Correlation between copy number variation genes (focal events) and selected clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1BV7FRP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1BV7FRP
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 63 focal events and 39 clinical features across 295 patients, 9 significant findings detected with Q value < 0.25.

  • amp_11q22.1 cnv correlated to 'YEARS_TO_BIRTH' and 'AGE_AT_DIAGNOSIS'.

  • del_3p14.2 cnv correlated to 'HISTOLOGICAL_TYPE' and 'TOBACCO_SMOKING_HISTORY'.

  • del_6q26 cnv correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

  • del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_16q11.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_16q23.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_18q21.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 63 focal events and 39 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY WEIGHT
KG
AT
DIAGNOSIS 		TUMOR
STATUS 		NEOPLASM
HISTOLOGIC
GRADE 		TOBACCO
SMOKING
YEAR
STOPPED 		TOBACCO
SMOKING
PACK
YEARS
SMOKED 		TOBACCO
SMOKING
HISTORY 		AGEBEGANSMOKINGINYEARS RADIATION
THERAPY
STATUS 		PREGNANCIES
COUNT
TOTAL 		PREGNANCIES
COUNT
STILLBIRTH 		PREGNANCY
SPONTANEOUS
ABORTION
COUNT 		PREGNANCIES
COUNT
LIVE
BIRTH 		PREGNANCY
THERAPEUTIC
ABORTION
COUNT 		PREGNANCIES
COUNT
ECTOPIC 		POS
LYMPH
NODE
LOCATION 		MENOPAUSE
STATUS 		LYMPHOVASCULAR
INVOLVEMENT 		LYMPH
NODES
EXAMINED
HE
COUNT 		LYMPH
NODES
EXAMINED 		KERATINIZATION
SQUAMOUS
CELL 		INITIAL
PATHOLOGIC
DX
YEAR 		HISTORY
HORMONAL
CONTRACEPTIVES
USE 		HEIGHT
CM
AT
DIAGNOSIS 		CORPUS
INVOLVEMENT 		CHEMO
CONCURRENT
TYPE 		CERVIX
SUV
RESULTS 		AGE
AT
DIAGNOSIS 		CLINICAL
STAGE
nCNV (%) 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 Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test
amp 11q22 1 47 (16%) 248 0.824
(1.00) 		0.000111
(0.0456) 		0.386
(0.921) 		1
(1.00) 		1
(1.00) 		0.637
(0.97) 		0.686
(0.981) 		0.0211
(0.452) 		0.965
(1.00) 		0.0234
(0.471) 		0.38
(0.921) 		0.285
(0.869) 		1
(1.00) 		0.0251
(0.486) 		0.279
(0.866) 		0.0211
(0.452) 		0.64
(0.971) 		0.69
(0.981) 		1
(1.00) 		0.947
(1.00) 		0.23
(0.84) 		0.512
(0.953) 		0.994
(1.00) 		0.436
(0.943) 		0.351
(0.906) 		0.924
(1.00) 		0.00215
(0.352) 		0.519
(0.953) 		0.965
(1.00) 		0.434
(0.94) 		0.274
(0.866) 		0.00252
(0.378) 		0.717
(0.988) 		0.172
(0.774) 		0.191
(0.792) 		0.308
(0.885) 		0.147
(0.749) 		9.19e-05
(0.0451) 		0.599
(0.969)
del 3p14 2 134 (45%) 161 0.668
(0.981) 		0.993
(1.00) 		0.0291
(0.504) 		0.00575
(0.416) 		0.752
(0.996) 		0.0719
(0.661) 		8e-05
(0.0451) 		0.61
(0.969) 		0.00323
(0.378) 		0.872
(1.00) 		0.262
(0.857) 		0.0114
(0.444) 		0.127
(0.712) 		0.127
(0.712) 		0.0982
(0.692) 		0.61
(0.969) 		0.00053
(0.186) 		0.639
(0.971) 		1
(1.00) 		0.8
(1.00) 		0.15
(0.749) 		0.488
(0.953) 		0.851
(1.00) 		0.812
(1.00) 		0.151
(0.749) 		0.103
(0.694) 		0.963
(1.00) 		0.00574
(0.416) 		0.00323
(0.378) 		0.349
(0.906) 		0.394
(0.921) 		0.0166
(0.452) 		0.047
(0.557) 		0.666
(0.981) 		0.596
(0.969) 		0.681
(0.981) 		0.063
(0.637) 		0.987
(1.00) 		0.0365
(0.53)
del 6q26 100 (34%) 195 0.106
(0.694) 		0.65
(0.976) 		0.789
(1) 		0.604
(0.969) 		1
(1.00) 		1
(1.00) 		0.303
(0.881) 		0.407
(0.921) 		0.384
(0.921) 		0.245
(0.857) 		0.342
(0.902) 		0.514
(0.953) 		0.555
(0.964) 		0.0782
(0.663) 		0.125
(0.712) 		0.407
(0.921) 		0.692
(0.982) 		0.969
(1.00) 		0.536
(0.957) 		0.625
(0.969) 		0.417
(0.93) 		0.15
(0.749) 		0.532
(0.954) 		0.475
(0.949) 		0.967
(1.00) 		0.861
(1.00) 		0.282
(0.866) 		0.598
(0.969) 		0.384
(0.921) 		0.24
(0.856) 		0.855
(1.00) 		0.000747
(0.229) 		0.689
(0.981) 		0.0327
(0.524) 		0.596
(0.969) 		0.476
(0.949) 		0.089
(0.683) 		0.591
(0.969) 		0.367
(0.916)
del 10q23 31 86 (29%) 209 0.379
(0.921) 		0.000904
(0.247) 		0.355
(0.907) 		0.271
(0.862) 		0.706
(0.985) 		0.291
(0.871) 		0.981
(1.00) 		0.949
(1.00) 		0.0998
(0.692) 		0.0167
(0.452) 		1
(1.00) 		0.369
(0.917) 		0.129
(0.712) 		0.00889
(0.444) 		0.266
(0.857) 		0.949
(1.00) 		0.102
(0.692) 		0.127
(0.712) 		1
(1.00) 		0.0817
(0.667) 		0.842
(1.00) 		0.701
(0.985) 		0.0103
(0.444) 		0.815
(1.00) 		0.698
(0.984) 		0.0206
(0.452) 		0.0197
(0.452) 		0.198
(0.796) 		0.0998
(0.692) 		0.242
(0.857) 		0.0909
(0.687) 		0.016
(0.452) 		0.524
(0.953) 		0.241
(0.857) 		0.767
(0.998) 		1
(1.00) 		0.526
(0.953) 		0.00121
(0.284) 		0.4
(0.921)
del 16q11 2 53 (18%) 242 0.823
(1.00) 		0.406
(0.921) 		0.842
(1.00) 		0.0156
(0.452) 		1
(1.00) 		0.155
(0.749) 		2e-05
(0.0246) 		0.265
(0.857) 		0.0762
(0.663) 		0.402
(0.921) 		0.771
(0.998) 		0.894
(1.00) 		1
(1.00) 		0.493
(0.953) 		0.491
(0.953) 		0.265
(0.857) 		0.313
(0.89) 		0.22
(0.828) 		1
(1.00) 		0.305
(0.881) 		0.888
(1.00) 		0.518
(0.953) 		0.591
(0.969) 		0.962
(1.00) 		0.0865
(0.673) 		0.82
(1.00) 		0.117
(0.707) 		0.402
(0.921) 		0.0762
(0.663) 		0.761
(0.998) 		0.0717
(0.661) 		0.743
(0.994) 		0.796
(1.00) 		0.504
(0.953) 		0.113
(0.705) 		1
(1.00) 		0.342
(0.902) 		0.447
(0.948)
del 16q23 1 55 (19%) 240 0.421
(0.934) 		0.245
(0.857) 		0.927
(1.00) 		0.316
(0.891) 		0.686
(0.981) 		1
(1.00) 		5e-05
(0.0409) 		0.265
(0.857) 		0.39
(0.921) 		0.00795
(0.444) 		0.378
(0.921) 		0.5
(0.953) 		0.49
(0.953) 		0.224
(0.84) 		0.616
(0.969) 		0.265
(0.857) 		0.513
(0.953) 		0.983
(1.00) 		0.551
(0.962) 		0.105
(0.694) 		0.888
(1.00) 		0.46
(0.949) 		0.439
(0.943) 		0.0277
(0.503) 		0.318
(0.891) 		1
(1.00) 		0.762
(0.998) 		0.667
(0.981) 		0.39
(0.921) 		0.939
(1.00) 		0.14
(0.735) 		0.428
(0.934) 		0.913
(1.00) 		0.383
(0.921) 		0.519
(0.953) 		1
(1.00) 		0.206
(0.811) 		0.979
(1.00)
del 18q21 2 82 (28%) 213 0.681
(0.981) 		0.561
(0.966) 		0.62
(0.969) 		0.355
(0.907) 		0.149
(0.749) 		0.473
(0.949) 		1e-05
(0.0246) 		0.588
(0.969) 		0.0506
(0.561) 		0.908
(1.00) 		0.603
(0.969) 		0.144
(0.747) 		0.288
(0.869) 		0.257
(0.857) 		0.975
(1.00) 		0.588
(0.969) 		0.411
(0.922) 		0.385
(0.921) 		1
(1.00) 		0.0926
(0.687) 		0.126
(0.712) 		0.803
(1.00) 		0.174
(0.774) 		0.854
(1.00) 		0.9
(1.00) 		0.474
(0.949) 		0.664
(0.981) 		0.0494
(0.558) 		0.0506
(0.561) 		0.872
(1.00) 		0.68
(0.981) 		0.0214
(0.452) 		0.627
(0.969) 		0.428
(0.934) 		0.0386
(0.53) 		0.122
(0.712) 		0.514
(0.953) 		0.0699
(0.653)
amp 1p31 3 96 (33%) 199 0.332
(0.899) 		0.00423
(0.399) 		0.338
(0.9) 		0.86
(1.00) 		0.497
(0.953) 		0.492
(0.953) 		0.244
(0.857) 		0.193
(0.793) 		0.539
(0.959) 		0.473
(0.949) 		0.102
(0.692) 		0.767
(0.998) 		0.768
(0.998) 		0.879
(1.00) 		0.596
(0.969) 		0.193
(0.793) 		0.475
(0.949) 		0.825
(1.00) 		1
(1.00) 		0.0116
(0.444) 		0.386
(0.921) 		0.875
(1.00) 		0.271
(0.862) 		0.149
(0.749) 		0.93
(1.00) 		0.525
(0.953) 		0.0157
(0.452) 		0.861
(1.00) 		0.539
(0.959) 		0.518
(0.953) 		0.375
(0.921) 		0.501
(0.953) 		0.0425
(0.533) 		0.36
(0.913) 		0.777
(0.999) 		0.786
(1) 		0.464
(0.949) 		0.00355
(0.396) 		0.395
(0.921)
amp 1q21 3 158 (54%) 137 0.542
(0.962) 		0.24
(0.857) 		0.0283
(0.504) 		0.635
(0.97) 		0.182
(0.781) 		0.745
(0.994) 		0.241
(0.857) 		0.722
(0.989) 		0.6
(0.969) 		0.00539
(0.416) 		0.506
(0.953) 		0.172
(0.774) 		0.168
(0.767) 		0.374
(0.921) 		0.723
(0.989) 		0.722
(0.989) 		0.86
(1.00) 		0.597
(0.969) 		0.56
(0.966) 		0.14
(0.735) 		0.482
(0.949) 		0.537
(0.958) 		0.219
(0.828) 		0.962
(1.00) 		0.00536
(0.416) 		0.685
(0.981) 		0.336
(0.899) 		0.62
(0.969) 		0.6
(0.969) 		0.914
(1.00) 		1
(1.00) 		0.733
(0.994) 		0.277
(0.866) 		0.0438
(0.537) 		0.612
(0.969) 		0.344
(0.902) 		0.291
(0.871) 		0.198
(0.796) 		0.334
(0.899)
amp 1q44 152 (52%) 143 0.342
(0.902) 		0.333
(0.899) 		0.0547
(0.582) 		0.522
(0.953) 		0.182
(0.781) 		1
(1.00) 		0.0788
(0.663) 		0.34
(0.902) 		0.31
(0.89) 		0.0245
(0.485) 		0.269
(0.862) 		0.332
(0.899) 		0.408
(0.922) 		0.209
(0.814) 		0.815
(1.00) 		0.34
(0.902) 		0.613
(0.969) 		0.757
(0.998) 		1
(1.00) 		0.735
(0.994) 		0.482
(0.949) 		0.546
(0.962) 		0.767
(0.998) 		0.465
(0.949) 		0.3
(0.881) 		0.882
(1.00) 		0.168
(0.767) 		0.0683
(0.645) 		0.31
(0.89) 		0.837
(1.00) 		0.496
(0.953) 		0.715
(0.987) 		0.363
(0.916) 		0.13
(0.712) 		1
(1.00) 		0.129
(0.712) 		0.807
(1.00) 		0.278
(0.866) 		0.739
(0.994)
amp 2p24 3 79 (27%) 216 0.772
(0.998) 		0.929
(1.00) 		0.616
(0.969) 		0.715
(0.987) 		0.48
(0.949) 		0.363
(0.916) 		0.544
(0.962) 		0.168
(0.767) 		0.476
(0.949) 		0.504
(0.953) 		1
(1.00) 		0.468
(0.949) 		0.536
(0.957) 		0.447
(0.948) 		0.138
(0.729) 		0.168
(0.767) 		0.804
(1.00) 		0.68
(0.981) 		1
(1.00) 		0.412
(0.922) 		0.178
(0.778) 		0.265
(0.857) 		0.409
(0.922) 		0.759
(0.998) 		0.0727
(0.663) 		0.906
(1.00) 		1
(1.00) 		0.706
(0.985) 		0.476
(0.949) 		0.609
(0.969) 		0.844
(1.00) 		0.822
(1.00) 		0.577
(0.969) 		0.665
(0.981) 		0.391
(0.921) 		0.5
(0.953) 		0.014
(0.452) 		0.897
(1.00) 		0.398
(0.921)
amp 2q33 1 41 (14%) 254 0.933
(1.00) 		0.29
(0.871) 		0.873
(1.00) 		0.0793
(0.663) 		1
(1.00) 		0.637
(0.97) 		0.554
(0.963) 		0.788
(1) 		0.0373
(0.53) 		0.311
(0.89) 		0.743
(0.994) 		0.0496
(0.558) 		0.847
(1.00) 		0.834
(1.00) 		0.447
(0.948) 		0.788
(1) 		0.627
(0.969) 		0.0667
(0.645) 		0.459
(0.949) 		0.633
(0.97) 		0.333
(0.899) 		0.684
(0.981) 		0.592
(0.969) 		0.559
(0.966) 		0.0206
(0.452) 		1
(1.00) 		0.594
(0.969) 		0.0478
(0.557) 		0.0373
(0.53) 		0.486
(0.953) 		0.605
(0.969) 		0.128
(0.712) 		0.213
(0.822) 		0.577
(0.969) 		0.411
(0.922) 		0.229
(0.84) 		0.268
(0.861) 		0.723
(0.989)
amp 3q26 31 227 (77%) 68 0.957
(1.00) 		0.779
(1) 		0.258
(0.857) 		0.0407
(0.53) 		1
(1.00) 		0.0751
(0.663) 		0.0101
(0.444) 		0.961
(1.00) 		0.013
(0.449) 		0.0154
(0.452) 		0.447
(0.948) 		0.116
(0.705) 		1
(1.00) 		0.811
(1.00) 		0.74
(0.994) 		0.961
(1.00) 		0.744
(0.994) 		0.0498
(0.558) 		0.382
(0.921) 		0.021
(0.452) 		0.147
(0.749) 		0.834
(1.00) 		0.0936
(0.687) 		0.471
(0.949) 		0.0484
(0.557) 		0.251
(0.857) 		0.619
(0.969) 		0.249
(0.857) 		0.013
(0.449) 		0.572
(0.968) 		0.689
(0.981) 		0.551
(0.962) 		1
(1.00) 		0.249
(0.857) 		1
(1.00) 		0.0399
(0.53) 		0.836
(1.00) 		0.89
(1.00)
amp 3q28 224 (76%) 71 0.708
(0.985) 		0.802
(1.00) 		0.262
(0.857) 		0.0464
(0.554) 		0.258
(0.857) 		0.334
(0.899) 		0.00721
(0.444) 		0.907
(1.00) 		0.0257
(0.49) 		0.239
(0.853) 		1
(1.00) 		0.174
(0.774) 		0.626
(0.969) 		0.763
(0.998) 		0.74
(0.994) 		0.907
(1.00) 		0.738
(0.994) 		0.0988
(0.692) 		0.459
(0.949) 		0.0353
(0.53) 		0.147
(0.749) 		1
(1.00) 		0.238
(0.853) 		0.596
(0.969) 		0.0484
(0.557) 		0.25
(0.857) 		0.509
(0.953) 		0.706
(0.985) 		0.0257
(0.49) 		0.749
(0.994) 		0.689
(0.981) 		0.338
(0.9) 		0.928
(1.00) 		0.167
(0.767) 		1
(1.00) 		0.0783
(0.663) 		0.745
(0.994) 		0.977
(1.00)
amp 4q12 21 (7%) 274 0.287
(0.869) 		0.553
(0.963) 		0.0425
(0.533) 		0.364
(0.916) 		0.519
(0.953) 		1
(1.00) 		0.412
(0.922) 		0.987
(1.00) 		0.827
(1.00) 		0.433
(0.94) 		1
(1.00) 		0.404
(0.921) 		0.782
(1) 		0.0945
(0.691) 		0.0683
(0.645) 		0.987
(1.00) 		0.491
(0.953) 		0.676
(0.981) 		1
(1.00) 		0.39
(0.921) 		0.515
(0.953) 		0.625
(0.969) 		0.282
(0.866) 		0.444
(0.948) 		0.786
(1) 		0.695
(0.983) 		0.676
(0.981) 		0.209
(0.814) 		0.827
(1.00) 		0.846
(1.00) 		0.725
(0.99) 		0.266
(0.857) 		0.0524
(0.567) 		0.77
(0.998) 		0.587
(0.969) 		1
(1.00) 		0.571
(0.968) 		0.572
(0.968) 		0.0743
(0.663)
amp 5p15 33 138 (47%) 157 0.901
(1.00) 		0.618
(0.969) 		0.176
(0.776) 		1
(1.00) 		0.0949
(0.692) 		0.148
(0.749) 		0.00991
(0.444) 		0.549
(0.962) 		0.894
(1.00) 		0.699
(0.984) 		0.267
(0.857) 		0.981
(1.00) 		0.68
(0.981) 		0.0407
(0.53) 		0.971
(1.00) 		0.549
(0.962) 		0.621
(0.969) 		0.446
(0.948) 		0.56
(0.966) 		0.205
(0.808) 		0.583
(0.969) 		0.872
(1.00) 		0.0102
(0.444) 		0.0896
(0.684) 		0.525
(0.953) 		0.369
(0.917) 		0.659
(0.981) 		0.495
(0.953) 		0.894
(1.00) 		0.114
(0.705) 		0.125
(0.712) 		0.394
(0.921) 		0.786
(1) 		0.946
(1.00) 		1
(1.00) 		0.02
(0.452) 		0.665
(0.981) 		0.709
(0.985) 		0.011
(0.444)
amp 6p21 33 82 (28%) 213 0.338
(0.9) 		0.866
(1.00) 		0.91
(1.00) 		0.477
(0.949) 		1
(1.00) 		0.724
(0.989) 		0.367
(0.916) 		0.155
(0.749) 		0.551
(0.962) 		0.788
(1) 		0.802
(1.00) 		0.506
(0.953) 		0.0485
(0.557) 		0.0885
(0.683) 		0.944
(1.00) 		0.155
(0.749) 		0.501
(0.953) 		0.361
(0.914) 		1
(1.00) 		0.327
(0.897) 		0.843
(1.00) 		0.619
(0.969) 		0.354
(0.907) 		1
(1.00) 		0.104
(0.694) 		1
(1.00) 		0.383
(0.921) 		0.568
(0.968) 		0.551
(0.962) 		0.693
(0.982) 		0.846
(1.00) 		0.121
(0.712) 		0.23
(0.84) 		0.48
(0.949) 		0.234
(0.848) 		0.3
(0.881) 		0.562
(0.966) 		0.806
(1.00) 		0.443
(0.948)
amp 7p11 2 52 (18%) 243 0.111
(0.705) 		0.92
(1.00) 		0.0169
(0.452) 		0.17
(0.77) 		0.179
(0.778) 		0.139
(0.732) 		0.403
(0.921) 		0.0375
(0.53) 		0.0787
(0.663) 		0.528
(0.953) 		1
(1.00) 		0.23
(0.84) 		0.012
(0.445) 		0.123
(0.712) 		0.489
(0.953) 		0.0375
(0.53) 		0.397
(0.921) 		0.345
(0.903) 		0.188
(0.79) 		0.354
(0.907) 		0.934
(1.00) 		0.148
(0.749) 		0.391
(0.921) 		0.596
(0.969) 		0.947
(1.00) 		0.126
(0.712) 		0.851
(1.00) 		0.0364
(0.53) 		0.0787
(0.663) 		0.788
(1) 		0.513
(0.953) 		0.193
(0.793) 		1
(1.00) 		0.885
(1.00) 		1
(1.00) 		1
(1.00) 		0.966
(1.00) 		0.0173
(0.452)
amp 8q24 21 127 (43%) 168 0.515
(0.953) 		0.591
(0.969) 		0.0664
(0.645) 		0.42
(0.934) 		0.32
(0.891) 		0.414
(0.926) 		0.231
(0.84) 		0.349
(0.906) 		0.47
(0.949) 		0.822
(1.00) 		1
(1.00) 		0.898
(1.00) 		0.327
(0.897) 		0.194
(0.793) 		0.257
(0.857) 		0.349
(0.906) 		0.715
(0.987) 		0.52
(0.953) 		0.543
(0.962) 		0.65
(0.976) 		0.582
(0.969) 		0.893
(1.00) 		0.721
(0.989) 		0.666
(0.981) 		0.48
(0.949) 		0.301
(0.881) 		0.835
(1.00) 		0.389
(0.921) 		0.47
(0.949) 		0.15
(0.749) 		0.865
(1.00) 		0.595
(0.969) 		0.291
(0.871) 		0.895
(1.00) 		0.194
(0.793) 		0.496
(0.953) 		0.961
(1.00) 		0.593
(0.969) 		0.182
(0.781)
amp 9p24 1 63 (21%) 232 0.237
(0.852) 		0.157
(0.749) 		0.189
(0.79) 		0.00505
(0.416) 		0.684
(0.981) 		0.327
(0.897) 		0.76
(0.998) 		0.0828
(0.667) 		0.0111
(0.444) 		0.0423
(0.533) 		0.771
(0.998) 		0.125
(0.712) 		0.23
(0.84) 		0.35
(0.906) 		0.394
(0.921) 		0.0828
(0.667) 		0.349
(0.906) 		0.548
(0.962) 		1
(1.00) 		0.423
(0.934) 		0.674
(0.981) 		0.112
(0.705) 		0.0545
(0.582) 		0.235
(0.848) 		0.99
(1.00) 		0.365
(0.916) 		0.577
(0.969) 		0.228
(0.84) 		0.0111
(0.444) 		0.185
(0.789) 		0.136
(0.724) 		0.011
(0.444) 		0.16
(0.757) 		0.459
(0.949) 		0.734
(0.994) 		0.267
(0.857) 		0.85
(1.00) 		0.14
(0.735) 		0.249
(0.857)
amp 11p12 23 (8%) 272 0.615
(0.969) 		0.027
(0.502) 		0.26
(0.857) 		0.312
(0.89) 		0.563
(0.966) 		0.399
(0.921) 		0.635
(0.97) 		0.261
(0.857) 		0.0389
(0.53) 		0.299
(0.881) 		0.0459
(0.551) 		0.0754
(0.663) 		0.324
(0.894) 		0.261
(0.857) 		0.261
(0.857) 		0.23
(0.84) 		0.679
(0.981) 		0.459
(0.949) 		0.102
(0.692) 		0.515
(0.953) 		0.426
(0.934) 		0.627
(0.969) 		0.322
(0.892) 		0.197
(0.796) 		0.598
(0.969) 		0.32
(0.891) 		0.0389
(0.53) 		0.971
(1.00) 		0.284
(0.866) 		0.5
(0.953) 		0.188
(0.79) 		0.427
(0.934) 		1
(1.00) 		0.346
(0.903) 		0.659
(0.981) 		0.0248
(0.486) 		0.804
(1.00)
amp 11q13 3 41 (14%) 254 0.988
(1.00) 		0.344
(0.902) 		0.944
(1.00) 		0.452
(0.949) 		0.614
(0.969) 		0.809
(1.00) 		0.619
(0.969) 		0.0373
(0.53) 		0.219
(0.828) 		0.422
(0.934) 		0.319
(0.891) 		0.107
(0.694) 		0.692
(0.982) 		0.0143
(0.452) 		1
(1.00) 		0.0373
(0.53) 		0.423
(0.934) 		0.207
(0.811) 		1
(1.00) 		0.814
(1.00) 		0.333
(0.899) 		0.755
(0.998) 		0.813
(1.00) 		0.663
(0.981) 		0.63
(0.969) 		1
(1.00) 		0.634
(0.97) 		0.453
(0.949) 		0.219
(0.828) 		0.388
(0.921) 		0.466
(0.949) 		0.181
(0.781) 		0.547
(0.962) 		0.87
(1.00) 		0.69
(0.981) 		0.424
(0.934) 		0.0677
(0.645) 		0.324
(0.894) 		0.392
(0.921)
amp 13q22 1 65 (22%) 230 0.387
(0.921) 		0.447
(0.948) 		0.127
(0.712) 		0.696
(0.983) 		0.115
(0.705) 		0.334
(0.899) 		0.706
(0.985) 		0.354
(0.907) 		0.1
(0.692) 		0.726
(0.99) 		0.0302
(0.51) 		0.634
(0.97) 		0.0991
(0.692) 		0.763
(0.998) 		0.913
(1.00) 		0.354
(0.907) 		0.384
(0.921) 		0.0929
(0.687) 		0.53
(0.953) 		0.857
(1.00) 		0.683
(0.981) 		0.514
(0.953) 		0.609
(0.969) 		0.143
(0.745) 		0.927
(1.00) 		0.426
(0.934) 		0.915
(1.00) 		0.0729
(0.663) 		0.1
(0.692) 		0.48
(0.949) 		0.671
(0.981) 		0.455
(0.949) 		0.315
(0.89) 		0.516
(0.953) 		0.516
(0.953) 		0.448
(0.948) 		0.494
(0.953) 		0.104
(0.694)
amp 13q34 69 (23%) 226 0.398
(0.921) 		0.882
(1.00) 		0.973
(1.00) 		1
(1.00) 		1
(1.00) 		0.716
(0.987) 		0.74
(0.994) 		0.94
(1.00) 		0.48
(0.949) 		0.733
(0.994) 		0.297
(0.878) 		0.974
(1.00) 		0.336
(0.899) 		0.217
(0.828) 		0.211
(0.815) 		0.94
(1.00) 		0.0929
(0.687) 		0.629
(0.969) 		0.0452
(0.547) 		0.831
(1.00) 		0.54
(0.96) 		0.46
(0.949) 		0.644
(0.974) 		0.747
(0.994) 		0.0344
(0.529) 		0.606
(0.969) 		0.624
(0.969) 		0.154
(0.749) 		0.48
(0.949) 		0.687
(0.981) 		0.156
(0.749) 		0.473
(0.949) 		1
(1.00) 		0.455
(0.949) 		0.186
(0.79) 		0.201
(0.8) 		0.936
(1.00) 		0.631
(0.969)
amp 15q26 1 76 (26%) 219 0.597
(0.969) 		0.0313
(0.515) 		0.115
(0.705) 		0.463
(0.949) 		0.114
(0.705) 		0.269
(0.862) 		0.132
(0.715) 		0.86
(1.00) 		0.82
(1.00) 		0.222
(0.835) 		0.622
(0.969) 		0.857
(1.00) 		0.637
(0.97) 		0.201
(0.8) 		0.296
(0.877) 		0.86
(1.00) 		0.282
(0.866) 		0.623
(0.969) 		1
(1.00) 		0.0363
(0.53) 		0.801
(1.00) 		0.652
(0.976) 		0.0484
(0.557) 		0.151
(0.749) 		0.372
(0.921) 		0.173
(0.774) 		0.249
(0.857) 		0.701
(0.985) 		0.82
(1.00) 		0.889
(1.00) 		1
(1.00) 		0.721
(0.989) 		0.0692
(0.649) 		0.264
(0.857) 		0.552
(0.962) 		1
(1.00) 		0.193
(0.793) 		0.026
(0.492) 		0.504
(0.953)
amp 16p13 13 65 (22%) 230 0.547
(0.962) 		0.427
(0.934) 		0.118
(0.707) 		0.252
(0.857) 		0.69
(0.981) 		0.692
(0.982) 		0.997
(1.00) 		0.313
(0.89) 		0.0847
(0.667) 		0.293
(0.872) 		0.771
(0.998) 		0.394
(0.921) 		0.234
(0.848) 		0.88
(1.00) 		0.166
(0.767) 		0.313
(0.89) 		0.447
(0.948) 		0.531
(0.953) 		1
(1.00) 		0.0148
(0.452) 		0.683
(0.981) 		0.597
(0.969) 		0.0216
(0.452) 		0.701
(0.985) 		0.0215
(0.452) 		0.65
(0.976) 		0.333
(0.899) 		0.561
(0.966) 		0.0847
(0.667) 		0.517
(0.953) 		1
(1.00) 		0.303
(0.881) 		0.193
(0.793) 		0.508
(0.953) 		0.351
(0.906) 		0.255
(0.857) 		0.469
(0.949) 		0.745
(0.994)
amp 17q12 55 (19%) 240 1
(1.00) 		0.707
(0.985) 		0.244
(0.857) 		0.661
(0.981) 		1
(1.00) 		0.845
(1.00) 		0.11
(0.705) 		0.19
(0.79) 		0.315
(0.89) 		0.853
(1.00) 		0.386
(0.921) 		0.575
(0.969) 		0.49
(0.953) 		0.136
(0.724) 		0.156
(0.749) 		0.19
(0.79) 		0.317
(0.891) 		0.668
(0.981) 		1
(1.00) 		0.0822
(0.667) 		0.261
(0.857) 		0.256
(0.857) 		0.261
(0.857) 		0.269
(0.862) 		0.421
(0.934) 		0.818
(1.00) 		0.98
(1.00) 		0.663
(0.981) 		0.315
(0.89) 		0.736
(0.994) 		0.466
(0.949) 		0.672
(0.981) 		0.91
(1.00) 		0.0814
(0.667) 		1
(1.00) 		1
(1.00) 		0.396
(0.921) 		0.75
(0.994) 		0.847
(1.00)
amp 17q25 1 74 (25%) 221 0.76
(0.998) 		0.819
(1.00) 		0.155
(0.749) 		0.263
(0.857) 		0.258
(0.857) 		1
(1.00) 		0.0847
(0.667) 		0.21
(0.815) 		0.0609
(0.621) 		0.583
(0.969) 		0.325
(0.895) 		0.36
(0.913) 		0.527
(0.953) 		0.0854
(0.67) 		0.828
(1.00) 		0.21
(0.815) 		0.331
(0.899) 		0.256
(0.857) 		1
(1.00) 		0.177
(0.778) 		0.166
(0.767) 		0.844
(1.00) 		0.181
(0.781) 		0.35
(0.906) 		0.429
(0.936) 		1
(1.00) 		0.858
(1.00) 		0.0796
(0.663) 		0.0609
(0.621) 		0.397
(0.921) 		0.105
(0.694) 		0.903
(1.00) 		0.396
(0.921) 		0.482
(0.949) 		0.774
(0.998) 		1
(1.00) 		0.396
(0.921) 		0.877
(1.00) 		0.225
(0.84)
amp 19p13 3 39 (13%) 256 0.125
(0.712) 		0.338
(0.9) 		0.367
(0.916) 		0.36
(0.913) 		0.596
(0.969) 		0.814
(1.00) 		0.901
(1.00) 		0.585
(0.969) 		0.0834
(0.667) 		0.844
(1.00) 		1
(1.00) 		0.506
(0.953) 		0.681
(0.981) 		0.865
(1.00) 		0.586
(0.969) 		0.585
(0.969) 		0.262
(0.857) 		0.0407
(0.53) 		1
(1.00) 		0.32
(0.892) 		0.816
(1.00) 		0.278
(0.866) 		0.0286
(0.504) 		0.0818
(0.667) 		0.703
(0.985) 		1
(1.00) 		0.7
(0.985) 		0.1
(0.692) 		0.0834
(0.667) 		0.52
(0.953) 		0.0205
(0.452) 		0.891
(1.00) 		0.198
(0.796) 		0.0537
(0.576) 		1
(1.00) 		1
(1.00) 		0.659
(0.981) 		0.288
(0.869) 		0.217
(0.828)
amp 19p13 2 43 (15%) 252 0.0266
(0.5) 		0.53
(0.953) 		0.541
(0.962) 		0.532
(0.954) 		1
(1.00) 		0.664
(0.981) 		0.591
(0.969) 		0.863
(1.00) 		0.464
(0.949) 		0.589
(0.969) 		0.744
(0.994) 		0.972
(1.00) 		0.174
(0.774) 		0.874
(1.00) 		0.382
(0.921) 		0.863
(1.00) 		0.194
(0.793) 		0.0487
(0.557) 		1
(1.00) 		0.609
(0.969) 		0.816
(1.00) 		0.204
(0.808) 		0.164
(0.767) 		0.652
(0.976) 		0.166
(0.767) 		1
(1.00) 		0.567
(0.968) 		0.811
(1.00) 		0.464
(0.949) 		0.228
(0.84) 		0.00151
(0.286) 		0.352
(0.907) 		0.533
(0.954) 		0.128
(0.712) 		0.12
(0.711) 		0.638
(0.971) 		0.571
(0.968) 		0.466
(0.949) 		0.781
(1)
amp 19q13 13 93 (32%) 202 0.612
(0.969) 		0.119
(0.709) 		0.0304
(0.51) 		0.0846
(0.667) 		0.277
(0.866) 		0.724
(0.989) 		0.516
(0.953) 		0.756
(0.998) 		0.106
(0.694) 		0.828
(1.00) 		0.469
(0.949) 		0.871
(1.00) 		0.551
(0.962) 		0.774
(0.998) 		0.806
(1.00) 		0.756
(0.998) 		0.019
(0.452) 		0.514
(0.953) 		0.56
(0.966) 		0.124
(0.712) 		0.757
(0.998) 		0.0511
(0.563) 		0.0439
(0.537) 		0.704
(0.985) 		0.135
(0.724) 		0.13
(0.712) 		0.301
(0.881) 		0.281
(0.866) 		0.106
(0.694) 		0.331
(0.899) 		0.144
(0.747) 		0.475
(0.949) 		0.602
(0.969) 		0.606
(0.969) 		0.253
(0.857) 		0.844
(1.00) 		0.753
(0.997) 		0.114
(0.705) 		0.167
(0.767)
amp 20q11 21 135 (46%) 160 0.652
(0.976) 		0.0273
(0.503) 		0.011
(0.444) 		0.336
(0.899) 		0.341
(0.902) 		0.748
(0.994) 		0.652
(0.976) 		0.918
(1.00) 		0.208
(0.813) 		0.0305
(0.51) 		0.115
(0.705) 		0.153
(0.749) 		0.584
(0.969) 		0.64
(0.971) 		0.678
(0.981) 		0.918
(1.00) 		0.26
(0.857) 		0.674
(0.981) 		0.56
(0.966) 		0.0681
(0.645) 		0.726
(0.99) 		0.967
(1.00) 		0.166
(0.767) 		0.791
(1.00) 		0.526
(0.953) 		0.118
(0.707) 		0.296
(0.877) 		0.739
(0.994) 		0.208
(0.813) 		0.581
(0.969) 		0.388
(0.921) 		0.294
(0.872) 		0.787
(1) 		0.407
(0.921) 		0.609
(0.969) 		0.411
(0.922) 		0.493
(0.953) 		0.0198
(0.452) 		0.551
(0.962)
amp 21q22 13 48 (16%) 247 0.282
(0.866) 		0.163
(0.767) 		0.272
(0.865) 		1
(1.00) 		1
(1.00) 		0.829
(1.00) 		0.522
(0.953) 		0.748
(0.994) 		0.776
(0.998) 		0.956
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.26
(0.857) 		0.242
(0.857) 		0.53
(0.953) 		0.748
(0.994) 		0.514
(0.953) 		0.892
(1.00) 		0.459
(0.949) 		0.998
(1.00) 		0.328
(0.899) 		0.814
(1.00) 		0.982
(1.00) 		0.404
(0.921) 		0.947
(1.00) 		0.196
(0.796) 		0.396
(0.921) 		1
(1.00) 		0.776
(0.998) 		0.637
(0.97) 		0.0393
(0.53) 		0.945
(1.00) 		0.438
(0.943) 		0.472
(0.949) 		0.686
(0.981) 		1
(1.00) 		0.96
(1.00) 		0.178
(0.778) 		0.234
(0.848)
amp xq28 75 (25%) 220 0.0578
(0.602) 		0.343
(0.902) 		0.12
(0.71) 		0.273
(0.866) 		0.448
(0.948) 		0.0391
(0.53) 		0.089
(0.683) 		0.523
(0.953) 		0.571
(0.968) 		0.12
(0.711) 		0.789
(1) 		0.879
(1.00) 		0.746
(0.994) 		0.427
(0.934) 		0.107
(0.694) 		0.523
(0.953) 		0.712
(0.987) 		0.425
(0.934) 		0.459
(0.949) 		0.299
(0.881) 		0.8
(1.00) 		0.448
(0.948) 		0.351
(0.906) 		0.895
(1.00) 		0.756
(0.998) 		0.623
(0.969) 		0.628
(0.969) 		1
(1.00) 		0.571
(0.968) 		0.824
(1.00) 		0.544
(0.962) 		0.0738
(0.663) 		0.524
(0.953) 		0.276
(0.866) 		0.553
(0.963) 		1
(1.00) 		0.955
(1.00) 		0.308
(0.885) 		0.672
(0.981)
del 1p36 23 40 (14%) 255 0.631
(0.969) 		0.0644
(0.639) 		0.571
(0.968) 		0.797
(1.00) 		0.08
(0.664) 		0.314
(0.89) 		0.00727
(0.444) 		0.0174
(0.452) 		0.894
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.686
(0.981) 		0.236
(0.849) 		0.664
(0.981) 		0.864
(1.00) 		0.0174
(0.452) 		0.621
(0.969) 		0.366
(0.916) 		0.53
(0.953) 		0.796
(1.00) 		0.874
(1.00) 		0.387
(0.921) 		0.474
(0.949) 		0.426
(0.934) 		0.684
(0.981) 		0.689
(0.981) 		0.397
(0.921) 		0.8
(1.00) 		0.894
(1.00) 		0.273
(0.865) 		0.357
(0.911) 		0.28
(0.866) 		0.764
(0.998) 		0.326
(0.896) 		0.463
(0.949) 		0.255
(0.857) 		0.0716
(0.661) 		0.506
(0.953)
del 1p13 2 34 (12%) 261 0.0566
(0.594) 		0.97
(1.00) 		0.729
(0.993) 		0.281
(0.866) 		0.115
(0.705) 		0.808
(1.00) 		0.785
(1) 		0.696
(0.983) 		0.577
(0.969) 		0.76
(0.998) 		1
(1.00) 		0.937
(1.00) 		0.0935
(0.687) 		0.546
(0.962) 		0.696
(0.983) 		0.0433
(0.534) 		0.247
(0.857) 		1
(1.00) 		0.0782
(0.663) 		0.483
(0.949) 		0.0755
(0.663) 		0.551
(0.962) 		0.0726
(0.663) 		0.898
(1.00) 		1
(1.00) 		0.596
(0.969) 		0.527
(0.953) 		0.577
(0.969) 		0.919
(1.00) 		0.0561
(0.594) 		0.0773
(0.663) 		0.548
(0.962) 		0.457
(0.949) 		1
(1.00) 		0.175
(0.776) 		0.995
(1.00) 		0.454
(0.949)
del 2q22 1 65 (22%) 230 0.819
(1.00) 		0.566
(0.967) 		0.41
(0.922) 		0.85
(1.00) 		1
(1.00) 		0.849
(1.00) 		0.43
(0.937) 		0.303
(0.881) 		0.611
(0.969) 		0.198
(0.796) 		0.592
(0.969) 		0.704
(0.985) 		1
(1.00) 		0.264
(0.857) 		0.332
(0.899) 		0.303
(0.881) 		0.455
(0.949) 		0.23
(0.84) 		0.551
(0.962) 		0.989
(1.00) 		0.888
(1.00) 		0.673
(0.981) 		0.293
(0.872) 		0.0581
(0.602) 		0.816
(1.00) 		0.45
(0.949) 		0.256
(0.857) 		0.424
(0.934) 		0.611
(0.969) 		0.118
(0.707) 		0.844
(1.00) 		0.378
(0.921) 		0.423
(0.934) 		0.331
(0.899) 		0.021
(0.452) 		1
(1.00) 		0.225
(0.84) 		0.522
(0.953) 		0.498
(0.953)
del 2q37 1 129 (44%) 166 0.996
(1.00) 		0.0104
(0.444) 		0.482
(0.949) 		0.521
(0.953) 		0.182
(0.781) 		0.744
(0.994) 		0.0519
(0.567) 		0.592
(0.969) 		0.47
(0.949) 		0.546
(0.962) 		0.502
(0.953) 		0.338
(0.9) 		0.489
(0.953) 		0.982
(1.00) 		0.0141
(0.452) 		0.592
(0.969) 		0.104
(0.694) 		0.399
(0.921) 		0.56
(0.966) 		0.911
(1.00) 		0.19
(0.792) 		0.646
(0.975) 		0.882
(1.00) 		0.344
(0.902) 		0.973
(1.00) 		0.306
(0.882) 		0.277
(0.866) 		1
(1.00) 		0.47
(0.949) 		0.00432
(0.399) 		0.612
(0.969) 		0.989
(1.00) 		0.744
(0.994) 		0.852
(1.00) 		0.3
(0.881) 		0.683
(0.981) 		0.96
(1.00) 		0.0158
(0.452) 		0.712
(0.987)
del 4q21 3 103 (35%) 192 0.114
(0.705) 		0.966
(1.00) 		0.27
(0.862) 		0.0101
(0.444) 		0.0937
(0.687) 		0.0188
(0.452) 		0.0293
(0.504) 		0.63
(0.969) 		0.00863
(0.444) 		0.116
(0.705) 		1
(1.00) 		0.00439
(0.399) 		0.148
(0.749) 		0.0107
(0.444) 		0.287
(0.869) 		0.63
(0.969) 		0.121
(0.711) 		0.798
(1.00) 		1
(1.00) 		0.673
(0.981) 		0.616
(0.969) 		0.446
(0.948) 		0.247
(0.857) 		0.365
(0.916) 		0.641
(0.972) 		0.228
(0.84) 		0.928
(1.00) 		0.479
(0.949) 		0.00863
(0.444) 		0.351
(0.906) 		0.599
(0.969) 		0.247
(0.857) 		0.744
(0.994) 		0.705
(0.985) 		0.149
(0.749) 		0.694
(0.983) 		0.157
(0.749) 		0.981
(1.00) 		0.363
(0.916)
del 4q22 1 100 (34%) 195 0.354
(0.907) 		0.867
(1.00) 		0.23
(0.84) 		0.0846
(0.667) 		0.304
(0.881) 		0.00383
(0.399) 		0.0386
(0.53) 		0.61
(0.969) 		0.0417
(0.533) 		0.251
(0.857) 		0.636
(0.97) 		0.0288
(0.504) 		0.387
(0.921) 		0.00132
(0.284) 		0.208
(0.813) 		0.61
(0.969) 		0.457
(0.949) 		0.714
(0.987) 		0.543
(0.962) 		0.893
(1.00) 		0.651
(0.976) 		0.717
(0.988) 		0.369
(0.917) 		0.778
(0.999) 		0.585
(0.969) 		0.109
(0.704) 		0.943
(1.00) 		0.274
(0.866) 		0.0417
(0.533) 		0.485
(0.952) 		0.858
(1.00) 		0.287
(0.869) 		0.591
(0.969) 		0.855
(1.00) 		0.391
(0.921) 		0.826
(1.00) 		0.157
(0.749) 		0.885
(1.00) 		0.538
(0.959)
del 4q35 2 114 (39%) 181 0.569
(0.968) 		0.32
(0.891) 		0.291
(0.871) 		0.319
(0.891) 		1
(1.00) 		0.0679
(0.645) 		0.0751
(0.663) 		0.175
(0.776) 		0.304
(0.881) 		0.737
(0.994) 		0.179
(0.779) 		0.205
(0.808) 		1
(1.00) 		0.0191
(0.452) 		0.305
(0.881) 		0.175
(0.776) 		0.628
(0.969) 		0.219
(0.828) 		0.56
(0.966) 		0.656
(0.98) 		0.0618
(0.628) 		0.27
(0.862) 		0.703
(0.985) 		0.598
(0.969) 		0.805
(1.00) 		0.398
(0.921) 		0.403
(0.921) 		0.605
(0.969) 		0.304
(0.881) 		0.564
(0.967) 		0.392
(0.921) 		0.395
(0.921) 		0.406
(0.921) 		0.616
(0.969) 		0.786
(1) 		0.687
(0.981) 		0.393
(0.921) 		0.326
(0.896) 		0.512
(0.953)
del 5q12 1 76 (26%) 219 0.0789
(0.663) 		0.963
(1.00) 		0.498
(0.953) 		0.263
(0.857) 		1
(1.00) 		0.845
(1.00) 		0.528
(0.953) 		0.13
(0.712) 		0.0667
(0.645) 		0.833
(1.00) 		0.447
(0.948) 		0.0401
(0.53) 		0.159
(0.754) 		0.513
(0.953) 		0.0487
(0.557) 		0.13
(0.712) 		0.46
(0.949) 		0.402
(0.921) 		1
(1.00) 		0.466
(0.949) 		0.155
(0.749) 		0.189
(0.79) 		0.775
(0.998) 		0.0913
(0.687) 		0.959
(1.00) 		0.63
(0.969) 		0.576
(0.969) 		0.182
(0.781) 		0.0667
(0.645) 		0.848
(1.00) 		0.704
(0.985) 		0.245
(0.857) 		0.928
(1.00) 		0.768
(0.998) 		1
(1.00) 		0.255
(0.857) 		0.0307
(0.51) 		0.93
(1.00) 		0.179
(0.778)
del 5q35 2 71 (24%) 224 0.737
(0.994) 		0.536
(0.957) 		0.136
(0.724) 		0.709
(0.985) 		0.283
(0.866) 		0.692
(0.982) 		0.321
(0.892) 		0.367
(0.916) 		0.0318
(0.515) 		0.885
(1.00) 		1
(1.00) 		0.305
(0.881) 		0.631
(0.969) 		0.169
(0.768) 		0.41
(0.922) 		0.367
(0.916) 		0.466
(0.949) 		0.924
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.166
(0.767) 		0.278
(0.866) 		0.629
(0.969) 		0.0477
(0.557) 		0.53
(0.953) 		0.459
(0.949) 		1
(1.00) 		0.131
(0.713) 		0.0318
(0.515) 		0.91
(1.00) 		0.186
(0.79) 		0.745
(0.994) 		0.82
(1.00) 		0.385
(0.921) 		0.776
(0.998) 		0.315
(0.89) 		0.209
(0.814) 		0.567
(0.968) 		0.403
(0.921)
del 6p24 2 46 (16%) 249 0.681
(0.981) 		0.848
(1.00) 		0.787
(1) 		0.277
(0.866) 		0.686
(0.981) 		0.656
(0.98) 		0.126
(0.712) 		0.394
(0.921) 		0.136
(0.724) 		0.508
(0.953) 		0.523
(0.953) 		0.294
(0.872) 		0.565
(0.967) 		0.857
(1.00) 		0.106
(0.694) 		0.394
(0.921) 		0.925
(1.00) 		1
(1.00) 		1
(1.00) 		0.467
(0.949) 		0.454
(0.949) 		0.111
(0.705) 		0.607
(0.969) 		0.331
(0.899) 		0.819
(1.00) 		0.678
(0.981) 		0.281
(0.866) 		0.383
(0.921) 		0.136
(0.724) 		0.194
(0.793) 		0.51
(0.953) 		0.224
(0.84) 		0.386
(0.921) 		0.474
(0.949) 		0.519
(0.953) 		0.713
(0.987) 		0.0376
(0.53) 		0.808
(1.00) 		0.984
(1.00)
del 7q34 60 (20%) 235 0.187
(0.79) 		0.0863
(0.673) 		0.557
(0.966) 		0.219
(0.828) 		1
(1.00) 		0.68
(0.981) 		0.775
(0.998) 		0.112
(0.705) 		0.0217
(0.452) 		0.933
(1.00) 		0.603
(0.969) 		0.735
(0.994) 		0.242
(0.857) 		0.748
(0.994) 		0.856
(1.00) 		0.112
(0.705) 		0.518
(0.953) 		0.249
(0.857) 		0.583
(0.969) 		0.776
(0.998) 		0.202
(0.804) 		0.776
(0.998) 		0.612
(0.969) 		0.092
(0.687) 		0.287
(0.869) 		0.868
(1.00) 		0.561
(0.966) 		0.216
(0.828) 		0.0217
(0.452) 		0.349
(0.906) 		0.418
(0.931) 		0.72
(0.989) 		0.748
(0.994) 		0.697
(0.984) 		0.755
(0.998) 		0.795
(1.00) 		0.591
(0.969) 		0.077
(0.663) 		0.854
(1.00)
del 8p23 3 104 (35%) 191 0.0042
(0.399) 		0.264
(0.857) 		0.888
(1.00) 		0.502
(0.953) 		0.732
(0.994) 		0.604
(0.969) 		0.936
(1.00) 		0.529
(0.953) 		0.3
(0.881) 		0.79
(1.00) 		1
(1.00) 		0.924
(1.00) 		0.064
(0.639) 		0.438
(0.943) 		0.199
(0.798) 		0.529
(0.953) 		0.345
(0.903) 		0.0338
(0.529) 		1
(1.00) 		0.84
(1.00) 		0.966
(1.00) 		0.164
(0.767) 		0.979
(1.00) 		0.68
(0.981) 		0.986
(1.00) 		0.708
(0.985) 		0.873
(1.00) 		0.153
(0.749) 		0.3
(0.881) 		0.519
(0.953) 		0.215
(0.827) 		0.319
(0.891) 		0.494
(0.953) 		0.748
(0.994) 		0.596
(0.969) 		1
(1.00) 		0.136
(0.724) 		0.23
(0.84) 		0.571
(0.968)
del 8p23 1 97 (33%) 198 0.00743
(0.444) 		0.166
(0.767) 		0.954
(1.00) 		0.498
(0.953) 		0.725
(0.99) 		0.288
(0.869) 		0.781
(1) 		0.318
(0.891) 		0.236
(0.848) 		0.323
(0.893) 		0.812
(1.00) 		0.857
(1.00) 		0.0286
(0.504) 		0.236
(0.848) 		0.0219
(0.452) 		0.318
(0.891) 		0.586
(0.969) 		0.123
(0.712) 		0.56
(0.966) 		0.789
(1) 		0.757
(0.998) 		0.197
(0.796) 		0.968
(1.00) 		1
(1.00) 		0.698
(0.984) 		0.861
(1.00) 		0.838
(1.00) 		0.101
(0.692) 		0.236
(0.848) 		0.433
(0.94) 		0.367
(0.916) 		0.779
(1) 		0.967
(1.00) 		0.776
(0.998) 		0.786
(1) 		1
(1.00) 		0.13
(0.712) 		0.145
(0.748) 		0.441
(0.947)
del 11p15 1 102 (35%) 193 0.41
(0.922) 		0.00308
(0.378) 		0.533
(0.954) 		0.387
(0.921) 		0.494
(0.953) 		0.739
(0.994) 		0.114
(0.705) 		0.229
(0.84) 		0.177
(0.778) 		0.106
(0.694) 		0.648
(0.976) 		0.227
(0.84) 		0.2
(0.798) 		0.0958
(0.692) 		0.516
(0.953) 		0.229
(0.84) 		0.802
(1.00) 		0.327
(0.897) 		0.551
(0.962) 		0.1
(0.692) 		0.0531
(0.572) 		0.512
(0.953) 		0.127
(0.712) 		0.901
(1.00) 		0.0124
(0.449) 		0.518
(0.953) 		0.00814
(0.444) 		0.375
(0.921) 		0.177
(0.778) 		0.499
(0.953) 		0.719
(0.989) 		0.803
(1.00) 		0.0758
(0.663) 		0.13
(0.712) 		1
(1.00) 		0.206
(0.811) 		0.958
(1.00) 		0.00193
(0.338) 		0.166
(0.767)
del 11q23 3 162 (55%) 133 0.938
(1.00) 		0.0145
(0.452) 		0.788
(1) 		0.749
(0.994) 		0.741
(0.994) 		0.871
(1.00) 		0.0122
(0.449) 		0.599
(0.969) 		0.671
(0.981) 		0.2
(0.799) 		0.188
(0.79) 		0.731
(0.994) 		0.406
(0.921) 		0.765
(0.998) 		0.902
(1.00) 		0.599
(0.969) 		0.748
(0.994) 		0.03
(0.51) 		1
(1.00) 		0.151
(0.749) 		0.482
(0.949) 		0.771
(0.998) 		0.393
(0.921) 		0.67
(0.981) 		0.0343
(0.529) 		0.89
(1.00) 		0.0193
(0.452) 		0.134
(0.724) 		0.671
(0.981) 		0.5
(0.953) 		0.864
(1.00) 		0.0382
(0.53) 		0.498
(0.953) 		0.897
(1.00) 		0.437
(0.943) 		0.331
(0.899) 		0.661
(0.981) 		0.0216
(0.452) 		0.00868
(0.444)
del 11q25 160 (54%) 135 0.452
(0.949) 		0.15
(0.749) 		0.628
(0.969) 		0.873
(1.00) 		0.739
(0.994) 		0.871
(1.00) 		0.0192
(0.452) 		0.71
(0.985) 		0.885
(1.00) 		0.179
(0.778) 		0.0753
(0.663) 		0.677
(0.981) 		0.168
(0.767) 		0.684
(0.981) 		0.618
(0.969) 		0.71
(0.985) 		0.61
(0.969) 		0.0564
(0.594) 		1
(1.00) 		0.262
(0.857) 		0.482
(0.949) 		0.771
(0.998) 		0.696
(0.983) 		0.469
(0.949) 		0.0343
(0.529) 		0.89
(1.00) 		0.0637
(0.639) 		0.0671
(0.645) 		0.885
(1.00) 		0.643
(0.974) 		1
(1.00) 		0.0182
(0.452) 		0.839
(1.00) 		0.419
(0.932) 		0.437
(0.943) 		0.339
(0.901) 		0.807
(1.00) 		0.195
(0.793) 		0.0224
(0.458)
del 13q12 11 98 (33%) 197 0.376
(0.921) 		0.954
(1.00) 		0.0792
(0.663) 		0.0796
(0.663) 		0.288
(0.869) 		1
(1.00) 		0.00323
(0.378) 		0.58
(0.969) 		0.0114
(0.444) 		0.0892
(0.683) 		0.345
(0.902) 		0.126
(0.712) 		0.473
(0.949) 		0.0872
(0.676) 		0.664
(0.981) 		0.58
(0.969) 		0.059
(0.606) 		0.109
(0.702) 		1
(1.00) 		0.149
(0.749) 		0.967
(1.00) 		0.583
(0.969) 		0.195
(0.793) 		0.665
(0.981) 		0.252
(0.857) 		0.86
(1.00) 		0.63
(0.969) 		0.288
(0.869) 		0.0114
(0.444) 		0.473
(0.949) 		0.723
(0.989) 		0.0232
(0.47) 		0.641
(0.972) 		0.572
(0.968) 		0.253
(0.857) 		0.261
(0.857) 		0.317
(0.891) 		0.91
(1.00) 		0.01
(0.444)
del 13q14 2 118 (40%) 177 0.277
(0.866) 		0.126
(0.712) 		0.0047
(0.412) 		0.0459
(0.551) 		0.517
(0.953) 		0.25
(0.857) 		0.0195
(0.452) 		0.322
(0.892) 		0.0151
(0.452) 		0.0184
(0.452) 		0.645
(0.975) 		0.95
(1.00) 		0.26
(0.857) 		0.00912
(0.444) 		0.0406
(0.53) 		0.322
(0.892) 		0.0157
(0.452) 		0.0361
(0.53) 		1
(1.00) 		0.033
(0.524) 		0.967
(1.00) 		0.526
(0.953) 		0.00826
(0.444) 		0.473
(0.949) 		0.0366
(0.53) 		0.629
(0.969) 		0.736
(0.994) 		0.385
(0.921) 		0.0151
(0.452) 		0.667
(0.981) 		0.731
(0.994) 		0.0384
(0.53) 		0.824
(1.00) 		0.384
(0.921) 		0.0913
(0.687) 		0.0837
(0.667) 		0.651
(0.976) 		0.0961
(0.692) 		0.0127
(0.449)
del 14q32 31 50 (17%) 245 0.648
(0.976) 		0.102
(0.692) 		0.703
(0.985) 		1
(1.00) 		0.117
(0.707) 		0.654
(0.978) 		0.0985
(0.692) 		0.44
(0.946) 		0.278
(0.866) 		0.632
(0.969) 		0.757
(0.998) 		0.933
(1.00) 		0.563
(0.966) 		0.0132
(0.451) 		0.938
(1.00) 		0.44
(0.946) 		0.0643
(0.639) 		0.956
(1.00) 		1
(1.00) 		0.0813
(0.667) 		0.377
(0.921) 		0.446
(0.948) 		0.289
(0.871) 		0.172
(0.774) 		0.517
(0.953) 		0.927
(1.00) 		0.118
(0.708) 		0.506
(0.953) 		0.278
(0.866) 		0.474
(0.949) 		0.813
(1.00) 		0.525
(0.953) 		0.386
(0.921) 		0.625
(0.969) 		1
(1.00) 		0.343
(0.902) 		0.114
(0.705) 		0.789
(1)
del 15q21 1 70 (24%) 225 0.805
(1.00) 		0.0112
(0.444) 		0.216
(0.828) 		0.234
(0.848) 		0.393
(0.921) 		0.13
(0.712) 		0.00564
(0.416) 		0.785
(1) 		0.59
(0.969) 		0.0291
(0.504) 		1
(1.00) 		0.924
(1.00) 		0.873
(1.00) 		0.0118
(0.445) 		0.155
(0.749) 		0.785
(1) 		0.632
(0.969) 		0.715
(0.987) 		1
(1.00) 		0.849
(1.00) 		0.93
(1.00) 		0.0752
(0.663) 		0.314
(0.89) 		0.863
(1.00) 		0.844
(1.00) 		0.887
(1.00) 		0.0574
(0.6) 		0.818
(1.00) 		0.59
(0.969) 		0.432
(0.94) 		0.513
(0.953) 		0.673
(0.981) 		0.373
(0.921) 		0.643
(0.974) 		0.724
(0.989) 		0.292
(0.872) 		0.733
(0.994) 		0.0135
(0.452) 		0.133
(0.718)
del 17p12 109 (37%) 186 0.4
(0.921) 		0.0195
(0.452) 		0.831
(1.00) 		0.604
(0.969) 		1
(1.00) 		0.622
(0.969) 		0.572
(0.968) 		0.526
(0.953) 		0.93
(1.00) 		0.167
(0.767) 		0.646
(0.975) 		0.198
(0.796) 		0.0334
(0.526) 		0.0524
(0.567) 		0.715
(0.987) 		0.526
(0.953) 		0.0507
(0.561) 		0.434
(0.94) 		1
(1.00) 		0.832
(1.00) 		0.46
(0.949) 		0.69
(0.981) 		0.157
(0.749) 		0.0493
(0.558) 		0.632
(0.969) 		0.681
(0.981) 		0.532
(0.954) 		1
(1.00) 		0.93
(1.00) 		0.405
(0.921) 		0.602
(0.969) 		0.621
(0.969) 		0.266
(0.857) 		0.411
(0.922) 		0.787
(1) 		0.689
(0.981) 		0.119
(0.71) 		0.0249
(0.486) 		0.702
(0.985)
del 17q25 3 51 (17%) 244 0.417
(0.93) 		0.703
(0.985) 		0.988
(1.00) 		0.409
(0.922) 		0.649
(0.976) 		0.822
(1.00) 		0.104
(0.694) 		0.245
(0.857) 		0.763
(0.998) 		0.261
(0.857) 		1
(1.00) 		0.492
(0.953) 		0.565
(0.967) 		0.305
(0.881) 		0.343
(0.902) 		0.245
(0.857) 		0.0981
(0.692) 		0.373
(0.921) 		1
(1.00) 		0.948
(1.00) 		0.314
(0.89) 		0.434
(0.94) 		0.805
(1.00) 		0.574
(0.969) 		0.149
(0.749) 		0.822
(1.00) 		0.885
(1.00) 		1
(1.00) 		0.763
(0.998) 		0.259
(0.857) 		0.678
(0.981) 		0.738
(0.994) 		1
(1.00) 		0.156
(0.749) 		0.458
(0.949) 		1
(1.00) 		0.958
(1.00) 		0.523
(0.953) 		0.422
(0.934)
del 19p13 3 105 (36%) 190 0.00266
(0.378) 		0.623
(0.969) 		0.591
(0.969) 		0.864
(1.00) 		0.723
(0.989) 		0.404
(0.921) 		0.315
(0.89) 		0.382
(0.921) 		0.974
(1.00) 		0.167
(0.767) 		0.099
(0.692) 		0.509
(0.953) 		0.00139
(0.284) 		0.116
(0.705) 		0.592
(0.969) 		0.382
(0.921) 		0.995
(1.00) 		0.589
(0.969) 		1
(1.00) 		0.999
(1.00) 		0.101
(0.692) 		0.358
(0.912) 		0.656
(0.98) 		0.127
(0.712) 		0.681
(0.981) 		0.802
(1.00) 		0.622
(0.969) 		0.479
(0.949) 		0.974
(1.00) 		0.556
(0.966) 		0.367
(0.916) 		0.497
(0.953) 		0.968
(1.00) 		0.107
(0.694) 		1
(1.00) 		0.828
(1.00) 		0.082
(0.667) 		0.558
(0.966) 		0.994
(1.00)
del 19q13 33 38 (13%) 257 0.361
(0.914) 		0.199
(0.798) 		0.949
(1.00) 		0.81
(1.00) 		0.614
(0.969) 		1
(1.00) 		0.113
(0.705) 		0.401
(0.921) 		0.766
(0.998) 		0.455
(0.949) 		0.474
(0.949) 		0.478
(0.949) 		0.685
(0.981) 		0.123
(0.712) 		0.835
(1.00) 		0.401
(0.921) 		0.99
(1.00) 		0.0966
(0.692) 		1
(1.00) 		0.708
(0.985) 		0.333
(0.899) 		0.855
(1.00) 		0.388
(0.921) 		0.141
(0.735) 		0.684
(0.981) 		0.927
(1.00) 		0.213
(0.822) 		1
(1.00) 		0.766
(0.998) 		0.735
(0.994) 		0.77
(0.998) 		0.484
(0.951) 		0.663
(0.981) 		0.916
(1.00) 		0.458
(0.949) 		0.28
(0.866) 		0.659
(0.981) 		0.218
(0.828) 		0.251
(0.857)
del 20p12 1 36 (12%) 259 0.145
(0.748) 		0.282
(0.866) 		0.565
(0.967) 		0.639
(0.971) 		1
(1.00) 		0.1
(0.692) 		0.787
(1) 		0.0935
(0.687) 		0.531
(0.953) 		0.622
(0.969) 		1
(1.00) 		0.283
(0.866) 		0.069
(0.649) 		0.99
(1.00) 		0.95
(1.00) 		0.0935
(0.687) 		0.0858
(0.671) 		0.932
(1.00) 		0.298
(0.881) 		0.652
(0.976) 		0.877
(1.00) 		0.708
(0.985) 		0.494
(0.953) 		0.745
(0.994) 		0.52
(0.953) 		0.401
(0.921) 		0.835
(1.00) 		1
(1.00) 		0.531
(0.953) 		0.358
(0.912) 		0.437
(0.943) 		0.607
(0.969) 		0.29
(0.871) 		0.713
(0.987) 		0.724
(0.989) 		0.577
(0.969) 		0.37
(0.919) 		0.693
(0.983)
del 21q11 2 58 (20%) 237 0.0358
(0.53) 		0.169
(0.768) 		0.0442
(0.538) 		0.219
(0.828) 		0.69
(0.981) 		0.14
(0.735) 		0.624
(0.969) 		0.562
(0.966) 		0.0647
(0.639) 		0.342
(0.902) 		0.052
(0.567) 		0.0986
(0.692) 		0.174
(0.774) 		0.0428
(0.533) 		0.562
(0.966) 		0.0331
(0.524) 		0.0244
(0.485) 		0.459
(0.949) 		0.0286
(0.504) 		0.314
(0.89) 		0.839
(1.00) 		0.0424
(0.533) 		0.154
(0.749) 		0.766
(0.998) 		0.0584
(0.603) 		0.964
(1.00) 		0.835
(1.00) 		0.0647
(0.639) 		0.188
(0.79) 		0.667
(0.981) 		0.156
(0.749) 		0.444
(0.948) 		0.448
(0.948) 		0.351
(0.906) 		0.73
(0.993) 		0.153
(0.749) 		0.0405
(0.53)
del 22q13 32 88 (30%) 207 0.144
(0.747) 		0.215
(0.827) 		0.383
(0.921) 		0.226
(0.84) 		0.494
(0.953) 		0.373
(0.921) 		0.277
(0.866) 		0.549
(0.962) 		0.768
(0.998) 		0.819
(1.00) 		0.804
(1.00) 		0.761
(0.998) 		1
(1.00) 		0.531
(0.953) 		0.134
(0.723) 		0.549
(0.962) 		0.463
(0.949) 		0.149
(0.749) 		0.258
(0.857) 		0.00957
(0.444) 		0.145
(0.748) 		0.572
(0.968) 		0.02
(0.452) 		0.64
(0.971) 		0.9
(1.00) 		0.861
(1.00) 		0.19
(0.79) 		0.218
(0.828) 		0.768
(0.998) 		0.193
(0.793) 		0.715
(0.987) 		0.937
(1.00) 		0.876
(1.00) 		0.187
(0.79) 		0.171
(0.774) 		0.246
(0.857) 		0.651
(0.976) 		0.247
(0.857) 		0.16
(0.757)
del xp11 3 72 (24%) 223 0.427
(0.934) 		0.205
(0.808) 		0.807
(1.00) 		0.57
(0.968) 		0.686
(0.981) 		0.425
(0.934) 		0.097
(0.692) 		0.522
(0.953) 		1
(1.00) 		0.096
(0.692) 		0.113
(0.705) 		0.666
(0.981) 		0.336
(0.899) 		0.472
(0.949) 		0.178
(0.778) 		0.522
(0.953) 		0.382
(0.921) 		0.359
(0.913) 		0.284
(0.866) 		0.353
(0.907) 		0.759
(0.998) 		0.122
(0.712) 		0.108
(0.699) 		0.581
(0.969) 		0.644
(0.974) 		0.244
(0.857) 		0.279
(0.866) 		0.847
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.105
(0.694) 		0.092
(0.687) 		0.0715
(0.661) 		0.726
(0.99) 		0.0682
(0.645) 		1
(1.00) 		0.225
(0.84) 		0.181
(0.781) 		0.504
(0.953)
del xq21 33 60 (20%) 235 0.0275
(0.503) 		0.427
(0.934) 		0.775
(0.998) 		0.434
(0.94) 		0.37
(0.919) 		0.843
(1.00) 		0.154
(0.749) 		0.763
(0.998) 		0.47
(0.949) 		0.187
(0.79) 		0.414
(0.926) 		0.164
(0.767) 		0.0415
(0.533) 		0.48
(0.949) 		0.575
(0.969) 		0.763
(0.998) 		0.684
(0.981) 		0.623
(0.969) 		0.188
(0.79) 		0.172
(0.774) 		0.583
(0.969) 		0.414
(0.926) 		0.0318
(0.515) 		0.952
(1.00) 		0.585
(0.969) 		0.102
(0.692) 		0.079
(0.663) 		1
(1.00) 		0.47
(0.949) 		0.906
(1.00) 		0.0432
(0.534) 		0.76
(0.998) 		0.813
(1.00) 		0.766
(0.998) 		0.116
(0.705) 		0.132
(0.715) 		0.635
(0.97) 		0.395
(0.921) 		0.876
(1.00)
'amp_11q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.000111 (Wilcoxon-test), Q value = 0.046

Table S1.  Gene #16: 'amp_11q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 293 48.1 (13.8)
AMP PEAK 16(11Q22.1) MUTATED 47 40.9 (12.6)
AMP PEAK 16(11Q22.1) WILD-TYPE 246 49.5 (13.6)

Figure S1.  Get High-res Image Gene #16: 'amp_11q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_11q22.1' versus 'AGE_AT_DIAGNOSIS'

P value = 9.19e-05 (Wilcoxon-test), Q value = 0.045

Table S2.  Gene #16: 'amp_11q22.1' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

nPatients Mean (Std.Dev)
ALL 295 48.2 (13.8)
AMP PEAK 16(11Q22.1) MUTATED 47 40.9 (12.6)
AMP PEAK 16(11Q22.1) WILD-TYPE 248 49.6 (13.6)

Figure S2.  Get High-res Image Gene #16: 'amp_11q22.1' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

'del_3p14.2' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.045

Table S3.  Gene #33: 'del_3p14.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE ENDOCERVICAL TYPE OF ADENOCARCINOMA ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
ALL 6 242 6 21 3 17
DEL PEAK 5(3P14.2) MUTATED 2 124 1 1 1 5
DEL PEAK 5(3P14.2) WILD-TYPE 4 118 5 20 2 12

Figure S3.  Get High-res Image Gene #33: 'del_3p14.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_3p14.2' versus 'TOBACCO_SMOKING_HISTORY'

P value = 0.00053 (Fisher's exact test), Q value = 0.19

Table S4.  Gene #33: 'del_3p14.2' versus Clinical Feature #17: 'TOBACCO_SMOKING_HISTORY'

nPatients CURRENT REFORMED SMOKER FOR < OR = 15 YEARS CURRENT REFORMED SMOKER FOR > 15 YEARS CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED CURRENT SMOKER LIFELONG NON-SMOKER
ALL 38 9 3 62 143
DEL PEAK 5(3P14.2) MUTATED 16 2 3 40 53
DEL PEAK 5(3P14.2) WILD-TYPE 22 7 0 22 90

Figure S4.  Get High-res Image Gene #33: 'del_3p14.2' versus Clinical Feature #17: 'TOBACCO_SMOKING_HISTORY'

'del_6q26' versus 'INITIAL_PATHOLOGIC_DX_YEAR'

P value = 0.000747 (Wilcoxon-test), Q value = 0.23

Table S5.  Gene #40: 'del_6q26' versus Clinical Feature #32: 'INITIAL_PATHOLOGIC_DX_YEAR'

nPatients Mean (Std.Dev)
ALL 293 2008.5 (4.6)
DEL PEAK 12(6Q26) MUTATED 98 2007.2 (5.2)
DEL PEAK 12(6Q26) WILD-TYPE 195 2009.2 (4.2)

Figure S5.  Get High-res Image Gene #40: 'del_6q26' versus Clinical Feature #32: 'INITIAL_PATHOLOGIC_DX_YEAR'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.000904 (Wilcoxon-test), Q value = 0.25

Table S6.  Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 293 48.1 (13.8)
DEL PEAK 16(10Q23.31) MUTATED 86 52.2 (14.5)
DEL PEAK 16(10Q23.31) WILD-TYPE 207 46.4 (13.2)

Figure S6.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.025

Table S7.  Gene #52: 'del_16q11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE ENDOCERVICAL TYPE OF ADENOCARCINOMA ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
ALL 6 242 6 21 3 17
DEL PEAK 24(16Q11.2) MUTATED 0 32 5 9 1 6
DEL PEAK 24(16Q11.2) WILD-TYPE 6 210 1 12 2 11

Figure S7.  Get High-res Image Gene #52: 'del_16q11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_16q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.041

Table S8.  Gene #53: 'del_16q23.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE ENDOCERVICAL TYPE OF ADENOCARCINOMA ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
ALL 6 242 6 21 3 17
DEL PEAK 25(16Q23.1) MUTATED 0 34 4 9 2 6
DEL PEAK 25(16Q23.1) WILD-TYPE 6 208 2 12 1 11

Figure S8.  Get High-res Image Gene #53: 'del_16q23.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_18q21.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.025

Table S9.  Gene #56: 'del_18q21.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE ENDOCERVICAL TYPE OF ADENOCARCINOMA ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
ALL 6 242 6 21 3 17
DEL PEAK 28(18Q21.2) MUTATED 0 55 1 14 2 10
DEL PEAK 28(18Q21.2) WILD-TYPE 6 187 5 7 1 7

Figure S9.  Get High-res Image Gene #56: 'del_18q21.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/19779737/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/19775059/CESC-TP.merged_data.txt

  • Number of patients = 295

  • Number of significantly focal cnvs = 63

  • Number of selected clinical features = 39

  • 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

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.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[3] 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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