LowPass Copy number analysis (GISTIC2)
Colorectal Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
Maintained by Spring Yingchun Liu (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): LowPass Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1H70D4W
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 2.0.19 (Firehose task version: 125).

Summary

There were 103 tumor samples used in this analysis: 18 significant arm-level results, 17 significant focal amplifications, and 22 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
14q11.2 7.2295e-14 1.4905e-13 chr14:21755002-22026999 9
7p14.1 3.982e-12 3.982e-12 chr7:38261002-38623533 4
17q12 1.1252e-08 1.1252e-08 chr17:35082002-35176999 0 [MRM1]
8p11.23 4.6004e-05 0.00047568 chr8:38205002-38377749 4
5q31.1 0.00064892 0.00064892 chr5:134286002-134292999 1
19q13.11 0.0021523 0.0021523 chr19:24004001-32804999 19
7q34 0.0044813 0.0044813 chr7:141733001-142634599 13
3p11.1 0.0050087 0.0050087 chr3:90396629-95001225 6
8q24.21 0.0098773 0.0098773 chr8:128117002-129060999 10
20q12 0.014589 0.014589 chr20:41559002-43781999 32
8p11.21 0.007744 0.029515 chr8:40314002-40700999 1
13q12.13 0.061815 0.061815 chr13:24754770-32619999 56
10q22.3 0.062344 0.062344 chr10:73024002-82901999 86
14q32.33 0.083571 0.14738 chr14:105385002-105601542 5
13q21.33 0.16165 0.16165 chr13:72457001-73040584 0 [DACH1]
12p12.1 0.17028 0.22469 chr12:24548909-26825461 16
12p13.33 0.14408 0.79834 chr12:1-133851895 1200
Genes in Wide Peak

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

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

Genes
SALL2
TOX4
SUPT16H
METTL3
RPGRIP1
CHD8
RAB2B
SNORD8
SNORD9
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p14.1.

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

Genes
AMPH
STARD3NL
TARP
LOC100506776
Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
LETM2
C8orf86
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q31.1.

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

Genes
PCBD2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
CCNE1
UQCRFS1
URI1
ZNF254
ZNF536
POP4
TSHZ3
PLEKHF1
C19orf12
DKFZp566F0947
LOC148145
LOC148189
LOC284395
VSTM2B
RPSAP58
ZNF726
LOC100101266
LOC100505835
THEG5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q34.

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

Genes
EPHB6
PRSS1
PRSS2
MGAM
TRPV6
TRPV5
LOC93432
PRSS58
TRY6
LOC730441
LOC100124692
MOXD2P
MTRNR2L6
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p11.1.

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

Genes
PROS1
NSUN3
ARL13B
DHFRL1
LOC255025
STX19
Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1206
hsa-mir-1205
hsa-mir-1204
POU5F1B
PVT1
LOC727677
MIR1205
MIR1206
MIR1204
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q12.

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

Genes
ADA
HNF4A
KCNS1
MYBL2
SRSF6
STK4
YWHAB
WISP2
SGK2
TOMM34
SERINC3
PTPRT
PKIG
L3MBTL1
IFT52
C20orf111
JPH2
KCNK15
GDAP1L1
LOC79015
TTPAL
PABPC1L
TOX2
FITM2
WFDC12
RIMS4
R3HDML
GTSF1L
WFDC5
MIR3646
LOC100505783
LOC100505826
Genes in Wide Peak

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

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

Genes
ZMAT4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.13.

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

Genes
CDX2
FLT3
PARP4
ALOX5AP
ATP12A
CDK8
FLT1
GPR12
GTF3A
HMGB1
PDX1
PABPC3
UBL3
RNF6
RPL21
SLC7A1
MTMR6
NUPL1
FRY
USPL1
HSPH1
WASF3
MTUS2
SNORD102
POLR1D
POMP
ATP8A2
CENPJ
RNF17
KATNAL1
C13orf33
RXFP2
TEX26
B3GALTL
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
SPATA13
LNX2
PAN3
SLC46A3
C1QTNF9
TPTE2P6
RASL11A
SHISA2
ATP5EP2
LOC440131
SNORA27
TPTE2P1
PRHOXNB
RPL21P28
LINC00426
PAN3-AS1
TEX26-AS1
Genes in Wide Peak

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

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

Genes
hsa-mir-606
ADK
ANXA7
ANXA11
CAMK2G
KCNMA1
MAT1A
P4HA1
PLAU
PPP3CB
PSAP
RPS24
SFTPD
VCL
VDAC2
NDST2
MBL1P
DLG5
CHST3
SEC24C
SPOCK2
PPIF
MICU1
POLR3A
ECD
KIAA0913
DNAJC9
KAT6B
NUDT13
AP3M1
ASCC1
MRPS16
DUSP13
DDIT4
DNAJB12
SLC29A3
ZMIZ1
MYOZ1
CDH23
C10orf54
SYNPO2L
FAM213A
TSPAN14
C10orf11
C10orf58
DYDC2
PLA2G12B
ZNF503
MCU
CHCHD1
ZMYND17
TTC18
COMTD1
ANAPC16
SAMD8
DYDC1
EIF5AL1
USP54
FUT11
OIT3
LOC219347
PLAC9
ZCCHC24
UNC5B
ZNF503-AS1
LOC283050
FAM149B1
DUPD1
SH2D4B
C10orf105
C10orf55
C10orf103
LOC439990
LOC642361
LOC650623
SFTPA1
AGAP5
BMS1P4
SFTPA2
LOC100128292
ZNF503-AS2
LOC100132987
LOC100288974
MIR1256
LOC100507331
MIR4676
Genes in Wide Peak

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

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

Genes
GPR132
CDCA4
AHNAK2
C14orf79
PLD4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
hsa-mir-4302
BCAT1
ITPR2
LRMP
SOX5
SSPN
RASSF8
CASC1
BHLHE41
LINC00477
LYRM5
IFLTD1
C12orf77
MIR4302
LOC100506451
Genes in Wide Peak

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

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

Genes
ALDH2
ATF1
BCL7A
BTG1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
MLL2
HMGA2
WIF1
ZNF384
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
ACACB
ACADS
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ARL1
ART4
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
SCARB1
CD63
CD69
CDK2
CDKN1B
CHD4
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CREBL2
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
DDX11
ATN1
EPYC
DTX1
DUSP6
PHC1
EIF2B1
EIF4B
CELA1
ELK3
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GRIN2B
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTA4H
LTBR
LUM
LYZ
M6PR
MARS
METTL1
KITLG
MGP
MGST1
MIP
MMP17
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NDUFA9
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
POU6F1
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAB1
PRKAG1
PRPH
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAN
RAP1B
RARG
RBMS2
RDH5
RECQL
RFC5
RFX4
RNY5
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SNRPF
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
SYT1
TAC3
TARBP2
TBX5
TBX3
HNF1A
TDG
TEAD4
TMBIM6
TFCP2
TSPAN8
TMPO
TNFRSF1A
TPI1
NR2C1
HSP90B1
TULP3
TXNRD1
UBC
UBE2N
UNG
VDR
VWF
WNT1
WNT10B
ZNF10
ZNF26
ZNF84
ZNF140
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
DYRK2
PPFIBP1
PPFIA2
CSDA
LGR5
MAPKAPK5
DENR
RDH16
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
GPRC5A
KRT75
SCAF11
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
KIAA0748
KIAA0528
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
CLEC2B
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
RNF41
MPHOSPH9
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
LEPREL2
DCTN2
AKAP3
CCT2
SLCO1B1
RAD51AP1
CAMKK2
AVIL
PTGES3
KLRAP1
ZNF268
FRS2
TSPAN9
TRAFD1
OS9
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
PHLDA1
R3HDM2
MLXIP
RPH3A
KLRK1
P2RX2
RAB21
STK38L
FBXO21
FAIM2
MON2
SETD1B
UHRF1BP1L
ERC1
DDN
ANKLE2
TMEM194A
CUX2
KIAA1033
TBC1D30
ESYT1
TENC1
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
ABCB9
CBX5
ISCU
RIMBP2
ANP32D
ATP6V0A2
SMUG1
LEMD3
CORO1C
GABARAPL1
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
FBXW8
GALNT8
HSPB8
SNORD59A
GLS2
HCAR1
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CCDC41
IRAK4
ING4
GPN3
DDX47
GLTP
MRPL51
CLEC1B
CLEC1A
C12orf47
C1RL
ERGIC2
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TM7SF3
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
MAGOHB
SLC6A15
FAM90A1
RIC8B
C12orf35
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
CAND1
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
ARNTL2
CHPT1
PARP11
ANO2
C12orf4
C12orf5
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHDC5
PITPNM2
DIP2B
KIAA1467
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
C12orf44
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
OBFC2B
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
RPAP3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
FLJ13224
TCTN2
PLBD1
PYROXD1
NANOG
DNAJC22
NAA25
SLC24A6
ADAMTS20
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
C12orf39
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
C12orf32
NRIP2
INHBE
RBP5
TMTC1
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
C12orf26
TMEM117
TCHP
COQ5
LLPH
WIBG
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
EFCAB4B
TUBA1C
ZC3H10
ORAI1
RNFT2
C12orf34
ALG10
SPRYD3
C12orf52
MFSD5
MGC14436
C12orf62
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
FAM113B
C12orf65
TMEM132C
CCDC64
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
TMEM132B
OSBPL8
ARHGEF25
C12orf56
IQCD
LOC116437
AGAP2
DCD
RAB3IP
LOH12CR1
MUCL1
DEPDC4
LRRK2
CCDC38
C12orf59
FAM186A
C12orf45
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
HIST4H4
ERP27
FGD4
AEBP2
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
BRI3BP
KRT72
PRICKLE1
AMDHD1
SLC2A14
BCDIN3D
ALG10B
GLIPR1L2
FAM101A
ZNF664
LINC00477
LYRM5
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
KRT80
A2ML1
LOC144571
C12orf66
C12orf60
FBXL14
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
IFLTD1
DENND5B
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
CLEC4C
DSTNP2
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
C12orf53
DCP1B
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
C12orf33
GNN
MSRB3
METTL20
LRRC43
OR6C74
OR6C3
TCP11L2
LOC255411
LOC255480
LOC256021
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
POC1B
OTOGL
MATL2963
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
GPR133
MORN3
LOC283392
LOC283403
LOC283404
C12orf61
DPY19L2
CLEC9A
C12orf36
GAS2L3
LINC00485
LOC283440
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
C12orf40
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
LOC338758
C1QL4
TMEM119
KRT79
LOC338799
C12orf74
FAM19A2
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
PTPRQ
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
RPL13AP20
REP15
C12orf68
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
LOC389634
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
MKRN9P
C12orf76
LOC400084
FLJ37505
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
MIR26A2
C12orf37
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
DBX2
FLJ12825
TMEM198B
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
TSPAN11
OR9K2
MIR148B
MIR331
EID3
LOH12CR2
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC574538
HIGD1C
POU5F1P3
LOC642846
MAP1LC3B2
LOC643339
LOC643770
GLYCAM1
LOC647589
FAM86FP
PRB2
LRTM2
HNRNPA1P10
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA34
SNORA49
SNORA53
LOC678655
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
MIR617
MIR618
MIR620
LOC728084
C12orf73
SKP1P2
LOC728739
C12orf71
SLC15A5
MRS2P2
HOTAIR
MIR920
LOC100128191
LOC100128554
LOC100129361
LOC100130238
LOC100130776
LOC100131138
LOC100131733
LOC100190940
LOC100233209
LOC100240734
LOC100240735
LOC100271702
LOC100286844
MANSC4
LOC100287314
LINC00173
LOC100287944
LOC100288778
ZNF605
LOC100292680
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1178
MIR1244-1
MIR1251
LOC100335030
SNORA70G
MIR1244-3
MIR1244-2
MIR4302
MIR4303
MIR4304
KLRF2
LOC100499405
MIR3685
MIR3649
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506314
LOC100506393
LOC100506451
LOC100506649
LOC100506660
LOC100506668
LOC100506844
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507250
LOC100507377
LOC100507424
BLOC1S1-RDH5
POC1B-GALNT4
KLRC4-KLRK1
ZNF664-FAM101A
PRH1-PRR4
MIR4699
MIR4498
MIR548AL
MIR4701
MIR3974
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4698
LOC100652846
LOC100652999

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 - 22 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
16p13.3 1.5124e-16 3.3524e-10 chr16:6593002-6632999 1
8p21.2 2.6583e-08 2.0117e-07 chr8:25028827-25046375 1
8p11.22 8.679e-08 8.1336e-07 chr8:39414002-39506157 2
16p13.3 1.0481e-14 2.8656e-05 chr16:6430387-6584999 1
1p36.11 0.00017684 0.00070133 chr1:12260002-31849999 302
17p12 0.0050224 0.0050224 chr17:10790001-12049999 6
3p14.2 0.0058512 0.0058512 chr3:59581001-61095999 1
18q21.1 0.0058512 0.0058512 chr18:46423304-51382016 29
1p31.1 0.0013131 0.007313 chr1:72538002-72584999 1
4q22.1 0.001028 0.0082349 chr4:91472002-91637999 1
4q22.1 0.0012268 0.0082958 chr4:91961002-92192999 1
16q23.1 0.010299 0.010299 chr16:77052002-77268999 2
6q26 0.011624 0.011624 chr6:162251002-162599000 1
20p12.1 0.072806 0.072806 chr20:14524002-15243000 2
5q12.1 0.027377 0.091012 chr5:59251002-59637999 1
1p21.3 0.025542 0.094816 chr1:95905221-119639999 187
4q35.1 0.10186 0.10186 chr4:152739002-191154276 169
19q13.11 0.11786 0.11786 chr19:24004001-32820288 19
11q22.3 0.16588 0.16588 chr11:102555446-125418372 242
3q26.32 0.1813 0.1813 chr3:176146018-176612000 0 [TBL1XR1]
5q35.3 0.068095 0.21171 chr5:180010144-180915260 24
3p11.1 0.24413 0.24413 chr3:90393563-95010999 6
Genes in Wide Peak

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

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

Genes
RBFOX1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

Genes
DOCK5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.22.

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

Genes
ADAM18
LOC100130964
Genes in Wide Peak

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

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

Genes
RBFOX1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
PAX7
SDHB
ARID1A
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
ALPL
C1QA
C1QB
C1QC
CAPZB
CASP9
RUNX3
CDA
CDC42
CD52
RCC1
CLCNKA
CLCNKB
CNR2
DDOST
E2F2
ECE1
EPHA2
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
FUCA1
IFI6
GALE
SFN
GPR3
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
NBL1
OPRD1
PAFAH2
PLA2G2A
PLA2G5
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC9A1
TAF12
TCEA3
TCEB3
TNFRSF1B
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
FCN3
AKR7A2
ALDH4A1
EIF4G3
MAP3K6
DHRS3
SNRNP40
C1orf38
SDC3
CROCC
PUM1
ZBTB40
PTPRU
CELA3A
WASF2
HNRNPR
SRRM1
CNKSR1
PDPN
GMEB1
NUDC
SRSF10
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
CTRC
DNAJC8
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
CELA3B
PADI4
TMEM50A
STX12
CLIC4
SYF2
C1orf144
LDLRAP1
PLA2G2D
RNU11
HSPB7
AHDC1
SMPDL3B
PRO0611
LINC00339
PADI1
PLA2G2E
HP1BP3
CELA2B
ZNF593
MECR
MRTO4
YTHDF2
ZCCHC17
PADI3
WNT4
FBXO42
RNF186
GPN2
FBLIM1
MED18
PQLC2
TRNAU1AP
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
RCC2
FAM54B
C1orf63
PITHD1
MAN1C1
NIPAL3
SEPN1
KIF17
GRHL3
IL22RA1
CELA2A
GPATCH3
PLA2G2F
CEP85
PINK1
PRAMEF1
PRAMEF2
PHACTR4
C1orf135
EFHD2
RSG1
NKAIN1
MUL1
LIN28A
AGMAT
FAM110D
DHDDS
ZNF436
TAS1R2
ACTL8
SH3BGRL3
SESN2
TMEM222
USP48
NBPF3
ZDHHC18
DDI2
TRIM63
CROCCP2
SYTL1
IGSF21
SNHG12
C1orf201
UBXN11
C1orf158
ATPIF1
CROCCP3
FHAD1
RAB42
FAM46B
C1orf172
LRRC38
AADACL3
IFFO2
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf213
PDIK1L
C1orf64
IL28RA
FAM43B
PAQR7
FAM76A
C1orf126
AKR7L
TMCO4
ZNF683
LOC284632
SLC25A34
ESPNP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
SPATA21
CATSPER4
TMEM82
TRNP1
CD164L2
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
PRAMEF7
LOC644961
PRAMEF19
PRAMEF20
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
LOC729059
PRAMEF14
FLJ37453
LOC100129196
MIR1976
MIR3115
MIR4253
MIR3917
MIR3675
LOC100506730
LOC100506801
LOC100506963
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR378F
RCAN3AS
Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
DNAH9
ZNF18
SHISA6
MIR744
Genes in Wide Peak

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

Table S22.  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 18q21.1.

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

Genes
hsa-mir-4320
hsa-mir-1539
DCC
SMAD4
SMAD7
MBD1
ME2
MYO5B
MAPK4
RPL17
LIPG
ACAA2
SNORD58B
SNORD58A
CXXC1
MEX3C
DYM
ELAC1
MRO
SKA1
CCDC11
C18orf32
SCARNA17
SNORD58C
LOC100287225
MIR1539
MIR4320
RPL17-C18ORF32
MIR4744
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.1.

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

Genes
NEGR1
Genes in Wide Peak

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

Table S25.  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 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 16q23.1.

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

Genes
MON1B
SYCE1L
Genes in Wide Peak

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

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

Genes
PARK2
Genes in Wide Peak

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

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

Genes
MACROD2
MACROD2-AS1
Genes in Wide Peak

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

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

Genes
PDE4D
Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
VCAM1
WNT2B
CSDE1
TTF2
CDC14A
RTCD1
SLC16A4
CD101
LRIG2
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
PTPN22
CHIA
GPSM2
SLC25A24
SNX7
DPH5
GPR88
CCDC76
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
AMIGO1
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1OS
FAM40A
DNAJA1P5
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
LPPR5
FNDC7
SASS6
UBL4B
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
FRRS1
MIR137HG
MIR137
MIR197
FLJ31662
LOC440600
BCL2L15
PGCP1
SRG7
CYMP
LOC643441
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729987
MIR942
LOC100128787
LOC100129138
LOC100129269
LOC100129620
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100506343
MIR2682
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
AGA
SLC25A4
ANXA2P1
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PLRG1
PPID
MSMO1
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
DUX2
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
DKFZP434I0714
DCHS2
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
MND1
TKTL2
CBR4
FHDC1
MGC45800
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
C4orf45
TRIM60
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
RNF175
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
MIR3140
MIR4276
MIR3945
MIR3688-1
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR4453
MIR3688-2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.11.

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

Genes
CCNE1
UQCRFS1
URI1
ZNF254
ZNF536
POP4
TSHZ3
PLEKHF1
C19orf12
DKFZp566F0947
LOC148145
LOC148189
LOC284395
VSTM2B
RPSAP58
ZNF726
LOC100101266
LOC100505835
THEG5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

Table S34.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
VWA5A
MCAM
MMP1
MMP3
MMP8
MMP10
MMP12
MMP13
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
SLN
SORL1
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
ZNF259
USP2
HTR3B
ZW10
UBE4A
FEZ1
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
MMP27
ABCG4
ROBO3
C11orf1
RNF26
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
MFRP
BCO2
TMPRSS13
DCUN1D5
KIAA1826
BUD13
TMEM25
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
PANX3
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf65
MPZL3
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
LOC100288077
LOC100288346
BACE1-AS
MIR4301
LOC100499227
MIR3656
CASP12
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.3.

Table S35.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FLT4
MGAT1
GNB2L1
BTNL3
OR4F3
BTNL8
OR4F16
TRIM7
TRIM52
TRIM41
SCGB3A1
OR2Y1
BTNL9
OR2V2
SNORD95
SNORD96A
ZFP62
LOC729678
OR4F29
LOC100132062
LOC100132287
LOC100133331
MIR4638
LOC100859930
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

Table S36.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PROS1
NSUN3
ARL13B
DHFRL1
LOC255025
STX19
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 18 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 0.02 -1.51 1 0.21 5.77 2.64e-08
1q 1955 0.21 4.47 1.93e-05 0.13 1.72 0.155
2p 924 0.07 -2.67 1 0.02 -3.87 1
2q 1556 0.11 -0.174 1 0.02 -2.79 1
3p 1062 0.05 -2.86 1 0.06 -2.61 1
3q 1139 0.09 -1.72 1 0.02 -3.5 1
4p 489 0.01 -4.01 1 0.31 2.68 0.0166
4q 1049 0.04 -2.84 1 0.27 3.06 0.00545
5p 270 0.11 -2.64 1 0.13 -2.22 1
5q 1427 0.08 -1.27 1 0.17 1.22 0.374
6p 1173 0.12 -0.737 1 0.04 -2.78 1
6q 839 0.11 -1.63 1 0.07 -2.8 1
7p 641 0.49 7.51 1.67e-13 0.06 -2.56 1
7q 1277 0.41 7.86 1.55e-14 0.05 -2.05 1
8p 580 0.38 3.31 0.00209 0.57 8.5 0
8q 859 0.49 8.04 5.92e-15 0.16 -0.331 1
9p 422 0.15 -1.59 1 0.08 -3.08 1
9q 1113 0.09 -1.57 1 0.09 -1.82 1
10p 409 0.06 -3.54 1 0.09 -2.9 1
10q 1268 0.04 -2.57 1 0.14 0.0615 1
11p 862 0.08 -2.31 1 0.08 -2.31 1
11q 1515 0.07 -1.54 1 0.12 0.175 1
12p 575 0.16 -0.818 1 0.14 -1.47 1
12q 1447 0.12 0.0347 1 0.08 -1.36 1
13q 654 0.55 9.24 0 0.04 -2.6 1
14q 1341 0.04 -2.37 1 0.28 4.33 4.26e-05
15q 1355 0.03 -2.52 1 0.34 6.09 4.6e-09
16p 872 0.15 -0.533 1 0.06 -2.89 1
16q 702 0.16 -0.629 1 0.06 -3.12 1
17p 683 0.04 -2.66 1 0.53 8.84 0
17q 1592 0.10 -0.48 1 0.10 -0.48 1
18p 143 0.05 -2.93 1 0.59 8.46 0
18q 446 0.05 -2.33 1 0.65 10.9 0
19p 995 0.11 -1.32 1 0.07 -2.54 1
19q 1709 0.11 0.397 1 0.07 -1.15 1
20p 355 0.56 7.85 1.55e-14 0.26 0.813 0.64
20q 753 0.71 13.6 0 0.15 -0.477 1
21q 509 0.04 -3.71 1 0.23 0.626 0.759
22q 921 0.03 -3.38 1 0.25 2.1 0.0716
Xq 1312 0.41 7.83 1.55e-14 0.12 -0.245 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/COADREAD-TP/4425380/segmentationfile.txt

  • Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/COADREAD-TP/4425380/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 103 Input Tumor Samples.

Tumor Sample Names
TCGA-A6-2671-01A-01D-1405-02
TCGA-A6-2674-01A-02D-1167-02
TCGA-A6-2676-01A-01D-1167-02
TCGA-A6-2678-01A-01D-1167-02
TCGA-A6-2679-01A-02D-1405-02
TCGA-A6-2680-01A-01D-1405-02
TCGA-A6-2681-01A-01D-1405-02
TCGA-A6-2683-01A-01D-1167-02
TCGA-A6-2684-01A-01D-1405-02
TCGA-A6-3807-01A-01D-1167-02

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.

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)
[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)
[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)