Head and Neck Squamous Cell Carcinoma: Correlation between copy number variation genes and selected clinical features
(primary solid tumor cohort)
(primary solid tumor cohort)
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction
This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Summary
Testing the association between copy number variation of 72 peak regions and 11 clinical features across 309 patients, 3 significant findings detected with Q value < 0.25.
-
Del Peak 7(3p14.2) cnvs correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Del Peak 8(3p12.2) cnvs correlated to 'Time to Death' and 'NUMBERPACKYEARSSMOKED'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 72 regions and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.
|
Clinical Features |
Time to Death |
AGE | GENDER |
PATHOLOGY T |
PATHOLOGY N |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET | ||
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | t-test | Fisher's exact test | t-test | |
| Del Peak 8(3p12 2) | 219 (71%) | 90 |
0.000275 (0.217) |
0.689 (1.00) |
0.328 (1.00) |
0.126 (1.00) |
0.103 (1.00) |
0.0381 (1.00) |
0.773 (1.00) |
8.79e-05 (0.0696) |
0.0109 (1.00) |
0.00872 (1.00) |
0.759 (1.00) |
| Del Peak 7(3p14 2) | 232 (75%) | 77 |
0.000381 (0.301) |
0.448 (1.00) |
0.0398 (1.00) |
0.0495 (1.00) |
0.0349 (1.00) |
0.013 (1.00) |
0.446 (1.00) |
0.00494 (1.00) |
0.00402 (1.00) |
0.000139 (0.11) |
0.739 (1.00) |
| Amp Peak 1(1q21 2) | 72 (23%) | 237 |
0.43 (1.00) |
0.135 (1.00) |
0.653 (1.00) |
0.953 (1.00) |
0.221 (1.00) |
0.813 (1.00) |
0.211 (1.00) |
0.427 (1.00) |
0.127 (1.00) |
0.0769 (1.00) |
0.823 (1.00) |
| Amp Peak 2(2q11 2) | 67 (22%) | 242 |
0.493 (1.00) |
0.556 (1.00) |
0.355 (1.00) |
0.00615 (1.00) |
0.725 (1.00) |
0.0856 (1.00) |
1 (1.00) |
0.244 (1.00) |
0.142 (1.00) |
0.154 (1.00) |
0.418 (1.00) |
| Amp Peak 3(2q31 2) | 65 (21%) | 244 |
0.178 (1.00) |
0.918 (1.00) |
0.877 (1.00) |
0.356 (1.00) |
0.396 (1.00) |
0.807 (1.00) |
0.871 (1.00) |
0.0558 (1.00) |
0.664 (1.00) |
0.00379 (1.00) |
0.356 (1.00) |
| Amp Peak 4(2q32 2) | 57 (18%) | 252 |
0.457 (1.00) |
0.873 (1.00) |
0.742 (1.00) |
0.582 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.865 (1.00) |
0.0585 (1.00) |
0.111 (1.00) |
0.0503 (1.00) |
0.468 (1.00) |
| Amp Peak 5(3q26 33) | 231 (75%) | 78 |
0.136 (1.00) |
0.0626 (1.00) |
0.0271 (1.00) |
0.473 (1.00) |
0.151 (1.00) |
0.0635 (1.00) |
0.365 (1.00) |
0.00723 (1.00) |
0.0247 (1.00) |
0.18 (1.00) |
0.181 (1.00) |
| Amp Peak 6(5p15 33) | 139 (45%) | 170 |
0.506 (1.00) |
0.074 (1.00) |
0.095 (1.00) |
0.292 (1.00) |
0.201 (1.00) |
0.312 (1.00) |
0.0463 (1.00) |
0.828 (1.00) |
0.0314 (1.00) |
0.317 (1.00) |
0.152 (1.00) |
| Amp Peak 7(5p12) | 116 (38%) | 193 |
0.638 (1.00) |
0.266 (1.00) |
0.239 (1.00) |
0.432 (1.00) |
0.333 (1.00) |
0.745 (1.00) |
0.0137 (1.00) |
0.758 (1.00) |
0.29 (1.00) |
0.454 (1.00) |
0.901 (1.00) |
| Amp Peak 8(6p12 1) | 63 (20%) | 246 |
0.61 (1.00) |
0.23 (1.00) |
0.874 (1.00) |
0.525 (1.00) |
0.969 (1.00) |
0.571 (1.00) |
0.189 (1.00) |
0.54 (1.00) |
0.195 (1.00) |
0.663 (1.00) |
0.424 (1.00) |
| Amp Peak 9(6q12) | 59 (19%) | 250 |
0.39 (1.00) |
0.695 (1.00) |
0.747 (1.00) |
0.682 (1.00) |
1 (1.00) |
0.57 (1.00) |
0.0293 (1.00) |
0.861 (1.00) |
0.0846 (1.00) |
0.532 (1.00) |
0.0155 (1.00) |
| Amp Peak 10(7p11 2) | 132 (43%) | 177 |
0.0405 (1.00) |
0.0869 (1.00) |
0.797 (1.00) |
0.0525 (1.00) |
0.378 (1.00) |
0.655 (1.00) |
0.691 (1.00) |
0.565 (1.00) |
0.0934 (1.00) |
0.184 (1.00) |
0.08 (1.00) |
| Amp Peak 11(7q22 1) | 109 (35%) | 200 |
0.0344 (1.00) |
0.63 (1.00) |
0.352 (1.00) |
0.0359 (1.00) |
0.264 (1.00) |
0.225 (1.00) |
0.27 (1.00) |
0.0152 (1.00) |
0.0212 (1.00) |
0.00118 (0.922) |
0.59 (1.00) |
| Amp Peak 12(8p11 23) | 98 (32%) | 211 |
0.22 (1.00) |
0.982 (1.00) |
0.892 (1.00) |
0.172 (1.00) |
0.416 (1.00) |
0.242 (1.00) |
0.887 (1.00) |
0.422 (1.00) |
0.716 (1.00) |
0.595 (1.00) |
0.517 (1.00) |
| Amp Peak 13(8q11 21) | 177 (57%) | 132 |
0.621 (1.00) |
0.407 (1.00) |
0.607 (1.00) |
0.998 (1.00) |
0.534 (1.00) |
0.559 (1.00) |
0.507 (1.00) |
0.947 (1.00) |
0.107 (1.00) |
0.0898 (1.00) |
0.233 (1.00) |
| Amp Peak 14(8q24 21) | 220 (71%) | 89 |
0.398 (1.00) |
0.249 (1.00) |
0.481 (1.00) |
0.587 (1.00) |
0.000529 (0.416) |
0.223 (1.00) |
0.662 (1.00) |
0.613 (1.00) |
0.581 (1.00) |
0.772 (1.00) |
0.0761 (1.00) |
| Amp Peak 15(9p23) | 73 (24%) | 236 |
0.711 (1.00) |
0.508 (1.00) |
0.133 (1.00) |
0.675 (1.00) |
0.271 (1.00) |
0.417 (1.00) |
0.877 (1.00) |
0.213 (1.00) |
0.98 (1.00) |
0.462 (1.00) |
0.934 (1.00) |
| Amp Peak 16(9p13 3) | 87 (28%) | 222 |
0.831 (1.00) |
0.83 (1.00) |
0.57 (1.00) |
0.471 (1.00) |
0.521 (1.00) |
0.462 (1.00) |
0.884 (1.00) |
0.444 (1.00) |
0.73 (1.00) |
0.294 (1.00) |
0.673 (1.00) |
| Amp Peak 17(11p13) | 60 (19%) | 249 |
0.371 (1.00) |
0.0765 (1.00) |
0.52 (1.00) |
0.478 (1.00) |
0.349 (1.00) |
0.64 (1.00) |
0.739 (1.00) |
0.00829 (1.00) |
0.829 (1.00) |
0.458 (1.00) |
0.126 (1.00) |
| Amp Peak 18(11p11 2) | 60 (19%) | 249 |
0.144 (1.00) |
0.854 (1.00) |
0.334 (1.00) |
0.806 (1.00) |
0.072 (1.00) |
0.815 (1.00) |
0.619 (1.00) |
0.112 (1.00) |
0.297 (1.00) |
0.385 (1.00) |
0.834 (1.00) |
| Amp Peak 19(11q13 3) | 141 (46%) | 168 |
0.00334 (1.00) |
0.249 (1.00) |
0.798 (1.00) |
0.324 (1.00) |
0.162 (1.00) |
0.189 (1.00) |
0.185 (1.00) |
0.0157 (1.00) |
0.0697 (1.00) |
0.012 (1.00) |
0.384 (1.00) |
| Amp Peak 20(12p13 33) | 109 (35%) | 200 |
0.782 (1.00) |
0.338 (1.00) |
0.352 (1.00) |
0.539 (1.00) |
0.635 (1.00) |
0.948 (1.00) |
0.491 (1.00) |
0.258 (1.00) |
0.127 (1.00) |
0.181 (1.00) |
0.115 (1.00) |
| Amp Peak 21(12q15) | 63 (20%) | 246 |
0.464 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.556 (1.00) |
0.67 (1.00) |
0.242 (1.00) |
0.416 (1.00) |
0.0923 (1.00) |
0.197 (1.00) |
0.386 (1.00) |
0.475 (1.00) |
| Amp Peak 22(13q22 1) | 67 (22%) | 242 |
0.125 (1.00) |
0.0786 (1.00) |
0.538 (1.00) |
0.611 (1.00) |
0.493 (1.00) |
0.671 (1.00) |
0.426 (1.00) |
0.0678 (1.00) |
0.908 (1.00) |
0.328 (1.00) |
0.0727 (1.00) |
| Amp Peak 23(14q11 2) | 86 (28%) | 223 |
0.877 (1.00) |
0.689 (1.00) |
0.887 (1.00) |
0.907 (1.00) |
0.905 (1.00) |
0.902 (1.00) |
0.559 (1.00) |
0.29 (1.00) |
0.156 (1.00) |
0.907 (1.00) |
0.455 (1.00) |
| Amp Peak 24(15q26 3) | 67 (22%) | 242 |
0.00676 (1.00) |
0.388 (1.00) |
1 (1.00) |
0.51 (1.00) |
0.99 (1.00) |
0.967 (1.00) |
0.522 (1.00) |
0.545 (1.00) |
0.925 (1.00) |
0.313 (1.00) |
0.765 (1.00) |
| Amp Peak 25(17q12) | 53 (17%) | 256 |
0.067 (1.00) |
0.195 (1.00) |
0.174 (1.00) |
0.415 (1.00) |
0.55 (1.00) |
0.177 (1.00) |
0.381 (1.00) |
0.387 (1.00) |
0.867 (1.00) |
0.0149 (1.00) |
0.588 (1.00) |
| Amp Peak 26(18p11 31) | 99 (32%) | 210 |
0.144 (1.00) |
0.0715 (1.00) |
0.000977 (0.765) |
0.358 (1.00) |
0.709 (1.00) |
0.0543 (1.00) |
0.572 (1.00) |
0.0612 (1.00) |
0.0733 (1.00) |
0.0716 (1.00) |
0.23 (1.00) |
| Amp Peak 27(18q11 2) | 70 (23%) | 239 |
0.959 (1.00) |
0.0162 (1.00) |
0.0331 (1.00) |
0.327 (1.00) |
0.809 (1.00) |
0.914 (1.00) |
0.347 (1.00) |
0.192 (1.00) |
0.22 (1.00) |
0.122 (1.00) |
0.791 (1.00) |
| Amp Peak 28(20q11 22) | 141 (46%) | 168 |
0.88 (1.00) |
0.154 (1.00) |
0.305 (1.00) |
0.653 (1.00) |
0.481 (1.00) |
0.79 (1.00) |
0.596 (1.00) |
0.48 (1.00) |
0.215 (1.00) |
0.87 (1.00) |
0.0574 (1.00) |
| Amp Peak 29(Xq28) | 95 (31%) | 214 |
0.399 (1.00) |
0.655 (1.00) |
0.89 (1.00) |
0.181 (1.00) |
0.358 (1.00) |
0.98 (1.00) |
0.0637 (1.00) |
0.516 (1.00) |
0.0814 (1.00) |
0.316 (1.00) |
0.267 (1.00) |
| Del Peak 1(1p36 13) | 65 (21%) | 244 |
0.119 (1.00) |
0.0419 (1.00) |
0.276 (1.00) |
0.225 (1.00) |
0.569 (1.00) |
0.495 (1.00) |
0.198 (1.00) |
0.0227 (1.00) |
0.317 (1.00) |
0.121 (1.00) |
0.17 (1.00) |
| Del Peak 2(1p13 2) | 76 (25%) | 233 |
0.233 (1.00) |
0.189 (1.00) |
1 (1.00) |
0.319 (1.00) |
0.267 (1.00) |
0.286 (1.00) |
0.648 (1.00) |
0.0144 (1.00) |
0.42 (1.00) |
0.149 (1.00) |
0.438 (1.00) |
| Del Peak 3(2q21 2) | 38 (12%) | 271 |
0.635 (1.00) |
0.248 (1.00) |
0.0804 (1.00) |
0.362 (1.00) |
0.102 (1.00) |
0.844 (1.00) |
0.424 (1.00) |
0.557 (1.00) |
0.431 (1.00) |
0.604 (1.00) |
0.844 (1.00) |
| Del Peak 4(2q22 1) | 63 (20%) | 246 |
0.467 (1.00) |
0.444 (1.00) |
0.266 (1.00) |
0.104 (1.00) |
0.143 (1.00) |
0.223 (1.00) |
0.416 (1.00) |
0.0612 (1.00) |
0.538 (1.00) |
0.289 (1.00) |
0.872 (1.00) |
| Del Peak 5(2q36 2) | 94 (30%) | 215 |
0.182 (1.00) |
0.845 (1.00) |
0.335 (1.00) |
0.0125 (1.00) |
0.484 (1.00) |
0.293 (1.00) |
0.776 (1.00) |
0.0141 (1.00) |
0.0137 (1.00) |
0.176 (1.00) |
0.283 (1.00) |
| Del Peak 6(3p24 1) | 228 (74%) | 81 |
0.000618 (0.485) |
0.571 (1.00) |
0.0286 (1.00) |
0.00381 (1.00) |
0.00974 (1.00) |
0.00606 (1.00) |
0.881 (1.00) |
0.00137 (1.00) |
0.00124 (0.964) |
0.00143 (1.00) |
0.79 (1.00) |
| Del Peak 9(4p16 3) | 133 (43%) | 176 |
0.0359 (1.00) |
0.137 (1.00) |
0.304 (1.00) |
0.436 (1.00) |
0.6 (1.00) |
0.334 (1.00) |
0.424 (1.00) |
0.409 (1.00) |
0.0252 (1.00) |
0.0123 (1.00) |
0.869 (1.00) |
| Del Peak 10(4p15 2) | 134 (43%) | 175 |
0.0869 (1.00) |
0.166 (1.00) |
0.439 (1.00) |
0.427 (1.00) |
0.56 (1.00) |
0.24 (1.00) |
0.427 (1.00) |
0.0687 (1.00) |
0.019 (1.00) |
0.00193 (1.00) |
0.779 (1.00) |
| Del Peak 11(4q22 1) | 98 (32%) | 211 |
0.482 (1.00) |
0.926 (1.00) |
0.892 (1.00) |
0.789 (1.00) |
0.974 (1.00) |
0.785 (1.00) |
0.478 (1.00) |
0.267 (1.00) |
0.109 (1.00) |
0.0906 (1.00) |
0.284 (1.00) |
| Del Peak 12(4q35 2) | 125 (40%) | 184 |
0.131 (1.00) |
0.587 (1.00) |
0.07 (1.00) |
0.143 (1.00) |
0.988 (1.00) |
0.5 (1.00) |
0.591 (1.00) |
0.856 (1.00) |
0.0115 (1.00) |
0.0332 (1.00) |
0.0398 (1.00) |
| Del Peak 13(5q11 2) | 130 (42%) | 179 |
0.377 (1.00) |
0.144 (1.00) |
0.12 (1.00) |
0.169 (1.00) |
0.258 (1.00) |
0.733 (1.00) |
0.288 (1.00) |
0.000524 (0.413) |
0.0355 (1.00) |
0.00859 (1.00) |
0.451 (1.00) |
| Del Peak 14(5q35 3) | 122 (39%) | 187 |
0.349 (1.00) |
0.2 (1.00) |
0.193 (1.00) |
0.0978 (1.00) |
0.307 (1.00) |
0.352 (1.00) |
0.421 (1.00) |
0.0446 (1.00) |
0.0938 (1.00) |
0.0168 (1.00) |
0.467 (1.00) |
| Del Peak 15(6p25 3) | 64 (21%) | 245 |
0.24 (1.00) |
0.192 (1.00) |
0.345 (1.00) |
0.0144 (1.00) |
0.923 (1.00) |
0.37 (1.00) |
1 (1.00) |
0.272 (1.00) |
0.76 (1.00) |
0.292 (1.00) |
0.164 (1.00) |
| Del Peak 16(7q31 1) | 48 (16%) | 261 |
0.688 (1.00) |
0.0162 (1.00) |
0.86 (1.00) |
0.978 (1.00) |
0.302 (1.00) |
0.524 (1.00) |
0.466 (1.00) |
0.732 (1.00) |
0.0331 (1.00) |
0.0501 (1.00) |
0.00641 (1.00) |
| Del Peak 17(7q36 1) | 78 (25%) | 231 |
0.0246 (1.00) |
0.661 (1.00) |
0.241 (1.00) |
0.747 (1.00) |
0.128 (1.00) |
0.278 (1.00) |
1 (1.00) |
0.931 (1.00) |
0.261 (1.00) |
0.289 (1.00) |
0.211 (1.00) |
| Del Peak 18(8p23 2) | 175 (57%) | 134 |
0.00782 (1.00) |
0.0802 (1.00) |
0.439 (1.00) |
0.748 (1.00) |
0.567 (1.00) |
0.895 (1.00) |
0.69 (1.00) |
0.0404 (1.00) |
0.408 (1.00) |
0.748 (1.00) |
0.791 (1.00) |
| Del Peak 19(9p23) | 142 (46%) | 167 |
0.486 (1.00) |
0.21 (1.00) |
0.702 (1.00) |
0.402 (1.00) |
0.901 (1.00) |
0.95 (1.00) |
0.508 (1.00) |
0.0173 (1.00) |
0.00564 (1.00) |
0.00191 (1.00) |
0.617 (1.00) |
| Del Peak 20(9p21 3) | 180 (58%) | 129 |
0.0147 (1.00) |
0.267 (1.00) |
0.44 (1.00) |
0.603 (1.00) |
0.976 (1.00) |
0.654 (1.00) |
0.422 (1.00) |
0.0827 (1.00) |
0.0189 (1.00) |
0.00089 (0.698) |
0.275 (1.00) |
| Del Peak 21(9q21 11) | 58 (19%) | 251 |
0.855 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.938 (1.00) |
0.788 (1.00) |
0.699 (1.00) |
1 (1.00) |
0.155 (1.00) |
0.477 (1.00) |
0.147 (1.00) |
0.285 (1.00) |
| Del Peak 22(9q34 3) | 51 (17%) | 258 |
0.564 (1.00) |
0.599 (1.00) |
0.303 (1.00) |
0.802 (1.00) |
0.858 (1.00) |
0.925 (1.00) |
0.477 (1.00) |
0.279 (1.00) |
0.313 (1.00) |
0.659 (1.00) |
0.759 (1.00) |
| Del Peak 23(10p15 3) | 103 (33%) | 206 |
0.128 (1.00) |
0.69 (1.00) |
0.892 (1.00) |
0.179 (1.00) |
0.0615 (1.00) |
0.304 (1.00) |
0.0692 (1.00) |
0.11 (1.00) |
0.412 (1.00) |
0.634 (1.00) |
0.389 (1.00) |
| Del Peak 24(10p11 21) | 98 (32%) | 211 |
0.211 (1.00) |
0.709 (1.00) |
0.495 (1.00) |
0.252 (1.00) |
0.69 (1.00) |
0.578 (1.00) |
0.0645 (1.00) |
0.477 (1.00) |
0.258 (1.00) |
0.31 (1.00) |
0.338 (1.00) |
| Del Peak 25(10q23 31) | 80 (26%) | 229 |
0.252 (1.00) |
0.594 (1.00) |
0.309 (1.00) |
0.875 (1.00) |
0.95 (1.00) |
0.807 (1.00) |
0.763 (1.00) |
0.129 (1.00) |
0.969 (1.00) |
0.175 (1.00) |
0.0182 (1.00) |
| Del Peak 26(11p15 4) | 98 (32%) | 211 |
0.056 (1.00) |
0.479 (1.00) |
0.495 (1.00) |
0.802 (1.00) |
0.0611 (1.00) |
0.625 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.264 (1.00) |
0.0824 (1.00) |
0.998 (1.00) |
| Del Peak 27(11q23 1) | 150 (49%) | 159 |
0.672 (1.00) |
0.288 (1.00) |
0.00711 (1.00) |
0.949 (1.00) |
0.113 (1.00) |
0.825 (1.00) |
0.599 (1.00) |
0.0701 (1.00) |
0.922 (1.00) |
0.12 (1.00) |
0.112 (1.00) |
| Del Peak 28(12q24 33) | 37 (12%) | 272 |
0.448 (1.00) |
0.701 (1.00) |
0.844 (1.00) |
0.638 (1.00) |
0.779 (1.00) |
0.887 (1.00) |
0.688 (1.00) |
0.475 (1.00) |
0.215 (1.00) |
0.134 (1.00) |
0.692 (1.00) |
| Del Peak 29(13q12 11) | 139 (45%) | 170 |
0.828 (1.00) |
0.544 (1.00) |
0.248 (1.00) |
0.073 (1.00) |
0.15 (1.00) |
0.0279 (1.00) |
1 (1.00) |
0.0382 (1.00) |
0.281 (1.00) |
0.166 (1.00) |
0.377 (1.00) |
| Del Peak 30(13q14 2) | 131 (42%) | 178 |
0.0163 (1.00) |
0.281 (1.00) |
0.368 (1.00) |
0.786 (1.00) |
0.244 (1.00) |
0.486 (1.00) |
1 (1.00) |
0.131 (1.00) |
0.377 (1.00) |
0.753 (1.00) |
0.131 (1.00) |
| Del Peak 31(14q11 2) | 45 (15%) | 264 |
0.314 (1.00) |
0.19 (1.00) |
0.72 (1.00) |
0.127 (1.00) |
0.524 (1.00) |
0.291 (1.00) |
1 (1.00) |
0.0158 (1.00) |
0.32 (1.00) |
0.566 (1.00) |
0.246 (1.00) |
| Del Peak 32(14q32 32) | 47 (15%) | 262 |
0.293 (1.00) |
0.472 (1.00) |
0.214 (1.00) |
0.0738 (1.00) |
0.649 (1.00) |
0.437 (1.00) |
0.363 (1.00) |
0.332 (1.00) |
0.769 (1.00) |
0.454 (1.00) |
0.463 (1.00) |
| Del Peak 33(15q15 1) | 76 (25%) | 233 |
0.593 (1.00) |
0.663 (1.00) |
0.462 (1.00) |
0.149 (1.00) |
0.193 (1.00) |
0.589 (1.00) |
0.22 (1.00) |
0.587 (1.00) |
0.0743 (1.00) |
0.302 (1.00) |
0.624 (1.00) |
| Del Peak 34(16q12 1) | 52 (17%) | 257 |
0.319 (1.00) |
0.809 (1.00) |
0.5 (1.00) |
0.922 (1.00) |
0.588 (1.00) |
0.634 (1.00) |
0.218 (1.00) |
0.448 (1.00) |
0.269 (1.00) |
0.0181 (1.00) |
0.634 (1.00) |
| Del Peak 35(16q23 3) | 62 (20%) | 247 |
0.225 (1.00) |
0.425 (1.00) |
0.633 (1.00) |
0.599 (1.00) |
0.205 (1.00) |
0.495 (1.00) |
0.744 (1.00) |
0.962 (1.00) |
0.44 (1.00) |
0.0411 (1.00) |
0.244 (1.00) |
| Del Peak 36(17q25 3) | 41 (13%) | 268 |
0.865 (1.00) |
0.954 (1.00) |
1 (1.00) |
0.48 (1.00) |
0.132 (1.00) |
0.417 (1.00) |
0.25 (1.00) |
0.988 (1.00) |
0.379 (1.00) |
0.212 (1.00) |
0.961 (1.00) |
| Del Peak 37(18q21 2) | 162 (52%) | 147 |
0.158 (1.00) |
0.579 (1.00) |
0.0218 (1.00) |
0.593 (1.00) |
0.69 (1.00) |
0.502 (1.00) |
0.43 (1.00) |
0.000451 (0.355) |
0.00121 (0.941) |
0.0249 (1.00) |
0.721 (1.00) |
| Del Peak 38(18q23) | 173 (56%) | 136 |
0.0948 (1.00) |
0.215 (1.00) |
0.0731 (1.00) |
0.565 (1.00) |
0.633 (1.00) |
0.692 (1.00) |
0.425 (1.00) |
0.00235 (1.00) |
0.00172 (1.00) |
0.118 (1.00) |
0.317 (1.00) |
| Del Peak 39(19p13 3) | 105 (34%) | 204 |
0.0255 (1.00) |
0.301 (1.00) |
0.787 (1.00) |
0.785 (1.00) |
0.595 (1.00) |
0.518 (1.00) |
0.404 (1.00) |
0.146 (1.00) |
0.515 (1.00) |
0.625 (1.00) |
0.217 (1.00) |
| Del Peak 40(19q13 43) | 59 (19%) | 250 |
0.0445 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.015 (1.00) |
0.902 (1.00) |
0.318 (1.00) |
0.405 (1.00) |
0.969 (1.00) |
0.0643 (1.00) |
0.44 (1.00) |
0.0276 (1.00) |
| Del Peak 41(Xp21 3) | 100 (32%) | 209 |
0.0288 (1.00) |
0.393 (1.00) |
0.786 (1.00) |
0.0356 (1.00) |
0.00973 (1.00) |
0.461 (1.00) |
0.158 (1.00) |
0.185 (1.00) |
0.404 (1.00) |
0.398 (1.00) |
0.653 (1.00) |
| Del Peak 42(Xp11 3) | 103 (33%) | 206 |
0.00145 (1.00) |
0.931 (1.00) |
0.684 (1.00) |
0.08 (1.00) |
0.0514 (1.00) |
0.621 (1.00) |
0.124 (1.00) |
0.0334 (1.00) |
0.0427 (1.00) |
0.03 (1.00) |
0.436 (1.00) |
| Del Peak 43(Xq21 33) | 53 (17%) | 256 |
0.352 (1.00) |
0.833 (1.00) |
0.612 (1.00) |
0.5 (1.00) |
0.976 (1.00) |
0.214 (1.00) |
0.599 (1.00) |
0.984 (1.00) |
0.991 (1.00) |
0.122 (1.00) |
0.31 (1.00) |
'Del Peak 7(3p14.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'
P value = 0.000139 (Fisher's exact test), Q value = 0.11
Table S1. Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #10: 'TOBACCOSMOKINGHISTORYINDICATOR'
| nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
|---|---|---|---|---|
| ALL | 81 | 56 | 97 | 64 |
| DEL PEAK 7(3P14.2) MUTATED | 70 | 35 | 79 | 38 |
| DEL PEAK 7(3P14.2) WILD-TYPE | 11 | 21 | 18 | 26 |
Figure S1. Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #10: 'TOBACCOSMOKINGHISTORYINDICATOR'
'Del Peak 8(3p12.2) mutation analysis' versus 'Time to Death'
P value = 0.000275 (logrank test), Q value = 0.22
Table S2. Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 306 | 121 | 0.1 - 210.9 (14.2) |
| DEL PEAK 8(3P12.2) MUTATED | 216 | 98 | 0.1 - 210.9 (13.1) |
| DEL PEAK 8(3P12.2) WILD-TYPE | 90 | 23 | 0.1 - 156.5 (20.4) |
Figure S2. Get High-res Image Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
'Del Peak 8(3p12.2) mutation analysis' versus 'NUMBERPACKYEARSSMOKED'
P value = 8.79e-05 (t-test), Q value = 0.07
Table S3. Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #8: 'NUMBERPACKYEARSSMOKED'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 167 | 49.8 (37.1) |
| DEL PEAK 8(3P12.2) MUTATED | 124 | 55.2 (39.3) |
| DEL PEAK 8(3P12.2) WILD-TYPE | 43 | 34.3 (24.4) |
Figure S3. Get High-res Image Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #8: 'NUMBERPACKYEARSSMOKED'
Methods & Data
Input
-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Clinical data file = HNSC-TP.clin.merged.picked.txt
-
Number of patients = 309
-
Number of copy number variation regions = 72
-
Number of selected clinical features = 11
-
Exclude regions that fewer than K tumors have alterations, K = 3
Survival analysis
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
Student's t-test analysis
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 cnvs using 't.test' function in R
Fisher's exact test
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
Q value calculation
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.
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
[5] GISTIC_version2
Copyright © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.