This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 26 peak regions and 7 clinical features across 144 patients, 11 significant findings detected with Q value < 0.25.
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Amp Peak 1(1q32.1) cnvs correlated to 'Time to Death'.
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Amp Peak 5(12q14.1) cnvs correlated to 'Time to Death'.
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Amp Peak 6(19q13.2) cnvs correlated to 'Time to Death'.
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Del Peak 1(1p36.23) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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Del Peak 11(9p21.3) cnvs correlated to 'Time to Death' and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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Del Peak 12(10q26.13) cnvs correlated to 'Time to Death'.
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Del Peak 18(19q13.41) cnvs correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 19(19q13.43) cnvs correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 20(22q13.31) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 26 regions and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 11 significant findings detected.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 1(1p36 23) | 51 (35%) | 93 |
0.786 (1.00) |
0.00714 (1.00) |
0.297 (1.00) |
0.82 (1.00) |
3.19e-10 (5.74e-08) |
0.000334 (0.0575) |
0.73 (1.00) |
Del Peak 11(9p21 3) | 46 (32%) | 98 |
0.000164 (0.0286) |
0.00196 (0.331) |
0.857 (1.00) |
0.741 (1.00) |
0.142 (1.00) |
0.000115 (0.0201) |
0.153 (1.00) |
Amp Peak 1(1q32 1) | 13 (9%) | 131 |
0.000374 (0.0639) |
0.00246 (0.414) |
0.559 (1.00) |
0.152 (1.00) |
0.401 (1.00) |
0.242 (1.00) |
0.778 (1.00) |
Amp Peak 5(12q14 1) | 10 (7%) | 134 |
0.000268 (0.0463) |
0.206 (1.00) |
0.745 (1.00) |
0.739 (1.00) |
0.278 (1.00) |
0.74 (1.00) |
0.205 (1.00) |
Amp Peak 6(19q13 2) | 9 (6%) | 135 |
2.69e-06 (0.000479) |
0.0101 (1.00) |
0.732 (1.00) |
0.44 (1.00) |
0.907 (1.00) |
0.314 (1.00) |
0.166 (1.00) |
Del Peak 12(10q26 13) | 34 (24%) | 110 |
5.75e-06 (0.00102) |
0.0046 (0.754) |
0.429 (1.00) |
0.896 (1.00) |
0.00311 (0.513) |
0.322 (1.00) |
1 (1.00) |
Del Peak 18(19q13 41) | 67 (47%) | 77 |
0.0384 (1.00) |
0.478 (1.00) |
0.738 (1.00) |
0.512 (1.00) |
1.05e-07 (1.88e-05) |
0.0925 (1.00) |
0.242 (1.00) |
Del Peak 19(19q13 43) | 75 (52%) | 69 |
0.0165 (1.00) |
0.824 (1.00) |
0.867 (1.00) |
0.472 (1.00) |
3.9e-05 (0.00687) |
0.127 (1.00) |
0.187 (1.00) |
Del Peak 20(22q13 31) | 16 (11%) | 128 |
0.0223 (1.00) |
0.444 (1.00) |
0.79 (1.00) |
0.361 (1.00) |
0.000687 (0.117) |
0.792 (1.00) |
1 (1.00) |
Amp Peak 2(4q12) | 8 (6%) | 136 |
0.775 (1.00) |
0.787 (1.00) |
0.726 (1.00) |
0.396 (1.00) |
0.0548 (1.00) |
1 (1.00) |
0.0322 (1.00) |
Amp Peak 3(7p11 2) | 32 (22%) | 112 |
0.00294 (0.489) |
0.0157 (1.00) |
0.227 (1.00) |
0.452 (1.00) |
0.0196 (1.00) |
0.152 (1.00) |
0.55 (1.00) |
Amp Peak 4(12p13 32) | 20 (14%) | 124 |
0.944 (1.00) |
0.107 (1.00) |
0.0924 (1.00) |
0.441 (1.00) |
0.112 (1.00) |
1 (1.00) |
0.0905 (1.00) |
Del Peak 2(1q44) | 6 (4%) | 138 |
0.679 (1.00) |
0.0628 (1.00) |
0.236 (1.00) |
0.742 (1.00) |
0.534 (1.00) |
0.685 (1.00) |
1 (1.00) |
Del Peak 3(2p25 3) | 5 (3%) | 139 |
0.522 (1.00) |
0.644 (1.00) |
0.652 (1.00) |
0.468 (1.00) |
0.0619 (1.00) |
1 (1.00) |
0.0271 (1.00) |
Del Peak 4(2q37 3) | 18 (12%) | 126 |
0.886 (1.00) |
0.249 (1.00) |
1 (1.00) |
0.708 (1.00) |
0.159 (1.00) |
0.31 (1.00) |
0.621 (1.00) |
Del Peak 5(3p14 3) | 6 (4%) | 138 |
0.868 (1.00) |
0.371 (1.00) |
1 (1.00) |
0.0661 (1.00) |
0.402 (1.00) |
1 (1.00) |
|
Del Peak 6(3q13 31) | 10 (7%) | 134 |
0.866 (1.00) |
0.514 (1.00) |
0.0434 (1.00) |
0.128 (1.00) |
0.254 (1.00) |
0.74 (1.00) |
0.745 (1.00) |
Del Peak 7(3q29) | 12 (8%) | 132 |
0.928 (1.00) |
0.46 (1.00) |
0.233 (1.00) |
0.428 (1.00) |
0.0622 (1.00) |
0.762 (1.00) |
1 (1.00) |
Del Peak 8(4q35 1) | 33 (23%) | 111 |
0.394 (1.00) |
0.884 (1.00) |
0.427 (1.00) |
0.804 (1.00) |
0.591 (1.00) |
0.841 (1.00) |
0.324 (1.00) |
Del Peak 9(6p24 1) | 9 (6%) | 135 |
0.382 (1.00) |
0.332 (1.00) |
0.3 (1.00) |
0.769 (1.00) |
0.0631 (1.00) |
0.0846 (1.00) |
0.494 (1.00) |
Del Peak 10(6q12) | 8 (6%) | 136 |
0.0541 (1.00) |
0.362 (1.00) |
0.0211 (1.00) |
0.779 (1.00) |
0.00616 (1.00) |
0.144 (1.00) |
1 (1.00) |
Del Peak 13(11p15 5) | 24 (17%) | 120 |
0.139 (1.00) |
0.0448 (1.00) |
0.823 (1.00) |
0.301 (1.00) |
0.00635 (1.00) |
0.261 (1.00) |
0.377 (1.00) |
Del Peak 14(11q14 1) | 7 (5%) | 137 |
0.268 (1.00) |
0.724 (1.00) |
0.14 (1.00) |
0.315 (1.00) |
0.376 (1.00) |
0.702 (1.00) |
1 (1.00) |
Del Peak 15(14q24 3) | 31 (22%) | 113 |
0.00267 (0.445) |
0.705 (1.00) |
0.00794 (1.00) |
0.193 (1.00) |
0.042 (1.00) |
1 (1.00) |
1 (1.00) |
Del Peak 16(15q21 1) | 15 (10%) | 129 |
0.459 (1.00) |
0.46 (1.00) |
0.583 (1.00) |
0.457 (1.00) |
0.234 (1.00) |
0.283 (1.00) |
0.424 (1.00) |
Del Peak 17(17q25 3) | 4 (3%) | 140 |
0.364 (1.00) |
0.222 (1.00) |
0.634 (1.00) |
0.557 (1.00) |
0.648 (1.00) |
0.62 (1.00) |
P value = 0.000374 (logrank test), Q value = 0.064
Table S1. Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 144 | 48 | 0.0 - 211.2 (18.0) |
AMP PEAK 1(1Q32.1) MUTATED | 13 | 7 | 4.1 - 90.8 (11.6) |
AMP PEAK 1(1Q32.1) WILD-TYPE | 131 | 41 | 0.0 - 211.2 (19.0) |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D1V1.png)
P value = 0.000268 (logrank test), Q value = 0.046
Table S2. Gene #5: 'Amp Peak 5(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 144 | 48 | 0.0 - 211.2 (18.0) |
AMP PEAK 5(12Q14.1) MUTATED | 10 | 8 | 7.7 - 80.0 (15.2) |
AMP PEAK 5(12Q14.1) WILD-TYPE | 134 | 40 | 0.0 - 211.2 (18.5) |
Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D5V1.png)
P value = 2.69e-06 (logrank test), Q value = 0.00048
Table S3. Gene #6: 'Amp Peak 6(19q13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 144 | 48 | 0.0 - 211.2 (18.0) |
AMP PEAK 6(19Q13.2) MUTATED | 9 | 6 | 0.0 - 43.9 (15.0) |
AMP PEAK 6(19Q13.2) WILD-TYPE | 135 | 42 | 0.1 - 211.2 (18.9) |
Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(19q13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D6V1.png)
P value = 3.19e-10 (Fisher's exact test), Q value = 5.7e-08
Table S4. Gene #7: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 50 | 35 | 58 |
DEL PEAK 1(1P36.23) MUTATED | 6 | 6 | 39 |
DEL PEAK 1(1P36.23) WILD-TYPE | 44 | 29 | 19 |
Figure S4. Get High-res Image Gene #7: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D7V5.png)
P value = 0.000334 (Fisher's exact test), Q value = 0.057
Table S5. Gene #7: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 58 | 86 |
DEL PEAK 1(1P36.23) MUTATED | 31 | 20 |
DEL PEAK 1(1P36.23) WILD-TYPE | 27 | 66 |
Figure S5. Get High-res Image Gene #7: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D7V6.png)
P value = 0.000164 (logrank test), Q value = 0.029
Table S6. Gene #17: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 144 | 48 | 0.0 - 211.2 (18.0) |
DEL PEAK 11(9P21.3) MUTATED | 46 | 21 | 4.1 - 117.4 (18.4) |
DEL PEAK 11(9P21.3) WILD-TYPE | 98 | 27 | 0.0 - 211.2 (17.8) |
Figure S6. Get High-res Image Gene #17: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D17V1.png)
P value = 0.000115 (Fisher's exact test), Q value = 0.02
Table S7. Gene #17: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 58 | 86 |
DEL PEAK 11(9P21.3) MUTATED | 8 | 38 |
DEL PEAK 11(9P21.3) WILD-TYPE | 50 | 48 |
Figure S7. Get High-res Image Gene #17: 'Del Peak 11(9p21.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D17V6.png)
P value = 5.75e-06 (logrank test), Q value = 0.001
Table S8. Gene #18: 'Del Peak 12(10q26.13) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 144 | 48 | 0.0 - 211.2 (18.0) |
DEL PEAK 12(10Q26.13) MUTATED | 34 | 21 | 4.0 - 154.1 (16.7) |
DEL PEAK 12(10Q26.13) WILD-TYPE | 110 | 27 | 0.0 - 211.2 (22.2) |
Figure S8. Get High-res Image Gene #18: 'Del Peak 12(10q26.13) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D18V1.png)
P value = 1.05e-07 (Fisher's exact test), Q value = 1.9e-05
Table S9. Gene #24: 'Del Peak 18(19q13.41) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 50 | 35 | 58 |
DEL PEAK 18(19Q13.41) MUTATED | 12 | 11 | 43 |
DEL PEAK 18(19Q13.41) WILD-TYPE | 38 | 24 | 15 |
Figure S9. Get High-res Image Gene #24: 'Del Peak 18(19q13.41) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D24V5.png)
P value = 3.9e-05 (Fisher's exact test), Q value = 0.0069
Table S10. Gene #25: 'Del Peak 19(19q13.43) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 50 | 35 | 58 |
DEL PEAK 19(19Q13.43) MUTATED | 17 | 14 | 43 |
DEL PEAK 19(19Q13.43) WILD-TYPE | 33 | 21 | 15 |
Figure S10. Get High-res Image Gene #25: 'Del Peak 19(19q13.43) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D25V5.png)
P value = 0.000687 (Fisher's exact test), Q value = 0.12
Table S11. Gene #26: 'Del Peak 20(22q13.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 50 | 35 | 58 |
DEL PEAK 20(22Q13.31) MUTATED | 12 | 3 | 1 |
DEL PEAK 20(22Q13.31) WILD-TYPE | 38 | 32 | 57 |
Figure S11. Get High-res Image Gene #26: 'Del Peak 20(22q13.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D26V5.png)
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Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
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Clinical data file = LGG.clin.merged.picked.txt
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Number of patients = 144
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Number of copy number variation regions = 26
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Number of selected clinical features = 7
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Exclude regions that fewer than K tumors have alterations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene cnvs using 't.test' 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.