3.62e-05 (logrank test), Q value = 0.0012
Table S76. Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
14Q LOSS MUTATED | 69 | 24 | 0.1 - 130.8 (18.8) |
14Q LOSS WILD-TYPE | 401 | 70 | 0.0 - 211.2 (18.6) |
Figure S76. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'
![](D66V1.png)
P value = 0.00031 (Wilcoxon-test), Q value = 0.0068
Table S77. Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
14Q LOSS MUTATED | 70 | 48.5 (13.2) |
14Q LOSS WILD-TYPE | 401 | 42.1 (13.3) |
Figure S77. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D66V2.png)
P value = 0.000239 (Wilcoxon-test), Q value = 0.0059
Table S78. Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
16P LOSS MUTATED | 11 | 58.5 (10.3) |
16P LOSS WILD-TYPE | 460 | 42.7 (13.3) |
Figure S78. Get High-res Image Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D68V2.png)
P value = 0.000301 (Wilcoxon-test), Q value = 0.0068
Table S79. Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
16Q LOSS MUTATED | 19 | 55.3 (14.3) |
16Q LOSS WILD-TYPE | 452 | 42.5 (13.2) |
Figure S79. Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D69V2.png)
P value = 0.00732 (logrank test), Q value = 0.087
Table S80. Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
17P LOSS MUTATED | 12 | 3 | 0.1 - 23.7 (14.6) |
17P LOSS WILD-TYPE | 458 | 91 | 0.0 - 211.2 (18.8) |
Figure S80. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'
![](D70V1.png)
P value = 0.00311 (Wilcoxon-test), Q value = 0.049
Table S81. Gene #70: '17p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
17P LOSS MUTATED | 6 | 73.3 (10.3) |
17P LOSS WILD-TYPE | 263 | 88.1 (11.8) |
Figure S81. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D70V4.png)
P value = 0.0344 (Wilcoxon-test), Q value = 0.24
Table S82. Gene #71: '17q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
17Q LOSS MUTATED | 4 | 75.0 (12.9) |
17Q LOSS WILD-TYPE | 265 | 87.9 (11.9) |
Figure S82. Get High-res Image Gene #71: '17q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D71V4.png)
P value = 0.00447 (Wilcoxon-test), Q value = 0.06
Table S83. Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
18P LOSS MUTATED | 63 | 47.9 (14.4) |
18P LOSS WILD-TYPE | 408 | 42.3 (13.1) |
Figure S83. Get High-res Image Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D72V2.png)
P value = 0.0346 (Wilcoxon-test), Q value = 0.24
Table S84. Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
18Q LOSS MUTATED | 58 | 46.9 (14.4) |
18Q LOSS WILD-TYPE | 413 | 42.5 (13.2) |
Figure S84. Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D73V2.png)
P value = 0.0191 (logrank test), Q value = 0.18
Table S85. Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
19Q LOSS MUTATED | 192 | 31 | 0.1 - 182.3 (20.2) |
19Q LOSS WILD-TYPE | 278 | 63 | 0.0 - 211.2 (18.2) |
Figure S85. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'
![](D75V1.png)
P value = 0.0258 (Wilcoxon-test), Q value = 0.2
Table S86. Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
19Q LOSS MUTATED | 192 | 44.5 (12.6) |
19Q LOSS WILD-TYPE | 279 | 42.1 (13.9) |
Figure S86. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D75V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
Table S87. Gene #75: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
19Q LOSS MUTATED | 21 | 38 | 134 |
19Q LOSS WILD-TYPE | 155 | 80 | 44 |
Figure S87. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D75V5.png)
P value = 0.000655 (Wilcoxon-test), Q value = 0.012
Table S88. Gene #77: '21q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
21Q LOSS MUTATED | 21 | 78.6 (14.6) |
21Q LOSS WILD-TYPE | 248 | 88.5 (11.4) |
Figure S88. Get High-res Image Gene #77: '21q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D77V4.png)
P value = 0.0218 (Fisher's exact test), Q value = 0.19
Table S89. Gene #77: '21q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 176 | 118 | 178 |
21Q LOSS MUTATED | 18 | 5 | 6 |
21Q LOSS WILD-TYPE | 158 | 113 | 172 |
Figure S89. Get High-res Image Gene #77: '21q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'
![](D77V5.png)
P value = 1.93e-05 (logrank test), Q value = 0.00069
Table S90. Gene #78: '22q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
22Q LOSS MUTATED | 50 | 20 | 0.1 - 156.2 (18.1) |
22Q LOSS WILD-TYPE | 420 | 74 | 0.0 - 211.2 (18.7) |
Figure S90. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #1: 'Time to Death'
![](D78V1.png)
P value = 1.87e-05 (Wilcoxon-test), Q value = 0.00069
Table S91. Gene #78: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 471 | 43.1 (13.4) |
22Q LOSS MUTATED | 50 | 51.3 (14.0) |
22Q LOSS WILD-TYPE | 421 | 42.1 (13.0) |
Figure S91. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D78V2.png)
P value = 0.0284 (Wilcoxon-test), Q value = 0.22
Table S92. Gene #78: '22q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 87.7 (12.0) |
22Q LOSS MUTATED | 28 | 82.1 (15.2) |
22Q LOSS WILD-TYPE | 241 | 88.4 (11.4) |
Figure S92. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
![](D78V4.png)
P value = 0.00725 (logrank test), Q value = 0.087
Table S93. Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 470 | 94 | 0.0 - 211.2 (18.7) |
XQ LOSS MUTATED | 64 | 19 | 0.1 - 134.3 (16.6) |
XQ LOSS WILD-TYPE | 406 | 75 | 0.0 - 211.2 (19.0) |
Figure S93. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'
![](D80V1.png)
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Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/15087637/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/15082624/LGG-TP.merged_data.txt
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Number of patients = 472
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Number of significantly arm-level cnvs = 80
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Number of selected clinical features = 8
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Exclude regions that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.