Kidney Renal Clear 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 2.0.16a (cga svn revision 43808).

Summary

There were 493 tumor samples used in this analysis: 28 significant arm-level results, 12 significant focal amplifications, and 18 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 - 12 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
--- | --- | --- | --- | ---
5q35.1 | 1.3883e-64 | 1.3883e-64 | chr5:157747359-180359088 | 180
3q26.32 | 7.4693e-07 | 7.4693e-07 | chr3:177793108-179141923 | 7
Xq11.2 | 0.00094749 | 0.00094749 | chrX:64003371-64052730 | 0 [ZC4H2]
Xp11.4 | 0.00221 | 0.00221 | chrX:40732510-40742477 | 0 [LOC100132831]
Xp22.2 | 0.0025448 | 0.0025448 | chrX:12175654-12177681 | 1
4q32.1 | 0.0049629 | 0.0049629 | chr4:159611309-161247218 | 7
7q36.3 | 0.033144 | 0.033144 | chr7:113660257-159138663 | 356
1q32.1 | 0.012618 | 0.089594 | chr1:203699717-205218424 | 24
1q24.1 | 0.046529 | 0.089619 | chr1:120522602-208325243 | 839
8q24.22 | 0.14276 | 0.14276 | chr8:71705506-146364022 | 413
17q24.3 | 0.16004 | 0.16004 | chr17:52619790-81195210 | 413
10p14 | 0.18511 | 0.18511 | chr10:1-16776063 | 103

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.1.

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

Genes
EBF1
NPM1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
ADRA1B
BNIP1
CANX
CCNG1
CLTB
NKX2-5
DBN1
DOCK2
DRD1
DUSP1
F12
FABP6
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GRK6
GRM6
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
IL12B
KCNMB1
LCP2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
RARS
SLC34A1
SLIT3
SNCB
STK10
ZNF354A
TTC1
STC2
FGF18
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
ADAMTS2
MAML1
GFPT2
SLU7
RGS14
CPLX2
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
ATP10B
N4BP3
FAF2
WWC1
FBXW11
ZNF346
TSPAN17
PRELID1
MAT2B
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
CCDC99
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
C5orf54
GMCL1P1
RMND5B
CCNJL
PANK3
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
MXD3
THOC3
AGXT2L2
UNC5A
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
PWWP2A
C1QTNF2
ZNF354B
C5orf47
C5orf58
OR2Y1
NUDCD2
UBLCP1
C5orf41
RNF145
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
LOC285626
LOC285627
LOC285629
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
FBLL1
C5orf25
MIR103A1
MIR146A
MIR218-2
FLJ16171
MIR340
LOC643201
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
LOC728554
AACSP1
LOC729678
FAM196B
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR4281
MIR3912
LOC100507387
MIR4634
MIR378E
LOC100859930

Genes in Wide Peak

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

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

Genes
PIK3CA
KCNMB2
KCNMB3
ZNF639
MFN1
GNB4
ZMAT3

Genes in Wide Peak

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

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

Genes
FRMPD4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q32.1.

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

Genes
ETFDH
PPID
RAPGEF2
FNIP2
C4orf45
MIR3688-1
MIR3688-2

Genes in Wide Peak

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

Table S5. 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-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
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
TFEC
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
NAA38
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
MIR3666
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

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

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

Genes
MDM4
ATP2B4
KISS1
PIK3C2B
RBBP5
REN
SNRPE
CNTN2
SOX13
ZC3H11A
TMCC2
LRRN2
PLEKHA6
NFASC
DSTYK
LAX1
ETNK2
LINC00260
PPP1R15B
LOC127841
GOLT1A
LINC00303
TMEM81
ZBED6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q24.1.

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

Genes
ABL2
ARNT
BCL9
ELK4
FCGR2B
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
TPR
PDE4DIP
SLC45A3
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
ADORA1
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
AVPR1B
BGLAP
C4BPA
C4BPB
CACNA1E
CACNA1S
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD34
CD48
CHI3L1
CHIT1
CHRNB2
CKS1B
CLK2
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSRP1
CTSE
CTSK
CTSS
CD55
DHX9
DPT
ECM1
EIF2D
EFNA1
EFNA3
EFNA4
ELF3
ENSA
ETV3
F5
F13B
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GBA
GBAP1
GJA5
GJA8
GLUL
GPR25
HDGF
CFH
CFHR1
CFHR2
MR1
HSPA6
HSPA7
IFI16
IL6R
IL10
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
KISS1
LAD1
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NHLH1
NIT1
NPR1
DDR2
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PRELP
PRKAB2
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPRC
PEX19
RAB13
RABIF
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
CNTN2
VPS72
THBS3
TCHH
TNNI1
TNNT2
TNR
TOP1P1
CCT3
TUFT1
TNFSF4
UCK2
USF1
DAP3
NPHS2
BTG2
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
DYRK3
RGS5
PPFIA4
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
TNFSF18
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
AIM2
RASAL2
ADAMTS4
SEC22B
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
KIF14
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
PIAS3
TIMM17A
LRRN2
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
KDM5B
CFHR4
CFHR3
OCLM
JTB
MTMR11
MLLT11
SLC27A3
IL24
TDRKH
CD160
CELF3
PMF1
DUSP12
VPS45
PLEKHA6
KIAA0907
KIFAP3
ATF6
KIF21B
NMNAT2
NFASC
POGZ
GLT25D2
RGL1
SYT11
PRRC2C
RPRD2
CAMSAP2
SRGAP2
SMG5
NCSTN
CRB1
GPR161
ZNF281
SNAPIN
PHLDA3
RUSC1
CA14
DSTYK
CCDC19
LMOD1
NBPF14
BRP44
OLFML2B
C1orf43
DNM3
TOR1AIP1
CHTOP
LCE2B
OPTC
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
USP21
CACYBP
SLC39A1
RNF115
KLHL20
LAMTOR2
UBE2T
TMOD4
NME7
IL19
CERS2
CRNN
IL20
DCAF8
F11R
GLRX2
BOLA1
ZBTB7B
RRNAD1
ADIPOR1
APH1A
PLEKHO1
ACP6
IER5
UCHL5
C1orf9
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CYB5R1
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
RALGPS2
MSTO1
DARS2
GOLPH3L
KLHDC8A
ETNK2
KIRREL
YY1AP1
YOD1
UBE2Q1
ITLN1
IPO9
C1orf112
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
LHX9
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
KIAA1614
FAM5B
C1orf114
SLAMF7
CADM3
PRUNE
KLHL12
LGR6
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
TOR3A
RFWD2
RGS18
NUCKS1
MRPL9
INTS3
SCNM1
C1orf116
MGC4473
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
C1orf129
TARS2
EDEM3
FLAD1
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
FCAMR
C1orf49
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
LINC00260
FCRLA
ANKRD36BP1
PPP1R15B
MAEL
RGS8
NAV1
SEC16B
AQP10
LHX4
SLAMF9
PYGO2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
PIGM
IGSF8
LEMD1
C1orf85
PGLYRP3
GNRHR2
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
AXDND1
HIST2H3C
ATP6V1G3
OR10J5
DCST2
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
NEK7
ITLN2
CREB3L4
C1orf51
LOC148696
LOC148709
PTPRVP
HFE2
ANKRD35
FAM163A
MFSD4
PM20D1
LELP1
RC3H1
DCST1
METTL11B
FAM78B
SHISA4
BNIPL
LRRC71
PYHIN1
DENND1B
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
FLJ23867
KRTCAP2
CRTC2
TMEM9
SLC41A1
LCE5A
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
SLC9A11
NBPF15
LINC00303
LOC284576
LOC284578
LOC284581
ANKRD34A
RUSC1-AS1
LOC284648
DKFZP564C196
C1orf204
C1orf111
LOC284688
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
ANKRD45
FAM5C
C1orf110
FAM58BP
OR10R2
FCRL6
KCNT2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
CYCSP52
LOC375010
PEAR1
SFT2D2
RPS10P7
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
TMEM81
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
C1orf220
NBPF9
LOC401980
APOBEC4
MIR181B1
MIR199A2
MIR181A1
MIR214
MIR29B2
MIR29C
MIR9-1
RGS21
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
C1orf186
OR10J3
MIR135B
KPRP
LCE6A
SUMO1P3
C1orf98
HIST2H4B
PRR9
MIR488
SNORD74
RPL31P11
LOC641515
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
TMEM183B
FAM72B
PCP4L1
SCARNA3
SCARNA4
SNORA42
SNORA77
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
FAM72A
LOC730102
LOC730159
LOC730227
PPIAL4E
PFN1P2
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131234
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
GM140
LOC100288079
LOC100289211
MIR1231
MIR1278
MIR1295A
MIR548F1
LOC100302401
ZBED6
MIR3119-1
MIR3120
MIR4257
MIR3119-2
MIR4258
MIR3121
MIR3658
LOC100505633
LOC100505666
LOC100505795
LOC100505918
LOC100506023
LOC100506046
KDM5B-AS1
PMF1-BGLAP
LOC100527964
TNFAIP8L2-SCNM1
MIR4424
MIR4735
MIR4654
DNM3OS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.22.

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

Genes
COX6C
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
hsa-mir-1273
hsa-mir-875
hsa-mir-3150
hsa-mir-3149
hsa-mir-2052
ADCY8
ANGPT1
ANXA13
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CYC1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
GEM
GLI4
GML
GPR20
GPT
GRINA
HAS2
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LY6E
LY6H
MATN2
MMP16
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PLEC
PMP2
POLR2K
POU5F1B
PKIA
PTK2
PVT1
PEX2
RAD21
RPL7
RPL8
RPL30
SDC2
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
LY6D
JRK
EIF3H
DGAT1
GPAA1
RIPK2
WISP1
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
LRRC14
TTC35
RIMS2
MTSS1
PTDSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
COLEC10
KHDRBS3
POP1
WWP1
STMN2
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
ZFPM2
HEY1
SCRIB
LRRC6
LY96
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
SNORA72
OPLAH
PABPC1
KCNV1
STAU2
MTBP
EIF2C2
MRPS28
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
FAM82B
ZNF706
VPS28
FAM203A
KCNK9
C8orf55
UBR5
FAM49B
AZIN1
OTUD6B
CHRAC1
GDAP1
EXOSC4
PDP1
CNGB3
LY6K
ESRP1
TMEM70
TRMT12
OXR1
WDYHV1
UBE2W
LAPTM4B
C8orf39
TMEM55A
SLC39A4
SYBU
INTS8
PAG1
GSDMC
JPH1
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
PLEKHF2
ZFAND1
ZFHX4
GSDMD
NIPAL2
BAALC
ZNF696
GRHL2
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SHARPIN
EPPK1
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NACAP1
NCALD
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
PSKH2
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
WDR67
HPYR1
TP53INP1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
TOP1MT
ZNF572
FAM92A1
C8orf38
ABRA
LYPD2
TMEM71
DCAF4L2
RALYL
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
TMEM74
FAM91A1
C8orf84
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
REXO1L1
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
C8orf83
DPY19L4
FBXO43
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
SLC10A5
SPATC1
CA13
LOC389676
RBM12B
FLJ43860
MAFA
LOC392232
GDF6
C8orf59
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
FLJ39080
FLJ46284
FLJ42969
C8orf85
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
ZNF704
C8orf69
LINC00051
C8orf73
SCXB
LINC00535
RAD21-AS1
FABP9
FABP12
FER1L6
MIR599
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR875
MIR937
MIR939
LOC100127983
LOC100128126
LOC100128338
SCXA
LOC100130231
CCDC166
LOC100130301
LRRC69
LOC100131726
LOC100132891
LOC100133669
LOC100192378
LOC100288181
REXO1L2P
LOC100288748
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR2052
MIR1208
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3150B
MIR3610
LOC100507117
ZHX1-C8ORF76
MIR378D2
MIR4661
MIR4663
MIR4472-1
MIR4664
MIR4471
LOC100616530
PCAT1
LINC00536
FSBP

Genes in Wide Peak

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

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

Genes
CD79B
CLTC
DDX5
HLF
PRKAR1A
ASPSCR1
BRIP1
MSI2
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NPTX1
P4HB
PDE6G
PECAM1
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
PPM1D
DGKE
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
RAB40B
TLK2
POLG2
CD300A
TMC6
DDX42
PPM1E
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
SDK2
FAM20A
BCAS3
TMEM104
RNF43
MKS1
C17orf80
CCDC40
WIPI1
SMG8
TMEM100
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45L
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
DNAI2
SMURF2
ENGASE
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
USP32
CBX2
FAM104A
MGC16275
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
DYNLL2
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
NOTUM
TMC8
ANKFN1
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MTVR2
STXBP4
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
LRRC37A3
RNF126P1
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
MIR142
MIR21
MIR301A
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LOC645638
TBC1D3P1-DHX40P1
LOC653653
LINC00338
SCARNA20
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR634
MIR635
MIR636
MIR657
LOC729683
PRCD
MIR454
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3614
MIR3678
MIR3615
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4729
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515

Genes in Wide Peak

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

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

Genes
GATA3
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PHYH
PRKCQ
RSU1
ITGA8
PRPF18
AKR1C3
CDC123
PTER
NMT2
USP6NL
OPTN
NET1
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
SEPHS1
KIN
DIP2C
LARP4B
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
CAMK1D
SFMBT2
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
FBXO18
RBM17
IDI2
UCN3
SFTA1P
LOC219731
UCMA
C10orf111
FAM171A1
BEND7
LOC254312
C10orf47
LOC282980
LOC283070
LOC338588
AKR1CL1
TUBB8
tAKR
C1QL3
LINC00200
LOC399708
LOC399715
FLJ45983
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
ADARB2-AS1
MEIG1
LOC100192204
LOC100216001
MIR1265
MIR3155A
LOC100507034
LOC100507127
MIR4480
MIR3155B

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 - 18 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
--- | --- | --- | --- | ---
3p25.3 | 1.2037e-49 | 5.2132e-24 | chr3:10545784-15710586 | 50
9p21.3 | 4.6075e-21 | 2.333e-17 | chr9:21865498-21997722 | 2
3p21.32 | 8.0315e-50 | 2.7235e-17 | chr3:24533315-53529383 | 340
2q37.3 | 4.3184e-15 | 4.3184e-15 | chr2:237410659-243199373 | 76
1p36.23 | 2.9762e-11 | 5.692e-10 | chr1:1-29567782 | 488
8p23.2 | 1.9387e-08 | 1.9397e-08 | chr8:2079140-6262191 | 1
9p24.1 | 9.5604e-09 | 6.3461e-07 | chr9:8310705-12693402 | 1
6q26 | 2.9852e-09 | 0.0002954 | chr6:107234267-171115067 | 366
4q34.3 | 0.00049564 | 0.00049563 | chr4:173959175-191154276 | 87
1p31.1 | 2.4464e-06 | 0.0005323 | chr1:71699756-74522473 | 2
6q26 | 2.2625e-10 | 0.0005323 | chr6:107234267-171115067 | 366
3p12.2 | 2.5507e-05 | 0.00093209 | chr3:75363575-84688247 | 12
10q23.31 | 0.010251 | 0.010657 | chr10:89574877-90034038 | 3
13q13.3 | 0.02111 | 0.021036 | chr13:1-72013697 | 261
14q24.3 | 0.020747 | 0.021036 | chr14:56181301-107349540 | 493
1q43 | 0.0369 | 0.035464 | chr1:211603844-249250621 | 298
3q11.2 | 0.16064 | 0.15364 | chr3:94709811-162895238 | 440
Xq23 | 0.23084 | 0.23489 | chrX:89573967-155270560 | 507

Genes in Wide Peak

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

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

Genes
PPARG
RAF1
XPC
hsa-mir-4270
BTD
FBLN2
HRH1
RPL32
SLC6A1
SLC6A6
SLC6A11
SYN2
TIMP4
NR2C2
WNT7A
COLQ
SH3BP5
VGLL4
IQSEC1
ATG7
CAND2
NUP210
CAPN7
MKRN2
HACL1
LSM3
C3orf19
TMEM40
ZFYVE20
MRPS25
TMEM43
HDAC11
TSEN2
GRIP2
C3orf20
EAF1
CHCHD4
METTL6
TAMM41
FGD5
LOC285370
LOC285375
COL6A4P1
TPRXL
SNORA7A
LOC100129480
LOC100132526
MIR4270
FGD5-AS1
LOC100505696

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.32.

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

Genes
CTNNB1
MLH1
MYD88
BAP1
SETD2
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
RHOA
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DOCK3
DUSP7
CELSR3
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RARB
SNORA62
RPL29
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
TKT
CLEC3B
TNNC1
TOP2B
UBA7
UBP1
USP4
UQCRC1
VIPR1
ZNF35
IFRD2
MAPKAPK3
SEMA3B
MANF
EOMES
HYAL3
HYAL2
BSN
LIMD1
CCRL2
RPL14
SEC22C
RRP9
LRRFIP2
CACNA2D2
SLC22A14
SLC22A13
SLC4A7
VPRBP
IP6K1
EPM2AIP1
TRANK1
DLEC1
EXOG
XYLB
OXSR1
PDCD6IP
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
CRTAP
NPRL2
CXCR6
CSPG5
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
CLASP2
RAD54L2
STAB1
GPD1L
NBEAL2
KLHL18
LARS2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
DNAH1
HIGD1A
SUSD5
GNL3
RBMS3
SPCS1
PRSS50
RBM15B
GMPPB
VILL
ABHD5
DYNC1LI1
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
C3orf75
SNRK
QRICH1
CMTM6
SLC25A38
ULK4
OXSM
ANO10
DALRD3
NGLY1
DCP1A
GLT8D1
ZNF167
SEMA3G
KIF15
PCBP4
KIAA1143
HHATL
WDR48
RNF123
KIF9
AZI2
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
WDR82
RTP3
ATRIP
NICN1
MON1A
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
ZBTB47
CMTM7
OSBPL10
ZNF501
LRRC3B
GPR62
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf45
CCDC12
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
XIRP1
TTC21A
KLHDC8B
STT3B
ZNF620
ALS2CL
TMIE
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
C3orf23
ZNF660
FLJ39534
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
MIR564
FAM198A
CCR2
SNORD19B
C3orf74
LOC100128640
NRADDP
LOC100132146
BSN-AS2
PRSS46
MIR1226
MIR711
MIR4271
KRBOX1
IQCF4
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4443
MIR4792
MIR4442
LUST

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD99
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

Table S16. 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 9p24.1.

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
ACAT2
AMD1
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GJA1
GPR6
GPR31
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
RPS12
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
NR2E1
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
SNX3
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
AKAP7
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
SEC63
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
OSTM1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TFB1M
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
SOBP
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
HYMAI
PDSS2
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
BEND3
C6orf115
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
FNDC1
RSPO3
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
FAM54A
SFT2D1
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FAM26F
FLJ46906
LOC441177
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
MIR548B
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
ADAM29
SCRG1
FAM149A
FBXO8
DUX2
PDLIM3
GALNT7
CLDN22
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.1.

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

Genes
NEGR1
NEGR1-IT1

Genes in Wide Peak

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

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

Genes
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
ACAT2
AMD1
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GJA1
GPR6
GPR31
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
RPS12
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
NR2E1
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
SNX3
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
AKAP7
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
SEC63
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
OSTM1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TFB1M
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
SOBP
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
HYMAI
PDSS2
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
BEND3
C6orf115
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
FNDC1
RSPO3
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
FAM54A
SFT2D1
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FAM26F
FLJ46906
LOC441177
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
MIR548B
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.2.

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

Genes
hsa-mir-4273
hsa-mir-1324
GBE1
ROBO1
ROBO2
LOC401074
FLJ20518
FAM86DP
ZNF717
FRG2C
MIR1324
MIR4273

Genes in Wide Peak

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

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

Genes
PTEN
CFL1P1
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.3.

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
XPO4
PCDH20
MRP63
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
LINC00550
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3169
MIR3613
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
NDUFB1
SIX6
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
TIMM9
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
C14orf101
CDCA4
C14orf102
ATG2B
UBR7
C14orf105
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
ACTR10
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNTL1
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
C14orf149
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
C14orf37
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
SLC35F4
COX8C
ASPG
RAB15
FLJ31306
TOMM20L
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
C14orf38
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
HNRNPU
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
RPS6KC1
RNU5F-1
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
PPPDE1
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
SLC30A10
ZNF692
IARS2
ENAH
NUP133
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR194-1
MIR215
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
DUSP5P
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
SNORA36B
SNORA16B
LOC728463
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3124
MIR3122
MIR3620
MIR3916
PROX1-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.2.

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

Genes
FOXL2
CBLB
GATA2
MLF1
RPN1
GMPS
TFG
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
AADAC
ACPP
ADCY5
ADPRH
AGTR1
ALCAM
ATP1B3
ATP6V1A
ATR
CASR
CD80
CD86
CD47
COL8A1
CP
CPA3
CPB1
CPOX
CSTA
DRD3
EPHB1
GAP43
GOLGB1
GP9
GPR15
GSK3B
GTF2E1
GYG1
HCLS1
HGD
IL12A
ITGB5
KPNA1
KPNA4
LSAMP
TM4SF1
MBNL1
MCM2
MME
CD200
MYLK
NCK1
NDUFB4
P2RY1
PCCB
PFN2
PIK3CB
PLOD2
PLS1
PLSCR1
PLXNA1
PPP2R3A
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
RHO
RPL24
RYK
SHOX2
SIAH2
SLC15A2
SLCO2A1
HLTF
SSR3
TF
TFDP2
TM4SF4
TRH
TRPC1
UPK1B
UMPS
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
SOX14
BFSP2
RUVBL1
B4GALT4
B3GALNT1
SNX4
NR1I2
MBD4
H1FX
KALRN
SLC33A1
COPB2
CHST2
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
TSC22D2
TOMM70A
P2RY14
SMC4
COX17
CD96
STAG1
ST3GAL6
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
FSTL1
MRPL3
FILIP1L
RNF13
MGLL
MRAS
COPG
MYH15
PLCH1
TMCC1
PLXND1
DNAJC13
U2SURP
C3orf27
ANAPC13
ARMC8
C3orf17
ABI3BP
WWTR1
PVRL3
TIPARP
ARHGEF26
ZBTB20
OR5K1
OR5H1
FAM162A
PCOLCE2
SEC22A
NPHP3
ATP2C1
ZBTB11
MORC1
SERP1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
SCHIP1
PIK3R4
PODXL2
TRAT1
IMPG2
NMD3
COMMD2
A4GNT
DBR1
CLDN18
TIMMDC1
RSRC1
PLA1A
AMOTL2
CCRL1
RAB6B
SELT
FBXO40
P2RY13
IL20RB
GPR87
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
RG9MTD1
SLC41A3
SLC35A5
TMEM45A
IFT57
MSL2
FAIM
SLC25A36
DPPA4
TMEM39A
ABHD10
CDV3
IFT122
TBC1D23
WDR52
EAF2
CLDND1
MUC13
SUCNR1
LXN
C3orf37
MRPS22
NIT2
POGLUT1
BBX
CCNL1
PLSCR2
PLSCR4
PCNP
SENP7
ISY1
HEG1
KIAA1257
ARHGAP31
IFT80
KIAA1407
KIAA1524
SRPRB
BPESC1
EEFSEC
CLSTN2
POPDC2
NFKBIZ
ATG3
MFSD1
CCDC14
P2RY12
TMEM108
OR5H6
OR5H2
ZXDC
ZBED2
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC48
NEK11
UBA5
C3orf36
ARL14
NAA50
CEP63
CEP70
ABTB1
TMEM22
OR5AC2
PARP9
ESYT3
EIF2A
ARL6
ZIC4
ACAD11
CHCHD6
C3orf26
HPS3
SLC12A8
RETNLB
CCDC54
MINA
GPR128
DIRC2
GFM1
C3orf15
PHLDB2
LOC90246
C3orf25
BOC
FAM55C
SPSB4
ACPL2
TXNRD3
OSBPL11
LRRC58
TM4SF18
MED12L
CLRN1-AS1
CPNE4
CCDC58
OTOL1
ZPLD1
CD200R1
DCBLD2
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
GRK7
FAM172BP
RPL32P3
H1FOO
PISRT1
DTX3L
LOC151658
PPM1L
DPPA2
CCDC80
BTLA
ROPN1B
C3orf22
C3orf55
C3orf79
SPICE1
NUDT16P1
LOC152225
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
CHST13
KBTBD12
DHX36
DZIP1L
ALG1L
GABRR3
PTPLB
TIGIT
LOC201651
C3orf58
KIAA2018
ZBTB38
ZDHHC23
NUP210P1
COL6A5
GK5
PLCXD2
GCET2
LSAMP-AS3
SLC9A9
LOC285205
EPHA6
DNAJB8-AS1
RABL3
IGSF10
C3orf33
SLC9A10
LOC285359
ILDR1
TRIM59
TRIM42
RAB43
KY
LOC339874
LOC339894
H1FX-AS1
LOC344595
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
NME9
LNP1
CCDC37
NPHP3-AS1
NMNAT3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIR15B
MIR16-2
MIR198
ARGFX
TMEM30C
ALG1L2
TXNRD3NB
TMEM14E
COL6A4P2
LOC646903
PA2G4P4
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
MIR548A3
MIR567
MIR568
FAM86HP
PRR23A
LOC730091
LOC100009676
LOC100125556
WWTR1-AS1
LOC100129550
ZBTB20-AS1
TIPARP-AS1
LOC100289361
MIR1280
MIR548I1
LOC100302640
MIR548H2
MIR548G
LOC100498859
MIR3919
MIR3921
IQCJ-SCHIP1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
LOC100507032
LOC100507389
ARHGEF26-AS1
LOC100507537
NPHP3-ACAD11
ISY1-RAB43
MIR4796
MIR4788
MIR4446

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq23.

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
hsa-mir-448
hsa-mir-1911
hsa-mir-1264
hsa-mir-4329
hsa-mir-652
hsa-mir-548m
AGTR2
ABCD1
SLC25A5
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
BTK
CAPN6
CD40LG
CDR1
CETN2
CLIC2
CNGA2
COL4A5
COL4A6
CSTF2
CTAG1B
TEX28
DCX
TIMM8A
DIAPH2
DKC1
DNASE1L1
DRP2
TSC22D3
DUSP9
EMD
F8
F9
ACSL4
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
CENPI
G6PD
GABRA3
GABRE
OPN1MW
GDI1
GLA
GLUD2
GRIA3
GUCY2F
HCFC1
HMGB3
HNRNPH2
HPRT1
HTR2C
IDH3G
IDS
IGSF1
IL9R
IL13RA1
IL13RA2
IRAK1
L1CAM
LAMP2
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
NAP1L3
NDUFA1
OCRL
PAK3
PLP1
PLS3
PLXNB3
PRPS1
PSMD10
OPN1LW
RENBP
RPL10
RPL39
RPL36A
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
SERPINA7
TDGF1P3
TSPAN6
TRPC5
UBE2A
VBP1
XPNPEP2
ZIC3
ZNF75D
RNF113A
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
CUL4B
IRS4
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
CLDN2
FAM50A
AIFM1
CXorf1
GPR50
TCEAL1
RAB33A
ARHGEF6
MORF4L2
GPRASP1
ARMCX2
MAGEC1
AMMECR1
ZBTB33
MAMLD1
BCAP31
ODZ1
SPRY3
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
PGRMC1
TMSB15A
MID2
TREX2
SLC6A14
SEPT6
ATP1B4
KCNE1L
LDOC1
FAM127B
IL1RAPL2
SRPK3
SNORA70
SNORA69
SNORD61
NGFRAP1
NOX1
SRPX2
RBMX
PCDH11X
HTATSF1
MCTS1
C1GALT1C1
RPA4
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
WBP5
RAB9B
LUZP4
TFDP3
ARMCX1
MAGEC2
VGLL1
ARMCX3
RBMX2
MST4
SASH3
TAF7L
ARMCX6
WDR44
NUP62CL
TBC1D8B
CXorf48
FAM70A
CXorf57
TMLHE
RBM41
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45B
BEX1
GABRQ
NXT2
NKRF
NXF5
NXF4
NXF3
NXF2
TEX13B
TEX13A
MOSPD1
BEX4
TCEAL7
THOC2
KIAA1210
PCDH19
RGAG1
PDZD4
LRCH2
RAP2C
TMEM35
FAM3A
BCORL1
CXorf56
TNMD
SPANXD
SPANXC
ARMCX5
UPF3B
FUNDC2
PRRG3
BRCC3
NKAP
RNF128
MAP7D3
MORC4
LONRF3
ALG13
TCEAL4
TRMT2B
ESX1
BHLHB9
GPR101
CD99L2
H2AFB3
USP26
TMEM164
PHF6
ZMAT1
RHOXF2
TMEM185A
SLITRK2
BEX2
MGC16121
PNMA6A
TCEAL3
FATE1
HS6ST2
FRMD7
KLHL13
TCEAL8
CHRDL1
CXorf40A
FAM58A
RIPPLY1
MMGT1
SYTL4
PNMA5
GPRASP2
ATG4A
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
CXorf41
MUM1L1
FAM199X
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
RBMXL3
DOCK11
TCEAL2
PABPC5
RAB40A
AMOT
CSAG1
FMR1NB
LOC158696
ARHGAP36
AKAP14
RHOXF1
NKAPP1
TCEAL6
H2BFWT
FAM122B
FAM122C
ZCCHC12
SPANXE
SPANXF1
CXorf61
SLC25A43
NRK
DDX26B
ZNF449
VMA21
TMEM31
CTAG1A
CT47A11
MAGEA2B
RAB40AL
ATP11C
RP1-177G6.2
H2BFM
LOC286437
LOC286467
FAM133A
TMSB15B
LINC00204B
BEX5
TCEAL5
LOC340544
VSIG1
DCAF12L2
ZCCHC16
LHFPL1
SOWAHD
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
ARL13A
LINC00086
MCART6
DKFZp686D0853
XKRX
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
LOC442459
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR448
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
CT47B1
LOC643486
ZCCHC18
CXorf69
LINC00087
CT47A7
MIR542
SNORA35
SNORA36A
SNORA56
SNORD96B
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
NXF2B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
CT45A2
H2BFXP
MIR767
MIR766
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129520
LOC100129662
HSFX2
CXorf64
LOC100131434
ARMCX4
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
LOC100287765
MIR1184-1
MIR1912
MIR1298
MIR1256
MIR320D2
MIR1277
MIR1911
MIR1264
SLC25A5-AS1
MIR718
MIR764
MIR2114
LOC100329135
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
MIR4329
HSFX1
LOC100506757
CT47A12
LOC100507404
ARMCX5-GPRASP2
RPL36A-HNRNPH2
MAGEA10-MAGEA5
MIR3978

Arm-level results

Table 3. Get Full Table Arm-level significance table - 28 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.04 | -3.16 | 1 | 0.12 | 3.34 | 0.0014
1q | 1955 | 0.10 | 1.23 | 0.312 | 0.08 | -0.311 | 1
2p | 924 | 0.15 | 2.39 | 0.0284 | 0.03 | -5.14 | 1
2q | 1556 | 0.15 | 3.96 | 0.000136 | 0.03 | -4.34 | 1
3p | 1062 | 0.08 | -1.2 | 1 | 0.75 | 45.2 | 0
3q | 1139 | 0.13 | 1.4 | 0.25 | 0.23 | 8.48 | 0
4p | 489 | 0.02 | -6.23 | 1 | 0.14 | 1.45 | 0.196
4q | 1049 | 0.02 | -5.67 | 1 | 0.13 | 1.7 | 0.128
5p | 270 | 0.36 | 15.5 | 0 | 0.02 | -5.99 | 1
5q | 1427 | 0.39 | 21.8 | 0 | 0.01 | -4.96 | 1
6p | 1173 | 0.02 | -5.52 | 1 | 0.20 | 6.65 | 7.14e-11
6q | 839 | 0.02 | -5.93 | 1 | 0.25 | 9.48 | 0
7p | 641 | 0.32 | 13.9 | 0 | 0.01 | -6.23 | 1
7q | 1277 | 0.33 | 16.4 | 0 | 0.01 | -5.62 | 1
8p | 580 | 0.05 | -4.19 | 1 | 0.29 | 11.6 | 0
8q | 859 | 0.11 | -0.019 | 1 | 0.16 | 2.76 | 0.0088
9p | 422 | 0.03 | -5.46 | 1 | 0.30 | 11.4 | 0
9q | 1113 | 0.03 | -4.89 | 1 | 0.30 | 13.7 | 0
10p | 409 | 0.03 | -5.81 | 1 | 0.13 | 0.408 | 0.759
10q | 1268 | 0.02 | -5.22 | 1 | 0.17 | 5 | 1.13e-06
11p | 862 | 0.05 | -4.35 | 1 | 0.03 | -5.42 | 1
11q | 1515 | 0.05 | -3.65 | 1 | 0.04 | -3.8 | 1
12p | 575 | 0.23 | 7.21 | 1.83e-12 | 0.01 | -6.47 | 1
12q | 1447 | 0.23 | 9.74 | 0 | 0.01 | -5.75 | 1
13q | 654 | 0.05 | -4.45 | 1 | 0.14 | 1.4 | 0.2
14q | 1341 | 0.05 | -3.09 | 1 | 0.43 | 24.2 | 0
15q | 1355 | 0.05 | -3.73 | 1 | 0.07 | -1.89 | 1
16p | 872 | 0.20 | 5.94 | 7.19e-09 | 0.03 | -5.53 | 1
16q | 702 | 0.18 | 4.37 | 2.5e-05 | 0.04 | -5.05 | 1
17p | 683 | 0.05 | -4.67 | 1 | 0.10 | -1.53 | 1
17q | 1592 | 0.06 | -2.81 | 1 | 0.06 | -2.37 | 1
18p | 143 | 0.06 | -4.14 | 1 | 0.20 | 4.1 | 7.52e-05
18q | 446 | 0.06 | -3.87 | 1 | 0.20 | 5.13 | 6.43e-07
19p | 995 | 0.10 | -1.02 | 1 | 0.02 | -5.77 | 1
19q | 1709 | 0.10 | 0.886 | 0.501 | 0.01 | -5.67 | 1
20p | 355 | 0.21 | 5.55 | 6.28e-08 | 0.02 | -6.17 | 1
20q | 753 | 0.21 | 6.55 | 1.6e-10 | 0.02 | -6.22 | 1
21q | 509 | 0.10 | -1.36 | 1 | 0.11 | -0.717 | 1
22q | 921 | 0.08 | -2.41 | 1 | 0.08 | -2.41 | 1
Xq | 1312 | 0.06 | -2.78 | 1 | 0.12 | 1.02 | 0.361

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRC/1971234/2.GDAC_MergeDataFiles.Finished/KIRC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 493 Input Tumor Samples.

Tumor Sample Names
TCGA-A3-3306-01A-01D-0858-01
TCGA-A3-3307-01A-01D-0858-01
TCGA-A3-3308-01A-02D-1322-01
TCGA-A3-3311-01A-02D-1322-01
TCGA-A3-3313-01A-02D-1322-01
TCGA-A3-3316-01A-01D-0858-01
TCGA-A3-3317-01A-02D-1322-01
TCGA-A3-3319-01A-02D-1322-01
TCGA-A3-3320-01A-02D-1322-01
TCGA-A3-3322-01A-02D-1322-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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