This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 30 focal events and 15 clinical features across 484 patients, 12 significant findings detected with Q value < 0.25.
-
del_2p23.1 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
del_2q35 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
del_8p23.2 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
del_8p22 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
del_8p12 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
del_8q24.22 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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del_9q21.13 cnv correlated to 'NEOPLASM.DISEASESTAGE'.
-
del_11p15.1 cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.
-
del_18q22.2 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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del_xq22.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
RADIATIONEXPOSURE |
EXTRATHYROIDAL EXTENSION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
MULTIFOCALITY |
TUMOR SIZE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Chi-square 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 | t-test | Fisher's exact test | t-test | |
del 11p15 1 | 7 (1%) | 477 |
0.00126 (0.544) |
0.000522 (0.228) |
1.47e-07 (6.47e-05) |
0.228 (1.00) |
0.449 (1.00) |
0.0964 (1.00) |
0.0164 (1.00) |
0.822 (1.00) |
0.187 (1.00) |
1 (1.00) |
0.545 (1.00) |
0.526 (1.00) |
0.0813 (1.00) |
0.709 (1.00) |
0.0356 (1.00) |
del xq22 3 | 4 (1%) | 480 |
0.753 (1.00) |
0.084 (1.00) |
1.61e-06 (0.000708) |
0.0583 (1.00) |
0.123 (1.00) |
0.107 (1.00) |
0.0598 (1.00) |
1 (1.00) |
1 (1.00) |
0.116 (1.00) |
0.639 (1.00) |
0.313 (1.00) |
1.35e-25 (6.01e-23) |
1 (1.00) |
0.887 (1.00) |
del 2p23 1 | 12 (2%) | 472 |
0.694 (1.00) |
0.677 (1.00) |
0.015 (1.00) |
0.892 (1.00) |
0.0201 (1.00) |
0.0247 (1.00) |
0.529 (1.00) |
0.00397 (1.00) |
1 (1.00) |
1 (1.00) |
0.0824 (1.00) |
0.536 (1.00) |
2.7e-09 (1.19e-06) |
1 (1.00) |
0.859 (1.00) |
del 2q35 | 12 (2%) | 472 |
0.259 (1.00) |
0.135 (1.00) |
0.000707 (0.307) |
0.647 (1.00) |
0.00732 (1.00) |
0.0247 (1.00) |
0.529 (1.00) |
0.0229 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.292 (1.00) |
0.271 (1.00) |
1.23e-25 (5.51e-23) |
0.779 (1.00) |
0.117 (1.00) |
del 8p23 2 | 4 (1%) | 480 |
0.872 (1.00) |
0.981 (1.00) |
0.189 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.374 (1.00) |
0.0598 (1.00) |
0.463 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
1.35e-25 (6.01e-23) |
1 (1.00) |
0.89 (1.00) |
del 8p22 | 4 (1%) | 480 |
0.872 (1.00) |
0.981 (1.00) |
0.189 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.374 (1.00) |
0.0598 (1.00) |
0.463 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
1.35e-25 (6.01e-23) |
1 (1.00) |
0.89 (1.00) |
del 8p12 | 4 (1%) | 480 |
0.872 (1.00) |
0.981 (1.00) |
0.189 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.374 (1.00) |
0.0598 (1.00) |
0.463 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
1.35e-25 (6.01e-23) |
1 (1.00) |
0.89 (1.00) |
del 8q24 22 | 7 (1%) | 477 |
0.843 (1.00) |
0.39 (1.00) |
0.104 (1.00) |
0.79 (1.00) |
0.0611 (1.00) |
0.741 (1.00) |
0.0164 (1.00) |
0.154 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.526 (1.00) |
1.32e-25 (5.89e-23) |
1 (1.00) |
0.342 (1.00) |
del 9q21 13 | 22 (5%) | 462 |
0.0288 (1.00) |
0.0221 (1.00) |
1.28e-09 (5.64e-07) |
0.191 (1.00) |
0.64 (1.00) |
0.0151 (1.00) |
0.324 (1.00) |
0.711 (1.00) |
0.483 (1.00) |
0.585 (1.00) |
0.0671 (1.00) |
0.572 (1.00) |
0.239 (1.00) |
0.666 (1.00) |
0.113 (1.00) |
del 18q22 2 | 5 (1%) | 479 |
0.708 (1.00) |
0.27 (1.00) |
0.312 (1.00) |
0.187 (1.00) |
0.623 (1.00) |
0.689 (1.00) |
1 (1.00) |
0.569 (1.00) |
1 (1.00) |
1 (1.00) |
0.442 (1.00) |
1 (1.00) |
7.2e-05 (0.0315) |
0.38 (1.00) |
0.305 (1.00) |
amp xq22 3 | 15 (3%) | 469 |
0.121 (1.00) |
0.339 (1.00) |
0.0101 (1.00) |
0.566 (1.00) |
0.416 (1.00) |
0.699 (1.00) |
0.0147 (1.00) |
0.534 (1.00) |
1 (1.00) |
1 (1.00) |
0.0132 (1.00) |
0.791 (1.00) |
0.948 (1.00) |
0.303 (1.00) |
0.668 (1.00) |
del 1q24 2 | 3 (1%) | 481 |
0.605 (1.00) |
0.872 (1.00) |
0.802 (1.00) |
0.806 (1.00) |
0.499 (1.00) |
0.135 (1.00) |
0.568 (1.00) |
0.233 (1.00) |
1 (1.00) |
1 (1.00) |
0.608 (1.00) |
1 (1.00) |
1 (1.00) |
0.177 (1.00) |
|
del 5p15 2 | 4 (1%) | 480 |
0.894 (1.00) |
0.243 (1.00) |
0.739 (1.00) |
0.629 (1.00) |
0.372 (1.00) |
0.197 (1.00) |
0.578 (1.00) |
0.0297 (1.00) |
1 (1.00) |
1 (1.00) |
0.411 (1.00) |
0.0694 (1.00) |
0.184 (1.00) |
0.34 (1.00) |
0.278 (1.00) |
del 6q22 31 | 7 (1%) | 477 |
0.00817 (1.00) |
0.123 (1.00) |
0.365 (1.00) |
0.79 (1.00) |
0.372 (1.00) |
0.0097 (1.00) |
0.39 (1.00) |
0.822 (1.00) |
0.187 (1.00) |
0.218 (1.00) |
0.383 (1.00) |
0.755 (1.00) |
0.00208 (0.894) |
0.459 (1.00) |
0.0166 (1.00) |
del 7q34 | 4 (1%) | 480 |
0.747 (1.00) |
0.82 (1.00) |
0.793 (1.00) |
0.554 (1.00) |
0.623 (1.00) |
1 (1.00) |
1 (1.00) |
0.124 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.231 (1.00) |
0.628 (1.00) |
0.189 (1.00) |
del 10q21 2 | 12 (2%) | 472 |
0.512 (1.00) |
0.782 (1.00) |
0.975 (1.00) |
0.733 (1.00) |
0.338 (1.00) |
0.509 (1.00) |
0.529 (1.00) |
0.558 (1.00) |
0.3 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.492 (1.00) |
0.761 (1.00) |
0.081 (1.00) |
del 10q23 31 | 12 (2%) | 472 |
0.508 (1.00) |
0.123 (1.00) |
0.0217 (1.00) |
0.78 (1.00) |
0.0201 (1.00) |
0.0717 (1.00) |
0.318 (1.00) |
0.341 (1.00) |
1 (1.00) |
1 (1.00) |
0.696 (1.00) |
0.624 (1.00) |
0.00131 (0.563) |
1 (1.00) |
0.00954 (1.00) |
del 13q12 3 | 16 (3%) | 468 |
0.625 (1.00) |
0.00257 (1.00) |
0.22 (1.00) |
0.569 (1.00) |
0.0875 (1.00) |
0.129 (1.00) |
0.148 (1.00) |
0.53 (1.00) |
0.379 (1.00) |
0.00184 (0.791) |
0.767 (1.00) |
0.791 (1.00) |
0.0629 (1.00) |
0.803 (1.00) |
0.308 (1.00) |
del 13q21 31 | 18 (4%) | 466 |
0.637 (1.00) |
0.0753 (1.00) |
0.886 (1.00) |
0.782 (1.00) |
0.0321 (1.00) |
0.305 (1.00) |
0.276 (1.00) |
0.611 (1.00) |
0.0913 (1.00) |
0.00239 (1.00) |
0.567 (1.00) |
0.655 (1.00) |
0.000607 (0.264) |
0.475 (1.00) |
0.498 (1.00) |
del 15q25 3 | 9 (2%) | 475 |
0.557 (1.00) |
0.804 (1.00) |
0.316 (1.00) |
0.529 (1.00) |
0.0678 (1.00) |
0.0423 (1.00) |
0.456 (1.00) |
0.0907 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.251 (1.00) |
1 (1.00) |
0.195 (1.00) |
del 16q23 3 | 6 (1%) | 478 |
0.0862 (1.00) |
0.03 (1.00) |
0.000576 (0.251) |
0.0148 (1.00) |
0.449 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.17 (1.00) |
1 (1.00) |
0.218 (1.00) |
0.0582 (1.00) |
0.0721 (1.00) |
0.46 (1.00) |
1 (1.00) |
0.469 (1.00) |
del 17p13 1 | 7 (1%) | 477 |
0.589 (1.00) |
0.68 (1.00) |
0.527 (1.00) |
0.14 (1.00) |
0.449 (1.00) |
0.342 (1.00) |
0.681 (1.00) |
0.154 (1.00) |
0.015 (1.00) |
0.25 (1.00) |
0.183 (1.00) |
0.755 (1.00) |
0.932 (1.00) |
1 (1.00) |
0.0926 (1.00) |
del 18p11 21 | 4 (1%) | 480 |
0.759 (1.00) |
0.543 (1.00) |
0.189 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.374 (1.00) |
1 (1.00) |
0.463 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.00208 (0.894) |
0.628 (1.00) |
0.233 (1.00) |
del 19p13 2 | 7 (1%) | 477 |
0.135 (1.00) |
0.175 (1.00) |
0.665 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.39 (1.00) |
1 (1.00) |
1 (1.00) |
0.0281 (1.00) |
1 (1.00) |
0.19 (1.00) |
0.459 (1.00) |
0.00215 (0.919) |
|
del 21q21 1 | 9 (2%) | 475 |
0.839 (1.00) |
0.0708 (1.00) |
0.00838 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.706 (1.00) |
0.661 (1.00) |
1 (1.00) |
1 (1.00) |
0.611 (1.00) |
0.396 (1.00) |
0.899 (1.00) |
0.314 (1.00) |
0.655 (1.00) |
del 22q13 1 | 84 (17%) | 400 |
0.499 (1.00) |
0.899 (1.00) |
0.698 (1.00) |
0.525 (1.00) |
0.315 (1.00) |
0.578 (1.00) |
0.498 (1.00) |
0.27 (1.00) |
0.481 (1.00) |
0.332 (1.00) |
0.305 (1.00) |
0.474 (1.00) |
0.315 (1.00) |
0.225 (1.00) |
0.863 (1.00) |
del 22q13 2 | 84 (17%) | 400 |
0.499 (1.00) |
0.899 (1.00) |
0.698 (1.00) |
0.525 (1.00) |
0.315 (1.00) |
0.578 (1.00) |
0.498 (1.00) |
0.27 (1.00) |
0.481 (1.00) |
0.332 (1.00) |
0.305 (1.00) |
0.474 (1.00) |
0.315 (1.00) |
0.225 (1.00) |
0.863 (1.00) |
del 22q13 31 | 84 (17%) | 400 |
0.499 (1.00) |
0.899 (1.00) |
0.698 (1.00) |
0.525 (1.00) |
0.315 (1.00) |
0.578 (1.00) |
0.498 (1.00) |
0.27 (1.00) |
0.481 (1.00) |
0.332 (1.00) |
0.305 (1.00) |
0.474 (1.00) |
0.315 (1.00) |
0.225 (1.00) |
0.863 (1.00) |
del 22q13 32 | 85 (18%) | 399 |
0.497 (1.00) |
0.942 (1.00) |
0.699 (1.00) |
0.512 (1.00) |
0.261 (1.00) |
0.6 (1.00) |
0.589 (1.00) |
0.193 (1.00) |
0.481 (1.00) |
0.218 (1.00) |
0.271 (1.00) |
0.474 (1.00) |
0.275 (1.00) |
0.184 (1.00) |
0.863 (1.00) |
del xq22 1 | 6 (1%) | 478 |
0.729 (1.00) |
0.209 (1.00) |
0.000803 (0.348) |
0.214 (1.00) |
0.685 (1.00) |
0.189 (1.00) |
0.0459 (1.00) |
1 (1.00) |
1 (1.00) |
0.185 (1.00) |
0.353 (1.00) |
0.317 (1.00) |
0.811 (1.00) |
0.422 (1.00) |
0.473 (1.00) |
P value = 2.7e-09 (t-test), Q value = 1.2e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 2(2P23.1) MUTATED | 10 | 0.3 (0.9) |
DEL PEAK 2(2P23.1) WILD-TYPE | 375 | 3.6 (6.3) |
P value = 1.23e-25 (t-test), Q value = 5.5e-23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 3(2Q35) MUTATED | 8 | 0.0 (0.0) |
DEL PEAK 3(2Q35) WILD-TYPE | 377 | 3.6 (6.2) |
P value = 1.35e-25 (t-test), Q value = 6e-23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 9(8P23.2) MUTATED | 4 | 0.0 (0.0) |
DEL PEAK 9(8P23.2) WILD-TYPE | 381 | 3.6 (6.2) |
P value = 1.35e-25 (t-test), Q value = 6e-23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 10(8P22) MUTATED | 4 | 0.0 (0.0) |
DEL PEAK 10(8P22) WILD-TYPE | 381 | 3.6 (6.2) |
P value = 1.35e-25 (t-test), Q value = 6e-23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 11(8P12) MUTATED | 4 | 0.0 (0.0) |
DEL PEAK 11(8P12) WILD-TYPE | 381 | 3.6 (6.2) |
P value = 1.32e-25 (t-test), Q value = 5.9e-23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 12(8Q24.22) MUTATED | 5 | 0.0 (0.0) |
DEL PEAK 12(8Q24.22) WILD-TYPE | 380 | 3.6 (6.2) |
P value = 1.28e-09 (Chi-square test), Q value = 5.6e-07
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 274 | 50 | 106 | 2 | 44 | 6 |
DEL PEAK 13(9Q21.13) MUTATED | 8 | 5 | 3 | 2 | 3 | 1 |
DEL PEAK 13(9Q21.13) WILD-TYPE | 266 | 45 | 103 | 0 | 41 | 5 |
P value = 0.000522 (t-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 47.1 (15.6) |
DEL PEAK 16(11P15.1) MUTATED | 7 | 68.1 (8.7) |
DEL PEAK 16(11P15.1) WILD-TYPE | 477 | 46.8 (15.4) |
P value = 1.47e-07 (Chi-square test), Q value = 6.5e-05
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 274 | 50 | 106 | 2 | 44 | 6 |
DEL PEAK 16(11P15.1) MUTATED | 1 | 1 | 4 | 1 | 0 | 0 |
DEL PEAK 16(11P15.1) WILD-TYPE | 273 | 49 | 102 | 1 | 44 | 6 |
P value = 7.2e-05 (t-test), Q value = 0.032
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 24(18Q22.2) MUTATED | 5 | 0.4 (0.9) |
DEL PEAK 24(18Q22.2) WILD-TYPE | 380 | 3.6 (6.2) |
P value = 1.61e-06 (Chi-square test), Q value = 0.00071
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 274 | 50 | 106 | 2 | 44 | 6 |
DEL PEAK 34(XQ22.3) MUTATED | 0 | 4 | 0 | 0 | 0 | 0 |
DEL PEAK 34(XQ22.3) WILD-TYPE | 274 | 46 | 106 | 2 | 44 | 6 |
P value = 1.35e-25 (t-test), Q value = 6e-23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 385 | 3.6 (6.2) |
DEL PEAK 34(XQ22.3) MUTATED | 4 | 0.0 (0.0) |
DEL PEAK 34(XQ22.3) WILD-TYPE | 381 | 3.6 (6.2) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = THCA-TP.merged_data.txt
-
Number of patients = 484
-
Number of significantly focal cnvs = 30
-
Number of selected clinical features = 15
-
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 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 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 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.