(primary blood tumor (peripheral) cohort)
This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 41 genes and 3 clinical features across 196 patients, 4 significant findings detected with Q value < 0.25.
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DNMT3A mutation correlated to 'Time to Death'.
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TP53 mutation correlated to 'Time to Death'.
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IDH2 mutation correlated to 'AGE'.
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FLJ43860 mutation correlated to 'Time to Death'.
Clinical Features |
Time to Death |
AGE | GENDER | ||
nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | |
DNMT3A | 49 (25%) | 147 |
0.000602 (0.0662) |
0.0517 (1.00) |
0.248 (1.00) |
TP53 | 11 (6%) | 185 |
7.75e-06 (0.000876) |
0.00306 (0.334) |
0.351 (1.00) |
IDH2 | 18 (9%) | 178 |
0.897 (1.00) |
3.57e-05 (0.004) |
1 (1.00) |
FLJ43860 | 3 (2%) | 193 |
0.00055 (0.061) |
0.754 (1.00) |
0.253 (1.00) |
NPM1 | 47 (24%) | 149 |
0.223 (1.00) |
0.985 (1.00) |
0.132 (1.00) |
FLT3 | 52 (27%) | 144 |
0.204 (1.00) |
0.365 (1.00) |
0.516 (1.00) |
IDH1 | 20 (10%) | 176 |
0.925 (1.00) |
0.339 (1.00) |
0.478 (1.00) |
NRAS | 18 (9%) | 178 |
0.88 (1.00) |
0.523 (1.00) |
0.626 (1.00) |
RUNX1 | 17 (9%) | 179 |
0.232 (1.00) |
0.106 (1.00) |
0.802 (1.00) |
WT1 | 12 (6%) | 184 |
0.325 (1.00) |
0.0417 (1.00) |
0.773 (1.00) |
KRAS | 8 (4%) | 188 |
0.498 (1.00) |
0.435 (1.00) |
0.472 (1.00) |
TET2 | 15 (8%) | 181 |
0.869 (1.00) |
0.171 (1.00) |
0.286 (1.00) |
U2AF1 | 10 (5%) | 186 |
0.462 (1.00) |
0.00354 (0.382) |
0.0234 (1.00) |
PHF6 | 6 (3%) | 190 |
0.882 (1.00) |
0.234 (1.00) |
0.0328 (1.00) |
PTPN11 | 7 (4%) | 189 |
0.373 (1.00) |
0.677 (1.00) |
1 (1.00) |
KIT | 7 (4%) | 189 |
0.905 (1.00) |
0.485 (1.00) |
0.704 (1.00) |
C17ORF97 | 5 (3%) | 191 |
0.631 (1.00) |
0.408 (1.00) |
0.379 (1.00) |
ETV6 | 5 (3%) | 191 |
0.471 (1.00) |
0.278 (1.00) |
0.379 (1.00) |
SMC3 | 6 (3%) | 190 |
0.178 (1.00) |
0.584 (1.00) |
0.413 (1.00) |
FAM5C | 5 (3%) | 191 |
0.121 (1.00) |
0.044 (1.00) |
0.379 (1.00) |
MUC4 | 7 (4%) | 189 |
0.149 (1.00) |
0.5 (1.00) |
1 (1.00) |
CYP21A2 | 4 (2%) | 192 |
0.0175 (1.00) |
0.554 (1.00) |
1 (1.00) |
NOTCH2NL | 3 (2%) | 193 |
0.807 (1.00) |
0.253 (1.00) |
|
AP3S1 | 3 (2%) | 193 |
0.741 (1.00) |
0.534 (1.00) |
0.592 (1.00) |
SMC1A | 5 (3%) | 191 |
0.479 (1.00) |
0.0219 (1.00) |
0.379 (1.00) |
TRIM48 | 3 (2%) | 193 |
0.202 (1.00) |
0.592 (1.00) |
|
C5ORF25 | 3 (2%) | 193 |
0.0882 (1.00) |
0.195 (1.00) |
0.0919 (1.00) |
CCDC74A | 3 (2%) | 193 |
0.523 (1.00) |
0.347 (1.00) |
0.253 (1.00) |
OR11H12 | 3 (2%) | 193 |
0.528 (1.00) |
0.374 (1.00) |
0.592 (1.00) |
OR5H6 | 3 (2%) | 193 |
0.0468 (1.00) |
0.592 (1.00) |
|
LILRA3 | 3 (2%) | 193 |
0.878 (1.00) |
0.592 (1.00) |
|
NMUR2 | 3 (2%) | 193 |
0.928 (1.00) |
1 (1.00) |
|
STAG2 | 4 (2%) | 192 |
0.397 (1.00) |
0.325 (1.00) |
0.331 (1.00) |
SUZ12 | 3 (2%) | 193 |
0.879 (1.00) |
0.253 (1.00) |
|
SCRN3 | 3 (2%) | 193 |
0.0536 (1.00) |
0.592 (1.00) |
|
DIS3 | 3 (2%) | 193 |
0.724 (1.00) |
0.592 (1.00) |
|
VPS26B | 3 (2%) | 193 |
0.588 (1.00) |
0.96 (1.00) |
0.253 (1.00) |
ZNF275 | 3 (2%) | 193 |
0.0715 (1.00) |
0.592 (1.00) |
|
EZH2 | 3 (2%) | 193 |
0.115 (1.00) |
1 (1.00) |
|
ANKRD24 | 3 (2%) | 193 |
0.177 (1.00) |
0.761 (1.00) |
1 (1.00) |
QRICH2 | 4 (2%) | 192 |
0.608 (1.00) |
0.0269 (1.00) |
1 (1.00) |
P value = 0.000602 (logrank test), Q value = 0.066
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 172 | 108 | 0.9 - 94.1 (12.0) |
DNMT3A MUTATED | 45 | 34 | 0.9 - 37.0 (9.0) |
DNMT3A WILD-TYPE | 127 | 74 | 0.9 - 94.1 (15.0) |
P value = 7.75e-06 (logrank test), Q value = 0.00088
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 172 | 108 | 0.9 - 94.1 (12.0) |
TP53 MUTATED | 10 | 10 | 1.0 - 17.0 (6.0) |
TP53 WILD-TYPE | 162 | 98 | 0.9 - 94.1 (13.0) |
P value = 3.57e-05 (t-test), Q value = 0.004
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 196 | 55.0 (16.2) |
IDH2 MUTATED | 18 | 64.6 (7.9) |
IDH2 WILD-TYPE | 178 | 54.0 (16.5) |
P value = 0.00055 (logrank test), Q value = 0.061
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 172 | 108 | 0.9 - 94.1 (12.0) |
FLJ43860 MUTATED | 3 | 3 | 1.0 - 9.0 (2.0) |
FLJ43860 WILD-TYPE | 169 | 105 | 0.9 - 94.1 (12.0) |
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Mutation data file = LAML-TB.mutsig.cluster.txt
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Clinical data file = LAML-TP.clin.merged.picked.txt
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Number of patients = 196
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Number of significantly mutated genes = 41
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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.