Cervical Squamous Cell Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16 (cga svn revision 38839).

Summary

There were 36 tumor samples used in this analysis: 14 significant arm-level results, 13 significant focal amplifications, and 17 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 - 13 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
--- | --- | --- | --- | ---
11q22.1 | 0.00020212 | 0.0027819 | chr11:101256134-101818609 | 7
20q11.21 | 0.00647 | 0.00647 | chr20:26020583-29820251 | 20
9p24.1 | 0.019988 | 0.019988 | chr9:5649828-5709211 | 1
16p13.13 | 0.037252 | 0.037252 | chr16:11785794-11835481 | 1
3q26.1 | 0.019988 | 0.041082 | chr3:166992045-199501827 | 210
11q13.3 | 0.041082 | 0.041082 | chr11:69516254-70078801 | 6
7p11.2 | 0.057281 | 0.057281 | chr7:55018826-55426994 | 2
21q22.2 | 0.064467 | 0.064467 | chr21:38710567-39610234 | 5
13q22.1 | 0.071279 | 0.071279 | chr13:73093889-73119658 | 0 [KLF12]
8q24.21 | 0.045931 | 0.074639 | chr8:129098497-129100915 | 1
3q26.1 | 0.034255 | 0.10186 | chr3:163643792-163719647 | 0 [OTOL1]
8q24.21 | 0.081818 | 0.17435 | chr8:129524135-129592226 | 0 [hsa-mir-1208]
8q24.21 | 0.041082 | 0.99915 | chr8:1-146274826 | 745

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.1.

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

Genes
BIRC3
BIRC2
YAP1
KIAA1377
C11orf70
TMEM123
ANGPTL5

Genes in Wide Peak

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

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

Genes
hsa-mir-663
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
DEFB118
NCRNA00028
C20orf191
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
MIR663
PSIMCT-1

Genes in Wide Peak

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

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

Genes
KIAA1432

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p13.13.

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

Genes
BCAR4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.1.

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
CLDN11
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SKIL
SLC2A2
SST
TERC
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
FYTTD1
ARPM1
MGC2889
LRCH3
C3orf34
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
C3orf50
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
C3orf59
C3orf21
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
NAALADL2
TCTEX1D2
C3orf43
SDHALP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
SOX2OT
WDR53
LOC348840
LRRC33
TMEM212
FLJ42393
SNORD2
SNORA4
C3orf65
LOC647309
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHALP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
SNAR-I
MIR1224

Genes in Wide Peak

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

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

Genes
hsa-mir-548k
CTTN
PPFIA1
FADD
SHANK2
ANO1

Genes in Wide Peak

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

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

Genes
EGFR
LANCL2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q22.2.

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

Genes
ERG
ETS2
PSMG1
BRWD1
NCRNA00114

Genes in Wide Peak

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

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

Genes
PVT1

Genes in Wide Peak

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

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

Genes
COX6C
EXT1
FGFR1
MYC
PCM1
PLAG1
TCEA1
WRN
RECQL4
NCOA2
WHSC1L1
CHCHD7
HOOK3
hsa-mir-1234
hsa-mir-661
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1206
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-1273
hsa-mir-875
hsa-mir-2052
hsa-mir-124-2
hsa-mir-486
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ADCY8
ADRA1A
ADRB3
ANGPT1
ANGPT2
ANK1
ANXA13
ASAH1
ASPH
ATP6V1B2
ATP6V1C1
BAI1
BLK
BMP1
POLR3D
BNIP3L
OSGIN2
CA1
CA2
CA3
CA8
CALB1
RUNX1T1
CDH17
CEBPD
CHRNA2
CHRNB3
CLU
CRH
CTSB
CYC1
CYP7A1
CYP11B1
CYP11B2
ADAM3A
DECR1
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4
DPYS
DPYSL2
DUSP4
E2F5
EEF1D
EGR3
EIF4EBP1
EPB49
EPHX2
CLN8
EXTL3
EYA1
FABP4
FABP5
PTK2B
FDFT1
FGL1
FNTA
ADAM2
GATA4
GEM
GFRA2
GLI4
GML
GNRH1
NPBWR1
GPR20
GPT
GRINA
GSR
GTF2E2
HAS2
NRG1
HNF4G
HSF1
IKBKB
IL7
IMPA1
IDO1
EIF3E
KCNQ3
KCNS2
LOXL2
LPL
LY6E
LY6H
LYN
MATN2
MCM4
MMP16
MOS
MSR1
MSRA
MYBL1
NBN
NDUFB9
NEFM
NEFL
NFKBIL2
NKX3-1
NOV
ODF1
TNFRSF11B
OPRK1
PDE7A
PDGFRL
ENPP2
PENK
PLAT
PLEC1
PNOC
PMP2
POLB
POLR2K
POU5F1B
PPP2CB
PPP2R2A
PPP3CC
PKIA
PRKDC
PTK2
PVT1
PXMP3
RAB2A
RAD21
RP1
RPL7
RPL8
RPL30
RPS20
SDC2
SDCBP
SFRP1
SFTPC
ST3GAL1
SLA
SLC7A2
SLC18A1
SLC20A2
SNAI2
SNTB1
SPAG1
SQLE
STAR
STC1
STK3
TACC1
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
UBE2V2
COL14A1
UQCRB
VDAC3
YWHAZ
ZNF7
ZNF16
FZD3
TUSC3
UBXN8
MYST3
PSCA
FZD6
NSMAF
LY6D
RGS20
JRK
TNKS
EIF3H
DGAT1
GPAA1
ADAM18
ADAM9
ADAM7
RIPK2
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
GGH
WISP1
CPNE3
FOXH1
CHRNA6
TRPA1
DOK2
ASH2L
MTMR7
CCNE2
EBAG9
MYOM2
DLGAP2
MSC
MFHAS1
KCNB2
CYP7B1
BAG4
ENTPD4
ARHGEF10
MTFR1
LRRC14
TTC35
RIMS2
ST18
TOX
MTSS1
PTDSS1
PHYHIP
RB1CC1
ZNF623
KIAA0196
KBTBD11
HHLA1
SORBS3
TRIB1
HRSP12
NPM2
DLC1
NDRG1
PGCP
SPAG11B
LYPLA1
ARFGEF1
COLEC10
KHDRBS3
DCTN6
PNMA2
ADAM28
POP1
AP3M2
COPS5
RBPMS
WWP1
STMN2
PTP4A3
ERLIN2
LZTS1
PROSC
RNF139
ZHX1
PUF60
ZHX2
DENND3
XPO7
TRIM35
ZC3H3
EFR3A
RRS1
SULF1
RHOBTB2
ARC
BOP1
DDHD2
KIF13B
PSD3
ZFPM2
HEY1
TRAM1
LEPROTL1
SCRIB
KIAA0146
SLC39A14
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
GPR124
KIAA1429
C8orf71
RGS22
FBXL6
PTTG3P
FBXO25
FGF20
SNORA72
SNORD54
OPLAH
PABPC1
KCNV1
STAU2
MTBP
DKK4
EIF2C2
LSM1
ADAMDEC1
BHLHE22
MRPS28
COMMD5
MRPL13
ATAD2
DDEF1IT1
MRPL15
CNOT7
CPSF1
PURG
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
FAM164A
PHF20L1
LACTB2
FAM82B
ZNF706
GOLGA7
VPS28
ZDHHC2
C8orf30A
KCNK9
SLC25A37
C8orf55
UBR5
SCARA3
FAM49B
AZIN1
ATP6V1H
OTUD6B
TMEM66
CHRAC1
SNTG1
GDAP1
EXOSC4
PDP1
CNGB3
LY6K
KCTD9
ESRP1
IMPAD1
TMEM70
PINX1
TRMT12
OXR1
WDYHV1
PIWIL2
ELP3
THAP1
ARMC1
INTS10
CCDC25
UBE2W
BRF2
AGPAT5
LAPTM4B
C8orf39
TMEM55A
SLC39A4
CHD7
GOLSYN
INTS8
INTS9
CSGALNACT1
HR
PAG1
PBK
ZNF395
DEFB103A
BIN3
TEX15
GSDMC
C8orf44
JPH1
C8orf4
ENY2
CPA6
SLURP1
SLC45A4
MTUS1
C8orf79
ZFAT
KIAA1967
ZNF250
PLEKHA2
SH2D4A
PRDM14
SNX16
NECAB1
PDLIM2
SOX17
CSMD1
EBF2
FAM160B2
DEPDC6
PYCRL
C8orf33
ZBTB10
LYNX1
MTMR9
DUSP26
C8orf51
DSCC1
DERL1
GPR172A
HMBOX1
EFCAB1
MCPH1
PPP1R3B
PLEKHF2
ZMAT4
ZFAND1
ZFHX4
GSDMD
NIPAL2
RNF122
CSPP1
BAALC
NUDT18
ZNF696
GRHL2
DOCK5
FLJ14107
VCPIP1
ZNF703
C8orf41
RAB11FIP1
PREX2
REEP4
KIAA1688
ZNF34
SLC25A32
TM7SF4
STMN4
RNF170
SLCO5A1
SHARPIN
EPPK1
SCRT1
SOX7
FAM167A
AMAC1L2
C8orf12
CRISPLD1
TRAPPC9
TM2D2
TATDN1
NACAP1
NCALD
SGK196
MAF1
UTP23
GINS4
PPAPDC1B
MAK16
TRIM55
FUT10
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
FAM86B1
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
ERI1
ZNF251
KIFC2
TMEM67
LONRF1
CHMP7
MTDH
CHMP4C
PKHD1L1
NAPRT1
WDR67
HPYR1
RP1L1
TP53INP1
TGS1
MFSD3
MAL2
XKR4
CSMD3
RHPN1
FBXO32
C8orf40
SLC26A7
PCMTD1
CTHRC1
OSR2
C8orf34
TOP1MT
CLDN23
ZNF572
GOT1L1
FAM92A1
VPS37A
C8orf38
TMEM68
ABRA
LYPD2
NKX2-6
TMEM71
SGCZ
ADHFE1
UBXN2B
PXDNL
AGPAT6
UNC5D
LETM2
DCAF4L2
RALYL
HGSNAT
DEFB104A
PRAGMIN
PEBP4
CDCA2
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
ESCO2
FBXO16
LOC157627
FAM84B
C8orf37
VPS13B
C8orf42
ERICH1
SLC7A13
TDH
TMEM74
FAM91A1
C8orf48
C8orf45
CLVS1
NKX6-3
KCNU1
C8orf84
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ZNF596
IDO2
SDR16C5
ADCK5
TSNARE1
R3HCC1
T-SP1
C8orf74
HTRA4
ADAM32
C8orf47
LGI3
MAPK15
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
ATP6V0D2
NEIL2
YTHDF3
C8orf46
REXO1L1
ADAM5P
FLJ10661
XKR6
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
EFHA2
ZNF252
TMED10P
C8orf77
C8orf31
ZFP41
SCARA5
LOC286135
RNF5P1
C8orf83
DPY19L4
FBXO43
NKAIN3
LRRC67
GPIHBP1
LOC340357
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
POTEA
SLC10A5
LOC349196
SPATC1
USP17L2
CA13
XKR5
C8orf80
C8orf86
FAM150A
XKR9
RBM12B
FLJ43860
MAFA
LOC392196
GDF6
LOC401463
C8orf59
SAMD12
MIR124-1
MIR124-2
MIR30B
MIR30D
MIR320A
DEFB103B
MGC70857
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
REXO1L2P
C8orf85
LRRC24
SDR16C6
DEFA10P
C8orf22
MIR383
BEYLA
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
ZFATAS
HAS2AS
DEFB135
DEFB136
DEFB134
ZNF704
C8orf75
MBOAT4
NCRNA00051
MIR486
DEFB109P1B
SNHG6
SNORD87
C8orf73
SCXB
LOC643763
RPL23AP53
FAM90A14
FABP9
FABP12
FAM86B2
SPAG11A
FER1L6
MIR596
MIR597
MIR598
MIR599
MIR661
LOC727677
HEATR7A
LOC728024
DEFA1B
FAM90A20
FAM90A19
ZNF705D
OC90
LOC731779
MIR875
MIR937
MIR939
SCXA
LOC100130274
LRRC69
LOC100131726
ZNF705G
FAM66E
FAM66D
FAM66A
SBF1P1
LOC100133669
LOC100192378

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 - 17 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
--- | --- | --- | --- | ---
3p14.2 | 1.2157e-07 | 1.2157e-07 | chr3:59009803-61522370 | 1
2q37.1 | 2.2714e-05 | 2.2714e-05 | chr2:213855358-242951149 | 247
6q26 | 0.0024205 | 0.0024205 | chr6:161613089-163073197 | 1
11q24.3 | 0.0010424 | 0.0024205 | chr11:17358096-134452384 | 1067
10q23.2 | 0.012697 | 0.012697 | chr10:89302988-89611040 | 3
3p22.1 | 0.079247 | 0.079247 | chr3:40553687-42109081 | 2
21q21.1 | 0.081912 | 0.079247 | chr21:18174997-25682320 | 4
11q14.1 | 0.02917 | 0.1053 | chr11:78825689-90243998 | 38
1p36.23 | 0.12708 | 0.12708 | chr1:1-222417645 | 2009
4q35.1 | 0.077278 | 0.15258 | chr4:174672203-191273063 | 67
7q31.33 | 0.14687 | 0.15258 | chr7:109385398-154370149 | 312
4q32.3 | 0.12708 | 0.16217 | chr4:167241131-174329125 | 13
20p12.1 | 0.18818 | 0.17837 | chr20:6695556-29311252 | 100
10q26.2 | 0.19982 | 0.19982 | chr10:97355027-135374737 | 308
5q12.1 | 0.20931 | 0.21755 | chr5:1-180857866 | 961
9p24.3 | 0.23217 | 0.23217 | chr9:1-140273252 | 890
13q32.3 | 0.23222 | 0.23217 | chr13:1-114142980 | 363

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.1.

Table S12. 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
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
IL8RA
IL8RB
IL8RBP
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
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
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
C2orf24
STK36
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
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
TIGD1
CCDC108
C2orf72
C2orf85
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 6q26.

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CCND1
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
LMO2
MEN1
MLL
NUMA1
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
hsa-mir-100
hsa-mir-125b-1
hsa-mir-34c
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-548k
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-130a
hsa-mir-129-2
hsa-mir-610
ACAT1
ACP2
ACRV1
ACTN3
ADRBK1
APLNR
ALDH3B1
ALDH3B2
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
ARHGAP1
PHOX2A
ARL2
ARRB1
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
CLNS1A
CNTF
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
EEF1G
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GTF2H1
GUCY1A2
H2AFX
HMBS
SLC29A2
HSPA8
HSPB2
DNAJC4
HTR3A
IGHMBP2
IL10RA
IL18
INCENP
INPPL1
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYBPC3
MYO7A
MYOD1
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
OMP
OPCML
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PGA5
PGR
PLCB3
POLR2G
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PSMC3
PTPRCAP
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
SNORD15A
ROM1
RPS3
RPS6KB2
RPS25
SAA1
SAA2
SAA3P
SAA4
SC5DL
SCN2B
SCN4B
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SORL1
SPI1
SPTBN2
SRPR
SSRP1
ST14
STX3
STX5
ABCC8
TAGLN
TCN1
TECTA
THRSP
THY1
TM7SF2
TPH1
TRAF6
TRPC6
TSG101
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WNT11
SF1
ZFPL1
ZBTB16
ZNF202
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIA1
SLC43A1
DGKZ
CHST1
BARX2
API5
MADD
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
AIP
SYT7
SART1
USP2
SLC6A5
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MED17
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
CEP57
RICS
KIAA0652
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
PRG3
YAP1
RBM14
CDC42EP2
EIF3M
NXF1
KAT5
HYOU1
SSSCA1
HTATIP2
DRAP1
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CUGBP1
POLD3
OR5I1
STARD10
NEU3
ME3
GPR83
YIF1A
SFRS2B
EHD1
STIP1
CLP1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
HPS5
GPR44
SLCO2B1
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
NUP160
NCAPD3
FNBP4
SIK3
CLCF1
VSIG2
BACE1
FAM89B
SNHG1
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
C11orf41
PRDX5
POU2F3
ABTB2
BRMS1
C11orf20
CHRDL2
PAMR1
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
PPP1R14B
OR8G2
OR8B8
OR8G1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
ACAD8
B3GAT1
RAB30
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
COMMD9
DDX25
PACSIN3
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
KCNK4
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
TMEM216
CHCHD8
SLC15A3
PHF21A
MS4A4A
WIT1
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
RSF1
SPA17
FXYD6
C11orf24
CNTN5
SIAE
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39
TRIM44
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
C11orf59
VPS37C
ANO1
NADSYN1
FAM86C
C11orf57
NAT10
CCDC87
SAPS3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
ELMOD1
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
TMPRSS4
GPR137
C11orf60
C11orf75
C11orf30
PRDM10
PRDM11
CABP4
SLC17A6
TRIM49
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
ATPGD1
SYT13
USP28
LRRC4C
POLD4
KRTAP5-8
PLEKHB1
MS4A7
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
ALX4
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
KLC2
TUT1
MRPL11
TMEM135
KCTD14
C11orf95
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
E2F8
CCDC82
ALG9
ZNF408
ASAM
NAT11
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
GDPD5
CLPB
UNC93B1
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
RNASEH2C
TMEM126A
DCUN1D5
EIF1AD
NUDT22
ARFGAP2
KIAA1826
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
SPRYD5
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
RELT
UBASH3B
C11orf70
LGALS12
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
NAV2
ATG16L2
GLB1L2
TSPAN18
ESAM
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
VPS26B
GLB1L3
CDCA5
RPLP0P2
SAAL1
SLC22A9
SNORD15B
TIRAP
CARD16
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRF
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
C11orf74
OR4C46
OR4X2
OR4B1
GYLTL1B
SLC36A4
FAT3
TRIM64
TMEM45B
DBX1
CASP12
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
DNAJC24
C11orf46
OR8I2
LDLRAD3
XRRA1
MUC15
C11orf94
FAM76B
SESN3
PIWIL4
FLJ32810
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
SPTY2D1
TMEM86A
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
GPHA2
ADAMTS15
B3GNT6
METT5D1
MPZL3
IMMP1L
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
MRPL21
TPCN2
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
C11orf66
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
OR4C3
OR4S1
EML3
TMEM151A
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR10AG1
OR5J2
OR4C13
OR4C12
C11orf85
SLC25A45
NEAT1
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
LOC283174
OR9G4
C11orf64
P4HA3
PGM2L1
KLHL35
KCTD21
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LOC283267
IGSF22
LUZP2
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
TBX10
C11orf34
RTN4RL2
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
KRTAP5-10
SLC22A25
FIBIN
LOC387763
SLC22A10
SPDYC
LIPT2
C11orf90
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
GUCY2E
TRIM77
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
FAM180B
PCNXL3
C11orf87
C11orf92
C11orf88
LOC399959
PATE2
PATE4
SNX19
OR4A47
OR4C45
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR34B
MIR34C
DDI1
BLID
LOC440040
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
NCRNA00167
LOC441601
OR5B3
MIR326
CCDC73
LOC494141
BDNFOS
MS4A13
OR8U8
OR9G9
SCARNA9
HEPN1
TRIM64B
TRIM53
UBTFL1
BTBD18
PGA3
PGA4
LOC643923
CLDN25
LOC645332
LOC646813
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
MIR610
MIR611
MIR612
LOC729384
LOC729799
METTL12
C11orf83
LOC100126784
LOC100128239
LOC100130987
C11orf91
LOC100133315
PATE3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.2.

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

Genes
PAPSS2
ATAD1
CFLP1

Genes in Wide Peak

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

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

Genes
CTNNB1
ULK4

Genes in Wide Peak

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

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

Genes
NCAM2
PRSS7
CHODL
C21orf131

Genes in Wide Peak

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

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

Genes
PICALM
hsa-mir-1261
CTSC
DLG2
GRM5
PRCP
TYR
FZD4
EED
NAALAD2
ME3
PRSS23
RAB38
CHORDC1
RAB30
NOX4
C11orf73
PCF11
SYTL2
TMEM126B
TRIM49
CREBZF
CCDC90B
CCDC81
TMEM135
TMEM126A
TRIM64
FOLH1B
C11orf82
CCDC83
FAM181B
CCDC89
ANKRD42
TRIM77
TRIM64B
TRIM53
UBTFL1
LOC729384

Genes in Wide Peak

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

Table S19. 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
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-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
ADAR
ADORA1
ADORA3
AGL
AK2
AK3L1
ALDH9A1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
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
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
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
GBA
GBAP
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GLUL
GNAI3
GNAT2
GNB1
GNG5
SFN
GPR3
GPR25
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
HCRTR1
HDAC1
HDGF
CFH
CFHR1
CFHR2
ZBTB48
MR1
HLX
HMGN2
HMGCL
HMGCS2
HPCA
HSD3B1
HSD3B2
HSD11B1
HSPA6
HSPA7
IGSF3
HSPG2
HTR1D
HTR6
ID3
IFI16
CYR61
IL6R
IL10
IL12RB2
TNFRSF9
ILF2
INPP5B
INSRR
IPP
IRF6
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNH1
KCNJ9
KCNJ10
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
STMN1
LEPR
LMNA
LMX1A
LOR
LY9
TACSTD2
MAGOH
MARK1
MATN1
MCL1
CD46
SMCP
MEF2D
MFAP2
MGST3
MNDA
MOV10
MPZ
MSH4
MTF1
MTHFR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NASP
NBL1
NCF2
NDUFS2
NDUFS5
NEK2
NFIA
NFYC
NGF
NHLH1
NHLH2
NIT1
NPPA
NPPB
NPR1
NRD1
YBX1
ROR1
DDR2
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
PSMA5
PSMB2
PSMB4
PSMD4
PTAFR
PTGER3
PTGFR
PTGFRN
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PTPRF
PEX19
ABCD3
RAB3B
RAB13
RABGGTB
RABIF
RAP1A
RAP1GAP
RBBP4
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RHCE
RHD
RIT1
RLF
RNASEL
RNF2
RNPEP
SNORD21
RORC
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RPS27
RSC1A1
RXRG
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
TROVE2
SSR2
AURKAPS1
STXBP3
XCL2
SYCP1
TAF12
TAF13
CNTN2
TBX15
TCEA3
TCEB3
VPS72
TGFB2
TGFBR3
THBS3
TCHH
TIE1
TLR5
TNFRSF1B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TP73
TRAF5
CCT3
TSHB
TTC4
TUFT1
TNFSF4
TNFRSF4
UCK2
UQCRH
UROD
USF1
USP1
USH2A
VCAM1
WNT2B
ZSCAN20
ZBTB17
SLC30A1
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
DAP3
NPHS2
BTG2
PTP4A2
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
SNHG3
NR0B2
RAD54L
DYRK3
TTF2
RGS5
PPFIA4
PIK3R3
MMP23B
MMP23A
KCNAB2
ITGA10
LMO4
FCN3
BLZF1
CDC14A
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
ARHGEF2
DEDD
ZMYM4
ZMYM6
XPR1
FAIM3
DHRS3
MAPKAPK2
GPR37L1
GPR52
SFRS11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
AIM2
RASAL2
C1orf38
ADAMTS4
TMEM59
SEC22B
CHD1L
H6PD
SOX13
PRDX6
CLCA3P
CLCA2
ISG15
IKBKE
PLCH2
HS2ST1
IPO13
SDC3
SLC25A44
KIAA0040
KDM4A
CROCC
PUM1
NOS1AP
KIAA0562
RIMS3
KIAA0494
ARHGEF11
DNAJC6
CEP350
LRIG2
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
KLHL21
SLC35E2
DENND4B
RABGAP1L
TMCC2
FAM20B
ZBTB40
LPGAT1
MFN2
KIF14
RBM8A
NR1I3
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
C1orf61
CAP1
LRRC41
SEMA6C
HBXIP
SLC19A2
IFI44
POLR3C
IVNS1ABP
TXNIP
PDPN
PMVK
KHDRBS1
GMEB1
FAM189B
AP4B1
NUDC
PHTF1
MASP2
NES
KDM5B
AHCYL1
SFRS13A
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
CLCA4
MTF2
DNAJC8
NTNG1
PLEKHA6
CLSTN1
FOXJ3
KIAA0907
WDR47
KIFAP3
ATF6
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
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
ICMT
MACF1
LRRC8B
ZNF281
SNAPIN
LPAR3
PADI4
DDAH1
TMEM50A
PHLDA3
RUSC1
CA14
KPNA6
SSBP3
STX12
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
INTS7
OLFML2B
C1orf43
CLIC4
NSL1
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
DNM3
TOR1AIP1
C1orf77
C1orf144
LDLRAP1
SERBP1
NOC2L
PTPN22
PHGDH
FBXO2
LCE2B
OPTC
FBXO6
PLA2G2D
AK5
MYCBP
OR10J1
HEYL
EIF2C1
OR4F3
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORA66
SNORD47
SNORD45B
SNORD45A
SNORD44
SNORD55
RNU11
RNF11
USP21
FOXD3
C1orf107
TRAPPC3
CACYBP
HSPB7
CHIA
SLC39A1
ARHGEF16
AHDC1
RNF115
KLHL20
TEKT2
SMPDL3B
ANGPTL3
ROBLD3
FLVCR1
PRO0611
UBE2T
HSPC157
SSU72
TMOD4
GNL2
GPSM2
UBIAD1
NME7
ALG6
NENF
PADI1
IL19
LASS2
SLC25A24
PLA2G2E
DNTTIP2
WDR8
CRNN
G0S2
IL20
SLC45A1
DCAF8
HP1BP3
F11R
TMED5
RRP15
GLRX2
BOLA1
CELA2B
ZNF593
ZBTB7B
ZNF691
TXNDC12
TNNI3K
C1orf66
ADIPOR1
SH3GLB1
MECR
APH1A
UTP11L
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
CD244
GPR88
ERRFI1
DPM3
WNT4
YIPF1
FBXO42
MRPS21
CCDC76
TMCO1
ADAMTSL4
CRCT1
RNF186
SPATA6
MXRA8
L1TD1
HES2
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
TMEM51
RALGPS2
GPATCH2
BSDC1
XKR8
TMEM39B
PRPF38B
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
NBPF1
IARS2
MAP7D1
IPO9
TMEM48
NECAP2
IQCC
C1orf112
HHAT
DNAJC11
RCOR3
C1orf106
C1orf103
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
RCC2
C1orf183
DMAP1
AJAP1
GNG12
RAG1AP1
C1orf91
FAM54B
SERTAD4
CCBL2
SLAMF8
CDC42SE1
UBQLN4
TMEM167B
OLFML3
SMYD2
LHX9
OTUD7B
CTNNBIP1
C1orf63
AGTRAP
C1orf128
RAB25
PGLYRP4
RHBG
MAN1C1
SCYL3
CAMK1G
NIPAL3
SEPN1
ATP8B2
KIAA0495
VANGL2
PBXIP1
S100A14
PLEKHG5
GATAD2B
AMIGO1
LRRC47
ODF2L
CGN
KIAA1324
PTCHD2
IGSF9
LRRC7
KIF17
ZNF687
ZSWIM5
POGK
KIAA1522
HCN3
CACHD1
MIER1
KIAA1614
FAM5B
HES4
C1orf114
GRHL3
SLAMF7
CADM3
PTBP2
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
SEMA4A
TOR3A
RFWD2
RGS18
PLA2G2F
HIAT1
NUCKS1
SMAP2
ATPAF1
MOSC1
S100PBP
MEAF6
DEM1
CCDC21
NMNAT1
ELOVL1
AIDA
VWA1
DCLRE1B
MRPS15
MRPL9
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
INTS3
NADK
ZNF643
C1orf163
PHACTR4
C1orf135
SCNM1
ERI3
C1orf50
WDR77
C1orf116
MGC4473
CCDC28B
EFHD2
MMEL1
C1orf89
FCRL2
DLEU2L
OR4F5
NKAIN1
EPS8L3
CDC73
MRPL24
MUL1
TNFAIP8L2
C1orf54
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
NOL9
PPCS
LIN28
C1orf113
TTLL7
SNIP1
C1orf115
HHIPL2
VASH2
AGMAT
WDR78
ZMYM1
NCRNA00115
RPAP2
MORN1
GRRP1
KIAA0319L
DHDDS
PAQR6
DENND2D
GPR177
GPR157
TRIM46
C1orf129
RPF1
SIKE1
ZC3H12A
SPSB1
TARS2
TRIM45
EDEM3
FLAD1
TRAF3IP3
GLTPD1
ZNF436
TAS1R2
TAS1R1
NPL
GJA9
OR4F16
OR6N2
OR6K2
SYNC
CFHR5
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
STK40
TM2D1
FCAMR
REG4
TMEM222
C1orf49
PLEKHN1
HORMAD1
TOMM40L
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
SLC25A33
TMEM79
DDI2
ACBD6
LZIC
PROK1
EFCAB7
ZBTB37
NT5C1A
LCE3D
TRIM63
PSRC1
FAM167B
C1orf97
MGC12982
C1orf170
CROCCL1
FCRLA
ANKRD36BL1
HPDL
C1orf203
AGBL4
MFSD2A
PPP1R15B
ATG4C
MAEL
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
DISP1
SNHG12
FAM40A
RGS8
DOCK7
KIAA1751
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
PIGM
IGSF8
C1orf158
LEMD1
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
C1orf85
MED8
KTI12
C1orf212
ADC
TMEM54
C1orf59
TOE1
ERMAP
PGLYRP3
CSMD2
MYSM1
GNRHR2
CROCCL2
FHAD1
SLAMF6
OSBPL9
SLC26A9
LOC115110
OMA1
RAB42
FCRL1
FCRL3
LRRC42
GBP4
GBP5
FAM46B
FMO9P
RBP7
TSEN15
FAM129A
ACAP3
TADA1
THEM4
SH2D1B
SSX2IP
UBE2J2
OLFM3
GABPB2
TCHHL1
RPTN
C1orf231
TDRD10
SHE
C1orf172
AADACL3
PUSL1
B3GALT6
WDR63
KLHDC9
C1orf125
C1orf161
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LYPLAL1
ATP6V1G3
ASB17
TYW3
C1orf173
LRRIQ3
TPRG1L
C1orf93
MYOM3
DMBX1
OR10J5
TMCO2
ZNF684
C1orf83
PODN
LRRC39
GJB4
HMGB4
RNF19B
DCST2
ZNF648
TEDDM1
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
LIX1L
SPATA17
KLF17
TMEM125
C1orf182
IQGAP3
APOA1BP
ARHGEF19
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
LOC148696
LOC148709
PTPRV
HFE2
ANKRD35
FAM163A
MFSD4
PM20D1
SLC30A7
CCDC27
C1orf213
KNCN
MOBKL2C
GLIS1
LELP1
RC3H1
MGC27382
DCDC2B
ZNF362
DCST1
MANEAL
IL23R
METTL11B
FAM78B
SHISA4
PDIK1L
BNIPL
CLDN19
WDR65
C1orf210
C1orf84
CCDC24
BTBD19
CCDC17
C1orf92
C1orf64
LOC149620
PYHIN1
C1orf227
FAM71A
SLC2A7
DENND2C
GBP6
LPPR5
FNDC7
DENND1B
TDRD5
TOR1AIP2
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
SPRR4
KANK4
SASS6
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
SPAG17
SLFNL1
KRTCAP2
CRTC2
C1orf126
HIPK1
SLC44A5
ATAD3C
AKR7L
AFARP1
TMEM9
FNDC5
EPHX4
TTLL10
AKNAD1
SLC41A1
LCE5A
TMCO4
MCOLN2
COL24A1
PCSK9
SYT14
ST6GALNAC3
ZNF683
ARHGAP30
C1orf192
NEGR1
ASPM
CYP4X1
MAGI3
TIPRL
NPHP4
BEST4
FAM19A3
C1orf230
THEM5
SLC9A11
CYP4A22
C1orf185
LOC284551
NBPF15
C1orf157
LOC284578
FAM41C
FAM102B
SYPL2
CYB561D1
ANKRD34A
C1orf104
LOC284632
RSPO1
EPHA10
LOC284661
C1orf204
C1orf111
LOC284688
ZNF326
BTBD8
RIMKLA
SLC25A34
ESPNP
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BA
FAM151A
S100A7A
LINGO4
RXFP4
ANKRD45
C1orf174
KLHL17
C1orf70
TMEM52
FAM5C
MTMR9L
ZBTB8OS
TFAP2E
C1orf110
FAM58B
LOC339524
C1orf228
ZNF642
RD3
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
CCDC18
MYBPHL
OR10R2
FCRL6
KCNT2
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
SERINC2
FAM159A
FAM131C
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PADI6
RGSL1
BMP8A
ZBTB41
CYCSP52
C1orf187
SPATA21
CCDC23
C1orf223
C1orf175
FAM73A
PEAR1
SFT2D2
MIA3
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
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
UOX
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
LOC400759
C1orf226
LOC400794
C1orf220
LOC400804
NBPF20
FAM177B
PRAMEF3
LDLRAD2
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
LOC441869
PRAMEF7
LOC441897
OR10J3
MIR135B
KPRP
LCE6A
SUMO1P3
LOC492303
RBMXL1
C1orf190
PEF1
MIR429
HIST2H4B
C1orf133
MIR488
CYB5RL
SNORD74
RPL31P11
FAM138F
LOC642502
LOC642587
LQK1
CYMP
KIAA0754
LOC643837
TMEM88B
PPIAL4G
C1orf200
PPIAL4D
LOC645166
PRAMEF19
PRAMEF20
FAM138A
LOC645676
S100A7L2
LOC646471
LOC647121
LOC648740
LOC649330
ZBTB8A
NBPF6
PPIAL4B
GPR89A
LOC653566
PPIAL4C
HIST2H3D
PRAMEF22
PRAMEF15
WASH5P
TMEM183B
FAM72B
PRAMEF16
PCP4L1
FAM138C
SCARNA3
SCARNA2
SCARNA4
SCARNA1
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
SNHG3-RCC1
C1orf152
MIR765
MIR942
MIR190B
MIR760
MIR921
LOC100128003
LOC100128071
LOC100128842
C1orf68
MSTO2P
LOC100129534
FLJ39609
LOC100130557
TSTD1
LOC100132062
LOC100132111
LOC100132287
NBPF10
FCGR1C
LOC100133331
LOC100133612
C2CD4D
LOC100286793
LOC100288778
LOC100302401

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
MLL3
CREB3L2
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
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
IFRD1
IMPDH1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
PRSS2
TAS2R38
PTN
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
FAM131B
DOCK4
FAM115A
ABCF2
AASS
FAM3C
FASTK
ZNF277
ABCB8
TFEC
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
C7orf54
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
C7orf68
MDFIC
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
LSM8
GPR85
TAS2R5
CHPF2
ING3
LRRN3
CHCHD3
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ZNF398
EXOC4
GALNT11
LRRC4
TMEM168
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7OT1
ST7OT2
ST7OT3
CADPS2
CPA5
FOXP2
TSGA14
C7orf29
TSGA13
AGAP3
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
TRYX3
MOXD2
ASZ1
ASB15
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF783
ZNF746
ATP6V0E2
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
FABP5L3
UBN2
TAS2R39
TAS2R40
TAS2R41
FLJ40852
FAM115C
ZNF775
ATG9B
C7orf53
LOC286016
MESTIT1
ST7OT4
TAS2R60
CTAGE6
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
LOC441294
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF5L
GIMAP6
WEE2
MIR490
ZNF862
PL-5283
ACTR3C
MIR592
MIR593
LOC728743
TMEM229A
LUZP6
MIR671
LOC100124692
LOC100128542
CTAGE4
LOC100128822
LOC100132707
LOC100134229
LOC100134713

Genes in Wide Peak

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

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

Genes
CLCN3
NEK1
MFAP3L
ANXA10
PALLD
SPOCK3
AADAT
C4orf27
DDX60
SH3RF1
CBR4
DDX60L
GALNTL6

Genes in Wide Peak

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

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

Genes
hsa-mir-663
JAG1
BFSP1
BMP2
ENTPD6
CST1
CST2
CST3
CST4
CST5
FOXA2
INSM1
NKX2-2
PAX1
PCSK2
PLCB4
PYGB
RRBP1
SNAP25
SNRPB2
SSTR4
THBD
ZNF133
MKKS
CST7
GINS1
CST8
SEC23B
POLR3F
RBBP9
DSTN
XRN2
BTBD3
CD93
NINL
PLCB1
FLRT3
C20orf103
C20orf26
ABHD12
ZNF337
SNX5
HSPC072
NXT1
VSX1
NAT5
CRNKL1
ESF1
HAO1
RIN2
C20orf12
SPTLC3
KIF16B
TASP1
PLK1S1
TMX4
OTOR
C20orf3
PAK7
RALGAPA2
CSRP2BP
SLC24A3
OVOL2
NAPB
ANKRD5
GZF1
C20orf7
TMEM90B
SEL1L2
ACSS1
GGTLC1
C20orf72
DTD1
C20orf94
CSTL1
CST9L
CST9
MACROD2
C20orf56
BANF2
NANP
C20orf79
ISM1
CST11
C20orf191
CSTT
DEFB115
LOC284788
LOC284798
FAM182A
FRG1B
LOC388789
NKX2-4
SNORD17
MIR663
FAM182B
LOC100130264
LOC100134868
LOC100270804
PET117

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.2.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-2110
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-608
hsa-mir-1287
hsa-mir-607
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2E1
CYP17A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HMX2
HPS1
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
ALDH18A1
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
DNMBP
FRAT2
RP11-529I10.4
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
CHST15
ACSL5
CCNJ
ZRANB1
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CWF19L1
PI4K2A
HIF1AN
BRWD2
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
C10orf84
LHPP
MMS19
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
C10orf119
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
C10orf79
LRRC27
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
ITPRIP
C10orf75
MTG1
NCRNA00081
FANK1
OPALIN
SYCE1
DHDPSL
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
SFXN2
PDZD8
C10orf32
GSTO2
C10orf78
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
NKX2-3
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
C10orf93
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
CC2D2B
ARMS2
C10orf122
GUCY2G
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FOXI2
GOLGA7B
FAM45A
C10orf62
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
LOC653543
LOC653544
LOC653545
LOC653548
SNORA12
MIR608
MIR609
LOC728410
LOC729020
TLX1NB
C10orf131
LOC100169752
NCRNA00093
LOC100270710

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

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

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-1303
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-1974
hsa-mir-9-2
hsa-mir-582
hsa-mir-449b
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-887
ADCY2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGF10
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NDUFS6
NEUROG1
NPR3
NPY6R
OCLN
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
PURA
RAD17
RARS
RASA1
RASGRF2
RPL37
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP1
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
SRP19
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
C5orf13
TRIP13
CNOT8
RAB9P1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5OS
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
SDCCAG10
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
POLS
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
HISPPD1
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
OTP
SKIV2L2
NNT
TTC33
ZNF346
AMACR
SSBP2
BHMT2
TNFAIP8
NIPBL
LOC25845
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
FBXO4
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1L
MAT2B
SLC27A6
SNX24
MRPL22
RNASEN
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MGC29506
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
FAM134B
FAM105A
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
MTMR12
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
PCDH24
GIN1
WDR55
ANKHD1
NSUN2
CCDC99
THG1L
WDR70
AGGF1
WDR41
BRIX1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
ANKH
CCL28
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
AHRR
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1L
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
C5orf23
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
CARD6
TRIM52
HAVCR2
AGXT2L2
C5orf62
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
LMBRD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C1QTNF3
C5orf26
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
HEATR7B2
EGFLAM
PRRC1
C5orf33
UGT3A1
CAPSL
JMY
C5orf58
ZNF474
CCDC127
OR2Y1
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
C5orf37
GPR151
STARD4
WDR36
LOC134466
NUDCD2
UBLCP1
ACOT12
ANKRD43
SHROOM1
C5orf24
SFRS12
C5orf20
SLC38A9
SLC36A2
SPINK5L3
C5orf41
CEP120
LOC153328
TMEM167A
MBLAC2
TMEM161B
SRFBP1
PLEKHG4B
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
LOC153684
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
MGC42105
LIX1
ZNF366
FAM151B
S100Z
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
LVRN
SLC36A1
RICTOR
EIF4E1B
LOC255167
RASGEF1C
ANKRD31
SERINC5
LOC257358
SH3PXD2B
LOC285593
FAM153A
ARL10
C5orf36
GPR150
DTWD2
RELL2
NBPF22P
LOC285627
LOC285629
C5orf51
SLC36A3
KIF4B
OR2V2
FLJ37543
RNF180
SFRS12IP1
ZNF454
C5orf60
LOC285692
LOC285696
RGMB
RFESD
CHSY3
SLC6A19
TMEM173
FAM170A
LOC340074
ARSI
LOC340094
ANKRD34B
PFN3
ZNF879
PLCXD3
IRGM
FBLL1
ACTBL2
FAM174A
MTX3
CATSPER3
SLC6A18
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
C5orf34
MAST4
C5orf25
RNF138P1
LRRC14B
C5orf39
ISCA1L
C5orf48
LOC389332
LOC389333
C5orf46
FLJ41603
FLJ33360
RGS7BP
FLJ44606
SPINK6
ANKHD1-EIF4EBP3
MIR103-1
MIR143
MIR145
MIR146A
MIR218-2
SPINK5L2
C5orf40
MARCH11
LOC441089
FLJ42709
C5orf56
MIR340
C5orf53
GPX8
TIFAB
MIR449A
CTXN3
SNORD72
SNORD95
SNORD96A
ECSCR
TMEM232
C5orf43
GRXCR2
SPINK9
ZFP62
FLJ33630
LOC644936
CCNI2
LOC645323
CBY3
LOC647859
ANKRD33B
GUSBP3
GTF2H2B
FAM153C
LOC653391
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR548C
MIR548D2
MIR580
MIR581
MIR583
MIR585
SNHG4
LOC728264
GTF2H2C
LOC728411
SERF1B
LOC728554
SDHAP3
LOC728613
LOC728723
AACSL
LOC729678
OR4F29
GTF2H2D
SNORD123
MIR886
MIR874
LOC100129716
CCDC152
LRRC70
FAM196B
LOC100132062
LOC100132287
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100286948
TMED7-TICAM2
NCRUPAR
LOC100303749
LOC100310782

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.3.

Table S26. 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 13q32.3.

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
hsa-mir-1267
hsa-mir-623
hsa-mir-92a-1
hsa-mir-622
hsa-mir-1297
hsa-mir-15a
hsa-mir-621
hsa-mir-320d-1
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3L1
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
OR7E37P
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
C13orf1
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NARG1L
RNASEH2B
DHRS12
GRTP1
C13orf34
C13orf18
C13orf23
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
C13orf27
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
C13orf16
LOC121838
LOC121952
CSNK1A1L
RXFP2
C13orf26
SLAIN1
PRR20A
C13orf28
RNF113B
LOC144776
C13orf30
C13orf31
HNRNPA1L2
FAM10A4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
C13orf39
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
LOC220115
LOC220429
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
DKFZp686A1627
HS6ST3
DAOA
C13orf29
ZNF828
OR7E156P
SUGT1L1
SIAH3
KCNRG
FLJ37307
SLC46A3
LOC284232
UBAC2
C1QTNF9
FREM2
NEK5
FAM70B
LOC348021
LOC374491
THSD1P
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
C13orf36
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
ALG11
C13orf37
PCOTH
SNORA27
FLJ44054
LOC643677
LOC646405
PRHOXNB
ZAR1L
LOC646982
SERPINE3
LOC647288
SNORA31
MIR548A2
MIR621
MIR623
FAM155A
C13orf38
PRR20B
PRR20C
PRR20D
PRR20E
LOC100101938
RPL21P28
FKSG29
LOC100188949
LOC100190939
LOC100288730

Arm-level results

Table 3. Get Full Table Arm-level significance table - 14 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.34 | 3.13 | 0.0106 | 0.04 | -1.51 | 0.991
1q | 1572 | 0.56 | 6.73 | 1.67e-10 | 0.00 | -1.7 | 0.991
2p | 753 | 0.14 | -0.2 | 0.987 | 0.00 | -2.35 | 0.991
2q | 1235 | 0.09 | -1.03 | 0.987 | 0.06 | -1.46 | 0.991
3p | 853 | 0.30 | 1.86 | 0.175 | 0.53 | 5.85 | 9.73e-08
3q | 917 | 0.61 | 7.18 | 1.39e-11 | 0.29 | 1.65 | 0.243
4p | 366 | 0.00 | -1.88 | 0.987 | 0.44 | 4.95 | 4.94e-06
4q | 865 | 0.00 | -2.23 | 0.987 | 0.22 | 1.19 | 0.35
5p | 207 | 0.30 | 2.31 | 0.0823 | 0.22 | 1.06 | 0.379
5q | 1246 | 0.09 | -0.867 | 0.987 | 0.38 | 3.75 | 0.000876
6p | 937 | 0.28 | 2.05 | 0.13 | 0.15 | -0.0443 | 0.968
6q | 692 | 0.24 | 1.36 | 0.373 | 0.24 | 1.36 | 0.336
7p | 508 | 0.06 | -1.34 | 0.987 | 0.15 | -0.0538 | 0.968
7q | 1071 | 0.09 | -0.911 | 0.987 | 0.12 | -0.485 | 0.991
8p | 495 | 0.16 | 0.135 | 0.987 | 0.34 | 3.06 | 0.00716
8q | 697 | 0.26 | 1.67 | 0.231 | 0.18 | 0.412 | 0.737
9p | 343 | 0.06 | -1.39 | 0.987 | 0.12 | -0.529 | 0.991
9q | 916 | 0.03 | -1.89 | 0.987 | 0.11 | -0.609 | 0.991
10p | 312 | 0.11 | -0.635 | 0.987 | 0.24 | 1.49 | 0.297
10q | 1050 | 0.07 | -1.24 | 0.987 | 0.21 | 0.886 | 0.431
11p | 731 | 0.04 | -1.55 | 0.987 | 0.31 | 2.7 | 0.0192
11q | 1279 | 0.05 | -1.27 | 0.987 | 0.46 | 5.03 | 4.74e-06
12p | 484 | 0.14 | -0.186 | 0.987 | 0.22 | 1.08 | 0.379
12q | 1162 | 0.03 | -1.9 | 0.987 | 0.11 | -0.616 | 0.991
13q | 554 | 0.00 | -2.23 | 0.987 | 0.22 | 1.2 | 0.35
14q | 1144 | 0.09 | -1.03 | 0.987 | 0.06 | -1.46 | 0.991
15q | 1132 | 0.09 | -1.03 | 0.987 | 0.06 | -1.46 | 0.991
16p | 719 | 0.06 | -1.5 | 0.987 | 0.06 | -1.5 | 0.991
16q | 562 | 0.06 | -1.49 | 0.987 | 0.06 | -1.49 | 0.991
17p | 575 | 0.04 | -1.49 | 0.987 | 0.34 | 3.18 | 0.00568
17q | 1321 | 0.06 | -1.56 | 0.987 | 0.03 | -1.99 | 0.991
18p | 117 | 0.10 | -0.697 | 0.987 | 0.21 | 1.01 | 0.382
18q | 340 | 0.00 | -2.22 | 0.987 | 0.22 | 1.21 | 0.35
19p | 870 | 0.13 | -0.343 | 0.987 | 0.16 | 0.0818 | 0.959
19q | 1452 | 0.21 | 0.871 | 0.748 | 0.07 | -1.25 | 0.991
20p | 295 | 0.19 | 0.748 | 0.806 | 0.00 | -2.26 | 0.991
20q | 627 | 0.33 | 3.07 | 0.0106 | 0.00 | -2.06 | 0.991
21q | 422 | 0.12 | -0.466 | 0.987 | 0.09 | -0.894 | 0.991
22q | 764 | 0.03 | -1.89 | 0.987 | 0.11 | -0.605 | 0.991

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/CESC/1216778/2.GDAC_MergeDataFiles.Finished/CESC.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 36 Input Tumor Samples.

Tumor Sample Names
TCGA-BI-A0VR-01A-11D-A10T-01
TCGA-BI-A0VS-01A-11D-A10T-01
TCGA-BI-A20A-01A-11D-A14V-01
TCGA-C5-A0TN-01A-21D-A14V-01
TCGA-C5-A1BE-01B-11D-A13V-01
TCGA-C5-A1BF-01B-11D-A13V-01
TCGA-C5-A1BI-01B-11D-A13V-01
TCGA-C5-A1BJ-01A-11D-A13V-01
TCGA-C5-A1BK-01B-11D-A13V-01
TCGA-C5-A1BL-01A-11D-A13V-01

Figure 3. Segmented copy number profiles in the input data

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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

- Maintainer = Dan DiCara

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