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

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1DR2SSZ

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 75 arm-level events and 9 clinical features across 68 patients, 13 significant findings detected with Q value < 0.25.

2Q GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death'.
13Q GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death'.
19Q GAIN MUTATION ANALYSIS cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
2P LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
7Q LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death'.
8Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
14Q LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'NUMBER.OF.LYMPH.NODES'.
16P LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
16Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
19P LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
19Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
XQ LOSS MUTATION ANALYSIS 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 75 arm-level events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 13 significant findings detected.


		Clinical Features	Time to Death	AGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	NUMBERPACKYEARSSMOKED	NUMBER OF LYMPH NODES
	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
14Q LOSS MUTATION ANALYSIS	4 (6%)	64	0 (0)	0.566 (1.00)	0.603 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.574 (1.00)		0.000251 (0.151)
2Q GAIN MUTATION ANALYSIS	4 (6%)	64	0 (0)	0.163 (1.00)	0.27 (1.00)	1 (1.00)	1 (1.00)	0.479 (1.00)	0.574 (1.00)
13Q GAIN MUTATION ANALYSIS	3 (4%)	65	0 (0)	0.91 (1.00)	1 (1.00)	1 (1.00)	0.339 (1.00)	0.384 (1.00)	1 (1.00)
19Q GAIN MUTATION ANALYSIS	15 (22%)	53	0.00514 (1.00)	0.257 (1.00)	1 (1.00)	0.329 (1.00)	0.586 (1.00)	0.801 (1.00)	0.000124 (0.0755)	0.944 (1.00)	0.238 (1.00)
2P LOSS MUTATION ANALYSIS	3 (4%)	65	0.4 (1.00)	0.517 (1.00)	1 (1.00)	0.545 (1.00)	0.588 (1.00)	1 (1.00)	0.505 (1.00)		0.000251 (0.151)
7Q LOSS MUTATION ANALYSIS	10 (15%)	58	5.74e-06 (0.0035)	0.182 (1.00)	0.43 (1.00)	0.104 (1.00)	0.0775 (1.00)	1 (1.00)	0.00357 (1.00)	0.935 (1.00)	0.0569 (1.00)
8Q LOSS MUTATION ANALYSIS	5 (7%)	63	0.89 (1.00)	0.142 (1.00)	0.603 (1.00)	0.292 (1.00)	0.377 (1.00)	1 (1.00)	0.272 (1.00)		0.000251 (0.151)
16P LOSS MUTATION ANALYSIS	6 (9%)	62	0.91 (1.00)	0.254 (1.00)	0.155 (1.00)	0.16 (1.00)	0.284 (1.00)	0.103 (1.00)	0.333 (1.00)		0.000247 (0.15)
16Q LOSS MUTATION ANALYSIS	9 (13%)	59	0.673 (1.00)	0.122 (1.00)	0.245 (1.00)	0.0439 (1.00)	0.774 (1.00)	0.00491 (1.00)	0.187 (1.00)		0.000235 (0.143)
19P LOSS MUTATION ANALYSIS	8 (12%)	60	0.559 (1.00)	0.299 (1.00)	1 (1.00)	0.16 (1.00)	0.705 (1.00)	0.675 (1.00)	0.347 (1.00)		0.000247 (0.15)
19Q LOSS MUTATION ANALYSIS	5 (7%)	63	0.293 (1.00)	0.873 (1.00)	1 (1.00)	0.292 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)		0.000247 (0.15)
XQ LOSS MUTATION ANALYSIS	15 (22%)	53	0.000123 (0.0749)	0.665 (1.00)	0.521 (1.00)	0.513 (1.00)	0.653 (1.00)	0.801 (1.00)	0.0649 (1.00)	0.145 (1.00)	0.341 (1.00)
1P GAIN MUTATION ANALYSIS	20 (29%)	48	0.277 (1.00)	0.85 (1.00)	0.782 (1.00)	0.774 (1.00)	0.893 (1.00)	0.712 (1.00)	0.532 (1.00)	0.581 (1.00)	0.68 (1.00)
1Q GAIN MUTATION ANALYSIS	30 (44%)	38	0.252 (1.00)	0.68 (1.00)	0.187 (1.00)	1 (1.00)	1 (1.00)	0.913 (1.00)	0.367 (1.00)	0.598 (1.00)	0.449 (1.00)
2P GAIN MUTATION ANALYSIS	9 (13%)	59	0.656 (1.00)	0.103 (1.00)	0.22 (1.00)	1 (1.00)	0.75 (1.00)	0.473 (1.00)	1 (1.00)		0.815 (1.00)
3P GAIN MUTATION ANALYSIS	11 (16%)	57	0.873 (1.00)	0.894 (1.00)	0.726 (1.00)	0.28 (1.00)	1 (1.00)	0.134 (1.00)	1 (1.00)		0.218 (1.00)
3Q GAIN MUTATION ANALYSIS	40 (59%)	28	0.633 (1.00)	1 (1.00)	0.792 (1.00)	0.424 (1.00)	0.239 (1.00)	0.00415 (1.00)	0.368 (1.00)	0.625 (1.00)	0.164 (1.00)
4P GAIN MUTATION ANALYSIS	3 (4%)	65		0.158 (1.00)		0.333 (1.00)		1 (1.00)	0.505 (1.00)
5P GAIN MUTATION ANALYSIS	20 (29%)	48	0.508 (1.00)	0.851 (1.00)	0.382 (1.00)	1 (1.00)	1 (1.00)	0.142 (1.00)	1 (1.00)	0.471 (1.00)	0.557 (1.00)
5Q GAIN MUTATION ANALYSIS	6 (9%)	62	0.19 (1.00)	0.683 (1.00)	1 (1.00)	0.657 (1.00)	1 (1.00)	1 (1.00)	0.595 (1.00)		0.759 (1.00)
6P GAIN MUTATION ANALYSIS	14 (21%)	54	0.975 (1.00)	0.144 (1.00)	1 (1.00)	0.516 (1.00)	0.694 (1.00)	0.407 (1.00)	1 (1.00)	0.7 (1.00)	0.0139 (1.00)
6Q GAIN MUTATION ANALYSIS	6 (9%)	62	0.997 (1.00)	0.454 (1.00)	1 (1.00)	0.654 (1.00)	0.191 (1.00)	1 (1.00)	1 (1.00)		0.0757 (1.00)
7P GAIN MUTATION ANALYSIS	6 (9%)	62	0.746 (1.00)	0.595 (1.00)	0.329 (1.00)	1 (1.00)	1 (1.00)	0.63 (1.00)	0.595 (1.00)		0.319 (1.00)
7Q GAIN MUTATION ANALYSIS	8 (12%)	60	0.6 (1.00)	0.357 (1.00)	1 (1.00)	1 (1.00)	0.75 (1.00)	0.675 (1.00)	0.0502 (1.00)		0.429 (1.00)
8P GAIN MUTATION ANALYSIS	12 (18%)	56	0.676 (1.00)	0.276 (1.00)	1 (1.00)	0.735 (1.00)	1 (1.00)	0.75 (1.00)	0.701 (1.00)	0.913 (1.00)	0.967 (1.00)
8Q GAIN MUTATION ANALYSIS	17 (25%)	51	0.987 (1.00)	0.437 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.913 (1.00)	0.992 (1.00)
9P GAIN MUTATION ANALYSIS	8 (12%)	60	0.521 (1.00)	0.615 (1.00)	0.43 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)		0.815 (1.00)
9Q GAIN MUTATION ANALYSIS	9 (13%)	59	0.539 (1.00)	0.647 (1.00)	0.48 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.673 (1.00)		0.815 (1.00)
10P GAIN MUTATION ANALYSIS	5 (7%)	63	0.518 (1.00)	0.446 (1.00)	0.155 (1.00)	0.323 (1.00)	1 (1.00)	1 (1.00)	0.575 (1.00)		0.302 (1.00)
11P GAIN MUTATION ANALYSIS	3 (4%)	65		0.0691 (1.00)		1 (1.00)		0.384 (1.00)	1 (1.00)
12P GAIN MUTATION ANALYSIS	10 (15%)	58	0.782 (1.00)	0.109 (1.00)	0.292 (1.00)	1 (1.00)	0.5 (1.00)	1 (1.00)	0.418 (1.00)	0.365 (1.00)	0.53 (1.00)
12Q GAIN MUTATION ANALYSIS	10 (15%)	58	0.946 (1.00)	0.162 (1.00)	0.726 (1.00)	1 (1.00)	0.806 (1.00)	0.522 (1.00)	0.418 (1.00)		0.53 (1.00)
14Q GAIN MUTATION ANALYSIS	8 (12%)	60	0.595 (1.00)	0.763 (1.00)	0.684 (1.00)	0.677 (1.00)	1 (1.00)	0.675 (1.00)	1 (1.00)		0.961 (1.00)
15Q GAIN MUTATION ANALYSIS	8 (12%)	60	0.124 (1.00)	0.678 (1.00)	0.0157 (1.00)	1 (1.00)	1 (1.00)	0.675 (1.00)	0.665 (1.00)		0.178 (1.00)
16P GAIN MUTATION ANALYSIS	7 (10%)	61	0.629 (1.00)	0.667 (1.00)	0.0418 (1.00)	0.677 (1.00)	0.75 (1.00)	1 (1.00)	1 (1.00)		0.458 (1.00)
16Q GAIN MUTATION ANALYSIS	6 (9%)	62	0.586 (1.00)	0.545 (1.00)	0.0157 (1.00)	1 (1.00)	1 (1.00)	0.63 (1.00)	1 (1.00)		0.684 (1.00)
17P GAIN MUTATION ANALYSIS	4 (6%)	64	0.151 (1.00)	0.921 (1.00)	0.113 (1.00)	0.104 (1.00)	1 (1.00)	0.479 (1.00)	0.185 (1.00)		0.389 (1.00)
17Q GAIN MUTATION ANALYSIS	6 (9%)	62	0.221 (1.00)	0.494 (1.00)	0.0157 (1.00)	0.391 (1.00)	0.718 (1.00)	0.63 (1.00)	0.595 (1.00)		0.492 (1.00)
18P GAIN MUTATION ANALYSIS	6 (9%)	62	0.399 (1.00)	0.05 (1.00)	0.17 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.595 (1.00)		0.339 (1.00)
18Q GAIN MUTATION ANALYSIS	4 (6%)	64	0.698 (1.00)	0.196 (1.00)	0.113 (1.00)	0.595 (1.00)	1 (1.00)	1 (1.00)	0.185 (1.00)		0.964 (1.00)
19P GAIN MUTATION ANALYSIS	12 (18%)	56	0.664 (1.00)	0.0846 (1.00)	1 (1.00)	0.191 (1.00)	0.828 (1.00)	1 (1.00)	0.0123 (1.00)		0.572 (1.00)
20P GAIN MUTATION ANALYSIS	19 (28%)	49	0.107 (1.00)	0.805 (1.00)	0.771 (1.00)	0.253 (1.00)	0.883 (1.00)	0.594 (1.00)	0.512 (1.00)	0.219 (1.00)	0.467 (1.00)
20Q GAIN MUTATION ANALYSIS	23 (34%)	45	0.404 (1.00)	0.502 (1.00)	0.163 (1.00)	0.584 (1.00)	0.899 (1.00)	0.539 (1.00)	0.529 (1.00)	0.17 (1.00)	0.669 (1.00)
21Q GAIN MUTATION ANALYSIS	9 (13%)	59	0.0393 (1.00)	0.0937 (1.00)	0.684 (1.00)	0.677 (1.00)	1 (1.00)	0.689 (1.00)	0.377 (1.00)		0.339 (1.00)
22Q GAIN MUTATION ANALYSIS	9 (13%)	59	0.38 (1.00)	0.0658 (1.00)	0.43 (1.00)	0.423 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)		0.458 (1.00)
XQ GAIN MUTATION ANALYSIS	8 (12%)	60	0.902 (1.00)	0.835 (1.00)	0.245 (1.00)	0.708 (1.00)	1 (1.00)	1 (1.00)	0.665 (1.00)		0.291 (1.00)
1P LOSS MUTATION ANALYSIS	3 (4%)	65		0.624 (1.00)		1 (1.00)		1 (1.00)	0.105 (1.00)
1Q LOSS MUTATION ANALYSIS	3 (4%)	65	0.182 (1.00)	0.489 (1.00)	0.545 (1.00)	0.256 (1.00)	1 (1.00)	1 (1.00)	0.00726 (1.00)		0.48 (1.00)
2Q LOSS MUTATION ANALYSIS	7 (10%)	61	0.976 (1.00)	0.664 (1.00)	0.684 (1.00)	0.677 (1.00)	1 (1.00)	0.666 (1.00)	0.147 (1.00)		0.435 (1.00)
3P LOSS MUTATION ANALYSIS	18 (26%)	50	0.371 (1.00)	0.202 (1.00)	0.545 (1.00)	0.0337 (1.00)	0.872 (1.00)	0.193 (1.00)	0.04 (1.00)	0.627 (1.00)	0.301 (1.00)
4P LOSS MUTATION ANALYSIS	29 (43%)	39	0.453 (1.00)	0.102 (1.00)	1 (1.00)	0.427 (1.00)	0.639 (1.00)	0.0139 (1.00)	0.241 (1.00)	0.722 (1.00)	0.478 (1.00)
4Q LOSS MUTATION ANALYSIS	14 (21%)	54	0.0229 (1.00)	0.224 (1.00)	0.343 (1.00)	0.103 (1.00)	0.844 (1.00)	0.489 (1.00)	0.144 (1.00)	0.961 (1.00)	0.171 (1.00)
5P LOSS MUTATION ANALYSIS	4 (6%)	64	0.000856 (0.515)	0.431 (1.00)	0.289 (1.00)	0.104 (1.00)	1 (1.00)	1 (1.00)	0.185 (1.00)		0.159 (1.00)
5Q LOSS MUTATION ANALYSIS	16 (24%)	52	0.0117 (1.00)	0.0746 (1.00)	0.226 (1.00)	0.545 (1.00)	0.851 (1.00)	0.294 (1.00)	0.726 (1.00)	0.657 (1.00)	0.777 (1.00)
6P LOSS MUTATION ANALYSIS	7 (10%)	61	0.883 (1.00)	0.0623 (1.00)	1 (1.00)	0.0892 (1.00)	1 (1.00)	1 (1.00)	0.33 (1.00)	0.168 (1.00)	0.424 (1.00)
6Q LOSS MUTATION ANALYSIS	13 (19%)	55	0.261 (1.00)	0.0331 (1.00)	1 (1.00)	0.513 (1.00)	0.465 (1.00)	0.469 (1.00)	0.275 (1.00)	0.0429 (1.00)	0.595 (1.00)
7P LOSS MUTATION ANALYSIS	6 (9%)	62	0.446 (1.00)	0.801 (1.00)	1 (1.00)	0.391 (1.00)	0.514 (1.00)	1 (1.00)	0.0141 (1.00)	0.976 (1.00)	0.36 (1.00)
8P LOSS MUTATION ANALYSIS	20 (29%)	48	0.153 (1.00)	0.648 (1.00)	0.557 (1.00)	0.771 (1.00)	0.876 (1.00)	0.0596 (1.00)	0.743 (1.00)	0.223 (1.00)	0.823 (1.00)
9P LOSS MUTATION ANALYSIS	11 (16%)	57	0.0149 (1.00)	0.461 (1.00)	1 (1.00)	1 (1.00)	0.626 (1.00)	0.533 (1.00)	0.684 (1.00)	0.586 (1.00)	0.461 (1.00)
9Q LOSS MUTATION ANALYSIS	7 (10%)	61	0.292 (1.00)	0.323 (1.00)	1 (1.00)	1 (1.00)	0.531 (1.00)	0.223 (1.00)	0.627 (1.00)		0.956 (1.00)
10P LOSS MUTATION ANALYSIS	14 (21%)	54	0.00934 (1.00)	0.132 (1.00)	0.737 (1.00)	0.0848 (1.00)	0.277 (1.00)	0.795 (1.00)	0.031 (1.00)	0.813 (1.00)	0.0703 (1.00)
10Q LOSS MUTATION ANALYSIS	16 (24%)	52	0.0136 (1.00)	0.207 (1.00)	0.757 (1.00)	0.0253 (1.00)	0.29 (1.00)	1 (1.00)	0.291 (1.00)	0.562 (1.00)	0.0424 (1.00)
11P LOSS MUTATION ANALYSIS	22 (32%)	46	0.645 (1.00)	0.996 (1.00)	0.58 (1.00)	0.782 (1.00)	0.477 (1.00)	0.037 (1.00)	0.523 (1.00)	0.451 (1.00)	0.245 (1.00)
11Q LOSS MUTATION ANALYSIS	26 (38%)	42	0.81 (1.00)	0.082 (1.00)	0.418 (1.00)	0.595 (1.00)	1 (1.00)	0.572 (1.00)	1 (1.00)	0.247 (1.00)	0.491 (1.00)
12P LOSS MUTATION ANALYSIS	11 (16%)	57	0.312 (1.00)	0.103 (1.00)	0.472 (1.00)	0.474 (1.00)	0.618 (1.00)	1 (1.00)	0.437 (1.00)	0.845 (1.00)	0.625 (1.00)
13Q LOSS MUTATION ANALYSIS	20 (29%)	48	0.269 (1.00)	0.925 (1.00)	0.782 (1.00)	0.151 (1.00)	0.521 (1.00)	0.142 (1.00)	1 (1.00)	0.498 (1.00)	0.366 (1.00)
15Q LOSS MUTATION ANALYSIS	6 (9%)	62	0.792 (1.00)	0.773 (1.00)	1 (1.00)	0.654 (1.00)	0.718 (1.00)	1 (1.00)	1 (1.00)		0.884 (1.00)
17P LOSS MUTATION ANALYSIS	17 (25%)	51	0.157 (1.00)	0.176 (1.00)	0.757 (1.00)	1 (1.00)	0.13 (1.00)	0.265 (1.00)	0.737 (1.00)	0.578 (1.00)	0.556 (1.00)
17Q LOSS MUTATION ANALYSIS	5 (7%)	63	0.357 (1.00)	0.0865 (1.00)	1 (1.00)	0.595 (1.00)	0.377 (1.00)	1 (1.00)	0.272 (1.00)		0.395 (1.00)
18P LOSS MUTATION ANALYSIS	10 (15%)	58	0.279 (1.00)	0.0766 (1.00)	0.147 (1.00)	0.705 (1.00)	1 (1.00)	0.707 (1.00)	0.0254 (1.00)	0.0333 (1.00)	0.758 (1.00)
18Q LOSS MUTATION ANALYSIS	16 (24%)	52	0.815 (1.00)	0.324 (1.00)	0.226 (1.00)	0.0692 (1.00)	0.308 (1.00)	0.197 (1.00)	0.291 (1.00)	0.365 (1.00)	0.237 (1.00)
20P LOSS MUTATION ANALYSIS	7 (10%)	61	0.807 (1.00)	0.664 (1.00)	0.655 (1.00)	1 (1.00)	1 (1.00)	0.356 (1.00)	0.33 (1.00)	0.141 (1.00)	0.339 (1.00)
20Q LOSS MUTATION ANALYSIS	3 (4%)	65		0.16 (1.00)		1 (1.00)		1 (1.00)	1 (1.00)
21Q LOSS MUTATION ANALYSIS	10 (15%)	58	0.257 (1.00)	0.214 (1.00)	0.726 (1.00)	1 (1.00)	0.806 (1.00)	0.522 (1.00)	1 (1.00)		0.65 (1.00)
22Q LOSS MUTATION ANALYSIS	9 (13%)	59	0.461 (1.00)	0.225 (1.00)	0.704 (1.00)	0.708 (1.00)	0.425 (1.00)	0.302 (1.00)	0.377 (1.00)		0.513 (1.00)

'2Q GAIN MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S1. Gene #4: '2Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	66	10	0.1 - 177.0 (6.4)
2Q GAIN MUTATED	3	0	0.7 - 1.8 (1.4)
2Q GAIN WILD-TYPE	63	10	0.1 - 177.0 (6.9)

Figure S1. Get High-res Image Gene #4: '2Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'13Q GAIN MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S2. Gene #22: '13Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	66	10	0.1 - 177.0 (6.4)
13Q GAIN MUTATED	3	0	0.1 - 1.4 (0.6)
13Q GAIN WILD-TYPE	63	10	0.1 - 177.0 (6.9)

Figure S2. Get High-res Image Gene #22: '13Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'19Q GAIN MUTATION STATUS' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000124 (Fisher's exact test), Q value = 0.075

Table S3. Gene #32: '19Q GAIN MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	14	54
19Q GAIN MUTATED	9	6
19Q GAIN WILD-TYPE	5	48

Figure S3. Get High-res Image Gene #32: '19Q GAIN MUTATION STATUS' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'2P LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000251 (t-test), Q value = 0.15

Table S4. Gene #40: '2P LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	57	0.7 (1.3)
2P LOSS MUTATED	3	0.0 (0.0)
2P LOSS WILD-TYPE	54	0.7 (1.4)

Figure S4. Get High-res Image Gene #40: '2P LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'7Q LOSS MUTATION STATUS' versus 'Time to Death'

P value = 5.74e-06 (logrank test), Q value = 0.0035

Table S5. Gene #50: '7Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	66	10	0.1 - 177.0 (6.4)
7Q LOSS MUTATED	10	5	0.7 - 40.9 (8.4)
7Q LOSS WILD-TYPE	56	5	0.1 - 177.0 (6.4)

Figure S5. Get High-res Image Gene #50: '7Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'8Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000251 (t-test), Q value = 0.15

Table S6. Gene #52: '8Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	57	0.7 (1.3)
8Q LOSS MUTATED	3	0.0 (0.0)
8Q LOSS WILD-TYPE	54	0.7 (1.4)

Figure S6. Get High-res Image Gene #52: '8Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'14Q LOSS MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S7. Gene #61: '14Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	66	10	0.1 - 177.0 (6.4)
14Q LOSS MUTATED	4	0	0.1 - 1.8 (1.4)
14Q LOSS WILD-TYPE	62	10	0.1 - 177.0 (7.4)

Figure S7. Get High-res Image Gene #61: '14Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'14Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000251 (t-test), Q value = 0.15

Table S8. Gene #61: '14Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	57	0.7 (1.3)
14Q LOSS MUTATED	3	0.0 (0.0)
14Q LOSS WILD-TYPE	54	0.7 (1.4)

Figure S8. Get High-res Image Gene #61: '14Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'16P LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000247 (t-test), Q value = 0.15

Table S9. Gene #63: '16P LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	57	0.7 (1.3)
16P LOSS MUTATED	4	0.0 (0.0)
16P LOSS WILD-TYPE	53	0.7 (1.4)

Figure S9. Get High-res Image Gene #63: '16P LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'16Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000235 (t-test), Q value = 0.14

Table S10. Gene #64: '16Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	57	0.7 (1.3)
16Q LOSS MUTATED	7	0.0 (0.0)
16Q LOSS WILD-TYPE	50	0.8 (1.4)

Figure S10. Get High-res Image Gene #64: '16Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'19P LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000247 (t-test), Q value = 0.15

Table S11. Gene #69: '19P LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	57	0.7 (1.3)
19P LOSS MUTATED	4	0.0 (0.0)
19P LOSS WILD-TYPE	53	0.7 (1.4)

Figure S11. Get High-res Image Gene #69: '19P LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'19Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000247 (t-test), Q value = 0.15

Table S12. Gene #70: '19Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	57	0.7 (1.3)
19Q LOSS MUTATED	4	0.0 (0.0)
19Q LOSS WILD-TYPE	53	0.7 (1.4)

Figure S12. Get High-res Image Gene #70: '19Q LOSS MUTATION STATUS' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'XQ LOSS MUTATION STATUS' versus 'Time to Death'

P value = 0.000123 (logrank test), Q value = 0.075

Table S13. Gene #75: 'XQ LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	66	10	0.1 - 177.0 (6.4)
XQ LOSS MUTATED	15	6	0.1 - 95.1 (5.5)
XQ LOSS WILD-TYPE	51	4	0.1 - 177.0 (6.8)

Figure S13. Get High-res Image Gene #75: 'XQ LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = CESC-TP.clin.merged.picked.txt
Number of patients = 68
Number of significantly arm-level cnvs = 75
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)

Made with Nozzle