This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 30 arm-level events and 6 molecular subtypes across 191 patients, 28 significant findings detected with P value < 0.05 and Q value < 0.25.
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8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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11p gain cnv correlated to 'CN_CNMF'.
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11q gain cnv correlated to 'CN_CNMF'.
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19p gain cnv correlated to 'CN_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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21q gain cnv correlated to 'CN_CNMF'.
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22q gain cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'CN_CNMF'.
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7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF'.
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16q loss cnv correlated to 'CN_CNMF'.
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17p loss cnv correlated to 'CN_CNMF'.
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17q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'CN_CNMF'.
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xq loss cnv correlated to 'CN_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
7q loss | 20 (10%) | 171 |
1e-05 (0.00174) |
3e-05 (0.00504) |
0.00601 (0.805) |
1e-05 (0.00174) |
0.00142 (0.214) |
0.00088 (0.136) |
7p loss | 17 (9%) | 174 |
0.00013 (0.0214) |
0.00029 (0.047) |
0.00097 (0.149) |
1e-05 (0.00174) |
0.00382 (0.535) |
0.00295 (0.425) |
8p gain | 22 (12%) | 169 |
0.001 (0.153) |
0.00047 (0.0757) |
0.0287 (1.00) |
0.00082 (0.128) |
0.01 (1.00) |
0.016 (1.00) |
8q gain | 23 (12%) | 168 |
0.0017 (0.25) |
0.0016 (0.237) |
0.0134 (1.00) |
0.00173 (0.253) |
0.00721 (0.956) |
0.0146 (1.00) |
11p gain | 4 (2%) | 187 |
0.00066 (0.105) |
0.147 (1.00) |
0.467 (1.00) |
0.365 (1.00) |
0.519 (1.00) |
0.022 (1.00) |
11q gain | 7 (4%) | 184 |
2e-05 (0.00338) |
0.0121 (1.00) |
0.0655 (1.00) |
0.0737 (1.00) |
0.291 (1.00) |
0.0154 (1.00) |
19p gain | 5 (3%) | 186 |
0.00078 (0.122) |
0.645 (1.00) |
1 (1.00) |
0.864 (1.00) |
0.579 (1.00) |
1 (1.00) |
19q gain | 5 (3%) | 186 |
0.00071 (0.112) |
0.646 (1.00) |
1 (1.00) |
0.865 (1.00) |
0.578 (1.00) |
1 (1.00) |
21q gain | 8 (4%) | 183 |
1e-05 (0.00174) |
0.23 (1.00) |
0.126 (1.00) |
0.524 (1.00) |
0.0813 (1.00) |
0.409 (1.00) |
22q gain | 9 (5%) | 182 |
0.00124 (0.188) |
0.0178 (1.00) |
0.136 (1.00) |
0.0162 (1.00) |
0.0567 (1.00) |
0.0132 (1.00) |
5q loss | 6 (3%) | 185 |
6e-05 (0.00996) |
0.0302 (1.00) |
0.224 (1.00) |
0.632 (1.00) |
0.0314 (1.00) |
0.0329 (1.00) |
15q loss | 4 (2%) | 187 |
0.00052 (0.0832) |
0.57 (1.00) |
0.0657 (1.00) |
0.366 (1.00) |
0.0236 (1.00) |
0.186 (1.00) |
16q loss | 4 (2%) | 187 |
0.00159 (0.237) |
0.149 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.0147 (1.00) |
0.0217 (1.00) |
17p loss | 13 (7%) | 178 |
1e-05 (0.00174) |
0.00418 (0.574) |
0.156 (1.00) |
0.00192 (0.278) |
0.162 (1.00) |
0.00345 (0.49) |
17q loss | 7 (4%) | 184 |
3e-05 (0.00504) |
0.216 (1.00) |
0.0685 (1.00) |
0.233 (1.00) |
0.04 (1.00) |
0.0475 (1.00) |
18p loss | 5 (3%) | 186 |
0.00021 (0.0342) |
0.0687 (1.00) |
1 (1.00) |
0.865 (1.00) |
0.248 (1.00) |
0.185 (1.00) |
18q loss | 4 (2%) | 187 |
0.00157 (0.235) |
0.148 (1.00) |
0.468 (1.00) |
0.864 (1.00) |
0.101 (1.00) |
0.186 (1.00) |
xq loss | 5 (3%) | 186 |
0.00013 (0.0214) |
0.145 (1.00) |
0.224 (1.00) |
0.632 (1.00) |
0.00347 (0.49) |
0.00482 (0.656) |
1p gain | 3 (2%) | 188 |
0.00552 (0.745) |
0.266 (1.00) |
0.185 (1.00) |
0.588 (1.00) |
0.0906 (1.00) |
0.0936 (1.00) |
4p gain | 4 (2%) | 187 |
0.0266 (1.00) |
0.0483 (1.00) |
0.341 (1.00) |
0.835 (1.00) |
||
4q gain | 4 (2%) | 187 |
0.0256 (1.00) |
0.05 (1.00) |
0.342 (1.00) |
0.833 (1.00) |
||
10q gain | 3 (2%) | 188 |
0.0119 (1.00) |
0.27 (1.00) |
0.187 (1.00) |
0.588 (1.00) |
0.554 (1.00) |
0.0949 (1.00) |
13q gain | 6 (3%) | 185 |
0.033 (1.00) |
0.0303 (1.00) |
0.125 (1.00) |
0.0837 (1.00) |
0.799 (1.00) |
0.0729 (1.00) |
17q gain | 3 (2%) | 188 |
0.00856 (1.00) |
0.302 (1.00) |
1 (1.00) |
0.589 (1.00) |
0.484 (1.00) |
0.305 (1.00) |
xq gain | 3 (2%) | 188 |
0.00296 (0.425) |
0.88 (1.00) |
0.893 (1.00) |
0.0459 (1.00) |
||
3p loss | 3 (2%) | 188 |
0.00719 (0.956) |
0.268 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.0607 (1.00) |
0.0926 (1.00) |
3q loss | 3 (2%) | 188 |
0.0075 (0.982) |
0.264 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.062 (1.00) |
0.092 (1.00) |
12p loss | 4 (2%) | 187 |
0.0084 (1.00) |
0.0949 (1.00) |
0.373 (1.00) |
0.393 (1.00) |
0.484 (1.00) |
0.185 (1.00) |
19p loss | 4 (2%) | 187 |
0.00416 (0.574) |
0.536 (1.00) |
0.468 (1.00) |
0.866 (1.00) |
0.312 (1.00) |
0.247 (1.00) |
19q loss | 4 (2%) | 187 |
0.00406 (0.564) |
0.534 (1.00) |
0.465 (1.00) |
0.865 (1.00) |
0.311 (1.00) |
0.248 (1.00) |
P value = 0.001 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
8P GAIN MUTATED | 11 | 1 | 10 | 0 |
8P GAIN WILD-TYPE | 136 | 13 | 17 | 3 |
P value = 0.00047 (Fisher's exact test), Q value = 0.076
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
8P GAIN MUTATED | 2 | 1 | 16 | 0 | 2 |
8P GAIN WILD-TYPE | 44 | 43 | 45 | 14 | 18 |
P value = 0.00082 (Fisher's exact test), Q value = 0.13
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 |
P value = 0.0017 (Fisher's exact test), Q value = 0.25
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
8Q GAIN MUTATED | 12 | 1 | 10 | 0 |
8Q GAIN WILD-TYPE | 135 | 13 | 17 | 3 |
P value = 0.0016 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
8Q GAIN MUTATED | 2 | 2 | 16 | 0 | 2 |
8Q GAIN WILD-TYPE | 44 | 42 | 45 | 14 | 18 |
P value = 0.00066 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
11P GAIN MUTATED | 0 | 3 | 1 | 0 |
11P GAIN WILD-TYPE | 147 | 11 | 26 | 3 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
11Q GAIN MUTATED | 0 | 4 | 3 | 0 |
11Q GAIN WILD-TYPE | 147 | 10 | 24 | 3 |
P value = 0.00078 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
19P GAIN MUTATED | 0 | 1 | 4 | 0 |
19P GAIN WILD-TYPE | 147 | 13 | 23 | 3 |
P value = 0.00071 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
19Q GAIN MUTATED | 0 | 1 | 4 | 0 |
19Q GAIN WILD-TYPE | 147 | 13 | 23 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
21Q GAIN MUTATED | 0 | 0 | 8 | 0 |
21Q GAIN WILD-TYPE | 147 | 14 | 19 | 3 |
P value = 0.00124 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
22Q GAIN MUTATED | 2 | 2 | 5 | 0 |
22Q GAIN WILD-TYPE | 145 | 12 | 22 | 3 |
P value = 6e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
5Q LOSS MUTATED | 0 | 0 | 6 | 0 |
5Q LOSS WILD-TYPE | 147 | 14 | 21 | 3 |
P value = 0.00013 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
7P LOSS MUTATED | 7 | 0 | 8 | 2 |
7P LOSS WILD-TYPE | 140 | 14 | 19 | 1 |
P value = 0.00029 (Fisher's exact test), Q value = 0.047
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
7P LOSS MUTATED | 1 | 0 | 14 | 1 | 1 |
7P LOSS WILD-TYPE | 45 | 44 | 47 | 13 | 19 |
P value = 0.00097 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 70 | 52 | 44 |
7P LOSS MUTATED | 13 | 0 | 3 |
7P LOSS WILD-TYPE | 57 | 52 | 41 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
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 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
7Q LOSS MUTATED | 8 | 0 | 10 | 2 |
7Q LOSS WILD-TYPE | 139 | 14 | 17 | 1 |
P value = 3e-05 (Fisher's exact test), Q value = 0.005
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 44 | 61 | 14 | 20 |
7Q LOSS MUTATED | 1 | 0 | 17 | 1 | 1 |
7Q LOSS WILD-TYPE | 45 | 44 | 44 | 13 | 19 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
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 |
P value = 0.00142 (Fisher's exact test), Q value = 0.21
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 |
P value = 0.00088 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 34 | 78 |
7Q LOSS MUTATED | 1 | 8 | 10 |
7Q LOSS WILD-TYPE | 66 | 26 | 68 |
P value = 0.00052 (Fisher's exact test), Q value = 0.083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
15Q LOSS MUTATED | 0 | 0 | 3 | 1 |
15Q LOSS WILD-TYPE | 147 | 14 | 24 | 2 |
P value = 0.00159 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
16Q LOSS MUTATED | 0 | 0 | 4 | 0 |
16Q LOSS WILD-TYPE | 147 | 14 | 23 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
17P LOSS MUTATED | 0 | 0 | 13 | 0 |
17P LOSS WILD-TYPE | 147 | 14 | 14 | 3 |
P value = 3e-05 (Fisher's exact test), Q value = 0.005
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
17Q LOSS MUTATED | 0 | 0 | 7 | 0 |
17Q LOSS WILD-TYPE | 147 | 14 | 20 | 3 |
P value = 0.00021 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
18P LOSS MUTATED | 0 | 0 | 5 | 0 |
18P LOSS WILD-TYPE | 147 | 14 | 22 | 3 |
P value = 0.00157 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
18Q LOSS MUTATED | 0 | 0 | 4 | 0 |
18Q LOSS WILD-TYPE | 147 | 14 | 23 | 3 |
P value = 0.00013 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 147 | 14 | 27 | 3 |
XQ LOSS MUTATED | 0 | 0 | 4 | 1 |
XQ LOSS WILD-TYPE | 147 | 14 | 23 | 2 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtypes file = LAML-TB.transferedmergedcluster.txt
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Number of patients = 191
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Number of significantly arm-level cnvs = 30
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Number of molecular subtypes = 6
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Exclude genes that fewer than K tumors have mutations, K = 3
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
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.
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.