(primary blood tumor (peripheral) cohort)
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 20 arm-level results and 3 clinical features across 191 patients, 6 significant findings detected with Q value < 0.25.
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Amp Peak 6(21q22.2) cnv correlated to 'Time to Death'.
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Del Peak 2(3p13) cnv correlated to 'Time to Death'.
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Del Peak 3(3q26.31) cnv correlated to 'AGE'.
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Del Peak 4(5q31.2) cnv correlated to 'Time to Death'.
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Del Peak 10(12p13.2) cnv correlated to 'Time to Death'.
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Del Peak 11(12q21.33) cnv correlated to 'AGE'.
Clinical Features |
Time to Death |
AGE | GENDER | ||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | |
Amp Peak 6(21q22 2) | 14 (7%) | 177 |
0.000742 (0.0415) |
0.0657 (1.00) |
0.0922 (1.00) |
Del Peak 2(3p13) | 9 (5%) | 182 |
4.2e-05 (0.00239) |
0.16 (1.00) |
0.185 (1.00) |
Del Peak 3(3q26 31) | 3 (2%) | 188 |
0.00241 (0.13) |
0.252 (1.00) |
|
Del Peak 4(5q31 2) | 18 (9%) | 173 |
0.00346 (0.183) |
0.00583 (0.297) |
0.0464 (1.00) |
Del Peak 10(12p13 2) | 10 (5%) | 181 |
0.00107 (0.059) |
0.581 (1.00) |
0.351 (1.00) |
Del Peak 11(12q21 33) | 3 (2%) | 188 |
8.84e-17 (5.13e-15) |
0.252 (1.00) |
|
Amp Peak 1(1p33) | 7 (4%) | 184 |
0.34 (1.00) |
0.0372 (1.00) |
1 (1.00) |
Amp Peak 2(1q43) | 7 (4%) | 184 |
0.737 (1.00) |
0.0234 (1.00) |
1 (1.00) |
Amp Peak 3(11q23 3) | 17 (9%) | 174 |
0.117 (1.00) |
0.0106 (0.53) |
0.45 (1.00) |
Amp Peak 4(13q31 3) | 7 (4%) | 184 |
0.929 (1.00) |
0.0714 (1.00) |
1 (1.00) |
Amp Peak 5(20q11 21) | 3 (2%) | 188 |
0.116 (1.00) |
0.372 (1.00) |
0.252 (1.00) |
Del Peak 5(7p12 1) | 16 (8%) | 175 |
0.075 (1.00) |
0.21 (1.00) |
0.604 (1.00) |
Del Peak 6(7q32 3) | 23 (12%) | 168 |
0.0282 (1.00) |
0.0883 (1.00) |
0.656 (1.00) |
Del Peak 7(7q34) | 24 (13%) | 167 |
0.0706 (1.00) |
0.0807 (1.00) |
0.512 (1.00) |
Del Peak 9(9q21 32) | 5 (3%) | 186 |
0.899 (1.00) |
0.744 (1.00) |
0.378 (1.00) |
Del Peak 12(16q23 1) | 9 (5%) | 182 |
0.126 (1.00) |
0.11 (1.00) |
0.513 (1.00) |
Del Peak 13(17p13 2) | 15 (8%) | 176 |
0.0431 (1.00) |
0.226 (1.00) |
0.0565 (1.00) |
Del Peak 14(17q11 2) | 13 (7%) | 178 |
0.0303 (1.00) |
0.547 (1.00) |
0.775 (1.00) |
Del Peak 15(18p11 21) | 9 (5%) | 182 |
0.00548 (0.285) |
0.175 (1.00) |
0.185 (1.00) |
Del Peak 16(20q13 13) | 4 (2%) | 187 |
0.0395 (1.00) |
0.113 (1.00) |
0.627 (1.00) |
P value = 0.000742 (logrank test), Q value = 0.042
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 168 | 106 | 0.9 - 94.1 (12.0) |
AMP PEAK 6(21Q22.2) MUTATED | 12 | 10 | 1.0 - 24.0 (5.4) |
AMP PEAK 6(21Q22.2) WILD-TYPE | 156 | 96 | 0.9 - 94.1 (12.5) |
P value = 4.2e-05 (logrank test), Q value = 0.0024
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 168 | 106 | 0.9 - 94.1 (12.0) |
DEL PEAK 2(3P13) MUTATED | 8 | 7 | 1.0 - 14.0 (2.0) |
DEL PEAK 2(3P13) WILD-TYPE | 160 | 99 | 0.9 - 94.1 (12.5) |
P value = 0.00241 (t-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 191 | 55.2 (16.1) |
DEL PEAK 3(3Q26.31) MUTATED | 3 | 74.0 (3.6) |
DEL PEAK 3(3Q26.31) WILD-TYPE | 188 | 54.9 (16.0) |
P value = 0.00346 (logrank test), Q value = 0.18
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 168 | 106 | 0.9 - 94.1 (12.0) |
DEL PEAK 4(5Q31.2) MUTATED | 17 | 15 | 1.0 - 73.0 (10.0) |
DEL PEAK 4(5Q31.2) WILD-TYPE | 151 | 91 | 0.9 - 94.1 (12.9) |
P value = 0.00107 (logrank test), Q value = 0.059
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 168 | 106 | 0.9 - 94.1 (12.0) |
DEL PEAK 10(12P13.2) MUTATED | 8 | 8 | 1.0 - 22.1 (7.0) |
DEL PEAK 10(12P13.2) WILD-TYPE | 160 | 98 | 0.9 - 94.1 (12.5) |
P value = 8.84e-17 (t-test), Q value = 5.1e-15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 191 | 55.2 (16.1) |
DEL PEAK 11(12Q21.33) MUTATED | 3 | 72.0 (1.0) |
DEL PEAK 11(12Q21.33) WILD-TYPE | 188 | 55.0 (16.0) |
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Mutation data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = LAML-TB.clin.merged.picked.txt
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Number of patients = 191
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Number of significantly arm-level cnvs = 20
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Number of selected clinical features = 3
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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 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 mutations 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.