Correlation between copy number variation genes (focal) and selected clinical features
Brain Lower Grade Glioma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1M61HGK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1M61HGK
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.

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle