Thyroid Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features<BR>(primary solid tumor cohort)

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.

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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