Breast Invasive Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16a (cga svn revision 43808).

Summary

There were 866 tumor samples used in this analysis: 26 significant arm-level results, 28 significant focal amplifications, and 40 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 28 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
11q13.3 | 1.3335e-173 | 1.082e-158 | chr11:69400218-69487994 | 2
8q24.21 | 1.8717e-77 | 1.8717e-77 | chr8:128657453-128779930 | 1
8p11.23 | 1.0805e-78 | 1.7757e-69 | chr8:37487106-37610505 | 3
17q12 | 9.1914e-125 | 1.9675e-66 | chr17:37789433-37899687 | 9
17q23.1 | 8.9123e-69 | 1.0754e-46 | chr17:57921224-57946881 | 1
20q13.2 | 1.2486e-41 | 1.2486e-41 | chr20:52145875-52373091 | 1
1q21.3 | 5.3689e-32 | 9.3144e-23 | chr1:150345471-150706805 | 11
6q21 | 9.9126e-14 | 9.9126e-14 | chr6:107206856-107290700 | 2
15q26.3 | 7.6758e-12 | 7.6758e-12 | chr15:98907098-99674749 | 5
3q26.32 | 1.683e-11 | 1.683e-11 | chr3:176494151-179797799 | 13
12q15 | 1.7897e-11 | 1.7897e-11 | chr12:69265279-69983634 | 10
1p22.3 | 1.0946e-10 | 1.197e-10 | chr1:85979933-86002734 | 1
1q44 | 3.1641e-17 | 4.0142e-08 | chr1:233299470-249250621 | 136
12p13.33 | 3.5692e-05 | 3.5692e-05 | chr12:1-1291266 | 13
8p11.21 | 3.8594e-29 | 4.523e-05 | chr8:42155813-42254056 | 4
10q22.3 | 4.573e-05 | 4.573e-05 | chr10:80467192-82012440 | 17
11q14.1 | 1.384e-55 | 0.00021241 | chr11:76855255-78169088 | 17
10p15.1 | 0.00073328 | 0.00073328 | chr10:3730052-6398978 | 28
6p23 | 0.0011615 | 0.0011615 | chr6:12431411-15555356 | 12
11p13 | 0.0023667 | 0.0029197 | chr11:32402479-33859313 | 16
4q13.3 | 0.0054045 | 0.0054045 | chr4:73389847-75049413 | 18
14q21.1 | 0.0060331 | 0.0060331 | chr14:37963714-38073152 | 2
19q12 | 0.00021674 | 0.0060331 | chr19:29772775-30862416 | 7
19q13.42 | 0.0028092 | 0.012845 | chr19:55524376-58776467 | 116
3p26.1 | 0.018707 | 0.018707 | chr3:3911146-5277098 | 8
13q12.3 | 0.023521 | 0.086012 | chr13:30394777-31229520 | 6
13q34 | 0.022038 | 0.12926 | chr13:93345298-115169878 | 109
17p11.2 | 0.14154 | 0.16723 | chr17:20801837-21012802 | 1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

Table S1. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CCND1
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

Table S2. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MYC

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

Table S3. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERLIN2
ZNF703
LOC728024

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

Table S4. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERBB2
GRB7
PNMT
TCAP
STARD3
PPP1R1B
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

Table S5. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TUBD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

Table S6. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZNF217

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

Table S7. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-4257
CTSS
ECM1
ENSA
MCL1
RPRD2
ADAMTSL4
GOLPH3L
TARS2
HORMAD1
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

Table S8. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-587
LOC100422737

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

Table S9. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IGF1R
SYNM
PGPEP1L
FAM169B
MIR4714

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

Table S10. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PIK3CA
ACTL6A
NDUFB5
USP13
KCNMB2
KCNMB3
ZNF639
PEX5L
MFN1
MRPL47
GNB4
ZMAT3
TBL1XR1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q15.

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-1279
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
MIR1279
MIR3913-2
MIR3913-1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p22.3.

Table S12. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DDAH1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q44.

Table S13. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
ACTN2
ADSS
CHML
LYST
CHRM3
GNG4
HNRNPU
KCNK1
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
ZNF124
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZNF238
SDCCAG8
RBM34
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
PPPDE1
SCCPDH
ARID4B
KIF26B
HEATR1
ZNF692
ERO1LB
FMN2
ZNF695
ZP4
TFB2M
GREM2
SMYD3
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2G3
OR2G2
OR2C3
EFCAB2
KIAA1804
ZNF496
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
EDARADD
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR2W5
OR13G1
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LGALS8-AS1
MIR1537
LINC00184
MIR3123
MIR3124
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4677
MIR4671
MIR4427

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

Table S14. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
KDM5A
NINJ2
RAD52
SLC6A12
SLC6A13
ERC1
WNK1
CCDC77
B4GALNT3
IQSEC3
LOC574538
FAM138D
LOC100288778

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

Table S15. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IKBKB
POLB
VDAC3
DKK4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.3.

Table S16. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ANXA11
SFTPD
MBL1P
PPIF
ZMIZ1
FAM213A
EIF5AL1
LOC219347
PLAC9
ZCCHC24
LOC283050
LOC439990
LOC642361
LOC650623
SFTPA1
SFTPA2
LOC100288974

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q14.1.

Table S17. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CLNS1A
MYO7A
NDUFC2
PAK1
THRSP
GAB2
C11orf67
RSF1
USP35
KCTD14
ALG8
NARS2
INTS4
GDPD4
AQP11
KCTD21
NDUFC2-KCTD14

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.1.

Table S18. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3155
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IL2RA
IL15RA
PFKFB3
AKR1C3
NET1
CALML5
ANKRD16
FAM208B
ASB13
TUBAL3
AKR1E2
FBXO18
RBM17
UCN3
LOC338588
AKR1CL1
tAKR
LOC399715
LOC100216001
MIR3155A
MIR3155B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p23.

Table S19. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
JARID2
CD83
RANBP9
SIRT5
TBC1D7
NOL7
GFOD1
CCDC90A
DTNBP1
RNF182
PHACTR1
LOC100130357

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

Table S20. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
WT1
CD59
CSTF3
HIPK3
EIF3M
C11orf41
FBXO3
WT1-AS
TCP11L1
PRRG4
QSER1
DEPDC7
LINC00294
LOC338739
CCDC73
C11orf91

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

Table S21. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
AFM
AFP
ALB
CXCL1
CXCL2
CXCL3
IL8
PF4
PF4V1
PPBP
CXCL6
CXCL5
ADAMTS3
PPBPL2
ANKRD17
RASSF6
COX18
MTHFD2L

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.1.

Table S22. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FOXA1
MIPOL1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q12.

Table S23. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CCNE1
URI1
POP4
PLEKHF1
C19orf12
LOC284395
VSTM2B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.42.

Table S24. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-1274b
FKBP1AP1
IL11
PEG3
PTPRH
RPL28
AURKC
SYT5
TNNI3
TNNT1
ZNF17
ZNF134
ZNF135
ZNF154
ZNF264
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
U2AF2
PPP6R1
ZIM2
HSPBP1
ZNF544
UBE2S
CCDC106
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
ZNF416
NAT14
VN1R1
ZNF304
ZNF471
USP29
ZNF71
ZNF667
ZSCAN18
ZSCAN5A
ZNF329
ZNF419
ISOC2
ZNF552
ZNF671
ZNF606
BRSK1
SUV420H2
ZNF587
FIZ1
GALP
ZNF628
ZNF551
ZNF835
RDH13
ZIM3
ZNF543
COX6B2
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
ZNF550
ZNF579
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZNF530
C19orf51
ZNF773
LOC386758
TMEM238
ZNF470
ZNF749
ZNF805
ZNF772
DUXA
SBK2
SHISA7
ZNF814
MIMT1
LOC100128252
LOC100128398
SGK110
PEG3-AS1
ZNF587B
ZNF865

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p26.1.

Table S25. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ITPR1
SETMAR
BHLHE40
EDEM1
ARL8B
SUMF1
EGOT
LOC100507582

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.3.

Table S26. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
HMGB1
UBL3
USPL1
KATNAL1
LOC440131
LINC00426

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q34.

Table S27. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
FGF14
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
RAP2A
GRK1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
OXGR1
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
TEX29
METTL21CP1
SPACA7
RNF113B
GPR180
CLYBL
METTL21C
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
FAM70B
C13orf35
FLJ44054
CCDC168
FLJ41484
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
MIR3170
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4705

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p11.2.

Table S28. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
USP22

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 40 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
8p23.2 | 4.6582e-41 | 1.2268e-40 | chr8:2079140-6262191 | 1
13q14.2 | 1.1938e-33 | 1.1938e-33 | chr13:48833767-49064807 | 2
1p36.13 | 6.1558e-34 | 7.0259e-30 | chr1:11321154-23038731 | 169
19p13.3 | 4.6831e-29 | 4.6831e-29 | chr19:1103802-1943798 | 35
3p14.3 | 2.7861e-25 | 2.7736e-25 | chr3:55883233-61547330 | 26
11q23.2 | 1.9038e-41 | 2.4311e-22 | chr11:105010192-118315445 | 114
10q23.31 | 1.4533e-27 | 2.8137e-22 | chr10:89615138-90034038 | 2
17p12 | 2.3964e-17 | 3.0626e-17 | chr17:11896630-12456081 | 3
15q12 | 4.7931e-16 | 4.7931e-16 | chr15:28096454-31198928 | 22
4q35.2 | 8.5786e-14 | 8.6431e-14 | chr4:178911874-191154276 | 64
11p15.5 | 1.0248e-13 | 1.0086e-13 | chr11:1-2468266 | 95
9p21.3 | 8.7385e-22 | 1.3802e-13 | chr9:21865498-22448737 | 4
6q27 | 1.0516e-17 | 1.5973e-13 | chr6:167548608-168862573 | 12
2q37.3 | 2.1095e-11 | 2.1095e-11 | chr2:237038083-243199373 | 79
17q12 | 4.1799e-11 | 4.8636e-11 | chr17:31957152-33257606 | 8
14q24.3 | 5.7945e-10 | 5.8299e-10 | chr14:65054827-99640110 | 246
7q36.1 | 5.9774e-10 | 5.9409e-10 | chr7:151817415-152136074 | 1
16q24.3 | 1.6362e-08 | 1.6185e-08 | chr16:88525832-90354753 | 49
21q11.2 | 1.726e-08 | 1.7882e-08 | chr21:1-15482604 | 16
5q11.2 | 2.2749e-10 | 5.448e-07 | chr5:53838110-60632719 | 36
6q15 | 6.6742e-11 | 1.3219e-06 | chr6:79945370-111983004 | 139
18q23 | 6.0929e-06 | 6.0929e-06 | chr18:67515151-78077248 | 39
6p25.3 | 0.00013043 | 0.00013279 | chr6:1-7327845 | 45
10q26.3 | 7.5581e-12 | 0.00028179 | chr10:129922812-135534747 | 52
11q25 | 1.5845e-36 | 0.00074545 | chr11:132204656-135006516 | 15
12p13.1 | 0.001048 | 0.0010591 | chr12:12418624-13714562 | 23
1p21.2 | 1.2975e-07 | 0.0015663 | chr1:79319634-119577924 | 282
20p13 | 0.0035972 | 0.0035972 | chr20:1-815752 | 18
4p16.3 | 0.0040773 | 0.0040735 | chr4:1-1215099 | 26
12q24.31 | 1.2171e-06 | 0.0042956 | chr12:113335426-133851895 | 192
8p11.21 | 0.0016166 | 0.012581 | chr8:42883855-47753079 | 4
7p22.3 | 0.018259 | 0.018039 | chr7:1-2344938 | 31
9p13.1 | 0.00093438 | 0.040995 | chr9:38619152-71152237 | 50
9p24.1 | 6.1113e-06 | 0.046019 | chr9:7799607-12693402 | 1
11q13.1 | 0.00011116 | 0.051592 | chr11:63886540-65684611 | 90
19q13.32 | 0.066785 | 0.066329 | chr19:46717474-48279236 | 44
5q21.3 | 7.907e-05 | 0.12937 | chr5:61923094-128802514 | 279
12q23.1 | 5.9217e-05 | 0.1409 | chr12:99124001-100431272 | 2
22q13.32 | 0.20266 | 0.19899 | chr22:46365895-51304566 | 69
9q34.3 | 0.11343 | 0.23555 | chr9:131703171-141213431 | 208

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

Table S29. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CSMD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

Table S30. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.13.

Table S31. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PAX7
SDHB
hsa-mir-1256
hsa-mir-1290
ALPL
C1QA
C1QB
C1QC
CAPZB
CASP9
TNFRSF8
CDA
CDC42
CLCN6
CLCNKA
CLCNKB
DDOST
ECE1
EPHA2
EPHA8
HSPG2
HTR6
MFAP2
MTHFR
NBL1
NPPA
NPPB
PLA2G2A
PLA2G5
PLOD1
RAP1GAP
RSC1A1
TNFRSF1B
ZBTB17
PRDM2
AKR7A2
ALDH4A1
EIF4G3
DHRS3
CROCC
ZBTB40
MFN2
CELA3A
MAD2L2
PDPN
MST1P2
MST1P9
PADI2
CTRC
AKR7A3
SPEN
KIAA0090
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
CELA3B
PADI4
C1orf144
FBXO2
FBXO6
PLA2G2D
HSPB7
LINC00339
UBIAD1
PADI1
PLA2G2E
HP1BP3
CELA2B
MRTO4
PADI3
WNT4
FBXO42
RNF186
FBLIM1
PQLC2
TMEM51
ARHGEF10L
VPS13D
CAMK2N1
NBPF1
NECAP2
RCC2
AGTRAP
PTCHD2
KIF17
MIIP
CELA2A
PLA2G2F
PINK1
PRAMEF1
PRAMEF2
EFHD2
RSG1
MUL1
AGMAT
TAS1R2
ACTL8
USP48
NBPF3
DDI2
CROCCP2
IGSF21
KIAA2013
C1orf158
FBXO44
CROCCP3
FHAD1
LRRC38
AADACL3
IFFO2
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf64
FAM43B
C1orf126
AKR7L
TMCO4
SLC25A34
ESPNP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
TMEM82
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
PRAMEF3
LDLRAD2
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
PRAMEF7
PRAMEF19
PRAMEF20
LOC649330
PRAMEF22
PRAMEF15
PRAMEF16
SNORA59B
SNORA59A
PRAMEF14
FLJ37453
NPPA-AS1
MIR3675
LOC100506730
LOC100506801
C1orf151-NBL1
MIR4695
MIR4632

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.3.

Table S32. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
STK11
TCF3
hsa-mir-1909
ATP5D
CIRBP
EFNA2
GAMT
GPX4
RPS15
APC2
UQCR11
SBNO2
DAZAP1
MBD3
PCSK4
C19orf24
REXO1
FAM108A1
KLF16
MUM1
MIDN
REEP6
SCAMP4
ADAT3
PLK5
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
ADAMTSL5
NDUFS7
ONECUT3
MEX3D
LOC100288123
MIR1909

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.3.

Table S33. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FHIT
ARF4
DNASE1L3
FLNB
PDHB
SLMAP
ACOX2
HESX1
RPP14
FAM107A
FAM208A
APPL1
ARHGEF3
IL17RD
PXK
ABHD6
FAM3D
ASB14
C3orf67
KCTD6
DNAH12
PDE12
FAM116A
CCDC66
SPATA12
MIR3938

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

Table S34. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATM
DDX10
PAFAH1B2
POU2AF1
SDHD
PCSK7
hsa-mir-4301
hsa-mir-34c
ACAT1
APOA1
APOA4
APOC3
FXYD2
CD3D
CD3E
CD3G
CRYAB
DLAT
DRD2
FDX1
GRIA4
GUCY1A2
HSPB2
HTR3A
IL10RA
IL18
NCAM1
NNMT
NPAT
PPP2R1B
PTS
RDX
SCN2B
SCN4B
SLN
TAGLN
ZBTB16
CUL5
ZNF259
HTR3B
ZW10
UBE4A
RBM7
MPZL2
ATP5L
CEP164
EXPH5
SIK2
SIK3
BACE1
CADM1
REXO2
TIMM8B
SIDT2
FXYD6
C11orf71
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
TEX12
TMPRSS4
DSCAML1
ARHGAP20
USP28
AASDHPPT
C11orf1
ALG9
TMPRSS5
BCO2
TMPRSS13
KIAA1826
BUD13
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
MPZL3
ANKK1
RNF214
LOC283143
C11orf53
C11orf34
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
LOC643923
CLDN25
LOC100132078
LOC100288346
BACE1-AS
MIR4301
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4491
LOC100652768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.31.

Table S35. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PTEN
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

Table S36. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MAP2K4
hsa-mir-744
MIR744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
APBA2
TJP1
HERC2
FAM189A1
DKFZP434L187
NDNL2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
GOLGA8G
HERC2P9
WHAMMP2
LOC646278
LOC653075
GOLGA8F
ULK4P2
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4509-3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

Table S38. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DUX4
hsa-mir-1305
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ZFP42
ENPP6
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
HRAS
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
ASCL2
CD81
CD151
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
LSP1
MUC2
MUC6
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
SCT
TALDO1
TH
TSPAN4
TNNI2
TNNT3
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
C11orf21
TRPM5
IGF2-AS1
BET1L
CEND1
CDHR5
TOLLIP
PIDD
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
MOB2
SYT8
ODF3
LRRC56
LOC143666
SCGB1C1
NLRP6
NS3BP
LOC255512
C11orf35
H19
EFCAB4A
TMEM80
ANO9
LOC338651
B4GALNT4
PDDC1
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
MIR483
SNORA52
LOC653486
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.3.

Table S40. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

Table S41. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MLLT4
GPR31
KIF25
TCP10
C6orf123
UNC93A
FRMD1
TTLL2
DACT2
TCP10L2
MLLT4-AS1
HGC6.3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

Table S42. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
FLJ43879
MIR149
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q12.

Table S43. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CCL1
CCL2
CCL7
CCL8
CCL11
CCL13
TMEM132E
C17orf102

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.3.

Table S44. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
DIO2
DLST
EIF2S1
ERH
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
IFI27
ITPK1
LTBP2
MAX
ATXN3
MAP3K9
ALDH6A1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
SEL1L
SRSF5
SLC8A3
SLC10A1
SPTB
TGFB3
VRK1
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
RPS6KA5
NRXN3
SPTLC2
TCL1B
RGS6
KIAA0247
KIAA0317
MED6
VTI1B
FBLN5
BATF
NPC2
AHSA1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
SNW1
PCNX
TTLL5
ANGEL1
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
C14orf109
PLEK2
MLH3
PRO1768
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
ATP6V1D
C14orf129
ASB2
ZFYVE1
CPSF2
KCNK10
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
GALNTL1
PLEKHH1
UNC79
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
IRF2BPL
MPP5
OTUB2
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
SLIRP
DNAL1
RPS6KL1
IFI27L2
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
IFT43
AK7
IFI27L1
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
SAMD15
EML5
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
C14orf55
ITPK1-AS1
SNORD56B
SERPINA9
VSX2
COX8C
RAB15
SERPINA13
C14orf64
HEATR4
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
LINC00238
CCDC88C
ACOT1
ACOT6
LOC645431
SYNDIG1L
SCARNA13
SNORA79
LOC731223
SNORA11B
LOC100129345
LOC100289511
MIR1260A
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
LOC100628307

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.1.

Table S45. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MLL3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

Table S46. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CBFA2T3
FANCA
AFG3L1P
APRT
C16orf3
CDH15
CYBA
DPEP1
GALNS
GAS8
MC1R
MVD
CHMP1A
RPL13
SPG7
CDK10
C16orf7
PIEZO1
TUBB3
PRDM7
TCF25
CPNE7
IL17C
ANKRD11
TRAPPC2L
DEF8
DBNDD1
CDT1
SPIRE2
CENPBD1
ZNF276
RNF166
SPATA2L
C16orf55
ZC3H18
SLC22A31
MGC23284
ZNF778
ACSF3
LINC00304
SNAI3
CTU2
PABPN1L
LOC400558
SNORD68
LOC100128881
LOC100130015
LOC100287036
MIR4722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

Table S47. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
TPTE
C21orf15
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
POTED
ANKRD20A11P
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

Table S48. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IL6ST
hsa-mir-582
hsa-mir-449c
ERCC8
GZMA
GZMK
MAP3K1
PDE4D
PPAP2A
CCNO
PLK2
ESM1
SKIV2L2
PART1
DHX29
DDX4
DEPDC1B
GPBP1
ANKRD55
ELOVL7
NDUFAF2
RAB3C
C5orf35
IL31RA
SLC38A9
MIER3
CDC20B
GAPT
IDAS
ACTBL2
RNF138P1
GPX8
MIR449A
C5orf43
MIR449B
MIR449C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q15.

Table S49. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
BCKDHB
CCNC
CGA
CNR1
EPHA7
FOXO3
GABRR1
GABRR2
GPR6
GRIK2
HTR1E
ME1
NT5E
PGM3
POU3F2
PREP
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WASF1
TBX18
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDK19
MDN1
UFL1
ORC3
PNISR
IBTK
FBXL4
SNORD50A
SESN1
OSTM1
NDUFAF4
CYB5R4
C6orf203
CDC40
UBE2J1
COQ3
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
FAM46A
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
SLC16A10
RIPPLY2
PM20D2
SRSF12
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
LACE1
MMS22L
SCML4
CEP57L1
PPIL6
GJB7
SNHG5
LINC00222
LIN28B
GSTM2P1
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
C6orf186
LOC100130890
MIR2113
MIR548H3
LOC100422737
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

Table S50. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
SOCS6
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
SALL3
TIMM21
ZNF407
CNDP2
RBFA
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

Table S51. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IRF4
BPHL
SERPINB1
F13A1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TUBB2A
RIPK1
PRPF4B
CDYL
LY86
ECI2
FARS2
RPP40
FAM50B
NRN1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
FOXQ1
HUS1B
C6orf195
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
MYLK4
TUBB2B
PSMG4
DKFZP686I15217
C6orf201
PPP1R3G
MIR3691
LOC100507194
LOC100508120
MIR4645

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

Table S52. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DUX4
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
ADAM8
BNIP3
CYP2E1
ECHS1
INPP5A
MGMT
UTF1
GLRX3
DPYSL4
TUBGCP2
DUX2
VENTX
CALY
TTC40
PPP2R2D
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
CTAGE7P
C10orf91
PWWP2B
PAOX
EBF3
TCERG1L
C10orf125
JAKMIP3
STK32C
LOC387723
FLJ46300
LOC399829
SPRNP1
FRG2B
SPRN
MIR202
LOC619207
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
MIR378C
MIR4297
MIR3944

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

Table S53. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
OPCML
IGSF9B
NCAPD3
ACAD8
B3GAT1
THYN1
JAM3
GLB1L2
VPS26B
GLB1L3
SPATA19
LOC283174
LOC283177
LOC100128239
MIR4697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

Table S54. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-614
hsa-mir-613
CDKN1B
CREBL2
EMP1
GPR19
GPRC5A
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
DUSP16
APOLD1
GSG1
HTR7P1
LOH12CR1
C12orf36
RPL13AP20
LOH12CR2
MIR613
MIR614
LOC100506314

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p21.2.

Table S55. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
TSPAN2
BCAS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
PTPN22
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p13.

Table S56. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CSNK2A1
SOX12
TCF15
RBCK1
TRIB3
NRSN2
DEFB126
ZCCHC3
SCRT2
C20orf54
TBC1D20
C20orf96
SRXN1
DEFB127
DEFB129
DEFB125
DEFB128
DEFB132

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.3.

Table S57. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-571
ATP5I
DGKQ
GAK
IDUA
MYL5
PDE6B
ZNF141
PCGF3
SPON2
CPLX1
SLC26A1
FGFRL1
PIGG
ABCA11P
MFSD7
TMEM175
ZNF595
ZNF721
ZNF718
RNF212
ZNF876P
ZNF732
LOC100129917
LOC100130872
TMED11P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.31.

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BCL7A
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
ACADS
SCARB1
COX6A1
DTX1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PLA2G1B
POLE
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RPLP0
CLIP1
SFSWAP
TBX5
TBX3
HNF1A
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
ULK1
RASAL1
DENR
OASL
DYNLL1
SRSF9
HRK
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RBM19
RNF10
MPHOSPH9
CAMKK2
ZNF268
TMED2
GCN1L1
SDS
RAB35
SNRNP35
CIT
FZD10
MLXIP
P2RX2
FBXO21
SETD1B
ANKLE2
MED13L
SIRT4
ABCB9
RIMBP2
ATP6V0A2
FBXW8
HSPB8
HCAR1
GALNT9
ARL6IP4
TAOK3
POP5
ANAPC5
TRIAP1
TPCN1
RHOF
VSIG10
TESC
SBNO1
ZCCHC8
CHFR
WSB2
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
LHX5
SUDS3
C12orf43
VPS33A
RSRC2
AACS
DDX54
NOC4L
B3GNT4
OGFOD2
VPS37B
C12orf49
TCTN2
SLC24A6
RNF34
CCDC92
PUS1
COQ5
SRRM4
CCDC62
KDM2B
UNC119B
ORAI1
RNFT2
C12orf52
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
TMEM132D
SLC15A4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
LOC144742
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
LRRC43
LOC255480
GPR133
MORN3
KSR2
GATC
HNF1A-AS1
DDX51
HCAR2
LOC338799
EP400NL
RILPL1
IL31
CCDC42B
TMEM233
SETD8
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
MAP1LC3B2
LOC647589
SNORA49
MIR620
LOC100128554
LOC100130238
LOC100190940
LINC00173
ZNF605
MIR1178
MIR4304
MIR3612
MIR3908
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4498
MIR4472-2
MIR4700

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.21.

Table S59. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FNTA
SGK196
HGSNAT
POTEA

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.3.

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-339
GPER
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
ADAP1
SUN1
INTS1
FTSJ2
GET4
CYP2W1
HEATR2
FAM20C
MICALL2
PSMG3
C7orf50
ZFAND2A
COX19
KIAA1908
GPR146
TMEM184A
TFAMP1
UNCX
ELFN1
FLJ44511
LOC442497
MIR339
LOC100288524
MIR4655

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p13.1.

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-1299
PGM5
ZNF658
FAM75A7
CNTNAP3
ANKRD20A1
FAM201A
CBWD5
LOC286297
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
FAM74A1
FAM74A4
ZNF658B
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.1.

Table S62. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PTPRD

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q13.1.

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MEN1
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
ARL2
BAD
C11orf2
MRPL49
ZNHIT2
CAPN1
CFL1
CTSW
ESRRA
FAU
FKBP2
DNAJC4
LTBP3
MAP3K11
OVOL1
PLCB3
PPP2R5B
PYGM
MAP4K2
RELA
DPF2
SIPA1
TM7SF2
VEGFB
SF1
ZFPL1
FOSL1
RPS6KA4
FIBP
NRXN2
NAALADL1
KCNK7
RASGRP2
CDC42EP2
KAT5
SSSCA1
EHD1
STIP1
CCDC85B
ATG2A
FAM89B
POLA2
PRDX5
C11orf20
PPP1R14B
SAC3D1
SNX15
EFEMP2
KCNK4
TRMT112
CDC42BPG
SLC22A11
GPR137
SCYL1
MUS81
FERMT3
TRPT1
FRMD8
RNASEH2C
NUDT22
SYVN1
DKFZp761E198
CDCA5
BATF2
SLC22A12
GPHA2
TIGD3
LOC254100
EHBP1L1
SNX32
C11orf85
SLC25A45
NEAT1
CCDC88B
MALAT1
SPDYC
PCNXL3
MIR192
MIR194-2
SLC22A20
MIR612
LOC100130348
MIR1237
ARL2-SNX15
MIR4489
MIR4690

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3191
hsa-mir-320e
C5AR1
CALM3
AP2S1
ARHGAP35
NPAS1
PPP5C
PTGIR
SLC1A5
SLC8A2
NAPA
DHX34
SAE1
KPTN
ZC3H4
PRKD2
CCDC9
BBC3
GPR77
STRN4
GLTSCR2
GLTSCR1
EHD2
TMEM160
PNMAL1
MEIS3
PNMAL2
HIF3A
FKRP
CCDC8
ZNF541
GNG8
DACT3
PRR24
IGFL1
SNORD23
SNAR-E
MIR3191
MIR3190
MIR320E
LOC100505681
LOC100506012
LOC100506068

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.3.

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
APC
PIK3R1
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
TRIM23
ARSB
ALDH7A1
BHMT
BTF3
CAMK4
CAST
CCNB1
CCNH
CDK7
CDO1
CETN3
CHD1
CKMT2
AP3S1
COX7C
CRHBP
HAPLN1
CSNK1G3
VCAN
DMXL1
DHFR
EFNA5
F2R
F2RL1
F2RL2
FBN2
FER
FOXD1
GLRX
GTF2H2
HEXB
HMGCR
HSD17B4
HTR1A
KCNN2
TNPO1
LMNB1
LNPEP
LOX
CD180
MAN2A1
MAP1B
MCC
MEF2C
MSH3
NAIP
PAM
PCSK1
PGGT1B
PMCHL2
PPIC
RAD17
RASA1
RASGRF2
RPS23
SLC12A2
SMN1
SMN2
SNX2
SRP19
TAF9
TBCA
NR2F1
THBS4
XRCC4
ST8SIA4
REEP5
SERF1A
ENC1
AP3B1
PDE8B
ATG12
NREP
RAB9BP1
HOMER1
SCAMP1
CARTPT
SNCAIP
TTC37
ZFYVE16
PJA2
EDIL3
COL4A3BP
LHFPL2
CWC27
NSA2
POLR3G
IQGAP2
SMA4
SMA5
ADAMTS6
RHOBTB3
ELL2
SV2C
MRPS27
PPIP5K2
PPWD1
OTP
SSBP2
BHMT2
TNFAIP8
FAM169A
RNU5E-1
RNU5D-1
SLC27A6
SNX24
DMGDH
TMED7
ISOC1
GCNT4
PRR16
COMMD10
POLK
ERAP1
PHAX
FLJ11235
SGTB
GIN1
AGGF1
WDR41
TRIM36
RIOK2
BDP1
ERBB2IP
FEM1C
NLN
ZNF608
SEMA6A
ARRDC3
ANKRA2
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
MCTP1
PTCD2
C5orf44
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
MEGF10
SPZ1
TSLP
C5orf30
SLC25A46
MRPS36
ATP6AP1L
PRDM6
FTMT
EPB41L4A-AS1
MARCH3
FCHO2
LYSMD3
SLCO6A1
PRRC1
JMY
ZNF474
POU5F2
TMEM171
TMEM174
POC5
STARD4
WDR36
ACOT12
SREK1
CEP120
TMEM167A
MBLAC2
TMEM161B
SRFBP1
MARVELD2
ARSK
FAM81B
CCDC112
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
CCDC125
C5orf27
CMYA5
AQPEP
ANKRD31
SERINC5
KIAA0825
GPR150
DTWD2
NBPF22P
RNF180
SREK1IP1
RGMB
RFESD
FAM170A
ANKRD34B
FAM174A
MTX3
SLCO4C1
TICAM2
MAST4
C5orf48
RGS7BP
C5orf63
MIR9-2
CRSP8P
FLJ42709
FLJ35946
CTXN3
TMEM232
LOC644100
FLJ33630
LOC644936
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR583
GTF2H2C
LOC728342
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
LOC100131067
FAM159B
LOC100133050
LOC100170939
LOC100272216
LOC100289230
LOC100289673
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR1244-3
MIR1244-2
MIR4280
MTRNR2L2
MIR3607
MIR3660
LOC100505678
LOC100505841
LOC100505894
OCLN
MIR4804
MIR4633
MIR3977
MIR4460
MIR4803

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ANKS1B
FAM71C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

Table S67. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3201
hsa-let-7b
ACR
ARSA
CHKB
CPT1B
TYMP
PPARA
MAPK11
MAPK12
SBF1
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
FAM19A5
NCAPH2
GTSE1
MOV10L1
TTC38
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR3201
MIR3619
MIR4763
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.3.

Table S68. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
ABCA2
ABO
ASS1
C8G
CACNA1B
ENTPD2
CEL
CELP
COL5A1
CRAT
DBH
SARDH
TOR1A
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PPP2R4
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
FUBP3
CLIC3
GTF3C5
GTF3C4
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
NOXA1
USP20
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
DOLK
SETX
PMPCA
EXOSC2
NCS1
NUP188
COBRA1
NELF
GPSM1
DKFZP434A062
GBGT1
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
TOR1B
METTL11A
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
PRRX2
C9orf78
FBXW5
C9orf167
EXD3
C9orf86
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
GPR107
PRDM12
CARD9
DDX31
MRPL41
EHMT1
AIF1L
UCK1
NTNG2
PRRC2B
PPAPDC3
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
SAPCD2
C9orf69
UAP1L1
ARRDC1
WDR85
TMEM203
ZMYND19
NACC2
C9orf116
LCN8
FAM69B
ASB6
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LINC00094
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
C9orf106
LCN10
C9orf173
NRARP
FAM163B
FLJ40292
TUBBP5
RNF224
SNORA17
SNORA43
SNORD62B
MIR602
RNF208
DNLZ
LOC100128593
LOC100129722
LOC100130954
LOC100131193
FAM157B
RNU6ATAC
LOC100272217
LOC100289341
MIR4292
MIR3621
MIR3689A
MIR3689B
LOC100506190
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR4479

Arm-level results

Table 3. Get Full Table Arm-level significance table - 26 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.21 | 0.933 | 0.638 | 0.31 | 7.86 | 8.88e-15
1q | 1955 | 0.64 | 30 | 0 | 0.34 | 6.97 | 6.33e-12
2p | 924 | 0.12 | -7.12 | 1 | 0.19 | -2.92 | 1
2q | 1556 | 0.07 | -9.22 | 1 | 0.21 | -0.518 | 1
3p | 1062 | 0.14 | -5.62 | 1 | 0.20 | -2.01 | 1
3q | 1139 | 0.20 | -1.77 | 1 | 0.12 | -6.82 | 1
4p | 489 | 0.10 | -8.63 | 1 | 0.34 | 5.63 | 2.59e-08
4q | 1049 | 0.09 | -8.26 | 1 | 0.30 | 4.49 | 8.83e-06
5p | 270 | 0.30 | 2.43 | 0.0335 | 0.20 | -3.34 | 1
5q | 1427 | 0.22 | 0.191 | 1 | 0.26 | 2.45 | 0.0135
6p | 1173 | 0.21 | -1.09 | 1 | 0.23 | 0.367 | 0.549
6q | 839 | 0.17 | -4.23 | 1 | 0.31 | 4.26 | 2.28e-05
7p | 641 | 0.29 | 2.63 | 0.0247 | 0.16 | -5.22 | 1
7q | 1277 | 0.23 | 0.716 | 0.79 | 0.16 | -3.86 | 1
8p | 580 | 0.31 | 3.04 | 0.0079 | 0.57 | 19.7 | 0
8q | 859 | 0.51 | 17.2 | 0 | 0.25 | 0.644 | 0.452
9p | 422 | 0.17 | -5.03 | 1 | 0.34 | 5.49 | 5.39e-08
9q | 1113 | 0.14 | -5.39 | 1 | 0.30 | 4.44 | 1.06e-05
10p | 409 | 0.21 | -2.69 | 1 | 0.22 | -2.24 | 1
10q | 1268 | 0.13 | -6.1 | 1 | 0.24 | 1.04 | 0.272
11p | 862 | 0.16 | -4.96 | 1 | 0.30 | 3.57 | 0.000379
11q | 1515 | 0.13 | -5.17 | 1 | 0.38 | 11.2 | 0
12p | 575 | 0.23 | -1.62 | 1 | 0.18 | -4.08 | 1
12q | 1447 | 0.19 | -1.88 | 1 | 0.14 | -5.12 | 1
13q | 654 | 0.14 | -5.5 | 1 | 0.44 | 12.6 | 0
14q | 1341 | 0.18 | -2.86 | 1 | 0.27 | 2.92 | 0.00351
15q | 1355 | 0.12 | -6.2 | 1 | 0.32 | 6.47 | 1.77e-10
16p | 872 | 0.42 | 10.2 | 0 | 0.42 | 10.2 | 0
16q | 702 | 0.21 | -1.43 | 1 | 0.65 | 26.1 | 0
17p | 683 | 0.14 | -4.58 | 1 | 0.62 | 24.9 | 0
17q | 1592 | 0.25 | 2.47 | 0.0335 | 0.34 | 8.2 | 5.55e-16
18p | 143 | 0.22 | -2.63 | 1 | 0.37 | 6.17 | 1.12e-09
18q | 446 | 0.19 | -3.61 | 1 | 0.35 | 5.85 | 7.67e-09
19p | 995 | 0.19 | -2.64 | 1 | 0.23 | -0.581 | 1
19q | 1709 | 0.23 | 1.3 | 0.385 | 0.22 | 0.576 | 0.471
20p | 355 | 0.41 | 9.65 | 0 | 0.16 | -5.52 | 1
20q | 753 | 0.43 | 12.6 | 0 | 0.09 | -7.92 | 1
21q | 509 | 0.22 | -1.99 | 1 | 0.21 | -2.71 | 1
22q | 921 | 0.17 | -3.57 | 1 | 0.48 | 15.9 | 0
Xq | 1312 | 0.17 | -3.43 | 1 | 0.23 | 0.38 | 0.549

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1970999/2.GDAC_MergeDataFiles.Finished/BRCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 866 Input Tumor Samples.

Tumor Sample Names
TCGA-A1-A0SB-01A-11D-A141-01
TCGA-A1-A0SD-01A-11D-A111-01
TCGA-A1-A0SE-01A-11D-A087-01
TCGA-A1-A0SF-01A-11D-A141-01
TCGA-A1-A0SG-01A-11D-A141-01
TCGA-A1-A0SH-01A-11D-A087-01
TCGA-A1-A0SI-01A-11D-A141-01
TCGA-A1-A0SJ-01A-11D-A087-01
TCGA-A1-A0SK-01A-12D-A087-01
TCGA-A1-A0SM-01A-11D-A087-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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