Correlation between copy number variations of arm-level result and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1ZW1JZ8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZW1JZ8
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 32 arm-level events and 6 molecular subtypes across 191 patients, 79 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1p gain cnv correlated to 'CN_CNMF'.

- 4p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 4q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

- 8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 10q gain cnv correlated to 'CN_CNMF'.

- 11p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- 11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 17q 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', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- xp gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- xq gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- 3p loss cnv correlated to 'CN_CNMF'.

- 3q loss cnv correlated to 'CN_CNMF'.

- 5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

- 12p loss cnv correlated to 'CN_CNMF'.

- 15q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

- 16q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 17q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 18p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

- 19p loss cnv correlated to 'CN_CNMF'.

- 19q loss cnv correlated to 'CN_CNMF'.

- xp loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- xq loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 32 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, 79 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
8p gain | 22 (12%) | 169 | 0.00091 (0.00793) | 0.00025 (0.0032) | 0.0287 (0.0795) | 0.00084 (0.00793) | 0.00981 (0.0349) | 0.0163 (0.0497)
8q gain | 23 (12%) | 168 | 0.00147 (0.0101) | 0.00039 (0.00452) | 0.0135 (0.0454) | 0.00184 (0.0112) | 0.00711 (0.0268) | 0.0145 (0.0462)
7p loss | 17 (9%) | 174 | 4e-05 (0.000698) | 0.00016 (0.00236) | 0.00095 (0.00793) | 1e-05 (0.00024) | 0.00358 (0.0181) | 0.00339 (0.0181)
7q loss | 20 (10%) | 171 | 1e-05 (0.00024) | 2e-05 (0.000427) | 0.00585 (0.0252) | 1e-05 (0.00024) | 0.00143 (0.0101) | 0.00084 (0.00793)
22q gain | 9 (5%) | 182 | 0.00095 (0.00793) | 0.00425 (0.0204) | 0.137 (0.258) | 0.0168 (0.0504) | 0.0562 (0.132) | 0.0132 (0.0452)
5q loss | 6 (3%) | 185 | 1e-05 (0.00024) | 0.00682 (0.0262) | 0.226 (0.364) | 0.633 (0.769) | 0.0312 (0.082) | 0.0327 (0.0848)
17p loss | 13 (7%) | 178 | 1e-05 (0.00024) | 0.00187 (0.0112) | 0.157 (0.292) | 0.00138 (0.0101) | 0.161 (0.296) | 0.00385 (0.019)
11q gain | 7 (4%) | 184 | 1e-05 (0.00024) | 0.0298 (0.0795) | 0.0667 (0.147) | 0.0736 (0.159) | 0.291 (0.443) | 0.0149 (0.0462)
16q loss | 4 (2%) | 187 | 0.00108 (0.00864) | 0.0556 (0.132) | 0.785 (0.923) | 1 (1.00) | 0.0145 (0.0462) | 0.0224 (0.0643)
17q loss | 7 (4%) | 184 | 1e-05 (0.00024) | 0.112 (0.218) | 0.0667 (0.147) | 0.234 (0.375) | 0.0375 (0.0959) | 0.0491 (0.119)
xp loss | 5 (3%) | 186 | 0.00012 (0.00192) | 0.199 (0.345) | 0.224 (0.364) | 0.631 (0.769) | 0.00353 (0.0181) | 0.00501 (0.0224)
xq loss | 5 (3%) | 186 | 4e-05 (0.000698) | 0.201 (0.345) | 0.224 (0.364) | 0.631 (0.769) | 0.0033 (0.0181) | 0.0048 (0.0219)
4p gain | 4 (2%) | 187 | 0.0294 (0.0795) | 0.00755 (0.0274) |  |  | 0.342 (0.501) | 0.837 (0.962)
4q gain | 4 (2%) | 187 | 0.0292 (0.0795) | 0.0074 (0.0273) |  |  | 0.342 (0.501) | 0.833 (0.962)
11p gain | 4 (2%) | 187 | 0.0007 (0.00747) | 0.43 (0.597) | 0.465 (0.625) | 0.369 (0.533) | 0.523 (0.682) | 0.0221 (0.0643)
13q gain | 6 (3%) | 185 | 0.0418 (0.106) | 0.00655 (0.0259) | 0.124 (0.238) | 0.0845 (0.178) | 0.801 (0.932) | 0.0736 (0.159)
xp gain | 3 (2%) | 188 | 0.00183 (0.0112) | 0.699 (0.837) |  |  | 0.892 (0.978) | 0.0468 (0.115)
xq gain | 3 (2%) | 188 | 0.00159 (0.0105) | 0.701 (0.837) |  |  | 0.891 (0.978) | 0.0469 (0.115)
15q loss | 4 (2%) | 187 | 0.0004 (0.00452) | 0.55 (0.707) | 0.0662 (0.147) | 0.369 (0.533) | 0.0228 (0.0645) | 0.186 (0.326)
18p loss | 5 (3%) | 186 | 0.00018 (0.00247) | 0.0207 (0.0613) | 1 (1.00) | 0.864 (0.962) | 0.249 (0.386) | 0.185 (0.326)
1p gain | 3 (2%) | 188 | 0.00441 (0.0207) | 0.209 (0.349) | 0.185 (0.326) | 0.592 (0.733) | 0.0911 (0.185) | 0.0927 (0.185)
10q gain | 3 (2%) | 188 | 0.0148 (0.0462) | 0.21 (0.349) | 0.184 (0.326) | 0.59 (0.733) | 0.552 (0.707) | 0.0924 (0.185)
17q gain | 3 (2%) | 188 | 0.00626 (0.0257) | 0.702 (0.837) | 1 (1.00) | 0.591 (0.733) | 0.482 (0.634) | 0.304 (0.459)
19p gain | 5 (3%) | 186 | 0.0141 (0.0462) | 0.249 (0.386) | 1 (1.00) | 0.867 (0.962) | 0.581 (0.733) | 1 (1.00)
19q gain | 5 (3%) | 186 | 0.0126 (0.0441) | 0.248 (0.386) | 1 (1.00) | 0.864 (0.962) | 0.578 (0.733) | 1 (1.00)
21q gain | 8 (4%) | 183 | 1e-05 (0.00024) | 0.112 (0.218) | 0.125 (0.239) | 0.525 (0.682) | 0.0829 (0.177) | 0.412 (0.582)
3p loss | 3 (2%) | 188 | 0.00662 (0.0259) | 0.211 (0.349) | 0.788 (0.923) | 1 (1.00) | 0.0611 (0.141) | 0.0926 (0.185)
3q loss | 3 (2%) | 188 | 0.0063 (0.0257) | 0.21 (0.349) | 0.788 (0.923) | 1 (1.00) | 0.0622 (0.142) | 0.0922 (0.185)
12p loss | 4 (2%) | 187 | 0.00591 (0.0252) | 0.431 (0.597) | 0.376 (0.538) | 0.39 (0.554) | 0.481 (0.634) | 0.186 (0.326)
18q loss | 4 (2%) | 187 | 0.00118 (0.00906) | 0.0566 (0.132) | 0.467 (0.625) | 0.865 (0.962) | 0.101 (0.2) | 0.183 (0.326)
19p loss | 4 (2%) | 187 | 0.00318 (0.018) | 0.432 (0.597) | 0.469 (0.625) | 0.864 (0.962) | 0.31 (0.464) | 0.246 (0.386)
19q loss | 4 (2%) | 187 | 0.003 (0.0175) | 0.436 (0.598) | 0.468 (0.625) | 0.863 (0.962) | 0.311 (0.464) | 0.252 (0.386)

'1p gain' versus 'CN_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.021

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
1P GAIN MUTATED | 0 | 2 | 1 | 0
1P GAIN WILD-TYPE | 148 | 12 | 26 | 2

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

'4p gain' versus 'CN_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.08

Table S2. Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
4P GAIN MUTATED | 1 | 0 | 3 | 0
4P GAIN WILD-TYPE | 147 | 14 | 24 | 2

Figure S2. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.027

Table S3. Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
4P GAIN MUTATED | 0 | 0 | 4 | 0
4P GAIN WILD-TYPE | 33 | 61 | 43 | 44

Figure S3. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.08

Table S4. Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
4Q GAIN MUTATED | 1 | 0 | 3 | 0
4Q GAIN WILD-TYPE | 147 | 14 | 24 | 2

Figure S4. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.027

Table S5. Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
4Q GAIN MUTATED | 0 | 0 | 4 | 0
4Q GAIN WILD-TYPE | 33 | 61 | 43 | 44

Figure S5. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0079

Table S6. 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 S6. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0032

Table S7. Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
8P GAIN MUTATED | 1 | 16 | 3 | 1
8P GAIN WILD-TYPE | 32 | 45 | 44 | 43

Figure S7. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.08

Table S8. Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 52 | 44
8P GAIN MUTATED | 13 | 2 | 3
8P GAIN WILD-TYPE | 57 | 50 | 41

Figure S8. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0079

Table S9. 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 S9. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00981 (Fisher's exact test), Q value = 0.035

Table S10. Gene #4: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
8P GAIN MUTATED | 2 | 9 | 3 | 7
8P GAIN WILD-TYPE | 56 | 28 | 38 | 36

Figure S10. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.05

Table S11. Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
8P GAIN MUTATED | 3 | 8 | 10
8P GAIN WILD-TYPE | 64 | 26 | 68

Figure S11. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.01

Table S12. 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 S12. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0045

Table S13. Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
8Q GAIN MUTATED | 1 | 16 | 4 | 1
8Q GAIN WILD-TYPE | 32 | 45 | 43 | 43

Figure S13. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.045

Table S14. Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 52 | 44
8Q GAIN MUTATED | 14 | 2 | 3
8Q GAIN WILD-TYPE | 56 | 50 | 41

Figure S14. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.011

Table S15. 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 S15. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00711 (Fisher's exact test), Q value = 0.027

Table S16. Gene #5: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
8Q GAIN MUTATED | 2 | 9 | 3 | 8
8Q GAIN WILD-TYPE | 56 | 28 | 38 | 35

Figure S16. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.046

Table S17. Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
8Q GAIN MUTATED | 3 | 8 | 11
8Q GAIN WILD-TYPE | 64 | 26 | 67

Figure S17. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.046

Table S18. Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
10Q GAIN MUTATED | 0 | 1 | 2 | 0
10Q GAIN WILD-TYPE | 148 | 13 | 25 | 2

Figure S18. Get High-res Image Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0075

Table S19. 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 S19. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.064

Table S20. Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
11P GAIN MUTATED | 0 | 3 | 1
11P GAIN WILD-TYPE | 67 | 31 | 77

Figure S20. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S21. 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 S21. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.08

Table S22. Gene #8: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
11Q GAIN MUTATED | 0 | 6 | 1 | 0
11Q GAIN WILD-TYPE | 33 | 55 | 46 | 44

Figure S22. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.046

Table S23. Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
11Q GAIN MUTATED | 0 | 4 | 3
11Q GAIN WILD-TYPE | 67 | 30 | 75

Figure S23. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.11

Table S24. Gene #9: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
13Q GAIN MUTATED | 2 | 1 | 3 | 0
13Q GAIN WILD-TYPE | 146 | 13 | 24 | 2

Figure S24. Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.026

Table S25. Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
13Q GAIN MUTATED | 0 | 6 | 0 | 0
13Q GAIN WILD-TYPE | 33 | 55 | 47 | 44

Figure S25. Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.026

Table S26. Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
17Q GAIN MUTATED | 0 | 0 | 3 | 0
17Q GAIN WILD-TYPE | 148 | 14 | 24 | 2

Figure S26. Get High-res Image Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.046

Table S27. Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
19P GAIN MUTATED | 1 | 1 | 3 | 0
19P GAIN WILD-TYPE | 147 | 13 | 24 | 2

Figure S27. Get High-res Image Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.044

Table S28. Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
19Q GAIN MUTATED | 1 | 1 | 3 | 0
19Q GAIN WILD-TYPE | 147 | 13 | 24 | 2

Figure S28. 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 = 0.00024

Table S29. 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 S29. Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0079

Table S30. 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 S30. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.02

Table S31. Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
22Q GAIN MUTATED | 0 | 8 | 1 | 0
22Q GAIN WILD-TYPE | 33 | 53 | 46 | 44

Figure S31. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.05

Table S32. Gene #14: '22q 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
22Q GAIN MUTATED | 0 | 1 | 0 | 8 | 0 | 0
22Q GAIN WILD-TYPE | 16 | 12 | 14 | 47 | 26 | 42

Figure S32. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.045

Table S33. Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
22Q GAIN MUTATED | 0 | 4 | 5
22Q GAIN WILD-TYPE | 67 | 30 | 73

Figure S33. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.011

Table S34. Gene #15: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
XP GAIN MUTATED | 0 | 1 | 1 | 1
XP GAIN WILD-TYPE | 148 | 13 | 26 | 1

Figure S34. Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.12

Table S35. Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
XP GAIN MUTATED | 1 | 2 | 0
XP GAIN WILD-TYPE | 66 | 32 | 78

Figure S35. Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.011

Table S36. Gene #16: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
XQ GAIN MUTATED | 0 | 1 | 1 | 1
XQ GAIN WILD-TYPE | 148 | 13 | 26 | 1

Figure S36. Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.12

Table S37. Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
XQ GAIN MUTATED | 1 | 2 | 0
XQ GAIN WILD-TYPE | 66 | 32 | 78

Figure S37. Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00662 (Fisher's exact test), Q value = 0.026

Table S38. Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S38. Get High-res Image Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.0063 (Fisher's exact test), Q value = 0.026

Table S39. Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S39. Get High-res Image Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S40. Gene #19: '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 S40. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00682 (Fisher's exact test), Q value = 0.026

Table S41. Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
5Q LOSS MUTATED | 0 | 6 | 0 | 0
5Q LOSS WILD-TYPE | 33 | 55 | 47 | 44

Figure S41. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.082

Table S42. Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
5Q LOSS MUTATED | 0 | 3 | 2 | 0
5Q LOSS WILD-TYPE | 58 | 34 | 39 | 43

Figure S42. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.085

Table S43. Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
5Q LOSS MUTATED | 0 | 3 | 2
5Q LOSS WILD-TYPE | 67 | 31 | 76

Figure S43. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7e-04

Table S44. Gene #20: '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 S44. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0024

Table S45. Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
7P LOSS MUTATED | 0 | 14 | 1 | 2
7P LOSS WILD-TYPE | 33 | 47 | 46 | 42

Figure S45. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0079

Table S46. Gene #20: '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 S46. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S47. Gene #20: '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 S47. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.018

Table S48. Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
7P LOSS MUTATED | 1 | 9 | 3 | 4
7P LOSS WILD-TYPE | 57 | 28 | 38 | 39

Figure S48. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00339 (Fisher's exact test), Q value = 0.018

Table S49. Gene #20: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
7P LOSS MUTATED | 1 | 7 | 9
7P LOSS WILD-TYPE | 66 | 27 | 69

Figure S49. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S50. Gene #21: '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 S50. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S51. Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
7Q LOSS MUTATED | 0 | 17 | 1 | 2
7Q LOSS WILD-TYPE | 33 | 44 | 46 | 42

Figure S51. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.025

Table S52. Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 70 | 52 | 44
7Q LOSS MUTATED | 13 | 1 | 3
7Q LOSS WILD-TYPE | 57 | 51 | 41

Figure S52. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S53. Gene #21: '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 S53. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.01

Table S54. Gene #21: '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 S54. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0079

Table S55. Gene #21: '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 S55. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00591 (Fisher's exact test), Q value = 0.025

Table S56. Gene #22: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
12P LOSS MUTATED | 1 | 0 | 2 | 1
12P LOSS WILD-TYPE | 147 | 14 | 25 | 1

Figure S56. Get High-res Image Gene #22: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0045

Table S57. Gene #23: '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 S57. Get High-res Image Gene #23: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.064

Table S58. Gene #23: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
15Q LOSS MUTATED | 0 | 3 | 0 | 1
15Q LOSS WILD-TYPE | 58 | 34 | 41 | 42

Figure S58. Get High-res Image Gene #23: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0086

Table S59. Gene #24: '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 S59. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.046

Table S60. Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
16Q LOSS MUTATED | 0 | 3 | 1 | 0
16Q LOSS WILD-TYPE | 58 | 34 | 40 | 43

Figure S60. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.064

Table S61. Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
16Q LOSS MUTATED | 0 | 3 | 1
16Q LOSS WILD-TYPE | 67 | 31 | 77

Figure S61. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S62. Gene #25: '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 S62. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.011

Table S63. Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
17P LOSS MUTATED | 0 | 10 | 3 | 0
17P LOSS WILD-TYPE | 33 | 51 | 44 | 44

Figure S63. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.01

Table S64. Gene #25: '17p 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
17P LOSS MUTATED | 0 | 0 | 0 | 12 | 0 | 1
17P LOSS WILD-TYPE | 16 | 13 | 14 | 43 | 26 | 41

Figure S64. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.019

Table S65. Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
17P LOSS MUTATED | 0 | 4 | 9
17P LOSS WILD-TYPE | 67 | 30 | 69

Figure S65. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S66. Gene #26: '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 S66. Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.096

Table S67. Gene #26: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
17Q LOSS MUTATED | 0 | 4 | 1 | 2
17Q LOSS WILD-TYPE | 58 | 33 | 40 | 41

Figure S67. Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.12

Table S68. Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
17Q LOSS MUTATED | 0 | 3 | 4
17Q LOSS WILD-TYPE | 67 | 31 | 74

Figure S68. Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0025

Table S69. Gene #27: '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 S69. Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.061

Table S70. Gene #27: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 33 | 61 | 47 | 44
18P LOSS MUTATED | 0 | 5 | 0 | 0
18P LOSS WILD-TYPE | 33 | 56 | 47 | 44

Figure S70. Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0091

Table S71. Gene #28: '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 S71. Get High-res Image Gene #28: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.018

Table S72. Gene #29: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
19P LOSS MUTATED | 0 | 1 | 3 | 0
19P LOSS WILD-TYPE | 148 | 13 | 24 | 2

Figure S72. Get High-res Image Gene #29: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.017

Table S73. Gene #30: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 14 | 27 | 2
19Q LOSS MUTATED | 0 | 1 | 3 | 0
19Q LOSS WILD-TYPE | 148 | 13 | 24 | 2

Figure S73. Get High-res Image Gene #30: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0019

Table S74. Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S74. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.018

Table S75. Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
XP LOSS MUTATED | 0 | 4 | 1 | 0
XP LOSS WILD-TYPE | 58 | 33 | 40 | 43

Figure S75. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00501 (Fisher's exact test), Q value = 0.022

Table S76. Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
XP LOSS MUTATED | 0 | 4 | 1
XP LOSS WILD-TYPE | 67 | 30 | 77

Figure S76. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7e-04

Table S77. Gene #32: '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 S77. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.018

Table S78. Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 58 | 37 | 41 | 43
XQ LOSS MUTATED | 0 | 4 | 1 | 0
XQ LOSS WILD-TYPE | 58 | 33 | 40 | 43

Figure S78. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0048 (Fisher's exact test), Q value = 0.022

Table S79. Gene #32: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 34 | 78
XQ LOSS MUTATED | 0 | 4 | 1
XQ LOSS WILD-TYPE | 67 | 30 | 77

Figure S79. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

- Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/15087096/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/15098833/LAML-TB.transferedmergedcluster.txt

- Number of patients = 191

- Number of significantly arm-level cnvs = 32

- 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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