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

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

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/C189149Q

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 79 arm-level events and 9 clinical features across 494 patients, 22 significant findings detected with Q value < 0.25.

5p gain cnv correlated to 'AGE'.
20p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
20q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
4p loss cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.
4q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
5p loss cnv correlated to 'PATHOLOGY.T.STAGE'.
9p loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
9q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
13q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
14q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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 79 arm-level events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 22 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
	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
4q loss	65 (13%)	429	1.93e-06 (0.00116)	0.905 (1.00)	1.67e-05 (0.00995)	8.49e-06 (0.00509)	0.468 (1.00)	0.00275 (1.00)	0.401 (1.00)	0.193 (1.00)
9p loss	142 (29%)	352	3.1e-05 (0.0184)	0.091 (1.00)	1.75e-05 (0.0104)	9.01e-05 (0.0532)	0.0977 (1.00)	0.00393 (1.00)	0.000792 (0.455)	0.576 (1.00)
9q loss	145 (29%)	349	0.000152 (0.0898)	0.05 (1.00)	1.82e-06 (0.0011)	7.87e-06 (0.00472)	0.172 (1.00)	0.00265 (1.00)	0.000853 (0.489)	0.487 (1.00)
20p gain	109 (22%)	385	0.163 (1.00)	0.156 (1.00)	5.29e-05 (0.0313)	4.21e-06 (0.00253)	0.548 (1.00)	0.0105 (1.00)	0.00197 (1.00)	0.373 (1.00)
20q gain	112 (23%)	382	0.124 (1.00)	0.0463 (1.00)	3.64e-05 (0.0216)	1.56e-05 (0.00935)	0.24 (1.00)	0.0171 (1.00)	0.00918 (1.00)	0.373 (1.00)
4p loss	71 (14%)	423	7.09e-06 (0.00426)	0.977 (1.00)	0.000484 (0.281)	0.000354 (0.207)	0.727 (1.00)	0.0206 (1.00)	1 (1.00)	0.13 (1.00)
13q loss	69 (14%)	425	0.000513 (0.297)	0.553 (1.00)	0.000224 (0.131)	3.99e-06 (0.00241)	0.325 (1.00)	0.0317 (1.00)	0.34 (1.00)	0.669 (1.00)
14q loss	207 (42%)	287	0.00253 (1.00)	0.127 (1.00)	4.71e-05 (0.0279)	0.000189 (0.112)	0.00237 (1.00)	0.00163 (0.926)	0.0691 (1.00)	0.0872 (1.00)
5p gain	183 (37%)	311	0.0513 (1.00)	0.000334 (0.195)	0.176 (1.00)	0.307 (1.00)	0.622 (1.00)	0.899 (1.00)	0.0186 (1.00)	0.572 (1.00)
5p loss	7 (1%)	487	0.0198 (1.00)	0.29 (1.00)	0.00185 (1.00)	0.000195 (0.115)	1 (1.00)	0.0798 (1.00)	0.242 (1.00)
19p loss	11 (2%)	483	0.000205 (0.12)	0.0394 (1.00)	0.0315 (1.00)	0.000986 (0.564)	1 (1.00)	0.39 (1.00)	0.755 (1.00)
1p gain	21 (4%)	473	0.00142 (0.809)	0.198 (1.00)	0.209 (1.00)	0.27 (1.00)	0.216 (1.00)	0.35 (1.00)	0.815 (1.00)	0.482 (1.00)
1q gain	49 (10%)	445	0.15 (1.00)	0.0574 (1.00)	0.13 (1.00)	0.135 (1.00)	0.417 (1.00)	0.837 (1.00)	0.636 (1.00)	0.499 (1.00)
2p gain	74 (15%)	420	0.793 (1.00)	0.113 (1.00)	0.168 (1.00)	0.427 (1.00)	1 (1.00)	0.487 (1.00)	0.791 (1.00)	0.491 (1.00)
2q gain	75 (15%)	419	0.639 (1.00)	0.157 (1.00)	0.308 (1.00)	0.671 (1.00)	1 (1.00)	0.393 (1.00)	0.294 (1.00)	0.387 (1.00)
3p gain	18 (4%)	476	0.0972 (1.00)	0.858 (1.00)	0.128 (1.00)	0.276 (1.00)	0.0376 (1.00)	0.0461 (1.00)	0.45 (1.00)	0.328 (1.00)
3q gain	56 (11%)	438	0.456 (1.00)	0.606 (1.00)	0.00238 (1.00)	0.000541 (0.313)	0.00543 (1.00)	0.00278 (1.00)	0.766 (1.00)	0.193 (1.00)
4p gain	13 (3%)	481	0.104 (1.00)	0.862 (1.00)	0.466 (1.00)	0.21 (1.00)	0.501 (1.00)	1 (1.00)	0.557 (1.00)
4q gain	13 (3%)	481	0.306 (1.00)	0.862 (1.00)	0.573 (1.00)	0.755 (1.00)	0.46 (1.00)	0.702 (1.00)	1 (1.00)
5q gain	196 (40%)	298	0.0867 (1.00)	0.000617 (0.356)	0.473 (1.00)	0.485 (1.00)	1 (1.00)	0.9 (1.00)	0.0423 (1.00)	0.572 (1.00)
6p gain	10 (2%)	484	0.93 (1.00)	0.961 (1.00)	0.58 (1.00)	0.407 (1.00)	1 (1.00)	0.659 (1.00)	0.506 (1.00)
6q gain	8 (2%)	486	0.851 (1.00)	0.517 (1.00)	0.47 (1.00)	0.462 (1.00)	1 (1.00)	1 (1.00)	0.273 (1.00)
7p gain	165 (33%)	329	0.934 (1.00)	0.392 (1.00)	0.0687 (1.00)	0.132 (1.00)	0.451 (1.00)	0.0178 (1.00)	0.00498 (1.00)	0.711 (1.00)
7q gain	166 (34%)	328	0.562 (1.00)	0.444 (1.00)	0.0149 (1.00)	0.0663 (1.00)	0.443 (1.00)	0.00234 (1.00)	0.0126 (1.00)	0.528 (1.00)
8p gain	28 (6%)	466	0.549 (1.00)	0.327 (1.00)	0.00199 (1.00)	0.00176 (0.998)	0.607 (1.00)	0.177 (1.00)	0.546 (1.00)	0.757 (1.00)
8q gain	57 (12%)	437	0.244 (1.00)	0.0805 (1.00)	0.00905 (1.00)	0.005 (1.00)	0.441 (1.00)	0.121 (1.00)	0.302 (1.00)	0.471 (1.00)
9p gain	14 (3%)	480	0.481 (1.00)	0.31 (1.00)	0.82 (1.00)	0.077 (1.00)	1 (1.00)	0.707 (1.00)	0.0234 (1.00)
9q gain	12 (2%)	482	0.949 (1.00)	0.339 (1.00)	0.231 (1.00)	0.00317 (1.00)	1 (1.00)	1 (1.00)	0.121 (1.00)
10p gain	16 (3%)	478	0.931 (1.00)	0.247 (1.00)	0.666 (1.00)	0.19 (1.00)	0.0854 (1.00)	0.725 (1.00)	1 (1.00)	0.887 (1.00)
10q gain	12 (2%)	482	0.688 (1.00)	0.0407 (1.00)	0.806 (1.00)	0.884 (1.00)	0.264 (1.00)	1 (1.00)	0.356 (1.00)	0.81 (1.00)
11p gain	30 (6%)	464	0.987 (1.00)	0.764 (1.00)	0.0244 (1.00)	0.0122 (1.00)	1 (1.00)	0.114 (1.00)	1 (1.00)	0.484 (1.00)
11q gain	28 (6%)	466	0.497 (1.00)	0.828 (1.00)	0.148 (1.00)	0.0799 (1.00)	1 (1.00)	0.418 (1.00)	1 (1.00)
12p gain	116 (23%)	378	0.00999 (1.00)	0.0326 (1.00)	0.00125 (0.715)	0.00469 (1.00)	0.259 (1.00)	0.0275 (1.00)	0.657 (1.00)	0.268 (1.00)
12q gain	117 (24%)	377	0.0156 (1.00)	0.0832 (1.00)	0.000859 (0.492)	0.00304 (1.00)	0.259 (1.00)	0.0286 (1.00)	0.657 (1.00)	0.268 (1.00)
13q gain	22 (4%)	472	0.107 (1.00)	0.336 (1.00)	0.178 (1.00)	0.275 (1.00)	1 (1.00)	0.364 (1.00)	0.261 (1.00)
14q gain	16 (3%)	478	0.161 (1.00)	0.563 (1.00)	0.279 (1.00)	0.00814 (1.00)	1 (1.00)	0.292 (1.00)	1 (1.00)
15q gain	26 (5%)	468	0.257 (1.00)	0.38 (1.00)	0.633 (1.00)	0.481 (1.00)	0.216 (1.00)	0.58 (1.00)	0.833 (1.00)	0.349 (1.00)
16p gain	103 (21%)	391	0.267 (1.00)	0.204 (1.00)	0.217 (1.00)	0.127 (1.00)	0.133 (1.00)	0.544 (1.00)	0.908 (1.00)	0.449 (1.00)
16q gain	95 (19%)	399	0.212 (1.00)	0.262 (1.00)	0.228 (1.00)	0.0821 (1.00)	0.212 (1.00)	1 (1.00)	0.811 (1.00)	0.31 (1.00)
17p gain	24 (5%)	470	0.949 (1.00)	0.4 (1.00)	0.083 (1.00)	0.812 (1.00)	0.216 (1.00)	0.0216 (1.00)	1 (1.00)	0.74 (1.00)
17q gain	30 (6%)	464	0.46 (1.00)	0.409 (1.00)	0.532 (1.00)	0.754 (1.00)	0.301 (1.00)	0.202 (1.00)	0.844 (1.00)	0.471 (1.00)
18p gain	25 (5%)	469	0.0417 (1.00)	0.664 (1.00)	0.677 (1.00)	0.894 (1.00)	1 (1.00)	0.401 (1.00)	0.0826 (1.00)
18q gain	25 (5%)	469	0.102 (1.00)	0.52 (1.00)	0.557 (1.00)	0.822 (1.00)	0.607 (1.00)	0.401 (1.00)	0.0826 (1.00)
19p gain	50 (10%)	444	0.798 (1.00)	0.659 (1.00)	0.0196 (1.00)	0.04 (1.00)	0.397 (1.00)	0.0213 (1.00)	0.349 (1.00)	0.716 (1.00)
19q gain	56 (11%)	438	0.749 (1.00)	0.418 (1.00)	0.00599 (1.00)	0.017 (1.00)	0.428 (1.00)	0.00954 (1.00)	0.372 (1.00)	0.716 (1.00)
21q gain	48 (10%)	446	0.601 (1.00)	0.116 (1.00)	0.242 (1.00)	0.125 (1.00)	1 (1.00)	0.53 (1.00)	0.43 (1.00)	0.297 (1.00)
22q gain	40 (8%)	454	0.464 (1.00)	0.484 (1.00)	0.839 (1.00)	0.129 (1.00)	1 (1.00)	0.655 (1.00)	0.388 (1.00)	0.829 (1.00)
xq gain	26 (5%)	468	0.963 (1.00)	0.956 (1.00)	0.0585 (1.00)	0.0816 (1.00)	1 (1.00)	0.0459 (1.00)	0.403 (1.00)	0.328 (1.00)
1p loss	58 (12%)	436	0.395 (1.00)	0.084 (1.00)	0.446 (1.00)	0.00814 (1.00)	1 (1.00)	0.334 (1.00)	0.244 (1.00)	0.297 (1.00)
1q loss	37 (7%)	457	0.477 (1.00)	0.491 (1.00)	0.819 (1.00)	0.071 (1.00)	0.637 (1.00)	0.243 (1.00)	0.859 (1.00)	0.484 (1.00)
2p loss	14 (3%)	480	0.796 (1.00)	0.927 (1.00)	0.412 (1.00)	0.12 (1.00)	1 (1.00)	0.707 (1.00)	0.78 (1.00)
2q loss	14 (3%)	480	0.812 (1.00)	0.908 (1.00)	0.562 (1.00)	0.216 (1.00)	1 (1.00)	0.707 (1.00)	0.78 (1.00)
3p loss	357 (72%)	137	0.584 (1.00)	0.751 (1.00)	0.0126 (1.00)	0.0258 (1.00)	0.788 (1.00)	0.128 (1.00)	0.027 (1.00)	0.0785 (1.00)
3q loss	100 (20%)	394	0.69 (1.00)	0.0103 (1.00)	0.622 (1.00)	0.307 (1.00)	0.747 (1.00)	0.758 (1.00)	0.00314 (1.00)	0.384 (1.00)
5q loss	6 (1%)	488	0.0548 (1.00)	0.231 (1.00)	0.00581 (1.00)	0.000452 (0.263)	1 (1.00)	0.237 (1.00)	0.421 (1.00)
6p loss	99 (20%)	395	0.277 (1.00)	0.377 (1.00)	0.0589 (1.00)	0.0389 (1.00)	0.0061 (1.00)	0.279 (1.00)	0.00201 (1.00)	0.122 (1.00)
6q loss	124 (25%)	370	0.65 (1.00)	0.832 (1.00)	0.273 (1.00)	0.194 (1.00)	0.00149 (0.843)	0.668 (1.00)	0.0634 (1.00)	0.21 (1.00)
7q loss	3 (1%)	491	0.529 (1.00)	0.559 (1.00)	0.127 (1.00)	0.011 (1.00)	0.0732 (1.00)	1 (1.00)	0.555 (1.00)
8p loss	134 (27%)	360	0.281 (1.00)	0.55 (1.00)	0.423 (1.00)	0.371 (1.00)	0.779 (1.00)	0.266 (1.00)	0.136 (1.00)	0.893 (1.00)
8q loss	64 (13%)	430	0.645 (1.00)	0.918 (1.00)	0.663 (1.00)	0.544 (1.00)	0.454 (1.00)	1 (1.00)	0.0239 (1.00)	0.654 (1.00)
10p loss	66 (13%)	428	0.334 (1.00)	0.381 (1.00)	0.0906 (1.00)	0.0125 (1.00)	0.14 (1.00)	0.584 (1.00)	0.331 (1.00)	0.0269 (1.00)
10q loss	86 (17%)	408	0.475 (1.00)	0.513 (1.00)	0.0958 (1.00)	0.00267 (1.00)	0.322 (1.00)	0.624 (1.00)	0.105 (1.00)	0.112 (1.00)
11p loss	18 (4%)	476	0.0091 (1.00)	0.145 (1.00)	0.458 (1.00)	0.457 (1.00)	0.16 (1.00)	0.503 (1.00)	1 (1.00)	0.81 (1.00)
11q loss	23 (5%)	471	0.00902 (1.00)	0.0228 (1.00)	0.697 (1.00)	0.641 (1.00)	0.244 (1.00)	0.381 (1.00)	0.502 (1.00)	0.887 (1.00)
12p loss	3 (1%)	491	0.321 (1.00)	0.755 (1.00)	0.49 (1.00)	0.743 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
12q loss	4 (1%)	490	0.955 (1.00)	0.343 (1.00)	0.173 (1.00)	0.414 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
15q loss	35 (7%)	459	0.00213 (1.00)	0.829 (1.00)	0.00113 (0.648)	0.000511 (0.296)	1 (1.00)	0.0135 (1.00)	0.0661 (1.00)	0.484 (1.00)
16p loss	9 (2%)	485	0.134 (1.00)	0.842 (1.00)	0.257 (1.00)	0.00987 (1.00)	0.369 (1.00)	1 (1.00)	1 (1.00)
16q loss	13 (3%)	481	0.218 (1.00)	0.916 (1.00)	0.292 (1.00)	0.00393 (1.00)	0.46 (1.00)	1 (1.00)	1 (1.00)
17p loss	45 (9%)	449	0.406 (1.00)	0.414 (1.00)	0.275 (1.00)	0.26 (1.00)	0.375 (1.00)	0.0491 (1.00)	0.143 (1.00)	0.0261 (1.00)
17q loss	28 (6%)	466	0.542 (1.00)	0.832 (1.00)	0.357 (1.00)	0.353 (1.00)	1 (1.00)	0.177 (1.00)	0.312 (1.00)
18p loss	91 (18%)	403	0.00196 (1.00)	0.125 (1.00)	0.00062 (0.357)	0.000451 (0.263)	1 (1.00)	0.0775 (1.00)	0.222 (1.00)	0.494 (1.00)
18q loss	93 (19%)	401	0.0084 (1.00)	0.14 (1.00)	0.0124 (1.00)	0.00762 (1.00)	1 (1.00)	0.0833 (1.00)	0.148 (1.00)	0.569 (1.00)
19q loss	4 (1%)	490	0.004 (1.00)	0.831 (1.00)	0.244 (1.00)	0.00312 (1.00)	1 (1.00)	0.117 (1.00)	1 (1.00)
20p loss	8 (2%)	486	0.827 (1.00)	0.702 (1.00)	0.726 (1.00)	0.616 (1.00)	1 (1.00)	0.362 (1.00)	1 (1.00)
20q loss	3 (1%)	491	0.799 (1.00)	0.181 (1.00)	0.243 (1.00)	0.111 (1.00)		0.399 (1.00)	1 (1.00)
21q loss	53 (11%)	441	0.574 (1.00)	0.592 (1.00)	0.204 (1.00)	0.00464 (1.00)	0.095 (1.00)	1 (1.00)	0.761 (1.00)	0.505 (1.00)
22q loss	38 (8%)	456	0.0023 (1.00)	0.269 (1.00)	0.0202 (1.00)	0.171 (1.00)	1 (1.00)	0.0647 (1.00)	0.727 (1.00)	0.115 (1.00)
xq loss	46 (9%)	448	0.141 (1.00)	0.483 (1.00)	0.538 (1.00)	0.246 (1.00)	0.359 (1.00)	0.673 (1.00)	0.142 (1.00)

'5p gain' versus 'AGE'

P value = 0.000334 (t-test), Q value = 0.2

Table S1. Gene #9: '5p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	493	60.6 (12.2)
5P GAIN MUTATED	183	63.1 (11.8)
5P GAIN WILD-TYPE	310	59.1 (12.2)

Figure S1. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.29e-05 (Fisher's exact test), Q value = 0.031

Table S2. Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
20P GAIN MUTATED	32	12	39	26
20P GAIN WILD-TYPE	205	42	86	52

Figure S2. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'PATHOLOGY.T.STAGE'

P value = 4.21e-06 (Fisher's exact test), Q value = 0.0025

Table S3. Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
20P GAIN MUTATED	33	13	57	6
20P GAIN WILD-TYPE	209	52	119	5

Figure S3. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.022

Table S4. Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
20Q GAIN MUTATED	33	12	41	26
20Q GAIN WILD-TYPE	204	42	84	52

Figure S4. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'PATHOLOGY.T.STAGE'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0093

Table S5. Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
20Q GAIN MUTATED	35	13	59	5
20Q GAIN WILD-TYPE	207	52	117	6

Figure S5. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'Time to Death'

P value = 7.09e-06 (logrank test), Q value = 0.0043

Table S6. Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
4P LOSS MUTATED	71	38	0.5 - 90.3 (25.7)
4P LOSS WILD-TYPE	422	125	0.1 - 120.6 (37.2)

Figure S6. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

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

P value = 0.000354 (Fisher's exact test), Q value = 0.21

Table S7. Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
4P LOSS MUTATED	21	8	38	4
4P LOSS WILD-TYPE	221	57	138	7

Figure S7. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4q loss' versus 'Time to Death'

P value = 1.93e-06 (logrank test), Q value = 0.0012

Table S8. Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
4Q LOSS MUTATED	65	36	1.0 - 90.3 (23.3)
4Q LOSS WILD-TYPE	428	127	0.1 - 120.6 (37.2)

Figure S8. Get High-res Image Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.01

Table S9. Gene #48: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
4Q LOSS MUTATED	15	6	24	20
4Q LOSS WILD-TYPE	222	48	101	58

Figure S9. Get High-res Image Gene #48: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 8.49e-06 (Fisher's exact test), Q value = 0.0051

Table S10. Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
4Q LOSS MUTATED	16	8	36	5
4Q LOSS WILD-TYPE	226	57	140	6

Figure S10. Get High-res Image Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000195 (Fisher's exact test), Q value = 0.11

Table S11. Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
5P LOSS MUTATED	0	3	2	2
5P LOSS WILD-TYPE	242	62	174	9

Figure S11. Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9p loss' versus 'Time to Death'

P value = 3.1e-05 (logrank test), Q value = 0.018

Table S12. Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
9P LOSS MUTATED	142	67	0.2 - 109.9 (34.9)
9P LOSS WILD-TYPE	351	96	0.1 - 120.6 (37.0)

Figure S12. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.01

Table S13. Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
9P LOSS MUTATED	48	11	50	33
9P LOSS WILD-TYPE	189	43	75	45

Figure S13. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 9.01e-05 (Fisher's exact test), Q value = 0.053

Table S14. Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
9P LOSS MUTATED	51	15	71	5
9P LOSS WILD-TYPE	191	50	105	6

Figure S14. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9q loss' versus 'Time to Death'

P value = 0.000152 (logrank test), Q value = 0.09

Table S15. Gene #57: '9q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
9Q LOSS MUTATED	145	67	0.2 - 109.9 (36.4)
9Q LOSS WILD-TYPE	348	96	0.1 - 120.6 (37.0)

Figure S15. Get High-res Image Gene #57: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.0011

Table S16. Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
9Q LOSS MUTATED	45	14	52	34
9Q LOSS WILD-TYPE	192	40	73	44

Figure S16. Get High-res Image Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 7.87e-06 (Fisher's exact test), Q value = 0.0047

Table S17. Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
9Q LOSS MUTATED	48	18	75	4
9Q LOSS WILD-TYPE	194	47	101	7

Figure S17. Get High-res Image Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000224 (Fisher's exact test), Q value = 0.13

Table S18. Gene #64: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
13Q LOSS MUTATED	23	2	25	19
13Q LOSS WILD-TYPE	214	52	100	59

Figure S18. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'13q loss' versus 'PATHOLOGY.T.STAGE'

P value = 3.99e-06 (Fisher's exact test), Q value = 0.0024

Table S19. Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
13Q LOSS MUTATED	25	3	34	7
13Q LOSS WILD-TYPE	217	62	142	4

Figure S19. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'14q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.71e-05 (Fisher's exact test), Q value = 0.028

Table S20. Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
14Q LOSS MUTATED	74	26	63	44
14Q LOSS WILD-TYPE	163	28	62	34

Figure S20. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'14q loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000189 (Fisher's exact test), Q value = 0.11

Table S21. Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
14Q LOSS MUTATED	79	34	91	3
14Q LOSS WILD-TYPE	163	31	85	8

Figure S21. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'19p loss' versus 'Time to Death'

P value = 0.000205 (logrank test), Q value = 0.12

Table S22. Gene #73: '19p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
19P LOSS MUTATED	11	9	1.4 - 109.9 (28.5)
19P LOSS WILD-TYPE	482	154	0.1 - 120.6 (37.0)

Figure S22. Get High-res Image Gene #73: '19p loss' versus Clinical Feature #1: 'Time to Death'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = KIRC-TP.merged_data.txt
Number of patients = 494
Number of significantly arm-level cnvs = 79
Number of selected clinical features = 9
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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