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 110 tumor samples used in this analysis: 44 significant arm-level results, 27 significant focal amplifications, and 24 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 - 27 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
--- | --- | --- | --- | ---
14q13.3 | 1.9114e-20 | 1.9114e-20 | chr14:36190002-36479999 | 2
8q24.21 | 1.8076e-15 | 1.6594e-14 | chr8:128150002-128209999 | 1
12q15 | 8.1683e-09 | 8.1683e-09 | chr12:69110002-69209999 | 0 [CPSF6]
5p15.33 | 2.7645e-06 | 2.7645e-06 | chr5:1030001-1350000 | 9
7p11.2 | 4.1099e-06 | 4.1099e-06 | chr7:54680001-55520000 | 7
11q13.3 | 0.0001419 | 0.0001419 | chr11:68860002-70000000 | 16
1q21.2 | 0.00034477 | 0.00034477 | chr1:119990001-156200000 | 343
Xq27.3 | 0.00076877 | 0.00076877 | chrX:145300001-155960000 | 173
19q12 | 0.0035841 | 0.0035841 | chr19:29620001-29880000 | 3
8q24.3 | 1.7225e-09 | 0.0073734 | chr8:144170002-145138636 | 46
20q13.33 | 3.2499e-05 | 0.0075838 | chr20:62820002-64444167 | 68
20q13.2 | 0.00025593 | 0.01267 | chr20:53340002-54059999 | 6
4q12 | 0.016092 | 0.016092 | chr4:54240001-55139999 | 4
17q23.1 | 0.016092 | 0.016092 | chr17:47650001-83257441 | 580
12p11.21 | 0.017505 | 0.02994 | chr12:32300002-32520000 | 2
Yq11.223 | 0.037304 | 0.037304 | chrY:20120002-20180000 | 0 [TTTY10]
13q31.1 | 0.044371 | 0.044371 | chr13:86200002-86280000 | 0 [SLITRK6]
1p34.2 | 0.047503 | 0.047503 | chr1:39800002-42080000 | 29
21p12 | 0.047503 | 0.047503 | chr21:6780001-6950000 | 1
6p21.1 | 0.058953 | 0.058953 | chr6:41530002-42000000 | 13
5q35.1 | 0.081515 | 0.081515 | chr5:169550001-181538259 | 169
Xp22.33 | 0.083882 | 0.083882 | chrX:1-150000 | 0 [PLCXD1]
14q32.33 | 0.045692 | 0.10635 | chr14:105520002-107043718 | 14
20p11.21 | 0.13766 | 0.13766 | chr20:22110001-23599999 | 18
8q13.1 | 0.0044146 | 0.15485 | chr8:62850002-69660000 | 49
6q27 | 0.19175 | 0.19175 | chr6:170590001-170805979 | 0 [PDCD2]
12p13.33 | 0.10919 | 0.21437 | chr12:1-789999 | 15

Genes in Wide Peak

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

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

Genes
MBIP
SFTA3

Genes in Wide Peak

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

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

Genes
MIR1208

Genes in Wide Peak

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

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

Genes
TERT
SLC12A7
CLPTM1L
NKD2
SLC6A19
SLC6A18
MIR4457
MIR4635
CTD-3080P12.3

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2
VOPP1
EGFR-AS1
LOC100996654
ELDR

Genes in Wide Peak

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

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

Genes
CCND1
FGF3
FGF4
IGHMBP2
FGF19
MYEOV
MRGPRD
MRGPRF
MRPL21
TPCN2
ORAOV1
LOC338694
MIR3164
MRGPRF-AS1
LINC01488
LOC102724265

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
MUC1
NOTCH2
TPM3
PDE4DIP
ADAR
CHRNB2
CKS1B
CLK2
CTSK
CTSS
DRD5P2
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LMNA
LOR
MCL1
SMCP
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RIT1
RNU1-4
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SSR2
VPS72
THBS3
TCHH
TUFT1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
PRPF3
ARHGEF2
SEC22B
CHD1L
SLC25A44
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
RNVU1-7
RNU1-3
RNU1-2
RNU1-1
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
C1orf56
MSTO1
GOLPH3L
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
ATP8B2
LINC00869
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE1
SEMA4A
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
MEX3A
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
DCST2
LIX1L
S100A16
CREB3L4
CIART
HFE2
ANKRD35
NBPF12
LELP1
DCST1
BNIPL
SPRR4
NUDT4P2
PDIA3P1
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
FLG-AS1
RXFP4
LOC343052
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
NOTCH2NL
LINC01138
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
NUDT4P1
HIST2H2BF
NBPF18P
KPRP
LCE6A
FAM72C
ADAMTSL4-AS1
PRR9
PPIAL4G
FAM231D
NBPF13P
PPIAL4D
LOC645166
ASH1L-AS1
POU5F1P4
S100A7L2
EMBP1
SRGAP2B
SRGAP2C
PPIAL4A
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA4
SNORA80E
MIR554
MIR555
MIR92B
FAM72D
NBPF8
LINC00623
LOC728989
PPIAL4E
PFN1P2
PDZK1P1
MIR190B
C1orf68
MSTO2P
LOC100131107
LOC100132057
LOC100132111
NBPF10
FCGR1CP
C2CD4D
NBPF20
HYDIN2
LINC00624
MIR4257
MIR4258
LOC100505666
LOC100505824
LOC100507670
TNFAIP8L2-SCNM1
MIR5698
MIR5087
SRGAP2-AS1
FALEC
UBE2Q1-AS1
SRGAP2D
RNVU1-8
LOC101927429
LOC101927468
GBAT2
LOC101928009
LOC101928034
LOC101928120
LOC101928979
NBPF25P
LOC101929798
RNVU1-4
RNVU1-14
RNVU1-15
RNVU1-20
RNVU1-17
RNVU1-3
RNVU1-1
RNVU1-6
RNVU1-19
MIR6737
MIR6738
MIR6878
MIR6736
MIR6077
MIR8083
CH17-408M7.1
LOC103091866
LOC105371433
SCARNA26A
SCARNA26B

Genes in Wide Peak

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

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

Genes
MTCP1
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CETN2
CLIC2
CNGA2
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
HCFC1
HMGB3
IDH3G
IDS
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MECP2
MPP1
MTM1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
FAM50A
TMEM257
GPR50
MAMLD1
BCAP31
SPRY3
ZNF275
TREX2
SRPK3
SNORA70
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
GABRQ
PDZD4
FAM3A
FUNDC2
PRRG3
BRCC3
CD99L2
TMEM185A
SLITRK2
PNMA6A
FATE1
CXorf40A
FAM58A
PNMA5
RAB39B
PASD1
GAB3
PNCK
ZFP92
CSAG1
FMR1NB
CH17-340M24.3
VMA21
CTAG1A
MAGEA2B
CSAG3
MIR105-1
MIR105-2
MIR224
H2AFB2
H2AFB1
F8A2
CXorf40B
MIR452
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
MIR767
FMR1-AS1
MIR509-2
MIR890
MIR891B
MIR888
MIR892B
MIR509-3
MIR891A
MIR892A
GPR50-AS1
CXorf51A
HSFX2
CSAG4
LINC00893
SMIM9
FAM223A
CMC4
LINC00894
MIR1184-1
MIR513C
MIR718
MIR513B
MIR2114
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
MAGEA10-MAGEA5
MIR664B
HCFC1-AS1
LCA10
OPN1MW3
LINC00850
MAGEA8-AS1
LOC101927830
LOC101928917
MIR6858
MIR892C
LOC105373368
LOC105373378
LOC105373383
LOC105377213

Genes in Wide Peak

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

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

Genes
CCNE1
PLEKHF1
C19orf12

Genes in Wide Peak

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

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

Genes
RECQL4
GPT
HSF1
TONSL
RPL8
ZNF7
ZNF16
DGAT1
FOXH1
LRRC14
BOP1
FBXL6
COMMD5
CPSF1
CYHR1
VPS28
SLC39A4
ZNF250
C8orf33
SLC52A2
ARHGAP39
ZNF34
SCRT1
PPP1R16A
ZNF251
KIFC2
MFSD3
ADCK5
ZNF252P
TMED10P1
ZNF252P-AS1
ZNF517
TMEM249
C8orf82
LRRC24
SCX
MROH1
MIR939
TONSL-AS1
MIR1234
LOC101928902
MIR6848
MIR7112
MIR6850
MIR6893
MIR6849

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
hsa-mir-941-3
CHRNA4
COL9A3
EEF1A2
NPBWR2
KCNQ2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
TCFL5
DIDO1
PRPF6
GMEB2
STMN3
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
GID8
PCMTD2
ARFGAP1
SLC2A4RG
ZNF512B
COL20A1
SLC17A9
LOC63930
FNDC11
PPDPF
BIRC7
DNAJC5
ZGPAT
HELZ2
BHLHE23
NKAIN4
ZBTB46
SAMD10
ABHD16B
LINC00266-1
LKAAEAR1
LINC00176
MIR124-3
MIR647
HAR1A
HAR1B
UCKL1-AS1
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100130587
DPH3P1
LINC00029
LINC01056
FLJ16779
MIR1914
MIR4326
MIR3196
LOC100505771
RTEL1-TNFRSF6B
ZBTB46-AS1
MIR6813

Genes in Wide Peak

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

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

Genes
ZNF217
BCAS1
TSHZ2
SUMO1P1
LOC101927770
LOC105372672

Genes in Wide Peak

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

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

Genes
KDR
KIT
PDGFRA
LOC339978

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
CD79B
CLTC
COL1A1
DDX5
HLF
PRKAR1A
ASPSCR1
BRIP1
MSI2
CANT1
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
ATP5G1
CA4
CACNG1
CD7
CDK3
CHAD
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
DLX3
DLX4
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
GIP
GNGT2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
ICAM2
MRPL58
FOXK2
ITGA3
ITGB4
KCNJ2
KCNJ16
KPNB1
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NFE2L1
NGFR
NME1
NME2
NPTX1
P4HB
PDE6G
PDK2
PECAM1
PHB
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGCA
SGSH
SMARCD2
SUMO2
SOX9
SP2
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
SPOP
PPM1D
DGKE
CBX4
SKAP1
DNAH17
ABCC3
RGS9
GALR2
SPHK1
CACNA1G
SOCS3
SPAG9
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
TSPOAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
TBKBP1
TMEM94
EIF4A3
MRC2
HELZ
MED13
TOM1L1
TOB1
ALYREF
SLC35B1
DCAF7
CALCOCO2
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
HOXB13
APPBP2
ST6GALNAC2
IGF2BP1
GNA13
SEPT9
CD300C
CBX1
RAB40B
TLK2
KAT7
POLG2
NXPH3
SNF8
CD300A
TMC6
DDX42
ZNF652
PPM1E
ARSG
CEP131
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
SNX11
TBX21
NT5C
CDR2L
MRPS7
UTP18
RNFT1
HN1
TUBD1
DCXR
TACO1
ABI3
COPZ2
MRPL27
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
LUC7L3
SDK2
FAM20A
MBTD1
BCAS3
TMEM104
RNF43
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
PNPO
SMG8
TMEM100
RSAD1
LRRC59
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45B
CA10
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
XYLT2
DNAI2
SMURF2
ENGASE
SPATA20
MRPL38
UBE2Z
CARD14
MFSD11
PRR15L
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
OGFOD3
ZNF750
NUP85
MYO15B
ACSF2
FAAP100
CDK5RAP3
SP6
LIMD2
KCNH6
FAM117A
VMP1
TSPAN10
MYCBPAP
QRICH2
PRAC1
KIF2B
USP32
PPP1R9B
CBX2
FAM104A
MGC16275
FBF1
UNK
LRRC46
SCRN2
CEP95
TRIM47
ANKRD40
STRADA
PRR29
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
OSBPL7
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
WFIKKN2
FLJ40194
B4GALNT2
MRPL10
TBC1D16
AFMID
DYNLL2
MGAT5B
TEPSIN
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146795
LOC146880
EME1
NOTUM
TMC8
ANKFN1
MARCH10
TMEM92
PHOSPHO1
CEP112
SAMD14
CENPX
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MTVR2
STXBP4
CACNA1G-AS1
TAC4
MYADML2
NPB
LINC00469
FADS6
HID1
TSEN54
UBALD2
LINC00868
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
TTLL6
LOC284080
C17orf47
SLC26A11
ENDOV
GDPD1
NDUFAF8
LINC00482
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
OXLD1
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
MCRIP1
GPR142
ZACN
PRAC2
HILS1
LRRC37A3
RNF126P1
YPEL2
LOC388406
C17orf82
BTBD17
AATK-AS1
RPL23AP87
TOB1-AS1
PRR29-AS1
KCNJ2-AS1
SOX9-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
HOXB-AS3
MIR10A
MIR142
MIR152
MIR196A1
MIR21
MIR301A
MXRA7
LOC440446
TBC1D3P2
PLEKHM1P1
LOC440461
BAIAP2-AS1
MIR338
CPSF4L
SMIM5
WFDC21P
TBC1D3P1-DHX40P1
LOC653653
NME1-NME2
SNHG20
SCARNA20
SCARNA16
SNORA50C
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR548D2
MIR633
MIR634
MIR635
MIR636
MIR657
FLJ45513
LOC729683
PRCD
MIR454
SNORA38B
LOC100130370
LOC100130520
SMIM6
TNRC6C-AS1
CD300LD
LOC100132174
PRO1804
LOC100134391
TEN1
C17orf99
LOC100287042
LOC100288866
LOC100294362
MIR1203
MIR1250
MIR4316
MIR3065
MIR3186
MIR4315-2
MIR3185
MIR4315-1
LINC00674
LINC00673
MIR3614
MIR3678
MIR3615
MIR548AA2
SP2-AS1
C17orf112
TSPOAP1-AS1
LOC100507002
RNF157-AS1
SNHG16
LOC100507351
C1QTNF1-AS1
MIR1273E
TEN1-CDK3
MIR1268B
MIR4739
MIR4525
MIR4729
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
HP09025
CEP295NL
MIR4524B
HOXB-AS1
LOC100996291
DNAH17-AS1
LOC101927166
LOC101927207
LOC101927230
LOC101927274
LOC101927539
LOC101927557
CCDC182
LOC101927666
SEPT4-AS1
LINC01476
LOC101927755
LOC101927855
LOC101927877
PRKCA-AS1
LOC101928021
LINC01482
LINC01483
LINC01028
CASC17
LOC101928205
LOC101928251
LOC101928514
LOC101928674
LOC101928710
LOC101928738
LOC101928766
LOC101928855
LOC101929511
LOC101929552
MIR6080
MIR6129
MIR6165
MIR6786
MIR6787
MIR6868
MIR6516
MIR6785
MIR8059
LINC01152
LINC01497
LOC102723505
LOC102723517
HID1-AS1
LOC102724532
LOC102724596
TBX2-AS1
TMEM92-AS1
ABCA9-AS1
LOC105274304
THRA1/BTR
LOC105371814
LOC105371824
LOC105371849
LOC105371899
LOC105371907
LOC105371925
SNHG25
CRAT40
SNORD134

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p11.21.

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

Genes
BICD1
FGD4

Genes in Wide Peak

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

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

Genes
COL9A2
CTPS1
EDN2
MYCL
NFYC
PPT1
RLF
KCNQ4
RIMS3
ZMPSTE24
CAP1
SCMH1
TRIT1
HIVEP3
SMAP2
EXO5
ZFP69B
MFSD2A
TMCO2
ZNF684
CITED4
SLFNL1
ZFP69
MIR30C1
MIR30E
NFYC-AS1
FOXO6
SLFNL1-AS1
LOC101929901

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21p12.

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

Genes
MIR8069-1

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
BYSL
MDFI
PGC
MED20
FRS3
USP49
PRICKLE4
FOXP4
TOMM6
MIR4641
FOXP4-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.1.

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

Genes
NPM1
TLX3
NSD1
RANBP17
BNIP1
CANX
CLTB
NKX2-5
DBN1
DOCK2
DRD1
DUSP1
F12
FGFR4
FOXI1
FLT4
GABRP
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
KCNMB1
LCP2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
SLC34A1
SNCB
STK10
ZNF354A
STC2
FGF18
SQSTM1
ATP6V0E1
PDLIM7
ADAMTS2
MAML1
GFPT2
RACK1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
FBXW11
ZNF346
TSPAN17
OR2V1
PRELID1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
SPDL1
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
CNOT6
GMCL1P1
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
PHYKPL
UNC5A
TRIM41
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
ZNF354B
C5orf47
C5orf58
OR2Y1
CREBRF
BTNL9
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
LINC01366
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
OR2V2
ZNF454
C5orf60
PRR7-AS1
PFN3
ZNF879
SIMC1
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
SMIM23
CBY3
FAM153C
SNORA74B
LOC728554
AACSP1
LINC00847
OR4F29
FAM196B
LOC100132062
LOC100268168
LOC100288254
MIR1229
MIR1271
MIR4281
MIR3912
LINC01187
LOC100507387
TRIM52-AS1
MIR4634
MIR4638
MIR378E
MIR5003
HEIH
LOC100996385
LOC100996419
CTD-2270F17.1
LOC101928093
LINC01484
LINC01485
LINC01411
LOC101928445
CTC-338M12.4
MIR8056
MIR8089
LINC01574
LOC102577426
LOC105377716
LOC105377763

Genes in Wide Peak

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

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

Genes
ELK2AP
ADAM6
FAM30A
TMEM121
LINC00226
LINC00221
MIR4507
MIR4538
MIR4539
MIR4537
MIR5195
MIR7641-2
MIR8071-1
LOC105370697

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.21.

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

Genes
FOXA2
SSTR4
THBD
CST8
CD93
NXT1
NAPB
GZF1
CSTL1
CST9L
LINC00261
CST11
CST13P
LINC00656
LOC284788
LINC01431
LINC01427
LINC01384

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q13.1.

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

Genes
CRH
MYBL1
PDE7A
TTPA
GGH
CYP7B1
MTFR1
ARFGEF1
COPS5
RRS1
SULF1
SGK3
PTTG3P
BHLHE22
ARMC1
C8orf44
CPA6
CSPP1
VCPIP1
PREX2
TRIM55
DNAJC5B
C8orf34
ADHFE1
MCMDC2
YTHDF3
C8orf46
NKAIN3
LINC01289
LINC01299
PPP1R42
C8orf34-AS1
LOC401463
MIR124-2
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
MIR124-2HG
LINC00967
RRS1-AS1
LINC01592
LINC01603
C8orf44-SGK3
YTHDF3-AS1
LOC102724612
LOC102724623
LOC102724708

Genes in Wide Peak

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

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

Genes
KDM5A
NINJ2
SLC6A12
SLC6A13
WNK1
CCDC77
B4GALNT3
IQSEC3
LOC574538
FAM138D
LOC100049716
LOC100288778
LOC101929384
LOC102723544
LOC105369595

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 - 24 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 | 1.8077e-25 | 4.8129e-21 | chr9:21860002-22450000 | 4
21p11.2 | 1.0581e-15 | 3.6453e-13 | chr21:7820002-8989999 | 11
17p13.1 | 1.3823e-12 | 1.3823e-12 | chr17:130002-19300000 | 407
13q11 | 3.141e-11 | 3.141e-11 | chr13:1-18870000 | 2
Yq11.223 | 1.0788e-08 | 1.0788e-08 | chrY:23190002-23940000 | 2
8p23.1 | 1.8609e-07 | 1.8609e-07 | chr8:1-30999999 | 284
22p11.2 | 2.6301e-07 | 2.6301e-07 | chr22:10960002-16939999 | 14
Xp22.33 | 1.2271e-05 | 1.2271e-05 | chrX:1-150909999 | 985
6q16.3 | 1.4456e-05 | 2.814e-05 | chr6:74050002-170805979 | 561
1p13.3 | 0.00019428 | 0.00019972 | chr1:75610001-119940000 | 369
4q35.2 | 0.00033408 | 0.0003557 | chr4:187670001-190179999 | 10
21q11.2 | 4.6002e-08 | 0.00060533 | chr21:9820002-14110000 | 13
9p23 | 2.6146e-10 | 0.0063756 | chr9:7790001-10630000 | 5
3p24.1 | 0.014089 | 0.014265 | chr3:1-94019999 | 680
5q15 | 0.016268 | 0.015324 | chr5:44800001-152989999 | 756
22q13.32 | 0.018705 | 0.01864 | chr22:43850001-50818468 | 98
12p13.1 | 0.022369 | 0.022689 | chr12:30001-133275309 | 1340
Xq28 | 0.028676 | 0.029533 | chrX:154570002-155999999 | 29
18q21.31 | 0.032129 | 0.032201 | chr18:24760002-80373285 | 265
10q25.1 | 0.051523 | 0.049831 | chr10:45140002-133797422 | 766
15q13.1 | 0.068661 | 0.068134 | chr15:1-71800000 | 590
16q24.3 | 0.068134 | 0.068134 | chr16:72080001-90338345 | 199
19q13.33 | 0.068134 | 0.068134 | chr19:38620002-58617616 | 850
6p11.2 | 0.086235 | 0.24726 | chr6:1-170805979 | 1400

Genes in Wide Peak

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

Table S23. 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 21p11.2.

Table S24. 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 17p13.1.

Table S25. 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
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
MNT
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
PMP22
POLR2A
PRPSAP2
PSMB6
RCVRN
RPA1
RPL26
SCO1
SHBG
SHMT1
SLC2A4
SOX15
SREBF1
VAMP2
TOP3A
UBB
UBE2G1
TRPV1
YWHAE
ZNF18
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
CCDC144A
ACAP1
KIAA0753
SGSM2
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
CLEC10A
MYBBP1A
FBXW10
PRPF8
TRIM16
RAI1
KIF1C
GRAP
GABARAP
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
MPRIP
CLUH
SMG6
WSCD1
CTDNEP1
TNFRSF13B
PIK3R5
ELP5
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
SNORD49A
SNORD3B-1
PELP1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
TVP23B
GLOD4
YBX2
MYO15A
TRPV2
ANKFY1
RASD1
INPP5K
FAM64A
XAF1
BORCS6
ALKBH5
TTC19
SLC52A1
MED9
WRAP53
MRM3
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
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
CDRT15
CFAP52
CCDC42
PIK3R6
ODF4
KCTD11
TRIM16L
MFSD6L
TRPV3
SLC16A11
FBXO39
USP32P1
DHRS7C
TVP23C
CENPV
FLCN
PLD6
SLC16A13
C17orf74
SPNS3
USP32P2
TBC1D28
TMEM256
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
LINC00670
CDRT4
CCDC144B
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
KRT17P5
SMTNL2
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
EVPLL
SNORA48
SNORD10
OR1D4
SCGB1C2
LGALS9C
SCARNA21
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
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
COX10-AS1
EPN2-IT1
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 13q11.

Table S26. 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 Yq11.223.

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

Genes
DAZ3
DAZ2

Genes in Wide Peak

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

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

Genes
PCM1
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
DMTN
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
GSR
GTF2E2
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
UBXN8
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
FBXO25
FGF20
ADAMDEC1
CNOT7
ZDHHC2
SLC25A37
SCARA3
SARAF
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
AGPAT5
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
MTUS1
KIAA1456
CCAR2
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
HMBOX1
MCPH1
PPP1R3B
NUDT18
DOCK5
BIN3-IT1
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
FAM167A-AS1
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
NKX2-6
SGCZ
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
ESCO2
FBXO16
LINC00599
FAM87A
TDRP
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FAM86B3P
XKR6
LOC286059
LOC286083
MICU3
LOC286114
SCARA5
FAM183CP
LOC340357
LINC00965
USP17L2
XKR5
FAM90A25P
LOC389641
NUGGC
USP17L8
LOC392196
USP17L7
LOC401442
USP17L1
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A7P
FAM90A10P
DEFA8P
DEFA9P
DEFA10P
MIR383
C8orf58
C8orf49
DEFB135
DEFB136
DEFB134
ERICH1-AS1
LINC00589
MBOAT4
DEFB109P1B
RPL23AP53
USP17L4
USP17L3
LOC649352
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA11P
DEFA1B
ZNF705D
FAM90A2P
LOC729732
RBPMS-AS1
FAM66B
LOC100128993
PRR23D1
ZNF705G
FAM66E
ZNF705B
FAM66D
FAM66A
PRR23D2
LOC100287015
DEFB4B
MIR1322
MIR548I3
MIR548H4
MIR4287
MIR548V
MIR3148
MIR4288
MIR4286
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
MIR3674
LOC100506990
LOC100507071
LOC100507156
SMIM18
DLGAP2-AS1
MCPH1-AS1
MIR4659A
MIR4660
MIR4659B
GS1-24F4.2
MIR5692A2
MIR5692A1
LZTS1-AS1
LINC00681
LOC101927752
LOC101927815
LOC101928058
LOC101929066
LOC101929128
LOC101929172
LINCR-0001
LOC101929229
LOC101929237
LOC101929269
LOC101929294
LOC101929315
EXTL3-AS1
LOC101929450
LOC101929470
MIR6841
MIR6842
MIR6843
MIR6876
MIR7160
MIR7641-2
MIR8055
LOC102467222
LOC102725080
KBTBD11-OT1
SNORA99

Genes in Wide Peak

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

Table S29. 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 Xp22.33.

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

Genes
ATRX
ELF4
GATA1
GPC3
MSN
NONO
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
CRLF2
P2RY8
hsa-mir-220a
hsa-mir-362
hsa-mir-1308
ABCB7
AGTR2
NR0B1
ALAS2
AMELX
SLC25A5
SLC25A6
XIAP
SHROOM2
AR
ARAF
ARHGAP6
ARR3
STS
ARSD
ARSE
ARSF
ASMT
ATP7A
BMX
BRS3
BTK
CACNA1F
S100G
CAPN6
CD40LG
CDR1
CDX4
CHM
CLCN4
CLCN5
COL4A5
COL4A6
COX7B
CSF2RA
CSTF2
CYBB
CYLC1
DCX
DDX3X
TIMM8A
DIAPH2
DLG3
DMD
DRP2
TSC22D3
EDA
EFNB1
EIF1AX
EIF2S3
ELK1
F9
ACSL4
FANCB
GPC4
FGD1
FGF13
FHL1
VEGFD
FMR1
AFF2
CENPI
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
GJB1
GK
GLA
GLRA2
GLUD2
GPM6B
CXCR3
LPAR4
GPR34
GRIA3
GRPR
GUCY2F
HSD17B10
HCCS
HNRNPH2
HPRT1
ERAS
HTR2C
IDS
IGBP1
IGSF1
IL2RG
IL3RA
IL13RA1
IL13RA2
ANOS1
KCND1
LAMP2
PRICKLE3
SH2D1A
MAGEA8
MAGEA9
MAGEA11
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
MCF2
CD99
MID1
FOXO4
CITED1
MTM1
NAP1L2
NAP1L3
NDP
NDUFA1
NHS
GPR143
TBC1D25
OCRL
OPHN1
OTC
P2RY4
PAK3
CDK16
PDHA1
PDK3
CFP
PFKFB1
PGK1
PHEX
PHKA1
PHKA2
PIGA
PIN4
PLP1
PLP2
PLS3
POLA1
POU3F4
PPEF1
PRKX
PRPS1
PRPS2
PRRG1
PSMD10
RBBP7
RBM3
RP2
RPGR
RPL39
RPL36A
RPS4X
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SH3BGRL
SHOX
SLC16A2
SMARCA1
SMS
SOX3
SRD5A1P1
SSX5
CDKL5
SUV39H1
SYN1
SYP
TAF1
SERPINA7
TBL1X
DYNLT3
TDGF1P3
TIMP1
TSPAN7
TSPAN6
TMSB4X
TRO
TRPC5
UBA1
UBE2A
SLC35A2
XG
XIST
XK
XPNPEP2
ZFX
ZIC3
ZNF711
ZNF182
ZNF41
ZNF75D
ZNF157
RNF113A
ZXDA
GTPBP6
PUDP
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
SRPX
UXT
CUL4B
IRS4
OGT
OFD1
PIR
INE2
INE1
CASK
ASMTL
PAGE1
MTMR1
FGF16
AKAP4
APLN
AP1S2
GYG2
FAM127A
SLC25A14
CLDN2
RGN
AIFM1
TMEM257
REPS2
ZBED1
ZMYM3
BMP15
MED14
TCEAL1
RAB33A
RAB9A
TSIX
ITM2A
ARHGEF6
PCYT1B
MAGED1
XAGE2
PAGE4
MORF4L2
GPRASP1
STARD8
FRMPD4
JADE3
ARMCX2
HEPH
MAGEC1
AMMECR1
MED12
ZBTB33
HDAC6
MAMLD1
HUWE1
PQBP1
ADGRG2
ATP6AP2
TENM1
SSX3
TIMM17B
RRAGB
SCML2
SLC9A6
ENOX2
PRDX4
EBP
STAG2
RAI2
PLAC1
CYSLTR1
UTP14A
DIAPH2-AS1
PGRMC1
MAGED2
MSL3
TMSB15A
PIM2
MID2
IL1RAPL1
WDR45
PRAF2
CA5B
SLC6A14
KLF8
VSIG4
CNKSR2
IQSEC2
PHF8
SEPT6
ARHGEF9
ATP1B4
ACOT9
KCNE5
LDOC1
SMPX
GSPT2
KIF4A
FTSJ1
HYPM
MXRA5
EGFL6
FAM127B
IL1RAPL2
ITGB1BP2
VCX
GAGE12I
GAGE2E
SNORA69
SNORD61
RNU6-1
BEX3
NOX1
FAM155B
INGX
GPR82
GPKOW
SRPX2
APEX2
RBMX
PCDH11X
RPS6KA6
P2RY10
HTATSF1
PCSK1N
PPP2R3B
CCDC22
MCTS1
MAGEH1
FAM156A
C1GALT1C1
SNX12
RPA4
UBQLN2
SH3KBP1
SPANXA1
FOXP3
TBX22
ZDHHC9
RLIM
TCEAL9
RAB9B
LUZP4
PDZD11
PBDC1
TFDP3
TLR7
ARMCX1
TLR8
MBTPS2
MAGEC2
VGLL1
VCX2
VCX3A
ARMCX3
TAF9B
RBMX2
STK26
CPXCR1
CHIC1
FTHL17
GPR173
NLGN3
SASH3
TAF7L
SPIN2A
ARMCX6
WDR44
NDUFB11
GNL3L
ERCC6L
NUP62CL
GDPD2
BCOR
TBC1D8B
FAM120C
GEMIN8
CT55
TMEM255A
CXorf57
NUDT11
RBM41
PLCXD1
SAGE1
OTUD5
ZNF280C
MTMR8
KRBOX4
TXLNG
MBNL3
WWC3
FAM45BP
BEX1
HDAC8
ZC4H2
NXT2
NKRF
NXF5
NXF4
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
MOSPD1
BEX4
CTPS2
CHST7
TCEAL7
GRIPAP1
THOC2
ZNF630
TMEM27
SHROOM4
KIAA1210
NLGN4X
PCDH19
RGAG1
LRCH2
MAGEE1
RAP2C
MID1IP1
ACE2
TMEM35A
EDA2R
NYX
BCORL1
DUSP21
CXorf56
DMRTC1
TSPYL2
TNMD
PJA1
SPANXD
SPANXC
WDR13
PORCN
ARMCX5
UPF3B
WNK3
APOO
HMGN5
NKAP
RNF128
MAP7D3
MORC4
CXorf36
LONRF3
ALG13
MAGIX
TCEAL4
TRMT2B
POF1B
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
ESX1
BHLHB9
MAGED4B
LAS1L
GPR101
TMEM47
CD99L2
USP26
FRMD8P1
MAGT1
TMEM164
PHF6
FRMPD3
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
SLC9A7
BEX2
MIR503HG
SLC7A3
TCEAL3
CCNB3
PPP1R3F
CCDC120
TSR2
HS6ST2
FRMD7
KLHL13
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
CXorf40A
RIPPLY1
LINC01278
ATXN3L
SLC38A5
MMGT1
ACRC
SYAP1
SYTL4
SYTL5
GPRASP2
ATG4A
DACH2
SLITRK4
SPANXN3
MAGEC3
BEND2
DCAF12L1
DGKK
MAP2K4P1
PIH1D3
MUM1L1
FAM199X
AMER1
APOOL
HDX
FUNDC1
ADGRG4
PTCHD1
PPP4R3CP
MAGEB10
DCAF8L1
VENTXP1
OTUD6A
UPRT
MAGEE2
MAGEB16
FOXR2
ACTRT1
GPR119
PAGE3
RBMXL3
DOCK11
SPIN4
ASB11
ASB9
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
ZNF645
FMR1NB
USP27X-AS1
FAAH2
ZXDB
LINC00889
FAM47A
MOSPD2
ARHGAP36
RIBC1
AKAP14
RHOXF1
NKAPP1
MAGEB6
CXorf65
AWAT1
AWAT2
ZDHHC15
USP51
TCEAL6
H2BFWT
CXorf38
FAM122B
FAM122C
DDX53
FAM46D
SPIN3
FAM47B
SUPT20HL2
TCEANC
ZCCHC12
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
CT83
LINC01560
SLC25A43
FAM226A
ZCCHC5
NRK
INTS6L
ZNF449
TMEM31
PAGE2
DHRSX
BRWD3
CXorf58
CT47A11
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX8
SSX9
RAB40AL
LINC00685
ATP11C
LINC00632
NLRP2B
H2BFM
LOC286437
LINC01281
YIPF6
CFAP47
FIRRE
UBE2E4P
TTC3P1
FAM133A
MAGEB18
TMSB15B
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
MORF4L2-AS1
VSIG1
ZC3H12B
SATL1
DCAF12L2
LOC340581
CA5BP1
ZCCHC16
LHFPL1
CXorf67
ZNF81
ITIH6
LANCL3
MPC1L
DCAF8L2
SOWAHD
OR13H1
CCDC160
CXorf66
DGAT2L6
RAB41
ARSH
MAGEB5
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
PAGE2B
ZCCHC13
LOC389895
UBE2NL
LOC389906
LOC392452
CXXC1P1
GLOD5
FLJ44635
ARL13A
SMIM10L2A
CD99P1
LOC401585
ZNF674-AS1
SLC25A53
LINC00890
XKRX
YY2
MIRLET7F2
MIR106A
MIR188
MIR19B2
MIR221
MIR222
MIR223
MIR92A2
MIR98
VCX3B
FTH1P18
LINC00891
RPS26P11
GLRA4
FAM127C
CT45A3
CT45A5
SPANXN4
PGAM4
FAM47C
UQCRBP1
XRCC6P5
MIR325
MIR374A
SPIN2B
SPANXN1
SPANXN2
SPANXN5
MIR361
MIR384
MIR424
CT45A6
CT45A1
CXorf40B
SSX4B
LINC01420
JPX
MIR448
MIR450A1
MIR362
MIR363
MIR20B
MIR18B
MIR500A
MIR501
MIR502
MIR450A2
MIR503
MIR504
MIR505
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
ZNF674
DANT2
CT47B1
BRDTP1
ZCCHC18
SMIM10
SMIM10L2B
GAGE2B
GAGE13
GAGE12G
LOC645188
MAGEB17
PABPC1L2B
NAP1L6
XAGE1B
CT47A7
MIR545
MIR542
SCARNA23
SNORA11
SNORA35
SNORD96B
MIR421
MIR532
MIR651
MIR652
MIR660
LINC01545
SSX2B
FAM156B
CT47A10
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGED4
MAGEA9B
SPANXB1
CT45A2
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE2A
LOC729609
LINC00106
H2BFXP
MIR766
GAGE12F
GS1-600G8.3
GAGE8
SNORA11C
SNORA11D
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR374B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100126447
LINC00892
CXorf51A
LOC100129291
LINC00684
LINC01546
LINC00633
TEX13C
FGF13-AS1
HSFX2
SUPT20HL1
CXorf49
PRR32
LINC00893
ARMCX4
UBE2DNL
PHKA2-AS1
LOC100132304
GAGE12D
XGY2
LOC100132831
LINC01203
UXT-AS1
SCARNA9L
LINC00894
LOC100287728
LINC00630
CLDN34
MIR513C
MIR1468
MIR1912
MIR1298
MIR320D2
MIR1321
MIR548I4
MIR1277
MIR1911
MIR548F5
MIR1264
FTX
SLC25A5-AS1
MIR548M
MIR513B
MIR764
MIR2114
TRPC5OS
LINC00102
LOC100421746
MIR514B
MIR500B
MIR4328
MIR4329
MTRNR2L10
MIR374C
MIR23C
MIR3937
MIR3672
MIR676
MIR3690
MIR3915
HSFX1
LINC00629
LOC100506790
CT47A12
ARMCX5-GPRASP2
RPL36A-HNRNPH2
PIR-FIGF
MIR548AN
MIR4769
MIR4536-1
MIR4454
MIR4768
MIR1587
MIR548AJ2
MIR4770
MIR548AM
MIR4767
MIR3978
MIR4666B
MIR548AX
PTCHD1-AS
NHS-AS1
SYP-AS1
ZFX-AS1
DLG3-AS1
PHEX-AS1
PRKX-AS1
MED14OS
PPEF1-AS1
EIF1AX-AS1
PCYT1B-AS1
HS6ST2-AS1
DDX26B-AS1
ZNF630-AS1
FRMPD3-AS1
MID1IP1-AS1
ARHGEF9-IT1
LINC00269
TCP11X2
LOC101059915
CHMP1B2P
CT45A7
LINC00850
MAGEA8-AS1
LINC01284
PLS3-AS1
LINC01282
LOC101927476
LOC101927501
LINC01204
LINC01186
LOC101927635
LOC101928128
LOC101928201
LOC101928259
LINC01285
LOC101928335
LOC101928336
PABPC1L2B-AS1
LOC101928358
LOC101928389
LOC101928402
LOC101928437
MIR325HG
LOC101928495
RAP2C-AS1
LOC101928627
LOC101928917
RHOXF1P1
RHOXF1-AS1
RNU6-7
MIR6087
MIR6089
MIR6134
MIR6857
MIR6895
MIR7641-2
MIR6086
MIR892C
MIR6894
MIR8088
LINC01496
KANTR
CT45A10
CT45A9
PABPC5-AS1
GAGE10
RNU6-2
LINC01201
LINC01402
GS1-594A7.3
LINC01456
LOC105373156
LOC105373185
LOC105373300
LOC105373338
XACT
SNORA109

Genes in Wide Peak

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

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
FGFR1OP
GOPC
hsa-mir-2113
ACAT2
AIM1
AMD1
ARG1
BCKDHB
CCNC
CGA
CCR6
CNR1
COL10A1
COL12A1
COX7A2
CTGF
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GPR31
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
ME1
MAP3K4
MAP3K5
AFDN
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLG
PLN
POU3F2
PREP
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
UTRN
EZR
VIP
RNF217-AS1
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
CEP162
ANKRD6
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
HEY2
HEBP2
ORC3
BRD7P3
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
SENP6
TIAM2
FBXL4
LINC01558
FBXO5
RGS17
SNORD50A
PDE7B
FILIP1
SESN1
DLL1
OSTM1
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
MPC1
HECA
COQ3
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
PHF10
QRSL1
VNN3
FAM46A
TMEM30A
ERMARD
ECHDC1
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
SMIM8
ADGRG6
ARFGEF3
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
TMEM181
ZBTB2
BEND3
ABRACL
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
LINC01590
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
ARMT1
FAM184A
ZDHHC14
MANEA
ADGB
FRMD1
AGPAT4-IT1
LINC00574
LCAL1
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
LINC01621
UBE3D
LINC00473
MFSD4B
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
MTFR2
SFT2D1
KLHL32
TMEM200A
NUS1
GINM1
IL22RA2
SLC18B1
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
PM20D2
SRSF12
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
LINC01312
SLC2A12
LINC01010
PNLDC1
RNF217
NKAIN2
CFAP206
BVES-AS1
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
C6orf163
CCDC162P
AK9
NT5DC1
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
PHACTR2-AS1
CEP57L1
PPIL6
LINC01268
FLJ34503
DCBLD1
LOC285762
PACRG-AS1
PRR18
LOC285804
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
GJB7
HMGA1P7
SNHG5
SUMO4
CENPW
SOGA3
LINC00222
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
TCP10L2
LOC401286
LINC00242
LINC01624
GTF2H5
FAM26F
FLJ46906
LINC00602
LOC441178
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
FAM229B
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LINC01625
RPS18P9
LOC645967
RAET1K
AFDN-AS1
SNORA20
SNORA29
SNORD50B
MIR548A2
MIR548B
MIR587
MIR588
MCHR2-AS1
TPI1P3
METTL24
KATNBL1P6
STXBP5-AS1
TMEM242
LOC729603
PACRG-AS3
LIN28B-AS1
HGC6.3
UST-AS1
TRAPPC3L
LOC100129518
LOC100130476
TSTD3
C6orf99
LOC100131532
LINC00271
LOC100132735
CD24
AIRN
LOC100287632
HMGN3-AS1
LOC100289495
NHEG1
MIR1913
MIR2113
MIR1202
LOC100422737
MIR1273C
MIR3144
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
SYNE1-AS1
KIF25-AS1
LOC100506804
SMLR1
LINC01013
TARID
LOC100507406
GVQW2
LOC100507477
LINC01277
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
MIR548AJ1
MIR4459
MIR548AI
MIR4463
MIR4644
MIR548H5
RAET1E-AS1
RPS6KA2-AS1
SYNJ2-IT1
RPS6KA2-IT1
LOC100996634
EZR-AS1
MANEA-AS1
LOC101927314
LOC101927365
LOC101927640
LOC101927686
LOC101927768
LOC101927919
HRAT13
LOC101928140
LOC101928231
LOC101928304
LOC101928429
LOC101928461
LOC101928516
LOC101928540
MEI4
LOC101928661
LINC01526
LOC101928820
LOC101928911
LOC101928936
LOC101929057
CASC6
LOC101929122
PACRG-AS2
LOC101929297
LOC101929420
LOC101929460
LINC01615
LOC101929504
LOC101929523
ARMC2-AS1
MIR7161
MIR7641-2
LOC102723649
LOC102723831
LOC102724053
LOC102724152
TBX18-AS1
LOC102724357
LOC102724511
LOC103352541
NCOA7-AS1
LOC105377879
LINC01611
LOC105377924
LOC105377962
LOC105377967
LOC105377975
LOC105378047
LOC105378052
LOC105378068
LOC105378098
MEAT6
LOC105378123
LOC105378127
LOC105378137
LOC105378146
LUADT1
SNORA98

Genes in Wide Peak

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

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

Genes
NRAS
BCL10
TRIM33
RBM15
ABCA4
ACADM
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DLSTP1
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCA
FUBP1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
PLPPR4
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
LAMTOR5
IFI44
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
ADGRL2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
HAO2
SNX7
DPH5
GPR88
TRMT13
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
KYAT3
TMEM167B
OLFML3
TMIGD3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ADGRL4
MFSD14A
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
ST6GALNAC5
GPR61
REG4
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1-AS1
STRIP1
ZNF697
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
LRRC39
HSD3BP4
DRAM2
PIFO
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
CHIAP2
DENND2C
GBP6
PLPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LINC01140
CCDC18
MYBPHL
BARHL2
NBPF7
MIGA1
NEXN-AS1
GBP7
C1orf146
FAM69A
SLC6A17
C1orf137
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
LINC01555
FLJ31662
LOC440600
LOC440602
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SPATA42
CYMP
LOC643355
LOC643441
LINC00622
LOC646626
SETSIP
ACTG1P4
NBPF6
SCARNA2
SNORD45C
MIR553
LOC729930
LOC729970
LOC729987
MIR942
MIR760
LINC01349
LOC100129046
LOC100129138
LINC01160
LOC100129620
CCDC18-AS1
AP4B1-AS1
MIR320B1
MIR548N
MIR4256
SPATA1
LINC01364
RTCA-AS1
FAM212B-AS1
SLC16A1-AS1
TMEM56-RWDD3
MIR378G
MIR548AC
MIR2682
MIR4423
DPYD-AS1
DPYD-AS2
VAV3-AS1
KCNC4-AS1
KCND3-AS1
HAO2-IT1
KCND3-IT1
LOC100996251
LOC100996263
LOC100996630
LOC100996635
LINC01356
LAMTOR5-AS1
LOC101927342
LOC101927412
LOC101927434
LINC01361
LOC101927560
LOC101927587
LOC101927844
PKN2-AS1
LINC01057
LOC101928098
LOC101928118
LOC101928241
LOC101928270
LOC101928370
LOC101928436
LOC101928476
LOC101928718
HIPK1-AS1
LOC101928977
LOC101928995
LOC101929023
LOC101929099
LOC101929147
MIR7852
MIR7856
MIR7156
LOC102606465
LOC102723661
LINC01461
LINC01397
LINC01307
LINC01525
WARS2-IT1
LOC105378828
LOC105378853
LOC105378933

Genes in Wide Peak

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

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

Genes
DUX4
FRG1
ZFP42
TRIML2
TRIML1
LINC01060
FRG2
DBET
LINC01262
LINC01596

Genes in Wide Peak

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

Table S34. 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
MIR3118-1
MIR3156-3
MIR8069-1
LOC102724188

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
PTPRD
TMEM261
PTPRD-AS1
PTPRD-AS2
LOC105375972

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p24.1.

Table S36. 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 5q15.

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

Genes
APC
CD74
IL6ST
PDGFRB
PIK3R1
hsa-mir-886
hsa-mir-1244-2
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BTF3
CAMK4
CAMK2A
CAMLG
CAST
CCNB1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
CTNNA1
DMXL1
DHFR
DIAPH1
DPYSL3
SLC26A2
HBEGF
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
FAT2
FBN2
FER
FGF1
FOXD1
GDF9
GFRA3
GLRA1
GLRX
GM2A
GPX3
NR3C1
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HMGCR
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL9
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNN2
KIF2A
TNPO1
LECT2
LMNB1
LNPEP
LOX
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFA2
NDUFS4
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PURA
RAD17
RASA1
RASGRF2
RPS14
RPS23
SKP1
SLC6A7
SLC12A2
SLC22A4
SLC22A5
SMN1
SMN2
SNX2
SPARC
SPINK1
SPOCK1
SRP19
TAF7
TAF9
TBCA
TCF7
TCOF1
NR2F1
TGFBI
THBS4
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PLPP1
PDE8B
EIF4EBP3
PCDHGB4
CDC23
HDAC3
P4HA2
HSPB3
ATG12
NREP
RAB9BP1
HOMER1
MYOT
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
TTC37
PCDHGA8
PCDHA9
ZFYVE16
MATR3
KIAA0141
JAKMIP2
PJA2
DDX46
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
APBB3
CCNO
TNIP1
NSA2
FST
POLR3G
PLK2
IQGAP2
SEC24A
MRPS30
BRD8
TCERG1
HNRNPA0
SPINK5
SMA4
SMA5
ESM1
KIF3A
ADAMTS6
SYNPO
RHOBTB3
ABLIM3
ELL2
SV2C
HMGXB3
ARHGAP26
FSTL4
MRPS27
SEPT8
PPIP5K2
ACSL6
JADE2
PPWD1
HARS2
OTP
SKIV2L2
SSBP2
BHMT2
TNFAIP8
PART1
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
FBXL21
KLHL3
SNORD63
SNORA74A
PKD2L2
UQCRQ
AFF4
IL17B
DIMT1
SLC27A6
SNX24
PCDHB1
DMGDH
TMED7
ISOC1
SAR1B
DCTN4
IPO11
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
LARS
CXXC5
RAPGEF6
ERAP1
KDM3B
PHAX
PELO
RBM27
DHX29
EPB41L4A-AS2
DDX4
SGTB
ARL15
PCDHB18P
PCDHB17P
ZCCHC10
GIN1
WDR55
ANKHD1
AGGF1
WDR41
LOC55338
TMCO6
TRIM36
RBM22
RIOK2
DEPDC1B
BDP1
ERBIN
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
NLN
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
MCCC2
EPB41L4A
CENPK
ERAP2
ARHGEF28
SIL1
ARAP3
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PCYOX1L
SH3TC2
PARP8
ANKRD55
TXNDC15
MCTP1
PTCD2
ELOVL7
TRAPPC13
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
ADGRV1
PCBD2
UTP15
ZCCHC9
PSD2
SLF1
ZBED3
GFM2
CYSTM1
MEGF10
SPINK7
SPZ1
SMIM3
TSLP
FCHSD1
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
NDUFAF2
ZNF300
MYOZ3
MRPS36
ATP6AP1L
PRDM6
FTMT
FNIP1
SNX18
SLC35A4
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
LEAP2
SCGB3A2
SETD9
IL31RA
EMB
SLCO6A1
PPARGC1B
PRRC1
JMY
ZNF474
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
POC5
GPR151
STARD4
WDR36
ZNF300P1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
DCANP1
SLC38A9
MGC32805
SLC36A2
SPINK13
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
JAKMIP2-AS1
ZMAT2
MARVELD2
ARSK
FAM81B
CCDC112
PRELID2
SH3RF2
PLAC8L1
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
SPATA24
DNAJC18
CCDC125
LINC01554
GAPT
CMYA5
STK32A
LVRN
SLC36A1
LOC255187
ANKRD31
SERINC5
LOC257396
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
SLC36A3
C5orf64
RNF180
SREK1IP1
RGMB
LINC00491
RFESD
CHSY3
TMEM173
FAM170A
C5orf66-AS2
LOC340074
ARSI
LOC340090
ANKRD34B
IRGM
MCIDAS
ACTBL2
FAM174A
MTX3
CATSPER3
HCN1
SLCO4C1
TICAM2
DND1
MAST4
RNF138P1
TEX43
LOC389332
PROB1
C5orf46
ARHGEF37
RGS7BP
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
MIR9-2
SPINK14
FLJ31104
LOC441081
LOC441086
CRSP8P
NR2F1-AS1
C5orf56
IGIP
GPX8
MIR378A
TIFAB
RGMB-AS1
LOC553103
MIR449A
CTXN3
ECSCR
LOC642366
TMEM232
SMIM15
GRXCR2
SPINK9
ARL14EPL
LOC644285
LOC644762
LINC01184
LOC644936
CCNI2
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR449B
MIR581
MIR582
MIR583
MIR584
SNHG4
CARMN
GTF2H2C
LINC00992
SERF1B
CCDC192
MEIKIN
ZBED3-AS1
SCAMP1-AS1
ANKDD1B
LOC729080
GTF2H2C_2
LOC731157
GUSBP9
VTRNA2-1
MIR874
KIAA1024L
ARRDC3-AS1
LOC100130172
LRRC70
CKMT2-AS1
FAM159B
LOC100133050
LOC100287592
LOC100289230
LOC100289673
MIR1289-2
MIR548F3
MIR1244-1
MIR548P
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR1244-2
MIR4280
MTRNR2L2
MIR3607
MIR3655
MIR3660
MIR3936
MIR3661
LINC01024
LOC100505658
STARD4-AS1
HNCAT21
LOC100505841
LOC100505878
TMEM161B-AS1
LUCAT1
LOC100506526
OCLN
MIR4804
MIR4633
MIR4461
MIR4459
MIR4454
MIR3977
MIR4460
MIR548AE2
MIR4803
SPRY4-IT1
LOC100652758
LINC01023
MIR5197
MIR5687
MIR5692C1
MIR5706
LINC00492
P4HA2-AS1
NREP-AS1
ARHGAP26-AS1
PPP2R2B-IT1
ARHGAP26-IT1
C5orf66
LINCR-0003
IPO11-LRRC70
LOC101926905
LOC101926941
LOC101926975
LOC101927023
LOC101927059
LOC101927078
CTB-113P19.1
LOC101927100
CTB-12O2.1
LINC01470
LOC101927190
SEMA6A-AS1
HRAT56
LOC101927357
LOC101927379
LOC101927421
LOC101927460
LOC101927488
TH2LCRR
LOC101927934
C5orf66-AS1
C5orf67
LOC101928505
LOC101928539
LOC101928569
LOC101928600
CTC-436P18.1
LOC101928651
LOC101928769
LOC101928794
LOC101928858
LOC101928885
LOC101928924
LINC01333
LOC101929109
LOC101929154
CTD-2201I18.1
LOC101929380
MEF2C-AS1
LINC01339
LOC101929696
LOC101929710
LOC101929719
AK6
MIR6499
MIR6830
MIR6831
LOC102467080
LOC102467081
LOC102467147
LOC102467212
LOC102467213
LOC102467214
LOC102467216
LOC102467217
LOC102467223
LOC102467224
LOC102467225
LOC102467226
LOC102467655
LOC102477328
LOC102503427
LINC01335
RASGRF2-AS1
LINC01338
LOC102546226
LINC01340
LOC102546228
LOC102546229
LOC102546294
LOC102546298
LOC102723557
LOC102724392
CTD-2151A2.1
ADAMTS19-AS1
LINC01337
LINC01170
LINC01331
LINC01336
LINC01033
LINC01386
LOC105379030
LOC105379054
LOC105379143
LOC105379176
LOC105379183
LOC105379192
LOC105379194
LINC01455
WSPAR
GRPEL2-AS1
TRPC7-AS2

Genes in Wide Peak

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

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

Genes
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
SAMM50
ATXN10
FAM19A5
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
PRR34
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
ALG12
CRELD2
ADM2
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LMF2
PHF21B
KLHDC7B
PNPLA5
PRR34-AS1
CDPF1
GTSE1-AS1
LOC284930
LOC284933
RPL23AP82
C22orf34
CHKB-CPT1B
LINC00207
MIRLET7BHG
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
LINC00229
DENND6B
PIM3
ODF3B
PRR5-ARHGAP8
TBC1D22A-AS1
SYCE3
LOC730668
LINC01310
CHKB-AS1
LINC00899
MIR1249
MIR3201
MIR3619
MIR3667
NUP50-AS1
LINC01589
MIR4763
MIR4762
MIR4535
LOC101927526
LL22NC03-75H12.2
MIR6821
LOC105373100

Genes in Wide Peak

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

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

Genes
ALDH2
ATF1
BCL7A
BTG1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
HMGA2
WIF1
ZNF384
hsa-mir-616
hsa-mir-1244-3
A2M
A2MP1
ACACB
ACADS
ASIC1
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ARL1
ART4
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
SCARB1
CD63
CD69
CDK2
CDKN1B
CHD4
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CREBL2
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
DDX11
ATN1
EPYC
DTX1
DUSP6
PHC1
EIF2B1
EIF4B
CELA1
ELK3
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GRIN2B
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTA4H
LTBR
LUM
LYZ
M6PR
MARS
METTL1
KITLG
MGP
MGST1
MIP
MMP17
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NDUFA9
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
POU6F1
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAB1
PRKAG1
PRPH
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAN
RAP1B
RARG
RBMS2
RDH5
RECQL
RFC5
RFX4
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SNRPF
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
SYT1
TAC3
TARBP2
TBX5
TBX3
HNF1A
TDG
TEAD4
TMBIM6
TFCP2
TSPAN8
TMPO
TNFRSF1A
TPI1
NR2C1
HSP90B1
TULP3
TXNRD1
UBC
UBE2N
UNG
VDR
VWF
WNT1
WNT10B
ZNF10
ZNF26
ZNF84
ZNF140
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
KMT2D
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
DYRK2
PPFIBP1
PPFIA2
YBX3
LGR5
MAPKAPK5
DENR
RDH16
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1A
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
GPRC5A
KRT75
SCAF11
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
TESPA1
C2CD5
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
CLEC2B
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
RNF41
MPHOSPH9
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
P3H3
DCTN2
AKAP3
CCT2
SLCO1B1
RAD51AP1
CAMKK2
AVIL
PTGES3
KLRA1P
ZNF268
FRS2
TSPAN9
TRAFD1
OS9
TMED2
ERP29
CKAP4
GCN1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
PHLDA1
R3HDM2
MLXIP
RPH3A
KLRK1
P2RX2
RAB21
STK38L
FBXO21
FAIM2
MON2
SETD1B
UHRF1BP1L
ERC1
DDN
ANKLE2
NEMP1
CUX2
KIAA1033
TBC1D30
ESYT1
TNS2
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
ABCB9
CBX5
ISCU
RIMBP2
ANP32D
ATP6V0A2
SMUG1
LEMD3
CORO1C
GABARAPL1
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
FBXW8
GALNT8
HSPB8
OR7E47P
SNORD59A
RNU4-2
RNU4-1
GLS2
HCAR1
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CEP83
IRAK4
ING4
GPN3
DDX47
GLTP
MRPL51
CLEC1B
CLEC1A
MAPKAPK5-AS1
C1RL
ERGIC2
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TM7SF3
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
MAGOHB
SLC6A15
FAM90A1
RIC8B
KIAA1551
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
CAND1
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
ARNTL2
CHPT1
PARP11
ANO2
C12orf4
TIGAR
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHL42
PITPNM2
DIP2B
FAM234B
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
ATG101
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
NABP2
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
RPAP3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
FLJ13224
TCTN2
PLBD1
PYROXD1
NANOG
DNAJC22
NAA25
SLC8B1
ADAMTS20
CEP290
RNF34
CCDC92
MTERF2
PUS1
ACAD10
SPX
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
RHNO1
NRIP2
INHBE
RBP5
TMTC1
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
METTL25
TMEM117
TCHP
COQ5
LLPH
PYM1
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
CRACR2A
TUBA1C
ZC3H10
ORAI1
RNFT2
FAM222A
ALG10
SPRYD3
RITA1
MFSD5
FAM222A-AS1
COX14
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
TMEM263
FMNL3
CERS5
C12orf29
ATP23
PCED1B
C12orf65
TMEM132C
BICDL1
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
TMEM132B
OSBPL8
ARHGEF25
C12orf56
IQCD
LINC01257
AGAP2
DCD
RAB3IP
BORCS5
MUCL1
DEPDC4
LRRK2
CCDC38
TMEM52B
FAM186A
C12orf45
OR2AP1
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
HIST4H4
ERP27
FGD4
AEBP2
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
BRI3BP
KRT72
PRICKLE1
AMDHD1
SLC2A14
BCDIN3D
ALG10B
GLIPR1L2
RFLNA
ZNF664
LINC00477
ETFRF1
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
SOCS2-AS1
CEP83-AS1
KRT80
CFAP54
A2ML1
A2M-AS1
C12orf66
C12orf60
FBXL14
RAD9B
FAM109A
LINC00934
KRT19P2
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
LMNTD1
DENND5B
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
CLEC4C
DSTNP2
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
MYRFL
PLBD2
FAM71C
RMST
CCER1
PIANP
DCP1B
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
LINC00612
TTC41P
MSRB3
ETFBKMT
LRRC43
OR6C74
OR6C3
TCP11L2
LINC00935
TBX5-AS1
LINC01619
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
POC1B
OTOGL
C1RL-AS1
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
LOC283352
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
ADGRD1
MORN3
TRHDE-AS1
C12orf80
LINC00592
LINC01465
DPY19L2
CLEC9A
LINC01559
GAS2L3
LINC00485
LOC283440
MYO1H
HECTD4
KSR2
GATC
HNF1A-AS1
C12orf40
MUC19
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
LINC00936
C1QL4
TMEM119
KRT79
LOC338797
LINC01089
C12orf74
FAM19A2
LINC01252
SLCO1B7
SMCO2
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
PTPRQ
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
RPL13AP20
REP15
CCDC184
C12orf75
CFAP73
TMEM233
KMT5A
LINC00944
LINC00937
OR6C1
OR6C75
OR6C76
OR6C70
LOC400002
LINC00938
LOC400043
FLJ41278
MKRN9P
C12orf76
LINC00939
FLJ37505
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
MIR26A2
LOC414300
LINC00615
IQSEC3
ZNF705A
FAM66C
DDX12P
SMCO3
H3F3C
DBX2
FLJ12825
TMEM198B
PLEKHG7
LOC440117
FZD10-AS1
TSPAN11
OR9K2
MIR148B
MIR331
EID3
LOH12CR2
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC574538
HIGD1C
POU5F1P3
LOC642846
MAP1LC3B2
LOC643339
LOC643711
LOC643770
GLYCAM1
LOC645177
LOC645485
ANHX
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA2C
SNORA49
SNORA53
CD27-AS1
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
MIR616
MIR617
MIR618
MIR619
MIR620
LOC728084
C12orf73
SKP1P2
LOC728739
C12orf71
SLC15A5
MRS2P2
LOC100049716
HOTAIR
MIR920
KRT73-AS1
TMPO-AS1
LOC100128554
THCAT155
SMIM10L1
LOC100129940
LOC100130075
LOC100130238
AGAP2-AS1
LINC01405
USP30-AS1
PGAM1P5
RNU7-1
LOC100190940
PCED1B-AS1
LOC100240734
LOC100240735
LINC00940
BCDIN3D-AS1
MANSC4
LINC00941
LINC00173
LOC100287944
LOC100288798
ZNF605
LINC00942
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1302-1
MIR1178
MIR1244-1
MIR1251
LOC100335030
SNORA70G
MIR1244-3
MIR1244-2
MIR4302
MIR4303
MIR4304
KLRF2
LINC00987
MIR3685
MIR3649
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3657
MIR3913-1
MIR3908
LOC100505978
LOC100506125
LOC100506159
LOC100506314
LOC100506393
RASSF8-AS1
LINC01234
LOC100506551
LOC100506606
PXN-AS1
DDX11-AS1
NRAV
LOC100506691
LOC100506844
LOC100506869
LRCOL1
LOC100507065
CLIP1-AS1
LOC100507091
LOC100507175
LOC100507195
LINC00943
LOC100507250
LOC100507377
LOC100507424
BLOC1S1-RDH5
POC1B-GALNT4
KLRC4-KLRK1
ZNF664-FAM101A
PRH1-PRR4
MIR4699
MIR4498
MIR4496
MIR4701
MIR3974
MIR4495
MIR4419B
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4494
MIR4698
CACNA1C-AS1
LOC100652999
MIR5188
MIR5700
MIR548AQ
LINC00507
RERG-AS1
CACNA1C-AS4
CACNA1C-AS2
DENND5B-AS1
HOXC-AS1
HOXC-AS2
HOXC-AS3
HOXC13-AS
CACNA1C-IT2
CACNA1C-IT3
IFNG-AS1
LOC100996671
LOC100996679
OVCH1-AS1
ZNF891
LOC101593348
LOC101927038
LOC101927058
LOC101927267
LOC101927292
LOC101927318
LOC101927415
LOC101927464
LOC101927583
LOC101927592
LOC101927616
LOC101927637
LOC101927653
LOC101927694
LOC101927735
LOC101927901
LOC101927905
LINC01479
LOC101928002
LOC101928030
LINC01481
LOC101928100
LOC101928137
LINC01486
LOC101928162
TESC-AS1
PLBD1-AS1
LINC01489
LOC101928416
LINC01490
LOC101928441
LOC101928449
LOC101928471
LOC101928530
LOC101928597
LOC101928617
ARNTL2-AS1
LOC101928731
LOC101928937
LOC101929058
LOC101929084
CASC18
LOC101929162
LOC101929384
LOC101929549
LOC101929584
LOC101930452
PCBP2-OT1
CISTR
MIR6074
MIR6125
MIR6502
MIR6758
MIR6760
MIR6761
MIR6762
MIR6861
MIR7107
MIR7641-2
MIR7844
MIR6763
MIR6757
MIR6880
MIR7106
MIR6505
MIR6759
MIR8072
MIR7851
THRIL
LOC102723544
LINC01498
LOC102724020
LOC102724050
LOC102724421
LOC102724663
LOC102724933
LLPH-AS1
CCND2-AS1
TMEM5-AS1
LHX5-AS1
LINC00508
LOC105369187
LOC105369595
LOC105369632
LOC105369635
LOC105369691
LOC105369723
LOC105369738
LOC105369739
LOC105369747
LOC105369781
LOC105369785
LOC105369860
LOC105369879
LOC105369891
LOC105369893
LOC105369911
LOC105369920
LOC105369921
LOC105369945
KCCAT198
LOC105369971
LOC105369980
LOC105370014
LOC105370016
LOC105370024
LOC105370068
CRAT8
XLOC_009911
LRP1-AS
LACAT8
SNORD133
SNORA105C
PRH1-TAS2R14
LOC107161159

Genes in Wide Peak

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

Table S40. 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 18q21.31.

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

Genes
BCL2
SS18
MALT1
ZNF521
AQP4
ATP5A1
CDH2
CDH7
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MEP1B
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TAF4B
TCF4
TTR
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
ZNF271P
TXNL4A
MAPRE2
POLI
ADNP2
TRAPPC8
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
RPRD1A
ZNF532
ELP2
ELAC1
ZNF407
CNDP2
CELF4
KIAA1328
KLHL14
KIAA1468
EPG5
GAREM1
CCDC102B
RBFA
PQLC1
FHOD3
CCDC68
ASXL3
NETO1
KATNAL2
CHST9
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
INO80C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
SLC25A52
DSG4
AQP4-AS1
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CFAP53
GTSCR1
DOK6
RNF152
LINC00305
ZNF396
LOC284241
KCTD1
DYNAP
BOD1L2
LINC00907
SIGLEC15
ZADH2
SMIM21
LINC00908
HMSD
LOC284294
LOC339298
CPLX4
CCDC178
ATP9B
OACYLP
LINC01538
LOC400655
LINC00909
C18orf65
LINC00683
LOC400661
MIR122
MIR187
HSBP1L1
WBP11P1
RNF165
C18orf32
KC6
LOC643542
C18orf63
MIR924HG
SKOR2
SCARNA17
SNORA37
PCAT18
TCEB3CL
ZSCAN30
SNORD58C
MIR924
PARD6G-AS1
LOC100131655
LINC01630
MIR302F
MIR1539
MIR4319
MIR4318
MIR4320
MIR3929
LINC01539
LOC100505549
LINC01541
LOC100505797
LOC100505817
LOC100505853
RBFADN
LINC01543
TCEB3CL2
RPL17-C18orf32
MIR4528
MIR3975
MIR4527
MIR4529
MIR3591
MIR4743
MIR4744
DSG2-AS1
MIR5583-2
MIR5011
MIR5583-1
MIR548AV
LINC-ROR
LINC01544
LOC101060542
LOC101927229
LINC01416
LOC101927322
LOC101927481
LOC101927606
LOC101927651
DSCAS
LINC01029
DSG1-AS1
LOC101927809
LINC01477
LINC01478
SLC14A2-AS1
LOC101927989
LOC101928167
MIR8057
LOC102724651
LOC102724913
SNHG22
LOC105372038
LOC105372068
LOC105372069
LOC105372071
TCF4-AS1
LOC105372179
LOC105667213
SNORA108
SNORA111

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.1.

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

Genes
BMPR1A
FGFR2
TLX1
NFKB2
PRF1
PTEN
NCOA4
SUFU
DUX4
hsa-mir-3158-1
ACADSB
ACTA2
ADAM8
ADD3
ADK
ADRA2A
ADRB1
ALOX5
ANK3
ANXA2P3
ANXA7
ANXA11
FAS
ARL3
BNIP3
CAMK2G
CASP7
ENTPD1
CDK1
CHAT
CHUK
ABCC2
COL13A1
COL17A1
COX15
CPN1
CTBP2
CTSLP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNA2
DNTT
DOCK1
DUSP5
ECHS1
EGR2
EIF4EBP2
EMX2
ERCC6
FGF8
GDF2
GDF10
GFRA1
GLUD1
GLUD1P3
GOT1
PRLHR
GPR26
GRK5
GRID1
HABP2
HELLS
HHEX
HK1
HMX2
HNRNPH3
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KCNMA1
KIF11
ABLIM1
LIPA
MAT1A
MBL2
MGMT
MKI67
MSMB
MXI1
NDUFB8
NODAL
NRAP
OAT
P4HA1
PAX2
PCBD1
PDE6C
PGAM1
PITX3
PLAU
PNLIP
PNLIPRP1
PNLIPRP2
PPA1
PPP1R3C
PPP3CB
NPY4R
SRGN
PRKG1
MAPK8
HTRA1
PSAP
PSD
PTPRE
ALDH18A1
RBP3
RBP4
RGR
RGS10
RPL21
RPS24
SCD
SFRP5
SFTPD
FBXW4
SLC18A2
SLC18A3
SLIT1
SNCG
SUPV3L1
TACR2
TAF5
TCF7L2
TECTB
TFAM
TIAL1
TLL2
UBE2D1
UROS
VCL
VDAC2
WNT8B
XPNPEP1
CCDC6
SLC25A16
SHOC2
ADAM12
UTF1
PARG
NDST2
MBL1P
LIPF
EIF3A
GBF1
LDB1
SGPL1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL1
BUB3
DDX21
LGI1
NOLC1
DLG5
GSTO1
CHST3
BAG3
VPS26A
MINPP1
KIF20B
SEC24C
SH3PXD2A
FAM53B
GPRIN2
SLK
SPOCK2
ZNF518A
RHOBTB1
DCLRE1A
FRAT1
PPIF
ACTR1A
SMNDC1
NPM3
MICU1
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
TUBGCP2
PRDX3
ADIRF
VAX1
ATE1
POLR3A
ZWINT
LDB3
SEC23IP
ECD
RAB11FIP2
CPEB3
INPP5F
ZNF365
DKK1
NT5C2
PDCD11
SORCS3
ZSWIM8
WAPL
PPRC1
FAM175B
RRP12
TBC1D12
DNAJC9
DNMBP
CSTF2T
FRAT2
SIRT1
KAT6B
TSPAN15
IFIT5
DPCD
SEC31B
NUDT13
ATRNL1
HERC4
PTPN20
EDRF1
LRIT1
TCTN3
KIF1BP
C10orf12
ANKRD2
CNNM1
MYOF
AP3M1
ANKRD1
GHITM
PALD1
PDCD4
VENTX
R3HCC1L
POLL
CTNNA3
BLNK
A1CF
NRBF2
KCNIP2
CUZD1
CALY
NEUROG3
ASCC1
EXOSC1
MRPS16
CALHM2
CUTC
PLCE1
DUSP13
CHST15
ACSL5
PANK1
CCSER2
EXOC6
FAM35A
DDIT4
CCNJ
MARCH5
ZRANB1
CFAP46
NSMCE4A
DNAJB12
CNNM2
WBP1L
CCDC186
CRTAC1
CEP55
LRRC20
CWF19L1
SLC29A3
RNLS
PI4K2A
H2AFY2
HIF1AN
RUFY2
WDR11
SLF2
CCAR1
OGDHL
DHX32
PPP2R2D
CISD1
TDRD1
DNAJC12
ASAH2
BCCIP
C10orf2
SAR1A
TM9SF3
ENTPD7
ZMIZ1
AS3MT
STAMBPL1
GPAM
SHTN1
FAM160B1
WDFY4
SEMA4G
ARHGAP22
MYOZ1
PLEKHA1
AVPI1
HPSE2
FAM204A
CDH23
LHPP
PBLD
NPFFR1
C10orf54
MMS19
NOC3L
IKZF5
ZDHHC6
PCDH15
CUEDC2
DDX50
FBXL15
OR13A1
C10orf76
HPS6
MMRN2
MFSD13A
MCMBP
SYNPO2L
C10orf95
PLEKHS1
PDZD7
OBFC1
C10orf88
UBTD1
BICC1
TMEM254
HKDC1
CFAP43
TET1
LRRC27
TNKS2
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
SYT15
C10orf11
PCGF6
ARID5B
LOXL4
ZDHHC16
FAM213A
DYDC2
PCGF5
ADGRA1
LZTS2
PHYHIPL
LCOR
NKX6-2
MRPL43
AFAP1L2
PLA2G12B
MYPN
PYROXD2
USMG5
ZNF503
AIFM2
ADO
ATAD1
ARHGAP19
JMJD1C-AS1
KNDC1
ITPRIP
OLMALINC
MCU
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
ZFAND4
OPN4
HOGA1
SORCS1
C10orf71
PRAP1
ZNF511
CHCHD1
MSS51
CFAP70
C10orf90
BTBD16
FAM24A
PSTK
ZNF488
PIK3AP1
MORN4
ZFYVE27
MMP21
COMTD1
FRA10AC1
ANKRD22
SFXN2
PDZD8
AGAP4
BORCS7
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
ANAPC16
PNLIPRP3
SFXN4
CPXM2
ADAMTS14
ACSM6
SAMD8
LIPJ
CFL1P1
TRUB1
FRMPD2
VTI1A
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
CACUL1
USP54
NKX2-3
SLC35G1
CFAP58
FAM170B
C10orf128
FUT11
OIT3
C10orf91
PWWP2B
LINC00858
ANTXRL
EMX2OS
PLPP4
VSTM4
PAOX
FAM24B
TMEM254-AS1
PLAC9
C10orf107
TMEM26
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
TBATA
ATOH7
SLC16A9
FAM13C
MARCH8
REEP3
JMJD1C
ZNF503-AS1
IPMK
FAM21C
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
SGMS1
PIPSL
PGBD3
C10orf53
FUOM
JAKMIP3
STK32C
BLOC1S2
RBM20
PDCD4-AS1
FLJ37201
LINC01553
LOC283038
LOC283045
ZMIZ1-AS1
WDR11-AS1
FAM149B1
FFAR4
KCNK18
ANKRD30BP3
DUPD1
LIPM
CYP26C1
VWA2
NANOS1
LRIT2
HMX3
LRRTM3
NHLRC2
CCDC172
DMBT1P1
FAM21A
SH2D4B
C10orf99
SLC16A12
CC2D2B
ENO4
ARMS2
TEX36
LINC00959
GUCY2GP
NKX1-2
BMS1P5
LBX1-AS1
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
LINC01164
LINC01168
SPRNP1
GOLGA7B
LINC01561
FAM45A
MIR107
C10orf105
C10orf62
AGAP6
GLUD1P7
AGAP12P
C10orf55
FAM35BP
LINC00595
DNAJC9-AS1
FAM35DP
LINC00857
LINC00863
IFIT1B
FRG2B
MIR346
LRRC18
SPRN
MIR146B
MIR202
NPS
SCART1
SNORA19
LOC642361
AGAP9
BMS1P6
HOST2
FAM196A
FAM25A
LIPK
LIPN
LINC00865
LINC00842
FAM25C
DRGX
RPL13AP6
BEND3P3
ANXA8
AGAP7P
ASAH2B
SFTPA1
SNORA12
SNORD98
MIR605
MIR606
MIR607
MIR608
MIR609
ANXA8L1
NUTM2A
NUTM2D
NUTM2A-AS1
LINC00864
PARGP1
ENTPD1-AS1
FAM133CP
HNRNPA1P33
RPL13AP5
FRMPD2B
UNC5B-AS1
RPEL1
AGAP5
BMS1P4
SFTPA2
NUTM2B
LOC729815
POU5F1P5
TLX1NB
MIR936
C10orf131
PLCE1-AS1
ADGRA1-AS1
DLG5-AS1
LOC100130698
ATE1-AS1
ZNF503-AS2
ACTA2-AS1
FAM25BP
LINC00856
FAM25G
KLLN
TEX36-AS1
HECTD2-AS1
DNMBP-AS1
TIMM23
BMS1P21
KCNIP2-AS1
MIR1287
MIR1296
MIR1307
MIR548F1
MIR2110
MIR1254-1
FAS-AS1
MIR548E
FAM21EP
MIR378C
MIR4297
MIR3157
MIR4294
MIR3158-1
MIR4295
MIR3156-1
MIR3158-2
MIR4296
MTRNR2L5
MIR3924
MIR3941
MIR3663
MIR3944
SLIT1-AS1
LINC00866
RPARP-AS1
SH3PXD2A-AS1
CFAP58-AS1
SORCS3-AS1
ADD3-AS1
LINC00867
FAM170B-AS1
C10orf71-AS1
PRKG1-AS1
LINC00844
MRLN
LINC00845
ZSWIM8-AS1
GRID1-AS1
TNKS2-AS1
MARK2P9
BORCS7-ASMT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4676
MIR4678
MIR4682
MIR4482
MIR4484
MIR4681
MIR4685
TIMM23B
LINC00502
ANTXRLP1
CH17-360D5.1
NUTM2B-AS1
LINC00601
FANK1-AS1
SLC16A12-AS1
LINC01375
LOC101926942
PLCE1-AS2
LOC101927278
LINC01475
LINC01163
LINC01514
LOC101927419
LOC101927472
TCERG1L-AS1
LOC101927523
LOC101927549
LINC01166
MIR202HG
LOC101927692
MIR3663HG
FAM53B-AS1
EDRF1-AS1
LINC01468
TMEM26-AS1
LOC101928887
LINC01515
LOC101928961
LOC101928994
PPP3CB-AS1
LOC101929165
LOC101929234
KCNMA1-AS3
KCNMA1-AS2
KCNMA1-AS1
LOC101929574
NRG3-AS1
LINC01519
LOC101929646
LOC101929662
LINC01520
MIR6507
MIR6715B
MIR7152
MIR6715A
MIR7151
LOC102723377
LOC102723439
LOC102723665
LOC102723703
LOC102724323
NEURL1-AS1
LOC102724589
LOC102724593
LOC102724719
LOC103344931
LINC01435
LINC01167
SGMS1-AS1
LOC105378292
LOC105378311
LOC105378330
LOC105378349
LOC105378367
LOC105378385
LOC105378397
XLOC_008559
LOC105378430
LOC105378470
AS-PTPRE
CCEPR
SNORA87
LOC107001062

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.1.

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

Genes
BUB1B
TCF12
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
NBEAP1
BNIP2
CA12
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
SMAD3
SMAD6
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OAZ2
OCA2
PLCB2
PPIB
MAPK6
MAP2K1
MAP2K5
RAB27A
RAD51
RORA
RPL4
RPLP1
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SORD
SPINT1
SRP14
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
UBE3A
MKRN3
SLC30A4
PWAR5
ANP32A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
ALDH1A2
HERC2
HERC1
SNURF
USP8
CCNB2
SLC28A2
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
PIGB
KIF23
IGDCC3
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
USP3
SLC12A6
BCL2L10
PDCD7
FEM1B
RASGRP1
SERF2
DENND4A
SNAPC5
CORO2B
GNB5
ARPP19
CLPX
SLC27A2
GPR176
CHP1
OIP5
ITGA11
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
DAPK2
EID1
NPAP1
HYPK
TMEM87A
RPAP1
GLCE
DKFZP434L187
PYGO1
BLOC1S6
GREM1
RNU6-1
RNU5A-1
RNU5B-1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
RPS27L
NDUFAF1
RSL24D1
NUSAP1
EMC4
RASL12
SPG21
SPTBN5
HACD3
CTDSPL2
KLF13
RAB8B
DUOX1
CSNK1G1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
PARP16
TIPIN
CLN6
ZNF770
ZWILCH
FLJ10038
UACA
HAUS2
RMDN3
DNAJC17
LARP6
MNS1
NOP10
MYO5C
NSMCE3
FAM214A
EMC7
THAP10
PAK6
DTWD1
KNL1
AVEN
ATP10A
GJD2
STARD9
VPS18
IGDCC4
SQRDL
ZNF106
IQCH
RFX7
SPATA5L1
CHAC1
NOX5
ICE2
AAGAB
KATNBL1
SLTM
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
PIF1
SPG11
ELL3
PLEKHO2
POLR2M
VWA9
NIPA2
APH1B
TLN2
FAM96A
C15orf48
MEGF11
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
SNORD107
CALML4
LDHAL6B
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
MTFMT
SLC51B
NIPA1
PLA2G4E
TRIM69
PWAR1
TERB2
LOC145694
C2CD4A
FAM81A
GCOM1
LOC145783
C15orf65
DRAIC
LOC145845
C15orf61
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
FAM227B
CT62
MGC15885
LCTL
UBR1
PATL2
SPESP1
LPCAT4
GOLGA2P11
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
HMGN2P46
SLC24A5
PRTG
LINC00926
EWSAT1
LOC283683
GOLGA6L2
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD115-1
WHAMMP3
GLDN
FMN1
SNORD64
PWAR4
PWARSN
RBPMS2
ANKDD1A
LINC01193
MRPL42P5
USP50
TEX9
IGHV1OR15-1
C15orf52
TNFAIP8L3
C2CD4B
GOLGA8EP
OR4M2
OR4N3P
HERC2P10
KBTBD13
UBAP1L
SKOR1
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR190A
MIR211
LINC00593
NF1P2
GOLGA6L22
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
MIR422A
LINC00929
CKMT1A
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
EIF3J-AS1
CHEK2P2
LOC646214
CXADRP2
PDCD6IPP2
IGHV1OR15-3
REREP3
GOLGA8S
GOLGA8J
GOLGA8T
GOLGA8K
GOLGA8M
HSP90AB4P
SCARNA14
MIR626
MIR627
MIR628
MIR629
ANP32AP1
GOLGA6L6
LOC727924
GOLGA8O
GOLGA6L7P
GOLGA8H
PIN4P1
OIP5-AS1
GOLGA8CP
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-8
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-41
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
GABPB1-AS1
LOC100129973
LOC100130111
USP3-AS1
SRP14-AS1
ANKRD63
LOC100131315
HERC2P7
GOLGA8F
DCAF13P3
GOLGA8DP
JMJD7
PLA2G4B
POTEB2
WHAMMP1
LOC100288637
LOC100289656
MIR1233-1
MIR1272
MIR1266
MIR1268A
MIR1282
NDUFAF4P1
MIR2116
LOC100419583
LOC100422556
MIR3118-3
MIR1233-2
MIR4311
MIR3118-4
MIR3118-2
MIR4312
MIR4310
MIR3942
INAFM2
RAD51-AS1
IQCH-AS1
DPH6-AS1
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4512
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4511
MIR4712
MIR4715
TMCO5B
MYZAP
MIR5701-2
MIR5701-1
SNORD116-30
SNORD115-46
LOC100996255
POTEB
RORA-AS2
GOLGA8R
LOC101927079
LOC101928042
LOC101928134
LOC101928174
LOC101928227
EHD4-AS1
PLA2G4E-AS1
LOC101928414
LINC01491
PIGBOS1
LINC01413
LIPC-AS1
LOC101928725
RORA-AS1
PWRN3
GABRG3-AS1
LOC101928907
LOC101928988
LOC101929076
LOC101929151
THSD4-AS2
THSD4-AS1
RNU6-7
MIR6085
MIR7973-2
MIR8067
MIR7973-1
MIR8063
LINC01169
LOC102723344
LOC102723481
LOC102723493
POTEB3
LOC102725022
RNU6-2
PWRN4
PCAT29
SALRNA3
SALRNA2
LOC105370757
LOC105370792
LOC105370802
LOC105370829
LOC105370941
LOC105370943
BUB1B-PAK6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

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

Genes
CBFA2T3
FANCA
MAF
AFG3L1P
APRT
ZFHX3
GAS8-AS1
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
VPS9D1
KIAA0513
PIEZO1
DHX38
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCO1
TERF2IP
NECAB2
KLHDC4
DEF8
TXNL4B
BANP
RFWD3
ZDHHC7
CENPN
CMC2
JPH3
VAT1L
TLDC1
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
SNAI3-AS1
LINC00311
LDHD
MLKL
ZNF778
ACSF3
LINC00304
HCCAT5
LOC283922
NUDT7
SNAI3
LOC339059
FAM92B
CTU2
C16orf47
PABPN1L
LOC400548
FENDRR
LOC400553
LOC400558
C16orf74
NPIPB15
CTRB2
LOC440390
CLEC18B
SNORD68
LINC00917
VPS9D1-AS1
LOC100129617
LOC100129697
URAHP
SYCE1L
LOC100287036
LOC100289580
MIR1910
MIR3182
LINC01568
LOC100506281
LINC01082
C16orf95
MIR4720
MIR4722
MIR4719
MIR5093
MIR5189
PRCAT47
FAM157C
LINC01081
LOC101927793
LOC101927817
LINC01572
LOC101928035
LOC101928203
LINC01229
LINC01227
LOC101928417
LOC101928446
LOC101928557
LOC101928614
LOC101928659
LOC101928682
LOC101928708
LOC101928737
LOC101928880
MIR6504
MIR6775
MIR7854
MIR8058
MIR6774
MAFTRR
LOC102724084
LOC102724163
LOC102724344
LOC102724467
FOXC2-AS1
LOC105371414
LOC105376772

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
AKT2
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-643
hsa-mir-220c
A1BG
ACTN4
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB3
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL2
KIR2DL3
KIR2DL4
KIR2DS1
KIR2DS3
KIR2DS4
KIR2DS5
KIR3DL1
KIR3DL2
KIR3DS1
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PTGIR
PTPRH
PVR
NECTIN2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
SYMPK
MIA
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2B
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA2
HNRNPUL1
CLASRP
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
SIRT2
CYP2G1P
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
C5AR2
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
PRX
SPTBN4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
CENPBD1P1
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
COQ8B
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
KMT5C
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
TIMM50
SHKBP1
CCDC114
LOC93429
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
C19orf84
SPACA6
ZNF480
ZNF534
ZNF578
ERVV-1
SMIM17
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542P
ZNF582
ZNF583
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
EID2
ZNF780B
ZNF525
SPACA4
NLRP7
CADM4
ADM5
ZNF584
ZSCAN4
NLRP11
TMEM86B
INAFM1
ZNF549
NAPSB
IL4I1
IFNL2
IFNL3
IFNL1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
EMC10
MGC45922
KLK9
SIGLEC17P
SIGLECL1
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
ZNF546
MYPOP
NANOS2
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
DNAAF3
ZNF233
LILRA5
B3GNT8
IGFL1
C19orf68
ZNF773
ZNF582-AS1
CEACAM22P
CEACAM16
BLOC1S3
BHMG1
IGFL3
ZNF808
ZNF888
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ACP7
PINLYP
ZNF818P
ZNF805
ZNF321P
LGALS17A
LOC400706
SIGLEC16
LOC400710
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
CCER2
LOC645553
FAM90A27P
SBK2
RNF225
PSG10P
LGALS7B
PHLDB3
SEC1P
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
CCDC61
CEACAM18
SHISA7
RFPL4AL1
LINC01530
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A12
ZNF667-AS1
LOC100128398
LOC100129083
LOC100129935
SBK3
BSPH1
MZF1-AS1
KIR2DS2
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A10
SNAR-C2
SNAR-C4
SNAR-E
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
ERICH4
SNAR-A14
ERVV-2
EML2-AS1
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
PCAT19
LOC100505585
LOC100505622
NAPA-AS1
LOC100505715
CARD8-AS1
PPP5D1
PTOV1-AS1
DACT3-AS1
GFY
ZNF865
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
MIR5088
NUCB1-AS1
LIPE-AS1
LOC101059948
IFNL4
ZNF350-AS1
LINC01480
LOC101928063
LOC101928295
PTOV1-AS2
LOC101928517
ZNF649-AS1
LOC101928804
LOC101928886
ZIM2-AS1
LOC101930071
SPACA6P-AS
MIR6088
MIR6796
MIR6797
MIR6799
MIR6800
MIR6802
MIR6804
MIR6805
MIR6806
MIR8074
MIR8077
MIR8085
MIR6719
MIR6807
MIR8061
MIR6798
MIR6803
MIR7975
MIR6801
ZNF528-AS1
LENG8-AS1
LOC105372419
LOC105372440
LOC105372441
LOC105372444
LOC105372476
LOC105372483
LOC105447645
PLA2G4C-AS1
GLTSCR2-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p11.2.

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

Genes
PRDM1
CCND3
DAXX
FANCE
HMGA1
IRF4
MYB
PIM1
POU5F1
TRIM27
ROS1
TNFAIP3
DEK
TFEB
HIST1H4I
FGFR1OP
GOPC
hsa-mir-2113
ABCF1
ACAT2
CRISP1
AGER
AIF1
AIM1
AMD1
ARG1
ATP6V1G2
ADGRB3
BAK1
BCKDHB
CFB
BMP5
BMP6
DST
BPHL
BTN1A1
BYSL
C2
C4A
C4B
DDR1
RUNX2
CCNC
CDC5L
CDKN1A
CDSN
CGA
CLIC1
CLPS
CCR6
CNR1
COL9A1
COL10A1
COL11A2
COL12A1
COL19A1
COX7A2
ATF6B
MAPK14
CSNK2B
CTGF
CYP21A2
CYP21A1P
DNAH8
DXO
DSP
E2F3
EDN1
EEF1A1
SERPINB1
SLC29A1
EPB41L2
EPHA7
EYA4
ESR1
F13A1
FABP7
FKBP5
FOXF2
FOXC1
FOXO3
FRK
FUCA2
FYN
GABBR1
GABRR1
GABRR2
GCNT2
GJA1
GCLC
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPR6
GPR31
GPX5
GRIK2
GRM1
GRM4
GSTA1
GSTA2
GSTA3
GSTA4
GTF2H4
GUCA1A
GUCA1B
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HCRTR2
HDAC2
HFE
HIVEP1
HIVEP2
HLA-A
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSF2
HSPA1A
HSPA1B
HSPA1L
HSP90AB1
HTR1B
HTR1E
ID4
IFNGR1
IGF2R
IL17A
IMPG1
ITPR3
JARID2
KIFC1
KIF25
KPNA5
LAMA2
LAMA4
LPA
LTA
LTB
MARCKS
MAK
MAN1A1
MAS1
MCM3
MDFI
ME1
MEA1
MAP3K4
MAP3K5
MEP1A
MICB
MLN
AFDN
MOCS1
MOG
MSH5
MUT
MYO6
RPL10A
NEDD9
NEU1
NFKBIE
NFKBIL1
NFYA
NMBR
NQO2
NOTCH4
NT5E
OPRM1
PARK2
PBX2
PCMT1
PDCD2
ENPP1
ENPP3
PEX6
PEX7
PGC
PGK2
PGM3
PHF1
SERPINB6
SERPINB9
PKHD1
PLAGL1
PLG
PLN
POLH
POU3F2
PPARD
PPP1R10
PPP2R5D
PREP
PRIM2
PKIB
MAPK13
PRL
PSMB1
PSMB8
PSMB9
PTK7
PTPRK
RGL2
PRPH2
REV3L
RHAG
RING1
BRD2
RNF5
RPS6KA2
RPS10
RPS12
RPS18
RREB1
RXRB
VPS52
ATXN1
SRSF3
SGK1
SIM1
SKIV2L
SLC17A1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SNRPC
SOD2
SOX4
SRF
SRPK1
SSR1
ELOVL4
T
TAF11
MAP3K7
TAP1
TAP2
TAPBP
TBCC
TBP
TCF19
TCF21
TCP1
TCP10
TCP11
TCTE3
PPP1R11
DYNLT1
TEAD3
TFAP2A
TFAP2B
THBS2
NR2E1
TNF
TNXA
TNXB
TPBG
TPD52L1
TPMT
CRISP2
TSPYL1
TTK
TUBB2A
TULP1
UTRN
VARS
VEGFA
EZR
VIP
ZNF76
ZNF165
TRIM26
ZNF184
ZSCAN26
ZKSCAN8
ZSCAN9
ZNF204P
PTP4A1
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
OR2H2
NELFE
LST1
PLA2G7
RNF217-AS1
EPM2A
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
STX7
CMAHP
DHX16
SUPT3H
PEX3
GCM1
DDO
RNASET2
KCNK5
STX11
B3GALT4
SNX3
RNGTT
RIPK1
CD164
SYNGAP1
WISP3
STK19
IER3
SYNJ2
VNN2
VNN1
PRPF4B
WASF1
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
TAAR5
MAP7
TBX18
LATS1
GCM2
WDR46
ZBTB22
TAAR2
TAAR3
CD83
HMGN3
PPT2
CDYL
NCR2
MED23
QKI
LY86
FHL5
AKAP7
ATG5
MED20
SLC25A27
TBPL1
EEF1E1
BAG2
POLR1C
MAD2L1BP
WTAP
AKAP12
MDC1
TRAM2
KIAA0408
PHACTR2
FAM65B
ZSCAN12
BCLAF1
CUL7
ZBTB24
KIAA0319
SNAP91
FIG4
NUP153
CASP8AP2
RANBP9
SLC17A4
UST
TRIM10
FLOT1
RCAN2
SLC17A2
HCG9
PRSS16
CRISP3
TRDN
CITED2
BTN3A3
BTN2A2
ECI2
PFDN6
HMGN4
TRIM38
CAP2
SYNCRIP
UBD
AGPAT1
SLC35A1
SCGN
DNPH1
C6orf10
FARS2
FUT9
CNPY3
TRAF3IP2
HBS1L
SLC17A3
RPP40
FRS3
PDE10A
SLC22A7
HCP5
EHMT2
SMPDL3A
APOBEC2
PNRC1
ASCC3
RAB32
TRIM31
KATNA1
BTN3A2
BTN3A1
BTN2A1
CAPN11
BVES
NUDT3
SEC63
NRM
STK38
SCAF8
CEP162
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
CMTR1
CDK19
CUL9
TAB2
MDN1
TSPYL4
ANKS1A
UBR2
SASH1
SYNE1
UFL1
SIRT5
PHF3
HEY2
DAAM2
GLTSCR1L
DDAH2
HEBP2
ORC3
CD2AP
BRD7P3
MTCH1
ZNF318
SPDEF
MTO1
ASF1A
YIPF3
USP49
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
OR2B6
TIAM2
FBXL4
LINC01558
FAM50B
FBXO9
FBXO5
SLC17A5
OR12D2
OR11A1
RGS17
OR2W1
OR2J2
OR2H1
SNORD52
SNORD50A
SNORD48
PDE7B
FILIP1
BRPF3
GNMT
TNFRSF21
SESN1
TINAG
DLL1
OSTM1
MRPS18B
TMEM14A
MRPL18
NDUFAF4
C6orf15
MYLIP
ABT1
DSE
PRICKLE4
PACSIN1
ZNRD1
CLDN20
NOX3
DEF6
C6orf48
SLC35B3
HDDC2
GMNN
MRPL2
TFB1M
CYB5R4
TUBE1
C6orf203
TBC1D7
NRN1
CYP39A1
CDC40
RWDD1
AIG1
NOL7
SNX9
FAM8A1
UBE2J1
DCDC2
ETV7
TMEM14C
VTA1
LGSN
TDP2
CUTA
PPIL1
MPC1
HECA
RAB23
COQ3
CLIC5
IL20RA
TREM2
TREM1
UNC93A
HCG4
GFOD1
HMGCLL1
MTRF1L
CCHCR1
GTPBP2
BTN2A3P
AHI1
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
MRPS18A
MRPS10
LRRC1
PHF10
QRSL1
VNN3
TMEM63B
DDX43
FAM46A
CARMIL1
TBC1D22B
TMEM30A
EXOC2
SAYSD1
ERMARD
LMBRD1
TRERF1
ACOT13
ECHDC1
APOM
BTNL2
KCNQ5
TRIM39
AGPAT4
WRNIP1
DUSP22
TULP4
RARS2
HYMAI
PDSS2
LYRM4
SMIM8
VARS2
ADGRG6
ARFGEF3
NHSL1
LYRM2
SNX14
MRS2
PLEKHG1
ARID1B
LRFN2
AARS2
XPO5
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
CPNE5
LSM2
C6orf47
LY6G5B
ABRACL
RRAGD
LY6G6D
ENPP5
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
ZFAND3
SLC22A23
LINC01590
BLOC1S5
MCUR1
GPSM3
FKBPL
KIF13A
PERP
SMOC2
POPDC3
ZSCAN31
ALDH8A1
C6orf106
MICAL1
MRPL14
DLK2
LY6G6E
ULBP3
OR2A4
ARMT1
OGFRL1
FAM184A
ZDHHC14
ZNF322
MANEA
ADGB
TREML2
RPP21
LINC00472
ATAT1
FRMD1
AGPAT4-IT1
LINC00574
LCAL1
CCDC170
MYCT1
ZKSCAN3
ULBP2
ULBP1
ZSCAN16
LPAL2
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRR3
KHDC1
ZNRD1ASP
PRRT1
EGFL8
HCG4B
GPR63
TXNDC5
COL21A1
C6orf62
OR5V1
OR2B2
PPP1R14C
OR12D3
SPACA1
RNF146
TMEM14B
SF3B5
TAAR8
SH3BGRL2
RIOK1
TFAP2D
KCNK16
RSPH3
TTLL2
DTNBP1
ARMC2
FBXO30
RPF2
UQCC2
L3MBTL3
FAM120B
MCHR2
PGBD1
FAXC
FNDC1
TTBK1
GJA10
RTN4IP1
ADTRP
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
HIST1H2AH
HIST1H2BK
PPIL4
PAQR8
SLC22A16
RRP36
LINC01621
KCNK17
ABCC10
TRIM15
KLC4
UBE3D
MLIP
LINC00473
MFSD4B
TJAP1
ARHGAP18
POM121L2
SYTL3
FOXQ1
GTF3C6
MRAP2
RWDD2A
IL17F
MTFR2
SFT2D1
EFHC1
BTBD9
KLHL32
TMEM200A
ZBED9
MB21D1
FOXP4
KLHDC3
NUS1
GINM1
SLC26A8
IL22RA2
MAS1L
SLC18B1
SLC16A10
IP6K3
TAGAP
RN7SK
TAF8
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
SDHAF4
CD109
RAET1E
PM20D2
SRSF12
C6orf141
HUS1B
TRIM40
DPCR1
NRSN1
LOC153910
ZC2HC1B
SNRNP48
CNKSR3
RAET1L
SAMD3
LINC01312
SLC2A12
LINC01010
MBOAT1
HDGFL1
PNLDC1
RNF217
NKAIN2
KHDC3L
CFAP206
LINC01600
BVES-AS1
LOC154449
CCDC167
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
PSORS1C1
PSORS1C2
PPP1R18
PTCRA
OSTCP1
TCTE1
KHDRBS2
TRIM39-RPP21
TUBB
C6orf163
PIP5K1P1
CCDC162P
AK9
NT5DC1
FAM26D
ZUFSP
FAM162B
TBC1D32
BEND6
GSTA5
OPN5
ADGRF4
ADGRF5
TDRD6
SPATS1
C6orf223
RSPH9
LRRC73
TREML5P
ADCY10P1
OARD1
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
SMIM13
SYCP2L
LINC00518
PXDC1
SERPINB9P1
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
ADGRF2
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
TOB2P1
FAM217A
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
HCG27
TMEM244
MMS22L
WDR27
FAM26E
MCM9
RNF144B
HIST1H2BA
SCML4
GPX6
SHPRH
NCR3
LY6G6F
MDGA1
ADGRF1
ZNF311
LINC00326
PHACTR2-AS1
CEP57L1
PPIL6
LINC01268
FLJ34503
DCBLD1
LOC285762
LOC285766
LINC01622
LY86-AS1
CAGE1
PACRG-AS1
PRR18
LOC285804
LOC285819
HLA-F-AS1
HCG22
LOC285847
PNPLA1
TREML4
RPL7L1
TAAR6
SLC35D3
ZC3H12D
MYLK4
DPPA5
IFITM4P
CLPSL1
TREML1
TREML3P
RSPH4A
ECT2L
EYS
ZNF391
ZFP57
TUBB2B
SLC35B2
C6orf52
NUP43
HCG26
C6orf58
RAET1G
KAAG1
GUSBP4
GJB7
NHLRC1
ZKSCAN4
GUSBP2
LINC00533
HMGA1P7
SNHG5
SUMO4
CENPW
SOGA3
LINC00222
CEP85L
C6orf120
VN1R10P
HIST1H2APS1
THEMIS
PSMG4
SFTA2
CLPSL2
C6orf222
GLYATL3
GFRAL
LIN28B
SAMD5
IYD
MUC21
LINC01011
HTATSF1P2
STMND1
CASC15
LINC01623
LINC00243
MCCD1
SAPCD1
LINC00336
RAB44
LINC00951
LOC401261
CRIP3
TRAM2-AS1
KLHL31
DKFZp451B082
TCP10L2
LOC401286
LINC00242
LINC01624
DEFB133
C6orf201
GTF2H5
ERVFRD-1
MIR206
MIR219A1
MIR30A
MIR30C2
HCG14
HCG23
HCG25
HCG16
HCG24
HCG18
HCG17
LINC00266-3
C6orf226
TMEM151B
LOC441155
OOEP
FAM26F
FLJ46906
LINC00602
LOC441178
OR2B3
OR2J3
OR14J1
OR10C1
ATP6V0CP3
PTCHD4
SLC25A51P1
GSTM2P1
RFPL4B
MIR133B
GGNBP1
HCG11
KU-MEL-3
LOC554223
SNORD101
SNORD100
SNORA33
FAM229B
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LINC01625
RPS18P9
LOC645967
RAET1K
C6orf132
RPS16P5
PPP1R3G
ZNF192P1
AFDN-AS1
SNORA20
SNORA29
SNORA38
SNORD50B
SNORD32B
SNORD84
SNORD117
MIR548A1
MIR548A2
MIR548B
MIR586
MIR587
MIR588
MCHR2-AS1
TPI1P3
METTL24
HULC
KATNBL1P6
NBAT1
STXBP5-AS1
TMEM242
LINC01556
LOC729603
PACRG-AS3
LOC730101
GSTA7P
TDRG1
LIN28B-AS1
TMEM170B
SCARNA27
MIR877
HGC6.3
UST-AS1
TRAPPC3L
KHDC1L
ZSCAN16-AS1
LYRM4-AS1
LOC100129518
LOC100129636
TFAP2A-AS1
LOC100130357
LOC100130476
PSORS1C3
TSTD3
C6orf99
LOC100131047
LOC100131289
LOC100131532
LINC00271
LINC01512
LOC100132735
LINC00240
CD24
TOMM6
LOC100270746
AIRN
LOC100287632
ANKRD66
HMGN3-AS1
LOC100289495
LOC100294145
NHEG1
MIR1275
MIR1913
MIR2113
MIR1236
MIR1202
LOC100422737
MIR1273C
MIR548U
MIR3143
MIR3144
MIR3145
MIR4282
MTRNR2L9
MIR3918
MIR3939
MIR3934
MIR3668
MIR3662
MIR3925
MIR3692
MIR3691
SYNE1-AS1
LOC100505530
LOC100505635
KIF25-AS1
LOC100506188
LOC100506207
ELOVL2-AS1
JARID2-AS1
LOC100506804
LOC100506885
LINC01012
LOC100507194
SMLR1
LINC01013
TARID
LINC01015
KCNQ5-IT1
HCG8
LOC100507406
MICA
GVQW2
PSMB8-AS1
LOC100507477
LINC01277
LOC100507506
LOC100507547
LOC100507557
LINC01016
MUC22
GMDS-AS1
CAHM
BLOC1S5-TXNDC5
EEF1E1-BLOC1S5
RPS10-NUDT3
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4464
MIR4647
MIR4466
MIR4643
MIR4641
MIR4465
MIR548AJ1
MIR3135B
MIR4646
MIR4459
MIR4640
MIR4639
MIR4645
MIR548AI
MIR4642
MIR4463
MIR4462
MIR4644
MIR548H5
RAET1E-AS1
MIR5689
MIR5004
MIR5683
MIR5690
MIR5685
RPS6KA2-AS1
KCNQ5-AS1
MLIP-IT1
SYNJ2-IT1
RPS6KA2-IT1
LINC00581
LOC100996634
FOXP4-AS1
LINCMD1
PANDAR
EZR-AS1
LOC101926898
LOC101926915
LOC101926934
LOC101926962
LOC101927020
LOC101927048
LOC101927082
LOC101927136
LINC01564
LOC101927189
LOC101927211
MANEA-AS1
LOC101927314
LOC101927365
LOC101927640
LOC101927686
LOC101927691
FOXCUT
LOC101927730
LOC101927759
LOC101927768
LOC101927919
LOC101927950
LOC101927972
HRAT13
LOC101928140
LOC101928191
LOC101928231
LOC101928253
LOC101928280
LOC101928304
LOC101928307
EVADR
LOC101928429
LOC101928433
LOC101928461
LOC101928489
LOC101928491
LOC101928516
LOC101928519
LOC101928540
MEI4
C6orf229
LOC101928661
LOC101928663
LINC01526
LOC101928820
LOC101928911
LOC101928936
LOC101929006
LOC101929057
CASC6
LOC101929122
LOC101929163
LOC101929188
PACRG-AS2
LOC101929243
LOC101929297
LOC101929420
LOC101929460
LINC01615
LOC101929504
LOC101929523
LOC101929555
LOC101929705
ARMC2-AS1
LOC101929726
LOC101930010
C2-AS1
LINC01108
MIR6833
MIR6834
MIR6835
MIR6891
MIR7111
MIR7161
MIR7641-2
MIR6721
MIR6720
MIR6832
MIR6780B
MIR6873
MIR7159
MIR7853
HCG21
LOC102723649
LOC102723831
LOC102723883
LINC01626
LOC102724053
LOC102724096
LOC102724152
TBX18-AS1
LOC102724357
LOC102724511
LINC01276
LOC103352541
NCOA7-AS1
SAPCD1-AS1
TRIM31-AS1
LOC105374952
LOC105374960
LOC105374972
LOC105374988
HCG20
LOC105375014
LOC105375075
LOC105377879
LINC01611
LOC105377924
LOC105377962
LOC105377967
LOC105377975
LOC105378047
LOC105378052
LOC105378068
LOC105378098
MEAT6
LOC105378123
LOC105378127
LOC105378137
LOC105378146
LUADT1
MDC1-AS1
DDX39B-AS1
HLA-DQB1-AS1
SNORA98
SNORD141A
MIR5689HG
LINC00680
LINC00680-GUSBP4
TBC1D7-LOC100130357
CNPY3-GNMT

Arm-level results

Table 3. Get Full Table Arm-level significance table - 44 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 | Del z-score | Del q-value
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1p | 3092 | 0.29 | 0.34 | 2.53 | 0.0344 | 0.15 | 0.21 | -0.534 | 1
1q | 2863 | 0.58 | 0.61 | 9.05 | 0 | 0.05 | 0.11 | -2.02 | 1
2p | 1500 | 0.20 | 0.22 | -1.03 | 1 | 0.07 | 0.09 | -3.63 | 1
2q | 2495 | 0.19 | 0.21 | -0.744 | 1 | 0.09 | 0.11 | -2.85 | 1
3p | 1531 | 0.08 | 0.12 | -2.71 | 1 | 0.33 | 0.36 | 2.21 | 0.0384
3q | 1708 | 0.16 | 0.22 | -0.831 | 1 | 0.25 | 0.29 | 0.807 | 0.503
4p | 693 | 0.07 | 0.09 | -4.01 | 1 | 0.17 | 0.19 | -2.02 | 1
4q | 1467 | 0.06 | 0.08 | -4 | 1 | 0.17 | 0.18 | -1.77 | 1
5p | 456 | 0.51 | 0.54 | 5.86 | 3.7e-08 | 0.05 | 0.11 | -2.77 | 1
5q | 2185 | 0.24 | 0.29 | 0.84 | 0.601 | 0.17 | 0.23 | -0.457 | 1
6p | 1664 | 0.16 | 0.19 | -1.57 | 1 | 0.13 | 0.15 | -2.31 | 1
6q | 1304 | 0.09 | 0.12 | -2.88 | 1 | 0.26 | 0.29 | 0.582 | 0.641
7p | 926 | 0.53 | 0.56 | 6.56 | 6.31e-10 | 0.05 | 0.12 | -2.53 | 1
7q | 1717 | 0.44 | 0.48 | 5.03 | 2.54e-06 | 0.08 | 0.15 | -2.01 | 1
8p | 795 | 0.18 | 0.26 | -0.28 | 1 | 0.30 | 0.37 | 1.97 | 0.0614
8q | 1249 | 0.30 | 0.34 | 1.67 | 0.207 | 0.12 | 0.17 | -1.92 | 1
9p | 621 | 0.06 | 0.12 | -2.6 | 1 | 0.48 | 0.51 | 5.38 | 3.56e-07
9q | 1610 | 0.05 | 0.09 | -2.95 | 1 | 0.48 | 0.50 | 5.76 | 4.99e-08
10p | 767 | 0.12 | 0.15 | -2.46 | 1 | 0.24 | 0.27 | -0.142 | 0.9
10q | 1968 | 0.06 | 0.08 | -3.52 | 1 | 0.25 | 0.26 | 0.242 | 0.829
11p | 1162 | 0.19 | 0.25 | -0.416 | 1 | 0.23 | 0.28 | 0.296 | 0.829
11q | 2133 | 0.21 | 0.26 | 0.213 | 1 | 0.19 | 0.24 | -0.158 | 0.9
12p | 804 | 0.21 | 0.27 | -0.132 | 1 | 0.22 | 0.28 | 0.0436 | 0.841
12q | 2055 | 0.19 | 0.24 | -0.189 | 1 | 0.21 | 0.26 | 0.18 | 0.829
13p | 0 | 0.05 | 0.10 | -3.23 | 1 | 0.45 | 0.48 | 4.32 | 4.25e-05
13q | 1092 | 0.04 | 0.06 | -3.62 | 1 | 0.44 | 0.45 | 4.29 | 4.35e-05
14p | 0 | 0.24 | 0.34 | 1.02 | 0.526 | 0.31 | 0.40 | 2.34 | 0.0307
14q | 1829 | 0.25 | 0.27 | 0.358 | 1 | 0.09 | 0.12 | -2.8 | 1
15p | 0 | 0.08 | 0.17 | -1.91 | 1 | 0.52 | 0.56 | 6.11 | 8.17e-09
15q | 2082 | 0.02 | 0.03 | -3.83 | 1 | 0.46 | 0.47 | 5.34 | 3.63e-07
16p | 1378 | 0.32 | 0.36 | 2.19 | 0.0761 | 0.12 | 0.17 | -1.76 | 1
16q | 1070 | 0.25 | 0.31 | 0.875 | 0.601 | 0.21 | 0.28 | 0.172 | 0.829
17p | 937 | 0.20 | 0.26 | -0.322 | 1 | 0.22 | 0.27 | 0.0308 | 0.841
17q | 2298 | 0.27 | 0.33 | 1.79 | 0.175 | 0.16 | 0.23 | -0.427 | 1
18p | 212 | 0.06 | 0.10 | -3.48 | 1 | 0.35 | 0.38 | 2.11 | 0.0469
18q | 644 | 0.06 | 0.11 | -2.99 | 1 | 0.42 | 0.45 | 3.85 | 0.000256
19p | 1331 | 0.12 | 0.20 | -1.17 | 1 | 0.41 | 0.46 | 4.47 | 2.33e-05
19q | 2402 | 0.13 | 0.18 | -1.26 | 1 | 0.30 | 0.34 | 2.29 | 0.0334
20p | 583 | 0.22 | 0.28 | 0.0232 | 1 | 0.22 | 0.28 | 0.0232 | 0.841
20q | 1092 | 0.26 | 0.32 | 1.08 | 0.514 | 0.17 | 0.23 | -0.686 | 1
21p | 92 | 0.04 | 0.06 | -4.16 | 1 | 0.38 | 0.40 | 2.48 | 0.0242
21q | 750 | 0.12 | 0.18 | -1.85 | 1 | 0.34 | 0.38 | 2.35 | 0.0307
22p | 2 | 0.04 | 0.06 | -3.95 | 1 | 0.43 | 0.44 | 3.51 | 0.0009
22q | 1258 | 0.03 | 0.05 | -3.82 | 1 | 0.45 | 0.46 | 4.52 | 2.16e-05
Xp | 945 | 0.41 | 0.46 | 4.27 | 7.76e-05 | 0.12 | 0.20 | -1.29 | 1
Xq | 1533 | 0.44 | 0.48 | 5.02 | 2.54e-06 | 0.09 | 0.16 | -1.77 | 1
Yp | 113 | 0.22 | 0.51 | 3.39 | 0.00237 | 0.57 | 0.73 | 9.14 | 0
Yq | 245 | 0.15 | 0.37 | 1.28 | 0.4 | 0.58 | 0.69 | 8.63 | 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-e7058367-eaa6-44b5-aab5-1ec08acf146a/cptac3_luad_cnv.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 110 Input Tumor Samples.

Tumor Sample Names
11LU013_TP
11LU016_TP
11LU022_TP
11LU035_TP
C3L-00001_TP
C3L-00009_TP
C3L-00080_TP
C3L-00083_TP
C3L-00093_TP
C3L-00094_TP

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