This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 36 focal events and 17 clinical features across 499 patients, 38 significant findings detected with Q value < 0.25.
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amp_1q31.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', 'TUMOR_SIZE', and 'RACE'.
-
amp_4q31.21 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
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amp_5q21.1 cnv correlated to 'PATHOLOGIC_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
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amp_5q33.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
-
amp_22q11.21 cnv correlated to 'RESIDUAL_TUMOR'.
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amp_xq22.3 cnv correlated to 'GENDER' and 'EXTRATHYROIDAL_EXTENSION'.
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del_2p23.1 cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.
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del_2q22.1 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
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del_2q37.3 cnv correlated to 'PATHOLOGIC_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
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del_9p21.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.
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del_9q22.33 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.
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del_10q23.31 cnv correlated to 'TUMOR_SIZE'.
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del_13q12.3 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_EXPOSURE'.
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del_13q14.3 cnv correlated to 'RADIATION_EXPOSURE'.
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del_16q23.3 cnv correlated to 'PATHOLOGIC_STAGE'.
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del_17p13.1 cnv correlated to 'TUMOR_SIZE'.
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del_19p13.2 cnv correlated to 'TUMOR_SIZE'.
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del_19p13.12 cnv correlated to 'TUMOR_SIZE'.
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del_21q21.1 cnv correlated to 'PATHOLOGIC_STAGE'.
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del_xq28 cnv correlated to 'PATHOLOGIC_STAGE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RADIATION EXPOSURE |
EXTRATHYROIDAL EXTENSION |
RESIDUAL TUMOR |
NUMBER OF LYMPH NODES |
MULTIFOCALITY |
TUMOR SIZE |
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 | 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 | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
amp 1q31 2 | 29 (6%) | 470 |
0.234 (0.775) |
5.12e-05 (0.00783) |
1e-05 (0.00408) |
2e-05 (0.00408) |
0.000629 (0.0482) |
1 (1.00) |
0.666 (1.00) |
0.303 (0.87) |
0.00601 (0.175) |
1 (1.00) |
2e-05 (0.00408) |
0.0423 (0.364) |
0.0293 (0.31) |
0.124 (0.574) |
0.00305 (0.111) |
0.00327 (0.111) |
0.0279 (0.299) |
amp 5q33 1 | 21 (4%) | 478 |
0.0358 (0.348) |
0.0131 (0.236) |
0.00338 (0.111) |
0.556 (1.00) |
0.0191 (0.266) |
1 (1.00) |
0.312 (0.879) |
0.465 (1.00) |
0.0901 (0.487) |
1 (1.00) |
0.0278 (0.299) |
0.395 (0.971) |
0.01 (0.214) |
1 (1.00) |
0.0825 (0.462) |
1 (1.00) |
0.623 (1.00) |
del 2q22 1 | 10 (2%) | 489 |
0.619 (1.00) |
0.264 (0.823) |
0.0253 (0.299) |
0.797 (1.00) |
0.0149 (0.246) |
1 (1.00) |
0.732 (1.00) |
0.495 (1.00) |
0.00482 (0.147) |
1 (1.00) |
0.15 (0.646) |
0.455 (1.00) |
0.00663 (0.178) |
1 (1.00) |
0.349 (0.925) |
1 (1.00) |
1 (1.00) |
amp 5q21 1 | 23 (5%) | 476 |
0.081 (0.462) |
0.022 (0.282) |
0.00793 (0.187) |
0.706 (1.00) |
0.0168 (0.254) |
1 (1.00) |
0.226 (0.775) |
0.809 (1.00) |
0.338 (0.905) |
1 (1.00) |
0.0477 (0.369) |
0.41 (0.989) |
0.00793 (0.187) |
0.834 (1.00) |
0.165 (0.687) |
0.222 (0.775) |
1 (1.00) |
amp xq22 3 | 15 (3%) | 484 |
0.16 (0.673) |
0.375 (0.964) |
0.181 (0.7) |
0.576 (1.00) |
0.416 (1) |
1 (1.00) |
0.0147 (0.246) |
0.566 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.0101 (0.214) |
0.791 (1.00) |
0.308 (0.879) |
0.302 (0.87) |
0.77 (1.00) |
0.8 (1.00) |
1 (1.00) |
del 2p23 1 | 12 (2%) | 487 |
0.619 (1.00) |
0.711 (1.00) |
0.0452 (0.364) |
0.868 (1.00) |
0.0201 (0.268) |
1 (1.00) |
0.742 (1.00) |
1 (1.00) |
0.0027 (0.111) |
1 (1.00) |
0.0756 (0.446) |
0.45 (1.00) |
0.0109 (0.216) |
0.779 (1.00) |
0.931 (1.00) |
1 (1.00) |
1 (1.00) |
del 2q37 3 | 13 (3%) | 486 |
0.236 (0.775) |
0.139 (0.611) |
0.0128 (0.236) |
0.449 (1.00) |
0.0372 (0.356) |
1 (1.00) |
0.349 (0.925) |
0.548 (1.00) |
0.0443 (0.364) |
0.383 (0.964) |
0.236 (0.775) |
0.234 (0.775) |
0.0155 (0.25) |
0.779 (1.00) |
0.0524 (0.377) |
0.759 (1.00) |
1 (1.00) |
del 9p21 3 | 20 (4%) | 479 |
0.049 (0.369) |
0.00966 (0.214) |
0.00023 (0.0282) |
0.177 (0.69) |
1 (1.00) |
0.202 (0.753) |
0.441 (1.00) |
0.465 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.0601 (0.394) |
0.479 (1.00) |
0.123 (0.574) |
0.172 (0.69) |
0.105 (0.549) |
0.888 (1.00) |
0.379 (0.964) |
del 9q22 33 | 27 (5%) | 472 |
0.0642 (0.406) |
0.000623 (0.0482) |
0.00035 (0.0357) |
0.116 (0.572) |
0.294 (0.868) |
0.3 (0.87) |
0.503 (1.00) |
0.669 (1.00) |
1 (1.00) |
1 (1.00) |
0.0908 (0.487) |
0.824 (1.00) |
0.901 (1.00) |
0.692 (1.00) |
0.0189 (0.266) |
0.83 (1.00) |
1 (1.00) |
del 13q12 3 | 16 (3%) | 483 |
0.0274 (0.299) |
0.00132 (0.0805) |
0.121 (0.574) |
0.896 (1.00) |
0.0876 (0.479) |
1 (1.00) |
0.15 (0.646) |
0.0592 (0.394) |
0.49 (1.00) |
0.00166 (0.0922) |
0.78 (1.00) |
0.791 (1.00) |
0.137 (0.608) |
0.802 (1.00) |
0.238 (0.775) |
0.863 (1.00) |
0.615 (1.00) |
amp 4q31 21 | 9 (2%) | 490 |
0.221 (0.775) |
0.0396 (0.364) |
0.257 (0.809) |
0.637 (1.00) |
0.0679 (0.415) |
1 (1.00) |
1 (1.00) |
0.676 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.805 (1.00) |
0.637 (1.00) |
0.0108 (0.216) |
0.313 (0.879) |
0.116 (0.572) |
0.0179 (0.261) |
1 (1.00) |
amp 22q11 21 | 7 (1%) | 492 |
0.785 (1.00) |
0.817 (1.00) |
0.224 (0.775) |
0.614 (1.00) |
1 (1.00) |
1 (1.00) |
0.198 (0.742) |
1 (1.00) |
0.372 (0.961) |
1 (1.00) |
0.748 (1.00) |
0.0127 (0.236) |
0.693 (1.00) |
1 (1.00) |
0.213 (0.775) |
0.317 (0.882) |
0.396 (0.971) |
del 10q23 31 | 12 (2%) | 487 |
0.568 (1.00) |
0.206 (0.762) |
0.0445 (0.364) |
0.765 (1.00) |
0.0201 (0.268) |
1 (1.00) |
0.319 (0.885) |
0.754 (1.00) |
0.327 (0.898) |
1 (1.00) |
0.708 (1.00) |
0.623 (1.00) |
0.0273 (0.299) |
1 (1.00) |
0.00234 (0.11) |
1 (1.00) |
1 (1.00) |
del 13q14 3 | 20 (4%) | 479 |
0.0445 (0.364) |
0.0457 (0.364) |
0.616 (1.00) |
0.968 (1.00) |
0.0449 (0.364) |
1 (1.00) |
0.441 (1.00) |
0.468 (1.00) |
0.532 (1.00) |
0.00345 (0.111) |
0.404 (0.982) |
0.76 (1.00) |
0.083 (0.462) |
0.494 (1.00) |
0.24 (0.775) |
1 (1.00) |
1 (1.00) |
del 16q23 3 | 6 (1%) | 493 |
0.186 (0.71) |
0.0506 (0.373) |
0.00215 (0.11) |
0.0163 (0.254) |
0.449 (1.00) |
0.12 (0.574) |
1 (1.00) |
0.419 (1.00) |
0.175 (0.69) |
0.213 (0.775) |
0.0644 (0.406) |
0.0729 (0.442) |
0.856 (1.00) |
1 (1.00) |
0.42 (1.00) |
0.473 (1.00) |
1 (1.00) |
del 17p13 1 | 8 (2%) | 491 |
0.575 (1.00) |
0.901 (1.00) |
0.147 (0.643) |
0.0312 (0.313) |
0.724 (1.00) |
1 (1.00) |
1 (1.00) |
0.478 (1.00) |
0.222 (0.775) |
0.274 (0.83) |
0.06 (0.394) |
0.339 (0.905) |
0.909 (1.00) |
0.731 (1.00) |
0.0141 (0.246) |
0.582 (1.00) |
1 (1.00) |
del 19p13 2 | 7 (1%) | 492 |
0.129 (0.596) |
0.166 (0.687) |
0.495 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.392 (0.971) |
0.715 (1.00) |
1 (1.00) |
0.0267 (0.299) |
1 (1.00) |
0.187 (0.71) |
0.46 (1.00) |
0.00278 (0.111) |
0.759 (1.00) |
1 (1.00) |
|
del 19p13 12 | 8 (2%) | 491 |
0.1 (0.53) |
0.263 (0.823) |
0.267 (0.826) |
0.881 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.448 (1.00) |
1 (1.00) |
1 (1.00) |
0.0267 (0.299) |
0.601 (1.00) |
0.281 (0.846) |
1 (1.00) |
0.00769 (0.187) |
0.137 (0.608) |
1 (1.00) |
|
del 21q21 1 | 9 (2%) | 490 |
0.686 (1.00) |
0.107 (0.553) |
0.00669 (0.178) |
0.265 (0.823) |
1 (1.00) |
1 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.622 (1.00) |
0.398 (0.971) |
0.736 (1.00) |
0.313 (0.879) |
0.465 (1.00) |
0.296 (0.868) |
1 (1.00) |
del xq28 | 4 (1%) | 495 |
0.753 (1.00) |
0.223 (0.775) |
0.00098 (0.0666) |
0.0483 (0.369) |
0.123 (0.574) |
0.0611 (0.394) |
0.302 (0.87) |
1 (1.00) |
0.112 (0.572) |
0.644 (1.00) |
0.31 (0.879) |
0.041 (0.364) |
1 (1.00) |
0.656 (1.00) |
1 (1.00) |
||
amp 13q14 2 | 6 (1%) | 493 |
0.744 (1.00) |
0.476 (1.00) |
0.118 (0.572) |
0.705 (1.00) |
0.372 (0.961) |
1 (1.00) |
1 (1.00) |
0.676 (1.00) |
0.232 (0.775) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.041 (0.364) |
1 (1.00) |
0.91 (1.00) |
0.48 (1.00) |
1 (1.00) |
amp xp11 22 | 8 (2%) | 491 |
0.0583 (0.394) |
0.0495 (0.369) |
0.0307 (0.313) |
0.398 (0.971) |
0.449 (1.00) |
1 (1.00) |
0.688 (1.00) |
1 (1.00) |
0.222 (0.775) |
0.274 (0.83) |
0.0255 (0.299) |
0.238 (0.775) |
0.117 (0.572) |
0.48 (1.00) |
0.177 (0.69) |
0.666 (1.00) |
1 (1.00) |
del 1q42 13 | 5 (1%) | 494 |
0.575 (1.00) |
0.461 (1.00) |
0.793 (1.00) |
0.517 (1.00) |
0.623 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.555 (1.00) |
1 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.392 (0.971) |
1 (1.00) |
0.0423 (0.364) |
1 (1.00) |
0.0471 (0.369) |
del 4q34 3 | 5 (1%) | 494 |
0.602 (1.00) |
0.742 (1.00) |
0.115 (0.572) |
0.174 (0.69) |
0.623 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.135 (0.608) |
1 (1.00) |
0.289 (0.863) |
0.38 (0.964) |
0.0533 (0.379) |
0.58 (1.00) |
1 (1.00) |
del 5p15 2 | 4 (1%) | 495 |
0.86 (1.00) |
0.182 (0.702) |
0.226 (0.775) |
0.631 (1.00) |
0.372 (0.961) |
1 (1.00) |
0.578 (1.00) |
0.631 (1.00) |
0.223 (0.775) |
1 (1.00) |
0.425 (1.00) |
0.0677 (0.415) |
0.865 (1.00) |
0.338 (0.905) |
0.21 (0.774) |
0.316 (0.882) |
0.332 (0.904) |
del 7q34 | 4 (1%) | 495 |
0.713 (1.00) |
0.757 (1.00) |
0.47 (1.00) |
0.503 (1.00) |
0.623 (1.00) |
1 (1.00) |
1 (1.00) |
0.631 (1.00) |
0.132 (0.602) |
1 (1.00) |
0.644 (1.00) |
1 (1.00) |
0.47 (1.00) |
0.628 (1.00) |
0.0875 (0.479) |
1 (1.00) |
1 (1.00) |
del 8p23 2 | 4 (1%) | 495 |
0.82 (1.00) |
0.913 (1.00) |
0.173 (0.69) |
0.872 (1.00) |
0.248 (0.787) |
1 (1.00) |
0.0611 (0.394) |
0.631 (1.00) |
0.452 (1.00) |
1 (1.00) |
0.645 (1.00) |
1 (1.00) |
0.0773 (0.446) |
1 (1.00) |
0.737 (1.00) |
1 (1.00) |
|
del 8p22 | 4 (1%) | 495 |
0.82 (1.00) |
0.913 (1.00) |
0.171 (0.69) |
0.871 (1.00) |
0.248 (0.787) |
1 (1.00) |
0.0611 (0.394) |
0.631 (1.00) |
0.45 (1.00) |
1 (1.00) |
0.644 (1.00) |
1 (1.00) |
0.0773 (0.446) |
1 (1.00) |
0.737 (1.00) |
1 (1.00) |
|
del 8p12 | 4 (1%) | 495 |
0.82 (1.00) |
0.913 (1.00) |
0.171 (0.69) |
0.871 (1.00) |
0.248 (0.787) |
1 (1.00) |
0.0611 (0.394) |
0.631 (1.00) |
0.451 (1.00) |
1 (1.00) |
0.642 (1.00) |
1 (1.00) |
0.0773 (0.446) |
1 (1.00) |
0.737 (1.00) |
1 (1.00) |
|
del 8q24 22 | 7 (1%) | 492 |
0.754 (1.00) |
0.409 (0.989) |
0.113 (0.572) |
0.796 (1.00) |
0.0611 (0.394) |
1 (1.00) |
0.017 (0.254) |
0.433 (1.00) |
0.152 (0.649) |
1 (1.00) |
0.758 (1.00) |
0.524 (1.00) |
0.041 (0.364) |
1 (1.00) |
0.27 (0.83) |
1 (1.00) |
1 (1.00) |
del 10p12 31 | 7 (1%) | 492 |
0.626 (1.00) |
0.59 (1.00) |
0.382 (0.964) |
0.74 (1.00) |
0.0302 (0.313) |
1 (1.00) |
0.392 (0.971) |
1 (1.00) |
0.816 (1.00) |
1 (1.00) |
0.757 (1.00) |
1 (1.00) |
0.0221 (0.282) |
0.708 (1.00) |
0.0818 (0.462) |
0.732 (1.00) |
1 (1.00) |
del 10q21 2 | 12 (2%) | 487 |
0.571 (1.00) |
0.971 (1.00) |
0.828 (1.00) |
0.741 (1.00) |
0.338 (0.905) |
1 (1.00) |
0.742 (1.00) |
0.754 (1.00) |
0.531 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.352 (0.928) |
0.761 (1.00) |
0.0352 (0.348) |
0.842 (1.00) |
0.61 (1.00) |
del 15q25 3 | 8 (2%) | 491 |
0.574 (1.00) |
0.754 (1.00) |
0.241 (0.775) |
0.73 (1.00) |
0.122 (0.574) |
0.0915 (0.487) |
0.688 (1.00) |
1 (1.00) |
0.0458 (0.364) |
1 (1.00) |
0.601 (1.00) |
0.786 (1.00) |
0.135 (0.608) |
0.731 (1.00) |
0.0758 (0.446) |
0.666 (1.00) |
0.396 (0.971) |
del 18q21 33 | 5 (1%) | 494 |
0.61 (1.00) |
0.36 (0.946) |
0.232 (0.775) |
0.155 (0.661) |
0.623 (1.00) |
1 (1.00) |
1 (1.00) |
0.366 (0.958) |
0.553 (1.00) |
1 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.174 (0.69) |
0.38 (0.964) |
0.838 (1.00) |
1 (1.00) |
0.0251 (0.299) |
del 22q13 1 | 89 (18%) | 410 |
0.238 (0.775) |
0.458 (1.00) |
0.679 (1.00) |
0.861 (1.00) |
0.326 (0.898) |
0.644 (1.00) |
0.43 (1.00) |
0.0673 (0.415) |
0.162 (0.68) |
0.332 (0.904) |
0.551 (1.00) |
0.295 (0.868) |
0.513 (1.00) |
0.286 (0.857) |
0.579 (1.00) |
0.431 (1.00) |
1 (1.00) |
del 22q13 32 | 90 (18%) | 409 |
0.237 (0.775) |
0.487 (1.00) |
0.7 (1.00) |
0.888 (1.00) |
0.272 (0.83) |
0.649 (1.00) |
0.511 (1.00) |
0.0523 (0.377) |
0.116 (0.572) |
0.218 (0.775) |
0.483 (1.00) |
0.294 (0.868) |
0.433 (1.00) |
0.197 (0.742) |
0.579 (1.00) |
0.455 (1.00) |
1 (1.00) |
P value = 5.12e-05 (Wilcoxon-test), Q value = 0.0078
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 499 | 47.3 (15.8) |
AMP PEAK 1(1Q31.2) MUTATED | 29 | 59.9 (17.3) |
AMP PEAK 1(1Q31.2) WILD-TYPE | 470 | 46.5 (15.3) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0041
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
AMP PEAK 1(1Q31.2) MUTATED | 7 | 0 | 12 | 1 | 9 | 0 |
AMP PEAK 1(1Q31.2) WILD-TYPE | 275 | 50 | 99 | 1 | 37 | 6 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0041
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 142 | 165 | 167 | 23 |
AMP PEAK 1(1Q31.2) MUTATED | 2 | 4 | 18 | 5 |
AMP PEAK 1(1Q31.2) WILD-TYPE | 140 | 161 | 149 | 18 |
P value = 0.000629 (Fisher's exact test), Q value = 0.048
nPatients | 0 | 1 |
---|---|---|
ALL | 225 | 224 |
AMP PEAK 1(1Q31.2) MUTATED | 5 | 22 |
AMP PEAK 1(1Q31.2) WILD-TYPE | 220 | 202 |
P value = 0.00601 (Fisher's exact test), Q value = 0.18
nPatients | OTHER, SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 7 | 356 | 100 | 36 |
AMP PEAK 1(1Q31.2) MUTATED | 0 | 25 | 0 | 4 |
AMP PEAK 1(1Q31.2) WILD-TYPE | 7 | 331 | 100 | 32 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0041
nPatients | MINIMAL (T3) | MODERATE/ADVANCED (T4A) | NONE | VERY ADVANCED (T4B) |
---|---|---|---|---|
ALL | 132 | 18 | 330 | 1 |
AMP PEAK 1(1Q31.2) MUTATED | 14 | 4 | 10 | 1 |
AMP PEAK 1(1Q31.2) WILD-TYPE | 118 | 14 | 320 | 0 |
P value = 0.00305 (Wilcoxon-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 401 | 3.0 (1.6) |
AMP PEAK 1(1Q31.2) MUTATED | 24 | 3.8 (1.5) |
AMP PEAK 1(1Q31.2) WILD-TYPE | 377 | 2.9 (1.6) |
P value = 0.00327 (Fisher's exact test), Q value = 0.11
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 52 | 27 | 329 |
AMP PEAK 1(1Q31.2) MUTATED | 1 | 1 | 5 | 21 |
AMP PEAK 1(1Q31.2) WILD-TYPE | 0 | 51 | 22 | 308 |
P value = 0.0108 (Wilcoxon-test), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 386 | 3.6 (6.0) |
AMP PEAK 3(4Q31.21) MUTATED | 8 | 0.1 (0.4) |
AMP PEAK 3(4Q31.21) WILD-TYPE | 378 | 3.6 (6.0) |
P value = 0.00793 (Fisher's exact test), Q value = 0.19
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
AMP PEAK 4(5Q21.1) MUTATED | 8 | 7 | 5 | 1 | 2 | 0 |
AMP PEAK 4(5Q21.1) WILD-TYPE | 274 | 43 | 106 | 1 | 44 | 6 |
P value = 0.00793 (Wilcoxon-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 386 | 3.6 (6.0) |
AMP PEAK 4(5Q21.1) MUTATED | 15 | 0.8 (1.9) |
AMP PEAK 4(5Q21.1) WILD-TYPE | 371 | 3.7 (6.1) |
P value = 0.0131 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 499 | 47.3 (15.8) |
AMP PEAK 5(5Q33.1) MUTATED | 21 | 55.7 (14.8) |
AMP PEAK 5(5Q33.1) WILD-TYPE | 478 | 46.9 (15.7) |
P value = 0.00338 (Fisher's exact test), Q value = 0.11
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
AMP PEAK 5(5Q33.1) MUTATED | 7 | 7 | 5 | 1 | 1 | 0 |
AMP PEAK 5(5Q33.1) WILD-TYPE | 275 | 43 | 106 | 1 | 45 | 6 |
P value = 0.01 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 386 | 3.6 (6.0) |
AMP PEAK 5(5Q33.1) MUTATED | 14 | 1.4 (3.8) |
AMP PEAK 5(5Q33.1) WILD-TYPE | 372 | 3.6 (6.0) |
P value = 0.0127 (Fisher's exact test), Q value = 0.24
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 383 | 51 | 4 | 30 |
AMP PEAK 7(22Q11.21) MUTATED | 2 | 2 | 0 | 2 |
AMP PEAK 7(22Q11.21) WILD-TYPE | 381 | 49 | 4 | 28 |
P value = 0.0147 (Fisher's exact test), Q value = 0.25
nPatients | FEMALE | MALE |
---|---|---|
ALL | 365 | 134 |
AMP PEAK 9(XQ22.3) MUTATED | 15 | 0 |
AMP PEAK 9(XQ22.3) WILD-TYPE | 350 | 134 |
P value = 0.0101 (Fisher's exact test), Q value = 0.21
nPatients | MINIMAL (T3) | MODERATE/ADVANCED (T4A) | NONE | VERY ADVANCED (T4B) |
---|---|---|---|---|
ALL | 132 | 18 | 330 | 1 |
AMP PEAK 9(XQ22.3) MUTATED | 1 | 0 | 13 | 1 |
AMP PEAK 9(XQ22.3) WILD-TYPE | 131 | 18 | 317 | 0 |
P value = 0.0027 (Fisher's exact test), Q value = 0.11
nPatients | OTHER, SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 7 | 356 | 100 | 36 |
DEL PEAK 2(2P23.1) MUTATED | 1 | 4 | 7 | 0 |
DEL PEAK 2(2P23.1) WILD-TYPE | 6 | 352 | 93 | 36 |
P value = 0.0109 (Wilcoxon-test), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 386 | 3.6 (6.0) |
DEL PEAK 2(2P23.1) MUTATED | 9 | 0.3 (1.0) |
DEL PEAK 2(2P23.1) WILD-TYPE | 377 | 3.6 (6.0) |
P value = 0.0149 (Fisher's exact test), Q value = 0.25
nPatients | 0 | 1 |
---|---|---|
ALL | 225 | 224 |
DEL PEAK 3(2Q22.1) MUTATED | 7 | 0 |
DEL PEAK 3(2Q22.1) WILD-TYPE | 218 | 224 |
P value = 0.00482 (Fisher's exact test), Q value = 0.15
nPatients | OTHER, SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 7 | 356 | 100 | 36 |
DEL PEAK 3(2Q22.1) MUTATED | 0 | 3 | 7 | 0 |
DEL PEAK 3(2Q22.1) WILD-TYPE | 7 | 353 | 93 | 36 |
P value = 0.00663 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 386 | 3.6 (6.0) |
DEL PEAK 3(2Q22.1) MUTATED | 7 | 0.0 (0.0) |
DEL PEAK 3(2Q22.1) WILD-TYPE | 379 | 3.6 (6.0) |
P value = 0.0128 (Fisher's exact test), Q value = 0.24
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
DEL PEAK 4(2Q37.3) MUTATED | 4 | 6 | 2 | 0 | 1 | 0 |
DEL PEAK 4(2Q37.3) WILD-TYPE | 278 | 44 | 109 | 2 | 45 | 6 |
P value = 0.0155 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 386 | 3.6 (6.0) |
DEL PEAK 4(2Q37.3) MUTATED | 8 | 0.2 (0.7) |
DEL PEAK 4(2Q37.3) WILD-TYPE | 378 | 3.6 (6.0) |
P value = 0.00966 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 499 | 47.3 (15.8) |
DEL PEAK 15(9P21.3) MUTATED | 20 | 56.8 (16.0) |
DEL PEAK 15(9P21.3) WILD-TYPE | 479 | 46.9 (15.6) |
P value = 0.00023 (Fisher's exact test), Q value = 0.028
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
DEL PEAK 15(9P21.3) MUTATED | 7 | 5 | 4 | 2 | 1 | 1 |
DEL PEAK 15(9P21.3) WILD-TYPE | 275 | 45 | 107 | 0 | 45 | 5 |
P value = 0.000623 (Wilcoxon-test), Q value = 0.048
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 499 | 47.3 (15.8) |
DEL PEAK 16(9Q22.33) MUTATED | 27 | 59.2 (19.0) |
DEL PEAK 16(9Q22.33) WILD-TYPE | 472 | 46.6 (15.3) |
P value = 0.00035 (Fisher's exact test), Q value = 0.036
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
DEL PEAK 16(9Q22.33) MUTATED | 10 | 5 | 4 | 2 | 5 | 1 |
DEL PEAK 16(9Q22.33) WILD-TYPE | 272 | 45 | 107 | 0 | 41 | 5 |
P value = 0.00234 (Wilcoxon-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 401 | 3.0 (1.6) |
DEL PEAK 19(10Q23.31) MUTATED | 9 | 4.6 (1.5) |
DEL PEAK 19(10Q23.31) WILD-TYPE | 392 | 2.9 (1.6) |
P value = 0.00132 (Wilcoxon-test), Q value = 0.081
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 499 | 47.3 (15.8) |
DEL PEAK 20(13Q12.3) MUTATED | 16 | 60.7 (15.5) |
DEL PEAK 20(13Q12.3) WILD-TYPE | 483 | 46.8 (15.6) |
P value = 0.00166 (Fisher's exact test), Q value = 0.092
nPatients | NO | YES |
---|---|---|
ALL | 420 | 17 |
DEL PEAK 20(13Q12.3) MUTATED | 11 | 4 |
DEL PEAK 20(13Q12.3) WILD-TYPE | 409 | 13 |
P value = 0.00345 (Fisher's exact test), Q value = 0.11
nPatients | NO | YES |
---|---|---|
ALL | 420 | 17 |
DEL PEAK 21(13Q14.3) MUTATED | 14 | 4 |
DEL PEAK 21(13Q14.3) WILD-TYPE | 406 | 13 |
P value = 0.00215 (Fisher's exact test), Q value = 0.11
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
DEL PEAK 24(16Q23.3) MUTATED | 0 | 0 | 3 | 0 | 2 | 1 |
DEL PEAK 24(16Q23.3) WILD-TYPE | 282 | 50 | 108 | 2 | 44 | 5 |
P value = 0.0141 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 401 | 3.0 (1.6) |
DEL PEAK 25(17P13.1) MUTATED | 7 | 4.5 (1.6) |
DEL PEAK 25(17P13.1) WILD-TYPE | 394 | 2.9 (1.6) |
P value = 0.00278 (Wilcoxon-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 401 | 3.0 (1.6) |
DEL PEAK 27(19P13.2) MUTATED | 4 | 5.8 (0.6) |
DEL PEAK 27(19P13.2) WILD-TYPE | 397 | 2.9 (1.6) |
P value = 0.00769 (Wilcoxon-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 401 | 3.0 (1.6) |
DEL PEAK 28(19P13.12) MUTATED | 5 | 5.2 (1.6) |
DEL PEAK 28(19P13.12) WILD-TYPE | 396 | 2.9 (1.6) |
P value = 0.00669 (Fisher's exact test), Q value = 0.18
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
DEL PEAK 30(21Q21.1) MUTATED | 1 | 4 | 2 | 0 | 2 | 0 |
DEL PEAK 30(21Q21.1) WILD-TYPE | 281 | 46 | 109 | 2 | 44 | 6 |
P value = 0.00098 (Fisher's exact test), Q value = 0.067
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 282 | 50 | 111 | 2 | 46 | 6 |
DEL PEAK 33(XQ28) MUTATED | 0 | 4 | 0 | 0 | 0 | 0 |
DEL PEAK 33(XQ28) WILD-TYPE | 282 | 46 | 111 | 2 | 46 | 6 |
-
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/THCA-TP/22511444/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/22507188/THCA-TP.merged_data.txt
-
Number of patients = 499
-
Number of significantly focal cnvs = 36
-
Number of selected clinical features = 17
-
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.