Correlation between copy number variation genes (focal events) and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1KH0KZ3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1KH0KZ3
Overview
Introduction

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

Summary

Testing the association between copy number variation 21 focal events and 6 molecular subtypes across 191 patients, 33 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1p33 cnv correlated to 'CN_CNMF'.

- amp_11q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- amp_19p13.2 cnv correlated to 'CN_CNMF'.

- amp_21q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

- del_3p13 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- del_5q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_7p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- del_7q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_7q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_12p13.2 cnv correlated to 'CN_CNMF'.

- del_12q21.33 cnv correlated to 'CN_CNMF'.

- del_16q23.1 cnv correlated to 'CN_CNMF'.

- del_17p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_17q11.2 cnv correlated to 'CN_CNMF'.

- del_18p11.21 cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 21 focal events and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 33 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
del 7p12 1 | 16 (8%) | 175 | 0.0004 (0.0424) | 0.000667 (0.0693) | 0.00172 (0.163) | 0.00272 (0.247) | 0.00598 (0.496) | 0.00167 (0.161)
del 5q31 2 | 18 (9%) | 173 | 1.77e-13 (2.14e-11) | 6.11e-05 (0.0069) | 0.00512 (0.445) | 0.0923 (1.00) | 0.000865 (0.0882) | 0.000478 (0.0502)
del 7q34 | 24 (13%) | 167 | 6.26e-07 (7.39e-05) | 7.4e-05 (0.00829) | 0.0212 (1.00) | 0.0212 (1.00) | 0.00105 (0.106) | 2.31e-05 (0.00264)
amp 21q22 2 | 14 (7%) | 177 | 5.15e-13 (6.17e-11) | 0.00156 (0.153) | 0.00336 (0.299) | 0.337 (1.00) | 0.00177 (0.167) | 0.0173 (1.00)
del 7q32 3 | 23 (12%) | 168 | 2.38e-07 (2.84e-05) | 0.000189 (0.0203) | 0.0374 (1.00) | 0.022 (1.00) | 0.00295 (0.265) | 9.24e-05 (0.0102)
del 17p13 2 | 15 (8%) | 176 | 1.4e-14 (1.71e-12) | 0.00105 (0.106) | 0.0106 (0.782) | 0.0211 (1.00) | 0.087 (1.00) | 0.00141 (0.14)
amp 11q23 3 | 17 (9%) | 174 | 8.57e-21 (1.05e-18) | 8.51e-05 (0.00944) | 0.358 (1.00) | 0.784 (1.00) | 0.746 (1.00) | 0.915 (1.00)
del 3p13 | 9 (5%) | 182 | 0.00015 (0.0163) | 0.137 (1.00) | 0.0349 (1.00) | 0.718 (1.00) | 0.012 (0.878) | 0.00166 (0.161)
amp 1p33 | 7 (4%) | 184 | 0.000671 (0.0693) | 0.00516 (0.445) | 0.124 (1.00) | 0.665 (1.00) | 0.00989 (0.741) | 0.23 (1.00)
amp 19p13 2 | 6 (3%) | 185 | 0.000137 (0.0149) | 0.581 (1.00) | 0.857 (1.00) | 0.664 (1.00) | 0.895 (1.00) | 0.863 (1.00)
del 12p13 2 | 10 (5%) | 181 | 2.12e-05 (0.00243) | 0.00776 (0.621) | 0.197 (1.00) | 0.167 (1.00) | 0.0682 (1.00) | 0.0217 (1.00)
del 12q21 33 | 3 (2%) | 188 | 0.00197 (0.181) | 0.38 (1.00) | 0.186 (1.00) | 0.552 (1.00) | 0.00827 (0.645) | 0.00696 (0.571)
del 16q23 1 | 9 (5%) | 182 | 0.00182 (0.169) | 0.0648 (1.00) | 0.332 (1.00) | 1 (1.00) | 0.0442 (1.00) | 0.0493 (1.00)
del 17q11 2 | 13 (7%) | 178 | 1.33e-06 (0.000155) | 0.029 (1.00) | 0.151 (1.00) | 0.222 (1.00) | 0.136 (1.00) | 0.00924 (0.702)
del 18p11 21 | 9 (5%) | 182 | 3.46e-06 (0.000401) | 0.00832 (0.645) | 0.381 (1.00) | 0.718 (1.00) | 0.213 (1.00) | 0.0914 (1.00)
amp 1q43 | 7 (4%) | 184 | 0.0047 (0.413) | 0.00516 (0.445) | 0.373 (1.00) | 0.425 (1.00) | 0.137 (1.00) | 0.121 (1.00)
amp 13q31 3 | 7 (4%) | 184 | 0.0849 (1.00) | 0.00516 (0.445) | 0.0668 (1.00) | 0.0965 (1.00) | 0.735 (1.00) | 0.143 (1.00)
amp 20q11 21 | 3 (2%) | 188 | 0.00767 (0.621) | 0.185 (1.00) |  | 0.55 (1.00) |  |
del 3q26 31 | 3 (2%) | 188 | 0.00767 (0.621) | 0.185 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.0618 (1.00) | 0.0481 (1.00)
del 9q21 32 | 5 (3%) | 186 | 0.256 (1.00) | 0.416 (1.00) | 0.176 (1.00) | 0.664 (1.00) | 0.183 (1.00) | 0.108 (1.00)
del 20q13 13 | 4 (2%) | 187 | 0.0259 (1.00) | 0.0808 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.125 (1.00) | 0.222 (1.00)

'amp_1p33' versus 'CN_CNMF'

P value = 0.000671 (Fisher's exact test), Q value = 0.069

Table S1. Gene #1: 'amp_1p33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
AMP PEAK 1(1P33) MUTATED | 1 | 3 | 3 | 0
AMP PEAK 1(1P33) WILD-TYPE | 146 | 11 | 24 | 3

Figure S1. Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q23.3' versus 'CN_CNMF'

P value = 8.57e-21 (Fisher's exact test), Q value = 1.1e-18

Table S2. Gene #3: 'amp_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
AMP PEAK 3(11Q23.3) MUTATED | 0 | 14 | 3 | 0
AMP PEAK 3(11Q23.3) WILD-TYPE | 147 | 0 | 24 | 3

Figure S2. Get High-res Image Gene #3: 'amp_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q23.3' versus 'METHLYATION_CNMF'

P value = 8.51e-05 (Chi-square test), Q value = 0.0094

Table S3. Gene #3: 'amp_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) MUTATED | 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_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.000137 (Fisher's exact test), Q value = 0.015

Table S4. Gene #5: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
AMP PEAK 5(19P13.2) MUTATED | 0 | 1 | 5 | 0
AMP PEAK 5(19P13.2) WILD-TYPE | 147 | 13 | 22 | 3

Figure S4. Get High-res Image Gene #5: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'CN_CNMF'

P value = 5.15e-13 (Fisher's exact test), Q value = 6.2e-11

Table S5. Gene #7: 'amp_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
AMP PEAK 7(21Q22.2) MUTATED | 0 | 0 | 13 | 1
AMP PEAK 7(21Q22.2) WILD-TYPE | 147 | 14 | 14 | 2

Figure S5. Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'METHLYATION_CNMF'

P value = 0.00156 (Chi-square test), Q value = 0.15

Table S6. Gene #7: 'amp_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 7(21Q22.2) MUTATED | 1 | 0 | 11 | 0 | 1
AMP PEAK 7(21Q22.2) WILD-TYPE | 45 | 44 | 50 | 14 | 19

Figure S6. Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_21q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.17

Table S7. Gene #7: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

Figure S7. Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.016

Table S8. Gene #8: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 2(3P13) MUTATED | 2 | 0 | 7 | 0
DEL PEAK 2(3P13) WILD-TYPE | 145 | 14 | 20 | 3

Figure S8. Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.16

Table S9. Gene #8: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S9. Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.2' versus 'CN_CNMF'

P value = 1.77e-13 (Fisher's exact test), Q value = 2.1e-11

Table S10. Gene #10: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 4(5Q31.2) MUTATED | 1 | 1 | 15 | 1
DEL PEAK 4(5Q31.2) WILD-TYPE | 146 | 13 | 12 | 2

Figure S10. Get High-res Image Gene #10: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'METHLYATION_CNMF'

P value = 6.11e-05 (Chi-square test), Q value = 0.0069

Table S11. Gene #10: 'del_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) MUTATED | 1 | 0 | 15 | 0 | 2
DEL PEAK 4(5Q31.2) WILD-TYPE | 45 | 44 | 46 | 14 | 18

Figure S11. Get High-res Image Gene #10: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.2' versus 'MIRSEQ_CNMF'

P value = 0.000865 (Fisher's exact test), Q value = 0.088

Table S12. Gene #10: 'del_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) MUTATED | 1 | 10 | 3 | 3
DEL PEAK 4(5Q31.2) WILD-TYPE | 57 | 27 | 38 | 40

Figure S12. Get High-res Image Gene #10: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000478 (Fisher's exact test), Q value = 0.05

Table S13. Gene #10: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S13. Get High-res Image Gene #10: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7p12.1' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.042

Table S14. Gene #11: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 5(7P12.1) MUTATED | 7 | 0 | 8 | 1
DEL PEAK 5(7P12.1) WILD-TYPE | 140 | 14 | 19 | 2

Figure S14. Get High-res Image Gene #11: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7p12.1' versus 'METHLYATION_CNMF'

P value = 0.000667 (Chi-square test), Q value = 0.069

Table S15. Gene #11: 'del_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) MUTATED | 1 | 0 | 13 | 1 | 1
DEL PEAK 5(7P12.1) WILD-TYPE | 45 | 44 | 48 | 13 | 19

Figure S15. Get High-res Image Gene #11: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.16

Table S16. Gene #11: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S16. Get High-res Image Gene #11: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.25

Table S17. Gene #11: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S17. Get High-res Image Gene #11: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.16

Table S18. Gene #11: 'del_7p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S18. Get High-res Image Gene #11: 'del_7p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q32.3' versus 'CN_CNMF'

P value = 2.38e-07 (Fisher's exact test), Q value = 2.8e-05

Table S19. Gene #12: 'del_7q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 6(7Q32.3) MUTATED | 8 | 2 | 10 | 3
DEL PEAK 6(7Q32.3) WILD-TYPE | 139 | 12 | 17 | 0

Figure S19. Get High-res Image Gene #12: 'del_7q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q32.3' versus 'METHLYATION_CNMF'

P value = 0.000189 (Chi-square test), Q value = 0.02

Table S20. Gene #12: 'del_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) MUTATED | 1 | 1 | 17 | 2 | 2
DEL PEAK 6(7Q32.3) WILD-TYPE | 45 | 43 | 44 | 12 | 18

Figure S20. Get High-res Image Gene #12: 'del_7q32.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.01

Table S21. Gene #12: 'del_7q32.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S21. Get High-res Image Gene #12: 'del_7q32.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 6.26e-07 (Fisher's exact test), Q value = 7.4e-05

Table S22. Gene #13: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 7(7Q34) MUTATED | 9 | 2 | 10 | 3
DEL PEAK 7(7Q34) WILD-TYPE | 138 | 12 | 17 | 0

Figure S22. Get High-res Image Gene #13: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 7.4e-05 (Chi-square test), Q value = 0.0083

Table S23. Gene #13: 'del_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) MUTATED | 1 | 1 | 18 | 2 | 2
DEL PEAK 7(7Q34) WILD-TYPE | 45 | 43 | 43 | 12 | 18

Figure S23. Get High-res Image Gene #13: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.11

Table S24. Gene #13: 'del_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) MUTATED | 2 | 12 | 5 | 4
DEL PEAK 7(7Q34) WILD-TYPE | 56 | 25 | 36 | 39

Figure S24. Get High-res Image Gene #13: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0026

Table S25. Gene #13: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S25. Get High-res Image Gene #13: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.0024

Table S26. Gene #15: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 10(12P13.2) MUTATED | 2 | 0 | 7 | 1
DEL PEAK 10(12P13.2) WILD-TYPE | 145 | 14 | 20 | 2

Figure S26. Get High-res Image Gene #15: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q21.33' versus 'CN_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.18

Table S27. Gene #16: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 11(12Q21.33) MUTATED | 0 | 0 | 2 | 1
DEL PEAK 11(12Q21.33) WILD-TYPE | 147 | 14 | 25 | 2

Figure S27. Get High-res Image Gene #16: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.17

Table S28. Gene #17: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 12(16Q23.1) MUTATED | 3 | 0 | 6 | 0
DEL PEAK 12(16Q23.1) WILD-TYPE | 144 | 14 | 21 | 3

Figure S28. Get High-res Image Gene #17: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 1.4e-14 (Fisher's exact test), Q value = 1.7e-12

Table S29. Gene #18: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 13(17P13.2) MUTATED | 0 | 0 | 15 | 0
DEL PEAK 13(17P13.2) WILD-TYPE | 147 | 14 | 12 | 3

Figure S29. Get High-res Image Gene #18: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00105 (Chi-square test), Q value = 0.11

Table S30. Gene #18: 'del_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) MUTATED | 0 | 1 | 12 | 0 | 2
DEL PEAK 13(17P13.2) WILD-TYPE | 46 | 43 | 49 | 14 | 18

Figure S30. Get High-res Image Gene #18: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.14

Table S31. Gene #18: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S31. Get High-res Image Gene #18: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00016

Table S32. Gene #19: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 14(17Q11.2) MUTATED | 2 | 2 | 9 | 0
DEL PEAK 14(17Q11.2) WILD-TYPE | 145 | 12 | 18 | 3

Figure S32. Get High-res Image Gene #19: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.21' versus 'CN_CNMF'

P value = 3.46e-06 (Fisher's exact test), Q value = 4e-04

Table S33. Gene #20: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
DEL PEAK 15(18P11.21) MUTATED | 1 | 0 | 8 | 0
DEL PEAK 15(18P11.21) WILD-TYPE | 146 | 14 | 19 | 3

Figure S33. Get High-res Image Gene #20: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

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

- Number of patients = 191

- Number of significantly focal cnvs = 21

- Number of molecular subtypes = 6

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

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

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

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] 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)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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