Correlation between copy number variations of arm-level result and selected clinical features

Thyroid Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C12N50BM

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 42 arm-level results and 15 clinical features across 421 patients, 42 significant findings detected with Q value < 0.25.

1q gain cnv correlated to 'EXTRATHYROIDAL.EXTENSION' and 'NEOPLASM.DISEASESTAGE'.
4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
4q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
5p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
5q gain cnv correlated to 'DISTANT.METASTASIS', 'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.
7p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.
7q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.
12p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
12q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
13q 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' and 'NEOPLASM.DISEASESTAGE'.
16q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.
17p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
17q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
19p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
19q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
20p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.
20q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.
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'.
6q loss cnv correlated to 'Time to Death'.
9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.
9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.
10p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
10q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
11p loss cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.
11q loss cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.
13q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
19p loss cnv correlated to 'Time to Death'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 42 arm-level results and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 42 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
5q gain	0 (0%)	410	0.00139 (0.738)	0.008 (1.00)	1 (1.00)	0.25 (1.00)	0.314 (1.00)	1 (1.00)	0.000218 (0.117)	0.0351 (1.00)	0.156 (1.00)	0.828 (1.00)	1.04e-21 (5.98e-19)		1.68e-05 (0.00922)	0.224 (1.00)	0.057 (1.00)
1q gain	0 (0%)	403	0.0639 (1.00)	0.00122 (0.655)	0.416 (1.00)	0.0941 (1.00)	0.463 (1.00)	1 (1.00)	0.867 (1.00)	4.34e-06 (0.0024)	0.00641 (1.00)	0.0201 (1.00)	0.33 (1.00)		3.37e-05 (0.0183)	0.225 (1.00)	0.0333 (1.00)
7p gain	0 (0%)	409	0.132 (1.00)	0.0191 (1.00)	0.738 (1.00)	0.0947 (1.00)	1 (1.00)	1 (1.00)	0.00238 (1.00)	0.0206 (1.00)	0.12 (1.00)	0.309 (1.00)	1.01e-21 (5.87e-19)		1.05e-05 (0.00577)	0.381 (1.00)	0.269 (1.00)
7q gain	0 (0%)	407	0.151 (1.00)	0.011 (1.00)	0.533 (1.00)	0.0565 (1.00)	1 (1.00)	1 (1.00)	0.00406 (1.00)	0.0414 (1.00)	0.0171 (1.00)	0.167 (1.00)	1.01e-21 (5.87e-19)		9.51e-05 (0.0515)	0.413 (1.00)	0.278 (1.00)
16p gain	0 (0%)	412	0.0515 (1.00)	0.139 (1.00)	0.12 (1.00)	0.566 (1.00)	1 (1.00)	1 (1.00)	0.0909 (1.00)	0.0343 (1.00)	0.0603 (1.00)	0.148 (1.00)	1.11e-21 (6.32e-19)		3.53e-05 (0.0192)	1 (1.00)	0.567 (1.00)
16q gain	0 (0%)	414	0.0448 (1.00)	0.0726 (1.00)	0.199 (1.00)	0.326 (1.00)	1 (1.00)	1 (1.00)	0.0955 (1.00)	0.0233 (1.00)	0.24 (1.00)	0.335 (1.00)	1.13e-21 (6.43e-19)		5.12e-07 (0.000284)	0.704 (1.00)	0.46 (1.00)
20p gain	0 (0%)	414	0.119 (1.00)	0.0677 (1.00)	0.684 (1.00)	0.125 (1.00)	1 (1.00)	1 (1.00)	0.00929 (1.00)	0.0233 (1.00)	0.24 (1.00)	0.718 (1.00)	1.13e-21 (6.43e-19)		2.98e-07 (0.000166)	0.704 (1.00)	0.0763 (1.00)
20q gain	0 (0%)	414	0.119 (1.00)	0.0677 (1.00)	0.684 (1.00)	0.125 (1.00)	1 (1.00)	1 (1.00)	0.00929 (1.00)	0.0233 (1.00)	0.24 (1.00)	0.718 (1.00)	1.13e-21 (6.43e-19)		2.98e-07 (0.000166)	0.704 (1.00)	0.0763 (1.00)
11p loss	0 (0%)	414	0.00162 (0.858)	0.000427 (0.23)	0.0132 (1.00)	0.831 (1.00)	0.212 (1.00)	1 (1.00)	0.0955 (1.00)	0.548 (1.00)	0.584 (1.00)	0.493 (1.00)	0.0855 (1.00)		1.36e-06 (0.000752)	0.704 (1.00)	0.0337 (1.00)
11q loss	0 (0%)	412	0.00416 (1.00)	7.15e-05 (0.0387)	0.00132 (0.705)	1 (1.00)	0.265 (1.00)	1 (1.00)	0.0909 (1.00)	0.8 (1.00)	0.712 (1.00)	0.603 (1.00)	0.266 (1.00)		2.97e-05 (0.0162)	1 (1.00)	0.0127 (1.00)
4p gain	0 (0%)	417	0.0044 (1.00)	0.123 (1.00)	1 (1.00)	0.479 (1.00)	0.127 (1.00)	1 (1.00)	0.105 (1.00)	1 (1.00)	0.307 (1.00)	0.294 (1.00)	1.13e-21 (6.43e-19)		0.655 (1.00)	0.324 (1.00)	0.587 (1.00)
4q gain	0 (0%)	417	0.0044 (1.00)	0.123 (1.00)	1 (1.00)	0.479 (1.00)	0.127 (1.00)	1 (1.00)	0.105 (1.00)	1 (1.00)	0.307 (1.00)	0.294 (1.00)	1.13e-21 (6.43e-19)		0.655 (1.00)	0.324 (1.00)	0.587 (1.00)
5p gain	0 (0%)	409	0.0193 (1.00)	0.00308 (1.00)	1 (1.00)	0.345 (1.00)	0.337 (1.00)	1 (1.00)	0.00238 (1.00)	0.0514 (1.00)	0.175 (1.00)	0.844 (1.00)	0.0605 (1.00)		2.58e-05 (0.0141)	0.381 (1.00)	0.0293 (1.00)
12p gain	0 (0%)	412	0.623 (1.00)	0.201 (1.00)	0.459 (1.00)	0.0899 (1.00)	1 (1.00)	1 (1.00)	0.00137 (0.728)	0.607 (1.00)	0.0951 (1.00)	0.603 (1.00)	1.06e-21 (6.09e-19)		0.0364 (1.00)	0.19 (1.00)	0.607 (1.00)
12q gain	0 (0%)	411	0.623 (1.00)	0.16 (1.00)	0.463 (1.00)	0.0339 (1.00)	1 (1.00)	1 (1.00)	0.00104 (0.556)	0.506 (1.00)	0.03 (1.00)	0.515 (1.00)	1.06e-21 (6.09e-19)		0.0741 (1.00)	0.346 (1.00)	0.607 (1.00)
13q gain	0 (0%)	418	0.799 (1.00)	0.267 (1.00)	1 (1.00)	0.233 (1.00)	1 (1.00)	1 (1.00)	0.13 (1.00)	1 (1.00)	0.462 (1.00)	1 (1.00)	1.16e-21 (6.49e-19)		0.047 (1.00)	0.084 (1.00)	0.378 (1.00)
14q gain	0 (0%)	413	0.617 (1.00)	0.147 (1.00)	0.686 (1.00)	0.214 (1.00)	1 (1.00)	1 (1.00)	0.0346 (1.00)	1 (1.00)	0.116 (1.00)	0.55 (1.00)	1.11e-21 (6.32e-19)		0.0134 (1.00)	0.146 (1.00)	0.387 (1.00)
17p gain	0 (0%)	410	0.505 (1.00)	0.245 (1.00)	0.303 (1.00)	0.25 (1.00)	1 (1.00)	1 (1.00)	0.126 (1.00)	0.677 (1.00)	0.156 (1.00)	0.555 (1.00)	0.000126 (0.0683)		0.00965 (1.00)	0.546 (1.00)	0.438 (1.00)
17q gain	0 (0%)	409	0.505 (1.00)	0.388 (1.00)	0.31 (1.00)	0.345 (1.00)	1 (1.00)	1 (1.00)	0.0704 (1.00)	0.689 (1.00)	0.12 (1.00)	0.592 (1.00)	1.57e-05 (0.00863)		0.0205 (1.00)	0.771 (1.00)	0.648 (1.00)
19p gain	0 (0%)	417	0.771 (1.00)	0.0671 (1.00)	1 (1.00)	0.117 (1.00)	1 (1.00)	1 (1.00)	0.105 (1.00)	1 (1.00)	0.307 (1.00)	0.294 (1.00)	1.13e-21 (6.43e-19)		0.655 (1.00)	0.324 (1.00)	0.305 (1.00)
19q gain	0 (0%)	416	0.0161 (1.00)	0.0282 (1.00)	0.605 (1.00)	0.178 (1.00)	0.156 (1.00)	1 (1.00)	0.0282 (1.00)	1 (1.00)	0.197 (1.00)	0.364 (1.00)	1.11e-21 (6.32e-19)		0.378 (1.00)	0.658 (1.00)	0.193 (1.00)
2p loss	0 (0%)	414	0.853 (1.00)	0.208 (1.00)	0.684 (1.00)	0.125 (1.00)	1 (1.00)	1 (1.00)	0.0955 (1.00)	0.308 (1.00)	0.0752 (1.00)	0.493 (1.00)	1.06e-21 (6.09e-19)		0.00524 (1.00)	0.704 (1.00)	0.682 (1.00)
2q loss	0 (0%)	415	0.853 (1.00)	0.0423 (1.00)	1 (1.00)	0.0614 (1.00)	1 (1.00)	1 (1.00)	0.188 (1.00)	0.344 (1.00)	0.123 (1.00)	0.431 (1.00)	1.08e-21 (6.2e-19)		0.000937 (0.503)	0.412 (1.00)	0.716 (1.00)
3q loss	0 (0%)	418	0.901 (1.00)	0.212 (1.00)	1 (1.00)	0.233 (1.00)	1 (1.00)	1 (1.00)	0.13 (1.00)	0.604 (1.00)	0.462 (1.00)	1 (1.00)	1.16e-21 (6.49e-19)		0.047 (1.00)	0.584 (1.00)	0.231 (1.00)
6q loss	0 (0%)	418	3.21e-05 (0.0175)	0.184 (1.00)	1 (1.00)	0.233 (1.00)	1 (1.00)	0.0828 (1.00)	0.13 (1.00)	0.604 (1.00)	0.462 (1.00)	1 (1.00)			0.047 (1.00)	1 (1.00)	0.225 (1.00)
9p loss	0 (0%)	413	0.8 (1.00)	0.22 (1.00)	0.425 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.398 (1.00)	0.772 (1.00)	0.83 (1.00)	1 (1.00)	0.336 (1.00)		1.27e-07 (7.1e-05)	1 (1.00)	0.106 (1.00)
9q loss	0 (0%)	409	0.00198 (1.00)	0.0112 (1.00)	0.51 (1.00)	0.749 (1.00)	0.337 (1.00)	0.409 (1.00)	0.317 (1.00)	0.0459 (1.00)	0.72 (1.00)	0.483 (1.00)	0.991 (1.00)		6.18e-17 (3.45e-14)	1 (1.00)	0.0479 (1.00)
10p loss	0 (0%)	416	0.879 (1.00)	0.0227 (1.00)	0.605 (1.00)	0.585 (1.00)	1 (1.00)	1 (1.00)	0.246 (1.00)	1 (1.00)	0.197 (1.00)	1 (1.00)	1.13e-21 (6.43e-19)		0.00729 (1.00)	0.658 (1.00)	0.201 (1.00)
10q loss	0 (0%)	417	0.931 (1.00)	0.0057 (1.00)	0.268 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.369 (1.00)	1 (1.00)	0.307 (1.00)	1 (1.00)	1.16e-21 (6.49e-19)		0.074 (1.00)	0.324 (1.00)	0.217 (1.00)
13q loss	0 (0%)	412	0.103 (1.00)	0.0373 (1.00)	0.241 (1.00)	0.0899 (1.00)	0.265 (1.00)	0.00305 (1.00)	0.0909 (1.00)	0.607 (1.00)	0.093 (1.00)	0.461 (1.00)	1.04e-21 (5.98e-19)		0.231 (1.00)	0.19 (1.00)	0.642 (1.00)
19p loss	0 (0%)	418	5.48e-06 (0.00302)	0.0819 (1.00)	0.16 (1.00)	0.653 (1.00)	1 (1.00)	0.122 (1.00)	0.603 (1.00)	0.604 (1.00)	0.471 (1.00)	1 (1.00)			0.0664 (1.00)	0.259 (1.00)
11p gain	0 (0%)	417	0.618 (1.00)	0.725 (1.00)	1 (1.00)	0.479 (1.00)	1 (1.00)	1 (1.00)	0.369 (1.00)	0.416 (1.00)	0.453 (1.00)	1 (1.00)			0.655 (1.00)	0.634 (1.00)	0.139 (1.00)
11q gain	0 (0%)	418	0.621 (1.00)	0.736 (1.00)	0.574 (1.00)	0.653 (1.00)	1 (1.00)	1 (1.00)	0.603 (1.00)	0.604 (1.00)	0.471 (1.00)	1 (1.00)			0.813 (1.00)	0.259 (1.00)	0.321 (1.00)
18p gain	0 (0%)	418	0.669 (1.00)	0.876 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.603 (1.00)	1 (1.00)	0.471 (1.00)	1 (1.00)			0.813 (1.00)	1 (1.00)	0.327 (1.00)
18q gain	0 (0%)	418	0.669 (1.00)	0.876 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.603 (1.00)	1 (1.00)	0.471 (1.00)	1 (1.00)			0.813 (1.00)	1 (1.00)	0.327 (1.00)
1p loss	0 (0%)	418	0.901 (1.00)	0.192 (1.00)	0.574 (1.00)	0.233 (1.00)	1 (1.00)	1 (1.00)	0.603 (1.00)	0.604 (1.00)	0.462 (1.00)	1 (1.00)			0.047 (1.00)	1 (1.00)
15q loss	0 (0%)	416	0.777 (1.00)	0.769 (1.00)	0.336 (1.00)	0.0194 (1.00)	1 (1.00)	1 (1.00)	0.0443 (1.00)	1 (1.00)	0.484 (1.00)	1 (1.00)	0.579 (1.00)		0.0191 (1.00)	1 (1.00)	0.407 (1.00)
17p loss	0 (0%)	417	0.696 (1.00)	0.556 (1.00)	0.576 (1.00)	0.479 (1.00)	0.00594 (1.00)	1 (1.00)	0.369 (1.00)	0.139 (1.00)	0.539 (1.00)	1 (1.00)	0.379 (1.00)		0.112 (1.00)	0.634 (1.00)	0.277 (1.00)
18p loss	0 (0%)	418	0.879 (1.00)	0.939 (1.00)	0.574 (1.00)	0.653 (1.00)	1 (1.00)	1 (1.00)	0.603 (1.00)	0.604 (1.00)	0.797 (1.00)	1 (1.00)	0.0277 (1.00)		0.0664 (1.00)	1 (1.00)	0.389 (1.00)
18q loss	0 (0%)	418	0.879 (1.00)	0.939 (1.00)	0.574 (1.00)	0.653 (1.00)	1 (1.00)	1 (1.00)	0.603 (1.00)	0.604 (1.00)	0.797 (1.00)	1 (1.00)	0.0277 (1.00)		0.0664 (1.00)	1 (1.00)	0.389 (1.00)
21q loss	0 (0%)	415	0.892 (1.00)	0.00855 (1.00)	0.647 (1.00)	0.794 (1.00)	1 (1.00)	1 (1.00)	0.474 (1.00)	0.344 (1.00)	0.647 (1.00)	0.662 (1.00)	0.994 (1.00)		0.0204 (1.00)	0.091 (1.00)	0.985 (1.00)
22q loss	0 (0%)	367	0.339 (1.00)	0.146 (1.00)	0.738 (1.00)	0.0216 (1.00)	0.232 (1.00)	0.708 (1.00)	0.397 (1.00)	0.175 (1.00)	0.252 (1.00)	0.899 (1.00)	0.201 (1.00)		0.281 (1.00)	0.378 (1.00)	0.783 (1.00)

'1q gain' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 4.34e-06 (Fisher's exact test), Q value = 0.0024

Table S1. Gene #1: '1q gain' versus Clinical Feature #8: 'EXTRATHYROIDAL.EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	113	13	275	1
1Q GAIN CNV	10	3	4	1
1Q GAIN WILD-TYPE	103	10	271	0

Figure S1. Get High-res Image Gene #1: '1q gain' versus Clinical Feature #8: 'EXTRATHYROIDAL.EXTENSION'

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.37e-05 (Chi-square test), Q value = 0.018

Table S2. Gene #1: '1q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
1Q GAIN CNV	3	1	8	1	5	0
1Q GAIN WILD-TYPE	234	43	86	1	31	5

Figure S2. Get High-res Image Gene #1: '1q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S3. Gene #2: '4p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
4P GAIN CNV	4	0.0 (0.0)
4P GAIN WILD-TYPE	324	3.6 (6.2)

Figure S3. Get High-res Image Gene #2: '4p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S4. Gene #3: '4q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
4Q GAIN CNV	4	0.0 (0.0)
4Q GAIN WILD-TYPE	324	3.6 (6.2)

Figure S4. Get High-res Image Gene #3: '4q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'5p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.58e-05 (Chi-square test), Q value = 0.014

Table S5. Gene #4: '5p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
5P GAIN CNV	2	4	5	1	0	0
5P GAIN WILD-TYPE	235	40	89	1	36	5

Figure S5. Get High-res Image Gene #4: '5p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'5q gain' versus 'DISTANT.METASTASIS'

P value = 0.000218 (Fisher's exact test), Q value = 0.12

Table S6. Gene #5: '5q gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

nPatients	M0	M1	MX
ALL	235	8	177
5Q GAIN CNV	0	0	11
5Q GAIN WILD-TYPE	235	8	166

Figure S6. Get High-res Image Gene #5: '5q gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

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

P value = 1.04e-21 (t-test), Q value = 6e-19

Table S7. Gene #5: '5q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
5Q GAIN CNV	8	0.0 (0.0)
5Q GAIN WILD-TYPE	320	3.6 (6.3)

Figure S7. Get High-res Image Gene #5: '5q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'5q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.68e-05 (Chi-square test), Q value = 0.0092

Table S8. Gene #5: '5q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
5Q GAIN CNV	2	4	4	1	0	0
5Q GAIN WILD-TYPE	235	40	90	1	36	5

Figure S8. Get High-res Image Gene #5: '5q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.01e-21 (t-test), Q value = 5.9e-19

Table S9. Gene #6: '7p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
7P GAIN CNV	9	0.0 (0.0)
7P GAIN WILD-TYPE	319	3.6 (6.3)

Figure S9. Get High-res Image Gene #6: '7p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.05e-05 (Chi-square test), Q value = 0.0058

Table S10. Gene #6: '7p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
7P GAIN CNV	3	5	3	1	0	0
7P GAIN WILD-TYPE	234	39	91	1	36	5

Figure S10. Get High-res Image Gene #6: '7p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.01e-21 (t-test), Q value = 5.9e-19

Table S11. Gene #7: '7q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
7Q GAIN CNV	9	0.0 (0.0)
7Q GAIN WILD-TYPE	319	3.6 (6.3)

Figure S11. Get High-res Image Gene #7: '7q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.51e-05 (Chi-square test), Q value = 0.051

Table S12. Gene #7: '7q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
7Q GAIN CNV	4	5	4	1	0	0
7Q GAIN WILD-TYPE	233	39	90	1	36	5

Figure S12. Get High-res Image Gene #7: '7q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.06e-21 (t-test), Q value = 6.1e-19

Table S13. Gene #10: '12p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
12P GAIN CNV	7	0.0 (0.0)
12P GAIN WILD-TYPE	321	3.6 (6.2)

Figure S13. Get High-res Image Gene #10: '12p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.06e-21 (t-test), Q value = 6.1e-19

Table S14. Gene #11: '12q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
12Q GAIN CNV	7	0.0 (0.0)
12Q GAIN WILD-TYPE	321	3.6 (6.2)

Figure S14. Get High-res Image Gene #11: '12q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'13q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-21 (t-test), Q value = 6.5e-19

Table S15. Gene #12: '13q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
13Q GAIN CNV	3	0.0 (0.0)
13Q GAIN WILD-TYPE	325	3.6 (6.2)

Figure S15. Get High-res Image Gene #12: '13q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.11e-21 (t-test), Q value = 6.3e-19

Table S16. Gene #13: '14q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
14Q GAIN CNV	5	0.0 (0.0)
14Q GAIN WILD-TYPE	323	3.6 (6.2)

Figure S16. Get High-res Image Gene #13: '14q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.11e-21 (t-test), Q value = 6.3e-19

Table S17. Gene #14: '16p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
16P GAIN CNV	5	0.0 (0.0)
16P GAIN WILD-TYPE	323	3.6 (6.2)

Figure S17. Get High-res Image Gene #14: '16p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'16p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.53e-05 (Chi-square test), Q value = 0.019

Table S18. Gene #14: '16p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
16P GAIN CNV	3	3	2	1	0	0
16P GAIN WILD-TYPE	234	41	92	1	36	5

Figure S18. Get High-res Image Gene #14: '16p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S19. Gene #15: '16q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
16Q GAIN CNV	4	0.0 (0.0)
16Q GAIN WILD-TYPE	324	3.6 (6.2)

Figure S19. Get High-res Image Gene #15: '16q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'16q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.12e-07 (Chi-square test), Q value = 0.00028

Table S20. Gene #15: '16q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
16Q GAIN CNV	2	3	1	1	0	0
16Q GAIN WILD-TYPE	235	41	93	1	36	5

Figure S20. Get High-res Image Gene #15: '16q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.000126 (t-test), Q value = 0.068

Table S21. Gene #16: '17p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
17P GAIN CNV	8	0.5 (1.4)
17P GAIN WILD-TYPE	320	3.6 (6.3)

Figure S21. Get High-res Image Gene #16: '17p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.57e-05 (t-test), Q value = 0.0086

Table S22. Gene #17: '17q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
17Q GAIN CNV	9	0.4 (1.3)
17Q GAIN WILD-TYPE	319	3.6 (6.3)

Figure S22. Get High-res Image Gene #17: '17q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S23. Gene #20: '19p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
19P GAIN CNV	4	0.0 (0.0)
19P GAIN WILD-TYPE	324	3.6 (6.2)

Figure S23. Get High-res Image Gene #20: '19p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.11e-21 (t-test), Q value = 6.3e-19

Table S24. Gene #21: '19q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
19Q GAIN CNV	5	0.0 (0.0)
19Q GAIN WILD-TYPE	323	3.6 (6.2)

Figure S24. Get High-res Image Gene #21: '19q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S25. Gene #22: '20p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
20P GAIN CNV	4	0.0 (0.0)
20P GAIN WILD-TYPE	324	3.6 (6.2)

Figure S25. Get High-res Image Gene #22: '20p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.98e-07 (Chi-square test), Q value = 0.00017

Table S26. Gene #22: '20p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
20P GAIN CNV	1	3	2	1	0	0
20P GAIN WILD-TYPE	236	41	92	1	36	5

Figure S26. Get High-res Image Gene #22: '20p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S27. Gene #23: '20q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
20Q GAIN CNV	4	0.0 (0.0)
20Q GAIN WILD-TYPE	324	3.6 (6.2)

Figure S27. Get High-res Image Gene #23: '20q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.98e-07 (Chi-square test), Q value = 0.00017

Table S28. Gene #23: '20q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
20Q GAIN CNV	1	3	2	1	0	0
20Q GAIN WILD-TYPE	236	41	92	1	36	5

Figure S28. Get High-res Image Gene #23: '20q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.06e-21 (t-test), Q value = 6.1e-19

Table S29. Gene #25: '2p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
2P LOSS CNV	7	0.0 (0.0)
2P LOSS WILD-TYPE	321	3.6 (6.2)

Figure S29. Get High-res Image Gene #25: '2p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.08e-21 (t-test), Q value = 6.2e-19

Table S30. Gene #26: '2q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
2Q LOSS CNV	6	0.0 (0.0)
2Q LOSS WILD-TYPE	322	3.6 (6.2)

Figure S30. Get High-res Image Gene #26: '2q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.16e-21 (t-test), Q value = 6.5e-19

Table S31. Gene #27: '3q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
3Q LOSS CNV	3	0.0 (0.0)
3Q LOSS WILD-TYPE	325	3.6 (6.2)

Figure S31. Get High-res Image Gene #27: '3q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'6q loss' versus 'Time to Death'

P value = 3.21e-05 (logrank test), Q value = 0.017

Table S32. Gene #28: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	416	10	0.0 - 147.4 (9.3)
6Q LOSS CNV	3	1	1.6 - 33.5 (21.4)
6Q LOSS WILD-TYPE	413	9	0.0 - 147.4 (9.3)

Figure S32. Get High-res Image Gene #28: '6q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.27e-07 (Chi-square test), Q value = 7.1e-05

Table S33. Gene #29: '9p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
9P LOSS CNV	1	4	2	1	0	0
9P LOSS WILD-TYPE	236	40	92	1	36	5

Figure S33. Get High-res Image Gene #29: '9p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.18e-17 (Chi-square test), Q value = 3.4e-14

Table S34. Gene #30: '9q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
9Q LOSS CNV	1	5	2	2	2	0
9Q LOSS WILD-TYPE	236	39	92	0	34	5

Figure S34. Get High-res Image Gene #30: '9q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S35. Gene #31: '10p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
10P LOSS CNV	4	0.0 (0.0)
10P LOSS WILD-TYPE	324	3.6 (6.2)

Figure S35. Get High-res Image Gene #31: '10p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'10q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-21 (t-test), Q value = 6.5e-19

Table S36. Gene #32: '10q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
10Q LOSS CNV	3	0.0 (0.0)
10Q LOSS WILD-TYPE	325	3.6 (6.2)

Figure S36. Get High-res Image Gene #32: '10q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'11p loss' versus 'AGE'

P value = 0.000427 (t-test), Q value = 0.23

Table S37. Gene #33: '11p loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	421	46.6 (15.6)
11P LOSS CNV	7	68.1 (8.7)
11P LOSS WILD-TYPE	414	46.2 (15.4)

Figure S37. Get High-res Image Gene #33: '11p loss' versus Clinical Feature #2: 'AGE'

'11p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.36e-06 (Chi-square test), Q value = 0.00075

Table S38. Gene #33: '11p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
11P LOSS CNV	1	1	4	1	0	0
11P LOSS WILD-TYPE	236	43	90	1	36	5

Figure S38. Get High-res Image Gene #33: '11p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'AGE'

P value = 7.15e-05 (t-test), Q value = 0.039

Table S39. Gene #34: '11q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	421	46.6 (15.6)
11Q LOSS CNV	9	67.0 (8.9)
11Q LOSS WILD-TYPE	412	46.1 (15.4)

Figure S39. Get High-res Image Gene #34: '11q loss' versus Clinical Feature #2: 'AGE'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.97e-05 (Chi-square test), Q value = 0.016

Table S40. Gene #34: '11q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	237	44	94	2	36	5
11Q LOSS CNV	1	2	4	1	1	0
11Q LOSS WILD-TYPE	236	42	90	1	35	5

Figure S40. Get High-res Image Gene #34: '11q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.04e-21 (t-test), Q value = 6e-19

Table S41. Gene #35: '13q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	328	3.5 (6.2)
13Q LOSS CNV	8	0.0 (0.0)
13Q LOSS WILD-TYPE	320	3.6 (6.3)

Figure S41. Get High-res Image Gene #35: '13q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'19p loss' versus 'Time to Death'

P value = 5.48e-06 (logrank test), Q value = 0.003

Table S42. Gene #40: '19p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	416	10	0.0 - 147.4 (9.3)
19P LOSS CNV	3	1	0.9 - 33.5 (15.8)
19P LOSS WILD-TYPE	413	9	0.0 - 147.4 (9.3)

Figure S42. Get High-res Image Gene #40: '19p loss' versus Clinical Feature #1: 'Time to Death'

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 = 421
Number of significantly arm-level cnvs = 42
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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