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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1S46QPH

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 29 focal events and 11 clinical features across 198 patients, 37 significant findings detected with Q value < 0.25.

amp_7q22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE'.
del_1p36.32 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_5p14.2 cnv correlated to '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_6q27 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_11q22.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_11q24.2 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_15q13.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.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_xp11.22 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 29 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 37 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 1p36 32	39 (20%)	159	4.88e-05 (0.0139)	0.465 (1.00)	1e-05 (0.00301)	2e-05 (0.00582)	0.0395 (1.00)	0.0959 (1.00)	0.0173 (1.00)	0.0157 (1.00)	0.568 (1.00)	0.396 (1.00)	1 (1.00)
del 3p22 1	17 (9%)	181	1.1e-06 (0.000339)	0.236 (1.00)	1e-05 (0.00301)	4e-05 (0.0115)	0.34 (1.00)	0.124 (1.00)	0.583 (1.00)	0.152 (1.00)	0.568 (1.00)	0.509 (1.00)	1 (1.00)
del 9p21 3	29 (15%)	169	0.000527 (0.144)	0.553 (1.00)	1e-05 (0.00301)	1e-05 (0.00301)	0.00558 (1.00)	0.026 (1.00)	0.0017 (0.456)	0.0492 (1.00)	0.0283 (1.00)	0.0464 (1.00)	0.358 (1.00)
del 11q22 3	20 (10%)	178	6.48e-06 (0.00196)	0.0959 (1.00)	4e-05 (0.0115)	0.0001 (0.0283)	0.0155 (1.00)	0.335 (1.00)	0.303 (1.00)	0.219 (1.00)	0.815 (1.00)	0.411 (1.00)	1 (1.00)
del 11q24 2	20 (10%)	178	1.75e-06 (0.000538)	0.052 (1.00)	1e-05 (0.00301)	1e-05 (0.00301)	0.0391 (1.00)	0.335 (1.00)	0.606 (1.00)	0.219 (1.00)	0.405 (1.00)	0.551 (1.00)	1 (1.00)
del 15q13 3	25 (13%)	173	7.44e-06 (0.00225)	0.088 (1.00)	0.00011 (0.031)	3e-05 (0.00864)	0.00315 (0.828)	0.125 (1.00)	0.241 (1.00)	0.0223 (1.00)		0.489 (1.00)	1 (1.00)
del xp11 22	20 (10%)	178	2.8e-06 (0.000855)	0.395 (1.00)	0.00015 (0.042)	0.00011 (0.031)	0.0461 (1.00)	0.824 (1.00)	0.00319 (0.835)	0.469 (1.00)	0.792 (1.00)	0.038 (1.00)	1 (1.00)
del 4q34 3	24 (12%)	174	0.0192 (1.00)	0.317 (1.00)	6e-05 (0.017)	0.00024 (0.0665)	0.0823 (1.00)	0.437 (1.00)	0.00745 (1.00)	0.469 (1.00)		0.16 (1.00)	1 (1.00)
del 5q35 2	11 (6%)	187	0.193 (1.00)	0.00797 (1.00)	0.00081 (0.22)	2e-05 (0.00582)	0.116 (1.00)	0.339 (1.00)	0.0161 (1.00)			0.591 (1.00)	0.335 (1.00)
del 6q27	23 (12%)	175	0.184 (1.00)	0.623 (1.00)	0.00019 (0.053)	1e-05 (0.00301)	0.156 (1.00)	0.657 (1.00)	0.00583 (1.00)	0.44 (1.00)	0.441 (1.00)	0.0461 (1.00)	0.599 (1.00)
del 19p13 3	17 (9%)	181	2.23e-05 (0.00645)	0.763 (1.00)	0.00156 (0.42)	0.00064 (0.175)	0.0959 (1.00)	0.342 (1.00)	0.583 (1.00)	0.0103 (1.00)	0.792 (1.00)	0.587 (1.00)	0.601 (1.00)
del 22q12 2	50 (25%)	148	0.00682 (1.00)	0.338 (1.00)	1e-05 (0.00301)	1e-05 (0.00301)	0.00704 (1.00)	0.0405 (1.00)	0.0039 (1.00)	0.496 (1.00)	0.538 (1.00)	0.123 (1.00)	0.428 (1.00)
amp 7q22 1	122 (62%)	76	0.396 (1.00)	0.183 (1.00)	0.00024 (0.0665)	0.0113 (1.00)	0.456 (1.00)	0.633 (1.00)	0.149 (1.00)	0.086 (1.00)	0.885 (1.00)	0.763 (1.00)	0.288 (1.00)
del 5p14 2	10 (5%)	188	0.00951 (1.00)	0.138 (1.00)	0.00682 (1.00)	0.00024 (0.0665)	0.0117 (1.00)	0.453 (1.00)	0.0666 (1.00)	0.49 (1.00)		1 (1.00)	0.294 (1.00)
del 6q22 31	20 (10%)	178	0.697 (1.00)	0.738 (1.00)	0.00603 (1.00)	0.00023 (0.0639)	0.118 (1.00)	0.388 (1.00)	0.0169 (1.00)	0.768 (1.00)	0.617 (1.00)	0.0476 (1.00)	1 (1.00)
del 16q24 1	9 (5%)	189	1.05e-05 (0.00305)	0.186 (1.00)	0.0442 (1.00)	0.132 (1.00)	0.0789 (1.00)	0.187 (1.00)	0.453 (1.00)	0.49 (1.00)		1 (1.00)	1 (1.00)
del 19q13 42	16 (8%)	182	5.38e-06 (0.00164)	0.608 (1.00)	0.00298 (0.787)	0.00249 (0.66)	0.436 (1.00)	0.278 (1.00)	0.567 (1.00)	0.152 (1.00)		0.295 (1.00)	1 (1.00)
del xq28	19 (10%)	179	2.69e-06 (0.000824)	0.0952 (1.00)	0.00174 (0.465)	0.00495 (1.00)	0.0459 (1.00)	0.836 (1.00)	0.00693 (1.00)	0.322 (1.00)		0.0752 (1.00)	1 (1.00)
amp 2p23 2	39 (20%)	159	0.505 (1.00)	0.512 (1.00)	0.338 (1.00)	0.565 (1.00)	0.0631 (1.00)	0.0343 (1.00)	0.33 (1.00)	0.886 (1.00)	0.479 (1.00)	0.673 (1.00)	1 (1.00)
amp 2q32 1	45 (23%)	153	0.605 (1.00)	0.986 (1.00)	0.0335 (1.00)	0.118 (1.00)	0.324 (1.00)	0.0187 (1.00)	0.577 (1.00)	0.719 (1.00)	0.782 (1.00)	0.272 (1.00)	1 (1.00)
amp 3p12 1	59 (30%)	139	0.997 (1.00)	0.485 (1.00)	0.0643 (1.00)	0.0309 (1.00)	1 (1.00)	0.195 (1.00)	0.497 (1.00)	0.0383 (1.00)	0.0695 (1.00)	0.308 (1.00)	0.724 (1.00)
amp 3q26 31	73 (37%)	125	0.15 (1.00)	0.759 (1.00)	0.322 (1.00)	0.327 (1.00)	1 (1.00)	0.0228 (1.00)	0.518 (1.00)	0.154 (1.00)	0.537 (1.00)	0.309 (1.00)	0.489 (1.00)
amp 17q25 2	145 (73%)	53	0.979 (1.00)	0.18 (1.00)	0.257 (1.00)	0.439 (1.00)	0.821 (1.00)	0.0054 (1.00)	0.0769 (1.00)	0.989 (1.00)	0.385 (1.00)	0.491 (1.00)	0.691 (1.00)
amp 19p13 2	22 (11%)	176	0.74 (1.00)	0.0128 (1.00)	0.788 (1.00)	0.0445 (1.00)	0.614 (1.00)	0.527 (1.00)	0.461 (1.00)	0.734 (1.00)		0.174 (1.00)	1 (1.00)
del 2q37 3	9 (5%)	189	0.697 (1.00)	0.24 (1.00)	0.0293 (1.00)	0.0125 (1.00)	1 (1.00)	0.785 (1.00)	0.126 (1.00)		0.511 (1.00)	1 (1.00)	1 (1.00)
del 6p12 3	18 (9%)	180	0.45 (1.00)	0.95 (1.00)	0.0011 (0.298)	0.00194 (0.516)	0.0928 (1.00)	0.304 (1.00)	0.416 (1.00)	0.753 (1.00)	0.273 (1.00)	0.145 (1.00)	1 (1.00)
del 10p11 21	12 (6%)	186	0.00691 (1.00)	0.956 (1.00)	0.00131 (0.354)	0.00351 (0.916)	0.0688 (1.00)	0.226 (1.00)	0.0432 (1.00)	0.317 (1.00)		0.302 (1.00)	1 (1.00)
del 14q11 2	40 (20%)	158	0.00559 (1.00)	0.908 (1.00)	0.00774 (1.00)	0.00385 (1.00)	0.0925 (1.00)	0.423 (1.00)	0.0194 (1.00)	0.196 (1.00)	0.293 (1.00)	0.758 (1.00)	0.686 (1.00)
del 21q22 3	33 (17%)	165	0.317 (1.00)	0.651 (1.00)	0.0162 (1.00)	0.00735 (1.00)	0.645 (1.00)	0.226 (1.00)	0.0926 (1.00)	0.105 (1.00)	1 (1.00)	0.486 (1.00)	1 (1.00)

'amp_7q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.066

Table S1. Gene #5: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
AMP PEAK 5(7Q22.1) MUTATED	86	4	15	8
AMP PEAK 5(7Q22.1) WILD-TYPE	36	7	27	4

Figure S1. Get High-res Image Gene #5: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_1p36.32' versus 'Time to Death'

P value = 4.88e-05 (logrank test), Q value = 0.014

Table S2. Gene #8: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 1(1P36.32) MUTATED	34	5	2.0 - 3760.0 (215.5)
DEL PEAK 1(1P36.32) WILD-TYPE	139	2	2.0 - 5925.0 (582.0)

Figure S2. Get High-res Image Gene #8: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

'del_1p36.32' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S3. Gene #8: 'del_1p36.32' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 1(1P36.32) MUTATED	10	3	19	5
DEL PEAK 1(1P36.32) WILD-TYPE	112	8	23	7

Figure S3. Get High-res Image Gene #8: 'del_1p36.32' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_1p36.32' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0058

Table S4. Gene #8: 'del_1p36.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 1(1P36.32) MUTATED	12	5	22
DEL PEAK 1(1P36.32) WILD-TYPE	118	13	28

Figure S4. Get High-res Image Gene #8: 'del_1p36.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p22.1' versus 'Time to Death'

P value = 1.1e-06 (logrank test), Q value = 0.00034

Table S5. Gene #10: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 3(3P22.1) MUTATED	15	4	4.0 - 2429.0 (205.0)
DEL PEAK 3(3P22.1) WILD-TYPE	158	3	2.0 - 5925.0 (542.0)

Figure S5. Get High-res Image Gene #10: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

'del_3p22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S6. Gene #10: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 3(3P22.1) MUTATED	2	1	11	3
DEL PEAK 3(3P22.1) WILD-TYPE	120	10	31	9

Figure S6. Get High-res Image Gene #10: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S7. Gene #10: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 3(3P22.1) MUTATED	3	2	12
DEL PEAK 3(3P22.1) WILD-TYPE	127	16	38

Figure S7. Get High-res Image Gene #10: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.017

Table S8. Gene #11: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 4(4Q34.3) MUTATED	6	2	14	2
DEL PEAK 4(4Q34.3) WILD-TYPE	116	9	28	10

Figure S8. Get High-res Image Gene #11: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.00024 (Fisher's exact test), Q value = 0.066

Table S9. Gene #11: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 4(4Q34.3) MUTATED	7	4	13
DEL PEAK 4(4Q34.3) WILD-TYPE	123	14	37

Figure S9. Get High-res Image Gene #11: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5p14.2' versus 'PATHOLOGY.T.STAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.066

Table S10. Gene #12: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 5(5P14.2) MUTATED	1	1	8
DEL PEAK 5(5P14.2) WILD-TYPE	129	17	42

Figure S10. Get High-res Image Gene #12: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5q35.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00081 (Fisher's exact test), Q value = 0.22

Table S11. Gene #13: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 6(5Q35.2) MUTATED	1	1	7	1
DEL PEAK 6(5Q35.2) WILD-TYPE	121	10	35	11

Figure S11. Get High-res Image Gene #13: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 2e-05 (Fisher's exact test), Q value = 0.0058

Table S12. Gene #13: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 6(5Q35.2) MUTATED	1	1	9
DEL PEAK 6(5Q35.2) WILD-TYPE	129	17	41

Figure S12. Get High-res Image Gene #13: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

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

P value = 0.00023 (Fisher's exact test), Q value = 0.064

Table S13. Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 8(6Q22.31) MUTATED	7	0	13
DEL PEAK 8(6Q22.31) WILD-TYPE	123	18	37

Figure S13. Get High-res Image Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_6q27' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.053

Table S14. Gene #16: 'del_6q27' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 9(6Q27) MUTATED	7	0	13	2
DEL PEAK 9(6Q27) WILD-TYPE	115	11	29	10

Figure S14. Get High-res Image Gene #16: 'del_6q27' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_6q27' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S15. Gene #16: 'del_6q27' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 9(6Q27) MUTATED	7	0	16
DEL PEAK 9(6Q27) WILD-TYPE	123	18	34

Figure S15. Get High-res Image Gene #16: 'del_6q27' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p21.3' versus 'Time to Death'

P value = 0.000527 (logrank test), Q value = 0.14

Table S16. Gene #17: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 10(9P21.3) MUTATED	22	4	4.0 - 2839.0 (288.5)
DEL PEAK 10(9P21.3) WILD-TYPE	151	3	2.0 - 5925.0 (541.0)

Figure S16. Get High-res Image Gene #17: '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 = 0.003

Table S17. Gene #17: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 10(9P21.3) MUTATED	6	0	15	6
DEL PEAK 10(9P21.3) WILD-TYPE	116	11	27	6

Figure S17. Get High-res Image Gene #17: '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 = 0.003

Table S18. Gene #17: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 10(9P21.3) MUTATED	7	2	20
DEL PEAK 10(9P21.3) WILD-TYPE	123	16	30

Figure S18. Get High-res Image Gene #17: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q22.3' versus 'Time to Death'

P value = 6.48e-06 (logrank test), Q value = 0.002

Table S19. Gene #19: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 12(11Q22.3) MUTATED	16	4	4.0 - 3760.0 (228.5)
DEL PEAK 12(11Q22.3) WILD-TYPE	157	3	2.0 - 5925.0 (516.0)

Figure S19. Get High-res Image Gene #19: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

'del_11q22.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S20. Gene #19: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 12(11Q22.3) MUTATED	4	2	10	4
DEL PEAK 12(11Q22.3) WILD-TYPE	118	9	32	8

Figure S20. Get High-res Image Gene #19: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1e-04 (Fisher's exact test), Q value = 0.028

Table S21. Gene #19: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 12(11Q22.3) MUTATED	5	2	13
DEL PEAK 12(11Q22.3) WILD-TYPE	125	16	37

Figure S21. Get High-res Image Gene #19: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q24.2' versus 'Time to Death'

P value = 1.75e-06 (logrank test), Q value = 0.00054

Table S22. Gene #20: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 13(11Q24.2) MUTATED	15	4	4.0 - 3760.0 (223.0)
DEL PEAK 13(11Q24.2) WILD-TYPE	158	3	2.0 - 5925.0 (513.5)

Figure S22. Get High-res Image Gene #20: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'

'del_11q24.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S23. Gene #20: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 13(11Q24.2) MUTATED	3	2	11	4
DEL PEAK 13(11Q24.2) WILD-TYPE	119	9	31	8

Figure S23. Get High-res Image Gene #20: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_11q24.2' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.003

Table S24. Gene #20: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 13(11Q24.2) MUTATED	4	2	14
DEL PEAK 13(11Q24.2) WILD-TYPE	126	16	36

Figure S24. Get High-res Image Gene #20: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_15q13.3' versus 'Time to Death'

P value = 7.44e-06 (logrank test), Q value = 0.0022

Table S25. Gene #22: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 15(15Q13.3) MUTATED	19	4	3.0 - 5925.0 (207.0)
DEL PEAK 15(15Q13.3) WILD-TYPE	154	3	2.0 - 3950.0 (528.5)

Figure S25. Get High-res Image Gene #22: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

'del_15q13.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.031

Table S26. Gene #22: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 15(15Q13.3) MUTATED	7	1	11	5
DEL PEAK 15(15Q13.3) WILD-TYPE	115	10	31	7

Figure S26. Get High-res Image Gene #22: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 3e-05 (Fisher's exact test), Q value = 0.0086

Table S27. Gene #22: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 15(15Q13.3) MUTATED	8	1	16
DEL PEAK 15(15Q13.3) WILD-TYPE	122	17	34

Figure S27. Get High-res Image Gene #22: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_16q24.1' versus 'Time to Death'

P value = 1.05e-05 (logrank test), Q value = 0.0031

Table S28. Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 16(16Q24.1) MUTATED	5	2	21.0 - 1967.0 (87.0)
DEL PEAK 16(16Q24.1) WILD-TYPE	168	5	2.0 - 5925.0 (509.0)

Figure S28. Get High-res Image Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'Time to Death'

P value = 2.23e-05 (logrank test), Q value = 0.0065

Table S29. Gene #24: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 17(19P13.3) MUTATED	16	3	4.0 - 1967.0 (228.0)
DEL PEAK 17(19P13.3) WILD-TYPE	157	4	2.0 - 5925.0 (510.0)

Figure S29. Get High-res Image Gene #24: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

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

P value = 0.00064 (Fisher's exact test), Q value = 0.17

Table S30. Gene #24: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 17(19P13.3) MUTATED	5	1	11
DEL PEAK 17(19P13.3) WILD-TYPE	125	17	39

Figure S30. Get High-res Image Gene #24: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_19q13.42' versus 'Time to Death'

P value = 5.38e-06 (logrank test), Q value = 0.0016

Table S31. Gene #25: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 18(19Q13.42) MUTATED	16	4	29.0 - 2839.0 (218.5)
DEL PEAK 18(19Q13.42) WILD-TYPE	157	3	2.0 - 5925.0 (510.0)

Figure S31. Get High-res Image Gene #25: '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 = 0.003

Table S32. Gene #27: 'del_22q12.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 20(22Q12.2) MUTATED	16	3	22	7
DEL PEAK 20(22Q12.2) WILD-TYPE	106	8	20	5

Figure S32. Get High-res Image Gene #27: '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 = 0.003

Table S33. Gene #27: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 20(22Q12.2) MUTATED	18	5	27
DEL PEAK 20(22Q12.2) WILD-TYPE	112	13	23

Figure S33. Get High-res Image Gene #27: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xp11.22' versus 'Time to Death'

P value = 2.8e-06 (logrank test), Q value = 0.00085

Table S34. Gene #28: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 21(XP11.22) MUTATED	16	4	4.0 - 2429.0 (246.5)
DEL PEAK 21(XP11.22) WILD-TYPE	157	3	2.0 - 5925.0 (516.0)

Figure S34. Get High-res Image Gene #28: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'

'del_xp11.22' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.042

Table S35. Gene #28: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	122	11	42	12
DEL PEAK 21(XP11.22) MUTATED	4	1	11	2
DEL PEAK 21(XP11.22) WILD-TYPE	118	10	31	10

Figure S35. Get High-res Image Gene #28: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_xp11.22' versus 'PATHOLOGY.T.STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.031

Table S36. Gene #28: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	130	18	50
DEL PEAK 21(XP11.22) MUTATED	5	2	13
DEL PEAK 21(XP11.22) WILD-TYPE	125	16	37

Figure S36. Get High-res Image Gene #28: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xq28' versus 'Time to Death'

P value = 2.69e-06 (logrank test), Q value = 0.00082

Table S37. Gene #29: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Year
ALL	173	7	2.0 - 5925.0 (508.0)
DEL PEAK 22(XQ28) MUTATED	14	3	3.0 - 1967.0 (160.0)
DEL PEAK 22(XQ28) WILD-TYPE	159	4	2.0 - 5925.0 (516.0)

Figure S37. Get High-res Image Gene #29: '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 = 198
Number of significantly focal cnvs = 29
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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