SNP6 Copy number analysis (GISTIC2)
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 2.0.23.

Summary

There were 110 tumor samples used in this analysis: 29 significant arm-level results, 39 significant focal amplifications, and 40 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 - 39 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
3q26.33 | 2.9855e-37 | 2.9855e-37 | chr3:181680270-182865155 | 6
8p11.23 | 2.3035e-20 | 2.3035e-20 | chr8:38281868-38626020 | 5
11q13.3 | 4.9498e-14 | 2.2324e-13 | chr11:69619064-70581423 | 13
5p15.2 | 1.8906e-08 | 1.8906e-08 | chr5:13265365-13266262 | 0 [DNAH5]
8q24.21 | 3.3931e-08 | 3.3931e-08 | chr8:127166717-127970555 | 12
7p11.2 | 1.9848e-06 | 1.9848e-06 | chr7:54395184-54397284 | 0 [LINC01445]
11q21 | 5.7811e-06 | 3.7459e-05 | chr11:96562424-96566636 | 0 [LOC105369443]
14q13.1 | 0.00013735 | 0.00013735 | chr14:34348215-34350419 | 0 [SPTSSA]
Xp21.3 | 0.00034988 | 0.00034988 | chrX:26085791-26087188 | 0 [MAGEB18]
19q13.11 | 0.00039347 | 0.00039347 | chr19:33204397-33457669 | 6
2q31.1 | 0.00049784 | 0.00049784 | chr2:169465230-169468481 | 0 [BBS5]
9p13.3 | 0.0020435 | 0.0020435 | chr9:35563972-36754816 | 34
18p11.32 | 0.0028522 | 0.0028522 | chr18:1629032-1630055 | 0 [LINC00470]
4q13.3 | 0.0013518 | 0.0042701 | chr4:70620934-70623231 | 0 [ENAM]
12p12.1 | 0.0055721 | 0.0055721 | chr12:24723955-25355706 | 7
6q12 | 0.0063274 | 0.0064237 | chr6:67232899-67234938 | 0 [LOC102723883]
20p11.22 | 0.0069402 | 0.0069402 | chr20:22081801-22084218 | 0 [LINC01432]
5q32 | 0.00034988 | 0.0076833 | chr5:145740576-145741273 | 0 [PRELID2]
4p12 | 0.0048205 | 0.0086693 | chr4:46762045-46763547 | 1
21q21.1 | 0.012038 | 0.012038 | chr21:16970634-16973377 | 0 [MIR99AHG]
Xq22.3 | 0.012038 | 0.012038 | chrX:107905794-109989371 | 16
Yq11.221 | 0.016014 | 0.016014 | chrY:12512884-12514081 | 0 [GYG2P1]
2p24.3 | 0.0021829 | 0.02144 | chr2:16143430-16148533 | 0 [GACAT3]
1q21.2 | 0.023511 | 0.023511 | chr1:119727351-175354241 | 644
5q31.1 | 0.010662 | 0.026873 | chr5:135803396-135808293 | 0 [MIR5692C1]
2p24.2 | 0.0084235 | 0.029924 | chr2:18294092-18295501 | 0 [RDH14]
20q11.22 | 0.029924 | 0.029924 | chr20:26219450-35801235 | 112
6p21.1 | 0.036421 | 0.038422 | chr6:43963421-43963918 | 0 [LINC01512]
4q12 | 0.012038 | 0.047804 | chr4:52389402-57504744 | 46
13q21.33 | 0.012578 | 0.068432 | chr13:70591229-70593026 | 0 [LINC00348]
16p13.13 | 0.068432 | 0.068432 | chr16:10697260-10698657 | 0 [TEKT5]
13q21.31 | 0.012972 | 0.078297 | chr13:61961483-61962744 | 0 [LINC00358]
15q25.3 | 0.095614 | 0.095614 | chr15:87882798-87884595 | 1
13q34 | 0.013423 | 0.13631 | chr13:112571276-113915739 | 30
9q31.1 | 0.14 | 0.14 | chr9:101494795-101497221 | 0 [TMEM246]
1p32.1 | 0.15955 | 0.15955 | chr1:58719280-58731664 | 0 [MYSM1]
18q12.1 | 0.063349 | 0.18171 | chr18:21251780-32624707 | 64
10p14 | 0.23955 | 0.23955 | chr10:9380131-9398288 | 0 [LOC101928272]
18q12.1 | 0.039532 | 1 | chr18:1-80373285 | 410

Genes in Wide Peak

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

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

Genes
SOX2
ATP11B
SOX2-OT
FLJ46066
LINC01206
LOC105374244

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
FGFR1
WHSC1L1
LETM2
RNF5P1
C8orf86

Genes in Wide Peak

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

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

Genes
CCND1
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
SHANK2
ANO1
ORAOV1
ANO1-AS2
MIR548K
LOC101928443

Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
PVT1
TMEM75
CASC8
CASC11
MIR1205
MIR1204
CCAT1
CCAT2
CASC21
CASC19

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
CEBPA
CEBPG
LRP3
PEPD
SLC7A10
CEBPA-AS1

Genes in Wide Peak

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

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

Genes
CA9
CCIN
CD72
CLTA
NPR2
RMRP
TESK1
TLN1
TPM2
RECK
RGP1
MELK
GNE
CREB3
SPAG8
SIT1
TMEM8B
OR2S2
GBA2
HINT2
ARHGEF39
LINC00950
RNF38
GLIPR2
LINC00961
CCDC107
FAM221B
OR13J1
HRCT1
MSMP
MIR4667
LOC101926948
MIR6852
MIR6853

Genes in Wide Peak

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

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

Genes
KRAS
BCAT1
LRMP
CASC1
ETFRF1
C12orf77
LOC645177

Genes in Wide Peak

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

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

Genes
COX7B2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq22.3.

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

Genes
COL4A5
COL4A6
ACSL4
GUCY2F
PSMD10
IRS4
MID2
KCNE5
NXT2
TEX13B
ATG4A
VSIG1
MIR4454
LOC101928335
LOC101928358
MIR6087

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
PDE4DIP
hsa-mir-3119-1
ADAR
ALDH9A1
APCS
APOA2
FASLG
SERPINC1
ATP1A2
ATP1A4
ATP1B1
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
DPT
DRD5P2
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
F5
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
ACKR1
GBA
GBAP1
GJA5
GJA8
HDGF
HMGCS2
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYOC
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PIGC
PI4KB
PKLR
PRRX1
POU2F1
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RNU1-4
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
XCL2
VPS72
THBS3
TCHH
TNR
TOP1P1
CCT3
TUFT1
TNFSF4
UCK2
USF1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
ADAM15
PEX11B
CREG1
CD84
SELENBP1
TNFSF18
MPZL1
SH2D2A
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
GPR52
AIM2
ADAMTS4
SEC22B
CHD1L
PRDX6
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RABGAP1L
RBM8A
NR1I3
SCAMP3
GPA33
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
CELF3
PMF1
DUSP12
VPS45
KIAA0907
KIFAP3
ATF6
POGZ
SYT11
PRRC2C
RPRD2
SMG5
NCSTN
GPR161
SNAPIN
RUSC1
CA14
CFAP45
NBPF14
MPC2
OLFML2B
C1orf43
DNM3
CHTOP
PHGDH
LCE2B
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
RNVU1-7
RNU1-3
RNU1-2
RNU1-1
USP21
CACYBP
SLC39A1
RNF115
KLHL20
LAMTOR2
TMOD4
NME7
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
ACP6
SUCO
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
DARS2
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
C1orf112
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
LINC00869
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
CCDC181
SLAMF7
CADM3
PRUNE1
HAPLN2
GAS5
BCAN
TNN
MRPS14
SEMA4A
MRPL9
INTS3
SCNM1
LINC00626
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
MROH9
TARS2
FLAD1
OR6N2
OR6K2
NECTIN4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
NUF2
REG4
HORMAD1
TOMM40L
POLR3GL
TMEM79
ZBTB37
LCE3D
FCRLA
ANKRD36BP1
MAEL
AQP10
SLAMF9
PYGO2
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
PIGM
IGSF8
GLMP
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
FMO9P
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
TSACC
IQGAP3
NAXE
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
CIART
HFE2
ANKRD35
NBPF12
LELP1
RC3H1
DCST1
METTL11B
FAM78B
BNIPL
LRRC71
PYHIN1
SPRR4
TTC24
NUDT4P2
PDIA3P1
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
CFAP126
TIPRL
RIIAD1
THEM5
SLC9C2
NBPF15
ANKRD34A
RUSC1-AS1
C1orf204
C1orf111
LINC01142
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
FLG-AS1
RXFP4
ANKRD45
CCDC190
LOC343052
OR10R2
FCRL6
NBPF7
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
PEAR1
SFT2D2
ILDR2
NOTCH2NL
LINC01138
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
NBPF9
MIR199A2
MIR214
MIR9-1
NUDT4P1
HIST2H2BF
ETV3L
LRRC52
LOC440700
NBPF18P
OR10J3
KPRP
LCE6A
SUMO1P3
FAM72C
ADAMTSL4-AS1
PRR9
SNORD74
RPL31P11
PPIAL4G
FAM231D
NBPF13P
PPIAL4D
LOC645166
ASH1L-AS1
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2B
SRGAP2C
PPIAL4A
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA4
SNORA80E
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
FAM72D
NBPF8
LINC00623
LOC728989
LOC729867
LOC730159
PPIAL4E
PFN1P2
MIR765
PDZK1P1
MIR190B
MIR921
C1orf68
MSTO2P
LOC100131107
TSTD1
CADM3-AS1
LOC100132057
LOC100132111
NBPF10
FCGR1CP
LOC100147773
C2CD4D
NBPF20
HYDIN2
LINC00624
MIR1295A
MIR1255B2
LOC100422212
MIR3119-1
MIR4259
MIR3120
MIR4257
MIR3119-2
MIR4258
MIR3658
LINC01133
LOC100505666
LOC100505795
LOC100505824
LOC100505918
LOC100506023
GAS5-AS1
LOC100507670
PMF1-BGLAP
TNFAIP8L2-SCNM1
MIR4654
DNM3OS
MIR1295B
MIR5698
MIR5087
MIR5187
SRGAP2-AS1
FALEC
UBE2Q1-AS1
DNM3-IT1
SRGAP2D
RNVU1-8
LOC101927429
LOC101927468
GBAT2
LOC101928009
LOC101928034
LOC101928120
LOC101928177
LOC101928372
LOC101928404
LINC01363
LOC101928565
LOC101928596
LOC101928650
LOC101928673
LOC101928696
LOC101928979
NBPF25P
LOC101929798
RNVU1-4
RNVU1-14
RNVU1-15
RNVU1-20
RNVU1-17
RNVU1-3
RNVU1-1
RNVU1-6
RNVU1-19
LINC00970
MIR6737
MIR6738
MIR6878
MIR6736
MIR6077
MIR8083
CH17-408M7.1
LOC102724601
LOC103091866
LOC105371433
LOC105371458
SCARNA26A
SCARNA26B
SNORA103
POP3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.22.

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

Genes
ASXL1
AHCY
ASIP
BCL2L1
DNMT3B
E2F1
FOXS1
GGT7
GSS
HCK
ID1
EIF6
PLAGL2
SNTA1
SPAG4
GDF5
EIF2S2
CPNE1
NFS1
CBFA2T2
KIF3B
RBM39
TM9SF4
RBM12
PROCR
MMP24
CEP250
PXMP4
RALY
MAPRE1
TPX2
NCOA6
POFUT1
TRPC4AP
REM1
PHF20
BPIFA1
ERGIC3
CDK5RAP1
UQCC1
EDEM2
ACSS2
MYH7B
TP53INP2
NECAB3
FER1L4
BPIFB2
HM13
PDRG1
DYNLRB1
ITCH
MAP1LC3A
COX4I2
ZNF341
MYLK2
BPIFB1
DEFB118
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
MLLT10P1
BPIFA2
NOL4L
CCM2L
SUN5
ROMO1
FAM83C-AS1
C20orf173
LINC00028
LOC149950
COMMD7
BPIFB4
TTLL9
ACTL10
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1BP
C20orf203
BPIFA4P
XKR7
BPIFB3
MIR499A
FRG2EP
MIR644A
FRG1CP
MIR1289-1
MIR1825
MIR3193
MIR499B
MIR4477A
MIR4755
HM13-AS1
MMP24-AS1
RALY-AS1
LOC101929698
ZNF341-AS1
MIR7641-2
FRG1DP
ABALON
LOC105379477
LINC01598

Genes in Wide Peak

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

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

Genes
KDR
KIT
PDGFRA
CHIC2
FIP1L1
IGFBP7
POLR2B
PPAT
REST
SPINK2
SRP72
CLOCK
CEP135
PAICS
NMU
EXOC1
TMEM165
DANCR
KIAA1211
USP46
RASL11B
SRD5A3
NOA1
HOPX
LNX1
ARL9
AASDH
PDCL2
LINC01618
SCFD2
GSX2
IGFBP7-AS1
LOC339978
RPL21P44
USP46-AS1
LOC644145
SNORA26
ERVMER34-1
LOC100506444
SRD5A3-AS1
THEGL
MIR4449
LNX1-AS1
LNX1-AS2
LOC101928851
MIR7641-2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q25.3.

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

Genes
NTRK3

Genes in Wide Peak

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

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

Genes
ATP4B
F7
F10
GAS6
LAMP1
GRK1
TFDP1
CUL4A
PROZ
TUBGCP3
ATP11A
MCF2L
TMCO3
DCUN1D2
PCID2
GRTP1
ADPRHL1
TMEM255B
ATP11AUN
LINC00452
GAS6-AS1
LINC00552
MCF2L-AS1
GAS6-AS2
GRTP1-AS1
LINC00454
ATP11A-AS1
LOC101928841
MIR8075
F10-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q12.1.

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

Genes
SS18
ZNF521
AQP4
CDH2
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
GATA6
LAMA3
MEP1B
NPC1
RBBP8
SNRPD1
TAF4B
TTR
RIOK3
B4GALT6
TRAPPC8
CABYR
C18orf8
RNF138
RNF125
IMPACT
MIB1
HRH4
CTAGE1
GAREM1
GREB1L
CHST9
TMEM241
CABLES1
ESCO1
OSBPL1A
TTC39C
PSMA8
SLC25A52
DSG4
AQP4-AS1
ANKRD29
ABHD3
KCTD1
MIR1-2
MIR133A1
WBP11P1
PCAT18
LOC729950
GATA6-AS1
MIR302F
MIR320C1
MIR320C2
LINC01543
MIR4741
DSG2-AS1
LOC101927571
DSCAS
DSG1-AS1
MIR8057
MIR133A1HG
TTC39C-AS1
LOC105372028
LOC105372038

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q12.1.

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

Genes
BCL2
SS18
MALT1
ZNF521
ADCYAP1
AQP4
ATP5A1
LDLRAD4
CDH2
CDH7
CETN1
CIDEA
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GATA6
GNAL
GRP
IMPA2
LAMA3
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC2R
MC4R
MC5R
ME2
MEP1B
MYO5B
NARS
NDUFV2
NFATC1
NPC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
PTPN2
PTPRM
RAB27B
RBBP8
RIT2
ROCK1
RPL17
SERPINB3
SERPINB4
SLC14A1
SNRPD1
SYT4
TAF4B
TCF4
TGIF1
TTR
TYMS
YES1
ZBTB14
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
RNMT
MYOM1
NAPG
RIOK3
TNFRSF11A
MBD2
PSTPIP2
PIAS2
USP14
CTDP1
VAPA
DLGAP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
LPIN2
CTIF
THOC1
PPP4R1
TSHZ1
NDC80
ACAA2
MYL12A
PRELID3A
CD226
ZNF271P
TXNL4A
RALBP1
AFG3L2
MAPRE2
RAB31
POLI
ADNP2
TRAPPC8
EPB41L3
PHLPP1
ANKRD12
MTCL1
NEDD4L
WDR7
SMCHD1
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
CABYR
SNORD58B
SNORD58A
CLUL1
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
C18orf8
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
CEP192
RPRD1A
ZNF532
ELP2
IMPACT
ELAC1
ENOSF1
ZNF407
CNDP2
LINC00470
CELF4
SPIRE1
PSMG2
TWSG1
CHMP1B
MIB1
KIAA1328
KLHL14
KIAA1468
EPG5
HRH4
PIEZO2
CTAGE1
GAREM1
METTL4
MPPE1
ARHGAP28
CCDC102B
RBFA
CEP76
GREB1L
PQLC1
FHOD3
CCDC68
ASXL3
COLEC12
NETO1
SEH1L
KATNAL2
CHST9
C18orf21
MRO
EMILIN2
HDHD2
TXNDC2
ZNF397
PARD6G
TUBB6
CNDP1
DLGAP1-AS2
TMEM241
SERPINB12
SERPINB11
SEC11C
L3MBTL4
CABLES1
DSEL
MYL12B
ESCO1
OSBPL1A
HAUS1
ALPK2
FAM210A
LOXHD1
INO80C
TTC39C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
SLC25A52
DSG4
AQP4-AS1
ANKRD29
APCDD1
LINC00526
ZNF519
C18orf54
TCEB3C
ABHD3
FBXO15
RAB12
DLGAP1-AS3
ZBTB7C
SKA1
CFAP53
GTSCR1
DOK6
RNF152
LINC00305
ZNF396
DLGAP1-AS5
LAMA1
CYP4F35P
LOC284241
KCTD1
DYNAP
BOD1L2
LINC00907
SIGLEC15
ZADH2
SMIM21
LINC00908
HMSD
LOC284294
LINC00667
LRRC30
LOC339298
CPLX4
ANKRD62
ANKRD30B
CCDC178
ATP9B
POTEC
OACYLP
LINC00668
LINC01443
LINC01538
LOC400655
LINC00909
C18orf65
LINC00683
LOC400661
MIR1-2
MIR122
MIR133A1
MIR187
CXADRP3
ANKRD20A5P
HSBP1L1
WBP11P1
RNF165
TYMSOS
C18orf61
C18orf32
KC6
AKAIN1
LOC643542
C18orf63
LOC644669
CBX3P2
MIR3976HG
TMEM200C
SLC35G4
MIR924HG
DLGAP1-AS1
SKOR2
SCARNA17
SNORA37
ROCK1P1
LOC727896
PCAT18
TCEB3CL
LOC729950
ZSCAN30
SNORD58C
MIR924
GATA6-AS1
LINC01387
PARD6G-AS1
LOC100131655
LOC100192426
GACAT2
LINC01630
LDLRAD4-AS1
MIR302F
MIR320C1
MIR320C2
MIR1539
MIR4319
MIR4317
MIR4318
MIR4320
MIR3156-2
MIR3929
LINC01539
LOC100505549
GAPLINC
LINC01541
LOC100505797
LOC100505817
LOC100505853
RBFADN
LINC01543
TCEB3CL2
RPL17-C18orf32
MIR4526
MIR4741
MIR4528
MIR3976
MIR3975
MIR4527
MIR4529
MIR3591
MIR4743
MIR4744
DSG2-AS1
MIR5583-2
MIR5011
MIR5583-1
MIR5190
MIR548AV
LINC-ROR
LOC100996324
LINC01544
LOC101060542
DLGAP1-AS4
L3MBTL4-AS1
LOC101927168
LOC101927188
LOC101927229
LINC01416
NDUFV2-AS1
LOC101927322
PPP4R1-AS1
LINC01254
LOC101927410
LINC01255
LOC101927481
LOC101927571
LOC101927606
LINC01444
LOC101927651
DSCAS
LINC01029
DSG1-AS1
LOC101927809
LINC01477
LINC01478
SLC14A2-AS1
LOC101927989
LOC101928167
MIR6718
MIR7153
MIR6788
MIR8057
MIR8078
MIR133A1HG
LOC102723376
TTC39C-AS1
LOC102724651
LOC102724913
SNHG22
LOC104968399
LOC105371998
LOC105372028
LOC105372038
LOC105372068
LOC105372069
LOC105372071
TCF4-AS1
LOC105372179
LOC105376854
LOC105667213
SNORA108
SNORA111

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 - 40 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 2.5114e-40 | 2.5114e-40 | chr9:21862204-21997447 | 2
8p23.2 | 3.4264e-15 | 3.4264e-15 | chr8:2129481-6406417 | 2
17p13.3 | 2.4855e-08 | 2.4855e-08 | chr17:1-16031979 | 335
3p12.1 | 2.8396e-08 | 2.6433e-08 | chr3:77646286-94014253 | 22
13q31.2 | 1.4891e-06 | 1.7697e-06 | chr13:86933577-87623081 | 1
10q23.31 | 3.7693e-06 | 3.5381e-06 | chr10:87838309-88274557 | 2
4p15.33 | 1.2505e-05 | 8.7976e-05 | chr4:14888143-15004496 | 1
Yq11.23 | 0.00028559 | 0.00028284 | chrY:13479852-57227415 | 57
18q12.3 | 1.1921e-05 | 0.00033829 | chr18:43277606-44544179 | 1
11p15.4 | 0.00072302 | 0.00076036 | chr11:3164691-3227879 | 2
13q11 | 0.00072302 | 0.0010275 | chr13:1-18868622 | 2
6q22.1 | 0.0015334 | 0.0015524 | chr6:93419398-117675473 | 125
1p13.2 | 8.9432e-05 | 0.0016661 | chr1:100738513-149927868 | 304
2q22.1 | 0.00033829 | 0.0052907 | chr2:140576645-142885137 | 1
Xq22.3 | 0.0085253 | 0.0088562 | chrX:108149812-108773392 | 4
5q12.1 | 1.1918e-05 | 0.022466 | chr5:58858255-60489091 | 2
16q21 | 0.011093 | 0.028815 | chr16:65167689-66371798 | 1
18q23 | 0.00023544 | 0.030983 | chr18:50187271-80373285 | 145
4q34.1 | 3.9904e-05 | 0.034885 | chr4:152099336-190214555 | 185
4q22.1 | 0.0010675 | 0.034885 | chr4:79299357-190214555 | 533
11q22.3 | 0.045791 | 0.043877 | chr11:90223009-135086622 | 419
15q21.3 | 0.045639 | 0.043877 | chr15:53761150-55065845 | 1
19p13.2 | 0.063814 | 0.065499 | chr19:1-27791982 | 713
21q22.3 | 0.063814 | 0.065499 | chr21:37267534-46709983 | 159
2q36.2 | 0.0021881 | 0.082325 | chr2:208817895-242193529 | 324
16q24.2 | 0.018643 | 0.082325 | chr16:76559187-90338345 | 163
14q21.2 | 0.086683 | 0.087151 | chr14:45252277-46503538 | 1
19q13.32 | 0.084371 | 0.087151 | chr19:36202239-58617616 | 911
4p12 | 0.028041 | 0.094639 | chr4:44722496-46735637 | 2
6p12.3 | 0.11429 | 0.11688 | chr6:1-51618701 | 741
22q13.32 | 0.11555 | 0.11688 | chr22:48270279-48781801 | 4
7q36.3 | 0.11816 | 0.12127 | chr7:108454740-159345973 | 413
1p36.12 | 0.014792 | 0.13554 | chr1:1-149927868 | 1522
16p13.3 | 0.13671 | 0.13554 | chr16:1-26031661 | 438
21p11.2 | 0.15368 | 0.15589 | chr21:6852736-14109327 | 35
5p12 | 0.0018617 | 0.19584 | chr5:44815307-50830121 | 2
5q35.2 | 0.0093696 | 0.20414 | chr5:51393999-181538259 | 1004
5q23.1 | 0.0015548 | 0.21061 | chr5:44815307-181538259 | 1010
Xp21.1 | 0.21263 | 0.21061 | chrX:1-53054082 | 386
20q13.33 | 0.24784 | 0.24509 | chr20:34550134-64444167 | 422

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2A-AS1

Genes in Wide Peak

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

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

Genes
CSMD1
LOC101927815

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.3.

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

Genes
PER1
MAP2K4
TP53
GAS7
USP6
ABR
ACADVL
ADORA2B
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
COX10
CLDN7
CRK
CTNS
DLG4
DNAH9
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MEIS3P1
MNT
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
PMP22
POLR2A
PSMB6
RCVRN
RPA1
RPL26
SCO1
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF18
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
MYH13
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
GLP2R
NTN1
STX8
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
ARHGAP44
HS3ST3B1
HS3ST3A1
CLEC10A
MYBBP1A
PRPF8
TRIM16
KIF1C
GABARAP
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
CLUH
SMG6
WSCD1
CTDNEP1
PIK3R5
ELP5
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
BORCS6
TTC19
SLC52A1
WRAP53
MRM3
VPS53
NCBP3
TSR1
DHX33
ADPRM
PLSCR3
ZNF286A
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
ELAC2
SRR
NXN
TEKT3
MIS12
METTL16
PHF23
FAM57A
CTC1
NDEL1
PITPNM3
EMC6
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
NAA38
NEURL4
ZNF594
HES7
SPATA22
MGC12916
TXNDC17
MIR22HG
TMEM88
MYOCD
CDRT7
CDRT8
CDRT15P1
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
ZSWIM7
DNAH2
RTN4RL1
CDRT15
CFAP52
CCDC42
PIK3R6
ODF4
KCTD11
MFSD6L
TRPV3
SLC16A11
FBXO39
DHRS7C
TVP23C
SLC16A13
C17orf74
SPNS3
TMEM256
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
LINC00670
CDRT4
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
TBC1D26
RFLNB
CDRT1
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
SHISA6
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
GSG1L2
PIRT
CDRT15P2
SNORA48
SNORD10
OR1D4
SCGB1C2
SCARNA21
SNORD91A
SNORD91B
SNORD118
BHLHA9
TLCD2
LOC728392
MIR744
LOC100128006
LOC100128288
MYHAS
C17orf107
LOC100130950
DBIL5P
LINC00675
MIR1253
MIR548H3
PITPNA-AS1
MIR3183
MIR4314
LOC100506371
LOC100506388
ALOX12-AS1
MIR497HG
MAGOH2P
RNASEK-C17orf49
TMEM256-PLSCR3
TVP23C-CDRT4
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4731
MIR4520-1
MIR4521
MIR5096
MIR4520-2
MIR1269B
ALOX15P1
COX10-AS1
LOC100996842
TMEM220-AS1
LOC101559451
LOC101927727
LOC101927839
LOC101927911
LOC101928000
LOC101928266
LOC101928418
LOC101928475
LOC101928567
MIR6776
MIR6864
MIR6865
MIR6883
LOC102724009
LOC103021295
LOC105371430
LOC105371485
LOC105371506
LOC105371592

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.1.

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

Genes
EPHA3
GBE1
HTR1F
POU1F1
PROS1
ROBO1
CGGBP1
CHMP2B
ZNF654
CADM2
C3orf38
VGLL3
LINC00971
LOC728290
MIR3923
MIR4795
LINC00506
MIR5688
CADM2-AS2
LOC101927374
LOC101927494
SNORA95

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q31.2.

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

Genes
MIR4500

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.33.

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

Genes
CPEB2-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Yq11.23.

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

Genes
DAZ1
IL9R
RBMY1A1
VAMP7
KDM5D
PRY
XKRY
BPY2
VCY
CDY1
EIF1AY
TMSB4Y
CDY2A
SPRY3
NLGN4Y
DAZ3
DAZ2
DAZ4
TTTY5
TTTY9A
TTTY13
TTTY14
GOLGA2P2Y
TTTY6
HSFY1
CSPG4P1Y
TTTY3
TTTY4
RPS4Y2
HSFY2
RBMY2EP
RBMY2FP
RBMY1F
CDY2B
TTTY10
TXLNGY
TTTY17A
BCORP1
FAM41AY1
VCY1B
RBMY1B
RBMY1D
RBMY1E
RBMY1J
FAM224B
FAM224A
TTTY6B
BPY2B
TTTY3B
TTTY4B
TTTY17B
DDX11L16
WASIR1
PRORY
LOC100652931
NLGN4Y-AS1
LOC101929148

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.3.

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

Genes
LINC01478

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
MRGPRG-AS1
MRGPRG

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q11.

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

Genes
FAM230C
LINC00417

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.1.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-2113
AIM1
AMD1
CCNC
COL10A1
FOXO3
FRK
FYN
GPR6
GRIK2
HDAC2
KPNA5
LAMA4
MARCKS
POU3F2
PREP
REV3L
SIM1
SMPD2
NR2E1
TSPYL1
DDO
SNX3
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
FUT9
TRAF3IP2
ASCC3
BVES
SEC63
CDK19
TSPYL4
UFL1
PNISR
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
COQ3
SOBP
QRSL1
PDSS2
HACE1
BEND3
PRDM13
POPDC3
MICAL1
MANEA
GPR63
ARMC2
RPF2
MCHR2
FAXC
RTN4IP1
USP45
SLC22A16
MFSD4B
GTF3C6
KLHL32
SLC16A10
BVES-AS1
CCDC162P
AK9
NT5DC1
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
VGLL2
LACE1
MMS22L
FAM26E
SCML4
CEP57L1
PPIL6
LINC01268
FLJ34503
DCBLD1
RSPH4A
LINC00222
LIN28B
FAM26F
GSTM2P1
RFPL4B
FAM229B
TSG1
TRAF3IP2-AS1
MIR587
MCHR2-AS1
TPI1P3
METTL24
LIN28B-AS1
TRAPPC3L
TSTD3
CD24
MIR2113
LOC100422737
MIR548AI
LOC100996634
MANEA-AS1
LOC101927314
LOC101927365
LOC101927640
LOC101927686
LOC101927768
LOC101927919
ARMC2-AS1
MIR7641-2
LOC105377924
LOC105377962

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
ADORA3
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DRD5P2
S1PR1
CELSR2
EXTL2
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
RAP1A
RNU1-4
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
TTF2
ITGA10
PEX11B
SLC16A4
CD101
SEC22B
CHD1L
LRIG2
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
LAMTOR5
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
CD160
DDX20
NTNG1
WDR47
CLCC1
NBPF14
PTPN22
PHGDH
RNVU1-7
RNU1-3
RNU1-2
RNU1-1
CHIA
RNF115
GPSM2
SLC25A24
BOLA1
HAO2
ACP6
GPR89B
DPH5
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
LINC00869
TMIGD3
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
ATP1A1-AS1
STRIP1
ZNF697
DNAJA1P5
HENMT1
GNRHR2
OLFM3
MAB21L3
ATXN7L2
C1orf194
LIX1L
HSD3BP4
DRAM2
PIFO
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
SLC30A7
NBPF12
CHIAP2
DENND2C
FNDC7
UBL4B
NUDT4P2
PDIA3P1
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
MYBPHL
NBPF7
SLC6A17
C1orf137
NOTCH2NL
LINC01138
LOC388692
NBPF9
MIR197
LOC440600
LOC440602
BCL2L15
NUDT4P1
HIST2H2BF
PGCP1
FAM72C
SPATA42
CYMP
LOC643355
LOC643441
LINC00622
PPIAL4G
FAM231D
NBPF13P
PPIAL4D
LOC645166
EMBP1
SRGAP2B
ACTG1P4
NBPF6
SRGAP2C
PPIAL4A
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
FAM72D
NBPF8
LINC00623
LOC728989
PPIAL4E
PFN1P2
PDZK1P1
MIR942
LOC100129138
LINC01160
LOC100132057
NBPF10
FCGR1CP
AP4B1-AS1
NBPF20
HYDIN2
LINC00624
MIR320B1
MIR4256
LOC100505824
FAM212B-AS1
SLC16A1-AS1
MIR548AC
MIR5087
SRGAP2-AS1
VAV3-AS1
KCNC4-AS1
KCND3-AS1
HAO2-IT1
KCND3-IT1
LOC100996251
LOC100996263
LINC01356
SRGAP2D
LAMTOR5-AS1
RNVU1-8
LOC101927429
LOC101927468
LOC101928370
LOC101928436
LOC101928476
LOC101928718
HIPK1-AS1
LOC101928977
LOC101928979
LOC101928995
LOC101929023
LOC101929099
LOC101929147
NBPF25P
LOC101929798
RNVU1-4
RNVU1-14
RNVU1-15
RNVU1-20
RNVU1-17
RNVU1-3
RNVU1-1
RNVU1-6
RNVU1-19
MIR7852
MIR6736
MIR6077
LOC102606465
CH17-408M7.1
LOC103091866
LINC01397
LINC01307
LINC01525
WARS2-IT1
LOC105378933

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

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

Genes
MIR7157

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
COL4A5
COL4A6
IRS4
LOC101928358

Genes in Wide Peak

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

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

Genes
PDE4D
MIR582

Genes in Wide Peak

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

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

Genes
LINC00922

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
CDH7
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD4
MBD1
MBP
MC4R
ME2
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
CXXC1
ST8SIA3
MEX3C
TMX3
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
MRO
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
SKA1
CFAP53
GTSCR1
DOK6
RNF152
LINC00305
LOC284241
DYNAP
BOD1L2
ZADH2
SMIM21
LINC00908
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
OACYLP
LINC01538
LOC400655
LINC00909
C18orf65
LINC00683
LOC400661
MIR122
HSBP1L1
LOC643542
C18orf63
SNORA37
PARD6G-AS1
LOC100131655
LINC01630
LINC01539
LOC100505549
LINC01541
LOC100505797
LOC100505817
LOC100505853
RBFADN
MIR4528
MIR4529
MIR3591
MIR5011
MIR548AV
LINC-ROR
LINC01544
LOC101060542
LOC101927229
LINC01416
LOC101927322
LOC101927481
LOC101927606
LOC101927651
LINC01029
LOC101927989
LOC101928167
LOC102724651
LOC102724913
TCF4-AS1
LOC105372179
SNORA108

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.1.

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

Genes
FBXW7
DUX4
hsa-mir-1979
AGA
SLC25A4
ANXA2P1
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PLRG1
PPID
MSMO1
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ASIC5
GALNT7
CLDN22
DKFZP434I0714
DCHS2
HPF1
MARCH1
NEIL3
TMEM144
TMA16
UFSP2
DDX60
CDKN2AIP
TENM3
LRP2BP
PDGFC
FSTL5
STOX2
CFAP97
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
CENPU
HAND2-AS1
MAP9
WWC2
CEP44
SNX25
MND1
TKTL2
CBR4
FHDC1
LOC90768
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
WWC2-AS2
FAM218A
C4orf45
TRIM60
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
PRIMPOL
TRIML2
CCDC110
CYP4V2
F11-AS1
LINC01098
RNF175
LOC339975
TRIML1
LOC340017
ANKRD37
LOC389247
TRIM61
HELT
LINC01060
FAM92A1P2
LOC441052
C4orf47
GALNTL6
FRG2
SLED1
FLJ38576
MIR578
LINC00290
LOC728175
LOC729870
MIR3945HG
CLDN24
MIR1305
LOC100419170
DBET
MIR548T
MIR3140
MIR4276
MIR3945
MIR3688-1
LINC01207
APELA
LOC100506085
LOC100506107
LOC100506122
LINC01093
LOC100506272
MIR4455
MIR4453
MIR4454
MIR3688-2
LOC100996286
LOC101928052
LOC101928131
LINC01179
LINC01612
LOC101928314
LOC101928509
LOC101928551
LOC101928590
LINC01099
WWC2-AS1
LINC01262
LOC101930370
DEAR
MIR6082
LOC102723766
LOC102724776
LVCAT8
LOC105377590
LINC01596

Genes in Wide Peak

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

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

Genes
IL2
RAP1GDS1
TET2
FBXW7
DUX4
hsa-mir-1979
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AGA
ANK2
SLC25A4
ANXA2P1
ANXA5
ATOH1
BMP3
BMPR1B
CAMK2D
CASP3
CASP6
CCNA2
LRBA
CDS1
CLGN
CENPE
CLCN3
CPE
CTSO
DCTD
DMP1
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGF5
FGG
FRG1
GAB1
GK2
GK3P
GLRB
GPM6A
GRIA2
GRID2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HMGB2
HNRNPD
HPGD
IBSP
CFI
IL15
ING2
IRF2
KLKB1
MAD2L1
SMAD1
MANBA
MGST2
AFF1
NR3C2
MTNR1A
MTTP
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PDHA2
GATB
PITX2
PKD2
PLRG1
EXOSC9
POU4F2
PPID
PPP3CA
PRKG2
MAPK10
PTPN13
ABCE1
RPL34
RPS3A
MSMO1
SFRP2
SNCA
SPP1
TACR3
TDO2
TLL1
TLR2
TLR3
TRPC3
UBE2D3
UCP1
UGT8
VEGFC
GLRA3
SPARCL1
SMARCA5
SORBS2
PRSS12
UNC5C
LAMTOR3
PDE5A
SAP30
INPP4B
HERC3
SNORD73A
PAPSS1
LRAT
AIMP1
NDST3
ABCG2
HAND2
RAPGEF2
MFAP3L
SEC24D
HNRNPDL
TSPAN5
FAM13A
SPRY1
ANAPC10
PGRMC2
SEC24B
MAB21L2
PDLIM5
RRH
PLK4
HPSE
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
MMRN1
WDFY3
PALLD
TBC1D9
METAP1
KIAA0922
TRIM2
ANP32C
SLC7A11
NOCT
FAM149A
FBXO8
PPA2
DAPP1
DKK2
INTU
COQ2
ARFIP1
PDLIM3
HPGDS
ZNF330
SPOCK3
MRPS18C
COPS4
AADAT
HSD17B11
LEF1
HERC5
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ASIC5
GALNT7
NUDT9
CLDN22
GAR1
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
HPF1
HERC6
MCUB
MARCH1
BANK1
LARP1B
BBS7
NEIL3
TMEM144
TMA16
UFSP2
ZGRF1
AP1AR
MAML3
DDX60
CDKN2AIP
TENM3
TMEM184C
LRP2BP
PDGFC
FSTL5
BDH2
SMARCAD1
MEPE
STOX2
PRDM8
INTS12
ANKRD50
RNF150
KLHL8
PCDH10
CFAP97
FNIP2
SH3RF1
METTL14
ENOPH1
OSTC
IL21
RXFP1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
HHIP
NDST4
ETNPPL
ELOVL6
NDNF
FAT4
ARSJ
ARHGAP10
CENPU
THAP9
HAND2-AS1
GSTCD
MAP9
TNIP3
JADE1
SCD5
DNAJB14
WWC2
NAA15
ABHD18
ALPK1
CXXC4
CEP44
SETD7
PLA2G12A
SLC25A31
RAB33B
ARHGAP24
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
COL25A1
USP38
MGARP
NAA11
GPAT3
CBR4
PIGY
FHDC1
FLJ20021
LOC90768
PRMT9
DDX60L
NAF1
TIFA
TRMT10A
TBCK
HELQ
CYP2U1
DDIT4L
WDR17
PCAT4
ANTXR2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
C4orf32
SPATA4
C4orf36
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
MGAT4D
WWC2-AS2
FAM218A
PPM1K
C4orf45
RASGEF1B
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
TIGD2
RBM46
SGMS2
SYNPO2
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
PRIMPOL
TRIML2
C4orf22
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
NAP1L5
LINC01091
CYP4V2
F11-AS1
RPL34-AS1
LINC01098
FAM13A-AS1
GPRIN3
RNF175
STPG2
LOC339975
TRIML1
LOC340017
PRSS48
LRIT3
SLC10A6
HSD17B13
ANKRD37
PCNAP1
LOC389247
TRIM61
HELT
CCSER1
LINC01061
C4orf3
LINC01060
FAM92A1P2
WDFY3-AS2
MIR302A
LINC00575
TMEM150C
GUSBP5
LOC441052
C4orf47
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
SLC7A11-AS1
LINC00616
LEF1-AS1
SLED1
SNCA-AS1
TNRC18P1
CEP170P1
LOC645513
HHIP-AS1
C4orf51
FLJ38576
SNORA24
MIR575
MIR576
MIR577
MIR578
LINC00290
LOC728175
LOC729218
LOC729307
CETN4P
FAM160A1
LOC729870
MIR3945HG
SNHG8
MIR297
SMARCA5-AS1
SCOC-AS1
CLDN24
PP12613
MIR1243
MIR1255A
MIR2054
MIR1305
MIR1973
MIR548G
LOC100419170
DBET
MIR548T
MIR3140
MIR3139
MIR4276
THAP9-AS1
MIR3945
MIR3684
MIR3688-1
LINC01095
LINC01207
APELA
LINC00989
LOC100506085
LOC100506107
LOC100506122
LINC01093
LOC100506272
LOC100506746
BMPR1B-AS1
LOC100507053
GIMD1
LOC100507487
LINC00613
LOC100507639
SEC24B-AS1
MIR4455
MIR4453
MIR4454
MIR4799
MIR3688-2
MIR4451
MIR4452
MIR5705
LINC00499
LINC01216
ARHGEF38-IT1
LOC100996286
LOC100996694
IL21-AS1
STPG2-AS1
GTF2IP12
LINC01365
LOC101927087
LOC101927282
LOC101927305
LOC101927359
LOC101927636
SMAD1-AS2
LOC101927849
LOC101928052
LOC101928131
LINC01179
LINC01612
LOC101928314
LOC101928509
LOC101928551
LOC101928590
LINC01099
WWC2-AS1
LOC101928942
LINC01262
LOC101928978
LOC101929064
LOC101929134
LOC101929194
LOC101929210
LOC101929353
LOC101929448
LOC101929468
LOC101929529
LOC101929577
LOC101929595
LOC101929621
LOC101929741
LOC101929762
LOC101930370
DEAR
MIR7849
MIR8066
MIR8082
MIR6082
LOC102723704
LOC102723766
LOC102724776
LINC01378
SMAD1-AS1
LINC01256
TET2-AS1
LOC105369192
LOC105377348
LOC105377448
LOC105377458
LOC105377480
LVCAT8
LOC105377590
LINC01596
LOC105377621
LOC105377623
SNORD143
SNORD144
SNORA101A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
MAML2
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
KMT2A
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PTS
NECTIN1
RDX
RPS25
SC5D
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPRA
ST14
TAGLN
TECTA
THY1
TRPC6
UPK2
ZBTB16
ZNF202
CUL5
BARX2
JRKL
ZPR1
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
C2CD2L
RBM7
MPZL2
YAP1
HYOU1
ATP5L
GPR83
SRSF8
ADAMTS8
TREH
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
PANX1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
C11orf54
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
CWC15
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
ANKRD49
TTC12
C11orf57
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
SMCO4
PRDM10
DSCAML1
GRAMD1B
CEP126
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
JAM3
BCO2
TMEM133
TMPRSS13
DCUN1D5
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
SNORD14C
SNORD14D
SNORD14E
DIXDC1
CEP295
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
SLC36A4
FAT3
TMEM45B
COLCA2
PIH1D2
NXPE1
NXPE2
JAML
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
DEUP1
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANGPTL5
ANKK1
RNF214
LOC283140
LINC00900
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
C11orf44
MIR4697HG
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
HEPHL1
PLET1
VSTM5
LOC387810
IZUMO1R
KDM4E
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
COLCA1
C11orf88
MIR100HG
PATE2
PATE4
ST3GAL4-AS1
SNX19
LOC403312
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CASP1P2
CARD17
LINC00167
SCARNA9
HEPN1
C11orf97
LOC643733
LOC643923
CLDN25
LOC646522
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
LOC100128239
LOC100128386
LOC100129203
LOC100131626
LOC100132078
LOC100132686
PATE3
WTAPP1
NCAM1-AS1
MIR1261
MIR1304
MIR548L
BACE1-AS
MIR4301
MIR3167
MIR1260B
USP2-AS1
MIR3920
MIR3656
CASP12
LOC100507283
SENCR
LOC100507431
LOC100507548
TMPRSS4-AS1
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768
JRKL-AS1
KIRREL3-AS2
NTM-IT
LOC101054525
LOC101928424
LOC101928535
LOC101928823
LOC101928847
LOC101928940
LOC101928985
LOC101929011
LOC101929089
LOC101929208
DISC1FP1
LOC101929227
LOC101929295
LOC101929340
LOC101929427
LOC101929473
LOC101929497
LOC101929517
LOC101929538
LINC01395
NTM-AS1
LOC101929653
MIR6756
MIR7641-1
MIR7641-2
MIR6090
MIR6716
MIR8052
LOC102723838
LOC102723895
LOC102724301
LOC103611081
PKNOX2-AS1
APOA1-AS
LOC105369431
LOC105369438
LOC105369443
LOC105369473
LOC105369486
LOC105369507
LOC105369509
LOC105369532
STT3A-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.3.

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

Genes
UNC13C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

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

Genes
GNA11
JAK3
LYL1
MLLT1
SH3GL1
SMARCA4
STK11
TCF3
TPM4
ELL
FSTL3
BRD4
hsa-mir-1270-1
hsa-mir-220b
ACP5
AES
AMH
ASNA1
ATP5D
AZU1
HCN2
BSG
BST2
C3
CACNA1A
CALR
CAPS
CD70
ADGRE5
CDC34
CDKN2D
CIRBP
CNN1
CNN2
COMP
CSNK1G2
NCAN
DAPK3
CFD
DHPS
DNASE2
DNM2
DNMT1
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
ELAVL3
ADGRE1
EPOR
NR2F6
FARSA
FCER2
FUT3
FUT5
FUT6
GAMT
GCDH
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
DNAJB1
ICAM1
ICAM3
ICAM4
IL12RB1
ILF3
INSL3
INSR
JUNB
JUND
KCNN1
LDLR
CYP4F3
MAN2B1
MATK
BORCS8-MEF2B
RAB8A
MYO1F
GADD45B
MYO9B
HNRNPM
NDUFA7
NDUFB7
NFIC
NFIX
NOTCH3
NRTN
OAZ1
P2RY11
PALM
PDE4A
PDE4C
PIK3R2
PIN1
POLR2E
POLRMT
PRKACA
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTGER1
PTPRS
RAB3A
RAD23A
UPF1
RFX1
RFX2
RPL18A
RPS15
RPS28
SAFB
CCL25
SGTA
SLC1A6
SLC5A5
SNAPC2
STXBP2
TBXA2R
PRDX2
THOP1
ICAM5
TLE2
TYK2
UBA52
VAV1
ZNF14
ZNF708
ZNF20
ZNF43
ZNF69
ZNF85
ZNF90
ZNF91
ZNF99
ZNF121
ZNF136
ZNF177
ZNF208
MADCAM1
SF3A2
CLPP
RANBP3
CYP4F2
KHSRP
PLPP2
RFXANK
EIF3G
STX10
S1PR4
TNFSF14
TNFSF9
AP1M1
AP3D1
F2RL3
LPAR2
RAB11B
CRLF1
S1PR2
TRIP10
LONP1
MED26
HOMER3
IL27RA
GDF15
TECR
ZNF254
RAB3D
APBA3
IER2
SAFB2
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
SUGP2
EBI3
DDX39A
ZNF443
PLIN3
AKAP8
APC2
B3GNT3
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4A
IFI30
TIMM44
CARM1
SEMA6B
CHERP
RNASEH2A
KLF1
CERS1
GIPC1
ZNF266
PNPLA6
UQCR11
ILVBL
TMED1
CDC37
CYP4F8
COPE
ADGRL1
SBNO2
MAST1
UNC13A
KDM4B
MAST3
FCHO1
ZFR2
SIN3B
ARHGEF18
CRTC1
MAU2
PIP5K1C
ARHGAP45
CASP14
FKBP8
SHC2
TMEM59L
PGLS
LSM4
RPL36
KANK2
FAM32A
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
SNORD37
RNU6-1
AKAP8L
FGF22
ARRDC2
TJP3
CPAMD8
NMRK2
C19orf53
BABAM1
UHRF1
HOOK2
SLC39A3
TNPO2
ADGRE2
CD209
COL5A3
RDH8
MRPL4
NDUFA13
ANGPTL4
MARCH2
GMIP
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
ISYNA1
SIRT6
PIAS4
LSM7
ZNF44
TM6SF2
MBD3
S1PR5
MIER2
DDX49
PCSK4
ZNF562
GATAD2A
BEST2
FBXL12
PGPEP1
CC2D1A
TMEM161A
C19orf24
C19orf60
PLEKHJ1
MAP1S
KLHL26
C19orf66
FEM1A
ZNF823
STAP2
TRMT1
BTBD2
RNF126
CCDC94
ASF1B
USE1
ANGPTL8
MYDGF
ZNF253
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
ATP13A1
RGL3
SLC44A2
MCOLN1
WDR18
REXO1
ZNF490
DOCK6
ZNF492
CAMSAP3
ZNF317
ANO8
SUGP1
CYP4F11
ZNF77
CACTIN
EPS15L1
WIZ
UBL5
CELF5
PLPPR2
RASAL3
MRPL34
KRI1
ZSWIM4
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
TMEM38A
SLC25A23
SMIM7
ZNF426
C19orf57
FSD1
ZNF557
ABHD8
CERS4
OCEL1
COLGALT1
TLE6
EPHX3
PODNL1
SLC35E1
PLPPR3
DENND1C
ZNF442
ZNF556
LRRC8E
PRR36
ZNF430
UBXN6
PBX4
KIAA1683
OR4F17
CCDC130
ACSBG2
ADAMTS10
QTRT1
ABHD17A
ZNF93
DOHH
PLVAP
RTBDN
ANGPTL6
KLF16
USHBP1
TSSK6
PRAM1
C19orf44
MRI1
FBXW9
ALKBH7
WDR83
ZNF414
ELOF1
DOT1L
ZNF333
FBN3
ZNF559
KISS1R
ADGRE3
CREB3L3
GTPBP3
HDGFRP2
MPV17L2
LMNB2
RAX2
MUM1
HSH2D
MPND
ATG4D
ATCAY
SYDE1
MBD3L1
MIDN
SAMD1
DCAF15
GADD45GIP1
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
ZNF486
DPP9
ZNF682
R3HDM4
TMEM259
TPGS1
CRB3
REEP6
PEX11G
ZNF561
OLFM2
HAUS8
MVB12A
ARMC6
MUC16
ZNF101
FDX1L
NACC1
IZUMO4
SCAMP4
ADAT3
MISP3
ZNF257
PGLYRP2
CCDC124
ZNF554
EVI5L
NXNL1
CCDC151
ZNF653
GRIN3B
MRPL54
LRG1
CIB3
RLN3
RAVER1
OR7D4
OR7G1
OR1M1
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
MISP
LRRC25
OR1I1
NR2C2AP
CCDC105
CYP4F22
PLK5
LINC00661
OR10H4
ANKLE1
C2CD4C
ZNF358
ILF3-AS1
ZNF560
ZNF563
SPC24
TICAM1
CIRBP-AS1
ZNRF4
CILP2
ZNF558
ZNF98
ZNF738
ZNF714
ZNF681
C19orf25
ATP8B3
LINC00905
DIRAS1
ZNF555
ZNF846
OR7D2
ZNF791
ZNF564
ZNF709
ZNF433
PRR22
ZNF676
ZNF100
SSBP4
ZNF431
ANKRD24
ZNF675
MCEMP1
ZNF627
DAND5
ZNF626
FAM129C
CBARP
CSNK1G2-AS1
C19orf38
SYCE2
KANK3
TINCR
CATSPERD
ACTL9
OR2Z1
ZNF561-AS1
ZNF763
ZNF844
SMIM24
MIR7-3HG
SLC25A41
MBD3L5
OR10H5
NWD1
SLC25A42
LINC00663
ZNF493
ODF3L2
LOC284454
ADGRE4P
ADAMTSL5
CLEC4G
NANOS3
PALM3
ZNF429
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
YJEFN3
LOC374890
WASH5P
SLC27A1
LYPLA2P2
C3P1
ZNF788
CLEC17A
CYP4F24P
ZNF728
RPSAP58
ONECUT3
LOC390877
OR7G2
OR7G3
OR7A10
MEX3D
LINC01002
PRSS57
VMAC
LINC00664
ZNF833P
HAPLN4
CTXN1
CACTIN-AS1
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR7-3
PLIN5
CLEC4GP1
ZNF506
GOLGA2P9
ZNF724
FLJ25758
MIR181D
LOC641367
LINGO3
ARRDC5
FAM138A
C19orf67
UCA1
MBD3L4
MBD3L3
FAM138C
ZNF826P
HNRNPA1P10
SNORD105
PPAN-P2RY11
MIR637
MIR638
MIR639
MIR640
PLIN4
ZNF878
LOC729966
BORCS8
ZNF726
HAVCR1P1
SNORD105B
ZGLP1
LINC01233
LOC100128568
C19orf71
LOC100128573
ZNF730
ZNF737
TMEM221
DPP9-AS1
PET100
IPO5P1
MEF2B
ZNF729
LOC100288123
LOC100289333
MIR1470
MIR1270
MIR1909
MIR1181
MIR1238
MIR1268A
MIR1302-2
MIR1227
MIR1302-9
MIR3188
MIR1302-10
MIR3187
MIR1302-11
MIR4322
MIR3189
MIR4321
MIR3940
LOC100507373
RAB11B-AS1
TGFBR3L
ZNF559-ZNF177
ZNF625-ZNF20
MIR4747
MIR4746
MIR4748
MIR4745
MIR5695
MIR4999
MIR5684
MIR5589
LOC100996349
LOC100996351
LOC101928238
LOC101928464
LOC101928602
LOC101928844
LOC101928845
LOC101929124
LOC101929144
LOC101929164
RNU6-7
MIR6790
MIR6791
MIR6792
MIR6795
MIR6885
MIR6886
MIR7850
MIR7974
MIR6794
MIR1199
MIR6515
MIR6789
MIR6793
MIR7108
LOC102724279
LOC102724360
LOC102725254
RNU6-2
LINC01224
BISPR
LOC105372273
LOC105372280
LOC105372288
SNORD135
SNORA104

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
ERG
TMPRSS2
ADARB1
AIRE
PTTG1IP
C21orf2
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
DYRK1A
ETS2
HMGN1
PRMT2
ITGB2
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
U2AF1
UBE2G2
WRB
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DSCR4
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
BACE2
C2CD2
DNMT3L
ZBTB21
UBASH3A
BRWD1
SLC37A1
PCBP3
C21orf58
YBEY
TSPEAR-AS1
TSPEAR
LINC00112
LINC00111
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
COL18A1
LRRC3
SPATC1L
LINC01547
DSCR8
FAM207A
RSPH1
UMODL1
ERVH48-1
LINC00313
B3GALT5-AS1
LINC00334
TSPEAR-AS2
MCM3AP-AS1
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
UMODL1-AS1
PLAC4
DSCR10
LINC00323
LINC00319
AATBC
KRTAP12-2
KRTAP12-1
KRTAP10-10
PICSAR
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00316
LINC00114
LOC400867
LOC642852
LINC00163
SSR4P1
LINC00322
LOC100129027
MIR3197
ITGB2-AS1
DSCAM-AS1
MIR4760
MIR5692B
LRRC3-AS1
DIP2A-IT1
BRWD1-AS1
COL18A1-AS2
DSCAM-IT1
LOC101928233
LOC101928311
LOC101928398
TCONS_00029157
LOC101928435
TRPM2-AS
LINC01424
LOC101928796
LOC101930094
MIR6070
MIR6814
MIR6815
MIR6508
LOC102724354
LOC102724428
U2AF1L5
LOC102724652
LINC01423
BRWD1-IT2
LOC105372833
FRGCA
SNORA91
WRB-SH3BGR

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q36.2.

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-1244-1
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
CNOT9
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ASIC4
DOCK10
MREG
PECR
C2orf83
MFF
ACKR3
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
LOC93463
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERF4
UBE2F
OTOS
COPS9
OR6B3
LOC150935
PKI55
KANSL1L
LINC01107
LOC151174
ERFE
CCDC140
SLC23A3
LINC00608
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
DAW1
C2orf57
TIGD1
LOC200772
CFAP65
C2orf72
RTP5
LOC285095
UNC80
RUFY4
DUSP28
MROH2A
ESPNL
ECEL1P2
SPATA3-AS1
CATIP
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
LOC440934
MIR375
LOC643387
LINC00607
LOC646736
PRSS56
AQP12B
SNORA75
LOC654841
SCARNA6
SCARNA5
MIR562
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3133
MIR3131
MIR4268
MIR3132
MIR4269
AGAP1-IT1
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4438
MIR4440
MIR4786
MIR4441
MIR5001
MIR5702
MIR5703
VWC2L-IT1
LOC100996693
CAPN10-AS1
LINC01237
LOC101928020
LOC101928103
LOC101928111
LINC01280
LOC101928327
CATIP-AS1
LINC01494
LOC101928881
MIR6513
MIR6809
MIR6811
MIR6810
LOC102723927
LANCL1-AS1
LOC102724849
LOC102725079
MIR9500
CATIP-AS2
LINC01614
LOC105373876
DIRC3-AS1
LOC105373878
LINC01173

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
AFG3L1P
APRT
GAS8-AS1
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
PRDM7
MON1B
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
CMC2
JPH3
VAT1L
TLDC1
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ADAMTS18
SNAI3-AS1
LINC00311
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
LOC339059
FAM92B
CTU2
PABPN1L
LOC400548
FENDRR
LOC400553
LOC400558
C16orf74
LOC440390
SNORD68
LINC00917
VPS9D1-AS1
LOC100129617
LOC100129697
URAHP
SYCE1L
LOC100287036
LOC100289580
MIR1910
MIR3182
LINC01082
C16orf95
MIR4720
MIR4722
MIR4719
MIR5093
MIR5189
PRCAT47
FAM157C
LINC01081
LOC101927793
LOC101927817
LOC101928203
LINC01229
LINC01227
LOC101928417
LOC101928446
LOC101928557
LOC101928614
LOC101928659
LOC101928682
LOC101928708
LOC101928737
LOC101928880
MIR6504
MIR6775
MIR7854
MIR8058
MIR6774
MAFTRR
LOC102724084
LOC102724163
LOC102724344
LOC102724467
FOXC2-AS1
LOC105371414

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.2.

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

Genes
LINC00871

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

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

Genes
AKT2
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-643
hsa-mir-220c
A1BG
ACTN4
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB3
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL2
KIR2DL3
KIR2DL4
KIR2DS1
KIR2DS3
KIR2DS4
KIR2DS5
KIR3DL1
KIR3DL2
KIR3DS1
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
NECTIN2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF146
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2B
SPINT2
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA2
HNRNPUL1
CLASRP
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
PPP6R1
CARD8
SIRT2
CYP2G1P
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
ZNF345
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
C5AR2
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
ZFP14
ZNF529
PRX
SPTBN4
MARK4
CATSPERG
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
CENPBD1P1
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
COQ8B
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
WDR87
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
SNORD35B
ZNF347
ZNF577
ZNF607
KMT5C
C19orf48
ZBTB45
ZNF382
ZNF587
FIZ1
ZNF566
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
ZNF461
ZNF585B
TIMM50
SHKBP1
CCDC114
LOC93429
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
C19orf84
SPACA6
ZNF480
ZNF534
ZNF578
ERVV-1
SMIM17
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
NLRP4
ZNF542P
ZNF582
ZNF583
FAM98C
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
ZNF540
ZNF525
SPACA4
ZNF585A
NLRP7
GGN
CADM4
ADM5
ZNF584
ZSCAN4
NLRP11
TMEM86B
INAFM1
ZNF549
NAPSB
IL4I1
IFNL2
IFNL3
IFNL1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
EMC10
MGC45922
KLK9
SIGLEC17P
SIGLECL1
ZNF615
ZNF841
LOC284379
ZFP82
ZNF790-AS1
LOC284412
VSTM1
TMEM150B
FAM71E2
HKR1
VN1R2
VN1R4
NLRP9
ZNF260
ZNF546
MYPOP
NANOS2
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
DNAAF3
ZNF233
LILRA5
ZNF829
ZNF568
B3GNT8
IGFL1
C19orf68
ZNF773
ZNF582-AS1
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
BHMG1
IGFL3
ZNF808
ZNF888
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF793
ACP7
PINLYP
ZNF818P
ZNF805
SPRED3
ZNF321P
LGALS17A
LOC400706
SIGLEC16
LOC400710
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
CCER2
LOC644189
LOC644554
LOC645553
FAM90A27P
SBK2
RNF225
PSG10P
LGALS7B
PHLDB3
SEC1P
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
LOC728485
LOC728752
CCDC61
CEACAM18
SHISA7
RFPL4AL1
LINC01530
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A12
ZNF667-AS1
LOC100128398
LOC100129083
LOC100129935
SBK3
BSPH1
MZF1-AS1
KIR2DS2
LOC100134317
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A10
SNAR-C2
SNAR-C4
SNAR-E
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
ERICH4
SNAR-A14
ERVV-2
EML2-AS1
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
PCAT19
LOC100505585
LOC100505622
NAPA-AS1
LOC100505715
CARD8-AS1
PPP5D1
PTOV1-AS1
DACT3-AS1
LINC00665
GFY
ZNF865
ZNF571-AS1
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
LOC100631378
MIR5088
NUCB1-AS1
LIPE-AS1
LOC101059948
IFNL4
ZNF350-AS1
ZNF529-AS1
LINC01534
LINC01535
ZNF793-AS1
LINC01480
LOC101928063
LOC101928295
PTOV1-AS2
LOC101928517
ZNF649-AS1
LOC101928804
LOC101928886
ZIM2-AS1
LOC101930071
SPACA6P-AS
MIR6088
MIR6796
MIR6797
MIR6799
MIR6800
MIR6802
MIR6804
MIR6805
MIR6806
MIR8074
MIR8077
MIR8085
MIR6719
MIR6807
MIR8061
MIR6798
MIR6803
MIR7975
MIR6801
ZNF528-AS1
LENG8-AS1
LOC105372397
LOC105372419
LOC105372440
LOC105372441
LOC105372444
LOC105372476
LOC105372483
LOC105447645
PLA2G4C-AS1
GLTSCR2-AS1

Genes in Wide Peak

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

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

Genes
GABRA2
GABRG1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p12.3.

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

Genes
CCND3
DAXX
FANCE
HMGA1
IRF4
PIM1
POU5F1
TRIM27
DEK
TFEB
HIST1H4I
ABCF1
CRISP1
AGER
AIF1
ATP6V1G2
BAK1
CFB
BMP6
BPHL
BTN1A1
BYSL
C2
C4A
C4B
DDR1
RUNX2
CDC5L
CDKN1A
CDSN
CLIC1
CLPS
COL11A2
ATF6B
MAPK14
CSNK2B
CYP21A2
CYP21A1P
DNAH8
DXO
DSP
E2F3
EDN1
SERPINB1
SLC29A1
F13A1
FKBP5
FOXF2
FOXC1
GABBR1
GCNT2
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPX5
GRM4
GTF2H4
GUCA1A
GUCA1B
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
HLA-A
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSPA1A
HSPA1B
HSPA1L
HSP90AB1
ID4
ITPR3
JARID2
KIFC1
LTA
LTB
MAK
MDFI
MEA1
MEP1A
MICB
MLN
MOCS1
MOG
MSH5
MUT
RPL10A
NEDD9
NEU1
NFKBIE
NFKBIL1
NFYA
NQO2
NOTCH4
PBX2
PEX6
PGC
PGK2
PHF1
SERPINB6
SERPINB9
POLH
PPARD
PPP1R10
PPP2R5D
MAPK13
PRL
PSMB8
PSMB9
PTK7
RGL2
PRPH2
RHAG
RING1
BRD2
RNF5
RPS10
RPS18
RREB1
RXRB
VPS52
ATXN1
SRSF3
SKIV2L
SLC17A1
SNRPC
SOX4
SRF
SRPK1
SSR1
TAF11
TAP1
TAP2
TAPBP
TBCC
TCF19
TCP11
PPP1R11
TEAD3
TFAP2A
TFAP2B
TNF
TNXA
TNXB
TPMT
CRISP2
TUBB2A
TULP1
VARS
VEGFA
ZNF76
ZNF165
TRIM26
ZNF184
ZSCAN26
ZKSCAN8
ZSCAN9
ZNF204P
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
OR2H2
NELFE
LST1
PLA2G7
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
CMAHP
DHX16
SUPT3H
KCNK5
B3GALT4
RIPK1
SYNGAP1
STK19
IER3
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
GCM2
WDR46
ZBTB22
CD83
PPT2
CDYL
NCR2
LY86
MED20
SLC25A27
EEF1E1
POLR1C
MAD2L1BP
MDC1
FAM65B
ZSCAN12
CUL7
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
FLOT1
RCAN2
SLC17A2
HCG9
PRSS16
CRISP3
BTN3A3
BTN2A2
ECI2
PFDN6
HMGN4
TRIM38
CAP2
UBD
AGPAT1
SCGN
DNPH1
C6orf10
FARS2
CNPY3
SLC17A3
RPP40
FRS3
SLC22A7
HCP5
EHMT2
APOBEC2
TRIM31
BTN3A2
BTN3A1
BTN2A1
CAPN11
NUDT3
NRM
STK38
ENPP4
CMTR1
CUL9
ANKS1A
UBR2
SIRT5
DAAM2
GLTSCR1L
DDAH2
CD2AP
MTCH1
ZNF318
SPDEF
YIPF3
USP49
OR2B6
FAM50B
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
SNORD52
SNORD48
BRPF3
GNMT
TNFRSF21
MRPS18B
C6orf15
MYLIP
ABT1
PRICKLE4
PACSIN1
ZNRD1
DEF6
C6orf48
SLC35B3
GMNN
MRPL2
TBC1D7
NRN1
CYP39A1
NOL7
FAM8A1
DCDC2
ETV7
TMEM14C
TDP2
CUTA
PPIL1
CLIC5
TREM2
TREM1
HCG4
GFOD1
CCHCR1
GTPBP2
BTN2A3P
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
CENPQ
MRPS18A
MRPS10
TMEM63B
CARMIL1
TBC1D22B
EXOC2
SAYSD1
TRERF1
ACOT13
APOM
BTNL2
TRIM39
WRNIP1
DUSP22
LYRM4
VARS2
MRS2
LRFN2
AARS2
XPO5
CPNE5
LSM2
C6orf47
LY6G5B
LY6G6D
ENPP5
ZFAND3
SLC22A23
BLOC1S5
MCUR1
GPSM3
FKBPL
KIF13A
ZSCAN31
C6orf106
MRPL14
DLK2
LY6G6E
ZNF322
TREML2
RPP21
ATAT1
ZKSCAN3
ZSCAN16
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRR3
ZNRD1ASP
PRRT1
EGFL8
HCG4B
TXNDC5
C6orf62
OR5V1
OR2B2
OR12D3
TMEM14B
RIOK1
TFAP2D
KCNK16
DTNBP1
UQCC2
PGBD1
TTBK1
ADTRP
HIST1H2AH
HIST1H2BK
RRP36
KCNK17
ABCC10
TRIM15
KLC4
TJAP1
POM121L2
FOXQ1
BTBD9
ZBED9
FOXP4
KLHDC3
SLC26A8
MAS1L
IP6K3
TAF8
C6orf141
HUS1B
TRIM40
DPCR1
NRSN1
SNRNP48
MBOAT1
HDGFL1
LINC01600
CCDC167
PSORS1C1
PSORS1C2
PPP1R18
PTCRA
TCTE1
TRIM39-RPP21
TUBB
PIP5K1P1
OPN5
ADGRF4
ADGRF5
TDRD6
SPATS1
C6orf223
RSPH9
LRRC73
TREML5P
ADCY10P1
OARD1
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
SMIM13
SYCP2L
LINC00518
PXDC1
SERPINB9P1
ADGRF2
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
TOB2P1
FAM217A
DEFB110
DEFB112
DEFB113
DEFB114
HCG27
RNF144B
HIST1H2BA
GPX6
NCR3
LY6G6F
MDGA1
ADGRF1
ZNF311
LOC285766
LINC01622
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
HCG22
LOC285847
PNPLA1
TREML4
RPL7L1
MYLK4
IFITM4P
CLPSL1
TREML1
TREML3P
ZNF391
ZFP57
TUBB2B
SLC35B2
C6orf52
HCG26
KAAG1
NHLRC1
ZKSCAN4
GUSBP2
LINC00533
VN1R10P
HIST1H2APS1
PSMG4
SFTA2
CLPSL2
C6orf222
GLYATL3
MUC21
LINC01011
HTATSF1P2
STMND1
CASC15
LINC01623
LINC00243
MCCD1
SAPCD1
LINC00336
RAB44
LINC00951
LOC401261
CRIP3
DEFB133
C6orf201
ERVFRD-1
MIR219A1
HCG14
HCG23
HCG25
HCG16
HCG24
HCG18
HCG17
LINC00266-3
C6orf226
TMEM151B
OR2B3
OR2J3
OR14J1
OR10C1
ATP6V0CP3
PTCHD4
GGNBP1
HCG11
KU-MEL-3
LOC554223
C6orf132
PPP1R3G
ZNF192P1
SNORA38
SNORD32B
SNORD84
SNORD117
MIR548A1
MIR586
HULC
NBAT1
LINC01556
TDRG1
TMEM170B
SCARNA27
MIR877
ZSCAN16-AS1
LYRM4-AS1
LOC100129636
TFAP2A-AS1
LOC100130357
PSORS1C3
LOC100131047
LOC100131289
LINC01512
LINC00240
TOMM6
LOC100270746
ANKRD66
LOC100294145
MIR1275
MIR1236
MIR3143
MIR3934
MIR3925
MIR3691
LOC100505530
LOC100505635
LOC100506207
ELOVL2-AS1
JARID2-AS1
LOC100506885
LINC01012
LOC100507194
LINC01015
HCG8
MICA
PSMB8-AS1
LOC100507506
LOC100507547
LINC01016
MUC22
GMDS-AS1
BLOC1S5-TXNDC5
EEF1E1-BLOC1S5
RPS10-NUDT3
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4647
MIR4641
MIR3135B
MIR4646
MIR4640
MIR4639
MIR4645
MIR4642
MIR4462
MIR5689
MIR5004
MIR5683
MIR5690
LINC00581
FOXP4-AS1
PANDAR
LOC101926898
LOC101926915
LOC101926934
LOC101926962
LOC101927020
LOC101927048
LOC101927691
FOXCUT
LOC101927730
LOC101927759
LOC101927950
LOC101927972
LOC101928191
LOC101928253
LOC101928433
LOC101928491
LOC101928519
C6orf229
LOC101928663
LOC101929006
LOC101929163
LOC101929188
LOC101929243
LOC101929555
LOC101929705
LOC101929726
C2-AS1
LINC01108
MIR6833
MIR6834
MIR6835
MIR6891
MIR7111
MIR7641-2
MIR6721
MIR6720
MIR6832
MIR6780B
MIR6873
MIR7159
MIR7853
HCG21
LOC102724096
LINC01276
SAPCD1-AS1
TRIM31-AS1
LOC105374952
LOC105374960
LOC105374972
LOC105374988
HCG20
LOC105375014
LOC105375075
MDC1-AS1
DDX39B-AS1
HLA-DQB1-AS1
MIR5689HG
TBC1D7-LOC100130357
CNPY3-GNMT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

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

Genes
FAM19A5
LOC284933
MIR3201
MIR4535

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
CREB3L2
hsa-mir-1975
hsa-mir-96
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
RNY1
RNY3
RNY4
RNY5
SHH
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
TCAF1
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ZNF277
ABCB8
TFEC
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
RNU6-1
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
LSM8
COPG2IT1
GPR85
TAS2R5
CHPF2
ING3
LRRN3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767P
CPED1
TTC26
KDM7A
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
MGAM2
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
BMT2
LOC154761
CLEC2L
FMC1
LINC00689
FEZF1-AS1
IQUB
C7orf77
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
THAP5
GIMAP7
ZNF467
ZNF800
GIMAP1
PAXIP1-AS1
C7orf33
TRY2P
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
WEE2-AS1
EPHA1-AS1
TCAF2
ZNF775
LINC00996
ATG9B
LSMEM1
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
BLACE
CTAGE6
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
LINC-PINT
RNF148
FEZF1
FAM180A
LOC389602
OR2A25
IQCA1L
OR2A5
LINC00998
POT1-AS1
PRRT4
RAB19
OR2A7
OR2A20P
ATP6V0E2-AS1
LINC01000
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
MNX1-AS1
C7orf73
TCAF2P1
ACTR3C
MIR592
MIR593
MIR595
ARHGEF34P
LOC728743
TMEM229A
LUZP6
MIR671
HTR5A-AS1
CTAGE4
LINC01003
LOC100129148
LOC100130705
LOC100130880
WDR86-AS1
PAXIP1-AS2
JHDM1D-AS1
NDUFB2-AS1
CTAGE8
SMKR1
MOXD2P
ZNF783
MIR548F4
MTRNR2L6
MIR3654
MIR3907
MIR3666
PRKAG2-AS1
LOC100506302
LINC01006
DOCK4-AS1
LOC100506585
LOC100506682
LOC100506860
MKLN1-AS
LOC100506937
TMEM178B
LOC100507507
GIMAP1-GIMAP5
MIR4468
MIR5707
LOC100996249
LINC01510
C7orf55-LUC7L2
LOC101927914
LOC101928012
HRAT17
LOC101928211
LOC101928254
LOC101928283
LOC101928333
OR2A1-AS1
LOC101928605
LOC101928700
LOC101928782
LOC101928807
LOC101928861
LOC101929998
RNU6-7
RNU6-8
MIR6133
MIR6509
MIR6892
MIR6132
GHET1
LINC01393
LOC102724434
LOC102724555
RNU6-2
LINC01287
LINC01392
LVCAT5
LOC105375483
LOC105375504
LOC105375512
LOC105375545
LOC105375556
LINC01022

Genes in Wide Peak

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

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

Genes
BCL9
CDKN2C
EPS15
JAK1
JUN
LCK
MPL
MUTYH
NOTCH2
NRAS
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
BCL10
PDE4DIP
THRAP3
TRIM33
PRDM16
RBM15
MDS2
hsa-mir-551a
ABCA4
ACADM
ADORA3
AGL
AK2
AK4
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
RERE
ATP1A1
ATP5F1
ATP6V0B
ADGRB2
BMP8B
BRDT
C1QA
C1QB
C1QC
C8A
C8B
CA6
CAPZA1
CAPZB
CASP9
CASQ2
RUNX3
CD2
TNFRSF8
CD53
CD58
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CHI3L2
CLCA1
CLCN6
CLCNKA
CLCNKB
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
CORT
CPT2
CRYZ
CSF1
CSF3R
CTBS
CTH
CTPS1
CYP2J2
CYP4A11
CYP4B1
DAB1
DBT
GADD45A
DDOST
DFFA
DFFB
DHCR24
DIO1
DLSTP1
DPH2
DPYD
DR1
DRD5P2
DVL1
E2F2
ECE1
S1PR1
EDN2
PHC2
CELSR2
MEGF6
EPHA2
ELAVL4
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EXTL2
EYA3
F3
FAAH
FABP3
FCGR1A
FCGR1B
FGR
FHL3
FOXE3
FOXD2
FMO5
MTOR
FUCA1
IFI6
GABRD
GALE
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GNAI3
GNAT2
GNB1
GNG5
SFN
GPR3
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HMGCS2
HPCA
HSD3B1
HSD3B2
IGSF3
HSPG2
HTR1D
HTR6
ID3
CYR61
IL12RB2
TNFRSF9
INPP5B
IPP
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
STMN1
LEPR
TACSTD2
MAGOH
MATN1
MFAP2
MOV10
MSH4
MTF1
MTHFR
MYCL
NASP
NBL1
NDUFS5
NFIA
NFYC
NGF
NHLH2
NPPA
NPPB
NRDC
YBX1
ROR1
OPRD1
ORC1
OVGP1
PAFAH2
PRDX1
PDE4B
PDZK1
PEX10
PEX14
PGD
PGM1
PIK3CD
PIN1P1
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKAA2
PRKAB2
PRKACB
PKN2
PRKCZ
PSMA5
PSMB2
PTAFR
PTGER3
PTGFR
PTGFRN
PTPRF
ABCD3
RAB3B
RABGGTB
RAP1A
RAP1GAP
RBBP4
RHCE
RHD
RLF
RNU1-4
SNORA73A
SNORD21
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RSC1A1
SORT1
SARS
SCNN1D
SCP2
SRSF4
ST3GAL3
STIL
SKI
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SLC16A1
SRM
STXBP3
SYCP1
TAF12
TAF13
TBX15
TCEA3
TCEB3
TGFBR3
TIE1
TNFRSF1B
TP73
TSHB
TTC4
TNFRSF4
UQCRH
UROD
USP1
VCAM1
WNT2B
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
PTP4A2
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
SNHG3
NR0B2
RAD54L
TTF2
PIK3R3
MMP23B
MMP23A
KCNAB2
ITGA10
LMO4
FCN3
CDC14A
YARS
MKNK1
AKR7A2
PLPP3
RTCA
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
FPGT
PEX11B
PER3
FUBP1
EIF2B3
ARTN
MAP3K6
DIRAS3
SLC16A4
KCNQ4
ZMYM4
ZMYM6
DHRS3
SRSF11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
THEMIS2
TMEM59
SEC22B
CHD1L
H6PD
CLCA3P
CLCA2
ISG15
PLCH2
HS2ST1
IPO13
SDC3
KDM4A
CROCC
PUM1
CEP104
RIMS3
EFCAB14
DNAJC6
LRIG2
PLPPR4
SV2A
KLHL21
SLC35E2
ZBTB40
MFN2
RBM8A
INSL5
PIGK
PTPRU
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
PATJ
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
BCAS2
AKR1A1
WARS2
CEPT1
PIAS3
TESK2
PPIE
VAV3
MAD2L2
PPIH
CAP1
LRRC41
LAMTOR5
IFI44
POLR3C
TXNIP
PDPN
KHDRBS1
GMEB1
AP4B1
NUDC
PHTF1
MASP2
AHCYL1
SRSF10
WDR3
MAN1A2
UTS2
SF3A3
IFI44L
EBNA1BP2
KIF2C
RER1
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
MST1P2
DDX20
MST1L
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLCA4
MTF2
DNAJC8
NTNG1
CLSTN1
FOXJ3
WDR47
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
USP33
WDTC1
EMC1
KIF1B
MAST2
NCDN
CLCC1
SLC35D1
PLEKHM2
OTUD3
KAZN
CAMTA1
ADGRL2
KIAA1107
ZCCHC11
SZT2
DNAJC16
UBR4
USP24
ATP13A2
ITGB3BP
TARDBP
CELA3B
SLC35A3
ICMT
MACF1
LRRC8B
LPAR3
PADI4
DDAH1
TMEM50A
KPNA6
SSBP3
STX12
NBPF14
CLIC4
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
SZRD1
LDLRAP1
SERBP1
NOC2L
PTPN22
PHGDH
FBXO2
FBXO6
PLA2G2D
AK5
MYCBP
HEYL
AGO1
SNORA73B
SNORA66
SNORD45B
SNORD45A
SNORD55
RNU11
RNU6-1
RNU5F-1
RNU5E-1
RNU5D-1
RNVU1-7
RNU1-3
RNU1-2
RNU1-1
RNF11
FOXD3
TRAPPC3
HSPB7
CHIA
ARHGEF16
AHDC1
RNF115
TEKT2
SMPDL3B
ANGPTL3
LINC00339
SSU72
GNL2
GPSM2
UBIAD1
ALG6
PADI1
SLC25A24
PLA2G2E
DNTTIP2
WRAP73
SLC45A1
HP1BP3
TMED5
BOLA1
CELA2B
ZNF593
ZNF691
TXNDC12
TNNI3K
SH3GLB1
MECR
UTP11
SDF4
MRTO4
HAO2
ACP6
TMEM69
MRPL37
HOOK1
SNX7
HPCAL4
YTHDF2
GPR89B
ZCCHC17
DPH5
HSPB11
PADI3
CMPK1
GPR88
ERRFI1
WNT4
YIPF1
FBXO42
TRMT13
RNF186
SPATA6
MXRA8
L1TD1
HES2
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf123
C1orf159
AURKAIP1
TTC22
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
PRPF38B
CDCA8
LRRC8D
ARHGEF10L
PRMT6
RNF220
VPS13D
EVA1B
ATAD3A
TMEM57
TRIM62
RAVER2
PANK4
ECHDC2
FGGY
MCOLN3
SLC22A15
CAMK2N1
RNPC3
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
NBPF1
MAP7D1
NDC1
NECAP2
IQCC
DNAJC11
LRIF1
CTTNBP2NL
RCC2
FAM212B
DMAP1
AJAP1
GNG12
TMEM234
MTFR1L
KYAT3
TMEM167B
OLFML3
CTNNBIP1
RSRP1
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
LINC00869
TMIGD3
PLEKHG5
AMIGO1
LRRC47
ODF2L
KIAA1324
DISP3
LRRC7
KIF17
ZSWIM5
KIAA1522
CACHD1
MIER1
HES4
GRHL3
PTBP2
DNASE2B
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ADGRL4
TINAGL1
P3H1
PLA2G2F
MFSD14A
SMAP2
ATPAF1
S100PBP
MEAF6
EXO5
CEP85
NMNAT1
ELOVL1
VWA1
DCLRE1B
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZFP69B
COA7
PHACTR4
AUNIP
ERI3
C1orf50
WDR77
CCDC28B
EFHD2
MMEL1
RSG1
DLEU2L
OR4F5
NKAIN1
EPS8L3
MUL1
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
NOL9
PPCS
LIN28A
SH3D21
TTLL7
SNIP1
AGMAT
WDR78
ZMYM1
LINC00115
RPAP2
MORN1
FAM110D
KIAA0319L
DHDDS
DENND2D
WLS
GPR157
RPF1
SIKE1
ZC3H12A
SPSB1
TRIM45
CPTP
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
ANKRD13C
TSSK3
CCNL2
VANGL1
ST6GALNAC5
HYI
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
GPR61
STK40
TM2D1
REG4
TMEM222
PLEKHN1
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
SLC25A33
DDI2
LZIC
PROK1
EFCAB7
NT5C1A
TRIM63
PSRC1
FAM167B
FOXD2-AS1
PERM1
CROCCP2
HPDL
ATP1A1-AS1
AGBL4
MFSD2A
ATG4C
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
STRIP1
DOCK7
CFAP74
KIAA2013
THAP3
STPG1
SPOCD1
ZNF697
BTF3L4
UBXN11
NEXN
C1orf158
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
MED8
KTI12
SMIM12
AZIN2
TMEM54
HENMT1
TOE1
ERMAP
CSMD2
MYSM1
GNRHR2
CROCCP3
FHAD1
OSBPL9
LOC115110
OMA1
RAB42
LRRC42
GBP4
GBP5
FAM46B
RBP7
ACAP3
SSX2IP
UBE2J2
OLFM3
CCDC163
KDF1
LRRC38
AADACL3
PUSL1
B3GALT6
WDR63
MAB21L3
IFFO2
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
ERICH3
LRRIQ3
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
TCEANC2
PODN
LRRC39
GJB4
HMGB4
RNF19B
A3GALT2
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
LIX1L
HSD3BP4
KLF17
TMEM125
ARHGEF19
DRAM2
PIFO
C1orf162
ACTRT2
MIB2
SYT6
C1orf127
SAMD11
LOC148413
SAMD13
C1orf52
PHF13
TMEM56
NBPF4
UBE2U
LINC00337
HFE2
ANKRD35
SLC30A7
CCDC27
ZNF436-AS1
KNCN
MOB3C
GLIS1
NBPF12
MGC27382
DCDC2B
ZNF362
LINC01225
MANEAL
IL23R
PDIK1L
CLDN19
CFAP57
C1orf210
CCDC24
BTBD19
CCDC17
C1orf64
CHIAP2
SLC2A7
DENND2C
GBP6
PLPPR5
FNDC7
CALML6
IFNLR1
CYP4Z2P
CITED4
SLC25A3P1
LEXM
KANK4
SASS6
FAM43B
HFM1
PAQR7
UBL4B
NUDT4P2
PDIA3P1
OXCT2P1
AGO3
AGO4
ALG14
FAM76A
LINC00466
C1orf168
TMEM201
TMEM61
CYP4Z1
FAAP20
CDCP2
SLC5A9
CC2D1B
NBPF11
NUDT17
TXLNA
TCTEX1D1
SPAG17
SLFNL1
TMEM51-AS1
HIPK1
SLC44A5
ATAD3C
AKR7L
AKR7A2P1
FNDC5
EPHX4
LINC01342
TTLL10
AKNAD1
TMCO4
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
ZNF683
NEGR1
CYP4X1
MAGI3
NPHP4
BEST4
FAM19A3
C1orf167
CYP4A22
C1orf185
LINC01226
NBPF15
FAM41C
FAM102B
SYPL2
CYB561D1
ANKRD34A
LOC284632
RSPO1
EPHA10
LOC284661
ZNF326
BTBD8
RIMKLA
SLC25A34
ESPNP
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
FAM151A
LINC01343
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LINC01141
LINC01140
LOC339539
C1orf228
ZFP69
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF10
CCDC18
MYBPHL
BARHL2
NBPF7
TCTEX1D4
SERINC2
FAM159A
FAM131C
PADI6
BMP8A
DRAXIN
SPATA21
SVBP
TEX38
MROH7
MIGA1
NEXN-AS1
AGRN
CENPS
CATSPER4
NSUN4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
TRABD2B
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
C1orf137
NOTCH2NL
LINC01138
LOC388692
HES3
PRAMEF12
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINT1L
UOX
FRRS1
TMEM200B
FAM87B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
LINC01144
C1orf141
GBP1P1
FLJ27354
MIR137HG
NBPF9
RNF223
LDLRAD2
CSMD2-AS1
MIR101-1
MIR137
MIR186
MIR197
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
MGC34796
LHX8
LINC01555
LINC00982
PRAMEF11
PRAMEF6
HNRNPCL2
UQCRHL
MINOS1
SLC2A1-AS1
FAM183A
ZYG11A
FLJ31662
LOC440600
LOC440602
BCL2L15
NUDT4P1
HIST2H2BF
ANKRD65
PRAMEF7
PRAMEF25
PGCP1
GEMIN8P4
RBMXL1
LURAP1
PEF1
MIR429
FAM72C
CYB5RL
SSBP3-AS1
SPATA42
CYMP
KIAA0754
LOC643355
LOC643441
LINC01128
TMEM88B
FNDC10
RPS14P3
LINC00622
PPIAL4G
FAM231D
NBPF13P
ACTG1P20
PIK3CD-AS1
NFIA-AS1
PPIAL4D
LOC645166
PRAMEF26
PRAMEF33P
PRAMEF19
PRAMEF20
FAM138A
LACTBL1
LOC646471
LOC646626
SETSIP
EMBP1
SRGAP2B
ACTG1P4
PRAMEF34P
HNRNPCL3
ZBTB8A
NBPF6
LOC653160
SRGAP2C
PPIAL4A
GPR89A
PPIAL4C
HIST2H3D
PRAMEF22
PRAMEF15
WASH7P
FAM72B
FAM138C
SCARNA2
SCARNA1
FAM138D
SNORA44
SNORA55
SNORA61
SNORA59A
SNORA16A
SNORD45C
SNORD103C
SNORD99
SNORD103A
MIR551A
MIR552
MIR553
C1orf195
ZBTB8B
LINC01137
PPIEL
CCDC30
CDK11A
SLC35E2B
LINC01346
FAM72D
NBPF8
LINC00623
RPS15AP10
LOC728989
FAAHP1
C1orf234
HSD52
PRAMEF14
FAM231A
FAM231C
FLJ37453
LOC729737
OR4F29
LOC729930
LOC729970
LOC729987
PPIAL4E
PFN1P2
PDZK1P1
MIR942
MIR760
FAM229A
LINC01349
LOC100129046
LOC100129138
MATN1-AS1
LINC01160
LOC100129534
LOC100129620
LOC100129924
EFCAB14-AS1
LOC100130417
NFYC-AS1
LINC01135
CCDC18-AS1
LOC100132057
LOC100132062
FOXO6
LOC100132147
NBPF10
FCGR1CP
ZRANB2-AS1
KDM4A-AS1
FAM231B
LOC100133331
LINC01134
DDX11L1
AP4B1-AS1
TTC34
LOC100288069
NBPF20
HYDIN2
GNG12-AS1
LINC00624
MIR320B1
MIR548N
MIR1256
MIR1976
MIR1290
MIR1302-2
MIR1262
MIR761
NPPA-AS1
MIR1302-9
MIR1302-10
MIR3115
MIR3117
MIR4255
MIR3116-1
MIR4253
MIR1302-11
MIR3116-2
MIR4251
MIR1273D
MIR4252
MIR4256
MIR4254
MIR3659
MIR3917
MIR3605
MIR3671
MIR3675
SPATA1
LINC01364
LOC100505824
LOC100505887
ENO1-AS1
RTCA-AS1
LOC100506022
TMEM35B
FAM212B-AS1
SLC16A1-AS1
LOC100506730
LOC100506801
TCEB3-AS1
LOC100506985
SLFNL1-AS1
MKNK1-AS1
LOC100507564
LOC100507634
APITD1-CORT
FPGT-TNNI3K
GJA9-MYCBP
MROH7-TTC4
TMEM56-RWDD3
MINOS1-NBL1
MIR4695
MIR1273G
MIR1273F
MIR4420
MIR4419A
MIR3972
MIR4421
MIR4422
MIR4781
MIR378G
MIR4794
MIR4425
MIR548AC
MIR4684
MIR4711
MIR4689
MIR5096
MIR4418
MIR4632
MIR2682
MIR5095
MIR4423
MIR4417
MIR378F
RCAN3AS
MIR5581
MIR5585
MIR5087
MIR5697
MIR5584
NEGR1-IT1
ZRANB2-AS2
PINK1-AS
SRGAP2-AS1
DPYD-AS1
DPYD-AS2
MTOR-AS1
VAV3-AS1
KCNC4-AS1
KCND3-AS1
LINC00853
HAO2-IT1
ERI3-IT1
KCND3-IT1
AGBL4-IT1
LOC100996251
LOC100996263
FOXD3-AS1
LINC01355
NFIA-AS2
LOC100996583
LOC100996630
LOC100996635
LINC01356
SRGAP2D
HNRNPCL4
LAMTOR5-AS1
RNVU1-8
DAB1-AS1
LINC01358
LOC101926944
LOC101926964
ROR1-AS1
LINC01359
LOC101927139
DEPDC1-AS1
LOC101927244
LINC01360
ERICH3-AS1
LOC101927342
LOC101927412
LOC101927429
LOC101927434
LOC101927468
LINC01361
LOC101927560
LOC101927587
LOC101927844
LOC101927876
PKN2-AS1
LOC101927895
UBXN10-AS1
LOC101928043
LINC01057
LOC101928098
LOC101928118
LOC101928163
LOC101928241
LOC101928270
LOC101928303
LOC101928324
LOC101928370
LOC101928436
LOC101928460
LOC101928476
LOC101928626
LOC101928718
LOC101928728
HIPK1-AS1
LOC101928977
LOC101928979
LOC101928995
LOC101929023
PIK3CD-AS2
LOC101929099
LOC101929147
LOC101929181
LOC101929406
LOC101929464
LOC101929516
LOC101929536
LOC101929592
LOC101929626
LINC01398
LOC101929721
NBPF25P
LOC101929798
LOC101929901
LOC101929935
PRAMEF27
RNVU1-4
RNVU1-14
RNVU1-15
RNVU1-20
RNVU1-17
RNVU1-3
RNVU1-1
RNU6-7
RNVU1-6
RNVU1-19
RNU6-8
MIR6068
MIR6079
MIR6084
MIR6723
MIR6726
MIR6727
MIR6728
MIR6731
MIR6732
MIR6733
MIR6735
MIR7846
MIR7852
MIR7856
MIR6859-2
MIR6859-3
MIR6736
MIR6077
MIR6127
MIR6500
MIR6730
MIR6734
MIR6808
MIR6859-1
MIR6729
MIR7156
LOC102606465
LOC102723661
LINC01389
TTC39A-AS1
LOC102724312
LOC102724450
LOC102724539
LOC102724552
CH17-408M7.1
LOC102724571
LOC102724659
LOC103091866
RNU6-2
LINC01461
LINC01397
TXNDC12-AS1
LINC01307
LINC01525
WARS2-IT1
LOC105376736
LOC105376805
LOC105378591
LOC105378614
LOC105378663
LOC105378683
LOC105378732
LOC105378828
LOC105378853
LOC105378933
MIR34AHG
SNORD128
SNORA110

Genes in Wide Peak

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

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

Genes
TNFRSF17
CREBBP
ERCC4
CIITA
MYH11
TSC2
SOCS1
PALB2
ABAT
ABCA3
ADCY9
AQP8
ABCC6
ARHGDIG
ATP6V0C
CCNF
CDR2
CLCN7
CRYM
ECI1
DNASE1
DNASE1L2
E4F1
EMP2
GFER
GP2
GRIN2A
GSPT1
HAGH
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
IGFALS
MEFV
MPG
ABCC1
NUBP1
NDUFAB1
NDUFB10
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PARN
PDPK1
PKD1
PLK1
PMM2
PPL
PRKCB
PRM1
PRM2
RBBP6
RPL3L
RPS2
RPS15A
ACSM3
SCNN1B
SCNN1G
SRL
CAPN15
SSTR5
TCEB2
TFAP4
TNP2
TPSAB1
UBE2I
UMOD
UQCRC2
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
ZP2
USP7
NPRL3
SNN
AXIN1
PLA2G10
RGS11
CACNA1H
BAIAP3
RHBDL1
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
SYNGR3
IL32
NPIPA1
SLC9A3R2
LITAF
KIAA0430
SEC14L5
RAB11FIP3
CCP110
IFT140
TELO2
HS3ST2
NUBP2
ZNF263
TRAP1
COQ7
MSLN
IGSF6
STUB1
CACNG3
MRPL28
ERN2
TBL3
RNPS1
PRSS21
PDXDC1
SMG1
CLUAP1
GGA2
NPIPB3
MAPK8IP3
ARL6IP1
CLEC16A
MGRN1
NOMO1
TPSD1
SRRM2
CARHSP1
TPSG1
RAB26
TMEM186
ZNF500
DECR2
RSL1D1
OR1F2P
SNORA64
SNORD60
TNRC6A
DEXI
C16orf72
ZC3H7A
UBN1
EEF2K
CDIP1
SOX8
AMDHD2
PAM16
TXNDC11
METTL9
NAGPA
BFAR
TNFRSF12A
LCMT1
GDE1
GPRC5B
POLR3K
MSRB1
SYT17
GNG13
KCTD5
RRN3
RBFOX1
NDE1
ZSCAN32
HCFC1R1
ACSM5
ARHGAP17
CPPED1
DNAH3
THUMPD1
LUC7L
POLR3E
ALG1
UBFD1
C16orf62
TMEM159
LYRM1
NMRAL1
TBC1D24
USP31
MKL2
CASKIN1
CRAMP1
RAB40C
PRM3
TMEM8A
CHTF18
CHP2
PRSS22
XYLT1
MLST8
RHBDF1
MMP25
NARFL
LINC00235
TPSB2
HS3ST6
PDIA2
UNKL
LINC00254
LMF1
FAM173A
MRPS34
METRN
METTL22
THOC6
KREMEN2
CORO7
SNRNP25
ROGDI
TMEM204
TMC5
NAA60
TMC7
ATF7IP2
C16orf59
LOC81691
ZNF205-AS1
FAHD1
PRSS27
FAM234A
WDR24
TRAF7
FLYWCH1
HAGHL
NUDT16L1
METTL26
MCRIP2
SLX4
DCTN5
GNPTG
GLYR1
GLIS2
ZSCAN10
C16orf45
RHOT2
ZNF598
HN1L
SPSB3
TIGD7
COG7
SNX29
ERI2
RPUSD1
FLYWCH2
VASN
SLC5A11
TSR3
RMI2
ACSM1
WFIKKN1
NTAN1
FOPNL
ACSM2A
DCUN1D3
NOXO1
CCDC78
IQCK
ZG16B
PRSS30P
PAQR4
GPR139
ANKS3
UBALD1
SEPT12
EARS2
VWA3A
OTOA
TEKT5
RNF151
PRR35
FBXL16
SSTR5-AS1
ZNF597
BICDL2
C16orf89
C16orf71
ITPRIPL2
EEF2KMT
WDR90
EME2
CASP16P
NLRC3
PDILT
MEIOB
MPV17L
PDZD9
ANKS4B
PRSS33
NOMO2
NPW
BRICD5
PGP
LINC00514
LINC00921
LOC283887
NHLRC4
C16orf91
TMEM114
PKD1P1
JMJD8
C16orf96
ZKSCAN2
ACSM2B
PRSS41
SLC7A5P2
PRR25
C1QTNF8
PTX4
BCAR4
KNOP1
CRYM-AS1
LINC01567
NOMO3
SMIM22
NPIPB4
LOC554206
SNORA10
MIR193B
MIR484
SMG1P1
NPIPA3
NPIPA2
FLJ42627
CCDC154
C16orf90
ABCA17P
LOC652276
ABCC6P1
LOC653786
SNORA78
MIR662
CLEC19A
LOC729652
SHISA9
ABCC6P2
RRN3P1
C16orf52
SNHG9
CEMP1
TVP23A
MIR940
MIR365A
LOC100128770
SRRM2-AS1
MIR193BHG
RRN3P3
WASIR2
NPIPB5
LOC100134368
MIR1225
LOC100190986
SMG1P3
DDX11L10
LOC100288162
NPIPA5
MIR1972-1
MIR548H2
MIR3180-3
MIR3180-1
MIR3179-2
MIR1972-2
MIR548W
MIR3180-2
MIR3179-1
MIR3178
MIR3179-3
MIR3177
MIR3176
MTRNR2L4
MIR3677
MIR3180-4
MIR3670-1
MIR3180-5
MIR3680-1
LOC100505915
LCMT1-AS2
SNHG19
ERVK13-1
MMP25-AS1
ZNF213-AS1
LINC01569
NAGPA-AS1
CORO7-PAM16
MIR4718
MIR4717
MIR4516
SNX29P1
MIR3670-2
MIR5587
NPIPA7
GLIS2-AS1
LINC01570
LOC101927009
LOC101927131
LOC101927311
LOC101927348
LOC101927814
LMF1-AS1
LOC101929613
MIR6126
MIR6506
MIR6511B1
MIR6767
MIR6768
MIR6770-1
MIR6511A3
MIR8065
MIR6770-2
MIR6859-2
MIR6859-3
MIR6511B2
MIR1273H
MIR6511A1
MIR6769A
MIR6859-1
MIR6511A2
LOC102723385
LCMT1-AS1
LOC102723692
LOC102724927
MIR3670-3
MIR3179-4
LINC01195
LINC01177
PKD1P6-NPIPP1
LOC105371038
LOC105371046
LOC105371049
LOC105371083
MFSD13B
LOC105371184
LOC105447648
LOC106660606

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21p11.2.

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

Genes
BAGE
TPTE
CYP4F29P
SMIM11A
BAGE4
BAGE3
BAGE2
ANKRD30BP2
POTED
ANKRD20A11P
MGC39584
MIR663A
RNA5-8S5
RNA18S5
RNA28S5
TEKT4P2
MIR3118-1
MIR3156-3
MIR3687-1
MIR3648-1
LOC100507412
RNA45S5
C21orf140
MIR6724-1
MIR8069-1
LOC102723360
KCNE1B
SMIM11B
LOC102724188
LOC102724219
LOC102724843
MIR6724-2
MIR6724-3
LOC105379511
LOC105379514

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p12.

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

Genes
EMB
HCN1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

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

Genes
APC
CD74
EBF1
IL6ST
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-886
hsa-mir-1244-2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
NAIP
NDUFA2
NDUFS4
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PLPP1
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
ATG12
PTTG1
PDLIM7
NREP
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
APBB3
CCNO
TNIP1
RACK1
NSA2
FST
SLU7
POLR3G
RGS14
PLK2
IQGAP2
SEC24A
CPLX2
FAXDC2
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
SOX30
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
JADE2
LARP1
PPWD1
HARS2
OTP
SKIV2L2
ZNF346
SSBP2
BHMT2
TNFAIP8
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR2V1
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
IPO11
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
NEURL1B
DHX29
EPB41L4A-AS2
DDX4
FAM193B
SGTB
ARL15
PCDHB18P
PCDHB17P
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
SPDL1
THG1L
AGGF1
WDR41
LOC55338
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
DEPDC1B
BDP1
RNF130
ERBIN
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
NLN
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
ZBED8
MCCC2
EPB41L4A
CENPK
ERAP2
ARHGEF28
SIL1
GMCL1P1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
ELOVL7
TRAPPC13
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
ADGRV1
PCBD2
UTP15
ZCCHC9
PSD2
SLF1
THOC3
ZBED3
GFM2
CYSTM1
MEGF10
SPINK7
SPZ1
TRIM52
HAVCR2
PHYKPL
SMIM3
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
LEAP2
SCGB3A2
ZNF354B
SETD9
IL31RA
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
C5orf58
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
DCANP1
SLC38A9
MGC32805
SLC36A2
SPINK13
CREBRF
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
JAKMIP2-AS1
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
CCDC125
LINC01554
GAPT
CMYA5
STK32A
LVRN
SLC36A1
EIF4E1B
LOC255187
RASGEF1C
ANKRD31
SERINC5
LINC01366
LOC257396
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
RGMB
LINC00491
RFESD
CHSY3
PRR7-AS1
TMEM173
FAM170A
C5orf66-AS2
LOC340074
ARSI
LOC340090
ANKRD34B
PFN3
ZNF879
IRGM
FBLL1
MCIDAS
ACTBL2
FAM174A
MTX3
CATSPER3
NIPAL4
SLCO4C1
TICAM2
DND1
MAST4
SIMC1
RNF138P1
SAP30L-AS1
TEX43
LOC389332
PROB1
C5orf46
ARHGEF37
RGS7BP
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
FLJ31104
LOC441081
LOC441086
CRSP8P
NR2F1-AS1
C5orf56
FLJ16171
MIR340
IGIP
GPX8
MIR378A
TIFAB
RGMB-AS1
LOC553103
MIR449A
CTXN3
SNORD95
SNORD96A
ECSCR
TMEM232
SMIM15
LOC643201
GRXCR2
SPINK9
ZFP62
ARL14EPL
LOC644285
LOC644762
LINC01184
LOC644936
SMIM23
CCNI2
LINC00461
CBY3
LOC647859
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR581
MIR582
MIR583
MIR584
MIR585
SNHG4
LOC728095
CARMN
GTF2H2C
LINC00992
SERF1B
LOC728554
CCDC192
MEIKIN
ZBED3-AS1
SCAMP1-AS1
ANKDD1B
LOC729080
AACSP1
LINC00847
OR4F29
GTF2H2C_2
LOC731157
GUSBP9
VTRNA2-1
MIR874
KIAA1024L
ARRDC3-AS1
LOC100130172
LRRC70
CKMT2-AS1
FAM196B
LOC100132062
FAM159B
LOC100133050
C5orf52
LOC100268168
LOC100288254
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR548F3
MIR1294
MIR1271
MIR103B1
MIR1303
MIR1244-1
MIR548P
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MTRNR2L2
MIR3607
MIR3655
MIR3660
MIR3912
MIR3936
MIR3661
LINC01024
LOC100505658
STARD4-AS1
HNCAT21
LOC100505841
LOC100505878
TMEM161B-AS1
LUCAT1
LOC100506526
OCLN
LINC01187
LOC100507387
TRIM52-AS1
MIR4804
MIR4633
MIR4634
MIR4461
MIR4459
MIR4454
MIR3977
MIR378H
MIR4460
MIR548AE2
MIR4638
MIR4803
MIR378E
SPRY4-IT1
LOC100652758
LINC01023
MIR5197
MIR5687
MIR5003
MIR5692C1
MIR5706
HEIH
LINC00492
P4HA2-AS1
NREP-AS1
ARHGAP26-AS1
PPP2R2B-IT1
ARHGAP26-IT1
LOC100996385
LOC100996419
C5orf66
LINCR-0003
IPO11-LRRC70
LOC101926905
LOC101926941
LOC101926975
LOC101927023
LOC101927059
LOC101927078
CTB-113P19.1
LOC101927100
CTB-12O2.1
LINC01470
LOC101927190
SEMA6A-AS1
HRAT56
LOC101927357
LOC101927379
LOC101927421
LOC101927460
LOC101927488
LOC101927697
LOC101927740
TH2LCRR
LOC101927766
HMMR-AS1
LOC101927835
CTB-178M22.2
LOC101927908
LOC101927934
C5orf66-AS1
LOC101927969
CTD-2270F17.1
LOC101928093
LINC01484
LINC01485
LINC01411
LOC101928445
C5orf67
LOC101928505
LOC101928539
LOC101928569
LOC101928600
CTC-436P18.1
CTC-338M12.4
LOC101928651
LOC101928769
LOC101928794
LOC101928858
LOC101928885
LOC101928924
LINC01333
LOC101929109
LOC101929154
CTD-2201I18.1
LOC101929380
MEF2C-AS1
LINC01339
LOC101929696
LOC101929710
LOC101929719
AK6
MIR6499
MIR6830
MIR6831
MIR8056
MIR8089
LOC102467080
LOC102467081
LOC102467147
LOC102467212
LOC102467213
LOC102467214
LOC102467216
LOC102467217
LOC102467223
LOC102467224
LOC102467225
LOC102467226
LOC102467655
LOC102477328
LOC102503427
LINC01335
RASGRF2-AS1
LINC01338
LOC102546226
LINC01340
LOC102546228
LOC102546229
LOC102546294
LOC102546298
LOC102546299
CTB-7E3.1
LINC01574
LOC102577426
LOC102723557
LOC102724392
LOC102724404
CTD-2151A2.1
ADAMTS19-AS1
LINC01337
LINC01170
LINC01331
LINC01202
LINC01336
LINC01033
LINC01386
LOC105377682
LOC105377716
LOC105377763
LOC105379030
LOC105379054
LOC105379143
LOC105379176
LOC105379183
LOC105379192
LOC105379194
LINC01455
WSPAR
GRPEL2-AS1
TRPC7-AS2
MIR3142HG

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q23.1.

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

Genes
APC
CD74
EBF1
IL6ST
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-886
hsa-mir-1244-2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
NAIP
NDUFA2
NDUFS4
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PLPP1
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
ATG12
PTTG1
PDLIM7
NREP
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
APBB3
CCNO
TNIP1
RACK1
NSA2
FST
SLU7
POLR3G
RGS14
PLK2
IQGAP2
SEC24A
CPLX2
FAXDC2
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
SOX30
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
JADE2
LARP1
PPWD1
HARS2
OTP
SKIV2L2
ZNF346
SSBP2
BHMT2
TNFAIP8
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR2V1
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
IPO11
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
NEURL1B
DHX29
EPB41L4A-AS2
DDX4
FAM193B
SGTB
ARL15
PCDHB18P
PCDHB17P
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
SPDL1
THG1L
AGGF1
WDR41
LOC55338
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
DEPDC1B
BDP1
RNF130
ERBIN
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
NLN
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
ZBED8
MCCC2
EPB41L4A
CENPK
ERAP2
ARHGEF28
SIL1
GMCL1P1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
ELOVL7
TRAPPC13
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
ADGRV1
PCBD2
UTP15
ZCCHC9
PSD2
SLF1
THOC3
ZBED3
GFM2
CYSTM1
MEGF10
SPINK7
SPZ1
TRIM52
HAVCR2
PHYKPL
SMIM3
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
LEAP2
SCGB3A2
ZNF354B
SETD9
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
C5orf58
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
DCANP1
SLC38A9
MGC32805
SLC36A2
SPINK13
CREBRF
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
JAKMIP2-AS1
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
CCDC125
LINC01554
GAPT
CMYA5
STK32A
LVRN
SLC36A1
EIF4E1B
LOC255187
RASGEF1C
ANKRD31
SERINC5
LINC01366
LOC257396
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
RGMB
LINC00491
RFESD
CHSY3
PRR7-AS1
TMEM173
FAM170A
C5orf66-AS2
LOC340074
ARSI
LOC340090
ANKRD34B
PFN3
ZNF879
IRGM
FBLL1
MCIDAS
ACTBL2
FAM174A
MTX3
CATSPER3
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
MAST4
SIMC1
RNF138P1
SAP30L-AS1
TEX43
LOC389332
PROB1
C5orf46
ARHGEF37
RGS7BP
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
FLJ31104
LOC441081
LOC441086
CRSP8P
NR2F1-AS1
C5orf56
FLJ16171
MIR340
IGIP
GPX8
MIR378A
TIFAB
RGMB-AS1
LOC553103
MIR449A
CTXN3
SNORD95
SNORD96A
ECSCR
LOC642366
TMEM232
SMIM15
LOC643201
GRXCR2
SPINK9
ZFP62
ARL14EPL
LOC644285
LOC644762
LINC01184
LOC644936
SMIM23
CCNI2
LINC00461
CBY3
LOC647859
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR581
MIR582
MIR583
MIR584
MIR585
SNHG4
LOC728095
CARMN
GTF2H2C
LINC00992
SERF1B
LOC728554
CCDC192
MEIKIN
ZBED3-AS1
SCAMP1-AS1
ANKDD1B
LOC729080
AACSP1
LINC00847
OR4F29
GTF2H2C_2
LOC731157
GUSBP9
VTRNA2-1
MIR874
KIAA1024L
ARRDC3-AS1
LOC100130172
LRRC70
CKMT2-AS1
FAM196B
LOC100132062
FAM159B
LOC100133050
C5orf52
LOC100268168
LOC100287592
LOC100288254
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR548F3
MIR1294
MIR1271
MIR103B1
MIR1303
MIR1244-1
MIR548P
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MTRNR2L2
MIR3607
MIR3655
MIR3660
MIR3912
MIR3936
MIR3661
LINC01024
LOC100505658
STARD4-AS1
HNCAT21
LOC100505841
LOC100505878
TMEM161B-AS1
LUCAT1
LOC100506526
OCLN
LINC01187
LOC100507387
TRIM52-AS1
MIR4804
MIR4633
MIR4634
MIR4461
MIR4459
MIR4454
MIR3977
MIR378H
MIR4460
MIR548AE2
MIR4638
MIR4803
MIR378E
SPRY4-IT1
LOC100652758
LINC01023
MIR5197
MIR5687
MIR5003
MIR5692C1
MIR5706
HEIH
LINC00492
P4HA2-AS1
NREP-AS1
ARHGAP26-AS1
PPP2R2B-IT1
ARHGAP26-IT1
LOC100996385
LOC100996419
C5orf66
LINCR-0003
IPO11-LRRC70
LOC101926905
LOC101926941
LOC101926975
LOC101927023
LOC101927059
LOC101927078
CTB-113P19.1
LOC101927100
CTB-12O2.1
LINC01470
LOC101927190
SEMA6A-AS1
HRAT56
LOC101927357
LOC101927379
LOC101927421
LOC101927460
LOC101927488
LOC101927697
LOC101927740
TH2LCRR
LOC101927766
HMMR-AS1
LOC101927835
CTB-178M22.2
LOC101927908
LOC101927934
C5orf66-AS1
LOC101927969
CTD-2270F17.1
LOC101928093
LINC01484
LINC01485
LINC01411
LOC101928445
C5orf67
LOC101928505
LOC101928539
LOC101928569
LOC101928600
CTC-436P18.1
CTC-338M12.4
LOC101928651
LOC101928769
LOC101928794
LOC101928858
LOC101928885
LOC101928924
LINC01333
LOC101929109
LOC101929154
CTD-2201I18.1
LOC101929380
MEF2C-AS1
LINC01339
LOC101929696
LOC101929710
LOC101929719
AK6
MIR6499
MIR6830
MIR6831
MIR8056
MIR8089
LOC102467080
LOC102467081
LOC102467147
LOC102467212
LOC102467213
LOC102467214
LOC102467216
LOC102467217
LOC102467223
LOC102467224
LOC102467225
LOC102467226
LOC102467655
LOC102477328
LOC102503427
LINC01335
RASGRF2-AS1
LINC01338
LOC102546226
LINC01340
LOC102546228
LOC102546229
LOC102546294
LOC102546298
LOC102546299
CTB-7E3.1
LINC01574
LOC102577426
LOC102723557
LOC102724392
LOC102724404
CTD-2151A2.1
ADAMTS19-AS1
LINC01337
LINC01170
LINC01331
LINC01202
LINC01336
LINC01033
LINC01386
LOC105377682
LOC105377716
LOC105377763
LOC105379030
LOC105379054
LOC105379143
LOC105379176
LOC105379183
LOC105379192
LOC105379194
LINC01455
WSPAR
GRPEL2-AS1
TRPC7-AS2
MIR3142HG

Genes in Wide Peak

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

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

Genes
GATA1
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
CRLF2
P2RY8
hsa-mir-362
hsa-mir-1308
NR0B1
AMELX
SLC25A6
SHROOM2
ARAF
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT
BMX
CACNA1F
S100G
CLCN4
CLCN5
CSF2RA
CYBB
DDX3X
DMD
EIF1AX
EIF2S3
ELK1
FANCB
VEGFD
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
GK
GLRA2
GPM6B
GPR34
GRPR
HCCS
ERAS
IL3RA
ANOS1
KCND1
PRICKLE3
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
CD99
MID1
NDP
NHS
GPR143
TBC1D25
OTC
CDK16
PDHA1
PDK3
CFP
PHEX
PHKA2
PIGA
PLP2
POLA1
PPEF1
PRKX
PRPS2
PRRG1
RBBP7
RBM3
RP2
RPGR
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SHOX
SMS
SSX5
CDKL5
SUV39H1
SYN1
SYP
TBL1X
DYNLT3
TIMP1
TSPAN7
TMSB4X
UBA1
SLC35A2
XG
XK
ZFX
ZNF182
ZNF41
ZNF157
GTPBP6
PUDP
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SRPX
UXT
OFD1
PIR
INE2
INE1
CASK
ASMTL
PAGE1
AKAP4
AP1S2
GYG2
RGN
REPS2
ZBED1
BMP15
MED14
RAB9A
PCYT1B
MAGED1
XAGE2
PAGE4
FRMPD4
JADE3
HDAC6
PQBP1
ADGRG2
ATP6AP2
SSX3
TIMM17B
SCML2
PRDX4
EBP
RAI2
MSL3
PIM2
IL1RAPL1
WDR45
PRAF2
CA5B
CNKSR2
ACOT9
SMPX
GSPT2
FTSJ1
HYPM
MXRA5
EGFL6
VCX
GAGE12I
GAGE2E
GPR82
GPKOW
PCSK1N
PPP2R3B
CCDC22
FAM156A
SH3KBP1
FOXP3
TLR7
TLR8
MBTPS2
VCX2
VCX3A
FTHL17
NDUFB11
BCOR
GEMIN8
NUDT11
PLCXD1
OTUD5
KRBOX4
TXLNG
WWC3
CTPS2
CHST7
GRIPAP1
ZNF630
TMEM27
SHROOM4
NLGN4X
MID1IP1
ACE2
NYX
DUSP21
WDR13
PORCN
APOO
CXorf36
MAGIX
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
MAGED4B
TMEM47
SLC9A7
CCNB3
PPP1R3F
CCDC120
ATXN3L
SLC38A5
SYAP1
SYTL5
BEND2
DGKK
FUNDC1
PTCHD1
PPP4R3CP
MAGEB10
DCAF8L1
VENTXP1
MAGEB16
ASB11
ASB9
ZNF645
USP27X-AS1
FAM47A
MOSPD2
MAGEB6
CXorf38
DDX53
FAM47B
SUPT20HL2
TCEANC
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
LINC01560
DHRSX
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX8
SSX9
LINC00685
LINC01281
CFAP47
UBE2E4P
MAGEB18
CA5BP1
CXorf67
ZNF81
LANCL3
MPC1L
DCAF8L2
ARSH
MAGEB5
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
LOC389906
LOC392452
CXXC1P1
GLOD5
CD99P1
LOC401585
ZNF674-AS1
YY2
MIR188
MIR221
MIR222
VCX3B
FTH1P18
FAM47C
SPANXN5
SSX4B
MIR362
MIR500A
MIR501
MIR502
ZNF674
GAGE2B
GAGE13
GAGE12G
MAGEB17
XAGE1B
SCARNA23
MIR532
MIR651
MIR660
LINC01545
SSX2B
FAM156B
MAGED4
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE2A
LOC729609
LINC00106
GAGE12F
GS1-600G8.3
GAGE8
SNORA11C
SNORA11D
LINC01546
SUPT20HL1
PHKA2-AS1
GAGE12D
XGY2
LOC100132831
LINC01203
UXT-AS1
SCARNA9L
CLDN34
MIR548F5
LINC00102
MIR500B
MIR23C
MIR3937
MIR3690
MIR3915
PIR-FIGF
MIR4769
MIR4768
MIR1587
MIR548AJ2
MIR4770
MIR548AM
MIR4767
MIR4666B
MIR548AX
PTCHD1-AS
NHS-AS1
SYP-AS1
ZFX-AS1
PHEX-AS1
PRKX-AS1
MED14OS
PPEF1-AS1
EIF1AX-AS1
PCYT1B-AS1
ZNF630-AS1
MID1IP1-AS1
LINC01284
LINC01282
LOC101927476
LOC101927501
LINC01204
LINC01186
LOC101927635
LOC101928201
LOC101928389
LOC101928627
MIR6089
MIR6134
MIR7641-2
MIR6086
MIR8088
LINC01496
GAGE10
GS1-594A7.3
LINC01456
LOC105373156
LOC105373185

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20q13.33.

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

Genes
GNAS
TOP1
MAFB
SS18L1
hsa-mir-941-3
hsa-mir-1259
ADA
ATP5E
BMP7
BPI
CD40
CDH4
CEBPB
CHRNA4
COL9A3
CSE1L
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
EPB41L1
EYA2
GGT7
GHRH
NPBWR2
GSS
HNF4A
EIF6
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
LBP
MC3R
MMP9
MYBL2
MYT1
NFATC2
NNAT
NTSR1
OPRL1
PCK1
PFDN4
PI3
PLCG1
PLTP
CTSA
PPP1R3D
PSMA7
PTGIS
PTK6
PTPN1
RBL1
RPN2
RPS21
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SPAG4
SRC
SRMS
STAU1
STK4
AURKA
TAF4
TCEA2
TFAP2C
TGM2
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF217
GDF5
NCOA3
RAE1
BCAS1
STX16
TNFRSF6B
MATN4
DPM1
WISP2
CPNE1
NFS1
VAPB
B4GALT5
RBM39
TTI1
SPATA2
OSBPL2
ACOT8
ATP9A
SGK2
RBM12
ARFRP1
RGS19
SYCP2
MYL9
WFDC2
PROCR
ARFGEF2
TCFL5
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
CEP250
HRH3
RBPJL
DLGAP4
ZHX3
NCOA6
SLC9A8
ADNP
ZMYND8
SPO11
PRPF6
SAMHD1
AAR2
L3MBTL1
PPP1R16B
TRPC4AP
MTG2
GMEB2
SNORD12C
SNORA71B
SNORA71A
TP53TG5
MOCS3
SLCO4A1
STMN3
SLC35C2
PRELID3B
IFT52
PHF20
SCAND1
NELFCD
RTFDC1
OSER1
PIGT
ERGIC3
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
GID8
UQCC1
PCMTD2
MRGBP
PPP4R1L
RBM38
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
EDEM2
DOK5
DBNDD2
ACSS2
RNF114
SULF2
C20orf24
CTNNBL1
SLC2A4RG
PMEPA1
CASS4
EPPIN
RALGAPB
JPH2
SALL4
ZNFX1
RAB22A
NDRG3
SLC12A5
ZNF512B
PREX1
COL20A1
MYH7B
NCOA5
TP53INP2
RPRD1B
TGIF2
CDH26
KCNK15
DHX35
MANBAL
SLC17A9
ELMO2
ZNF335
LOC63930
PCIF1
FAM217B
CDH22
SLC13A3
LPIN3
GDAP1L1
LINC01260
FNDC11
PPDPF
LOC79160
TTPAL
BIRC7
NPEPL1
ACTR5
DSN1
FER1L4
DNAJC5
PABPC1L
TUBB1
ZBP1
SLC2A10
FAM83D
CABLES2
SLA2
CHD6
MAP1LC3A
PARD6B
ZGPAT
TOX2
HELZ2
KIAA1755
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
TP53RK
DNTTIP1
FAM210B
PHACTR3
BHLHE23
NKAIN4
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
OCSTAMP
TSHZ2
C20orf85
ZNF831
MIR1-1HG
PIGU
HMGB3P1
FAM83C
GATA5
SLC32A1
ZBTB46
WFDC3
GCNT7
CBLN4
CTCFL
MROH8
SAMD10
ABHD16B
SOGA1
TLDC2
RIMS4
ANKRD60
ROMO1
NEURL2
ZSWIM3
WFDC10A
LINC01620
FAM83C-AS1
LINC00266-1
WFDC6
C20orf173
FAM65C
RBBP8NL
CNBD2
R3HDML
LOC149684
ADIG
GTSF1L
WFDC5
APCDD1L-AS1
GNAS-AS1
LSM14B
WFDC13
APCDD1L
LKAAEAR1
FAM209A
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LINC01270
C20orf197
MIR646HG
LOC339568
ARHGAP40
TMEM189
TMEM189-UBE2V1
SNHG17
FAM209B
SPINT4
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
ZFAS1
MIR499A
NORAD
SNORA71E
SNORA60
SNORA71C
SNORA71D
SNORD12
MIR645
MIR646
MIR647
LOC729296
SYS1-DBNDD2
HAR1A
HAR1B
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
SLCO4A1-AS1
LOC100128988
LOC100130587
ZNF663P
LOC100131496
DPH3P1
LINC00029
LINC01056
FLJ16779
LOC100287792
MIR1289-1
MIR1914
MIR1302-5
MIR1257
MIR3195
MIR4325
MIR3194
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
MIR3617
LINC01370
LOC100505771
OSER1-AS1
STK4-AS1
LINC01272
LOC100506175
LOC100506384
LOC100506470
EPPIN-WFDC6
TGIF2-C20orf24
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR499B
MIR548O2
MIR4756
MIR4758
MIR4532
MIR4533
MIR548AG2
LINC00659
LINC00489
TRERNA1
LINC01523
OGFR-AS1
MMP24-AS1
DLGAP4-AS1
PLCG1-AS1
LOC101927159
HNF4A-AS1
LINC01430
LOC101927377
LINC01522
LINC01273
CEBPB-AS1
LINC01271
ADNP-AS1
LINC01429
LINC01524
LOC101927770
LINC01441
LOC101927932
LOC101928048
LAMA5-AS1
ZBTB46-AS1
MIR6812
MIR6813
MIR6871
CSE1L-AS1
LINC01440
BMP7-AS1
LOC105372626
LOC105372653
LOC105372672
LOC105372682
LOC105372695
NKILA
KCNK15-AS1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 29 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Frequency Score | Amp Z score | Amp Q value | Del Frequency | Del Frequency Score | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1p | 3092 | 0.10 | 0.14 | -1.24 | 1 | 0.24 | 0.27 | 1.82 | 0.116
1q | 2863 | 0.32 | 0.37 | 3.84 | 0.000443 | 0.11 | 0.17 | -0.747 | 1
2p | 1500 | 0.36 | 0.38 | 2.14 | 0.0547 | 0.04 | 0.06 | -4.03 | 1
2q | 2495 | 0.23 | 0.24 | 0.408 | 0.73 | 0.06 | 0.07 | -3.26 | 1
3p | 1531 | 0.18 | 0.33 | 0.915 | 0.423 | 0.46 | 0.56 | 5.77 | 3.67e-08
3q | 1708 | 0.50 | 0.60 | 6.94 | 9.02e-11 | 0.15 | 0.31 | 0.627 | 0.623
4p | 693 | 0.03 | 0.06 | -3.89 | 1 | 0.54 | 0.56 | 5.03 | 1.31e-06
4q | 1467 | 0.03 | 0.05 | -3.76 | 1 | 0.48 | 0.49 | 4.66 | 7.49e-06
5p | 456 | 0.54 | 0.63 | 5.8 | 8.02e-08 | 0.13 | 0.29 | -0.69 | 1
5q | 2185 | 0.10 | 0.20 | -0.774 | 1 | 0.51 | 0.57 | 7.41 | 9.86e-13
6p | 1664 | 0.22 | 0.25 | -0.526 | 1 | 0.11 | 0.15 | -2.55 | 1
6q | 1304 | 0.14 | 0.17 | -2.45 | 1 | 0.17 | 0.20 | -1.91 | 1
7p | 926 | 0.40 | 0.45 | 2.81 | 0.0107 | 0.10 | 0.17 | -2.36 | 1
7q | 1717 | 0.32 | 0.35 | 1.82 | 0.108 | 0.08 | 0.11 | -2.96 | 1
8p | 795 | 0.30 | 0.40 | 1.47 | 0.197 | 0.26 | 0.36 | 0.828 | 0.532
8q | 1249 | 0.40 | 0.48 | 3.85 | 0.000443 | 0.17 | 0.29 | -0.156 | 0.943
9p | 621 | 0.12 | 0.27 | -0.958 | 1 | 0.53 | 0.61 | 5.69 | 4.87e-08
9q | 1610 | 0.10 | 0.19 | -1.4 | 1 | 0.50 | 0.55 | 5.96 | 1.5e-08
10p | 767 | 0.16 | 0.22 | -1.83 | 1 | 0.28 | 0.33 | 0.161 | 0.854
10q | 1968 | 0.05 | 0.07 | -3.74 | 1 | 0.29 | 0.30 | 1.04 | 0.452
11p | 1162 | 0.14 | 0.20 | -1.94 | 1 | 0.28 | 0.32 | 0.47 | 0.676
11q | 2133 | 0.15 | 0.19 | -1.23 | 1 | 0.19 | 0.22 | -0.454 | 1
12p | 804 | 0.46 | 0.48 | 3.36 | 0.00205 | 0.04 | 0.07 | -4.04 | 1
12q | 2055 | 0.27 | 0.28 | 0.698 | 0.543 | 0.05 | 0.06 | -3.75 | 1
13p | 0 | 0.10 | 0.24 | -1.76 | 1 | 0.56 | 0.63 | 5.31 | 3.26e-07
13q | 1092 | 0.03 | 0.06 | -3.63 | 1 | 0.54 | 0.56 | 5.61 | 6.76e-08
14q | 1829 | 0.17 | 0.25 | -0.307 | 1 | 0.30 | 0.37 | 2.24 | 0.0459
15p | 0 | 0.15 | 0.24 | -2.21 | 1 | 0.35 | 0.42 | 1.01 | 0.452
15q | 2082 | 0.10 | 0.12 | -2.6 | 1 | 0.23 | 0.25 | 0.0981 | 0.867
16p | 1378 | 0.12 | 0.16 | -2.41 | 1 | 0.25 | 0.28 | -0.103 | 0.943
16q | 1070 | 0.12 | 0.17 | -2.47 | 1 | 0.29 | 0.33 | 0.447 | 0.676
17p | 937 | 0.16 | 0.22 | -1.79 | 1 | 0.26 | 0.31 | -0.106 | 0.943
17q | 2298 | 0.27 | 0.31 | 1.6 | 0.16 | 0.13 | 0.18 | -1.12 | 1
18p | 212 | 0.25 | 0.32 | -0.592 | 1 | 0.23 | 0.30 | -0.905 | 1
18q | 644 | 0.16 | 0.22 | -2.14 | 1 | 0.25 | 0.30 | -0.657 | 1
19p | 1331 | 0.15 | 0.18 | -2.18 | 1 | 0.17 | 0.20 | -1.83 | 1
19q | 2402 | 0.24 | 0.28 | 1.07 | 0.374 | 0.14 | 0.19 | -0.912 | 1
20p | 583 | 0.44 | 0.46 | 2.72 | 0.0126 | 0.05 | 0.08 | -4.03 | 1
20q | 1092 | 0.43 | 0.45 | 3.27 | 0.00252 | 0.06 | 0.10 | -3.43 | 1
21p | 92 | 0.09 | 0.17 | -2.95 | 1 | 0.49 | 0.53 | 3.52 | 0.000937
21q | 750 | 0.05 | 0.08 | -4.07 | 1 | 0.41 | 0.43 | 2.3 | 0.0419
22p | 2 | 0.30 | 0.42 | 0.98 | 0.405 | 0.30 | 0.42 | 0.98 | 0.452
22q | 1258 | 0.41 | 0.48 | 3.82 | 0.000443 | 0.14 | 0.24 | -0.903 | 1
Xp | 945 | 0.34 | 0.44 | 2.58 | 0.0178 | 0.23 | 0.35 | 0.65 | 0.623
Xq | 1533 | 0.37 | 0.46 | 3.7 | 0.000633 | 0.19 | 0.30 | 0.438 | 0.676
Yp | 113 | 0.26 | 0.69 | 4.36 | 0.000104 | 0.63 | 0.85 | 8.99 | 0
Yq | 245 | 0.24 | 0.68 | 4.14 | 0.0002 | 0.65 | 0.85 | 9.36 | 0

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 = /cromwell_root/fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55/c49d2584-2f4b-481e-b176-6c78f2b67d71/aggregate_data_workflow/1b599a59-dfb3-4d22-9c4d-ae8b08202bfc/call-aggregate_data/CPTAC3-LSCC-v1.CNV__wgs.seg.txt

- Markers File = ./this_file_does_not_exist.txt

- Reference Genome = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/gistic2.refgene.hg38.UCSC.add_miR.160920.mat

- CNV Files = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg38_GDC_SNP6_CNV_list.161107.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.98

- 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 110 Input Tumor Samples.

Tumor Sample Names
C3L-00081
C3L-00415
C3L-00445
C3L-00568
C3L-00603
C3L-00904
C3L-00923
C3L-00927
C3L-00965
C3L-00993

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.

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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