Correlation between copy number variation genes and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C10000DF
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 and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10000DF
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 20 peak regions and 6 molecular subtypes across 191 patients, 35 significant findings detected with Q value < 0.25.

- Amp Peak 1(1p33) cnvs correlated to 'CN_CNMF'.

- Amp Peak 3(11q23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Amp Peak 4(13q31.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 5(20q11.21) cnvs correlated to 'CN_CNMF'.

- Amp Peak 6(21q22.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

- Del Peak 2(3p13) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 4(5q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 5(7p12.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 6(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 7(7q34) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 10(12p13.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 12(16q23.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 13(17p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 14(17q11.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 15(18p11.21) cnvs correlated to 'CN_CNMF'.

- Del Peak 16(20q13.13) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 20 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 35 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nCNV (%) | nWild-Type | Chi-square test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
Del Peak 5(7p12 1) | 0 (0%) | 175 | 2.4e-07 (2.64e-05) | 0.000667 (0.064) | 0.00179 (0.155) | 0.00272 (0.225) | 0.00595 (0.452) | 0.00176 (0.155)
Del Peak 4(5q31 2) | 0 (0%) | 173 | 6.32e-15 (7.27e-13) | 6.11e-05 (0.00623) | 0.0053 (0.413) | 0.0923 (1.00) | 0.000809 (0.0769) | 0.00042 (0.0407)
Del Peak 6(7q32 3) | 0 (0%) | 168 | 8.78e-07 (9.31e-05) | 0.000189 (0.0186) | 0.0384 (1.00) | 0.022 (1.00) | 0.00255 (0.214) | 9.87e-05 (0.00977)
Del Peak 7(7q34) | 0 (0%) | 167 | 2.83e-06 (0.000298) | 7.4e-05 (0.00748) | 0.0221 (1.00) | 0.0212 (1.00) | 0.000836 (0.0786) | 1.55e-05 (0.00161)
Amp Peak 6(21q22 2) | 0 (0%) | 177 | 9.35e-32 (1.08e-29) | 0.00156 (0.14) | 0.00336 (0.276) | 0.337 (1.00) | 0.00177 (0.155) | 0.0173 (1.00)
Del Peak 13(17p13 2) | 0 (0%) | 176 | 1.68e-14 (1.91e-12) | 0.00105 (0.0981) | 0.0113 (0.765) | 0.0211 (1.00) | 0.0874 (1.00) | 0.00133 (0.123)
Amp Peak 3(11q23 3) | 0 (0%) | 174 | 4.87e-33 (5.7e-31) | 8.51e-05 (0.00851) | 0.373 (1.00) | 0.784 (1.00) | 0.746 (1.00) | 0.945 (1.00)
Del Peak 2(3p13) | 0 (0%) | 182 | 0.00179 (0.155) | 0.137 (1.00) | 0.0349 (1.00) | 0.718 (1.00) | 0.012 (0.806) | 0.00166 (0.147)
Amp Peak 1(1p33) | 0 (0%) | 184 | 4.86e-07 (5.2e-05) | 0.00516 (0.413) | 0.124 (1.00) | 0.665 (1.00) | 0.00989 (0.682) | 0.23 (1.00)
Amp Peak 4(13q31 3) | 0 (0%) | 184 | 1.96e-10 (2.2e-08) | 0.00516 (0.413) | 0.0668 (1.00) | 0.0965 (1.00) | 0.735 (1.00) | 0.143 (1.00)
Amp Peak 5(20q11 21) | 0 (0%) | 188 | 0.00135 (0.123) | 0.185 (1.00) |  | 0.55 (1.00) |  |
Del Peak 10(12p13 2) | 0 (0%) | 181 | 8.25e-13 (9.33e-11) | 0.00776 (0.566) | 0.197 (1.00) | 0.167 (1.00) | 0.0682 (1.00) | 0.0217 (1.00)
Del Peak 12(16q23 1) | 0 (0%) | 182 | 2.61e-07 (2.84e-05) | 0.0648 (1.00) | 0.332 (1.00) | 1 (1.00) | 0.0442 (1.00) | 0.0493 (1.00)
Del Peak 14(17q11 2) | 0 (0%) | 178 | 1.72e-05 (0.00177) | 0.029 (1.00) | 0.156 (1.00) | 0.222 (1.00) | 0.136 (1.00) | 0.00838 (0.595)
Del Peak 15(18p11 21) | 0 (0%) | 182 | 4.63e-07 (5e-05) | 0.00832 (0.595) | 0.381 (1.00) | 0.718 (1.00) | 0.213 (1.00) | 0.0914 (1.00)
Del Peak 16(20q13 13) | 0 (0%) | 187 | 9.73e-10 (1.08e-07) | 0.0808 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.125 (1.00) | 0.222 (1.00)
Amp Peak 2(1q43) | 0 (0%) | 184 | 0.0063 (0.473) | 0.00516 (0.413) | 0.373 (1.00) | 0.425 (1.00) | 0.137 (1.00) | 0.121 (1.00)
Del Peak 3(3q26 31) | 0 (0%) | 188 | 0.00355 (0.287) | 0.185 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.0618 (1.00) | 0.0481 (1.00)
Del Peak 9(9q21 32) | 0 (0%) | 186 | 0.63 (1.00) | 0.416 (1.00) | 0.176 (1.00) | 0.664 (1.00) | 0.183 (1.00) | 0.108 (1.00)
Del Peak 11(12q21 33) | 0 (0%) | 188 | 0.057 (1.00) | 0.38 (1.00) | 0.186 (1.00) | 0.552 (1.00) | 0.00827 (0.595) | 0.00696 (0.515)

'Amp Peak 1(1p33)' versus 'CN_CNMF'

P value = 4.86e-07 (Chi-square test), Q value = 5.2e-05

Table S1. Gene #1: 'Amp Peak 1(1p33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
AMP PEAK 1(1P33) CNV | 0 | 3 | 0 | 4 | 0
AMP PEAK 1(1P33) WILD-TYPE | 142 | 12 | 15 | 14 | 1

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(11q23.3)' versus 'CN_CNMF'

P value = 4.87e-33 (Chi-square test), Q value = 5.7e-31

Table S2. Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
AMP PEAK 3(11Q23.3) CNV | 0 | 14 | 0 | 2 | 1
AMP PEAK 3(11Q23.3) WILD-TYPE | 142 | 1 | 15 | 16 | 0

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(11q23.3)' versus 'METHLYATION_CNMF'

P value = 8.51e-05 (Chi-square test), Q value = 0.0085

Table S3. Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
AMP PEAK 3(11Q23.3) CNV | 0 | 0 | 12 | 4 | 1
AMP PEAK 3(11Q23.3) WILD-TYPE | 46 | 44 | 49 | 10 | 19

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(11q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(13q31.3)' versus 'CN_CNMF'

P value = 1.96e-10 (Chi-square test), Q value = 2.2e-08

Table S4. Gene #4: 'Amp Peak 4(13q31.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
AMP PEAK 4(13Q31.3) CNV | 0 | 1 | 0 | 6 | 0
AMP PEAK 4(13Q31.3) WILD-TYPE | 142 | 14 | 15 | 12 | 1

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(13q31.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(20q11.21)' versus 'CN_CNMF'

P value = 0.00135 (Chi-square test), Q value = 0.12

Table S5. Gene #5: 'Amp Peak 5(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
AMP PEAK 5(20Q11.21) CNV | 0 | 0 | 2 | 1 | 0
AMP PEAK 5(20Q11.21) WILD-TYPE | 142 | 15 | 13 | 17 | 1

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(21q22.2)' versus 'CN_CNMF'

P value = 9.35e-32 (Chi-square test), Q value = 1.1e-29

Table S6. Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
AMP PEAK 6(21Q22.2) CNV | 0 | 0 | 13 | 1 | 0
AMP PEAK 6(21Q22.2) WILD-TYPE | 142 | 15 | 2 | 17 | 1

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(21q22.2)' versus 'METHLYATION_CNMF'

P value = 0.00156 (Chi-square test), Q value = 0.14

Table S7. Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
AMP PEAK 6(21Q22.2) CNV | 1 | 0 | 11 | 0 | 1
AMP PEAK 6(21Q22.2) WILD-TYPE | 45 | 44 | 50 | 14 | 19

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 6(21q22.2)' versus 'MIRSEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.15

Table S8. Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
AMP PEAK 6(21Q22.2) CNV | 1 | 4 | 7 | 0
AMP PEAK 6(21Q22.2) WILD-TYPE | 57 | 33 | 34 | 43

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 2(3p13)' versus 'CN_CNMF'

P value = 0.00179 (Chi-square test), Q value = 0.15

Table S9. Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 2(3P13) CNV | 2 | 1 | 3 | 3 | 0
DEL PEAK 2(3P13) WILD-TYPE | 140 | 14 | 12 | 15 | 1

Figure S9. Get High-res Image Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(3p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.15

Table S10. Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 79 | 65
DEL PEAK 2(3P13) CNV | 5 | 0 | 3
DEL PEAK 2(3P13) WILD-TYPE | 30 | 79 | 62

Figure S10. Get High-res Image Gene #7: 'Del Peak 2(3p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(5q31.2)' versus 'CN_CNMF'

P value = 6.32e-15 (Chi-square test), Q value = 7.3e-13

Table S11. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 4(5Q31.2) CNV | 1 | 1 | 7 | 8 | 1
DEL PEAK 4(5Q31.2) WILD-TYPE | 141 | 14 | 8 | 10 | 0

Figure S11. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 4(5q31.2)' versus 'METHLYATION_CNMF'

P value = 6.11e-05 (Chi-square test), Q value = 0.0062

Table S12. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
DEL PEAK 4(5Q31.2) CNV | 1 | 0 | 15 | 0 | 2
DEL PEAK 4(5Q31.2) WILD-TYPE | 45 | 44 | 46 | 14 | 18

Figure S12. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 4(5q31.2)' versus 'MIRSEQ_CNMF'

P value = 0.000809 (Fisher's exact test), Q value = 0.077

Table S13. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
DEL PEAK 4(5Q31.2) CNV | 1 | 10 | 3 | 3
DEL PEAK 4(5Q31.2) WILD-TYPE | 57 | 27 | 38 | 40

Figure S13. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 4(5q31.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.041

Table S14. Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 79 | 65
DEL PEAK 4(5Q31.2) CNV | 10 | 3 | 4
DEL PEAK 4(5Q31.2) WILD-TYPE | 25 | 76 | 61

Figure S14. Get High-res Image Gene #9: 'Del Peak 4(5q31.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(7p12.1)' versus 'CN_CNMF'

P value = 2.4e-07 (Chi-square test), Q value = 2.6e-05

Table S15. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 5(7P12.1) CNV | 7 | 1 | 0 | 7 | 1
DEL PEAK 5(7P12.1) WILD-TYPE | 135 | 14 | 15 | 11 | 0

Figure S15. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(7p12.1)' versus 'METHLYATION_CNMF'

P value = 0.000667 (Chi-square test), Q value = 0.064

Table S16. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
DEL PEAK 5(7P12.1) CNV | 1 | 0 | 13 | 1 | 1
DEL PEAK 5(7P12.1) WILD-TYPE | 45 | 44 | 48 | 13 | 19

Figure S16. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 5(7p12.1)' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.15

Table S17. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 52 | 44
DEL PEAK 5(7P12.1) CNV | 12 | 0 | 3
DEL PEAK 5(7P12.1) WILD-TYPE | 58 | 52 | 41

Figure S17. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 5(7p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.23

Table S18. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 110 | 56
DEL PEAK 5(7P12.1) CNV | 15 | 0
DEL PEAK 5(7P12.1) WILD-TYPE | 95 | 56

Figure S18. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(7p12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.15

Table S19. Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 79 | 65
DEL PEAK 5(7P12.1) CNV | 9 | 3 | 4
DEL PEAK 5(7P12.1) WILD-TYPE | 26 | 76 | 61

Figure S19. Get High-res Image Gene #10: 'Del Peak 5(7p12.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(7q32.3)' versus 'CN_CNMF'

P value = 8.78e-07 (Chi-square test), Q value = 9.3e-05

Table S20. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 6(7Q32.3) CNV | 7 | 3 | 5 | 7 | 1
DEL PEAK 6(7Q32.3) WILD-TYPE | 135 | 12 | 10 | 11 | 0

Figure S20. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(7q32.3)' versus 'METHLYATION_CNMF'

P value = 0.000189 (Chi-square test), Q value = 0.019

Table S21. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
DEL PEAK 6(7Q32.3) CNV | 1 | 1 | 17 | 2 | 2
DEL PEAK 6(7Q32.3) WILD-TYPE | 45 | 43 | 44 | 12 | 18

Figure S21. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 6(7q32.3)' versus 'MIRSEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.21

Table S22. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
DEL PEAK 6(7Q32.3) CNV | 2 | 11 | 5 | 4
DEL PEAK 6(7Q32.3) WILD-TYPE | 56 | 26 | 36 | 39

Figure S22. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 6(7q32.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.87e-05 (Fisher's exact test), Q value = 0.0098

Table S23. Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 79 | 65
DEL PEAK 6(7Q32.3) CNV | 12 | 3 | 7
DEL PEAK 6(7Q32.3) WILD-TYPE | 23 | 76 | 58

Figure S23. Get High-res Image Gene #11: 'Del Peak 6(7q32.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(7q34)' versus 'CN_CNMF'

P value = 2.83e-06 (Chi-square test), Q value = 3e-04

Table S24. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 7(7Q34) CNV | 8 | 3 | 5 | 7 | 1
DEL PEAK 7(7Q34) WILD-TYPE | 134 | 12 | 10 | 11 | 0

Figure S24. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(7q34)' versus 'METHLYATION_CNMF'

P value = 7.4e-05 (Chi-square test), Q value = 0.0075

Table S25. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
DEL PEAK 7(7Q34) CNV | 1 | 1 | 18 | 2 | 2
DEL PEAK 7(7Q34) WILD-TYPE | 45 | 43 | 43 | 12 | 18

Figure S25. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(7q34)' versus 'MIRSEQ_CNMF'

P value = 0.000836 (Fisher's exact test), Q value = 0.079

Table S26. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
DEL PEAK 7(7Q34) CNV | 2 | 12 | 5 | 4
DEL PEAK 7(7Q34) WILD-TYPE | 56 | 25 | 36 | 39

Figure S26. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 7(7q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.0016

Table S27. Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 79 | 65
DEL PEAK 7(7Q34) CNV | 13 | 3 | 7
DEL PEAK 7(7Q34) WILD-TYPE | 22 | 76 | 58

Figure S27. Get High-res Image Gene #12: 'Del Peak 7(7q34)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(12p13.2)' versus 'CN_CNMF'

P value = 8.25e-13 (Chi-square test), Q value = 9.3e-11

Table S28. Gene #14: 'Del Peak 10(12p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 10(12P13.2) CNV | 1 | 1 | 0 | 8 | 0
DEL PEAK 10(12P13.2) WILD-TYPE | 141 | 14 | 15 | 10 | 1

Figure S28. Get High-res Image Gene #14: 'Del Peak 10(12p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(16q23.1)' versus 'CN_CNMF'

P value = 2.61e-07 (Chi-square test), Q value = 2.8e-05

Table S29. Gene #16: 'Del Peak 12(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 12(16Q23.1) CNV | 2 | 1 | 1 | 4 | 1
DEL PEAK 12(16Q23.1) WILD-TYPE | 140 | 14 | 14 | 14 | 0

Figure S29. Get High-res Image Gene #16: 'Del Peak 12(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(17p13.2)' versus 'CN_CNMF'

P value = 1.68e-14 (Chi-square test), Q value = 1.9e-12

Table S30. Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 13(17P13.2) CNV | 0 | 1 | 5 | 8 | 1
DEL PEAK 13(17P13.2) WILD-TYPE | 142 | 14 | 10 | 10 | 0

Figure S30. Get High-res Image Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(17p13.2)' versus 'METHLYATION_CNMF'

P value = 0.00105 (Chi-square test), Q value = 0.098

Table S31. Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
DEL PEAK 13(17P13.2) CNV | 0 | 1 | 12 | 0 | 2
DEL PEAK 13(17P13.2) WILD-TYPE | 46 | 43 | 49 | 14 | 18

Figure S31. Get High-res Image Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(17p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.12

Table S32. Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 79 | 65
DEL PEAK 13(17P13.2) CNV | 7 | 1 | 7
DEL PEAK 13(17P13.2) WILD-TYPE | 28 | 78 | 58

Figure S32. Get High-res Image Gene #17: 'Del Peak 13(17p13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(17q11.2)' versus 'CN_CNMF'

P value = 1.72e-05 (Chi-square test), Q value = 0.0018

Table S33. Gene #18: 'Del Peak 14(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 14(17Q11.2) CNV | 2 | 3 | 3 | 5 | 0
DEL PEAK 14(17Q11.2) WILD-TYPE | 140 | 12 | 12 | 13 | 1

Figure S33. Get High-res Image Gene #18: 'Del Peak 14(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(18p11.21)' versus 'CN_CNMF'

P value = 4.63e-07 (Chi-square test), Q value = 5e-05

Table S34. Gene #19: 'Del Peak 15(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 15(18P11.21) CNV | 1 | 0 | 3 | 5 | 0
DEL PEAK 15(18P11.21) WILD-TYPE | 141 | 15 | 12 | 13 | 1

Figure S34. Get High-res Image Gene #19: 'Del Peak 15(18p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(20q13.13)' versus 'CN_CNMF'

P value = 9.73e-10 (Chi-square test), Q value = 1.1e-07

Table S35. Gene #20: 'Del Peak 16(20q13.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 142 | 15 | 15 | 18 | 1
DEL PEAK 16(20Q13.13) CNV | 0 | 0 | 4 | 0 | 0
DEL PEAK 16(20Q13.13) WILD-TYPE | 142 | 15 | 11 | 18 | 1

Figure S35. Get High-res Image Gene #20: 'Del Peak 16(20q13.13)' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

- Molecular subtype file = LAML-TB.transferedmergedcluster.txt

- Number of patients = 191

- Number of copy number variation regions = 20

- Number of molecular subtypes = 6

- Exclude regions that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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)
[4] GISTIC_version2
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