SNP6 Copy number analysis (GISTIC2)
Brain Lower Grade Glioma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C11V5C7K
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C11V5C7K
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 2.0.19 (Firehose task version: 125).

Summary

There were 269 tumor samples used in this analysis: 21 significant arm-level results, 20 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 - 20 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
--- | --- | --- | --- | ---
7p11.2 | 5.1703e-36 | 5.1703e-36 | chr7:54942676-55107468 | 1
12q14.1 | 1.0993e-16 | 1.0993e-16 | chr12:58125396-58163019 | 6
1q32.1 | 3.9701e-10 | 2.286e-09 | chr1:204309639-204610897 | 6
8q24.12 | 2.286e-09 | 2.286e-09 | chr8:113422063-143672987 | 122
12p13.32 | 2.286e-09 | 5.3095e-09 | chr12:3585779-4603697 | 8
4q12 | 8.7304e-07 | 8.7304e-07 | chr4:55120558-55218631 | 1
7q32.3 | 1.4583e-06 | 1.4583e-06 | chr7:129888335-131642364 | 19
10p15.3 | 0.00075166 | 0.00075166 | chr10:1-6398978 | 46
11q23.3 | 0.0038587 | 0.0038587 | chr11:116705101-135006516 | 195
Xp11.22 | 0.0051153 | 0.0051153 | chrX:53659048-56536223 | 26
13q33.3 | 0.013941 | 0.013941 | chr13:106988965-111100017 | 12
3q26.32 | 0.022399 | 0.022399 | chr3:176689358-184282891 | 55
19p13.3 | 0.029216 | 0.029216 | chr19:713557-968485 | 15
17q25.1 | 0.049694 | 0.049694 | chr17:52273528-81195210 | 413
19q13.2 | 0.061858 | 0.061858 | chr19:40246077-40291097 | 1
1q22 | 0.080514 | 0.11205 | chr1:120527362-164991045 | 472
Xp22.33 | 0.17555 | 0.17555 | chrX:1-34033668 | 165
3p24.3 | 0.21736 | 0.21736 | chr3:1-55279563 | 491
12p12.1 | 0.0011572 | 0.22217 | chr12:1-40547378 | 343
18q23 | 0.24214 | 0.24214 | chr18:14656199-78077248 | 258

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
MARCH9
AGAP2

Genes in Wide Peak

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

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

Genes
MDM4
PIK3C2B
LRRN2
PLEKHA6
PPP1R15B
LOC127841

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.12.

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

Genes
EXT1
MYC
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
hsa-mir-2053
ADCY8
ANXA13
BAI1
GPR20
HAS2
KCNQ3
NDUFB9
NOV
TNFRSF11B
ENPP2
POU5F1B
PTK2
PVT1
RAD21
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
COL14A1
EIF3H
WISP1
MTSS1
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
KHDRBS3
PTP4A3
RNF139
ZHX1
ZHX2
DENND3
EFR3A
LRRC6
MTBP
EIF2C2
MRPL13
ATAD2
ASAP1-IT1
ASAP1
FAM135B
PHF20L1
KCNK9
FAM49B
CHRAC1
TRMT12
WDYHV1
GSDMC
SLC45A4
ZFAT
DEPTOR
DSCC1
DERL1
TRAPPC9
TATDN1
UTP23
C8orf76
FAM83A
MED30
WDR67
HPYR1
MAL2
CSMD3
FBXO32
ZNF572
TMEM71
TMEM65
LOC157381
FAM84B
FAM91A1
SLC30A8
COL22A1
TSNARE1
NSMCE2
LOC286094
KLHL38
FLJ43860
SAMD12
MIR30B
MIR30D
FER1L6-AS1
C8orf85
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
RAD21-AS1
FER1L6
LOC727677
LOC728724
OC90
LOC731779
LOC100130231
LOC100131726
MIR1205
MIR1206
MIR1207
MIR1204
MIR2053
MIR1208
MIR3610
LOC100507117
ZHX1-C8ORF76
MIR4663
MIR4472-1
PCAT1
LINC00536

Genes in Wide Peak

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

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

Genes
CCND2
FGF6
FGF23
PRMT8
PARP11
C12orf4
C12orf5
EFCAB4B

Genes in Wide Peak

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

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

Genes
PDGFRA

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q32.3.

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

Genes
hsa-mir-29b-1
hsa-mir-335
CPA1
CPA2
MEST
MKLN1
PODXL
COPG2
CPA4
CPA5
CEP41
TSGA13
KLF14
MESTIT1
FLJ43663
MIR29A
MIR29B1
MIR335
LOC646329

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q23.3.

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

Genes
CBL
DDX6
FLI1
MLL
PAFAH1B2
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
ACRV1
APLP2
APOA1
ARCN1
FXYD2
CXCR5
CD3D
CD3E
CD3G
CHEK1
DPAGT1
ETS1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
IL10RA
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NFRKB
NRGN
OPCML
PVRL1
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZNF202
BARX2
USP2
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
PHLDB1
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
POU2F3
HINFP
OR8G2
OR8B8
OR8G1
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
C11orf61
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
JAM3
TMPRSS13
KIRREL3
TMEM25
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
TMEM45B
AMICA1
TTC36
PATE1
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
RNF214
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
LINC00167
HEPN1
LOC649133
RPL23AP64
LOC100128239
PATE3
BACE1-AS
MIR3167
LOC100499227
MIR3656
LOC100507392
LOC100526771
FXYD6-FXYD2
MIR4697
MIR4493
MIR4492
LOC100652768

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.22.

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

Genes
ALAS2
FGD1
PFKFB1
TRO
HUWE1
RRAGB
MAGED2
KLF8
PHF8
APEX2
MAGEH1
GNL3L
FAM120C
WNK3
TSR2
FAM104B
PAGE5
FOXR2
PAGE3
USP51
PAGE2
ITIH6
PAGE2B
SNORA11
MTRNR2L10
MIR4536-1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q33.3.

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

Genes
hsa-mir-1267
COL4A1
COL4A2
EFNB2
LIG4
IRS2
TNFSF13B
MYO16
ARGLU1
ABHD13
LINC00460
FAM155A

Genes in Wide Peak

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

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

Genes
PIK3CA
SOX2
hsa-mir-1224
ACTL6A
AP2M1
CLCN2
DVL3
EIF4G1
EPHB3
NDUFB5
POLR2H
PSMD2
THPO
FXR1
CHRD
EIF2B5
USP13
ECE2
ABCC5
ALG3
KCNMB2
MCF2L2
ATP11B
LAMP3
KCNMB3
ZNF639
PEX5L
DCUN1D1
KLHL24
ABCF3
PARL
MFN1
YEATS2
MCCC1
MRPL47
GNB4
ZMAT3
TBL1XR1
MAP6D1
B3GNT5
KLHL6
VWA5B2
CAMK2N2
DNAJC19
FAM131A
TTC14
HTR3C
HTR3D
HTR3E
CCDC39
SOX2-OT
FLJ46066
SNORD66
MIR1224
LOC100505687

Genes in Wide Peak

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

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

Genes
hsa-mir-3187
AZU1
CFD
ARID3A
ELANE
PALM
PRTN3
PTBP1
MED16
LPPR3
KISS1R
R3HDM4
C19orf21
MIR3187
MIR4745

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
LEUTX

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
PDE4DIP
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
APCS
APOA2
ATP1A2
ATP1A4
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO5
DARC
GBA
GBAP1
GJA5
GJA8
HDGF
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LMNA
LOR
LY9
MCL1
SMCP
MEF2D
MNDA
MPZ
MTX1
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PI4KB
PKLR
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
USF1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
PEA15
B4GALT3
ADAM15
PEX11B
CD84
SELENBP1
SH2D2A
FCGR2C
PRPF3
ARHGEF2
DEDD
AIM2
ADAMTS4
SEC22B
CHD1L
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
PMF1
DUSP12
VPS45
KIAA0907
ATF6
POGZ
SYT11
RPRD2
SMG5
NCSTN
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
OLFML2B
C1orf43
CHTOP
LCE2B
OR10J1
USP21
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
ACP6
GPR89B
HSD17B7
UFC1
OAZ3
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
FAM63A
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
NUF2
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
AQP10
SLAMF9
PYGO2
NUP210L
MEX3A
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
HIST2H3C
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
LRRC71
PYHIN1
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
C1orf204
C1orf111
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
C1orf110
OR10R2
FCRL6
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
LOC375010
PEAR1
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
NBPF9
MIR9-1
HIST2H2BF
ETV3L
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
PRR9
RPL31P11
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA4
SNORA42
MIR554
MIR555
MIR556
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR765
MIR190B
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505633
LOC100505666
LOC100505795
PMF1-BGLAP
TNFAIP8L2-SCNM1
MIR4654

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.33.

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

Genes
CRLF2
P2RY8
hsa-mir-548f-5
hsa-mir-1308
hsa-mir-651
NR0B1
AMELX
SLC25A6
SHROOM2
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT
BMX
S100G
CLCN4
CSF2RA
DMD
EIF1AX
EIF2S3
FANCB
FIGF
GK
GLRA2
GPM6B
GRPR
HCCS
IL3RA
KAL1
MAGEB1
MAGEB2
MAGEB3
MAGEB4
CD99
MID1
NHS
GPR143
PDHA1
PDK3
PHEX
PHKA2
PIGA
POLA1
PPEF1
PRKX
PRPS2
RBBP7
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SHOX
SMS
CDKL5
TBL1X
TMSB4X
XG
ZFX
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
OFD1
PIR
INE2
ASMTL
AP1S2
GYG2
REPS2
ZBED1
RAB9A
PCYT1B
FRMPD4
GPR64
SCML2
PRDX4
RAI2
MSL3
IL1RAPL1
CA5B
CNKSR2
ACOT9
SMPX
MXRA5
EGFL6
VCX
PPP2R3B
SH3KBP1
TLR7
TLR8
MBTPS2
VCX2
VCX3A
FTHL17
GEMIN8
PLCXD1
TXLNG
WWC3
CTPS2
TMEM27
NLGN4X
ACE2
APOO
ASMTL-AS1
CXorf21
KLHL15
ATXN3L
SYAP1
BEND2
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
ASB11
ASB9
ZNF645
MOSPD2
MAGEB6
DDX53
FAM48B2
TCEANC
ARX
FAM9A
FAM9B
FAM9C
DHRSX
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
PPP2R3B-AS1
MAGEB18
CA5BP1
DCAF8L2
ARSH
TLR8-AS1
MAP3K15
LOC389906
CD99P1
YY2
VCX3B
SCARNA23
MIR651
LOC729609
LOC100093698
CXorf28
FAM48B1
LOC100132163
XGPY2
LOC100133123
SCARNA9L
LOC100288814
LINC00102
MIR23C
MIR3690
PIR-FIGF
MIR4768
MIR4770
MIR4767

Genes in Wide Peak

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

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

Genes
CTNNB1
FANCD2
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
SETD2
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
RHOA
ATP2B2
BTD
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DOCK3
DUSP7
CELSR3
FBLN2
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPX1
GRM2
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RAB5A
RARB
SNORA62
RPL15
RPL29
RPL32
SATB1
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT7A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SEMA3B
MANF
COLQ
EOMES
HYAL3
CAMK1
BHLHE40
HYAL2
KAT2B
BSN
LIMD1
CCRL2
RPL14
SEC22C
RRP9
LRRFIP2
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
VPRBP
TBC1D5
TATDN2
IP6K1
EPM2AIP1
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
NPRL2
CXCR6
CSPG5
CHL1
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
CAND2
CLASP2
RAD54L2
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
KLHL18
LARS2
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
DNAH1
HIGD1A
SUSD5
HACL1
TTLL3
GNL3
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LINC00312
LMCD1
VILL
C3orf32
TRNT1
ABHD5
DYNC1LI1
C3orf18
CRBN
SS18L2
C3orf19
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
C3orf75
SNRK
QRICH1
CMTM6
SLC25A38
ULK4
OXSM
ANO10
DALRD3
ARL8B
SETD5
TMEM40
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
TMEM111
BRK1
ZNF167
RAD18
SEMA3G
KIF15
PCBP4
LRTM1
KIAA1143
HHATL
WDR48
LRRN1
SELK
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
WDR82
TSEN2
GRIP2
RTP3
C3orf20
ATRIP
NICN1
MON1A
JAGN1
GHRLOS2
IL17RC
ABHD14B
C3orf39
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
ZNF501
C3orf24
LRRC3B
GALNTL2
GPR62
KCNH8
LYZL4
KBTBD5
TRIM71
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf45
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
FGD5
CIDECP
CNTN4
XIRP1
TTC21A
KLHDC8B
STT3B
ZNF620
ALS2CL
TMIE
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
C3orf23
ZNF660
FLJ39534
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
COL6A4P1
TPRXL
ZNF445
LHFPL4
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VENTXP7
LOC401052
IQCF3
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
SNORA7A
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
MIR563
MIR564
FAM198A
CCR2
ESRG
SNORD19B
MIR885
EGOT
GHRLOS
C3orf74
LOC100128640
NRADDP
LOC100129480
LOC100132146
LOC100132526
BSN-AS2
PRSS46
LOC100288428
MIR1226
MIR711
MIR4270
MIR4271
MIR3714
FGD5-AS1
LOC100505696
KRBOX1
IQCF4
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4791
MIR4790
MIR548AC
MIR4443
MIR4792
MIR4442
LUST

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
CCND2
ETV6
KRAS
KDM5A
ZNF384
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
ABCD2
APOBEC1
ARHGDIB
ART4
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
DDX11
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
GYS2
IAPP
ITPR2
KCNA1
KCNA5
KCNA6
KCNJ8
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LDHB
LRMP
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NINJ2
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PKP2
PRB1
PRB3
PRB4
PRH1
PRH2
PTHLH
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
RECQL
SCNN1A
ST8SIA1
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SOX5
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
SSPN
KLRC4
PPFIBP1
CSDA
DYRK4
GPRC5A
CD163
MED21
GDF3
CLSTN3
KIAA0528
NCAPD2
CLEC2B
DNM1L
ABCC9
LPCAT3
KLRG1
LRRC23
EMG1
IPO8
LEPREL2
AKAP3
SLCO1B1
RAD51AP1
KLRAP1
TSPAN9
STRAP
RASSF8
PRR4
PHB2
KLRK1
STK38L
ERC1
GABARAPL1
IFFO1
NECAP1
FGFR1OP2
CLEC4E
GALNT8
GPR162
SLCO1B3
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
GOLT1B
YARS2
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
ERGIC2
KLRF1
WBP11
TM7SF3
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
MAGOHB
FAM90A1
C12orf35
PLEKHG6
CASC1
CCDC91
STYK1
ETNK1
GPRC5D
KIF21A
FAR2
ASUN
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
CMAS
PRMT8
ARNTL2
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KLHDC5
KIAA1467
FAM60A
MRPS35
CLEC7A
WNK1
CAPRIN2
BHLHE41
BCL2L14
ADIPOR2
RERGL
FLJ13224
PLBD1
PYROXD1
NANOG
C12orf39
DUSP16
WNT5B
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
TMTC1
CCDC77
ACRBP
SPSB2
EFCAB4B
ALG10
RERG
PLCZ1
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
C12orf57
SLC2A13
LOH12CR1
C12orf59
HIST4H4
ERP27
FGD4
AEBP2
SLC2A14
ALG10B
LINC00477
LYRM5
CPNE8
A2ML1
LOC144571
C12orf60
FBXL14
CLEC12A
CLECL1
IFLTD1
DENND5B
CLEC4C
DSTNP2
AMN1
C12orf77
C12orf53
DCP1B
C12orf33
METTL20
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
B4GALNT3
CLEC9A
C12orf36
LOC283440
C12orf40
CLEC4D
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
REP15
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
TSPAN11
LOH12CR2
LOC574538
POU5F1P3
LOC642846
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
C12orf71
SLC15A5
MIR920
LOC100129361
LOC100271702
MANSC4
LOC100287314
LOC100288778
LOC100292680
MIR1244-1
MIR1244-3
MIR1244-2
MIR4302
KLRF2
LOC100499405
MIR3649
LOC100506314
LOC100506393
LOC100506451
LOC100506660
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846

Genes in Wide Peak

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

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

Genes
BCL2
SS18
MALT1
ZNF521
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
hsa-mir-187
hsa-mir-302f
hsa-mir-320c-2
hsa-mir-1-2
hsa-mir-320c-1
hsa-mir-3156-2
AQP4
ATP5A1
CDH2
CDH7
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GATA6
GRP
LAMA3
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MEP1B
MYO5B
NARS
NFATC1
NPC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RBBP8
RIT2
ROCK1
RPL17
SERPINB3
SERPINB4
SLC14A1
SNRPD1
SYT4
TAF4B
TCF4
TTR
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
RIOK3
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
ZNF271
TXNL4A
MAPRE2
POLI
ADNP2
TRAPPC8
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
CABYR
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
C18orf8
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
RPRD1A
ZNF532
ELP2
IMPACT
ELAC1
ZNF407
CNDP2
CELF4
MIB1
KIAA1328
KLHL14
KIAA1468
EPG5
HRH4
CTAGE1
FAM59A
CCDC102B
RBFA
GREB1L
PQLC1
FHOD3
CCDC68
ASXL3
NETO1
KATNAL2
CHST9
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
TMEM241
SERPINB12
SERPINB11
SEC11C
CABLES1
DSEL
ESCO1
OSBPL1A
HAUS1
ALPK2
LOXHD1
INO80C
TTC39C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
MCART2
DSG4
CHST9-AS1
ANKRD29
C18orf54
TCEB3C
ABHD3
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
ZNF396
KCTD1
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ANKRD30B
C18orf34
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR1-2
MIR122
MIR133A1
MIR187
HSBP1L1
WBP11P1
RNF165
C18orf32
KC6
LOC643542
C18orf63
LOC644669
LOC647946
SCARNA17
SNORA37
LOC728606
TCEB3CL
LOC729950
ZSCAN30
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR302F
MIR320C1
MIR320C2
MIR1539
MIR4319
MIR4318
MIR4320
MIR3156-2
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4741
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744
LOC100652770

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
--- | --- | --- | --- | ---
9p21.3 | 1.9065e-58 | 1.9065e-58 | chr9:21865498-22448737 | 4
19q13.42 | 5.032e-19 | 5.032e-19 | chr19:53856554-59128983 | 249
4q35.2 | 2.8884e-11 | 2.8884e-11 | chr4:165499372-191154276 | 116
10q26.3 | 2.2293e-09 | 2.2841e-09 | chr10:117705523-135534747 | 150
2q37.3 | 2.8912e-13 | 9.101e-09 | chr2:239463774-243199373 | 54
14q24.3 | 8.3732e-07 | 8.2417e-07 | chr14:62199756-96851110 | 259
11p15.5 | 4.2129e-06 | 3.9817e-06 | chr11:1-5968920 | 184
18q23 | 0.00046613 | 0.00044933 | chr18:74979706-78077248 | 12
22q13.31 | 0.00044933 | 0.00044933 | chr22:47571204-48018269 | 1
6q24.3 | 0.0041617 | 0.0043271 | chr6:112670088-171115067 | 321
6p25.3 | 0.0051639 | 0.0051639 | chr6:1-2833738 | 13
3p21.2 | 0.0074887 | 0.0074887 | chr3:43761442-58179027 | 253
13q34 | 0.0025929 | 0.0083857 | chr13:114620052-115169878 | 4
1p36.31 | 0.0063363 | 0.0091588 | chr1:3771349-10107464 | 58
1p32.3 | 0.0079788 | 0.011832 | chr1:50879767-51569162 | 3
2q37.1 | 6.8972e-11 | 0.031017 | chr2:232576432-243199373 | 131
13q14.2 | 9.6309e-05 | 0.046122 | chr13:1-86367939 | 290
5q35.2 | 0.051369 | 0.051858 | chr5:122370812-180915260 | 547
12q12 | 0.051858 | 0.051858 | chr12:33046522-121420319 | 747
17q25.3 | 0.1027 | 0.10328 | chr17:80379333-81195210 | 12
2p25.3 | 0.11988 | 0.12238 | chr2:1-27652307 | 168
Xp22.2 | 0.12577 | 0.12238 | chrX:3474210-11155728 | 25
11q25 | 0.15466 | 0.15933 | chr11:132204656-135006516 | 15
18p11.32 | 0.19051 | 0.19152 | chr18:1-2850630 | 16
Xq21.1 | 0.22015 | 0.21585 | chrX:76710176-77102528 | 1
1q43 | 0.23398 | 0.24213 | chr1:180912007-249250621 | 534
13q21.33 | 0.00014311 | 0.51533 | chr13:1-115169878 | 414
13q21.2 | 1.7752e-05 | 0.80299 | chr13:1-115169878 | 414

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
A1BG
FCAR
FKBP1AP1
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR1
LAIR2
NDUFA3
CNOT3
PEG3
PRKCG
PTPRH
RPL28
RPS5
RPS9
AURKC
SYT5
TNNI3
TNNT1
ZNF8
ZNF17
MZF1
ZNF132
ZNF134
ZNF135
ZNF154
UBE2M
ZNF264
NCR1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
LILRB1
LILRB5
SLC27A5
LILRB4
LILRA1
LILRB3
LILRA3
LILRA2
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
ZNF324
PRPF31
CHMP2A
ZNF544
UBE2S
CCDC106
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
NLRP2
ZNF416
ZNF446
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
ZNF71
CACNG8
CACNG7
CACNG6
ZNF667
ZSCAN18
MGC2752
TSEN34
MBOAT7
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
ZNF419
ISOC2
ZNF552
ZNF671
ZNF606
BRSK1
SUV420H2
ZBTB45
ZNF587
FIZ1
GALP
ZNF628
KIR3DX1
ZNF551
ZNF835
ZNF765
NLRP12
MYADM
LENG9
RDH13
ZIM3
LENG8
KIR3DL3
ZNF837
ZNF543
COX6B2
OSCAR
ZNF813
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF497
ZNF550
ZNF579
ZNF525
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
LOC284379
VSTM1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
ZNF773
LOC386758
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF772
TARM1
MIR371A
MIR372
MIR373
A1BG-AS1
DPRX
DUXA
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
LOC646862
SHISA7
ZNF814
MIMT1
MIR935
LOC100128252
LOC100128398
SGK110
LOC100131691
PEG3-AS1
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
ZNF865
MIR4754
MIR4752
MIR371B

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
AGA
SLC25A4
CASP3
CLCN3
CPE
DCTD
F11
ACSL1
FAT1
FRG1
GK3P
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
MSMO1
TLL1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
FAM149A
FBXO8
DUX2
PDLIM3
SPOCK3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SH3RF1
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
CBR4
MGC45800
DDX60L
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
TRIM60
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229

Genes in Wide Peak

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

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

Genes
FGFR2
DUX4
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
ACADSB
ADAM8
BNIP3
CTBP2
CYP2E1
DMBT1
DOCK1
ECHS1
EMX2
GFRA1
PRLHR
GPR26
GRK5
HMX2
INPP5A
MGMT
MKI67
OAT
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PTPRE
RGS10
SLC18A2
TIAL1
UROS
ADAM12
UTF1
EIF3A
BUB3
BAG3
FAM53B
GLRX3
DPYSL4
TACC2
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
FAM175B
C10orf137
DUX2
VENTX
CUZD1
CALY
CHST15
ZRANB1
TTC40
NSMCE4A
WDR11
DHX32
PPP2R2D
FAM45B
BCCIP
KIAA1598
PLEKHA1
FAM204A
LHPP
IKZF5
MCMBP
C10orf88
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
FANK1
SYCE1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
PDZD8
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf82
C10orf46
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CASC2
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
LOC283038
LOC283089
KCNK18
NANOS1
HMX3
C10orf96
FLJ46361
ENO4
ARMS2
C10orf122
LOC387723
NKX1-2
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
FAM45A
FRG2B
SPRN
MIR202
NPS
LOC619207
SNORA19
FAM196A
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
LOC100169752
MIR378C
MIR4297
MIR4296
MIR3941
MIR3663
MIR3944
FAM24B-CUZD1
MIR4682
MIR4484
MIR4681

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
HDAC4
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
RNPEPL1
GAL3ST2
C2orf54
ING5
MGC16025
TWIST2
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
LOC150935
LOC200772
CXXC11
DUSP28
AQP12A
OR6B2
FLJ43879
MIR149
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.3.

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

Genes
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
HSPA2
IFI27
ITPK1
LTBP2
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5E
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
SEL1L
SRSF5
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
TCL1B
RGS6
KIAA0247
KIAA0317
MED6
VTI1B
FBLN5
BATF
NPC2
AHSA1
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
C14orf109
PLEK2
MLH3
KCNH5
PRO1768
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
ATP6V1D
ASB2
ZFYVE1
CPSF2
KCNK10
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
UNC79
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
IRF2BPL
MPP5
OTUB2
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
SGPP1
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
IFT43
WDR89
IFI27L1
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
SAMD15
EML5
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf55
ITPK1-AS1
SNORD56B
SERPINA9
VSX2
COX8C
RAB15
SERPINA13
HEATR4
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
LINC00238
CCDC88C
TEX21P
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
SCARNA13
SNORA79
LOC731223
SNORA11B
LOC100289511
MIR1260A
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

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

Genes
CARS
HRAS
NUP98
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
RHOG
ART1
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
IGF2
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
TRIM21
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IFITM2
OR7E12P
KCNQ1OT1
PKP3
SIRT3
OR52A1
PGAP2
C11orf21
TRPM5
UBQLN3
IGF2-AS1
BET1L
CEND1
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
TRIM5
SYT8
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
SCGB1C1
NLRP6
NS3BP
LOC255512
C11orf35
OR51F1
OR51B5
OR51V1
H19
EFCAB4A
TMEM80
C11orf36
ANO9
LOC338651
B4GALNT4
OR52B6
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TRIM6-TRIM34
MIR483
SNORA52
LOC650368
LOC653486
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686
MIR4687

Genes in Wide Peak

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

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

Genes
NFATC1
CTDP1
TXNL4A
ADNP2
KCNG2
SALL3
RBFA
PQLC1
PARD6G
ATP9B
HSBP1L1
LOC100130522

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q24.3.

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

Genes
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
ACAT2
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FRK
FUCA2
GJA1
GPR31
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PKIB
PSMB1
PTPRK
RPS6KA2
RPS12
SGK1
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
RNASET2
STX11
SYNJ2
VNN2
VNN1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
AKAP7
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
UST
TRDN
CITED2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
SCAF8
TAB2
TSPYL4
SASH1
SYNE1
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
DLL1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TFB1M
RWDD1
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
C6orf115
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
TTLL2
FBXO30
L3MBTL3
FAM120B
FNDC1
RSPO3
LRP11
LTV1
SERAC1
REPS1
PPIL4
LINC00473
ARHGAP18
SYTL3
FAM54A
SFT2D1
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
C6orf191
WDR27
FAM26E
MCM9
SHPRH
LINC00326
LOC285740
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
CENPW
C6orf174
CEP85L
C6orf120
THEMIS
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FAM26F
FLJ46906
LOC441177
SNORD101
SNORD100
SNORA33
LOC643623
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
MIR548B
TPI1P3
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
IRF4
FOXF2
FOXC1
GMDS
EXOC2
WRNIP1
DUSP22
FOXQ1
HUS1B
C6orf195
LOC285768
MYLK4
LOC100508120

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.2.

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

Genes
BAP1
SETD2
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
HYAL3
HYAL2
HESX1
BSN
LIMD1
CCRL2
RRP9
CACNA2D2
VPRBP
IP6K1
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
RAD54L2
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
PTPN23
DNAH1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
QRICH1
DALRD3
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
SEMA3G
KIF15
PCBP4
LRTM1
KIAA1143
SELK
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
WDR82
RTP3
ATRIP
NICN1
MON1A
ABHD14B
UCN2
ZNF502
RFT1
ACTR8
ZNF501
GPR62
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf45
ASB14
CCDC12
KLHDC8B
DNAH12
PDE12
FAM116A
ALS2CL
TMIE
FBXW12
CCDC66
C3orf23
ZNF660
FLJ39534
CCDC36
PRSS42
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR138-1
MIR191
TMEM89
IQCF6
C3orf78
MIR425
LOC644714
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
MIR564
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
LOC100132146
BSN-AS2
PRSS46
MIR1226
MIR711
MIR4271
MIR3938
IQCF4
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4443
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q34.

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

Genes
CDC16
RASA3
UPF3A
CHAMP1

Genes in Wide Peak

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

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

Genes
RPL22
hsa-mir-34a
hsa-mir-4252
RERE
CA6
DFFB
ENO1
ZBTB48
TNFRSF9
PIK3CD
SLC2A5
KCNAB2
TNFRSF25
PER3
VAMP3
H6PD
KLHL21
UTS2
PARK7
ACOT7
CLSTN1
CAMTA1
ICMT
CHD5
SLC45A1
ERRFI1
HES2
DNAJC11
AJAP1
CTNNBIP1
PLEKHG5
NMNAT1
NOL9
GPR157
SPSB1
TAS1R1
ESPN
SLC25A33
LZIC
THAP3
RBP7
PHF13
SLC2A7
TMEM201
NPHP4
LOC284661
C1orf174
GPR153
RNF207
HES3
MIR34A
C1orf200
LOC728716
LOC100133612
MIR4252
ENO1-AS1
MIR4689
MIR4417

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p32.3.

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

Genes
CDKN2C
FAF1
DMRTA2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

Table S37. 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-3169
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
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
CPB2
DACH1
EDNRB
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
POU4F1
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
UCHL3
ZMYM2
IFT88
TNFSF11
SCEL
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
SAP18
DLEU1
N4BP2L2
PIBF1
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
MRP63
RNF219
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
COMMD6
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
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 5q35.2.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDX1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
NKX2-5
CTNNA1
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HINT1
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
LCP2
LECT2
LMNB1
LTC4S
SMAD5
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SPARC
SPINK1
SPOCK1
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
MRPL22
PCDHB1
KCNIP1
ZNF354C
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
ZNF608
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
LYRM7
TRIM41
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
LOC153469
ZMAT2
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
LOC340037
TMEM173
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
DND1
C5orf25
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
FLJ33630
CCNI2
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
VTRNA2-1
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1289-2
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100507387
MIR4633
MIR4634
MIR4461
MIR4460
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

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

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

Genes
ALDH2
ATF1
BTG1
CDK4
DDIT3
HOXC11
HOXC13
MDM2
NACA
PTPN11
MLL2
HMGA2
WIF1
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
ACACB
ACADS
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
AQP2
AQP5
AQP6
ARF3
ARL1
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
CACNB3
CCNT1
CD63
CDK2
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
EPYC
DTX1
DUSP6
EIF4B
CELA1
ELK3
ERBB3
B4GALNT1
BLOC1S1
GLI1
GNS
GPD1
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
KCNC2
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
LRP1
LTA4H
LUM
LYZ
MARS
METTL1
KITLG
MIP
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NELL2
NFE2
NFYB
NOS1
CNOT2
SLC11A2
NTS
OAS1
OAS2
OAS3
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE1B
PFDN5
PFKM
SLC25A3
PLA2G1B
PMCH
POU6F1
PPP1CC
PPP1R1A
PRIM1
PRKAB1
PRKAG1
PRPH
TWF1
PTPRB
PTPRR
PXN
RAB5B
RAP1B
RARG
RBMS2
RDH5
RFC5
RFX4
RNY5
RPL6
RPL41
RPLP0
RPS26
TSPAN31
ATXN2
SCN8A
SELPLG
SHMT2
PMEL
SMARCC2
SMARCD1
SNRPF
SP1
STAT2
STAT6
SUOX
SYT1
TAC3
TARBP2
TBX5
TBX3
TDG
TMBIM6
TFCP2
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBE2N
UNG
VDR
WNT1
WNT10B
MAP3K12
TUBA1A
AAAS
YEATS4
ALX1
BRAP
EEA1
SOAT2
RASAL1
DYRK2
PPFIA2
LGR5
MAPKAPK5
RDH16
NPFF
HSD17B6
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
ENDOU
TIMELESS
KRT75
SCAF11
RASSF9
SLC16A7
DDX23
CABP1
SLC4A8
WSCD2
ESPL1
SART3
MLEC
DAZAP2
GIT2
KIAA0748
ZBTB39
NUAK1
RBM19
RNF10
PAN2
USP15
NR1H4
SH2B3
TROAP
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
RNF41
GDF11
TMEM5
CNPY2
TUBA1B
RAPGEF3
MCRS1
DCTN2
CCT2
AVIL
PTGES3
FRS2
TRAFD1
OS9
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
BAZ2A
IRAK3
GALNT6
NXPH4
XPOT
GPR182
COPZ1
PHLDA1
R3HDM2
RPH3A
RAB21
FBXO21
FAIM2
MON2
UHRF1BP1L
DDN
TMEM194A
CUX2
KIAA1033
TBC1D30
ESYT1
TENC1
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
CBX5
ISCU
ANP32D
SMUG1
LEMD3
CORO1C
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
ZNF385A
FBXW8
HSPB8
SNORD59A
GLS2
RND1
UTP20
KCNMB4
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
IL22
DHH
CCDC53
PLEKHA8P1
CCDC41
IRAK4
GPN3
GLTP
C12orf47
FKBP11
TAOK3
KRT76
POP5
CSAD
BIN2
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
TPCN1
GPR84
SLC38A2
SSH1
PRR13
VSIG10
KANSL2
TESC
PARPBP
SLC38A4
SLC6A15
RIC8B
APPL2
TMEM19
DRAM1
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
KIF21A
SLC48A1
SCYL2
POLR3B
LMBR1L
FGD6
IL26
CAND1
WSB2
NDUFA12
MDM1
ANKS1B
NDUFA4L2
CHPT1
NUP107
SMAGP
TMCC3
PPM1H
SRGAP1
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
NTN4
TRPV4
C12orf10
C12orf44
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
TBC1D15
SLC26A10
SPATS2
TMEM106C
NUP37
OBFC2B
DDX54
GNPTAB
TCTN1
ACSS3
RPAP3
BBS10
C12orf49
PIP4K2C
DNAJC22
NAA25
SLC24A6
ADAMTS20
CEP290
MTERFD3
ACAD10
SLC38A1
CSRNP2
PUS7L
GLT8D2
THAP2
INHBE
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
C12orf26
TMEM117
TCHP
COQ5
LLPH
WIBG
SARNP
HVCN1
SRRM4
CAPS2
UNC119B
USP30
TUBA1C
ZC3H10
RNFT2
C12orf34
ALG10
SPRYD3
C12orf52
MFSD5
MGC14436
C12orf62
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
TMEM116
UBE3B
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
FAM113B
CCDC64
HELB
MARCH9
COQ10A
KRT71
LARP4
SDSL
SLC2A13
MBD6
OSBPL8
ARHGEF25
C12orf56
IQCD
AGAP2
DCD
RAB3IP
MUCL1
DEPDC4
LRRK2
CCDC38
FAM186A
C12orf45
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
KRT72
PRICKLE1
AMDHD1
BCDIN3D
ALG10B
GLIPR1L2
CPNE8
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
KRT80
C12orf66
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
KRT78
DTX3
METTL7B
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
GNN
MSRB3
OR6C74
OR6C3
TCP11L2
LOC255411
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
LOC283332
LOC283335
ZNF740
RASSF3
OR6C6
ANKRD52
SLC39A5
SPRYD4
LOC283392
LOC283403
LOC283404
C12orf61
DPY19L2
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
MMAB
LOC338758
C1QL4
TMEM119
KRT79
C12orf74
FAM19A2
SYT10
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
KRT77
PTPRQ
C12orf42
LRRC10
C12orf68
C12orf75
CCDC42B
TMEM233
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
MKRN9P
C12orf76
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR196A2
MIR26A2
C12orf37
DBX2
FLJ12825
TMEM198B
PLEKHG7
NUDT4P1
OR9K2
MIR148B
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
HIGD1C
MAP1LC3B2
LOC643339
LOC643770
GLYCAM1
HNRNPA1P10
SNORA2A
SNORA2B
SNORA34
SNORA53
SNORD59B
MIR548C
MIR615
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
MRS2P2
HOTAIR
LOC100128191
LOC100130776
LOC100131138
LOC100131733
LOC100233209
LOC100240734
LOC100240735
LOC100286844
LINC00173
LOC100287944
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1178
MIR1251
LOC100335030
SNORA70G
MIR4303
MIR3685
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
LOC100505978
LOC100506649
LOC100506668
LOC100506844
LOC100507250
LOC100507377
BLOC1S1-RDH5
POC1B-GALNT4
MIR4699
MIR4498
MIR548AL
MIR4701
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4698
LOC100652999

Genes in Wide Peak

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

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

Genes
FOXK2
TBCD
RAB40B
NARF
WDR45L
FN3K
C17orf62
FN3KRP
ZNF750
B3GNTL1
METRNL
FLJ43681

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.3.

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

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ADCY3
APOB
RHOB
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
FTH1P3
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
SNX17
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
MAPRE3
EFR3B
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
ITSN2
TRAPPC12
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
HS1BP3
COLEC11
CENPO
SMC6
NOL10
C2orf44
FAM49A
ABHD1
EPT1
RSAD2
CCDC164
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
FAM84A
GDF7
GPR113
UBXN2A
CYS1
ATP6V1C2
RNASEH1
FAM150B
DNAJC5G
IAH1
FLJ33534
C2orf70
C2orf53
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
PFN4
LOC375190
LOC386597
MFSD2B
PTRHD1
LOC400940
LINC00487
FLJ12334
FAM110C
LOC645949
C2orf84
LOC727982
RAD51AP2
DNAJC27-AS1
LOC730811
OST4
MIR1301
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505624
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.2.

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

Genes
hsa-mir-651
SHROOM2
STS
CLCN4
HCCS
KAL1
MID1
GPR143
PRKX
TBL1X
HDHD1
PNPLA4
VCX
VCX2
VCX3A
WWC3
NLGN4X
FAM9A
FAM9B
LOC389906
VCX3B
MIR651
LOC100288814
MIR4770
MIR4767

Genes in Wide Peak

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

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

Genes
OPCML
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 18p11.32.

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

Genes
ADCYAP1
CETN1
TYMS
YES1
USP14
THOC1
NDC80
SMCHD1
CLUL1
ENOSF1
LINC00470
METTL4
COLEC12
C18orf56
CBX3P2
ROCK1P1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.1.

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

Genes
ATRX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

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

Genes
ELK4
FH
MDM4
TPR
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ARF1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
DHX9
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GLUL
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
MR1
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NCF2
NEK2
NID1
NVL
CDK18
PDC
PFKFB2
PIGR
PIK3C2B
PKP1
PLA2G4A
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTGS2
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS1
RGS2
RGS7
RGS13
RGS16
RNASEL
RNF2
RNPEP
RYR2
SNRPE
SRP9
TROVE2
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
B3GALT2
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GPR37L1
GGPS1
SOX13
IKBKE
TMEM63A
TOMM20
URB2
CEP170
ZC3H11A
SMG7
TMCC2
LPGAT1
KIF14
AKT3
ARPC5
PRG4
STX6
BPNT1
TIMM17A
LRRN2
ZNF238
IVNS1ABP
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
OCLM
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NMNAT2
NFASC
GLT25D2
RGL1
FBXO28
CAMSAP2
SRGAP2
CRB1
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
GLRX2
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
IER5
UCHL5
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
SWT1
LAX1
C1orf27
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
KLHL12
LGR6
TFB2M
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
EDEM3
TRAF3IP3
SH3BP5L
NPL
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
SHCBP1L
TRMT1L
NUAK2
DDX59
RASSF5
HMCN1
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
RGS8
WNT3A
NAV1
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
TSEN15
FAM129A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
ASPM
PGBD2
OR2L13
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
LOC284648
DKFZP564C196
HNRNPU-AS1
LIN9
VN1R5
FAM5C
ZNF678
PRSS38
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
RGSL1
IRF2BP2
ZBTB41
MIA3
C1orf95
FAM89A
RPS10P7
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR194-1
MIR205
MIR181A1
MIR215
MIR29B2
MIR29C
RGS21
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SNORA14B
SNORA36B
SNORA77
SNORA16B
LOC728463
FAM72A
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
GM140
LOC100288079
MIR1182
MIR1537
MIR1231
MIR1278
MIR548F1
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
KDM5B-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4735
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.33.

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.2.

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Arm-level results

Table 3. Get Full Table Arm-level significance table - 21 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 | 0.05 | -1.4 | 1 | 0.32 | 15 | 0
1q | 1955 | 0.05 | -1.49 | 1 | 0.06 | -0.825 | 1
2p | 924 | 0.02 | -3.49 | 1 | 0.05 | -1.96 | 1
2q | 1556 | 0.02 | -3.49 | 1 | 0.03 | -2.61 | 1
3p | 1062 | 0.03 | -2.98 | 1 | 0.06 | -1.23 | 1
3q | 1139 | 0.03 | -2.7 | 1 | 0.07 | -0.514 | 1
4p | 489 | 0.03 | -2.97 | 1 | 0.14 | 3.98 | 0.000138
4q | 1049 | 0.01 | -3.79 | 1 | 0.19 | 6.7 | 7.09e-11
5p | 270 | 0.01 | -3.91 | 1 | 0.08 | -0.221 | 1
5q | 1427 | 0.00 | -4.33 | 1 | 0.07 | -0.375 | 1
6p | 1173 | 0.02 | -3.18 | 1 | 0.06 | -0.775 | 1
6q | 839 | 0.01 | -3.69 | 1 | 0.14 | 3.72 | 0.000331
7p | 641 | 0.25 | 10.3 | 0 | 0.01 | -3.63 | 1
7q | 1277 | 0.32 | 14.8 | 0 | 0.01 | -3.37 | 1
8p | 580 | 0.10 | 1.09 | 0.614 | 0.04 | -2.17 | 1
8q | 859 | 0.12 | 2.67 | 0.0378 | 0.03 | -2.78 | 1
9p | 422 | 0.04 | -2.01 | 1 | 0.27 | 11.4 | 0
9q | 1113 | 0.05 | -1.89 | 1 | 0.10 | 1.16 | 0.287
10p | 409 | 0.12 | 2.11 | 0.141 | 0.19 | 6.41 | 4.15e-10
10q | 1268 | 0.01 | -3.71 | 1 | 0.21 | 8.11 | 1.78e-15
11p | 862 | 0.08 | -0.0371 | 1 | 0.14 | 3.87 | 0.000195
11q | 1515 | 0.11 | 1.95 | 0.17 | 0.05 | -1.34 | 1
12p | 575 | 0.08 | -0.193 | 1 | 0.06 | -0.845 | 1
12q | 1447 | 0.03 | -2.78 | 1 | 0.11 | 2.05 | 0.0508
13q | 654 | 0.01 | -3.65 | 1 | 0.24 | 9.82 | 0
14q | 1341 | 0.01 | -3.86 | 1 | 0.16 | 4.91 | 2.29e-06
15q | 1355 | 0.02 | -3.12 | 1 | 0.08 | 0.166 | 0.914
16p | 872 | 0.03 | -2.6 | 1 | 0.03 | -2.6 | 1
16q | 702 | 0.04 | -2.1 | 1 | 0.05 | -1.66 | 1
17p | 683 | 0.02 | -3.27 | 1 | 0.05 | -1.97 | 1
17q | 1592 | 0.02 | -3.26 | 1 | 0.03 | -2.82 | 1
18p | 143 | 0.04 | -2.29 | 1 | 0.14 | 3.55 | 0.000591
18q | 446 | 0.03 | -3.02 | 1 | 0.13 | 3.06 | 0.0032
19p | 995 | 0.16 | 4.83 | 8.95e-06 | 0.08 | 0.0513 | 0.959
19q | 1709 | 0.08 | 0.216 | 1 | 0.38 | 18 | 0
20p | 355 | 0.10 | 1.15 | 0.614 | 0.01 | -3.84 | 1
20q | 753 | 0.10 | 1.16 | 0.614 | 0.00 | -4.3 | 1
21q | 509 | 0.05 | -1.73 | 1 | 0.09 | 0.658 | 0.568
22q | 921 | 0.03 | -2.8 | 1 | 0.11 | 2.22 | 0.0355
Xq | 1312 | 0.08 | 0.0607 | 1 | 0.16 | 4.64 | 7.7e-06

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

- Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LGG-TP/4393170/GDAC_MergeDataFiles_4311741/LGG-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 269 Input Tumor Samples.

Tumor Sample Names
TCGA-CS-4938-01B-11D-1892-01
TCGA-CS-4941-01A-01D-1466-01
TCGA-CS-4942-01A-01D-1466-01
TCGA-CS-4943-01A-01D-1466-01
TCGA-CS-4944-01A-01D-1466-01
TCGA-CS-5390-01A-02D-1466-01
TCGA-CS-5393-01A-01D-1466-01
TCGA-CS-5394-01A-01D-1466-01
TCGA-CS-5395-01A-01D-1466-01
TCGA-CS-5396-01A-02D-1466-01

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

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

- 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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