SNP6 Copy number analysis (GISTIC2)
Mesothelioma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C10R9N2T
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C10R9N2T
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 37 tumor samples used in this analysis: 13 significant arm-level results, 4 significant focal amplifications, and 19 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 - 4 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
--- | --- | --- | --- | ---
17q24.3 | 0.07091 | 0.07091 | chr17:59456590-69535200 | 100
12p11.21 | 0.10629 | 0.10629 | chr12:30605286-31010936 | 3
20p12.1 | 0.1592 | 0.1592 | chr20:17384587-17397548 | 1
19q13.43 | 0.24013 | 0.24013 | chr19:58648280-59128983 | 25

Genes in Wide Peak

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

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

Genes
CD79B
DDX5
PRKAR1A
BRIP1
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
APOH
CACNG1
CSH1
CSH2
CSHL1
CYB561
ACE
ERN1
BPTF
GH1
GH2
ICAM2
KCNJ2
KCNJ16
KPNA2
MAP3K3
PECAM1
PRKCA
MAP2K6
PSMC5
PSMD12
SCN4A
SMARCD2
TBX2
AXIN2
RGS9
SLC16A6
TBX4
MRC2
HELZ
MED13
DCAF7
ABCA10
ABCA9
ABCA8
GNA13
TLK2
POLG2
DDX42
ARSG
ABCA6
ABCA5
NOL11
TANC2
PITPNC1
CACNG5
CACNG4
TACO1
AMZ2
FAM20A
BCAS3
WIPI1
TEX2
CCDC47
INTS2
SMURF2
LIMD2
KCNH6
CEP95
STRADA
C17orf72
FTSJ3
TCAM1P
EFCAB3
LOC146880
MARCH10
CEP112
AMZ2P1
C17orf58
MILR1
METTL2A
NACA2
LRRC37A3
C17orf82
KCNJ2-AS1
TBC1D3P2
PLEKHM1P
LOC440461
SNORA76
SNORD104
MIR634
MIR635
LOC729683
SNORA38B
MIR548W
MIR4315-2
MIR4315-1
LOC100499466
MIR4524A
MIR3064
MIR5047

Genes in Wide Peak

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

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

Genes
IPO8
CAPRIN2
LOC100287314

Genes in Wide Peak

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

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

Genes
PCSK2

Genes in Wide Peak

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

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

Genes
A1BG
RPS5
ZNF8
MZF1
ZNF132
UBE2M
TRIM28
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
MGC2752
ZNF329
ZBTB45
ZNF837
ZNF497
ZNF584
ZSCAN22
ZNF324B
A1BG-AS1
LOC646862
LOC100131691
MIR4754

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 - 19 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 | 1.3279e-28 | 1.3279e-28 | chr9:21865498-22448737 | 4
3p21.1 | 1.9424e-10 | 1.9424e-10 | chr3:52423190-52468508 | 2
15q15.1 | 4.6583e-05 | 4.3197e-05 | chr15:1-45063816 | 321
16p13.3 | 0.00078859 | 0.00078922 | chr16:5144019-7771745 | 1
1p22.1 | 0.00045401 | 0.0018908 | chr1:77746246-118172220 | 290
4q26 | 0.0063018 | 0.0065557 | chr4:115598111-117226382 | 3
10q24.1 | 0.01001 | 0.0097964 | chr10:93165832-135534747 | 388
16q24.1 | 0.0065557 | 0.015326 | chr16:69976034-90354753 | 201
5q23.2 | 0.018775 | 0.019054 | chr5:101702788-132953522 | 125
6q22.31 | 0.021347 | 0.020061 | chr6:100835058-163737599 | 334
14q32.31 | 0.023803 | 0.024883 | chr14:78865413-107349540 | 292
10p15.1 | 0.040627 | 0.039021 | chr10:1-15904270 | 100
13q13.3 | 0.049605 | 0.048936 | chr13:1-76435634 | 274
1p36.23 | 0.006984 | 0.057934 | chr1:1-35137980 | 556
22q12.2 | 0.099026 | 0.10027 | chr22:29969457-30128393 | 2
14q11.2 | 0.12083 | 0.12319 | chr14:1-23134074 | 73
2q35 | 0.21123 | 0.21973 | chr2:181840208-243199373 | 459
10q22.3 | 0.22469 | 0.22419 | chr10:76788059-89611620 | 73
16q21 | 0.061167 | 0.23924 | chr16:1-90354753 | 967

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
BAP1
PHF7

Genes in Wide Peak

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

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

Genes
BUB1B
C15orf55
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
EPB42
GABRA5
GABRB3
GABRG3
GANC
GCHFR
PDIA3
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
TGM5
PPIP5K1
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
GREM1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
ZFP106
CHAC1
C15orf29
WDR76
TMEM62
SPG11
ELL3
NIPA2
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
TRIM69
PAR1
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1282
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

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

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

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
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
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FUBP1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
TSPAN2
BCAS2
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
MAN1A2
IFI44L
DNAJB4
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
AK5
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q26.

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

Genes
hsa-mir-1973
NDST4
MIR1973

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q24.1.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HELLS
HHEX
HMX2
HPS1
IDE
INPP5A
KIF11
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
BTAF1
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
EXOC6
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
OPALIN
SYCE1
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
SFXN2
PDZD8
C10orf32
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
TRUB1
VTI1A
LOC143188
HECTD2
FGFBP3
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
LOC283038
LOC283089
O3FAR1
KCNK18
CYP26C1
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
C10orf62
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
DUX4L2
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100169752
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4483
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.1.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
AARS
AP1G1
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
ST3GAL2
SPG7
TAT
ZNF19
ZNF23
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
ADAT1
CHST5
COG4
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
TXNL4B
BANP
PDPR
RFWD3
DDX19A
ZNF821
ZDHHC7
VAC14
FTSJD1
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
IL34
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
CTRB2
CLEC18B
SNORD68
SNORD71
SNORD111
LOC727710
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130894
SYCE1L
LOC100287036
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
LOC100506083
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q23.2.

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

Genes
APC
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
ALDH7A1
CAMK4
CDO1
AP3S1
CSF2
CSNK1G3
DMXL1
EFNA5
FBN2
FER
GDF9
HINT1
HSD17B4
HSPA4
IL3
IL4
IL5
IL13
IRF1
KCNN2
LMNB1
LOX
MAN2A1
MCC
PAM
PGGT1B
PPIC
SLC12A2
SLC22A4
SLC22A5
SNX2
SRP19
REEP5
PDLIM4
P4HA2
ATG12
NREP
RAB9BP1
SNCAIP
PJA2
RAD50
KIF3A
FSTL4
SEPT8
PPIP5K2
ACSL6
TNFAIP8
UQCRQ
AFF4
SLC27A6
SNX24
TMED7
ISOC1
PRR16
COMMD10
RAPGEF6
PHAX
FLJ11235
ZCCHC10
GIN1
TRIM36
FEM1C
CDC42SE2
ZNF608
SEMA6A
EPB41L4A
FBXL17
YTHDC2
GRAMD3
NUDT12
TSSK1B
MEGF10
TSLP
C5orf30
LYRM7
SLC25A46
PRDM6
FTMT
FNIP1
EPB41L4A-AS1
MARCH3
LEAP2
SLCO6A1
PRRC1
ZNF474
STARD4
WDR36
SOWAHA
SHROOM1
CEP120
SRFBP1
CCDC112
DCP2
ADAMTS19
AQPEP
DTWD2
CHSY3
FAM170A
TICAM2
C5orf48
C5orf63
C5orf56
LOC553103
CTXN3
TMEM232
LOC644100
FLJ33630
CCNI2
SNORA13
LOC728342
LOC100289673
MIR1289-2
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
MIR3936
LOC100505678
LOC100505841
MIR4633
MIR4460

Genes in Wide Peak

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

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
STL
GOPC
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
ACAT2
AIM1
AMD1
ARG1
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PREP
PKIB
PTPRK
REV3L
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
TCF21
TCP1
DYNLT1
NR2E1
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
STX11
SNX3
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
SMPDL3A
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
FBXO5
RGS17
PDE7B
SESN1
OSTM1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TFB1M
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
VTA1
HECA
IL20RA
MTRF1L
AHI1
RMND1
SOBP
QRSL1
VNN3
ECHDC1
AGPAT4
TULP4
HYMAI
PDSS2
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
HACE1
TMEM181
ZBTB2
BEND3
C6orf115
PBOV1
TRMT11
PERP
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
AGPAT4-IT1
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
ARMC2
FBXO30
RPF2
L3MBTL3
FNDC1
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
KIAA1919
ARHGAP18
SYTL3
GTF3C6
FAM54A
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
BVES-AS1
OLIG3
TXLNB
OSTCP1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
CENPW
C6orf174
LINC00222
CEP85L
THEMIS
LIN28B
SAMD5
IYD
GTF2H5
FAM26F
FLJ46906
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
SNORA20
SNORA29
MIR548B
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
LOC100128176
BET3L
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100287632
NHEG1
LOC100422737
MIR3145
MIR3918
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
MIR4466
MIR4465
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.31.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
GALC
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
MTA1
RPS6KA5
NRXN3
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
PTPN21
RCOR1
PACS2
PPP1R13B
FLRT2
KIF26A
C14orf109
PRO1768
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
UNC79
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
CEP128
TTC7B
C14orf49
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
CCDC85C
ITPK1-AS1
SERPINA9
LINC00226
LINC00221
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
MIR1247
MIR1185-1
MIR1185-2
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392
LOC100628307

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.1.

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

Genes
GATA3
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PHYH
PRKCQ
ITGA8
PRPF18
AKR1C3
CDC123
NMT2
USP6NL
OPTN
NET1
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
SEPHS1
KIN
DIP2C
LARP4B
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
CAMK1D
SFMBT2
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
FBXO18
RBM17
IDI2
UCN3
SFTA1P
LOC219731
UCMA
C10orf111
FAM171A1
BEND7
LOC254312
C10orf47
LOC282980
LOC283070
LOC338588
AKR1CL1
TUBB8
tAKR
LINC00200
LOC399708
LOC399715
FLJ45983
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
ADARB2-AS1
MEIG1
LOC100192204
LOC100216001
MIR1265
MIR3155A
LOC100507034
LOC100507127
MIR4480
MIR3155B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.3.

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
KLF5
CDK8
RCBTB2
CPB2
DACH1
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
UCHL3
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
PIBF1
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
XPO4
PCDH20
MRP63
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
COMMD6
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3169
MIR3613
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
LCK
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
AK2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
YARS
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
S100PBP
CEP85
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCP2
SYTL1
IGSF21
C1orf94
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
ADC
TMEM54
CSMD2
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
HMGB4
RNF19B
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR4254
MIR3917
MIR3605
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.2.

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

Genes
NF2
CABP7

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-1201
ANG
APEX1
DAD1
HNRNPC
PNP
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TOX4
PARP2
EDDM3A
SUPT16H
OR10G3
OR10G2
OR4E2
SLC39A2
ZNF219
OSGEP
ARHGEF40
METTL3
RPGRIP1
NDRG2
CHD8
ABHD4
EDDM3B
METTL17
OR4K5
OR11H2
OR4K1
OR4K15
RNASE7
RAB2B
RPPH1
TMEM55B
TTC5
RNASE11
TPPP2
RNASE8
OR4K14
OR4L1
OR11H6
KLHL33
LOC283624
SNORD8
RNASE10
OR6S1
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
SNORD9
SNORD126

Genes in Wide Peak

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

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

Genes
ATIC
CREB1
ACSL3
IDH1
PAX3
PMS1
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
AOX1
KIF1A
BARD1
BCS1L
BMPR2
BOK
CASP8
CASP10
CD28
CHRND
CHRNG
CLK1
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CYP27A1
DES
DTYMK
EEF1B2
EPHA4
ERBB4
FN1
FRZB
GBX2
MSTN
GLS
GPC1
GPR1
GPR35
HDLBP
AGFG1
DNAJB2
HSPD1
HSPE1
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP1
INPP5D
IRS1
ITGA4
ITGAV
KCNJ13
MAP2
MYO1B
MYL1
NAB1
NCL
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPPC
ORC2
PDCD1
PDE1A
PDE6D
SERPINE2
PLCL1
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
SSFA2
STAT1
STAT4
TFPI
TNP1
TNS1
TUBA4A
SUMO1
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
FZD7
SDPR
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
CFLAR
PER2
CDK5R2
RQCD1
LRRFIP1
STK17B
GPR55
TRIP12
GTF3C3
ECEL1
EIF4E2
TTLL4
BZW1
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
ABI2
CALCRL
RAMP1
SPEG
LANCL1
NMUR1
UBE2E3
STK25
NCKAP1
COPS8
CAPN10
SP140
IKZF2
FASTKD2
PASK
ATG4B
SATB2
OBSL1
SF3B1
DNPEP
TMEFF2
SH3BP4
KCNE4
NGEF
SNORD82
MOB4
PNKD
SNED1
SPATS2L
GIGYF2
TRAF3IP1
ABCA12
HIBCH
SNORD51
CNPPD1
STK36
CPS1-IT1
ICOS
GMPPA
SLC40A1
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
GULP1
SCLY
NOP58
ASB1
CAB39
PRKAG3
PPIL3
DNAJC10
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
MFSD6
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
STRADB
HES6
ACCN4
DOCK10
MREG
WDR12
PECR
ZC3H15
DNAH7
C2orf83
MFF
CXCR7
RNPEPL1
SLC39A10
CYP20A1
HECW2
MARCH4
WDFY1
NYAP2
ALS2
ZDBF2
USP37
CTDSP1
MPP4
NIF3L1
PCGEM1
GAL3ST2
TMBIM1
OSGEPL1
RAB17
RNF25
COPS7B
OBFC2A
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
TRAK2
BOLL
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
C2orf47
SPAG16
CHPF
IQCA1
ALS2CR8
NHEJ1
FAM124B
TM4SF20
C2orf54
PGAP1
TUBA4B
ARMC9
COQ10B
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
WDR75
RHBDD1
C2orf88
ING5
PLCD4
MGC16025
ANKRD44
ZNF804A
TMEM169
DNER
MARS2
B3GNT7
SP140L
ORMDL1
STK11IP
DIRC1
MOGAT1
AGAP1
TWIST2
PARD3B
NUP35
TYW5
DIS3L2
NEU4
ICA1L
RFTN2
AP1S3
SGPP2
KCTD18
ALS2CR12
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
DUSP19
FLJ32063
OTOS
MYEOV2
OR6B3
ANKAR
FAM117B
LOC150935
PKI55
C2orf67
ZSWIM2
LOC151171
LOC151174
METTL21A
CCNYL1
PPP1R1C
SGOL2
ALS2CR11
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
FAM171B
PIKFYVE
LOC200726
TIGD1
LOC200772
C2orf69
CCDC108
C2orf72
CCDC150
CXXC11
FAM126B
UNC80
RUFY4
DUSP28
ESPNL
AOX2P
ECEL1P2
FONG
LOC348761
CERKL
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
FSIP2
C2orf66
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
SNORA41
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
SNORD11
SNORD70
MIR561
D2HGDH
LOC728323
DIRC3
SNORD11B
LOC100129175
PP14571
LOC100130451
LOC100130452
TMEM194B
LOC100286922
MIR1471
MIR1245A
MIR1244-1
MIR548F2
LOC100329109
BOK-AS1
MIR1244-3
MIR1244-2
MIR3129
MIR3131
MIR4268
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
MIR3606
LOC100507140
LOC100507443
HSPE1-MOB4
UBE2F-SCLY
MIR4439
MIR4437
MIR4776-1
MIR4777
MIR1245B
MIR2467
MIR4775
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
BMPR1A
hsa-mir-346
hsa-mir-606
ANXA11
GLUD1
GRID1
KCNMA1
MAT1A
RGR
RPS24
SFTPD
SNCG
VDAC2
MBL1P
PAPSS2
DLG5
MINPP1
PPIF
NRG3
C10orf116
POLR3A
LDB3
WAPAL
LRIT1
GHITM
DUSP13
FAM190B
FAM35A
ZMIZ1
MMRN2
FAM213A
TSPAN14
C10orf11
C10orf58
DYDC2
ZNF503
ATAD1
CDHR1
OPN4
COMTD1
AGAP11
SAMD8
CFL1P1
DYDC1
EIF5AL1
LOC170425
LOC219347
PLAC9
ZCCHC24
ZNF503-AS1
LOC283050
DUPD1
LRIT2
SH2D4B
C10orf99
LOC439990
LOC439994
MIR346
LOC642361
FAM25A
LOC650623
SFTPA1
FAM22A
FAM22D
LOC728190
LOC728218
SFTPA2
LOC100128292
ZNF503-AS2
LOC100132987
LOC100288974
LOC100507470
MIR4678

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q21.

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

Genes
TNFRSF17
CBFA2T3
CBFB
CDH1
CDH11
CREBBP
CYLD
ERCC4
FANCA
FUS
MAF
CIITA
MYH11
TSC2
SOCS1
HERPUD1
IL21R
PALB2
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
hsa-mir-762
hsa-mir-548w
hsa-mir-3179-3
hsa-mir-3180-2
hsa-mir-484
hsa-mir-1972-1
hsa-mir-3180-1
hsa-mir-365-1
hsa-mir-548h-2
hsa-mir-3178
hsa-mir-940
hsa-mir-1225
hsa-mir-3177
hsa-mir-662
hsa-mir-3176
AARS
ABAT
ABCA3
ADCY7
ADCY9
AP1G1
AFG3L1P
AGRP
ALDOA
AMFR
AQP8
APRT
ABCC6
ARHGDIG
ZFHX3
ATP2A1
ATP6V0C
BBS2
C16orf3
CA5A
CA7
CALB2
CBLN1
CCNF
CD19
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CDR2
CES1
CETP
CLCN7
CLN3
CNGB1
COX4I1
COX6A2
CRYM
CSNK2A2
CTF1
CTRB1
CTRL
CYBA
ECI1
DHODH
NQO1
SEPT1
DNASE1
DNASE1L2
DYNC1LI2
DPEP1
E2F4
E4F1
EMP2
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GFER
GLG1
GNAO1
GOT2
GP2
GRIN2A
GSPT1
GTF3C1
HAGH
HAS3
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
IGFALS
IL4R
ITGAD
ITGAL
ITGAM
ITGAX
KARS
KIFC3
KIF22
LCAT
MAZ
MC1R
CHST6
MEFV
MMP2
MMP15
MPG
ABCC1
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
MVD
NUBP1
NDUFAB1
NDUFB10
NFATC3
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PARN
CHMP1A
PDPK1
PHKB
PHKG2
PKD1
PLCG2
PLK1
PMM2
POLR2C
PPL
PPP4C
PRKCB
MAPK3
PRM1
PRM2
PRSS8
PSKH1
PSMB10
PSMD7
RBBP6
RBL2
RPL3L
RPL13
RPS2
RPS15A
RRAD
ACSM3
SALL1
SCNN1B
SCNN1G
SRL
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC5A2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SOLH
SPG7
SPN
SSTR5
SULT1A2
STX4
SULT1A1
SULT1A3
TAT
TBX6
TCEB2
TERF2
TFAP4
TGFB1I1
TK2
TNP2
TPSAB1
TUFM
UBE2I
UMOD
UQCRC2
ZNF19
ZNF23
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
ZP2
USP7
NPRL3
GAN
SLC7A5
SNN
AXIN1
PLA2G10
DOC2A
HIRIP3
CDK10
EIF3C
TRADD
MBTPS1
RGS11
CES2
NAE1
CACNA1H
BAIAP3
NOL3
TAF1C
RHBDL1
SLC7A6
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
USP10
ATP6V0D1
SYNGR3
IL32
BCL7C
NPIP
GPR56
TAOK2
SLC9A3R2
LITAF
BCAR1
C16orf7
KIAA0430
N4BP1
NUP93
SEC14L5
ZNF646
RAB11FIP3
CCP110
SETD1A
IFT140
KIAA0513
PIEZO1
DHX38
IST1
RNF40
TELO2
ATP2C2
HS3ST4
HS3ST2
MVP
NUBP2
ZNF263
TRAP1
CLEC3A
CHST4
MPHOSPH6
NUTF2
COQ7
MSLN
IGSF6
IRX5
STUB1
DNAJA2
BCKDK
KATNB1
ZNF267
COX4NB
CACNG3
TUBB3
CD2BP2
CDIPT
CFDP1
MRPL28
ERN2
TBL3
CTCF
NFAT5
SRCAP
RNPS1
PRSS21
NUDT21
WWP2
PRDM7
CORO1A
DDX19B
ATXN2L
GABARAPL2
MON1B
SEPHS2
TCF25
CNOT1
PHLPP2
PDXDC1
SMG1
CLUAP1
GGA2
ZNF423
NPIPL3
MAPK8IP3
ZCCHC14
KIAA0182
ARL6IP1
XPO6
KIAA0556
CLEC16A
MGRN1
ATMIN
RPGRIP1L
ZNF629
COTL1
MLYCD
NOMO1
TPSD1
SF3B3
QPRT
CES3
SRRM2
ADAT1
CHST5
ARL2BP
CARHSP1
ORC6
EDC4
PLA2G15
TP53TG3
TPSG1
RAB26
COG4
TMEM186
PLEKHG4
SH2B1
TBC1D10B
ZNF500
DECR2
DKFZP434H168
RSL1D1
OR1F2P
LRRC29
SEZ6L2
NUPR1
SNORA64
SNORD60
LAT
CPNE7
VPS4A
IL17C
TOX3
TNRC6A
DEXI
NOB1
C16orf72
ZC3H7A
CCDC113
TMEM208
C16orf80
PYCARD
FHOD1
BRD7
ANKRD11
ZDHHC1
UBN1
MYLPF
EEF2K
OSGIN1
C16orf5
SOX8
PARD6A
AMDHD2
PAM16
TXNDC11
PLLP
METTL9
NAGPA
CKLF
BFAR
AHSP
TNFRSF12A
ZNF771
NIP7
LCMT1
GDE1
FAM96B
GINS2
TPPP3
TRAPPC2L
GPRC5B
CES1P1
POLR3K
SEPX1
WWOX
SYT17
GNG13
BCMO1
TERF2IP
KCTD5
PRMT7
NECAB2
FBXL19
RRN3
RBFOX1
KLHDC4
HYDIN
NDE1
DEF8
DUS2L
CHTF8
ZNF434
LPCAT2
TXNL4B
BANP
HCFC1R1
ACSM5
HEATR3
PDPR
ARHGAP17
RFWD3
SLC38A7
OGFOD1
LRRC36
DDX19A
CPPED1
FBXL8
SMPD3
ZNF821
DNAH3
THUMPD1
ZDHHC7
LUC7L
VAC14
DOK4
POLR3E
VPS35
FTSJD1
DDX28
TSNAXIP1
CENPN
APOBR
ALG1
UBFD1
C16orf61
COQ9
CIAPIN1
C16orf62
TMEM159
LYRM1
THAP11
JPH3
NMRAL1
TBC1D24
USP31
MKL2
CASKIN1
PDP2
ZNF319
CRAMP1L
RANBP10
VAT1L
KIAA1609
RAB40C
WFDC1
PRM3
TMEM8A
CHTF18
CHP2
PRSS22
NOD2
XYLT1
PDF
DPEP2
DPEP3
MLST8
PAPD5
RHBDF1
FBRS
MMP25
AKTIP
NARFL
LINC00235
TPSB2
HS3ST6
PDIA2
UNKL
LINC00254
C16orf58
MTHFSD
GINS3
LMF1
NDRG4
ACD
ZNF747
FAM173A
MRPS34
PRR14
VKORC1
METRN
DBNDD1
SLX1B
FTO
DCTPP1
METTL22
FA2H
GDPD3
IRX6
IRX3
THOC6
KREMEN2
C16orf53
FAM65A
TMEM231
CORO7
TMCO7
SNRNP25
ROGDI
C16orf57
TMEM204
ZNF768
WDR59
ZNF668
ELMO3
KLHL36
FBXO31
ARMC5
SHCBP1
JMJD5
TMC5
RABEP2
NAA60
TMC7
SETD6
ESRP2
FAM192A
ATF7IP2
CENPT
C16orf59
CHD9
C16orf70
HSD3B7
CYB5B
CMIP
ITFG1
GFOD2
CDT1
MAP1LC3B
LOC81691
NETO2
MGC3771
FAHD1
SLC7A5P1
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
YPEL3
FAM57B
LONP2
PRSS27
SPNS1
ITFG3
C16orf48
SLC7A6OS
KAT8
NLRC5
WDR24
CCDC135
TRAF7
FLYWCH1
HAGHL
CAPNS2
NUDT16L1
C16orf13
FAM195A
COG8
SLX4
SPIRE2
DCTN5
MT4
GNPTG
ZNF469
GLYR1
GLIS2
GPT2
B3GNT9
ZSCAN10
NFATC2IP
CIRH1A
ZNRF1
ABCC11
NKD1
CNTNAP4
C16orf45
RHOT2
RSPRY1
C16orf93
ZNF598
HN1L
SPSB3
TIGD7
MYLK3
MARVELD3
COG7
SNX29
MTSS1L
ZNF764
CENPBD1
ZNF276
CCDC102A
KCNG4
ORAI3
SDR42E1
ABCC12
PRRT2
ERI2
STX1B
CCDC101
RPUSD1
CMTM1
PKD1L2
FLYWCH2
VASN
ZNF689
SLC5A11
C16orf42
RNF166
RMI2
ACSM1
WFIKKN1
EXOSC6
C16orf46
NTAN1
FOPNL
DNAAF1
ACSM2A
DCUN1D3
NRN1L
CMTM3
C16orf78
SPATA2L
C16orf55
NOXO1
CCDC78
ANKRD26P1
IQCK
ZG16B
PRSS30P
PAQR4
ZC3H18
GPR139
CDYL2
ANKS3
FAM100A
SEPT12
ZNF720
TMEM219
EARS2
SNX20
TMEM170A
SLC38A8
VWA3A
OTOA
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
TEKT5
RNF151
C16orf11
FBXL16
LOC146336
C16orf92
GSG1L
SLC22A31
IL34
ZNF597
CCDC64B
TMED6
LOC146481
FLJ30679
LOC146513
ZNF785
ZNF688
PRSS36
C16orf89
C16orf71
ZFPM1
ADAD2
ITPRIPL2
C16orf82
ZFP1
ADAMTS18
FAM86A
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
WDR90
EME2
NLRC3
NSMCE1
ZNF48
PDILT
CPNE2
GPR114
PRSS54
CES5A
GPR97
IL27
KCTD13
ASPHD1
C16orf73
MPV17L
PDZD9
CNEP1R1
ANKS4B
PRSS33
PYDC1
NOMO2
CCDC79
CES4A
EXOC3L1
LOC283856
LINC00304
LOC283867
NPW
C16orf79
PGP
LINC00514
FLJ39639
LOC283888
C16orf54
INO80E
HTA
LOC283914
LOC283922
NUDT7
FBXL19-AS1
ZNF843
NHLRC4
C16orf91
TMEM114
PDXDC2P
CLEC18C
MT1DP
SNAI3
PKD1P1
PRSS53
JMJD8
FAM92B
C16orf96
ZKSCAN2
ATXN1L
PKD1L3
ACSM2B
CLEC18A
CTU2
PRSS41
TEPP
SLC6A10P
SLC7A5P2
PRR25
SBK1
LOC388242
C16orf87
LOC388276
C16orf86
C1QTNF8
PTX4
LOC390705
CES1P2
PABPN1L
BCAR4
C16orf88
CRYM-AS1
FLJ21408
FLJ26245
LOC400548
LOC400550
LOC400558
MSLNL
C16orf74
MIR138-2
MIR140
NOMO3
LOC440335
SNX29P2
LOC440354
LOC440356
CSDAP1
HERC2P4
CTRB2
MIR328
SULT1A4
TRIM72
CLEC18B
SLX1A
BOLA2
LOC554206
SNORA10
MIR193B
LOC595101
SNORD68
UBE2MP1
LOC606724
LOC613037
LOC613038
MIR484
LOC641298
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
FLJ42627
CCDC154
C16orf90
LINC00273
ABCA17P
LOC652276
ABCC6P1
KIAA0895L
RRN3P2
TP53TG3C
LOC653786
ZG16
BOLA2B
SNORA30
SNORA46
SNORA50
SNORA78
SNORD71
SNORD111
MIR548D2
MIR662
LOC727710
EIF3CL
LOC729264
TP53TG3B
LOC729513
SHISA9
ABCC6P2
RRN3P1
C16orf52
LOC732275
SNHG9
CEMP1
FAM18A
SNORD111B
MIR940
MIR365A
LOC100128788
LOC100128881
LOC100129617
LOC100130015
LOC100130700
LOC100130894
SYCE1L
RRN3P3
LOC100132247
KIAA0664L3
LOC100134368
MIR1225
LOC100190986
LOC100271836
DDX11L10
LOC100287036
LOC100289092
MIR1538
MIR1972-1
MIR1910
MIR762
SNORA70D
MIR3180-3
MIR3182
MIR3180-1
MIR3179-2
MIR548X
MIR1972-2
MIR3180-2
MIR3179-1
MIR3178
MIR3179-3
MIR3177
MIR3176
MTRNR2L4
MIR3677
MIR3180-4
MIR3935
MIR548AA2
MIR3180-5
LOC100505619
LOC100505865
LOC100506083
LOC100506172
C16orf95
LOC100506655
ERVK13-1
LOC100507501
LOC100507577
LOC100507589
SLX1A-SULT1A3
SLX1B-SULT1A4
CORO7-PAM16
CKLF-CMTM1
MIR4720
MIR4722
MIR4719
MIR4718
MIR4519
MIR4717
MIR4721
MIR4516
MIR548AE2
MIR4518
MIR4517
SNX29P1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 13 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.10 | -0.45 | 0.984 | 0.21 | 1.37 | 0.262
1q | 1955 | 0.29 | 2.71 | 0.133 | 0.07 | -0.877 | 0.988
2p | 924 | 0.03 | -2.05 | 0.984 | 0.06 | -1.63 | 0.988
2q | 1556 | 0.06 | -1.36 | 0.984 | 0.09 | -0.92 | 0.988
3p | 1062 | 0.23 | 1.3 | 0.557 | 0.07 | -1.23 | 0.988
3q | 1139 | 0.26 | 1.8 | 0.356 | 0.07 | -1.15 | 0.988
4p | 489 | 0.05 | -1.43 | 0.984 | 0.44 | 4.58 | 2.32e-05
4q | 1049 | 0.04 | -1.44 | 0.984 | 0.39 | 4 | 0.000183
5p | 270 | 0.31 | 2.33 | 0.2 | 0.08 | -1.24 | 0.988
5q | 1427 | 0.21 | 1.06 | 0.644 | 0.10 | -0.665 | 0.988
6p | 1173 | 0.06 | -1.31 | 0.984 | 0.17 | 0.392 | 0.818
6q | 839 | 0.00 | -2.01 | 0.984 | 0.41 | 4.21 | 0.000104
7p | 641 | 0.27 | 1.84 | 0.356 | 0.00 | -2.26 | 0.988
7q | 1277 | 0.20 | 0.911 | 0.668 | 0.07 | -1.23 | 0.988
8p | 580 | 0.16 | -0.0689 | 0.984 | 0.16 | -0.0689 | 0.988
8q | 859 | 0.17 | 0.274 | 0.984 | 0.06 | -1.39 | 0.988
9p | 422 | 0.05 | -1.5 | 0.984 | 0.42 | 4.09 | 0.000143
9q | 1113 | 0.00 | -2.14 | 0.984 | 0.30 | 2.53 | 0.0286
10p | 409 | 0.08 | -1.2 | 0.984 | 0.31 | 2.39 | 0.0372
10q | 1268 | 0.07 | -1.17 | 0.984 | 0.23 | 1.39 | 0.262
11p | 862 | 0.17 | 0.275 | 0.984 | 0.06 | -1.39 | 0.988
11q | 1515 | 0.15 | 0.182 | 0.984 | 0.12 | -0.252 | 0.988
12p | 575 | 0.19 | 0.549 | 0.972 | 0.03 | -1.9 | 0.988
12q | 1447 | 0.19 | 0.902 | 0.668 | 0.03 | -1.7 | 0.988
13q | 654 | 0.05 | -1.27 | 0.984 | 0.50 | 5.59 | 2.25e-07
14q | 1341 | 0.10 | -0.64 | 0.984 | 0.46 | 5.27 | 9.2e-07
15q | 1355 | 0.13 | -0.166 | 0.984 | 0.21 | 1.12 | 0.378
16p | 872 | 0.24 | 1.31 | 0.557 | 0.10 | -0.759 | 0.988
16q | 702 | 0.25 | 1.43 | 0.557 | 0.17 | 0.212 | 0.925
17p | 683 | 0.11 | -0.744 | 0.984 | 0.26 | 1.7 | 0.18
17q | 1592 | 0.21 | 1.13 | 0.644 | 0.10 | -0.615 | 0.988
18p | 143 | 0.09 | -1.15 | 0.984 | 0.15 | -0.359 | 0.988
18q | 446 | 0.07 | -1.32 | 0.984 | 0.26 | 1.5 | 0.245
19p | 995 | 0.12 | -0.554 | 0.984 | 0.09 | -0.974 | 0.988
19q | 1709 | 0.09 | -0.817 | 0.984 | 0.09 | -0.817 | 0.988
20p | 355 | 0.10 | -0.966 | 0.984 | 0.21 | 0.632 | 0.659
20q | 753 | 0.06 | -1.52 | 0.984 | 0.11 | -0.694 | 0.988
21q | 509 | 0.03 | -1.96 | 0.984 | 0.17 | 0.0718 | 0.988
22q | 921 | 0.12 | -0.223 | 0.984 | 0.81 | 10.9 | 0
Xq | 1312 | 0.03 | -1.74 | 0.984 | 0.19 | 0.845 | 0.531

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

- Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/MESO-TP/8017629/GDAC_MergeDataFiles_6754310/MESO-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 37 Input Tumor Samples.

Tumor Sample Names
TCGA-LK-A4NW-01A-11D-A34B-01
TCGA-LK-A4NY-01A-11D-A34B-01
TCGA-LK-A4NZ-01A-12D-A34B-01
TCGA-LK-A4O0-01A-11D-A34B-01
TCGA-LK-A4O2-01A-11D-A34B-01
TCGA-LK-A4O4-01A-11D-A34B-01
TCGA-LK-A4O5-01A-11D-A34B-01
TCGA-LK-A4O6-01A-11D-A34B-01
TCGA-LK-A4O7-01A-11D-A34B-01
TCGA-MQ-A4KX-01A-11D-A34B-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle