Thyroid Adenocarcinoma: Correlation between copy number variation genes (focal) and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 25 arm-level results and 15 clinical features across 309 patients, 15 significant findings detected with Q value < 0.25.

  • Amp Peak 1(Xq22.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 2(2p23.1) cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 3(2q35) cnv correlated to 'HISTOLOGICAL.TYPE',  'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 10(8q24.22) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 11(9q21.13) cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 14(11p15.1) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 15(13q12.3) cnv correlated to 'RADIATIONEXPOSURE'.

  • Del Peak 17(15q25.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 26(21q21.1) cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 31(Xq22.1) cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 32(Xq22.3) cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 25 arm-level results and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RADIATIONEXPOSURE DISTANT
METASTASIS 		EXTRATHYROIDAL
EXTENSION 		LYMPH
NODE
METASTASIS 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE 		MULTIFOCALITY TUMOR
SIZE
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 Fisher's exact test Chi-square test Fisher's exact test t-test t-test Chi-square test Fisher's exact test t-test
Del Peak 3(2q35) 8 (3%) 301 1
(1.00) 		0.0119
(1.00) 		0.685
(1.00) 		0.0004
(0.134) 		1
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.733
(1.00) 		0.174
(1.00) 		0.172
(1.00) 		1.93e-15
(6.67e-13) 		6.91e-05
(0.0234) 		1
(1.00) 		0.134
(1.00)
Del Peak 2(2p23 1) 9 (3%) 300 1
(1.00) 		0.151
(1.00) 		0.461
(1.00) 		0.0193
(1.00) 		1
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.27
(1.00) 		0.144
(1.00) 		0.581
(1.00) 		1.89e-15
(6.57e-13) 		0.000558
(0.186) 		1
(1.00) 		0.869
(1.00)
Del Peak 32(Xq22 3) 4 (1%) 305 1
(1.00) 		0.0625
(1.00) 		0.0474
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.138
(1.00) 		0.168
(1.00) 		0.609
(1.00) 		0.374
(1.00) 		0.288
(1.00) 		2e-15
(6.88e-13) 		8.3e-07
(0.000282) 		1
(1.00) 		0.385
(1.00)
Amp Peak 1(Xq22 3) 7 (2%) 302 1
(1.00) 		0.098
(1.00) 		0.2
(1.00) 		0.133
(1.00) 		1
(1.00) 		1
(1.00) 		0.2
(1.00) 		1
(1.00) 		0.342
(1.00) 		0.477
(1.00) 		1.96e-15
(6.77e-13) 		0.462
(1.00) 		1
(1.00) 		0.323
(1.00)
Del Peak 10(8q24 22) 5 (2%) 304 1
(1.00) 		0.0552
(1.00) 		0.0976
(1.00) 		0.0281
(1.00) 		1
(1.00) 		1
(1.00) 		0.696
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.355
(1.00) 		2.04e-15
(6.94e-13) 		0.0034
(1.00) 		1
(1.00) 		0.158
(1.00)
Del Peak 11(9q21 13) 9 (3%) 300 1
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.345
(1.00) 		0.329
(1.00) 		0.268
(1.00) 		0.27
(1.00) 		0.274
(1.00) 		0.581
(1.00) 		0.845
(1.00) 		0.000112
(0.0378) 		1
(1.00) 		0.327
(1.00)
Del Peak 14(11p15 1) 4 (1%) 305 0.00468
(1.00) 		0.0308
(1.00) 		0.254
(1.00) 		0.141
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.609
(1.00) 		0.374
(1.00) 		0.288
(1.00) 		2e-15
(6.88e-13) 		0.492
(1.00) 		0.622
(1.00) 		0.203
(1.00)
Del Peak 15(13q12 3) 10 (3%) 299 0.00468
(1.00) 		0.0126
(1.00) 		0.0702
(1.00) 		0.106
(1.00) 		0.375
(1.00) 		0.000357
(0.12) 		0.217
(1.00) 		0.562
(1.00) 		0.29
(1.00) 		0.464
(1.00) 		0.0381
(1.00) 		0.099
(1.00) 		0.75
(1.00) 		0.105
(1.00)
Del Peak 17(15q25 3) 4 (1%) 305 1
(1.00) 		0.24
(1.00) 		0.575
(1.00) 		0.141
(1.00) 		1
(1.00) 		1
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.374
(1.00) 		0.478
(1.00) 		2e-15
(6.88e-13) 		0.0394
(1.00) 		0.622
(1.00) 		0.527
(1.00)
Del Peak 26(21q21 1) 7 (2%) 302 1
(1.00) 		0.00405
(1.00) 		0.682
(1.00) 		0.439
(1.00) 		1
(1.00) 		1
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.341
(1.00) 		0.188
(1.00) 		0.979
(1.00) 		0.000223
(0.075) 		1
(1.00) 		0.595
(1.00)
Del Peak 31(Xq22 1) 6 (2%) 303 1
(1.00) 		0.174
(1.00) 		0.034
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.219
(1.00) 		0.275
(1.00) 		0.418
(1.00) 		0.465
(1.00) 		0.23
(1.00) 		0.676
(1.00) 		0.000428
(0.143) 		0.684
(1.00) 		0.803
(1.00)
Del Peak 6(6q22 31) 4 (1%) 305 0.00468
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.609
(1.00) 		0.773
(1.00) 		1
(1.00) 		0.00876
(1.00) 		0.0665
(1.00) 		0.622
(1.00) 		0.0277
(1.00)
Del Peak 8(7q34) 4 (1%) 305 1
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.244
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.773
(1.00) 		1
(1.00) 		0.401
(1.00) 		0.685
(1.00) 		0.622
(1.00) 		0.256
(1.00)
Del Peak 12(10q21 2) 7 (2%) 302 1
(1.00) 		0.551
(1.00) 		0.682
(1.00) 		0.0648
(1.00) 		0.28
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.588
(1.00) 		0.682
(1.00) 		0.319
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.0189
(1.00)
Del Peak 13(10q23 31) 8 (3%) 301 1
(1.00) 		0.0192
(1.00) 		0.412
(1.00) 		0.0233
(1.00) 		1
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.733
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.0686
(1.00) 		0.0078
(1.00) 		1
(1.00) 		0.03
(1.00)
Del Peak 16(13q14 3) 13 (4%) 296 0.00468
(1.00) 		0.171
(1.00) 		0.32
(1.00) 		0.164
(1.00) 		0.112
(1.00) 		0.000886
(0.294) 		0.33
(1.00) 		0.459
(1.00) 		0.157
(1.00) 		0.845
(1.00) 		0.0445
(1.00) 		0.484
(1.00) 		0.378
(1.00) 		0.274
(1.00)
Del Peak 19(16q23 3) 3 (1%) 306 1
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.0215
(1.00) 		1
(1.00) 		0.138
(1.00) 		1
(1.00) 		0.198
(1.00) 		0.709
(1.00) 		0.219
(1.00) 		0.0653
(1.00) 		0.143
(1.00) 		1
(1.00)
Del Peak 20(17p13 1) 5 (2%) 304 1
(1.00) 		0.928
(1.00) 		0.339
(1.00) 		0.363
(1.00) 		0.0177
(1.00) 		1
(1.00) 		0.412
(1.00) 		0.11
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.188
(1.00) 		0.371
(1.00) 		0.277
(1.00)
Del Peak 21(18p11 21) 3 (1%) 306 1
(1.00) 		0.971
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.0653
(1.00) 		0.0384
(1.00) 		1
(1.00) 		0.655
(1.00)
Del Peak 22(18q22 2) 3 (1%) 306 1
(1.00) 		0.971
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.0653
(1.00) 		0.0384
(1.00) 		1
(1.00) 		0.655
(1.00)
Del Peak 23(19p13 2) 3 (1%) 306 1
(1.00) 		0.109
(1.00) 		0.573
(1.00) 		0.0425
(1.00) 		1
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.592
(1.00) 		0.0257
(1.00) 		0.219
(1.00) 		0.691
(1.00) 		0.247
(1.00)
Del Peak 27(22q13 1) 55 (18%) 254 0.724
(1.00) 		0.647
(1.00) 		0.73
(1.00) 		0.0651
(1.00) 		0.478
(1.00) 		0.473
(1.00) 		0.826
(1.00) 		0.386
(1.00) 		0.575
(1.00) 		0.467
(1.00) 		0.566
(1.00) 		0.845
(1.00) 		0.226
(1.00) 		0.321
(1.00)
Del Peak 28(22q13 2) 55 (18%) 254 0.724
(1.00) 		0.647
(1.00) 		0.73
(1.00) 		0.0651
(1.00) 		0.478
(1.00) 		0.473
(1.00) 		0.826
(1.00) 		0.386
(1.00) 		0.575
(1.00) 		0.467
(1.00) 		0.566
(1.00) 		0.845
(1.00) 		0.226
(1.00) 		0.321
(1.00)
Del Peak 29(22q13 31) 55 (18%) 254 0.724
(1.00) 		0.647
(1.00) 		0.73
(1.00) 		0.0651
(1.00) 		0.478
(1.00) 		0.473
(1.00) 		0.826
(1.00) 		0.386
(1.00) 		0.575
(1.00) 		0.467
(1.00) 		0.566
(1.00) 		0.845
(1.00) 		0.226
(1.00) 		0.321
(1.00)
Del Peak 30(22q13 32) 56 (18%) 253 0.724
(1.00) 		0.692
(1.00) 		0.61
(1.00) 		0.0377
(1.00) 		0.478
(1.00) 		0.473
(1.00) 		0.838
(1.00) 		0.386
(1.00) 		0.517
(1.00) 		0.467
(1.00) 		0.5
(1.00) 		0.854
(1.00) 		0.176
(1.00) 		0.321
(1.00)
'Amp Peak 1(Xq22.3) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.96e-15 (t-test), Q value = 6.8e-13

Table S1.  Gene #1: 'Amp Peak 1(Xq22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 248 2.7 (5.1)
AMP PEAK 1(XQ22.3) MUTATED 5 0.0 (0.0)
AMP PEAK 1(XQ22.3) WILD-TYPE 243 2.8 (5.1)

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(Xq22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 2(2p23.1) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.89e-15 (t-test), Q value = 6.6e-13

Table S2.  Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 248 2.7 (5.1)
DEL PEAK 2(2P23.1) MUTATED 7 0.0 (0.0)
DEL PEAK 2(2P23.1) WILD-TYPE 241 2.8 (5.1)

Figure S2.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 2(2p23.1) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000558 (Chi-square test), Q value = 0.19

Table S3.  Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
ALL 177 33 67 28 3
DEL PEAK 2(2P23.1) MUTATED 3 5 1 0 0
DEL PEAK 2(2P23.1) WILD-TYPE 174 28 66 28 3

Figure S3.  Get High-res Image Gene #2: 'Del Peak 2(2p23.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 3(2q35) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4e-04 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients OTHER THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL 20 183 75 31
DEL PEAK 3(2Q35) MUTATED 4 1 3 0
DEL PEAK 3(2Q35) WILD-TYPE 16 182 72 31

Figure S4.  Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 3(2q35) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.93e-15 (t-test), Q value = 6.7e-13

Table S5.  Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 248 2.7 (5.1)
DEL PEAK 3(2Q35) MUTATED 6 0.0 (0.0)
DEL PEAK 3(2Q35) WILD-TYPE 242 2.8 (5.1)

Figure S5.  Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 3(2q35) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.91e-05 (Chi-square test), Q value = 0.023

Table S6.  Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
ALL 177 33 67 28 3
DEL PEAK 3(2Q35) MUTATED 1 5 2 0 0
DEL PEAK 3(2Q35) WILD-TYPE 176 28 65 28 3

Figure S6.  Get High-res Image Gene #3: 'Del Peak 3(2q35) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 10(8q24.22) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.04e-15 (t-test), Q value = 6.9e-13

Table S7.  Gene #6: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 248 2.7 (5.1)
DEL PEAK 10(8Q24.22) MUTATED 3 0.0 (0.0)
DEL PEAK 10(8Q24.22) WILD-TYPE 245 2.8 (5.1)

Figure S7.  Get High-res Image Gene #6: 'Del Peak 10(8q24.22) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 11(9q21.13) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000112 (Chi-square test), Q value = 0.038

Table S8.  Gene #7: 'Del Peak 11(9q21.13) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
ALL 177 33 67 28 3
DEL PEAK 11(9Q21.13) MUTATED 2 5 0 2 0
DEL PEAK 11(9Q21.13) WILD-TYPE 175 28 67 26 3

Figure S8.  Get High-res Image Gene #7: 'Del Peak 11(9q21.13) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 14(11p15.1) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 6.9e-13

Table S9.  Gene #10: 'Del Peak 14(11p15.1) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 248 2.7 (5.1)
DEL PEAK 14(11P15.1) MUTATED 4 0.0 (0.0)
DEL PEAK 14(11P15.1) WILD-TYPE 244 2.8 (5.1)

Figure S9.  Get High-res Image Gene #10: 'Del Peak 14(11p15.1) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 15(13q12.3) mutation analysis' versus 'RADIATIONEXPOSURE'

P value = 0.000357 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #11: 'Del Peak 15(13q12.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

nPatients NO YES
ALL 258 13
DEL PEAK 15(13Q12.3) MUTATED 5 4
DEL PEAK 15(13Q12.3) WILD-TYPE 253 9

Figure S10.  Get High-res Image Gene #11: 'Del Peak 15(13q12.3) mutation analysis' versus Clinical Feature #6: 'RADIATIONEXPOSURE'

'Del Peak 17(15q25.3) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 6.9e-13

Table S11.  Gene #13: 'Del Peak 17(15q25.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 248 2.7 (5.1)
DEL PEAK 17(15Q25.3) MUTATED 4 0.0 (0.0)
DEL PEAK 17(15Q25.3) WILD-TYPE 244 2.8 (5.1)

Figure S11.  Get High-res Image Gene #13: 'Del Peak 17(15q25.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 26(21q21.1) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000223 (Chi-square test), Q value = 0.075

Table S12.  Gene #19: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
ALL 177 33 67 28 3
DEL PEAK 26(21Q21.1) MUTATED 0 4 1 2 0
DEL PEAK 26(21Q21.1) WILD-TYPE 177 29 66 26 3

Figure S12.  Get High-res Image Gene #19: 'Del Peak 26(21q21.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 31(Xq22.1) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000428 (Chi-square test), Q value = 0.14

Table S13.  Gene #24: 'Del Peak 31(Xq22.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
ALL 177 33 67 28 3
DEL PEAK 31(XQ22.1) MUTATED 1 4 1 0 0
DEL PEAK 31(XQ22.1) WILD-TYPE 176 29 66 28 3

Figure S13.  Get High-res Image Gene #24: 'Del Peak 31(Xq22.1) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'Del Peak 32(Xq22.3) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-15 (t-test), Q value = 6.9e-13

Table S14.  Gene #25: 'Del Peak 32(Xq22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 248 2.7 (5.1)
DEL PEAK 32(XQ22.3) MUTATED 4 0.0 (0.0)
DEL PEAK 32(XQ22.3) WILD-TYPE 244 2.8 (5.1)

Figure S14.  Get High-res Image Gene #25: 'Del Peak 32(Xq22.3) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 32(Xq22.3) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.3e-07 (Chi-square test), Q value = 0.00028

Table S15.  Gene #25: 'Del Peak 32(Xq22.3) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVC
ALL 177 33 67 28 3
DEL PEAK 32(XQ22.3) MUTATED 0 4 0 0 0
DEL PEAK 32(XQ22.3) WILD-TYPE 177 29 67 28 3

Figure S15.  Get High-res Image Gene #25: 'Del Peak 32(Xq22.3) mutation analysis' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

  • Clinical data file = THCA-TP.clin.merged.picked.txt

  • Number of patients = 309

  • Number of significantly arm-level cnvs = 25

  • Number of selected clinical features = 15

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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)
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