SNP6 Copy number analysis (GISTIC2) - Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1TM78VW

Overview

Introduction

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

Summary

There were 206 tumor samples used in this analysis: 24 significant arm-level results, 23 significant focal amplifications, and 34 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 - 23 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
11q22.1	1.4767e-27	2.954e-23	chr11:101586586-102266642	6
3q26.31	1.0456e-24	2.1187e-16	chr3:168026373-172485872	32
20q11.21	1.2763e-09	1.2763e-09	chr20:30204825-30356590	3
8q24.21	4.9583e-09	4.9583e-09	chr8:128754838-128772049	0 [MYC]
19q13.2	1.6403e-06	1.6403e-06	chr19:38370469-39622696	34
9p24.1	3.7827e-06	3.7827e-06	chr9:5302096-5565600	5
3q28	4.5113e-26	3.8068e-06	chr3:188970430-198022430	85
13q22.1	3.9675e-06	3.9675e-06	chr13:73929290-73956005	0 [KLF5]
17q12	2.0186e-05	2.0186e-05	chr17:37853555-37869191	1
16p13.13	3.9153e-05	3.9153e-05	chr16:11667206-11927980	5
1q21.3	0.00040817	0.00040817	chr1:149890534-155333392	199
17q25.1	0.0010324	0.0010324	chr17:72723443-74083947	58
11q13.3	3.2726e-05	0.0016314	chr11:69512115-70747182	11
Xq28	0.0051618	0.0051618	chrX:142436434-155270560	178
5p15.33	0.0072163	0.0072163	chr5:1-12142832	73
11p13	0.017812	0.017812	chr11:34553850-37753926	17
1p31.3	0.042676	0.042676	chr1:61416174-62488521	3
2q32.3	0.077715	0.077715	chr2:168816244-203250823	215
7p11.2	0.077715	0.077715	chr7:54944574-55769800	4
4q12	0.090894	0.090894	chr4:55996856-56580180	6
2p24.3	0.15735	0.15735	chr2:1-45898529	287
6p21.33	0.18137	0.18137	chr6:1-37826192	520
15q26.1	0.19008	0.19008	chr15:71968338-102531392	304

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.1.

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

Genes
BIRC3
BIRC2
YAP1
KIAA1377
C11orf70
ANGPTL5

Genes in Wide Peak

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

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

Genes
hsa-mir-569
hsa-mir-551b
ECT2
MECOM
GHSR
CLDN11
PLD1
PRKCI
SKIL
SLC2A2
TERC
SEC62
TNFSF10
TNIK
GPR160
MYNN
EIF5A2
NCEH1
SLC7A14
FNDC3B
LRRC31
PHC3
ARPM1
EGFEM1P
LRRC34
RPL22L1
LRRIQ4
SAMD7
TMEM212
MIR551B
MIR569
LOC100128164

Genes in Wide Peak

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

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

Genes
BCL2L1
TPX2
COX4I2

Genes in Wide Peak

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

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

Genes
ACTN4
ECH1
HNRNPL
LGALS4
LGALS7
NFKBIB
PSMD8
MRPS12
RYR1
DPF1
KCNK6
PAK4
SPINT2
MAP4K1
SIRT2
SIPA1L3
EIF3K
SARS2
CATSPERG
C19orf33
WDR87
YIF1B
PPP1R14A
FBXO17
RASGRP4
RINL
FBXO27
FAM98C
CAPN12
GGN
PAPL
SPRED3
LOC643669
LGALS7B

Genes in Wide Peak

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

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

Genes
CD274
RLN1
RLN2
C9orf46
PDCD1LG2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q28.

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

Genes
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
APOD
BDH1
CPN2
DLG1
FGF12
GP5
HES1
IL1RAP
MFI2
MUC4
OPA1
PAK2
PCYT1A
PPP1R2
RPL35A
TP63
CLDN1
KIAA0226
TNK2
CLDN16
NCBP2
ACAP2
UBXN7
PIGX
LEPREL1
LSG1
HRASLS
ATP13A3
PIGZ
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
CEP19
LMLN
TMEM44
TM4SF19
ZDHHC19
LRRC15
FAM43A
TMEM207
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
TCTEX1D2
C3orf43
SDHAP1
UTS2D
TPRG1
OSTN
ATP13A5
WDR53
ANKRD18DP
LRRC33
FLJ34208
LOC401109
GMNC
LOC647323
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
SNAR-I
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797

Genes in Wide Peak

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

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

Genes
ERBB2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p13.13.

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

Genes
SNN
LITAF
ZC3H7A
TXNDC11
BCAR4

Genes in Wide Peak

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

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

Genes
ARNT
MUC1
TPM3
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
ADAR
CHRNB2
CKS1B
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FDPS
FLG
GBA
GBAP1
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PI4KB
PKLR
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
PIP5K1A
ANXA9
ADAM15
SELENBP1
PRPF3
SETDB1
UBAP2L
DENND4B
SCAMP3
SF3B4
HAX1
SEMA6C
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CELF3
VPS45
POGZ
RPRD2
SNAPIN
RUSC1
CA14
C1orf43
CHTOP
LCE2B
SLC39A1
TMOD4
CERS2
CRNN
ZBTB7B
APH1A
PLEKHO1
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
DCST2
S100A16
CREB3L4
C1orf51
LELP1
DCST1
BNIPL
SPRR4
LCE4A
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
RUSC1-AS1
S100A7A
LINGO4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LYSMD1
HRNR
FLG2
C1orf189
KPRP
LCE6A
PRR9
S100A7L2
MIR554
MIR555
MIR92B
MIR190B
C1orf68
LOC100132111
C2CD4D
MIR4257
MIR4258
LOC100505666
TNFAIP8L2-SCNM1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
ACOX1
CDK3
EVPL
FDXR
GALK1
GRB2
GRIN2C
H3F3B
ICT1
ITGB4
LLGL2
SUMO2
SRP68
GALR2
SLC16A5
SLC9A3R1
RECQL5
KIAA0195
ATP5H
GGA3
EXOC7
KCTD2
WBP2
NAT9
SAP30BP
NT5C
CDR2L
MRPS7
HN1
TMEM104
MIF4GD
CASKIN2
SLC25A19
MRPL38
ARMC7
NUP85
MYO15B
FBF1
UNK
TRIM47
OTOP2
USH1G
TRIM65
UNC13D
FADS6
C17orf28
TSEN54
RAB37
OTOP3
ZACN
C17orf109
C17orf110
TEN1
LOC100287042
MIR3678
MIR3615
TEN1-CDK3
MIR4738

Genes in Wide Peak

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

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

Genes
hsa-mir-548k
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
SHANK2
ANO1
MIR548K
MIR3664

Genes in Wide Peak

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

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

Genes
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
HCFC1
HMGB3
IDH3G
IDS
IL9R
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MECP2
MPP1
MTM1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
FAM50A
CXorf1
GPR50
MAMLD1
BCAP31
SPRY3
ZNF275
TREX2
SRPK3
SNORA70
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
GABRQ
PDZD4
FAM3A
FUNDC2
PRRG3
BRCC3
CD99L2
H2AFB3
TMEM185A
SLITRK2
PNMA6A
FATE1
CXorf40A
FAM58A
PNMA5
RAB39B
SLITRK4
SPANXN3
PASD1
GAB3
PNCK
ZFP92
CSAG1
FMR1NB
VMA21
CTAG1A
MAGEA2B
LINC00204B
UBE2NL
CSAG3
MIR105-1
MIR105-2
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
CXorf40B
MIR452
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
CSAG2
MIR767
FMR1-AS1
MIR509-2
MIR890
MIR891B
MIR888
MIR892B
MIR509-3
MIR891A
MIR892A
CXorf51A
HSFX2
LOC100131434
CXorf68
LINC00204A
CXorf51B
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR718
MIR2114
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
LOC100507404
MAGEA10-MAGEA5

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
CD44
RAG1
RAG2
SLC1A2
TRAF6
PDHX
FJX1
PAMR1
EHF
COMMD9
APIP
TRIM44
PRR5L
C11orf74
LDLRAD3
MIR3973
MIR1343

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p31.3.

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

Genes
NFIA
INADL
TM2D1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q32.3.

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

Genes
CHN1
HOXD11
HOXD13
NFE2L2
PMS1
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
AOX1
ATP5G3
BMPR2
CASP8
CASP10
CHRNA1
CLK1
COL3A1
COL5A2
ATF2
DLX1
DLX2
DYNC1I2
FRZB
GAD1
MSTN
GLS
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HSPD1
HSPE1
INPP1
ITGA6
ITGA4
ITGAV
LRP2
MYO1B
NAB1
NDUFB3
NEUROD1
ORC2
PDE1A
PDK1
PLCL1
SP3
SSB
SSFA2
STAT1
STAT4
TFPI
TTN
SUMO1
WIPF1
FZD7
SDPR
HAT1
AGPS
PRKRA
SLC25A12
ABCB11
CFLAR
STK17B
GTF3C3
PPIG
CIR1
BZW1
TLK1
DHRS9
CALCRL
KBTBD10
UBE2E3
MTX2
NCKAP1
RAPGEF4
SATB2
SF3B1
TMEFF2
MOB4
GORASP2
SPATS2L
HIBCH
STK39
METTL5
OLA1
SLC40A1
PDE11A
GULP1
NOP58
FKBP7
ZAK
PPIL3
DNAJC10
ASNSD1
MFSD6
STRADB
ZC3H15
DNAH7
SLC39A10
SPC25
HECW2
ALS2
CWC22
G6PC2
MPP4
NIF3L1
PCGEM1
OSGEPL1
OBFC2A
CDK15
TMEM237
CFLAR-AS1
PLEKHA3
TRAK2
BOLL
C2orf47
SCRN3
FASTKD1
METTL8
CYBRD1
PGAP1
DCAF17
COQ10B
KIAA1715
CDCA7
WDR75
C2orf88
LOC91149
SESTD1
ANKRD44
ZNF804A
TTC30A
MARS2
ORMDL1
OSBPL6
NOSTRIN
DIRC1
NUP35
TYW5
RBM45
BBS5
C2orf77
RFTN2
UBR3
KCTD18
ALS2CR12
MYO3B
DUSP19
FLJ32063
ANKAR
TTC30B
ZSWIM2
ZNF385B
KLHL23
PPP1R1C
SGOL2
ALS2CR11
GPR155
FAM171B
C2orf69
HNRNPA3
CERS6
METAP1D
CCDC150
CCDC141
LOC285084
FAM126B
MLK7-AS1
EVX2
AOX2P
FONG
LOC375295
CERKL
SP5
LOC401022
FSIP2
C2orf66
MIR10B
LOC440925
PHOSPHO2
DFNB59
SNORD11
SNORD70
MIR561
SNORD11B
MIR933
LOC100130452
LOC100130691
TMEM194B
SP9
MIR1246
MIR548N
MIR1258
MIR1245A
MIR3128
MIR3129
MIR3606
LOC100505695
LOC100506783
LOC100506866
LOC100507140
PHOSPHO2-KLHL23
HSPE1-MOB4
MIR4437
MIR1245B
MIR4774
MIR4444-1
LOC100861402

Genes in Wide Peak

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

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

Genes
EGFR
LANCL2
VOPP1
FKBP9L

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
CLOCK
NMU
TMEM165
SRD5A3
PDCL2
LOC100506462

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.3.

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

Genes
ALK
DNMT3A
MYCN
NCOA1
EML4
hsa-mir-558
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ADCY3
APOB
RHOB
ZFP36L2
CAD
CENPA
CYP1B1
DDX1
DTNB
E2F6
FKBP1B
FOSL2
FTH1P3
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
LTBP1
MATN3
MPV17
ODC1
VIT
POMC
PPM1B
PPM1G
PPP1CB
PRKCE
EIF2AK2
RPS7
RRM2
SDC1
SRSF7
SIX3
SLC3A1
SLC8A1
SOS1
SOX11
SPAST
SRD5A2
STRN
ADAM17
TPO
TSSC1
UCN
VSNL1
XDH
SLC30A3
PXDN
KLF11
MAP4K3
ASAP2
SLC5A6
EIF2B4
TAF1B
COX7A2L
ITGB1BP1
OTOF
ROCK2
TP53I3
MRPL33
BRE
PREPL
FEZ2
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
LRPPRC
PDIA6
CEBPZ
MYCNOS
CDC42EP3
CGREF1
SIX2
RAB10
YWHAQ
EMILIN1
GPN1
MAPRE3
SLC4A1AP
EFR3B
MYT1L
WDR43
LPIN1
PUM2
HAAO
NTSR2
PRKD3
RASGRP3
QPCT
FAM98A
IFT172
SH3YL1
SNORD53
TRIB2
GRHL1
NRBP1
EHD3
ITSN2
MEMO1
TRAPPC12
CRIM1
DNAJC27
C2orf28
NBAS
DYNC2LI1
SF3B14
YPEL5
CPSF3
SNTG2
ATAD2B
HEATR5B
TMEM214
C2orf18
TRMT61B
SRBD1
ASXL2
ADI1
C2orf56
TTC27
SLC30A6
ALLC
DPYSL5
TRIM54
BIRC6
KIDINS220
MTA3
WDR35
RDH14
NLRC4
AGBL5
C2orf43
THADA
RBKS
ATL2
ABCG5
ABCG8
HS1BP3
FNDC4
COLEC11
CENPO
GALNT14
CCDC121
SMC6
CLIP4
CAMKMT
GEMIN6
NOL10
C2orf44
THUMPD2
FAM49A
LBH
C2orf16
YIPF4
ZNF512
DPY30
ABHD1
EPT1
DHX57
PKDCC
RSAD2
CAPN13
CCDC164
HNRPLL
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
PLEKHH2
OSR1
TTC32
ZNF513
GALM
TMEM178
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
PLB1
MYADML
FAM84A
FAM82A1
GDF7
GPR113
OXER1
FAM179A
UBXN2A
KCNG3
CYS1
KRTCAP3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
FAM150B
LINC00486
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
C2orf70
C2orf53
LOC339788
LINC00299
LOC339822
MSGN1
CDKL4
GEN1
C2orf48
PFN4
LOC375190
LOC375196
LOC386597
MFSD2B
C2orf71
LOC388942
PTRHD1
SULT6B1
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
CAPN14
FAM110C
LOC645949
C2orf84
SNORD92
MIR558
LOC727982
LOC728730
LOC728819
RAD51AP2
DNAJC27-AS1
MORN2
LOC730811
LOC100128590
OST4
LOC100129726
ARHGEF33
LOC100271832
LOC100288911
MIR1301
LOC100302650
SNORA80B
MIR4261
MIR4263
MIR3125
MIR4262
LOC100505624
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4765
MIR4757
MIR4429
MIR548AD

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.33.

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

Genes
DAXX
FANCE
HMGA1
IRF4
PIM1
POU5F1
TRIM27
DEK
HIST1H4I
hsa-mir-1275
hsa-mir-219-1
hsa-mir-1236
hsa-mir-877
hsa-mir-3143
hsa-mir-548a-1
ABCF1
AGER
AIF1
ATP6V1G2
BAK1
CFB
BMP6
BPHL
BTN1A1
C2
C4A
C4B
DDR1
CDKN1A
CDSN
CLIC1
CLPS
COL11A2
ATF6B
MAPK14
CSNK2B
CYP21A2
CYP21A1P
DOM3Z
DSP
E2F3
EDN1
SERPINB1
F13A1
FKBP5
FOXF2
FOXC1
GABBR1
GCNT2
GMDS
GMPR
GNL1
GPLD1
GPX5
GRM4
GTF2H4
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
HLA-A
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSPA1A
HSPA1B
HSPA1L
ID4
ITPR3
JARID2
KIFC1
LTA
LTB
MAK
MICB
MLN
MOG
MSH5
RPL10A
NEDD9
NEU1
NFKBIL1
NQO2
NOTCH4
PBX2
PHF1
SERPINB6
SERPINB9
PPARD
PPP1R10
MAPK13
PRL
PSMB8
PSMB9
RGL2
RING1
BRD2
RNF5
RPS10
RPS18
RREB1
RXRB
VPS52
ATXN1
SRSF3
SKIV2L
SLC17A1
SNRPC
SOX4
SRPK1
SSR1
TAF11
TAP1
TAP2
TAPBP
TCF19
TCP11
PPP1R11
TEAD3
TFAP2A
TNF
TNXA
TNXB
TPMT
TUBB2A
TULP1
VARS
ZNF76
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204P
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
OR2H2
RDBP
LST1
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
CMAHP
DHX16
B3GALT4
RIPK1
SYNGAP1
STK19
IER3
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
GCM2
WDR46
ZBTB22
CD83
PPT2
CDYL
LY86
EEF1E1
MDC1
FAM65B
ZSCAN12
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
FLOT1
SLC17A2
HCG9
PRSS16
BTN3A3
BTN2A2
ECI2
PFDN6
HMGN4
TRIM38
CAP2
UBD
AGPAT1
SCGN
C6orf10
FARS2
SLC17A3
RPP40
HCP5
EHMT2
TRIM31
BTN3A2
BTN3A1
BTN2A1
NUDT3
NRM
STK38
FTSJD2
ANKS1A
SIRT5
DDAH2
MTCH1
SPDEF
OR2B6
FAM50B
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
SNORD52
SNORD48
BRPF3
MRPS18B
C6orf15
MYLIP
ABT1
PACSIN1
ZNRD1
DEF6
C6orf48
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
ETV7
TMEM14C
TDP2
CUTA
PPIL1
HCG4
GFOD1
CCHCR1
BTN2A3P
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
TBC1D22B
EXOC2
ACOT13
APOM
BTNL2
TRIM39
WRNIP1
DUSP22
LYRM4
VARS2
MRS2
CPNE5
LSM2
C6orf47
LY6G5B
LY6G6D
ZFAND3
SLC22A23
MUTED
CCDC90A
GPSM3
FKBPL
KIF13A
ZNF323
C6orf106
LY6G6E
ZNF322
RPP21
ATAT1
ZKSCAN3
ZSCAN16
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRR3
ZNRD1-AS1
PRRT1
EGFL8
HCG4B
TXNDC5
C6orf62
OR5V1
OR2B2
OR12D3
TMEM14B
RIOK1
DTNBP1
MNF1
PGBD1
ADTRP
HIST1H2AH
HIST1H2BK
TRIM15
POM121L2
FOXQ1
SCAND3
SLC26A8
MAS1L
IP6K3
HUS1B
TRIM40
DPCR1
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
CCDC167
PSORS1C1
PSORS1C2
PPP1R18
TRIM39-RPP21
TUBB
PIP5K1P1
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
TOB2P1
FAM217A
HCG27
RNF144B
HIST1H2BA
GPX6
NCR3
LY6G6F
MDGA1
ZNF311
LOC285768
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
HCG22
LOC285847
PNPLA1
RNF5P1
MYLK4
IFITM4P
CLPSL1
ZNF391
ZFP57
TUBB2B
C6orf52
HCG26
KAAG1
NHLRC1
ZKSCAN4
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
SFTA2
CLPSL2
C6orf222
MUC21
DKFZP686I15217
FLJ23152
LINC00340
LOC401242
MCCD1
SAPCD1
LINC00336
C6orf201
ERVFRD-1
MIR219-1
HCG23
HCG25
HCG18
OR2B3
OR2J3
OR14J1
OR10C1
GGNBP1
HCG11
LOC554223
PPP1R3G
SNORA38
SNORD32B
SNORD84
SNORD117
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
MIR877
LOC100129636
LOC100130275
LOC100130357
PSORS1C3
LOC100131289
LINC00240
LOC100270746
LOC100293534
LOC100294145
MIR1275
MIR1236
MIR3143
MIR3925
MIR3691
LOC100506207
LOC100506409
LOC100507173
LOC100507194
LOC100507362
MICA
LOC100507463
LOC100507547
LOC100507584
MUC22
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
RPS10-NUDT3
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4646
MIR4640
MIR4639
MIR4645
MIR4462

Genes in Wide Peak

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

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

Genes
BLM
IDH2
NTRK3
PML
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
ACAN
ALDH1A3
ANPEP
BBS4
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
FES
HEXA
IDH3A
IGF1R
IL16
IREB2
ISG20
ISLR
LOXL1
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
MYO9A
NEO1
NMB
FURIN
PCSK6
PDE8A
PKM2
PLIN1
POLG
PSMA4
PTPN9
RASGRF1
RCN2
RLBP1
RPS17
SH3GL3
SNRPA1
NR2F2
TYRO3P
AP3B2
ST8SIA2
SEMA7A
PEX11A
IQGAP1
PSTPIP1
PRC1
SLC28A1
COX5A
STOML1
HOMER2
ZNF592
SV2B
ARNT2
NR2E3
HCN4
SCAMP2
SNUPN
TSPAN3
AP3S2
HMG20A
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
ARIH1
SIN3A
ULK3
FBXO22
VPS33B
MRPL46
OR4F4
NPTN
SLCO3A1
SCAPER
HDGFRP3
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2
RPP25
COMMD4
ZSCAN2
DET1
LINS
FANCI
IMP3
DNAJA4
MCTP2
SELS
GOLGA6B
MESP1
UNC45A
C15orf39
RGMA
WDR93
PARP6
C15orf17
ADAMTSL3
KIAA1199
ALPK3
ISLR2
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
KLHL25
CPEB1
AEN
ISL2
TTC23
MRPS11
EFTUD1
NEIL1
LRRK1
LMAN1L
PEAK1
THSD4
C15orf34
CCDC33
EDC3
AGSK1
TM2D3
WDR61
CD276
STARD5
C15orf5
ADPGK
FAM103A1
MEX3B
LINGO1
WDR73
UBL7
C15orf42
RCCD1
LOC91450
ARRDC4
LOC91948
UBE2Q2
C15orf40
SENP8
TARSL2
HIGD2B
LRRC28
C15orf27
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
NRG4
LINC00052
C15orf26
TBC1D21
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
GRAMD2
CERS3
LOC253044
LOC254559
SNX33
C15orf60
C15orf37
LOC283688
LOC283692
LOC283693
FAM154B
LOC283731
LOC283738
LOC283761
FAM169B
TMEM202
LOC338963
GOLGA6A
TMC3
ZNF774
C15orf38
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
C15orf59
LOC388152
UBE2Q2P1
FLJ42289
ANKRD34C
C15orf58
OR4F6
OR4F15
LOC390660
ST20
FAM174B
LOC400456
MIR184
MIR7-2
MIR9-3
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
CPLX3
LOC645752
SH2D7
LOC646938
GOLGA6L10
LOC648809
GOLGA6C
GOLGA6D
SCARNA15
FBXO22-AS1
MIR549
MIR630
MIR631
LOC727849
LOC727915
ASB9P1
LOC729739
LOC729911
FAM138E
DNM1P35
UBE2Q2P3
UBE2Q2P2
LOC100144604
GPCRLTM7
DDX11L1
LOC100287559
LOC100287616
DDX11L9
MIR1276
MIR1179
MIR1469
MIR3175
MIR4313
RPS17L
LOC100505679
LOC100506874
LOC100507217
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
MIR4514
MIR4513
MIR3529
MIR4515
MIR4714

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 - 34 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
11q25	1.7009e-24	1.6937e-24	chr11:118392854-135006516	165
2q22.1	1.2924e-18	1.4825e-16	chr2:139655617-143637838	1
19p13.3	6.6867e-16	6.6867e-16	chr19:1103802-1210605	2
4q35.2	6.4266e-10	1.6504e-09	chr4:187133825-191154276	21
2q37.1	3.4978e-30	9.1217e-09	chr2:213401694-243199373	285
10q23.31	1.0013e-08	9.4281e-09	chr10:89506488-89621060	2
13q14.2	7.3263e-11	2.88e-07	chr13:40171063-52436675	97
2q37.3	1.005e-29	9.6011e-06	chr2:206480055-243199373	334
20p12.1	9.4907e-05	9.4907e-05	chr20:14302876-16252980	3
6q26	0.00048062	0.00048062	chr6:147518548-171115067	140
16q23.1	0.00094222	0.00095447	chr16:78129058-79627770	1
1p36.31	0.0016414	0.0034571	chr1:1-25758654	399
14q32.31	0.0040729	0.004227	chr14:81404075-107349540	288
17q25.3	0.0051443	0.0052534	chr17:76236955-81195210	108
3p14.2	0.0060943	0.0061179	chr3:53923579-93777876	111
11p15.1	0.0066758	0.0066287	chr11:1-30035954	375
13q12.11	5.1691e-08	0.0071565	chr13:1-39920285	127
22q13.32	0.011255	0.010771	chr22:48668582-49176545	5
Xq21.33	0.010771	0.010771	chrX:96134519-98718611	1
16q12.1	0.011863	0.011429	chr16:31772318-65320530	138
15q21.1	0.015337	0.015133	chr15:34148119-60309441	260
7q34	0.015866	0.01613	chr7:114658966-159138663	353
4q22.1	0.0091254	0.035648	chr4:90844993-93240505	1
8p23.3	0.049366	0.050351	chr8:1-10754510	88
19q13.33	0.04949	0.050351	chr19:45569944-59128983	604
6p24.2	0.068819	0.06604	chr6:1-25082104	130
5q35.2	0.07566	0.07566	chr5:174955585-175224904	1
18q21.2	0.07374	0.07566	chr18:48514396-48705371	1
21q11.2	0.081044	0.081044	chr21:1-33786418	121
1p13.2	0.060643	0.082733	chr1:78217678-149898950	387
5q22.3	0.091328	0.091423	chr5:44813655-133938162	384
17p12	0.099573	0.10138	chr17:11896630-12456081	3
Xp11.3	0.1367	0.1367	chrX:44702452-45008304	2
4q21.3	0.03704	0.25036	chr4:87373401-87746054	1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

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

Genes
CBL
DDX6
FLI1
ARHGEF12
hsa-mir-3167
hsa-mir-100
ACRV1
APLP2
ARCN1
CXCR5
CHEK1
DPAGT1
ETS1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NFRKB
NRGN
OPCML
PVRL1
RPS25
SC5DL
ST3GAL4
SORL1
SRPR
ST14
TECTA
THY1
UPK2
ZNF202
BARX2
USP2
EI24
FEZ1
ARHGAP32
C2CD2L
HYOU1
ADAMTS8
TREH
IGSF9B
PHLDB1
NCAPD3
VSIG2
TRIM29
POU2F3
HINFP
OR8G2
OR8B8
OR8G1
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
TRAPPC4
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
IFT46
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
C11orf61
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
JAM3
KIRREL3
TMEM25
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
TMEM45B
TTC36
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
LINC00167
HEPN1
LOC649133
RPL23AP64
LOC100128239
PATE3
MIR3167
LOC100499227
MIR3656
LOC100507392
MIR4697
MIR4493
MIR4492

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
GPX4
SBNO2

Genes in Wide Peak

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

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

Genes
DUX4
F11
FAT1
FRG1
HSP90AA4P
KLKB1
MTNR1A
DUX2
ZFP42
TRIML2
LOC285441
LOC339975
TRIML1
LOC401164
DUX4L4
FRG2
DUX4L6
DUX4L5
DUX4L3
DUX4L2
LOC100288255

Genes in Wide Peak

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

Table S26. Genes in bold are cancer genes as defined by The Sanger Institute: 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
IKZF2
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
LOC100130451
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
ATAD1
CFL1P1

Genes in Wide Peak

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

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

Genes
LCP1
RB1
TTL
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
TPT1
TNFSF11
SUCLA2
DLEU2
TSC22D1
ITM2B
MTRF1
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
WBP4
AKAP11
FNDC3A
KIAA0564
ZC3H13
LRCH1
INTS6
NUFIP1
C13orf15
MED4
DNAJC15
PHF11
ENOX1
RCBTB1
NUDT15
KIAA1704
CYSLTR2
SPRYD7
COG6
NAA16
RNASEH2B
DHRS12
KIAA0226L
CDADC1
CAB39L
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
LINC00284
FAM216B
LACC1
LINC00330
ST13P4
DGKH
CCDC122
FAM194B
SPERT
DLEU7
FAM124A
CTAGE10P
SLC25A30
SUGT1P3
SIAH3
KCNRG
LINC00282
KCTD4
SERP2
LINC00548
MIR15A
MIR16-1
TSC22D1-AS1
SERPINE3
SNORA31
MIR621
TPT1-AS1
MIR320D1
MIR4305
MIR3613
OR7E37P
LOC100507240
LOC100509894
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
ATIC
CREB1
ACSL3
IDH1
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CYP27A1
DES
DTYMK
EEF1B2
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
NDUFS1
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
FASTKD2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
SNORD51
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
ZDBF2
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
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
METTL21A
CCNYL1
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
PIKFYVE
LOC200726
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
SNORA41
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
LOC100329109
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
LOC100507443
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4775
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
FLRT3
MACROD2
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
ACAT2
CCR6
ESR1
GPR31
IGF2R
KIF25
LPA
MAS1
MAP3K4
OPRM1
PARK2
PCMT1
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
EZR
VIP
RNASET2
SYNJ2
LATS1
QKI
WTAP
AKAP12
UST
PDE10A
KATNA1
SCAF8
TAB2
SASH1
SYNE1
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
TFB1M
SNX9
BRP44L
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
PLEKHG1
ARID1B
TMEM181
ZBTB2
SMOC2
ULBP3
C6orf211
ZDHHC14
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RSPH3
TTLL2
FAM120B
FNDC1
LRP11
SERAC1
PPIL4
LINC00473
SYTL3
SFT2D1
C6orf72
TAGAP
STXBP5
PACRG
RAET1E
CNKSR3
RAET1L
PNLDC1
LOC154449
DACT2
C6orf118
OSTCP1
WDR27
LOC285796
PRR18
ZC3H12D
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
LOC441177
RAET1K
MLLT4-AS1
SNORA20
SNORA29
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LOC100289495
MIR1913
MIR3918
MIR3939
MIR3692
CAHM
MIR4466
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
MDS2
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
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
MTOR
FUCA1
GABRD
GALE
GNB1
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RHCE
RHD
RPL11
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
LUZP1
PRDM2
MMP23B
MMP23A
KCNAB2
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
ANGPTL7
HNRNPR
SRRM1
UBE4B
MAD2L2
PDPN
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLSTN1
AKR7A3
SPEN
KDM1A
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
CLIC4
SYF2
CHD5
C1orf144
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
ARHGEF10L
VPS13D
ATAD3A
PANK4
CAMK2N1
ASAP3
PNRC2
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
PLA2G2F
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
AGMAT
LINC00115
MORN1
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
USP48
NBPF3
SLC25A33
DDI2
LZIC
C1orf170
CROCCP2
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf201
C1orf158
FBXO44
CROCCP3
FHAD1
LOC115110
RBP7
ACAP3
UBE2J2
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC649330
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
GALC
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
MTA1
RPS6KA5
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
PTPN21
RCOR1
PACS2
PPP1R13B
FLRT2
KIF26A
C14orf109
PRO1768
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
UNC79
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
TTC7B
C14orf49
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
CCDC85C
ITPK1-AS1
SERPINA9
LINC00226
LINC00221
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
MIR1247
MIR1185-1
MIR1185-2
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q25.3.

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

Genes
ASPSCR1
CANT1
hsa-mir-3186
hsa-mir-1250
ACTG1
ARHGDIA
CD7
CSNK1D
SLC25A10
FASN
GAA
GCGR
UTS2R
GPS1
FOXK2
LGALS3BP
MAFG
NPTX1
P4HB
PDE6G
PYCR1
PCYT2
RAC3
RFNG
MRPL12
SECTM1
SGSH
TBCD
TIMP2
CBX4
DNAH17
SOCS3
SLC16A3
HGS
CYTH1
PGS1
AATK
EIF4A3
ALYREF
BAIAP2
RAB40B
AZI1
FSCN2
NARF
DCXR
ANAPC11
SIRT7
CCDC40
NPLOC4
WDR45L
CBX8
RPTOR
BAHCC1
USP36
RNF213
DUS1L
FN3K
ENGASE
CARD14
C17orf62
CHMP6
FN3KRP
C17orf101
ZNF750
C17orf70
TSPAN10
CBX2
MAFG-AS1
C1QTNF1
PPP1R27
SLC38A10
TBC1D16
C17orf56
B3GNTL1
RBFOX3
NOTUM
STRA13
LRRC45
MYADML2
NPB
CCDC57
HEXDC
SLC26A11
ENDOV
C17orf89
LINC00482
TMEM105
METRNL
ENPP7
C17orf90
CCDC137
ARL16
FAM195B
AATK-AS1
FLJ43681
TEX19
FLJ90757
MIR338
MIR657
LOC100294362
MIR1250
MIR3065
MIR3186
LOC100507410
MIR4739
MIR4740
MIR4730
LOC100653515

Genes in Wide Peak

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

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

Genes
FHIT
MITF
FOXP1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
ARF4
C3orf51
DNASE1L3
EPHA3
FLNB
GBE1
GPR27
HTR1F
CNTN3
PDHB
POU1F1
PROS1
PTPRG
ROBO1
ROBO2
ATXN7
TMF1
WNT5A
SLMAP
ACOX2
CGGBP1
CADPS
SUCLG2
HESX1
UBA3
MAGI1
PSMD6
ARL6IP5
RPP14
FAM107A
PDZRN3
FRMD4B
FAM208A
RYBP
CHMP2B
LRIG1
ERC2
APPL1
ARHGEF3
IL17RD
PXK
FEZF2
EBLN2
SHQ1
ZNF654
CACNA2D3
LMOD3
ADAMTS9
ABHD6
LRTM1
C3orf14
PROK2
THOC7
ID2B
KBTBD8
SLC25A26
FAM3D
C3orf49
SNTN
SYNPR
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
ARL13B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
C3orf64
C3orf38
CCDC66
LOC285401
EIF4E3
SPATA12
VGLL3
LOC401074
FAM19A1
STX19
LOC440970
FLJ20518
FAM86DP
MIR548A2
GXYLT2
ESRG
ZNF717
LOC100287879
FRG2C
MIR1284
MIR1324
MIR3136
MIR4272
MIR4273
MIR3938
LOC100506994
LOC100507062
ADAMTS9-AS2
MIR4795
MIR4444-1
LOC100652759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.1.

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

Genes
CARS
FANCF
HRAS
LMO1
NUP98
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
SERGEF
OR5E1P
OR10A3
FXC1
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
LIN7C
LGR4
PIDD
KCNQ1DN
SOX6
PARVA
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
NAV2
SYT8
CCDC34
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
NS3BP
METTL15
OR56B4
ANO5
LOC255512
OR52B2
C11orf35
OR51F1
SVIP
MRGPRX1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
B7H6
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
NAV2-AS4
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
LOC494141
BDNF-AS1
MIR483
SNORA3
SNORA52
LOC644656
RASSF10
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
MIR610
INS-IGF2
MUC5B
LOC729013
MIR675
LOC100126784
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
LOC100500938
MIR210HG
LOC100506305
LOC100506540
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR4694
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

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

Genes
BRCA2
CDX2
FLT3
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
CDK8
FGF9
FLT1
GJA3
GJB2
GPR12
GTF3A
HMGB1
PDX1
MAB21L1
SMAD9
MIPEP
PABPC3
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TRPC4
TUBA3C
ZMYM2
IFT88
CCNA1
MTMR6
DCLK1
ZMYM5
KL
NUPL1
FRY
USPL1
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
EXOSC8
PDS5B
SPG20
MTUS2
SACS
LATS2
SNORD102
NBEA
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
PSPC1
TNFRSF19
FAM48A
CENPJ
RNF17
XPO4
MRP63
PROSER1
KATNAL1
C13orf33
STARD13
N4BP2L1
TPTE2
CG030
CSNK1A1L
RXFP2
TEX26
B3GALTL
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
ZDHHC20
PAN3
PHF2P1
SLC46A3
ANKRD20A9P
C1QTNF9
FREM2
LINC00442
TPTE2P6
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERTM1
LINC00547
ATP5EP2
LOC440131
C1QTNF9B-AS1
SNORA27
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
CCDC169
ANKRD26P3
RPL21P28
LINC00426
LINC00421
PAN3-AS1
MIR548F5
MIR2276
LINC00327
TEX26-AS1
SPG20OS
CCDC169-SOHLH2
MIR4499

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
FAM19A5
LOC284933
MIR3201
MIR4535

Genes in Wide Peak

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

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

Genes
RPA4

Genes in Wide Peak

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

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

Genes
CDH11
CYLD
HERPUD1
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
ADCY7
AMFR
BBS2
CBLN1
CDH8
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
PHKB
POLR2C
RBL2
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC12A3
GPR56
N4BP1
NUP93
IRX5
DNAJA2
KATNB1
ZNF267
NUDT21
CNOT1
ZNF423
RPGRIP1L
ARL2BP
ORC6
TP53TG3
DKFZP434H168
TOX3
CCDC113
C16orf80
BRD7
PLLP
CES1P1
LPCAT2
HEATR3
SLC38A7
OGFOD1
DOK4
VPS35
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
FTO
IRX6
IRX3
C16orf57
SHCBP1
SETD6
FAM192A
CHD9
ITFG1
NETO2
LONP2
NLRC5
CCDC135
CAPNS2
MT4
GPT2
ABCC11
NKD1
RSPRY1
MYLK3
CCDC102A
ABCC12
C16orf78
ANKRD26P1
SNX20
LOC146481
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
LOC283856
LOC283914
MT1DP
TEPP
SLC6A10P
C16orf87
LOC388276
LOC390705
CES1P2
FLJ26245
MIR138-2
HERC2P4
UBE2MP1
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
LINC00273
TP53TG3C
SNORA46
SNORA50
LOC729264
TP53TG3B
LOC100130700
MIR3935
LOC100505619
LOC100507577
MIR548AE2

Genes in Wide Peak

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

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

Genes
BUB1B
TCF12
FLJ27352
C15orf55
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
ACTC1
ADAM10
AQP9
B2M
BNIP2
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ONECUT1
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
MYO1E
MYO5A
NEDD4
PLCB2
MAPK6
RAB27A
RAD51
SLC12A1
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
CEP152
MAPKBP1
GOLGA8A
RTF1
MGA
DMXL2
VPS39
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PYGO1
PLDN
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
PPP1R14D
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
LDHAL6B
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145663
FAM81A
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
FAM98B
PLA2G4D
GLDN
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
HSP90AB4P
MIR626
MIR627
MIR628
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100129387
LOC100131089
ANKRD63
LOC100132724
JMJD7
PLA2G4B
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR2116
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4510
MIR4716
MIR4713
MIR4712
MYZAP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q34.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
TFEC
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
NAA38
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

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

Genes
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
ANGPT2
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
CLN8
MSRA
TNKS
MYOM2
DLGAP2
MFHAS1
ARHGEF10
KBTBD11
SPAG11B
FBXO25
PINX1
AGPAT5
DEFB103B
CSMD1
MCPH1
PPP1R3B
SOX7
ERI1
RP1L1
CLDN23
DEFB104A
LOC157273
SGK223
LOC157627
C8orf42
ERICH1
ZNF596
DEFT1P
PRSS55
C8orf74
DEFB105A
DEFB106A
DEFB107A
FLJ10661
LOC286083
LOC349196
XKR5
MIR124-1
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
DEFB107B
DEFB104B
DEFB106B
DEFB105B
DEFB109P1B
RPL23AP53
FAM90A14
SPAG11A
MIR596
MIR597
DEFA1B
FAM90A20
FAM90A19
FAM66B
ZNF705G
FAM66E
LOC100132396
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR4659A
MIR4660
MIR4659B
LOC100652791

Genes in Wide Peak

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

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

Genes
ERCC2
KLK2
PPP2R1A
TFPT
ZNF331
hsa-mir-1274b
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
A1BG
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
CKM
AP2S1
CRX
DBP
DMPK
DMWD
EMP3
ERCC1
ETFB
FCAR
FCGRT
FKBP1AP1
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
RPS5
RPS9
RPS11
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SYT5
TNNI3
TNNT1
TULP2
NR1H2
VASP
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF175
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
UBE2M
CYTH2
ZNF264
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
FBXO46
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
CABP5
SPHK2
MEIS3
SLC17A7
NAT14
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
RSPH6A
ZNF611
MED25
BCL2L12
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
ZNF616
ZNF766
EXOC3L2
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
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
IGFL1
ZNF773
LOC386758
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF321P
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
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
LOC646862
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
SGK110
BSPH1
LOC100131691
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
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
MIR3191
MIR3190
MIR320E
MIR4324
MIR642B
LOC100505681
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4751

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.2.

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

Genes
IRF4
DEK
hsa-mir-548a-1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
GPLD1
HIVEP1
ID4
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
ALDH5A1
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
FAM65B
KIAA0319
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
GFOD1
ELOVL2
CDKAL1
PAK1IP1
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
MUTED
CCDC90A
KIF13A
TXNDC5
C6orf62
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
PIP5K1P1
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
RNF144B
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
KAAG1
NHLRC1
PSMG4
DKFZP686I15217
FLJ23152
LINC00340
C6orf201
ERVFRD-1
PPP1R3G
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

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

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

Genes
HRH2

Genes in Wide Peak

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

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

Genes
SMAD4

Genes in Wide Peak

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

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

Genes
hsa-mir-4327
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
APP
ATP5J
BACH1
BAGE
CXADR
GABPA
GRIK1
NCAM2
TMPRSS15
SOD1
HSPA13
TIAM1
TPTE
NRIP1
CLDN8
ADAMTS1
URB1
RWDD2B
USP16
CCT8
BTG3
ADAMTS5
LTN1
CLDN17
N6AMT1
USP25
HUNK
RBM11
MIS18A
LINC00158
CHODL-AS1
LINC00113
C21orf15
LINC00308
MRPL39
C21orf91
MRAP
C21orf7
SCAF4
JAM2
SAMSN1
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
MIR155HG
CYYR1
LINC00161
KRTAP13-1
CHODL
ANKRD30BP2
LIPI
ABCC13
LINC00189
C21orf91-OT1
LINC00314
KRTAP15-1
D21S2088E
LINC00307
LINC00515
KRTAP13-4
POTED
KRTAP7-1
KRTAP8-1
KRTAP11-1
KRTAP19-1
KRTAP13-2
KRTAP13-3
KRTAP23-1
KRTAP6-1
KRTAP6-2
KRTAP6-3
KRTAP19-2
KRTAP19-3
KRTAP19-4
KRTAP19-5
KRTAP19-6
KRTAP19-7
KRTAP20-1
KRTAP20-2
KRTAP21-1
KRTAP21-2
KRTAP22-1
KRTAP20-3
LOC339622
LINC00317
LINC00320
LOC388813
LINC00478
KRTAP26-1
ANKRD20A11P
MIRLET7C
MIR125B2
MIR155
MIR99A
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
KRTAP19-8
KRTAP25-1
TEKT4P2
KRTAP20-4
KRTAP22-2
KRTAP21-3
GRIK1-AS2
MIR4327
MIR3156-3
MIR3687
MIR3648
C21orf37
LINC00159
MIR4759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

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

Genes
BCL9
NOTCH2
NRAS
BCL10
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FCGR1B
FMO5
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
TTF2
ITGA10
LMO4
CDC14A
RTCD1
PEX11B
FUBP1
SLC16A4
CD101
SEP15
ARHGAP29
SEC22B
CHD1L
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
CD160
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
PTPN22
PHGDH
SNORA66
CHIA
RNF115
GPSM2
SLC25A24
DNTTIP2
TMED5
BOLA1
SH3GLB1
HAO2
ACP6
SNX7
GPR89B
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
FAM91A2
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
GPR61
REG4
SYDE2
ZNF644
LRRC8C
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
NEXN
DNAJA1P5
HENMT1
GNRHR2
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LRRC39
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
HFE2
ANKRD35
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
PPIAL4A
HFM1
UBL4B
PDIA3P
ALG14
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
ZNF326
BTBD8
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
FAM73A
LOC375010
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
NBPF9
MIR137
MIR197
C1orf180
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
PGCP1
GEMIN8P4
RBMXL1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC646626
EMBP1
SRGAP2P2
LOC648740
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
MIR548D1
MIR553
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130000
LOC100131564
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q22.3.

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

Genes
APC
IL6ST
PIK3R1
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
ALDH7A1
BHMT
BTF3
CAMK4
CAST
CCNB1
CCNH
CDK7
CDO1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
COX7C
CRHBP
HAPLN1
CSF2
CSNK1G3
VCAN
DMXL1
DHFR
EFNA5
F2R
F2RL1
F2RL2
FBN2
FER
FOXD1
GDF9
GLRX
GTF2H2
GZMA
GZMK
HEXB
HINT1
HMGCR
HSD17B4
HSPA4
HTR1A
IL3
IL4
IL5
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNN2
KIF2A
TNPO1
LMNB1
LNPEP
LOX
CD180
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
PAM
PCSK1
PDE4D
PGGT1B
PMCHL2
PPIC
PPP2CA
RAD17
RASA1
RASGRF2
RPS23
SKP1
SLC12A2
SLC22A4
SLC22A5
SMN1
SMN2
SNX2
SRP19
TAF9
TBCA
TCF7
NR2F1
THBS4
UBE2B
VDAC1
XRCC4
ST8SIA4
REEP5
SERF1A
ENC1
AP3B1
PDLIM4
PPAP2A
PDE8B
P4HA2
HSPB3
ATG12
NREP
RAB9BP1
HOMER1
SCAMP1
CARTPT
SNCAIP
TTC37
ZFYVE16
PJA2
EDIL3
COL4A3BP
RAD50
LHFPL2
CWC27
CCNO
NSA2
FST
POLR3G
PLK2
IQGAP2
SMA4
SMA5
ESM1
KIF3A
ADAMTS6
RHOBTB3
ELL2
SV2C
FSTL4
MRPS27
SEPT8
PPIP5K2
ACSL6
PHF15
PPWD1
OTP
SKIV2L2
SSBP2
BHMT2
TNFAIP8
PART1
FAM169A
RNU5E-1
RNU5D-1
UQCRQ
AFF4
DIMT1
SLC27A6
SNX24
DMGDH
TMED7
ISOC1
IPO11
CDKL3
GCNT4
PRR16
COMMD10
POLK
RAPGEF6
ERAP1
PHAX
PELO
DHX29
FLJ11235
DDX4
SGTB
ARL15
ZCCHC10
GIN1
AGGF1
WDR41
TRIM36
RIOK2
DEPDC1B
BDP1
ERBB2IP
FEM1C
C5orf15
CDC42SE2
NLN
ZNF608
SEMA6A
ARRDC3
ZSWIM6
ANKRA2
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PARP8
ANKRD55
MCTP1
PTCD2
ELOVL7
C5orf44
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
MEGF10
SPZ1
TSLP
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
NDUFAF2
MRPS36
ATP6AP1L
PRDM6
FTMT
FNIP1
SNX18
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
LEAP2
C5orf35
IL31RA
EMB
SLCO6A1
PRRC1
JMY
ZNF474
POU5F2
TMEM171
TMEM174
POC5
STARD4
WDR36
ACOT12
SOWAHA
SHROOM1
SREK1
SLC38A9
CEP120
TMEM167A
MBLAC2
TMEM161B
SRFBP1
MARVELD2
ARSK
FAM81B
CCDC112
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
CCDC125
C5orf27
GAPT
CMYA5
AQPEP
ANKRD31
SERINC5
LOC257396
KIAA0825
GPR150
DTWD2
NBPF22P
C5orf64
RNF180
SREK1IP1
RGMB
RFESD
CHSY3
FAM170A
ANKRD34B
IDAS
ACTBL2
FAM174A
MTX3
HCN1
SLCO4C1
TICAM2
MAST4
RNF138P1
C5orf48
RGS7BP
C5orf63
MIR9-2
CRSP8P
FLJ42709
C5orf56
GPX8
FLJ35946
LOC553103
MIR449A
CTXN3
LOC642366
TMEM232
C5orf43
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR449B
MIR581
MIR583
GTF2H2C
LOC728342
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
LRRC70
LOC100131067
FAM159B
LOC100133050
LOC100170939
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR1244-2
MIR4280
MTRNR2L2
MIR3607
MIR3660
MIR3936
MIR3661
LOC100505678
LOC100505841
LOC100505894
OCLN
MIR4804
MIR4633
MIR3977
MIR4460
MIR4803

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
MIR744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.3.

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.3.

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

Genes
PTPN13

Arm-level results

Table 3. Get Full Table Arm-level significance table - 24 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	0.32	5.86	2.36e-08	0.06	-3.55	1
1q	1955	0.48	11.6	0	0.08	-2.51	1
2p	924	0.23	1.31	0.38	0.08	-3.58	1
2q	1556	0.13	-1.75	1	0.15	-1.1	1
3p	1062	0.25	1.89	0.147	0.41	7.53	3.29e-13
3q	1139	0.61	14.7	0	0.23	1.18	0.282
4p	489	0.06	-3.87	1	0.43	8.22	4.44e-15
4q	1049	0.06	-4.1	1	0.31	4.3	4.82e-05
5p	270	0.34	4.41	3.47e-05	0.17	-1.14	1
5q	1427	0.16	-0.853	1	0.25	2.36	0.0264
6p	1173	0.20	0.625	0.887	0.20	0.625	0.56
6q	839	0.14	-1.5	1	0.29	3.47	0.00115
7p	641	0.13	-2.34	1	0.10	-3.12	1
7q	1277	0.12	-2.19	1	0.17	-0.579	1
8p	580	0.19	-0.263	1	0.35	5.19	9.02e-07
8q	859	0.29	3.26	0.00323	0.14	-1.72	1
9p	422	0.18	-0.798	1	0.23	1.03	0.337
9q	1113	0.18	-0.396	1	0.20	0.395	0.66
10p	409	0.09	-3.38	1	0.24	1.38	0.21
10q	1268	0.05	-4.23	1	0.26	2.84	0.00808
11p	862	0.05	-4.24	1	0.34	5.18	9.02e-07
11q	1515	0.06	-3.65	1	0.40	8	1.33e-14
12p	575	0.19	-0.109	1	0.15	-1.5	1
12q	1447	0.15	-0.977	1	0.06	-4.08	1
13q	654	0.11	-2.7	1	0.31	3.79	0.000379
14q	1341	0.15	-1.04	1	0.13	-1.85	1
15q	1355	0.20	0.68	0.887	0.16	-0.603	1
16p	872	0.16	-1.24	1	0.15	-1.55	1
16q	702	0.13	-2.1	1	0.17	-0.694	1
17p	683	0.08	-3.34	1	0.33	4.72	7.99e-06
17q	1592	0.16	-0.562	1	0.12	-2.03	1
18p	143	0.16	-1.57	1	0.22	0.537	0.591
18q	446	0.10	-3.13	1	0.28	2.85	0.00808
19p	995	0.14	-1.44	1	0.26	2.32	0.0269
19q	1709	0.23	1.8	0.161	0.15	-0.816	1
20p	355	0.36	5.41	2.58e-07	0.12	-2.3	1
20q	753	0.38	6.62	2.45e-10	0.07	-3.63	1
21q	509	0.16	-1.26	1	0.18	-0.641	1
22q	921	0.15	-1.25	1	0.26	2.5	0.02
Xq	1312	0.13	-1.67	1	0.25	2.48	0.02

Methods & Data

Input

Description

Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).
Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).
Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.
CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End
Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.
Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.
Confidence Level: Confidence level used to calculate the region containing a driver.
Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.
Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).
Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/CESC-TP/9824476/GDAC_MergeDataFiles_9825750/CESC-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
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 206 Input Tumor Samples.

Tumor Sample Names
TCGA-BI-A0VR-01A-11D-A10T-01
TCGA-BI-A0VS-01A-11D-A10T-01
TCGA-BI-A20A-01A-11D-A14V-01
TCGA-C5-A0TN-01A-21D-A14V-01
TCGA-C5-A1BE-01B-11D-A13V-01
TCGA-C5-A1BF-01B-11D-A13V-01
TCGA-C5-A1BI-01B-11D-A13V-01
TCGA-C5-A1BJ-01A-11D-A13V-01
TCGA-C5-A1BK-01B-11D-A13V-01
TCGA-C5-A1BL-01A-11D-A13V-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:

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)

[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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