Correlation between copy number variation genes (focal events) and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1S75FQ9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1S75FQ9
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 16 focal events and 6 molecular subtypes across 191 patients, 47 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_1p33 cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- amp_11q23.3 cnv correlated to 'METHLYATION_CNMF'.

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

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

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

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

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

- del_12p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_12q21.33 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- del_16q23.1 cnv correlated to 'CN_CNMF'.

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

- del_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- del_18p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 16 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, 47 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 | 0.00138 (0.00883) | 4e-05 (0.000768) | 0.00455 (0.0175) | 0.00068 (0.0062) | 0.00109 (0.00805) | 0.00109 (0.00805)
del 7p12 1 | 16 (8%) | 175 | 1e-05 (0.00048) | 0.00071 (0.0062) | 0.00227 (0.0109) | 1e-05 (0.00048) | 0.0189 (0.0477) | 0.00701 (0.0217)
del 7q32 3 | 23 (12%) | 168 | 2e-05 (0.00048) | 0.00062 (0.0062) | 0.0445 (0.0994) | 2e-05 (0.00048) | 0.00431 (0.0175) | 0.00172 (0.00933)
del 17p13 2 | 15 (8%) | 176 | 0.0218 (0.0538) | 0.00055 (0.0062) | 0.0128 (0.0352) | 0.00022 (0.00352) | 0.0668 (0.128) | 0.00126 (0.00864)
del 17q11 2 | 13 (7%) | 178 | 0.0159 (0.0424) | 0.0058 (0.0206) | 0.17 (0.247) | 0.00676 (0.0216) | 0.0188 (0.0477) | 0.00376 (0.0172)
amp 21q22 2 | 14 (7%) | 177 | 0.07 (0.132) | 0.00169 (0.00933) | 0.00402 (0.0175) | 0.0371 (0.0847) | 0.00597 (0.0206) | 0.0668 (0.128)
amp 1p33 | 7 (4%) | 184 | 0.809 (0.872) | 0.0471 (0.0996) | 0.148 (0.222) | 0.13 (0.2) | 0.00736 (0.0221) | 0.0486 (0.0996)
del 12p13 2 | 10 (5%) | 181 | 0.00032 (0.00439) | 0.0045 (0.0175) | 0.197 (0.273) | 0.0737 (0.136) | 0.126 (0.198) | 0.00977 (0.0284)
del 18p11 21 | 9 (5%) | 182 | 0.00175 (0.00933) | 0.0125 (0.0352) | 0.481 (0.57) | 0.334 (0.425) | 0.218 (0.29) | 0.0325 (0.076)
del 3p13 | 8 (4%) | 183 | 0.0545 (0.109) | 0.114 (0.186) | 0.0778 (0.141) | 0.237 (0.311) | 0.0466 (0.0996) | 0.0487 (0.0996)
del 12q21 33 | 3 (2%) | 188 | 0.131 (0.2) | 0.784 (0.855) | 0.262 (0.34) | 0.589 (0.666) | 0.00621 (0.0206) | 0.00616 (0.0206)
amp 11q23 3 | 17 (9%) | 174 | 0.098 (0.168) | 0.00197 (0.00995) | 0.373 (0.465) | 0.203 (0.274) | 0.481 (0.57) | 0.187 (0.265)
del 16q23 1 | 9 (5%) | 182 | 0.0302 (0.0724) | 0.0847 (0.151) | 1 (1.00) | 0.86 (0.917) | 0.097 (0.168) | 0.104 (0.173)
amp 20q11 21 | 3 (2%) | 188 | 0.391 (0.481) | 0.336 (0.425) |  |  |  |
del 9q21 32 | 5 (3%) | 186 | 0.502 (0.588) | 0.572 (0.662) | 0.178 (0.254) | 0.599 (0.669) | 0.199 (0.273) | 0.105 (0.173)
del 20q13 13 | 4 (2%) | 187 | 0.904 (0.954) | 0.16 (0.237) | 0.784 (0.855) | 0.589 (0.666) | 0.12 (0.193) | 0.411 (0.5)

'amp_1p33' versus 'METHLYATION_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.1

Table S1. Gene #1: 'amp_1p33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
AMP PEAK 1(1P33) MUTATED | 0 | 1 | 6 | 0 | 0
AMP PEAK 1(1P33) WILD-TYPE | 23 | 24 | 54 | 35 | 42

Figure S1. Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p33' versus 'MIRSEQ_CNMF'

P value = 0.00736 (Fisher's exact test), Q value = 0.022

Table S2. Gene #1: 'amp_1p33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
AMP PEAK 1(1P33) MUTATED | 1 | 1 | 1 | 0 | 4
AMP PEAK 1(1P33) WILD-TYPE | 56 | 30 | 38 | 33 | 15

Figure S2. Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_1p33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.1

Table S3. Gene #1: 'amp_1p33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
AMP PEAK 1(1P33) MUTATED | 0 | 3 | 4
AMP PEAK 1(1P33) WILD-TYPE | 67 | 31 | 74

Figure S3. Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q23.3' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.01

Table S4. Gene #2: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
AMP PEAK 2(11Q23.3) MUTATED | 0 | 0 | 13 | 1 | 3
AMP PEAK 2(11Q23.3) WILD-TYPE | 23 | 25 | 47 | 34 | 39

Figure S4. Get High-res Image Gene #2: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_21q22.2' versus 'METHLYATION_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0093

Table S5. Gene #4: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
AMP PEAK 4(21Q22.2) MUTATED | 1 | 0 | 11 | 1 | 0
AMP PEAK 4(21Q22.2) WILD-TYPE | 22 | 25 | 49 | 34 | 42

Figure S5. Get High-res Image Gene #4: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_21q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00402 (Fisher's exact test), Q value = 0.017

Table S6. Gene #4: 'amp_21q22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
AMP PEAK 4(21Q22.2) MUTATED | 10 | 1 | 0
AMP PEAK 4(21Q22.2) WILD-TYPE | 61 | 49 | 45

Figure S6. Get High-res Image Gene #4: 'amp_21q22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_21q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.085

Table S7. Gene #4: 'amp_21q22.2' 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
AMP PEAK 4(21Q22.2) MUTATED | 0 | 0 | 1 | 9 | 0 | 1
AMP PEAK 4(21Q22.2) WILD-TYPE | 16 | 13 | 13 | 46 | 26 | 41

Figure S7. Get High-res Image Gene #4: 'amp_21q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_21q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.021

Table S8. Gene #4: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
AMP PEAK 4(21Q22.2) MUTATED | 1 | 3 | 0 | 5 | 3
AMP PEAK 4(21Q22.2) WILD-TYPE | 56 | 28 | 39 | 28 | 16

Figure S8. Get High-res Image Gene #4: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.1

Table S9. Gene #5: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
DEL PEAK 1(3P13) MUTATED | 0 | 3 | 1 | 1 | 2
DEL PEAK 1(3P13) WILD-TYPE | 57 | 28 | 38 | 32 | 17

Figure S9. Get High-res Image Gene #5: 'del_3p13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.1

Table S10. Gene #5: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 1(3P13) MUTATED | 0 | 3 | 4
DEL PEAK 1(3P13) WILD-TYPE | 67 | 31 | 74

Figure S10. Get High-res Image Gene #5: 'del_3p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.2' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0088

Table S11. Gene #6: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 2(5Q31.2) MUTATED | 0 | 10 | 4 | 4
DEL PEAK 2(5Q31.2) WILD-TYPE | 49 | 34 | 51 | 39

Figure S11. Get High-res Image Gene #6: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00077

Table S12. Gene #6: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
DEL PEAK 2(5Q31.2) MUTATED | 1 | 0 | 15 | 2 | 0
DEL PEAK 2(5Q31.2) WILD-TYPE | 22 | 25 | 45 | 33 | 42

Figure S12. Get High-res Image Gene #6: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.2' versus 'MRNASEQ_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.017

Table S13. Gene #6: 'del_5q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
DEL PEAK 2(5Q31.2) MUTATED | 13 | 1 | 2
DEL PEAK 2(5Q31.2) WILD-TYPE | 58 | 49 | 43

Figure S13. Get High-res Image Gene #6: 'del_5q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0062

Table S14. Gene #6: '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 2(5Q31.2) MUTATED | 0 | 0 | 0 | 14 | 0 | 2
DEL PEAK 2(5Q31.2) WILD-TYPE | 16 | 13 | 14 | 41 | 26 | 40

Figure S14. Get High-res Image Gene #6: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.008

Table S15. Gene #6: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
DEL PEAK 2(5Q31.2) MUTATED | 1 | 7 | 2 | 2 | 5
DEL PEAK 2(5Q31.2) WILD-TYPE | 56 | 24 | 37 | 31 | 14

Figure S15. Get High-res Image Gene #6: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.008

Table S16. Gene #6: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S16. Get High-res Image Gene #6: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S17. Gene #7: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 3(7P12.1) MUTATED | 0 | 6 | 0 | 10
DEL PEAK 3(7P12.1) WILD-TYPE | 49 | 38 | 55 | 33

Figure S17. Get High-res Image Gene #7: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7p12.1' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0062

Table S18. Gene #7: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
DEL PEAK 3(7P12.1) MUTATED | 1 | 1 | 13 | 0 | 1
DEL PEAK 3(7P12.1) WILD-TYPE | 22 | 24 | 47 | 35 | 41

Figure S18. Get High-res Image Gene #7: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.011

Table S19. Gene #7: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
DEL PEAK 3(7P12.1) MUTATED | 12 | 0 | 3
DEL PEAK 3(7P12.1) WILD-TYPE | 59 | 50 | 42

Figure S19. Get High-res Image Gene #7: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S20. Gene #7: '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 3(7P12.1) MUTATED | 0 | 0 | 0 | 15 | 0 | 0
DEL PEAK 3(7P12.1) WILD-TYPE | 16 | 13 | 14 | 40 | 26 | 42

Figure S20. Get High-res Image Gene #7: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.048

Table S21. Gene #7: 'del_7p12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
DEL PEAK 3(7P12.1) MUTATED | 1 | 7 | 4 | 2 | 2
DEL PEAK 3(7P12.1) WILD-TYPE | 56 | 24 | 35 | 31 | 17

Figure S21. Get High-res Image Gene #7: 'del_7p12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00701 (Fisher's exact test), Q value = 0.022

Table S22. Gene #7: 'del_7p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 3(7P12.1) MUTATED | 1 | 6 | 9
DEL PEAK 3(7P12.1) WILD-TYPE | 66 | 28 | 69

Figure S22. Get High-res Image Gene #7: 'del_7p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q32.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S23. Gene #8: 'del_7q32.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 4(7Q32.3) MUTATED | 2 | 7 | 0 | 14
DEL PEAK 4(7Q32.3) WILD-TYPE | 47 | 37 | 55 | 29

Figure S23. Get High-res Image Gene #8: 'del_7q32.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q32.3' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0062

Table S24. Gene #8: 'del_7q32.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
DEL PEAK 4(7Q32.3) MUTATED | 1 | 2 | 17 | 1 | 2
DEL PEAK 4(7Q32.3) WILD-TYPE | 22 | 23 | 43 | 34 | 40

Figure S24. Get High-res Image Gene #8: 'del_7q32.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q32.3' versus 'MRNASEQ_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.099

Table S25. Gene #8: 'del_7q32.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
DEL PEAK 4(7Q32.3) MUTATED | 13 | 2 | 4
DEL PEAK 4(7Q32.3) WILD-TYPE | 58 | 48 | 41

Figure S25. Get High-res Image Gene #8: 'del_7q32.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S26. Gene #8: 'del_7q32.3' 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(7Q32.3) MUTATED | 1 | 1 | 0 | 17 | 0 | 0
DEL PEAK 4(7Q32.3) WILD-TYPE | 15 | 12 | 14 | 38 | 26 | 42

Figure S26. Get High-res Image Gene #8: 'del_7q32.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q32.3' versus 'MIRSEQ_CNMF'

P value = 0.00431 (Fisher's exact test), Q value = 0.017

Table S27. Gene #8: 'del_7q32.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
DEL PEAK 4(7Q32.3) MUTATED | 2 | 10 | 5 | 3 | 2
DEL PEAK 4(7Q32.3) WILD-TYPE | 55 | 21 | 34 | 30 | 17

Figure S27. Get High-res Image Gene #8: 'del_7q32.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.0093

Table S28. Gene #8: 'del_7q32.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 4(7Q32.3) MUTATED | 2 | 9 | 11
DEL PEAK 4(7Q32.3) WILD-TYPE | 65 | 25 | 67

Figure S28. Get High-res Image Gene #8: 'del_7q32.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0044

Table S29. Gene #10: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 6(12P13.2) MUTATED | 0 | 8 | 1 | 1
DEL PEAK 6(12P13.2) WILD-TYPE | 49 | 36 | 54 | 42

Figure S29. Get High-res Image Gene #10: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.2' versus 'METHLYATION_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.017

Table S30. Gene #10: 'del_12p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
DEL PEAK 6(12P13.2) MUTATED | 0 | 0 | 9 | 1 | 0
DEL PEAK 6(12P13.2) WILD-TYPE | 23 | 25 | 51 | 34 | 42

Figure S30. Get High-res Image Gene #10: 'del_12p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00977 (Fisher's exact test), Q value = 0.028

Table S31. Gene #10: 'del_12p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 6(12P13.2) MUTATED | 0 | 4 | 6
DEL PEAK 6(12P13.2) WILD-TYPE | 67 | 30 | 72

Figure S31. Get High-res Image Gene #10: 'del_12p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12q21.33' versus 'MIRSEQ_CNMF'

P value = 0.00621 (Fisher's exact test), Q value = 0.021

Table S32. Gene #11: 'del_12q21.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
DEL PEAK 7(12Q21.33) MUTATED | 0 | 3 | 0 | 0 | 0
DEL PEAK 7(12Q21.33) WILD-TYPE | 57 | 28 | 39 | 33 | 19

Figure S32. Get High-res Image Gene #11: 'del_12q21.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_12q21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00616 (Fisher's exact test), Q value = 0.021

Table S33. Gene #11: 'del_12q21.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 7(12Q21.33) MUTATED | 0 | 3 | 0
DEL PEAK 7(12Q21.33) WILD-TYPE | 67 | 31 | 78

Figure S33. Get High-res Image Gene #11: 'del_12q21.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.072

Table S34. Gene #12: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 8(16Q23.1) MUTATED | 1 | 4 | 0 | 4
DEL PEAK 8(16Q23.1) WILD-TYPE | 48 | 40 | 55 | 39

Figure S34. Get High-res Image Gene #12: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.054

Table S35. Gene #13: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 9(17P13.2) MUTATED | 0 | 7 | 5 | 3
DEL PEAK 9(17P13.2) WILD-TYPE | 49 | 37 | 50 | 40

Figure S35. Get High-res Image Gene #13: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0062

Table S36. Gene #13: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
DEL PEAK 9(17P13.2) MUTATED | 0 | 0 | 12 | 3 | 0
DEL PEAK 9(17P13.2) WILD-TYPE | 23 | 25 | 48 | 32 | 42

Figure S36. Get High-res Image Gene #13: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.035

Table S37. Gene #13: 'del_17p13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
DEL PEAK 9(17P13.2) MUTATED | 12 | 2 | 1
DEL PEAK 9(17P13.2) WILD-TYPE | 59 | 48 | 44

Figure S37. Get High-res Image Gene #13: 'del_17p13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0035

Table S38. Gene #13: '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 9(17P13.2) MUTATED | 0 | 0 | 0 | 14 | 0 | 1
DEL PEAK 9(17P13.2) WILD-TYPE | 16 | 13 | 14 | 41 | 26 | 41

Figure S38. Get High-res Image Gene #13: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0086

Table S39. Gene #13: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 9(17P13.2) MUTATED | 0 | 5 | 10
DEL PEAK 9(17P13.2) WILD-TYPE | 67 | 29 | 68

Figure S39. Get High-res Image Gene #13: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.042

Table S40. Gene #14: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 10(17Q11.2) MUTATED | 0 | 7 | 4 | 2
DEL PEAK 10(17Q11.2) WILD-TYPE | 49 | 37 | 51 | 41

Figure S40. Get High-res Image Gene #14: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.021

Table S41. Gene #14: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
DEL PEAK 10(17Q11.2) MUTATED | 0 | 0 | 9 | 4 | 0
DEL PEAK 10(17Q11.2) WILD-TYPE | 23 | 25 | 51 | 31 | 42

Figure S41. Get High-res Image Gene #14: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00676 (Fisher's exact test), Q value = 0.022

Table S42. Gene #14: 'del_17q11.2' 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 10(17Q11.2) MUTATED | 0 | 1 | 0 | 11 | 0 | 1
DEL PEAK 10(17Q11.2) WILD-TYPE | 16 | 12 | 14 | 44 | 26 | 41

Figure S42. Get High-res Image Gene #14: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.048

Table S43. Gene #14: 'del_17q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
DEL PEAK 10(17Q11.2) MUTATED | 1 | 2 | 3 | 2 | 5
DEL PEAK 10(17Q11.2) WILD-TYPE | 56 | 29 | 36 | 31 | 14

Figure S43. Get High-res Image Gene #14: 'del_17q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.017

Table S44. Gene #14: 'del_17q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 10(17Q11.2) MUTATED | 0 | 4 | 9
DEL PEAK 10(17Q11.2) WILD-TYPE | 67 | 30 | 69

Figure S44. Get High-res Image Gene #14: 'del_17q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_18p11.21' versus 'CN_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0093

Table S45. Gene #15: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
DEL PEAK 11(18P11.21) MUTATED | 0 | 7 | 1 | 1
DEL PEAK 11(18P11.21) WILD-TYPE | 49 | 37 | 54 | 42

Figure S45. Get High-res Image Gene #15: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.21' versus 'METHLYATION_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.035

Table S46. Gene #15: 'del_18p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
DEL PEAK 11(18P11.21) MUTATED | 0 | 0 | 8 | 1 | 0
DEL PEAK 11(18P11.21) WILD-TYPE | 23 | 25 | 52 | 34 | 42

Figure S46. Get High-res Image Gene #15: 'del_18p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.076

Table S47. Gene #15: 'del_18p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
DEL PEAK 11(18P11.21) MUTATED | 0 | 3 | 5
DEL PEAK 11(18P11.21) WILD-TYPE | 67 | 31 | 73

Figure S47. Get High-res Image Gene #15: 'del_18p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = all_lesions.txt from GISTIC pipeline

- Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/22529563/transformed.cor.cli.txt

- Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/LAML-TB.transferedmergedcluster.txt

- Number of patients = 191

- Number of significantly focal cnvs = 16

- 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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