Correlation between copy number variation genes (focal events) and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C14M935D
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C14M935D
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 28 focal events and 10 clinical features across 163 patients, 31 significant findings detected with Q value < 0.25.

- amp_7q22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- amp_17q25.2 cnv correlated to 'PATHOLOGY.M.STAGE'.

- del_1p36.31 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- del_3p22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- del_4q34.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- del_5p14.2 cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.

- del_5q35.2 cnv correlated to 'PATHOLOGY.T.STAGE'.

- del_6q21 cnv correlated to 'PATHOLOGY.T.STAGE'.

- del_6q22.31 cnv correlated to 'PATHOLOGY.T.STAGE'.

- del_9p21.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- del_11q22.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- del_11q24.2 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- del_15q15.2 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- del_16q24.1 cnv correlated to 'Time to Death'.

- del_xp11.22 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- del_xq28 cnv correlated to 'Time to Death'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 28 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 31 significant findings detected.

|  | Clinical Features | Time to Death | AGE | NEOPLASM DISEASESTAGE | PATHOLOGY T STAGE | PATHOLOGY N STAGE | PATHOLOGY M STAGE | GENDER | KARNOFSKY PERFORMANCE SCORE | NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | t-test | t-test
del 1p36 31 | 35 (21%) | 128 | 0.000879 (0.177) | 0.475 (1.00) | 1.99e-05 (0.00448) | 2.41e-05 (0.0054) | 0.013 (1.00) | 0.135 (1.00) | 0.0361 (1.00) | 0.301 (1.00) | 0.453 (1.00) |
del 9p21 3 | 24 (15%) | 139 | 5.18e-05 (0.0115) | 0.272 (1.00) | 3.19e-07 (7.34e-05) | 2.02e-06 (0.000461) | 0.00914 (1.00) | 0.00761 (1.00) | 0.00288 (0.576) | 0.314 (1.00) |  |
del 11q22 3 | 17 (10%) | 146 | 0.000127 (0.0279) | 0.114 (1.00) | 0.000152 (0.0329) | 0.000633 (0.13) | 0.0444 (1.00) | 0.0974 (1.00) | 0.401 (1.00) | 0.792 (1.00) |  |
del 11q24 2 | 17 (10%) | 146 | 3.61e-05 (0.00806) | 0.0593 (1.00) | 0.000152 (0.0329) | 0.000633 (0.13) | 0.0776 (1.00) | 0.0974 (1.00) | 0.589 (1.00) | 0.792 (1.00) |  |
del 15q15 2 | 21 (13%) | 142 | 2.86e-07 (6.61e-05) | 0.0511 (1.00) | 0.000171 (0.0368) | 0.000141 (0.0308) | 0.0057 (1.00) | 0.0523 (1.00) | 0.204 (1.00) | 0.348 (1.00) |  |
del xp11 22 | 18 (11%) | 145 | 0.000314 (0.0662) | 0.333 (1.00) | 0.000432 (0.089) | 0.000217 (0.0463) | 0.0836 (1.00) | 0.696 (1.00) | 0.00486 (0.942) | 0.467 (1.00) |  |
del 3p22 1 | 15 (9%) | 148 | 0.0198 (1.00) | 0.149 (1.00) | 6.41e-06 (0.00145) | 5.12e-05 (0.0114) | 0.361 (1.00) | 0.114 (1.00) | 0.386 (1.00) | 0.754 (1.00) | 0.453 (1.00) |
del 4q34 3 | 18 (11%) | 145 | 0.0288 (1.00) | 0.18 (1.00) | 0.00108 (0.217) | 0.000411 (0.0852) | 0.0698 (1.00) | 0.23 (1.00) | 0.00486 (0.942) | 0.754 (1.00) |  |
del 5p14 2 | 10 (6%) | 153 | 6.3e-05 (0.0139) | 0.185 (1.00) | 0.0109 (1.00) | 0.000382 (0.0799) | 0.0122 (1.00) | 0.359 (1.00) | 0.0673 (1.00) | 0.104 (1.00) |  |
amp 7q22 1 | 97 (60%) | 66 | 0.049 (1.00) | 0.518 (1.00) | 0.000276 (0.0584) | 0.00432 (0.851) | 0.54 (1.00) | 0.314 (1.00) | 0.166 (1.00) | 0.159 (1.00) | 0.354 (1.00) | 0.837 (1.00)
amp 17q25 2 | 120 (74%) | 43 | 0.871 (1.00) | 0.239 (1.00) | 0.296 (1.00) | 0.395 (1.00) | 0.891 (1.00) | 0.000359 (0.0753) | 0.0319 (1.00) | 0.667 (1.00) |  |
del 5q35 2 | 10 (6%) | 153 | 0.00872 (1.00) | 0.0436 (1.00) | 0.00438 (0.859) | 0.000382 (0.0799) | 0.0903 (1.00) | 0.434 (1.00) | 0.0673 (1.00) |  |  |
del 6q21 | 16 (10%) | 147 | 0.206 (1.00) | 0.902 (1.00) | 0.0157 (1.00) | 0.000811 (0.165) | 0.169 (1.00) | 0.445 (1.00) | 0.00717 (1.00) | 0.459 (1.00) | 0.315 (1.00) |
del 6q22 31 | 17 (10%) | 146 | 0.0437 (1.00) | 0.857 (1.00) | 0.00578 (1.00) | 0.000217 (0.0463) | 0.139 (1.00) | 0.304 (1.00) | 0.0105 (1.00) | 0.459 (1.00) | 0.315 (1.00) |
del 16q24 1 | 7 (4%) | 156 | 1.82e-06 (0.000417) | 0.57 (1.00) | 0.0363 (1.00) | 0.269 (1.00) | 0.192 (1.00) | 0.216 (1.00) | 0.199 (1.00) |  |  |
del xq28 | 17 (10%) | 146 | 5.1e-06 (0.00116) | 0.113 (1.00) | 0.00351 (0.699) | 0.0134 (1.00) | 0.0836 (1.00) | 0.632 (1.00) | 0.0105 (1.00) | 0.469 (1.00) |  |
amp 2p23 2 | 32 (20%) | 131 | 0.262 (1.00) | 0.356 (1.00) | 0.46 (1.00) | 0.873 (1.00) | 0.408 (1.00) | 0.0307 (1.00) | 0.196 (1.00) | 0.537 (1.00) | 0.331 (1.00) | 0.477 (1.00)
amp 2q32 1 | 39 (24%) | 124 | 0.461 (1.00) | 0.856 (1.00) | 0.0642 (1.00) | 0.172 (1.00) | 0.72 (1.00) | 0.0174 (1.00) | 0.424 (1.00) | 0.531 (1.00) |  |
amp 3q22 3 | 56 (34%) | 107 | 0.373 (1.00) | 0.478 (1.00) | 0.295 (1.00) | 0.0523 (1.00) | 1 (1.00) | 0.533 (1.00) | 0.591 (1.00) | 0.126 (1.00) | 0.354 (1.00) |
amp 19p13 2 | 19 (12%) | 144 | 0.543 (1.00) | 0.0568 (1.00) | 0.889 (1.00) | 0.0541 (1.00) | 0.521 (1.00) | 0.903 (1.00) | 0.595 (1.00) | 0.268 (1.00) |  |
del 2q37 3 | 8 (5%) | 155 | 0.681 (1.00) | 0.151 (1.00) | 0.018 (1.00) | 0.00691 (1.00) |  | 0.534 (1.00) | 0.0538 (1.00) |  |  |
del 5q15 | 11 (7%) | 152 | 0.00642 (1.00) | 0.0301 (1.00) | 0.0357 (1.00) | 0.00535 (1.00) | 0.0903 (1.00) | 0.389 (1.00) | 0.0886 (1.00) |  |  |
del 10p11 21 | 11 (7%) | 152 | 0.822 (1.00) | 0.823 (1.00) | 0.006 (1.00) | 0.0109 (1.00) | 0.0556 (1.00) | 0.52 (1.00) | 0.0886 (1.00) | 0.792 (1.00) |  |
del 14q11 2 | 34 (21%) | 129 | 0.00577 (1.00) | 0.68 (1.00) | 0.00494 (0.949) | 0.00745 (1.00) | 0.118 (1.00) | 0.17 (1.00) | 0.141 (1.00) | 0.448 (1.00) |  |
del 14q32 2 | 34 (21%) | 129 | 0.00427 (0.845) | 0.639 (1.00) | 0.00494 (0.949) | 0.00745 (1.00) | 0.0476 (1.00) | 0.183 (1.00) | 0.141 (1.00) | 0.448 (1.00) | 0.413 (1.00) | 0.00474 (0.925)
del 19p13 3 | 16 (10%) | 147 | 0.0285 (1.00) | 0.946 (1.00) | 0.00802 (1.00) | 0.00614 (1.00) | 0.209 (1.00) | 0.412 (1.00) | 0.568 (1.00) | 0.268 (1.00) |  |
del 19q13 42 | 15 (9%) | 148 | 0.179 (1.00) | 0.792 (1.00) | 0.0167 (1.00) | 0.0135 (1.00) | 0.651 (1.00) | 0.512 (1.00) | 0.386 (1.00) | 0.754 (1.00) |  |
del 21q22 3 | 31 (19%) | 132 | 0.577 (1.00) | 0.661 (1.00) | 0.0139 (1.00) | 0.00747 (1.00) | 0.872 (1.00) | 0.143 (1.00) | 0.129 (1.00) | 0.711 (1.00) | 0.332 (1.00) |

'amp_7q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000276 (Fisher's exact test), Q value = 0.058

Table S1. Gene #4: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
AMP PEAK 4(7Q22.1) MUTATED | 67 | 4 | 12 | 6
AMP PEAK 4(7Q22.1) WILD-TYPE | 28 | 7 | 25 | 4

Figure S1. Get High-res Image Gene #4: 'amp_7q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_17q25.2' versus 'PATHOLOGY.M.STAGE'

P value = 0.000359 (Fisher's exact test), Q value = 0.075

Table S2. Gene #5: 'amp_17q25.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 62 | 6 | 82
AMP PEAK 5(17Q25.2) MUTATED | 35 | 4 | 70
AMP PEAK 5(17Q25.2) WILD-TYPE | 27 | 2 | 12

Figure S2. Get High-res Image Gene #5: 'amp_17q25.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_1p36.31' versus 'Time to Death'

P value = 0.000879 (logrank test), Q value = 0.18

Table S3. Gene #7: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 1(1P36.31) MUTATED | 35 | 7 | 0.1 - 123.6 (7.7)
DEL PEAK 1(1P36.31) WILD-TYPE | 115 | 10 | 0.0 - 194.8 (16.6)

Figure S3. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

'del_1p36.31' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0045

Table S4. Gene #7: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 1(1P36.31) MUTATED | 9 | 3 | 17 | 4
DEL PEAK 1(1P36.31) WILD-TYPE | 86 | 8 | 20 | 6

Figure S4. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_1p36.31' versus 'PATHOLOGY.T.STAGE'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.0054

Table S5. Gene #7: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 1(1P36.31) MUTATED | 11 | 4 | 20
DEL PEAK 1(1P36.31) WILD-TYPE | 91 | 13 | 24

Figure S5. Get High-res Image Gene #7: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.41e-06 (Fisher's exact test), Q value = 0.0014

Table S6. Gene #9: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 3(3P22.1) MUTATED | 1 | 1 | 10 | 3
DEL PEAK 3(3P22.1) WILD-TYPE | 94 | 10 | 27 | 7

Figure S6. Get High-res Image Gene #9: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_3p22.1' versus 'PATHOLOGY.T.STAGE'

P value = 5.12e-05 (Fisher's exact test), Q value = 0.011

Table S7. Gene #9: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 3(3P22.1) MUTATED | 2 | 2 | 11
DEL PEAK 3(3P22.1) WILD-TYPE | 100 | 15 | 33

Figure S7. Get High-res Image Gene #9: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00108 (Fisher's exact test), Q value = 0.22

Table S8. Gene #10: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 4(4Q34.3) MUTATED | 4 | 2 | 10 | 2
DEL PEAK 4(4Q34.3) WILD-TYPE | 91 | 9 | 27 | 8

Figure S8. Get High-res Image Gene #10: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_4q34.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.000411 (Fisher's exact test), Q value = 0.085

Table S9. Gene #10: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 4(4Q34.3) MUTATED | 4 | 3 | 11
DEL PEAK 4(4Q34.3) WILD-TYPE | 98 | 14 | 33

Figure S9. Get High-res Image Gene #10: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5p14.2' versus 'Time to Death'

P value = 6.3e-05 (logrank test), Q value = 0.014

Table S10. Gene #11: 'del_5p14.2' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 5(5P14.2) MUTATED | 9 | 4 | 0.1 - 63.7 (6.6)
DEL PEAK 5(5P14.2) WILD-TYPE | 141 | 13 | 0.0 - 194.8 (14.4)

Figure S10. Get High-res Image Gene #11: 'del_5p14.2' versus Clinical Feature #1: 'Time to Death'

'del_5p14.2' versus 'PATHOLOGY.T.STAGE'

P value = 0.000382 (Fisher's exact test), Q value = 0.08

Table S11. Gene #11: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 5(5P14.2) MUTATED | 1 | 1 | 8
DEL PEAK 5(5P14.2) WILD-TYPE | 101 | 16 | 36

Figure S11. Get High-res Image Gene #11: 'del_5p14.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5q35.2' versus 'PATHOLOGY.T.STAGE'

P value = 0.000382 (Fisher's exact test), Q value = 0.08

Table S12. Gene #13: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 7(5Q35.2) MUTATED | 1 | 1 | 8
DEL PEAK 7(5Q35.2) WILD-TYPE | 101 | 16 | 36

Figure S12. Get High-res Image Gene #13: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_6q21' versus 'PATHOLOGY.T.STAGE'

P value = 0.000811 (Fisher's exact test), Q value = 0.16

Table S13. Gene #14: 'del_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 8(6Q21) MUTATED | 5 | 0 | 11
DEL PEAK 8(6Q21) WILD-TYPE | 97 | 17 | 33

Figure S13. Get High-res Image Gene #14: 'del_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_6q22.31' versus 'PATHOLOGY.T.STAGE'

P value = 0.000217 (Fisher's exact test), Q value = 0.046

Table S14. Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 9(6Q22.31) MUTATED | 5 | 0 | 12
DEL PEAK 9(6Q22.31) WILD-TYPE | 97 | 17 | 32

Figure S14. Get High-res Image Gene #15: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p21.3' versus 'Time to Death'

P value = 5.18e-05 (logrank test), Q value = 0.011

Table S15. Gene #16: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 10(9P21.3) MUTATED | 22 | 7 | 0.1 - 93.3 (10.5)
DEL PEAK 10(9P21.3) WILD-TYPE | 128 | 10 | 0.0 - 194.8 (14.9)

Figure S15. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.19e-07 (Fisher's exact test), Q value = 7.3e-05

Table S16. Gene #16: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 10(9P21.3) MUTATED | 4 | 0 | 12 | 6
DEL PEAK 10(9P21.3) WILD-TYPE | 91 | 11 | 25 | 4

Figure S16. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_9p21.3' versus 'PATHOLOGY.T.STAGE'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.00046

Table S17. Gene #16: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 10(9P21.3) MUTATED | 5 | 2 | 17
DEL PEAK 10(9P21.3) WILD-TYPE | 97 | 15 | 27

Figure S17. Get High-res Image Gene #16: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q22.3' versus 'Time to Death'

P value = 0.000127 (logrank test), Q value = 0.028

Table S18. Gene #18: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 12(11Q22.3) MUTATED | 16 | 5 | 0.1 - 123.6 (8.3)
DEL PEAK 12(11Q22.3) WILD-TYPE | 134 | 12 | 0.0 - 194.8 (14.6)

Figure S18. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

'del_11q22.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000152 (Fisher's exact test), Q value = 0.033

Table S19. Gene #18: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 12(11Q22.3) MUTATED | 3 | 2 | 8 | 4
DEL PEAK 12(11Q22.3) WILD-TYPE | 92 | 9 | 29 | 6

Figure S19. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_11q22.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.000633 (Fisher's exact test), Q value = 0.13

Table S20. Gene #18: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 12(11Q22.3) MUTATED | 4 | 2 | 11
DEL PEAK 12(11Q22.3) WILD-TYPE | 98 | 15 | 33

Figure S20. Get High-res Image Gene #18: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q24.2' versus 'Time to Death'

P value = 3.61e-05 (logrank test), Q value = 0.0081

Table S21. Gene #19: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 13(11Q24.2) MUTATED | 16 | 6 | 0.1 - 123.6 (9.9)
DEL PEAK 13(11Q24.2) WILD-TYPE | 134 | 11 | 0.0 - 194.8 (14.5)

Figure S21. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #1: 'Time to Death'

'del_11q24.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000152 (Fisher's exact test), Q value = 0.033

Table S22. Gene #19: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 13(11Q24.2) MUTATED | 3 | 2 | 8 | 4
DEL PEAK 13(11Q24.2) WILD-TYPE | 92 | 9 | 29 | 6

Figure S22. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_11q24.2' versus 'PATHOLOGY.T.STAGE'

P value = 0.000633 (Fisher's exact test), Q value = 0.13

Table S23. Gene #19: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 13(11Q24.2) MUTATED | 4 | 2 | 11
DEL PEAK 13(11Q24.2) WILD-TYPE | 98 | 15 | 33

Figure S23. Get High-res Image Gene #19: 'del_11q24.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_15q15.2' versus 'Time to Death'

P value = 2.86e-07 (logrank test), Q value = 6.6e-05

Table S24. Gene #22: 'del_15q15.2' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 16(15Q15.2) MUTATED | 20 | 7 | 0.1 - 194.8 (8.2)
DEL PEAK 16(15Q15.2) WILD-TYPE | 130 | 10 | 0.0 - 129.9 (14.6)

Figure S24. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #1: 'Time to Death'

'del_15q15.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000171 (Fisher's exact test), Q value = 0.037

Table S25. Gene #22: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 16(15Q15.2) MUTATED | 5 | 1 | 9 | 5
DEL PEAK 16(15Q15.2) WILD-TYPE | 90 | 10 | 28 | 5

Figure S25. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_15q15.2' versus 'PATHOLOGY.T.STAGE'

P value = 0.000141 (Fisher's exact test), Q value = 0.031

Table S26. Gene #22: 'del_15q15.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 16(15Q15.2) MUTATED | 6 | 1 | 14
DEL PEAK 16(15Q15.2) WILD-TYPE | 96 | 16 | 30

Figure S26. Get High-res Image Gene #22: 'del_15q15.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_16q24.1' versus 'Time to Death'

P value = 1.82e-06 (logrank test), Q value = 0.00042

Table S27. Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 17(16Q24.1) MUTATED | 6 | 3 | 0.7 - 21.6 (9.5)
DEL PEAK 17(16Q24.1) WILD-TYPE | 144 | 14 | 0.0 - 194.8 (14.5)

Figure S27. Get High-res Image Gene #23: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

'del_xp11.22' versus 'Time to Death'

P value = 0.000314 (logrank test), Q value = 0.066

Table S28. Gene #27: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 21(XP11.22) MUTATED | 17 | 5 | 0.1 - 79.9 (10.1)
DEL PEAK 21(XP11.22) WILD-TYPE | 133 | 12 | 0.0 - 194.8 (14.4)

Figure S28. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #1: 'Time to Death'

'del_xp11.22' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000432 (Fisher's exact test), Q value = 0.089

Table S29. Gene #27: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
DEL PEAK 21(XP11.22) MUTATED | 3 | 1 | 10 | 2
DEL PEAK 21(XP11.22) WILD-TYPE | 92 | 10 | 27 | 8

Figure S29. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_xp11.22' versus 'PATHOLOGY.T.STAGE'

P value = 0.000217 (Fisher's exact test), Q value = 0.046

Table S30. Gene #27: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
DEL PEAK 21(XP11.22) MUTATED | 4 | 2 | 12
DEL PEAK 21(XP11.22) WILD-TYPE | 98 | 15 | 32

Figure S30. Get High-res Image Gene #27: 'del_xp11.22' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xq28' versus 'Time to Death'

P value = 5.1e-06 (logrank test), Q value = 0.0012

Table S31. Gene #28: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
DEL PEAK 22(XQ28) MUTATED | 16 | 5 | 0.1 - 25.1 (9.9)
DEL PEAK 22(XQ28) WILD-TYPE | 134 | 12 | 0.0 - 194.8 (14.5)

Figure S31. Get High-res Image Gene #28: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

- Clinical data file = KIRP-TP.merged_data.txt

- Number of patients = 163

- Number of significantly focal cnvs = 28

- Number of selected clinical features = 10

- Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

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

Student's t-test analysis

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

Fisher's exact test

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

Q value calculation

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.

Download Results

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle