SNP6 Copy number analysis (GISTIC2)
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 2.0.23.

Summary

There were 108 tumor samples used in this analysis: 31 significant arm-level results, 29 significant focal amplifications, and 30 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 - 29 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
3q26.33 1.4984e-55 1.4984e-55 chr3:181620001-182869999 6
8p11.23 1.851e-22 5.765e-22 chr8:38280002-38700000 5
11q13.3 3.6022e-12 3.6022e-12 chr11:69530002-70740000 14
19q13.12 2.7299e-08 3.0558e-08 chr19:37260002-37320000 3
8q24.21 7.8182e-10 5.0676e-06 chr8:126620001-128620000 19
17q25.3 5.0505e-05 5.0505e-05 chr17:81880002-82089999 20
7p22.3 9.0017e-05 9.0017e-05 chr7:1410002-1509999 2
9p24.3 0.00018604 0.00018604 chr9:1-789999 14
19p13.3 0.0010745 0.0010745 chr19:1-280000 9
15q26.3 0.0015499 0.0015499 chr15:101940002-101991189 10
7q21.3 0.0026129 0.0026129 chr7:93400001-97120000 29
20q11.21 0.002847 0.002847 chr20:31300002-32360000 33
19q13.43 0.0020838 0.0031238 chr19:58360002-58617616 20
2p15 0.019002 0.019002 chr2:36020001-69600000 221
4q12 0.019002 0.019002 chr4:52290001-56719999 39
9q34.3 0.01935 0.01935 chr9:138250002-138394717 0 [FAM157B]
1q23.3 0.027882 0.027882 chr1:161420002-161690000 8
13p11.2 0.038947 0.038947 chr13:16100002-16219999 0 [FAM230C]
12p13.33 0.051972 0.051972 chr12:40002-790000 13
14q13.3 0.058946 0.058946 chr14:36430002-38030000 12
6p25.3 0.079981 0.079981 chr6:1-89999 0 [LINC00266-3]
2q31.2 0.11182 0.11182 chr2:177110001-177370000 6
22p11.2 0.15899 0.15899 chr22:11370002-11510000 0 [LOC102723769]
12q15 0.19988 0.19988 chr12:66650001-72370000 50
21q21.1 0.2097 0.2097 chr21:10330001-18980000 36
8q24.3 1.9316e-08 0.21615 chr8:142440002-142549999 1
5p15.33 0.027388 0.23573 chr5:1-1299999 27
5p13.2 0.010759 0.29139 chr5:33930002-50839999 93
8q11.21 0.0090234 0.36612 chr8:49200001-49810000 1
Genes in Wide Peak

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

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

Genes
SOX2
ATP11B
SOX2-OT
FLJ46066
LINC01206
LOC105374244
Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
LETM2
RNF5P1
C8orf86
Genes in Wide Peak

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

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

Genes
CCND1
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
SHANK2
ANO1
ORAOV1
ANO1-AS2
MIR548K
SHANK2-AS1
LOC101928443
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.12.

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

Genes
LOC284412
HKR1
LINC01535
Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
PVT1
TMEM75
CASC8
CASC11
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
CCAT1
PCAT1
CCAT2
PRNCR1
LINC00824
CASC21
CASC19
PCAT2
Genes in Wide Peak

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

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

Genes
ASPSCR1
FASN
GPS1
MAFG
PYCR1
PCYT2
RAC3
RFNG
ALYREF
DCXR
ANAPC11
SIRT7
DUS1L
MAFG-AS1
NOTUM
CENPX
LRRC45
MYADML2
NPB
SNORD134
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.3.

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

Genes
INTS1
MICALL2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.3.

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

Genes
FOXD4
KANK1
CBWD1
DOCK8
C9orf66
FAM138A
FAM138C
WASH1
DDX11L5
MIR1302-2
MIR1302-9
MIR1302-10
MIR1302-11
PGM5P3-AS1
Genes in Wide Peak

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

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

Genes
OR4F17
WASH5P
LINC01002
FAM138A
FAM138C
MIR1302-2
MIR1302-9
MIR1302-10
MIR1302-11
Genes in Wide Peak

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

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

Genes
WASH3P
FAM138E
DDX11L9
MIR1302-2
MIR1302-9
MIR1302-10
MIR1302-11
MIR6859-2
MIR6859-3
MIR6859-1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.3.

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

Genes
CALCR
COL1A2
DLX5
DLX6
DYNC1I1
GNG11
GNGT1
PDK4
PON1
PON2
PON3
SHFM1
TFPI2
SGCE
SLC25A13
BET1
PEG10
ASB4
PPP1R9A
SDHAF3
CASD1
DLX6-AS1
C7orf76
MIR489
MIR591
MIR653
LOC100506136
MIR4652
LOC105375401
Genes in Wide Peak

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

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

Genes
ASXL1
BCL2L1
FOXS1
HCK
ID1
PLAGL2
KIF3B
TM9SF4
TPX2
POFUT1
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TSPY26P
CCM2L
LINC00028
TTLL9
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
XKR7
MIR1825
MIR3193
HM13-AS1
MIR7641-2
ABALON
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.43.

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

Genes
RPS5
MZF1
ZNF132
UBE2M
TRIM28
SLC27A5
ZNF324
CHMP2A
ZNF446
CENPBD1P1
ZBTB45
ZNF837
ZNF497
ZNF584
ZNF324B
RNF225
MZF1-AS1
MIR4754
MIR6807
LOC105372483
Genes in Wide Peak

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

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

Genes
MSH6
MSH2
REL
EML4
BCL11A
ACYP2
BCYRN1
ZFP36L2
CALM2
CYP1B1
EPAS1
EFEMP1
FSHR
GFPT1
FOXN2
LHCGR
EPCAM
MDH1
MEIS1
MTIF2
OTX1
PEX13
VIT
PIGF
PLEK
PPM1B
PPP3R1
PRKCE
EIF2AK2
RAB1A
RPS27A
SRSF7
SIX3
SLC1A4
SLC3A1
SLC8A1
SOS1
SPTBN1
STRN
UGP2
VRK2
XPO1
MAP4K3
COX7A2L
NRXN1
CRIPT
PREPL
FEZ2
SOCS5
USP34
SERTAD2
ARHGAP25
ACTR2
LRPPRC
CEBPZ
C1D
CCT4
CDC42EP3
B3GNT2
SIX2
PROKR1
GPR75
GTF2A1L
STON1
AAK1
CEP68
PSME4
EHBP1
RHOQ
HAAO
PRKD3
QPCT
CNRIP1
NFU1
ERLEC1
BMP10
LGALSL
WDPCP
ASB3
CRIM1
VPS54
DYNC2LI1
ETAA1
HEATR5B
AFTPH
FANCL
SRBD1
NDUFAF7
CCDC88A
GKN1
KCNK12
PNO1
RPL23AP32
RTN4
PELI1
TTC7A
PPP4R3B
MTA3
THADA
ATL2
ABCG5
ABCG8
PAPOLG
CAMKMT
GEMIN6
FBXO11
THUMPD2
FAM161A
ANTXR1
KIAA1841
PNPT1
MCFD2
ATP6V1E2
DHX57
PKDCC
HNRNPLL
CFAP36
CCDC85A
WDR92
PPP1R21
C2orf73
CLHC1
PLEKHH2
GALM
TMEM178A
AHSA2
COMMD1
PUS10
LINC00309
RMDN2
OXER1
KCNG3
GKN2
APLF
TMEM17
SPRED2
GPATCH11
C2orf61
CYP1B1-AS1
STON1-GTF2A1L
LOC339803
C2orf74
LOC339807
CDKL4
PRORSD1P
LOC375196
LOC388942
TMEM247
LINC01118
TSPYL6
SULT6B1
C2orf91
LINC01121
EML6
LINC01122
LINC01185
LOC400958
MIR216A
MIR217
CHAC2
FBXO48
HCG2040054
LOC644838
MIR559
LOC728730
C1GALT1C1L
LOC729348
MORN2
LOC730100
MEIS1-AS3
SNORA36C
SNORA70B
MIR216B
SLC8A1-AS1
LOC100129434
LINC01126
LOC100132215
LINC01119
DBIL5P2
ARHGEF33
LOC100288911
GPR75-ASB3
MIR3126
MIR3682
CEBPZOS
SIX3-AS1
LOC100506142
LOC100507006
LOC100507073
MIR4433A
MIR4426
MIR4434
MIR4431
MIR4778
MIR4432
MIR5192
MEIS1-AS2
LOC101060019
RMDN2-AS1
LOC101805491
LOC101927043
LOC101927165
LOC101927285
LOC101927402
LOC101927438
LOC101927577
LOC101927661
LOC101927701
LINC00211
LOC101929596
LOC101929723
MIR4433B
MIR548BA
LOC102723824
LOC102723854
LINC01628
LOC102800447
MIR8485
MIR217HG
LOC105374596
MIR4432HG
Genes in Wide Peak

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

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

Genes
KDR
KIT
PDGFRA
CHIC2
FIP1L1
PPAT
SRP72
CLOCK
CEP135
PAICS
NMU
EXOC1
TMEM165
DANCR
KIAA1211
USP46
RASL11B
SRD5A3
HOPX
LNX1
ARL9
AASDH
PDCL2
LINC01618
SCFD2
GSX2
LOC339978
RPL21P44
USP46-AS1
LOC644145
SNORA26
ERVMER34-1
LOC100506444
SRD5A3-AS1
THEGL
MIR4449
LNX1-AS1
LNX1-AS2
MIR7641-2
Genes in Wide Peak

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

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

Genes
FCGR2B
FCGR2A
FCGR3A
FCGR3B
HSPA6
HSPA7
FCGR2C
RPL31P11
Genes in Wide Peak

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

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

Genes
KDM5A
NINJ2
SLC6A12
SLC6A13
WNK1
CCDC77
B4GALNT3
IQSEC3
LOC574538
LOC100049716
LOC101929384
LOC102723544
LOC105369595
Genes in Wide Peak

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

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

Genes
NKX2-1
FOXA1
PAX9
NKX2-8
SLC25A21
MIPOL1
SFTA3
TTC6
LINC00517
SLC25A21-AS1
NKX2-1-AS1
MIR4503
Genes in Wide Peak

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

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

Genes
NFE2L2
HNRNPA3
LOC100130691
MIR3128
MIR4444-1
MIR6512
Genes in Wide Peak

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

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

Genes
MDM2
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
TSPAN8
YEATS4
DYRK2
LGR5
CCT2
FRS2
CPSF6
RAB21
GRIP1
KCNMB4
TRHDE
IL22
TMEM19
SLC35E3
IL26
CAND1
MDM1
NUP107
TBC1D15
THAP2
RAB3IP
TPH2
BEST3
ZFC3H1
MYRFL
TRHDE-AS1
LRRC10
MRS2P2
LOC100130075
MIR1279
SNORA70G
MIR3913-2
MIR3913-1
LOC100507175
LOC100507195
LOC100507250
IFNG-AS1
LOC101927901
LINC01479
LOC101928002
LINC01481
LOC102724421
Genes in Wide Peak

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

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

Genes
BAGE
CXADR
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CYP4F29P
CHODL-AS1
C21orf91
SAMSN1
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
POTED
LOC388813
MIR99AHG
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
MIR548X
MIR3118-1
MIR3156-3
LINC01549
SAMSN1-AS1
MIR548XHG
MIR8069-1
LOC102724188
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.3.

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

Genes
ADGRB1
Genes in Wide Peak

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

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

Genes
SDHA
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
NKD2
EXOC3-AS1
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100288152
LOC100506688
MIR4456
MIR4635
LOC100996325
CTD-3080P12.3
HRAT5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.2.

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

Genes
LIFR
hsa-mir-1274a
C6
C7
C9
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
ZNF131
OSMR
NUP155
PAIP1
MRPS30
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
SLC45A2
RXFP3
WDR70
BRIX1
CCL28
TMEM267
AGXT2
C5orf42
PARP8
SPEF2
CARD6
LMBRD2
C1QTNF3
EMB
MROH2B
EGFLAM
NADK2
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1K
RANBP3L
RICTOR
C5orf51
PLCXD3
HCN1
C5orf34
ANXA2R
SNORD72
FLJ32255
NIPBL-AS1
LOC648987
MIR580
CCDC152
LOC100132356
MIR3650
LOC100506406
EGFLAM-AS2
LIFR-AS1
LOC100506548
LOC100506639
BRCAT54
C1QTNF3-AMACR
NNT-AS1
EGFLAM-AS4
GDNF-AS1
OXCT1-AS1
LINC01265
LOC101926940
LOC101926960
FGF10-AS1
LOC101929745
OSMR-AS1
MIR7641-2
LINC00603
BRCAT107
LOC105374727
LOC105374729
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.21.

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

Genes
LOC100507464

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 - 30 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
9p21.3 3.0737e-45 3.0737e-45 chr9:21860002-22449999 4
8p23.2 5.8018e-28 5.8018e-28 chr8:2130002-6410000 3
Xq28 3.4088e-25 1.1452e-24 chrX:154570002-156000000 29
Yq11.23 1.1758e-14 1.4865e-13 chrY:9910002-56959204 58
Xp22.33 2.0343e-15 4.9058e-12 chrX:1-3279999 29
1p13.3 1.0152e-07 1.0152e-07 chr1:100730002-119370000 184
10q23.31 7.1958e-06 7.4317e-06 chr10:87850002-88280000 2
5q12.1 2.0295e-05 2.0295e-05 chr5:58850001-60490000 2
4q35.2 6.7567e-05 6.7886e-05 chr4:173310001-190179999 88
13q14.2 4.4553e-06 6.7886e-05 chr13:48280002-48500000 3
2q22.1 5.2359e-05 0.00021111 chr2:140570002-142879999 1
17p13.2 1.8508e-07 0.00041814 chr17:1-20720000 427
3p13 3.9175e-06 0.0014437 chr3:45790001-89110000 352
13q11 5.9354e-06 0.003055 chr13:1-18870000 2
21p11.2 0.00025533 0.003055 chr21:7820002-8989999 11
4p16.3 0.0034472 0.0034472 chr4:1-9790000 147
18q22.1 0.0053584 0.0053064 chr18:39750002-80373285 197
Xq22.3 0.0017655 0.0065709 chrX:108140002-108790000 4
17p11.1 8.8998e-08 0.0071392 chr17:21290002-27129999 7
19p13.3 0.0077433 0.0077188 chr19:70001-16650000 560
2q37.1 0.0034472 0.022005 chr2:208820002-242193529 324
Yq12 2.6376e-05 0.027561 chrY:25730002-57227415 5
22p11.2 0.036634 0.035705 chr22:10960001-16940000 14
14q11.2 0.037211 0.036857 chr14:1-20069999 22
11p15.5 0.042737 0.042434 chr11:130002-31269999 418
Xp21.1 0.00057554 0.079295 chrX:11110001-55910000 369
3p11.1 0.0023636 0.093069 chr3:1-94010000 680
21p11.2 0.0036436 0.098282 chr21:9120002-14110000 16
11q21 0.11733 0.11709 chr11:74720002-135086622 527
16q24.2 0.19446 0.19666 chr16:76640001-90338345 162
Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
CDKN2A-AS1
CDKN2B-AS1
Genes in Wide Peak

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

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

Genes
CSMD1
LOC100287015
LOC101927815
Genes in Wide Peak

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

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

Genes
MTCP1
CLIC2
DKC1
F8
MPP1
VAMP7
VBP1
F8A1
SPRY3
CTAG2
TMLHE
FUNDC2
BRCC3
RAB39B
GAB3
CTAG1A
H2AFB2
H2AFB1
F8A2
SNORA36A
SNORA56
SMIM9
FAM223A
CMC4
MIR1184-1
MIR1184-3
MIR1184-2
MIR664B
LOC101927830
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Yq11.23.

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

Genes
DAZ1
RBMY1A1
UTY
KDM5D
USP9Y
DDX3Y
PRY
XKRY
BPY2
VCY
CDY1
EIF1AY
TMSB4Y
CDY2A
NLGN4Y
DAZ3
DAZ2
DAZ4
TTTY15
TTTY5
TTTY9A
TTTY13
TTTY14
GOLGA2P2Y
TTTY6
HSFY1
CSPG4P1Y
TTTY3
TTTY4
RPS4Y2
HSFY2
RBMY2EP
RBMY2FP
RBMY1F
CDY2B
TTTY10
TXLNGY
TTTY17A
TTTY23
BCORP1
FAM41AY1
GYG2P1
VCY1B
RBMY1B
RBMY1D
RBMY1E
RBMY1J
FAM224B
FAM224A
TTTY6B
BPY2B
TTTY3B
TTTY4B
TTTY17B
PRORY
LOC100652931
NLGN4Y-AS1
LOC101929148
Genes in Wide Peak

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

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

Genes
CRLF2
P2RY8
SLC25A6
ARSD
ARSE
ARSF
ASMT
CSF2RA
IL3RA
CD99
SHOX
XG
GTPBP6
AKAP17A
ASMTL
GYG2
ZBED1
PPP2R3B
PLCXD1
ASMTL-AS1
DHRSX
LINC00685
ARSH
CD99P1
LINC00106
XGY2
LINC00102
MIR3690
MIR6089
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.3.

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

Genes
NRAS
TRIM33
RBM15
ADORA3
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
S1PR1
CELSR2
EXTL2
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
TTF2
SLC16A4
CD101
LRIG2
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
LAMTOR5
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
NTNG1
WDR47
CLCC1
PTPN22
CHIA
GPSM2
SLC25A24
DPH5
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
TMIGD3
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1-AS1
STRIP1
DNAJA1P5
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
DRAM2
PIFO
C1orf162
SYT6
NBPF4
SLC30A7
CHIAP2
DENND2C
FNDC7
UBL4B
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
C1orf137
MIR197
LOC440600
LOC440602
BCL2L15
PGCP1
SPATA42
CYMP
LOC643355
LOC643441
ACTG1P4
NBPF6
SCARNA2
MIR942
LOC100129138
LINC01160
AP4B1-AS1
MIR320B1
MIR4256
FAM212B-AS1
SLC16A1-AS1
MIR548AC
VAV3-AS1
KCNC4-AS1
KCND3-AS1
KCND3-IT1
LOC100996251
LOC100996263
LINC01356
LAMTOR5-AS1
LOC101928370
LOC101928436
LOC101928476
LOC101928718
HIPK1-AS1
LOC101928977
LOC101928995
LOC101929023
LOC101929099
LOC101929147
MIR7852
LOC102606465
LINC01397
LINC01307
LINC01525
WARS2-IT1
LOC105378933
Genes in Wide Peak

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

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

Genes
PTEN
KLLN
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
PDE4D
MIR582
Genes in Wide Peak

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

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

Genes
DUX4
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
ADAM29
SCRG1
FAM149A
FBXO8
PDLIM3
CLDN22
NEIL3
UFSP2
CDKN2AIP
TENM3
LRP2BP
STOX2
CFAP97
SPCS3
TRAPPC11
CENPU
HAND2-AS1
WWC2
CEP44
SNX25
LOC90768
WDR17
ZFP42
SPATA4
ENPP6
ASB5
WWC2-AS2
RWDD4
PRIMPOL
TRIML2
CCDC110
CYP4V2
F11-AS1
LINC01098
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LINC01060
FAM92A1P2
C4orf47
FRG2
SLED1
FLJ38576
LINC00290
LOC728175
MIR3945HG
CLDN24
MIR1305
DBET
MIR4276
MIR3945
LINC01093
LOC100506272
MIR4455
LOC101928509
LOC101928551
LOC101928590
LINC01099
WWC2-AS1
LINC01262
LOC102723766
LVCAT8
LOC105377590
LINC01596
Genes in Wide Peak

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

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

Genes
RB1
LPAR6
LINC00441
Genes in Wide Peak

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

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

Genes
MIR7157
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.2.

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

Genes
PER1
MAP2K4
TP53
GAS7
USP6
ABR
ACADVL
ADORA2B
ALDH3A1
ALDH3A2
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
COX10
CLDN7
CRK
CTNS
DLG4
DNAH9
DPH1
DRG2
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
FOXO3B
FLII
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
LLGL1
MEIS3P1
MFAP4
MNT
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
PMP22
POLR2A
MAPK7
PRPSAP2
PSMB6
RCVRN
RPA1
RPL26
SCO1
SHBG
SHMT1
SLC2A4
SOX15
SREBF1
VAMP2
TOP3A
UBB
UBE2G1
TRPV1
YWHAE
ZNF18
RNF112
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
COPS3
SCARF1
TNK1
MYH13
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
GLP2R
NTN1
STX8
PIGL
RPH3AL
FXR2
MPDU1
SPAG7
NCOR1
ULK2
CCDC144A
ACAP1
KIAA0753
SGSM2
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
CLEC10A
MYBBP1A
FBXW10
PRPF8
TRIM16
RAI1
KIF1C
GRAP
AKAP10
GABARAP
NLRP1
ARHGEF15
EPN2
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
MPRIP
CLUH
SMG6
WSCD1
CTDNEP1
TNFRSF13B
PIK3R5
ELP5
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
SNORD49A
SNORD3B-1
PELP1
B9D1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
TVP23B
GLOD4
YBX2
MYO15A
TRPV2
ANKFY1
RASD1
INPP5K
FAM64A
XAF1
BORCS6
ALKBH5
TTC19
SLC52A1
MED9
WRAP53
MRM3
SLC47A1
VPS53
NCBP3
TSR1
DHX33
NT5M
ADPRM
PLSCR3
ZNF286A
ZNF287
ZNF624
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
ELAC2
SRR
NXN
TEKT3
MIS12
GID4
METTL16
PHF23
FAM57A
FAM106A
CTC1
NDEL1
PITPNM3
DRC3
EMC6
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
NAA38
NEURL4
ZNF594
HES7
SPATA22
MGC12916
TXNDC17
MIR22HG
ATPAF2
TMEM88
SPECC1
MYOCD
CDRT7
CDRT8
CDRT15P1
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
LRRC75A-AS1
ZSWIM7
MIEF2
SLC5A10
SMCR5
SMCR8
TOM1L2
DNAH2
RTN4RL1
SLC47A2
CDRT15
CFAP52
CCDC42
PIK3R6
ODF4
KCTD11
TRIM16L
MFSD6L
TRPV3
SLC16A11
FBXO39
USP32P1
DHRS7C
TVP23C
CENPV
FLCN
PLD6
SLC16A13
C17orf74
SPNS3
USP32P2
TBC1D28
TMEM256
BCL6B
CDRT15L2
LOC284009
VMO1
LOC284023
LINC00324
LINC00670
CDRT4
CCDC144B
SLC13A5
TMEM102
LGALS9B
TUSC5
LOC339166
TMEM95
KRT17P5
SMTNL2
CCDC144CP
TBC1D26
RFLNB
CDRT1
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
SHISA6
LRRC75A
LOC388436
OR3A4P
SLC25A35
C17orf97
MED11
KRT16P2
FLJ35934
GRAPL
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
GSG1L2
PIRT
CDRT15P2
FAM83G
KRT16P3
EVPLL
SNORA48
SNORD10
OR1D4
SCGB1C2
LGALS9C
SCARNA21
SNORA59A
SNORD49B
SNORD65
SNORD91A
SNORD91B
MIR33B
SNORD118
BHLHA9
TLCD2
LOC728392
KRT16P1
ZNF286B
SNORD3A
SNORD3C
SNORD3D
MIR744
LOC100128006
LOC100128288
MYHAS
FAM106CP
C17orf107
LOC100130950
DBIL5P
LINC00675
MIR1288
MIR1253
MIR1180
MIR548H3
PITPNA-AS1
MIR3183
MIR4314
LOC100506371
LOC100506388
ALOX12-AS1
MIR497HG
MAGOH2P
RNASEK-C17orf49
TMEM256-PLSCR3
TVP23C-CDRT4
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4731
MIR4520-1
MIR4521
MIR5096
MIR4520-2
MIR1269B
ALOX15P1
RAI1-AS1
EPN2-AS1
COX10-AS1
EPN2-IT1
FAM106B
LOC100996842
TMEM220-AS1
LOC101559451
LOC101927727
LOC101927839
LOC101927911
LOC101928000
LOC101928266
LOC101928418
LOC101928475
LOC101928567
MIR6776
MIR6777
MIR6864
MIR6865
MIR6883
MIR6778
LOC102724009
LOC103021295
LOC105371430
LOC105371485
LOC105371506
SMCR2
LOC105371592
Genes in Wide Peak

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

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

Genes
FHIT
MITF
BAP1
FOXP1
SETD2
PBRM1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ERC2-IT1
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GBE1
GNAI2
GNAT1
XCR1
GPR27
GPX1
GRM2
HTR1F
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
CNTN3
PDHB
PFKFB4
PLXNB1
POU1F1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
ROBO1
ROBO2
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TKT
TMF1
TNNC1
UBA7
USP4
UQCRC1
WNT5A
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
BSN
CCRL2
UBA3
RRP9
MAGI1
CACNA2D2
DCAF1
IP6K1
PSMD6
PARP3
RBM6
RBM5
NME6
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SCAP
LAMB2P1
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
RYBP
NAT6
ABHD14A
POC1A
NDUFAF3
PTPN23
CHMP2B
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
IL17RD
ELP6
QRICH1
PXK
FEZF2
EBLN2
DALRD3
SHQ1
ZNF654
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
LMOD3
SEMA3G
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
SELK
PROK2
RNF123
KIF9
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
LRRC2-AS1
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
UCN2
RFT1
ACTR8
SLC25A26
GPR62
FAM3D
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
LSMEM2
ASB14
FAM19A4
CCDC12
PPP4R2
PRICKLE2
C3orf67
KCTD6
KLHDC8B
LINC00870
DNAH12
PDE12
DENND6A
CADM2
ALS2CL
TMIE
EOGT
FBXW12
C3orf38
LINC00877
CCDC66
KIF9-AS1
LINC00698
EIF4E3
CCDC36
PRSS42
SPATA12
C3orf62
TMEM110
PRSS45
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LINC00960
MIRLET7G
MIR135A1
MIR191
FAM19A1
TMEM89
IQCF6
SMIM4
LINC00971
MIR425
SPINK8
ARIH2OS
C3orf84
SNORD19
FAM86DP
SNORD69
MIR566
GXYLT2
LOC728290
CCR2
ESRG
SNORD19B
LINC00696
SEMA3F-AS1
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LINC00994
FRG2C
MIR1284
MIR1324
MIR1226
MIR2115
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
MIR3923
PRKAR2A-AS1
IQCF4
PTPRG-AS1
PSMD6-AS2
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4444-1
MIR4443
PRICKLE2-AS1
RBM5-AS1
LINC00506
MIR5688
MIR5193
MAGI1-AS1
ITIH4-AS1
SYNPR-AS1
CADM2-AS2
THOC7-AS1
GLYCTK-AS1
ARHGEF3-AS1
CACNA2D3-AS1
PRICKLE2-AS2
PRICKLE2-AS3
FCF1P2
SUCLG2-AS1
SAMMSON
PDZRN3-AS1
LOC101927296
LOC101927374
LOC101927494
SEMA3B-AS1
IQCF5-AS1
LOC101929054
LOC101929159
C3orf67-AS1
ADAMTS9-AS1
RASSF1-AS1
MIR5787
MIR6823
MIR6824
MIR6872
MIR6890
MIR8064
LOC102724297
CELSR3-AS1
MIR548BB
FOXP1-AS1
LOC105377102
LOC105377105
FAM3D-AS1
LOC105377143
LOC105377146
LOC105377162
ARF4-AS1
SNORD136
SNORA94
SNORA95
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q11.

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

Genes
FAM230C
LINC00417
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21p11.2.

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

Genes
MIR663A
RNA5-8S5
RNA18S5
RNA28S5
MIR3687-1
MIR3648-1
LOC100507412
RNA45S5
MIR6724-1
MIR6724-2
MIR6724-3
Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
NELFA
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
KIAA0232
LINC01587
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
NSG1
GPR78
STX18
FGFRL1
CYTL1
SH3TC1
NKX1-1
PIGG
BLOC1S4
STK32B
LYAR
TBC1D14
SORCS2
UVSSA
ZFYVE28
AFAP1
TNIP2
HAUS3
ABCA11P
GRPEL1
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
CTBP1-AS2
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
ZNF595
JAKMIP1
FAM53A
TRMT44
ZBTB49
ZNF721
ZNF718
CCDC96
CTBP1-AS
CRIPAK
LOC285484
DOK7
LINC00955
RNF212
NOP14-AS1
NAT8L
MSANTD1
FAM86EP
POLN
LOC389199
USP17L6P
USP17L9P
C4orf48
CFAP99
MIR95
ZNF876P
DEFB131
LOC650293
ZNF732
SCARNA22
MIR571
USP17L24
USP17L25
USP17L26
USP17L27
USP17L28
USP17L29
USP17L30
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L15
MIR548I2
TMED11P
MIR4274
STX18-AS1
MIR378D1
MIR4800
MIR4798
HTT-AS
LOC101928279
LOC101928306
LINC01396
STX18-IT1
LOC105374344
LOC105374366
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

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

Genes
BCL2
MALT1
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
CFAP53
GTSCR1
DOK6
RNF152
LINC00305
LOC284241
DYNAP
BOD1L2
LINC00907
SIGLEC15
ZADH2
SMIM21
LINC00908
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
OACYLP
LINC01538
LOC400655
LINC00909
C18orf65
LINC00683
LOC400661
MIR122
HSBP1L1
RNF165
C18orf32
KC6
LOC643542
C18orf63
SKOR2
SCARNA17
SNORA37
TCEB3CL
SNORD58C
PARD6G-AS1
LOC100131655
LINC01630
MIR1539
MIR4319
MIR4320
LINC01539
LOC100505549
LINC01541
LOC100505797
LOC100505817
LOC100505853
RBFADN
TCEB3CL2
RPL17-C18orf32
MIR4528
MIR4527
MIR4529
MIR3591
MIR4743
MIR4744
MIR5011
MIR548AV
LINC-ROR
LINC01544
LOC101060542
LOC101927229
LINC01416
LOC101927322
LOC101927481
LOC101927606
LOC101927651
LINC01029
LINC01477
LINC01478
SLC14A2-AS1
LOC101927989
LOC101928167
LOC102724651
LOC102724913
SNHG22
TCF4-AS1
LOC105372179
LOC105667213
SNORA108
Genes in Wide Peak

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

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

Genes
COL4A5
COL4A6
IRS4
LOC101928358
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p11.1.

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

Genes
KCNJ12
FAM27E5
FLJ36000
C17orf51
KCNJ18
MTRNR2L1
LOC105371703
Genes in Wide Peak

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

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

Genes
GNA11
LYL1
MLLT1
SH3GL1
SMARCA4
STK11
TCF3
TPM4
FSTL3
BRD4
hsa-mir-220b
ACP5
AES
AMH
ASNA1
ATP5D
AZU1
HCN2
BSG
C3
CACNA1A
CALR
CAPS
CD70
ADGRE5
CDC34
CDKN2D
CIRBP
CNN1
CNN2
CSNK1G2
DAPK3
CFD
DHPS
DNASE2
DNM2
DNMT1
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
ELAVL3
ADGRE1
EPOR
FARSA
FCER2
FUT3
FUT5
FUT6
GAMT
GCDH
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
DNAJB1
ICAM1
ICAM3
ICAM4
ILF3
INSR
JUNB
LDLR
CYP4F3
MAN2B1
MATK
RAB8A
MYO1F
GADD45B
HNRNPM
NDUFA7
NDUFB7
NFIC
NFIX
NOTCH3
NRTN
OAZ1
P2RY11
PALM
PDE4A
PIN1
POLR2E
POLRMT
PRKACA
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTGER1
PTPRS
RAD23A
RFX1
RFX2
RPS15
RPS28
SAFB
CCL25
SGTA
SLC1A6
SNAPC2
STXBP2
TBXA2R
PRDX2
THOP1
ICAM5
TLE2
TYK2
VAV1
ZNF20
ZNF69
ZNF121
ZNF136
ZNF177
MADCAM1
SF3A2
CLPP
RANBP3
CYP4F2
KHSRP
PLPP2
EIF3G
STX10
S1PR4
TNFSF14
TNFSF9
AP1M1
AP3D1
RAB11B
S1PR2
TRIP10
LONP1
MED26
IL27RA
TECR
RAB3D
APBA3
IER2
SAFB2
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
EBI3
DDX39A
ZNF443
PLIN3
AKAP8
APC2
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4A
TIMM44
CARM1
SEMA6B
CHERP
RNASEH2A
KLF1
GIPC1
ZNF266
PNPLA6
UQCR11
ILVBL
TMED1
CDC37
CYP4F8
ADGRL1
SBNO2
MAST1
KDM4B
ZFR2
ARHGEF18
PIP5K1C
ARHGAP45
CASP14
SHC2
RPL36
KANK2
FAM32A
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7A5
OR7C1
SNORD41
SNORD37
RNU6-1
AKAP8L
FGF22
TJP3
NMRK2
C19orf53
UHRF1
HOOK2
SLC39A3
TNPO2
ADGRE2
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
SIRT6
PIAS4
LSM7
ZNF44
MBD3
S1PR5
MIER2
PCSK4
ZNF562
BEST2
FBXL12
CC2D1A
C19orf24
PLEKHJ1
C19orf66
FEM1A
ZNF823
STAP2
TRMT1
BTBD2
RNF126
CCDC94
ASF1B
ANGPTL8
MYDGF
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
RGL3
SLC44A2
MCOLN1
WDR18
REXO1
ZNF490
DOCK6
CAMSAP3
ZNF317
CYP4F11
ZNF77
CACTIN
EPS15L1
WIZ
UBL5
CELF5
PLPPR2
RASAL3
KRI1
ZSWIM4
CYP4F12
YIPF2
C19orf43
SLC25A23
ZNF426
C19orf57
FSD1
ZNF557
CERS4
TLE6
EPHX3
PODNL1
SLC35E1
PLPPR3
DENND1C
ZNF442
ZNF556
LRRC8E
PRR36
UBXN6
OR4F17
CCDC130
ACSBG2
ADAMTS10
QTRT1
ABHD17A
DOHH
RTBDN
ANGPTL6
KLF16
PRAM1
C19orf44
MRI1
FBXW9
ALKBH7
WDR83
ZNF414
ELOF1
DOT1L
ZNF333
FBN3
ZNF559
KISS1R
ADGRE3
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
HSH2D
MPND
ATG4D
ATCAY
SYDE1
MBD3L1
MIDN
SAMD1
DCAF15
GADD45GIP1
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
DPP9
R3HDM4
TMEM259
TPGS1
CRB3
REEP6
PEX11G
ZNF561
OLFM2
MUC16
FDX1L
NACC1
IZUMO4
SCAMP4
ADAT3
MISP3
PGLYRP2
ZNF554
EVI5L
CCDC151
ZNF653
GRIN3B
MRPL54
LRG1
CIB3
RLN3
RAVER1
OR7D4
OR7G1
OR1M1
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
MISP
OR1I1
CCDC105
CYP4F22
PLK5
LINC00661
OR10H4
C2CD4C
ZNF358
ILF3-AS1
ZNF560
ZNF563
SPC24
TICAM1
CIRBP-AS1
ZNRF4
ZNF558
C19orf25
ATP8B3
LINC00905
DIRAS1
ZNF555
ZNF846
OR7D2
ZNF791
ZNF564
ZNF709
ZNF433
PRR22
ANKRD24
MCEMP1
ZNF627
DAND5
CBARP
CSNK1G2-AS1
C19orf38
SYCE2
KANK3
TINCR
CATSPERD
ACTL9
OR2Z1
ZNF561-AS1
ZNF763
ZNF844
SMIM24
MIR7-3HG
SLC25A41
MBD3L5
OR10H5
ODF3L2
LOC284454
ADGRE4P
ADAMTSL5
CLEC4G
NANOS3
PALM3
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
LYPLA2P2
C3P1
ZNF788
CLEC17A
CYP4F24P
ONECUT3
LOC390877
OR7G2
OR7G3
OR7A10
MEX3D
LINC01002
PRSS57
VMAC
ZNF833P
CTXN1
CACTIN-AS1
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
MIR181D
LINGO3
ARRDC5
FAM138A
C19orf67
UCA1
MBD3L4
MBD3L3
FAM138C
HNRNPA1P10
SNORD105
PPAN-P2RY11
MIR637
MIR638
MIR639
PLIN4
ZNF878
SNORD105B
ZGLP1
LOC100128568
C19orf71
LOC100128573
DPP9-AS1
PET100
LOC100288123
LOC100289333
MIR1470
MIR1909
MIR1181
MIR1238
MIR1268A
MIR1302-2
MIR1227
MIR1302-9
MIR1302-10
MIR3187
MIR1302-11
MIR4322
MIR4321
MIR3940
LOC100507373
RAB11B-AS1
TGFBR3L
ZNF559-ZNF177
ZNF625-ZNF20
MIR4747
MIR4746
MIR4748
MIR4745
MIR5695
MIR4999
MIR5684
MIR5589
LOC100996351
LOC101928238
LOC101928464
LOC101928602
LOC101928844
LOC101928845
RNU6-7
MIR6790
MIR6791
MIR6792
MIR6795
MIR6885
MIR6886
MIR7850
MIR7974
MIR6794
MIR1199
MIR6515
MIR6789
MIR6793
MIR7108
LOC102724279
RNU6-2
LOC105372273
LOC105372280
LOC105372288
SNORD135
SNORA104
Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-1244-1
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
CNOT9
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ASIC4
DOCK10
MREG
PECR
C2orf83
MFF
ACKR3
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
LOC93463
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERF4
UBE2F
OTOS
COPS9
OR6B3
LOC150935
PKI55
KANSL1L
LINC01107
LOC151174
ERFE
CCDC140
SLC23A3
LINC00608
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
DAW1
C2orf57
TIGD1
LOC200772
CFAP65
C2orf72
RTP5
LOC285095
UNC80
RUFY4
DUSP28
MROH2A
ESPNL
ECEL1P2
SPATA3-AS1
CATIP
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
LOC440934
MIR375
LOC643387
LINC00607
LOC646736
PRSS56
AQP12B
SNORA75
LOC654841
SCARNA6
SCARNA5
MIR562
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3133
MIR3131
MIR4268
MIR3132
MIR4269
AGAP1-IT1
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4438
MIR4440
MIR4786
MIR4441
MIR5001
MIR5702
MIR5703
VWC2L-IT1
LOC100996693
CAPN10-AS1
LINC01237
LOC101928020
LOC101928103
LOC101928111
LINC01280
LOC101928327
CATIP-AS1
LINC01494
LOC101928881
MIR6513
MIR6809
MIR6811
MIR6810
LOC102723927
LANCL1-AS1
LOC102724849
LOC102725079
MIR9500
CATIP-AS2
LINC01614
LOC105373876
DIRC3-AS1
LOC105373878
LINC01173
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Yq12.

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

Genes
IL9R
VAMP7
SPRY3
DDX11L16
WASIR1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22p11.2.

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

Genes
ANKRD62P1-PARP4P3
POTEH
HSFY1P1
OR11H1
CCT8L2
XKR3
TPTEP1
DUXAP8
POTEH-AS1
BMS1P17
LOC101929350
LOC102723769
LINC01297
BMS1P22
Genes in Wide Peak

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

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

Genes
OR4K5
OR11H2
OR4K1
OR4K15
OR4K14
OR4L1
OR4N2
OR4K2
OR4K13
POTEG
OR11H12
OR4Q3
OR4M1
DUXAP10
POTEM
LOC642426
LINC01296
LOC100508046
POTEH-AS1
BMS1P17
LOC101929572
BMS1P22
Genes in Wide Peak

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

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

Genes
CARS
FANCF
HRAS
LMO1
NUP98
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
MPPED2
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
FSHB
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC5AC
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
SERGEF
OR5E1P
OR10A3
TIMM10B
SNORD14A
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
LIN7C
LGR4
PIDD1
KCNQ1DN
SOX6
PARVA
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
PGGHG
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
SNORD14B
NAV2
SYT8
CCDC34
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
ARL14EP
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
LOC171391
METTL15
OR56B4
ANO5
TOLLIP-AS1
OR52B2
LMNTD2
OR51F1
SVIP
MRGPRX1
OR51B5
KRT8P41
SBF2-AS1
CSNK2A3
OR51V1
H19
CRACR2B
TMEM80
IGSF22
OR10A4
OLFML1
LOC283299
MRGPRG-AS1
NLRP10
NLRP14
ANO9
LUZP2
KRTAP5-AS1
KCNQ1-AS1
B4GALNT4
OR52L1
OR2AG2
OR52B6
OTOG
OR10A2
OVCH2
PDDC1
GALNT18
NCR3LG1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
NAV2-AS4
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
TMEM9B-AS1
LOC494141
BDNF-AS
MIR483
SNORA3A
SNORA52
LOC644656
RASSF10
TSSC2
SNORA23
SNORA3B
SNORA54
SNORD97
MIR610
INS-IGF2
MUC5B
ZBED5-AS1
MIR675
LOC100126784
MRVI1-AS1
CAND1.11
FAM99B
MRPL23-AS1
MIR302E
MIR3159
MIR4298
MIR4299
MTRNR2L8
CCDC179
LOC100506082
MIR210HG
LOC100506258
LINC00958
SPTY2D1-AS1
DCDC5
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR4694
MIR4687
MIR5691
NAV2-AS5
NAV2-AS2
LINC00678
PANO1
LOC101927503
LINC01150
CD81-AS1
LOC101927708
OLFM5P
TUB-AS1
LOC101928008
LOC101928053
LOC101928132
MIR6073
MIR6743
MIR8054
MIR8070
MIR8087
MIR7847
MIR6744
MIR8068
MIR6124
LOC102723330
LINC01495
LOC102724784
LOC102724957
HOTS
BGLT3
CASC23
BBOX1-AS1
LINC01219
LOC105376554
LOC105376575
LOC105376599
LOC105376671
LINC01616
SNORD131
Genes in Wide Peak

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

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

Genes
GATA1
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
hsa-mir-362
hsa-mir-1308
NR0B1
ALAS2
AMELX
ARAF
ARHGAP6
BMX
CACNA1F
S100G
CLCN5
CYBB
DDX3X
DMD
EIF1AX
EIF2S3
ELK1
FANCB
FGD1
VEGFD
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
GK
GLRA2
GPM6B
GPR34
GRPR
HSD17B10
HCCS
ERAS
KCND1
PRICKLE3
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
NDP
NHS
TBC1D25
OTC
CDK16
PDHA1
PDK3
CFP
PFKFB1
PHEX
PHKA2
PIGA
PLP2
POLA1
PPEF1
PRPS2
PRRG1
RBBP7
RBM3
RP2
RPGR
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SMS
SSX5
CDKL5
SUV39H1
SYN1
SYP
DYNLT3
TIMP1
TSPAN7
TMSB4X
TRO
UBA1
SLC35A2
XK
ZFX
ZNF182
ZNF41
ZNF157
ZRSR2
USP11
USP9X
RBM10
SMC1A
SRPX
UXT
OFD1
PIR
INE2
INE1
CASK
PAGE1
AKAP4
AP1S2
RGN
REPS2
BMP15
MED14
RAB9A
PCYT1B
MAGED1
XAGE2
PAGE4
FRMPD4
JADE3
HDAC6
HUWE1
PQBP1
ADGRG2
ATP6AP2
SSX3
TIMM17B
RRAGB
SCML2
PRDX4
EBP
RAI2
MAGED2
MSL3
PIM2
IL1RAPL1
WDR45
PRAF2
CA5B
CNKSR2
IQSEC2
PHF8
ACOT9
SMPX
GSPT2
FTSJ1
HYPM
EGFL6
GAGE12I
GAGE2E
GPR82
GPKOW
APEX2
PCSK1N
CCDC22
MAGEH1
FAM156A
SH3KBP1
FOXP3
TLR7
TLR8
MBTPS2
FTHL17
GPR173
NDUFB11
GNL3L
BCOR
FAM120C
GEMIN8
NUDT11
OTUD5
KRBOX4
TXLNG
CTPS2
CHST7
GRIPAP1
ZNF630
TMEM27
SHROOM4
MID1IP1
ACE2
NYX
DUSP21
TSPYL2
WDR13
PORCN
WNK3
APOO
CXorf36
MAGIX
CXorf21
EFHC2
KLHL15
PPP1R2P9
MAGED4B
TMEM47
SLC9A7
CCNB3
PPP1R3F
CCDC120
TSR2
FAM104B
PAGE5
ATXN3L
SLC38A5
SYAP1
SYTL5
BEND2
DGKK
FUNDC1
PTCHD1
PPP4R3CP
MAGEB10
DCAF8L1
VENTXP1
MAGEB16
FOXR2
PAGE3
ASB11
ASB9
ZNF645
USP27X-AS1
FAM47A
MOSPD2
RIBC1
MAGEB6
USP51
CXorf38
DDX53
FAM47B
SUPT20HL2
TCEANC
ARX
XAGE3
XAGE5
NUDT10
FAM9C
LINC01560
PAGE2
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX8
SSX9
LINC01281
CFAP47
UBE2E4P
MAGEB18
CA5BP1
CXorf67
ZNF81
ITIH6
LANCL3
MPC1L
DCAF8L2
MAGEB5
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
PAGE2B
LOC392452
CXXC1P1
GLOD5
LOC401585
ZNF674-AS1
YY2
MIRLET7F2
MIR188
MIR221
MIR222
MIR98
FTH1P18
FAM47C
SPANXN5
SSX4B
MIR362
MIR500A
MIR501
MIR502
ZNF674
GAGE2B
GAGE13
GAGE12G
MAGEB17
XAGE1B
SCARNA23
SNORA11
MIR532
MIR660
LINC01545
SSX2B
FAM156B
MAGED4
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE2A
LOC729609
GAGE12F
GS1-600G8.3
GAGE8
SNORA11C
SNORA11D
SUPT20HL1
PHKA2-AS1
GAGE12D
LOC100132831
LINC01203
UXT-AS1
SCARNA9L
MIR548F5
LOC100421746
MIR500B
MTRNR2L10
MIR23C
MIR3937
MIR3915
PIR-FIGF
MIR4769
MIR4536-1
MIR4768
MIR1587
MIR548AJ2
MIR548AM
MIR4666B
MIR548AX
PTCHD1-AS
NHS-AS1
SYP-AS1
ZFX-AS1
PHEX-AS1
MED14OS
PPEF1-AS1
EIF1AX-AS1
PCYT1B-AS1
ZNF630-AS1
MID1IP1-AS1
LINC01284
LINC01282
LOC101927476
LOC101927501
LINC01204
LINC01186
LOC101927635
LOC101928389
LOC101928627
MIR6134
MIR6857
MIR6895
MIR7641-2
MIR6086
MIR6894
MIR8088
LINC01496
KANTR
GAGE10
GS1-594A7.3
LINC01456
LOC105373185
SNORA109
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

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

Genes
CTNNB1
FANCD2
FHIT
MITF
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
FOXP1
SETD2
PBRM1
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
ERC2-IT1
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
ACKR2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
EPHA3
FBLN2
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
GRM7
HRH1
HTR1F
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
POU1F1
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
WNT7A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
CGGBP1
BHLHE40
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
DCAF1
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
CXCR6
CSPG5
CHL1
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CAND2
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
RYBP
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LINC00312
LMCD1
ARHGEF3
VILL
SSUH2
TRNT1
ABHD5
DYNC1LI1
C3orf18
CRBN
SS18L2
CCDC174
SHISA5
ZDHHC3
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
ELP6
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ARL8B
SETD5
ZNF654
TMEM40
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
EMC3
BRK1
ZKSCAN7
LMOD3
RAD18
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
LRRN1
SELK
PROK2
RNF123
CIDEC
RBSN
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
THOC7
WDR82
TSEN2
GRIP2
RTP3
LRRC2-AS1
C3orf20
ATRIP
NICN1
MON1A
JAGN1
KBTBD8
LINC00852
IL17RC
ABHD14B
POMGNT2
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
FANCD2OS
LRRC3B
GALNT15
GPR62
KCNH8
FAM3D
LYZL4
KLHL40
TRIM71
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
LSMEM2
ASB14
FAM19A4
SGO1
PP2D1
EFHB
CPNE9
CCDC12
PPP4R2
LINC00691
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
FGD5
LOC152274
CIDECP
CNTN4
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LINC00870
DNAH12
PDE12
DENND6A
CADM2
ZNF620
ALS2CL
TMIE
EOGT
FBXW12
C3orf38
ENTPD3-AS1
ZNF619
ZNF621
LINC00877
LINC00692
CCDC66
TCAIM
ZNF852
ZNF660
KIF9-AS1
SUMF1
RPUSD3
PRRT3
LINC00606
LINC00620
DPH3
LINC00698
EIF4E3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
COL6A4P1
TPRXL
ZNF445
SPATA12
LHFPL4
TOPAZ1
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
VENTXP7
LOC401052
IQCF3
LINC00960
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
THUMPD3-AS1
EIF1B-AS1
TMEM89
IQCF6
SMIM4
LINC00971
EMC3-AS1
MIR425
SNORA6
SNORA7A
TMPPE
LIMD1-AS1
THRB-AS1
LINC00693
SPINK8
ARIH2OS
C3orf84
SNORD19
FAM86DP
SNORD69
MIR563
MIR564
MIR566
GXYLT2
LOC728290
LOC729083
FAM198A
CCR2
ESRG
SNORD19B
MIR885
EGOT
GHRLOS
LINC00696
ACVR2B-AS1
SEMA3F-AS1
NRADDP
MKRN2OS
ZNF717
LOC100132146
FGD5P1
BSN-AS2
PRSS46
LINC00994
LMCD1-AS1
FRG2C
SRGAP3-AS3
MIR1284
MIR1324
MIR1226
MIR2115
MIR711
MIR3136
MIR4270
MIR3135A
MIR378B
MIR4272
MIR4271
MIR4273
MIR3134
MIR466
MIR3938
MIR3923
MIR3714
FGD5-AS1
SH3BP5-AS1
UBE2E2-AS1
KRBOX1
KRBOX1-AS1
PRKAR2A-AS1
IQCF4
PTPRG-AS1
PSMD6-AS2
ADAMTS9-AS2
BHLHE40-AS1
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4791
MIR4790
MIR4444-1
MIR4443
MIR4792
MIR4442
PRICKLE2-AS1
RBM5-AS1
LINC00506
MIR5688
MIR5193
GRM7-AS1
SNRK-AS1
CNTN4-AS1
CNTN4-AS2
RBMS3-AS1
RBMS3-AS3
MAGI1-AS1
ITIH4-AS1
VIPR1-AS1
SYNPR-AS1
SGO1-AS1
PRRT3-AS1
CADM2-AS2
THOC7-AS1
SLC6A1-AS1
UBE2E1-AS1
ZNF197-AS1
HDAC11-AS1
GLYCTK-AS1
CCDC13-AS1
ARHGEF3-AS1
OSBPL10-AS1
ZNF385D-AS1
ZNF385D-AS2
CACNA2D3-AS1
PRICKLE2-AS2
PRICKLE2-AS3
ATP2B2-IT2
LARS2-AS1
ITPR1-AS1
LINC00690
LOC100996624
FCF1P2
SUCLG2-AS1
SAMMSON
CHL1-AS1
LINC01266
PDZRN3-AS1
LOC101927296
GRM7-AS3
LOC101927374
LOC101927394
LOC101927416
LOC101927494
LINC01267
SATB1-AS1
LOC101927829
LOC101927854
LOC101928135
ITGA9-AS1
LOC101928323
SEMA3B-AS1
IQCF5-AS1
LOC101929054
LOC101929159
C3orf67-AS1
ADAMTS9-AS1
RASSF1-AS1
MIR5787
MIR548AY
MIR6823
MIR6824
MIR6872
MIR6890
MIR8064
MIR6822
LOC102723448
LOC102724231
LOC102724297
CELSR3-AS1
MIR548BB
FOXP1-AS1
GRM7-AS2
LOC105376955
LOC105376975
LOC105376997
LOC105377102
LOC105377105
FAM3D-AS1
LOC105377143
LOC105377146
LOC105377162
ARF4-AS1
SNORD136
SNORA93
SNORA94
SNORA95
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21p11.2.

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

Genes
BAGE
TPTE
CYP4F29P
BAGE4
BAGE3
BAGE2
ANKRD30BP2
POTED
ANKRD20A11P
MGC39584
MIR3118-1
MIR3156-3
MIR8069-1
LOC102724188
LOC105379511
LOC105379514
Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
PICALM
PCSK7
ARHGEF12
MAML2
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
ARRB1
FXYD2
CXCR5
CAPN5
CASP1
CASP4
CASP5
SERPINH1
CD3D
CD3E
CD3G
CTSC
CHEK1
CLNS1A
CRYAB
DLAT
DLG2
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
LRRC32
GRIA4
GRIK4
GRM5
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MAP6
MCAM
KMT2A
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYO7A
NCAM1
NDUFC2
NFRKB
NNMT
NPAT
NRGN
OMP
OPCML
PAK1
PGR
PPP2R1B
PRCP
THAP12
PTS
NECTIN1
RDX
SNORD15A
RPS3
RPS25
SC5D
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPRA
ST14
TAGLN
TECTA
THRSP
THY1
TRPC6
TYR
UPK2
UVRAG
WNT11
ZBTB16
ZNF202
CUL5
FZD4
BARX2
OR7E2P
JRKL
EED
ZPR1
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
SPCS2
GAB2
C2CD2L
NAALAD2
RBM7
MPZL2
YAP1
HYOU1
ATP5L
NEU3
ME3
GPR83
SRSF8
ADAMTS8
PRSS23
TREH
SLCO2B1
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
RAB38
CADM1
PANX1
POU2F3
TSKU
HINFP
REXO2
TENM4
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
CHORDC1
ACAD8
B3GAT1
RAB30
DCPS
C11orf54
AAMDC
ZBTB44
THYN1
DDX25
NOX4
NTM
CDON
SIDT2
TRAPPC4
HIKESHI
CWC15
PCF11
RSF1
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
SYTL2
ANKRD49
TTC12
C11orf57
ACER3
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TMEM126B
TEX12
CRTAM
TMPRSS4
IFT46
SMCO4
EMSY
PRDM10
TRIM49
DSCAML1
GRAMD1B
USP35
CEP126
ARHGAP20
USP28
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TMEM135
KCTD14
ALG8
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
NARS2
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
MOGAT2
PDGFD
TMPRSS5
GDPD5
PUS3
JAM3
BCO2
TMEM133
TMPRSS13
TMEM126A
DCUN1D5
MSANTD4
KIRREL3
DGAT2
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
SNORD14C
SNORD14D
SNORD14E
DIXDC1
CEP295
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
INTS4
VPS26B
GLB1L3
SNORD15B
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
SLC36A4
FAT3
TRIM64
TMEM45B
COLCA2
PIH1D2
NXPE1
NXPE2
JAML
XRRA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
DEUP1
PATE1
C11orf65
ADAMTS15
B3GNT6
MPZL3
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
GDPD4
DDIAS
CCDC83
HEPACAM
OAF
FAM181B
CCDC89
ANGPTL5
RNF169
ANKK1
RNF214
AQP11
LOC283140
LINC00900
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
C11orf44
MIR4697HG
LOC283177
KLHL35
LOC283214
KCTD21
CCDC84
TMEM225
OR8D4
ANKRD42
C11orf53
LOC341056
OR2AT4
HEPHL1
PLET1
VSTM5
LOC387810
GUCY2EP
TRIM77
IZUMO1R
KDM4E
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
TRIM49D1
C11orf87
COLCA1
C11orf88
MIR100HG
PATE2
PATE4
ST3GAL4-AS1
SNX19
LOC403312
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CASP1P2
CARD17
LINC00167
MIR326
SCARNA9
HEPN1
TRIM64B
TRIM53AP
TRIM49C
UBTFL1
C11orf97
LOC643733
LOC643923
CLDN25
LOC646029
LOC646522
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49D2
MIR708
LOC100128239
LOC100128386
LOC100129203
LOC100131626
LOC100132078
LOC100132686
PATE3
WTAPP1
NCAM1-AS1
KCTD21-AS1
MIR1261
MIR1304
MIR548L
SNORA70E
BACE1-AS
MIR4300
MIR4301
MIR3167
MIR1260B
MIR3166
USP2-AS1
MIR3920
MIR3656
LOC100506127
RAB30-AS1
LOC100506368
CASP12
TPBGL
LOC100507283
SENCR
LOC100507431
LOC100507548
TMPRSS4-AS1
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4696
MIR4693
LOC100652768
MIR5579
GRM5-AS1
JRKL-AS1
KIRREL3-AS2
NTM-IT
LOC101054525
LOC101928424
LOC101928535
LOC101928823
LOC101928837
LOC101928847
LOC101928865
LOC101928896
LOC101928940
LOC101928944
LOC101928985
MIR4300HG
LOC101929011
LOC101929089
LOC101929208
DISC1FP1
LOC101929227
LOC101929295
LOC101929340
LOC101929427
LOC101929473
LOC101929497
LOC101929517
LOC101929538
LINC01395
NTM-AS1
LOC101929653
MIR6755
MIR6756
MIR7641-1
MIR7641-2
MIR6090
MIR6716
MIR8052
LOC102723838
LOC102723895
LOC102724301
LOC103611081
PKNOX2-AS1
APOA1-AS
LOC105369423
LOC105369431
LOC105369438
LOC105369443
LOC105369473
LOC105369486
LOC105369507
LOC105369509
LOC105369532
STT3A-AS1
PCF11-AS1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.2.

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

Genes
CBFA2T3
FANCA
MAF
AFG3L1P
APRT
GAS8-AS1
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
PRDM7
MON1B
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
CMC2
JPH3
VAT1L
TLDC1
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ADAMTS18
SNAI3-AS1
LINC00311
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
LOC339059
FAM92B
CTU2
PABPN1L
LOC400548
FENDRR
LOC400553
LOC400558
C16orf74
LOC440390
SNORD68
LINC00917
VPS9D1-AS1
LOC100129617
LOC100129697
URAHP
SYCE1L
LOC100287036
LOC100289580
MIR1910
MIR3182
LINC01082
C16orf95
MIR4720
MIR4722
MIR4719
MIR5093
MIR5189
PRCAT47
FAM157C
LINC01081
LOC101927793
LOC101927817
LINC01229
LINC01227
LOC101928417
LOC101928446
LOC101928557
LOC101928614
LOC101928659
LOC101928682
LOC101928708
LOC101928737
LOC101928880
MIR6504
MIR6775
MIR7854
MIR8058
MIR6774
MAFTRR
LOC102724084
LOC102724163
LOC102724344
LOC102724467
FOXC2-AS1
LOC105371414
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 31 significant results found. The significance cutoff is at Q value=0.25.

Arm # Genes Amp Frequency Amp Frequency Score Amp Z score Amp Q value Del Frequency Del Frequency Score Del Z score Del Q value
1p 3092 0.15 0.21 -1.68 1 0.30 0.35 1.03 0.301
1q 2863 0.35 0.41 2.18 0.0774 0.15 0.23 -1.44 1
2p 1500 0.46 0.47 2.3 0.0648 0.02 0.03 -5.22 1
2q 2495 0.31 0.33 0.15 1 0.05 0.07 -4.7 1
3p 1531 0.23 0.54 2.54 0.0375 0.57 0.75 7.27 1.39e-12
3q 1708 0.40 0.61 4.4 0.000131 0.34 0.57 3.6 0.000597
4p 693 0.05 0.12 -3.69 1 0.61 0.64 5.04 1.01e-06
4q 1467 0.04 0.09 -3.71 1 0.60 0.62 5.49 1.37e-07
5p 456 0.63 0.70 5.88 9.62e-08 0.10 0.28 -1.71 1
5q 2185 0.14 0.36 0.29 1 0.61 0.71 7.63 1.13e-13
6p 1664 0.29 0.36 0.0566 1 0.20 0.29 -1.32 1
6q 1304 0.24 0.31 -1.19 1 0.22 0.29 -1.49 1
7p 926 0.44 0.49 2.13 0.0788 0.12 0.21 -2.8 1
7q 1717 0.33 0.38 0.481 0.974 0.12 0.18 -3.1 1
8p 795 0.31 0.43 0.727 0.862 0.30 0.43 0.589 0.494
8q 1249 0.43 0.52 2.87 0.0165 0.19 0.32 -0.848 1
9p 621 0.11 0.27 -1.83 1 0.58 0.66 5.11 7.71e-07
9q 1610 0.13 0.28 -1.18 1 0.54 0.62 5.2 5.41e-07
10p 767 0.19 0.29 -1.86 1 0.35 0.43 0.714 0.456
10q 1968 0.09 0.15 -3.37 1 0.38 0.42 1.53 0.152
11p 1162 0.17 0.24 -2.54 1 0.30 0.36 -0.445 0.948
11q 2133 0.16 0.22 -2.31 1 0.27 0.32 -0.393 0.948
12p 804 0.56 0.58 3.84 0.000992 0.04 0.08 -4.39 1
12q 2055 0.33 0.36 0.393 0.98 0.07 0.11 -4.12 1
13p 0 0.13 0.31 -1.56 1 0.58 0.67 4.78 3.49e-06
13q 1092 0.08 0.20 -2.5 1 0.58 0.64 5.23 5.15e-07
14p 0 0.27 0.40 -0.404 1 0.33 0.46 0.528 0.512
14q 1829 0.24 0.38 0.454 0.974 0.36 0.48 2.37 0.0251
15p 0 0.19 0.33 -1.59 1 0.41 0.51 1.5 0.153
15q 2082 0.21 0.34 -0.0352 1 0.37 0.47 2.54 0.017
16p 1378 0.16 0.25 -1.96 1 0.38 0.45 1.6 0.137
16q 1070 0.15 0.24 -2.34 1 0.39 0.46 1.47 0.155
17p 937 0.25 0.36 -0.401 1 0.31 0.42 0.594 0.494
17q 2298 0.30 0.39 1.13 0.514 0.24 0.34 0.2 0.664
18p 212 0.25 0.35 -1.28 1 0.28 0.37 -0.861 1
18q 644 0.19 0.28 -2.11 1 0.33 0.41 0.18 0.664
19p 1331 0.19 0.27 -1.79 1 0.29 0.36 -0.289 0.921
19q 2402 0.27 0.36 0.595 0.946 0.25 0.34 0.279 0.645
20p 583 0.45 0.49 1.88 0.131 0.08 0.15 -3.91 1
20q 1092 0.48 0.54 3.14 0.00808 0.10 0.20 -2.85 1
21p 92 0.08 0.15 -4.27 1 0.44 0.48 1.26 0.218
21q 750 0.09 0.18 -3.4 1 0.47 0.52 2.53 0.017
22p 2 0.11 0.21 -3.38 1 0.46 0.52 1.87 0.0813
22q 1258 0.36 0.56 3.16 0.00808 0.35 0.55 3.03 0.00422
Xp 945 0.01 0.06 -2.78 1 0.84 0.85 9.84 0
Xq 1533 0.00 0.00 -3.29 1 0.82 0.82 9.97 0
Yp 113 0.01 0.25 -0.695 1 0.96 0.97 11.5 0
Yq 245 0.00 0.00 -1.46 1 0.97 0.97 11.7 0
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 = /cromwell_root/fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55/cfa7a2c5-5d9d-41c1-bca5-29ac294918db/aggregate_data_workflow/aefc661b-6bee-4a45-8f2c-3bb695390093/call-aggregate_data/CPTAC3-LSCC-v3beta.CNV__wgs_wxs_pool_cn.seg.txt

  • Markers File = ./this_file_does_not_exist.txt

  • Reference Genome = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/gistic2.refgene.hg38.UCSC.add_miR.160920.mat

  • CNV Files = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg38_GDC_SNP6_CNV_list.161107.txt

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.98

  • 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 108 Input Tumor Samples.

Tumor Sample Names
C3L-00081
C3L-00415
C3L-00445
C3L-00568
C3L-00603
C3L-00904
C3L-00923
C3L-00927
C3L-00965
C3L-00993

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.

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)
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