This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 50 focal events and 10 clinical features across 134 patients, 9 significant findings detected with Q value < 0.25.
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del_10p15.3 cnv correlated to 'YEARS_TO_BIRTH'.
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del_10q23.1 cnv correlated to 'YEARS_TO_BIRTH'.
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del_10q26.3 cnv correlated to 'YEARS_TO_BIRTH'.
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del_19q13.33 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'RADIATION_THERAPY'.
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del_19q13.42 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'RADIATION_THERAPY'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
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 | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 19q13 33 | 47 (35%) | 87 |
0.152 (0.84) |
0.000526 (0.0458) |
0.00053 (0.0458) |
0.372 (0.965) |
0.128 (0.84) |
0.619 (1.00) |
3.99e-05 (0.0193) |
0.482 (0.993) |
0.765 (1.00) |
1 (1.00) |
del 19q13 42 | 46 (34%) | 88 |
0.143 (0.84) |
0.000278 (0.0458) |
0.00055 (0.0458) |
0.299 (0.965) |
0.128 (0.84) |
0.613 (1.00) |
7.74e-05 (0.0193) |
0.616 (1.00) |
0.768 (1.00) |
1 (1.00) |
del 10p15 3 | 72 (54%) | 62 |
0.531 (1.00) |
0.00228 (0.143) |
0.16 (0.84) |
0.494 (1.00) |
0.203 (0.921) |
0.125 (0.84) |
0.0541 (0.731) |
0.0365 (0.677) |
0.0524 (0.731) |
0.766 (1.00) |
del 10q23 1 | 62 (46%) | 72 |
0.294 (0.965) |
0.00195 (0.139) |
0.0683 (0.821) |
0.293 (0.965) |
0.0303 (0.677) |
0.328 (0.965) |
0.0315 (0.677) |
0.0719 (0.821) |
0.471 (0.993) |
0.139 (0.84) |
del 10q26 3 | 66 (49%) | 68 |
0.33 (0.965) |
0.0043 (0.239) |
0.0181 (0.565) |
0.371 (0.965) |
0.0262 (0.677) |
0.364 (0.965) |
0.152 (0.84) |
0.0333 (0.677) |
0.785 (1.00) |
0.363 (0.965) |
amp 1q21 2 | 63 (47%) | 71 |
0.909 (1.00) |
0.163 (0.84) |
0.625 (1.00) |
0.954 (1.00) |
0.532 (1.00) |
0.619 (1.00) |
0.347 (0.965) |
0.933 (1.00) |
0.267 (0.965) |
0.0678 (0.821) |
amp 2p24 1 | 53 (40%) | 81 |
0.671 (1.00) |
0.888 (1.00) |
0.923 (1.00) |
0.261 (0.965) |
0.351 (0.965) |
0.64 (1.00) |
0.468 (0.993) |
0.142 (0.84) |
0.673 (1.00) |
0.364 (0.965) |
amp 3p13 | 30 (22%) | 104 |
0.356 (0.965) |
0.323 (0.965) |
0.98 (1.00) |
0.767 (1.00) |
1 (1.00) |
0.207 (0.934) |
0.782 (1.00) |
0.971 (1.00) |
0.473 (0.993) |
0.296 (0.965) |
amp 3q27 3 | 41 (31%) | 93 |
0.858 (1.00) |
0.772 (1.00) |
0.754 (1.00) |
0.11 (0.84) |
1 (1.00) |
0.583 (1.00) |
0.608 (1.00) |
0.504 (1.00) |
0.483 (0.993) |
0.344 (0.965) |
amp 4q12 | 19 (14%) | 115 |
0.387 (0.977) |
0.274 (0.965) |
0.554 (1.00) |
0.917 (1.00) |
1 (1.00) |
1 (1.00) |
0.165 (0.84) |
0.855 (1.00) |
1 (1.00) |
1 (1.00) |
amp 7p22 1 | 116 (87%) | 18 |
0.603 (1.00) |
0.581 (1.00) |
0.712 (1.00) |
0.834 (1.00) |
0.668 (1.00) |
0.421 (0.993) |
0.487 (0.998) |
0.864 (1.00) |
0.392 (0.986) |
0.164 (0.84) |
amp 7q11 22 | 110 (82%) | 24 |
0.735 (1.00) |
0.665 (1.00) |
0.337 (0.965) |
0.265 (0.965) |
1 (1.00) |
0.545 (1.00) |
1 (1.00) |
0.468 (0.993) |
0.816 (1.00) |
0.123 (0.84) |
amp 8q11 23 | 114 (85%) | 20 |
0.355 (0.965) |
0.923 (1.00) |
0.45 (0.993) |
0.702 (1.00) |
0.668 (1.00) |
0.0869 (0.837) |
0.196 (0.911) |
0.327 (0.965) |
0.298 (0.965) |
0.655 (1.00) |
amp 8q23 3 | 101 (75%) | 33 |
0.254 (0.965) |
0.573 (1.00) |
0.149 (0.84) |
0.287 (0.965) |
0.713 (1.00) |
0.221 (0.965) |
0.0994 (0.84) |
0.179 (0.878) |
0.846 (1.00) |
0.467 (0.993) |
amp 12p13 33 | 129 (96%) | 5 |
0.745 (1.00) |
0.577 (1.00) |
0.419 (0.993) |
0.72 (1.00) |
1 (1.00) |
0.179 (0.878) |
0.652 (1.00) |
1 (1.00) |
1 (1.00) |
|
amp 12p12 1 | 131 (98%) | 3 |
0.791 (1.00) |
0.552 (1.00) |
0.305 (0.965) |
1 (1.00) |
1 (1.00) |
0.408 (0.993) |
1 (1.00) |
1 (1.00) |
||
amp 12p11 21 | 128 (96%) | 6 |
0.714 (1.00) |
0.651 (1.00) |
0.897 (1.00) |
0.764 (1.00) |
1 (1.00) |
0.243 (0.965) |
0.398 (0.99) |
1 (1.00) |
0.407 (0.993) |
|
amp 12q15 | 90 (67%) | 44 |
0.551 (1.00) |
0.0233 (0.677) |
0.473 (0.993) |
0.659 (1.00) |
0.481 (0.993) |
1 (1.00) |
0.313 (0.965) |
0.483 (0.993) |
0.57 (1.00) |
0.517 (1.00) |
amp 16q21 | 19 (14%) | 115 |
0.349 (0.965) |
0.371 (0.965) |
0.306 (0.965) |
0.296 (0.965) |
1 (1.00) |
0.465 (0.993) |
0.737 (1.00) |
0.855 (1.00) |
1 (1.00) |
0.062 (0.795) |
amp 20q11 21 | 41 (31%) | 93 |
0.546 (1.00) |
0.173 (0.865) |
0.0303 (0.677) |
0.0118 (0.49) |
0.481 (0.993) |
0.307 (0.965) |
0.0777 (0.823) |
0.373 (0.965) |
0.482 (0.993) |
1 (1.00) |
amp 22q11 21 | 54 (40%) | 80 |
0.858 (1.00) |
0.101 (0.84) |
0.0762 (0.823) |
0.909 (1.00) |
0.152 (0.84) |
0.152 (0.84) |
0.0136 (0.524) |
0.134 (0.84) |
0.781 (1.00) |
0.539 (1.00) |
del 1p36 31 | 29 (22%) | 105 |
0.0435 (0.705) |
0.781 (1.00) |
0.118 (0.84) |
0.869 (1.00) |
1 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.641 (1.00) |
0.692 (1.00) |
0.0564 (0.742) |
del 1p31 1 | 26 (19%) | 108 |
0.0284 (0.677) |
0.811 (1.00) |
0.68 (1.00) |
0.607 (1.00) |
0.712 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.0871 (0.837) |
0.423 (0.993) |
1 (1.00) |
del 1q42 12 | 9 (7%) | 125 |
0.0533 (0.731) |
0.522 (1.00) |
0.379 (0.971) |
0.45 (0.993) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.149 (0.84) |
0.079 (0.823) |
0.522 (1.00) |
del 2q37 3 | 13 (10%) | 121 |
0.137 (0.84) |
0.609 (1.00) |
0.708 (1.00) |
0.431 (0.993) |
0.643 (1.00) |
1 (1.00) |
0.69 (1.00) |
0.111 (0.84) |
0.0159 (0.565) |
0.0945 (0.84) |
del 3p26 2 | 40 (30%) | 94 |
0.652 (1.00) |
0.344 (0.965) |
0.338 (0.965) |
0.0523 (0.731) |
0.509 (1.00) |
0.322 (0.965) |
0.611 (1.00) |
0.767 (1.00) |
0.298 (0.965) |
0.752 (1.00) |
del 4q22 2 | 100 (75%) | 34 |
0.302 (0.965) |
0.119 (0.84) |
0.317 (0.965) |
0.0698 (0.821) |
0.026 (0.677) |
1 (1.00) |
0.419 (0.993) |
0.364 (0.965) |
0.352 (0.965) |
0.732 (1.00) |
del 5p15 2 | 91 (68%) | 43 |
0.997 (1.00) |
0.694 (1.00) |
0.333 (0.965) |
0.118 (0.84) |
1 (1.00) |
0.592 (1.00) |
0.454 (0.993) |
0.269 (0.965) |
0.566 (1.00) |
0.517 (1.00) |
del 5p14 3 | 93 (69%) | 41 |
0.951 (1.00) |
0.841 (1.00) |
0.453 (0.993) |
0.0384 (0.686) |
1 (1.00) |
0.583 (1.00) |
0.303 (0.965) |
0.482 (0.993) |
0.645 (1.00) |
0.752 (1.00) |
del 5q12 1 | 95 (71%) | 39 |
0.898 (1.00) |
0.571 (1.00) |
0.131 (0.84) |
0.00576 (0.288) |
0.738 (1.00) |
0.58 (1.00) |
0.0366 (0.677) |
0.197 (0.911) |
0.644 (1.00) |
0.745 (1.00) |
del 6p22 3 | 19 (14%) | 115 |
0.91 (1.00) |
0.326 (0.965) |
0.66 (1.00) |
0.62 (1.00) |
0.668 (1.00) |
0.465 (0.993) |
0.0422 (0.705) |
0.872 (1.00) |
0.779 (1.00) |
0.671 (1.00) |
del 6q26 | 22 (16%) | 112 |
0.338 (0.965) |
0.0732 (0.821) |
0.11 (0.84) |
0.661 (1.00) |
1 (1.00) |
0.131 (0.84) |
0.525 (1.00) |
0.958 (1.00) |
1 (1.00) |
0.688 (1.00) |
del 7q11 22 | 3 (2%) | 131 |
0.777 (1.00) |
0.94 (1.00) |
0.799 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.535 (1.00) |
1 (1.00) |
0.267 (0.965) |
|
del 7q35 | 12 (9%) | 122 |
0.575 (1.00) |
0.305 (0.965) |
0.554 (1.00) |
0.866 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.284 (0.965) |
1 (1.00) |
0.0172 (0.565) |
del 9p24 3 | 63 (47%) | 71 |
0.962 (1.00) |
0.592 (1.00) |
0.224 (0.965) |
0.955 (1.00) |
0.54 (1.00) |
0.348 (0.965) |
0.157 (0.84) |
0.933 (1.00) |
0.694 (1.00) |
1 (1.00) |
del 9p23 | 59 (44%) | 75 |
0.879 (1.00) |
0.686 (1.00) |
0.232 (0.965) |
0.831 (1.00) |
1 (1.00) |
0.322 (0.965) |
0.0935 (0.84) |
0.902 (1.00) |
0.598 (1.00) |
0.766 (1.00) |
del 9q33 3 | 52 (39%) | 82 |
0.173 (0.865) |
0.551 (1.00) |
0.403 (0.993) |
0.675 (1.00) |
0.755 (1.00) |
0.64 (1.00) |
1 (1.00) |
0.241 (0.965) |
0.449 (0.993) |
0.364 (0.965) |
del 9q34 2 | 52 (39%) | 82 |
0.252 (0.965) |
0.377 (0.97) |
0.422 (0.993) |
0.679 (1.00) |
0.755 (1.00) |
0.64 (1.00) |
1 (1.00) |
0.319 (0.965) |
0.447 (0.993) |
0.124 (0.84) |
del 11p15 5 | 85 (63%) | 49 |
0.861 (1.00) |
0.248 (0.965) |
0.895 (1.00) |
0.709 (1.00) |
0.184 (0.879) |
1 (1.00) |
0.225 (0.965) |
0.361 (0.965) |
0.763 (1.00) |
0.75 (1.00) |
del 11p12 | 90 (67%) | 44 |
0.625 (1.00) |
0.211 (0.94) |
0.989 (1.00) |
0.403 (0.993) |
0.0838 (0.837) |
1 (1.00) |
0.0739 (0.821) |
0.483 (0.993) |
0.656 (1.00) |
0.753 (1.00) |
del 11q12 3 | 104 (78%) | 30 |
0.934 (1.00) |
0.371 (0.965) |
0.997 (1.00) |
0.273 (0.965) |
0.159 (0.84) |
1 (1.00) |
0.0437 (0.705) |
0.356 (0.965) |
0.147 (0.84) |
0.708 (1.00) |
del 11q24 3 | 110 (82%) | 24 |
0.469 (0.993) |
0.587 (1.00) |
0.791 (1.00) |
0.457 (0.993) |
0.1 (0.84) |
1 (1.00) |
0.121 (0.84) |
0.129 (0.84) |
0.00777 (0.353) |
0.381 (0.973) |
del 13q34 | 102 (76%) | 32 |
0.313 (0.965) |
0.181 (0.879) |
0.642 (1.00) |
0.163 (0.84) |
0.159 (0.84) |
1 (1.00) |
0.102 (0.84) |
0.873 (1.00) |
0.331 (0.965) |
0.73 (1.00) |
del 16q23 1 | 61 (46%) | 73 |
0.105 (0.84) |
0.663 (1.00) |
0.506 (1.00) |
0.292 (0.965) |
1 (1.00) |
0.123 (0.84) |
0.0541 (0.731) |
0.795 (1.00) |
0.688 (1.00) |
1 (1.00) |
del 16q23 3 | 62 (46%) | 72 |
0.638 (1.00) |
0.425 (0.993) |
0.368 (0.965) |
0.691 (1.00) |
0.755 (1.00) |
0.123 (0.84) |
0.153 (0.84) |
0.795 (1.00) |
0.779 (1.00) |
1 (1.00) |
del 18p11 32 | 106 (79%) | 28 |
0.386 (0.977) |
0.257 (0.965) |
0.446 (0.993) |
0.228 (0.965) |
0.426 (0.993) |
1 (1.00) |
1 (1.00) |
0.252 (0.965) |
0.673 (1.00) |
1 (1.00) |
del 18q22 3 | 113 (84%) | 21 |
0.453 (0.993) |
0.258 (0.965) |
0.445 (0.993) |
0.083 (0.837) |
0.671 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.48 (0.993) |
0.783 (1.00) |
1 (1.00) |
del 20p12 1 | 27 (20%) | 107 |
0.291 (0.965) |
0.896 (1.00) |
0.337 (0.965) |
0.576 (1.00) |
0.113 (0.84) |
0.194 (0.911) |
0.565 (1.00) |
0.506 (1.00) |
0.573 (1.00) |
0.716 (1.00) |
del xp21 1 | 23 (17%) | 111 |
0.325 (0.965) |
0.763 (1.00) |
0.527 (1.00) |
0.202 (0.921) |
0.185 (0.879) |
1 (1.00) |
0.529 (1.00) |
0.308 (0.965) |
0.0503 (0.731) |
0.411 (0.993) |
del xq27 3 | 25 (19%) | 109 |
0.296 (0.965) |
0.293 (0.965) |
0.0341 (0.677) |
0.398 (0.99) |
0.426 (0.993) |
0.564 (1.00) |
0.549 (1.00) |
0.829 (1.00) |
0.826 (1.00) |
0.235 (0.965) |
P value = 0.00228 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
DEL PEAK 18(10P15.3) MUTATED | 72 | 29.8 (8.6) |
DEL PEAK 18(10P15.3) WILD-TYPE | 62 | 34.5 (9.5) |
P value = 0.00195 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
DEL PEAK 19(10Q23.1) MUTATED | 62 | 29.6 (8.9) |
DEL PEAK 19(10Q23.1) WILD-TYPE | 72 | 34.0 (9.2) |
P value = 0.0043 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
DEL PEAK 20(10Q26.3) MUTATED | 66 | 29.8 (8.8) |
DEL PEAK 20(10Q26.3) WILD-TYPE | 68 | 34.1 (9.4) |
P value = 0.000526 (Wilcoxon-test), Q value = 0.046
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
DEL PEAK 30(19Q13.33) MUTATED | 47 | 28.8 (9.5) |
DEL PEAK 30(19Q13.33) WILD-TYPE | 87 | 33.7 (8.8) |
P value = 0.00053 (Fisher's exact test), Q value = 0.046
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
DEL PEAK 30(19Q13.33) MUTATED | 19 | 2 | 3 | 3 | 4 | 4 | 0 | 0 | 1 | 0 | 4 | 3 |
DEL PEAK 30(19Q13.33) WILD-TYPE | 27 | 16 | 23 | 8 | 0 | 2 | 1 | 1 | 1 | 1 | 2 | 2 |
P value = 3.99e-05 (Fisher's exact test), Q value = 0.019
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
DEL PEAK 30(19Q13.33) MUTATED | 47 | 0 |
DEL PEAK 30(19Q13.33) WILD-TYPE | 64 | 21 |
P value = 0.000278 (Wilcoxon-test), Q value = 0.046
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
DEL PEAK 31(19Q13.42) MUTATED | 46 | 28.7 (9.6) |
DEL PEAK 31(19Q13.42) WILD-TYPE | 88 | 33.7 (8.7) |
P value = 0.00055 (Fisher's exact test), Q value = 0.046
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
DEL PEAK 31(19Q13.42) MUTATED | 18 | 2 | 3 | 3 | 4 | 4 | 0 | 0 | 1 | 0 | 4 | 3 |
DEL PEAK 31(19Q13.42) WILD-TYPE | 28 | 16 | 23 | 8 | 0 | 2 | 1 | 1 | 1 | 1 | 2 | 2 |
P value = 7.74e-05 (Fisher's exact test), Q value = 0.019
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
DEL PEAK 31(19Q13.42) MUTATED | 46 | 0 |
DEL PEAK 31(19Q13.42) WILD-TYPE | 65 | 21 |
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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/TGCT-TP/22533662/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/TGCT-TP/22507091/TGCT-TP.merged_data.txt
-
Number of patients = 134
-
Number of significantly focal cnvs = 50
-
Number of selected clinical features = 10
-
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.