Stomach Adenocarcinoma: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16a (cga svn revision 43808).

Summary

There were 237 tumor samples used in this analysis: 25 significant arm-level results, 26 significant focal amplifications, and 46 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 - 26 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
--- | --- | --- | --- | ---
17q12 | 1.7491e-27 | 1.7491e-27 | chr17:37854508-37904210 | 4
19q12 | 1.0637e-20 | 1.0637e-20 | chr19:30183172-30442829 | 3
12p12.1 | 7.2121e-16 | 7.2121e-16 | chr12:25348817-25414737 | 2
8q24.21 | 9.5883e-14 | 9.5883e-14 | chr8:128627168-128754688 | 1
7q21.2 | 7.9615e-12 | 1.039e-11 | chr7:92104677-92571116 | 6
20q13.2 | 5.1491e-10 | 5.1491e-10 | chr20:51973663-52624581 | 4
8p23.1 | 7.6099e-10 | 7.6099e-10 | chr8:11547791-11638987 | 2
18q11.2 | 6.686e-09 | 6.686e-09 | chr18:19594807-19775976 | 1
6p21.1 | 8.1683e-09 | 1.2612e-08 | chr6:43593968-44065071 | 7
12q15 | 1.0907e-07 | 1.0907e-07 | chr12:69120903-70036889 | 14
11q13.3 | 2.7878e-06 | 2.9514e-06 | chr11:69150824-70241934 | 10
7p11.2 | 2.6745e-06 | 5.2968e-06 | chr7:55035101-55514022 | 2
10q26.13 | 8.7536e-05 | 8.7536e-05 | chr10:123172617-123425303 | 1
15q26.1 | 0.00017999 | 0.00017999 | chr15:90778391-91404476 | 8
11p13 | 0.00041649 | 0.00044039 | chr11:34932338-35197156 | 4
3q26.31 | 0.00086614 | 0.00086614 | chr3:162110637-185642387 | 116
1q42.3 | 0.00020237 | 0.0011017 | chr1:234915915-235130525 | 0 [LOC100506810]
13q22.1 | 0.00071986 | 0.0011298 | chr13:73642878-73944996 | 1
5p13.1 | 0.0017293 | 0.0017293 | chr5:36010845-44248189 | 53
13q12.3 | 0.0093662 | 0.011823 | chr13:31027893-34420150 | 20
1p36.22 | 0.024806 | 0.024806 | chr1:10686864-11093740 | 5
9p24.1 | 0.039958 | 0.039958 | chr9:5047445-5711052 | 9
1q21.3 | 0.013007 | 0.057042 | chr1:120523956-158514634 | 361
Xq27.3 | 0.072546 | 0.072546 | chrX:122656947-155270560 | 308
6q12 | 0.069627 | 0.1393 | chr6:63506061-64996026 | 4
9q34.3 | 0.24777 | 0.24777 | chr9:139857913-140151408 | 31

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's Cancer Gene Census [7].

Genes
ERBB2
GRB7
MIEN1
MIR4728

Genes in Wide Peak

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

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

Genes
CCNE1
URI1
C19orf12

Genes in Wide Peak

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

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

Genes
KRAS
LYRM5

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's Cancer Gene Census [7].

Genes
MYC

Genes in Wide Peak

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

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

Genes
CDK6
PEX1
RBM48
MGC16142
FAM133B
LOC728066

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
ZNF217
BCAS1
TSHZ2
SUMO1P1

Genes in Wide Peak

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

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

Genes
GATA4
NEIL2

Genes in Wide Peak

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

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

Genes
GATA6

Genes in Wide Peak

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

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

Genes
VEGFA
MAD2L1BP
GTPBP2
MRPS18A
C6orf223
RSPH9
LOC100132354

Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
SLC35E3
NUP107
LRRC10
MIR1279
MIR3913-2
MIR3913-1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
EGFR
LANCL2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q26.13.

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

Genes
FGFR2

Genes in Wide Peak

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

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

Genes
BLM
CRTC3
IQGAP1
GABARAPL3
NGRN
ZNF774
C15orf58
TTLL13

Genes in Wide Peak

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

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

Genes
CD44
PDHX
APIP
MIR1343

Genes in Wide Peak

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

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

Genes
PIK3CA
SOX2
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
ACTL6A
BCHE
AP2M1
CLCN2
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
GHSR
NDUFB5
CLDN11
SERPINI1
SERPINI2
PLD1
POLR2H
PRKCI
PSMD2
TRA2B
SI
SKIL
SLC2A2
TERC
THPO
SEC62
FXR1
CHRD
TNFSF10
EIF2B5
USP13
MAP3K13
ECE2
ABCC5
ALG3
KCNMB2
IGF2BP2
PDCD10
SLITRK3
NLGN1
TNIK
MCF2L2
ATP11B
VPS8
GPR160
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DCUN1D1
KLHL24
ABCF3
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
MRPL47
NCEH1
SLC7A14
SENP2
GNB4
MAGEF1
ZMAT3
FNDC3B
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
SPATA16
B3GNT5
ARPM1
KLHL6
VWA5B2
TMEM41A
EGFEM1P
CAMK2N2
DNAJC19
FAM131A
TTC14
WDR49
LRRC34
HTR3C
LIPH
HTR3D
RPL22L1
NAALADL2
HTR3E
C3orf70
CCDC39
LOC339926
LRRIQ4
SAMD7
SOX2-OT
TMEM212
FLJ46066
LOC646168
C3orf65
LOC647107
SNORD66
MIR551B
MIR569
LOC100128164
MIR1224
LOC100505687
MIR4789

Genes in Wide Peak

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

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

Genes
KLF5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.1.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
C6
C7
C9
DAB2
FYB
GDNF
GHR
HMGCS1
OXCT1
PRKAA1
PTGER4
RPL37
SEPP1
SKP2
SLC1A3
ZNF131
OSMR
NUP155
PAIP1
NNT
TTC33
NIPBL
FBXO4
WDR70
CCL28
C5orf28
C5orf42
CARD6
LMBRD2
HEATR7B2
EGFLAM
NADKD1
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR3650
LOC100506548
EGFLAM-AS4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.3.

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

Genes
BRCA2
ALOX5AP
HMGB1
RFC3
KL
FRY
USPL1
N4BP2L2
HSPH1
PDS5B
C13orf33
STARD13
N4BP2L1
CG030
RXFP2
TEX26
B3GALTL
EEF1DP3
ZAR1L
TEX26-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.22.

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

Genes
PEX14
MASP2
TARDBP
CASZ1
C1orf127

Genes in Wide Peak

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

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

Genes
JAK2
CD274
INSL4
RLN1
RLN2
INSL6
C9orf46
KIAA1432
PDCD1LG2

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
MUC1
NOTCH2
NTRK1
PRCC
TPM3
PDE4DIP
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
BGLAP
CD1A
CD1B
CD1C
CD1D
CD1E
CD5L
CHRNB2
CKS1B
CLK2
CRABP2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
HDGF
IL6R
ILF2
INSRR
IVL
KCNN3
LMNA
LOR
MCL1
SMCP
MEF2D
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
SH2D2A
PRPF3
ARHGEF2
SEC22B
CHD1L
SLC25A44
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
PMF1
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SMG5
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
HORMAD1
POLR3GL
TMEM79
LCE3D
AQP10
PYGO2
NUP210L
MEX3A
C1orf85
PGLYRP3
GNRHR2
FCRL1
FCRL3
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
LRRC71
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
OR10R2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
LOC375010
PEAR1
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
OR10K2
OR10K1
NBPF9
MIR9-1
HIST2H2BF
ETV3L
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA4
SNORA42
MIR554
MIR555
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR765
MIR190B
C1orf68
MSTO2P
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505666
PMF1-BGLAP
TNFAIP8L2-SCNM1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq27.3.

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
ABCD1
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CD40LG
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
HCFC1
HMGB3
HPRT1
IDH3G
IDS
IGSF1
IL9R
IRAK1
L1CAM
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
OCRL
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
VBP1
XPNPEP2
ZIC3
ZNF75D
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
CXorf1
GPR50
RAB33A
ARHGEF6
MAGEC1
MAMLD1
BCAP31
ODZ1
SPRY3
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
TREX2
LDOC1
FAM127B
SRPK3
SNORA70
SNORD61
RBMX
HTATSF1
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
CXorf48
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45B
GABRQ
MOSPD1
THOC2
PDZD4
RAP2C
FAM3A
BCORL1
SPANXD
SPANXC
FUNDC2
PRRG3
BRCC3
MAP7D3
GPR101
CD99L2
H2AFB3
USP26
PHF6
TMEM185A
SLITRK2
MGC16121
PNMA6A
FATE1
HS6ST2
FRMD7
CXorf40A
FAM58A
MMGT1
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
CSAG1
FMR1NB
LOC158696
ARHGAP36
FAM122B
FAM122C
SPANXE
SPANXF1
DDX26B
ZNF449
VMA21
CTAG1A
MAGEA2B
ATP11C
RP1-177G6.2
LOC286467
LINC00204B
DCAF12L2
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
LINC00086
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
CXorf69
LINC00087
MIR542
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
CT45A2
MIR767
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129520
LOC100129662
HSFX2
CXorf64
LOC100131434
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR320D2
MIR718
MIR2114
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
LOC100506757
LOC100507404
MAGEA10-MAGEA5

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's Cancer Gene Census [7].

Genes
PTP4A1
PHF3
LGSN
EYS

Genes in Wide Peak

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

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

Genes
ABCA2
ENTPD2
FUT7
GRIN1
PTGDS
SSNA1
CLIC3
TUBB4B
MAN1B1
COBRA1
NDOR1
ANAPC2
DPP7
NPDC1
SAPCD2
UAP1L1
TMEM203
SLC34A3
C9orf142
TPRN
C9orf169
LRRC26
LCNL1
C9orf139
FAM166A
C9orf173
RNF224
RNF208
LOC100129722
LOC100289341
MIR3621

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 - 46 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
--- | --- | --- | --- | ---
16q23.1 | 1.4269e-42 | 1.4269e-42 | chr16:78129058-79627770 | 1
5q11.2 | 1.2752e-32 | 1.2752e-32 | chr5:58260298-59787985 | 3
4q22.1 | 2.2613e-28 | 6.3172e-25 | chr4:91148280-93240505 | 1
9p24.1 | 1.3454e-26 | 1.1684e-22 | chr9:8310705-12693402 | 1
9p21.3 | 3.6917e-30 | 4.1625e-17 | chr9:21865498-21997722 | 2
3p14.2 | 2.1678e-17 | 2.7127e-16 | chr3:59034763-61547330 | 1
6p25.3 | 1.4186e-13 | 1.4186e-13 | chr6:1608837-2252425 | 2
20p12.1 | 1.2572e-12 | 1.2702e-12 | chr20:14690293-15165995 | 1
7q31.1 | 5.5475e-14 | 3.4578e-10 | chr7:109599468-111366370 | 2
18q21.2 | 2.5504e-12 | 9.6506e-10 | chr18:48472083-48705371 | 2
1p36.11 | 4.4639e-09 | 1.5832e-08 | chr1:26900639-27433459 | 11
Xp21.2 | 1.2813e-08 | 3.7603e-08 | chrX:30870233-32661893 | 3
6q26 | 4.7815e-10 | 6.6719e-08 | chr6:161693099-163153207 | 1
4q35.1 | 7.1979e-13 | 1.8981e-06 | chr4:178911874-186321446 | 34
3q26.31 | 3.0294e-05 | 3.0125e-05 | chr3:173999806-175760559 | 2
19p13.3 | 3.6817e-05 | 3.6364e-05 | chr19:2473582-4772399 | 72
2q32.1 | 1.3665e-06 | 4.7199e-05 | chr2:187373995-187560595 | 1
17p12 | 0.00013096 | 0.00013344 | chr17:10740609-13933317 | 13
21q11.2 | 0.00017148 | 0.00017148 | chr21:1-16335988 | 22
10q23.31 | 7.4533e-06 | 0.00017613 | chr10:89506488-90034038 | 4
7q36.3 | 3.511e-07 | 0.00043228 | chr7:157210222-159138663 | 11
2q37.2 | 0.00017148 | 0.001115 | chr2:235913227-237079324 | 2
11p15.5 | 0.00112 | 0.001115 | chr11:2441018-3115942 | 10
12p13.31 | 0.0012105 | 0.0012105 | chr12:7307243-18417317 | 148
11q23.2 | 0.0013592 | 0.0013011 | chr11:102955092-135006516 | 292
16p13.3 | 0.0013592 | 0.0013011 | chr16:5144019-7771745 | 1
22q13.31 | 0.0013626 | 0.0013592 | chr22:45736500-51304566 | 75
8p23.2 | 0.005269 | 0.005115 | chr8:1-6262191 | 15
15q15.1 | 0.0011652 | 0.0057341 | chr15:33536714-59733125 | 256
3p26.1 | 0.00016082 | 0.0087676 | chr3:1-6903296 | 16
1q44 | 0.013536 | 0.01321 | chr1:245282267-245913707 | 1
Xq21.33 | 0.018813 | 0.018918 | chrX:94288568-98718611 | 4
17q24.3 | 0.021186 | 0.021577 | chr17:70116519-70595192 | 2
4p16.3 | 0.046464 | 0.046482 | chr4:1-15685350 | 153
6q27 | 0.00024205 | 0.050903 | chr6:166070110-171115067 | 42
Xp22.2 | 0.010385 | 0.050903 | chrX:9891764-11137490 | 4
10p14 | 0.053073 | 0.053132 | chr10:1-26507905 | 156
2q33.3 | 0.0012105 | 0.088752 | chr2:204826225-206558638 | 1
19q13.11 | 0.088757 | 0.088752 | chr19:32083224-36216055 | 70
14q13.3 | 0.096613 | 0.098436 | chr14:37635653-38677651 | 3
14q32.33 | 0.14954 | 0.14532 | chr14:92629600-107349540 | 248
18q22.3 | 3.199e-06 | 0.17906 | chr18:39097457-78077248 | 165
10q22.2 | 0.069182 | 0.21469 | chr10:76992208-78629541 | 6
1p31.1 | 0.034312 | 0.22716 | chr1:33427321-149898950 | 792
9p13.1 | 0.19098 | 0.22716 | chr9:23820136-135288260 | 707
15q11.2 | 0.0022021 | 0.2526 | chr15:1-86686002 | 732

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
PTPRD

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's Cancer Gene Census [7].

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

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

Genes
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
LRRN3
IMMP2L

Genes in Wide Peak

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

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

Genes
SMAD4
ELAC1

Genes in Wide Peak

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

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

Genes
ARID1A
SFN
NR0B2
NUDC
GPN2
PIGV
GPATCH3
ZDHHC18
FAM46B
C1orf172
TRNP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.2.

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

Genes
hsa-mir-548f-5
DMD
FTHL17

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
hsa-mir-1305
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ENPP6
C4orf38
RWDD4
CCDC111
ANKRD37
LOC389247
HELT
FAM92A3
SLED1
LINC00290
LOC728175
LOC731424
CLDN24
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

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

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
hsa-mir-7-3
hsa-mir-637
AES
DAPK3
EEF2
GNA15
GNG7
MATK
GADD45B
NFIC
MAP2K2
SGTA
TBXA2R
THOP1
TLE2
S1PR4
APBA3
CHAF1A
EBI3
HMG20B
SEMA6B
ZFR2
PIP5K1C
SNORD37
TJP3
ITGB1BP3
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
STAP2
CCDC94
C19orf10
NCLN
SHD
ZNF77
C19orf29
CELF5
FSD1
TLE6
ZNF556
UBXN6
DOHH
CREB3L3
HDGFRP2
RAX2
MPND
ATCAY
DPP9
ZNF554
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
MFSD12
GIPC3
DIRAS1
ZNF555
ANKRD24
C19orf77
C19orf29-AS1
MIR7-3
PLIN5
MIR637
PLIN4
C19orf71
LOC100131094
MIR4746

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q32.1.

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

Genes
ITGAV

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-548h-3
hsa-mir-744
DNAH9
ZNF18
ARHGAP44
HS3ST3A1
ELAC2
MYOCD
CDRT15P1
FLJ34690
SHISA6
MIR744

Genes in Wide Peak

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

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

Genes
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
HSPA13
TPTE
RBM11
C21orf15
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
LIPI
ABCC13
POTED
LOC388813
ANKRD20A11P
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

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

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

Genes
PTEN
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

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

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

Genes
hsa-mir-595
hsa-mir-153-2
PTPRN2
VIPR2
NCAPG2
WDR60
ESYT2
LOC154822
MIR153-2
MIR595
LOC100506585

Genes in Wide Peak

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

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

Genes
GBX2
AGAP1

Genes in Wide Peak

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

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

Genes
CARS
CDKN1C
KCNQ1
NAP1L4
SLC22A18
SLC22A18AS
PHLDA2
KCNQ1OT1
KCNQ1DN
SNORA54

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.31.

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C3AR1
CD69
CDKN1B
CREBL2
PHC1
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
PEX5
PZP
SLC2A3
MFAP5
KLRC4
CSDA
GPRC5A
CD163
GDF3
CLEC2B
KLRG1
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
NECAP1
CLEC4E
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
MANSC1
MAGOHB
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
NANOG
DUSP16
APOLD1
GSG1
RERG
HTR7P1
CLEC6A
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
CD163L1
CLEC9A
C12orf36
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
KLRC4-KLRK1
PRH1-PRR4
MIR3974

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

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

Genes
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100128239
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
hsa-let-7b
ACR
ARSA
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
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR3201
MIR3619
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

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

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

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53
MIR596

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
BUB1B
TCF12
FLJ27352
C15orf55
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
ACTC1
ADAM10
AQP9
B2M
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
MYO1E
MYO5A
NEDD4
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SLC12A1
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
USP8
CCNB2
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
CEP152
MAPKBP1
GOLGA8A
RTF1
MGA
DMXL2
VPS39
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PYGO1
PLDN
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
PPP1R14D
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
LDHAL6B
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145663
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
FAM98B
PLA2G4D
GLDN
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
HSP90AB4P
MIR626
MIR627
MIR628
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100129387
LOC100131089
ANKRD63
LOC100132724
JMJD7
PLA2G4B
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR2116
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4510
MIR4716
MIR4713
MIR4712
MYZAP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.1.

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

Genes
IL5RA
ITPR1
SETMAR
BHLHE40
EDEM1
CHL1
CNTN6
TRNT1
CRBN
ARL8B
LRRN1
CNTN4
SUMF1
EGOT
LOC100507582
MIR4790

Genes in Wide Peak

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

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

Genes
KIF26B

Genes in Wide Peak

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

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

Genes
hsa-mir-548m
DIAPH2
RPA4
LOC643486

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

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

Genes
SOX9
LOC100499467

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.3.

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

Genes
FGFR3
WHSC1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
NKX3-2
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
RAB28
KIAA0232
WDR1
HS3ST1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
FBXL5
D4S234E
GPR78
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
CNO
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
CC2D2A
KIAA1530
ZFYVE28
AFAP1
TNIP2
HAUS3
ABCA11P
GRPEL1
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
CPEB2
EVC2
OTOP1
ZNF595
LOC152742
JAKMIP1
FAM53A
METTL19
ZBTB49
ZNF721
ZNF718
CCDC96
BOD1L
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285547
LOC285548
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
USP17L6P
USP17
HSP90AB2P
C4orf48
LOC402160
LOC441009
ZNF876P
DEFB131
LOC650293
ZNF732
SCARNA22
MIR572
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR3138
LOC100507266
MIR378D1
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
CCR6
GPR31
KIF25
PDCD2
PSMB1
RPS6KA2
T
TBP
TCP10
TCTE3
THBS2
RNASET2
C6orf123
DLL1
BRP44L
UNC93A
PHF10
C6orf70
SMOC2
FRMD1
C6orf208
TTLL2
FAM120B
LINC00473
SFT2D1
LOC154449
DACT2
WDR27
PRR18
C6orf120
TCP10L2
LINC00242
LOC441177
MLLT4-AS1
HGC6.3
LOC100289495
MIR1913
MIR3939
MIR4644

Genes in Wide Peak

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

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

Genes
CLCN4
MID1
WWC3
LOC100288814

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p14.

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

Genes
GATA3
MLLT10
hsa-mir-603
hsa-mir-1915
hsa-mir-511-2
hsa-mir-511-1
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
BMI1
CACNB2
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
TRDMT1
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PIP4K2A
PRKCQ
RSU1
VIM
STAM
CUBN
ITGA8
PRPF18
AKR1C3
CDC123
PTPLA
PTER
NMT2
SPAG6
USP6NL
OPTN
NET1
NEBL
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
MSRB2
SEPHS1
KIN
DIP2C
LARP4B
COMMD3
GTPBP4
UPF2
HSPA14
CALML5
MYO3A
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
KIAA1217
PRTFDC1
CAMK1D
GPR158
ARHGAP21
SFMBT2
DNAJC1
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
THNSL1
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
FBXO18
PLXDC2
RBM17
IDI2
UCN3
SFTA1P
ENKUR
ARMC3
LOC219731
OTUD1
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
LOC254312
C10orf47
PTF1A
C10orf67
LOC282980
LOC283070
LOC338588
ST8SIA6
AKR1CL1
EBLN1
TUBB8
C10orf113
C10orf140
tAKR
C1QL3
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf114
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
MIR511-1
MIR511-2
ADARB2-AS1
MEIG1
TMEM236
MIR603
LOC100128098
LOC100128511
LOC100128811
LOC100129213
LOC100130992
PRINS
LOC100192204
LOC100216001
MIR1265
MIR1915
MIR3155A
LOC100499489
LOC100507034
LOC100507127
COMMD3-BMI1
MIR4480
MIR4675
MIR3155B

Genes in Wide Peak

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

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

Genes
PARD3B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.11.

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

Genes
CEBPA
ATP4A
CD22
CEBPG
COX6B1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
LRP3
MAG
PEPD
FXYD1
FXYD3
SCN1B
USF2
PDCD5
KIAA0355
UBA2
TMEM147
UPK1A
SLC7A9
ZNF507
HAUS5
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
GPATCH1
ZNF302
SLC7A10
GRAMD1A
HAMP
CHST8
KCTD15
RBM42
LOC80054
ANKRD27
PDCD2L
CEP89
RHPN2
ZNF30
C19orf40
TDRD12
DMKN
WDR88
WTIP
ZNF792
DPY19L3
ZNF599
FAM187B
LGI4
SCGB2B2
ZNF181
SBSN
RGS9BP
KRTDAP
NUDT19
LOC400684
LOC400685
SCGB1B2P
LOC100128675
LOC100128682
SCGB2B3P
LOC100506469
LOC100652909

Genes in Wide Peak

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

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

Genes
FOXA1
MIPOL1
LOC100129794

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
ATP5A1
CDH7
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TCF4
ZNF236
SLC14A2
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
EPG5
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
KATNAL2
MRO
HDHD2
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
RNF165
C18orf32
LOC643542
C18orf63
SCARNA17
SNORA37
TCEB3CL
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR1539
MIR4319
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4529
MIR3591
MIR4743
MIR4744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q22.2.

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

Genes
hsa-mir-606
C10orf11
ZNF503
COMTD1
ZNF503-AS1
ZNF503-AS2

Genes in Wide Peak

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

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

Genes
BCL9
CDKN2C
EPS15
JAK1
JUN
MPL
MUTYH
MYCL1
NOTCH2
NRAS
SFPQ
TAL1
BCL10
PDE4DIP
THRAP3
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
ABCA4
ACADM
ADORA3
AGL
AK2
AK4
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
ATP6V0B
BMP8B
BRDT
C8A
C8B
CAPZA1
CASQ2
CD2
CD53
CD58
CDC20
CHI3L2
CLCA1
PLK3
CNN3
COL8A2
COL9A2
COL11A1
CPT2
CRYZ
CSF1
CSF3R
CTBS
CTH
CTPS
CYP2J2
CYP4A11
CYP4B1
DAB1
DBT
GADD45A
DHCR24
DIO1
DPH2
DPYD
DR1
S1PR1
EDN2
PHC2
CELSR2
ELAVL4
EXTL2
F3
FAAH
FCGR1A
FCGR1B
FHL3
FOXE3
FOXD2
FMO5
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GNAI3
GNAT2
GNG5
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
IL12RB2
INPP5B
IPP
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
LEPR
TACSTD2
MAGOH
MOV10
MSH4
MTF1
NASP
NDUFS5
NFIA
NFYC
NGF
NHLH2
NRD1
YBX1
ROR1
ORC1
OVGP1
PRDX1
PDE4B
PDZK1
PGM1
PIN1P1
POU3F1
PPT1
PRKAA2
PRKAB2
PRKACB
PKN2
PSMA5
PSMB2
PTGER3
PTGFR
PTGFRN
PTPRF
ABCD3
RAB3B
RABGGTB
RAP1A
RLF
SNORD21
RPE65
RPL5
RPS8
SORT1
SARS
SCP2
ST3GAL3
STIL
SLC1A7
SLC2A1
SLC6A9
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TIE1
TSHB
TTC4
UQCRH
UROD
USP1
VCAM1
WNT2B
ZSCAN20
DNALI1
LRP8
BSND
CSDE1
EVI5
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
RAD54L
TTF2
PIK3R3
ITGA10
LMO4
CDC14A
MKNK1
PPAP2B
RTCD1
PTCH2
B4GALT2
PABPC4
FPGT
PEX11B
FUBP1
EIF2B3
ARTN
DIRAS3
SLC16A4
KCNQ4
ZMYM4
ZMYM6
SRSF11
ZFYVE9
CD101
SEP15
ZRANB2
ARHGAP29
TMEM59
SEC22B
CHD1L
CLCA3P
CLCA2
HS2ST1
IPO13
KDM4A
RIMS3
KIAA0494
DNAJC6
LRIG2
LPPR4
SV2A
RBM8A
INSL5
PIGK
TSPAN2
TSPAN1
PDZK1IP1
INADL
ZMPSTE24
BCAS2
AKR1A1
WARS2
CEPT1
PIAS3
TESK2
PPIE
VAV3
PPIH
CAP1
LRRC41
HBXIP
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
SF3A3
IFI44L
EBNA1BP2
KIF2C
DNAJB4
ADAM30
FAF1
CD160
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
FOXJ3
WDR47
SCMH1
TTC39A
USP33
MAST2
NCDN
CLCC1
SLC35D1
LPHN2
KIAA1107
ZCCHC11
SZT2
USP24
ITGB3BP
SLC35A3
MACF1
LRRC8B
LPAR3
DDAH1
SSBP3
NBPF14
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
SERBP1
PTPN22
PHGDH
AK5
MYCBP
HEYL
EIF2C1
SNORA66
SNORD45B
SNORD45A
SNORD55
RNF11
FOXD3
TRAPPC3
CHIA
RNF115
TEKT2
ANGPTL3
GNL2
GPSM2
ALG6
SLC25A24
DNTTIP2
TMED5
BOLA1
ZNF691
TXNDC12
TNNI3K
SH3GLB1
UTP11L
HAO2
ACP6
TMEM69
MRPL37
HOOK1
SNX7
HPCAL4
GPR89B
DPH5
HSPB11
CMPK1
GPR88
YIPF1
CCDC76
SPATA6
L1TD1
RSBN1
ZNHIT6
LEPROT
TRIT1
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
RHBDL2
ADPRHL2
C1orf109
C1orf123
TTC22
PRPF38B
CDCA8
LRRC8D
PRMT6
RNF220
FAM176B
TRIM62
RAVER2
ECHDC2
FGGY
MCOLN3
SLC22A15
RNPC3
POMGNT1
LRRC40
DEPDC1
MAP7D1
TMEM48
LRIF1
CTTNBP2NL
FAM212B
DMAP1
GNG12
CCBL2
TMEM167B
OLFML3
FAM91A2
AMIGO1
ODF2L
KIAA1324
LRRC7
ZSWIM5
CACHD1
MIER1
PTBP2
DNASE2B
DLGAP3
HIVEP3
GPBP1L1
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
LEPRE1
HIAT1
SMAP2
ATPAF1
MEAF6
DEM1
ELOVL1
DCLRE1B
MRPS15
ZNF643
SELRC1
ERI3
C1orf50
WDR77
DLEU2L
EPS8L3
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
PPCS
SH3D21
TTLL7
SNIP1
WDR78
ZMYM1
RPAP2
KIAA0319L
DENND2D
WLS
RPF1
SIKE1
ZC3H12A
TRIM45
GJA9
ANKRD13C
VANGL1
ST6GALNAC5
HYI
GPR61
STK40
TM2D1
REG4
SYDE2
ZNF644
ZMYND12
LRRC8C
SGIP1
POLR3GL
PROK1
EFCAB7
NT5C1A
PSRC1
MGC12982
HPDL
ATP1A1OS
AGBL4
MFSD2A
ATG4C
PRPF38A
LSM10
C1orf94
FAM40A
DOCK7
ZNF697
BTF3L4
NEXN
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
MED8
KTI12
C1orf212
ADC
HENMT1
TOE1
ERMAP
CSMD2
MYSM1
GNRHR2
OSBPL9
OMA1
LRRC42
GBP4
GBP5
SSX2IP
OLFM3
CCDC163P
WDR63
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
DMBX1
TMCO2
ZNF684
TCEANC2
PODN
LRRC39
GJB4
HMGB4
C1orf122
OSCP1
C1orf216
C1orf87
LIX1L
HSD3BP4
KLF17
TMEM125
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
UBE2U
HFE2
ANKRD35
SLC30A7
KNCN
MOB3C
GLIS1
MGC27382
ZNF362
MANEAL
IL23R
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
CYP4Z2P
CITED4
FLJ40434
C1orf177
KANK4
SASS6
PPIAL4A
HFM1
UBL4B
PDIA3P
EIF2C3
EIF2C4
ALG14
LINC00466
C1orf168
TMEM61
CYP4Z1
CDCP2
SLC5A9
CC2D1B
NBPF11
NUDT17
TCTEX1D1
SPAG17
SLFNL1
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
NEGR1
CYP4X1
MAGI3
BEST4
FAM19A3
CYP4A22
C1orf185
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
RSPO1
EPHA10
ZNF326
BTBD8
RIMKLA
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
FAM151A
LOC339442
TFAP2E
LOC339524
C1orf228
ZNF642
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
FAM159A
BMP8A
CCDC23
ATPAF1-AS1
HEATR8
FAM73A
LOC375010
NSUN4
LOC388630
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
SKINTL
UOX
FRRS1
LOC400752
C1orf141
GBP1P1
FLJ27354
MIR137HG
NBPF9
LOC402779
MIR101-1
MIR137
MIR186
MIR197
MIR30C1
MIR30E
LHX8
C1orf180
FLJ32224
FAM183A
ZYG11A
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
PGCP1
GEMIN8P4
RBMXL1
LURAP1
HIST2H4B
CYB5RL
SRG7
CYMP
KIAA0754
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC646626
EMBP1
SRGAP2P2
LOC648740
NBPF6
LOC653160
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
SNORA55
SNORD45C
MIR548D1
MIR553
HIST2H2AA4
LOC728431
PPIEL
CCDC30
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729041
HSD52
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100129924
LOC100130000
LOC100130197
LOC100130557
LOC100131060
LOC100131564
NBPF10
FCGR1C
ZRANB2-AS1
LOC100132774
LOC100286793
LOC100287722
LOC100289178
LOC100289211
MIR320B1
MIR1262
MIR761
MIR3117
MIR4255
MIR4256
MIR3659
MIR3605
MIR3671
MIR548AA1
LOC100505768
ZMYM6NB
LOC100506343
LOC100507178
LOC100507423
LOC100507564
LOC100507634
FPGT-TNNI3K
GJA9-MYCBP
HEATR8-TTC4
TMEM56-RWDD3
MIR4422
MIR4781
MIR4794
MIR4711
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p13.1.

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

Genes
ABL1
FANCC
FANCG
GNAQ
OMD
PAX5
SET
SYK
TAL2
XPA
NR4A3
NUP214
FNBP1
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
hsa-mir-873
ABCA1
ACO1
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
ANXA2P2
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
CA9
CCIN
CCBL1
TNFSF8
CD72
CDK9
CKS2
CLTA
CNTFR
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
DBC1
DNM1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FOXE1
FPGS
FXN
NR5A1
GALT
GAS1
NR6A1
GCNT1
GGTA1P
B4GALT1
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IL11RA
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGS1
PTPN3
RAD23B
RGS3
RMRP
RORB
RPL12
CCL19
CCL21
SHB
SPTAN1
STXBP1
TEK
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TTF1
TXN
UGCG
VCP
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
CTNNAL1
FBP2
DPM2
FUBP3
PRPF4
KLF4
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
RGP1
TRIM14
MELK
RUSC2
ZBTB5
TNFSF15
PTBP3
GNE
SH2D3C
TOPORS
RABEPK
SIGMAR1
LAMC3
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
CCL27
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
PTENP1
AKAP2
RPL35
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
SMC5
FAM120A
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA1045
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
CIZ1
DNAJB5
DCAF12
DFNB31
NIPSNAP3A
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
TRUB2
DNAI1
ST6GALNAC4
INVS
SIT1
SPINK4
TOR1B
TOR2A
METTL11A
PKN3
PSAT1
UBQLN1
SLC2A8
ST6GALNAC6
STOML2
DEC1
PCA3
EXOSC3
FAM108B1
COQ4
CERCAM
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
SHC3
POLE3
NANS
MRPL50
RC3H2
EPB41L4B
C9orf11
TBC1D13
FAM22F
DIRAS2
ASPN
BSPRY
APTX
TEX10
LPPR1
UBE2R2
FAM206A
C9orf95
STX17
NOL8
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDK5RAP2
UBAP2
BARX1
RNF20
LRRC8A
OR2S2
IFNK
SH3GLB2
DOLPP1
KIAA1161
BDAG1
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
NAA35
SLC28A3
SUSD1
POLR1E
IPPK
FAM129B
LRRC19
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
MOB3B
C9orf82
CNTNAP3
SVEP1
RMI1
TRPM3
PTGES2
IFT74
FAM214B
GKAP1
AKNA
MIR600HG
URM1
ISCA1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
COL27A1
ALG2
FGD3
FAM125B
WDR34
LRSAM1
C9orf30
MCART1
MRRF
RBM18
FP588
KIF12
PALM2
SLC25A25
WDR31
ZNF618
FAM122A
GRIN3A
TMC1
RNF183
C9orf41
C9orf57
C9orf85
C9orf135
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19P
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
RNF38
GLIPR2
DAB2IP
LINC00032
LINGO2
NXNL2
OR1Q1
TTLL11
RASEF
FAM201A
RG9MTD3
TTC16
LOC158257
FAM120AOS
LINC00475
LOC158376
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
OLFML2A
C9orf71
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
FAM205A
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LOC286297
TUSC1
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
LOC340508
LOC340515
GPR144
FAM75D5
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
ENHO
AQP7P1
PTAR1
C9orf102
SWI5
C9orf50
KGFLP1
FAM205B
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
LOC389791
IER5L
C9orf128
OR13J1
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
FAM102A
LOC401497
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR32
MIR7-1
C9orf106
C9orf103
LOC415056
LOC440173
LOC440896
SUGT1P1
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
ANKRD18B
LOC441461
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
LOC572558
PGM5P2
MIR455
NRON
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75C2
HRCT1
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
SNORD62B
MSMP
SNORD90
MIR600
MIR601
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
SNORD121A
SNORD121B
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LINC00476
LOC100129034
UNQ6494
LOC100129250
LOC100129316
LOC100132077
LOC100132352
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
LINC00092
LOC100272217
LOC100286938
LOC100288842
LOC100289019
MIR548H3
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR3154
MIR2861
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3910-1
MIR3911
MIR3910-2
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506422
LOC100506710
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR4667
MIR3960
MIR4540
MIR4475
MIR4478
MIR2964A
MIR4670
MIR4672
MIR4476

Genes in Wide Peak

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

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

Genes
BUB1B
PML
TCF12
FLJ27352
C15orf55
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
BBS4
BCL2A1
NBEAP1
BNC1
BNIP2
CA12
CAPN3
CHRM5
CHRNA3
CHRNA5
CHRNA7
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IDH3A
IL16
IPW
IREB2
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2C1
MAP1A
MEIS2
MFAP1
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
NMB
OAZ2
OCA2
PDE8A
PKM2
PLCB2
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SH3GL3
SLC12A1
SNRPN
SNX1
SORD
SPINT1
SRP14
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
UBE3A
MKRN3
SLC30A4
AP3B2
PAR5
ANP32A
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
ALDH1A2
HERC2
HERC1
SNURF
PSTPIP1
USP8
CCNB2
SLC28A2
SLC28A1
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
ARNT2
USP3
SLC12A6
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
RASGRP1
SERF2
DENND4A
SNAPC5
HMG20A
CORO2B
CIB2
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
SLC27A2
ADAMTS7
AKAP13
GPR176
CHP
OIP5
ITGA11
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
CYFIP1
ACSBG1
KIAA1024
MGA
DMXL2
VPS39
FAM189A1
TMED3
AP4E1
SEC11A
CCNDBP1
DAPK2
EID1
C15orf2
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
GREM1
NPTN
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
HDGFRP3
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
RASL12
SPG21
SPTBN5
PTPLAD1
CTDSPL2
KLF13
RAB8B
BTBD1
TM6SF1
DUOX1
CSNK1G1
ZFAND6
MAGEL2
DLL4
SCAND2
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZNF770
ZSCAN2
ZWILCH
FLJ10038
UACA
HAUS2
FAM82A2
DNAJC17
IMP3
LARP6
MNS1
DNAJA4
NOP10
GOLGA6B
MYO5C
NDNL2
FAM214A
C15orf24
C15orf39
THAP10
PAK6
PARP6
DTWD1
CASC5
AVEN
C15orf17
ADAMTSL3
ATP10A
KIAA1199
GJD2
STARD9
ALPK3
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
ZFP106
KLHL25
CPEB1
IQCH
ISL2
RFX7
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
AAGAB
LMAN1L
C15orf29
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
AGSK1
SPG11
ELL3
PLEKHO2
WDR61
CD276
STARD5
POLR2M
C15orf44
NIPA2
C15orf5
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
WDR73
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LOC91450
CALML4
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
C15orf40
SENP8
MTFMT
OSTBETA
HIGD2B
C15orf27
NIPA1
AGPHD1
WHAMM
FSD2
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145837
LOC145845
C15orf61
TMCO5A
NRG4
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
RHOV
SCAMP5
C15orf33
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
SPESP1
LOC253044
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
HMGN2P46
SLC24A5
PRTG
LOC283663
LINC00277
C15orf60
LOC283683
C15orf37
LOC283688
LOC283692
LOC283693
OR4N4
LOC283710
FAM154B
LOC283731
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
TMEM202
LOC338963
WHAMMP3
POTEB
GLDN
GOLGA6A
TMC3
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
LOC348120
MRPL42P5
USP50
TEX9
GOLGA6L5
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
LOC388152
UBE2Q2P1
GOLGA8E
OR4M2
OR4N3P
KBTBD13
UBAP1L
SKOR1
ANKRD34C
LOC390660
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
ST20
DUOXA2
MIR184
MIR190A
MIR211
C15orf50
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
LOC503519
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC645752
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
SH2D7
LOC646938
GOLGA6L10
LOC648809
LOC653061
LOC653075
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA15
SCARNA14
FBXO22-AS1
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727849
LOC727924
LOC728758
OIP5-AS1
LOC729739
GOLGA8C
LOC729911
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
DNM1P35
LOC100128714
LOC100129387
LOC100130855
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
UBE2Q2P3
UBE2Q2P2
JMJD7
PLA2G4B
LOC100287559
LOC100287616
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1276
MIR1233-1
MIR1272
MIR1266
MIR1282
LOC100306975
MIR548H4
MIR2116
MIR1233-2
MIR4311
MIR4312
MIR4310
MIR4313
MIR3942
RPS17L
LOC100505648
LOC100505679
LOC100506686
LOC100506874
LOC100507466
ST20-MTHFS
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4514
MIR4513
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4511
MIR4509-3
MIR4712
MIR4515
MIR4715
TMCO5B
MYZAP

Arm-level results

Table 3. Get Full Table Arm-level significance table - 25 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.07 | -1.4 | 1 | 0.14 | 1.83 | 0.0897
1q | 1955 | 0.22 | 4.94 | 1.91e-06 | 0.08 | -1.2 | 1
2p | 924 | 0.14 | -1.17 | 1 | 0.07 | -3.97 | 1
2q | 1556 | 0.12 | -0.591 | 1 | 0.08 | -2.52 | 1
3p | 1062 | 0.08 | -3.22 | 1 | 0.21 | 1.7 | 0.112
3q | 1139 | 0.15 | -0.218 | 1 | 0.12 | -1.66 | 1
4p | 489 | 0.05 | -4.62 | 1 | 0.32 | 4.59 | 1.66e-05
4q | 1049 | 0.02 | -4.91 | 1 | 0.30 | 5.71 | 2.32e-07
5p | 270 | 0.18 | -1.2 | 1 | 0.17 | -1.48 | 1
5q | 1427 | 0.05 | -3.74 | 1 | 0.21 | 3.08 | 0.00383
6p | 1173 | 0.18 | 0.705 | 0.961 | 0.11 | -2.04 | 1
6q | 839 | 0.15 | -1.22 | 1 | 0.15 | -1.07 | 1
7p | 641 | 0.38 | 7.33 | 8.91e-13 | 0.10 | -2.87 | 1
7q | 1277 | 0.35 | 8.16 | 1.11e-15 | 0.11 | -1.62 | 1
8p | 580 | 0.37 | 6.16 | 2.46e-09 | 0.29 | 3.07 | 0.00383
8q | 859 | 0.48 | 11.8 | 0 | 0.13 | -1.42 | 1
9p | 422 | 0.13 | -2.44 | 1 | 0.33 | 4.6 | 1.66e-05
9q | 1113 | 0.16 | -0.224 | 1 | 0.25 | 3.26 | 0.0028
10p | 409 | 0.19 | -0.51 | 1 | 0.18 | -0.793 | 1
10q | 1268 | 0.15 | -0.0801 | 1 | 0.18 | 1.23 | 0.243
11p | 862 | 0.10 | -2.87 | 1 | 0.13 | -1.64 | 1
11q | 1515 | 0.11 | -1.23 | 1 | 0.12 | -0.708 | 1
12p | 575 | 0.17 | -0.929 | 1 | 0.14 | -1.8 | 1
12q | 1447 | 0.15 | 0.278 | 1 | 0.11 | -1.43 | 1
13q | 654 | 0.32 | 5.07 | 1.15e-06 | 0.13 | -2.09 | 1
14q | 1341 | 0.04 | -4.27 | 1 | 0.22 | 2.94 | 0.00507
15q | 1355 | 0.10 | -1.95 | 1 | 0.16 | 0.566 | 0.571
16p | 872 | 0.16 | -0.632 | 1 | 0.18 | -0.0218 | 0.925
16q | 702 | 0.14 | -1.62 | 1 | 0.21 | 1.04 | 0.312
17p | 683 | 0.08 | -3.52 | 1 | 0.33 | 5.49 | 2.76e-07
17q | 1592 | 0.11 | -1.03 | 1 | 0.16 | 1.26 | 0.243
18p | 143 | 0.18 | -1.35 | 1 | 0.28 | 2.03 | 0.0599
18q | 446 | 0.11 | -2.8 | 1 | 0.35 | 5.54 | 2.76e-07
19p | 995 | 0.11 | -2.15 | 1 | 0.25 | 3.14 | 0.00373
19q | 1709 | 0.17 | 1.72 | 0.19 | 0.20 | 2.98 | 0.00486
20p | 355 | 0.52 | 11.6 | 0 | 0.12 | -2.47 | 1
20q | 753 | 0.58 | 15.5 | 0 | 0.05 | -3.53 | 1
21q | 509 | 0.07 | -4.22 | 1 | 0.32 | 4.57 | 1.66e-05
22q | 921 | 0.10 | -2.63 | 1 | 0.29 | 4.43 | 2.68e-05
Xq | 1312 | 0.12 | -1.11 | 1 | 0.16 | 0.223 | 0.785

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/STAD-TP/2330022/2.GDAC_MergeDataFiles.Finished/STAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 237 Input Tumor Samples.

Tumor Sample Names
TCGA-B7-5816-01A-21D-1599-01
TCGA-B7-5818-01A-11D-1599-01
TCGA-BR-4183-01A-02D-1130-01
TCGA-BR-4184-01A-01D-1130-01
TCGA-BR-4187-01A-01D-1130-01
TCGA-BR-4188-01A-01D-1130-01
TCGA-BR-4191-01A-02D-1130-01
TCGA-BR-4201-01A-01D-1130-01
TCGA-BR-4253-01A-01D-1130-01
TCGA-BR-4255-01A-01D-1130-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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