Bladder Urothelial Carinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16 (cga svn revision 38839).

Summary

There were 35 tumor samples used in this analysis: 17 significant arm-level results, 17 significant focal amplifications, and 14 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 - 17 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
--- | --- | --- | --- | ---
6p22.3 | 9.91e-06 | 9.91e-06 | chr6:19833818-23096030 | 8
1q23.3 | 0.001261 | 0.001261 | chr1:159160335-159567617 | 24
12q15 | 0.001944 | 0.001944 | chr12:67407170-68461877 | 13
17q12 | 0.0020227 | 0.0095515 | chr17:35058337-35159341 | 7
11q13.2 | 0.021537 | 0.021537 | chr11:68876335-69704851 | 6
19q13.13 | 0.028123 | 0.028123 | chr19:42525035-44578035 | 54
8q22.3 | 0.012482 | 0.031997 | chr8:99524488-103789516 | 25
9p21.3 | 0.050945 | 0.050945 | chr9:20000313-20943334 | 4
1p34.2 | 0.052209 | 0.052209 | chr1:39300820-41999023 | 39
3p25.2 | 0.052209 | 0.052209 | chr3:11691872-12831403 | 10
7p11.2 | 0.12014 | 0.12014 | chr7:50769929-62280486 | 26
17q11.2 | 0.10187 | 0.12477 | chr17:28028389-28283153 | 2
12p13.33 | 0.12918 | 0.12918 | chr12:539572-4221251 | 25
8p11.21 | 0.14031 | 0.14031 | chr8:41532176-42222195 | 8
4p16.3 | 0.17753 | 0.17753 | chr4:1401560-2593900 | 18
6q21 | 0.18071 | 0.18071 | chr6:107205627-107666415 | 6
8q24.21 | 0.032261 | 0.183 | chr8:127650793-129858315 | 7

Genes in Wide Peak

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

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

Genes
E2F3
ID4
PRL
SOX4
CDKAL1
MBOAT1
HDGFL1
FLJ22536

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
SDHC
APOA2
FCER1G
MPZ
NDUFS2
NIT1
PFDN2
PPOX
USF1
B4GALT3
DEDD
ADAMTS4
NR1I3
USP21
F11R
UFC1
PVRL4
TOMM40L
KLHDC9
ITLN2
ARHGAP30
LOC642502
PCP4L1
TSTD1

Genes in Wide Peak

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

Table S3. 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

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
PNMT
TCAP
STARD3
C17orf37
PGAP3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
CCND1
FGF3
FGF4
FGF19
ANO1
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.13.

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

Genes
ACTN4
ECH1
HNRNPL
LGALS4
LGALS7
NFKBIB
PSMD8
MRPS12
RYR1
DPF1
KCNK6
GMFG
PAK4
SPINT2
MAP4K1
ZFP30
SIRT2
SIPA1L3
EIF3K
ZNF571
PAF1
SARS2
SAMD4B
MED29
LRFN1
CATSPERG
C19orf33
WDR87
ZNF527
ZNF607
YIF1B
PPP1R14A
FBXO17
RASGRP4
ZNF573
RINL
FBXO27
FAM98C
CAPN12
ZNF569
ZNF570
ZNF781
ZNF540
GGN
IL28A
IL28B
IL29
HKR1
NCCRP1
SYCN
ZNF793
PAPL
SPRED3
LGALS7B

Genes in Wide Peak

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

Table S7. 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
ODF1
POLR2K
SPAG1
STK3
KLF10
YWHAZ
RNF19A
RGS22
PABPC1
RRM2B
ZNF706
UBR5
GRHL2
NACAP1
NCALD
OSR2
ANKRD46
VPS13B
SNX31
FBXO43
MIR599
MIR875

Genes in Wide Peak

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

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

Genes
MLLT3
hsa-mir-491
KIAA1797
MIR491

Genes in Wide Peak

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

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

Genes
MYCL1
hsa-mir-30c-1
BMP8B
COL9A2
CTPS
EDN2
NFYC
PPT1
RLF
PABPC4
KCNQ4
RIMS3
ZMPSTE24
PPIE
CAP1
SCMH1
MACF1
HEYL
HPCAL4
TRIT1
HIVEP3
OXCT2
SMAP2
DEM1
ZNF643
NT5C1A
MFSD2A
TMCO2
ZNF684
CITED4
SLFNL1
ZNF642
BMP8A
MIR30C1
MIR30E
KIAA0754
SNORA55
LOC728448
LOC100130557

Genes in Wide Peak

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

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

Genes
PPARG
RAF1
SYN2
TIMP4
VGLL4
CAND2
MKRN2
TMEM40
TSEN2
C3orf31

Genes in Wide Peak

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

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

Genes
EGFR
CCT6A
GBAS
GRB10
HPVC1
PHKG1
PSPH
COBL
SEC61G
SUMF2
CHCHD2
MRPS17
LANCL2
VOPP1
ZNF479
VSTM2A
DKFZp434L192
POM121L12
SEPT14
ZNF713
FKBP9L
LOC389493
ZNF716
LOC442308
LOC650226
SNORA15

Genes in Wide Peak

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

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

Genes
MYO1D
TMEM98

Genes in Wide Peak

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

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

Genes
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
PARP11
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
EFCAB4B
CACNA2D4
FBXL14
DCP1B
B4GALNT3
HSN2
LRTM2
LOC100292680

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
hsa-mir-486
ANK1
PLAT
MYST3
AP3M2
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
hsa-mir-943
LETM1
RNF4
WHSC2
SLBP
TACC3
MXD4
ZFYVE28
HAUS3
TMEM129
FAM53A
NAT8L
POLN
C4orf48
SCARNA22
MIR943

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

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

Genes
hsa-mir-587
C6orf203
QRSL1
PDSS2
BEND3
LOC553137

Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1208
hsa-mir-1206
hsa-mir-1204
POU5F1B
PVT1
LOC727677

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 3.1786e-32 | 3.1786e-32 | chr9:21855498-22438737 | 4
2q22.1 | 0.0003466 | 0.0010461 | chr2:139248662-143354308 | 1
17p12 | 0.001221 | 0.001221 | chr17:10040108-15280519 | 28
4q22.1 | 0.0033997 | 0.0033997 | chr4:91092757-93459528 | 2
2q37.1 | 0.011567 | 0.015953 | chr2:215984621-242951149 | 242
3p14.2 | 0.046582 | 0.046582 | chr3:59009803-61522370 | 1
5q11.2 | 0.016628 | 0.053578 | chr5:45730220-57785752 | 37
10q26.3 | 0.063834 | 0.063834 | chr10:121457373-133628884 | 60
15q13.3 | 0.087731 | 0.087731 | chr15:22478867-30800105 | 118
6q25.2 | 0.1177 | 0.11712 | chr6:153490906-155760257 | 7
6q21 | 0.13513 | 0.14829 | chr6:97351134-131948859 | 147
6p25.2 | 0.22949 | 0.22949 | chr6:1-12405964 | 71
11p15.4 | 0.23636 | 0.2394 | chr11:1-134452384 | 1357
5q12.2 | 0.015953 | 1 | chr5:1-180857866 | 961

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2BAS

Genes in Wide Peak

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

Table S19. 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 17p12.

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

Genes
MAP2K4
hsa-mir-548h-3
hsa-mir-744
COX10
DNAH9
MYH1
MYH2
MYH3
MYH4
MYH8
PMP22
SCO1
ZNF18
MYH13
RICH2
HS3ST3B1
HS3ST3A1
C17orf48
ELAC2
TEKT3
MGC12916
MYOCD
CDRT15P
CDRT15
TMEM220
SHISA6
PIRT
MIR744

Genes in Wide Peak

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

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

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

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

Genes
ACSL3
PAX3
FEV
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
hsa-mir-153-1
hsa-mir-375
hsa-mir-26b
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
IL8RA
IL8RB
IL8RBP
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
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
C2orf24
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
KIAA1486
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
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
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
TIGD1
CCDC108
C2orf72
C2orf85
RUFY4
DUSP28
ESPNL
ECEL1P2
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
PP14571

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
IL6ST
hsa-mir-449b
hsa-mir-581
GZMA
GZMK
ISL1
ITGA1
ITGA2
MAP3K1
MOCS2
NDUFS4
PPAP2A
HSPB3
CCNO
FST
ESM1
SKIV2L2
PELO
DHX29
DDX4
ARL15
GPBP1
PARP8
ANKRD55
SNX18
C5orf35
IL31RA
EMB
SLC38A9
MIER3
CDC20B
ACTBL2
RNF138P1
GPX8
MIR449A
MIR449B
MIR581

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
FGFR2
ACADSB
CTBP2
DMBT1
DOCK1
GPR26
HMX2
MGMT
MKI67
OAT
HTRA1
PTPRE
UROS
ADAM12
BUB3
FAM53B
GLRX3
TACC2
ATE1
SEC23IP
INPP5F
FAM175B
C10orf137
CUZD1
CHST15
ZRANB1
NSMCE4A
BRWD2
DHX32
PPP2R2D
BCCIP
PLEKHA1
LHPP
IKZF5
C10orf119
C10orf88
FANK1
C10orf90
BTBD16
FAM24A
PSTK
MMP21
CLRN3
CPXM2
PPAPDC1A
FAM24B
EBF3
TCERG1L
HMX3
FLJ46361
ARMS2
C10orf122
NKX1-2
C10orf120
LOC399815
METTL10
FOXI2
NPS
FAM196A
LOC100169752

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.3.

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

Genes
hsa-mir-211
APBA2
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
OCA2
SCG5
SNRPN
TJP1
UBE3A
PAR5
HERC2
SNURF
ARHGAP11A
MTMR15
FAM189A1
DKFZP434L187
KLF13
MTMR10
NDNL2
ATP10A
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
SNORD107
PAR1
OTUD7A
GOLGA8G
SNORD108
SNORD109A
SNORD109B
SNORD115-1
SNORD64
PAR4
PAR-SN
MIR211
WHAMML2
SNORD116-19
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
HBII-52-24
HBII-52-27
HBII-52-28
HBII-52-45
HBII-52-46
GOLGA8F
FAM7A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.2.

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

Genes
OPRM1
RBM16
IPCEF1
TIAM2
CLDN20
TFB1M
CNKSR3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q21.

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

Genes
PRDM1
ROS1
STL
GOPC
hsa-mir-588
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
ARG1
CCNC
COL10A1
EPB41L2
FABP7
FOXO3
FRK
FYN
GJA1
GPR6
GRIK2
HDAC2
HSF2
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
SIM1
SMPD2
NR2E1
TPD52L1
TSPYL1
DDO
SNX3
CD164
WISP3
WASF1
AKAP7
ATG5
KIAA0408
ZBTB24
FIG4
TRDN
TRAF3IP2
SMPDL3A
ASCC3
BVES
SEC63
CDC2L6
TSPYL4
HEY2
BRD7P3
ASF1A
SFRS18
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
HDDC2
TUBE1
C6orf203
CDC40
RWDD1
COQ3
SOBP
QRSL1
ECHDC1
PDSS2
SERINC1
HACE1
BEND3
PRDM13
TRMT11
POPDC3
MICAL1
FAM184A
GPR63
RNF146
ARMC2
RPF2
L3MBTL3
MCHR2
C6orf168
RTN4IP1
RSPO3
USP45
SLC22A16
KIAA1919
ARHGAP18
GTF3C6
KLHL32
TMEM200A
NUS1
SLC16A10
CLVS2
NCOA7
HINT3
SAMD3
RNF217
NKAIN2
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
C6orf167
FAM26E
MCM9
SCML4
LOC285733
C6orf182
PPIL6
FLJ34503
DCBLD1
RSPH4A
C6orf58
C6orf173
C6orf174
C6orf204
THEMIS
LIN28B
FAM26F
LOC442245
RFPL4B
LOC553137
C6orf225
MIR548B
LOC728402
C6orf186
BET3L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.2.

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

Genes
IRF4
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CDYL
LY86
EEF1E1
PECI
FARS2
RPP40
FAM50B
SLC35B3
NRN1
TMEM14C
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
TXNDC5
TMEM14B
RIOK1
C6orf105
FOXQ1
HUS1B
SNRNP48
C6orf195
MGC26597
LOC221710
SYCP2L
C6orf218
C6orf145
C6orf146
LOC285768
LOC285780
CAGE1
MYLK4
TUBB2B
C6orf52
FAM136B
PSMG4
DKFZP686I15217
C6orf201
HERV-FRD
PPP1R3G
HULC
TMEM170B
SCARNA27

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
BIRC3
ATM
CCND1
CARS
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
HRAS
LMO1
LMO2
MEN1
MLL
NUMA1
NUP98
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
hsa-mir-100
hsa-mir-125b-1
hsa-mir-34c
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-548k
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-130a
hsa-mir-129-2
hsa-mir-610
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-210
ACAT1
ACP2
ACRV1
ACTN3
ADM
ADRBK1
AP2A2
APLNR
ALDH3B1
ALDH3B2
AMPD3
APBB1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
RHOG
ARHGAP1
PHOX2A
ARL2
ARNTL
ARRB1
ART1
ASCL2
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CCKBR
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
TPP1
CLNS1A
CNGA4
CNTF
COPB1
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSD
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GTF2H1
GUCY1A2
H2AFX
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HMBS
SLC29A2
HPX
HSPA8
HSPB2
DNAJC4
HTR3A
IGF2
IGHMBP2
IL10RA
IL18
ILK
INCENP
INS
INPPL1
IRF7
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KCNQ1
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LSP1
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MUC2
MUC6
MYBPC3
MYO7A
MYOD1
NAP1L4
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
NUCB2
OMP
OPCML
SLC22A18
SLC22A18AS
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PDE3B
PGA5
PGR
PIK3C2A
PLCB3
POLR2G
POLR2L
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PSMA1
PSMC3
PSMD13
PTH
PTPRCAP
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
RNH1
SNORD15A
ROM1
MRPL23
RPL27A
RPLP2
RPS3
RPS6KB2
RPS13
RPS25
RRM1
SAA1
SAA2
SAA3P
SAA4
SC5DL
SCN2B
SCN4B
SCT
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SMPD1
SORL1
SPI1
SPTBN2
SRPR
TRIM21
SSRP1
ST5
ST14
STIM1
STX3
STX5
ABCC8
TAGLN
TAF10
TALDO1
TCN1
TEAD1
TECTA
TH
THRSP
THY1
TSPAN4
TM7SF2
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TRPC6
TSG101
PHLDA2
TUB
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WEE1
WNT11
SF1
ZFPL1
ZNF143
ZBTB16
ZNF195
ZNF202
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIBP2
PPFIA1
SLC43A1
IFITM1
DGKZ
CHST1
BARX2
API5
MADD
OR6A2
DCHS1
EIF3F
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
BRSK2
AIP
SYT7
SART1
USP2
SLC6A5
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MED17
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
MICAL2
CTR9
CEP57
RICS
KIAA0652
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
TRIM66
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
TSPAN32
TSSC4
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
MRVI1
TRIM22
PRG3
IFITM3
YAP1
SPON1
RBM14
CDC42EP2
EIF3M
NXF1
DEAF1
KAT5
HYOU1
IPO7
SSSCA1
HTATIP2
IFITM2
DRAP1
TRIM3
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CUGBP1
POLD3
OR5I1
STARD10
NEU3
ME3
GPR83
LYVE1
YIF1A
SFRS2B
EHD1
C11orf58
STIP1
CLP1
KCNQ1OT1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
PKP3
HPS5
GPR44
SLCO2B1
RRAS2
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
SWAP70
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
DENND5A
NUP160
NCAPD3
FNBP4
RRP8
SIK3
SIRT3
CLCF1
OR52A1
VSIG2
BACE1
FAM89B
SNHG1
ARFIP2
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
C11orf41
PRDX5
POU2F3
ABTB2
BRMS1
C11orf20
CHRDL2
PAMR1
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
PPP1R14B
OR8G2
OR8B8
OR8G1
OR10A3
FXC1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
ACAD8
B3GAT1
DKK3
RBMXL2
RAB30
PGAP2
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
COMMD9
DDX25
C11orf21
PACSIN3
TRPM5
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
UBQLN3
KCNK4
RNF141
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
IGF2AS
TMEM216
BET1L
CEND1
CHCHD8
SLC15A3
PHF21A
MS4A4A
WIT1
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
CYB5R2
RSF1
SPA17
FXYD6
C11orf24
TRIM34
MUPCDH
CNTN5
SIAE
TOLLIP
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39
TRIM44
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
C11orf59
USP47
VPS37C
ANO1
TRIM68
NADSYN1
FAM86C
C11orf57
NAT10
CCDC87
SAPS3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
LRDD
ELMOD1
KCNQ1DN
SOX6
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
PARVA
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
MMP26
TMPRSS4
C11orf17
C11orf16
TMEM9B
NRIP3
ASCL3
GPR137
C11orf60
C11orf75
C11orf30
PRDM10
PRDM11
CABP4
CHRNA10
SLC17A6
TRIM49
PNPLA2
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
ATPGD1
SYT13
USP28
PHRF1
LRRC4C
SCUBE2
POLD4
KRTAP5-8
PLEKHB1
MS4A7
ZBED5
CREBZF
CARD18
SIGIRR
CCDC90B
CCDC81
AASDHPPT
ALX4
RIC8A
MRPL17
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
EPS8L2
KLC2
TUT1
MRPL11
TMEM135
STK33
KCTD14
C11orf95
CHID1
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
OR51G1
OR51B4
OR51B2
OR52N1
FAM118B
RIC3
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
E2F8
SLC25A22
CCDC82
ALG9
ZNF408
ASAM
NAT11
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
ATHL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
PTDSS2
HCCA2
GDPD5
CLPB
UNC93B1
SBF2
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
FAM160A2
RNASEH2C
FAR1
TMEM126A
DCUN1D5
BTBD10
EIF1AD
NUDT22
ARFGAP2
KIAA1826
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
SPRYD5
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
MICALCL
RELT
UBASH3B
C11orf70
LGALS12
TRIM5
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
NAV2
ATG16L2
GLB1L2
SYT8
TSPAN18
ESAM
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
PRKCDBP
VPS26B
GLB1L3
CDCA5
RPLP0P2
SAAL1
ODF3
SLC22A9
SNORD15B
TIRAP
CARD16
OSBPL5
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
LRRC56
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRE
MRGPRF
ART5
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIMP1
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
SLC36A4
FAT3
TRIM64
TMEM45B
CYP2R1
DBX1
CASP12
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
XRRA1
UBQLNL
MUC15
LOC143666
C11orf94
FAM76B
SESN3
PIWIL4
FLJ32810
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
C11orf42
GPHA2
ADAMTS15
NLRP6
B3GNT6
METT5D1
MPZL3
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
MRPL21
TPCN2
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
C11orf66
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
TMEM151A
OR51F1
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
FLJ46111
CSNK2A1P
OR51V1
H19
C11orf85
SLC25A45
NEAT1
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
LOC283174
OR9G4
C11orf64
P4HA3
PGM2L1
KLHL35
KCTD21
EFCAB4A
TMEM80
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LOC283267
IGSF22
OR10A4
OLFML1
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
B4GALNT4
OR52L1
OR2AG2
OR52B6
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
OR10A2
OVCH2
TBX10
PDDC1
C11orf34
RTN4RL2
GALNTL4
DKFZp686O24166
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
KRTAP5-10
SLC22A25
IFITM5
FAM99A
OR56B1
GVIN1
INSC
FIBIN
LOC387763
SLC22A10
SPDYC
LIPT2
C11orf90
OR52K1
OR52I1
OR51D1
OR52A4
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
GUCY2E
TRIM77
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
FAM180B
PCNXL3
C11orf87
C11orf92
C11orf88
LOC399959
PATE2
PATE4
SNX19
OR51T1
OR51A4
OR51A2
OR4A47
OR4C45
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR210
MIR34B
MIR34C
DDI1
BLID
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440040
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
NCRNA00167
LOC441601
OR5B3
MIR326
TRIM6-TRIM34
CCDC73
LOC494141
BDNFOS
MS4A13
OR8U8
OR9G9
SCARNA9
MIR483
SNORA3
SNORA52
HEPN1
TRIM64B
TRIM53
UBTFL1
BTBD18
PGA3
PGA4
LOC643923
CLDN25
RASSF10
LOC645332
LOC646813
RPL23AP64
LOC650368
SNORA8
SNORA1
SNORA18
SNORA23
SNORA40
SNORA45
SNORA54
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
SNORD97
MIR610
MIR611
MIR612
INS-IGF2
MUC5B
LOC729384
LOC729799
METTL12
C11orf83
MIR675
LOC100126784
LOC100128239
LOC100130987
C11orf91
FAM99B
LOC100133161
LOC100133315
LOC100133545
PATE3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.2.

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

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-1303
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-1974
hsa-mir-9-2
hsa-mir-582
hsa-mir-449b
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-887
ADCY2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGF10
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NDUFS6
NEUROG1
NPR3
NPY6R
OCLN
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
PURA
RAD17
RARS
RASA1
RASGRF2
RPL37
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP1
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
SRP19
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
C5orf13
TRIP13
CNOT8
RAB9P1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5OS
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
SDCCAG10
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
POLS
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
HISPPD1
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
OTP
SKIV2L2
NNT
TTC33
ZNF346
AMACR
SSBP2
BHMT2
TNFAIP8
NIPBL
LOC25845
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
FBXO4
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1L
MAT2B
SLC27A6
SNX24
MRPL22
RNASEN
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MGC29506
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
FAM134B
FAM105A
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
MTMR12
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
PCDH24
GIN1
WDR55
ANKHD1
NSUN2
CCDC99
THG1L
WDR70
AGGF1
WDR41
BRIX1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
ANKH
CCL28
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
AHRR
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1L
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
C5orf23
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
CARD6
TRIM52
HAVCR2
AGXT2L2
C5orf62
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
LMBRD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C1QTNF3
C5orf26
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
HEATR7B2
EGFLAM
PRRC1
C5orf33
UGT3A1
CAPSL
JMY
C5orf58
ZNF474
CCDC127
OR2Y1
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
C5orf37
GPR151
STARD4
WDR36
LOC134466
NUDCD2
UBLCP1
ACOT12
ANKRD43
SHROOM1
C5orf24
SFRS12
C5orf20
SLC38A9
SLC36A2
SPINK5L3
C5orf41
CEP120
LOC153328
TMEM167A
MBLAC2
TMEM161B
SRFBP1
PLEKHG4B
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
LOC153684
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
MGC42105
LIX1
ZNF366
FAM151B
S100Z
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
LVRN
SLC36A1
RICTOR
EIF4E1B
LOC255167
RASGEF1C
ANKRD31
SERINC5
LOC257358
SH3PXD2B
LOC285593
FAM153A
ARL10
C5orf36
GPR150
DTWD2
RELL2
NBPF22P
LOC285627
LOC285629
C5orf51
SLC36A3
KIF4B
OR2V2
FLJ37543
RNF180
SFRS12IP1
ZNF454
C5orf60
LOC285692
LOC285696
RGMB
RFESD
CHSY3
SLC6A19
TMEM173
FAM170A
LOC340074
ARSI
LOC340094
ANKRD34B
PFN3
ZNF879
PLCXD3
IRGM
FBLL1
ACTBL2
FAM174A
MTX3
CATSPER3
SLC6A18
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
C5orf34
MAST4
C5orf25
RNF138P1
LRRC14B
C5orf39
ISCA1L
C5orf48
LOC389332
LOC389333
C5orf46
FLJ41603
FLJ33360
RGS7BP
FLJ44606
SPINK6
ANKHD1-EIF4EBP3
MIR103-1
MIR143
MIR145
MIR146A
MIR218-2
SPINK5L2
C5orf40
MARCH11
LOC441089
FLJ42709
C5orf56
MIR340
C5orf53
GPX8
TIFAB
MIR449A
CTXN3
SNORD72
SNORD95
SNORD96A
ECSCR
TMEM232
C5orf43
GRXCR2
SPINK9
ZFP62
FLJ33630
LOC644936
CCNI2
LOC645323
CBY3
LOC647859
ANKRD33B
GUSBP3
GTF2H2B
FAM153C
LOC653391
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR548C
MIR548D2
MIR580
MIR581
MIR583
MIR585
SNHG4
LOC728264
GTF2H2C
LOC728411
SERF1B
LOC728554
SDHAP3
LOC728613
LOC728723
AACSL
LOC729678
OR4F29
GTF2H2D
SNORD123
MIR886
MIR874
LOC100129716
CCDC152
LRRC70
FAM196B
LOC100132062
LOC100132287
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100286948
TMED7-TICAM2
NCRUPAR
LOC100303749
LOC100310782

Arm-level results

Table 3. Get Full Table Arm-level significance table - 17 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.03 | -1.14 | 0.977 | 0.03 | -1.14 | 0.99
1q | 1572 | 0.09 | -0.217 | 0.977 | 0.00 | -1.85 | 0.99
2p | 753 | 0.20 | 0.59 | 0.832 | 0.00 | -2.34 | 0.99
2q | 1235 | 0.09 | -0.576 | 0.977 | 0.06 | -1.05 | 0.99
3p | 853 | 0.26 | 1.59 | 0.245 | 0.15 | -0.0983 | 0.99
3q | 917 | 0.31 | 2.73 | 0.0312 | 0.00 | -2.06 | 0.99
4p | 366 | 0.11 | -1.17 | 0.977 | 0.22 | 0.345 | 0.99
4q | 865 | 0.07 | -1.21 | 0.977 | 0.21 | 0.925 | 0.533
5p | 207 | 0.17 | -0.466 | 0.977 | 0.20 | -0.101 | 0.99
5q | 1246 | 0.11 | -0.256 | 0.977 | 0.22 | 1.65 | 0.215
6p | 937 | 0.06 | -1.42 | 0.977 | 0.06 | -1.42 | 0.99
6q | 692 | 0.03 | -1.97 | 0.977 | 0.15 | -0.328 | 0.99
7p | 508 | 0.29 | 1.67 | 0.245 | 0.04 | -1.85 | 0.99
7q | 1071 | 0.21 | 1.16 | 0.434 | 0.04 | -1.56 | 0.99
8p | 495 | 0.12 | -0.827 | 0.977 | 0.31 | 1.87 | 0.17
8q | 697 | 0.32 | 2.31 | 0.0818 | 0.16 | -0.103 | 0.99
9p | 343 | 0.21 | 0.154 | 0.977 | 0.52 | 4.48 | 7.28e-05
9q | 916 | 0.11 | -0.545 | 0.977 | 0.48 | 5.39 | 1.37e-06
10p | 312 | 0.29 | 1.27 | 0.395 | 0.15 | -0.576 | 0.99
10q | 1050 | 0.11 | -0.487 | 0.977 | 0.22 | 1.3 | 0.375
11p | 731 | 0.00 | -1.99 | 0.977 | 0.43 | 4.2 | 0.000171
11q | 1279 | 0.00 | -1.85 | 0.977 | 0.29 | 3.01 | 0.0103
12p | 484 | 0.25 | 0.947 | 0.558 | 0.11 | -0.989 | 0.99
12q | 1162 | 0.24 | 1.92 | 0.177 | 0.07 | -0.863 | 0.99
13q | 554 | 0.15 | -0.422 | 0.977 | 0.26 | 1.14 | 0.411
14q | 1144 | 0.07 | -0.881 | 0.977 | 0.24 | 1.89 | 0.17
15q | 1132 | 0.06 | -1.22 | 0.977 | 0.06 | -1.22 | 0.99
16p | 719 | 0.06 | -1.52 | 0.977 | 0.12 | -0.69 | 0.99
16q | 562 | 0.09 | -1.25 | 0.977 | 0.09 | -1.25 | 0.99
17p | 575 | 0.09 | -1.06 | 0.977 | 0.39 | 3.25 | 0.00559
17q | 1321 | 0.31 | 3.24 | 0.00775 | 0.23 | 1.81 | 0.173
18p | 117 | 0.11 | -1.39 | 0.977 | 0.22 | 0.0541 | 0.99
18q | 340 | 0.12 | -1.04 | 0.977 | 0.28 | 1.2 | 0.406
19p | 870 | 0.18 | 0.37 | 0.977 | 0.03 | -1.78 | 0.99
19q | 1452 | 0.29 | 3.44 | 0.0056 | 0.00 | -1.72 | 0.99
20p | 295 | 0.31 | 1.58 | 0.245 | 0.12 | -1 | 0.99
20q | 627 | 0.41 | 3.48 | 0.0056 | 0.14 | -0.458 | 0.99
21q | 422 | 0.16 | -0.487 | 0.977 | 0.10 | -1.26 | 0.99
22q | 764 | 0.10 | -0.989 | 0.977 | 0.12 | -0.571 | 0.99

Methods & Data
Input

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/BLCA/1215414/2.GDAC_MergeDataFiles.Finished/BLCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

- Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

- CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt

- Amplification Threshold = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 35 Input Tumor Samples.

Tumor Sample Names
TCGA-BL-A0C8-01A-11D-A10T-01
TCGA-BL-A13I-01A-11D-A13V-01
TCGA-BL-A13J-01A-11D-A10T-01
TCGA-BT-A0S7-01A-11D-A10T-01
TCGA-BT-A0YX-01A-11D-A10T-01
TCGA-BT-A20J-01A-11D-A14V-01
TCGA-BT-A20N-01A-11D-A14V-01
TCGA-BT-A20O-01A-21D-A14V-01
TCGA-BT-A20P-01A-11D-A14V-01
TCGA-BT-A20Q-01A-11D-A14V-01

Figure 3. Segmented copy number profiles in the input data

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- 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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- Maintainer = Dan DiCara

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