SNP6 Copy number analysis (GISTIC2)
Testicular Germ Cell Tumors (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1M044B9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1M044B9
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 2.0.21 (Firehose task version: 127).

Summary

There were 150 tumor samples used in this analysis: 27 significant arm-level results, 15 significant focal amplifications, and 32 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 15 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
12p13.33 | 2.9312e-21 | 4.565e-16 | chr12:1-11799340 | 196
4q12 | 5.0882e-09 | 5.0882e-09 | chr4:55115758-57515684 | 24
12p12.1 | 1.8303e-22 | 1.4226e-08 | chr12:21282954-28751389 | 49
22q11.21 | 2.3802e-06 | 2.3802e-06 | chr22:18613558-22141824 | 100
8q11.23 | 1.2888e-05 | 1.2888e-05 | chr8:54495678-57712567 | 28
3q27.3 | 7.3752e-05 | 7.3752e-05 | chr3:164340364-194094109 | 196
20q11.21 | 8.2343e-05 | 8.2343e-05 | chr20:26197900-29850834 | 3
12q15 | 0.00039669 | 0.00039669 | chr12:69164647-72373494 | 26
2p24.1 | 0.0022955 | 0.0022955 | chr2:1-50469812 | 336
7p22.1 | 0.020942 | 0.020942 | chr7:1-10259096 | 93
16q21 | 0.029676 | 0.029676 | chr16:31845698-71612345 | 299
12p11.21 | 1.7975e-16 | 0.032655 | chr12:29472999-39228082 | 34
7q11.22 | 0.060793 | 0.060793 | chr7:63322037-111706330 | 405
1q21.2 | 0.093723 | 0.093723 | chr1:75763492-207387595 | 1163
8q23.3 | 0.13957 | 0.13957 | chr8:70954721-146364022 | 443

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
CCND2
KDM5A
ZNF384
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
C1R
SCARNA12
DSTNP2
RPL13P5
RN7SL380P
SCARNA11|ENSG00000251898.1
SCARNA10
MRPL51
RN7SL391P
RN7SL69P
NDUFA9
C12orf5
FKBP4
CBX3P4
CACNA1C
LINC00940
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
A2M
APOBEC1
C1S
C3AR1
CD4
CD9
CD27
CD69
CHD4
ATN1
PHC1
ENO2
FGF6
FOXM1
GAPDH
GNB3
KCNA1
KCNA5
KCNA6
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LTBR
M6PR
NINJ2
NOP2
NTF3
OLR1
PRB1
PRB3
PRB4
PRH1
PTMS
PTPN6
PEX5
PZP
RAD52
SCNN1A
SLC2A3
SLC6A12
SLC6A13
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
YBX3
DYRK4
CD163
GDF3
CLSTN3
NCAPD2
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
RAD51AP1
KLRAP1
TSPAN9
PRR4
PHB2
KLRK1
ERC1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
COPS7A
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
ING4
CLEC1B
CLEC1A
C1RL
KLRF1
TAPBPL
FAM90A1
PLEKHG6
STYK1
FOXJ2
ITFG2
PRMT8
PARP11
ANO2
C12orf4
LPAR5
AICDA
RIMKLB
CLEC7A
WNK1
ADIPOR2
NANOG
WNT5B
CDCA3
RHNO1
NRIP2
RBP5
CCDC77
ACRBP
SPSB2
EFCAB4B
CACNA2D4
CLEC6A
C12orf57
TMEM52B
SLC2A14
A2ML1
FBXL14
CLEC12A
CLECL1
CLEC4C
PIANP
DCP1B
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CD163L1
B4GALNT3
CLEC9A
CLEC4D
ACSM4
TAS2R42
DPPA3
NANOGNB
CLEC2A
CLEC12B
LINC00937
MIR141
MIR200C
IQSEC3
ZNF705A
PRB2
LRTM2
MIR3649

Genes in Wide Peak

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

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

Genes
KDR
KIT
PDGFRA
FIP1L1
ARL9
SRP72
RNA5SP162
KIAA1211
RNA5SP161
RN7SKP30
RN7SL822P
RN7SL424P
PPAT
CLOCK
CEP135
PAICS
NMU
EXOC1
TMEM165
SRD5A3
HOPX
AASDH
PDCL2
THEGL

Genes in Wide Peak

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

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

Genes
KRAS
RNA5SP355
RN7SKP15
ARNTL2
TM7SF3
RNA5SP354
SSPN
RN7SKP262
RN7SL38P
C12orf39
PYROXD1
BCAT1
GYS2
IAPP
ITPR2
KCNJ8
LDHB
LRMP
PTHLH
RECQL
ST8SIA1
SLCO1A2
SOX5
PPFIBP1
MED21
C2CD5
ABCC9
SLCO1B1
RASSF8
STK38L
FGFR1OP2
GOLT1B
CASC1
CCDC91
ETNK1
ASUN
CMAS
KLHL42
MRPS35
BHLHE41
LINC00477
LYRM5
IFLTD1
C12orf77
SMCO2
REP15
C12orf71
MIR920
MANSC4

Genes in Wide Peak

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

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

Genes
CLTCL1
RN7SL280P
RN7SKP221
SCARNA18|ENSG00000252605.1
SCARNA17|ENSG00000252143.1
snoU13|ENSG00000252799.1
TMEM191C
snoU13|ENSG00000252402.1
SCARNA17|ENSG00000252020.1
SCARNA18|ENSG00000252314.1
RN7SKP63
FAM230C
GGT2
FAM230B
POM121L7
BCRP2
P2RX6P
P2RX6
RN7SL389P
POM121L4P
SMPD4P1
RN7SL812P
USP41
FAM230A
RN7SKP131
SCARNA18|ENSG00000252024.1
SCARNA17|ENSG00000252571.1
snoU13|ENSG00000271796.1
PI4KAP1
GGTLC3
MIR1286
SNORA77|ENSG00000264346.1
MIR1306
MIR4761
GP1BB
MRPL40
RN7SL168P
SNORA15|ENSG00000251940.1
GSC2
DGCR5
GGT3P
PEX26
ARVCF
COMT
CRKL
SERPIND1
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
SNAP29
DGCR2
TXNRD2
USP18
HIC2
TSSK2
SDF2L1
PPIL2
TRMT2A
YPEL1
ZDHHC8
MED15
TUBA8
DGCR8
GNB1L
RTN4R
C22orf29
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
TUBA3FP
C22orf39
TANGO2
AIFM3
RIMBP3C
YDJC
CCDC116
PI4KAP2
MIR130B
MIR185
RIMBP3B
MIR649
MIR301B
MIR3618

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.23.

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

Genes
PLAG1
TCEA1
CHCHD7
LINC00968
SDR16C6P
SNORA3|ENSG00000221093.1
SNORD54
RPS20
RN7SL323P
RN7SL798P
SNORA1|ENSG00000199405.1
RNA5SP265
XKR4
RN7SL250P
RNU105C
RNU6ATAC32P
MRPL15
LYN
MOS
PENK
RP1
RGS20
LYPLA1
ATP6V1H
SOX17
TGS1
TMEM68
SDR16C5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q27.3.

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

Genes
PIK3CA
BCL6
EIF4A2
ETV5
LPP
SOX2
LINC00887
RN7SL215P
RN7SL447P
snoU13|ENSG00000238902.1
RN7SKP222
RN7SKP296
RN7SL486P
MIR944
MIR28
snoU13|ENSG00000239093.1
RTP4
SNORA4|ENSG00000263776.1
SNORA63|ENSG00000200320.1
SNORA81|ENSG00000221420.2
SNORA63|ENSG00000200418.1
SNORD2|ENSG00000238942.1
KNG1
CRYGS
RN7SL637P
TRA2B
MIR548AQ
SENP2
snoU13|ENSG00000239146.1
SNORD66|ENSG00000212158.1
MIR1224
CYP2AB1P
SNORA4|ENSG00000251730.1
SNORA63|ENSG00000199363.1
SNORA81|ENSG00000253092.1
SNORA63|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
RN7SL229P
U8|ENSG00000201810.1
RNA5SP149
snoU13|ENSG00000239096.1
GNB4
SNORA25|ENSG00000201957.1
RNA5SP148
SNORA18|ENSG00000200288.1
RN7SKP52
LINC00578
LINC00501
RNA5SP147
snoU13|ENSG00000271842.1
MIR4789
RN7SKP40
RN7SKP234
snoU13|ENSG00000239141.1
SNORA72|ENSG00000200355.1
RN7SL141P
PP13439
snoU13|ENSG00000238359.1
MIR569
RNY5P3
CLDN11
TERC
EGFEM1P
RN7SKP298
ACTL6A
AHSG
BCHE
AP2M1
CLCN2
CPN2
DGKG
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
HRG
HES1
IL1RAP
NDUFB5
OPA1
SERPINI1
SERPINI2
PLD1
POLR2H
PRKCI
MASP1
PSMD2
RFC4
SI
ST6GAL1
SKIL
SLC2A2
SST
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
ECE2
ABCC5
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
TNIK
MCF2L2
ATP11B
VPS8
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
KLHL24
TBCCD1
LEPREL1
ABCF3
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
MAGEF1
ZMAT3
FNDC3B
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
SPATA16
B3GNT5
ATP13A4
ACTRT3
KLHL6
VWA5B2
TMEM41A
CAMK2N2
RPL39L
DNAJC19
FAM131A
LRRC15
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
CCDC50
PYDC2
HTR3C
LIPH
HTR3D
RPL22L1
NAALADL2
UTS2B
HTR3E
C3orf70
TPRG1
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
TMEM212
C3orf65
GMNC
MIR551B
MIR4448

Genes in Wide Peak

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

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

Genes
DEFB115
FRG1B
MIR663A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q15.

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

Genes
MDM2
RAB21
SNORA17|ENSG00000212461.1
MYRFL
RN7SL804P
SLC35E3
CPM
LYZ
CNOT2
PTPRB
PTPRR
TSPAN8
YEATS4
LGR5
CCT2
FRS2
CPSF6
KCNMB4
TMEM19
TBC1D15
THAP2
RAB3IP
TPH2
BEST3
ZFC3H1
LRRC10

Genes in Wide Peak

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

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

Genes
ALK
DNMT3A
MSH6
MSH2
MYCN
NCOA1
EML4
SNORA75|ENSG00000212580.1
RN7SKP224
KCNK12
MIR559
RN7SKP119
BCYRN1
RHOQ
RN7SL817P
RN7SL414P
SLC3A1
snoU13|ENSG00000239052.1
RN7SKP66
SNORD75|ENSG00000221300.1
snoZ247
HNRNPA1P57
SNORA67|ENSG00000252473.1
RN7SL96P
GEMIN6
LINC00211
RN7SL602P
RNA5SP92
RNA5SP91
SNORD112|ENSG00000252502.1
LINC00486
MIR4765
MIR558
YIPF4
DPY30
SRD5A2
EHD3
RNA5SP90
SNORA64|ENSG00000207187.1
RN7SL516P
SNORD53
SNORD92
RNA5SP89
FOSL2
MIR4263
RBKS
SNORA36|ENSG00000206731.1
UCN
TCF23
KCNK3
RN7SL856P
EFR3B
SNORD14
PTRHD1
RNA5SP88
SCARNA21|ENSG00000251805.1
PFN4
RN7SL610P
UBXN2A
RN7SKP27
RNA5SP87
RN7SL117P
TDRD15
GDF7
RNA5SP86
RN7SL140P
LINC00954
SNORA40|ENSG00000212455.1
RN7SKP168
SNORA40|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13|ENSG00000238371.1
LINC00276
MIR3125
SNORD18|ENSG00000238503.1
MIR548S
RN7SL674P
RNA5SP85
RNA5SP84
LINC00570
RN7SL832P
SNORA80B
SNORA51|ENSG00000206898.1
RN7SL66P
SNORA2|ENSG00000206647.1
SNORA26|ENSG00000212558.1
snoU13|ENSG00000238462.1
IAH1
snoU13|ENSG00000238888.1
MBOAT2
RNU6ATAC37P
RN7SKP112
FLJ30594
SNORA31|ENSG00000252238.1
RN7SL531P
DCDC2C
SNORA73|ENSG00000252531.1
snoU13|ENSG00000238722.1
TMEM18
FAM110C
ACP1
ADCY3
APOB
RHOB
ZFP36L2
CAD
CALM2
CENPA
CYP1B1
DDX1
DTNB
E2F6
EPAS1
FKBP1B
FSHR
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
FOXN2
ID2
KCNF1
KCNS3
KHK
KIF3C
LHCGR
LTBP1
EPCAM
MATN3
MPV17
ODC1
VIT
PIGF
POMC
PPM1B
PPM1G
PPP1CB
PRKCE
EIF2AK2
RPS7
RRM2
SDC1
SRSF7
SIX3
SLC8A1
SOS1
SOX11
SPAST
STRN
ADAM17
TPO
TSSC1
VSNL1
XDH
SLC30A3
PXDN
KLF11
MAP4K3
ASAP2
SLC5A6
EIF2B4
TAF1B
COX7A2L
ITGB1BP1
NRXN1
OTOF
CRIPT
ROCK2
TP53I3
MRPL33
BRE
PREPL
FEZ2
SOCS5
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
LRPPRC
PDIA6
CEBPZ
CDC42EP3
CGREF1
SIX2
RAB10
YWHAQ
GTF2A1L
STON1
EMILIN1
GPN1
MAPRE3
SLC4A1AP
MYT1L
WDR43
LPIN1
PUM2
HAAO
NTSR2
PRKD3
RASGRP3
QPCT
FAM98A
IFT172
SH3YL1
TRIB2
GRHL1
NRBP1
ITSN2
MEMO1
TRAPPC12
CRIM1
DNAJC27
ATRAID
NBAS
DYNC2LI1
SF3B14
YPEL5
CPSF3
SNTG2
ATAD2B
HEATR5B
TMEM214
SLC35F6
TRMT61B
SRBD1
ASXL2
ADI1
NDUFAF7
TTC27
SLC30A6
ALLC
DPYSL5
TRIM54
TTC7A
BIRC6
KIDINS220
MTA3
WDR35
RDH14
NLRC4
AGBL5
C2orf43
THADA
ATL2
ABCG5
ABCG8
HS1BP3
FNDC4
COLEC11
CENPO
GALNT14
CCDC121
SMC6
CLIP4
CAMKMT
NOL10
FBXO11
C2orf44
THUMPD2
FAM49A
LBH
C2orf16
ZNF512
ABHD1
EPT1
MCFD2
ATP6V1E2
DHX57
PKDCC
RSAD2
CAPN13
DRC1
HNRNPLL
NT5C1B
KLHL29
PPP1R21
CMPK2
CIB4
PLEKHH2
OSR1
TTC32
ZNF513
GALM
TMEM178A
C2orf50
PQLC3
GAREML
PLB1
MYADML
FAM84A
RMDN2
GPR113
OXER1
FAM179A
KCNG3
CYS1
KRTCAP3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
GPATCH11
FAM150B
C2orf61
DNAJC5G
C2orf70
C2orf53
LINC00299
MSGN1
CDKL4
GEN1
C2orf48
FAM228B
MFSD2B
C2orf71
TMEM247
SULT6B1
LINC00487
C2orf91
CAPN14
FAM228A
RAD51AP2
MORN2
OST4
ARHGEF33
MIR1301
MIR4261
MIR4262
MIR3681
MIR4757
MIR4429
MIR548AD

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.1.

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

Genes
PMS2
CARD11
RPA3
PMS2CL
GRID2IP
FLJ20306
RN7SL851P
SNORA42|ENSG00000207217.1
RN7SL556P
ZNF815P
MIR589
snoU13|ENSG00000238394.1
ZNF890P
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
ACTB
GNA12
GPER
ICA1
LFNG
NUDT1
PDGFA
PRKAR1B
RAC1
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KDELR2
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
C1GALT1
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM220A
ZFAND2A
GLCCI1
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
SLC29A4
RSPH10B
COL28A1
OCM
RSPH10B2
ANKRD61
MIR3683
MIR4656

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q21.

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

Genes
CDH11
CBFB
CDH1
CYLD
HERPUD1
TAT
SNORD112|ENSG00000251700.1
RNU6ATAC25P
FLJ00418
SNORD111|ENSG00000221066.1
SNORD111B
SF3B3
RN7SL279P
RN7SL407P
snoU13|ENSG00000238734.1
FKSG63
PDXDC2P
MIR140
SNORA62|ENSG00000252443.1
snoU13|ENSG00000238683.1
COG8
CHTF8
RPS2P45
RNA5SP429
snoU109|ENSG00000252640.1
snoU109|ENSG00000252040.1
snoU13|ENSG00000238343.1
SLC7A6OS
SNORA48|ENSG00000212445.1
CTRL
NUTF2
RN7SKP118
TRADD
RN7SL543P
LINC00920
RNA5SP428
LINC00922
snoU13|ENSG00000238507.1
RN7SKP76
RN7SL143P
SLC38A7
snoU13|ENSG00000239121.1
SNORA50|ENSG00000206952.2
SNORA46|ENSG00000207493.1
RN7SL645P
TEPP
MT1DP
MT1M
MT1E
MT1L
MT2A
OGFOD1
MIR3935
IRX6
RN7SL841P
CRNDE
FTO
RNA5SP427
snoU13|ENSG00000238645.1
CASC16
LINC00919
RN7SKP142
HNRNPA1P48
RNA5SP426
NKD1
SNORD112|ENSG00000252077.1
snoU13|ENSG00000238544.1
SNORA70|ENSG00000252526.1
RNY4P3
snoU13|ENSG00000239038.1
snoU13|ENSG00000239013.1
RN7SL54P
LONP2
RNA5SP425
RNA5SP424
ITFG1
snoU13|ENSG00000238834.1
MYLK3
VPS35
ANKRD26P1
RNA5SP423
RNA5SP422
RNA5SP421
RNA5SP420
RNA5SP419
RNA5SP418
RNA5SP417
RNA5SP416
RNA5SP415
RNA5SP413
RNA5SP410
RNA5SP409
RNA5SP408
RNA5SP407
RNA5SP406
LINC00273
ARHGAP23P1
HERC2P8
HERC2P5
TP53TG3
TP53TG3D
HERC2P4
AARS
ADCY7
AGRP
AMFR
BBS2
CA7
CALB2
CBLN1
CDH3
CDH5
CDH8
CDH16
CES1
CETP
CNGB1
CSNK2A2
NQO1
DYNC1LI2
E2F4
GNAO1
GOT2
HAS3
HSD11B2
HSF4
KIFC3
LCAT
MMP2
MMP15
MT1A
MT1B
MT1F
MT1G
MT1H
MT1JP
MT1X
MT3
NFATC3
PHKB
POLR2C
PSKH1
PSMB10
RBL2
RRAD
SALL1
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
TERF2
TK2
ZNF19
ZNF23
CES2
NAE1
NOL3
SLC7A6
ATP6V0D1
GPR56
N4BP1
NUP93
CHST4
IRX5
DNAJA2
KATNB1
ZNF267
CTCF
NFAT5
NUDT21
WWP2
DDX19B
CNOT1
ZNF423
RPGRIP1L
CES3
ARL2BP
ORC6
EDC4
PLA2G15
COG4
PLEKHG4
LRRC29
VPS4A
TOX3
NOB1
CCDC113
TMEM208
C16orf80
FHOD1
BRD7
ZDHHC1
PARD6A
PLLP
CKLF
NIP7
FAM96B
TPPP3
CES1P1
PRMT7
HYDIN
DUS2L
CHTF8
LPCAT2
HEATR3
PDPR
LRRC36
DDX19A
FBXL8
SMPD3
VAC14
DOK4
FTSJD1
DDX28
TSNAXIP1
COQ9
CIAPIN1
THAP11
PDP2
ZNF319
RANBP10
NOD2
PDF
DPEP2
DPEP3
PAPD5
AKTIP
GINS3
NDRG4
ACD
IRX3
FAM65A
TANGO6
USB1
ELMO3
SHCBP1
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
CYB5B
GFOD2
NETO2
ENKD1
NLRC5
CCDC135
CAPNS2
MT4
GPT2
B3GNT9
CIRH1A
ABCC11
RSPRY1
MTSS1L
CCDC102A
ABCC12
CMTM1
EXOSC6
NRN1L
CMTM3
C16orf78
SNX20
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
IL34
TMED6
FUK
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
CCDC79
CES4A
EXOC3L1
CLEC18C
CLEC18A
SLC6A10P
C16orf87
C16orf97
C16orf86
MIR328
KIAA0895L
TP53TG3C
TP53TG3B
MIR1538

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p11.21.

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

Genes
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112|ENSG00000251863.1
SNORA25|ENSG00000252204.1
STMN1P1
snoU13|ENSG00000239033.1
snoU13|ENSG00000238661.1
SNORA75|ENSG00000212533.1
LINC00941
RNA5SP356
U3|ENSG00000253052.1
ERGIC2
BICD1
DDX11
PKP2
DNM1L
IPO8
YARS2
KIAA1551
FAR2
FAM60A
CAPRIN2
TMTC1
FGD4
CPNE8
DENND5B
AMN1
METTL20
OVCH1
H3F3C
TSPAN11

Genes in Wide Peak

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

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

Genes
CDK6
ELN
HIP1
AKAP9
SBDS
RNA5SP237
snoU13|ENSG00000238922.1
FLJ00325
U3|ENSG00000238297.1
snoU109|ENSG00000238832.1
RNA5SP236
SNORD112|ENSG00000251911.1
RN7SL8P
LHFPL3
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
MIR4658
MIR106B
MIR93
MIR25
AZGP1P1
SNORA40|ENSG00000222966.1
CYP3A4
snoU13|ENSG00000239133.1
MYH16
snoU13|ENSG00000238459.1
MIR3609
RN7SL13P
RN7SL478P
RN7SKP104
RN7SL252P
SHFM1
MIR591
PON1
snoU13|ENSG00000238384.1
RN7SKP129
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
snoU13|ENSG00000238739.1
DPY19L2P4
SNORA67|ENSG00000207094.1
snoU13|ENSG00000238587.1
LINC00972
SEMA3A
RNA5SP235
MIR1255B1
RN7SL35P
RN7SL869P
RNA5SP234
RSBN1L
snoU13|ENSG00000238453.1
RN7SL212P
snoU13|ENSG00000238935.1
TMEM120A
SNORA14A
CCL24
RN7SL642P
NSUN5P1
STAG3L1
GATSL2
GATSL1
STAG3L2
RNA5SP233
MIR590
LINC00035
RN7SL265P
GTF2IRD2P1
NCF1B
RN7SL625P
RN7SL377P
RNA5SP232
RN7SKP75
RN7SL371P
RNA5SP231
PMS2P4
RN7SL43P
GTF2IRD1P1
snoU13|ENSG00000238841.1
snoU13|ENSG00000252265.1
VKORC1L1
SNORA15|ENSG00000206785.1
SNORA22|ENSG00000206634.1
CCT6P1
INTS4L2
SNORA63|ENSG00000200130.1
SNORA63|ENSG00000252102.1
INTS4L1
SNORA15|ENSG00000207062.1
SNORA22|ENSG00000207344.1
CCT6P3
ZNF117
ZNF273
ZNF736
ZNF727
ACHE
ASL
ASNS
AZGP1
CACNA2D1
CALCR
KRIT1
CD36
AP1S1
COL1A2
CLDN4
CLDN3
CUX1
CYP3A7
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
SLC26A3
EPHB4
EPO
GNAI1
GNB2
GNGT1
GPR22
GRM3
GTF2I
GUSB
HGF
AGFG2
HSPB1
LAMB1
LIMK1
LRCH4
MCM7
DNAJB9
MDH2
NPTX2
NRCAM
OCM2
ORC5
SERPINE1
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PMS2P3
POLR2J
PON2
PON3
POR
PRKAR2B
RELN
PSMC2
PTPN12
RFC2
SRI
SRPK2
STX1A
SYPL1
TAC1
TAF6
TFR2
TRIP6
VGF
ZAN
EIF4H
CLIP2
LAT2
YWHAG
ZNF3
ZKSCAN1
ZSCAN21
ZNF138
ZP3
MTERF
TFPI2
TRRAP
FZD1
FZD9
TPST1
FKBP6
BUD31
SGCE
PLOD3
BAZ1B
CLDN12
AP4M1
BCL7B
PMPCB
ATP5J2
GTF2IRD1
SEMA3E
DOCK4
MAGI2
POM121
DMTF1
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
BET1
CCL26
COG5
ZNHIT1
SEMA3C
ARPC1A
STAG3
FGL2
CPSF4
DBF4
COPS6
DUS4L
TP53TG1
PDAP1
LAMB4
LMTK2
POMZP3
PEG10
ZKSCAN5
CLDN15
BRI3
TECPR1
PTCD1
AUTS2
FBXO24
TBL2
STEAP1
HBP1
DNAJC2
CRCP
RABGEF1
PCLO
PILRA
PNPLA8
FIS1
MLXIPL
ACTL6B
ZNF107
SRRT
STYXL1
ASB4
ADAM22
GSAP
ANKIB1
PUS7
LRRN3
CROT
ALKBH4
SAMD9
ZCWPW1
TMEM248
TYW1
C7orf43
PPP1R9A
CCDC132
NSUN5
KMT2E
BAIAP2L1
SLC25A40
BCAP29
MEPCE
SLC12A9
ACN9
SMURF1
PHTF2
RHBDD2
CCDC146
RINT1
WBSCR17
MOSPD3
GIGYF1
CYP3A43
CASD1
STAG3L4
ZNF655
PVRIG
TMEM243
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ORAI2
UPK3B
OR2AE1
WBSCR16
TSC22D4
TRIM56
ABHD11
CALN1
ARMC10
IMMP2L
RBM48
ZNF394
GTF2IRD2
DNAJC30
TMEM60
GTPBP10
TRIM4
MYL10
DTX2
WBSCR22
WBSCR28
TRIM50
COL26A1
SRCRB4D
MUC17
RUNDC3B
KCTD7
C7orf66
WBSCR27
VPS37D
ZNF92
ZNF679
THAP5
CCDC71L
BHLHA15
SAMD9L
C7orf62
ZNF804B
ZSCAN25
FAM200A
PPP1R35
GPC2
SRRM3
KIAA1324L
LRWD1
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
MBLAC1
FAM133B
NSUN5P2
STEAP2
LINC00174
ZNF789
ZNF680
GNAT3
MOGAT3
GJC3
DPY19L2P2
GATS
TRIM73
NAT16
SLC26A5
TRIM74
GTF2IRD2B
LAMTOR4
RPL13AP17
LRRD1
C7orf76
KPNA7
C7orf61
UFSP1
TYW1B
SPDYE3
SPDYE2
STAG3L3
POLR2J3
NCF1
POM121C
EFCAB10
UPK3BL
RASA4B
SPDYE2B
MIR548O
MIR4284
MIR4652
MIR4651
MIR5692C2
MIR5692A1

Genes in Wide Peak

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

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

Genes
SDHC
ABL2
ARNT
BCL9
ELK4
FCGR2B
MDM4
MUC1
NOTCH2
NRAS
NTRK1
PBX1
PRCC
TPM3
TPR
BCL10
PDE4DIP
TRIM33
RBM15
SLC45A3
snoU13|ENSG00000238401.1
FAIM3
IL20
SNORD112|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72|ENSG00000201944.1
SNORD112|ENSG00000252946.1
SCARNA20|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77|ENSG00000221643.1
RABIF
PCAT6
SNORA70|ENSG00000253042.1
U6|ENSG00000272262.1
snoU13|ENSG00000239046.1
snoU13|ENSG00000238571.1
PTPRVP
GPR37L1
SNORA70|ENSG00000206637.1
MIR1231
MIR5191
RPS10P7
ASCL5
LINC00862
MIR181A1HG
MIR4735
U3|ENSG00000252241.1
MIR1278
snoU109|ENSG00000238754.1
RN7SKP126
RNA5SP73
RN7SKP156
RNA5SP72
SNORD112|ENSG00000252790.1
RN7SL654P
RNA5SP71
RN7SKP229
RNA5SP70
KIAA1614
U6|ENSG00000272292.1
MIR3121
LHX4
RN7SL230P
IFRG15
RN7SL374P
SNORA67|ENSG00000201619.1
SNORA67|ENSG00000212338.1
TOR3A
SNORA63|ENSG00000201791.1
RNA5SP69
C1orf220
LINC00083
MIR488
SCARNA3
snoU13|ENSG00000238872.1
RNA5SP68
RNA5SP67
SNORD78|ENSG00000208317.1
GAS5
RN7SKP160
snoU13|ENSG00000238430.1
ANKRD45
snoU13|ENSG00000251817.1
TNFSF18
SNORD112|ENSG00000252354.1
DNM3OS
SCARNA20|ENSG00000253060.1
RN7SL425P
snoU13|ENSG00000238859.1
RN7SL269P
RN7SL333P
C1orf112
F5
RNA5SP66
LINC00970
LINC00626
ANKRD36BP1
SFT2D2
MIR1255B2
snoU13|ENSG00000238325.1
RNA5SP65
POGK
MIR921
RNA5SP64
UCK2
TMCO1
SNORD112|ENSG00000252359.1
U3|ENSG00000212538.1
RNA5SP63
RNA5SP62
SNORD112|ENSG00000252740.1
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13|ENSG00000238843.1
BGLAP
SNORA26|ENSG00000252236.1
SCARNA4|ENSG00000252808.1
SNORA42|ENSG00000207475.1
snoU13|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
LINC00622
snoU13|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
ACTBP12
RN7SL235P
RN7SL653P
BARHL2
U3|ENSG00000199666.1
RN7SKP272
snoU13|ENSG00000239176.1
GBP1P1
GBP6
RN7SL583P
RNA5SP52
RNA5SP51
SNORD81|ENSG00000199934.1
C1orf52
CTBS
SPATA1
RPF1
UOX
SNORA2|ENSG00000199959.1
TTLL7
RN7SKP247
RNA5SP23
RNA5SP22
GIPC2
DNAJB4
RNA5SP21
RN7SL370P
RNA5SP20
ST6GALNAC5
ST6GALNAC3
SNORD45B
SNORD45A
SNORD45C
ABCA4
ACADM
ADAR
ADORA1
ADORA3
AGL
ALDH9A1
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
RHOC
ASTN1
SERPINC1
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
BRDT
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPZA1
CASQ1
CASQ2
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
CD48
CD53
CD58
CHI3L1
CHI3L2
CHIT1
CHRNB2
CKS1B|ENSG00000173207.8
CLCA1
CLK2
CNN3
COL11A1
COPA
CRABP2
CRP
CSF1
CSRP1
CTSE
CTSK
CTSS
DBT
DHX9
DPT
DPYD
ECM1
S1PR1
EIF2D
EFNA1
EFNA3
EFNA4
CELSR2
ELF3
ENSA
ETV3
EXTL2
F3
F13B
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GBA
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GLUL
GNAT2
GNG5
GPR25
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HDGF
CFH
CFHR1
CFHR2
MR1
HMGCS2
HSD3B1
HSD3B2
HSPA6
IGSF3
IFI16
CYR61
IL6R
IL10
ILF2
INSRR
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNJ10
KCNN3
KISS1
LAD1
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MOV10
MPZ
MSH4
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NGF
NHLH1
NHLH2
NIT1
NPR1
DDR2
OVGP1
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PRRX1
POU2F1
PPOX
PRELP
PRKAB2
PRKACB
PKN2
PSMA5
PSMB4
PSMD4
PTGFR
PTGFRN
PTGS2
QSOX1
PTPN7
PTPRC
PEX19
ABCD3
RAB13
RABGGTB
RAP1A
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPL5
RPS27
RXRG
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SLC16A1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
STXBP3
XCL2
SYCP1
CNTN2
TBX15
VPS72
TGFBR3
THBS3
TCHH
TNNI1
TNNT2
TNR
CCT3
TSHB
TUFT1
TNFSF4
USF1
VCAM1
CSDE1
EVI5
DAP3
NPHS2
BTG2
CDC7
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
DYRK3
RGS5
PPFIA4
ITGA10
LMO4
BLZF1
CDC14A
RTCA
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
FUBP1
RAB7L1
SELENBP1
MPZL1
SH2D2A
ANGPTL1
TBX19
SLC16A4
PRPF3
ARHGEF2
DEDD
XPR1
MAPKAPK2
GPR52
CD101
AIM2
RASAL2
CHD1L
SOX13
PRDX6
CLCA3P
CLCA2
IKBKE
HS2ST1
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
KIF14
RBM8A
NR1I3
PIGK
SCAMP3
ARPC5
TSPAN2
PRG4
GPA33
STX6
SF3B4
BCAS2
WARS2
CEPT1
PIAS3
TIMM17A
LRRN2
VAV3
HAX1
C1orf61
SEMA6C
LAMTOR5
SLC19A2
IFI44
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
AP4B1
PHTF1
NES
KDM5B
AHCYL1
CFHR4
CFHR3
OCLM
JTB
MTMR11
IFI44L
SLC27A3
IL24
TDRKH
ADAM30
CD160
GLMN
DDX20
PMF1
DUSP12
VPS45
CLCA4
MTF2
NTNG1
PLEKHA6
KIAA0907
WDR47
KIFAP3
ATF6
USP33
KIF21B
NMNAT2
NFASC
POGZ
COLGALT2
CLCC1
RGL1
SYT11
PRRC2C
RPRD2
LPHN2
CAMSAP2
KIAA1107
SMG5
NCSTN
CRB1
GPR161
SLC35A3
LRRC8B
ZNF281
SNAPIN
LPAR3
DDAH1
PHLDA3
RUSC1
CA14
DSTYK
CCDC19
LMOD1
NBPF14
MPC2
OLFML2B
C1orf43
RWDD3
ZZZ3
DNM3
TOR1AIP1
CHTOP
PTPN22
PHGDH
LCE2B
OPTC
AK5
OR10J1
USP21
CACYBP
CHIA
SLC39A1
KLHL20
LAMTOR2
UBE2T
TMOD4
GPSM2
NME7
IL19
CERS2
SLC25A24
CRNN
DCAF8
F11R
TMED5
GLRX2
BOLA1
ZBTB7B
RRNAD1
ADIPOR1
SH3GLB1
APH1A
PLEKHO1
HAO2
IER5
SNX7
UCHL5
SUCO
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CYB5R1
CD244
GPR88
DPM3
MRPS21
TRMT13
ADAMTSL4
CRCT1
RSBN1
ZNHIT6
SWT1
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
LAX1
DUSP23
C1orf27
C1orf56
RALGPS2
PRPF38B
LRRC8D
MSTO1
DARS2
PRMT6
GOLPH3L
KLHDC8A
ETNK2
KIRREL
YY1AP1
MCOLN3
SLC22A15
YOD1
UBE2Q1
RNPC3
ITLN1
IPO9
C1orf106
LRIF1
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
FAM212B
SLC50A1
CCBL2
SLAMF8
CDC42SE1
UBQLN4
OLFML3
LHX9
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
AMIGO1
ODF2L
CGN
IGSF9
ZNF687
HCN3
FAM5B
CCDC181
SLAMF7
CADM3
PTBP2
PRUNE
DNASE2B
KLHL12
LGR6
HAPLN2
PAPPA2
BCAN
TNN
MRPS14
ELTD1
SEMA4A
RFWD2
RGS18
HIAT1
NUCKS1
DCLRE1B
MRPL9
INTS3
SCNM1
WDR77
C1orf116
FCRL2
EPS8L3
CDC73
MRPL24
TNFAIP8L2
C1orf54
VTCN1
PAQR6
TRIM46
MROH9
SIKE1
TARS2
TRIM45
EDEM3
FLAD1
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
VANGL1
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
GPR61
FCAMR
REG4
TEX35
HORMAD1
TOMM40L
SYDE2
ZNF644
LRRC8C
POLR3GL
TMEM79
ACBD6
PROK1
ZBTB37
LCE3D
PSRC1
FCRLA
PPP1R15B
MAEL
STRIP1
RGS8
NAV1
SEC16B
AQP10
SLAMF9
PYGO2
ZNF697
IGFN1
NUP210L
NEXN
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
PIGM
IGSF8
LEMD1
C1orf85
HENMT1
PGLYRP3
SLAMF6
SLC26A9
FCRL1
FCRL3
GBP4
GBP5
FMO9P
TSEN15
FAM129A
TADA1
SH2D1B
SSX2IP
OLFM3
GABPB2
TCHHL1
RPTN
TDRD10
SHE
WDR63
KLHDC9
AXDND1
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ATP6V1G3
ASB17
OR10J5
LRRC39
DCST2
ZNF648
TEDDM1
ARL8A
SYT2
GOLT1A
UHMK1
FCRLB
LIX1L
TSACC
IQGAP3
APOA1BP
DRAM2
PIFO
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
NEK7
ITLN2
SYT6
CREB3L4
SAMD13
C1orf51
TMEM56
NBPF4
HFE2
ANKRD35
FAM163A
MFSD4
PM20D1
SLC30A7
NBPF12
LELP1
RC3H1
DCST1
METTL11B
FAM78B
SHISA4
BNIPL
LRRC71
CHIAP2
PYHIN1
FNDC7
DENND1B
TDRD5
TOR1AIP2
SPRR4
SASS6
PPIAL4A
HFM1
TTC24
UBL4B
LCE4A
NBPF11
SPAG17
KRTCAP2
CRTC2
HIPK1
SLC44A5
TMEM9
EPHX4
AKNAD1
SLC41A1
LCE5A
MCOLN2
COL24A1
ARHGAP30
C1orf192
ASPM
MAGI3
TIPRL
FAM19A3
RIIAD1
THEM5
SLC9C2
NBPF16
LINC00303
FAM102B
SYPL2
CYB561D1
ANKRD34A
C1orf204
ZNF326
BTBD8
HIST2H2AB
PPM1J
S100A7A
RXFP4
FAM5C
C1orf110
CCDC18
MYBPHL
OR10R2
FCRL6
KCNT2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
FAM73A
PEAR1
ILDR2
GBP7
C1orf146
FAM69A
SLC6A17
C1orf137
NOTCH2NL
LYSMD1
HRNR
FLG2
FMO6P
LINC00272
C1orf53
TMEM81
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
C1ORF220
NBPF9
APOBEC4
MIR181B1
MIR197
MIR199A2
MIR181A1
MIR214
RGS21
C1orf180
HIST2H2BF
ETV3L
LRRC52
OR10J3
MIR135B
KPRP
LCE6A
RBMXL1
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
NBPF6
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR557
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
MIR760
C1orf68
TSTD1
C2CD4D
NBPF20
MIR320B1
MIR1295A
MIR4257
MIR378G
MIR4424
MIR137HG
MIR4423

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q23.3.

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

Genes
EXT1
COX6C
MYC
RECQL4
NCOA2
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25|ENSG00000251744.1
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
SNORD112|ENSG00000252559.1
TMEM74
RNA5SP275
snoU13|ENSG00000238687.1
RIMS2
MIR3151
RNU6ATAC8P
snoU13|ENSG00000238533.1
snoU13|ENSG00000238372.1
RN7SL563P
NACAP1
RN7SKP249
RN7SL685P
RNU6ATAC41P
MIR1273A
SNORD77|ENSG00000212414.1
RN7SL350P
RN7SKP85
KCNS2
NIPAL2
SNORA72|ENSG00000207067.1
LAPTM4B
U3|ENSG00000207215.1
PTDSS1
snoU13|ENSG00000238791.1
FSBP
RNA5SP274
LINC00535
RN7SKP231
snoU13|ENSG00000239134.1
MIR4661
RN7SL777P
RNA5SP273
LINC00534
RNA5SP272
MMP16
REXO1L10P|ENSG00000255940.1
REXO1L11P
REXO1L10P|ENSG00000270416.1
snoU13|ENSG00000238566.1
SLC10A5
IMPA1P
RN7SL308P
RN7SL107P
SNORA20|ENSG00000206649.1
RN7SL41P
snoU13|ENSG00000238595.1
CASC9
RNA5SP271
U8|ENSG00000200191.1
RN7SL19P
snoU13|ENSG00000238450.1
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
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
LY6E
LY6H
MATN2
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PLEC
PMP2
POLR2K
PKIA
PTK2
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
GPAA1
RIPK2
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
LRRC14
EMC2
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
CPQ
KHDRBS3
POP1
WWP1
STMN2
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
LRRC6
LY96
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
OPLAH
PABPC1
KCNV1
STAU2
MTBP
AGO2
MRPS28
COMMD5
MRPL13
ATAD2
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
RMDN1
ZNF706
VPS28
FAM203A
KCNK9
THEM6
UBR5
FAM49B
AZIN1
OTUD6B
CHRAC1
GDAP1
EXOSC4
PDP1
CNGB3
ESRP1
TMEM70
TRMT12
OXR1
WDYHV1
UBE2W
TMEM55A
SLC39A4
SYBU
INTS8
PAG1
GSDMC
JPH1
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
PRDM14
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
DSCC1
DERL1
SLC52A2
PLEKHF2
ZFAND1
ZFHX4
GSDMD
BAALC
GRHL2
ARHGAP39
ZNF34
SLC25A32
DCSTAMP
SHARPIN
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NCALD
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
PSKH2
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
TBC1D31
TP53INP1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
TOP1MT
ZNF572
FAM92A1
NDUFAF6
ABRA
LYPD2
TMEM71
DCAF4L2
RALYL
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
FAM91A1
SBSPON
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
REXO1L1
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
TRIQK
DPY19L4
FBXO43
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
CA13
XKR9
C8orf87
RBM12B
MROH5
MAFA
GDF6
C8orf59
SAMD12
MIR30B
MIR30D
LRRC24
ZNF704
MROH6
FABP9
FABP12
FER1L6
MIR548A3
MIR599
MROH1
FAM203B
OC90
MIR875
LRRC69
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3150B
MIR3610
MIR378D2
MIR4662B
MIR4663
MIR4664
MIR4471
MIR5680
MIR5194
MIR5708
MIR5681A

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 - 32 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
--- | --- | --- | --- | ---
11q24.2 | 2.2772e-15 | 2.4652e-15 | chr11:124894569-124967486 | 1
4q22.2 | 2.1323e-11 | 2.1323e-11 | chr4:92521823-94741521 | 2
10q26.3 | 3.5798e-07 | 3.5798e-07 | chr10:134944852-135534747 | 18
6p22.3 | 6.5289e-07 | 6.5289e-07 | chr6:15109824-15538684 | 2
16q23.1 | 5.3117e-05 | 5.4046e-05 | chr16:76579192-90354753 | 135
18q22.2 | 5.4046e-05 | 5.4046e-05 | chr18:63200038-78077248 | 50
18p11.32 | 0.00044581 | 0.00047272 | chr18:1-893521 | 11
1p36.31 | 0.00025881 | 0.00070255 | chr1:1-48649489 | 789
9p23 | 5.0434e-05 | 0.0013188 | chr9:7887952-12687261 | 3
6q26 | 0.0041389 | 0.0041389 | chr6:154677895-171115067 | 99
19q13.41 | 0.0050233 | 0.0052801 | chr19:48083041-59128983 | 479
5q12.1 | 0.0094715 | 0.0094715 | chr5:58998410-59780946 | 2
Xp21.1 | 0.035723 | 0.036469 | chrX:32117084-32611359 | 2
1p31.1 | 0.0152 | 0.04615 | chr1:62146229-77102451 | 87
9q33.3 | 0.021162 | 0.04615 | chr9:129609858-130003734 | 3
3p26.2 | 0.047631 | 0.047631 | chr3:1-50611550 | 444
7q11.22 | 0.060458 | 0.059005 | chr7:69000716-70601215 | 2
10p15.3 | 0.060727 | 0.059005 | chr10:1-7202930 | 57
2q37.3 | 0.066033 | 0.069443 | chr2:220768880-243199373 | 192
9q34.2 | 0.029396 | 0.069443 | chr9:136602059-137007089 | 3
9p24.3 | 7.5754e-05 | 0.069443 | chr9:1-71039939 | 321
11q12.3 | 0.033605 | 0.091452 | chr11:40133134-74383980 | 574
13q34 | 0.091452 | 0.091452 | chr13:114202593-114304134 | 1
Xq27.3 | 0.091452 | 0.091452 | chrX:103806756-155270560 | 438
11p15.5 | 0.097934 | 0.1009 | chr11:1-63334217 | 735
5p15.2 | 0.11377 | 0.1144 | chr5:1-16049923 | 73
5p14.3 | 0.13538 | 0.14014 | chr5:22139046-37813156 | 53
7q36.1 | 0.13232 | 0.14014 | chr7:108534673-159138663 | 382
10q23.1 | 0.15892 | 0.15826 | chr10:82406275-85904649 | 1
1q42.12 | 0.1741 | 0.17376 | chr1:204529809-249250621 | 415
20p12.1 | 0.20523 | 0.20183 | chr20:1-16555385 | 145
11p12 | 0.13142 | 0.20863 | chr11:30405520-106894520 | 820

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.2.

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

Genes
SLC37A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.2.

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

Genes
RNA5SP164
GRID2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
MIR3944
TUBGCP2
ADAM8
CYP2E1
ECHS1
UTF1
VENTX
CALY
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
PAOX
FUOM
FRG2B
SPRN
MIR202

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p22.3.

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

Genes
RN7SL332P
JARID2

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13|ENSG00000239186.1
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
MIR3182
RN7SL134P
snoU13|ENSG00000238321.1
RN7SKP190
7SK|ENSG00000260682.2
MIR4720
GAN
PKD1L2
CMC2
RNA5SP431
PIH1
MON1B
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
PRDM7
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
JPH3
VAT1L
WFDC1
MTHFSD
DBNDD1
KLHL36
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
CENPBD1
ZNF276
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
SLC38A8
ADAD2
ADAMTS18
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
C16orf74
SYCE1L
MIR1910
C16orf95
MIR4719
MIR5093

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.2.

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
CDH7
CYB5A
MBP
NFATC1
ZNF236
CTDP1
SOCS6
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
CDH19
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
PQLC1
NETO1
PARD6G
CNDP1
DSEL
FAM69C
CBLN2
FBXO15
GTSCR1
DOK6
LINC00908
ATP9B
LINC00909
HSBP1L1
C18orf63
MIR5011

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.32.

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

Genes
RN7SKP146
CETN1
ROCK1P1
TYMS
YES1
USP14
THOC1
CLUL1
ENOSF1
COLEC12
C18orf56

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
LCK
MPL
MUTYH
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
SKINTL
TRABD2B
LINC00853
CYP4A22
CYP4Z2P
KNCN
LINC00505
NSUN4
TMEM69
snoU13|ENSG00000238945.1
RNA5SP47
BTBD19
SNORD38B
SNORD38A
SNORD46|ENSG00000200913.1
SNORD55
MIR5584
RN7SL479P
RNA5SP46
RNA5SP45
RN7SL326P
MIR30C1
MIR30E
BMP8B
SNORA55
BMP8A
RNA5SP44
MYCBP
SNORA63|ENSG00000252448.1
snoU13|ENSG00000238871.1
MIR5581
MEAF6
RNA5SP43
SNORA63|ENSG00000201448.1
RN7SL131P
RN7SL281P
PSMB2
RNY5P1
SNORA62|ENSG00000201542.1
RN7SL503P
RN7SL136P
ZMYM6
SNORD112|ENSG00000252728.1
SMIM12
RNA5SP42
RN7SKP16
MIR3605
FKSG48
ZBTB8OS
ZBTB8B
RN7SL122P
MTMR9LP
MIR5585
MIR4254
FABP3
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18|ENSG00000252691.1
SCARNA17|ENSG00000252190.1
MAN1C1
snoU13|ENSG00000238889.1
SYF2
snoU13|ENSG00000238986.1
RN7SL857P
snoU13|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16|ENSG00000252404.1
RN7SL451P
SNORA77|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
AK2
ALPL
RERE
ATP6V0B
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
PLK3
CNR2
COL8A2
COL9A2
COL16A1
CORT
CSF3R
CTPS1
CYP4A11
CYP4B1
DDOST
DFFB
DPH2
DVL1
E2F2
ECE1
EDN2
PHC2
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FAAH
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
INPP5B
IPP
STMN1
MATN1
MFAP2
MTF1
MTHFR
MYCL
NASP
NBL1
NDUFS5
NFYC
NPPA
NPPB
YBX1
OPRD1
PAFAH2
PRDX1
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKCZ
PTAFR
PTPRF
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RPS8
RSC1A1
SCNN1D
SRSF4
ST3GAL3
STIL
SKI
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TIE1
TNFRSF1B
TP73
TNFRSF4
UQCRH
UROD
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LAPTM5
PTP4A2
SNHG3
NR0B2
RAD54L
PIK3R3
MMP23B
KCNAB2
FCN3
YARS
MKNK1
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
PER3
EIF2B3
ARTN
MAP3K6
KCNQ4
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
THEMIS2
H6PD
ISG15
PLCH2
IPO13
KDM4A
CROCC
PUM1
CEP104
RIMS3
EFCAB14
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
TSPAN1
CELA3A
PDZK1IP1
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
AKR1A1
TESK2
PPIE
MAD2L2
PPIH
CAP1
LRRC41
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
EBNA1BP2
KIF2C
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
FOXJ3
SCMH1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
MAST2
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
SZT2
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
STX12
CLIC4
MMACHC
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HEYL
AGO1
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
SSU72
GNL2
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF691
MECR
UTP11L
SDF4
MRTO4
HPCAL4
YTHDF2
ZCCHC17
PADI3
CMPK1
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
RNF220
VPS13D
EVA1B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
POMGNT1
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
DMAP1
AJAP1
TMEM234
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
ZSWIM5
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
PLA2G2F
SMAP2
ATPAF1
S100PBP
EXO5
CEP85
NMNAT1
ELOVL1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZFP69B
PHACTR4
AUNIP
ERI3
C1orf50
CCDC28B
EFHD2
MMEL1
RSG1
NKAIN1
MUL1
TMEM53
AKIRIN1
HECTD3
YRDC
NOL9
PPCS
LIN28A
SH3D21
SNIP1
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
HYI
SESN2
ESPN
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
ZMYND12
NBPF3
LZIC
NT5C1A
TRIM63
FAM167B
C1orf170
HPDL
MFSD2A
SYTL1
IGSF21
LSM10
C1orf94
KIAA2013
THAP3
STPG1
SPOCD1
UBXN11
FBXO44
ATPIF1
MED8
ADC
TMEM54
TOE1
ERMAP
CSMD2
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
GJB4
HMGB4
RNF19B
A3GALT2
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
KLF17
TMEM125
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
MOB3C
DCDC2B
ZNF362
MANEAL
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
CCDC17
SLC2A7
CALML6
IFNLR1
CITED4
FAM43B
PAQR7
AGO3
AGO4
FAM76A
TMEM201
CYP4Z1
C1orf86
TXLNA
SLFNL1
ATAD3C
AKR7L
FNDC5
TTLL10
TMCO4
ZNF683
CYP4X1
NPHP4
BEST4
RSPO1
EPHA10
RIMKLA
SLC25A34
C1orf174
KLHL17
TMEM52
TFAP2E
C1orf228
ZFP69
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
TCTEX1D4
SERINC2
FAM131C
SPATA21
CCDC23
TEX38
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
FAM183A
ANKRD65
PRAMEF7
LURAP1
PEF1
MIR429
KIAA0754
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
ZBTB8A
PRAMEF22
PRAMEF15
PRAMEF16
MIR552
CCDC30
CDK11A
SLC35E2B
C1orf234
OR4F29
FAM229A
FOXO6
MIR4255
MIR4253
MIR1273D
MIR4252
MIR3659
MIR3917
MIR3675
ZMYM6NB
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
RN7SL5P
SNORD27|ENSG00000251699.1
PTPRD

Genes in Wide Peak

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

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

Genes
FGFR1OP
MLLT4
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13|ENSG00000239136.1
AIRN
SNORA29
SNORA20|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
ACAT2
CCR6
IGF2R
KIF25
LPA
MAS1
MAP3K4
PARK2
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCTE3
DYNLT1
THBS2
EZR
RNASET2
SYNJ2
QKI
WTAP
PDE10A
SCAF8
TIAM2
C6orf123
DLL1
MRPL18
CLDN20
NOX3
SNX9
MPC1
UNC93A
PHF10
C6orf70
AGPAT4
TULP4
ARID1B
TMEM181
SMOC2
ZDHHC14
FRMD1
LINC00574
LPAL2
RSPH3
FAM120B
FNDC1
SERAC1
SYTL3
TAGAP
PACRG
PNLDC1
DACT2
C6orf118
OSTCP1
WDR27
PRR18
C6orf120
TCP10L2
LINC00242
GTF2H5
TMEM242
MIR1202
MIR1273C
MIR3918
MIR3939
MIR4466

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.41.

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

Genes
PPP2R1A
KLK2
TFPT
ZNF331
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13|ENSG00000239137.1
KIR3DX1
LILRA6
LENG1
NDUFA3
MIR935
MIR371B
RN7SL317P
ZNF813
ZNF761
FAM90A28P
FAM90A27P
ZNF321P
ZNF888
ZNF600
ZNF137P
MIR643
snoU13|ENSG00000238630.1
HCCAT3
FPR1
snoU13|ENSG00000238486.1
SIGLEC5
CEACAM18
SIGLEC22P
SIGLEC17P
KLK13
KLK9
KLKP1
SNORD88C
SNORD88A
SNORD88B
LRRC4B
SPIB
RN7SL324P
NAPSB
SIGLEC16
U3|ENSG00000221125.1
MIR4751
MIR4750
MIR4749
ADM5
MIR5088
BCL2L12
SNORD35B
SNORD35A
SNORD34
SNORD33|ENSG00000199631.1
SNORD32A
MIR4324
RN7SL708P
RN7SL345P
SEC1P
DBP
GRWD1
C19orf68
CABP5
TPRX2P
SNORD23|ENSG00000221803.1
RN7SL322P
A1BG
AP2A1
KLK3
BAX
BCAT2
CA11
CD33
SIGLEC6
CD37
CGB
CRX
EMP3
ETFB
FCAR
FCGRT
FLT3LG
FPR2
FPR3
FTL
FUT1
FUT2
GPR32
GRIN2D
GYS1
HAS1
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
MYBPC2
NKG7
CNOT3
NTF4
NUCB1
PEG3
POLD1
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTPRH
RPL18
RPL28
RPS5
RPS9
RPS11
RRAS
CLEC11A
SEPW1
SNRNP70
SPIB
AURKC
SULT2B1
SULT2A1
TNNI3
TNNT1
TULP2
NR1H2
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF135
ZNF154
ZNF175
TEAD2
PPFIA3
PLA2G4C
SIGLEC5
UBE2M
CYTH2
NCR1
NAPSA
KLK4
ZNF432
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
ZNF324
KLK5
ZNF473
PRPF31
FGF21
SIGLEC7
DKKL1
SIGLEC9
SIGLEC8
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
FAM83E
EPS8L1
RASIP1
PIH1D1
C19orf73
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SPHK2
SLC17A7
NAT14
VN1R1
RCN3
ZNF304
TTYH1
PRR12
ZNF471
USP29
PLEKHA4
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
ZNF649
ZSCAN18
RPL23AP79
TSEN34
MBOAT7
ZSCAN5A
ZNF329
TBC1D17
ZNF419
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
ZNF611
MED25
SYT3
AKT1S1
ZNF528
BRSK1
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
ZNF551
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
ACPT
CGB5
CGB7
LENG9
CGB8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LINC00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
TMEM190
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF320
ZNF497
ZNF550
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TPRX1
MAMSTR
IZUMO1
EMC10
KLK9
SIGLECL1
ZNF615
ZNF841
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
DNAAF3
LILRA5
ZNF773
ZNF808
ZNF470
ZNF749
ZNF324B
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR371A
MIR372
MIR373
DPRX
ASPDH
MIR498
MIR520E
MIR519E
MIR520F
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
SHISA7
SIGLEC14
SGK110
BSPH1
ZNF587B
MIR1323
ZNF865
MIR4754
MIR4752

Genes in Wide Peak

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

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

Genes
FKSG52
MIR582

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
MIR3915
RNA5SP501

Genes in Wide Peak

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

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

Genes
JAK1
ST6GALNAC3
SNORD45B
SNORD45A
SNORD45C
LRRC53
RNU4ATAC8P
RNA5SP50
RN7SKP19
NEGR1
MIR186
RN7SL242P
PIN1P1
RN7SL538P
MIR1262
RN7SL392P
RNU4ATAC4P
SNORA31|ENSG00000252433.1
MIR3117
RN7SL854P
snoU13|ENSG00000238931.1
LEPROT
MIR4794
RN7SL130P
DLEU2L
RN7SL488P
LINC00466
RNA5SP49
RN7SL180P
ACADM
AK4
CRYZ
CTH
GADD45A
IL12RB2
MSH4
ROR1
PDE4B
PGM1
PTGER3
RABGGTB
RPE65
USP1
FPGT
DIRAS3
SRSF11
ZRANB2
DNAJC6
INSL5
INADL
HHLA3
SLC35D1
ITGB3BP
SERBP1
FOXD3
ANGPTL3
ALG6
L1TD1
LEPR
RAVER2
LRRC40
DEPDC1
GNG12
LRRC7
CACHD1
MIER1
WDR78
WLS
ANKRD13C
TM2D1
SGIP1
EFCAB7
ATG4C
DOCK7
ASB17
TYW3
C1orf173
LRRIQ3
UBE2U
IL23R
KANK4
TCTEX1D1
SLC44A5
C1orf141
LHX8
MIR3671
TNNI3K

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q33.3.

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

Genes
RALGPS1
ANGPTL2
ZBTB34

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.2.

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

Genes
VHL
CTNNB1
FANCD2
MLH1
MYD88
PPARG
RAF1
XPC
SRGAP3
SETD2
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13|ENSG00000238350.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000251938.1
PRSS44
PRSS45
SNORD77|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
U8|ENSG00000212145.2
RN7SKP58
SCARNA21|ENSG00000252409.1
ZNF621
SNORA64|ENSG00000202517.1
RN7SL411P
SNORA62|ENSG00000202363.1
SNORA6
MIR26A1
ITGA9
RNA5SP129
snoU13|ENSG00000238929.1
RNU6ATAC4P
TRANK1
HSPD1P6
RN7SKP227
RNA5SP128
RN7SL296P
TMPPE
CCR4
TRIM71
snoU13|ENSG00000238646.1
SNORA25|ENSG00000201701.1
OSBPL10
STT3B
RNA5SP127
U3|ENSG00000199927.1
LINC00693
CMC1
RN7SL859P
SNORD5|ENSG00000272166.1
RNA5SP126
RNA5SP125
RN7SL216P
LINC00691
UBE2E2
HMGB1P5
RNY4P22
MIR3135A
U7|ENSG00000271841.1
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13|ENSG00000238345.1
snoU13|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13|ENSG00000239126.1
EGOT
SNORA43|ENSG00000253049.1
RN7SKP144
RN7SL120P
ACAA1
ACVR2B
AMT
APEH
RHOA
ATP2B2
BTD
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CCR1
CCR3
CCR5
CCR8
ACKR2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
CELSR3
FBLN2
GNAI2
GOLGA4
XCR1
GPX1
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PTH1R
QARS
RAB5A
RARB
RPL15
RPL32
SATB1
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SMARCC1
STAC
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
CLEC3B
TOP2B
UBA7
UBE2E1
UBP1
USP4
UQCRC1
VIPR1
ZNF35
BRPF1
IFRD2
COLQ
EOMES
HYAL3
CAMK1
BHLHE40
HYAL2
KAT2B
BSN
ACKR5
RPL14
SEC22C
LRRFIP2
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
TBC1D5
TATDN2
IP6K1
EPM2AIP1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
NPRL2
CXCR6
CHL1
ARPP21
CCR9
USP19
CYB561D2
TMEM115
WDR6
RASSF1
TREX1
SCN11A
TUSC2
TRAK1
DHX30
SACM1L
SCAP
EXOSC7
CAND2
CLASP2
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
KLHL18
LARS2
CAPN7
MKRN2
NAT6
FBXL2
CNOT10
TMEM158
THUMPD3
MYRIP
PTPN23
SUSD5
HACL1
TTLL3
CNTN6
RBMS3
NKIRAS1
PRSS50
GMPPB
LMCD1
VILL
SSUH2
TRNT1
DYNC1LI1
C3orf18
CRBN
SS18L2
CCDC174
SHISA5
ZMYND10
TMA7
ZNF589
IP6K2
NCKIPSD
GHRL
LZTFL1
P4HTM
SLC6A20
ELP6
SNRK
QRICH1
CMTM6
SLC25A38
ULK4
OXSM
ANO10
DALRD3
ARL8B
SETD5
TMEM40
NGLY1
BRK1
ZKSCAN7
RAD18
KIF15
KIAA1143
HHATL
WDR48
LRRN1
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
TSEN2
C3orf20
ATRIP
NICN1
MON1A
JAGN1
IL17RC
GTDC2
EAF1
DCLK3
UCN2
ZNF502
OXNAD1
CMTM7
ZNF501
FANCD2OS
LRRC3B
GALNT15
KCNH8
LYZL4
KLHL40
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
LSMEM2
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
ZCWPW2
NEK10
CMTM8
CCDC13
FGD5
CNTN4
XIRP1
TTC21A
KLHDC8B
ZNF620
ALS2CL
TMIE
FBXW12
ZNF619
LINC00692
TCAIM
SUMF1
RPUSD3
PRRT3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
TPRXL
ZNF445
TOPAZ1
AMIGO3
ZNF662
CDHR4
FAM212A
MIR191
MIR425
GLB1
SPINK8
ARIH2OS
C3orf84
MIR563
FAM198A
CCR2
PRSS46
MIR378B
MIR4271
MIR3714
KRBOX1
MIR4791
MIR4790
MIR4443
MIR4792
MIR4442

Genes in Wide Peak

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

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

Genes
RN7SL371P
AUTS2

Genes in Wide Peak

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

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

Genes
LINC00707
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
CALML3
AKR1C4
KLF6
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
PFKFB3
PFKP
PRKCQ
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
ASB13
TUBAL3
AKR1E2
FBXO18
RBM17
IDI2
UCN3
LINC00200
PRR26

Genes in Wide Peak

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

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

Genes
ACSL3
PAX3
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13|ENSG00000238852.1
SGPP2
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
SAG
CCL20
SP100
SPP2
SCG2
CUL3
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
FARSB
ARL4C
RAMP1
NMUR1
STK25
CAPN10
SP140
PASK
ATG4B
SH3BP4
KCNE4
NGEF
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
PID1
ATG16L1
USP40
HJURP
HES6
DOCK10
C2orf83
MFF
ACKR3
WDFY1
NYAP2
GAL3ST2
RAB17
COPS7B
MRPL44
TRPM8
MLPH
IQCA1
FAM124B
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
DNER
B3GNT7
SP140L
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
CCDC140
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
C2orf72
DUSP28
MROH2A
ESPNL
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4268
MIR4269
MIR4786
MIR5001
MIR5702
MIR5703

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.2.

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

Genes
BRD3
LINC00094
VAV2

Genes in Wide Peak

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

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

Genes
FANCG
JAK2
MLLT3
NFIB
PAX5
CD274
CBWD3
PGM5P2
RNA5SP284
SNORA70|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
SNX18P3
IGFBPL1
snoU13|ENSG00000238313.1
U8|ENSG00000200026.1
SHB
RN7SKP171
RN7SL463P
MIR4476
MIR4540
LINC00961
RGP1
RN7SL22P
RMRP
MIR4667
RN7SL338P
FLJ00273
FAM205CP
FAM205B
GALT
RN7SKP24
KIAA1161
RNA5SP282
RN7SKP114
SNORD121A
SNORD121B
RNU4ATAC11P
PTENP1
RNU4ATAC15P
TMEM215
GVQW1
RNA5SP281
snoU13|ENSG00000239155.1
LINC00032
RNA5SP280
RN7SL100P
SNORA31|ENSG00000252580.1
RN7SKP120
RMRPP5
DMRTA1
RN7SL151P
SNORD39|ENSG00000264379.1
MIR31HG
IFNA6
KLHL9
PTPLAD2
SNORA30|ENSG00000202189.1
MIR491
MIR4474
MIR4473
ACER2
snoU13|ENSG00000238348.1
RN7SL158P
SCARNA8
RN7SKP258
MIR3152
RN7SL720P
RN7SL98P
RN7SL157P
LINC00583
LURAP1L
RN7SL849P
RN7SL5P
SNORD27|ENSG00000251699.1
RN7SL123P
snoU13|ENSG00000252110.1
RN7SL25P
C9orf38
MLANA
snoU13|ENSG00000238654.1
INSL4
AK3
CDC37L1
CARM1P1
RN7SL592P
RNA5SP279
RN7SL412P
FAM138C
ACO1
PLIN2
ALDH1B1
NUDT2
AQP3
AQP7
BAG1
CA9
CCIN
CD72
CDKN2A
CDKN2B
CLTA
CNTFR
DMRT1
ELAVL2
FOXD4
GALT
B4GALT1
GLDC
DNAJA1
IFNA1
IFNA2
IFNA4
IFNA5
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
IL11RA
MTAP
NDUFB6
NFX1
NPR2
PRSS3
PTPRD
RFX3
RLN1
RLN2
RPS6
CCL19
CCL21
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TEK
TESK1
TLN1
TPM2
TYRP1
VCP
VLDLR
RECK
MPDZ
CER1
PLAA
GRHPR
MELK
RUSC2
ZBTB5
KIAA0020
GNE
RCL1
TOPORS
SIGMAR1
CREB3
UNC13B
DMRT2
RRAGA
CCL27
PSIP1
INSL6
DCTN3
FRMPD1
KDM4C
KANK1
KIAA1045
DDX58
SLC24A2
DNAJB5
DCAF12
ZNF658
SPATA31A7
SPAG8
FBXO10
RANBP6
DNAI1
SIT1
SPINK4
STOML2
EXOSC3
C9orf53
UBAP1
CHMP5
TMEM8B
EQTN
BNC2
HAUS6
APTX
CNTLN
FOCAD
UBE2R2
SPATA6L
SMU1
DENND4C
UBAP2
PLGRKT
CBWD1
OR2S2
IFNK
KIAA1432
GBA2
DMRT3
POLR1E
LRRC19
NOL6
DCAF10
MOB3B
CAAP1
CNTNAP3
ERMP1
IFT74
FAM214B
PDCD1LG2
DOCK8
ZCCHC7
ANKRD20A1
HINT2
C9orf24
PIGO
ARHGEF39
TPD52L3
IL33
C9orf123
SLC25A51
ADAMTSL1
UHRF2
TAF1L
ARID3C
RPP25L
C9orf131
RNF38
GLIPR2
C9orf66
LINGO2
TTC39B
TRMT10B
FAM154A
FREM1
KIAA2026
ATP8B5P
KCNV2
GLIS3
C9orf72
CCDC171
FAM219A
CCDC107
CBWD5
ANKRD18A
FAM205A
TUSC1
FOXD4L3
IFNE
ZDHHC21
KIF24
FOXD4L4
ENHO
SPATA31A6
FAM221B
OR13J1
TOMM5
FAM74A4
PPAPDC2
MIR31
ANKRD20A3
ANKRD20A2
ANKRD18B
FAM27A
SPATA31A2
SPATA31A4
CBWD6
HRCT1
SPATA31A1
FOXD4L6
FOXD4L5
MSMP
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
MIR876
MIR873
C9orf92
IZUMO3
FAM27E3
FAM27C
FAM27B
MIR1299
MIR4477A
MIR4665
MIR4475

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q12.3.

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

Genes
CCND1
DDB2
EXT2
MEN1
NUMA1
CREB3L1
SNORA7|ENSG00000206913.1
RNA5SP343
UCP2
RN7SKP243
MRPL48
MIR139
snoU13|ENSG00000238768.1
RNA5SP342
ZNF705E
ENPP7P8
UNC93B6
MIR3664
MIR548K
FGF3
MIR3164
TPCN2
MIR4691
FAM86C2P
DOC2GP
C11orf72
RN7SL59P
PTPRCAP
RN7SKP239
POLD4
snoU13|ENSG00000238892.1
SYT12
U3|ENSG00000252709.1
RN7SL12P
RBM14
ZDHHC24
SNORA43|ENSG00000201733.1
snoU13|ENSG00000238763.1
snoU13|ENSG00000238752.1
GAL3ST3
AP5B1
RN7SL309P
MIR4489
MIR4690
MALAT1
POLA2
SLC22A20
FAU
RN7SL114P
MIR1237
TEX40
VEGFB
OTUB1
RN7SL596P
C11orf95
SLC22A10
RN7SL259P
SNHG1
RN7SL119P
TMEM223
C11orf83
SNORA57|ENSG00000206597.1
METTL12
MIR3654
MIR1908
MIR611
RPLP0P2
SYT7
RN7SL23P
SDHAF2
PGA4
PGA3
MS4A18
MS4A4E
MS4A2
OOSP1
RN7SKP192
MIR3162
RN7SL435P
RN7SL42P
GLYATL1P2
BTBD18
C11orf31
RTN4RL2
RN7SKP259
RNA5SP341
PRG2
P2RX3
snoU13|ENSG00000238692.1
OR5G5P
TRIM51HP
TRIM49B
OR4C5
MIR3161
RNA5SP340
snoU13|ENSG00000252447.1
KBTBD4
PTPMT1
RN7SL652P
RN7SL772P
SNORD67|ENSG00000212135.1
SNORD67|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
PHF21A
CHST1
CD82
C11orf96
RN7SKP287
HNRNPKP3
ACP2
ACTN3
ADRBK1
APLNR
ALDH3B1
ALDH3B2
ARHGAP1
PHOX2A
ARL2
BAD
BBS1
SERPING1
VPS51
MRPL49
ZNHIT2
MYRF
TMEM258
DAGLA
CAPN1
CD5
CD6
MS4A1
MS4A3
CFL1
CHKA
CHRM1
CHRM4
CNTF
COX8A
CPT1A
CRY2
CST6
CTNND1
CTSW
DDB1
DHCR7
EEF1G
MARK2
CTTN
ESRRA
F2
FEN1
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FTH1
GIF
GNG3
GSTP1
SLC29A2
DNAJC4
IGHMBP2
INCENP
INPPL1
FADS1
FADS3
LRP4
LRP5
LTBP3
MDK
SCGB2A1
SCGB2A2
MAP3K11
MYBPC3
NDUFS3
NDUFV1
NDUFS8
OSBP
OVOL1
P2RY2
P2RY6
PC
PDE2A
PGA5
PLCB3
POLR2G
PPP1CA
PPP2R5B
PSMC3
PTPRJ
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAPSN
RARRES3
RELA
DPF2
ROM1
RPS6KB2
SIPA1
SLC3A2
SPI1
SPTBN2
SSRP1
STX3
STX5
TCN1
TM7SF2
UCP3
SCGB1A1
BEST1
SF1
ZFPL1
FOSL1
PPFIA1
SLC43A1
DGKZ
API5
MADD
CTSF
FADD
BANF1
RPS6KA4
AIP
SART1
FIBP
MTA2
UBE2L6
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
PITPNM1
RIN1
MTL5
ATG13
CKAP5
ARHGEF17
FCHSD2
FGF19
CCS
RCE1
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
KCNK7
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
PRG3
CDC42EP2
NXF1
KAT5
SSSCA1
DRAP1
TAF6L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
YIF1A
EHD1
STIP1
CLP1
SF3B2
CCDC85B
B3GNT1
PLA2G16
PTGDR2
ZP1
SHANK2
KDM2A
ATG2A
GANAB
FAM168A
DTX4
NUP160
FNBP4
CLCF1
FAM89B
FLRT1
MTCH2
PRDX5
BRMS1
ANAPC15
ZDHHC5
ATL3
C2CD3
DAK
B3GAT3
OR5L2
PPP1R14B
TIMM10
MYEOV
BSCL2
PRPF19
MACROD1
SLC43A3
PACSIN3
SAC3D1
SNX15
RHOD
EFEMP2
KCNK4
UBXN1
TMX2
GAL
SUV420H1
HSD17B12
TMEM216
COA4
SLC15A3
MS4A4A
PPME1
CABP2
TRMT112
TMEM138
C11orf24
WDR74
MS4A12
MRPL16
SSH3
TMEM132A
HRASLS2
LAMTOR1
VPS37C
ANO1
NADSYN1
FAM86C1
CCDC87
PPP6R3
RNF121
SLC35C1
CDC42BPG
AMBRA1
PACS1
KBTBD4
TTC17
SLC22A11
GPR137
PRDM11
CABP4
CD248
CORO1B
SCYL1
CARNS1
SYT13
LRRC4C
PLEKHB1
MS4A7
ALX4
FAM111A
MS4A6A
MS4A5
KLC2
TUT1
MRPL11
LRFN4
AHNAK
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
C11orf80
ZNF408
NAA40
AGBL2
ZBTB3
CPSF7
ASRGL1
TMEM134
MUS81
PAAF1
INTS5
ZFP91
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
CLPB
UNC93B1
RAB1B
C11orf68
MS4A8
FERMT3
TRPT1
RBM4B
FRMD8
RNASEH2C
EIF1AD
NUDT22
ARFGAP2
SYVN1
ACCS
MS4A14
TRIM51
RELT
LGALS12
TNKS1BP1
ATG16L2
TSPAN18
SLC39A13
ACY3
GLYATL1
CDCA5
SLC22A9
C1QTNF4
BATF2
SLC22A12
MRGPRD
MRGPRF
ARAP1
CATSPER1
HRASLS5
OR4C46
OR4X2
OR4B1
GYLTL1B
OR8I2
C11orf94
C11orf84
GPHA2
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
MRPL21
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYB561A3
PPP1R32
ORAOV1
LRTOMT
TIGD3
LRRN4CL
HNRNPUL2
ALKBH3
MS4A6E
DEFB108B
PELI3
EHBP1L1
SNX32
TSGA10IP
CNIH2
C11orf86
NUDT8
OR4C3
OR4S1
EML3
TMEM151A
NPAS4
OR10AG1
OR5J2
OR4C13
OR4C12
C11orf85
SLC25A45
OR9G4
LINC00301
P4HA3
PGM2L1
CCDC88B
TTC9C
SLC22A24
RCOR2
OR5F1
OR5AP2
ANKRD13D
MS4A10
TBX10
FAM111B
TMEM179B
TBC1D10C
DNAJB13
SLC22A25
SPDYC
LIPT2
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
FAM180B
PCNXL3
OR4A47
SCGB1D4
MIR130A
MIR192
OR5B3
MS4A13
TRIM64C
NEAT1
MIR670
MIR3165
MIR3163
RBM4
MIR548AL
MIR4487
MIR4692
MIR4488

Genes in Wide Peak

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

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

Genes
TFDP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq27.3.

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

Genes
ELF4
GPC3
MTCP1
WASH6P|ENSG00000182484.10
WASIR1|ENSG00000185203.7
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36|ENSG00000251846.1
RN7SL687P
RN7SL667P
snoU13|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
MIR452
MIR224
U3|ENSG00000253009.1
LINC00894
LINC00893
RN7SKP267
CXorf51A
CXorf51B
RNA5SP517
SPANXN1
RN7SKP189
RN7SKP149
RN7SKP81
snoU13|ENSG00000239188.1
RNA5SP516
SPANXD
SPANXA2
SPANXA1
RN7SL727P
MIR505
SNORA18|ENSG00000252719.1
RNU6ATAC23P
snoU13|ENSG00000238485.1
MIR504
RN7SKP31
RN7SL325P
SNORD61|ENSG00000206979.1
MIR934
snoU13|ENSG00000239080.1
RNA5SP515
LINC00086
LINC00633
LINC00087
SMIM10
LINC00629
GPC4
SNORA8|ENSG00000207100.1
RNA5SP514
RN7SL191P
FAM45B
RNA5SP513
DCAF12L2
snoU13|ENSG00000238626.1
SNORA40|ENSG00000252693.1
snoU13|ENSG00000239058.1
RN7SL29P
U3|ENSG00000212321.1
CT47A12
MCTS1
snoU13|ENSG00000272179.1
RHOXF2B
NDUFA1
SNORA69|ENSG00000206622.1
MIR766
RN7SL118P
SNORA35|ENSG00000239182.1
MIR1277
RN7SL712P
SNORA64|ENSG00000252441.1
SNORA35|ENSG00000271907.1
MIR448
MIR1911
SNORA35|ENSG00000208839.1
SNORD30
RN7SL93P
U3|ENSG00000201674.1
snoU13|ENSG00000238811.1
RN7SL266P
MIR4329
ZCCHC16
TRPC5OS
RNA5SP512
RN7SL661P
LINC00890
TDGF1P3
GNG5P2
SNORD96B
MIR3978
MIR652
MID2
NCBP2L
RBM41
MIR548AN
AGTR2
ABCD1
SLC25A5
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CAPN6
CD40LG
CDR1
CLIC2
CNGA2
COL4A5
COL4A6
CTAG1B
TEX28
DCX
DKC1
DNASE1L1
TSC22D3
DUSP9
EMD
F8
F9
ACSL4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
GDI1
GLUD2
GRIA3
GUCY2F
HCFC1
HMGB3
HPRT1
HTR2C
IDH3G
IDS
IGSF1
IL9R|ENSG00000124334.12
IL13RA1
IL13RA2
IRAK1
L1CAM
LAMP2
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
OCRL
PAK3
PLS3
PLXNB3
PRPS1
PSMD10
OPN1LW
RENBP
RPL10
RPL39
SLC6A8
SMARCA1
SOX3
SSR4
VAMP7|ENSG00000124333.10
TAZ
SERPINA7
TRPC5
UBE2A
VBP1
XPNPEP2
ZIC3
ZNF75D
RNF113A
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
CUL4B
IRS4
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
CLDN2
FAM50A
AIFM1
TMEM257
GPR50
RAB33A
ARHGEF6
MAGEC1
AMMECR1
ZBTB33
MAMLD1
BCAP31
TENM1
SPRY3|ENSG00000168939.6
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
PGRMC1
TREX2
SLC6A14
SEPT6
ATP1B4
KCNE1L
LDOC1
FAM127B
IL1RAPL2
SRPK3
RBMX
HTATSF1
C1GALT1C1
PNMA3
CTAG2
NSDHL
ZDHHC9
LUZP4
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
WDR44
NUP62CL
TBC1D8B
CXorf48
TMEM255A
CXorf57
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
NXT2
NKRF
TEX13B
TEX13A
MOSPD1
THOC2
KIAA1210
RGAG1
PDZD4
LRCH2
RAP2C
FAM3A
BCORL1
CXorf56
SPANXC
UPF3B
PRRG3
BRCC3
NKAP
RNF128
MAP7D3
MORC4
LONRF3
ALG13
GPR101
CD99L2
H2AFB3
USP26
TMEM164
PHF6
FRMPD3
RHOXF2
TMEM185A
SLITRK2
FATE1
HS6ST2
FRMD7
KLHL13
CHRDL1
CXorf40A
FAM58A
RIPPLY1
MMGT1
PNMA5
ATG4A
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
PIH1D3
MUM1L1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
RBMXL3
DOCK11
AMOT
CSAG1
FMR1NB
ARHGAP36
AKAP14
RHOXF1
NKAPP1
FAM122B
FAM122C
ZCCHC12
CXorf61
SLC25A43
NRK
DDX26B
ZNF449
VMA21
CTAG1A
CT47A11
ATP11C
LINC00632
VSIG1
LHFPL1
SOWAHD
OR13H1
CCDC160
CXorf66
UBE2NL
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
SPANXN2
MIR503HG
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR450A2
MIR503
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR510
MIR514A1
MIR514A2
MIR514A3
CT47B1
CT47A7
MIR542
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
OPN1MW2
SPANXB1
CT45A2
MIR767
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR891A
MIR892A
LINC00892
HSFX2
CXorf64
SMIM9
SPANXB2
CMC4
PNMA6C
MIR513C
MIR1912
MIR1298
MIR320D2
MIR718
MIR513B
MIR764
MIR2114
MIR514B
MIR4330
MIR3672
HSFX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

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

Genes
CARS
DDB2
EXT2
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
CREB3L1
SLC22A10
RN7SL259P
SNHG1
RN7SL119P
TMEM223
C11orf83
SNORA57|ENSG00000206597.1
METTL12
MIR3654
MIR1908
MIR611
RPLP0P2
SYT7
RN7SL23P
SDHAF2
PGA4
PGA3
MS4A18
MS4A4E
MS4A2
OOSP1
RN7SKP192
MIR3162
RN7SL435P
RN7SL42P
GLYATL1P2
BTBD18
C11orf31
RTN4RL2
RN7SKP259
RNA5SP341
PRG2
P2RX3
snoU13|ENSG00000238692.1
OR5G5P
TRIM51HP
TRIM49B
OR4C5
MIR3161
RNA5SP340
snoU13|ENSG00000252447.1
KBTBD4
PTPMT1
RN7SL652P
RN7SL772P
SNORD67|ENSG00000212135.1
SNORD67|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
PHF21A
CHST1
CD82
C11orf96
RN7SKP287
HNRNPKP3
SNORA31|ENSG00000251838.1
TRAF6
COMMD9
MIR3973
TRIM44
MIR1343
EHF
CD59
C11orf91
EIF3M
U3|ENSG00000212551.1
DNAJC24
ARL14EP
RN7SL240P
RN7SKP158
LINC00678
RNA5SP339
SVIP
RNA5SP338
RNA5SP337
RNA5SP336
SLC6A5
SNORA1|ENSG00000207407.1
MIR4486
RNA5SP335
RNA5SP334
RNA5SP333
SAA3P
TPH1
SNORD14B
SNORD14A
OR7E14P
RN7SKP90
C11orf58
RN7SL188P
PSMA1
RNA5SP332
SPON1
RNA5SP331
RN7SKP151
LINC00958
SCARNA16|ENSG00000252329.1
PARVA
SNORD97
LYVE1
RNU6ATAC33P
ADM
RN7SKP50
RN7SL56P
snoU13|ENSG00000238387.1
SNORA23
MIR5691
RNA5SP330
SNORA45
SNORA3|ENSG00000200983.1
SCARNA20|ENSG00000252778.1
OR10AB1P
GVINP1
TAF10
RRP8
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62|ENSG00000201980.1
OR51C1P
SNORA7|ENSG00000206976.1
snoU13|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
ACP2
AP2A2
APLNR
AMPD3
APBB1
RHOG
ARHGAP1
ARNTL
ART1
ASCL2
BDNF
SERPING1
MPPED2
MYRF
TMEM258
DAGLA
CALCA
CALCB
CAT
CCKBR
CD5
CD6
MS4A1
MS4A3
CD44
CD81
CD151
CDKN1C
CHRM1
CHRM4
TPP1
CNGA4
CNTF
COPB1
CRY2
CSTF3
CTNND1
CTSD
DDB1
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
F2
FEN1
FOLH1
FSHB
FTH1
GAS2
GIF
GNG3
GTF2H1
HBB
HBD
HBE1
HBG2
HPX
IGF2
ILK
INCENP
INS
IRF7
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
FADS1
FADS3
LRP4
LSP1|ENSG00000130592.9
CAPRIN1
MDK
SCGB2A1
SCGB2A2
MUC2
MUC6
MYBPC3
MYOD1
NAP1L4
NDUFS3
NELL1
NUCB2
SLC22A18
OSBP
PAX6
PDE3B
PGA5
PIK3C2A
POLR2G
POLR2L
PSMA1
PSMC3
PSMD13
PTH
PTPRJ
RAB3IL1
RAG1
RAG2
RAPSN
RARRES3
RCN1
RNH1
ROM1
MRPL23
RPL27A
RPS13
RRM1
SAA1
SAA2
SAA4
SLC1A2
SLC3A2
SMPD1
SPI1
TRIM21
SSRP1
ST5
STIM1
STX3
STX5
ABCC8
TALDO1
TCN1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TSG101
PHLDA2
TUB
SCGB1A1
BEST1
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
BBOX1
PPFIBP2
SLC43A1
IFITM1
DGKZ
API5
MADD
OR6A2
DCHS1
EIF3F
BRSK2
MTA2
UBE2L6
SLC22A6
SLC22A8
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
MICAL2
CTR9
ATG13
CKAP5
TRIM66
NR1H3
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
GLYAT
MRVI1
TRIM22
PRG3
IFITM3
NXF1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
TAF6L
SCGB1D2
SCGB1D1
CELF1
OR5I1
CLP1
PKP3
HPS5
PTGDR2
RRAS2
ZP1
SWAP70
GANAB
DTX4
DENND5A
NUP160
FNBP4
SIRT3
OR52A1
ARFIP2
MTCH2
FJX1
KIAA1549L
ABTB2
PAMR1
ZDHHC5
DAK
B3GAT3
FBXO3
SERGEF
OR5L2
OR10A3
TIMM10B
TIMM10
BSCL2
ELP4
DKK3
RBMXL2
PGAP2
PRPF19
SLC43A3
PACSIN3
TRPM5
UBQLN3
RNF141
UBXN1
APIP
TMX2
HSD17B12
TMEM216
BET1L
CEND1
SLC15A3
MS4A4A
TMEM138
CYB5R2
CDHR5
TOLLIP
ZDHHC13
WDR74
MS4A12
MRPL16
TMEM132A
HRASLS2
USP47
VPS37C
TRIM68
NAT10
UEVLD
LIN7C
SLC35C1
TCP11L1
LGR4
PIDD
KCNQ1DN
SOX6
AMBRA1
KBTBD4
TTC17
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
PRDM11
CHRNA10
SLC17A6
PNPLA2
SYT13
PHRF1
LRRC4C
SCUBE2
MS4A7
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
FAM111A
ANO3
MS4A6A
MS4A5
EPS8L2
TUT1
STK33
CHID1
AHNAK
PRRG4
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ZNF408
QSER1
AGBL2
ZBTB3
CPSF7
PRR5L
ASRGL1
ATHL1
INTS5
ZFP91
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
PTDSS2
SBF2
KIF18A
MS4A8
FAM160A2
FAR1
BTBD10
ARFGAP2
ACCS
MS4A14
TRIM51
PTPN5
MICALCL
LGALS12
TRIM5
TNKS1BP1
NAV2
SYT8
TSPAN18
CCDC34
SLC39A13
DEPDC7
GLYATL1
PRKCDBP
SAAL1
SLC22A9
OSBPL5
C1QTNF4
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
CYP2R1
DBX1
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
C11orf94
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
METTL15
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYB561A3
PPP1R32
LRRN4CL
HNRNPUL2
ALKBH3
MS4A6E
OR52B2
OR4C3
OR4S1
C11orf35
EML3
OR51F1
MRGPRX1
OR10AG1
OR5J2
OR4C13
OR4C12
CSNK2A3
OR51V1
OR9G4
LINC00301
EFCAB4A
TTC9C
SLC22A24
IGSF22
OR10A4
OLFML1
NLRP10
NLRP14
ANO9
LUZP2
OR5F1
OR5AP2
B4GALNT4
OR52L1
OR2AG2
OR52B6
OTOG
DCDC1
MS4A10
OR10A2
OVCH2
PDDC1
GALNT18
NCR3LG1
FAM111B
TMEM179B
MRGPRG
SLC22A25
IFITM5
FAM99A
OR56B1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
LINC00610
FAM180B
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
SCGB1D4
MIR130A
MIR210
TMEM41B
OR5B3
CCDC73
MS4A13
TRIM64C
MIR610
MUC5B
MIR302E
MIR670
MIR3159
MIR4298
MIR4299
MTRNR2L8
CCDC179
MIR4686
MIR4487
MIR4694
MIR4687
MIR4488

Genes in Wide Peak

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

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

Genes
RNA5SP178
MIR887
U8|ENSG00000202269.1
MIR4637
FAM105A
CT49
ANKRD33B
CMBL
FAM173B
RNA5SP177
SNORD123
MIR4636
RNA5SP176
RN7SKP79
UBE2QL1
RN7SKP73
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
ADCY2
CTNND2
DAP
DNAH5
MTRR
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
IRX4
TAS2R1
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
C5orf55
C5orf49
C5orf38
IRX2
ADAMTS16
SLC6A19
SLC6A18
MIR4277
MIR4458
MIR4457
MIR4456

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p14.3.

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

Genes
WDR70
RN7SL37P
RNA5SP181
LMBRD2
U3|ENSG00000201368.1
BRIX1
C1QTNF3
MIR579
snoU13|ENSG00000238864.1
RN7SKP207
SNORA18|ENSG00000252601.1
SNORD29
SNORA40|ENSG00000252083.1
C5orf17
RN7SL572P
CDH6
CDH9
CDH10
IL7R
NPR3
PMCHL1
PRLR
RAD1
SKP2
SLC1A3
TARS
NUP155
SUB1
PDZD2
AMACR
NIPBL
RAI14
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
C5orf22
PRDM9
GOLPH3
AGXT2
C5orf42
SPEF2
ADAMTS12
NADK2
UGT3A1
CAPSL
DNAJC21
TTC23L
UGT3A2
RANBP3L
MIR580
MIR4279

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.1.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1|ENSG00000271739.1
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13|ENSG00000238922.1
FLJ00325
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CAV1
CAV2
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
FAM3C
FASTK
ZNF277
ABCB8
TFEC
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
TES
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
GPR85
TAS2R5
CHPF2
ING3
LRRN3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
CPED1
TTC26
JHDM1D
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
C7orf60
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
LSMEM1
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.1.

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

Genes
NRG3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.12.

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

Genes
ELK4
FH
SLC45A3
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13|ENSG00000239094.1
snoU13|ENSG00000238545.1
MIR4742
snoU13|ENSG00000238856.1
MIR320B2
SNORA72|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13|ENSG00000238576.1
snoU13|ENSG00000238798.1
U3|ENSG00000221673.1
RNA5SP76
SLC30A10
U3|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
SERTAD4
MIR4260
MIR205HG
MIR29B2
MIR29C
snoU13|ENSG00000238401.1
FAIM3
IL20
SNORD112|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72|ENSG00000201944.1
SNORD112|ENSG00000252946.1
SCARNA20|ENSG00000251861.1
RNA5SP75
RNA5SP74
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
C4BPA
C4BPB
CAPN2
CD34
CENPF
CHML
LYST
CR1
CR1L
CR2
CTSE
CD55
EIF2D
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PLXNA2
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RBBP5
RGS7
RYR2
SRP9
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
ZNF124
HIST3H3
GNPAT
DYRK3
CDC42BPA
DEGS1
KMO
RAB7L1
TAF1A
EXO1
MAPKAPK2
GGPS1
IKBKE
TMEM63A
TOMM20
URB2
CEP170
TMCC2
LPGAT1
AKT3
BPNT1
LRRN2
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
IL24
DUSP10
COG2
RBM34
NFASC
FBXO28
ABCB10
OPN3
DSTYK
RAB3GAP2
INTS7
AHCTF1
NSL1
OR2M4
OR2L2
OR2T1
RPS6KC1
DIEXF
TAF5L
DISC1
FLVCR1
CNIH4
PYCR2
NENF
IL19
G0S2
RRP15
DESI2
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
TMEM206
YOD1
BATF3
ZNF692
IARS2
HHAT
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
RHOU
TFB2M
GREM2
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
NUAK2
RASSF5
MIXL1
SPRTN
FCAMR
OBSCN
EFCAB2
MLK4
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
LEMD1
NLRP3
SLC26A9
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
B3GALNT2
MFSD4
PM20D1
GCSAML
CNIH3
EXOC8
C1orf227
FAM71A
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
SLC41A1
OR2T6
SYT14
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
TMEM81
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
C1orf132
TRIM67
MAP1LC3C
OR13G1
MIR135B
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

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

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

Genes
RNA5SP475
RN7SL864P
RN7SKP111
LINC00687
C20orf187
JAG1
RNU105B
TMX4
RN7SL547P
snoR26
RN7SL498P
LINC00654
LINC00658
SNORA26|ENSG00000212517.1
RNA5SP474
RN7SL514P
snoU13|ENSG00000252058.1
SNORA31|ENSG00000252096.1
MIR103A2
MAVS
U3|ENSG00000201346.1
RN7SL839P
RN7SL555P
TMEM239
SNORD57
SNORD56|ENSG00000229686.1
SNORD86
SNORA51|ENSG00000271798.1
SNORD110
MIR1292
SNORD119
RN7SL561P
TCF15
CSNK2A1
DEFB128
DEFB127
DEFB126
DEFB125
ADRA1D
JAG1
AVP
BMP2
CDC25B
CENPB
CHGB
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PCNA
PDYN
PLCB4
PRNP
PTPRA
SIGLEC1
SNAP25
SNRPB
SOX12
TGM3
MKKS
ATRN
CDS2
PSMF1
SNPH
LZTS3
RASSF2
SLC23A2
SIRPB1
NOP56
RBCK1
RNF24
UBOX5
BTBD3
PLCB1
PRND
FLRT3
LAMP5
SPEF1
C20orf194
SDCBP2
TMEM230
ANGPT4
ESF1
TRMT6
HAO1
SMOX
CRLS1
C20orf27
SPTLC3
AP5S1
TMEM74B
SIRPG
FERMT1
KIF16B
TASP1
NSFL1C
GPCPD1
CPXM1
PAK7
EBF4
TRIB3
FASTKD5
ANKEF1
GFRA4
VPS16
PCED1A
MRPS26
DDRGK1
NDUFAF5
ZNF343
NRSN2
PANK2
ADAM33
SEL1L2
FAM110A
SLC4A11
MCM8
ZCCHC3
SCRT2
SLC52A3
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
PROKR2
SLX4IP
C20orf96
MACROD2
SRXN1
ISM1
DEFB129
SIRPA
STK35
PRNT
C20orf196
LRRN4
SIRPB2
RSPO4
TGM6
DEFB132
C20orf202
RAD21L1
TMEM239

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p12.

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

Genes
MAML2
BIRC3
CCND1
DDB2
EXT2
LMO2
MEN1
NUMA1
WT1
PICALM
CREB3L1
RNA5SP348
MMP12
WTAPP1
snoU13|ENSG00000239154.1
snoU13|ENSG00000252679.1
MIR3920
snoU13|ENSG00000238388.1
RN7SKP115
RN7SL222P
RN7SKP53
RNA5SP347
RNA5SP346
RNA5SP345
SRSF8
SRSF8
MIR548L
VSTM5
RN7SL195P
snoU13|ENSG00000238437.1
MED17
SNORA40|ENSG00000210825.1
SNORA18|ENSG00000207145.1
SNORD5|ENSG00000239195.1
SNORA8|ENSG00000207304.1
SNORA1|ENSG00000206834.1
SNORD6
SNORA32|ENSG00000206799.1
SNORA25|ENSG00000207112.1
SCARNA9
RN7SL223P
SLC36A4
snoU13|ENSG00000239086.1
DISC1FP1
CHORDC1
SNORD56|ENSG00000207299.1
TRIM49D1
TRIM64B
TRIM77
FOLH1B
GRM5
TMEM135
RN7SL225P
snoU13|ENSG00000238666.1
PCF11
SNORA70E
snoU13|ENSG00000238995.1
SNORD112|ENSG00000252592.1
DKFZP434E1119
ACER3
GUCY2EP
RNA5SP344
UVRAG
RN7SL786P
MOGAT2
SNORD15B
SNORD15A
MIR326
NEU3
RN7SL239P
MIR4696
SNORD43|ENSG00000212277.1
RN7SKP297
SNORA7|ENSG00000206913.1
RNA5SP343
UCP2
RN7SKP243
MRPL48
MIR139
snoU13|ENSG00000238768.1
RNA5SP342
ZNF705E
ENPP7P8
UNC93B6
MIR3664
MIR548K
FGF3
MIR3164
TPCN2
MIR4691
FAM86C2P
DOC2GP
C11orf72
RN7SL59P
PTPRCAP
RN7SKP239
POLD4
snoU13|ENSG00000238892.1
SYT12
U3|ENSG00000252709.1
RN7SL12P
RBM14
ZDHHC24
SNORA43|ENSG00000201733.1
snoU13|ENSG00000238763.1
snoU13|ENSG00000238752.1
GAL3ST3
AP5B1
RN7SL309P
MIR4489
MIR4690
MALAT1
POLA2
SLC22A20
FAU
RN7SL114P
MIR1237
TEX40
VEGFB
OTUB1
RN7SL596P
C11orf95
SLC22A10
RN7SL259P
SNHG1
RN7SL119P
TMEM223
C11orf83
SNORA57|ENSG00000206597.1
METTL12
MIR3654
MIR1908
MIR611
RPLP0P2
SYT7
RN7SL23P
SDHAF2
PGA4
PGA3
MS4A18
MS4A4E
MS4A2
OOSP1
RN7SKP192
MIR3162
RN7SL435P
RN7SL42P
GLYATL1P2
BTBD18
C11orf31
RTN4RL2
RN7SKP259
RNA5SP341
PRG2
P2RX3
snoU13|ENSG00000238692.1
OR5G5P
TRIM51HP
TRIM49B
OR4C5
MIR3161
RNA5SP340
snoU13|ENSG00000252447.1
KBTBD4
PTPMT1
RN7SL652P
RN7SL772P
SNORD67|ENSG00000212135.1
SNORD67|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
PHF21A
CHST1
CD82
C11orf96
RN7SKP287
HNRNPKP3
SNORA31|ENSG00000251838.1
TRAF6
COMMD9
MIR3973
TRIM44
MIR1343
EHF
CD59
C11orf91
EIF3M
U3|ENSG00000212551.1
DNAJC24
ACP2
ACTN3
ADRBK1
APLNR
ALDH3B1
ALDH3B2
BIRC2
ARHGAP1
PHOX2A
ARL2
ARRB1
BAD
BBS1
SERPING1
CAPN5
VPS51
MRPL49
ZNHIT2
MPPED2
MYRF
TMEM258
DAGLA
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CD5
CD6
MS4A1
MS4A3
CD44
CFL1
CTSC
CHKA
CHRM1
CHRM4
CLNS1A
CNTF
COX8A
CPT1A
CRY2
CST6
CSTF3
CTNND1
CTSW
DDB1
DHCR7
DLG2
EEF1G
ELF5
MARK2
CTTN
ESRRA
F2
FEN1
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FTH1
FUT4
LRRC32
GIF
GNG3
GRIA4
GSTP1
GUCY1A2
SLC29A2
DNAJC4
IGHMBP2
INCENP
INPPL1
FADS1
FADS3
LRP4
LRP5
LTBP3
CAPRIN1
MAP6
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP13
MRE11A
MTNR1B
MYBPC3
MYO7A
NDUFC2
NDUFS3
NDUFV1
NDUFS8
OMP
OSBP
OVOL1
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PGA5
PGR
PLCB3
POLR2G
PPP1CA
PPP2R5B
PRCP
PRKRIR
PSMC3
PTPRJ
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RCN1
RELA
DPF2
ROM1
RPS3
RPS6KB2
SIPA1
SLC1A2
SLC3A2
SPI1
SPTBN2
SSRP1
STX3
STX5
TCN1
THRSP
TM7SF2
TRPC6
TYR
UCP3
SCGB1A1
BEST1
WNT11
SF1
ZFPL1
PDHX
FOSL1
FZD4
PPFIA1
SLC43A1
DGKZ
API5
MADD
JRKL
CTSF
EED
FADD
BANF1
MTMR2
RPS6KA4
AIP
SART1
FIBP
MTA2
UBE2L6
MMP20
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
PITPNM1
RIN1
MTL5
CEP57
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
KCNK7
HIPK3
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
PRG3
YAP1
CDC42EP2
NXF1
KAT5
SSSCA1
DRAP1
TAF6L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
ME3
GPR83
YIF1A
EHD1
STIP1
CLP1
SF3B2
CCDC85B
B3GNT1
PRSS23
PLA2G16
PTGDR2
SLCO2B1
ZP1
SHANK2
KDM2A
ENDOD1
ATG2A
GANAB
FAM168A
DTX4
NUP160
FNBP4
CLCF1
FAM89B
RAB38
FLRT1
MTCH2
PANX1
FJX1
KIAA1549L
PRDX5
ABTB2
BRMS1
CHRDL2
PAMR1
ANAPC15
ZDHHC5
ATL3
TSKU
C2CD3
DAK
TENM4
B3GAT3
FBXO3
OR5L2
PPP1R14B
TIMM10
MYEOV
BSCL2
ELP4
RAB30
PRPF19
C11orf54
AAMDC
MACROD1
SLC43A3
PACSIN3
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
KCNK4
UBXN1
APIP
TMX2
GAL
SUV420H1
HSD17B12
TMEM216
COA4
SLC15A3
MS4A4A
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
RSF1
C11orf24
CNTN5
WDR74
SYTL2
ANKRD49
MS4A12
MRPL16
SSH3
TMEM132A
HRASLS2
LAMTOR1
VPS37C
ANO1
NADSYN1
FAM86C1
NAT10
CCDC87
PPP6R3
RNF121
SLC35C1
TCP11L1
CDC42BPG
AMBRA1
PACS1
KDM4D
KBTBD4
TTC17
TMEM126B
SLC22A11
GPR137
SMCO4
C11orf30
PRDM11
CABP4
TRIM49
CD248
CORO1B
SCYL1
USP35
KIAA1377
CARNS1
SYT13
LRRC4C
PLEKHB1
MS4A7
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
ALX4
FAM111A
MMP27
MS4A6A
MS4A5
KLC2
TUT1
MRPL11
KCTD14
LRFN4
AHNAK
ALG8
PRRG4
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
DYNC2H1
C11orf80
NARS2
CCDC82
ZNF408
NAA40
QSER1
AGBL2
ZBTB3
CPSF7
PRR5L
ASRGL1
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
GDPD5
CLPB
UNC93B1
RAB1B
C11orf68
MS4A8
FERMT3
TRPT1
RBM4B
FRMD8
TMEM133
RNASEH2C
TMEM126A
DCUN1D5
EIF1AD
NUDT22
ARFGAP2
MSANTD4
SYVN1
DGAT2
ACCS
MS4A14
TRIM51
RELT
C11orf70
LGALS12
TNKS1BP1
KIAA1731
ATG16L2
TSPAN18
SLC39A13
DEPDC7
ACY3
INTS4
GLYATL1
CDCA5
SLC22A9
CARD16
C1QTNF4
TMEM123
BATF2
SLC22A12
MRGPRD
MRGPRF
ARAP1
CATSPER1
HRASLS5
C11orf74
OR4C46
OR4X2
OR4B1
GYLTL1B
FAT3
OR8I2
LDLRAD3
XRRA1
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
C11orf84
AMOTL1
CCDC67
GPHA2
B3GNT6
IMMP1L
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
MRPL21
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYB561A3
PPP1R32
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
MS4A6E
DEFB108B
PELI3
ANGPTL5
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
C11orf86
NUDT8
OR4C3
OR4S1
EML3
TMEM151A
NPAS4
AQP11
OR10AG1
OR5J2
OR4C13
OR4C12
C11orf85
SLC25A45
OR9G4
LINC00301
P4HA3
PGM2L1
KLHL35
KCTD21
CCDC88B
TTC9C
SLC22A24
RCOR2
OR5F1
OR5AP2
ANKRD13D
ANKRD42
DCDC1
MS4A10
OR2AT4
HEPHL1
TBX10
FAM111B
TMEM179B
TBC1D10C
DNAJB13
SLC22A25
SPDYC
LIPT2
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
FOLR4
KDM4E
LINC00610
FAM180B
PCNXL3
OR4A47
SCGB1D4
MIR130A
MIR192
DDI1
CARD17
OR5B3
CCDC73
MS4A13
TRIM49C
TRIM64C
NEAT1
MIR708
MIR1261
MIR1304
MIR670
MIR4300
MIR3165
MIR1260B
MIR3163
MIR3166
CASP12
TPBGL
RBM4
MIR4490
MIR548AL
MIR4487
MIR4692
MIR4693
MIR4488
MIR5579

Arm-level results

Table 3. Get Full Table Arm-level significance table - 27 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1300 | 0.28 | 1.11 | 0.445 | 0.17 | -1.81 | 1
1q | 1195 | 0.43 | 4.64 | 8.91e-06 | 0.10 | -3.38 | 1
2p | 624 | 0.32 | -0.412 | 1 | 0.05 | -6.17 | 1
2q | 967 | 0.29 | 0.00592 | 1 | 0.06 | -5.13 | 1
3p | 644 | 0.23 | -2.46 | 1 | 0.24 | -2.05 | 1
3q | 733 | 0.27 | -1.17 | 1 | 0.21 | -2.58 | 1
4p | 289 | 0.05 | -5.14 | 1 | 0.63 | 6.16 | 1.58e-09
4q | 670 | 0.02 | -4.19 | 1 | 0.72 | 10.3 | 0
5p | 183 | 0.13 | -3.73 | 1 | 0.72 | 7.9 | 7.22e-15
5q | 905 | 0.06 | -3.59 | 1 | 0.69 | 10.4 | 0
6p | 710 | 0.19 | -3.35 | 1 | 0.13 | -4.63 | 1
6q | 556 | 0.17 | -4.31 | 1 | 0.13 | -5 | 1
7p | 389 | 0.82 | 11.4 | 0 | 0.07 | -3.32 | 1
7q | 783 | 0.71 | 10.4 | 0 | 0.07 | -3.61 | 1
8p | 338 | 0.80 | 10.2 | 0 | 0.32 | -0.734 | 1
8q | 551 | 0.76 | 10.5 | 0 | 0.19 | -2.09 | 1
9p | 301 | 0.17 | -3.89 | 1 | 0.47 | 2.31 | 0.0276
9q | 700 | 0.18 | -2.83 | 1 | 0.44 | 2.79 | 0.00813
10p | 253 | 0.08 | -5.3 | 1 | 0.53 | 3.72 | 0.000368
10q | 738 | 0.10 | -4.08 | 1 | 0.51 | 4.84 | 2.56e-06
11p | 509 | 0.19 | -2.37 | 1 | 0.70 | 8.71 | 0
11q | 975 | 0.06 | -2.86 | 1 | 0.79 | 13.6 | 0
12p | 339 | 0.97 | 15.2 | 0 | 0.20 | -0.797 | 1
12q | 904 | 0.66 | 9.88 | 0 | 0.02 | -4.31 | 1
13q | 560 | 0.03 | -4.04 | 1 | 0.76 | 10.7 | 0
14q | 938 | 0.39 | 2.56 | 0.021 | 0.20 | -1.94 | 1
15q | 810 | 0.42 | 2.71 | 0.0152 | 0.29 | -0.324 | 1
16p | 559 | 0.15 | -4.15 | 1 | 0.33 | -0.339 | 1
16q | 455 | 0.13 | -4.63 | 1 | 0.38 | 0.564 | 0.674
17p | 415 | 0.35 | -0.303 | 1 | 0.34 | -0.43 | 1
17q | 972 | 0.38 | 2.3 | 0.0389 | 0.17 | -2.56 | 1
18p | 104 | 0.09 | -3.67 | 1 | 0.80 | 9.67 | 0
18q | 275 | 0.07 | -3.37 | 1 | 0.82 | 11.1 | 0
19p | 681 | 0.35 | 0.593 | 0.851 | 0.44 | 2.7 | 0.00997
19q | 935 | 0.29 | 0.0173 | 1 | 0.44 | 3.69 | 0.000373
20p | 234 | 0.28 | -2.45 | 1 | 0.26 | -2.7 | 1
20q | 448 | 0.28 | -1.85 | 1 | 0.16 | -4.4 | 1
21q | 258 | 0.84 | 11.5 | 0 | 0.08 | -3.12 | 1
22q | 564 | 0.36 | 0.439 | 0.944 | 0.40 | 1.34 | 0.224
Xq | 668 | 0.17 | -3.56 | 1 | 0.23 | -2.29 | 1

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

- Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

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/TGCT-TP/11449416/GDAC_MergeDataFiles_11451880/TGCT-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

- Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.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

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 150 Input Tumor Samples.

Tumor Sample Names
TCGA-2G-AAEW-01A-11D-A42X-01
TCGA-2G-AAEX-01A-11D-A42X-01
TCGA-2G-AAF1-01A-11D-A42X-01
TCGA-2G-AAF4-01A-11D-A42X-01
TCGA-2G-AAF6-01A-11D-A42X-01
TCGA-2G-AAF8-01A-11D-A42X-01
TCGA-2G-AAFE-01A-11D-A42X-01
TCGA-2G-AAFG-01A-11D-A42X-01
TCGA-2G-AAFH-01A-12D-A42X-01
TCGA-2G-AAFI-01A-21D-A42X-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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- 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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