This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 82 arm-level events and 12 clinical features across 370 patients, 31 significant findings detected with Q value < 0.25.
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2p gain cnv correlated to 'GENDER'.
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2q gain cnv correlated to 'GENDER'.
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6q gain cnv correlated to 'ETHNICITY'.
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8q gain cnv correlated to 'GENDER'.
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12p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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20p gain cnv correlated to 'Time to Death'.
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22q gain cnv correlated to 'PATHOLOGY_T_STAGE'.
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3p loss cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
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4q loss cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.
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6q loss cnv correlated to 'YEARS_TO_BIRTH'.
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7q loss cnv correlated to 'Time to Death'.
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10q loss cnv correlated to 'RACE'.
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12p loss cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_N_STAGE'.
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12q loss cnv correlated to 'PATHOLOGIC_STAGE'.
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15q loss cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.
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16p loss cnv correlated to 'RACE'.
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16q loss cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.
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17p loss cnv correlated to 'PATHOLOGIC_STAGE'.
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17q loss cnv correlated to 'PATHOLOGIC_STAGE' and 'HISTOLOGICAL_TYPE'.
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18p loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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22q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
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xp loss 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 |
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 | |
3p loss | 52 (14%) | 318 |
0.759 (1.00) |
0.187 (0.685) |
0.00239 (0.181) |
0.00383 (0.192) |
0.0523 (0.468) |
0.447 (0.873) |
0.199 (0.7) |
0.618 (0.968) |
0.00082 (0.115) |
0.742 (1.00) |
0.951 (1.00) |
0.708 (1.00) |
4q loss | 146 (39%) | 224 |
0.172 (0.669) |
0.00228 (0.181) |
0.754 (1.00) |
0.66 (0.995) |
1 (1.00) |
0.319 (0.77) |
0.0883 (0.554) |
1 (1.00) |
0.514 (0.926) |
0.281 (0.75) |
0.00065 (0.107) |
0.442 (0.868) |
12p loss | 66 (18%) | 304 |
0.422 (0.858) |
0.587 (0.963) |
0.00731 (0.244) |
0.324 (0.77) |
0.00507 (0.192) |
0.168 (0.665) |
0.884 (1.00) |
0.367 (0.814) |
0.786 (1.00) |
0.122 (0.595) |
0.683 (1.00) |
1 (1.00) |
15q loss | 67 (18%) | 303 |
0.00477 (0.192) |
0.849 (1.00) |
0.0257 (0.395) |
0.00647 (0.236) |
0.087 (0.554) |
0.583 (0.96) |
1 (1.00) |
1 (1.00) |
0.789 (1.00) |
0.663 (0.995) |
0.109 (0.573) |
1 (1.00) |
16q loss | 145 (39%) | 225 |
0.0889 (0.554) |
0.000393 (0.0964) |
0.255 (0.741) |
0.127 (0.604) |
1 (1.00) |
1 (1.00) |
0.304 (0.762) |
0.491 (0.907) |
0.517 (0.929) |
0.56 (0.955) |
2e-05 (0.0197) |
0.442 (0.868) |
17q loss | 40 (11%) | 330 |
0.0725 (0.528) |
0.508 (0.92) |
0.00768 (0.244) |
0.178 (0.674) |
0.0278 (0.402) |
0.388 (0.828) |
0.281 (0.75) |
0.606 (0.963) |
0.00295 (0.189) |
0.925 (1.00) |
0.0288 (0.402) |
0.667 (0.996) |
22q loss | 70 (19%) | 300 |
0.424 (0.858) |
0.173 (0.669) |
0.0576 (0.495) |
0.0232 (0.387) |
0.448 (0.873) |
1 (1.00) |
0.32 (0.77) |
0.669 (0.996) |
0.00747 (0.244) |
0.0229 (0.387) |
0.00406 (0.192) |
0.048 (0.468) |
2p gain | 43 (12%) | 327 |
0.186 (0.683) |
0.051 (0.468) |
0.0717 (0.528) |
0.133 (0.613) |
0.0392 (0.438) |
0.0662 (0.509) |
4.32e-05 (0.0213) |
0.606 (0.963) |
0.328 (0.773) |
0.119 (0.594) |
0.154 (0.652) |
1 (1.00) |
2q gain | 40 (11%) | 330 |
0.255 (0.741) |
0.409 (0.843) |
0.0951 (0.565) |
0.141 (0.633) |
0.33 (0.773) |
0.0662 (0.509) |
0.00049 (0.0964) |
0.605 (0.963) |
0.295 (0.762) |
0.277 (0.75) |
0.425 (0.858) |
0.408 (0.843) |
6q gain | 67 (18%) | 303 |
0.605 (0.963) |
0.302 (0.762) |
0.0408 (0.444) |
0.0816 (0.55) |
1 (1.00) |
0.0186 (0.359) |
0.386 (0.826) |
1 (1.00) |
1 (1.00) |
0.135 (0.617) |
0.232 (0.73) |
0.00308 (0.189) |
8q gain | 184 (50%) | 186 |
0.983 (1.00) |
0.22 (0.72) |
0.0728 (0.528) |
0.226 (0.726) |
0.108 (0.573) |
1 (1.00) |
0.0012 (0.132) |
0.101 (0.565) |
0.52 (0.932) |
0.885 (1.00) |
0.0373 (0.422) |
0.62 (0.969) |
12p gain | 40 (11%) | 330 |
0.0895 (0.554) |
0.536 (0.938) |
0.54 (0.942) |
0.158 (0.652) |
1 (1.00) |
1 (1.00) |
0.473 (0.893) |
0.605 (0.963) |
0.00506 (0.192) |
0.79 (1.00) |
0.308 (0.762) |
1 (1.00) |
16q gain | 17 (5%) | 353 |
0.574 (0.96) |
0.00815 (0.251) |
0.0307 (0.403) |
0.129 (0.604) |
0.155 (0.652) |
1 (1.00) |
1 (1.00) |
0.349 (0.796) |
0.00187 (0.18) |
0.432 (0.859) |
0.359 (0.806) |
0.129 (0.604) |
20p gain | 107 (29%) | 263 |
0.0071 (0.244) |
0.0344 (0.419) |
0.235 (0.732) |
0.178 (0.674) |
1 (1.00) |
0.0878 (0.554) |
0.268 (0.747) |
1 (1.00) |
0.859 (1.00) |
0.287 (0.753) |
0.925 (1.00) |
0.781 (1.00) |
22q gain | 48 (13%) | 322 |
0.593 (0.963) |
0.841 (1.00) |
0.03 (0.402) |
0.00466 (0.192) |
0.321 (0.77) |
1 (1.00) |
0.246 (0.741) |
0.613 (0.963) |
0.493 (0.907) |
0.313 (0.762) |
0.922 (1.00) |
0.708 (1.00) |
6q loss | 94 (25%) | 276 |
0.391 (0.83) |
0.00271 (0.189) |
0.391 (0.83) |
0.886 (1.00) |
0.167 (0.664) |
1 (1.00) |
0.0541 (0.476) |
0.461 (0.881) |
0.401 (0.836) |
0.823 (1.00) |
0.644 (0.984) |
0.77 (1.00) |
7q loss | 21 (6%) | 349 |
0.00113 (0.132) |
0.271 (0.747) |
0.955 (1.00) |
0.788 (1.00) |
1 (1.00) |
1 (1.00) |
0.0521 (0.468) |
0.418 (0.854) |
1 (1.00) |
0.19 (0.687) |
0.0924 (0.561) |
1 (1.00) |
10q loss | 78 (21%) | 292 |
0.11 (0.573) |
0.959 (1.00) |
0.737 (1.00) |
0.144 (0.638) |
1 (1.00) |
0.579 (0.96) |
0.682 (1.00) |
0.69 (1.00) |
0.0423 (0.448) |
0.486 (0.905) |
0.00022 (0.0722) |
1 (1.00) |
12q loss | 36 (10%) | 334 |
0.209 (0.708) |
0.1 (0.565) |
0.00424 (0.192) |
0.477 (0.897) |
0.265 (0.746) |
0.0584 (0.495) |
1 (1.00) |
1 (1.00) |
0.253 (0.741) |
0.156 (0.652) |
0.313 (0.762) |
0.66 (0.995) |
16p loss | 108 (29%) | 262 |
0.034 (0.419) |
0.0108 (0.279) |
0.524 (0.933) |
0.412 (0.847) |
1 (1.00) |
0.601 (0.963) |
0.272 (0.747) |
0.0642 (0.509) |
0.858 (1.00) |
0.0766 (0.535) |
0.00422 (0.192) |
0.577 (0.96) |
17p loss | 185 (50%) | 185 |
0.0108 (0.279) |
0.552 (0.951) |
0.00358 (0.192) |
0.015 (0.315) |
0.247 (0.741) |
0.623 (0.969) |
0.911 (1.00) |
1 (1.00) |
0.46 (0.881) |
0.307 (0.762) |
0.663 (0.995) |
0.32 (0.77) |
18p loss | 74 (20%) | 296 |
0.739 (1.00) |
0.467 (0.885) |
0.341 (0.786) |
0.808 (1.00) |
0.113 (0.578) |
1 (1.00) |
0.163 (0.657) |
0.381 (0.821) |
0.00201 (0.18) |
0.92 (1.00) |
0.832 (1.00) |
1 (1.00) |
xp loss | 95 (26%) | 275 |
0.304 (0.762) |
0.126 (0.601) |
0.961 (1.00) |
0.571 (0.96) |
1 (1.00) |
1 (1.00) |
0.00477 (0.192) |
0.701 (1.00) |
0.405 (0.842) |
0.521 (0.932) |
0.429 (0.859) |
0.77 (1.00) |
1p gain | 62 (17%) | 308 |
0.814 (1.00) |
0.0302 (0.402) |
0.688 (1.00) |
0.265 (0.746) |
1 (1.00) |
1 (1.00) |
0.0517 (0.468) |
1 (1.00) |
1 (1.00) |
0.397 (0.835) |
0.14 (0.63) |
0.0846 (0.554) |
1q gain | 226 (61%) | 144 |
0.841 (1.00) |
0.64 (0.983) |
0.258 (0.741) |
0.36 (0.806) |
0.0578 (0.495) |
0.301 (0.762) |
0.494 (0.907) |
0.737 (1.00) |
0.0544 (0.476) |
0.813 (1.00) |
0.136 (0.618) |
0.431 (0.859) |
3p gain | 35 (9%) | 335 |
0.221 (0.72) |
0.592 (0.963) |
0.654 (0.992) |
0.809 (1.00) |
0.246 (0.741) |
0.346 (0.791) |
0.13 (0.605) |
1 (1.00) |
1 (1.00) |
0.236 (0.732) |
0.764 (1.00) |
0.66 (0.995) |
3q gain | 38 (10%) | 332 |
0.0402 (0.444) |
0.677 (1.00) |
0.668 (0.996) |
0.775 (1.00) |
0.265 (0.746) |
0.356 (0.803) |
0.145 (0.638) |
0.607 (0.963) |
0.665 (0.996) |
0.27 (0.747) |
0.645 (0.984) |
0.231 (0.73) |
4p gain | 27 (7%) | 343 |
0.108 (0.573) |
0.698 (1.00) |
0.663 (0.995) |
0.641 (0.983) |
1 (1.00) |
1 (1.00) |
0.197 (0.698) |
0.494 (0.907) |
1 (1.00) |
0.886 (1.00) |
1 (1.00) |
1 (1.00) |
4q gain | 7 (2%) | 363 |
0.916 (1.00) |
0.253 (0.741) |
0.757 (1.00) |
0.685 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.176 (0.674) |
0.582 (0.96) |
0.281 (0.75) |
5p gain | 134 (36%) | 236 |
0.0458 (0.459) |
0.118 (0.594) |
0.389 (0.829) |
0.1 (0.565) |
0.553 (0.951) |
1 (1.00) |
0.729 (1.00) |
0.299 (0.762) |
0.523 (0.933) |
0.853 (1.00) |
0.738 (1.00) |
0.795 (1.00) |
5q gain | 110 (30%) | 260 |
0.125 (0.601) |
0.0419 (0.448) |
0.941 (1.00) |
0.516 (0.928) |
0.562 (0.955) |
1 (1.00) |
0.0516 (0.468) |
0.0248 (0.394) |
0.858 (1.00) |
0.71 (1.00) |
0.875 (1.00) |
1 (1.00) |
6p gain | 116 (31%) | 254 |
0.366 (0.814) |
0.434 (0.86) |
0.195 (0.696) |
0.0964 (0.565) |
0.554 (0.951) |
0.0968 (0.565) |
0.4 (0.836) |
0.282 (0.75) |
0.547 (0.946) |
0.635 (0.981) |
0.334 (0.774) |
0.0509 (0.468) |
7p gain | 109 (29%) | 261 |
0.766 (1.00) |
0.0471 (0.468) |
0.645 (0.984) |
0.701 (1.00) |
0.19 (0.687) |
1 (1.00) |
0.328 (0.773) |
1 (1.00) |
0.533 (0.938) |
0.893 (1.00) |
0.152 (0.651) |
0.577 (0.96) |
7q gain | 110 (30%) | 260 |
0.563 (0.955) |
0.0217 (0.382) |
0.465 (0.885) |
0.375 (0.82) |
0.2 (0.7) |
1 (1.00) |
1 (1.00) |
0.461 (0.881) |
0.536 (0.938) |
1 (1.00) |
0.0611 (0.499) |
0.269 (0.747) |
8p gain | 73 (20%) | 297 |
0.324 (0.77) |
0.15 (0.651) |
0.941 (1.00) |
0.929 (1.00) |
1 (1.00) |
1 (1.00) |
0.162 (0.657) |
0.0672 (0.509) |
0.807 (1.00) |
0.163 (0.657) |
0.203 (0.705) |
1 (1.00) |
9p gain | 19 (5%) | 351 |
0.849 (1.00) |
0.227 (0.726) |
0.0673 (0.509) |
0.144 (0.638) |
1 (1.00) |
0.218 (0.719) |
0.323 (0.77) |
1 (1.00) |
0.0867 (0.554) |
0.184 (0.68) |
0.282 (0.75) |
0.556 (0.952) |
9q gain | 19 (5%) | 351 |
0.96 (1.00) |
0.328 (0.773) |
0.151 (0.651) |
0.209 (0.708) |
1 (1.00) |
0.205 (0.707) |
0.0733 (0.528) |
1 (1.00) |
0.414 (0.848) |
0.183 (0.68) |
0.87 (1.00) |
0.577 (0.96) |
10p gain | 58 (16%) | 312 |
0.185 (0.682) |
0.021 (0.375) |
0.243 (0.741) |
0.161 (0.657) |
1 (1.00) |
0.12 (0.594) |
1 (1.00) |
0.635 (0.981) |
0.584 (0.96) |
0.853 (1.00) |
0.562 (0.955) |
0.307 (0.762) |
10q gain | 36 (10%) | 334 |
0.61 (0.963) |
0.207 (0.707) |
0.108 (0.573) |
0.151 (0.651) |
1 (1.00) |
0.0547 (0.476) |
0.576 (0.96) |
0.574 (0.96) |
0.642 (0.983) |
0.916 (1.00) |
1 (1.00) |
0.206 (0.707) |
11p gain | 18 (5%) | 352 |
0.508 (0.92) |
0.872 (1.00) |
0.349 (0.796) |
0.324 (0.77) |
1 (1.00) |
0.205 (0.707) |
0.605 (0.963) |
1 (1.00) |
1 (1.00) |
0.0238 (0.39) |
0.731 (1.00) |
1 (1.00) |
11q gain | 20 (5%) | 350 |
0.426 (0.858) |
0.855 (1.00) |
0.293 (0.76) |
0.209 (0.708) |
1 (1.00) |
0.242 (0.741) |
0.462 (0.882) |
1 (1.00) |
1 (1.00) |
0.0345 (0.419) |
0.759 (1.00) |
1 (1.00) |
12q gain | 47 (13%) | 323 |
0.841 (1.00) |
0.526 (0.933) |
0.102 (0.566) |
0.101 (0.565) |
0.357 (0.803) |
1 (1.00) |
0.319 (0.77) |
0.608 (0.963) |
0.0888 (0.554) |
0.4 (0.836) |
0.448 (0.873) |
1 (1.00) |
13q gain | 23 (6%) | 347 |
0.212 (0.713) |
0.908 (1.00) |
0.0989 (0.565) |
0.623 (0.969) |
0.207 (0.707) |
0.242 (0.741) |
0.107 (0.573) |
0.449 (0.873) |
1 (1.00) |
0.211 (0.71) |
0.534 (0.938) |
0.247 (0.741) |
14q gain | 22 (6%) | 348 |
0.481 (0.902) |
0.393 (0.831) |
0.31 (0.762) |
0.555 (0.951) |
1 (1.00) |
0.18 (0.679) |
0.353 (0.799) |
1 (1.00) |
0.114 (0.579) |
0.0884 (0.554) |
0.183 (0.68) |
1 (1.00) |
15q gain | 33 (9%) | 337 |
0.545 (0.944) |
0.941 (1.00) |
0.738 (1.00) |
0.362 (0.808) |
1 (1.00) |
1 (1.00) |
0.696 (1.00) |
1 (1.00) |
0.34 (0.786) |
0.91 (1.00) |
0.639 (0.983) |
0.648 (0.987) |
16p gain | 32 (9%) | 338 |
0.253 (0.741) |
0.0256 (0.395) |
0.114 (0.58) |
0.398 (0.835) |
0.236 (0.732) |
1 (1.00) |
1 (1.00) |
0.178 (0.674) |
0.014 (0.315) |
0.744 (1.00) |
0.46 (0.881) |
1 (1.00) |
17p gain | 30 (8%) | 340 |
0.843 (1.00) |
0.613 (0.963) |
0.257 (0.741) |
0.191 (0.687) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.576 (0.96) |
0.128 (0.604) |
0.304 (0.762) |
0.38 (0.821) |
17q gain | 93 (25%) | 277 |
0.804 (1.00) |
0.595 (0.963) |
0.233 (0.732) |
0.163 (0.657) |
1 (1.00) |
0.27 (0.747) |
0.0955 (0.565) |
1 (1.00) |
0.603 (0.963) |
0.0902 (0.555) |
0.0688 (0.517) |
0.571 (0.96) |
18p gain | 36 (10%) | 334 |
0.795 (1.00) |
0.308 (0.762) |
0.333 (0.774) |
0.191 (0.687) |
1 (1.00) |
0.346 (0.791) |
0.707 (1.00) |
0.608 (0.963) |
1 (1.00) |
0.106 (0.573) |
0.0161 (0.325) |
1 (1.00) |
18q gain | 28 (8%) | 342 |
0.73 (1.00) |
0.0974 (0.565) |
0.226 (0.726) |
0.181 (0.679) |
1 (1.00) |
0.278 (0.75) |
0.529 (0.936) |
1 (1.00) |
1 (1.00) |
0.0451 (0.459) |
0.036 (0.42) |
1 (1.00) |
19p gain | 56 (15%) | 314 |
0.425 (0.858) |
0.65 (0.988) |
0.11 (0.573) |
0.668 (0.996) |
1 (1.00) |
0.0135 (0.315) |
0.0299 (0.402) |
1 (1.00) |
0.131 (0.608) |
0.117 (0.591) |
0.064 (0.509) |
0.718 (1.00) |
19q gain | 71 (19%) | 299 |
0.507 (0.92) |
0.491 (0.907) |
0.143 (0.638) |
0.504 (0.92) |
1 (1.00) |
0.0248 (0.394) |
0.257 (0.741) |
1 (1.00) |
0.217 (0.718) |
0.313 (0.762) |
0.283 (0.75) |
0.53 (0.936) |
20q gain | 112 (30%) | 258 |
0.0197 (0.359) |
0.0639 (0.509) |
0.172 (0.669) |
0.121 (0.594) |
1 (1.00) |
0.596 (0.963) |
0.467 (0.885) |
0.73 (1.00) |
0.859 (1.00) |
0.451 (0.873) |
0.889 (1.00) |
1 (1.00) |
21q gain | 26 (7%) | 344 |
0.438 (0.866) |
0.715 (1.00) |
0.0292 (0.402) |
0.0149 (0.315) |
1 (1.00) |
1 (1.00) |
0.828 (1.00) |
1 (1.00) |
0.522 (0.933) |
0.0195 (0.359) |
0.378 (0.821) |
1 (1.00) |
xp gain | 41 (11%) | 329 |
0.741 (1.00) |
0.474 (0.894) |
0.975 (1.00) |
0.859 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.258 (0.741) |
1 (1.00) |
0.575 (0.96) |
0.37 (0.816) |
0.687 (1.00) |
xq gain | 60 (16%) | 310 |
0.336 (0.778) |
0.571 (0.96) |
0.992 (1.00) |
0.845 (1.00) |
1 (1.00) |
1 (1.00) |
0.132 (0.611) |
0.157 (0.652) |
0.77 (1.00) |
0.854 (1.00) |
0.35 (0.796) |
1 (1.00) |
1p loss | 78 (21%) | 292 |
0.84 (1.00) |
0.256 (0.741) |
0.265 (0.746) |
0.381 (0.821) |
0.537 (0.939) |
0.0505 (0.468) |
0.173 (0.669) |
0.214 (0.715) |
0.26 (0.746) |
0.373 (0.82) |
0.29 (0.758) |
1 (1.00) |
1q loss | 20 (5%) | 350 |
0.0606 (0.499) |
0.584 (0.96) |
0.724 (1.00) |
0.895 (1.00) |
0.155 (0.652) |
1 (1.00) |
0.22 (0.72) |
1 (1.00) |
0.432 (0.859) |
0.439 (0.866) |
0.745 (1.00) |
1 (1.00) |
2p loss | 33 (9%) | 337 |
0.766 (1.00) |
0.421 (0.858) |
0.251 (0.741) |
0.486 (0.905) |
0.217 (0.718) |
1 (1.00) |
0.434 (0.86) |
0.535 (0.938) |
0.222 (0.72) |
0.299 (0.762) |
0.242 (0.741) |
0.38 (0.821) |
2q loss | 38 (10%) | 332 |
0.746 (1.00) |
0.104 (0.57) |
0.487 (0.905) |
0.962 (1.00) |
0.265 (0.746) |
1 (1.00) |
0.854 (1.00) |
0.598 (0.963) |
0.273 (0.749) |
0.112 (0.578) |
0.258 (0.741) |
1 (1.00) |
3q loss | 41 (11%) | 329 |
0.426 (0.858) |
0.104 (0.57) |
0.0142 (0.315) |
0.0411 (0.444) |
0.0344 (0.419) |
1 (1.00) |
0.293 (0.76) |
0.605 (0.963) |
0.00998 (0.273) |
0.798 (1.00) |
0.88 (1.00) |
1 (1.00) |
4p loss | 105 (28%) | 265 |
0.452 (0.873) |
0.0665 (0.509) |
0.217 (0.718) |
0.199 (0.7) |
1 (1.00) |
0.0794 (0.539) |
0.0363 (0.42) |
1 (1.00) |
0.858 (1.00) |
0.305 (0.762) |
0.0163 (0.325) |
0.255 (0.741) |
5p loss | 29 (8%) | 341 |
0.331 (0.773) |
0.0302 (0.402) |
0.455 (0.877) |
0.313 (0.762) |
0.246 (0.741) |
1 (1.00) |
0.412 (0.847) |
0.494 (0.907) |
0.0451 (0.459) |
0.891 (1.00) |
0.372 (0.819) |
1 (1.00) |
5q loss | 37 (10%) | 333 |
0.0842 (0.554) |
0.0353 (0.419) |
0.155 (0.652) |
0.01 (0.273) |
0.275 (0.749) |
1 (1.00) |
0.711 (1.00) |
0.586 (0.962) |
0.0123 (0.302) |
1 (1.00) |
0.62 (0.969) |
1 (1.00) |
6p loss | 31 (8%) | 339 |
0.814 (1.00) |
0.989 (1.00) |
0.549 (0.948) |
0.278 (0.75) |
0.236 (0.732) |
1 (1.00) |
0.0454 (0.459) |
0.508 (0.92) |
1 (1.00) |
0.811 (1.00) |
0.172 (0.669) |
0.632 (0.979) |
7p loss | 16 (4%) | 354 |
0.0848 (0.554) |
0.543 (0.944) |
0.966 (1.00) |
0.828 (1.00) |
1 (1.00) |
1 (1.00) |
0.167 (0.664) |
0.331 (0.773) |
1 (1.00) |
0.396 (0.835) |
0.639 (0.983) |
0.511 (0.922) |
8p loss | 196 (53%) | 174 |
0.174 (0.669) |
0.165 (0.66) |
0.157 (0.652) |
0.507 (0.92) |
1 (1.00) |
1 (1.00) |
0.739 (1.00) |
1 (1.00) |
0.071 (0.528) |
0.504 (0.92) |
0.451 (0.873) |
0.61 (0.963) |
8q loss | 45 (12%) | 325 |
0.876 (1.00) |
0.908 (1.00) |
0.731 (1.00) |
0.78 (1.00) |
0.294 (0.76) |
0.428 (0.858) |
0.0613 (0.499) |
0.606 (0.963) |
0.732 (1.00) |
0.472 (0.893) |
0.891 (1.00) |
0.704 (1.00) |
9p loss | 119 (32%) | 251 |
0.101 (0.565) |
0.0784 (0.536) |
0.386 (0.826) |
0.888 (1.00) |
0.25 (0.741) |
0.106 (0.573) |
0.12 (0.594) |
0.726 (1.00) |
1 (1.00) |
0.243 (0.741) |
0.331 (0.773) |
0.102 (0.566) |
9q loss | 110 (30%) | 260 |
0.075 (0.531) |
0.796 (1.00) |
0.135 (0.617) |
0.576 (0.96) |
0.0232 (0.387) |
0.074 (0.528) |
0.225 (0.726) |
1 (1.00) |
1 (1.00) |
0.305 (0.762) |
0.682 (1.00) |
0.163 (0.657) |
10p loss | 47 (13%) | 323 |
0.287 (0.753) |
0.367 (0.814) |
0.487 (0.905) |
0.183 (0.68) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.613 (0.963) |
0.0883 (0.554) |
0.591 (0.963) |
0.197 (0.698) |
1 (1.00) |
11p loss | 63 (17%) | 307 |
0.323 (0.77) |
0.631 (0.979) |
0.015 (0.315) |
0.00989 (0.273) |
0.0735 (0.528) |
0.545 (0.944) |
0.882 (1.00) |
1 (1.00) |
0.019 (0.359) |
0.282 (0.75) |
0.286 (0.753) |
0.307 (0.762) |
11q loss | 72 (19%) | 298 |
0.428 (0.858) |
0.325 (0.771) |
0.0596 (0.497) |
0.0778 (0.536) |
0.113 (0.578) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0319 (0.413) |
0.406 (0.842) |
0.504 (0.92) |
0.195 (0.696) |
13q loss | 122 (33%) | 248 |
0.27 (0.747) |
0.911 (1.00) |
0.0277 (0.402) |
0.00928 (0.273) |
0.271 (0.747) |
0.605 (0.963) |
0.0979 (0.565) |
0.724 (1.00) |
0.353 (0.799) |
0.159 (0.655) |
0.868 (1.00) |
1 (1.00) |
14q loss | 109 (29%) | 261 |
0.0497 (0.468) |
0.0762 (0.535) |
0.0945 (0.565) |
0.0353 (0.419) |
0.229 (0.728) |
0.601 (0.963) |
0.393 (0.831) |
1 (1.00) |
0.262 (0.746) |
0.777 (1.00) |
0.0345 (0.419) |
0.785 (1.00) |
18q loss | 79 (21%) | 291 |
0.781 (1.00) |
0.996 (1.00) |
0.287 (0.753) |
1 (1.00) |
0.125 (0.601) |
0.227 (0.726) |
0.221 (0.72) |
0.0852 (0.554) |
0.0115 (0.29) |
0.443 (0.869) |
0.986 (1.00) |
0.345 (0.791) |
19p loss | 52 (14%) | 318 |
0.0452 (0.459) |
0.0261 (0.395) |
0.675 (1.00) |
0.375 (0.82) |
0.382 (0.822) |
1 (1.00) |
0.152 (0.651) |
0.61 (0.963) |
1 (1.00) |
0.653 (0.992) |
0.0497 (0.468) |
0.713 (1.00) |
19q loss | 39 (11%) | 331 |
0.201 (0.703) |
0.0129 (0.31) |
0.426 (0.858) |
0.376 (0.821) |
0.312 (0.762) |
1 (1.00) |
0.145 (0.638) |
1 (1.00) |
1 (1.00) |
0.453 (0.874) |
0.0165 (0.325) |
0.687 (1.00) |
20p loss | 26 (7%) | 344 |
0.961 (1.00) |
0.059 (0.496) |
0.0924 (0.561) |
0.312 (0.762) |
1 (1.00) |
0.29 (0.758) |
0.828 (1.00) |
0.479 (0.9) |
0.151 (0.651) |
0.622 (0.969) |
0.19 (0.687) |
0.3 (0.762) |
20q loss | 13 (4%) | 357 |
0.36 (0.806) |
0.229 (0.728) |
0.262 (0.746) |
0.723 (1.00) |
1 (1.00) |
1 (1.00) |
0.562 (0.955) |
0.274 (0.749) |
0.121 (0.595) |
0.299 (0.762) |
0.0649 (0.509) |
0.406 (0.842) |
21q loss | 110 (30%) | 260 |
0.0278 (0.402) |
0.169 (0.667) |
0.377 (0.821) |
0.953 (1.00) |
1 (1.00) |
0.0999 (0.565) |
0.0516 (0.468) |
1 (1.00) |
0.369 (0.815) |
0.544 (0.944) |
0.526 (0.933) |
1 (1.00) |
xq loss | 74 (20%) | 296 |
0.854 (1.00) |
0.078 (0.536) |
0.934 (1.00) |
0.659 (0.995) |
0.487 (0.905) |
0.582 (0.96) |
0.0367 (0.42) |
1 (1.00) |
0.235 (0.732) |
0.779 (1.00) |
0.123 (0.595) |
0.748 (1.00) |
P value = 4.32e-05 (Fisher's exact test), Q value = 0.021
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
2P GAIN MUTATED | 26 | 17 |
2P GAIN WILD-TYPE | 92 | 235 |
P value = 0.00049 (Fisher's exact test), Q value = 0.096
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
2Q GAIN MUTATED | 23 | 17 |
2Q GAIN WILD-TYPE | 95 | 235 |
P value = 0.00308 (Fisher's exact test), Q value = 0.19
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 16 | 335 |
6Q GAIN MUTATED | 8 | 56 |
6Q GAIN WILD-TYPE | 8 | 279 |
P value = 0.0012 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
8Q GAIN MUTATED | 44 | 140 |
8Q GAIN WILD-TYPE | 74 | 112 |
P value = 0.00506 (Fisher's exact test), Q value = 0.19
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
12P GAIN MUTATED | 0 | 36 | 4 |
12P GAIN WILD-TYPE | 3 | 324 | 3 |
P value = 0.00187 (Fisher's exact test), Q value = 0.18
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
16Q GAIN MUTATED | 2 | 14 | 1 |
16Q GAIN WILD-TYPE | 1 | 346 | 6 |
P value = 0.0071 (logrank test), Q value = 0.24
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
20P GAIN MUTATED | 105 | 48 | 0.3 - 114.3 (18.2) |
20P GAIN WILD-TYPE | 259 | 81 | 0.0 - 120.8 (20.2) |
P value = 0.00466 (Fisher's exact test), Q value = 0.19
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
22Q GAIN MUTATED | 13 | 17 | 16 | 2 |
22Q GAIN WILD-TYPE | 170 | 78 | 61 | 10 |
P value = 0.00239 (Fisher's exact test), Q value = 0.18
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 |
3P LOSS MUTATED | 13 | 15 | 0 | 15 | 2 | 2 | 0 | 1 | 1 |
3P LOSS WILD-TYPE | 160 | 72 | 3 | 47 | 7 | 5 | 2 | 0 | 1 |
P value = 0.00383 (Fisher's exact test), Q value = 0.19
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
3P LOSS MUTATED | 15 | 16 | 18 | 3 |
3P LOSS WILD-TYPE | 168 | 79 | 59 | 9 |
P value = 0.00082 (Fisher's exact test), Q value = 0.12
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
3P LOSS MUTATED | 2 | 46 | 4 |
3P LOSS WILD-TYPE | 1 | 314 | 3 |
P value = 0.00228 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
4Q LOSS MUTATED | 144 | 57.1 (13.4) |
4Q LOSS WILD-TYPE | 222 | 61.0 (12.8) |
P value = 0.00065 (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 |
4Q LOSS MUTATED | 1 | 80 | 9 | 56 |
4Q LOSS WILD-TYPE | 1 | 78 | 8 | 127 |
P value = 0.00271 (Wilcoxon-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
6Q LOSS MUTATED | 93 | 63.1 (12.3) |
6Q LOSS WILD-TYPE | 273 | 58.2 (13.3) |
P value = 0.00113 (logrank test), Q value = 0.13
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
7Q LOSS MUTATED | 21 | 13 | 0.2 - 76.4 (13.6) |
7Q LOSS WILD-TYPE | 343 | 116 | 0.0 - 120.8 (20.1) |
P value = 0.00022 (Fisher's exact test), Q value = 0.072
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
10Q LOSS MUTATED | 0 | 40 | 10 | 28 |
10Q LOSS WILD-TYPE | 2 | 118 | 7 | 155 |
P value = 0.00731 (Fisher's exact test), Q value = 0.24
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 |
12P LOSS MUTATED | 24 | 18 | 1 | 9 | 4 | 2 | 2 | 1 | 0 |
12P LOSS WILD-TYPE | 149 | 69 | 2 | 53 | 5 | 5 | 0 | 0 | 2 |
P value = 0.00507 (Fisher's exact test), Q value = 0.19
nPatients | 0 | 1 |
---|---|---|
ALL | 254 | 3 |
12P LOSS MUTATED | 42 | 3 |
12P LOSS WILD-TYPE | 212 | 0 |
P value = 0.00424 (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 |
12Q LOSS MUTATED | 12 | 10 | 1 | 6 | 2 | 0 | 2 | 1 | 0 |
12Q LOSS WILD-TYPE | 161 | 77 | 2 | 56 | 7 | 7 | 0 | 0 | 2 |
P value = 0.00477 (logrank test), Q value = 0.19
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 364 | 129 | 0.0 - 120.8 (19.8) |
15Q LOSS MUTATED | 64 | 31 | 0.2 - 102.7 (13.3) |
15Q LOSS WILD-TYPE | 300 | 98 | 0.0 - 120.8 (20.9) |
P value = 0.00647 (Fisher's exact test), Q value = 0.24
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 183 | 95 | 77 | 12 |
15Q LOSS MUTATED | 22 | 23 | 21 | 1 |
15Q LOSS WILD-TYPE | 161 | 72 | 56 | 11 |
P value = 0.00422 (Fisher's exact test), Q value = 0.19
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
16P LOSS MUTATED | 0 | 61 | 6 | 40 |
16P LOSS WILD-TYPE | 2 | 97 | 11 | 143 |
P value = 0.000393 (Wilcoxon-test), Q value = 0.096
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 366 | 59.4 (13.2) |
16Q LOSS MUTATED | 144 | 56.9 (12.9) |
16Q LOSS WILD-TYPE | 222 | 61.1 (13.1) |
P value = 2e-05 (Fisher's exact test), Q value = 0.02
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
16Q LOSS MUTATED | 0 | 84 | 7 | 51 |
16Q LOSS WILD-TYPE | 2 | 74 | 10 | 132 |
P value = 0.00358 (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 |
17P LOSS MUTATED | 70 | 50 | 2 | 34 | 4 | 7 | 2 | 1 | 1 |
17P LOSS WILD-TYPE | 103 | 37 | 1 | 28 | 5 | 0 | 0 | 0 | 1 |
P value = 0.00768 (Fisher's exact test), Q value = 0.24
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 |
17Q LOSS MUTATED | 10 | 12 | 0 | 9 | 2 | 2 | 1 | 1 | 0 |
17Q LOSS WILD-TYPE | 163 | 75 | 3 | 53 | 7 | 5 | 1 | 0 | 2 |
P value = 0.00295 (Fisher's exact test), Q value = 0.19
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
17Q LOSS MUTATED | 2 | 35 | 3 |
17Q LOSS WILD-TYPE | 1 | 325 | 4 |
P value = 0.00201 (Fisher's exact test), Q value = 0.18
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
18P LOSS MUTATED | 3 | 68 | 3 |
18P LOSS WILD-TYPE | 0 | 292 | 4 |
P value = 0.00747 (Fisher's exact test), Q value = 0.24
nPatients | FIBROLAMELLAR CARCINOMA | HEPATOCELLULAR CARCINOMA | HEPATOCHOLANGIOCARCINOMA (MIXED) |
---|---|---|---|
ALL | 3 | 360 | 7 |
22Q LOSS MUTATED | 3 | 65 | 2 |
22Q LOSS WILD-TYPE | 0 | 295 | 5 |
P value = 0.00406 (Fisher's exact test), Q value = 0.19
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 158 | 17 | 183 |
22Q LOSS MUTATED | 1 | 22 | 8 | 39 |
22Q LOSS WILD-TYPE | 1 | 136 | 9 | 144 |
P value = 0.00477 (Fisher's exact test), Q value = 0.19
nPatients | FEMALE | MALE |
---|---|---|
ALL | 118 | 252 |
XP LOSS MUTATED | 19 | 76 |
XP LOSS WILD-TYPE | 99 | 176 |
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22531240/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 arm-level cnvs = 82
-
Number of selected clinical features = 12
-
Exclude regions that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.