Correlation between copy number variation genes (focal events) and selected clinical features
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 59 focal events and 12 clinical features across 165 patients, 5 significant findings detected with Q value < 0.25.

  • amp_8p11.21 cnv correlated to 'RESIDUAL_TUMOR'.

  • amp_13q22.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_20q11.21 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_20q11.23 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_20q13.31 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 59 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 5 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE
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 Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test
amp 8p11 21 70 (42%) 95 0.51
(0.957) 		0.664
(0.987) 		0.173
(0.814) 		0.411
(0.899) 		0.672
(0.987) 		0.074
(0.754) 		0.753
(0.993) 		0.609
(0.975) 		0.156
(0.799) 		0.001
(0.16) 		0.346
(0.888) 		0.825
(1.00)
amp 13q22 1 120 (73%) 45 0.791
(1.00) 		0.663
(0.987) 		0.771
(0.997) 		0.193
(0.833) 		0.153
(0.799) 		1
(1.00) 		0.485
(0.945) 		0.179
(0.814) 		0.00113
(0.16) 		0.624
(0.976) 		0.0581
(0.71) 		0.473
(0.934)
amp 20q11 21 146 (88%) 19 0.814
(1.00) 		0.0825
(0.754) 		0.204
(0.84) 		0.558
(0.975) 		0.0986
(0.754) 		0.739
(0.992) 		1
(1.00) 		0.733
(0.992) 		0.000663
(0.156) 		0.71
(0.987) 		0.156
(0.799) 		0.0988
(0.754)
amp 20q11 23 147 (89%) 18 0.899
(1.00) 		0.169
(0.814) 		0.259
(0.86) 		0.594
(0.975) 		0.0372
(0.628) 		0.309
(0.871) 		1
(1.00) 		1
(1.00) 		0.000447
(0.156) 		0.709
(0.987) 		0.156
(0.799) 		0.0852
(0.754)
amp 20q13 31 148 (90%) 17 0.925
(1.00) 		0.26
(0.86) 		0.293
(0.868) 		0.609
(0.975) 		0.0635
(0.731) 		0.311
(0.873) 		0.799
(1.00) 		1
(1.00) 		0.000447
(0.156) 		0.595
(0.975) 		0.221
(0.84) 		0.118
(0.773)
amp 1q21 3 48 (29%) 117 0.929
(1.00) 		0.646
(0.987) 		0.803
(1.00) 		0.102
(0.754) 		0.469
(0.928) 		0.619
(0.975) 		0.734
(0.992) 		0.275
(0.863) 		1
(1.00) 		0.58
(0.975) 		0.507
(0.957) 		0.171
(0.814)
amp 1q32 2 48 (29%) 117 0.446
(0.921) 		0.976
(1.00) 		0.686
(0.987) 		0.0235
(0.536) 		0.276
(0.863) 		0.803
(1.00) 		1
(1.00) 		0.285
(0.868) 		1
(1.00) 		0.57
(0.975) 		0.126
(0.79) 		0.118
(0.773)
amp 5q22 3 20 (12%) 145 0.147
(0.799) 		0.298
(0.868) 		0.68
(0.987) 		0.883
(1.00) 		0.851
(1.00) 		0.509
(0.957) 		0.637
(0.987) 		0.46
(0.928) 		0.374
(0.895) 		0.84
(1.00) 		0.737
(0.992) 		1
(1.00)
amp 6p21 1 54 (33%) 111 0.874
(1.00) 		0.861
(1.00) 		0.134
(0.799) 		0.415
(0.899) 		0.00617
(0.358) 		0.0139
(0.428) 		0.406
(0.899) 		0.101
(0.754) 		0.062
(0.731) 		0.174
(0.814) 		0.0117
(0.395) 		0.179
(0.814)
amp 8p11 23 53 (32%) 112 0.164
(0.802) 		0.355
(0.888) 		0.21
(0.84) 		0.219
(0.84) 		0.323
(0.886) 		0.148
(0.799) 		0.0941
(0.754) 		0.593
(0.975) 		0.222
(0.841) 		0.0097
(0.395) 		0.147
(0.799) 		1
(1.00)
amp 8q24 21 109 (66%) 56 0.266
(0.86) 		0.343
(0.888) 		0.199
(0.84) 		0.497
(0.955) 		0.624
(0.976) 		0.353
(0.888) 		0.743
(0.992) 		0.795
(1.00) 		0.0328
(0.611) 		0.408
(0.899) 		0.706
(0.987) 		0.329
(0.888)
amp 10q22 2 11 (7%) 154 0.38
(0.895) 		0.702
(0.987) 		0.848
(1.00) 		0.935
(1.00) 		0.914
(1.00) 		0.662
(0.987) 		0.756
(0.993) 		0.339
(0.888) 		0.585
(0.975) 		1
(1.00) 		0.619
(0.975) 		1
(1.00)
amp 11p15 5 45 (27%) 120 0.307
(0.871) 		0.913
(1.00) 		0.592
(0.975) 		0.963
(1.00) 		0.189
(0.826) 		0.809
(1.00) 		1
(1.00) 		0.41
(0.899) 		0.114
(0.773) 		1
(1.00) 		0.208
(0.84) 		0.103
(0.754)
amp 11q13 3 28 (17%) 137 0.669
(0.987) 		0.0462
(0.633) 		0.662
(0.987) 		0.604
(0.975) 		0.354
(0.888) 		0.384
(0.895) 		1
(1.00) 		0.297
(0.868) 		0.468
(0.928) 		0.26
(0.86) 		0.297
(0.868) 		0.00471
(0.358)
amp 12p13 33 41 (25%) 124 0.85
(1.00) 		0.256
(0.86) 		0.754
(0.993) 		0.384
(0.895) 		0.604
(0.975) 		0.597
(0.975) 		0.588
(0.975) 		0.257
(0.86) 		0.305
(0.871) 		0.504
(0.957) 		0.62
(0.975) 		0.107
(0.754)
amp 12p12 1 40 (24%) 125 0.353
(0.888) 		0.289
(0.868) 		0.537
(0.971) 		0.325
(0.886) 		0.596
(0.975) 		0.788
(1.00) 		0.716
(0.987) 		0.779
(0.997) 		0.183
(0.814) 		0.323
(0.886) 		0.605
(0.975) 		0.0939
(0.754)
amp 13q12 13 126 (76%) 39 0.102
(0.754) 		0.188
(0.826) 		0.074
(0.754) 		0.0637
(0.731) 		0.0116
(0.395) 		0.798
(1.00) 		0.717
(0.987) 		0.555
(0.975) 		0.00229
(0.27) 		1
(1.00) 		0.0076
(0.358) 		0.121
(0.773)
amp 13q12 2 125 (76%) 40 0.273
(0.863) 		0.0964
(0.754) 		0.0936
(0.754) 		0.0651
(0.731) 		0.0174
(0.474) 		1
(1.00) 		0.368
(0.891) 		0.394
(0.895) 		0.00279
(0.283) 		1
(1.00) 		0.0076
(0.358) 		0.151
(0.799)
amp 15q26 1 13 (8%) 152 0.943
(1.00) 		0.818
(1.00) 		0.634
(0.987) 		0.462
(0.928) 		0.27
(0.86) 		0.213
(0.84) 		0.263
(0.86) 		0.178
(0.814) 		0.288
(0.868) 		0.343
(0.888) 		0.378
(0.895) 		1
(1.00)
amp 16p11 2 47 (28%) 118 0.663
(0.987) 		0.673
(0.987) 		0.0934
(0.754) 		0.612
(0.975) 		0.0764
(0.754) 		0.0465
(0.633) 		0.607
(0.975) 		0.41
(0.899) 		0.0109
(0.395) 		0.0387
(0.631) 		0.144
(0.799) 		0.0967
(0.754)
amp 17q12 46 (28%) 119 0.179
(0.814) 		0.33
(0.888) 		0.831
(1.00) 		0.851
(1.00) 		0.269
(0.86) 		0.321
(0.886) 		0.299
(0.868) 		0.267
(0.86) 		0.35
(0.888) 		0.137
(0.799) 		0.97
(1.00) 		0.0731
(0.754)
amp 17q24 1 39 (24%) 126 0.351
(0.888) 		0.25
(0.86) 		0.417
(0.899) 		0.264
(0.86) 		0.261
(0.86) 		0.117
(0.773) 		1
(1.00) 		0.555
(0.975) 		0.0392
(0.631) 		0.199
(0.84) 		0.756
(0.993) 		0.73
(0.992)
amp 19p13 2 36 (22%) 129 0.561
(0.975) 		0.887
(1.00) 		0.267
(0.86) 		0.217
(0.84) 		0.68
(0.987) 		0.797
(1.00) 		0.706
(0.987) 		0.536
(0.971) 		0.0412
(0.633) 		0.723
(0.989) 		0.488
(0.948) 		0.0186
(0.476)
amp xp22 2 32 (19%) 133 0.833
(1.00) 		0.895
(1.00) 		0.035
(0.62) 		0.858
(1.00) 		0.54
(0.971) 		0.256
(0.86) 		0.238
(0.86) 		0.76
(0.996) 		0.469
(0.928) 		0.319
(0.885) 		0.782
(0.998) 		0.0581
(0.71)
del 1p36 11 75 (45%) 90 0.568
(0.975) 		0.615
(0.975) 		0.725
(0.989) 		0.106
(0.754) 		0.325
(0.886) 		0.377
(0.895) 		0.877
(1.00) 		0.209
(0.84) 		0.566
(0.975) 		0.714
(0.987) 		0.0557
(0.705) 		0.0081
(0.358)
del 1p33 53 (32%) 112 0.291
(0.868) 		0.51
(0.957) 		0.914
(1.00) 		0.537
(0.971) 		0.412
(0.899) 		1
(1.00) 		0.868
(1.00) 		0.424
(0.902) 		0.0643
(0.731) 		0.854
(1.00) 		0.491
(0.95) 		0.0195
(0.477)
del 1p13 2 54 (33%) 111 0.476
(0.937) 		0.644
(0.987) 		0.148
(0.799) 		0.212
(0.84) 		0.817
(1.00) 		1
(1.00) 		1
(1.00) 		0.424
(0.902) 		0.227
(0.851) 		0.953
(1.00) 		0.315
(0.881) 		0.191
(0.829)
del 2p12 13 (8%) 152 0.718
(0.987) 		0.0264
(0.55) 		0.774
(0.997) 		1
(1.00) 		0.442
(0.919) 		1
(1.00) 		0.577
(0.975) 		0.394
(0.895) 		1
(1.00) 		1
(1.00) 		0.766
(0.997) 		1
(1.00)
del 3p14 2 31 (19%) 134 0.341
(0.888) 		0.573
(0.975) 		0.175
(0.814) 		0.25
(0.86) 		0.776
(0.997) 		0.16
(0.801) 		0.0158
(0.448) 		0.768
(0.997) 		0.702
(0.987) 		0.116
(0.773) 		0.621
(0.975) 		0.0679
(0.739)
del 3q26 31 18 (11%) 147 0.307
(0.871) 		0.404
(0.899) 		0.0803
(0.754) 		0.725
(0.989) 		0.351
(0.888) 		0.0328
(0.611) 		0.0437
(0.633) 		0.3
(0.868) 		0.0043
(0.358) 		0.263
(0.86) 		0.156
(0.799) 		0.131
(0.791)
del 4p13 60 (36%) 105 0.0948
(0.754) 		0.704
(0.987) 		0.791
(1.00) 		0.772
(0.997) 		0.349
(0.888) 		1
(1.00) 		0.147
(0.799) 		0.198
(0.84) 		0.377
(0.895) 		0.654
(0.987) 		0.297
(0.868) 		0.78
(0.997)
del 4q22 1 73 (44%) 92 0.0549
(0.705) 		0.46
(0.928) 		0.455
(0.928) 		0.431
(0.908) 		0.591
(0.975) 		0.511
(0.957) 		0.16
(0.801) 		0.209
(0.84) 		0.395
(0.895) 		0.491
(0.95) 		0.302
(0.868) 		1
(1.00)
del 4q35 1 72 (44%) 93 0.433
(0.908) 		0.779
(0.997) 		0.445
(0.92) 		0.538
(0.971) 		0.385
(0.895) 		1
(1.00) 		0.348
(0.888) 		0.217
(0.84) 		0.156
(0.799) 		0.364
(0.889) 		0.251
(0.86) 		0.429
(0.906)
del 5q12 1 53 (32%) 112 0.705
(0.987) 		0.555
(0.975) 		0.719
(0.987) 		0.928
(1.00) 		0.974
(1.00) 		0.24
(0.86) 		0.407
(0.899) 		0.796
(1.00) 		0.224
(0.844) 		0.904
(1.00) 		0.962
(1.00) 		0.18
(0.814)
del 5q22 2 59 (36%) 106 0.669
(0.987) 		0.366
(0.891) 		0.636
(0.987) 		0.466
(0.928) 		0.569
(0.975) 		1
(1.00) 		0.416
(0.899) 		1
(1.00) 		0.135
(0.799) 		0.881
(1.00) 		0.67
(0.987) 		0.0222
(0.524)
del 6p25 3 24 (15%) 141 0.26
(0.86) 		0.346
(0.888) 		0.35
(0.888) 		0.231
(0.858) 		0.41
(0.899) 		0.743
(0.992) 		0.665
(0.987) 		0.327
(0.886) 		0.383
(0.895) 		0.69
(0.987) 		0.283
(0.868) 		0.119
(0.773)
del 6q26 30 (18%) 135 0.482
(0.945) 		0.963
(1.00) 		0.392
(0.895) 		0.403
(0.899) 		0.104
(0.754) 		1
(1.00) 		0.157
(0.799) 		0.217
(0.84) 		0.0125
(0.403) 		0.62
(0.975) 		0.557
(0.975) 		0.136
(0.799)
del 7q31 1 4 (2%) 161 0.612
(0.975) 		0.215
(0.84) 		0.875
(1.00) 		1
(1.00) 		0.531
(0.971) 		1
(1.00) 		1
(1.00) 		0.074
(0.754) 		0.291
(0.868) 		1
(1.00) 		0.695
(0.987)
del 8p23 2 100 (61%) 65 0.336
(0.888) 		0.26
(0.86) 		0.388
(0.895) 		0.204
(0.84) 		0.541
(0.971) 		0.505
(0.957) 		1
(1.00) 		1
(1.00) 		0.769
(0.997) 		0.298
(0.868) 		0.229
(0.852) 		1
(1.00)
del 8p11 21 45 (27%) 120 0.801
(1.00) 		0.503
(0.957) 		0.252
(0.86) 		0.896
(1.00) 		0.919
(1.00) 		0.464
(0.928) 		0.162
(0.801) 		0.768
(0.997) 		0.75
(0.993) 		0.569
(0.975) 		0.583
(0.975) 		1
(1.00)
del 10q21 1 41 (25%) 124 0.589
(0.975) 		0.578
(0.975) 		0.675
(0.987) 		0.716
(0.987) 		0.812
(1.00) 		0.129
(0.79) 		0.588
(0.975) 		0.00766
(0.358) 		0.0929
(0.754) 		0.744
(0.992) 		0.719
(0.987) 		0.689
(0.987)
del 10q25 2 48 (29%) 117 0.243
(0.86) 		0.455
(0.928) 		0.714
(0.987) 		0.162
(0.801) 		0.683
(0.987) 		0.22
(0.84) 		0.864
(1.00) 		0.0487
(0.651) 		0.0542
(0.705) 		0.284
(0.868) 		0.964
(1.00) 		1
(1.00)
del 11q22 3 38 (23%) 127 0.452
(0.928) 		0.862
(1.00) 		0.341
(0.888) 		0.447
(0.921) 		0.939
(1.00) 		0.0278
(0.563) 		0.584
(0.975) 		0.237
(0.86) 		0.0341
(0.619) 		0.182
(0.814) 		0.978
(1.00) 		0.0861
(0.754)
del 12p13 1 33 (20%) 132 0.173
(0.814) 		0.977
(1.00) 		0.359
(0.889) 		0.936
(1.00) 		0.124
(0.781) 		0.256
(0.86) 		0.846
(1.00) 		1
(1.00) 		0.465
(0.928) 		0.595
(0.975) 		0.654
(0.987) 		1
(1.00)
del 12q22 26 (16%) 139 0.89
(1.00) 		0.215
(0.84) 		0.12
(0.773) 		0.845
(1.00) 		1
(1.00) 		0.369
(0.892) 		1
(1.00) 		0.744
(0.992) 		0.694
(0.987) 		0.425
(0.902) 		1
(1.00) 		0.664
(0.987)
del 14q11 2 70 (42%) 95 0.95
(1.00) 		0.541
(0.971) 		0.596
(0.975) 		0.648
(0.987) 		0.387
(0.895) 		0.377
(0.895) 		0.753
(0.993) 		0.0774
(0.754) 		0.0431
(0.633) 		0.0925
(0.754) 		0.717
(0.987) 		0.409
(0.899)
del 14q31 1 72 (44%) 93 0.743
(0.992) 		0.962
(1.00) 		0.278
(0.868) 		0.189
(0.826) 		0.0815
(0.754) 		0.825
(1.00) 		0.531
(0.971) 		0.217
(0.84) 		0.00712
(0.358) 		0.433
(0.908) 		0.73
(0.992) 		0.401
(0.899)
del 15q21 1 79 (48%) 86 0.617
(0.975) 		0.876
(1.00) 		0.439
(0.916) 		0.39
(0.895) 		0.521
(0.966) 		0.828
(1.00) 		0.211
(0.84) 		0.141
(0.799) 		1
(1.00) 		0.82
(1.00) 		0.116
(0.773) 		0.419
(0.899)
del 15q22 33 77 (47%) 88 0.709
(0.987) 		0.941
(1.00) 		0.15
(0.799) 		0.0295
(0.581) 		0.274
(0.863) 		1
(1.00) 		0.531
(0.971) 		0.318
(0.885) 		1
(1.00) 		0.604
(0.975) 		0.0461
(0.633) 		1
(1.00)
del 16p13 3 13 (8%) 152 0.363
(0.889) 		0.699
(0.987) 		0.129
(0.79) 		0.75
(0.993) 		0.182
(0.814) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.255
(0.86) 		1
(1.00) 		0.953
(1.00) 		1
(1.00)
del 16q23 1 23 (14%) 142 0.673
(0.987) 		0.498
(0.955) 		0.0256
(0.55) 		0.6
(0.975) 		0.0188
(0.476) 		0.748
(0.993) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.308
(0.871) 		0.645
(0.987)
del 17p11 2 113 (68%) 52 0.516
(0.962) 		0.0672
(0.739) 		0.742
(0.992) 		0.0157
(0.448) 		0.855
(1.00) 		1
(1.00) 		0.614
(0.975) 		0.419
(0.899) 		0.118
(0.773) 		0.909
(1.00) 		0.815
(1.00) 		0.58
(0.975)
del 18q21 2 145 (88%) 20 0.518
(0.963) 		0.418
(0.899) 		0.0987
(0.754) 		0.00775
(0.358) 		0.106
(0.754) 		0.044
(0.633) 		1
(1.00) 		0.687
(0.987) 		0.656
(0.987) 		0.555
(0.975) 		0.0368
(0.628) 		1
(1.00)
del 18q22 1 141 (85%) 24 0.654
(0.987) 		0.361
(0.889) 		0.089
(0.754) 		0.0423
(0.633) 		0.352
(0.888) 		0.203
(0.84) 		0.665
(0.987) 		0.458
(0.928) 		0.393
(0.895) 		0.775
(0.997) 		0.128
(0.79) 		0.164
(0.802)
del 19p13 3 37 (22%) 128 0.542
(0.971) 		0.848
(1.00) 		0.796
(1.00) 		0.36
(0.889) 		0.66
(0.987) 		0.297
(0.868) 		0.713
(0.987) 		0.233
(0.86) 		0.3
(0.868) 		0.855
(1.00) 		0.465
(0.928) 		0.261
(0.86)
del 20p12 1 49 (30%) 116 0.0264
(0.55) 		0.612
(0.975) 		0.336
(0.888) 		0.954
(1.00) 		0.706
(0.987) 		0.811
(1.00) 		0.495
(0.954) 		0.776
(0.997) 		0.535
(0.971) 		0.686
(0.987) 		0.234
(0.86) 		0.111
(0.773)
del 21q11 2 73 (44%) 92 0.637
(0.987) 		0.59
(0.975) 		0.574
(0.975) 		0.0897
(0.754) 		0.385
(0.895) 		0.506
(0.957) 		0.64
(0.987) 		1
(1.00) 		0.152
(0.799) 		0.289
(0.868) 		0.443
(0.919) 		1
(1.00)
del 22q13 31 68 (41%) 97 0.0783
(0.754) 		0.096
(0.754) 		0.421
(0.901) 		0.262
(0.86) 		0.0108
(0.395) 		0.363
(0.889) 		0.527
(0.971) 		1
(1.00) 		0.562
(0.975) 		0.516
(0.962) 		0.148
(0.799) 		1
(1.00)
del xp22 33 34 (21%) 131 0.766
(0.997) 		0.609
(0.975) 		0.955
(1.00) 		0.714
(0.987) 		0.845
(1.00) 		0.586
(0.975) 		0.7
(0.987) 		0.364
(0.889) 		0.719
(0.987) 		0.846
(1.00) 		0.484
(0.945) 		1
(1.00)
'amp_8p11.21' versus 'RESIDUAL_TUMOR'

P value = 0.001 (Fisher's exact test), Q value = 0.16

Table S1.  Gene #6: 'amp_8p11.21' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 123 2 12 4
AMP PEAK 6(8P11.21) MUTATED 41 2 9 3
AMP PEAK 6(8P11.21) WILD-TYPE 82 0 3 1

Figure S1.  Get High-res Image Gene #6: 'amp_8p11.21' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

'amp_13q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00113 (Fisher's exact test), Q value = 0.16

Table S2.  Gene #15: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 146 13
AMP PEAK 15(13Q22.1) MUTATED 112 4
AMP PEAK 15(13Q22.1) WILD-TYPE 34 9

Figure S2.  Get High-res Image Gene #15: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.000663 (Fisher's exact test), Q value = 0.16

Table S3.  Gene #21: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 146 13
AMP PEAK 21(20Q11.21) MUTATED 135 7
AMP PEAK 21(20Q11.21) WILD-TYPE 11 6

Figure S3.  Get High-res Image Gene #21: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q11.23' versus 'HISTOLOGICAL_TYPE'

P value = 0.000447 (Fisher's exact test), Q value = 0.16

Table S4.  Gene #22: 'amp_20q11.23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 146 13
AMP PEAK 22(20Q11.23) MUTATED 136 7
AMP PEAK 22(20Q11.23) WILD-TYPE 10 6

Figure S4.  Get High-res Image Gene #22: 'amp_20q11.23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q13.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.000447 (Fisher's exact test), Q value = 0.16

Table S5.  Gene #23: 'amp_20q13.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 146 13
AMP PEAK 23(20Q13.31) MUTATED 136 7
AMP PEAK 23(20Q13.31) WILD-TYPE 10 6

Figure S5.  Get High-res Image Gene #23: 'amp_20q13.31' versus Clinical Feature #9: '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/READ-TP/19781847/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/19775480/READ-TP.merged_data.txt

  • Number of patients = 165

  • Number of significantly focal cnvs = 59

  • Number of selected clinical features = 12

  • 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.

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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