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

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

Summary

There were 86 tumor samples used in this analysis: 19 significant arm-level results, 22 significant focal amplifications, and 29 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 - 22 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
6p22.3 | 1.4627e-21 | 1.4627e-21 | chr6:20361033-21757620 | 4
8q22.2 | 2.8441e-12 | 2.32e-10 | chr8:101180651-102354063 | 9
1q23.3 | 3.8622e-10 | 3.8622e-10 | chr1:161032152-161086944 | 4
3p25.2 | 6.4541e-10 | 6.4541e-10 | chr3:12481505-12491536 | 0 [PPARG]
11q13.3 | 2.9265e-09 | 2.9265e-09 | chr11:69464719-70027203 | 6
19q12 | 2.4183e-07 | 2.4183e-07 | chr19:30245583-30529931 | 2
7p11.2 | 9.5403e-06 | 9.5403e-06 | chr7:54286143-56022730 | 10
12q15 | 2.1122e-05 | 2.1122e-05 | chr12:69120903-70175610 | 16
10p15.1 | 0.0003082 | 0.0003082 | chr10:4197255-6398978 | 27
17q12 | 0.0011087 | 0.0015275 | chr17:37813857-37905815 | 8
4p16.3 | 0.0055855 | 0.0055855 | chr4:1752421-1817427 | 2
1p34.2 | 0.0056607 | 0.0056607 | chr1:39531274-40539227 | 17
8p11.23 | 0.0082157 | 0.0082157 | chr8:36905670-37763904 | 7
22q11.23 | 0.014768 | 0.014768 | chr22:22281639-26820434 | 70
5p15.33 | 0.018395 | 0.018395 | chr5:1-15331281 | 81
20q11.21 | 0.028443 | 0.028443 | chr20:30064458-31121563 | 26
16p11.2 | 0.04376 | 0.04376 | chr16:28605319-30334145 | 61
17q11.2 | 0.014768 | 0.05794 | chr17:27386448-27864389 | 6
8q24.21 | 2.6052e-07 | 0.066402 | chr8:119209188-146364022 | 211
6q21 | 0.15379 | 0.15379 | chr6:107302810-107457456 | 2
12p13.32 | 0.21034 | 0.21034 | chr12:1-8309432 | 124
13q22.1 | 0.21688 | 0.21688 | chr13:67509993-115169878 | 157

Genes in Wide Peak

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

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

Genes
E2F3
SOX4
CDKAL1
LINC00340

Genes in Wide Peak

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

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

Genes
SPAG1
YWHAZ
RNF19A
PABPC1
ZNF706
ANKRD46
SNX31
FLJ42969
MIR4471

Genes in Wide Peak

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

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

Genes
PFDN2
PVRL4
KLHDC9
ARHGAP30

Genes in Wide Peak

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

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

Genes
CCND1
FGF3
FGF4
FGF19
ANO1
ORAOV1

Genes in Wide Peak

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

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

Genes
CCNE1
URI1

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
MRPS17
LANCL2
VOPP1
VSTM2A
LOC285878
SEPT14
ZNF713
FKBP9L

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
hsa-mir-3155
CALML3
AKR1C4
AKR1C1
AKR1C2
GDI2
IL2RA
IL15RA
PFKFB3
AKR1C3
NET1
CALML5
ANKRD16
FAM208B
ASB13
TUBAL3
AKR1E2
FBXO18
RBM17
UCN3
LOC338588
AKR1CL1
tAKR
LOC399715
LOC100216001
MIR3155A
MIR3155B

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
PNMT
TCAP
STARD3
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

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

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

Genes
FGFR3
LETM1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ERLIN2
PROSC
GPR124
BRF2
ZNF703
RAB11FIP1
LOC728024

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ASXL1
hsa-mir-1825
hsa-mir-3193
BCL2L1
FOXS1
HCK
ID1
PLAGL2
KIF3B
TM9SF4
TPX2
POFUT1
REM1
HM13
PDRG1
COX4I2
MYLK2
DUSP15
TSPY26P
C20orf112
C20orf160
LINC00028
TTLL9
XKR7
PSIMCT-1
MIR3193

Genes in Wide Peak

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

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

Genes
ALDOA
ATP2A1
CD19
KIF22
MAZ
PPP4C
MAPK3
SPN
SULT1A2
SULT1A1
SULT1A3
TBX6
TUFM
DOC2A
HIRIP3
EIF3C
TAOK2
MVP
CDIPT
CORO1A
ATXN2L
QPRT
SH2B1
SEZ6L2
LAT
SLX1B
GDPD3
C16orf53
RABEP2
SLC7A5P1
YPEL3
FAM57B
SPNS1
NFATC2IP
PRRT2
TMEM219
C16orf92
KCTD13
ASPHD1
C16orf54
INO80E
LOC388242
SNX29P2
LOC440354
LOC440356
SULT1A4
SLX1A
BOLA2
LOC595101
LOC606724
LOC613037
LOC613038
RRN3P2
ZG16
BOLA2B
EIF3CL
LOC100289092
SLX1A-SULT1A3
SLX1B-SULT1A4
MIR4721
MIR4517

Genes in Wide Peak

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

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

Genes
CRYBA1
TIAF1
NUFIP2
TAOK1
MYO18A
MIR4523

Genes in Wide Peak

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

Table S18. 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-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
ADCY8
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
POU5F1B
PTK2
PVT1
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
JRK
DGAT1
GPAA1
WISP1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
KHDRBS3
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
C8orf55
FAM49B
CHRAC1
EXOSC4
LY6K
TRMT12
WDYHV1
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
GSDMD
ZNF696
ARHGAP39
ZNF34
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
MAF1
PARP10
C8orf76
TIGD5
FAM83A
PPP1R16A
ZNF251
KIFC2
NAPRT1
WDR67
HPYR1
MFSD3
MAL2
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
TMEM65
LOC157381
FAM84B
FAM91A1
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
SPATC1
FLJ43860
MAFA
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
C8orf73
SCXB
FER1L6
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR937
MIR939
LOC100128338
SCXA
LOC100130231
CCDC166
LOC100131726
LOC100133669
LOC100288181
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR1208
LOC100507117
ZHX1-C8ORF76
MIR4663
MIR4472-1
MIR4664
PCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

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

Genes
C6orf203
BEND3

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

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 - 29 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 | 5.9073e-47 | 1.357e-45 | chr9:21865498-22448737 | 4
5q11.2 | 6.6605e-09 | 6.6605e-09 | chr5:58260298-59787985 | 3
2q22.1 | 4.0754e-08 | 4.2025e-07 | chr2:139655617-143637838 | 1
13q14.2 | 1.1701e-06 | 1.1701e-06 | chr13:45382430-50471178 | 39
4q22.1 | 5.7425e-06 | 1.7413e-05 | chr4:90844993-93240505 | 1
16p13.3 | 7.6082e-05 | 7.6135e-05 | chr16:3029029-4013466 | 34
17p12 | 0.00011404 | 0.00011949 | chr17:14131834-15999789 | 19
6q22.31 | 0.0014245 | 0.0014245 | chr6:92230434-122757952 | 130
10q23.31 | 0.0032676 | 0.0032676 | chr10:89617158-91063177 | 17
15q12 | 0.0050497 | 0.0051122 | chr15:1-32934882 | 168
2q34 | 2.9364e-05 | 0.0093461 | chr2:213401694-214143899 | 3
19p13.3 | 0.013136 | 0.013317 | chr19:1-9203991 | 287
2q37.1 | 0.0010542 | 0.036753 | chr2:214143901-243199373 | 281
6p25.3 | 0.042133 | 0.042571 | chr6:1-4026921 | 29
11p15.4 | 0.07006 | 0.070635 | chr11:1-135006516 | 1478
16q23.1 | 0.088002 | 0.086273 | chr16:78129058-79627770 | 1
Xq23 | 0.086273 | 0.086273 | chrX:77910652-128658341 | 239
1p36.11 | 0.089446 | 0.088646 | chr1:1-117645743 | 1232
8p23.1 | 0.10817 | 0.10817 | chr8:1-39792913 | 303
9q22.33 | 0.113 | 0.11097 | chr9:101016723-101979393 | 5
3p14.1 | 0.020403 | 0.12578 | chr3:40211012-88046665 | 367
9p24.1 | 0.0036188 | 0.12578 | chr9:1-21008376 | 83
12p13.2 | 0.12958 | 0.13163 | chr12:3980957-24365820 | 246
22q13.32 | 0.14542 | 0.14542 | chr22:34146369-51304566 | 271
3p21.31 | 0.025941 | 0.16067 | chr3:25755999-84920597 | 438
4q31.21 | 0.088002 | 0.16562 | chr4:90804644-191154276 | 397
14q32.31 | 0.24602 | 0.24257 | chr14:1-107349540 | 788
3p11.2 | 0.10817 | 0.33256 | chr3:1-198022430 | 1276
3p14.2 | 0.0043233 | 0.72395 | chr3:1-198022430 | 1276

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

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

Table S24. 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 13q14.2.

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

Genes
LCP1
RB1
RCBTB2
CPB2
ESD
MLNR
GTF2F2
HTR2A
KPNA3
TPT1
SUCLA2
ITM2B
LPAR6
FNDC3A
ZC3H13
LRCH1
NUFIP1
MED4
PHF11
RCBTB1
NUDT15
KIAA1704
CYSLTR2
KIAA0226L
CDADC1
CAB39L
COG3
SETDB2
EBPL
ARL11
FAM194B
SPERT
CTAGE10P
SLC25A30
SIAH3
KCTD4
SNORA31
TPT1-AS1
LOC100509894

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
CREBBP
DNASE1
MEFV
OR1F1
OR2C1
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
CLDN6
CLDN9
IL32
ZNF263
TRAP1
CLUAP1
OR1F2P
TNFRSF12A
ZNF434
HCFC1R1
MMP25
THOC6
NAA60
MGC3771
SLX4
ZSCAN10
TIGD7
ZNF597
CCDC64B
NLRC3
LINC00514
FLJ39639
C16orf90
MTRNR2L4

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
CCNC
COL10A1
EPHA7
FOXO3
FRK
FYN
GJA1
GPR6
GRIK2
HDAC2
HSF2
KPNA5
LAMA4
MARCKS
MAN1A1
PLN
POU3F2
PREP
REV3L
SIM1
SMPD2
NR2E1
TSPYL1
DDO
SNX3
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
FUT9
TRAF3IP2
ASCC3
BVES
SEC63
CDK19
TSPYL4
UFL1
BRD7P3
ASF1A
PNISR
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
COQ3
SOBP
QRSL1
PDSS2
HACE1
BEND3
PRDM13
POPDC3
MICAL1
FAM184A
MANEA
GPR63
ARMC2
RPF2
MCHR2
FAXC
RTN4IP1
USP45
SLC22A16
KIAA1919
GTF3C6
KLHL32
NUS1
SLC16A10
BVES-AS1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
RSPH4A
LINC00222
CEP85L
LIN28B
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
LOC100130890
LOC100287632
MIR2113
MIR548H3
LOC100422737
MIR4643

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
IKZF2
MIR4776-1
MIR4776-2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
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
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
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
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

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

Genes
IRF4
BPHL
SERPINB1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
TUBB2A
RIPK1
FAM50B
EXOC2
WRNIP1
DUSP22
SLC22A23
FOXQ1
HUS1B
C6orf195
PXDC1
MGC39372
LOC285768
MYLK4
TUBB2B
PSMG4
DKFZP686I15217
LOC100507194
LOC100508120
MIR4645

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CCND1
CARS
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
HRAS
LMO1
LMO2
MEN1
MLL
NUMA1
NUP98
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
hsa-mir-3163
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-3162
hsa-mir-130a
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ACAT1
ACP2
ACRV1
ACTN3
ADM
ADRBK1
AP2A2
APLNR
ALDH3B1
ALDH3B2
AMPD3
APBB1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
RHOG
ARHGAP1
PHOX2A
ARL2
ARNTL
ARRB1
ART1
ASCL2
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CCKBR
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
TPP1
CLNS1A
CNGA4
CNTF
COPB1
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSD
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GTF2H1
GUCY1A2
H2AFX
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HMBS
SLC29A2
HPX
HSPA8
HSPB2
DNAJC4
HTR3A
IGF2
IGHMBP2
IL10RA
IL18
ILK
INCENP
INS
INPPL1
IRF7
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KCNQ1
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LSP1
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MUC2
MUC6
MYBPC3
MYO7A
MYOD1
NAP1L4
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
NUCB2
OMP
OPCML
SLC22A18
SLC22A18AS
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PDE3B
PGA5
PGR
PIK3C2A
PLCB3
POLR2G
POLR2L
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PSMA1
PSMC3
PSMD13
PTH
PTPRCAP
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
RNH1
SNORD15A
ROM1
MRPL23
RPL27A
RPLP2
RPS3
RPS6KB2
RPS13
RPS25
RRM1
SAA1
SAA2
SAA3P
SAA4
SC5DL
SCN2B
SCN4B
SCT
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SMPD1
SORL1
SPI1
SPTBN2
SRPR
TRIM21
SSRP1
ST5
ST14
STIM1
STX3
STX5
ABCC8
TAGLN
TAF10
TALDO1
TCN1
TEAD1
TECTA
TH
THRSP
THY1
TSPAN4
TM7SF2
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TRPC6
TSG101
PHLDA2
TUB
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WEE1
WNT11
SF1
ZFPL1
ZNF143
ZBTB16
ZNF195
ZNF202
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIBP2
PPFIA1
SLC43A1
IFITM1
DGKZ
CHST1
BARX2
API5
MADD
OR7E2P
OR6A2
DCHS1
EIF3F
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
BRSK2
AIP
SYT7
SART1
USP2
SLC6A5
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MED17
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
MICAL2
CTR9
CEP57
ARHGAP32
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
TRIM66
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
TSPAN32
TSSC4
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
MRVI1
TRIM22
PRG3
IFITM3
YAP1
SPON1
RBM14
CDC42EP2
EIF3M
NXF1
DEAF1
KAT5
HYOU1
IPO7
SSSCA1
HTATIP2
IFITM2
DRAP1
TRIM3
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
OR7E14P
OR7E12P
NEU3
ME3
GPR83
LYVE1
YIF1A
SRSF8
EHD1
C11orf58
STIP1
CLP1
KCNQ1OT1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
PKP3
HPS5
PTGDR2
SLCO2B1
RRAS2
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
SWAP70
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
DENND5A
NUP160
NCAPD3
FNBP4
RRP8
SIK3
SIRT3
CLCF1
OR52A1
VSIG2
BACE1
FAM89B
SNHG1
ARFIP2
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
C11orf41
PRDX5
POU2F3
ABTB2
BRMS1
C11orf20
CHRDL2
PAMR1
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
PPP1R14B
OR8G2
OR8B8
OR8G1
OR10A3
FXC1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
ACAD8
B3GAT1
DKK3
RBMXL2
RAB30
PGAP2
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
COMMD9
DDX25
C11orf21
PACSIN3
TRPM5
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
UBQLN3
KCNK4
RNF141
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
IGF2-AS1
TMEM216
BET1L
CEND1
CHCHD8
SLC15A3
PHF21A
MS4A4A
WT1-AS
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
CYB5R2
RSF1
SPA17
FXYD6
C11orf24
TRIM34
CDHR5
CNTN5
SIAE
TOLLIP
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39A
TRIM44
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
USP47
VPS37C
ANO1
TRIM68
NADSYN1
FAM86C1
C11orf57
NAT10
CCDC87
PPP6R3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
PIDD
ELMOD1
KCNQ1DN
SOX6
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
PARVA
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
MMP26
TMPRSS4
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
GPR137
IFT46
C11orf75
C11orf30
PRDM10
PRDM11
CABP4
CHRNA10
SLC17A6
TRIM49
PNPLA2
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
CARNS1
SYT13
USP28
PHRF1
LRRC4C
SCUBE2
POLD4
KRTAP5-8
PLEKHB1
MS4A7
ZBED5
CREBZF
CARD18
SIGIRR
CCDC90B
CCDC81
AASDHPPT
ALX4
RIC8A
MRPL17
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
EPS8L2
KLC2
TUT1
MRPL11
TMEM135
STK33
KCTD14
C11orf95
CHID1
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
OR51G1
OR51B4
OR51B2
OR52N1
FAM118B
RIC3
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
E2F8
SLC25A22
CCDC82
ALG9
ZNF408
CLMP
NAA40
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
ATHL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
PTDSS2
MOB2
GDPD5
CLPB
UNC93B1
SBF2
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
FAM160A2
RNASEH2C
FAR1
TMEM126A
DCUN1D5
BTBD10
EIF1AD
NUDT22
ARFGAP2
KIAA1826
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
SPRYD5
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
MICALCL
RELT
UBASH3B
C11orf70
LGALS12
TRIM5
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
NAV2
ATG16L2
GLB1L2
SYT8
TSPAN18
ESAM
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
PRKCDBP
VPS26B
GLB1L3
CDCA5
RPLP0P2
SAAL1
ODF3
SLC22A9
SNORD15B
TIRAP
CARD16
OSBPL5
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
LRRC56
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRE
MRGPRF
ART5
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
SLC36A4
FAT3
TRIM64
TMEM45B
CYP2R1
DBX1
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
LOC120824
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
XRRA1
UBQLNL
MUC15
LOC143666
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
C11orf42
GPHA2
ADAMTS15
NLRP6
NS3BP
B3GNT6
METTL15
MPZL3
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
MRPL21
TPCN2
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
PPP1R32
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
LOC254100
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
TMEM151A
OR51F1
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
KRT8P41
LOC283104
CSNK2A1P
OR51V1
LOC283116
H19
C11orf85
SLC25A45
NEAT1
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
OR9G4
LOC283194
LINC00301
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
EFCAB4A
TMEM80
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
OR10A2
OVCH2
TBX10
PDDC1
C11orf34
RTN4RL2
GALNTL4
B7H6
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
KRTAP5-10
SLC22A25
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
SLC22A10
SPDYC
LIPT2
VSTM5
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
NAV2-AS4
HNRNPKP3
FAM180B
PCNXL3
FLJ42102
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
OR4C45
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR210
MIR34B
MIR34C
DDI1
BLID
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
LOC440040
LOC440041
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
LINC00167
LOC441601
OR5B3
MIR326
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
MS4A13
OR8U8
OR9G9
SCARNA9
MIR483
SNORA3
SNORA52
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
BTBD18
LOC643733
PGA3
PGA4
LOC643923
LOC644656
CLDN25
RASSF10
FAM86C2P
TRIM64C
LOC646813
LOC649133
RPL23AP64
LOC650368
LOC653486
SNORA8
SNORA1
SNORA18
SNORA23
SNORA40
SNORA45
SNORA54
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
SNORD97
MIR610
MIR611
MIR612
INS-IGF2
MUC5B
LOC729013
TRIM49L1
LOC729799
METTL12
C11orf83
MIR675
MIR708
LOC100126784
LOC100128239
LOC100129216
MRVI1-AS1
LOC100130348
LOC100130987
C11orf91
LOC100132078
FAM99B
LOC100133161
LOC100133315
MRPL23-AS1
PATE3
LOC100288077
LOC100288346
MIR1304
MIR1908
MIR1237
MIR548K
MIR670
SNORA70E
BACE1-AS
MIR4300
MIR3160-2
MIR3160-1
MIR4301
MIR3162
MIR3167
MIR3165
MIR1260B
MIR4298
MIR4299
MTRNR2L8
LOC100499227
MIR3654
MIR3920
MIR3656
MIR3664
MIR3680-1
LOC100500938
MIR210HG
LOC100506233
LOC100506305
LOC100506368
LOC100506540
DCDC5
CASP12
LOC100507050
LOC100507205
LOC100507300
LOC100507392
LOC100507401
RBM14-RBM4
LOC100526771
TMX2-CTNND1
SAA2-SAA4
ARL2-SNX15
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
HNRNPUL2-BSCL2
MIR4486
MIR4697
MIR4686
MIR4490
MIR4485
MIR4489
MIR4690
MIR3973
MIR4493
MIR4491
MIR4688
MIR4492
MIR4696
MIR4691
MIR4692
MIR4694
MIR1343
MIR4687
MIR4693
MIR4488
LOC100652768

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq23.

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

Genes
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
hsa-mir-448
hsa-mir-1911
hsa-mir-1264
hsa-mir-4329
hsa-mir-652
hsa-mir-548m
hsa-mir-361
hsa-mir-548i-4
hsa-mir-4328
AGTR2
SLC25A5
XIAP
BTK
CAPN6
CHM
COL4A5
COL4A6
CSTF2
CYLC1
DCX
TIMM8A
DIAPH2
DRP2
TSC22D3
ACSL4
CENPI
GLA
GLUD2
LPAR4
GRIA3
GUCY2F
HNRNPH2
HTR2C
IL13RA1
IL13RA2
LAMP2
SH2D1A
NAP1L3
NDUFA1
PAK3
PLP1
PLS3
POU3F4
PRPS1
PSMD10
RPL39
RPL36A
SH3BGRL
SMARCA1
SERPINA7
TDGF1P3
TSPAN6
TRPC5
UBE2A
ZNF711
RNF113A
CUL4B
IRS4
CLDN2
TCEAL1
ITM2A
MORF4L2
GPRASP1
ARMCX2
AMMECR1
ZBTB33
ODZ1
STAG2
PGRMC1
TMSB15A
MID2
SLC6A14
SEPT6
ATP1B4
KCNE1L
IL1RAPL2
SNORA69
NGFRAP1
NOX1
SRPX2
PCDH11X
RPS6KA6
P2RY10
MCTS1
C1GALT1C1
RPA4
TBX22
WBP5
RAB9B
LUZP4
ARMCX1
ARMCX3
CPXCR1
TAF7L
ARMCX6
WDR44
NUP62CL
TBC1D8B
FAM70A
CXorf57
RBM41
BEX1
NXT2
NKRF
NXF5
NXF4
NXF3
NXF2
KLHL4
TEX13B
TEX13A
BEX4
TCEAL7
THOC2
KIAA1210
PCDH19
RGAG1
LRCH2
TMEM35
CXorf56
TNMD
ARMCX5
UPF3B
HMGN5
NKAP
RNF128
MORC4
LONRF3
ALG13
TCEAL4
TRMT2B
POF1B
ESX1
BHLHB9
TMEM164
ZMAT1
RHOXF2
GPR174
BEX2
TCEAL3
KLHL13
TGIF2LX
TCEAL8
CHRDL1
RIPPLY1
SYTL4
GPRASP2
ATG4A
DACH2
DCAF12L1
CXorf41
MUM1L1
FAM199X
APOOL
HDX
ACTRT1
RBMXL3
DOCK11
TCEAL2
PABPC5
RAB40A
AMOT
AKAP14
RHOXF1
NKAPP1
TCEAL6
H2BFWT
FAM46D
ZCCHC12
CXorf61
SLC25A43
ZCCHC5
NRK
TMEM31
BRWD3
CT47A11
RAB40AL
H2BFM
LOC286437
FAM133A
TMSB15B
BEX5
TCEAL5
LOC340544
VSIG1
SATL1
DCAF12L2
ZCCHC16
LHFPL1
SOWAHD
ARL13A
MCART6
DKFZp686D0853
XKRX
GLRA4
LOC442459
MIR448
CT47B1
LOC643486
ZCCHC18
CT47A7
SNORA35
SNORD96B
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
NXF2B
H2BFXP
MIR766
LOC100129520
CXorf64
ARMCX4
UBE2DNL
LOC100287765
MIR1912
MIR1298
MIR1256
MIR1277
MIR1911
MIR1264
SLC25A5-AS1
MIR764
LOC100329135
MIR4328
MIR4329
CT47A12
ARMCX5-GPRASP2
RPL36A-HNRNPH2
MIR3978

Genes in Wide Peak

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

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

Genes
CDKN2C
EPS15
JAK1
JUN
LCK
MPL
MUTYH
MYCL1
NRAS
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
BCL10
THRAP3
TRIM33
PRDM16
RBM15
MDS2
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ABCA4
ACADM
ADORA3
AGL
AK2
AK4
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
CDK11B
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
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GBP1
GBP2
GBP3
GFI1
GJA4
GJB3
GJB5
GCLM
GNAI3
GNAT2
GNB1
GNG5
SFN
GPR3
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
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
ORC1
OVGP1
PAFAH2
PRDX1
PDE4B
PEX10
PEX14
PGD
PGM1
PIK3CD
PIN1P1
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKAA2
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
SRSF4
ST3GAL3
STIL
SKI
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SLC16A1
SRM
STXBP3
SYCP1
TAF12
TAF13
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
BCAR3
SNHG3
NR0B2
RAD54L
TTF2
PIK3R3
MMP23B
MMP23A
KCNAB2
LMO4
FCN3
CDC14A
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
FPGT
PER3
FUBP1
EIF2B3
ARTN
MAP3K6
DIRAS3
SLC16A4
KCNQ4
ZMYM4
ZMYM6
DHRS3
SRSF11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
C1orf38
TMEM59
H6PD
CLCA3P
CLCA2
ISG15
PLCH2
HS2ST1
IPO13
SDC3
KDM4A
CROCC
PUM1
CEP104
RIMS3
KIAA0494
DNAJC6
LRIG2
LPPR4
KLHL21
SLC35E2
ZBTB40
MFN2
INSL5
PIGK
PTPRU
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
BCAS2
AKR1A1
CEPT1
TESK2
PPIE
VAV3
MAD2L2
PPIH
CAP1
LRRC41
HBXIP
IFI44
PDPN
KHDRBS1
GMEB1
AP4B1
NUDC
PHTF1
MASP2
AHCYL1
SRSF10
UTS2
SF3A3
IFI44L
EBNA1BP2
KIF2C
RER1
DNAJB4
RCAN3
FAF1
GLMN
HHLA3
MST1P2
DDX20
MST1P9
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
KAZN
CAMTA1
LPHN2
KIAA1107
ZCCHC11
SZT2
DNAJC16
UBR4
USP24
ATP13A2
ITGB3BP
TARDBP
CELA3B
SLC35A3
ICMT
MACF1
LRRC8B
LPAR3
PADI4
DDAH1
TMEM50A
KPNA6
SSBP3
STX12
CLIC4
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
C1orf144
LDLRAP1
SERBP1
NOC2L
PTPN22
FBXO2
FBXO6
PLA2G2D
AK5
MYCBP
HEYL
EIF2C1
OR4F3
SNORA66
SNORD45B
SNORD45A
SNORD55
RNU11
RNF11
FOXD3
TRAPPC3
HSPB7
CHIA
ARHGEF16
AHDC1
TEKT2
SMPDL3B
ANGPTL3
PRO0611
LINC00339
SSU72
GNL2
GPSM2
UBIAD1
ALG6
PADI1
SLC25A24
PLA2G2E
DNTTIP2
WRAP73
SLC45A1
HP1BP3
TMED5
CELA2B
ZNF593
ZNF691
TXNDC12
TNNI3K
SH3GLB1
MECR
UTP11L
SDF4
MRTO4
TMEM69
MRPL37
HOOK1
SNX7
HPCAL4
YTHDF2
ZCCHC17
DPH5
HSPB11
PADI3
CMPK1
GPR88
ERRFI1
WNT4
YIPF1
FBXO42
CCDC76
RNF186
SPATA6
MXRA8
L1TD1
HES2
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
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
LRIF1
CTTNBP2NL
RCC2
FAM212B
DMAP1
AJAP1
GNG12
TMEM234
FAM54B
CCBL2
TMEM167B
OLFML3
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
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
LEPRE1
PLA2G2F
HIAT1
SMAP2
ATPAF1
S100PBP
MEAF6
DEM1
CEP85
NMNAT1
ELOVL1
VWA1
DCLRE1B
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZNF643
SELRC1
PHACTR4
C1orf135
ERI3
C1orf50
WDR77
CCDC28B
EFHD2
MMEL1
RSG1
DLEU2L
OR4F5
NKAIN1
EPS8L3
MUL1
TMEM53
AKIRIN1
HECTD3
BEND5
YRDC
ZYG11B
NOL9
PPCS
LIN28A
SH3D21
TTLL7
SNIP1
AGMAT
WDR78
ZMYM1
LINC00115
RPAP2
MORN1
FAM110D
KIAA0319L
DHDDS
DENND2D
WLS
GPR157
RPF1
SIKE1
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
ANKRD13C
TSSK3
CCNL2
VANGL1
ST6GALNAC5
HYI
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
GPR61
STK40
TM2D1
TMEM222
PLEKHN1
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
SLC25A33
DDI2
LZIC
PROK1
EFCAB7
NT5C1A
TRIM63
PSRC1
FAM167B
MGC12982
C1orf170
CROCCP2
HPDL
ATP1A1OS
AGBL4
MFSD2A
ATG4C
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
FAM40A
DOCK7
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
BTF3L4
UBXN11
NEXN
C1orf158
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
MED8
KTI12
C1orf212
ADC
TMEM54
HENMT1
TOE1
ERMAP
CSMD2
MYSM1
CROCCP3
FHAD1
OSBPL9
LOC115110
OMA1
RAB42
LRRC42
GBP4
GBP5
FAM46B
RBP7
ACAP3
SSX2IP
UBE2J2
OLFM3
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
WDR63
MAB21L3
IFFO2
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
TCEANC2
PODN
LRRC39
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
KLF17
TMEM125
ARHGEF19
DRAM2
C1orf88
C1orf162
ACTRT2
MIB2
SYT6
C1orf127
SAMD11
LOC148413
SAMD13
C1orf52
PHF13
TMEM56
NBPF4
UBE2U
SLC30A7
CCDC27
C1orf213
KNCN
MOB3C
GLIS1
MGC27382
DCDC2B
ZNF362
LOC149086
MANEAL
IL23R
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
C1orf64
RP11-165H20.1
SLC2A7
DENND2C
GBP6
LPPR5
FNDC7
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
KANK4
SASS6
FAM43B
HFM1
PAQR7
UBL4B
EIF2C3
EIF2C4
ALG14
FAM76A
LINC00466
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
TXLNA
TCTEX1D1
SLFNL1
C1orf126
HIPK1
SLC44A5
ATAD3C
AKR7L
AKR7A2P1
FNDC5
EPHX4
LOC254099
TTLL10
AKNAD1
TMCO4
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
ZNF683
NEGR1
CYP4X1
MAGI3
NPHP4
BEST4
FAM19A3
CYP4A22
C1orf185
LOC284551
FAM41C
FAM102B
SYPL2
CYB561D1
LOC284632
RSPO1
EPHA10
LOC284661
ZNF326
BTBD8
RIMKLA
SLC25A34
ESPNP
PPM1J
FAM151A
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
LOC339524
C1orf228
ZNF642
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
CCDC18
MYBPHL
BARHL2
HSP90B3P
TCTEX1D4
SERINC2
FAM159A
FAM131C
PADI6
BMP8A
C1orf187
SPATA21
CCDC23
ATPAF1-AS1
HEATR8
FAM73A
AGRN
APITD1
CATSPER4
NSUN4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LOC388630
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
UOX
FRRS1
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
GBP1P1
FLJ27354
MIR137HG
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR101-1
MIR137
MIR186
MIR197
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
LHX8
C1orf180
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
FLJ32224
FAM183A
ZYG11A
FLJ31662
LOC440600
BCL2L15
ANKRD65
PRAMEF7
PGCP1
GEMIN8P4
RBMXL1
LURAP1
PEF1
MIR429
CYB5RL
FAM138F
SRG7
CYMP
KIAA0754
LOC643441
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC646626
LOC648740
LOC649330
ZBTB8A
NBPF6
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA2
SCARNA1
SNORA44
SNORA55
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD45C
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR548D1
MIR551A
MIR553
ZBTB8B
LOC728431
PPIEL
CCDC30
CDK11A
SLC35E2B
LOC728716
RPS15AP10
LOC729041
LOC729059
HSD52
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC729970
LOC729987
MIR942
MIR760
LOC100128071
LOC100128787
LOC100129046
LOC100129138
LOC100129196
LOC100129269
LOC100129534
LOC100129620
LOC100129924
LOC100130197
LOC100130417
LOC100130557
LOC100131060
LOC100131564
LOC100132062
LOC100132287
ZRANB2-AS1
LOC100132774
LOC100133331
LOC100133445
LOC100133612
DDX11L1
LOC100287722
TTC34
LOC100288069
LOC100289178
MIR320B1
MIR1976
MIR1262
MIR761
NPPA-AS1
MIR3115
MIR3117
MIR4255
MIR4253
MIR4251
MIR4252
MIR4256
MIR4254
MIR3659
MIR3917
MIR3605
MIR3671
MIR548AA1
MIR3675
LOC100505768
ENO1-AS1
ZMYM6NB
LOC100506343
LOC100506730
LOC100506801
LOC100506963
LOC100507178
LOC100507423
LOC100507564
LOC100507634
APITD1-CORT
FPGT-TNNI3K
GJA9-MYCBP
HEATR8-TTC4
TMEM56-RWDD3
C1orf151-NBL1
MIR4695
MIR4420
MIR4422
MIR4781
MIR4794
MIR4684
MIR4711
MIR4689
MIR4632
MIR2682
MIR4423
MIR4417
MIR378F
RCAN3AS
NEGR1-IT1
ZRANB2-AS2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
COL15A1
TGFBR1
GABBR2
GALNT12
ANKS6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

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

Genes in Wide Peak

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

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

Genes
JAK2
MLLT3
NFIB
CD274
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
PLIN2
DMRT1
FOXD4
MLANA
GLDC
INSL4
PTPRD
RFX3
RLN1
RLN2
RPS6
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TYRP1
VLDLR
MPDZ
CER1
KIAA0020
RCL1
DMRT2
RRAGA
PSIP1
INSL6
KDM4C
KANK1
SLC24A2
RANBP6
AK3
BNC2
HAUS6
CNTLN
KIAA1797
C9orf68
CDC37L1
DENND4C
C9orf46
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
C9orf66
TTC39B
FAM154A
FREM1
KIAA2026
KCNV2
GLIS3
C9orf93
LURAP1L
ZDHHC21
ACER2
LOC389705
FLJ35024
FLJ41200
PPAPDC2
MIR101-2
MIR491
FAM138C
SCARNA8
C9orf146
WASH1
MIR3152
MIR4473
MIR4665
MIR4474

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
CTNNB1
FHIT
MITF
MLH1
MYD88
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
SNORA62
ROBO1
ROBO2
RPL29
ATXN7
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
TKT
TMF1
CLEC3B
TNNC1
UBA7
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
EOMES
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SLC4A7
VPRBP
IP6K1
EPM2AIP1
PSMD6
TRANK1
DLEC1
EXOG
XYLB
OXSR1
PDCD6IP
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
CRTAP
ARL6IP5
NPRL2
CXCR6
CSPG5
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
GNL3
RBMS3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
VILL
ABHD5
DYNC1LI1
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
KIF9
AZI2
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
LRRC3B
GPR62
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
SNORA6
TMPPE
LOC644714
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
LOC100128640
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4444-1
MIR4443
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q31.21.

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

Genes
IL2
RAP1GDS1
DUX4
TET2
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AGA
ANK2
SLC25A4
ANXA2P1
ANXA5
ATOH1
BMPR1B
CAMK2D
CASP3
CASP6
CCNA2
LRBA
CLGN
CENPE
CLCN3
CPE
CTSO
DCTD
EDNRA
EGF
EIF4E
ELF2
ENPEP
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGG
FRG1
GAB1
GK3P
GLRB
GPM6A
GRIA2
GRID2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HMGB2
HPGD
HSP90AA4P
CFI
IL15
ING2
IRF2
KLKB1
MAD2L1
SMAD1
MANBA
MGST2
NR3C2
MTNR1A
MTTP
NDUFC1
NEK1
NFKB1
NPY1R
NPY2R
NPY5R
PDHA2
PET112
PITX2
PLRG1
EXOSC9
POU4F2
PPID
PPP3CA
ABCE1
RPL34
RPS3A
MSMO1
SFRP2
TACR3
TDO2
TLL1
TLR2
TLR3
TRPC3
UBE2D3
UCP1
UGT8
VEGFC
GLRA3
SMARCA5
SORBS2
PRSS12
UNC5C
LAMTOR3
PDE5A
SAP30
INPP4B
SNORD73A
PAPSS1
LRAT
AIMP1
NDST3
HAND2
RAPGEF2
MFAP3L
SEC24D
TSPAN5
SPRY1
ANAPC10
PGRMC2
SEC24B
MAB21L2
PDLIM5
RRH
PLK4
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
MMRN1
PALLD
TBC1D9
METAP1
KIAA0922
TRIM2
ANP32C
SLC7A11
CCRN4L
FAM149A
FBXO8
DUX2
PPA2
DAPP1
DKK2
INTU
ARFIP1
PDLIM3
HPGDS
ZNF330
SPOCK3
AADAT
LEF1
FAM198B
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
CLDN22
GAR1
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
C4orf27
CCDC109B
MARCH1
BANK1
LARP1B
BBS7
NEIL3
TMEM144
C4orf43
UFSP2
C4orf21
AP1AR
MAML3
DDX60
CDKN2AIP
ODZ3
TMEM184C
LRP2BP
PDGFC
FSTL5
BDH2
SMARCAD1
STOX2
INTS12
ANKRD50
RNF150
PCDH10
KIAA1430
FNIP2
SH3RF1
METTL14
OSTC
IL21
RXFP1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
HHIP
NDST4
AGXT2L1
ELOVL6
NDNF
FAT4
ARSJ
ARHGAP10
MLF1IP
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
DNAJB14
WWC2
NAA15
C4orf29
ALPK1
CXXC4
CEP44
SETD7
PLA2G12A
SLC25A31
RAB33B
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
KIAA1109
COL25A1
USP38
C4orf49
CBR4
FHDC1
FLJ20021
MGC45800
PRMT10
DDX60L
NAF1
TIFA
RG9MTD2
TBCK
CYP2U1
DDIT4L
WDR17
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
C4orf32
SPATA4
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
C4orf38
C4orf39
C4orf45
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
RBM46
SGMS2
SYNPO2
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
LOC285419
CYP4V2
LOC285441
LOC285456
LOC285501
RNF175
C4orf37
LOC339975
TRIML1
LOC340017
PRSS48
LRIT3
ANKRD37
PCNAP1
LOC389247
TRIM61
HELT
FAM190A
FLJ14186
C4orf3
LOC401164
FAM92A3
MIR302A
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC641364
LOC641365
LOC641518
SLED1
CEP170P1
LOC645513
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
SNORA24
MIR577
MIR578
LINC00290
LOC728175
DUX4L2
CETN4P
FAM160A1
LOC731424
SNHG8
LOC100129858
CLDN24
PP12613
LOC100288255
MIR1243
MIR2054
MIR1305
MIR1973
MIR3140
MIR4276
MIR3945
MIR3684
MIR3688-1
LOC100505545
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4453
MIR4799
MIR3688-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.31.

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

Genes
AKT1
KTN1
NKX2-1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
NIN
CCNB1IP1
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
SERPINA3
ACTN1
ACYP1
ANG
APEX1
ARF6
ARG2
ARHGAP5
BCL2L2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
ENTPD5
CDKN3
CEBPE
CFL2
FOXN3
CHGA
CKB
CMA1
LTB4R
CRIP1
CRIP2
CTSG
DAD1
COCH
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FKBP3
FOXG1
FNTB
FOS
FUT8
GALC
GCH1
GMFB
GPR33
GPX2
GSTZ1
GTF2A1
BRF1
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
MGAT2
CTAGE5
ATXN3
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NDUFB1
NEDD8
NFATC4
NFKBIA
NOVA1
PNP
NRL
SIX6
OTX2
OXA1L
PAX9
SERPINA5
PCK2
PGF
SERPINA1
SERPINA4
PIGH
PNN
POLE2
PPM1A
PPP2R5C
PPP2R5E
PRKCH
PRKD1
LGMN
PSEN1
PSMA3
PSMA6
PSMB5
PSMC1
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
MOK
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPL36AL
RPS29
RTN1
SALL2
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGFB3
TGM1
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
PABPN1
DPF3
GPR68
GPR65
GEMIN2
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
CDKL1
DCAF5
ALKBH1
EIF2B2
AP1G2
SLC7A7
MTA1
NEMF
PNMA1
RPS6KA5
CPNE6
NRXN3
AKAP6
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
KIAA0125
KIAA0317
TOX4
TECPR2
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
FBLN5
BATF
TM9SF1
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
EDDM3A
DHRS4
PAPOLA
ACOT2
TMED10
FERMT2
RIPK3
PTPN21
AP4S1
C14orf1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
VASH1
ATG14
ZBTB1
SNW1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
RCOR1
SYNE2
PACS2
SCFD1
KHNYN
ANGEL1
PPP1R13B
SLC7A8
ZFYVE26
TTC9
KLHDC2
FLRT2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
NKX2-8
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
PRO1768
CHMP4A
STXBP6
GPR132
POMT2
STRN3
SLC39A2
ERO1L
COQ6
FAM158A
ATL1
FCF1
RDH11
SERPINA10
GLRX5
ZNF219
COX16
GMPR2
SLC22A17
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
MBIP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
GNG2
KLHL28
C14orf101
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
CDCA4
C14orf102
RNF31
ATG2B
RBM23
UBR7
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SYNJ2BP
SLC39A9
MEG3
C14orf167
G2E3
FLVCR2
OSGEP
C14orf118
SMEK1
ARHGEF40
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
EAPP
ACTR10
YLPM1
METTL3
LTB4R2
KCNK13
C14orf162
SDR39U1
C14orf132
DDX24
RPGRIP1
ADCK1
TMEM63C
PELI2
RHOJ
NDRG2
GALNTL1
PLEKHH1
NYNRIN
TXNDC16
TRMT5
UNC79
HOMEZ
BEGAIN
CHD8
FANCM
PPP4R4
ZNF410
NGB
RBM25
SNX6
SAV1
C14orf93
ABHD4
C14orf133
NPAS3
SMOC1
MOAP1
DIO3OS
EDDM3B
IRF2BPL
MPP5
CDH24
INF2
C14orf135
GPR135
METTL17
IL25
GNPNAT1
OTUB2
ZFYVE21
MEG8
THTPA
OR4K5
OR11H2
WDR25
OR4K1
METTL21D
LINC00341
ZC2HC1C
C14orf169
IPO4
CLMN
CATSPERB
ZC3H14
RIN3
L2HGDH
C14orf159
C14orf45
NUBPL
DCAF11
TMEM121
DDHD1
OR4K15
SGPP1
TMX1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
FSCB
SETD3
BRMS1L
APOPT1
HHIPL1
JPH4
C14orf142
RNASE7
INSM2
ARHGAP5-AS1
RAB2B
AJUBA
STON2
ZFHX2
KIAA1737
RPPH1
SLC25A21
PAPLN
FAM181A
BTBD6
EFCAB11
LRRC16B
PPP1R3E
TMEM55B
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
TTC5
MAPK1IP1L
EGLN3
C14orf126
IFT43
WDR89
C14orf149
AHNAK2
TRIM9
TRMT61A
DHRS1
CMTM5
MIA2
TDRD9
ANKRD9
AK7
IFI27L1
C14orf28
TRAPPC6B
C14orf79
PLD4
ADSSL1
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
KLHL33
RPL10L
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
MIPOL1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
MDP1
TTC7B
LRFN5
FAM71D
TMEM229B
C14orf49
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
SAMD15
C14orf21
EML5
SPTSSA
MGC23270
ADCY4
C14orf183
RALGAPA1
SFTA3
FBXO33
NUDT14
LINC00521
SERPINA11
IGBP1P1
LOC283547
C14orf182
LOC283553
GPR137C
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
LOC283624
TSSK4
FAM177A1
KIAA0284
C14orf80
DHRS4L2
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD8
SNORD56B
SERPINA9
LINC00226
LINC00221
RNASE10
VSX2
OR6S1
SLC35F4
COX8C
ASPG
RAB15
FLJ31306
TBPL2
C14orf23
TOMM20L
SERPINA13
C14orf64
RTL1
TMEM179
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
POTEG
MIR127
MIR134
MIR136
MIR154
MIR203
MIR208A
MIR299
C14orf165
OR11H12
RNASE13
LINC00238
CCDC88C
OR4Q3
OR4M1
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
RNASE12
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
POTEM
LOC642426
ECRP
C14orf176
CBLN3
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
SNORD9
MIR411
MIR624
MIR654
MIR655
MIR656
DHRS4L1
C14orf38
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORD127
SNORD126
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR208B
MIR889
ZBTB42
KTN1-AS1
LOC100129345
LOC100129794
LOC100131366
LOC100288846
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR4309
MIR3173
MIR4308
MIR4307
MIR548Y
LOC100505967
LOC100506071
LOC100506321
LOC100506433
LOC100507043
NEDD8-MDP1
BCL2L2-PABPN1
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4503
MIR4710
MIR548AI
MIR4707
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.2.

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

Genes
BCL6
FOXL2
CBLB
CTNNB1
EIF4A2
ETV5
FANCD2
FHIT
GATA2
LPP
MITF
MLF1
MLH1
MYD88
PIK3CA
PPARG
RAF1
RPN1
SOX2
TFRC
VHL
XPC
BAP1
GMPS
SRGAP3
TFG
FOXP1
SETD2
PBRM1
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
AADAC
ACAA1
ACPP
ACTL6A
ACVR2B
ACY1
ADCY5
ADPRH
AGTR1
AHSG
ALAS1
ALCAM
AMT
APEH
APOD
ARF4
RHOA
ATP1B3
ATP2B2
ATP6V1A
ATR
BCHE
BDH1
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CASR
CAV3
CCK
CD80
CD86
ENTPD3
CD47
CDC25A
CISH
AP2M1
CLCN2
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CP
CPA3
CPB1
CPN2
CPOX
CRYGS
CSTA
CX3CR1
CYP8B1
DAG1
DGKG
DAZL
DLG1
DNASE1L3
DOCK3
DRD3
DUSP7
DVL3
ECT2
CELSR3
EHHADH
EIF4G1
EPHA3
EPHB1
EPHB3
MECOM
FBLN2
FGF12
FLNB
GAP43
GBE1
GHSR
GLB1
GNAI2
GNAT1
GOLGA4
GOLGB1
GP5
GP9
XCR1
GPR15
GPR27
GPX1
GRM2
GRM7
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRH1
HRG
HES1
HTR1F
HYAL1
IL1RAP
IL5RA
IL12A
IMPDH2
IRAK2
ITGA9
ITGB5
ITIH1
ITIH3
ITIH4
ITPR1
KNG1
KPNA1
KPNA4
LAMB2
RPSA
LSAMP
LTF
TM4SF1
MAP4
MBNL1
MCM2
MFI2
MME
MOBP
CD200
MST1
MST1R
MUC4
MYL3
MYLK
NCK1
NDUFB4
NDUFB5
NKTR
OGG1
OPA1
CLDN11
OXTR
P2RY1
PAK2
CNTN3
PCCB
PCYT1A
PDHB
PFKFB4
PFN2
SERPINI1
SERPINI2
PIK3CB
PLCD1
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
PLXNB1
POLR2H
POU1F1
PPP1R2
PPP2R3A
PRKAR2A
PRKCD
PRKCI
PROS1
MASP1
PSMD2
PTH1R
PTPRG
PTX3
QARS
RAB5A
RAP2B
RARB
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
SNORA62
ROBO1
ROBO2
RPL15
RPL24
RPL29
RPL32
RPL35A
RYK
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC6A1
SLC6A6
SLC6A11
SLC15A2
SLCO2A1
HLTF
SMARCC1
SSR3
SST
STAC
NEK4
SYN2
TCTA
TDGF1
TERC
TF
TFDP2
TGM4
TGFBR2
THPO
THRB
TIMP4
TKT
SEC62
TM4SF4
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
TRH
TRPC1
UBA7
UBE2E1
UBE2E2
UBP1
UPK1B
UMPS
USP4
UQCRC1
CLRN1
VIPR1
WNT5A
WNT7A
ZIC1
CNBP
ZNF35
ZNF80
ZNF148
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
RAB7A
KCNAB1
FXR1
COLQ
ACOX2
EOMES
HYAL3
SOX14
BFSP2
CAMK1
CGGBP1
BHLHE40
RUVBL1
CADPS
TP63
CHRD
HYAL2
B4GALT4
B3GALNT1
SNX4
TNFSF10
SUCLG2
HESX1
KAT2B
NR1I2
EIF2B5
BSN
MBD4
H1FX
USP13
LIMD1
KALRN
CCRL2
UBA3
RPL14
CLDN1
SEC22C
RRP9
MAP3K13
SLC33A1
LRRFIP2
MAGI1
CACNA2D2
COPB2
ADIPOQ
SLC22A14
SLC22A13
CHST2
SH3BP5
SLC4A7
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
VGLL4
EDEM1
KIAA0226
ECE2
VPRBP
TBC1D5
TATDN2
IP6K1
TSC22D2
EPM2AIP1
PSMD6
TOMM70A
TRANK1
IQSEC1
P2RY14
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
SMC4
ABCC5
COX17
ARPC4
ZNF197
RBM6
RBM5
TNK2
ALG3
NME6
CTDSPL
CD96
KCNMB2
STAG1
EIF1B
TRAIP
ST3GAL6
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
IGF2BP2
CXCR6
CSPG5
CLDN16
POLQ
CHL1
ARPP21
CCR9
ALDH1L1
USP19
PDIA5
SLC38A3
CYB561D2
TMEM115
TOPBP1
RPP14
HHLA2
FSTL1
FAM107A
WDR6
RASSF1
NISCH
MRPL3
PDCD10
FILIP1L
TREX1
SCN11A
TUSC2
RNF13
MGLL
TWF2
MRAS
COPG
SLITRK3
NLGN1
TRAK1
DHX30
SACM1L
NCBP2
SCAP
LAMB2P1
MYH15
PLCH1
EXOSC7
TMCC1
PDZRN3
TNIK
CAND2
MCF2L2
CLASP2
PLXND1
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
ATP11B
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
DNAJC13
U2SURP
VPS8
LARS2
RYBP
C3orf27
CAPN7
ACAP2
MKRN2
NAT6
FBXL2
ANAPC13
ARMC8
ABHD14A
C3orf17
POC1A
ABI3BP
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
WWTR1
PVRL3
TIPARP
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
UBXN7
ERC2
APPL1
HACL1
ARHGEF26
ZBTB20
TTLL3
OR5K1
OR5H1
GNL3
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
ZBTB11
MORC1
SERP1
CNTN6
LSM3
RBMS3
GOLIM4
NKIRAS1
SPCS1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
PRSS50
RBM15B
GPR171
GMPPB
SEC61A1
LINC00312
SCHIP1
LMCD1
PIK3R4
PODXL2
ARHGEF3
TRAT1
VILL
IMPG2
C3orf32
NMD3
TRNT1
ABHD5
COMMD2
DYNC1LI1
A4GNT
C3orf18
DBR1
CRBN
SS18L2
ZNF639
CLDN18
C3orf19
SHISA5
TIMMDC1
ZDHHC3
RSRC1
ZMYND10
PLA1A
TEX264
CCDC72
ZNF589
HEMK1
AMOTL2
IP6K2
SFMBT1
NCKIPSD
PHF7
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
GHRL
P2RY13
IL20RB
GPR87
TLR9
DCUN1D1
SEMA5B
XRN1
WDR5B
LZTFL1
PARP14
P4HTM
SLC6A20
IL17RD
GRAMD1C
ROPN1
KLHL24
SIDT1
C3orf75
SNRK
QRICH1
PXK
CMTM6
RG9MTD1
SLC41A3
PIGX
SLC25A38
ULK4
OXSM
SLC35A5
TMEM45A
FEZF2
IFT57
EBLN2
ANO10
DALRD3
SHQ1
MSL2
TBCCD1
FAIM
SLC25A36
ARL8B
SETD5
DPPA4
LEPREL1
TMEM39A
ZNF654
TMEM40
ABCF3
LSG1
ABHD10
CHDH
PARL
IL17RB
CDV3
MFN1
YEATS2
IFT122
NGLY1
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
TMEM111
EAF2
BRK1
ZNF167
MYNN
LMOD3
EIF5A2
CLDND1
MUC13
SUCNR1
RAD18
SEMA3G
MCCC1
LXN
C3orf37
MRPS22
NIT2
POGLUT1
BBX
KIF15
ADAMTS9
CCNL1
PLSCR2
PCBP4
PLSCR4
PCNP
HRASLS
MRPL47
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
ISY1
HHATL
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
WDR48
LRRN1
KIAA1524
SLC7A14
SRPRB
SELK
SENP2
GNB4
BPESC1
PROK2
EEFSEC
RNF123
NSUN3
CIDEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZFYVE20
KIF9
NFKBIZ
AZI2
ZMAT3
MTMR14
ATG3
MRPS25
CSRNP1
GORASP1
MFSD1
CCDC14
FNDC3B
P2RY12
CDCP1
CCDC71
NT5DC2
SLC26A6
TMEM108
CRELD1
CAMKV
TMEM43
OR5H6
OR5H2
ZXDC
ZBED2
LRRC2
FYCO1
ATP13A3
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC51
TBL1XR1
ZBBX
ZNF385D
LRRC31
CCDC48
NEK11
UBA5
HDAC11
MAP6D1
PHC3
C3orf36
ARL14
THOC7
NAA50
PIGZ
CEP63
CEP70
ABTB1
WDR82
TMEM22
TSEN2
GRIP2
OR5AC2
RTP3
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
C3orf20
ID2B
ARL6
ZIC4
ATRIP
ACAD11
IQCG
ATP13A4
FYTTD1
NICN1
CHCHD6
MON1A
C3orf26
HPS3
ARPM1
JAGN1
KBTBD8
SLC12A8
GHRLOS2
RETNLB
CCDC54
MGC2889
IL17RC
ABHD14B
LRCH3
MINA
GPR128
C3orf39
DIRC2
CEP19
EAF1
DCLK3
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
UCN2
LOC90246
C3orf25
TMEM41A
ZNF502
BOC
FAM55C
RFT1
OXNAD1
SPSB4
ACPL2
ZBTB47
TMEM44
EGFEM1P
ACTR8
CAMK2N2
CMTM7
TXNRD3
OSBPL10
OSBPL11
SLC25A26
ZNF501
C3orf24
LRRC58
LRRC3B
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
GALNTL2
GPR62
CPNE4
CCDC58
KCNH8
DNAJC19
OTOL1
FAM3D
ZPLD1
LYZL4
KBTBD5
TRIM71
FAM131A
CD200R1
CHCHD4
ZDHHC19
DCBLD2
LRRC15
FAM43A
TPRA1
TMEM42
UROC1
FAM194A
NUDT16
COL6A6
GRK7
FAM172BP
TMEM207
METTL6
TAMM41
IL17RE
RTP1
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
RPL32P3
H1FOO
PISRT1
ASB14
TTC14
DTX3L
FAM19A4
SGOL1
PP2D1
EFHB
LOC151658
PPM1L
WDR49
LRRC34
CPNE9
DPPA2
CCDC80
BTLA
CCDC12
MB21D2
PPP4R2
XXYLT1
ROPN1B
LOC152024
C3orf22
C3orf55
ZCWPW2
CMC1
NEK10
C3orf79
CCDC50
PYDC2
SPICE1
CMTM8
NUDT16P1
CCDC13
LOC152217
LOC152225
FGD5
CIDECP
CNTN4
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
XIRP1
RNF168
CHST13
PRICKLE2
KBTBD12
DHX36
HTR3C
DZIP1L
TTC21A
ALG1L
C3orf67
KCTD6
LIPH
ARL13B
DHFRL1
HTR3D
RPL22L1
OSTalpha
FBXO45
KLHDC8B
MUC20
GABRR3
PTPLB
STT3B
LOC201617
DNAH12
PDE12
FAM116A
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
CADM2
LOC253573
ZNF620
NAALADL2
ZDHHC23
LOC255025
NUP210P1
TCTEX1D2
C3orf43
SDHAP1
COL6A5
GK5
PLCXD2
GCET2
UTS2D
ALS2CL
TMIE
LSAMP-AS3
SLC9A9
C3orf64
LOC285205
EPHA6
DNAJB8-AS1
FBXW12
C3orf38
HTR3E
ENTPD3-AS1
ZNF619
ZNF621
RABL3
IGSF10
C3orf33
LOC285326
CCDC66
SLC9A10
C3orf23
ZNF660
FLJ39534
LOC285359
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
C3orf70
TPRG1
LOC285401
ILDR1
TRIM59
TRIM42
EIF4E3
RAB43
CCDC39
CCDC36
KY
LOC339862
LOC339874
C3orf35
LOC339894
GADL1
PRSS42
LOC339926
LPP-AS2
H1FX-AS1
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
ZNF860
TMPRSS7
CD200R1L
PAQR9
COL6A4P1
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
LNP1
CCDC37
NPHP3-AS1
TPRXL
ANKRD18DP
NMNAT3
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
LRRC33
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
VENTXP7
LOC401052
IQCF3
LOC401074
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR15B
MIR16-2
MIR191
MIR198
MIR26A1
FAM19A1
STX19
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
ARGFX
SNORA6
SNORA7A
SNORD2
SNORA4
TMPPE
TMEM30C
LOC644714
ALG1L2
LOC644990
LOC645206
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
SPINK8
C3orf71
LOC646498
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
FLJ20518
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
SNORA81
SNORD19
FAM86DP
SNORD66
SNORD69
MIR548A2
MIR548A3
MIR551B
MIR563
MIR564
MIR567
MIR568
MIR569
MIR570
GXYLT2
SDHAP2
FAM157A
FAM198A
CCR2
FAM86HP
PRR23A
LOC730091
ESRG
LOC100009676
SNORD19B
LOC100125556
MIR922
MIR885
MIR944
EGOT
GHRLOS
LOC100128023
WWTR1-AS1
LOC100128164
C3orf74
LOC100128640
NRADDP
LOC100129480
LOC100129550
ZBTB20-AS1
LOC100131551
LOC100131635
ZNF717
LOC100132146
LOC100132526
BSN-AS2
SNAR-I
MIR1224
TIPARP-AS1
PRSS46
LOC100287879
LOC100288428
FRG2C
LOC100289361
MIR1284
MIR1248
MIR1280
MIR548I1
MIR1324
MIR1226
LOC100302640
MIR548H2
MIR711
MIR548G
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
LOC100498859
MIR3919
MIR3921
MIR3938
MIR3714
IQCJ-SCHIP1
FGD5-AS1
LOC100505687
LOC100505696
KRBOX1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
IQCF4
LOC100506994
LOC100507032
MFI2-AS1
LOC100507062
LOC100507086
ADAMTS9-AS2
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
NPHP3-ACAD11
ISY1-RAB43
TM4SF19-TCTEX1D2
MIR4793
MIR4787
MIR4795
MIR4796
MIR4797
MIR4788
MIR4791
MIR4790
MIR548AC
MIR4444-1
MIR4789
MIR4443
MIR4792
MIR4446
MIR4442
LOC100652759
LUST

Genes in Wide Peak

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

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

Genes
BCL6
FOXL2
CBLB
CTNNB1
EIF4A2
ETV5
FANCD2
FHIT
GATA2
LPP
MITF
MLF1
MLH1
MYD88
PIK3CA
PPARG
RAF1
RPN1
SOX2
TFRC
VHL
XPC
BAP1
GMPS
SRGAP3
TFG
FOXP1
SETD2
PBRM1
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
AADAC
ACAA1
ACPP
ACTL6A
ACVR2B
ACY1
ADCY5
ADPRH
AGTR1
AHSG
ALAS1
ALCAM
AMT
APEH
APOD
ARF4
RHOA
ATP1B3
ATP2B2
ATP6V1A
ATR
BCHE
BDH1
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CASR
CAV3
CCK
CD80
CD86
ENTPD3
CD47
CDC25A
CISH
AP2M1
CLCN2
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CP
CPA3
CPB1
CPN2
CPOX
CRYGS
CSTA
CX3CR1
CYP8B1
DAG1
DGKG
DAZL
DLG1
DNASE1L3
DOCK3
DRD3
DUSP7
DVL3
ECT2
CELSR3
EHHADH
EIF4G1
EPHA3
EPHB1
EPHB3
MECOM
FBLN2
FGF12
FLNB
GAP43
GBE1
GHSR
GLB1
GNAI2
GNAT1
GOLGA4
GOLGB1
GP5
GP9
XCR1
GPR15
GPR27
GPX1
GRM2
GRM7
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRH1
HRG
HES1
HTR1F
HYAL1
IL1RAP
IL5RA
IL12A
IMPDH2
IRAK2
ITGA9
ITGB5
ITIH1
ITIH3
ITIH4
ITPR1
KNG1
KPNA1
KPNA4
LAMB2
RPSA
LSAMP
LTF
TM4SF1
MAP4
MBNL1
MCM2
MFI2
MME
MOBP
CD200
MST1
MST1R
MUC4
MYL3
MYLK
NCK1
NDUFB4
NDUFB5
NKTR
OGG1
OPA1
CLDN11
OXTR
P2RY1
PAK2
CNTN3
PCCB
PCYT1A
PDHB
PFKFB4
PFN2
SERPINI1
SERPINI2
PIK3CB
PLCD1
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
PLXNB1
POLR2H
POU1F1
PPP1R2
PPP2R3A
PRKAR2A
PRKCD
PRKCI
PROS1
MASP1
PSMD2
PTH1R
PTPRG
PTX3
QARS
RAB5A
RAP2B
RARB
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
SNORA62
ROBO1
ROBO2
RPL15
RPL24
RPL29
RPL32
RPL35A
RYK
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC6A1
SLC6A6
SLC6A11
SLC15A2
SLCO2A1
HLTF
SMARCC1
SSR3
SST
STAC
NEK4
SYN2
TCTA
TDGF1
TERC
TF
TFDP2
TGM4
TGFBR2
THPO
THRB
TIMP4
TKT
SEC62
TM4SF4
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
TRH
TRPC1
UBA7
UBE2E1
UBE2E2
UBP1
UPK1B
UMPS
USP4
UQCRC1
CLRN1
VIPR1
WNT5A
WNT7A
ZIC1
CNBP
ZNF35
ZNF80
ZNF148
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
RAB7A
KCNAB1
FXR1
COLQ
ACOX2
EOMES
HYAL3
SOX14
BFSP2
CAMK1
CGGBP1
BHLHE40
RUVBL1
CADPS
TP63
CHRD
HYAL2
B4GALT4
B3GALNT1
SNX4
TNFSF10
SUCLG2
HESX1
KAT2B
NR1I2
EIF2B5
BSN
MBD4
H1FX
USP13
LIMD1
KALRN
CCRL2
UBA3
RPL14
CLDN1
SEC22C
RRP9
MAP3K13
SLC33A1
LRRFIP2
MAGI1
CACNA2D2
COPB2
ADIPOQ
SLC22A14
SLC22A13
CHST2
SH3BP5
SLC4A7
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
VGLL4
EDEM1
KIAA0226
ECE2
VPRBP
TBC1D5
TATDN2
IP6K1
TSC22D2
EPM2AIP1
PSMD6
TOMM70A
TRANK1
IQSEC1
P2RY14
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
SMC4
ABCC5
COX17
ARPC4
ZNF197
RBM6
RBM5
TNK2
ALG3
NME6
CTDSPL
CD96
KCNMB2
STAG1
EIF1B
TRAIP
ST3GAL6
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
IGF2BP2
CXCR6
CSPG5
CLDN16
POLQ
CHL1
ARPP21
CCR9
ALDH1L1
USP19
PDIA5
SLC38A3
CYB561D2
TMEM115
TOPBP1
RPP14
HHLA2
FSTL1
FAM107A
WDR6
RASSF1
NISCH
MRPL3
PDCD10
FILIP1L
TREX1
SCN11A
TUSC2
RNF13
MGLL
TWF2
MRAS
COPG
SLITRK3
NLGN1
TRAK1
DHX30
SACM1L
NCBP2
SCAP
LAMB2P1
MYH15
PLCH1
EXOSC7
TMCC1
PDZRN3
TNIK
CAND2
MCF2L2
CLASP2
PLXND1
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
ATP11B
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
DNAJC13
U2SURP
VPS8
LARS2
RYBP
C3orf27
CAPN7
ACAP2
MKRN2
NAT6
FBXL2
ANAPC13
ARMC8
ABHD14A
C3orf17
POC1A
ABI3BP
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
WWTR1
PVRL3
TIPARP
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
UBXN7
ERC2
APPL1
HACL1
ARHGEF26
ZBTB20
TTLL3
OR5K1
OR5H1
GNL3
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
ZBTB11
MORC1
SERP1
CNTN6
LSM3
RBMS3
GOLIM4
NKIRAS1
SPCS1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
PRSS50
RBM15B
GPR171
GMPPB
SEC61A1
LINC00312
SCHIP1
LMCD1
PIK3R4
PODXL2
ARHGEF3
TRAT1
VILL
IMPG2
C3orf32
NMD3
TRNT1
ABHD5
COMMD2
DYNC1LI1
A4GNT
C3orf18
DBR1
CRBN
SS18L2
ZNF639
CLDN18
C3orf19
SHISA5
TIMMDC1
ZDHHC3
RSRC1
ZMYND10
PLA1A
TEX264
CCDC72
ZNF589
HEMK1
AMOTL2
IP6K2
SFMBT1
NCKIPSD
PHF7
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
GHRL
P2RY13
IL20RB
GPR87
TLR9
DCUN1D1
SEMA5B
XRN1
WDR5B
LZTFL1
PARP14
P4HTM
SLC6A20
IL17RD
GRAMD1C
ROPN1
KLHL24
SIDT1
C3orf75
SNRK
QRICH1
PXK
CMTM6
RG9MTD1
SLC41A3
PIGX
SLC25A38
ULK4
OXSM
SLC35A5
TMEM45A
FEZF2
IFT57
EBLN2
ANO10
DALRD3
SHQ1
MSL2
TBCCD1
FAIM
SLC25A36
ARL8B
SETD5
DPPA4
LEPREL1
TMEM39A
ZNF654
TMEM40
ABCF3
LSG1
ABHD10
CHDH
PARL
IL17RB
CDV3
MFN1
YEATS2
IFT122
NGLY1
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
TMEM111
EAF2
BRK1
ZNF167
MYNN
LMOD3
EIF5A2
CLDND1
MUC13
SUCNR1
RAD18
SEMA3G
MCCC1
LXN
C3orf37
MRPS22
NIT2
POGLUT1
BBX
KIF15
ADAMTS9
CCNL1
PLSCR2
PCBP4
PLSCR4
PCNP
HRASLS
MRPL47
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
ISY1
HHATL
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
WDR48
LRRN1
KIAA1524
SLC7A14
SRPRB
SELK
SENP2
GNB4
BPESC1
PROK2
EEFSEC
RNF123
NSUN3
CIDEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZFYVE20
KIF9
NFKBIZ
AZI2
ZMAT3
MTMR14
ATG3
MRPS25
CSRNP1
GORASP1
MFSD1
CCDC14
FNDC3B
P2RY12
CDCP1
CCDC71
NT5DC2
SLC26A6
TMEM108
CRELD1
CAMKV
TMEM43
OR5H6
OR5H2
ZXDC
ZBED2
LRRC2
FYCO1
ATP13A3
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC51
TBL1XR1
ZBBX
ZNF385D
LRRC31
CCDC48
NEK11
UBA5
HDAC11
MAP6D1
PHC3
C3orf36
ARL14
THOC7
NAA50
PIGZ
CEP63
CEP70
ABTB1
WDR82
TMEM22
TSEN2
GRIP2
OR5AC2
RTP3
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
C3orf20
ID2B
ARL6
ZIC4
ATRIP
ACAD11
IQCG
ATP13A4
FYTTD1
NICN1
CHCHD6
MON1A
C3orf26
HPS3
ARPM1
JAGN1
KBTBD8
SLC12A8
GHRLOS2
RETNLB
CCDC54
MGC2889
IL17RC
ABHD14B
LRCH3
MINA
GPR128
C3orf39
DIRC2
CEP19
EAF1
DCLK3
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
UCN2
LOC90246
C3orf25
TMEM41A
ZNF502
BOC
FAM55C
RFT1
OXNAD1
SPSB4
ACPL2
ZBTB47
TMEM44
EGFEM1P
ACTR8
CAMK2N2
CMTM7
TXNRD3
OSBPL10
OSBPL11
SLC25A26
ZNF501
C3orf24
LRRC58
LRRC3B
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
GALNTL2
GPR62
CPNE4
CCDC58
KCNH8
DNAJC19
OTOL1
FAM3D
ZPLD1
LYZL4
KBTBD5
TRIM71
FAM131A
CD200R1
CHCHD4
ZDHHC19
DCBLD2
LRRC15
FAM43A
TPRA1
TMEM42
UROC1
FAM194A
NUDT16
COL6A6
GRK7
FAM172BP
TMEM207
METTL6
TAMM41
IL17RE
RTP1
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
RPL32P3
H1FOO
PISRT1
ASB14
TTC14
DTX3L
FAM19A4
SGOL1
PP2D1
EFHB
LOC151658
PPM1L
WDR49
LRRC34
CPNE9
DPPA2
CCDC80
BTLA
CCDC12
MB21D2
PPP4R2
XXYLT1
ROPN1B
LOC152024
C3orf22
C3orf55
ZCWPW2
CMC1
NEK10
C3orf79
CCDC50
PYDC2
SPICE1
CMTM8
NUDT16P1
CCDC13
LOC152217
LOC152225
FGD5
CIDECP
CNTN4
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
XIRP1
RNF168
CHST13
PRICKLE2
KBTBD12
DHX36
HTR3C
DZIP1L
TTC21A
ALG1L
C3orf67
KCTD6
LIPH
ARL13B
DHFRL1
HTR3D
RPL22L1
OSTalpha
FBXO45
KLHDC8B
MUC20
GABRR3
PTPLB
STT3B
LOC201617
DNAH12
PDE12
FAM116A
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
CADM2
LOC253573
ZNF620
NAALADL2
ZDHHC23
LOC255025
NUP210P1
TCTEX1D2
C3orf43
SDHAP1
COL6A5
GK5
PLCXD2
GCET2
UTS2D
ALS2CL
TMIE
LSAMP-AS3
SLC9A9
C3orf64
LOC285205
EPHA6
DNAJB8-AS1
FBXW12
C3orf38
HTR3E
ENTPD3-AS1
ZNF619
ZNF621
RABL3
IGSF10
C3orf33
LOC285326
CCDC66
SLC9A10
C3orf23
ZNF660
FLJ39534
LOC285359
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
C3orf70
TPRG1
LOC285401
ILDR1
TRIM59
TRIM42
EIF4E3
RAB43
CCDC39
CCDC36
KY
LOC339862
LOC339874
C3orf35
LOC339894
GADL1
PRSS42
LOC339926
LPP-AS2
H1FX-AS1
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
ZNF860
TMPRSS7
CD200R1L
PAQR9
COL6A4P1
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
LNP1
CCDC37
NPHP3-AS1
TPRXL
ANKRD18DP
NMNAT3
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
LRRC33
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
VENTXP7
LOC401052
IQCF3
LOC401074
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR15B
MIR16-2
MIR191
MIR198
MIR26A1
FAM19A1
STX19
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
ARGFX
SNORA6
SNORA7A
SNORD2
SNORA4
TMPPE
TMEM30C
LOC644714
ALG1L2
LOC644990
LOC645206
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
SPINK8
C3orf71
LOC646498
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
FLJ20518
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
SNORA81
SNORD19
FAM86DP
SNORD66
SNORD69
MIR548A2
MIR548A3
MIR551B
MIR563
MIR564
MIR567
MIR568
MIR569
MIR570
GXYLT2
SDHAP2
FAM157A
FAM198A
CCR2
FAM86HP
PRR23A
LOC730091
ESRG
LOC100009676
SNORD19B
LOC100125556
MIR922
MIR885
MIR944
EGOT
GHRLOS
LOC100128023
WWTR1-AS1
LOC100128164
C3orf74
LOC100128640
NRADDP
LOC100129480
LOC100129550
ZBTB20-AS1
LOC100131551
LOC100131635
ZNF717
LOC100132146
LOC100132526
BSN-AS2
SNAR-I
MIR1224
TIPARP-AS1
PRSS46
LOC100287879
LOC100288428
FRG2C
LOC100289361
MIR1284
MIR1248
MIR1280
MIR548I1
MIR1324
MIR1226
LOC100302640
MIR548H2
MIR711
MIR548G
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
LOC100498859
MIR3919
MIR3921
MIR3938
MIR3714
IQCJ-SCHIP1
FGD5-AS1
LOC100505687
LOC100505696
KRBOX1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
IQCF4
LOC100506994
LOC100507032
MFI2-AS1
LOC100507062
LOC100507086
ADAMTS9-AS2
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
NPHP3-ACAD11
ISY1-RAB43
TM4SF19-TCTEX1D2
MIR4793
MIR4787
MIR4795
MIR4796
MIR4797
MIR4788
MIR4791
MIR4790
MIR548AC
MIR4444-1
MIR4789
MIR4443
MIR4792
MIR4446
MIR4442
LOC100652759
LUST

Arm-level results

Table 3. Get Full Table Arm-level significance table - 19 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.25 | 1.4 | 0.295 | 0.11 | -1.76 | 1
1q | 1955 | 0.33 | 2.75 | 0.0149 | 0.13 | -1.41 | 1
2p | 924 | 0.32 | 0.276 | 0.978 | 0.18 | -2.19 | 1
2q | 1556 | 0.12 | -2.34 | 1 | 0.26 | 0.232 | 0.817
3p | 1062 | 0.42 | 2.26 | 0.0473 | 0.33 | 0.593 | 0.59
3q | 1139 | 0.49 | 4.11 | 0.000261 | 0.15 | -2.06 | 1
4p | 489 | 0.15 | -2.99 | 1 | 0.42 | 1.42 | 0.275
4q | 1049 | 0.08 | -3.48 | 1 | 0.40 | 2.17 | 0.067
5p | 270 | 0.39 | 0.419 | 0.9 | 0.40 | 0.582 | 0.59
5q | 1427 | 0.15 | -1.77 | 1 | 0.42 | 3.35 | 0.00374
6p | 1173 | 0.12 | -2.84 | 1 | 0.27 | -0.243 | 1
6q | 839 | 0.09 | -3.56 | 1 | 0.38 | 1.34 | 0.275
7p | 641 | 0.47 | 2.66 | 0.0173 | 0.06 | -3.91 | 1
7q | 1277 | 0.43 | 3.17 | 0.00546 | 0.13 | -2.22 | 1
8p | 580 | 0.30 | -0.583 | 1 | 0.54 | 3.65 | 0.00173
8q | 859 | 0.51 | 3.88 | 0.000518 | 0.13 | -2.58 | 1
9p | 422 | 0.33 | -0.384 | 1 | 0.56 | 3.71 | 0.00173
9q | 1113 | 0.27 | -0.239 | 1 | 0.44 | 2.78 | 0.0181
10p | 409 | 0.39 | 0.577 | 0.806 | 0.32 | -0.61 | 1
10q | 1268 | 0.13 | -2.42 | 1 | 0.33 | 1.21 | 0.326
11p | 862 | 0.11 | -3.03 | 1 | 0.48 | 3.31 | 0.00374
11q | 1515 | 0.12 | -2.15 | 1 | 0.38 | 2.69 | 0.0181
12p | 575 | 0.34 | -0.0164 | 1 | 0.15 | -3.09 | 1
12q | 1447 | 0.31 | 1.13 | 0.431 | 0.15 | -1.99 | 1
13q | 654 | 0.33 | -0.0464 | 1 | 0.30 | -0.581 | 1
14q | 1341 | 0.27 | 0.000331 | 1 | 0.32 | 1 | 0.397
15q | 1355 | 0.13 | -2.3 | 1 | 0.33 | 1.38 | 0.275
16p | 872 | 0.22 | -1.65 | 1 | 0.29 | -0.341 | 1
16q | 702 | 0.23 | -1.68 | 1 | 0.24 | -1.49 | 1
17p | 683 | 0.30 | -0.444 | 1 | 0.54 | 3.86 | 0.00173
17q | 1592 | 0.39 | 3.12 | 0.00546 | 0.18 | -1.1 | 1
18p | 143 | 0.35 | -0.448 | 1 | 0.44 | 1 | 0.397
18q | 446 | 0.24 | -1.55 | 1 | 0.50 | 2.69 | 0.0181
19p | 995 | 0.24 | -0.974 | 1 | 0.34 | 0.727 | 0.55
19q | 1709 | 0.38 | 3.1 | 0.00546 | 0.22 | -0.116 | 0.993
20p | 355 | 0.62 | 4.83 | 1.37e-05 | 0.19 | -2.16 | 1
20q | 753 | 0.65 | 6.28 | 6.68e-09 | 0.23 | -1.18 | 1
21q | 509 | 0.39 | 0.852 | 0.607 | 0.21 | -2.13 | 1
22q | 921 | 0.30 | -0.0942 | 1 | 0.38 | 1.37 | 0.275
Xq | 1312 | 0.22 | -0.822 | 1 | 0.27 | -0.0145 | 0.963

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BLCA/1668709/2.GDAC_MergeDataFiles.Finished/BLCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 86 Input Tumor Samples.

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

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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