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

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 12 clinical features across 528 patients, 73 significant findings detected with Q value < 0.25.

amp_1q24.1 cnv correlated to 'Time to Death'.
amp_1q32.1 cnv correlated to 'YEARS_TO_BIRTH'.
amp_3q26.32 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.
amp_5q35.1 cnv correlated to 'Time to Death', 'GENDER', and 'RACE'.
amp_7q31.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'GENDER'.
amp_8q24.22 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.
amp_10p14 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_T_STAGE'.
del_1p36.13 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
del_1p31.1 cnv correlated to 'PATHOLOGY_T_STAGE'.
del_3p25.3 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RACE'.
del_3p22.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'RACE'.
del_3p12.3 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.
del_3p12.2 cnv correlated to 'GENDER'.
del_3p11.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
del_3q11.2 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
del_4q34.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'RACE'.
del_6q26 cnv correlated to 'PATHOLOGY_N_STAGE', 'GENDER', and 'NUMBER_PACK_YEARS_SMOKED'.
del_6q26 cnv correlated to 'PATHOLOGY_N_STAGE', 'GENDER', and 'NUMBER_PACK_YEARS_SMOKED'.
del_8p23.2 cnv correlated to 'Time to Death' and 'ETHNICITY'.
del_9p23 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'GENDER'.
del_9p21.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', and 'GENDER'.
del_10q23.31 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.
del_13q13.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.
del_14q31.1 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 29 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 73 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	PATHOLOGIC STAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	KARNOFSKY PERFORMANCE SCORE	NUMBER PACK YEARS SMOKED	YEAR OF TOBACCO SMOKING ONSET	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	Wilcoxon-test	Fisher's exact test	Fisher's exact test
del 9p21 3	159 (30%)	369	4.25e-07 (7.4e-05)	0.0385 (0.205)	1e-05 (0.000435)	1e-05 (0.000435)	0.0126 (0.105)	0.000159 (0.00277)	0.000768 (0.00891)	0.315 (0.718)	0.91 (1.00)	0.935 (1.00)	0.0594 (0.265)	0.827 (1.00)
del 14q31 1	228 (43%)	300	0.000609 (0.00785)	0.0959 (0.346)	3e-05 (0.00087)	7e-05 (0.00152)	0.000258 (0.00408)	0.00114 (0.012)	0.17 (0.515)	0.0296 (0.181)	0.37 (0.767)	0.199 (0.528)	0.0395 (0.205)	1 (1.00)
del 9p23	152 (29%)	376	2.03e-05 (0.000642)	0.0226 (0.157)	1e-05 (0.000435)	2e-05 (0.000642)	0.0879 (0.338)	0.00173 (0.0172)	0.0019 (0.0184)	0.315 (0.718)	0.707 (0.988)	0.872 (1.00)	0.321 (0.725)	0.655 (0.958)
del 4q34 3	78 (15%)	450	0.000362 (0.00548)	0.56 (0.918)	1e-05 (0.000435)	1e-05 (0.000435)	0.714 (0.993)	0.0278 (0.179)	0.371 (0.767)	0.877 (1.00)			0.0247 (0.169)	0.579 (0.918)
amp 3q26 32	87 (16%)	441	0.106 (0.376)	0.991 (1.00)	5e-05 (0.00116)	0.00013 (0.00266)	0.0516 (0.246)	0.000414 (0.00577)	0.903 (1.00)	0.815 (1.00)	1 (1.00)		0.571 (0.918)	1 (1.00)
amp 7q31 2	175 (33%)	353	0.427 (0.818)	0.326 (0.733)	0.00766 (0.0684)	0.0395 (0.205)	0.306 (0.709)	0.00158 (0.0162)	0.016 (0.127)	0.138 (0.463)	0.154 (0.492)	0.233 (0.591)	0.081 (0.324)	0.27 (0.657)
amp 8q24 22	79 (15%)	449	0.0297 (0.181)	0.00692 (0.0634)	0.00111 (0.012)	0.00076 (0.00891)	0.728 (0.995)	0.0578 (0.265)	0.0747 (0.307)	0.523 (0.892)	0.8 (1.00)		0.256 (0.627)	0.229 (0.591)
amp 5q35 1	332 (63%)	196	0.041 (0.21)	0.183 (0.528)	0.343 (0.736)	0.241 (0.603)	0.192 (0.528)	0.306 (0.709)	0.0484 (0.234)	0.836 (1.00)	0.155 (0.492)	0.47 (0.847)	0.00254 (0.0239)	1 (1.00)
del 3p25 3	463 (88%)	65	0.88 (1.00)	0.512 (0.89)	0.0453 (0.222)	0.0011 (0.012)	1 (1.00)	0.848 (1.00)	0.783 (1.00)	0.279 (0.675)	0.619 (0.945)		5e-05 (0.00116)	1 (1.00)
del 3p22 2	465 (88%)	63	0.66 (0.962)	0.53 (0.896)	0.0182 (0.135)	0.0002 (0.00331)	1 (1.00)	0.563 (0.918)	0.89 (1.00)	0.482 (0.86)	0.619 (0.945)		1e-05 (0.000435)	1 (1.00)
del 6q26	151 (29%)	377	0.803 (1.00)	0.236 (0.595)	0.342 (0.736)	0.568 (0.918)	0.0177 (0.134)	0.588 (0.918)	0.0274 (0.179)	0.181 (0.528)	0.0337 (0.192)	0.643 (0.952)	0.0688 (0.292)	0.12 (0.414)
del 6q26	151 (29%)	377	0.826 (1.00)	0.194 (0.528)	0.341 (0.736)	0.568 (0.918)	0.0177 (0.134)	0.588 (0.918)	0.0161 (0.127)	0.181 (0.528)	0.0337 (0.192)	0.643 (0.952)	0.0702 (0.294)	0.12 (0.414)
del 13q13 3	81 (15%)	447	0.000668 (0.00831)	0.942 (1.00)	0.00015 (0.00275)	5e-05 (0.00116)	0.181 (0.528)	0.0652 (0.28)	0.802 (1.00)	0.665 (0.964)	0.478 (0.857)		0.0932 (0.345)	0.15 (0.487)
amp 10p14	20 (4%)	508	0.847 (1.00)	0.0424 (0.211)	0.189 (0.528)	0.0289 (0.181)	0.191 (0.528)	0.536 (0.896)	0.643 (0.952)	0.346 (0.737)			0.381 (0.781)	1 (1.00)
del 1p36 13	99 (19%)	429	0.0304 (0.182)	0.0362 (0.2)	0.629 (0.952)	0.365 (0.766)	0.763 (1.00)	1 (1.00)	0.163 (0.501)	0.46 (0.838)	0.919 (1.00)		1 (1.00)	0.315 (0.718)
del 3p12 3	339 (64%)	189	0.964 (1.00)	0.719 (0.993)	0.192 (0.528)	0.0268 (0.179)	0.192 (0.528)	0.441 (0.829)	0.000148 (0.00275)	0.69 (0.976)	0.913 (1.00)	0.871 (1.00)	0.13 (0.442)	1 (1.00)
del 3p11 1	237 (45%)	291	0.428 (0.818)	0.0419 (0.211)	0.635 (0.952)	0.704 (0.988)	0.805 (1.00)	0.386 (0.786)	1.67e-05 (0.000642)	0.5 (0.883)	0.523 (0.892)	0.684 (0.976)	0.703 (0.988)	0.415 (0.807)
del 3q11 2	161 (30%)	367	0.672 (0.966)	0.00991 (0.0862)	0.405 (0.8)	0.0885 (0.338)	0.409 (0.803)	0.689 (0.976)	8.29e-08 (2.88e-05)	0.164 (0.501)	0.588 (0.918)		0.19 (0.528)	0.372 (0.767)
del 8p23 2	154 (29%)	374	0.0325 (0.192)	0.131 (0.442)	0.0964 (0.346)	0.075 (0.307)	0.785 (1.00)	0.14 (0.466)	0.232 (0.591)	0.516 (0.892)	0.647 (0.954)	0.865 (1.00)	0.0541 (0.253)	0.0361 (0.2)
del 10q23 31	96 (18%)	432	0.198 (0.528)	0.46 (0.838)	0.0123 (0.105)	0.00038 (0.00551)	1 (1.00)	0.434 (0.825)	0.0593 (0.265)	0.792 (1.00)			0.147 (0.482)	0.427 (0.818)
amp 1q24 1	62 (12%)	466	0.0187 (0.136)	0.0803 (0.324)	0.117 (0.411)	0.0948 (0.346)	0.0624 (0.272)	0.194 (0.528)	0.575 (0.918)	0.401 (0.8)			0.534 (0.896)	0.52 (0.892)
amp 1q32 1	62 (12%)	466	0.0621 (0.272)	0.0211 (0.15)	0.0842 (0.329)	0.0828 (0.328)	0.462 (0.838)	0.352 (0.742)	0.575 (0.918)	0.401 (0.8)			0.532 (0.896)	0.2 (0.528)
del 1p31 1	77 (15%)	451	0.248 (0.617)	0.176 (0.528)	0.572 (0.918)	0.0388 (0.205)	0.3 (0.707)	0.73 (0.995)	0.0544 (0.253)	0.881 (1.00)			0.607 (0.939)	0.0916 (0.343)
del 3p12 2	305 (58%)	223	0.339 (0.736)	0.858 (1.00)	0.671 (0.966)	0.211 (0.548)	0.449 (0.836)	0.457 (0.838)	0.000479 (0.00642)	0.25 (0.618)	1 (1.00)	0.871 (1.00)	0.288 (0.686)	0.538 (0.896)
amp 4q32 1	16 (3%)	512	0.197 (0.528)	0.338 (0.736)	0.762 (1.00)	0.341 (0.736)	0.511 (0.89)	1 (1.00)	0.598 (0.929)	0.151 (0.487)			1 (1.00)	1 (1.00)
amp xq11 2	29 (5%)	499	0.643 (0.952)	0.297 (0.703)	0.287 (0.686)	0.347 (0.737)	1 (1.00)	0.411 (0.803)	1 (1.00)	0.587 (0.918)			0.0893 (0.338)	0.612 (0.943)
amp xq28	37 (7%)	491	0.556 (0.918)	0.504 (0.885)	0.456 (0.838)	0.643 (0.952)	1 (1.00)	0.211 (0.548)	0.859 (1.00)	0.331 (0.736)			1 (1.00)	0.394 (0.797)
del 1q44	44 (8%)	484	0.774 (1.00)	0.444 (0.831)	0.921 (1.00)	0.157 (0.493)	1 (1.00)	1 (1.00)	1 (1.00)	0.655 (0.958)			0.726 (0.995)	0.732 (0.995)
del 2q37 3	50 (9%)	478	0.88 (1.00)	0.718 (0.993)	0.44 (0.829)	0.688 (0.976)	1 (1.00)	0.403 (0.8)	0.163 (0.501)				0.761 (1.00)	0.492 (0.874)

'amp_1q24.1' versus 'Time to Death'

P value = 0.0187 (logrank test), Q value = 0.14

Table S1. Gene #1: 'amp_1q24.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
AMP PEAK 1(1Q24.1) MUTATED	62	29	0.4 - 129.4 (28.9)
AMP PEAK 1(1Q24.1) WILD-TYPE	464	146	0.1 - 149.2 (39.7)

Figure S1. Get High-res Image Gene #1: 'amp_1q24.1' versus Clinical Feature #1: 'Time to Death'

'amp_1q32.1' versus 'YEARS_TO_BIRTH'

P value = 0.0211 (Wilcoxon-test), Q value = 0.15

Table S2. Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
AMP PEAK 2(1Q32.1) MUTATED	62	63.4 (11.9)
AMP PEAK 2(1Q32.1) WILD-TYPE	465	60.1 (12.1)

Figure S2. Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.32' versus 'PATHOLOGIC_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S3. Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
AMP PEAK 3(3Q26.32) MUTATED	28	6	26	27
AMP PEAK 3(3Q26.32) WILD-TYPE	234	51	98	56

Figure S3. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0027

Table S4. Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
AMP PEAK 3(3Q26.32) MUTATED	29	8	46	4
AMP PEAK 3(3Q26.32) WILD-TYPE	239	61	134	7

Figure S4. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_N_STAGE'

P value = 0.0516 (Fisher's exact test), Q value = 0.25

Table S5. Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	234	17
AMP PEAK 3(3Q26.32) MUTATED	43	7
AMP PEAK 3(3Q26.32) WILD-TYPE	191	10

Figure S5. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.000414 (Fisher's exact test), Q value = 0.0058

Table S6. Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	418	78
AMP PEAK 3(3Q26.32) MUTATED	59	25
AMP PEAK 3(3Q26.32) WILD-TYPE	359	53

Figure S6. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_5q35.1' versus 'Time to Death'

P value = 0.041 (logrank test), Q value = 0.21

Table S7. Gene #5: 'amp_5q35.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
AMP PEAK 5(5Q35.1) MUTATED	332	104	0.1 - 149.2 (43.6)
AMP PEAK 5(5Q35.1) WILD-TYPE	194	71	0.1 - 126.3 (33.7)

Figure S7. Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #1: 'Time to Death'

'amp_5q35.1' versus 'GENDER'

P value = 0.0484 (Fisher's exact test), Q value = 0.23

Table S8. Gene #5: 'amp_5q35.1' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
AMP PEAK 5(5Q35.1) MUTATED	108	224
AMP PEAK 5(5Q35.1) WILD-TYPE	81	115

Figure S8. Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #7: 'GENDER'

'amp_5q35.1' versus 'RACE'

P value = 0.00254 (Fisher's exact test), Q value = 0.024

Table S9. Gene #5: 'amp_5q35.1' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	8	56	457
AMP PEAK 5(5Q35.1) MUTATED	3	25	299
AMP PEAK 5(5Q35.1) WILD-TYPE	5	31	158

Figure S9. Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #11: 'RACE'

'amp_7q31.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00766 (Fisher's exact test), Q value = 0.068

Table S10. Gene #6: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
AMP PEAK 6(7Q31.2) MUTATED	74	16	44	40
AMP PEAK 6(7Q31.2) WILD-TYPE	188	41	80	43

Figure S10. Get High-res Image Gene #6: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q31.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0395 (Fisher's exact test), Q value = 0.21

Table S11. Gene #6: 'amp_7q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
AMP PEAK 6(7Q31.2) MUTATED	76	21	74	4
AMP PEAK 6(7Q31.2) WILD-TYPE	192	48	106	7

Figure S11. Get High-res Image Gene #6: 'amp_7q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_7q31.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00158 (Fisher's exact test), Q value = 0.016

Table S12. Gene #6: 'amp_7q31.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	418	78
AMP PEAK 6(7Q31.2) MUTATED	128	39
AMP PEAK 6(7Q31.2) WILD-TYPE	290	39

Figure S12. Get High-res Image Gene #6: 'amp_7q31.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_7q31.2' versus 'GENDER'

P value = 0.016 (Fisher's exact test), Q value = 0.13

Table S13. Gene #6: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
AMP PEAK 6(7Q31.2) MUTATED	50	125
AMP PEAK 6(7Q31.2) WILD-TYPE	139	214

Figure S13. Get High-res Image Gene #6: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

'amp_8q24.22' versus 'Time to Death'

P value = 0.0297 (logrank test), Q value = 0.18

Table S14. Gene #7: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
AMP PEAK 7(8Q24.22) MUTATED	79	33	0.5 - 115.7 (31.3)
AMP PEAK 7(8Q24.22) WILD-TYPE	447	142	0.1 - 149.2 (40.7)

Figure S14. Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

'amp_8q24.22' versus 'YEARS_TO_BIRTH'

P value = 0.00692 (Wilcoxon-test), Q value = 0.063

Table S15. Gene #7: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
AMP PEAK 7(8Q24.22) MUTATED	79	63.8 (11.4)
AMP PEAK 7(8Q24.22) WILD-TYPE	448	59.9 (12.1)

Figure S15. Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.22' versus 'PATHOLOGIC_STAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.012

Table S16. Gene #7: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
AMP PEAK 7(8Q24.22) MUTATED	23	11	25	19
AMP PEAK 7(8Q24.22) WILD-TYPE	239	46	99	64

Figure S16. Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_T_STAGE'

P value = 0.00076 (Fisher's exact test), Q value = 0.0089

Table S17. Gene #7: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
AMP PEAK 7(8Q24.22) MUTATED	24	12	41	2
AMP PEAK 7(8Q24.22) WILD-TYPE	244	57	139	9

Figure S17. Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_10p14' versus 'YEARS_TO_BIRTH'

P value = 0.0424 (Wilcoxon-test), Q value = 0.21

Table S18. Gene #8: 'amp_10p14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
AMP PEAK 8(10P14) MUTATED	20	65.5 (10.5)
AMP PEAK 8(10P14) WILD-TYPE	507	60.3 (12.1)

Figure S18. Get High-res Image Gene #8: 'amp_10p14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10p14' versus 'PATHOLOGY_T_STAGE'

P value = 0.0289 (Fisher's exact test), Q value = 0.18

Table S19. Gene #8: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
AMP PEAK 8(10P14) MUTATED	9	5	4	2
AMP PEAK 8(10P14) WILD-TYPE	259	64	176	9

Figure S19. Get High-res Image Gene #8: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.13' versus 'Time to Death'

P value = 0.0304 (logrank test), Q value = 0.18

Table S20. Gene #11: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
DEL PEAK 1(1P36.13) MUTATED	99	43	0.5 - 130.7 (40.0)
DEL PEAK 1(1P36.13) WILD-TYPE	427	132	0.1 - 149.2 (38.7)

Figure S20. Get High-res Image Gene #11: 'del_1p36.13' versus Clinical Feature #1: 'Time to Death'

'del_1p36.13' versus 'YEARS_TO_BIRTH'

P value = 0.0362 (Wilcoxon-test), Q value = 0.2

Table S21. Gene #11: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
DEL PEAK 1(1P36.13) MUTATED	99	62.7 (11.7)
DEL PEAK 1(1P36.13) WILD-TYPE	428	60.0 (12.2)

Figure S21. Get High-res Image Gene #11: 'del_1p36.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p31.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0388 (Fisher's exact test), Q value = 0.21

Table S22. Gene #12: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 2(1P31.1) MUTATED	38	12	22	5
DEL PEAK 2(1P31.1) WILD-TYPE	230	57	158	6

Figure S22. Get High-res Image Gene #12: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p25.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0453 (Fisher's exact test), Q value = 0.22

Table S23. Gene #15: 'del_3p25.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 5(3P25.3) MUTATED	222	49	117	73
DEL PEAK 5(3P25.3) WILD-TYPE	40	8	7	10

Figure S23. Get High-res Image Gene #15: 'del_3p25.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p25.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0011 (Fisher's exact test), Q value = 0.012

Table S24. Gene #15: 'del_3p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 5(3P25.3) MUTATED	228	61	168	6
DEL PEAK 5(3P25.3) WILD-TYPE	40	8	12	5

Figure S24. Get High-res Image Gene #15: 'del_3p25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p25.3' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S25. Gene #15: 'del_3p25.3' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	8	56	457
DEL PEAK 5(3P25.3) MUTATED	6	38	412
DEL PEAK 5(3P25.3) WILD-TYPE	2	18	45

Figure S25. Get High-res Image Gene #15: 'del_3p25.3' versus Clinical Feature #11: 'RACE'

'del_3p22.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0182 (Fisher's exact test), Q value = 0.14

Table S26. Gene #16: 'del_3p22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 6(3P22.2) MUTATED	222	49	118	74
DEL PEAK 6(3P22.2) WILD-TYPE	40	8	6	9

Figure S26. Get High-res Image Gene #16: 'del_3p22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p22.2' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0033

Table S27. Gene #16: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 6(3P22.2) MUTATED	228	61	170	6
DEL PEAK 6(3P22.2) WILD-TYPE	40	8	10	5

Figure S27. Get High-res Image Gene #16: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p22.2' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S28. Gene #16: 'del_3p22.2' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	8	56	457
DEL PEAK 6(3P22.2) MUTATED	6	38	414
DEL PEAK 6(3P22.2) WILD-TYPE	2	18	43

Figure S28. Get High-res Image Gene #16: 'del_3p22.2' versus Clinical Feature #11: 'RACE'

'del_3p12.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0268 (Fisher's exact test), Q value = 0.18

Table S29. Gene #17: 'del_3p12.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 7(3P12.3) MUTATED	165	48	123	3
DEL PEAK 7(3P12.3) WILD-TYPE	103	21	57	8

Figure S29. Get High-res Image Gene #17: 'del_3p12.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p12.3' versus 'GENDER'

P value = 0.000148 (Fisher's exact test), Q value = 0.0027

Table S30. Gene #17: 'del_3p12.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 7(3P12.3) MUTATED	101	238
DEL PEAK 7(3P12.3) WILD-TYPE	88	101

Figure S30. Get High-res Image Gene #17: 'del_3p12.3' versus Clinical Feature #7: 'GENDER'

'del_3p12.2' versus 'GENDER'

P value = 0.000479 (Fisher's exact test), Q value = 0.0064

Table S31. Gene #18: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 8(3P12.2) MUTATED	90	215
DEL PEAK 8(3P12.2) WILD-TYPE	99	124

Figure S31. Get High-res Image Gene #18: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

'del_3p11.1' versus 'YEARS_TO_BIRTH'

P value = 0.0419 (Wilcoxon-test), Q value = 0.21

Table S32. Gene #19: 'del_3p11.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
DEL PEAK 9(3P11.1) MUTATED	237	61.8 (12.3)
DEL PEAK 9(3P11.1) WILD-TYPE	290	59.5 (11.8)

Figure S32. Get High-res Image Gene #19: 'del_3p11.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p11.1' versus 'GENDER'

P value = 1.67e-05 (Fisher's exact test), Q value = 0.00064

Table S33. Gene #19: 'del_3p11.1' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 9(3P11.1) MUTATED	61	176
DEL PEAK 9(3P11.1) WILD-TYPE	128	163

Figure S33. Get High-res Image Gene #19: 'del_3p11.1' versus Clinical Feature #7: 'GENDER'

'del_3q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.00991 (Wilcoxon-test), Q value = 0.086

Table S34. Gene #20: 'del_3q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
DEL PEAK 10(3Q11.2) MUTATED	161	62.8 (12.9)
DEL PEAK 10(3Q11.2) WILD-TYPE	366	59.5 (11.6)

Figure S34. Get High-res Image Gene #20: 'del_3q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3q11.2' versus 'GENDER'

P value = 8.29e-08 (Fisher's exact test), Q value = 2.9e-05

Table S35. Gene #20: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 10(3Q11.2) MUTATED	31	130
DEL PEAK 10(3Q11.2) WILD-TYPE	158	209

Figure S35. Get High-res Image Gene #20: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'Time to Death'

P value = 0.000362 (logrank test), Q value = 0.0055

Table S36. Gene #21: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
DEL PEAK 11(4Q34.3) MUTATED	78	41	0.6 - 133.7 (38.5)
DEL PEAK 11(4Q34.3) WILD-TYPE	448	134	0.1 - 149.2 (39.1)

Figure S36. Get High-res Image Gene #21: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S37. Gene #21: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 11(4Q34.3) MUTATED	19	7	30	22
DEL PEAK 11(4Q34.3) WILD-TYPE	243	50	94	61

Figure S37. Get High-res Image Gene #21: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S38. Gene #21: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 11(4Q34.3) MUTATED	20	9	43	6
DEL PEAK 11(4Q34.3) WILD-TYPE	248	60	137	5

Figure S38. Get High-res Image Gene #21: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q34.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0278 (Fisher's exact test), Q value = 0.18

Table S39. Gene #21: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	418	78
DEL PEAK 11(4Q34.3) MUTATED	59	19
DEL PEAK 11(4Q34.3) WILD-TYPE	359	59

Figure S39. Get High-res Image Gene #21: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q34.3' versus 'RACE'

P value = 0.0247 (Fisher's exact test), Q value = 0.17

Table S40. Gene #21: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	8	56	457
DEL PEAK 11(4Q34.3) MUTATED	1	2	73
DEL PEAK 11(4Q34.3) WILD-TYPE	7	54	384

Figure S40. Get High-res Image Gene #21: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0177 (Fisher's exact test), Q value = 0.13

Table S41. Gene #22: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	234	17
DEL PEAK 12(6Q26) MUTATED	56	9
DEL PEAK 12(6Q26) WILD-TYPE	178	8

Figure S41. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'GENDER'

P value = 0.0274 (Fisher's exact test), Q value = 0.18

Table S42. Gene #22: 'del_6q26' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 12(6Q26) MUTATED	43	108
DEL PEAK 12(6Q26) WILD-TYPE	146	231

Figure S42. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #7: 'GENDER'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0337 (Wilcoxon-test), Q value = 0.19

Table S43. Gene #22: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	21	28.3 (16.1)
DEL PEAK 12(6Q26) MUTATED	5	16.0 (13.7)
DEL PEAK 12(6Q26) WILD-TYPE	16	32.2 (15.2)

Figure S43. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0177 (Fisher's exact test), Q value = 0.13

Table S44. Gene #23: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	234	17
DEL PEAK 13(6Q26) MUTATED	56	9
DEL PEAK 13(6Q26) WILD-TYPE	178	8

Figure S44. Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'GENDER'

P value = 0.0161 (Fisher's exact test), Q value = 0.13

Table S45. Gene #23: 'del_6q26' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 13(6Q26) MUTATED	42	109
DEL PEAK 13(6Q26) WILD-TYPE	147	230

Figure S45. Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #7: 'GENDER'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0337 (Wilcoxon-test), Q value = 0.19

Table S46. Gene #23: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	21	28.3 (16.1)
DEL PEAK 13(6Q26) MUTATED	5	16.0 (13.7)
DEL PEAK 13(6Q26) WILD-TYPE	16	32.2 (15.2)

Figure S46. Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

'del_8p23.2' versus 'Time to Death'

P value = 0.0325 (logrank test), Q value = 0.19

Table S47. Gene #24: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
DEL PEAK 14(8P23.2) MUTATED	154	61	0.1 - 118.8 (37.1)
DEL PEAK 14(8P23.2) WILD-TYPE	372	114	0.1 - 149.2 (41.7)

Figure S47. Get High-res Image Gene #24: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'ETHNICITY'

P value = 0.0361 (Fisher's exact test), Q value = 0.2

Table S48. Gene #24: 'del_8p23.2' versus Clinical Feature #12: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	26	350
DEL PEAK 14(8P23.2) MUTATED	12	89
DEL PEAK 14(8P23.2) WILD-TYPE	14	261

Figure S48. Get High-res Image Gene #24: 'del_8p23.2' versus Clinical Feature #12: 'ETHNICITY'

'del_9p23' versus 'Time to Death'

P value = 2.03e-05 (logrank test), Q value = 0.00064

Table S49. Gene #25: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
DEL PEAK 15(9P23) MUTATED	151	73	0.5 - 133.7 (39.2)
DEL PEAK 15(9P23) WILD-TYPE	375	102	0.1 - 149.2 (38.7)

Figure S49. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.0226 (Wilcoxon-test), Q value = 0.16

Table S50. Gene #25: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
DEL PEAK 15(9P23) MUTATED	151	62.3 (11.7)
DEL PEAK 15(9P23) WILD-TYPE	376	59.8 (12.2)

Figure S50. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S51. Gene #25: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 15(9P23) MUTATED	51	12	49	38
DEL PEAK 15(9P23) WILD-TYPE	211	45	75	45

Figure S51. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00064

Table S52. Gene #25: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 15(9P23) MUTATED	55	16	76	5
DEL PEAK 15(9P23) WILD-TYPE	213	53	104	6

Figure S52. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_M_STAGE'

P value = 0.00173 (Fisher's exact test), Q value = 0.017

Table S53. Gene #25: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	418	78
DEL PEAK 15(9P23) MUTATED	111	35
DEL PEAK 15(9P23) WILD-TYPE	307	43

Figure S53. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'GENDER'

P value = 0.0019 (Fisher's exact test), Q value = 0.018

Table S54. Gene #25: 'del_9p23' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 15(9P23) MUTATED	39	113
DEL PEAK 15(9P23) WILD-TYPE	150	226

Figure S54. Get High-res Image Gene #25: 'del_9p23' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'Time to Death'

P value = 4.25e-07 (logrank test), Q value = 7.4e-05

Table S55. Gene #26: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
DEL PEAK 16(9P21.3) MUTATED	158	79	0.5 - 133.7 (37.8)
DEL PEAK 16(9P21.3) WILD-TYPE	368	96	0.1 - 149.2 (40.8)

Figure S55. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.0385 (Wilcoxon-test), Q value = 0.21

Table S56. Gene #26: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	527	60.5 (12.1)
DEL PEAK 16(9P21.3) MUTATED	158	62.1 (11.6)
DEL PEAK 16(9P21.3) WILD-TYPE	369	59.8 (12.3)

Figure S56. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S57. Gene #26: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 16(9P21.3) MUTATED	52	11	53	41
DEL PEAK 16(9P21.3) WILD-TYPE	210	46	71	42

Figure S57. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S58. Gene #26: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 16(9P21.3) MUTATED	56	15	82	6
DEL PEAK 16(9P21.3) WILD-TYPE	212	54	98	5

Figure S58. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0126 (Fisher's exact test), Q value = 0.1

Table S59. Gene #26: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	234	17
DEL PEAK 16(9P21.3) MUTATED	66	10
DEL PEAK 16(9P21.3) WILD-TYPE	168	7

Figure S59. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.000159 (Fisher's exact test), Q value = 0.0028

Table S60. Gene #26: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	418	78
DEL PEAK 16(9P21.3) MUTATED	115	39
DEL PEAK 16(9P21.3) WILD-TYPE	303	39

Figure S60. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.000768 (Fisher's exact test), Q value = 0.0089

Table S61. Gene #26: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	189	339
DEL PEAK 16(9P21.3) MUTATED	40	119
DEL PEAK 16(9P21.3) WILD-TYPE	149	220

Figure S61. Get High-res Image Gene #26: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_10q23.31' versus 'PATHOLOGIC_STAGE'

P value = 0.0123 (Fisher's exact test), Q value = 0.1

Table S62. Gene #27: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 17(10Q23.31) MUTATED	34	11	31	20
DEL PEAK 17(10Q23.31) WILD-TYPE	228	46	93	63

Figure S62. Get High-res Image Gene #27: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00038 (Fisher's exact test), Q value = 0.0055

Table S63. Gene #27: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 17(10Q23.31) MUTATED	34	12	44	6
DEL PEAK 17(10Q23.31) WILD-TYPE	234	57	136	5

Figure S63. Get High-res Image Gene #27: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q13.3' versus 'Time to Death'

P value = 0.000668 (logrank test), Q value = 0.0083

Table S64. Gene #28: 'del_13q13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
DEL PEAK 18(13Q13.3) MUTATED	80	38	0.5 - 112.1 (31.5)
DEL PEAK 18(13Q13.3) WILD-TYPE	446	137	0.1 - 149.2 (41.2)

Figure S64. Get High-res Image Gene #28: 'del_13q13.3' versus Clinical Feature #1: 'Time to Death'

'del_13q13.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0027

Table S65. Gene #28: 'del_13q13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 18(13Q13.3) MUTATED	27	4	29	21
DEL PEAK 18(13Q13.3) WILD-TYPE	235	53	95	62

Figure S65. Get High-res Image Gene #28: 'del_13q13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_13q13.3' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

Table S66. Gene #28: 'del_13q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 18(13Q13.3) MUTATED	29	5	41	6
DEL PEAK 18(13Q13.3) WILD-TYPE	239	64	139	5

Figure S66. Get High-res Image Gene #28: 'del_13q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q31.1' versus 'Time to Death'

P value = 0.000609 (logrank test), Q value = 0.0078

Table S67. Gene #29: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	526	175	0.1 - 149.2 (38.8)
DEL PEAK 19(14Q31.1) MUTATED	227	97	0.4 - 133.7 (36.8)
DEL PEAK 19(14Q31.1) WILD-TYPE	299	78	0.1 - 149.2 (42.7)

Figure S67. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

'del_14q31.1' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00087

Table S68. Gene #29: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	262	57	124	83
DEL PEAK 19(14Q31.1) MUTATED	85	27	65	49
DEL PEAK 19(14Q31.1) WILD-TYPE	177	30	59	34

Figure S68. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_14q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0015

Table S69. Gene #29: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	268	69	180	11
DEL PEAK 19(14Q31.1) MUTATED	91	35	98	4
DEL PEAK 19(14Q31.1) WILD-TYPE	177	34	82	7

Figure S69. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.000258 (Fisher's exact test), Q value = 0.0041

Table S70. Gene #29: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	234	17
DEL PEAK 19(14Q31.1) MUTATED	100	15
DEL PEAK 19(14Q31.1) WILD-TYPE	134	2

Figure S70. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q31.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00114 (Fisher's exact test), Q value = 0.012

Table S71. Gene #29: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	418	78
DEL PEAK 19(14Q31.1) MUTATED	171	48
DEL PEAK 19(14Q31.1) WILD-TYPE	247	30

Figure S71. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0296 (Wilcoxon-test), Q value = 0.18

Table S72. Gene #29: 'del_14q31.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	54	85.6 (25.8)
DEL PEAK 19(14Q31.1) MUTATED	21	72.4 (37.5)
DEL PEAK 19(14Q31.1) WILD-TYPE	33	93.9 (6.1)

Figure S72. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q31.1' versus 'RACE'

P value = 0.0395 (Fisher's exact test), Q value = 0.21

Table S73. Gene #29: 'del_14q31.1' versus Clinical Feature #11: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	8	56	457
DEL PEAK 19(14Q31.1) MUTATED	2	16	206
DEL PEAK 19(14Q31.1) WILD-TYPE	6	40	251

Figure S73. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #11: 'RACE'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/22531283/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/22506714/KIRC-TP.merged_data.txt
Number of patients = 528
Number of significantly focal cnvs = 29
Number of selected clinical features = 12
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.

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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