Correlation between copy number variations of arm-level result 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/C1GT5M1G
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/C1GT5M1G
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, 27 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', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 11p gain cnv correlated to 'CN_CNMF'.

- 11q 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, 27 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) | 4e-05 (0.00664) | 0.00618 (0.834) | 1e-05 (0.00174) | 0.00151 (0.226) | 0.00076 (0.119)
7p loss | 17 (9%) | 174 | 4e-05 (0.00664) | 0.00012 (0.0196) | 0.00096 (0.149) | 1e-05 (0.00174) | 0.00351 (0.495) | 0.00357 (0.5)
8p gain | 22 (12%) | 169 | 0.00084 (0.131) | 0.00049 (0.0784) | 0.0283 (1.00) | 0.00074 (0.117) | 0.0103 (1.00) | 0.0162 (1.00)
8q gain | 23 (12%) | 168 | 0.00145 (0.219) | 0.00152 (0.226) | 0.0131 (1.00) | 0.00157 (0.232) | 0.00719 (0.942) | 0.015 (1.00)
11p gain | 4 (2%) | 187 | 0.00071 (0.113) | 0.147 (1.00) | 0.467 (1.00) | 0.366 (1.00) | 0.527 (1.00) | 0.0226 (1.00)
11q gain | 7 (4%) | 184 | 2e-05 (0.00338) | 0.0126 (1.00) | 0.0664 (1.00) | 0.0744 (1.00) | 0.293 (1.00) | 0.016 (1.00)
21q gain | 8 (4%) | 183 | 1e-05 (0.00174) | 0.231 (1.00) | 0.126 (1.00) | 0.525 (1.00) | 0.0818 (1.00) | 0.411 (1.00)
22q gain | 9 (5%) | 182 | 0.00104 (0.16) | 0.0179 (1.00) | 0.134 (1.00) | 0.0163 (1.00) | 0.055 (1.00) | 0.0127 (1.00)
5q loss | 6 (3%) | 185 | 2e-05 (0.00338) | 0.0304 (1.00) | 0.225 (1.00) | 0.631 (1.00) | 0.0316 (1.00) | 0.0327 (1.00)
15q loss | 4 (2%) | 187 | 0.00045 (0.0724) | 0.571 (1.00) | 0.0665 (1.00) | 0.368 (1.00) | 0.023 (1.00) | 0.184 (1.00)
16q loss | 4 (2%) | 187 | 0.00126 (0.193) | 0.147 (1.00) | 0.785 (1.00) | 1 (1.00) | 0.0144 (1.00) | 0.0221 (1.00)
17p loss | 13 (7%) | 178 | 1e-05 (0.00174) | 0.00449 (0.62) | 0.157 (1.00) | 0.00191 (0.279) | 0.16 (1.00) | 0.00343 (0.487)
17q loss | 7 (4%) | 184 | 2e-05 (0.00338) | 0.214 (1.00) | 0.065 (1.00) | 0.233 (1.00) | 0.0391 (1.00) | 0.0485 (1.00)
18p loss | 5 (3%) | 186 | 0.00033 (0.0535) | 0.0685 (1.00) | 1 (1.00) | 0.866 (1.00) | 0.247 (1.00) | 0.186 (1.00)
18q loss | 4 (2%) | 187 | 0.00134 (0.204) | 0.145 (1.00) | 0.467 (1.00) | 0.865 (1.00) | 0.101 (1.00) | 0.184 (1.00)
xq loss | 5 (3%) | 186 | 6e-05 (0.00984) | 0.145 (1.00) | 0.221 (1.00) | 0.631 (1.00) | 0.00331 (0.473) | 0.00462 (0.633)
1p gain | 3 (2%) | 188 | 0.00412 (0.573) | 0.265 (1.00) | 0.187 (1.00) | 0.587 (1.00) | 0.0925 (1.00) | 0.0919 (1.00)
4p gain | 4 (2%) | 187 | 0.0286 (1.00) | 0.0485 (1.00) |  |  | 0.341 (1.00) | 0.835 (1.00)
4q gain | 4 (2%) | 187 | 0.028 (1.00) | 0.0495 (1.00) |  |  | 0.345 (1.00) | 0.834 (1.00)
10q gain | 3 (2%) | 188 | 0.0148 (1.00) | 0.266 (1.00) | 0.185 (1.00) | 0.589 (1.00) | 0.554 (1.00) | 0.0913 (1.00)
13q gain | 6 (3%) | 185 | 0.0418 (1.00) | 0.0293 (1.00) | 0.124 (1.00) | 0.0832 (1.00) | 0.802 (1.00) | 0.074 (1.00)
17q gain | 3 (2%) | 188 | 0.00621 (0.834) | 0.302 (1.00) | 1 (1.00) | 0.59 (1.00) | 0.482 (1.00) | 0.307 (1.00)
19p gain | 5 (3%) | 186 | 0.0127 (1.00) | 0.643 (1.00) | 1 (1.00) | 0.864 (1.00) | 0.578 (1.00) | 1 (1.00)
19q gain | 5 (3%) | 186 | 0.0127 (1.00) | 0.645 (1.00) | 1 (1.00) | 0.865 (1.00) | 0.581 (1.00) | 1 (1.00)
xq gain | 3 (2%) | 188 | 0.00174 (0.256) | 0.882 (1.00) |  |  | 0.891 (1.00) | 0.0452 (1.00)
3p loss | 3 (2%) | 188 | 0.00707 (0.933) | 0.264 (1.00) | 0.787 (1.00) | 1 (1.00) | 0.0615 (1.00) | 0.0918 (1.00)
3q loss | 3 (2%) | 188 | 0.0067 (0.891) | 0.266 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.0617 (1.00) | 0.0938 (1.00)
12p loss | 4 (2%) | 187 | 0.00599 (0.815) | 0.0952 (1.00) | 0.375 (1.00) | 0.39 (1.00) | 0.484 (1.00) | 0.185 (1.00)
19p loss | 4 (2%) | 187 | 0.00307 (0.442) | 0.536 (1.00) | 0.465 (1.00) | 0.865 (1.00) | 0.312 (1.00) | 0.248 (1.00)
19q loss | 4 (2%) | 187 | 0.00298 (0.432) | 0.536 (1.00) | 0.468 (1.00) | 0.864 (1.00) | 0.314 (1.00) | 0.251 (1.00)

'8p gain' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.13

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
8P GAIN MUTATED | 11 | 1 | 10 | 0
8P GAIN WILD-TYPE | 137 | 13 | 17 | 2

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

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.078

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 = 0.00074 (Fisher's exact test), Q value = 0.12

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 = 0.00145 (Fisher's exact test), Q value = 0.22

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
8Q GAIN MUTATED | 12 | 1 | 10 | 0
8Q GAIN WILD-TYPE | 136 | 13 | 17 | 2

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

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.23

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'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.23

Table S6. Gene #5: '8q 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
8Q GAIN MUTATED | 1 | 0 | 1 | 15 | 1 | 1
8Q GAIN WILD-TYPE | 15 | 13 | 13 | 40 | 25 | 41

Figure S6. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

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

Table S7. Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
11P GAIN MUTATED | 0 | 3 | 1 | 0
11P GAIN WILD-TYPE | 148 | 11 | 26 | 2

Figure S7. 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 S8. Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
11Q GAIN MUTATED | 0 | 4 | 3 | 0
11Q GAIN WILD-TYPE | 148 | 10 | 24 | 2

Figure S8. Get High-res Image Gene #8: '11q 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 S9. Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
21Q GAIN MUTATED | 0 | 0 | 8 | 0
21Q GAIN WILD-TYPE | 148 | 14 | 19 | 2

Figure S9. Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.16

Table S10. Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
22Q GAIN MUTATED | 2 | 2 | 5 | 0
22Q GAIN WILD-TYPE | 146 | 12 | 22 | 2

Figure S10. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

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

Table S11. Gene #18: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
5Q LOSS MUTATED | 0 | 0 | 6 | 0
5Q LOSS WILD-TYPE | 148 | 14 | 21 | 2

Figure S11. Get High-res Image Gene #18: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0066

Table S12. Gene #19: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
7P LOSS MUTATED | 7 | 0 | 9 | 1
7P LOSS WILD-TYPE | 141 | 14 | 18 | 1

Figure S12. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.02

Table S13. 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 S13. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.15

Table S14. 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 S14. 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 S15. 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 S15. 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 S16. Gene #20: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
7Q LOSS MUTATED | 8 | 0 | 11 | 1
7Q LOSS WILD-TYPE | 140 | 14 | 16 | 1

Figure S16. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0066

Table S17. 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 S17. 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 S18. 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 S18. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.23

Table S19. 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 S19. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.12

Table S20. 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 S20. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.072

Table S21. Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
15Q LOSS MUTATED | 0 | 0 | 3 | 1
15Q LOSS WILD-TYPE | 148 | 14 | 24 | 1

Figure S21. Get High-res Image Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.19

Table S22. Gene #23: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
16Q LOSS MUTATED | 0 | 0 | 4 | 0
16Q LOSS WILD-TYPE | 148 | 14 | 23 | 2

Figure S22. 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 S23. Gene #24: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
17P LOSS MUTATED | 0 | 0 | 13 | 0
17P LOSS WILD-TYPE | 148 | 14 | 14 | 2

Figure S23. Get High-res Image Gene #24: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'CN_CNMF'

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

Table S24. Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
17Q LOSS MUTATED | 0 | 0 | 7 | 0
17Q LOSS WILD-TYPE | 148 | 14 | 20 | 2

Figure S24. Get High-res Image Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.053

Table S25. Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
18P LOSS MUTATED | 0 | 0 | 5 | 0
18P LOSS WILD-TYPE | 148 | 14 | 22 | 2

Figure S25. Get High-res Image Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.2

Table S26. Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
18Q LOSS MUTATED | 0 | 0 | 4 | 0
18Q LOSS WILD-TYPE | 148 | 14 | 23 | 2

Figure S26. Get High-res Image Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0098

Table S27. Gene #30: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
XQ LOSS MUTATED | 0 | 0 | 4 | 1
XQ LOSS WILD-TYPE | 148 | 14 | 23 | 1

Figure S27. 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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