Liver Hepatocellular 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 2.0.16 (cga svn revision 38839).

Summary

There were 53 tumor samples used in this analysis: 21 significant arm-level results, 15 significant focal amplifications, and 35 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 - 15 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
11q13.2 9.6605e-05 9.6605e-05 chr11:68713597-68771449 0 [MYEOV]
6p21.1 0.0097933 0.0097933 chr6:43876809-43886368 0 [VEGFA]
1q23.3 0.0097933 0.011247 chr1:158773709-159925403 40
13q33.3 0.066106 0.066106 chr13:106978732-114142980 43
17q25.3 0.10175 0.10175 chr17:76596751-78239374 62
3q26.31 0.17594 0.17594 chr3:173737376-173779556 0 [TNFSF10]
7q21.13 0.17594 0.17594 chr7:90288913-92559550 15
16q11.2 0.17594 0.17594 chr16:31813563-46192072 20
5p15.33 0.18058 0.18058 chr5:1009672-1339515 5
6q12 0.18058 0.18058 chr6:67601419-67634943 0 [MCART3P]
4q13.3 0.19184 0.19184 chr4:74503551-74538973 2
5q31.1 0.20526 0.20526 chr5:133799381-133822028 0 [CDKN2AIPNL]
20q13.2 0.21798 0.21798 chr20:50693176-54369134 10
2p24.1 0.23604 0.23604 chr2:1-27538143 146
1q21.2 0.0072315 1 chr1:1-247249719 2207
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q23.3.

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

Genes
FCGR2B
SDHC
APOA2
CD48
FCER1G
FCGR2A
FCGR3A
FCGR3B
HSPA6
HSPA7
LY9
MPZ
NDUFS2
NIT1
PFDN2
PPOX
SLAMF1
USF1
B4GALT3
CD84
FCGR2C
DEDD
ADAMTS4
NR1I3
USP21
F11R
UFC1
CD244
ITLN1
SLAMF7
PVRL4
TOMM40L
KLHDC9
ITLN2
ARHGAP30
C1orf192
RPL31P11
LOC642502
PCP4L1
TSTD1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q33.3.

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

Genes
hsa-mir-1267
ATP4B
COL4A1
COL4A2
F7
F10
GAS6
ING1
LAMP1
LIG4
GRK1
SOX1
TFDP1
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
TUBGCP3
TNFSF13B
RASA3
MYO16
ATP11A
MCF2L
TMCO3
DCUN1D2
ANKRD10
RAB20
CARKD
PCID2
UPF3A
CARS2
GRTP1
ABHD13
ADPRHL1
C13orf16
C13orf28
C13orf29
ZNF828
FAM70B
C13orf35
FLJ44054
FAM155A
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

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

Genes
ASPSCR1
hsa-mir-1250
ACTG1
ARHGDIA
CD7
CSNK1D
SLC25A10
FASN
UTS2R
GPS1
FOXK2
MAFG
P4HB
PDE6G
PYCR1
PCYT2
RAC3
RFNG
MRPL12
SECTM1
SLC16A3
HGS
AATK
THOC4
BAIAP2
RAB40B
AZI1
FSCN2
NARF
DCXR
ANAPC11
SIRT7
NPLOC4
WDR45L
BAHCC1
DUS1L
C17orf62
C17orf101
C17orf70
TSPAN10
LOC92659
DYSFIP1
SLC38A10
C17orf56
NOTUM
STRA13
LRRC45
MYADML2
NPB
CCDC57
HEXDC
C17orf89
C17orf55
TMEM105
C17orf90
CCDC137
ARL16
LOC388428
TEX19
FLJ90757
MIR338
MIR657
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.13.

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

Genes
CDK6
AKAP9
hsa-mir-1285-1
KRIT1
CYP51A1
PEX1
PFTK1
MTERF
FZD1
ANKIB1
GATAD1
C7orf64
MGC16142
FAM133B
LOC401387
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q11.2.

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

Genes
hsa-mir-1826
PHKB
DNAJA2
ZNF267
ORC6L
TP53TG3
VPS35
SHCBP1
ITFG1
NETO2
GPT2
MYLK3
ANKRD26P1
LOC146481
LOC283914
SLC6A10P
C16orf87
HERC2P4
UBE2MP1
TP53TG3B
Genes in Wide Peak

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

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

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
Genes in Wide Peak

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

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

Genes
AFP
ALB
Genes in Wide Peak

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

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

Genes
CYP24A1
MC3R
PFDN4
ZNF217
BCAS1
DOK5
C20orf108
TSHZ2
CBLN4
SUMO1P1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.1.

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

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-1301
ACP1
ADCY3
APOB
RHOB
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
FTHL3P
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
SNX17
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
MAPRE3
EFR3B
MYT1L
LPIN1
PUM2
NTSR2
IFT172
SH3YL1
TRIB2
GRHL1
NRBP1
ITSN2
TTC15
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
HS1BP3
COLEC11
CENPO
SMC6
NOL10
C2orf44
FAM49A
ABHD1
SELI
RSAD2
C2orf39
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
LOC150622
TCF23
FAM84A
GDF7
GPR113
UBXN2A
CYS1
KRTCAP3
ATP6V1C2
RNASEH1
FAM150B
DNAJC5G
IAH1
C2orf70
C2orf53
LOC339788
MSGN1
GEN1
C2orf48
PFN4
LOC375190
MFSD2B
C2orf90
C2orf79
LOC400940
FAM110C
C2orf84
RAD51AP2
LOC730811
LOC100128731
SNORA80B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
ABL2
ARNT
BCL9
CDKN2C
ELK4
EPS15
FCGR2B
FH
JAK1
JUN
LCK
MDM4
MPL
MUC1
MUTYH
MYCL1
NOTCH2
NRAS
NTRK1
PAX7
PBX1
PRCC
RPL22
SDHB
SDHC
SFPQ
TAL1
TPM3
TPR
ARID1A
TNFRSF14
BCL10
PDE4DIP
THRAP3
TRIM33
PRDM16
RBM15
SLC45A3
MDS2
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-488
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
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-101-1
hsa-mir-30c-1
hsa-mir-552
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
ABCA4
ACADM
ACTA1
ACTN2
ADAR
ADORA1
ADORA3
PARP1
ADSS
AGL
AGT
AK2
AK3L1
ALDH9A1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
ARF1
RHOC
ASTN1
SERPINC1
ATF3
RERE
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
ATP5F1
ATP6V0B
AVPR1B
BAI2
BGLAP
BMP8B
BRDT
C1QA
C1QB
C1QC
C4BPA
C4BPB
C8A
C8B
CA6
CACNA1E
CACNA1S
CAPN2
CAPZA1
CAPZB
CASP9
CASQ1
CASQ2
RUNX3
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
TNFRSF8
CD34
CD48
CD53
CD58
CDA
CDC2L1
CDC20
CDC42
CD52
CENPF
RCC1
CHI3L1
CHI3L2
CHIT1
CHML
LYST
CHRM3
CHRNB2
CKS1B
CLCA1
CLCN6
CLCNKA
CLCNKB
CLK2
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
COPA
CORT
CPT2
CR1
CR1L
CR2
CRABP2
CRP
CRYZ
CSF1
CSF3R
CSRP1
CTBS
CTH
CTPS
CTSE
CTSK
CTSS
CYP2J2
CYP4A11
CYP4B1
DAB1
CD55
DBT
GADD45A
DDOST
DHX9
DFFA
DFFB
DHCR24
DIO1
DPH2
DPT
DPYD
DR1
DVL1
E2F2
ECE1
ECM1
S1PR1
EDN2
PHC2
LGTN
EFNA1
EFNA3
EFNA4
CELSR2
MEGF6
EPHA2
ELAVL4
ELF3
ENO1
ENSA
EPB41
EPHA8
EPHB2
EPHX1
EPRS
ESRRG
ETV3
EXTL1
EXTL2
EYA3
F3
F5
F13B
FAAH
FABP3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FGR
FHL3
FOXE3
FOXD2
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
MTOR
NR5A2
FUCA1
DARC
IFI6
GABRD
GALE
GALNT2
GBA
GBAP
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GLUL
GNAI3
GNAT2
GNB1
GNG4
GNG5
SFN
GPR3
GPR25
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
GUK1
H3F3A
HCRTR1
HDAC1
HDGF
CFH
CFHR1
CFHR2
ZBTB48
MR1
HLX
HMGN2
HMGCL
HMGCS2
HNRNPU
HPCA
HSD3B1
HSD3B2
HSD11B1
HSPA6
HSPA7
IGSF3
HSPG2
HTR1D
HTR6
ID3
IFI16
CYR61
IL6R
IL10
IL12RB2
TNFRSF9
ILF2
INPP5B
INSRR
IPP
IRF6
ITPKB
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNH1
KCNJ9
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
STMN1
LBR
LEPR
LGALS8
LMNA
LMX1A
LOR
LY9
TACSTD2
MAGOH
MARK1
MATN1
MCL1
CD46
SMCP
MEF2D
MFAP2
MGST3
MNDA
MOV10
MPZ
MSH4
MTF1
MTHFR
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NASP
NBL1
NCF2
NDUFS2
NDUFS5
NEK2
NFIA
NFYC
NGF
NHLH1
NHLH2
NID1
NIT1
NPPA
NPPB
NPR1
NRD1
YBX1
ROR1
DDR2
NVL
OPRD1
ORC1L
OVGP1
PAFAH2
PRDX1
PCTK3
PDC
PDE4B
PDZK1
PEX10
PEX14
PFDN2
PFKFB2
PGD
PGM1
PIGC
PIGR
PIK3C2B
PIK3CD
PI4KB
PIN1L
PKLR
PKP1
PLA2G2A
PLA2G4A
PLA2G5
PLOD1
PLXNA2
EXOSC10
PRRX1
POU2F1
POU3F1
PPOX
PPP1R8
PPP2R5A
PPT1
PRELP
PRKAA2
PRKAB2
PRKACB
PKN2
PRKCZ
PROX1
PSEN2
PSMA5
PSMB2
PSMB4
PSMD4
PTAFR
PTGER3
PTGFR
PTGFRN
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PTPRF
PEX19
ABCD3
RAB3B
RAB4A
RAB13
RABGGTB
RABIF
RAP1A
RAP1GAP
RBBP4
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RHCE
RHD
RIT1
RLF
RNASEL
RNF2
RNPEP
SNORD21
RORC
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RPS27
RSC1A1
RXRG
RYR2
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
SCNN1D
SCP2
XCL1
SELE
SELL
SELP
SFRS4
SHC1
ST3GAL3
STIL
SKI
SLAMF1
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SLC16A1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRM
SRP9
TROVE2
SSR2
AURKAPS1
STXBP3
XCL2
SYCP1
TAF12
TAF13
TARBP1
CNTN2
TBCE
TBX15
TCEA3
TCEB3
VPS72
TGFB2
LEFTY2
TGFBR3
THBS3
TCHH
TIE1
TLR5
GPR137B
TNFRSF1B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TP73
TRAF5
CCT3
TSHB
TSNAX
TTC4
TUFT1
TNFSF4
TNFRSF4
UCK2
UQCRH
UROD
USF1
USP1
USH2A
VCAM1
WNT2B
WNT9A
ZSCAN20
ZNF124
ZBTB17
SLC30A1
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
DAP3
NPHS2
BTG2
PTP4A2
HIST3H3
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
SNHG3
NR0B2
RAD54L
GNPAT
DYRK3
TTF2
CDC42BPA
RGS5
PPFIA4
PIK3R3
MMP23B
MMP23A
KCNAB2
ITGA10
LMO4
FCN3
BLZF1
CDC14A
DEGS1
KMO
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
VAMP4
PEA15
B4GALT3
B4GALT2
B3GALT2
TNFRSF25
ADAM15
PABPC4
TNFRSF18
FPGT
PEX11B
CREG1
CD84
PER3
FUBP1
EIF2B3
RAB7L1
SELENBP1
TNFSF18
TAF1A
MPZL1
SH2D2A
ARTN
MAP3K6
ANGPTL1
DIRAS3
TBX19
FCGR2C
SLC16A4
PRPF3
KCNQ4
EXO1
ARHGEF2
DEDD
ZMYM4
ZMYM6
XPR1
FAIM3
DHRS3
MAPKAPK2
GPR37L1
GPR52
SFRS11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
AIM2
GGPS1
RASAL2
C1orf38
ADAMTS4
TMEM59
SEC22B
CHD1L
H6PD
SOX13
PRDX6
CLCA3P
CLCA2
ISG15
IKBKE
PLCH2
HS2ST1
IPO13
SDC3
SLC25A44
KIAA0040
KDM4A
CROCC
PUM1
NOS1AP
TMEM63A
KIAA0562
RIMS3
TOMM20
KIAA0494
URB2
ARHGEF11
DNAJC6
CEP350
CEP170
LRIG2
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
KLHL21
SLC35E2
DENND4B
RABGAP1L
TMCC2
FAM20B
ZBTB40
LPGAT1
MFN2
KIF14
RBM8A
NR1I3
AKT3
INSL5
PIGK
SCAMP3
PTPRU
ARPC5
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
PRG4
ANGPTL7
GPA33
STX6
HNRNPR
SRRM1
CNKSR1
SF3B4
ZMPSTE24
UBE4B
BCAS2
AKR1A1
WARS2
BPNT1
CEPT1
PIAS3
TESK2
TIMM17A
LRRN2
PPIE
VAV3
HAX1
MAD2L2
PPIH
ZNF238
C1orf61
CAP1
LRRC41
SEMA6C
HBXIP
SLC19A2
IFI44
POLR3C
IVNS1ABP
TXNIP
PDPN
LEFTY1
SPHAR
PMVK
KHDRBS1
GMEB1
FAM189B
AP4B1
NUDC
PHTF1
MASP2
CAPN9
NES
KDM5B
AHCYL1
SFRS13A
SDCCAG8
CFHR4
CFHR3
WDR3
OCLM
JTB
MTMR11
MAN1A2
UTS2
SF3A3
MLLT11
IFI44L
EBNA1BP2
SLC27A3
KIF2C
IL24
TDRKH
RER1
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
TNRC4
MSTP2
DDX20
DUSP10
MSTP9
PADI2
PMF1
DUSP12
VPS45
LYPLA2
PARK7
CTRC
ACOT7
COG2
CLCA4
MTF2
DNAJC8
NTNG1
PLEKHA6
CLSTN1
FOXJ3
KIAA0907
WDR47
KIFAP3
ATF6
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
RBM34
USP33
WDTC1
KIF21B
NMNAT2
KIAA0090
KIF1B
NFASC
POGZ
GLT25D2
MAST2
NCDN
CLCC1
SLC35D1
RGL1
PLEKHM2
SYT11
BAT2D1
FBXO28
RPRD2
OTUD3
KIAA1026
CAMTA1
LPHN2
CAMSAP1L1
KIAA1107
ZCCHC11
KIAA0467
DNAJC16
UBR4
USP24
SRGAP2
SMG5
NCSTN
ATP13A2
CRB1
ITGB3BP
GPR161
TARDBP
CELA3B
SLC35A3
ABCB10
ICMT
MACF1
LRRC8B
ZNF281
SNAPIN
LPAR3
PADI4
DDAH1
TMEM50A
OPN3
PHLDA3
RUSC1
CA14
KPNA6
SSBP3
STX12
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
TRIM58
INTS7
OLFML2B
AHCTF1
C1orf43
CLIC4
NSL1
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
DNM3
TOR1AIP1
C1orf77
C1orf144
LDLRAP1
SERBP1
NOC2L
OR1C1
PTPN22
PHGDH
FBXO2
LCE2B
OR2M4
OR2L2
OR2L1P
OPTC
FBXO6
PLA2G2D
AK5
MYCBP
OR10J1
HEYL
EIF2C1
OR4F3
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORA66
SNORD47
SNORD45B
SNORD45A
SNORD44
SNORD55
RNU11
RNF11
USP21
FOXD3
C1orf107
TRAPPC3
TAF5L
CACYBP
HSPB7
CHIA
SLC39A1
DISC2
DISC1
ARHGEF16
AHDC1
RNF115
KLHL20
TEKT2
SMPDL3B
ANGPTL3
ROBLD3
FLVCR1
PRO0611
UBE2T
HSPC157
CNIH4
SSU72
TMOD4
GNL2
GPSM2
UBIAD1
PYCR2
NME7
ALG6
NENF
PADI1
IL19
LASS2
SLC25A24
PLA2G2E
DNTTIP2
WDR8
CRNN
G0S2
IL20
SLC45A1
DCAF8
HP1BP3
F11R
TMED5
RRP15
GLRX2
BOLA1
PPPDE1
CELA2B
ZNF593
ZBTB7B
ZNF691
TXNDC12
TNNI3K
C1orf66
ADIPOR1
SCCPDH
SH3GLB1
MECR
APH1A
UTP11L
TRIM17
KCTD3
SDF4
MRTO4
PLEKHO1
HAO2
ACP6
TMEM69
MRPL37
IER5
HOOK1
SNX7
UCHL5
C1orf9
HPCAL4
YTHDF2
GPR89B
HSD17B7
UFC1
DTL
ZCCHC17
METTL13
DPH5
HSPB11
OAZ3
PADI3
CYB5R1
CMPK1
ARID4B
CD244
GPR88
ERRFI1
DPM3
WNT4
YIPF1
FBXO42
MRPS21
CCDC76
TMCO1
ADAMTSL4
CRCT1
RNF186
SPATA6
EGLN1
MXRA8
L1TD1
HES2
KIAA1383
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
C1orf26
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
PQLC2
CASZ1
LAX1
RHBDL2
DUSP23
ADPRHL2
TRNAU1AP
C1orf27
C1orf109
C1orf56
CPSF3L
C1orf123
C1orf159
MOSC2
AURKAIP1
TTC22
MRPL20
AIM1L
SUSD4
KIF26B
TMEM51
RALGPS2
GPATCH2
BSDC1
XKR8
TMEM39B
PRPF38B
HEATR1
CDCA8
LRRC8D
MSTO1
DARS2
ARHGEF10L
PRMT6
RNF220
VPS13D
FAM176B
GOLPH3L
ATAD3A
TMEM57
KLHDC8A
TRIM62
ETNK2
RAVER2
PANK4
KIRREL
TMEM206
YY1AP1
ECHDC2
FGGY
MCOLN3
SLC22A15
YOD1
CAMK2N1
BATF3
SLC30A10
UBE2Q1
RNPC3
ITLN1
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
ZNF692
NBPF1
IARS2
MAP7D1
IPO9
TMEM48
NECAP2
IQCC
C1orf112
HHAT
DNAJC11
ENAH
NUP133
RCOR3
C1orf106
C1orf103
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
RCC2
C1orf183
DMAP1
AJAP1
GNG12
RAG1AP1
C1orf91
FAM54B
SERTAD4
CCBL2
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
TMEM167B
OLFML3
SMYD2
LHX9
OTUD7B
CABC1
CTNNBIP1
C1orf63
AGTRAP
C1orf128
RAB25
PGLYRP4
ZNF695
RHBG
MAN1C1
SCYL3
GJC2
CAMK1G
NIPAL3
SEPN1
ATP8B2
KIAA0495
VANGL2
PBXIP1
S100A14
PLEKHG5
GATAD2B
AMIGO1
LRRC47
ODF2L
CGN
KIAA1324
PTCHD2
IGSF9
LRRC7
SIPA1L2
KIF17
ZNF687
ZSWIM5
POGK
KIAA1522
HCN3
CACHD1
MIER1
KIAA1614
FAM5B
HES4
C1orf114
GRHL3
SLAMF7
ZP4
CADM3
PTBP2
RHOU
PRUNE
DNASE2B
DLGAP3
IL22RA1
HIVEP3
KLHL12
LGR6
GPBP1L1
HAPLN2
MIIP
GAS5
PAPPA2
CELA2A
BCAN
GPATCH3
TNN
MRPS14
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
TINAGL1
SPATA1
LEPRE1
TFB2M
SEMA4A
TOR3A
RFWD2
GREM2
RGS18
PLA2G2F
HIAT1
NUCKS1
SMAP2
ACBD3
SMYD3
ATPAF1
MOSC1
S100PBP
MEAF6
DEM1
CCDC21
ARV1
NMNAT1
ELOVL1
AIDA
VWA1
DCLRE1B
MRPS15
MRPL9
PINK1
JMJD4
MARCKSL1
PRAMEF1
PRAMEF2
INTS3
NADK
ZNF643
C1orf163
PHACTR4
C1orf135
SCNM1
ERI3
C1orf50
WDR77
C1orf116
MGC4473
CCDC28B
C1orf35
EFHD2
MMEL1
C1orf89
FCRL2
DLEU2L
OR4F5
NKAIN1
TTC13
EPS8L3
CDC73
MRPL24
MUL1
PGBD5
TNFAIP8L2
C1orf54
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
NOL9
PPCS
LIN28
C1orf113
TTLL7
SNIP1
C1orf115
HHIPL2
VASH2
AGMAT
WDR78
ZMYM1
NCRNA00115
ZNF669
RPAP2
ZNF672
MORN1
GRRP1
KIAA0319L
DHDDS
PAQR6
DENND2D
GPR177
PCNXL2
GPR157
TRIM46
C1orf129
RPF1
SIKE1
ZC3H12A
SPSB1
TARS2
WDR26
TRIM45
EDEM3
FLAD1
TRAF3IP3
GLTPD1
ZNF436
TAS1R2
TAS1R1
SH3BP5L
NPL
GJA9
OR4F16
OR6N2
OR6K2
OR2G3
OR2G2
OR2C3
SYNC
CFHR5
TRIM11
C1orf21
ACTL8
ANKRD13C
PVRL4
SNX27
ANP32E
C1orf14
C1orf25
TSSK3
CCNL2
NUAK2
VANGL1
ST6GALNAC5
ISG20L2
HYI
FCRL5
FCRL4
SH3BGRL3
DDX59
NUF2
RASSF5
SESN2
ESPN
TAS1R3
ATAD3B
HMCN1
GPR61
MIXL1
STK40
C1orf124
TM2D1
FCAMR
REG4
OBSCN
TMEM222
C1orf49
PLEKHN1
HORMAD1
TOMM40L
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
SLC25A33
TMEM79
C1orf57
EFCAB2
DDI2
ACBD6
LZIC
PROK1
KIAA1804
EFCAB7
ZBTB37
NT5C1A
LCE3D
TRIM63
PSRC1
FAM167B
C1orf97
MGC12982
C1orf170
CROCCL1
FCRLA
ANKRD36BL1
ZNF496
HPDL
C1orf203
AGBL4
MFSD2A
C1orf198
PPP1R15B
ATG4C
MAEL
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
DISP1
SNHG12
FAM40A
RGS8
DOCK7
KIAA1751
WNT3A
NAV1
SEC16B
AQP10
LHX4
SLAMF9
KIAA2013
THAP3
C1orf201
PYGO2
ANGEL2
SPOCD1
ZNF697
IGFN1
NUP210L
BTF3L4
UBXN11
NEXN
CENPL
DUSP27
RCSD1
MEX3A
C1orf156
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
C1orf158
LEMD1
ZNF670
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
C1orf85
MED8
KTI12
C1orf212
ADC
TMEM54
C1orf59
TOE1
NLRP3
ERMAP
PGLYRP3
CSMD2
MYSM1
GNRHR2
CROCCL2
FHAD1
SLAMF6
OSBPL9
SLC26A9
LOC115110
OMA1
RAB42
FCRL1
FCRL3
LRRC42
GBP4
GBP5
FAM46B
FMO9P
FAM36A
RBP7
TSEN15
FAM129A
SNAP47
ACAP3
TADA1
THEM4
SH2D1B
SSX2IP
UBE2J2
OLFM3
GABPB2
TCHHL1
RPTN
C1orf231
TDRD10
SHE
C1orf172
C1orf96
AADACL3
PUSL1
B3GALT6
WDR63
KLHDC9
C1orf125
C1orf161
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
ASB17
TYW3
C1orf173
LRRIQ3
TPRG1L
C1orf93
MYOM3
DMBX1
OR10J5
TMCO2
ZNF684
C1orf83
PODN
LRRC39
GJB4
HMGB4
RNF19B
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
SPATA17
EDARADD
KLF17
TMEM125
C1orf182
IQGAP3
APOA1BP
ARHGEF19
MRPL55
HIST3H2BB
DRAM2
C1orf88
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ACTRT2
MIB2
ITLN2
SYT6
C1orf74
CREB3L4
C1orf127
C1orf58
SAMD11
LOC148413
SAMD13
C1orf52
PHF13
C1orf51
TMEM56
NBPF4
UBE2U
SLC35F3
LOC148696
LOC148709
PTPRV
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
SLC30A7
CCDC27
C1orf213
KNCN
MOBKL2C
GLIS1
LELP1
RC3H1
MGC27382
DCDC2B
ZNF362
DCST1
CNIH3
LOC149134
MANEAL
IL23R
METTL11B
FAM78B
SHISA4
EXOC8
PDIK1L
BNIPL
CLDN19
WDR65
C1orf210
C1orf84
CCDC24
BTBD19
CCDC17
C1orf92
C1orf64
RNF187
LOC149620
PYHIN1
C1orf227
FAM71A
SLC2A7
DENND2C
GBP6
LPPR5
FNDC7
DENND1B
TDRD5
TOR1AIP2
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
SPRR4
KANK4
SASS6
C1orf55
CNST
FAM43B
PPIAL4A
HFM1
PAQR7
TTC24
C1orf65
UBL4B
PDIA3P
EIF2C3
EIF2C4
LCE4A
ALG14
FAM76A
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
LOC200030
NUDT17
FLJ23867
TXLNA
TCTEX1D1
PLD5
C1orf100
SPAG17
SLFNL1
KRTCAP2
CRTC2
C1orf126
C1orf69
HIPK1
SLC44A5
ATAD3C
AKR7L
AFARP1
TMEM9
FNDC5
EPHX4
TTLL10
AKNAD1
SLC41A1
OR2T6
LCE5A
TMCO4
MCOLN2
COL24A1
PCSK9
SYT14
ST6GALNAC3
C1orf101
ZNF683
ARHGAP30
C1orf192
NEGR1
ASPM
CYP4X1
MAGI3
TIPRL
NPHP4
BEST4
PGBD2
FAM19A3
C1orf230
THEM5
OR2L13
SLC9A11
OR14A16
CYP4A22
C1orf185
LOC284551
NBPF15
C1orf157
LOC284578
FAM41C
FAM102B
SYPL2
CYB561D1
ANKRD34A
C1orf104
LOC284632
RSPO1
EPHA10
LOC284661
C1orf204
C1orf111
LOC284688
ZNF326
BTBD8
NCRNA00201
RIMKLA
SLC25A34
ESPNP
LIN9
VN1R5
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BA
FAM151A
S100A7A
LINGO4
RXFP4
ANKRD45
C1orf174
KLHL17
C1orf70
TMEM52
FAM5C
MTMR9L
ZBTB8OS
TFAP2E
ZNF678
PRSS38
C1orf110
FAM58B
LOC339524
LOC339535
C1orf228
ZNF642
RD3
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
CCDC18
OR6F1
OR2W3
OR2T8
OR2T3
MYBPHL
OR10R2
FCRL6
KCNT2
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
OR2T29
SERINC2
FAM159A
FAM131C
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PADI6
RGSL1
BMP8A
IRF2BP2
ZBTB41
CYCSP52
C1orf187
SPATA21
CCDC23
C1orf223
C1orf175
FAM73A
PEAR1
SFT2D2
MIA3
C1orf95
FAM89A
AGRN
RPS10P7
APITD1
CATSPER4
NSUN4
GPR153
ILDR2
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
UOX
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
LOC400759
C1orf226
LOC400794
C1orf220
LOC400804
NBPF20
FAM177B
PRAMEF3
LDLRAD2
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR101-1
MIR137
MIR181B1
MIR186
MIR194-1
MIR197
MIR199A2
MIR200A
MIR200B
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
MIR30C1
MIR30E
MIR34A
MIR9-1
RGS21
LHX8
C1orf180
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
FAM183A
ZYG11A
BCL2L15
HIST2H2BF
ETV3L
LRRC52
C1orf186
TRIM67
MAP1LC3C
LOC440926
LOC441869
PRAMEF7
LOC441897
OR10J3
OR2W5
OR13G1
MIR135B
KPRP
LCE6A
SUMO1P3
LOC492303
RBMXL1
C1orf190
PEF1
MIR429
HIST2H4B
DUSP5P
C1orf133
MIR488
CYB5RL
SNORD74
RPL31P11
FAM138F
LOC642502
LOC642587
LQK1
CYMP
KIAA0754
LOC643837
TMEM88B
PPIAL4G
C1orf200
PPIAL4D
LOC645166
PRAMEF19
PRAMEF20
FAM138A
LOC645676
S100A7L2
LOC646471
LOC646627
LOC647121
LOC648740
LOC649330
ZBTB8A
NBPF6
PPIAL4B
GPR89A
LOC653566
PPIAL4C
HIST2H3D
PRAMEF22
PRAMEF15
WASH5P
TMEM183B
FAM72B
PRAMEF16
PCP4L1
FAM138C
SCARNA3
SCARNA2
SCARNA4
SCARNA1
SNORA14B
SNORA36B
SNORA42
SNORA44
SNORA55
SNORA61
SNORA77
SNORA59B
SNORA59A
SNORA16A
SNORD45C
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
SNORD85
SNORD99
SNORD103A
MIR551A
MIR553
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
ZBTB8B
LOC728448
CCDC30
CDC2L2
LOC728661
LOC728855
LOC728875
NBPF11
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729467
PRAMEF14
FAM72A
FLJ37453
OR4F29
PPIAL4E
LOC731275
SNHG3-RCC1
C1orf152
MIR765
MIR942
MIR190B
MIR760
MIR921
LOC100128003
LOC100128071
LOC100128842
C1orf68
MSTO2P
LOC100129534
LOC100130093
LOC100130331
FLJ39609
LOC100130557
TSTD1
LOC100132062
LOC100132111
LOC100132287
NBPF10
FCGR1C
LOC100133331
LOC100133612
C2CD4D
LOC100286793
LOC100288778
LOC100302401
TSNAX-DISC1

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 - 35 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
1p36.23 7.7868e-08 7.7868e-08 chr1:1-8309316 134
13q14.2 0.00030558 0.00085033 chr13:47731768-47962808 2
14q31.3 0.0059411 0.0059411 chr14:74536625-106368585 314
19p13.3 0.0075482 0.012098 chr19:6619605-6686925 1
2q34 0.017434 0.017434 chr2:208838538-242951149 261
10q26.2 0.012098 0.019034 chr10:123231113-135374737 91
8p23.2 0.022767 0.022462 chr8:2080589-6255647 1
22q13.31 0.024075 0.022806 chr22:40804400-49691432 109
2q23.1 0.027339 0.027339 chr2:138435310-165520964 67
18q21.2 0.039499 0.038451 chr18:46509167-46959369 4
9p21.3 0.04488 0.046925 chr9:21020852-23680570 26
10q23.31 0.012515 0.051476 chr10:88837980-90024018 11
16q24.2 0.059144 0.056098 chr16:70485567-88827254 147
13q32.3 0.066172 0.062681 chr13:99428994-100055448 3
3p21.1 0.088143 0.09176 chr3:52547488-52919124 13
4q22.3 0.0031499 0.09176 chr4:76699973-123507109 222
17p12 0.095983 0.092912 chr17:15832052-16062027 2
4q31.3 0.038028 0.12018 chr4:151397952-152240226 2
9p24.1 0.12242 0.12184 chr9:7786330-12683402 2
2p15 0.13818 0.13818 chr2:62267493-207340787 728
11q14.1 0.096761 0.14987 chr11:77555851-94349006 75
19p13.12 0.12184 0.16414 chr19:10621992-17905559 216
1p33 0.19242 0.19242 chr1:50652354-51210952 2
11q24.3 0.056755 0.19242 chr11:102421578-134452384 269
12q24.31 0.20028 0.19242 chr12:109829625-132349534 191
17p13.2 0.20077 0.19242 chr17:1-4658761 99
6q26 0.16298 0.20182 chr6:44330865-170899992 548
13q14.3 0.024497 0.20182 chr13:1-94080173 276
18q22.1 0.20308 0.20182 chr18:50644442-76117153 86
6q15 0.13818 0.22392 chr6:44330865-170414665 543
9q31.1 0.17657 0.22392 chr9:101620195-140273252 439
4q35.1 0.0026302 0.25613 chr4:1-191273063 806
7q34 0.24123 0.25613 chr7:1-158821424 1031
9q34.13 0.15068 0.25613 chr9:1-140273252 890
4q24 0.0031689 0.77436 chr4:1-191273063 806
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
CDC2L1
DFFB
DVL1
MEGF6
GABRD
GNB1
ZBTB48
TNFRSF9
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
PER3
VAMP3
ISG15
PLCH2
KIAA0562
KLHL21
SLC35E2
UTS2
RER1
PARK7
ACOT7
CAMTA1
ICMT
CHD5
NOC2L
OR4F3
ARHGEF16
SSU72
WDR8
SDF4
ERRFI1
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
DNAJC11
AJAP1
KIAA0495
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
OR4F5
NOL9
NCRNA00115
MORN1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
C1orf170
KIAA1751
THAP3
LOC115110
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
C1orf93
ACTRT2
MIB2
SAMD11
LOC148413
PHF13
CCDC27
CALML6
C1orf86
ATAD3C
TTLL10
NPHP4
FAM41C
LOC284661
C1orf174
KLHL17
C1orf70
TMEM52
AGRN
GPR153
FAM132A
HES5
LOC388588
RNF207
HES3
MIR200A
MIR200B
FLJ42875
LOC441869
MIR429
FAM138F
LOC643837
TMEM88B
FAM138A
WASH5P
FAM138C
MIR551A
CDC2L2
LOC728661
OR4F29
LOC100128003
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 13q14.2.

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

Genes
RB1
LPAR6
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.3.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-770
hsa-mir-345
hsa-mir-342
hsa-mir-1260
SERPINA3
ACYP1
BCYRN1
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DYNC1H1
EIF5
EML1
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
RAGE
SEL1L
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
ALKBH1
EIF2B2
MTA1
RPS6KA5
NRXN3
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
BATF
SIVA1
AHSA1
CYP46A1
PAPOLA
TMED10
PTPN21
C14orf1
VASH1
SNW1
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
FLRT2
KIF26A
C14orf109
MLH3
PRO1768
GPR132
POMT2
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
ADCK1
TMEM63C
KIAA1409
BEGAIN
PPP4R4
NGB
C14orf133
MOAP1
DIO3OS
C14orf4
INF2
OTUB2
ZFYVE21
MEG8
WDR25
C14orf139
FAM164C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
C14orf156
IFI27L2
SETD3
C14orf153
HHIPL1
C14orf142
STON2
KIAA1737
FAM181A
BTBD6
C14orf143
NEK9
C14orf73
WDR20
C14orf179
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
C14orf148
JDP2
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
C14orf72
GSC
SERPINA12
PRIMA1
C14orf166B
ISM2
C14orf145
TTC7B
C14orf49
C14orf174
EML5
MGC23270
NUDT14
C14orf48
SERPINA11
ZDHHC22
TMED8
C14orf178
C14orf86
SNHG10
C14orf177
C14orf68
C14orf70
KIAA0284
C14orf80
CCDC85C
NCRNA00203
SERPINA9
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
FLJ45244
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323
MIR337
MIR342
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR453
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
C14orf184
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
SNORD112
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-3
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-8
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
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100133469
Genes in Wide Peak

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

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

Genes
C3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q34.

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

Genes
ATIC
ACSL3
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
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
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 10q26.2.

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

Genes
FGFR2
DUX4
hsa-mir-202
ACADSB
ADAM8
BNIP3
CTBP2
CYP2E1
DMBT1
DOCK1
ECHS1
GPR26
HMX2
INPP5A
MGMT
MKI67
OAT
HTRA1
PTPRE
UROS
ADAM12
UTF1
BUB3
FAM53B
GLRX3
DPYSL4
TACC2
TUBGCP2
ATE1
FAM175B
C10orf137
VENTX
CUZD1
CALY
CHST15
ZRANB1
NSMCE4A
DHX32
PPP2R2D
BCCIP
PLEKHA1
LHPP
IKZF5
C10orf88
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
FANK1
SYCE1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
CLRN3
CPXM2
C10orf91
PWWP2B
PAOX
FAM24B
EBF3
C10orf93
TCERG1L
C10orf125
JAKMIP3
STK32C
HMX3
FLJ46361
ARMS2
C10orf122
NKX1-2
C10orf120
LOC399815
METTL10
FOXI2
FRG2B
SPRN
MIR202
NPS
LOC619207
FAM196A
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410
LOC100169752
Genes in Wide Peak

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

Table S17.  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 22q13.31.

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

Genes
hsa-let-7b
hsa-mir-1249
ACR
ARSA
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
NDUFA6
PPARA
MAPK11
MAPK12
SBF1
TCF20
UPK3A
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
C22orf9
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
RRP7A
MCAT
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
SCUBE1
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
POLDIP3
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
TTLL8
SERHL2
RNU12
ATP5L2
RPL23AP82
C22orf34
CHKB-CPT1B
NCRNA00207
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
C22orf41
LOC730668
LOC100144603
LOC100271722
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q23.1.

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

Genes
hsa-mir-1978
ACVR1
ACVR2A
RND3
CACNB4
DPP4
FAP
GCG
GPD2
GRB14
HNMT
ITGB6
KCNJ3
KIF5C
LY75
NEB
NR4A2
ORC4L
RBMS1
TNFAIP6
PKP4
KYNU
NMI
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
TBR1
GALNT5
NXPH2
COBLL1
PLA2R1
GCA
EPC2
ARL5A
MMADHC
BAZ2B
LRP1B
FIGN
RIF1
PRPF40A
MBD5
ARHGAP15
RPRM
SLC4A10
ERMN
IFIH1
MARCH7
GTDC1
TANC1
KCNH7
DAPL1
FMNL2
GALNT13
ACVR1C
LYPD6
LYPD6B
CCDC148
ARL6IP6
SLC38A11
WDSUB1
UPP2
SPOPL
RBM43
PABPCP2
Genes in Wide Peak

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

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

Genes
SMAD4
ME2
ELAC1
MRO
Genes in Wide Peak

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

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

Genes
hsa-mir-31
CDKN2A
CDKN2B
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
MTAP
C9orf53
KLHL9
DMRTA1
IFNE
MIR31
LOC554202
CDKN2BAS
Genes in Wide Peak

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

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

Genes
PTEN
PAPSS2
MINPP1
FAM35A
ATAD1
CFLP1
LOC439994
FAM22A
FAM22D
LOC728190
KILLIN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.2.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
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
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
TXNL4B
BANP
RFWD3
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
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
PKD1L3
CTU2
LOC390748
C16orf74
CTRB2
CLEC18B
SNORD68
LOC732275
LOC100129637
LOC100130015
SYCE1L
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q32.3.

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

Genes
PCCA
ZIC2
A2LD1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.1.

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

Genes
PBRM1
ITIH1
ITIH3
ITIH4
NEK4
GNL3
SPCS1
GLT8D1
TMEM110
MUSTN1
SNORD19
SNORD69
SNORD19B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.3.

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

Genes
RAP1GDS1
TET2
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ANK2
ANXA3
ANXA5
ART3
ATOH1
BMP3
BMPR1B
CAMK2D
CASP6
CCNA2
CCNG2
SCARB2
CDS1
CENPE
DMP1
DSPP
EGF
EIF4E
ENPEP
FABP2
FGF5
GK2
GRID2
H2AFZ
HADH
HNRNPD
IBSP
CFI
CXCL10
MAD2L1
MANBA
CXCL9
AFF1
MTTP
NFKB1
NKX6-1
PDHA2
PITX2
PKD2
EXOSC9
PPEF2
PPP3CA
PRKG2
MAPK10
PTPN13
RPL34
CXCL11
SNCA
SPP1
TACR3
TMSL3
TRPC3
UBE2D3
UGT8
SPARCL1
PRSS12
USO1
UNC5C
MAPKSP1
PDE5A
HERC3
STBD1
CDKL2
PAPSS1
AIMP1
NDST3
ABCG2
SEC24D
G3BP2
HNRPDL
TSPAN5
FAM13A
SEC24B
CXCL13
PDLIM5
RRH
HPSE
CCNI
PRDM5
SEC31A
MMRN1
WDFY3
METAP1
PPA2
DAPP1
DKK2
NAAA
COQ2
HPGDS
MRPS18C
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
MYOZ2
NUDT9
NUP54
GAR1
USP53
FLJ20184
HERC6
CCDC109B
BANK1
SDAD1
BBS7
C4orf21
AP1AR
BMP2K
SEPT11
BDH2
SMARCAD1
MEPE
PRDM8
INTS12
KLHL8
SHROOM3
METTL14
ENOPH1
OSTC
NEUROG2
SLC39A8
NDST4
AGXT2L1
MRPL1
ELOVL6
C4orf31
ARSJ
THAP9
GSTCD
TNIP3
SCD5
DNAJB14
FRAS1
ALPK1
CXXC4
PLA2G12A
ARHGAP24
C4orf17
QRFPR
FAM175A
KIAA1109
COL25A1
ARD1B
AGPAT9
PIGY
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
GDEP
ANTXR2
TMEM155
LIN54
C4orf32
C4orf36
TRAM1L1
NHEDC2
NHEDC1
PAQR3
C4orf26
PPM1K
RASGEF1B
TIGD2
SGMS2
SYNPO2
CNOT6L
C4orf22
NPNT
LOC256880
NAP1L5
LOC285456
FAM13AOS
GPRIN3
C4orf37
CCDC158
ANKRD56
LRIT3
SLC10A6
HSD17B13
PCNAP1
FAM190A
C4orf3
C4orf12
MIR302A
C4orf11
TMEM150C
EEF1AL7
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641518
CEP170L
SNORA24
MIR575
MIR577
SNHG8
FAM47E
LOC100192379
Genes in Wide Peak

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

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

Genes
NCOR1
TTC19
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q31.3.

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

Genes
LRBA
MAB21L2
Genes in Wide Peak

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

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

Genes
PTPRD
C9orf123
Genes in Wide Peak

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

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

Genes
CHN1
ERCC3
HOXD11
HOXD13
NFE2L2
PMS1
PAX8
TTL
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-1978
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-1285-2
ACTG2
ACVR1
ACVR2A
ADD2
ADRA2B
BIN1
ANXA4
AOX1
RND3
ATP5G3
ATP6V1B1
AUP1
BMPR2
BUB1
CACNB4
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CHRNA1
CLK1
CNGA3
COL3A1
COL5A2
COX5B
ATF2
CTLA4
CTNNA2
DARS
DBI
DCTN1
DGUOK
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DUSP2
EEF1B2
EGR4
EMX1
EN1
FABP1
FAP
FHL2
FRZB
GAD1
GALNT3
GCG
MSTN
GFPT1
GGCX
GLI2
GLS
GPD2
GPR1
GPR17
GPR39
GRB14
GYPC
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HSPD1
HSPE1
IL1A
IL1B
IL1R1
IL1RN
INHBB
INPP1
INPP4A
ITGA6
ITGA4
ITGAV
ITGB6
KCNJ3
KIF5C
AFF3
LCT
LIMS1
LRP2
LY75
MXD1
MAL
MAT2A
MCM6
MDH1
MEIS1
MGAT5
MYO1B
MYO7B
NAB1
NEB
NDUFB3
NDUFS1
NEUROD1
NPAS2
NPHP1
NR4A2
ORC2L
ORC4L
OTX1
REG3A
PCBP1
PDE1A
PDK1
PLCL1
PLEK
PLGLB2
PLGLB1
POLR2D
POU3F3
PPP3R1
PROC
PTPN4
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
REG1P
RPL31
RTKN
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
SFTPB
SLC1A4
SLC9A2
SLC20A1
SNRPG
SP3
SPR
SSB
SSFA2
STAT1
STAT4
SULT1C2
TACR1
C2orf3
TFPI
TGFA
TIA1
TNFAIP6
TSN
TTN
SUMO1
UGP2
WIPF1
ZAP70
ZNF2
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
DYSF
FZD7
SDPR
NCK2
DUSP11
PKP4
HAT1
AGPS
PRKRA
SLC25A12
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ST3GAL5
DDX18
KYNU
NAT8
NMI
TMSB10
IL1RL1
STK17B
GTF3C3
PPIG
CIAO1
TGFBRAP1
HS6ST1
MAP4K4
EIF2AK3
CHST10
CIR1
CYTIP
GCC2
EIF5B
BZW1
SERTAD2
MRPL19
ZEB2
TLK1
CD302
ARHGAP25
TANK
BCL2L11
ACTR3
ACTR2
ACTR1B
ABI2
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
SMYD5
KBTBD10
C1D
MERTK
UBE2E3
SEMA4F
CCT7
GNLY
STAMBP
TGOLN2
MTX2
B3GNT2
USP39
TBR1
MAP3K2
NCKAP1
VAMP5
MTHFD2
ARID5A
PROKR1
EDAR
IMMT
SNRNP27
RAPGEF4
TBC1D8
RABL2A
GALNT5
NXPH2
GPR45
MGAT4A
COBLL1
AAK1
PLA2R1
RAB3GAP1
RPIA
SNRNP200
CEP68
UBXN4
EXOC6B
EHBP1
SATB2
CLASP1
NCAPH
SF3B1
TMEM131
R3HDM1
PSD4
WBP1
TMEFF2
GCA
VAX2
MOBKL3
POLR1A
CNRIP1
UNC50
GORASP2
SPATS2L
RAB11FIP5
EPC2
ARL5A
HIBCH
PTPN18
CNNM4
CNNM3
IL1F5
SNORD51
IL1F8
IL1F7
IL1F6
SULT1C4
NFU1
MMADHC
BMP10
ZNF638
STK39
HTRA2
METTL5
HSPC159
OLA1
C2orf27A
TFCP2L1
ICOS
BAZ2B
SLC40A1
KCNIP3
CD207
ARHGEF4
PDE11A
TPRKB
FAHD2A
C2orf86
INSIG2
ANKRD39
FAM178B
RNF181
MRPL30
KRCC1
MRPL35
PCYOX1
GULP1
REV1
NAT8B
VPS54
LIPT1
NOP58
VPS24
FKBP7
ZAK
LRP1B
PPIL3
DNAJC10
ETAA1
CCDC93
ASNSD1
AFTPH
MFSD6
RETSAT
INO80D
SEMA4C
C2orf42
PTCD3
PLEKHB2
FIGN
RIF1
MOBKL1B
STEAP3
THNSL2
ACOXL
WDR33
STRADB
C2orf29
NAGK
SMPD4
TMEM127
PRPF40A
IWS1
LIMS2
KIAA1310
WDR12
MBD5
KDM3A
ARHGAP15
ZC3H15
CFC1
DNAH7
GKN1
IL1F9
RPRM
CYP26B1
POLE4
UGGT1
KCMF1
PNO1
STARD7
PELI1
SLC39A10
SLC4A10
CYP20A1
SPC25
ERMN
HECW2
DPP10
EPB41L5
ALS2
ZDBF2
CWC22
ANKRD36B
G6PC2
SLC4A5
MPP4
SLC5A7
NIF3L1
PCGEM1
IFIH1
OSGEPL1
GMCL1
TTC31
ANAPC1
RMND5A
MARCH7
OBFC2A
MRPS9
MRPS5
REEP1
RAPH1
PFTK2
ALS2CR4
NBEAL1
ANKRD57
PLEKHA3
TRAK2
BOLL
PDCL3
C2orf49
TMEM185B
OR7E91P
C2orf47
SAP130
SCRN3
FASTKD1
GTDC1
ALS2CR8
TTC21B
METTL8
CYBRD1
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
FAM128B
YSK4
UXS1
COQ10B
SLC35F5
TSGA10
THSD7B
TMEM177
KIAA1715
LMAN2L
TMEM163
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
CHCHD5
C2orf7
C2orf88
CCDC115
MKI67IP
C2orf40
ZC3H8
ST6GAL2
IL1F10
MCEE
LOXL3
PCGF1
MGC13005
MFSD9
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
TANC1
LBX2
KCNH7
FER1L5
CCDC74A
LOC90784
LOC91149
SESTD1
CCDC74B
ANKRD44
ZNF804A
TTC30A
DAPL1
IMP4
MARS2
NEURL3
SFXN5
ORMDL1
LIMS3
NCRNA00152
TUBA3E
TEX261
TUBA3D
FMNL2
GALNT13
OSBPL6
NOSTRIN
DIRC1
WDR92
LYPD1
MRPL53
PARD3B
RPL23AP7
C2orf89
TMEM150A
NUP35
XIRP2
C2orf60
NMS
LYG1
MITD1
CNTNAP5
FBLN7
RBM45
TRIM43
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
REG3G
RFTN2
C2orf76
ACVR1C
UBR3
KCTD18
ALS2CR12
LYPD6
LYPD6B
MDH1B
TMEM182
CCDC148
C2orf65
MYO3B
TMEM37
DUSP19
CKAP2L
CBWD2
TEKT4
LOC150527
FLJ32063
LOC150568
SMYD1
C2orf15
PROM2
ANKAR
FBXO41
TTC30B
GPAT2
ITPRIPL1
LOC150776
LOC150786
FAM117B
LOC151009
SEPT10
ZSWIM2
ZNF385B
LOC151162
ARL6IP6
KLHL23
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
FAHD2B
ASPRV1
WDSUB1
UPP2
LOC151534
GPR155
BZW1L1
LONRF2
CCDC138
FAM171B
C1QL2
CLEC4F
DQX1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
LOC200726
TMEM17
SPRED2
FAM123C
NCRNA00116
C2orf69
HNRNPA3
LASS6
MAP1D
LYG2
SH2D6
CCDC150
RNF149
CCDC141
LOC285033
LOC285074
FAM126B
PLGLA
RGPD4
SPOPL
CYP27C1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
EVX2
AOX2P
SH3RF3
GPR148
LRRTM1
ANKRD36
WASH2P
RBM43
CERKL
ZC3H6
LOC388955
C2orf78
BOLA3
C2orf81
LOC388965
C2orf68
SLC9A4
LOC389033
SP5
DYTN
PAIP2B
RGPD1
LOC401010
C2orf66
MIR10B
MIR128-1
C2orf27B
ASTL
FKSG73
LOC440895
LOC440905
LOC440925
SULT1C3
POTEE
C2orf64
PHOSPHO2
DFNB59
LOC541471
NCRNA00164
FBXO48
SNORA41
GGT8P
FLJ40330
TRIM43B
CFC1B
RGPD3
FAM128A
LOC654342
FAM138B
LOC654433
SNORD11
SNORD70
SNORD89
SNORD94
MIR561
RGPD8
POTEF
PABPCP2
LOC729121
ANKRD20B
LOC729234
RGPD6
RGPD2
RFX8
SNORD11B
SNORA36C
MIR933
LOC100130691
TMEM194B
SP9
LOC100132215
C2orf14
LOC100133985
RNU4ATAC
SNAR-H
LOC100189589
LIMS3-LOC440895
LOC100287216
Genes in Wide Peak

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

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

Genes
PICALM
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-708
CTSC
DLG2
FUT4
GRM5
MRE11A
MTNR1B
PRCP
TYR
FZD4
EED
MED17
GAB2
NAALAD2
ME3
GPR83
PRSS23
RAB38
PANX1
ODZ4
CHORDC1
RAB30
C11orf54
NOX4
C11orf73
CWC15
PCF11
SYTL2
ANKRD49
TMEM126B
C11orf75
TRIM49
USP35
CREBZF
CCDC90B
CCDC81
TMEM135
TAF1D
NARS2
TMEM126A
KIAA1731
SLC36A4
FAT3
TRIM64
PIWIL4
AMOTL1
CCDC67
FOLH1B
C11orf82
CCDC83
FAM181B
CCDC89
KCTD21
ANKRD42
HEPHL1
C11orf90
TRIM77
FOLR4
SCARNA9
TRIM64B
TRIM53
UBTFL1
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
LOC729384
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.12.

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

Genes
JAK3
LYL1
SMARCA4
TPM4
BRD4
hsa-mir-1470
hsa-mir-639
hsa-mir-181d
hsa-mir-199a-1
hsa-mir-638
ACP5
ASNA1
BST2
CACNA1A
CALR
CD97
CNN1
DHPS
DNASE2
DNM2
ELAVL3
EPOR
NR2F6
FARSA
GCDH
DNAJB1
ILF3
INSL3
JUNB
LDLR
CYP4F3
MAN2B1
RAB8A
MYO9B
NDUFB7
NFIX
NOTCH3
PRKACA
PKN1
PRKCSH
PTGER1
RAD23A
RFX1
RPL18A
SLC1A6
SLC5A5
PRDX2
ZNF20
ZNF69
ZNF136
CYP4F2
STX10
AP1M1
F2RL3
MED26
IL27RA
TECR
RAB3D
IER2
DDX39
ZNF443
AKAP8
B3GNT3
KLF2
CARM1
CHERP
RNASEH2A
KLF1
GIPC1
ILVBL
TMED1
CYP4F8
LPHN1
MAST1
UNC13A
FCHO1
SIN3B
CASP14
PGLS
KANK2
FAM32A
OR7A17
TSPAN16
OR10H3
OR10H2
OR10H1
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
AKAP8L
CPAMD8
C19orf53
C19orf62
HOOK2
TNPO2
EMR2
ECSIT
C19orf56
ZNF44
BEST2
CC2D1A
MAP1S
ZNF823
TRMT1
ASF1B
USE1
LOC55908
RGL3
ZNF490
DOCK6
ANO8
CYP4F11
EPS15L1
WIZ
LPPR2
RASAL3
MRPL34
ZSWIM4
CYP4F12
YIPF2
C19orf43
DDA1
TMEM38A
C19orf42
C19orf57
ABHD8
OCEL1
GLT25D1
EPHX3
PODNL1
SLC35E1
ZNF442
CCDC130
QTRT1
PLVAP
RTBDN
USHBP1
C19orf44
MRI1
FBXW9
MORG1
ELOF1
ZNF333
EMR3
GTPBP3
HSH2D
SYDE1
SAMD1
DCAF15
GADD45GIP1
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
HAUS8
FAM125A
NACC1
LOC113230
PGLYRP2
NXNL1
CCDC151
ZNF653
CIB3
RLN3
CALR3
ZNF441
ZNF491
ZNF440
C19orf39
CCDC159
OR1I1
CCDC105
CYP4F22
LOC126536
OR10H4
ANKLE1
LOC147727
ZNF563
SPC24
FLJ25328
ZNF791
ZNF564
ZNF709
ZNF433
ZNF627
DAND5
FAM129C
C19orf38
SYCE2
ZNF763
ZNF844
OR10H5
NWD1
NANOS3
PALM3
TMEM205
SLC27A1
ZNF788
CLEC17A
RPL18AP3
OR7A10
ZNF833
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR181D
UCA1
MIR638
MIR639
ZNF878
LOC100130932
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p33.

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

Genes
FAF1
DMRTA2
Genes in Wide Peak

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

Table S34.  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-100
hsa-mir-125b-1
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
RICS
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
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
C11orf60
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
ASAM
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
CASP12
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
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
LOC283174
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
LOC399959
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
NCRNA00167
HEPN1
LOC643923
CLDN25
RPL23AP64
LOC100128239
PATE3
Genes in Wide Peak

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

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

Genes
ALDH2
BCL7A
PTPN11
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
ACADS
SCARB1
COX6A1
DTX1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
MYL2
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PLA2G1B
POLE
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RPL6
RPLP0
CLIP1
ATXN2
SFRS8
TBX5
TBX3
HNF1A
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
BRAP
ULK1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SFRS9
HRK
GPR109B
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RBM19
RNF10
SH2B3
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
GCN1L1
SDS
RAB35
SNRNP35
CIT
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
ANKLE2
CUX2
MED13L
SIRT4
ABCB9
RIMBP2
ATP6V0A2
FBXW8
HSPB8
GPR81
GALNT9
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
TRIAP1
TPCN1
RHOF
VSIG10
TESC
SBNO1
ZCCHC8
CHFR
WSB2
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
LHX5
SUDS3
C12orf43
VPS33A
RSRC2
AACS
DDX54
NOC4L
B3GNT4
OGFOD2
VPS37B
C12orf49
TCTN2
C12orf30
SLC24A6
RNF34
CCDC92
PUS1
ACAD10
COQ5
SRRM4
CCDC62
KDM2B
UNC119B
ORAI1
RNFT2
C12orf52
TMEM116
C12orf65
TMEM132C
CCDC64
SDSL
MGC16384
TMEM132B
IQCD
LOC116437
TMEM132D
SLC15A4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
FAM109A
LOC144742
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
LRRC43
GPR133
MORN3
C12orf51
KSR2
NME2P1
GATC
C12orf27
DDX51
GPR109A
LOC338799
EP400NL
RILPL1
IL31
CCDC42B
TMEM233
SETD8
MAP1LC3B2
SNORA49
MIR620
LOC100128554
LOC100130238
LOC100190940
NCRNA00173
ZNF605
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.2.

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

Genes
hsa-mir-1253
hsa-mir-212
hsa-mir-22
ABR
ALOX15
ARRB2
ASPA
ATP2A3
CRK
CTNS
DPH1
HIC1
ITGAE
MNT
MYO1C
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PITPNA
SERPINF2
PSMB6
RPA1
UBE2G1
TRPV1
YWHAE
OR1A1
OR1D4
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SCARF1
TM4SF5
RPH3AL
SGSM2
MYBBP1A
PRPF8
RAP1GAP2
ZZEF1
KIAA0664
SMG6
SHPK
OR1A2
PELP1
TIMM22
TAX1BP3
GEMIN4
GLOD4
ANKFY1
INPP5K
RNMTL1
VPS53
C17orf85
TSR1
CXCL16
SRR
NXN
METT10D
FAM57A
TMEM93
RILP
GSG2
ZMYND15
CAMKK1
SPATA22
C17orf91
SMYD4
OVCA2
SLC43A2
CYB5D2
GGT6
SPNS2
WDR81
RTN4RL1
TRPV3
SPNS3
LOC284009
VMO1
TUSC5
SMTNL2
FAM101B
GLTPD2
OR3A4
C17orf97
MED11
MIR132
MIR212
MIR22
SNORD91A
SNORD91B
BHLHA9
TLCD2
ELP2P
LOC100306951
Genes in Wide Peak

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

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-548a-2
hsa-mir-588
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-30a
hsa-mir-133b
hsa-mir-586
ACAT2
CRISP1
AIM1
AMD1
ARG1
BAI3
BCKDHB
BMP5
DST
RUNX2
CCNC
CDC5L
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GCLC
GPR6
GPR31
GRIK2
GRM1
GSTA1
GSTA2
GSTA3
GSTA4
HCRTR2
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IL17A
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MCM3
ME1
MAP3K4
MAP3K5
MEP1A
MUT
MYO6
NFKBIE
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGK2
PGM3
PKHD1
PLAGL1
PLG
PLN
POU3F2
PREP
PRIM2
PKIB
PSMB1
PTPRK
REV3L
RHAG
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
TFAP2B
THBS2
NR2E1
TPBG
TPD52L1
CRISP2
TSPYL1
TTK
UTRN
EZR
VIP
PTP4A1
PLA2G7
EPM2A
STX7
SUPT3H
PEX3
GCM1
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
SLC25A27
TBPL1
BAG2
WTAP
AKAP12
TRAM2
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
RCAN2
CRISP3
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
RBM16
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
CDC2L6
MAP3K7IP2
MDN1
TSPYL4
SASH1
SYNE1
KIAA0776
PHF3
HEY2
HEBP2
ORC3L
CD2AP
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
SFRS18
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
TIAM2
FBXL4
C6orf123
FBXO9
FBXO5
SLC17A5
RGS17
SNORD50A
PDE7B
FILIP1
TNFRSF21
SESN1
TINAG
DLL1
OSTM1
TMEM14A
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CYP39A1
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
LGSN
BRP44L
HECA
RAB23
COQ3
CLIC5
IL20RA
UNC93A
HMGCLL1
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
LRRC1
PHF10
QRSL1
VNN3
NCRNA00120
DDX43
FAM46A
TMEM30A
C6orf70
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
AARS2
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
C6orf115
RRAGD
ENPP5
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
C6orf164
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
C6orf103
C6orf155
FRMD1
C6orf59
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
COL21A1
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
TFAP2D
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
MCHR2
C6orf168
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
PAQR8
SLC22A16
UBE2CBP
C6orf142
C6orf176
KIAA1919
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
IL17F
FAM54A
SFT2D1
EFHC1
KLHL32
TMEM200A
C6orf150
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SFRS13B
C6orf141
LOC153910
C6orf94
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCL
TCTE1
KHDRBS2
C6orf163
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
GPR111
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
C6orf191
C6orf167
WDR27
FAM26E
MCM9
SCML4
SHPRH
GPR110
LOC285733
LOC285735
LOC285740
C6orf182
PPIL6
FLJ34503
DCBLD1
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GUSBL2
GJB7
SNHG5
SUMO4
C6orf147
C6orf173
C6orf174
C6orf204
C6orf120
THEMIS
C6orf140
GFRAL
LIN28B
SAMD5
IYD
KLHL31
TCP10L2
C6orf122
DEFB133
GTF2H5
MIR206
MIR30A
MIR30C2
TMEM151B
OOEP
FAM26F
LOC441177
C6orf138
MCART3P
LOC442245
RFPL4B
MIR133B
LOC553137
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
CTAGE9
RAET1K
C6orf124
SNORA20
SNORA29
SNORD50B
MIR548B
MIR586
LOC728402
C6orf186
LOC729176
LOC729603
LOC730101
HGC6.3
BET3L
KHDC1L
C6orf217
LOC100287718
NHEG1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.3.

Table S38.  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-92a-1
hsa-mir-622
hsa-mir-1297
hsa-mir-15a
hsa-mir-621
hsa-mir-320d-1
PARP4
ALOX5AP
ATP12A
ATP7B
KLF5
BTF3L1
CDK8
RCBTB2
CLN5
CPB2
DACH1
DCT
EDNRB
ELF1
ESD
FGF9
GPC5
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
POU4F1
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
UCHL3
ZMYM2
IFT88
TNFSF11
SCEL
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
SAP18
DLEU1
N4BP2L2
PIBF1
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
OR7E37P
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
C13orf1
COG6
KLHL1
RBM26
XPO4
PCDH20
MRP63
RNF219
NARG1L
RNASEH2B
DHRS12
C13orf34
C13orf18
C13orf23
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
LOC121838
CSNK1A1L
RXFP2
C13orf26
SLAIN1
PRR20A
LOC144776
C13orf30
C13orf31
HNRNPA1L2
FAM10A4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
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
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
ALG11
C13orf37
PCOTH
SNORA27
LOC646405
PRHOXNB
ZAR1L
LOC646982
SERPINE3
LOC647288
SNORA31
MIR548A2
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 18q22.1.

Table S39.  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
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
C18orf55
RAX
ST8SIA3
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
C18orf22
PQLC1
CCDC68
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
CCBE1
CBLN2
FBXO15
DOK6
RNF152
C18orf20
ZADH2
C18orf62
LOC284276
HMSD
CPLX4
ATP9B
LOC390858
LOC400657
MIR122
HSBP1L1
LOC100130522
Genes in Wide Peak

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

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-548a-2
hsa-mir-588
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-30a
hsa-mir-133b
hsa-mir-586
ACAT2
CRISP1
AIM1
AMD1
ARG1
BAI3
BCKDHB
BMP5
DST
RUNX2
CCNC
CDC5L
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GCLC
GPR6
GPR31
GRIK2
GRM1
GSTA1
GSTA2
GSTA3
GSTA4
HCRTR2
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IL17A
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MCM3
ME1
MAP3K4
MAP3K5
MEP1A
MUT
MYO6
NFKBIE
NMBR
NT5E
OPRM1
PARK2
PCMT1
ENPP1
ENPP3
PEX7
PGK2
PGM3
PKHD1
PLAGL1
PLG
PLN
POU3F2
PREP
PRIM2
PKIB
PTPRK
REV3L
RHAG
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TCF21
TCP1
TCP10
TCTE3
DYNLT1
TFAP2B
THBS2
NR2E1
TPBG
TPD52L1
CRISP2
TSPYL1
TTK
UTRN
EZR
VIP
PTP4A1
PLA2G7
EPM2A
STX7
SUPT3H
PEX3
GCM1
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
SLC25A27
TBPL1
BAG2
WTAP
AKAP12
TRAM2
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
RCAN2
CRISP3
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
RBM16
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
CDC2L6
MAP3K7IP2
MDN1
TSPYL4
SASH1
SYNE1
KIAA0776
PHF3
HEY2
HEBP2
ORC3L
CD2AP
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
SFRS18
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
TIAM2
FBXL4
C6orf123
FBXO9
FBXO5
SLC17A5
RGS17
SNORD50A
PDE7B
FILIP1
TNFRSF21
SESN1
TINAG
OSTM1
TMEM14A
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CYP39A1
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
LGSN
BRP44L
HECA
RAB23
COQ3
CLIC5
IL20RA
UNC93A
HMGCLL1
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
LRRC1
PHF10
QRSL1
VNN3
NCRNA00120
DDX43
FAM46A
TMEM30A
C6orf70
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
AARS2
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
C6orf115
RRAGD
ENPP5
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
C6orf164
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
C6orf103
C6orf155
FRMD1
C6orf59
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
COL21A1
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
TFAP2D
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
MCHR2
C6orf168
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
PAQR8
SLC22A16
UBE2CBP
C6orf142
C6orf176
KIAA1919
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
IL17F
FAM54A
SFT2D1
EFHC1
KLHL32
TMEM200A
C6orf150
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SFRS13B
C6orf141
LOC153910
C6orf94
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCL
TCTE1
KHDRBS2
C6orf163
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
GPR111
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
C6orf191
C6orf167
WDR27
FAM26E
MCM9
SCML4
SHPRH
GPR110
LOC285733
LOC285735
LOC285740
C6orf182
PPIL6
FLJ34503
DCBLD1
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GUSBL2
GJB7
SNHG5
SUMO4
C6orf147
C6orf173
C6orf174
C6orf204
C6orf120
THEMIS
C6orf140
GFRAL
LIN28B
SAMD5
IYD
KLHL31
TCP10L2
C6orf122
DEFB133
GTF2H5
MIR206
MIR30A
MIR30C2
TMEM151B
OOEP
FAM26F
LOC441177
C6orf138
MCART3P
LOC442245
RFPL4B
MIR133B
LOC553137
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
CTAGE9
RAET1K
C6orf124
SNORA20
SNORA29
SNORD50B
MIR548B
MIR586
LOC728402
C6orf186
LOC729176
LOC729603
LOC730101
HGC6.3
BET3L
KHDC1L
C6orf217
LOC100287718
NHEG1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q31.1.

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

Genes
ABL1
NOTCH1
RALGDS
SET
TAL2
TSC1
NR4A3
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-126
hsa-mir-219-2
hsa-mir-199b
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
BAAT
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
SLC31A1
SLC31A2
CRAT
CYLC2
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FPGS
NR5A1
FUT7
NR6A1
GGTA1
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TLR4
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
TMEFF1
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
RALGPS1
ADAMTSL2
KIAA0649
SEC16A
TNFSF15
ROD1
SH2D3C
RABEPK
LAMC3
TUBB2C
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
SLC27A4
CEP110
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
PTGR1
TRIM32
SETX
ERP44
ZBTB43
PMPCA
ASTN2
FKBP15
KIAA0368
EXOSC2
FREQ
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
LOC26102
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
RAB14
C9orf78
POLE3
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
BSPRY
C9orf167
TEX10
LPPR1
EXD3
C9orf6
STX17
TMEM38B
NIPSNAP3B
STRBP
C9orf86
CDK5RAP2
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
SLC46A2
C9orf27
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
EHMT1
SVEP1
PTGES2
AKNA
C9orf45
URM1
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
C9orf125
NTNG2
BAT2L
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
FAM125B
WDR34
C9orf140
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
C9orf98
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
C9orf96
OLFML2A
QSOX2
LOC169834
C9orf91
NAIF1
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
NCRNA00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
C9orf75
C9orf109
FAM78A
OR13C9
OR13D1
LOC286367
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf119
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
LOC402377
SOHLH1
ZBTB34
MIR126
MIR147
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR32
C9orf106
LCN10
C9orf173
NRARP
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
FAM163B
FLJ40292
TUBBP5
SNORA17
SNORA43
SNORD62B
SNORD90
MIR548D1
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
C9orf110
LOC100129034
LOC100131193
FAM157B
RNU6ATAC
LOC100272217
LOC100289341
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
FGFR3
IL2
KDR
KIT
PDGFRA
RAP1GDS1
WHSC1
PHOX2B
DUX4
CHIC2
TET2
FBXW7
FIP1L1
hsa-mir-1305
hsa-mir-1979
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
hsa-mir-575
hsa-mir-1269
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-548i-2
hsa-mir-95
hsa-mir-943
hsa-mir-571
ADD1
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ADRA2C
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA2P1
ANXA3
ANXA5
APBB2
AREG
RHOH
ART3
ATOH1
ATP5I
NKX3-2
BMP3
BMPR1B
BST1
BTC
CAMK2D
CASP3
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
CD38
LRBA
CDS1
CLGN
CENPC1
CENPE
CLCN3
CNGA1
CPE
CRMP1
CSN1S1
CSN2
CSN3
CTBP1
CTSO
DGKQ
DCK
DCTD
DHX15
DMP1
DRD5
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
EPHA5
EREG
ETFDH
EVC
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGF5
FGG
FRG1
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GC
GK2
GK3P
GLRB
GNRHR
GPM6A
GRK4
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HTT
HGFAC
UBE2K
HMGB2
HNRNPD
HPGD
HTN1
HTN3
IBSP
IDUA
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
LETM1
LRPAP1
MAD2L1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MSX1
MTNR1A
MTTP
MUC7
MYL5
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PCDH7
PDE6B
PDHA2
PET112L
PF4
PF4V1
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPBP
PPID
PPP2R2C
PPP3CA
PRKG2
MAPK10
PTPN13
QDPR
REST
RFC1
RGS12
RNF4
ABCE1
RPL9
RPL34
RPS3A
S100P
SC4MOL
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SH3BP2
SNCA
SOD3
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
TDO2
TEC
TLL1
TLR1
TLR2
TLR3
TMSL3
TRPC3
TXK
UBE2D3
UCHL1
UCP1
UGDH
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
VEGFC
WFS1
WHSC2
ZNF141
SLBP
GLRA3
ACOX3
SPARCL1
SMARCA5
SORBS2
PRSS12
CPZ
NOP14
FAM193A
USO1
UNC5C
MAPKSP1
PDE5A
SLC4A4
SAP30
INPP4B
PROM1
HERC3
SNORD73A
STBD1
CDKL2
PAPSS1
LDB2
LRAT
AIMP1
NDST3
SLIT2
RAB28
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
KIAA0232
MFAP3L
SEC24D
G3BP2
WDR1
HS3ST1
FGFBP1
HNRPDL
TSPAN5
ENAM
C4orf6
FAM13A
MFSD10
SPRY1
MAEA
TLR6
PCGF3
ANAPC10
ATP8A1
SPON2
PGRMC2
SEC24B
TACC3
SLC30A9
CXCL13
SLC34A2
MAB21L2
PAICS
MXD4
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
CPLX1
HPSE
SLC26A1
NMU
SMR3B
NPFFR2
PPARGC1A
PPBPL2
MORF4
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
MAN2B2
ANP32C
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXL5
FBXO8
SMR3A
D4S234E
PPA2
DAPP1
DKK2
FAM184B
INTU
NAAA
GPR78
COQ2
ARFIP1
SULT1B1
PDLIM3
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
MRPS18C
LAP3
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
NUDT9
NUP54
STX18
FGFRL1
CLDN22
CYTL1
GAR1
SH3TC1
UGT2B28
RBM47
PCDH18
USP53
OTUD4
DCHS2
FLJ20184
PIGG
DCAF16
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
CCDC109B
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
UBA6
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
C4orf43
UFSP2
CNO
C4orf21
STK32B
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
CDKN2AIP
LYAR
ODZ3
N4BP2
TMEM184C
SEPT11
EXOC1
LRP2BP
TMEM165
PDGFC
TUBB4Q
SLC2A9
FSTL5
BDH2
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
KIAA0114
KIAA1211
RNF150
KIAA1239
TBC1D14
SORCS2
CC2D2A
KLHL8
PCDH10
KIAA1430
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
KIAA1530
METTL14
WDR19
ZFYVE28
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
AFAP1
GUF1
SPCS3
SCOC
C4orf41
NEUROG2
SLC39A8
NCAPG
HHIP
NDST4
AGXT2L1
USP46
MRPL1
RASL11B
ELOVL6
TNIP2
HAUS3
C4orf31
FAT4
ARSJ
SRD5A3
ARHGAP10
FLJ13197
MLF1IP
THAP9
NSUN7
UGT2A3
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
ABCA11P
SCD5
DNAJB14
TMEM156
WWC2
FRAS1
NARG1
CWH43
C4orf29
ALPK1
GRPEL1
MED28
CXXC4
KCNIP4
KIAA1712
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
FGFBP2
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
MFSD7
C4orf14
TMEM175
ABLIM2
HOPX
COL25A1
USP38
LNX1
C4orf49
LOC84740
ARD1B
AGPAT9
CBR4
PIGY
TMEM128
C4orf35
ZNF518B
FHDC1
MGC45800
PRMT10
CCDC149
DDX60L
YTHDC1
C4orf42
TMEM129
NAF1
MOBKL1A
TIFA
FAM114A1
RG9MTD2
MRFAP1
LOC93622
TADA2B
TBCK
HTRA3
HELQ
CYP2U1
C1QTNF7
MRFAP1L1
DDIT4L
CLNK
WDR17
ARAP2
GDEP
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
SPATA18
C4orf32
TMPRSS11B
GNPDA2
SPATA4
CPEB2
EVC2
ARL9
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
OTOP1
ENPP6
NHEDC2
ASB5
NHEDC1
ZNF827
SH3D19
NFXL1
NIPAL1
PAQR3
SHISA3
SCFD2
C4orf38
ZNF595
C4orf39
JAKMIP1
THAP6
C4orf26
KLB
FAM53A
PPM1K
C4orf45
C4orf23
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
MMAA
ZNF509
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
GSX2
ZNF721
SYNPO2
C4orf46
SLC10A4
TIGD4
TMEM154
C4orf34
TMEM192
RWDD4A
CCDC111
TAPT1
FLJ39653
TRIML2
CNOT6L
TECRL
LCORL
C4orf22
EPGN
ZNF718
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
CCDC96
BOD1L
C4orf7
NAP1L5
LOC285419
DCAF4L1
CYP4V2
LOC285456
CRIPAK
DOK7
RNF212
LOC285501
FAM13AOS
GPRIN3
COX18
YIPF7
FRYL
RNF175
LOC285548
LOC285550
C4orf37
CSN1S2A
C4orf10
CSN1S2B
ZAR1
CCDC158
TMPRSS11A
TRIML1
LRRC66
NAT8L
LOC340017
LOC344967
PRSS48
ANKRD56
LRIT3
C4orf44
SLC10A6
HSD17B13
LOC348926
ANKRD37
POLN
PCNAP1
NCRNA00099
KCTD8
C4orf50
C4orf52
BEND4
GRXCR1
TMPRSS11F
USP17L6P
USP17
HSP90AB2P
TRIM61
TRIM75
HELT
C4orf48
DTHD1
LOC401127
SYT14L
FLJ41562
C4orf40
AMTN
FAM190A
C4orf3
RPL21P44
FAM92A3
C4orf12
MIR218-1
MIR302A
C4orf11
MTHFD2L
TMEM150C
EEF1AL7
LOC441046
C4orf47
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC550112
UGT2A2
LOC641518
ZNF876P
SLED1
LOC644145
DEFB131
CLRN2
CEP170L
C4orf51
LOC650293
LOC653543
LOC653544
LOC653545
LOC653548
ZNF732
SCARNA22
SNORA24
SNORA26
MIR572
MIR573
MIR574
MIR575
MIR577
MIR578
PPBPL1
LOC728410
LOC729338
FAM160A1
FLJ36777
RELL1
PSAPL1
SNHG8
MIR943
FAM47E
LOC100130017
LOC100130872
LOC100192379
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q34.

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

Genes
BRAF
CDK6
EGFR
ELN
ETV1
EZH2
HIP1
HNRNPA2B1
HOXA9
HOXA11
HOXA13
MET
PMS2
SMO
AKAP9
IKZF1
SBDS
KIAA1549
MLL3
CREB3L2
CARD11
JAZF1
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
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
hsa-mir-548o
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
hsa-mir-590
hsa-mir-1200
hsa-mir-548n
hsa-mir-550-2
hsa-mir-550-1
hsa-mir-196b
hsa-mir-148a
hsa-mir-1183
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ABP1
ACHE
ACTB
ADCY1
ADCYAP1R1
AEBP1
AHR
AKR1B1
AMPH
AOAH
AQP1
ARF5
ASL
ASNS
AZGP1
OPN1SW
BLVRA
BPGM
CACNA2D1
CALCR
CALD1
CALU
CAMK2B
CAPZA2
CASP2
CAV1
CAV2
KRIT1
CCT6A
CD36
SEPT7
CDK5
CFTR
CHN2
CHRM2
AP1S1
CLCN1
CLK2P
COL1A2
CPA1
CPA2
CLDN4
CLDN3
CRHR2
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DGKB
DDC
DFNA5
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
EVX1
FLNC
GARS
GBAS
GBX1
GCK
GHRHR
GLI3
GNA12
GNAI1
GNB2
GNG11
GNGT1
GPR22
GPER
GPR37
GRB10
GRM3
GRM8
GTF2I
GTF2IP1
GUSB
HGF
MNX1
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
HPVC1
AGFG2
HSPB1
HTR5A
HUS1
ICA1
IFRD1
IGFBP1
IGFBP3
IL6
IMPDH1
INHBA
INSIG1
IRF5
ITGB8
KCND2
KCNH2
KEL
LAMB1
LEP
LFNG
LIMK1
LRCH4
MCM7
DNAJB9
MDH2
MEOX2
MEST
MKLN1
NUDT1
NDUFA4
NDUFA5
NDUFB2
NOS3
CNOT4
NPY
NPTX2
NRCAM
NRF1
OCM2
OGDH
ORC5L
SERPINE1
PAX4
PCOLCE
PDE1C
PDGFA
PDK4
SLC26A4
PEX1
PFTK1
PGAM2
ABCB1
ABCB4
PHKG1
PIK3CG
PIP
PMS2L1
PMS2L2
PMS2L4
PMS2L5
PMS2L3
PODXL
POLD2
POLR2J
PON1
PON2
PON3
POR
PPIA
PPP1R3A
PRKAR1B
PRKAR2B
PRSS1
PRSS2
RELN
PSMA2
PSMC2
PSPH
TAS2R38
PTN
PTPN12
PTPRN2
PTPRZ1
PURB
RAC1
RALA
RARRES2
RFC2
RHEB
RP9
RPA3
CCL24
SFRP4
SHH
SLC4A2
SLC13A1
SMARCD3
FSCN1
SP4
SPAM1
SRI
AKR1D1
SRPK2
SSBP1
STX1A
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
TWIST1
UBE2H
UPP1
VGF
VIPR2
ZAN
EIF4H
CLIP2
LAT2
WNT2
XRCC2
YWHAG
ZNF3
ZNF12
ZKSCAN1
ZSCAN21
ZNF138
ZP3
ZYX
AIMP2
MAFK
MTERF
SHFM1
TFPI2
ST7
ARHGEF5
ZNF212
TRRAP
FZD1
FZD9
MAD1L1
ZNF282
CUL1
TPST1
FKBP6
CDC2L5
EIF3B
DNAH11
TRIM24
TAX1BP1
BUD31
SGCE
SKAP2
MGAM
WASL
PLOD3
BAZ1B
CLDN12
DGKI
AP4M1
TBRG4
STK17A
CYTH3
BCL7B
ATP6V1F
ACCN3
PMPCB
ATP5J2
GTF2IRD1
CREB5
PDIA4
NFE2L3
PHF14
UBE3C
FAM131B
SEMA3E
DOCK4
HDAC9
FAM115A
RAPGEF5
SCRN1
KIAA0087
ELMO1
MAGI2
TRIL
POM121
KIAA0415
DMTF1
DNAJB6
ABCF2
MUC12
ARPC1B
ARL4A
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
RAMP3
BET1
CCL26
SEMA3A
NOD1
FAM3C
GPNMB
COG5
ZNHIT1
SEMA3C
AGR2
ARPC1A
SH2B2
IGF2BP3
YKT6
STAG3
ZNF273
C7orf16
FGL2
CPSF4
FASTK
DBF4
COPS6
KDELR2
ADAP1
ZPBP
DUS4L
NUPL2
HIBADH
ZNF277
INMT
ABCB8
TP53TG1
POU6F2
FKBP9
PDAP1
CBX3
TFEC
LAMB4
LMTK2
POMZP3
PAXIP1
KLHDC10
HECW1
AVL9
PEG10
SSPO
NACAD
SNX13
NUP205
COBL
IQCE
DPY19L1
UNC84A
KIAA0895
AHCYL2
NUDCD3
SEC61G
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
LSM5
ZKSCAN5
CLDN15
BRI3
TECPR1
SUMF2
POT1
SOSTDC1
KBTBD2
PTCD1
OSBPL3
CNTNAP2
AUTS2
HYALP1
WIPI2
TES
GIMAP2
INTS1
OR2F1
FBXO24
SLC13A4
TBL2
STEAP1
COPG2
HBP1
DNAJC2
TPK1
SND1
VPS41
TSPAN13
C7orf54
EIF2AK1
DENND2A
ZNF777
BBS9
CRCP
RABGEF1
POLM
PCLO
TMEM176B
BZW2
DBNL
HIPK2
WDR91
REPIN1
NPC1L1
SNX8
SNX10
TRA2A
C7orf68
FTSJ2
MDFIC
PILRB
PILRA
FSCN3
NXPH1
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
MLXIPL
CHCHD2
CPA4
NT5C3
TXNDC3
ZNF117
MRPS17
WNT16
ACTL6B
PRKAG2
ZNF107
ZC3HC1
SRRT
C7orf20
UBE2D4
C7orf28A
LUC7L2
MRPS33
STYXL1
ASB4
NUB1
MPP6
LSM8
ADAM22
PION
CYCS
GPR85
TAS2R5
STAG3L1
ANLN
ANKIB1
MIOS
RNF216
CHPF2
CPVL
PUS7
TOMM7
ING3
DDX56
TMEM106B
LRRN3
CROT
EPDR1
ZNF853
ALKBH4
SAMD9
NCAPG2
CYP2W1
HEATR2
CHCHD3
FKBP14
ZCWPW1
C7orf42
WDR60
RBM28
ZDHHC4
TYW1
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
CHST12
TRPV6
CDCA7L
PPP1R9A
CCDC132
URG4
NSUN5
RADIL
C7orf44
AGK
METTL2B
MLL5
LANCL2
BAIAP2L1
SLC25A40
BCAP29
KLHL7
STK31
MEPCE
TRPV5
ANKRD7
ZC3HAV1
PAPOLB
C1GALT1
FAM20C
SLC12A9
ACN9
C7orf36
AKR1B10
ANKMY2
TBX20
SMURF1
PHTF2
ACTR3B
KIAA1147
RHBDD2
FAM40B
ESYT2
ZNF398
CCDC146
RBAK
GATAD1
MYL7
EXOC4
RINT1
GALNT11
NEUROD6
FIGNL1
MYO1G
LRRC4
NPVF
HERPUD2
LMBR1
WBSCR17
TMEM168
C7orf4
NOM1
MOSPD3
GIGYF1
CCDC136
TNS3
PARP12
RABL5
CYP3A43
CASD1
STAG3L4
MRPS24
MRPL32
LRRC61
C7orf49
GGCT
C7orf25
ZNF655
C7orf26
PVRIG
C7orf23
GCC1
STEAP4
GAL3ST4
PRKRIP1
MICALL2
C7orf10
C7orf63
CBLL1
ZNF767
C7orf58
TTC26
FBXL18
C7orf69
ORAI2
TTYH3
UPK3B
EEPD1
JHDM1D
OR2AE1
VOPP1
WBSCR16
TSC22D4
TRIM56
ABHD11
TMUB1
CCM2
ZMIZ2
CALN1
ARMC10
TMEM120A
STARD3NL
IMMP2L
CTTNBP2
C7orf64
ZNF394
USP42
GTF2IRD2
MYH16
FAM188B
SLC37A3
PSMG3
DNAJC30
C7orf50
KRBA1
TNRC18
FAM126A
FAM71F1
PLEKHA8
C7orf70
POLR2J4
MGC16142
SLC35B4
TMEM209
TMEM60
SCIN
GTPBP10
TRIM4
OR6W1P
ZFAND2A
COX19
CCDC126
ZNF479
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7OT1
ST7OT2
ST7OT3
CADPS2
CPA5
FOXP2
H2AFV
TSGA14
GLCCI1
C7orf29
DTX2
WBSCR22
KIAA1908
TSGA13
GPR146
C7orf30
AGAP3
C7orf13
OR9A4
WBSCR28
TRIM50
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
C7orf57
SVOPL
MTPN
LRGUK
ASB10
TRYX3
MOXD2
C7orf11
SRCRB4D
C7orf31
ASZ1
MUC17
RNF32
ASB15
RUNDC3B
ABCA13
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
VKORC1L1
LOC154822
IQUB
KCTD7
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF783
ZNF746
ATP6V0E2
AMZ1
WBSCR27
SBDSP
VPS37D
NSUN5B
RBM33
AGR3
ZNF92
GALNTL5
ZNF679
RNF133
CDC14C
THAP5
FLJ36031
LOC168474
PKD1L1
GIMAP7
ZNF467
BHLHA15
BMPER
PER4
ZNF800
GIMAP1
WBSCR26
LOC202781
C7orf33
TMEM184A
SAMD9L
MGC26647
ZNF804B
FABP5L3
ZNF498
C7orf38
VWDE
PRPS1L1
TWISTNB
SP8
HOXA11AS
C7orf47
GPC2
C7orf27
SDK1
FOXK1
MMD2
DAGLB
C7orf28B
THSD7A
VSTM2A
DKFZp434L192
TMED4
DKFZP586I1420
C7orf41
PRR15
SRRM3
RSBN1L
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
FLJ23834
TMEM130
FERD3L
RPL23P8
C7orf51
SLC29A4
RSPH10B
CCDC129
ZNRF2
SEMA3D
CNPY4
POLR2J2
HEPACAM2
UBN2
FLJ35390
MBLAC1
TMEM196
MGC87042
RPS2P32
SUNC1
FAM133B
TAS2R39
TAS2R40
TAS2R41
NSUN5C
TFAMP1
STEAP2
POM121L12
CNPY1
INTS4L1
NCRNA00174
C7orf71
LOC285954
SPDYE1
C7orf40
FLJ40852
FAM115C
ZNF775
ATG9B
DLX6AS
ZNF789
LOC286002
C7orf53
LOC286016
MESTIT1
ST7OT4
TAS2R60
ZNF680
UNCX
COL28A1
ABCB5
C7orf46
FAM183B
CTAGE6
TSPAN33
AGBL3
SEPT14
MACC1
OR6V1
OR2A12
OR2A1
GNAT3
MOGAT3
FAM71F2
STRA8
KLRG2
ZNF713
LOC349114
WDR86
GJC3
DPY19L2P2
GATS
GPR141
FKBP9L
GSTK1
VWC2
TRIM73
C7orf52
SLC26A5
LHFPL3
KCP
TRIM74
FLJ43663
RNF148
NPSR1
LOC389458
LOC389493
SPDYE8P
GATSL1
GTF2IRD2B
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
ELFN1
TMEM195
GRID2IP
OR2A5
RPL13AP17
ZNF815
RASA4P
C7orf65
GTF2IRD2P
LOC401387
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
LOC402644
UFSP1
AAA1
MIR106B
MIR129-1
MIR148A
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
RNF216L
PMS2CL
LOC441204
LOC441208
RP9P
ZNF716
TYW1B
SPDYE7P
PMS2L11
SPDYE3
SPDYE2
AKR1B15
LOC441294
OR2A9P
LOC442308
ZNF727
OR2A2
DPY19L2P4
STAG3L3
STAG3L2
SPDYE5
EIF3IP1
LMOD2
MIR335
MIR339
MIR196B
ARHGEF5L
TARP
GIMAP6
LOC493754
WEE2
LOC541473
POLR2J3
DPY19L2P1
MIR489
MIR490
FDPSL2A
SEPT13
CCT6P1
ZNF862
LOC643955
WIPF3
INTS4L2
LOC646762
LOC646999
PL-5283
LOC649395
LOC650226
NCF1
ACTR3C
OCM
SNORA5A
NCF1B
NCF1C
SNORA5B
SNORA5C
SNORA9
SNORA14A
SNORA15
SNORA22
SNORD93
MIR550-1
MIR550-2
MIR589
MIR590
MIR591
MIR592
MIR593
MIR595
LOC723809
MIR653
RSPH10B2
LOC728743
LOC729156
GATSL2
SPDYE6
ISPD
TMEM229A
ZNF735
LUZP6
MIR671
LOC100093631
POM121C
LOC100124692
LOC100128542
CTAGE4
LOC100128822
RPL19P12
EFCAB10
C7orf72
LOC100132707
LOC100132832
LOC100133091
LOC100134229
LOC100134713
UPLP
LOC100216545
LOC100287704
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.13.

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

Genes
ABL1
FANCC
FANCG
GNAQ
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
hsa-mir-602
hsa-mir-126
hsa-mir-219-2
hsa-mir-199b
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-let-7d
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
hsa-mir-873
hsa-mir-31
hsa-mir-491
hsa-mir-101-2
hsa-mir-1302-2
ABCA1
ABCA2
ABO
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
ANXA2P2
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
TNFSF8
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CELP
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
MLANA
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
GGTA1
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
IL11RA
INSL4
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RMRP
RORB
RPL7A
RPL12
RPS6
RXRA
CCL19
CCL21
SH3GL2
SHB
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
UGCG
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
RGP1
TRIM14
MELK
RUSC2
KIAA0649
SEC16A
ZBTB5
KIAA0020
TNFSF15
ROD1
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB2C
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CEP110
WDR5
C9orf9
ADAMTS13
C9orf7
PSIP1
INSL6
SLC2A6
PTENP1
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA1045
KIAA0368
EXOSC2
FREQ
TDRD7
SLC44A1
ANGPTL2
NUP188
CCRK
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
LOC26102
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
PCA3
AK3
EXOSC3
FAM108B1
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
C9orf11
TBC1D13
FAM22F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
C9orf167
CNTLN
TEX10
LPPR1
KIAA1797
UBE2R2
EXD3
C9orf6
C9orf95
STX17
NOL8
C9orf68
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDC37L1
DENND4C
C9orf86
CDK5RAP2
UBAP2
C9orf46
CBWD1
KLHL9
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KIAA1161
KCNT1
KIAA1432
KIAA1529
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
C9orf27
C9orf80
ZNF462
DMRT3
PRDM12
MAK10
DMRTA1
SLC28A3
CARD9
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
MRPL41
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOBKL2B
C9orf82
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
KIAA1539
GKAP1
PDCD1LG2
AKNA
C9orf45
URM1
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
BAT2L
PPAPDC3
C9orf70
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
TPD52L3
WDR34
C9orf140
C9orf69
LRSAM1
IL33
C9orf123
C9orf30
UAP1L1
MCART1
MRRF
RBM18
ARRDC1
WDR85
ADAMTSL1
LOC92973
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf66
NCRNA00032
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
C9orf98
OR1Q1
TTLL11
RASEF
TTC39B
C9orf122
RG9MTD3
TTC16
FAM120AOS
FAM154A
C9orf44
FREM1
KIAA2026
LOC158376
LOC158381
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
PRUNE2
C9orf96
KCNV2
OLFML2A
C9orf71
QSOX2
GLIS3
LOC169834
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
C9orf93
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
C9orf144B
NCRNA00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
C9orf75
TUSC1
C9orf109
FAM78A
C9orf150
LOC286359
OR13C9
OR13D1
LOC286367
FOXD4L3
IFNE
ZDHHC21
ACER2
LOC340508
GPR144
FLJ43950
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
GLT6D1
ENHO
AQP7P1
PTAR1
C9orf102
C9orf119
C9orf50
PNPLA7
C9orf169
ENTPD8
ZNF322B
KGFLP1
LOC389705
C9orf144
FAM75A6
MGC21881
AQP7P2
FLJ43859
FLJ44082
FLJ46321
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
C9orf128
OR13J1
CTSL3
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FLJ35024
PTPLAD2
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
LOC402377
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR101-2
MIR126
MIR147
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR31
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC415056
LOC440173
LOC440839
LOC440896
SUGT1P
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
FAM27A
DNAJC25
DNAJC25-GNG10
LOC554202
LOC572558
MIR491
PGM5P2
MIR455
FAM138F
FAM75A2
LOC642313
LOC642929
FAM163B
FLJ40292
TUBBP5
CBWD6
FAM138A
LOC645961
HRCT1
FAM75A1
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM138C
SCARNA8
SNORA17
SNORA43
SNORD62B
MSMP
SNORD90
MIR548D1
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
ANKRD20A4
CCDC29
FAM166B
FOXD4L2
CDKN2BAS
SNORD121A
SNORD121B
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
C9orf110
C9orf130
LOC100129034
LOC100129066
LOC100130426
LOC100131193
FAM157B
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
NCRNA00092
LOC100272217
WASH1
LOC100289341
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q24.

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

Genes
FGFR3
IL2
KDR
KIT
PDGFRA
RAP1GDS1
WHSC1
PHOX2B
DUX4
CHIC2
TET2
FBXW7
FIP1L1
hsa-mir-1305
hsa-mir-1979
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
hsa-mir-575
hsa-mir-1269
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-548i-2
hsa-mir-95
hsa-mir-943
hsa-mir-571
ADD1
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ADRA2C
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA2P1
ANXA3
ANXA5
APBB2
AREG
RHOH
ART3
ATOH1
ATP5I
NKX3-2
BMP3
BMPR1B
BST1
BTC
CAMK2D
CASP3
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
CD38
LRBA
CDS1
CLGN
CENPC1
CENPE
CLCN3
CNGA1
CPE
CRMP1
CSN1S1
CSN2
CSN3
CTBP1
CTSO
DGKQ
DCK
DCTD
DHX15
DMP1
DRD5
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
EPHA5
EREG
ETFDH
EVC
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGF5
FGG
FRG1
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GC
GK2
GK3P
GLRB
GNRHR
GPM6A
GRK4
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HTT
HGFAC
UBE2K
HMGB2
HNRNPD
HPGD
HTN1
HTN3
IBSP
IDUA
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
LETM1
LRPAP1
MAD2L1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MSX1
MTNR1A
MTTP
MUC7
MYL5
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PCDH7
PDE6B
PDHA2
PET112L
PF4
PF4V1
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPBP
PPID
PPP2R2C
PPP3CA
PRKG2
MAPK10
PTPN13
QDPR
REST
RFC1
RGS12
RNF4
ABCE1
RPL9
RPL34
RPS3A
S100P
SC4MOL
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SH3BP2
SNCA
SOD3
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
TDO2
TEC
TLL1
TLR1
TLR2
TLR3
TMSL3
TRPC3
TXK
UBE2D3
UCHL1
UCP1
UGDH
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
VEGFC
WFS1
WHSC2
ZNF141
SLBP
GLRA3
ACOX3
SPARCL1
SMARCA5
SORBS2
PRSS12
CPZ
NOP14
FAM193A
USO1
UNC5C
MAPKSP1
PDE5A
SLC4A4
SAP30
INPP4B
PROM1
HERC3
SNORD73A
STBD1
CDKL2
PAPSS1
LDB2
LRAT
AIMP1
NDST3
SLIT2
RAB28
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
KIAA0232
MFAP3L
SEC24D
G3BP2
WDR1
HS3ST1
FGFBP1
HNRPDL
TSPAN5
ENAM
C4orf6
FAM13A
MFSD10
SPRY1
MAEA
TLR6
PCGF3
ANAPC10
ATP8A1
SPON2
PGRMC2
SEC24B
TACC3
SLC30A9
CXCL13
SLC34A2
MAB21L2
PAICS
MXD4
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
CPLX1
HPSE
SLC26A1
NMU
SMR3B
NPFFR2
PPARGC1A
PPBPL2
MORF4
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
MAN2B2
ANP32C
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXL5
FBXO8
SMR3A
D4S234E
PPA2
DAPP1
DKK2
FAM184B
INTU
NAAA
GPR78
COQ2
ARFIP1
SULT1B1
PDLIM3
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
MRPS18C
LAP3
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
NUDT9
NUP54
STX18
FGFRL1
CLDN22
CYTL1
GAR1
SH3TC1
UGT2B28
RBM47
PCDH18
USP53
OTUD4
DCHS2
FLJ20184
PIGG
DCAF16
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
CCDC109B
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
UBA6
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
C4orf43
UFSP2
CNO
C4orf21
STK32B
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
CDKN2AIP
LYAR
ODZ3
N4BP2
TMEM184C
SEPT11
EXOC1
LRP2BP
TMEM165
PDGFC
TUBB4Q
SLC2A9
FSTL5
BDH2
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
KIAA0114
KIAA1211
RNF150
KIAA1239
TBC1D14
SORCS2
CC2D2A
KLHL8
PCDH10
KIAA1430
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
KIAA1530
METTL14
WDR19
ZFYVE28
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
AFAP1
GUF1
SPCS3
SCOC
C4orf41
NEUROG2
SLC39A8
NCAPG
HHIP
NDST4
AGXT2L1
USP46
MRPL1
RASL11B
ELOVL6
TNIP2
HAUS3
C4orf31
FAT4
ARSJ
SRD5A3
ARHGAP10
FLJ13197
MLF1IP
THAP9
NSUN7
UGT2A3
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
ABCA11P
SCD5
DNAJB14
TMEM156
WWC2
FRAS1
NARG1
CWH43
C4orf29
ALPK1
GRPEL1
MED28
CXXC4
KCNIP4
KIAA1712
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
FGFBP2
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
MFSD7
C4orf14
TMEM175
ABLIM2
HOPX
COL25A1
USP38
LNX1
C4orf49
LOC84740
ARD1B
AGPAT9
CBR4
PIGY
TMEM128
C4orf35
ZNF518B
FHDC1
MGC45800
PRMT10
CCDC149
DDX60L
YTHDC1
C4orf42
TMEM129
NAF1
MOBKL1A
TIFA
FAM114A1
RG9MTD2
MRFAP1
LOC93622
TADA2B
TBCK
HTRA3
HELQ
CYP2U1
C1QTNF7
MRFAP1L1
DDIT4L
CLNK
WDR17
ARAP2
GDEP
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
SPATA18
C4orf32
TMPRSS11B
GNPDA2
SPATA4
CPEB2
EVC2
ARL9
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
OTOP1
ENPP6
NHEDC2
ASB5
NHEDC1
ZNF827
SH3D19
NFXL1
NIPAL1
PAQR3
SHISA3
SCFD2
C4orf38
ZNF595
C4orf39
JAKMIP1
THAP6
C4orf26
KLB
FAM53A
PPM1K
C4orf45
C4orf23
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
MMAA
ZNF509
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
GSX2
ZNF721
SYNPO2
C4orf46
SLC10A4
TIGD4
TMEM154
C4orf34
TMEM192
RWDD4A
CCDC111
TAPT1
FLJ39653
TRIML2
CNOT6L
TECRL
LCORL
C4orf22
EPGN
ZNF718
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
CCDC96
BOD1L
C4orf7
NAP1L5
LOC285419
DCAF4L1
CYP4V2
LOC285456
CRIPAK
DOK7
RNF212
LOC285501
FAM13AOS
GPRIN3
COX18
YIPF7
FRYL
RNF175
LOC285548
LOC285550
C4orf37
CSN1S2A
C4orf10
CSN1S2B
ZAR1
CCDC158
TMPRSS11A
TRIML1
LRRC66
NAT8L
LOC340017
LOC344967
PRSS48
ANKRD56
LRIT3
C4orf44
SLC10A6
HSD17B13
LOC348926
ANKRD37
POLN
PCNAP1
NCRNA00099
KCTD8
C4orf50
C4orf52
BEND4
GRXCR1
TMPRSS11F
USP17L6P
USP17
HSP90AB2P
TRIM61
TRIM75
HELT
C4orf48
DTHD1
LOC401127
SYT14L
FLJ41562
C4orf40
AMTN
FAM190A
C4orf3
RPL21P44
FAM92A3
C4orf12
MIR218-1
MIR302A
C4orf11
MTHFD2L
TMEM150C
EEF1AL7
LOC441046
C4orf47
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC550112
UGT2A2
LOC641518
ZNF876P
SLED1
LOC644145
DEFB131
CLRN2
CEP170L
C4orf51
LOC650293
LOC653543
LOC653544
LOC653545
LOC653548
ZNF732
SCARNA22
SNORA24
SNORA26
MIR572
MIR573
MIR574
MIR575
MIR577
MIR578
PPBPL1
LOC728410
LOC729338
FAM160A1
FLJ36777
RELL1
PSAPL1
SNHG8
MIR943
FAM47E
LOC100130017
LOC100130872
LOC100192379
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 21 significant results found.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 1731 0.17 0.209 0.991 0.24 1.58 0.172
1q 1572 0.60 8.94 0 0.05 -1.39 0.994
2p 753 0.19 1.22 0.36 0.02 -2.14 0.994
2q 1235 0.14 -0.0924 0.991 0.07 -1.53 0.994
3p 853 0.06 -1.45 0.991 0.12 -0.342 0.994
3q 917 0.10 -0.778 0.991 0.06 -1.52 0.994
4p 366 0.11 -0.309 0.991 0.17 0.839 0.46
4q 865 0.12 -0.218 0.991 0.27 2.7 0.0225
5p 207 0.28 3.38 0.00356 0.08 -0.877 0.994
5q 1246 0.30 3.12 0.0071 0.08 -1.15 0.994
6p 937 0.25 2.41 0.0388 0.05 -1.62 0.994
6q 692 0.12 -0.212 0.991 0.25 2.38 0.0374
7p 508 0.25 2.67 0.0246 0.05 -1.5 0.994
7q 1071 0.20 1.26 0.36 0.09 -0.907 0.994
8p 495 0.25 1.77 0.168 0.62 9.98 0
8q 697 0.50 7.15 8.16e-12 0.29 2.57 0.0247
9p 343 0.05 -1.45 0.991 0.25 2.78 0.0214
9q 916 0.05 -1.66 0.991 0.24 2.02 0.0775
10p 312 0.08 -0.878 0.991 0.10 -0.491 0.994
10q 1050 0.02 -2.14 0.991 0.23 1.87 0.101
11p 731 0.02 -2.3 0.991 0.10 -0.802 0.994
11q 1279 0.02 -2.35 0.991 0.15 0.17 0.887
12p 484 0.06 -1.41 0.991 0.08 -1.03 0.994
12q 1162 0.06 -1.76 0.991 0.02 -2.49 0.994
13q 554 0.00 -2.26 0.991 0.36 4.93 4.07e-06
14q 1144 0.03 -2.09 0.991 0.27 2.61 0.0247
15q 1132 0.09 -1.08 0.991 0.14 0.00837 0.968
16p 719 0.05 -1.6 0.991 0.24 2.13 0.0648
16q 562 0.00 -2.26 0.991 0.36 4.93 4.07e-06
17p 575 0.06 -0.947 0.991 0.67 11.6 0
17q 1321 0.31 3.38 0.00356 0.05 -1.59 0.994
18p 117 0.04 -1.58 0.991 0.16 0.781 0.471
18q 340 0.05 -1.61 0.991 0.18 1.09 0.336
19p 870 0.14 0.12 0.991 0.09 -0.986 0.994
19q 1452 0.17 0.341 0.991 0.11 -0.716 0.994
20p 295 0.20 1.54 0.242 0.05 -1.56 0.994
20q 627 0.25 2.52 0.0329 0.03 -2 0.994
21q 422 0.07 -1.18 0.991 0.18 1.11 0.336
22q 764 0.14 0.0316 0.991 0.19 1.14 0.336
Methods & Data
Input

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/LIHC/1216611/2.GDAC_MergeDataFiles.Finished/LIHC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

  • Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

  • Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

  • CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt

  • Amplification Threshold = 0.30

  • Deletion Threshold = 0.30

  • Cap Values = 2.0

  • Broad Length Cutoff = 0.5

  • Remove X-Chromosome = 1

  • Confidence Level = 0.99

  • Join Segment Size = 10

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 10000

Table 4.  Get Full Table First 10 out of 53 Input Tumor Samples.

Tumor Sample Names
TCGA-BC-4072-01B-11D-A151-01
TCGA-BC-4073-01B-02D-A12Y-01
TCGA-BC-A10Q-01A-11D-A12Y-01
TCGA-BC-A10R-01A-11D-A12Y-01
TCGA-BC-A10S-01A-22D-A12Y-01
TCGA-BC-A10T-01A-11D-A12Y-01
TCGA-BC-A10U-01A-11D-A12Y-01
TCGA-BC-A10W-01A-11D-A12Y-01
TCGA-BC-A10X-01A-11D-A12Y-01
TCGA-BC-A10Y-01A-11D-A12Y-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.

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)
[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)
[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)
Meta
  • Maintainer = Dan DiCara