Correlation between copy number variation genes (focal events) and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1C24V92
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/C1C24V92
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 20 focal events and 6 molecular subtypes across 191 patients, 36 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'.

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

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

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

- del_7q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', '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', 'MRNASEQ_CHIERARCHICAL', 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 20 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, 36 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
del 5q31 2 | 18 (9%) | 173 | 1e-05 (0.00116) | 9e-05 (0.00909) | 0.00534 (0.406) | 0.00084 (0.0764) | 0.00077 (0.0716) | 0.0013 (0.112)
del 7q34 | 24 (13%) | 167 | 1e-05 (0.00116) | 6e-05 (0.00618) | 0.0215 (1.00) | 1e-05 (0.00116) | 0.0008 (0.0736) | 0.00055 (0.0533)
del 7q34 | 24 (13%) | 167 | 1e-05 (0.00116) | 6e-05 (0.00618) | 0.0216 (1.00) | 2e-05 (0.00216) | 0.00092 (0.0819) | 0.00056 (0.0538)
del 7p12 1 | 16 (8%) | 175 | 0.00019 (0.019) | 0.00062 (0.0589) | 0.00186 (0.154) | 5e-05 (0.0052) | 0.00614 (0.454) | 0.00639 (0.46)
del 17p13 2 | 15 (8%) | 176 | 1e-05 (0.00116) | 0.00085 (0.0765) | 0.0114 (0.767) | 0.0002 (0.0198) | 0.0865 (1.00) | 0.00116 (0.102)
amp 21q22 2 | 14 (7%) | 177 | 1e-05 (0.00116) | 0.00214 (0.175) | 0.00327 (0.262) | 0.0361 (1.00) | 0.00167 (0.14) | 0.0673 (1.00)
amp 11q23 3 | 17 (9%) | 174 | 1e-05 (0.00116) | 2e-05 (0.00216) | 0.373 (1.00) | 0.201 (1.00) | 0.746 (1.00) | 0.187 (1.00)
amp 1p33 | 7 (4%) | 184 | 0.00049 (0.048) | 0.0116 (0.767) | 0.125 (1.00) | 0.13 (1.00) | 0.00951 (0.656) | 0.0492 (1.00)
amp 19p13 2 | 6 (3%) | 185 | 0.0029 (0.235) | 0.555 (1.00) | 0.857 (1.00) | 0.632 (1.00) | 0.895 (1.00) | 1 (1.00)
del 3p13 | 8 (4%) | 183 | 0.00072 (0.0677) | 0.297 (1.00) | 0.0676 (1.00) | 0.236 (1.00) | 0.0365 (1.00) | 0.0478 (1.00)
del 12p13 2 | 10 (5%) | 181 | 2e-05 (0.00216) | 0.00519 (0.4) | 0.199 (1.00) | 0.0723 (1.00) | 0.0697 (1.00) | 0.00959 (0.656)
del 12q21 33 | 3 (2%) | 188 | 0.00135 (0.115) | 0.304 (1.00) | 0.187 (1.00) | 0.587 (1.00) | 0.00843 (0.59) | 0.006 (0.45)
del 16q23 1 | 9 (5%) | 182 | 0.00121 (0.105) | 0.149 (1.00) | 0.33 (1.00) | 0.494 (1.00) | 0.043 (1.00) | 0.0657 (1.00)
del 17q11 2 | 13 (7%) | 178 | 1e-05 (0.00116) | 0.0224 (1.00) | 0.156 (1.00) | 0.00661 (0.469) | 0.136 (1.00) | 0.0035 (0.273)
del 18p11 21 | 9 (5%) | 182 | 2e-05 (0.00216) | 0.0178 (1.00) | 0.382 (1.00) | 0.335 (1.00) | 0.213 (1.00) | 0.0311 (1.00)
amp 1q43 | 7 (4%) | 184 | 0.00338 (0.267) | 0.0124 (0.808) | 0.377 (1.00) | 0.0364 (1.00) | 0.137 (1.00) | 0.015 (0.944)
amp 13q31 3 | 7 (4%) | 184 | 0.0807 (1.00) | 0.0124 (0.808) | 0.067 (1.00) | 0.0364 (1.00) | 0.737 (1.00) | 0.0566 (1.00)
amp 20q11 21 | 3 (2%) | 188 | 0.00618 (0.454) | 0.267 (1.00) |  |  |  |
del 9q21 32 | 5 (3%) | 186 | 0.236 (1.00) | 0.516 (1.00) | 0.176 (1.00) | 0.602 (1.00) | 0.182 (1.00) | 0.105 (1.00)
del 20q13 13 | 4 (2%) | 187 | 0.0288 (1.00) | 0.148 (1.00) | 0.787 (1.00) | 0.588 (1.00) | 0.126 (1.00) | 0.411 (1.00)

'amp_1p33' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.048

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
AMP PEAK 1(1P33) MUTATED | 1 | 3 | 3 | 0
AMP PEAK 1(1P33) WILD-TYPE | 147 | 11 | 24 | 2

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

'amp_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
AMP PEAK 3(11Q23.3) MUTATED | 0 | 14 | 3 | 0
AMP PEAK 3(11Q23.3) WILD-TYPE | 148 | 0 | 24 | 2

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 = 2e-05 (Fisher's exact test), Q value = 0.0022

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 = 0.0029 (Fisher's exact test), Q value = 0.23

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
AMP PEAK 5(19P13.2) MUTATED | 1 | 1 | 4 | 0
AMP PEAK 5(19P13.2) WILD-TYPE | 147 | 13 | 23 | 2

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 = 1e-05 (Fisher's exact test), Q value = 0.0012

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
AMP PEAK 7(21Q22.2) MUTATED | 0 | 0 | 14 | 0
AMP PEAK 7(21Q22.2) WILD-TYPE | 148 | 14 | 13 | 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 = 0.00214 (Fisher's exact test), Q value = 0.18

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 = 0.00167 (Fisher's exact test), Q value = 0.14

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 = 0.00072 (Fisher's exact test), Q value = 0.068

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 2(3P13) MUTATED | 2 | 0 | 6 | 0
DEL PEAK 2(3P13) WILD-TYPE | 146 | 14 | 21 | 2

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

'del_5q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S9. Gene #9: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 3(5Q31.2) MUTATED | 1 | 1 | 15 | 1
DEL PEAK 3(5Q31.2) WILD-TYPE | 147 | 13 | 12 | 1

Figure S9. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0091

Table S10. Gene #9: '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 3(5Q31.2) MUTATED | 1 | 0 | 15 | 0 | 2
DEL PEAK 3(5Q31.2) WILD-TYPE | 45 | 44 | 46 | 14 | 18

Figure S10. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.076

Table S11. Gene #9: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 14 | 55 | 26 | 42
DEL PEAK 3(5Q31.2) MUTATED | 0 | 0 | 0 | 14 | 0 | 2
DEL PEAK 3(5Q31.2) WILD-TYPE | 16 | 13 | 14 | 41 | 26 | 40

Figure S11. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.072

Table S12. Gene #9: '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 3(5Q31.2) MUTATED | 1 | 10 | 3 | 3
DEL PEAK 3(5Q31.2) WILD-TYPE | 57 | 27 | 38 | 40

Figure S12. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.11

Table S13. Gene #9: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 3(5Q31.2) MUTATED | 1 | 8 | 8
DEL PEAK 3(5Q31.2) WILD-TYPE | 66 | 26 | 70

Figure S13. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7p12.1' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.019

Table S14. Gene #10: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 4(7P12.1) MUTATED | 7 | 0 | 8 | 1
DEL PEAK 4(7P12.1) WILD-TYPE | 141 | 14 | 19 | 1

Figure S14. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7p12.1' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.059

Table S15. Gene #10: '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 4(7P12.1) MUTATED | 1 | 0 | 13 | 1 | 1
DEL PEAK 4(7P12.1) WILD-TYPE | 45 | 44 | 48 | 13 | 19

Figure S15. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.15

Table S16. Gene #10: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 52 | 44
DEL PEAK 4(7P12.1) MUTATED | 12 | 0 | 3
DEL PEAK 4(7P12.1) WILD-TYPE | 58 | 52 | 41

Figure S16. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0052

Table S17. Gene #10: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 14 | 55 | 26 | 42
DEL PEAK 4(7P12.1) MUTATED | 0 | 0 | 0 | 15 | 0 | 0
DEL PEAK 4(7P12.1) WILD-TYPE | 16 | 13 | 14 | 40 | 26 | 42

Figure S17. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S18. Gene #11: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 5(7Q34) MUTATED | 9 | 2 | 11 | 2
DEL PEAK 5(7Q34) WILD-TYPE | 139 | 12 | 16 | 0

Figure S18. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0062

Table S19. Gene #11: '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 5(7Q34) MUTATED | 1 | 1 | 18 | 2 | 2
DEL PEAK 5(7Q34) WILD-TYPE | 45 | 43 | 43 | 12 | 18

Figure S19. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S20. Gene #11: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 14 | 55 | 26 | 42
DEL PEAK 5(7Q34) MUTATED | 1 | 1 | 0 | 18 | 0 | 0
DEL PEAK 5(7Q34) WILD-TYPE | 15 | 12 | 14 | 37 | 26 | 42

Figure S20. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.074

Table S21. Gene #11: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

Figure S21. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.053

Table S22. Gene #11: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 5(7Q34) MUTATED | 2 | 10 | 11
DEL PEAK 5(7Q34) WILD-TYPE | 65 | 24 | 67

Figure S22. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S23. Gene #12: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 6(7Q34) MUTATED | 9 | 2 | 11 | 2
DEL PEAK 6(7Q34) WILD-TYPE | 139 | 12 | 16 | 0

Figure S23. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0062

Table S24. Gene #12: '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 6(7Q34) MUTATED | 1 | 1 | 18 | 2 | 2
DEL PEAK 6(7Q34) WILD-TYPE | 45 | 43 | 43 | 12 | 18

Figure S24. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S25. Gene #12: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 14 | 55 | 26 | 42
DEL PEAK 6(7Q34) MUTATED | 1 | 1 | 0 | 18 | 0 | 0
DEL PEAK 6(7Q34) WILD-TYPE | 15 | 12 | 14 | 37 | 26 | 42

Figure S25. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.082

Table S26. Gene #12: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
DEL PEAK 6(7Q34) MUTATED | 2 | 12 | 5 | 4
DEL PEAK 6(7Q34) WILD-TYPE | 56 | 25 | 36 | 39

Figure S26. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.054

Table S27. Gene #12: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 6(7Q34) MUTATED | 2 | 10 | 11
DEL PEAK 6(7Q34) WILD-TYPE | 65 | 24 | 67

Figure S27. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S28. Gene #14: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 10(12P13.2) MUTATED | 2 | 0 | 7 | 1
DEL PEAK 10(12P13.2) WILD-TYPE | 146 | 14 | 20 | 1

Figure S28. Get High-res Image Gene #14: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q21.33' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.11

Table S29. Gene #15: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 11(12Q21.33) MUTATED | 0 | 0 | 2 | 1
DEL PEAK 11(12Q21.33) WILD-TYPE | 148 | 14 | 25 | 1

Figure S29. Get High-res Image Gene #15: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.11

Table S30. Gene #16: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 12(16Q23.1) MUTATED | 3 | 0 | 6 | 0
DEL PEAK 12(16Q23.1) WILD-TYPE | 145 | 14 | 21 | 2

Figure S30. Get High-res Image Gene #16: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S31. Gene #17: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 13(17P13.2) MUTATED | 0 | 0 | 15 | 0
DEL PEAK 13(17P13.2) WILD-TYPE | 148 | 14 | 12 | 2

Figure S31. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.076

Table S32. Gene #17: '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 S32. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.02

Table S33. Gene #17: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 16 | 13 | 14 | 55 | 26 | 42
DEL PEAK 13(17P13.2) MUTATED | 0 | 0 | 0 | 14 | 0 | 1
DEL PEAK 13(17P13.2) WILD-TYPE | 16 | 13 | 14 | 41 | 26 | 41

Figure S33. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.1

Table S34. Gene #17: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 13(17P13.2) MUTATED | 0 | 5 | 10
DEL PEAK 13(17P13.2) WILD-TYPE | 67 | 29 | 68

Figure S34. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S35. Gene #18: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 14(17Q11.2) MUTATED | 2 | 2 | 9 | 0
DEL PEAK 14(17Q11.2) WILD-TYPE | 146 | 12 | 18 | 2

Figure S35. Get High-res Image Gene #18: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S36. Gene #19: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
DEL PEAK 15(18P11.21) MUTATED | 1 | 0 | 8 | 0
DEL PEAK 15(18P11.21) WILD-TYPE | 147 | 14 | 19 | 2

Figure S36. Get High-res Image Gene #19: '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 = 20

- 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

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] 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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