Head and Neck Squamous Cell Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.15 (cga svn revision 34144).

Summary

There were 165 tumor samples used in this analysis: 20 significant arm-level results, 30 significant focal amplifications, and 45 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 - 30 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
--- | --- | --- | --- | ---
11q13.3 | 1.3283e-95 | 1.3283e-95 | chr11:69722985-69914440 | 3
7p11.2 | 2.2259e-11 | 2.2259e-11 | chr7:54998999-55426994 | 2
8p12 | 4.0426e-07 | 4.0426e-07 | chr8:38263360-38405175 | 3
17q12 | 5.3242e-06 | 5.3242e-06 | chr17:35013152-35213123 | 10
20q11.22 | 1.5197e-05 | 1.5197e-05 | chr20:32121011-32596844 | 8
2q11.2 | 0.00066873 | 0.00090745 | chr2:96851006-96974656 | 5
18q11.2 | 0.0029612 | 0.0029612 | chr18:18916281-19244464 | 2
9p13.3 | 0.0015633 | 0.0039959 | chr9:35231249-36270787 | 32
18p11.31 | 0.0046028 | 0.0046028 | chr18:2820250-4738590 | 9
5p12 | 0.0054316 | 0.0078037 | chr5:43833357-43865407 | 0 [NNT]
3q26.32 | 0.0085717 | 0.0085717 | chr3:169846861-185125444 | 64
2q31.2 | 0.0051251 | 0.012645 | chr2:174045666-178702724 | 36
7q22.1 | 0.018545 | 0.018545 | chr7:102996265-103268879 | 1
8q24.21 | 0.020204 | 0.020204 | chr8:125448587-146274826 | 160
12q15 | 0.020204 | 0.020204 | chr12:67642939-68090477 | 5
11p13 | 0.079917 | 0.079917 | chr11:35774202-37260150 | 8
12p13.32 | 0.08813 | 0.08813 | chr12:1-5303065 | 44
14q24.1 | 0.092721 | 0.092721 | chr14:59508929-67913941 | 57
5p15.33 | 0.052028 | 0.11422 | chr5:433125-604389 | 6
15q26.3 | 0.12159 | 0.12159 | chr15:93715479-98856681 | 18
6p12.1 | 0.12389 | 0.13416 | chr6:52691465-56821346 | 21
21q21.1 | 0.14663 | 0.14663 | chr21:19337339-19694105 | 0 [PRSS7]
13q22.1 | 0.15644 | 0.15644 | chr13:72778415-73085147 | 0 [KLF12]
9p24.1 | 0.030577 | 0.17549 | chr9:5411313-5483683 | 2
12p11.21 | 0.17818 | 0.17818 | chr12:30616028-31331717 | 5
22q11.21 | 0.17818 | 0.17818 | chr22:17958537-20258915 | 47
4p12 | 0.18701 | 0.18701 | chr4:48322889-48441365 | 1
6q12 | 0.17818 | 0.19005 | chr6:64322832-64626846 | 3
9p23 | 0.033482 | 0.19386 | chr9:13387807-16494663 | 10
2q32.2 | 0.0046028 | 1 | chr2:1-242951149 | 1324

Genes in Wide Peak

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

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

Genes
hsa-mir-548k
PPFIA1
FADD

Genes in Wide Peak

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

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

Genes
EGFR
LANCL2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p12.

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

Genes
FGFR1
WHSC1L1
LETM2

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
NEUROD2
PNMT
TCAP
STARD3
IKZF3
PPP1R1B
C17orf37
PGAP3

Genes in Wide Peak

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

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

Genes
hsa-mir-644
AHCY
ASIP
EIF2S2
RALY
DYNLRB1
ITCH
MIR644

Genes in Wide Peak

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

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

Genes
CNNM3
ANKRD39
FAM178B
SEMA4C
ANKRD23

Genes in Wide Peak

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

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

Genes
C18orf45
CABLES1

Genes in Wide Peak

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

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

Genes
CA9
CCIN
CD72
CLTA
NPR2
RMRP
TESK1
TLN1
TPM2
RECK
RGP1
RUSC2
GNE
CREB3
UNC13B
SPAG8
SIT1
TMEM8B
OR2S2
GBA2
HINT2
C9orf100
LOC92973
GLIPR2
LOC158376
LOC158381
CCDC107
C9orf128
OR13J1
HRCT1
MSMP
FAM166B

Genes in Wide Peak

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

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

Genes
TGIF1
MYOM1
DLGAP1
LPIN2
MYL12A
EMILIN2
MYL12B
FLJ35776
LOC727896

Genes in Wide Peak

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

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

Genes
PIK3CA
SOX2
hsa-mir-569
ACTL6A
ECT2
MECOM
GHSR
NDUFB5
CLDN11
PLD1
PRKCI
SKIL
SLC2A2
TERC
SEC62
FXR1
TNFSF10
USP13
ABCC5
KCNMB2
NLGN1
TNIK
MCF2L2
ATP11B
GPR160
LAMP3
KCNMB3
ZNF639
PEX5L
DCUN1D1
KLHL24
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
MRPL47
NCEH1
SLC7A14
GNB4
ZMAT3
FNDC3B
TBL1XR1
LRRC31
MAP6D1
PHC3
SPATA16
B3GNT5
ARPM1
KLHL6
C3orf50
DNAJC19
TTC14
LRRC34
RPL22L1
NAALADL2
CCDC39
LRRIQ4
SAMD7
SOX2OT
TMEM212
MIR569
LOC100128164

Genes in Wide Peak

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

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

Genes
CHN1
HOXD11
HOXD13
NFE2L2
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
ATP5G3
CHRNA1
ATF2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
SP3
WIPF1
AGPS
CIR1
MTX2
OLA1
PDE11A
SCRN3
KIAA1715
TTC30A
RBM45
TTC30B
GPR155
HNRNPA3
EVX2
MIR10B
MIR933
LOC100130691
SP9

Genes in Wide Peak

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

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

Genes
RELN

Genes in Wide Peak

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

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

Genes
MYC
RECQL4
hsa-mir-1234
hsa-mir-661
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1206
hsa-mir-1204
ADCY8
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
NFKBIL2
PLEC1
POU5F1B
PTK2
PVT1
RPL8
ST3GAL1
SLA
SQLE
TG
TSTA3
ZNF7
ZNF16
PSCA
LY6D
JRK
DGAT1
GPAA1
WISP1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
KHDRBS3
PTP4A3
RNF139
PUF60
DENND3
ZC3H3
EFR3A
ARC
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
EIF2C2
COMMD5
DDEF1IT1
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
C8orf30A
KCNK9
C8orf55
FAM49B
CHRAC1
EXOSC4
LY6K
TRMT12
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
PYCRL
C8orf33
LYNX1
C8orf51
GPR172A
GSDMD
ZNF696
KIAA1688
ZNF34
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
MAF1
PARP10
TIGD5
PPP1R16A
ZNF251
KIFC2
NAPRT1
HPYR1
MFSD3
RHPN1
TOP1MT
ZNF572
LYPD2
TMEM71
TMEM65
LOC157381
FAM84B
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P
C8orf77
C8orf31
ZFP41
GPIHBP1
NRBP2
ZNF517
KIAA1875
C8ORFK29
SPATC1
FLJ43860
MAFA
MIR30B
MIR30D
MGC70857
LRRC24
ZFATAS
NCRNA00051
C8orf73
SCXB
MIR661
LOC727677
HEATR7A
OC90
LOC731779
MIR937
MIR939
SCXA
LOC100130274
LOC100133669

Genes in Wide Peak

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

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

Genes
hsa-mir-1279
CPM
LYZ
YEATS4
CPSF6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
RAG1
RAG2
TRAF6
COMMD9
TRIM44
PRR5L
C11orf74
LDLRAD3

Genes in Wide Peak

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

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

Genes
CCND2
KDM5A
CACNA1C
FGF6
FKBP4
FOXM1
KCNA1
KCNA5
KCNA6
NDUFA9
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
FGF23
DYRK4
AKAP3
RAD51AP1
TSPAN9
ERC1
GALNT8
ITFG2
PRMT8
PARP11
C12orf4
C12orf5
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
EFCAB4B
CACNA2D4
FBXL14
DCP1B
B4GALNT3
HSN2
IQSEC3
LRTM2
FAM138D
LOC100292680

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q24.1.

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

Genes
RAD51L1
GPHN
hsa-mir-625
hsa-mir-548h-1
ARG2
EIF2S1
ESR2
FNTB
FUT8
GPX2
HIF1A
HSPA2
MAX
MNAT1
MTHFD1
SIX6
PIGH
PPM1A
PPP2R5E
PRKCH
SIX1
SNAPC1
SPTB
ZBTB25
AKAP5
VTI1B
ZBTB1
SYNE2
ZFYVE26
PLEKHG3
PLEK2
KCNH5
RDH11
ATP6V1D
DHRS7
SIX4
RHOJ
PLEKHH1
TRMT5
MPP5
C14orf135
SGPP1
SYT16
CHURC1
WDR89
GPHB5
RDH12
C14orf50
SLC38A6
FAM71D
TMEM229B
TMEM30B
C14orf39
RAB15
C14orf53
LOC645431
FLJ43390

Genes in Wide Peak

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

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

Genes
SLC9A3
EXOC3
LOC25845
AHRR
C5orf55
LOC100310782

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
hsa-mir-1469
IGF1R
MEF2A
NR2F2
SYNM
TTC23
ARRDC4
LOC91948
LRRC28
LYSMD4
LOC145814
LOC145820
SPATA8
ADAMTS17
C15orf51
LASS3
FAM169B
FLJ42289

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p12.1.

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

Genes
BMP5
DST
GCLC
GSTA1
GSTA2
GSTA3
GSTA4
HCRTR2
GCM1
ICK
FBXO9
TINAG
HMGCLL1
LRRC1
ELOVL5
COL21A1
C6orf142
GSTA5
FAM83B
GFRAL
KLHL31

Genes in Wide Peak

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

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

Genes
CD274
C9orf46

Genes in Wide Peak

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

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

Genes
DDX11
IPO8
FAM60A
CAPRIN2
TSPAN11

Genes in Wide Peak

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

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

Genes
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
ARVCF
COMT
CRKL
GP1BB
SERPIND1
PI4KA
SEPT5
RANBP1
SLC7A4
TBX1
UBE2L3
ZNF74
LZTR1
P2RX6
SNAP29
TXNRD2
HIC2
TRMT2A
POM121L8P
ZDHHC8
MED15
DGCR8
GNB1L
RTN4R
C22orf29
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
MGC16703
C22orf25
LOC150197
AIFM3
RIMBP3C
POM121L4P
PI4KAP2
LOC400891
MIR185
FLJ39582
P2RX6P
RIMBP3B
PI4KAP1

Genes in Wide Peak

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

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

Genes
FRYL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
PTP4A1
PHF3
EYS

Genes in Wide Peak

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

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

Genes
NFIB
SNAPC3
CER1
PSIP1
BNC2
TTC39B
FREM1
C9orf93
ZDHHC21
LOC389705

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q32.2.

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

Genes
ALK
ATIC
CHN1
CREB1
DNMT3A
ERCC3
ACSL3
MSH6
HOXD11
HOXD13
IDH1
MSH2
MYCN
NFE2L2
PAX3
PMS1
REL
PAX8
NCOA1
EML4
BCL11A
FEV
TTL
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
hsa-mir-153-1
hsa-mir-375
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-1978
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-1285-2
hsa-mir-216b
hsa-mir-559
hsa-mir-558
hsa-mir-1301
AAMP
ACADL
ACP1
ACTG2
ACVR1
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
AGXT
ALPI
ALPP
ALPPL2
BIN1
ANXA4
AOX1
APOB
RHOB
RND3
ATP5G3
ATP6V1B1
KIF1A
AUP1
BARD1
BCS1L
BMPR2
BOK
ZFP36L2
BUB1
CACNB4
CAD
CALM2
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CENPA
CHRNA1
CHRND
CHRNG
CLK1
CNGA3
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
COX5B
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CTNNA2
CYP1B1
CYP27A1
DARS
DBI
DCTN1
DDX1
DES
DGUOK
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DTNB
DTYMK
DUSP2
E2F6
EEF1B2
EGR4
EMX1
EN1
EPAS1
EPHA4
ERBB4
FABP1
FAP
EFEMP1
FHL2
FKBP1B
FN1
FOSL2
FRZB
FSHR
FTHL3P
GAD1
GALNT3
GBX2
GCG
GCKR
MSTN
GFPT1
GGCX
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GTF3C2
GYPC
HADHA
HADHB
HDLBP
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HPCAL1
AGFG1
DNAJB2
HSPD1
HSPE1
FOXN2
HTR2B
ID2
SP110
IGFBP2
IGFBP5
IHH
IL1A
IL1B
IL1R1
IL1RN
IL8RA
IL8RB
IL8RBP
INHA
INHBB
INPP1
INPP4A
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNF1
KCNJ3
KCNJ13
KCNK3
KCNS3
KHK
KIF3C
KIF5C
AFF3
LCT
LHCGR
LIMS1
LRP2
LTBP1
LY75
EPCAM
MXD1
MAL
MAP2
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MYO1B
MTIF2
MYL1
MYO7B
NAB1
NCL
NEB
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPAS2
NPHP1
NPPC
NR4A2
ODC1
ORC2L
ORC4L
OTX1
REG3A
PCBP1
PDCD1
PDE1A
PDE6D
PDK1
PEX13
VIT
SERPINE2
PIGF
PLCL1
PLEK
PLGLB2
PLGLB1
POLR2D
POMC
POU3F3
PPM1B
PPM1G
PPP1CB
PPP1R7
PPP3R1
PRKCE
EIF2AK2
PROC
PSMD1
PTH2R
PTMA
PTPN4
PTPRN
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
REG1P
SNORD20
RPE
RPL31
RPL37A
RPS7
RPS27A
RRM2
RTKN
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
CCL20
SDC1
SFRS7
SFTPB
SIX3
SLC4A3
SLC1A4
SLC3A1
SLC8A1
SLC9A2
SLC11A1
SLC20A1
SNRPG
SOS1
SOX11
SP3
SP100
SPAST
SPP2
SPR
SPTBN1
SRD5A2
SSB
SSFA2
STAT1
STAT4
STRN
SULT1C2
ADAM17
TACR1
C2orf3
TFPI
TGFA
TIA1
TNFAIP6
TNP1
TNS1
TPO
TSN
TSSC1
TTN
TUBA4A
SUMO1
UCN
UGP2
VIL1
VRK2
VSNL1
WIPF1
WNT6
XDH
XPO1
XRCC5
ZAP70
ZNF2
ZNF142
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
FZD5
SCG2
DYSF
FZD7
SDPR
NCK2
DUSP11
CUL3
KLF11
MAP4K3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ASAP2
PER2
ST3GAL5
SLC5A6
DDX18
EIF2B4
CDK5R2
KYNU
TAF1B
NAT8
NMI
RQCD1
COX7A2L
TMSB10
IL1RL1
LRRFIP1
STK17B
ITGB1BP1
GPR55
TRIP12
GTF3C3
PPIG
NRXN1
OTOF
CIAO1
TGFBRAP1
HS6ST1
CRIPT
ECEL1
MAP4K4
EIF2AK3
EIF4E2
ROCK2
CHST10
TP53I3
CIR1
MRPL33
BRE
PREPL
CYTIP
FEZ2
GCC2
TTLL4
SOCS5
EIF5B
GREB1
BZW1
USP34
LAPTM4A
HDAC4
RNF144A
SNX17
SERTAD2
MRPL19
ZEB2
FARP2
TLK1
SUPT7L
CD302
ARHGAP25
TANK
BCL2L11
FARSB
ABCB6
ACTR3
ACTR2
ARPC2
PREB
ACTR1B
ARL4C
LRPPRC
PDIA6
ABI2
CEBPZ
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
SMYD5
KBTBD10
MYCNOS
C1D
MERTK
UBE2E3
STK25
SEMA4F
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
MTX2
CGREF1
B3GNT2
USP39
TBR1
SIX2
MAP3K2
NCKAP1
VAMP5
MTHFD2
ARID5A
PROKR1
RAB10
EDAR
COPS8
GPR75
YWHAQ
IMMT
SNRNP27
GTF2A1L
STON1
RAPGEF4
EMILIN1
CAPN10
TBC1D8
RABL2A
GALNT5
NXPH2
GPR45
SP140
MGAT4A
GPN1
IKZF2
COBLL1
AAK1
FASTKD2
MAPRE3
PLA2R1
RAB3GAP1
RPIA
SLC4A1AP
EFR3B
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
PASK
UBXN4
ATG4B
PSME4
EXOC6B
EHBP1
SATB2
CLASP1
OBSL1
PUM2
NCAPH
RHOQ
SF3B1
HAAO
TMEM131
R3HDM1
DNPEP
PSD4
WBP1
NTSR2
TMEFF2
SH3BP4
PRKD3
KCNE4
RASGRP3
NGEF
QPCT
GCA
VAX2
SNORD82
MOBKL3
POLR1A
CNRIP1
FAM98A
PNKD
UNC50
SNED1
GORASP2
SPATS2L
RAB11FIP5
GIGYF2
EPC2
TRAF3IP1
ABCA12
IFT172
ARL5A
HIBCH
PTPN18
CNNM4
CNNM3
IL1F5
SH3YL1
SNORD53
SNORD51
C2orf24
STK36
IL1F8
IL1F7
IL1F6
SULT1C4
NFU1
ERLEC1
MMADHC
BMP10
ZNF638
STK39
HTRA2
TRIB2
LOC29034
METTL5
HSPC159
OLA1
C2orf27A
GRHL1
TFCP2L1
ICOS
GMPPA
NRBP1
BAZ2B
SLC40A1
KCNIP3
EHD3
SMARCAL1
CD207
ITSN2
ANO7
ARHGEF4
PDE11A
TPRKB
FAHD2A
PRLH
C2orf86
MEMO1
THAP4
TTC15
ASB3
INSIG2
CRIM1
ANKRD39
FAM178B
RNF181
MRPL30
DNAJC27
ANKMY1
KRCC1
MRPL35
C2orf28
PCYOX1
GULP1
REV1
NAT8B
SCLY
VPS54
NBAS
LIPT1
NOP58
DYNC2LI1
SF3B14
YPEL5
VPS24
FKBP7
ASB1
CPSF3
CAB39
ZAK
LRP1B
PRKAG3
PPIL3
SNTG2
DNAJC10
ATAD2B
ETAA1
HEATR5B
CCDC93
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
AFTPH
MFSD6
TMEM214
RETSAT
INO80D
SEMA4C
C2orf18
C2orf42
TRMT61B
PID1
PTCD3
PLEKHB2
ATG16L1
FANCL
SRBD1
FIGN
ANKZF1
RIF1
USP40
MOBKL1B
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
HJURP
STRADB
C2orf56
HES6
ACCN4
C2orf29
NAGK
DOCK10
TTC27
SMPD4
TMEM127
PRPF40A
SLC30A6
IWS1
LIMS2
KIAA1310
MREG
CCDC88A
WDR12
MBD5
KDM3A
ALLC
PECR
ARHGAP15
ZC3H15
CFC1
DNAH7
GKN1
IL1F9
RPRM
CYP26B1
POLE4
KCNK12
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
C2orf83
MFF
RPL23AP32
CXCR7
RNPEPL1
RTN4
TRIM54
PELI1
SLC39A10
TTC7A
SMEK2
SLC4A10
CYP20A1
SPC25
BIRC6
ERMN
KIDINS220
MTA3
HECW2
WDR35
MARCH4
WDFY1
KIAA1486
DPP10
RDH14
EPB41L5
ALS2
ZDBF2
USP37
CWC22
ANKRD36B
G6PC2
SLC4A5
CTDSP1
NLRC4
MPP4
SLC5A7
NIF3L1
AGBL5
C2orf43
THADA
PCGEM1
RBKS
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
ATL2
ABCG5
ABCG8
RAB17
RNF25
HS1BP3
GMCL1
TTC31
ANAPC1
COPS7B
RMND5A
FNDC4
MARCH7
OBFC2A
PAPOLG
MRPS9
MRPS5
REEP1
RAPH1
PFTK2
ALS2CR4
NBEAL1
MRPL44
ANKRD57
PLEKHA3
TRAK2
BOLL
COLEC11
PDCL3
TRPM8
ATG9A
C2orf49
MLPH
TMEM185B
FAM134A
CENPO
OR7E91P
GLB1L
C2orf47
SPAG16
CHPF
SAP130
GALNT14
SCRN3
CCDC121
FASTKD1
SMC6
GTDC1
CLIP4
IQCA1
ALS2CR8
TTC21B
C2orf34
METTL8
GEMIN6
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
NOL10
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
TUBA4B
FAM128B
YSK4
UXS1
FBXO11
ARMC9
COQ10B
SLC35F5
EFHD1
C2orf44
SPHKAP
WNT10A
SLC19A3
TSGA10
THSD7B
THUMPD2
TMEM177
KIAA1715
ILKAP
FAM49A
LMAN2L
LBH
TMEM163
ITM2C
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
RHBDD1
CHCHD5
YIPF4
C2orf7
C2orf88
ING5
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
DPY30
MCEE
LOXL3
ABHD1
PCGF1
MGC13005
MFSD9
PLCD4
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
MGC16025
TANC1
SELI
LBX2
PNPT1
KCNH7
FER1L5
MCFD2
ATP6V1E2
CCDC74A
LOC90784
DHX57
LOC91149
SESTD1
CCDC74B
SGK493
ANKRD44
RSAD2
ZNF804A
TTC30A
DAPL1
CAPN13
TMEM169
DNER
C2orf39
IMP4
HNRPLL
MARS2
B3GNT7
NT5C1B
NEURL3
SP140L
SFXN5
ORMDL1
LIMS3
NCRNA00152
TUBA3E
CCDC104
TEX261
TUBA3D
STK11IP
FMNL2
CCDC85A
GALNT13
KLHL29
OSBPL6
NOSTRIN
DIRC1
WDR92
MOGAT1
LYPD1
MRPL53
AGAP1
PARD3B
RPL23AP7
KLRAQ1
C2orf89
TMEM150A
NUP35
XIRP2
C2orf60
NMS
LYG1
MITD1
DIS3L2
CMPK2
MBOAT2
CNTNAP5
TMEM18
FBLN7
NEU4
RBM45
C2orf73
TRIM43
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
CIB4
REG3G
RFTN2
C2orf63
PLEKHH2
AP1S3
C2orf76
SGPP2
ACVR1C
OSR1
TTC32
UBR3
KCTD18
ALS2CR12
ZNF513
SPATA3
LYPD6
LYPD6B
GALM
TMEM198
ZFAND2B
TMEM178
CPO
MDH1B
C2orf50
PQLC3
TMEM182
AHSA2
FBXO36
MTERFD2
CCDC148
C2orf65
MYO3B
TMEM37
UBE2F
DUSP19
CKAP2L
CBWD2
TEKT4
LOC150527
FLJ32063
LOC150568
SMYD1
C2orf15
LOC150622
OTOS
MYEOV2
OR6B3
COMMD1
PROM2
ANKAR
FBXO41
TTC30B
GPAT2
ITPRIPL1
LOC150776
LOC150786
FAM117B
TCF23
PUS10
LOC151009
SEPT10
C2orf67
PLB1
ZSWIM2
ZNF385B
LOC151162
LOC151174
ARL6IP6
FAM119A
CCNYL1
KLHL23
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
LOC151300
GPBAR1
FAHD2B
MYADML
FAM84A
FAM82A1
GDF7
SLC16A14
C2orf52
MSL3L2
ASPRV1
WDSUB1
UPP2
LOC151534
GPR155
BZW1L1
WDR69
LONRF2
CCDC138
GPR113
C2orf57
OXER1
FAM179A
FAM171B
C1QL2
UBXN2A
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
PIKFYVE
KRTCAP3
LOC200726
TMEM17
SPRED2
TIGD1
FAM123C
NCRNA00116
C2orf69
HNRNPA3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
LASS6
MAP1D
LYG2
CCDC108
C2orf72
SH2D6
CCDC150
RNF149
FAM150B
CCDC141
LOC285033
LOC285045
C2orf61
LOC285074
C2orf85
DNAJC5G
IAH1
C2orf58
FAM126B
UNC80
RUFY4
PLGLA
RGPD4
DUSP28
STON1-GTF2A1L
SPOPL
CYP27C1
ESPNL
C2orf70
C2orf53
LOC339788
C2orf74
MSGN1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
EVX2
CDKL4
PRDXDD1P
AOX2P
SH3RF3
GPR148
ECEL1P2
LRRTM1
GEN1
C2orf48
PFN4
LOC375190
LOC375196
ANKRD36
WASH2P
RBM43
CERKL
C2orf62
RBM44
AQP12A
ZC3H6
KLHL30
MFSD2B
C2orf71
LOC388946
TSPYL6
LOC388955
C2orf78
BOLA3
C2orf81
LOC388965
C2orf68
SLC9A4
LOC389033
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
C2orf90
C2orf79
SULT6B1
DYTN
LOC400940
EML6
PAIP2B
RGPD1
LOC401010
C2orf66
ASB18
VWC2L
MIR10B
MIR128-1
MIR149
MIR153-1
MIR216A
MIR217
MIR26B
C2orf27B
DNAJB3
ASTL
CAPN14
FKSG73
LOC440895
LOC440905
LOC440925
SULT1C3
POTEE
C2orf64
PHOSPHO2
CHAC2
MIR375
DFNB59
LOC541471
NCRNA00164
FBXO48
SNORA41
FAM110C
LOC643387
PRR21
GGT8P
FLJ40330
C2orf84
TRIM43B
CFC1B
AQP12B
RGPD3
FAM128A
SNORA75
LOC654342
FAM138B
LOC654433
SCARNA6
SCARNA5
SNORD11
SNORD70
SNORD89
SNORD92
SNORD94
MIR558
MIR559
MIR561
RGPD8
D2HGDH
LOC728323
POTEF
PABPCP2
LOC728819
LOC729121
ANKRD20B
LOC729234
RAD51AP2
RGPD6
DIRC3
RGPD2
MORN2
LOC730811
RFX8
SNORD11B
SNORA36C
SNORA70B
MIR216B
MIR933
LOC100128731
LOC100129726
PP14571
LOC100130691
TMEM194B
SP9
LOC100132215
C2orf14
LOC100133985
LOC100134259
RNU4ATAC
SNAR-H
LOC100189589
LOC100271715
LOC100271832
LIMS3-LOC440895
LOC100287216
LOC100302650
LOC100302652
SNORA80B

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 - 45 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 | 3.3255e-55 | 1.0692e-51 | chr9:21855498-21987722 | 2
3p14.2 | 1.3643e-20 | 3.4843e-20 | chr3:59009803-61522370 | 1
8p23.2 | 6.1117e-14 | 6.1117e-14 | chr8:2080589-6255647 | 1
4q35.2 | 3.5821e-09 | 6.7058e-09 | chr4:187447681-189156683 | 2
2q22.1 | 5.7799e-11 | 3.724e-08 | chr2:139248662-143354308 | 1
2q36.3 | 6.7058e-09 | 1.7536e-06 | chr2:213855358-242951149 | 247
10p11.22 | 7.5577e-06 | 7.5577e-06 | chr10:33662799-35344867 | 1
11q22.3 | 3.0762e-05 | 3.0762e-05 | chr11:103411263-124810439 | 213
14q32.32 | 7.1494e-05 | 0.00026793 | chr14:101892998-102636537 | 6
1p13.1 | 0.00062155 | 0.00062155 | chr1:111529809-165756937 | 548
13q12.12 | 0.00027912 | 0.0007397 | chr13:1-24589021 | 40
5q11.2 | 0.00012364 | 0.0012093 | chr5:58180924-59823742 | 3
17q25.3 | 0.0012093 | 0.0012093 | chr17:78197803-78496029 | 5
16q23.3 | 0.0012856 | 0.0017511 | chr16:80761244-82402288 | 1
3p12.3 | 0.00042259 | 0.0020542 | chr3:79897608-85095529 | 1
13q21.31 | 0.0011015 | 0.0020542 | chr13:60880247-65781730 | 2
1p36.13 | 0.0033057 | 0.0033057 | chr1:1-148117443 | 1215
7q31.1 | 0.0040831 | 0.0041385 | chr7:110512908-111163100 | 1
9p24.1 | 2.0033e-06 | 0.0063077 | chr9:7786330-12683402 | 2
4q22.1 | 0.00658 | 0.014717 | chr4:91092757-93459528 | 2
18q23 | 0.018205 | 0.018205 | chr18:56186185-76117153 | 62
19p13.3 | 0.018205 | 0.018571 | chr19:1-62963291 | 1500
2q21.2 | 3.0762e-05 | 0.029638 | chr2:133139822-134729105 | 1
5q35.2 | 0.033294 | 0.032301 | chr5:176454063-176664472 | 2
7q36.1 | 0.033294 | 0.032301 | chr7:131718011-158821424 | 216
16q12.1 | 0.018605 | 0.04253 | chr16:31679819-55026352 | 58
11q14.2 | 0.04923 | 0.049156 | chr11:85028471-100369355 | 73
10q23.31 | 0.073322 | 0.074833 | chr10:86074834-100991851 | 131
22q13.31 | 0.073259 | 0.074833 | chr22:41151625-49691432 | 103
6p24.1 | 0.10849 | 0.10849 | chr6:1-17413378 | 87
19q13.43 | 0.10632 | 0.10849 | chr19:9722799-63811651 | 1248
14q23.3 | 0.067019 | 0.10963 | chr14:66032906-66727865 | 1
5p11 | 0.0061147 | 0.1284 | chr5:43561332-64821431 | 67
15q15.1 | 0.031715 | 0.1284 | chr15:1-43194344 | 286
14q11.2 | 0.077856 | 0.13145 | chr14:1-34832416 | 180
21q22.3 | 0.13626 | 0.13145 | chr21:1-46944323 | 267
12q12 | 0.14841 | 0.14183 | chr12:19480356-60876690 | 408
16q13 | 0.068501 | 0.14183 | chr16:48078795-64169892 | 95
6q14.2 | 0.16779 | 0.16552 | chr6:58337167-152470396 | 371
9p21.2 | 0.0076487 | 0.17704 | chr9:27562512-28858209 | 3
11p15.5 | 0.18842 | 0.19701 | chr11:1-29999147 | 349
3p24.1 | 0.047932 | 0.21708 | chr3:28540267-31998644 | 5
10p15.1 | 0.21613 | 0.21708 | chr10:1-10871379 | 47
15q21.1 | 0.084537 | 0.21708 | chr15:37875934-80132022 | 431
5q15 | 0.050326 | 0.23007 | chr5:1-180857866 | 961

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

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

Genes
FAT1
MTNR1A

Genes in Wide Peak

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

Table S32. 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 2q36.3.

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
hsa-mir-153-1
hsa-mir-375
hsa-mir-26b
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
IL8RA
IL8RB
IL8RBP
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
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
C2orf24
STK36
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
KIAA1486
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
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
TIGD1
CCDC108
C2orf72
C2orf85
RUFY4
DUSP28
ESPNL
ECEL1P2
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
PP14571

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.22.

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

Genes
PARD3

Genes in Wide Peak

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

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

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-100
hsa-mir-125b-1
hsa-mir-34c
ACAT1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
VWA5A
MCAM
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
SLN
SORL1
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
ZNF259
USP2
HTR3B
ZW10
UBE4A
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
C11orf60
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
ABCG4
ROBO3
C11orf1
RNF26
NLRX1
C11orf61
ALG9
ASAM
PDZD3
C11orf63
CCDC15
TMPRSS5
MFRP
BCO2
TMPRSS13
KIAA1826
BUD13
TMEM25
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
PANX3
APOA5
CASP12
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf65
MPZL3
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
LOC399959
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
LOC643923
CLDN25
RPL23AP64

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.32.

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

Genes
TRAF3
CDC42BPB
TECPR2
RCOR1
AMN
ANKRD9

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NRAS
NTRK1
PBX1
PRCC
SDHC
TPM3
PDE4DIP
TRIM33
hsa-mir-921
hsa-mir-556
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-190b
hsa-mir-554
hsa-mir-942
hsa-mir-320b-1
ADAR
ADORA3
ALDH9A1
AMPD1
APCS
APOA2
RHOC
ATP1A1
ATP1A2
ATP1A4
ATP5F1
BGLAP
CAPZA1
CASQ1
CASQ2
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
CD48
CD58
CHI3L2
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO5
DARC
GBA
GBAP
GJA5
GJA8
HDGF
HMGCS2
HSD3B1
HSD3B2
HSPA6
HSPA7
IGSF3
IFI16
IL6R
ILF2
INSRR
IVL
KCND3
KCNJ9
KCNJ10
KCNN3
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MOV10
MPZ
MTX1
NDUFS2
NGF
NHLH1
NHLH2
NIT1
NPR1
DDR2
OVGP1
PDZK1
PFDN2
PI4KB
PKLR
POU2F1
PPOX
PRKAB2
PSMB4
PSMD4
PTGFRN
PEX19
RAB13
RAP1A
RFX5
RGS4
RIT1
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SLAMF1
SLC16A1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
SYCP1
TBX15
VPS72
THBS3
TCHH
CCT3
TSHB
TUFT1
UCK2
USF1
WNT2B
CSDE1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
TTF2
RGS5
ITGA10
PEA15
B4GALT3
ADAM15
PEX11B
CD84
SELENBP1
SH2D2A
FCGR2C
PRPF3
ARHGEF2
DEDD
CD101
AIM2
ADAMTS4
SEC22B
CHD1L
SLC25A44
NOS1AP
ARHGEF11
LRIG2
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
TSPAN2
GPA33
SF3B4
BCAS2
WARS2
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
AP4B1
PHTF1
NES
WDR3
JTB
MTMR11
MAN1A2
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
TNRC4
DDX20
PMF1
DUSP12
VPS45
KIAA0907
ATF6
POGZ
SYT11
RPRD2
SMG5
NCSTN
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
OLFML2B
C1orf43
C1orf77
PTPN22
PHGDH
LCE2B
OR10J1
USP21
CHIA
SLC39A1
RNF115
ROBLD3
TMOD4
LASS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
C1orf66
APH1A
PLEKHO1
HAO2
ACP6
GPR89B
HSD17B7
UFC1
OAZ3
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
RSBN1
GDAP2
FAM46C
GON4L
GPATCH4
ST7L
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
SLC22A15
UBE2Q1
ITLN1
FAM63A
ASH1L
LENEP
CTTNBP2NL
C1orf183
RAG1AP1
SLAMF8
CDC42SE1
UBQLN4
OLFML3
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
DCLRE1B
MRPL9
INTS3
SCNM1
WDR77
FCRL2
MRPL24
TNFAIP8L2
C1orf54
VTCN1
PAQR6
DENND2D
TRIM46
SIKE1
TARS2
TRIM45
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
VANGL1
ISG20L2
FCRL5
FCRL4
NUF2
REG4
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
C1orf203
MAEL
AQP10
SLAMF9
PYGO2
ZNF697
NUP210L
DUSP27
MEX3A
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
FMO9P
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
C1orf161
HIST2H3C
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
C1orf88
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
SYT6
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
FAM78B
BNIPL
C1orf92
LOC149620
PYHIN1
DENND2C
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
LOC200030
NUDT17
SPAG17
KRTCAP2
CRTC2
HIPK1
AFARP1
LCE5A
ARHGAP30
C1orf192
MAGI3
FAM19A3
C1orf230
THEM5
NBPF15
ANKRD34A
C1orf104
C1orf204
C1orf111
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BA
S100A7A
LINGO4
RXFP4
C1orf110
OR10R2
FCRL6
NBPF7
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
PEAR1
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
NBPF20
MIR9-1
BCL2L15
HIST2H2BF
ETV3L
LRRC52
LOC441897
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
RPL31P11
LOC642502
PPIAL4G
PPIAL4D
LOC645166
LOC645676
S100A7L2
LOC647121
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA4
SNORA42
MIR554
MIR555
MIR556
MIR92B
HIST2H2AA4
LOC728855
LOC728875
NBPF11
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
C1orf152
MIR765
MIR942
MIR190B
MIR921
C1orf68
MSTO2P
TSTD1
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.12.

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

Genes
PARP4
ATP12A
FGF9
GJA3
GJB2
MIPEP
PABPC3
SGCG
TUBA3C
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
PSPC1
TNFRSF19
CENPJ
RNF17
XPO4
MRP63
TPTE2
N6AMT2
SKA3
EFHA1
SPATA13
ZDHHC20
DKFZp686A1627
LOC284232
C1QTNF9
LOC348021
LOC374491
C1QTNF9B
PCOTH
LOC646405
LOC100101938

Genes in Wide Peak

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

Table S39. 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 17q25.3.

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

Genes
TBCD
RAB40B
FN3K
FN3KRP
ZNF750

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
CDH13

Genes in Wide Peak

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

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

Genes
GBE1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.31.

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

Genes
PCDH20
OR7E156P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.13.

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

Genes
BCL9
CDKN2C
EPS15
JAK1
JUN
LCK
MPL
MUTYH
MYCL1
NOTCH2
NRAS
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
BCL10
PDE4DIP
THRAP3
TRIM33
PRDM16
RBM15
MDS2
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-101-1
hsa-mir-30c-1
hsa-mir-552
hsa-mir-1976
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
ABCA4
ACADM
ADORA3
AGL
AK2
AK3L1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
RERE
ATP1A1
ATP5F1
ATP6V0B
BAI2
BMP8B
BRDT
C1QA
C1QB
C1QC
C8A
C8B
CA6
CAPZA1
CAPZB
CASP9
CASQ2
RUNX3
CD2
TNFRSF8
CD53
CD58
CDA
CDC2L1
CDC20
CDC42
CD52
RCC1
CHI3L2
CLCA1
CLCN6
CLCNKA
CLCNKB
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
CORT
CPT2
CRYZ
CSF1
CSF3R
CTBS
CTH
CTPS
CYP2J2
CYP4A11
CYP4B1
DAB1
DBT
GADD45A
DDOST
DFFA
DFFB
DHCR24
DIO1
DPH2
DPYD
DR1
DVL1
E2F2
ECE1
S1PR1
EDN2
PHC2
CELSR2
MEGF6
EPHA2
ELAVL4
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EXTL2
EYA3
F3
FAAH
FABP3
FCGR1A
FCGR1B
FGR
FHL3
FOXE3
FOXD2
FMO5
MTOR
FUCA1
IFI6
GABRD
GALE
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GNAI3
GNAT2
GNB1
GNG5
SFN
GPR3
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HMGCS2
HPCA
HSD3B1
HSD3B2
IGSF3
HSPG2
HTR1D
HTR6
ID3
CYR61
IL12RB2
TNFRSF9
INPP5B
IPP
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
STMN1
LEPR
TACSTD2
MAGOH
MATN1
MFAP2
MOV10
MSH4
MTF1
MTHFR
NASP
NBL1
NDUFS5
NFIA
NFYC
NGF
NHLH2
NPPA
NPPB
NRD1
YBX1
ROR1
OPRD1
ORC1L
OVGP1
PAFAH2
PRDX1
PDE4B
PDZK1
PEX10
PEX14
PGD
PGM1
PIK3CD
PIN1L
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKAA2
PRKAB2
PRKACB
PKN2
PRKCZ
PSMA5
PSMB2
PTAFR
PTGER3
PTGFR
PTGFRN
PTPRF
ABCD3
RAB3B
RABGGTB
RAP1A
RAP1GAP
RBBP4
RHCE
RHD
RLF
SNORD21
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RSC1A1
SORT1
SARS
SCNN1D
SCP2
SFRS4
ST3GAL3
STIL
SKI
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SLC16A1
SRM
STXBP3
SYCP1
TAF12
TAF13
TBX15
TCEA3
TCEB3
TGFBR3
TIE1
TNFRSF1B
TP73
TSHB
TTC4
TNFRSF4
UQCRH
UROD
USP1
VCAM1
WNT2B
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
PTP4A2
CDC7
HIST2H2AA3
HIST2H4A
BCAR3
SNHG3
NR0B2
RAD54L
TTF2
PIK3R3
MMP23B
MMP23A
KCNAB2
ITGA10
LMO4
FCN3
CDC14A
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
FPGT
PEX11B
PER3
FUBP1
EIF2B3
ARTN
MAP3K6
DIRAS3
SLC16A4
KCNQ4
ZMYM4
ZMYM6
DHRS3
SFRS11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
C1orf38
TMEM59
SEC22B
CHD1L
H6PD
CLCA3P
CLCA2
ISG15
PLCH2
HS2ST1
IPO13
SDC3
KDM4A
CROCC
PUM1
KIAA0562
RIMS3
KIAA0494
DNAJC6
LRIG2
LPPR4
KLHL21
SLC35E2
ZBTB40
MFN2
RBM8A
INSL5
PIGK
PTPRU
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
BCAS2
AKR1A1
WARS2
CEPT1
PIAS3
TESK2
PPIE
VAV3
MAD2L2
PPIH
CAP1
LRRC41
HBXIP
IFI44
POLR3C
TXNIP
PDPN
KHDRBS1
GMEB1
AP4B1
NUDC
PHTF1
MASP2
AHCYL1
SFRS13A
WDR3
MAN1A2
UTS2
SF3A3
IFI44L
EBNA1BP2
KIF2C
RER1
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
MSTP2
DDX20
MSTP9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLCA4
MTF2
DNAJC8
NTNG1
CLSTN1
FOXJ3
WDR47
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
USP33
WDTC1
KIAA0090
KIF1B
MAST2
NCDN
CLCC1
SLC35D1
PLEKHM2
OTUD3
KIAA1026
CAMTA1
LPHN2
KIAA1107
ZCCHC11
KIAA0467
DNAJC16
UBR4
USP24
ATP13A2
ITGB3BP
TARDBP
CELA3B
SLC35A3
ICMT
MACF1
LRRC8B
LPAR3
PADI4
DDAH1
TMEM50A
KPNA6
SSBP3
STX12
NBPF14
CLIC4
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
C1orf144
LDLRAP1
SERBP1
NOC2L
PTPN22
PHGDH
FBXO2
FBXO6
PLA2G2D
AK5
MYCBP
HEYL
EIF2C1
OR4F3
SNORA66
SNORD45B
SNORD45A
SNORD55
RNU11
RNF11
FOXD3
TRAPPC3
HSPB7
CHIA
ARHGEF16
AHDC1
RNF115
TEKT2
SMPDL3B
ANGPTL3
PRO0611
HSPC157
SSU72
GNL2
GPSM2
UBIAD1
ALG6
PADI1
SLC25A24
PLA2G2E
DNTTIP2
WDR8
SLC45A1
HP1BP3
TMED5
CELA2B
ZNF593
ZNF691
TXNDC12
TNNI3K
SH3GLB1
MECR
UTP11L
SDF4
MRTO4
HAO2
ACP6
TMEM69
MRPL37
HOOK1
SNX7
HPCAL4
YTHDF2
GPR89B
ZCCHC17
DPH5
HSPB11
PADI3
CMPK1
GPR88
ERRFI1
WNT4
YIPF1
FBXO42
CCDC76
RNF186
SPATA6
MXRA8
L1TD1
HES2
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf123
C1orf159
AURKAIP1
TTC22
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
PRPF38B
CDCA8
LRRC8D
ARHGEF10L
PRMT6
RNF220
VPS13D
FAM176B
ATAD3A
TMEM57
TRIM62
RAVER2
PANK4
ECHDC2
FGGY
MCOLN3
SLC22A15
CAMK2N1
RNPC3
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
NBPF1
MAP7D1
TMEM48
NECAP2
IQCC
DNAJC11
C1orf103
CTTNBP2NL
RCC2
C1orf183
DMAP1
AJAP1
GNG12
C1orf91
FAM54B
CCBL2
TMEM167B
OLFML3
CTNNBIP1
C1orf63
AGTRAP
C1orf128
MAN1C1
NIPAL3
SEPN1
KIAA0495
PLEKHG5
AMIGO1
LRRC47
ODF2L
KIAA1324
PTCHD2
LRRC7
KIF17
ZSWIM5
KIAA1522
CACHD1
MIER1
HES4
GRHL3
PTBP2
DNASE2B
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
TINAGL1
SPATA1
LEPRE1
PLA2G2F
HIAT1
SMAP2
ATPAF1
S100PBP
MEAF6
DEM1
CCDC21
NMNAT1
ELOVL1
VWA1
DCLRE1B
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZNF643
C1orf163
PHACTR4
C1orf135
ERI3
C1orf50
WDR77
CCDC28B
EFHD2
MMEL1
C1orf89
DLEU2L
OR4F5
NKAIN1
EPS8L3
MUL1
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
NOL9
PPCS
LIN28
C1orf113
TTLL7
SNIP1
AGMAT
WDR78
ZMYM1
NCRNA00115
RPAP2
MORN1
GRRP1
KIAA0319L
DHDDS
DENND2D
GPR177
GPR157
RPF1
SIKE1
ZC3H12A
SPSB1
TRIM45
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
ANKRD13C
TSSK3
CCNL2
VANGL1
ST6GALNAC5
HYI
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
GPR61
STK40
TM2D1
REG4
TMEM222
PLEKHN1
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
SLC25A33
DDI2
LZIC
PROK1
EFCAB7
NT5C1A
TRIM63
PSRC1
FAM167B
MGC12982
C1orf170
CROCCL1
HPDL
C1orf203
AGBL4
MFSD2A
ATG4C
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
FAM40A
DOCK7
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
ZNF697
BTF3L4
UBXN11
NEXN
C1orf158
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
MED8
KTI12
C1orf212
ADC
TMEM54
C1orf59
TOE1
ERMAP
CSMD2
MYSM1
GNRHR2
CROCCL2
FHAD1
OSBPL9
LOC115110
OMA1
RAB42
LRRC42
GBP4
GBP5
FAM46B
RBP7
ACAP3
SSX2IP
UBE2J2
OLFM3
C1orf231
C1orf172
AADACL3
PUSL1
B3GALT6
WDR63
C1orf161
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
TPRG1L
C1orf93
MYOM3
DMBX1
TMCO2
ZNF684
C1orf83
PODN
LRRC39
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
LIX1L
KLF17
TMEM125
ARHGEF19
DRAM2
C1orf88
C1orf162
ACTRT2
MIB2
SYT6
C1orf127
SAMD11
LOC148413
SAMD13
C1orf52
PHF13
TMEM56
NBPF4
UBE2U
HFE2
ANKRD35
SLC30A7
CCDC27
C1orf213
KNCN
MOBKL2C
GLIS1
MGC27382
DCDC2B
ZNF362
MANEAL
IL23R
PDIK1L
CLDN19
WDR65
C1orf210
C1orf84
CCDC24
BTBD19
CCDC17
C1orf64
LOC149620
SLC2A7
DENND2C
GBP6
LPPR5
FNDC7
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
KANK4
SASS6
FAM43B
PPIAL4A
HFM1
PAQR7
UBL4B
PDIA3P
EIF2C3
EIF2C4
ALG14
FAM76A
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
LOC200030
NUDT17
TXLNA
TCTEX1D1
SPAG17
SLFNL1
C1orf126
HIPK1
SLC44A5
ATAD3C
AKR7L
AFARP1
FNDC5
EPHX4
TTLL10
AKNAD1
TMCO4
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
ZNF683
NEGR1
CYP4X1
MAGI3
NPHP4
BEST4
FAM19A3
CYP4A22
C1orf185
LOC284551
NBPF15
FAM41C
FAM102B
SYPL2
CYB561D1
ANKRD34A
LOC284632
RSPO1
EPHA10
LOC284661
ZNF326
BTBD8
RIMKLA
SLC25A34
ESPNP
PPM1J
HIST2H3A
HIST2H2BA
FAM151A
C1orf174
KLHL17
C1orf70
TMEM52
MTMR9L
ZBTB8OS
TFAP2E
LOC339524
C1orf228
ZNF642
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
SERINC2
FAM159A
FAM131C
PADI6
BMP8A
C1orf187
SPATA21
CCDC23
C1orf223
C1orf175
FAM73A
AGRN
APITD1
CATSPER4
NSUN4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
UOX
FRRS1
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
LOC400759
NBPF20
PRAMEF3
LDLRAD2
MIR101-1
MIR137
MIR186
MIR197
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
LHX8
C1orf180
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
FAM183A
ZYG11A
BCL2L15
HIST2H2BF
LOC441869
PRAMEF7
LOC441897
LOC492303
RBMXL1
C1orf190
PEF1
MIR429
HIST2H4B
CYB5RL
FAM138F
CYMP
KIAA0754
LOC643837
TMEM88B
PPIAL4G
C1orf200
PPIAL4D
LOC645166
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC647121
LOC648740
LOC649330
ZBTB8A
NBPF6
PPIAL4B
GPR89A
LOC653566
PPIAL4C
HIST2H3D
PRAMEF22
PRAMEF15
WASH5P
FAM72B
PRAMEF16
FAM138C
SCARNA2
SCARNA1
SNORA44
SNORA55
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD45C
SNORD85
SNORD99
SNORD103A
MIR551A
MIR553
HIST2H2AA4
ZBTB8B
LOC728448
CCDC30
CDC2L2
LOC728661
LOC728855
LOC728875
NBPF11
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729467
PRAMEF14
FLJ37453
OR4F29
PPIAL4E
SNHG3-RCC1
C1orf152
MIR942
MIR760
LOC100128003
LOC100128071
LOC100128842
LOC100129534
FLJ39609
LOC100130557
LOC100132062
LOC100132287
NBPF10
FCGR1C
LOC100133331
LOC100133612
LOC100286793
LOC100288778

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
LRRN3

Genes in Wide Peak

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

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

Genes
PTPRD
C9orf123

Genes in Wide Peak

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

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

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

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

Genes
BCL2
CDH7
CYB5A
KDSR
GALR1
MBP
MC4R
NFATC1
SERPINB2
SERPINB5
SERPINB8
SERPINB10
SERPINB13
SERPINB3
SERPINB4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
C18orf55
TMX3
ZCCHC2
ZNF407
CNDP2
KIAA1468
CCDC102B
C18orf22
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
DSEL
FAM69C
CBLN2
FBXO15
DOK6
RNF152
C18orf20
ZADH2
C18orf62
LOC284276
HMSD
ATP9B
LOC400657
HSBP1L1
LOC100130522

Genes in Wide Peak

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

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

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
GNA11
JAK3
KLK2
LYL1
MLLT1
PPP2R1A
SH3GL1
SMARCA4
STK11
TCF3
TPM4
ELL
FSTL3
CIC
BRD4
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-519a-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-220c
hsa-mir-769
hsa-mir-642
hsa-mir-330
hsa-mir-641
hsa-mir-1270
hsa-mir-640
hsa-mir-1470
hsa-mir-639
hsa-mir-181d
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-1227
hsa-mir-1909
hsa-mir-1302-2
ACP5
ACTN4
AP2A1
AES
AMH
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ASNA1
ATP1A3
ATP4A
ATP5D
AXL
AZU1
BAX
BCAT2
BCKDHA
HCN2
CEACAM1
BLVRB
BSG
BST2
C3
C5AR1
CA11
CACNA1A
CALM3
CALR
CAPNS1
CAPS
CCNE1
CD22
CD33
SIGLEC6
CD37
CD70
CD97
CDC34
CDKN2D
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CIRBP
TBCB
CKM
AP2S1
CLC
CLPTM1
CNN1
CNN2
COMP
COX6B1
COX7A1
CRX
CSNK1G2
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DAPK3
DBP
CFD
DHPS
DMPK
DMWD
DNASE2
DNM2
DNMT1
ARID3A
ECH1
EEF2
EFNA2
MEGF8
ELANE
ELAVL1
ELAVL3
EMP3
EMR1
EPOR
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FARSA
FCAR
FCER2
FCGRT
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
FUT3
FUT5
FUT6
GAMT
GCDH
GDF1
GIPR
GNA15
GNG7
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
MKNK2
GPX4
GRIK5
GRIN2D
GRLF1
GSK3A
GTF2F1
GYS1
GZMM
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
DNAJB1
ICAM1
ICAM3
ICAM4
IL11
IL12RB1
ILF3
INSL3
INSR
IRF3
JUNB
JUND
KCNA7
KCNC3
KCNJ14
KCNN1
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LDLR
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
CYP4F3
BCAM
MAG
MAN2B1
MATK
LOC729991-MEF2B
RAB8A
MAP3K10
MYO1F
MYBPC2
GADD45B
MYO9B
HNRNPM
CEACAM6
NDUFA3
NDUFA7
NDUFB7
NFIC
NFIX
NFKBIB
NKG7
CNOT3
NOTCH3
NOVA2
NPAS1
NPHS1
NRTN
NTF4
NUCB1
OAZ1
P2RY11
PAFAH1B3
PALM
PDE4A
PDE4C
PEG3
PEPD
PIK3R2
PIN1
PLAUR
FXYD1
FXYD3
POLD1
POLR2E
POLR2I
POLRMT
POU2F2
PPP5C
PRKACA
PRKCG
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRRG2
KLK7
KLK6
KLK10
PRTN3
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTBP1
PTGER1
PTGIR
PTPRH
PTPRS
PVR
PVRL2
RAB3A
RAD23A
RELB
UPF1
RFX1
RFX2
RPL18
RPL18A
RPL28
MRPS12
RPS9
RPS11
RPS15
RPS16
RPS19
RPS28
RRAS
RTN2
RYR1
SAFB
CLEC11A
SCN1B
CCL25
SEPW1
SGTA
SLC1A5
SLC1A6
SLC5A5
SLC8A2
SNAPC2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
STXBP2
SULT2B1
SULT2A1
SUPT5H
SYT5
TBXA2R
PRDX2
TGFB1
THOP1
ICAM5
TLE2
TNNI3
TNNT1
TULP2
TYK2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
VAV1
XRCC1
ZFP36
ZNF14
ZNF708
ZNF17
ZNF20
ZNF28
ZNF43
ZNF45
ZNF69
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF121
ZNF134
ZNF136
ZNF137
ZNF146
ZNF154
ZNF155
ZNF175
ZNF177
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
MADCAM1
SF3A2
SYMPK
MIA
CLPP
DPF1
LTBP4
TEAD2
RANBP3
CYP4F2
PPFIA3
KHSRP
PLA2G4C
PPAP2C
RFXANK
EIF3G
STX10
S1PR4
C19orf2
TNFSF14
TNFSF9
NAPA
SIGLEC5
FCGBP
AP1M1
AP3D1
PGLYRP1
F2RL3
ARHGEF1
PDCD5
DYRK1B
LPAR2
RAB11B
CRLF1
NUMBL
CYTH2
S1PR2
ZNF235
TRIP10
LONP1
ZNF264
KCNK6
NCR1
MED26
HOMER3
IL27RA
NAPSA
GDF15
TECR
ZNF254
GMFG
RAB3D
APBA3
IER2
KLK4
SAFB2
ZNF432
DHX34
KIAA0355
ZNF536
MLL4
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
UBA2
SAE1
SFRS14
EBI3
DDX39
ZNF443
PLIN3
AKAP8
LILRB2
APC2
PAK4
B3GNT3
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4
TMEM147
IFI30
TOMM40
TIMM44
CARM1
SEMA6B
ZNF211
CHERP
RNASEH2A
RABAC1
TRAPPC2P1
SPINT2
KLF1
DLL3
LASS1
GIPC1
POP4
ZNF234
ZNF266
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
PNPLA6
KDELR1
UQCR
LILRB5
ILVBL
LILRB4
KLK11
TMED1
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
SFRS16
KPTN
SLC7A9
CDC37
MAP4K1
KLK8
CYP4F8
PNKP
COPE
U2AF2
ATF5
ZFP30
ZNF507
LPHN1
SAPS1
CARD8
SBNO2
SIRT2
MAST1
UNC13A
KDM4B
MAST3
SIPA1L3
FCHO1
ZC3H4
ZFR2
SIN3B
HAUS5
ARHGEF18
CRTC1
KIAA0892
PIP5K1C
FBXO46
ETHE1
RPL13A
HMHA1
SYNGR4
LILRA4
PRG1
CASP14
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
SHC2
TMEM59L
PGLS
LSM4
KLK5
ZNF345
PRKD2
RPL36
ZNF473
KANK2
CLIP3
FAM32A
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
SNORD37
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285A
AKAP8L
FGF22
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
TJP3
CPAMD8
SIGLEC9
SIGLEC8
GPR77
ITGB1BP3
DHDH
EIF3K
UBE2S
SLC6A16
C19orf53
C19orf62
LGALS13
UHRF1
CYP2S1
STRN4
CCDC106
HOOK2
EPN1
SERTAD3
SERTAD1
SLC39A3
GLTSCR2
GLTSCR1
TNPO2
EMR2
CD209
EHD2
KLK14
KLK12
COL5A3
RDH8
SHANK1
NOSIP
MRPL4
NDUFA13
ANGPTL4
ZNF580
HSD17B14
GP6
VRK3
MARCH2
ZNF571
GMIP
CD320
ECSIT
THEG
ZBTB7A
FZR1
C19orf56
ISYNA1
ZNF581
SIRT6
PIAS4
LSR
LSM7
ZNF44
TM6SF2
MBD3
PTOV1
S1PR5
FXYD7
FXYD5
RAB4B
MIER2
DDX49
PAF1
PCSK4
PPP1R12C
TRPM4
ZNF562
QPCTL
GATAD2A
BEST2
FBXL12
FAM83E
PGPEP1
CC2D1A
EPS8L1
RASIP1
TMEM161A
SARS2
TMEM160
C19orf24
PIH1D1
C19orf60
GPATCH1
SAMD4B
ATP5SL
PLEKHJ1
C19orf73
MAP1S
PNMAL1
TMEM143
KLHL26
ZNF444
C19orf66
FEM1A
ZNF823
KLK15
MED29
STAP2
TRMT1
BTBD2
NLRP2
RNF126
ZNF416
CCDC94
ASF1B
ZNF701
ZNF83
ZNF415
USE1
PSENEN
ZNF302
LOC55908
LIN37
C19orf10
C19orf61
ZNF253
IRGC
SLC7A10
PPAN
CABP5
RETN
SPHK2
LGALS14
EXOSC5
MEIS3
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
CEACAM19
SLC17A7
NAT14
CD177
ATP13A1
RGL3
SLC44A2
VN1R1
MCOLN1
RCN3
ZNF304
TTYH1
WDR18
REXO1
PNMAL2
ZNF490
PRR12
DOCK6
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
KIAA1543
USP29
PLEKHA4
ZFP14
ZNF317
ZNF529
PRX
ANO8
SPTBN4
MARK4
SF4
HAMP
CATSPERG
CYP4F11
ZNF71
ZNF77
SCAF1
C19orf29
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
UBL5
ZNF350
TSKS
BRUNOL5
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
LPPR2
ZNF574
PLEKHG2
RASAL3
MRPL34
KRI1
ZSWIM4
ZNF649
CYP4F12
YIPF2
C19orf43
DDA1
C19orf50
TMEM38A
TSEN34
KCTD15
SLC25A23
C19orf42
ZNF426
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
C19orf57
ZNF576
FSD1
ZNF557
LRFN3
ABHD8
LASS4
OCEL1
GLT25D1
TMEM149
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
TLE6
EPHX3
PODNL1
ZNF671
ZNF613
ADCK4
CNTD2
SLC35E1
LPPR3
DENND1C
ZNF442
ZNF702P
ZNF556
LOC80054
ZNF614
LRRC8E
FUZ
OPA3
ZNF430
ITPKC
UBXN6
PBX4
KIAA1683
B9D2
OR4F17
RSHL1
CCDC130
ACSBG2
ADAMTS10
ZNF611
MED25
QTRT1
FAM108A1
ZNF93
DOHH
PLVAP
RTBDN
BCL2L12
C19orf12
TEX101
GRWD1
ANGPTL6
KLF16
USHBP1
WDR87
TSSK6
CCDC8
KIRREL2
ANKRD27
PRAM1
C19orf44
ZNF541
MRI1
SYT3
FBXW9
ALKBH7
MORG1
PDCD2L
ZNF414
AKT1S1
ELOF1
ZNF528
DOT1L
BRSK1
ZNF333
FBN3
ZNF527
CNFN
ZNF559
SNORD35B
KISS1R
EMR3
ZNF347
CREB3L3
GTPBP3
HDGF2
ZNF577
MPV17L2
ZNF607
SUV420H2
C19orf48
NFKBID
LMNB2
RAX2
CCDC123
ZNF382
FIZ1
ZNF566
MUM1
HSH2D
MPND
ALKBH6
ATG4D
ATCAY
SYDE1
RHPN2
MBD3L1
GALP
SIGLEC10
SIGLEC12
ZNF628
MIDN
KIR3DX1
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
SAMD1
DCAF15
GADD45GIP1
ZNF835
YIF1B
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
ZNF486
DPP9
ZNF682
C19orf22
C19orf6
C19orf40
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
C19orf20
ZNF461
ZNF585B
CRB3
TIMM50
SHKBP1
REEP6
PEX11G
DMKN
ZNF561
OLFM2
CCDC114
HAUS8
FAM125A
DKFZp434J0226
ARMC6
ACPT
CGB5
DKFZp566F0947
MUC16
CGB7
LRRC4B
ZNF101
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
FDX1L
NACC1
PTH2
C19orf36
SCAMP4
ADAT3
LOC113230
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
LENG8
CCDC124
ZNF554
FBXO17
KIR3DL3
SNX26
EVI5L
RASGRP4
NXNL1
CCDC151
ZNF653
ZNF526
GRIN3B
MRPL54
LRG1
CIB3
RLN3
CLDND2
ZNF816A
ZNF543
CEACAM20
RAVER1
OR7D4
OR7G1
OR1M1
COX6B2
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
OSCAR
ZNF813
ZNF441
ZNF491
ZNF440
C19orf39
CCDC159
JOSD2
C19orf41
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
WDR88
TMIGD2
EID2B
TNFAIP8L1
ZNF57
IRGQ
ZNF428
JSRP1
MOBKL2A
C19orf28
GIPC3
NDUFA11
C19orf21
LRRC25
OR1I1
WTIP
ZNF792
NR2C2AP
HSPB6
CCDC105
CYP4F22
RINL
FBXO27
PLK5P
C19orf47
LOC126536
OR10H4
ANKLE1
C2CD4C
ZNF358
ZFP28
VSIG10L
NCRNA00085
ZNF480
ZNF534
ZNF578
ZNF548
FLJ40125
KLC3
LYPD4
LOC147727
ZNF560
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
ZNF563
SPC24
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
TTC9B
TICAM1
C19orf23
ZNRF4
ZNF599
FAM187B
CILP2
C19orf55
LOC148145
ZNF558
CDC42EP5
LOC148189
ZNF98
ZNF738
ZNF714
ZNF681
C19orf25
ATP8B3
FLJ25328
DIRAS1
ZNF555
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF550
ZNF296
DEDD2
ZNF846
OR7D2
ZNF579
ZNF791
ZNF564
ZNF709
ZNF433
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
PRR22
LGI4
C19orf46
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
ANKRD24
SPACA4
ZNF675
C19orf59
ZNF627
DAND5
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
C19orf76
ZSCAN4
NLRP11
TMEM86B
C19orf26
C19orf34
PRR24
C19orf38
ZNF549
SYCE2
NAPSB
KANK3
PLAC2
TMEM146
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
ZNF575
LYPD5
ZNF283
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
ACTL9
OR2Z1
ZNF763
ZNF844
SCGBL
WDR62
ZFP82
LOC284412
VSTM1
TMEM150B
FAM71E2
C19orf77
C19orf30
SLC25A41
MBD3L5
OR10H5
NWD1
SLC25A42
LOC284440
LOC284441
ZNF493
ODF3L2
HKR1
VN1R2
VN1R4
EMR4P
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
ADAMTSL5
CLEC4G
VSTM2B
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
ZNF677
RFPL4A
ZSCAN5B
NANOS3
PALM3
SELV
ZNF530
C19orf51
ZNF429
ZNF233
LILRA5
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
SLC27A1
C3P1
ZNF788
CLEC17A
RPSAP58
RGS9BP
KRTDAP
ZNF790
FLJ41856
CEACAM16
BLOC1S3
IGFL3
ZNF808
ZNF761
ZNF470
ZNF749
RPL18AP3
ONECUT3
OR7G2
OR7G3
OR7A10
NUDT19
ZNF793
PAPL
ZNF805
SPRED3
MEX3D
ZNF321
FLJ45445
PRSSL1
VMAC
LOC400696
SIGLEC16
FLJ26850
ZNF880
ZNF772
ZNF833
IGLON5
HAPLN4
CTXN1
MIRLET7E
MIR125A
MIR150
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR7-3
MIR99B
PLIN5
CLEC4GP1
ZNF506
PSG8
OLT-2
MIR330
MIR371
MIR372
MIR373
IGFL4
FLJ25758
DPRX
DUXA
ASPDH
MIR181D
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
LOC641367
TMEM91
FAM138F
LOC643719
SDHAF1
LINGO3
ARRDC5
FAM138A
SBK2
UCA1
PSG10
LGALS7B
PHLDB3
MBD3L4
MBD3L3
SEC1
FAM138C
ZNF826
SNORD23
SNORD88A
SNORD88B
SNORD88C
SNORD105
PPAN-P2RY11
MIR637
MIR638
MIR639
MIR641
MIR642
MIR643
RPL13AP5
PLIN4
CCDC61
ZNF878
CEACAM18
SHISA7
LOC729991
MIR769
KIR3DP1
SIGLEC14
MIMT1
LOC100101266
SNORD105B
ZGLP1
MIR220B
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
C19orf71
LOC100128573
LOC100128675
ZNF737
LOC100129935
LOC100130932
BSPH1
LOC100134317
PEG3AS
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
MEF2B

Genes in Wide Peak

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

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

Genes
NCKAP5

Genes in Wide Peak

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

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

Genes
NSD1
RAB24

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
ABP1
AKR1B1
BPGM
CALD1
CASP2
CDK5
CHRM2
CLCN1
DPP6
EN2
EPHA1
EPHB6
GBX1
MNX1
HTR5A
INSIG1
KCNH2
KEL
NDUFB2
NOS3
CNOT4
PIP
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
AKR1D1
SSBP1
TBXAS1
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
DGKI
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
NUP205
CLEC5A
MKRN1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
ATP6V0A4
TAS2R3
TAS2R4
PRKAG2
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
ESYT2
ZNF398
EXOC4
GALNT11
LMBR1
C7orf4
NOM1
PARP12
LRRC61
C7orf49
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
SLC35B4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
C7orf29
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
SVOPL
MTPN
LRGUK
ASB10
TRYX3
MOXD2
RNF32
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF783
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5L3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FLJ40852
FAM115C
ZNF775
ATG9B
TAS2R60
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
STRA8
KLRG2
WDR86
GSTK1
FAM180A
OR2A25
OR2A5
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
MIR153-2
AKR1B15
LOC441294
OR2A9P
OR2A2
ARHGEF5L
GIMAP6
WEE2
MIR490
ZNF862
PL-5283
ACTR3C
MIR595
LOC728743
LUZP6
MIR671
LOC100124692
LOC100128542
CTAGE4
LOC100128822
LOC100132707
LOC100134229
LOC100134713

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q12.1.

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

Genes
CYLD
hsa-mir-1826
ADCY7
AMFR
CBLN1
CES1
GNAO1
MMP2
PHKB
RBL2
SALL1
SIAH1
SLC6A2
N4BP1
IRX5
DNAJA2
ZNF267
ZNF423
RPGRIP1L
ORC6L
TP53TG3
DKFZP434H168
TOX3
BRD7
CES4
LPCAT2
HEATR3
VPS35
NOD2
PAPD5
AKTIP
FTO
IRX6
IRX3
SHCBP1
CHD9
ITFG1
NETO2
LONP2
CAPNS2
GPT2
ABCC11
NKD1
MYLK3
ABCC12
C16orf78
ANKRD26P1
SNX20
LOC146481
CES7
TMEM188
LOC283856
LOC283914
SLC6A10P
C16orf87
HERC2P4
UBE2MP1
TP53TG3B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.2.

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

Genes
PICALM
MAML2
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
CTSC
FUT4
GRM5
MRE11A
MTNR1B
TYR
FZD4
JRKL
EED
MTMR2
MED17
CEP57
NAALAD2
ME3
GPR83
SFRS2B
PRSS23
ENDOD1
RAB38
PANX1
CHORDC1
C11orf54
NOX4
C11orf73
CWC15
CNTN5
SYTL2
ANKRD49
KDM4D
C11orf75
TRIM49
CREBZF
CCDC81
TMEM135
TAF1D
CCDC82
TMEM126A
KIAA1731
SLC36A4
FAT3
TRIM64
FAM76B
SESN3
PIWIL4
FLJ32810
AMOTL1
CCDC67
FOLH1B
CCDC83
CCDC89
HEPHL1
C11orf90
TRIM77
FOLR4
KDM4DL
SCARNA9
TRIM64B
TRIM53
UBTFL1
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
LOC729384

Genes in Wide Peak

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

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

Genes
BMPR1A
PTEN
hsa-mir-1287
hsa-mir-607
hsa-mir-107
hsa-mir-346
ACTA2
FAS
ENTPD1
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP26A1
DNTT
GLUD1
GRID1
HELLS
HHEX
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
KIF11
LIPA
PDE6C
PGAM1
PPP1R3C
ALDH18A1
RBP4
SFRP5
SLIT1
SNCG
TLL2
LIPF
CH25H
BTAF1
PAPSS2
PDLIM1
LGI1
MINPP1
KIF20B
ZNF518A
FRAT1
RPP30
SORBS1
C10orf116
LDB3
CPEB3
WAPAL
RRP12
TBC1D12
FRAT2
IFIT5
TCTN3
C10orf12
ANKRD2
MYOF
ANKRD1
C10orf28
BLNK
EXOSC1
PLCE1
PANK1
FAM190B
EXOC6
FAM35A
CCNJ
MARCH5
CRTAC1
CEP55
RNLS
PI4K2A
TM9SF3
STAMBPL1
AVPI1
HPSE2
MMS19
NOC3L
MMRN2
UBTD1
TNKS2
MARVELD1
LOXL4
ZDHHC16
PCGF5
LCOR
PYROXD2
ATAD1
ARHGAP19
OPALIN
OPN4
DHDPSL
PIK3AP1
MORN4
ZFYVE27
C10orf4
ANKRD22
NUDT9P1
AGAP11
C10orf129
LIPJ
CFLP1
HECTD2
FGFBP3
TMEM20
PIPSL
FLJ37201
GPR120
LIPM
CYP26C1
SLC16A12
CC2D2B
GOLGA7B
MIR107
C10orf62
LOC439994
IFIT1L
MIR346
FAM25A
LIPK
LIPN
FAM22A
FAM22D
LOC728190
C10orf131
KILLIN
LOC100188947
LOC100270710

Genes in Wide Peak

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

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

Genes
hsa-let-7b
hsa-mir-1249
ACR
ARSA
BIK
TSPO
MPPED1
CHKB
CPT1B
CYB5R3
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
C22orf9
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
RRP7A
MCAT
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
SCUBE1
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
POLDIP3
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
RRP7B
SERHL
PHF21B
KLHDC7B
PNPLA5
LOC150381
C22orf40
CN5H6.4
TTLL8
SERHL2
RNU12
ATP5L2
RPL23AP82
C22orf34
CHKB-CPT1B
NCRNA00207
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.1.

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

Genes
IRF4
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
RANBP9
PECI
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
NOL7
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
CCDC90A
TXNDC5
TMEM14B
RIOK1
DTNBP1
C6orf105
C6orf114
FOXQ1
HUS1B
SNRNP48
C6orf195
MGC26597
RBM24
RNF182
PHACTR1
LOC221710
SYCP2L
C6orf218
C6orf145
C6orf146
LOC285768
LOC285780
CAGE1
MYLK4
TUBB2B
C6orf52
FAM136B
PSMG4
DKFZP686I15217
C6orf201
HERV-FRD
PPP1R3G
HULC
TMEM170B
SCARNA27

Genes in Wide Peak

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

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

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
JAK3
KLK2
LYL1
PPP2R1A
SMARCA4
TPM4
ELL
CIC
BRD4
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-519a-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-220c
hsa-mir-769
hsa-mir-642
hsa-mir-330
hsa-mir-641
hsa-mir-1270
hsa-mir-640
hsa-mir-1470
hsa-mir-639
hsa-mir-181d
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
A1BG
ACP5
ACTN4
AP2A1
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ASNA1
ATP1A3
ATP4A
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
BST2
C5AR1
CA11
CACNA1A
CALM3
CALR
CAPNS1
CCNE1
CD22
CD33
SIGLEC6
CD37
CD97
CDKN2D
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
TBCB
CKM
AP2S1
CLC
CLPTM1
CNN1
COMP
COX6B1
COX7A1
CRX
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DHPS
DMPK
DMWD
DNASE2
DNM2
DNMT1
ECH1
MEGF8
ELAVL3
EMP3
EPOR
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FARSA
FCAR
FCGRT
FKBP1P1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GCDH
GDF1
GIPR
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
GRIK5
GRIN2D
GRLF1
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
DNAJB1
ICAM1
ICAM3
ICAM4
IL11
IL12RB1
ILF3
INSL3
IRF3
JUNB
JUND
KCNA7
KCNC3
KCNJ14
KCNN1
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LDLR
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
CYP4F3
BCAM
MAG
MAN2B1
LOC729991-MEF2B
RAB8A
MAP3K10
MYBPC2
MYO9B
CEACAM6
NDUFA3
NDUFB7
NFIX
NFKBIB
NKG7
CNOT3
NOTCH3
NOVA2
NPAS1
NPHS1
NTF4
NUCB1
P2RY11
PAFAH1B3
PDE4A
PDE4C
PEG3
PEPD
PIK3R2
PIN1
PLAUR
FXYD1
FXYD3
POLD1
POLR2I
POU2F2
PPP5C
PRKACA
PRKCG
PKN1
PRKCSH
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGER1
PTGIR
PTPRH
PVR
PVRL2
RAB3A
RAD23A
RELB
UPF1
RFX1
RPL18
RPL18A
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SCN1B
SEPW1
SLC1A5
SLC1A6
SLC5A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
PRDX2
TGFB1
ICAM5
TNNI3
TNNT1
TULP2
TYK2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
XRCC1
ZFP36
ZNF8
ZNF14
ZNF708
ZNF17
ZNF20
ZNF28
MZF1
ZNF43
ZNF45
ZNF69
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF132
ZNF134
ZNF135
ZNF136
ZNF137
ZNF146
ZNF154
ZNF155
ZNF175
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
CYP4F2
PPFIA3
PLA2G4C
RFXANK
EIF3G
STX10
C19orf2
NAPA
SIGLEC5
FCGBP
AP1M1
PGLYRP1
F2RL3
UBE2M
ARHGEF1
PDCD5
DYRK1B
LPAR2
CRLF1
NUMBL
CYTH2
S1PR2
ZNF235
ZNF264
KCNK6
NCR1
MED26
HOMER3
IL27RA
NAPSA
GDF15
TECR
ZNF254
GMFG
RAB3D
IER2
KLK4
ZNF432
DHX34
KIAA0355
ZNF536
MLL4
KEAP1
AP1M2
UBA2
SAE1
SFRS14
TRIM28
ZNF256
DDX39
ZNF443
AKAP8
LILRB2
PAK4
B3GNT3
KLF2
TMEM147
IFI30
TOMM40
CARM1
ZNF211
CHERP
RNASEH2A
RABAC1
TRAPPC2P1
SPINT2
KLF1
DLL3
LASS1
GIPC1
POP4
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
KDELR1
LILRB5
ILVBL
SLC27A5
LILRB4
KLK11
TMED1
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
SFRS16
KPTN
SLC7A9
CDC37
MAP4K1
KLK8
CYP4F8
PNKP
COPE
U2AF2
ATF5
ZFP30
ZNF507
LPHN1
SAPS1
CARD8
SIRT2
MAST1
UNC13A
MAST3
SIPA1L3
FCHO1
ZC3H4
SIN3B
HAUS5
CRTC1
KIAA0892
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
CASP14
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
TMEM59L
PGLS
ZNF324
LSM4
KLK5
ZNF345
PRKD2
ZNF473
KANK2
CLIP3
FAM32A
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
OR7A17
TSPAN16
OR10H3
OR10H2
OR10H1
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285A
AKAP8L
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
CPAMD8
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
C19orf53
C19orf62
LGALS13
CYP2S1
STRN4
CCDC106
HOOK2
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
TNPO2
EMR2
EHD2
KLK14
KLK12
COL5A3
RDH8
SHANK1
NOSIP
MRPL4
NDUFA13
ZNF580
HSD17B14
GP6
VRK3
ZNF571
GMIP
ECSIT
C19orf56
ISYNA1
ZNF581
LSR
ZNF44
TM6SF2
PTOV1
S1PR5
FXYD7
FXYD5
RAB4B
DDX49
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
GATAD2A
BEST2
FBXL12
FAM83E
PGPEP1
CC2D1A
EPS8L1
RASIP1
TMEM161A
SARS2
TMEM160
PIH1D1
C19orf60
GPATCH1
SAMD4B
ATP5SL
C19orf73
MAP1S
PNMAL1
TMEM143
KLHL26
ZNF444
C19orf66
ZNF823
KLK15
MED29
TRMT1
NLRP2
ZNF416
ZNF446
ASF1B
ZNF701
ZNF83
ZNF415
USE1
PSENEN
ZNF302
LOC55908
LIN37
C19orf61
ZNF253
IRGC
SLC7A10
PPAN
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
ATP13A1
RGL3
SLC44A2
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
ZNF490
PRR12
DOCK6
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
USP29
PLEKHA4
ZFP14
ZNF529
PRX
ANO8
SPTBN4
MARK4
SF4
HAMP
CATSPERG
CYP4F11
ZNF71
SCAF1
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
UBL5
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
LPPR2
ZNF574
PLEKHG2
RASAL3
MRPL34
KRI1
ZSWIM4
ZNF649
ZSCAN18
MGC2752
CYP4F12
YIPF2
C19orf43
DDA1
C19orf50
TMEM38A
TSEN34
KCTD15
C19orf42
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
C19orf57
ZNF576
LRFN3
ABHD8
OCEL1
ZNF329
GLT25D1
TMEM149
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
EPHX3
PODNL1
ZNF671
ZNF613
ADCK4
CNTD2
SLC35E1
ZNF442
ZNF702P
LOC80054
ZNF606
ZNF614
FUZ
OPA3
ZNF430
ITPKC
PBX4
KIAA1683
B9D2
RSHL1
CCDC130
ZNF611
MED25
QTRT1
ZNF93
PLVAP
RTBDN
BCL2L12
C19orf12
TEX101
GRWD1
ANGPTL6
USHBP1
WDR87
TSSK6
CCDC8
KIRREL2
ANKRD27
C19orf44
ZNF541
MRI1
SYT3
FBXW9
MORG1
PDCD2L
AKT1S1
ELOF1
ZNF528
BRSK1
ZNF333
ZNF527
CNFN
SNORD35B
EMR3
ZNF347
GTPBP3
ZNF577
MPV17L2
ZNF607
SUV420H2
C19orf48
NFKBID
ZBTB45
CCDC123
ZNF382
ZNF587
FIZ1
ZNF566
HSH2D
ALKBH6
ATG4D
SYDE1
RHPN2
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
SAMD1
DCAF15
GADD45GIP1
ZNF835
YIF1B
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
ZNF486
ZNF682
C19orf40
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
ZNF461
ZNF585B
TIMM50
SHKBP1
DMKN
OLFM2
CCDC114
HAUS8
FAM125A
DKFZp434J0226
ARMC6
ACPT
CGB5
DKFZp566F0947
CGB7
LRRC4B
ZNF101
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
FDX1L
NACC1
PTH2
LOC113230
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
LENG8
CCDC124
FBXO17
KIR3DL3
SNX26
RASGRP4
NXNL1
CCDC151
ZNF653
ZNF526
ZNF837
CIB3
RLN3
CLDND2
ZNF816A
ZNF543
CEACAM20
RAVER1
COX6B2
CALR3
OSCAR
ZNF813
ZNF441
ZNF491
ZNF440
C19orf39
CCDC159
JOSD2
C19orf41
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
WDR88
EID2B
IRGQ
ZNF428
LRRC25
OR1I1
WTIP
ZNF792
NR2C2AP
HSPB6
CCDC105
CYP4F22
RINL
FBXO27
C19orf47
LOC126536
OR10H4
ANKLE1
ZFP28
VSIG10L
NCRNA00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
ZNF417
ZNF548
FLJ40125
KLC3
LYPD4
LOC147727
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
ZNF563
SPC24
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
TTC9B
ZNF599
FAM187B
CILP2
C19orf55
LOC148145
CDC42EP5
LOC148189
ZNF98
ZNF738
ZNF714
ZNF681
FLJ25328
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF846
ZNF579
ZNF791
ZNF564
ZNF709
ZNF433
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
LGI4
C19orf46
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
SPACA4
ZNF675
ZNF627
DAND5
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
C19orf38
ZNF549
SYCE2
NAPSB
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
ZNF575
LYPD5
ZNF283
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
ZNF763
ZNF844
SCGBL
WDR62
ZFP82
LOC284412
VSTM1
TMEM150B
FAM71E2
OR10H5
NWD1
SLC25A42
LOC284440
LOC284441
ZNF493
HKR1
VN1R2
VN1R4
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
VSTM2B
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
NANOS3
PALM3
SELV
ZNF530
C19orf51
ZNF429
ZNF233
LILRA5
TMEM205
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
SLC27A1
C3P1
ZNF788
CLEC17A
RPSAP58
RGS9BP
KRTDAP
ZNF790
FLJ41856
CEACAM16
BLOC1S3
IGFL3
ZNF808
ZNF761
ZNF470
ZNF749
ZNF324B
RPL18AP3
OR7A10
NUDT19
ZNF793
PAPL
ZNF805
SPRED3
ZNF321
LOC400696
SIGLEC16
FLJ26850
ZNF880
ZNF772
ZNF833
IGLON5
HAPLN4
MIRLET7E
MIR125A
MIR150
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR99B
ZNF506
PSG8
OLT-2
MIR330
MIR371
MIR372
MIR373
IGFL4
NCRNA00181
DPRX
DUXA
ASPDH
MIR181D
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
LOC641367
TMEM91
LOC643719
SDHAF1
SBK2
UCA1
PSG10
LGALS7B
PHLDB3
SEC1
ZNF826
SNORD23
SNORD88A
SNORD88B
SNORD88C
SNORD105
PPAN-P2RY11
MIR638
MIR639
MIR641
MIR642
MIR643
RPL13AP5
CCDC61
ZNF878
CEACAM18
SHISA7
LOC729991
ZNF814
MIR769
KIR3DP1
SIGLEC14
MIMT1
LOC100101266
SNORD105B
ZGLP1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128675
ZNF737
LOC100129935
LOC100130932
BSPH1
LOC100131691
LOC100134317
PEG3AS
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
MEF2B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

Table S59. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GPHN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p11.

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IL6ST
hsa-mir-582
hsa-mir-449b
hsa-mir-581
ERCC8
FGF10
GZMA
GZMK
HTR1A
ISL1
ITGA1
ITGA2
KIF2A
MAP3K1
MOCS2
NDUFS4
PDE4D
PPAP2A
HSPB3
SDCCAG10
CCNO
FST
PAIP1
PLK2
MRPS30
ESM1
ADAMTS6
SKIV2L2
NNT
PART1
DIMT1L
IPO11
PELO
DHX29
DDX4
ARL15
DEPDC1B
ZSWIM6
GPBP1
PARP8
ANKRD55
ELOVL7
NDUFAF2
SNX18
RAB3C
C5orf35
IL31RA
EMB
SLC38A9
MIER3
CDC20B
GAPT
FLJ37543
RNF180
SFRS12IP1
ACTBL2
HCN1
RNF138P1
ISCA1L
RGS7BP
GPX8
MIR449A
C5orf43
MIR449B
MIR581
LRRC70
FAM159B

Genes in Wide Peak

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

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BUB1B
C15orf55
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
hsa-mir-211
hsa-mir-1268
ACTC1
APBA2
B2M
BCL8
CAPN3
CHRM5
CHRNA7
CKMT1B
EPB42
GABRA5
GABRB3
GABRG3
GANC
GCHFR
PDIA3
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
TGM5
HISPPD2A
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
MTMR15
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
VPS18
ZFP106
CHAC1
C15orf29
WDR76
TMEM62
SPG11
ELL3
NIPA2
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
OR4N4
FAM98B
PLA2G4D
GOLGA6L1
GOLGA8G
GOLGA9P
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMML1
POTEB
FMN1
SNORD64
PAR4
PAR-SN
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
MIR211
NF1P1
WHAMML2
GOLGA8B
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC646214
CXADRP2
MIR626
MIR627
LOC723972
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
LOC729082
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
HBII-52-24
HBII-52-27
HBII-52-28
HBII-52-45
HBII-52-46
GOLGA8F
GOLGA8D
JMJD7
PLA2G4B
FAM7A2

Genes in Wide Peak

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

Table S62. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CCNB1IP1
hsa-mir-624
hsa-mir-208b
hsa-mir-208a
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
NP
NRL
OXA1L
PCK2
PRKD1
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
SRP54
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
AKAP6
KIAA0391
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
FAM12A
DHRS4
RIPK3
AP4S1
BAZ1A
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
PPP2R3C
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
FLJ10357
EAPP
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
SNX6
C14orf93
ABHD4
NPAS3
FAM12B
CDH24
METT11D1
IL25
THTPA
OR4K5
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
JPH4
RNASE7
C14orf128
RAB2B
JUB
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
EGLN3
C14orf126
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
C14orf21
C14orf147
ADCY4
C14orf19
TSSK4
FAM177A1
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
P704P
C14orf176
CBLN3
SNORD9
MIR624
DHRS4L1
SNORD126
MIR208B

Genes in Wide Peak

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

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RUNX1
ERG
TMPRSS2
OLIG2
hsa-mir-802
hsa-mir-155
hsa-mir-125b-2
ADARB1
AIRE
APP
ATP5J
ATP5O
BACH1
BAGE
PTTG1IP
C21orf2
TMEM50B
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
CXADR
DSCAM
RCAN1
DYRK1A
ETS2
GABPA
GART
GRIK1
HLCS
HMGN1
PRMT2
IFNAR1
IFNAR2
IFNGR2
IL10RB
ITGB2
KCNE1
KCNJ6
KCNJ15
LSS
MX1
MX2
NCAM2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PRSS7
PWP2
S100B
SH3BGR
ITSN1
SIM2
SLC5A3
SLC19A1
SUMO3
SOD1
SON
HSPA13
TFF1
TFF2
TFF3
TIAM1
TRAPPC10
TPTE
TRPM2
TTC3
U2AF1
UBE2G2
WRB
NRIP1
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
SYNJ1
MCM3AP
CLDN8
ADAMTS1
ABCG1
URB1
CRYZL1
DOPEY2
KCNE2
RWDD2B
DSCR4
DSCR3
B3GALT5
USP16
CCT8
WDR4
FTCD
BTG3
HSF2BP
ADAMTS5
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
RNF160
CLDN17
N6AMT1
USP25
DNMT3L
DONSON
HUNK
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
RBM11
PCBP3
C21orf58
C21orf57
NCRNA00160
FAM165B
C21orf49
C21orf45
NCRNA00159
NCRNA00158
NCRNA00157
C21orf29
NCRNA00113
NCRNA00112
NCRNA00111
SETD4
C21orf15
FAM3B
RIPK4
CLIC6
MRPL39
C21orf91
DNAJC28
C21orf62
MRAP
C21orf59
AGPAT3
C21orf7
SFRS15
JAM2
C21orf63
PRDM15
SAMSN1
TMPRSS3
MRPS6
C21orf96
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
C21orf70
RSPH1
UMODL1
C21orf66
C21orf82
C21orf84
C21orf88
C21orf90
MCM3APAS
MIR155HG
CYYR1
OLIG1
NCRNA00161
KRTAP13-1
TCP10L
CHODL
C21orf99
LIPI
ABCC13
LCA5L
IGSF5
SIK1
C21orf129
C21orf121
C21orf128
PLAC4
NCRNA00189
C21orf94
KRTAP15-1
DSCR9
DSCR10
C21orf71
KRTAP13-4
C21orf130
C21orf125
LOC284837
POTED
KRTAP7-1
KRTAP8-1
KRTAP11-1
KRTAP19-1
KRTAP13-2
KRTAP13-3
KRTAP23-1
KRTAP6-1
KRTAP6-2
KRTAP6-3
KRTAP19-2
KRTAP19-3
KRTAP19-4
KRTAP19-5
KRTAP19-6
KRTAP19-7
KRTAP20-1
KRTAP20-2
KRTAP21-1
KRTAP21-2
KRTAP22-1
KRTAP20-3
KRTAP12-2
KRTAP12-1
KRTAP10-10
NCRNA00162
NCRNA00175
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
C21orf131
C21orf34
KRTAP26-1
C21orf81
NCRNA00114
MIRLET7C
MIR125B2
MIR99A
LOC642852
NCRNA00110
KRTAP24-1
KRTAP27-1
SNORA80
C21orf122
KRTAP19-8
C21orf54
MIR802
KRTAP25-1
KRTAP20-4
KRTAP22-2
KRTAP21-3

Genes in Wide Peak

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

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATF1
CDK4
DDIT3
HOXC11
HOXC13
KRAS
NACA
MLL2
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
hsa-mir-920
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APOF
AQP2
AQP5
AQP6
ARF3
ATP5B
ATP5G2
BCAT1
BICD1
CACNB3
CCNT1
CD63
CDK2
CNTN1
COL2A1
CS
CYP27B1
DGKA
DDX11
EIF4B
CELA1
ERBB3
B4GALNT1
BLOC1S1
GLI1
GPD1
GYS2
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IAPP
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNJ8
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
LDHB
LRMP
LRP1
MARS
METTL1
MIP
MMP19
MYL6
MYO1A
NAB2
NELL2
NFE2
SLC11A2
PA2G4
PCBP2
PDE3A
PDE1B
PFDN5
PFKM
PKP2
POU6F1
PPP1R1A
PRIM1
PRKAG1
PRPH
PTHLH
TWF1
RAB5B
RARG
RBMS2
RDH5
RECQL
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
ST8SIA1
SILV
SLCO1A2
SMARCC2
SMARCD1
SOX5
SP1
STAT2
STAT6
SUOX
TAC3
TARBP2
TMBIM6
TFCP2
VDR
WNT1
WNT10B
MAP3K12
TUBA1A
SSPN
AAAS
SOAT2
PPFIBP1
RDH16
NPFF
HSD17B6
P11
TIMELESS
KRT75
SFRS2IP
SLC16A7
MED21
DDX23
SLC4A8
ESPL1
DAZAP2
KIAA0748
KIAA0528
ZBTB39
PAN2
TROAP
DNM1L
ABCC9
TSFM
CTDSP2
YAF2
RNF41
GDF11
CNPY2
TUBA1B
RAPGEF3
MCRS1
IPO8
DCTN2
SLCO1B1
AVIL
PTGES3
OS9
ATF7
BAZ2A
GALNT6
RASSF8
NXPH4
GPR182
COPZ1
R3HDM2
STK38L
FAIM2
DDN
TMEM194A
ESYT1
TENC1
KCNH3
CBX5
ANP32D
SMUG1
PRPF40B
METTL7A
LETMD1
FAM119B
ZNF385A
FGFR1OP2
SNORD59A
GLS2
RND1
SLCO1B3
ORMDL2
RACGAP1
SENP1
PDZRN4
DHH
GOLT1B
PLEKHA9
YARS2
IRAK4
ERGIC2
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
IL23A
HDAC7
TM7SF3
GPR84
SLCO1C1
SLC38A2
PRR13
C12orf41
SLC38A4
C12orf35
CASC1
CCDC91
ETNK1
KIF21A
SLC48A1
FAR2
LMBR1L
C12orf11
CMAS
DAD1L
NDUFA4L2
ARNTL2
SMAGP
KLHDC5
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
FAM60A
C12orf10
MRPS35
C12orf44
ARHGAP9
IKZF4
SLC26A10
SPATS2
CAPRIN2
TMEM106C
OBFC2B
BHLHE41
RPAP3
PIP4K2C
FLJ13224
PYROXD1
DNAJC22
ADAMTS20
C12orf39
SLC38A1
CSRNP2
PUS7L
INHBE
TMTC1
RACGAP1P
FAM186B
TMEM117
WIBG
SARNP
TUBA1C
ZC3H10
ALG10
SPRYD3
MFSD5
C12orf62
DNAJC14
ZCRB1
CCDC65
LACRT
FMNL3
LASS5
XRCC6BP1
FAM113B
MARCH9
COQ10A
KRT71
LARP4
SLC2A13
MBD6
GEFT
AGAP2
DCD
MUCL1
LRRK2
FAM186A
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
FGD4
AEBP2
ASB8
MYL6B
KRT72
PRICKLE1
BCDIN3D
ALG10B
C12orf67
LYRM5
CPNE8
LOC144438
KRT80
IFLTD1
DENND5B
GRASP
KRT78
AMN1
DTX3
METTL7B
C12orf77
ANO6
ARID2
STAC3
C12orf72
OR6C74
OR6C3
LOC255411
LOC283332
ZNF740
OR6C6
ANKRD52
SLC39A5
SPRYD4
LOC283404
C12orf40
GLT8D3
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
FAM19A2
LST-3TM12
C12orf70
OVCH1
SYT10
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
KRT77
REP15
C12orf68
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FIGNL2
OR6C65
OR6C68
MIR196A2
MIR26A2
H3F3C
DBX2
FLJ12825
TSPAN11
OR9K2
MIR148B
HIGD1C
GLYCAM1
HNRPA1L-2
SNORA2A
SNORA2B
SNORA34
SNORD59B
C12orf71
HOTAIR
MIR920
LOC100130776
LOC100133893
LOC100233209
LOC100240734
LOC100240735
LOC100286844

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q13.

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CDH11
CYLD
HERPUD1
hsa-mir-138-2
ADCY7
AMFR
BBS2
CDH8
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1M
MT1L
MT1X
MT2A
MT3
POLR2C
RBL2
SALL1
CCL17
CCL22
CX3CL1
SLC6A2
SLC12A3
GPR56
NUP93
IRX5
KATNB1
NUDT21
CNOT1
ZNF423
RPGRIP1L
ARL2BP
DKFZP434H168
TOX3
CCDC113
C16orf80
BRD7
PLLP
CES4
LPCAT2
HEATR3
SLC38A7
OGFOD1
DOK4
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
FTO
IRX6
IRX3
C16orf57
SETD6
FAM192A
CHD9
NLRC5
CCDC135
CAPNS2
MT4
NKD1
RSPRY1
CCDC102A
SNX20
CPNE2
GPR114
KLKBL4
CES7
GPR97
TMEM188
LOC283856
LOC283867
MT1DP
TEPP
MIR138-2
MT1IP
LOC644649
SNORA46
SNORA50

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.2.

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PRDM1
MYB
ROS1
TNFAIP3
STL
GOPC
hsa-mir-548a-2
hsa-mir-588
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-30a
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IMPG1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
ME1
MAP3K5
MYO6
NMBR
NT5E
PCMT1
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
RPS12
SGK1
SIM1
SMPD2
ELOVL4
MAP3K7
TCF21
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
UTRN
PTP4A1
EPM2A
STX7
PEX3
DDO
STX11
SNX3
RNGTT
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
FHL5
AKAP7
ATG5
TBPL1
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDC2L6
MAP3K7IP2
MDN1
TSPYL4
SASH1
KIAA0776
PHF3
HEY2
HEBP2
ORC3L
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
SFRS18
IBTK
MOXD1
SENP6
FBXL4
SLC17A5
SNORD50A
PDE7B
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
HDDC2
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
UBE2J1
VTA1
LGSN
HECA
COQ3
IL20RA
AHI1
RMND1
PHIP
SOBP
AKIRIN2
QRSL1
VNN3
NCRNA00120
DDX43
FAM46A
TMEM30A
LMBRD1
ECHDC1
KCNQ5
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
SERINC1
HACE1
FAM135A
ZBTB2
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
MANEA
C6orf103
C6orf155
C6orf97
ULBP2
ULBP1
KHDC1
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
ARMC2
FBXO30
RPF2
L3MBTL3
MCHR2
C6orf168
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
USP45
REPS1
PPIL4
SLC22A16
UBE2CBP
KIAA1919
ARHGAP18
GTF3C6
MRAP2
RWDD2A
FAM54A
KLHL32
TMEM200A
C6orf150
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SFRS13B
LOC153910
C6orf94
RAET1L
SAMD3
MGC34034
SLC2A12
RNF217
NKAIN2
C6orf221
C6orf165
PRSS35
LCA5
OLIG3
TXLNB
KHDRBS2
C6orf163
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
C6orf167
FAM26E
MCM9
SCML4
SHPRH
LOC285733
LOC285735
LOC285740
C6orf182
PPIL6
FLJ34503
DCBLD1
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GUSBL2
GJB7
SNHG5
SUMO4
C6orf147
C6orf173
C6orf174
C6orf204
THEMIS
LIN28B
SAMD5
IYD
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
LOC442245
RFPL4B
LOC553137
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
CTAGE9
RAET1K
SNORD50B
MIR548B
LOC728402
C6orf186
LOC729176
BET3L
KHDC1L
C6orf217
NHEG1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.2.

Table S67. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-876
LINGO2
MIR876

Genes in Wide Peak

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

Table S68. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CARS
FANCF
HRAS
LMO1
NUP98
hsa-mir-610
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
SERGEF
OR5E1P
OR10A3
FXC1
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2AS
BET1L
CEND1
CYB5R2
TRIM34
MUPCDH
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
LIN7C
LGR4
LRDD
KCNQ1DN
SOX6
PARVA
MMP26
C11orf17
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
HCCA2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
NAV2
SYT8
CCDC34
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIMP1
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
METT5D1
OR56B4
ANO5
LOC255512
OR52B2
C11orf35
OR51F1
SVIP
MRGPRX1
OR51B5
FLJ46111
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
IGSF22
OR10A4
OLFML1
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
DKFZp686O24166
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVIN1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A4
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
TRIM6-TRIM34
LOC494141
BDNFOS
MIR483
SNORA3
SNORA52
RASSF10
LOC650368
SNORA23
SNORA45
SNORA54
SNORD97
MIR610
INS-IGF2
MUC5B
MIR675
LOC100126784
FAM99B
LOC100133161
LOC100133545

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p24.1.

Table S69. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TGFBR2
RBMS3
OSBPL10
STT3B
GADL1

Genes in Wide Peak

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

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GATA3
ADARB2
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PRKCQ
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
KIN
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
C10orf18
C10orf110
SFMBT2
ASB13
TUBAL3
ITIH5
AKR1E2
TAF3
FBXO18
RBM17
IDI2
UCN3
LOC338588
AKR1CL1
TUBB8
tAKR
NCRNA00200
FLJ45983
C10orf108
LOC100216001

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

Table S71. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BUB1B
PML
TCF12
C15orf21
hsa-mir-549
hsa-mir-184
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-628
hsa-mir-1300
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
ADAM10
ANXA2
AQP9
B2M
BBS4
BCL2A1
BNIP2
CA12
CAPN3
CHRNA3
CHRNA5
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IDH3A
IL16
IREB2
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2C1
MAP1A
MFAP1
MPI
MYO1E
MYO5A
MYO9A
NEDD4
NEO1
OAZ2
PKM2
PLCB2
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RORA
RPL4
RPLP1
SLC12A1
SNX1
SORD
SPINT1
SRP14
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
SLC30A4
ANP32A
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
ALDH1A2
HERC1
PSTPIP1
USP8
CCNB2
SLC28A2
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
PIGB
KIF23
IGDCC3
HISPPD2A
SECISBP2L
KIAA0101
LCMT2
ARNT2
USP3
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
SERF2
DENND4A
SNAPC5
HMG20A
CORO2B
CIB2
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
SLC27A2
ADAMTS7
GPR176
CHP
OIP5
ITGA11
BAHD1
CEP152
MAPKBP1
ZNF609
TBC1D2B
RTF1
MESDC2
ACSBG1
KIAA1024
MGA
DMXL2
VPS39
TMED3
AP4E1
CCNDBP1
DAPK2
EID1
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
PYGO1
PLDN
FBXO22
NPTN
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
RPS27L
NDUFAF1
RSL24D1
NUSAP1
RASL12
SPG21
SPTBN5
PTPLAD1
CTDSPL2
RAB8B
DUOX1
CSNK1G1
ZFAND6
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZWILCH
FLJ10038
UACA
HAUS2
FAM82A2
DNAJC17
IMP3
LARP6
MNS1
DNAJA4
GOLGA6B
MYO5C
KIAA1370
C15orf39
THAP10
PAK6
PARP6
DTWD1
CASC5
C15orf17
KIAA1199
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
MESDC1
PPCDC
BRUNOL6
STRA6
ZFP106
IQCH
ISL2
RFX7
SPATA5L1
CHAC1
NOX5
NEIL1
NARG2
AAGAB
LMAN1L
SLTM
SGK269
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
C15orf28
C15orf34
PIF1
CCDC33
EDC3
SPG11
ELL3
PLEKHO2
WDR61
CD276
STARD5
GRINL1A
C15orf44
C15orf5
ADPGK
APH1B
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
SPPL2A
LINGO1
ZFYVE19
CGNL1
FRMD5
UBL7
DISP2
C15orf57
C15orf23
BMF
SHF
DUOXA1
LOC91450
CALML4
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
DIS3L
TGM7
CATSPER2
LEO1
SENP8
MTFMT
OSTbeta
HIGD2B
C15orf27
AGPHD1
PLA2G4E
TRIM69
C15orf43
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145837
C15orf61
NRG4
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
ODF3L1
ADAL
EXD1
RHOV
SCAMP5
C15orf33
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
SPESP1
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
SLC24A5
PRTG
LOC283663
TMEM84
C15orf60
C15orf37
LOC283731
PLA2G4D
FBXL22
TMEM202
GLDN
GOLGA6A
TMC3
RBPMS2
ANKDD1A
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
LOC390594
LOC390595
LBXCOR1
ANKRD34C
SHC4
CTXN2
ST20
DUOXA2
MIR184
MIR190
C15orf50
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645752
SH2D7
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA14
FBXO22OS
MIR548A3
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
LOC728758
LOC729082
MIR147B
DNM1P35
LOC100129387
LOC100132724
JMJD7
PLA2G4B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

Table S72. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-1303
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-1974
hsa-mir-9-2
hsa-mir-582
hsa-mir-449b
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-887
ADCY2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGF10
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NDUFS6
NEUROG1
NPR3
NPY6R
OCLN
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
PURA
RAD17
RARS
RASA1
RASGRF2
RPL37
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP1
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
SRP19
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
C5orf13
TRIP13
CNOT8
RAB9P1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5OS
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
SDCCAG10
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
POLS
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
HISPPD1
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
OTP
SKIV2L2
NNT
TTC33
ZNF346
AMACR
SSBP2
BHMT2
TNFAIP8
NIPBL
LOC25845
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
FBXO4
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1L
MAT2B
SLC27A6
SNX24
MRPL22
RNASEN
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MGC29506
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
FAM134B
FAM105A
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
MTMR12
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
PCDH24
GIN1
WDR55
ANKHD1
NSUN2
CCDC99
THG1L
WDR70
AGGF1
WDR41
BRIX1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
ANKH
CCL28
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
AHRR
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1L
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
C5orf23
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
CARD6
TRIM52
HAVCR2
AGXT2L2
C5orf62
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
LMBRD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C1QTNF3
C5orf26
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
HEATR7B2
EGFLAM
PRRC1
C5orf33
UGT3A1
CAPSL
JMY
C5orf58
ZNF474
CCDC127
OR2Y1
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
C5orf37
GPR151
STARD4
WDR36
LOC134466
NUDCD2
UBLCP1
ACOT12
ANKRD43
SHROOM1
C5orf24
SFRS12
C5orf20
SLC38A9
SLC36A2
SPINK5L3
C5orf41
CEP120
LOC153328
TMEM167A
MBLAC2
TMEM161B
SRFBP1
PLEKHG4B
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
LOC153684
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
MGC42105
LIX1
ZNF366
FAM151B
S100Z
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
LVRN
SLC36A1
RICTOR
EIF4E1B
LOC255167
RASGEF1C
ANKRD31
SERINC5
LOC257358
SH3PXD2B
LOC285593
FAM153A
ARL10
C5orf36
GPR150
DTWD2
RELL2
NBPF22P
LOC285627
LOC285629
C5orf51
SLC36A3
KIF4B
OR2V2
FLJ37543
RNF180
SFRS12IP1
ZNF454
C5orf60
LOC285692
LOC285696
RGMB
RFESD
CHSY3
SLC6A19
TMEM173
FAM170A
LOC340074
ARSI
LOC340094
ANKRD34B
PFN3
ZNF879
PLCXD3
IRGM
FBLL1
ACTBL2
FAM174A
MTX3
CATSPER3
SLC6A18
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
C5orf34
MAST4
C5orf25
RNF138P1
LRRC14B
C5orf39
ISCA1L
C5orf48
LOC389332
LOC389333
C5orf46
FLJ41603
FLJ33360
RGS7BP
FLJ44606
SPINK6
ANKHD1-EIF4EBP3
MIR103-1
MIR143
MIR145
MIR146A
MIR218-2
SPINK5L2
C5orf40
MARCH11
LOC441089
FLJ42709
C5orf56
MIR340
C5orf53
GPX8
TIFAB
MIR449A
CTXN3
SNORD72
SNORD95
SNORD96A
ECSCR
TMEM232
C5orf43
GRXCR2
SPINK9
ZFP62
FLJ33630
LOC644936
CCNI2
LOC645323
CBY3
LOC647859
ANKRD33B
GUSBP3
GTF2H2B
FAM153C
LOC653391
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR548C
MIR548D2
MIR580
MIR581
MIR583
MIR585
SNHG4
LOC728264
GTF2H2C
LOC728411
SERF1B
LOC728554
SDHAP3
LOC728613
LOC728723
AACSL
LOC729678
OR4F29
GTF2H2D
SNORD123
MIR886
MIR874
LOC100129716
CCDC152
LRRC70
FAM196B
LOC100132062
LOC100132287
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100286948
TMED7-TICAM2
NCRUPAR
LOC100303749
LOC100310782

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.06 | 0.528 | 0.702 | 0.10 | 2.6 | 0.0227
1q | 1572 | 0.16 | 4.93 | 5.29e-06 | 0.02 | -2.08 | 1
2p | 753 | 0.09 | -1.92 | 1 | 0.03 | -4 | 1
2q | 1235 | 0.09 | -0.322 | 1 | 0.04 | -2.33 | 1
3p | 853 | 0.16 | 0.907 | 0.508 | 0.57 | 16 | 0
3q | 917 | 0.56 | 16.2 | 0 | 0.20 | 1.99 | 0.0818
4p | 366 | 0.06 | -3.18 | 1 | 0.32 | 4.92 | 2.88e-06
4q | 865 | 0.04 | -3.02 | 1 | 0.16 | 1.29 | 0.277
5p | 207 | 0.29 | 2.99 | 0.0108 | 0.18 | -0.325 | 1
5q | 1246 | 0.08 | -0.414 | 1 | 0.22 | 5.35 | 3.37e-07
6p | 937 | 0.09 | -1.32 | 1 | 0.11 | -0.651 | 1
6q | 692 | 0.06 | -2.95 | 1 | 0.10 | -1.73 | 1
7p | 508 | 0.24 | 2.7 | 0.0194 | 0.06 | -3.26 | 1
7q | 1071 | 0.16 | 2.02 | 0.0769 | 0.07 | -1.47 | 1
8p | 495 | 0.26 | 2.91 | 0.0119 | 0.38 | 6.77 | 8.33e-11
8q | 697 | 0.47 | 11.6 | 0 | 0.11 | -0.974 | 1
9p | 343 | 0.22 | 1.2 | 0.373 | 0.33 | 4.78 | 4.97e-06
9q | 916 | 0.20 | 2.58 | 0.0239 | 0.16 | 1.28 | 0.277
10p | 312 | 0.04 | -4.18 | 1 | 0.16 | -0.519 | 1
10q | 1050 | 0.05 | -2.51 | 1 | 0.11 | -0.189 | 1
11p | 731 | 0.07 | -2.22 | 1 | 0.20 | 2.1 | 0.0699
11q | 1279 | 0.11 | 0.507 | 0.702 | 0.33 | 10.4 | 0
12p | 484 | 0.19 | 0.787 | 0.56 | 0.07 | -2.84 | 1
12q | 1162 | 0.10 | -0.091 | 1 | 0.03 | -2.77 | 1
13q | 554 | 0.07 | -2.87 | 1 | 0.20 | 1.42 | 0.253
14q | 1144 | 0.16 | 2.42 | 0.034 | 0.09 | -0.702 | 1
15q | 1132 | 0.05 | -2.43 | 1 | 0.06 | -1.71 | 1
16p | 719 | 0.07 | -2.52 | 1 | 0.07 | -2.52 | 1
16q | 562 | 0.07 | -3.06 | 1 | 0.09 | -2.27 | 1
17p | 575 | 0.10 | -1.67 | 1 | 0.15 | -0.296 | 1
17q | 1321 | 0.11 | 0.965 | 0.502 | 0.07 | -0.868 | 1
18p | 117 | 0.21 | 0.264 | 0.858 | 0.28 | 2.48 | 0.0287
18q | 340 | 0.12 | -1.54 | 1 | 0.38 | 6.41 | 7.23e-10
19p | 870 | 0.06 | -2.36 | 1 | 0.07 | -2.15 | 1
19q | 1452 | 0.06 | -0.512 | 1 | 0.07 | -0.23 | 1
20p | 295 | 0.26 | 2.35 | 0.0363 | 0.13 | -1.61 | 1
20q | 627 | 0.25 | 3.38 | 0.00359 | 0.13 | -0.566 | 1
21q | 422 | 0.04 | -4.03 | 1 | 0.21 | 1.25 | 0.277
22q | 764 | 0.12 | -0.505 | 1 | 0.08 | -1.96 | 1

Methods & Data
Input

Table 4. Get Full Table First 10 out of 165 Input Tumor Samples.

Tumor Sample Names
TCGA-BA-4074-01A-01D-1432-01
TCGA-BA-4075-01A-01D-1432-01
TCGA-BA-4076-01A-01D-1432-01
TCGA-BA-4077-01B-01D-1432-01
TCGA-BA-4078-01A-01D-1432-01
TCGA-BA-5149-01A-01D-1510-01
TCGA-BA-5151-01A-01D-1432-01
TCGA-BA-5152-01A-02D-1869-01
TCGA-BA-5153-01A-01D-1432-01
TCGA-BA-5555-01A-01D-1510-01

Figure 3. Segmented copy number profiles in the input data

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
Meta

- Maintainer = Dan DiCara

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