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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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 (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18914HD

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 69 arm-level events and 10 clinical features across 163 patients, 47 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'Time to Death'.
1q gain cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
6q gain cnv correlated to 'Time to Death'.
7p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
7q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
8q gain cnv correlated to 'Time to Death'.
17p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.M.STAGE'.
17q gain cnv correlated to 'PATHOLOGY.M.STAGE'.
3p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
3q loss cnv correlated to 'Time to Death'.
4p loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'GENDER'.
4q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
5p loss cnv correlated to 'Time to Death'.
5q loss cnv correlated to 'Time to Death'.
9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
11q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
13q loss cnv correlated to 'Time to Death' and 'GENDER'.
15q loss cnv correlated to 'Time to Death'.
16p loss cnv correlated to 'Time to Death'.
16q loss cnv correlated to 'Time to Death'.
17p loss cnv correlated to 'Time to Death' and 'NEOPLASM.DISEASESTAGE'.
18p loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
18q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
22q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
xq loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 69 arm-level events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 significant findings detected.


		Clinical Features	Time to Death	AGE	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	KARNOFSKY PERFORMANCE SCORE	NUMBERPACKYEARSSMOKED	YEAROFTOBACCOSMOKINGONSET
	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	t-test	t-test	t-test
4p loss	15 (9%)	148	0.000358 (0.177)	0.00867 (1.00)	5.58e-05 (0.0283)	1.58e-05 (0.00818)	0.00898 (1.00)	0.536 (1.00)	4e-05 (0.0204)	0.792 (1.00)
1q gain	13 (8%)	150	3.52e-05 (0.018)	0.666 (1.00)	1.29e-05 (0.00671)	3.26e-05 (0.0168)	0.408 (1.00)	0.133 (1.00)	0.0629 (1.00)	0.478 (1.00)
11q loss	14 (9%)	149	2.48e-05 (0.0128)	0.331 (1.00)	0.000129 (0.0644)	5.22e-05 (0.0266)	0.0641 (1.00)	0.0824 (1.00)	0.36 (1.00)	0.792 (1.00)
18p loss	26 (16%)	137	5.21e-05 (0.0266)	0.18 (1.00)	7.2e-05 (0.0363)	5.11e-06 (0.0027)	0.0607 (1.00)	0.0774 (1.00)	0.063 (1.00)	0.724 (1.00)
18q loss	28 (17%)	135	5.21e-05 (0.0266)	0.28 (1.00)	8.45e-06 (0.00444)	5.88e-06 (0.0031)	0.029 (1.00)	0.0938 (1.00)	0.0442 (1.00)	0.724 (1.00)
xq loss	20 (12%)	143	6.67e-05 (0.0337)	0.174 (1.00)	0.000495 (0.243)	0.000194 (0.0965)	0.0526 (1.00)	0.213 (1.00)	0.0169 (1.00)	0.469 (1.00)
17p gain	99 (61%)	64	0.0569 (1.00)	0.0561 (1.00)	1.59e-05 (0.00826)	0.000589 (0.289)	0.215 (1.00)	1.07e-05 (0.00561)	0.0546 (1.00)	0.254 (1.00)	0.369 (1.00)
3p loss	14 (9%)	149	0.0103 (1.00)	0.177 (1.00)	1.8e-05 (0.0093)	0.000186 (0.0926)	0.669 (1.00)	0.11 (1.00)	0.761 (1.00)	0.792 (1.00)	0.453 (1.00)
4q loss	16 (10%)	147	0.0112 (1.00)	0.0535 (1.00)	0.000432 (0.213)	0.000146 (0.073)	0.0698 (1.00)	0.165 (1.00)	0.000894 (0.435)	0.754 (1.00)
9p loss	21 (13%)	142	0.00952 (1.00)	0.561 (1.00)	1.43e-05 (0.00744)	8.13e-05 (0.0409)	0.119 (1.00)	0.034 (1.00)	0.00886 (1.00)	0.314 (1.00)
9q loss	23 (14%)	140	0.00179 (0.862)	0.587 (1.00)	5.93e-05 (0.03)	1.49e-05 (0.00777)	0.0607 (1.00)	0.24 (1.00)	0.0248 (1.00)	0.325 (1.00)
13q loss	16 (10%)	147	1.05e-05 (0.00549)	0.0404 (1.00)	0.00285 (1.00)	0.000696 (0.34)	0.0444 (1.00)	0.489 (1.00)	0.000123 (0.0618)	0.467 (1.00)
17p loss	8 (5%)	155	4.03e-14 (2.16e-11)	0.753 (1.00)	0.000306 (0.152)	0.00691 (1.00)	0.00807 (1.00)	0.0499 (1.00)	0.0538 (1.00)	0.478 (1.00)
22q loss	39 (24%)	124	0.0393 (1.00)	0.395 (1.00)	2.02e-06 (0.00107)	3.32e-06 (0.00176)	0.0619 (1.00)	0.185 (1.00)	0.00138 (0.669)	0.447 (1.00)
1p gain	4 (2%)	159	7.98e-06 (0.0042)	0.444 (1.00)	0.0212 (1.00)	0.0129 (1.00)	0.0803 (1.00)	0.18 (1.00)	0.0816 (1.00)
6q gain	5 (3%)	158	1.53e-09 (8.19e-07)	0.166 (1.00)	0.0285 (1.00)	0.0441 (1.00)	0.0803 (1.00)	0.0127 (1.00)	0.637 (1.00)	0.548 (1.00)
7p gain	95 (58%)	68	0.0607 (1.00)	0.466 (1.00)	0.000467 (0.23)	0.0068 (1.00)	0.662 (1.00)	0.223 (1.00)	0.123 (1.00)	0.159 (1.00)	0.354 (1.00)	0.837 (1.00)
7q gain	96 (59%)	67	0.0546 (1.00)	0.402 (1.00)	0.000276 (0.137)	0.00554 (1.00)	0.54 (1.00)	0.314 (1.00)	0.118 (1.00)	0.159 (1.00)	0.354 (1.00)	0.837 (1.00)
8q gain	15 (9%)	148	1.56e-06 (0.000828)	0.789 (1.00)	0.00568 (1.00)	0.00185 (0.888)	0.0444 (1.00)	0.349 (1.00)	0.0715 (1.00)	0.566 (1.00)
17q gain	112 (69%)	51	0.481 (1.00)	0.124 (1.00)	0.0431 (1.00)	0.144 (1.00)	0.443 (1.00)	0.000504 (0.247)	0.199 (1.00)	0.667 (1.00)
3q loss	4 (2%)	159	3.96e-11 (2.12e-08)	0.21 (1.00)	0.00511 (1.00)	0.0129 (1.00)	0.192 (1.00)	0.18 (1.00)	0.584 (1.00)
5p loss	7 (4%)	156	1.91e-10 (1.02e-07)	0.0911 (1.00)	0.0161 (1.00)	0.0045 (1.00)	0.0396 (1.00)	0.163 (1.00)	0.0262 (1.00)
5q loss	7 (4%)	156	8.61e-08 (4.58e-05)	0.0351 (1.00)	0.0272 (1.00)	0.0045 (1.00)	0.0152 (1.00)	0.163 (1.00)	0.0262 (1.00)
15q loss	18 (11%)	145	2.65e-08 (1.41e-05)	0.119 (1.00)	0.00732 (1.00)	0.00478 (1.00)	0.112 (1.00)	0.125 (1.00)	0.178 (1.00)	0.666 (1.00)
16p loss	4 (2%)	159	3.35e-05 (0.0172)	0.648 (1.00)	0.13 (1.00)	0.115 (1.00)		1 (1.00)	0.0816 (1.00)
16q loss	5 (3%)	158	3.35e-05 (0.0172)	0.316 (1.00)	0.0748 (1.00)	0.205 (1.00)	0.273 (1.00)	1 (1.00)	0.161 (1.00)
2p gain	31 (19%)	132	0.259 (1.00)	0.34 (1.00)	0.0987 (1.00)	0.76 (1.00)	0.669 (1.00)	0.00328 (1.00)	0.516 (1.00)	0.534 (1.00)	0.331 (1.00)	0.477 (1.00)
2q gain	33 (20%)	130	0.392 (1.00)	0.695 (1.00)	0.0242 (1.00)	0.799 (1.00)	0.223 (1.00)	0.00479 (1.00)	0.4 (1.00)	0.531 (1.00)	0.331 (1.00)	0.477 (1.00)
3p gain	46 (28%)	117	0.415 (1.00)	0.763 (1.00)	0.0508 (1.00)	0.0326 (1.00)	1 (1.00)	0.381 (1.00)	0.85 (1.00)	0.0416 (1.00)	0.368 (1.00)
3q gain	55 (34%)	108	0.17 (1.00)	0.464 (1.00)	0.161 (1.00)	0.0885 (1.00)	1 (1.00)	0.169 (1.00)	0.718 (1.00)	0.113 (1.00)	0.357 (1.00)
4p gain	6 (4%)	157	0.0202 (1.00)	0.00484 (1.00)	0.0433 (1.00)	0.542 (1.00)	0.501 (1.00)	0.18 (1.00)	0.669 (1.00)
4q gain	5 (3%)	158	0.333 (1.00)	0.0155 (1.00)	0.259 (1.00)	0.612 (1.00)	0.167 (1.00)	0.69 (1.00)	1 (1.00)
5p gain	24 (15%)	139	0.679 (1.00)	0.893 (1.00)	0.202 (1.00)	0.137 (1.00)	0.558 (1.00)	0.385 (1.00)	0.637 (1.00)	0.401 (1.00)
5q gain	24 (15%)	139	0.679 (1.00)	0.422 (1.00)	0.202 (1.00)	0.327 (1.00)	1 (1.00)	0.385 (1.00)	0.637 (1.00)	0.401 (1.00)
6p gain	7 (4%)	156	0.00143 (0.691)	0.577 (1.00)	0.00775 (1.00)	0.0045 (1.00)	0.277 (1.00)	0.0257 (1.00)	1 (1.00)	0.548 (1.00)
8p gain	11 (7%)	152	0.00353 (1.00)	0.969 (1.00)	0.165 (1.00)	0.0845 (1.00)	0.296 (1.00)	0.848 (1.00)	0.308 (1.00)
9p gain	3 (2%)	160	0.107 (1.00)	0.931 (1.00)	0.0557 (1.00)	0.0704 (1.00)		0.627 (1.00)	1 (1.00)
10p gain	5 (3%)	158	0.465 (1.00)	0.927 (1.00)	0.162 (1.00)	0.377 (1.00)		0.321 (1.00)	1 (1.00)
10q gain	5 (3%)	158	0.465 (1.00)	0.927 (1.00)	0.162 (1.00)	0.377 (1.00)		0.321 (1.00)	1 (1.00)
11p gain	8 (5%)	155	0.0524 (1.00)	0.638 (1.00)	0.0363 (1.00)	0.0404 (1.00)	0.588 (1.00)	0.0191 (1.00)	0.698 (1.00)
11q gain	7 (4%)	156	0.466 (1.00)	0.449 (1.00)	0.186 (1.00)	0.0625 (1.00)	0.738 (1.00)	0.163 (1.00)	0.199 (1.00)
12p gain	66 (40%)	97	0.804 (1.00)	0.681 (1.00)	0.319 (1.00)	0.601 (1.00)	0.818 (1.00)	0.126 (1.00)	0.0233 (1.00)	0.847 (1.00)	0.29 (1.00)
12q gain	66 (40%)	97	0.804 (1.00)	0.681 (1.00)	0.319 (1.00)	0.601 (1.00)	0.818 (1.00)	0.126 (1.00)	0.0233 (1.00)	0.847 (1.00)	0.29 (1.00)
13q gain	18 (11%)	145	0.906 (1.00)	0.762 (1.00)	0.601 (1.00)	0.804 (1.00)	0.738 (1.00)	1 (1.00)	0.788 (1.00)	0.153 (1.00)
14q gain	3 (2%)	160			0.069 (1.00)	0.0281 (1.00)		0.627 (1.00)	0.215 (1.00)
15q gain	4 (2%)	159	0.478 (1.00)	0.588 (1.00)	0.486 (1.00)	0.412 (1.00)		0.69 (1.00)	0.584 (1.00)
16p gain	86 (53%)	77	0.785 (1.00)	0.158 (1.00)	0.792 (1.00)	0.943 (1.00)	1 (1.00)	0.323 (1.00)	0.01 (1.00)	0.674 (1.00)	0.369 (1.00)
16q gain	83 (51%)	80	0.227 (1.00)	0.353 (1.00)	0.545 (1.00)	0.513 (1.00)	0.742 (1.00)	0.081 (1.00)	0.0597 (1.00)	0.207 (1.00)	0.369 (1.00)
18p gain	8 (5%)	155	0.888 (1.00)	0.903 (1.00)	0.294 (1.00)	0.545 (1.00)		0.149 (1.00)	1 (1.00)	0.548 (1.00)
18q gain	5 (3%)	158	0.355 (1.00)	0.962 (1.00)	0.59 (1.00)	0.612 (1.00)		0.419 (1.00)	1 (1.00)
19p gain	3 (2%)	160	0.626 (1.00)	0.344 (1.00)	0.481 (1.00)	0.438 (1.00)	1 (1.00)	0.627 (1.00)	1 (1.00)
19q gain	3 (2%)	160	0.626 (1.00)	0.344 (1.00)	0.481 (1.00)	0.438 (1.00)	1 (1.00)	0.627 (1.00)	1 (1.00)
20p gain	55 (34%)	108	0.635 (1.00)	0.148 (1.00)	0.51 (1.00)	0.476 (1.00)	0.787 (1.00)	0.867 (1.00)	0.594 (1.00)	0.641 (1.00)
20q gain	57 (35%)	106	0.38 (1.00)	0.116 (1.00)	0.224 (1.00)	0.271 (1.00)	0.512 (1.00)	1 (1.00)	0.591 (1.00)	0.641 (1.00)
21q gain	9 (6%)	154	0.011 (1.00)	0.0647 (1.00)	1 (1.00)	1 (1.00)		0.192 (1.00)	1 (1.00)	0.905 (1.00)
xq gain	51 (31%)	112	0.577 (1.00)	0.738 (1.00)	0.00285 (1.00)	0.00676 (1.00)	0.608 (1.00)	0.337 (1.00)	0.065 (1.00)	0.268 (1.00)	0.373 (1.00)
1p loss	20 (12%)	143	0.0379 (1.00)	0.815 (1.00)	0.0626 (1.00)	0.124 (1.00)	0.296 (1.00)	0.915 (1.00)	0.308 (1.00)	0.13 (1.00)
1q loss	11 (7%)	152	0.506 (1.00)	0.333 (1.00)	0.268 (1.00)	0.577 (1.00)	0.654 (1.00)	0.467 (1.00)	0.735 (1.00)	0.314 (1.00)
6p loss	11 (7%)	152	0.0121 (1.00)	0.428 (1.00)	0.0275 (1.00)	0.0295 (1.00)	0.0582 (1.00)	0.833 (1.00)	0.0886 (1.00)	0.157 (1.00)
6q loss	15 (9%)	148	0.206 (1.00)	0.92 (1.00)	0.0361 (1.00)	0.0025 (1.00)	0.169 (1.00)	0.347 (1.00)	0.015 (1.00)	0.754 (1.00)
8p loss	6 (4%)	157	0.00199 (0.95)	0.534 (1.00)	0.0505 (1.00)	0.542 (1.00)	0.0803 (1.00)	0.0257 (1.00)	0.366 (1.00)
8q loss	4 (2%)	159	0.0317 (1.00)	0.3 (1.00)	0.0791 (1.00)	0.412 (1.00)		0.18 (1.00)	0.584 (1.00)
10p loss	11 (7%)	152	0.208 (1.00)	0.87 (1.00)	0.00632 (1.00)	0.0109 (1.00)	0.0556 (1.00)	0.0872 (1.00)	0.308 (1.00)	0.44 (1.00)
10q loss	11 (7%)	152	0.15 (1.00)	0.442 (1.00)	0.00231 (1.00)	0.00535 (1.00)	0.0248 (1.00)	0.168 (1.00)	0.308 (1.00)	0.355 (1.00)
11p loss	10 (6%)	153	0.000775 (0.378)	0.105 (1.00)	0.0256 (1.00)	0.0541 (1.00)	0.192 (1.00)	0.467 (1.00)	0.169 (1.00)
14q loss	31 (19%)	132	0.0128 (1.00)	0.991 (1.00)	0.00198 (0.95)	0.00514 (1.00)	0.0776 (1.00)	0.108 (1.00)	0.0511 (1.00)	0.448 (1.00)
19p loss	12 (7%)	151	0.744 (1.00)	0.171 (1.00)	0.0381 (1.00)	0.0367 (1.00)	0.192 (1.00)	0.263 (1.00)	0.348 (1.00)	0.754 (1.00)	0.315 (1.00)
19q loss	11 (7%)	152	0.000889 (0.433)	0.948 (1.00)	0.00135 (0.655)	0.00197 (0.945)	0.192 (1.00)	0.134 (1.00)	0.0886 (1.00)	0.754 (1.00)
21q loss	31 (19%)	132	0.577 (1.00)	0.661 (1.00)	0.0139 (1.00)	0.00747 (1.00)	0.872 (1.00)	0.143 (1.00)	0.129 (1.00)	0.711 (1.00)	0.332 (1.00)

'1p gain' versus 'Time to Death'

P value = 7.98e-06 (logrank test), Q value = 0.0042

Table S1. Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
1P GAIN MUTATED	3	1	2.0 - 7.9 (3.7)
1P GAIN WILD-TYPE	147	16	0.0 - 194.8 (14.4)

Figure S1. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'Time to Death'

P value = 3.52e-05 (logrank test), Q value = 0.018

Table S2. Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
1Q GAIN MUTATED	12	3	0.7 - 30.3 (3.8)
1Q GAIN WILD-TYPE	138	14	0.0 - 194.8 (14.9)

Figure S2. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0067

Table S3. Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
1Q GAIN MUTATED	1	0	9	3
1Q GAIN WILD-TYPE	94	11	28	7

Figure S3. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1q gain' versus 'PATHOLOGY.T.STAGE'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.017

Table S4. Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
1Q GAIN MUTATED	2	0	11
1Q GAIN WILD-TYPE	100	17	33

Figure S4. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'6q gain' versus 'Time to Death'

P value = 1.53e-09 (logrank test), Q value = 8.2e-07

Table S5. Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
6Q GAIN MUTATED	5	3	1.9 - 13.6 (7.9)
6Q GAIN WILD-TYPE	145	14	0.0 - 194.8 (14.6)

Figure S5. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000467 (Fisher's exact test), Q value = 0.23

Table S6. Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
7P GAIN MUTATED	66	4	12	6
7P GAIN WILD-TYPE	29	7	25	4

Figure S6. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000276 (Fisher's exact test), Q value = 0.14

Table S7. Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
7Q GAIN MUTATED	67	4	12	6
7Q GAIN WILD-TYPE	28	7	25	4

Figure S7. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'8q gain' versus 'Time to Death'

P value = 1.56e-06 (logrank test), Q value = 0.00083

Table S8. Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
8Q GAIN MUTATED	15	5	0.2 - 43.2 (6.6)
8Q GAIN WILD-TYPE	135	12	0.0 - 194.8 (14.7)

Figure S8. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0083

Table S9. Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
17P GAIN MUTATED	70	6	13	2
17P GAIN WILD-TYPE	25	5	24	8

Figure S9. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17p gain' versus 'PATHOLOGY.M.STAGE'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0056

Table S10. Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	62	6	82
17P GAIN MUTATED	26	1	62
17P GAIN WILD-TYPE	36	5	20

Figure S10. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'17q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000504 (Fisher's exact test), Q value = 0.25

Table S11. Gene #30: '17q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	62	6	82
17Q GAIN MUTATED	32	3	66
17Q GAIN WILD-TYPE	30	3	16

Figure S11. Get High-res Image Gene #30: '17q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'3p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.0093

Table S12. Gene #41: '3p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
3P LOSS MUTATED	1	1	9	3
3P LOSS WILD-TYPE	94	10	28	7

Figure S12. Get High-res Image Gene #41: '3p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'3p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000186 (Fisher's exact test), Q value = 0.093

Table S13. Gene #41: '3p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
3P LOSS MUTATED	2	2	10
3P LOSS WILD-TYPE	100	15	34

Figure S13. Get High-res Image Gene #41: '3p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'3q loss' versus 'Time to Death'

P value = 3.96e-11 (logrank test), Q value = 2.1e-08

Table S14. Gene #42: '3q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
3Q LOSS MUTATED	4	3	3.7 - 21.6 (6.4)
3Q LOSS WILD-TYPE	146	14	0.0 - 194.8 (14.3)

Figure S14. Get High-res Image Gene #42: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'Time to Death'

P value = 0.000358 (logrank test), Q value = 0.18

Table S15. Gene #43: '4p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
4P LOSS MUTATED	14	4	0.1 - 79.9 (5.1)
4P LOSS WILD-TYPE	136	13	0.0 - 194.8 (14.9)

Figure S15. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.58e-05 (Fisher's exact test), Q value = 0.028

Table S16. Gene #43: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
4P LOSS MUTATED	2	1	11	1
4P LOSS WILD-TYPE	93	10	26	9

Figure S16. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0082

Table S17. Gene #43: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
4P LOSS MUTATED	2	1	12
4P LOSS WILD-TYPE	100	16	32

Figure S17. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'GENDER'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S18. Gene #43: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	49	114
4P LOSS MUTATED	12	3
4P LOSS WILD-TYPE	37	111

Figure S18. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000432 (Fisher's exact test), Q value = 0.21

Table S19. Gene #44: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
4Q LOSS MUTATED	3	1	10	2
4Q LOSS WILD-TYPE	92	10	27	8

Figure S19. Get High-res Image Gene #44: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4q loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000146 (Fisher's exact test), Q value = 0.073

Table S20. Gene #44: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
4Q LOSS MUTATED	3	2	11
4Q LOSS WILD-TYPE	99	15	33

Figure S20. Get High-res Image Gene #44: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p loss' versus 'Time to Death'

P value = 1.91e-10 (logrank test), Q value = 1e-07

Table S21. Gene #45: '5p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
5P LOSS MUTATED	7	4	0.7 - 22.9 (6.6)
5P LOSS WILD-TYPE	143	13	0.0 - 194.8 (14.4)

Figure S21. Get High-res Image Gene #45: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'Time to Death'

P value = 8.61e-08 (logrank test), Q value = 4.6e-05

Table S22. Gene #46: '5q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
5Q LOSS MUTATED	7	3	0.7 - 22.9 (3.7)
5Q LOSS WILD-TYPE	143	14	0.0 - 194.8 (14.4)

Figure S22. Get High-res Image Gene #46: '5q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0074

Table S23. Gene #51: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
9P LOSS MUTATED	4	0	10	5
9P LOSS WILD-TYPE	91	11	27	5

Figure S23. Get High-res Image Gene #51: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 8.13e-05 (Fisher's exact test), Q value = 0.041

Table S24. Gene #51: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
9P LOSS MUTATED	5	2	14
9P LOSS WILD-TYPE	97	15	30

Figure S24. Get High-res Image Gene #51: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.93e-05 (Fisher's exact test), Q value = 0.03

Table S25. Gene #52: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
9Q LOSS MUTATED	5	1	12	4
9Q LOSS WILD-TYPE	90	10	25	6

Figure S25. Get High-res Image Gene #52: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.0078

Table S26. Gene #52: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
9Q LOSS MUTATED	6	1	16
9Q LOSS WILD-TYPE	96	16	28

Figure S26. Get High-res Image Gene #52: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'11q loss' versus 'Time to Death'

P value = 2.48e-05 (logrank test), Q value = 0.013

Table S27. Gene #56: '11q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
11Q LOSS MUTATED	13	5	0.1 - 123.6 (8.9)
11Q LOSS WILD-TYPE	137	12	0.0 - 194.8 (14.6)

Figure S27. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000129 (Fisher's exact test), Q value = 0.064

Table S28. Gene #56: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
11Q LOSS MUTATED	2	1	7	4
11Q LOSS WILD-TYPE	93	10	30	6

Figure S28. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.027

Table S29. Gene #56: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
11Q LOSS MUTATED	2	1	11
11Q LOSS WILD-TYPE	100	16	33

Figure S29. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'Time to Death'

P value = 1.05e-05 (logrank test), Q value = 0.0055

Table S30. Gene #57: '13q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
13Q LOSS MUTATED	16	5	0.1 - 86.8 (3.4)
13Q LOSS WILD-TYPE	134	12	0.0 - 194.8 (14.9)

Figure S30. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'GENDER'

P value = 0.000123 (Fisher's exact test), Q value = 0.062

Table S31. Gene #57: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	49	114
13Q LOSS MUTATED	12	4
13Q LOSS WILD-TYPE	37	110

Figure S31. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #7: 'GENDER'

'15q loss' versus 'Time to Death'

P value = 2.65e-08 (logrank test), Q value = 1.4e-05

Table S32. Gene #59: '15q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
15Q LOSS MUTATED	17	6	0.1 - 34.8 (6.8)
15Q LOSS WILD-TYPE	133	11	0.0 - 194.8 (14.6)

Figure S32. Get High-res Image Gene #59: '15q loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'Time to Death'

P value = 3.35e-05 (logrank test), Q value = 0.017

Table S33. Gene #60: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
16P LOSS MUTATED	3	2	0.7 - 21.6 (11.1)
16P LOSS WILD-TYPE	147	15	0.0 - 194.8 (14.1)

Figure S33. Get High-res Image Gene #60: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'Time to Death'

P value = 3.35e-05 (logrank test), Q value = 0.017

Table S34. Gene #61: '16q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
16Q LOSS MUTATED	4	2	0.7 - 21.6 (7.0)
16Q LOSS WILD-TYPE	146	15	0.0 - 194.8 (14.3)

Figure S34. Get High-res Image Gene #61: '16q loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'Time to Death'

P value = 4.03e-14 (logrank test), Q value = 2.2e-11

Table S35. Gene #62: '17p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
17P LOSS MUTATED	6	4	0.2 - 11.3 (6.8)
17P LOSS WILD-TYPE	144	13	0.0 - 194.8 (14.6)

Figure S35. Get High-res Image Gene #62: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000306 (Fisher's exact test), Q value = 0.15

Table S36. Gene #62: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
17P LOSS MUTATED	1	1	2	4
17P LOSS WILD-TYPE	94	10	35	6

Figure S36. Get High-res Image Gene #62: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'Time to Death'

P value = 5.21e-05 (logrank test), Q value = 0.027

Table S37. Gene #63: '18p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
18P LOSS MUTATED	25	7	0.0 - 123.6 (7.6)
18P LOSS WILD-TYPE	125	10	0.0 - 194.8 (15.1)

Figure S37. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.2e-05 (Fisher's exact test), Q value = 0.036

Table S38. Gene #63: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
18P LOSS MUTATED	6	1	13	4
18P LOSS WILD-TYPE	89	10	24	6

Figure S38. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.11e-06 (Fisher's exact test), Q value = 0.0027

Table S39. Gene #63: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
18P LOSS MUTATED	6	3	17
18P LOSS WILD-TYPE	96	14	27

Figure S39. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'18q loss' versus 'Time to Death'

P value = 5.21e-05 (logrank test), Q value = 0.027

Table S40. Gene #64: '18q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
18Q LOSS MUTATED	26	7	0.0 - 123.6 (7.5)
18Q LOSS WILD-TYPE	124	10	0.0 - 194.8 (15.7)

Figure S40. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.45e-06 (Fisher's exact test), Q value = 0.0044

Table S41. Gene #64: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
18Q LOSS MUTATED	6	1	15	4
18Q LOSS WILD-TYPE	89	10	22	6

Figure S41. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.88e-06 (Fisher's exact test), Q value = 0.0031

Table S42. Gene #64: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
18Q LOSS MUTATED	7	3	18
18Q LOSS WILD-TYPE	95	14	26

Figure S42. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'22q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0011

Table S43. Gene #68: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
22Q LOSS MUTATED	10	3	19	5
22Q LOSS WILD-TYPE	85	8	18	5

Figure S43. Get High-res Image Gene #68: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'22q loss' versus 'PATHOLOGY.T.STAGE'

P value = 3.32e-06 (Fisher's exact test), Q value = 0.0018

Table S44. Gene #68: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
22Q LOSS MUTATED	13	3	23
22Q LOSS WILD-TYPE	89	14	21

Figure S44. Get High-res Image Gene #68: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'xq loss' versus 'Time to Death'

P value = 6.67e-05 (logrank test), Q value = 0.034

Table S45. Gene #69: 'xq loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
XQ LOSS MUTATED	19	6	0.1 - 79.9 (11.1)
XQ LOSS WILD-TYPE	131	11	0.0 - 194.8 (14.4)

Figure S45. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000495 (Fisher's exact test), Q value = 0.24

Table S46. Gene #69: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
XQ LOSS MUTATED	4	1	10	3
XQ LOSS WILD-TYPE	91	10	27	7

Figure S46. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'xq loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000194 (Fisher's exact test), Q value = 0.097

Table S47. Gene #69: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
XQ LOSS MUTATED	5	2	13
XQ LOSS WILD-TYPE	97	15	31

Figure S47. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = KIRP-TP.merged_data.txt
Number of patients = 163
Number of significantly arm-level cnvs = 69
Number of selected clinical features = 10
Exclude regions 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

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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] 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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