Copy number analysis (GISTIC2)
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C15B00C0
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Kidney Renal Papillary Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C15B00C0
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 127 tumor samples used in this analysis: 16 significant arm-level results, 9 significant focal amplifications, and 25 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 - 9 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
--- | --- | --- | --- | ---
19p13.2 | 7.5946e-10 | 7.5946e-10 | chr19:7296453-7397014 | 0 [INSR]
2q32.1 | 0.23083 | 0.23083 | chr2:186297358-186918006 | 1
3p14.1 | 0.23083 | 0.23083 | chr3:68089010-68094828 | 1
3q26.31 | 0.23083 | 0.23083 | chr3:145785598-198022430 | 334
5q35.2 | 0.23083 | 0.23083 | chr5:150936362-180915260 | 236
6p12.3 | 0.23083 | 0.23083 | chr6:49565389-49615406 | 1
7q22.1 | 0.23083 | 0.23083 | chr7:101454617-103862258 | 33
17q25.2 | 0.23083 | 0.23083 | chr17:48641966-81195210 | 430
19q13.11 | 0.23083 | 0.23083 | chr19:33878199-36222036 | 52

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q32.1.

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

Genes
FSIP2

Genes in Wide Peak

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

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

Genes
FAM19A1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.31.

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

Genes
BCL6
EIF4A2
ETV5
LPP
MLF1
PIK3CA
SOX2
TFRC
GMPS
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
AADAC
ACTL6A
AGTR1
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
GYG1
HRG
HES1
IL1RAP
IL12A
KNG1
KPNA4
TM4SF1
MBNL1
MFI2
MME
MUC4
NDUFB5
OPA1
CLDN11
P2RY1
PAK2
PCYT1A
PFN2
SERPINI1
SERPINI2
PLD1
PLOD2
PLSCR1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
PTX3
RAP2B
RARRES1
RFC4
SNORA63
RPL35A
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
HLTF
SSR3
SST
TERC
THPO
SEC62
TM4SF4
CLRN1
ZIC1
KCNAB1
FXR1
TP63
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
SLC33A1
ADIPOQ
KIAA0226
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
RNF13
SLITRK3
NLGN1
NCBP2
PLCH1
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
WWTR1
TIPARP
UBXN7
ARHGEF26
GPR160
FETUB
LAMP3
KCNMB3
SERP1
GOLIM4
GPR171
SCHIP1
NMD3
COMMD2
ZNF639
RSRC1
PEX5L
SELT
DNAJB11
P2RY13
GPR87
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
SUCNR1
MCCC1
LXN
CCNL1
PLSCR2
PLSCR4
HRASLS
MRPL47
NCEH1
IFT80
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
MFSD1
FNDC3B
P2RY12
ATP13A3
VEPH1
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
PIGZ
SPATA16
EIF2A
B3GNT5
ZIC4
IQCG
ATP13A4
FYTTD1
HPS3
ARPM1
MGC2889
LRCH3
CEP19
GFM1
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
FAM194A
TMEM207
RTP1
TTC14
PPM1L
WDR49
LRRC34
MB21D2
XXYLT1
C3orf55
C3orf79
CCDC50
PYDC2
LOC152217
SPTSSB
RNF168
DHX36
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
LOC201651
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
IGSF10
C3orf33
C3orf70
TPRG1
TRIM59
CCDC39
LOC339894
LOC339926
LPP-AS2
LRRIQ4
SAMD7
AADACL2
GPR149
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
PLSCR5
ANKUB1
LEKR1
TMEM212
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
SNORD2
SNORA4
TMEM14E
LOC646168
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
IQCJ
SCARNA7
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
LOC730091
MIR922
MIR944
LOC100128023
WWTR1-AS1
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
TIPARP-AS1
MIR1248
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
ARHGEF26-AS1
LOC100507537
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

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

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

Genes
EBF1
ITK
NPM1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
ADRA1B
ATOX1
BNIP1
CANX
CCNG1
CLTB
NKX2-5
DBN1
DOCK2
DRD1
DUSP1
F12
FABP6
FAT2
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GLRA1
GRK6
GRIA1
GRM6
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
IL12B
KCNMB1
LCP2
LTC4S
MFAP3
MGAT1
MSX2
MAPK9
PROP1
RARS
SGCD
SLC34A1
SLIT3
SNCB
SPARC
STK10
ZNF354A
TTC1
STC2
ADAM19
FGF18
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
ADAMTS2
CLINT1
MAML1
GFPT2
G3BP1
GNB2L1
SLU7
RGS14
CPLX2
C5orf4
FAM114A2
BTNL3
LMAN2
SOX30
MGAT4B
B4GALT7
RNF44
TBC1D9B
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
ZNF346
GEMIN5
TSPAN17
OR4F3
HAVCR1
CYFIP2
PRELID1
MAT2B
MRPL22
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
CCDC99
THG1L
GALNT10
NHP2
RNF130
NMUR2
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
C5orf54
GMCL1P1
RMND5B
CCNJL
PANK3
SAP30L
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
HAVCR2
AGXT2L2
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
UBTD2
SCGB3A1
SFXN1
GPRIN1
PWWP2A
C1QTNF2
ZNF354B
C5orf47
C5orf58
OR2Y1
LSM11
NUDCD2
UBLCP1
C5orf41
BTNL9
PPP1R2P3
FAM71B
RNF145
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
LOC285626
LOC285627
LOC285629
KIF4B
OR2V2
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
FBLL1
NIPAL4
C5orf25
FLJ38109
MIR103A1
MIR146A
MIR218-2
FNDC9
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
LOC728554
AACSP1
LOC729678
OR4F29
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3912
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

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

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

Genes
RHAG

Genes in Wide Peak

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

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

Genes
hsa-mir-548o
hsa-mir-4285
CUX1
ORC5
POLR2J
RELN
PSMC2
PMPCB
RASA4
LRRC17
SH2B2
DNAJC2
ALKBH4
PRKRIP1
ORAI2
ARMC10
LRWD1
FAM185A
FBXL13
NAPEPLD
POLR2J2
DPY19L2P2
SLC26A5
SPDYE2
POLR2J3
SPDYE6
RPL19P12
UPK3BL
LOC100289561
SPDYE2L
MIR4285
MIR4467
LOC100630923

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.2.

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

Genes
CD79B
CLTC
DDX5
HLF
PRKAR1A
ASPSCR1
BRIP1
MSI2
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NME1
NME2
NPTX1
P4HB
PDE6G
PECAM1
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
PPM1D
DGKE
CBX4
DNAH17
ABCC3
RGS9
GALR2
SPHK1
CACNA1G
SOCS3
SPAG9
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
TOB1
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
RAB40B
TLK2
POLG2
CD300A
TMC6
DDX42
PPM1E
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
UTP18
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
LUC7L3
SDK2
FAM20A
MBTD1
BCAS3
TMEM104
RNF43
MKS1
LINC00483
C17orf80
CCDC40
WIPI1
SMG8
TMEM100
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45L
CA10
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
DNAI2
SMURF2
ENGASE
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
KIF2B
USP32
CBX2
FAM104A
MGC16275
FBF1
UNK
CEP95
TRIM47
ANKRD40
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
WFIKKN2
TBC1D16
AFMID
DYNLL2
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
NOTUM
TMC8
ANKFN1
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MTVR2
STXBP4
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
LRRC37A3
RNF126P1
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
LOC400604
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
MIR142
MIR21
MIR301A
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LOC645638
TBC1D3P1-DHX40P1
LOC653653
NME1-NME2
LINC00338
SCARNA20
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR634
MIR635
MIR636
MIR657
LOC729683
PRCD
MIR454
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3614
MIR3678
MIR3615
LOC100506650
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4729
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515

Genes in Wide Peak

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

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

Genes
ATP4A
CD22
COX6B1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
MAG
PEPD
FXYD1
FXYD3
SCN1B
USF2
KIAA0355
MLL4
UBA2
TMEM147
UPK1A
HAUS5
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
ZNF302
GRAMD1A
HAMP
CHST8
KCTD15
RBM42
PDCD2L
ZNF30
DMKN
WTIP
ZNF792
ZNF599
FAM187B
LGI4
SCGB2B2
ZNF181
SBSN
KRTDAP
LOC400685
SCGB1B2P
LOC100128675
LOC100128682
SCGB2B3P
LOC100506469
LOC100652909

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 3.9073e-13 | 3.9073e-13 | chr9:21865498-22448737 | 4
1p36.31 | 0.00091293 | 0.00091293 | chr1:1-7832211 | 138
2q37.3 | 0.0062542 | 0.0062542 | chr2:232223718-243199373 | 141
3p22.1 | 0.0062542 | 0.0062542 | chr3:41280645-42218893 | 1
19q13.42 | 0.0062542 | 0.014378 | chr19:45825627-57684043 | 527
6q22.31 | 0.032252 | 0.032076 | chr6:123955968-125232805 | 1
11q22.3 | 0.032029 | 0.032076 | chr11:102916368-132208800 | 278
Xq28 | 0.041293 | 0.041293 | chrX:151843350-152761709 | 21
22q12.2 | 0.04784 | 0.047287 | chr22:22120154-32558809 | 160
19p13.3 | 0.049441 | 0.050574 | chr19:1033227-6135900 | 162
6p12.3 | 0.09044 | 0.09044 | chr6:44235214-63054935 | 88
14q11.2 | 0.027334 | 0.09044 | chr14:1-33303273 | 183
5q35.2 | 0.095823 | 0.12581 | chr5:174422375-177410415 | 51
6q26 | 0.12581 | 0.12581 | chr6:136573457-171115067 | 199
14q23.3 | 0.047287 | 0.12581 | chr14:58869576-81577655 | 189
5p15.2 | 0.13778 | 0.13966 | chr5:1-31329532 | 101
19q13.2 | 0.011894 | 0.13966 | chr19:41244888-57684043 | 671
Xq21.31 | 0.14485 | 0.14591 | chrX:91074436-92938656 | 2
14q32.2 | 0.04435 | 0.14962 | chr14:97027760-98099702 | 1
4q32.1 | 0.16724 | 0.16479 | chr4:123643386-191154276 | 255
15q12 | 0.16511 | 0.16479 | chr15:1-76562737 | 622
2p11.2 | 0.18034 | 0.18034 | chr2:43447767-119918675 | 498
10p15.3 | 0.17152 | 0.18034 | chr10:1-10842676 | 58
5q15 | 0.16379 | 0.18849 | chr5:92743026-160280696 | 476
12q24.33 | 0.19453 | 0.18849 | chr12:129468996-131078424 | 6

Genes in Wide Peak

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

Table S9. 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 1p36.31.

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

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
CDK11B
DFFB
DVL1
MEGF6
GABRD
GNB1
ZBTB48
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
RER1
ACOT7
CAMTA1
ICMT
CHD5
NOC2L
OR4F3
ARHGEF16
SSU72
WRAP73
SDF4
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
DNAJC11
AJAP1
TP73-AS1
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
OR4F5
NOL9
LINC00115
MORN1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
C1orf170
KIAA1751
THAP3
LOC115110
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
LOC148413
PHF13
CCDC27
CALML6
C1orf86
ATAD3C
LOC254099
TTLL10
NPHP4
FAM41C
LOC284661
C1orf174
KLHL17
TMEM240
TMEM52
AGRN
GPR153
FAM132A
HES5
LOC388588
RNF207
HES3
RNF223
MIR200A
MIR200B
FLJ42875
ANKRD65
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
FAM138A
WASH7P
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR4251
MIR4252
MIR4689
MIR4417

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
PPP1R7
PTMA
SNORD20
SAG
SPP2
DGKD
PER2
LRRFIP1
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
C2orf54
EFHD1
ILKAP
ING5
MGC16025
B3GNT7
AGAP1
TWIST2
DIS3L2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LINC00471
MSL3P1
C2orf57
TIGD1
LOC200772
CXXC11
DUSP28
ESPNL
ECEL1P2
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR4269
UBE2F-SCLY
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p22.1.

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

Genes
ULK4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.42.

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

Genes
ERCC2
KLK2
PPP2R1A
TFPT
ZNF331
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
DBP
DMPK
DMWD
EMP3
ERCC1
ETFB
FCAR
FCGRT
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
MYBPC2
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PEG3
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTGIR
PTPRH
RPL18
RPL28
RPS9
RPS11
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SPIB
SULT2B1
SULT2A1
SYT5
TNNI3
TNNT1
TULP2
NR1H2
VASP
ZNF28
ZNF137P
ZNF175
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
CYTH2
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
LILRB2
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
FBXO46
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
DHDH
UBE2S
SLC6A16
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF701
ZNF83
ZNF415
CABP5
SPHK2
MEIS3
SLC17A7
NAT14
RCN3
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
TSEN34
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
TBC1D17
ISOC2
MYH14
ZNF665
ZNF613
ZNF702P
ZNF614
FUZ
OPA3
RSPH6A
ZNF611
MED25
BCL2L12
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
CLDND2
ZNF816
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
PPM1N
KLC3
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
C19orf76
NLRP11
TMEM86B
PRR24
NAPSB
IL4I1
SSC5D
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
C19orf81
ZNF677
RFPL4A
ZSCAN5B
C19orf51
LILRA5
IGFL1
LOC386758
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF321P
SIGLEC16
FLJ26850
ZNF880
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC646508
SBK2
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100129083
SGK110
BSPH1
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SNAR-A14
ERVV-2
LOC100287177
MIR1283-2
MIR1323
MIR1283-1
MIR3191
MIR3190
MIR320E
MIR4324
MIR642B
LOC100505681
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
MIR4752
MIR371B
MIR4749
MIR4750
MIR4751

Genes in Wide Peak

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

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

Genes
NKAIN2

Genes in Wide Peak

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

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

Genes
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NCAM1
NFRKB
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
ZBTB44
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq28.

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

Genes
CETN2
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
ZNF185
ZNF275
TREX2
PNMA3
NSDHL
HAUS7
PNMA6A
PNMA5
ZFP92
CSAG1
MAGEA2B
CSAG3
CSAG2
PNMA6C
PNMA6D

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.2.

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

Genes
BCR
EWSR1
MN1
NF2
SMARCB1
CHEK2
hsa-mir-3200
hsa-mir-3199-2
hsa-mir-548j
hsa-mir-650
ADORA2A
ADRBK2
AP1B1
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
DDT
GGT1
GGT5
GNAZ
GSTT1
GSTT2
IGLL1
LIF
LIMK2
MIF
MMP11
DRG1
NEFH
OSM
MAPK1
RFPL1
SLC5A1
SMTN
SNRPD3
TCN2
TOP1P2
VPREB1
XBP1
YWHAH
ZNF70
TPST2
NIPSNAP1
THOC5
MTMR3
TOP3B
GAL3ST1
RAB36
PPM1F
DEPDC5
SFI1
SF3A1
RASL10A
GAS2L1
RFPL1-AS1
MORC2
TTC28
SPECC1L
PES1
CABIN1
PRAME
SEC14L2
SEZ6L
PATZ1
PITPNB
PISD
OSBP2
AP1B1P1
TFIP11
C22orf31
GSTTP1
C22orf24
RHBDD3
POM121L1P
FBXW4P1
INPP5J
RTDR1
POM121L9P
UQCR10
VPREB3
PLA2G3
C22orf43
MTFP1
UPB1
TUG1
ZMAT5
SUSD2
EIF4ENIF1
ASPHD2
SLC2A11
C22orf13
TBC1D10A
KREMEN1
ZNRF3
ASCC2
MYO18B
KIAA1656
KIAA1671
HPS4
GGTLC2
GUSBP11
DERL3
IGLL3P
LRP5L
RNF185
LOC96610
PIK3IP1
ZNF280A
SGSM1
EMID1
SELM
ZNF280B
ZDHHC8P1
C22orf15
HSCB
CCDC117
HORMAD2
DUSP18
MORC2-AS1
C22orf42
CABP7
RNF215
PRR14L
TMEM211
SEC14L3
RGL4
LOC284889
TTC28-AS1
SEC14L4
SLC35E4
SDC4P
FAM211B
LOC391322
CHCHD10
SRRD
PIWIL3
MIAT
CCDC157
BCRP3
C22orf45
POM121L10P
LOC648691
CES5AP1
GATSL3
GSTTP2
GSTT2B
MIR650
SEC14L6
DDTL
SNORD125
LOC100128531
MIR548J
MIR3200
MIR3199-2
MIR3199-1
IGLL5
MIR3653
MIR3928

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
STK11
TCF3
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
AES
AMH
ATP5D
CAPS
CIRBP
CSNK1G2
DAPK3
EEF2
EFNA2
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
MATK
GADD45B
NFIC
NRTN
OAZ1
POLR2E
MAP2K2
PTPRS
RFX2
RPS15
SAFB
SGTA
TBXA2R
THOP1
TLE2
SF3A2
RANBP3
S1PR4
AP3D1
LONP1
APBA3
SAFB2
CHAF1A
EBI3
PLIN3
APC2
ABCA7
HMG20B
SEMA6B
UQCR11
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
RPL36
TIMM13
DAZAP1
SNORD37
TJP3
ITGB1BP3
UHRF1
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
CCDC94
C19orf10
NCLN
SPPL2B
DUS3L
SHD
REXO1
ZNF77
C19orf29
CELF5
FSD1
TLE6
ZNF556
UBXN6
FAM108A1
DOHH
KLF16
DOT1L
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
MRPL54
LRG1
C19orf70
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
PLK5
TICAM1
CIRBP-AS1
ZNRF4
C19orf25
ATP8B3
DIRAS1
ZNF555
PRR22
ANKRD24
C19orf26
CSNK1G2-AS1
PLAC2
TMEM146
C19orf77
MIR7-3HG
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
ONECUT3
MEX3D
VMAC
C19orf29-AS1
MIR7-3
PLIN5
LINGO3
ARRDC5
MIR637
PLIN4
C19orf71
LOC100131094
LOC100288123
MIR1909
MIR1227
MIR4321
MIR4747
MIR4746

Genes in Wide Peak

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

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

Genes
hsa-mir-548u
hsa-mir-133b
hsa-mir-586
CRISP1
BMP5
DST
RUNX2
CDC5L
GCLC
GSTA1
GSTA2
GSTA3
GSTA4
HCRTR2
IL17A
MCM3
MEP1A
MUT
PGK2
PKHD1
PRIM2
RHAG
TFAP2B
CRISP2
PLA2G7
SUPT3H
GCM1
SLC25A27
BAG2
TRAM2
RCAN2
CRISP3
ICK
ENPP4
CD2AP
ZNF451
FBXO9
TNFRSF21
TINAG
TMEM14A
CYP39A1
RAB23
CLIC5
HMGCLL1
CENPQ
LRRC1
AARS2
KIAA1586
ENPP5
ELOVL5
COL21A1
TFAP2D
PAQR8
MLIP
IL17F
EFHC1
C6orf141
TCTE1
KHDRBS2
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
FAM83B
GPR111
DEFB110
DEFB112
DEFB113
DEFB114
GPR110
GUSBP4
GLYATL3
GFRAL
KLHL31
DEFB133
MIR206
TMEM151B
PTCHD4
MIR133B
RPS16P5
MIR586
LOC730101
GSTA7P
LOC100287718
MIR4642

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GPR33
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
PNP
NRL
OXA1L
PCK2
PRKD1
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
AKAP6
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
AP4S1
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
JPH4
RNASE7
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
C14orf126
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
C14orf21
ADCY4
LOC283624
TSSK4
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
CBLN3
SNORD9
MIR624
DHRS4L1
SNORD126
MIR208B
MIR4307
LOC100505967
LOC100506071
NEDD8-MDP1
BCL2L2-PABPN1
MIR548AI
MIR4707

Genes in Wide Peak

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

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

Genes
NSD1
hsa-mir-4281
hsa-mir-1271
CLTB
DBN1
DRD1
F12
FGFR4
GRK6
HK3
HRH2
SLC34A1
SNCB
PDLIM7
RGS14
CPLX2
LMAN2
B4GALT7
RNF44
FAF2
ZNF346
TSPAN17
PRELID1
DDX41
NOP16
UIMC1
RAB24
FAM193B
TMED9
CDHR2
KIAA1191
DOK3
PRR7
MXD3
THOC3
UNC5A
SFXN1
GPRIN1
HIGD2A
FAM153B
LOC202181
EIF4E1B
FAM153A
ARL10
LOC340037
PFN3
C5orf25
LOC643201
LOC728554
MIR4281
LOC100507387

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
MLLT4
TNFAIP3
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
ACAT2
CCR6
ESR1
FUCA2
GPR31
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
PEX7
PLAGL1
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
PEX3
RNASET2
STX11
SYNJ2
MAP7
LATS1
QKI
WTAP
AKAP12
PHACTR2
BCLAF1
UST
CITED2
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
HEBP2
CCDC28A
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
TFB1M
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
C6orf115
PBOV1
PERP
SMOC2
ULBP3
C6orf211
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
RSPH3
TTLL2
FBXO30
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
LINC00473
SYTL3
SFT2D1
C6orf72
IL22RA2
TAGAP
ADAT2
STXBP5
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
PNLDC1
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
WDR27
SHPRH
LOC285740
LOC285796
PRR18
SLC35D3
ZC3H12D
ECT2L
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FLJ46906
LOC441177
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LOC100132735
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3692
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
TSHR
GPHN
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
ACTN1
ACYP1
ARG2
ZFP36L1
ENTPD5
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GPX2
GSTZ1
HIF1A
HSPA2
LTBP2
MAX
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SIX6
PGF
PIGH
PPM1A
PPP2R5E
PRKCH
PSEN1
ABCD4
RAD51B
RTN1
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
ZBTB25
DPF3
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
NRXN3
AKAP5
SPTLC2
RGS6
KIAA0247
KIAA0586
KIAA0317
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
TIMM9
MLH3
KCNH5
POMT2
COQ6
FCF1
RDH11
COX16
DACT1
ATP6V1D
JKAMP
DHRS7
SIX4
ZFYVE1
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
YLPM1
C14orf162
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
TRMT5
ZNF410
NGB
RBM25
C14orf133
SMOC1
IRF2BPL
MPP5
C14orf135
GPR135
ZC2HC1C
C14orf169
C14orf45
SGPP1
SLIRP
DNAL1
RPS6KL1
SYT16
KIAA1737
PAPLN
CHURC1
C14orf43
LIN52
NEK9
IFT43
WDR89
C14orf149
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
RDH12
ADAM21P1
PPP1R36
SLC38A6
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
FAM71D
TMEM229B
TMEM30B
SAMD15
PROX2
ZDHHC22
TMED8
C14orf178
C14orf55
C14orf39
SNORD56B
VSX2
RAB15
HEATR4
FLJ22447
PLEKHD1
LINC00238
TEX21P
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
C14orf38
LOC731223
LOC100289511
MIR1260A
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p15.2.

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

Genes
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
CDH6
CDH9
CDH10
CDH12
CDH18
CTNND2
DAP
DNAH5
MTRR
MYO10
NDUFS6
PMCHL1
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
BASP1
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
PP7080
IRX4
TAS2R1
FAM134B
FAM105A
NSUN2
CEP72
ANKH
PRDM9
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285577
LOC285692
LOC285696
SLC6A19
LOC340094
LOC340107
SLC6A18
LRRC14B
FLJ33360
LOC401177
TAG
MARCH11
LOC442132
LOC643401
ANKRD33B
GUSBP1
SDHAP3
LOC728613
LOC729506
LOC729862
SNORD123
LOC100130744
MIR4277
MIR4278
LOC100505738
LOC100505806
LOC100506688
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
MEGF8
EMP3
ERCC1
ERF
ETFB
FCAR
FCGRT
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
LIPE
BCAM
MYBPC2
CEACAM6
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
RPS9
RPS11
RPS19
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
SULT2B1
SULT2A1
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZNF28
ZNF45
ZNF221
ZNF222
ZNF137P
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
ARHGEF1
CYTH2
ZNF235
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
LILRB2
TOMM40
RABAC1
ZNF234
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
CYP2G1P
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
DHDH
UBE2S
SLC6A16
CYP2S1
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
RAB4B
PPP1R12C
TRPM4
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
RCN3
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
ELSPBP1
LIN7B
HIF3A
ZNF574
ZNF649
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
TBC1D17
GEMIN7
ISOC2
MYH14
ZNF665
ZNF613
ZNF702P
ZNF614
FUZ
OPA3
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF526
CLDND2
ZNF816
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
IRGQ
ZNF428
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF296
DEDD2
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
CADM4
C19orf76
NLRP11
TMEM86B
PRR24
NAPSB
IL4I1
SSC5D
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
C19orf51
ZNF233
LILRA5
B3GNT8
IGFL1
LOC386758
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
LOC390940
ZNF321P
SIGLEC16
FLJ26850
ZNF880
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
LOC646508
SBK2
PSG10P
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100129083
SGK110
BSPH1
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
ERVV-2
LOC100287177
LOC100289650
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.31.

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

Genes
NAP1L3
PCDH11X

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.2.

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

Genes
VRK1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.1.

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
AGA
SLC25A4
ANXA2P1
CASP3
LRBA
CLGN
CLCN3
CPE
CTSO
DCTD
EDNRA
ELF2
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGF2
FGG
FRG1
GAB1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
HMGB2
HPGD
HSP90AA4P
IL15
ING2
IRF2
KLKB1
SMAD1
MGST2
NR3C2
MTNR1A
NDUFC1
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
POU4F2
PPID
ABCE1
RPS3A
MSMO1
SFRP2
TDO2
TLL1
TLR2
TLR3
UCP1
VEGFC
GLRA3
SMARCA5
SORBS2
SAP30
INPP4B
SNORD73A
LRAT
HAND2
RAPGEF2
MFAP3L
SPRY1
ANAPC10
PGRMC2
MAB21L2
PLK4
ADAM29
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
PALLD
TBC1D9
KIAA0922
TRIM2
ANP32C
SLC7A11
CCRN4L
FAM149A
FBXO8
DUX2
INTU
ARFIP1
PDLIM3
ZNF330
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
PCDH18
DKFZP434I0714
OTUD4
DCHS2
C4orf27
MARCH1
LARP1B
NEIL3
TMEM144
C4orf43
UFSP2
MAML3
DDX60
CDKN2AIP
ODZ3
TMEM184C
LRP2BP
PDGFC
FSTL5
STOX2
ANKRD50
RNF150
PCDH10
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
SCOC
TRAPPC11
HHIP
FAT4
ARHGAP10
MLF1IP
NBLA00301
MAP9
PHF17
WWC2
NAA15
C4orf29
CEP44
SETD7
SLC25A31
RAB33B
SNX25
TTC29
MND1
SLC10A7
TKTL2
USP38
C4orf49
CBR4
FHDC1
MGC45800
PRMT10
DDX60L
NAF1
WDR17
SCLT1
C4orf33
PABPC4L
ZFP42
SPATA4
ENPP6
ASB5
ZNF827
SH3D19
C4orf38
C4orf39
C4orf45
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
ELMOD2
CCDC110
MFSD8
LOC285419
CYP4V2
LOC285441
LOC285501
RNF175
LOC339975
TRIML1
LOC340017
PRSS48
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
LOC641364
LOC641365
SLED1
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
CETN4P
FAM160A1
LOC731424
LOC100129858
CLDN24
LOC100288255
MIR2054
MIR1305
MIR3140
MIR4276
MIR3945
MIR3688-1
LOC100505545
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR4453
MIR4799
MIR3688-2

Genes in Wide Peak

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

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

Genes
BUB1B
PML
TCF12
FLJ27352
C15orf55
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
BBS4
NBEAP1
BNIP2
CA12
CAPN3
CHRM5
CHRNA7
CKMT1B
CLK3
CSK
CSPG4
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IPW
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2C1
MAP1A
MEIS2
MFAP1
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
OAZ2
OCA2
PKM2
PLCB2
PPIB
MAPK6
MAP2K1
MAP2K5
PTPN9
RAB27A
RAD51
RORA
RPL4
RPLP1
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SORD
SPINT1
SRP14
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
UBE3A
MKRN3
SLC30A4
PAR5
ANP32A
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
ALDH1A2
HERC2
HERC1
SNURF
USP8
CCNB2
SLC28A2
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
PIGB
KIF23
IGDCC3
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
USP3
SLC12A6
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
FEM1B
RASGRP1
SERF2
DENND4A
SNAPC5
CORO2B
ARID3B
GNB5
ARPP19
CLPX
SLC27A2
GPR176
CHP
OIP5
ITGA11
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
DAPK2
EID1
C15orf2
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
GREM1
NPTN
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
RASL12
SPG21
SPTBN5
PTPLAD1
CTDSPL2
KLF13
RAB8B
DUOX1
CSNK1G1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZNF770
ZWILCH
FLJ10038
UACA
HAUS2
FAM82A2
DNAJC17
IMP3
LARP6
MNS1
NOP10
GOLGA6B
MYO5C
NDNL2
FAM214A
C15orf24
C15orf39
THAP10
PAK6
PARP6
DTWD1
CASC5
AVEN
C15orf17
ATP10A
GJD2
STARD9
ISLR2
VPS18
IGDCC4
SQRDL
PPCDC
CELF6
STRA6
ZFP106
IQCH
RFX7
SPATA5L1
CHAC1
NOX5
NEIL1
NARG2
AAGAB
LMAN1L
C15orf29
SLTM
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
SPG11
ELL3
PLEKHO2
CD276
POLR2M
C15orf44
NIPA2
ADPGK
APH1B
TLN2
FAM96A
C15orf48
MEGF11
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CALML4
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
SENP8
MTFMT
OSTBETA
HIGD2B
C15orf27
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145837
LOC145845
C15orf61
TMCO5A
NRG4
ZSCAN29
TTBK2
CDAN1
STRC
TBC1D21
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
RHOV
SCAMP5
C15orf33
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
SPESP1
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
HMGN2P46
SLC24A5
PRTG
LOC283663
LINC00277
C15orf60
LOC283683
OR4N4
LOC283710
LOC283731
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
TMEM202
WHAMMP3
POTEB
GLDN
GOLGA6A
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
LOC348120
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
GOLGA8E
OR4M2
OR4N3P
KBTBD13
UBAP1L
SKOR1
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR190A
MIR211
C15orf50
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC440288
LOC503519
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA14
FBXO22-AS1
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
LOC729739
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
MIR147B
DNM1P35
LOC100128714
LOC100129387
LOC100130855
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
LOC100287559
LOC100287616
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1272
MIR1266
MIR1282
LOC100306975
MIR548H4
MIR2116
MIR1233-2
MIR4311
MIR4312
MIR4310
MIR4313
MIR3942
LOC100505648
LOC100506686
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4513
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4511
MIR4509-3
MIR4712
MIR4715
TMCO5B
MYZAP

Genes in Wide Peak

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

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

Genes
MSH6
MSH2
REL
PAX8
BCL11A
TTL
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
hsa-mir-3127
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
hsa-mir-216b
hsa-mir-559
ACTG2
ACYP2
ADD2
ADRA2B
ANXA4
ATP6V1B1
AUP1
ZFP36L2
BUB1
CALM2
CAPG
CD8A
CD8B
CNGA3
COX5B
CTNNA2
DCTN1
DGUOK
LOC1720
DNAH6
DOK1
DUSP2
EGR4
EMX1
EN1
EPAS1
FABP1
EFEMP1
FHL2
FSHR
GFPT1
GGCX
HK2
TLX2
FOXN2
IL1A
IL1B
IL1R1
IL1RN
INPP4A
AFF3
LHCGR
LIMS1
EPCAM
MXD1
MAL
MAT2A
MDH1
MEIS1
MTIF2
NPAS2
NPHP1
OTX1
REG3A
PCBP1
PEX13
PIGF
PLEK
PLGLB2
PLGLB1
POU3F3
PPM1B
PPP3R1
PRKCE
RAB1A
RANBP2
REG1A
REG1B
REG1P
RPL31
RPS27A
RTKN
SFTPB
SIX3
SLC1A4
SLC3A1
SLC9A2
SLC20A1
SNRPG
SPR
SPTBN1
SULT1C2
TACR1
GCFC2
TGFA
TIA1
UGP2
VRK2
XPO1
ZAP70
ZNF2
ALMS1
MOGS
RNF103
IL1R2
MALL
DYSF
NCK2
DUSP11
VAMP8
MARCO
SUCLG1
IL18RAP
IL1RL2
IL18R1
ST3GAL5
DDX18
NAT8
TMSB10
IL1RL1
NRXN1
CIAO1
TGFBRAP1
CRIPT
MAP4K4
EIF2AK3
CHST10
PREPL
GCC2
SOCS5
EIF5B
USP34
SERTAD2
MRPL19
ARHGAP25
BCL2L11
ACTR3
ACTR2
ACTR1B
LRPPRC
TXNDC9
MPHOSPH10
SMYD5
C1D
MERTK
SEMA4F
CCT7
CCT4
GNLY
STAMBP
TGOLN2
B3GNT2
USP39
SIX2
VAMP5
MTHFD2
ARID5A
PROKR1
EDAR
GPR75
IMMT
SNRNP27
GTF2A1L
STON1
TBC1D8
RABL2A
GPR45
MGAT4A
AAK1
RPIA
SNRNP200
CEP68
PSME4
EXOC6B
EHBP1
NCAPH
RHOQ
TMEM131
PSD4
WBP1
VAX2
POLR1A
CNRIP1
UNC50
RAB11FIP5
CNNM4
CNNM3
IL36RN
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
BMP10
ZNF638
HTRA2
LGALSL
KCNIP3
CD207
TPRKB
FAHD2A
WDPCP
ASB3
INSIG2
ANKRD39
FAM178B
RNF181
MRPL30
KRCC1
MRPL35
PCYOX1
REV1
NAT8B
VPS54
LIPT1
DYNC2LI1
CHMP3
ETAA1
CCDC93
AFTPH
RETSAT
SEMA4C
C2orf42
PTCD3
FANCL
SRBD1
MOB1A
THNSL2
ACOXL
C2orf29
NAGK
TMEM127
KANSL3
CCDC88A
KDM3A
GKN1
IL36G
CYP26B1
POLE4
KCNK12
KCMF1
PNO1
STARD7
RPL23AP32
RTN4
PELI1
TTC7A
SMEK2
DPP10
ANKRD36B
SLC4A5
SLC5A7
THADA
ABCG5
ABCG8
GMCL1
TTC31
ANAPC1
RMND5A
PAPOLG
MRPS9
MRPS5
REEP1
SOWAHC
PDCL3
C2orf49
OR7E91P
CAMKMT
ANKRD53
LRRTM4
UXS1
FBXO11
SLC35F5
TSGA10
LMAN2L
TCF7L1
INO80B
WDR54
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
CHCHD5
PRADC1
C2orf40
ZC3H8
KIAA1841
ST6GAL2
IL1F10
MCEE
LOXL3
PCGF1
DDX11L2
MFSD9
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LBX2
PNPT1
FER1L5
MCFD2
ATP6V1E2
LOC90499
LOC90784
NEURL3
SFXN5
LIMS3
LINC00152
CCDC104
TEX261
CCDC85A
WDR92
MRPL53
RPL23AP7
PPP1R21
C2orf89
TMEM150A
NMS
LYG1
MITD1
FBLN7
C2orf73
TRIM43
REG3G
C2orf63
PLEKHH2
TMEM182
AHSA2
C2orf65
CKAP2L
CBWD2
TEKT4
LOC150568
SMYD1
C2orf15
COMMD1
PROM2
FBXO41
GPAT2
ITPRIPL1
PUS10
LINC00309
LOC151009
SEPT10
SULT1C2P1
FAHD2B
ASPRV1
LOC151534
LONRF2
CCDC138
C1QL2
CLEC4F
DQX1
FOXD4L1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
TMEM17
SPRED2
LINC00116
LYG2
SH2D6
LOC284950
RNF149
LOC284998
LOC285000
LOC285033
C2orf61
LOC285074
PLGLA
RGPD4
STON1-GTF2A1L
LOC339803
C2orf74
LOC339807
C2orf55
FIGLA
NOTO
FOXI3
PRORSD1P
SH3RF3
LRRTM1
ANKRD36
WASH2P
ZC3H6
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
SLC9A4
LOC389023
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
FLJ42351
MIR216A
MIR217
ASTL
ACTR3BP2
LOC440894
LOC440895
LOC440900
LOC442028
SULT1C3
COA5
CHAC2
LOC541471
FBXO48
LOC644838
GGT8P
ANKRD36BP2
TRIM43B
RGPD3
LOC654342
FAM138B
LOC654433
SNORD89
SNORD94
MIR559
RGPD8
LOC728537
LOC728819
LOC729121
ANKRD20A8P
LOC729234
RGPD6
RGPD2
RFX8
SNORA36C
SNORA70B
MIR216B
LOC100129726
LOC100132215
LOC100133985
LOC100134259
DBIL5P2
SNAR-H
LOC100189589
LIMS3-LOC440895
LOC100286979
LOC100287010
LOC100287216
LOC100288570
LIMS3L
GPR75-ASB3
MIR4265
MIR4264
MIR3127
MIR4267
MIR4266
MIR3126
LOC100499194
MIR3682
LOC100506123
LOC100506421
BOLA3-AS1
LOC100507334
RNF103-CHMP3
INO80B-WBP1
MIR4436B1
MIR4772
MIR4779
MIR4782
MIR4435-2
MIR4426
MIR4436A
MIR4434
MIR4780
MIR4778
MIR4432
MIR548AD
MIR4435-1
LOC100630918

Genes in Wide Peak

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

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

Genes
GATA3
hsa-mir-3155
ADARB2
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PRKCQ
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
KIN
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
IDI2-AS1
SFMBT2
ASB13
TUBAL3
ITIH5
AKR1E2
TAF3
FBXO18
RBM17
IDI2
UCN3
SFTA1P
LOC282980
LOC338588
AKR1CL1
TUBB8
tAKR
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf108
LOC439949
ADARB2-AS1
LOC100216001
MIR3155A
LOC100507034
LOC100507127
MIR3155B

Genes in Wide Peak

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

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

Genes
APC
CD74
EBF1
ITK
PDGFRB
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
CAMK4
CAMK2A
CAMLG
CAST
CD14
CDC25C
CDO1
CDX1
CHD1
AP3S1
CSF1R
CSF2
CSNK1A1
CSNK1G3
CTNNA1
DMXL1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EFNA5
EGR1
ETF1
FABP6
FAT2
FBN2
FER
FGF1
GDF9
GFRA3
GLRA1
GLRX
GM2A
GPX3
GRIA1
NR3C1
HARS
HINT1
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNN2
LECT2
LMNB1
LNPEP
LOX
SMAD5
MAN2A1
MCC
MFAP3
NDUFA2
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
PURA
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC22A4
SLC22A5
SNX2
SPARC
SPINK1
SPOCK1
SRP19
TAF7
TCF7
TCOF1
NR2F1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
ST8SIA4
REEP5
NME5
PDLIM4
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
P4HA2
ATG12
PTTG1
NREP
CNOT8
RAB9BP1
HAND1
MED7
MYOT
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
PJA2
DDX46
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
SLU7
SEC24A
C5orf4
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
KIF3A
SYNPO
RHOBTB3
ABLIM3
ELL2
HMGXB3
ARHGAP26
FSTL4
ATP10B
SEPT8
PPIP5K2
ACSL6
PHF15
LARP1
HARS2
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
IL17B
SLC27A6
SNX24
MRPL22
PCDHB1
TMED7
ISOC1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
LARS
CXXC5
RAPGEF6
ERAP1
KDM3B
PHAX
RBM27
FLJ11235
PCDHB18
PCDHB17
ZCCHC10
GIN1
WDR55
ANKHD1
THG1L
TMCO6
TRIM36
GALNT10
RBM22
RIOK2
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
C5orf54
EPB41L4A
ERAP2
SIL1
ARAP3
FBXL17
YTHDC2
GRAMD3
PCYOX1L
CCNJL
SH3TC2
SAP30L
TXNDC15
MCTP1
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
NUDT12
SLC4A9
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
PCBD2
PSD2
ANKRD32
C5orf32
MEGF10
SPINK7
HAVCR2
C5orf62
TSLP
FCHSD1
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
TIMD4
ZNF300
MYOZ3
PRDM6
FTMT
FNIP1
SLC35A4
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
LEAP2
SCGB3A2
SLCO6A1
PPARGC1B
PRRC1
ZNF474
POU5F2
AFAP1L1
GRPEL2
LSM11
GPR151
STARD4
WDR36
ZNF300P1
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
CEP120
SLC25A48
SRFBP1
LOC153469
ZMAT2
ARSK
FAM81B
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
DCP2
LIX1
ADAMTS19
SPATA24
DNAJC18
C5orf27
STK32A
AQPEP
SLC36A1
KIAA0825
GPR150
DTWD2
RELL2
LOC285626
LOC285627
SLC36A3
KIF4B
RGMB
RFESD
CHSY3
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
IRGM
FAM174A
CATSPER3
NIPAL4
SLCO4C1
TICAM2
DND1
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
MIR146A
SPINK14
FNDC9
FLJ42709
C5orf56
IGIP
TIFAB
FLJ35946
LOC553103
CTXN3
ECSCR
TMEM232
GRXCR2
SPINK9
LOC644100
FLJ33630
CCNI2
SNORA13
MIR583
SNHG4
MIR143HG
LOC728342
LOC729080
VTRNA2-1
MIR874
LOC100133050
C5orf52
LOC100289230
LOC100289673
MIR1289-2
MIR1244-1
TMED7-TICAM2
MIR2277
MIR1244-3
MIR1244-2
MIR3142
MIR3141
MIR3655
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505841
MIR4633
MIR4461
MIR4460

Genes in Wide Peak

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

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

Genes
PIWIL1
FZD10
RIMBP2
TMEM132D
FLJ31485
LOC100190940

Arm-level results

Table 3. Get Full Table Arm-level significance table - 16 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.02 | -2.88 | 1 | 0.13 | 1.04 | 0.742
1q | 1955 | 0.09 | -0.385 | 1 | 0.07 | -1.21 | 1
2p | 924 | 0.14 | 0.448 | 0.77 | 0.02 | -3.34 | 1
2q | 1556 | 0.15 | 1.43 | 0.218 | 0.01 | -3.36 | 1
3p | 1062 | 0.27 | 5.04 | 7.07e-07 | 0.09 | -0.764 | 1
3q | 1139 | 0.31 | 6.46 | 1.89e-10 | 0.03 | -2.48 | 1
4p | 489 | 0.04 | -2.79 | 1 | 0.10 | -1.07 | 1
4q | 1049 | 0.04 | -2.8 | 1 | 0.11 | -0.504 | 1
5p | 270 | 0.15 | 0.508 | 0.765 | 0.07 | -1.89 | 1
5q | 1427 | 0.13 | 0.73 | 0.621 | 0.07 | -1.37 | 1
6p | 1173 | 0.03 | -2.81 | 1 | 0.08 | -1.26 | 1
6q | 839 | 0.03 | -3.17 | 1 | 0.10 | -0.662 | 1
7p | 641 | 0.54 | 13.7 | 0 | 0.00 | -2.95 | 1
7q | 1277 | 0.55 | 15.3 | 0 | 0.00 | -2.74 | 1
8p | 580 | 0.08 | -1.56 | 1 | 0.04 | -2.79 | 1
8q | 859 | 0.10 | -0.923 | 1 | 0.03 | -3.19 | 1
9p | 422 | 0.02 | -3.54 | 1 | 0.14 | 0.118 | 1
9q | 1113 | 0.01 | -3.51 | 1 | 0.16 | 1.37 | 0.572
10p | 409 | 0.03 | -3.16 | 1 | 0.07 | -1.95 | 1
10q | 1268 | 0.03 | -3.08 | 1 | 0.07 | -1.52 | 1
11p | 862 | 0.04 | -2.69 | 1 | 0.07 | -1.68 | 1
11q | 1515 | 0.03 | -2.89 | 1 | 0.10 | -0.238 | 1
12p | 575 | 0.35 | 7.28 | 7.36e-13 | 0.00 | -3.51 | 1
12q | 1447 | 0.35 | 8.32 | 0 | 0.00 | -3.25 | 1
13q | 654 | 0.13 | 0.114 | 1 | 0.12 | -0.378 | 1
14q | 1341 | 0.03 | -2.71 | 1 | 0.20 | 3.03 | 0.0164
15q | 1355 | 0.02 | -3.25 | 1 | 0.10 | -0.373 | 1
16p | 872 | 0.50 | 12.8 | 0 | 0.06 | -1.53 | 1
16q | 702 | 0.49 | 12 | 0 | 0.06 | -1.66 | 1
17p | 683 | 0.56 | 14.3 | 0 | 0.10 | -0.593 | 1
17q | 1592 | 0.64 | 19 | 0 | 0.00 | -2.39 | 1
18p | 143 | 0.07 | -2.11 | 1 | 0.18 | 1.45 | 0.572
18q | 446 | 0.05 | -2.53 | 1 | 0.19 | 1.85 | 0.325
19p | 995 | 0.02 | -3.5 | 1 | 0.06 | -1.97 | 1
19q | 1709 | 0.02 | -3.2 | 1 | 0.06 | -1.58 | 1
20p | 355 | 0.33 | 6.38 | 2.91e-10 | 0.02 | -3.01 | 1
20q | 753 | 0.35 | 7.75 | 2.33e-14 | 0.00 | -3.44 | 1
21q | 509 | 0.06 | -2.29 | 1 | 0.17 | 1.13 | 0.742
22q | 921 | 0.01 | -3.32 | 1 | 0.26 | 4.75 | 4.03e-05
Xq | 1312 | 0.33 | 6.85 | 1.47e-11 | 0.22 | 3.06 | 0.0164

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/KIRP-TP/3023993/2.GDAC_MergeDataFiles.Finished/KIRP-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

- Reference Genome = /xchip/cga/reference/gistic2/hg19_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 127 Input Tumor Samples.

Tumor Sample Names
TCGA-A4-7286-01A-11D-2135-01
TCGA-A4-7287-01A-11D-2135-01
TCGA-A4-7288-01A-11D-2135-01
TCGA-A4-7583-01A-11D-2135-01
TCGA-A4-7584-01A-11D-2135-01
TCGA-A4-7585-01A-11D-2135-01
TCGA-A4-7732-01A-11D-2135-01
TCGA-A4-7734-01A-11D-2135-01
TCGA-A4-7828-01A-11D-2135-01
TCGA-A4-7915-01A-11D-2200-01

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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