LowPass Copy number analysis (GISTIC2)
Prostate Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by Spring Yingchun Liu (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): LowPass Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C13X85K1
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 115 tumor samples used in this analysis: 16 significant arm-level results, 4 significant focal amplifications, and 16 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 - 4 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
5q31.1 2.4231e-05 2.4231e-05 chr5:135102172-135142341 1
10p11.1 0.019986 0.019986 chr10:38771600-38888819 0 [SEPT7P9]
7p15.2 0.031008 0.031008 chr7:23747603-33899458 80
8p11.23 0.090124 0.090124 chr8:36722500-37773697 8
Genes in Wide Peak

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

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

Genes
MIR5692C1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p15.2.

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

Genes
HOXA13
HNRNPA2B1
HOXA9
HOXA11
JAZF1
RNA5SP229
snoU13|ENSG00000252706.1
RN7SL505P
RP9P
SNORA31|ENSG00000251999.1
AQP1
CRHR2
MIR550A1
snoU13|ENSG00000238906.1
TRIL
RN7SL365P
EVX1
HOTTIP
HOTAIRM1
U3|ENSG00000202233.1
CYCS
snoU13|ENSG00000239098.1
RNA5SP228
snoU13|ENSG00000238849.1
ADCYAP1R1
AQP1
CHN2
DFNA5
GARS
GHRHR
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
NPY
PDE1C
RP9
TAX1BP1
SKAP2
CREB5
NFE2L3
SCRN1
KIAA0087
NOD1
PPP1R17
HIBADH
INMT
FKBP9
CBX3
AVL9
LSM5
KBTBD2
OSBPL3
BBS9
SNX10
NT5C3A
MPP6
CPVL
FKBP14
STK31
NEUROD6
NPVF
GGCT
FAM188B
PLEKHA8
C7orf31
C7orf41
PRR15
CCDC129
ZNRF2
C7orf71
MIR148A
MIR196B
WIPF3
MIR550A2
MIR550A3
Genes in Wide Peak

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

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

Genes
RN7SL709P
BRF2
ZNF703
ERLIN2
PROSC
GPR124
RAB11FIP1
KCNU1

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 - 16 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
10q23.31 1.1524e-29 1.1524e-29 chr10:89605005-90036483 5
21q22.2 9.4171e-15 9.4171e-15 chr21:39900175-42862782 25
6q14.3 2.5979e-08 2.5979e-08 chr6:84879631-87907117 11
16q24.1 5.3598e-06 5.3598e-06 chr16:78508930-90354753 128
13q14.11 6.0495e-05 6.0495e-05 chr13:37403671-58065063 167
17q21.31 0.00014529 0.00014529 chr17:41809000-42771669 33
3p13 0.0012346 0.0012346 chr3:70330075-72954816 13
5q15 0.0019191 0.0019191 chr5:96716255-100717422 6
11q23.2 0.0079663 0.0079663 chr11:113676693-114556953 12
2q22.1 0.0083212 0.0083212 chr2:136747893-149637131 25
8p21.2 0.0037559 0.008686 chr8:9632689-27470746 148
5q13.2 0.017059 0.017059 chr5:54459221-77689173 153
17p13.1 0.030995 0.030995 chr17:6726127-7961035 73
12p13.1 0.049968 0.049968 chr12:11587862-14028033 27
1p31.3 0.13253 0.13253 chr1:63261852-67387711 30
8p11.21 0.096041 0.22375 chr8:33955044-47636734 73
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
CFL1P1
RNLS
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.2.

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

Genes
ERG
TMPRSS2
FAM3B
LINC00323
SNORA51|ENSG00000207147.1
MIR4760
snoU13|ENSG00000238556.1
SNORA62|ENSG00000272015.1
DSCAM
ETS2
HMGN1
MX1
MX2
PCP4
SH3BGR
WRB
PSMG1
B3GALT5
BACE2
BRWD1
C21orf88
LCA5L
IGSF5
LINC00114
MIR3197
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.3.

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

Genes
RN7SKP209
RN7SL643P
SNHG5
CGA
HTR1E
NT5E
TBX18
SYNCRIP
KIAA1009
ZNF292
SNX14
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.1.

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

Genes
CBFA2T3
FANCA
MAF
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13|ENSG00000239186.1
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
MIR3182
RN7SL134P
snoU13|ENSG00000238321.1
RN7SKP190
7SK|ENSG00000260682.2
MIR4720
GAN
PKD1L2
CMC2
RNA5SP431
PIH1
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
MPHOSPH6
EMC8
TUBB3
PRDM7
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
JPH3
WFDC1
MTHFSD
DBNDD1
KLHL36
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
CENPBD1
ZNF276
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
SLC38A8
ADAD2
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
C16orf74
MIR1910
C16orf95
MIR5093
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.11.

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

Genes
LCP1
RB1
LHFP
RN7SKP6
snoU13|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31|ENSG00000199477.1
SNORA31|ENSG00000253051.1
7SK|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116|ENSG00000212553.1
RNY4P14
snoU13|ENSG00000238408.1
LINC00366
LINC00571
RNA5SP26
RN7SKP1
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
SMAD9
NEK3
PCDH8
TPT1
TRPC4
TNFSF11
SUCLA2
ITM2B
MTRF1
UTP14C
LPAR6
TRIM13
MRPS31
DLEU1
OLFM4
POSTN
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
VWA8
ZC3H13
LRCH1
INTS6
CKAP2
NUFIP1
RGCC
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
ENOX1
RCBTB1
NUDT15
KIAA1704
SUPT20H
THSD1
CYSLTR2
SPRYD7
COG6
SMIM2
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
CDADC1
CAB39L
CCDC70
COG3
SETDB2
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
CSNK1A1L
PRR20A
FAM216B
LACC1
HNRNPA1L2
DGKH
CCDC122
STOML3
FAM194B
SPERT
FAM124A
LRRC63
SLC25A30
SIAH3
KCNRG
FREM2
NEK5
KCTD4
NHLRC3
SERP2
DLEU2
ALG11
SERPINE3
MIR621
PRR20B
PRR20C
PRR20D
PRR20E
MIR759
MIR320D1
MIR3168
MIR4305
MIR3613
MIR4703
MIR5007
MIR5693
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

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

Genes
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
C17orf105
DUSP3
GRN
ITGA2B
MPP2
MPP3
PPY
PYY
SLC4A1
UBTF
HDAC5
RUNDC3A
FAM215A
SOST
SLC25A39
ATXN7L3
C17orf53
TMUB2
TMEM101
G6PC3
ASB16
LSM12
CCDC43
CD300LG
NAGS
FAM171A2
C17orf104
Genes in Wide Peak

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

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

Genes
FOXP1
GXYLT2
RNA5SP136
snoU13|ENSG00000238568.1
RYBP
LINC00870
LINC00877
RN7SL271P
GPR27
SHQ1
PROK2
EIF4E3
MIR1284
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
MIR548P
RN7SKP62
CHD1
ST8SIA4
RGMB
FAM174A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

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

Genes
snoU13|ENSG00000238724.1
HTR3A
NNMT
ZBTB16
HTR3B
RBM7
REXO2
C11orf71
NXPE4
USP28
NXPE1
NXPE2
Genes in Wide Peak

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

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

Genes
SNORA48|ENSG00000212181.1
RNA5SP106
snoU13|ENSG00000238860.1
snR65|ENSG00000253036.1
TEX41
RN7SL283P
SNORA72|ENSG00000206901.1
RN7SKP286
NXPH2
RNA5SP105
RN7SKP141
ACVR2A
HNMT
KIF5C
ORC4
CXCR4
KYNU
ZEB2
EPC2
LRP1B
MBD5
ARHGAP15
GTDC1
THSD7B
SPOPL
Genes in Wide Peak

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

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

Genes
PCM1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13|ENSG00000238466.1
U3|ENSG00000251944.1
SNORA62|ENSG00000201157.1
RNA5SP256
MIR548V
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
LINC00529
MIR598
SNORD112|ENSG00000252565.1
SOX7
RNA5SP252
PRSS51
snoU13|ENSG00000238496.1
snoU13|ENSG00000239065.1
NAT1
NAT2
ADRA1A
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DPYSL2
EGR3
DMTN
EPHX2
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
LOXL2
LPL
MSR1
MSRA
NEFM
PDGFRL
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
DLC1
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
PSD3
SLC39A14
ADAMDEC1
CNOT7
KCTD9
PINX1
PIWIL2
INTS10
CSGALNACT1
HR
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
MTMR9
DOCK5
REEP4
STMN4
SOX7
FAM167A
SLC35G5
FAM86B1
LONRF1
CHMP7
RP1L1
VPS37A
SGCZ
PEBP4
CDCA2
TDH
C8orf48
R3HCC1
PRSS55
C8orf74
LGI3
DEFB130|ENSG00000232948.1
NEIL2
XKR6
MICU3
USP17L2
LINC00599
MIR320A
C8orf58
DEFB135
DEFB136
ZNF705D
MIR548H4
MIR4286
MIR5692A2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.2.

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

Genes
IL6ST
PIK3R1
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13|ENSG00000238688.1
RNA5SP186
POLK
SNORA40|ENSG00000212363.1
RN7SL814P
MIR4804
RN7SL153P
MIR4803
snoU13|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13|ENSG00000238334.1
SNORA50|ENSG00000220986.1
RN7SL103P
7SK|ENSG00000249352.3
U8|ENSG00000212249.2
snoU13|ENSG00000238400.1
SNORA76|ENSG00000252904.1
RN7SL169P
HTR1A
CKS1B|ENSG00000268942.1
KIF2A
RN7SKP157
FKSG52
MIR582
GAPT
snoU13|ENSG00000238899.1
snoU13|ENSG00000238717.1
RNU6ATAC2P
RNA5SP185
RNA5SP184
snoU13|ENSG00000238326.1
RNA5SP183
MIR5687
MIR449C
MIR449B
MIR449A
GPX8
TRIM23
BTF3
CCNB1
CDK7
ERCC8
CRHBP
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
TNPO1
CD180
MAP1B
MAP3K1
NAIP
PDE4D
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
SCAMP1
CARTPT
COL4A3BP
CWC27
CCNO
NSA2
PLK2
IQGAP2
ADAMTS6
SV2C
MRPS27
PPWD1
SKIV2L2
PART1
FAM169A
DIMT1
IPO11
GCNT4
DHX29
DDX4
SGTB
AGGF1
DEPDC1B
BDP1
ERBB2IP
NLN
ZSWIM6
ANKRA2
MCCC2
CENPK
ARHGEF28
SLC30A5
CENPH
GPBP1
ANKRD55
PTCD2
ELOVL7
TRAPPC13
UTP15
GFM2
NDUFAF2
MRPS36
FCHO2
RAB3C
SETD9
IL31RA
TMEM171
TMEM174
POC5
SREK1
SLC38A9
MARVELD2
MIER3
CDC20B
ZNF366
CCDC125
ANKRD31
C5orf64
RNF180
SREK1IP1
MCIDAS
ACTBL2
MAST4
RGS7BP
SMIM15
GTF2H2C
SERF1B
ANKDD1B
LRRC70
FAM159B
OCLN
MIR548AE2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

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

Genes
TP53
snoU13|ENSG00000238676.1
SCARNA21|ENSG00000252835.1
RPL29P2
snoU13|ENSG00000251860.1
SNORD10
SNORA48|ENSG00000209582.1
SNORA67|ENSG00000264772.2
SLC35G6
GABARAP
ALOX12P2
TEKT1
ACADVL
ALOX12
ALOX15B
ASGR1
ASGR2
ATP1B2
CD68
CHD3
CHRNB1
CLDN7
DLG4
DVL2
EFNB3
EIF4A1
EIF5A
FGF11
GPS2
GUCY2D
POLR2A
SHBG
SLC2A4
SOX15
TNK1
TNFSF13
KCNAB3
FXR2
MPDU1
ACAP1
CLEC10A
KDM6B
CTDNEP1
ELP5
SENP3
YBX2
WRAP53
PLSCR3
NLGN2
ZBTB4
TRAPPC1
PHF23
LSMD1
NEURL4
TMEM88
SAT2
CNTROB
CYB5D1
C17orf49
DNAH2
KCTD11
SLC16A11
SLC16A13
C17orf74
TMEM256
BCL6B
TMEM102
TMEM95
SPEM1
TNFSF12
RNASEK
MIR324
MIR497HG
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
ETV6
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
CDKN1B
CREBL2
EMP1
GPR19
LRP6
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
APOLD1
GSG1
LOH12CR1
C12orf36
PRB2
MIR614
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.3.

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

Genes
JAK1
MIR3117
RN7SL854P
snoU13|ENSG00000238931.1
LEPROT
MIR4794
RN7SL130P
DLEU2L
RN7SL488P
LINC00466
RNA5SP49
AK4
ROR1
PDE4B
PGM1
DNAJC6
INSL5
ITGB3BP
FOXD3
ALG6
LEPR
RAVER2
CACHD1
WDR78
SGIP1
EFCAB7
ATG4C
UBE2U
TCTEX1D1
MIR3671
Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
HOOK3
RN7SKP41
U3|ENSG00000201329.1
POTEA
RN7SL806P
snoU13|ENSG00000238714.1
SNORD112|ENSG00000238966.1
RN7SL149P
MIR486
SNORD65|ENSG00000238936.1
MIR548AO
IDO1
ADAM3A
ADAM5
SNORD38|ENSG00000207199.1
PLEKHA2
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
RNA5SP264
RN7SKP201
ADRB3
ANK1
CHRNB3
EIF4EBP1
FNTA
ADAM2
IKBKB
PLAT
POLB
SFRP1
SLC20A2
TACC1
VDAC3
KAT6A
ADAM18
ADAM9
CHRNA6
ASH2L
BAG4
AP3M2
ERLIN2
PROSC
DDHD2
GPR124
DKK4
LSM1
GOLGA7
THAP1
C8orf4
ZMAT4
RAB11FIP1
RNF170
TM2D2
SGK196
GINS4
PPAPDC1B
SMIM19
GOT1L1
AGPAT6
UNC5D
LETM2
HGSNAT
KCNU1
IDO2
HTRA4
ADAM32
C8orf86
MIR4469
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 16 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 0.02 0.989 0.807 0.02 0.989 0.496
1q 1195 0.03 2.36 0.0731 0.00 -1.13 0.952
2p 624 0.00 -1.7 0.979 0.01 -1.11 0.952
2q 967 0.00 -1.38 0.979 0.03 1.5 0.221
3p 644 0.04 1.35 0.505 0.01 -1.04 0.952
3q 733 0.08 4.07 0.000944 0.00 -1.55 0.952
4p 289 0.00 -1.95 0.979 0.02 -0.923 0.952
4q 670 0.01 -1.06 0.979 0.00 -1.67 0.952
5p 183 0.00 -2.04 0.979 0.01 -1.54 0.952
5q 905 0.00 -1.45 0.979 0.01 -0.764 0.952
6p 710 0.00 -1.62 0.979 0.02 -0.389 0.952
6q 556 0.00 -1.7 0.979 0.08 3.46 0.00106
7p 389 0.07 2.48 0.0661 0.01 -1.27 0.952
7q 783 0.07 3.62 0.00199 0.00 -1.52 0.952
8p 338 0.01 -0.873 0.979 0.37 20.6 0
8q 551 0.09 3.81 0.00141 0.10 4.95 2.17e-06
9p 301 0.01 -1.4 0.979 0.03 -0.368 0.952
9q 700 0.03 0.217 0.979 0.00 -1.63 0.952
10p 253 0.00 -1.95 0.979 0.04 0.591 0.708
10q 738 0.01 -0.89 0.979 0.08 4.12 9.46e-05
11p 509 0.01 -1.22 0.979 0.01 -1.22 0.952
11q 975 0.01 -0.625 0.979 0.04 1.55 0.221
12p 339 0.02 -0.689 0.979 0.12 5.08 1.26e-06
12q 904 0.04 1.36 0.505 0.02 -0.0183 0.952
13q 560 0.01 -1.05 0.979 0.11 5.26 5.69e-07
14q 938 0.00 -1.42 0.979 0.02 -0.00486 0.952
15q 810 0.01 -0.872 0.979 0.02 -0.22 0.952
16p 559 0.02 -0.588 0.979 0.01 -1.16 0.952
16q 455 0.01 -1.12 0.979 0.13 6.56 2.68e-10
17p 415 0.00 -1.74 0.979 0.14 6.9 3.35e-11
17q 972 0.00 -1.39 0.979 0.01 -0.667 0.952
18p 104 0.00 -1.99 0.979 0.10 3.82 0.000296
18q 275 0.00 -1.82 0.979 0.16 7.41 1.27e-12
19p 681 0.00 -1.63 0.979 0.03 0.799 0.606
19q 935 0.00 -1.42 0.979 0.02 -0.0106 0.952
20p 234 0.01 -1.45 0.979 0.04 0.0641 0.952
20q 448 0.04 0.426 0.979 0.03 -0.122 0.952
21q 258 0.01 -1.44 0.979 0.03 -0.423 0.952
22q 564 0.00 -1.73 0.979 0.03 0.573 0.708
Xq 668 0.01 -1.06 0.979 0.00 -1.67 0.952
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/PRAD-TP/11542039/segmentationfile.txt

  • Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/PRAD-TP/11542039/markersfile.txt

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

  • CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

  • Amplification Threshold = 0.3

  • Deletion Threshold = 0.3

  • Cap Values = 2

  • Broad Length Cutoff = 0.5

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 10

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 10000

  • Gene GISTIC = 0

Table 4.  Get Full Table First 10 out of 115 Input Tumor Samples.

Tumor Sample Names
TCGA-CH-5741-01A-11D-1572-02
TCGA-CH-5743-01A-21D-1572-02
TCGA-CH-5744-01A-11D-1572-02
TCGA-CH-5745-01A-11D-1572-02
TCGA-CH-5746-01A-11D-1572-02
TCGA-CH-5748-01A-11D-1572-02
TCGA-CH-5750-01A-11D-1572-02
TCGA-CH-5751-01A-11D-1572-02
TCGA-CH-5752-01A-11D-1572-02
TCGA-CH-5754-01A-11D-1572-02

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)