This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 21 focal events and 11 clinical features across 87 patients, 15 significant findings detected with Q value < 0.25.
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del_1p36.31 cnv correlated to 'Time to Death'.
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del_2q35 cnv correlated to 'Time to Death' and 'GENDER'.
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del_3p21.1 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
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del_4q26 cnv correlated to 'Time to Death'.
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del_4q34.3 cnv correlated to 'Time to Death'.
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del_5q23.2 cnv correlated to 'Time to Death'.
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del_9p21.3 cnv correlated to 'Time to Death'.
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del_10p15.3 cnv correlated to 'Time to Death' and 'RADIATION_THERAPY'.
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del_10q25.2 cnv correlated to 'Time to Death'.
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del_14q32.31 cnv correlated to 'Time to Death'.
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del_15q15.1 cnv correlated to 'Time to Death' and 'KARNOFSKY_PERFORMANCE_SCORE'.
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del_16q24.1 cnv correlated to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
del 2q35 | 17 (20%) | 70 |
0.00831 (0.174) |
0.397 (0.882) |
0.766 (1.00) |
0.82 (1.00) |
0.313 (0.797) |
0.566 (0.932) |
0.0129 (0.213) |
0.376 (0.851) |
0.655 (0.964) |
0.319 (0.8) |
|
del 10p15 3 | 28 (32%) | 59 |
6.76e-07 (9.72e-05) |
0.598 (0.946) |
0.036 (0.397) |
0.186 (0.711) |
0.367 (0.851) |
0.551 (0.932) |
1 (1.00) |
0.00408 (0.106) |
0.058 (0.446) |
0.102 (0.589) |
0.211 (0.743) |
del 15q15 1 | 28 (32%) | 59 |
0.000648 (0.0374) |
0.993 (1.00) |
0.561 (0.932) |
0.764 (1.00) |
0.888 (1.00) |
1 (1.00) |
1 (1.00) |
0.801 (1.00) |
0.00382 (0.106) |
0.191 (0.711) |
0.42 (0.903) |
del 1p36 31 | 33 (38%) | 54 |
0.000204 (0.0157) |
0.93 (1.00) |
0.956 (1.00) |
0.644 (0.959) |
0.949 (1.00) |
0.268 (0.764) |
0.776 (1.00) |
0.804 (1.00) |
0.0751 (0.469) |
0.935 (1.00) |
0.818 (1.00) |
del 3p21 1 | 48 (55%) | 39 |
0.884 (1.00) |
0.864 (1.00) |
0.224 (0.743) |
0.703 (0.99) |
0.672 (0.971) |
1 (1.00) |
0.782 (1.00) |
0.813 (1.00) |
0.0102 (0.197) |
0.179 (0.711) |
0.824 (1.00) |
del 4q26 | 38 (44%) | 49 |
0.00112 (0.052) |
0.566 (0.932) |
0.388 (0.87) |
0.106 (0.589) |
0.447 (0.924) |
0.251 (0.762) |
0.28 (0.779) |
0.477 (0.932) |
0.0471 (0.409) |
0.151 (0.648) |
0.131 (0.633) |
del 4q34 3 | 41 (47%) | 46 |
0.00453 (0.106) |
0.147 (0.648) |
0.634 (0.953) |
0.31 (0.797) |
0.546 (0.932) |
0.238 (0.743) |
0.58 (0.932) |
1 (1.00) |
0.0471 (0.409) |
0.304 (0.797) |
0.0778 (0.473) |
del 5q23 2 | 17 (20%) | 70 |
0.00239 (0.0919) |
0.249 (0.762) |
1 (1.00) |
0.52 (0.932) |
1 (1.00) |
0.462 (0.932) |
0.179 (0.711) |
0.228 (0.743) |
0.0751 (0.469) |
0.875 (1.00) |
0.448 (0.924) |
del 9p21 3 | 51 (59%) | 36 |
8.42e-07 (9.72e-05) |
0.41 (0.893) |
0.765 (1.00) |
0.447 (0.924) |
0.668 (0.971) |
0.0672 (0.469) |
1 (1.00) |
1 (1.00) |
0.801 (1.00) |
0.649 (0.962) |
0.853 (1.00) |
del 10q25 2 | 31 (36%) | 56 |
0.00458 (0.106) |
0.776 (1.00) |
0.725 (1.00) |
0.585 (0.932) |
0.716 (1.00) |
0.255 (0.764) |
1 (1.00) |
0.616 (0.953) |
0.131 (0.633) |
0.62 (0.953) |
0.482 (0.932) |
del 14q32 31 | 39 (45%) | 48 |
0.0116 (0.206) |
0.932 (1.00) |
0.481 (0.932) |
0.14 (0.647) |
0.67 (0.971) |
0.238 (0.743) |
0.0503 (0.415) |
1 (1.00) |
0.0207 (0.266) |
0.0266 (0.307) |
0.126 (0.633) |
del 16q24 1 | 22 (25%) | 65 |
0.0142 (0.219) |
0.721 (1.00) |
0.626 (0.953) |
0.969 (1.00) |
0.224 (0.743) |
0.545 (0.932) |
0.107 (0.589) |
0.58 (0.932) |
0.181 (0.711) |
0.263 (0.764) |
|
del 1p21 3 | 37 (43%) | 50 |
0.0265 (0.307) |
0.298 (0.797) |
0.314 (0.797) |
0.128 (0.633) |
0.355 (0.845) |
1 (1.00) |
0.581 (0.932) |
0.23 (0.743) |
0.152 (0.648) |
0.967 (1.00) |
0.964 (1.00) |
del 6q22 1 | 41 (47%) | 46 |
0.574 (0.932) |
0.848 (1.00) |
0.14 (0.647) |
0.832 (1.00) |
0.577 (0.932) |
0.565 (0.932) |
0.422 (0.903) |
0.342 (0.831) |
0.574 (0.932) |
0.763 (1.00) |
0.529 (0.932) |
del 6q26 | 36 (41%) | 51 |
0.223 (0.743) |
0.87 (1.00) |
0.236 (0.743) |
0.816 (1.00) |
0.0737 (0.469) |
0.268 (0.764) |
1 (1.00) |
0.467 (0.932) |
0.683 (0.971) |
0.856 (1.00) |
0.791 (1.00) |
del 8p23 2 | 18 (21%) | 69 |
0.426 (0.903) |
0.294 (0.797) |
0.335 (0.823) |
0.16 (0.672) |
0.755 (1.00) |
1 (1.00) |
0.506 (0.932) |
0.566 (0.932) |
0.0751 (0.469) |
0.264 (0.764) |
0.232 (0.743) |
del 11q23 2 | 18 (21%) | 69 |
0.0657 (0.469) |
0.626 (0.953) |
0.184 (0.711) |
0.55 (0.932) |
1 (1.00) |
0.558 (0.932) |
0.506 (0.932) |
0.548 (0.932) |
0.307 (0.797) |
0.348 (0.837) |
|
del 12p13 31 | 11 (13%) | 76 |
0.0184 (0.266) |
0.361 (0.85) |
0.375 (0.851) |
0.939 (1.00) |
0.585 (0.932) |
1 (1.00) |
0.681 (0.971) |
0.278 (0.779) |
0.194 (0.711) |
0.193 (0.711) |
|
del 13q14 11 | 44 (51%) | 43 |
0.0207 (0.266) |
0.575 (0.932) |
0.0466 (0.409) |
0.62 (0.953) |
0.0378 (0.397) |
0.237 (0.743) |
0.103 (0.589) |
0.633 (0.953) |
0.838 (1.00) |
0.904 (1.00) |
0.58 (0.932) |
del 16p13 3 | 6 (7%) | 81 |
0.753 (1.00) |
0.0425 (0.409) |
0.128 (0.633) |
0.0478 (0.409) |
0.583 (0.932) |
1 (1.00) |
0.304 (0.797) |
1 (1.00) |
0.0674 (0.469) |
0.132 (0.633) |
|
del 22q12 2 | 68 (78%) | 19 |
0.0529 (0.421) |
0.825 (1.00) |
0.409 (0.893) |
0.151 (0.648) |
0.869 (1.00) |
0.556 (0.932) |
0.327 (0.813) |
0.569 (0.932) |
0.635 (0.953) |
0.37 (0.851) |
0.685 (0.971) |
P value = 0.000204 (logrank test), Q value = 0.016
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 1(1P36.31) MUTATED | 32 | 31 | 1.3 - 49.0 (12.2) |
DEL PEAK 1(1P36.31) WILD-TYPE | 53 | 42 | 0.7 - 91.7 (22.6) |
P value = 0.00831 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 3(2Q35) MUTATED | 17 | 17 | 1.9 - 29.1 (12.7) |
DEL PEAK 3(2Q35) WILD-TYPE | 68 | 56 | 0.7 - 91.7 (18.7) |
P value = 0.0129 (Fisher's exact test), Q value = 0.21
nPatients | FEMALE | MALE |
---|---|---|
ALL | 16 | 71 |
DEL PEAK 3(2Q35) MUTATED | 7 | 10 |
DEL PEAK 3(2Q35) WILD-TYPE | 9 | 61 |
P value = 0.0102 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 77.6 (31.5) |
DEL PEAK 4(3P21.1) MUTATED | 9 | 93.3 (7.1) |
DEL PEAK 4(3P21.1) WILD-TYPE | 8 | 60.0 (39.3) |
P value = 0.00112 (logrank test), Q value = 0.052
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 5(4Q26) MUTATED | 38 | 36 | 1.9 - 68.7 (13.5) |
DEL PEAK 5(4Q26) WILD-TYPE | 47 | 37 | 0.7 - 91.7 (23.6) |
P value = 0.00453 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 6(4Q34.3) MUTATED | 41 | 38 | 2.5 - 68.7 (13.6) |
DEL PEAK 6(4Q34.3) WILD-TYPE | 44 | 35 | 0.7 - 91.7 (23.8) |
P value = 0.00239 (logrank test), Q value = 0.092
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 7(5Q23.2) MUTATED | 17 | 17 | 3.5 - 41.5 (11.9) |
DEL PEAK 7(5Q23.2) WILD-TYPE | 68 | 56 | 0.7 - 91.7 (20.1) |
P value = 8.42e-07 (logrank test), Q value = 9.7e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 11(9P21.3) MUTATED | 50 | 47 | 0.7 - 41.5 (13.0) |
DEL PEAK 11(9P21.3) WILD-TYPE | 35 | 26 | 2.8 - 91.7 (27.2) |
P value = 6.76e-07 (logrank test), Q value = 9.7e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 12(10P15.3) MUTATED | 27 | 26 | 0.7 - 28.3 (10.8) |
DEL PEAK 12(10P15.3) WILD-TYPE | 58 | 47 | 1.3 - 91.7 (23.5) |
P value = 0.00408 (Fisher's exact test), Q value = 0.11
nPatients | NO | YES |
---|---|---|
ALL | 62 | 24 |
DEL PEAK 12(10P15.3) MUTATED | 25 | 2 |
DEL PEAK 12(10P15.3) WILD-TYPE | 37 | 22 |
P value = 0.00458 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 13(10Q25.2) MUTATED | 30 | 28 | 0.7 - 55.1 (11.7) |
DEL PEAK 13(10Q25.2) WILD-TYPE | 55 | 45 | 1.3 - 91.7 (20.7) |
P value = 0.0116 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 17(14Q32.31) MUTATED | 38 | 35 | 1.3 - 77.6 (13.5) |
DEL PEAK 17(14Q32.31) WILD-TYPE | 47 | 38 | 0.7 - 91.7 (21.8) |
P value = 0.000648 (logrank test), Q value = 0.037
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 18(15Q15.1) MUTATED | 27 | 26 | 0.7 - 41.5 (12.7) |
DEL PEAK 18(15Q15.1) WILD-TYPE | 58 | 47 | 1.9 - 91.7 (20.1) |
P value = 0.00382 (Wilcoxon-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 17 | 77.6 (31.5) |
DEL PEAK 18(15Q15.1) MUTATED | 6 | 50.0 (41.0) |
DEL PEAK 18(15Q15.1) WILD-TYPE | 11 | 92.7 (6.5) |
P value = 0.0142 (logrank test), Q value = 0.22
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
DEL PEAK 20(16Q24.1) MUTATED | 21 | 19 | 1.3 - 49.0 (14.7) |
DEL PEAK 20(16Q24.1) WILD-TYPE | 64 | 54 | 0.7 - 91.7 (21.3) |
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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/MESO-TP/22533663/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/MESO-TP/22507181/MESO-TP.merged_data.txt
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Number of patients = 87
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Number of significantly focal cnvs = 21
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Number of selected clinical features = 11
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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.