Lung Squamous Cell 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 2.0.15 (cga svn revision 34144).

Summary

There were 211 tumor samples used in this analysis: 25 significant arm-level results, 28 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 - 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
--- | --- | --- | --- | ---
3q26.33 | 3.7589e-46 | 3.7589e-46 | chr3:184069946-184285567 | 3
8p12 | 1.944e-40 | 1.944e-40 | chr8:38287525-38370893 | 2
11q13.3 | 1.7587e-27 | 1.9545e-27 | chr11:69408710-69588487 | 0 [ANO1]
7p11.2 | 6.9009e-14 | 6.9009e-14 | chr7:54749279-55481516 | 3
2p16.1 | 2.0079e-12 | 2.0079e-12 | chr2:60382630-61008146 | 3
4q12 | 3.66e-08 | 3.66e-08 | chr4:55960066-56202497 | 4
8q24.21 | 4.547e-07 | 4.547e-07 | chr8:128071511-128693092 | 2
18q11.2 | 8.2941e-07 | 8.2941e-07 | chr18:22007290-22278528 | 2
22q11.21 | 6.588e-06 | 6.588e-06 | chr22:19200757-19740490 | 17
9p13.3 | 1.7518e-05 | 1.7518e-05 | chr9:34997337-35036417 | 1
19q13.13 | 8.0263e-07 | 0.00010246 | chr19:43029012-43993845 | 22
12q15 | 0.0023772 | 0.0023772 | chr12:65424056-70146921 | 26
14q13.3 | 0.0028692 | 0.0028692 | chr14:35852736-37332424 | 8
1p34.2 | 0.004513 | 0.004513 | chr1:39525916-40423375 | 18
1q22 | 0.0063428 | 0.0063428 | chr1:121045320-171649835 | 519
6q22.31 | 0.0098908 | 0.0098908 | chr6:124765242-125815717 | 5
17q25.1 | 0.012558 | 0.012558 | chr17:68709195-69657523 | 7
7q21.2 | 0.016778 | 0.016778 | chr7:91312491-93095567 | 21
6q12 | 0.028804 | 0.028804 | chr6:63725884-66170398 | 4
2q31.2 | 0.043752 | 0.043752 | chr2:177780568-177863084 | 3
16p12.1 | 0.055567 | 0.055567 | chr16:24972464-26907093 | 4
19q12 | 0.0054439 | 0.062079 | chr19:33389816-35460315 | 8
21q21.1 | 0.062079 | 0.062079 | chr21:1-19807858 | 28
15q26.3 | 0.072938 | 0.072938 | chr15:86853989-100338915 | 91
20q11.21 | 0.11496 | 0.11496 | chr20:26020583-30093702 | 27
5p15.2 | 0.12985 | 0.12985 | chr5:1-18514934 | 71
11p11.2 | 0.11725 | 0.13869 | chr11:45871288-46949201 | 19
19q13.42 | 0.13255 | 0.21221 | chr19:60244636-61435811 | 47

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
ATP11B
DCUN1D1
MCCC1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p12.

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

Genes
WHSC1L1
LETM2

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p16.1.

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

Genes
REL
BCL11A
PAPOLG

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
CLOCK
NMU
TMEM165
PDCL2

Genes in Wide Peak

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

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

Genes
POU5F1B
LOC727677

Genes in Wide Peak

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

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

Genes
TAF4B
PSMA8

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q11.21.

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

Genes
hsa-mir-649
CRKL
SERPIND1
PI4KA
SLC7A4
LZTR1
P2RX6
SNAP29
MED15
THAP7
TMEM191A
MGC16703
AIFM3
POM121L4P
LOC400891
FLJ39582
P2RX6P

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
C9orf131

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.13.

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

Genes
ACTN4
LGALS4
LGALS7
PSMD8
RYR1
DPF1
KCNK6
SPINT2
MAP4K1
SIPA1L3
EIF3K
CATSPERG
C19orf33
WDR87
YIF1B
PPP1R14A
RASGRP4
FAM98C
CAPN12
GGN
SPRED3
LGALS7B

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
hsa-mir-1279
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
TSPAN8
YEATS4
DYRK2
LGR5
CCT2
FRS2
CPSF6
KCNMB4
IL22
SLC35E3
IL26
CAND1
MDM1
NUP107
RAB3IP
BEST3
LRRC10

Genes in Wide Peak

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

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

Genes
NKX2-1
FOXA1
PAX9
NKX2-8
MBIP
SLC25A21
MIPOL1
SFTA3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MYCL1
BMP8B
PPT1
RLF
PABPC4
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
OXCT2
NT5C1A
MFSD2A
BMP8A
KIAA0754
SNORA55
LOC728448

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NTRK1
PBX1
PRCC
SDHC
TPM3
PDE4DIP
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-190b
hsa-mir-554
ADAR
ALDH9A1
APCS
APOA2
FASLG
ATP1A2
ATP1A4
ATP1B1
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
DPT
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
F5
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
DARC
GBA
GBAP
GJA5
GJA8
HDGF
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYOC
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PIGC
PI4KB
PKLR
PRRX1
POU2F1
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
XCL2
VPS72
THBS3
TCHH
TOP1P1
CCT3
TUFT1
TNFSF4
UCK2
USF1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
ADAM15
PEX11B
CREG1
CD84
SELENBP1
TNFSF18
MPZL1
SH2D2A
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
AIM2
ADAMTS4
SEC22B
CHD1L
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
GPA33
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
TNRC4
PMF1
DUSP12
VPS45
KIAA0907
KIFAP3
ATF6
POGZ
SYT11
BAT2D1
RPRD2
SMG5
NCSTN
GPR161
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
BRP44
OLFML2B
C1orf43
DNM3
C1orf77
LCE2B
OR10J1
USP21
SLC39A1
RNF115
ROBLD3
TMOD4
NME7
LASS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
C1orf66
APH1A
PLEKHO1
ACP6
C1orf9
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
C1orf112
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
RAG1AP1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
C1orf114
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
MGC4473
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
C1orf129
TARS2
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
NUF2
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
ANKRD36BL1
MAEL
AQP10
SLAMF9
PYGO2
NUP210L
DUSP27
RCSD1
MEX3A
C1orf156
GORAB
C1orf105
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
FMO9P
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
HIST2H3C
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
METTL11B
FAM78B
BNIPL
C1orf92
PYHIN1
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
LOC200030
NUDT17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
TIPRL
C1orf230
THEM5
NBPF15
ANKRD34A
C1orf104
C1orf204
C1orf111
LOC284688
HIST2H2AB
HIST2H3A
S100A7A
LINGO4
RXFP4
C1orf110
OR10R2
FCRL6
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
PEAR1
SFT2D2
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
NBPF20
MIR199A2
MIR214
MIR9-1
HIST2H2BF
ETV3L
LRRC52
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
RPL31P11
LOC642502
PPIAL4G
PPIAL4D
LOC645166
LOC645676
S100A7L2
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
PCP4L1
SCARNA4
SNORA42
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
LOC728855
LOC728875
NBPF11
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
C1orf152
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
TSTD1
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q22.31.

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

Genes
STL
TPD52L1
HDDC2
RNF217
NKAIN2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
COG1
CDC42EP4
SDK2
C17orf80
FAM104A
C17orf54
CPSF4L

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
hsa-mir-489
hsa-mir-1285-1
CALCR
KRIT1
CYP51A1
PEX1
MTERF
ANKIB1
SAMD9
CCDC132
GATAD1
C7orf64
MGC16142
SAMD9L
HEPACAM2
FAM133B
LOC401387
MIR489
MIR653

Genes in Wide Peak

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

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

Genes
PTP4A1
PHF3
LGSN
EYS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q31.2.

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

Genes
NFE2L2
HNRNPA3
LOC100130691

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p12.1.

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

Genes
AQP8
HS3ST4
LCMT1
ZKSCAN2

Genes in Wide Peak

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

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

Genes
CCNE1
UQCRFS1
C19orf2
POP4
PLEKHF1
C19orf12
LOC148145
VSTM2B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q21.1.

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

Genes
hsa-mir-125b-2
BAGE
CXADR
PRSS7
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
NCRNA00157
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
C21orf99
LIPI
ABCC13
POTED
C21orf34
C21orf81
MIRLET7C
MIR125B2
MIR99A

Genes in Wide Peak

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

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

Genes
BLM
IDH2
CRTC3
hsa-mir-1302-2
hsa-mir-1469
hsa-mir-9-3
hsa-mir-7-2
ACAN
ALDH1A3
ANPEP
CHD2
FES
IGF1R
ISG20
MAN2A2
MEF2A
MFGE8
FURIN
PCSK6
PLIN1
POLG
RLBP1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
ABHD2
CHSY1
SYNM
GABARAPL3
VPS33B
OR4F4
SLCO3A1
NGRN
RHCG
DET1
LINS1
FANCI
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
AEN
TTC23
LRRK1
TM2D3
C15orf42
RCCD1
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
LOC145814
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
ADAMTS17
C15orf51
LASS3
LOC254559
LOC283761
FAM169B
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
WASH3P
FLJ42289
C15orf58
OR4F6
OR4F15
FAM174B
MIR7-2
MIR9-3
TTLL13
FAM138E
LOC100144604
LOC100288778

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-663
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
C20orf160
NCRNA00028
C20orf191
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
MIR663
PSIMCT-1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.2.

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

Genes
hsa-mir-887
ADCY2
CTNND2
DAP
DNAH5
MTRR
MYO10
NDUFS6
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
BASP1
SLC12A7
POLS
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
LOC25845
IRX4
TAS2R1
FAM134B
FAM105A
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285692
LOC285696
SLC6A19
LOC340094
SLC6A18
LRRC14B
FLJ33360
MARCH11
ANKRD33B
SDHAP3
LOC728613
SNORD123
LOC100310782

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p11.2.

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

Genes
CREB3L1
ARHGAP1
CHRM4
F2
LRP4
MDK
DGKZ
PEX16
MAPK8IP1
KIAA0652
CKAP5
PHF21A
AMBRA1
C11orf49
ZNF408
GYLTL1B
C11orf94
HARBI1
SNORD67

Genes in Wide Peak

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

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

Genes
IL11
PTPRH
RPL28
SYT5
TNNI3
TNNT1
U2AF2
SAPS1
HSPBP1
UBE2S
CCDC106
EPN1
ZNF580
ZNF581
PPP1R12C
EPS8L1
ZNF444
NAT14
ZSCAN5A
ISOC2
BRSK1
SUV420H2
FIZ1
GALP
ZNF628
RDH13
COX6B2
NLRP13
NLRP8
NLRP5
ZNF787
TMEM190
ZNF524
ZNF784
NLRP4
ZNF579
NLRP11
TMEM86B
SSC5D
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
C19orf51
SBK2
SHISA7

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
--- | --- | --- | --- | ---
9p21.3 | 3.7363e-81 | 2.8121e-72 | chr9:21855498-21986995 | 2
2q22.1 | 1.3951e-20 | 8.2635e-19 | chr2:139248662-143354308 | 1
8p23.2 | 3.5585e-14 | 9.2216e-13 | chr8:2080589-6255647 | 1
10q23.31 | 1.7926e-11 | 1.7926e-11 | chr10:89607138-90024018 | 2
5q11.2 | 9.2963e-10 | 9.2963e-10 | chr5:58296055-59823742 | 3
3p14.2 | 4.2538e-09 | 1.1952e-07 | chr3:59009803-61522370 | 1
2q37.3 | 2.5851e-08 | 1.7041e-05 | chr2:208390444-242951149 | 268
6q26 | 0.00040723 | 0.00040723 | chr6:161613089-163073197 | 1
11p15.5 | 0.00053733 | 0.00052942 | chr11:1-5098845 | 139
3p25.2 | 1.0527e-05 | 0.0010295 | chr3:11568528-11808472 | 1
9p21.2 | 2.7332e-14 | 0.0017708 | chr9:27562512-32375942 | 4
9p13.1 | 3.1206e-06 | 0.0023592 | chr9:38609152-78983232 | 85
4q35.2 | 2.9442e-07 | 0.0027227 | chr4:183326192-191273063 | 49
21q21.1 | 0.0033784 | 0.0034209 | chr21:1-21293802 | 29
1p13.1 | 0.00082933 | 0.004129 | chr1:103339163-144126225 | 168
20p12.1 | 0.0054788 | 0.0054788 | chr20:14250876-15984135 | 2
11q24.3 | 0.0067742 | 0.0067742 | chr11:126375629-134452384 | 32
3p11.2 | 0.00017846 | 0.0090642 | chr3:77779180-95076656 | 11
3p14.1 | 3.9639e-06 | 0.012183 | chr3:68676953-87070815 | 28
17q11.2 | 0.016666 | 0.016438 | chr17:26307851-26673293 | 6
4q22.1 | 0.0015066 | 0.018621 | chr4:91092757-93459528 | 2
18q23 | 0.01992 | 0.01992 | chr18:71130474-76117153 | 18
15q11.2 | 0.005207 | 0.02927 | chr15:1-47070162 | 311
1p36.12 | 0.0065654 | 0.032616 | chr1:1-33741020 | 511
7q11.22 | 0.023229 | 0.035345 | chr7:66423810-70239151 | 1
4q34.3 | 6.3706e-06 | 0.043818 | chr4:171246607-191273063 | 72
16p13.3 | 0.048546 | 0.048356 | chr16:1-7328344 | 209
4p15.31 | 0.045061 | 0.05196 | chr4:20336563-21999843 | 2
7q31.33 | 0.038137 | 0.056388 | chr7:108310780-147750120 | 244
13q12.11 | 0.021354 | 0.064195 | chr13:1-28497722 | 70
19p13.3 | 0.064992 | 0.06566 | chr19:1-13721363 | 419
22q11.21 | 0.076337 | 0.072813 | chr22:1-18213813 | 47
10p15.3 | 0.079927 | 0.080027 | chr10:1-4683335 | 15
4p16.2 | 0.053991 | 0.093143 | chr4:1-5067215 | 70
4q32.3 | 0.0049654 | 0.093143 | chr4:143166997-191273063 | 178
4p12 | 0.10907 | 0.12228 | chr4:41847185-52409225 | 27
16q24.3 | 0.12228 | 0.12228 | chr16:70168187-88827254 | 153
14q21.3 | 0.15584 | 0.15584 | chr14:1-61292206 | 309
8p23.3 | 4.0183e-06 | 0.16538 | chr8:1-2780982 | 13
9p24.1 | 0.00025666 | 0.17605 | chr9:4850981-14995054 | 27
13q14.2 | 0.010666 | 0.17605 | chr13:1-72205527 | 234
15q21.1 | 0.013256 | 0.1901 | chr15:1-52708651 | 350
4q23 | 0.056622 | 0.22405 | chr4:95893013-164308535 | 245
7q36.3 | 0.077406 | 0.22405 | chr7:130833759-158821424 | 217
19q13.33 | 0.23816 | 0.23419 | chr19:42572590-63811651 | 775
3q13.31 | 0.17245 | 0.24658 | chr3:1-199501827 | 1158

Genes in Wide Peak

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

Table S28. 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 2q22.1.

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

Genes
LRP1B

Genes in Wide Peak

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

Table S30. 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 10q23.31.

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

Genes
PTEN
KILLIN

Genes in Wide Peak

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

Table S32. 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 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 2q37.3.

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

Genes
ATIC
ACSL3
IDH1
PAX3
FEV
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
hsa-mir-153-1
hsa-mir-375
hsa-mir-26b
hsa-mir-548f-2
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
IL8RA
IL8RB
IL8RBP
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
C2orf24
STK36
LOC29034
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
KIAA1486
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
C2orf67
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
PIKFYVE
TIGD1
CCDC108
C2orf72
C2orf85
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
ASB18
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
PP14571

Genes in Wide Peak

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

Table S35. 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 11p15.5.

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

Genes
CARS
HRAS
NUP98
hsa-mir-483
hsa-mir-675
hsa-mir-210
AP2A2
RHOG
ART1
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
TRIM21
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
KCNQ1OT1
PKP3
SIRT3
PGAP2
C11orf21
TRPM5
IGF2AS
BET1L
CEND1
MUPCDH
TOLLIP
TRIM68
LRDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
OR51G1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
HCCA2
SYT8
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR52B4
C11orf40
OR52I2
OR51E1
LOC143666
SCGB1C1
NLRP6
LOC255512
C11orf35
OR51F1
H19
EFCAB4A
TMEM80
C11orf36
ANO9
LOC338651
B4GALNT4
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR52K1
OR52I1
OR51D1
OR51T1
OR51A4
OR51A2
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
MIR483
SNORA52
LOC650368
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
LOC100133545

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.2.

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

Genes
VGLL4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.2.

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

Genes
hsa-mir-873
LINGO2
MIR876
MIR873

Genes in Wide Peak

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

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

Genes
hsa-mir-204
hsa-mir-1299
ALDH1A1
ANXA1
APBA1
KLF9
FXN
GCNT1
PCSK5
PGM5
PRKACG
RORB
ZFAND5
PIP5K1B
FAM189A2
TJP2
GDA
SMC5
TMEM2
ZNF658
FAM75A7
OSTF1
PCA3
FAM108B1
C9orf95
C9orf40
RFK
CNTNAP3
TRPM3
ANKRD20A1
FAM122A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
TRPM6
C9orf122
PRUNE2
C9orf71
CBWD5
MAMDC2
FOXD4L3
FOXD4L4
AQP7P1
PTAR1
KGFLP1
FAM75A6
MGC21881
AQP7P2
FAM74A1
FAM74A4
ZNF658B
MIR204
LOC440839
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
FOXB2
CBWD3
FAM27A
LOC572558
PGM5P2
FAM75A2
LOC642929
CBWD6
FAM75A1
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
ANKRD20A4
CCDC29
FOXD4L2
LOC100130426
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

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

Table S40. 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
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
TUBB4Q
STOX2
KIAA1430
C4orf41
MLF1IP
WWC2
SNX25
ZFP42
ENPP6
C4orf38
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
TRIML1
ANKRD37
HELT
FAM92A3
C4orf47
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

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

Genes
hsa-mir-125b-2
BAGE
CXADR
PRSS7
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
NCRNA00157
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
C21orf99
LIPI
ABCC13
POTED
C21orf131
C21orf34
C21orf81
MIRLET7C
MIR125B2
MIR99A

Genes in Wide Peak

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

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

Genes
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
ADORA3
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CSF1
CELSR2
FCGR1B
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
TTF2
SLC16A4
CD101
SEC22B
LRIG2
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
DDX20
NTNG1
WDR47
CLCC1
PTPN22
PHGDH
CHIA
GPSM2
SLC25A24
HAO2
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
C1orf103
CTTNBP2NL
C1orf183
TMEM167B
OLFML3
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
PROK1
PSRC1
C1orf203
FAM40A
ZNF697
C1orf59
C1orf161
ATXN7L2
C1orf194
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
LOC149620
DENND2C
FNDC7
PPIAL4A
UBL4B
SPAG17
HIPK1
AFARP1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
HIST2H2BA
MYBPHL
NBPF7
SLC6A17
NOTCH2NL
FLJ39739
NBPF20
MIR197
BCL2L15
LOC441897
CYMP
PPIAL4G
LOC647121
LOC648740
NBPF6
PPIAL4B
PPIAL4C
FAM72B
SCARNA2
LOC728855
LOC728875
C1orf152
MIR942
NBPF10
LOC100286793

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

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

Genes
FLI1
APLP2
ETS1
KCNJ1
KCNJ5
NFRKB
OPCML
ST14
BARX2
RICS
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
PRDM10
TP53AIP1
JAM3
GLB1L2
VPS26B
GLB1L3
TMEM45B
ADAMTS15
C11orf45
SPATA19
LOC283174
SNX19
NCRNA00167
LOC100128239

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.2.

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

Genes
EPHA3
GBE1
HTR1F
POU1F1
ROBO1
CGGBP1
CHMP2B
ZNF654
CADM2
C3orf38
VGLL3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
MITF
FOXP1
hsa-mir-1324
hsa-mir-1284
GBE1
GPR27
CNTN3
ROBO1
ROBO2
TMF1
UBA3
ARL6IP5
PDZRN3
FRMD4B
RYBP
FLJ10213
SHQ1
LMOD3
PROK2
FAM19A4
PPP4R2
CADM2
C3orf64
EIF4E3
FAM86D
GLT8D4
ZNF717
FRG2C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

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

Genes
NF1
EVI2A
EVI2B
OMG
RNF135
DPRXP4

Genes in Wide Peak

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

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

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

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

Genes
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TXNL4A
ADNP2
KCNG2
SALL3
C18orf22
PQLC1
PARD6G
C18orf62
LOC284276
ATP9B
HSBP1L1
LOC100130522

Genes in Wide Peak

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

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

Genes
BUB1B
C15orf55
C15orf21
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
hsa-mir-211
hsa-mir-1268
ACTC1
APBA2
B2M
BCL8
CAPN3
CHRM5
CHRNA7
CKMT1B
DUT
EPB42
FBN1
GABRA5
GABRB3
GABRG3
GANC
GATM
GCHFR
PDIA3
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
SLC28A2
TGM5
HISPPD2A
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
MTMR15
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
SLC24A5
OR4N4
FAM98B
PLA2G4D
GOLGA6L1
GOLGA8G
GOLGA9P
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMML1
POTEB
FMN1
SNORD64
PAR4
PAR-SN
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P1
WHAMML2
GOLGA8B
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC646214
CXADRP2
MIR548A3
MIR626
MIR627
LOC723972
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
LOC729082
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
HBII-52-24
HBII-52-27
HBII-52-28
HBII-52-45
HBII-52-46
MIR147B
GOLGA8F
GOLGA8D
JMJD7
PLA2G4B
FAM7A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.12.

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

Genes
LCK
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
AK2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC2L1
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SFRS4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
YARS
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
KIAA0562
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SFRS13A
UTS2
RER1
RCAN3
MSTP2
MSTP9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KIAA1026
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
HSPC157
SSU72
UBIAD1
PADI1
PLA2G2E
WDR8
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
C1orf91
FAM54B
CTNNBIP1
C1orf63
AGTRAP
C1orf128
MAN1C1
NIPAL3
SEPN1
KIAA0495
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
S100PBP
CCDC21
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
C1orf89
OR4F5
NKAIN1
MUL1
NOL9
LIN28
AGMAT
NCRNA00115
MORN1
GRRP1
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCL1
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
ADC
TMEM54
CROCCL2
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
C1orf93
MYOM3
RNF19B
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
FNDC5
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
C1orf70
TMEM52
MTMR9L
ZBTB8OS
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
LOC441869
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653566
PRAMEF22
PRAMEF15
WASH5P
PRAMEF16
FAM138C
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
MIR551A
ZBTB8B
CDC2L2
LOC728661
PRAMEF14
FLJ37453
OR4F29
SNHG3-RCC1
LOC100128003
LOC100128071
LOC100128842
LOC100129534
FLJ39609
LOC100132062
LOC100132287
LOC100133331
LOC100133612
LOC100288778

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.22.

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

Genes
AUTS2

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MORF4
ADAM29
SCRG1
FAM149A
FBXO8
PDLIM3
GALNT7
CLDN22
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
TUBB4Q
STOX2
KIAA1430
SPCS3
C4orf41
MLF1IP
NBLA00301
WWC2
KIAA1712
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
TRIML1
ANKRD37
HELT
FAM92A3
C4orf47
GALNTL6
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

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

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

Genes
CREBBP
TSC2
hsa-mir-940
hsa-mir-1225
hsa-mir-662
ABCA3
ADCY9
ARHGDIG
ATP6V0C
CCNF
CLCN7
DCI
DNASE1
DNASE1L2
E4F1
GFER
HAGH
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
IGFALS
MEFV
MPG
NDUFB10
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PDPK1
PKD1
PPL
RPL3L
RPS2
SRL
SOLH
SSTR5
TCEB2
TFAP4
TPSAB1
UBE2I
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
C16orf35
AXIN1
RGS11
CACNA1H
BAIAP3
RHBDL1
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
SYNGR3
IL32
SLC9A3R2
SEC14L5
RAB11FIP3
IFT140
TELO2
NUBP2
ZNF263
TRAP1
MSLN
STUB1
MRPL28
TBL3
RNPS1
PRSS21
CLUAP1
MAPK8IP3
MGRN1
TPSD1
SRRM2
TPSG1
RAB26
ZNF500
DECR2
OR1F2P
SNORA64
SNORD60
UBN1
C16orf5
SOX8
AMDHD2
Magmas
NAGPA
TNFRSF12A
POLR3K
SEPX1
GNG13
KCTD5
ZNF434
HCFC1R1
LUC7L
ALG1
NMRAL1
TBC1D24
CASKIN1
CRAMP1L
RAB40C
TMEM8A
CHTF18
PRSS22
MLST8
RHBDF1
MMP25
NARFL
C16orf10
TPSB2
HS3ST6
PDIA2
UNKL
LMF1
FAM173A
MRPS34
METRN
THOC6
KREMEN2
CORO7
SNRNP25
ROGDI
TMEM204
NAT15
C16orf59
MGC3771
FAHD1
PRSS27
ITFG3
WDR24
TRAF7
FLYWCH1
HAGHL
NUDT16L1
C16orf13
FAM195A
BTBD12
GNPTG
GLYR1
GLIS2
ZSCAN10
RHOT2
ZNF598
HN1L
SPSB3
TIGD7
RPUSD1
FLYWCH2
VASN
C16orf42
WFIKKN1
NOXO1
CCDC78
ZG16B
TMPRSS8
PAQR4
ANKS3
FAM100A
SEPT12
RNF151
C16orf11
FBXL16
LOC146336
ZNF597
CCDC64B
C16orf89
C16orf71
FAM86A
WDR90
EME2
NLRC3
C16orf73
PRSS33
NPW
C16orf79
PGP
NHLRC4
C16orf91
JMJD8
LOC342346
TESSP1
PRR25
C1QTNF8
C16orf38
MSLNL
LOC440335
SNORA10
FLJ42627
CCDC154
C16orf90
ABCA17P
LOC652276
SNORA78
MIR662
SNHG9
CEMP1
MIR940
LOC100128788
LOC100134368
MIR1225
LOC100288778

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

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

Genes
KCNIP4
NCRNA00099

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.33.

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

Genes
BRAF
MET
SMO
KIAA1549
CREB3L2
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CFTR
CHRM2
CLCN1
CPA1
CPA2
EPHA1
EPHB6
FLNC
GPR37
GRM8
IFRD1
IMPDH1
IRF5
KCND2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
CNOT4
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
PRSS2
TAS2R38
PTN
PTPRZ1
SLC13A1
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
WNT2
ZYX
ST7
ARHGEF5
TRIM24
MGAM
WASL
DGKI
ATP6V1F
FAM131B
DOCK4
FAM115A
AASS
FAM3C
ZNF277
TFEC
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
OR2F1
SLC13A4
COPG2
TPK1
SND1
C7orf54
DENND2A
HIPK2
WDR91
C7orf68
MDFIC
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
ZC3HC1
LUC7L2
MRPS33
LSM8
GPR85
TAS2R5
ING3
LRRN3
CHCHD3
RBM28
TMEM140
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
KIAA1147
FAM40B
EXOC4
LRRC4
TMEM168
CCDC136
PARP12
C7orf49
GCC1
C7orf58
TTC26
JHDM1D
IMMP2L
CTTNBP2
SLC37A3
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7OT1
ST7OT2
ST7OT3
CADPS2
CPA5
FOXP2
TSGA14
TSGA13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
TRYX3
MOXD2
ASZ1
ASB15
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
IQUB
C7orf66
TMEM213
RNF133
ZNF800
UBN2
TAS2R39
TAS2R40
TAS2R41
FLJ40852
FAM115C
C7orf53
LOC286016
MESTIT1
ST7OT4
TAS2R60
CTAGE6
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
OR2A42
FLJ45340
MIR129-1
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
LOC441294
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF5L
WEE2
MIR490
PL-5283
MIR592
MIR593
TMEM229A
LUZP6
LOC100124692
CTAGE4
LOC100134229
LOC100134713

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

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

Genes
CDX2
FLT3
PARP4
ATP12A
CDK8
FGF9
FLT1
GJA3
GJB2
GPR12
GTF3A
PDX1
MIPEP
PABPC3
RNF6
RPL21
SGCG
TUBA3C
ZMYM2
IFT88
MTMR6
ZMYM5
NUPL1
SAP18
GJB6
WASF3
SACS
LATS2
SNORD102
POLR1D
CRYL1
POMP
ATP8A2
IL17D
MPHOSPH8
PSPC1
TNFRSF19
CENPJ
RNF17
XPO4
MRP63
TPTE2
FAM123A
USP12
MTIF3
GSX1
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
ZDHHC20
PAN3
DKFZp686A1627
SLC46A3
LOC284232
C1QTNF9
LOC348021
LOC374491
RASL11A
C1QTNF9B
SHISA2
ATP5EP2
PCOTH
SNORA27
LOC646405
PRHOXNB
LOC100101938
RPL21P28
LOC100288730

Genes in Wide Peak

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

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

Genes
GNA11
LYL1
MLLT1
SH3GL1
SMARCA4
STK11
TCF3
FSTL3
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-1227
hsa-mir-1909
hsa-mir-1302-2
ACP5
AES
AMH
ASNA1
ATP5D
AZU1
HCN2
BSG
C3
CACNA1A
CALR
CAPS
CD70
CDC34
CDKN2D
CIRBP
CNN1
CNN2
CSNK1G2
DAPK3
CFD
DHPS
DNASE2
DNM2
DNMT1
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
ELAVL3
EMR1
EPOR
FARSA
FCER2
FUT3
FUT5
FUT6
GAMT
GCDH
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
ICAM1
ICAM3
ICAM4
ILF3
INSR
JUNB
LDLR
MAN2B1
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NFIX
NRTN
OAZ1
P2RY11
PALM
PDE4A
PIN1
POLR2E
POLRMT
PRKCSH
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RAD23A
RFX2
RPS15
RPS28
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
PRDX2
THOP1
ICAM5
TLE2
TYK2
VAV1
ZNF20
ZNF69
ZNF121
ZNF136
ZNF177
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
EIF3G
STX10
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
S1PR2
TRIP10
LONP1
RAB3D
APBA3
IER2
SAFB2
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
EBI3
ZNF443
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4
TIMM44
CARM1
SEMA6B
RNASEH2A
KLF1
ZNF266
PNPLA6
UQCR
TMED1
CDC37
SBNO2
MAST1
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
KANK2
TIMM13
TSPAN16
DAZAP1
OR7E24
SNORD41
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
HOOK2
SLC39A3
TNPO2
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
ECSIT
THEG
ZBTB7A
FZR1
C19orf56
SIRT6
PIAS4
LSM7
ZNF44
MBD3
S1PR5
MIER2
PCSK4
ZNF562
BEST2
FBXL12
C19orf24
PLEKHJ1
C19orf66
FEM1A
ZNF823
STAP2
TRMT1
BTBD2
RNF126
CCDC94
LOC55908
C19orf10
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
RGL3
SLC44A2
MCOLN1
WDR18
REXO1
ZNF490
DOCK6
KIAA1543
ZNF317
ZNF77
C19orf29
UBL5
BRUNOL5
LPPR2
KRI1
YIPF2
C19orf43
SLC25A23
ZNF426
FSD1
ZNF557
LASS4
TLE6
LPPR3
DENND1C
ZNF442
ZNF556
LRRC8E
UBXN6
OR4F17
ACSBG2
ADAMTS10
QTRT1
FAM108A1
DOHH
RTBDN
ANGPTL6
KLF16
PRAM1
FBXW9
ALKBH7
MORG1
ZNF414
ELOF1
DOT1L
FBN3
ZNF559
KISS1R
CREB3L3
HDGF2
LMNB2
RAX2
MUM1
MPND
ATG4D
ATCAY
MBD3L1
MIDN
GADD45GIP1
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
DPP9
C19orf22
C19orf6
C19orf20
CRB3
REEP6
PEX11G
ZNF561
OLFM2
MUC16
FDX1L
NACC1
C19orf36
SCAMP4
ADAT3
ZNF554
EVI5L
CCDC151
ZNF653
GRIN3B
MRPL54
LRG1
RAVER1
OR7D4
OR7G1
OR1M1
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
ZNF441
ZNF491
ZNF440
C19orf39
CCDC159
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOBKL2A
C19orf28
GIPC3
NDUFA11
C19orf21
PLK5P
C2CD4C
ZNF358
LOC147727
ZNF560
ZNF563
SPC24
TICAM1
C19orf23
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
ZNF846
OR7D2
ZNF791
ZNF564
ZNF709
ZNF433
PRR22
ANKRD24
C19orf59
ZNF627
DAND5
C19orf26
C19orf34
C19orf38
SYCE2
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
ZNF763
ZNF844
C19orf77
C19orf30
SLC25A41
MBD3L5
ODF3L2
EMR4P
ADAMTSL5
CLEC4G
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
C3P1
ZNF788
ONECUT3
OR7G2
OR7G3
MEX3D
FLJ45445
PRSSL1
VMAC
ZNF833
CTXN1
MIR199A1
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
FAM138F
LINGO3
ARRDC5
FAM138A
MBD3L4
MBD3L3
FAM138C
SNORD105
PPAN-P2RY11
MIR637
MIR638
PLIN4
ZNF878
SNORD105B
ZGLP1
MIR220B
C19orf71
LOC100128573

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.21.

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

Genes
CLTCL1
hsa-mir-648
ATP6V1E1
BID
GGT3P
GP1BB
GSC2
SEPT5
PRODH
SLC25A1
TBX1
CLDN5
HIRA
UFD1L
DGCR6
DGCR14
CDC45L
DGCR2
USP18
TSSK2
IL17RA
POTEH
BCL2L13
DGCR11
DGCR9
DGCR5
DGCR10
HSFYP1
CECR6
CECR5
CECR2
TUBA8
CECR1
PEX26
MICAL3
MRPL40
OR11H1
SLC25A18
GAB4
C22orf39
CCT8L2
XKR3
LOC150185
psiTPTE22
CECR7
CECR4
FLJ41941

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

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

Genes
ADARB2
KLF6
IDI1
PFKP
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
C10orf110
IDI2
TUBB8
NCRNA00200
C10orf108

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.2.

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

Genes
FGFR3
WHSC1
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
CTBP1
DGKQ
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
RGS12
RNF4
SH3BP2
WHSC2
ZNF141
SLBP
NOP14
FAM193A
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
D4S234E
STX18
FGFRL1
PIGG
LYAR
KIAA1530
ZFYVE28
TNIP2
HAUS3
ABCA11P
MFSD7
TMEM175
TMEM128
C4orf42
TMEM129
OTOP1
ZNF595
FAM53A
ZNF509
ZNF721
ZNF718
CRIPAK
DOK7
RNF212
C4orf10
NAT8L
C4orf44
LOC348926
POLN
C4orf48
ZNF876P
ZNF732
SCARNA22
MIR943
LOC100130872

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.3.

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-1979
hsa-mir-548g
AGA
SLC25A4
ANXA2P1
CASP3
LRBA
CLCN3
CPE
CTSO
DCTD
EDNRA
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GAB1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
HMGB2
HPGD
ING2
IRF2
KLKB1
SMAD1
NR3C2
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112L
PLRG1
POU4F2
PPID
ABCE1
RPS3A
SC4MOL
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SMARCA5
SORBS2
SAP30
INPP4B
SNORD73A
LRAT
HAND2
RAPGEF2
MFAP3L
ANAPC10
MAB21L2
MORF4
ADAM29
LSM6
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
OTUD4
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
TMEM184C
LRP2BP
PDGFC
TUBB4Q
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
C4orf41
HHIP
ARHGAP10
MLF1IP
NBLA00301
MAP9
WWC2
KIAA1712
SNX25
TTC29
MND1
SLC10A7
TKTL2
USP38
CBR4
FHDC1
MGC45800
PRMT10
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
ZNF827
SH3D19
C4orf38
C4orf39
C4orf45
DCLK2
TRIM60
MMAA
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
RNF175
TRIML1
LOC340017
PRSS48
ANKRD37
TRIM61
TRIM75
HELT
FAM92A3
LOC441046
C4orf47
GALNTL6
FRG2
SLED1
C4orf51
LOC653543
LOC653544
LOC653545
LOC653548
MIR578
LOC728410
FAM160A1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p12.

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

Genes
CNGA1
GABRA2
GABRA4
GABRB1
GABRG1
TEC
TXK
ATP8A1
CORIN
OCIAD1
COMMD8
ATP10D
SLAIN2
GUF1
CWH43
OCIAD2
GNPDA2
NFXL1
NIPAL1
SHISA3
COX7B2
SLC10A4
YIPF7
FRYL
ZAR1
KCTD8
GRXCR1

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
AP1G1
AFG3L1
APRT
ZFHX3
C16orf3
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
FAM38A
DHX38
KIAA0174
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
TXNL4B
BANP
RFWD3
ZNF821
ZDHHC7
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
MARVELD3
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
LRRC50
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
FLJ30679
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LDHD
MLKL
ZNF778
ACSF3
C16orf81
HTA
LOC283922
NUDT7
SNAI3
FAM92B
ATXN1L
PKD1L3
CTU2
LOC390748
C16orf74
CTRB2
CLEC18B
SNORD68
SNORD71
LOC732275
LOC100129637
LOC100130015
SYCE1L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.3.

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

Genes
KTN1
NKX2-1
NIN
CCNB1IP1
hsa-mir-624
hsa-mir-208b
hsa-mir-208a
hsa-mir-1201
ANG
APEX1
ARF6
ARHGAP5
BCL2L2
BMP4
CDKN3
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
FKBP3
FOXG1
GCH1
GMFB
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
LGALS3
MGAT2
CTAGE5
MMP14
MNAT1
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
NP
NRL
SIX6
OTX2
OXA1L
PAX9
PCK2
PNN
POLE2
PPM1A
PRKCH
PRKD1
PSMA3
PSMA6
PSMB5
PSMC6
PSME1
PSME2
PTGDR
PTGER2
PYGL
RABGGTA
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPL36AL
RPS29
RTN1
SALL2
SIX1
SOS2
SRP54
SSTR1
STYX
TEP1
TGM1
PABPN1
SIP1
CDKL1
AP1G2
SLC7A7
SDCCAG1
CPNE6
AKAP6
KIAA0391
KIAA0586
DLGAP5
TOX4
REC8
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
TM9SF1
EXOC5
CGRRF1
FAM12A
DHRS4
FERMT2
RIPK3
AP4S1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
KIAA0831
ACIN1
DAAM1
SAMD4A
FAM179B
SCFD1
KHNYN
SLC7A8
KLHDC2
HECTD1
HEATR5A
NGDN
LRP10
NKX2-8
TINF2
TIMM9
OR10G3
OR10G2
OR4E2
ATP5S
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
ERO1L
FAM158A
ATL1
ZNF219
GMPR2
SLC22A17
DACT1
JKAMP
MBIP
DHRS7
C14orf166
SIX4
GNG2
KLHL28
C14orf101
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
RNF31
RBM23
C14orf104
C14orf105
C14orf106
C14orf167
G2E3
OSGEP
FLJ10357
MUDENG
EAPP
ACTR10
METTL3
LTB4R2
SDR39U1
RPGRIP1
PELI2
NDRG2
NYNRIN
TXNDC16
TRMT5
HOMEZ
CHD8
FANCM
SNX6
SAV1
C14orf93
ABHD4
NPAS3
FAM12B
CDH24
C14orf135
GPR135
METT11D1
IL25
GNPNAT1
THTPA
OR4K5
OR4K1
C14orf138
IPO4
L2HGDH
NUBPL
DCAF11
DDHD1
OR4K15
TMX1
FSCB
BRMS1L
JPH4
RNASE7
INSM2
C14orf128
RAB2B
JUB
RPPH1
SLC25A21
LRRC16B
PPP1R3E
TMEM55B
TTC5
MAPK1IP1L
EGLN3
C14orf126
C14orf149
TRIM9
DHRS1
CMTM5
MIA2
C14orf28
TRAPPC6B
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
PPIL5
KLHDC1
FRMD6
SOCS4
NAT12
KLHL33
RPL10L
MIPOL1
SLC38A6
C14orf37
ABHD12B
MDP1
LRFN5
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
C14orf21
C14orf147
ADCY4
C14orf183
RALGAPA1
SFTA3
FBXO33
C14orf19
C14orf182
GPR137C
TSSK4
FAM177A1
DHRS4L2
C14orf39
SNORD8
RNASE10
OR6S1
SLC35F4
FLJ31306
TBPL2
C14orf23
TOMM20L
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
P704P
C14orf176
CBLN3
RPL13AP3
C14orf34
SNORD9
MIR624
DHRS4L1
C14orf38
SNORD127
SNORD126
MIR208B
C14orf33
OTX2OS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

Table S66. 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
C8orf42
ERICH1
ZNF596
OR4F21
RPL23AP53
MIR596

Genes in Wide Peak

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

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

Genes
JAK2
NFIB
CD274
MLANA
GLDC
INSL4
PTPRD
RLN1
RLN2
TYRP1
MPDZ
CER1
INSL6
KDM4C
RANBP6
C9orf46
KIAA1432
ERMP1
PDCD1LG2
TPD52L3
IL33
C9orf123
UHRF2
FREM1
KIAA2026
C9orf150
ZDHHC21

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
hsa-mir-1297
hsa-mir-15a
hsa-mir-621
hsa-mir-320d-1
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
DACH1
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
OR7E37P
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
C13orf1
COG6
KLHL1
XPO4
PCDH20
MRP63
NARG1L
RNASEH2B
DHRS12
C13orf18
C13orf23
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LOC121838
CSNK1A1L
RXFP2
C13orf26
PRR20A
C13orf30
C13orf31
HNRNPA1L2
FAM10A4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
LOC220115
LOC220429
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
DKFZp686A1627
OR7E156P
SUGT1L1
SIAH3
KCNRG
FLJ37307
SLC46A3
LOC284232
C1QTNF9
FREM2
NEK5
LOC348021
LOC374491
THSD1P
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
C13orf36
MIR15A
MIR16-1
ATP5EP2
ALG11
C13orf37
PCOTH
SNORA27
LOC646405
PRHOXNB
ZAR1L
LOC646982
SERPINE3
SNORA31
MIR621
C13orf38
PRR20B
PRR20C
PRR20D
PRR20E
LOC100101938
RPL21P28
LOC100188949
LOC100190939
LOC100288730

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

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

Genes
BUB1B
C15orf55
C15orf21
hsa-mir-1300
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
hsa-mir-211
hsa-mir-1268
ACTC1
APBA2
B2M
BCL8
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
OCA2
PLCB2
MAPK6
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
USP8
SLC28A2
COPS2
TGM5
HISPPD2A
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
MTMR15
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
MYO5C
NDNL2
KIAA1370
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SLC24A5
OR4N4
FAM98B
PLA2G4D
GOLGA6L1
GOLGA8G
GOLGA9P
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMML1
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
MRPL42P5
USP50
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P1
WHAMML2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC646214
CXADRP2
MIR548A3
MIR626
MIR627
LOC723972
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
LOC729082
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
HBII-52-24
HBII-52-27
HBII-52-28
HBII-52-45
HBII-52-46
MIR147B
LOC100129387
GOLGA8F
LOC100132724
GOLGA8D
JMJD7
PLA2G4B
FAM7A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q23.

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

Genes
IL2
RAP1GDS1
TET2
FBXW7
hsa-mir-548g
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ANK2
ANXA2P1
ANXA5
BMPR1B
CAMK2D
CASP6
CCNA2
LRBA
CLGN
CENPE
CTSO
EDNRA
EGF
EIF4E
ELF2
ENPEP
ETFDH
FABP2
FGA
FGB
FGF2
FGG
GAB1
GLRB
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
CFI
IL15
MAD2L1
SMAD1
MANBA
MGST2
NR3C2
MTTP
NDUFC1
NFKB1
NPY2R
PDHA2
PET112L
PITX2
PLRG1
EXOSC9
POU4F2
PPID
PPP3CA
ABCE1
RPL34
RPS3A
SFRP2
TACR3
TDO2
TLR2
TRPC3
UBE2D3
UCP1
UGT8
SMARCA5
PRSS12
UNC5C
MAPKSP1
PDE5A
INPP4B
SNORD73A
PAPSS1
LRAT
AIMP1
NDST3
RAPGEF2
SEC24D
TSPAN5
SPRY1
ANAPC10
PGRMC2
SEC24B
MAB21L2
RRH
PLK4
PRDM5
LSM6
NUDT6
HSPA4L
TBC1D9
METAP1
KIAA0922
TRIM2
SLC7A11
CCRN4L
PPA2
DAPP1
DKK2
INTU
ARFIP1
ZNF330
LEF1
FAM198B
LARP7
EMCN
MYOZ2
ACCN5
GAR1
PCDH18
USP53
OTUD4
DCHS2
FLJ20184
CCDC109B
BANK1
LARP1B
BBS7
TMEM144
C4orf21
AP1AR
MAML3
TMEM184C
PDGFC
FSTL5
BDH2
INTS12
ANKRD50
RNF150
PCDH10
FNIP2
METTL14
OSTC
IL21
RXFP1
SCOC
NEUROG2
SLC39A8
HHIP
NDST4
AGXT2L1
ELOVL6
C4orf31
FAT4
ARSJ
ARHGAP10
GSTCD
MAP9
TNIP3
PHF17
DNAJB14
NARG1
C4orf29
ALPK1
CXXC4
SETD7
PLA2G12A
SLC25A31
RAB33B
TTC29
MND1
SLC10A7
C4orf17
QRFPR
KIAA1109
COL25A1
USP38
C4orf49
FHDC1
PRMT10
NAF1
TIFA
RG9MTD2
TBCK
CYP2U1
DDIT4L
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
C4orf32
TRAM1L1
NHEDC2
NHEDC1
ZNF827
SH3D19
C4orf45
SPATA5
BBS12
DCLK2
MMAA
RBM46
SGMS2
SYNPO2
C4orf46
TIGD4
TMEM154
ELMOD2
NPNT
MFSD8
LOC256880
LOC285419
LOC285456
RNF175
C4orf37
LOC340017
PRSS48
LRIT3
PCNAP1
C4orf3
MIR302A
EEF1AL7
LOC441046
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641518
CEP170L
C4orf51
SNORA24
MIR577
LOC729338
FAM160A1
SNHG8
LOC100192379

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
ABP1
AKR1B1
BPGM
CALD1
CASP2
CDK5
CHRM2
CLCN1
DPP6
EN2
EPHA1
EPHB6
GBX1
MNX1
HTR5A
INSIG1
KCNH2
KEL
NDUFB2
NOS3
CNOT4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
AKR1D1
SSBP1
TBXAS1
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
DGKI
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
NUP205
CLEC5A
MKRN1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
ATP6V0A4
TAS2R3
TAS2R4
PRKAG2
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
ESYT2
ZNF398
EXOC4
GALNT11
LMBR1
C7orf4
NOM1
PARP12
LRRC61
C7orf49
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
SLC35B4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
C7orf29
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
SVOPL
MTPN
LRGUK
ASB10
TRYX3
MOXD2
RNF32
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF783
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5L3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FLJ40852
FAM115C
ZNF775
ATG9B
TAS2R60
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
STRA8
KLRG2
WDR86
GSTK1
FAM180A
OR2A25
OR2A5
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
MIR153-2
AKR1B15
LOC441294
OR2A9P
OR2A2
ARHGEF5L
GIMAP6
WEE2
MIR490
ZNF862
PL-5283
ACTR3C
MIR595
LOC728743
LUZP6
MIR671
LOC100124692
LOC100128542
CTAGE4
LOC100128822
LOC100132707
LOC100134229
LOC100134713

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
AKT2
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-519a-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-220c
hsa-mir-769
hsa-mir-642
hsa-mir-330
hsa-mir-641
A1BG
ACTN4
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1P1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
GRLF1
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
SFRS16
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
SAPS1
CARD8
SIRT2
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285A
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
C19orf61
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
PRX
SPTBN4
MARK4
CATSPERG
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSHL1
ZNF611
MED25
BCL2L12
TEX101
GRWD1
WDR87
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
ZNF607
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
TIMM50
SHKBP1
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816A
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
C19orf41
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
NCRNA00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
ZNF417
ZNF548
FLJ40125
KLC3
LYPD4
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
TTC9B
CDC42EP5
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF781
EID2
ZNF780B
ZNF540
ZNF525
SPACA4
NLRP7
GGN
CADM4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
ZNF575
LYPD5
ZNF283
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
ZNF546
MYPOP
NANOS2
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
C19orf51
ZNF233
LILRA5
B3GNT8
IGFL1
ZNF773
FLJ41856
CEACAM16
BLOC1S3
IGFL3
ZNF808
ZNF761
ZNF470
ZNF749
ZNF324B
ZNF793
PAPL
ZNF805
SPRED3
ZNF321
LOC400696
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
OLT-2
MIR330
MIR371
MIR372
MIR373
IGFL4
NCRNA00181
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
SBK2
PSG10
LGALS7B
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
ZNF814
MIR769
KIR3DP1
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100129935
BSPH1
LOC100131691
PEG3AS
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
BCL6
FOXL2
CBLB
CTNNB1
EIF4A2
ETV5
FANCD2
FHIT
GATA2
LPP
MITF
MLF1
MLH1
MYD88
PIK3CA
PPARG
RAF1
RPN1
SOX2
TFRC
VHL
XPC
BAP1
GMPS
SRGAP3
TFG
FOXP1
SETD2
PBRM1
hsa-mir-922
hsa-mir-570
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-198
hsa-mir-568
hsa-mir-567
hsa-mir-1324
hsa-mir-1284
hsa-mir-135a-1
hsa-let-7g
hsa-mir-566
hsa-mir-191
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-563
hsa-mir-885
AADAC
ACAA1
ACPP
ACTL6A
ACVR2B
ACY1
ADCY5
ADPRH
AGTR1
AHSG
ALAS1
ALCAM
AMT
APEH
APOD
ARF4
RHOA
ATP1B3
ATP2B2
ATP6V1A
ATR
BCHE
BDH1
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CASR
CAV3
CCK
CD80
CD86
ENTPD3
CD47
CDC25A
CISH
AP2M1
CLCN2
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CP
CPA3
CPB1
CPN2
CPOX
CRYGS
CSTA
CX3CR1
CYP8B1
DAG1
DGKG
DAZL
DLG1
DNASE1L3
DOCK3
DRD3
DUSP7
DVL3
ECT2
CELSR3
EHHADH
EIF4G1
EPHA3
EPHB1
EPHB3
MECOM
FBLN2
FGF12
FLNB
GAP43
GBE1
GHSR
GLB1
GNAI2
GNAT1
GOLGA4
GOLGB1
GP5
GP9
XCR1
GPR15
GPR27
GPX1
GRM2
GRM7
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRH1
HRG
HES1
HTR1F
HYAL1
IL1RAP
IL5RA
IL12A
IMPDH2
IRAK2
ITGA9
ITGB5
ITIH1
ITIH3
ITIH4
ITPR1
KNG1
KPNA1
KPNA4
LAMB2
RPSA
LSAMP
LTF
TM4SF1
MAP4
MBNL1
MCM2
MFI2
MME
MOBP
CD200
MST1
MST1R
MUC4
MYL3
MYLK
NCK1
NDUFB4
NDUFB5
NKTR
OGG1
OPA1
CLDN11
OXTR
P2RY1
PAK2
CNTN3
PCCB
PCYT1A
PDHB
PFKFB4
PFN2
SERPINI1
SERPINI2
PIK3CB
PLCD1
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
PLXNB1
POLR2H
POU1F1
PPP1R2
PPP2R3A
PRKAR2A
PRKCD
PRKCI
PROS1
MASP1
PSMD2
PTH1R
PTPRG
PTX3
QARS
RAB5A
RAP2B
RARB
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
SNORA62
ROBO1
ROBO2
RPL15
RPL24
RPL29
RPL32
RPL35A
RYK
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC6A1
SLC6A6
SLC6A11
SLC15A2
SLCO2A1
HLTF
SMARCC1
SSR3
SST
STAC
NEK4
SYN2
TCTA
TDGF1
TERC
TF
TFDP2
TGM4
TGFBR2
THPO
THRB
TIMP4
TKT
SEC62
TM4SF4
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
TRH
TRPC1
UBA7
UBE2E1
UBE2E2
UBP1
UPK1B
UMPS
USP4
UQCRC1
CLRN1
VIPR1
WNT5A
WNT7A
ZIC1
CNBP
ZNF35
ZNF80
ZNF148
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
RAB7A
KCNAB1
FXR1
COLQ
ACOX2
EOMES
HYAL3
SOX14
BFSP2
CAMK1
CGGBP1
BHLHE40
RUVBL1
CADPS
TP63
CHRD
HYAL2
B4GALT4
B3GALNT1
SNX4
TNFSF10
SUCLG2
HESX1
KAT2B
NR1I2
EIF2B5
BSN
MBD4
H1FX
USP13
LIMD1
KALRN
CCRL2
UBA3
RPL14
CLDN1
SEC22C
RRP9
MAP3K13
SLC33A1
LRRFIP2
MAGI1
CACNA2D2
COPB2
ADIPOQ
SLC22A14
SLC22A13
CHST2
SH3BP5
SLC4A7
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
VGLL4
EDEM1
KIAA0226
ECE2
VPRBP
TBC1D5
TATDN2
IP6K1
TSC22D2
EPM2AIP1
PSMD6
TOMM70A
TRANK1
IQSEC1
P2RY14
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
SMC4
ABCC5
COX17
ARPC4
ZNF197
RBM6
RBM5
TNK2
ALG3
NME6
CTDSPL
CD96
KCNMB2
STAG1
EIF1B
TRAIP
ST3GAL6
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
TUSC4
IGF2BP2
CXCR6
CSPG5
CLDN16
POLQ
CHL1
ARPP-21
CCR9
ALDH1L1
USP19
PDIA5
SLC38A3
CYB561D2
TMEM115
TOPBP1
RPP14
HHLA2
FSTL1
FAM107A
WDR6
RASSF1
NISCH
MRPL3
PDCD10
FILIP1L
TREX1
SCN11A
TUSC2
RNF13
MGLL
TWF2
MRAS
COPG
SLITRK3
NLGN1
TRAK1
DHX30
SACM1L
NCBP2
SCAP
LAMB2L
MYH15
PLCH1
EXOSC7
TMCC1
PDZRN3
TNIK
CAND2
MCF2L2
CLASP2
PLXND1
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
ATP11B
NBEAL2
NUP210
PLCL2
ANKRD28
C3orf63
KLHL18
DNAJC13
SR140
VPS8
LARS2
RYBP
C3orf27
CAPN7
ACAP2
MKRN2
NAT6
FBXL2
ANAPC13
ARMC8
ABHD14A
C3orf17
WDR51A
ABI3BP
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
WWTR1
PVRL3
TIPARP
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
UBXN7
ERC2
APPL1
HACL1
SGEF
ZBTB20
TTLL3
OR5K1
OR5H1
GNL3
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
ZBTB11
MORC1
SERP1
CNTN6
LSM3
RBMS3
GOLIM4
NKIRAS1
SPCS1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
PRSS50
RBM15B
GPR171
GMPPB
SEC61A1
LOH3CR2A
SCHIP1
LMCD1
PIK3R4
PODXL2
ARHGEF3
TRAT1
VILL
IMPG2
C3orf32
NMD3
TRNT1
ABHD5
COMMD2
DYNC1LI1
A4GNT
C3orf18
DBR1
CRBN
SS18L2
ZNF639
CLDN18
C3orf19
SHISA5
C3orf1
ZDHHC3
RSRC1
ZMYND10
PLA1A
TEX264
CCDC72
ZNF589
HEMK1
AMOTL2
IP6K2
SFMBT1
NCKIPSD
PHF7
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
GHRL
P2RY13
IL20RB
GPR87
TLR9
DCUN1D1
SEMA5B
XRN1
WDR5B
LZTFL1
PARP14
P4HTM
SLC6A20
IL17RD
GRAMD1C
ROPN1
KLHL24
SIDT1
C3orf75
SNRK
QRICH1
PXK
CMTM6
RG9MTD1
SLC41A3
PIGX
SLC25A38
ULK4
OXSM
SLC35A5
TMEM45A
FEZF2
IFT57
FLJ10213
ANO10
DALRD3
SHQ1
MSL2
TBCCD1
FAIM
SLC25A36
ARL8B
SETD5
DPPA4
LEPREL1
TMEM39A
ZNF654
TMEM40
ABCF3
LSG1
ABHD10
CHDH
PARL
IL17RB
CDV3
MFN1
YEATS2
IFT122
NGLY1
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
TMEM111
EAF2
C3orf10
ZNF167
MYNN
LMOD3
EIF5A2
CLDND1
MUC13
SUCNR1
RAD18
SEMA3G
MCCC1
LXN
C3orf37
MRPS22
NIT2
KTELC1
BBX
KIF15
ADAMTS9
CCNL1
PLSCR2
PCBP4
PLSCR4
PCNP
HRASLS
MRPL47
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
ISY1
HHATL
HEG1
KIAA1257
CDGAP
NCEH1
IFT80
KIAA1407
WDR48
LRRN1
KIAA1524
SLC7A14
SRPRB
SELK
SENP2
GNB4
BPESC1
PROK2
EEFSEC
RNF123
NSUN3
CIDEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZFYVE20
KIF9
NFKBIZ
AZI2
ZMAT3
MTMR14
ATG3
MRPS25
CSRNP1
GORASP1
MFSD1
CCDC14
FNDC3B
P2RY12
CDCP1
CCDC71
NT5DC2
SLC26A6
TMEM108
CRELD1
CAMKV
TMEM43
OR5H6
OR5H2
ZXDC
ZBED2
LRRC2
FYCO1
ATP13A3
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC51
TBL1XR1
ZBBX
ZNF385D
LRRC31
CCDC48
NEK11
UBA5
HDAC11
MAP6D1
PHC3
C3orf36
ARL14
THOC7
NAT13
PIGZ
CEP63
CEP70
ABTB1
WDR82
TMEM22
TSEN2
GRIP2
OR5AC2
RTP3
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
C3orf20
ID2B
ARL6
ZIC4
ATRIP
ACAD11
IQCG
ATP13A4
FYTTD1
NICN1
CHCHD6
MON1A
C3orf26
HPS3
ARPM1
JAGN1
KBTBD8
SLC12A8
C3orf42
RETNLB
CCDC54
MGC2889
IL17RC
ABHD14B
LRCH3
MINA
GPR128
C3orf39
DIRC2
C3orf34
EAF1
DCLK3
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
UCN2
LOC90246
C3orf25
TMEM41A
ZNF502
BOC
FAM55C
RFT1
OXNAD1
SPSB4
ACPL2
ZBTB47
TMEM44
C3orf50
ACTR8
CAMK2N2
CMTM7
OSBPL10
OSBPL11
SLC25A26
ZNF501
C3orf24
LRRC58
LRRC3B
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1OS
GALNTL2
GPR62
CPNE4
CCDC58
KCNH8
DNAJC19
OTOL1
FAM3D
ZPLD1
LYZL4
KBTBD5
TRIM71
FAM131A
CD200R1
CHCHD4
ZDHHC19
CRYBG3
DCBLD2
LRRC15
FAM43A
TPRA1
TMEM42
UROC1
FAM194A
NUDT16
COL6A6
GRK7
TMEM207
METTL6
C3orf31
IL17RE
RTP1
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
RPL32P3
H1FOO
PISRT1
ASB14
TTC14
DTX3L
FAM19A4
SGOL1
C3orf48
EFHB
LOC151658
PPM1L
WDR49
LRRC34
CPNE9
DPPA2
CCDC80
BTLA
CCDC12
C3orf59
PPP4R2
C3orf21
ROPN1B
LOC152024
C3orf22
C3orf55
ZCWPW2
CMC1
NEK10
C3orf79
CCDC50
PYDC2
CCDC52
CMTM8
NUDT16P
CCDC13
LOC152217
LOC152225
FGD5
CIDECP
CNTN4
IGSF11
C3orf30
PARP15
C3orf57
DNAJB8
GPR156
XIRP1
RNF168
CHST13
PRICKLE2
KBTBD12
DHX36
HTR3C
DZIP1L
TTC21A
ALG1L
C3orf67
KCTD6
LIPH
ARL13B
DHFRL1
HTR3D
RPL22L1
OSTalpha
FBXO45
KLHDC8B
MUC20
GABRR3
PTPLB
STT3B
DNAH12
PDE12
FAM116A
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
CADM2
ZNF620
NAALADL2
ZDHHC23
LOC255025
TCTEX1D2
C3orf43
SDHALP1
COL29A1
GK5
PLCXD2
GCET2
UTS2D
ALS2CL
TMIE
LOC285194
SLC9A9
C3orf64
LOC285205
EPHA6
FBXW12
C3orf38
HTR3E
ZNF619
ZNF621
RABL3
IGSF10
C3orf33
CCDC66
SLC9A10
C3orf23
ZNF660
LOC285359
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
C3orf70
TPRG1
LOC285401
ILDR1
TRIM59
TRIM42
EIF4E3
RAB43
CCDC39
CCDC36
KY
C3orf35
GADL1
PRSS42
C3orf47
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
ZNF860
TMPRSS7
CD200R1L
PAQR9
DVWA
RTP2
OSTN
ATP13A5
SOX2OT
TXNDC6
WDR53
LNP1
CCDC37
NCRNA00119
TPRXL
LOC348840
NMNAT3
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
LRRC33
PRSS45
AMIGO3
ZNF662
CDH29
C3orf54
IQCF2
IQCF5
MUSTN1
VGLL3
PRR23B
PRR23C
PLSCR5
C3orf16
LEKR1
TMEM212
VENTXP7
LOC401052
IQCF3
FLJ25363
C3orf72
LOC401093
FLJ42393
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR15B
MIR16-2
MIR191
MIR198
MIR26A1
FAM19A1
STX19
LOC440944
TMEM89
IQCF6
LOC440957
MIR425
ARGFX
SNORA6
SNORA7A
SNORD2
SNORA4
TMPPE
TMEM30C
ALG1L2
TXNRD3IT1
TMEM14E
COL6A4P2
SPINK8
C3orf71
LOC646498
C3orf65
PA2G4P4
LOC647309
IQCJ
SCARNA7
C3orf66
SNORA7B
SNORA58
SNORA81
SNORD19
FAM86D
SNORD66
SNORD69
MIR551B
MIR563
MIR564
MIR567
MIR568
MIR569
MIR570
GLT8D4
SDHALP2
FAM157A
FAM198A
CCR2
LOC729375
PRR23A
HESRG
LOC100009676
SNORD19B
LOC100125556
MIR922
MIR885
MIR944
EGOT
GHRLOS
LOC100128023
LOC100128164
C3orf74
LOC100128640
LOC100129354
LOC100129550
LOC100131551
ZNF717
SNAR-I
MIR1224
LOC100287227
FRG2C
LOC100302640

Arm-level results

Table 3. Get Full Table Arm-level significance table - 25 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.11 | -1.21 | 1 | 0.19 | 1.8 | 0.1
1q | 1572 | 0.29 | 5.5 | 1.81e-07 | 0.05 | -3.68 | 1
2p | 753 | 0.25 | 1.99 | 0.0752 | 0.03 | -5.36 | 1
2q | 1235 | 0.14 | -1.15 | 1 | 0.02 | -5.32 | 1
3p | 853 | 0.19 | -0.0103 | 1 | 0.54 | 12.7 | 0
3q | 917 | 0.64 | 15.5 | 0 | 0.35 | 4.34 | 2.32e-05
4p | 366 | 0.05 | -4.17 | 1 | 0.46 | 8.94 | 0
4q | 865 | 0.03 | -4.26 | 1 | 0.45 | 9.69 | 0
5p | 207 | 0.54 | 9.76 | 0 | 0.43 | 5.92 | 6.82e-09
5q | 1246 | 0.09 | -2.13 | 1 | 0.51 | 13 | 0
6p | 937 | 0.12 | -2.44 | 1 | 0.11 | -2.76 | 1
6q | 692 | 0.06 | -4.48 | 1 | 0.13 | -2.46 | 1
7p | 508 | 0.31 | 3.64 | 0.000694 | 0.11 | -2.96 | 1
7q | 1071 | 0.28 | 3.65 | 0.000694 | 0.08 | -3.29 | 1
8p | 495 | 0.19 | -0.367 | 1 | 0.48 | 9.37 | 0
8q | 697 | 0.39 | 6.82 | 5.96e-11 | 0.13 | -1.83 | 1
9p | 343 | 0.15 | -1.73 | 1 | 0.48 | 9.37 | 0
9q | 916 | 0.14 | -1.23 | 1 | 0.35 | 5.79 | 1.37e-08
10p | 312 | 0.07 | -4.56 | 1 | 0.23 | 0.63 | 0.607
10q | 1050 | 0.06 | -4.01 | 1 | 0.26 | 2.93 | 0.00501
11p | 731 | 0.10 | -3.1 | 1 | 0.17 | -0.769 | 1
11q | 1279 | 0.11 | -2.31 | 1 | 0.11 | -2.15 | 1
12p | 484 | 0.28 | 2.9 | 0.0067 | 0.00 | -6.22 | 1
12q | 1162 | 0.18 | 0.119 | 1 | 0.04 | -4.66 | 1
13q | 554 | 0.04 | -4.73 | 1 | 0.37 | 6.2 | 1.62e-09
14q | 1144 | 0.14 | -1.03 | 1 | 0.20 | 1.09 | 0.361
15q | 1132 | 0.13 | -1.64 | 1 | 0.13 | -1.48 | 1
16p | 719 | 0.09 | -3.52 | 1 | 0.16 | -1.03 | 1
16q | 562 | 0.08 | -4.01 | 1 | 0.18 | -0.8 | 1
17p | 575 | 0.10 | -2.86 | 1 | 0.38 | 6.17 | 1.69e-09
17q | 1321 | 0.21 | 1.71 | 0.131 | 0.16 | -0.117 | 1
18p | 117 | 0.18 | -1.42 | 1 | 0.17 | -1.71 | 1
18q | 340 | 0.13 | -2.66 | 1 | 0.24 | 0.889 | 0.456
19p | 870 | 0.21 | 0.769 | 0.616 | 0.20 | 0.3 | 0.828
19q | 1452 | 0.25 | 3.36 | 0.0017 | 0.14 | -0.696 | 1
20p | 295 | 0.31 | 3.32 | 0.00174 | 0.07 | -4.34 | 1
20q | 627 | 0.30 | 3.64 | 0.000694 | 0.07 | -3.85 | 1
21q | 422 | 0.08 | -3.6 | 1 | 0.35 | 4.87 | 1.95e-06
22q | 764 | 0.29 | 3.63 | 0.000694 | 0.11 | -2.55 | 1

Methods & Data
Input

Table 4. Get Full Table First 10 out of 211 Input Tumor Samples.

Tumor Sample Names
TCGA-18-3406-01A-01D-0978-01
TCGA-18-3408-01A-01D-0978-01
TCGA-18-3409-01A-01D-0978-01
TCGA-18-3412-01A-01D-0978-01
TCGA-18-3414-01A-01D-0978-01
TCGA-18-3415-01A-01D-0978-01
TCGA-18-3416-01A-01D-0978-01
TCGA-18-3417-01A-01D-1439-01
TCGA-18-3419-01A-01D-0978-01
TCGA-18-3421-01A-01D-0978-01

Figure 3. Segmented copy number profiles in the input data

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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- Maintainer = Dan DiCara

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