This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 29 focal events and 12 clinical features across 528 patients, 73 significant findings detected with Q value < 0.25.
-
amp_1q24.1 cnv correlated to 'Time to Death'.
-
amp_1q32.1 cnv correlated to 'YEARS_TO_BIRTH'.
-
amp_3q26.32 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.
-
amp_5q35.1 cnv correlated to 'Time to Death', 'GENDER', and 'RACE'.
-
amp_7q31.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'GENDER'.
-
amp_8q24.22 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.
-
amp_10p14 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_T_STAGE'.
-
del_1p36.13 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
-
del_1p31.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
del_3p25.3 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RACE'.
-
del_3p22.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RACE'.
-
del_3p12.3 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.
-
del_3p12.2 cnv correlated to 'GENDER'.
-
del_3p11.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
-
del_3q11.2 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
-
del_4q34.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'RACE'.
-
del_6q26 cnv correlated to 'PATHOLOGY_N_STAGE', 'GENDER', and 'NUMBER_PACK_YEARS_SMOKED'.
-
del_6q26 cnv correlated to 'PATHOLOGY_N_STAGE', 'GENDER', and 'NUMBER_PACK_YEARS_SMOKED'.
-
del_8p23.2 cnv correlated to 'Time to Death' and 'ETHNICITY'.
-
del_9p23 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'GENDER'.
-
del_9p21.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', and 'GENDER'.
-
del_10q23.31 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.
-
del_13q13.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.
-
del_14q31.1 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
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 | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 9p21 3 | 159 (30%) | 369 |
4.25e-07 (7.4e-05) |
0.0385 (0.205) |
1e-05 (0.000435) |
1e-05 (0.000435) |
0.0126 (0.105) |
0.000159 (0.00277) |
0.000768 (0.00891) |
0.315 (0.718) |
0.91 (1.00) |
0.935 (1.00) |
0.0594 (0.265) |
0.827 (1.00) |
del 14q31 1 | 228 (43%) | 300 |
0.000609 (0.00785) |
0.0959 (0.346) |
3e-05 (0.00087) |
7e-05 (0.00152) |
0.000258 (0.00408) |
0.00114 (0.012) |
0.17 (0.515) |
0.0296 (0.181) |
0.37 (0.767) |
0.199 (0.528) |
0.0395 (0.205) |
1 (1.00) |
del 9p23 | 152 (29%) | 376 |
2.03e-05 (0.000642) |
0.0226 (0.157) |
1e-05 (0.000435) |
2e-05 (0.000642) |
0.0879 (0.338) |
0.00173 (0.0172) |
0.0019 (0.0184) |
0.315 (0.718) |
0.707 (0.988) |
0.872 (1.00) |
0.321 (0.725) |
0.655 (0.958) |
del 4q34 3 | 78 (15%) | 450 |
0.000362 (0.00548) |
0.56 (0.918) |
1e-05 (0.000435) |
1e-05 (0.000435) |
0.714 (0.993) |
0.0278 (0.179) |
0.371 (0.767) |
0.877 (1.00) |
0.0247 (0.169) |
0.579 (0.918) |
||
amp 3q26 32 | 87 (16%) | 441 |
0.106 (0.376) |
0.991 (1.00) |
5e-05 (0.00116) |
0.00013 (0.00266) |
0.0516 (0.246) |
0.000414 (0.00577) |
0.903 (1.00) |
0.815 (1.00) |
1 (1.00) |
0.571 (0.918) |
1 (1.00) |
|
amp 7q31 2 | 175 (33%) | 353 |
0.427 (0.818) |
0.326 (0.733) |
0.00766 (0.0684) |
0.0395 (0.205) |
0.306 (0.709) |
0.00158 (0.0162) |
0.016 (0.127) |
0.138 (0.463) |
0.154 (0.492) |
0.233 (0.591) |
0.081 (0.324) |
0.27 (0.657) |
amp 8q24 22 | 79 (15%) | 449 |
0.0297 (0.181) |
0.00692 (0.0634) |
0.00111 (0.012) |
0.00076 (0.00891) |
0.728 (0.995) |
0.0578 (0.265) |
0.0747 (0.307) |
0.523 (0.892) |
0.8 (1.00) |
0.256 (0.627) |
0.229 (0.591) |
|
amp 5q35 1 | 332 (63%) | 196 |
0.041 (0.21) |
0.183 (0.528) |
0.343 (0.736) |
0.241 (0.603) |
0.192 (0.528) |
0.306 (0.709) |
0.0484 (0.234) |
0.836 (1.00) |
0.155 (0.492) |
0.47 (0.847) |
0.00254 (0.0239) |
1 (1.00) |
del 3p25 3 | 463 (88%) | 65 |
0.88 (1.00) |
0.512 (0.89) |
0.0453 (0.222) |
0.0011 (0.012) |
1 (1.00) |
0.848 (1.00) |
0.783 (1.00) |
0.279 (0.675) |
0.619 (0.945) |
5e-05 (0.00116) |
1 (1.00) |
|
del 3p22 2 | 465 (88%) | 63 |
0.66 (0.962) |
0.53 (0.896) |
0.0182 (0.135) |
0.0002 (0.00331) |
1 (1.00) |
0.563 (0.918) |
0.89 (1.00) |
0.482 (0.86) |
0.619 (0.945) |
1e-05 (0.000435) |
1 (1.00) |
|
del 6q26 | 151 (29%) | 377 |
0.803 (1.00) |
0.236 (0.595) |
0.342 (0.736) |
0.568 (0.918) |
0.0177 (0.134) |
0.588 (0.918) |
0.0274 (0.179) |
0.181 (0.528) |
0.0337 (0.192) |
0.643 (0.952) |
0.0688 (0.292) |
0.12 (0.414) |
del 6q26 | 151 (29%) | 377 |
0.826 (1.00) |
0.194 (0.528) |
0.341 (0.736) |
0.568 (0.918) |
0.0177 (0.134) |
0.588 (0.918) |
0.0161 (0.127) |
0.181 (0.528) |
0.0337 (0.192) |
0.643 (0.952) |
0.0702 (0.294) |
0.12 (0.414) |
del 13q13 3 | 81 (15%) | 447 |
0.000668 (0.00831) |
0.942 (1.00) |
0.00015 (0.00275) |
5e-05 (0.00116) |
0.181 (0.528) |
0.0652 (0.28) |
0.802 (1.00) |
0.665 (0.964) |
0.478 (0.857) |
0.0932 (0.345) |
0.15 (0.487) |
|
amp 10p14 | 20 (4%) | 508 |
0.847 (1.00) |
0.0424 (0.211) |
0.189 (0.528) |
0.0289 (0.181) |
0.191 (0.528) |
0.536 (0.896) |
0.643 (0.952) |
0.346 (0.737) |
0.381 (0.781) |
1 (1.00) |
||
del 1p36 13 | 99 (19%) | 429 |
0.0304 (0.182) |
0.0362 (0.2) |
0.629 (0.952) |
0.365 (0.766) |
0.763 (1.00) |
1 (1.00) |
0.163 (0.501) |
0.46 (0.838) |
0.919 (1.00) |
1 (1.00) |
0.315 (0.718) |
|
del 3p12 3 | 339 (64%) | 189 |
0.964 (1.00) |
0.719 (0.993) |
0.192 (0.528) |
0.0268 (0.179) |
0.192 (0.528) |
0.441 (0.829) |
0.000148 (0.00275) |
0.69 (0.976) |
0.913 (1.00) |
0.871 (1.00) |
0.13 (0.442) |
1 (1.00) |
del 3p11 1 | 237 (45%) | 291 |
0.428 (0.818) |
0.0419 (0.211) |
0.635 (0.952) |
0.704 (0.988) |
0.805 (1.00) |
0.386 (0.786) |
1.67e-05 (0.000642) |
0.5 (0.883) |
0.523 (0.892) |
0.684 (0.976) |
0.703 (0.988) |
0.415 (0.807) |
del 3q11 2 | 161 (30%) | 367 |
0.672 (0.966) |
0.00991 (0.0862) |
0.405 (0.8) |
0.0885 (0.338) |
0.409 (0.803) |
0.689 (0.976) |
8.29e-08 (2.88e-05) |
0.164 (0.501) |
0.588 (0.918) |
0.19 (0.528) |
0.372 (0.767) |
|
del 8p23 2 | 154 (29%) | 374 |
0.0325 (0.192) |
0.131 (0.442) |
0.0964 (0.346) |
0.075 (0.307) |
0.785 (1.00) |
0.14 (0.466) |
0.232 (0.591) |
0.516 (0.892) |
0.647 (0.954) |
0.865 (1.00) |
0.0541 (0.253) |
0.0361 (0.2) |
del 10q23 31 | 96 (18%) | 432 |
0.198 (0.528) |
0.46 (0.838) |
0.0123 (0.105) |
0.00038 (0.00551) |
1 (1.00) |
0.434 (0.825) |
0.0593 (0.265) |
0.792 (1.00) |
0.147 (0.482) |
0.427 (0.818) |
||
amp 1q24 1 | 62 (12%) | 466 |
0.0187 (0.136) |
0.0803 (0.324) |
0.117 (0.411) |
0.0948 (0.346) |
0.0624 (0.272) |
0.194 (0.528) |
0.575 (0.918) |
0.401 (0.8) |
0.534 (0.896) |
0.52 (0.892) |
||
amp 1q32 1 | 62 (12%) | 466 |
0.0621 (0.272) |
0.0211 (0.15) |
0.0842 (0.329) |
0.0828 (0.328) |
0.462 (0.838) |
0.352 (0.742) |
0.575 (0.918) |
0.401 (0.8) |
0.532 (0.896) |
0.2 (0.528) |
||
del 1p31 1 | 77 (15%) | 451 |
0.248 (0.617) |
0.176 (0.528) |
0.572 (0.918) |
0.0388 (0.205) |
0.3 (0.707) |
0.73 (0.995) |
0.0544 (0.253) |
0.881 (1.00) |
0.607 (0.939) |
0.0916 (0.343) |
||
del 3p12 2 | 305 (58%) | 223 |
0.339 (0.736) |
0.858 (1.00) |
0.671 (0.966) |
0.211 (0.548) |
0.449 (0.836) |
0.457 (0.838) |
0.000479 (0.00642) |
0.25 (0.618) |
1 (1.00) |
0.871 (1.00) |
0.288 (0.686) |
0.538 (0.896) |
amp 4q32 1 | 16 (3%) | 512 |
0.197 (0.528) |
0.338 (0.736) |
0.762 (1.00) |
0.341 (0.736) |
0.511 (0.89) |
1 (1.00) |
0.598 (0.929) |
0.151 (0.487) |
1 (1.00) |
1 (1.00) |
||
amp xq11 2 | 29 (5%) | 499 |
0.643 (0.952) |
0.297 (0.703) |
0.287 (0.686) |
0.347 (0.737) |
1 (1.00) |
0.411 (0.803) |
1 (1.00) |
0.587 (0.918) |
0.0893 (0.338) |
0.612 (0.943) |
||
amp xq28 | 37 (7%) | 491 |
0.556 (0.918) |
0.504 (0.885) |
0.456 (0.838) |
0.643 (0.952) |
1 (1.00) |
0.211 (0.548) |
0.859 (1.00) |
0.331 (0.736) |
1 (1.00) |
0.394 (0.797) |
||
del 1q44 | 44 (8%) | 484 |
0.774 (1.00) |
0.444 (0.831) |
0.921 (1.00) |
0.157 (0.493) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.655 (0.958) |
0.726 (0.995) |
0.732 (0.995) |
||
del 2q37 3 | 50 (9%) | 478 |
0.88 (1.00) |
0.718 (0.993) |
0.44 (0.829) |
0.688 (0.976) |
1 (1.00) |
0.403 (0.8) |
0.163 (0.501) |
0.761 (1.00) |
0.492 (0.874) |
P value = 0.0187 (logrank test), Q value = 0.14
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
AMP PEAK 1(1Q24.1) MUTATED | 62 | 29 | 0.4 - 129.4 (28.9) |
AMP PEAK 1(1Q24.1) WILD-TYPE | 464 | 146 | 0.1 - 149.2 (39.7) |
P value = 0.0211 (Wilcoxon-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
AMP PEAK 2(1Q32.1) MUTATED | 62 | 63.4 (11.9) |
AMP PEAK 2(1Q32.1) WILD-TYPE | 465 | 60.1 (12.1) |
P value = 5e-05 (Fisher's exact test), Q value = 0.0012
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
AMP PEAK 3(3Q26.32) MUTATED | 28 | 6 | 26 | 27 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 234 | 51 | 98 | 56 |
P value = 0.00013 (Fisher's exact test), Q value = 0.0027
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
AMP PEAK 3(3Q26.32) MUTATED | 29 | 8 | 46 | 4 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 239 | 61 | 134 | 7 |
P value = 0.0516 (Fisher's exact test), Q value = 0.25
nPatients | 0 | 1 |
---|---|---|
ALL | 234 | 17 |
AMP PEAK 3(3Q26.32) MUTATED | 43 | 7 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 191 | 10 |
P value = 0.000414 (Fisher's exact test), Q value = 0.0058
nPatients | 0 | 1 |
---|---|---|
ALL | 418 | 78 |
AMP PEAK 3(3Q26.32) MUTATED | 59 | 25 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 359 | 53 |
P value = 0.041 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
AMP PEAK 5(5Q35.1) MUTATED | 332 | 104 | 0.1 - 149.2 (43.6) |
AMP PEAK 5(5Q35.1) WILD-TYPE | 194 | 71 | 0.1 - 126.3 (33.7) |
P value = 0.0484 (Fisher's exact test), Q value = 0.23
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
AMP PEAK 5(5Q35.1) MUTATED | 108 | 224 |
AMP PEAK 5(5Q35.1) WILD-TYPE | 81 | 115 |
P value = 0.00254 (Fisher's exact test), Q value = 0.024
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 56 | 457 |
AMP PEAK 5(5Q35.1) MUTATED | 3 | 25 | 299 |
AMP PEAK 5(5Q35.1) WILD-TYPE | 5 | 31 | 158 |
P value = 0.00766 (Fisher's exact test), Q value = 0.068
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
AMP PEAK 6(7Q31.2) MUTATED | 74 | 16 | 44 | 40 |
AMP PEAK 6(7Q31.2) WILD-TYPE | 188 | 41 | 80 | 43 |
P value = 0.0395 (Fisher's exact test), Q value = 0.21
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
AMP PEAK 6(7Q31.2) MUTATED | 76 | 21 | 74 | 4 |
AMP PEAK 6(7Q31.2) WILD-TYPE | 192 | 48 | 106 | 7 |
P value = 0.00158 (Fisher's exact test), Q value = 0.016
nPatients | 0 | 1 |
---|---|---|
ALL | 418 | 78 |
AMP PEAK 6(7Q31.2) MUTATED | 128 | 39 |
AMP PEAK 6(7Q31.2) WILD-TYPE | 290 | 39 |
P value = 0.016 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
AMP PEAK 6(7Q31.2) MUTATED | 50 | 125 |
AMP PEAK 6(7Q31.2) WILD-TYPE | 139 | 214 |
P value = 0.0297 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
AMP PEAK 7(8Q24.22) MUTATED | 79 | 33 | 0.5 - 115.7 (31.3) |
AMP PEAK 7(8Q24.22) WILD-TYPE | 447 | 142 | 0.1 - 149.2 (40.7) |
P value = 0.00692 (Wilcoxon-test), Q value = 0.063
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
AMP PEAK 7(8Q24.22) MUTATED | 79 | 63.8 (11.4) |
AMP PEAK 7(8Q24.22) WILD-TYPE | 448 | 59.9 (12.1) |
P value = 0.00111 (Fisher's exact test), Q value = 0.012
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
AMP PEAK 7(8Q24.22) MUTATED | 23 | 11 | 25 | 19 |
AMP PEAK 7(8Q24.22) WILD-TYPE | 239 | 46 | 99 | 64 |
P value = 0.00076 (Fisher's exact test), Q value = 0.0089
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
AMP PEAK 7(8Q24.22) MUTATED | 24 | 12 | 41 | 2 |
AMP PEAK 7(8Q24.22) WILD-TYPE | 244 | 57 | 139 | 9 |
P value = 0.0424 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
AMP PEAK 8(10P14) MUTATED | 20 | 65.5 (10.5) |
AMP PEAK 8(10P14) WILD-TYPE | 507 | 60.3 (12.1) |
P value = 0.0289 (Fisher's exact test), Q value = 0.18
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
AMP PEAK 8(10P14) MUTATED | 9 | 5 | 4 | 2 |
AMP PEAK 8(10P14) WILD-TYPE | 259 | 64 | 176 | 9 |
P value = 0.0304 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
DEL PEAK 1(1P36.13) MUTATED | 99 | 43 | 0.5 - 130.7 (40.0) |
DEL PEAK 1(1P36.13) WILD-TYPE | 427 | 132 | 0.1 - 149.2 (38.7) |
P value = 0.0362 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
DEL PEAK 1(1P36.13) MUTATED | 99 | 62.7 (11.7) |
DEL PEAK 1(1P36.13) WILD-TYPE | 428 | 60.0 (12.2) |
P value = 0.0388 (Fisher's exact test), Q value = 0.21
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 2(1P31.1) MUTATED | 38 | 12 | 22 | 5 |
DEL PEAK 2(1P31.1) WILD-TYPE | 230 | 57 | 158 | 6 |
P value = 0.0453 (Fisher's exact test), Q value = 0.22
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 5(3P25.3) MUTATED | 222 | 49 | 117 | 73 |
DEL PEAK 5(3P25.3) WILD-TYPE | 40 | 8 | 7 | 10 |
P value = 0.0011 (Fisher's exact test), Q value = 0.012
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 5(3P25.3) MUTATED | 228 | 61 | 168 | 6 |
DEL PEAK 5(3P25.3) WILD-TYPE | 40 | 8 | 12 | 5 |
P value = 5e-05 (Fisher's exact test), Q value = 0.0012
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 56 | 457 |
DEL PEAK 5(3P25.3) MUTATED | 6 | 38 | 412 |
DEL PEAK 5(3P25.3) WILD-TYPE | 2 | 18 | 45 |
P value = 0.0182 (Fisher's exact test), Q value = 0.14
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 6(3P22.2) MUTATED | 222 | 49 | 118 | 74 |
DEL PEAK 6(3P22.2) WILD-TYPE | 40 | 8 | 6 | 9 |
P value = 2e-04 (Fisher's exact test), Q value = 0.0033
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 6(3P22.2) MUTATED | 228 | 61 | 170 | 6 |
DEL PEAK 6(3P22.2) WILD-TYPE | 40 | 8 | 10 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 56 | 457 |
DEL PEAK 6(3P22.2) MUTATED | 6 | 38 | 414 |
DEL PEAK 6(3P22.2) WILD-TYPE | 2 | 18 | 43 |
P value = 0.0268 (Fisher's exact test), Q value = 0.18
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 7(3P12.3) MUTATED | 165 | 48 | 123 | 3 |
DEL PEAK 7(3P12.3) WILD-TYPE | 103 | 21 | 57 | 8 |
P value = 0.000148 (Fisher's exact test), Q value = 0.0027
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 7(3P12.3) MUTATED | 101 | 238 |
DEL PEAK 7(3P12.3) WILD-TYPE | 88 | 101 |
P value = 0.000479 (Fisher's exact test), Q value = 0.0064
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 8(3P12.2) MUTATED | 90 | 215 |
DEL PEAK 8(3P12.2) WILD-TYPE | 99 | 124 |
P value = 0.0419 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
DEL PEAK 9(3P11.1) MUTATED | 237 | 61.8 (12.3) |
DEL PEAK 9(3P11.1) WILD-TYPE | 290 | 59.5 (11.8) |
P value = 1.67e-05 (Fisher's exact test), Q value = 0.00064
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 9(3P11.1) MUTATED | 61 | 176 |
DEL PEAK 9(3P11.1) WILD-TYPE | 128 | 163 |
P value = 0.00991 (Wilcoxon-test), Q value = 0.086
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
DEL PEAK 10(3Q11.2) MUTATED | 161 | 62.8 (12.9) |
DEL PEAK 10(3Q11.2) WILD-TYPE | 366 | 59.5 (11.6) |
P value = 8.29e-08 (Fisher's exact test), Q value = 2.9e-05
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 10(3Q11.2) MUTATED | 31 | 130 |
DEL PEAK 10(3Q11.2) WILD-TYPE | 158 | 209 |
P value = 0.000362 (logrank test), Q value = 0.0055
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
DEL PEAK 11(4Q34.3) MUTATED | 78 | 41 | 0.6 - 133.7 (38.5) |
DEL PEAK 11(4Q34.3) WILD-TYPE | 448 | 134 | 0.1 - 149.2 (39.1) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 11(4Q34.3) MUTATED | 19 | 7 | 30 | 22 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 243 | 50 | 94 | 61 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 11(4Q34.3) MUTATED | 20 | 9 | 43 | 6 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 248 | 60 | 137 | 5 |
P value = 0.0278 (Fisher's exact test), Q value = 0.18
nPatients | 0 | 1 |
---|---|---|
ALL | 418 | 78 |
DEL PEAK 11(4Q34.3) MUTATED | 59 | 19 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 359 | 59 |
P value = 0.0247 (Fisher's exact test), Q value = 0.17
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 56 | 457 |
DEL PEAK 11(4Q34.3) MUTATED | 1 | 2 | 73 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 7 | 54 | 384 |
P value = 0.0177 (Fisher's exact test), Q value = 0.13
nPatients | 0 | 1 |
---|---|---|
ALL | 234 | 17 |
DEL PEAK 12(6Q26) MUTATED | 56 | 9 |
DEL PEAK 12(6Q26) WILD-TYPE | 178 | 8 |
P value = 0.0274 (Fisher's exact test), Q value = 0.18
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 12(6Q26) MUTATED | 43 | 108 |
DEL PEAK 12(6Q26) WILD-TYPE | 146 | 231 |
P value = 0.0337 (Wilcoxon-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 28.3 (16.1) |
DEL PEAK 12(6Q26) MUTATED | 5 | 16.0 (13.7) |
DEL PEAK 12(6Q26) WILD-TYPE | 16 | 32.2 (15.2) |
P value = 0.0177 (Fisher's exact test), Q value = 0.13
nPatients | 0 | 1 |
---|---|---|
ALL | 234 | 17 |
DEL PEAK 13(6Q26) MUTATED | 56 | 9 |
DEL PEAK 13(6Q26) WILD-TYPE | 178 | 8 |
P value = 0.0161 (Fisher's exact test), Q value = 0.13
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 13(6Q26) MUTATED | 42 | 109 |
DEL PEAK 13(6Q26) WILD-TYPE | 147 | 230 |
P value = 0.0337 (Wilcoxon-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 21 | 28.3 (16.1) |
DEL PEAK 13(6Q26) MUTATED | 5 | 16.0 (13.7) |
DEL PEAK 13(6Q26) WILD-TYPE | 16 | 32.2 (15.2) |
P value = 0.0325 (logrank test), Q value = 0.19
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
DEL PEAK 14(8P23.2) MUTATED | 154 | 61 | 0.1 - 118.8 (37.1) |
DEL PEAK 14(8P23.2) WILD-TYPE | 372 | 114 | 0.1 - 149.2 (41.7) |
P value = 0.0361 (Fisher's exact test), Q value = 0.2
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 26 | 350 |
DEL PEAK 14(8P23.2) MUTATED | 12 | 89 |
DEL PEAK 14(8P23.2) WILD-TYPE | 14 | 261 |
P value = 2.03e-05 (logrank test), Q value = 0.00064
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
DEL PEAK 15(9P23) MUTATED | 151 | 73 | 0.5 - 133.7 (39.2) |
DEL PEAK 15(9P23) WILD-TYPE | 375 | 102 | 0.1 - 149.2 (38.7) |
P value = 0.0226 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
DEL PEAK 15(9P23) MUTATED | 151 | 62.3 (11.7) |
DEL PEAK 15(9P23) WILD-TYPE | 376 | 59.8 (12.2) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 15(9P23) MUTATED | 51 | 12 | 49 | 38 |
DEL PEAK 15(9P23) WILD-TYPE | 211 | 45 | 75 | 45 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00064
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 15(9P23) MUTATED | 55 | 16 | 76 | 5 |
DEL PEAK 15(9P23) WILD-TYPE | 213 | 53 | 104 | 6 |
P value = 0.00173 (Fisher's exact test), Q value = 0.017
nPatients | 0 | 1 |
---|---|---|
ALL | 418 | 78 |
DEL PEAK 15(9P23) MUTATED | 111 | 35 |
DEL PEAK 15(9P23) WILD-TYPE | 307 | 43 |
P value = 0.0019 (Fisher's exact test), Q value = 0.018
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 15(9P23) MUTATED | 39 | 113 |
DEL PEAK 15(9P23) WILD-TYPE | 150 | 226 |
P value = 4.25e-07 (logrank test), Q value = 7.4e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
DEL PEAK 16(9P21.3) MUTATED | 158 | 79 | 0.5 - 133.7 (37.8) |
DEL PEAK 16(9P21.3) WILD-TYPE | 368 | 96 | 0.1 - 149.2 (40.8) |
P value = 0.0385 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 527 | 60.5 (12.1) |
DEL PEAK 16(9P21.3) MUTATED | 158 | 62.1 (11.6) |
DEL PEAK 16(9P21.3) WILD-TYPE | 369 | 59.8 (12.3) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 16(9P21.3) MUTATED | 52 | 11 | 53 | 41 |
DEL PEAK 16(9P21.3) WILD-TYPE | 210 | 46 | 71 | 42 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00043
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 16(9P21.3) MUTATED | 56 | 15 | 82 | 6 |
DEL PEAK 16(9P21.3) WILD-TYPE | 212 | 54 | 98 | 5 |
P value = 0.0126 (Fisher's exact test), Q value = 0.1
nPatients | 0 | 1 |
---|---|---|
ALL | 234 | 17 |
DEL PEAK 16(9P21.3) MUTATED | 66 | 10 |
DEL PEAK 16(9P21.3) WILD-TYPE | 168 | 7 |
P value = 0.000159 (Fisher's exact test), Q value = 0.0028
nPatients | 0 | 1 |
---|---|---|
ALL | 418 | 78 |
DEL PEAK 16(9P21.3) MUTATED | 115 | 39 |
DEL PEAK 16(9P21.3) WILD-TYPE | 303 | 39 |
P value = 0.000768 (Fisher's exact test), Q value = 0.0089
nPatients | FEMALE | MALE |
---|---|---|
ALL | 189 | 339 |
DEL PEAK 16(9P21.3) MUTATED | 40 | 119 |
DEL PEAK 16(9P21.3) WILD-TYPE | 149 | 220 |
P value = 0.0123 (Fisher's exact test), Q value = 0.1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 17(10Q23.31) MUTATED | 34 | 11 | 31 | 20 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 228 | 46 | 93 | 63 |
P value = 0.00038 (Fisher's exact test), Q value = 0.0055
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 17(10Q23.31) MUTATED | 34 | 12 | 44 | 6 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 234 | 57 | 136 | 5 |
P value = 0.000668 (logrank test), Q value = 0.0083
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
DEL PEAK 18(13Q13.3) MUTATED | 80 | 38 | 0.5 - 112.1 (31.5) |
DEL PEAK 18(13Q13.3) WILD-TYPE | 446 | 137 | 0.1 - 149.2 (41.2) |
P value = 0.00015 (Fisher's exact test), Q value = 0.0027
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 18(13Q13.3) MUTATED | 27 | 4 | 29 | 21 |
DEL PEAK 18(13Q13.3) WILD-TYPE | 235 | 53 | 95 | 62 |
P value = 5e-05 (Fisher's exact test), Q value = 0.0012
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 18(13Q13.3) MUTATED | 29 | 5 | 41 | 6 |
DEL PEAK 18(13Q13.3) WILD-TYPE | 239 | 64 | 139 | 5 |
P value = 0.000609 (logrank test), Q value = 0.0078
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 526 | 175 | 0.1 - 149.2 (38.8) |
DEL PEAK 19(14Q31.1) MUTATED | 227 | 97 | 0.4 - 133.7 (36.8) |
DEL PEAK 19(14Q31.1) WILD-TYPE | 299 | 78 | 0.1 - 149.2 (42.7) |
P value = 3e-05 (Fisher's exact test), Q value = 0.00087
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 262 | 57 | 124 | 83 |
DEL PEAK 19(14Q31.1) MUTATED | 85 | 27 | 65 | 49 |
DEL PEAK 19(14Q31.1) WILD-TYPE | 177 | 30 | 59 | 34 |
P value = 7e-05 (Fisher's exact test), Q value = 0.0015
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 268 | 69 | 180 | 11 |
DEL PEAK 19(14Q31.1) MUTATED | 91 | 35 | 98 | 4 |
DEL PEAK 19(14Q31.1) WILD-TYPE | 177 | 34 | 82 | 7 |
P value = 0.000258 (Fisher's exact test), Q value = 0.0041
nPatients | 0 | 1 |
---|---|---|
ALL | 234 | 17 |
DEL PEAK 19(14Q31.1) MUTATED | 100 | 15 |
DEL PEAK 19(14Q31.1) WILD-TYPE | 134 | 2 |
P value = 0.00114 (Fisher's exact test), Q value = 0.012
nPatients | 0 | 1 |
---|---|---|
ALL | 418 | 78 |
DEL PEAK 19(14Q31.1) MUTATED | 171 | 48 |
DEL PEAK 19(14Q31.1) WILD-TYPE | 247 | 30 |
P value = 0.0296 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 85.6 (25.8) |
DEL PEAK 19(14Q31.1) MUTATED | 21 | 72.4 (37.5) |
DEL PEAK 19(14Q31.1) WILD-TYPE | 33 | 93.9 (6.1) |
P value = 0.0395 (Fisher's exact test), Q value = 0.21
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 56 | 457 |
DEL PEAK 19(14Q31.1) MUTATED | 2 | 16 | 206 |
DEL PEAK 19(14Q31.1) WILD-TYPE | 6 | 40 | 251 |
-
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/KIRC-TP/22531283/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/22506714/KIRC-TP.merged_data.txt
-
Number of patients = 528
-
Number of significantly focal cnvs = 29
-
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.