LowPass Copy number analysis (GISTIC2)
Prostate Adenocarcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1ST7N91
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/C1ST7N91
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 2.0.20 (Firehose task version: 126).

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 | 0 [SLC25A48]
10p11.1 | 0.019986 | 0.019986 | chr10:38771600-38888819 | 0 [LOC399744]
7p15.3 | 0.031008 | 0.031008 | chr7:23747603-33899458 | 91
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 7p15.3.

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

Genes
HNRNPA2B1
HOXA9
HOXA11
HOXA13
JAZF1
hsa-mir-550-2
hsa-mir-550-1
hsa-mir-196b
hsa-mir-148a
ADCYAP1R1
AQP1
CHN2
CRHR2
DFNA5
EVX1
GARS
GHRHR
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
NPY
PDE1C
RP9
TAX1BP1
SKAP2
CREB5
NFE2L3
SCRN1
KIAA0087
TRIL
NOD1
PPP1R17
HIBADH
INMT
FKBP9
CBX3
AVL9
LSM5
KBTBD2
OSBPL3
BBS9
SNX10
NT5C3
MPP6
CYCS
CPVL
FKBP14
STK31
NEUROD6
NPVF
GGCT
FAM188B
PLEKHA8
C7orf31
HOXA11-AS1
DKFZP586I1420
C7orf41
PRR15
CCDC129
ZNRF2
C7orf71
LOC401320
LOC401321
MIR148A
LOC441204
ZNRF2P1
RP9P
DPY19L2P3
MIR196B
WIPF3
LOC646762
MIR550A1
MIR550A2
JAZF1-AS1
DPY19L1P1
LOC100130673
LOC100133311
ZNRF2P2
HOTTIP
MIR550B2
MIR550B1
HOTAIRM1
LOC100506497
INMT-FAM188B
HOXA10-HOXA9
MIR550A3

Genes in Wide Peak

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

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

Genes
ERLIN2
PROSC
GPR124
BRF2
ZNF703
RAB11FIP1
KCNU1
LOC728024

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 | 4
21q22.2 | 9.4171e-15 | 9.4171e-15 | chr21:39900175-42862782 | 26
6q14.3 | 2.5979e-08 | 2.5979e-08 | chr6:84879631-87907117 | 11
16q23.3 | 5.3598e-06 | 5.3598e-06 | chr16:78508930-90354753 | 122
13q14.11 | 6.0495e-05 | 6.0495e-05 | chr13:37403671-58065063 | 137
17q21.31 | 0.00014529 | 0.00014529 | chr17:41809000-42771669 | 30
3p13 | 0.0012346 | 0.0012346 | chr3:70330075-72954816 | 10
5q15 | 0.0019191 | 0.0019191 | chr5:96716255-100717422 | 8
11q23.2 | 0.0079663 | 0.0079663 | chr11:113676693-114556953 | 11
2q22.1 | 0.0083212 | 0.0083212 | chr2:136747893-149637131 | 19
8p21.2 | 0.0037559 | 0.008686 | chr8:9632689-27470746 | 146
5q13.1 | 0.017059 | 0.017059 | chr5:54459221-77689173 | 132
17p13.1 | 0.030995 | 0.030995 | chr17:6726127-7961035 | 81
12p13.1 | 0.049968 | 0.049968 | chr12:11587862-14028033 | 31
1p31.3 | 0.13253 | 0.13253 | chr1:63261852-67387711 | 28
8p11.21 | 0.096041 | 0.22375 | chr8:33955044-47636734 | 65

Genes in Wide Peak

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

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

Genes
PTEN
RNLS
CFL1P1
KLLN

Genes in Wide Peak

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

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

Genes
ERG
TMPRSS2
hsa-mir-3197
DSCAM
ETS2
HMGN1
MX1
MX2
PCP4
SH3BGR
WRB
PSMG1
B3GALT5
BACE2
BRWD1
FAM3B
C21orf88
LCA5L
IGSF5
PLAC4
BRWD1-IT2
LINC00323
LINC00114
MIR3197
DSCAM-AS1
MIR4760

Genes in Wide Peak

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

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

Genes
CGA
HTR1E
NT5E
TBX18
SYNCRIP
KIAA1009
ZNF292
SNORD50A
SNX14
SNHG5
SNORD50B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
C16orf7
KIAA0513
PIEZO1
ATP2C2
MPHOSPH6
COX4NB
TUBB3
PRDM7
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
C16orf61
JPH3
KIAA1609
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
MGC23284
LINC00311
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722

Genes in Wide Peak

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

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

Genes
LCP1
RB1
LHFP
TTL
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
SMAD9
NEK3
PCDH8
RFXAP
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
ITM2B
MTRF1
UTP14C
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
KIAA0564
ZC3H13
LRCH1
INTS6
CKAP2
NUFIP1
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
CDADC1
CAB39L
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
LINC00284
CSNK1A1L
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
SUGT1P3
SIAH3
KCNRG
LINC00282
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
LINC00547
LINC00548
MIR15A
MIR16-1
ALG11
TSC22D1-AS1
SERPINE3
SNORA31
MIR621
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR759
MIR320D1
MIR4305
MIR3613
OR7E37P
LOC100507240
LOC100509894
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
DUSP3
FZD2
GRN
ITGA2B
MPP2
MPP3
PPY
PYY
SLC4A1
UBTF
HDAC5
RUNDC3A
GPATCH8
FAM215A
SOST
SLC25A39
ATXN7L3
C17orf53
TMUB2
TMEM101
G6PC3
ASB16
LSM12
CCDC43
CD300LG
NAGS
C17orf105
FAM171A2
C17orf104
C17orf65

Genes in Wide Peak

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

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

Genes
FOXP1
hsa-mir-1284
GPR27
RYBP
SHQ1
PROK2
LOC201617
EIF4E3
GXYLT2
MIR1284

Genes in Wide Peak

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

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

Genes
hsa-mir-548p
CHD1
ST8SIA4
RGMB
FAM174A
FLJ35946
LOC100133050
LOC100289230

Genes in Wide Peak

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

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

Genes
HTR3A
NNMT
ZBTB16
HTR3B
RBM7
REXO2
C11orf71
FAM55D
USP28
FAM55A
FAM55B

Genes in Wide Peak

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

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

Genes
ACVR2A
HNMT
KIF5C
ORC4
CXCR4
KYNU
ZEB2
NXPH2
EPC2
LRP1B
MBD5
ARHGAP15
GTDC1
THSD7B
SPOPL
DKFZp686O1327
LOC647012
PABPC1P2
ZEB2-AS1

Genes in Wide Peak

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

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

Genes
PCM1
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
NAT1
NAT2
ADRA1A
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DPYSL2
EGR3
EPB49
EPHX2
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
ENTPD4
PHYHIP
SORBS3
NPM2
DLC1
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
PSD3
SLC39A14
FGF20
ADAMDEC1
CNOT7
ZDHHC2
SLC25A37
KCTD9
PINX1
PIWIL2
INTS10
CSGALNACT1
HR
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
MTMR9
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
FAM86B1
LONRF1
CHMP7
RP1L1
VPS37A
NKX2-6
SGCZ
PEBP4
CDCA2
LOC157627
TDH
C8orf48
R3HCC1
PRSS55
C8orf74
LGI3
DEFB109P1
DEFB130
NEIL2
LOC254896
XKR6
LOC286059
EFHA2
LOC286114
LOC340357
USP17L2
FAM90A25P
LOC389641
LOC392196
MIR124-1
MIR320A
MIR383
C8orf58
DEFB135
DEFB136
DEFB134
FAM86B2
MIR598
ZNF705D
LOC100128993
FAM66D
FAM66A
LOC100133267
MIR1322
MIR3926-2
MIR3926-1
LOC100506990
LOC100507156

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.1.

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

Genes
IL6ST
PIK3R1
hsa-mir-582
hsa-mir-449c
TRIM23
BTF3
CCNB1
CDK7
ERCC8
CRHBP
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
HTR1A
KIF2A
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
SMA4
SMA5
ADAMTS6
SV2C
MRPS27
PPWD1
OTP
SKIV2L2
PART1
FAM169A
DIMT1
IPO11
GCNT4
POLK
DHX29
DDX4
SGTB
AGGF1
WDR41
DEPDC1B
BDP1
ERBB2IP
NLN
ZSWIM6
ANKRA2
MCCC2
CENPK
RGNEF
SLC30A5
CENPH
GPBP1
ANKRD55
PTCD2
ELOVL7
C5orf44
UTP15
ZBED3
GFM2
NDUFAF2
MRPS36
FCHO2
RAB3C
C5orf35
IL31RA
TMEM171
TMEM174
POC5
SREK1
SLC38A9
MARVELD2
MIER3
CDC20B
ZNF366
S100Z
CCDC125
GAPT
ANKRD31
C5orf64
RNF180
SREK1IP1
IDAS
ACTBL2
MAST4
RNF138P1
RGS7BP
GPX8
MIR449A
C5orf43
LOC647859
GUSBP3
GTF2H2B
SNORA47
MIR449B
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LRRC70
FAM159B
LOC100170939
LOC100272216
NCRUPAR
LOC100303749
MIR449C
OCLN
MIR4804
MIR4803

Genes in Wide Peak

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

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

Genes
TP53
hsa-mir-324
hsa-mir-497
ACADVL
ALOX12
ALOX12P2
ALOX15B
ASGR1
ASGR2
ATP1B2
CD68
CHD3
CHRNB1
CLDN7
DLG4
DVL2
EFNB3
EIF4A1
EIF5A
FGF11
GPS2
GUCY2D
POLR2A
SHBG
SLC2A4
SOX15
TNK1
TNFSF13
TNFSF12
KCNAB3
FXR2
MPDU1
ACAP1
CLEC10A
GABARAP
KDM6B
CTDNEP1
C17orf81
SENP3
SNORA67
YBX2
WRAP53
PLSCR3
NLGN2
ZBTB4
TRAPPC1
PHF23
TEKT1
LSMD1
NEURL4
TMEM88
SAT2
CNTROB
RPL29P2
CYB5D1
C17orf49
DNAH2
KCTD11
SLC16A11
SLC16A13
C17orf74
C17orf61
BCL6B
LOC284023
TMEM102
TMEM95
SPEM1
MIR195
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
SNORA48
SNORD10
SCARNA21
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
SENP3-EIF4A1

Genes in Wide Peak

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

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
CDKN1B
CREBL2
EMP1
GPR19
GRIN2B
LRP6
GPRC5A
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
DUSP16
APOLD1
GSG1
HTR7P1
LOH12CR1
C12orf36
LOC338817
RPL13AP20
LOH12CR2
MIR613
MIR614
MIR1244-1
MIR1244-3
MIR1244-2
LOC100506314

Genes in Wide Peak

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

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

Genes
JAK1
hsa-mir-3117
hsa-mir-101-1
AK4
LEPR
ROR1
PDE4B
PGM1
DNAJC6
INSL5
ITGB3BP
FOXD3
ALG6
LEPROT
RAVER2
CACHD1
DLEU2L
WDR78
SGIP1
EFCAB7
ATG4C
UBE2U
LINC00466
TCTEX1D1
MIR101-1
MIR3117
MIR3671
MIR4794

Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
HOOK3
hsa-mir-486
ADRB3
ANK1
CHRNB3
ADAM3A
EIF4EBP1
FNTA
ADAM2
IKBKB
IDO1
PLAT
POLB
SFRP1
SLC20A2
STAR
TACC1
VDAC3
KAT6A
ADAM18
ADAM9
CHRNA6
ASH2L
BAG4
AP3M2
ERLIN2
PROSC
DDHD2
GPR124
DKK4
LSM1
GOLGA7
THAP1
BRF2
C8orf4
PLEKHA2
ZMAT4
ZNF703
RAB11FIP1
RNF170
TM2D2
SGK196
GINS4
PPAPDC1B
C8orf40
GOT1L1
AGPAT6
UNC5D
LETM2
HGSNAT
NKX6-3
KCNU1
IDO2
HTRA4
ADAM32
ADAM5P
RNF5P1
POTEA
C8orf86
MIR486
LOC728024
LOC100130964
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 | 2121 | 0.02 | 1.21 | 0.568 | 0.02 | 1.21 | 0.35
1q | 1955 | 0.03 | 2.6 | 0.0466 | 0.00 | -1.07 | 0.954
2p | 924 | 0.00 | -1.75 | 0.981 | 0.01 | -1.17 | 0.954
2q | 1556 | 0.00 | -1.36 | 0.981 | 0.03 | 1.55 | 0.222
3p | 1062 | 0.04 | 1.38 | 0.482 | 0.01 | -1.02 | 0.954
3q | 1139 | 0.08 | 3.97 | 0.00142 | 0.00 | -1.58 | 0.954
4p | 489 | 0.00 | -1.96 | 0.981 | 0.02 | -0.932 | 0.954
4q | 1049 | 0.01 | -1.08 | 0.981 | 0.00 | -1.68 | 0.954
5p | 270 | 0.00 | -2.07 | 0.981 | 0.01 | -1.58 | 0.954
5q | 1427 | 0.00 | -1.46 | 0.981 | 0.01 | -0.776 | 0.954
6p | 1173 | 0.00 | -1.61 | 0.981 | 0.02 | -0.359 | 0.954
6q | 839 | 0.00 | -1.73 | 0.981 | 0.08 | 3.33 | 0.00174
7p | 641 | 0.07 | 2.46 | 0.0557 | 0.01 | -1.27 | 0.954
7q | 1277 | 0.07 | 3.67 | 0.0016 | 0.00 | -1.51 | 0.954
8p | 580 | 0.01 | -0.87 | 0.981 | 0.37 | 20.6 | 0
8q | 859 | 0.09 | 3.72 | 0.0016 | 0.10 | 4.85 | 4.13e-06
9p | 422 | 0.01 | -1.46 | 0.981 | 0.03 | -0.448 | 0.954
9q | 1113 | 0.03 | 0.2 | 0.981 | 0.00 | -1.63 | 0.954
10p | 409 | 0.00 | -1.97 | 0.981 | 0.04 | 0.553 | 0.725
10q | 1268 | 0.01 | -0.824 | 0.981 | 0.08 | 4.34 | 3.63e-05
11p | 862 | 0.01 | -1.21 | 0.981 | 0.01 | -1.21 | 0.954
11q | 1515 | 0.01 | -0.656 | 0.981 | 0.04 | 1.48 | 0.23
12p | 575 | 0.02 | -0.69 | 0.981 | 0.12 | 5.08 | 1.54e-06
12q | 1447 | 0.04 | 1.38 | 0.482 | 0.02 | -0.00844 | 0.954
13q | 654 | 0.01 | -1.22 | 0.981 | 0.11 | 4.66 | 8.87e-06
14q | 1341 | 0.00 | -1.51 | 0.981 | 0.02 | -0.182 | 0.954
15q | 1355 | 0.01 | -0.821 | 0.981 | 0.02 | -0.154 | 0.954
16p | 872 | 0.02 | -0.622 | 0.981 | 0.01 | -1.19 | 0.954
16q | 702 | 0.01 | -1.16 | 0.981 | 0.13 | 6.42 | 6.62e-10
17p | 683 | 0.00 | -1.75 | 0.981 | 0.14 | 6.88 | 4.02e-11
17q | 1592 | 0.00 | -1.36 | 0.981 | 0.01 | -0.617 | 0.954
18p | 143 | 0.00 | -2.02 | 0.981 | 0.10 | 3.7 | 0.00048
18q | 446 | 0.00 | -1.83 | 0.981 | 0.16 | 7.32 | 2.4e-12
19p | 995 | 0.00 | -1.69 | 0.981 | 0.03 | 0.665 | 0.723
19q | 1709 | 0.00 | -1.27 | 0.981 | 0.02 | 0.3 | 0.899
20p | 355 | 0.01 | -1.49 | 0.981 | 0.04 | 0.00824 | 0.954
20q | 753 | 0.04 | 0.436 | 0.981 | 0.03 | -0.113 | 0.954
21q | 509 | 0.01 | -1.41 | 0.981 | 0.03 | -0.376 | 0.954
22q | 921 | 0.00 | -1.73 | 0.981 | 0.03 | 0.574 | 0.725
Xq | 1312 | 0.01 | -0.877 | 0.981 | 0.00 | -1.53 | 0.954

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/6154864/segmentationfile.txt

- Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/PRAD-TP/6154864/markersfile.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

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

- Amplification Threshold = 0.3

- Deletion Threshold = 0.3

- Cap Values = 2

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

- Gene GISTIC = 0

Table 4. Get Full Table First 10 out of 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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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