Correlation between copy number variation genes (focal) 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 subtypes identified by 43 different clustering approaches and 6 clinical features across 207 patients, 15 significant findings detected with Q value < 0.25.

2 subtypes identified in current cancer cohort by 'Amp Peak 1(1q32.1) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 2(4q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 3(7p11.2) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 4(7q32.3) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 5(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 6(10p15.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 7(10q11.21) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 8(11q23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 9(12p13.32) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 10(12p11.22) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 11(12q14.1) mutation analysis'. These subtypes correlate to 'Time to Death'.
2 subtypes identified in current cancer cohort by 'Amp Peak 12(19p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 13(19q13.2) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 14(Xp22.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 15(Xq11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.31) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
2 subtypes identified in current cancer cohort by 'Del Peak 2(1p32.3) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE' and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
2 subtypes identified in current cancer cohort by 'Del Peak 3(1q43) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 4(2q37.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 5(3p21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 6(3q29) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 7(4q33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 8(4q35.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 9(5q35.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 10(6p24.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 11(6q24.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 12(8p23.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 13(9p21.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'AGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
2 subtypes identified in current cancer cohort by 'Del Peak 14(10q26.2) mutation analysis'. These subtypes correlate to 'Time to Death'.
2 subtypes identified in current cancer cohort by 'Del Peak 15(11p15.5) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 16(11q25) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 17(12q24.11) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 18(13q14.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 19(13q34) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 20(14q24.3) mutation analysis'. These subtypes correlate to 'Time to Death'.
2 subtypes identified in current cancer cohort by 'Del Peak 21(15q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 22(17q25.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 23(18p11.32) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 24(18q23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 25(19q13.42) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
2 subtypes identified in current cancer cohort by 'Del Peak 26(22q13.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 27(Xp22.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 28(Xq21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between subtypes identified by 43 different clustering approaches and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.


Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION
Statistical Tests	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test
Amp Peak 1(1q32 1)	0.0615 (1.00)	0.000116 (0.0288)	0.378 (1.00)	0.0855 (1.00)	0.182 (1.00)	0.377 (1.00)
Amp Peak 2(4q12)	0.953 (1.00)	0.606 (1.00)	0.748 (1.00)	0.325 (1.00)	0.0461 (1.00)	0.748 (1.00)
Amp Peak 3(7p11 2)	0.00366 (0.868)	0.000626 (0.153)	0.109 (1.00)	0.604 (1.00)	0.0547 (1.00)	0.34 (1.00)
Amp Peak 4(7q32 3)	0.247 (1.00)	8.46e-05 (0.0212)	0.0283 (1.00)	0.844 (1.00)	0.384 (1.00)	0.0416 (1.00)
Amp Peak 5(8q24 21)	0.903 (1.00)	0.56 (1.00)	0.0837 (1.00)	0.332 (1.00)	0.011 (1.00)	0.119 (1.00)
Amp Peak 6(10p15 1)	0.739 (1.00)	0.00528 (1.00)	0.127 (1.00)	0.636 (1.00)	0.00415 (0.976)	0.255 (1.00)
Amp Peak 7(10q11 21)	0.782 (1.00)	0.692 (1.00)	0.636 (1.00)		0.0125 (1.00)	1 (1.00)
Amp Peak 8(11q23 3)	0.605 (1.00)	0.0473 (1.00)	0.349 (1.00)	0.568 (1.00)	0.35 (1.00)	0.266 (1.00)
Amp Peak 9(12p13 32)	0.899 (1.00)	0.0809 (1.00)	0.176 (1.00)	0.47 (1.00)	0.486 (1.00)	0.848 (1.00)
Amp Peak 10(12p11 22)	0.906 (1.00)	0.193 (1.00)	0.0521 (1.00)	0.448 (1.00)	0.297 (1.00)	0.631 (1.00)
Amp Peak 11(12q14 1)	1.49e-05 (0.00378)	0.0516 (1.00)	0.564 (1.00)	0.466 (1.00)	0.117 (1.00)	0.568 (1.00)
Amp Peak 12(19p13 3)	0.828 (1.00)	0.0993 (1.00)	0.869 (1.00)	0.338 (1.00)	0.0146 (1.00)	0.744 (1.00)
Amp Peak 13(19q13 2)	6.78e-05 (0.0171)	0.00011 (0.0274)	0.792 (1.00)	0.508 (1.00)	0.396 (1.00)	0.593 (1.00)
Amp Peak 14(Xp22 33)	0.579 (1.00)	0.877 (1.00)	1 (1.00)	0.611 (1.00)	0.00384 (0.905)	0.407 (1.00)
Amp Peak 15(Xq11 2)	0.666 (1.00)	0.451 (1.00)	0.163 (1.00)	0.687 (1.00)	0.00489 (1.00)	0.424 (1.00)
Del Peak 1(1p36 31)	0.93 (1.00)	0.00114 (0.276)	0.474 (1.00)	0.85 (1.00)	7.71e-13 (1.97e-10)	0.00432 (1.00)
Del Peak 2(1p32 3)	0.139 (1.00)	0.0029 (0.691)	0.771 (1.00)	0.952 (1.00)	7.56e-15 (1.94e-12)	0.000489 (0.12)
Del Peak 3(1q43)	0.942 (1.00)	0.546 (1.00)	0.369 (1.00)	0.244 (1.00)	0.491 (1.00)	0.768 (1.00)
Del Peak 4(2q37 3)	0.818 (1.00)	0.0889 (1.00)	1 (1.00)	0.542 (1.00)	0.114 (1.00)	0.242 (1.00)
Del Peak 5(3p21 1)	0.288 (1.00)	0.0149 (1.00)	0.634 (1.00)	0.674 (1.00)	0.362 (1.00)	0.147 (1.00)
Del Peak 6(3q29)	0.381 (1.00)	0.655 (1.00)	0.1 (1.00)	0.0446 (1.00)	0.159 (1.00)	0.481 (1.00)
Del Peak 7(4q33)	0.614 (1.00)	0.813 (1.00)	0.164 (1.00)	0.532 (1.00)	0.133 (1.00)	0.284 (1.00)
Del Peak 8(4q35 2)	0.56 (1.00)	0.759 (1.00)	0.125 (1.00)	0.663 (1.00)	0.0924 (1.00)	0.361 (1.00)
Del Peak 9(5q35 2)	0.0993 (1.00)	0.34 (1.00)	0.305 (1.00)	0.31 (1.00)	0.11 (1.00)	0.0376 (1.00)
Del Peak 10(6p24 1)	0.0458 (1.00)	0.525 (1.00)	0.31 (1.00)	0.698 (1.00)	0.00129 (0.31)	0.127 (1.00)
Del Peak 11(6q24 3)	0.0186 (1.00)	0.482 (1.00)	0.43 (1.00)	0.56 (1.00)	0.0243 (1.00)	0.0026 (0.62)
Del Peak 12(8p23 2)	0.362 (1.00)	0.514 (1.00)	1 (1.00)	0.249 (1.00)	0.133 (1.00)	0.332 (1.00)
Del Peak 13(9p21 3)	3.01e-05 (0.00761)	0.000488 (0.12)	1 (1.00)	0.367 (1.00)	0.0451 (1.00)	0.000267 (0.0659)
Del Peak 14(10q26 2)	0.000151 (0.0374)	0.0104 (1.00)	0.0717 (1.00)	0.33 (1.00)	0.0167 (1.00)	0.765 (1.00)
Del Peak 15(11p15 5)	0.381 (1.00)	0.0493 (1.00)	0.0598 (1.00)	0.671 (1.00)	0.00928 (1.00)	0.304 (1.00)
Del Peak 16(11q25)	0.0051 (1.00)	0.944 (1.00)	0.246 (1.00)	0.864 (1.00)	0.623 (1.00)	0.568 (1.00)
Del Peak 17(12q24 11)	0.861 (1.00)	0.286 (1.00)	0.305 (1.00)	0.34 (1.00)	0.11 (1.00)	0.681 (1.00)
Del Peak 18(13q14 2)	0.462 (1.00)	0.853 (1.00)	0.648 (1.00)	0.0725 (1.00)	0.0745 (1.00)	0.095 (1.00)
Del Peak 19(13q34)	0.361 (1.00)	0.528 (1.00)	0.506 (1.00)	0.433 (1.00)	0.551 (1.00)	0.138 (1.00)
Del Peak 20(14q24 3)	0.000981 (0.238)	0.184 (1.00)	0.0455 (1.00)	0.994 (1.00)	0.0652 (1.00)	0.411 (1.00)
Del Peak 21(15q21 3)	0.15 (1.00)	0.34 (1.00)	1 (1.00)	0.212 (1.00)	0.646 (1.00)	0.681 (1.00)
Del Peak 22(17q25 3)	0.606 (1.00)	0.454 (1.00)	0.761 (1.00)	0.731 (1.00)	1 (1.00)	1 (1.00)
Del Peak 23(18p11 32)	0.822 (1.00)	0.852 (1.00)	0.225 (1.00)	0.349 (1.00)	0.875 (1.00)	0.0439 (1.00)
Del Peak 24(18q23)	0.722 (1.00)	0.383 (1.00)	0.699 (1.00)	0.843 (1.00)	0.876 (1.00)	0.0826 (1.00)
Del Peak 25(19q13 42)	0.0266 (1.00)	0.629 (1.00)	0.888 (1.00)	0.566 (1.00)	9.51e-08 (2.42e-05)	0.889 (1.00)
Del Peak 26(22q13 31)	0.116 (1.00)	0.281 (1.00)	0.319 (1.00)	0.733 (1.00)	0.0023 (0.552)	1 (1.00)
Del Peak 27(Xp22 31)	0.54 (1.00)	0.489 (1.00)	0.319 (1.00)	0.675 (1.00)	0.831 (1.00)	0.411 (1.00)
Del Peak 28(Xq21 1)	0.582 (1.00)	0.233 (1.00)	0.55 (1.00)	0.957 (1.00)	0.206 (1.00)	0.844 (1.00)

Clustering Approach #1: 'Amp Peak 1(1q32.1) mutation analysis'

Table S1. Description of clustering approach #1: 'Amp Peak 1(1q32.1) mutation analysis'

Cluster Labels	AMP PEAK 1(1Q32.1) MUTATED	AMP PEAK 1(1Q32.1) WILD-TYPE
Number of samples	23	184

'Amp Peak 1(1q32.1) mutation analysis' versus 'AGE'

P value = 0.000116 (t-test), Q value = 0.029

Table S2. Clustering Approach #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	207	43.1 (13.4)
AMP PEAK 1(1Q32.1) MUTATED	23	53.2 (11.4)
AMP PEAK 1(1Q32.1) WILD-TYPE	184	41.8 (13.1)

Figure S1. Get High-res Image Clustering Approach #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #2: 'Amp Peak 2(4q12) mutation analysis'

Table S3. Description of clustering approach #2: 'Amp Peak 2(4q12) mutation analysis'

Cluster Labels	AMP PEAK 2(4Q12) MUTATED	AMP PEAK 2(4Q12) WILD-TYPE
Number of samples	10	197

Clustering Approach #3: 'Amp Peak 3(7p11.2) mutation analysis'

Table S4. Description of clustering approach #3: 'Amp Peak 3(7p11.2) mutation analysis'

Cluster Labels	AMP PEAK 3(7P11.2) MUTATED	AMP PEAK 3(7P11.2) WILD-TYPE
Number of samples	53	154

'Amp Peak 3(7p11.2) mutation analysis' versus 'AGE'

P value = 0.000626 (t-test), Q value = 0.15

Table S5. Clustering Approach #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	207	43.1 (13.4)
AMP PEAK 3(7P11.2) MUTATED	53	48.7 (13.4)
AMP PEAK 3(7P11.2) WILD-TYPE	154	41.2 (12.9)

Figure S2. Get High-res Image Clustering Approach #3: 'Amp Peak 3(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #4: 'Amp Peak 4(7q32.3) mutation analysis'

Table S6. Description of clustering approach #4: 'Amp Peak 4(7q32.3) mutation analysis'

Cluster Labels	AMP PEAK 4(7Q32.3) MUTATED	AMP PEAK 4(7Q32.3) WILD-TYPE
Number of samples	73	134

'Amp Peak 4(7q32.3) mutation analysis' versus 'AGE'

P value = 8.46e-05 (t-test), Q value = 0.021

Table S7. Clustering Approach #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	207	43.1 (13.4)
AMP PEAK 4(7Q32.3) MUTATED	73	48.1 (13.1)
AMP PEAK 4(7Q32.3) WILD-TYPE	134	40.4 (12.9)

Figure S3. Get High-res Image Clustering Approach #4: 'Amp Peak 4(7q32.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #5: 'Amp Peak 5(8q24.21) mutation analysis'

Table S8. Description of clustering approach #5: 'Amp Peak 5(8q24.21) mutation analysis'

Cluster Labels	AMP PEAK 5(8Q24.21) MUTATED	AMP PEAK 5(8Q24.21) WILD-TYPE
Number of samples	42	165

Clustering Approach #6: 'Amp Peak 6(10p15.1) mutation analysis'

Table S9. Description of clustering approach #6: 'Amp Peak 6(10p15.1) mutation analysis'

Cluster Labels	AMP PEAK 6(10P15.1) MUTATED	AMP PEAK 6(10P15.1) WILD-TYPE
Number of samples	33	174

Clustering Approach #7: 'Amp Peak 7(10q11.21) mutation analysis'

Table S10. Description of clustering approach #7: 'Amp Peak 7(10q11.21) mutation analysis'

Cluster Labels	AMP PEAK 7(10Q11.21) MUTATED	AMP PEAK 7(10Q11.21) WILD-TYPE
Number of samples	4	203

Clustering Approach #8: 'Amp Peak 8(11q23.3) mutation analysis'

Table S11. Description of clustering approach #8: 'Amp Peak 8(11q23.3) mutation analysis'

Cluster Labels	AMP PEAK 8(11Q23.3) MUTATED	AMP PEAK 8(11Q23.3) WILD-TYPE
Number of samples	35	172

Clustering Approach #9: 'Amp Peak 9(12p13.32) mutation analysis'

Table S12. Description of clustering approach #9: 'Amp Peak 9(12p13.32) mutation analysis'

Cluster Labels	AMP PEAK 9(12P13.32) MUTATED	AMP PEAK 9(12P13.32) WILD-TYPE
Number of samples	32	175

Clustering Approach #10: 'Amp Peak 10(12p11.22) mutation analysis'

Table S13. Description of clustering approach #10: 'Amp Peak 10(12p11.22) mutation analysis'

Cluster Labels	AMP PEAK 10(12P11.22) MUTATED	AMP PEAK 10(12P11.22) WILD-TYPE
Number of samples	19	188

Clustering Approach #11: 'Amp Peak 11(12q14.1) mutation analysis'

Table S14. Description of clustering approach #11: 'Amp Peak 11(12q14.1) mutation analysis'

Cluster Labels	AMP PEAK 11(12Q14.1) MUTATED	AMP PEAK 11(12Q14.1) WILD-TYPE
Number of samples	13	194

'Amp Peak 11(12q14.1) mutation analysis' versus 'Time to Death'

P value = 1.49e-05 (logrank test), Q value = 0.0038

Table S15. Clustering Approach #11: 'Amp Peak 11(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	206	51	0.0 - 211.2 (13.4)
AMP PEAK 11(12Q14.1) MUTATED	13	9	1.2 - 80.0 (12.4)
AMP PEAK 11(12Q14.1) WILD-TYPE	193	42	0.0 - 211.2 (13.4)

Figure S4. Get High-res Image Clustering Approach #11: 'Amp Peak 11(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

Clustering Approach #12: 'Amp Peak 12(19p13.3) mutation analysis'

Table S16. Description of clustering approach #12: 'Amp Peak 12(19p13.3) mutation analysis'

Cluster Labels	AMP PEAK 12(19P13.3) MUTATED	AMP PEAK 12(19P13.3) WILD-TYPE
Number of samples	48	159

Clustering Approach #13: 'Amp Peak 13(19q13.2) mutation analysis'

Table S17. Description of clustering approach #13: 'Amp Peak 13(19q13.2) mutation analysis'

Cluster Labels	AMP PEAK 13(19Q13.2) MUTATED	AMP PEAK 13(19Q13.2) WILD-TYPE
Number of samples	15	192

'Amp Peak 13(19q13.2) mutation analysis' versus 'Time to Death'

P value = 6.78e-05 (logrank test), Q value = 0.017

Table S18. Clustering Approach #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	206	51	0.0 - 211.2 (13.4)
AMP PEAK 13(19Q13.2) MUTATED	15	6	0.0 - 43.9 (10.6)
AMP PEAK 13(19Q13.2) WILD-TYPE	191	45	0.1 - 211.2 (14.3)

Figure S5. Get High-res Image Clustering Approach #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 13(19q13.2) mutation analysis' versus 'AGE'

P value = 0.00011 (t-test), Q value = 0.027

Table S19. Clustering Approach #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	207	43.1 (13.4)
AMP PEAK 13(19Q13.2) MUTATED	15	53.1 (8.0)
AMP PEAK 13(19Q13.2) WILD-TYPE	192	42.3 (13.5)

Figure S6. Get High-res Image Clustering Approach #13: 'Amp Peak 13(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #14: 'Amp Peak 14(Xp22.33) mutation analysis'

Table S20. Description of clustering approach #14: 'Amp Peak 14(Xp22.33) mutation analysis'

Cluster Labels	AMP PEAK 14(XP22.33) MUTATED	AMP PEAK 14(XP22.33) WILD-TYPE
Number of samples	14	193

Clustering Approach #15: 'Amp Peak 15(Xq11.2) mutation analysis'

Table S21. Description of clustering approach #15: 'Amp Peak 15(Xq11.2) mutation analysis'

Cluster Labels	AMP PEAK 15(XQ11.2) MUTATED	AMP PEAK 15(XQ11.2) WILD-TYPE
Number of samples	29	178

Clustering Approach #16: 'Del Peak 1(1p36.31) mutation analysis'

Table S22. Description of clustering approach #16: 'Del Peak 1(1p36.31) mutation analysis'

Cluster Labels	DEL PEAK 1(1P36.31) MUTATED	DEL PEAK 1(1P36.31) WILD-TYPE
Number of samples	80	127

'Del Peak 1(1p36.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.71e-13 (Fisher's exact test), Q value = 2e-10

Table S23. Clustering Approach #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	63	54	89
DEL PEAK 1(1P36.31) MUTATED	9	11	60
DEL PEAK 1(1P36.31) WILD-TYPE	54	43	29

Figure S7. Get High-res Image Clustering Approach #16: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Clustering Approach #17: 'Del Peak 2(1p32.3) mutation analysis'

Table S24. Description of clustering approach #17: 'Del Peak 2(1p32.3) mutation analysis'

Cluster Labels	DEL PEAK 2(1P32.3) MUTATED	DEL PEAK 2(1P32.3) WILD-TYPE
Number of samples	74	133

'Del Peak 2(1p32.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.56e-15 (Fisher's exact test), Q value = 1.9e-12

Table S25. Clustering Approach #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	63	54	89
DEL PEAK 2(1P32.3) MUTATED	7	8	59
DEL PEAK 2(1P32.3) WILD-TYPE	56	46	30

Figure S8. Get High-res Image Clustering Approach #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 2(1p32.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000489 (Fisher's exact test), Q value = 0.12

Table S26. Clustering Approach #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	104	103
DEL PEAK 2(1P32.3) MUTATED	25	49
DEL PEAK 2(1P32.3) WILD-TYPE	79	54

Figure S9. Get High-res Image Clustering Approach #17: 'Del Peak 2(1p32.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #18: 'Del Peak 3(1q43) mutation analysis'

Table S27. Description of clustering approach #18: 'Del Peak 3(1q43) mutation analysis'

Cluster Labels	DEL PEAK 3(1Q43) MUTATED	DEL PEAK 3(1Q43) WILD-TYPE
Number of samples	12	195

Clustering Approach #19: 'Del Peak 4(2q37.3) mutation analysis'

Table S28. Description of clustering approach #19: 'Del Peak 4(2q37.3) mutation analysis'

Cluster Labels	DEL PEAK 4(2Q37.3) MUTATED	DEL PEAK 4(2Q37.3) WILD-TYPE
Number of samples	31	176

Clustering Approach #20: 'Del Peak 5(3p21.1) mutation analysis'

Table S29. Description of clustering approach #20: 'Del Peak 5(3p21.1) mutation analysis'

Cluster Labels	DEL PEAK 5(3P21.1) MUTATED	DEL PEAK 5(3P21.1) WILD-TYPE
Number of samples	19	188

Clustering Approach #21: 'Del Peak 6(3q29) mutation analysis'

Table S30. Description of clustering approach #21: 'Del Peak 6(3q29) mutation analysis'

Cluster Labels	DEL PEAK 6(3Q29) MUTATED	DEL PEAK 6(3Q29) WILD-TYPE
Number of samples	20	187

Clustering Approach #22: 'Del Peak 7(4q33) mutation analysis'

Table S31. Description of clustering approach #22: 'Del Peak 7(4q33) mutation analysis'

Cluster Labels	DEL PEAK 7(4Q33) MUTATED	DEL PEAK 7(4Q33) WILD-TYPE
Number of samples	60	147

Clustering Approach #23: 'Del Peak 8(4q35.2) mutation analysis'

Table S32. Description of clustering approach #23: 'Del Peak 8(4q35.2) mutation analysis'

Cluster Labels	DEL PEAK 8(4Q35.2) MUTATED	DEL PEAK 8(4Q35.2) WILD-TYPE
Number of samples	61	146

Clustering Approach #24: 'Del Peak 9(5q35.2) mutation analysis'

Table S33. Description of clustering approach #24: 'Del Peak 9(5q35.2) mutation analysis'

Cluster Labels	DEL PEAK 9(5Q35.2) MUTATED	DEL PEAK 9(5Q35.2) WILD-TYPE
Number of samples	27	180

Clustering Approach #25: 'Del Peak 10(6p24.1) mutation analysis'

Table S34. Description of clustering approach #25: 'Del Peak 10(6p24.1) mutation analysis'

Cluster Labels	DEL PEAK 10(6P24.1) MUTATED	DEL PEAK 10(6P24.1) WILD-TYPE
Number of samples	17	190

Clustering Approach #26: 'Del Peak 11(6q24.3) mutation analysis'

Table S35. Description of clustering approach #26: 'Del Peak 11(6q24.3) mutation analysis'

Cluster Labels	DEL PEAK 11(6Q24.3) MUTATED	DEL PEAK 11(6Q24.3) WILD-TYPE
Number of samples	30	177

Clustering Approach #27: 'Del Peak 12(8p23.2) mutation analysis'

Table S36. Description of clustering approach #27: 'Del Peak 12(8p23.2) mutation analysis'

Cluster Labels	DEL PEAK 12(8P23.2) MUTATED	DEL PEAK 12(8P23.2) WILD-TYPE
Number of samples	10	197

Clustering Approach #28: 'Del Peak 13(9p21.3) mutation analysis'

Table S37. Description of clustering approach #28: 'Del Peak 13(9p21.3) mutation analysis'

Cluster Labels	DEL PEAK 13(9P21.3) MUTATED	DEL PEAK 13(9P21.3) WILD-TYPE
Number of samples	74	133

'Del Peak 13(9p21.3) mutation analysis' versus 'Time to Death'

P value = 3.01e-05 (logrank test), Q value = 0.0076

Table S38. Clustering Approach #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	206	51	0.0 - 211.2 (13.4)
DEL PEAK 13(9P21.3) MUTATED	73	26	0.1 - 117.4 (14.7)
DEL PEAK 13(9P21.3) WILD-TYPE	133	25	0.0 - 211.2 (13.4)

Figure S10. Get High-res Image Clustering Approach #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 13(9p21.3) mutation analysis' versus 'AGE'

P value = 0.000488 (t-test), Q value = 0.12

Table S39. Clustering Approach #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	207	43.1 (13.4)
DEL PEAK 13(9P21.3) MUTATED	74	47.5 (13.2)
DEL PEAK 13(9P21.3) WILD-TYPE	133	40.7 (13.0)

Figure S11. Get High-res Image Clustering Approach #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 13(9p21.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000267 (Fisher's exact test), Q value = 0.066

Table S40. Clustering Approach #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	104	103
DEL PEAK 13(9P21.3) MUTATED	50	24
DEL PEAK 13(9P21.3) WILD-TYPE	54	79

Figure S12. Get High-res Image Clustering Approach #28: 'Del Peak 13(9p21.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #29: 'Del Peak 14(10q26.2) mutation analysis'

Table S41. Description of clustering approach #29: 'Del Peak 14(10q26.2) mutation analysis'

Cluster Labels	DEL PEAK 14(10Q26.2) MUTATED	DEL PEAK 14(10Q26.2) WILD-TYPE
Number of samples	65	142

'Del Peak 14(10q26.2) mutation analysis' versus 'Time to Death'

P value = 0.000151 (logrank test), Q value = 0.037

Table S42. Clustering Approach #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	206	51	0.0 - 211.2 (13.4)
DEL PEAK 14(10Q26.2) MUTATED	65	29	0.1 - 156.2 (12.4)
DEL PEAK 14(10Q26.2) WILD-TYPE	141	22	0.0 - 211.2 (14.3)

Figure S13. Get High-res Image Clustering Approach #29: 'Del Peak 14(10q26.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

Clustering Approach #30: 'Del Peak 15(11p15.5) mutation analysis'

Table S43. Description of clustering approach #30: 'Del Peak 15(11p15.5) mutation analysis'

Cluster Labels	DEL PEAK 15(11P15.5) MUTATED	DEL PEAK 15(11P15.5) WILD-TYPE
Number of samples	43	164

Clustering Approach #31: 'Del Peak 16(11q25) mutation analysis'

Table S44. Description of clustering approach #31: 'Del Peak 16(11q25) mutation analysis'

Cluster Labels	DEL PEAK 16(11Q25) MUTATED	DEL PEAK 16(11Q25) WILD-TYPE
Number of samples	13	194

Clustering Approach #32: 'Del Peak 17(12q24.11) mutation analysis'

Table S45. Description of clustering approach #32: 'Del Peak 17(12q24.11) mutation analysis'

Cluster Labels	DEL PEAK 17(12Q24.11) MUTATED	DEL PEAK 17(12Q24.11) WILD-TYPE
Number of samples	27	180

Clustering Approach #33: 'Del Peak 18(13q14.2) mutation analysis'

Table S46. Description of clustering approach #33: 'Del Peak 18(13q14.2) mutation analysis'

Cluster Labels	DEL PEAK 18(13Q14.2) MUTATED	DEL PEAK 18(13Q14.2) WILD-TYPE
Number of samples	62	145

Clustering Approach #34: 'Del Peak 19(13q34) mutation analysis'

Table S47. Description of clustering approach #34: 'Del Peak 19(13q34) mutation analysis'

Cluster Labels	DEL PEAK 19(13Q34) MUTATED	DEL PEAK 19(13Q34) WILD-TYPE
Number of samples	48	159

Clustering Approach #35: 'Del Peak 20(14q24.3) mutation analysis'

Table S48. Description of clustering approach #35: 'Del Peak 20(14q24.3) mutation analysis'

Cluster Labels	DEL PEAK 20(14Q24.3) MUTATED	DEL PEAK 20(14Q24.3) WILD-TYPE
Number of samples	48	159

'Del Peak 20(14q24.3) mutation analysis' versus 'Time to Death'

P value = 0.000981 (logrank test), Q value = 0.24

Table S49. Clustering Approach #35: 'Del Peak 20(14q24.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	206	51	0.0 - 211.2 (13.4)
DEL PEAK 20(14Q24.3) MUTATED	48	22	0.2 - 130.8 (17.4)
DEL PEAK 20(14Q24.3) WILD-TYPE	158	29	0.0 - 211.2 (12.4)

Figure S14. Get High-res Image Clustering Approach #35: 'Del Peak 20(14q24.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

Clustering Approach #36: 'Del Peak 21(15q21.3) mutation analysis'

Table S50. Description of clustering approach #36: 'Del Peak 21(15q21.3) mutation analysis'

Cluster Labels	DEL PEAK 21(15Q21.3) MUTATED	DEL PEAK 21(15Q21.3) WILD-TYPE
Number of samples	26	181

Clustering Approach #37: 'Del Peak 22(17q25.3) mutation analysis'

Table S51. Description of clustering approach #37: 'Del Peak 22(17q25.3) mutation analysis'

Cluster Labels	DEL PEAK 22(17Q25.3) MUTATED	DEL PEAK 22(17Q25.3) WILD-TYPE
Number of samples	11	196

Clustering Approach #38: 'Del Peak 23(18p11.32) mutation analysis'

Table S52. Description of clustering approach #38: 'Del Peak 23(18p11.32) mutation analysis'

Cluster Labels	DEL PEAK 23(18P11.32) MUTATED	DEL PEAK 23(18P11.32) WILD-TYPE
Number of samples	29	178

Clustering Approach #39: 'Del Peak 24(18q23) mutation analysis'

Table S53. Description of clustering approach #39: 'Del Peak 24(18q23) mutation analysis'

Cluster Labels	DEL PEAK 24(18Q23) MUTATED	DEL PEAK 24(18Q23) WILD-TYPE
Number of samples	32	175

Clustering Approach #40: 'Del Peak 25(19q13.42) mutation analysis'

Table S54. Description of clustering approach #40: 'Del Peak 25(19q13.42) mutation analysis'

Cluster Labels	DEL PEAK 25(19Q13.42) MUTATED	DEL PEAK 25(19Q13.42) WILD-TYPE
Number of samples	111	96

'Del Peak 25(19q13.42) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.51e-08 (Fisher's exact test), Q value = 2.4e-05

Table S55. Clustering Approach #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	63	54	89
DEL PEAK 25(19Q13.42) MUTATED	20	23	67
DEL PEAK 25(19Q13.42) WILD-TYPE	43	31	22

Figure S15. Get High-res Image Clustering Approach #40: 'Del Peak 25(19q13.42) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Clustering Approach #41: 'Del Peak 26(22q13.31) mutation analysis'

Table S56. Description of clustering approach #41: 'Del Peak 26(22q13.31) mutation analysis'

Cluster Labels	DEL PEAK 26(22Q13.31) MUTATED	DEL PEAK 26(22Q13.31) WILD-TYPE
Number of samples	29	178

Clustering Approach #42: 'Del Peak 27(Xp22.31) mutation analysis'

Table S57. Description of clustering approach #42: 'Del Peak 27(Xp22.31) mutation analysis'

Cluster Labels	DEL PEAK 27(XP22.31) MUTATED	DEL PEAK 27(XP22.31) WILD-TYPE
Number of samples	48	159

Clustering Approach #43: 'Del Peak 28(Xq21.1) mutation analysis'

Table S58. Description of clustering approach #43: 'Del Peak 28(Xq21.1) mutation analysis'

Cluster Labels	DEL PEAK 28(XQ21.1) MUTATED	DEL PEAK 28(XQ21.1) WILD-TYPE
Number of samples	29	178

Methods & Data

Input

Cluster data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = LGG-TP.clin.merged.picked.txt
Number of patients = 207
Number of clustering approaches = 43
Number of selected clinical features = 6
Exclude small clusters that include fewer than K patients, 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 two tumor subtypes using 't.test' function in R

Fisher's exact test

For binary clinical features, 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] 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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