SNP6 Copy number analysis (GISTIC2)
Mesothelioma (Primary solid tumor)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1DZ07R6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1DZ07R6
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.22 (Firehose task version: 140).

Summary

There were 87 tumor samples used in this analysis: 21 significant arm-level results, 0 significant focal amplifications, and 21 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.

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 1. Get Full Table Deletions Table - 21 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 | 1.0694e-72 | 1.0694e-72 | chr9:21931610-22448737 | 3
3p21.1 | 4.0443e-31 | 4.0443e-31 | chr3:52321313-52468508 | 4
16p13.3 | 3.1518e-12 | 3.1518e-12 | chr16:5144019-7780235 | 2
1p21.3 | 5.9874e-12 | 3.2892e-10 | chr1:87602082-113949401 | 201
15q15.1 | 4.5411e-10 | 4.4847e-10 | chr15:33485762-45026122 | 146
22q12.2 | 2.969e-05 | 2.9861e-05 | chr22:29969457-30128393 | 2
1p36.31 | 2.434e-07 | 6.1158e-05 | chr1:1-31262836 | 501
10q25.2 | 0.00015289 | 0.000159 | chr10:89566631-133918419 | 379
13q14.11 | 0.0010209 | 0.0010461 | chr13:1-66543128 | 337
16q24.1 | 0.001069 | 0.0010461 | chr16:76902147-90354753 | 135
11q23.2 | 0.0023183 | 0.0023534 | chr11:107434707-115499061 | 78
10p15.3 | 0.0040398 | 0.0042546 | chr10:1-11047562 | 69
6q26 | 0.0023534 | 0.0049795 | chr6:137363836-171115067 | 193
2q35 | 0.014499 | 0.014499 | chr2:206480055-240227399 | 291
8p23.2 | 0.088476 | 0.088476 | chr8:1-4985851 | 15
14q32.31 | 0.088547 | 0.088476 | chr14:50793385-107349540 | 565
4q26 | 0.075661 | 0.15527 | chr4:54323711-139058686 | 408
4q34.3 | 0.10007 | 0.17338 | chr4:160426521-191154276 | 131
12p13.31 | 0.17495 | 0.17338 | chr12:4663718-21591846 | 222
6q22.1 | 0.05642 | 0.19352 | chr6:57206295-158935117 | 481
5q23.2 | 0.20184 | 0.19723 | chr5:44806004-180915260 | 907

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53

Genes in Wide Peak

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

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

Genes
BAP1
DNAH1
PHF7
MIR135A1

Genes in Wide Peak

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

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

Genes
SNORA40|ENSG00000252138.1
RBFOX1

Genes in Wide Peak

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

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

Genes
RBM15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
ACTBP12
RN7SL235P
RN7SL653P
BARHL2
U3|ENSG00000199666.1
RN7SKP272
snoU13|ENSG00000239176.1
GBP1P1
GBP6
RN7SL583P
RNA5SP52
ABCA4
ADORA3
AGL
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
BRDT
CAPZA1
CD53
CHI3L2
CNN3
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
OVGP1
PKN2
PSMA5
ABCD3
RAP1A
RPL5
SORT1
SARS
SLC16A1
STXBP3
TGFBR3
VCAM1
EVI5
CDC7
BCAR3
LMO4
CDC14A
RTCA
SLC16A4
LPPR4
CEPT1
VAV3
LAMTOR5
AHCYL1
GLMN
DDX20
MTF2
NTNG1
WDR47
CLCC1
KIAA1107
SLC35A3
LRRC8B
RWDD3
CHIA
GPSM2
SLC25A24
TMED5
SNX7
GPR88
TRMT13
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
AMIGO1
PTBP2
HIAT1
WDR77
EPS8L3
GPR61
ZNF644
LRRC8C
PROK1
PSRC1
STRIP1
HENMT1
GBP4
GBP5
OLFM3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
PIFO
C1orf162
TMEM56
NBPF4
SLC30A7
CHIAP2
FNDC7
SASS6
HFM1
UBL4B
EPHX4
AKNAD1
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
CCDC18
MYBPHL
GBP7
C1orf146
FAM69A
SLC6A17
FRRS1
MIR197
RBMXL1
NBPF6
MIR760
MIR378G
MIR137HG

Genes in Wide Peak

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

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

Genes
BUB1B
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13|ENSG00000238494.1
snoU13|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13|ENSG00000238564.1
THBS1
FAM98B
U3|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18|ENSG00000252425.1
SLC12A6
TMCO5B
ACTC1
CAPN3
CHRM5
CKMT1B
EPB42
GANC
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
RYR3
SPINT1
SRP14
TP53BP1
TYRO3
EIF3J
SNAP23
TGM5
PPIP5K1
AQR
LCMT2
RASGRP1
GPR176
CHP1
OIP5
BAHD1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
SERF2
TMEM87A
RPAP1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
DLL4
INO80
PPP1R14D
ZNF770
HAUS2
RMDN3
DNAJC17
NOP10
EMC7
PAK6
CASC5
AVEN
STARD9
VPS18
ZNF106
CHAC1
KATNBL1
WDR76
TMEM62
SPG11
ELL3
C15orf41
ZFYVE19
FRMD5
DISP2
DPH6
C15orf57
KNSTRN
BMF
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
NUTM1
PLA2G4D
C15orf52
C15orf53
C15orf54
GOLGA8B
EIF2AK4
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4510

Genes in Wide Peak

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

Table S6. 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 1p36.31.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
MIR4420
SCARNA24|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18|ENSG00000252691.1
SCARNA17|ENSG00000252190.1
MAN1C1
snoU13|ENSG00000238889.1
SYF2
snoU13|ENSG00000238986.1
RN7SL857P
snoU13|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16|ENSG00000252404.1
RN7SL451P
SNORA77|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
MMP23B
KCNAB2
FCN3
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
THEMIS2
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
AHDC1
SMPDL3B
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
MECR
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
AUNIP
EFHD2
MMEL1
RSG1
MUL1
NOL9
LIN28A
LINC00115
MORN1
FAM110D
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SESN2
ESPN
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
C1orf170
SYTL1
IGSF21
KIAA2013
THAP3
STPG1
UBXN11
FBXO44
ATPIF1
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
C1orf234
OR4F29
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.2.

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

Genes
PTEN
FGFR2
TLX1
NFKB2
SUFU
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19|ENSG00000222588.1
SNORA19|ENSG00000207468.1
U3|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13|ENSG00000239125.1
SMNDC1
RN7SL450P
U4|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112|ENSG00000253068.1
FGF8
snoU13|ENSG00000239091.1
SNORD112|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12|ENSG00000212464.1
ERLIN1
snoU13|ENSG00000238472.1
COX15
ENTPD7
snoU13|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13|ENSG00000238991.1
ANKRD22
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
ACADSB
ACTA2
ADD3
ADRA2A
ADRB1
FAS
ARL3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
CPN1
CTBP2
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
EMX2
GFRA1
GOT1
PRLHR
GRK5
HABP2
HELLS
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT3
KIF11
ABLIM1
LIPA
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
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
KIF20B
SH3PXD2A
FAM53B
SLK
DCLRE1A
FRAT1
ACTR1A
NPM3
GLRX3
RPP30
TACC2
SORBS1
MGEA5
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
PDCD4
R3HCC1L
POLL
BLNK
KCNIP2
CUZD1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
EXOC6
CCNJ
MARCH5
ZRANB1
NSMCE4A
CNNM2
WBP1L
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
WDR11
FAM178A
DHX32
TDRD1
BCCIP
C10orf2
TM9SF3
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
PLEKHS1
PDZD7
C10orf88
UBTD1
WDR96
TNKS2
TRIM8
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
LZTS2
LCOR
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
BBIP1
FANK1
OPALIN
HOGA1
SORCS1
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
C10orf32
GSTO2
SFR1
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
TRUB1
VTI1A
HECTD2
FGFBP3
C10orf82
CACUL1
SLC35G1
CCDC147
PPAPDC1A
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
RBM20
FFAR4
KCNK18
LIPM
CYP26C1
NANOS1
HMX3
CCDC172
SLC16A12
CC2D2B
ARMS2
TEX36
C10orf120
FOXI2
GOLGA7B
C10orf85
C10orf62
IFIT1B
MIR146B
FAM196A
LIPK
LIPN
MIR607
TLX1NB
C10orf131
KLLN
MIR1307
MIR2110
MIR378C
MIR3157
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.11.

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

Genes
CDX2
BRCA2
FLT3
LCP1
RB1
LHFP
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31|ENSG00000199477.1
SNORA31|ENSG00000253051.1
7SK|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116|ENSG00000212553.1
RNY4P14
snoU13|ENSG00000238408.1
LINC00366
LINC00571
RNA5SP26
RN7SKP1
ARL2BPP3
DCLK1
LINC00445
LINC00457
SNORA25|ENSG00000199196.1
LINC00423
RNY1P4
SNORA16|ENSG00000212293.1
ZAR1L
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
LINC00365
LINC00544
LINC00572
LINC00297
MTUS2
RN7SL272P
URAD
LINC00543
GSX1
RNY1P1
SNORA27|ENSG00000207051.1
SNORD102
LINC00415
RNY1P3
RN7SL741P
RN7SL289P
PABPC3
LSP1|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
MIR2276
ANKRD20A19P
LINC00352
LINC00327
LINC00362
RNY3P4
LINC00621
SNORD36|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27|ENSG00000252128.1
snoU13|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PCDH8
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
ZMYM2
IFT88
TNFSF11
SUCLA2
CCNA1
MTMR6
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
VWA8
ZC3H13
SPG20
LRCH1
SACS
INTS6
LATS2
CKAP2
NUFIP1
NBEA
PCDH17
RGCC
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
ENOX1
RCBTB1
NUDT15
KIAA1704
TNFRSF19
SUPT20H
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
XPO4
PCDH20
MRP63
SMIM2
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
EBPL
MEDAG
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
HNRNPA1L2
B3GALTL
DGKH
CCDC122
STOML3
AMER2
USP12
MTIF3
FAM194B
SPERT
FAM124A
LRRC63
N6AMT2
SKA3
MICU2
SPATA13
LNX2
SLC25A30
PAN3
SIAH3
KCNRG
SLC46A3
C1QTNF9
FREM2
NEK5
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
DLEU2
ATP5EP2
ALG11
SERPINE3
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
MIR759
MIR320D1
MIR3168
MIR4305
MIR3169
MIR3613
SPG20OS
SOHLH2
MIR548X2
MIR4703
MIR5007
MIR5693

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13|ENSG00000239186.1
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
MIR3182
RN7SL134P
snoU13|ENSG00000238321.1
RN7SKP190
7SK|ENSG00000260682.2
MIR4720
GAN
PKD1L2
CMC2
RNA5SP431
PIH1
MON1B
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
PRDM7
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
JPH3
VAT1L
WFDC1
MTHFSD
DBNDD1
KLHL36
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
CENPBD1
ZNF276
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
SLC38A8
ADAD2
ADAMTS18
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
C16orf74
SYCE1L
MIR1910
C16orf95
MIR4719
MIR5093

Genes in Wide Peak

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

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

Genes
SDHD
ATM
DDX10
POU2AF1
SDHD
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
ACAT1
CRYAB
DLAT
DRD2
FDX1
HTR3A
IL18
NCAM1
NNMT
NPAT
PPP2R1B
PTS
RDX
SLN
ZBTB16
CUL5
HTR3B
ZW10
RBM7
EXPH5
CADM1
REXO2
TIMM8B
C11orf71
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
TEX12
ARHGAP20
USP28
C11orf1
TMPRSS5
BCO2
DIXDC1
ZC3H12C
FDXACB1
C11orf52
C11orf93
PIH1D2
NXPE1
NXPE2
KDELC2
LAYN
C11orf65
ANKK1
C11orf53
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CLDN25
MIR4301
MIR4491

Genes in Wide Peak

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

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

Genes
GATA3
LINC00710
SFTA1P
LINC00709
RNA5SP299
LINC00708
TAF3
LINC00707
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PRKCQ
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
KIN
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
SFMBT2
ASB13
TUBAL3
ITIH5
AKR1E2
FBXO18
RBM17
IDI2
UCN3
LINC00200
PRR26

Genes in Wide Peak

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

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

Genes
FGFR1OP
MLLT4
TNFAIP3
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13|ENSG00000239136.1
AIRN
SNORA29
SNORA20|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
ACAT2
CCR6
ESR1
FUCA2
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LPA
MAS1
MAP3K4
NMBR
OPRM1
PARK2
PCMT1
PDCD2
PLAGL1
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
RNASET2
SYNJ2
LATS1
QKI
WTAP
AKAP12
PHACTR2
UST
CITED2
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
CCDC28A
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
AIG1
SNX9
MPC1
HECA
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
ABRACL
PBOV1
PERP
SMOC2
ULBP3
C6orf211
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
RSPH3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
SYTL3
IL22RA2
TAGAP
PACRG
RAET1E
ZC2HC1B
RAET1L
PNLDC1
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
WDR27
SHPRH
PRR18
ECT2L
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
TMEM242
MIR1202
MIR1273C
MIR3918
MIR3939
MIR3668
MIR4466
MIR4465

Genes in Wide Peak

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

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

Genes
ACSL3
ATIC
CREB1
IDH1
PAX3
FEV
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
snoU13|ENSG00000238736.1
snoU13|ENSG00000238428.1
CXCR2P1
DIRC3
RN7SKP43
RNA5SP120
RPL37A
MREG
LINC00607
snoU13|ENSG00000238663.1
SNORA70|ENSG00000207274.1
VWC2L
MIR4438
MIR548F2
RNA5SP119
RPE
RNA5SP118
RNA5SP117
CRYGEP
snoU13|ENSG00000238582.1
RNA5SP116
MIR2355
FASTKD2
RN7SKP260
RN7SKP200
SNORA41|ENSG00000207406.1
SNORD51|ENSG00000207047.2
NDUFS1
Vault|ENSG00000252485.1
RN7SKP178
AAMP
ACADL
ALPI
ALPP
ALPPL2
BARD1
BCS1L
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CYP27A1
DES
EEF1B2
EPHA4
ERBB4
FN1
GBX2
GPR1
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NEU2
PDE6D
SERPINE2
PSMD1
PTH2R
PTMA
PTPRN
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
WNT6
XRCC5
ZNF142
FZD5
SCG2
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
SP140
IKZF2
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
PNKD
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
PRLH
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ASIC4
DOCK10
PECR
C2orf83
MFF
ACKR3
MARCH4
WDFY1
NYAP2
ZDBF2
USP37
CTDSP1
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
PLCD4
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
AP1S3
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
UBE2F
KANSL1L
METTL21A
CCNYL1
CCDC140
SLC23A3
GPBAR1
SLC16A14
LINC00471
DAW1
C2orf57
PIKFYVE
TIGD1
CCDC108
C2orf72
UNC80
RUFY4
MROH2A
ESPNL
C2orf62
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
DYTN
ASB18
MIR375
PRSS56
MIR1471
MIR4268
MIR3132
MIR4269
MIR4775
MIR5001
MIR5702
MIR5703

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
AKT1
KTN1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
NIN
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3|ENSG00000200693.1
WDR89
SCARNA20|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112|ENSG00000252380.1
SIX1
U3|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
RN7SKP99
NAA30
RN7SL461P
LINC00520
RPL13AP3
TBPL2
MIR4308
RNU6ATAC9P
RN7SL588P
ERO1L
RNA5SP385
LINC00640
LINC00519
SNORA70|ENSG00000201376.1
TMX1
snoU83B
RN7SL452P
CDKL1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
CDKN3
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FOS
FUT8
GALC
GCH1
GMFB
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
PSMC6
PTGDR
PTGER2
ABCD4
PYGL
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SLC8A3
SNAPC1
SPTB
STYX
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
DLGAP5
AREL1
TECPR2
MED6
CNIH
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
PAPOLA
ACOT2
TMED10
FERMT2
PTPN21
WDHD1
MAP4K5
NID2
VASH1
ATG14
ZBTB1
SNW1
PCNX
DAAM1
SAMD4A
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
TIMM9
MLH3
KCNH5
GPR132
POMT2
COQ6
ATL1
FCF1
RDH11
SERPINA10
COX16
DACT1
EVL
GSKIP
CINP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
GNG2
TMEM260
FBXO34
CDCA4
NRDE2
ATG2B
UBR7
C14orf105
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
AP5M1
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNT16
PLEKHH1
TXNDC16
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
SAV1
VIPAS39
SMOC1
MOAP1
IRF2BPL
MPP5
INF2
PCNXL4
GNPNAT1
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
DDHD1
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
MAPK1IP1L
IFT43
L3HYPDH
AHNAK2
TRIM9
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
FRMD6
SOCS4
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
RDH12
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
ABHD12B
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SYNE3
TMEM30B
EML5
NUDT14
LINC00521
SERPINA11
GPR137C
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
C14orf39
CCDC85C
SERPINA9
VSX2
SLC35F4
LRRC9
COX8C
ASPG
RAB15
TOMM20L
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
LINC00238
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4505
MIR4708
MIR151B
MIR4710
MIR2392
MIR5694
MIR5580

Genes in Wide Peak

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

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

Genes
IL2
KDR
KIT
PDGFRA
RAP1GDS1
CHIC2
TET2
LINC00616
LINC00613
PCDH10
SNORA70|ENSG00000252014.1
RN7SL205P
RNY5P4
snoU13|ENSG00000238802.1
HSPA4L
INTU
RN7SL335P
QRFPR
RN7SKP137
MAD2L1
SNORA11|ENSG00000221245.1
C4orf3
CEP170P1
SNHG8
NT5C3AP1
MTRNR2L13
RN7SL808P
MIR577
RN7SL184P
TIFA
C4orf32
ENPEP
RN7SL275P
CCDC109B
MIR576
RN7SL55P
SNORD112|ENSG00000252566.1
GIMD1
RN7SL89P
SNORA31|ENSG00000252136.1
TACR3
BDH2
CISD2
snoU13|ENSG00000238948.1
RN7SL728P
MIR1255A
ADH1B
PCNAP1
MIR3684
EIF4E
RN7SKP28
RNA5SP164
RN7SKP248
GPRIN3
RN7SKP244
RNU6ATAC31P
IBSP
snoU13|ENSG00000238652.1
RN7SL681P
RN7SKP96
MIR4451
RN7SKP48
RN7SL552P
MRPS18C
snoR442|ENSG00000252834.1
MIR575
LINC00575
SNORD42|ENSG00000202440.1
HNRNPD
SNORA31|ENSG00000252762.1
SNORA75|ENSG00000212620.1
OR7E94P
LINC00989
NAA11
RN7SL127P
MIR5096
snoU13|ENSG00000238816.1
SNORD75|ENSG00000221711.1
MIR548AH
MIR4450
SNORD50|ENSG00000199857.1
CDKL2
BTC
PPBPP2
RN7SL218P
PPBP
PF4
PF4V1
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
RNA5SP163
snoU13|ENSG00000238318.1
CSN1S2AP
SULT1B1
UGT2A1
UGT2A2
UGT2B10
TMPRSS11BNL
FTLP10
TMPRSS11GP
SNORA62|ENSG00000202374.1
GNRHR
UBA6
TECRL
snoU13|ENSG00000238925.1
snoU13|ENSG00000238541.1
snoU13|ENSG00000238579.1
NOA1
RN7SL357P
RN7SL492P
ARL9
SRP72
RNA5SP162
KIAA1211
RNA5SP161
RN7SKP30
RN7SL822P
RN7SL424P
snoU13|ENSG00000238753.1
GSX2
ADH1A
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
ALB
AMBN
ANK2
ANXA3
ANXA5
AREG
ART3
ATOH1
BMP3
BMPR1B
CAMK2D
CASP6
CCNA2
CCNG2
SCARB2
CDS1
CENPC
CENPE
CSN1S1
CSN2
CSN3
DCK
DMP1
DSPP
EGF
EPHA5
EREG
FABP2
FGF2
FGF5
GC
GK2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
H2AFZ
HADH
HTN1
HTN3
CFI
IGFBP7
IGJ
IL8
CXCL10
MANBA
CXCL9
AFF1
MTTP
MUC7
NFKB1
PDHA2
PITX2
PKD2
EXOSC9
POLR2B
PPEF2
PPAT
PPP3CA
PRKG2
MAPK10
PTPN13
REST
RPL34
CXCL6
CXCL11
CXCL5
SNCA
SPINK2
SPP1
STATH
SULT1E1
TRPC3
UBE2D3
UGT2B4
UGT2B7
UGT2B15
UGT2B17
UGT8
SPARCL1
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
HERC3
PAPSS1
AIMP1
NDST3
TMPRSS11D
ABCG2
ADAMTS3
CLOCK
CEP135
SEC24D
G3BP2
HNRNPDL
TSPAN5
ENAM
FAM13A
SPRY1
PGRMC2
SEC24B
CXCL13
PAICS
PDLIM5
RRH
UGT2B11
PLK4
HPSE
NMU
SMR3B
NPFFR2
UGT2A1
CCNI
PRDM5
NUDT6
SEC31A
RUFY3
MMRN1
WDFY3
METAP1
LPHN3
PARM1
RCHY1
ANKRD17
STAP1
SMR3A
PPA2
DAPP1
DKK2
NAAA
COQ2
HPGDS
TMPRSS11E
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
MYOZ2
NUDT9
NUP54
GAR1
UGT2B28
PCDH18
USP53
ARHGEF38
ODAM
HERC6
BANK1
LARP1B
SDAD1
BBS7
C4orf21
AP1AR
BMP2K
SEPT11
EXOC1
TMEM165
SMARCAD1
MEPE
PRDM8
UTP3
INTS12
ANKRD50
KLHL8
SHROOM3
METTL14
ENOPH1
PROL1
OSTC
IL21
NEUROG2
SLC39A8
NDST4
ETNPPL
MRPL1
ELOVL6
NDNF
FAT4
ARSJ
SRD5A3
THAP9
UGT2A3
GSTCD
TNIP3
PHF17
SCD5
DNAJB14
FRAS1
C4orf29
ALPK1
CXXC4
PLA2G12A
SLC25A31
ARHGAP24
C4orf17
FAM175A
KIAA1109
HOPX
COL25A1
LNX1
AGPAT9
PIGY
CABS1
YTHDC1
MOB1B
TRMT10A
TBCK
HELQ
CYP2U1
DDIT4L
PCAT4
ANTXR2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
LIN54
TMPRSS11B
AASDH
PDCL2
C4orf36
TRAM1L1
SLC9B2
SLC9B1
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
SPATA5
BBS12
TIGD2
RASSF6
SGMS2
SYNPO2
CNOT6L
C4orf22
EPGN
NPNT
MFSD8
FDCSP
NAP1L5
COX18
STPG2
CCDC158
TMPRSS11A
SOWAHB
LRIT3
SLC10A6
HSD17B13
TMPRSS11F
C4orf40
AMTN
CCSER1
MIR302A
MTHFD2L
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
AREGB
MIR297
FAM47E
MIR1269A
THEGL
MIR548AG1
MIR4452
FAM47E
MIR5705
PYURF

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
AGA
SLC25A4
CASP3
CLCN3
CPE
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY5R
MSMO1
TLL1
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
ANXA10
KLHL2
PALLD
FAM149A
FBXO8
SPOCK3
AADAT
GALNT7
CLDN22
C4orf27
MARCH1
NEIL3
TMA16
DDX60
CDKN2AIP
TENM3
LRP2BP
FSTL5
STOX2
KIAA1430
SH3RF1
SPCS3
TRAPPC11
MLF1IP
WWC2
CEP44
SNX25
TKTL2
CBR4
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
FAM218A
TRIM60
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
TRIM61
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR4276
MIR3945
MIR4455

Genes in Wide Peak

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

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

Genes
ETV6
ZNF384
LST3
AEBP2
RN7SL67P
RN7SL459P
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
C1R
SCARNA12
DSTNP2
RPL13P5
RN7SL380P
SCARNA11|ENSG00000251898.1
SCARNA10
MRPL51
RN7SL391P
RN7SL69P
NDUFA9
A2M
APOBEC1
ARHGDIB
C1S
C3AR1
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
GAPDH
GNB3
GPR19
GUCY2C
IAPP
KCNA1
KCNA5
KCNA6
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LRP6
LTBR
M6PR
MGP
MGST1
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PTMS
PTPN6
PTPRO
PEX5
PZP
SCNN1A
SLC2A3
SLCO1A2
VAMP1
TNFRSF1A
TPI1
VWF
MFAP5
USP5
MLF2
KLRC4
YBX3
DYRK4
CD163
GDF3
CLSTN3
NCAPD2
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
SLCO1B1
KLRAP1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
SLCO1B3
COPS7A
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
HEBP1
DERA
ING4
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
ANO2
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
NANOG
APOLD1
GSG1
CDCA3
RBP5
ACRBP
SPSB2
RERG
PLCZ1
CAPZA3
CLEC6A
C12orf57
LOH12CR1
TMEM52B
HIST4H4
SLC2A14
A2ML1
CLEC12A
CLECL1
CLEC4C
PIANP
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CD163L1
CLEC9A
C12orf36
CLEC4D
SLCO1B7
ACSM4
TAS2R42
DPPA3
NANOGNB
CLEC2A
CLEC12B
LINC00937
MIR141
MIR200C
ZNF705A
SMCO3
PRB2
MIR614
SLC15A5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.1.

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
GOPC
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
snoU13|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18|ENSG00000252249.1
U3|ENSG00000221455.1
U3|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73|ENSG00000222145.1
RN7SL183P
snoU13|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70|ENSG00000206886.1
RNA5SP210
SNORD112|ENSG00000252932.1
HTR1B
U6|ENSG00000272445.1
snoU13|ENSG00000239132.1
RNA5SP209
RN7SKP163
U3|ENSG00000221332.1
MB21D1
snoU13|ENSG00000238464.1
OOEP
OGFRL1
U3|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65|ENSG00000212229.1
FKBP1C
LINC00680
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1E
IFNGR1
IMPG1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
ME1
MAP3K5
MYO6
NMBR
NT5E
OPRM1
PCMT1
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
SGK1
SIM1
SMPD2
ELOVL4
MAP3K7
TCF21
NR2E1
TPBG
TPD52L1
TTK
UTRN
VIP
PTP4A1
EPM2A
DDO
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
HMGN3
MED23
FHL5
AKAP7
ATG5
AKAP12
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
PHF3
HEY2
ORC3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
SENP6
TIAM2
FBXL4
FBXO5
SLC17A5
RGS17
PDE7B
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
LGSN
HECA
COQ3
IL20RA
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
QRSL1
VNN3
DDX43
FAM46A
TMEM30A
LMBRD1
ECHDC1
KCNQ5
TULP4
RARS2
PDSS2
SMIM8
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
FAM135A
ZBTB2
BEND3
ABRACL
RRAGD
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
CCDC170
MYCT1
ULBP2
ULBP1
KHDC1
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
ARMC2
L3MBTL3
MCHR2
FAXC
GJA10
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
UBE3D
ARHGAP18
GTF3C6
MRAP2
MTFR2
KLHL32
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
RIPPLY2
IRAK1BP1
TAAR9
TAAR1
NCOA7
HINT3
CD109
RAET1E
PM20D2
SRSF12
ZC2HC1B
RAET1L
SAMD3
RNF217
NKAIN2
KHDC3L
C6orf165
PRSS35
LCA5
OLIG3
TXLNB
KHDRBS2
C6orf163
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
MMS22L
MCM9
SHPRH
CEP57L1
PPIL6
DCBLD1
TAAR6
SLC35D3
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GJB7
SUMO4
CENPW
SOGA3
CEP85L
THEMIS
LIN28B
SAMD5
IYD
GTF2H5
MIR30A
MIR30C2
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR587
MIR588
METTL24
TMEM242
TRAPPC3L
KHDC1L
MIR2113
MIR1202
MIR1273C
MIR548U
MIR3144
MIR4282
MTRNR2L9
MIR3668
SMLR1
MIR4464
MIR4466
MIR4643
MIR4465
MIR548AJ1
MIR548AI
MIR4463
MIR548H5

Genes in Wide Peak

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

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

Genes
APC
CD74
EBF1
IL6ST
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
TRIM52
SNORD95|ENSG00000264549.1
SNORD96A
LINC00847
MIR340
RN7SKP150
MIR1229
HMGB3P22
RN7SL71P
ZNF879
ZNF354B
AACSP1
RN7SKP70
RN7SL646P
RN7SL562P
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
RN7SKP148
snoU13|ENSG00000239026.1
NSG2
RNA5SP200
SNORA74B
ATP6V0E1
MIR5003
SNORA57|ENSG00000212529.1
C5orf50
SNORA70|ENSG00000206909.1
RN7SL339P
snoU13|ENSG00000252387.1
RN7SL623P
MIR4454
KCNMB1
LCP2
C5orf58
MIR378E
MIR585
MIR103A1
PANK3
FBLL1
SNORA40|ENSG00000253065.1
RN7SKP60
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68|ENSG00000252458.1
LSM11
THG1L
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
RNA5SP198
RN7SKP232
RNA5SP197
ZNF300P1
snoU13|ENSG00000239191.1
snoU13|ENSG00000238369.1
MIR378A
RN7SL868P
U3|ENSG00000221043.1
MIR143HG
RN7SKP145
MIR584
SH3TC2
SPINK13
RN7SL791P
RNA5SP196
GPR151
RN7SKP246
KCTD16
RN7SL87P
RN7SL68P
PCDHGB8P
PCDHB18
PCDHB17
PCDHA14
WDR55
MIR3655
SNORA27|ENSG00000200235.1
SNORD45|ENSG00000200051.1
CYSTM1
PURA
TMEM173
ECSCR
RN7SKP64
RNA5SP195
SNORA74A
SNORA74|ENSG00000252213.1
RNA5SP194
RN7SL867P
snoU13|ENSG00000238745.1
SNORD63|ENSG00000206989.1
SNORD63|ENSG00000222937.1
RN7SL682P
snoU13|ENSG00000238605.1
NPY6R
MIR874
RNA5SP193
FBXL21
TIFAB
MIR4461
MIR4461
PCBD2
RN7SL541P
PPP2CA
SKP1
snoU13|ENSG00000238796.1
HSPA4
LEAP2
UQCRQ
RNA5SP192
snoZ6|ENSG00000253067.1
HINT1
RNA5SP191
RNU6ATAC10P
KIAA1024L
MIR4633
C5orf63
RN7SKP117
RN7SL711P
RN7SL689P
snoU13|ENSG00000239103.1
snoU13|ENSG00000252295.1
snoU13|ENSG00000239067.1
snoU13|ENSG00000239084.1
RNA5SP190
RN7SL174P
TNFAIP8
MIR5706
snoU13|ENSG00000239011.1
DTWD2
ARL14EPL
AP3S1
RN7SKP89
RNU4ATAC13P
ZRSR1
SRP19
FLJ11235
SNORA13
RN7SKP57
CAMK4
SNORA51|ENSG00000207177.1
MIR548F3
TMEM232
RN7SKP230
FER
RN7SKP122
RN7SL782P
SNORA31|ENSG00000252337.1
RNA5SP189
RN7SL255P
LINC00491
LINC00492
RN7SKP68
RNA5SP188
RN7SL802P
MIR548P
RN7SKP62
GPR150
LUCAT1
SNORA70|ENSG00000206958.1
RNA5SP187
RN7SL629P
RN7SKP34
MIR3607
COX7C
NBPF22P
RN7SKP295
SCARNA18|ENSG00000238835.1
RN7SL378P
SSBP2
SNORA31|ENSG00000251828.1
snoU13|ENSG00000239159.1
MTX3
HOMER1
SNORA18|ENSG00000206592.1
RNY3P1
BHMT2
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13|ENSG00000238688.1
RNA5SP186
POLK
SNORA40|ENSG00000212363.1
RN7SL814P
MIR4804
RN7SL153P
MIR4803
snoU13|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13|ENSG00000238334.1
SNORA50|ENSG00000220986.1
RN7SL103P
7SK|ENSG00000249352.3
U8|ENSG00000212249.2
snoU13|ENSG00000238400.1
SNORA76|ENSG00000252904.1
RN7SL169P
HTR1A
CKS1B|ENSG00000268942.1
KIF2A
RN7SKP157
FKSG52
MIR582
GAPT
snoU13|ENSG00000238899.1
snoU13|ENSG00000238717.1
RNU6ATAC2P
RNA5SP185
RNA5SP184
snoU13|ENSG00000238326.1
RNA5SP183
MIR5687
MIR449C
MIR449B
MIR449A
GPX8
GZMK
MIR4459
RN7SL801P
MIR581
PELO
ITGA1
RNA5SP182
snoU13|ENSG00000238702.1
HCN1
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
CLTB
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
HARS
HEXB
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
ISL1
ITGA2
KCNN2
TNPO1
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
NAIP
NDUFA2
NDUFS4
NEUROG1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2R2B
MAPK9
PROP1
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATG12
PTTG1
PDLIM7
NREP
CNOT8
HAND1
MED7
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
APBB3
CCNO
TNIP1
GNB2L1
NSA2
FST
SLU7
POLR3G
RGS14
PLK2
IQGAP2
SEC24A
CPLX2
FAXDC2
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
PPWD1
HARS2
SKIV2L2
ZNF346
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
KLHL3
TSPAN17
OR4F3
OR2V1
HAVCR1
CYFIP2
PKD2L2
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
IPO11
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
RBM27
NEURL1B
DHX29
DDX4
FAM193B
SGTB
ARL15
TMED9
ZCCHC10
CDHR2
GIN1
SPDL1
AGGF1
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
NLN
ZNF608
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
MCCC2
EPB41L4A
CENPK
ERAP2
ARHGEF28
SIL1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PCYOX1L
CCNJL
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
ELOVL7
TRAPPC13
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
PSD2
ANKRD32
THOC3
GFM2
MEGF10
SPINK7
SPZ1
HAVCR2
PHYKPL
SMIM3
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
FCHO2
RAB3C
LYSMD3
SCGB3A2
SETD9
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
POC5
STARD4
WDR36
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC38A9
SLC36A2
CREBRF
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
CCDC125
C5orf27
CMYA5
STK32A
AQPEP
SLC36A1
RASGEF1C
ANKRD31
SERINC5
EFCAB9
SH3PXD2B
FAM153A
KIAA0825
RELL2
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
RGMB
RFESD
CHSY3
FAM170A
ARSI
ANKRD34B
PFN3
IRGM
MCIDAS
ACTBL2
FAM174A
CATSPER3
NIPAL4
SLCO4C1
DND1
MAST4
SIMC1
C5orf48
PROB1
C5orf46
ARHGEF37
RGS7BP
SPINK6
ANKHD1
MIR143
MIR145
MIR146A
LINC00461
SPINK14
FNDC9
C5orf56
IGIP
CTXN3
SMIM15
GRXCR2
SPINK9
ZFP62
CCNI2
CBY3
FAM153C
MIR583
GTF2H2C
SERF1B
ANKDD1B
LRRC70
FAM196B
FAM159B
C5orf52
MIR1303
TICAM2
MIR2277
MIR4280
MIR3141
MTRNR2L2
MIR3660
MIR3912
MIR3936
MIR3661
OCLN
MIR4634
MIR378H
MIR4460
MIR548AE2
MIR4638
MIR5197
MIR5692C1

Arm-level results

Table 2. Get Full Table Arm-level significance table - 21 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1300 | 0.09 | -0.924 | 0.997 | 0.12 | -0.0223 | 1
1q | 1195 | 0.24 | 2.92 | 0.0182 | 0.03 | -2.42 | 1
2p | 624 | 0.05 | -2.49 | 0.997 | 0.07 | -1.94 | 1
2q | 967 | 0.07 | -1.67 | 0.997 | 0.06 | -1.96 | 1
3p | 644 | 0.22 | 1.71 | 0.224 | 0.11 | -0.775 | 1
3q | 733 | 0.24 | 2.38 | 0.0718 | 0.10 | -0.968 | 1
4p | 289 | 0.02 | -2.78 | 0.997 | 0.40 | 6.01 | 7.56e-09
4q | 670 | 0.04 | -2.24 | 0.997 | 0.40 | 6.62 | 2.43e-10
5p | 183 | 0.29 | 3.14 | 0.0149 | 0.06 | -2.12 | 1
5q | 905 | 0.16 | 0.486 | 0.997 | 0.15 | 0.202 | 0.907
6p | 710 | 0.09 | -1.42 | 0.997 | 0.10 | -1.14 | 1
6q | 556 | 0.05 | -2.06 | 0.997 | 0.36 | 5.32 | 3.55e-07
7p | 389 | 0.29 | 3.4 | 0.0138 | 0.00 | -3.38 | 1
7q | 783 | 0.26 | 3.07 | 0.0149 | 0.03 | -2.58 | 1
8p | 338 | 0.16 | 0.122 | 0.997 | 0.17 | 0.389 | 0.907
8q | 551 | 0.17 | 0.474 | 0.997 | 0.05 | -2.28 | 1
9p | 301 | 0.03 | -2.62 | 0.997 | 0.33 | 4.33 | 3.46e-05
9q | 700 | 0.05 | -2.27 | 0.997 | 0.26 | 3.03 | 0.00412
10p | 253 | 0.05 | -2.39 | 0.997 | 0.30 | 3.45 | 0.00115
10q | 738 | 0.04 | -2.35 | 0.997 | 0.23 | 2.14 | 0.0504
11p | 509 | 0.14 | -0.175 | 0.997 | 0.05 | -2.37 | 1
11q | 975 | 0.15 | 0.264 | 0.997 | 0.07 | -1.76 | 1
12p | 339 | 0.22 | 1.5 | 0.304 | 0.06 | -2.26 | 1
12q | 904 | 0.21 | 1.95 | 0.15 | 0.03 | -2.64 | 1
13q | 560 | 0.09 | -1.18 | 0.997 | 0.40 | 6.41 | 7.43e-10
14q | 938 | 0.04 | -2.07 | 0.997 | 0.41 | 7.34 | 2.19e-12
15q | 810 | 0.12 | -0.539 | 0.997 | 0.15 | 0.308 | 0.907
16p | 559 | 0.20 | 1.31 | 0.388 | 0.11 | -0.877 | 1
16q | 455 | 0.20 | 1.13 | 0.485 | 0.17 | 0.317 | 0.907
17p | 415 | 0.12 | -0.653 | 0.997 | 0.29 | 3.36 | 0.00145
17q | 972 | 0.21 | 1.98 | 0.15 | 0.10 | -0.888 | 1
18p | 104 | 0.10 | -1.48 | 0.997 | 0.11 | -1.21 | 1
18q | 275 | 0.05 | -2.44 | 0.997 | 0.17 | 0.24 | 0.907
19p | 681 | 0.15 | 0.0579 | 0.997 | 0.08 | -1.62 | 1
19q | 935 | 0.14 | -0.0039 | 0.997 | 0.09 | -1.15 | 1
20p | 234 | 0.11 | -1.18 | 0.997 | 0.18 | 0.408 | 0.907
20q | 448 | 0.12 | -0.874 | 0.997 | 0.04 | -2.79 | 1
21q | 258 | 0.08 | -1.92 | 0.997 | 0.14 | -0.584 | 1
22q | 564 | 0.10 | -0.623 | 0.997 | 0.79 | 16.5 | 0
Xp | 418 | 0.09 | -1.44 | 0.997 | 0.35 | 4.99 | 1.52e-06
Xq | 668 | 0.10 | -0.969 | 0.997 | 0.35 | 5.08 | 1.12e-06

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/22230047/GDAC_MergeDataFiles_12185773/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_GENCODE_v18_20140127.mat

- CNV Files = /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 3. Get Full Table First 10 out of 87 Input Tumor Samples.

Tumor Sample Names
TCGA-3H-AB3K-01A-11D-A39Q-01
TCGA-3H-AB3L-01A-11D-A39Q-01
TCGA-3H-AB3M-01A-11D-A39Q-01
TCGA-3H-AB3O-01A-11D-A39Q-01
TCGA-3H-AB3S-01A-21D-A39Q-01
TCGA-3H-AB3T-01A-11D-A39Q-01
TCGA-3H-AB3U-01A-21D-A39Q-01
TCGA-3H-AB3X-01A-11D-A39Q-01
TCGA-3U-A98D-01A-12D-A39Q-01
TCGA-3U-A98E-01A-11D-A39Q-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
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