This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 94 focal events and 12 clinical features across 625 patients, 47 significant findings detected with Q value < 0.25.
-
amp_1p36.22 cnv correlated to 'GENDER'.
-
amp_1p34.2 cnv correlated to 'RADIATION_THERAPY'.
-
amp_1q42.3 cnv correlated to 'YEARS_TO_BIRTH'.
-
amp_3q26.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'RACE'.
-
amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
amp_5p13.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
amp_6q21 cnv correlated to 'Time to Death'.
-
amp_7p22.3 cnv correlated to 'GENDER'.
-
amp_7p11.2 cnv correlated to 'GENDER'.
-
amp_7q21.2 cnv correlated to 'GENDER'.
-
amp_8p23.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
-
amp_9q34.3 cnv correlated to 'Time to Death'.
-
amp_12p12.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
amp_14q13.3 cnv correlated to 'GENDER'.
-
amp_17q12 cnv correlated to 'PATHOLOGY_M_STAGE' and 'GENDER'.
-
amp_20q13.2 cnv correlated to 'GENDER'.
-
del_4q34.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.
-
del_7q31.1 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'GENDER'.
-
del_7q36.3 cnv correlated to 'PATHOLOGIC_STAGE'.
-
del_8p23.2 cnv correlated to 'GENDER'.
-
del_9p21.3 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'GENDER'.
-
del_10p15.3 cnv correlated to 'Time to Death'.
-
del_10p11.21 cnv correlated to 'PATHOLOGY_T_STAGE' and 'RACE'.
-
del_10q22.3 cnv correlated to 'RACE'.
-
del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
del_11p15.5 cnv correlated to 'GENDER'.
-
del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
del_13q12.11 cnv correlated to 'GENDER'.
-
del_13q21.31 cnv correlated to 'RADIATION_THERAPY'.
-
del_18q12.2 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
del_18q21.2 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
del_19p13.3 cnv correlated to 'GENDER'.
-
del_22q11.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
del_22q13.31 cnv correlated to 'PATHOLOGIC_STAGE'.
-
del_xp22.2 cnv correlated to 'GENDER'.
-
del_xp21.1 cnv correlated to 'GENDER'.
-
del_xp11.3 cnv correlated to 'GENDER'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
NUMBER PACK YEARS SMOKED |
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 | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 7q31 1 | 127 (20%) | 498 |
0.119 (0.534) |
0.0412 (0.384) |
0.00081 (0.0798) |
0.00556 (0.174) |
0.00744 (0.207) |
0.304 (0.711) |
0.0015 (0.0942) |
0.799 (0.975) |
1 (1.00) |
0.105 (0.508) |
0.364 (0.76) |
0.699 (0.943) |
del 9p21 3 | 334 (53%) | 291 |
0.393 (0.773) |
0.887 (1.00) |
0.00827 (0.207) |
0.002 (0.115) |
0.0954 (0.491) |
0.87 (1.00) |
0.0037 (0.143) |
0.079 (0.47) |
0.171 (0.586) |
0.25 (0.667) |
0.214 (0.626) |
0.221 (0.635) |
amp 3q26 2 | 287 (46%) | 338 |
0.675 (0.931) |
0.0146 (0.267) |
0.00307 (0.128) |
0.968 (1.00) |
0.664 (0.925) |
0.739 (0.949) |
0.0647 (0.448) |
0.0128 (0.264) |
0.197 (0.608) |
0.0964 (0.491) |
0.00104 (0.0838) |
0.0655 (0.448) |
amp 8p23 1 | 229 (37%) | 396 |
0.514 (0.842) |
0.00428 (0.146) |
0.442 (0.812) |
0.382 (0.77) |
0.754 (0.949) |
1 (1.00) |
0.00055 (0.0776) |
0.391 (0.773) |
0.444 (0.812) |
0.279 (0.703) |
0.442 (0.812) |
0.532 (0.851) |
amp 17q12 | 222 (36%) | 403 |
0.294 (0.707) |
0.444 (0.812) |
0.0308 (0.347) |
0.716 (0.948) |
0.768 (0.955) |
0.00809 (0.207) |
0.00448 (0.149) |
0.194 (0.608) |
0.691 (0.941) |
0.221 (0.635) |
0.0125 (0.264) |
1 (1.00) |
del 4q34 3 | 300 (48%) | 325 |
0.148 (0.559) |
0.0102 (0.244) |
0.0038 (0.143) |
0.176 (0.586) |
0.467 (0.815) |
0.32 (0.719) |
0.54 (0.854) |
0.304 (0.711) |
0.924 (1.00) |
0.881 (1.00) |
0.852 (0.996) |
1 (1.00) |
del 10p11 21 | 102 (16%) | 523 |
0.178 (0.586) |
0.53 (0.85) |
0.0297 (0.342) |
0.00428 (0.146) |
0.915 (1.00) |
1 (1.00) |
0.345 (0.747) |
0.0969 (0.491) |
0.407 (0.785) |
0.0561 (0.441) |
0.00075 (0.0798) |
0.396 (0.774) |
amp 1p36 22 | 101 (16%) | 524 |
0.927 (1.00) |
0.911 (1.00) |
0.208 (0.616) |
0.0916 (0.491) |
0.971 (1.00) |
0.82 (0.982) |
0.00079 (0.0798) |
0.0893 (0.491) |
0.238 (0.649) |
0.143 (0.558) |
0.215 (0.627) |
0.393 (0.773) |
amp 1p34 2 | 95 (15%) | 530 |
0.96 (1.00) |
0.149 (0.56) |
0.0659 (0.448) |
0.177 (0.586) |
0.437 (0.812) |
0.34 (0.742) |
0.145 (0.559) |
0.00139 (0.0925) |
0.884 (1.00) |
0.681 (0.935) |
0.384 (0.77) |
0.673 (0.93) |
amp 1q42 3 | 244 (39%) | 381 |
0.329 (0.729) |
0.00269 (0.128) |
0.513 (0.842) |
0.0529 (0.435) |
0.941 (1.00) |
0.734 (0.949) |
0.0195 (0.294) |
0.0569 (0.441) |
0.522 (0.846) |
0.839 (0.992) |
0.0219 (0.296) |
1 (1.00) |
amp 5p15 33 | 228 (36%) | 397 |
0.849 (0.996) |
0.723 (0.949) |
0.291 (0.707) |
1e-05 (0.00564) |
0.876 (1.00) |
1 (1.00) |
0.0232 (0.3) |
0.199 (0.609) |
0.167 (0.583) |
0.602 (0.889) |
0.0234 (0.3) |
0.754 (0.949) |
amp 5p13 1 | 216 (35%) | 409 |
0.948 (1.00) |
0.779 (0.963) |
0.769 (0.955) |
0.00822 (0.207) |
0.428 (0.803) |
0.486 (0.82) |
0.231 (0.642) |
0.914 (1.00) |
0.919 (1.00) |
0.915 (1.00) |
0.288 (0.707) |
1 (1.00) |
amp 6q21 | 111 (18%) | 514 |
0.00134 (0.0925) |
0.565 (0.866) |
0.0288 (0.335) |
0.555 (0.864) |
0.408 (0.785) |
0.0149 (0.267) |
0.423 (0.796) |
0.789 (0.969) |
0.337 (0.742) |
0.57 (0.866) |
0.0585 (0.441) |
1 (1.00) |
amp 7p22 3 | 353 (56%) | 272 |
0.536 (0.851) |
0.285 (0.707) |
0.216 (0.627) |
0.0392 (0.378) |
0.794 (0.973) |
1 (1.00) |
0.000393 (0.0739) |
0.533 (0.851) |
0.851 (0.996) |
0.459 (0.815) |
0.576 (0.872) |
0.23 (0.642) |
amp 7p11 2 | 339 (54%) | 286 |
0.441 (0.812) |
0.0655 (0.448) |
0.304 (0.711) |
0.0118 (0.262) |
0.932 (1.00) |
0.183 (0.599) |
0.00484 (0.156) |
0.409 (0.785) |
0.535 (0.851) |
0.694 (0.942) |
0.0618 (0.448) |
1 (1.00) |
amp 7q21 2 | 317 (51%) | 308 |
0.974 (1.00) |
0.942 (1.00) |
0.942 (1.00) |
0.0753 (0.466) |
0.548 (0.86) |
0.741 (0.949) |
0.00213 (0.115) |
0.303 (0.711) |
0.178 (0.586) |
0.262 (0.686) |
0.0986 (0.492) |
0.764 (0.955) |
amp 9q34 3 | 185 (30%) | 440 |
0.00629 (0.187) |
0.021 (0.296) |
0.727 (0.949) |
0.364 (0.76) |
0.286 (0.707) |
0.717 (0.948) |
0.0438 (0.389) |
0.0311 (0.347) |
0.52 (0.846) |
0.022 (0.296) |
0.589 (0.884) |
0.516 (0.844) |
amp 12p12 1 | 207 (33%) | 418 |
0.239 (0.649) |
0.234 (0.646) |
0.0591 (0.441) |
0.00214 (0.115) |
0.872 (1.00) |
0.723 (0.949) |
0.0405 (0.384) |
0.23 (0.642) |
0.0587 (0.441) |
0.381 (0.77) |
0.141 (0.555) |
1 (1.00) |
amp 14q13 3 | 113 (18%) | 512 |
0.144 (0.558) |
0.101 (0.495) |
0.168 (0.583) |
0.324 (0.723) |
0.746 (0.949) |
1 (1.00) |
0.00881 (0.216) |
0.0253 (0.313) |
0.664 (0.925) |
0.75 (0.949) |
0.306 (0.711) |
0.118 (0.534) |
amp 20q13 2 | 416 (67%) | 209 |
0.101 (0.495) |
0.0374 (0.369) |
0.585 (0.882) |
0.192 (0.608) |
0.0415 (0.384) |
0.863 (1.00) |
0.00301 (0.128) |
0.383 (0.77) |
0.964 (1.00) |
0.208 (0.616) |
0.968 (1.00) |
1 (1.00) |
del 7q36 3 | 165 (26%) | 460 |
0.295 (0.707) |
0.462 (0.815) |
0.00092 (0.0798) |
0.0822 (0.475) |
0.124 (0.543) |
0.571 (0.866) |
0.196 (0.608) |
0.816 (0.982) |
0.669 (0.928) |
0.544 (0.859) |
0.6 (0.889) |
1 (1.00) |
del 8p23 2 | 214 (34%) | 411 |
0.833 (0.992) |
0.279 (0.703) |
0.198 (0.609) |
0.0485 (0.421) |
0.482 (0.819) |
0.384 (0.77) |
0.000315 (0.0739) |
0.0832 (0.476) |
0.651 (0.922) |
0.0657 (0.448) |
0.157 (0.576) |
0.331 (0.733) |
del 10p15 3 | 131 (21%) | 494 |
0.00726 (0.207) |
0.956 (1.00) |
0.209 (0.616) |
0.359 (0.759) |
0.324 (0.723) |
0.838 (0.992) |
0.0406 (0.384) |
0.615 (0.889) |
0.294 (0.707) |
0.514 (0.842) |
0.0319 (0.353) |
0.704 (0.945) |
del 10q22 3 | 135 (22%) | 490 |
0.18 (0.591) |
0.117 (0.53) |
0.639 (0.907) |
0.017 (0.286) |
0.881 (1.00) |
0.842 (0.993) |
0.241 (0.653) |
0.802 (0.977) |
0.122 (0.537) |
0.318 (0.718) |
0.00128 (0.0925) |
0.256 (0.68) |
del 10q23 31 | 183 (29%) | 442 |
0.0984 (0.492) |
0.0436 (0.389) |
0.965 (1.00) |
0.00796 (0.207) |
0.889 (1.00) |
0.717 (0.948) |
0.565 (0.866) |
0.497 (0.832) |
0.083 (0.476) |
0.857 (0.998) |
0.015 (0.267) |
0.506 (0.837) |
del 11p15 5 | 175 (28%) | 450 |
0.696 (0.942) |
0.271 (0.701) |
0.0881 (0.487) |
0.0242 (0.304) |
0.591 (0.886) |
0.853 (0.997) |
0.00827 (0.207) |
0.028 (0.332) |
0.152 (0.565) |
0.447 (0.814) |
0.141 (0.555) |
0.481 (0.819) |
del 12q23 1 | 110 (18%) | 515 |
0.805 (0.978) |
0.31 (0.714) |
0.367 (0.762) |
0.00291 (0.128) |
0.825 (0.986) |
0.657 (0.924) |
1 (1.00) |
0.139 (0.554) |
0.196 (0.608) |
0.356 (0.758) |
0.163 (0.582) |
0.189 (0.608) |
del 13q12 11 | 138 (22%) | 487 |
0.471 (0.815) |
0.106 (0.509) |
0.0567 (0.441) |
0.015 (0.267) |
0.259 (0.683) |
0.689 (0.94) |
5.21e-05 (0.0196) |
0.0867 (0.486) |
0.559 (0.866) |
0.202 (0.609) |
0.269 (0.697) |
0.26 (0.683) |
del 13q21 31 | 126 (20%) | 499 |
0.831 (0.991) |
0.0811 (0.471) |
0.0218 (0.296) |
0.0135 (0.264) |
0.312 (0.717) |
0.147 (0.559) |
0.0286 (0.335) |
0.00231 (0.119) |
0.163 (0.582) |
0.57 (0.866) |
0.0512 (0.431) |
0.445 (0.812) |
del 18q12 2 | 292 (47%) | 333 |
0.137 (0.554) |
0.362 (0.759) |
0.417 (0.788) |
1e-05 (0.00564) |
0.843 (0.994) |
0.868 (1.00) |
0.114 (0.522) |
0.471 (0.815) |
1 (1.00) |
0.125 (0.543) |
0.46 (0.815) |
0.222 (0.635) |
del 18q21 2 | 323 (52%) | 302 |
0.491 (0.826) |
0.548 (0.86) |
0.551 (0.863) |
0.00038 (0.0739) |
0.809 (0.98) |
0.869 (1.00) |
0.0661 (0.448) |
0.302 (0.711) |
0.914 (1.00) |
0.235 (0.646) |
0.315 (0.718) |
0.0342 (0.361) |
del 19p13 3 | 249 (40%) | 376 |
0.0648 (0.448) |
0.942 (1.00) |
0.672 (0.93) |
0.0548 (0.441) |
0.457 (0.815) |
1 (1.00) |
0.000905 (0.0798) |
0.17 (0.586) |
0.268 (0.696) |
0.433 (0.808) |
0.0332 (0.356) |
1 (1.00) |
del 22q11 1 | 230 (37%) | 395 |
0.0937 (0.491) |
0.149 (0.559) |
0.0351 (0.361) |
0.0005 (0.0776) |
0.788 (0.969) |
0.734 (0.949) |
0.277 (0.703) |
0.109 (0.52) |
0.684 (0.937) |
0.82 (0.982) |
0.254 (0.677) |
1 (1.00) |
del 22q13 31 | 235 (38%) | 390 |
0.0957 (0.491) |
0.521 (0.846) |
0.00616 (0.187) |
0.166 (0.583) |
0.176 (0.586) |
0.394 (0.773) |
0.322 (0.721) |
0.396 (0.774) |
0.507 (0.837) |
0.899 (1.00) |
0.139 (0.554) |
0.754 (0.949) |
del xp22 2 | 151 (24%) | 474 |
0.459 (0.815) |
0.059 (0.441) |
0.209 (0.616) |
0.294 (0.707) |
0.214 (0.626) |
0.7 (0.943) |
0.00289 (0.128) |
0.633 (0.906) |
0.741 (0.949) |
0.0991 (0.492) |
0.0652 (0.448) |
0.158 (0.576) |
del xp21 1 | 146 (23%) | 479 |
0.506 (0.837) |
0.365 (0.76) |
0.262 (0.686) |
0.666 (0.925) |
0.238 (0.649) |
0.165 (0.583) |
0.00361 (0.143) |
0.903 (1.00) |
0.63 (0.902) |
0.696 (0.942) |
0.743 (0.949) |
0.021 (0.296) |
del xp11 3 | 148 (24%) | 477 |
0.741 (0.949) |
0.155 (0.571) |
0.0851 (0.482) |
0.205 (0.613) |
0.196 (0.608) |
0.324 (0.723) |
0.00396 (0.144) |
0.227 (0.638) |
0.291 (0.707) |
0.747 (0.949) |
0.173 (0.586) |
0.139 (0.554) |
amp 1q21 3 | 249 (40%) | 376 |
0.414 (0.786) |
0.0704 (0.451) |
0.301 (0.711) |
0.0242 (0.304) |
0.71 (0.946) |
0.61 (0.889) |
0.129 (0.545) |
0.092 (0.491) |
0.892 (1.00) |
0.87 (1.00) |
0.121 (0.535) |
1 (1.00) |
amp 2q12 2 | 155 (25%) | 470 |
0.836 (0.992) |
0.372 (0.767) |
0.0113 (0.257) |
0.0186 (0.294) |
0.499 (0.835) |
0.556 (0.864) |
0.128 (0.545) |
1 (1.00) |
0.777 (0.963) |
0.926 (1.00) |
0.194 (0.608) |
1 (1.00) |
amp 6p21 1 | 192 (31%) | 433 |
0.167 (0.583) |
0.0207 (0.296) |
0.0918 (0.491) |
0.0453 (0.397) |
0.112 (0.522) |
0.468 (0.815) |
0.106 (0.509) |
0.823 (0.985) |
0.135 (0.554) |
0.757 (0.949) |
0.078 (0.469) |
1 (1.00) |
amp 6q12 | 141 (23%) | 484 |
0.0114 (0.257) |
0.691 (0.941) |
0.0943 (0.491) |
0.471 (0.815) |
0.335 (0.739) |
0.315 (0.718) |
0.464 (0.815) |
0.805 (0.978) |
0.113 (0.522) |
0.661 (0.924) |
0.354 (0.757) |
0.472 (0.815) |
amp 8p11 21 | 272 (44%) | 353 |
0.45 (0.815) |
0.465 (0.815) |
0.0873 (0.487) |
0.444 (0.812) |
0.168 (0.583) |
0.506 (0.837) |
0.077 (0.469) |
0.756 (0.949) |
0.412 (0.786) |
0.98 (1.00) |
0.768 (0.955) |
0.765 (0.955) |
amp 8q24 21 | 454 (73%) | 171 |
0.635 (0.906) |
0.386 (0.77) |
0.731 (0.949) |
0.257 (0.68) |
0.249 (0.667) |
0.711 (0.946) |
0.116 (0.528) |
1 (1.00) |
0.128 (0.545) |
0.392 (0.773) |
0.296 (0.71) |
1 (1.00) |
amp 9p24 1 | 91 (15%) | 534 |
0.479 (0.817) |
0.706 (0.945) |
0.897 (1.00) |
0.68 (0.934) |
0.267 (0.696) |
1 (1.00) |
0.385 (0.77) |
0.305 (0.711) |
0.948 (1.00) |
0.603 (0.889) |
0.202 (0.609) |
0.677 (0.931) |
amp 9p13 3 | 132 (21%) | 493 |
0.413 (0.786) |
0.839 (0.992) |
0.113 (0.522) |
0.444 (0.812) |
0.725 (0.949) |
0.838 (0.992) |
0.592 (0.886) |
0.383 (0.77) |
0.796 (0.973) |
0.223 (0.636) |
0.912 (1.00) |
0.237 (0.649) |
amp 10p11 22 | 169 (27%) | 456 |
0.967 (1.00) |
0.665 (0.925) |
0.18 (0.591) |
0.0605 (0.446) |
0.978 (1.00) |
0.573 (0.867) |
0.622 (0.894) |
0.645 (0.916) |
0.0454 (0.397) |
0.121 (0.536) |
0.147 (0.559) |
0.735 (0.949) |
amp 10q22 2 | 125 (20%) | 500 |
0.562 (0.866) |
0.524 (0.848) |
0.0877 (0.487) |
0.13 (0.545) |
0.513 (0.842) |
0.675 (0.931) |
0.743 (0.949) |
0.37 (0.766) |
0.0328 (0.356) |
0.0376 (0.369) |
0.139 (0.554) |
0.131 (0.545) |
amp 10q26 13 | 119 (19%) | 506 |
0.274 (0.702) |
0.887 (1.00) |
0.0148 (0.267) |
0.157 (0.576) |
0.881 (1.00) |
0.519 (0.845) |
0.911 (1.00) |
0.896 (1.00) |
0.734 (0.949) |
0.069 (0.45) |
0.244 (0.656) |
0.227 (0.638) |
amp 11p13 | 138 (22%) | 487 |
0.119 (0.534) |
0.525 (0.848) |
0.251 (0.668) |
0.0308 (0.347) |
0.478 (0.817) |
0.0699 (0.451) |
0.0262 (0.322) |
0.213 (0.626) |
0.0968 (0.491) |
0.0992 (0.492) |
0.0732 (0.461) |
1 (1.00) |
amp 11q13 3 | 218 (35%) | 407 |
0.705 (0.945) |
0.56 (0.866) |
0.13 (0.545) |
0.923 (1.00) |
0.166 (0.583) |
0.486 (0.82) |
0.0542 (0.44) |
0.0511 (0.431) |
0.81 (0.98) |
0.273 (0.701) |
0.0274 (0.329) |
0.754 (0.949) |
amp 12q15 | 161 (26%) | 464 |
0.177 (0.586) |
0.228 (0.64) |
0.284 (0.707) |
0.553 (0.863) |
0.414 (0.786) |
0.058 (0.441) |
0.194 (0.608) |
0.814 (0.982) |
0.346 (0.748) |
0.877 (1.00) |
0.134 (0.55) |
1 (1.00) |
amp 13q12 3 | 216 (35%) | 409 |
0.6 (0.889) |
0.11 (0.521) |
0.422 (0.796) |
0.9 (1.00) |
0.188 (0.608) |
0.382 (0.77) |
0.927 (1.00) |
0.387 (0.77) |
0.42 (0.793) |
0.019 (0.294) |
0.147 (0.559) |
0.755 (0.949) |
amp 13q22 1 | 243 (39%) | 382 |
0.309 (0.714) |
0.801 (0.977) |
0.757 (0.949) |
0.818 (0.982) |
0.194 (0.608) |
1 (1.00) |
0.0589 (0.441) |
0.597 (0.889) |
0.0968 (0.491) |
0.204 (0.611) |
0.307 (0.712) |
0.113 (0.522) |
amp 15q26 1 | 168 (27%) | 457 |
0.545 (0.859) |
0.992 (1.00) |
0.355 (0.757) |
0.169 (0.586) |
0.286 (0.707) |
0.131 (0.545) |
0.0932 (0.491) |
0.2 (0.609) |
0.571 (0.866) |
0.0349 (0.361) |
0.131 (0.545) |
0.292 (0.707) |
amp 18p11 32 | 178 (28%) | 447 |
0.458 (0.815) |
0.634 (0.906) |
0.0493 (0.424) |
0.275 (0.702) |
0.353 (0.757) |
0.459 (0.815) |
0.208 (0.616) |
0.569 (0.866) |
0.414 (0.786) |
0.577 (0.872) |
0.123 (0.539) |
0.308 (0.712) |
amp 18q11 2 | 198 (32%) | 427 |
0.707 (0.946) |
0.127 (0.545) |
0.46 (0.815) |
0.472 (0.815) |
0.718 (0.948) |
0.477 (0.817) |
0.925 (1.00) |
1 (1.00) |
0.379 (0.77) |
0.699 (0.943) |
0.273 (0.701) |
0.746 (0.949) |
amp 19q12 | 185 (30%) | 440 |
0.955 (1.00) |
0.617 (0.889) |
0.931 (1.00) |
0.152 (0.565) |
0.407 (0.785) |
1 (1.00) |
0.292 (0.707) |
0.735 (0.949) |
0.35 (0.752) |
0.468 (0.815) |
0.0806 (0.471) |
1 (1.00) |
amp 19q13 43 | 164 (26%) | 461 |
0.763 (0.955) |
0.849 (0.996) |
0.501 (0.837) |
0.315 (0.718) |
0.372 (0.767) |
0.848 (0.996) |
0.319 (0.719) |
1 (1.00) |
0.809 (0.98) |
0.231 (0.642) |
0.0527 (0.435) |
0.736 (0.949) |
amp xq28 | 155 (25%) | 470 |
0.908 (1.00) |
0.241 (0.653) |
0.46 (0.815) |
0.522 (0.847) |
0.795 (0.973) |
1 (1.00) |
0.0844 (0.481) |
0.905 (1.00) |
0.374 (0.768) |
0.316 (0.718) |
0.0726 (0.46) |
0.161 (0.582) |
del 1p36 11 | 210 (34%) | 415 |
0.22 (0.635) |
0.954 (1.00) |
0.174 (0.586) |
0.276 (0.702) |
0.454 (0.815) |
1 (1.00) |
0.138 (0.554) |
0.443 (0.812) |
0.0202 (0.296) |
0.78 (0.963) |
0.446 (0.812) |
1 (1.00) |
del 1p13 2 | 156 (25%) | 469 |
0.0949 (0.491) |
0.82 (0.982) |
0.0746 (0.465) |
0.0662 (0.448) |
0.0964 (0.491) |
1 (1.00) |
0.0429 (0.389) |
0.552 (0.863) |
0.856 (0.998) |
0.401 (0.78) |
0.289 (0.707) |
0.47 (0.815) |
del 1q44 | 46 (7%) | 579 |
0.199 (0.609) |
0.0218 (0.296) |
0.615 (0.889) |
0.536 (0.851) |
0.57 (0.866) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.143 (0.558) |
0.553 (0.863) |
0.269 (0.697) |
1 (1.00) |
del 1q44 | 43 (7%) | 582 |
0.504 (0.837) |
0.744 (0.949) |
0.163 (0.582) |
0.819 (0.982) |
0.46 (0.815) |
0.504 (0.837) |
0.729 (0.949) |
1 (1.00) |
0.133 (0.549) |
0.886 (1.00) |
0.648 (0.918) |
1 (1.00) |
del 2q22 1 | 126 (20%) | 499 |
0.658 (0.924) |
0.139 (0.554) |
0.605 (0.889) |
0.613 (0.889) |
0.605 (0.889) |
1 (1.00) |
1 (1.00) |
0.164 (0.582) |
0.0233 (0.3) |
0.603 (0.889) |
0.755 (0.949) |
0.128 (0.545) |
del 2q32 1 | 87 (14%) | 538 |
0.567 (0.866) |
0.571 (0.866) |
0.916 (1.00) |
0.513 (0.842) |
0.164 (0.582) |
0.339 (0.742) |
1 (1.00) |
0.766 (0.955) |
0.294 (0.707) |
0.386 (0.77) |
1 (1.00) |
0.373 (0.768) |
del 2q33 3 | 85 (14%) | 540 |
0.897 (1.00) |
0.459 (0.815) |
0.784 (0.966) |
0.225 (0.637) |
0.791 (0.971) |
0.338 (0.742) |
0.612 (0.889) |
0.655 (0.924) |
0.592 (0.886) |
0.341 (0.742) |
0.475 (0.816) |
1 (1.00) |
del 2q37 2 | 122 (20%) | 503 |
0.718 (0.948) |
0.136 (0.554) |
0.793 (0.973) |
0.837 (0.992) |
0.709 (0.946) |
0.0591 (0.441) |
0.826 (0.986) |
0.303 (0.711) |
0.895 (1.00) |
0.162 (0.582) |
0.508 (0.838) |
0.227 (0.638) |
del 3p26 2 | 250 (40%) | 375 |
0.778 (0.963) |
0.489 (0.824) |
0.472 (0.815) |
0.486 (0.82) |
0.34 (0.742) |
0.402 (0.781) |
0.0746 (0.465) |
0.463 (0.815) |
0.817 (0.982) |
0.749 (0.949) |
0.411 (0.786) |
0.756 (0.949) |
del 3p14 2 | 282 (45%) | 343 |
0.0778 (0.469) |
0.374 (0.768) |
0.0154 (0.267) |
0.0636 (0.448) |
0.0335 (0.356) |
0.317 (0.718) |
0.481 (0.819) |
0.836 (0.992) |
0.385 (0.77) |
0.671 (0.93) |
0.0231 (0.3) |
0.545 (0.859) |
del 3q11 1 | 98 (16%) | 527 |
0.217 (0.628) |
0.14 (0.555) |
0.661 (0.924) |
0.283 (0.707) |
0.341 (0.742) |
0.656 (0.924) |
0.399 (0.779) |
0.393 (0.773) |
0.0688 (0.45) |
0.739 (0.949) |
0.952 (1.00) |
1 (1.00) |
del 3q26 31 | 65 (10%) | 560 |
0.932 (1.00) |
0.461 (0.815) |
0.608 (0.889) |
0.4 (0.78) |
0.361 (0.759) |
0.787 (0.969) |
0.569 (0.866) |
0.608 (0.889) |
0.558 (0.866) |
0.326 (0.725) |
0.609 (0.889) |
|
del 4p16 3 | 271 (43%) | 354 |
0.224 (0.636) |
0.537 (0.851) |
0.295 (0.707) |
0.127 (0.545) |
0.196 (0.608) |
0.131 (0.545) |
0.0133 (0.264) |
0.533 (0.851) |
0.928 (1.00) |
0.375 (0.768) |
0.388 (0.77) |
1 (1.00) |
del 4p15 2 | 269 (43%) | 356 |
0.0368 (0.369) |
0.366 (0.762) |
0.192 (0.608) |
0.127 (0.545) |
0.81 (0.98) |
0.243 (0.656) |
0.0271 (0.329) |
0.348 (0.751) |
0.705 (0.945) |
0.201 (0.609) |
0.195 (0.608) |
1 (1.00) |
del 4q22 1 | 298 (48%) | 327 |
0.0679 (0.45) |
0.139 (0.554) |
0.0411 (0.384) |
0.018 (0.291) |
0.235 (0.646) |
1 (1.00) |
0.0796 (0.47) |
0.301 (0.711) |
0.965 (1.00) |
0.615 (0.889) |
0.34 (0.742) |
0.56 (0.866) |
del 5q12 1 | 282 (45%) | 343 |
0.602 (0.889) |
0.609 (0.889) |
0.0196 (0.294) |
0.0657 (0.448) |
0.298 (0.711) |
0.868 (1.00) |
0.0526 (0.435) |
0.536 (0.851) |
0.484 (0.82) |
0.928 (1.00) |
0.381 (0.77) |
1 (1.00) |
del 6p25 3 | 188 (30%) | 437 |
0.325 (0.723) |
0.284 (0.707) |
0.45 (0.815) |
0.12 (0.534) |
0.987 (1.00) |
0.357 (0.758) |
0.634 (0.906) |
0.26 (0.683) |
0.597 (0.889) |
0.989 (1.00) |
1 (1.00) |
0.19 (0.608) |
del 6q16 3 | 147 (24%) | 478 |
0.746 (0.949) |
0.908 (1.00) |
0.616 (0.889) |
0.0688 (0.45) |
0.449 (0.815) |
0.072 (0.459) |
0.0176 (0.289) |
0.11 (0.521) |
0.663 (0.925) |
0.0697 (0.451) |
0.316 (0.718) |
0.72 (0.948) |
del 6q26 | 152 (24%) | 473 |
0.532 (0.851) |
0.596 (0.889) |
0.203 (0.61) |
0.0158 (0.271) |
0.858 (0.998) |
1 (1.00) |
0.0671 (0.448) |
0.465 (0.815) |
0.148 (0.559) |
0.238 (0.649) |
0.479 (0.817) |
0.718 (0.948) |
del 9p23 | 302 (48%) | 323 |
0.694 (0.942) |
0.562 (0.866) |
0.0595 (0.442) |
0.0421 (0.386) |
0.15 (0.561) |
0.408 (0.785) |
0.0352 (0.361) |
0.216 (0.627) |
0.177 (0.586) |
0.616 (0.889) |
0.778 (0.963) |
0.362 (0.759) |
del 9q21 11 | 175 (28%) | 450 |
0.0959 (0.491) |
0.926 (1.00) |
0.279 (0.703) |
0.301 (0.711) |
0.848 (0.996) |
1 (1.00) |
0.0972 (0.491) |
0.91 (1.00) |
1 (1.00) |
0.0121 (0.262) |
0.16 (0.581) |
1 (1.00) |
del 11q25 | 178 (28%) | 447 |
0.194 (0.608) |
0.318 (0.718) |
0.0497 (0.425) |
0.0643 (0.448) |
0.362 (0.759) |
0.709 (0.946) |
0.0151 (0.267) |
0.0671 (0.448) |
0.297 (0.711) |
0.207 (0.616) |
0.617 (0.889) |
0.0861 (0.486) |
del 12p13 1 | 113 (18%) | 512 |
0.19 (0.608) |
0.0771 (0.469) |
0.188 (0.608) |
0.0969 (0.491) |
0.96 (1.00) |
0.661 (0.924) |
0.91 (1.00) |
0.292 (0.707) |
0.56 (0.866) |
0.113 (0.522) |
0.379 (0.77) |
0.677 (0.931) |
del 14q23 3 | 187 (30%) | 438 |
0.385 (0.77) |
0.517 (0.844) |
0.266 (0.694) |
0.599 (0.889) |
0.0376 (0.369) |
0.275 (0.702) |
0.444 (0.812) |
1 (1.00) |
0.747 (0.949) |
0.904 (1.00) |
0.505 (0.837) |
0.735 (0.949) |
del 15q11 2 | 183 (29%) | 442 |
0.441 (0.812) |
0.621 (0.893) |
0.456 (0.815) |
0.0136 (0.264) |
0.527 (0.849) |
0.855 (0.998) |
0.443 (0.812) |
0.176 (0.586) |
0.876 (1.00) |
0.423 (0.796) |
0.688 (0.94) |
0.736 (0.949) |
del 16p13 3 | 177 (28%) | 448 |
0.202 (0.609) |
0.106 (0.509) |
0.0221 (0.296) |
0.0107 (0.252) |
0.103 (0.5) |
0.197 (0.608) |
0.0194 (0.294) |
1 (1.00) |
0.626 (0.898) |
0.458 (0.815) |
0.851 (0.996) |
1 (1.00) |
del 16p13 3 | 153 (24%) | 472 |
0.317 (0.718) |
0.147 (0.559) |
0.0324 (0.355) |
0.0365 (0.369) |
0.0808 (0.471) |
0.244 (0.656) |
0.0665 (0.448) |
0.813 (0.982) |
0.588 (0.884) |
0.475 (0.816) |
0.492 (0.826) |
0.714 (0.948) |
del 16q23 1 | 265 (42%) | 360 |
0.958 (1.00) |
0.429 (0.804) |
0.0795 (0.47) |
0.615 (0.889) |
0.176 (0.586) |
0.0177 (0.289) |
0.0761 (0.469) |
0.604 (0.889) |
0.967 (1.00) |
0.69 (0.941) |
0.701 (0.944) |
0.353 (0.757) |
del 17p12 | 267 (43%) | 358 |
0.768 (0.955) |
0.171 (0.586) |
0.873 (1.00) |
0.232 (0.642) |
0.752 (0.949) |
0.315 (0.718) |
0.0133 (0.264) |
0.118 (0.534) |
0.163 (0.582) |
0.781 (0.964) |
0.304 (0.711) |
0.344 (0.746) |
del 17q24 3 | 103 (16%) | 522 |
0.617 (0.889) |
0.0541 (0.44) |
0.36 (0.759) |
0.0994 (0.492) |
0.288 (0.707) |
0.658 (0.924) |
0.41 (0.786) |
0.059 (0.441) |
0.176 (0.586) |
0.745 (0.949) |
0.188 (0.608) |
0.7 (0.943) |
del 20p12 1 | 72 (12%) | 553 |
0.683 (0.936) |
0.935 (1.00) |
0.88 (1.00) |
0.432 (0.808) |
0.936 (1.00) |
1 (1.00) |
0.585 (0.882) |
0.0781 (0.469) |
0.471 (0.815) |
0.753 (0.949) |
0.906 (1.00) |
0.287 (0.707) |
del 21q11 2 | 286 (46%) | 339 |
0.638 (0.907) |
0.0383 (0.372) |
0.817 (0.982) |
0.153 (0.565) |
0.357 (0.758) |
0.739 (0.949) |
0.93 (1.00) |
0.408 (0.785) |
0.924 (1.00) |
0.486 (0.82) |
0.569 (0.866) |
0.369 (0.765) |
del 21q22 13 | 305 (49%) | 320 |
0.66 (0.924) |
0.285 (0.707) |
0.711 (0.946) |
0.529 (0.85) |
0.884 (1.00) |
0.409 (0.785) |
0.726 (0.949) |
0.47 (0.815) |
0.0435 (0.389) |
0.145 (0.559) |
0.197 (0.608) |
0.222 (0.635) |
del xq11 2 | 105 (17%) | 520 |
0.997 (1.00) |
0.881 (1.00) |
0.933 (1.00) |
0.526 (0.849) |
0.84 (0.992) |
0.177 (0.586) |
0.102 (0.499) |
0.0943 (0.491) |
0.548 (0.86) |
0.958 (1.00) |
0.932 (1.00) |
0.39 (0.772) |
del xq21 33 | 98 (16%) | 527 |
0.475 (0.816) |
0.954 (1.00) |
0.528 (0.849) |
0.501 (0.837) |
0.35 (0.752) |
0.637 (0.907) |
0.278 (0.703) |
0.113 (0.522) |
0.147 (0.559) |
0.446 (0.812) |
0.86 (1) |
0.66 (0.924) |
P value = 0.00079 (Fisher's exact test), Q value = 0.08
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 1(1P36.22) MUTATED | 16 | 85 |
AMP PEAK 1(1P36.22) WILD-TYPE | 169 | 355 |
P value = 0.00139 (Fisher's exact test), Q value = 0.092
nPatients | NO | YES |
---|---|---|
ALL | 445 | 119 |
AMP PEAK 2(1P34.2) MUTATED | 56 | 30 |
AMP PEAK 2(1P34.2) WILD-TYPE | 389 | 89 |
P value = 0.00269 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 616 | 64.8 (11.2) |
AMP PEAK 4(1Q42.3) MUTATED | 240 | 63.2 (10.4) |
AMP PEAK 4(1Q42.3) WILD-TYPE | 376 | 65.7 (11.6) |
P value = 0.00307 (Fisher's exact test), Q value = 0.13
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
AMP PEAK 6(3Q26.2) MUTATED | 3 | 9 | 18 | 12 | 47 | 43 | 23 | 37 | 29 | 25 | 19 | 3 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 7 | 12 | 29 | 21 | 40 | 44 | 5 | 58 | 43 | 21 | 30 | 1 |
P value = 0.00104 (Fisher's exact test), Q value = 0.084
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
AMP PEAK 6(3Q26.2) MUTATED | 79 | 10 | 0 | 162 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 55 | 7 | 1 | 230 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0056
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
AMP PEAK 7(5P15.33) MUTATED | 12 | 53 | 127 | 26 |
AMP PEAK 7(5P15.33) WILD-TYPE | 43 | 83 | 156 | 98 |
P value = 0.00822 (Fisher's exact test), Q value = 0.21
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
AMP PEAK 8(5P13.1) MUTATED | 12 | 50 | 112 | 32 |
AMP PEAK 8(5P13.1) WILD-TYPE | 43 | 86 | 171 | 92 |
P value = 0.00134 (logrank test), Q value = 0.092
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 599 | 245 | 0.0 - 122.3 (13.9) |
AMP PEAK 11(6Q21) MUTATED | 107 | 56 | 0.7 - 68.0 (12.9) |
AMP PEAK 11(6Q21) WILD-TYPE | 492 | 189 | 0.0 - 122.3 (14.4) |
P value = 0.000393 (Fisher's exact test), Q value = 0.074
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 12(7P22.3) MUTATED | 84 | 269 |
AMP PEAK 12(7P22.3) WILD-TYPE | 101 | 171 |
P value = 0.00484 (Fisher's exact test), Q value = 0.16
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 13(7P11.2) MUTATED | 84 | 255 |
AMP PEAK 13(7P11.2) WILD-TYPE | 101 | 185 |
P value = 0.00213 (Fisher's exact test), Q value = 0.11
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 14(7Q21.2) MUTATED | 76 | 241 |
AMP PEAK 14(7Q21.2) WILD-TYPE | 109 | 199 |
P value = 0.00428 (Wilcoxon-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 616 | 64.8 (11.2) |
AMP PEAK 15(8P23.1) MUTATED | 225 | 66.4 (11.1) |
AMP PEAK 15(8P23.1) WILD-TYPE | 391 | 63.9 (11.2) |
P value = 0.00055 (Fisher's exact test), Q value = 0.078
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 15(8P23.1) MUTATED | 87 | 142 |
AMP PEAK 15(8P23.1) WILD-TYPE | 98 | 298 |
P value = 0.00629 (logrank test), Q value = 0.19
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 599 | 245 | 0.0 - 122.3 (13.9) |
AMP PEAK 20(9Q34.3) MUTATED | 177 | 58 | 0.4 - 122.3 (13.4) |
AMP PEAK 20(9Q34.3) WILD-TYPE | 422 | 187 | 0.0 - 116.4 (14.0) |
P value = 0.00214 (Fisher's exact test), Q value = 0.11
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
AMP PEAK 26(12P12.1) MUTATED | 14 | 40 | 115 | 29 |
AMP PEAK 26(12P12.1) WILD-TYPE | 41 | 96 | 168 | 95 |
P value = 0.00881 (Fisher's exact test), Q value = 0.22
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 30(14Q13.3) MUTATED | 22 | 91 |
AMP PEAK 30(14Q13.3) WILD-TYPE | 163 | 349 |
P value = 0.00809 (Fisher's exact test), Q value = 0.21
nPatients | 0 | 1 |
---|---|---|
ALL | 524 | 39 |
AMP PEAK 32(17Q12) MUTATED | 169 | 21 |
AMP PEAK 32(17Q12) WILD-TYPE | 355 | 18 |
P value = 0.00448 (Fisher's exact test), Q value = 0.15
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 32(17Q12) MUTATED | 50 | 172 |
AMP PEAK 32(17Q12) WILD-TYPE | 135 | 268 |
P value = 0.00301 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
AMP PEAK 37(20Q13.2) MUTATED | 107 | 309 |
AMP PEAK 37(20Q13.2) WILD-TYPE | 78 | 131 |
P value = 0.0102 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 616 | 64.8 (11.2) |
DEL PEAK 16(4Q34.3) MUTATED | 295 | 66.0 (10.5) |
DEL PEAK 16(4Q34.3) WILD-TYPE | 321 | 63.6 (11.7) |
P value = 0.0038 (Fisher's exact test), Q value = 0.14
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
DEL PEAK 16(4Q34.3) MUTATED | 2 | 6 | 20 | 22 | 39 | 37 | 20 | 46 | 39 | 26 | 16 | 3 |
DEL PEAK 16(4Q34.3) WILD-TYPE | 8 | 15 | 27 | 11 | 48 | 50 | 8 | 49 | 33 | 20 | 33 | 1 |
P value = 0.00081 (Fisher's exact test), Q value = 0.08
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
DEL PEAK 21(7Q31.1) MUTATED | 1 | 5 | 4 | 9 | 19 | 21 | 15 | 22 | 9 | 5 | 8 | 2 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 9 | 16 | 43 | 24 | 68 | 66 | 13 | 73 | 63 | 41 | 41 | 2 |
P value = 0.00556 (Fisher's exact test), Q value = 0.17
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 21(7Q31.1) MUTATED | 14 | 23 | 71 | 14 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 41 | 113 | 212 | 110 |
P value = 0.00744 (Fisher's exact test), Q value = 0.21
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 207 | 187 | 98 | 96 |
DEL PEAK 21(7Q31.1) MUTATED | 36 | 53 | 21 | 12 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 171 | 134 | 77 | 84 |
P value = 0.0015 (Fisher's exact test), Q value = 0.094
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 21(7Q31.1) MUTATED | 23 | 104 |
DEL PEAK 21(7Q31.1) WILD-TYPE | 162 | 336 |
P value = 0.00092 (Fisher's exact test), Q value = 0.08
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
DEL PEAK 22(7Q36.3) MUTATED | 1 | 6 | 5 | 9 | 23 | 33 | 14 | 27 | 11 | 10 | 13 | 3 |
DEL PEAK 22(7Q36.3) WILD-TYPE | 9 | 15 | 42 | 24 | 64 | 54 | 14 | 68 | 61 | 36 | 36 | 1 |
P value = 0.000315 (Fisher's exact test), Q value = 0.074
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 23(8P23.2) MUTATED | 44 | 170 |
DEL PEAK 23(8P23.2) WILD-TYPE | 141 | 270 |
P value = 0.00827 (Fisher's exact test), Q value = 0.21
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
DEL PEAK 25(9P21.3) MUTATED | 3 | 12 | 21 | 18 | 54 | 48 | 23 | 47 | 34 | 18 | 26 | 4 |
DEL PEAK 25(9P21.3) WILD-TYPE | 7 | 9 | 26 | 15 | 33 | 39 | 5 | 48 | 38 | 28 | 23 | 0 |
P value = 0.002 (Fisher's exact test), Q value = 0.11
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 25(9P21.3) MUTATED | 31 | 78 | 162 | 47 |
DEL PEAK 25(9P21.3) WILD-TYPE | 24 | 58 | 121 | 77 |
P value = 0.0037 (Fisher's exact test), Q value = 0.14
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 25(9P21.3) MUTATED | 82 | 252 |
DEL PEAK 25(9P21.3) WILD-TYPE | 103 | 188 |
P value = 0.00726 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 599 | 245 | 0.0 - 122.3 (13.9) |
DEL PEAK 27(10P15.3) MUTATED | 127 | 60 | 0.1 - 115.7 (12.6) |
DEL PEAK 27(10P15.3) WILD-TYPE | 472 | 185 | 0.0 - 122.3 (14.8) |
P value = 0.00428 (Fisher's exact test), Q value = 0.15
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 28(10P11.21) MUTATED | 6 | 29 | 53 | 9 |
DEL PEAK 28(10P11.21) WILD-TYPE | 49 | 107 | 230 | 115 |
P value = 0.00075 (Fisher's exact test), Q value = 0.08
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
DEL PEAK 28(10P11.21) MUTATED | 32 | 7 | 0 | 51 |
DEL PEAK 28(10P11.21) WILD-TYPE | 102 | 10 | 1 | 341 |
P value = 0.00128 (Fisher's exact test), Q value = 0.092
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
DEL PEAK 29(10Q22.3) MUTATED | 36 | 9 | 0 | 71 |
DEL PEAK 29(10Q22.3) WILD-TYPE | 98 | 8 | 1 | 321 |
P value = 0.00796 (Fisher's exact test), Q value = 0.21
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 30(10Q23.31) MUTATED | 14 | 51 | 83 | 23 |
DEL PEAK 30(10Q23.31) WILD-TYPE | 41 | 85 | 200 | 101 |
P value = 0.00827 (Fisher's exact test), Q value = 0.21
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 31(11P15.5) MUTATED | 38 | 137 |
DEL PEAK 31(11P15.5) WILD-TYPE | 147 | 303 |
P value = 0.00291 (Fisher's exact test), Q value = 0.13
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 34(12Q23.1) MUTATED | 16 | 18 | 58 | 12 |
DEL PEAK 34(12Q23.1) WILD-TYPE | 39 | 118 | 225 | 112 |
P value = 5.21e-05 (Fisher's exact test), Q value = 0.02
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 35(13Q12.11) MUTATED | 22 | 116 |
DEL PEAK 35(13Q12.11) WILD-TYPE | 163 | 324 |
P value = 0.00231 (Fisher's exact test), Q value = 0.12
nPatients | NO | YES |
---|---|---|
ALL | 445 | 119 |
DEL PEAK 36(13Q21.31) MUTATED | 82 | 38 |
DEL PEAK 36(13Q21.31) WILD-TYPE | 363 | 81 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0056
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 44(18Q12.2) MUTATED | 22 | 62 | 158 | 36 |
DEL PEAK 44(18Q12.2) WILD-TYPE | 33 | 74 | 125 | 88 |
P value = 0.00038 (Fisher's exact test), Q value = 0.074
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 45(18Q21.2) MUTATED | 27 | 69 | 167 | 45 |
DEL PEAK 45(18Q21.2) WILD-TYPE | 28 | 67 | 116 | 79 |
P value = 0.000905 (Fisher's exact test), Q value = 0.08
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 46(19P13.3) MUTATED | 55 | 194 |
DEL PEAK 46(19P13.3) WILD-TYPE | 130 | 246 |
P value = 5e-04 (Fisher's exact test), Q value = 0.078
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
DEL PEAK 50(22Q11.1) MUTATED | 28 | 43 | 119 | 30 |
DEL PEAK 50(22Q11.1) WILD-TYPE | 27 | 93 | 164 | 94 |
P value = 0.00616 (Fisher's exact test), Q value = 0.19
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
DEL PEAK 51(22Q13.31) MUTATED | 6 | 2 | 19 | 12 | 29 | 28 | 18 | 42 | 30 | 14 | 17 | 3 |
DEL PEAK 51(22Q13.31) WILD-TYPE | 4 | 19 | 28 | 21 | 58 | 59 | 10 | 53 | 42 | 32 | 32 | 1 |
P value = 0.00289 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 52(XP22.2) MUTATED | 30 | 121 |
DEL PEAK 52(XP22.2) WILD-TYPE | 155 | 319 |
P value = 0.00361 (Fisher's exact test), Q value = 0.14
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 53(XP21.1) MUTATED | 29 | 117 |
DEL PEAK 53(XP21.1) WILD-TYPE | 156 | 323 |
P value = 0.00396 (Fisher's exact test), Q value = 0.14
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
DEL PEAK 54(XP11.3) MUTATED | 30 | 118 |
DEL PEAK 54(XP11.3) WILD-TYPE | 155 | 322 |
-
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/STES-TP/22532764/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/22507048/STES-TP.merged_data.txt
-
Number of patients = 625
-
Number of significantly focal cnvs = 94
-
Number of selected clinical features = 12
-
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.