Correlation between copy number variations of arm-level result 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/C1X066F1
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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X066F1
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, 58 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'MIRSEQ_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 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

  • 21q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 22q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • xp gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to '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'.

  • 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 'MIRSEQ_CHIERARCHICAL'.

  • 18p 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, 58 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
7p loss 17 (9%) 174 1e-05
(0.000384) 		0.00042
(0.0134) 		0.00111
(0.0194) 		1e-05
(0.000384) 		0.00658
(0.0486) 		0.00293
(0.0316)
7q loss 20 (10%) 171 1e-05
(0.000384) 		1e-05
(0.000384) 		0.00978
(0.0626) 		1e-05
(0.000384) 		0.00296
(0.0316) 		0.0008
(0.0171)
8p gain 22 (12%) 169 0.959
(1.00) 		0.00223
(0.0268) 		0.0273
(0.109) 		0.00076
(0.0171) 		0.0683
(0.212) 		0.0165
(0.0835)
8q gain 23 (12%) 168 0.886
(0.989) 		0.00558
(0.045) 		0.0141
(0.08) 		0.00182
(0.0233) 		0.0618
(0.198) 		0.0142
(0.08)
22q gain 9 (5%) 182 0.239
(0.455) 		0.0121
(0.0749) 		0.148
(0.345) 		0.0163
(0.0835) 		0.00067
(0.0171) 		0.0136
(0.08)
17p loss 13 (7%) 178 0.0171
(0.0843) 		0.00356
(0.0344) 		0.171
(0.377) 		0.00157
(0.0233) 		0.195
(0.407) 		0.00358
(0.0344)
5q loss 6 (3%) 185 0.302
(0.523) 		0.0223
(0.101) 		0.228
(0.452) 		0.632
(0.795) 		0.0325
(0.122) 		0.032
(0.122)
16q loss 4 (2%) 187 0.0357
(0.128) 		0.161
(0.361) 		0.789
(0.925) 		1
(1.00) 		0.0237
(0.101) 		0.023
(0.101)
xp loss 5 (3%) 186 0.00926
(0.0626) 		0.308
(0.523) 		0.23
(0.452) 		0.633
(0.795) 		0.00563
(0.045) 		0.00504
(0.044)
xq loss 5 (3%) 186 0.00945
(0.0626) 		0.307
(0.523) 		0.228
(0.452) 		0.631
(0.795) 		0.00598
(0.0459) 		0.00495
(0.044)
4p gain 4 (2%) 187 0.0359
(0.128) 		0.0259
(0.108) 		0.592
(0.758) 		0.835
(0.96)
4q gain 4 (2%) 187 0.0354
(0.128) 		0.0265
(0.108) 		0.593
(0.758) 		0.833
(0.96)
11p gain 5 (3%) 186 0.443
(0.645) 		0.306
(0.523) 		0.231
(0.452) 		0.235
(0.452) 		0.0151
(0.0807) 		0.0321
(0.122)
11q gain 7 (4%) 184 0.233
(0.452) 		0.0728
(0.221) 		0.0767
(0.223) 		0.0747
(0.221) 		0.00177
(0.0233) 		0.015
(0.0807)
13q gain 6 (3%) 185 0.423
(0.629) 		0.0238
(0.101) 		0.149
(0.345) 		0.0832
(0.235) 		0.00182
(0.0233) 		0.0736
(0.221)
1p gain 3 (2%) 188 0.56
(0.742) 		0.336
(0.555) 		0.261
(0.486) 		0.588
(0.758) 		0.00105
(0.0194) 		0.0919
(0.245)
21q gain 8 (4%) 183 0.126
(0.31) 		0.215
(0.445) 		0.149
(0.345) 		0.525
(0.725) 		0.0498
(0.165) 		0.409
(0.62)
xp gain 3 (2%) 188 0.794
(0.925) 		0.479
(0.672) 		0.443
(0.645) 		0.046
(0.159)
xq gain 3 (2%) 188 0.795
(0.925) 		0.478
(0.672) 		0.442
(0.645) 		0.047
(0.159)
3p loss 3 (2%) 188 0.0227
(0.101) 		0.338
(0.555) 		0.787
(0.925) 		1
(1.00) 		0.101
(0.255) 		0.0921
(0.245)
3q loss 3 (2%) 188 0.0217
(0.101) 		0.336
(0.555) 		0.785
(0.925) 		1
(1.00) 		0.101
(0.255) 		0.0932
(0.245)
17q loss 7 (4%) 184 0.0858
(0.239) 		0.149
(0.345) 		0.0782
(0.224) 		0.236
(0.452) 		0.119
(0.297) 		0.0471
(0.159)
18p loss 5 (3%) 186 0.00909
(0.0626) 		0.0647
(0.204) 		1
(1.00) 		0.865
(0.972) 		0.269
(0.486) 		0.185
(0.392)
10q gain 3 (2%) 188 0.447
(0.645) 		0.337
(0.555) 		0.262
(0.486) 		0.587
(0.758) 		0.159
(0.361) 		0.093
(0.245)
17q gain 3 (2%) 188 0.795
(0.925) 		0.783
(0.925) 		1
(1.00) 		0.589
(0.758) 		0.664
(0.827) 		0.303
(0.523)
19p gain 5 (3%) 186 0.399
(0.62) 		0.265
(0.486) 		1
(1.00) 		0.865
(0.972) 		0.409
(0.62) 		1
(1.00)
19q gain 5 (3%) 186 0.397
(0.62) 		0.267
(0.486) 		1
(1.00) 		0.866
(0.972) 		0.41
(0.62) 		1
(1.00)
12p loss 4 (2%) 187 0.538
(0.728) 		0.502
(0.698) 		0.381
(0.614) 		0.389
(0.62) 		0.398
(0.62) 		0.184
(0.392)
15q loss 4 (2%) 187 0.539
(0.728) 		0.45
(0.645) 		0.0968
(0.251) 		0.369
(0.601) 		0.143
(0.345) 		0.185
(0.392)
18q loss 4 (2%) 187 0.538
(0.728) 		0.162
(0.361) 		0.475
(0.672) 		0.864
(0.972) 		0.0617
(0.198) 		0.186
(0.392)
19p loss 3 (2%) 188 0.56
(0.742) 		0.783
(0.925) 		0.787
(0.925) 		1
(1.00) 		0.283
(0.503) 		0.413
(0.62)
19q loss 3 (2%) 188 0.559
(0.742) 		0.783
(0.925) 		0.787
(0.925) 		1
(1.00) 		0.283
(0.503) 		0.413
(0.62)
'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.019

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
1P GAIN MUTATED 0 0 0 0 3
1P GAIN WILD-TYPE 57 31 39 33 16

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
4P GAIN MUTATED 0 3 0 1
4P GAIN WILD-TYPE 49 41 55 42

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

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
4P GAIN MUTATED 2 0 0 2 0
4P GAIN WILD-TYPE 21 25 60 33 42

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

'4q gain' versus 'CN_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
4Q GAIN MUTATED 0 3 0 1
4Q GAIN WILD-TYPE 49 41 55 42

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

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
4Q GAIN MUTATED 2 0 0 2 0
4Q GAIN WILD-TYPE 21 25 60 33 42

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

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.027

Table S6.  Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
8P GAIN MUTATED 2 2 15 1 1
8P GAIN WILD-TYPE 21 23 45 34 41

Figure S6.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.11

Table S7.  Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 50 45
8P GAIN MUTATED 13 2 3
8P GAIN WILD-TYPE 58 48 42

Figure S7.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.017

Table S8.  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 S8.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.083

Table S9.  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 S9.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00558 (Fisher's exact test), Q value = 0.045

Table S10.  Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
8Q GAIN MUTATED 2 2 15 2 1
8Q GAIN WILD-TYPE 21 23 45 33 41

Figure S10.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.08

Table S11.  Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 50 45
8Q GAIN MUTATED 14 2 3
8Q GAIN WILD-TYPE 57 48 42

Figure S11.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.023

Table S12.  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 S12.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.08

Table S13.  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 S13.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.081

Table S14.  Gene #7: '11p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
11P GAIN MUTATED 1 1 0 0 3
11P GAIN WILD-TYPE 56 30 39 33 16

Figure S14.  Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.12

Table S15.  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 2
11P GAIN WILD-TYPE 67 31 76

Figure S15.  Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.023

Table S16.  Gene #8: '11q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
11Q GAIN MUTATED 1 2 0 0 4
11Q GAIN WILD-TYPE 56 29 39 33 15

Figure S16.  Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.081

Table S17.  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 S17.  Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.1

Table S18.  Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
13Q GAIN MUTATED 0 0 6 0 0
13Q GAIN WILD-TYPE 23 25 54 35 42

Figure S18.  Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.023

Table S19.  Gene #9: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
13Q GAIN MUTATED 1 1 0 0 4
13Q GAIN WILD-TYPE 56 30 39 33 15

Figure S19.  Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #13: '21q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
21Q GAIN MUTATED 1 2 0 4 0
21Q GAIN WILD-TYPE 56 29 39 29 19

Figure S20.  Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.075

Table S21.  Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
22Q GAIN MUTATED 0 0 8 1 0
22Q GAIN WILD-TYPE 23 25 52 34 42

Figure S21.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.083

Table S22.  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 S22.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.017

Table S23.  Gene #14: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
22Q GAIN MUTATED 0 2 1 1 5
22Q GAIN WILD-TYPE 57 29 38 32 14

Figure S23.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.08

Table S24.  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 S24.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.16

Table S25.  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 S25.  Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.16

Table S26.  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 S26.  Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.1

Table S27.  Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
3P LOSS MUTATED 0 3 0 0
3P LOSS WILD-TYPE 49 41 55 43

Figure S27.  Get High-res Image Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.1

Table S28.  Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
3Q LOSS MUTATED 0 3 0 0
3Q LOSS WILD-TYPE 49 41 55 43

Figure S28.  Get High-res Image Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.1

Table S29.  Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
5Q LOSS MUTATED 0 0 6 0 0
5Q LOSS WILD-TYPE 23 25 54 35 42

Figure S29.  Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.12

Table S30.  Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
5Q LOSS MUTATED 0 3 0 1 1
5Q LOSS WILD-TYPE 57 28 39 32 18

Figure S30.  Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.12

Table S31.  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 S31.  Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S32.  Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
7P LOSS MUTATED 0 5 0 12
7P LOSS WILD-TYPE 49 39 55 31

Figure S32.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.013

Table S33.  Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
7P LOSS MUTATED 1 1 14 0 1
7P LOSS WILD-TYPE 22 24 46 35 41

Figure S33.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.019

Table S34.  Gene #20: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 50 45
7P LOSS MUTATED 13 0 3
7P LOSS WILD-TYPE 58 50 42

Figure S34.  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 = 0.00038

Table S35.  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 S35.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.049

Table S36.  Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
7P LOSS MUTATED 1 8 4 2 2
7P LOSS WILD-TYPE 56 23 35 31 17

Figure S36.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.032

Table S37.  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 S37.  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 = 0.00038

Table S38.  Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
7Q LOSS MUTATED 1 6 0 13
7Q LOSS WILD-TYPE 48 38 55 30

Figure S38.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S39.  Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
7Q LOSS MUTATED 1 1 17 0 1
7Q LOSS WILD-TYPE 22 24 43 35 41

Figure S39.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.063

Table S40.  Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 50 45
7Q LOSS MUTATED 13 1 3
7Q LOSS WILD-TYPE 58 49 42

Figure S40.  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 = 0.00038

Table S41.  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 S41.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.032

Table S42.  Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
7Q LOSS MUTATED 1 9 4 3 2
7Q LOSS WILD-TYPE 56 22 35 30 17

Figure S42.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.017

Table S43.  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 S43.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.13

Table S44.  Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
16Q LOSS MUTATED 0 3 0 1
16Q LOSS WILD-TYPE 49 41 55 42

Figure S44.  Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.1

Table S45.  Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
16Q LOSS MUTATED 0 3 0 1 0
16Q LOSS WILD-TYPE 57 28 39 32 19

Figure S45.  Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.1

Table S46.  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 S46.  Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.084

Table S47.  Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
17P LOSS MUTATED 0 7 3 3
17P LOSS WILD-TYPE 49 37 52 40

Figure S47.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.034

Table S48.  Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 25 60 35 42
17P LOSS MUTATED 0 0 10 3 0
17P LOSS WILD-TYPE 23 25 50 32 42

Figure S48.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.023

Table S49.  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 S49.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.034

Table S50.  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 S50.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.16

Table S51.  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 S51.  Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00909 (Fisher's exact test), Q value = 0.063

Table S52.  Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
18P LOSS MUTATED 0 4 0 1
18P LOSS WILD-TYPE 49 40 55 42

Figure S52.  Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.063

Table S53.  Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
XP LOSS MUTATED 0 4 0 1
XP LOSS WILD-TYPE 49 40 55 42

Figure S53.  Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00563 (Fisher's exact test), Q value = 0.045

Table S54.  Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
XP LOSS MUTATED 0 4 0 1 0
XP LOSS WILD-TYPE 57 27 39 32 19

Figure S54.  Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 0.044

Table S55.  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 S55.  Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.063

Table S56.  Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 44 55 43
XQ LOSS MUTATED 0 4 0 1
XQ LOSS WILD-TYPE 49 40 55 42

Figure S56.  Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.046

Table S57.  Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 57 31 39 33 19
XQ LOSS MUTATED 0 4 0 1 0
XQ LOSS WILD-TYPE 57 27 39 32 19

Figure S57.  Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00495 (Fisher's exact test), Q value = 0.044

Table S58.  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 S58.  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/22529564/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/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.

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)
Copyright © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle