This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 79 arm-level events and 12 clinical features across 242 patients, 2 significant findings detected with Q value < 0.25.
-
5Q GAIN MUTATION ANALYSIS cnv correlated to 'BRESLOW.THICKNESS'.
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10Q LOSS MUTATION ANALYSIS cnv correlated to 'AGE'.
Clinical Features |
Time from Specimen Diagnosis to Death |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
MELANOMA ULCERATION |
MELANOMA PRIMARY KNOWN |
BRESLOW THICKNESS |
GENDER | ||
nCNV (%) | nWild-Type | logrank test | logrank test | t-test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | t-test | Fisher's exact test | |
5Q GAIN MUTATION ANALYSIS | 27 (11%) | 215 |
0.667 (1.00) |
0.21 (1.00) |
0.943 (1.00) |
0.779 (1.00) |
0.343 (1.00) |
0.238 (1.00) |
0.312 (1.00) |
0.0977 (1.00) |
0.246 (1.00) |
0.349 (1.00) |
0.000158 (0.15) |
1 (1.00) |
10Q LOSS MUTATION ANALYSIS | 145 (60%) | 97 |
0.663 (1.00) |
0.612 (1.00) |
0.000247 (0.234) |
0.0461 (1.00) |
0.712 (1.00) |
0.154 (1.00) |
0.363 (1.00) |
0.0549 (1.00) |
0.409 (1.00) |
0.551 (1.00) |
0.621 (1.00) |
0.0614 (1.00) |
1P GAIN MUTATION ANALYSIS | 55 (23%) | 187 |
0.922 (1.00) |
0.905 (1.00) |
0.528 (1.00) |
0.0267 (1.00) |
0.236 (1.00) |
0.551 (1.00) |
0.441 (1.00) |
0.085 (1.00) |
0.698 (1.00) |
0.819 (1.00) |
0.78 (1.00) |
0.754 (1.00) |
1Q GAIN MUTATION ANALYSIS | 110 (45%) | 132 |
0.833 (1.00) |
0.526 (1.00) |
0.869 (1.00) |
0.61 (1.00) |
0.55 (1.00) |
0.847 (1.00) |
0.306 (1.00) |
0.0623 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.792 (1.00) |
2P GAIN MUTATION ANALYSIS | 49 (20%) | 193 |
0.203 (1.00) |
0.103 (1.00) |
0.77 (1.00) |
0.45 (1.00) |
0.969 (1.00) |
0.312 (1.00) |
0.932 (1.00) |
0.531 (1.00) |
0.419 (1.00) |
0.466 (1.00) |
0.74 (1.00) |
1 (1.00) |
2Q GAIN MUTATION ANALYSIS | 47 (19%) | 195 |
0.0504 (1.00) |
0.0405 (1.00) |
0.587 (1.00) |
0.389 (1.00) |
0.882 (1.00) |
0.116 (1.00) |
0.907 (1.00) |
0.62 (1.00) |
0.682 (1.00) |
0.809 (1.00) |
0.824 (1.00) |
0.621 (1.00) |
3P GAIN MUTATION ANALYSIS | 36 (15%) | 206 |
0.548 (1.00) |
0.0259 (1.00) |
0.0533 (1.00) |
0.119 (1.00) |
0.0958 (1.00) |
0.0856 (1.00) |
0.41 (1.00) |
0.452 (1.00) |
1 (1.00) |
0.586 (1.00) |
0.00206 (1.00) |
0.854 (1.00) |
3Q GAIN MUTATION ANALYSIS | 45 (19%) | 197 |
0.411 (1.00) |
0.0117 (1.00) |
0.0139 (1.00) |
0.332 (1.00) |
0.069 (1.00) |
0.021 (1.00) |
0.051 (1.00) |
0.456 (1.00) |
0.187 (1.00) |
1 (1.00) |
0.00214 (1.00) |
0.736 (1.00) |
4P GAIN MUTATION ANALYSIS | 36 (15%) | 206 |
0.969 (1.00) |
0.561 (1.00) |
0.161 (1.00) |
0.828 (1.00) |
0.065 (1.00) |
0.391 (1.00) |
0.874 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.997 (1.00) |
0.355 (1.00) |
4Q GAIN MUTATION ANALYSIS | 31 (13%) | 211 |
0.825 (1.00) |
0.544 (1.00) |
0.0906 (1.00) |
0.481 (1.00) |
0.203 (1.00) |
0.535 (1.00) |
0.677 (1.00) |
0.392 (1.00) |
0.813 (1.00) |
0.557 (1.00) |
0.997 (1.00) |
1 (1.00) |
5P GAIN MUTATION ANALYSIS | 43 (18%) | 199 |
0.194 (1.00) |
0.0227 (1.00) |
0.855 (1.00) |
0.603 (1.00) |
0.0218 (1.00) |
0.207 (1.00) |
0.113 (1.00) |
0.232 (1.00) |
0.0531 (1.00) |
0.201 (1.00) |
0.000603 (0.57) |
0.171 (1.00) |
6P GAIN MUTATION ANALYSIS | 95 (39%) | 147 |
0.557 (1.00) |
0.667 (1.00) |
0.854 (1.00) |
0.0168 (1.00) |
0.121 (1.00) |
0.317 (1.00) |
0.14 (1.00) |
0.164 (1.00) |
1 (1.00) |
0.691 (1.00) |
0.632 (1.00) |
0.347 (1.00) |
6Q GAIN MUTATION ANALYSIS | 30 (12%) | 212 |
0.314 (1.00) |
0.482 (1.00) |
0.94 (1.00) |
0.273 (1.00) |
0.215 (1.00) |
0.131 (1.00) |
0.0292 (1.00) |
0.288 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.0829 (1.00) |
0.426 (1.00) |
7P GAIN MUTATION ANALYSIS | 122 (50%) | 120 |
0.708 (1.00) |
0.706 (1.00) |
0.386 (1.00) |
0.28 (1.00) |
0.0681 (1.00) |
0.559 (1.00) |
0.418 (1.00) |
0.374 (1.00) |
0.513 (1.00) |
0.33 (1.00) |
0.457 (1.00) |
0.432 (1.00) |
7Q GAIN MUTATION ANALYSIS | 123 (51%) | 119 |
0.782 (1.00) |
0.665 (1.00) |
0.104 (1.00) |
0.446 (1.00) |
0.0331 (1.00) |
0.757 (1.00) |
0.503 (1.00) |
0.658 (1.00) |
0.513 (1.00) |
0.846 (1.00) |
0.474 (1.00) |
0.358 (1.00) |
8P GAIN MUTATION ANALYSIS | 79 (33%) | 163 |
0.741 (1.00) |
0.586 (1.00) |
0.167 (1.00) |
0.15 (1.00) |
0.783 (1.00) |
0.688 (1.00) |
0.592 (1.00) |
0.419 (1.00) |
0.374 (1.00) |
0.678 (1.00) |
0.975 (1.00) |
0.483 (1.00) |
8Q GAIN MUTATION ANALYSIS | 111 (46%) | 131 |
0.464 (1.00) |
0.349 (1.00) |
0.0118 (1.00) |
0.122 (1.00) |
0.619 (1.00) |
0.178 (1.00) |
0.405 (1.00) |
0.674 (1.00) |
1 (1.00) |
0.436 (1.00) |
0.847 (1.00) |
0.896 (1.00) |
9P GAIN MUTATION ANALYSIS | 14 (6%) | 228 |
0.621 (1.00) |
0.33 (1.00) |
0.507 (1.00) |
0.0177 (1.00) |
0.147 (1.00) |
0.505 (1.00) |
0.849 (1.00) |
0.933 (1.00) |
0.201 (1.00) |
0.228 (1.00) |
0.0062 (1.00) |
0.784 (1.00) |
9Q GAIN MUTATION ANALYSIS | 15 (6%) | 227 |
0.648 (1.00) |
0.958 (1.00) |
0.576 (1.00) |
0.0229 (1.00) |
0.0455 (1.00) |
0.505 (1.00) |
0.622 (1.00) |
0.924 (1.00) |
0.125 (1.00) |
0.227 (1.00) |
0.00321 (1.00) |
0.591 (1.00) |
10P GAIN MUTATION ANALYSIS | 7 (3%) | 235 |
0.539 (1.00) |
0.223 (1.00) |
0.651 (1.00) |
1 (1.00) |
0.306 (1.00) |
0.745 (1.00) |
0.532 (1.00) |
0.00622 (1.00) |
1 (1.00) |
0.0428 (1.00) |
0.027 (1.00) |
1 (1.00) |
11P GAIN MUTATION ANALYSIS | 23 (10%) | 219 |
0.396 (1.00) |
0.514 (1.00) |
0.868 (1.00) |
0.29 (1.00) |
0.248 (1.00) |
0.0312 (1.00) |
0.823 (1.00) |
0.836 (1.00) |
0.521 (1.00) |
0.0477 (1.00) |
0.48 (1.00) |
0.501 (1.00) |
11Q GAIN MUTATION ANALYSIS | 19 (8%) | 223 |
0.505 (1.00) |
0.87 (1.00) |
0.645 (1.00) |
0.253 (1.00) |
0.223 (1.00) |
0.061 (1.00) |
0.772 (1.00) |
0.904 (1.00) |
1 (1.00) |
0.0186 (1.00) |
0.194 (1.00) |
0.626 (1.00) |
12P GAIN MUTATION ANALYSIS | 39 (16%) | 203 |
0.523 (1.00) |
0.499 (1.00) |
0.253 (1.00) |
0.55 (1.00) |
0.123 (1.00) |
0.0856 (1.00) |
0.056 (1.00) |
0.445 (1.00) |
1 (1.00) |
0.287 (1.00) |
0.697 (1.00) |
0.593 (1.00) |
12Q GAIN MUTATION ANALYSIS | 21 (9%) | 221 |
0.77 (1.00) |
0.399 (1.00) |
0.271 (1.00) |
0.53 (1.00) |
0.733 (1.00) |
0.261 (1.00) |
0.0035 (1.00) |
0.836 (1.00) |
1 (1.00) |
1 (1.00) |
0.484 (1.00) |
1 (1.00) |
13Q GAIN MUTATION ANALYSIS | 60 (25%) | 182 |
0.184 (1.00) |
0.283 (1.00) |
0.689 (1.00) |
0.0681 (1.00) |
0.273 (1.00) |
0.267 (1.00) |
0.26 (1.00) |
0.407 (1.00) |
0.562 (1.00) |
0.822 (1.00) |
0.491 (1.00) |
0.761 (1.00) |
14Q GAIN MUTATION ANALYSIS | 25 (10%) | 217 |
0.737 (1.00) |
0.744 (1.00) |
0.479 (1.00) |
0.763 (1.00) |
0.883 (1.00) |
0.655 (1.00) |
0.578 (1.00) |
0.849 (1.00) |
0.602 (1.00) |
0.749 (1.00) |
0.701 (1.00) |
0.282 (1.00) |
15Q GAIN MUTATION ANALYSIS | 48 (20%) | 194 |
0.884 (1.00) |
0.712 (1.00) |
0.924 (1.00) |
0.599 (1.00) |
0.19 (1.00) |
0.336 (1.00) |
0.291 (1.00) |
0.544 (1.00) |
0.4 (1.00) |
0.626 (1.00) |
0.964 (1.00) |
1 (1.00) |
16P GAIN MUTATION ANALYSIS | 32 (13%) | 210 |
0.462 (1.00) |
0.726 (1.00) |
0.44 (1.00) |
0.617 (1.00) |
0.275 (1.00) |
0.0231 (1.00) |
0.00697 (1.00) |
0.43 (1.00) |
1 (1.00) |
0.389 (1.00) |
0.958 (1.00) |
0.698 (1.00) |
16Q GAIN MUTATION ANALYSIS | 26 (11%) | 216 |
0.276 (1.00) |
0.754 (1.00) |
0.6 (1.00) |
0.486 (1.00) |
0.368 (1.00) |
0.0633 (1.00) |
0.011 (1.00) |
0.379 (1.00) |
1 (1.00) |
0.217 (1.00) |
0.803 (1.00) |
1 (1.00) |
17P GAIN MUTATION ANALYSIS | 28 (12%) | 214 |
0.228 (1.00) |
0.386 (1.00) |
0.334 (1.00) |
0.646 (1.00) |
0.286 (1.00) |
0.828 (1.00) |
0.415 (1.00) |
0.379 (1.00) |
0.0354 (1.00) |
0.76 (1.00) |
0.873 (1.00) |
0.418 (1.00) |
17Q GAIN MUTATION ANALYSIS | 48 (20%) | 194 |
0.873 (1.00) |
0.951 (1.00) |
0.000996 (0.939) |
0.663 (1.00) |
0.148 (1.00) |
0.961 (1.00) |
0.304 (1.00) |
0.666 (1.00) |
0.225 (1.00) |
1 (1.00) |
0.904 (1.00) |
0.511 (1.00) |
18P GAIN MUTATION ANALYSIS | 38 (16%) | 204 |
0.488 (1.00) |
0.958 (1.00) |
0.48 (1.00) |
0.783 (1.00) |
0.00305 (1.00) |
0.149 (1.00) |
0.389 (1.00) |
0.021 (1.00) |
0.105 (1.00) |
0.794 (1.00) |
0.475 (1.00) |
0.151 (1.00) |
18Q GAIN MUTATION ANALYSIS | 33 (14%) | 209 |
0.725 (1.00) |
0.279 (1.00) |
0.497 (1.00) |
0.702 (1.00) |
0.000833 (0.786) |
0.113 (1.00) |
0.303 (1.00) |
0.529 (1.00) |
0.131 (1.00) |
0.575 (1.00) |
0.606 (1.00) |
0.255 (1.00) |
19P GAIN MUTATION ANALYSIS | 37 (15%) | 205 |
0.353 (1.00) |
0.273 (1.00) |
0.94 (1.00) |
0.696 (1.00) |
0.926 (1.00) |
0.852 (1.00) |
0.957 (1.00) |
0.431 (1.00) |
0.159 (1.00) |
0.423 (1.00) |
0.671 (1.00) |
0.207 (1.00) |
19Q GAIN MUTATION ANALYSIS | 40 (17%) | 202 |
0.495 (1.00) |
0.125 (1.00) |
0.571 (1.00) |
0.517 (1.00) |
0.971 (1.00) |
0.973 (1.00) |
0.646 (1.00) |
0.468 (1.00) |
0.172 (1.00) |
0.601 (1.00) |
0.602 (1.00) |
0.0761 (1.00) |
20P GAIN MUTATION ANALYSIS | 95 (39%) | 147 |
0.234 (1.00) |
0.627 (1.00) |
0.189 (1.00) |
0.806 (1.00) |
0.146 (1.00) |
0.108 (1.00) |
0.0593 (1.00) |
0.223 (1.00) |
0.241 (1.00) |
0.321 (1.00) |
0.0481 (1.00) |
0.687 (1.00) |
20Q GAIN MUTATION ANALYSIS | 117 (48%) | 125 |
0.924 (1.00) |
0.192 (1.00) |
0.0541 (1.00) |
0.319 (1.00) |
0.0583 (1.00) |
0.167 (1.00) |
0.271 (1.00) |
0.125 (1.00) |
0.408 (1.00) |
0.338 (1.00) |
0.0556 (1.00) |
1 (1.00) |
21Q GAIN MUTATION ANALYSIS | 43 (18%) | 199 |
0.826 (1.00) |
0.574 (1.00) |
0.661 (1.00) |
0.333 (1.00) |
0.0647 (1.00) |
0.417 (1.00) |
0.345 (1.00) |
0.488 (1.00) |
0.101 (1.00) |
0.616 (1.00) |
0.114 (1.00) |
0.732 (1.00) |
22Q GAIN MUTATION ANALYSIS | 83 (34%) | 159 |
0.302 (1.00) |
0.14 (1.00) |
0.711 (1.00) |
0.415 (1.00) |
0.47 (1.00) |
0.365 (1.00) |
0.237 (1.00) |
0.955 (1.00) |
0.603 (1.00) |
0.838 (1.00) |
0.296 (1.00) |
0.782 (1.00) |
XQ GAIN MUTATION ANALYSIS | 30 (12%) | 212 |
0.456 (1.00) |
0.578 (1.00) |
0.313 (1.00) |
0.335 (1.00) |
0.235 (1.00) |
0.678 (1.00) |
0.349 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.773 (1.00) |
0.448 (1.00) |
0.163 (1.00) |
1P LOSS MUTATION ANALYSIS | 33 (14%) | 209 |
0.219 (1.00) |
0.0405 (1.00) |
0.136 (1.00) |
0.762 (1.00) |
0.151 (1.00) |
0.497 (1.00) |
0.201 (1.00) |
0.864 (1.00) |
0.337 (1.00) |
0.392 (1.00) |
0.804 (1.00) |
1 (1.00) |
1Q LOSS MUTATION ANALYSIS | 15 (6%) | 227 |
0.35 (1.00) |
0.457 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.982 (1.00) |
0.602 (1.00) |
0.924 (1.00) |
0.755 (1.00) |
0.227 (1.00) |
0.357 (1.00) |
0.591 (1.00) |
2P LOSS MUTATION ANALYSIS | 29 (12%) | 213 |
0.908 (1.00) |
0.308 (1.00) |
0.876 (1.00) |
0.961 (1.00) |
0.583 (1.00) |
0.0695 (1.00) |
0.507 (1.00) |
0.418 (1.00) |
0.816 (1.00) |
0.547 (1.00) |
0.484 (1.00) |
0.315 (1.00) |
2Q LOSS MUTATION ANALYSIS | 28 (12%) | 214 |
0.153 (1.00) |
0.75 (1.00) |
0.774 (1.00) |
0.961 (1.00) |
0.743 (1.00) |
0.0892 (1.00) |
0.351 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.219 (1.00) |
0.681 (1.00) |
0.418 (1.00) |
3P LOSS MUTATION ANALYSIS | 36 (15%) | 206 |
0.297 (1.00) |
0.414 (1.00) |
0.562 (1.00) |
0.906 (1.00) |
0.663 (1.00) |
0.382 (1.00) |
0.404 (1.00) |
0.862 (1.00) |
0.634 (1.00) |
0.785 (1.00) |
0.208 (1.00) |
0.854 (1.00) |
3Q LOSS MUTATION ANALYSIS | 30 (12%) | 212 |
0.376 (1.00) |
0.375 (1.00) |
0.945 (1.00) |
0.855 (1.00) |
0.841 (1.00) |
0.0925 (1.00) |
0.415 (1.00) |
0.866 (1.00) |
0.314 (1.00) |
1 (1.00) |
0.253 (1.00) |
0.691 (1.00) |
4P LOSS MUTATION ANALYSIS | 45 (19%) | 197 |
0.936 (1.00) |
0.89 (1.00) |
0.34 (1.00) |
0.397 (1.00) |
0.283 (1.00) |
0.745 (1.00) |
0.625 (1.00) |
0.458 (1.00) |
0.428 (1.00) |
0.314 (1.00) |
0.0411 (1.00) |
0.0419 (1.00) |
4Q LOSS MUTATION ANALYSIS | 47 (19%) | 195 |
0.726 (1.00) |
0.785 (1.00) |
0.136 (1.00) |
0.526 (1.00) |
0.4 (1.00) |
0.51 (1.00) |
0.478 (1.00) |
0.0507 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.0255 (1.00) |
0.0191 (1.00) |
5P LOSS MUTATION ANALYSIS | 54 (22%) | 188 |
0.968 (1.00) |
0.976 (1.00) |
0.92 (1.00) |
0.766 (1.00) |
0.5 (1.00) |
0.226 (1.00) |
0.827 (1.00) |
0.46 (1.00) |
0.0541 (1.00) |
0.102 (1.00) |
0.562 (1.00) |
0.636 (1.00) |
5Q LOSS MUTATION ANALYSIS | 66 (27%) | 176 |
0.409 (1.00) |
0.797 (1.00) |
0.826 (1.00) |
0.743 (1.00) |
0.865 (1.00) |
0.106 (1.00) |
0.923 (1.00) |
0.682 (1.00) |
0.199 (1.00) |
0.389 (1.00) |
0.858 (1.00) |
0.769 (1.00) |
6P LOSS MUTATION ANALYSIS | 46 (19%) | 196 |
0.0348 (1.00) |
0.0718 (1.00) |
0.772 (1.00) |
0.731 (1.00) |
0.565 (1.00) |
0.509 (1.00) |
0.676 (1.00) |
0.854 (1.00) |
1 (1.00) |
1 (1.00) |
0.359 (1.00) |
0.867 (1.00) |
6Q LOSS MUTATION ANALYSIS | 116 (48%) | 126 |
0.379 (1.00) |
0.747 (1.00) |
0.264 (1.00) |
0.564 (1.00) |
0.792 (1.00) |
0.171 (1.00) |
0.509 (1.00) |
0.97 (1.00) |
1 (1.00) |
1 (1.00) |
0.0946 (1.00) |
0.429 (1.00) |
7P LOSS MUTATION ANALYSIS | 12 (5%) | 230 |
0.855 (1.00) |
0.942 (1.00) |
0.272 (1.00) |
0.326 (1.00) |
0.151 (1.00) |
0.0106 (1.00) |
0.344 (1.00) |
0.95 (1.00) |
1 (1.00) |
1 (1.00) |
0.648 (1.00) |
0.769 (1.00) |
7Q LOSS MUTATION ANALYSIS | 11 (5%) | 231 |
0.481 (1.00) |
0.935 (1.00) |
0.552 (1.00) |
0.234 (1.00) |
0.298 (1.00) |
0.37 (1.00) |
0.606 (1.00) |
0.957 (1.00) |
0.714 (1.00) |
1 (1.00) |
0.722 (1.00) |
1 (1.00) |
8P LOSS MUTATION ANALYSIS | 42 (17%) | 200 |
0.654 (1.00) |
0.441 (1.00) |
0.117 (1.00) |
0.428 (1.00) |
0.264 (1.00) |
0.111 (1.00) |
0.951 (1.00) |
0.413 (1.00) |
0.117 (1.00) |
0.616 (1.00) |
0.0904 (1.00) |
0.864 (1.00) |
8Q LOSS MUTATION ANALYSIS | 16 (7%) | 226 |
0.0297 (1.00) |
0.635 (1.00) |
0.364 (1.00) |
0.405 (1.00) |
0.627 (1.00) |
0.218 (1.00) |
0.91 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.232 (1.00) |
0.641 (1.00) |
0.187 (1.00) |
9P LOSS MUTATION ANALYSIS | 159 (66%) | 83 |
0.0545 (1.00) |
0.666 (1.00) |
0.954 (1.00) |
0.226 (1.00) |
0.544 (1.00) |
0.321 (1.00) |
0.766 (1.00) |
0.254 (1.00) |
0.302 (1.00) |
1 (1.00) |
0.946 (1.00) |
0.073 (1.00) |
9Q LOSS MUTATION ANALYSIS | 125 (52%) | 117 |
0.519 (1.00) |
0.412 (1.00) |
0.173 (1.00) |
0.219 (1.00) |
0.264 (1.00) |
0.747 (1.00) |
0.532 (1.00) |
0.393 (1.00) |
0.87 (1.00) |
0.241 (1.00) |
0.866 (1.00) |
0.048 (1.00) |
10P LOSS MUTATION ANALYSIS | 129 (53%) | 113 |
0.372 (1.00) |
0.95 (1.00) |
0.0208 (1.00) |
0.119 (1.00) |
0.828 (1.00) |
0.194 (1.00) |
0.564 (1.00) |
0.458 (1.00) |
0.186 (1.00) |
1 (1.00) |
0.443 (1.00) |
0.0174 (1.00) |
11P LOSS MUTATION ANALYSIS | 84 (35%) | 158 |
0.308 (1.00) |
0.496 (1.00) |
0.0824 (1.00) |
0.574 (1.00) |
0.76 (1.00) |
0.962 (1.00) |
0.176 (1.00) |
0.609 (1.00) |
0.173 (1.00) |
0.414 (1.00) |
0.624 (1.00) |
0.00355 (1.00) |
11Q LOSS MUTATION ANALYSIS | 94 (39%) | 148 |
0.945 (1.00) |
0.777 (1.00) |
0.624 (1.00) |
0.877 (1.00) |
0.44 (1.00) |
0.982 (1.00) |
0.0923 (1.00) |
0.669 (1.00) |
0.0126 (1.00) |
0.554 (1.00) |
0.925 (1.00) |
0.000462 (0.437) |
12P LOSS MUTATION ANALYSIS | 34 (14%) | 208 |
0.955 (1.00) |
0.539 (1.00) |
0.53 (1.00) |
0.312 (1.00) |
0.869 (1.00) |
0.865 (1.00) |
0.99 (1.00) |
0.0503 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.0758 (1.00) |
0.347 (1.00) |
12Q LOSS MUTATION ANALYSIS | 41 (17%) | 201 |
0.548 (1.00) |
0.888 (1.00) |
0.93 (1.00) |
0.223 (1.00) |
0.867 (1.00) |
0.87 (1.00) |
0.524 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.11 (1.00) |
0.38 (1.00) |
13Q LOSS MUTATION ANALYSIS | 50 (21%) | 192 |
0.981 (1.00) |
0.486 (1.00) |
0.298 (1.00) |
0.49 (1.00) |
0.401 (1.00) |
0.077 (1.00) |
0.49 (1.00) |
0.00709 (1.00) |
0.438 (1.00) |
0.639 (1.00) |
0.0079 (1.00) |
0.629 (1.00) |
14Q LOSS MUTATION ANALYSIS | 73 (30%) | 169 |
0.634 (1.00) |
0.998 (1.00) |
0.181 (1.00) |
0.304 (1.00) |
0.378 (1.00) |
0.515 (1.00) |
0.581 (1.00) |
0.332 (1.00) |
0.721 (1.00) |
0.676 (1.00) |
0.385 (1.00) |
0.252 (1.00) |
15Q LOSS MUTATION ANALYSIS | 31 (13%) | 211 |
0.344 (1.00) |
0.714 (1.00) |
0.676 (1.00) |
0.27 (1.00) |
0.352 (1.00) |
0.0236 (1.00) |
0.328 (1.00) |
0.413 (1.00) |
0.807 (1.00) |
0.776 (1.00) |
0.105 (1.00) |
0.555 (1.00) |
16P LOSS MUTATION ANALYSIS | 46 (19%) | 196 |
0.901 (1.00) |
0.433 (1.00) |
0.0948 (1.00) |
0.437 (1.00) |
0.687 (1.00) |
0.627 (1.00) |
0.704 (1.00) |
0.533 (1.00) |
0.839 (1.00) |
0.468 (1.00) |
0.262 (1.00) |
0.0113 (1.00) |
16Q LOSS MUTATION ANALYSIS | 69 (29%) | 173 |
0.579 (1.00) |
0.214 (1.00) |
0.114 (1.00) |
0.302 (1.00) |
0.0513 (1.00) |
0.244 (1.00) |
0.637 (1.00) |
0.788 (1.00) |
0.594 (1.00) |
0.666 (1.00) |
0.353 (1.00) |
0.0284 (1.00) |
17P LOSS MUTATION ANALYSIS | 86 (36%) | 156 |
0.233 (1.00) |
0.184 (1.00) |
0.139 (1.00) |
0.0974 (1.00) |
0.429 (1.00) |
0.937 (1.00) |
0.972 (1.00) |
0.64 (1.00) |
0.612 (1.00) |
0.841 (1.00) |
0.248 (1.00) |
0.217 (1.00) |
17Q LOSS MUTATION ANALYSIS | 43 (18%) | 199 |
0.217 (1.00) |
0.029 (1.00) |
0.696 (1.00) |
0.569 (1.00) |
0.316 (1.00) |
0.976 (1.00) |
0.496 (1.00) |
0.079 (1.00) |
1 (1.00) |
1 (1.00) |
0.56 (1.00) |
0.39 (1.00) |
18P LOSS MUTATION ANALYSIS | 68 (28%) | 174 |
0.277 (1.00) |
0.291 (1.00) |
0.815 (1.00) |
0.861 (1.00) |
0.109 (1.00) |
0.846 (1.00) |
0.766 (1.00) |
0.295 (1.00) |
0.574 (1.00) |
0.282 (1.00) |
0.779 (1.00) |
1 (1.00) |
18Q LOSS MUTATION ANALYSIS | 62 (26%) | 180 |
0.372 (1.00) |
0.152 (1.00) |
0.771 (1.00) |
0.88 (1.00) |
0.104 (1.00) |
0.822 (1.00) |
0.388 (1.00) |
0.38 (1.00) |
0.706 (1.00) |
0.655 (1.00) |
0.598 (1.00) |
0.764 (1.00) |
19P LOSS MUTATION ANALYSIS | 47 (19%) | 195 |
0.487 (1.00) |
0.755 (1.00) |
0.781 (1.00) |
0.452 (1.00) |
0.326 (1.00) |
0.384 (1.00) |
0.708 (1.00) |
0.075 (1.00) |
0.533 (1.00) |
0.809 (1.00) |
0.25 (1.00) |
0.0319 (1.00) |
19Q LOSS MUTATION ANALYSIS | 48 (20%) | 194 |
0.97 (1.00) |
0.803 (1.00) |
0.742 (1.00) |
0.599 (1.00) |
0.663 (1.00) |
0.285 (1.00) |
0.822 (1.00) |
0.0661 (1.00) |
0.836 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.0484 (1.00) |
20P LOSS MUTATION ANALYSIS | 15 (6%) | 227 |
0.778 (1.00) |
0.997 (1.00) |
0.322 (1.00) |
0.252 (1.00) |
0.98 (1.00) |
1 (1.00) |
0.332 (1.00) |
0.15 (1.00) |
0.485 (1.00) |
0.409 (1.00) |
0.808 (1.00) |
0.787 (1.00) |
20Q LOSS MUTATION ANALYSIS | 4 (2%) | 238 |
0.779 (1.00) |
0.715 (1.00) |
0.93 (1.00) |
0.176 (1.00) |
0.57 (1.00) |
0.684 (1.00) |
0.238 (1.00) |
0.994 (1.00) |
1 (1.00) |
0.413 (1.00) |
0.712 (1.00) |
0.157 (1.00) |
21Q LOSS MUTATION ANALYSIS | 50 (21%) | 192 |
0.704 (1.00) |
0.888 (1.00) |
0.379 (1.00) |
0.465 (1.00) |
0.412 (1.00) |
0.875 (1.00) |
0.506 (1.00) |
0.497 (1.00) |
0.548 (1.00) |
0.152 (1.00) |
0.215 (1.00) |
0.104 (1.00) |
22Q LOSS MUTATION ANALYSIS | 26 (11%) | 216 |
0.435 (1.00) |
0.386 (1.00) |
0.417 (1.00) |
0.623 (1.00) |
0.249 (1.00) |
0.387 (1.00) |
0.298 (1.00) |
0.365 (1.00) |
0.282 (1.00) |
1 (1.00) |
0.193 (1.00) |
1 (1.00) |
XQ LOSS MUTATION ANALYSIS | 68 (28%) | 174 |
0.312 (1.00) |
0.82 (1.00) |
0.922 (1.00) |
0.176 (1.00) |
0.0445 (1.00) |
0.267 (1.00) |
0.162 (1.00) |
0.00744 (1.00) |
0.466 (1.00) |
0.192 (1.00) |
0.494 (1.00) |
0.00828 (1.00) |
P value = 0.000158 (t-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 181 | 3.6 (5.2) |
5Q GAIN MUTATED | 18 | 1.6 (1.4) |
5Q GAIN WILD-TYPE | 163 | 3.8 (5.4) |
P value = 0.000247 (t-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 238 | 55.5 (15.9) |
10Q LOSS MUTATED | 141 | 52.5 (16.3) |
10Q LOSS WILD-TYPE | 97 | 59.9 (14.2) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = SKCM-TM.clin.merged.picked.txt
-
Number of patients = 242
-
Number of significantly arm-level cnvs = 79
-
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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.