This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 61 focal events and 5 clinical features across 56 patients, no significant finding detected with Q value < 0.25.
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No focal cnvs related to clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RACE | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 1q22 | 42 (75%) | 14 |
0.631 (1.00) |
0.576 (0.979) |
1 (1.00) |
0.355 (0.977) |
0.233 (0.977) |
amp 2p14 | 28 (50%) | 28 |
0.223 (0.977) |
0.768 (1.00) |
0.00582 (0.566) |
0.38 (0.977) |
0.144 (0.977) |
amp 2q13 | 29 (52%) | 27 |
0.671 (1.00) |
0.345 (0.977) |
0.055 (0.887) |
1 (1.00) |
0.594 (0.979) |
amp 3p25 1 | 20 (36%) | 36 |
0.175 (0.977) |
0.392 (0.977) |
1 (1.00) |
0.939 (1.00) |
0.451 (0.979) |
amp 3q26 2 | 37 (66%) | 19 |
0.579 (0.979) |
0.382 (0.977) |
1 (1.00) |
0.481 (0.979) |
0.761 (1.00) |
amp 4p16 3 | 25 (45%) | 31 |
0.209 (0.977) |
0.343 (0.977) |
0.17 (0.977) |
0.0645 (0.895) |
0.359 (0.977) |
amp 5p13 2 | 26 (46%) | 30 |
0.856 (1.00) |
0.902 (1.00) |
0.29 (0.977) |
0.837 (1.00) |
0.317 (0.977) |
amp 6p24 2 | 37 (66%) | 19 |
0.12 (0.977) |
0.0963 (0.977) |
0.776 (1.00) |
1 (1.00) |
0.759 (1.00) |
amp 8p11 21 | 33 (59%) | 23 |
0.888 (1.00) |
0.14 (0.977) |
1 (1.00) |
0.61 (0.99) |
0.407 (0.978) |
amp 8q11 23 | 38 (68%) | 18 |
0.972 (1.00) |
0.226 (0.977) |
0.154 (0.977) |
0.474 (0.979) |
0.259 (0.977) |
amp 8q24 21 | 42 (75%) | 14 |
0.339 (0.977) |
0.902 (1.00) |
0.766 (1.00) |
0.069 (0.915) |
0.282 (0.977) |
amp 8q24 21 | 40 (71%) | 16 |
0.0968 (0.977) |
0.574 (0.979) |
0.384 (0.977) |
0.197 (0.977) |
0.147 (0.977) |
amp 10q22 2 | 26 (46%) | 30 |
0.508 (0.979) |
0.111 (0.977) |
0.785 (1.00) |
0.698 (1.00) |
0.888 (1.00) |
amp 11q13 1 | 19 (34%) | 37 |
0.309 (0.977) |
0.446 (0.979) |
0.394 (0.977) |
0.937 (1.00) |
0.497 (0.979) |
amp 12q12 | 22 (39%) | 34 |
0.431 (0.979) |
0.512 (0.979) |
0.78 (1.00) |
0.781 (1.00) |
0.106 (0.977) |
amp 12q15 | 17 (30%) | 39 |
0.927 (1.00) |
0.108 (0.977) |
0.552 (0.979) |
0.756 (1.00) |
0.147 (0.977) |
amp 13q31 3 | 25 (45%) | 31 |
0.675 (1.00) |
0.276 (0.977) |
0.417 (0.978) |
0.337 (0.977) |
0.781 (1.00) |
amp 16p11 2 | 20 (36%) | 36 |
0.443 (0.979) |
0.134 (0.977) |
0.576 (0.979) |
0.562 (0.979) |
0.76 (1.00) |
amp 17q12 | 27 (48%) | 29 |
0.862 (1.00) |
0.889 (1.00) |
0.182 (0.977) |
0.7 (1.00) |
1 (1.00) |
amp 17q25 1 | 32 (57%) | 24 |
0.833 (1.00) |
0.0588 (0.887) |
0.784 (1.00) |
0.832 (1.00) |
0.597 (0.979) |
amp 19p13 2 | 19 (34%) | 37 |
0.999 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.519 (0.979) |
0.495 (0.979) |
amp 19q12 | 45 (80%) | 11 |
0.506 (0.979) |
0.82 (1.00) |
0.485 (0.979) |
0.623 (1.00) |
0.688 (1.00) |
amp 20q11 21 | 48 (86%) | 8 |
0.476 (0.979) |
0.535 (0.979) |
0.262 (0.977) |
0.377 (0.977) |
0.0489 (0.887) |
amp 20q11 21 | 48 (86%) | 8 |
0.791 (1.00) |
0.87 (1.00) |
0.711 (1.00) |
0.18 (0.977) |
0.0492 (0.887) |
amp xp11 21 | 28 (50%) | 28 |
0.721 (1.00) |
0.0136 (0.566) |
1 (1.00) |
0.269 (0.977) |
1 (1.00) |
del 1p36 21 | 19 (34%) | 37 |
0.824 (1.00) |
0.148 (0.977) |
0.566 (0.979) |
0.036 (0.845) |
1 (1.00) |
del 2q22 1 | 11 (20%) | 45 |
0.0596 (0.887) |
0.877 (1.00) |
0.191 (0.977) |
0.00098 (0.299) |
0.556 (0.979) |
del 3p14 2 | 37 (66%) | 19 |
0.823 (1.00) |
0.979 (1.00) |
1 (1.00) |
0.938 (1.00) |
0.05 (0.887) |
del 3q13 31 | 22 (39%) | 34 |
0.289 (0.977) |
0.425 (0.979) |
0.407 (0.978) |
0.47 (0.979) |
0.459 (0.979) |
del 4q22 1 | 37 (66%) | 19 |
0.95 (1.00) |
0.562 (0.979) |
0.259 (0.977) |
0.322 (0.977) |
0.757 (1.00) |
del 4q34 3 | 37 (66%) | 19 |
0.458 (0.979) |
0.646 (1.00) |
0.573 (0.979) |
0.148 (0.977) |
0.226 (0.977) |
del 5q12 1 | 26 (46%) | 30 |
0.726 (1.00) |
0.324 (0.977) |
0.0611 (0.887) |
0.517 (0.979) |
1 (1.00) |
del 6q26 | 10 (18%) | 46 |
0.519 (0.979) |
0.872 (1.00) |
0.736 (1.00) |
0.363 (0.977) |
0.514 (0.979) |
del 7q11 22 | 12 (21%) | 44 |
0.174 (0.977) |
0.889 (1.00) |
0.347 (0.977) |
0.643 (1.00) |
1 (1.00) |
del 7q36 2 | 20 (36%) | 36 |
0.238 (0.977) |
0.669 (1.00) |
0.78 (1.00) |
0.489 (0.979) |
0.515 (0.979) |
del 8p23 2 | 33 (59%) | 23 |
0.38 (0.977) |
0.745 (1.00) |
1 (1.00) |
0.649 (1.00) |
0.156 (0.977) |
del 9p23 | 34 (61%) | 22 |
0.593 (0.979) |
0.0167 (0.566) |
0.579 (0.979) |
0.215 (0.977) |
0.878 (1.00) |
del 9q21 13 | 39 (70%) | 17 |
0.333 (0.977) |
0.568 (0.979) |
1 (1.00) |
0.706 (1.00) |
0.411 (0.978) |
del 9q33 3 | 39 (70%) | 17 |
0.152 (0.977) |
0.284 (0.977) |
0.145 (0.977) |
0.566 (0.979) |
0.865 (1.00) |
del 10q23 31 | 20 (36%) | 36 |
0.669 (1.00) |
0.532 (0.979) |
0.776 (1.00) |
0.56 (0.979) |
0.234 (0.977) |
del 11p15 5 | 25 (45%) | 31 |
0.113 (0.977) |
0.895 (1.00) |
0.0139 (0.566) |
0.05 (0.887) |
0.595 (0.979) |
del 11q14 1 | 26 (46%) | 30 |
0.803 (1.00) |
0.22 (0.977) |
0.79 (1.00) |
0.207 (0.977) |
0.884 (1.00) |
del 11q23 2 | 26 (46%) | 30 |
0.63 (1.00) |
0.246 (0.977) |
0.79 (1.00) |
0.205 (0.977) |
0.447 (0.979) |
del 12q23 1 | 20 (36%) | 36 |
0.0925 (0.977) |
0.031 (0.845) |
0.576 (0.979) |
0.819 (1.00) |
1 (1.00) |
del 12q24 31 | 20 (36%) | 36 |
0.151 (0.977) |
0.244 (0.977) |
1 (1.00) |
0.939 (1.00) |
1 (1.00) |
del 13q12 11 | 30 (54%) | 26 |
0.402 (0.978) |
0.344 (0.977) |
0.597 (0.979) |
0.333 (0.977) |
0.6 (0.979) |
del 13q14 2 | 32 (57%) | 24 |
0.894 (1.00) |
0.567 (0.979) |
0.417 (0.978) |
0.58 (0.979) |
0.596 (0.979) |
del 14q21 1 | 28 (50%) | 28 |
0.23 (0.977) |
0.38 (0.977) |
0.111 (0.977) |
0.159 (0.977) |
0.244 (0.977) |
del 15q11 2 | 41 (73%) | 15 |
0.823 (1.00) |
0.251 (0.977) |
0.557 (0.979) |
0.508 (0.979) |
0.203 (0.977) |
del 15q15 1 | 43 (77%) | 13 |
0.344 (0.977) |
0.217 (0.977) |
0.339 (0.977) |
0.785 (1.00) |
1 (1.00) |
del 16p13 3 | 33 (59%) | 23 |
0.899 (1.00) |
0.967 (1.00) |
0.583 (0.979) |
0.833 (1.00) |
0.0152 (0.566) |
del 16q23 1 | 39 (70%) | 17 |
0.0135 (0.566) |
0.239 (0.977) |
0.145 (0.977) |
0.0146 (0.566) |
0.295 (0.977) |
del 17p13 1 | 42 (75%) | 14 |
0.553 (0.979) |
0.94 (1.00) |
0.766 (1.00) |
0.923 (1.00) |
0.174 (0.977) |
del 17q21 32 | 19 (34%) | 37 |
0.0266 (0.811) |
0.35 (0.977) |
0.394 (0.977) |
1 (1.00) |
0.188 (0.977) |
del 18q22 2 | 26 (46%) | 30 |
0.438 (0.979) |
0.278 (0.977) |
1 (1.00) |
0.314 (0.977) |
0.0134 (0.566) |
del 19p13 3 | 47 (84%) | 9 |
0.409 (0.978) |
0.269 (0.977) |
1 (1.00) |
0.375 (0.977) |
0.0349 (0.845) |
del 19q13 33 | 17 (30%) | 39 |
0.341 (0.977) |
0.837 (1.00) |
0.772 (1.00) |
0.811 (1.00) |
0.478 (0.979) |
del 20p12 1 | 9 (16%) | 47 |
0.702 (1.00) |
0.688 (1.00) |
0.48 (0.979) |
0.663 (1.00) |
0.371 (0.977) |
del 22q13 31 | 40 (71%) | 16 |
0.784 (1.00) |
0.388 (0.977) |
0.772 (1.00) |
0.384 (0.977) |
1 (1.00) |
del xp21 1 | 18 (32%) | 38 |
0.32 (0.977) |
0.304 (0.977) |
1 (1.00) |
0.103 (0.977) |
1 (1.00) |
del xq25 | 23 (41%) | 33 |
0.899 (1.00) |
0.297 (0.977) |
0.783 (1.00) |
0.831 (1.00) |
0.769 (1.00) |
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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/19782452/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCS-TP/19775681/UCS-TP.merged_data.txt
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Number of patients = 56
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Number of significantly focal cnvs = 61
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Number of selected clinical features = 5
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Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
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.