This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 11 genes and 17 clinical features across 400 patients, 13 significant findings detected with Q value < 0.25.
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BRAF mutation correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'EXTRATHYROIDAL_EXTENSION'.
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NRAS mutation correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
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NUP93 mutation correlated to 'HISTOLOGICAL_TYPE'.
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DNMT3A mutation correlated to 'Time to Death'.
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ITGAL mutation correlated to 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', and 'EXTRATHYROIDAL_EXTENSION'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
RADIATION EXPOSURE |
EXTRATHYROIDAL EXTENSION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
MULTIFOCALITY |
TUMOR SIZE |
RACE | ETHNICITY | ||
nMutated (%) | 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
BRAF | 239 (60%) | 161 |
0.956 (1.00) |
0.335 (1.00) |
0.00137 (0.0259) |
0.00122 (0.0259) |
0.000777 (0.0207) |
1 (1.00) |
0.245 (1.00) |
1e-05 (0.000623) |
0.0322 (0.376) |
0.595 (1.00) |
1e-05 (0.000623) |
0.358 (1.00) |
0.0239 (0.298) |
1 (1.00) |
0.234 (1.00) |
0.917 (1.00) |
0.437 (1.00) |
NRAS | 34 (8%) | 366 |
0.474 (1.00) |
0.548 (1.00) |
0.0384 (0.399) |
0.145 (0.82) |
0.000139 (0.00519) |
0.442 (1.00) |
0.84 (1.00) |
2e-05 (0.000935) |
0.61 (1.00) |
1 (1.00) |
0.187 (0.921) |
0.689 (1.00) |
0.00152 (0.0259) |
0.371 (1.00) |
0.527 (1.00) |
0.0986 (0.683) |
0.0576 (0.47) |
ITGAL | 4 (1%) | 396 |
0.0353 (0.388) |
0.0164 (0.236) |
0.00038 (0.0118) |
0.143 (0.82) |
0.348 (1.00) |
1 (1.00) |
0.0527 (0.47) |
0.712 (1.00) |
1 (1.00) |
1 (1.00) |
0.00146 (0.0259) |
0.0967 (0.683) |
0.627 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.263 (1.00) |
|
NUP93 | 4 (1%) | 396 |
0.883 (1.00) |
0.51 (1.00) |
0.547 (1.00) |
0.734 (1.00) |
0.348 (1.00) |
1 (1.00) |
1 (1.00) |
0.014 (0.218) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.517 (1.00) |
0.411 (1.00) |
0.34 (1.00) |
0.998 (1.00) |
0.199 (0.933) |
1 (1.00) |
DNMT3A | 3 (1%) | 397 |
0 (0) |
0.136 (0.819) |
0.0612 (0.477) |
0.166 (0.88) |
1 (1.00) |
1 (1.00) |
0.574 (1.00) |
0.656 (1.00) |
1 (1.00) |
0.123 (0.768) |
0.258 (1.00) |
0.418 (1.00) |
0.724 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
HRAS | 14 (4%) | 386 |
0.486 (1.00) |
0.338 (1.00) |
0.344 (1.00) |
0.78 (1.00) |
0.388 (1.00) |
0.249 (1.00) |
0.76 (1.00) |
0.0217 (0.29) |
1 (1.00) |
1 (1.00) |
0.688 (1.00) |
0.2 (0.933) |
0.686 (1.00) |
0.792 (1.00) |
0.716 (1.00) |
0.107 (0.713) |
0.615 (1.00) |
EIF1AX | 6 (2%) | 394 |
0.0578 (0.47) |
0.0562 (0.47) |
0.92 (1.00) |
1 (1.00) |
0.625 (1.00) |
1 (1.00) |
0.176 (0.889) |
0.0727 (0.543) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.28 (1.00) |
0.774 (1.00) |
0.666 (1.00) |
0.468 (1.00) |
1 (1.00) |
|
PPM1D | 5 (1%) | 395 |
0.852 (1.00) |
0.158 (0.867) |
0.231 (1.00) |
0.288 (1.00) |
1 (1.00) |
1 (1.00) |
0.605 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.111 (0.719) |
0.353 (1.00) |
1 (1.00) |
0.516 (1.00) |
1 (1.00) |
1 (1.00) |
|
KRAS | 4 (1%) | 396 |
0.869 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.206 (0.941) |
0.625 (1.00) |
1 (1.00) |
0.576 (1.00) |
0.471 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.419 (1.00) |
0.281 (1.00) |
1 (1.00) |
0.749 (1.00) |
1 (1.00) |
|
DLC1 | 4 (1%) | 396 |
0.0517 (0.47) |
0.782 (1.00) |
0.73 (1.00) |
1 (1.00) |
0.605 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.385 (1.00) |
0.517 (1.00) |
0.627 (1.00) |
0.573 (1.00) |
1 (1.00) |
0.263 (1.00) |
|
NLRP6 | 3 (1%) | 397 |
0.624 (1.00) |
0.437 (1.00) |
0.788 (1.00) |
0.169 (0.88) |
0.605 (1.00) |
1 (1.00) |
0.653 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.359 (1.00) |
0.598 (1.00) |
1 (1.00) |
P value = 0.00137 (Fisher's exact test), Q value = 0.026
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 230 | 45 | 83 | 2 | 32 | 6 |
BRAF MUTATED | 131 | 19 | 59 | 0 | 25 | 4 |
BRAF WILD-TYPE | 99 | 26 | 24 | 2 | 7 | 2 |
P value = 0.00122 (Fisher's exact test), Q value = 0.026
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 117 | 137 | 129 | 15 |
BRAF MUTATED | 69 | 67 | 89 | 13 |
BRAF WILD-TYPE | 48 | 70 | 40 | 2 |
P value = 0.000777 (Fisher's exact test), Q value = 0.021
nPatients | 0 | 1 |
---|---|---|
ALL | 189 | 170 |
BRAF MUTATED | 99 | 119 |
BRAF WILD-TYPE | 90 | 51 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00062
nPatients | OTHER SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 6 | 281 | 83 | 30 |
BRAF MUTATED | 3 | 193 | 15 | 28 |
BRAF WILD-TYPE | 3 | 88 | 68 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00062
nPatients | MINIMAL (T3) | MODERATE/ADVANCED (T4A) | NONE | VERY ADVANCED (T4B) |
---|---|---|---|---|
ALL | 103 | 11 | 272 | 1 |
BRAF MUTATED | 80 | 11 | 143 | 0 |
BRAF WILD-TYPE | 23 | 0 | 129 | 1 |
P value = 0.000139 (Fisher's exact test), Q value = 0.0052
nPatients | 0 | 1 |
---|---|---|
ALL | 189 | 170 |
NRAS MUTATED | 27 | 5 |
NRAS WILD-TYPE | 162 | 165 |
P value = 2e-05 (Fisher's exact test), Q value = 0.00093
nPatients | OTHER SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 6 | 281 | 83 | 30 |
NRAS MUTATED | 0 | 15 | 19 | 0 |
NRAS WILD-TYPE | 6 | 266 | 64 | 30 |
P value = 0.00152 (Wilcoxon-test), Q value = 0.026
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 303 | 3.4 (6.0) |
NRAS MUTATED | 25 | 1.0 (2.4) |
NRAS WILD-TYPE | 278 | 3.6 (6.2) |
P value = 0.014 (Fisher's exact test), Q value = 0.22
nPatients | OTHER SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 6 | 281 | 83 | 30 |
NUP93 MUTATED | 1 | 1 | 1 | 1 |
NUP93 WILD-TYPE | 5 | 280 | 82 | 29 |
P value = 0 (logrank test), Q value = 0
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 399 | 13 | 0.1 - 169.3 (21.0) |
DNMT3A MUTATED | 3 | 1 | 1.0 - 7.7 (6.8) |
DNMT3A WILD-TYPE | 396 | 12 | 0.1 - 169.3 (21.2) |
P value = 0.0164 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 400 | 47.1 (15.7) |
ITGAL MUTATED | 4 | 64.8 (3.5) |
ITGAL WILD-TYPE | 396 | 46.9 (15.7) |
P value = 0.00038 (Fisher's exact test), Q value = 0.012
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 230 | 45 | 83 | 2 | 32 | 6 |
ITGAL MUTATED | 0 | 1 | 0 | 1 | 2 | 0 |
ITGAL WILD-TYPE | 230 | 44 | 83 | 1 | 30 | 6 |
P value = 0.00146 (Fisher's exact test), Q value = 0.026
nPatients | MINIMAL (T3) | MODERATE/ADVANCED (T4A) | NONE | VERY ADVANCED (T4B) |
---|---|---|---|---|
ALL | 103 | 11 | 272 | 1 |
ITGAL MUTATED | 0 | 1 | 2 | 1 |
ITGAL WILD-TYPE | 103 | 10 | 270 | 0 |
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Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
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Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/15165022/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/15092795/THCA-TP.merged_data.txt
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Number of patients = 400
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Number of significantly mutated genes = 11
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Number of selected clinical features = 17
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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.