Thyroid Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
(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 arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 36 arm-level results and 15 clinical features across 309 patients, 29 significant findings detected with Q value < 0.25.

- 4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 4q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 5p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 5q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 7p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 7q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 12p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 12q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 14q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 16p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 16q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 17p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 17q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 19p gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'NUMBER.OF.LYMPH.NODES'.

- 19q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 20p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 20q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 2p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 2q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

- 3q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 10p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 11p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 11q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 13q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 15q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 36 arm-level results and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 29 significant findings detected.

|  | Clinical Features | Time to Death | AGE | GENDER | HISTOLOGICAL TYPE | RADIATIONS RADIATION REGIMENINDICATION | RADIATIONEXPOSURE | DISTANT METASTASIS | EXTRATHYROIDAL EXTENSION | LYMPH NODE METASTASIS | COMPLETENESS OF RESECTION | NUMBER OF LYMPH NODES | TUMOR STAGECODE | NEOPLASM DISEASESTAGE | MULTIFOCALITY | TUMOR SIZE
| 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 | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | Fisher's exact test | t-test
19p gain | 3 (1%) | 306 | 1 (1.00) | 0.186 (1.00) | 1 (1.00) | 0.000234 (0.11) | 1 (1.00) | 1 (1.00) | 0.277 (1.00) | 1 (1.00) | 0.53 (1.00) | 0.219 (1.00) | 2.04e-15 (9.77e-13) |  | 0.691 (1.00) | 1 (1.00) | 0.557 (1.00)
2q loss | 6 (2%) | 303 | 1 (1.00) | 0.0372 (1.00) | 1 (1.00) | 0.018 (1.00) | 1 (1.00) | 1 (1.00) | 0.275 (1.00) | 0.418 (1.00) | 0.171 (1.00) | 0.418 (1.00) | 1.93e-15 (9.45e-13) |  | 0.000428 (0.201) | 0.684 (1.00) | 0.322 (1.00)
4p gain | 4 (1%) | 305 | 0.00468 (1.00) | 0.118 (1.00) | 1 (1.00) | 0.365 (1.00) | 0.17 (1.00) | 1 (1.00) | 0.168 (1.00) | 1 (1.00) | 0.374 (1.00) | 0.288 (1.00) | 2e-15 (9.72e-13) |  | 0.492 (1.00) | 0.622 (1.00) | 0.429 (1.00)
4q gain | 4 (1%) | 305 | 0.00468 (1.00) | 0.118 (1.00) | 1 (1.00) | 0.365 (1.00) | 0.17 (1.00) | 1 (1.00) | 0.168 (1.00) | 1 (1.00) | 0.374 (1.00) | 0.288 (1.00) | 2e-15 (9.72e-13) |  | 0.492 (1.00) | 0.622 (1.00) | 0.429 (1.00)
5p gain | 9 (3%) | 300 | 0.00468 (1.00) | 0.0351 (1.00) | 1 (1.00) | 0.0193 (1.00) | 0.345 (1.00) | 1 (1.00) | 0.00842 (1.00) | 0.745 (1.00) | 0.149 (1.00) | 0.581 (1.00) | 1.89e-15 (9.39e-13) |  | 0.00967 (1.00) | 0.501 (1.00) | 0.0735 (1.00)
5q gain | 9 (3%) | 300 | 0.00468 (1.00) | 0.0351 (1.00) | 1 (1.00) | 0.0193 (1.00) | 0.345 (1.00) | 1 (1.00) | 0.00842 (1.00) | 0.745 (1.00) | 0.149 (1.00) | 0.581 (1.00) | 1.89e-15 (9.39e-13) |  | 0.00967 (1.00) | 0.501 (1.00) | 0.0735 (1.00)
7p gain | 11 (4%) | 298 | 1 (1.00) | 0.036 (1.00) | 1 (1.00) | 0.0257 (1.00) | 1 (1.00) | 1 (1.00) | 0.023 (1.00) | 0.449 (1.00) | 0.0924 (1.00) | 0.299 (1.00) | 1.82e-15 (9.1e-13) |  | 0.00306 (1.00) | 0.541 (1.00) | 0.17 (1.00)
7q gain | 13 (4%) | 296 | 1 (1.00) | 0.02 (1.00) | 0.742 (1.00) | 0.00409 (1.00) | 1 (1.00) | 1 (1.00) | 0.0478 (1.00) | 0.803 (1.00) | 0.0137 (1.00) | 0.114 (1.00) | 1.82e-15 (9.1e-13) |  | 0.00986 (1.00) | 0.572 (1.00) | 0.161 (1.00)
12p gain | 9 (3%) | 300 | 1 (1.00) | 0.181 (1.00) | 0.461 (1.00) | 0.0193 (1.00) | 1 (1.00) | 1 (1.00) | 0.00842 (1.00) | 0.745 (1.00) | 0.149 (1.00) | 0.581 (1.00) | 1.89e-15 (9.39e-13) |  | 0.0196 (1.00) | 0.501 (1.00) | 0.367 (1.00)
12q gain | 10 (3%) | 299 | 1 (1.00) | 0.141 (1.00) | 0.46 (1.00) | 0.0134 (1.00) | 1 (1.00) | 1 (1.00) | 0.00361 (1.00) | 0.562 (1.00) | 0.054 (1.00) | 0.627 (1.00) | 1.89e-15 (9.39e-13) |  | 0.0426 (1.00) | 0.75 (1.00) | 0.367 (1.00)
14q gain | 6 (2%) | 303 | 1 (1.00) | 0.256 (1.00) | 0.342 (1.00) | 0.0844 (1.00) | 1 (1.00) | 1 (1.00) | 0.0574 (1.00) | 1 (1.00) | 0.183 (1.00) | 0.418 (1.00) | 2e-15 (9.72e-13) |  | 0.0384 (1.00) | 0.214 (1.00) | 0.468 (1.00)
16p gain | 8 (3%) | 301 | 1 (1.00) | 0.251 (1.00) | 0.207 (1.00) | 0.183 (1.00) | 1 (1.00) | 1 (1.00) | 0.356 (1.00) | 1 (1.00) | 0.0428 (1.00) | 0.172 (1.00) | 1.96e-15 (9.58e-13) |  | 0.139 (1.00) | 1 (1.00) | 0.475 (1.00)
16q gain | 6 (2%) | 303 | 1 (1.00) | 0.152 (1.00) | 0.342 (1.00) | 0.501 (1.00) | 1 (1.00) | 1 (1.00) | 0.275 (1.00) | 1 (1.00) | 0.183 (1.00) | 0.418 (1.00) | 2e-15 (9.72e-13) |  | 0.0384 (1.00) | 0.684 (1.00) | 0.425 (1.00)
17p gain | 8 (3%) | 301 | 1 (1.00) | 0.306 (1.00) | 0.207 (1.00) | 0.0216 (1.00) | 1 (1.00) | 1 (1.00) | 0.161 (1.00) | 0.327 (1.00) | 0.174 (1.00) | 0.531 (1.00) | 1.93e-15 (9.45e-13) |  | 0.00888 (1.00) | 0.723 (1.00) | 0.476 (1.00)
17q gain | 9 (3%) | 300 | 1 (1.00) | 0.466 (1.00) | 0.119 (1.00) | 0.0429 (1.00) | 1 (1.00) | 1 (1.00) | 0.0682 (1.00) | 0.27 (1.00) | 0.149 (1.00) | 0.581 (1.00) | 1.89e-15 (9.39e-13) |  | 0.0212 (1.00) | 1 (1.00) | 0.75 (1.00)
19q gain | 4 (1%) | 305 | 0.00468 (1.00) | 0.0697 (1.00) | 1 (1.00) | 0.00146 (0.683) | 0.17 (1.00) | 1 (1.00) | 0.168 (1.00) | 0.609 (1.00) | 0.374 (1.00) | 0.288 (1.00) | 2e-15 (9.72e-13) |  | 0.492 (1.00) | 1 (1.00) | 0.311 (1.00)
20p gain | 5 (2%) | 304 | 1 (1.00) | 0.279 (1.00) | 0.339 (1.00) | 0.0281 (1.00) | 1 (1.00) | 1 (1.00) | 0.121 (1.00) | 0.406 (1.00) | 0.149 (1.00) | 1 (1.00) | 2.04e-15 (9.77e-13) |  | 0.00997 (1.00) | 1 (1.00) | 0.149 (1.00)
20q gain | 5 (2%) | 304 | 1 (1.00) | 0.279 (1.00) | 0.339 (1.00) | 0.0281 (1.00) | 1 (1.00) | 1 (1.00) | 0.121 (1.00) | 0.406 (1.00) | 0.149 (1.00) | 1 (1.00) | 2.04e-15 (9.77e-13) |  | 0.00997 (1.00) | 1 (1.00) | 0.149 (1.00)
2p loss | 7 (2%) | 302 | 1 (1.00) | 0.189 (1.00) | 1 (1.00) | 0.0482 (1.00) | 1 (1.00) | 1 (1.00) | 0.2 (1.00) | 0.309 (1.00) | 0.112 (1.00) | 0.477 (1.00) | 1.89e-15 (9.39e-13) |  | 0.00258 (1.00) | 1 (1.00) | 0.896 (1.00)
3q loss | 3 (1%) | 306 | 1 (1.00) | 0.2 (1.00) | 0.573 (1.00) | 0.0563 (1.00) | 1 (1.00) | 1 (1.00) | 0.277 (1.00) | 1 (1.00) | 0.53 (1.00) | 1 (1.00) | 2.04e-15 (9.77e-13) |  | 0.0256 (1.00) | 1 (1.00) | 0.147 (1.00)
9p loss | 5 (2%) | 304 | 1 (1.00) | 0.923 (1.00) | 0.339 (1.00) | 0.554 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.406 (1.00) | 0.552 (1.00) | 1 (1.00) | 0.47 (1.00) |  | 3.76e-05 (0.0178) | 1 (1.00) | 0.467 (1.00)
9q loss | 7 (2%) | 302 | 1 (1.00) | 0.34 (1.00) | 1 (1.00) | 0.158 (1.00) | 0.28 (1.00) | 0.294 (1.00) | 0.498 (1.00) | 0.309 (1.00) | 0.512 (1.00) | 1 (1.00) | 0.734 (1.00) |  | 8.55e-06 (0.00405) | 1 (1.00) | 0.486 (1.00)
10p loss | 4 (1%) | 305 | 1 (1.00) | 0.0668 (1.00) | 1 (1.00) | 0.202 (1.00) | 1 (1.00) | 1 (1.00) | 0.643 (1.00) | 0.609 (1.00) | 0.374 (1.00) | 1 (1.00) | 2.04e-15 (9.77e-13) |  | 0.00104 (0.486) | 1 (1.00) | 0.147 (1.00)
11p loss | 4 (1%) | 305 | 0.00468 (1.00) | 0.0308 (1.00) | 0.254 (1.00) | 0.141 (1.00) | 0.17 (1.00) | 1 (1.00) | 0.168 (1.00) | 0.609 (1.00) | 0.374 (1.00) | 0.288 (1.00) | 2e-15 (9.72e-13) |  | 0.492 (1.00) | 0.622 (1.00) | 0.203 (1.00)
11q loss | 5 (2%) | 304 | 0.00468 (1.00) | 0.0185 (1.00) | 0.0976 (1.00) | 0.0947 (1.00) | 0.208 (1.00) | 1 (1.00) | 0.121 (1.00) | 0.406 (1.00) | 0.256 (1.00) | 0.355 (1.00) | 1.96e-15 (9.58e-13) |  | 0.159 (1.00) | 1 (1.00) | 0.203 (1.00)
13q loss | 9 (3%) | 300 | 0.00468 (1.00) | 0.0329 (1.00) | 0.231 (1.00) | 0.0651 (1.00) | 0.345 (1.00) | 0.00424 (1.00) | 0.268 (1.00) | 0.745 (1.00) | 0.144 (1.00) | 0.408 (1.00) | 1.86e-15 (9.24e-13) |  | 0.143 (1.00) | 0.501 (1.00) | 0.402 (1.00)
15q loss | 3 (1%) | 306 | 1 (1.00) | 0.405 (1.00) | 1 (1.00) | 0.0425 (1.00) | 1 (1.00) | 1 (1.00) | 0.277 (1.00) | 1 (1.00) | 0.53 (1.00) | 1 (1.00) | 2.04e-15 (9.77e-13) |  | 0.0256 (1.00) | 1 (1.00) | 0.354 (1.00)
1q gain | 10 (3%) | 299 | 1 (1.00) | 0.133 (1.00) | 0.712 (1.00) | 0.153 (1.00) | 0.375 (1.00) | 1 (1.00) | 1 (1.00) | 0.00345 (1.00) | 0.357 (1.00) | 0.157 (1.00) | 0.402 (1.00) |  | 0.1 (1.00) | 0.335 (1.00) | 0.277 (1.00)
11p gain | 3 (1%) | 306 | 1 (1.00) | 0.718 (1.00) | 0.573 (1.00) | 0.0143 (1.00) | 1 (1.00) | 1 (1.00) | 0.277 (1.00) | 1 (1.00) | 0.544 (1.00) | 1 (1.00) |  |  | 0.441 (1.00) | 1 (1.00) | 0.0131 (1.00)
1p loss | 3 (1%) | 306 | 1 (1.00) | 0.181 (1.00) | 1 (1.00) | 0.431 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.53 (1.00) | 1 (1.00) |  |  | 0.0256 (1.00) | 1 (1.00) |
10q loss | 3 (1%) | 306 | 1 (1.00) | 0.0336 (1.00) | 0.573 (1.00) | 0.431 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.53 (1.00) | 1 (1.00) |  |  | 0.0256 (1.00) | 1 (1.00) |
17p loss | 4 (1%) | 305 | 1 (1.00) | 0.525 (1.00) | 0.575 (1.00) | 0.798 (1.00) | 0.0109 (1.00) | 1 (1.00) | 0.643 (1.00) | 0.0488 (1.00) | 0.291 (1.00) | 1 (1.00) | 0.587 (1.00) |  | 0.071 (1.00) | 0.622 (1.00) | 0.227 (1.00)
18p loss | 3 (1%) | 306 | 1 (1.00) | 0.971 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.861 (1.00) | 1 (1.00) | 0.0653 (1.00) |  | 0.0384 (1.00) | 1 (1.00) | 0.655 (1.00)
18q loss | 3 (1%) | 306 | 1 (1.00) | 0.971 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.861 (1.00) | 1 (1.00) | 0.0653 (1.00) |  | 0.0384 (1.00) | 1 (1.00) | 0.655 (1.00)
21q loss | 5 (2%) | 304 | 1 (1.00) | 0.0267 (1.00) | 0.6 (1.00) | 0.314 (1.00) | 1 (1.00) | 1 (1.00) | 0.412 (1.00) | 0.406 (1.00) | 0.552 (1.00) | 0.557 (1.00) | 0.981 (1.00) |  | 0.00437 (1.00) | 0.371 (1.00) | 0.683 (1.00)
22q loss | 42 (14%) | 267 | 1 (1.00) | 0.277 (1.00) | 1 (1.00) | 0.00071 (0.333) | 0.23 (1.00) | 0.699 (1.00) | 0.575 (1.00) | 0.111 (1.00) | 0.189 (1.00) | 0.614 (1.00) | 0.611 (1.00) |  | 0.364 (1.00) | 0.406 (1.00) | 0.559 (1.00)

'4p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 9.7e-13

Table S1. Gene #2: '4p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
4P GAIN MUTATED | 4 | 0.0 (0.0)
4P GAIN WILD-TYPE | 244 | 2.8 (5.1)

Figure S1. Get High-res Image Gene #2: '4p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'4q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 9.7e-13

Table S2. Gene #3: '4q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
4Q GAIN MUTATED | 4 | 0.0 (0.0)
4Q GAIN WILD-TYPE | 244 | 2.8 (5.1)

Figure S2. Get High-res Image Gene #3: '4q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'5p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.89e-15 (t-test), Q value = 9.4e-13

Table S3. Gene #4: '5p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
5P GAIN MUTATED | 7 | 0.0 (0.0)
5P GAIN WILD-TYPE | 241 | 2.8 (5.1)

Figure S3. Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'5q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.89e-15 (t-test), Q value = 9.4e-13

Table S4. Gene #5: '5q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
5Q GAIN MUTATED | 7 | 0.0 (0.0)
5Q GAIN WILD-TYPE | 241 | 2.8 (5.1)

Figure S4. Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'7p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.82e-15 (t-test), Q value = 9.1e-13

Table S5. Gene #6: '7p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
7P GAIN MUTATED | 9 | 0.0 (0.0)
7P GAIN WILD-TYPE | 239 | 2.8 (5.1)

Figure S5. Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'7q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.82e-15 (t-test), Q value = 9.1e-13

Table S6. Gene #7: '7q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
7Q GAIN MUTATED | 9 | 0.0 (0.0)
7Q GAIN WILD-TYPE | 239 | 2.8 (5.1)

Figure S6. Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'12p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.89e-15 (t-test), Q value = 9.4e-13

Table S7. Gene #9: '12p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
12P GAIN MUTATED | 7 | 0.0 (0.0)
12P GAIN WILD-TYPE | 241 | 2.8 (5.1)

Figure S7. Get High-res Image Gene #9: '12p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'12q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.89e-15 (t-test), Q value = 9.4e-13

Table S8. Gene #10: '12q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
12Q GAIN MUTATED | 7 | 0.0 (0.0)
12Q GAIN WILD-TYPE | 241 | 2.8 (5.1)

Figure S8. Get High-res Image Gene #10: '12q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'14q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 9.7e-13

Table S9. Gene #11: '14q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
14Q GAIN MUTATED | 4 | 0.0 (0.0)
14Q GAIN WILD-TYPE | 244 | 2.8 (5.1)

Figure S9. Get High-res Image Gene #11: '14q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'16p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.96e-15 (t-test), Q value = 9.6e-13

Table S10. Gene #12: '16p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
16P GAIN MUTATED | 5 | 0.0 (0.0)
16P GAIN WILD-TYPE | 243 | 2.8 (5.1)

Figure S10. Get High-res Image Gene #12: '16p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'16q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 9.7e-13

Table S11. Gene #13: '16q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
16Q GAIN MUTATED | 4 | 0.0 (0.0)
16Q GAIN WILD-TYPE | 244 | 2.8 (5.1)

Figure S11. Get High-res Image Gene #13: '16q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'17p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.93e-15 (t-test), Q value = 9.4e-13

Table S12. Gene #14: '17p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
17P GAIN MUTATED | 6 | 0.0 (0.0)
17P GAIN WILD-TYPE | 242 | 2.8 (5.1)

Figure S12. Get High-res Image Gene #14: '17p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'17q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.89e-15 (t-test), Q value = 9.4e-13

Table S13. Gene #15: '17q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
17Q GAIN MUTATED | 7 | 0.0 (0.0)
17Q GAIN WILD-TYPE | 241 | 2.8 (5.1)

Figure S13. Get High-res Image Gene #15: '17q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'19p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000234 (Fisher's exact test), Q value = 0.11

Table S14. Gene #16: '19p gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients | OTHER | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
--- | --- | --- | --- | ---
ALL | 20 | 183 | 75 | 31
19P GAIN MUTATED | 3 | 0 | 0 | 0
19P GAIN WILD-TYPE | 17 | 183 | 75 | 31

Figure S14. Get High-res Image Gene #16: '19p gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'19p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.04e-15 (t-test), Q value = 9.8e-13

Table S15. Gene #16: '19p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
19P GAIN MUTATED | 3 | 0.0 (0.0)
19P GAIN WILD-TYPE | 245 | 2.8 (5.1)

Figure S15. Get High-res Image Gene #16: '19p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'19q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 9.7e-13

Table S16. Gene #17: '19q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
19Q GAIN MUTATED | 4 | 0.0 (0.0)
19Q GAIN WILD-TYPE | 244 | 2.8 (5.1)

Figure S16. Get High-res Image Gene #17: '19q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20p gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.04e-15 (t-test), Q value = 9.8e-13

Table S17. Gene #18: '20p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
20P GAIN MUTATED | 3 | 0.0 (0.0)
20P GAIN WILD-TYPE | 245 | 2.8 (5.1)

Figure S17. Get High-res Image Gene #18: '20p gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20q gain mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.04e-15 (t-test), Q value = 9.8e-13

Table S18. Gene #19: '20q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
20Q GAIN MUTATED | 3 | 0.0 (0.0)
20Q GAIN WILD-TYPE | 245 | 2.8 (5.1)

Figure S18. Get High-res Image Gene #19: '20q gain mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2p loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.89e-15 (t-test), Q value = 9.4e-13

Table S19. Gene #21: '2p loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
2P LOSS MUTATED | 7 | 0.0 (0.0)
2P LOSS WILD-TYPE | 241 | 2.8 (5.1)

Figure S19. Get High-res Image Gene #21: '2p loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2q loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.93e-15 (t-test), Q value = 9.4e-13

Table S20. Gene #22: '2q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
2Q LOSS MUTATED | 6 | 0.0 (0.0)
2Q LOSS WILD-TYPE | 242 | 2.8 (5.1)

Figure S20. Get High-res Image Gene #22: '2q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2q loss mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000428 (Chi-square test), Q value = 0.2

Table S21. Gene #22: '2q loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | ---
ALL | 177 | 33 | 67 | 28 | 3
2Q LOSS MUTATED | 1 | 4 | 1 | 0 | 0
2Q LOSS WILD-TYPE | 176 | 29 | 66 | 28 | 3

Figure S21. Get High-res Image Gene #22: '2q loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'3q loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.04e-15 (t-test), Q value = 9.8e-13

Table S22. Gene #23: '3q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
3Q LOSS MUTATED | 3 | 0.0 (0.0)
3Q LOSS WILD-TYPE | 245 | 2.8 (5.1)

Figure S22. Get High-res Image Gene #23: '3q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'9p loss mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.76e-05 (Chi-square test), Q value = 0.018

Table S23. Gene #24: '9p loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | ---
ALL | 177 | 33 | 67 | 28 | 3
9P LOSS MUTATED | 1 | 4 | 0 | 0 | 0
9P LOSS WILD-TYPE | 176 | 29 | 67 | 28 | 3

Figure S23. Get High-res Image Gene #24: '9p loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'9q loss mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.55e-06 (Chi-square test), Q value = 0.0041

Table S24. Gene #25: '9q loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | ---
ALL | 177 | 33 | 67 | 28 | 3
9Q LOSS MUTATED | 1 | 5 | 0 | 1 | 0
9Q LOSS WILD-TYPE | 176 | 28 | 67 | 27 | 3

Figure S24. Get High-res Image Gene #25: '9q loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'10p loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.04e-15 (t-test), Q value = 9.8e-13

Table S25. Gene #26: '10p loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
10P LOSS MUTATED | 3 | 0.0 (0.0)
10P LOSS WILD-TYPE | 245 | 2.8 (5.1)

Figure S25. Get High-res Image Gene #26: '10p loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'11p loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 9.7e-13

Table S26. Gene #28: '11p loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
11P LOSS MUTATED | 4 | 0.0 (0.0)
11P LOSS WILD-TYPE | 244 | 2.8 (5.1)

Figure S26. Get High-res Image Gene #28: '11p loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'11q loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.96e-15 (t-test), Q value = 9.6e-13

Table S27. Gene #29: '11q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
11Q LOSS MUTATED | 5 | 0.0 (0.0)
11Q LOSS WILD-TYPE | 243 | 2.8 (5.1)

Figure S27. Get High-res Image Gene #29: '11q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'13q loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.86e-15 (t-test), Q value = 9.2e-13

Table S28. Gene #30: '13q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
13Q LOSS MUTATED | 8 | 0.0 (0.0)
13Q LOSS WILD-TYPE | 240 | 2.8 (5.1)

Figure S28. Get High-res Image Gene #30: '13q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'15q loss mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.04e-15 (t-test), Q value = 9.8e-13

Table S29. Gene #31: '15q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 248 | 2.7 (5.1)
15Q LOSS MUTATED | 3 | 0.0 (0.0)
15Q LOSS WILD-TYPE | 245 | 2.8 (5.1)

Figure S29. Get High-res Image Gene #31: '15q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

- Mutation data file = broad_values_by_arm.mutsig.cluster.txt

- Clinical data file = THCA-TP.clin.merged.picked.txt

- Number of patients = 309

- Number of significantly arm-level cnvs = 36

- Number of selected clinical features = 15

- Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

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

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 mutations 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

Chi-square test

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

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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)
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