This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 61 focal events and 12 clinical features across 370 patients, 46 significant findings detected with Q value < 0.25.
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amp_1q21.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
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amp_2p24.1 cnv correlated to 'GENDER'.
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amp_2q33.1 cnv correlated to 'GENDER'.
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amp_8q24.21 cnv correlated to 'GENDER' and 'RACE'.
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amp_10p15.1 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.
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amp_17p11.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.
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amp_17q25.3 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.
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amp_19p13.12 cnv correlated to 'GENDER'.
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amp_xq28 cnv correlated to 'GENDER'.
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del_3p13 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
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del_4p16.3 cnv correlated to 'GENDER'.
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del_4q21.3 cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.
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del_4q24 cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.
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del_4q35.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'RACE'.
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del_6q27 cnv correlated to 'YEARS_TO_BIRTH'.
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del_7q36.3 cnv correlated to 'Time to Death' and 'GENDER'.
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del_10q23.31 cnv correlated to 'RACE'.
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del_12p12.1 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_N_STAGE'.
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del_12q24.33 cnv correlated to 'PATHOLOGIC_STAGE'.
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del_16q23.1 cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.
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del_17p13.1 cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.
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del_17p11.2 cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.
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del_19p13.3 cnv correlated to 'RACE'.
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del_22q12.1 cnv correlated to 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
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del_22q13.32 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
del 22q13 32 | 83 (22%) | 287 |
0.565 (0.883) |
0.287 (0.747) |
0.00958 (0.2) |
0.00356 (0.133) |
0.121 (0.587) |
1 (1.00) |
0.352 (0.779) |
1 (1.00) |
0.0134 (0.233) |
0.0413 (0.428) |
0.00103 (0.0838) |
0.112 (0.587) |
amp 10p15 1 | 72 (19%) | 298 |
0.0146 (0.233) |
0.295 (0.747) |
0.00616 (0.167) |
0.00508 (0.155) |
1 (1.00) |
0.18 (0.661) |
0.779 (0.977) |
0.687 (0.925) |
0.805 (0.991) |
0.685 (0.924) |
0.484 (0.861) |
0.53 (0.882) |
del 3p13 | 73 (20%) | 297 |
0.591 (0.884) |
0.137 (0.61) |
0.00129 (0.0858) |
0.00352 (0.133) |
0.0977 (0.568) |
0.174 (0.66) |
0.0173 (0.264) |
0.217 (0.661) |
0.00271 (0.124) |
1 (1.00) |
0.608 (0.892) |
0.747 (0.959) |
del 4q35 1 | 172 (46%) | 198 |
0.00606 (0.167) |
0.000583 (0.0567) |
0.487 (0.861) |
0.241 (0.686) |
1 (1.00) |
0.623 (0.893) |
0.0572 (0.483) |
0.514 (0.863) |
0.351 (0.779) |
0.216 (0.661) |
4e-05 (0.0122) |
1 (1.00) |
del 22q12 1 | 79 (21%) | 291 |
0.754 (0.962) |
0.166 (0.648) |
0.0507 (0.47) |
0.0135 (0.233) |
0.487 (0.861) |
1 (1.00) |
0.341 (0.777) |
1 (1.00) |
0.0121 (0.227) |
0.0781 (0.539) |
0.00676 (0.171) |
0.105 (0.585) |
amp 8q24 21 | 231 (62%) | 139 |
0.651 (0.899) |
0.128 (0.592) |
0.0287 (0.339) |
0.59 (0.884) |
0.0329 (0.37) |
0.601 (0.889) |
0.000211 (0.0257) |
0.492 (0.863) |
0.75 (0.96) |
0.566 (0.883) |
1e-05 (0.00732) |
0.117 (0.587) |
amp 17p11 2 | 46 (12%) | 324 |
0.602 (0.889) |
0.361 (0.783) |
0.0132 (0.233) |
0.00463 (0.147) |
1 (1.00) |
0.447 (0.842) |
0.867 (1.00) |
0.606 (0.892) |
1 (1.00) |
0.0196 (0.274) |
0.647 (0.898) |
0.421 (0.83) |
amp 17q25 3 | 145 (39%) | 225 |
0.236 (0.684) |
0.739 (0.958) |
0.00889 (0.191) |
0.00363 (0.133) |
1 (1.00) |
1 (1.00) |
0.11 (0.587) |
0.491 (0.863) |
0.449 (0.842) |
0.0522 (0.478) |
0.232 (0.681) |
0.299 (0.747) |
del 4q21 3 | 171 (46%) | 199 |
0.301 (0.747) |
0.000187 (0.0257) |
0.781 (0.977) |
0.641 (0.897) |
1 (1.00) |
0.622 (0.893) |
0.317 (0.747) |
1 (1.00) |
0.392 (0.814) |
0.399 (0.82) |
0.00225 (0.11) |
0.0751 (0.53) |
del 4q24 | 173 (47%) | 197 |
0.107 (0.587) |
0.00195 (0.102) |
0.679 (0.924) |
0.549 (0.883) |
1 (1.00) |
0.623 (0.893) |
0.373 (0.787) |
1 (1.00) |
0.347 (0.779) |
0.342 (0.777) |
0.0101 (0.205) |
0.122 (0.587) |
del 7q36 3 | 34 (9%) | 336 |
0.00637 (0.167) |
0.683 (0.924) |
0.859 (1.00) |
0.542 (0.883) |
1 (1.00) |
1 (1.00) |
0.00315 (0.133) |
0.574 (0.883) |
0.623 (0.893) |
0.0433 (0.432) |
0.887 (1.00) |
1 (1.00) |
del 12p12 1 | 78 (21%) | 292 |
0.339 (0.777) |
0.873 (1.00) |
0.0108 (0.209) |
0.47 (0.86) |
0.00887 (0.191) |
0.215 (0.661) |
0.892 (1.00) |
0.213 (0.661) |
0.149 (0.63) |
0.0704 (0.522) |
0.638 (0.897) |
1 (1.00) |
del 16q23 1 | 162 (44%) | 208 |
0.218 (0.661) |
0.00148 (0.0903) |
0.308 (0.747) |
0.151 (0.63) |
1 (1.00) |
1 (1.00) |
0.261 (0.708) |
0.308 (0.747) |
0.443 (0.842) |
0.85 (1.00) |
5e-05 (0.0122) |
0.798 (0.985) |
del 17p13 1 | 226 (61%) | 144 |
0.00787 (0.18) |
0.542 (0.883) |
0.0629 (0.5) |
0.0145 (0.233) |
0.287 (0.747) |
0.3 (0.747) |
0.649 (0.898) |
0.743 (0.959) |
0.874 (1.00) |
0.313 (0.747) |
0.254 (0.704) |
0.607 (0.892) |
del 17p11 2 | 195 (53%) | 175 |
0.00412 (0.137) |
0.726 (0.95) |
0.0168 (0.262) |
0.014 (0.233) |
0.249 (0.696) |
0.625 (0.893) |
0.911 (1.00) |
1 (1.00) |
0.591 (0.884) |
0.138 (0.61) |
0.952 (1.00) |
0.453 (0.847) |
amp 1q21 3 | 271 (73%) | 99 |
0.0406 (0.428) |
0.943 (1.00) |
0.574 (0.883) |
0.823 (1.00) |
0.163 (0.641) |
0.575 (0.883) |
0.614 (0.893) |
0.699 (0.936) |
0.0108 (0.209) |
0.429 (0.836) |
0.22 (0.661) |
1 (1.00) |
amp 2p24 1 | 65 (18%) | 305 |
0.0485 (0.459) |
0.0915 (0.551) |
0.219 (0.661) |
0.153 (0.63) |
0.0768 (0.535) |
0.131 (0.598) |
0.00187 (0.102) |
1 (1.00) |
0.643 (0.897) |
0.515 (0.863) |
0.156 (0.633) |
1 (1.00) |
amp 2q33 1 | 64 (17%) | 306 |
0.162 (0.64) |
0.695 (0.932) |
0.0531 (0.48) |
0.073 (0.524) |
0.479 (0.861) |
0.168 (0.65) |
0.000109 (0.0199) |
0.366 (0.783) |
0.634 (0.896) |
0.624 (0.893) |
0.275 (0.735) |
0.495 (0.863) |
amp 19p13 12 | 69 (19%) | 301 |
0.372 (0.787) |
0.628 (0.896) |
0.207 (0.661) |
0.855 (1.00) |
1 (1.00) |
0.021 (0.274) |
0.00621 (0.167) |
1 (1.00) |
0.204 (0.661) |
0.22 (0.661) |
0.335 (0.773) |
0.515 (0.863) |
amp xq28 | 87 (24%) | 283 |
0.35 (0.779) |
0.191 (0.661) |
0.98 (1.00) |
0.931 (1.00) |
1 (1.00) |
0.578 (0.883) |
0.00062 (0.0567) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.563 (0.883) |
0.379 (0.796) |
del 4p16 3 | 85 (23%) | 285 |
0.204 (0.661) |
0.436 (0.841) |
0.345 (0.778) |
0.59 (0.884) |
0.544 (0.883) |
0.245 (0.691) |
0.00784 (0.18) |
1 (1.00) |
0.848 (1.00) |
0.194 (0.661) |
0.0311 (0.356) |
0.219 (0.661) |
del 6q27 | 136 (37%) | 234 |
0.926 (1.00) |
0.00124 (0.0858) |
0.449 (0.842) |
0.973 (1.00) |
0.557 (0.883) |
0.305 (0.747) |
0.299 (0.747) |
0.496 (0.863) |
0.387 (0.808) |
0.245 (0.691) |
0.51 (0.863) |
0.184 (0.661) |
del 10q23 31 | 97 (26%) | 273 |
0.241 (0.686) |
0.418 (0.83) |
0.24 (0.686) |
0.0188 (0.274) |
1 (1.00) |
0.577 (0.883) |
1 (1.00) |
0.454 (0.847) |
0.086 (0.547) |
0.544 (0.883) |
0.007 (0.171) |
1 (1.00) |
del 12q24 33 | 59 (16%) | 311 |
0.114 (0.587) |
0.291 (0.747) |
0.004 (0.137) |
0.232 (0.681) |
0.424 (0.834) |
0.152 (0.63) |
0.128 (0.592) |
1 (1.00) |
0.594 (0.884) |
0.949 (1.00) |
0.386 (0.807) |
0.724 (0.95) |
del 19p13 3 | 87 (24%) | 283 |
0.185 (0.661) |
0.259 (0.708) |
0.353 (0.779) |
0.148 (0.63) |
0.572 (0.883) |
1 (1.00) |
0.513 (0.863) |
0.69 (0.928) |
1 (1.00) |
0.81 (0.995) |
0.0138 (0.233) |
0.77 (0.973) |
amp 1q42 2 | 268 (72%) | 102 |
0.48 (0.861) |
0.98 (1.00) |
0.192 (0.661) |
0.595 (0.884) |
1 (1.00) |
0.575 (0.883) |
0.618 (0.893) |
0.706 (0.941) |
0.51 (0.863) |
0.859 (1.00) |
0.311 (0.747) |
0.777 (0.975) |
amp 3q26 31 | 77 (21%) | 293 |
0.356 (0.782) |
0.41 (0.826) |
0.835 (1.00) |
0.735 (0.957) |
0.471 (0.86) |
0.587 (0.884) |
0.784 (0.979) |
1 (1.00) |
0.822 (1.00) |
0.583 (0.884) |
0.205 (0.661) |
0.345 (0.778) |
amp 4p14 | 54 (15%) | 316 |
0.214 (0.661) |
0.0431 (0.432) |
0.559 (0.883) |
0.257 (0.708) |
1 (1.00) |
1 (1.00) |
0.269 (0.721) |
1 (1.00) |
1 (1.00) |
0.547 (0.883) |
0.87 (1.00) |
0.718 (0.95) |
amp 5p15 33 | 163 (44%) | 207 |
0.0687 (0.522) |
0.558 (0.883) |
0.168 (0.65) |
0.0436 (0.432) |
0.259 (0.708) |
0.632 (0.896) |
0.736 (0.957) |
0.193 (0.661) |
0.443 (0.842) |
0.91 (1.00) |
0.22 (0.661) |
0.798 (0.985) |
amp 5q35 3 | 135 (36%) | 235 |
0.386 (0.807) |
0.113 (0.587) |
0.472 (0.86) |
0.694 (0.932) |
0.555 (0.883) |
0.631 (0.896) |
0.249 (0.696) |
0.299 (0.747) |
0.105 (0.585) |
0.12 (0.587) |
0.489 (0.863) |
1 (1.00) |
amp 6p25 2 | 159 (43%) | 211 |
0.133 (0.605) |
0.983 (1.00) |
0.117 (0.587) |
0.0836 (0.547) |
1 (1.00) |
0.317 (0.747) |
0.368 (0.784) |
0.311 (0.747) |
0.445 (0.842) |
0.723 (0.95) |
0.913 (1.00) |
0.123 (0.59) |
amp 6p21 1 | 158 (43%) | 212 |
0.365 (0.783) |
0.0928 (0.552) |
0.403 (0.826) |
0.409 (0.826) |
0.266 (0.719) |
0.315 (0.747) |
0.0918 (0.551) |
0.085 (0.547) |
0.302 (0.747) |
0.721 (0.95) |
0.882 (1.00) |
0.3 (0.747) |
amp 6q12 | 109 (29%) | 261 |
0.407 (0.826) |
0.637 (0.897) |
0.018 (0.269) |
0.0561 (0.483) |
0.195 (0.661) |
0.583 (0.884) |
0.328 (0.76) |
0.0667 (0.514) |
0.144 (0.63) |
0.337 (0.775) |
0.455 (0.847) |
0.255 (0.706) |
amp 6q12 | 83 (22%) | 287 |
0.281 (0.74) |
0.313 (0.747) |
0.399 (0.82) |
0.148 (0.63) |
1 (1.00) |
0.203 (0.661) |
0.352 (0.779) |
0.214 (0.661) |
0.299 (0.747) |
0.395 (0.816) |
0.305 (0.747) |
0.056 (0.483) |
amp 7q31 2 | 120 (32%) | 250 |
0.989 (1.00) |
0.0819 (0.547) |
0.368 (0.784) |
0.543 (0.883) |
0.234 (0.681) |
1 (1.00) |
0.476 (0.861) |
0.48 (0.861) |
0.411 (0.826) |
0.762 (0.968) |
0.145 (0.63) |
0.414 (0.826) |
amp 9q34 2 | 47 (13%) | 323 |
0.619 (0.893) |
0.393 (0.816) |
0.181 (0.661) |
0.037 (0.41) |
1 (1.00) |
0.438 (0.841) |
0.74 (0.958) |
1 (1.00) |
1 (1.00) |
0.157 (0.633) |
0.633 (0.896) |
0.443 (0.842) |
amp 11q13 3 | 57 (15%) | 313 |
0.748 (0.959) |
0.414 (0.826) |
0.207 (0.661) |
0.0984 (0.568) |
1 (1.00) |
0.511 (0.863) |
0.643 (0.897) |
0.366 (0.783) |
0.759 (0.966) |
0.0574 (0.483) |
0.893 (1.00) |
0.483 (0.861) |
amp 13q32 3 | 67 (18%) | 303 |
0.115 (0.587) |
0.345 (0.778) |
0.568 (0.883) |
0.509 (0.863) |
0.448 (0.842) |
0.577 (0.883) |
0.0304 (0.353) |
0.205 (0.661) |
0.189 (0.661) |
0.408 (0.826) |
0.776 (0.975) |
1 (1.00) |
amp 13q33 3 | 67 (18%) | 303 |
0.109 (0.587) |
0.366 (0.783) |
0.881 (1.00) |
0.954 (1.00) |
0.448 (0.842) |
0.569 (0.883) |
0.112 (0.587) |
0.212 (0.661) |
0.191 (0.661) |
0.753 (0.962) |
0.218 (0.661) |
1 (1.00) |
amp 15q26 3 | 54 (15%) | 316 |
0.946 (1.00) |
0.0482 (0.459) |
0.486 (0.861) |
0.234 (0.681) |
1 (1.00) |
0.494 (0.863) |
0.43 (0.836) |
1 (1.00) |
0.548 (0.883) |
0.706 (0.941) |
0.843 (1.00) |
0.0613 (0.499) |
amp 19q13 11 | 91 (25%) | 279 |
0.669 (0.915) |
0.292 (0.747) |
0.0753 (0.53) |
0.373 (0.787) |
1 (1.00) |
0.0407 (0.428) |
0.198 (0.661) |
1 (1.00) |
0.462 (0.85) |
0.0895 (0.551) |
0.207 (0.661) |
0.557 (0.883) |
amp 20q13 13 | 124 (34%) | 246 |
0.047 (0.458) |
0.0489 (0.459) |
0.112 (0.587) |
0.0809 (0.547) |
0.26 (0.708) |
0.617 (0.893) |
0.156 (0.633) |
0.724 (0.95) |
1 (1.00) |
0.216 (0.661) |
0.534 (0.883) |
0.787 (0.981) |
amp 20q13 33 | 128 (35%) | 242 |
0.0892 (0.551) |
0.0912 (0.551) |
0.105 (0.585) |
0.122 (0.587) |
1 (1.00) |
0.153 (0.63) |
0.0611 (0.499) |
0.724 (0.95) |
0.745 (0.959) |
0.514 (0.863) |
0.658 (0.903) |
0.792 (0.985) |
del 1p36 31 | 162 (44%) | 208 |
0.529 (0.882) |
0.478 (0.861) |
0.912 (1.00) |
0.729 (0.953) |
1 (1.00) |
0.342 (0.777) |
0.177 (0.66) |
0.0834 (0.547) |
0.135 (0.61) |
0.17 (0.65) |
0.0707 (0.522) |
0.314 (0.747) |
del 1p36 11 | 142 (38%) | 228 |
0.949 (1.00) |
0.91 (1.00) |
0.545 (0.883) |
0.53 (0.882) |
0.566 (0.883) |
0.314 (0.747) |
0.731 (0.954) |
1 (1.00) |
0.279 (0.74) |
0.15 (0.63) |
0.115 (0.587) |
0.298 (0.747) |
del 2q22 1 | 52 (14%) | 318 |
0.137 (0.61) |
0.148 (0.63) |
0.649 (0.898) |
1 (1.00) |
0.357 (0.782) |
1 (1.00) |
1 (1.00) |
0.36 (0.783) |
0.533 (0.883) |
0.303 (0.747) |
0.537 (0.883) |
1 (1.00) |
del 2q37 3 | 62 (17%) | 308 |
0.548 (0.883) |
0.0664 (0.514) |
0.412 (0.826) |
0.431 (0.836) |
0.0641 (0.504) |
1 (1.00) |
0.766 (0.971) |
1 (1.00) |
0.09 (0.551) |
0.458 (0.849) |
0.196 (0.661) |
0.721 (0.95) |
del 8p23 2 | 247 (67%) | 123 |
0.815 (0.999) |
0.0541 (0.48) |
0.128 (0.592) |
0.411 (0.826) |
1 (1.00) |
0.304 (0.747) |
0.408 (0.826) |
1 (1.00) |
0.16 (0.639) |
0.905 (1.00) |
0.652 (0.899) |
1 (1.00) |
del 8p12 | 242 (65%) | 128 |
0.67 (0.915) |
0.21 (0.661) |
0.323 (0.757) |
0.645 (0.897) |
1 (1.00) |
0.301 (0.747) |
0.64 (0.897) |
0.504 (0.863) |
0.432 (0.836) |
0.775 (0.975) |
0.621 (0.893) |
0.592 (0.884) |
del 9p21 3 | 150 (41%) | 220 |
0.1 (0.573) |
0.0796 (0.545) |
0.601 (0.889) |
0.561 (0.883) |
0.568 (0.883) |
1 (1.00) |
0.427 (0.836) |
0.327 (0.76) |
1 (1.00) |
0.201 (0.661) |
0.233 (0.681) |
0.0713 (0.522) |
del 9q31 3 | 119 (32%) | 251 |
0.226 (0.671) |
0.903 (1.00) |
0.0695 (0.522) |
0.182 (0.661) |
0.0262 (0.314) |
0.085 (0.547) |
0.905 (1.00) |
0.725 (0.95) |
1 (1.00) |
0.176 (0.66) |
0.975 (1.00) |
0.281 (0.74) |
del 10q26 13 | 105 (28%) | 265 |
0.113 (0.587) |
0.794 (0.985) |
0.42 (0.83) |
0.0386 (0.422) |
1 (1.00) |
0.581 (0.884) |
0.712 (0.948) |
0.456 (0.847) |
0.213 (0.661) |
0.365 (0.783) |
0.0205 (0.274) |
1 (1.00) |
del 11q14 1 | 77 (21%) | 293 |
0.481 (0.861) |
0.205 (0.661) |
0.126 (0.592) |
0.0874 (0.551) |
0.129 (0.592) |
1 (1.00) |
0.683 (0.924) |
1 (1.00) |
0.0415 (0.428) |
0.499 (0.863) |
0.502 (0.863) |
0.0252 (0.308) |
del 11q23 3 | 93 (25%) | 277 |
0.674 (0.918) |
0.151 (0.63) |
0.362 (0.783) |
0.507 (0.863) |
0.172 (0.655) |
1 (1.00) |
1 (1.00) |
0.461 (0.85) |
0.103 (0.582) |
0.661 (0.906) |
0.187 (0.661) |
0.245 (0.691) |
del 13q14 2 | 179 (48%) | 191 |
0.0208 (0.274) |
0.237 (0.684) |
0.285 (0.747) |
0.0219 (0.276) |
0.622 (0.893) |
1 (1.00) |
0.094 (0.555) |
0.744 (0.959) |
0.682 (0.924) |
0.427 (0.836) |
0.157 (0.633) |
0.614 (0.893) |
del 14q23 3 | 131 (35%) | 239 |
0.25 (0.696) |
0.186 (0.661) |
0.461 (0.85) |
0.437 (0.841) |
0.56 (0.883) |
0.64 (0.897) |
0.415 (0.826) |
1 (1.00) |
0.178 (0.66) |
0.794 (0.985) |
0.02 (0.274) |
0.593 (0.884) |
del 14q32 33 | 133 (36%) | 237 |
0.805 (0.991) |
0.0986 (0.568) |
0.177 (0.66) |
0.0726 (0.524) |
0.557 (0.883) |
0.634 (0.896) |
0.908 (1.00) |
0.496 (0.863) |
0.0626 (0.5) |
0.87 (1.00) |
0.12 (0.587) |
0.795 (0.985) |
del 15q26 3 | 79 (21%) | 291 |
0.0214 (0.274) |
0.938 (1.00) |
0.0856 (0.547) |
0.0205 (0.274) |
0.121 (0.587) |
0.575 (0.883) |
0.892 (1.00) |
1 (1.00) |
0.268 (0.721) |
0.767 (0.972) |
0.225 (0.671) |
1 (1.00) |
del 18q21 2 | 94 (25%) | 276 |
0.821 (1.00) |
0.824 (1.00) |
0.328 (0.76) |
0.937 (1.00) |
0.158 (0.634) |
0.277 (0.737) |
0.126 (0.592) |
0.228 (0.676) |
0.0244 (0.302) |
0.505 (0.863) |
0.966 (1.00) |
0.56 (0.883) |
del 20p12 1 | 29 (8%) | 341 |
0.501 (0.863) |
0.314 (0.747) |
0.186 (0.661) |
0.656 (0.902) |
1 (1.00) |
0.324 (0.757) |
0.534 (0.883) |
0.15 (0.63) |
0.18 (0.661) |
0.59 (0.884) |
0.169 (0.65) |
0.353 (0.779) |
del xq26 2 | 67 (18%) | 303 |
0.116 (0.587) |
0.0603 (0.499) |
0.507 (0.863) |
0.317 (0.747) |
0.464 (0.851) |
0.587 (0.884) |
0.773 (0.975) |
0.22 (0.661) |
0.192 (0.661) |
0.483 (0.861) |
0.0545 (0.48) |
0.747 (0.959) |
P value = 0.0108 (Fisher's exact test), Q value = 0.21
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
AMP PEAK 1(1Q21.3) MUTATED | 0 | 267 | 4 |
AMP PEAK 1(1Q21.3) WILD-TYPE | 3 | 93 | 3 |
P value = 0.00187 (Fisher's exact test), Q value = 0.1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
AMP PEAK 3(2P24.1) MUTATED | 32 | 33 |
AMP PEAK 3(2P24.1) WILD-TYPE | 86 | 219 |
P value = 0.000109 (Fisher's exact test), Q value = 0.02
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
AMP PEAK 4(2Q33.1) MUTATED | 34 | 30 |
AMP PEAK 4(2Q33.1) WILD-TYPE | 84 | 222 |
P value = 0.000211 (Fisher's exact test), Q value = 0.026
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
AMP PEAK 14(8Q24.21) MUTATED | 57 | 174 |
AMP PEAK 14(8Q24.21) WILD-TYPE | 61 | 78 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0073
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
AMP PEAK 14(8Q24.21) MUTATED | 2 | 119 | 11 | 92 |
AMP PEAK 14(8Q24.21) WILD-TYPE | 0 | 39 | 6 | 91 |
P value = 0.0146 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
AMP PEAK 16(10P15.1) MUTATED | 71 | 32 | 0.3 - 114.3 (15.5) |
AMP PEAK 16(10P15.1) WILD-TYPE | 293 | 97 | 0.0 - 120.8 (20.8) |
P value = 0.00616 (Fisher's exact test), Q value = 0.17
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
AMP PEAK 16(10P15.1) MUTATED | 23 | 22 | 0 | 19 | 2 | 0 | 0 | 0 | 2 |
AMP PEAK 16(10P15.1) WILD-TYPE | 150 | 65 | 3 | 43 | 7 | 7 | 2 | 1 | 0 |
P value = 0.00508 (Fisher's exact test), Q value = 0.15
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
AMP PEAK 16(10P15.1) MUTATED | 23 | 24 | 22 | 3 |
AMP PEAK 16(10P15.1) WILD-TYPE | 160 | 71 | 55 | 9 |
P value = 0.0132 (Fisher's exact test), Q value = 0.23
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
AMP PEAK 21(17P11.2) MUTATED | 17 | 7 | 1 | 15 | 3 | 1 | 1 | 0 | 0 |
AMP PEAK 21(17P11.2) WILD-TYPE | 156 | 80 | 2 | 47 | 6 | 6 | 1 | 1 | 2 |
P value = 0.00463 (Fisher's exact test), Q value = 0.15
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
AMP PEAK 21(17P11.2) MUTATED | 17 | 8 | 19 | 2 |
AMP PEAK 21(17P11.2) WILD-TYPE | 166 | 87 | 58 | 10 |
P value = 0.00889 (Fisher's exact test), Q value = 0.19
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
AMP PEAK 22(17Q25.3) MUTATED | 54 | 37 | 0 | 32 | 7 | 3 | 1 | 0 | 1 |
AMP PEAK 22(17Q25.3) WILD-TYPE | 119 | 50 | 3 | 30 | 2 | 4 | 1 | 1 | 1 |
P value = 0.00363 (Fisher's exact test), Q value = 0.13
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
AMP PEAK 22(17Q25.3) MUTATED | 57 | 41 | 39 | 8 |
AMP PEAK 22(17Q25.3) WILD-TYPE | 126 | 54 | 38 | 4 |
P value = 0.00621 (Fisher's exact test), Q value = 0.17
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
AMP PEAK 23(19P13.12) MUTATED | 32 | 37 |
AMP PEAK 23(19P13.12) WILD-TYPE | 86 | 215 |
P value = 0.00062 (Fisher's exact test), Q value = 0.057
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
AMP PEAK 27(XQ28) MUTATED | 15 | 72 |
AMP PEAK 27(XQ28) WILD-TYPE | 103 | 180 |
P value = 0.00129 (Fisher's exact test), Q value = 0.086
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
DEL PEAK 5(3P13) MUTATED | 20 | 22 | 0 | 17 | 3 | 3 | 1 | 1 | 1 |
DEL PEAK 5(3P13) WILD-TYPE | 153 | 65 | 3 | 45 | 6 | 4 | 1 | 0 | 1 |
P value = 0.00352 (Fisher's exact test), Q value = 0.13
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
DEL PEAK 5(3P13) MUTATED | 23 | 25 | 21 | 4 |
DEL PEAK 5(3P13) WILD-TYPE | 160 | 70 | 56 | 8 |
P value = 0.00271 (Fisher's exact test), Q value = 0.12
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
DEL PEAK 5(3P13) MUTATED | 1 | 67 | 5 |
DEL PEAK 5(3P13) WILD-TYPE | 2 | 293 | 2 |
P value = 0.00784 (Fisher's exact test), Q value = 0.18
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
DEL PEAK 6(4P16.3) MUTATED | 17 | 68 |
DEL PEAK 6(4P16.3) WILD-TYPE | 101 | 184 |
P value = 0.000187 (Wilcoxon-test), Q value = 0.026
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
DEL PEAK 7(4Q21.3) MUTATED | 169 | 57.1 (13.4) |
DEL PEAK 7(4Q21.3) WILD-TYPE | 197 | 61.4 (12.7) |
P value = 0.00225 (Fisher's exact test), Q value = 0.11
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 7(4Q21.3) MUTATED | 1 | 89 | 9 | 68 |
DEL PEAK 7(4Q21.3) WILD-TYPE | 1 | 69 | 8 | 115 |
P value = 0.00195 (Wilcoxon-test), Q value = 0.1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
DEL PEAK 8(4Q24) MUTATED | 171 | 57.5 (13.5) |
DEL PEAK 8(4Q24) WILD-TYPE | 195 | 61.1 (12.6) |
P value = 0.0101 (Fisher's exact test), Q value = 0.2
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 8(4Q24) MUTATED | 1 | 88 | 9 | 71 |
DEL PEAK 8(4Q24) WILD-TYPE | 1 | 70 | 8 | 112 |
P value = 0.00606 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
DEL PEAK 9(4Q35.1) MUTATED | 168 | 69 | 0.2 - 120.8 (17.1) |
DEL PEAK 9(4Q35.1) WILD-TYPE | 196 | 60 | 0.0 - 114.3 (21.1) |
P value = 0.000583 (Wilcoxon-test), Q value = 0.057
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
DEL PEAK 9(4Q35.1) MUTATED | 169 | 57.2 (13.2) |
DEL PEAK 9(4Q35.1) WILD-TYPE | 197 | 61.3 (12.9) |
P value = 4e-05 (Fisher's exact test), Q value = 0.012
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 9(4Q35.1) MUTATED | 1 | 95 | 10 | 66 |
DEL PEAK 9(4Q35.1) WILD-TYPE | 1 | 63 | 7 | 117 |
P value = 0.00124 (Wilcoxon-test), Q value = 0.086
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
DEL PEAK 10(6Q27) MUTATED | 135 | 62.6 (12.3) |
DEL PEAK 10(6Q27) WILD-TYPE | 231 | 57.6 (13.4) |
P value = 0.00637 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
DEL PEAK 11(7Q36.3) MUTATED | 34 | 18 | 0.2 - 90.3 (12.9) |
DEL PEAK 11(7Q36.3) WILD-TYPE | 330 | 111 | 0.0 - 120.8 (20.5) |
P value = 0.00315 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
DEL PEAK 11(7Q36.3) MUTATED | 19 | 15 |
DEL PEAK 11(7Q36.3) WILD-TYPE | 99 | 237 |
P value = 0.007 (Fisher's exact test), Q value = 0.17
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 16(10Q23.31) MUTATED | 0 | 46 | 10 | 40 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 2 | 112 | 7 | 143 |
P value = 0.0108 (Fisher's exact test), Q value = 0.21
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
DEL PEAK 20(12P12.1) MUTATED | 30 | 20 | 1 | 11 | 5 | 2 | 2 | 1 | 0 |
DEL PEAK 20(12P12.1) WILD-TYPE | 143 | 67 | 2 | 51 | 4 | 5 | 0 | 0 | 2 |
P value = 0.00887 (Fisher's exact test), Q value = 0.19
nPatients | 0 | 1 |
---|---|---|
ALL | 254 | 3 |
DEL PEAK 20(12P12.1) MUTATED | 51 | 3 |
DEL PEAK 20(12P12.1) WILD-TYPE | 203 | 0 |
P value = 0.004 (Fisher's exact test), Q value = 0.14
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
DEL PEAK 21(12Q24.33) MUTATED | 20 | 16 | 2 | 10 | 4 | 1 | 1 | 1 | 1 |
DEL PEAK 21(12Q24.33) WILD-TYPE | 153 | 71 | 1 | 52 | 5 | 6 | 1 | 0 | 1 |
P value = 0.00148 (Wilcoxon-test), Q value = 0.09
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
DEL PEAK 26(16Q23.1) MUTATED | 161 | 57.5 (12.8) |
DEL PEAK 26(16Q23.1) WILD-TYPE | 205 | 61.0 (13.3) |
P value = 5e-05 (Fisher's exact test), Q value = 0.012
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 26(16Q23.1) MUTATED | 0 | 91 | 7 | 60 |
DEL PEAK 26(16Q23.1) WILD-TYPE | 2 | 67 | 10 | 123 |
P value = 0.00787 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
DEL PEAK 27(17P13.1) MUTATED | 222 | 90 | 0.0 - 120.8 (19.0) |
DEL PEAK 27(17P13.1) WILD-TYPE | 142 | 39 | 0.3 - 114.3 (20.9) |
P value = 0.0145 (Fisher's exact test), Q value = 0.23
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
DEL PEAK 27(17P13.1) MUTATED | 100 | 65 | 49 | 11 |
DEL PEAK 27(17P13.1) WILD-TYPE | 83 | 30 | 28 | 1 |
P value = 0.00412 (logrank test), Q value = 0.14
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
DEL PEAK 28(17P11.2) MUTATED | 191 | 81 | 0.0 - 120.8 (19.1) |
DEL PEAK 28(17P11.2) WILD-TYPE | 173 | 48 | 0.2 - 114.3 (20.8) |
P value = 0.014 (Fisher's exact test), Q value = 0.23
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
DEL PEAK 28(17P11.2) MUTATED | 82 | 58 | 45 | 9 |
DEL PEAK 28(17P11.2) WILD-TYPE | 101 | 37 | 32 | 3 |
P value = 0.0138 (Fisher's exact test), Q value = 0.23
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 30(19P13.3) MUTATED | 0 | 51 | 3 | 33 |
DEL PEAK 30(19P13.3) WILD-TYPE | 2 | 107 | 14 | 150 |
P value = 0.0135 (Fisher's exact test), Q value = 0.23
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
DEL PEAK 32(22Q12.1) MUTATED | 29 | 31 | 16 | 3 |
DEL PEAK 32(22Q12.1) WILD-TYPE | 154 | 64 | 61 | 9 |
P value = 0.0121 (Fisher's exact test), Q value = 0.23
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
DEL PEAK 32(22Q12.1) MUTATED | 3 | 74 | 2 |
DEL PEAK 32(22Q12.1) WILD-TYPE | 0 | 286 | 5 |
P value = 0.00676 (Fisher's exact test), Q value = 0.17
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 32(22Q12.1) MUTATED | 1 | 25 | 8 | 44 |
DEL PEAK 32(22Q12.1) WILD-TYPE | 1 | 133 | 9 | 139 |
P value = 0.00958 (Fisher's exact test), Q value = 0.2
nPatients | STAGE I | STAGE II | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|
ALL | 173 | 87 | 3 | 62 | 9 | 7 | 2 | 1 | 2 |
DEL PEAK 33(22Q13.32) MUTATED | 26 | 25 | 1 | 16 | 4 | 3 | 1 | 1 | 0 |
DEL PEAK 33(22Q13.32) WILD-TYPE | 147 | 62 | 2 | 46 | 5 | 4 | 1 | 0 | 2 |
P value = 0.00356 (Fisher's exact test), Q value = 0.13
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
DEL PEAK 33(22Q13.32) MUTATED | 28 | 30 | 20 | 5 |
DEL PEAK 33(22Q13.32) WILD-TYPE | 155 | 65 | 57 | 7 |
P value = 0.0134 (Fisher's exact test), Q value = 0.23
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
DEL PEAK 33(22Q13.32) MUTATED | 3 | 78 | 2 |
DEL PEAK 33(22Q13.32) WILD-TYPE | 0 | 282 | 5 |
P value = 0.00103 (Fisher's exact test), Q value = 0.084
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
DEL PEAK 33(22Q13.32) MUTATED | 2 | 24 | 7 | 48 |
DEL PEAK 33(22Q13.32) WILD-TYPE | 0 | 134 | 10 | 135 |
-
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/LIHC-TP/22531241/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/22506983/LIHC-TP.merged_data.txt
-
Number of patients = 370
-
Number of significantly focal cnvs = 61
-
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.