Correlation between copy number variation genes (focal events) and selected clinical features

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1PN94HM

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 31 focal events and 11 clinical features across 221 patients, 39 significant findings detected with Q value < 0.25.

amp_7q31.2 cnv correlated to 'NEOPLASM.DISEASESTAGE'.
del_1p36.31 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_3p22.1 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_4q34.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
del_5q35.2 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
del_6q22.31 cnv correlated to 'PATHOLOGY.T.STAGE'.
del_6q25.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
del_9p21.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_10q21.1 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
del_11q22.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_11q23.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_15q13.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'PATHOLOGY.N.STAGE'.
del_16q24.1 cnv correlated to 'Time to Death'.
del_19p13.3 cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.
del_19q13.42 cnv correlated to 'Time to Death'.
del_22q12.2 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
del_xp11.4 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_xq28 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 31 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 39 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	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Wilcoxon-test	Fisher's exact test	Fisher's exact test
del 15q13 3	28 (13%)	193	8.62e-05 (0.0259)	0.144 (1.00)	0.00034 (0.1)	0.00013 (0.0387)	0.00084 (0.242)	0.119 (1.00)	0.376 (1.00)	0.0107 (1.00)	0.248 (1.00)	0.523 (1.00)	1 (1.00)
del 1p36 31	42 (19%)	179	0.000239 (0.0708)	0.471 (1.00)	1e-05 (0.00319)	1e-05 (0.00319)	0.00531 (1.00)	0.324 (1.00)	0.0354 (1.00)	0.00653 (1.00)	0.852 (1.00)	0.632 (1.00)	1 (1.00)
del 3p22 1	19 (9%)	202	2.53e-05 (0.00784)	0.187 (1.00)	5e-05 (0.0152)	0.00018 (0.0535)	0.171 (1.00)	0.074 (1.00)	0.792 (1.00)	0.0791 (1.00)	0.95 (1.00)	0.613 (1.00)	1 (1.00)
del 9p21 3	30 (14%)	191	0.00079 (0.228)	0.424 (1.00)	1e-05 (0.00319)	1e-05 (0.00319)	0.0014 (0.395)	0.02 (1.00)	0.0021 (0.589)	0.0224 (1.00)	0.0234 (1.00)	0.0736 (1.00)	0.612 (1.00)
del 11q22 3	22 (10%)	199	1.36e-06 (0.000441)	0.084 (1.00)	7e-05 (0.0211)	4e-05 (0.0123)	0.019 (1.00)	0.288 (1.00)	0.456 (1.00)	0.181 (1.00)	0.619 (1.00)	0.119 (1.00)	1 (1.00)
del 11q23 3	21 (10%)	200	3.42e-07 (0.000111)	0.0856 (1.00)	1e-05 (0.00319)	2e-05 (0.00622)	0.018 (1.00)	0.298 (1.00)	0.616 (1.00)	0.181 (1.00)	1 (1.00)	0.126 (1.00)	1 (1.00)
del xp11 4	23 (10%)	198	3.61e-06 (0.00116)	0.286 (1.00)	1e-05 (0.00319)	4e-05 (0.0123)	0.112 (1.00)	0.766 (1.00)	0.0132 (1.00)	0.681 (1.00)	0.322 (1.00)	0.0119 (1.00)	1 (1.00)
del 4q34 3	26 (12%)	195	0.122 (1.00)	0.612 (1.00)	3e-05 (0.00927)	8e-05 (0.0241)	0.0839 (1.00)	0.315 (1.00)	0.0186 (1.00)	0.403 (1.00)	0.522 (1.00)	0.0317 (1.00)	1 (1.00)
del 5q35 2	11 (5%)	210	0.148 (1.00)	0.0064 (1.00)	0.00054 (0.157)	5e-05 (0.0152)	0.0855 (1.00)	0.386 (1.00)	0.0139 (1.00)			0.601 (1.00)	0.3 (1.00)
del 6q25 3	23 (10%)	198	0.679 (1.00)	0.927 (1.00)	0.00053 (0.154)	4e-05 (0.0123)	0.109 (1.00)	0.581 (1.00)	0.00302 (0.831)	0.361 (1.00)	0.981 (1.00)	0.056 (1.00)	1 (1.00)
del 10q21 1	15 (7%)	206	0.0384 (1.00)	0.622 (1.00)	3e-05 (0.00927)	0.00047 (0.138)	0.0385 (1.00)	0.439 (1.00)	0.137 (1.00)	0.181 (1.00)		0.332 (1.00)	1 (1.00)
del 19p13 3	17 (8%)	204	9.48e-06 (0.00303)	0.902 (1.00)	0.00108 (0.308)	0.00039 (0.115)	0.0376 (1.00)	0.319 (1.00)	0.578 (1.00)	0.00728 (1.00)	0.496 (1.00)	0.591 (1.00)	1 (1.00)
del 22q12 2	53 (24%)	168	0.00414 (1.00)	0.172 (1.00)	1e-05 (0.00319)	1e-05 (0.00319)	0.00367 (1.00)	0.0413 (1.00)	0.000874 (0.251)	0.297 (1.00)	0.595 (1.00)	0.185 (1.00)	0.411 (1.00)
amp 7q31 2	133 (60%)	88	0.409 (1.00)	0.0811 (1.00)	0.00052 (0.152)	0.0422 (1.00)	0.349 (1.00)	0.7 (1.00)	0.0937 (1.00)	0.0286 (1.00)	0.678 (1.00)	0.867 (1.00)	0.304 (1.00)
del 6q22 31	21 (10%)	200	0.657 (1.00)	0.87 (1.00)	0.00475 (1.00)	0.0001 (0.0299)	0.0874 (1.00)	0.391 (1.00)	0.0196 (1.00)	0.5 (1.00)	0.981 (1.00)	0.06 (1.00)	1 (1.00)
del 16q24 1	10 (5%)	211	1.94e-06 (0.000624)	0.106 (1.00)	0.0143 (1.00)	0.0312 (1.00)	0.192 (1.00)	0.383 (1.00)	0.476 (1.00)	0.532 (1.00)		0.268 (1.00)	1 (1.00)
del 19q13 42	16 (7%)	205	1.68e-06 (0.000544)	0.754 (1.00)	0.00148 (0.416)	0.00128 (0.364)	0.239 (1.00)	0.302 (1.00)	0.401 (1.00)	0.12 (1.00)		0.266 (1.00)	1 (1.00)
del xq28	19 (9%)	202	1.22e-06 (0.000397)	0.0646 (1.00)	0.00097 (0.277)	0.00213 (0.594)	0.0226 (1.00)	0.666 (1.00)	0.00611 (1.00)	0.27 (1.00)		0.0991 (1.00)	1 (1.00)
amp 2p23 2	40 (18%)	181	0.482 (1.00)	0.339 (1.00)	0.32 (1.00)	0.503 (1.00)	0.0211 (1.00)	0.0236 (1.00)	0.336 (1.00)	0.606 (1.00)	0.544 (1.00)	0.683 (1.00)	0.681 (1.00)
amp 2q32 1	47 (21%)	174	0.559 (1.00)	0.643 (1.00)	0.0322 (1.00)	0.12 (1.00)	0.251 (1.00)	0.017 (1.00)	0.587 (1.00)	0.463 (1.00)	0.741 (1.00)	0.29 (1.00)	1 (1.00)
amp 3q27 1	77 (35%)	144	0.236 (1.00)	0.68 (1.00)	0.355 (1.00)	0.147 (1.00)	1 (1.00)	0.0858 (1.00)	0.435 (1.00)	0.155 (1.00)	0.56 (1.00)	0.253 (1.00)	0.5 (1.00)
amp 5q35 2	32 (14%)	189	0.89 (1.00)	0.728 (1.00)	0.147 (1.00)	0.184 (1.00)	1 (1.00)	0.352 (1.00)	0.832 (1.00)	0.305 (1.00)	0.895 (1.00)	0.327 (1.00)	0.361 (1.00)
amp 17q25 2	158 (71%)	63	0.963 (1.00)	0.0517 (1.00)	0.289 (1.00)	0.418 (1.00)	0.91 (1.00)	0.00851 (1.00)	0.102 (1.00)	0.897 (1.00)	0.918 (1.00)	0.398 (1.00)	0.702 (1.00)
amp 19p13 2	23 (10%)	198	0.64 (1.00)	0.00821 (1.00)	0.836 (1.00)	0.102 (1.00)	0.769 (1.00)	0.582 (1.00)	0.473 (1.00)	0.969 (1.00)		0.24 (1.00)	1 (1.00)
del 2p12	4 (2%)	217	0.53 (1.00)	0.683 (1.00)	0.0962 (1.00)	0.135 (1.00)		0.118 (1.00)	1 (1.00)			1 (1.00)	1 (1.00)
del 2q22 1	7 (3%)	214	0.0265 (1.00)	0.146 (1.00)	0.00442 (1.00)	0.018 (1.00)	0.217 (1.00)	0.217 (1.00)	0.104 (1.00)			1 (1.00)	1 (1.00)
del 2q37 3	10 (5%)	211	0.651 (1.00)	0.51 (1.00)	0.00942 (1.00)	0.00301 (0.831)	1 (1.00)	0.807 (1.00)	0.0338 (1.00)		0.221 (1.00)	0.782 (1.00)	1 (1.00)
del 5p15 33	10 (5%)	211	0.216 (1.00)	0.126 (1.00)	0.00651 (1.00)	0.00232 (0.643)	0.004 (1.00)	0.359 (1.00)	0.153 (1.00)			1 (1.00)	0.263 (1.00)
del 6p12 3	19 (9%)	202	0.394 (1.00)	0.813 (1.00)	0.00131 (0.371)	0.00223 (0.62)	0.0471 (1.00)	0.307 (1.00)	0.429 (1.00)	0.934 (1.00)	0.477 (1.00)	0.167 (1.00)	1 (1.00)
del 14q11 2	44 (20%)	177	0.00931 (1.00)	0.762 (1.00)	0.0195 (1.00)	0.0101 (1.00)	0.0356 (1.00)	0.438 (1.00)	0.0608 (1.00)	0.0995 (1.00)	0.129 (1.00)	0.916 (1.00)	0.69 (1.00)
del 14q24 2	42 (19%)	179	0.00699 (1.00)	0.433 (1.00)	0.00875 (1.00)	0.00443 (1.00)	0.0177 (1.00)	0.238 (1.00)	0.0354 (1.00)	0.0445 (1.00)	0.0822 (1.00)	1 (1.00)	1 (1.00)

'amp_7q31.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00052 (Fisher's exact test), Q value = 0.15

Table S1. Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
AMP PEAK 5(7Q31.2) MUTATED	92	7	15	10
AMP PEAK 5(7Q31.2) WILD-TYPE	45	9	28	3

Figure S1. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_1p36.31' versus 'Time to Death'

P value = 0.000239 (logrank test), Q value = 0.071

Table S2. Gene #8: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 1(1P36.31) MUTATED	38	5	2.0 - 3760.0 (288.5)
DEL PEAK 1(1P36.31) WILD-TYPE	156	2	2.0 - 5925.0 (590.5)

Figure S2. Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

'del_1p36.31' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S3. Gene #8: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 1(1P36.31) MUTATED	13	3	19	4
DEL PEAK 1(1P36.31) WILD-TYPE	124	13	24	9

Figure S3. Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_1p36.31' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S4. Gene #8: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 1(1P36.31) MUTATED	16	4	22
DEL PEAK 1(1P36.31) WILD-TYPE	130	18	29

Figure S4. Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p22.1' versus 'Time to Death'

P value = 2.53e-05 (logrank test), Q value = 0.0078

Table S5. Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 5(3P22.1) MUTATED	18	4	4.0 - 2429.0 (317.0)
DEL PEAK 5(3P22.1) WILD-TYPE	176	3	2.0 - 5925.0 (578.0)

Figure S5. Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

'del_3p22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.015

Table S6. Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 5(3P22.1) MUTATED	4	1	11	3
DEL PEAK 5(3P22.1) WILD-TYPE	133	15	32	10

Figure S6. Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_3p22.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.053

Table S7. Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 5(3P22.1) MUTATED	5	2	12
DEL PEAK 5(3P22.1) WILD-TYPE	141	20	39

Figure S7. Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0093

Table S8. Gene #13: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 6(4Q34.3) MUTATED	6	2	15	2
DEL PEAK 6(4Q34.3) WILD-TYPE	131	14	28	11

Figure S8. Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_4q34.3' versus 'PATHOLOGY.T.STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.024

Table S9. Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 6(4Q34.3) MUTATED	8	4	14
DEL PEAK 6(4Q34.3) WILD-TYPE	138	18	37

Figure S9. Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5q35.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00054 (Fisher's exact test), Q value = 0.16

Table S10. Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 8(5Q35.2) MUTATED	1	1	7	1
DEL PEAK 8(5Q35.2) WILD-TYPE	136	15	36	12

Figure S10. Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_5q35.2' versus 'PATHOLOGY.T.STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.015

Table S11. Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 8(5Q35.2) MUTATED	1	1	9
DEL PEAK 8(5Q35.2) WILD-TYPE	145	21	42

Figure S11. Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_6q22.31' versus 'PATHOLOGY.T.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.03

Table S12. Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 10(6Q22.31) MUTATED	8	0	13
DEL PEAK 10(6Q22.31) WILD-TYPE	138	22	38

Figure S12. Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_6q25.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00053 (Fisher's exact test), Q value = 0.15

Table S13. Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 11(6Q25.3) MUTATED	8	0	12	2
DEL PEAK 11(6Q25.3) WILD-TYPE	129	16	31	11

Figure S13. Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_6q25.3' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

Table S14. Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 11(6Q25.3) MUTATED	8	0	15
DEL PEAK 11(6Q25.3) WILD-TYPE	138	22	36

Figure S14. Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p21.3' versus 'Time to Death'

P value = 0.00079 (logrank test), Q value = 0.23

Table S15. Gene #19: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 12(9P21.3) MUTATED	24	4	4.0 - 2839.0 (355.0)
DEL PEAK 12(9P21.3) WILD-TYPE	170	3	2.0 - 5925.0 (578.0)

Figure S15. Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S16. Gene #19: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 12(9P21.3) MUTATED	7	0	15	6
DEL PEAK 12(9P21.3) WILD-TYPE	130	16	28	7

Figure S16. Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_9p21.3' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S17. Gene #19: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 12(9P21.3) MUTATED	8	2	20
DEL PEAK 12(9P21.3) WILD-TYPE	138	20	31

Figure S17. Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_10q21.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0093

Table S18. Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 13(10Q21.1) MUTATED	3	0	11	1
DEL PEAK 13(10Q21.1) WILD-TYPE	134	16	32	12

Figure S18. Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_10q21.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.00047 (Fisher's exact test), Q value = 0.14

Table S19. Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 13(10Q21.1) MUTATED	5	0	10
DEL PEAK 13(10Q21.1) WILD-TYPE	141	22	41

Figure S19. Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q22.3' versus 'Time to Death'

P value = 1.36e-06 (logrank test), Q value = 0.00044

Table S20. Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 14(11Q22.3) MUTATED	18	4	4.0 - 3760.0 (223.5)
DEL PEAK 14(11Q22.3) WILD-TYPE	176	3	2.0 - 5925.0 (578.0)

Figure S20. Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

'del_11q22.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.021

Table S21. Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 14(11Q22.3) MUTATED	5	2	11	4
DEL PEAK 14(11Q22.3) WILD-TYPE	132	14	32	9

Figure S21. Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_11q22.3' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

Table S22. Gene #21: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 14(11Q22.3) MUTATED	6	2	14
DEL PEAK 14(11Q22.3) WILD-TYPE	140	20	37

Figure S22. Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q23.3' versus 'Time to Death'

P value = 3.42e-07 (logrank test), Q value = 0.00011

Table S23. Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 15(11Q23.3) MUTATED	17	4	4.0 - 3760.0 (208.0)
DEL PEAK 15(11Q23.3) WILD-TYPE	177	3	2.0 - 5925.0 (578.0)

Figure S23. Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

'del_11q23.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S24. Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 15(11Q23.3) MUTATED	3	2	12	4
DEL PEAK 15(11Q23.3) WILD-TYPE	134	14	31	9

Figure S24. Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_11q23.3' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0062

Table S25. Gene #22: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 15(11Q23.3) MUTATED	4	2	15
DEL PEAK 15(11Q23.3) WILD-TYPE	142	20	36

Figure S25. Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_15q13.3' versus 'Time to Death'

P value = 8.62e-05 (logrank test), Q value = 0.026

Table S26. Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 18(15Q13.3) MUTATED	22	4	3.0 - 5925.0 (207.5)
DEL PEAK 18(15Q13.3) WILD-TYPE	172	3	2.0 - 3950.0 (578.5)

Figure S26. Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

'del_15q13.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00034 (Fisher's exact test), Q value = 0.1

Table S27. Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 18(15Q13.3) MUTATED	9	1	11	5
DEL PEAK 18(15Q13.3) WILD-TYPE	128	15	32	8

Figure S27. Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_15q13.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.039

Table S28. Gene #25: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 18(15Q13.3) MUTATED	11	1	16
DEL PEAK 18(15Q13.3) WILD-TYPE	135	21	35

Figure S28. Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_15q13.3' versus 'PATHOLOGY.N.STAGE'

P value = 0.00084 (Fisher's exact test), Q value = 0.24

Table S29. Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients	N0	N1	N2
ALL	39	20	4
DEL PEAK 18(15Q13.3) MUTATED	3	10	1
DEL PEAK 18(15Q13.3) WILD-TYPE	36	10	3

Figure S29. Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_16q24.1' versus 'Time to Death'

P value = 1.94e-06 (logrank test), Q value = 0.00062

Table S30. Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 19(16Q24.1) MUTATED	6	2	13.0 - 1967.0 (69.5)
DEL PEAK 19(16Q24.1) WILD-TYPE	188	5	2.0 - 5925.0 (543.5)

Figure S30. Get High-res Image Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'Time to Death'

P value = 9.48e-06 (logrank test), Q value = 0.003

Table S31. Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 20(19P13.3) MUTATED	16	3	4.0 - 1967.0 (330.5)
DEL PEAK 20(19P13.3) WILD-TYPE	178	4	2.0 - 5925.0 (543.5)

Figure S31. Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.11

Table S32. Gene #27: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 20(19P13.3) MUTATED	5	1	11
DEL PEAK 20(19P13.3) WILD-TYPE	141	21	40

Figure S32. Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_19q13.42' versus 'Time to Death'

P value = 1.68e-06 (logrank test), Q value = 0.00054

Table S33. Gene #28: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 21(19Q13.42) MUTATED	16	4	29.0 - 2839.0 (325.5)
DEL PEAK 21(19Q13.42) WILD-TYPE	178	3	2.0 - 5925.0 (543.5)

Figure S33. Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

'del_22q12.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S34. Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 22(22Q12.2) MUTATED	19	3	22	7
DEL PEAK 22(22Q12.2) WILD-TYPE	118	13	21	6

Figure S34. Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_22q12.2' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S35. Gene #29: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 22(22Q12.2) MUTATED	21	5	27
DEL PEAK 22(22Q12.2) WILD-TYPE	125	17	24

Figure S35. Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xp11.4' versus 'Time to Death'

P value = 3.61e-06 (logrank test), Q value = 0.0012

Table S36. Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 23(XP11.4) MUTATED	19	4	4.0 - 2429.0 (307.0)
DEL PEAK 23(XP11.4) WILD-TYPE	175	3	2.0 - 5925.0 (578.0)

Figure S36. Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

'del_xp11.4' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S37. Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	137	16	43	13
DEL PEAK 23(XP11.4) MUTATED	4	1	14	2
DEL PEAK 23(XP11.4) WILD-TYPE	133	15	29	11

Figure S37. Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_xp11.4' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

Table S38. Gene #30: 'del_xp11.4' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	146	22	51
DEL PEAK 23(XP11.4) MUTATED	6	2	15
DEL PEAK 23(XP11.4) WILD-TYPE	140	20	36

Figure S38. Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xq28' versus 'Time to Death'

P value = 1.22e-06 (logrank test), Q value = 4e-04

Table S39. Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	194	7	2.0 - 5925.0 (540.5)
DEL PEAK 24(XQ28) MUTATED	14	3	3.0 - 1967.0 (265.0)
DEL PEAK 24(XQ28) WILD-TYPE	180	4	2.0 - 5925.0 (578.0)

Figure S39. Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = KIRP-TP.merged_data.txt
Number of patients = 221
Number of significantly focal cnvs = 31
Number of selected clinical features = 11
Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

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] 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)

[3] 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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