SNP6 Copy number analysis (GISTIC2)
Pancreatic Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C11G0K6X
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 184 tumor samples used in this analysis: 21 significant arm-level results, 25 significant focal amplifications, and 38 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 - 25 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
8q24.21 6.1329e-13 6.1329e-13 chr8:128671421-128679033 0 [MYC]
18q11.2 6.1329e-13 6.1329e-13 chr18:19704037-19953596 3
19q13.2 5.1055e-10 5.1055e-10 chr19:39817101-39931030 10
9p13.3 1.717e-05 1.717e-05 chr9:35244633-35808362 21
1p12 8.757e-05 0.00016347 chr1:120204209-120523901 5
7q22.1 0.00031763 0.00031763 chr7:97568629-99200083 31
12p13.33 0.00035603 0.00049982 chr12:1-4109959 35
17q12 0.0011738 0.0011738 chr17:37726424-37951087 11
Xq27.1 0.0022718 0.0022718 chrX:138564705-138580557 0 [F9]
12p11.21 0.0020074 0.0027368 chr12:31421842-31442221 1
12q15 0.0030751 0.0030751 chr12:68307608-71340084 24
8p11.22 0.023829 0.034784 chr8:37097564-38558525 21
4p16.3 0.042508 0.042508 chr4:1-2148628 44
17p11.2 0.060274 0.060274 chr17:19277362-19597719 9
Xp22.11 0.063463 0.063463 chrX:23975644-23983593 0 [CXorf58]
20p11.23 0.075581 0.075581 chr20:20117297-22259357 11
6p21.31 0.11164 0.11164 chr6:34073534-34891140 15
2q36.2 0.12363 0.12363 chr2:183058658-243199373 464
19p13.2 0.13696 0.13696 chr19:7313873-7398264 0 [INSR]
1q21.3 0.063036 0.14953 chr1:120523903-204808169 789
15q26.1 0.16394 0.16394 chr15:61298614-102531392 421
3q26.2 0.18751 0.18751 chr3:148386857-198022430 349
8p11.21 0.072892 0.1927 chr8:39698409-41157238 6
3p12.2 0.2335 0.2335 chr3:82203546-82960457 0 [GBE1]
1p34.2 0.24554 0.24554 chr1:37413199-44557362 110
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
snoU13|ENSG00000238907.1
RNU6ATAC20P
GATA6
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
RN7SL566P
RPS16
SUPT5H
ZFP36
GMFG
PAF1
SAMD4B
MED29
PLEKHG2
MIR4530
Genes in Wide Peak

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

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

Genes
RGP1
RN7SL22P
RMRP
MIR4667
CA9
CD72
NPR2
TESK1
TLN1
TPM2
RUSC2
CREB3
UNC13B
SPAG8
SIT1
GBA2
ARHGEF39
ATP8B5P
CCDC107
MSMP
FAM166B
Genes in Wide Peak

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

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

Genes
NOTCH2
HMGCS2
ADAM30
PHGDH
REG4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
snoU13|ENSG00000239133.1
MYH16
snoU13|ENSG00000238459.1
MIR3609
RN7SL13P
RN7SL478P
NPTX2
OCM2
TRRAP
BUD31
ATP5J2
ARPC1B
ARPC1A
CPSF4
PDAP1
LMTK2
ZKSCAN5
BRI3
TECPR1
PTCD1
BAIAP2L1
SMURF1
ZNF655
ZNF394
BHLHA15
FAM200A
TMEM130
ZNF789
KPNA7
MIR5692C2
MIR5692A1
Genes in Wide Peak

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

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

Genes
KDM5A
FKBP4
CBX3P4
CACNA1C
LINC00940
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
PARP11
WNK1
ADIPOR2
WNT5B
RHNO1
NRIP2
CCDC77
EFCAB4B
CACNA2D4
FBXL14
DCP1B
B4GALNT3
IQSEC3
LRTM2
MIR3649
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
GRB7
STARD3
PPP1R1B
MIEN1
PGAP3
Genes in Wide Peak

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

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

Genes
FAM60A
Genes in Wide Peak

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

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

Genes
MDM2
MYRFL
RN7SL804P
SLC35E3
SNORA70G
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
YEATS4
CCT2
FRS2
CPSF6
KCNMB4
IL22
IL26
MDM1
NUP107
RAB3IP
BEST3
LRRC10
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.22.

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

Genes
FGFR1
WHSC1L1
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
ADRB3
EIF4EBP1
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
RAB11FIP1
PPAPDC1B
GOT1L1
LETM2
C8orf86
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

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

Genes
FGFR3
WHSC1
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ATP5I
CTBP1
DGKQ
GAK
IDUA
LETM1
MYL5
PDE6B
NELFA
SLBP
MAEA
PCGF3
SPON2
TACC3
CPLX1
SLC26A1
FGFRL1
PIGG
UVSSA
MFSD7
TMEM175
TMEM129
FAM53A
CRIPAK
RNF212
NAT8L
POLN
C4orf48
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p11.2.

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

Genes
SNORA31|ENSG00000252349.1
SNORA59B
ALDH3A2
MFAP4
MAPK7
RNF112
B9D1
SLC47A1
SLC47A2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.23.

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

Genes
PAX1
RN7SKP140
RNA5SP477
PLK1S1
LINC00237
RN7SL607P
RN7SL690P
INSM1
XRN2
C20orf26
RALGAPA2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.31.

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

Genes
HMGA1
SNRPC
snoU13|ENSG00000238484.1
RN7SL200P
snoU13|ENSG00000239059.1
NUDT3
GRM4
RPS10
TAF11
ANKS1A
SPDEF
PACSIN1
UHRF1BP1
C6orf106
C6orf1
Genes in Wide Peak

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

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

Genes
ACSL3
ATIC
CREB1
IDH1
PAX3
PMS1
FEV
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
snoU13|ENSG00000238736.1
snoU13|ENSG00000238428.1
CXCR2P1
DIRC3
RN7SKP43
RNA5SP120
RPL37A
MREG
LINC00607
snoU13|ENSG00000238663.1
SNORA70|ENSG00000207274.1
VWC2L
MIR4438
MIR548F2
RNA5SP119
RPE
RNA5SP118
RNA5SP117
CRYGEP
snoU13|ENSG00000238582.1
RNA5SP116
MIR2355
FASTKD2
RN7SKP260
RN7SKP200
SNORA41|ENSG00000207406.1
SNORD51|ENSG00000207047.2
NDUFS1
Vault|ENSG00000252485.1
RN7SKP178
RN7SL670P
SNORA1|ENSG00000202059.1
WDR12
RN7SL40P
RN7SL753P
SNORD11|ENSG00000238317.1
SNORD11B
SNORD70|ENSG00000212309.1
SNORD70|ENSG00000212534.1
snoU13|ENSG00000238770.1
RN7SL694P
ORC2
RNA5SP115
AOX2P
RN7SL717P
PLCL1
RFTN2
MOB4
SNORA4|ENSG00000202434.1
C2orf66
SCARNA16|ENSG00000252923.1
RN7SL820P
snoU13|ENSG00000239161.1
SNORD59|ENSG00000252517.1
PCGEM1
NABP1
RN7SKP179
TMEM194B
MIR3129
MIR1245A
DIRC1
GULP1
RNA5SP114
RN7SKP42
U8|ENSG00000212581.1
snoU13|ENSG00000238306.1
SNORA77|ENSG00000221498.1
DNAJC10
RN7SL267P
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
AOX1
KIF1A
BARD1
BCS1L
BMPR2
BOK
CASP8
CASP10
CD28
CHRNG
CLK1
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CYP27A1
DES
DTYMK
EEF1B2
EPHA4
ERBB4
FN1
FRZB
GBX2
MSTN
GLS
GPC1
GPR1
GPR35
HDLBP
AGFG1
DNAJB2
HSPD1
HSPE1
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
INHA
INPP1
INPP5D
IRS1
ITGAV
KCNJ13
MAP2
MYO1B
MYL1
NAB1
NDUFA10
NDUFB3
SEPT2
NEU2
PDCD1
PDE1A
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
STAT1
STAT4
TFPI
TNP1
TNS1
TUBA4A
SUMO1
WNT6
XRCC5
ZNF142
FZD5
SCG2
FZD7
SDPR
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
CFLAR
PER2
CDK5R2
RQCD1
LRRFIP1
STK17B
GPR55
TRIP12
GTF3C3
ECEL1
EIF4E2
TTLL4
BZW1
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
ABI2
CALCRL
RAMP1
SPEG
LANCL1
NMUR1
STK25
NCKAP1
CAPN10
SP140
IKZF2
PASK
ATG4B
SATB2
OBSL1
SF3B1
DNPEP
TMEFF2
SH3BP4
KCNE4
NGEF
MOB4
PNKD
SNED1
SPATS2L
GIGYF2
TRAF3IP1
ABCA12
HIBCH
CNPPD1
STK36
ICOS
GMPPA
SLC40A1
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
NOP58
ASB1
CAB39
PRKAG3
PPIL3
ASNSD1
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
MFSD6
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
STRADB
HES6
ASIC4
DOCK10
PECR
ZC3H15
DNAH7
C2orf83
MFF
ACKR3
SLC39A10
CYP20A1
HECW2
MARCH4
WDFY1
NYAP2
ALS2
ZDBF2
USP37
CTDSP1
MPP4
NIF3L1
GAL3ST2
TMBIM1
OSGEPL1
RAB17
RNF25
COPS7B
RAPH1
CDK15
TMEM237
NBEAL1
MRPL44
TRAK2
BOLL
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
C2orf47
SPAG16
CHPF
IQCA1
CARF
NHEJ1
FAM124B
TM4SF20
C2orf54
PGAP1
TUBA4B
ARMC9
COQ10B
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
WDR75
RHBDD1
C2orf88
ING5
PLCD4
ANKRD44
ZNF804A
TMEM169
DNER
MARS2
B3GNT7
SP140L
ORMDL1
STK11IP
MOGAT1
AGAP1
TWIST2
PARD3B
NUP35
TYW5
DIS3L2
NEU4
ICA1L
AP1S3
KCTD18
ALS2CR12
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
DUSP19
OTOS
MYEOV2
OR6B3
ANKAR
FAM117B
KANSL1L
ZSWIM2
METTL21A
CCNYL1
SGOL2
ALS2CR11
CCDC140
SLC23A3
GPBAR1
SLC16A14
LINC00471
DAW1
C2orf57
FAM171B
PIKFYVE
TIGD1
C2orf69
CCDC108
C2orf72
CCDC150
FAM126B
UNC80
RUFY4
DUSP28
MROH2A
ESPNL
FTCDNL1
C2orf62
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
FSIP2
ASB18
MIR375
PRR21
PRSS56
AQP12B
MIR561
D2HGDH
MIR1471
MIR4268
MIR3132
MIR4269
MIR548AE1
MIR4775
MIR4786
MIR5001
MIR5702
MIR5703
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
SDHC
ABL2
ARNT
BCL9
FCGR2B
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
TPM3
TPR
PDE4DIP
SCARNA20|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77|ENSG00000221643.1
RABIF
PCAT6
SNORA70|ENSG00000253042.1
U6|ENSG00000272262.1
snoU13|ENSG00000239046.1
snoU13|ENSG00000238571.1
PTPRVP
GPR37L1
SNORA70|ENSG00000206637.1
MIR1231
MIR5191
RPS10P7
ASCL5
LINC00862
MIR181A1HG
MIR4735
U3|ENSG00000252241.1
MIR1278
snoU109|ENSG00000238754.1
RN7SKP126
RNA5SP73
RN7SKP156
RNA5SP72
SNORD112|ENSG00000252790.1
RN7SL654P
RNA5SP71
RN7SKP229
RNA5SP70
KIAA1614
U6|ENSG00000272292.1
MIR3121
LHX4
RN7SL230P
IFRG15
RN7SL374P
SNORA67|ENSG00000201619.1
SNORA67|ENSG00000212338.1
TOR3A
SNORA63|ENSG00000201791.1
RNA5SP69
C1orf220
LINC00083
MIR488
SCARNA3
snoU13|ENSG00000238872.1
RNA5SP68
RNA5SP67
SNORD78|ENSG00000208317.1
GAS5
RN7SKP160
snoU13|ENSG00000238430.1
ANKRD45
snoU13|ENSG00000251817.1
TNFSF18
SNORD112|ENSG00000252354.1
DNM3OS
SCARNA20|ENSG00000253060.1
RN7SL425P
snoU13|ENSG00000238859.1
RN7SL269P
RN7SL333P
C1orf112
F5
RNA5SP66
LINC00970
LINC00626
ANKRD36BP1
SFT2D2
MIR1255B2
snoU13|ENSG00000238325.1
RNA5SP65
POGK
MIR921
RNA5SP64
UCK2
TMCO1
SNORD112|ENSG00000252359.1
U3|ENSG00000212538.1
RNA5SP63
RNA5SP62
SNORD112|ENSG00000252740.1
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13|ENSG00000238843.1
BGLAP
SNORA26|ENSG00000252236.1
SCARNA4|ENSG00000252808.1
SNORA42|ENSG00000207475.1
snoU13|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
ADORA1
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
CACNA1E
CACNA1S
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
CHI3L1
CHIT1
CHRNB2
CKS1B|ENSG00000173207.8
CLK2
COPA
CRABP2
CRP
CSRP1
CTSK
CTSS
DHX9
DPT
ECM1
EFNA1
EFNA3
EFNA4
ELF3
ENSA
ETV3
F13B
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GBA
GJA5
GJA8
GLUL
GPR25
HDGF
CFH
CFHR1
CFHR2
MR1
HSPA6
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ10
KCNN3
KISS1
LAD1
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDC
PDZK1
PFDN2
PIGC
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PRRX1
POU2F1
PPOX
PRELP
PRKAB2
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPRC
PEX19
RAB13
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
VPS72
THBS3
TCHH
TNNI1
TNNT2
TNR
CCT3
TUFT1
TNFSF4
USF1
DAP3
NPHS2
BTG2
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
PPFIA4
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
SELENBP1
MPZL1
SH2D2A
ANGPTL1
TBX19
PRPF3
ARHGEF2
DEDD
XPR1
GPR52
AIM2
RASAL2
CHD1L
SOX13
PRDX6
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
FAM20B
KIF14
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
PIAS3
TIMM17A
LRRN2
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
KDM5B
CFHR4
CFHR3
OCLM
JTB
MTMR11
SLC27A3
TDRKH
CD160
PMF1
DUSP12
VPS45
PLEKHA6
KIAA0907
KIFAP3
ATF6
KIF21B
NMNAT2
NFASC
POGZ
COLGALT2
RGL1
SYT11
PRRC2C
RPRD2
CAMSAP2
SMG5
NCSTN
CRB1
GPR161
ZNF281
SNAPIN
PHLDA3
RUSC1
CA14
CCDC19
LMOD1
NBPF14
MPC2
OLFML2B
C1orf43
DNM3
TOR1AIP1
CHTOP
LCE2B
OPTC
OR10J1
USP21
CACYBP
SLC39A1
KLHL20
LAMTOR2
UBE2T
TMOD4
NME7
CERS2
CRNN
DCAF8
F11R
GLRX2
BOLA1
ZBTB7B
RRNAD1
ADIPOR1
APH1A
PLEKHO1
IER5
UCHL5
SUCO
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CYB5R1
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
RALGPS2
MSTO1
DARS2
GOLPH3L
ETNK2
KIRREL
YY1AP1
UBE2Q1
ITLN1
IPO9
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
LHX9
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
FAM5B
CCDC181
SLAMF7
CADM3
PRUNE
KLHL12
LGR6
HAPLN2
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
RFWD2
RGS18
MRPL9
INTS3
SCNM1
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
MROH9
TARS2
EDEM3
FLAD1
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
HMCN1
TEX35
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
FCRLA
PPP1R15B
MAEL
RGS8
NAV1
SEC16B
AQP10
SLAMF9
PYGO2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
PIGM
IGSF8
C1orf85
PGLYRP3
SLAMF6
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
AXDND1
ATP6V1G3
OR10J5
DCST2
ZNF648
TEDDM1
ARL8A
SYT2
GOLT1A
UHMK1
FCRLB
LIX1L
TSACC
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
NEK7
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
FAM163A
NBPF12
LELP1
RC3H1
DCST1
METTL11B
FAM78B
SHISA4
BNIPL
LRRC71
PYHIN1
DENND1B
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
LCE4A
NBPF11
KRTCAP2
CRTC2
TMEM9
LCE5A
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
SLC9C2
NBPF16
LINC00303
ANKRD34A
C1orf204
HIST2H2AB
S100A7A
RXFP4
FAM5C
C1orf110
OR10R2
FCRL6
KCNT2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
PEAR1
ILDR2
NOTCH2NL
LYSMD1
HRNR
FLG2
FMO6P
LINC00272
C1orf53
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
C1ORF220
NBPF9
APOBEC4
MIR181B1
MIR199A2
MIR181A1
MIR214
RGS21
HIST2H2BF
ETV3L
LRRC52
OR10J3
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR557
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
TSTD1
C2CD4D
NBPF20
MIR1295A
MIR4257
MIR4424
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
IDH2
NTRK3
PML
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109|ENSG00000239197.1
snoU13|ENSG00000238981.1
RN7SL363P
SNORD18|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
SNORD74|ENSG00000200206.1
RNA5SP400
RN7SL428P
CSPG4P12
SNORA25|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
HDGFRP3
SCARNA15|ENSG00000252690.2
GOLGA6L10|ENSG00000254374.2
RN7SL410P
GOLGA6L9|ENSG00000196648.6
UBE2Q2P3
RN7SL256P
RN7SL61P
CSPG4P8
UBE2Q2P2
TMC3
STARD5
LINC00927
SNORD112|ENSG00000251881.1
C15orf37
MTHFS
ANKRD34C
CTSH
ACSBG1
IDH3A
SNORA63|ENSG00000199633.1
SH2D7
MIR1827
RN7SL214P
RN7SL278P
RN7SKP217
NRG4
RN7SL510P
SNORD112|ENSG00000252372.1
RN7SL319P
DNM1P35
SNX33
ANP32BP1
DNM1P34
RN7SL327P
GOLGA6D
RN7SL489P
GOLGA6C
SCARNA20|ENSG00000252722.1
RPP25
COX5A
SCAMP2
SNORD77|ENSG00000212279.2
RN7SL429P
C15orf59
RN7SL853P
GOLGA6B
RN7SL485P
TMEM202
RNA5SP399
NR2E3
RPL29P30
MIR629
LINC00593
U3|ENSG00000207119.1
RNA5SP398
SNORA77|ENSG00000221376.1
RN7SL438P
MIR4312
FEM1B
CALML4
SNORD18A
SNORD16
SNORD18B
SNORD18C
MIR4512
MAP2K1
SCARNA14
TIPIN
MIR4511
snoU13|ENSG00000238311.1
snoU13|ENSG00000238715.1
SNORA24|ENSG00000206903.1
CLPX
MTFMT
RN7SL348P
MIR1272
RN7SL707P
RN7SL595P
SNORA48|ENSG00000252774.1
USP3
CA12
MIR190A
RN7SL613P
ACAN
ALDH1A3
ANPEP
BBS4
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
FES
HEXA
IGF1R
IL16
IREB2
ISLR
LOXL1
SMAD3
SMAD6
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
MYO9A
NEO1
NMB
OAZ2
FURIN
PCSK6
PDE8A
PKM
PLIN1
POLG
PPIB
MAP2K5
PSMA4
PTPN9
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
SH3GL3
SNRPA1
SNX1
NR2F2
TLE3
TPM1
AP3B2
ANP32A
ST8SIA2
SEMA7A
CILP
PIAS1
RAB11A
PEX11A
IQGAP1
HERC1
PSTPIP1
PRC1
SLC28A1
SLC24A1
TRIP4
STOML1
HOMER2
KIF23
IGDCC3
ZNF592
KIAA0101
SV2B
ARNT2
HCN4
SNUPN
PDCD7
TSPAN3
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
ARID3B
MORF4L1
ABHD2
ADAMTS7
AKAP13
ITGA11
CHSY1
ZNF609
TBC1D2B
MESDC2
KIAA1024
SYNM
TMED3
SEC11A
DAPK2
ARIH1
SIN3A
ULK3
GLCE
FBXO22
VPS33B
MRPL46
OR4F4
NPTN
SLCO3A1
SCAPER
RPS27L
RASL12
SPG21
NGRN
RHCG
PTPLAD1
RAB8B
BTBD1
TM6SF1
CSNK1G1
ZFAND6
SCAND2P
VPS13C
LRRC49
PAQR5
DPP8
COMMD4
PARP16
CLN6
ZSCAN2
ZWILCH
DET1
UACA
FANCI
IMP3
LARP6
DNAJA4
MCTP2
VIMP
UNC45A
C15orf39
THAP10
RGMA
WDR93
PARP6
FAM219B
ADAMTSL3
KIAA1199
ALPK3
ISLR2
IGDCC4
ABHD17C
MESDC1
PPCDC
CELF6
STRA6
KLHL25
CPEB1
AEN
IQCH
ISL2
TTC23
MRPS11
NOX5
EFTUD1
NEIL1
LRRK1
AAGAB
LMAN1L
PEAK1
SNX22
THSD4
PIF1
CCDC33
EDC3
TM2D3
PLEKHO2
WDR61
CD276
VWA9
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
MEGF11
LINGO1
WDR73
UBL7
TICRR
RCCD1
ARRDC4
LINC00923
UBE2Q2
LACTB
DIS3L
C15orf40
SENP8
SLC51B
TARSL2
HIGD2B
LRRC28
C15orf27
AGBL1
HYKK
WHAMM
FSD2
ASB7
C2CD4A
LYSMD4
PGPEP1L
C15orf61
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
C15orf26
TBC1D21
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
CT62
GRAMD2
LCTL
CERS3
SPESP1
LINC00277
C15orf60
C15ORF37
FAM154B
FAM169B
FBXL22
GOLGA6A
RBPMS2
ANKDD1A
KIF7
ZNF710
HDDC3
C2CD4B
UBE2Q2P1
SPATA41
KBTBD13
UBAP1L
SKOR1
GDPGP1
OR4F6
OR4F15
ST20
FAM174B
MIR184
GOLGA6L9|ENSG00000197978.8
TTLL13
MIR422A
CPLX3
GOLGA6L10|ENSG00000205281.6
MIR549
MIR630
MIR631
MIR1276
MIR1179
MIR3174
MIR4311
MIR4313
MIR3713
RPS17L
MIR4514
MIR4513
MIR4515
MIR548AP
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
PIK3CA
BCL6
EIF4A2
ETV5
LPP
MLF1
SOX2
TFRC
GMPS
FAM157A
FYTTD1
snoU13|ENSG00000238491.1
MIR4797
U4|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
RN7SL36P
MIR3137
LINC00884
LINC00887
RN7SL215P
RN7SL447P
snoU13|ENSG00000238902.1
RN7SKP222
RN7SKP296
RN7SL486P
MIR944
MIR28
snoU13|ENSG00000239093.1
RTP4
SNORA4|ENSG00000263776.1
SNORA63|ENSG00000200320.1
SNORA81|ENSG00000221420.2
SNORA63|ENSG00000200418.1
SNORD2|ENSG00000238942.1
KNG1
CRYGS
RN7SL637P
TRA2B
MIR548AQ
SENP2
snoU13|ENSG00000239146.1
SNORD66|ENSG00000212158.1
MIR1224
CYP2AB1P
SNORA4|ENSG00000251730.1
SNORA63|ENSG00000199363.1
SNORA81|ENSG00000253092.1
SNORA63|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
RN7SL229P
U8|ENSG00000201810.1
RNA5SP149
snoU13|ENSG00000239096.1
GNB4
SNORA25|ENSG00000201957.1
RNA5SP148
SNORA18|ENSG00000200288.1
RN7SKP52
LINC00578
LINC00501
RNA5SP147
snoU13|ENSG00000271842.1
MIR4789
RN7SKP40
RN7SKP234
snoU13|ENSG00000239141.1
SNORA72|ENSG00000200355.1
RN7SL141P
PP13439
snoU13|ENSG00000238359.1
MIR569
RNY5P3
CLDN11
TERC
EGFEM1P
RN7SKP298
MIR720
snoU13|ENSG00000238398.1
CT64
SPTSSB
PPM1L
SNORA72|ENSG00000207084.1
KRT8P12
SCARNA7
MIR15B
C3orf80
MIR3919
SHOX2
RN7SKP46
RNA5SP146
CCNL1
LINC00881
LINC00880
RN7SKP177
LINC00886
snoU13|ENSG00000271922.1
U8|ENSG00000201398.1
RN7SL300P
RAP2B
SUCNR1
IGSF10
P2RY12
RNA5SP145
FAM188B2
snoU13|ENSG00000243321.2
ANKUB1
TM4SF4
CPHL1P
AADAC
ACTL6A
AGTR1
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
GYG1
HRG
HES1
IL1RAP
IL12A
KPNA4
TM4SF1
MBNL1
MFI2
MME
MUC4
NDUFB5
OPA1
P2RY1
PAK2
PCYT1A
PFN2
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
PTX3
RARRES1
RFC4
RPL35A
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
HLTF
SSR3
SST
THPO
SEC62
CLRN1
KCNAB1
FXR1
TP63
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
SLC33A1
ADIPOQ
KIAA0226
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
RNF13
SLITRK3
NLGN1
NCBP2
PLCH1
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
WWTR1
TIPARP
ARHGEF26
GPR160
FETUB
LAMP3
KCNMB3
SERP1
GOLIM4
GPR171
SCHIP1
NMD3
COMMD2
ZNF639
RSRC1
PEX5L
SELT
DNAJB11
P2RY13
GPR87
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
LXN
HRASLS
MRPL47
NCEH1
IFT80
SLC7A14
MAGEF1
ZMAT3
MFSD1
FNDC3B
ATP13A3
VEPH1
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
PIGZ
SPATA16
EIF2A
B3GNT5
IQCG
ATP13A4
HPS3
ACTRT3
LRCH3
CEP19
GFM1
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
TM4SF18
RPL39L
MED12L
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
FAM194A
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
XXYLT1
C3orf55
C3orf79
CCDC50
PYDC2
RNF168
DHX36
HTR3C
LIPH
HTR3D
RPL22L1
SLC51A
FBXO45
MUC20
SENP5
NAALADL2
TCTEX1D2
SMCO1
UTS2B
HTR3E
C3orf33
C3orf70
TPRG1
TRIM59
CCDC39
LRRIQ4
SAMD7
AADACL2
GPR149
RTP2
OSTN
ATP13A5
WDR53
ANKRD18DP
NRROS
LEKR1
TMEM212
LINC00885
TMEM14E
C3orf65
GMNC
IQCJ
MIR551B
MIR570
MIR922
MIR1263
MIR4448
MIR5186
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
MIR548AO
IDO1
SFRP1
C8orf4
ZMAT4
IDO2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MPL
RNA5SP46
RNA5SP45
RN7SL326P
MIR30C1
MIR30E
BMP8B
SNORA55
BMP8A
RNA5SP44
MYCBP
SNORA63|ENSG00000252448.1
snoU13|ENSG00000238871.1
MIR5581
MEAF6
RNA5SP43
ATP6V0B
CDC20
COL9A2
CTPS1
DPH2
EDN2
FHL3
GRIK3
GUCA2A
GUCA2B
INPP5B
MTF1
MYCL
NDUFS5
NFYC
YBX1
POU3F1
PPT1
PTPRF
RLF
ST3GAL3
SLC2A1
SLC6A9
TIE1
DNALI1
B4GALT2
PABPC4
ARTN
KCNQ4
IPO13
KDM4A
RIMS3
ZMPSTE24
PPIE
PPIH
CAP1
SF3A3
EBNA1BP2
FOXJ3
SCMH1
SZT2
MACF1
HEYL
GNL2
ZNF691
UTP11L
HPCAL4
TRIT1
RHBDL2
C1orf109
CDCA8
HIVEP3
OXCT2
RRAGC
LEPRE1
SMAP2
EXO5
ELOVL1
ZFP69B
C1orf50
AKIRIN1
YRDC
PPCS
SNIP1
ZC3H12A
GJA9
HYI
ZMYND12
NT5C1A
MFSD2A
MED8
ERMAP
TMCO2
ZNF684
C1orf122
TMEM125
MANEAL
CLDN19
WDR65
C1orf210
CCDC24
CITED4
SLFNL1
RSPO1
EPHA10
RIMKLA
ZFP69
CCDC23
FAM183A
KIAA0754
CCDC30
FOXO6
MIR4255
MIR3659

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 - 38 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 1.0175e-92 1.0175e-92 chr9:21959052-21977193 1
18q21.2 2.1191e-32 2.1191e-32 chr18:48491525-48650073 3
17q22 1.839e-08 1.839e-08 chr17:55754312-57936913 40
1p36.11 2.3492e-06 0.00013762 chr1:26795113-27650365 20
5q14.2 0.00021798 0.00021798 chr5:65889312-90466295 144
17p12 0.0012972 0.0013492 chr17:11866892-12456081 4
12p13.1 0.0030925 0.0035374 chr12:3709766-22700847 241
6p25.2 0.00024922 0.0042402 chr6:1-19439844 119
11p15.4 0.012782 0.011964 chr11:1-13933964 281
1p36.32 0.00066415 0.020752 chr1:1-24288183 381
4q34.3 0.023971 0.02376 chr4:151493422-191154276 184
22q13.32 8.4644e-05 0.02376 chr22:43902280-51304566 85
8p23.2 0.025599 0.025351 chr8:1-29007074 233
3p21.31 0.027427 0.028089 chr3:41286244-69823854 342
6p22.2 0.0018425 0.028967 chr6:26187784-26235299 9
7q36.1 0.030018 0.032152 chr7:104644244-159138663 413
19q13.33 0.031084 0.032152 chr19:46475664-59128983 522
19p13.2 0.0064388 0.032152 chr19:11040707-11207540 2
22q13.31 0.00011836 0.032628 chr22:43558927-51304566 88
16q23.1 0.038483 0.040828 chr16:78098006-79299841 3
19p13.3 0.005647 0.046902 chr19:1-7112175 229
12q24.33 0.0028269 0.055218 chr12:75782484-133851895 473
12q21.33 0.0016105 0.065229 chr12:68037089-133851895 513
4q22.1 0.078852 0.078852 chr4:90844993-93240505 2
Xp21.1 0.08346 0.08346 chrX:30870233-32611359 3
13q14.2 0.096268 0.094409 chr13:48875329-49563699 5
21q11.2 0.094032 0.094409 chr21:1-34407260 97
18p11.31 0.11354 0.11463 chr18:1-5145388 32
15q15.1 0.12349 0.12349 chr15:1-87572429 695
14q11.2 0.14238 0.14238 chr14:1-107349540 938
10q23.33 0.16002 0.15839 chr10:82101948-135534747 444
10p15.3 0.16002 0.16394 chr10:1-15137499 110
2q14.3 0.18947 0.18947 chr2:1-243199373 1591
Xq11.2 0.18215 0.18947 chrX:62570171-64136373 6
6q25.3 0.20444 0.20488 chr6:57206295-171115067 558
12q12 0.028089 0.20488 chr12:31797043-68556857 407
9q22.33 0.2404 0.2484 chr9:88160239-134602961 442
4p15.31 0.24963 0.26186 chr4:1-191154276 959
Genes in Wide Peak

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

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

Genes
C9orf53
Genes in Wide Peak

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

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

Genes
RN7SL695P
SMAD4
ELAC1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q22.

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

Genes
CLTC
MIR4729
PRR11
MIR301A
MIR454
RN7SL716P
PPM1E
U3|ENSG00000212195.1
DYNLL2
SRSF1
VEZF1
MRPS23
RN7SKP94
LPO
MPO
TRIM37
SEPT4
RAD51C
SUPT4H1
EPX
MTMR4
BZRAP1
OR4D1
PTRH2
RNF43
MKS1
SMG8
TEX14
DHX40
VMP1
HSF5
OR4D2
C17orf47
GDPD1
SKA2
YPEL2
CUEDC1
MIR142
MIR21
MIR4736
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
ARID1A
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
SFN
RPS6KA1
SLC9A1
NR0B2
NUDC
WDTC1
PIGV
GPATCH3
FAM46B
C1orf172
TRNP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q14.2.

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

Genes
PIK3R1
SNORA70|ENSG00000206958.1
RNA5SP187
RN7SL629P
RN7SKP34
MIR3607
COX7C
NBPF22P
RN7SKP295
SCARNA18|ENSG00000238835.1
RN7SL378P
SSBP2
SNORA31|ENSG00000251828.1
snoU13|ENSG00000239159.1
MTX3
HOMER1
SNORA18|ENSG00000206592.1
RNY3P1
BHMT2
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13|ENSG00000238688.1
RNA5SP186
POLK
SNORA40|ENSG00000212363.1
RN7SL814P
MIR4804
RN7SL153P
MIR4803
snoU13|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13|ENSG00000238334.1
SNORA50|ENSG00000220986.1
RN7SL103P
7SK|ENSG00000249352.3
U8|ENSG00000212249.2
ARSB
BHMT
BTF3
CCNB1
CCNH
CDK7
CETN3
CKMT2
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
TNPO1
CD180
MAP1B
MEF2C
MSH3
NAIP
PMCHL2
RAD17
RASA1
RASGRF2
RPS23
SMN1
SMN2
TAF9
TBCA
THBS4
XRCC4
SERF1A
ENC1
AP3B1
PDE8B
SCAMP1
CARTPT
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
NSA2
POLR3G
IQGAP2
SV2C
MRPS27
FAM169A
DMGDH
GCNT4
AGGF1
BDP1
ANKRA2
MCCC2
ARHGEF28
SLC30A5
CENPH
PTCD2
ATG10
GPR98
UTP15
ZCCHC9
GFM2
SPZ1
MRPS36
ATP6AP1L
FCHO2
LYSMD3
JMY
TMEM171
TMEM174
POC5
ACOT12
TMEM167A
MBLAC2
TMEM161B
MARVELD2
PAPD4
ZNF366
FAM151B
CCDC125
CMYA5
ANKRD31
SERINC5
ANKRD34B
MAST4
LINC00461
GTF2H2C
SERF1B
ANKDD1B
MIR4280
MTRNR2L2
MIR3660
OCLN
Genes in Wide Peak

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

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

Genes
MAP2K4
MIR744
RPL21P122
ZNF18
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
CCND2
ETV6
ZNF384
C12orf39
PYROXD1
LST3
AEBP2
RN7SL67P
RN7SL459P
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
C1R
SCARNA12
DSTNP2
RPL13P5
RN7SL380P
SCARNA11|ENSG00000251898.1
SCARNA10
MRPL51
RN7SL391P
RN7SL69P
NDUFA9
C12orf5
A2M
APOBEC1
ARHGDIB
C1S
C3AR1
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
GAPDH
GNB3
GPR19
GUCY2C
GYS2
IAPP
KCNA1
KCNA5
KCNA6
KCNJ8
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LDHB
LRP6
LTBR
M6PR
MGP
MGST1
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PTMS
PTPN6
PTPRO
PEX5
PZP
RECQL
SCNN1A
ST8SIA1
SLC2A3
SLCO1A2
VAMP1
TNFRSF1A
TPI1
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
YBX3
DYRK4
CD163
GDF3
CLSTN3
C2CD5
NCAPD2
ABCC9
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
SLCO1B1
RAD51AP1
KLRAP1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
SLCO1B3
COPS7A
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
HEBP1
GOLT1B
DERA
ING4
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
CMAS
PARP11
ANO2
C12orf4
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
NANOG
APOLD1
GSG1
CDCA3
RBP5
ACRBP
SPSB2
EFCAB4B
RERG
PLCZ1
CAPZA3
CLEC6A
C12orf57
LOH12CR1
TMEM52B
HIST4H4
SLC2A14
A2ML1
CLEC12A
CLECL1
CLEC4C
PIANP
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CD163L1
CLEC9A
C12orf36
CLEC4D
SLCO1B7
ACSM4
TAS2R42
DPPA3
NANOGNB
CLEC2A
CLEC12B
LINC00937
MIR141
MIR200C
ZNF705A
SMCO3
PRB2
MIR614
SLC15A5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.2.

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

Genes
IRF4
DEK
RNA5SP205
snoU13|ENSG00000238458.1
RNA5SP204
STMND1
U3|ENSG00000251793.1
MIR4639
RN7SL332P
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
FAM8A1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
MCUR1
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
KDM1B
RBM24
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
RNF144B
CAGE1
MYLK4
TUBB2B
NHLRC1
PSMG4
C6orf201
PPP1R3G
MIR548A1
TMEM170B
MIR4645
MIR5689
MIR5683
Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
RNA5SP331
RN7SKP151
LINC00958
SCARNA16|ENSG00000252329.1
PARVA
SNORD97
LYVE1
RNU6ATAC33P
ADM
RN7SKP50
RN7SL56P
snoU13|ENSG00000238387.1
SNORA23
MIR5691
RNA5SP330
SNORA45
SNORA3|ENSG00000200983.1
SCARNA20|ENSG00000252778.1
OR10AB1P
GVINP1
TAF10
RRP8
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62|ENSG00000201980.1
OR51C1P
SNORA7|ENSG00000206976.1
snoU13|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
EIF4G2
HBB
HBD
HBE1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
PTH
RNH1
MRPL23
RPL27A
RRM1
SMPD1
TRIM21
ST5
STIM1
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
MRVI1
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
PKP3
SWAP70
DENND5A
SIRT3
OR52A1
ARFIP2
OR10A3
TIMM10B
DKK3
RBMXL2
PGAP2
TRPM5
UBQLN3
RNF141
BET1L
CEND1
CYB5R2
CDHR5
TOLLIP
USP47
TRIM68
PIDD
KCNQ1DN
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
SBF2
FAM160A2
FAR1
BTBD10
MICALCL
TRIM5
SYT8
PRKCDBP
OSBPL5
LRRC56
MRGPRE
ART5
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
OR56B4
OR52B2
C11orf35
OR51F1
CSNK2A3
OR51V1
EFCAB4A
OR10A4
OLFML1
NLRP10
NLRP14
ANO9
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNT18
MRGPRG
IFITM5
FAM99A
OR56B1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
TMEM41B
MUC5B
MIR302E
MIR4298
MIR4299
MTRNR2L8
MIR4686
MIR4687
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
MDS2
snoU13|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16|ENSG00000252404.1
RN7SL451P
SNORA77|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
TNFRSF8
CDA
CDK11B
CDC42
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
EPHA2
ENO1
EPHA8
EPHB2
MTOR
FUCA1
GABRD
GALE
GNB1
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RPL11
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
LUZP1
PRDM2
MMP23B
KCNAB2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
ANGPTL7
HNRNPR
UBE4B
MAD2L2
PDPN
MASP2
UTS2
RER1
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLSTN1
SPEN
KDM1A
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
CHD5
SZRD1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
ARHGEF10L
VPS13D
ATAD3A
PANK4
CAMK2N1
ASAP3
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
AGTRAP
PITHD1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
MIIP
CELA2A
PLA2G2F
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
EFHD2
MMEL1
RSG1
MUL1
NOL9
LINC00115
MORN1
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
ATAD3B
PLEKHN1
USP48
NBPF3
LZIC
C1orf170
IGSF21
KIAA2013
THAP3
FBXO44
FHAD1
RBP7
ACAP3
UBE2J2
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
SLC2A7
CALML6
FAM43B
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
C1orf234
OR4F29
MIR4253
MIR1273D
MIR4252
MIR3675
APITD1
MIR4419A
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697
Genes in Wide Peak

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

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

Genes
DUX4
FBXW7
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
C4orf45
U3|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
SNORD73A
SNORD73
RNA5SP168
AGA
SLC25A4
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGG
FRG1
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
PPID
RPS3A
MSMO1
SFRP2
TDO2
TLL1
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
MAB21L2
ADAM29
ANXA10
KLHL2
PALLD
KIAA0922
TRIM2
FAM149A
FBXO8
ARFIP1
SPOCK3
AADAT
FAM198B
ASIC5
GALNT7
CLDN22
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
TMA16
DDX60
CDKN2AIP
TENM3
LRP2BP
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
MLF1IP
MAP9
WWC2
CEP44
SNX25
MND1
TKTL2
CBR4
FHDC1
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
SH3D19
FAM218A
TRIM60
RBM46
C4orf46
TIGD4
RWDD4
CCDC111
TRIML2
CCDC110
RNF175
TRIML1
PRSS48
ANKRD37
TRIM61
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
FAM160A1
CLDN24
MIR1305
MIR3140
MIR4276
MIR3945
MIR4455
MIR4453
Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
LINC00229
ACR
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
CRELD2
ADM2
TRABD
PNPLA3
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LMF2
PHF21B
KLHDC7B
PNPLA5
C22orf34
LINC00207
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535
Genes in Wide Peak

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

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

Genes
PCM1
RN7SL781P
RNA5SP260
RNA5SP259
MIR4287
snoU13|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13|ENSG00000238466.1
U3|ENSG00000251944.1
SNORA62|ENSG00000201157.1
RNA5SP256
MIR548V
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
LINC00529
MIR598
SNORD112|ENSG00000252565.1
SOX7
RNA5SP252
PRSS51
snoU13|ENSG00000238496.1
snoU13|ENSG00000239065.1
MIR597
U3|ENSG00000252543.1
SNORA70|ENSG00000207244.1
RN7SL178P
SGK223
ALG1L13P
FAM86B3P
LRLE1
FAM85B
FAM90A24P
FAM66E
DEFB105A
DEFB105B
DEFB103B
ZNF705G
FAM66B
XKR5
MIR4659A
AGPAT5
RN7SKP159
RN7SL318P
SNORA70|ENSG00000206661.1
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
EGR3
DMTN
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
LOXL2
LPL
MSR1
MSRA
NEFM
PDGFRL
PNOC
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
DOK2
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
PSD3
SLC39A14
FBXO25
ADAMDEC1
CNOT7
SCARA3
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
HMBOX1
MCPH1
PPP1R3B
DOCK5
REEP4
STMN4
SOX7
FAM167A
SLC35G5
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
SGCZ
DEFB104A
PEBP4
CDCA2
ESCO2
FBXO16
TDRP
ERICH1
TDH
C8orf48
ZNF596
R3HCC1
PRSS55
C8orf74
LGI3
DEFB106A
DEFB107A
DEFB130|ENSG00000232948.1
NEIL2
XKR6
MICU3
SCARA5
USP17L2
NUGGC
LINC00599
MIR320A
DEFB103A
DEFB107B
DEFB104B
DEFB106B
C8orf58
DEFB135
DEFB136
SPAG11A
MIR596
DEFA1B
ZNF705D
ZNF705B
DEFB4B
MIR548I3
MIR548H4
MIR4288
MIR4286
MIR3622B
MIR4660
MIR5692A2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.31.

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

Genes
FHIT
BAP1
SETD2
PBRM1
RN7SL418P
MIR3136
RNA5SP135
RN7SL482P
U3|ENSG00000200222.1
SNTN
RNA5SP134
LINC00698
RN7SL863P
PTPRG
U3|ENSG00000212211.1
NPCDR1
RPP14
RNU6ATAC26P
PDE12
snoU13|ENSG00000238905.1
HESX1
RNA5SP133
RN7SKP45
MIR3938
ESRG
CHDH
SNORD63|ENSG00000251987.1
SNORA26|ENSG00000212608.1
SNORD38|ENSG00000207109.1
RN7SL821P
snoU13|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19|ENSG00000222345.1
SNORD19B|ENSG00000238862.1
SNORD19|ENSG00000212493.1
SNORD19B|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13|ENSG00000238350.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000251938.1
PRSS44
PRSS45
SNORD77|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
U8|ENSG00000212145.2
RN7SKP58
SCARNA21|ENSG00000252409.1
ALAS1
AMT
APEH
ARF4
RHOA
CACNA1D
SLC25A20
CAMP
CCK
CDC25A
CISH
CCR1
CCR3
CCR5
ACKR2
COL7A1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
NKTR
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
TMF1
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
SUCLG2
BSN
ACKR5
UBA3
SEC22C
RRP9
MAGI1
CACNA2D2
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CCR9
USP19
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
EXOSC7
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
PTPN23
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SS18L2
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
ELP6
SNRK
QRICH1
PXK
ULK4
FEZF2
ANO10
DALRD3
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZKSCAN7
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
SELK
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
GTDC2
UCN2
ZNF502
RFT1
ACTR8
SLC25A26
ZNF501
GPR62
FAM3D
LYZL4
KLHL40
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SYNPR
LSMEM2
ASB14
FAM19A4
CCDC12
CCDC13
PRICKLE2
C3orf67
KCTD6
KLHDC8B
DNAH12
DENND6A
ALS2CL
TMIE
EOGT
FBXW12
CCDC66
TCAIM
CCDC36
PRSS42
ZNF445
SPATA12
TOPAZ1
TMEM110
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
FAM19A1
MIR425
SPINK8
ARIH2OS
C3orf84
FAM198A
CCR2
PRSS46
MIR4271
KRBOX1
MIR4787
MIR4443
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p22.2.

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

Genes
HIST1H4E
HIST1H2BF
HIST1H2AD
HIST1H1D
HIST1H2AE
HIST1H2BG
HIST1H3D
HIST1H3E
HIST1H4D
Genes in Wide Peak

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

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1|ENSG00000271739.1
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13|ENSG00000238922.1
FLJ00325
U3|ENSG00000238297.1
snoU109|ENSG00000238832.1
RNA5SP236
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CAV1
CAV2
CFTR
CHRM2
CLCN1
CPA1
CPA2
DLD
DPP6
SLC26A3
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR22
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRCAM
NRF1
PAX4
SLC26A4
PIK3CG
PIP
PODXL
PPP1R3A
PRKAR2B
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
NAMPT
FAM3C
COG5
FASTK
DUS4L
ZNF277
ABCB8
TFEC
LAMB4
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
TES
GIMAP2
OR2F1
SLC13A4
HBP1
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
GPR85
TAS2R5
CHPF2
PUS7
ING3
LRRN3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
KMT2E
BCAP29
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
CBLL1
ZNF767
CPED1
TTC26
JHDM1D
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
C7orf60
CLEC2L
C7orf55
IQUB
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
ATXN7L1
CDHR3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
LSMEM1
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
EFCAB10
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
PPP2R1A
KLK2
TFPT
ZNF331
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13|ENSG00000239137.1
KIR3DX1
LILRA6
LENG1
NDUFA3
MIR935
MIR371B
RN7SL317P
ZNF813
ZNF761
FAM90A28P
FAM90A27P
ZNF321P
ZNF888
ZNF600
ZNF137P
MIR643
snoU13|ENSG00000238630.1
HCCAT3
FPR1
snoU13|ENSG00000238486.1
SIGLEC5
CEACAM18
SIGLEC22P
SIGLEC17P
KLK13
KLK9
KLKP1
SNORD88C
SNORD88A
SNORD88B
LRRC4B
SPIB
RN7SL324P
NAPSB
SIGLEC16
U3|ENSG00000221125.1
MIR4751
MIR4750
MIR4749
ADM5
MIR5088
BCL2L12
SNORD35B
SNORD35A
SNORD34
SNORD33|ENSG00000199631.1
SNORD32A
MIR4324
RN7SL708P
RN7SL345P
SEC1P
DBP
GRWD1
C19orf68
CABP5
TPRX2P
SNORD23|ENSG00000221803.1
RN7SL322P
RN7SL533P
snoU13|ENSG00000252071.1
MIR320E
RN7SL364P
PGLYRP1
A1BG
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
EMP3
ETFB
FCAR
FCGRT
FLT3LG
FPR2
FPR3
FTL
FUT1
FUT2
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
MYBPC2
NKG7
CNOT3
NPAS1
NTF4
NUCB1
PEG3
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTGIR
PTPRH
RPL18
RPL28
RPS5
RPS9
RPS11
RRAS
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SPIB
AURKC
SULT2B1
SULT2A1
TNNI3
TNNT1
TULP2
NR1H2
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF135
ZNF154
ZNF175
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
UBE2M
CYTH2
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
ZNF324
KLK5
PRKD2
ZNF473
CCDC9
PRPF31
FGF21
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
C5AR2
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
STRN4
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SPHK2
MEIS3
SLC17A7
NAT14
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
ZSCAN18
RPL23AP79
TSEN34
MBOAT7
FKRP
ZSCAN5A
ZNF329
TBC1D17
ZNF419
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
ZNF611
MED25
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
ZNF551
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
ACPT
CGB5
CGB7
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LINC00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
TMEM190
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
DACT3
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF320
ZNF497
ZNF550
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TPRX1
MAMSTR
IZUMO1
EMC10
KLK9
SIGLECL1
ZNF615
ZNF841
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
DNAAF3
LILRA5
IGFL1
ZNF773
IGFL3
ZNF808
ZNF470
ZNF749
ZNF324B
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR371A
MIR372
MIR373
IGFL4
DPRX
ASPDH
MIR498
MIR520E
MIR519E
MIR520F
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
CCDC61
SHISA7
MIR769
SIGLEC14
SGK110
BSPH1
ZNF587B
MIR1323
MIR3191
PPP5D1
ZNF865
MIR4754
MIR4752
Genes in Wide Peak

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

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

Genes
SMARCA4
RN7SL192P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
LINC00229
SCUBE1
ACR
MPPED1
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
TTLL12
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
CRELD2
ADM2
TRABD
PNPLA3
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LMF2
PHF21B
KLHDC7B
PNPLA5
C22orf34
LINC00207
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535
Genes in Wide Peak

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

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

Genes
RNA5SP431
PIH1
WWOX
Genes in Wide Peak

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

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

Genes
MLLT1
GNA11
SH3GL1
STK11
TCF3
FSTL3
EMR4P
MIR3940
ACER1
CAPS
VMAC
RN7SL626P
MIR4747
UHRF1
RN7SL121P
LRG1
HDGFRP2
RN7SL528P
RN7SL84P
PIAS4
SNORD37|ENSG00000206775.1
MIR637
RN7SL202P
SNORD38|ENSG00000252408.1
FZR1
RN7SL866P
ZNF554
SPPL2B
LINGO3
MIR4321
MIR1227
RN7SL226P
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
AES
AMH
ATP5D
AZU1
HCN2
BSG
C3
CD70
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
EEF2
EFNA2
ELANE
EMR1
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
MATK
GADD45B
NFIC
NRTN
OAZ1
PALM
POLRMT
MAP2K2
PSPN
PRTN3
PTBP1
PTPRS
RFX2
RPS15
SAFB
SGTA
TBXA2R
THOP1
TLE2
VAV1
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
S1PR4
TNFSF14
TNFSF9
AP3D1
TRIP10
LONP1
APBA3
SAFB2
MED16
CHAF1A
SH2D3A
EBI3
PLIN3
APC2
ABCA7
HMG20B
TUBB4A
SEMA6B
UQCR11
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
SHC2
RPL36
TIMM13
DAZAP1
FGF22
TJP3
NMRK2
SLC39A3
THEG
ZBTB7A
SIRT6
LSM7
MBD3
MIER2
PCSK4
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
NCLN
GPR108
DUS3L
SHD
WDR18
REXO1
ZNF77
CACTIN
CELF5
SLC25A23
FSD1
ZNF557
TLE6
LPPR3
DENND1C
ZNF556
UBXN6
ACSBG2
ABHD17A
DOHH
KLF16
ALKBH7
DOT1L
KISS1R
CREB3L3
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
R3HDM4
TMEM259
TPGS1
CRB3
REEP6
IZUMO4
SCAMP4
ADAT3
GRIN3B
MRPL54
C19orf70
MBD3L2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
MISP
PLK5
C2CD4C
TICAM1
ZNRF4
C19orf25
ATP8B3
DIRAS1
ZNF555
PRR22
ANKRD24
C19orf26
TINCR
CATSPERD
C19orf77
SLC25A41
MBD3L5
ODF3L2
ADAMTSL5
TMPRSS9
C19orf35
HSD11B1L
MEX3D
PRSS57
PLIN5
ARRDC5
MBD3L4
MBD3L3
PLIN4
C19orf71
MIR3187
MIR4746
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.33.

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

Genes
BCL7A
BTG1
ALDH2
PTPN11
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13|ENSG00000238822.1
RN7SL534P
snoU13|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38|ENSG00000201042.1
RNA5SP374
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56|ENSG00000200112.1
RN7SL865P
SNORA27|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40|ENSG00000264043.2
FICD
RNA5SP371
SNORD74|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13|ENSG00000238914.1
U8|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13|ENSG00000238800.1
SLC5A8
snoU13|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13|ENSG00000239073.1
SNORD74|ENSG00000201502.1
snoU13|ENSG00000238361.1
snoU13|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
LTA4H
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SYT1
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
KERA
KRR1
PRDM4
CIT
PWP1
NUDT4
FZD10
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
UTP20
MRPL42
IFT81
CCDC59
FAM216A
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
METTL25
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
CCDC64
SDSL
OSBPL8
IQCD
DEPDC4
CCDC38
TMEM132D
SLC15A4
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
RAD9B
FAM109A
TMTC2
TMTC3
C12orf50
ALDH1L2
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
CCER1
SLC17A8
LRRC43
TCP11L2
C12orf79
POC1B
OTOGL
GPR133
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
DDX51
MMAB
HCAR2
TMEM119
C12orf74
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
CLLU1OS
CLLU1
MIR492
C12orf73
ZNF605
MIR1251
MIR4303
MIR3685
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR5188
MIR5700
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.33.

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

Genes
BCL7A
BTG1
ALDH2
MDM2
PTPN11
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13|ENSG00000238822.1
RN7SL534P
snoU13|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38|ENSG00000201042.1
RNA5SP374
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56|ENSG00000200112.1
RN7SL865P
SNORA27|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40|ENSG00000264043.2
FICD
RNA5SP371
SNORD74|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13|ENSG00000238914.1
U8|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13|ENSG00000238800.1
SLC5A8
snoU13|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13|ENSG00000239073.1
SNORD74|ENSG00000201502.1
snoU13|ENSG00000238361.1
snoU13|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
U8|ENSG00000201809.1
RAB21
SNORA17|ENSG00000212461.1
MYRFL
RN7SL804P
SLC35E3
SNORA70G
DYRK2
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CPM
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
STX2
GOLGA3
GTF2H3
HAL
HPD
IFNG
IGF1
KCNC2
LTA4H
LYZ
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
CNOT2
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PTPRB
PTPRR
PXMP2
PXN
RAP1B
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
YEATS4
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CCT2
CAMKK2
ZNF268
FRS2
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
CPSF6
KERA
KRR1
PRDM4
CIT
PWP1
NUDT4
FZD10
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
UTP20
KCNMB4
MRPL42
IFT81
CCDC59
FAM216A
TRHDE
SYCP3
CHST11
GALNT9
IL22
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
CHFR
FGD6
IL26
WSB2
NDUFA12
DIABLO
MDM1
ANKS1B
CHPT1
NUP107
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
METTL25
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
CCDC64
SDSL
OSBPL8
IQCD
RAB3IP
DEPDC4
CCDC38
TMEM132D
SLC15A4
TPH2
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
RAD9B
FAM109A
TMTC2
TMTC3
C12orf50
ALDH1L2
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
CCER1
SLC17A8
LRRC43
TCP11L2
C12orf79
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
DDX51
MMAB
HCAR2
TMEM119
C12orf74
EP400NL
RILPL1
C12orf42
LRRC10
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
C12orf73
ZNF605
MIR1251
MIR4303
MIR3685
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR5188
MIR5700
Genes in Wide Peak

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

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

Genes
RN7SKP248
CCSER1
Genes in Wide Peak

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

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

Genes
MIR3915
RNA5SP501
FTHL17
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

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

Genes
RB1
LINC00462
RCBTB2
LPAR6
CYSLTR2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

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

Genes
OLIG2
SNORA70|ENSG00000207098.1
C21orf62
C21orf49
C21ORF59
TCP10L
LINC00846
RNA5SP490
SNORA33|ENSG00000252045.1
SNORA80
RN7SL109P
LINC00159
SNORA81|ENSG00000238390.1
LINC00307
snoU13|ENSG00000239171.1
LINC00189
U3|ENSG00000212479.1
RWDD2B
N6AMT1
LINC00113
LINC00515
snoU13|ENSG00000238314.1
RNA5SP489
7SK|ENSG00000232512.2
RN7SL609P
LINC00308
LINC00317
LINC00320
RN7SKP147
RN7SL163P
SNORD74|ENSG00000201025.1
snoU13|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
APP
ATP5J
CXADR
GABPA
GRIK1
NCAM2
TMPRSS15
SOD1
HSPA13
TIAM1
TPTE
NRIP1
SYNJ1
CLDN8
ADAMTS1
URB1
USP16
CCT8
BTG3
ADAMTS5
LTN1
CLDN17
USP25
HUNK
RBM11
MIS18A
LINC00158
MRPL39
C21orf91
MRAP
C21orf59
MAP3K7CL
SCAF4
JAM2
EVA1C
SAMSN1
C21orf119
PAXBP1
CYYR1
LINC00161
CHODL
LIPI
ABCC13
LINC00314
POTED
LINC00478
MIRLET7C
MIR125B2
MIR155HG
MIR99A
BACH1
MIR4327
MIR548X
MIR3687
C21orf37
MIR4759
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.31.

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

Genes
snoU13|ENSG00000238790.1
snoU13|ENSG00000238445.1
RN7SL39P
snoU13|ENSG00000238863.1
SNORA70|ENSG00000252258.1
EMILIN2
snoU13|ENSG00000238425.1
CBX3P2
snoU109|ENSG00000238575.1
RN7SKP72
LINC00470
RN7SKP146
CETN1
ROCK1P1
ADCYAP1
TGIF1
TYMS
YES1
MYOM1
USP14
DLGAP1
LPIN2
THOC1
NDC80
MYL12A
SMCHD1
CLUL1
ENOSF1
METTL4
COLEC12
MYL12B
C18orf56
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
BUB1B
PML
TCF12
SNORD74|ENSG00000200206.1
RNA5SP400
RN7SL428P
CSPG4P12
SNORA25|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
HDGFRP3
SCARNA15|ENSG00000252690.2
GOLGA6L10|ENSG00000254374.2
RN7SL410P
GOLGA6L9|ENSG00000196648.6
UBE2Q2P3
RN7SL256P
RN7SL61P
CSPG4P8
UBE2Q2P2
TMC3
STARD5
LINC00927
SNORD112|ENSG00000251881.1
C15orf37
MTHFS
ANKRD34C
CTSH
ACSBG1
IDH3A
SNORA63|ENSG00000199633.1
SH2D7
MIR1827
RN7SL214P
RN7SL278P
RN7SKP217
NRG4
RN7SL510P
SNORD112|ENSG00000252372.1
RN7SL319P
DNM1P35
SNX33
ANP32BP1
DNM1P34
RN7SL327P
GOLGA6D
RN7SL489P
GOLGA6C
SCARNA20|ENSG00000252722.1
RPP25
COX5A
SCAMP2
SNORD77|ENSG00000212279.2
RN7SL429P
C15orf59
RN7SL853P
GOLGA6B
RN7SL485P
TMEM202
RNA5SP399
NR2E3
RPL29P30
MIR629
LINC00593
U3|ENSG00000207119.1
RNA5SP398
SNORA77|ENSG00000221376.1
RN7SL438P
MIR4312
FEM1B
CALML4
SNORD18A
SNORD16
SNORD18B
SNORD18C
MIR4512
MAP2K1
SCARNA14
TIPIN
MIR4511
snoU13|ENSG00000238311.1
snoU13|ENSG00000238715.1
SNORA24|ENSG00000206903.1
CLPX
MTFMT
RN7SL348P
MIR1272
RN7SL707P
RN7SL595P
SNORA48|ENSG00000252774.1
USP3
CA12
MIR190A
RN7SL613P
RNA5SP397
RNA5SP396
snoU13|ENSG00000238767.1
MIR2116
C15ORF31
U3|ENSG00000200318.1
RN7SKP95
snoU13|ENSG00000239100.1
MYZAP
LINC00926
snoU13|ENSG00000239035.1
RN7SL568P
snoU13|ENSG00000238513.1
PYGO1
MIR628
RSL24D1
ONECUT1
MIR1266
U6|ENSG00000272337.1
RN7SL354P
RNA5SP395
U6|ENSG00000271819.1
RN7SL494P
RNA5SP394
FGF7
RN7SL307P
RN7SL577P
RN7SKP139
FKSG62
RN7SKP101
SNORD11|ENSG00000238819.1
SNORA41|ENSG00000207516.1
HMGN2P46
snoU13|ENSG00000238583.1
SLC30A4
SNORA11|ENSG00000261709.2
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13|ENSG00000238494.1
snoU13|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13|ENSG00000238564.1
THBS1
FAM98B
U3|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77|ENSG00000212415.1
snoU13|ENSG00000238342.1
RN7SL286P
RN7SL539P
GOLGA8O
U8|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18|ENSG00000206849.1
MIR211
RN7SL82P
U8|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
RNA5SP391
LINC00929
SNORA48|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64|ENSG00000270704.2
SNHG14
SNURF
snoU13|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13|ENSG00000239083.1
CHEK2P2
RN7SL584P
ACTC1
ADAM10
ANXA2
APBA2
AQP9
BBS4
BCL2A1
BNC1
BNIP2
CAPN3
CHRM5
CHRNA3
CHRNA5
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
IL16
IREB2
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2C1
MAP1A
MEIS2
MFAP1
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
NMB
OAZ2
OCA2
PDE8A
PKM
PLCB2
PPIB
MAPK6
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SH3GL3
SLC12A1
SNRPN
SNX1
SPINT1
SRP14
TJP1
TLE3
TP53BP1
TPM1
TYRO3
UBE3A
MKRN3
AP3B2
ANP32A
SEMA7A
CILP
PIAS1
EIF3J
RAB11A
SNAP23
ALDH1A2
HERC2
HERC1
PSTPIP1
USP8
CCNB2
SLC28A2
SLC28A1
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
ARNT2
BCL2L10
HCN4
SNUPN
PDCD7
TSPAN3
RASGRP1
DENND4A
SNAPC5
HMG20A
CORO2B
CIB2
ARID3B
GNB5
ARPP19
MORF4L1
SLC27A2
ADAMTS7
AKAP13
GPR176
CHP1
OIP5
ITGA11
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
CYFIP1
KIAA1024
MGA
DMXL2
VPS39
FAM189A1
TMED3
AP4E1
SEC11A
DAPK2
EID1
NPAP1
SERF2
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
BLOC1S6
FBXO22
GREM1
NPTN
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
RPS27L
NDUFAF1
NUSAP1
EMC4
RASL12
SPG21
SPTBN5
PTPLAD1
CTDSPL2
KLF13
RAB8B
BTBD1
TM6SF1
DUOX1
CSNK1G1
ZFAND6
DLL4
SCAND2P
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
COMMD4
PARP16
CLN6
ZNF770
ZSCAN2
ZWILCH
UACA
HAUS2
RMDN3
DNAJC17
IMP3
LARP6
MNS1
DNAJA4
NOP10
MYO5C
NDNL2
FAM214A
EMC7
C15orf39
THAP10
PAK6
PARP6
DTWD1
CASC5
AVEN
FAM219B
ADAMTSL3
KIAA1199
STARD9
ALPK3
ISLR2
VPS18
IGDCC4
SQRDL
ABHD17C
MESDC1
PPCDC
CELF6
STRA6
ZNF106
KLHL25
CPEB1
IQCH
ISL2
RFX7
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
AAGAB
LMAN1L
KATNBL1
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
PIF1
CCDC33
EDC3
SPG11
ELL3
PLEKHO2
WDR61
CD276
POLR2M
VWA9
NIPA2
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
WDR73
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
C15orf40
SENP8
SLC51B
HIGD2B
C15orf27
NIPA1
AGBL1
HYKK
WHAMM
FSD2
PLA2G4E
TRIM69
C15orf43
C2CD4A
FAM81A
C15orf65
C15orf61
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
RHOV
SCAMP5
FAM227B
CT62
GRAMD2
LCTL
UBR1
PATL2
SPESP1
LPCAT4
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
SLC24A5
PRTG
LINC00277
C15orf60
GOLGA6L2
C15ORF37
FAM154B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
FBXL22
GLDN
GOLGA6A
FMN1
RBPMS2
ANKDD1A
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
UBE2Q2P1
GOLGA8EP
OR4M2
KBTBD13
UBAP1L
SKOR1
SHC4
CTXN2
C15orf53
C15orf54
ST20
DUOXA2
MIR184
HERC2P9
GOLGA8B
EIF2AK4
UNC13C
GOLGA6L9|ENSG00000197978.8
MIR422A
CKMT1A
CPLX3
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
GOLGA6L10|ENSG00000205281.6
MIR549
MIR630
MIR631
MIR147B
ANKRD63
JMJD7
PLA2G4B
POTEB2
MIR1276
MIR1282
MIR4311
MIR4313
MIR3713
RPS17L
MIR4514
MIR4513
MIR4508
MIR4510
MIR4716
MIR4713
MIR4712
MIR4515
GCOM1
MIR548AP
POTEB
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q11.2.

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

Genes
AKT1
KTN1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
NIN
CCNB1IP1
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3|ENSG00000200693.1
WDR89
SCARNA20|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112|ENSG00000252380.1
SIX1
U3|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
RN7SKP99
NAA30
RN7SL461P
LINC00520
RPL13AP3
TBPL2
MIR4308
RNU6ATAC9P
RN7SL588P
ERO1L
RNA5SP385
LINC00640
LINC00519
SNORA70|ENSG00000201376.1
TMX1
snoU83B
RN7SL452P
CDKL1
MIR4504
RN7SKP193
ARF6
RN7SL2
RN7SL3
RNU6ATAC30P
RPL36AL
RN7SL1
RNA5SP384
SNORD112|ENSG00000251824.1
LINC00648
SNORA25|ENSG00000251735.1
LINC00871
SNORD127
SNORD58
snoU13|ENSG00000238501.1
SNORA31|ENSG00000251858.1
FBXO33
LINC00639
LINC00517
SNORA42|ENSG00000200385.1
TTC6
MIR4503
SLC25A21
RN7SKP257
DPPA3P2
RN7SKP21
PTCSC3
snoU13|ENSG00000238718.1
SNORA31|ENSG00000253059.1
KIAA0391
RN7SL660P
GPR33
MIR624
BNIP3P1
LINC00645
SNORD37|ENSG00000212270.1
TM9SF1
RNA5SP383
DHRS4L1
LINC00596
RN7SKP205
MIR208B
MIR208A
PABPN1
C14orf164
SNORA73|ENSG00000252114.1
SNORD41|ENSG00000212302.1
OR6J1
TRAC
TRAJ1
TRAJ2
TRAJ3
TRAJ4
TRAJ5
TRAJ6
TRAJ7
TRAJ8
TRAJ9
TRAJ10
TRAJ11
TRAJ12
TRAJ13
TRAJ14
TRAJ16
TRAJ17
TRAJ18
TRAJ19
TRAJ20
TRAJ21
TRAJ22
TRAJ23
TRAJ24
TRAJ25
TRAJ26
TRAJ27
TRAJ28
TRAJ29
TRAJ30
TRAJ31
TRAJ32
TRAJ33
TRAJ34
TRAJ35
TRAJ36
TRAJ37
TRAJ38
TRAJ39
TRAJ40
TRAJ41
TRAJ42
TRAJ43
TRAJ44
TRAJ45
TRAJ46
TRAJ47
TRAJ48
TRAJ49
TRAJ50
TRAJ52
TRAJ53
TRAJ54
TRAJ56
TRAJ57
TRAJ58
TRAJ59
TRAJ61
TRDV3
TRDC
TRDJ3
TRDJ2
TRDJ4
TRDJ1
TRDD3
TRDD2
TRDD1
TRDV2
TRAV41
TRAV40
TRAV39
TRAV36DV7
TRAV35
TRAV34
TRAV30
TRAV29DV5
TRAV27
TRAV25
TRAV24
TRDV1
TRAV23DV6
TRAV22
TRAV21
TRAV20
TRAV19
TRAV18
TRAV17
TRAV16
TRAV14DV4
TRAV10
TRAV7
TRAV6
TRAV5
TRAV4
TRAV3
TRAV2
RN7SL650P
SNORD8
SNORD9
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
OR4Q2
snoU13|ENSG00000238492.1
MED15P6
LINC00516
MED15P1
SERPINA3
ACTN1
ACYP1
ANG
APEX1
ARG2
ARHGAP5
BCL2L2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
CDKN3
CEBPE
CFL2
FOXN3
CHGA
CKB
CMA1
LTB4R
CRIP1
CRIP2
CTSG
DAD1
COCH
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FKBP3
FOXG1
FOS
FUT8
GALC
GCH1
GMFB
GPX2
GSTZ1
GTF2A1
BRF1
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
MGAT2
CTAGE5
ATXN3
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
NRL
OTX2
OXA1L
PAX9
SERPINA5
PCK2
PGF
SERPINA1
SERPINA4
PIGH
PNN
POLE2
PPM1A
PPP2R5C
PRKCH
PRKD1
LGMN
PSEN1
PSMA3
PSMA6
PSMB5
PSMC1
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
MOK
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPS29
RTN1
SALL2
SEL1L
SRSF5
SLC8A3
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGM1
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
GEMIN2
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
AP1G2
SLC7A7
MTA1
NEMF
PNMA1
RPS6KA5
CPNE6
AKAP6
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
AREL1
TOX4
TECPR2
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
FBLN5
BATF
TM9SF1
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
EDDM3A
DHRS4
PAPOLA
ACOT2
TMED10
FERMT2
RIPK3
PTPN21
AP4S1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
VASH1
ATG14
ZBTB1
SNW1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
RCOR1
SYNE2
PACS2
SCFD1
KHNYN
ANGEL1
PPP1R13B
SLC7A8
ZFYVE26
TTC9
KLHDC2
FLRT2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
CHMP4A
STXBP6
GPR132
POMT2
STRN3
SLC39A2
COQ6
EMC9
ATL1
FCF1
RDH11
SERPINA10
ZNF219
COX16
GMPR2
SLC22A17
DACT1
EVL
GSKIP
CINP
MBIP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
GNG2
KLHL28
TMEM260
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
CDCA4
NRDE2
RNF31
ATG2B
RBM23
UBR7
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SLC39A9
G2E3
FLVCR2
OSGEP
GPATCH2L
SMEK1
ARHGEF40
BTBD7
AP5M1
TDP1
ZNF839
SPATA7
EAPP
YLPM1
METTL3
LTB4R2
KCNK13
SDR39U1
DDX24
RPGRIP1
ADCK1
TMEM63C
PELI2
RHOJ
NDRG2
GALNT16
PLEKHH1
NYNRIN
TXNDC16
TRMT5
UNC79
HOMEZ
BEGAIN
CHD8
FANCM
PPP4R4
ZNF410
NGB
RBM25
SNX6
SAV1
C14orf93
ABHD4
VIPAS39
NPAS3
SMOC1
MOAP1
EDDM3B
IRF2BPL
MPP5
CDH24
INF2
PCNXL4
METTL17
IL25
GNPNAT1
OTUB2
ZFYVE21
THTPA
OR4K5
WDR25
OR4K1
METTL21D
LINC00341
ZC2HC1C
IPO4
CLMN
CATSPERB
ZC3H14
RIN3
L2HGDH
C14orf159
CCDC176
NUBPL
DCAF11
TMEM121
DDHD1
OR4K15
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
FSCB
SETD3
BRMS1L
HHIPL1
JPH4
C14orf142
RNASE7
INSM2
RAB2B
AJUBA
STON2
ZFHX2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
LRRC16B
PPP1R3E
TMEM55B
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
MAPK1IP1L
EGLN3
DTD2
IFT43
L3HYPDH
AHNAK2
TRIM9
TRMT61A
DHRS1
CMTM5
MIA2
TDRD9
ANKRD9
AK7
IFI27L1
C14orf28
TRAPPC6B
PLD4
ADSSL1
RNASE11
TPPP2
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
KLHL33
RPL10L
RDH12
GSC
SERPINA12
PRIMA1
MIPOL1
PPP1R36
SLC38A6
ABHD12B
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
MDP1
TTC7B
LRFN5
FAM71D
TMEM229B
SYNE3
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
NOP9
EML5
SPTSSA
ADCY4
C14orf183
RALGAPA1
SFTA3
NUDT14
LINC00521
SERPINA11
C14orf182
GPR137C
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
TSSK4
FAM177A1
CEP170B
C14orf80
DHRS4L2
C14orf39
CCDC85C
SERPINA9
RNASE10
VSX2
OR6S1
SLC35F4
LRRC9
COX8C
ASPG
RAB15
C14orf23
TOMM20L
SERPINA13P
C14orf64
RTL1
TMEM179
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
PLEKHD1
C14orf180
POTEG
MIR127
MIR136
MIR154
MIR203
OR11H12
RNASE13
LINC00238
CCDC88C
OR4Q3
OR4M1
MIR323A
MIR337
MIR345
MIR370
RNASE12
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
POTEM
TMEM253
CBLN3
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4307
MIR548Y
MIR4505
MIR4708
MIR151B
MIR4710
MIR4707
MIR2392
MIR5694
MIR5580
LINC00609
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.33.

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

Genes
PTEN
BMPR1A
FGFR2
TLX1
NFKB2
SUFU
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19|ENSG00000222588.1
SNORA19|ENSG00000207468.1
U3|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13|ENSG00000239125.1
SMNDC1
RN7SL450P
U4|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112|ENSG00000253068.1
FGF8
snoU13|ENSG00000239091.1
SNORD112|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12|ENSG00000212464.1
ERLIN1
snoU13|ENSG00000238472.1
COX15
ENTPD7
snoU13|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13|ENSG00000238991.1
ANKRD22
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
AGAP11
U3|ENSG00000252189.1
MIR346
RNA5SP322
RN7SKP238
RN7SKP84
LINC00858
RGR
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
FAS
ARL3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
CPN1
CTBP2
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
GLUD1
GOT1
PRLHR
GRK5
GRID1
HABP2
HELLS
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
DCLRE1A
FRAT1
ACTR1A
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
NRG3
MGEA5
PRDX3
ADIRF
VAX1
ATE1
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
LRIT1
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
GHITM
PDCD4
VENTX
R3HCC1L
POLL
BLNK
KCNIP2
CUZD1
CALY
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
CCSER2
EXOC6
FAM35A
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
WBP1L
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
WDR11
FAM178A
DHX32
TDRD1
BCCIP
C10orf2
TM9SF3
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
MCMBP
C10orf95
PLEKHS1
PDZD7
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
TSPAN14
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
FAM213A
DYDC2
PCGF5
GPR123
LZTS2
LCOR
MRPL43
AFAP1L2
PYROXD2
USMG5
ATAD1
ARHGAP19
KNDC1
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
OPN4
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
C10orf32
GSTO2
SFR1
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
TRUB1
VTI1A
HECTD2
FGFBP3
C10orf82
CACUL1
SLC35G1
CCDC147
PWWP2B
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
FUOM
JAKMIP3
STK32C
RBM20
FFAR4
KCNK18
LIPM
CYP26C1
NANOS1
LRIT2
HMX3
CCDC172
SH2D4B
C10orf99
SLC16A12
CC2D2B
ARMS2
TEX36
C10orf120
FOXI2
GOLGA7B
C10orf85
C10orf62
IFIT1B
FRG2B
SPRN
MIR146B
MIR202
FAM196A
FAM25A
LIPK
LIPN
MIR607
NUTM2A
NUTM2D
TLX1NB
C10orf131
KLLN
MIR1307
MIR2110
MIR378C
MIR3157
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601
Genes in Wide Peak

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

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

Genes
GATA3
ACBD7
MEIG1
CDNF
RNA5SP302
RNA5SP301
RNA5SP300
MIR4480
RNU6ATAC39P
SNORD45|ENSG00000252438.1
RN7SL198P
RN7SL232P
snoU13|ENSG00000238900.1
U6|ENSG00000272507.1
LINC00710
SFTA1P
LINC00709
RNA5SP299
LINC00708
TAF3
LINC00707
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PHYH
PRKCQ
PRPF18
AKR1C3
CDC123
USP6NL
OPTN
NET1
PITRM1
CELF2
ZMYND11
NUDT5
WDR37
SEPHS1
KIN
DIP2C
LARP4B
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
CAMK1D
SFMBT2
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
ITIH5
AKR1E2
FAM107B
CCDC3
FBXO18
RBM17
IDI2
UCN3
UCMA
BEND7
PROSER2
LINC00200
PRR26
MIR1265
MIR548Q
MIR4293
MIR548AK
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q14.3.

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

Genes
ACSL3
HOXD11
TTL
ALK
ATIC
CHN1
CREB1
DNMT3A
ERCC3
MSH6
HOXD13
IDH1
MSH2
MYCN
NFE2L2
PAX3
PMS1
REL
PAX8
NCOA1
EML4
BCL11A
FEV
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
snoU13|ENSG00000238736.1
snoU13|ENSG00000238428.1
CXCR2P1
DIRC3
RN7SKP43
RNA5SP120
RPL37A
MREG
LINC00607
snoU13|ENSG00000238663.1
SNORA70|ENSG00000207274.1
VWC2L
MIR4438
MIR548F2
RNA5SP119
RPE
RNA5SP118
RNA5SP117
CRYGEP
snoU13|ENSG00000238582.1
RNA5SP116
MIR2355
FASTKD2
RN7SKP260
RN7SKP200
SNORA41|ENSG00000207406.1
SNORD51|ENSG00000207047.2
NDUFS1
Vault|ENSG00000252485.1
RN7SKP178
RN7SL670P
SNORA1|ENSG00000202059.1
WDR12
RN7SL40P
RN7SL753P
SNORD11|ENSG00000238317.1
SNORD11B
SNORD70|ENSG00000212309.1
SNORD70|ENSG00000212534.1
snoU13|ENSG00000238770.1
RN7SL694P
ORC2
RNA5SP115
AOX2P
RN7SL717P
PLCL1
RFTN2
MOB4
SNORA4|ENSG00000202434.1
C2orf66
SCARNA16|ENSG00000252923.1
RN7SL820P
snoU13|ENSG00000239161.1
SNORD59|ENSG00000252517.1
PCGEM1
NABP1
RN7SKP179
TMEM194B
MIR3129
MIR1245A
DIRC1
GULP1
RNA5SP114
RN7SKP42
U8|ENSG00000212581.1
snoU13|ENSG00000238306.1
SNORA77|ENSG00000221498.1
DNAJC10
RN7SL267P
RNA5SP113
RNU6ATAC19P
SNORA43|ENSG00000202216.1
snoU13|ENSG00000238339.1
ACA59|ENSG00000252000.1
PLEKHA3
TTC30A
TTC30B
snoU13|ENSG00000238295.1
MIR3128
RNA5SP112
RNU6ATAC14P
HOXD9
EVX2
KIAA1715
ATP5G3
SP9
RN7SL65P
snoU13|ENSG00000239041.1
PDK1
snoU13|ENSG00000238572.1
METAP1D
snoU13|ENSG00000238567.1
ERICH2
U3|ENSG00000252981.1
SNORA51|ENSG00000206961.1
G6PC2
MIR4774
RN7SL813P
RN7SL95P
snoU13|ENSG00000238662.1
RN7SKP152
RN7SL455P
RNA5SP111
RNA5SP110
SNORA70F
FIGN
RNA5SP109
GCA
snoU13|ENSG00000238570.1
TBR1
RN7SL423P
MIR4785
RMRPP3
MARCH7
snoZ5
RN7SL393P
RN7SKP281
GALNT5
snoU13|ENSG00000238481.1
snoU13|ENSG00000238543.1
RNA5SP107
SNORD56|ENSG00000200377.1
ARL5A
RN7SL124P
SNORA48|ENSG00000212181.1
RNA5SP106
snoU13|ENSG00000238860.1
snR65|ENSG00000253036.1
TEX41
RN7SL283P
SNORA72|ENSG00000206901.1
RN7SKP286
NXPH2
RNA5SP105
RN7SKP141
SNORA40|ENSG00000208308.1
snoU13|ENSG00000238337.1
MIR5590
RNA5SP104
RN7SKP93
RN7SKP154
RN7SKP103
RN7SL701P
MIR4784
CYP4F31P
SCARNA4|ENSG00000252829.2
CYP4F30P
CFC1
POTEI
CYP4F43P
snoU13|ENSG00000238546.1
RNA5SP103
RN7SL206P
RNY4P7
RNA5SP102
RN7SKP102
snoU13|ENSG00000238341.1
RNU4ATAC
TMEM185B
snoU13|ENSG00000238368.1
PCDP1
RN7SL468P
RN7SL111P
HTR5BP
snoU13|ENSG00000238520.1
U3|ENSG00000212182.1
snoU13|ENSG00000239077.1
MIR4782
RPL23AP7
FAM138B
IL1A
CKAP2L
NT5DC4
snoU13|ENSG00000238951.1
RN7SL297P
LIMS3L
LIMS3|ENSG00000257207.4
LINC00116
MIR4436B2
SH3RF3
SULT1C2P1
RGPD4
GACAT1
CD8BP
PLGLA
C2orf49
POU3F3
SNORA72|ENSG00000207249.1
U3|ENSG00000199727.1
MFSD9
MIR4772
FLJ20373
CREG2
SNORD89
RN7SL548P
RN7SL360P
snoU13|ENSG00000238328.1
PDCL3
RN7SL611P
MRPL30
COX5B
ANKRD36B
RN7SL313P
snoU13|ENSG00000238760.1
RNA5SP101
CNNM3
MIR3127
FER1L5
CIAO1
TMEM127
FAHD2CP
RN7SL210P
ANKRD36C
LINC00342
FLJ14082
RN7SL575P
ANKRD20A8P
SLC9B1P2
RNA5SP100
IGKJ1
IGKJ2
IGKJ3
IGKJ4
IGKJ5
IGKC
ANKRD36BP2
FOXI3
snoU13|ENSG00000239049.1
RNY4P15
snoU13|ENSG00000238979.1
RGPD2
PLGLB2
PLGLB1
SNORA19|ENSG00000251974.1
U8|ENSG00000202537.1
MIR4779
SNORD94
RN7SKP83
ATOH8
C2orf68
RNF181
RN7SL126P
RN7SL830P
RN7SL251P
RN7SL113P
SNORD112|ENSG00000252298.1
RN7SL201P
RNA5SP99
REG1P
RNA5SP98
RN7SKP164
RN7SKP203
MRPL19
snoU13|ENSG00000239018.1
U3|ENSG00000221638.1
snoU109|ENSG00000238410.1
snoU13|ENSG00000238521.1
POLE4
SEMA4F
PCGF1
CCDC142
MRPL53
C2orf81
MTHFD2
MOB1A
MGC10955
RNA5SP97
NOTO
SNORD78|ENSG00000212378.1
RN7SL160P
snoU13|ENSG00000239064.1
RN7SL470P
snoU13|ENSG00000239072.1
snoU13|ENSG00000238465.1
SNRNP27
GMCL1
snoU13|ENSG00000238708.1
SNORA36C
RN7SL604P
AAK1
RNA5SP96
MIR3126
FBXO48
C1D
Vault|ENSG00000251900.1
RN7SL635P
SNORA74|ENSG00000272025.1
snoU13|ENSG00000238696.1
RN7SL211P
RN7SL341P
LINC00309
ACA59|ENSG00000251775.1
RPS4XP5
DBIL5P2
RN7SL18P
snoU13|ENSG00000238809.1
RN7SL51P
COMMD1
SNORA70B
C2orf74
RNA5SP95
RN7SL632P
RN7SL361P
RNA5SP94
SNORD78|ENSG00000212168.1
snoU13|ENSG00000238690.1
RNA5SP93
RN7SKP208
SNORA12|ENSG00000212175.1
PRORSD1P
MIR3682
snoU13|ENSG00000238756.1
ASB3
SCARNA16|ENSG00000251942.1
SNORA75|ENSG00000212580.1
RN7SKP224
KCNK12
MIR559
RN7SKP119
BCYRN1
RHOQ
RN7SL817P
RN7SL414P
SLC3A1
snoU13|ENSG00000239052.1
RN7SKP66
SNORD75|ENSG00000221300.1
snoZ247
HNRNPA1P57
SNORA67|ENSG00000252473.1
RN7SL96P
GEMIN6
LINC00211
RN7SL602P
RNA5SP92
RNA5SP91
SNORD112|ENSG00000252502.1
LINC00486
MIR4765
MIR558
YIPF4
DPY30
SRD5A2
EHD3
RNA5SP90
SNORA64|ENSG00000207187.1
RN7SL516P
SNORD53
SNORD92
RNA5SP89
FOSL2
MIR4263
RBKS
SNORA36|ENSG00000206731.1
UCN
TCF23
KCNK3
RN7SL856P
EFR3B
SNORD14
PTRHD1
RNA5SP88
SCARNA21|ENSG00000251805.1
PFN4
RN7SL610P
UBXN2A
RN7SKP27
RNA5SP87
RN7SL117P
TDRD15
GDF7
RNA5SP86
RN7SL140P
LINC00954
SNORA40|ENSG00000212455.1
RN7SKP168
SNORA40|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13|ENSG00000238371.1
LINC00276
MIR3125
SNORD18|ENSG00000238503.1
MIR548S
RN7SL674P
RNA5SP85
RNA5SP84
LINC00570
RN7SL832P
SNORA80B
SNORA51|ENSG00000206898.1
RN7SL66P
SNORA2|ENSG00000206647.1
SNORA26|ENSG00000212558.1
snoU13|ENSG00000238462.1
IAH1
snoU13|ENSG00000238888.1
MBOAT2
RNU6ATAC37P
RN7SKP112
FLJ30594
SNORA31|ENSG00000252238.1
RN7SL531P
DCDC2C
SNORA73|ENSG00000252531.1
snoU13|ENSG00000238722.1
TMEM18
FAM110C
AAMP
ACADL
ACP1
ACTG2
ACVR1
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
AGXT
ALPI
ALPP
ALPPL2
BIN1
ANXA4
AOX1
APOB
RHOB
RND3
ATP6V1B1
KIF1A
AUP1
BARD1
BCS1L
BMPR2
BOK
ZFP36L2
BUB1
CACNB4
CAD
CALM2
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CENPA
CHRNA1
CHRNG
CLK1
CNGA3
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CTNNA2
CYP1B1
CYP27A1
DARS
DBI
DCTN1
DDX1
DES
DGUOK
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DTNB
DTYMK
DUSP2
E2F6
EEF1B2
EGR4
EMX1
EN1
EPAS1
EPHA4
ERBB4
FABP1
FAP
EFEMP1
FHL2
FKBP1B
FN1
FRZB
FSHR
GAD1
GALNT3
GBX2
GCG
GCKR
MSTN
GFPT1
GGCX
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GTF3C2
GYPC
HADHA
HADHB
HDLBP
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD10
HOXD12
HPCAL1
AGFG1
DNAJB2
HSPD1
HSPE1
FOXN2
HTR2B
ID2
SP110
IGFBP2
IGFBP5
IHH
IL1B
IL1R1
IL1RN
CXCR1
CXCR2
INHA
INHBB
INPP1
INPP4A
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNF1
KCNJ3
KCNJ13
KCNS3
KHK
KIF3C
KIF5C
AFF3
LCT
LHCGR
LIMS1
LRP2
LTBP1
LY75
EPCAM
MXD1
MAL
MAP2
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MYO1B
MTIF2
MYL1
MYO7B
NAB1
NEB
NDUFA10
NDUFB3
SEPT2
NEU2
NEUROD1
NPAS2
NPHP1
NR4A2
ODC1
ORC4
OTX1
REG3A
PCBP1
PDCD1
PDE1A
PDE6D
PEX13
VIT
SERPINE2
PIGF
PLEK
POLR2D
POMC
PPM1B
PPM1G
PPP1CB
PPP1R7
PPP3R1
PRKCE
EIF2AK2
PROC
PSMD1
PTH2R
PTMA
PTPN4
PTPRN
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
RPL31
RPS7
RPS27A
RRM2
RTKN
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
CCL20
SDC1
SRSF7
SFTPB
SIX3
SLC4A3
SLC1A4
SLC8A1
SLC9A2
SLC11A1
SLC20A1
SNRPG
SOS1
SOX11
SP3
SP100
SPAST
SPP2
SPR
SPTBN1
SSB
SSFA2
STAT1
STAT4
STRN
SULT1C2
ADAM17
TACR1
GCFC2
TFPI
TGFA
TIA1
TNFAIP6
TNP1
TNS1
TPO
TSN
TSSC1
TTN
TUBA4A
SUMO1
UGP2
VRK2
VSNL1
WIPF1
WNT6
XDH
XPO1
XRCC5
ZAP70
ZNF2
ZNF142
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
FZD5
SCG2
DYSF
FZD7
SDPR
NCK2
DUSP11
CUL3
KLF11
MAP4K3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ASAP2
PER2
ST3GAL5
SLC5A6
DDX18
EIF2B4
CDK5R2
KYNU
TAF1B
NAT8
NMI
RQCD1
COX7A2L
TMSB10
IL1RL1
LRRFIP1
STK17B
ITGB1BP1
GPR55
TRIP12
GTF3C3
PPIG
NRXN1
OTOF
TGFBRAP1
HS6ST1
CRIPT
ECEL1
MAP4K4
EIF2AK3
EIF4E2
ROCK2
CHST10
TP53I3
CIR1
MRPL33
BRE
PREPL
CYTIP
FEZ2
GCC2
TTLL4
SOCS5
EIF5B
GREB1
BZW1
USP34
LAPTM4A
HDAC4
RNF144A
SNX17
SERTAD2
ZEB2
FARP2
TLK1
SUPT7L
CD302
ARHGAP25
TANK
BCL2L11
FARSB
ABCB6
ACTR3
ACTR2
ARPC2
PREB
ACTR1B
ARL4C
LRPPRC
PDIA6
ABI2
CEBPZ
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
SMYD5
KLHL41
MERTK
UBE2E3
STK25
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
MTX2
CGREF1
B3GNT2
USP39
SIX2
MAP3K2
NCKAP1
VAMP5
ARID5A
PROKR1
RAB10
EDAR
GPR75
YWHAQ
IMMT
GTF2A1L
STON1
RAPGEF4
EMILIN1
CAPN10
TBC1D8
RABL2A
GPR45
SP140
MGAT4A
GPN1
IKZF2
COBLL1
MAPRE3
PLA2R1
RAB3GAP1
RPIA
SLC4A1AP
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
PASK
UBXN4
ATG4B
PSME4
EXOC6B
EHBP1
SATB2
CLASP1
OBSL1
PUM2
NCAPH
SF3B1
HAAO
TMEM131
R3HDM1
DNPEP
PSD4
WBP1
NTSR2
TMEFF2
SH3BP4
PRKD3
KCNE4
RASGRP3
NGEF
QPCT
VAX2
MOB4
POLR1A
CNRIP1
FAM98A
PNKD
UNC50
SNED1
GORASP2
SPATS2L
RAB11FIP5
GIGYF2
EPC2
TRAF3IP1
ABCA12
IFT172
HIBCH
PTPN18
CNNM4
IL36RN
SH3YL1
CNPPD1
STK36
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
MMADHC
BMP10
ZNF638
STK39
HTRA2
TRIB2
METTL5
LGALSL
OLA1
C2orf27A
GRHL1
TFCP2L1
ICOS
GMPPA
NRBP1
BAZ2B
SLC40A1
KCNIP3
SMARCAL1
CD207
ITSN2
ANO7
ARHGEF4
PDE11A
TPRKB
FAHD2A
PRLH
WDPCP
MEMO1
THAP4
TRAPPC12
INSIG2
CRIM1
ANKRD39
FAM178B
C2orf15
DNAJC27
ANKMY1
KRCC1
MRPL35
ATRAID
PCYOX1
REV1
SCLY
VPS54
NBAS
LIPT1
NOP58
DYNC2LI1
SF3B14
YPEL5
FKBP7
ASB1
CPSF3
CAB39
MLTK
LRP1B
PRKAG3
PPIL3
SNTG2
ATAD2B
ETAA1
HEATR5B
CCDC93
ASNSD1
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
AFTPH
MFSD6
TMEM214
RETSAT
INO80D
SEMA4C
SLC35F6
C2orf42
TRMT61B
PID1
PTCD3
PLEKHB2
ATG16L1
FANCL
SRBD1
ANKZF1
RIF1
USP40
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
HJURP
STRADB
NDUFAF7
HES6
ASIC4
CNOT11
NAGK
DOCK10
TTC27
SMPD4
PRPF40A
SLC30A6
IWS1
LIMS2
KANSL3
CCDC88A
MBD5
KDM3A
ALLC
PECR
ARHGAP15
ZC3H15
DNAH7
GKN1
IL36G
RPRM
CYP26B1
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
C2orf83
MFF
ACKR3
RTN4
TRIM54
PELI1
SLC39A10
TTC7A
SMEK2
SLC4A10
CYP20A1
SPC25
BIRC6
ERMN
KIDINS220
MTA3
HECW2
WDR35
MARCH4
WDFY1
NYAP2
DPP10
RDH14
EPB41L5
ALS2
ZDBF2
USP37
CWC22
SLC4A5
CTDSP1
NLRC4
MPP4
SLC5A7
NIF3L1
AGBL5
C2orf43
THADA
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
ATL2
ABCG5
ABCG8
RAB17
RNF25
HS1BP3
TTC31
ANAPC1
COPS7B
RMND5A
FNDC4
PAPOLG
MRPS9
MRPS5
REEP1
RAPH1
CDK15
TMEM237
NBEAL1
MRPL44
SOWAHC
TRAK2
BOLL
COLEC11
TRPM8
ATG9A
MLPH
FAM134A
CENPO
GLB1L
C2orf47
SPAG16
CHPF
SAP130
GALNT14
SCRN3
CCDC121
FASTKD1
SMC6
GTDC1
CLIP4
IQCA1
CARF
TTC21B
CAMKMT
METTL8
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
NOL10
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
TUBA4B
MZT2B
MAP3K19
UXS1
FBXO11
ARMC9
COQ10B
SLC35F5
EFHD1
C2orf44
SPHKAP
WNT10A
SLC19A3
TSGA10
THSD7B
THUMPD2
TMEM177
ILKAP
FAM49A
LMAN2L
LBH
TMEM163
ITM2C
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM161A
EVA1A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
RHBDD1
CHCHD5
PRADC1
C2orf88
ING5
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
MCEE
LOXL3
ABHD1
PLCD4
SFT2D3
ZNF514
FAM136A
TMEM87B
FLJ14816
TANC1
EPT1
LBX2
PNPT1
KCNH7
MCFD2
ATP6V1E2
CCDC74A
DHX57
SESTD1
CCDC74B
PKDCC
ANKRD44
RSAD2
ZNF804A
DAPL1
CAPN13
TMEM169
DNER
DRC1
IMP4
HNRNPLL
MARS2
B3GNT7
NT5C1B
NEURL3
SP140L
SFXN5
ORMDL1
LIMS3|ENSG00000256977.6
LINC00152
TUBA3E
CCDC104
TEX261
TUBA3D
STK11IP
FMNL2
CCDC85A
GALNT13
KLHL29
OSBPL6
NOSTRIN
WDR92
MOGAT1
LYPD1
AGAP1
TWIST2
PARD3B
PPP1R21
TRABD2A
TMEM150A
NUP35
XIRP2
TYW5
NMS
LYG1
MITD1
DIS3L2
CMPK2
CNTNAP5
FBLN7
NEU4
RBM45
C2orf73
TRIM43
BBS5
CCDC173
ACMSD
ICA1L
FAM168B
CIB4
REG3G
CLHC1
PLEKHH2
AP1S3
C2orf76
ACVR1C
OSR1
TTC32
UBR3
KCTD18
ALS2CR12
ZNF513
SPATA3
LYPD6
LYPD6B
GALM
TMEM198
ZFAND2B
TMEM178A
CPO
MDH1B
C2orf50
PQLC3
TMEM182
AHSA2
FBXO36
MTERFD2
CCDC148
M1AP
MYO3B
TMEM37
UBE2F
DUSP19
CBWD2
TEKT4
SMYD1
OTOS
MYEOV2
OR6B3
PROM2
ANKAR
FBXO41
GPAT2
ITPRIPL1
FAM117B
GAREML
PUS10
SEPT10
KANSL1L
PLB1
ZSWIM2
ZNF385B
ARL6IP6
METTL21A
CCNYL1
KLHL23
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
GPBAR1
FAHD2B
MYADML
FAM84A
RMDN2
SLC16A14
LINC00471
ASPRV1
WDSUB1
UPP2
GPR155
DAW1
LONRF2
CCDC138
GPR113
C2orf57
OXER1
FAM179A
FAM171B
C1QL2
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
VWA3B
ALMS1P
TET3
GKN2
TEX37
ANKRD23
APLF
PIKFYVE
KRTCAP3
TMEM17
SPRED2
TIGD1
AMER3
C2orf69
HNRNPA3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
GPATCH11
CERS6
LYG2
CCDC108
C2orf72
SH2D6
CCDC150
RNF149
FAM150B
CCDC141
C2orf61
DNAJC5G
FAM126B
UNC80
RUFY4
DUSP28
SPOPL
CYP27C1
MROH2A
ESPNL
C2orf70
C2orf53
LINC00299
MSGN1
KIAA1211L
FIGLA
NCKAP5
CDKL4
GPR148
LRRTM1
GEN1
C2orf48
FTCDNL1
FAM228B
ANKRD36
WASH2P
RBM43
CERKL
C2orf62
AQP12A
ZC3H6
KLHL30
MFSD2B
C2orf71
TMEM247
TSPYL6
C2orf78
BOLA3
FUNDC2P2
SLC9A4
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
SULT6B1
DYTN
LINC00487
C2orf91
EML6
PAIP2B
RGPD1
FSIP2
ASB18
MIR10B
MIR216A
MIR217
C2orf27B
ASTL
CAPN14
SULT1C3
POTEE
COA5
PHOSPHO2
CHAC2
MIR375
DFNB59
ANKRD30BL
PRR21
PRSS56
FAM228A
CFC1B
AQP12B
RGPD3
POTEJ
MZT2A
MIR561
RGPD8
D2HGDH
POTEF
RAD51AP2
RGPD6
MORN2
RFX8
MIR216B
MIR933
OST4
ARHGEF33
MIR1471
MIR1258
MIR1301
MIR663B
MIR4265
MIR4264
MIR4261
MIR4268
MIR4267
MIR4262
MIR4266
MIR3132
MIR4269
MIR3679
MIR3681
CHMP3
MIR4783
MIR4437
MIR4433
MIR548AE1
MIR4757
MIR4775
MIR4436A
MIR4786
MIR4431
MIR4780
MIR4778
MIR4429
MIR4432
MIR548AD
MIR5000
MIR5696
MIR4436B1
MIR5001
MIR5702
MIR5703
MIR5192
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq11.2.

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

Genes
RN7SL799P
ARHGEF9
MTMR8
AMER1
ASB12
MIR1468
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.3.

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

Genes
FGFR1OP
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
GOPC
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13|ENSG00000239136.1
AIRN
SNORA29
SNORA20|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
snoU13|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18|ENSG00000252249.1
U3|ENSG00000221455.1
U3|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73|ENSG00000222145.1
RN7SL183P
snoU13|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70|ENSG00000206886.1
RNA5SP210
SNORD112|ENSG00000252932.1
HTR1B
U6|ENSG00000272445.1
snoU13|ENSG00000239132.1
RNA5SP209
RN7SKP163
U3|ENSG00000221332.1
MB21D1
snoU13|ENSG00000238464.1
OOEP
OGFRL1
U3|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65|ENSG00000212229.1
FKBP1C
LINC00680
ACAT2
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1E
IFNGR1
IGF2R
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
ME1
MAP3K4
MAP3K5
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLG
PLN
POU3F2
PREP
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TBP
TCF21
TCP1
TCTE3
DYNLT1
THBS2
NR2E1
TPBG
TPD52L1
TTK
UTRN
EZR
VIP
PTP4A1
EPM2A
DDO
RNASET2
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
WTAP
AKAP12
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
PHF3
HEY2
ORC3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
SENP6
TIAM2
FBXL4
C6orf123
FBXO5
SLC17A5
RGS17
PDE7B
FILIP1
SESN1
DLL1
OSTM1
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
LGSN
MPC1
HECA
COQ3
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
PHF10
QRSL1
VNN3
DDX43
FAM46A
TMEM30A
C6orf70
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
PDSS2
SMIM8
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
ABRACL
RRAGD
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
SMOC2
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
RSPH3
ARMC2
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
GJA10
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
UBE3D
ARHGAP18
SYTL3
GTF3C6
MRAP2
MTFR2
KLHL32
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAGAP
RIPPLY2
IRAK1BP1
TAAR9
TAAR1
NCOA7
HINT3
PACRG
CD109
RAET1E
PM20D2
SRSF12
ZC2HC1B
RAET1L
SAMD3
PNLDC1
RNF217
NKAIN2
KHDC3L
C6orf165
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
KHDRBS2
C6orf163
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
MMS22L
WDR27
MCM9
SHPRH
CEP57L1
PPIL6
DCBLD1
PRR18
TAAR6
SLC35D3
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GJB7
SUMO4
CENPW
SOGA3
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
MIR30A
MIR30C2
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR587
MIR588
METTL24
TMEM242
TRAPPC3L
KHDC1L
MIR2113
MIR1202
MIR1273C
MIR548U
MIR3144
MIR4282
MTRNR2L9
MIR3918
MIR3939
MIR3668
SMLR1
MIR4464
MIR4466
MIR4643
MIR4465
MIR548AJ1
MIR548AI
MIR4463
MIR548H5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q12.

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

Genes
ATF1
CDK4
DDIT3
HOXC11
HOXC13
NACA
HMGA2
WIF1
DYRK2
CAND1
snoU13|ENSG00000238528.1
RN7SKP166
TMBIM4
RNA5SP362
RPSAP52
RNU6ATAC42P
snoU13|ENSG00000238592.1
MIR548C
SNORD83
XPOT
snoU13|ENSG00000238440.1
RPS11P6
AVPR1A
LDHAL6CP
snoU13|ENSG00000238475.1
SNORD112|ENSG00000252883.1
SNORA19|ENSG00000251822.1
RN7SKP65
MIR26A2
snoU13|ENSG00000238436.1
RN7SL312P
MIR1228
HBCBP
RDH16
SNORA48|ENSG00000212383.1
RN7SL809P
SNORD59A
RBMS2
RNF41
RN7SL770P
MMP19
TMEM198B
ORMDL2
GLYCAM1
RN7SL744P
MIR148B
RN7SL390P
MIR615
HOXC8
HOTAIR
HOXC12
RN7SKP289
SNORD81|ENSG00000223213.1
KRT121P
LINC00592
C12orf80
OR7E47P
POU6F1
U6|ENSG00000272028.1
HIGD1C
RN7SL519P
MIR1293
AQP6
AQP5
BCDIN3D
PRPH
WNT1
snoU13|ENSG00000238395.1
MIR4701
SNORA2B
SNORA2A
SNORA34
DKFZP779L1853
RPAP3
SNORA64|ENSG00000199566.1
SCAF11
RN7SL246P
RNA5SP361
SNORA74|ENSG00000252917.1
RN7SL10P
RNA5SP360
MUC19
SNORA22|ENSG00000199571.1
ABCD2
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112|ENSG00000251863.1
SNORA25|ENSG00000252204.1
STMN1P1
ASIC1
ACVR1B
ACVRL1
ADCY6
AMHR2
APOF
AQP2
ARF3
ATP5B
ATP5G2
BICD1
CACNB3
CCNT1
CD63
CDK2
CNTN1
COL2A1
CS
CYP27B1
DGKA
EIF4B
CELA1
ERBB3
B4GALNT1
BLOC1S1
GLI1
GNS
GPD1
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC9
HOXC10
IFNG
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
LRP1
MARS
METTL1
MIP
MYL6
MYO1A
NAB2
NELL2
NFE2
SLC11A2
PA2G4
PCBP2
PDE1B
PFDN5
PFKM
PKP2
PPP1R1A
PRIM1
PRKAG1
TWF1
RAB5B
RARG
RDH5
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
PMEL
SMARCC2
SMARCD1
SP1
STAT2
STAT6
SUOX
TAC3
TARBP2
TMBIM6
TFCP2
VDR
WNT10B
MAP3K12
TUBA1A
KMT2D
AAAS
SOAT2
NPFF
HSD17B6
ENDOU
TIMELESS
KRT75
SLC16A7
DDX23
SLC4A8
ESPL1
DAZAP2
TESPA1
ZBTB39
PAN2
USP15
TROAP
DNM1L
TSFM
CTDSP2
YAF2
GDF11
TMEM5
CNPY2
TUBA1B
RAPGEF3
MCRS1
DCTN2
AVIL
PTGES3
OS9
ATF7
BAZ2A
IRAK3
GALNT6
NXPH4
GPR182
COPZ1
R3HDM2
FAIM2
MON2
DDN
TMEM194A
TBC1D30
ESYT1
TENC1
KCNH3
GRIP1
CBX5
ANP32D
SMUG1
LEMD3
PRPF40B
METTL7A
LETMD1
METTL21B
ZNF385A
GLS2
RND1
TBK1
RACGAP1
SENP1
PDZRN4
DHH
PLEKHA8P1
YARS2
IRAK4
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
IL23A
HDAC7
TMBIM4
GPR84
SLC38A2
PRR13
KANSL2
SLC38A4
KIAA1551
KIF21A
SLC48A1
LMBR1L
NDUFA4L2
SMAGP
PPM1H
SRGAP1
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
C12orf10
C12orf44
ARHGAP9
IKZF4
SLC26A10
SPATS2
TMEM106C
NABP2
PIP4K2C
DNAJC22
ADAMTS20
SLC38A1
CSRNP2
PUS7L
INHBE
FAM186B
TMEM117
LLPH
WIBG
SARNP
TUBA1C
ZC3H10
SPRYD3
MFSD5
COX14
DNAJC14
ZCRB1
CCDC65
LACRT
FMNL3
CERS5
XRCC6BP1
PCED1B
HELB
MARCH9
COQ10A
KRT71
LARP4
SLC2A13
MBD6
ARHGEF25
C12orf56
AGAP2
DCD
MUCL1
LRRK2
FAM186A
OR2AP1
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
FGD4
ASB8
MYL6B
KRT72
PRICKLE1
CPNE8
KRT80
C12orf66
GRASP
KRT78
AMN1
DTX3
METTL7B
ANO6
ARID2
STAC3
MSRB3
METTL20
OR6C74
OR6C3
LINC00935
ZNF740
RASSF3
OR6C6
ANKRD52
SLC39A5
SPRYD4
C12orf61
DPY19L2
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
FAM19A2
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
KRT77
C12orf68
OR6C1
OR6C75
OR6C76
OR6C70
OR6C65
OR6C68
MIRLET7I
MIR196A2
H3F3C
DBX2
OR9K2
MIR616
MIR4494
MIR4698
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.33.

Table S57.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ABL1
FANCC
OMD
SET
SYK
TAL2
XPA
NR4A3
NUP214
FNBP1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13|ENSG00000238530.1
MIR455
COL27A1
FKBP15
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
snoU13|ENSG00000238746.1
RNA5SP288
MIR27B
MIR23B
MIR2278
PCAT7
ZNF169
snoU13|ENSG00000238792.1
MIRLET7DHG
CENPP
SNORA84
snoU13|ENSG00000238996.1
LINC00475
LINC00484
MIR3153
SHC3
U3|ENSG00000252299.1
U6|ENSG00000271923.1
SPATA31C1
SNORA26|ENSG00000212421.1
RN7SKP264
ABCA1
AK1
ALAD
ALDOB
AMBP
ASS1
AUH
BAAT
C5
CCBL1
CDK9
CKS2
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL
CYLC2
DAPK1
DBC1
DNM1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FOXE1
FPGS
NR5A1
GAS1
NR6A1
GLE1
GNG10
GOLGA1
GOLGA2
GSN
HSD17B3
HSPA5
TNC
IARS
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
ROR2
ODF2
OGN
ORM1
ORM2
PAPPA
PDCL
PBX3
PHF2
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGS1
PTPN3
RAD23B
RGS3
RPL12
SPTAN1
STXBP1
TGFBR1
TLR4
TMOD1
TRAF1
TXN
CORO2A
ZFP37
ZNF79
ZNF189
IKBKAP
CDC14B
TMEFF1
CTNNAL1
FBP2
DPM2
FUBP3
PRPF4
KLF4
LHX2
PTGES
GABBR2
RALGPS1
TRIM14
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
ZER1
SEMA4D
ANP32B
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
USP20
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
AKAP2
RPL35
DOLK
ZNF510
HABP4
PTGR1
TRIM32
ERP44
ZBTB43
FAM120A
ASTN2
AGTPBP1
BICD2
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
RABGAP1
TMEM245
CIZ1
DFNB31
NIPSNAP3A
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
LHX6
OR1L3
OR1L1
OR1J2
TRUB2
ST6GALNAC4
INVS
TOR1B
TOR2A
NTMT1
PKN3
SLC2A8
ST6GALNAC6
DEC1
COQ4
CERCAM
GOLM1
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
MRPL50
RC3H2
EPB41L4B
TBC1D13
NUTM2F
DIRAS2
ASPN
BSPRY
TEX10
FAM206A
NOL8
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
CDK5RAP2
BARX1
RNF20
LRRC8A
SH3GLB2
DOLPP1
ZBTB26
DENND1A
GPR107
SLC46A2
ZNF462
PRDM12
NAA35
SUSD1
IPPK
FAM129B
WNK2
SECISBP2
C9orf16
MAPKAP1
ZCCHC6
GALNT12
SVEP1
PTGES2
AKNA
ISCA1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
GARNL3
HSDL2
C9orf89
HIATL2
HIATL1
PPAPDC3
ZDHHC12
FAM73B
C9orf3
FIBCD1
FGD3
MVB12B
WDR34
LRSAM1
MRRF
KIF12
PALM2
SLC25A25
WDR31
ZNF618
GRIN3A
RNF183
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
DAB2IP
NXNL2
OR1Q1
TTLL11
TTC16
FAM120AOS
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
OLFML2A
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CDC26
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
CRB2
SCAI
C9orf117
C9orf47
SPATA31E1
FAM78A
OR13C9
OR13D1
GPR144
QRFP
OR1J1
OR1B1
MURC
ERCC6L2
SWI5
C9orf50
C9orf153
IER5L
CTSL3P
OR13C2
OR1L6
OR5C1
OR1K1
FAM102A
C9orf170
C9orf152
SNX30
WDR38
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
NUTM2G
C9orf129
DNAJC25
MIR600HG
MIR3074
MIR3154
MIR4291
MIR4290
MIR4289
CCDC180
MIR3911
MIR3927
MIR3960
MIR4478
MIR4670
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

Table S58.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
IL2
FGFR3
KDR
KIT
PDGFRA
RAP1GDS1
WHSC1
PHOX2B
DUX4
CHIC2
TET2
FBXW7
FIP1L1
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
C4orf45
U3|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
SNORD73A
SNORD73
RNA5SP168
RNA5SP167
RNA5SP166
RN7SL254P
MIR4799
RNA5SP165
TMEM184C
RN7SKP235
ANAPC10
HHIP
MIR3139
USP38
snoU13|ENSG00000238695.1
RN7SL152P
UCP1
SNORD112|ENSG00000252300.1
RN7SKP253
RN7SKP237
ACA64|ENSG00000239005.1
RN7SL311P
RN7SL382P
LINC00500
LINC00499
LINC00498
LINC00616
LINC00613
PCDH10
SNORA70|ENSG00000252014.1
RN7SL205P
RNY5P4
snoU13|ENSG00000238802.1
HSPA4L
INTU
RN7SL335P
QRFPR
RN7SKP137
MAD2L1
SNORA11|ENSG00000221245.1
C4orf3
CEP170P1
SNHG8
NT5C3AP1
MTRNR2L13
RN7SL808P
MIR577
RN7SL184P
TIFA
C4orf32
ENPEP
RN7SL275P
CCDC109B
MIR576
RN7SL55P
SNORD112|ENSG00000252566.1
GIMD1
RN7SL89P
SNORA31|ENSG00000252136.1
TACR3
BDH2
CISD2
snoU13|ENSG00000238948.1
RN7SL728P
MIR1255A
ADH1B
PCNAP1
MIR3684
EIF4E
RN7SKP28
RNA5SP164
RN7SKP248
GPRIN3
RN7SKP244
RNU6ATAC31P
IBSP
snoU13|ENSG00000238652.1
RN7SL681P
RN7SKP96
MIR4451
RN7SKP48
RN7SL552P
MRPS18C
snoR442|ENSG00000252834.1
MIR575
LINC00575
SNORD42|ENSG00000202440.1
HNRNPD
SNORA31|ENSG00000252762.1
SNORA75|ENSG00000212620.1
OR7E94P
LINC00989
NAA11
RN7SL127P
MIR5096
snoU13|ENSG00000238816.1
SNORD75|ENSG00000221711.1
MIR548AH
MIR4450
SNORD50|ENSG00000199857.1
CDKL2
BTC
PPBPP2
RN7SL218P
PPBP
PF4
PF4V1
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
RNA5SP163
snoU13|ENSG00000238318.1
CSN1S2AP
SULT1B1
UGT2A1
UGT2A2
UGT2B10
TMPRSS11BNL
FTLP10
TMPRSS11GP
SNORA62|ENSG00000202374.1
GNRHR
UBA6
TECRL
snoU13|ENSG00000238925.1
snoU13|ENSG00000238541.1
snoU13|ENSG00000238579.1
NOA1
RN7SL357P
RN7SL492P
ARL9
SRP72
RNA5SP162
KIAA1211
RNA5SP161
RN7SKP30
RN7SL822P
RN7SL424P
snoU13|ENSG00000238753.1
GSX2
SNORA26|ENSG00000212490.1
SNORA26|ENSG00000212588.1
DANCR
snoU13|ENSG00000239068.1
NIPAL1
RN7SKP215
snoU13|ENSG00000238301.1
RN7SKP199
RN7SL193P
RN7SL691P
RN7SKP82
SLC30A9
LINC00682
RNA5SP160
snoU13|ENSG00000238351.1
RHOH
SNORA51|ENSG00000201863.1
RNA5SP159
RN7SL558P
SMIM14
MIR5591
RNA5SP158
DTHD1
snoU13|ENSG00000238694.1
RN7SL101P
SNORD74|ENSG00000200999.1
RN7SL16P
snoU13|ENSG00000238383.1
RNA5SP157
FAM184B
MED28
RN7SL315P
snoU13|ENSG00000238536.1
SNORA75|ENSG00000206780.1
ZEB2P1
CD38
FAM200B
RN7SKP170
SNORA63|ENSG00000202449.1
LINC00504
HSP90AB2P
RNA5SP156
HS3ST1
CLNK
RNA5SP155
MIR3138
RNA5SP154
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADH1A
ADH1C
ADH4
ADH5
ADH6
ADH7
ADRA2C
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA3
ANXA5
APBB2
AREG
ART3
ATOH1
ATP5I
BMP3
BMPR1B
BST1
CAMK2D
CASP3
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
LRBA
CDS1
CLGN
CENPC
CENPE
CLCN3
CNGA1
CPE
CRMP1
CSN1S1
CSN2
CSN3
CTBP1
CTSO
DGKQ
DCK
DCTD
DHX15
DMP1
DRD5
DSPP
EDNRA
EGF
ELF2
EPHA5
EREG
ETFDH
EVC
F11
FABP2
ACSL1
FAT1
FGA
FGF2
FGF5
FGG
FRG1
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GC
GK2
GLRB
GPM6A
GRK4
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HTT
HGFAC
UBE2K
HMX1
HPGD
HTN1
HTN3
IDUA
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
LETM1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MSX1
MTNR1A
MTTP
MUC7
MYL5
NDUFC1
NEK1
NFKB1
NPY1R
NPY2R
NPY5R
PCDH7
PDE6B
PDHA2
PET112
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPID
PPP2R2C
PPP3CA
PRKG2
MAPK10
PTPN13
QDPR
REST
RFC1
RGS12
RNF4
ABCE1
RPL9
RPL34
RPS3A
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SH3BP2
SNCA
SOD3
SPINK2
SPP1
STATH
SULT1E1
TDO2
TEC
TLL1
TLR1
TRPC3
TXK
UBE2D3
UCHL1
UGDH
UGT2B4
UGT2B7
UGT2B15
UGT2B17
UGT8
VEGFC
WFS1
NELFA
SLBP
GLRA3
ACOX3
SPARCL1
SMARCA5
SORBS2
PRSS12
CPZ
NOP14
FAM193A
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
PROM1
HERC3
PAPSS1
LDB2
LRAT
AIMP1
NDST3
SLIT2
RAB28
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
KIAA0232
MFAP3L
SEC24D
G3BP2
WDR1
FGFBP1
HNRNPDL
TSPAN5
ENAM
C4orf6
FAM13A
MFSD10
SPRY1
MAEA
TLR6
PCGF3
ATP8A1
SPON2
PGRMC2
SEC24B
TACC3
CXCL13
SLC34A2
MAB21L2
PAICS
MXD4
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
CPLX1
HPSE
SLC26A1
NMU
SMR3B
NPFFR2
PPARGC1A
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
MAN2B2
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXL5
FBXO8
SMR3A
NSG1
PPA2
DAPP1
DKK2
NAAA
COQ2
ARFIP1
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
LAP3
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ASIC5
GALNT7
NUDT9
NUP54
STX18
FGFRL1
CLDN22
CYTL1
GAR1
SH3TC1
UGT2B28
RBM47
PCDH18
USP53
OTUD4
DCHS2
ARHGEF38
PIGG
DCAF16
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
TMA16
BLOC1S4
C4orf21
STK32B
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
CDKN2AIP
LYAR
TENM3
N4BP2
SEPT11
EXOC1
LRP2BP
TMEM165
SLC2A9
FSTL5
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
RNF150
KIAA1239
TBC1D14
SORCS2
CC2D2A
KLHL8
KIAA1430
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
UVSSA
METTL14
WDR19
ZFYVE28
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
AFAP1
GUF1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
NCAPG
NDST4
ETNPPL
USP46
MRPL1
RASL11B
ELOVL6
TNIP2
HAUS3
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
MLF1IP
THAP9
NSUN7
UGT2A3
GSTCD
MAP9
TNIP3
PHF17
SCD5
DNAJB14
TMEM156
WWC2
FRAS1
NAA15
CWH43
C4orf29
ALPK1
CXXC4
KCNIP4
CEP44
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
FGFBP2
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
FAM175A
KIAA1109
MFSD7
TMEM175
ABLIM2
HOPX
COL25A1
LNX1
MGARP
AGPAT9
CBR4
PIGY
TMEM128
CABS1
ZNF518B
FHDC1
PRMT10
CCDC149
DDX60L
YTHDC1
TMEM129
NAF1
MOB1B
FAM114A1
TRMT10A
MRFAP1
TADA2B
TBCK
HTRA3
HELQ
CYP2U1
C1QTNF7
MRFAP1L1
DDIT4L
WDR17
ARAP2
PCAT4
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
SPATA18
TMPRSS11B
GNPDA2
SPATA4
CPEB2
EVC2
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
OTOP1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
NFXL1
PAQR3
SHISA3
SCFD2
FAM218A
JAKMIP1
THAP6
C4orf26
KLB
FAM53A
PPM1K
TRMT44
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
FREM3
MMAA
ZBTB49
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
SYNPO2
C4orf46
SLC10A4
TIGD4
RWDD4
CCDC111
TAPT1
TRIML2
CNOT6L
LCORL
C4orf22
EPGN
ELMOD2
NPNT
CCDC110
MFSD8
CCDC96
BOD1L1
FDCSP
NAP1L5
DCAF4L1
CRIPAK
DOK7
RNF212
COX18
YIPF7
FRYL
RNF175
STPG2
ZAR1
CCDC158
TMPRSS11A
TRIML1
LRRC66
NAT8L
PRSS48
SOWAHB
LRIT3
SLC10A6
HSD17B13
ANKRD37
POLN
KCTD8
SMIM20
BEND4
GRXCR1
TMPRSS11F
TRIM61
HELT
C4orf48
C4orf40
AMTN
CCSER1
MIR302A
MTHFD2L
TMEM150C
GUSBP5
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
DEFB131
CLRN2
C4orf51
DUX4L7
DUX4L6
DUX4L5
DUX4L3
MIR572
MIR573
MIR574
AREGB
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
DUX4L2
USP17L30
FAM160A1
RELL1
PSAPL1
MIR297
FAM47E
CLDN24
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR1269A
MIR1305
MIR548I2
MIR548G
MIR3140
MIR4276
MIR3945
THEGL
MIR4455
MIR4453
MIR378D1
MIR4802
MIR4800
MIR4801
MIR4449
MIR548AG1
MIR4452
FAM47E
MIR5091
MIR5705
PYURF
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 21 significant results found. The significance cutoff is at Q value=0.25.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 1300 0.08 -0.856 1 0.24 5.84 1.48e-08
1q 1195 0.26 6.03 3.22e-08 0.10 -0.471 1
2p 624 0.08 -2.38 1 0.06 -2.96 1
2q 967 0.09 -1.45 1 0.03 -3.74 1
3p 644 0.05 -3.06 1 0.22 2.74 0.0102
3q 733 0.12 -0.839 1 0.12 -0.642 1
4p 289 0.06 -3.4 1 0.15 -0.497 1
4q 670 0.04 -3.52 1 0.15 0.186 0.897
5p 183 0.16 -0.497 1 0.06 -3.53 1
5q 905 0.10 -1.07 1 0.10 -1.27 1
6p 710 0.06 -2.57 1 0.36 8.51 0
6q 556 0.04 -3.05 1 0.47 12 0
7p 389 0.28 4.62 2.54e-05 0.03 -4.04 1
7q 783 0.26 4.96 7.13e-06 0.04 -3.39 1
8p 338 0.15 -0.27 1 0.28 4.23 4.29e-05
8q 551 0.25 3.78 0.000785 0.16 0.409 0.803
9p 301 0.07 -2.53 1 0.43 9.47 0
9q 700 0.08 -2.1 1 0.25 4.32 3.51e-05
10p 253 0.07 -3.2 1 0.21 1.47 0.187
10q 738 0.08 -1.93 1 0.18 1.41 0.198
11p 509 0.07 -2.83 1 0.10 -1.7 1
11q 975 0.08 -1.82 1 0.11 -0.777 1
12p 339 0.16 0.0667 1 0.15 -0.297 1
12q 904 0.14 0.452 1 0.17 1.67 0.146
13q 560 0.18 1.03 0.67 0.13 -0.671 1
14q 938 0.15 1.08 0.67 0.10 -0.971 1
15q 810 0.09 -1.57 1 0.18 1.62 0.151
16p 559 0.13 -0.78 1 0.07 -2.88 1
16q 455 0.13 -0.89 1 0.09 -2.38 1
17p 415 0.07 -2.44 1 0.46 11.2 0
17q 972 0.10 -0.775 1 0.13 0.26 0.883
18p 104 0.19 0.345 1 0.37 6.66 9e-11
18q 275 0.10 -1.57 1 0.63 16.6 0
19p 681 0.09 -1.81 1 0.12 -0.639 1
19q 935 0.16 1.21 0.67 0.08 -1.67 1
20p 234 0.20 1.06 0.67 0.14 -0.719 1
20q 448 0.25 3.42 0.00247 0.04 -3.65 1
21q 258 0.02 -4.51 1 0.32 5.58 6e-08
22q 564 0.06 -2.98 1 0.26 4.24 4.29e-05
Xq 668 0.07 -2.75 1 0.12 -0.999 1
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PAAD-TP/11448552/GDAC_MergeDataFiles_11451133/PAAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

  • Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat

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

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 184 Input Tumor Samples.

Tumor Sample Names
TCGA-2J-AAB1-01A-11D-A40V-01
TCGA-2J-AAB4-01A-12D-A40V-01
TCGA-2J-AAB6-01A-11D-A40V-01
TCGA-2J-AAB8-01A-12D-A40V-01
TCGA-2J-AAB9-01A-11D-A40V-01
TCGA-2J-AABA-01A-21D-A40V-01
TCGA-2J-AABE-01A-12D-A40V-01
TCGA-2J-AABF-01A-31D-A40V-01
TCGA-2J-AABH-01A-21D-A40V-01
TCGA-2J-AABI-01A-12D-A40V-01

Figure 3.  Segmented copy number profiles in the input data

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

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

Region Data

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

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

  2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

  1. Cytoband

  2. Q value

  3. Residual Q value

  4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

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