This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 76 focal events and 14 clinical features across 522 patients, 73 significant findings detected with Q value < 0.25.
-
amp_2q11.2 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
amp_3q26.33 cnv correlated to 'GENDER'.
-
amp_7p11.2 cnv correlated to 'Time to Death'.
-
amp_7q21.3 cnv correlated to 'Time to Death' and 'RACE'.
-
amp_8p11.23 cnv correlated to 'RACE'.
-
amp_8q24.21 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
-
amp_9p24.1 cnv correlated to 'GENDER'.
-
amp_9p23 cnv correlated to 'GENDER' and 'NUMBER_PACK_YEARS_SMOKED'.
-
amp_9q34.3 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
amp_13q34 cnv correlated to 'YEARS_TO_BIRTH'.
-
amp_18p11.31 cnv correlated to 'GENDER'.
-
amp_18q11.2 cnv correlated to 'GENDER'.
-
amp_xq28 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
-
del_1p36.21 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_1p13.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_2q21.2 cnv correlated to 'GENDER'.
-
del_2q22.1 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.
-
del_2q36.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'NUMBER_PACK_YEARS_SMOKED', 'RACE', and 'ETHNICITY'.
-
del_3p26.2 cnv correlated to 'GENDER', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
-
del_3p24.1 cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', 'GENDER', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
-
del_3p14.2 cnv correlated to 'Time to Death', 'GENDER', 'NUMBER_PACK_YEARS_SMOKED', 'NUMBER_OF_LYMPH_NODES', and 'RACE'.
-
del_3p12.1 cnv correlated to 'Time to Death', 'GENDER', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
-
del_4p15.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_5q12.1 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.
-
del_5q15 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.
-
del_5q35.3 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_7q31.1 cnv correlated to 'PATHOLOGY_N_STAGE'.
-
del_8p23.2 cnv correlated to 'Time to Death'.
-
del_9p23 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_9p21.3 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_10p15.3 cnv correlated to 'Time to Death' and 'NUMBER_OF_LYMPH_NODES'.
-
del_10p11.21 cnv correlated to 'RACE'.
-
del_11q23.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_N_STAGE', 'GENDER', 'RADIATION_THERAPY', and 'NUMBER_OF_LYMPH_NODES'.
-
del_13q14.2 cnv correlated to 'RACE'.
-
del_14q11.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
del_14q32.32 cnv correlated to 'RADIATION_THERAPY'.
-
del_17p11.2 cnv correlated to 'RACE'.
-
del_17q25.3 cnv correlated to 'ETHNICITY'.
-
del_18q23 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.
-
del_19p13.3 cnv correlated to 'Time to Death'.
-
del_21q22.3 cnv correlated to 'RACE'.
-
del_xp22.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'NUMBER_OF_LYMPH_NODES'.
-
del_xp21.3 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
-
del_xq21.33 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
NUMBER OF LYMPH NODES |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 2q36 2 | 157 (30%) | 365 |
0.438 (0.797) |
0.627 (0.9) |
0.012 (0.225) |
0.00207 (0.11) |
0.428 (0.786) |
1 (1.00) |
0.747 (0.963) |
0.337 (0.715) |
1 (1.00) |
0.0113 (0.215) |
0.319 (0.707) |
0.905 (1.00) |
0.0093 (0.198) |
0.0141 (0.238) |
del 3p24 1 | 368 (70%) | 154 |
0.00893 (0.198) |
0.217 (0.63) |
0.423 (0.784) |
0.00534 (0.165) |
0.146 (0.574) |
1 (1.00) |
0.0035 (0.13) |
0.916 (1.00) |
0.0719 (0.436) |
7.33e-05 (0.0189) |
0.589 (0.883) |
0.0614 (0.399) |
0.00023 (0.0223) |
1 (1.00) |
del 3p14 2 | 372 (71%) | 150 |
0.0027 (0.125) |
0.21 (0.629) |
0.447 (0.801) |
0.129 (0.544) |
0.0554 (0.376) |
1 (1.00) |
0.00635 (0.171) |
0.673 (0.922) |
0.0465 (0.349) |
0.000107 (0.0189) |
0.495 (0.832) |
0.014 (0.238) |
0.00173 (0.1) |
1 (1.00) |
del 11q23 1 | 246 (47%) | 276 |
0.885 (1.00) |
0.00342 (0.13) |
0.856 (0.997) |
0.917 (1.00) |
0.0006 (0.0479) |
1 (1.00) |
4.97e-06 (0.00529) |
0.00124 (0.0824) |
0.432 (0.788) |
0.216 (0.63) |
0.245 (0.664) |
0.000219 (0.0223) |
0.0388 (0.338) |
0.314 (0.704) |
del 3p12 1 | 343 (66%) | 179 |
0.00438 (0.15) |
0.909 (1.00) |
0.272 (0.68) |
0.229 (0.641) |
0.153 (0.579) |
1 (1.00) |
0.0165 (0.246) |
0.839 (0.988) |
0.557 (0.861) |
8.33e-05 (0.0189) |
0.336 (0.715) |
0.157 (0.58) |
0.00179 (0.1) |
1 (1.00) |
del 3p26 2 | 348 (67%) | 174 |
0.0328 (0.326) |
0.836 (0.987) |
0.607 (0.89) |
0.0279 (0.309) |
0.375 (0.745) |
1 (1.00) |
0.00331 (0.13) |
0.682 (0.929) |
0.121 (0.524) |
0.00116 (0.0824) |
0.429 (0.786) |
0.102 (0.481) |
9e-05 (0.0189) |
0.833 (0.987) |
amp 7q21 3 | 169 (32%) | 353 |
0.00354 (0.13) |
0.175 (0.604) |
0.775 (0.967) |
0.0618 (0.399) |
0.284 (0.683) |
1 (1.00) |
0.673 (0.922) |
0.752 (0.963) |
0.0811 (0.457) |
0.0427 (0.348) |
0.791 (0.97) |
0.634 (0.904) |
0.00055 (0.0479) |
0.525 (0.844) |
amp 9p23 | 124 (24%) | 398 |
0.113 (0.502) |
0.034 (0.326) |
0.925 (1.00) |
0.671 (0.922) |
0.0525 (0.363) |
1 (1.00) |
0.00241 (0.116) |
0.172 (0.599) |
0.592 (0.884) |
0.0102 (0.204) |
0.263 (0.676) |
0.0439 (0.349) |
0.877 (1.00) |
0.485 (0.83) |
del 2q22 1 | 121 (23%) | 401 |
0.612 (0.892) |
0.0729 (0.436) |
0.0127 (0.23) |
0.00725 (0.18) |
0.747 (0.963) |
0.288 (0.687) |
0.0346 (0.326) |
0.169 (0.599) |
0.775 (0.967) |
0.181 (0.609) |
0.552 (0.859) |
0.693 (0.929) |
0.382 (0.746) |
0.631 (0.902) |
del 5q12 1 | 215 (41%) | 307 |
0.867 (1.00) |
0.45 (0.801) |
0.809 (0.975) |
0.0514 (0.363) |
0.325 (0.71) |
1 (1.00) |
0.0352 (0.326) |
0.552 (0.859) |
0.61 (0.89) |
0.00626 (0.171) |
0.357 (0.728) |
0.308 (0.704) |
0.00217 (0.11) |
0.15 (0.574) |
del 5q15 | 226 (43%) | 296 |
0.669 (0.922) |
0.27 (0.68) |
0.742 (0.963) |
0.0307 (0.324) |
0.765 (0.966) |
1 (1.00) |
0.0587 (0.39) |
0.768 (0.967) |
0.521 (0.844) |
0.0111 (0.215) |
0.701 (0.931) |
0.793 (0.97) |
0.00968 (0.202) |
0.224 (0.635) |
del 10p15 3 | 170 (33%) | 352 |
0.0077 (0.182) |
0.588 (0.883) |
0.211 (0.629) |
0.0223 (0.276) |
0.0413 (0.346) |
1 (1.00) |
0.345 (0.723) |
0.532 (0.849) |
0.0347 (0.326) |
0.749 (0.963) |
0.787 (0.97) |
0.0132 (0.233) |
0.0456 (0.349) |
0.668 (0.922) |
del 18q23 | 288 (55%) | 234 |
0.186 (0.616) |
0.171 (0.599) |
0.954 (1.00) |
0.1 (0.479) |
0.896 (1.00) |
1 (1.00) |
0.321 (0.709) |
0.495 (0.832) |
0.0479 (0.349) |
0.017 (0.247) |
0.331 (0.711) |
0.247 (0.666) |
0.00435 (0.15) |
0.156 (0.58) |
del xp22 2 | 157 (30%) | 365 |
0.0439 (0.349) |
0.87 (1.00) |
0.292 (0.691) |
0.0607 (0.399) |
0.107 (0.499) |
0.257 (0.675) |
0.133 (0.548) |
0.524 (0.844) |
0.346 (0.723) |
0.0157 (0.245) |
0.505 (0.838) |
0.00063 (0.0479) |
0.346 (0.723) |
0.661 (0.921) |
amp 2q11 2 | 107 (20%) | 415 |
0.471 (0.814) |
0.851 (0.994) |
0.264 (0.676) |
0.00586 (0.171) |
0.255 (0.672) |
1 (1.00) |
0.18 (0.609) |
0.218 (0.63) |
0.759 (0.963) |
0.087 (0.462) |
0.405 (0.765) |
0.428 (0.786) |
0.452 (0.802) |
0.449 (0.801) |
amp 3q26 33 | 380 (73%) | 142 |
0.52 (0.844) |
0.0525 (0.363) |
0.111 (0.502) |
0.718 (0.944) |
0.21 (0.629) |
1 (1.00) |
0.00541 (0.165) |
0.195 (0.622) |
0.377 (0.746) |
0.0343 (0.326) |
0.419 (0.78) |
0.0398 (0.343) |
0.46 (0.807) |
0.822 (0.981) |
amp 7p11 2 | 222 (43%) | 300 |
3.54e-05 (0.0188) |
0.493 (0.832) |
0.778 (0.968) |
0.031 (0.324) |
0.785 (0.97) |
0.403 (0.765) |
0.842 (0.988) |
0.323 (0.71) |
0.149 (0.574) |
0.134 (0.549) |
0.446 (0.801) |
0.606 (0.89) |
0.0469 (0.349) |
0.689 (0.929) |
amp 8p11 23 | 161 (31%) | 361 |
0.312 (0.704) |
0.834 (0.987) |
0.0194 (0.262) |
0.0895 (0.462) |
0.217 (0.63) |
0.298 (0.693) |
0.67 (0.922) |
0.753 (0.963) |
0.109 (0.502) |
0.149 (0.574) |
0.609 (0.89) |
0.208 (0.629) |
0.00643 (0.171) |
1 (1.00) |
amp 8q24 21 | 386 (74%) | 136 |
0.0697 (0.434) |
0.541 (0.854) |
0.17 (0.599) |
0.199 (0.622) |
0.0615 (0.399) |
0.215 (0.63) |
1 (1.00) |
0.741 (0.963) |
0.478 (0.821) |
0.823 (0.981) |
0.0408 (0.345) |
0.0162 (0.246) |
0.875 (1.00) |
0.254 (0.672) |
amp 9p24 1 | 126 (24%) | 396 |
0.188 (0.617) |
0.0379 (0.336) |
0.886 (1.00) |
0.745 (0.963) |
0.196 (0.622) |
1 (1.00) |
0.000125 (0.019) |
0.211 (0.629) |
0.592 (0.884) |
0.0188 (0.256) |
0.167 (0.599) |
0.0906 (0.462) |
0.979 (1.00) |
0.252 (0.669) |
amp 9q34 3 | 177 (34%) | 345 |
0.0766 (0.443) |
0.0793 (0.449) |
0.133 (0.548) |
0.00851 (0.193) |
0.248 (0.666) |
1 (1.00) |
0.917 (1.00) |
0.836 (0.987) |
1 (1.00) |
0.775 (0.967) |
0.917 (1.00) |
0.444 (0.801) |
0.692 (0.929) |
0.203 (0.627) |
amp 13q34 | 106 (20%) | 416 |
0.0281 (0.309) |
0.0143 (0.238) |
0.277 (0.681) |
0.153 (0.579) |
0.155 (0.58) |
1 (1.00) |
0.326 (0.711) |
0.72 (0.945) |
1 (1.00) |
0.726 (0.951) |
0.131 (0.547) |
0.693 (0.929) |
0.769 (0.967) |
0.212 (0.629) |
amp 18p11 31 | 156 (30%) | 366 |
0.12 (0.523) |
0.451 (0.801) |
0.0533 (0.364) |
0.0478 (0.349) |
0.192 (0.62) |
0.262 (0.676) |
0.00023 (0.0223) |
0.24 (0.655) |
0.647 (0.913) |
0.0408 (0.345) |
0.787 (0.97) |
0.443 (0.801) |
0.257 (0.675) |
0.276 (0.681) |
amp 18q11 2 | 106 (20%) | 416 |
0.6 (0.889) |
0.0775 (0.443) |
0.33 (0.711) |
0.827 (0.985) |
0.857 (0.997) |
0.168 (0.599) |
0.00993 (0.203) |
0.331 (0.711) |
0.113 (0.502) |
0.285 (0.683) |
0.702 (0.931) |
0.847 (0.991) |
0.129 (0.544) |
0.323 (0.71) |
amp xq28 | 150 (29%) | 372 |
0.177 (0.608) |
0.408 (0.768) |
0.553 (0.859) |
0.106 (0.494) |
0.233 (0.648) |
0.246 (0.666) |
0.384 (0.746) |
1 (1.00) |
0.807 (0.974) |
0.861 (0.998) |
0.548 (0.859) |
0.014 (0.238) |
0.76 (0.963) |
0.509 (0.841) |
del 1p36 21 | 95 (18%) | 427 |
0.364 (0.734) |
0.0531 (0.364) |
0.277 (0.681) |
0.528 (0.844) |
0.657 (0.918) |
1 (1.00) |
0.609 (0.89) |
0.306 (0.704) |
0.0331 (0.326) |
0.00326 (0.13) |
0.111 (0.502) |
0.925 (1.00) |
0.376 (0.745) |
0.794 (0.97) |
del 1p13 2 | 133 (25%) | 389 |
0.0868 (0.462) |
0.0351 (0.326) |
0.54 (0.854) |
0.313 (0.704) |
0.96 (1.00) |
0.241 (0.655) |
0.91 (1.00) |
0.499 (0.832) |
0.464 (0.809) |
0.00612 (0.171) |
0.609 (0.89) |
0.709 (0.936) |
0.191 (0.619) |
0.817 (0.979) |
del 2q21 2 | 78 (15%) | 444 |
0.676 (0.925) |
0.262 (0.676) |
0.113 (0.502) |
0.803 (0.973) |
0.263 (0.676) |
1 (1.00) |
0.00804 (0.186) |
0.893 (1.00) |
0.703 (0.931) |
0.366 (0.736) |
0.0476 (0.349) |
0.262 (0.676) |
0.555 (0.859) |
0.262 (0.676) |
del 4p15 2 | 208 (40%) | 314 |
0.286 (0.683) |
0.51 (0.841) |
0.748 (0.963) |
0.385 (0.746) |
0.498 (0.832) |
1 (1.00) |
0.0202 (0.264) |
0.274 (0.68) |
0.718 (0.944) |
0.0152 (0.242) |
0.317 (0.706) |
0.282 (0.683) |
0.174 (0.602) |
1 (1.00) |
del 5q35 3 | 199 (38%) | 323 |
0.731 (0.955) |
0.223 (0.633) |
0.792 (0.97) |
0.0654 (0.417) |
0.641 (0.911) |
1 (1.00) |
0.222 (0.633) |
0.548 (0.859) |
0.314 (0.704) |
0.0126 (0.23) |
0.493 (0.832) |
0.558 (0.861) |
0.138 (0.555) |
0.404 (0.765) |
del 7q31 1 | 77 (15%) | 445 |
0.41 (0.772) |
0.0338 (0.326) |
0.593 (0.884) |
0.755 (0.963) |
0.0164 (0.246) |
1 (1.00) |
1 (1.00) |
0.593 (0.884) |
0.7 (0.931) |
0.0246 (0.292) |
0.114 (0.505) |
0.149 (0.574) |
0.404 (0.765) |
0.782 (0.97) |
del 8p23 2 | 305 (58%) | 217 |
0.00729 (0.18) |
0.0203 (0.264) |
0.787 (0.97) |
0.206 (0.629) |
0.345 (0.723) |
1 (1.00) |
0.23 (0.642) |
0.235 (0.648) |
0.0728 (0.436) |
0.554 (0.859) |
0.978 (1.00) |
0.15 (0.574) |
0.393 (0.751) |
0.152 (0.579) |
del 9p23 | 239 (46%) | 283 |
0.52 (0.844) |
0.504 (0.838) |
0.762 (0.963) |
0.278 (0.681) |
0.814 (0.978) |
0.466 (0.809) |
0.0478 (0.349) |
0.845 (0.99) |
0.869 (1.00) |
0.000175 (0.0223) |
0.239 (0.652) |
0.836 (0.987) |
0.123 (0.53) |
0.32 (0.707) |
del 9p21 3 | 302 (58%) | 220 |
0.0174 (0.25) |
0.525 (0.844) |
0.29 (0.69) |
0.0318 (0.326) |
0.651 (0.916) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.333 (0.712) |
0.00135 (0.0847) |
0.208 (0.629) |
0.78 (0.97) |
0.0855 (0.462) |
0.687 (0.929) |
del 10p11 21 | 163 (31%) | 359 |
0.0714 (0.436) |
0.76 (0.963) |
0.333 (0.712) |
0.132 (0.548) |
0.373 (0.742) |
1 (1.00) |
0.11 (0.502) |
0.092 (0.462) |
0.112 (0.502) |
0.733 (0.955) |
0.953 (1.00) |
0.138 (0.555) |
0.00512 (0.165) |
0.669 (0.922) |
del 13q14 2 | 217 (42%) | 305 |
0.327 (0.711) |
0.0942 (0.462) |
0.429 (0.786) |
0.854 (0.997) |
0.278 (0.681) |
0.393 (0.751) |
0.0451 (0.349) |
0.277 (0.681) |
0.198 (0.622) |
0.669 (0.922) |
0.574 (0.876) |
0.202 (0.626) |
0.0152 (0.242) |
0.217 (0.63) |
del 14q11 2 | 75 (14%) | 447 |
0.616 (0.895) |
0.352 (0.728) |
0.522 (0.844) |
0.496 (0.832) |
0.772 (0.967) |
1 (1.00) |
0.161 (0.59) |
0.0518 (0.363) |
0.283 (0.683) |
0.0111 (0.215) |
0.656 (0.917) |
0.286 (0.683) |
0.353 (0.728) |
0.0358 (0.329) |
del 14q32 32 | 75 (14%) | 447 |
0.196 (0.622) |
0.349 (0.723) |
0.314 (0.704) |
0.521 (0.844) |
0.596 (0.886) |
1 (1.00) |
0.0487 (0.353) |
0.0166 (0.246) |
0.693 (0.929) |
0.816 (0.979) |
0.578 (0.878) |
0.878 (1.00) |
0.343 (0.722) |
0.558 (0.861) |
del 17p11 2 | 99 (19%) | 423 |
0.198 (0.622) |
0.803 (0.973) |
0.182 (0.609) |
0.776 (0.967) |
0.359 (0.731) |
0.188 (0.617) |
0.614 (0.893) |
0.215 (0.63) |
0.525 (0.844) |
0.355 (0.728) |
0.928 (1.00) |
0.654 (0.917) |
0.00283 (0.125) |
0.124 (0.53) |
del 17q25 3 | 71 (14%) | 451 |
0.842 (0.988) |
0.324 (0.71) |
0.686 (0.929) |
0.0755 (0.439) |
0.089 (0.462) |
1 (1.00) |
0.313 (0.704) |
0.259 (0.676) |
0.166 (0.597) |
0.299 (0.693) |
0.459 (0.807) |
0.619 (0.895) |
0.83 (0.987) |
0.0145 (0.238) |
del 19p13 3 | 175 (34%) | 347 |
0.00756 (0.182) |
0.607 (0.89) |
0.0852 (0.462) |
0.296 (0.693) |
0.102 (0.481) |
0.33 (0.711) |
0.601 (0.889) |
0.531 (0.849) |
0.223 (0.633) |
0.297 (0.693) |
0.0902 (0.462) |
0.164 (0.594) |
0.775 (0.967) |
0.394 (0.751) |
del 21q22 3 | 208 (40%) | 314 |
0.749 (0.963) |
0.847 (0.991) |
0.975 (1.00) |
0.0966 (0.469) |
0.383 (0.746) |
1 (1.00) |
0.268 (0.678) |
0.367 (0.737) |
1 (1.00) |
0.0179 (0.254) |
0.788 (0.97) |
0.44 (0.799) |
0.00694 (0.18) |
0.683 (0.929) |
del xp21 3 | 159 (30%) | 363 |
0.343 (0.722) |
0.728 (0.952) |
0.279 (0.682) |
0.123 (0.53) |
0.212 (0.629) |
0.283 (0.683) |
0.336 (0.715) |
0.596 (0.886) |
0.348 (0.723) |
0.0729 (0.436) |
0.7 (0.931) |
0.0092 (0.198) |
0.884 (1.00) |
0.382 (0.746) |
del xq21 33 | 80 (15%) | 442 |
0.805 (0.973) |
0.968 (1.00) |
0.102 (0.481) |
0.669 (0.922) |
0.148 (0.574) |
0.141 (0.563) |
0.784 (0.97) |
0.507 (0.839) |
0.103 (0.481) |
0.717 (0.944) |
0.491 (0.832) |
0.00524 (0.165) |
0.634 (0.904) |
0.574 (0.876) |
amp 2q31 2 | 112 (21%) | 410 |
0.198 (0.622) |
0.522 (0.844) |
0.454 (0.803) |
0.393 (0.751) |
0.189 (0.617) |
1 (1.00) |
0.0936 (0.462) |
0.026 (0.297) |
0.762 (0.963) |
0.0524 (0.363) |
0.907 (1.00) |
0.138 (0.555) |
0.206 (0.629) |
0.0871 (0.462) |
amp 5p15 33 | 240 (46%) | 282 |
0.833 (0.987) |
0.0187 (0.256) |
0.293 (0.692) |
0.579 (0.878) |
0.0331 (0.326) |
0.445 (0.801) |
0.0473 (0.349) |
0.0642 (0.412) |
0.742 (0.963) |
0.29 (0.69) |
0.173 (0.602) |
0.0934 (0.462) |
0.044 (0.349) |
0.156 (0.58) |
amp 5p12 | 205 (39%) | 317 |
0.576 (0.878) |
0.118 (0.516) |
0.373 (0.742) |
0.411 (0.772) |
0.0596 (0.394) |
1 (1.00) |
0.188 (0.617) |
0.0739 (0.439) |
0.591 (0.884) |
0.543 (0.854) |
0.769 (0.967) |
0.102 (0.481) |
0.758 (0.963) |
0.15 (0.574) |
amp 6p12 1 | 110 (21%) | 412 |
0.79 (0.97) |
0.134 (0.549) |
0.796 (0.972) |
0.266 (0.676) |
0.688 (0.929) |
1 (1.00) |
0.468 (0.81) |
0.812 (0.977) |
1 (1.00) |
0.472 (0.814) |
0.909 (1.00) |
0.697 (0.931) |
0.0579 (0.389) |
1 (1.00) |
amp 6q12 | 96 (18%) | 426 |
0.431 (0.788) |
0.192 (0.62) |
0.894 (1.00) |
0.347 (0.723) |
0.804 (0.973) |
1 (1.00) |
0.799 (0.973) |
0.385 (0.746) |
0.364 (0.734) |
0.75 (0.963) |
0.0228 (0.279) |
0.564 (0.866) |
0.183 (0.609) |
0.297 (0.693) |
amp 8q11 21 | 310 (59%) | 212 |
0.947 (1.00) |
0.891 (1.00) |
0.13 (0.546) |
0.329 (0.711) |
0.525 (0.844) |
0.356 (0.728) |
0.841 (0.988) |
0.113 (0.502) |
0.724 (0.948) |
0.863 (0.999) |
0.228 (0.639) |
0.369 (0.739) |
0.569 (0.871) |
0.31 (0.704) |
amp 9p13 3 | 139 (27%) | 383 |
0.542 (0.854) |
0.254 (0.672) |
0.54 (0.854) |
0.92 (1.00) |
0.406 (0.766) |
1 (1.00) |
0.0939 (0.462) |
0.583 (0.882) |
0.804 (0.973) |
0.295 (0.693) |
0.115 (0.507) |
0.202 (0.626) |
0.876 (1.00) |
0.182 (0.609) |
amp 11p13 | 102 (20%) | 420 |
0.278 (0.681) |
0.448 (0.801) |
0.183 (0.609) |
0.868 (1.00) |
0.0989 (0.476) |
1 (1.00) |
0.619 (0.895) |
0.0909 (0.462) |
0.755 (0.963) |
0.0673 (0.424) |
0.311 (0.704) |
0.881 (1.00) |
0.379 (0.746) |
0.201 (0.626) |
amp 11q13 3 | 229 (44%) | 293 |
0.0452 (0.349) |
0.16 (0.59) |
0.5 (0.833) |
0.517 (0.844) |
0.211 (0.629) |
1 (1.00) |
0.426 (0.785) |
0.922 (1.00) |
0.196 (0.622) |
0.0342 (0.326) |
0.604 (0.89) |
0.182 (0.609) |
0.27 (0.68) |
1 (1.00) |
amp 12p13 33 | 167 (32%) | 355 |
0.931 (1.00) |
0.962 (1.00) |
0.92 (1.00) |
0.983 (1.00) |
0.536 (0.854) |
1 (1.00) |
0.0718 (0.436) |
0.833 (0.987) |
1 (1.00) |
0.553 (0.859) |
0.62 (0.895) |
0.247 (0.666) |
0.183 (0.609) |
0.669 (0.922) |
amp 12q15 | 103 (20%) | 419 |
0.872 (1.00) |
0.0385 (0.338) |
0.614 (0.893) |
0.662 (0.921) |
0.216 (0.63) |
1 (1.00) |
0.902 (1.00) |
0.9 (1.00) |
0.755 (0.963) |
0.0752 (0.439) |
0.38 (0.746) |
0.0914 (0.462) |
0.0954 (0.466) |
0.799 (0.973) |
amp 13q22 1 | 105 (20%) | 417 |
0.0299 (0.322) |
0.0898 (0.462) |
0.835 (0.987) |
0.207 (0.629) |
0.561 (0.863) |
1 (1.00) |
0.462 (0.809) |
1 (1.00) |
0.758 (0.963) |
0.537 (0.854) |
0.162 (0.591) |
0.934 (1.00) |
0.273 (0.68) |
0.316 (0.706) |
amp 15q26 3 | 105 (20%) | 417 |
0.0308 (0.324) |
0.671 (0.922) |
0.759 (0.963) |
0.125 (0.53) |
0.889 (1.00) |
1 (1.00) |
0.902 (1.00) |
0.466 (0.809) |
0.3 (0.693) |
0.368 (0.738) |
0.389 (0.749) |
0.956 (1.00) |
0.622 (0.895) |
0.8 (0.973) |
amp 17q12 | 91 (17%) | 431 |
0.199 (0.622) |
0.0749 (0.439) |
0.128 (0.543) |
0.193 (0.62) |
0.743 (0.963) |
0.194 (0.621) |
0.435 (0.793) |
0.898 (1.00) |
0.186 (0.615) |
0.0249 (0.292) |
0.226 (0.636) |
0.718 (0.944) |
0.82 (0.98) |
0.0287 (0.312) |
amp 20q11 22 | 227 (43%) | 295 |
0.52 (0.844) |
0.212 (0.629) |
0.541 (0.854) |
0.495 (0.832) |
0.962 (1.00) |
1 (1.00) |
0.486 (0.83) |
0.492 (0.832) |
0.623 (0.895) |
0.79 (0.97) |
0.171 (0.599) |
0.672 (0.922) |
0.583 (0.882) |
0.542 (0.854) |
del 1q44 | 48 (9%) | 474 |
0.0375 (0.336) |
0.421 (0.783) |
0.806 (0.974) |
0.478 (0.821) |
0.864 (0.999) |
1 (1.00) |
0.495 (0.832) |
0.0211 (0.27) |
0.646 (0.913) |
0.695 (0.929) |
0.145 (0.574) |
0.273 (0.68) |
0.481 (0.825) |
0.295 (0.693) |
del 4p16 3 | 205 (39%) | 317 |
0.138 (0.555) |
0.475 (0.818) |
0.36 (0.731) |
0.273 (0.68) |
0.762 (0.963) |
0.351 (0.726) |
0.0266 (0.301) |
0.37 (0.74) |
0.251 (0.669) |
0.0511 (0.363) |
0.342 (0.722) |
0.301 (0.694) |
0.387 (0.747) |
0.684 (0.929) |
del 4q21 3 | 156 (30%) | 366 |
0.82 (0.98) |
0.231 (0.644) |
0.222 (0.633) |
0.0451 (0.349) |
0.917 (1.00) |
1 (1.00) |
1 (1.00) |
0.398 (0.757) |
0.506 (0.838) |
0.17 (0.599) |
0.0467 (0.349) |
0.425 (0.784) |
0.332 (0.712) |
0.0775 (0.443) |
del 4q22 1 | 169 (32%) | 353 |
0.319 (0.707) |
0.549 (0.859) |
0.309 (0.704) |
0.312 (0.704) |
0.882 (1.00) |
1 (1.00) |
0.527 (0.844) |
0.348 (0.723) |
0.22 (0.633) |
0.0918 (0.462) |
0.085 (0.462) |
0.515 (0.844) |
0.356 (0.728) |
0.137 (0.555) |
del 4q35 2 | 213 (41%) | 309 |
0.643 (0.911) |
0.653 (0.917) |
0.0824 (0.457) |
0.068 (0.426) |
0.494 (0.832) |
0.393 (0.751) |
0.0874 (0.462) |
0.236 (0.648) |
0.26 (0.676) |
0.443 (0.801) |
0.499 (0.832) |
0.623 (0.895) |
0.521 (0.844) |
0.841 (0.988) |
del 6p25 3 | 96 (18%) | 426 |
0.0744 (0.439) |
0.283 (0.683) |
0.183 (0.609) |
0.0931 (0.462) |
0.526 (0.844) |
1 (1.00) |
0.0975 (0.472) |
0.899 (1.00) |
1 (1.00) |
0.317 (0.706) |
0.362 (0.734) |
0.638 (0.908) |
0.0419 (0.346) |
0.794 (0.97) |
del 7q36 1 | 132 (25%) | 390 |
0.0508 (0.363) |
0.691 (0.929) |
0.415 (0.775) |
0.577 (0.878) |
0.164 (0.594) |
1 (1.00) |
0.364 (0.734) |
0.265 (0.676) |
0.792 (0.97) |
0.148 (0.574) |
0.237 (0.649) |
0.38 (0.746) |
0.327 (0.711) |
0.643 (0.911) |
del 9q21 11 | 108 (21%) | 414 |
0.451 (0.801) |
0.234 (0.648) |
0.569 (0.871) |
0.607 (0.89) |
0.684 (0.929) |
0.262 (0.676) |
0.393 (0.751) |
0.904 (1.00) |
0.386 (0.747) |
0.0369 (0.336) |
0.661 (0.921) |
0.518 (0.844) |
0.161 (0.59) |
0.622 (0.895) |
del 9q34 3 | 79 (15%) | 443 |
0.704 (0.931) |
0.456 (0.804) |
0.299 (0.693) |
0.858 (0.997) |
0.975 (1.00) |
0.147 (0.574) |
0.89 (1.00) |
0.893 (1.00) |
0.465 (0.809) |
0.0219 (0.274) |
0.327 (0.711) |
0.857 (0.997) |
0.424 (0.784) |
0.563 (0.866) |
del 10q23 31 | 138 (26%) | 384 |
0.634 (0.904) |
0.691 (0.929) |
0.487 (0.831) |
0.285 (0.683) |
0.917 (1.00) |
1 (1.00) |
0.0253 (0.293) |
0.217 (0.63) |
0.609 (0.89) |
0.0581 (0.389) |
0.265 (0.676) |
0.891 (1.00) |
0.466 (0.809) |
0.171 (0.599) |
del 11p15 5 | 163 (31%) | 359 |
0.269 (0.679) |
0.86 (0.998) |
0.0399 (0.343) |
0.546 (0.858) |
0.0277 (0.309) |
1 (1.00) |
0.339 (0.718) |
0.0249 (0.292) |
0.0203 (0.264) |
0.772 (0.967) |
0.891 (1.00) |
0.089 (0.462) |
0.0331 (0.326) |
0.19 (0.618) |
del 12q24 33 | 63 (12%) | 459 |
0.703 (0.931) |
0.587 (0.883) |
0.892 (1.00) |
0.311 (0.704) |
0.525 (0.844) |
1 (1.00) |
0.65 (0.916) |
0.449 (0.801) |
0.423 (0.784) |
0.92 (1.00) |
0.941 (1.00) |
0.601 (0.889) |
0.0428 (0.348) |
0.221 (0.633) |
del 13q12 11 | 233 (45%) | 289 |
0.582 (0.882) |
0.682 (0.929) |
0.0824 (0.457) |
0.11 (0.502) |
0.0832 (0.459) |
0.445 (0.801) |
0.0376 (0.336) |
0.695 (0.929) |
0.734 (0.955) |
0.0825 (0.457) |
0.385 (0.746) |
0.0873 (0.462) |
0.0182 (0.254) |
0.154 (0.579) |
del 15q15 1 | 124 (24%) | 398 |
0.46 (0.807) |
0.682 (0.929) |
0.414 (0.775) |
0.169 (0.599) |
0.554 (0.859) |
1 (1.00) |
0.354 (0.728) |
0.356 (0.728) |
0.042 (0.346) |
0.654 (0.917) |
0.586 (0.883) |
0.645 (0.913) |
0.777 (0.968) |
0.159 (0.589) |
del 16q23 1 | 98 (19%) | 424 |
0.913 (1.00) |
0.224 (0.635) |
0.236 (0.648) |
0.588 (0.883) |
0.0664 (0.42) |
1 (1.00) |
0.207 (0.629) |
0.139 (0.557) |
0.266 (0.676) |
0.472 (0.814) |
0.249 (0.666) |
0.109 (0.502) |
0.497 (0.832) |
1 (1.00) |
del 16q23 3 | 105 (20%) | 417 |
0.618 (0.895) |
0.248 (0.666) |
0.309 (0.704) |
0.226 (0.636) |
0.0779 (0.443) |
1 (1.00) |
0.462 (0.809) |
0.148 (0.574) |
0.298 (0.693) |
0.81 (0.975) |
0.385 (0.746) |
0.0728 (0.436) |
0.413 (0.773) |
0.454 (0.803) |
del 19q13 43 | 97 (19%) | 425 |
0.18 (0.609) |
0.175 (0.603) |
0.0915 (0.462) |
0.0231 (0.28) |
0.7 (0.931) |
1 (1.00) |
0.899 (1.00) |
0.901 (1.00) |
1 (1.00) |
0.63 (0.902) |
0.0217 (0.274) |
0.967 (1.00) |
0.656 (0.917) |
0.124 (0.53) |
P value = 0.00586 (Fisher's exact test), Q value = 0.17
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 50 | 137 | 100 | 173 |
AMP PEAK 1(2Q11.2) MUTATED | 5 | 19 | 27 | 44 |
AMP PEAK 1(2Q11.2) WILD-TYPE | 45 | 118 | 73 | 129 |
P value = 0.00541 (Fisher's exact test), Q value = 0.16
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
AMP PEAK 3(3Q26.33) MUTATED | 89 | 291 |
AMP PEAK 3(3Q26.33) WILD-TYPE | 51 | 91 |
P value = 3.54e-05 (logrank test), Q value = 0.019
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
AMP PEAK 8(7P11.2) MUTATED | 220 | 112 | 0.1 - 172.7 (18.3) |
AMP PEAK 8(7P11.2) WILD-TYPE | 300 | 107 | 0.1 - 211.0 (23.0) |
P value = 0.00354 (logrank test), Q value = 0.13
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
AMP PEAK 9(7Q21.3) MUTATED | 169 | 90 | 0.1 - 172.7 (19.8) |
AMP PEAK 9(7Q21.3) WILD-TYPE | 351 | 129 | 0.1 - 211.0 (21.2) |
P value = 0.00055 (Fisher's exact test), Q value = 0.048
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
AMP PEAK 9(7Q21.3) MUTATED | 1 | 1 | 27 | 138 |
AMP PEAK 9(7Q21.3) WILD-TYPE | 1 | 10 | 21 | 308 |
P value = 0.00643 (Fisher's exact test), Q value = 0.17
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
AMP PEAK 10(8P11.23) MUTATED | 0 | 0 | 22 | 134 |
AMP PEAK 10(8P11.23) WILD-TYPE | 2 | 11 | 26 | 312 |
P value = 0.0162 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
AMP PEAK 12(8Q24.21) MUTATED | 315 | 2.3 (4.0) |
AMP PEAK 12(8Q24.21) WILD-TYPE | 93 | 1.9 (5.1) |
P value = 0.000125 (Fisher's exact test), Q value = 0.019
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
AMP PEAK 13(9P24.1) MUTATED | 51 | 75 |
AMP PEAK 13(9P24.1) WILD-TYPE | 89 | 307 |
P value = 0.00241 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
AMP PEAK 14(9P23) MUTATED | 47 | 77 |
AMP PEAK 14(9P23) WILD-TYPE | 93 | 305 |
P value = 0.0102 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
AMP PEAK 14(9P23) MUTATED | 69 | 37.8 (27.2) |
AMP PEAK 14(9P23) WILD-TYPE | 224 | 48.4 (37.2) |
P value = 0.00851 (Fisher's exact test), Q value = 0.19
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 50 | 137 | 100 | 173 |
AMP PEAK 16(9Q34.3) MUTATED | 11 | 39 | 37 | 75 |
AMP PEAK 16(9Q34.3) WILD-TYPE | 39 | 98 | 63 | 98 |
P value = 0.0143 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 521 | 60.9 (11.9) |
AMP PEAK 22(13Q34) MUTATED | 105 | 58.4 (12.6) |
AMP PEAK 22(13Q34) WILD-TYPE | 416 | 61.5 (11.7) |
P value = 0.00023 (Fisher's exact test), Q value = 0.022
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
AMP PEAK 25(18P11.31) MUTATED | 25 | 131 |
AMP PEAK 25(18P11.31) WILD-TYPE | 115 | 251 |
P value = 0.00993 (Fisher's exact test), Q value = 0.2
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
AMP PEAK 26(18Q11.2) MUTATED | 18 | 88 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 122 | 294 |
P value = 0.014 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
AMP PEAK 28(XQ28) MUTATED | 122 | 2.4 (3.1) |
AMP PEAK 28(XQ28) WILD-TYPE | 286 | 2.1 (4.7) |
P value = 0.00326 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 1(1P36.21) MUTATED | 62 | 58.0 (46.4) |
DEL PEAK 1(1P36.21) WILD-TYPE | 231 | 42.6 (31.1) |
P value = 0.00612 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 2(1P13.2) MUTATED | 70 | 56.0 (43.7) |
DEL PEAK 2(1P13.2) WILD-TYPE | 223 | 42.7 (31.7) |
P value = 0.00804 (Fisher's exact test), Q value = 0.19
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
DEL PEAK 4(2Q21.2) MUTATED | 31 | 47 |
DEL PEAK 4(2Q21.2) WILD-TYPE | 109 | 335 |
P value = 0.0127 (Fisher's exact test), Q value = 0.23
nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVB | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 27 | 76 | 82 | 252 | 12 | 1 |
DEL PEAK 5(2Q22.1) MUTATED | 2 | 13 | 20 | 65 | 6 | 1 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 25 | 63 | 62 | 187 | 6 | 0 |
P value = 0.00725 (Fisher's exact test), Q value = 0.18
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 50 | 137 | 100 | 173 |
DEL PEAK 5(2Q22.1) MUTATED | 5 | 27 | 24 | 54 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 45 | 110 | 76 | 119 |
P value = 0.012 (Fisher's exact test), Q value = 0.22
nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVB | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 27 | 76 | 82 | 252 | 12 | 1 |
DEL PEAK 6(2Q36.2) MUTATED | 3 | 17 | 33 | 73 | 6 | 0 |
DEL PEAK 6(2Q36.2) WILD-TYPE | 24 | 59 | 49 | 179 | 6 | 1 |
P value = 0.00207 (Fisher's exact test), Q value = 0.11
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 50 | 137 | 100 | 173 |
DEL PEAK 6(2Q36.2) MUTATED | 7 | 33 | 41 | 55 |
DEL PEAK 6(2Q36.2) WILD-TYPE | 43 | 104 | 59 | 118 |
P value = 0.0113 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 6(2Q36.2) MUTATED | 92 | 51.8 (33.7) |
DEL PEAK 6(2Q36.2) WILD-TYPE | 201 | 43.2 (35.8) |
P value = 0.0093 (Fisher's exact test), Q value = 0.2
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 6(2Q36.2) MUTATED | 1 | 6 | 22 | 125 |
DEL PEAK 6(2Q36.2) WILD-TYPE | 1 | 5 | 26 | 321 |
P value = 0.0141 (Fisher's exact test), Q value = 0.24
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 26 | 459 |
DEL PEAK 6(2Q36.2) MUTATED | 14 | 134 |
DEL PEAK 6(2Q36.2) WILD-TYPE | 12 | 325 |
P value = 0.00331 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
DEL PEAK 7(3P26.2) MUTATED | 79 | 269 |
DEL PEAK 7(3P26.2) WILD-TYPE | 61 | 113 |
P value = 0.00116 (Wilcoxon-test), Q value = 0.082
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 7(3P26.2) MUTATED | 204 | 49.3 (37.2) |
DEL PEAK 7(3P26.2) WILD-TYPE | 89 | 38.0 (29.4) |
P value = 9e-05 (Fisher's exact test), Q value = 0.019
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 7(3P26.2) MUTATED | 2 | 6 | 44 | 285 |
DEL PEAK 7(3P26.2) WILD-TYPE | 0 | 5 | 4 | 161 |
P value = 0.00893 (logrank test), Q value = 0.2
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
DEL PEAK 8(3P24.1) MUTATED | 366 | 168 | 0.1 - 211.0 (20.6) |
DEL PEAK 8(3P24.1) WILD-TYPE | 154 | 51 | 0.4 - 169.4 (22.1) |
P value = 0.00534 (Fisher's exact test), Q value = 0.16
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 50 | 137 | 100 | 173 |
DEL PEAK 8(3P24.1) MUTATED | 28 | 90 | 79 | 132 |
DEL PEAK 8(3P24.1) WILD-TYPE | 22 | 47 | 21 | 41 |
P value = 0.0035 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
DEL PEAK 8(3P24.1) MUTATED | 85 | 283 |
DEL PEAK 8(3P24.1) WILD-TYPE | 55 | 99 |
P value = 7.33e-05 (Wilcoxon-test), Q value = 0.019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 8(3P24.1) MUTATED | 216 | 49.8 (37.2) |
DEL PEAK 8(3P24.1) WILD-TYPE | 77 | 34.8 (26.8) |
P value = 0.00023 (Fisher's exact test), Q value = 0.022
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 8(3P24.1) MUTATED | 1 | 7 | 45 | 304 |
DEL PEAK 8(3P24.1) WILD-TYPE | 1 | 4 | 3 | 142 |
P value = 0.0027 (logrank test), Q value = 0.12
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
DEL PEAK 9(3P14.2) MUTATED | 370 | 170 | 0.1 - 211.0 (20.5) |
DEL PEAK 9(3P14.2) WILD-TYPE | 150 | 49 | 0.4 - 172.7 (22.5) |
P value = 0.00635 (Fisher's exact test), Q value = 0.17
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
DEL PEAK 9(3P14.2) MUTATED | 87 | 285 |
DEL PEAK 9(3P14.2) WILD-TYPE | 53 | 97 |
P value = 0.000107 (Wilcoxon-test), Q value = 0.019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 9(3P14.2) MUTATED | 220 | 49.5 (37.0) |
DEL PEAK 9(3P14.2) WILD-TYPE | 73 | 35.0 (27.4) |
P value = 0.014 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
DEL PEAK 9(3P14.2) MUTATED | 304 | 2.4 (4.7) |
DEL PEAK 9(3P14.2) WILD-TYPE | 104 | 1.5 (2.6) |
P value = 0.00173 (Fisher's exact test), Q value = 0.1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 9(3P14.2) MUTATED | 1 | 7 | 44 | 308 |
DEL PEAK 9(3P14.2) WILD-TYPE | 1 | 4 | 4 | 138 |
P value = 0.00438 (logrank test), Q value = 0.15
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
DEL PEAK 10(3P12.1) MUTATED | 341 | 159 | 0.1 - 211.0 (21.1) |
DEL PEAK 10(3P12.1) WILD-TYPE | 179 | 60 | 0.4 - 180.2 (21.5) |
P value = 0.0165 (Fisher's exact test), Q value = 0.25
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
DEL PEAK 10(3P12.1) MUTATED | 80 | 263 |
DEL PEAK 10(3P12.1) WILD-TYPE | 60 | 119 |
P value = 8.33e-05 (Wilcoxon-test), Q value = 0.019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 10(3P12.1) MUTATED | 202 | 49.2 (33.5) |
DEL PEAK 10(3P12.1) WILD-TYPE | 91 | 38.6 (38.4) |
P value = 0.00179 (Fisher's exact test), Q value = 0.1
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 10(3P12.1) MUTATED | 1 | 7 | 42 | 281 |
DEL PEAK 10(3P12.1) WILD-TYPE | 1 | 4 | 6 | 165 |
P value = 0.0152 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 12(4P15.2) MUTATED | 128 | 48.7 (29.4) |
DEL PEAK 12(4P15.2) WILD-TYPE | 165 | 43.7 (39.3) |
P value = 0.00626 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 16(5Q12.1) MUTATED | 125 | 51.8 (38.4) |
DEL PEAK 16(5Q12.1) WILD-TYPE | 168 | 41.5 (32.3) |
P value = 0.00217 (Fisher's exact test), Q value = 0.11
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 16(5Q12.1) MUTATED | 1 | 3 | 31 | 173 |
DEL PEAK 16(5Q12.1) WILD-TYPE | 1 | 8 | 17 | 273 |
P value = 0.0111 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 17(5Q15) MUTATED | 131 | 50.8 (37.7) |
DEL PEAK 17(5Q15) WILD-TYPE | 162 | 41.9 (32.9) |
P value = 0.00968 (Fisher's exact test), Q value = 0.2
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 17(5Q15) MUTATED | 1 | 5 | 31 | 182 |
DEL PEAK 17(5Q15) WILD-TYPE | 1 | 6 | 17 | 264 |
P value = 0.0126 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 18(5Q35.3) MUTATED | 114 | 49.6 (30.1) |
DEL PEAK 18(5Q35.3) WILD-TYPE | 179 | 43.5 (38.2) |
P value = 0.0164 (Fisher's exact test), Q value = 0.25
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 179 | 68 | 168 | 8 |
DEL PEAK 20(7Q31.1) MUTATED | 18 | 17 | 29 | 0 |
DEL PEAK 20(7Q31.1) WILD-TYPE | 161 | 51 | 139 | 8 |
P value = 0.00729 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
DEL PEAK 22(8P23.2) MUTATED | 304 | 145 | 0.1 - 180.2 (19.9) |
DEL PEAK 22(8P23.2) WILD-TYPE | 216 | 74 | 0.4 - 211.0 (22.6) |
P value = 0.000175 (Wilcoxon-test), Q value = 0.022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 23(9P23) MUTATED | 142 | 50.9 (30.3) |
DEL PEAK 23(9P23) WILD-TYPE | 151 | 41.2 (39.0) |
P value = 0.00135 (Wilcoxon-test), Q value = 0.085
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 24(9P21.3) MUTATED | 179 | 48.6 (29.5) |
DEL PEAK 24(9P21.3) WILD-TYPE | 114 | 41.6 (42.7) |
P value = 0.0077 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
DEL PEAK 27(10P15.3) MUTATED | 170 | 85 | 0.4 - 172.7 (19.0) |
DEL PEAK 27(10P15.3) WILD-TYPE | 350 | 134 | 0.1 - 211.0 (22.4) |
P value = 0.0132 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
DEL PEAK 27(10P15.3) MUTATED | 140 | 2.8 (5.8) |
DEL PEAK 27(10P15.3) WILD-TYPE | 268 | 1.9 (3.2) |
P value = 0.00512 (Fisher's exact test), Q value = 0.16
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 28(10P11.21) MUTATED | 0 | 5 | 25 | 131 |
DEL PEAK 28(10P11.21) WILD-TYPE | 2 | 6 | 23 | 315 |
P value = 0.00342 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 521 | 60.9 (11.9) |
DEL PEAK 31(11Q23.1) MUTATED | 245 | 59.5 (11.3) |
DEL PEAK 31(11Q23.1) WILD-TYPE | 276 | 62.1 (12.4) |
P value = 6e-04 (Fisher's exact test), Q value = 0.048
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 179 | 68 | 168 | 8 |
DEL PEAK 31(11Q23.1) MUTATED | 65 | 26 | 96 | 3 |
DEL PEAK 31(11Q23.1) WILD-TYPE | 114 | 42 | 72 | 5 |
P value = 4.97e-06 (Fisher's exact test), Q value = 0.0053
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
DEL PEAK 31(11Q23.1) MUTATED | 43 | 203 |
DEL PEAK 31(11Q23.1) WILD-TYPE | 97 | 179 |
P value = 0.00124 (Fisher's exact test), Q value = 0.082
nPatients | NO | YES |
---|---|---|
ALL | 162 | 301 |
DEL PEAK 31(11Q23.1) MUTATED | 59 | 158 |
DEL PEAK 31(11Q23.1) WILD-TYPE | 103 | 143 |
P value = 0.000219 (Wilcoxon-test), Q value = 0.022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
DEL PEAK 31(11Q23.1) MUTATED | 178 | 2.9 (5.3) |
DEL PEAK 31(11Q23.1) WILD-TYPE | 230 | 1.7 (3.2) |
P value = 0.0152 (Fisher's exact test), Q value = 0.24
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 34(13Q14.2) MUTATED | 2 | 3 | 28 | 178 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 0 | 8 | 20 | 268 |
P value = 0.0111 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 35(14Q11.2) MUTATED | 46 | 57.7 (37.0) |
DEL PEAK 35(14Q11.2) WILD-TYPE | 247 | 43.7 (34.7) |
P value = 0.0166 (Fisher's exact test), Q value = 0.25
nPatients | NO | YES |
---|---|---|
ALL | 162 | 301 |
DEL PEAK 36(14Q32.32) MUTATED | 14 | 51 |
DEL PEAK 36(14Q32.32) WILD-TYPE | 148 | 250 |
P value = 0.00283 (Fisher's exact test), Q value = 0.13
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 40(17P11.2) MUTATED | 0 | 2 | 19 | 75 |
DEL PEAK 40(17P11.2) WILD-TYPE | 2 | 9 | 29 | 371 |
P value = 0.0145 (Fisher's exact test), Q value = 0.24
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 26 | 459 |
DEL PEAK 41(17Q25.3) MUTATED | 8 | 57 |
DEL PEAK 41(17Q25.3) WILD-TYPE | 18 | 402 |
P value = 0.017 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 42(18Q23) MUTATED | 166 | 50.5 (40.3) |
DEL PEAK 42(18Q23) WILD-TYPE | 127 | 39.9 (26.6) |
P value = 0.00435 (Fisher's exact test), Q value = 0.15
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 42(18Q23) MUTATED | 2 | 8 | 36 | 233 |
DEL PEAK 42(18Q23) WILD-TYPE | 0 | 3 | 12 | 213 |
P value = 0.00756 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 520 | 219 | 0.1 - 211.0 (21.1) |
DEL PEAK 43(19P13.3) MUTATED | 174 | 83 | 0.1 - 153.9 (18.5) |
DEL PEAK 43(19P13.3) WILD-TYPE | 346 | 136 | 0.1 - 211.0 (22.3) |
P value = 0.00694 (Fisher's exact test), Q value = 0.18
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
DEL PEAK 45(21Q22.3) MUTATED | 1 | 7 | 28 | 166 |
DEL PEAK 45(21Q22.3) WILD-TYPE | 1 | 4 | 20 | 280 |
P value = 0.0157 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
DEL PEAK 46(XP22.2) MUTATED | 96 | 52.6 (38.5) |
DEL PEAK 46(XP22.2) WILD-TYPE | 197 | 42.6 (33.3) |
P value = 0.00063 (Wilcoxon-test), Q value = 0.048
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
DEL PEAK 46(XP22.2) MUTATED | 126 | 3.1 (5.5) |
DEL PEAK 46(XP22.2) WILD-TYPE | 282 | 1.8 (3.6) |
P value = 0.0092 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
DEL PEAK 47(XP21.3) MUTATED | 128 | 2.8 (5.3) |
DEL PEAK 47(XP21.3) WILD-TYPE | 280 | 1.9 (3.8) |
P value = 0.00524 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
DEL PEAK 48(XQ21.33) MUTATED | 57 | 3.7 (7.2) |
DEL PEAK 48(XQ21.33) WILD-TYPE | 351 | 2.0 (3.6) |
-
Copy number data file = all_lesions.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/22508724/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/22506490/HNSC-TP.merged_data.txt
-
Number of patients = 522
-
Number of significantly focal cnvs = 76
-
Number of selected clinical features = 14
-
Exclude genes 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.