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

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

21 April 2013 | analyses__2013_04_21

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): Kidney Renal Clear Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1JQ0XZ0

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 30 arm-level results and 8 clinical features across 493 patients, 26 significant findings detected with Q value < 0.25.

Amp Peak 3(3q26.32) cnv correlated to 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
Amp Peak 7(8q24.22) cnv correlated to 'PATHOLOGY.T'.
Del Peak 6(3p21.32) cnv correlated to 'PATHOLOGY.T' and 'TUMOR.STAGE'.
Del Peak 8(3q11.2) cnv correlated to 'GENDER'.
Del Peak 9(4q34.3) cnv correlated to 'Time to Death', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
Del Peak 13(9p23) cnv correlated to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
Del Peak 14(9p21.3) cnv correlated to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
Del Peak 15(10q23.31) cnv correlated to 'PATHOLOGY.T'.
Del Peak 16(13q13.3) cnv correlated to 'Time to Death', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
Del Peak 17(14q31.1) cnv correlated to 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 arm-level results and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 26 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	PATHOLOGY T	PATHOLOGY N	PATHOLOGICSPREAD(M)	TUMOR STAGE
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 13(9p23)	0 (0%)	349	0.000138 (0.0304)	0.0136 (1.00)	0.00361 (0.744)	0.656 (1.00)	1.39e-05 (0.0032)	0.262 (1.00)	0.000876 (0.187)	5.62e-06 (0.0013)
Del Peak 14(9p21 3)	0 (0%)	341	2.03e-06 (0.000473)	0.0261 (1.00)	0.00144 (0.303)	0.656 (1.00)	1.01e-07 (2.4e-05)	0.0589 (1.00)	6.93e-05 (0.0156)	3.39e-08 (8.03e-06)
Del Peak 17(14q31 1)	0 (0%)	275	0.00179 (0.374)	0.055 (1.00)	0.393 (1.00)	0.0872 (1.00)	0.000107 (0.0238)	0.000113 (0.0249)	0.00101 (0.216)	2.42e-05 (0.00553)
Amp Peak 3(3q26 32)	0 (0%)	413	0.156 (1.00)	0.903 (1.00)	0.442 (1.00)	0.152 (1.00)	0.000107 (0.0238)	0.0593 (1.00)	7.09e-05 (0.0159)	2.55e-05 (0.00579)
Del Peak 9(4q34 3)	0 (0%)	417	0.000557 (0.12)	0.568 (1.00)	0.433 (1.00)	0.0261 (1.00)	4.27e-07 (9.98e-05)	1 (1.00)	0.00862 (1.00)	2.7e-06 (0.000626)
Del Peak 16(13q13 3)	0 (0%)	417	0.000848 (0.182)	0.884 (1.00)	0.794 (1.00)	0.748 (1.00)	1.48e-05 (0.0034)	0.325 (1.00)	0.0377 (1.00)	0.000348 (0.0762)
Del Peak 6(3p21 32)	0 (0%)	58	0.498 (1.00)	0.704 (1.00)	0.772 (1.00)	0.0817 (1.00)	3.34e-05 (0.00756)	1 (1.00)	0.333 (1.00)	0.00053 (0.115)
Amp Peak 7(8q24 22)	0 (0%)	420	0.0527 (1.00)	0.0214 (1.00)	0.11 (1.00)	0.297 (1.00)	0.00112 (0.237)	0.74 (1.00)	0.053 (1.00)	0.00241 (0.5)
Del Peak 8(3q11 2)	0 (0%)	343	0.635 (1.00)	0.0111 (1.00)	1.32e-07 (3.1e-05)	0.749 (1.00)	0.134 (1.00)	0.787 (1.00)	0.591 (1.00)	0.45 (1.00)
Del Peak 15(10q23 31)	0 (0%)	403	0.217 (1.00)	0.209 (1.00)	0.0272 (1.00)	0.764 (1.00)	0.000477 (0.104)	1 (1.00)	0.333 (1.00)	0.0177 (1.00)
Amp Peak 1(1q24 1)	0 (0%)	433	0.2 (1.00)	0.164 (1.00)	0.666 (1.00)	0.499 (1.00)	0.157 (1.00)	0.0751 (1.00)	0.339 (1.00)	0.298 (1.00)
Amp Peak 2(1q32 1)	0 (0%)	434	0.437 (1.00)	0.0725 (1.00)	0.771 (1.00)	0.499 (1.00)	0.164 (1.00)	0.482 (1.00)	0.703 (1.00)	0.24 (1.00)
Amp Peak 4(4q32 1)	0 (0%)	479	0.0584 (1.00)	0.416 (1.00)	0.258 (1.00)	0.411 (1.00)	0.265 (1.00)	0.574 (1.00)	0.462 (1.00)	0.415 (1.00)
Amp Peak 5(5q35 1)	0 (0%)	182	0.0454 (1.00)	0.0923 (1.00)	0.141 (1.00)	0.944 (1.00)	0.295 (1.00)	0.31 (1.00)	0.366 (1.00)	0.629 (1.00)
Amp Peak 6(7q36 3)	0 (0%)	330	0.724 (1.00)	0.806 (1.00)	0.0352 (1.00)	0.57 (1.00)	0.0563 (1.00)	0.443 (1.00)	0.00523 (1.00)	0.0202 (1.00)
Amp Peak 8(10p14)	0 (0%)	477	0.234 (1.00)	0.423 (1.00)	0.594 (1.00)	0.887 (1.00)	0.013 (1.00)	0.188 (1.00)	0.288 (1.00)	0.0494 (1.00)
Amp Peak 9(17q24 3)	0 (0%)	456	0.0512 (1.00)	0.0662 (1.00)	0.858 (1.00)	0.471 (1.00)	0.482 (1.00)	0.359 (1.00)	0.244 (1.00)	0.857 (1.00)
Amp Peak 10(Xp22 2)	0 (0%)	458	0.468 (1.00)	0.676 (1.00)	0.854 (1.00)	0.726 (1.00)	0.0837 (1.00)	0.668 (1.00)	0.0897 (1.00)	0.0108 (1.00)
Amp Peak 11(Xp11 4)	0 (0%)	457	0.759 (1.00)	0.712 (1.00)	0.857 (1.00)	0.726 (1.00)	0.0695 (1.00)	0.668 (1.00)	0.0509 (1.00)	0.00533 (1.00)
Amp Peak 12(Xq11 2)	0 (0%)	461	0.803 (1.00)	0.145 (1.00)	0.706 (1.00)	0.726 (1.00)	0.179 (1.00)	0.647 (1.00)	0.31 (1.00)	0.0584 (1.00)
Del Peak 1(1p36 23)	0 (0%)	395	0.0495 (1.00)	0.123 (1.00)	0.123 (1.00)	0.284 (1.00)	0.111 (1.00)	1 (1.00)	0.0844 (1.00)	0.168 (1.00)
Del Peak 2(1p31 1)	0 (0%)	421	0.219 (1.00)	0.0726 (1.00)	0.016 (1.00)	0.284 (1.00)	0.0536 (1.00)	0.722 (1.00)	0.294 (1.00)	0.181 (1.00)
Del Peak 3(1q43)	0 (0%)	455	0.704 (1.00)	0.335 (1.00)	1 (1.00)		0.0712 (1.00)	0.374 (1.00)	1 (1.00)	0.749 (1.00)
Del Peak 4(2q37 3)	0 (0%)	445	0.673 (1.00)	0.63 (1.00)	0.153 (1.00)		0.822 (1.00)	1 (1.00)	0.402 (1.00)	0.556 (1.00)
Del Peak 5(3p25 3)	0 (0%)	61	0.783 (1.00)	0.788 (1.00)	0.569 (1.00)	0.0817 (1.00)	0.00144 (0.303)	1 (1.00)	0.707 (1.00)	0.0129 (1.00)
Del Peak 7(3p12 2)	0 (0%)	210	0.614 (1.00)	0.761 (1.00)	0.00221 (0.461)	0.741 (1.00)	0.217 (1.00)	0.626 (1.00)	0.53 (1.00)	0.231 (1.00)
Del Peak 10(6q26)	0 (0%)	351	0.565 (1.00)	0.287 (1.00)	0.012 (1.00)	0.256 (1.00)	0.621 (1.00)	0.0195 (1.00)	0.41 (1.00)	0.32 (1.00)
Del Peak 11(6q26)	0 (0%)	351	0.589 (1.00)	0.226 (1.00)	0.00648 (1.00)	0.256 (1.00)	0.621 (1.00)	0.0195 (1.00)	0.41 (1.00)	0.32 (1.00)
Del Peak 12(8p23 2)	0 (0%)	347	0.0385 (1.00)	0.139 (1.00)	0.256 (1.00)	0.893 (1.00)	0.176 (1.00)	0.786 (1.00)	0.055 (1.00)	0.14 (1.00)
Del Peak 18(Xq23)	0 (0%)	438	0.287 (1.00)	0.669 (1.00)	0.234 (1.00)		0.297 (1.00)	0.657 (1.00)	0.168 (1.00)	0.142 (1.00)

'Amp Peak 3(3q26.32)' versus 'PATHOLOGY.T'

P value = 0.000107 (Fisher's exact test), Q value = 0.024

Table S1. Gene #3: 'Amp Peak 3(3q26.32)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
AMP PEAK 3(3Q26.32) CNV	24	8	44	4
AMP PEAK 3(3Q26.32) WILD-TYPE	218	56	132	7

Figure S1. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Amp Peak 3(3q26.32)' versus 'PATHOLOGICSPREAD(M)'

P value = 7.09e-05 (Fisher's exact test), Q value = 0.016

Table S2. Gene #3: 'Amp Peak 3(3q26.32)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
AMP PEAK 3(3Q26.32) CNV	55	25
AMP PEAK 3(3Q26.32) WILD-TYPE	362	51

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Amp Peak 3(3q26.32)' versus 'TUMOR.STAGE'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.0058

Table S3. Gene #3: 'Amp Peak 3(3q26.32)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
AMP PEAK 3(3Q26.32) CNV	23	6	25	26
AMP PEAK 3(3Q26.32) WILD-TYPE	215	46	98	54

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 7(8q24.22)' versus 'PATHOLOGY.T'

P value = 0.00112 (Fisher's exact test), Q value = 0.24

Table S4. Gene #7: 'Amp Peak 7(8q24.22)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
AMP PEAK 7(8Q24.22) CNV	21	11	39	2
AMP PEAK 7(8Q24.22) WILD-TYPE	221	53	137	9

Figure S4. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 6(3p21.32)' versus 'PATHOLOGY.T'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.0076

Table S5. Gene #18: 'Del Peak 6(3p21.32)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 6(3P21.32) CNV	209	52	168	6
DEL PEAK 6(3P21.32) WILD-TYPE	33	12	8	5

Figure S5. Get High-res Image Gene #18: 'Del Peak 6(3p21.32)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 6(3p21.32)' versus 'TUMOR.STAGE'

P value = 0.00053 (Fisher's exact test), Q value = 0.12

Table S6. Gene #18: 'Del Peak 6(3p21.32)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 6(3P21.32) CNV	205	40	119	71
DEL PEAK 6(3P21.32) WILD-TYPE	33	12	4	9

Figure S6. Get High-res Image Gene #18: 'Del Peak 6(3p21.32)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 8(3q11.2)' versus 'GENDER'

P value = 1.32e-07 (Fisher's exact test), Q value = 3.1e-05

Table S7. Gene #20: 'Del Peak 8(3q11.2)' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	171	322
DEL PEAK 8(3Q11.2) CNV	27	123
DEL PEAK 8(3Q11.2) WILD-TYPE	144	199

Figure S7. Get High-res Image Gene #20: 'Del Peak 8(3q11.2)' versus Clinical Feature #3: 'GENDER'

'Del Peak 9(4q34.3)' versus 'Time to Death'

P value = 0.000557 (logrank test), Q value = 0.12

Table S8. Gene #21: 'Del Peak 9(4q34.3)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 9(4Q34.3) CNV	76	38	0.2 - 91.4 (35.1)
DEL PEAK 9(4Q34.3) WILD-TYPE	414	120	0.1 - 111.0 (35.2)

Figure S8. Get High-res Image Gene #21: 'Del Peak 9(4q34.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 9(4q34.3)' versus 'PATHOLOGY.T'

P value = 4.27e-07 (Fisher's exact test), Q value = 1e-04

Table S9. Gene #21: 'Del Peak 9(4q34.3)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 9(4Q34.3) CNV	19	8	43	6
DEL PEAK 9(4Q34.3) WILD-TYPE	223	56	133	5

Figure S9. Get High-res Image Gene #21: 'Del Peak 9(4q34.3)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 9(4q34.3)' versus 'TUMOR.STAGE'

P value = 2.7e-06 (Fisher's exact test), Q value = 0.00063

Table S10. Gene #21: 'Del Peak 9(4q34.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 9(4Q34.3) CNV	18	6	30	22
DEL PEAK 9(4Q34.3) WILD-TYPE	220	46	93	58

Figure S10. Get High-res Image Gene #21: 'Del Peak 9(4q34.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 13(9p23)' versus 'Time to Death'

P value = 0.000138 (logrank test), Q value = 0.03

Table S11. Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 13(9P23) CNV	143	65	0.2 - 109.9 (36.1)
DEL PEAK 13(9P23) WILD-TYPE	347	93	0.1 - 111.0 (34.6)

Figure S11. Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 13(9p23)' versus 'PATHOLOGY.T'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0032

Table S12. Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 13(9P23) CNV	50	15	74	5
DEL PEAK 13(9P23) WILD-TYPE	192	49	102	6

Figure S12. Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 13(9p23)' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000876 (Fisher's exact test), Q value = 0.19

Table S13. Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
DEL PEAK 13(9P23) CNV	109	35
DEL PEAK 13(9P23) WILD-TYPE	308	41

Figure S13. Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 13(9p23)' versus 'TUMOR.STAGE'

P value = 5.62e-06 (Fisher's exact test), Q value = 0.0013

Table S14. Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 13(9P23) CNV	48	11	49	36
DEL PEAK 13(9P23) WILD-TYPE	190	41	74	44

Figure S14. Get High-res Image Gene #25: 'Del Peak 13(9p23)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 14(9p21.3)' versus 'Time to Death'

P value = 2.03e-06 (logrank test), Q value = 0.00047

Table S15. Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 14(9P21.3) CNV	152	72	0.2 - 109.9 (31.5)
DEL PEAK 14(9P21.3) WILD-TYPE	338	86	0.1 - 111.0 (36.2)

Figure S15. Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 14(9p21.3)' versus 'PATHOLOGY.T'

P value = 1.01e-07 (Fisher's exact test), Q value = 2.4e-05

Table S16. Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 14(9P21.3) CNV	51	14	81	6
DEL PEAK 14(9P21.3) WILD-TYPE	191	50	95	5

Figure S16. Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 14(9p21.3)' versus 'PATHOLOGICSPREAD(M)'

P value = 6.93e-05 (Fisher's exact test), Q value = 0.016

Table S17. Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
DEL PEAK 14(9P21.3) CNV	113	39
DEL PEAK 14(9P21.3) WILD-TYPE	304	37

Figure S17. Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 14(9p21.3)' versus 'TUMOR.STAGE'

P value = 3.39e-08 (Fisher's exact test), Q value = 8e-06

Table S18. Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 14(9P21.3) CNV	49	10	52	41
DEL PEAK 14(9P21.3) WILD-TYPE	189	42	71	39

Figure S18. Get High-res Image Gene #26: 'Del Peak 14(9p21.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 15(10q23.31)' versus 'PATHOLOGY.T'

P value = 0.000477 (Fisher's exact test), Q value = 0.1

Table S19. Gene #27: 'Del Peak 15(10q23.31)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 15(10Q23.31) CNV	31	10	43	6
DEL PEAK 15(10Q23.31) WILD-TYPE	211	54	133	5

Figure S19. Get High-res Image Gene #27: 'Del Peak 15(10q23.31)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 16(13q13.3)' versus 'Time to Death'

P value = 0.000848 (logrank test), Q value = 0.18

Table S20. Gene #28: 'Del Peak 16(13q13.3)' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 16(13Q13.3) CNV	75	34	0.1 - 89.4 (28.5)
DEL PEAK 16(13Q13.3) WILD-TYPE	415	124	0.1 - 111.0 (36.3)

Figure S20. Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 16(13q13.3)' versus 'PATHOLOGY.T'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.0034

Table S21. Gene #28: 'Del Peak 16(13q13.3)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 16(13Q13.3) CNV	28	3	39	6
DEL PEAK 16(13Q13.3) WILD-TYPE	214	61	137	5

Figure S21. Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 16(13q13.3)' versus 'TUMOR.STAGE'

P value = 0.000348 (Fisher's exact test), Q value = 0.076

Table S22. Gene #28: 'Del Peak 16(13q13.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 16(13Q13.3) CNV	27	2	27	20
DEL PEAK 16(13Q13.3) WILD-TYPE	211	50	96	60

Figure S22. Get High-res Image Gene #28: 'Del Peak 16(13q13.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 17(14q31.1)' versus 'PATHOLOGY.T'

P value = 0.000107 (Fisher's exact test), Q value = 0.024

Table S23. Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 17(14Q31.1) CNV	83	35	96	4
DEL PEAK 17(14Q31.1) WILD-TYPE	159	29	80	7

Figure S23. Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 17(14q31.1)' versus 'PATHOLOGY.N'

P value = 0.000113 (Fisher's exact test), Q value = 0.025

Table S24. Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	0	1
ALL	228	18
DEL PEAK 17(14Q31.1) CNV	96	16
DEL PEAK 17(14Q31.1) WILD-TYPE	132	2

Figure S24. Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 17(14q31.1)' versus 'PATHOLOGICSPREAD(M)'

P value = 0.00101 (Fisher's exact test), Q value = 0.22

Table S25. Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
DEL PEAK 17(14Q31.1) CNV	171	47
DEL PEAK 17(14Q31.1) WILD-TYPE	246	29

Figure S25. Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 17(14q31.1)' versus 'TUMOR.STAGE'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.0055

Table S26. Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 17(14Q31.1) CNV	79	25	68	46
DEL PEAK 17(14Q31.1) WILD-TYPE	159	27	55	34

Figure S26. Get High-res Image Gene #29: 'Del Peak 17(14q31.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

Methods & Data

Input

Mutation data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = KIRC-TP.clin.merged.picked.txt
Number of patients = 493
Number of significantly arm-level cnvs = 30
Number of selected clinical features = 8
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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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