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

Thyroid Adenocarcinoma (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/C1GF0S63

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 57 arm-level events and 15 clinical features across 484 patients, 53 significant findings detected with Q value < 0.25.

1q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
3p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
4q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
5q gain cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
7p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.
7q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
8q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.
9q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
11p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
11q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
12p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
12q gain cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.
13q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
16p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
16q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.
17p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.
17q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.
18p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
18q 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 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
20q gain cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
21q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
xq gain cnv correlated to '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'.
8p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
8q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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 'NEOPLASM.DISEASESTAGE'.
11q loss cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.
13q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
17q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
xq loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 57 arm-level events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.


		Clinical Features	Time to Death	AGE	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RADIATIONEXPOSURE	EXTRATHYROIDAL EXTENSION	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES	MULTIFOCALITY	TUMOR SIZE
	nCNV (%)	nWild-Type	logrank test	t-test	Chi-square 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	Fisher's exact test	Fisher's exact test	Fisher's exact test	t-test	Fisher's exact test	t-test
5q gain	16 (3%)	468	0.0222 (1.00)	0.0146 (1.00)	0.000152 (0.122)	0.685 (1.00)	0.0057 (1.00)	0.000165 (0.131)	0.774 (1.00)	0.0442 (1.00)	0.379 (1.00)	1 (1.00)	0.0292 (1.00)	0.414 (1.00)	1.12e-25 (9.45e-23)	0.803 (1.00)	0.173 (1.00)
20p gain	12 (2%)	472	0.337 (1.00)	0.0946 (1.00)	4.82e-05 (0.0389)	0.569 (1.00)	0.0678 (1.00)	0.00016 (0.128)	0.529 (1.00)	0.00447 (1.00)	1 (1.00)	1 (1.00)	0.0224 (1.00)	0.856 (1.00)	1.23e-25 (1.03e-22)	1 (1.00)	0.133 (1.00)
20q gain	12 (2%)	472	0.337 (1.00)	0.0946 (1.00)	4.82e-05 (0.0389)	0.569 (1.00)	0.0678 (1.00)	0.00016 (0.128)	0.529 (1.00)	0.00447 (1.00)	1 (1.00)	1 (1.00)	0.0224 (1.00)	0.856 (1.00)	1.23e-25 (1.03e-22)	1 (1.00)	0.133 (1.00)
1q gain	23 (5%)	461	0.162 (1.00)	0.000699 (0.551)	9.09e-06 (0.00736)	0.000207 (0.164)	0.002 (1.00)	0.691 (1.00)	0.345 (1.00)	0.0269 (1.00)	0.499 (1.00)	0.585 (1.00)	0.000324 (0.257)	0.0261 (1.00)	0.541 (1.00)	0.0545 (1.00)	0.0541 (1.00)
7p gain	17 (4%)	467	0.372 (1.00)	0.0573 (1.00)	8.98e-05 (0.0722)	0.794 (1.00)	0.003 (1.00)	0.00591 (1.00)	1 (1.00)	0.019 (1.00)	1 (1.00)	1 (1.00)	0.0101 (1.00)	0.414 (1.00)	1.09e-25 (9.25e-23)	1 (1.00)	0.707 (1.00)
12q gain	15 (3%)	469	0.513 (1.00)	0.165 (1.00)	0.0797 (1.00)	0.922 (1.00)	0.00176 (1.00)	0.00025 (0.199)	0.769 (1.00)	0.00648 (1.00)	1 (1.00)	1 (1.00)	0.203 (1.00)	0.546 (1.00)	1.15e-25 (9.67e-23)	1 (1.00)	0.984 (1.00)
16q gain	13 (3%)	471	0.228 (1.00)	0.133 (1.00)	0.000188 (0.149)	0.715 (1.00)	0.0371 (1.00)	0.0094 (1.00)	1 (1.00)	0.0521 (1.00)	1 (1.00)	1 (1.00)	0.0168 (1.00)	0.236 (1.00)	1.2e-25 (1.01e-22)	1 (1.00)	0.758 (1.00)
17p gain	16 (3%)	468	0.419 (1.00)	0.103 (1.00)	3.32e-05 (0.0269)	0.851 (1.00)	0.036 (1.00)	0.00786 (1.00)	1 (1.00)	0.0442 (1.00)	1 (1.00)	1 (1.00)	0.767 (1.00)	0.326 (1.00)	1.51e-06 (0.00123)	1 (1.00)	0.41 (1.00)
17q gain	17 (4%)	467	0.419 (1.00)	0.169 (1.00)	8.98e-05 (0.0722)	0.863 (1.00)	0.0206 (1.00)	0.00591 (1.00)	1 (1.00)	0.0677 (1.00)	1 (1.00)	1 (1.00)	0.694 (1.00)	0.329 (1.00)	2.11e-07 (0.000172)	0.806 (1.00)	0.588 (1.00)
11q loss	9 (2%)	475	0.00264 (1.00)	9.49e-05 (0.0761)	5.53e-06 (0.00449)	0.207 (1.00)	0.503 (1.00)	0.12 (1.00)	0.00184 (1.00)	1 (1.00)	0.234 (1.00)	1 (1.00)	0.798 (1.00)	0.513 (1.00)	0.254 (1.00)	1 (1.00)	0.0136 (1.00)
xq loss	3 (1%)	481	0.753 (1.00)	0.182 (1.00)	8.6e-05 (0.0692)	0.223 (1.00)	0.248 (1.00)	0.135 (1.00)	0.175 (1.00)	0.645 (1.00)	1 (1.00)	1 (1.00)	0.608 (1.00)	1 (1.00)	1.38e-25 (1.13e-22)	1 (1.00)
3p gain	3 (1%)	481	0.0121 (1.00)	0.0169 (1.00)	4.07e-05 (0.0329)	0.12 (1.00)	1 (1.00)	0.0114 (1.00)	0.568 (1.00)	0.233 (1.00)	1 (1.00)	1 (1.00)	0.608 (1.00)	0.0232 (1.00)		1 (1.00)	0.629 (1.00)
4p gain	5 (1%)	479	0.026 (1.00)	0.0543 (1.00)	0.356 (1.00)	0.704 (1.00)	0.0611 (1.00)	0.0294 (1.00)	1 (1.00)	0.186 (1.00)	0.137 (1.00)	1 (1.00)	1 (1.00)	0.389 (1.00)	1.32e-25 (1.1e-22)	0.187 (1.00)	0.305 (1.00)
4q gain	5 (1%)	479	0.026 (1.00)	0.0543 (1.00)	0.356 (1.00)	0.704 (1.00)	0.0611 (1.00)	0.0294 (1.00)	1 (1.00)	0.186 (1.00)	0.137 (1.00)	1 (1.00)	1 (1.00)	0.389 (1.00)	1.32e-25 (1.1e-22)	0.187 (1.00)	0.305 (1.00)
7q gain	19 (4%)	465	0.387 (1.00)	0.0406 (1.00)	0.000403 (0.319)	0.93 (1.00)	0.003 (1.00)	0.00949 (1.00)	0.792 (1.00)	0.0119 (1.00)	1 (1.00)	1 (1.00)	0.0219 (1.00)	0.259 (1.00)	1.09e-25 (9.25e-23)	1 (1.00)	0.649 (1.00)
8q gain	7 (1%)	477	0.108 (1.00)	0.371 (1.00)	2.21e-06 (0.0018)	0.41 (1.00)	1 (1.00)	0.0964 (1.00)	0.681 (1.00)	0.822 (1.00)	1 (1.00)	1 (1.00)	0.00831 (1.00)	0.39 (1.00)	0.00208 (1.00)	0.13 (1.00)	0.282 (1.00)
9q gain	4 (1%)	480	0.698 (1.00)	0.0156 (1.00)	0.0679 (1.00)	0.629 (1.00)	0.623 (1.00)	1 (1.00)	0.29 (1.00)	0.463 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.000171 (0.136)	0.34 (1.00)	0.00997 (1.00)
11p gain	6 (1%)	478	0.559 (1.00)	0.775 (1.00)	0.936 (1.00)	0.761 (1.00)	0.123 (1.00)	0.189 (1.00)	0.195 (1.00)	0.256 (1.00)	1 (1.00)	1 (1.00)	0.353 (1.00)	0.46 (1.00)	1.35e-25 (1.12e-22)	0.224 (1.00)	0.563 (1.00)
11q gain	5 (1%)	479	0.562 (1.00)	0.807 (1.00)	0.961 (1.00)	0.891 (1.00)	0.248 (1.00)	0.249 (1.00)	0.613 (1.00)	0.569 (1.00)	1 (1.00)	1 (1.00)	0.442 (1.00)	0.389 (1.00)	1.38e-25 (1.13e-22)	0.0648 (1.00)	0.829 (1.00)
12p gain	14 (3%)	470	0.513 (1.00)	0.193 (1.00)	0.0518 (1.00)	0.916 (1.00)	0.00176 (1.00)	0.000559 (0.441)	0.769 (1.00)	0.0172 (1.00)	1 (1.00)	1 (1.00)	0.244 (1.00)	0.455 (1.00)	1.15e-25 (9.67e-23)	0.792 (1.00)	0.984 (1.00)
13q gain	5 (1%)	479	0.731 (1.00)	0.166 (1.00)	0.0172 (1.00)	0.704 (1.00)	0.123 (1.00)	0.249 (1.00)	1 (1.00)	0.186 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1.35e-25 (1.12e-22)	0.666 (1.00)	0.655 (1.00)
16p gain	15 (3%)	469	0.236 (1.00)	0.19 (1.00)	0.00102 (0.805)	0.878 (1.00)	0.0201 (1.00)	0.0162 (1.00)	0.769 (1.00)	0.101 (1.00)	1 (1.00)	1 (1.00)	0.0352 (1.00)	0.13 (1.00)	1.17e-25 (9.87e-23)	0.794 (1.00)	0.752 (1.00)
18p gain	6 (1%)	478	0.617 (1.00)	0.745 (1.00)	0.936 (1.00)	0.761 (1.00)	0.0611 (1.00)	0.476 (1.00)	0.66 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.389 (1.00)	1.35e-25 (1.12e-22)	0.691 (1.00)	0.611 (1.00)
18q gain	6 (1%)	478	0.617 (1.00)	0.745 (1.00)	0.936 (1.00)	0.761 (1.00)	0.0611 (1.00)	0.476 (1.00)	0.66 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.389 (1.00)	1.35e-25 (1.12e-22)	0.691 (1.00)	0.611 (1.00)
19p gain	8 (2%)	476	0.734 (1.00)	0.0788 (1.00)	0.867 (1.00)	0.612 (1.00)	0.0302 (1.00)	0.00251 (1.00)	0.218 (1.00)	0.00895 (1.00)	1 (1.00)	1 (1.00)	0.593 (1.00)	0.458 (1.00)	1.26e-25 (1.05e-22)	0.152 (1.00)	0.219 (1.00)
19q gain	10 (2%)	474	0.0329 (1.00)	0.028 (1.00)	0.747 (1.00)	0.328 (1.00)	0.0149 (1.00)	0.0011 (0.864)	0.14 (1.00)	0.00564 (1.00)	0.256 (1.00)	1 (1.00)	0.515 (1.00)	0.688 (1.00)	1.23e-25 (1.03e-22)	0.524 (1.00)	0.145 (1.00)
21q gain	5 (1%)	479	0.617 (1.00)	0.043 (1.00)	0.764 (1.00)	0.56 (1.00)	0.248 (1.00)	0.689 (1.00)	0.613 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	0.313 (1.00)	1.38e-25 (1.13e-22)	0.0648 (1.00)	0.313 (1.00)
xq gain	9 (2%)	475	0.0873 (1.00)	0.0759 (1.00)	6.53e-06 (0.0053)	0.485 (1.00)	0.285 (1.00)	0.0244 (1.00)	0.456 (1.00)	0.343 (1.00)	1 (1.00)	0.31 (1.00)	0.0236 (1.00)	0.0841 (1.00)	0.656 (1.00)	0.314 (1.00)	0.544 (1.00)
2p loss	10 (2%)	474	0.72 (1.00)	0.282 (1.00)	0.00329 (1.00)	0.697 (1.00)	0.00732 (1.00)	0.0135 (1.00)	0.731 (1.00)	0.00564 (1.00)	1 (1.00)	1 (1.00)	0.141 (1.00)	0.451 (1.00)	1.2e-25 (1.01e-22)	1 (1.00)	0.695 (1.00)
2q loss	10 (2%)	474	0.576 (1.00)	0.257 (1.00)	0.00329 (1.00)	0.823 (1.00)	0.0149 (1.00)	0.0135 (1.00)	0.731 (1.00)	0.00564 (1.00)	1 (1.00)	1 (1.00)	0.141 (1.00)	0.451 (1.00)	1.23e-25 (1.03e-22)	1 (1.00)	0.481 (1.00)
3q loss	4 (1%)	480	0.598 (1.00)	0.646 (1.00)	0.201 (1.00)	0.629 (1.00)	0.248 (1.00)	0.107 (1.00)	1 (1.00)	0.463 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	1.38e-25 (1.13e-22)	1 (1.00)	0.101 (1.00)
8p loss	4 (1%)	480	0.872 (1.00)	0.981 (1.00)	0.189 (1.00)	1 (1.00)	0.248 (1.00)	0.374 (1.00)	0.0598 (1.00)	0.463 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	1.35e-25 (1.12e-22)	1 (1.00)	0.89 (1.00)
8q loss	4 (1%)	480	0.872 (1.00)	0.981 (1.00)	0.189 (1.00)	1 (1.00)	0.248 (1.00)	0.374 (1.00)	0.0598 (1.00)	0.463 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	1.35e-25 (1.12e-22)	1 (1.00)	0.89 (1.00)
9q loss	22 (5%)	462	0.0288 (1.00)	0.0221 (1.00)	1.28e-09 (1.04e-06)	0.191 (1.00)	0.64 (1.00)	0.0151 (1.00)	0.324 (1.00)	0.711 (1.00)	0.483 (1.00)	0.585 (1.00)	0.0671 (1.00)	0.572 (1.00)	0.239 (1.00)	0.666 (1.00)	0.113 (1.00)
10p loss	7 (1%)	477	0.588 (1.00)	0.334 (1.00)	0.104 (1.00)	0.26 (1.00)	0.0302 (1.00)	0.0964 (1.00)	0.39 (1.00)	0.394 (1.00)	1 (1.00)	1 (1.00)	0.753 (1.00)	1 (1.00)	1.32e-25 (1.1e-22)	0.709 (1.00)	0.0511 (1.00)
10q loss	6 (1%)	478	0.648 (1.00)	0.338 (1.00)	0.455 (1.00)	0.328 (1.00)	0.0611 (1.00)	0.189 (1.00)	0.195 (1.00)	0.785 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1.35e-25 (1.12e-22)	0.422 (1.00)	0.0462 (1.00)
11p loss	7 (1%)	477	0.00126 (0.988)	0.000522 (0.413)	1.47e-07 (0.00012)	0.228 (1.00)	0.449 (1.00)	0.0964 (1.00)	0.0164 (1.00)	0.822 (1.00)	0.187 (1.00)	1 (1.00)	0.545 (1.00)	0.526 (1.00)	0.0813 (1.00)	0.709 (1.00)	0.0356 (1.00)
13q loss	14 (3%)	470	0.381 (1.00)	0.0446 (1.00)	0.6 (1.00)	0.591 (1.00)	0.0108 (1.00)	0.365 (1.00)	0.539 (1.00)	0.469 (1.00)	0.341 (1.00)	0.000719 (0.566)	0.626 (1.00)	0.674 (1.00)	1.07e-14 (8.76e-12)	0.792 (1.00)	0.153 (1.00)
17q loss	4 (1%)	480	0.806 (1.00)	0.368 (1.00)	0.793 (1.00)	0.629 (1.00)	0.123 (1.00)	0.374 (1.00)	1 (1.00)	0.463 (1.00)	0.111 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1.38e-25 (1.13e-22)	1 (1.00)	0.486 (1.00)
1p gain	3 (1%)	481	0.92 (1.00)	0.305 (1.00)	0.0215 (1.00)	1 (1.00)	0.623 (1.00)	0.135 (1.00)	1 (1.00)	0.342 (1.00)	1 (1.00)	0.0785 (1.00)	1 (1.00)	0.233 (1.00)	0.151 (1.00)	1 (1.00)
5p gain	19 (4%)	465	0.0856 (1.00)	0.0015 (1.00)	0.00056 (0.442)	0.527 (1.00)	0.112 (1.00)	0.00128 (1.00)	0.603 (1.00)	0.118 (1.00)	0.434 (1.00)	1 (1.00)	0.0305 (1.00)	0.48 (1.00)	0.00621 (1.00)	0.816 (1.00)	0.122 (1.00)
8p gain	6 (1%)	478	0.628 (1.00)	0.636 (1.00)	0.936 (1.00)	0.906 (1.00)	0.623 (1.00)	0.189 (1.00)	1 (1.00)	0.785 (1.00)	1 (1.00)	1 (1.00)	0.353 (1.00)	0.46 (1.00)	0.00208 (1.00)	0.224 (1.00)	0.425 (1.00)
9p gain	3 (1%)	481	0.703 (1.00)	0.0791 (1.00)	0.0433 (1.00)	0.806 (1.00)	0.248 (1.00)	0.608 (1.00)	1 (1.00)	0.233 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)		0.598 (1.00)	0.0614 (1.00)
14q gain	11 (2%)	473	0.536 (1.00)	0.0292 (1.00)	0.00229 (1.00)	0.38 (1.00)	0.0678 (1.00)	0.0347 (1.00)	0.302 (1.00)	0.0629 (1.00)	1 (1.00)	1 (1.00)	0.825 (1.00)	0.494 (1.00)	0.0176 (1.00)	0.123 (1.00)	0.312 (1.00)
1p loss	4 (1%)	480	0.601 (1.00)	0.605 (1.00)	0.201 (1.00)	0.629 (1.00)	0.248 (1.00)	0.374 (1.00)	0.578 (1.00)	0.463 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)		0.628 (1.00)	0.177 (1.00)
1q loss	3 (1%)	481	0.605 (1.00)	0.872 (1.00)	0.802 (1.00)	0.806 (1.00)	0.499 (1.00)	0.135 (1.00)	0.568 (1.00)	0.233 (1.00)	1 (1.00)	1 (1.00)	0.608 (1.00)	1 (1.00)		1 (1.00)	0.177 (1.00)
3p loss	3 (1%)	481	0.661 (1.00)	0.671 (1.00)	0.802 (1.00)	0.806 (1.00)	0.499 (1.00)	0.135 (1.00)	1 (1.00)	0.645 (1.00)	1 (1.00)	1 (1.00)	0.608 (1.00)	1 (1.00)		0.598 (1.00)	0.0829 (1.00)
6p loss	4 (1%)	480	0.633 (1.00)	0.421 (1.00)	0.803 (1.00)	1 (1.00)	1 (1.00)	0.107 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	0.551 (1.00)		1 (1.00)	0.0253 (1.00)
6q loss	7 (1%)	477	0.00817 (1.00)	0.123 (1.00)	0.365 (1.00)	0.79 (1.00)	0.372 (1.00)	0.0097 (1.00)	0.39 (1.00)	0.822 (1.00)	0.187 (1.00)	0.218 (1.00)	0.383 (1.00)	0.755 (1.00)	0.00208 (1.00)	0.459 (1.00)	0.0166 (1.00)
9p loss	18 (4%)	466	0.416 (1.00)	0.204 (1.00)	0.00266 (1.00)	0.341 (1.00)	1 (1.00)	0.0258 (1.00)	0.276 (1.00)	0.758 (1.00)	1 (1.00)	1 (1.00)	0.694 (1.00)	0.595 (1.00)	0.00724 (1.00)	0.633 (1.00)	0.187 (1.00)
15q loss	8 (2%)	476	0.56 (1.00)	0.705 (1.00)	0.217 (1.00)	0.724 (1.00)	0.122 (1.00)	0.0621 (1.00)	0.688 (1.00)	0.0532 (1.00)	1 (1.00)	1 (1.00)	0.593 (1.00)	0.785 (1.00)	0.389 (1.00)	0.731 (1.00)	0.086 (1.00)
17p loss	7 (1%)	477	0.589 (1.00)	0.68 (1.00)	0.527 (1.00)	0.14 (1.00)	0.449 (1.00)	0.342 (1.00)	0.681 (1.00)	0.154 (1.00)	0.015 (1.00)	0.25 (1.00)	0.183 (1.00)	0.755 (1.00)	0.932 (1.00)	1 (1.00)	0.0926 (1.00)
18p loss	4 (1%)	480	0.759 (1.00)	0.543 (1.00)	0.189 (1.00)	0.344 (1.00)	1 (1.00)	0.374 (1.00)	1 (1.00)	0.463 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	0.00208 (1.00)	0.628 (1.00)	0.233 (1.00)
18q loss	4 (1%)	480	0.759 (1.00)	0.543 (1.00)	0.189 (1.00)	0.344 (1.00)	1 (1.00)	0.374 (1.00)	1 (1.00)	0.463 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	0.00208 (1.00)	0.628 (1.00)	0.233 (1.00)
19p loss	5 (1%)	479	0.129 (1.00)	0.522 (1.00)	0.312 (1.00)	1 (1.00)	1 (1.00)	0.689 (1.00)	0.613 (1.00)	1 (1.00)	1 (1.00)	0.0141 (1.00)	1 (1.00)	0.633 (1.00)		0.38 (1.00)	0.0195 (1.00)
21q loss	8 (2%)	476	0.849 (1.00)	0.0978 (1.00)	0.00879 (1.00)	0.175 (1.00)	0.724 (1.00)	0.773 (1.00)	0.445 (1.00)	0.857 (1.00)	1 (1.00)	1 (1.00)	0.215 (1.00)	1 (1.00)	0.983 (1.00)	0.152 (1.00)	0.672 (1.00)
22q loss	84 (17%)	400	0.499 (1.00)	0.899 (1.00)	0.698 (1.00)	0.525 (1.00)	0.315 (1.00)	0.578 (1.00)	0.498 (1.00)	0.27 (1.00)	0.481 (1.00)	0.332 (1.00)	0.305 (1.00)	0.474 (1.00)	0.315 (1.00)	0.225 (1.00)	0.863 (1.00)

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.09e-06 (Chi-square test), Q value = 0.0074

Table S1. Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
1Q GAIN MUTATED	6	0	9	1	7	0
1Q GAIN WILD-TYPE	268	50	97	1	37	6

Figure S1. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.000207 (Fisher's exact test), Q value = 0.16

Table S2. Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	139	161	161	21
1Q GAIN MUTATED	2	3	14	4
1Q GAIN WILD-TYPE	137	158	147	17

Figure S2. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'3p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.07e-05 (Chi-square test), Q value = 0.033

Table S3. Gene #3: '3p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
3P GAIN MUTATED	1	1	0	0	0	1
3P GAIN WILD-TYPE	273	49	106	2	44	5

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

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

P value = 1.32e-25 (t-test), Q value = 1.1e-22

Table S4. Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
4P GAIN MUTATED	5	0.0 (0.0)
4P GAIN WILD-TYPE	380	3.6 (6.2)

Figure S4. Get High-res Image Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.32e-25 (t-test), Q value = 1.1e-22

Table S5. Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
4Q GAIN MUTATED	5	0.0 (0.0)
4Q GAIN WILD-TYPE	380	3.6 (6.2)

Figure S5. Get High-res Image Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'5q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000152 (Chi-square test), Q value = 0.12

Table S6. Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
5Q GAIN MUTATED	5	5	5	1	0	0
5Q GAIN WILD-TYPE	269	45	101	1	44	6

Figure S6. Get High-res Image Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'5q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000165 (Fisher's exact test), Q value = 0.13

Table S7. Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	265	9	209
5Q GAIN MUTATED	1	0	15
5Q GAIN WILD-TYPE	264	9	194

Figure S7. Get High-res Image Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.12e-25 (t-test), Q value = 9.5e-23

Table S8. Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
5Q GAIN MUTATED	12	0.0 (0.0)
5Q GAIN WILD-TYPE	373	3.7 (6.3)

Figure S8. Get High-res Image Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.98e-05 (Chi-square test), Q value = 0.072

Table S9. Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
7P GAIN MUTATED	7	6	3	1	0	0
7P GAIN WILD-TYPE	267	44	103	1	44	6

Figure S9. Get High-res Image Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.09e-25 (t-test), Q value = 9.3e-23

Table S10. Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
7P GAIN MUTATED	13	0.0 (0.0)
7P GAIN WILD-TYPE	372	3.7 (6.3)

Figure S10. Get High-res Image Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.09e-25 (t-test), Q value = 9.3e-23

Table S11. Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
7Q GAIN MUTATED	13	0.0 (0.0)
7Q GAIN WILD-TYPE	372	3.7 (6.3)

Figure S11. Get High-res Image Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.21e-06 (Chi-square test), Q value = 0.0018

Table S12. Gene #11: '8q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
8Q GAIN MUTATED	3	1	2	1	0	0
8Q GAIN WILD-TYPE	271	49	104	1	44	6

Figure S12. Get High-res Image Gene #11: '8q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000171 (t-test), Q value = 0.14

Table S13. Gene #13: '9q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
9Q GAIN MUTATED	3	0.3 (0.6)
9Q GAIN WILD-TYPE	382	3.6 (6.2)

Figure S13. Get High-res Image Gene #13: '9q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.35e-25 (t-test), Q value = 1.1e-22

Table S14. Gene #14: '11p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
11P GAIN MUTATED	4	0.0 (0.0)
11P GAIN WILD-TYPE	381	3.6 (6.2)

Figure S14. Get High-res Image Gene #14: '11p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.38e-25 (t-test), Q value = 1.1e-22

Table S15. Gene #15: '11q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
11Q GAIN MUTATED	3	0.0 (0.0)
11Q GAIN WILD-TYPE	382	3.6 (6.2)

Figure S15. Get High-res Image Gene #15: '11q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.15e-25 (t-test), Q value = 9.7e-23

Table S16. Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
12P GAIN MUTATED	11	0.0 (0.0)
12P GAIN WILD-TYPE	374	3.7 (6.3)

Figure S16. Get High-res Image Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'12q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.2

Table S17. Gene #17: '12q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	265	9	209
12Q GAIN MUTATED	1	0	14
12Q GAIN WILD-TYPE	264	9	195

Figure S17. Get High-res Image Gene #17: '12q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.15e-25 (t-test), Q value = 9.7e-23

Table S18. Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
12Q GAIN MUTATED	11	0.0 (0.0)
12Q GAIN WILD-TYPE	374	3.7 (6.3)

Figure S18. Get High-res Image Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.35e-25 (t-test), Q value = 1.1e-22

Table S19. Gene #18: '13q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
13Q GAIN MUTATED	4	0.0 (0.0)
13Q GAIN WILD-TYPE	381	3.6 (6.2)

Figure S19. Get High-res Image Gene #18: '13q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.17e-25 (t-test), Q value = 9.9e-23

Table S20. Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
16P GAIN MUTATED	10	0.0 (0.0)
16P GAIN WILD-TYPE	375	3.6 (6.3)

Figure S20. Get High-res Image Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'16q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000188 (Chi-square test), Q value = 0.15

Table S21. Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
16Q GAIN MUTATED	6	4	2	1	0	0
16Q GAIN WILD-TYPE	268	46	104	1	44	6

Figure S21. Get High-res Image Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.2e-25 (t-test), Q value = 1e-22

Table S22. Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
16Q GAIN MUTATED	9	0.0 (0.0)
16Q GAIN WILD-TYPE	376	3.6 (6.2)

Figure S22. Get High-res Image Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.32e-05 (Chi-square test), Q value = 0.027

Table S23. Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
17P GAIN MUTATED	6	6	3	1	0	0
17P GAIN WILD-TYPE	268	44	103	1	44	6

Figure S23. Get High-res Image Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.51e-06 (t-test), Q value = 0.0012

Table S24. Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
17P GAIN MUTATED	12	0.6 (1.4)
17P GAIN WILD-TYPE	373	3.6 (6.3)

Figure S24. Get High-res Image Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.98e-05 (Chi-square test), Q value = 0.072

Table S25. Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
17Q GAIN MUTATED	7	6	3	1	0	0
17Q GAIN WILD-TYPE	267	44	103	1	44	6

Figure S25. Get High-res Image Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 2.11e-07 (t-test), Q value = 0.00017

Table S26. Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
17Q GAIN MUTATED	13	0.5 (1.3)
17Q GAIN WILD-TYPE	372	3.7 (6.3)

Figure S26. Get High-res Image Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.35e-25 (t-test), Q value = 1.1e-22

Table S27. Gene #24: '18p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
18P GAIN MUTATED	4	0.0 (0.0)
18P GAIN WILD-TYPE	381	3.6 (6.2)

Figure S27. Get High-res Image Gene #24: '18p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.35e-25 (t-test), Q value = 1.1e-22

Table S28. Gene #25: '18q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
18Q GAIN MUTATED	4	0.0 (0.0)
18Q GAIN WILD-TYPE	381	3.6 (6.2)

Figure S28. Get High-res Image Gene #25: '18q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.26e-25 (t-test), Q value = 1e-22

Table S29. Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
19P GAIN MUTATED	7	0.0 (0.0)
19P GAIN WILD-TYPE	378	3.6 (6.2)

Figure S29. Get High-res Image Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.23e-25 (t-test), Q value = 1e-22

Table S30. Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
19Q GAIN MUTATED	8	0.0 (0.0)
19Q GAIN WILD-TYPE	377	3.6 (6.2)

Figure S30. Get High-res Image Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.82e-05 (Chi-square test), Q value = 0.039

Table S31. Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
20P GAIN MUTATED	4	4	3	1	0	0
20P GAIN WILD-TYPE	270	46	103	1	44	6

Figure S31. Get High-res Image Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S32. Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	265	9	209
20P GAIN MUTATED	0	0	12
20P GAIN WILD-TYPE	265	9	197

Figure S32. Get High-res Image Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.23e-25 (t-test), Q value = 1e-22

Table S33. Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
20P GAIN MUTATED	8	0.0 (0.0)
20P GAIN WILD-TYPE	377	3.6 (6.2)

Figure S33. Get High-res Image Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.82e-05 (Chi-square test), Q value = 0.039

Table S34. Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
20Q GAIN MUTATED	4	4	3	1	0	0
20Q GAIN WILD-TYPE	270	46	103	1	44	6

Figure S34. Get High-res Image Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S35. Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	265	9	209
20Q GAIN MUTATED	0	0	12
20Q GAIN WILD-TYPE	265	9	197

Figure S35. Get High-res Image Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.23e-25 (t-test), Q value = 1e-22

Table S36. Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
20Q GAIN MUTATED	8	0.0 (0.0)
20Q GAIN WILD-TYPE	377	3.6 (6.2)

Figure S36. Get High-res Image Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'21q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.38e-25 (t-test), Q value = 1.1e-22

Table S37. Gene #30: '21q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
21Q GAIN MUTATED	3	0.0 (0.0)
21Q GAIN WILD-TYPE	382	3.6 (6.2)

Figure S37. Get High-res Image Gene #30: '21q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'xq gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.53e-06 (Chi-square test), Q value = 0.0053

Table S38. Gene #31: 'xq gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
XQ GAIN MUTATED	3	3	2	1	0	0
XQ GAIN WILD-TYPE	271	47	104	1	44	6

Figure S38. Get High-res Image Gene #31: 'xq gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.2e-25 (t-test), Q value = 1e-22

Table S39. Gene #34: '2p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
2P LOSS MUTATED	9	0.0 (0.0)
2P LOSS WILD-TYPE	376	3.6 (6.2)

Figure S39. Get High-res Image Gene #34: '2p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.23e-25 (t-test), Q value = 1e-22

Table S40. Gene #35: '2q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
2Q LOSS MUTATED	8	0.0 (0.0)
2Q LOSS WILD-TYPE	377	3.6 (6.2)

Figure S40. Get High-res Image Gene #35: '2q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.38e-25 (t-test), Q value = 1.1e-22

Table S41. Gene #37: '3q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
3Q LOSS MUTATED	3	0.0 (0.0)
3Q LOSS WILD-TYPE	382	3.6 (6.2)

Figure S41. Get High-res Image Gene #37: '3q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.35e-25 (t-test), Q value = 1.1e-22

Table S42. Gene #40: '8p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
8P LOSS MUTATED	4	0.0 (0.0)
8P LOSS WILD-TYPE	381	3.6 (6.2)

Figure S42. Get High-res Image Gene #40: '8p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.35e-25 (t-test), Q value = 1.1e-22

Table S43. Gene #41: '8q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
8Q LOSS MUTATED	4	0.0 (0.0)
8Q LOSS WILD-TYPE	381	3.6 (6.2)

Figure S43. Get High-res Image Gene #41: '8q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.28e-09 (Chi-square test), Q value = 1e-06

Table S44. Gene #43: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
9Q LOSS MUTATED	8	5	3	2	3	1
9Q LOSS WILD-TYPE	266	45	103	0	41	5

Figure S44. Get High-res Image Gene #43: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.32e-25 (t-test), Q value = 1.1e-22

Table S45. Gene #44: '10p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
10P LOSS MUTATED	5	0.0 (0.0)
10P LOSS WILD-TYPE	380	3.6 (6.2)

Figure S45. Get High-res Image Gene #44: '10p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.35e-25 (t-test), Q value = 1.1e-22

Table S46. Gene #45: '10q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
10Q LOSS MUTATED	4	0.0 (0.0)
10Q LOSS WILD-TYPE	381	3.6 (6.2)

Figure S46. Get High-res Image Gene #45: '10q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.47e-07 (Chi-square test), Q value = 0.00012

Table S47. Gene #46: '11p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
11P LOSS MUTATED	1	1	4	1	0	0
11P LOSS WILD-TYPE	273	49	102	1	44	6

Figure S47. Get High-res Image Gene #46: '11p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'AGE'

P value = 9.49e-05 (t-test), Q value = 0.076

Table S48. Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	484	47.1 (15.6)
11Q LOSS MUTATED	9	67.0 (8.9)
11Q LOSS WILD-TYPE	475	46.8 (15.4)

Figure S48. Get High-res Image Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.53e-06 (Chi-square test), Q value = 0.0045

Table S49. Gene #47: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
11Q LOSS MUTATED	1	2	4	1	1	0
11Q LOSS WILD-TYPE	273	48	102	1	43	6

Figure S49. Get High-res Image Gene #47: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.07e-14 (t-test), Q value = 8.8e-12

Table S50. Gene #48: '13q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
13Q LOSS MUTATED	10	0.2 (0.6)
13Q LOSS WILD-TYPE	375	3.6 (6.3)

Figure S50. Get High-res Image Gene #48: '13q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.38e-25 (t-test), Q value = 1.1e-22

Table S51. Gene #51: '17q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
17Q LOSS MUTATED	3	0.0 (0.0)
17Q LOSS WILD-TYPE	382	3.6 (6.2)

Figure S51. Get High-res Image Gene #51: '17q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'xq loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.6e-05 (Chi-square test), Q value = 0.069

Table S52. Gene #57: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	274	50	106	2	44	6
XQ LOSS MUTATED	0	3	0	0	0	0
XQ LOSS WILD-TYPE	274	47	106	2	44	6

Figure S52. Get High-res Image Gene #57: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'xq loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.38e-25 (t-test), Q value = 1.1e-22

Table S53. Gene #57: 'xq loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.2)
XQ LOSS MUTATED	3	0.0 (0.0)
XQ LOSS WILD-TYPE	382	3.6 (6.2)

Figure S53. Get High-res Image Gene #57: 'xq loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = THCA-TP.merged_data.txt
Number of patients = 484
Number of significantly arm-level cnvs = 57
Number of selected clinical features = 15
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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[4] 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)

[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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