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 303 patients, 27 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'.

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

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

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

- 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, 27 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%) | 300 | 1 (1.00) | 0.186 (1.00) | 0.575 (1.00) | 0.000248 (0.117) | 1 (1.00) | 1 (1.00) | 0.279 (1.00) | 1 (1.00) | 0.529 (1.00) | 0.222 (1.00) | 3.19e-15 (1.53e-12) |  | 0.703 (1.00) | 1 (1.00) | 0.558 (1.00)
4p gain | 4 (1%) | 299 | 0.00468 (1.00) | 0.118 (1.00) | 1 (1.00) | 0.371 (1.00) | 0.173 (1.00) | 1 (1.00) | 0.17 (1.00) | 1 (1.00) | 0.374 (1.00) | 0.292 (1.00) | 3.14e-15 (1.52e-12) |  | 0.502 (1.00) | 0.623 (1.00) | 0.43 (1.00)
4q gain | 4 (1%) | 299 | 0.00468 (1.00) | 0.118 (1.00) | 1 (1.00) | 0.371 (1.00) | 0.173 (1.00) | 1 (1.00) | 0.17 (1.00) | 1 (1.00) | 0.374 (1.00) | 0.292 (1.00) | 3.14e-15 (1.52e-12) |  | 0.502 (1.00) | 0.623 (1.00) | 0.43 (1.00)
5p gain | 9 (3%) | 294 | 0.00468 (1.00) | 0.0351 (1.00) | 1 (1.00) | 0.0215 (1.00) | 0.351 (1.00) | 1 (1.00) | 0.0112 (1.00) | 0.746 (1.00) | 0.153 (1.00) | 0.585 (1.00) | 2.97e-15 (1.47e-12) |  | 0.0112 (1.00) | 0.501 (1.00) | 0.0739 (1.00)
5q gain | 9 (3%) | 294 | 0.00468 (1.00) | 0.0351 (1.00) | 1 (1.00) | 0.0215 (1.00) | 0.351 (1.00) | 1 (1.00) | 0.0112 (1.00) | 0.746 (1.00) | 0.153 (1.00) | 0.585 (1.00) | 2.97e-15 (1.47e-12) |  | 0.0112 (1.00) | 0.501 (1.00) | 0.0739 (1.00)
7p gain | 11 (4%) | 292 | 1 (1.00) | 0.0361 (1.00) | 0.737 (1.00) | 0.0296 (1.00) | 1 (1.00) | 1 (1.00) | 0.0236 (1.00) | 0.451 (1.00) | 0.0947 (1.00) | 0.301 (1.00) | 2.86e-15 (1.42e-12) |  | 0.00371 (1.00) | 0.541 (1.00) | 0.171 (1.00)
7q gain | 13 (4%) | 290 | 1 (1.00) | 0.0201 (1.00) | 0.529 (1.00) | 0.00532 (1.00) | 1 (1.00) | 1 (1.00) | 0.0503 (1.00) | 0.804 (1.00) | 0.0152 (1.00) | 0.116 (1.00) | 2.86e-15 (1.42e-12) |  | 0.0116 (1.00) | 0.573 (1.00) | 0.162 (1.00)
12p gain | 10 (3%) | 293 | 1 (1.00) | 0.141 (1.00) | 0.461 (1.00) | 0.0155 (1.00) | 1 (1.00) | 1 (1.00) | 0.00495 (1.00) | 0.563 (1.00) | 0.0579 (1.00) | 0.63 (1.00) | 2.97e-15 (1.47e-12) |  | 0.0481 (1.00) | 0.75 (1.00) | 0.369 (1.00)
12q gain | 10 (3%) | 293 | 1 (1.00) | 0.141 (1.00) | 0.461 (1.00) | 0.0155 (1.00) | 1 (1.00) | 1 (1.00) | 0.00495 (1.00) | 0.563 (1.00) | 0.0579 (1.00) | 0.63 (1.00) | 2.97e-15 (1.47e-12) |  | 0.0481 (1.00) | 0.75 (1.00) | 0.369 (1.00)
14q gain | 6 (2%) | 297 | 1 (1.00) | 0.257 (1.00) | 0.343 (1.00) | 0.0949 (1.00) | 1 (1.00) | 1 (1.00) | 0.0589 (1.00) | 1 (1.00) | 0.192 (1.00) | 0.422 (1.00) | 3.14e-15 (1.52e-12) |  | 0.043 (1.00) | 0.214 (1.00) | 0.47 (1.00)
16p gain | 8 (3%) | 295 | 1 (1.00) | 0.252 (1.00) | 0.208 (1.00) | 0.212 (1.00) | 1 (1.00) | 1 (1.00) | 0.361 (1.00) | 1 (1.00) | 0.0468 (1.00) | 0.174 (1.00) | 3.08e-15 (1.5e-12) |  | 0.151 (1.00) | 1 (1.00) | 0.477 (1.00)
16q gain | 6 (2%) | 297 | 1 (1.00) | 0.152 (1.00) | 0.343 (1.00) | 0.503 (1.00) | 1 (1.00) | 1 (1.00) | 0.279 (1.00) | 1 (1.00) | 0.192 (1.00) | 0.422 (1.00) | 3.14e-15 (1.52e-12) |  | 0.043 (1.00) | 0.684 (1.00) | 0.426 (1.00)
17p gain | 8 (3%) | 295 | 1 (1.00) | 0.307 (1.00) | 0.208 (1.00) | 0.0224 (1.00) | 1 (1.00) | 1 (1.00) | 0.165 (1.00) | 0.33 (1.00) | 0.18 (1.00) | 0.535 (1.00) | 3.02e-15 (1.47e-12) |  | 0.0104 (1.00) | 0.723 (1.00) | 0.478 (1.00)
17q gain | 9 (3%) | 294 | 1 (1.00) | 0.467 (1.00) | 0.118 (1.00) | 0.0467 (1.00) | 1 (1.00) | 1 (1.00) | 0.0705 (1.00) | 0.273 (1.00) | 0.153 (1.00) | 0.585 (1.00) | 2.97e-15 (1.47e-12) |  | 0.0242 (1.00) | 1 (1.00) | 0.752 (1.00)
19q gain | 4 (1%) | 299 | 0.00468 (1.00) | 0.0697 (1.00) | 1 (1.00) | 0.00151 (0.705) | 0.173 (1.00) | 1 (1.00) | 0.17 (1.00) | 0.61 (1.00) | 0.374 (1.00) | 0.292 (1.00) | 3.14e-15 (1.52e-12) |  | 0.502 (1.00) | 1 (1.00) | 0.312 (1.00)
20p gain | 5 (2%) | 298 | 1 (1.00) | 0.279 (1.00) | 0.336 (1.00) | 0.0333 (1.00) | 1 (1.00) | 1 (1.00) | 0.123 (1.00) | 0.406 (1.00) | 0.158 (1.00) | 1 (1.00) | 3.19e-15 (1.53e-12) |  | 0.0115 (1.00) | 1 (1.00) | 0.149 (1.00)
20q gain | 5 (2%) | 298 | 1 (1.00) | 0.279 (1.00) | 0.336 (1.00) | 0.0333 (1.00) | 1 (1.00) | 1 (1.00) | 0.123 (1.00) | 0.406 (1.00) | 0.158 (1.00) | 1 (1.00) | 3.19e-15 (1.53e-12) |  | 0.0115 (1.00) | 1 (1.00) | 0.149 (1.00)
2p loss | 7 (2%) | 296 | 1 (1.00) | 0.189 (1.00) | 0.684 (1.00) | 0.0496 (1.00) | 1 (1.00) | 1 (1.00) | 0.203 (1.00) | 0.311 (1.00) | 0.112 (1.00) | 0.48 (1.00) | 2.97e-15 (1.47e-12) |  | 0.0031 (1.00) | 1 (1.00) | 0.9 (1.00)
2q loss | 6 (2%) | 297 | 1 (1.00) | 0.0373 (1.00) | 1 (1.00) | 0.0186 (1.00) | 1 (1.00) | 1 (1.00) | 0.279 (1.00) | 0.42 (1.00) | 0.171 (1.00) | 0.422 (1.00) | 3.02e-15 (1.47e-12) |  | 0.000534 (0.251) | 0.684 (1.00) | 0.325 (1.00)
3q loss | 3 (1%) | 300 | 1 (1.00) | 0.2 (1.00) | 1 (1.00) | 0.0585 (1.00) | 1 (1.00) | 1 (1.00) | 0.279 (1.00) | 1 (1.00) | 0.529 (1.00) | 1 (1.00) | 3.19e-15 (1.53e-12) |  | 0.0285 (1.00) | 1 (1.00) | 0.147 (1.00)
9p loss | 5 (2%) | 298 | 1 (1.00) | 0.922 (1.00) | 0.336 (1.00) | 0.559 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.406 (1.00) | 0.55 (1.00) | 1 (1.00) | 0.456 (1.00) |  | 4.92e-05 (0.0232) | 0.681 (1.00) | 0.477 (1.00)
9q loss | 7 (2%) | 296 | 1 (1.00) | 0.34 (1.00) | 0.684 (1.00) | 0.163 (1.00) | 0.284 (1.00) | 0.298 (1.00) | 0.502 (1.00) | 0.311 (1.00) | 0.513 (1.00) | 1 (1.00) | 0.745 (1.00) |  | 1.14e-05 (0.00541) | 0.72 (1.00) | 0.5 (1.00)
11p loss | 4 (1%) | 299 | 0.00468 (1.00) | 0.0307 (1.00) | 0.262 (1.00) | 0.171 (1.00) | 0.173 (1.00) | 1 (1.00) | 0.17 (1.00) | 0.61 (1.00) | 0.374 (1.00) | 0.292 (1.00) | 3.14e-15 (1.52e-12) |  | 0.502 (1.00) | 0.623 (1.00) | 0.204 (1.00)
11q loss | 5 (2%) | 298 | 0.00468 (1.00) | 0.0185 (1.00) | 0.103 (1.00) | 0.0977 (1.00) | 0.212 (1.00) | 1 (1.00) | 0.123 (1.00) | 0.406 (1.00) | 0.256 (1.00) | 0.359 (1.00) | 3.08e-15 (1.5e-12) |  | 0.169 (1.00) | 1 (1.00) | 0.204 (1.00)
13q loss | 9 (3%) | 294 | 0.00468 (1.00) | 0.0329 (1.00) | 0.236 (1.00) | 0.0753 (1.00) | 0.351 (1.00) | 0.00442 (1.00) | 0.273 (1.00) | 0.746 (1.00) | 0.144 (1.00) | 0.407 (1.00) | 2.91e-15 (1.44e-12) |  | 0.154 (1.00) | 0.501 (1.00) | 0.404 (1.00)
15q loss | 3 (1%) | 300 | 1 (1.00) | 0.405 (1.00) | 0.575 (1.00) | 0.0437 (1.00) | 1 (1.00) | 1 (1.00) | 0.279 (1.00) | 1 (1.00) | 0.529 (1.00) | 1 (1.00) | 3.19e-15 (1.53e-12) |  | 0.0285 (1.00) | 1 (1.00) | 0.355 (1.00)
1q gain | 8 (3%) | 295 | 1 (1.00) | 0.161 (1.00) | 0.419 (1.00) | 0.307 (1.00) | 0.318 (1.00) | 1 (1.00) | 0.754 (1.00) | 0.0035 (1.00) | 0.3 (1.00) | 0.289 (1.00) | 0.438 (1.00) |  | 0.0803 (1.00) | 0.169 (1.00) | 0.61 (1.00)
11p gain | 3 (1%) | 300 | 1 (1.00) | 0.718 (1.00) | 1 (1.00) | 0.0218 (1.00) | 1 (1.00) | 1 (1.00) | 0.279 (1.00) | 1 (1.00) | 0.555 (1.00) | 1 (1.00) |  |  | 0.445 (1.00) | 0.619 (1.00) | 0.013 (1.00)
1p loss | 3 (1%) | 300 | 1 (1.00) | 0.181 (1.00) | 0.575 (1.00) | 0.541 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.529 (1.00) | 1 (1.00) |  |  | 0.0285 (1.00) | 0.619 (1.00) |
10p loss | 3 (1%) | 300 | 1 (1.00) | 0.0335 (1.00) | 1 (1.00) | 0.541 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.529 (1.00) | 1 (1.00) |  |  | 0.0285 (1.00) | 1 (1.00) |
10q loss | 3 (1%) | 300 | 1 (1.00) | 0.0335 (1.00) | 1 (1.00) | 0.541 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.529 (1.00) | 1 (1.00) |  |  | 0.0285 (1.00) | 1 (1.00) |
17p loss | 4 (1%) | 299 | 1 (1.00) | 0.526 (1.00) | 0.575 (1.00) | 0.799 (1.00) | 0.0113 (1.00) | 1 (1.00) | 0.644 (1.00) | 0.05 (1.00) | 0.274 (1.00) | 1 (1.00) | 0.573 (1.00) |  | 0.075 (1.00) | 0.366 (1.00) | 0.227 (1.00)
18p loss | 3 (1%) | 300 | 1 (1.00) | 0.97 (1.00) | 0.575 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.862 (1.00) | 1 (1.00) | 0.0615 (1.00) |  | 0.0425 (1.00) | 0.619 (1.00) | 0.665 (1.00)
18q loss | 3 (1%) | 300 | 1 (1.00) | 0.97 (1.00) | 0.575 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.862 (1.00) | 1 (1.00) | 0.0615 (1.00) |  | 0.0425 (1.00) | 0.619 (1.00) | 0.665 (1.00)
21q loss | 5 (2%) | 298 | 1 (1.00) | 0.0267 (1.00) | 0.602 (1.00) | 0.317 (1.00) | 1 (1.00) | 1 (1.00) | 0.415 (1.00) | 0.406 (1.00) | 0.55 (1.00) | 0.556 (1.00) | 0.993 (1.00) |  | 0.00498 (1.00) | 0.371 (1.00) | 0.686 (1.00)
22q loss | 39 (13%) | 264 | 1 (1.00) | 0.327 (1.00) | 1 (1.00) | 0.000578 (0.271) | 0.229 (1.00) | 0.7 (1.00) | 0.552 (1.00) | 0.161 (1.00) | 0.119 (1.00) | 0.632 (1.00) | 0.448 (1.00) |  | 0.458 (1.00) | 0.304 (1.00) | 0.739 (1.00)

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

P value = 3.14e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
4P GAIN MUTATED | 4 | 0.0 (0.0)
4P GAIN WILD-TYPE | 238 | 2.8 (5.2)

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 = 3.14e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
4Q GAIN MUTATED | 4 | 0.0 (0.0)
4Q GAIN WILD-TYPE | 238 | 2.8 (5.2)

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 = 2.97e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
5P GAIN MUTATED | 7 | 0.0 (0.0)
5P GAIN WILD-TYPE | 235 | 2.9 (5.2)

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 = 2.97e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
5Q GAIN MUTATED | 7 | 0.0 (0.0)
5Q GAIN WILD-TYPE | 235 | 2.9 (5.2)

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 = 2.86e-15 (t-test), Q value = 1.4e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
7P GAIN MUTATED | 9 | 0.0 (0.0)
7P GAIN WILD-TYPE | 233 | 2.9 (5.2)

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 = 2.86e-15 (t-test), Q value = 1.4e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
7Q GAIN MUTATED | 9 | 0.0 (0.0)
7Q GAIN WILD-TYPE | 233 | 2.9 (5.2)

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 = 2.97e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
12P GAIN MUTATED | 7 | 0.0 (0.0)
12P GAIN WILD-TYPE | 235 | 2.9 (5.2)

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 = 2.97e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
12Q GAIN MUTATED | 7 | 0.0 (0.0)
12Q GAIN WILD-TYPE | 235 | 2.9 (5.2)

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 = 3.14e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
14Q GAIN MUTATED | 4 | 0.0 (0.0)
14Q GAIN WILD-TYPE | 238 | 2.8 (5.2)

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 = 3.08e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
16P GAIN MUTATED | 5 | 0.0 (0.0)
16P GAIN WILD-TYPE | 237 | 2.8 (5.2)

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 = 3.14e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
16Q GAIN MUTATED | 4 | 0.0 (0.0)
16Q GAIN WILD-TYPE | 238 | 2.8 (5.2)

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 = 3.02e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
17P GAIN MUTATED | 6 | 0.0 (0.0)
17P GAIN WILD-TYPE | 236 | 2.8 (5.2)

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 = 2.97e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
17Q GAIN MUTATED | 7 | 0.0 (0.0)
17Q GAIN WILD-TYPE | 235 | 2.9 (5.2)

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 = 0.000248 (Fisher's exact test), Q value = 0.12

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 | 178 | 75 | 30
19P GAIN MUTATED | 3 | 0 | 0 | 0
19P GAIN WILD-TYPE | 17 | 178 | 75 | 30

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 = 3.19e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
19P GAIN MUTATED | 3 | 0.0 (0.0)
19P GAIN WILD-TYPE | 239 | 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 = 3.14e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
19Q GAIN MUTATED | 4 | 0.0 (0.0)
19Q GAIN WILD-TYPE | 238 | 2.8 (5.2)

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 = 3.19e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
20P GAIN MUTATED | 3 | 0.0 (0.0)
20P GAIN WILD-TYPE | 239 | 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 = 3.19e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
20Q GAIN MUTATED | 3 | 0.0 (0.0)
20Q GAIN WILD-TYPE | 239 | 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 = 2.97e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
2P LOSS MUTATED | 7 | 0.0 (0.0)
2P LOSS WILD-TYPE | 235 | 2.9 (5.2)

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 = 3.02e-15 (t-test), Q value = 1.5e-12

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
2Q LOSS MUTATED | 6 | 0.0 (0.0)
2Q LOSS WILD-TYPE | 236 | 2.8 (5.2)

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

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

P value = 3.19e-15 (t-test), Q value = 1.5e-12

Table S21. Gene #23: '3q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
3Q LOSS MUTATED | 3 | 0.0 (0.0)
3Q LOSS WILD-TYPE | 239 | 2.8 (5.1)

Figure S21. 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 = 4.92e-05 (Chi-square test), Q value = 0.023

Table S22. Gene #24: '9p loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | ---
ALL | 173 | 33 | 66 | 27 | 3
9P LOSS MUTATED | 1 | 4 | 0 | 0 | 0
9P LOSS WILD-TYPE | 172 | 29 | 66 | 27 | 3

Figure S22. 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 = 1.14e-05 (Chi-square test), Q value = 0.0054

Table S23. Gene #25: '9q loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | ---
ALL | 173 | 33 | 66 | 27 | 3
9Q LOSS MUTATED | 1 | 5 | 0 | 1 | 0
9Q LOSS WILD-TYPE | 172 | 28 | 66 | 26 | 3

Figure S23. Get High-res Image Gene #25: '9q loss mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 3.14e-15 (t-test), Q value = 1.5e-12

Table S24. Gene #28: '11p loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
11P LOSS MUTATED | 4 | 0.0 (0.0)
11P LOSS WILD-TYPE | 238 | 2.8 (5.2)

Figure S24. 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 = 3.08e-15 (t-test), Q value = 1.5e-12

Table S25. Gene #29: '11q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
11Q LOSS MUTATED | 5 | 0.0 (0.0)
11Q LOSS WILD-TYPE | 237 | 2.8 (5.2)

Figure S25. 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 = 2.91e-15 (t-test), Q value = 1.4e-12

Table S26. Gene #30: '13q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
13Q LOSS MUTATED | 8 | 0.0 (0.0)
13Q LOSS WILD-TYPE | 234 | 2.9 (5.2)

Figure S26. 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 = 3.19e-15 (t-test), Q value = 1.5e-12

Table S27. Gene #31: '15q loss mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 242 | 2.8 (5.1)
15Q LOSS MUTATED | 3 | 0.0 (0.0)
15Q LOSS WILD-TYPE | 239 | 2.8 (5.1)

Figure S27. 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 = 303

- 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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