SNP6 Copy number analysis (GISTIC2)

Esophageal Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1QJ7G5S

Overview

Introduction

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

Summary

There were 184 tumor samples used in this analysis: 26 significant arm-level results, 31 significant focal amplifications, and 54 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 - 31 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
11q13.3	1.6976e-102	1.6976e-102	chr11:69647998-69671074	0 [FGF3]
8q24.21	1.6335e-32	1.6335e-32	chr8:128702020-128724664	0 [MYC]
17q12	9.7604e-23	9.7604e-23	chr17:37737580-37930169	11
3q26.2	1.0457e-19	1.0457e-19	chr3:169464943-169746250	8
6p21.1	6.5276e-14	6.5276e-14	chr6:43657128-43847055	1
7q21.2	5.3897e-14	7.1594e-14	chr7:91837002-93854668	20
7p11.2	5.0759e-13	1.06e-12	chr7:54942676-55390810	1
12p12.1	7.9453e-11	1.2081e-10	chr12:24880663-25593511	7
18q11.2	6.5867e-08	6.5867e-08	chr18:19613596-19648445	0 [RNU6ATAC20P]
19q12	8.1334e-08	8.1334e-08	chr19:30243979-30405684	1
12q15	1.8352e-06	2.2431e-06	chr12:69499276-70210091	9
8p11.21	1.9125e-06	3.7415e-06	chr8:42155813-42518767	6
8p23.1	4.0241e-06	1.3941e-05	chr8:11355603-12562991	20
5p15.33	0.00022938	0.00022938	chr5:1-938697	16
19p13.2	0.00032485	0.00032485	chr19:7304493-7397014	0 [INSR]
1q42.3	6.8833e-05	0.00077076	chr1:234915915-235019265	1
1p34.2	0.0023035	0.0023035	chr1:40264205-40567215	5
9p13.3	0.0050003	0.0050003	chr9:35533693-35696801	12
18p11.32	0.01273	0.01273	chr18:983189-2081265	2
2q14.2	0.0039343	0.04283	chr2:117471735-123226137	30
11p13	0.032974	0.090258	chr11:33149811-35674319	20
15q26.1	0.092304	0.092304	chr15:89828332-102531392	102
13q22.1	0.11396	0.11396	chr13:73630948-74089174	3
Xq28	0.11396	0.11396	chrX:152735103-153624575	38
2q31.1	0.026996	0.14496	chr2:173028657-173414076	1
14q21.1	0.15164	0.15164	chr14:35399861-39058108	29
1q23.3	0.0027902	0.15891	chr1:120523956-171983088	551
6q23.3	0.19702	0.19702	chr6:135500891-135715565	3
4q21.1	0.20626	0.20626	chr4:73135093-77631886	50
9q34.3	0.21556	0.21556	chr9:140086046-140219867	14
11p13	0.020259	1	chr11:1-135006516	1484

Genes in Wide Peak

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

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

Genes
ERBB2
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
GRB7
STARD3
PPP1R1B
MIEN1
PGAP3

Genes in Wide Peak

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

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

Genes
TERC
SEC62
MYNN
LRRC31
ACTRT3
LRRC34
LRRIQ4
SAMD7

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
VEGFA

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
CALCR
KRIT1
GNGT1
PEX1
TFPI2
BET1
ANKIB1
SAMD9
CCDC132
RBM48
SAMD9L
HEPACAM2
FAM133B
MIR4652

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

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

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

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

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

Genes
RN7SL804P
LYZ
YEATS4
CCT2
FRS2
CPSF6
RAB3IP
BEST3
LRRC10

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
IKBKB
POLB
SLC20A2
VDAC3
DKK4
SMIM19

Genes in Wide Peak

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

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

Genes
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130\|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
BLK
CTSB
FDFT1
GATA4
FAM86B1
DEFB130\|ENSG00000232948.1
NEIL2
USP17L2
DEFB135
DEFB136
ZNF705D

Genes in Wide Peak

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

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

Genes
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC9A3
TRIP13
PDCD6
TPPP
EXOC3
CEP72
AHRR
BRD9
ZDHHC11
C5orf55
MIR4456

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.3.

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

Genes
RNY4P16

Genes in Wide Peak

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

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

Genes
MYCL
PPT1
CAP1
TRIT1
MFSD2A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
RN7SL22P
RMRP
MIR4667
CA9
CD72
TESK1
TPM2
RUSC2
SIT1
ARHGEF39
CCDC107
FAM166B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.32.

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

Genes
RN7SKP72
LINC00470

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238341.1
RNU4ATAC
TMEM185B
snoU13\|ENSG00000238368.1
PCDP1
RN7SL468P
RN7SL111P
HTR5BP
DBI
EN1
GLI2
INHBB
PTPN4
RALB
SCTR
TSN
MARCO
DDX18
CLASP1
TFCP2L1
INSIG2
CCDC93
STEAP3
EPB41L5
TMEM177
MKI67IP
FLJ14816
C2orf76
TMEM37
C1QL2

Genes in Wide Peak

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

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

Genes
LMO2
MIR1343
EHF
CD59
C11orf91
CAT
CD44
CSTF3
ELF5
CAPRIN1
SLC1A2
PDHX
HIPK3
FJX1
KIAA1549L
ABTB2
PAMR1
FBXO3
APIP
NAT10

Genes in Wide Peak

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

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

Genes
BLM
IDH2
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13\|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109\|ENSG00000239197.1
snoU13\|ENSG00000238981.1
RN7SL363P
SNORD18\|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ALDH1A3
ANPEP
CHD2
FES
IGF1R
MAN2A2
MEF2A
FURIN
PCSK6
PLIN1
POLG
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CHSY1
SYNM
VPS33B
OR4F4
SLCO3A1
NGRN
RHCG
FANCI
MCTP2
VIMP
UNC45A
RGMA
WDR93
TTC23
LRRK1
TM2D3
TICRR
RCCD1
ARRDC4
LINC00923
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
C15orf32
MESP2
SPATA8
ADAMTS17
DNM1P46
CERS3
FAM169B
KIF7
ZNF710
HDDC3
SPATA41
GDPGP1
OR4F6
OR4F15
FAM174B
TTLL13
MIR3174

Genes in Wide Peak

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

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

Genes
LINC00393
RNY1P8
KLF5

Genes in Wide Peak

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

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

Genes
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36\|ENSG00000251846.1
RN7SL687P
ABCD1
ARHGAP4
ATP2B3
AVPR2
BGN
TEX28
DUSP9
EMD
FLNA
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
TMEM187
TKTL1
BCAP31
TREX2
SRPK3
HAUS7
PDZD4
FAM58A
PNCK
OPN1MW2
MIR718

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q31.1.

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

Genes
ITGA6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.1.

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

Genes
LINC00517
SNORA42\|ENSG00000200385.1
TTC6
MIR4503
SLC25A21
RN7SKP257
DPPA3P2
RN7SKP21
PTCSC3
snoU13\|ENSG00000238718.1
SNORA31\|ENSG00000253059.1
KIAA0391
FOXA1
NFKBIA
PAX9
PSMA6
SRP54
SSTR1
KIAA0391
MBIP
PPP2R3C
BRMS1L
INSM2
MIPOL1
CLEC14A
RALGAPA1
SFTA3
FAM177A1
LINC00609

Genes in Wide Peak

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

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

Genes
SDHC
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PBX1
PRCC
TPM3
PDE4DIP
SCARNA20\|ENSG00000253060.1
RN7SL425P
snoU13\|ENSG00000238859.1
RN7SL269P
RN7SL333P
C1orf112
F5
RNA5SP66
LINC00970
LINC00626
ANKRD36BP1
SFT2D2
MIR1255B2
snoU13\|ENSG00000238325.1
RNA5SP65
POGK
MIR921
RNA5SP64
UCK2
TMCO1
SNORD112\|ENSG00000252359.1
U3\|ENSG00000212538.1
RNA5SP63
RNA5SP62
SNORD112\|ENSG00000252740.1
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64\|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64\|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13\|ENSG00000238843.1
BGLAP
SNORA26\|ENSG00000252236.1
SCARNA4\|ENSG00000252808.1
SNORA42\|ENSG00000207475.1
snoU13\|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59\|ENSG00000252682.1
SNORA58\|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3\|ENSG00000252669.1
snoU13\|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31\|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13\|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
ALDH9A1
APCS
APOA2
ATP1A2
ATP1A4
ATP1B1
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
CHRNB2
CKS1B\|ENSG00000173207.8
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
DPT
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
DARC
GBA
GJA5
GJA8
HDGF
HSPA6
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ10
KCNN3
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYOC
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PI4KB
PKLR
PRRX1
POU2F1
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
XCL2
VPS72
THBS3
TCHH
CCT3
TUFT1
USF1
DAP3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
ADAM15
PEX11B
CREG1
CD84
SELENBP1
MPZL1
SH2D2A
TBX19
PRPF3
ARHGEF2
DEDD
AIM2
CHD1L
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
GPA33
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
SLC27A3
TDRKH
CD160
PMF1
DUSP12
VPS45
KIAA0907
KIFAP3
ATF6
POGZ
SYT11
PRRC2C
RPRD2
SMG5
NCSTN
GPR161
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
MPC2
OLFML2B
C1orf43
DNM3
CHTOP
LCE2B
OR10J1
USP21
SLC39A1
LAMTOR2
TMOD4
NME7
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
CCDC181
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
MROH9
TARS2
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
NUF2
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
MAEL
AQP10
SLAMF9
PYGO2
NUP210L
DUSP27
RCSD1
MEX3A
METTL18
GORAB
PIGM
IGSF8
C1orf85
PGLYRP3
SLAMF6
FCRL1
FCRL3
FMO9P
TADA1
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
TSACC
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
NBPF12
LELP1
DCST1
METTL11B
FAM78B
BNIPL
LRRC71
PYHIN1
SPRR4
PPIAL4A
TTC24
LCE4A
NBPF11
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
TIPRL
RIIAD1
THEM5
NBPF16
ANKRD34A
C1orf204
HIST2H2AB
S100A7A
RXFP4
C1orf110
OR10R2
FCRL6
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PEAR1
ILDR2
NOTCH2NL
LYSMD1
HRNR
FLG2
FMO6P
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
NBPF9
HIST2H2BF
ETV3L
LRRC52
OR10J3
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR557
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
TSTD1
C2CD4D
NBPF20
MIR1295A
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q23.3.

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

Genes
MYB
AHI1
MIR548A2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q21.1.

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

Genes
MIR548AH
MIR4450
SNORD50\|ENSG00000199857.1
CDKL2
BTC
PPBPP2
RN7SL218P
PPBP
PF4
PF4V1
SNORA3\|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
AFM
AFP
ALB
AREG
ART3
SCARB2
EREG
CXCL1
CXCL2
CXCL3
IL8
CXCL10
CXCL9
PPEF2
CXCL6
CXCL11
CXCL5
USO1
ADAMTS3
G3BP2
PARM1
RCHY1
ANKRD17
NAAA
NUP54
SDAD1
SHROOM3
THAP6
C4orf26
RASSF6
EPGN
COX18
CCDC158
MTHFD2L
AREGB
FAM47E
FAM47E

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
RNF224
TUBB4B
NELFB
NDOR1
TOR4A
EXD3
TMEM203
SLC34A3
TPRN
C9orf169
FAM166A
C9orf173
NRARP
RNF208

Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
MAML2
BIRC3
ATM
CCND1
CARS
CBL
DDB2
DDX10
EXT2
FANCF
FLI1
HRAS
LMO1
LMO2
MEN1
NUMA1
NUP98
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
ARHGEF12
CREB3L1
snoU13\|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13\|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8\|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13\|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64\|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11\|ENSG00000252992.1
RNY4P6
ZNF259
snoU13\|ENSG00000238625.1
LINC00900
snoU13\|ENSG00000239153.1
ACA59\|ENSG00000252870.1
snoU13\|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39\|ENSG00000264997.1
RNA5SP349
RNA5SP348
MMP12
WTAPP1
snoU13\|ENSG00000239154.1
snoU13\|ENSG00000252679.1
MIR3920
snoU13\|ENSG00000238388.1
RN7SKP115
RN7SL222P
RN7SKP53
RNA5SP347
RNA5SP346
RNA5SP345
SRSF8
SRSF8
MIR548L
VSTM5
RN7SL195P
snoU13\|ENSG00000238437.1
MED17
SNORA40\|ENSG00000210825.1
SNORA18\|ENSG00000207145.1
SNORD5\|ENSG00000239195.1
SNORA8\|ENSG00000207304.1
SNORA1\|ENSG00000206834.1
SNORD6
SNORA32\|ENSG00000206799.1
SNORA25\|ENSG00000207112.1
SCARNA9
RN7SL223P
SLC36A4
snoU13\|ENSG00000239086.1
DISC1FP1
CHORDC1
SNORD56\|ENSG00000207299.1
TRIM49D1
TRIM64B
TRIM77
FOLH1B
GRM5
TMEM135
RN7SL225P
snoU13\|ENSG00000238666.1
PCF11
SNORA70E
snoU13\|ENSG00000238995.1
SNORD112\|ENSG00000252592.1
DKFZP434E1119
ACER3
GUCY2EP
RNA5SP344
UVRAG
RN7SL786P
MOGAT2
SNORD15B
SNORD15A
MIR326
NEU3
RN7SL239P
MIR4696
SNORD43\|ENSG00000212277.1
RN7SKP297
SNORA7\|ENSG00000206913.1
RNA5SP343
UCP2
RN7SKP243
MRPL48
MIR139
snoU13\|ENSG00000238768.1
RNA5SP342
ZNF705E
ENPP7P8
UNC93B6
MIR3664
MIR548K
FGF3
MIR3164
TPCN2
MIR4691
FAM86C2P
DOC2GP
C11orf72
RN7SL59P
PTPRCAP
RN7SKP239
POLD4
snoU13\|ENSG00000238892.1
SYT12
U3\|ENSG00000252709.1
RN7SL12P
RBM14
ZDHHC24
SNORA43\|ENSG00000201733.1
snoU13\|ENSG00000238763.1
snoU13\|ENSG00000238752.1
GAL3ST3
AP5B1
RN7SL309P
MIR4489
MIR4690
MALAT1
POLA2
SLC22A20
FAU
RN7SL114P
MIR1237
TEX40
VEGFB
OTUB1
RN7SL596P
C11orf95
SLC22A10
RN7SL259P
SNHG1
RN7SL119P
TMEM223
C11orf83
SNORA57\|ENSG00000206597.1
METTL12
MIR3654
MIR1908
MIR611
RPLP0P2
SYT7
RN7SL23P
SDHAF2
PGA4
PGA3
MS4A18
MS4A4E
MS4A2
OOSP1
RN7SKP192
MIR3162
RN7SL435P
RN7SL42P
GLYATL1P2
BTBD18
C11orf31
RTN4RL2
RN7SKP259
RNA5SP341
PRG2
P2RX3
snoU13\|ENSG00000238692.1
OR5G5P
TRIM51HP
TRIM49B
OR4C5
MIR3161
RNA5SP340
snoU13\|ENSG00000252447.1
KBTBD4
PTPMT1
RN7SL652P
RN7SL772P
SNORD67\|ENSG00000212135.1
SNORD67\|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
PHF21A
CHST1
CD82
C11orf96
RN7SKP287
HNRNPKP3
SNORA31\|ENSG00000251838.1
TRAF6
COMMD9
MIR3973
TRIM44
MIR1343
EHF
CD59
C11orf91
EIF3M
U3\|ENSG00000212551.1
DNAJC24
ARL14EP
RN7SL240P
RN7SKP158
LINC00678
RNA5SP339
SVIP
RNA5SP338
RNA5SP337
RNA5SP336
SLC6A5
SNORA1\|ENSG00000207407.1
MIR4486
RNA5SP335
RNA5SP334
RNA5SP333
SAA3P
TPH1
SNORD14B
SNORD14A
OR7E14P
RN7SKP90
C11orf58
RN7SL188P
PSMA1
RNA5SP332
SPON1
RNA5SP331
RN7SKP151
LINC00958
SCARNA16\|ENSG00000252329.1
PARVA
SNORD97
LYVE1
RNU6ATAC33P
ADM
RN7SKP50
RN7SL56P
snoU13\|ENSG00000238387.1
SNORA23
MIR5691
RNA5SP330
SNORA45
SNORA3\|ENSG00000200983.1
SCARNA20\|ENSG00000252778.1
OR10AB1P
GVINP1
TAF10
RRP8
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62\|ENSG00000201980.1
OR51C1P
SNORA7\|ENSG00000206976.1
snoU13\|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
ACAT1
ACP2
ACRV1
ACTN3
ADRBK1
AP2A2
APLNR
ALDH3B1
ALDH3B2
AMPD3
APBB1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
RHOG
ARHGAP1
PHOX2A
ARL2
ARNTL
ARRB1
ART1
ASCL2
FXYD2
BAD
BBS1
BDNF
SERPING1
CAPN5
VPS51
MRPL49
ZNHIT2
MPPED2
MYRF
TMEM258
DAGLA
CALCA
CALCB
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CCKBR
CD3D
CD3E
CD5
CD6
MS4A1
MS4A3
CD44
CD81
CD151
CDKN1C
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
TPP1
CLNS1A
CNGA4
CNTF
COPB1
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSD
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FDX1
FEN1
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GSTP1
GTF2H1
GUCY1A2
H2AFX
HBB
HBD
HBE1
HBG2
HMBS
SLC29A2
HPX
HSPA8
DNAJC4
HTR3A
IGF2
IGHMBP2
IL10RA
IL18
ILK
INCENP
INS
INPPL1
IRF7
STT3A
KCNA4
KCNC1
KCNJ1
KCNJ11
KCNQ1
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LSP1\|ENSG00000130592.9
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
KMT2A
MMP1
MMP3
MMP7
MMP8
MMP10
MMP13
MRE11A
MTNR1B
MUC2
MUC6
MYBPC3
MYO7A
MYOD1
NAP1L4
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
NUCB2
OMP
OPCML
SLC22A18
OSBP
OVOL1
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PDE3B
PGA5
PGR
PIK3C2A
PLCB3
POLR2G
POLR2L
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRKRIR
PSMA1
PSMC3
PSMD13
PTH
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RCN1
RDX
RELA
DPF2
RNH1
ROM1
MRPL23
RPL27A
RPS3
RPS6KB2
RPS13
RRM1
SAA1
SAA2
SAA4
SCN2B
SCN4B
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SMPD1
SORL1
SPI1
SPTBN2
SRPR
TRIM21
SSRP1
ST5
ST14
STIM1
STX3
STX5
ABCC8
TAGLN
TALDO1
TCN1
TEAD1
TECTA
TH
THRSP
TSPAN4
TM7SF2
TNNI2
TNNT3
TRPC6
TSG101
PHLDA2
TUB
TYR
UCP3
SCGB1A1
UPK2
BEST1
WEE1
WNT11
SF1
ZFPL1
ZNF143
ZBTB16
ZNF195
ZNF202
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIBP2
PPFIA1
SLC43A1
IFITM1
DGKZ
BARX2
API5
MADD
OR6A2
DCHS1
EIF3F
JRKL
CTSF
EED
FADD
BANF1
MTMR2
RPS6KA4
BRSK2
AIP
SART1
USP2
FIBP
HTR3B
ZW10
MTA2
UBE2L6
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
MICAL2
CTR9
CEP57
ARHGAP32
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
TRIM66
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
TSPAN32
TSSC4
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
MRVI1
TRIM22
PRG3
IFITM3
YAP1
CDC42EP2
NXF1
DEAF1
KAT5
HYOU1
IPO7
SSSCA1
HTATIP2
IFITM2
DRAP1
TRIM3
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
ME3
GPR83
YIF1A
EHD1
STIP1
CLP1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
PKP3
HPS5
PTGDR2
SLCO2B1
RRAS2
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
SWAP70
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
DENND5A
NUP160
NCAPD3
FNBP4
SIK3
SIRT3
CLCF1
OR52A1
VSIG2
BACE1
FAM89B
ARFIP2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
KIAA1549L
PRDX5
POU2F3
ABTB2
BRMS1
CHRDL2
PAMR1
ANAPC15
ZDHHC5
ATL3
TSKU
REXO2
C2CD3
DAK
TENM4
B3GAT3
FBXO3
SERGEF
OR5L2
PPP1R14B
OR8B8
OR10A3
TIMM10B
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
ACAD8
B3GAT1
DKK3
RBMXL2
RAB30
PGAP2
PRPF19
DCPS
C11orf54
AAMDC
MACROD1
SLC43A3
ZBTB44
THYN1
DDX25
PACSIN3
TRPM5
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
UBQLN3
KCNK4
RNF141
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
TMEM216
BET1L
CEND1
COA4
SLC15A3
MS4A4A
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
CYB5R2
RSF1
SPA17
FXYD6
C11orf24
CDHR5
CNTN5
SIAE
TOLLIP
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39A
BTG4
NXPE4
SYTL2
ANKRD49
MS4A12
MRPL16
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
USP47
VPS37C
ANO1
TRIM68
NADSYN1
FAM86C1
C11orf57
NAT10
CCDC87
PPP6R3
UEVLD
RNF121
LIN7C
SLC35C1
TCP11L1
LGR4
PIDD
ELMOD1
KCNQ1DN
SOX6
CDC42BPG
FOXRED1
AMBRA1
PACS1
KDM4D
KBTBD4
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
GPR137
IFT46
SMCO4
C11orf30
PRDM10
PRDM11
CABP4
CHRNA10
SLC17A6
TRIM49
PNPLA2
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
CARNS1
SYT13
USP28
PHRF1
LRRC4C
SCUBE2
PLEKHB1
MS4A7
ZBED5
CREBZF
CARD18
SIGIRR
CCDC90B
CCDC81
AASDHPPT
ALX4
RIC8A
MRPL17
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
EPS8L2
KLC2
TUT1
MRPL11
STK33
KCTD14
CHID1
LRFN4
AHNAK
ALG8
PRRG4
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
OR51G1
OR51B4
OR51B2
OR52N1
FAM118B
RIC3
DYNC2H1
NLRX1
MSANTD2
C11orf80
NARS2
E2F8
SLC25A22
CCDC82
ZNF408
CLMP
NAA40
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
ATHL1
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
PTDSS2
GDPD5
CLPB
UNC93B1
SBF2
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
FAM160A2
RNASEH2C
FAR1
TMEM126A
DCUN1D5
BTBD10
EIF1AD
NUDT22
ARFGAP2
MSANTD4
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
TRIM51
BUD13
TMEM25
PTPN5
RPUSD4
MICALCL
RELT
UBASH3B
C11orf70
LGALS12
TRIM5
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
NAV2
ATG16L2
GLB1L2
SYT8
TSPAN18
ESAM
CCDC34
SLC39A13
DEPDC7
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
PRKCDBP
VPS26B
GLB1L3
CDCA5
SAAL1
SLC22A9
TIRAP
CARD16
OSBPL5
C1QTNF4
C1QTNF5
TMEM123
LRRC56
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRE
MRGPRF
ART5
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
FAT3
TMEM45B
CYP2R1
DBX1
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
XRRA1
UBQLNL
MUC15
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf84
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
C11orf42
GPHA2
ADAMTS15
NLRP6
B3GNT6
METTL15
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
MRPL21
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYB561A3
PPP1R32
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
MS4A6E
DEFB108B
PELI3
ANGPTL5
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
C11orf86
NUDT8
ANKK1
OR52B2
OR4C3
OR4S1
C11orf35
EML3
TMEM151A
OR51F1
RNF214
MRGPRX1
NPAS4
AQP11
OR10AG1
OR5J2
OR4C13
OR4C12
CSNK2A3
OR51V1
C11orf85
SLC25A45
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
OR9G4
LINC00301
P4HA3
PGM2L1
KLHL35
KCTD21
EFCAB4A
CCDC88B
TTC9C
SLC22A24
RCOR2
IGSF22
OR10A4
OLFML1
NLRP10
NLRP14
ANO9
LUZP2
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
B4GALNT4
OR52L1
OR2AG2
OR52B6
OTOG
DCDC1
C11orf53
MS4A10
OR2AT4
HEPHL1
OR10A2
OVCH2
TBX10
PDDC1
GALNT18
NCR3LG1
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MRGPRG
SLC22A25
IFITM5
FAM99A
OR56B1
INSC
FIBIN
SPDYC
LIPT2
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
FOLR4
KDM4E
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
LINC00610
FAM180B
PCNXL3
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR130A
MIR192
MIR210
MIR34B
MIR34C
DDI1
BLID
TMEM41B
CARD17
OR5B3
CCDC73
MS4A13
HEPN1
TRIM49C
CLDN25
TRIM64C
MIR610
NEAT1
MUC5B
MIR708
PATE3
MIR1261
MIR1304
MIR302E
MIR670
MIR4300
MIR4301
MIR3165
MIR1260B
MIR3159
MIR4298
MIR4299
MIR3163
MIR3166
MTRNR2L8
CCDC179
CASP12
TPBGL
RBM4
MIR4697
MIR4686
MIR4490
MIR548AL
MIR4487
MIR4493
MIR4491
MIR4492
MIR4692
MIR4694
MIR4687
MIR4693
MIR4488
MIR5579

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 - 54 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	2.9078e-138	2.4083e-133	chr9:21931610-22003135	2
16q23.1	5.0482e-78	5.0482e-78	chr16:78098006-79031486	1
4q22.1	1.3509e-40	1.0655e-39	chr4:91271445-93240505	1
Xp21.1	6.6507e-36	5.6969e-35	chrX:32117084-32611359	2
5q12.1	1.0479e-31	1.0479e-31	chr5:58998410-59780946	2
2q22.1	3.1052e-27	3.3401e-25	chr2:140708948-143637838	2
6p25.3	3.4705e-23	3.4705e-23	chr6:1608837-2624052	2
7q31.1	9.2943e-30	4.4051e-23	chr7:110746146-111366370	1
3p14.2	4.7823e-22	1.854e-14	chr3:59702822-61026498	2
8p23.2	1.1835e-13	6.7787e-13	chr8:2112968-4251283	2
18q21.2	6.9633e-16	2.2584e-11	chr18:48472083-48650073	3
20p12.1	2.1972e-08	2.1367e-08	chr20:14301156-15274325	2
19p13.3	7.2998e-08	1.5323e-07	chr19:1103802-1189539	2
10p11.21	2.6686e-06	5.2712e-06	chr10:34059131-35328087	1
11q25	5.5793e-06	5.757e-06	chr11:130433734-135006516	18
Xp11.3	9.0779e-09	9.2071e-06	chrX:44702452-45008304	2
7q36.3	3.0944e-13	8.1681e-05	chr7:157210222-158385117	3
1p13.2	2.1743e-05	9.3243e-05	chr1:112530734-118507228	63
4p15.2	0.00010587	0.00010576	chr4:20726855-22351071	1
2q33.3	1.073e-06	0.00017761	chr2:204826225-206558638	1
3p14.3	1.5153e-09	0.0002594	chr3:53923579-55500153	3
21q22.12	4.4895e-05	0.00029893	chr21:36102470-37096497	1
3q26.31	0.00057283	0.00057283	chr3:174345545-175760559	3
1q44	0.00076305	0.00076305	chr1:245290228-247052144	7
Xq21.33	0.00083722	0.0012889	chrX:96134519-96599519	2
11p15.4	0.0019779	0.0020128	chr11:1-3686943	97
17q25.3	0.0023963	0.0023662	chr17:80604514-80902410	6
6q26	0.00094945	0.0025064	chr6:161693099-163153207	1
3q11.1	1.504e-06	0.0029688	chr3:90078624-93767487	3
13q14.2	0.00021653	0.003916	chr13:48875329-49064807	2
1p36.11	0.00092771	0.0040921	chr1:12821076-31774502	310
10q23.31	0.00051951	0.005533	chr10:89183250-92501260	32
22q11.1	0.0069291	0.0069902	chr22:1-18218209	21
18q12.2	6.9551e-06	0.0083866	chr18:36593175-39537209	2
16p13.3	0.013804	0.014	chr16:1-1758773	78
3p26.2	8.605e-06	0.039475	chr3:3220635-4535479	3
12q23.1	0.041117	0.040234	chr12:73057951-117648232	307
15q11.2	0.041924	0.042038	chr15:1-31198928	93
21q11.2	0.00029098	0.060922	chr21:1-19650435	31
18q22.3	1.2898e-05	0.066334	chr18:56469085-78077248	87
17p12	0.083857	0.087212	chr17:11060240-25626166	144
Xq11.2	0.039421	0.087212	chrX:62570171-64711702	7
6q16.3	0.041558	0.092423	chr6:64422619-119281181	254
10p15.3	0.046512	0.10785	chr10:1-6469154	55
19q11	0.044018	0.12444	chr19:23553827-29422400	7
10q21.1	0.046149	0.13557	chr10:38686143-71563405	192
13q12.11	0.0046735	0.14419	chr13:1-28577687	98
9p23	3.2805e-08	0.17469	chr9:1-12687261	53
13q21.31	0.022017	0.17469	chr13:57458876-69271491	30
14q23.3	0.17906	0.17469	chr14:66963153-67658112	1
18p11.23	0.17431	0.17469	chr18:2802589-12313664	59
21q21.1	0.00055511	0.20678	chr21:1-30909774	66
8p12	0.041117	0.21801	chr8:17940701-47750537	204
4q34.3	0.0008746	0.22604	chr4:170189485-191154276	99

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
PIH1

Genes in Wide Peak

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

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

Genes
RN7SKP248

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
MIR3915
RNA5SP501

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

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

Genes
FKSG52
MIR582

Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
snoU13\|ENSG00000238922.1

Genes in Wide Peak

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

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

Genes
U3\|ENSG00000212211.1
NPCDR1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

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

Genes
RN7SL872P
RNA5SP251

Genes in Wide Peak

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

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

Genes
RN7SL695P
SMAD4
ELAC1

Genes in Wide Peak

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

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

Genes
RNA5SP475
FLRT3

Genes in Wide Peak

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

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

Genes
GPX4
SBNO2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

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

Genes
PARD3

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
OPCML
IGSF9B
NCAPD3
ACAD8
B3GAT1
THYN1
NTM
JAM3
GLB1L2
VPS26B
GLB1L3
SPATA19
C11orf44
SNX19
MIR4697

Genes in Wide Peak

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

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
MIR595
PTPRN2
MIR5707

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
WDR3
SNORA40\|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3\|ENSG00000221040.1
SNORA42\|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13\|ENSG00000238975.1
WNT2B
snoU13\|ENSG00000238761.1
snoU13\|ENSG00000239111.1
AMPD1
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD58
IGSF3
MOV10
NGF
NHLH2
PTGFRN
SLC16A1
SYCP1
TSHB
CSDE1
CD101
TSPAN2
BCAS2
AP4B1
PHTF1
PTPN22
RSBN1
GDAP2
FAM46C
ST7L
SLC22A15
CTTNBP2NL
OLFML3
DCLRE1B
VTCN1
SIKE1
TRIM45
VANGL1
MAB21L3
SYT6
HIPK1
MAGI3
FAM19A3
PPM1J
C1orf137
MIR320B1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.2.

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

Genes
KCNIP4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q33.3.

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

Genes
PARD3B

Genes in Wide Peak

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

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

Genes
ESRG
CACNA2D3
LRTM1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.12.

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

Genes
MIR802

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000271842.1
MIR4789
RN7SKP40

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q44.

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

Genes
SNORA25\|ENSG00000252011.1
SNORD112\|ENSG00000252495.1
SCCPDH
KIF26B
TFB2M
SMYD3
CNST

Genes in Wide Peak

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

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

Genes
RN7SL74P
RPA4

Genes in Wide Peak

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

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

Genes
CARS
HRAS
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
ART1
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1\|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
RNH1
MRPL23
TALDO1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
TRPM5
BET1L
CEND1
CDHR5
TOLLIP
PIDD
KCNQ1DN
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
SYT8
OSBPL5
LRRC56
MRGPRE
ART5
SCGB1C1
NLRP6
C11orf35
EFCAB4A
ANO9
B4GALNT4
PDDC1
MRGPRG
IFITM5
FAM99A
IFITM10
MIR210
MUC5B
MIR4298
MIR4686

Genes in Wide Peak

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

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

Genes
MIR4525
RAB40B
TBCD
FN3K
FN3KRP
ZNF750

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.1.

Table S56. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
U3\|ENSG00000212598.1
PROS1
STX19

Genes in Wide Peak

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

Table S57. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RB1
LPAR6

Genes in Wide Peak

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

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PAX7
SDHB
ARID1A
MDS2
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24\|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13\|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18\|ENSG00000252691.1
SCARNA17\|ENSG00000252190.1
MAN1C1
snoU13\|ENSG00000238889.1
SYF2
snoU13\|ENSG00000238986.1
RN7SL857P
snoU13\|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13\|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13\|ENSG00000239020.1
PADI6
MIR3972
U1\|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1\|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13\|ENSG00000238818.1
DDI2
AGMAT
SCARNA21\|ENSG00000251866.1
C1orf195
SCARNA11\|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
ALPL
C1QA
C1QB
C1QC
CAPZB
CASP9
RUNX3
CDA
CDC42
CD52
RCC1
CLCNKA
CLCNKB
CNR2
DDOST
E2F2
ECE1
EPHA2
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
FUCA1
IFI6
GALE
SFN
GPR3
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
NBL1
OPRD1
PAFAH2
PLA2G2A
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC9A1
TAF12
TCEA3
TCEB3
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
FCN3
ALDH4A1
EIF4G3
MAP3K6
SNRNP40
THEMIS2
CROCC
PUM1
ZBTB40
PTPRU
CELA3A
WASF2
HNRNPR
SRRM1
CNKSR1
PDPN
GMEB1
NUDC
SRSF10
RCAN3
PADI2
LYPLA2
CTRC
DNAJC8
SPEN
KDM1A
WDTC1
EMC1
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
CELA3B
PADI4
TMEM50A
STX12
CLIC4
SZRD1
LDLRAP1
HSPB7
AHDC1
SMPDL3B
PADI1
HP1BP3
CELA2B
MECR
MRTO4
YTHDF2
PADI3
WNT4
FBXO42
RNF186
FBLIM1
MED18
PQLC2
TRNAU1AP
TMEM51
XKR8
ARHGEF10L
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
RCC2
MTFR1L
C1orf63
PITHD1
NIPAL3
SEPN1
KIF17
GRHL3
IL22RA1
CELA2A
GPATCH3
PLA2G2F
CEP85
PINK1
PRAMEF1
PRAMEF2
PHACTR4
AUNIP
EFHD2
RSG1
NKAIN1
MUL1
LIN28A
FAM110D
DHDDS
ZNF436
TAS1R2
ACTL8
SESN2
TMEM222
USP48
NBPF3
TRIM63
SYTL1
IGSF21
STPG1
UBXN11
ATPIF1
FHAD1
FAM46B
C1orf172
LRRC38
IFFO2
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
C1orf213
PDIK1L
IFNLR1
FAM43B
PAQR7
FAM76A
AKR7L
TMCO4
ZNF683
SLC25A34
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
CATSPER4
TMEM82
TRNP1
CD164L2
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
PRAMEF11
PRAMEF6
MINOS1
PRAMEF7
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
C1orf234
MIR4253
MIR3917
MIR3675
MIR4419A
MIR4425
MIR4418
MIR378F

Genes in Wide Peak

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

Table S59. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PTEN
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13\|ENSG00000238991.1
ANKRD22
SNORD74\|ENSG00000200891.1
RN7SL78P
CFL1P1
ACTA2
FAS
IFIT2
IFIT3
LIPA
LIPF
CH25H
PAPSS2
MINPP1
KIF20B
IFIT5
PANK1
RNLS
STAMBPL1
ATAD1
LIPJ
LIPM
SLC16A12
IFIT1B
LIPK
LIPN
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.1.

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13\|ENSG00000251737.1
RN7SL843P
CECR9
CECR3
CECR7
HSFY1P1
TPTEP1
KCNMB3P1
OR11H1
POTEH
ATP6V1E1
IL17RA
BCL2L13
CECR6
CECR5
CECR2
CECR1
SLC25A18
GAB4
CCT8L2
XKR3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LINC00669
RN7SKP182

Genes in Wide Peak

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

Table S62. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CCDC154
PRSS29P
C1QTNF8
MSLNL
METRN
MIR3176
MIR5587
ITFG3
HBZ
SNRNP25
POLR3K
WASIR2
WASH4P
DDX11L10
ARHGDIG
CLCN7
HBA1
HBA2
HBM
HBQ1
MPG
NME4
CAPN15
SSTR5
TPSAB1
UBE2I
NPRL3
AXIN1
RGS11
CACNA1H
BAIAP3
RHBDL1
PIGQ
RAB11FIP3
IFT140
TELO2
MSLN
STUB1
MRPL28
TPSD1
TPSG1
DECR2
SOX8
GNG13
LUC7L
CRAMP1L
RAB40C
TMEM8A
CHTF18
RHBDF1
NARFL
TPSB2
PDIA2
UNKL
LMF1
FAM173A
TMEM204
ITFG3
WDR24
HAGHL
C16orf13
FAM195A
GNPTG
RHOT2
HN1L
RPUSD1
TSR3
WFIKKN1
CCDC78
C16orf11
FBXL16
WDR90
NHLRC4
C16orf91
JMJD8
PRR25
PTX4
MIR662

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.2.

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SETMAR
LRRN1
SUMF1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BTG1
ALDH2
PTPN11
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56\|ENSG00000200112.1
RN7SL865P
SNORA27\|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7\|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50\|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40\|ENSG00000264043.2
FICD
RNA5SP371
SNORD74\|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13\|ENSG00000238914.1
U8\|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13\|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13\|ENSG00000238800.1
SLC5A8
snoU13\|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13\|ENSG00000239073.1
SNORD74\|ENSG00000201502.1
snoU13\|ENSG00000238361.1
snoU13\|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3\|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13\|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70\|ENSG00000251893.2
GLIPR1
U8\|ENSG00000201809.1
ACACB
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
CMKLR1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
HAL
IGF1
KCNC2
LTA4H
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NTS
OAS1
OAS2
OAS3
PAH
CDK17
SLC25A3
PMCH
PPP1CC
RFX4
RPL6
ATXN2
SELPLG
SYT1
TBX5
TBX3
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UNG
ALX1
BRAP
EEA1
RASAL1
PPFIA2
MAPKAPK5
GALNT4
CRADD
LIN7A
SOCS2
RASSF9
WSCD2
SART3
GIT2
NUAK1
RBM19
NR1H4
SH2B3
ARPC3
PLXNC1
TRAFD1
ERP29
CKAP4
METAP2
SDS
KERA
KRR1
PRDM4
PWP1
NUDT4
RPH3A
FBXO21
UHRF1BP1L
CUX2
KIAA1033
MED13L
ZDHHC17
ISCU
CORO1C
MGAT4C
FBXW8
UTP20
MRPL42
IFT81
CCDC59
FAM216A
SYCP3
CHST11
CCDC53
CCDC41
GPN3
GLTP
ANAPC7
NT5DC3
VPS29
TPCN1
SSH1
TESC
PARPBP
SLC6A15
RIC8B
APPL2
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
FGD6
NDUFA12
ANKS1B
CHPT1
TMCC3
NTN4
TRPV4
ACTR6
NUP37
DDX54
GNPTAB
TCTN1
ACSS3
BBS10
C12orf49
NAA25
SLC24A6
CEP290
MTERFD3
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
METTL25
TCHP
HVCN1
CAPS2
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
SDSL
OSBPL8
IQCD
DEPDC4
CCDC38
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
AMDHD1
GLIPR1L2
TSPAN19
E2F7
RAD9B
FAM109A
TMTC2
TMTC3
C12orf50
ALDH1L2
CCDC63
PLBD2
FAM71C
CCER1
SLC17A8
TCP11L2
C12orf79
GLIPR1L1
POC1B
OTOGL
GAS2L3
MYO1H
HECTD4
MMAB
TMEM119
C12orf74
C12orf42
C12orf75
CCDC42B
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
C12orf73
MIR1251
MIR4303
MIR3685
MIR4495
MIR4497
MIR5700

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL82P
U8\|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8\|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8\|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8\|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
RNA5SP391
LINC00929
SNORA48\|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115\|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64\|ENSG00000270704.2
SNHG14
SNURF
snoU13\|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13\|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13\|ENSG00000239083.1
CHEK2P2
RN7SL584P
APBA2
GABRA5
GABRB3
GABRG3
NDN
OCA2
SNRPN
TJP1
UBE3A
MKRN3
HERC2
CYFIP1
FAM189A1
NPAP1
NDNL2
NIPA2
CHRFAM7A
ARHGAP11B
TUBGCP5
NIPA1
GOLGA6L2
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
GOLGA8EP
OR4M2
HERC2P9
POTEB2
MIR4508
POTEB

Genes in Wide Peak

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

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL163P
SNORD74\|ENSG00000201025.1
snoU13\|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70\|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
CXADR
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
C21orf91
SAMSN1
CHODL
LIPI
ABCC13
POTED
LINC00478
MIRLET7C
MIR125B2
MIR99A
MIR3687
C21orf37

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.3.

Table S67. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BCL2
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25\|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
snoU13\|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8\|ENSG00000199713.1
RN7SL112P
CDH7
CYB5A
KDSR
GRP
LMAN1
MBP
MC4R
NFATC1
SERPINB2
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
SERPINB3
SERPINB4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
VPS4B
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
PIGN
RTTN
KCNG2
CDH20
CDH19
TIMM21
RAX
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
FAM69C
CCBE1
CBLN2
FBXO15
GTSCR1
DOK6
LINC00305
LINC00908
HMSD
CPLX4
ATP9B
LINC00909
HSBP1L1
C18orf63
MIR5011

Genes in Wide Peak

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

Table S68. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MAP2K4
MTND1P15
UBBP4
RN7SL426P
TMEM11
KRT16P3
NOS2P3
USP32P3
UPF3AP2
RN7SL17P
U6\|ENSG00000266839.2
CCDC144CP
SNORA31\|ENSG00000252349.1
SNORA59B
MIR1180
SNORD3C
SNORD3A
GRAPL
SNORD3D
GRAP
FAM83G
RN7SL627P
ZNF286B
TBC1D28
RN7SL639P
KRT16P1
KRT17P2
SMCR8
snoU13\|ENSG00000238691.1
MIR33B
SMCR5
SMCR2
RN7SL775P
TBC1D27
KRT17P1
KRT16P2
USP32P1
RN7SL620P
ZNF287
MIR1288
RN7SL442P
RNA5SP436
ZNF286A
SNORA74\|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13\|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
SNORA74\|ENSG00000252305.1
MIR548H3
RN7SL550P
MIR744
RPL21P122
RN7SL601P
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FLII
KCNJ12
LLGL1
MFAP4
PMP22
MAPK7
MAP2K3
PRPSAP2
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
DHRS7B
B9D1
TVP23B
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
ZNF286A
ZNF624
ELAC2
TEKT3
GID4
FAM106A
LRRC48
ATPAF2
SPECC1
MYOCD
ZSWIM7
SMCR7
SLC5A10
TOM1L2
SLC47A2
TRIM16L
TVP23C
CENPV
FLCN
PLD6
USP32P2
CDRT15L2
C17orf103
LINC00670
CDRT4
CCDC144B
FAM27L
LGALS9B
CCDC144NL
C17orf51
TBC1D26
CDRT1
SHISA6
FAM211A
EVPLL
LGALS9C
MTRNR2L1
MIR4522
MIR1269B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq11.2.

Table S69. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL799P
ARHGEF9
MTMR8
ZC4H2
AMER1
ASB12
MIR1468

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.3.

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PRDM1
ROS1
GOPC
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13\|ENSG00000238563.1
U3\|ENSG00000253091.1
snoU13\|ENSG00000239095.1
snoU13\|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13\|ENSG00000238775.1
SNORA40\|ENSG00000212587.1
RN7SL617P
snoU13\|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13\|ENSG00000238974.1
SNORA73\|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33\|ENSG00000202283.1
snoU13\|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18\|ENSG00000252249.1
U3\|ENSG00000221455.1
U3\|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13\|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73\|ENSG00000222145.1
RN7SL183P
snoU13\|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70\|ENSG00000206886.1
RNA5SP210
SNORD112\|ENSG00000252932.1
HTR1B
U6\|ENSG00000272445.1
snoU13\|ENSG00000239132.1
RNA5SP209
RN7SKP163
U3\|ENSG00000221332.1
MB21D1
snoU13\|ENSG00000238464.1
OOEP
OGFRL1
U3\|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65\|ENSG00000212229.1
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COX7A2
EEF1A1
EPHA7
FOXO3
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
REV3L
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
MTO1
ASF1A
PNISR
IBTK
SENP6
FBXL4
SLC17A5
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
SMIM8
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
BACH2
SMAP1
C6orf164
MICAL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
MCHR2
FAXC
GJA10
USP45
SLC22A16
UBE3D
GTF3C6
MRAP2
KLHL32
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
CD109
PM20D2
SRSF12
KHDC3L
C6orf165
PRSS35
LCA5
C6orf163
AK9
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
MCM9
CEP57L1
PPIL6
DCBLD1
DPPA5
RSPH4A
EYS
GJB7
CEP85L
LIN28B
MIR30A
MIR30C2
FAM26F
RFPL4B
FAM229B
MIR587
METTL24
TRAPPC3L
KHDC1L
MIR2113
MIR4282
MIR4464
MIR4643
MIR548AI
MIR4463

Genes in Wide Peak

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

Table S71. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8\|ENSG00000251909.1
AKR1CL1
U8\|ENSG00000239142.1
U8\|ENSG00000251740.1
U8\|ENSG00000239148.1
U8\|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
CALML3
AKR1C4
KLF6
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
PFKFB3
PFKP
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
ASB13
TUBAL3
AKR1E2
FBXO18
RBM17
IDI2
UCN3
LINC00200
PRR26

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q11.

Table S72. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13\|ENSG00000238514.1
LINC00662
ZNF726
ZNF254
ZNF681
ZNF675
RPSAP58

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.1.

Table S73. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RET
NCOA4
NEUROG3
RN7SL373P
SNORD98
snoU13\|ENSG00000251926.1
SLC25A16
LINC00849
RNA5SP319
RN7SKP202
RN7SL220P
RN7SL394P
LRRTM3
snoU13\|ENSG00000239000.1
snoR442\|ENSG00000252203.1
MIR1296
RN7SL591P
LINC00845
LINC00948
LINC00844
RN7SKP196
snoU13\|ENSG00000238970.1
SNORD2\|ENSG00000238707.1
snoU13\|ENSG00000238355.1
MIR548F1
RNA5SP318
MIR605
RMRPP4
RNA5SP317
LINC00843
SNORA74\|ENSG00000223111.1
SNORA74\|ENSG00000223182.1
RNA5SP316
FAM25D
FAM21D
PARG
C10orf53
DRGX
C10orf128
WDFY4
RNA5SP315
RN7SL527P
GLUD1P2
RNA5SP314
RNA5SP313
ASAH2C
C10orf43
ANTXRLP1
RN7SL453P
BMS1P2
RNA5SP312
AGAP10
LINC00842
GPRIN2
RN7SL248P
FAM35BP
RNA5SP311
RNA5SP310
FAM25E
RSU1P2
CEP164P1
TMEM72
LINC00841
LINC00840
LINC00619
ZNF487
U3\|ENSG00000221400.1
RNU6ATAC11P
snoU13\|ENSG00000238732.1
ZNF33B
ZNF37BP
CCNYL2
ALOX5
ANXA8L2
ANK3
CDK1
CHAT
DNA2
EGR2
ERCC6
GDF2
GDF10
HK1
HNRNPF
HNRNPH3
MBL2
MSMB
NPY4R
SRGN
PRKG1
MAPK8
RBP3
CXCL12
SLC18A3
SUPV3L1
TACR2
TFAM
UBE2D1
ZNF22
ZNF32
ZNF33B
CCDC6
ZNF239
DDX21
VPS26A
BMS1
RHOBTB1
C10orf10
ZWINT
ZNF365
DKK1
CSTF2T
SIRT1
TSPAN15
HERC4
PTPN20B
KIAA1279
CTNNA3
A1CF
NRBF2
FXYD4
CSGALNACT2
RUFY2
FAM21B
CCAR1
OGDHL
CISD1
DNAJC12
ASAH2
ARHGAP22
PBLD
PCDH15
DDX50
OR13A1
BICC1
HKDC1
TET1
SYT15
RASSF4
ARID5B
PHYHIPL
MYPN
LINC00839
ADO
ZFAND4
C10orf71
ZNF488
AGAP4
FRMPD2
FAM170B
ANTXRL
VSTM4
C10orf107
TMEM26
STOX1
C10orf35
RTKN2
ATOH7
SLC16A9
FAM13C
MARCH8
C10orf25
ZNF485
RASGEF1A
REEP3
JMJD1C
IPMK
FAM21C
SGMS1
C10orf40
FAM21A
BMS1P5
AGAP6
LRRC18
AGAP9
FAM25C
PTPN20A
ANXA8
TIMM23B
AGAP7
ASAH2B
BMS1P1
ANXA8L1
AGAP8
FAM25B
FAM25G
TIMM23
MIR4294
MTRNR2L5
MIR3924
MIR5100
PGBD3

Genes in Wide Peak

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

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CDX2
RN7SL272P
URAD
LINC00543
GSX1
RNY1P1
SNORA27\|ENSG00000207051.1
SNORD102
LINC00415
RNY1P3
RN7SL741P
RN7SL289P
PABPC3
LSP1\|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
MIR2276
ANKRD20A19P
LINC00352
LINC00327
LINC00362
RNY3P4
LINC00621
SNORD36\|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13\|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27\|ENSG00000252128.1
snoU13\|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13\|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
PARP4
ATP12A
CDK8
FGF9
GJA3
GJB2
GPR12
GTF3A
PDX1
MIPEP
RNF6
RPL21
SGCG
ZMYM2
IFT88
MTMR6
ZMYM5
NUPL1
SAP18
GJB6
WASF3
SACS
LATS2
POLR1D
CRYL1
ATP8A2
IL17D
MPHOSPH8
TNFRSF19
CENPJ
RNF17
XPO4
MRP63
TPTE2
AMER2
USP12
MTIF3
N6AMT2
SKA3
MICU2
SPATA13
LNX2
C1QTNF9
RASL11A
C1QTNF9B
SHISA2
ATP5EP2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

Table S75. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
JAK2
CD274
RN7SL5P
SNORD27\|ENSG00000251699.1
RN7SL123P
snoU13\|ENSG00000252110.1
RN7SL25P
C9orf38
MLANA
snoU13\|ENSG00000238654.1
INSL4
AK3
CDC37L1
CARM1P1
RN7SL592P
RNA5SP279
RN7SL412P
FAM138C
DMRT1
FOXD4
GLDC
PTPRD
RFX3
RLN1
RLN2
SLC1A1
SMARCA2
VLDLR
KIAA0020
RCL1
DMRT2
INSL6
KDM4C
KANK1
RANBP6
SPATA6L
PLGRKT
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
TPD52L3
IL33
C9orf123
UHRF2
C9orf66
KIAA2026
KCNV2
GLIS3
PPAPDC2
MIR4665

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.31.

Table S76. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
PCDH9
PCDH17
PCDH20
TDRD3
DIAPH3
PRR20A
PRR20B
PRR20C
PRR20D
PRR20E
MIR3169
MIR4704
MIR548X2

Genes in Wide Peak

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

Table S77. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GPHN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.23.

Table S78. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CIDEA
ANKRD62
NPIPB1P
APCDD1
snoU13\|ENSG00000239031.1
RNA5SP450
RNA5SP449
RN7SL862P
snoU13\|ENSG00000239087.1
RN7SL50P
U3\|ENSG00000199856.1
SNORA48\|ENSG00000212626.1
RN7SL537P
LINC00668
RN7SL282P
RPL6P27
RN7SL723P
TMEM200C
SNORD112\|ENSG00000252572.1
snR65\|ENSG00000252576.1
LINC00526
LINC00667
C18orf42
snoU13\|ENSG00000238790.1
snoU13\|ENSG00000238445.1
RN7SL39P
snoU13\|ENSG00000238863.1
SNORA70\|ENSG00000252258.1
EMILIN2
GNAL
IMPA2
NDUFV2
PTPRM
TGIF1
ZBTB14
MYOM1
NAPG
VAPA
DLGAP1
LPIN2
PPP4R1
MYL12A
RALBP1
RAB31
EPB41L3
ANKRD12
SOGA2
TWSG1
CHMP1B
PIEZO2
MPPE1
ARHGAP28
TXNDC2
L3MBTL4
MYL12B
RAB12
LAMA1
LRRC30
MIR3976

Genes in Wide Peak

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

Table S79. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13\|ENSG00000239171.1
LINC00189
U3\|ENSG00000212479.1
RWDD2B
N6AMT1
LINC00113
LINC00515
snoU13\|ENSG00000238314.1
RNA5SP489
7SK\|ENSG00000232512.2
RN7SL609P
LINC00308
LINC00317
LINC00320
RN7SKP147
RN7SL163P
SNORD74\|ENSG00000201025.1
snoU13\|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70\|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
APP
ATP5J
CXADR
GABPA
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
ADAMTS1
USP16
CCT8
BTG3
ADAMTS5
LTN1
USP25
RBM11
LINC00158
MRPL39
C21orf91
MAP3K7CL
JAM2
SAMSN1
CYYR1
LINC00161
CHODL
LIPI
ABCC13
LINC00314
POTED
LINC00478
MIRLET7C
MIR125B2
MIR155HG
MIR99A
MIR548X
MIR3687
C21orf37
MIR4759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p12.

Table S80. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR1
WRN
WHSC1L1
HOOK3
RN7SKP41
U3\|ENSG00000201329.1
POTEA
RN7SL806P
snoU13\|ENSG00000238714.1
SNORD112\|ENSG00000238966.1
RN7SL149P
MIR486
SNORD65\|ENSG00000238936.1
MIR548AO
IDO1
ADAM3A
ADAM5
SNORD38\|ENSG00000207199.1
PLEKHA2
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
RNA5SP264
RN7SKP201
RN7SL457P
RN7SL621P
SNORA70\|ENSG00000252505.1
SNORD13
RNA5SP263
RNA5SP262
RNA5SP261
UBXN8
TUBBP1
FAM183CP
LINC00589
RN7SL781P
RNA5SP260
RNA5SP259
MIR4287
snoU13\|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67\|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13\|ENSG00000238466.1
U3\|ENSG00000251944.1
SNORA62\|ENSG00000201157.1
NAT1
NAT2
ADRA1A
ADRB3
ANK1
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CHRNB3
CLU
DPYSL2
DUSP4
EGR3
EIF4EBP1
DMTN
EPHX2
EXTL3
PTK2B
FNTA
ADAM2
GFRA2
GNRH1
GSR
GTF2E2
NRG1
IKBKB
LOXL2
LPL
NEFM
PLAT
PNOC
POLB
PPP2CB
PPP2R2A
PPP3CC
SFRP1
SFTPC
SLC18A1
SLC20A2
STC1
TACC1
VDAC3
FZD3
KAT6A
ADAM18
ADAM9
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
CHRNA6
DOK2
ASH2L
BAG4
ENTPD4
PHYHIP
SORBS3
NPM2
DCTN6
PNMA2
ADAM28
AP3M2
RBPMS
ERLIN2
LZTS1
PROSC
XPO7
TRIM35
RHOBTB2
DDHD2
KIF13B
PSD3
LEPROTL1
SLC39A14
GPR124
DKK4
LSM1
ADAMDEC1
PURG
GOLGA7
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
THAP1
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
C8orf4
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
DUSP26
HMBOX1
ZMAT4
RNF122
DOCK5
TTI2
RAB11FIP1
REEP4
STMN4
RNF170
TM2D2
SGK196
GINS4
PPAPDC1B
MAK16
FUT10
CHMP7
SMIM19
GOT1L1
AGPAT6
UNC5D
LETM2
HGSNAT
PEBP4
CDCA2
ESCO2
FBXO16
KCNU1
IDO2
R3HCC1
HTRA4
ADAM32
LGI3
SCARA5
NUGGC
C8orf86
MIR320A
C8orf58
MBOAT4
MIR548H4
MIR3148
MIR4288
MIR3622B
SMIM18
MIR4469

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

Table S81. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31\|ENSG00000253013.1
TLR3
snoU13\|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13\|ENSG00000239116.1
snoU13\|ENSG00000238596.1
snoU13\|ENSG00000238319.1
U3\|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173
snoU13\|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51\|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
FAM149A
FBXO8
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
WWC2
CEP44
SNX25
WDR17
ZFP42
SPATA4
ENPP6
ASB5
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR4276
MIR3945
MIR4455

Arm-level results

Table 3. Get Full Table Arm-level significance table - 26 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	1300	0.23	0.353	1	0.28	1.72	0.1
1q	1195	0.37	3.77	0.000535	0.21	-0.692	1
2p	624	0.35	-0.197	1	0.10	-5.81	1
2q	967	0.27	-0.355	1	0.14	-3.88	1
3p	644	0.25	-1.85	1	0.63	7.68	3.11e-13
3q	733	0.46	3.21	0.00384	0.39	1.34	0.179
4p	289	0.22	-3.5	1	0.64	5.84	2.55e-08
4q	670	0.17	-3.59	1	0.53	5.09	1.01e-06
5p	183	0.48	0.892	0.745	0.51	1.67	0.106
5q	905	0.13	-3.4	1	0.55	7.15	8.69e-12
6p	710	0.26	-1.99	1	0.27	-1.63	1
6q	556	0.21	-3.82	1	0.27	-2.39	1
7p	389	0.63	5.94	1.46e-08	0.26	-2.63	1
7q	783	0.54	6.03	1.09e-08	0.25	-1.56	1
8p	338	0.52	2.35	0.0471	0.58	4	0.000157
8q	551	0.61	6.37	1.94e-09	0.33	-0.796	1
9p	301	0.16	-4.59	1	0.61	5.12	1.01e-06
9q	700	0.25	-2.07	1	0.45	2.94	0.00727
10p	253	0.28	-3.41	1	0.36	-1.47	1
10q	738	0.20	-3.2	1	0.34	0.147	0.745
11p	509	0.27	-2.49	1	0.38	0.134	0.745
11q	975	0.21	-1.78	1	0.39	2.86	0.00857
12p	339	0.36	-1.1	1	0.29	-2.74	1
12q	904	0.24	-1.59	1	0.22	-1.98	1
13q	560	0.37	0.0624	1	0.48	2.72	0.0104
14q	938	0.35	1.41	0.35	0.33	1.03	0.29
15q	810	0.23	-2.07	1	0.37	1.56	0.125
16p	559	0.29	-1.79	1	0.40	0.852	0.358
16q	455	0.27	-2.72	1	0.38	-0.133	0.884
17p	415	0.24	-3.25	1	0.50	2.68	0.0105
17q	972	0.26	-0.544	1	0.20	-2.16	1
18p	104	0.40	-1.11	1	0.56	2.45	0.0189
18q	275	0.26	-2.78	1	0.66	6.18	4.36e-09
19p	681	0.19	-3.43	1	0.44	2.71	0.0104
19q	935	0.26	-0.784	1	0.38	2.33	0.025
20p	234	0.64	5.43	2.27e-07	0.30	-2.26	1
20q	448	0.65	6.97	6.45e-11	0.16	-3.9	1
21q	258	0.22	-3.6	1	0.64	5.67	5.59e-08
22q	564	0.28	-1.92	1	0.47	2.74	0.0104
Xq	668	0.24	-2.46	1	0.30	-1.13	1

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/ESCA-TP/11447006/GDAC_MergeDataFiles_10782610/ESCA-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_GENCODE_v18_20140127.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 184 Input Tumor Samples.

Tumor Sample Names
TCGA-2H-A9GF-01A-11D-A37B-01
TCGA-2H-A9GH-01A-11D-A37B-01
TCGA-2H-A9GI-01A-11D-A37B-01
TCGA-2H-A9GJ-01A-11D-A37B-01
TCGA-2H-A9GK-01A-11D-A37B-01
TCGA-2H-A9GL-01A-12D-A37B-01
TCGA-2H-A9GM-01A-11D-A37B-01
TCGA-2H-A9GN-01A-11D-A37B-01
TCGA-2H-A9GO-01A-11D-A37B-01
TCGA-2H-A9GQ-01A-11D-A37B-01

Figure 3. Segmented copy number profiles in the input data

Output

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

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

Region Data

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

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.
Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').
Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

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

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

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

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

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

[2] GISTIC version 1

[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)

[4] GISTIC version 2

[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)

[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)

[7] The Sanger Institute: Cancer Gene Census

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