Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
17 April 2019  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 95 arm-level events and 2 molecular subtypes across 110 patients, 54 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 2p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 18p gain cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • xp gain cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'LINCRNA_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 21p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • 22p loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • yp loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

  • yq loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'LINCRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 95 arm-level events and 2 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 54 significant findings detected.

Clinical
Features 		MRNA
CHIERARCHICAL 		LINCRNA
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test
1p gain 32 (29%) 78 0.0229
(0.124) 		0.0286
(0.139)
2p gain 23 (21%) 87 0.00555
(0.0662) 		0.0186
(0.114)
2q gain 21 (19%) 89 0.0167
(0.11) 		0.0353
(0.156)
5q gain 26 (24%) 84 0.0156
(0.11) 		0.00038
(0.0361)
7p gain 58 (53%) 52 0.0301
(0.139) 		0.00974
(0.0839)
7q gain 48 (44%) 62 0.0205
(0.117) 		0.0323
(0.146)
16p gain 37 (34%) 73 0.00023
(0.0361) 		0.00248
(0.0581)
20p gain 24 (22%) 86 0.0472
(0.175) 		0.04
(0.161)
1p loss 16 (15%) 94 0.0266
(0.136) 		0.0123
(0.0897)
3p loss 36 (33%) 74 0.00372
(0.0622) 		0.0299
(0.139)
3q loss 27 (25%) 83 0.00628
(0.0662) 		0.00301
(0.0581)
5q loss 19 (17%) 91 0.00163
(0.0581) 		0.00243
(0.0581)
10q loss 28 (25%) 82 0.0496
(0.175) 		0.0271
(0.136)
11p loss 27 (25%) 83 0.0102
(0.0839) 		0.011
(0.087)
16p loss 15 (14%) 95 0.00668
(0.0662) 		0.0414
(0.161)
18p loss 40 (36%) 70 0.0209
(0.117) 		0.00536
(0.0662)
18q loss 46 (42%) 64 0.0369
(0.156) 		0.012
(0.0897)
21p loss 42 (38%) 68 0.0174
(0.11) 		0.0065
(0.0662)
21q loss 38 (35%) 72 0.0201
(0.117) 		0.00306
(0.0581)
yp loss 63 (57%) 47 0.00668
(0.0662) 		0.00219
(0.0581)
yq loss 64 (58%) 46 0.0497
(0.175) 		0.00393
(0.0622)
10q gain 7 (6%) 103 0.355
(0.564) 		0.0408
(0.161)
12p gain 23 (21%) 87 0.0398
(0.161) 		0.113
(0.27)
16q gain 28 (25%) 82 0.026
(0.136) 		0.0909
(0.24)
18p gain 8 (7%) 102 0.0169
(0.11) 		0.0765
(0.229)
18q gain 7 (6%) 103 0.0433
(0.164) 		0.226
(0.413)
21q gain 16 (15%) 94 0.396
(0.593) 		0.0495
(0.175)
xp gain 46 (42%) 64 0.0365
(0.156) 		0.884
(0.933)
12p loss 24 (22%) 86 0.0948
(0.244) 		0.00201
(0.0581)
12q loss 23 (21%) 87 0.109
(0.27) 		0.00172
(0.0581)
15q loss 52 (47%) 58 0.086
(0.234) 		0.00975
(0.0839)
22p loss 47 (43%) 63 0.00553
(0.0662) 		0.521
(0.704)
22q loss 49 (45%) 61 0.00697
(0.0662) 		0.627
(0.759)
1q gain 66 (60%) 44 0.299
(0.502) 		0.455
(0.654)
3p gain 10 (9%) 100 0.765
(0.855) 		0.839
(0.901)
3q gain 18 (16%) 92 0.607
(0.744) 		0.487
(0.67)
4p gain 8 (7%) 102 1
(1.00) 		0.808
(0.884)
4q gain 7 (6%) 103 0.416
(0.608) 		0.13
(0.291)
5p gain 57 (52%) 53 0.409
(0.602) 		0.21
(0.398)
6p gain 20 (18%) 90 0.777
(0.863) 		0.326
(0.534)
6q gain 10 (9%) 100 1
(1.00) 		0.644
(0.774)
8p gain 20 (18%) 90 0.201
(0.389) 		0.861
(0.919)
8q gain 34 (31%) 76 0.604
(0.744) 		0.965
(0.996)
9p gain 7 (6%) 103 0.534
(0.704) 		0.289
(0.494)
9q gain 5 (5%) 105 1
(1.00) 		0.73
(0.834)
10p gain 15 (14%) 95 0.086
(0.234) 		0.276
(0.485)
11p gain 21 (19%) 89 0.283
(0.492) 		0.16
(0.337)
11q gain 24 (22%) 86 0.837
(0.901) 		0.561
(0.725)
12q gain 22 (20%) 88 0.0873
(0.234) 		0.232
(0.42)
13p gain 7 (6%) 103 0.537
(0.704) 		0.477
(0.661)
13q gain 4 (4%) 106 0.687
(0.796) 		0.469
(0.659)
14p gain 26 (24%) 84 0.805
(0.884) 		0.717
(0.825)
14q gain 27 (25%) 83 0.96
(0.996) 		0.142
(0.311)
15p gain 9 (8%) 101 0.109
(0.27) 		0.189
(0.382)
17p gain 22 (20%) 88 0.593
(0.744) 		0.684
(0.796)
17q gain 30 (27%) 80 0.891
(0.935) 		0.156
(0.334)
19p gain 14 (13%) 96 0.196
(0.384) 		0.314
(0.524)
19q gain 15 (14%) 95 0.266
(0.473) 		0.384
(0.579)
20q gain 29 (26%) 81 0.0546
(0.189) 		0.17
(0.35)
21p gain 4 (4%) 106 0.363
(0.564) 		0.377
(0.574)
22p gain 4 (4%) 106 0.687
(0.796) 		0.472
(0.659)
22q gain 3 (3%) 107 0.333
(0.54) 		0.259
(0.465)
xq gain 49 (45%) 61 0.103
(0.262) 		0.97
(0.996)
yp gain 24 (22%) 86 0.0657
(0.208) 		0.22
(0.406)
yq gain 17 (15%) 93 0.365
(0.564) 		0.75
(0.843)
1q loss 6 (5%) 104 0.559
(0.725) 		0.653
(0.775)
2p loss 8 (7%) 102 0.574
(0.733) 		0.472
(0.659)
2q loss 10 (9%) 100 0.362
(0.564) 		0.369
(0.565)
4p loss 19 (17%) 91 0.064
(0.207) 		0.191
(0.382)
4q loss 19 (17%) 91 0.0643
(0.207) 		0.0692
(0.216)
5p loss 7 (6%) 103 0.215
(0.401) 		0.15
(0.325)
6p loss 19 (17%) 91 0.113
(0.27) 		0.123
(0.281)
6q loss 31 (28%) 79 0.136
(0.301) 		0.119
(0.279)
7p loss 8 (7%) 102 0.46
(0.657) 		0.167
(0.348)
7q loss 9 (8%) 101 0.675
(0.796) 		0.127
(0.287)
8p loss 33 (30%) 77 0.196
(0.384) 		0.215
(0.401)
8q loss 15 (14%) 95 0.285
(0.492) 		0.295
(0.5)
9p loss 53 (48%) 57 0.538
(0.704) 		0.365
(0.564)
9q loss 54 (49%) 56 0.535
(0.704) 		0.527
(0.704)
10p loss 26 (24%) 84 0.0815
(0.231) 		0.114
(0.27)
11q loss 22 (20%) 88 0.121
(0.281) 		0.175
(0.358)
13p loss 50 (45%) 60 0.354
(0.564) 		0.832
(0.901)
13q loss 48 (44%) 62 0.586
(0.743) 		0.0726
(0.222)
14p loss 34 (31%) 76 0.931
(0.972) 		0.32
(0.529)
14q loss 10 (9%) 100 0.0772
(0.229) 		0.407
(0.602)
15p loss 58 (53%) 52 0.0942
(0.244) 		0.0558
(0.189)
16q loss 24 (22%) 86 0.0786
(0.229) 		0.084
(0.234)
17p loss 24 (22%) 86 0.511
(0.698) 		1
(1.00)
17q loss 18 (16%) 92 1
(1.00) 		0.575
(0.733)
19p loss 45 (41%) 65 0.0638
(0.207) 		0.0794
(0.229)
19q loss 35 (32%) 75 0.81
(0.884) 		0.733
(0.834)
20p loss 26 (24%) 84 0.597
(0.744) 		0.206
(0.396)
20q loss 21 (19%) 89 0.744
(0.842) 		0.648
(0.774)
xp loss 13 (12%) 97 0.867
(0.92) 		0.612
(0.745)
xq loss 11 (10%) 99 0.602
(0.744) 		0.435
(0.631)
'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
1P GAIN MUTATED 5 6 21
1P GAIN WILD-TYPE 28 21 29

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'1p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.14

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
1P GAIN MUTATED 7 5 20
1P GAIN WILD-TYPE 26 25 27

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00555 (Fisher's exact test), Q value = 0.066

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
2P GAIN MUTATED 12 7 4
2P GAIN WILD-TYPE 21 20 46

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
2P GAIN MUTATED 10 9 4
2P GAIN WILD-TYPE 23 21 43

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.11

Table S5.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
2Q GAIN MUTATED 10 7 4
2Q GAIN WILD-TYPE 23 20 46

Figure S5.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
2Q GAIN MUTATED 8 9 4
2Q GAIN WILD-TYPE 25 21 43

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'5q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.11

Table S7.  Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
5Q GAIN MUTATED 3 5 18
5Q GAIN WILD-TYPE 30 22 32

Figure S7.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'5q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.036

Table S8.  Gene #10: '5q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
5Q GAIN MUTATED 3 3 20
5Q GAIN WILD-TYPE 30 27 27

Figure S8.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.14

Table S9.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
7P GAIN MUTATED 11 17 30
7P GAIN WILD-TYPE 22 10 20

Figure S9.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00974 (Fisher's exact test), Q value = 0.084

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
7P GAIN MUTATED 10 19 29
7P GAIN WILD-TYPE 23 11 18

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.12

Table S11.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
7Q GAIN MUTATED 9 17 22
7Q GAIN WILD-TYPE 24 10 28

Figure S11.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #14: '7q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
7Q GAIN MUTATED 9 18 21
7Q GAIN WILD-TYPE 24 12 26

Figure S12.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'10q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.16

Table S13.  Gene #20: '10q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
10Q GAIN MUTATED 5 0 2
10Q GAIN WILD-TYPE 28 30 45

Figure S13.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 0.16

Table S14.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
12P GAIN MUTATED 12 3 8
12P GAIN WILD-TYPE 21 24 42

Figure S14.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.036

Table S15.  Gene #30: '16p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
16P GAIN MUTATED 5 5 27
16P GAIN WILD-TYPE 28 22 23

Figure S15.  Get High-res Image Gene #30: '16p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.058

Table S16.  Gene #30: '16p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
16P GAIN MUTATED 5 8 24
16P GAIN WILD-TYPE 28 22 23

Figure S16.  Get High-res Image Gene #30: '16p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.14

Table S17.  Gene #31: '16q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
16Q GAIN MUTATED 5 4 19
16Q GAIN WILD-TYPE 28 23 31

Figure S17.  Get High-res Image Gene #31: '16q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.11

Table S18.  Gene #34: '18p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
18P GAIN MUTATED 6 1 1
18P GAIN WILD-TYPE 27 26 49

Figure S18.  Get High-res Image Gene #34: '18p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.16

Table S19.  Gene #35: '18q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
18Q GAIN MUTATED 5 1 1
18Q GAIN WILD-TYPE 28 26 49

Figure S19.  Get High-res Image Gene #35: '18q gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.17

Table S20.  Gene #38: '20p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
20P GAIN MUTATED 11 7 6
20P GAIN WILD-TYPE 22 20 44

Figure S20.  Get High-res Image Gene #38: '20p gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.16

Table S21.  Gene #38: '20p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
20P GAIN MUTATED 10 9 5
20P GAIN WILD-TYPE 23 21 42

Figure S21.  Get High-res Image Gene #38: '20p gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'21q gain' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.17

Table S22.  Gene #41: '21q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
21Q GAIN MUTATED 1 5 10
21Q GAIN WILD-TYPE 32 25 37

Figure S22.  Get High-res Image Gene #41: '21q gain' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'xp gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.16

Table S23.  Gene #44: 'xp gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
XP GAIN MUTATED 18 6 22
XP GAIN WILD-TYPE 15 21 28

Figure S23.  Get High-res Image Gene #44: 'xp gain' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.14

Table S24.  Gene #48: '1p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
1P LOSS MUTATED 9 4 3
1P LOSS WILD-TYPE 24 23 47

Figure S24.  Get High-res Image Gene #48: '1p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.09

Table S25.  Gene #48: '1p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
1P LOSS MUTATED 9 5 2
1P LOSS WILD-TYPE 24 25 45

Figure S25.  Get High-res Image Gene #48: '1p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00372 (Fisher's exact test), Q value = 0.062

Table S26.  Gene #52: '3p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
3P LOSS MUTATED 17 3 16
3P LOSS WILD-TYPE 16 24 34

Figure S26.  Get High-res Image Gene #52: '3p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.14

Table S27.  Gene #52: '3p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
3P LOSS MUTATED 16 5 15
3P LOSS WILD-TYPE 17 25 32

Figure S27.  Get High-res Image Gene #52: '3p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.066

Table S28.  Gene #53: '3q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
3Q LOSS MUTATED 14 2 11
3Q LOSS WILD-TYPE 19 25 39

Figure S28.  Get High-res Image Gene #53: '3q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.058

Table S29.  Gene #53: '3q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
3Q LOSS MUTATED 15 3 9
3Q LOSS WILD-TYPE 18 27 38

Figure S29.  Get High-res Image Gene #53: '3q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.058

Table S30.  Gene #57: '5q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
5Q LOSS MUTATED 9 8 2
5Q LOSS WILD-TYPE 24 19 48

Figure S30.  Get High-res Image Gene #57: '5q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.058

Table S31.  Gene #57: '5q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
5Q LOSS MUTATED 7 10 2
5Q LOSS WILD-TYPE 26 20 45

Figure S31.  Get High-res Image Gene #57: '5q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.17

Table S32.  Gene #67: '10q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
10Q LOSS MUTATED 4 6 18
10Q LOSS WILD-TYPE 29 21 32

Figure S32.  Get High-res Image Gene #67: '10q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.14

Table S33.  Gene #67: '10q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
10Q LOSS MUTATED 3 9 16
10Q LOSS WILD-TYPE 30 21 31

Figure S33.  Get High-res Image Gene #67: '10q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.084

Table S34.  Gene #68: '11p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
11P LOSS MUTATED 10 11 6
11P LOSS WILD-TYPE 23 16 44

Figure S34.  Get High-res Image Gene #68: '11p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.087

Table S35.  Gene #68: '11p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
11P LOSS MUTATED 8 13 6
11P LOSS WILD-TYPE 25 17 41

Figure S35.  Get High-res Image Gene #68: '11p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'12p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.058

Table S36.  Gene #70: '12p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
12P LOSS MUTATED 1 7 16
12P LOSS WILD-TYPE 32 23 31

Figure S36.  Get High-res Image Gene #70: '12p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'12q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.058

Table S37.  Gene #71: '12q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
12Q LOSS MUTATED 1 6 16
12Q LOSS WILD-TYPE 32 24 31

Figure S37.  Get High-res Image Gene #71: '12q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'15q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00975 (Fisher's exact test), Q value = 0.084

Table S38.  Gene #77: '15q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
15Q LOSS MUTATED 9 14 29
15Q LOSS WILD-TYPE 24 16 18

Figure S38.  Get High-res Image Gene #77: '15q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'16p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00668 (Fisher's exact test), Q value = 0.066

Table S39.  Gene #78: '16p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
16P LOSS MUTATED 5 8 2
16P LOSS WILD-TYPE 28 19 48

Figure S39.  Get High-res Image Gene #78: '16p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'16p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.16

Table S40.  Gene #78: '16p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
16P LOSS MUTATED 4 8 3
16P LOSS WILD-TYPE 29 22 44

Figure S40.  Get High-res Image Gene #78: '16p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.12

Table S41.  Gene #82: '18p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
18P LOSS MUTATED 6 10 24
18P LOSS WILD-TYPE 27 17 26

Figure S41.  Get High-res Image Gene #82: '18p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00536 (Fisher's exact test), Q value = 0.066

Table S42.  Gene #82: '18p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
18P LOSS MUTATED 5 12 23
18P LOSS WILD-TYPE 28 18 24

Figure S42.  Get High-res Image Gene #82: '18p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.16

Table S43.  Gene #83: '18q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
18Q LOSS MUTATED 8 12 26
18Q LOSS WILD-TYPE 25 15 24

Figure S43.  Get High-res Image Gene #83: '18q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.09

Table S44.  Gene #83: '18q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
18Q LOSS MUTATED 7 14 25
18Q LOSS WILD-TYPE 26 16 22

Figure S44.  Get High-res Image Gene #83: '18q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'21p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.11

Table S45.  Gene #88: '21p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
21P LOSS MUTATED 19 10 13
21P LOSS WILD-TYPE 14 17 37

Figure S45.  Get High-res Image Gene #88: '21p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'21p loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0065 (Fisher's exact test), Q value = 0.066

Table S46.  Gene #88: '21p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
21P LOSS MUTATED 17 15 10
21P LOSS WILD-TYPE 16 15 37

Figure S46.  Get High-res Image Gene #88: '21p loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.12

Table S47.  Gene #89: '21q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
21Q LOSS MUTATED 17 10 11
21Q LOSS WILD-TYPE 16 17 39

Figure S47.  Get High-res Image Gene #89: '21q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.058

Table S48.  Gene #89: '21q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
21Q LOSS MUTATED 16 14 8
21Q LOSS WILD-TYPE 17 16 39

Figure S48.  Get High-res Image Gene #89: '21q loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'22p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.066

Table S49.  Gene #90: '22p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
22P LOSS MUTATED 21 12 14
22P LOSS WILD-TYPE 12 15 36

Figure S49.  Get High-res Image Gene #90: '22p loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00697 (Fisher's exact test), Q value = 0.066

Table S50.  Gene #91: '22q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
22Q LOSS MUTATED 22 11 16
22Q LOSS WILD-TYPE 11 16 34

Figure S50.  Get High-res Image Gene #91: '22q loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'yp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00668 (Fisher's exact test), Q value = 0.066

Table S51.  Gene #94: 'yp loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
YP LOSS MUTATED 25 17 21
YP LOSS WILD-TYPE 8 10 29

Figure S51.  Get High-res Image Gene #94: 'yp loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'yp loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.058

Table S52.  Gene #94: 'yp loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
YP LOSS MUTATED 25 20 18
YP LOSS WILD-TYPE 8 10 29

Figure S52.  Get High-res Image Gene #94: 'yp loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

'yq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 0.17

Table S53.  Gene #95: 'yq loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 27 50
YQ LOSS MUTATED 24 17 23
YQ LOSS WILD-TYPE 9 10 27

Figure S53.  Get High-res Image Gene #95: 'yq loss' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'yq loss' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00393 (Fisher's exact test), Q value = 0.062

Table S54.  Gene #95: 'yq loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 30 47
YQ LOSS MUTATED 25 20 19
YQ LOSS WILD-TYPE 8 10 28

Figure S54.  Get High-res Image Gene #95: 'yq loss' versus Molecular Subtype #2: 'LINCRNA_CHIERARCHICAL'

Methods & Data
Input

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

  • Processed Copy number data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/038fcf2f-32c7-437e-beb7-ded16a017a25/correlate_genomic_events_all/d2cdaeae-8d2e-46f5-b7bd-6cd908ffe652/call-preprocess_genomic_event/transformed.cor.cli.txt

  • Molecular subtypes file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/69dd18b3-97fe-4143-b0f4-32e5d55e929d/aggregate_clusters_workflow/d44c315a-761b-4b72-be1f-cb969be36102/call-aggregate_clusters/CPTAC3-LUAD-TP.transposedmergedcluster.txt

  • Number of patients = 110

  • Number of significantly arm-level cnvs = 95

  • Number of molecular subtypes = 2

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

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] 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)
[2] 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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