SNP6 Copy number analysis (GISTIC2) - Lung Squamous Cell Carcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Lung Squamous Cell 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/C1W9582B

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 501 tumor samples used in this analysis: 29 significant arm-level results, 30 significant focal amplifications, and 53 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 - 30 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
3q26.33	4.4921e-200	4.4921e-200	chr3:181401404-182481981	4
8p11.23	4.1358e-83	4.1358e-83	chr8:38170522-38247105	2
11q13.3	2.7776e-76	2.7776e-76	chr11:69699947-70248899	5
8q24.21	2.1362e-28	2.1362e-28	chr8:128297257-128423649	1
4q12	5.8288e-18	5.8288e-18	chr4:56246865-56507740	5
7p11.2	3.4268e-17	3.957e-17	chr7:54781785-55694877	5
2p16.1	4.3767e-17	4.3767e-17	chr2:60450758-61267829	9
5p15.33	5.0697e-19	1.7481e-13	chr5:1-1428010	25
9p13.3	6.0114e-11	6.0114e-11	chr9:35109573-36060450	30
19q13.2	3.093e-25	6.7191e-10	chr19:38271451-39302021	25
19q12	2.1821e-17	3.9199e-08	chr19:30287570-30465652	2
1q21.2	1.7136e-06	1.7136e-06	chr1:120523956-153556563	210
20q11.21	1.41e-05	1.41e-05	chr20:26196264-30564096	26
22q11.21	2.5961e-05	2.5961e-05	chr22:18613558-22141228	100
2q31.2	3.8119e-05	3.8119e-05	chr2:178083264-178154838	3
15q26.3	7.8929e-05	7.8929e-05	chr15:98033377-102531392	38
7q21.2	0.00017796	0.00018728	chr7:91474555-93654751	24
12q15	0.0010006	0.0010006	chr12:67813808-71115184	25
17q25.1	0.0012371	0.0012371	chr17:70468942-76301198	123
5p12	8.4135e-10	0.0015517	chr5:30913798-50133343	87
18q11.2	0.0057202	0.0057202	chr18:23753292-24419705	5
12p13.33	0.0079006	0.0079006	chr12:1-3480534	32
13q34	0.0091281	0.0091281	chr13:113773700-114847012	20
6q12	0.0007358	0.014955	chr6:63706479-65073682	5
14q13.3	0.0084074	0.02394	chr14:36625634-38262673	14
6p12.1	0.0017819	0.057782	chr6:54187909-56484757	8
Xq28	0.075128	0.075128	chrX:147462113-155270560	142
14q32.33	0.090245	0.19931	chr14:98935959-107349540	181
18p11.32	0.22098	0.22098	chr18:1-923766	12
20p12.2	0.23448	0.23448	chr20:11194380-11393881	0 [C20orf187]

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
SOX2
RN7SKP265
RNA5SP150
RN7SL703P

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
WHSC1L1
LETM2

Genes in Wide Peak

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

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

Genes
MIR548K
CTTN
PPFIA1
FADD
ANO1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
CASC8

Genes in Wide Peak

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

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

Genes
RN7SKP30
CLOCK
NMU
TMEM165
PDCL2

Genes in Wide Peak

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

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

Genes
EGFR
SNORA73\|ENSG00000252054.1
SEC61G
LANCL2
VOPP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p16.1.

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

Genes
REL
BCL11A
RNA5SP95
RN7SL632P
RN7SL361P
PEX13
PAPOLG
PUS10
MIR4432

Genes in Wide Peak

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

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

Genes
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
SLC6A19
SLC6A18
MIR4457
MIR4456

Genes in Wide Peak

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

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

Genes
LINC00961
RGP1
RN7SL22P
RMRP
MIR4667
CA9
CD72
NPR2
TESK1
TLN1
TPM2
RECK
RUSC2
CREB3
UNC13B
SPAG8
SIT1
TMEM8B
OR2S2
GBA2
FAM214B
HINT2
ARHGEF39
ATP8B5P
CCDC107
FAM221B
OR13J1
HRCT1
MSMP
FAM166B

Genes in Wide Peak

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

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

Genes
ACTN4
SPRED3
snoU13\|ENSG00000238838.1
RN7SL663P
LGALS4
LGALS7
PSMD8
RYR1
DPF1
KCNK6
SPINT2
MAP4K1
SIPA1L3
EIF3K
CATSPERG
C19orf33
WDR87
YIF1B
PPP1R14A
RASGRP4
ZNF573
FAM98C
CAPN12
GGN
LGALS7B

Genes in Wide Peak

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

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

Genes
CCNE1
URI1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
ARNT
BCL9
NOTCH2
PDE4DIP
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
CTSK
CTSS
ECM1
ENSA
FCGR1A
FLG
FMO5
GJA5
GJA8
IVL
LOR
MCL1
SMCP
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
TCHH
TUFT1
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
CHD1L
SETDB1
SV2A
RBM8A
SF3B4
PIAS3
SEMA6C
POLR3C
TXNIP
MTMR11
TDRKH
CD160
VPS45
POGZ
RPRD2
CA14
NBPF14
LCE2B
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
FAM63A
CDC42SE1
PGLYRP4
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
PGLYRP3
GABPB2
TCHHL1
RPTN
LIX1L
C1orf51
HFE2
ANKRD35
NBPF12
LELP1
BNIPL
SPRR4
PPIAL4A
LCE4A
NBPF11
LCE5A
RIIAD1
THEM5
NBPF16
ANKRD34A
HIST2H2AB
S100A7A
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
NOTCH2NL
LYSMD1
HRNR
FLG2
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
C1orf68
C2CD4D
NBPF20
MIR4257

Genes in Wide Peak

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

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

Genes
XKR7
LINC00028
DEFB122
SNORA40\|ENSG00000212134.1
RNA5SP480
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB123
DEFB124
FRG1B
MIR663A
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q11.21.

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

Genes
CLTCL1
RN7SL280P
RN7SKP221
SCARNA18\|ENSG00000252605.1
SCARNA17\|ENSG00000252143.1
snoU13\|ENSG00000252799.1
TMEM191C
snoU13\|ENSG00000252402.1
SCARNA17\|ENSG00000252020.1
SCARNA18\|ENSG00000252314.1
RN7SKP63
FAM230C
GGT2
FAM230B
POM121L7
BCRP2
P2RX6P
P2RX6
RN7SL389P
POM121L4P
SMPD4P1
RN7SL812P
USP41
FAM230A
RN7SKP131
SCARNA18\|ENSG00000252024.1
SCARNA17\|ENSG00000252571.1
snoU13\|ENSG00000271796.1
PI4KAP1
GGTLC3
MIR1286
SNORA77\|ENSG00000264346.1
MIR1306
MIR4761
GP1BB
MRPL40
RN7SL168P
SNORA15\|ENSG00000251940.1
GSC2
DGCR5
GGT3P
PEX26
ARVCF
COMT
CRKL
SERPIND1
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
SNAP29
DGCR2
TXNRD2
USP18
HIC2
TSSK2
SDF2L1
PPIL2
TRMT2A
YPEL1
ZDHHC8
MED15
TUBA8
DGCR8
GNB1L
RTN4R
C22orf29
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
TUBA3FP
C22orf39
TANGO2
AIFM3
RIMBP3C
YDJC
CCDC116
PI4KAP2
MIR130B
MIR185
RIMBP3B
MIR649
MIR301B
MIR3618

Genes in Wide Peak

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

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

Genes
NFE2L2
MIR3128
HNRNPA3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13\|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
VIMP
TTC23
LRRK1
TM2D3
ARRDC4
LINC00923
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
ADAMTS17
DNM1P46
CERS3
FAM169B
SPATA41
OR4F6
OR4F15

Genes in Wide Peak

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

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

Genes
CDK6
AKAP9
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
CALCR
KRIT1
CYP51A1
GNGT1
PEX1
MTERF
TFPI2
BET1
ANKIB1
SAMD9
CCDC132
RBM48
SAMD9L
HEPACAM2
FAM133B
LRRD1
MIR4652

Genes in Wide Peak

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

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

Genes
MDM2
MYRFL
RN7SL804P
SLC35E3
SNORA70G
DYRK2
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
YEATS4
CCT2
FRS2
CPSF6
KCNMB4
IL22
IL26
MDM1
NUP107
RAB3IP
BEST3
LRRC10

Genes in Wide Peak

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

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

Genes
FLJ45079
LINC00338
LINC00868
MIR636
SNORD1B
SNHG16
PRCD
snoU13\|ENSG00000238418.1
MYO15B
RN7SL573P
MIR3615
CD300LD
GPRC5C
RNA5SP448
LINC00469
SSTR2
SCARNA24\|ENSG00000252274.1
RN7SKP180
LINC00511
AANAT
ACOX1
BIRC5
CDK3
EVPL
FDXR
FOXJ1
GALK1
GRB2
GRIN2C
H3F3B
ICT1
ITGB4
LLGL2
PRPSAP1
RPL38
SEC14L1
SRSF2
SUMO2
SRP68
TK1
GALR2
SPHK1
SLC16A5
SYNGR2
SLC9A3R1
COG1
RECQL5
KIAA0195
ATP5H
ST6GALNAC2
SEPT9
CD300C
CD300A
TMC6
GGA3
JMJD6
EXOC7
KCTD2
WBP2
CDC42EP4
NAT9
SAP30BP
NT5C
CDR2L
MRPS7
HN1
SDK2
TMEM104
C17orf80
ST6GALNAC1
MIF4GD
CASKIN2
TNRC6C
SLC25A19
UBE2O
DNAI2
MRPL38
MFSD11
ARMC7
RHBDF2
NUP85
QRICH2
FAM104A
FBF1
UNK
TRIM47
OTOP2
TTYH2
CYGB
RNF157
METTL23
USH1G
CD300LB
KIF19
AFMID
MGAT5B
CD300LF
C17orf77
TMC8
SLC39A11
TRIM65
UNC13D
FADS6
HID1
TSEN54
UBALD2
TMEM235
RAB37
CD300E
OTOP3
GPR142
ZACN
BTBD17
MXRA7
CPSF4L
SMIM5
SMIM6
TEN1
C17orf99
MIR4316
MIR3678
MIR3615
MIR4738

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p12.

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

Genes
LIFR
HCN1
RN7SL383P
FGF10
CCL28
ANXA2R
SNORD72
RPL37
SNORA57\|ENSG00000212567.1
SNORA63\|ENSG00000199552.1
LINC00604
LINC00603
WDR70
RN7SL37P
RNA5SP181
LMBRD2
U3\|ENSG00000201368.1
BRIX1
C1QTNF3
MIR579
snoU13\|ENSG00000238864.1
C6
C7
C9
CDH6
DAB2
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
C5orf22
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
EMB
MROH2B
EGFLAM
NADK2
UGT3A1
CAPSL
DNAJC21
TTC23L
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
C5orf34
MIR580
CCDC152
MIR4279
MIR3650

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
U3\|ENSG00000265369.2
U3\|ENSG00000252921.1
TAF4B
PSMA8
KCTD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
KDM5A
FKBP4
CBX3P4
CACNA1C
LINC00940
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
WNK1
ADIPOR2
WNT5B
RHNO1
NRIP2
CCDC77
CACNA2D4
FBXL14
DCP1B
B4GALNT3
IQSEC3
LRTM2
MIR3649

Genes in Wide Peak

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

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

Genes
LINC00565
LINC00452
LINC00453
LINC00454
GRK1
DCUN1D2
ATP4B
F7
F10
GAS6
LAMP1
TFDP1
CUL4A
PROZ
RASA3
TMCO3
PCID2
GRTP1
ADPRHL1
TMEM255B

Genes in Wide Peak

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

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

Genes
FKBP1C
PTP4A1
PHF3
LGSN
EYS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.3.

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

Genes
SNORA42\|ENSG00000200385.1
TTC6
MIR4503
SLC25A21
RN7SKP257
DPPA3P2
RN7SKP21
PTCSC3
FOXA1
PAX9
MBIP
MIPOL1
SFTA3
LINC00609

Genes in Wide Peak

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

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

Genes
FAM83B
BMP5
DST
HCRTR2
TINAG
HMGCLL1
COL21A1
GFRAL

Genes in Wide Peak

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

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

Genes
MTCP1
WASH6P\|ENSG00000182484.10
WASIR1\|ENSG00000185203.7
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70\|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36\|ENSG00000251846.1
RN7SL687P
RN7SL667P
snoU13\|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
MIR452
MIR224
U3\|ENSG00000253009.1
LINC00894
LINC00893
RN7SKP267
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
AFF2
G6PD
GABRA3
GABRE
GDI1
HCFC1
HMGB3
IDH3G
IDS
IL9R\|ENSG00000124334.12
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MECP2
MPP1
MTM1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7\|ENSG00000124333.10
TAZ
VBP1
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
MTMR1
FAM50A
GPR50
MAMLD1
BCAP31
SPRY3\|ENSG00000168939.6
ZNF275
TREX2
SRPK3
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
PDZD4
FAM3A
PRRG3
BRCC3
CD99L2
H2AFB3
TMEM185A
FATE1
CXorf40A
FAM58A
PNMA5
RAB39B
PASD1
GAB3
PNCK
ZFP92
CSAG1
VMA21
CTAG1A
H2AFB2
H2AFB1
CXorf40B
MAGEA9B
OPN1MW2
MIR767
HSFX2
SMIM9
CMC4
PNMA6C
MIR718
MIR2114
MIR4330
HSFX1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.33.

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

Genes
AKT1
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51\|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13\|ENSG00000238853.1
RN7SL546P
snoU13\|ENSG00000239061.1
RN7SL472P
LINC00524
U3\|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113\|ENSG00000222185.1
SNORD112\|ENSG00000252009.1
SNORD113\|ENSG00000222095.1
SNORD113\|ENSG00000201710.1
SNORD113\|ENSG00000201036.1
SNORD113\|ENSG00000201500.1
SNORD113\|ENSG00000200150.1
SNORD112\|ENSG00000251918.1
SNORD112\|ENSG00000252144.1
SNORD112\|ENSG00000251949.1
SNORD112\|ENSG00000252873.1
SNORD112\|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6\|ENSG00000272439.1
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
BRF1
HSP90AA1
JAG2
KLC1
MARK3
PPP2R5C
MOK
TNFAIP2
TRAF3
WARS
XRCC3
DLK1
MTA1
BAG5
C14orf2
CDC42BPB
TECPR2
SIVA1
CYP46A1
RCOR1
PACS2
PPP1R13B
KIF26A
GPR132
EVL
CINP
CDCA4
ZNF839
BEGAIN
INF2
ZFYVE21
WDR25
TMEM121
AMN
SETD3
HHIPL1
BTBD6
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
PLD4
ADSSL1
SLC25A29
NUDT14
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
ASPG
RTL1
TMEM179
C14orf180
MIR127
MIR136
MIR154
MIR203
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1197
MIR1193
MIR4309
MIR151B
MIR4710
MIR2392

Genes in Wide Peak

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

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

Genes
RN7SKP146
CETN1
ROCK1P1
ADCYAP1
TYMS
YES1
USP14
THOC1
CLUL1
ENOSF1
COLEC12
C18orf56

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 - 53 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	2.0009e-198	2.0998e-177	chr9:21931610-22003135	2
8p23.2	6.4476e-71	6.4476e-71	chr8:3548028-4251283	2
2q22.1	1.9677e-60	2.8611e-54	chr2:140708948-143637838	2
10q23.31	2.5283e-34	2.5283e-34	chr10:89617158-89755074	3
5q12.1	9.1228e-23	2.5212e-21	chr5:58998410-59780946	2
11p15.5	1.9803e-13	2.1158e-13	chr11:1-4406284	107
1p13.1	1.6941e-17	2.7936e-13	chr1:114515579-119426205	44
19p13.3	3.8308e-13	3.8308e-13	chr19:1-987570	35
4q22.1	2.4944e-13	2.5986e-10	chr4:91271445-93240505	1
13q14.2	6.9725e-16	4.7639e-10	chr13:48875329-49064807	2
3p25.3	1.5298e-15	5.8624e-10	chr3:11593014-11833472	1
18q23	1.2116e-09	1.2282e-09	chr18:74335369-78077248	17
4q35.2	2.1038e-22	3.575e-09	chr4:187179487-191154276	18
Xq22.3	2.7755e-08	2.6554e-08	chrX:107382193-108023686	3
2q37.1	7.3252e-20	3.3958e-08	chr2:213401694-243199373	284
10p15.2	7.7225e-08	8.1275e-08	chr10:1-5197880	32
19q13.32	6.9498e-07	6.9169e-07	chr19:47351962-48473973	29
16q23.1	1.2757e-06	1.319e-06	chr16:78098006-79299841	3
16p13.3	3.9987e-06	4.0547e-06	chr16:3764793-4004422	1
3p13	1.6072e-24	7.5254e-06	chr3:70016017-71729299	2
13q12.11	1.4499e-10	7.5254e-06	chr13:1-21149718	22
7q36.3	1.6044e-06	9.357e-06	chr7:151211607-159138663	39
11q25	3.364e-09	1.2705e-05	chr11:127277502-135006516	36
4q32.3	9.5408e-13	1.7376e-05	chr4:164439857-165912961	4
1p36.11	3.7093e-08	6.1781e-05	chr1:1-29218916	493
15q21.1	1.0506e-07	0.00014012	chr15:44953604-45026122	2
6p25.3	0.00022496	0.00023306	chr6:1-9597208	61
4p15.2	0.00059836	0.00059691	chr4:20726855-22351071	1
3p12.3	2.7982e-17	0.00076581	chr3:75363575-78166985	9
17q25.3	0.00041886	0.00078086	chr17:80031841-81195210	24
9q21.11	3.2117e-08	0.00173	chr9:38619152-71152237	57
Xp21.1	3.3395e-05	0.0023429	chrX:30865118-34644819	7
7q11.22	0.0011144	0.0044864	chr7:69000716-70601215	2
14q11.2	0.0053185	0.0053185	chr14:1-27379462	267
21q11.2	0.0018832	0.0060229	chr21:1-21729079	33
Xp11.3	0.00019677	0.0076974	chrX:44702452-45008304	2
21q22.3	0.0035474	0.0095807	chr21:42217276-44075429	28
6q26	0.0011653	0.011453	chr6:161693099-163153207	1
9p21.1	1.2213e-24	0.01342	chr9:27572512-28982153	3
11q22.1	0.00018048	0.014024	chr11:90647136-100513772	54
Xp22.2	0.00028912	0.01701	chrX:9687508-11137490	5
22q11.21	0.01005	0.01894	chr22:1-22096801	124
22q13.32	0.0070245	0.021309	chr22:45736500-51304566	66
3p12.3	3.2336e-18	0.02225	chr3:78209676-86177974	9
17q11.2	0.0043711	0.025874	chr17:29326736-29722618	5
12q24.31	0.033578	0.033275	chr12:94698881-133851895	391
15q11.2	0.00014443	0.042038	chr15:1-40988962	175
17p11.2	0.023699	0.04773	chr17:20793028-21031068	1
6q22.31	0.0068288	0.061839	chr6:123955968-125285408	1
9p23	7.0182e-14	0.12347	chr9:7887952-12687261	3
2p25.3	0.1431	0.14614	chr2:1-22149177	116
3q11.1	4.0276e-09	0.15163	chr3:87325722-93767487	9
5q31.1	0.0017745	0.24095	chr5:64777655-180915260	828

Genes in Wide Peak

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

Table S30. 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 8p23.2.

Table S31. 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 2q22.1.

Table S32. 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 10q23.31.

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

Genes
PTEN
SNORD74\|ENSG00000200891.1
KLLN

Genes in Wide Peak

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

Table S34. 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 11p15.5.

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

Genes
CARS
HRAS
NUP98
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
AP2A2
RHOG
ART1
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1\|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
RNH1
MRPL23
RRM1
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
PGAP2
TRPM5
BET1L
CEND1
CDHR5
TOLLIP
PIDD
KCNQ1DN
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
SYT8
OSBPL5
LRRC56
MRGPRE
ART5
OR52B4
SCGB1C1
NLRP6
C11orf35
EFCAB4A
ANO9
B4GALNT4
PDDC1
MRGPRG
IFITM5
FAM99A
IFITM10
MIR210
MUC5B
MIR4298
MIR4686
MIR4687

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RNA5SP56
WDR3
SNORA40\|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3\|ENSG00000221040.1
SNORA42\|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
AMPD1
ATP1A1
CASQ2
CD2
CD58
IGSF3
NGF
NHLH2
PTGFRN
SYCP1
TSHB
CSDE1
CD101
TSPAN2
BCAS2
GDAP2
FAM46C
SLC22A15
OLFML3
VTCN1
SIKE1
TRIM45
VANGL1
MAB21L3
SYT6
SPAG17
C1orf137
MIR320B1

Genes in Wide Peak

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

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

Genes
FSTL3
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
AZU1
HCN2
BSG
CDC34
ELANE
GZMM
PALM
POLRMT
PRTN3
PTBP1
MADCAM1
PPAP2C
MED16
SHC2
FGF22
THEG
MIER2
RNF126
LPPR3
KISS1R
R3HDM4
TPGS1
MISP
C2CD4C
ODF3L2
PRSS57
MIR3187

Genes in Wide Peak

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

Table S38. 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 13q14.2.

Table S39. 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 3p25.3.

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

Genes
VGLL4

Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25\|ENSG00000199392.1
GALR1
MBP
NFATC1
ZNF236
CTDP1
TXNL4A
ADNP2
KCNG2
PQLC1
PARD6G
ATP9B
HSBP1L1

Genes in Wide Peak

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

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
F11
FAT1
FRG1
MTNR1A
ZFP42
TRIML2
TRIML1
DUX4L4
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
COL4A5
COL4A6
IRS4

Genes in Wide Peak

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

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

Genes
ACSL3
ATIC
PAX3
FEV
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39\|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6\|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13\|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75\|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112\|ENSG00000251801.1
SNORA25\|ENSG00000272237.1
RNA5SP121
SNORA48\|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13\|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3\|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
snoU13\|ENSG00000238736.1
snoU13\|ENSG00000238428.1
CXCR2P1
DIRC3
RN7SKP43
RNA5SP120
RPL37A
MREG
LINC00607
snoU13\|ENSG00000238663.1
SNORA70\|ENSG00000207274.1
VWC2L
MIR4438
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
INHA
INPP5D
IRS1
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ASIC4
DOCK10
PECR
C2orf83
MFF
ACKR3
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
CCDC140
SLC23A3
GPBAR1
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
CCDC108
C2orf72
RUFY4
DUSP28
MROH2A
ESPNL
C2orf62
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
MIR375
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4268
MIR3132
MIR4269
MIR4786
MIR5001
MIR5702
MIR5703

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.2.

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

Genes
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
KLF6
AKR1C2
IDI1
PFKP
AKR1C3
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
AKR1E2
IDI2
LINC00200
PRR26

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

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

Genes
TPRX2P
SNORD23\|ENSG00000221803.1
RN7SL322P
RN7SL533P
snoU13\|ENSG00000252071.1
C5AR1
CRX
ARHGAP35
NPAS1
SEPW1
SLC8A2
SULT2A1
NAPA
DHX34
SAE1
KPTN
ZC3H4
CCDC9
BBC3
C5AR2
GLTSCR2
GLTSCR1
EHD2
TMEM160
MEIS3
ZNF541
PRR24
TPRX1
MIR3191

Genes in Wide Peak

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

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

Genes
RNA5SP431
PIH1
WWOX

Genes in Wide Peak

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

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

Genes
CREBBP

Genes in Wide Peak

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

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

Genes
FOXP1
MIR1284

Genes in Wide Peak

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

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

Genes
MIR4499
LINC00556
snoU13\|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
GJA3
GJB2
ZMYM2
ZMYM5
GJB6
CRYL1
MPHOSPH8
TPTE2

Genes in Wide Peak

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

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

Genes
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26\|ENSG00000212590.1
snoU13\|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13\|ENSG00000239045.1
DPP6
EN2
MNX1
INSIG1
PTPRN2
VIPR2
XRCC2
UBE3C
DNAJB6
PAXIP1
PRKAG2
NCAPG2
WDR60
ACTR3B
ESYT2
KMT2C
GALNT11
LMBR1
NOM1
C7orf13
RNF32
RBM33
GALNTL5
CNPY1
BLACE
MIR5707

Genes in Wide Peak

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

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

Genes
FLI1
snoU13\|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
APLP2
ETS1
KCNJ1
NFRKB
OPCML
ST14
BARX2
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
PRDM10
TP53AIP1
JAM3
GLB1L2
VPS26B
GLB1L3
TMEM45B
ADAMTS15
C11orf45
SPATA19
C11orf44
SNX19
MIR4697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.3.

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

Genes
RN7SKP105
MARCH1
FAM218A
TRIM61

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
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
C1orf158
snoU13\|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70\|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13\|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16\|ENSG00000252404.1
RN7SL451P
SNORA77\|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13\|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
KCNAB2
FCN3
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
THEMIS2
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
AHDC1
SMPDL3B
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
AUNIP
EFHD2
MMEL1
RSG1
MUL1
NOL9
LIN28A
LINC00115
MORN1
FAM110D
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SESN2
ESPN
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
C1orf170
SYTL1
IGSF21
KIAA2013
THAP3
STPG1
UBXN11
FBXO44
ATPIF1
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
C1orf234
OR4F29
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

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

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

Genes
B2M
PATL2

Genes in Wide Peak

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

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

Genes
IRF4
HULC
snoU13\|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13\|ENSG00000238801.1
RNA5SP202
snoU13\|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13\|ENSG00000238438.1
BMP6
BPHL
DSP
SERPINB1
F13A1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TUBB2A
RIPK1
PRPF4B
CDYL
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
NRN1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
TXNDC5
RIOK1
FOXQ1
HUS1B
SNRNP48
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
PSMG4
C6orf201
PPP1R3G
MIR4645
MIR5683

Genes in Wide Peak

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

Table S57. 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 3p12.3.

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

Genes
RN7SL647P
RN7SL92P
ZNF717
LINC00960
FAM86DP
ROBO2
FRG2C
MIR1324
MIR4273

Genes in Wide Peak

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

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

Genes
MIR4525
RAB40B
snoU13\|ENSG00000238403.1
snoU13\|ENSG00000238947.1
CD7
CSNK1D
FASN
UTS2R
FOXK2
SECTM1
TBCD
SLC16A3
NARF
WDR45B
FN3K
C17orf62
FN3KRP
OGFOD3
ZNF750
B3GNTL1
CCDC57
HEXDC
METRNL
TEX19

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.11.

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

Genes
CBWD3
PGM5P2
RNA5SP284
SNORA70\|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70\|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70\|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70\|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
PGM5
ZNF658
SPATA31A7
CNTNAP3
ANKRD20A1
CBWD5
FOXD4L3
FOXD4L4
SPATA31A6
FAM74A4
ANKRD20A3
ANKRD20A2
FAM27A
SPATA31A2
SPATA31A4
CBWD6
SPATA31A1
FOXD4L6
FOXD4L5
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR4477A

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238969.1
MIR548F5
MIR3915
RNA5SP501
DMD
FTHL17
FAM47A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.22.

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

Genes
RN7SL371P
AUTS2

Genes in Wide Peak

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

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

Genes
CCNB1IP1
SNORD37\|ENSG00000212270.1
TM9SF1
RNA5SP383
DHRS4L1
LINC00596
RN7SKP205
MIR208B
MIR208A
PABPN1
C14orf164
SNORA73\|ENSG00000252114.1
SNORD41\|ENSG00000212302.1
OR6J1
TRAC
TRAJ1
TRAJ2
TRAJ3
TRAJ4
TRAJ5
TRAJ6
TRAJ7
TRAJ8
TRAJ9
TRAJ10
TRAJ11
TRAJ12
TRAJ13
TRAJ14
TRAJ16
TRAJ17
TRAJ18
TRAJ19
TRAJ20
TRAJ21
TRAJ22
TRAJ23
TRAJ24
TRAJ25
TRAJ26
TRAJ27
TRAJ28
TRAJ29
TRAJ30
TRAJ31
TRAJ32
TRAJ33
TRAJ34
TRAJ35
TRAJ36
TRAJ37
TRAJ38
TRAJ39
TRAJ40
TRAJ41
TRAJ42
TRAJ43
TRAJ44
TRAJ45
TRAJ46
TRAJ47
TRAJ48
TRAJ49
TRAJ50
TRAJ52
TRAJ53
TRAJ54
TRAJ56
TRAJ57
TRAJ58
TRAJ59
TRAJ61
TRDV3
TRDC
TRDJ3
TRDJ2
TRDJ4
TRDJ1
TRDD3
TRDD2
TRDD1
TRDV2
TRAV41
TRAV40
TRAV39
TRAV36DV7
TRAV35
TRAV34
TRAV30
TRAV29DV5
TRAV27
TRAV25
TRAV24
TRDV1
TRAV23DV6
TRAV22
TRAV21
TRAV20
TRAV19
TRAV18
TRAV17
TRAV16
TRAV14DV4
TRAV10
TRAV7
TRAV6
TRAV5
TRAV4
TRAV3
TRAV2
RN7SL650P
SNORD8
SNORD9
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79\|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
OR4Q2
snoU13\|ENSG00000238492.1
MED15P6
LINC00516
MED15P1
ANG
APEX1
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
NRL
OXA1L
PCK2
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TGM1
AP1G2
SLC7A7
CPNE6
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
SUPT16H
ACIN1
KHNYN
SLC7A8
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
SLC39A2
EMC9
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR4K1
IPO4
DCAF11
OR4K15
JPH4
RNASE7
RAB2B
AJUBA
ZFHX2
LRRC16B
PPP1R3E
TMEM55B
DHRS1
CMTM5
RNASE11
TPPP2
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
NOP9
ADCY4
TSSK4
DHRS4L2
RNASE10
OR6S1
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
TMEM253
CBLN3
MIR4307
MIR4707

Genes in Wide Peak

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

Table S64. 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
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
C21orf91
SAMSN1
CHODL
LIPI
ABCC13
POTED
LINC00478
MIRLET7C
MIR125B2
MIR99A
MIR548X
MIR3687
C21orf37

Genes in Wide Peak

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

Table S65. 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 21q22.3.

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

Genes
TMPRSS2
RNA5SP492
SNORA3\|ENSG00000251778.1
LINC00112
LINC00111
snoU13\|ENSG00000252771.1
SNORA32\|ENSG00000207503.1
FAM3B
LINC00323
MX1
MX2
TFF1
TFF2
TFF3
ABCG1
BACE2
C2CD2
ZBTB21
UBASH3A
SLC37A1
RIPK4
PRDM15
TMPRSS3
RSPH1
UMODL1
LINC00479
C21orf128
MIR3197

Genes in Wide Peak

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

Table S67. 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 9p21.1.

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

Genes
LINGO2
MIR876
MIR873

Genes in Wide Peak

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

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

Genes
MAML2
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
FUT4
MRE11A
MTNR1B
JRKL
MTMR2
CEP57
GPR83
ENDOD1
PANX1
C11orf54
CWC15
CNTN5
ANKRD49
KDM4D
SMCO4
TAF1D
CCDC82
KIAA1731
FAT3
FAM76B
SESN3
PIWIL4
AMOTL1
CCDC67
HEPHL1
FOLR4
KDM4E
MIR1304
MIR1260B

Genes in Wide Peak

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

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

Genes
SHROOM2
CLCN4
MID1
GPR143
WWC3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.21.

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

Genes
CLTCL1
RN7SL280P
RN7SKP221
SCARNA18\|ENSG00000252605.1
SCARNA17\|ENSG00000252143.1
snoU13\|ENSG00000252799.1
TMEM191C
snoU13\|ENSG00000252402.1
SCARNA17\|ENSG00000252020.1
SCARNA18\|ENSG00000252314.1
RN7SKP63
FAM230C
GGT2
FAM230B
POM121L7
BCRP2
P2RX6P
P2RX6
RN7SL389P
POM121L4P
SMPD4P1
RN7SL812P
USP41
FAM230A
RN7SKP131
SCARNA18\|ENSG00000252024.1
SCARNA17\|ENSG00000252571.1
snoU13\|ENSG00000271796.1
PI4KAP1
GGTLC3
MIR1286
SNORA77\|ENSG00000264346.1
MIR1306
MIR4761
GP1BB
MRPL40
RN7SL168P
SNORA15\|ENSG00000251940.1
GSC2
DGCR5
GGT3P
PEX26
LINC00528
snoU13\|ENSG00000251737.1
RN7SL843P
CECR9
CECR3
CECR7
HSFY1P1
TPTEP1
KCNMB3P1
OR11H1
POTEH
ARVCF
ATP6V1E1
BID
COMT
CRKL
SERPIND1
PI4KA
SEPT5
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
SNAP29
DGCR2
TXNRD2
USP18
HIC2
TSSK2
SDF2L1
PPIL2
IL17RA
BCL2L13
TRMT2A
CECR6
CECR5
CECR2
YPEL1
ZDHHC8
MED15
TUBA8
CECR1
DGCR8
GNB1L
MICAL3
RTN4R
C22orf29
THAP7
SLC25A18
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
TUBA3FP
GAB4
C22orf39
TANGO2
CCT8L2
XKR3
AIFM3
RIMBP3C
YDJC
CCDC116
PI4KAP2
MIR130B
MIR185
RIMBP3B
MIR648
MIR649
MIR301B
MIR3618

Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
ACR
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
TTC38
MIOX
TRMU
PANX2
CERK
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535

Genes in Wide Peak

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

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

Genes
snoZ40
MIR5688
LINC00971
RN7SL751P
RN7SKP61
GBE1
ROBO1
CADM2
MIR3923

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

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

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.31.

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

Genes
BCL7A
ALDH2
PTPN11
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13\|ENSG00000238822.1
RN7SL534P
snoU13\|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9\|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9\|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70\|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13\|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38\|ENSG00000201042.1
RNA5SP374
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
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DTX1
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
LTA4H
MMP17
MSI1
MVK
MYBPC1
MYL2
NFYB
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
CDK2AP1
BRAP
ULK1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
PRDM4
CIT
PWP1
FZD10
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
FBXW8
HSPB8
UTP20
IFT81
FAM216A
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf65
CCDC64
SDSL
IQCD
DEPDC4
CCDC38
TMEM132D
SLC15A4
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
RAD9B
FAM109A
ALDH1L2
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
SLC17A8
LRRC43
TCP11L2
GPR133
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
DDX51
MMAB
HCAR2
TMEM119
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MIR135A2
MIR331
EID3
MIR492
C12orf73
ZNF605
MIR1251
MIR4303
MIR3685
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR5188
MIR5700

Genes in Wide Peak

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

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

Genes
BUB1B
RN7SL376P
snoU13\|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13\|ENSG00000238564.1
THBS1
FAM98B
U3\|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18\|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77\|ENSG00000212415.1
snoU13\|ENSG00000238342.1
RN7SL286P
RN7SL539P
GOLGA8O
U8\|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18\|ENSG00000206849.1
MIR211
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
ACTC1
APBA2
CHRM5
GABRA5
GABRB3
GABRG3
IVD
MEIS2
TRPM1
NDN
OCA2
PLCB2
RYR3
SCG5
SNRPN
SRP14
TJP1
UBE3A
MKRN3
HERC2
AQR
ARHGAP11A
RASGRP1
GPR176
BAHD1
FAN1
GOLGA8A
CYFIP1
FAM189A1
NPAP1
GREM1
RPUSD2
EMC4
KLF13
MTMR10
ZNF770
NOP10
NDNL2
EMC7
PAK6
CASC5
AVEN
KATNBL1
NIPA2
C15orf41
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
CHST14
TUBGCP5
NIPA1
TMCO5A
OTUD7A
SPRED1
PGBD4
FSIP1
LPCAT4
NUTM1
GOLGA6L2
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
FMN1
C15orf52
GOLGA8EP
OR4M2
C15orf53
C15orf54
HERC2P9
GOLGA8B
EIF2AK4
GOLGA8N
C15orf56
PHGR1
ANKRD63
POTEB2
MIR4508
MIR4510
POTEB

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p11.2.

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

Genes
USP22

Genes in Wide Peak

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

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

Genes
NKAIN2

Genes in Wide Peak

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

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

Genes
RN7SL5P
SNORD27\|ENSG00000251699.1
PTPRD

Genes in Wide Peak

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

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

Genes
MYCN
RN7SL117P
TDRD15
GDF7
RNA5SP86
RN7SL140P
LINC00954
SNORA40\|ENSG00000212455.1
RN7SKP168
SNORA40\|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13\|ENSG00000238371.1
LINC00276
MIR3125
SNORD18\|ENSG00000238503.1
MIR548S
RN7SL674P
RNA5SP85
RNA5SP84
LINC00570
RN7SL832P
SNORA80B
SNORA51\|ENSG00000206898.1
RN7SL66P
SNORA2\|ENSG00000206647.1
SNORA26\|ENSG00000212558.1
snoU13\|ENSG00000238462.1
IAH1
snoU13\|ENSG00000238888.1
MBOAT2
RNU6ATAC37P
RN7SKP112
FLJ30594
SNORA31\|ENSG00000252238.1
RN7SL531P
DCDC2C
SNORA73\|ENSG00000252531.1
snoU13\|ENSG00000238722.1
TMEM18
FAM110C
ACP1
APOB
RHOB
DDX1
E2F6
HPCAL1
ID2
KCNF1
KCNS3
MATN3
ODC1
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
ROCK2
GREB1
LAPTM4A
RNF144A
PDIA6
YWHAQ
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
TRAPPC12
NBAS
CPSF3
SNTG2
ADI1
ALLC
KIDINS220
WDR35
RDH14
C2orf43
HS1BP3
COLEC11
SMC6
NOL10
FAM49A
RSAD2
NT5C1B
CMPK2
OSR1
TTC32
C2orf50
PQLC3
FAM84A
CYS1
ATP6V1C2
RNASEH1
FAM150B
LINC00299
MSGN1
GEN1
C2orf48
LINC00487
RAD51AP2
MIR4261
MIR4262
MIR3681
MIR4757
MIR4429

Genes in Wide Peak

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

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

Genes
U3\|ENSG00000212598.1
HTR1F
RNU6ATAC6P
EPHA3
PROS1
CGGBP1
ZNF654
C3orf38
STX19

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q31.1.

Table S82. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
APC
CD74
EBF1
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
TRIM52
SNORD95\|ENSG00000264549.1
SNORD96A
LINC00847
MIR340
RN7SKP150
MIR1229
HMGB3P22
RN7SL71P
ZNF879
ZNF354B
AACSP1
RN7SKP70
RN7SL646P
RN7SL562P
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
RN7SKP148
snoU13\|ENSG00000239026.1
NSG2
RNA5SP200
SNORA74B
ATP6V0E1
MIR5003
SNORA57\|ENSG00000212529.1
C5orf50
SNORA70\|ENSG00000206909.1
RN7SL339P
snoU13\|ENSG00000252387.1
RN7SL623P
MIR4454
KCNMB1
LCP2
C5orf58
MIR378E
MIR585
MIR103A1
PANK3
FBLL1
SNORA40\|ENSG00000253065.1
RN7SKP60
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68\|ENSG00000252458.1
LSM11
THG1L
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
RNA5SP198
RN7SKP232
RNA5SP197
ZNF300P1
snoU13\|ENSG00000239191.1
snoU13\|ENSG00000238369.1
MIR378A
RN7SL868P
U3\|ENSG00000221043.1
MIR143HG
RN7SKP145
MIR584
SH3TC2
SPINK13
RN7SL791P
RNA5SP196
GPR151
RN7SKP246
KCTD16
RN7SL87P
RN7SL68P
PCDHGB8P
PCDHB18
PCDHB17
PCDHA14
WDR55
MIR3655
SNORA27\|ENSG00000200235.1
SNORD45\|ENSG00000200051.1
CYSTM1
PURA
TMEM173
ECSCR
RN7SKP64
RNA5SP195
SNORA74A
SNORA74\|ENSG00000252213.1
RNA5SP194
RN7SL867P
snoU13\|ENSG00000238745.1
SNORD63\|ENSG00000206989.1
SNORD63\|ENSG00000222937.1
RN7SL682P
snoU13\|ENSG00000238605.1
NPY6R
MIR874
RNA5SP193
FBXL21
TIFAB
MIR4461
MIR4461
PCBD2
RN7SL541P
PPP2CA
SKP1
snoU13\|ENSG00000238796.1
HSPA4
LEAP2
UQCRQ
RNA5SP192
snoZ6\|ENSG00000253067.1
HINT1
RNA5SP191
RNU6ATAC10P
KIAA1024L
MIR4633
C5orf63
RN7SKP117
RN7SL711P
RN7SL689P
snoU13\|ENSG00000239103.1
snoU13\|ENSG00000252295.1
snoU13\|ENSG00000239067.1
snoU13\|ENSG00000239084.1
RNA5SP190
RN7SL174P
TNFAIP8
MIR5706
snoU13\|ENSG00000239011.1
DTWD2
ARL14EPL
AP3S1
RN7SKP89
RNU4ATAC13P
ZRSR1
SRP19
FLJ11235
SNORA13
RN7SKP57
CAMK4
SNORA51\|ENSG00000207177.1
MIR548F3
TMEM232
RN7SKP230
FER
RN7SKP122
RN7SL782P
SNORA31\|ENSG00000252337.1
RNA5SP189
RN7SL255P
LINC00491
LINC00492
RN7SKP68
RNA5SP188
RN7SL802P
MIR548P
RN7SKP62
GPR150
LUCAT1
SNORA70\|ENSG00000206958.1
RNA5SP187
RN7SL629P
RN7SKP34
MIR3607
COX7C
NBPF22P
RN7SKP295
SCARNA18\|ENSG00000238835.1
RN7SL378P
SSBP2
SNORA31\|ENSG00000251828.1
snoU13\|ENSG00000239159.1
MTX3
HOMER1
SNORA18\|ENSG00000206592.1
RNY3P1
BHMT2
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13\|ENSG00000238688.1
RNA5SP186
POLK
SNORA40\|ENSG00000212363.1
RN7SL814P
MIR4804
RN7SL153P
MIR4803
snoU13\|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13\|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13\|ENSG00000238334.1
SNORA50\|ENSG00000220986.1
RN7SL103P
7SK\|ENSG00000249352.3
U8\|ENSG00000212249.2
snoU13\|ENSG00000238400.1
SNORA76\|ENSG00000252904.1
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
CLTB
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
HARS
HEXB
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNN2
TNPO1
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MFAP3
MGAT1
MSH3
MSX2
NAIP
NDUFA2
NEUROG1
PAM
PCDH1
PCDHGC3
PCSK1
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2R2B
MAPK9
PROP1
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATG12
PTTG1
PDLIM7
NREP
CNOT8
HAND1
MED7
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
APBB3
TNIP1
GNB2L1
NSA2
SLU7
POLR3G
RGS14
IQGAP2
SEC24A
CPLX2
FAXDC2
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
PPWD1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
KLHL3
TSPAN17
OR4F3
OR2V1
HAVCR1
CYFIP2
PKD2L2
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
SGTB
TMED9
ZCCHC10
CDHR2
GIN1
SPDL1
AGGF1
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
NLN
ZNF608
SEMA6A
ARRDC3
PCDHB16
ANKRA2
HMHB1
C5orf54
MCCC2
EPB41L4A
CENPK
ERAP2
ARHGEF28
SIL1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
PCYOX1L
CCNJL
SAP30L
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
TRAPPC13
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
PSD2
ANKRD32
THOC3
GFM2
MEGF10
SPINK7
SPZ1
HAVCR2
PHYKPL
SMIM3
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
FCHO2
LYSMD3
SCGB3A2
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
POC5
STARD4
WDR36
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC36A2
CREBRF
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
PAPD4
DCP2
LIX1
ZNF366
FAM151B
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
CCDC125
C5orf27
CMYA5
STK32A
AQPEP
SLC36A1
RASGEF1C
ANKRD31
SERINC5
EFCAB9
SH3PXD2B
FAM153A
KIAA0825
RELL2
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
RGMB
RFESD
CHSY3
FAM170A
ARSI
ANKRD34B
PFN3
IRGM
FAM174A
CATSPER3
NIPAL4
SLCO4C1
DND1
MAST4
SIMC1
C5orf48
PROB1
C5orf46
ARHGEF37
SPINK6
ANKHD1
MIR143
MIR145
MIR146A
LINC00461
SPINK14
FNDC9
C5orf56
IGIP
CTXN3
GRXCR2
SPINK9
ZFP62
CCNI2
CBY3
FAM153C
MIR583
GTF2H2C
SERF1B
ANKDD1B
FAM196B
C5orf52
MIR1303
TICAM2
MIR2277
MIR4280
MIR3141
MTRNR2L2
MIR3660
MIR3912
MIR3936
MIR3661
OCLN
MIR4634
MIR378H
MIR4460
MIR4638
MIR5197
MIR5692C1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 29 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	0.21	-3.32	1	0.40	4.81	2.19e-06
1q	1195	0.42	4.87	2.48e-06	0.28	-0.973	1
2p	624	0.45	3.41	0.00131	0.11	-9.18	1
2q	967	0.30	-1.69	1	0.13	-8.22	1
3p	644	0.25	-2.61	1	0.82	20.4	0
3q	733	0.67	12.1	0	0.57	6.93	7.51e-12
4p	289	0.15	-7.26	1	0.68	11.5	0
4q	670	0.10	-7.77	1	0.62	11.6	0
5p	183	0.65	8.17	2.22e-15	0.60	6.04	2.3e-09
5q	905	0.18	-4.01	1	0.75	19	0
6p	710	0.27	-3.88	1	0.30	-2.81	1
6q	556	0.23	-6.28	1	0.29	-3.83	1
7p	389	0.53	5.52	9.57e-08	0.26	-4.65	1
7q	783	0.48	5.38	1.83e-07	0.21	-5.07	1
8p	338	0.36	-1.27	1	0.70	12.4	0
8q	551	0.54	6.69	1.13e-10	0.28	-3.49	1
9p	301	0.29	-3.35	1	0.71	12.8	0
9q	700	0.34	-0.959	1	0.61	10.3	0
10p	253	0.25	-5.75	1	0.52	4.17	3.77e-05
10q	738	0.14	-7.37	1	0.51	6.67	4.24e-11
11p	509	0.21	-6.6	1	0.41	0.865	0.369
11q	975	0.24	-3.76	1	0.35	0.985	0.324
12p	339	0.48	3.21	0.00242	0.18	-7.95	1
12q	904	0.33	-0.399	1	0.15	-7.64	1
13q	560	0.20	-5.13	1	0.67	12.9	0
14q	938	0.39	1.88	0.0935	0.45	4.47	1.03e-05
15q	810	0.29	-2.48	1	0.36	0.509	0.509
16p	559	0.24	-5.31	1	0.40	0.8	0.385
16q	455	0.25	-5.09	1	0.45	2.32	0.0215
17p	415	0.26	-3.94	1	0.69	12.4	0
17q	972	0.36	1.11	0.38	0.31	-0.712	1
18p	104	0.38	-1.97	1	0.43	-0.36	1
18q	275	0.32	-3.57	1	0.49	2.84	0.00499
19p	681	0.31	-2.13	1	0.45	3.27	0.00128
19q	935	0.39	1.96	0.0826	0.36	0.748	0.395
20p	234	0.56	5.84	1.73e-08	0.21	-6.76	1
20q	448	0.54	6.39	6.78e-10	0.21	-6.13	1
21q	258	0.24	-5.61	1	0.60	7.65	4.04e-14
22q	564	0.55	6.77	8.56e-11	0.35	-0.942	1
Xq	668	0.17	-7.88	1	0.30	-3.21	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/LUSC-TP/11448144/GDAC_MergeDataFiles_11450826/LUSC-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 501 Input Tumor Samples.

Tumor Sample Names
TCGA-18-3406-01A-01D-0978-01
TCGA-18-3407-01A-01D-1969-01
TCGA-18-3408-01A-01D-0978-01
TCGA-18-3409-01A-01D-0978-01
TCGA-18-3410-01A-01D-1969-01
TCGA-18-3411-01A-01D-1969-01
TCGA-18-3412-01A-01D-0978-01
TCGA-18-3414-01A-01D-0978-01
TCGA-18-3415-01A-01D-0978-01
TCGA-18-3416-01A-01D-0978-01

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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