Stomach Adenocarcinoma: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 306 tumor samples used in this analysis: 26 significant arm-level results, 29 significant focal amplifications, and 46 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 - 29 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
--- | --- | --- | --- | ---
17q12 | 5.8394e-43 | 5.8394e-43 | chr17:37854508-37876018 | 1
19q12 | 8.5145e-31 | 8.5145e-31 | chr19:30287570-30358836 | 1
12p12.1 | 2.8021e-22 | 2.8021e-22 | chr12:25348817-25414737 | 2
8q24.21 | 1.0519e-19 | 1.0519e-19 | chr8:128627168-128754688 | 1
7q21.2 | 8.5005e-19 | 1.0267e-18 | chr7:92104677-92557998 | 6
8p23.1 | 1.355e-13 | 1.355e-13 | chr8:11547791-11638987 | 2
20q13.2 | 1.5462e-12 | 1.5462e-12 | chr20:52148496-52552779 | 2
18q11.2 | 2.6039e-11 | 2.6039e-11 | chr18:19594807-19766958 | 1
6p21.1 | 7.7029e-11 | 1.1184e-10 | chr6:43593968-43811746 | 5
11q13.3 | 1.4417e-10 | 1.5106e-10 | chr11:69150824-69595013 | 4
12q15 | 3.7309e-10 | 3.7309e-10 | chr12:69120903-69586302 | 4
15q26.1 | 7.4432e-07 | 7.4432e-07 | chr15:90778391-91264459 | 8
1q42.3 | 3.3758e-07 | 8.6186e-06 | chr1:234915915-235243263 | 0 [TOMM20]
10q26.13 | 2.576e-05 | 2.576e-05 | chr10:123172617-123399846 | 1
11p13 | 3.3964e-05 | 3.5469e-05 | chr11:35244045-35263023 | 1
3q26.2 | 6.149e-05 | 6.149e-05 | chr3:163127738-184706041 | 105
7p11.2 | 9.4088e-08 | 0.00013765 | chr7:55035101-55424026 | 1
13q22.1 | 7.321e-05 | 0.00014237 | chr13:73642878-73944996 | 1
1q21.3 | 7.0832e-05 | 0.0020942 | chr1:149930853-151725358 | 55
9p24.1 | 0.0055148 | 0.0055148 | chr9:5047445-5711052 | 9
Xq26.2 | 0.0090117 | 0.0090117 | chrX:126233464-155270560 | 298
6q12 | 0.0092652 | 0.017367 | chr6:63903355-64323832 | 2
13q12.3 | 0.013178 | 0.033418 | chr13:30946447-34420150 | 21
7p22.3 | 0.012819 | 0.037064 | chr7:1-13958817 | 102
9q34.3 | 0.048 | 0.048 | chr9:139834793-140290845 | 37
1p36.22 | 0.068074 | 0.068074 | chr1:10686864-11093740 | 5
6q21 | 0.046733 | 0.080123 | chr6:107098934-107221941 | 2
5p13.1 | 0.0024858 | 0.12482 | chr5:33718161-50133343 | 75
5p15.33 | 0.066402 | 0.21708 | chr5:1-15332573 | 81

Genes in Wide Peak

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

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

Genes
ERBB2

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
LYRM5

Genes in Wide Peak

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

Table S4. 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 7q21.2.

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

Genes
CDK6
PEX1
RBM48
MGC16142
FAM133B
LOC728066

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p23.1.

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

Genes
GATA4
NEIL2

Genes in Wide Peak

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

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

Genes
ZNF217
SUMO1P1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
GATA6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
VEGFA
MAD2L1BP
GTPBP2
MRPS18A
RSPH9

Genes in Wide Peak

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

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

Genes
CCND1
FGF4
FGF19
ORAOV1

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
MDM2
CPM
SLC35E3
NUP107

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
CRTC3
IQGAP1
GABARAPL3
NGRN
ZNF774
C15orf58
TTLL13

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q26.13.

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

Genes
FGFR2

Genes in Wide Peak

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

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

Genes
CD44

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
PIK3CA
SOX2
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
ACTL6A
BCHE
AP2M1
CLCN2
DVL3
ECT2
EIF4G1
EPHB3
MECOM
GHSR
NDUFB5
CLDN11
SERPINI1
SERPINI2
PLD1
POLR2H
PRKCI
PSMD2
SI
SKIL
SLC2A2
TERC
THPO
SEC62
FXR1
CHRD
TNFSF10
EIF2B5
USP13
ECE2
ABCC5
ALG3
KCNMB2
PDCD10
SLITRK3
NLGN1
TNIK
MCF2L2
ATP11B
VPS8
GPR160
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DCUN1D1
KLHL24
ABCF3
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
MRPL47
NCEH1
SLC7A14
GNB4
MAGEF1
ZMAT3
FNDC3B
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
SPATA16
B3GNT5
ARPM1
KLHL6
VWA5B2
EGFEM1P
CAMK2N2
DNAJC19
FAM131A
TTC14
WDR49
LRRC34
HTR3C
HTR3D
RPL22L1
NAALADL2
HTR3E
CCDC39
LRRIQ4
SAMD7
SOX2-OT
TMEM212
FLJ46066
LOC646168
SNORD66
MIR551B
MIR569
LOC100128164
MIR1224
LOC100505687
MIR4789

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q22.1.

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

Genes
KLF5

Genes in Wide Peak

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

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

Genes
ARNT
hsa-mir-554
hsa-mir-4257
CTSK
CTSS
ECM1
ENSA
MCL1
PI4KB
PSMB4
PSMD4
RFX5
VPS72
TUFT1
PIP5K1A
ANXA9
SELENBP1
PRPF3
SETDB1
SEMA6C
MLLT11
CELF3
VPS45
POGZ
RPRD2
CA14
TMOD4
CERS2
APH1A
PLEKHO1
MRPS21
ADAMTSL4
C1orf56
GOLPH3L
FAM63A
CDC42SE1
OTUD7B
CGN
ZNF687
PRUNE
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
GABPB2
C1orf51
BNIPL
RIIAD1
LYSMD1
MIR554
MIR4257
TNFAIP8L2-SCNM1

Genes in Wide Peak

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

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

Genes
JAK2
CD274
INSL4
RLN1
RLN2
INSL6
C9orf46
KIAA1432
PDCD1LG2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq26.2.

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CD40LG
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
HCFC1
HMGB3
HPRT1
IDH3G
IDS
IGSF1
IL9R
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
OCRL
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
VBP1
XPNPEP2
ZIC3
ZNF75D
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
CXorf1
GPR50
RAB33A
ARHGEF6
MAGEC1
MAMLD1
BCAP31
SPRY3
SLC9A6
ENOX2
PLAC1
UTP14A
ZNF275
TREX2
LDOC1
FAM127B
SRPK3
SNORA70
SNORD61
RBMX
HTATSF1
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
CXorf48
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45B
GABRQ
MOSPD1
PDZD4
RAP2C
FAM3A
BCORL1
SPANXD
SPANXC
FUNDC2
PRRG3
BRCC3
MAP7D3
GPR101
CD99L2
H2AFB3
USP26
PHF6
TMEM185A
SLITRK2
MGC16121
PNMA6A
FATE1
HS6ST2
FRMD7
CXorf40A
FAM58A
MMGT1
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
CSAG1
FMR1NB
LOC158696
ARHGAP36
FAM122B
FAM122C
SPANXE
SPANXF1
DDX26B
ZNF449
VMA21
CTAG1A
MAGEA2B
ATP11C
RP1-177G6.2
LOC286467
LINC00204B
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
LINC00086
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
CXorf69
LINC00087
MIR542
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
CT45A2
MIR767
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129662
HSFX2
LOC100131434
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR320D2
MIR718
MIR2114
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
LOC100506757
LOC100507404
MAGEA10-MAGEA5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
PTP4A1
LGSN

Genes in Wide Peak

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

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

Genes
BRCA2
ALOX5AP
HMGB1
RFC3
KL
FRY
USPL1
N4BP2L2
HSPH1
PDS5B
C13orf33
STARD13
N4BP2L1
CG030
RXFP2
TEX26
B3GALTL
EEF1DP3
ZAR1L
LINC00426
TEX26-AS1

Genes in Wide Peak

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

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

Genes
ETV1
PMS2
CARD11
hsa-mir-589
hsa-mir-339
ACTB
GNA12
GPER
ICA1
LFNG
NUDT1
NDUFA4
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
PHF14
KIAA0415
ARL4A
KDELR2
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
TMEM106B
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
C1GALT1
FAM20C
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
C7orf70
SCIN
ZFAND2A
COX19
GLCCI1
KIAA1908
GPR146
AMZ1
PER4
TMEM184A
VWDE
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
SLC29A4
RSPH10B
TFAMP1
UNCX
COL28A1
LOC389458
ELFN1
GRID2IP
ZNF815
RNF216P1
PMS2CL
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
MIR589
RSPH10B2
LOC729852
LOC100131257
LOC100288524
RBAK-LOC389458
MIR4648
MIR4655
MIR4656

Genes in Wide Peak

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

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

Genes
ABCA2
C8G
ENTPD2
FUT7
GRIN1
PTGDS
SSNA1
CLIC3
TUBB4B
MAN1B1
COBRA1
NDOR1
ANAPC2
DPP7
FBXW5
C9orf167
EXD3
NPDC1
SAPCD2
UAP1L1
TMEM203
SLC34A3
LCN12
C9orf142
TPRN
C9orf169
LRRC26
LCNL1
C9orf139
FAM166A
C9orf173
NRARP
RNF224
RNF208
LOC100129722
LOC100289341
MIR3621

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.22.

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

Genes
PEX14
MASP2
TARDBP
CASZ1
C1orf127

Genes in Wide Peak

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

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

Genes
QRSL1
LOC100422737

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.1.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
C6
C7
C9
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
ZNF131
OSMR
NUP155
PAIP1
MRPS30
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
SLC45A2
RXFP3
WDR70
BRIX1
CCL28
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

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

Genes
hsa-mir-4278
hsa-mir-4277
ADCY2
CTNND2
DAP
DNAH5
MTRR
NDUFS6
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
KIAA0947
PP7080
IRX4
TAS2R1
FAM105A
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285577
LOC285692
SLC6A19
LOC340094
SLC6A18
LRRC14B
FLJ33360
TAG
LOC442132
ANKRD33B
SDHAP3
LOC728613
LOC729506
SNORD123
LOC100130744
MIR4277
MIR4278
LOC100505738
LOC100505806
LOC100506688
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635

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 - 46 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
--- | --- | --- | --- | ---
16q23.1 | 1.0642e-67 | 1.0642e-67 | chr16:78129058-79627770 | 1
5q11.2 | 1.6415e-46 | 1.6415e-46 | chr5:58260298-59787985 | 3
4q22.1 | 2.9166e-48 | 3.1995e-45 | chr4:91148280-93240505 | 1
9p24.1 | 5.0319e-33 | 1.3913e-28 | chr9:8310705-12693402 | 1
3p14.2 | 7.0289e-27 | 1.3271e-24 | chr3:59034763-61547330 | 1
6p25.3 | 1.0953e-22 | 1.0953e-22 | chr6:1608837-2252425 | 2
9p21.3 | 1.4363e-34 | 3.2614e-20 | chr9:21865498-21997722 | 2
20p12.1 | 4.1048e-20 | 4.1048e-20 | chr20:14302876-15179819 | 2
18q21.2 | 5.2564e-20 | 6.0707e-16 | chr18:48514396-48705371 | 1
7q31.1 | 6.2778e-19 | 1.0931e-13 | chr7:110725672-111366370 | 1
6q26 | 3.3001e-13 | 3.3001e-13 | chr6:161693099-163153207 | 1
Xp21.2 | 1.2311e-13 | 8.1639e-13 | chrX:30870233-32661893 | 3
1p36.11 | 2.2445e-10 | 1.1611e-09 | chr1:26752993-27277495 | 13
4q34.3 | 5.7693e-15 | 1.8379e-07 | chr4:178911874-186321446 | 34
3q26.31 | 3.6947e-06 | 3.5694e-06 | chr3:173999806-175760559 | 2
21q11.2 | 4.0363e-07 | 4.4173e-06 | chr21:1-16335988 | 22
2q32.1 | 1.0536e-06 | 4.5097e-06 | chr2:187373995-187560595 | 1
10q23.31 | 4.9912e-06 | 0.00010869 | chr10:89506488-90034038 | 4
19p13.3 | 0.00020492 | 0.00020022 | chr19:2473582-4675277 | 68
17p12 | 0.00030655 | 0.00030049 | chr17:10740609-13975082 | 13
21q22.13 | 3.4744e-05 | 0.00057255 | chr21:38638578-38997673 | 1
2q37.2 | 0.00029564 | 0.00061514 | chr2:235913227-237079324 | 2
16p13.3 | 0.00080304 | 0.00080037 | chr16:5144019-7771745 | 1
11p15.4 | 0.0014716 | 0.0015059 | chr11:2441018-3249828 | 13
7q36.3 | 1.1475e-07 | 0.0016988 | chr7:157210222-159138663 | 11
22q13.31 | 0.0018012 | 0.0017347 | chr22:45996783-51304566 | 72
11q23.2 | 0.0022161 | 0.0021545 | chr11:102955092-135006516 | 292
Xp22.2 | 0.00024869 | 0.0022751 | chrX:9891764-11137490 | 4
3p26.1 | 4.5097e-06 | 0.002802 | chr3:1-6903296 | 16
12p13.31 | 0.0048003 | 0.0047133 | chr12:6980182-18417317 | 168
9p13.1 | 0.004072 | 0.0052421 | chr9:38619152-71322791 | 51
8p23.2 | 0.0057573 | 0.005988 | chr8:1-6262191 | 15
17q24.3 | 0.0086526 | 0.0086741 | chr17:70116519-70595192 | 2
1q44 | 0.0090627 | 0.0093724 | chr1:245282267-247047608 | 7
15q15.1 | 0.0013385 | 0.0119 | chr15:37383162-59733125 | 226
18q23 | 4.6105e-10 | 0.012811 | chr18:51061400-78077248 | 106
14q32.33 | 0.019433 | 0.0194 | chr14:93152307-107349540 | 246
19q13.11 | 0.023948 | 0.02442 | chr19:32083224-36216055 | 70
Xq21.33 | 0.024454 | 0.02442 | chrX:94288568-98718611 | 4
10q22.2 | 0.010805 | 0.070623 | chr10:77168623-78629541 | 2
1p13.2 | 0.0078123 | 0.096084 | chr1:68692745-149898950 | 426
10p14 | 0.10125 | 0.10205 | chr10:1-32095975 | 192
14q13.3 | 0.10784 | 0.11073 | chr14:37635653-38677651 | 3
13q14.2 | 0.11191 | 0.11569 | chr13:1-115169878 | 414
15q11.2 | 0.0017578 | 0.20793 | chr15:1-34158528 | 173
20p12.1 | 4.1048e-20 | 1 | chr20:1-63025520 | 672

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
WWOX

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
FAM190A

Genes in Wide Peak

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

Table S32. 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 3p14.2.

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
FLRT3
MACROD2-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
SMAD4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
LRRN3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.2.

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

Genes
hsa-mir-548f-5
DMD
FTHL17

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
ARID1A
hsa-mir-1976
SFN
HMGN2
RPS6KA1
NR0B2
NUDC
GPN2
PIGV
GPATCH3
DHDDS
ZDHHC18
MIR1976

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
hsa-mir-1305
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ENPP6
C4orf38
RWDD4
CCDC111
ANKRD37
LOC389247
HELT
FAM92A3
SLED1
LINC00290
LOC728175
LOC731424
CLDN24
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

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

Table S44. 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
HSPA13
TPTE
RBM11
C21orf15
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
LIPI
ABCC13
POTED
LOC388813
ANKRD20A11P
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q32.1.

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

Genes
ITGAV

Genes in Wide Peak

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

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

Genes
PTEN
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
hsa-mir-637
AES
DAPK3
EEF2
GNA15
GNG7
MATK
GADD45B
NFIC
MAP2K2
SGTA
TBXA2R
THOP1
TLE2
S1PR4
APBA3
CHAF1A
EBI3
HMG20B
SEMA6B
ZFR2
PIP5K1C
SNORD37
TJP3
ITGB1BP3
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
STAP2
CCDC94
C19orf10
NCLN
SHD
ZNF77
C19orf29
CELF5
FSD1
TLE6
ZNF556
UBXN6
DOHH
CREB3L3
HDGFRP2
RAX2
MPND
ATCAY
ZNF554
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
MFSD12
GIPC3
DIRAS1
ZNF555
ANKRD24
C19orf77
C19orf29-AS1
PLIN5
MIR637
PLIN4
C19orf71
MIR4746

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-548h-3
hsa-mir-744
DNAH9
ZNF18
ARHGAP44
HS3ST3A1
ELAC2
MYOCD
CDRT15P1
FLJ34690
SHISA6
MIR744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.13.

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

Genes
DYRK1A

Genes in Wide Peak

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

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

Genes
GBX2
AGAP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

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

Genes
RBFOX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
CARS
CDKN1C
KCNQ1
NAP1L4
SLC22A18
SLC22A18AS
PHLDA2
KCNQ1OT1
KCNQ1DN
OSBPL5
C11orf36
MRGPRG
SNORA54

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
hsa-mir-595
hsa-mir-153-2
PTPRN2
VIPR2
NCAPG2
WDR60
ESYT2
LOC154822
MIR153-2
MIR595
LOC100506585

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

Table S54. 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
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
ATXN10
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
MIR4762
MIR4535

Genes in Wide Peak

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

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

Genes
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100128239
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.2.

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

Genes
CLCN4
MID1
WWC3
LOC100288814

Genes in Wide Peak

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

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

Genes
IL5RA
ITPR1
SETMAR
BHLHE40
EDEM1
CHL1
CNTN6
TRNT1
CRBN
ARL8B
LRRN1
CNTN4
SUMF1
EGOT
LOC100507582
MIR4790

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.31.

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CD69
CDKN1B
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
GPR19
GRIN2B
GUCY2C
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTPN6
PTPRO
PEX5
PZP
SLC2A3
MFAP5
KLRC4
CSDA
GPRC5A
CD163
GDF3
CLSTN3
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
KLRAP1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
NECAP1
CLEC4E
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
MAGOHB
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
NANOG
DUSP16
APOLD1
GSG1
RBP5
RERG
HTR7P1
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
CLEC9A
C12orf36
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
SCARNA12
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
KLRC4-KLRK1
PRH1-PRR4
MIR3974

Genes in Wide Peak

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

Table S59. 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
C9orf71
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 8p23.2.

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

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53
MIR596

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

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

Genes
SOX9
LOC100499467

Genes in Wide Peak

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

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

Genes
SCCPDH
KIF26B
TFB2M
SMYD3
LOC149134
CNST
LOC255654

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
BUB1B
TCF12
FLJ27352
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
ADAM10
AQP9
B2M
CAPN3
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
ITPKA
IVD
LIPC
LTK
MAP1A
MFAP1
MYO1E
MYO5A
NEDD4
PLCB2
MAPK6
RAB27A
RAD51
SLC12A1
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
USP8
CCNB2
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
SECISBP2L
LCMT2
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
CEP152
MAPKBP1
RTF1
MGA
DMXL2
VPS39
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PYGO1
PLDN
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
PPP1R14D
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
MYO5C
FAM214A
PAK6
DTWD1
CASC5
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
C15orf48
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
C15orf57
C15orf23
BMF
SHF
DUOXA1
LDHAL6B
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145663
GCOM1
LOC145783
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
SPRED1
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
FAM98B
PLA2G4D
GLDN
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
HSP90AB4P
MIR626
MIR627
MIR628
LOC728758
OIP5-AS1
MIR147B
LOC100129387
LOC100131089
ANKRD63
LOC100132724
JMJD7
PLA2G4B
MIR1266
MIR1282
LOC100306975
MIR2116
MIR4310
LOC100505648
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4716
MIR4713
MIR4712
MYZAP

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
CYB5A
FECH
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
ST8SIA3
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
DOK6
RNF152
LINC00305
C18orf26
BOD1P
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
SNORA37
LOC100130522
LOC100131655
LOC100505474
LOC100505549
LOC100505776
LOC100505817
MIR4529
MIR3591

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.33.

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

Genes
AKT1
TCL1A
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
SERPINA3
BDKRB1
BDKRB2
SERPINA6
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ADAM6
DLK1
CCNK
MTA1
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
C14orf109
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CDCA4
ATG2B
UBR7
MEG3
BTBD7
ZNF839
C14orf132
DDX24
UNC79
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
TMEM121
AMN
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
FAM181A
BTBD6
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
C14orf49
MGC23270
NUDT14
LINC00521
SERPINA11
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
CCDC85C
ITPK1-AS1
SERPINA9
LINC00226
LINC00221
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
MIR1247
MIR1185-1
MIR1185-2
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.11.

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

Genes
CEBPA
ATP4A
CD22
CEBPG
COX6B1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
LRP3
MAG
PEPD
FXYD1
FXYD3
SCN1B
USF2
PDCD5
KIAA0355
UBA2
TMEM147
UPK1A
SLC7A9
ZNF507
HAUS5
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
GPATCH1
ZNF302
SLC7A10
GRAMD1A
HAMP
CHST8
KCTD15
RBM42
LOC80054
ANKRD27
PDCD2L
CEP89
RHPN2
ZNF30
C19orf40
TDRD12
DMKN
WDR88
WTIP
ZNF792
DPY19L3
ZNF599
FAM187B
LGI4
SCGB2B2
ZNF181
SBSN
RGS9BP
KRTDAP
NUDT19
LOC400684
LOC400685
SCGB1B2P
LOC100128675
LOC100128682
SCGB2B3P
LOC100506469
LOC100652909

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
hsa-mir-548m
DIAPH2
RPA4
LOC643486

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q22.2.

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

Genes
hsa-mir-606
C10orf11

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

Table S69. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BCL9
NOTCH2
NRAS
BCL10
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
ABCA4
ACADM
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
CTH
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FCGR1B
FMO5
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PDZK1
PIN1P1
PRKAB2
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPE65
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
TTF2
ITGA10
LMO4
CDC14A
RTCD1
FPGT
PEX11B
FUBP1
SLC16A4
SRSF11
CD101
SEP15
ZRANB2
ARHGAP29
SEC22B
CHD1L
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
SV2A
RBM8A
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
CD160
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
ZZZ3
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
CHIA
RNF115
GPSM2
SLC25A24
DNTTIP2
TMED5
BOLA1
TNNI3K
SH3GLB1
HAO2
ACP6
SNX7
GPR89B
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRRC40
DEPDC1
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
FAM91A2
AMIGO1
ODF2L
KIAA1324
LRRC7
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
REG4
SYDE2
ZNF644
LRRC8C
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
NEXN
DNAJA1P5
HENMT1
GNRHR2
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
HFE2
ANKRD35
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
PPIAL4A
HFM1
UBL4B
PDIA3P
ALG14
NBPF11
NUDT17
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
NEGR1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
ZNF326
BTBD8
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
FAM73A
LOC375010
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
NBPF9
MIR137
MIR186
MIR197
LHX8
C1orf180
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
PGCP1
GEMIN8P4
RBMXL1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC646626
EMBP1
SRGAP2P2
LOC648740
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
SNORD45C
MIR548D1
MIR553
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130000
LOC100131564
NBPF10
FCGR1C
ZRANB2-AS1
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
FPGT-TNNI3K
TMEM56-RWDD3
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p14.

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GATA3
MLLT10
hsa-mir-938
hsa-mir-604
hsa-mir-603
hsa-mir-1915
hsa-mir-511-2
hsa-mir-511-1
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
BMI1
CACNB2
CALML3
AKR1C4
KLF6
MAP3K8
AKR1C1
AKR1C2
TRDMT1
GAD2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PIP4K2A
PRKCQ
RSU1
SVIL
ZEB1
VIM
STAM
CUBN
ITGA8
PRPF18
AKR1C3
CDC123
PTPLA
PTER
NMT2
SPAG6
USP6NL
ABI1
OPTN
NET1
NEBL
PITRM1
RPP38
CELF2
YME1L1
ZMYND11
NUDT5
ANKRD26
WDR37
MSRB2
SEPHS1
RAB18
KIN
DIP2C
LARP4B
COMMD3
GTPBP4
PDSS1
BAMBI
UPF2
HSPA14
WAC
CALML5
MYO3A
APBB1IP
ANKRD16
FAM208B
ARMC4
MTPAP
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
KIAA1217
PRTFDC1
CAMK1D
GPR158
ARHGAP21
KIAA1462
SFMBT2
DNAJC1
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
THNSL1
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
LYZL1
FBXO18
PLXDC2
MASTL
RBM17
ACBD5
IDI2
UCN3
LYZL2
MPP7
SFTA1P
ENKUR
ARMC3
LOC219731
OTUD1
LOC220906
ZNF438
ZEB1-AS1
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
LOC254312
C10orf47
PTF1A
C10orf67
LOC282980
LOC283070
MKX
LOC338588
ST8SIA6
AKR1CL1
EBLN1
TUBB8
PTCHD3
C10orf113
C10orf140
LINC00202
LOC387646
LOC387647
tAKR
C1QL3
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf114
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
MIR511-1
MIR511-2
ADARB2-AS1
MEIG1
LINC00264
TMEM236
MIR603
MIR604
LOC729668
LOC731789
MIR938
LOC100128098
LOC100128511
LOC100128811
LOC100129213
LOC100130992
PRINS
LOC100192204
LOC100216001
MIR1265
MIR1915
MIR3155A
LOC100499489
LOC100507034
LOC100507127
LOC100507605
COMMD3-BMI1
MIR4480
MIR4675
MIR3155B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q13.3.

Table S71. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FOXA1
MIPOL1
LOC100129794

Genes in Wide Peak

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

Table S72. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

Table S73. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
APBA2
NBEAP1
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
NDN
OCA2
RYR3
SCG5
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
ARHGAP11A
FAN1
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
GREM1
KLF13
MAGEL2
MTMR10
NDNL2
ATP10A
NIPA2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
OTUD7A
LOC283683
OR4N4
LOC283710
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
MIR211
NF1P2
HERC2P9
WHAMMP2
LOC503519
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GNAS
TOP1
MAFB
SS18L1
ASXL1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-1289-1
hsa-mir-499
hsa-mir-644
hsa-mir-1825
hsa-mir-3193
hsa-mir-663
hsa-mir-3192
hsa-mir-103-2-as
hsa-mir-1292
hsa-mir-3194
ADA
ADRA1D
JAG1
AHCY
ASIP
ATP5E
AVP
BCL2L1
BFSP1
BMP2
BMP7
BPI
ENTPD6
CD40
CDC25B
CDH4
CEBPB
CENPB
CHGB
CHRNA4
COL9A3
CSE1L
CSNK2A1
CST1
CST2
CST3
CST4
CST5
CSTF1
CTSZ
CYP24A1
DNMT3B
E2F1
EDN3
EEF1A2
EPB41L1
EYA2
FKBP1A
FOXS1
GGT7
GHRH
GNRH2
NPBWR2
GSS
HCK
FOXA2
HNF4A
ID1
IDH3B
INSM1
EIF6
ITPA
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
LBP
MC3R
MMP9
MYBL2
MYT1
NFATC2
NKX2-2
NNAT
NTSR1
OPRL1
OXT
PAX1
PCK1
PCNA
PCSK2
PDYN
PFDN4
PI3
PLAGL2
PLCB4
PLCG1
PLTP
CTSA
PPP1R3D
PRNP
PSMA7
PTGIS
PTK6
PTPN1
PTPRA
PYGB
RBL1
RPN2
RPS21
RRBP1
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SIGLEC1
SNAI1
SNAP25
SNRPB
SNRPB2
SNTA1
SOX12
SPAG4
SRC
SRMS
SSTR4
STAU1
STK4
AURKA
TAF4
TCEA2
TCF15
TFAP2C
TGM2
TGM3
THBD
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF133
ZNF217
MKKS
GDF5
NCOA3
ATRN
RAE1
CST7
BCAS1
STX16
CDS2
TNFRSF6B
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
VAPB
B4GALT5
KIF3B
PSMF1
RBM39
TTI1
SNPH
ProSAPiP1
RASSF2
TM9SF4
SPATA2
GINS1
OSBPL2
SLC23A2
ACOT8
CST8
ATP9A
SGK2
RBM12
ARFRP1
RGS19
SIRPB1
SYCP2
MYL9
WFDC2
SEC23B
NOP56
PROCR
ARFGEF2
RBCK1
POLR3F
TCFL5
RBBP9
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
DSTN
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
CEP250
RNF24
HRH3
PXMP4
RBPJL
XRN2
DLGAP4
UBOX5
BTBD3
RALY
CD93
MAPRE1
TPX2
NINL
ZHX3
NCOA6
PLCB1
SLC9A8
ADNP
POFUT1
ZMYND8
SPO11
PRND
FLRT3
LAMP5
PRPF6
SPEF1
SAMHD1
C20orf194
C20orf4
L3MBTL1
PPP1R16B
C20orf26
ABHD12
TRPC4AP
ZNF337
GTPBP5
GMEB2
SNORD12C
SNORA71B
SNORA71A
SNORD57
SNORD56
SDCBP2
SNX5
TP53TG5
MOCS3
SLCO4A1
REM1
C20orf30
HSPC072
NXT1
VSX1
STMN3
SLC35C2
SLMO2
IFT52
NAA20
PHF20
SCAND1
BPIFA1
CRNKL1
ANGPT4
TH1L
C20orf43
C20orf111
ESF1
PIGT
TRMT6
ERGIC3
CDK5RAP1
RTEL1
SOX18
HAO1
RIN2
SMOX
CRLS1
YTHDF1
LIME1
UCKL1
C20orf27
C20orf11
DZANK1
UQCC
PCMTD2
C20orf20
SPTLC3
C20orf29
TMEM74B
PPP4R1L
SIRPG
RBM38
FERMT1
KIF16B
TASP1
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
EDEM2
DOK5
PLK1S1
DBNDD2
ACSS2
RNF114
SULF2
NSFL1C
C20orf24
TMX4
CTNNBL1
GPCPD1
CPXM1
SLC2A4RG
OTOR
PMEPA1
CASS4
SPINLW1
C20orf3
PAK7
RALGAPB
JPH2
SALL4
ZNFX1
RALGAPA2
CSRP2BP
RAB22A
SLC24A3
NDRG3
SLC12A5
ZNF512B
MAVS
PREX1
EBF4
COL20A1
MYH7B
NCOA5
TRIB3
TP53INP2
RPRD1B
OVOL2
TGIF2
CDH26
FASTKD5
KCNK15
DHX35
MANBAL
NAPB
SLC17A9
ELMO2
ZNF335
ANKRD5
LOC63930
PCIF1
FAM217B
NECAB3
GFRA4
CDH22
GZF1
VPS16
FAM113A
SLC13A3
LPIN3
MRPS26
DDRGK1
GDAP1L1
LOC79015
C20orf195
C20orf7
PPDPF
ZNF343
TTPAL
BIRC7
NPEPL1
ACTR5
SYNDIG1
DSN1
NRSN2
PANK2
FER1L4
DNAJC5
ADAM33
PABPC1L
BPIFB2
SEL1L2
TUBB1
ZBP1
SLC2A10
HM13
PDRG1
FAM83D
DEFB126
CABLES2
FAM110A
DYNLRB1
ITCH
SLC4A11
SLA2
CHD6
MCM8
ACSS1
MAP1LC3A
PARD6B
ZGPAT
COX4I2
ZNF341
TOX2
ZCCHC3
MYLK2
PRIC285
KIAA1755
SCRT2
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
GGTLC1
C20orf72
DTD1
BPIFB1
TP53RK
C20orf54
DNTTIP1
FAM210B
PHACTR3
HSPA12B
DEFB118
TMC2
BHLHE23
NKAIN4
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
TBC1D20
SIRPD
C20orf141
PROKR2
C20orf94
CSTL1
CST9L
CST9
C20orf166
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
GATA5
MLLT10P1
SLC32A1
C20orf96
BPIFA2
ZBTB46
WFDC3
GCNT7
C20orf112
CBLN4
CTCFL
C20orf132
SAMD10
ABHD16B
C20orf160
KIAA0889
C20orf118
RIMS4
SUN5
MACROD2
SRXN1
ROMO1
NEURL2
LINC00261
ZSWIM3
WFDC10A
BANF2
NANP
LINC00266-1
DEFB127
C20orf79
ISM1
WFDC6
C20orf173
LINC00028
FAM65C
CST11
DEFB129
SIRPA
C20orf151
C20orf152
STK35
R3HDML
ADIG
GTSF1L
WFDC5
LOC149773
GNAS-AS1
PRNT
LOC149837
C20orf196
NCOR1P1
LOC149950
COMMD7
BPIFB4
LSM14B
WFDC13
APCDD1L
LRRN4
CSTT
TTLL9
ACTL10
C20orf201
FAM209A
LOC200261
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
DEFB125
DEFB128
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
SIRPB2
LOC284788
LOC284798
FAM182A
LOC284801
FRG1B
C20orf203
BPIFA4P
LOC339568
LOC339593
ARHGAP40
RSPO4
TGM6
XKR7
BPIFB3
TMEM189
TMEM189-UBE2V1
LINC00493
LOC388796
FAM209B
SPINT4
SUMO1P1
DEFB132
C20orf202
FLJ33581
MIR103A2
MIR1-1
MIR124-3
MIR133A2
MIR296
DZANK1-AS1
ZNFX1-AS1
MIR499A
RAD21L1
LOC643406
NKX2-4
LOC647979
SNORA39
SNORA51
SNORA60
SNORA71C
SNORA71D
SNORD12
SNORD17
SNORD86
SNORD110
MIR644A
MIR645
MIR647
MIR663A
LOC728228
FAM182B
SYS1-DBNDD2
HAR1A
HAR1B
PSIMCT-1
SNORD119
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
LOC100128496
LOC100130264
ZNF663
LOC100131208
LOC100131496
DPH3P1
LOC100134015
LOC100134868
LINC00029
LOC100144597
FLJ16779
LOC100270679
LOC100270804
LOC100287792
TMEM239
LOC100289473
MIR1914
MIR1292
MIR1257
MIR103B2
PCNA-AS1
PET117
MACROD2-AS1
MIR3192
MIR4325
MIR3194
MIR3193
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505536
LOC100505783
LOC100505815
LOC100505826
LOC100506384
LOC100507495
LOC100507629
SPINLW1-WFDC6
TGIF2-C20ORF24
FKBP1A-SDCBP2
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR499B
MIR4756
MIR4758
MIR4532
MIR4533
MIR4755
MIR5095
LOC100652730

Arm-level results

Table 3. Get Full Table Arm-level significance table - 26 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.10 | -0.593 | 1 | 0.14 | 1.6 | 0.129
1q | 1955 | 0.22 | 5.3 | 2.92e-07 | 0.09 | -1.67 | 1
2p | 924 | 0.16 | -0.563 | 1 | 0.05 | -5.16 | 1
2q | 1556 | 0.15 | 0.296 | 1 | 0.07 | -3.46 | 1
3p | 1062 | 0.10 | -2.94 | 1 | 0.22 | 2.41 | 0.0214
3q | 1139 | 0.18 | 0.516 | 0.993 | 0.14 | -1.29 | 1
4p | 489 | 0.05 | -5.5 | 1 | 0.33 | 5.48 | 2.11e-07
4q | 1049 | 0.02 | -5.83 | 1 | 0.32 | 6.82 | 1.78e-10
5p | 270 | 0.16 | -1.87 | 1 | 0.19 | -0.895 | 1
5q | 1427 | 0.05 | -4.16 | 1 | 0.23 | 3.6 | 0.000631
6p | 1173 | 0.18 | 0.651 | 0.937 | 0.12 | -1.86 | 1
6q | 839 | 0.15 | -1.34 | 1 | 0.15 | -1.48 | 1
7p | 641 | 0.40 | 9.12 | 0 | 0.10 | -3.22 | 1
7q | 1277 | 0.35 | 8.84 | 0 | 0.11 | -1.85 | 1
8p | 580 | 0.42 | 8.99 | 0 | 0.31 | 4.13 | 8.96e-05
8q | 859 | 0.51 | 14.6 | 0 | 0.14 | -1.41 | 1
9p | 422 | 0.14 | -2.45 | 1 | 0.32 | 4.6 | 1.23e-05
9q | 1113 | 0.16 | -0.123 | 1 | 0.23 | 2.9 | 0.00581
10p | 409 | 0.22 | 0.46 | 0.993 | 0.17 | -1.4 | 1
10q | 1268 | 0.16 | 0.0761 | 1 | 0.17 | 0.359 | 0.685
11p | 862 | 0.11 | -3.07 | 1 | 0.14 | -1.87 | 1
11q | 1515 | 0.11 | -1.45 | 1 | 0.13 | -0.852 | 1
12p | 575 | 0.19 | -0.0953 | 1 | 0.15 | -2.01 | 1
12q | 1447 | 0.17 | 0.938 | 0.696 | 0.11 | -1.85 | 1
13q | 654 | 0.35 | 6.59 | 1.22e-10 | 0.12 | -2.46 | 1
14q | 1341 | 0.05 | -4.31 | 1 | 0.23 | 3.34 | 0.00139
15q | 1355 | 0.09 | -2.95 | 1 | 0.19 | 1.53 | 0.141
16p | 872 | 0.14 | -1.45 | 1 | 0.21 | 1.34 | 0.189
16q | 702 | 0.12 | -2.74 | 1 | 0.23 | 1.8 | 0.0907
17p | 683 | 0.08 | -4.2 | 1 | 0.33 | 6.13 | 8.74e-09
17q | 1592 | 0.11 | -1.27 | 1 | 0.16 | 0.693 | 0.489
18p | 143 | 0.18 | -1.36 | 1 | 0.28 | 2.57 | 0.0145
18q | 446 | 0.12 | -2.81 | 1 | 0.35 | 5.99 | 1.38e-08
19p | 995 | 0.12 | -2.11 | 1 | 0.27 | 4.1 | 9.24e-05
19q | 1709 | 0.17 | 1.68 | 0.206 | 0.21 | 3.52 | 0.000795
20p | 355 | 0.53 | 13.6 | 0 | 0.11 | -2.9 | 1
20q | 753 | 0.58 | 17.8 | 0 | 0.04 | -4.33 | 1
21q | 509 | 0.08 | -4.53 | 1 | 0.32 | 5.18 | 8.73e-07
22q | 921 | 0.10 | -2.89 | 1 | 0.29 | 5.12 | 1.03e-06
Xq | 1312 | 0.15 | -0.417 | 1 | 0.13 | -1.28 | 1

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/STAD-TP/2842896/2.GDAC_MergeDataFiles.Finished/STAD-TP.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 306 Input Tumor Samples.

Tumor Sample Names
TCGA-B7-5816-01A-21D-1599-01
TCGA-B7-5818-01A-11D-1599-01
TCGA-BR-4183-01A-02D-1130-01
TCGA-BR-4184-01A-01D-1130-01
TCGA-BR-4187-01A-01D-1130-01
TCGA-BR-4188-01A-01D-1130-01
TCGA-BR-4191-01A-02D-1130-01
TCGA-BR-4201-01A-01D-1130-01
TCGA-BR-4253-01A-01D-1130-01
TCGA-BR-4255-01A-01D-1130-01

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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