Correlation between copy number variations of arm-level result and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1BR8QXK
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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1BR8QXK
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 30 arm-level events and 6 molecular subtypes across 191 patients, 28 significant findings detected with P value < 0.05 and Q value < 0.25.

- 8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 11p gain cnv correlated to 'CN_CNMF'.

- 11q gain cnv correlated to 'CN_CNMF'.

- 19p gain cnv correlated to 'CN_CNMF'.

- 19q gain cnv correlated to 'CN_CNMF'.

- 21q gain cnv correlated to 'CN_CNMF'.

- 22q gain cnv correlated to 'CN_CNMF'.

- 5q loss cnv correlated to 'CN_CNMF'.

- 7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 15q loss cnv correlated to 'CN_CNMF'.

- 16q loss cnv correlated to 'CN_CNMF'.

- 17p loss cnv correlated to 'CN_CNMF'.

- 17q loss cnv correlated to 'CN_CNMF'.

- 18p loss cnv correlated to 'CN_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

- xq loss 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 30 arm-level 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, 28 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
7q loss | 20 (10%) | 171 | 1e-05 (0.00174) | 3e-05 (0.00504) | 0.00601 (0.805) | 1e-05 (0.00174) | 0.00142 (0.214) | 0.00088 (0.136)
7p loss | 17 (9%) | 174 | 0.00013 (0.0214) | 0.00029 (0.047) | 0.00097 (0.149) | 1e-05 (0.00174) | 0.00382 (0.535) | 0.00295 (0.425)
8p gain | 22 (12%) | 169 | 0.001 (0.153) | 0.00047 (0.0757) | 0.0287 (1.00) | 0.00082 (0.128) | 0.01 (1.00) | 0.016 (1.00)
8q gain | 23 (12%) | 168 | 0.0017 (0.25) | 0.0016 (0.237) | 0.0134 (1.00) | 0.00173 (0.253) | 0.00721 (0.956) | 0.0146 (1.00)
11p gain | 4 (2%) | 187 | 0.00066 (0.105) | 0.147 (1.00) | 0.467 (1.00) | 0.365 (1.00) | 0.519 (1.00) | 0.022 (1.00)
11q gain | 7 (4%) | 184 | 2e-05 (0.00338) | 0.0121 (1.00) | 0.0655 (1.00) | 0.0737 (1.00) | 0.291 (1.00) | 0.0154 (1.00)
19p gain | 5 (3%) | 186 | 0.00078 (0.122) | 0.645 (1.00) | 1 (1.00) | 0.864 (1.00) | 0.579 (1.00) | 1 (1.00)
19q gain | 5 (3%) | 186 | 0.00071 (0.112) | 0.646 (1.00) | 1 (1.00) | 0.865 (1.00) | 0.578 (1.00) | 1 (1.00)
21q gain | 8 (4%) | 183 | 1e-05 (0.00174) | 0.23 (1.00) | 0.126 (1.00) | 0.524 (1.00) | 0.0813 (1.00) | 0.409 (1.00)
22q gain | 9 (5%) | 182 | 0.00124 (0.188) | 0.0178 (1.00) | 0.136 (1.00) | 0.0162 (1.00) | 0.0567 (1.00) | 0.0132 (1.00)
5q loss | 6 (3%) | 185 | 6e-05 (0.00996) | 0.0302 (1.00) | 0.224 (1.00) | 0.632 (1.00) | 0.0314 (1.00) | 0.0329 (1.00)
15q loss | 4 (2%) | 187 | 0.00052 (0.0832) | 0.57 (1.00) | 0.0657 (1.00) | 0.366 (1.00) | 0.0236 (1.00) | 0.186 (1.00)
16q loss | 4 (2%) | 187 | 0.00159 (0.237) | 0.149 (1.00) | 0.785 (1.00) | 1 (1.00) | 0.0147 (1.00) | 0.0217 (1.00)
17p loss | 13 (7%) | 178 | 1e-05 (0.00174) | 0.00418 (0.574) | 0.156 (1.00) | 0.00192 (0.278) | 0.162 (1.00) | 0.00345 (0.49)
17q loss | 7 (4%) | 184 | 3e-05 (0.00504) | 0.216 (1.00) | 0.0685 (1.00) | 0.233 (1.00) | 0.04 (1.00) | 0.0475 (1.00)
18p loss | 5 (3%) | 186 | 0.00021 (0.0342) | 0.0687 (1.00) | 1 (1.00) | 0.865 (1.00) | 0.248 (1.00) | 0.185 (1.00)
18q loss | 4 (2%) | 187 | 0.00157 (0.235) | 0.148 (1.00) | 0.468 (1.00) | 0.864 (1.00) | 0.101 (1.00) | 0.186 (1.00)
xq loss | 5 (3%) | 186 | 0.00013 (0.0214) | 0.145 (1.00) | 0.224 (1.00) | 0.632 (1.00) | 0.00347 (0.49) | 0.00482 (0.656)
1p gain | 3 (2%) | 188 | 0.00552 (0.745) | 0.266 (1.00) | 0.185 (1.00) | 0.588 (1.00) | 0.0906 (1.00) | 0.0936 (1.00)
4p gain | 4 (2%) | 187 | 0.0266 (1.00) | 0.0483 (1.00) |  |  | 0.341 (1.00) | 0.835 (1.00)
4q gain | 4 (2%) | 187 | 0.0256 (1.00) | 0.05 (1.00) |  |  | 0.342 (1.00) | 0.833 (1.00)
10q gain | 3 (2%) | 188 | 0.0119 (1.00) | 0.27 (1.00) | 0.187 (1.00) | 0.588 (1.00) | 0.554 (1.00) | 0.0949 (1.00)
13q gain | 6 (3%) | 185 | 0.033 (1.00) | 0.0303 (1.00) | 0.125 (1.00) | 0.0837 (1.00) | 0.799 (1.00) | 0.0729 (1.00)
17q gain | 3 (2%) | 188 | 0.00856 (1.00) | 0.302 (1.00) | 1 (1.00) | 0.589 (1.00) | 0.484 (1.00) | 0.305 (1.00)
xq gain | 3 (2%) | 188 | 0.00296 (0.425) | 0.88 (1.00) |  |  | 0.893 (1.00) | 0.0459 (1.00)
3p loss | 3 (2%) | 188 | 0.00719 (0.956) | 0.268 (1.00) | 0.785 (1.00) | 1 (1.00) | 0.0607 (1.00) | 0.0926 (1.00)
3q loss | 3 (2%) | 188 | 0.0075 (0.982) | 0.264 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.062 (1.00) | 0.092 (1.00)
12p loss | 4 (2%) | 187 | 0.0084 (1.00) | 0.0949 (1.00) | 0.373 (1.00) | 0.393 (1.00) | 0.484 (1.00) | 0.185 (1.00)
19p loss | 4 (2%) | 187 | 0.00416 (0.574) | 0.536 (1.00) | 0.468 (1.00) | 0.866 (1.00) | 0.312 (1.00) | 0.247 (1.00)
19q loss | 4 (2%) | 187 | 0.00406 (0.564) | 0.534 (1.00) | 0.465 (1.00) | 0.865 (1.00) | 0.311 (1.00) | 0.248 (1.00)

'8p gain' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.15

Table S1. Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
8P GAIN MUTATED | 11 | 1 | 10 | 0
8P GAIN WILD-TYPE | 136 | 13 | 17 | 3

Figure S1. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.076

Table S2. Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
8P GAIN MUTATED | 2 | 1 | 16 | 0 | 2
8P GAIN WILD-TYPE | 44 | 43 | 45 | 14 | 18

Figure S2. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.13

Table S3. Gene #4: '8p gain' 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
8P GAIN MUTATED | 1 | 0 | 0 | 15 | 1 | 1
8P GAIN WILD-TYPE | 15 | 13 | 14 | 40 | 25 | 41

Figure S3. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.25

Table S4. Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
8Q GAIN MUTATED | 12 | 1 | 10 | 0
8Q GAIN WILD-TYPE | 135 | 13 | 17 | 3

Figure S4. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.24

Table S5. Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
8Q GAIN MUTATED | 2 | 2 | 16 | 0 | 2
8Q GAIN WILD-TYPE | 44 | 42 | 45 | 14 | 18

Figure S5. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.1

Table S6. Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
11P GAIN MUTATED | 0 | 3 | 1 | 0
11P GAIN WILD-TYPE | 147 | 11 | 26 | 3

Figure S6. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0034

Table S7. Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
11Q GAIN MUTATED | 0 | 4 | 3 | 0
11Q GAIN WILD-TYPE | 147 | 10 | 24 | 3

Figure S7. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.12

Table S8. Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
19P GAIN MUTATED | 0 | 1 | 4 | 0
19P GAIN WILD-TYPE | 147 | 13 | 23 | 3

Figure S8. Get High-res Image Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.11

Table S9. Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
19Q GAIN MUTATED | 0 | 1 | 4 | 0
19Q GAIN WILD-TYPE | 147 | 13 | 23 | 3

Figure S9. Get High-res Image Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S10. Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
21Q GAIN MUTATED | 0 | 0 | 8 | 0
21Q GAIN WILD-TYPE | 147 | 14 | 19 | 3

Figure S10. Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.19

Table S11. Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
22Q GAIN MUTATED | 2 | 2 | 5 | 0
22Q GAIN WILD-TYPE | 145 | 12 | 22 | 3

Figure S11. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.01

Table S12. Gene #18: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
5Q LOSS MUTATED | 0 | 0 | 6 | 0
5Q LOSS WILD-TYPE | 147 | 14 | 21 | 3

Figure S12. Get High-res Image Gene #18: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.021

Table S13. Gene #19: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
7P LOSS MUTATED | 7 | 0 | 8 | 2
7P LOSS WILD-TYPE | 140 | 14 | 19 | 1

Figure S13. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.047

Table S14. Gene #19: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
7P LOSS MUTATED | 1 | 0 | 14 | 1 | 1
7P LOSS WILD-TYPE | 45 | 44 | 47 | 13 | 19

Figure S14. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.15

Table S15. Gene #19: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 52 | 44
7P LOSS MUTATED | 13 | 0 | 3
7P LOSS WILD-TYPE | 57 | 52 | 41

Figure S15. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S16. Gene #19: '7p loss' 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
7P LOSS MUTATED | 0 | 0 | 0 | 16 | 0 | 0
7P LOSS WILD-TYPE | 16 | 13 | 14 | 39 | 26 | 42

Figure S16. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S17. Gene #20: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
7Q LOSS MUTATED | 8 | 0 | 10 | 2
7Q LOSS WILD-TYPE | 139 | 14 | 17 | 1

Figure S17. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.005

Table S18. Gene #20: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 46 | 44 | 61 | 14 | 20
7Q LOSS MUTATED | 1 | 0 | 17 | 1 | 1
7Q LOSS WILD-TYPE | 45 | 44 | 44 | 13 | 19

Figure S18. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S19. Gene #20: '7q loss' 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
7Q LOSS MUTATED | 0 | 0 | 0 | 17 | 0 | 0
7Q LOSS WILD-TYPE | 16 | 13 | 14 | 38 | 26 | 42

Figure S19. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.21

Table S20. Gene #20: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
7Q LOSS MUTATED | 1 | 10 | 4 | 4
7Q LOSS WILD-TYPE | 57 | 27 | 37 | 39

Figure S20. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.14

Table S21. Gene #20: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
7Q LOSS MUTATED | 1 | 8 | 10
7Q LOSS WILD-TYPE | 66 | 26 | 68

Figure S21. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.083

Table S22. Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
15Q LOSS MUTATED | 0 | 0 | 3 | 1
15Q LOSS WILD-TYPE | 147 | 14 | 24 | 2

Figure S22. Get High-res Image Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.24

Table S23. Gene #23: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
16Q LOSS MUTATED | 0 | 0 | 4 | 0
16Q LOSS WILD-TYPE | 147 | 14 | 23 | 3

Figure S23. Get High-res Image Gene #23: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S24. Gene #24: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
17P LOSS MUTATED | 0 | 0 | 13 | 0
17P LOSS WILD-TYPE | 147 | 14 | 14 | 3

Figure S24. Get High-res Image Gene #24: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.005

Table S25. Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
17Q LOSS MUTATED | 0 | 0 | 7 | 0
17Q LOSS WILD-TYPE | 147 | 14 | 20 | 3

Figure S25. Get High-res Image Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.034

Table S26. Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
18P LOSS MUTATED | 0 | 0 | 5 | 0
18P LOSS WILD-TYPE | 147 | 14 | 22 | 3

Figure S26. Get High-res Image Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.24

Table S27. Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
18Q LOSS MUTATED | 0 | 0 | 4 | 0
18Q LOSS WILD-TYPE | 147 | 14 | 23 | 3

Figure S27. Get High-res Image Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.021

Table S28. Gene #30: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 147 | 14 | 27 | 3
XQ LOSS MUTATED | 0 | 0 | 4 | 1
XQ LOSS WILD-TYPE | 147 | 14 | 23 | 2

Figure S28. Get High-res Image Gene #30: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

- Number of patients = 191

- Number of significantly arm-level cnvs = 30

- Number of molecular subtypes = 6

- Exclude genes that fewer than K tumors have mutations, 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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