Correlation between copy number variation genes (focal events) and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1S75FQ9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1S75FQ9
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 16 focal events and 6 molecular subtypes across 191 patients, 47 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • amp_11q23.3 cnv correlated to 'METHLYATION_CNMF'.

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

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

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

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

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

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

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

  • del_16q23.1 cnv correlated to 'CN_CNMF'.

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 16 focal events and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 47 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 5q31 2 18 (9%) 173 0.00138
(0.00883) 		4e-05
(0.000768) 		0.00455
(0.0175) 		0.00068
(0.0062) 		0.00109
(0.00805) 		0.00109
(0.00805)
del 7p12 1 16 (8%) 175 1e-05
(0.00048) 		0.00071
(0.0062) 		0.00227
(0.0109) 		1e-05
(0.00048) 		0.0189
(0.0477) 		0.00701
(0.0217)
del 7q32 3 23 (12%) 168 2e-05
(0.00048) 		0.00062
(0.0062) 		0.0445
(0.0994) 		2e-05
(0.00048) 		0.00431
(0.0175) 		0.00172
(0.00933)
del 17p13 2 15 (8%) 176 0.0218
(0.0538) 		0.00055
(0.0062) 		0.0128
(0.0352) 		0.00022
(0.00352) 		0.0668
(0.128) 		0.00126
(0.00864)
del 17q11 2 13 (7%) 178 0.0159
(0.0424) 		0.0058
(0.0206) 		0.17
(0.247) 		0.00676
(0.0216) 		0.0188
(0.0477) 		0.00376
(0.0172)
amp 21q22 2 14 (7%) 177 0.07
(0.132) 		0.00169
(0.00933) 		0.00402
(0.0175) 		0.0371
(0.0847) 		0.00597
(0.0206) 		0.0668
(0.128)
amp 1p33 7 (4%) 184 0.809
(0.872) 		0.0471
(0.0996) 		0.148
(0.222) 		0.13
(0.2) 		0.00736
(0.0221) 		0.0486
(0.0996)
del 12p13 2 10 (5%) 181 0.00032
(0.00439) 		0.0045
(0.0175) 		0.197
(0.273) 		0.0737
(0.136) 		0.126
(0.198) 		0.00977
(0.0284)
del 18p11 21 9 (5%) 182 0.00175
(0.00933) 		0.0125
(0.0352) 		0.481
(0.57) 		0.334
(0.425) 		0.218
(0.29) 		0.0325
(0.076)
del 3p13 8 (4%) 183 0.0545
(0.109) 		0.114
(0.186) 		0.0778
(0.141) 		0.237
(0.311) 		0.0466
(0.0996) 		0.0487
(0.0996)
del 12q21 33 3 (2%) 188 0.131
(0.2) 		0.784
(0.855) 		0.262
(0.34) 		0.589
(0.666) 		0.00621
(0.0206) 		0.00616
(0.0206)
amp 11q23 3 17 (9%) 174 0.098
(0.168) 		0.00197
(0.00995) 		0.373
(0.465) 		0.203
(0.274) 		0.481
(0.57) 		0.187
(0.265)
del 16q23 1 9 (5%) 182 0.0302
(0.0724) 		0.0847
(0.151) 		1
(1.00) 		0.86
(0.917) 		0.097
(0.168) 		0.104
(0.173)
amp 20q11 21 3 (2%) 188 0.391
(0.481) 		0.336
(0.425)
del 9q21 32 5 (3%) 186 0.502
(0.588) 		0.572
(0.662) 		0.178
(0.254) 		0.599
(0.669) 		0.199
(0.273) 		0.105
(0.173)
del 20q13 13 4 (2%) 187 0.904
(0.954) 		0.16
(0.237) 		0.784
(0.855) 		0.589
(0.666) 		0.12
(0.193) 		0.411
(0.5)
'amp_1p33' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_1p33' versus 'MIRSEQ_CNMF'

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

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

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

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

'amp_1p33' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'amp_11q23.3' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_21q22.2' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_21q22.2' versus 'MRNASEQ_CNMF'

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

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

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

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

'amp_21q22.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S7.  Gene #4: 'amp_21q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
AMP PEAK 4(21Q22.2) MUTATED 0 0 1 9 0 1
AMP PEAK 4(21Q22.2) WILD-TYPE 16 13 13 46 26 41

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

'amp_21q22.2' versus 'MIRSEQ_CNMF'

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

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

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

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

'del_3p13' versus 'MIRSEQ_CNMF'

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

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

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

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

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_5q31.2' versus 'CN_CNMF'

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

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

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

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

'del_5q31.2' versus 'METHLYATION_CNMF'

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

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

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

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

'del_5q31.2' versus 'MRNASEQ_CNMF'

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

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

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

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

'del_5q31.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S14.  Gene #6: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 2(5Q31.2) MUTATED 0 0 0 14 0 2
DEL PEAK 2(5Q31.2) WILD-TYPE 16 13 14 41 26 40

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

'del_5q31.2' versus 'MIRSEQ_CNMF'

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

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

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

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

'del_5q31.2' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_7p12.1' versus 'CN_CNMF'

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

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

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

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

'del_7p12.1' versus 'METHLYATION_CNMF'

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

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

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

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

'del_7p12.1' versus 'MRNASEQ_CNMF'

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

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

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

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

'del_7p12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S20.  Gene #7: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 3(7P12.1) MUTATED 0 0 0 15 0 0
DEL PEAK 3(7P12.1) WILD-TYPE 16 13 14 40 26 42

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

'del_7p12.1' versus 'MIRSEQ_CNMF'

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

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

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

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

'del_7p12.1' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_7q32.3' versus 'CN_CNMF'

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

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

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

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

'del_7q32.3' versus 'METHLYATION_CNMF'

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

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

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

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

'del_7q32.3' versus 'MRNASEQ_CNMF'

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

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

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

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

'del_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S26.  Gene #8: 'del_7q32.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 4(7Q32.3) MUTATED 1 1 0 17 0 0
DEL PEAK 4(7Q32.3) WILD-TYPE 15 12 14 38 26 42

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

'del_7q32.3' versus 'MIRSEQ_CNMF'

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

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

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

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

'del_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_12p13.2' versus 'CN_CNMF'

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

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

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

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

'del_12p13.2' versus 'METHLYATION_CNMF'

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

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

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

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

'del_12p13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_12q21.33' versus 'MIRSEQ_CNMF'

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

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

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

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

'del_12q21.33' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_16q23.1' versus 'CN_CNMF'

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

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

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

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

'del_17p13.2' versus 'CN_CNMF'

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

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

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

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

'del_17p13.2' versus 'METHLYATION_CNMF'

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

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

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

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

'del_17p13.2' versus 'MRNASEQ_CNMF'

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

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

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

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

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S38.  Gene #13: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 9(17P13.2) MUTATED 0 0 0 14 0 1
DEL PEAK 9(17P13.2) WILD-TYPE 16 13 14 41 26 41

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

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_17q11.2' versus 'CN_CNMF'

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

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

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

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

'del_17q11.2' versus 'METHLYATION_CNMF'

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

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

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

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

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S42.  Gene #14: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
DEL PEAK 10(17Q11.2) MUTATED 0 1 0 11 0 1
DEL PEAK 10(17Q11.2) WILD-TYPE 16 12 14 44 26 41

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

'del_17q11.2' versus 'MIRSEQ_CNMF'

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

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

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

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

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'del_18p11.21' versus 'CN_CNMF'

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

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

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

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

'del_18p11.21' versus 'METHLYATION_CNMF'

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

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

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

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

'del_18p11.21' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

Methods & Data
Input

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

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

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

  • Number of patients = 191

  • Number of significantly focal cnvs = 16

  • Number of molecular subtypes = 6

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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