LowPass Copy number analysis (GISTIC2)
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Spring Yingchun Liu (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): LowPass Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C15T3JVV
Overview
Introduction

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

Summary

There were 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 1.5753e-13 3.4249e-13 chr14:21742002-22028999 10
7p14.1 4.9342e-12 4.9342e-12 chr7:38261002-38623533 19
17q12 6.3424e-09 6.3424e-09 chr17:35082002-35176999 0 [MRM1]
5q31.1 0.0006969 0.0006969 chr5:134286002-134292999 1
8p11.22 8.311e-05 0.00071179 chr8:38205002-38377749 5
19q13.11 0.0023698 0.0023698 chr19:24004001-32804999 20
7q34 0.0048806 0.0048806 chr7:141733001-142634599 17
3p11.1 0.0054364 0.0054364 chr3:90396629-95001225 6
8q24.21 0.011745 0.011745 chr8:128117002-129060999 7
20q13.11 0.016453 0.016453 chr20:41559002-43781999 35
8p11.21 0.0080987 0.032057 chr8:40314002-40700999 1
13q12.13 0.060547 0.060547 chr13:24754770-32619999 69
10q22.3 0.064891 0.064891 chr10:73024002-82901999 90
14q32.33 0.093056 0.16542 chr14:105385002-105601542 5
13q21.33 0.21104 0.21104 chr13:72457001-73040584 3
12p12.1 0.18641 0.24203 chr12:24548909-26825461 15
12p13.33 0.15438 0.80338 chr12:1-133851895 1243
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: Cancer Gene Census[7].

Genes
RN7SL650P
SNORD8
SNORD9
SALL2
TOX4
SUPT16H
METTL3
RPGRIP1
CHD8
RAB2B
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: Cancer Gene Census[7].

Genes
RN7SL83P
TRGV1
TRGV2
TRGV3
TRGV4
TRGV5
TRGV8
TRGV9
TRGV10
TRGV11
TRGJP1
TRGJP
TRGJ1
TRGC1
TRGJP2
TRGJ2
TRGC2
AMPH
STARD3NL
Genes in Wide Peak

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

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

Genes
PCBD2
Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
RPS20P22
LETM2
C8orf86
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: Cancer Gene Census[7].

Genes
RNA5SP472
RNA5SP471
THEG5
C19orf12
POP4
RN7SL340P
UQCRFS1
RNA5SP470
LINC00906
snoU13|ENSG00000238514.1
LINC00662
ZNF726
CCNE1
URI1
ZNF254
ZNF536
TSHZ3
PLEKHF1
VSTM2B
RPSAP58
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: Cancer Gene Census[7].

Genes
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
EPHB6
PRSS1
MGAM
TRPV6
TRPV5
PRSS58
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: Cancer Gene Census[7].

Genes
LINC00879
NSUN3
PROS1
ARL13B
DHFRL1
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: Cancer Gene Census[7].

Genes
MYC
TMEM75
POU5F1B
CASC8
CCAT1
MIR1205
PVT1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.11.

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

Genes
RN7SL31P
KCNK15
MIR3646
R3HDML
FITM2
RN7SL443P
SCARNA15|ENSG00000252193.1
RN7SL666P
RN7SKP100
ADA
HNF4A
KCNS1
MYBL2
SRSF6
STK4
YWHAB
WISP2
SGK2
TOMM34
SERINC3
PTPRT
PKIG
L3MBTL1
IFT52
OSER1
JPH2
GDAP1L1
TTPAL
PABPC1L
TOX2
WFDC12
RIMS4
C20orf62
GTSF1L
WFDC5
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: 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: Cancer Gene Census[7].

Genes
CDX2
FLT3
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
LINC00365
LINC00544
LINC00572
LINC00297
MTUS2
RN7SL272P
URAD
LINC00543
GSX1
RNY1P1
SNORA27|ENSG00000207051.1
SNORD102
LINC00415
RNY1P3
RN7SL741P
RN7SL289P
PABPC3
LSP1|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
PARP4
ALOX5AP
ATP12A
CDK8
FLT1
GPR12
GTF3A
HMGB1
PDX1
UBL3
RNF6
RPL21
SLC7A1
MTMR6
NUPL1
FRY
USPL1
HSPH1
WASF3
POLR1D
POMP
ATP8A2
CENPJ
RNF17
KATNAL1
MEDAG
RXFP2
TEX26
B3GALTL
AMER2
USP12
MTIF3
SPATA13
LNX2
PAN3
SLC46A3
C1QTNF9
RASL11A
SHISA2
ATP5EP2
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: Cancer Gene Census[7].

Genes
LINC00857
PLAC9
MBL1P
NUTM2E
NUTM2B
SFTPA1
SNORA71|ENSG00000201393.1
LINC00595
LINC00856
RN7SL284P
RNA5SP321
SNORA31|ENSG00000252888.1
RN7SL518P
MIR606
AP3M1
RMRPP1
GLUD1P3
BMS1P4
RNA5SP320
snoU13|ENSG00000238983.1
DNAJC9
FAM149B1
SNORA11|ENSG00000221164.1
MIR4676
SNORA36|ENSG00000200294.1
ASCC1
snoU13|ENSG00000238918.1
ADK
ANXA7
ANXA11
CAMK2G
KCNMA1
MAT1A
P4HA1
PLAU
PPP3CB
PSAP
RPS24
SFTPD
VCL
VDAC2
NDST2
DLG5
CHST3
SEC24C
SPOCK2
PPIF
MICU1
POLR3A
ECD
ZSWIM8
KAT6B
NUDT13
MRPS16
DUSP13
DDIT4
DNAJB12
SLC29A3
ZMIZ1
MYOZ1
CDH23
C10orf54
SYNPO2L
TMEM254
TSPAN14
C10orf11
FAM213A
DYDC2
PLA2G12B
ZNF503
MCU
CHCHD1
MSS51
TTC18
COMTD1
ANAPC16
SAMD8
DYDC1
EIF5AL1
USP54
FUT11
OIT3
ZCCHC24
UNC5B
DUPD1
SH2D4B
C10orf105
C10orf55
AGAP5
SFTPA2
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: Cancer Gene Census[7].

Genes
C14orf79
GPR132
CDCA4
AHNAK2
PLD4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q21.33.

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

Genes
SNORA68|ENSG00000251715.1
SNORD37|ENSG00000212377.1
RNA5SP32
Genes in Wide Peak

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

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

Genes
KRAS
RNA5SP354
SSPN
RN7SKP262
RN7SL38P
BCAT1
ITPR2
LRMP
RASSF8
CASC1
BHLHE41
LINC00477
LYRM5
IFLTD1
C12orf77
Genes in Wide Peak

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

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

Genes
BCL7A
BTG1
ALDH2
ATF1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
HMGA2
WIF1
ZNF384
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13|ENSG00000238822.1
RN7SL534P
snoU13|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38|ENSG00000201042.1
RNA5SP374
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56|ENSG00000200112.1
RN7SL865P
SNORA27|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40|ENSG00000264043.2
FICD
RNA5SP371
SNORD74|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13|ENSG00000238914.1
U8|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13|ENSG00000238800.1
SLC5A8
snoU13|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13|ENSG00000239073.1
SNORD74|ENSG00000201502.1
snoU13|ENSG00000238361.1
snoU13|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
U8|ENSG00000201809.1
RAB21
SNORA17|ENSG00000212461.1
MYRFL
RN7SL804P
SLC35E3
SNORA70G
DYRK2
CAND1
snoU13|ENSG00000238528.1
RN7SKP166
TMBIM4
RNA5SP362
RPSAP52
RNU6ATAC42P
snoU13|ENSG00000238592.1
MIR548C
SNORD83
XPOT
snoU13|ENSG00000238440.1
RPS11P6
AVPR1A
LDHAL6CP
snoU13|ENSG00000238475.1
SNORD112|ENSG00000252883.1
SNORA19|ENSG00000251822.1
RN7SKP65
MIR26A2
snoU13|ENSG00000238436.1
RN7SL312P
MIR1228
HBCBP
RDH16
SNORA48|ENSG00000212383.1
RN7SL809P
SNORD59A
RBMS2
RNF41
RN7SL770P
MMP19
TMEM198B
ORMDL2
GLYCAM1
RN7SL744P
MIR148B
RN7SL390P
MIR615
HOXC8
HOTAIR
HOXC12
RN7SKP289
SNORD81|ENSG00000223213.1
KRT121P
LINC00592
C12orf80
OR7E47P
POU6F1
U6|ENSG00000272028.1
HIGD1C
RN7SL519P
MIR1293
AQP6
AQP5
BCDIN3D
PRPH
WNT1
snoU13|ENSG00000238395.1
MIR4701
SNORA2B
SNORA2A
SNORA34
DKFZP779L1853
RPAP3
SNORA64|ENSG00000199566.1
SCAF11
RN7SL246P
RNA5SP361
SNORA74|ENSG00000252917.1
RN7SL10P
RNA5SP360
MUC19
SNORA22|ENSG00000199571.1
ABCD2
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112|ENSG00000251863.1
SNORA25|ENSG00000252204.1
STMN1P1
snoU13|ENSG00000239033.1
snoU13|ENSG00000238661.1
SNORA75|ENSG00000212533.1
LINC00941
RNA5SP356
U3|ENSG00000253052.1
ERGIC2
RNA5SP355
RN7SKP15
ARNTL2
TM7SF3
RNA5SP354
SSPN
RN7SKP262
RN7SL38P
C12orf39
PYROXD1
LST3
AEBP2
RN7SL67P
RN7SL459P
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
C1R
SCARNA12
DSTNP2
RPL13P5
RN7SL380P
SCARNA11|ENSG00000251898.1
SCARNA10
MRPL51
RN7SL391P
RN7SL69P
NDUFA9
C12orf5
FKBP4
CBX3P4
CACNA1C
LINC00940
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
A2M
ACACB
ACADS
ASIC1
ACVR1B
ACVRL1
ADCY6
AMHR2
APAF1
APOF
APOBEC1
AQP2
ARF3
ARHGDIB
ARL1
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
BCAT1
BICD1
C1S
C3AR1
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
EIF4B
CELA1
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC9
HOXC10
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
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
LYZ
M6PR
MARS
METTL1
MGP
MGST1
MIP
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRIM1
PRKAB1
PRKAG1
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAP1B
RARG
RDH5
RECQL
RFC5
RFX4
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
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
UNG
VDR
VWF
WNT10B
ZNF10
ZNF26
ZNF84
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
KMT2D
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
PPFIBP1
PPFIA2
YBX3
LGR5
MAPKAPK5
DENR
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
KRT75
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
TESPA1
C2CD5
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
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
ATF7
RAB35
CPSF6
KERA
KRR1
PRDM4
CIT
PWP1
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
PRR4
GPR182
PHB2
COPZ1
R3HDM2
RPH3A
KLRK1
P2RX2
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
GLS2
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
TBK1
RACGAP1
SENP1
FAM216A
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R7
TAS2R13
TAS2R10
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CCDC41
IRAK4
ING4
GPN3
DDX47
GLTP
CLEC1B
CLEC1A
C1RL
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
SLC6A15
FAM90A1
RIC8B
KIAA1551
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SVOP
STAB2
VEZT
GOLGA2B
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
CHPT1
PARP11
ANO2
C12orf4
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHL42
PITPNM2
DIP2B
KIAA1467
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
C12orf44
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
NABP2
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
TCTN2
NANOG
DNAJC22
NAA25
SLC24A6
ADAMTS20
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
RHNO1
NRIP2
INHBE
RBP5
TMTC1
KCTD10
FAM186B
USP44
SLC41A2
LRRIQ1
METTL25
TMEM117
TCHP
COQ5
LLPH
WIBG
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
EFCAB4B
TUBA1C
ZC3H10
RNFT2
FAM222A
SPRYD3
C12orf52
MFSD5
COX14
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
PCED1B
C12orf65
CCDC64
HELB
MARCH9
COQ10A
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
OSBPL8
ARHGEF25
C12orf56
IQCD
AGAP2
DCD
RAB3IP
LOH12CR1
MUCL1
DEPDC4
LRRK2
CCDC38
TMEM52B
FAM186A
OR2AP1
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
IKBIP
HIST4H4
FGD4
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
KRT72
PRICKLE1
AMDHD1
SLC2A14
GLIPR1L2
FAM101A
ZNF664
LINC00477
LYRM5
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
KRT80
A2ML1
C12orf66
FBXL14
RAD9B
FAM109A
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
IFLTD1
DENND5B
GRASP
CCDC63
CCDC60
CLEC4C
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
PLBD2
FAM71C
CCER1
PIANP
DCP1B
ANO6
ARID2
SLC17A8
STAC3
MSRB3
METTL20
LRRC43
OR6C74
OR6C3
TCP11L2
LINC00935
C12orf79
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
POC1B
OTOGL
CD163L1
ZNF740
RASSF3
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
GPR133
MORN3
C12orf61
DPY19L2
CLEC9A
C12orf36
GAS2L3
MYO1H
HECTD4
KSR2
C12orf40
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
C1QL4
TMEM119
KRT79
C12orf74
FAM19A2
SLCO1B7
SMCO2
OVCH1
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
KRT77
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
REP15
C12orf68
C12orf75
CCDC42B
TMEM233
SETD8
LINC00937
OR6C1
OR6C75
OR6C76
OR6C70
C12orf76
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
IQSEC3
ZNF705A
SMCO3
H3F3C
DBX2
PLEKHG7
TSPAN11
OR9K2
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
PRB2
LRTM2
MIR614
MIR616
C12orf73
C12orf71
SLC15A5
MIR920
MANSC4
ZNF605
MIR1251
MIR4303
MIR3685
MIR3649
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR4494
MIR4698
MIR5188
MIR5700

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 8.2011e-17 2.4787e-10 chr16:6593002-6632999 1
8p21.2 3.0684e-08 2.3544e-07 chr8:25028827-25046375 2
8p11.22 2.6304e-07 2.5798e-06 chr8:39414002-39506157 1
16p13.3 6.5239e-15 2.7074e-05 chr16:6430387-6584999 1
1p36.11 0.00019015 0.0007143 chr1:12260002-31849999 322
17p12 0.0052202 0.0052202 chr17:10790001-12049999 7
3p14.2 0.005747 0.005747 chr3:59581001-61097999 3
18q21.1 0.0060998 0.0060998 chr18:46423304-51382016 31
4q22.1 0.0010644 0.0085715 chr4:91472002-91637999 1
16q23.1 0.0085715 0.0085715 chr16:77057138-77268999 2
4q22.1 0.0012693 0.0085863 chr4:91961002-92192999 1
1p31.1 0.0032822 0.010772 chr1:72538002-72584999 1
6q26 0.012116 0.012116 chr6:162251002-162599000 1
20p12.1 0.039368 0.039368 chr20:14524002-15184999 1
5q12.1 0.029072 0.093781 chr5:59176002-59637999 1
1p21.3 0.039368 0.10293 chr1:95905221-119639999 185
4q35.1 0.10375 0.10375 chr4:152067002-191154276 179
19q13.11 0.1191 0.1191 chr19:24004001-32820288 20
11q22.3 0.1683 0.1683 chr11:102555446-125418372 253
4p16.3 0.1762 0.1762 chr4:1-9681000 137
3q26.32 0.18859 0.18859 chr3:176146018-176612000 1
5q35.3 0.074403 0.22406 chr5:180010144-180915260 19
Genes in Wide Peak

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

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

Genes
RBFOX1
Genes in Wide Peak

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

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

Genes
RN7SL651P
DOCK5
Genes in Wide Peak

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

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

Genes
ADAM18
Genes in Wide Peak

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

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

Genes
RBFOX1
Genes in Wide Peak

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

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

Genes
PAX7
SDHB
ARID1A
MDS2
FABP3
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18|ENSG00000252691.1
SCARNA17|ENSG00000252190.1
MAN1C1
snoU13|ENSG00000238889.1
SYF2
snoU13|ENSG00000238986.1
RN7SL857P
snoU13|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70|ENSG00000252969.1
ALPL
C1QA
C1QB
C1QC
CAPZB
CASP9
RUNX3
CDA
CDC42
CD52
RCC1
CLCNKA
CLCNKB
CNR2
DDOST
E2F2
ECE1
EPHA2
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
FUCA1
IFI6
GALE
SFN
GPR3
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
NBL1
OPRD1
PAFAH2
PLA2G2A
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC9A1
TAF12
TCEA3
TCEB3
TNFRSF1B
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
FCN3
ALDH4A1
EIF4G3
MAP3K6
DHRS3
SNRNP40
THEMIS2
CROCC
PUM1
ZBTB40
PTPRU
CELA3A
WASF2
HNRNPR
SRRM1
CNKSR1
PDPN
GMEB1
NUDC
SRSF10
RCAN3
PADI2
LYPLA2
CTRC
DNAJC8
SPEN
KDM1A
WDTC1
EMC1
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
CELA3B
PADI4
TMEM50A
STX12
CLIC4
SZRD1
LDLRAP1
HSPB7
AHDC1
SMPDL3B
PADI1
HP1BP3
CELA2B
MECR
MRTO4
YTHDF2
ZCCHC17
PADI3
WNT4
FBXO42
RNF186
FBLIM1
MED18
PQLC2
TRNAU1AP
TMEM51
XKR8
ARHGEF10L
VPS13D
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
RCC2
MTFR1L
C1orf63
PITHD1
NIPAL3
SEPN1
KIF17
GRHL3
IL22RA1
CELA2A
GPATCH3
PLA2G2F
CEP85
PINK1
PRAMEF1
PRAMEF2
PHACTR4
AUNIP
EFHD2
RSG1
NKAIN1
MUL1
LIN28A
FAM110D
DHDDS
ZNF436
TAS1R2
ACTL8
SESN2
TMEM222
USP48
NBPF3
TRIM63
SYTL1
IGSF21
STPG1
UBXN11
ATPIF1
FHAD1
FAM46B
C1orf172
LRRC38
AADACL3
IFFO2
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
C1orf213
PDIK1L
IFNLR1
FAM43B
PAQR7
FAM76A
AKR7L
TMCO4
ZNF683
SLC25A34
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
CATSPER4
TMEM82
TRNP1
CD164L2
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
PRAMEF11
PRAMEF6
MINOS1
PRAMEF7
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
C1orf234
MIR4253
MIR3917
MIR3675
MIR4419A
MIR4425
MIR4418
MIR378F
Genes in Wide Peak

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

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

Genes
MAP2K4
MIR744
RPL21P122
RN7SL601P
DNAH9
ZNF18
SHISA6
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: Cancer Gene Census[7].

Genes
FHIT
U3|ENSG00000212211.1
NPCDR1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.1.

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

Genes
DCC
snoU13|ENSG00000238885.1
RN7SL695P
ME2
RNA5SP458
RN7SL310P
RNA5SP457
SCARNA18|ENSG00000252139.1
SCARNA17|ENSG00000251992.1
SCARNA17|ENSG00000267322.1
SNORD58B
SNORD58A
SNORD58C
C18orf32
MIR4744
SMAD4
SMAD7
MBD1
MYO5B
MAPK4
RPL17
LIPG
ACAA2
CXXC1
MEX3C
DYM
ELAC1
MRO
SKA1
CCDC11
MIR1539
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: Cancer Gene Census[7].

Genes
CCSER1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
MON1B
SYCE1L
Genes in Wide Peak

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

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

Genes
CCSER1
Genes in Wide Peak

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

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

Genes
NEGR1
Genes in Wide Peak

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

Table S29.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 S30.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MACROD2
Genes in Wide Peak

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

Table S31.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 S32.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
NRAS
TRIM33
RBM15
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ADORA3
AGL
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TBX15
TSHB
VCAM1
CSDE1
CDC14A
RTCA
SLC16A4
CD101
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
LAMTOR5
AP4B1
PHTF1
AHCYL1
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
PTPN22
CHIA
GPSM2
SLC25A24
SNX7
GPR88
TRMT13
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
OLFML3
AMIGO1
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
STRIP1
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
LRRC39
DRAM2
PIFO
C1orf162
SYT6
NBPF4
SLC30A7
CHIAP2
FNDC7
SASS6
UBL4B
SPAG17
HIPK1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
C1orf137
FRRS1
MIR197
NBPF6
MIR320B1
MIR137HG
Genes in Wide Peak

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

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

Genes
DUX4
FBXW7
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
C4orf45
U3|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
AGA
SLC25A4
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGG
FRG1
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
PPID
MSMO1
SFRP2
TDO2
TLL1
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
PALLD
KIAA0922
TRIM2
FAM149A
FBXO8
ARFIP1
SPOCK3
AADAT
FAM198B
ASIC5
GALNT7
CLDN22
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
TMA16
DDX60
CDKN2AIP
TENM3
LRP2BP
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
MLF1IP
MAP9
WWC2
CEP44
SNX25
MND1
TKTL2
CBR4
FHDC1
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
SH3D19
FAM218A
TRIM60
RBM46
C4orf46
TIGD4
RWDD4
CCDC111
TRIML2
CCDC110
RNF175
TRIML1
PRSS48
ANKRD37
TRIM61
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
FAM160A1
CLDN24
MIR1305
MIR3140
MIR4276
MIR3945
MIR4455
MIR4453
Genes in Wide Peak

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

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

Genes
RNA5SP472
RNA5SP471
THEG5
C19orf12
POP4
RN7SL340P
UQCRFS1
RNA5SP470
LINC00906
snoU13|ENSG00000238514.1
LINC00662
ZNF726
CCNE1
URI1
ZNF254
ZNF536
TSHZ3
PLEKHF1
VSTM2B
RPSAP58
Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
RNA5SP348
MMP12
WTAPP1
ACAT1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
VWA5A
MCAM
KMT2A
MMP1
MMP3
MMP8
MMP10
MMP13
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
SLN
SORL1
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
USP2
HTR3B
ZW10
UBE4A
FEZ1
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
SCN3B
VPS11
TEX12
CRTAM
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
MMP27
ABCG4
ROBO3
C11orf1
RNF26
DYNC2H1
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
MFRP
BCO2
TMPRSS13
DCUN1D5
MSANTD4
BUD13
TMEM25
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
PANX3
APOA5
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
MIR4301
CASP12
MIR4493
MIR4491
MIR4492
MIR4693
Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
SH3BP2
WFS1
NELFA
SLBP
ACOX3
CPZ
NOP14
FAM193A
KIAA0232
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
NSG1
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
BLOC1S4
STK32B
LYAR
TBC1D14
SORCS2
UVSSA
ZFYVE28
AFAP1
TNIP2
HAUS3
MFSD7
TMEM175
ABLIM2
TMEM128
TMEM129
MRFAP1
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
JAKMIP1
FAM53A
TRMT44
ZBTB49
CCDC96
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
DEFB131
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
USP17L30
PSAPL1
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR548I2
MIR378D1
MIR4800
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.32.

Table S37.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RNA5SP147
Genes in Wide Peak

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

Table S38.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TRIM52
SNORD95|ENSG00000264549.1
SNORD96A
LINC00847
FLT4
MGAT1
GNB2L1
BTNL3
OR4F3
OR2V1
BTNL8
TRIM7
TRIM41
SCGB3A1
OR2Y1
BTNL9
OR2V2
ZFP62
MIR4638
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 1300 0.04 -1.04 1 0.21 5.88 1.34e-08
1q 1195 0.22 4.83 3.39e-06 0.13 1.75 0.147
2p 624 0.06 -2.85 1 0.02 -3.82 1
2q 967 0.10 -0.472 1 0.02 -2.81 1
3p 644 0.05 -2.91 1 0.07 -2.42 1
3q 733 0.09 -1.67 1 0.02 -3.47 1
4p 289 0.01 -4.1 1 0.31 2.47 0.0303
4q 670 0.04 -2.8 1 0.28 3.36 0.00195
5p 183 0.11 -2.71 1 0.13 -2.3 1
5q 905 0.08 -1.21 1 0.17 1.3 0.322
6p 710 0.12 -0.846 1 0.04 -2.87 1
6q 556 0.12 -1.31 1 0.07 -2.73 1
7p 389 0.49 7.29 1.02e-12 0.06 -2.64 1
7q 783 0.42 8.02 7.4e-15 0.05 -2.06 1
8p 338 0.38 3.12 0.00406 0.57 8.21 1.11e-15
8q 551 0.49 7.93 1.11e-14 0.19 0.292 0.911
9p 301 0.14 -1.63 1 0.07 -3.33 1
9q 700 0.09 -1.58 1 0.09 -1.83 1
10p 253 0.06 -3.6 1 0.10 -2.76 1
10q 738 0.05 -2.7 1 0.15 0.11 1
11p 509 0.09 -2.42 1 0.09 -2.19 1
11q 975 0.07 -1.41 1 0.12 0.341 0.911
12p 339 0.17 -0.928 1 0.15 -1.36 1
12q 904 0.12 0.0537 1 0.08 -1.34 1
13q 560 0.54 9.83 0 0.04 -2.42 1
14q 938 0.04 -2.1 1 0.28 5.01 1.54e-06
15q 810 0.03 -2.58 1 0.35 6.12 3.66e-09
16p 559 0.13 -1.08 1 0.06 -2.96 1
16q 455 0.14 -1.17 1 0.06 -3.2 1
17p 415 0.04 -2.73 1 0.53 8.61 0
17q 972 0.08 -1.09 1 0.12 0.365 0.911
18p 104 0.05 -2.93 1 0.60 8.54 0
18q 275 0.05 -2.39 1 0.65 10.7 0
19p 681 0.11 -1.16 1 0.07 -2.4 1
19q 935 0.11 -0.16 1 0.07 -1.58 1
20p 234 0.57 7.88 1.33e-14 0.25 0.491 0.911
20q 448 0.71 13.1 0 0.12 -1.01 1
21q 258 0.04 -3.91 1 0.23 0.287 0.911
22q 564 0.03 -3.41 1 0.26 2.24 0.0505
Xq 668 0.41 6.75 4.14e-11 0.12 -0.722 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/22507110/segmentationfile.txt

  • Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/COADREAD-TP/22507110/markersfile.txt

  • Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat

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

  • Amplification Threshold = 0.3

  • 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)