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

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C14M935D

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 28 focal events and 10 clinical features across 163 patients, 31 significant findings detected with Q value < 0.25.

amp_7q22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE'.
amp_17q25.2 cnv correlated to 'PATHOLOGY.M.STAGE'.
del_1p36.31 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_3p22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
del_4q34.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
del_5p14.2 cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.
del_5q35.2 cnv correlated to 'PATHOLOGY.T.STAGE'.
del_6q21 cnv correlated to 'PATHOLOGY.T.STAGE'.
del_6q22.31 cnv correlated to '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_15q15.2 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_16q24.1 cnv correlated to 'Time to Death'.
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 28 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 31 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	YEAROFTOBACCOSMOKINGONSET
	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	t-test
del 1p36 31	35 (21%)	128	0.000879 (0.177)	0.475 (1.00)	1.99e-05 (0.00448)	2.41e-05 (0.0054)	0.013 (1.00)	0.135 (1.00)	0.0361 (1.00)	0.301 (1.00)	0.453 (1.00)
del 9p21 3	24 (15%)	139	5.18e-05 (0.0115)	0.272 (1.00)	3.19e-07 (7.34e-05)	2.02e-06 (0.000461)	0.00914 (1.00)	0.00761 (1.00)	0.00288 (0.576)	0.314 (1.00)
del 11q22 3	17 (10%)	146	0.000127 (0.0279)	0.114 (1.00)	0.000152 (0.0329)	0.000633 (0.13)	0.0444 (1.00)	0.0974 (1.00)	0.401 (1.00)	0.792 (1.00)
del 11q24 2	17 (10%)	146	3.61e-05 (0.00806)	0.0593 (1.00)	0.000152 (0.0329)	0.000633 (0.13)	0.0776 (1.00)	0.0974 (1.00)	0.589 (1.00)	0.792 (1.00)
del 15q15 2	21 (13%)	142	2.86e-07 (6.61e-05)	0.0511 (1.00)	0.000171 (0.0368)	0.000141 (0.0308)	0.0057 (1.00)	0.0523 (1.00)	0.204 (1.00)	0.348 (1.00)
del xp11 22	18 (11%)	145	0.000314 (0.0662)	0.333 (1.00)	0.000432 (0.089)	0.000217 (0.0463)	0.0836 (1.00)	0.696 (1.00)	0.00486 (0.942)	0.467 (1.00)
del 3p22 1	15 (9%)	148	0.0198 (1.00)	0.149 (1.00)	6.41e-06 (0.00145)	5.12e-05 (0.0114)	0.361 (1.00)	0.114 (1.00)	0.386 (1.00)	0.754 (1.00)	0.453 (1.00)
del 4q34 3	18 (11%)	145	0.0288 (1.00)	0.18 (1.00)	0.00108 (0.217)	0.000411 (0.0852)	0.0698 (1.00)	0.23 (1.00)	0.00486 (0.942)	0.754 (1.00)
del 5p14 2	10 (6%)	153	6.3e-05 (0.0139)	0.185 (1.00)	0.0109 (1.00)	0.000382 (0.0799)	0.0122 (1.00)	0.359 (1.00)	0.0673 (1.00)	0.104 (1.00)
amp 7q22 1	97 (60%)	66	0.049 (1.00)	0.518 (1.00)	0.000276 (0.0584)	0.00432 (0.851)	0.54 (1.00)	0.314 (1.00)	0.166 (1.00)	0.159 (1.00)	0.354 (1.00)	0.837 (1.00)
amp 17q25 2	120 (74%)	43	0.871 (1.00)	0.239 (1.00)	0.296 (1.00)	0.395 (1.00)	0.891 (1.00)	0.000359 (0.0753)	0.0319 (1.00)	0.667 (1.00)
del 5q35 2	10 (6%)	153	0.00872 (1.00)	0.0436 (1.00)	0.00438 (0.859)	0.000382 (0.0799)	0.0903 (1.00)	0.434 (1.00)	0.0673 (1.00)
del 6q21	16 (10%)	147	0.206 (1.00)	0.902 (1.00)	0.0157 (1.00)	0.000811 (0.165)	0.169 (1.00)	0.445 (1.00)	0.00717 (1.00)	0.459 (1.00)	0.315 (1.00)
del 6q22 31	17 (10%)	146	0.0437 (1.00)	0.857 (1.00)	0.00578 (1.00)	0.000217 (0.0463)	0.139 (1.00)	0.304 (1.00)	0.0105 (1.00)	0.459 (1.00)	0.315 (1.00)
del 16q24 1	7 (4%)	156	1.82e-06 (0.000417)	0.57 (1.00)	0.0363 (1.00)	0.269 (1.00)	0.192 (1.00)	0.216 (1.00)	0.199 (1.00)
del xq28	17 (10%)	146	5.1e-06 (0.00116)	0.113 (1.00)	0.00351 (0.699)	0.0134 (1.00)	0.0836 (1.00)	0.632 (1.00)	0.0105 (1.00)	0.469 (1.00)
amp 2p23 2	32 (20%)	131	0.262 (1.00)	0.356 (1.00)	0.46 (1.00)	0.873 (1.00)	0.408 (1.00)	0.0307 (1.00)	0.196 (1.00)	0.537 (1.00)	0.331 (1.00)	0.477 (1.00)
amp 2q32 1	39 (24%)	124	0.461 (1.00)	0.856 (1.00)	0.0642 (1.00)	0.172 (1.00)	0.72 (1.00)	0.0174 (1.00)	0.424 (1.00)	0.531 (1.00)
amp 3q22 3	56 (34%)	107	0.373 (1.00)	0.478 (1.00)	0.295 (1.00)	0.0523 (1.00)	1 (1.00)	0.533 (1.00)	0.591 (1.00)	0.126 (1.00)	0.354 (1.00)
amp 19p13 2	19 (12%)	144	0.543 (1.00)	0.0568 (1.00)	0.889 (1.00)	0.0541 (1.00)	0.521 (1.00)	0.903 (1.00)	0.595 (1.00)	0.268 (1.00)
del 2q37 3	8 (5%)	155	0.681 (1.00)	0.151 (1.00)	0.018 (1.00)	0.00691 (1.00)		0.534 (1.00)	0.0538 (1.00)
del 5q15	11 (7%)	152	0.00642 (1.00)	0.0301 (1.00)	0.0357 (1.00)	0.00535 (1.00)	0.0903 (1.00)	0.389 (1.00)	0.0886 (1.00)
del 10p11 21	11 (7%)	152	0.822 (1.00)	0.823 (1.00)	0.006 (1.00)	0.0109 (1.00)	0.0556 (1.00)	0.52 (1.00)	0.0886 (1.00)	0.792 (1.00)
del 14q11 2	34 (21%)	129	0.00577 (1.00)	0.68 (1.00)	0.00494 (0.949)	0.00745 (1.00)	0.118 (1.00)	0.17 (1.00)	0.141 (1.00)	0.448 (1.00)
del 14q32 2	34 (21%)	129	0.00427 (0.845)	0.639 (1.00)	0.00494 (0.949)	0.00745 (1.00)	0.0476 (1.00)	0.183 (1.00)	0.141 (1.00)	0.448 (1.00)	0.413 (1.00)	0.00474 (0.925)
del 19p13 3	16 (10%)	147	0.0285 (1.00)	0.946 (1.00)	0.00802 (1.00)	0.00614 (1.00)	0.209 (1.00)	0.412 (1.00)	0.568 (1.00)	0.268 (1.00)
del 19q13 42	15 (9%)	148	0.179 (1.00)	0.792 (1.00)	0.0167 (1.00)	0.0135 (1.00)	0.651 (1.00)	0.512 (1.00)	0.386 (1.00)	0.754 (1.00)
del 21q22 3	31 (19%)	132	0.577 (1.00)	0.661 (1.00)	0.0139 (1.00)	0.00747 (1.00)	0.872 (1.00)	0.143 (1.00)	0.129 (1.00)	0.711 (1.00)	0.332 (1.00)

'amp_7q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000276 (Fisher's exact test), Q value = 0.058

Table S1. Gene #4: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
AMP PEAK 4(7Q22.1) MUTATED	67	4	12	6
AMP PEAK 4(7Q22.1) WILD-TYPE	28	7	25	4

Figure S1. Get High-res Image Gene #4: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_17q25.2' versus 'PATHOLOGY.M.STAGE'

P value = 0.000359 (Fisher's exact test), Q value = 0.075

Table S2. Gene #5: 'amp_17q25.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	MX
ALL	62	6	82
AMP PEAK 5(17Q25.2) MUTATED	35	4	70
AMP PEAK 5(17Q25.2) WILD-TYPE	27	2	12

Figure S2. Get High-res Image Gene #5: 'amp_17q25.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_1p36.31' versus 'Time to Death'

P value = 0.000879 (logrank test), Q value = 0.18

Table S3. Gene #7: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 1(1P36.31) MUTATED	35	7	0.1 - 123.6 (7.7)
DEL PEAK 1(1P36.31) WILD-TYPE	115	10	0.0 - 194.8 (16.6)

Figure S3. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

'del_1p36.31' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0045

Table S4. Gene #7: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 1(1P36.31) MUTATED	9	3	17	4
DEL PEAK 1(1P36.31) WILD-TYPE	86	8	20	6

Figure S4. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 2.41e-05 (Fisher's exact test), Q value = 0.0054

Table S5. Gene #7: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 1(1P36.31) MUTATED	11	4	20
DEL PEAK 1(1P36.31) WILD-TYPE	91	13	24

Figure S5. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.41e-06 (Fisher's exact test), Q value = 0.0014

Table S6. Gene #9: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 3(3P22.1) MUTATED	1	1	10	3
DEL PEAK 3(3P22.1) WILD-TYPE	94	10	27	7

Figure S6. Get High-res Image Gene #9: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 5.12e-05 (Fisher's exact test), Q value = 0.011

Table S7. Gene #9: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 3(3P22.1) MUTATED	2	2	11
DEL PEAK 3(3P22.1) WILD-TYPE	100	15	33

Figure S7. Get High-res Image Gene #9: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00108 (Fisher's exact test), Q value = 0.22

Table S8. Gene #10: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 4(4Q34.3) MUTATED	4	2	10	2
DEL PEAK 4(4Q34.3) WILD-TYPE	91	9	27	8

Figure S8. Get High-res Image Gene #10: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.000411 (Fisher's exact test), Q value = 0.085

Table S9. Gene #10: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 4(4Q34.3) MUTATED	4	3	11
DEL PEAK 4(4Q34.3) WILD-TYPE	98	14	33

Figure S9. Get High-res Image Gene #10: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5p14.2' versus 'Time to Death'

P value = 6.3e-05 (logrank test), Q value = 0.014

Table S10. Gene #11: 'del_5p14.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 5(5P14.2) MUTATED	9	4	0.1 - 63.7 (6.6)
DEL PEAK 5(5P14.2) WILD-TYPE	141	13	0.0 - 194.8 (14.4)

Figure S10. Get High-res Image Gene #11: 'del_5p14.2' versus Clinical Feature #1: 'Time to Death'

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

P value = 0.000382 (Fisher's exact test), Q value = 0.08

Table S11. Gene #11: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 5(5P14.2) MUTATED	1	1	8
DEL PEAK 5(5P14.2) WILD-TYPE	101	16	36

Figure S11. Get High-res Image Gene #11: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

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

P value = 0.000382 (Fisher's exact test), Q value = 0.08

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

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 7(5Q35.2) MUTATED	1	1	8
DEL PEAK 7(5Q35.2) WILD-TYPE	101	16	36

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

'del_6q21' versus 'PATHOLOGY.T.STAGE'

P value = 0.000811 (Fisher's exact test), Q value = 0.16

Table S13. Gene #14: 'del_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 8(6Q21) MUTATED	5	0	11
DEL PEAK 8(6Q21) WILD-TYPE	97	17	33

Figure S13. Get High-res Image Gene #14: 'del_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

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

P value = 0.000217 (Fisher's exact test), Q value = 0.046

Table S14. Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 9(6Q22.31) MUTATED	5	0	12
DEL PEAK 9(6Q22.31) WILD-TYPE	97	17	32

Figure S14. Get High-res Image Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p21.3' versus 'Time to Death'

P value = 5.18e-05 (logrank test), Q value = 0.011

Table S15. Gene #16: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 10(9P21.3) MUTATED	22	7	0.1 - 93.3 (10.5)
DEL PEAK 10(9P21.3) WILD-TYPE	128	10	0.0 - 194.8 (14.9)

Figure S15. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.19e-07 (Fisher's exact test), Q value = 7.3e-05

Table S16. Gene #16: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 10(9P21.3) MUTATED	4	0	12	6
DEL PEAK 10(9P21.3) WILD-TYPE	91	11	25	4

Figure S16. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 2.02e-06 (Fisher's exact test), Q value = 0.00046

Table S17. Gene #16: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 10(9P21.3) MUTATED	5	2	17
DEL PEAK 10(9P21.3) WILD-TYPE	97	15	27

Figure S17. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q22.3' versus 'Time to Death'

P value = 0.000127 (logrank test), Q value = 0.028

Table S18. Gene #18: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 12(11Q22.3) MUTATED	16	5	0.1 - 123.6 (8.3)
DEL PEAK 12(11Q22.3) WILD-TYPE	134	12	0.0 - 194.8 (14.6)

Figure S18. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

'del_11q22.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000152 (Fisher's exact test), Q value = 0.033

Table S19. Gene #18: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 12(11Q22.3) MUTATED	3	2	8	4
DEL PEAK 12(11Q22.3) WILD-TYPE	92	9	29	6

Figure S19. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.000633 (Fisher's exact test), Q value = 0.13

Table S20. Gene #18: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 12(11Q22.3) MUTATED	4	2	11
DEL PEAK 12(11Q22.3) WILD-TYPE	98	15	33

Figure S20. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q24.2' versus 'Time to Death'

P value = 3.61e-05 (logrank test), Q value = 0.0081

Table S21. Gene #19: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 13(11Q24.2) MUTATED	16	6	0.1 - 123.6 (9.9)
DEL PEAK 13(11Q24.2) WILD-TYPE	134	11	0.0 - 194.8 (14.5)

Figure S21. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'

'del_11q24.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000152 (Fisher's exact test), Q value = 0.033

Table S22. Gene #19: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 13(11Q24.2) MUTATED	3	2	8	4
DEL PEAK 13(11Q24.2) WILD-TYPE	92	9	29	6

Figure S22. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.000633 (Fisher's exact test), Q value = 0.13

Table S23. Gene #19: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 13(11Q24.2) MUTATED	4	2	11
DEL PEAK 13(11Q24.2) WILD-TYPE	98	15	33

Figure S23. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_15q15.2' versus 'Time to Death'

P value = 2.86e-07 (logrank test), Q value = 6.6e-05

Table S24. Gene #22: 'del_15q15.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 16(15Q15.2) MUTATED	20	7	0.1 - 194.8 (8.2)
DEL PEAK 16(15Q15.2) WILD-TYPE	130	10	0.0 - 129.9 (14.6)

Figure S24. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #1: 'Time to Death'

'del_15q15.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000171 (Fisher's exact test), Q value = 0.037

Table S25. Gene #22: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 16(15Q15.2) MUTATED	5	1	9	5
DEL PEAK 16(15Q15.2) WILD-TYPE	90	10	28	5

Figure S25. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_15q15.2' versus 'PATHOLOGY.T.STAGE'

P value = 0.000141 (Fisher's exact test), Q value = 0.031

Table S26. Gene #22: 'del_15q15.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 16(15Q15.2) MUTATED	6	1	14
DEL PEAK 16(15Q15.2) WILD-TYPE	96	16	30

Figure S26. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_16q24.1' versus 'Time to Death'

P value = 1.82e-06 (logrank test), Q value = 0.00042

Table S27. Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 17(16Q24.1) MUTATED	6	3	0.7 - 21.6 (9.5)
DEL PEAK 17(16Q24.1) WILD-TYPE	144	14	0.0 - 194.8 (14.5)

Figure S27. Get High-res Image Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

'del_xp11.22' versus 'Time to Death'

P value = 0.000314 (logrank test), Q value = 0.066

Table S28. Gene #27: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 21(XP11.22) MUTATED	17	5	0.1 - 79.9 (10.1)
DEL PEAK 21(XP11.22) WILD-TYPE	133	12	0.0 - 194.8 (14.4)

Figure S28. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'

'del_xp11.22' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000432 (Fisher's exact test), Q value = 0.089

Table S29. Gene #27: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	95	11	37	10
DEL PEAK 21(XP11.22) MUTATED	3	1	10	2
DEL PEAK 21(XP11.22) WILD-TYPE	92	10	27	8

Figure S29. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.000217 (Fisher's exact test), Q value = 0.046

Table S30. Gene #27: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3+T4
ALL	102	17	44
DEL PEAK 21(XP11.22) MUTATED	4	2	12
DEL PEAK 21(XP11.22) WILD-TYPE	98	15	32

Figure S30. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xq28' versus 'Time to Death'

P value = 5.1e-06 (logrank test), Q value = 0.0012

Table S31. Gene #28: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	150	17	0.0 - 194.8 (14.0)
DEL PEAK 22(XQ28) MUTATED	16	5	0.1 - 25.1 (9.9)
DEL PEAK 22(XQ28) WILD-TYPE	134	12	0.0 - 194.8 (14.5)

Figure S31. Get High-res Image Gene #28: '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 = 163
Number of significantly focal cnvs = 28
Number of selected clinical features = 10
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

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)

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