SNP6 Copy number analysis (GISTIC2)
Stomach Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
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 (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1K073R3
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 2.0.22 (Firehose task version: 140).

Summary

There were 441 tumor samples used in this analysis: 27 significant arm-level results, 36 significant focal amplifications, and 52 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 - 36 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 1.2178e-73 1.2178e-73 chr17:37854508-37876018 1
19q12 4.0012e-55 7.1023e-51 chr19:30287570-30358836 1
8q24.21 1.51e-35 1.51e-35 chr8:128714098-128729186 0 [MYC]
12p12.1 2.4608e-34 2.4608e-34 chr12:25339898-25414737 3
18q11.2 2.0923e-25 2.0923e-25 chr18:19594807-19790248 2
12q15 7.7245e-20 7.7245e-20 chr12:69281664-69978625 6
8p23.1 9.7666e-20 9.7666e-20 chr8:11547791-11638987 3
6p21.1 1.0258e-19 2.2377e-19 chr6:43845008-43936728 0 [C6orf223]
20q13.2 5.5657e-18 5.5657e-18 chr20:52246647-52427475 0 [ZNF217]
11q13.3 7.796e-18 8.153e-18 chr11:69406626-69595013 4
7q21.2 1.337e-27 2.1954e-15 chr7:91743151-92669786 10
15q26.1 1.6367e-12 1.6367e-12 chr15:90663892-90703835 1
1q42.3 2.6203e-13 2.1996e-11 chr1:235072499-235128859 0 [RN7SL668P]
3q26.2 5.0488e-11 5.0488e-11 chr3:169766260-170486763 6
7p11.2 1.0022e-11 3.7921e-09 chr7:55025387-55372336 1
13q22.1 3.8612e-08 1.0298e-07 chr13:73725494-73857708 1
6q21 1.0667e-07 2.7546e-07 chr6:107129118-107221941 0 [MIR587]
10q26.13 2.5741e-08 6.1855e-07 chr10:123172617-123399846 1
11p13 3.4401e-08 6.2887e-06 chr11:35244045-35263023 1
7q22.1 8.0319e-14 1.8593e-05 chr7:99549026-99679895 6
1q21.3 1.12e-06 0.00044589 chr1:150033346-151224319 45
10q22.2 6.569e-05 0.0018322 chr10:76839356-77572076 7
Xq27.3 0.0021069 0.0021069 chrX:138601616-155270560 201
1p36.22 0.003761 0.003761 chr1:10686864-11068052 3
5p13.1 3.3128e-05 0.0047133 chr5:38167585-44523118 38
9q34.3 0.0047873 0.0047873 chr9:139857644-140151408 33
9p24.1 0.0062179 0.0092958 chr9:4764022-5711052 10
9p13.2 0.00082114 0.012364 chr9:33804007-36412610 75
7p22.1 0.0078915 0.020485 chr7:1-7930534 90
10p11.22 0.021867 0.021867 chr10:31856589-33304482 7
5p15.33 0.0018322 0.043652 chr5:1-1891820 31
13q12.3 0.01734 0.055957 chr13:30754530-35520798 29
6q12 0.0056259 0.058323 chr6:64001177-64323832 2
11p11.2 0.01734 0.195 chr11:45847089-46475305 12
19q13.32 0.0018322 0.24148 chr19:44887619-45385167 15
14q21.3 0.2486 0.2486 chr14:50242323-50678361 10
Genes in Wide Peak

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

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

Genes
ERBB2
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: Cancer Gene Census[7].

Genes
CCNE1
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: Cancer Gene Census[7].

Genes
KRAS
CASC1
LYRM5
Genes in Wide Peak

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

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

Genes
RNU6ATAC20P
GATA6
Genes in Wide Peak

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

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

Genes
RN7SL804P
CPM
LYZ
YEATS4
FRS2
CPSF6
Genes in Wide Peak

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

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

Genes
C8orf49
GATA4
NEIL2
Genes in Wide Peak

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

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

Genes
CCND1
FGF4
FGF19
ORAOV1
Genes in Wide Peak

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

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

Genes
CDK6
RN7SL7P
GATAD1
KRIT1
CYP51A1
PEX1
ANKIB1
RBM48
FAM133B
LRRD1
Genes in Wide Peak

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

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

Genes
RN7SL755P
Genes in Wide Peak

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

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

Genes
CLDN11
PRKCI
SKIL
GPR160
SLC7A14
PHC3
Genes in Wide Peak

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

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

Genes
EGFR
Genes in Wide Peak

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

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

Genes
RNY1P8
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: Cancer Gene Census[7].

Genes
FGFR2
Genes in Wide Peak

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

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

Genes
CD44
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
AZGP1P1
SNORA40|ENSG00000222966.1
AZGP1
ZNF3
ZKSCAN1
ZSCAN21
Genes in Wide Peak

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

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

Genes
ARNT
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
CTSK
CTSS
ECM1
ENSA
MCL1
VPS72
PIP5K1A
ANXA9
PRPF3
SETDB1
SEMA6C
VPS45
RPRD2
CA14
TMOD4
CERS2
APH1A
PLEKHO1
MRPS21
ADAMTSL4
C1orf56
GOLPH3L
FAM63A
CDC42SE1
PRUNE
SCNM1
TNFAIP8L2
C1orf54
TARS2
ANP32E
HORMAD1
GABPB2
C1orf51
BNIPL
LYSMD1
MIR4257
Genes in Wide Peak

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

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

Genes
MIR606
VDAC2
DUSP13
C10orf11
ZNF503
COMTD1
SAMD8
Genes in Wide Peak

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

Table S18.  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
CXorf51A
CXorf51B
RNA5SP517
SPANXN1
RN7SKP189
RN7SKP149
RN7SKP81
snoU13|ENSG00000239188.1
RNA5SP516
SPANXD
SPANXA2
SPANXA1
RN7SL727P
MIR505
SNORA18|ENSG00000252719.1
RNU6ATAC23P
snoU13|ENSG00000238485.1
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CDR1
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
GDI1
HCFC1
HMGB3
IDH3G
IDS
IL9R|ENSG00000124334.12
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SOX3
SSR4
VAMP7|ENSG00000124333.10
TAZ
VBP1
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
MTMR1
FAM50A
TMEM257
GPR50
MAGEC1
MAMLD1
BCAP31
SPRY3|ENSG00000168939.6
ZNF275
TREX2
LDOC1
SRPK3
PNMA3
CTAG2
NSDHL
MAGEC2
TMLHE
PLXNA3
HAUS7
PDZD4
FAM3A
SPANXC
PRRG3
BRCC3
CD99L2
H2AFB3
TMEM185A
SLITRK2
FATE1
CXorf40A
FAM58A
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
GAB3
PNCK
ZFP92
CSAG1
FMR1NB
VMA21
CTAG1A
ATP11C
LINC00632
CXorf66
UBE2NL
SPANXN4
H2AFB2
H2AFB1
SPANXN2
CXorf40B
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR510
MIR514A1
MIR514A2
MIR514A3
MAGEA9B
OPN1MW2
SPANXB1
MIR767
MIR890
MIR891B
MIR888
MIR892B
MIR891A
MIR892A
HSFX2
SMIM9
SPANXB2
CMC4
PNMA6C
MIR513C
MIR320D2
MIR718
MIR513B
MIR2114
MIR514B
MIR4330
HSFX1
Genes in Wide Peak

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

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

Genes
PEX14
CASZ1
C1orf127
Genes in Wide Peak

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

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

Genes
LIFR
FGF10
CCL28
ANXA2R
SNORD72
RPL37
SNORA57|ENSG00000212567.1
SNORA63|ENSG00000199552.1
LINC00604
LINC00603
C6
C7
C9
DAB2
FYB
GHR
HMGCS1
OXCT1
PRKAA1
PTGER4
SEPP1
ZNF131
OSMR
PAIP1
NNT
TTC33
FBXO4
C5orf28
CARD6
MROH2B
EGFLAM
NIM1
RICTOR
C5orf51
PLCXD3
C5orf34
CCDC152
MIR3650
Genes in Wide Peak

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

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

Genes
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
ABCA2
ENTPD2
FUT7
GRIN1
PTGDS
SSNA1
TUBB4B
MAN1B1
NELFB
NDOR1
ANAPC2
DPP7
NPDC1
SAPCD2
UAP1L1
TMEM203
SLC34A3
C9orf142
TPRN
C9orf169
LRRC26
LCNL1
C9orf139
FAM166A
C9orf173
RNF208
Genes in Wide Peak

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

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

Genes
JAK2
CD274
INSL4
RLN1
RLN2
RCL1
INSL6
PLGRKT
KIAA1432
PDCD1LG2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.2.

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

Genes
FANCG
LINC00961
RGP1
RN7SL22P
RMRP
MIR4667
RN7SL338P
FLJ00273
FAM205CP
FAM205B
GALT
RN7SKP24
KIAA1161
RNA5SP282
RN7SKP114
SNORD121A
SNORD121B
RNU4ATAC11P
NUDT2
CA9
CCIN
CD72
CLTA
CNTFR
GALT
IL11RA
NPR2
CCL19
CCL21
TESK1
TLN1
TPM2
VCP
RECK
RUSC2
GNE
SIGMAR1
CREB3
UNC13B
CCL27
DCTN3
KIAA1045
DNAJB5
DCAF12
SPAG8
DNAI1
SIT1
STOML2
UBAP1
TMEM8B
UBE2R2
UBAP2
OR2S2
GBA2
FAM214B
HINT2
C9orf24
PIGO
ARHGEF39
ARID3C
RPP25L
C9orf131
RNF38
GLIPR2
ATP8B5P
FAM219A
CCDC107
FAM205A
KIF24
ENHO
FAM221B
OR13J1
HRCT1
MSMP
FAM166B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.1.

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

Genes
PMS2
CARD11
RPA3
PMS2CL
GRID2IP
FLJ20306
RN7SL851P
SNORA42|ENSG00000207217.1
RN7SL556P
ZNF815P
MIR589
snoU13|ENSG00000238394.1
ZNF890P
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
ACTB
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
RAC1
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KDELR2
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
GET4
CCZ1
MIOS
RNF216
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
C1GALT1
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM220A
ZFAND2A
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
SLC29A4
RSPH10B
COL28A1
OCM
RSPH10B2
ANKRD61
MIR3683
MIR4656
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p11.22.

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

Genes
CCDC7
RN7SL825P
ITGB1
KIF5B
C10orf68
EPC1
ARHGAP12
Genes in Wide Peak

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

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

Genes
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
IRX4
CEP72
AHRR
MRPL36
BRD9
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
SLC6A19
SLC6A18
MIR4277
MIR4457
MIR4456
Genes in Wide Peak

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

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

Genes
BRCA2
LINC00457
SNORA25|ENSG00000199196.1
LINC00423
RNY1P4
SNORA16|ENSG00000212293.1
ZAR1L
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
ALOX5AP
HMGB1
RFC3
KL
FRY
USPL1
N4BP2L2
HSPH1
PDS5B
NBEA
KATNAL1
MEDAG
STARD13
N4BP2L1
RXFP2
TEX26
B3GALTL
Genes in Wide Peak

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

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

Genes
PTP4A1
LGSN
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p11.2.

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

Genes
CREB3L1
MIR4688
PHF21A
CHRM4
CRY2
MDK
DGKZ
PEX16
MAPK8IP1
AMBRA1
GYLTL1B
C11orf94
Genes in Wide Peak

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

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

Genes
BCL3
CBLC
SNORA70|ENSG00000253027.1
snoZ6|ENSG00000252200.1
CEACAM22P
CEACAM20
ZNF180
BCAM
PVR
PVRL2
ZNF229
ZNF285
CEACAM19
IGSF23
CEACAM16
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.3.

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

Genes
RN7SKP193
ARF6
RN7SL2
RN7SL3
SOS2
NEMF
KLHDC2
METTL21D
C14orf183
C14orf182

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 - 52 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 5.2032e-147 5.2032e-147 chr16:78098006-79031486 1
5q12.1 2.1714e-87 8.0169e-85 chr5:58998410-59780946 2
4q22.1 1.373e-90 1.3185e-83 chr4:91271445-93240505 1
9p23 3.8915e-58 8.4591e-49 chr9:8885227-12687261 2
6p25.3 2.4628e-45 2.4628e-45 chr6:1608837-2624052 2
20p12.1 2.3484e-36 2.3484e-36 chr20:14301156-15274325 2
3p14.2 2.6651e-43 7.5254e-33 chr3:59701447-61026498 2
9p21.3 4.5257e-56 3.4236e-28 chr9:21931610-22003135 2
Xp21.1 3.3271e-27 2.4058e-25 chrX:32117084-32611359 2
18q21.2 3.3736e-29 4.4494e-25 chr18:48472083-48650073 3
7q31.1 1.1641e-33 4.9513e-25 chr7:110746146-111366370 1
6q26 1.2358e-25 2.2648e-22 chr6:161693099-163153207 1
3q26.31 1.6983e-19 1.6983e-19 chr3:174345545-175760559 3
1p36.11 3.0679e-18 1.6645e-16 chr1:26963410-27127934 4
4q35.1 2.1858e-27 2.1979e-11 chr4:179280062-186321446 36
10q23.31 5.928e-15 7.7856e-11 chr10:89506488-90034038 6
2q32.1 1.5882e-13 1.2457e-08 chr2:187373995-187560595 1
21q11.2 1.2217e-07 1.6636e-06 chr21:1-16335988 17
16p13.3 2.4826e-06 2.5171e-06 chr16:5144019-7780235 2
19p13.3 1.5798e-05 1.5592e-05 chr19:2473582-4675277 72
17p12 3.7518e-05 3.8183e-05 chr17:11866892-12456081 4
7q36.3 8.2812e-11 8.4589e-05 chr7:157210222-158385117 3
11q23.2 8.3734e-05 8.4589e-05 chr11:106886059-131242853 272
12p13.1 0.00030002 0.00031124 chr12:7176979-18235892 146
11p15.5 0.00031813 0.00031949 chr11:2441018-2892511 2
3p26.1 3.479e-10 0.00034388 chr3:3099461-5164768 11
2q37.2 2.9767e-06 0.00055914 chr2:235913227-237079324 3
10q22.3 2.8168e-06 0.00065093 chr10:77312101-78597839 4
Xp22.2 6.0353e-07 0.00087836 chrX:9891764-11137490 3
21q22.13 3.866e-05 0.0014903 chr21:38638578-38997673 1
1q44 0.0018105 0.0017816 chr1:245290228-247052144 7
Xq21.33 0.0025468 0.0026527 chrX:95661798-99356556 5
15q15.1 3.2335e-05 0.00268 chr15:41403242-41790986 7
2q33.3 2.003e-07 0.0030211 chr2:204826225-206558638 1
14q23.3 0.00031723 0.0030211 chr14:66963153-67658112 1
6q24.3 2.5441e-05 0.0069766 chr6:147706792-148595857 1
9q21.11 0.0014803 0.0075045 chr9:38619152-71322791 58
22q13.31 0.010201 0.010144 chr22:45736500-51304566 66
4p16.3 0.016966 0.01751 chr4:1297570-2848182 25
17q24.3 0.021534 0.021242 chr17:70116519-70642789 2
18q12.2 2.599e-07 0.022858 chr18:36593175-39537209 2
13q12.11 0.024986 0.025106 chr13:1-23727991 46
8p23.2 0.028548 0.028965 chr8:1-4985851 15
15q11.2 3.7853e-05 0.046144 chr15:1-31198928 93
3p21.1 1.0362e-08 0.048297 chr3:52560991-52727256 8
6q14.1 0.0044196 0.084889 chr6:62995384-117999812 252
14q32.32 0.0031145 0.094836 chr14:95939420-107349540 203
5q23.2 2.8835e-08 0.10621 chr5:80521963-135554491 245
19q13.11 0.1243 0.1243 chr19:31198022-36230173 79
10p15.3 0.13903 0.14244 chr10:1-32095975 223
1p13.2 0.0040659 0.15145 chr1:71512161-149898950 418
12q12 0.22179 0.22301 chr12:33514047-54185878 200
Genes in Wide Peak

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

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

Genes
PIH1
Genes in Wide Peak

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

Table S33.  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 4q22.1.

Table S34.  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 9p23.

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

Genes
RN7SL5P
SNORD27|ENSG00000251699.1
Genes in Wide Peak

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

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

Genes
FOXC1
GMDS
Genes in Wide Peak

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

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

Genes
RNA5SP475
FLRT3
Genes in Wide Peak

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

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

Genes
U3|ENSG00000212211.1
NPCDR1
Genes in Wide Peak

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

Table S39.  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 Xp21.1.

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

Genes
MIR3915
RNA5SP501
Genes in Wide Peak

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

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

Genes
RN7SL695P
SMAD4
ELAC1
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238922.1
Genes in Wide Peak

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

Table S43.  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 3q26.31.

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

Genes
snoU13|ENSG00000271842.1
MIR4789
RN7SKP40
Genes in Wide Peak

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

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

Genes
ARID1A
RN7SL501P
snoU13|ENSG00000238316.1
PIGV
Genes in Wide Peak

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

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

Genes
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
ENPP6
RWDD4
CCDC111
HELT
CLDN24
MIR1305
MIR3945
MIR4455
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
ATAD1
KLLN
Genes in Wide Peak

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

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

Genes
ITGAV
Genes in Wide Peak

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

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

Genes
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
HSPA13
TPTE
RBM11
SAMSN1
LIPI
ABCC13
POTED
MIR3687
Genes in Wide Peak

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

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

Genes
SNORA40|ENSG00000252138.1
RBFOX1
Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
RN7SL121P
LRG1
HDGFRP2
RN7SL528P
RN7SL84P
PIAS4
SNORD37|ENSG00000206775.1
MIR637
RN7SL202P
SNORD38|ENSG00000252408.1
FZR1
RN7SL866P
ZNF554
AES
DAPK3
EEF2
GNA15
GNG7
MATK
GADD45B
NFIC
MAP2K2
SGTA
TBXA2R
THOP1
TLE2
S1PR4
APBA3
CHAF1A
EBI3
HMG20B
SEMA6B
ZFR2
PIP5K1C
TJP3
NMRK2
SLC39A3
ZBTB7A
SIRT6
STAP2
CCDC94
C19orf10
NCLN
SHD
ZNF77
CACTIN
CELF5
FSD1
TLE6
ZNF556
UBXN6
DOHH
CREB3L3
RAX2
MPND
ATCAY
MRPL54
TMIGD2
TNFAIP8L1
ZNF57
MFSD12
GIPC3
DIRAS1
ZNF555
ANKRD24
C19orf77
PLIN5
PLIN4
C19orf71
MIR4746
Genes in Wide Peak

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

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

Genes
MAP2K4
MIR744
RPL21P122
ZNF18
Genes in Wide Peak

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

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

Genes
MIR595
PTPRN2
MIR5707
Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NCAM1
NFRKB
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
BARX2
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
EXPH5
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
DCPS
ZBTB44
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
HEPN1
CLDN25
PATE3
MIR4301
MIR4493
MIR4491
MIR4492
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
ETV6
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
C1R
A2M
APOBEC1
ARHGDIB
C3AR1
CD69
CDKN1B
CREBL2
PHC1
EMP1
EPS8
GPR19
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PTPRO
PEX5
PZP
SLC2A3
MFAP5
KLRC4
YBX3
CD163
GDF3
CLSTN3
KLRG1
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
NECAP1
CLEC4E
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
NANOG
APOLD1
GSG1
RBP5
RERG
CLEC6A
LOH12CR1
TMEM52B
HIST4H4
SLC2A14
A2ML1
CLEC12A
CLECL1
CLEC4C
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CD163L1
CLEC9A
C12orf36
CLEC4D
ACSM4
TAS2R42
DPPA3
NANOGNB
CLEC2A
CLEC12B
LINC00937
ZNF705A
SMCO3
PRB2
MIR614
SLC15A5
Genes in Wide Peak

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

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

Genes
KCNQ1OT1
KCNQ1
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000239126.1
EGOT
SNORA43|ENSG00000253049.1
IL5RA
ITPR1
SETMAR
BHLHE40
TRNT1
CRBN
LRRN1
SUMF1
Genes in Wide Peak

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

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

Genes
RN7SL204P
GBX2
AGAP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q22.3.

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

Genes
SNORA31|ENSG00000252888.1
RN7SL518P
MIR606
C10orf11
Genes in Wide Peak

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

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

Genes
CLCN4
MID1
WWC3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.13.

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

Genes
DYRK1A
Genes in Wide Peak

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

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

Genes
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
SCCPDH
KIF26B
TFB2M
SMYD3
CNST
Genes in Wide Peak

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

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

Genes
SNORA25|ENSG00000252296.1
RN7SL74P
RN7SKP194
DIAPH2
RPA4
Genes in Wide Peak

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

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

Genes
RN7SL497P
CHP1
OIP5
RTF1
NDUFAF1
NUSAP1
EXD1
Genes in Wide Peak

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

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

Genes
PARD3B
Genes in Wide Peak

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

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

Genes
GPHN
Genes in Wide Peak

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

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

Genes
SAMD5
Genes in Wide Peak

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

Table S68.  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
TMEM252
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 22q13.31.

Table S69.  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 4p16.3.

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

Genes
FGFR3
WHSC1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
LETM1
RNF4
SH3BP2
NELFA
SLBP
FAM193A
TACC3
MXD4
UVSSA
ZFYVE28
TNIP2
HAUS3
TMEM129
FAM53A
CRIPAK
NAT8L
POLN
C4orf48
MIR4800
Genes in Wide Peak

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

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

Genes
LINC00511
SOX9
Genes in Wide Peak

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

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

Genes
LINC00669
RN7SKP182
Genes in Wide Peak

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

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

Genes
RNY3P4
LINC00621
SNORD36|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27|ENSG00000252128.1
snoU13|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
FGF9
GJA3
GJB2
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
LATS2
CRYL1
IL17D
MPHOSPH8
XPO4
MRP63
TPTE2
N6AMT2
SKA3
MICU2
Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
TDRP
ERICH1
ZNF596
MIR596
Genes in Wide Peak

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

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

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

This is the comprehensive list of deleted genes in the wide peak for 3p21.1.

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

Genes
PBRM1
SNORD69
SNORD19|ENSG00000222345.1
SNORD19B|ENSG00000238862.1
SNORD19|ENSG00000212493.1
SNORD19B|ENSG00000252787.1
RNU6ATAC16P
SMIM4
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.1.

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

Genes
PRDM1
ROS1
GOPC
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
snoU13|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18|ENSG00000252249.1
U3|ENSG00000221455.1
U3|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73|ENSG00000222145.1
RN7SL183P
snoU13|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70|ENSG00000206886.1
RNA5SP210
SNORD112|ENSG00000252932.1
HTR1B
U6|ENSG00000272445.1
snoU13|ENSG00000239132.1
RNA5SP209
RN7SKP163
U3|ENSG00000221332.1
MB21D1
snoU13|ENSG00000238464.1
OOEP
OGFRL1
U3|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65|ENSG00000212229.1
FKBP1C
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COX7A2
EEF1A1
EPHA7
FOXO3
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
REV3L
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
PTP4A1
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
PHF3
ORC3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
LGSN
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
SMIM8
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
BACH2
SMAP1
C6orf164
MICAL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
MCHR2
FAXC
GJA10
USP45
SLC22A16
UBE3D
GTF3C6
MRAP2
KLHL32
SLC16A10
RIPPLY2
IRAK1BP1
CD109
PM20D2
SRSF12
KHDC3L
C6orf165
PRSS35
LCA5
C6orf163
AK9
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
VGLL2
LACE1
MMS22L
CEP57L1
PPIL6
DCBLD1
DPPA5
RSPH4A
EYS
GJB7
LIN28B
MIR30A
MIR30C2
FAM26F
RFPL4B
FAM229B
MIR587
METTL24
TRAPPC3L
KHDC1L
MIR2113
MIR4282
MIR4464
MIR4643
MIR548AI
MIR4463
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.32.

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

Genes
AKT1
TCL1A
TCL6
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
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
BDKRB1
BDKRB2
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
BRF1
HSP90AA1
JAG2
KLC1
MARK3
PPP2R5C
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DLK1
MTA1
BAG5
C14orf2
CDC42BPB
TCL1B
TECPR2
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
GPR132
EVL
GSKIP
CINP
CDCA4
ATG2B
ZNF839
BEGAIN
INF2
ZFYVE21
WDR25
TMEM121
AMN
SETD3
HHIPL1
BTBD6
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
PLD4
ADSSL1
SLC25A29
NUDT14
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
ASPG
C14orf64
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 deleted genes in the wide peak for 5q23.2.

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

Genes
APC
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
ALDH7A1
CAMLG
CAST
CCNH
CDO1
CETN3
CHD1
CKMT2
HAPLN1
CSF2
CSNK1G3
VCAN
DMXL1
EFNA5
FBN2
GDF9
GLRX
HSD17B4
IL3
IL4
IL5
IL9
IL13
IRF1
KCNN2
LECT2
LMNB1
LNPEP
LOX
SMAD5
MAN2A1
MCC
MEF2C
NEUROG1
PAM
PCSK1
PGGT1B
PITX1
PPIC
RASA1
RPS23
SLC12A2
SLC22A4
SLC22A5
SNX2
TCF7
NR2F1
TGFBI
UBE2B
VDAC1
XRCC4
ST8SIA4
REEP5
PDLIM4
P4HA2
ATG12
NREP
CXCL14
H2AFY
SNCAIP
TTC37
PJA2
DDX46
EDIL3
RAD50
POLR3G
SEC24A
KIF3A
RHOBTB3
ELL2
FSTL4
SEPT8
PPIP5K2
ACSL6
PHF15
AFF4
SLC27A6
SNX24
TMED7
ISOC1
SAR1B
CDKL3
PRR16
COMMD10
RAPGEF6
ERAP1
PHAX
ZCCHC10
GIN1
TRIM36
RIOK2
FEM1C
C5orf15
CDC42SE2
ZNF608
SEMA6A
ARRDC3
EPB41L4A
ERAP2
FBXL17
YTHDC2
GRAMD3
TXNDC15
MCTP1
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
ZCCHC9
ANKRD32
MEGF10
TSLP
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
ATP6AP1L
PRDM6
FTMT
FNIP1
MARCH3
LYSMD3
SLCO6A1
PRRC1
ZNF474
POU5F2
STARD4
WDR36
ACOT12
SOWAHA
SHROOM1
C5orf24
C5orf20
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
ARSK
FAM81B
CCDC112
DCP2
LIX1
ADAMTS19
C5orf27
AQPEP
KIAA0825
RGMB
RFESD
CHSY3
FAM170A
FAM174A
CATSPER3
SLCO4C1
C5orf48
LINC00461
C5orf56
CTXN3
CCNI2
MIR583
TICAM2
MIR2277
MIR4280
MIR3660
MIR3936
MIR3661
MIR4460
MIR5692C1
Genes in Wide Peak

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

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

Genes
CEBPA
KMT2B
RN7SL765P
RN7SL491P
GPR42
MIR5196
HAMP
LINC00904
SNORD111|ENSG00000252230.1
SCGB1B2P
WTIP
RN7SL154P
RN7SL150P
LRP3
C19orf40
RN7SKP22
RN7SL789P
SNORA68|ENSG00000201388.1
RNA5SP472
RNA5SP471
THEG5
ATP4A
CD22
CEBPG
COX6B1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
MAG
PEPD
FXYD1
FXYD3
SCN1B
USF2
PDCD5
KIAA0355
WBP7
UBA2
TMEM147
UPK1A
SLC7A9
ZNF507
HAUS5
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
GPATCH1
ZNF302
SLC7A10
TSHZ3
GRAMD1A
CHST8
KCTD15
RBM42
ANKRD27
PDCD2L
CEP89
RHPN2
ZNF30
TDRD12
DMKN
WDR88
ZNF792
DPY19L3
ZNF599
FAM187B
LGI4
SCGB2B2
ZNF181
SBSN
RGS9BP
KRTDAP
NUDT19
Genes in Wide Peak

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

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

Genes
GATA3
MLLT10
RNA5SP309
SVILP1
RN7SL63P
RN7SL241P
SNORD115|ENSG00000212411.1
MIR604
PTCHD3P1
RNA5SP308
LINC00837
RNU4ATAC6P
RN7SKP39
U3|ENSG00000222666.1
RN7SKP132
ARMC4P1
LINC00614
snoU13|ENSG00000238414.1
SNORA57|ENSG00000223027.1
LINC00264
RNA5SP307
RNA5SP306
RN7SKP220
RN7SKP241
RNA5SP305
MIR603
snoU13|ENSG00000238515.1
SNORA40|ENSG00000252049.1
RNA5SP304
RN7SKP37
RN7SKP219
MIR1915
CASC10
U3|ENSG00000251749.1
RNA5SP303
U3|ENSG00000200545.1
C10orf112
TMEM236|ENSG00000184040.7
MRC1L1
snoR442|ENSG00000251959.1
ST8SIA6
snoU13|ENSG00000238552.1
SNORA31|ENSG00000252537.1
snoU13|ENSG00000239130.1
ITGA8
NMT2
ACBD7
MEIG1
CDNF
RNA5SP302
RNA5SP301
RNA5SP300
MIR4480
RNU6ATAC39P
SNORD45|ENSG00000252438.1
RN7SL198P
RN7SL232P
snoU13|ENSG00000238900.1
U6|ENSG00000272507.1
LINC00710
SFTA1P
LINC00709
RNA5SP299
LINC00708
TAF3
LINC00707
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ATP5C1
BMI1
CACNB2
CALML3
AKR1C4
KLF6
MAP3K8
AKR1C2
TRDMT1
GAD2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PIP4K2A
PRKCQ
RSU1
SVIL
ZEB1
VIM
STAM
CUBN
PRPF18
AKR1C3
CDC123
PTPLA
PTER
SPAG6
USP6NL
ABI1
OPTN
NET1
NEBL
PITRM1
RPP38
CELF2
YME1L1
ZMYND11
NUDT5
ANKRD26
WDR37
MSRB2
SEPHS1
RAB18
KIN
DIP2C
LARP4B
COMMD3
GTPBP4
PDSS1
BAMBI
UPF2
HSPA14
WAC
CALML5
MYO3A
APBB1IP
ANKRD16
FAM208B
ARMC4
MTPAP
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
KIAA1217
PRTFDC1
CAMK1D
GPR158
ARHGAP21
KIAA1462
SFMBT2
DNAJC1
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
THNSL1
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
LYZL1
FBXO18
PLXDC2
MASTL
RBM17
ACBD5
IDI2
UCN3
LYZL2
MPP7
ENKUR
ARMC3
OTUD1
ZNF438
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
PROSER2
PTF1A
C10orf67
MKX
C10orf126
EBLN1
PTCHD3
C10orf113
SKIDA1
C10orf115
LRRC37A6P
C1QL3
LINC00200
PRR26
TMEM236|ENSG00000148483.7
MIR938
MIR1265
MIR548Q
MIR4293
MIR4675
MIR548AK
Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
NRAS
BCL10
PDE4DIP
TRIM33
RBM15
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
LINC00622
snoU13|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
ACTBP12
RN7SL235P
RN7SL653P
BARHL2
U3|ENSG00000199666.1
RN7SKP272
snoU13|ENSG00000239176.1
GBP1P1
GBP6
RN7SL583P
RNA5SP52
RNA5SP51
SNORD81|ENSG00000199934.1
C1orf52
CTBS
SPATA1
RPF1
UOX
SNORA2|ENSG00000199959.1
TTLL7
RN7SKP247
RNA5SP23
RNA5SP22
GIPC2
DNAJB4
RNA5SP21
RN7SL370P
RNA5SP20
ST6GALNAC5
ST6GALNAC3
SNORD45B
SNORD45A
SNORD45C
LRRC53
RNU4ATAC8P
RNA5SP50
RN7SKP19
NEGR1
MIR186
ABCA4
ACADM
ADORA3
AGL
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FMO5
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TBX15
TGFBR3
TSHB
VCAM1
CSDE1
EVI5
CDC7
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
ITGA10
LMO4
CDC14A
RTCA
FPGT
PEX11B
FUBP1
SLC16A4
CD101
ZRANB2
CHD1L
CLCA3P
CLCA2
HS2ST1
LPPR4
SV2A
RBM8A
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
LAMTOR5
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
IFI44L
ADAM30
CD160
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
ZZZ3
PTPN22
PHGDH
AK5
CHIA
GPSM2
SLC25A24
TMED5
BOLA1
SH3GLB1
HAO2
SNX7
GPR89B
GPR88
TRMT13
RSBN1
ZNHIT6
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
OLFML3
AMIGO1
ODF2L
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
REG4
SYDE2
ZNF644
LRRC8C
POLR3GL
PROK1
PSRC1
STRIP1
ZNF697
NEXN
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
LIX1L
DRAM2
PIFO
C1orf162
SYT6
SAMD13
TMEM56
NBPF4
HFE2
ANKRD35
SLC30A7
NBPF12
CHIAP2
FNDC7
SASS6
PPIAL4A
HFM1
UBL4B
NBPF11
SPAG17
HIPK1
SLC44A5
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
NBPF16
FAM102B
SYPL2
CYB561D1
ANKRD34A
ZNF326
BTBD8
HIST2H2AB
PPM1J
CCDC18
MYBPHL
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
C1orf137
NOTCH2NL
FRRS1
NBPF9
MIR197
LHX8
C1orf180
HIST2H2BF
RBMXL1
HIST2H4B
PPIAL4G
PPIAL4D
NBPF6
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
MIR760
NBPF20
MIR320B1
TNNI3K
MIR378G
MIR137HG
MIR4423
Genes in Wide Peak

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

Table S83.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ATF1
SNORD81|ENSG00000223213.1
KRT121P
LINC00592
C12orf80
OR7E47P
POU6F1
U6|ENSG00000272028.1
HIGD1C
RN7SL519P
MIR1293
AQP6
AQP5
BCDIN3D
PRPH
WNT1
snoU13|ENSG00000238395.1
MIR4701
SNORA2B
SNORA2A
SNORA34
DKFZP779L1853
RPAP3
SNORA64|ENSG00000199566.1
SCAF11
RN7SL246P
RNA5SP361
SNORA74|ENSG00000252917.1
RN7SL10P
RNA5SP360
MUC19
SNORA22|ENSG00000199571.1
ABCD2
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112|ENSG00000251863.1
ASIC1
ACVR1B
ACVRL1
ADCY6
AMHR2
AQP2
ARF3
ATP5G2
CACNB3
CCNT1
CNTN1
COL2A1
EIF4B
CELA1
GPD1
NR4A1
IGFBP6
ITGB7
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
NELL2
SLC11A2
PCBP2
PFDN5
PFKM
PRKAG1
TWF1
RARG
SCN8A
SMARCD1
SP1
TARBP2
TMBIM6
TFCP2
VDR
WNT10B
MAP3K12
TUBA1A
KMT2D
AAAS
SOAT2
NPFF
ENDOU
KRT75
DDX23
SLC4A8
ESPL1
DAZAP2
TROAP
YAF2
TUBA1B
RAPGEF3
MCRS1
ATF7
GALNT6
FAIM2
DDN
TENC1
KCNH3
ANP32D
PRPF40B
METTL7A
LETMD1
RND1
RACGAP1
SENP1
PDZRN4
DHH
PLEKHA8P1
IRAK4
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
HDAC7
SLC38A2
PRR13
KANSL2
SLC38A4
KIF21A
SLC48A1
LMBR1L
SMAGP
DIP2B
CALCOCO1
NCKAP5L
C12orf10
C12orf44
SPATS2
TMEM106C
DNAJC22
ADAMTS20
SLC38A1
CSRNP2
PUS7L
FAM186B
TMEM117
TUBA1C
SPRYD3
MFSD5
COX14
ZCRB1
CCDC65
FMNL3
CERS5
PCED1B
KRT71
LARP4
SLC2A13
LRRK2
FAM186A
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
KRT74
ASB8
KRT72
PRICKLE1
CPNE8
KRT80
GRASP
KRT78
ANO6
ARID2
LINC00935
ZNF740
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
ANKRD33
H1FNT
OR8S1
AMIGO2
KRT77
C12orf68
DBX2
MIR4494
MIR4698
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 27 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 0.11 -1.34 1 0.17 1.73 0.0936
1q 1195 0.23 4.89 2.6e-06 0.10 -2.45 1
2p 624 0.18 -1.63 1 0.07 -6.65 1
2q 967 0.16 -0.832 1 0.08 -4.69 1
3p 644 0.12 -3.92 1 0.26 2.29 0.0264
3q 733 0.22 1.13 0.531 0.17 -1.27 1
4p 289 0.07 -6.81 1 0.40 6.94 1.6e-11
4q 670 0.05 -6.54 1 0.39 9.39 0
5p 183 0.22 -1.85 1 0.23 -1.39 1
5q 905 0.09 -4.06 1 0.29 5.95 5.93e-09
6p 710 0.20 -0.332 1 0.15 -2.51 1
6q 556 0.18 -2.14 1 0.19 -1.65 1
7p 389 0.47 10.7 0 0.10 -5 1
7q 783 0.41 11 0 0.12 -3.25 1
8p 338 0.49 10 0 0.41 6.38 4.62e-10
8q 551 0.58 17.1 0 0.23 0.283 0.759
9p 301 0.18 -2.66 1 0.40 6.84 2.77e-11
9q 700 0.22 0.65 0.881 0.29 4.21 4.31e-05
10p 253 0.24 -0.545 1 0.21 -2.2 1
10q 738 0.17 -1.43 1 0.19 -0.485 1
11p 509 0.16 -3.29 1 0.18 -2.3 1
11q 975 0.18 0.553 0.915 0.18 0.215 0.773
12p 339 0.23 -0.618 1 0.19 -2.49 1
12q 904 0.19 0.66 0.881 0.15 -1.54 1
13q 560 0.38 7.64 6.24e-14 0.13 -3.78 1
14q 938 0.08 -4.4 1 0.27 4.86 2.22e-06
15q 810 0.11 -3.97 1 0.23 1.71 0.0936
16p 559 0.15 -3.01 1 0.27 2.54 0.0144
16q 455 0.13 -4.22 1 0.30 3.11 0.00254
17p 415 0.09 -5.79 1 0.41 8.04 6.07e-15
17q 972 0.17 -0.0711 1 0.20 1.28 0.207
18p 104 0.24 -1.22 1 0.35 3.31 0.00136
18q 275 0.16 -3.6 1 0.42 7.41 6.44e-13
19p 681 0.13 -3.44 1 0.32 5.67 2.98e-08
19q 935 0.20 1.19 0.531 0.26 3.94 0.000127
20p 234 0.57 14.7 0 0.12 -4.37 1
20q 448 0.63 19.4 0 0.06 -5.39 1
21q 258 0.08 -6.32 1 0.43 8.27 2.28e-15
22q 564 0.11 -4.64 1 0.36 6.66 8.19e-11
Xp 418 0.10 -6.02 1 0.18 -2.53 1
Xq 668 0.13 -3.61 1 0.15 -2.78 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/STAD-TP/22231921/GDAC_MergeDataFiles_12187016/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_GENCODE_v18_20140127.mat

  • CNV Files = /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.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 441 Input Tumor Samples.

Tumor Sample Names
TCGA-3M-AB46-01A-11D-A40Z-01
TCGA-3M-AB47-01A-22D-A40Z-01
TCGA-B7-5816-01A-21D-1599-01
TCGA-B7-5818-01A-11D-1599-01
TCGA-B7-A5TI-01A-11D-A31K-01
TCGA-B7-A5TJ-01A-11D-A31K-01
TCGA-B7-A5TK-01A-12D-A31K-01
TCGA-B7-A5TN-01A-21D-A31K-01
TCGA-BR-4183-01A-02D-1130-01
TCGA-BR-4184-01A-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

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)
[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)
[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)