LowPass Copy number analysis (GISTIC2)
Bladder Urothelial Carcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1VM49NS
Maintained by Spring Yingchun Liu (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): LowPass Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1VM49NS
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 2.0.20 (Firehose task version: 126).

Summary

There were 112 tumor samples used in this analysis: 22 significant arm-level results, 20 significant focal amplifications, and 13 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 - 20 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
--- | --- | --- | --- | ---
11q13.3 | 2.8499e-09 | 2.8499e-09 | chr11:70102480-70428787 | 5
1q23.3 | 7.5348e-09 | 7.5348e-09 | chr1:160624317-161190721 | 22
3p25.2 | 8.5225e-07 | 8.5225e-07 | chr3:11913848-12576749 | 4
7p11.2 | 1.3064e-06 | 1.3064e-06 | chr7:54594326-55726666 | 6
8q22.3 | 1.476e-06 | 1.476e-06 | chr8:100146645-103355705 | 23
12q15 | 4.8476e-06 | 4.8476e-06 | chr12:69121869-70436774 | 16
19q12 | 2.9408e-06 | 0.00019258 | chr19:30021330-30821093 | 6
8p11.23 | 0.00036289 | 0.00036289 | chr8:37127703-37944323 | 10
17q12 | 0.0003015 | 0.00097007 | chr17:37807774-38014602 | 9
6p22.3 | 0.00015209 | 0.0036879 | chr6:19262639-24823672 | 21
6p22.3 | 9.013e-06 | 0.0077752 | chr6:17727193-23861197 | 17
1p34.2 | 0.027548 | 0.027548 | chr1:39396332-40714877 | 22
16p12.1 | 0.0069281 | 0.033159 | chr16:23852373-27102172 | 14
19q13.2 | 0.00025063 | 0.041071 | chr19:37953039-41225744 | 99
10p14 | 0.048051 | 0.048051 | chr10:4082074-10859662 | 39
20q11.21 | 0.1314 | 0.1314 | chr20:25328497-30866238 | 46
22q11.23 | 0.14087 | 0.14087 | chr22:1-27271918 | 197
16p13.2 | 0.056724 | 0.18528 | chr16:6480817-13296512 | 38
4q13.3 | 0.18938 | 0.18938 | chr4:68533744-78216278 | 103
17q11.2 | 0.16176 | 0.19889 | chr17:20979844-34943690 | 183

Genes in Wide Peak

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

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

Genes
hsa-mir-548k
CTTN
PPFIA1
SHANK2
MIR548K

Genes in Wide Peak

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

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

Genes
CD48
FCER1G
LY9
NDUFS2
NIT1
PFDN2
PPOX
USF1
B4GALT3
DEDD
ADAMTS4
USP21
F11R
UFC1
CD244
ITLN1
SLAMF7
PVRL4
KLHDC9
ITLN2
ARHGAP30
TSTD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p25.2.

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

Genes
PPARG
SYN2
TIMP4
TSEN2

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2
VOPP1
VSTM2A
LOC285878

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q22.3.

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

Genes
COX6C
hsa-mir-1273
hsa-mir-875
POLR2K
SPAG1
YWHAZ
RNF19A
RGS22
PABPC1
RRM2B
ZNF706
UBR5
GRHL2
NACAP1
NCALD
ANKRD46
VPS13B
SNX31
FBXO43
FLJ42969
MIR599
MIR875
MIR4471

Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
SLC35E3
NUP107
RAB3IP
BEST3
LRRC10
MIR1279
MIR3913-2
MIR3913-1

Genes in Wide Peak

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

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

Genes
CCNE1
URI1
POP4
PLEKHF1
C19orf12
VSTM2B

Genes in Wide Peak

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

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

Genes
ADRB3
EIF4EBP1
ERLIN2
PROSC
GPR124
BRF2
ZNF703
RAB11FIP1
GOT1L1
LOC728024

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
PNMT
TCAP
STARD3
IKZF3
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

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

Genes
E2F3
GPLD1
ID4
PRL
SOX4
ALDH5A1
FAM65B
KIAA0319
GMNN
DCDC2
TDP2
CDKAL1
ACOT13
MRS2
C6orf62
NRSN1
MBOAT1
HDGFL1
KAAG1
LINC00340
LOC729177

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

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

Genes
DEK
hsa-mir-548a-1
E2F3
ID4
PRL
SOX4
TPMT
CDKAL1
KIF13A
MBOAT1
HDGFL1
KDM1B
RNF144B
NHLRC1
LINC00340
MIR548A1
LOC729177

Genes in Wide Peak

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

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

Genes
MYCL1
BMP8B
NDUFS5
PPT1
RLF
PABPC4
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
RHBDL2
OXCT2
AKIRIN1
NT5C1A
MFSD2A
TMCO2
BMP8A
KIAA0754
SNORA55
PPIEL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p12.1.

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

Genes
hsa-mir-548w
AQP8
PRKCB
RBBP6
HS3ST4
CACNG3
TNRC6A
LCMT1
ARHGAP17
SLC5A11
C16orf82
ZKSCAN2
LOC554206
LOC100506655

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
AKT2
hsa-mir-641
ACTN4
BLVRB
CLC
ECH1
FBL
HNRNPL
LGALS4
LGALS7
MAP3K10
NFKBIB
PSMC4
PSMD8
MRPS12
RPS16
RYR1
SUPT5H
ZFP36
DPF1
LTBP4
FCGBP
DYRK1B
NUMBL
KCNK6
GMFG
PAK4
SPINT2
DLL3
MAP4K1
ZFP30
SIRT2
SIPA1L3
PLD3
EIF3K
LGALS13
SERTAD3
SERTAD1
ZNF571
PAF1
SARS2
SAMD4B
MED29
LGALS14
LRFN1
PRX
SPTBN4
CATSPERG
C19orf33
PLEKHG2
ADCK4
CNTD2
ITPKC
WDR87
ZNF607
YIF1B
TIMM50
SHKBP1
PPP1R14A
FBXO17
RASGRP4
ZNF573
EID2B
RINL
FBXO27
C19orf47
HIPK4
FAM98C
CAPN12
LGALS16
TTC9B
ZNF569
ZNF570
ZNF781
EID2
ZNF780B
ZNF540
GGN
IL28A
IL28B
IL29
ZNF780A
ZNF546
NCCRP1
SYCN
LEUTX
SELV
ZNF793
PAPL
SPRED3
LGALS17A
LOC643669
LOC644554
LGALS7B
MIR641
LOC100129935
LOC100507433
MIR4530
LOC100631378

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p14.

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

Genes
GATA3
hsa-mir-3155
ATP5C1
CALML3
AKR1C4
AKR1C1
AKR1C2
GDI2
IL2RA
IL15RA
ITIH2
PFKFB3
PRKCQ
AKR1C3
NET1
KIN
CALML5
ANKRD16
FAM208B
SFMBT2
ASB13
TUBAL3
ITIH5
AKR1E2
TAF3
FBXO18
RBM17
UCN3
SFTA1P
LOC338588
AKR1CL1
tAKR
LOC399715
FLJ45983
LOC439949
LOC100216001
MIR3155A
LOC100507127
MIR3155B

Genes in Wide Peak

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

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

Genes
hsa-mir-1825
hsa-mir-3193
hsa-mir-663
BCL2L1
FOXS1
HCK
ID1
PLAGL2
KIF3B
TM9SF4
GINS1
TPX2
NINL
POFUT1
ABHD12
ZNF337
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TSPY26P
MLLT10P1
C20orf160
NANP
LINC00028
NCOR1P1
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FAM182A
LOC284801
FRG1B
XKR7
MIR663A
FAM182B
PSIMCT-1
LOC100134868
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q11.23.

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

Genes
BCR
SMARCB1
CLTCL1
hsa-mir-548j
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ADORA2A
ADRBK2
ARVCF
ATP6V1E1
BID
COMT
CRKL
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
DDT
GGT1
GGT3P
GGT5
GNAZ
GP1BB
GSC2
GSTT1
GSTT2
SERPIND1
IGLL1
MIF
MMP11
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
SNRPD3
TBX1
CLDN5
TOP1P2
HIRA
UBE2L3
UFD1L
VPREB1
ZNF70
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
TPST2
TOP3B
P2RX6
SNAP29
RAB36
PPM1F
DGCR2
TXNRD2
USP18
HIC2
SPECC1L
CABIN1
PRAME
SEZ6L
TSSK2
SDF2L1
PPIL2
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
TFIP11
GSTTP1
DGCR11
DGCR9
POM121L1P
DGCR5
DGCR10
FBXW4P1
TRMT2A
RTDR1
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L9P
POM121L8P
YPEL1
ZDHHC8
VPREB3
C22orf43
MED15
UPB1
TUBA8
CECR1
DGCR8
GNB1L
PEX26
SUSD2
ASPHD2
MICAL3
MRPL40
RTN4R
SLC2A11
C22orf29
THAP7
OR11H1
C22orf13
SLC25A18
TMEM191A
MYO18B
KLHL22
DGCR6L
RIMBP3
KIAA1671
HPS4
SCARF2
GGTLC2
GUSBP11
DERL3
IGLL3P
LRP5L
LOC96610
MGC16703
GAB4
C22orf39
C22orf25
ZNF280A
SGSM1
ZNF280B
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
C22orf15
CCDC116
TMEM211
POM121L4P
RGL4
LOC284865
LOC284889
PI4KAP2
TPTEP1
LOC388849
FAM211B
LOC391322
LOC400891
BCRP2
CHCHD10
SRRD
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
PIWIL3
MIAT
BCRP3
TMEM191C
C22orf45
POM121L10P
LOC648691
CES5AP1
GSTTP2
GSTT2B
MIR648
MIR650
TMEM191B
PI4KAP1
LOC729444
DDTL
MIR301B
LOC100128531
CECR7
CECR5-AS1
FLJ41941
MIR1286
MIR1306
MIR548J
MIR3198-1
IGLL5
MIR3618
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p13.2.

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

Genes
TNFRSF17
CIITA
SOCS1
hsa-mir-548h-2
ABAT
EMP2
GRIN2A
GSPT1
NUBP1
PMM2
PRM1
PRM2
TNP2
USP7
SNN
LITAF
CLEC16A
CARHSP1
TMEM186
RSL1D1
DEXI
C16orf72
ZC3H7A
TXNDC11
RBFOX1
CPPED1
PRM3
METTL22
ATF7IP2
SNX29
RMI2
TEKT5
TMEM114
BCAR4
SHISA9
FAM18A
MIR548X
MIR4718

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
AFM
AFP
ALB
AMBN
AREG
ART3
BTC
CCNG2
SCARB2
CSN1S1
CSN2
CSN3
DCK
EREG
GC
GNRHR
CXCL1
CXCL2
CXCL3
GRSF1
HTN1
HTN3
IGJ
IL8
CXCL10
CXCL9
MUC7
PF4
PF4V1
PPEF2
PPBP
CXCL6
CXCL11
CXCL5
STATH
SULT1E1
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
USO1
SLC4A4
STBD1
CDKL2
TMPRSS11D
ADAMTS3
G3BP2
ENAM
UGT2B11
SMR3B
NPFFR2
PPBPL2
UGT2A1
CCNI
RUFY3
PARM1
RCHY1
ANKRD17
SMR3A
NAAA
SULT1B1
TMPRSS11E
NUP54
UGT2B28
ODAM
SDAD1
UBA6
SEPT11
UTP3
SHROOM3
PROL1
UGT2A3
CABS1
YTHDC1
MOB1B
TMPRSS11B
THAP6
C4orf26
RASSF6
EPGN
FDCSP
COX18
CSN1S2AP
CCDC158
TMPRSS11A
SOWAHB
TMPRSS11F
SYT14L
TMPRSS11BNL
C4orf40
AMTN
MTHFD2L
LOC441025
LOC550112
LOC550113
UGT2A2
TMPRSS11GP
FAM47E
FTLP10
CSN1S2BP
MIR4450
FAM47E-STBD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q11.2.

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

Genes
NF1
TAF15
SUZ12
hsa-mir-632
hsa-mir-365-2
hsa-mir-3184
hsa-mir-144
ACCN1
AP2B1
ALDOC
BLMH
CPD
CRYBA1
EVI2A
EVI2B
FLOT2
KCNJ12
LGALS9
LIG3
MYO1D
NOS2
OMG
PEX12
MAP2K3
PSMD11
RAD51D
RPL23A
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SH3GL1P1
SH3GL1P2
SLC6A4
SUPT6H
TNFAIP1
VTN
ZNF207
FOXN1
TMEM11
KSR1
CDK5R1
SLC13A2
UNC119
TIAF1
ZNHIT3
GOSR1
CCL4L1
TRAF4
KIAA0100
SPAG5
CCT6B
SARM1
PPY2
PYY2
DHRS7B
TMEM98
POLDIP2
TBC1D29
WSB1
ERAL1
SNORD4B
SNORD4A
SNORD42B
SNORD42A
TMEM97
GIT1
PIPOX
CRLF3
NLK
NLE1
FNDC8
SLFN12
RHOT1
C17orf79
C17orf63
ADAP2
UTP6
LYZL6
NUFIP2
TAOK1
PHF12
C17orf75
MMP28
TEFM
GGNBP2
ATAD5
MYO19
RAB34
NSRP1
RNF135
RAB11FIP4
CORO6
SSH2
TP53I13
IFT20
ZNF830
SLFN11
RASL10B
PIGS
SLC46A1
LRRC37B
ABHD15
TLCD1
RFFL
TMEM132E
SPACA3
SGK494
SEZ6
ANKRD13B
C17orf50
SLFN13
SLC35G3
UNC45B
TMEM199
PROCA1
DHRS13
LRRC37BP1
SLFN5
RHBDL3
C17orf108
RDM1
GAS2L2
C17orf103
C17orf66
KRT18P55
NEK8
PIGW
FAM27L
FLJ36000
C17orf51
SLFN14
CCL14-CCL15
EFCAB5
TMIGD1
CCL4L2
MYO18A
C17orf102
MIR144
MIR193A
TBC1D3B
TBC1D3C
CCL3L3
TBC1D3P5
SUZ12P
MIR423
ARGFXP2
DPRXP4
MIR451A
SEBOX
TBC1D3G
SNORD7
MIR632
TBC1D3H
MIR365B
KCNJ18
MIR3184
MTRNR2L1
SPAG5-AS1
AA06
SLFN12L
RAD51L3-RFFL
MIR4523
MIR4724
MIR4733
MIR451B
MIR4522
MIR4732
MIR4723
MIR4725
RAB34

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 - 13 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 | 2.412e-52 | 2.412e-52 | chr9:21964593-22024723 | 4
8p22 | 7.1775e-06 | 7.1775e-06 | chr8:1-31636712 | 263
13q14.2 | 8.0013e-06 | 8.0013e-06 | chr13:47328496-51676610 | 34
2q36.3 | 8.6613e-06 | 1.4589e-05 | chr2:213561821-243199373 | 285
2q22.1 | 0.00065298 | 0.0015751 | chr2:141719260-142020472 | 1
4q22.1 | 0.0063669 | 0.020204 | chr4:91510636-92537601 | 1
5q12.1 | 0.041919 | 0.041919 | chr5:45373655-78981219 | 160
15q12 | 0.043859 | 0.043859 | chr15:1-42987954 | 281
6q21 | 0.049012 | 0.049012 | chr6:89342867-122609798 | 145
17p12 | 0.059527 | 0.059527 | chr17:10232869-12759217 | 20
3p12.3 | 0.080145 | 0.080145 | chr3:41449449-85171246 | 353
4q34.3 | 0.033936 | 0.15941 | chr4:155656891-191154276 | 148
6p25.3 | 0.16006 | 0.16006 | chr6:1-5266921 | 39

Genes in Wide Peak

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

Table S21. Genes in bold are cancer genes as defined by The Sanger Institute's 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 8p22.

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

Genes
PCM1
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
GSR
GTF2E2
NRG1
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
UBXN8
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
FBXO25
FGF20
ADAMDEC1
CNOT7
PURG
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
AGPAT5
INTS9
CSGALNACT1
HR
PBK
ZNF395
DEFB103B
BIN3
TEX15
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
HMBOX1
MCPH1
PPP1R3B
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
NKX2-6
SGCZ
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
ESCO2
FBXO16
LOC157627
C8orf42
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FLJ10661
XKR6
LOC286059
LOC286083
EFHA2
LOC286114
SCARA5
LOC286135
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
C8orf80
LOC392196
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
C8orf75
MBOAT4
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA1B
FAM90A20
FAM90A19
ZNF705D
LOC100128750
FAM66B
LOC100128993
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR4287
MIR3148
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
LOC100507341
MIR548O2
MIR4659A
MIR4660
MIR4659B
LOC100652791

Genes in Wide Peak

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

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

Genes
RB1
hsa-mir-15a
RCBTB2
ESD
MLNR
GUCY1B2
HTR2A
KPNA3
SUCLA2
DLEU2
ITM2B
LPAR6
TRIM13
DLEU1
FNDC3A
MED4
PHF11
RCBTB1
NUDT15
CYSLTR2
SPRYD7
RNASEH2B
CDADC1
CAB39L
SETDB2
EBPL
ARL11
ST13P4
DLEU7
CTAGE10P
KCNRG
MIR15A
MIR16-1
MIR3613

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q36.3.

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

Genes
ATIC
ACSL3
PAX3
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
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
IL6ST
PIK3R1
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
BHMT
BTF3
CCNB1
CDK7
ERCC8
CRHBP
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HTR1A
ISL1
ITGA1
ITGA2
KIF2A
TNPO1
CD180
MAP1B
MAP3K1
MOCS2
NAIP
NDUFS4
PDE4D
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
HOMER1
SCAMP1
CARTPT
COL4A3BP
LHFPL2
CWC27
CCNO
NSA2
FST
PLK2
IQGAP2
SMA4
SMA5
ESM1
ADAMTS6
SV2C
MRPS27
PPWD1
OTP
SKIV2L2
BHMT2
PART1
FAM169A
DIMT1
DMGDH
IPO11
GCNT4
POLK
PELO
DHX29
DDX4
SGTB
ARL15
AGGF1
WDR41
DEPDC1B
BDP1
ERBB2IP
NLN
ZSWIM6
ANKRA2
MCCC2
CENPK
RGNEF
SLC30A5
CENPH
GPBP1
PARP8
ANKRD55
PTCD2
ELOVL7
C5orf44
UTP15
ZBED3
GFM2
NDUFAF2
MRPS36
SNX18
FCHO2
RAB3C
C5orf35
IL31RA
EMB
JMY
TMEM171
TMEM174
POC5
SREK1
SLC38A9
MARVELD2
MIER3
CDC20B
PAPD4
ZNF366
S100Z
CCDC125
GAPT
ANKRD31
LOC257396
C5orf64
RNF180
SREK1IP1
IDAS
ACTBL2
HCN1
MAST4
RNF138P1
RGS7BP
GPX8
MIR449A
LOC642366
C5orf43
LOC647859
GUSBP3
GTF2H2B
SNORA47
MIR449B
MIR581
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LRRC70
FAM159B
LOC100170939
LOC100272216
NCRUPAR
LOC100303749
MIR449C
OCLN
MIR4804
MIR4803

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

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

Genes
BUB1B
C15orf55
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
NBEAP1
CAPN3
CHRM5
CHRNA7
GABRA5
GABRB3
GABRG3
GANC
GCHFR
IPW
ITPKA
IVD
LTK
MEIS2
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SPINT1
SRP14
THBS1
TJP1
TYRO3
UBE3A
MKRN3
PAR5
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
AQR
ARHGAP11A
SLC12A6
RASGRP1
GPR176
CHP
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
C15orf2
TMEM87A
RPAP1
DKFZP434L187
GREM1
RPUSD2
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
KLF13
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
ZFP106
CHAC1
C15orf29
NIPA2
C15orf41
ZFYVE19
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
TUBGCP5
NIPA1
PLA2G4E
PAR1
LOC145845
TMCO5A
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
EXD1
FSIP1
RHOV
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
LOC503519
C15orf62
C15orf56
PHGR1
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
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
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
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 6q21.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
CCNC
COL10A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
KPNA5
LAMA4
MARCKS
MAN1A1
PLN
POU3F2
PREP
REV3L
SIM1
SMPD2
MAP3K7
NR2E1
TSPYL1
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
CASP8AP2
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
ANKRD6
CDK19
MDN1
TSPYL4
UFL1
BRD7P3
ASF1A
PNISR
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
SOBP
QRSL1
PDSS2
LYRM2
HACE1
BEND3
RRAGD
PRDM13
BACH2
POPDC3
MICAL1
FAM184A
MANEA
GPR63
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
KIAA1919
GTF3C6
KLHL32
NUS1
SLC16A10
PM20D2
SRSF12
BVES-AS1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
RSPH4A
LINC00222
CEP85L
LIN28B
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
LOC100130890
LOC100287632
MIR2113
MIR548H3
LOC100422737
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
DNAH9
MYH1
MYH2
MYH3
MYH4
MYH8
SCO1
ZNF18
MYH13
ARHGAP44
C17orf48
MYOCD
FLJ34690
TMEM220
SHISA6
PIRT
MIR744
LOC100289255

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.3.

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

Genes
FHIT
MITF
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
CDC25A
CISH
CCR1
CCR3
CCR5
CCBP2
COL7A1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GBE1
GNAI2
GNAT1
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
ROBO1
ROBO2
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
TMF1
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
SEC22C
RRP9
MAGI1
CACNA2D2
VPRBP
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
PTPN23
DNAH1
HIGD1A
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
ABHD5
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
ULK4
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
SELK
PROK2
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
SLC25A26
ZNF501
GPR62
FAM3D
LYZL4
KBTBD5
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
CCDC13
PRICKLE2
C3orf67
KCTD6
KLHDC8B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ALS2CL
TMIE
C3orf64
FBXW12
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
PRSS42
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
LOC401074
MIRLET7G
MIR135A1
MIR138-1
MIR191
FAM19A1
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
LOC644714
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4444-1
MIR4443
LOC100652759
LUST

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
AGA
SLC25A4
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PPID
MSMO1
TDO2
TLL1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
ANP32C
FAM149A
FBXO8
DUX2
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
PDGFC
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
MLF1IP
NBLA00301
MAP9
WWC2
CEP44
SNX25
TKTL2
CBR4
MGC45800
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
C4orf45
TRIM60
RBM46
C4orf46
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
LOC340017
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
MIR3688-1
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR3688-2

Genes in Wide Peak

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

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

Genes
IRF4
BPHL
SERPINB1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
TUBB2A
RIPK1
PRPF4B
CDYL
ECI2
FARS2
RPP40
FAM50B
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
FOXQ1
HUS1B
C6orf195
PXDC1
MGC39372
FAM217A
LOC285768
MYLK4
TUBB2B
PSMG4
DKFZP686I15217
C6orf201
PPP1R3G
MIR3691
LOC100507194
LOC100508120
MIR4645

Arm-level results

Table 3. Get Full Table Arm-level significance table - 22 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 | -0.473 | 1 | 0.04 | -2.41 | 1
1q | 1955 | 0.31 | 5.72 | 1.04e-07 | 0.03 | -2.69 | 1
2p | 924 | 0.26 | 1.61 | 0.154 | 0.13 | -1.55 | 1
2q | 1556 | 0.09 | -1.76 | 1 | 0.19 | 1.11 | 0.446
3p | 1062 | 0.28 | 2.42 | 0.0309 | 0.19 | 0.0715 | 1
3q | 1139 | 0.32 | 3.83 | 0.000431 | 0.09 | -2.08 | 1
4p | 489 | 0.07 | -3.59 | 1 | 0.20 | -0.602 | 1
4q | 1049 | 0.02 | -3.91 | 1 | 0.23 | 1.11 | 0.446
5p | 270 | 0.33 | 1.98 | 0.0735 | 0.28 | 0.867 | 0.558
5q | 1427 | 0.09 | -1.6 | 1 | 0.35 | 5.31 | 7.36e-07
6p | 1173 | 0.08 | -2.43 | 1 | 0.15 | -0.644 | 1
6q | 839 | 0.00 | -4.63 | 1 | 0.23 | 0.859 | 0.558
7p | 641 | 0.31 | 2.47 | 0.0296 | 0.03 | -4.04 | 1
7q | 1277 | 0.25 | 2.12 | 0.0604 | 0.04 | -3.33 | 1
8p | 580 | 0.28 | 1.27 | 0.272 | 0.36 | 3.2 | 0.00454
8q | 859 | 0.40 | 5.18 | 1.11e-06 | 0.10 | -2.06 | 1
9p | 422 | 0.22 | -0.186 | 1 | 0.44 | 5.09 | 1.41e-06
9q | 1113 | 0.16 | -0.44 | 1 | 0.38 | 5.13 | 1.41e-06
10p | 409 | 0.32 | 2.09 | 0.0604 | 0.17 | -1.18 | 1
10q | 1268 | 0.10 | -1.65 | 1 | 0.25 | 2.17 | 0.0862
11p | 862 | 0.03 | -3.49 | 1 | 0.40 | 5.31 | 7.36e-07
11q | 1515 | 0.08 | -1.97 | 1 | 0.23 | 2.06 | 0.0995
12p | 575 | 0.20 | -0.509 | 1 | 0.11 | -2.52 | 1
12q | 1447 | 0.13 | -0.712 | 1 | 0.08 | -2.12 | 1
13q | 654 | 0.23 | 0.445 | 0.729 | 0.23 | 0.445 | 0.821
14q | 1341 | 0.11 | -1.54 | 1 | 0.19 | 0.519 | 0.805
15q | 1355 | 0.05 | -3 | 1 | 0.15 | -0.463 | 1
16p | 872 | 0.08 | -2.77 | 1 | 0.16 | -0.873 | 1
16q | 702 | 0.13 | -1.89 | 1 | 0.13 | -1.89 | 1
17p | 683 | 0.24 | 0.516 | 0.713 | 0.46 | 5.98 | 4.48e-08
17q | 1592 | 0.27 | 3.49 | 0.00137 | 0.12 | -0.813 | 1
18p | 143 | 0.20 | -1.07 | 1 | 0.17 | -1.63 | 1
18q | 446 | 0.05 | -3.79 | 1 | 0.29 | 1.54 | 0.276
19p | 995 | 0.19 | 0.109 | 0.962 | 0.15 | -0.96 | 1
19q | 1709 | 0.31 | 4.97 | 2.72e-06 | 0.03 | -2.96 | 1
20p | 355 | 0.46 | 5.57 | 1.74e-07 | 0.08 | -2.86 | 1
20q | 753 | 0.49 | 7.34 | 4.13e-12 | 0.07 | -2.61 | 1
21q | 509 | 0.25 | 0.822 | 0.514 | 0.12 | -2.34 | 1
22q | 921 | 0.13 | -1.6 | 1 | 0.25 | 1.35 | 0.354
Xq | 1312 | 0.27 | 2.75 | 0.0147 | 0.15 | -0.395 | 1

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/6154391/segmentationfile.txt

- Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/6154391/markersfile.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 = 0.3

- Deletion Threshold = 0.3

- Cap Values = 2

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

- Gene GISTIC = 0

Table 4. Get Full Table First 10 out of 112 Input Tumor Samples.

Tumor Sample Names
TCGA-BL-A0C8-01A-11D-A10R-02
TCGA-BL-A13I-01A-11D-A13U-02
TCGA-BL-A13J-01A-11D-A10R-02
TCGA-BL-A3JM-01A-12D-A21C-26
TCGA-BT-A0S7-01A-11D-A10R-02
TCGA-BT-A0YX-01A-11D-A10R-02
TCGA-BT-A20N-01A-11D-A14U-02
TCGA-BT-A20O-01A-21D-A14U-02
TCGA-BT-A20P-01A-11D-A14U-02
TCGA-BT-A20Q-01A-11D-A14U-02

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