This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 54 peak regions and 4 clinical features across 65 patients, one significant finding detected with Q value < 0.25.
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Del Peak 27(17p12) cnvs correlated to 'Time to Death'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 54 regions and 4 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.
|
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
||
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | |
| Del Peak 27(17p12) | 34 (52%) | 31 |
0.000822 (0.176) |
0.446 (1.00) |
1 (1.00) |
0.719 (1.00) |
| Amp Peak 1(1p34 2) | 16 (25%) | 49 |
0.217 (1.00) |
0.661 (1.00) |
0.372 (1.00) |
0.488 (1.00) |
| Amp Peak 2(1q23 3) | 32 (49%) | 33 |
0.568 (1.00) |
0.38 (1.00) |
1 (1.00) |
0.719 (1.00) |
| Amp Peak 3(3p25 2) | 28 (43%) | 37 |
0.0562 (1.00) |
0.218 (1.00) |
0.033 (1.00) |
0.181 (1.00) |
| Amp Peak 4(4p16 3) | 15 (23%) | 50 |
0.101 (1.00) |
0.618 (1.00) |
0.231 (1.00) |
0.95 (1.00) |
| Amp Peak 5(5p15 33) | 26 (40%) | 39 |
0.754 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.503 (1.00) |
| Amp Peak 6(6p22 3) | 26 (40%) | 39 |
0.389 (1.00) |
0.841 (1.00) |
0.597 (1.00) |
0.416 (1.00) |
| Amp Peak 7(6q12) | 9 (14%) | 56 |
0.282 (1.00) |
0.12 (1.00) |
0.706 (1.00) |
|
| Amp Peak 8(6q21) | 8 (12%) | 57 |
0.66 (1.00) |
0.486 (1.00) |
1 (1.00) |
|
| Amp Peak 9(7p11 2) | 35 (54%) | 30 |
0.615 (1.00) |
0.112 (1.00) |
1 (1.00) |
0.26 (1.00) |
| Amp Peak 10(8p11 23) | 20 (31%) | 45 |
0.683 (1.00) |
0.679 (1.00) |
0.78 (1.00) |
0.679 (1.00) |
| Amp Peak 11(8q22 2) | 41 (63%) | 24 |
0.504 (1.00) |
0.769 (1.00) |
0.0138 (1.00) |
0.377 (1.00) |
| Amp Peak 12(8q24 21) | 41 (63%) | 24 |
0.0973 (1.00) |
0.458 (1.00) |
0.0564 (1.00) |
0.588 (1.00) |
| Amp Peak 13(10p15 1) | 29 (45%) | 36 |
0.996 (1.00) |
0.0112 (1.00) |
1 (1.00) |
0.665 (1.00) |
| Amp Peak 14(11q13 3) | 26 (40%) | 39 |
0.812 (1.00) |
0.416 (1.00) |
0.791 (1.00) |
0.503 (1.00) |
| Amp Peak 15(12p13 32) | 20 (31%) | 45 |
0.683 (1.00) |
0.915 (1.00) |
0.0465 (1.00) |
0.861 (1.00) |
| Amp Peak 16(12q15) | 26 (40%) | 39 |
0.618 (1.00) |
0.959 (1.00) |
0.183 (1.00) |
0.938 (1.00) |
| Amp Peak 17(13q22 1) | 21 (32%) | 44 |
0.706 (1.00) |
0.644 (1.00) |
0.0992 (1.00) |
0.907 (1.00) |
| Amp Peak 18(16p11 2) | 23 (35%) | 42 |
0.844 (1.00) |
0.269 (1.00) |
0.277 (1.00) |
0.699 (1.00) |
| Amp Peak 19(17q11 2) | 30 (46%) | 35 |
0.62 (1.00) |
0.412 (1.00) |
0.794 (1.00) |
0.0739 (1.00) |
| Amp Peak 20(17q12) | 31 (48%) | 34 |
0.133 (1.00) |
0.349 (1.00) |
1 (1.00) |
0.179 (1.00) |
| Amp Peak 21(19q12) | 30 (46%) | 35 |
0.287 (1.00) |
0.264 (1.00) |
0.794 (1.00) |
0.893 (1.00) |
| Amp Peak 22(20q11 21) | 46 (71%) | 19 |
0.967 (1.00) |
0.841 (1.00) |
1 (1.00) |
0.913 (1.00) |
| Amp Peak 23(22q11 23) | 18 (28%) | 47 |
0.0253 (1.00) |
0.58 (1.00) |
0.0197 (1.00) |
0.921 (1.00) |
| Del Peak 1(1p36 11) | 11 (17%) | 54 |
0.414 (1.00) |
0.0563 (1.00) |
0.737 (1.00) |
0.533 (1.00) |
| Del Peak 2(2q22 1) | 19 (29%) | 46 |
0.749 (1.00) |
0.971 (1.00) |
0.159 (1.00) |
0.253 (1.00) |
| Del Peak 3(2q34) | 22 (34%) | 43 |
0.394 (1.00) |
0.928 (1.00) |
1 (1.00) |
0.665 (1.00) |
| Del Peak 4(2q37 1) | 27 (42%) | 38 |
0.571 (1.00) |
0.636 (1.00) |
0.116 (1.00) |
0.88 (1.00) |
| Del Peak 5(3p21 31) | 24 (37%) | 41 |
0.987 (1.00) |
0.121 (1.00) |
0.787 (1.00) |
0.677 (1.00) |
| Del Peak 6(3p14 2) | 24 (37%) | 41 |
0.335 (1.00) |
0.0301 (1.00) |
0.787 (1.00) |
0.677 (1.00) |
| Del Peak 7(3p14 1) | 22 (34%) | 43 |
0.701 (1.00) |
0.00699 (1.00) |
0.787 (1.00) |
0.513 (1.00) |
| Del Peak 8(3p11 2) | 15 (23%) | 50 |
0.265 (1.00) |
0.207 (1.00) |
0.118 (1.00) |
0.938 (1.00) |
| Del Peak 9(4q22 1) | 29 (45%) | 36 |
0.58 (1.00) |
0.316 (1.00) |
0.0364 (1.00) |
0.893 (1.00) |
| Del Peak 10(4q31 21) | 25 (38%) | 40 |
0.369 (1.00) |
0.598 (1.00) |
0.793 (1.00) |
0.671 (1.00) |
| Del Peak 11(5q11 2) | 27 (42%) | 38 |
0.435 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.699 (1.00) |
| Del Peak 12(6p25 3) | 16 (25%) | 49 |
0.505 (1.00) |
0.965 (1.00) |
0.372 (1.00) |
0.592 (1.00) |
| Del Peak 13(6q22 31) | 25 (38%) | 40 |
0.098 (1.00) |
0.162 (1.00) |
0.793 (1.00) |
0.498 (1.00) |
| Del Peak 14(8p23 1) | 31 (48%) | 34 |
0.896 (1.00) |
0.351 (1.00) |
0.6 (1.00) |
0.499 (1.00) |
| Del Peak 15(9p23) | 27 (42%) | 38 |
0.279 (1.00) |
0.924 (1.00) |
0.603 (1.00) |
0.285 (1.00) |
| Del Peak 16(9p21 3) | 36 (55%) | 29 |
0.208 (1.00) |
0.496 (1.00) |
0.603 (1.00) |
0.312 (1.00) |
| Del Peak 17(9q22 33) | 25 (38%) | 40 |
0.501 (1.00) |
0.471 (1.00) |
0.105 (1.00) |
0.475 (1.00) |
| Del Peak 18(10q23 31) | 27 (42%) | 38 |
0.946 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.416 (1.00) |
| Del Peak 19(11p15 4) | 34 (52%) | 31 |
0.832 (1.00) |
0.158 (1.00) |
1 (1.00) |
0.0425 (1.00) |
| Del Peak 20(11q25) | 20 (31%) | 45 |
0.493 (1.00) |
0.618 (1.00) |
0.78 (1.00) |
0.681 (1.00) |
| Del Peak 21(12p13 2) | 5 (8%) | 60 |
0.0931 (1.00) |
0.292 (1.00) |
1 (1.00) |
0.95 (1.00) |
| Del Peak 22(13q14 2) | 27 (42%) | 38 |
0.751 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.907 (1.00) |
| Del Peak 23(14q32 32) | 18 (28%) | 47 |
0.556 (1.00) |
0.755 (1.00) |
0.0197 (1.00) |
0.103 (1.00) |
| Del Peak 24(15q13 1) | 22 (34%) | 43 |
0.421 (1.00) |
0.724 (1.00) |
1 (1.00) |
0.302 (1.00) |
| Del Peak 25(16p13 3) | 22 (34%) | 43 |
0.888 (1.00) |
0.793 (1.00) |
0.787 (1.00) |
0.893 (1.00) |
| Del Peak 26(16q23 1) | 15 (23%) | 50 |
0.129 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.253 (1.00) |
| Del Peak 28(19p13 3) | 27 (42%) | 38 |
0.484 (1.00) |
0.902 (1.00) |
0.426 (1.00) |
0.498 (1.00) |
| Del Peak 29(22q13 32) | 24 (37%) | 41 |
0.531 (1.00) |
0.474 (1.00) |
0.0564 (1.00) |
0.253 (1.00) |
| Del Peak 30(Xq21 33) | 16 (25%) | 49 |
0.27 (1.00) |
0.398 (1.00) |
0.372 (1.00) |
0.679 (1.00) |
| Del Peak 31(Xq23) | 15 (23%) | 50 |
0.0766 (1.00) |
0.876 (1.00) |
0.351 (1.00) |
0.498 (1.00) |
P value = 0.000822 (logrank test), Q value = 0.18
Table S1. Gene #50: 'Del Peak 27(17p12) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 65 | 24 | 0.4 - 118.9 (7.8) |
| DEL PEAK 27(17P12) MUTATED | 34 | 12 | 0.4 - 118.9 (11.7) |
| DEL PEAK 27(17P12) WILD-TYPE | 31 | 12 | 1.5 - 17.3 (6.7) |
Figure S1. Get High-res Image Gene #50: 'Del Peak 27(17p12) mutation analysis' versus Clinical Feature #1: 'Time to Death'
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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 = BLCA.clin.merged.picked.txt
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Number of patients = 65
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Number of copy number variation regions = 54
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Number of selected clinical features = 4
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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.