Correlation between copy number variation genes (focal events) and selected clinical features
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1XW4J5S
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1XW4J5S
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, 25 significant findings detected with Q value < 0.25.

  • amp_11q22.1 cnv correlated to 'YEARS_TO_BIRTH',  'MENOPAUSE_STATUS',  'INITIAL_PATHOLOGIC_DX_YEAR', and 'AGE_AT_DIAGNOSIS'.

  • amp_19p13.2 cnv correlated to 'KERATINIZATION_SQUAMOUS_CELL'.

  • del_3p22.1 cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES',  'LYMPHOVASCULAR_INVOLVEMENT', and 'LYMPH_NODES_EXAMINED_HE_COUNT'.

  • del_3p14.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_4p16.3 cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'LYMPH_NODES_EXAMINED_HE_COUNT'.

  • del_4q22.1 cnv correlated to 'RADIATION_THERAPY' and 'NEOPLASM_HISTOLOGIC_GRADE'.

  • del_6q26 cnv correlated to 'INITIAL_PATHOLOGIC_DX_YEAR'.

  • del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH' and 'AGE_AT_DIAGNOSIS'.

  • del_11p15.1 cnv correlated to 'AGE_AT_DIAGNOSIS'.

  • del_16q11.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_16q23.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_18q21.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_19p13.3 cnv correlated to 'TUMOR_STATUS'.

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, 25 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 Wilcoxon-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
del 3p22 1 113 (38%) 182 0.188
(0.788) 		0.924
(1.00) 		0.0862
(0.654) 		0.000706
(0.153) 		0.742
(1) 		0.312
(0.888) 		0.00018
(0.0442) 		0.544
(0.961) 		3.18e-05
(0.0156) 		0.621
(0.968) 		0.356
(0.909) 		0.377
(0.922) 		0.0688
(0.635) 		0.408
(0.927) 		0.189
(0.788) 		0.544
(0.961) 		0.0475
(0.541) 		0.338
(0.9) 		1
(1.00) 		0.507
(0.957) 		0.278
(0.864) 		0.728
(0.996) 		0.761
(1.00) 		0.606
(0.967) 		0.165
(0.761) 		0.0905
(0.667) 		0.814
(1.00) 		0.0017
(0.205) 		3.18e-05
(0.0156) 		0.462
(0.953) 		0.387
(0.922) 		0.00405
(0.308) 		0.0763
(0.648) 		0.218
(0.816) 		0.104
(0.678) 		0.826
(1.00) 		0.063
(0.619) 		0.846
(1.00) 		0.0494
(0.541)
amp 11q22 1 47 (16%) 248 0.624
(0.968) 		0.000111
(0.0304) 		0.389
(0.922) 		1
(1.00) 		1
(1.00) 		0.641
(0.974) 		0.688
(0.986) 		0.0211
(0.427) 		0.965
(1.00) 		0.0238
(0.446) 		0.38
(0.922) 		0.285
(0.871) 		0.856
(1.00) 		0.0254
(0.459) 		0.279
(0.866) 		0.0211
(0.427) 		0.779
(1.00) 		0.69
(0.986) 		1
(1.00) 		0.947
(1.00) 		0.23
(0.828) 		0.512
(0.957) 		0.994
(1.00) 		0.436
(0.948) 		0.351
(0.907) 		0.947
(1.00) 		0.0023
(0.235) 		0.519
(0.957) 		0.965
(1.00) 		0.434
(0.948) 		0.274
(0.864) 		0.00252
(0.248) 		0.72
(0.995) 		0.172
(0.77) 		0.191
(0.788) 		0.308
(0.888) 		0.147
(0.745) 		9.19e-05
(0.0282) 		0.602
(0.966)
del 4p16 3 127 (43%) 168 0.442
(0.949) 		0.698
(0.99) 		0.136
(0.719) 		0.00175
(0.205) 		0.178
(0.773) 		0.00466
(0.318) 		9e-05
(0.0282) 		0.616
(0.968) 		0.00111
(0.181) 		0.281
(0.868) 		0.823
(1.00) 		0.31
(0.888) 		0.413
(0.928) 		0.202
(0.796) 		0.426
(0.942) 		0.616
(0.968) 		0.0928
(0.667) 		0.737
(0.999) 		1
(1.00) 		0.0769
(0.648) 		0.778
(1.00) 		0.941
(1.00) 		0.0522
(0.553) 		0.262
(0.857) 		0.525
(0.957) 		0.77
(1.00) 		1
(1.00) 		0.231
(0.828) 		0.00111
(0.181) 		0.256
(0.857) 		0.236
(0.835) 		0.04
(0.513) 		0.761
(1.00) 		0.376
(0.922) 		0.597
(0.966) 		0.679
(0.986) 		0.885
(1.00) 		0.701
(0.991) 		0.141
(0.73)
del 4q22 1 100 (34%) 195 0.378
(0.922) 		0.867
(1.00) 		0.23
(0.828) 		0.0846
(0.651) 		0.304
(0.885) 		0.00204
(0.218) 		0.0404
(0.513) 		0.61
(0.967) 		0.0417
(0.516) 		0.248
(0.85) 		0.636
(0.972) 		0.0288
(0.475) 		0.391
(0.922) 		0.00175
(0.205) 		0.208
(0.804) 		0.61
(0.967) 		0.216
(0.816) 		0.714
(0.994) 		0.543
(0.961) 		0.893
(1.00) 		0.651
(0.979) 		0.717
(0.995) 		0.369
(0.921) 		0.778
(1.00) 		0.585
(0.966) 		0.122
(0.7) 		0.963
(1.00) 		0.274
(0.864) 		0.0417
(0.516) 		0.485
(0.956) 		0.858
(1.00) 		0.287
(0.872) 		0.59
(0.966) 		0.855
(1.00) 		0.391
(0.922) 		0.827
(1.00) 		0.157
(0.745) 		0.885
(1.00) 		0.539
(0.961)
del 10q23 31 86 (29%) 209 0.408
(0.927) 		0.000904
(0.171) 		0.353
(0.907) 		0.271
(0.861) 		0.706
(0.991) 		0.471
(0.953) 		0.981
(1.00) 		0.949
(1.00) 		0.0998
(0.672) 		0.0164
(0.425) 		1
(1.00) 		0.369
(0.921) 		0.0724
(0.642) 		0.00882
(0.384) 		0.266
(0.857) 		0.949
(1.00) 		0.0247
(0.453) 		0.127
(0.703) 		1
(1.00) 		0.0817
(0.651) 		0.842
(1.00) 		0.701
(0.991) 		0.0103
(0.384) 		0.815
(1.00) 		0.698
(0.99) 		0.0273
(0.472) 		0.0187
(0.427) 		0.198
(0.79) 		0.0998
(0.672) 		0.242
(0.845) 		0.0909
(0.667) 		0.016
(0.424) 		0.526
(0.957) 		0.241
(0.845) 		0.767
(1.00) 		1
(1.00) 		0.526
(0.957) 		0.00121
(0.186) 		0.398
(0.925)
amp 19p13 2 43 (15%) 252 0.0564
(0.57) 		0.53
(0.957) 		0.539
(0.961) 		0.532
(0.957) 		1
(1.00) 		1
(1.00) 		0.589
(0.966) 		0.863
(1.00) 		0.464
(0.953) 		0.588
(0.966) 		0.744
(1) 		0.972
(1.00) 		0.336
(0.899) 		0.874
(1.00) 		0.382
(0.922) 		0.863
(1.00) 		0.667
(0.985) 		0.0487
(0.541) 		1
(1.00) 		0.609
(0.967) 		0.816
(1.00) 		0.204
(0.799) 		0.164
(0.761) 		0.652
(0.979) 		0.166
(0.761) 		0.921
(1.00) 		0.567
(0.966) 		0.811
(1.00) 		0.464
(0.953) 		0.228
(0.828) 		0.00151
(0.205) 		0.352
(0.907) 		0.535
(0.959) 		0.128
(0.703) 		0.12
(0.7) 		0.636
(0.972) 		0.571
(0.966) 		0.466
(0.953) 		0.783
(1.00)
del 3p14 2 134 (45%) 161 0.782
(1.00) 		0.993
(1.00) 		0.0308
(0.492) 		0.00575
(0.333) 		0.752
(1.00) 		0.136
(0.719) 		6e-05
(0.0246) 		0.61
(0.967) 		0.00323
(0.274) 		0.872
(1.00) 		0.263
(0.857) 		0.0114
(0.384) 		0.173
(0.772) 		0.129
(0.708) 		0.0982
(0.672) 		0.61
(0.967) 		0.0329
(0.5) 		0.639
(0.974) 		1
(1.00) 		0.8
(1.00) 		0.15
(0.745) 		0.488
(0.957) 		0.851
(1.00) 		0.812
(1.00) 		0.151
(0.745) 		0.123
(0.701) 		0.969
(1.00) 		0.00574
(0.333) 		0.00323
(0.274) 		0.349
(0.907) 		0.394
(0.922) 		0.0166
(0.425) 		0.0459
(0.532) 		0.666
(0.985) 		0.596
(0.966) 		0.682
(0.986) 		0.063
(0.619) 		0.987
(1.00) 		0.0384
(0.513)
del 6q26 100 (34%) 195 0.0826
(0.651) 		0.65
(0.979) 		0.786
(1.00) 		0.604
(0.967) 		1
(1.00) 		1
(1.00) 		0.303
(0.885) 		0.407
(0.927) 		0.384
(0.922) 		0.245
(0.847) 		0.342
(0.906) 		0.514
(0.957) 		0.563
(0.963) 		0.0792
(0.65) 		0.125
(0.703) 		0.407
(0.927) 		0.544
(0.961) 		0.969
(1.00) 		0.536
(0.959) 		0.625
(0.968) 		0.417
(0.935) 		0.15
(0.745) 		0.532
(0.957) 		0.475
(0.953) 		0.967
(1.00) 		0.578
(0.966) 		0.111
(0.689) 		0.598
(0.966) 		0.384
(0.922) 		0.24
(0.845) 		0.855
(1.00) 		0.000747
(0.153) 		0.686
(0.986) 		0.0327
(0.5) 		0.596
(0.966) 		0.474
(0.953) 		0.089
(0.666) 		0.591
(0.966) 		0.365
(0.919)
del 11p15 1 102 (35%) 193 0.499
(0.957) 		0.00308
(0.274) 		0.532
(0.957) 		0.387
(0.922) 		0.494
(0.957) 		1
(1.00) 		0.112
(0.689) 		0.229
(0.828) 		0.177
(0.773) 		0.105
(0.678) 		0.649
(0.979) 		0.227
(0.828) 		0.201
(0.794) 		0.0974
(0.672) 		0.516
(0.957) 		0.229
(0.828) 		0.63
(0.97) 		0.327
(0.892) 		0.551
(0.963) 		0.1
(0.672) 		0.0531
(0.554) 		0.512
(0.957) 		0.127
(0.703) 		0.901
(1.00) 		0.0124
(0.396) 		0.649
(0.979) 		0.0102
(0.384) 		0.375
(0.922) 		0.177
(0.773) 		0.499
(0.957) 		0.719
(0.995) 		0.803
(1.00) 		0.0748
(0.648) 		0.13
(0.709) 		1
(1.00) 		0.205
(0.799) 		0.958
(1.00) 		0.00193
(0.215) 		0.167
(0.761)
del 16q11 2 53 (18%) 242 0.803
(1.00) 		0.406
(0.927) 		0.841
(1.00) 		0.0156
(0.422) 		1
(1.00) 		0.297
(0.881) 		1e-05
(0.0123) 		0.265
(0.857) 		0.0762
(0.648) 		0.402
(0.927) 		0.771
(1.00) 		0.894
(1.00) 		1
(1.00) 		0.489
(0.957) 		0.491
(0.957) 		0.265
(0.857) 		0.235
(0.835) 		0.22
(0.816) 		1
(1.00) 		0.305
(0.885) 		0.888
(1.00) 		0.518
(0.957) 		0.591
(0.966) 		0.962
(1.00) 		0.0865
(0.654) 		0.766
(1.00) 		0.152
(0.745) 		0.402
(0.927) 		0.0762
(0.648) 		0.761
(1.00) 		0.0717
(0.642) 		0.743
(1) 		0.797
(1.00) 		0.504
(0.957) 		0.113
(0.689) 		1
(1.00) 		0.342
(0.906) 		0.446
(0.951)
del 16q23 1 55 (19%) 240 0.409
(0.927) 		0.245
(0.847) 		0.928
(1.00) 		0.316
(0.888) 		0.686
(0.986) 		0.834
(1.00) 		3e-05
(0.0156) 		0.265
(0.857) 		0.39
(0.922) 		0.00716
(0.384) 		0.378
(0.922) 		0.5
(0.957) 		0.602
(0.966) 		0.226
(0.828) 		0.616
(0.968) 		0.265
(0.857) 		0.437
(0.948) 		0.983
(1.00) 		0.551
(0.963) 		0.105
(0.678) 		0.888
(1.00) 		0.46
(0.953) 		0.439
(0.949) 		0.0277
(0.472) 		0.318
(0.888) 		1
(1.00) 		0.805
(1.00) 		0.667
(0.985) 		0.39
(0.922) 		0.939
(1.00) 		0.14
(0.727) 		0.428
(0.943) 		0.912
(1.00) 		0.383
(0.922) 		0.519
(0.957) 		1
(1.00) 		0.206
(0.801) 		0.979
(1.00)
del 18q21 2 82 (28%) 213 0.76
(1.00) 		0.561
(0.963) 		0.619
(0.968) 		0.355
(0.908) 		0.149
(0.745) 		0.588
(0.966) 		1e-05
(0.0123) 		0.588
(0.966) 		0.0506
(0.544) 		0.909
(1.00) 		0.603
(0.967) 		0.144
(0.735) 		0.291
(0.876) 		0.254
(0.857) 		0.975
(1.00) 		0.588
(0.966) 		0.0545
(0.558) 		0.385
(0.922) 		1
(1.00) 		0.0926
(0.667) 		0.126
(0.703) 		0.803
(1.00) 		0.174
(0.773) 		0.854
(1.00) 		0.9
(1.00) 		0.752
(1.00) 		0.712
(0.993) 		0.0494
(0.541) 		0.0506
(0.544) 		0.872
(1.00) 		0.68
(0.986) 		0.0214
(0.427) 		0.628
(0.97) 		0.428
(0.943) 		0.0386
(0.513) 		0.123
(0.701) 		0.514
(0.957) 		0.0699
(0.638)
del 19p13 3 105 (36%) 190 0.00426
(0.308) 		0.623
(0.968) 		0.588
(0.966) 		0.864
(1.00) 		0.723
(0.995) 		0.314
(0.888) 		0.315
(0.888) 		0.382
(0.922) 		0.974
(1.00) 		0.168
(0.761) 		0.0651
(0.63) 		0.509
(0.957) 		0.00169
(0.205) 		0.116
(0.689) 		0.592
(0.966) 		0.382
(0.922) 		0.96
(1.00) 		0.589
(0.966) 		1
(1.00) 		0.999
(1.00) 		0.101
(0.672) 		0.358
(0.912) 		0.656
(0.981) 		0.127
(0.703) 		0.681
(0.986) 		0.712
(0.993) 		0.418
(0.936) 		0.479
(0.953) 		0.974
(1.00) 		0.556
(0.963) 		0.367
(0.919) 		0.497
(0.957) 		0.968
(1.00) 		0.107
(0.678) 		1
(1.00) 		0.829
(1.00) 		0.082
(0.651) 		0.558
(0.963) 		0.994
(1.00)
amp 1p31 3 96 (33%) 199 0.244
(0.847) 		0.00423
(0.308) 		0.336
(0.899) 		0.86
(1.00) 		0.497
(0.957) 		0.862
(1.00) 		0.244
(0.847) 		0.193
(0.788) 		0.539
(0.961) 		0.471
(0.953) 		0.1
(0.672) 		0.767
(1.00) 		0.563
(0.963) 		0.878
(1.00) 		0.596
(0.966) 		0.193
(0.788) 		0.719
(0.995) 		0.825
(1.00) 		1
(1.00) 		0.0116
(0.384) 		0.386
(0.922) 		0.875
(1.00) 		0.271
(0.861) 		0.149
(0.745) 		0.93
(1.00) 		0.476
(0.953) 		0.0206
(0.427) 		0.861
(1.00) 		0.539
(0.961) 		0.518
(0.957) 		0.375
(0.922) 		0.501
(0.957) 		0.042
(0.516) 		0.36
(0.912) 		0.777
(1.00) 		0.788
(1.00) 		0.464
(0.953) 		0.00355
(0.291) 		0.394
(0.922)
amp 1q21 3 158 (54%) 137 0.464
(0.953) 		0.24
(0.845) 		0.0288
(0.475) 		0.635
(0.972) 		0.182
(0.778) 		0.512
(0.957) 		0.241
(0.845) 		0.722
(0.995) 		0.6
(0.966) 		0.00518
(0.329) 		0.505
(0.957) 		0.172
(0.772) 		0.138
(0.72) 		0.376
(0.922) 		0.723
(0.995) 		0.722
(0.995) 		0.885
(1.00) 		0.597
(0.966) 		0.56
(0.963) 		0.14
(0.727) 		0.482
(0.953) 		0.537
(0.96) 		0.219
(0.816) 		0.962
(1.00) 		0.00536
(0.329) 		0.734
(0.998) 		0.616
(0.968) 		0.62
(0.968) 		0.6
(0.966) 		0.914
(1.00) 		1
(1.00) 		0.733
(0.998) 		0.278
(0.864) 		0.0438
(0.526) 		0.612
(0.967) 		0.345
(0.906) 		0.291
(0.876) 		0.198
(0.79) 		0.329
(0.895)
amp 2p24 3 79 (27%) 216 0.811
(1.00) 		0.929
(1.00) 		0.615
(0.968) 		0.715
(0.995) 		0.48
(0.953) 		0.27
(0.861) 		0.544
(0.961) 		0.168
(0.761) 		0.476
(0.953) 		0.501
(0.957) 		1
(1.00) 		0.468
(0.953) 		0.543
(0.961) 		0.451
(0.953) 		0.138
(0.72) 		0.168
(0.761) 		0.474
(0.953) 		0.68
(0.986) 		1
(1.00) 		0.412
(0.927) 		0.178
(0.773) 		0.265
(0.857) 		0.409
(0.927) 		0.759
(1.00) 		0.0727
(0.642) 		0.795
(1.00) 		0.968
(1.00) 		0.706
(0.991) 		0.476
(0.953) 		0.609
(0.967) 		0.844
(1.00) 		0.822
(1.00) 		0.578
(0.966) 		0.665
(0.985) 		0.391
(0.922) 		0.5
(0.957) 		0.014
(0.417) 		0.897
(1.00) 		0.397
(0.924)
amp 2q33 1 41 (14%) 254 0.965
(1.00) 		0.29
(0.876) 		0.873
(1.00) 		0.0793
(0.65) 		1
(1.00) 		0.641
(0.974) 		0.553
(0.963) 		0.788
(1.00) 		0.0373
(0.513) 		0.309
(0.888) 		0.744
(1) 		0.0496
(0.541) 		0.848
(1.00) 		0.833
(1.00) 		0.447
(0.951) 		0.788
(1.00) 		0.915
(1.00) 		0.0667
(0.633) 		0.459
(0.953) 		0.633
(0.971) 		0.333
(0.896) 		0.684
(0.986) 		0.592
(0.966) 		0.559
(0.963) 		0.0206
(0.427) 		0.806
(1.00) 		0.624
(0.968) 		0.0478
(0.541) 		0.0373
(0.513) 		0.486
(0.957) 		0.605
(0.967) 		0.128
(0.703) 		0.213
(0.813) 		0.577
(0.966) 		0.411
(0.927) 		0.23
(0.828) 		0.268
(0.86) 		0.722
(0.995)
amp 3q26 31 227 (77%) 68 0.908
(1.00) 		0.779
(1.00) 		0.26
(0.857) 		0.0407
(0.513) 		1
(1.00) 		0.0676
(0.633) 		0.0101
(0.384) 		0.961
(1.00) 		0.013
(0.399) 		0.0157
(0.422) 		0.444
(0.951) 		0.116
(0.689) 		0.748
(1.00) 		0.811
(1.00) 		0.74
(1) 		0.961
(1.00) 		0.341
(0.906) 		0.0498
(0.541) 		0.382
(0.922) 		0.021
(0.427) 		0.147
(0.745) 		0.834
(1.00) 		0.0936
(0.667) 		0.471
(0.953) 		0.0484
(0.541) 		0.0854
(0.654) 		0.488
(0.957) 		0.249
(0.85) 		0.013
(0.399) 		0.572
(0.966) 		0.689
(0.986) 		0.551
(0.963) 		1
(1.00) 		0.249
(0.85) 		1
(1.00) 		0.0396
(0.513) 		0.836
(1.00) 		0.892
(1.00)
amp 4q12 21 (7%) 274 0.269
(0.86) 		0.553
(0.963) 		0.0423
(0.516) 		0.364
(0.917) 		0.519
(0.957) 		1
(1.00) 		0.413
(0.928) 		0.987
(1.00) 		0.827
(1.00) 		0.434
(0.948) 		1
(1.00) 		0.404
(0.927) 		1
(1.00) 		0.0957
(0.672) 		0.0683
(0.633) 		0.987
(1.00) 		0.313
(0.888) 		0.676
(0.986) 		1
(1.00) 		0.39
(0.922) 		0.515
(0.957) 		0.625
(0.968) 		0.282
(0.868) 		0.444
(0.951) 		0.786
(1.00) 		0.722
(0.995) 		0.697
(0.99) 		0.209
(0.805) 		0.827
(1.00) 		0.846
(1.00) 		0.725
(0.996) 		0.266
(0.857) 		0.0512
(0.544) 		0.77
(1.00) 		0.587
(0.966) 		1
(1.00) 		0.571
(0.966) 		0.572
(0.966) 		0.0726
(0.642)
amp 5p15 33 138 (47%) 157 0.991
(1.00) 		0.618
(0.968) 		0.174
(0.773) 		1
(1.00) 		0.0949
(0.671) 		0.143
(0.733) 		0.0103
(0.384) 		0.549
(0.963) 		0.894
(1.00) 		0.7
(0.991) 		0.269
(0.86) 		0.981
(1.00) 		0.683
(0.986) 		0.0406
(0.513) 		0.971
(1.00) 		0.549
(0.963) 		0.338
(0.9) 		0.446
(0.951) 		0.56
(0.963) 		0.205
(0.799) 		0.583
(0.966) 		0.872
(1.00) 		0.0102
(0.384) 		0.0896
(0.667) 		0.525
(0.957) 		0.582
(0.966) 		0.89
(1.00) 		0.495
(0.957) 		0.894
(1.00) 		0.114
(0.689) 		0.125
(0.703) 		0.394
(0.922) 		0.787
(1.00) 		0.946
(1.00) 		1
(1.00) 		0.0203
(0.427) 		0.665
(0.985) 		0.709
(0.992) 		0.0111
(0.384)
amp 6p21 33 82 (28%) 213 0.405
(0.927) 		0.866
(1.00) 		0.908
(1.00) 		0.477
(0.953) 		1
(1.00) 		0.859
(1.00) 		0.374
(0.922) 		0.155
(0.745) 		0.551
(0.963) 		0.789
(1.00) 		1
(1.00) 		0.506
(0.957) 		0.1
(0.672) 		0.0887
(0.666) 		0.944
(1.00) 		0.155
(0.745) 		0.135
(0.719) 		0.361
(0.912) 		1
(1.00) 		0.327
(0.893) 		0.843
(1.00) 		0.619
(0.968) 		0.354
(0.907) 		1
(1.00) 		0.104
(0.678) 		1
(1.00) 		0.415
(0.932) 		0.568
(0.966) 		0.551
(0.963) 		0.693
(0.99) 		0.846
(1.00) 		0.121
(0.7) 		0.227
(0.828) 		0.48
(0.953) 		0.234
(0.835) 		0.303
(0.885) 		0.562
(0.963) 		0.806
(1.00) 		0.444
(0.951)
amp 7p11 2 52 (18%) 243 0.121
(0.7) 		0.92
(1.00) 		0.0174
(0.425) 		0.17
(0.766) 		0.179
(0.775) 		0.199
(0.79) 		0.404
(0.927) 		0.0375
(0.513) 		0.0787
(0.65) 		0.528
(0.957) 		1
(1.00) 		0.23
(0.828) 		0.0231
(0.438) 		0.125
(0.703) 		0.489
(0.957) 		0.0375
(0.513) 		0.844
(1.00) 		0.345
(0.906) 		0.188
(0.788) 		0.354
(0.907) 		0.934
(1.00) 		0.148
(0.745) 		0.391
(0.922) 		0.596
(0.966) 		0.947
(1.00) 		0.14
(0.728) 		0.877
(1.00) 		0.0364
(0.513) 		0.0787
(0.65) 		0.788
(1.00) 		0.513
(0.957) 		0.193
(0.788) 		1
(1.00) 		0.885
(1.00) 		1
(1.00) 		1
(1.00) 		0.966
(1.00) 		0.0169
(0.425)
amp 8q24 21 127 (43%) 168 0.44
(0.949) 		0.591
(0.966) 		0.0676
(0.633) 		0.42
(0.938) 		0.32
(0.888) 		0.62
(0.968) 		0.229
(0.828) 		0.349
(0.907) 		0.47
(0.953) 		0.826
(1.00) 		1
(1.00) 		0.898
(1.00) 		0.218
(0.816) 		0.194
(0.788) 		0.257
(0.857) 		0.349
(0.907) 		0.436
(0.948) 		0.52
(0.957) 		0.543
(0.961) 		0.65
(0.979) 		0.582
(0.966) 		0.893
(1.00) 		0.721
(0.995) 		0.666
(0.985) 		0.48
(0.953) 		0.315
(0.888) 		0.693
(0.99) 		0.389
(0.922) 		0.47
(0.953) 		0.15
(0.745) 		0.865
(1.00) 		0.595
(0.966) 		0.288
(0.872) 		0.895
(1.00) 		0.194
(0.788) 		0.495
(0.957) 		0.961
(1.00) 		0.593
(0.966) 		0.184
(0.785)
amp 9p24 1 63 (21%) 232 0.195
(0.788) 		0.157
(0.745) 		0.188
(0.788) 		0.00505
(0.329) 		0.684
(0.986) 		0.33
(0.895) 		0.757
(1.00) 		0.0828
(0.651) 		0.0111
(0.384) 		0.0398
(0.513) 		0.771
(1.00) 		0.125
(0.703) 		0.313
(0.888) 		0.351
(0.907) 		0.394
(0.922) 		0.0828
(0.651) 		0.86
(1.00) 		0.548
(0.963) 		1
(1.00) 		0.423
(0.94) 		0.674
(0.986) 		0.112
(0.689) 		0.0545
(0.558) 		0.235
(0.835) 		0.99
(1.00) 		0.524
(0.957) 		0.441
(0.949) 		0.228
(0.828) 		0.0111
(0.384) 		0.185
(0.785) 		0.136
(0.719) 		0.011
(0.384) 		0.16
(0.754) 		0.459
(0.953) 		0.734
(0.998) 		0.266
(0.857) 		0.85
(1.00) 		0.14
(0.727) 		0.252
(0.857)
amp 11p12 23 (8%) 272 0.596
(0.966) 		0.027
(0.472) 		0.263
(0.857) 		0.312
(0.888) 		0.563
(0.963) 		0.558
(0.963) 		0.639
(0.974) 		0.261
(0.857) 		0.0389
(0.513) 		0.298
(0.881) 		0.0451
(0.532) 		0.0754
(0.648) 		0.317
(0.888) 		0.26
(0.857) 		0.261
(0.857) 		0.982
(1.00) 		0.679
(0.986) 		0.459
(0.953) 		0.102
(0.677) 		0.515
(0.957) 		0.426
(0.942) 		0.627
(0.97) 		0.322
(0.888) 		0.197
(0.79) 		0.633
(0.971) 		0.32
(0.888) 		0.0389
(0.513) 		0.971
(1.00) 		0.284
(0.869) 		0.5
(0.957) 		0.188
(0.788) 		0.427
(0.943) 		1
(1.00) 		0.346
(0.906) 		0.659
(0.985) 		0.0248
(0.453) 		0.806
(1.00)
amp 11q13 3 41 (14%) 254 0.962
(1.00) 		0.344
(0.906) 		0.945
(1.00) 		0.452
(0.953) 		0.614
(0.968) 		0.809
(1.00) 		0.622
(0.968) 		0.0373
(0.513) 		0.219
(0.816) 		0.421
(0.939) 		0.32
(0.888) 		0.107
(0.678) 		0.842
(1.00) 		0.0146
(0.422) 		1
(1.00) 		0.0373
(0.513) 		0.717
(0.995) 		0.207
(0.802) 		1
(1.00) 		0.814
(1.00) 		0.333
(0.896) 		0.755
(1.00) 		0.813
(1.00) 		0.663
(0.985) 		0.63
(0.97) 		1
(1.00) 		0.683
(0.986) 		0.453
(0.953) 		0.219
(0.816) 		0.388
(0.922) 		0.466
(0.953) 		0.181
(0.778) 		0.548
(0.963) 		0.87
(1.00) 		0.69
(0.986) 		0.424
(0.942) 		0.0677
(0.633) 		0.324
(0.889) 		0.39
(0.922)
amp 13q22 1 65 (22%) 230 0.469
(0.953) 		0.447
(0.951) 		0.127
(0.703) 		0.696
(0.99) 		0.115
(0.689) 		0.697
(0.99) 		0.708
(0.992) 		0.354
(0.907) 		0.1
(0.672) 		0.728
(0.996) 		0.0303
(0.49) 		0.634
(0.972) 		0.106
(0.678) 		0.764
(1.00) 		0.913
(1.00) 		0.354
(0.907) 		0.0946
(0.671) 		0.0929
(0.667) 		0.53
(0.957) 		0.857
(1.00) 		0.683
(0.986) 		0.514
(0.957) 		0.609
(0.967) 		0.143
(0.733) 		0.927
(1.00) 		0.373
(0.922) 		0.883
(1.00) 		0.0729
(0.642) 		0.1
(0.672) 		0.48
(0.953) 		0.671
(0.986) 		0.455
(0.953) 		0.316
(0.888) 		0.516
(0.957) 		0.516
(0.957) 		0.45
(0.953) 		0.494
(0.957) 		0.107
(0.678)
amp 13q34 69 (23%) 226 0.46
(0.953) 		0.882
(1.00) 		0.973
(1.00) 		1
(1.00) 		1
(1.00) 		0.854
(1.00) 		0.74
(1) 		0.94
(1.00) 		0.48
(0.953) 		0.733
(0.998) 		0.298
(0.881) 		0.974
(1.00) 		0.427
(0.942) 		0.216
(0.816) 		0.211
(0.807) 		0.94
(1.00) 		0.0201
(0.427) 		0.629
(0.97) 		0.0452
(0.532) 		0.831
(1.00) 		0.54
(0.961) 		0.46
(0.953) 		0.644
(0.976) 		0.747
(1.00) 		0.0344
(0.507) 		0.509
(0.957) 		0.565
(0.964) 		0.154
(0.745) 		0.48
(0.953) 		0.687
(0.986) 		0.156
(0.745) 		0.473
(0.953) 		1
(1.00) 		0.455
(0.953) 		0.186
(0.788) 		0.2
(0.792) 		0.936
(1.00) 		0.631
(0.97)
amp 15q26 1 76 (26%) 219 0.789
(1.00) 		0.0313
(0.493) 		0.115
(0.689) 		0.463
(0.953) 		0.114
(0.689) 		0.193
(0.788) 		0.132
(0.711) 		0.86
(1.00) 		0.82
(1.00) 		0.223
(0.826) 		0.62
(0.968) 		0.857
(1.00) 		0.536
(0.959) 		0.203
(0.796) 		0.296
(0.88) 		0.86
(1.00) 		0.943
(1.00) 		0.623
(0.968) 		1
(1.00) 		0.0363
(0.513) 		0.801
(1.00) 		0.652
(0.979) 		0.0484
(0.541) 		0.151
(0.745) 		0.372
(0.922) 		0.226
(0.828) 		0.333
(0.896) 		0.701
(0.991) 		0.82
(1.00) 		0.889
(1.00) 		1
(1.00) 		0.721
(0.995) 		0.069
(0.635) 		0.264
(0.857) 		0.552
(0.963) 		1
(1.00) 		0.193
(0.788) 		0.026
(0.464) 		0.504
(0.957)
amp 16p13 13 65 (22%) 230 0.562
(0.963) 		0.427
(0.942) 		0.115
(0.689) 		0.252
(0.857) 		0.69
(0.986) 		0.312
(0.888) 		0.996
(1.00) 		0.313
(0.888) 		0.0847
(0.651) 		0.292
(0.876) 		0.771
(1.00) 		0.394
(0.922) 		0.318
(0.888) 		0.882
(1.00) 		0.166
(0.761) 		0.313
(0.888) 		0.951
(1.00) 		0.531
(0.957) 		1
(1.00) 		0.0148
(0.422) 		0.683
(0.986) 		0.597
(0.966) 		0.0216
(0.427) 		0.701
(0.991) 		0.0215
(0.427) 		0.489
(0.957) 		0.344
(0.906) 		0.561
(0.963) 		0.0847
(0.651) 		0.517
(0.957) 		1
(1.00) 		0.303
(0.885) 		0.193
(0.788) 		0.508
(0.957) 		0.351
(0.907) 		0.257
(0.857) 		0.469
(0.953) 		0.748
(1.00)
amp 17q12 55 (19%) 240 0.93
(1.00) 		0.707
(0.992) 		0.243
(0.847) 		0.661
(0.985) 		1
(1.00) 		0.56
(0.963) 		0.112
(0.689) 		0.19
(0.788) 		0.315
(0.888) 		0.853
(1.00) 		0.385
(0.922) 		0.575
(0.966) 		0.606
(0.967) 		0.137
(0.72) 		0.156
(0.745) 		0.19
(0.788) 		0.235
(0.835) 		0.668
(0.985) 		1
(1.00) 		0.0822
(0.651) 		0.261
(0.857) 		0.256
(0.857) 		0.261
(0.857) 		0.269
(0.86) 		0.421
(0.938) 		0.651
(0.979) 		0.984
(1.00) 		0.663
(0.985) 		0.315
(0.888) 		0.736
(0.999) 		0.466
(0.953) 		0.672
(0.986) 		0.91
(1.00) 		0.0814
(0.651) 		1
(1.00) 		1
(1.00) 		0.396
(0.923) 		0.75
(1.00) 		0.847
(1.00)
amp 17q25 1 74 (25%) 221 0.757
(1.00) 		0.819
(1.00) 		0.157
(0.745) 		0.263
(0.857) 		0.258
(0.857) 		0.853
(1.00) 		0.0848
(0.651) 		0.21
(0.807) 		0.0609
(0.606) 		0.583
(0.966) 		0.322
(0.888) 		0.36
(0.912) 		0.533
(0.957) 		0.0857
(0.654) 		0.828
(1.00) 		0.21
(0.807) 		0.361
(0.912) 		0.256
(0.857) 		1
(1.00) 		0.177
(0.773) 		0.166
(0.761) 		0.844
(1.00) 		0.181
(0.778) 		0.35
(0.907) 		0.429
(0.943) 		0.919
(1.00) 		0.804
(1.00) 		0.0796
(0.65) 		0.0609
(0.606) 		0.397
(0.924) 		0.105
(0.678) 		0.903
(1.00) 		0.398
(0.924) 		0.482
(0.953) 		0.774
(1.00) 		1
(1.00) 		0.396
(0.923) 		0.877
(1.00) 		0.225
(0.828)
amp 19p13 3 39 (13%) 256 0.226
(0.828) 		0.338
(0.9) 		0.371
(0.922) 		0.36
(0.912) 		0.596
(0.966) 		1
(1.00) 		0.898
(1.00) 		0.585
(0.966) 		0.0834
(0.651) 		0.845
(1.00) 		1
(1.00) 		0.506
(0.957) 		0.683
(0.986) 		0.862
(1.00) 		0.586
(0.966) 		0.585
(0.966) 		0.532
(0.957) 		0.0407
(0.513) 		1
(1.00) 		0.32
(0.888) 		0.816
(1.00) 		0.278
(0.864) 		0.0286
(0.475) 		0.0818
(0.651) 		0.703
(0.991) 		1
(1.00) 		0.742
(1) 		0.1
(0.672) 		0.0834
(0.651) 		0.52
(0.957) 		0.0205
(0.427) 		0.891
(1.00) 		0.197
(0.79) 		0.0537
(0.555) 		1
(1.00) 		1
(1.00) 		0.659
(0.985) 		0.288
(0.872) 		0.217
(0.816)
amp 19q13 13 93 (32%) 202 0.462
(0.953) 		0.119
(0.698) 		0.0319
(0.493) 		0.0846
(0.651) 		0.277
(0.864) 		0.593
(0.966) 		0.516
(0.957) 		0.756
(1.00) 		0.106
(0.678) 		0.828
(1.00) 		0.346
(0.906) 		0.871
(1.00) 		0.466
(0.953) 		0.773
(1.00) 		0.806
(1.00) 		0.756
(1.00) 		0.988
(1.00) 		0.514
(0.957) 		0.56
(0.963) 		0.124
(0.701) 		0.757
(1.00) 		0.0511
(0.544) 		0.0439
(0.526) 		0.704
(0.991) 		0.135
(0.719) 		0.116
(0.689) 		0.327
(0.892) 		0.281
(0.868) 		0.106
(0.678) 		0.331
(0.895) 		0.144
(0.736) 		0.475
(0.953) 		0.6
(0.966) 		0.606
(0.967) 		0.253
(0.857) 		0.846
(1.00) 		0.753
(1.00) 		0.114
(0.689) 		0.167
(0.761)
amp 20q11 21 135 (46%) 160 0.596
(0.966) 		0.0273
(0.472) 		0.0113
(0.384) 		0.336
(0.899) 		0.341
(0.906) 		0.514
(0.957) 		0.654
(0.979) 		0.918
(1.00) 		0.208
(0.804) 		0.0313
(0.493) 		0.115
(0.689) 		0.153
(0.745) 		0.686
(0.986) 		0.644
(0.976) 		0.678
(0.986) 		0.918
(1.00) 		0.412
(0.928) 		0.674
(0.986) 		0.56
(0.963) 		0.0681
(0.633) 		0.726
(0.996) 		0.967
(1.00) 		0.166
(0.761) 		0.791
(1.00) 		0.526
(0.957) 		0.439
(0.949) 		0.215
(0.816) 		0.739
(1) 		0.208
(0.804) 		0.581
(0.966) 		0.388
(0.922) 		0.294
(0.876) 		0.785
(1.00) 		0.407
(0.927) 		0.609
(0.967) 		0.412
(0.927) 		0.493
(0.957) 		0.0198
(0.427) 		0.549
(0.963)
amp 21q22 13 48 (16%) 247 0.282
(0.868) 		0.163
(0.761) 		0.272
(0.864) 		1
(1.00) 		1
(1.00) 		0.665
(0.985) 		0.519
(0.957) 		0.748
(1.00) 		0.776
(1.00) 		0.955
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.258
(0.857) 		0.242
(0.845) 		0.53
(0.957) 		0.748
(1.00) 		0.481
(0.953) 		0.892
(1.00) 		0.459
(0.953) 		0.998
(1.00) 		0.328
(0.895) 		0.814
(1.00) 		0.982
(1.00) 		0.404
(0.927) 		0.947
(1.00) 		0.0984
(0.672) 		0.383
(0.922) 		1
(1.00) 		0.776
(1.00) 		0.637
(0.973) 		0.0393
(0.513) 		0.945
(1.00) 		0.439
(0.949) 		0.472
(0.953) 		0.686
(0.986) 		1
(1.00) 		0.96
(1.00) 		0.178
(0.773) 		0.234
(0.835)
amp xq28 75 (25%) 220 0.0529
(0.554) 		0.343
(0.906) 		0.12
(0.7) 		0.273
(0.864) 		0.448
(0.951) 		0.0227
(0.436) 		0.0887
(0.666) 		0.523
(0.957) 		0.571
(0.966) 		0.121
(0.7) 		0.789
(1.00) 		0.879
(1.00) 		0.639
(0.974) 		0.429
(0.943) 		0.107
(0.678) 		0.523
(0.957) 		0.684
(0.986) 		0.425
(0.942) 		0.459
(0.953) 		0.299
(0.883) 		0.8
(1.00) 		0.448
(0.951) 		0.351
(0.907) 		0.895
(1.00) 		0.756
(1.00) 		0.72
(0.995) 		0.588
(0.966) 		1
(1.00) 		0.571
(0.966) 		0.824
(1.00) 		0.544
(0.961) 		0.0738
(0.645) 		0.525
(0.957) 		0.276
(0.864) 		0.553
(0.963) 		1
(1.00) 		0.955
(1.00) 		0.308
(0.888) 		0.671
(0.986)
del 1p36 23 40 (14%) 255 0.653
(0.979) 		0.0644
(0.629) 		0.572
(0.966) 		0.797
(1.00) 		0.08
(0.651) 		0.316
(0.888) 		0.00757
(0.384) 		0.0174
(0.425) 		0.894
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.686
(0.986) 		0.319
(0.888) 		0.663
(0.985) 		0.864
(1.00) 		0.0174
(0.425) 		0.794
(1.00) 		0.366
(0.919) 		0.53
(0.957) 		0.796
(1.00) 		0.874
(1.00) 		0.387
(0.922) 		0.474
(0.953) 		0.426
(0.942) 		0.684
(0.986) 		0.574
(0.966) 		0.356
(0.909) 		0.8
(1.00) 		0.894
(1.00) 		0.273
(0.864) 		0.357
(0.91) 		0.28
(0.868) 		0.761
(1.00) 		0.326
(0.891) 		0.463
(0.953) 		0.254
(0.857) 		0.0716
(0.642) 		0.507
(0.957)
del 1p13 2 34 (12%) 261 0.0683
(0.633) 		0.97
(1.00) 		0.726
(0.996) 		0.281
(0.868) 		0.115
(0.689) 		1
(1.00) 		0.788
(1.00) 		0.696
(0.99) 		0.577
(0.966) 		0.76
(1.00) 		1
(1.00) 		0.937
(1.00) 		0.0893
(0.667) 		0.546
(0.962) 		0.696
(0.99) 		0.882
(1.00) 		0.247
(0.848) 		1
(1.00) 		0.0782
(0.65) 		0.483
(0.953) 		0.0755
(0.648) 		0.551
(0.963) 		0.0726
(0.642) 		0.898
(1.00) 		0.805
(1.00) 		0.636
(0.972) 		0.527
(0.957) 		0.577
(0.966) 		0.919
(1.00) 		0.0561
(0.57) 		0.0773
(0.649) 		0.548
(0.963) 		0.457
(0.953) 		1
(1.00) 		0.176
(0.773) 		0.995
(1.00) 		0.453
(0.953)
del 2q22 1 65 (22%) 230 0.759
(1.00) 		0.566
(0.965) 		0.411
(0.927) 		0.85
(1.00) 		1
(1.00) 		0.44
(0.949) 		0.43
(0.944) 		0.303
(0.885) 		0.611
(0.967) 		0.198
(0.79) 		0.598
(0.966) 		0.704
(0.991) 		1
(1.00) 		0.265
(0.857) 		0.332
(0.896) 		0.303
(0.885) 		0.841
(1.00) 		0.23
(0.828) 		0.551
(0.963) 		0.989
(1.00) 		0.888
(1.00) 		0.673
(0.986) 		0.293
(0.876) 		0.0581
(0.583) 		0.816
(1.00) 		0.542
(0.961) 		0.353
(0.907) 		0.424
(0.942) 		0.611
(0.967) 		0.118
(0.695) 		0.844
(1.00) 		0.378
(0.922) 		0.421
(0.938) 		0.331
(0.895) 		0.021
(0.427) 		1
(1.00) 		0.225
(0.828) 		0.522
(0.957) 		0.498
(0.957)
del 2q37 1 129 (44%) 166 0.938
(1.00) 		0.0104
(0.384) 		0.48
(0.953) 		0.521
(0.957) 		0.182
(0.778) 		0.743
(1) 		0.0507
(0.544) 		0.592
(0.966) 		0.47
(0.953) 		0.544
(0.961) 		0.501
(0.957) 		0.338
(0.9) 		0.586
(0.966) 		0.981
(1.00) 		0.0141
(0.417) 		0.592
(0.966) 		0.192
(0.788) 		0.399
(0.925) 		0.56
(0.963) 		0.911
(1.00) 		0.19
(0.788) 		0.646
(0.977) 		0.882
(1.00) 		0.344
(0.906) 		0.973
(1.00) 		0.242
(0.845) 		0.311
(0.888) 		1
(1.00) 		0.47
(0.953) 		0.00432
(0.308) 		0.612
(0.967) 		0.989
(1.00) 		0.744
(1) 		0.852
(1.00) 		0.3
(0.883) 		0.683
(0.986) 		0.96
(1.00) 		0.0158
(0.422) 		0.708
(0.992)
del 4q21 3 103 (35%) 192 0.132
(0.714) 		0.966
(1.00) 		0.269
(0.86) 		0.0101
(0.384) 		0.0937
(0.667) 		0.0167
(0.425) 		0.0291
(0.477) 		0.63
(0.97) 		0.00863
(0.384) 		0.114
(0.689) 		1
(1.00) 		0.00439
(0.308) 		0.118
(0.695) 		0.0112
(0.384) 		0.287
(0.872) 		0.63
(0.97) 		0.195
(0.788) 		0.798
(1.00) 		1
(1.00) 		0.673
(0.986) 		0.616
(0.968) 		0.446
(0.951) 		0.247
(0.848) 		0.365
(0.919) 		0.641
(0.974) 		0.296
(0.88) 		0.954
(1.00) 		0.479
(0.953) 		0.00863
(0.384) 		0.351
(0.907) 		0.599
(0.966) 		0.247
(0.848) 		0.747
(1.00) 		0.705
(0.991) 		0.149
(0.745) 		0.696
(0.99) 		0.157
(0.745) 		0.981
(1.00) 		0.363
(0.916)
del 4q35 2 114 (39%) 181 0.618
(0.968) 		0.32
(0.888) 		0.292
(0.876) 		0.319
(0.888) 		1
(1.00) 		0.0454
(0.532) 		0.0746
(0.648) 		0.175
(0.773) 		0.304
(0.885) 		0.737
(0.999) 		0.177
(0.773) 		0.205
(0.799) 		0.89
(1.00) 		0.0186
(0.427) 		0.305
(0.885) 		0.175
(0.773) 		0.735
(0.998) 		0.219
(0.816) 		0.56
(0.963) 		0.656
(0.981) 		0.0618
(0.612) 		0.27
(0.861) 		0.703
(0.991) 		0.598
(0.966) 		0.805
(1.00) 		0.442
(0.949) 		0.278
(0.864) 		0.605
(0.967) 		0.304
(0.885) 		0.564
(0.964) 		0.392
(0.922) 		0.395
(0.923) 		0.408
(0.927) 		0.616
(0.968) 		0.786
(1.00) 		0.689
(0.986) 		0.393
(0.922) 		0.326
(0.891) 		0.511
(0.957)
del 5q12 1 76 (26%) 219 0.0535
(0.555) 		0.963
(1.00) 		0.5
(0.957) 		0.263
(0.857) 		1
(1.00) 		1
(1.00) 		0.525
(0.957) 		0.13
(0.709) 		0.0667
(0.633) 		0.834
(1.00) 		0.447
(0.951) 		0.0401
(0.513) 		0.167
(0.761) 		0.513
(0.957) 		0.0487
(0.541) 		0.13
(0.709) 		0.718
(0.995) 		0.402
(0.927) 		1
(1.00) 		0.466
(0.953) 		0.155
(0.745) 		0.189
(0.788) 		0.775
(1.00) 		0.0913
(0.667) 		0.959
(1.00) 		0.775
(1.00) 		0.721
(0.995) 		0.182
(0.778) 		0.0667
(0.633) 		0.848
(1.00) 		0.704
(0.991) 		0.245
(0.847) 		0.927
(1.00) 		0.768
(1.00) 		1
(1.00) 		0.257
(0.857) 		0.0307
(0.492) 		0.93
(1.00) 		0.179
(0.776)
del 5q35 2 71 (24%) 224 0.594
(0.966) 		0.536
(0.959) 		0.137
(0.72) 		0.709
(0.992) 		0.283
(0.868) 		0.841
(1.00) 		0.324
(0.889) 		0.367
(0.919) 		0.0318
(0.493) 		0.884
(1.00) 		1
(1.00) 		0.305
(0.885) 		0.753
(1.00) 		0.168
(0.761) 		0.41
(0.927) 		0.367
(0.919) 		0.994
(1.00) 		0.924
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.166
(0.761) 		0.278
(0.864) 		0.629
(0.97) 		0.0477
(0.541) 		0.53
(0.957) 		0.528
(0.957) 		0.979
(1.00) 		0.131
(0.71) 		0.0318
(0.493) 		0.91
(1.00) 		0.186
(0.788) 		0.745
(1) 		0.82
(1.00) 		0.385
(0.922) 		0.776
(1.00) 		0.316
(0.888) 		0.209
(0.805) 		0.567
(0.966) 		0.401
(0.927)
del 6p24 2 46 (16%) 249 0.789
(1.00) 		0.848
(1.00) 		0.785
(1.00) 		0.277
(0.864) 		0.686
(0.986) 		0.823
(1.00) 		0.125
(0.703) 		0.394
(0.922) 		0.136
(0.719) 		0.508
(0.957) 		0.536
(0.959) 		0.294
(0.876) 		0.353
(0.907) 		0.856
(1.00) 		0.106
(0.678) 		0.394
(0.922) 		0.845
(1.00) 		1
(1.00) 		1
(1.00) 		0.467
(0.953) 		0.454
(0.953) 		0.111
(0.689) 		0.607
(0.967) 		0.331
(0.895) 		0.819
(1.00) 		0.598
(0.966) 		0.407
(0.927) 		0.383
(0.922) 		0.136
(0.719) 		0.194
(0.788) 		0.51
(0.957) 		0.224
(0.828) 		0.382
(0.922) 		0.474
(0.953) 		0.519
(0.957) 		0.714
(0.994) 		0.0376
(0.513) 		0.808
(1.00) 		0.985
(1.00)
del 7q34 60 (20%) 235 0.203
(0.797) 		0.0863
(0.654) 		0.555
(0.963) 		0.219
(0.816) 		1
(1.00) 		0.683
(0.986) 		0.775
(1.00) 		0.112
(0.689) 		0.0217
(0.427) 		0.931
(1.00) 		0.604
(0.967) 		0.735
(0.998) 		0.407
(0.927) 		0.743
(1) 		0.856
(1.00) 		0.112
(0.689) 		0.778
(1.00) 		0.249
(0.85) 		0.583
(0.966) 		0.776
(1.00) 		0.202
(0.796) 		0.776
(1.00) 		0.612
(0.967) 		0.092
(0.667) 		0.287
(0.872) 		0.841
(1.00) 		0.75
(1.00) 		0.216
(0.816) 		0.0217
(0.427) 		0.349
(0.907) 		0.418
(0.936) 		0.72
(0.995) 		0.75
(1.00) 		0.697
(0.99) 		0.755
(1.00) 		0.796
(1.00) 		0.591
(0.966) 		0.077
(0.648) 		0.854
(1.00)
del 8p23 3 104 (35%) 191 0.00681
(0.38) 		0.264
(0.857) 		0.891
(1.00) 		0.502
(0.957) 		0.732
(0.998) 		0.728
(0.996) 		0.937
(1.00) 		0.529
(0.957) 		0.3
(0.883) 		0.793
(1.00) 		1
(1.00) 		0.924
(1.00) 		0.048
(0.541) 		0.437
(0.948) 		0.199
(0.79) 		0.529
(0.957) 		0.0998
(0.672) 		0.0338
(0.506) 		1
(1.00) 		0.84
(1.00) 		0.966
(1.00) 		0.164
(0.761) 		0.979
(1.00) 		0.68
(0.986) 		0.986
(1.00) 		0.544
(0.961) 		0.917
(1.00) 		0.153
(0.745) 		0.3
(0.883) 		0.519
(0.957) 		0.215
(0.816) 		0.319
(0.888) 		0.491
(0.957) 		0.748
(1.00) 		0.596
(0.966) 		1
(1.00) 		0.136
(0.719) 		0.23
(0.828) 		0.575
(0.966)
del 8p23 1 97 (33%) 198 0.012
(0.389) 		0.166
(0.761) 		0.955
(1.00) 		0.498
(0.957) 		0.725
(0.996) 		0.373
(0.922) 		0.782
(1.00) 		0.318
(0.888) 		0.236
(0.835) 		0.323
(0.889) 		0.812
(1.00) 		0.857
(1.00) 		0.0153
(0.422) 		0.237
(0.837) 		0.0219
(0.427) 		0.318
(0.888) 		0.159
(0.749) 		0.123
(0.701) 		0.56
(0.963) 		0.789
(1.00) 		0.757
(1.00) 		0.197
(0.79) 		0.968
(1.00) 		1
(1.00) 		0.698
(0.99) 		0.671
(0.986) 		0.907
(1.00) 		0.101
(0.674) 		0.236
(0.835) 		0.433
(0.948) 		0.367
(0.919) 		0.779
(1.00) 		0.967
(1.00) 		0.776
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.13
(0.709) 		0.145
(0.738) 		0.44
(0.949)
del 11q23 3 162 (55%) 133 0.998
(1.00) 		0.0145
(0.422) 		0.786
(1.00) 		0.749
(1.00) 		0.741
(1) 		1
(1.00) 		0.0116
(0.384) 		0.599
(0.966) 		0.671
(0.986) 		0.198
(0.79) 		0.191
(0.788) 		0.731
(0.998) 		0.278
(0.864) 		0.768
(1.00) 		0.902
(1.00) 		0.599
(0.966) 		0.886
(1.00) 		0.03
(0.487) 		1
(1.00) 		0.151
(0.745) 		0.482
(0.953) 		0.771
(1.00) 		0.393
(0.922) 		0.67
(0.986) 		0.0343
(0.507) 		0.492
(0.957) 		0.0334
(0.504) 		0.134
(0.719) 		0.671
(0.986) 		0.5
(0.957) 		0.864
(1.00) 		0.0382
(0.513) 		0.501
(0.957) 		0.897
(1.00) 		0.437
(0.948) 		0.33
(0.895) 		0.661
(0.985) 		0.0216
(0.427) 		0.0083
(0.384)
del 11q25 160 (54%) 135 0.41
(0.927) 		0.15
(0.745) 		0.625
(0.968) 		0.873
(1.00) 		0.739
(1) 		1
(1.00) 		0.019
(0.427) 		0.71
(0.992) 		0.885
(1.00) 		0.175
(0.773) 		0.0768
(0.648) 		0.677
(0.986) 		0.106
(0.678) 		0.685
(0.986) 		0.618
(0.968) 		0.71
(0.992) 		0.6
(0.966) 		0.0564
(0.57) 		1
(1.00) 		0.262
(0.857) 		0.482
(0.953) 		0.771
(1.00) 		0.696
(0.99) 		0.469
(0.953) 		0.0343
(0.507) 		0.486
(0.957) 		0.12
(0.7) 		0.0671
(0.633) 		0.885
(1.00) 		0.643
(0.976) 		1
(1.00) 		0.0182
(0.427) 		0.838
(1.00) 		0.419
(0.936) 		0.437
(0.948) 		0.334
(0.897) 		0.807
(1.00) 		0.195
(0.788) 		0.0227
(0.436)
del 13q12 11 98 (33%) 197 0.294
(0.878) 		0.954
(1.00) 		0.0796
(0.65) 		0.0796
(0.65) 		0.288
(0.872) 		1
(1.00) 		0.00306
(0.274) 		0.58
(0.966) 		0.0114
(0.384) 		0.09
(0.667) 		0.346
(0.906) 		0.126
(0.703) 		0.394
(0.922) 		0.0846
(0.651) 		0.664
(0.985) 		0.58
(0.966) 		0.229
(0.828) 		0.109
(0.685) 		1
(1.00) 		0.149
(0.745) 		0.967
(1.00) 		0.583
(0.966) 		0.195
(0.788) 		0.665
(0.985) 		0.252
(0.857) 		0.665
(0.985) 		0.79
(1.00) 		0.288
(0.872) 		0.0114
(0.384) 		0.473
(0.953) 		0.723
(0.995) 		0.0232
(0.438) 		0.64
(0.974) 		0.572
(0.966) 		0.253
(0.857) 		0.262
(0.857) 		0.317
(0.888) 		0.91
(1.00) 		0.00983
(0.384)
del 13q14 2 118 (40%) 177 0.213
(0.813) 		0.126
(0.703) 		0.00531
(0.329) 		0.0459
(0.532) 		0.517
(0.957) 		0.325
(0.891) 		0.0181
(0.427) 		0.322
(0.888) 		0.0151
(0.422) 		0.0198
(0.427) 		0.646
(0.977) 		0.95
(1.00) 		0.168
(0.761) 		0.00951
(0.384) 		0.0406
(0.513) 		0.322
(0.888) 		0.0175
(0.425) 		0.0361
(0.513) 		1
(1.00) 		0.033
(0.5) 		0.967
(1.00) 		0.526
(0.957) 		0.00826
(0.384) 		0.473
(0.953) 		0.0366
(0.513) 		0.732
(0.998) 		0.922
(1.00) 		0.385
(0.922) 		0.0151
(0.422) 		0.667
(0.985) 		0.731
(0.998) 		0.0384
(0.513) 		0.825
(1.00) 		0.384
(0.922) 		0.0913
(0.667) 		0.0844
(0.651) 		0.651
(0.979) 		0.0961
(0.672) 		0.0126
(0.397)
del 14q32 31 50 (17%) 245 0.629
(0.97) 		0.102
(0.676) 		0.703
(0.991) 		1
(1.00) 		0.117
(0.694) 		0.82
(1.00) 		0.0979
(0.672) 		0.44
(0.949) 		0.278
(0.864) 		0.629
(0.97) 		0.756
(1.00) 		0.933
(1.00) 		0.45
(0.953) 		0.0118
(0.387) 		0.938
(1.00) 		0.44
(0.949) 		0.162
(0.761) 		0.956
(1.00) 		1
(1.00) 		0.0813
(0.651) 		0.377
(0.922) 		0.446
(0.951) 		0.289
(0.874) 		0.172
(0.772) 		0.517
(0.957) 		1
(1.00) 		0.0732
(0.642) 		0.506
(0.957) 		0.278
(0.864) 		0.474
(0.953) 		0.813
(1.00) 		0.525
(0.957) 		0.387
(0.922) 		0.625
(0.968) 		1
(1.00) 		0.345
(0.906) 		0.114
(0.689) 		0.789
(1.00)
del 15q21 1 70 (24%) 225 0.768
(1.00) 		0.0112
(0.384) 		0.216
(0.816) 		0.234
(0.835) 		0.393
(0.922) 		0.181
(0.778) 		0.00583
(0.333) 		0.785
(1.00) 		0.59
(0.966) 		0.0275
(0.472) 		1
(1.00) 		0.924
(1.00) 		0.753
(1.00) 		0.0106
(0.384) 		0.155
(0.745) 		0.785
(1.00) 		0.41
(0.927) 		0.715
(0.995) 		1
(1.00) 		0.849
(1.00) 		0.93
(1.00) 		0.0752
(0.648) 		0.314
(0.888) 		0.863
(1.00) 		0.844
(1.00) 		0.936
(1.00) 		0.0568
(0.572) 		0.818
(1.00) 		0.59
(0.966) 		0.432
(0.948) 		0.513
(0.957) 		0.673
(0.986) 		0.376
(0.922) 		0.643
(0.976) 		0.724
(0.995) 		0.292
(0.876) 		0.733
(0.998) 		0.0135
(0.41) 		0.132
(0.711)
del 17p12 109 (37%) 186 0.329
(0.895) 		0.0195
(0.427) 		0.833
(1.00) 		0.604
(0.967) 		1
(1.00) 		0.743
(1) 		0.573
(0.966) 		0.526
(0.957) 		0.93
(1.00) 		0.168
(0.761) 		0.646
(0.977) 		0.198
(0.79) 		0.0259
(0.464) 		0.0532
(0.554) 		0.715
(0.995) 		0.526
(0.957) 		0.17
(0.767) 		0.434
(0.948) 		1
(1.00) 		0.832
(1.00) 		0.46
(0.953) 		0.69
(0.986) 		0.157
(0.745) 		0.0493
(0.541) 		0.632
(0.971) 		0.815
(1.00) 		0.613
(0.968) 		1
(1.00) 		0.93
(1.00) 		0.405
(0.927) 		0.602
(0.966) 		0.621
(0.968) 		0.267
(0.857) 		0.411
(0.927) 		0.787
(1.00) 		0.69
(0.986) 		0.119
(0.699) 		0.0249
(0.453) 		0.704
(0.991)
del 17q25 3 51 (17%) 244 0.459
(0.953) 		0.703
(0.991) 		0.988
(1.00) 		0.409
(0.927) 		0.649
(0.979) 		0.654
(0.979) 		0.105
(0.678) 		0.245
(0.847) 		0.763
(1.00) 		0.258
(0.857) 		1
(1.00) 		0.492
(0.957) 		0.585
(0.966) 		0.308
(0.888) 		0.343
(0.906) 		0.245
(0.847) 		0.353
(0.907) 		0.373
(0.922) 		1
(1.00) 		0.948
(1.00) 		0.314
(0.888) 		0.434
(0.948) 		0.805
(1.00) 		0.574
(0.966) 		0.149
(0.745) 		0.85
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.763
(1.00) 		0.259
(0.857) 		0.678
(0.986) 		0.738
(1) 		1
(1.00) 		0.156
(0.745) 		0.458
(0.953) 		1
(1.00) 		0.958
(1.00) 		0.523
(0.957) 		0.425
(0.942)
del 19q13 33 38 (13%) 257 0.399
(0.925) 		0.199
(0.79) 		0.95
(1.00) 		0.81
(1.00) 		0.614
(0.968) 		1
(1.00) 		0.112
(0.689) 		0.401
(0.927) 		0.766
(1.00) 		0.457
(0.953) 		0.471
(0.953) 		0.478
(0.953) 		0.689
(0.986) 		0.122
(0.701) 		0.835
(1.00) 		0.401
(0.927) 		0.956
(1.00) 		0.0966
(0.672) 		1
(1.00) 		0.708
(0.992) 		0.333
(0.896) 		0.855
(1.00) 		0.388
(0.922) 		0.141
(0.728) 		0.684
(0.986) 		1
(1.00) 		0.314
(0.888) 		1
(1.00) 		0.766
(1.00) 		0.735
(0.998) 		0.77
(1.00) 		0.484
(0.955) 		0.666
(0.985) 		0.916
(1.00) 		0.458
(0.953) 		0.278
(0.864) 		0.659
(0.985) 		0.218
(0.816) 		0.253
(0.857)
del 20p12 1 36 (12%) 259 0.158
(0.745) 		0.282
(0.868) 		0.564
(0.964) 		0.639
(0.974) 		1
(1.00) 		0.229
(0.828) 		0.788
(1.00) 		0.0935
(0.667) 		0.531
(0.957) 		0.623
(0.968) 		1
(1.00) 		0.283
(0.868) 		0.0457
(0.532) 		0.99
(1.00) 		0.95
(1.00) 		0.0935
(0.667) 		0.0472
(0.541) 		0.932
(1.00) 		0.298
(0.881) 		0.652
(0.979) 		0.877
(1.00) 		0.708
(0.992) 		0.494
(0.957) 		0.745
(1) 		0.52
(0.957) 		0.376
(0.922) 		0.856
(1.00) 		1
(1.00) 		0.531
(0.957) 		0.358
(0.912) 		0.437
(0.948) 		0.607
(0.967) 		0.291
(0.876) 		0.713
(0.994) 		0.724
(0.995) 		0.577
(0.966) 		0.37
(0.922) 		0.694
(0.99)
del 21q11 2 58 (20%) 237 0.0178
(0.427) 		0.169
(0.764) 		0.042
(0.516) 		0.219
(0.816) 		0.69
(0.986) 		0.198
(0.79) 		0.631
(0.97) 		0.562
(0.963) 		0.0647
(0.629) 		0.336
(0.899) 		0.0524
(0.553) 		0.0986
(0.672) 		0.237
(0.837) 		0.043
(0.521) 		0.562
(0.963) 		0.0693
(0.635) 		0.0244
(0.453) 		0.459
(0.953) 		0.0286
(0.475) 		0.314
(0.888) 		0.839
(1.00) 		0.0424
(0.516) 		0.154
(0.745) 		0.766
(1.00) 		0.0447
(0.532) 		0.817
(1.00) 		0.835
(1.00) 		0.0647
(0.629) 		0.188
(0.788) 		0.667
(0.985) 		0.156
(0.745) 		0.443
(0.95) 		0.448
(0.951) 		0.351
(0.907) 		0.727
(0.996) 		0.153
(0.745) 		0.0415
(0.516)
del 22q13 32 87 (29%) 208 0.166
(0.761) 		0.261
(0.857) 		0.349
(0.907) 		0.301
(0.883) 		0.494
(0.957) 		0.363
(0.916) 		0.278
(0.864) 		0.559
(0.963) 		0.984
(1.00) 		0.899
(1.00) 		0.803
(1.00) 		0.728
(0.996) 		1
(1.00) 		0.63
(0.97) 		0.134
(0.719) 		0.559
(0.963) 		0.499
(0.957) 		0.0726
(0.642) 		0.533
(0.957) 		0.0113
(0.384) 		0.145
(0.738) 		0.572
(0.966) 		0.0279
(0.473) 		0.64
(0.974) 		0.9
(1.00) 		0.925
(1.00) 		0.143
(0.733) 		0.288
(0.872) 		0.984
(1.00) 		0.189
(0.788) 		0.854
(1.00) 		0.945
(1.00) 		0.874
(1.00) 		0.24
(0.845) 		0.177
(0.773) 		0.247
(0.848) 		0.651
(0.979) 		0.297
(0.881) 		0.153
(0.745)
del xp11 3 72 (24%) 223 0.488
(0.957) 		0.205
(0.799) 		0.803
(1.00) 		0.57
(0.966) 		0.686
(0.986) 		0.545
(0.961) 		0.096
(0.672) 		0.522
(0.957) 		1
(1.00) 		0.095
(0.671) 		0.113
(0.689) 		0.666
(0.985) 		0.529
(0.957) 		0.474
(0.953) 		0.178
(0.773) 		0.522
(0.957) 		0.697
(0.99) 		0.359
(0.912) 		0.284
(0.869) 		0.353
(0.907) 		0.759
(1.00) 		0.122
(0.701) 		0.108
(0.683) 		0.581
(0.966) 		0.644
(0.976) 		0.323
(0.889) 		0.386
(0.922) 		0.847
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.105
(0.678) 		0.092
(0.667) 		0.0727
(0.642) 		0.726
(0.996) 		0.0682
(0.633) 		1
(1.00) 		0.225
(0.828) 		0.181
(0.778) 		0.506
(0.957)
del xq21 33 59 (20%) 236 0.0707
(0.642) 		0.471
(0.953) 		0.737
(0.999) 		0.557
(0.963) 		0.37
(0.922) 		1
(1.00) 		0.146
(0.742) 		0.763
(1.00) 		0.47
(0.953) 		0.18
(0.776) 		0.779
(1.00) 		0.106
(0.678) 		0.0921
(0.667) 		0.393
(0.922) 		0.575
(0.966) 		0.763
(1.00) 		0.844
(1.00) 		0.623
(0.968) 		0.188
(0.788) 		0.176
(0.773) 		0.54
(0.961) 		0.504
(0.957) 		0.0263
(0.464) 		0.924
(1.00) 		0.53
(0.957) 		0.0984
(0.672) 		0.209
(0.805) 		1
(1.00) 		0.47
(0.953) 		0.906
(1.00) 		0.038
(0.513) 		0.6
(0.966) 		0.815
(1.00) 		0.793
(1.00) 		0.116
(0.689) 		0.121
(0.7) 		0.462
(0.953) 		0.437
(0.948) 		0.877
(1.00)
'amp_11q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.000111 (Wilcoxon-test), Q value = 0.03

Table S1.  Gene #14: 'amp_11q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 293 48.1 (13.8)
AMP PEAK 14(11Q22.1) MUTATED 47 40.9 (12.6)
AMP PEAK 14(11Q22.1) WILD-TYPE 246 49.5 (13.6)

Figure S1.  Get High-res Image Gene #14: 'amp_11q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_11q22.1' versus 'MENOPAUSE_STATUS'

P value = 0.0023 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #14: 'amp_11q22.1' versus Clinical Feature #27: 'MENOPAUSE_STATUS'

nPatients INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL) PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD) POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY) PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
ALL 3 25 82 121
AMP PEAK 14(11Q22.1) MUTATED 0 4 4 28
AMP PEAK 14(11Q22.1) WILD-TYPE 3 21 78 93

Figure S2.  Get High-res Image Gene #14: 'amp_11q22.1' versus Clinical Feature #27: 'MENOPAUSE_STATUS'

'amp_11q22.1' versus 'INITIAL_PATHOLOGIC_DX_YEAR'

P value = 0.00252 (Wilcoxon-test), Q value = 0.25

Table S3.  Gene #14: 'amp_11q22.1' versus Clinical Feature #32: 'INITIAL_PATHOLOGIC_DX_YEAR'

nPatients Mean (Std.Dev)
ALL 293 2008.5 (4.6)
AMP PEAK 14(11Q22.1) MUTATED 47 2006.4 (5.6)
AMP PEAK 14(11Q22.1) WILD-TYPE 246 2008.9 (4.3)

Figure S3.  Get High-res Image Gene #14: 'amp_11q22.1' versus Clinical Feature #32: 'INITIAL_PATHOLOGIC_DX_YEAR'

'amp_11q22.1' versus 'AGE_AT_DIAGNOSIS'

P value = 9.19e-05 (Wilcoxon-test), Q value = 0.028

Table S4.  Gene #14: 'amp_11q22.1' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

nPatients Mean (Std.Dev)
ALL 295 48.2 (13.8)
AMP PEAK 14(11Q22.1) MUTATED 47 40.9 (12.6)
AMP PEAK 14(11Q22.1) WILD-TYPE 248 49.6 (13.6)

Figure S4.  Get High-res Image Gene #14: 'amp_11q22.1' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

'amp_19p13.2' versus 'KERATINIZATION_SQUAMOUS_CELL'

P value = 0.00151 (Fisher's exact test), Q value = 0.21

Table S5.  Gene #22: 'amp_19p13.2' versus Clinical Feature #31: 'KERATINIZATION_SQUAMOUS_CELL'

nPatients KERATINIZING SQUAMOUS CELL CARCINOMA NON-KERATINIZING SQUAMOUS CELL CARCINOMA
ALL 49 117
AMP PEAK 22(19P13.2) MUTATED 14 10
AMP PEAK 22(19P13.2) WILD-TYPE 35 107

Figure S5.  Get High-res Image Gene #22: 'amp_19p13.2' versus Clinical Feature #31: 'KERATINIZATION_SQUAMOUS_CELL'

'del_3p22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.000706 (Fisher's exact test), Q value = 0.15

Table S6.  Gene #31: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 129 56
DEL PEAK 5(3P22.1) MUTATED 33 29
DEL PEAK 5(3P22.1) WILD-TYPE 96 27

Figure S6.  Get High-res Image Gene #31: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_3p22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00018 (Fisher's exact test), Q value = 0.044

Table S7.  Gene #31: 'del_3p22.1' 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 5(3P22.1) MUTATED 1 107 1 1 0 3
DEL PEAK 5(3P22.1) WILD-TYPE 5 135 5 20 3 14

Figure S7.  Get High-res Image Gene #31: 'del_3p22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_3p22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 3.18e-05 (Wilcoxon-test), Q value = 0.016

Table S8.  Gene #31: 'del_3p22.1' versus Clinical Feature #9: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 150 0.9 (2.1)
DEL PEAK 5(3P22.1) MUTATED 52 1.5 (2.1)
DEL PEAK 5(3P22.1) WILD-TYPE 98 0.6 (2.0)

Figure S8.  Get High-res Image Gene #31: 'del_3p22.1' versus Clinical Feature #9: 'NUMBER_OF_LYMPH_NODES'

'del_3p22.1' versus 'LYMPHOVASCULAR_INVOLVEMENT'

P value = 0.0017 (Fisher's exact test), Q value = 0.21

Table S9.  Gene #31: 'del_3p22.1' versus Clinical Feature #28: 'LYMPHOVASCULAR_INVOLVEMENT'

nPatients ABSENT PRESENT
ALL 71 74
DEL PEAK 5(3P22.1) MUTATED 15 34
DEL PEAK 5(3P22.1) WILD-TYPE 56 40

Figure S9.  Get High-res Image Gene #31: 'del_3p22.1' versus Clinical Feature #28: 'LYMPHOVASCULAR_INVOLVEMENT'

'del_3p22.1' versus 'LYMPH_NODES_EXAMINED_HE_COUNT'

P value = 3.18e-05 (Wilcoxon-test), Q value = 0.016

Table S10.  Gene #31: 'del_3p22.1' versus Clinical Feature #29: 'LYMPH_NODES_EXAMINED_HE_COUNT'

nPatients Mean (Std.Dev)
ALL 150 0.9 (2.1)
DEL PEAK 5(3P22.1) MUTATED 52 1.5 (2.1)
DEL PEAK 5(3P22.1) WILD-TYPE 98 0.6 (2.0)

Figure S10.  Get High-res Image Gene #31: 'del_3p22.1' versus Clinical Feature #29: 'LYMPH_NODES_EXAMINED_HE_COUNT'

'del_3p14.2' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S11.  Gene #32: '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 6(3P14.2) MUTATED 2 124 1 1 1 5
DEL PEAK 6(3P14.2) WILD-TYPE 4 118 5 20 2 12

Figure S11.  Get High-res Image Gene #32: 'del_3p14.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_4p16.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00175 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #33: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 129 56
DEL PEAK 7(4P16.3) MUTATED 41 32
DEL PEAK 7(4P16.3) WILD-TYPE 88 24

Figure S12.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'del_4p16.3' versus 'HISTOLOGICAL_TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.028

Table S13.  Gene #33: 'del_4p16.3' 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 7(4P16.3) MUTATED 2 117 3 1 0 4
DEL PEAK 7(4P16.3) WILD-TYPE 4 125 3 20 3 13

Figure S13.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_4p16.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00111 (Wilcoxon-test), Q value = 0.18

Table S14.  Gene #33: 'del_4p16.3' versus Clinical Feature #9: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 150 0.9 (2.1)
DEL PEAK 7(4P16.3) MUTATED 53 1.3 (1.8)
DEL PEAK 7(4P16.3) WILD-TYPE 97 0.7 (2.2)

Figure S14.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #9: 'NUMBER_OF_LYMPH_NODES'

'del_4p16.3' versus 'LYMPH_NODES_EXAMINED_HE_COUNT'

P value = 0.00111 (Wilcoxon-test), Q value = 0.18

Table S15.  Gene #33: 'del_4p16.3' versus Clinical Feature #29: 'LYMPH_NODES_EXAMINED_HE_COUNT'

nPatients Mean (Std.Dev)
ALL 150 0.9 (2.1)
DEL PEAK 7(4P16.3) MUTATED 53 1.3 (1.8)
DEL PEAK 7(4P16.3) WILD-TYPE 97 0.7 (2.2)

Figure S15.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #29: 'LYMPH_NODES_EXAMINED_HE_COUNT'

'del_4q22.1' versus 'RADIATION_THERAPY'

P value = 0.00204 (Fisher's exact test), Q value = 0.22

Table S16.  Gene #35: 'del_4q22.1' versus Clinical Feature #6: 'RADIATION_THERAPY'

nPatients NO YES
ALL 53 125
DEL PEAK 9(4Q22.1) MUTATED 10 54
DEL PEAK 9(4Q22.1) WILD-TYPE 43 71

Figure S16.  Get High-res Image Gene #35: 'del_4q22.1' versus Clinical Feature #6: 'RADIATION_THERAPY'

'del_4q22.1' versus 'NEOPLASM_HISTOLOGIC_GRADE'

P value = 0.00175 (Fisher's exact test), Q value = 0.21

Table S17.  Gene #35: 'del_4q22.1' versus Clinical Feature #14: 'NEOPLASM_HISTOLOGIC_GRADE'

nPatients G1 G2 G3 G4 GX
ALL 18 129 115 1 24
DEL PEAK 9(4Q22.1) MUTATED 2 34 54 0 8
DEL PEAK 9(4Q22.1) WILD-TYPE 16 95 61 1 16

Figure S17.  Get High-res Image Gene #35: 'del_4q22.1' versus Clinical Feature #14: 'NEOPLASM_HISTOLOGIC_GRADE'

'del_6q26' versus 'INITIAL_PATHOLOGIC_DX_YEAR'

P value = 0.000747 (Wilcoxon-test), Q value = 0.15

Table S18.  Gene #40: 'del_6q26' versus Clinical Feature #32: 'INITIAL_PATHOLOGIC_DX_YEAR'

nPatients Mean (Std.Dev)
ALL 293 2008.5 (4.6)
DEL PEAK 14(6Q26) MUTATED 98 2007.2 (5.2)
DEL PEAK 14(6Q26) WILD-TYPE 195 2009.2 (4.2)

Figure S18.  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 = 0.17

Table S19.  Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 293 48.1 (13.8)
DEL PEAK 18(10Q23.31) MUTATED 86 52.2 (14.5)
DEL PEAK 18(10Q23.31) WILD-TYPE 207 46.4 (13.2)

Figure S19.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'AGE_AT_DIAGNOSIS'

P value = 0.00121 (Wilcoxon-test), Q value = 0.19

Table S20.  Gene #44: 'del_10q23.31' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

nPatients Mean (Std.Dev)
ALL 295 48.2 (13.8)
DEL PEAK 18(10Q23.31) MUTATED 86 52.2 (14.5)
DEL PEAK 18(10Q23.31) WILD-TYPE 209 46.6 (13.2)

Figure S20.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

'del_11p15.1' versus 'AGE_AT_DIAGNOSIS'

P value = 0.00193 (Wilcoxon-test), Q value = 0.22

Table S21.  Gene #45: 'del_11p15.1' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

nPatients Mean (Std.Dev)
ALL 295 48.2 (13.8)
DEL PEAK 19(11P15.1) MUTATED 102 51.8 (13.5)
DEL PEAK 19(11P15.1) WILD-TYPE 193 46.3 (13.6)

Figure S21.  Get High-res Image Gene #45: 'del_11p15.1' versus Clinical Feature #38: 'AGE_AT_DIAGNOSIS'

'del_16q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S22.  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 26(16Q11.2) MUTATED 0 32 5 9 1 6
DEL PEAK 26(16Q11.2) WILD-TYPE 6 210 1 12 2 11

Figure S22.  Get High-res Image Gene #52: 'del_16q11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_16q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S23.  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 27(16Q23.1) MUTATED 0 34 4 9 2 6
DEL PEAK 27(16Q23.1) WILD-TYPE 6 208 2 12 1 11

Figure S23.  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 = 0.012

Table S24.  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 30(18Q21.2) MUTATED 0 55 1 14 2 10
DEL PEAK 30(18Q21.2) WILD-TYPE 6 187 5 7 1 7

Figure S24.  Get High-res Image Gene #56: 'del_18q21.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'TUMOR_STATUS'

P value = 0.00169 (Fisher's exact test), Q value = 0.21

Table S25.  Gene #57: 'del_19p13.3' versus Clinical Feature #13: 'TUMOR_STATUS'

nPatients TUMOR FREE WITH TUMOR
ALL 193 76
DEL PEAK 31(19P13.3) MUTATED 56 38
DEL PEAK 31(19P13.3) WILD-TYPE 137 38

Figure S25.  Get High-res Image Gene #57: 'del_19p13.3' versus Clinical Feature #13: 'TUMOR_STATUS'

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/22507940/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/22489370/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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