LowPass Copy number analysis (GISTIC2)
Stomach 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/C1Z60NJV
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 107 tumor samples used in this analysis: 20 significant arm-level results, 17 significant focal amplifications, and 19 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
19q12 8.9159e-10 8.9159e-10 chr19:29981243-30434489 6
12q15 1.076e-07 1.076e-07 chr12:68032120-70142158 20
8q24.21 3.7757e-06 3.7757e-06 chr8:128070146-128865434 6
20q13.2 0.00013853 0.00013853 chr20:51594458-53175651 8
12p12.1 0.00023194 0.00023194 chr12:24832434-25872659 8
8p23.1 0.000235 0.000235 chr8:10975654-12724285 31
7q21.2 0.00074501 0.00074501 chr7:90901353-97945867 58
18q11.2 0.0039842 0.0039842 chr18:19444890-20134873 6
7p11.2 0.0040235 0.0040235 chr7:54995267-55593325 3
10q26.13 0.0073872 0.0073872 chr10:122709888-123893564 5
17q12 0.0055736 0.0078855 chr17:35621565-39490730 94
6p21.1 0.015581 0.015581 chr6:43508397-44379101 23
1q42.3 0.037544 0.037544 chr1:234797952-235344760 6
13q22.1 0.067385 0.067385 chr13:73543082-74325003 6
15q26.1 0.10362 0.10362 chr15:87285740-102531392 116
11q13.3 0.11927 0.11927 chr11:67821083-70533128 26
17q12 0.18836 0.24899 chr17:31682027-36884102 87
Genes in Wide Peak

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

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

Genes
C19orf12
POP4
CCNE1
URI1
PLEKHF1
VSTM2B
Genes in Wide Peak

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

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

Genes
MDM2
RN7SL804P
SLC35E3
SNORA70G
DYRK2
CPM
IFNG
LYZ
RAP1B
YEATS4
CCT2
FRS2
CPSF6
IL22
IL26
MDM1
NUP107
RAB3IP
BEST3
LRRC10
Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
CASC8
CCAT1
PCAT2
PVT1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
RN7SKP184
CYP24A1
PFDN4
ZNF217
BCAS1
DOK5
TSHZ2
MIR4756
Genes in Wide Peak

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

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

Genes
KRAS
RN7SL38P
BCAT1
LRMP
CASC1
LYRM5
IFLTD1
C12orf77
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p23.1.

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

Genes
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
LINC00529
BLK
CTSB
FDFT1
GATA4
MTMR9
FAM167A
SLC35G5
FAM86B1
LONRF1
TDH
DEFB130|ENSG00000232948.1
NEIL2
XKR6
USP17L2
DEFB135
DEFB136
ZNF705D
MIR5692A2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
RN7SL13P
RN7SL478P
RN7SKP104
RN7SL252P
SHFM1
MIR591
PON1
snoU13|ENSG00000238384.1
RN7SKP129
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
ASNS
CALCR
KRIT1
COL1A2
CYP51A1
DLX5
DLX6
DYNC1I1
GNGT1
OCM2
PDK4
PEX1
PON2
PON3
TAC1
MTERF
TFPI2
SGCE
SLC25A13
BET1
LMTK2
PEG10
BRI3
TECPR1
ASB4
ANKIB1
SAMD9
PPP1R9A
CCDC132
BAIAP2L1
ACN9
CASD1
RBM48
BHLHA15
SAMD9L
HEPACAM2
FAM133B
LRRD1
C7orf76
MIR4652
MIR5692C2
MIR5692A1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
snoU13|ENSG00000238907.1
RNU6ATAC20P
RNA5SP451
GATA6
MIB1
CTAGE1
Genes in Wide Peak

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

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

Genes
EGFR
LANCL2
VOPP1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q26.13.

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

Genes
FGFR2
RN7SKP167
TACC2
ATE1
NSMCE4A
Genes in Wide Peak

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

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

Genes
RARA
ERBB2
LASP1
MLLT6
KRT223P
KRT222
KRT222
RNA5SP441
GJD3
RNY4P8
SNORD124
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
ARL5C
LINC00672
SNORA21|ENSG00000199293.1
SNORA21|ENSG00000252699.1
RPL23
RNA5SP440
CISD3
MIR4726
RN7SL102P
RN7SL458P
SOCS7
ACACA
CACNB1
CDC6
CCR7
CSF3
GRB7
IGFBP4
KRT10
KRT12
MED1
PSMB3
PSMD3
RPL19
SMARCE1
TADA2A
HNF1B
THRA
TOP2A
PCGF2
PIP4K2B
NR1D1
MED24
STARD3
DDX52
DUSP14
SYNRG
CASC3
KRT23
RAPGEFL1
CDK12
KRT20
CWC25
GSDMB
PLXDC1
ARHGAP23
SRCIN1
PPP1R1B
TBC1D3F
MIEN1
MRPL45
TNS4
FBXL20
PGAP3
ORMDL3
ZPBP2
KRT40
WIPF2
KRT25
TMEM99
KRT28
KRT24
C17orf78
GSDMA
MSL1
KRT27
LRRC37A11P
STAC2
KRT26
C17orf98
KRT39
GPR179
FBXO47
TBC1D3
C17orf96
LRRC3C
MIR4734
MIR4727
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
TCTE1
TMEM151B
RSPH9
SCARNA15|ENSG00000252218.1
CDC5L
SLC29A1
HSP90AB1
NFKBIE
POLH
VEGFA
MAD2L1BP
CAPN11
GTPBP2
MRPS18A
TMEM63B
AARS2
XPO5
MRPL14
SPATS1
C6orf223
SLC35B2
TMEM151B
MIR4647
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.3.

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

Genes
SNORA14B
RN7SL668P
RNY4P16
TOMM20
RBM34
ARID4B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q22.1.

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

Genes
LINC00392
LINC00393
RNY1P8
KLF5
PIBF1
KLF12
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
IDH2
NTRK3
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109|ENSG00000239197.1
snoU13|ENSG00000238981.1
RN7SL363P
SNORD18|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
ACAN
ALDH1A3
ANPEP
CHD2
FES
IGF1R
MAN2A2
MEF2A
MFGE8
FURIN
PCSK6
PLIN1
POLG
RLBP1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
ABHD2
CHSY1
SYNM
VPS33B
MRPL46
OR4F4
SLCO3A1
NGRN
RHCG
DET1
FANCI
MCTP2
VIMP
UNC45A
RGMA
WDR93
AEN
TTC23
MRPS11
LRRK1
TM2D3
TICRR
RCCD1
ARRDC4
LINC00923
TARSL2
LRRC28
AGBL1
ASB7
LYSMD4
PGPEP1L
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
ADAMTS17
DNM1P46
CERS3
FAM169B
KIF7
ZNF710
HDDC3
SPATA41
GDPGP1
OR4F6
OR4F15
FAM174B
TTLL13
MIR1179
MIR3174
Genes in Wide Peak

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

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

Genes
CCND1
MIR548K
FGF3
MIR3164
TPCN2
CHKA
CPT1A
CTTN
FGF4
IGHMBP2
LRP5
PPFIA1
FADD
MTL5
FGF19
SHANK2
MYEOV
GAL
SUV420H1
C11orf24
ANO1
PPP6R3
MRGPRD
MRGPRF
MRPL21
ORAOV1
Genes in Wide Peak

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

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

Genes
MLLT6
TAF15
MIR4726
RN7SL102P
RN7SL458P
SOCS7
HMGB1P24
MIR2909
RNA5SP439
CCL4L2
RN7SL301P
CCL4
CCL18
RN7SKP274
SNORD7
SLFN12L
SLFN5
Vault|ENSG00000252328.1
snoU13|ENSG00000238858.1
RNA5SP438
ACACA
ASIC2
AP2B1
LHX1
LIG3
PEX12
RAD51D
CCL1
CCL2
CCL3
CCL3L1
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL23
TADA2A
HNF1B
ZNHIT3
CCL4L1
CCT6B
DDX52
DUSP14
SYNRG
AATF
NLE1
FNDC8
SLFN12
LYZL6
ARHGAP23
MMP28
DHRS11
GGNBP2
MRM1
MYO19
SRCIN1
TBC1D3F
MRPL45
ZNF830
SLFN11
RASL10B
RFFL
TMEM132E
C17orf50
SLFN13
SLC35G3
UNC45B
RDM1
GAS2L2
C17orf66
PIGW
C17orf78
SLFN14
C17orf102
TBC1D3B
TBC1D3C
CCL3L3
GPR179
TBC1D3G
TBC1D3
TBC1D3H
C17orf96
MIR4734

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 - 19 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
9p23 5.7062e-09 5.7062e-09 chr9:9455034-9627050 1
16q23.1 3.9135e-08 3.9135e-08 chr16:78583111-78648685 1
5q12.1 1.8769e-07 1.8769e-07 chr5:59050959-59380706 1
9p21.3 6.3569e-07 6.3569e-07 chr9:21852135-21983214 3
6p25.3 2.3392e-05 2.3392e-05 chr6:1867395-2191114 1
3p14.2 0.00028751 0.00028751 chr3:59563588-61184955 3
4q34.3 0.00037796 0.0010767 chr4:170615980-191154276 98
18q21.2 0.0010767 0.0010767 chr18:38271779-78077248 180
1p36.11 0.001659 0.001659 chr1:26023101-28275742 64
22q13.31 0.0091074 0.0091074 chr22:45576204-51304566 71
10q23.31 0.011777 0.011777 chr10:88849958-89802725 15
7q36.1 0.014174 0.014174 chr7:129240874-159138663 283
2q37.2 0.017589 0.017589 chr2:233474044-243199373 104
4q22.1 0.0065341 0.018497 chr4:91690999-91950491 1
20p12.1 0.031996 0.031996 chr20:14390118-15232555 1
3p11.1 0.050646 0.050646 chr3:90309030-93822733 5
17q24.3 0.077942 0.077942 chr17:70127295-70640568 1
11p15.5 0.22053 0.22053 chr11:1-27836474 369
17p11.2 0.24847 0.24847 chr17:8529294-25479095 169
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
PTPRD
Genes in Wide Peak

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

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

Genes
WWOX
Genes in Wide Peak

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

Table S20.  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 9p21.3.

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

Genes
CDKN2A
MTAP
C9orf53
Genes in Wide Peak

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

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

Genes
GMDS
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 4q34.3.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HPGD
ING2
IRF2
KLKB1
MTNR1A
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
FAM149A
FBXO8
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
WWC2
CEP44
SNX25
WDR17
ZFP42
SPATA4
ENPP6
ASB5
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR4276
MIR3945
MIR4455
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
BCL2
MALT1
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
snoU13|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8|ENSG00000199713.1
RN7SL112P
SNORD28|ENSG00000252284.1
FECH
U3|ENSG00000212539.1
TXNL1
SNORA73|ENSG00000201816.1
RNA5SP459
SNORA37
DCC
snoU13|ENSG00000238885.1
RN7SL695P
ME2
RNA5SP458
RN7SL310P
RNA5SP457
SCARNA18|ENSG00000252139.1
SCARNA17|ENSG00000251992.1
SCARNA17|ENSG00000267322.1
SNORD58B
SNORD58A
SNORD58C
C18orf32
MIR4744
MIR4743
RNA5SP456
IER3IP1
RNF165
RN7SKP26
RNA5SP455
RNA5SP454
LINC00907
PIK3C3
ATP5A1
CDH7
CYB5A
KDSR
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TCF4
ZNF236
SLC14A2
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
LIPG
ONECUT2
VPS4B
CTIF
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
SETBP1
KCNG2
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
EPG5
CCDC102B
PQLC1
CCDC68
NETO1
KATNAL2
MRO
HDHD2
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
GTSCR1
DOK6
LINC00305
DYNAP
BOD1L2
SIGLEC15
LINC00908
HMSD
CPLX4
ATP9B
LINC00909
MIR122
HSBP1L1
C18orf63
SKOR2
TCEB3CL
MIR1539
MIR4319
TCEB3CL2
MIR4527
MIR4529
MIR5011
Genes in Wide Peak

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

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

Genes
ARID1A
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18|ENSG00000252691.1
SCARNA17|ENSG00000252190.1
MAN1C1
CD52
EXTL1
FGR
IFI6
SFN
GPR3
STMN1
PAFAH2
PPP1R8
RPA2
RPS6KA1
SLC9A1
SLC30A2
NR0B2
FCN3
MAP3K6
THEMIS2
WASF2
CNKSR1
NUDC
WDTC1
STX12
AHDC1
SMPDL3B
PIGV
MTFR1L
SEPN1
GPATCH3
CEP85
AUNIP
LIN28A
FAM110D
DHDDS
TMEM222
TRIM63
SYTL1
UBXN11
FAM46B
C1orf172
PDIK1L
PAQR7
FAM76A
ZNF683
CATSPER4
TRNP1
CD164L2
MIR3917
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
ACR
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
MIOX
TRMU
PANX2
CERK
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.31.

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

Genes
PTEN
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
GLUD1
PAPSS2
MINPP1
FAM35A
ATAD1
NUTM2A
NUTM2D
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.1.

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

Genes
BRAF
EZH2
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
AOC1
AKR1B1
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
GBX1
MNX1
INSIG1
KCNH2
KEL
MEST
MKLN1
NDUFB2
NOS3
CNOT4
NRF1
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
RARRES2
RHEB
SLC4A2
SMARCD3
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
DGKI
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
CLEC5A
MKRN1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
ATP6V0A4
TAS2R3
TAS2R4
CPA4
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LMBR1
NOM1
PARP12
LRRC61
C7orf49
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
CLEC2L
C7orf55
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
STRA8
WDR86
GSTK1
FAM180A
OR2A25
OR2A5
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
CTAGE4
CTAGE8
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707
Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PPP1R7
SAG
SPP2
DGKD
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
CAPN10
PASK
ATG4B
SH3BP4
NGEF
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
ATG16L1
USP40
HJURP
HES6
ACKR3
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
EFHD1
ILKAP
ING5
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
DUSP28
MROH2A
ESPNL
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
PRR21
AQP12B
D2HGDH
MIR4269
MIR4786
Genes in Wide Peak

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

Table S31.  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 20p12.1.

Table S32.  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 3p11.1.

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

Genes
NSUN3
PROS1
ARL13B
DHFRL1
STX19
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

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

Genes
LINC00511
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

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

Genes
CARS
FANCF
HRAS
LMO1
NUP98
LINC00678
RNA5SP339
SVIP
RNA5SP338
RNA5SP337
RNA5SP336
SLC6A5
SNORA1|ENSG00000207407.1
MIR4486
RNA5SP335
RNA5SP334
RNA5SP333
SAA3P
TPH1
SNORD14B
SNORD14A
OR7E14P
RN7SKP90
C11orf58
RN7SL188P
PSMA1
RNA5SP332
SPON1
RNA5SP331
RN7SKP151
LINC00958
SCARNA16|ENSG00000252329.1
PARVA
SNORD97
LYVE1
RNU6ATAC33P
ADM
RN7SKP50
RN7SL56P
snoU13|ENSG00000238387.1
SNORA23
MIR5691
RNA5SP330
SNORA45
SNORA3|ENSG00000200983.1
SCARNA20|ENSG00000252778.1
OR10AB1P
GVINP1
TAF10
RRP8
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62|ENSG00000201980.1
OR51C1P
SNORA7|ENSG00000206976.1
snoU13|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
GAS2
GTF2H1
HBB
HBD
HBE1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1|ENSG00000130592.9
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPS13
RRM1
SAA1
SAA2
SAA4
SMPD1
TRIM21
ST5
STIM1
ABCC8
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
PKP3
HPS5
RRAS2
SWAP70
DENND5A
SIRT3
OR52A1
ARFIP2
SERGEF
OR10A3
TIMM10B
DKK3
RBMXL2
PGAP2
TRPM5
UBQLN3
RNF141
BET1L
CEND1
CYB5R2
CDHR5
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
LIN7C
LGR4
PIDD
KCNQ1DN
SOX6
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
SBF2
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
NAV2
SYT8
CCDC34
PRKCDBP
SAAL1
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
OR56B4
ANO5
OR52B2
C11orf35
OR51F1
MRGPRX1
CSNK2A3
OR51V1
EFCAB4A
IGSF22
OR10A4
OLFML1
NLRP10
NLRP14
ANO9
LUZP2
B4GALNT4
OR52L1
OR2AG2
OR52B6
OTOG
OR10A2
OVCH2
PDDC1
GALNT18
NCR3LG1
MRGPRG
IFITM5
FAM99A
OR56B1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
TMEM41B
MUC5B
MIR302E
MIR3159
MIR4298
MIR4299
MTRNR2L8
CCDC179
MIR4686
MIR4694
MIR4687
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p11.2.

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

Genes
MAP2K4
GAS7
MTND1P15
UBBP4
RN7SL426P
TMEM11
KRT16P3
NOS2P3
USP32P3
UPF3AP2
RN7SL17P
U6|ENSG00000266839.2
CCDC144CP
SNORA31|ENSG00000252349.1
SNORA59B
MIR1180
SNORD3C
SNORD3A
GRAPL
SNORD3D
GRAP
FAM83G
RN7SL627P
ZNF286B
TBC1D28
RN7SL639P
KRT16P1
KRT17P2
SMCR8
snoU13|ENSG00000238691.1
MIR33B
SMCR5
SMCR2
RN7SL775P
TBC1D27
KRT17P1
KRT16P2
USP32P1
RN7SL620P
ZNF287
MIR1288
RN7SL442P
RNA5SP436
ZNF286A
SNORA74|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
SNORA74|ENSG00000252305.1
MIR548H3
RN7SL550P
MIR744
RPL21P122
RN7SL601P
LINC00675
MAGOH2
ADPRM
RCVRN
GLP2R
STX8
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FLII
KCNJ12
LLGL1
MFAP4
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
PMP22
MAPK7
MAP2K3
PRPSAP2
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
MYH13
NTN1
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
PIK3R5
DHRS7B
B9D1
TVP23B
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
ZNF286A
ZNF624
ELAC2
TEKT3
GID4
FAM106A
LRRC48
ATPAF2
SPECC1
MYOCD
USP43
ZSWIM7
SMCR7
SLC5A10
TOM1L2
SLC47A2
WDR16
CCDC42
PIK3R6
TRIM16L
MFSD6L
DHRS7C
TVP23C
CENPV
FLCN
PLD6
USP32P2
CDRT15L2
C17orf103
LINC00670
CDRT4
CCDC144B
FAM27L
LGALS9B
CCDC144NL
C17orf51
TBC1D26
CDRT1
SPDYE4
TMEM220
SHISA6
FAM211A
PIRT
EVPLL
LGALS9C
MTRNR2L1
MIR1269B
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 20 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 0.03 -0.322 1 0.07 1.71 0.173
1q 1195 0.09 2.06 0.0784 0.05 0.256 0.84
2p 624 0.05 -1.76 1 0.01 -3 0.999
2q 967 0.04 -1.15 1 0.03 -1.52 0.999
3p 644 0.03 -2.2 1 0.09 -0.334 0.999
3q 733 0.11 0.639 0.732 0.03 -1.96 0.999
4p 289 0.01 -3.31 1 0.17 1.26 0.318
4q 670 0.00 -3.07 1 0.15 1.98 0.12
5p 183 0.16 0.666 0.732 0.09 -1.4 0.999
5q 905 0.04 -1.09 1 0.14 2.5 0.0358
6p 710 0.07 -0.758 1 0.05 -1.4 0.999
6q 556 0.05 -1.78 1 0.07 -1.18 0.999
7p 389 0.33 6.68 9.39e-11 0.01 -2.76 0.999
7q 783 0.30 7.92 1.63e-14 0.04 -1.39 0.999
8p 338 0.27 4.22 8.07e-05 0.23 2.89 0.0213
8q 551 0.43 10.6 0 0.11 0.122 0.903
9p 301 0.08 -1.22 1 0.23 3.07 0.0213
9q 700 0.08 -0.324 1 0.09 -0.00478 0.956
10p 253 0.16 0.7 0.732 0.12 -0.354 0.999
10q 738 0.05 -1.3 1 0.08 -0.326 0.999
11p 509 0.06 -1.42 1 0.12 0.331 0.823
11q 975 0.06 -0.209 1 0.08 0.543 0.734
12p 339 0.11 -0.465 1 0.06 -1.83 0.999
12q 904 0.08 0.181 1 0.03 -1.61 0.999
13q 560 0.20 3.28 0.00263 0.03 -2.1 0.999
14q 938 0.01 -2.33 1 0.07 -0.129 0.999
15q 810 0.02 -2.16 1 0.10 0.894 0.53
16p 559 0.06 -1.28 1 0.13 0.814 0.554
16q 455 0.03 -2.4 1 0.16 1.61 0.197
17p 415 0.06 -1.7 1 0.21 2.78 0.0213
17q 972 0.09 0.9 0.669 0.05 -0.601 0.999
18p 104 0.15 0.249 1 0.11 -1.01 0.999
18q 275 0.09 -0.985 1 0.22 2.73 0.0213
19p 681 0.11 0.599 0.732 0.18 2.8 0.0213
19q 935 0.14 2.9 0.00832 0.11 1.44 0.248
20p 234 0.39 7.45 4.71e-13 0.09 -1.1 0.999
20q 448 0.50 12.5 0 0.02 -2.21 0.999
21q 258 0.02 -2.87 1 0.24 3.23 0.0213
22q 564 0.01 -2.88 1 0.16 1.92 0.122
Xq 668 0.21 4.08 0.000128 0.10 0.339 0.823
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/STAD-TP/22507709/segmentationfile.txt

  • Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/STAD-TP/22507709/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 107 Input Tumor Samples.

Tumor Sample Names
TCGA-B7-5816-01A-21D-1598-02
TCGA-B7-5818-01A-11D-1598-02
TCGA-BR-4183-01A-02D-1128-02
TCGA-BR-4184-01A-01D-1128-02
TCGA-BR-4187-01A-01D-1128-02
TCGA-BR-4188-01A-01D-1128-02
TCGA-BR-4191-01A-02D-1128-02
TCGA-BR-4201-01A-01D-1128-02
TCGA-BR-4253-01A-01D-1128-02
TCGA-BR-4255-01A-01D-1128-02

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)