Page 1
Query results of copy number alternations compared with Firehose Legacy study
Track_name track_typeTCGA-AA-3664TCGA-AG-A032TCGA-3L-AA1BTCGA-D5-5538TCGA-D5-5541TCGA-WS-AB45
American Joint Committee on Cancer Tumor Stage CodeCLINICALT3 T3 T2 T3 T3 T3
Sex CLINICALFemale Male Female Female Male Female
Diagnosis Age CLINICAL 74 68 61 60 63 52
A1CF CNA
ALDH2 CNA
AMER1 CNA Deep DeletionDeep DeletionDeep DeletionDeep DeletionDeep Deletion
AR CNA Amplification
ATRX CNA Deep DeletionDeep Deletion
BCL7A CNA
BMPR1A CNA Deep Deletion
CCDC6 CNA
CHST11 CNA
CLIP1 CNA
CYP2C8 CNA
FANCG CNA
FOXO4 CNA
HNF1A CNA
KAT6B CNA
MED12 CNA Deep DeletionDeep Deletion
MSN CNA
NCOA4 CNA
NCOR2 CNA
NONO CNA
NUTM2A CNA
NUTM2B CNA
POLE CNA
PRF1 CNA
PTPN11 CNA
RET CNA
SETD1B CNA
SH2B3 CNA
SS18 CNA
TBX3 CNA
TET1 CNA
USP44 CNA
ZCCHC8 CNA
ZMYM3 CNA
ZNF521 CNA
Page 2
Query results of copy number alternations compared with Firehose Legacy study
TCGA-AA-3680TCGA-AG-3890TCGA-AY-A54LTCGA-D5-6539TCGA-G4-6323TCGA-QG-A5YWTCGA-AY-A71XTCGA-F4-6461TCGA-4N-A93T
T4 T2 T2 T3 Tis T3 T2 T4b T4a
Female Male Female Female Male Female Female Female Male
67 62 74 45 50 55 54 41 67
Amplification
Deep DeletionDeep DeletionDeep DeletionDeep DeletionDeep DeletionDeep Deletion
Deep Deletion
Deep Deletion
Page 3
TCGA-4T-AA8HTCGA-5M-AAT4TCGA-5M-AAT5TCGA-5M-AAT6TCGA-5M-AATATCGA-5M-AATETCGA-A6-A5ZUTCGA-A6-A56BTCGA-A6-A565
T3 T3 T4a T3 T3 T3 T3
Female Male Female Male Male Male Female
42 74 40 76 59 57 34
Page 4
TCGA-A6-A566TCGA-A6-A567TCGA-A6-2671TCGA-A6-2672TCGA-A6-2674TCGA-A6-2675TCGA-A6-2676TCGA-A6-2677TCGA-A6-2678
T4 T3 T3 T3 T3 T3 T4 T3 T3
Female Male Male Female Male Male Female Female Female
55 56 85 82 71 78 75 68 43
Page 5
TCGA-A6-2679TCGA-A6-2680TCGA-A6-2681TCGA-A6-2682TCGA-A6-2683TCGA-A6-2684TCGA-A6-2685TCGA-A6-2686TCGA-A6-3807
T3 T3 T3 T4b T4 T2 T3 T3 T3
Female Female Female Male Female Female Female Female Female
73 72 73 70 57 75 48 81 53
Page 6
TCGA-A6-3809TCGA-A6-3810TCGA-A6-4105TCGA-A6-4107TCGA-A6-5656TCGA-A6-5657TCGA-A6-5659TCGA-A6-5660TCGA-A6-5661
T4 T3 T3 T3 T2 T3 T2 T3 T3
Female Male Male Female Male Male Male Male Female
71 62 79 57 74 65 82 73 80
Page 7
TCGA-A6-5662TCGA-A6-5664TCGA-A6-5665TCGA-A6-5666TCGA-A6-5667TCGA-A6-6137TCGA-A6-6138TCGA-A6-6140TCGA-A6-6141
T3 T4a T3 T4b T3 T3 T2 T3 T3
Male Male Female Male Female Male Male Male Male
46 80 84 78 40 55 61 62 31
Page 8
TCGA-A6-6142TCGA-A6-6648TCGA-A6-6649TCGA-A6-6650TCGA-A6-6651TCGA-A6-6652TCGA-A6-6653TCGA-A6-6654TCGA-A6-6780
T3 T3 T3 T3 T3 T3 T2 T3 T3
Female Male Male Female Female Male Male Female Male
56 56 66 69 55 59 82 65 74
Page 9
TCGA-A6-6781TCGA-A6-6782TCGA-AA-A00ATCGA-AA-A00DTCGA-AA-A00ETCGA-AA-A00FTCGA-AA-A00JTCGA-AA-A00KTCGA-AA-A00L
T4b T4a T3 T2 T3 T3 T4 T3 T3
Male Male Male Male Male Male Male Male Male
43 82 80 70 65 66 80 79 66
Page 10
TCGA-AA-A00NTCGA-AA-A00OTCGA-AA-A00QTCGA-AA-A00RTCGA-AA-A00UTCGA-AA-A00WTCGA-AA-A00ZTCGA-AA-A01CTCGA-AA-A01D
T4 T3 T4 T2 T3 T1 T3 T2 T3
Male Female Female Female Male Male Male Male Female
75 83 66 64 50 80 70 75 47
Page 11
TCGA-AA-A01FTCGA-AA-A01GTCGA-AA-A01ITCGA-AA-A01KTCGA-AA-A01PTCGA-AA-A01QTCGA-AA-A01RTCGA-AA-A01STCGA-AA-A01T
T3 T3 T2 T3 T3 T3 T3 T3 T3
Male Male Male Female Female Female Male Female Female
72 63 76 74 80 48 47 47 63
Page 12
TCGA-AA-A01VTCGA-AA-A01XTCGA-AA-A01ZTCGA-AA-A02ETCGA-AA-A02FTCGA-AA-A02HTCGA-AA-A02JTCGA-AA-A02OTCGA-AA-A02R
T2 T2 T3 T3 T3 T3 T3 T3 T3
Male Female Male Female Female Female Female Male Female
59 80 68 82 68 74 70 82 84
Page 13
TCGA-AA-A02WTCGA-AA-A02YTCGA-AA-A03FTCGA-AA-A03JTCGA-AA-A004TCGA-AA-A010TCGA-AA-A017TCGA-AA-A022TCGA-AA-A024
T2 T2 T3 T2 T3 T4 T3 T4 T3
Female Male Female Female Male Female Female Female Male
73 73 90 65 76 46 57 88 81
Page 14
TCGA-AA-A029TCGA-AA-3488TCGA-AA-3489TCGA-AA-3492TCGA-AA-3494TCGA-AA-3495TCGA-AA-3496TCGA-AA-3502TCGA-AA-3506
T3 T3 T3 T3 T3 T2 T3 T2 T2
Male Male Male Female Male Male Female Male Male
67 58 75 90 55 79 83 73 77
Page 15
TCGA-AA-3510TCGA-AA-3511TCGA-AA-3514TCGA-AA-3516TCGA-AA-3517TCGA-AA-3518TCGA-AA-3519TCGA-AA-3520TCGA-AA-3521
T3 T4 T2 T3 T3 T3 T3 T3 T3
Male Male Female Female Male Female Male Female Male
70 64 81 74 60 81 63 86 87
Page 16
TCGA-AA-3522TCGA-AA-3524TCGA-AA-3525TCGA-AA-3526TCGA-AA-3527TCGA-AA-3529TCGA-AA-3530TCGA-AA-3531TCGA-AA-3532
T3 T3 T3 T2 T3 T3 T2 T3 T3
Male Male Male Male Female Female Male Female Male
67 85 90 57 90 78 80 75 63
Page 17
TCGA-AA-3534TCGA-AA-3538TCGA-AA-3542TCGA-AA-3543TCGA-AA-3544TCGA-AA-3548TCGA-AA-3549TCGA-AA-3552TCGA-AA-3553
T3 T2 T3 T2 T2 T3 T2 T3 T2
Female Female Male Male Male Female Male Male Female
78 54 69 84 68 71 69 85 61
Page 18
TCGA-AA-3554TCGA-AA-3555TCGA-AA-3556TCGA-AA-3558TCGA-AA-3560TCGA-AA-3561TCGA-AA-3562TCGA-AA-3655TCGA-AA-3660
T3 T3 T2 T2 T3 T3 T3 T3 T3
Female Female Male Male Female Male Male Male Female
62 81 78 70 72 72 82 68 51
Page 19
TCGA-AA-3662TCGA-AA-3663TCGA-AA-3666TCGA-AA-3667TCGA-AA-3672TCGA-AA-3673TCGA-AA-3675TCGA-AA-3678TCGA-AA-3679
T4 T3 T3 T2 T3 T3 T3 T2 T3
Female Male Male Female Female Female Male Female Male
80 42 68 36 90 53 84 60 59
Page 20
TCGA-AA-3681TCGA-AA-3684TCGA-AA-3685TCGA-AA-3688TCGA-AA-3692TCGA-AA-3693TCGA-AA-3695TCGA-AA-3696TCGA-AA-3697
T3 T4 T3 T3 T3 T4 T3 T3 T3
Female Female Male Male Female Female Female Female Male
77 65 69 80 47 77 63 75 77
Page 21
TCGA-AA-3710TCGA-AA-3712TCGA-AA-3713TCGA-AA-3715TCGA-AA-3811TCGA-AA-3812TCGA-AA-3814TCGA-AA-3818TCGA-AA-3819
T3 T3 T3 T3 T3 T3 T3 T3 T3
Female Male Male Male Female Female Female Female Female
80 65 68 77 84 82 85 78 41
Page 22
TCGA-AA-3821TCGA-AA-3831TCGA-AA-3833TCGA-AA-3837TCGA-AA-3841TCGA-AA-3842TCGA-AA-3844TCGA-AA-3845TCGA-AA-3846
T2 T3 T3 T3 T3 T2 T3 T3 T3
Female Male Female Male Male Male Female Female Female
81 66 63 67 66 51 78 86 74
Page 23
TCGA-AA-3848TCGA-AA-3850TCGA-AA-3851TCGA-AA-3852TCGA-AA-3854TCGA-AA-3855TCGA-AA-3856TCGA-AA-3858TCGA-AA-3860
T3 T2 T3 T3 T2 T2 T3 T2 T3
Female Male Male Male Female Male Male Male Female
82 74 74 88 71 72 59 67 53
Page 24
TCGA-AA-3864TCGA-AA-3866TCGA-AA-3867TCGA-AA-3869TCGA-AA-3870TCGA-AA-3872TCGA-AA-3875TCGA-AA-3877TCGA-AA-3930
T3 T2 T3 T4 T3 T4 T1 T1 T3
Male Female Male Male Female Male Female Female Male
71 78 74 76 71 45 78 83 66
Page 25
TCGA-AA-3939TCGA-AA-3941TCGA-AA-3947TCGA-AA-3949TCGA-AA-3950TCGA-AA-3952TCGA-AA-3955TCGA-AA-3956TCGA-AA-3966
T3 T4 T4 T3 T3 T3 T2 T3 T3
Male Female Female Female Female Male Male Male Female
83 84 60 87 79 68 38 65 89
Page 26
TCGA-AA-3968TCGA-AA-3971TCGA-AA-3972TCGA-AA-3973TCGA-AA-3975TCGA-AA-3976TCGA-AA-3977TCGA-AA-3979TCGA-AA-3982
T2 T3 T3 T4 T2 T2 T2 T3 T3
Female Male Male Male Male Male Male Male Male
55 58 72 69 80 70 65 84 75
Page 27
TCGA-AA-3984TCGA-AA-3986TCGA-AA-3989TCGA-AA-3994TCGA-AD-A5EJTCGA-AD-A5EKTCGA-AD-5900TCGA-AD-6548TCGA-AD-6888
T3 T2 T3 T3 T3 T2 T2 T2 T3
Female Male Male Male Female Male Male Female Male
61 73 84 69 74 51 67 81 73
Page 28
TCGA-AD-6889TCGA-AD-6890TCGA-AD-6895TCGA-AD-6899TCGA-AD-6901TCGA-AD-6963TCGA-AD-6964TCGA-AD-6965TCGA-AF-A56K
T3 T1 T3 T4a T3 T3 T4a T4a T3
Male Male Male Male Male Male Male Male Male
76 65 84 84 78 58 58 62 56
Page 29
TCGA-AF-A56LTCGA-AF-A56NTCGA-AF-2687TCGA-AF-2689TCGA-AF-2690
T3 T3 T3 T3 T3
Female Female Male Female Female
48 47 57 41 76