Copy number analysis (GISTIC2)
Cervical Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C16Q1V71
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C16Q1V71
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 126 tumor samples used in this analysis: 23 significant arm-level results, 24 significant focal amplifications, and 28 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 - 24 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 | 4.1968e-20 | 1.1938e-16 | chr11:101685753-102266642 | 6
20q11.21 | 3.6301e-08 | 3.6301e-08 | chr20:29882209-30356590 | 17
3q26.2 | 1.1241e-13 | 6.5464e-08 | chr3:165509242-174622217 | 43
8q24.21 | 1.5117e-06 | 3.8454e-05 | chr8:128754838-128766079 | 0 [MYC]
13q22.1 | 8.0892e-05 | 8.0892e-05 | chr13:73913670-73956005 | 0 [KLF5]
3q28 | 4.1883e-14 | 0.00010918 | chr3:165509242-198022430 | 229
9p24.1 | 0.00011124 | 0.00011124 | chr9:5722416-5791681 | 2
11q13.3 | 6.5284e-05 | 0.0016421 | chr11:69386589-70450687 | 12
19q13.31 | 0.013189 | 0.013189 | chr19:44539543-45458234 | 33
17q25.1 | 0.026413 | 0.026413 | chr17:71814085-74083947 | 74
16p13.13 | 7.682e-05 | 0.031091 | chr16:11889060-11927917 | 2
Xq28 | 0.038184 | 0.038184 | chrX:137483690-155270560 | 209
4q12 | 0.070329 | 0.070329 | chr4:55996856-56580180 | 6
1q44 | 0.021321 | 0.087299 | chr1:224617386-249250621 | 218
2p24.3 | 0.096808 | 0.096808 | chr2:15893634-15902847 | 0 [DDX1]
14q24.1 | 0.16092 | 0.16092 | chr14:68651737-68669044 | 1
1q21.3 | 0.036659 | 0.17411 | chr1:119694388-200336921 | 719
15q26.2 | 0.18584 | 0.18584 | chr15:73811103-102531392 | 283
6q12 | 0.20949 | 0.20949 | chr6:63450050-65454973 | 4
17q12 | 0.20949 | 0.20949 | chr17:37848534-37869191 | 1
2q32.3 | 0.2175 | 0.2175 | chr2:162489153-204085634 | 244
8q24.21 | 0.00035994 | 0.23353 | chr8:120103075-146364022 | 208
6p21.33 | 0.24269 | 0.24269 | chr6:1-38072111 | 520
16p13.2 | 0.0040685 | 0.24269 | chr16:1-18809339 | 307

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's 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 20q11.21.

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

Genes
hsa-mir-3193
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
DEFB118
LINC00028
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
PSIMCT-1
MIR3193

Genes in Wide Peak

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

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

Genes
hsa-mir-569
hsa-mir-551b
BCHE
ECT2
MECOM
GHSR
CLDN11
SERPINI1
SERPINI2
PLD1
PRKCI
SKIL
SLC2A2
TERC
SEC62
TNFSF10
PDCD10
NLGN1
TNIK
GPR160
GOLIM4
MYNN
EIF5A2
NCEH1
SLC7A14
FNDC3B
ZBBX
LRRC31
PHC3
SPATA16
ARPM1
EGFEM1P
WDR49
LRRC34
RPL22L1
NAALADL2
LRRIQ4
SAMD7
TMEM212
LOC646168
MIR551B
MIR569
LOC100128164

Genes in Wide Peak

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

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
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
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
CLDN11
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SKIL
SLC2A2
SST
TERC
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
FYTTD1
ARPM1
MGC2889
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LOC339926
LPP-AS2
LRRIQ4
SAMD7
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
TMEM212
FLJ46066
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
LOC646168
C3orf65
GMNC
LOC647323
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789

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's Cancer Gene Census [7].

Genes
KIAA1432
ERMP1

Genes in Wide Peak

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

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

Genes
CCND1
hsa-mir-548k
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
SHANK2
ANO1
ORAOV1
MIR548K

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.31.

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

Genes
BCL3
CBLC
APOC1
APOC1P1
APOC2
APOC4
APOE
CLPTM1
BCAM
PVR
PVRL2
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF235
TOMM40
ZNF234
ZNF285
CEACAM19
CEACAM20
IGSF23
ZNF284
ZNF233
CEACAM22P
CEACAM16
LOC100379224
APOC4-APOC2
MIR4531

Genes in Wide Peak

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

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

Genes
ACOX1
CDK3
EVPL
FDXR
GALK1
GRB2
GRIN2C
H3F3B
ICT1
ITGB4
LLGL2
RPL38
SUMO2
SRP68
GALR2
SLC16A5
SLC9A3R1
RECQL5
KIAA0195
ATP5H
CD300C
CD300A
GGA3
EXOC7
KCTD2
WBP2
NAT9
SAP30BP
NT5C
CDR2L
MRPS7
HN1
TMEM104
GPRC5C
MIF4GD
CASKIN2
SLC25A19
DNAI2
MRPL38
ARMC7
NUP85
MYO15B
MGC16275
FBF1
UNK
TRIM47
OTOP2
TTYH2
USH1G
CD300LB
KIF19
CD300LF
C17orf77
TRIM65
UNC13D
LINC00469
FADS6
C17orf28
TSEN54
RAB37
CD300E
OTOP3
GPR142
ZACN
BTBD17
C17orf109
C17orf110
CD300LD
TEN1
LOC100287042
MIR3678
MIR3615
TEN1-CDK3
MIR4738

Genes in Wide Peak

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

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

Genes
ZC3H7A
BCAR4

Genes in Wide Peak

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

Table S10. Genes in bold are cancer genes as defined by The Sanger Institute's 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
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
FGF13
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
MCF2
MECP2
MPP1
MTM1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
FAM50A
CXorf1
GPR50
MAGEC1
MAMLD1
BCAP31
SPRY3
ZNF275
TREX2
LDOC1
SRPK3
SNORA70
PNMA3
SPANXA1
CTAG2
NSDHL
MAGEC2
TMLHE
PLXNA3
HAUS7
GABRQ
PDZD4
FAM3A
SPANXD
SPANXC
FUNDC2
PRRG3
BRCC3
CD99L2
H2AFB3
TMEM185A
SLITRK2
PNMA6A
FATE1
CXorf40A
FAM58A
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
GAB3
PNCK
ZFP92
CSAG1
FMR1NB
LOC158696
SPANXE
SPANXF1
VMA21
CTAG1A
MAGEA2B
ATP11C
RP1-177G6.2
LINC00204B
CXorf66
UBE2NL
CSAG3
MIR105-1
MIR105-2
SPANXN4
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
CXorf40B
MIR452
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
MIR767
FMR1-AS1
MIR509-2
MIR890
MIR891B
MIR888
MIR892B
MIR509-3
MIR891A
MIR892A
CXorf51A
LOC100129662
HSFX2
LOC100131434
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR320D2
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 4q12.

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute's 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 1q44.

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
CHML
LYST
CHRM3
EPHX1
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
LBR
LGALS8
MTR
NID1
PSEN2
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
LEFTY2
GPR137B
TSNAX
WNT9A
ZNF124
HIST3H3
GNPAT
CDC42BPA
KMO
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
AKT3
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
COG2
RBM34
ABCB10
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
TAF5L
DISC2
DISC1
PYCR2
PPPDE1
SCCPDH
TRIM17
ARID4B
EGLN1
KIAA1383
KIF26B
HEATR1
ZNF692
ENAH
NUP133
ERO1LB
FMN2
ADCK3
ZNF695
GJC2
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
ACBD3
SMYD3
ARV1
JMJD4
C1orf35
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
ZNF496
C1orf198
WNT3A
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf55
CNST
PLD5
C1orf100
IBA57
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf95
FAM89A
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
DUSP5P
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
MIR3123
MIR3124
MIR3620
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427

Genes in Wide Peak

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

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

Genes
RAD51B

Genes in Wide Peak

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

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

Genes
ABL2
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
TPR
PDE4DIP
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
BGLAP
CACNA1E
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
DHX9
DPT
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
F5
F13B
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
NR5A2
DARC
GBA
GBAP1
GJA5
GJA8
GLUL
HDGF
CFH
CFHR1
CFHR2
MR1
HMGCS2
HSD3B1
HSD3B2
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYOC
NCF2
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDC
PDZK1
PFDN2
PIGC
PI4KB
PKLR
PLA2G4A
PRRX1
POU2F1
PPOX
PRKAB2
PSMB4
PSMD4
PTGS2
QSOX1
PTPRC
PEX19
RAB13
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
VPS72
THBS3
TCHH
TNR
TOP1P1
CCT3
TUFT1
TNFSF4
UCK2
USF1
DAP3
NPHS2
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
SELENBP1
TNFSF18
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
XPR1
GPR52
AIM2
RASAL2
ADAMTS4
SEC22B
CHD1L
PRDX6
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
FAM20B
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
CFHR4
CFHR3
OCLM
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
CELF3
PMF1
DUSP12
VPS45
KIAA0907
KIFAP3
ATF6
NMNAT2
POGZ
GLT25D2
RGL1
SYT11
PRRC2C
RPRD2
SMG5
NCSTN
CRB1
GPR161
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
BRP44
OLFML2B
C1orf43
DNM3
TOR1AIP1
CHTOP
PHGDH
LCE2B
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
USP21
CACYBP
SLC39A1
RNF115
KLHL20
LAMTOR2
TMOD4
NME7
CERS2
CRNN
DCAF8
F11R
GLRX2
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
HAO2
ACP6
IER5
UCHL5
C1orf9
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
SWT1
GON4L
GPATCH4
DUSP23
C1orf27
C1orf56
RALGPS2
MSTO1
DARS2
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
C1orf112
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
LHX9
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
KIAA1614
FAM5B
C1orf114
SLAMF7
CADM3
PRUNE
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
TOR3A
RFWD2
RGS18
MRPL9
INTS3
SCNM1
MGC4473
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
C1orf129
TARS2
EDEM3
FLAD1
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
ISG20L2
FCRL5
FCRL4
NUF2
HMCN1
REG4
C1orf49
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
FCRLA
ANKRD36BP1
MAEL
RGS8
SEC16B
AQP10
LHX4
SLAMF9
PYGO2
ZNF697
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
AXDND1
HIST2H3C
ATP6V1G3
OR10J5
DCST2
ZNF648
TEDDM1
UHMK1
FCRLB
LIX1L
HSD3BP4
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
NEK7
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
FAM163A
LELP1
RC3H1
DCST1
METTL11B
FAM78B
BNIPL
LRRC71
PYHIN1
DENND1B
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
FLJ23867
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
SLC9A11
NBPF15
ANKRD34A
RUSC1-AS1
LOC284648
DKFZP564C196
C1orf204
C1orf111
LOC284688
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
ANKRD45
FAM5C
C1orf110
FAM58BP
OR10R2
FCRL6
KCNT2
NBPF7
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
CYCSP52
LOC375010
PEAR1
SFT2D2
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
C1orf220
NBPF9
APOBEC4
MIR181B1
MIR199A2
MIR181A1
MIR214
MIR9-1
RGS21
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
OR10J3
KPRP
LCE6A
SUMO1P3
C1orf98
HIST2H4B
PRR9
MIR488
SNORD74
RPL31P11
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA3
SCARNA4
SNORA42
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
LOC730102
LOC730159
PPIAL4E
PFN1P2
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131234
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
GM140
LOC100288079
LOC100289211
MIR1278
MIR1295A
MIR548F1
LOC100302401
MIR3119-1
MIR3120
MIR4257
MIR3119-2
MIR4258
MIR3121
MIR3658
LOC100505633
LOC100505666
LOC100505795
LOC100505918
LOC100506023
LOC100506046
PMF1-BGLAP
LOC100527964
TNFAIP8L2-SCNM1
MIR4424
MIR4735
MIR4654
DNM3OS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.2.

Table S15. Genes in bold are cancer genes as defined by The Sanger Institute's 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
ACAN
ALDH1A3
ANPEP
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
FES
IDH3A
IGF1R
IL16
IREB2
ISG20
ISLR
LOXL1
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
NMB
FURIN
PCSK6
PDE8A
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
SCAMP2
SNUPN
TSPAN3
AP3S2
HMG20A
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
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
MESP1
UNC45A
C15orf39
RGMA
WDR93
C15orf17
ADAMTSL3
KIAA1199
ALPK3
ISLR2
FAM108C1
MESDC1
PPCDC
STRA6
KLHL25
CPEB1
AEN
ISL2
TTC23
MRPS11
EFTUD1
NEIL1
LRRK1
LMAN1L
PEAK1
CCDC33
EDC3
AGSK1
TM2D3
WDR61
CD276
STARD5
C15orf5
FAM103A1
MEX3B
LINGO1
WDR73
UBL7
C15orf42
RCCD1
LOC91450
ARRDC4
LOC91948
UBE2Q2
C15orf40
TARSL2
LRRC28
C15orf27
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
NRG4
LINC00052
C15orf26
TBC1D21
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
CERS3
LOC253044
LOC254559
SNX33
C15orf60
C15orf37
LOC283688
LOC283692
LOC283693
FAM154B
LOC283731
LOC283738
LOC283761
FAM169B
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
MIR631
LOC727849
LOC727915
ASB9P1
LOC729739
LOC729911
FAM138E
DNM1P35
UBE2Q2P3
UBE2Q2P2
LOC100144604
GPCRLTM7
DDX11L1
LOC100287616
DDX11L9
MIR1276
MIR1179
MIR1469
MIR3175
MIR4313
RPS17L
LOC100505679
LOC100506874
LOC100507217
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
MIR4514
MIR4513
MIR3529
MIR4515
MIR4714

Genes in Wide Peak

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

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

Genes
PTP4A1
PHF3
LGSN
EYS

Genes in Wide Peak

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

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

Genes
ERBB2

Genes in Wide Peak

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

Table S18. Genes in bold are cancer genes as defined by The Sanger Institute's 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
DPP4
FAP
FRZB
GAD1
GALNT3
GCG
MSTN
GLS
GRB14
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HSPD1
HSPE1
INPP1
ITGA6
ITGA4
ITGAV
LRP2
MYO1B
NAB1
NDUFB3
NEUROD1
ORC2
PDE1A
PDK1
PLCL1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SP3
SSB
SSFA2
STAT1
STAT4
TFPI
TTN
SUMO1
WIPF1
FZD7
SDPR
HAT1
AGPS
PRKRA
SLC25A12
ABCB11
B3GALT1
CFLAR
STK17B
GTF3C3
PPIG
CIR1
BZW1
TLK1
DHRS9
CALCRL
KBTBD10
UBE2E3
MTX2
NCKAP1
RAPGEF4
COBLL1
SATB2
SF3B1
TMEFF2
GCA
MOB4
GORASP2
SPATS2L
HIBCH
STK39
METTL5
OLA1
SLC40A1
PDE11A
GULP1
NOP58
FKBP7
ZAK
PPIL3
DNAJC10
ASNSD1
MFSD6
FIGN
STRADB
WDR12
ZC3H15
DNAH7
SLC39A10
SLC4A10
SPC25
HECW2
ALS2
CWC22
G6PC2
MPP4
NIF3L1
PCGEM1
IFIH1
OSGEPL1
OBFC2A
CDK15
TMEM237
NBEAL1
CFLAR-AS1
PLEKHA3
TRAK2
BOLL
C2orf47
SCRN3
FASTKD1
ALS2CR8
TTC21B
METTL8
CYBRD1
CSRNP3
PGAP1
DCAF17
COQ10B
KIAA1715
CDCA7
WDR75
C2orf88
KCNH7
LOC91149
SESTD1
ANKRD44
ZNF804A
TTC30A
MARS2
ORMDL1
OSBPL6
NOSTRIN
DIRC1
NUP35
XIRP2
TYW5
RBM45
BBS5
C2orf77
ICA1L
RFTN2
UBR3
KCTD18
ALS2CR12
MYO3B
DUSP19
FLJ32063
ANKAR
TTC30B
FAM117B
ZSWIM2
ZNF385B
KLHL23
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
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
SNORA70F
MIR3128
MIR3129
MIR3606
LOC100505695
LOC100506124
LOC100506134
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 8q24.21.

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

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

Genes in Wide Peak

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

Table S20. Genes in bold are cancer genes as defined by The Sanger Institute's 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 16p13.2.

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

Genes
TNFRSF17
CREBBP
ERCC4
CIITA
MYH11
TSC2
SOCS1
hsa-mir-3179-3
hsa-mir-3180-2
hsa-mir-484
hsa-mir-1972-1
hsa-mir-3180-1
hsa-mir-365-1
hsa-mir-548h-2
hsa-mir-3178
hsa-mir-940
hsa-mir-1225
hsa-mir-3177
hsa-mir-662
hsa-mir-3176
ABAT
ABCA3
ADCY9
ABCC6
ARHGDIG
ATP6V0C
CCNF
CLCN7
ECI1
DNASE1
DNASE1L2
E4F1
EMP2
GFER
GRIN2A
GSPT1
HAGH
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
IGFALS
MEFV
MPG
ABCC1
NUBP1
NDUFB10
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PARN
PDPK1
PKD1
PMM2
PPL
PRM1
PRM2
RPL3L
RPS2
RPS15A
SRL
SOLH
SSTR5
TCEB2
TFAP4
TNP2
TPSAB1
UBE2I
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
USP7
NPRL3
SNN
AXIN1
PLA2G10
RGS11
CACNA1H
BAIAP3
RHBDL1
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
SYNGR3
IL32
NPIP
SLC9A3R2
LITAF
KIAA0430
SEC14L5
RAB11FIP3
IFT140
TELO2
NUBP2
ZNF263
TRAP1
MSLN
STUB1
MRPL28
TBL3
RNPS1
PRSS21
PDXDC1
CLUAP1
MAPK8IP3
ARL6IP1
CLEC16A
MGRN1
NOMO1
TPSD1
SRRM2
CARHSP1
TPSG1
RAB26
TMEM186
ZNF500
DECR2
RSL1D1
OR1F2P
SNORA64
SNORD60
DEXI
C16orf72
ZC3H7A
UBN1
C16orf5
SOX8
AMDHD2
PAM16
TXNDC11
NAGPA
BFAR
TNFRSF12A
POLR3K
SEPX1
GNG13
KCTD5
RRN3
RBFOX1
NDE1
ZNF434
HCFC1R1
CPPED1
LUC7L
ALG1
NMRAL1
TBC1D24
MKL2
CASKIN1
CRAMP1L
RAB40C
PRM3
TMEM8A
CHTF18
PRSS22
XYLT1
MLST8
RHBDF1
MMP25
NARFL
LINC00235
TPSB2
HS3ST6
PDIA2
UNKL
LINC00254
LMF1
FAM173A
MRPS34
METRN
METTL22
THOC6
KREMEN2
CORO7
SNRNP25
ROGDI
TMEM204
NAA60
ATF7IP2
C16orf59
MGC3771
FAHD1
PRSS27
ITFG3
WDR24
TRAF7
FLYWCH1
HAGHL
NUDT16L1
C16orf13
FAM195A
SLX4
GNPTG
GLYR1
GLIS2
ZSCAN10
C16orf45
RHOT2
ZNF598
HN1L
SPSB3
TIGD7
SNX29
RPUSD1
FLYWCH2
VASN
C16orf42
RMI2
WFIKKN1
NTAN1
FOPNL
NOXO1
CCDC78
ZG16B
PRSS30P
PAQR4
ANKS3
FAM100A
SEPT12
TEKT5
RNF151
C16orf11
FBXL16
LOC146336
ZNF597
CCDC64B
C16orf89
C16orf71
FAM86A
WDR90
EME2
NLRC3
C16orf73
MPV17L
PRSS33
NOMO2
NPW
C16orf79
PGP
LINC00514
FLJ39639
NHLRC4
C16orf91
TMEM114
PKD1P1
JMJD8
C16orf96
PRSS41
PRR25
C1QTNF8
PTX4
BCAR4
MSLNL
NOMO3
LOC440335
SNORA10
MIR193B
MIR484
FLJ42627
CCDC154
C16orf90
ABCA17P
LOC652276
ABCC6P1
SNORA78
MIR662
SHISA9
ABCC6P2
SNHG9
CEMP1
FAM18A
MIR940
MIR365A
LOC100128788
LOC100134368
MIR1225
DDX11L10
MIR3180-3
MIR3180-1
MIR3179-2
MIR548X
MIR3180-2
MIR3179-1
MIR3178
MIR3179-3
MIR3177
MIR3176
MTRNR2L4
MIR3677
MIR3180-4
MIR3180-5
ERVK13-1
LOC100507501
LOC100507589
CORO7-PAM16
MIR4718
MIR4717
MIR4516

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 - 28 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 | 4.2398e-18 | 4.2398e-18 | chr11:133400280-135006516 | 14
2q37.1 | 4.2398e-18 | 5.8439e-15 | chr2:219431536-243199373 | 245
19p13.3 | 4.99e-09 | 4.99e-09 | chr19:1103802-1210605 | 2
4q35.2 | 1.2129e-07 | 3.5505e-07 | chr4:187179487-188227950 | 4
13q13.3 | 4.9455e-07 | 4.6952e-07 | chr13:1-58051240 | 250
2q22.1 | 1.4345e-08 | 1.6025e-06 | chr2:139655617-143637838 | 1
10q23.31 | 0.00063403 | 0.0010717 | chr10:89313008-89621060 | 3
1p36.23 | 0.00075956 | 0.0011751 | chr1:1-28840301 | 471
6q26 | 0.0019703 | 0.0019703 | chr6:146758670-171115067 | 144
Xp11.3 | 0.0032473 | 0.0031981 | chrX:44702452-45008304 | 2
3p11.1 | 0.007507 | 0.0073959 | chr3:53923579-93777876 | 111
14q32.31 | 0.007972 | 0.0079803 | chr14:75748707-107349540 | 326
4q22.1 | 0.012581 | 0.031178 | chr4:90844993-93240505 | 1
6p24.3 | 0.020319 | 0.031178 | chr6:1-12292253 | 79
20p12.1 | 0.036378 | 0.0366 | chr20:13964029-16252980 | 3
15q15.1 | 0.051039 | 0.050497 | chr15:33357233-62146652 | 265
17p12 | 0.050334 | 0.050497 | chr17:1-19642951 | 387
16q23.1 | 0.053728 | 0.053194 | chr16:68869268-90354753 | 221
21q21.1 | 0.074412 | 0.074059 | chr21:1-33641721 | 116
17q25.3 | 0.085057 | 0.08647 | chr17:77084275-81195210 | 96
6p12.1 | 0.059017 | 0.10037 | chr6:38606560-63986983 | 183
11p15.1 | 0.11263 | 0.11456 | chr11:1-31533216 | 383
7q34 | 0.13194 | 0.13221 | chr7:81993261-159138663 | 619
16p11.2 | 0.13131 | 0.13221 | chr16:26148503-71205193 | 401
Xq21.33 | 0.16033 | 0.16504 | chrX:96134519-98718611 | 1
5q14.3 | 0.19455 | 0.18854 | chr5:44813655-137229204 | 419
10q26.3 | 0.12786 | 0.21534 | chr10:89728127-135534747 | 421
1p13.1 | 0.20396 | 0.22502 | chr1:58714075-149898950 | 487

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's Cancer Gene Census [7].

Genes
IGSF9B
NCAPD3
ACAD8
B3GAT1
THYN1
JAM3
GLB1L2
VPS26B
GLB1L3
SPATA19
LOC283174
LOC283177
LOC100128239
MIR4697

Genes in Wide Peak

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

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

Genes
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
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IHH
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
SAG
CCL20
SLC4A3
SP100
SPP2
TUBA4A
WNT6
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
CNPPD1
STK36
GMPPA
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
C2orf83
MFF
CXCR7
RNPEPL1
WDFY1
NYAP2
GAL3ST2
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
DUSP28
ESPNL
ECEL1P2
LOC348761
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
MIR153-1
DNAJB3
MIR375
LOC643387
PRR21
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
LOC100129175
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

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

Genes
F11
FAT1
MTNR1A
LOC285441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.3.

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
XPO4
MRP63
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
CDADC1
CAB39L
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3613
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
PAPSS2
ATAD1
CFL1P1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
AHDC1
SMPDL3B
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
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
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
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 6q26.

Table S30. Genes in bold are cancer genes as defined by The Sanger Institute's 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
RAB32
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
ADGB
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
LOC729176
LOC729178
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 Xp11.3.

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

Table S32. Genes in bold are cancer genes as defined by The Sanger Institute's 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 14q32.31.

Table S33. Genes in bold are cancer genes as defined by The Sanger Institute's 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
hsa-mir-1260
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
ESRRB
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
ALKBH1
MTA1
RPS6KA5
NRXN3
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
BATF
SIVA1
AHSA1
CYP46A1
PAPOLA
PTPN21
C14orf1
VASH1
SNW1
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
FLRT2
KIF26A
C14orf109
PRO1768
GPR132
POMT2
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
ADCK1
TMEM63C
UNC79
BEGAIN
PPP4R4
NGB
C14orf133
MOAP1
DIO3OS
IRF2BPL
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
SLIRP
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
C14orf166B
ISM2
CEP128
TTC7B
C14orf49
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
ZDHHC22
TMED8
C14orf178
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
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392
LOC100628307

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.3.

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

Genes
IRF4
BMP6
BPHL
DSP
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CDYL
LY86
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
NRN1
TMEM14C
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
C6orf195
PIP5K1P1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
PSMG4
DKFZP686I15217
C6orf201
ERVFRD-1
PPP1R3G
HULC
TMEM170B
SCARNA27
LOC100130275
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4645

Genes in Wide Peak

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

Table S36. Genes in bold are cancer genes as defined by The Sanger Institute's 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 15q15.1.

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute's 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
ANXA2
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
RORA
RYR3
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
NARG2
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
TMCO5B
MYZAP

Genes in Wide Peak

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

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

Genes
PER1
MAP2K4
TP53
GAS7
USP6
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
hsa-mir-4314
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ACADVL
ADORA2B
ALDH3A2
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
COX10
CLDN7
CRK
CTNS
DLG4
DNAH9
DPH1
DRG2
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
FOXO3B
FLII
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
LLGL1
MEIS3P1
MFAP4
MNT
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
PMP22
POLR2A
MAPK7
PRPSAP2
PSMB6
RCVRN
RPA1
RPL26
SCO1
SHBG
SHMT1
SLC2A4
SOX15
SREBF1
VAMP2
TOP3A
UBB
UBE2G1
TRPV1
YWHAE
ZNF18
RNF112
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
COPS3
SCARF1
TNK1
MYH13
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
GLP2R
NTN1
STX8
PIGL
RPH3AL
FXR2
MPDU1
SPAG7
NCOR1
CCDC144A
ACAP1
KIAA0753
SGSM2
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
CLEC10A
MYBBP1A
FBXW10
PRPF8
TRIM16
RAI1
KIF1C
GRAP
GABARAP
NLRP1
ARHGEF15
EPN2
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
MPRIP
KIAA0664
SMG6
WSCD1
CTDNEP1
TNFRSF13B
PIK3R5
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
SNORD49A
PELP1
B9D1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
FAM18B1
GLOD4
YBX2
MYO15A
TRPV2
ANKFY1
RASD1
INPP5K
FAM64A
XAF1
C17orf59
ALKBH5
TTC19
GPR172B
MED9
WRAP53
RNMTL1
SLC47A1
VPS53
C17orf85
TSR1
DHX33
NT5M
C17orf48
PLSCR3
ZNF286A
ZNF287
ZNF624
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
ELAC2
SRR
NXN
TEKT3
MIS12
C17orf39
METTL16
PHF23
FAM57A
FAM106A
CTC1
NDEL1
PITPNM3
LRRC48
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
LSMD1
NEURL4
ZNF594
HES7
SPATA22
MGC12916
TXNDC17
MIR22HG
ATPAF2
TMEM88
MYOCD
CDRT7
CDRT15P1
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
DNAH2
RTN4RL1
SLC47A2
CDRT15
WDR16
CCDC42
PIK3R6
ODF4
KCTD11
TRIM16L
MFSD6L
TRPV3
SLC16A11
FBXO39
USP32P1
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
SLC16A13
C17orf74
SPNS3
USP32P2
TBC1D28
C17orf61
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
FLJ34690
CDRT4
CCDC144B
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
LOC339240
SMTNL2
ALOX15P1
TBC1D26
FAM101B
CDRT1
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
SHISA6
FAM211A
OR3A4P
SLC25A35
C17orf97
MED11
KRT16P2
GRAPL
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
PIRT
CDRT15P2
FAM83G
EVPLL
SNORA48
SNORD10
OR1D4
LGALS9C
SCARNA21
SNORA59B
SNORA59A
SNORD49B
SNORD65
SNORD91A
SNORD91B
MIR33B
BHLHA9
TLCD2
LOC728392
ZNF286B
MIR744
LOC100128288
FAM106CP
C17orf107
LOC100130950
DBIL5P
LOC100289255
MIR1288
MIR1253
MIR1180
LOC100306951
MIR3183
MIR4314
MIR3676
LOC100506388
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
FAM18B2-CDRT4
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4731
MIR4520A
MIR4521
MIR4520B

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
AARS
AP1G1
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
NQO1
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HAS3
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
ST3GAL2
SNTB2
SPG7
TAT
TERF2
ZNF19
ZNF23
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
COX4NB
TUBB3
CFDP1
NFAT5
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
ADAT1
CHST5
COG4
CPNE7
VPS4A
IL17C
NOB1
ANKRD11
OSGIN1
NIP7
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
CHTF8
TXNL4B
BANP
PDPR
RFWD3
DDX19A
ZNF821
ZDHHC7
VAC14
FTSJD1
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
PDF
MTHFSD
DBNDD1
FA2H
TMEM231
TMCO7
WDR59
KLHL36
FBXO31
CYB5B
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
COG8
SPIRE2
ZNF469
CIRH1A
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
IL34
TMED6
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
MIR140
CTRB2
CLEC18B
SNORD68
SNORD71
SNORD111
LOC727710
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130894
SYCE1L
LOC100287036
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
LOC100506083
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

Table S40. Genes in bold are cancer genes as defined by The Sanger Institute's 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
RWDD2B
USP16
CCT8
BTG3
ADAMTS5
LTN1
CLDN17
N6AMT1
USP25
HUNK
RBM11
LINC00158
CHODL-AS1
LINC00113
C21orf15
LINC00308
MRPL39
C21orf91
C21orf7
SCAF4
JAM2
SAMSN1
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
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 17q25.3.

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

Genes
ASPSCR1
hsa-mir-3186
hsa-mir-1250
ACTG1
ARHGDIA
CD7
CSNK1D
SLC25A10
FASN
GAA
GCGR
UTS2R
GPS1
FOXK2
MAFG
NPTX1
P4HB
PDE6G
PYCR1
PCYT2
RAC3
RFNG
MRPL12
SECTM1
SGSH
TBCD
CBX4
SLC16A3
HGS
AATK
EIF4A3
ALYREF
BAIAP2
RAB40B
AZI1
FSCN2
NARF
DCXR
ANAPC11
SIRT7
CCDC40
NPLOC4
WDR45L
CBX8
RPTOR
BAHCC1
RNF213
DUS1L
FN3K
CARD14
C17orf62
CHMP6
FN3KRP
C17orf101
ZNF750
C17orf70
TSPAN10
CBX2
MAFG-AS1
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
MIR4739
MIR4740
MIR4730

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
hsa-mir-548u
hsa-mir-133b
hsa-mir-586
CRISP1
BMP5
DST
BYSL
RUNX2
CDC5L
DNAH8
SLC29A1
GCLC
GLO1
GLP1R
GSTA1
GSTA2
GSTA3
GSTA4
GUCA1A
GUCA1B
HCRTR2
HSP90AB1
IL17A
MCM3
MDFI
MEA1
MEP1A
MOCS1
MUT
NFKBIE
NFYA
PEX6
PGC
PGK2
PKHD1
POLH
PPP2R5D
PRIM2
PTK7
PRPH2
RHAG
SRF
TBCC
TFAP2B
CRISP2
VEGFA
PLA2G7
SUPT3H
GCM1
KCNK5
NCR2
MED20
SLC25A27
BAG2
POLR1C
MAD2L1BP
TRAM2
CUL7
RCAN2
CRISP3
C6orf108
CNPY3
FRS3
SLC22A7
APOBEC2
CAPN11
ICK
ENPP4
CUL9
UBR2
DAAM2
KIAA0240
CD2AP
ZNF318
YIPF3
USP49
ZNF451
FBXO9
GNMT
TNFRSF21
TINAG
TMEM14A
PRICKLE4
MRPL2
CYP39A1
RAB23
CLIC5
TREM2
TREM1
HMGCLL1
GTPBP2
CENPQ
MRPS18A
MRPS10
LRRC1
TMEM63B
SAYSD1
TRERF1
LRFN2
AARS2
XPO5
KIAA1586
ENPP5
ELOVL5
MRPL14
DLK2
TREML2
COL21A1
TFAP2D
KCNK16
TTBK1
PAQR8
RRP36
KCNK17
ABCC10
KLC4
MLIP
TJAP1
IL17F
EFHC1
FOXP4
KLHDC3
TAF8
C6orf141
PTCRA
TCTE1
KHDRBS2
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
RSPH9
LRRC73
TREML2P1
LOC221442
C6orf130
KIF6
FAM83B
GPR111
TSPO2
UNC5CL
DEFB110
DEFB112
DEFB113
DEFB114
GPR110
TREML4
RPL7L1
TREML1
TREML3
SLC35B2
GUSBP4
GLYATL3
GFRAL
FLJ41649
CRIP3
KLHL31
DEFB133
MIR206
C6orf226
TMEM151B
ATP6V0CP3
PTCHD4
MIR133B
C6orf132
RPS16P5
MIR586
LOC730101
GSTA7P
TDRG1
LOC100131047
LOC100132354
TOMM6
LOC100287718
MIR4647
MIR4641
MIR4642

Genes in Wide Peak

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

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

Genes
CARS
FANCF
HRAS
LMO1
NUP98
hsa-mir-610
hsa-mir-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
MPPED2
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
FSHB
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
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
DNAJC24
C11orf46
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
IMMP1L
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
DCDC1
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
DCDC5
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR4694
MIR4687

Genes in Wide Peak

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

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

Genes
BRAF
CDK6
EZH2
MET
SMO
AKAP9
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
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
ABP1
ACHE
AKR1B1
ARF5
ASNS
AZGP1
OPN1SW
BPGM
CALCR
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
KRIT1
CDK5
CFTR
CHRM2
AP1S1
CLCN1
COL1A2
CPA1
CPA2
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNB2
GNG11
GNGT1
GPR22
GPR37
GRM3
GRM8
MNX1
AGFG2
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PIP
PMS2P1
PODXL
POLR2J
PON1
PON2
PON3
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
PSMC2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
SRI
AKR1D1
SRPK2
SSBP1
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
ZNF3
ZKSCAN1
ZSCAN21
ZYX
MTERF
SHFM1
TFPI2
ST7
ARHGEF5
ZNF212
TRRAP
FZD1
ZNF282
CUL1
TRIM24
BUD31
SGCE
MGAM
WASL
PLOD3
CLDN12
DGKI
AP4M1
ATP6V1F
ACCN3
PMPCB
ATP5J2
PDIA4
UBE3C
FAM131B
SEMA3E
DOCK4
FAM115A
DMTF1
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
BET1
SEMA3A
FAM3C
COG5
ZNHIT1
ARPC1A
SH2B2
STAG3
CPSF4
FASTK
DBF4
COPS6
DUS4L
ZNF277
ABCB8
TP53TG1
PDAP1
TFEC
LAMB4
LMTK2
PAXIP1
KLHDC10
PEG10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
STEAP1
COPG2
HBP1
DNAJC2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
PCLO
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRB
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
LUC7L2
MRPS33
ASB4
NUB1
NAA38
ADAM22
GPR85
TAS2R5
ANKIB1
CHPF2
PUS7
ING3
LRRN3
CROT
ALKBH4
SAMD9
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
PPP1R9A
CCDC132
AGK
METTL2B
MLL5
BAIAP2L1
SLC25A40
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
GATAD1
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
RABL5
CYP3A43
CASD1
LRRC61
C7orf49
ZNF655
PVRIG
C7orf23
GCC1
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ZNF767
C7orf58
TTC26
ORAI2
JHDM1D
OR2AE1
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
RBM48
ZNF394
MYH16
SLC37A3
KRBA1
FAM71F1
MGC16142
SLC35B4
TMEM209
GTPBP10
TRIM4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
MUC17
RNF32
ASB15
RUNDC3B
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
BHLHA15
ZNF800
GIMAP1
LOC202781
C7orf33
SAMD9L
C7orf62
ZNF804B
FABP5P3
ZNF498
FAM200A
PPP1R35
GPC2
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
UBN2
MBLAC1
FAM133B
TAS2R39
TAS2R40
TAS2R41
STEAP2
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
DLX6-AS1
ZNF789
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
MOGAT3
FAM71F2
STRA8
KLRG2
WDR86
GJC3
DPY19L2P2
LOC349160
GATS
GSTK1
NAT16
SLC26A5
LHFPL3
KCP
FLJ43663
RNF148
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
OR2A5
LRRD1
FLJ42280
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
UFSP1
MIR106B
MIR129-1
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
SPDYE3
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
OR2A2
DPY19L2P4
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR489
MIR490
ZNF862
LOC645249
LOC645591
AZGP1P1
LOC646329
C7orf73
ACTR3C
MIR591
MIR592
MIR593
MIR595
LOC723809
MIR653
LOC728066
LOC728377
LOC728743
SPDYE6
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100129845
LOC100130705
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
LOC100287482
MOXD2P
LOC100289187
LOC100289561
ZNF783
MIR548F3
MIR548I4
SPDYE2L
MIR548F4
SAP25
MIR548T
MIR4285
MTRNR2L6
MIR3609
MIR3907
MIR3666
LOC100505483
LOC100506136
LOC100506585
LOC100507421
ATP5J2-PTCD1
GIMAP1-GIMAP5
MIR4653
MIR4652
MIR4468
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

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

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

Genes
CBFB
CDH1
CDH11
CYLD
FUS
HERPUD1
IL21R
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
hsa-mir-762
AARS
ADCY7
AGRP
ALDOA
AMFR
ATP2A1
BBS2
CA7
CBLN1
CD19
CDH3
CDH5
CDH8
CDH16
CES1
CETP
CLN3
CNGB1
COX6A2
CSNK2A2
CTF1
CTRL
NQO1
SEPT1
DYNC1LI2
E2F4
GNAO1
GOT2
GTF3C1
HAS3
HSD11B2
HSF4
IL4R
ITGAD
ITGAL
ITGAM
ITGAX
KIFC3
KIF22
LCAT
MAZ
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
NFATC3
PHKB
PHKG2
POLR2C
PPP4C
MAPK3
PRSS8
PSKH1
PSMB10
RBL2
RRAD
SALL1
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC5A2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SPN
SULT1A2
STX4
SULT1A1
SULT1A3
TBX6
TERF2
TGFB1I1
TK2
TUFM
DOC2A
HIRIP3
EIF3C
TRADD
CES2
NAE1
NOL3
SLC7A6
ATP6V0D1
BCL7C
GPR56
TAOK2
N4BP1
NUP93
ZNF646
SETD1A
RNF40
MVP
NUTF2
IRX5
DNAJA2
BCKDK
KATNB1
ZNF267
CD2BP2
CDIPT
CTCF
NFAT5
SRCAP
NUDT21
WWP2
CORO1A
DDX19B
ATXN2L
SEPHS2
CNOT1
ZNF423
XPO6
KIAA0556
RPGRIP1L
ZNF629
SF3B3
QPRT
CES3
ARL2BP
ORC6
EDC4
PLA2G15
TP53TG3
COG4
PLEKHG4
SH2B1
TBC1D10B
DKFZP434H168
LRRC29
SEZ6L2
NUPR1
LAT
VPS4A
TOX3
NOB1
CCDC113
TMEM208
C16orf80
PYCARD
FHOD1
BRD7
ZDHHC1
MYLPF
PARD6A
PLLP
CKLF
AHSP
ZNF771
NIP7
FAM96B
TPPP3
CES1P1
PRMT7
FBXL19
DUS2L
CHTF8
LPCAT2
HEATR3
PDPR
SLC38A7
OGFOD1
LRRC36
DDX19A
FBXL8
SMPD3
VAC14
DOK4
VPS35
DDX28
TSNAXIP1
APOBR
COQ9
CIAPIN1
THAP11
PDP2
ZNF319
RANBP10
NOD2
PDF
DPEP2
DPEP3
PAPD5
FBRS
AKTIP
C16orf58
GINS3
NDRG4
ACD
ZNF747
PRR14
VKORC1
SLX1B
FTO
DCTPP1
GDPD3
IRX6
IRX3
C16orf53
FAM65A
TMCO7
C16orf57
ZNF768
ZNF668
ELMO3
ARMC5
SHCBP1
JMJD5
RABEP2
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
HSD3B7
CYB5B
ITFG1
GFOD2
NETO2
SLC7A5P1
YPEL3
FAM57B
LONP2
SPNS1
C16orf48
SLC7A6OS
KAT8
NLRC5
CCDC135
CAPNS2
COG8
MT4
GPT2
B3GNT9
NFATC2IP
CIRH1A
ABCC11
NKD1
RSPRY1
C16orf93
MYLK3
MTSS1L
ZNF764
CCDC102A
ORAI3
ABCC12
PRRT2
STX1B
CCDC101
CMTM1
ZNF689
EXOSC6
NRN1L
CMTM3
C16orf78
ANKRD26P1
ZNF720
TMEM219
SNX20
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
C16orf92
GSG1L
IL34
TMED6
LOC146481
ZNF785
ZNF688
PRSS36
C16orf82
FUK
NSMCE1
ZNF48
CPNE2
GPR114
PRSS54
CES5A
GPR97
IL27
KCTD13
ASPHD1
CNEP1R1
PYDC1
CCDC79
CES4A
EXOC3L1
LOC283856
LOC283867
LOC283888
C16orf54
INO80E
LOC283914
FBXL19-AS1
ZNF843
PDXDC2P
CLEC18C
MT1DP
PRSS53
CLEC18A
TEPP
SLC6A10P
SBK1
LOC388242
C16orf87
LOC388276
C16orf86
LOC390705
CES1P2
FLJ21408
FLJ26245
MIR138-2
MIR140
SNX29P2
LOC440354
LOC440356
CSDAP1
HERC2P4
MIR328
SULT1A4
TRIM72
SLX1A
BOLA2
LOC595101
UBE2MP1
LOC606724
LOC613037
LOC613038
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
LINC00273
KIAA0895L
RRN3P2
TP53TG3C
ZG16
BOLA2B
SNORA30
SNORA46
SNORA50
SNORD111
EIF3CL
LOC729264
TP53TG3B
LOC729513
SNORD111B
LOC100130700
LOC100130894
KIAA0664L3
LOC100289092
MIR1538
MIR1972-1
MIR762
MIR1972-2
MIR3935
LOC100505619
LOC100505865
LOC100506083
LOC100507577
SLX1A-SULT1A3
SLX1B-SULT1A4
CKLF-CMTM1
MIR4519
MIR4721
MIR548AE2
MIR4518
MIR4517

Genes in Wide Peak

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

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

Genes
RPA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q14.3.

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

Genes
APC
IL6ST
PIK3R1
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
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
ALDH7A1
BHMT
BTF3
CAMK4
CAMLG
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
IL9
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNN2
KIF2A
TNPO1
LECT2
LMNB1
LNPEP
LOX
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
NEUROG1
NPY6R
PAM
PCSK1
PDE4D
PGGT1B
PITX1
PMCHL2
PPIC
PPP2CA
RAD17
RASA1
RASGRF2
RPS23
SKP1
SLC12A2
SLC22A4
SLC22A5
SMN1
SMN2
SNX2
SPOCK1
SRP19
TAF9
TBCA
TCF7
NR2F1
TGFBI
THBS4
UBE2B
VDAC1
XRCC4
ST8SIA4
REEP5
SERF1A
ENC1
AP3B1
PDLIM4
PPAP2A
PDE8B
P4HA2
HSPB3
ATG12
NREP
RAB9BP1
HOMER1
MYOT
SCAMP1
CXCL14
H2AFY
SMAD5-AS1
CARTPT
SNCAIP
TTC37
ZFYVE16
PJA2
DDX46
EDIL3
COL4A3BP
RAD50
LHFPL2
CWC27
CCNO
NSA2
FST
POLR3G
PLK2
IQGAP2
SEC24A
HNRNPA0
SMA4
SMA5
ESM1
KIF3A
ADAMTS6
RHOBTB3
ELL2
SV2C
FSTL4
MRPS27
SEPT8
PPIP5K2
ACSL6
PHF15
PPWD1
OTP
SKIV2L2
SSBP2
BHMT2
TNFAIP8
PART1
FAM169A
FBXL21
KLHL3
RNU5E-1
RNU5D-1
UQCRQ
AFF4
DIMT1
SLC27A6
SNX24
DMGDH
TMED7
ISOC1
SAR1B
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
TRPC7
NLN
ZNF608
SEMA6A
ARRDC3
ZSWIM6
ANKRA2
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PARP8
ANKRD55
TXNDC15
MCTP1
PTCD2
ELOVL7
C5orf44
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
PCBD2
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
C5orf24
SREK1
C5orf20
SLC38A9
CEP120
SLC25A48
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
LOC340073
LOC340074
ANKRD34B
IDAS
ACTBL2
FAM174A
MTX3
CATSPER3
HCN1
SLCO4C1
TICAM2
MAST4
RNF138P1
C5orf48
LOC389332
RGS7BP
C5orf63
MIR9-2
CRSP8P
FLJ42709
C5orf56
GPX8
TIFAB
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
VTRNA2-1
MIR874
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
MIR4461
MIR3977
MIR4460
MIR4803

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
FAS
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HELLS
HHEX
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
KIF20B
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
ANKRD1
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
EXOC6
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
OPALIN
SYCE1
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
ANKRD22
SFXN2
PDZD8
C10orf32
NUDT9P1
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
TRUB1
VTI1A
LOC143188
HECTD2
FGFBP3
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
FLJ37201
LOC283038
LOC283089
O3FAR1
KCNK18
LIPM
CYP26C1
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
C10orf62
IFIT1B
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
LIPK
LIPN
LOC643529
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
DUX4L2
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100169752
LOC100188947
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
FAS-AS1
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

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

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

Genes
BCL9
JAK1
JUN
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
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
ABCA4
ACADM
ADORA3
AGL
AK4
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
CTH
CYP2J2
DBT
GADD45A
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
IL12RB2
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
LEPR
TACSTD2
MOV10
MSH4
NFIA
NGF
NHLH2
ROR1
OVGP1
PDE4B
PDZK1
PGM1
PIN1P1
PRKAB2
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPE65
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
USP1
VCAM1
WNT2B
CSDE1
EVI5
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
TTF2
ITGA10
LMO4
CDC14A
RTCD1
FPGT
PEX11B
FUBP1
DIRAS3
SLC16A4
SRSF11
CD101
SEP15
ZRANB2
ARHGAP29
SEC22B
CHD1L
CLCA3P
CLCA2
HS2ST1
DNAJC6
LRIG2
LPPR4
SV2A
RBM8A
INSL5
PIGK
TSPAN2
INADL
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
CD160
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
SLC35D1
LPHN2
KIAA1107
ITGB3BP
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
ZZZ3
SERBP1
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
FOXD3
CHIA
RNF115
ANGPTL3
GPSM2
ALG6
SLC25A24
DNTTIP2
TMED5
BOLA1
TNNI3K
SH3GLB1
HAO2
ACP6
HOOK1
SNX7
GPR89B
DPH5
GPR88
CCDC76
L1TD1
RSBN1
ZNHIT6
LEPROT
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RAVER2
FGGY
MCOLN3
SLC22A15
RNPC3
LRRC40
DEPDC1
LRIF1
CTTNBP2NL
FAM212B
GNG12
CCBL2
TMEM167B
OLFML3
FAM91A2
AMIGO1
ODF2L
KIAA1324
LRRC7
CACHD1
MIER1
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
DLEU2L
EPS8L3
VTCN1
TTLL7
WDR78
RPAP2
DENND2D
WLS
RPF1
SIKE1
TRIM45
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
TM2D1
REG4
SYDE2
ZNF644
LRRC8C
SGIP1
POLR3GL
PROK1
EFCAB7
PSRC1
ATP1A1OS
ATG4C
FAM40A
DOCK7
ZNF697
NEXN
DNAJA1P5
HENMT1
MYSM1
GNRHR2
OMA1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
C1orf87
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
UBE2U
HFE2
ANKRD35
SLC30A7
MGC27382
IL23R
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
KANK4
SASS6
PPIAL4A
HFM1
UBL4B
PDIA3P
ALG14
LINC00466
NBPF11
NUDT17
TCTEX1D1
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
NEGR1
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
C1orf141
GBP1P1
FLJ27354
MIR137HG
NBPF9
MIR101-1
MIR137
MIR186
MIR197
LHX8
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
SNORD45C
MIR548D1
MIR553
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
HSD52
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130000
LOC100131060
LOC100131564
NBPF10
FCGR1C
ZRANB2-AS1
LOC100286793
LOC100287722
LOC100289178
LOC100289211
MIR320B1
MIR1262
MIR3117
MIR4256
MIR3671
MIR548AA1
LOC100505768
LOC100506343
FPGT-TNNI3K
TMEM56-RWDD3
MIR4794
MIR4711
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 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 | 0.34 | 4.65 | 1.67e-05 | 0.05 | -3.19 | 1
1q | 1955 | 0.49 | 8.6 | 0 | 0.07 | -2.32 | 1
2p | 924 | 0.21 | 0.197 | 1 | 0.10 | -2.57 | 1
2q | 1556 | 0.12 | -1.96 | 1 | 0.13 | -1.56 | 1
3p | 1062 | 0.26 | 1.42 | 0.346 | 0.39 | 5.04 | 3.14e-06
3q | 1139 | 0.61 | 11.3 | 0 | 0.18 | -0.272 | 0.963
4p | 489 | 0.06 | -3.16 | 1 | 0.44 | 6.46 | 2.07e-09
4q | 1049 | 0.06 | -3.35 | 1 | 0.31 | 2.98 | 0.00711
5p | 270 | 0.36 | 3.98 | 0.000229 | 0.19 | -0.529 | 0.968
5q | 1427 | 0.16 | -0.848 | 1 | 0.28 | 2.33 | 0.0305
6p | 1173 | 0.21 | 0.496 | 1 | 0.18 | -0.293 | 0.963
6q | 839 | 0.14 | -1.47 | 1 | 0.29 | 2.42 | 0.0282
7p | 641 | 0.12 | -2.34 | 1 | 0.12 | -2.34 | 1
7q | 1277 | 0.14 | -1.33 | 1 | 0.19 | -0.138 | 0.963
8p | 580 | 0.16 | -1.01 | 1 | 0.35 | 3.77 | 0.000832
8q | 859 | 0.26 | 1.54 | 0.307 | 0.14 | -1.38 | 1
9p | 422 | 0.17 | -1.05 | 1 | 0.21 | 0.103 | 0.933
9q | 1113 | 0.15 | -1.1 | 1 | 0.20 | 0.0846 | 0.933
10p | 409 | 0.12 | -1.99 | 1 | 0.26 | 1.47 | 0.175
10q | 1268 | 0.08 | -2.87 | 1 | 0.29 | 2.51 | 0.0239
11p | 862 | 0.07 | -3.06 | 1 | 0.33 | 3.41 | 0.00263
11q | 1515 | 0.09 | -2.39 | 1 | 0.38 | 5.2 | 2e-06
12p | 575 | 0.18 | -0.557 | 1 | 0.21 | 0.0222 | 0.935
12q | 1447 | 0.15 | -1.16 | 1 | 0.06 | -3.6 | 1
13q | 654 | 0.12 | -1.87 | 1 | 0.32 | 3.15 | 0.00471
14q | 1341 | 0.16 | -0.905 | 1 | 0.17 | -0.505 | 0.968
15q | 1355 | 0.18 | -0.41 | 1 | 0.18 | -0.41 | 0.968
16p | 872 | 0.16 | -1.01 | 1 | 0.14 | -1.6 | 1
16q | 702 | 0.12 | -1.97 | 1 | 0.19 | -0.216 | 0.963
17p | 683 | 0.08 | -2.88 | 1 | 0.32 | 3.15 | 0.00471
17q | 1592 | 0.18 | -0.345 | 1 | 0.12 | -1.76 | 1
18p | 143 | 0.15 | -1.59 | 1 | 0.22 | 0.132 | 0.933
18q | 446 | 0.10 | -2.58 | 1 | 0.29 | 2.24 | 0.035
19p | 995 | 0.16 | -0.947 | 1 | 0.29 | 2.37 | 0.0296
19q | 1709 | 0.27 | 2.09 | 0.106 | 0.18 | -0.321 | 0.963
20p | 355 | 0.37 | 4.38 | 4.66e-05 | 0.13 | -1.69 | 1
20q | 753 | 0.40 | 5.56 | 1.84e-07 | 0.06 | -3 | 1
21q | 509 | 0.21 | 0.198 | 1 | 0.22 | 0.389 | 0.82
22q | 921 | 0.14 | -1.49 | 1 | 0.28 | 2.22 | 0.035
Xq | 1312 | 0.18 | -0.319 | 1 | 0.29 | 2.63 | 0.0188

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/CESC-TP/3348173/GDAC_MergeDataFiles_3124084/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

Table 4. Get Full Table First 10 out of 126 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:

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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