Bladder Urothelial Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16a (cga svn revision 43808).

Summary

There were 97 tumor samples used in this analysis: 23 significant arm-level results, 27 significant focal amplifications, and 31 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 - 27 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
--- | --- | --- | --- | ---
6p22.3 | 2.3327e-26 | 2.3327e-26 | chr6:20361033-21757620 | 4
3p25.2 | 2.0398e-13 | 2.0398e-13 | chr3:12481505-12491536 | 0 [PPARG]
11q13.3 | 3.2995e-13 | 3.2995e-13 | chr11:69464719-69503929 | 2
1q23.3 | 4.5936e-14 | 7.1918e-13 | chr1:160979061-161109018 | 9
8q22.2 | 1.6611e-12 | 1.1958e-10 | chr8:101180651-102354063 | 9
7p11.2 | 3.0898e-08 | 3.0898e-08 | chr7:54993065-55397917 | 1
19q12 | 1.7259e-08 | 1.374e-07 | chr19:30148223-30537755 | 4
17q12 | 4.4466e-06 | 8.1206e-06 | chr17:37820993-37905815 | 7
10p15.1 | 3.7928e-05 | 3.7928e-05 | chr10:5610225-5844627 | 3
12q15 | 7.1817e-05 | 7.1817e-05 | chr12:69120903-70280714 | 16
1p34.2 | 0.003409 | 0.003409 | chr1:39581932-40539227 | 17
20q11.21 | 0.0048623 | 0.0048623 | chr20:30109883-30332464 | 8
4p16.3 | 0.0063081 | 0.0063081 | chr4:1738268-1817427 | 3
17q11.2 | 0.0015208 | 0.0095316 | chr17:27386448-27864389 | 6
5p15.33 | 0.024861 | 0.024861 | chr5:1-15332573 | 81
22q11.23 | 0.029384 | 0.029384 | chr22:22101516-27257657 | 81
8p11.23 | 0.016391 | 0.050891 | chr8:36905670-37763904 | 7
3q26.2 | 0.069422 | 0.069422 | chr3:147774141-198022430 | 327
1q21.3 | 4.3142e-05 | 0.079807 | chr1:120523956-153385355 | 201
16p11.2 | 0.084684 | 0.084684 | chr16:23463203-30907402 | 129
19q13.43 | 0.029384 | 0.086987 | chr19:51155789-59128983 | 352
8q24.21 | 1.5458e-07 | 0.11157 | chr8:119095748-146364022 | 212
6q12 | 0.11368 | 0.11368 | chr6:64050962-64133661 | 0 [LGSN]
13q22.1 | 0.14278 | 0.14278 | chr13:67514501-115169878 | 157
8p11.21 | 0.031517 | 0.19598 | chr8:41413019-42103038 | 8
12p13.32 | 0.23094 | 0.23094 | chr12:1-8700625 | 132
4q13.3 | 0.23615 | 0.23615 | chr4:72385235-74875451 | 17

Genes in Wide Peak

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

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

Genes
E2F3
SOX4
CDKAL1
LINC00340

Genes in Wide Peak

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

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

Genes
CCND1
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q23.3.

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

Genes
NIT1
PFDN2
USF1
DEDD
F11R
PVRL4
KLHDC9
ARHGAP30
TSTD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q22.2.

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

Genes
SPAG1
YWHAZ
RNF19A
PABPC1
ZNF706
ANKRD46
SNX31
FLJ42969
MIR4471

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q12.

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

Genes
CCNE1
URI1
PLEKHF1
C19orf12

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's Cancer Gene Census [7].

Genes
ERBB2
GRB7
PNMT
TCAP
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.1.

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

Genes
GDI2
FAM208B
ASB13

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's Cancer Gene Census [7].

Genes
MDM2
hsa-mir-1279
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
SLC35E3
NUP107
RAB3IP
BEST3
LRRC10
MIR1279
MIR3913-2
MIR3913-1

Genes in Wide Peak

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

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

Genes
MYCL1
BMP8B
PPT1
PABPC4
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
OXCT2
NT5C1A
MFSD2A
BMP8A
KIAA0754
SNORA55
PPIEL

Genes in Wide Peak

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

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

Genes
hsa-mir-3193
BCL2L1
ID1
TPX2
HM13
COX4I2
PSIMCT-1
MIR3193

Genes in Wide Peak

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

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

Genes
FGFR3
LETM1
TACC3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q11.2.

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

Genes
CRYBA1
TIAF1
NUFIP2
TAOK1
MYO18A
MIR4523

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

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

Genes
hsa-mir-4278
hsa-mir-4277
ADCY2
CTNND2
DAP
DNAH5
MTRR
NDUFS6
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
KIAA0947
PP7080
IRX4
TAS2R1
FAM105A
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285577
LOC285692
SLC6A19
LOC340094
SLC6A18
LRRC14B
FLJ33360
TAG
LOC442132
ANKRD33B
SDHAP3
LOC728613
LOC729506
SNORD123
LOC100130744
MIR4277
MIR4278
LOC100505738
LOC100505806
LOC100506688
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q11.23.

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

Genes
BCR
SMARCB1
hsa-mir-548j
hsa-mir-650
ADORA2A
ADRBK2
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
DDT
GGT1
GGT5
GNAZ
GSTT1
GSTT2
IGLL1
MIF
MMP11
MAPK1
SNRPD3
TOP1P2
VPREB1
ZNF70
TPST2
TOP3B
RAB36
PPM1F
SPECC1L
CABIN1
PRAME
SEZ6L
TFIP11
GSTTP1
POM121L1P
FBXW4P1
RTDR1
POM121L9P
VPREB3
C22orf43
UPB1
SUSD2
ASPHD2
SLC2A11
C22orf13
MYO18B
KIAA1671
HPS4
GGTLC2
GUSBP11
DERL3
IGLL3P
LRP5L
LOC96610
ZNF280A
SGSM1
ZNF280B
ZDHHC8P1
C22orf15
TMEM211
RGL4
LOC284889
FAM211B
LOC391322
CHCHD10
SRRD
PIWIL3
MIAT
BCRP3
C22orf45
POM121L10P
LOC648691
CES5AP1
GSTTP2
GSTT2B
MIR650
DDTL
LOC100128531
MIR548J
IGLL5

Genes in Wide Peak

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

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

Genes
ERLIN2
PROSC
GPR124
BRF2
ZNF703
RAB11FIP1
LOC728024

Genes in Wide Peak

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

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

Genes
BCL6
EIF4A2
ETV5
LPP
MLF1
PIK3CA
SOX2
TFRC
GMPS
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
AADAC
ACTL6A
AGTR1
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
GYG1
HRG
HES1
IL1RAP
IL12A
KNG1
KPNA4
TM4SF1
MBNL1
MFI2
MME
MUC4
NDUFB5
OPA1
CLDN11
P2RY1
PAK2
PCYT1A
PFN2
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
PTX3
RAP2B
RARRES1
RFC4
SNORA63
RPL35A
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
HLTF
SSR3
SST
TERC
THPO
SEC62
TM4SF4
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
UBXN7
ARHGEF26
GPR160
FETUB
LAMP3
KCNMB3
SERP1
GOLIM4
GPR171
SCHIP1
NMD3
COMMD2
ZNF639
RSRC1
PEX5L
SELT
DNAJB11
P2RY13
GPR87
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
SUCNR1
MCCC1
LXN
CCNL1
HRASLS
MRPL47
NCEH1
IFT80
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
MFSD1
FNDC3B
P2RY12
ATP13A3
VEPH1
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
PIGZ
SPATA16
EIF2A
B3GNT5
IQCG
ATP13A4
FYTTD1
HPS3
ARPM1
MGC2889
LRCH3
CEP19
GFM1
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
FAM194A
TMEM207
RTP1
TTC14
PPM1L
WDR49
LRRC34
MB21D2
XXYLT1
C3orf55
C3orf79
CCDC50
PYDC2
LOC152217
SPTSSB
RNF168
DHX36
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
LOC201651
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
IGSF10
C3orf33
C3orf70
TPRG1
TRIM59
CCDC39
LOC339894
LOC339926
LPP-AS2
LRRIQ4
SAMD7
AADACL2
GPR149
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
ANKUB1
LEKR1
TMEM212
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
SNORD2
SNORA4
TMEM14E
LOC646168
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
IQCJ
SCARNA7
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
LOC730091
MIR922
MIR944
LOC100128023
WWTR1-AS1
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
TIPARP-AS1
MIR1248
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
ARHGEF26-AS1
LOC100507537
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
NOTCH2
PDE4DIP
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
CTSK
CTSS
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
IVL
LOR
MCL1
SMCP
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A8
S100A9
S100A10
S100A11
S100A12
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
SV2A
RBM8A
SF3B4
PIAS3
SEMA6C
POLR3C
TXNIP
MTMR11
MLLT11
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
CA14
NBPF14
LCE2B
RNF115
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
FAM63A
CDC42SE1
OTUD7B
PGLYRP4
FAM91A2
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
HIST2H3C
LIX1L
C1orf51
HFE2
ANKRD35
LELP1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
LINGO4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
C1orf68
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
TNFAIP8L2-SCNM1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

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

Genes
IL21R
PALB2
hsa-mir-762
hsa-mir-548w
ALDOA
AQP8
ATP2A1
CD19
CLN3
SEPT1
GTF3C1
IL4R
ITGAL
KIF22
MAZ
NDUFAB1
PHKG2
PLK1
PPP4C
PRKCB
MAPK3
RBBP6
SPN
SULT1A2
SULT1A1
SULT1A3
TBX6
TUFM
DOC2A
HIRIP3
EIF3C
BCL7C
TAOK2
RNF40
HS3ST4
MVP
CACNG3
CD2BP2
CDIPT
ERN2
SRCAP
CORO1A
ATXN2L
SEPHS2
GGA2
XPO6
KIAA0556
ZNF629
QPRT
SH2B1
TBC1D10B
SEZ6L2
NUPR1
LAT
TNRC6A
MYLPF
ZNF771
LCMT1
ARHGAP17
APOBR
UBFD1
CHP2
FBRS
ZNF747
PRR14
SLX1B
DCTPP1
GDPD3
C16orf53
ZNF768
JMJD5
RABEP2
SLC7A5P1
YPEL3
FAM57B
SPNS1
DCTN5
NFATC2IP
C16orf93
COG7
ZNF764
PRRT2
CCDC101
ZNF689
SLC5A11
TMEM219
EARS2
C16orf92
GSG1L
ZNF785
ZNF688
C16orf82
NSMCE1
ZNF48
IL27
KCTD13
ASPHD1
LOC283888
C16orf54
INO80E
ZKSCAN2
SBK1
LOC388242
FLJ21408
SNX29P2
LOC440354
LOC440356
SULT1A4
SLX1A
BOLA2
LOC554206
LOC595101
LOC606724
LOC613037
LOC613038
RRN3P2
ZG16
BOLA2B
SNORA30
EIF3CL
LOC100289092
MIR762
LOC100506655
SLX1A-SULT1A3
SLX1B-SULT1A4
MIR4519
MIR4721
MIR4518
MIR4517

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.43.

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

Genes
KLK2
PPP2R1A
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
A1BG
KLK3
CD33
SIGLEC6
ETFB
FCAR
FKBP1AP1
FPR1
FPR2
FPR3
GPR32
HAS1
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LIM2
NDUFA3
NKG7
CNOT3
PEG3
PRKCG
KLK7
KLK6
KLK10
PTPRH
RPL28
RPS5
RPS9
CLEC11A
AURKC
SYT5
TNNI3
TNNT1
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF175
SIGLEC5
UBE2M
ZNF264
NCR1
KLK4
ZNF432
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
LILRB1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KLK8
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
ZNF324
KLK5
KLK13
PRPF31
SIGLEC7
SIGLEC9
SIGLEC8
CHMP2A
ZNF544
UBE2S
CCDC106
EPN1
KLK14
KLK12
SHANK1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
ZNF71
CACNG8
CACNG7
CACNG6
ZNF350
ZNF667
ZNF649
ZSCAN18
MGC2752
TSEN34
MBOAT7
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
ZNF419
ISOC2
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
ZNF611
ZNF528
BRSK1
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
ACPT
LENG9
BIRC8
RDH13
ZIM3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
ZNF813
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF579
ZNF525
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
ZNF773
LOC386758
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF321P
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR99B
TARM1
MIR371A
MIR372
MIR373
A1BG-AS1
DPRX
DUXA
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC646508
SBK2
LOC646862
SNORD88A
SNORD88B
SNORD88C
MIR643
CEACAM18
SHISA7
FLJ30403
ZNF814
SIGLEC14
MIMT1
MIR935
LOC100128252
LOC100128398
LOC100129083
SGK110
LOC100131691
PEG3-AS1
ERVV-2
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
ZNF865
ZNF816-ZNF321P
MIR4754
MIR4752
MIR371B

Genes in Wide Peak

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

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

Genes
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
ADCY8
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
POU5F1B
PTK2
PVT1
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
JRK
DGAT1
GPAA1
WISP1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
KHDRBS3
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
C8orf55
FAM49B
CHRAC1
EXOSC4
LY6K
TRMT12
WDYHV1
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
GSDMD
ZNF696
ARHGAP39
ZNF34
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
MAF1
PARP10
C8orf76
TIGD5
FAM83A
PPP1R16A
ZNF251
KIFC2
NAPRT1
WDR67
HPYR1
MFSD3
MAL2
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
TMEM65
LOC157381
FAM84B
FAM91A1
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
SPATC1
FLJ43860
MAFA
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
C8orf73
SCXB
FER1L6
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR937
MIR939
LOC100128338
SCXA
LOC100130231
CCDC166
LOC100131726
LOC100133669
LOC100288181
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR1208
LOC100507117
ZHX1-C8ORF76
MIR4663
MIR4472-1
MIR4664
PCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q22.1.

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
ATP4B
KLF5
BTF3P11
CLN5
COL4A1
COL4A2
DACH1
DCT
GPR183
EDNRB
EFNB2
F7
F10
FGF14
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
LMO7
PCCA
PCDH9
POU4F1
DNAJC3
RAP2A
GRK1
ATXN8OS
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
UCHL3
ZIC2
STK24
CUL4A
IRS2
SCEL
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
TBC1D4
GPC6
MBNL2
FARP1
SPRY2
ABCC4
TUBGCP3
PIBF1
TNFSF13B
SOX21
KLF12
RASA3
DZIP1
DIS3
MYO16
MYCBP2
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
FBXL3
OXGR1
NDFIP2
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
KLHL1
RBM26
UPF3A
KDELC1
CARS2
RNF219
GRTP1
BORA
SLITRK6
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
SLITRK1
KCTD12
TEX29
METTL21CP1
SLAIN1
SPACA7
RNF113B
LINC00410
GPR180
COMMD6
CLYBL
METTL21C
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
LINC00550
LINC00347
FAM70B
C13orf35
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
MZT1
MIR4500HG
FLJ44054
CCDC168
CTAGE11P
FLJ41484
MIR622
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
MIR3170
MIR3665
RBM26-AS1
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
PLAT
KAT6A
AP3M2
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
CCND2
KDM5A
ZNF384
hsa-mir-141
APOBEC1
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CHD4
ATN1
ENO2
FGF6
FKBP4
FOXM1
GAPDH
GNB3
KCNA1
KCNA5
KCNA6
LAG3
LTBR
NDUFA9
NINJ2
NOP2
NTF3
PTMS
PTPN6
PEX5
RAD52
SCNN1A
SLC2A3
SLC6A12
SLC6A13
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
USP5
MLF2
DYRK4
CD163
GDF3
CLSTN3
NCAPD2
LPCAT3
LRRC23
EMG1
LEPREL2
AKAP3
RAD51AP1
TSPAN9
PHB2
ERC1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
COPS7A
CLEC4A
ING4
MRPL51
C1RL
TAPBPL
FAM90A1
PLEKHG6
FOXJ2
ITFG2
PRMT8
PARP11
ANO2
C12orf4
C12orf5
LPAR5
WNK1
ADIPOR2
NANOG
WNT5B
CDCA3
C12orf32
NRIP2
RBP5
CCDC77
ACRBP
SPSB2
EFCAB4B
CACNA2D4
CLEC6A
C12orf57
SLC2A14
FBXL14
CLEC4C
DSTNP2
C12orf53
DCP1B
MATL2963
CD163L1
RPL13P5
B4GALNT3
LOC283440
CLEC4D
ACSM4
DPPA3
NANOGNB
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
LOC574538
POU5F1P3
FAM86FP
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
LOC100271702
LOC100288778
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
AFM
AFP
ALB
GC
CXCL1
IL8
PF4
PF4V1
PPBP
CXCL6
CXCL5
SLC4A4
ADAMTS3
NPFFR2
ANKRD17
RASSF6
COX18

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 - 31 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 | 1.6136e-51 | 7.4906e-49 | chr9:21865498-22448737 | 4
13q14.2 | 4.9582e-09 | 4.9582e-09 | chr13:48833767-49281290 | 3
5q11.2 | 1.3527e-08 | 1.3527e-08 | chr5:58260298-59787985 | 3
2q22.1 | 4.2759e-08 | 4.7339e-07 | chr2:139655617-143637838 | 1
16p13.3 | 9.0727e-07 | 9.0727e-07 | chr16:3764793-4013466 | 1
4q22.1 | 1.673e-06 | 6.9986e-06 | chr4:90844993-93240505 | 1
17p12 | 9.2451e-05 | 9.758e-05 | chr17:14131834-15999789 | 19
6q22.31 | 0.001928 | 0.0019057 | chr6:92231219-122722043 | 129
19p13.3 | 0.0033012 | 0.0033519 | chr19:1-9203991 | 287
10q23.31 | 0.0042856 | 0.0044043 | chr10:89617158-91063177 | 17
2q34 | 5.1482e-06 | 0.0054788 | chr2:213401694-214143899 | 3
6p25.3 | 0.0086043 | 0.0089998 | chr6:1-2624052 | 10
2q37.1 | 0.00025208 | 0.01505 | chr2:211398754-243199373 | 290
15q12 | 0.022886 | 0.023915 | chr15:1-33605300 | 172
16q23.1 | 0.027775 | 0.027331 | chr16:78129058-79627770 | 1
3p12.3 | 0.006632 | 0.032888 | chr3:40211012-93784545 | 375
1p36.11 | 0.035866 | 0.035866 | chr1:1-41240470 | 653
4q34.2 | 0.0089998 | 0.040377 | chr4:152324103-191154276 | 171
8p23.1 | 0.042331 | 0.042385 | chr8:1-39792913 | 303
Xq22.3 | 0.027269 | 0.042385 | chrX:107395766-108020483 | 3
3p14.2 | 0.00398 | 0.060249 | chr3:28426979-74571402 | 415
12p13.2 | 0.092325 | 0.093013 | chr12:1-24365820 | 283
22q13.32 | 0.092325 | 0.093013 | chr22:34146369-51304566 | 271
11p15.4 | 0.095839 | 0.099311 | chr11:1-56510219 | 567
14q32.33 | 0.10149 | 0.10327 | chr14:64696450-107349540 | 441
Xq21.33 | 0.026267 | 0.12628 | chrX:94288568-98718611 | 4
9p24.1 | 0.00026877 | 0.14076 | chr9:1-25677256 | 113
11q24.3 | 0.14532 | 0.14466 | chr11:17107164-135006516 | 1171
9q22.33 | 0.17983 | 0.17765 | chr9:38614979-115654245 | 343
1q32.3 | 0.19543 | 0.19543 | chr1:161333249-249250621 | 717
4p16.3 | 0.19089 | 0.19543 | chr4:1-47923843 | 264

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
RB1
RCBTB2
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
CREBBP

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
ADORA2B
MEIS3P1
PMP22
HS3ST3B1
TRIM16
TTC19
ZNF286A
TEKT3
MGC12916
CDRT7
ZSWIM7
CDRT15
FAM18B2
CDRT4
TBC1D26
CDRT1
CDRT15P2
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
CCNC
COL10A1
EPHA7
FOXO3
FRK
FYN
GJA1
GPR6
GRIK2
HDAC2
KPNA5
LAMA4
MARCKS
MAN1A1
PLN
POU3F2
PREP
REV3L
SIM1
SMPD2
NR2E1
TSPYL1
DDO
SNX3
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
FUT9
TRAF3IP2
ASCC3
BVES
SEC63
CDK19
TSPYL4
UFL1
BRD7P3
ASF1A
PNISR
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
COQ3
SOBP
QRSL1
PDSS2
HACE1
BEND3
PRDM13
POPDC3
MICAL1
FAM184A
MANEA
GPR63
ARMC2
RPF2
MCHR2
FAXC
RTN4IP1
USP45
SLC22A16
KIAA1919
GTF3C6
KLHL32
NUS1
SLC16A10
BVES-AS1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
RSPH4A
LINC00222
CEP85L
LIN28B
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
LOC100130890
LOC100287632
MIR2113
MIR548H3
LOC100422737
MIR4643

Genes in Wide Peak

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

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

Genes
GNA11
MLLT1
SH3GL1
STK11
TCF3
FSTL3
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
C3
CAPS
CD70
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
EMR1
FCER2
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
INSR
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NRTN
OAZ1
PALM
POLR2E
POLRMT
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RFX2
RPS15
RPS28
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
THOP1
TLE2
VAV1
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
TRIP10
LONP1
APBA3
SAFB2
MED16
CHAF1A
SH2D3A
EBI3
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4A
TIMM44
SEMA6B
PNPLA6
UQCR11
SBNO2
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
TIMM13
DAZAP1
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
SLC39A3
CD209
ANGPTL4
MARCH2
CD320
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
MCOLN1
WDR18
REXO1
CAMSAP3
ZNF77
C19orf29
CELF5
SLC25A23
FSD1
ZNF557
CERS4
TLE6
LPPR3
DENND1C
ZNF556
LRRC8E
FLJ22184
UBXN6
OR4F17
ACSBG2
ADAMTS10
FAM108A1
DOHH
KLF16
PRAM1
ALKBH7
ZNF414
DOT1L
FBN3
KISS1R
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATCAY
MBD3L1
MIDN
DPP9
R3HDM4
C19orf6
TPGS1
CRB3
REEP6
PEX11G
MUC16
IZUMO4
SCAMP4
ADAT3
ZNF554
EVI5L
GRIN3B
MRPL54
LRG1
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
C19orf21
PLK5
C2CD4C
ZNF358
TICAM1
CIRBP-AS1
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
PRR22
ANKRD24
C19orf59
C19orf26
CSNK1G2-AS1
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
ODF3L2
EMR4P
ADAMTSL5
CLEC4G
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
WASH5P
LOC388499
ONECUT3
MEX3D
FLJ45445
PRSS57
VMAC
CTXN1
C19orf29-AS1
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
FAM138F
LINGO3
ARRDC5
FAM138A
MBD3L4
MBD3L3
MIR637
PLIN4
C19orf71
LOC100128573
LOC100131094
C19orf79
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR3940
LOC100507567
LOC100507588
MIR4747
MIR4746
MIR4745

Genes in Wide Peak

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

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

Genes
PTEN
ACTA2
FAS
LIPA
LIPF
CH25H
RNLS
STAMBPL1
ANKRD22
LIPJ
LIPM
LIPK
LIPN
KLLN
FAS-AS1
MIR4679-1
MIR4679-2

Genes in Wide Peak

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

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

Genes
IKZF2
MIR4776-1
MIR4776-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

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

Genes
IRF4
FOXF2
FOXC1
GMDS
EXOC2
DUSP22
FOXQ1
HUS1B
LOC285768
LOC100508120

Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

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

Genes
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
APBA2
NBEAP1
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
NDN
OCA2
SCG5
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
ARHGAP11A
FAN1
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
GREM1
KLF13
MAGEL2
MTMR10
NDNL2
ATP10A
NIPA2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
OTUD7A
LOC283683
OR4N4
LOC283710
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
MIR211
NF1P2
HERC2P9
WHAMMP2
LOC503519
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715
TMCO5B

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's Cancer Gene Census [7].

Genes
WWOX

Genes in Wide Peak

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

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

Genes
CTNNB1
FHIT
MITF
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR5
CCBP2
COL7A1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
EPHA3
FLNB
GBE1
GNAI2
GNAT1
XCR1
GPR27
GPX1
GRM2
HTR1F
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLXNB1
POU1F1
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
ROBO1
ROBO2
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
TMF1
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
MAGI1
CACNA2D2
VPRBP
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
EIF1B
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
PTPN23
CHMP2B
DNAH1
HIGD1A
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
ABHD5
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
ULK4
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ZNF654
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
SELK
PROK2
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
SLC25A26
ZNF501
GPR62
FAM3D
LYZL4
KBTBD5
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
CCDC13
PRICKLE2
C3orf67
KCTD6
ARL13B
DHFRL1
KLHDC8B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
C3orf38
ENTPD3-AS1
ZNF619
ZNF621
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
PRSS42
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LOC401074
MIRLET7G
MIR135A1
MIR138-1
MIR191
FAM19A1
STX19
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
LOC644714
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4444-1
MIR4443
LOC100652759
LUST

Genes in Wide Peak

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

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

Genes
LCK
MYCL1
PAX7
RPL22
SDHB
SFPQ
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
AK2
ALPL
RERE
BAI2
BMP8B
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL8A2
COL9A2
COL16A1
CORT
CSF3R
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
FHL3
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
INPP5B
STMN1
MATN1
MFAP2
MTF1
MTHFR
NBL1
NDUFS5
NFYC
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKCZ
PSMB2
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
YARS
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
PABPC4
TNFRSF18
PER3
MAP3K6
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
RIMS3
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
PPIE
MAD2L2
CAP1
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
MYCBP
HEYL
EIF2C1
OR4F3
RNU11
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
PRO0611
LINC00339
SSU72
GNL2
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
UTP11L
SDF4
MRTO4
HPCAL4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
VPS13D
FAM176B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
MIIP
CELA2A
GPATCH3
CLSPN
OXCT2
RRAGC
TINAGL1
PLA2G2F
SMAP2
S100PBP
MEAF6
DEM1
CEP85
NMNAT1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZNF643
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
AKIRIN1
YRDC
NOL9
LIN28A
SH3D21
SNIP1
AGMAT
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
GPR157
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
NT5C1A
TRIM63
FAM167B
C1orf170
CROCCP2
MFSD2A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
C1orf212
ADC
TMEM54
CSMD2
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
TMCO2
ZNF684
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
LOC149086
MANEAL
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
EIF2C3
EIF2C4
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
RSPO1
EPHA10
LOC284661
SLC25A34
ESPNP
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
ZNF642
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
BMP8A
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
KIAA0754
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA55
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
LOC728431
PPIEL
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100130557
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4255
MIR4253
MIR4251
MIR4252
MIR4254
MIR3659
MIR3917
MIR3605
MIR3675
ENO1-AS1
ZMYM6NB
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
GJA9-MYCBP
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.2.

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
AGA
SLC25A4
ANXA2P1
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
PPID
MSMO1
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
DUX2
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
DKFZP434I0714
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
PDGFC
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
MLF1IP
NBLA00301
MAP9
WWC2
CEP44
SNX25
MND1
TKTL2
CBR4
FHDC1
MGC45800
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
C4orf45
TRIM60
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
RNF175
LOC339975
TRIML1
LOC340017
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
FAM160A1
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3140
MIR4276
MIR3945
MIR3688-1
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR4453
MIR3688-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.1.

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

Genes
FGFR1
PCM1
WRN
WHSC1L1
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ADRA1A
ADRB3
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
ADAM3A
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
EIF4EBP1
EPB49
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
ADAM2
GATA4
GFRA2
GNRH1
GSR
GTF2E2
NRG1
IDO1
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STAR
STC1
TACC1
FZD3
TUSC3
UBXN8
TNKS
ADAM18
ADAM9
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ASH2L
MTMR7
MYOM2
DLGAP2
MFHAS1
BAG4
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
DCTN6
PNMA2
ADAM28
RBPMS
ERLIN2
LZTS1
PROSC
XPO7
TRIM35
RHOBTB2
DDHD2
KIF13B
PSD3
LEPROTL1
SLC39A14
GPR124
FBXO25
FGF20
LSM1
ADAMDEC1
CNOT7
PURG
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
BRF2
AGPAT5
INTS9
CSGALNACT1
HR
PBK
ZNF395
DEFB103B
BIN3
TEX15
MTUS1
KIAA1456
KIAA1967
PLEKHA2
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
DUSP26
HMBOX1
MCPH1
PPP1R3B
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
TTI2
RAB11FIP1
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
TM2D2
PPAPDC1B
MAK16
FUT10
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
GOT1L1
VPS37A
NKX2-6
SGCZ
UNC5D
LETM2
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
ESCO2
FBXO16
LOC157627
C8orf42
ERICH1
TDH
C8orf48
KCNU1
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
HTRA4
ADAM32
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
ADAM5P
FLJ10661
XKR6
LOC286059
LOC286083
EFHA2
LOC286114
SCARA5
LOC286135
RNF5P1
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
C8orf80
C8orf86
LOC392196
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
C8orf75
MBOAT4
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
LOC728024
DEFA1B
FAM90A20
FAM90A19
ZNF705D
LOC100128750
FAM66B
LOC100128993
LOC100130964
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR4287
MIR3148
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
LOC100507341
MIR548O2
MIR4659A
MIR4660
MIR4659B
LOC100652791

Genes in Wide Peak

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

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

Genes
COL4A5
COL4A6
IRS4

Genes in Wide Peak

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

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

Genes
CTNNB1
FHIT
MITF
MLH1
MYD88
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
SNORA62
RPL29
ATXN7
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
TKT
TMF1
CLEC3B
TNNC1
UBA7
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
VPRBP
IP6K1
EPM2AIP1
PSMD6
TRANK1
DLEC1
EXOG
XYLB
OXSR1
PDCD6IP
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
CRTAP
ARL6IP5
NPRL2
CXCR6
CSPG5
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
GNL3
RBMS3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
VILL
ABHD5
DYNC1LI1
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
KIF9
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
GPR62
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
ZCWPW2
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
TMPPE
LOC644714
LOC645206
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
LOC100128640
NRADDP
LOC100132146
BSN-AS2
PRSS46
LOC100287879
MIR1284
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4443
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

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

Genes
CCND2
ETV6
KDM5A
ZNF384
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
GYS2
IAPP
KCNA1
KCNA5
KCNA6
KCNJ8
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LDHB
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NINJ2
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
RECQL
SCNN1A
ST8SIA1
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SOX5
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
CSDA
DYRK4
GPRC5A
CD163
GDF3
CLSTN3
KIAA0528
NCAPD2
CLEC2B
ABCC9
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
SLCO1B1
RAD51AP1
KLRAP1
TSPAN9
STRAP
PRR4
PHB2
KLRK1
ERC1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
SLCO1B3
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
GOLT1B
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
ETNK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
CMAS
PRMT8
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
WNK1
BCL2L14
ADIPOR2
RERGL
PLBD1
PYROXD1
NANOG
C12orf39
DUSP16
WNT5B
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
CCDC77
ACRBP
SPSB2
EFCAB4B
RERG
PLCZ1
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
SLC2A14
A2ML1
LOC144571
C12orf60
FBXL14
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf53
DCP1B
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
B4GALNT3
CLEC9A
C12orf36
LOC283440
CLEC4D
LOC338817
SLCO1B7
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
LOC574538
POU5F1P3
LOC642846
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
SLC15A5
MIR920
LOC100129361
LOC100271702
LOC100288778
LOC100292680
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
MIR3649
LOC100506314
LOC100506393
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846

Genes in Wide Peak

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

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

Genes
EP300
MYH9
PDGFB
MKL1
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
hsa-mir-33a
hsa-mir-1281
hsa-mir-659
ACR
ACO2
ADSL
ARSA
ATF4
BIK
TSPO
MPPED1
CHKB
CPT1B
CSF2RB
CSNK1E
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
MCHR1
H1F0
HMOX1
IL2RB
KCNJ4
LGALS1
LGALS2
MB
MCM5
MFNG
MGAT3
MPST
NAGA
NCF4
NDUFA6
NHP2L1
PMM1
POLR2F
PPARA
MAPK11
PVALB
RAC2
RANGAP1
RPL3
MAPK12
SBF1
SOX10
SREBF2
SSTR3
ST13
TCF20
TEF
TST
UPK3A
WNT7B
PLA2G6
GALR3
APOL1
EIF3D
CACNA1I
SYNGR1
GRAP2
PICK1
GTPBP1
APOBEC3B
CELSR1
PPP6R2
ZBED4
JOSD1
RBX1
SCO2
HMGXB4
TOM1
DNAL4
PKDREJ
CACNG2
TAB1
SLC25A17
DDX17
NUP50
TOB2
KDELR3
IFT27
TRIOBP
CDC42EP1
DMC1
RABL2B
PACSIN2
TNRC6B
GRAMD4
TTLL12
MLC1
ZC3H7B
KIAA0930
GCAT
CBX6
NPTXR
CBX7
SLC16A8
MAPK8IP2
RBFOX2
RASD2
SH3BP1
PLXNB2
MAFF
BRD1
ARHGAP8
APOL2
TBC1D22A
CBY1
SUN2
TTLL1
SAMM50
ATXN10
FAM19A5
TXN2
TMEM184B
SULT4A1
GGA1
RIBC2
ARFGAP3
SNORD43
SMC1B
CYTH4
CSDC2
RRP7A
MCAT
APOBEC3C
PPPDE2
SGSM3
CARD10
PARVB
NCAPH2
EIF3L
GTSE1
A4GALT
MOV10L1
SMCR7L
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
SEPT3
PANX2
TOMM22
PDXP
APOBEC3G
XPNPEP3
PARVG
CERK
EFCAB6
CENPM
ALG12
NOL12
CRELD2
C22orf46
KCTD17
CCDC134
ADM2
FOXRED2
BAIAP2L2
SCUBE1
TRABD
PNPLA3
APOL6
APOL5
APOL4
APOL3
SELO
L3MBTL2
HDAC10
LDOC1L
POLDIP3
C22orf23
PHF5A
KIAA1644
SHANK3
MICALL1
TUBGCP6
LOC90834
LMF2
ISX
RPS19BP1
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
FAM83F
ELFN2
C1QTNF6
TNFRSF13C
RNU86
SNORD83A
SNORD83B
ANKRD54
APOBEC3D
ENTHD1
DNAJB7
CHADL
MEI1
FAM109B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
TMPRSS6
APOBEC3H
WBP2NL
POLR3H
APOBEC3A
APOBEC3F
SERHL2
RNU12
ATP5L2
LOC284933
RPL23AP82
C22orf33
BK250D10.8
LOC339685
C22orf34
CHKB-CPT1B
LOC388906
LINC00207
LOC400927
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
MIR33A
LINC00229
FAM116B
PIM3
SHISA8
ODF3B
PRR5-ARHGAP8
SYCE3
LOC646851
MIR658
MIR659
LOC730668
LOC100128946
LOC100130899
LOC100132273
LOC100144603
LOC100271722
MIR1249
MIR1281
MIR3201
MIR3909
MIR3619
LOC100506241
LOC100506472
LOC100506714
MIR4763
MIR4534
MIR4762
MIR4766
MIR4535

Genes in Wide Peak

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

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

Genes
CARS
DDB2
EXT2
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
CREB3L1
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ACP2
ADM
AP2A2
AMPD3
APBB1
RHOG
ARHGAP1
ARNTL
ART1
ASCL2
BDNF
MPPED2
CALCA
CALCB
CAT
CCKBR
CD44
CD59
CD81
CD151
CDKN1C
CHRM4
TPP1
CNGA4
COPB1
CRY2
CSTF3
CTSD
DRD4
DUSP8
EIF4G2
ELF5
F2
FOLH1
FSHB
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
CD82
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LRP4
LSP1
CAPRIN1
MDK
MUC2
MUC6
MYBPC3
MYOD1
NAP1L4
NDUFS3
NELL1
NUCB2
SLC22A18
SLC22A18AS
PAX6
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMC3
PSMD13
PTH
PTPRJ
RAG1
RAG2
RAPSN
RCN1
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SLC1A2
SMPD1
SPI1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
BBOX1
PPFIBP2
IFITM1
DGKZ
CHST1
API5
MADD
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
PEX16
MAPK8IP1
TP53I11
MICAL2
CTR9
ATG13
CKAP5
TRIM66
NR1H3
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
EIF3M
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
CELF1
OR5I1
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
NUP160
FNBP4
RRP8
SIRT3
OR52A1
ARFIP2
MTCH2
FJX1
C11orf41
ABTB2
PAMR1
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
OR10A3
FXC1
ELP4
DKK3
RBMXL2
PGAP2
COMMD9
C11orf21
PACSIN3
TRPM5
UBQLN3
RNF141
APIP
HSD17B12
IGF2-AS1
BET1L
CEND1
PHF21A
WT1-AS
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
TRIM44
USP47
TRIM68
NAT10
UEVLD
LIN7C
SLC35C1
TCP11L1
LGR4
PIDD
KCNQ1DN
SOX6
AMBRA1
KBTBD4
PARVA
TTC17
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
PRDM11
CHRNA10
SLC17A6
PNPLA2
SYT13
PHRF1
LRRC4C
SCUBE2
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
PRRG4
C11orf49
TRIM48
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ZNF408
QSER1
AGBL2
PRR5L
ATHL1
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
PTDSS2
MOB2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
ARFGAP2
ACCS
SPRYD5
PTPN5
MICALCL
TRIM5
NAV2
SYT8
TSPAN18
CCDC34
SLC39A13
DEPDC7
PRKCDBP
SAAL1
ODF3
OSBPL5
C1QTNF4
PTPMT1
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
CYP2R1
DBX1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
LOC120824
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
C11orf94
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
NS3BP
METTL15
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
ALKBH3
LOC221122
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
OR51F1
SVIP
MRGPRX1
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
KRT8P41
LOC283104
CSNK2A1P
OR51V1
LOC283116
H19
EFCAB4A
TMEM80
HARBI1
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
OR5F1
OR5AP2
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
OR10A2
OVCH2
PDDC1
GALNTL4
B7H6
DKFZp779M0652
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
NAV2-AS4
HNRNPKP3
FAM180B
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
OR4C45
MIR129-2
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
LOC440040
LOC440041
LOC441601
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
OR8U8
OR9G9
MIR483
SNORA3
SNORA52
LOC644656
RASSF10
TRIM64C
LOC646813
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD67
SNORD97
MIR610
INS-IGF2
MUC5B
LOC729013
LOC729799
MIR675
LOC100126784
MRVI1-AS1
C11orf91
FAM99B
LOC100133161
MRPL23-AS1
MIR670
MIR3160-2
MIR3160-1
MIR4298
MIR4299
MTRNR2L8
LOC100500938
MIR210HG
LOC100506305
LOC100506540
DCDC5
LOC100507205
LOC100507300
LOC100507401
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR3973
MIR4688
MIR4694
MIR1343
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.33.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
hsa-mir-548m
DIAPH2
RPA4
LOC643486

Genes in Wide Peak

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

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

Genes
JAK2
MLLT3
NFIB
CD274
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
PLIN2
CDKN2A
CDKN2B
DMRT1
ELAVL2
FOXD4
MLANA
GLDC
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
INSL4
MTAP
PTPRD
RFX3
RLN1
RLN2
RPS6
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TYRP1
VLDLR
MPDZ
CER1
KIAA0020
RCL1
DMRT2
RRAGA
PSIP1
INSL6
KDM4C
KANK1
SLC24A2
RANBP6
AK3
C9orf53
BNC2
HAUS6
CNTLN
KIAA1797
C9orf68
CDC37L1
DENND4C
C9orf46
CBWD1
KLHL9
KIAA1432
DMRT3
DMRTA1
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
C9orf66
TTC39B
FAM154A
FREM1
KIAA2026
KCNV2
GLIS3
C9orf93
LURAP1L
IFNE
ZDHHC21
ACER2
LOC389705
FLJ35024
FLJ41200
PTPLAD2
PPAPDC2
MIR101-2
MIR31
FLJ35282
MIR31HG
MIR491
FAM138C
SCARNA8
CDKN2B-AS1
C9orf146
WASH1
MIR3152
MIR4473
MIR4665
MIR4474

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CCND1
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
LMO2
MEN1
MLL
NUMA1
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
hsa-mir-3163
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-3162
hsa-mir-130a
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
ACAT1
ACP2
ACRV1
ACTN3
ADRBK1
APLNR
ALDH3B1
ALDH3B2
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
ARHGAP1
PHOX2A
ARL2
ARRB1
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
CLNS1A
CNTF
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
EEF1G
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GTF2H1
GUCY1A2
H2AFX
HMBS
SLC29A2
HSPA8
HSPB2
DNAJC4
HTR3A
IGHMBP2
IL10RA
IL18
INCENP
INPPL1
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYBPC3
MYO7A
MYOD1
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
NUCB2
OMP
OPCML
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PGA5
PGR
PIK3C2A
PLCB3
POLR2G
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PSMC3
PTPRCAP
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
SNORD15A
ROM1
RPS3
RPS6KB2
RPS25
SAA1
SAA2
SAA3P
SAA4
SC5DL
SCN2B
SCN4B
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SORL1
SPI1
SPTBN2
SRPR
SSRP1
ST14
STX3
STX5
ABCC8
TAGLN
TCN1
TECTA
THRSP
THY1
TM7SF2
TPH1
TRAF6
TRPC6
TSG101
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WNT11
SF1
ZFPL1
ZBTB16
ZNF202
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIA1
SLC43A1
DGKZ
CHST1
BARX2
API5
MADD
OR7E2P
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
AIP
SYT7
SART1
USP2
SLC6A5
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MED17
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
CEP57
ARHGAP32
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
PRG3
YAP1
RBM14
CDC42EP2
EIF3M
NXF1
KAT5
HYOU1
SSSCA1
HTATIP2
DRAP1
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
NEU3
ME3
GPR83
YIF1A
SRSF8
EHD1
STIP1
CLP1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
HPS5
PTGDR2
SLCO2B1
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
NUP160
NCAPD3
FNBP4
SIK3
CLCF1
VSIG2
BACE1
FAM89B
SNHG1
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
C11orf41
PRDX5
POU2F3
ABTB2
BRMS1
C11orf20
CHRDL2
PAMR1
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
PPP1R14B
OR8G2
OR8B8
OR8G1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
ACAD8
B3GAT1
RAB30
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
COMMD9
DDX25
PACSIN3
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
KCNK4
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
TMEM216
CHCHD8
SLC15A3
PHF21A
MS4A4A
WT1-AS
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
RSF1
SPA17
FXYD6
C11orf24
CNTN5
SIAE
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39A
TRIM44
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
VPS37C
ANO1
NADSYN1
FAM86C1
C11orf57
NAT10
CCDC87
PPP6R3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
ELMOD1
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
TMPRSS4
GPR137
IFT46
C11orf75
C11orf30
PRDM10
PRDM11
CABP4
SLC17A6
TRIM49
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
CARNS1
SYT13
USP28
LRRC4C
POLD4
KRTAP5-8
PLEKHB1
MS4A7
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
ALX4
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
KLC2
TUT1
MRPL11
TMEM135
KCTD14
C11orf95
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
E2F8
CCDC82
ALG9
ZNF408
CLMP
NAA40
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
GDPD5
CLPB
UNC93B1
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
RNASEH2C
TMEM126A
DCUN1D5
EIF1AD
NUDT22
ARFGAP2
KIAA1826
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
SPRYD5
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
RELT
UBASH3B
C11orf70
LGALS12
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
NAV2
ATG16L2
GLB1L2
TSPAN18
ESAM
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
VPS26B
GLB1L3
CDCA5
RPLP0P2
SAAL1
SLC22A9
SNORD15B
TIRAP
CARD16
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRF
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
C11orf74
OR4C46
OR4X2
OR4B1
GYLTL1B
SLC36A4
FAT3
TRIM64
TMEM45B
DBX1
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
DNAJC24
C11orf46
OR8I2
LOC120824
LDLRAD3
XRRA1
MUC15
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
SPTY2D1
TMEM86A
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
GPHA2
ADAMTS15
B3GNT6
METTL15
MPZL3
IMMP1L
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
MRPL21
TPCN2
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
PPP1R32
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
LOC254100
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
OR4C3
OR4S1
EML3
TMEM151A
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR10AG1
OR5J2
OR4C13
OR4C12
LOC283116
C11orf85
SLC25A45
NEAT1
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
OR9G4
LOC283194
LINC00301
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LINC00294
IGSF22
LUZP2
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
LOC338739
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
TBX10
C11orf34
RTN4RL2
B7H6
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
KRTAP5-10
SLC22A25
FIBIN
C11orf96
SLC22A10
SPDYC
LIPT2
VSTM5
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
NAV2-AS4
HNRNPKP3
FAM180B
PCNXL3
FLJ42102
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
OR4A47
OR4C45
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR34B
MIR34C
DDI1
BLID
DKFZp686K1684
LOC440040
LOC440041
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
LINC00167
LOC441601
OR5B3
MIR326
CCDC73
LOC494141
BDNF-AS1
MS4A13
OR8U8
OR9G9
SCARNA9
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
BTBD18
LOC643733
PGA3
PGA4
LOC643923
CLDN25
FAM86C2P
TRIM64C
LOC646813
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
MIR610
MIR611
MIR612
TRIM49L1
LOC729799
METTL12
C11orf83
MIR708
LOC100126784
LOC100128239
LOC100129216
LOC100130348
LOC100130987
C11orf91
LOC100132078
LOC100133315
PATE3
LOC100288077
LOC100288346
MIR1304
MIR1908
MIR1237
MIR548K
MIR670
SNORA70E
BACE1-AS
MIR4300
MIR3160-2
MIR3160-1
MIR4301
MIR3162
MIR3167
MIR3165
MIR1260B
LOC100499227
MIR3654
MIR3920
MIR3656
MIR3664
MIR3680-1
LOC100500938
LOC100506233
LOC100506368
LOC100506540
DCDC5
CASP12
LOC100507050
LOC100507205
LOC100507300
LOC100507392
LOC100507401
RBM14-RBM4
LOC100526771
TMX2-CTNND1
SAA2-SAA4
ARL2-SNX15
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
HNRNPUL2-BSCL2
MIR4486
MIR4697
MIR4490
MIR4489
MIR4690
MIR3973
MIR4493
MIR4491
MIR4688
MIR4492
MIR4696
MIR4691
MIR4692
MIR4694
MIR1343
MIR4693
MIR4488
LOC100652768

Genes in Wide Peak

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

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

Genes
FANCC
GNAQ
OMD
SYK
TAL2
XPA
NR4A3
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
ABCA1
ALDH1A1
ALDOB
ANXA1
APBA1
AUH
BAAT
KLF9
CKS2
COL15A1
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
ECM2
LPAR1
S1PR3
FBP1
FKTN
FOXE1
FXN
GAS1
GCNT1
GNG10
HNRNPK
HSD17B3
IARS
MUSK
NCBP1
NFIL3
NINJ1
NTRK2
ROR2
OGN
PCSK5
PGM5
PHF2
PPP3R2
PRKACG
PTCH1
PTPN3
RAD23B
RORB
TGFBR1
TLE1
TLE4
TMOD1
TXN
UGCG
CORO2A
ZNF189
ZFAND5
PIP5K1B
IKBKAP
CDC14B
TMEFF1
CTNNAL1
FBP2
KLF4
FAM189A2
TJP2
GABBR2
GDA
GNA14
TRIM14
PTBP3
SEMA4D
ANP32B
SPTLC1
SMC2
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC35D2
AKAP2
ZNF510
HABP4
PTGR1
ERP44
SMC5
FAM120A
VPS13A
AGTPBP1
BICD2
KIAA0368
TDRD7
SLC44A1
CDK20
TMEM2
C9orf5
C9orf4
NIPSNAP3A
ZNF658
FAM75A7
OR2K2
OSTF1
INVS
PSAT1
UBQLN1
PCA3
FAM108B1
GOLM1
C9orf156
SHC3
NANS
MRPL50
EPB41L4B
FAM22F
DIRAS2
ASPN
TEX10
LPPR1
FAM206A
C9orf95
STX17
NOL8
C9orf40
TMEM38B
RFK
NIPSNAP3B
TBC1D2
HEMGN
KIF27
BARX1
RNF20
BDAG1
SLC46A2
C9orf80
ZNF462
NAA35
SLC28A3
SUSD1
IPPK
WNK2
SECISBP2
ZCCHC6
GALNT12
CNTNAP3
SVEP1
RMI1
TRPM3
GKAP1
ISCA1
ZNF484
FSD1L
CEP78
ANKRD20A1
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
HIATL1
C9orf3
ALG2
FGD3
C9orf30
PALM2
FAM122A
GRIN3A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
TRPM6
NXNL2
RASEF
FAM201A
LOC158257
FAM120AOS
LINC00475
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
C9orf71
ZNF169
C9orf21
ZNF367
ANKS6
SUSD3
CBWD5
TXNDC8
MAMDC2
FRMD3
C9orf47
C9orf79
LOC286238
LOC286297
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
LOC340508
LOC340515
FAM75D5
MURC
FOXD4L4
AQP7P1
PTAR1
C9orf102
KGFLP1
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
CTSL3
LOC392364
OR13C2
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR204
MIR23B
MIR24-1
MIR27B
MIR32
MIR7-1
C9orf103
LOC440173
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
LOC441461
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75C2
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
SNORA84
LOC100128076
LOC100128361
LINC00476
UNQ6494
LOC100129316
LOC100132077
LOC100132352
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
LINC00092
LOC100286938
MIR548H3
MIR2278
MIR548Q
MIR3074
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3910-1
MIR3910-2
MIR3651
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR4670

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q32.3.

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

Genes
ABL2
ELK4
FCGR2B
FH
MDM4
PBX1
TPR
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ALDH9A1
FASLG
ARF1
ASTN1
SERPINC1
ATF3
ATP1B1
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CD247
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
DHX9
DPT
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F5
F13B
FCGR2A
FCGR3A
FCGR3B
FMO1
FMO2
FMO3
FMO4
FMOD
NR5A2
GALNT2
GLUL
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
MR1
HLX
HNRNPU
HSD11B1
HSPA6
HSPA7
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
LMX1A
MARK1
CD46
MGST3
MTR
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NEK2
NID1
DDR2
NVL
CDK18
PDC
PFKFB2
PIGC
PIGR
PIK3C2B
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPP2R5A
PRELP
PROX1
PSEN2
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RNASEL
RNF2
RNPEP
RXRG
RYR2
XCL1
SELE
SELL
SELP
SNRPE
SOAT1
UAP1
SRP9
TROVE2
AURKAPS1
XCL2
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TRAF5
TSNAX
TNFSF4
UCK2
USH2A
WNT9A
ZNF124
SLC30A1
NPHS2
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
RGS5
PPFIA4
BLZF1
DEGS1
KMO
VAMP4
B3GALT2
CREG1
RAB7L1
TNFSF18
TAF1A
MPZL1
ANGPTL1
TBX19
FCGR2C
EXO1
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
GGPS1
RASAL2
SOX13
PRDX6
IKBKE
KIAA0040
NOS1AP
TMEM63A
TOMM20
URB2
CEP350
CEP170
ZC3H11A
SMG7
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
AKT3
ARPC5
PRG4
GPA33
STX6
BPNT1
TIMM17A
LRRN2
ZNF238
SLC19A2
IVNS1ABP
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
OCLM
IL24
DUSP10
DUSP12
COG2
PLEKHA6
KIFAP3
ATF6
RBM34
KIF21B
NMNAT2
NFASC
GLT25D2
RGL1
PRRC2C
FBXO28
CAMSAP2
SRGAP2
CRB1
GPR161
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
BRP44
TRIM58
INTS7
OLFML2B
AHCTF1
NSL1
DNM3
TOR1AIP1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
RNU5F-1
DIEXF
TAF5L
CACYBP
DISC2
DISC1
KLHL20
FLVCR1
UBE2T
CNIH4
PYCR2
NME7
NENF
IL19
G0S2
IL20
RRP15
GLRX2
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
IER5
UCHL5
C1orf9
HSD17B7
DTL
METTL13
CYB5R1
ARID4B
TMCO1
EGLN1
KIAA1383
SWT1
LAX1
C1orf27
MARC2
SUSD4
KIF26B
RALGPS2
GPATCH2
HEATR1
DARS2
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
C1orf112
HHAT
ENAH
NUP133
RCOR3
C1orf106
ADCY10
DCAF6
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
SCYL3
GJC2
CAMK1G
SIPA1L2
POGK
KIAA1614
FAM5B
C1orf114
ZP4
RHOU
KLHL12
LGR6
GAS5
PAPPA2
TNN
MRPS14
TFB2M
TOR3A
RFWD2
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
MGC4473
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
C1orf129
WDR26
EDEM3
TRAF3IP3
SH3BP5L
NPL
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
SHCBP1L
TRMT1L
NUAK2
DDX59
NUF2
RASSF5
HMCN1
MIXL1
C1orf124
FCAMR
OBSCN
C1orf49
NTPCR
EFCAB2
ACBD6
KIAA1804
ZBTB37
LINC00260
LINC00467
FCRLA
ANKRD36BP1
ZNF496
C1orf198
PPP1R15B
MAEL
DISP1
RGS8
WNT3A
NAV1
SEC16B
LHX4
ANGEL2
IGFN1
CENPL
DUSP27
RCSD1
METTL18
GORAB
C1orf105
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FMO9P
FAM36A
TSEN15
FAM129A
SNAP47
TADA1
SH2D1B
C1orf96
AXDND1
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
RC3H1
CNIH3
LOC149134
METTL11B
FAM78B
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
C1orf55
CNST
C1orf65
FLJ23867
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
C1orf192
ASPM
TIPRL
PGBD2
OR2L13
SLC9A11
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
LOC284648
DKFZP564C196
C1orf111
LOC284688
HNRNPU-AS1
LIN9
VN1R5
ANKRD45
FAM5C
ZNF678
PRSS38
C1orf110
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
RGSL1
IRF2BP2
ZBTB41
SFT2D2
MIA3
C1orf95
FAM89A
RPS10P7
ILDR2
FMO6P
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf226
LOC400794
C1orf220
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR194-1
MIR199A2
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
RGS21
LRRC52
LOC440700
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
MIR488
SNORD74
RPL31P11
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SCARNA3
SNORA14B
SNORA36B
SNORA77
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
MIR556
MIR557
LOC728463
FAM72A
LOC730102
LOC730159
LOC730227
LOC731275
MIR921
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
GM140
LOC100288079
MIR1182
MIR1537
MIR1231
MIR1278
MIR1295A
MIR548F1
MIR664
LOC100302401
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3119-1
MIR3123
MIR3124
MIR3120
MIR4260
MIR3122
MIR3119-2
MIR3121
MIR3620
MIR3658
MIR3916
LOC100505795
PROX1-AS1
LOC100505918
LOC100506023
LOC100506046
KDM5B-AS1
LOC100506795
LOC100506810
LOC100527964
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4424
MIR4677
MIR4735
MIR4671
MIR4654
MIR4427
MIR4742
DNM3OS
LINC00538

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
PHOX2B
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
APBB2
RHOH
ATP5I
NKX3-2
BST1
CCKAR
CD38
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GRK4
HTT
HGFAC
UBE2K
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RFC1
RGS12
RNF4
RPL9
S100P
SH3BP2
SOD3
TLR1
UCHL1
UGDH
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
TLR6
PCGF3
ATP8A1
SPON2
TACC3
SLC30A9
SLC34A2
MXD4
CORIN
PTTG2
CPLX1
SLC26A1
PPARGC1A
LIAS
LIMCH1
TBC1D1
SEL1L3
PDS5A
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
KLHL5
SEPSECS
KLF3
STX18
FGFRL1
CYTL1
SH3TC1
RBM47
PIGG
DCAF16
COMMD8
TMEM33
LGI2
PGM2
C4orf19
TBC1D19
PI4K2B
CNO
STK32B
CHRNA9
LYAR
N4BP2
SLC2A9
ATP10D
KIAA1239
TBC1D14
SORCS2
CC2D2A
STIM2
KIAA1530
WDR19
ZFYVE28
GBA3
AFAP1
GUF1
NCAPG
TNIP2
HAUS3
FLJ13197
NSUN7
ABCA11P
TMEM156
GRPEL1
MED28
KCNIP4
TLR10
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
FAM114A1
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
ARAP2
GNPDA2
CPEB2
EVC2
PACRGL
OTOP1
NFXL1
SHISA3
ZNF595
LOC152742
JAKMIP1
KLB
FAM53A
METTL19
GPR125
ZBTB49
COX7B2
ZNF721
C4orf34
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
DCAF4L1
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
YIPF7
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
NAT8L
LOC344967
C4orf44
FAM86EP
POLN
KCNIP4-IT1
KCTD8
C4orf52
BEND4
GRXCR1
USP17L6P
USP17
HSP90AB2P
C4orf48
DTHD1
LOC401127
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
MIR574
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
RELL1
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4802
MIR4800
MIR4801
MIR4798
HTT-AS1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.27 | 1.89 | 0.107 | 0.10 | -2.03 | 1
1q | 1955 | 0.34 | 3.18 | 0.00584 | 0.13 | -1.42 | 1
2p | 924 | 0.33 | 0.588 | 0.68 | 0.17 | -2.29 | 1
2q | 1556 | 0.14 | -2.13 | 1 | 0.26 | 0.502 | 0.615
3p | 1062 | 0.44 | 2.99 | 0.00928 | 0.32 | 0.528 | 0.615
3q | 1139 | 0.49 | 4.35 | 6.66e-05 | 0.17 | -1.86 | 1
4p | 489 | 0.13 | -3.39 | 1 | 0.42 | 1.49 | 0.229
4q | 1049 | 0.07 | -3.84 | 1 | 0.39 | 2.1 | 0.0799
5p | 270 | 0.43 | 1.27 | 0.338 | 0.42 | 0.968 | 0.469
5q | 1427 | 0.17 | -1.48 | 1 | 0.44 | 3.93 | 0.000557
6p | 1173 | 0.11 | -3.15 | 1 | 0.28 | 0.0822 | 0.85
6q | 839 | 0.08 | -3.83 | 1 | 0.39 | 1.73 | 0.168
7p | 641 | 0.44 | 2.27 | 0.0469 | 0.05 | -4.36 | 1
7q | 1277 | 0.40 | 2.84 | 0.0127 | 0.11 | -2.69 | 1
8p | 580 | 0.31 | -0.376 | 1 | 0.56 | 4.27 | 0.000341
8q | 859 | 0.52 | 4.45 | 5.85e-05 | 0.14 | -2.55 | 1
9p | 422 | 0.31 | -0.59 | 1 | 0.53 | 3.35 | 0.00328
9q | 1113 | 0.25 | -0.505 | 1 | 0.42 | 2.74 | 0.0175
10p | 409 | 0.38 | 0.612 | 0.68 | 0.31 | -0.681 | 1
10q | 1268 | 0.13 | -2.53 | 1 | 0.33 | 1.3 | 0.298
11p | 862 | 0.11 | -3.11 | 1 | 0.47 | 3.45 | 0.00282
11q | 1515 | 0.11 | -2.47 | 1 | 0.38 | 2.92 | 0.0115
12p | 575 | 0.35 | 0.313 | 0.838 | 0.12 | -3.65 | 1
12q | 1447 | 0.30 | 1.13 | 0.399 | 0.11 | -2.65 | 1
13q | 654 | 0.36 | 0.557 | 0.68 | 0.30 | -0.453 | 1
14q | 1341 | 0.26 | -0.021 | 1 | 0.31 | 0.931 | 0.469
15q | 1355 | 0.13 | -2.4 | 1 | 0.33 | 1.49 | 0.229
16p | 872 | 0.21 | -1.78 | 1 | 0.30 | -0.0031 | 0.872
16q | 702 | 0.25 | -1.39 | 1 | 0.26 | -1.22 | 1
17p | 683 | 0.28 | -0.617 | 1 | 0.54 | 4.14 | 0.000341
17q | 1592 | 0.35 | 2.49 | 0.0285 | 0.18 | -1.13 | 1
18p | 143 | 0.34 | -0.502 | 1 | 0.41 | 0.578 | 0.615
18q | 446 | 0.22 | -1.93 | 1 | 0.46 | 2.31 | 0.0528
19p | 995 | 0.24 | -1 | 1 | 0.33 | 0.617 | 0.615
19q | 1709 | 0.35 | 2.74 | 0.0155 | 0.22 | -0.128 | 0.918
20p | 355 | 0.62 | 5.34 | 9.3e-07 | 0.17 | -2.44 | 1
20q | 753 | 0.66 | 6.93 | 8.68e-11 | 0.18 | -1.75 | 1
21q | 509 | 0.37 | 0.667 | 0.68 | 0.21 | -2.18 | 1
22q | 921 | 0.31 | 0.173 | 0.908 | 0.35 | 0.873 | 0.479
Xq | 1312 | 0.21 | -0.996 | 1 | 0.27 | 0.154 | 0.836

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BLCA/1970944/2.GDAC_MergeDataFiles.Finished/BLCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 97 Input Tumor Samples.

Tumor Sample Names
TCGA-BL-A0C8-01A-11D-A10T-01
TCGA-BL-A13I-01A-11D-A13V-01
TCGA-BL-A13J-01A-11D-A10T-01
TCGA-BL-A3JM-01A-12D-A219-01
TCGA-BT-A0S7-01A-11D-A10T-01
TCGA-BT-A0YX-01A-11D-A10T-01
TCGA-BT-A20J-01A-11D-A14V-01
TCGA-BT-A20N-01A-11D-A14V-01
TCGA-BT-A20O-01A-21D-A14V-01
TCGA-BT-A20P-01A-11D-A14V-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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