Prostate Adenocarcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16 (cga svn revision 38839).

Summary

There were 100 tumor samples used in this analysis: 14 significant arm-level results, 0 significant focal amplifications, and 20 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.

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 1. Get Full Table Deletions Table - 20 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 | 8.1491e-22 | 8.1491e-22 | chr10:89617158-90348818 | 3
21q22.3 | 2.1911e-20 | 2.1911e-20 | chr21:42827479-43100702 | 1
6q14.3 | 2.3144e-14 | 2.3144e-14 | chr6:84138186-108885555 | 95
13q14.11 | 4.4314e-11 | 5.2751e-11 | chr13:38439710-49563699 | 72
3p13 | 2.771e-09 | 2.771e-09 | chr3:70016017-72941288 | 9
16q23.3 | 1.3067e-07 | 1.3067e-07 | chr16:83829806-90354753 | 100
17q21.31 | 4.5017e-07 | 4.3759e-07 | chr17:42019495-42651945 | 20
5q15 | 1.0115e-06 | 5.2804e-06 | chr5:96515472-101571689 | 8
2q22.3 | 0.00012462 | 0.00012462 | chr2:136875713-147346415 | 12
12p13.2 | 0.0010212 | 0.00098283 | chr12:10978771-13523791 | 48
8p21.3 | 0.0015442 | 0.0014211 | chr8:20109881-27951247 | 78
11q23.2 | 0.0025006 | 0.0023857 | chr11:111963481-116619072 | 28
1p31.3 | 0.010068 | 0.010068 | chr1:63986866-66261758 | 16
5q13.2 | 0.0010818 | 0.012619 | chr5:44813655-79598621 | 165
17p13.1 | 0.01417 | 0.014197 | chr17:6932141-7593565 | 53
18q23 | 0.026817 | 0.026936 | chr18:63200038-78077248 | 46
4q34.3 | 0.053635 | 0.053635 | chr4:177189490-182078895 | 5
1q42.2 | 0.085393 | 0.085393 | chr1:210847515-242252988 | 217
3q29 | 0.11003 | 0.11567 | chr3:172856243-198022430 | 188
7q36.1 | 0.19829 | 0.18836 | chr7:117882615-159138663 | 336

Genes in Wide Peak

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

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

Genes
PTEN
RNLS
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
TMPRSS2

Genes in Wide Peak

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

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
CCNC
CGA
CNR1
EPHA7
GABRR1
GABRR2
GRIK2
HTR1E
NT5E
POU3F2
PREP
SIM1
MAP3K7
NR2E1
SNX3
RNGTT
TBX18
FHL5
ATG5
SNAP91
CASP8AP2
SYNCRIP
SLC35A1
FUT9
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
ZNF292
MDN1
UFL1
ORC3
PNISR
FBXL4
SNORD50A
OSTM1
NDUFAF4
CYB5R4
C6orf203
UBE2J1
COQ3
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MANEA
GPR63
SPACA1
MCHR2
FAXC
GJA10
RTN4IP1
USP45
MRAP2
KLHL32
RIPPLY2
PM20D2
SRSF12
C6orf165
BVES-AS1
PRSS35
C6orf163
LACE1
MMS22L
SCML4
GJB7
SNHG5
LIN28B
TSG1
SNORD50B
LOC728012
LOC100130890
MIR2113
MIR548H3
LOC100422737
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
LCP1
RB1
LHFP
TTL
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
RCBTB2
CPB2
ELF1
ESD
FOXO1
GTF2F2
HTR2A
TPT1
TNFSF11
SUCLA2
TSC22D1
ITM2B
MTRF1
LPAR6
SLC25A15
MRPS31
WBP4
AKAP11
KIAA0564
ZC3H13
LRCH1
NUFIP1
C13orf15
MED4
DNAJC15
UFM1
ENOX1
NUDT15
KIAA1704
CYSLTR2
COG6
NAA16
KIAA0226L
PROSER1
COG3
KBTBD7
KBTBD6
EPSTI1
LINC00284
FAM216B
LACC1
LINC00330
DGKH
CCDC122
STOML3
FAM194B
SPERT
SLC25A30
SUGT1P3
SIAH3
FREM2
KCTD4
NHLRC3
SERP2
LINC00548
TSC22D1-AS1
SNORA31
MIR621
TPT1-AS1
MIR320D1
MIR4305
OR7E37P
LOC100507240
LOC100509894
LOC100616668

Genes in Wide Peak

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

Table S5. 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
MIR1284

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

Genes in Wide Peak

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

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

Genes
FZD2
GRN
ITGA2B
PYY
SLC4A1
UBTF
HDAC5
RUNDC3A
GPATCH8
SLC25A39
ATXN7L3
C17orf53
TMUB2
TMEM101
G6PC3
ASB16
LSM12
NAGS
FAM171A2
C17orf65

Genes in Wide Peak

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

Table S8. 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 2q22.3.

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

Genes
HNMT
KYNU
ZEB2
NXPH2
LRP1B
ARHGAP15
GTDC1
THSD7B
SPOPL
DKFZp686O1327
LOC647012
ZEB2-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

Table S10. 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
LRP6
PRB1
PRB3
PRB4
PRH1
PRH2
GPRC5A
PRR4
TAS2R13
TAS2R14
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
DUSP16
APOLD1
GSG1
HTR7P1
LOH12CR1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
LOC338817
TAS2R42
RPL13AP20
LOH12CR2
PRB2
MIR613
MIR614
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
LOC100506314
PRH1-PRR4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

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

Genes
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
ADRA1A
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
EGR3
EPB49
EPHX2
PTK2B
GFRA2
GNRH1
LOXL2
NEFM
NEFL
NKX3-1
PPP2R2A
PPP3CC
SFTPC
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
PNMA2
ADAM28
XPO7
TRIM35
RHOBTB2
SLC39A14
ADAMDEC1
SLC25A37
SCARA3
KCTD9
PIWIL2
CCDC25
HR
PBK
BIN3
KIAA1967
PDLIM2
EBF2
FAM160B2
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
CHMP7
NKX2-6
PEBP4
CDCA2
ESCO2
R3HCC1
LGI3
LOC254896
LOC286059
LOC286114
SCARA5
LOC389641
C8orf80
MIR320A
C8orf58
MIR4287
MIR3622A
MIR3622B
LOC100507156

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's Cancer Gene Census [7].

Genes
hsa-mir-4301
DRD2
HTR3A
IL18
NCAM1
NNMT
PTS
ZBTB16
HTR3B
ZW10
RBM7
CADM1
REXO2
C11orf71
FAM55D
TTC12
TEX12
USP28
TMPRSS5
BCO2
FAM55A
FAM55B
ANKK1
LOC283143
C11orf34
CLDN25
LOC100288346
MIR4301

Genes in Wide Peak

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

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

Genes
JAK1
hsa-mir-101-1
AK4
LEPR
ROR1
PGM1
DNAJC6
LEPROT
RAVER2
CACHD1
DLEU2L
EFCAB7
UBE2U
MIR101-1
MIR3671
MIR4794

Genes in Wide Peak

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

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
hsa-mir-581
TRIM23
ARSB
BHMT
BTF3
CCNB1
CDK7
ERCC8
CRHBP
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HTR1A
ISL1
ITGA1
ITGA2
KIF2A
TNPO1
CD180
MAP1B
MAP3K1
MOCS2
NAIP
NDUFS4
PDE4D
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
THBS4
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
HOMER1
SCAMP1
CARTPT
COL4A3BP
LHFPL2
CWC27
CCNO
NSA2
FST
PLK2
IQGAP2
SMA4
SMA5
ESM1
ADAMTS6
SV2C
MRPS27
PPWD1
OTP
SKIV2L2
BHMT2
PART1
FAM169A
DIMT1
DMGDH
IPO11
GCNT4
POLK
PELO
DHX29
DDX4
SGTB
ARL15
AGGF1
WDR41
DEPDC1B
BDP1
ERBB2IP
NLN
ZSWIM6
ANKRA2
MCCC2
CENPK
RGNEF
SLC30A5
CENPH
GPBP1
PARP8
ANKRD55
PTCD2
ELOVL7
C5orf44
UTP15
ZBED3
GFM2
NDUFAF2
MRPS36
SNX18
FCHO2
RAB3C
C5orf35
IL31RA
EMB
JMY
TMEM171
TMEM174
POC5
SREK1
SLC38A9
MARVELD2
MIER3
CDC20B
PAPD4
ZNF366
S100Z
CCDC125
GAPT
CMYA5
ANKRD31
SERINC5
LOC257396
C5orf64
RNF180
SREK1IP1
IDAS
ACTBL2
MTX3
HCN1
MAST4
RNF138P1
RGS7BP
GPX8
MIR449A
LOC642366
C5orf43
LOC644936
LOC647859
GUSBP3
GTF2H2B
SNORA47
MIR449B
MIR581
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
ACADVL
ASGR1
ASGR2
ATP1B2
CD68
CHRNB1
CLDN7
DLG4
DVL2
EIF4A1
EIF5A
FGF11
GPS2
POLR2A
SHBG
SLC2A4
SOX15
TNK1
TNFSF13
TNFSF12
FXR2
MPDU1
ACAP1
CLEC10A
GABARAP
CTDNEP1
C17orf81
SENP3
SNORA67
YBX2
PLSCR3
NLGN2
ZBTB4
PHF23
NEURL4
SAT2
KCTD11
SLC16A11
SLC16A13
C17orf74
C17orf61
TMEM102
TMEM95
SPEM1
TNFSF12-TNFSF13
MIR324
SLC35G6
SNORA48
SNORD10
C17orf61-PLSCR3
SENP3-EIF4A1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
CDH7
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
SOCS6
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
SALL3
CDH19
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
RBFA
PQLC1
NETO1
PARD6G
CNDP1
DSEL
FAM69C
CBLN2
FBXO15
DOK6
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
AGA
VEGFC
NEIL3
SPCS3
LOC285501

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.2.

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

Genes
FH
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
ACTA1
ACTN2
PARP1
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
ITPKB
KCNH1
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
LPGAT1
BPNT1
LEFTY1
SPHAR
CAPN9
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
INTS7
NSL1
RPS6KC1
RNU5F-1
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
GPATCH2
HEATR1
TMEM206
BATF3
SLC30A10
IARS2
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
GJC2
SIPA1L2
ZP4
RHOU
GREM2
ACBD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
PCNXL2
WDR26
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
KIAA1804
LINC00467
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
SNAP47
C1orf96
LYPLAL1
DNAH14
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
CNIH3
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
C1orf65
IBA57
LIN9
ZNF678
PRSS38
LOC339535
RD3
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf140
FAM177B
ZNF847P
MIR194-1
MIR215
TRIM67
MAP1LC3C
H3F3AP4
DUSP5P
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
SNORA14B
SNORA36B
SNORA16B
LOC728463
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3122
MIR3620
PROX1-AS1
LOC100506795
LOC100506810
MIR4753
MIR4666A
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
ACTL6A
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
EHHADH
EIF4G1
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
POLR2H
PPP1R2
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SST
THPO
FXR1
TP63
CHRD
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
NLGN1
NCBP2
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
FETUB
LAMP3
KCNMB3
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MCCC1
HRASLS
MRPL47
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
ATP13A3
TBL1XR1
MAP6D1
PIGZ
B3GNT5
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LOC339926
LPP-AS2
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
FLJ46066
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
C3orf65
GMNC
LOC647323
SNORA81
SNORD66
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CADPS2
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Arm-level results

Table 2. Get Full Table Arm-level significance table - 14 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.01 | 2.92 | 0.0138 | 0.01 | 2.92 | 0.00863
1q | 1955 | 0.02 | 2.81 | 0.0163 | 0.00 | -0.585 | 0.923
2p | 924 | 0.00 | -1.39 | 0.957 | 0.00 | -1.39 | 0.923
2q | 1556 | 0.00 | -0.975 | 0.957 | 0.01 | 0.0514 | 0.898
3p | 1062 | 0.03 | 1.03 | 0.741 | 0.01 | -0.507 | 0.923
3q | 1139 | 0.06 | 3.58 | 0.00227 | 0.01 | -0.401 | 0.923
4p | 489 | 0.01 | -0.966 | 0.957 | 0.02 | -0.341 | 0.923
4q | 1049 | 0.01 | -0.551 | 0.957 | 0.00 | -1.31 | 0.923
5p | 270 | 0.00 | -1.72 | 0.957 | 0.01 | -1.13 | 0.923
5q | 1427 | 0.01 | -0.126 | 0.957 | 0.01 | -0.126 | 0.923
6p | 1173 | 0.00 | -1.24 | 0.957 | 0.01 | -0.431 | 0.923
6q | 839 | 0.00 | -1.41 | 0.957 | 0.04 | 1.39 | 0.318
7p | 641 | 0.07 | 3.12 | 0.00868 | 0.01 | -0.803 | 0.923
7q | 1277 | 0.06 | 3.98 | 0.000672 | 0.00 | -1.14 | 0.923
8p | 580 | 0.00 | -1.2 | 0.957 | 0.42 | 25.7 | 0
8q | 859 | 0.09 | 4.54 | 0.000108 | 0.08 | 3.84 | 0.000345
9p | 422 | 0.01 | -0.998 | 0.957 | 0.03 | 0.227 | 0.866
9q | 1113 | 0.02 | 0.346 | 0.957 | 0.03 | 1.13 | 0.457
10p | 409 | 0.00 | -1.63 | 0.957 | 0.03 | 0.197 | 0.866
10q | 1268 | 0.01 | -0.309 | 0.957 | 0.02 | 0.541 | 0.675
11p | 862 | 0.00 | -1.43 | 0.957 | 0.00 | -1.43 | 0.923
11q | 1515 | 0.00 | -1.01 | 0.957 | 0.00 | -1.01 | 0.923
12p | 575 | 0.00 | -1.51 | 0.957 | 0.09 | 4.26 | 6.5e-05
12q | 1447 | 0.03 | 1.82 | 0.194 | 0.01 | -0.0786 | 0.923
13q | 654 | 0.00 | -1.42 | 0.957 | 0.15 | 8.44 | 0
14q | 1341 | 0.00 | -1.14 | 0.957 | 0.00 | -1.14 | 0.923
15q | 1355 | 0.00 | -1.12 | 0.957 | 0.01 | -0.228 | 0.923
16p | 872 | 0.02 | 0.0412 | 0.957 | 0.02 | 0.0412 | 0.898
16q | 702 | 0.01 | -0.699 | 0.957 | 0.12 | 6.64 | 1.48e-10
17p | 683 | 0.00 | -1.42 | 0.957 | 0.13 | 7.21 | 3.69e-12
17q | 1592 | 0.00 | -0.951 | 0.957 | 0.00 | -0.951 | 0.923
18p | 143 | 0.01 | -1.13 | 0.957 | 0.06 | 1.71 | 0.188
18q | 446 | 0.01 | -0.874 | 0.957 | 0.12 | 5.91 | 1.35e-08
19p | 995 | 0.00 | -1.33 | 0.957 | 0.03 | 0.905 | 0.548
19q | 1709 | 0.00 | -0.851 | 0.957 | 0.00 | -0.851 | 0.923
20p | 355 | 0.00 | -1.65 | 0.957 | 0.04 | 0.754 | 0.586
20q | 753 | 0.01 | -0.766 | 0.957 | 0.03 | 0.594 | 0.674
21q | 509 | 0.00 | -1.58 | 0.957 | 0.04 | 0.935 | 0.548
22q | 921 | 0.00 | -1.37 | 0.957 | 0.03 | 0.797 | 0.586

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.

- 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.

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/GDAC_MergeDataFilesPipeline/PRAD/1552030/2.GDAC_MergeDataFiles.Finished/PRAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.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 = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 3. Get Full Table First 10 out of 100 Input Tumor Samples.

Tumor Sample Names
TCGA-CH-5737-01A-11D-1574-01
TCGA-CH-5738-01A-11D-1574-01
TCGA-CH-5739-01A-11D-1574-01
TCGA-CH-5740-01A-11D-1574-01
TCGA-CH-5741-01A-11D-1574-01
TCGA-CH-5743-01A-21D-1574-01
TCGA-CH-5744-01A-11D-1574-01
TCGA-CH-5746-01A-11D-1574-01
TCGA-CH-5748-01A-11D-1574-01
TCGA-CH-5750-01A-11D-1574-01

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- 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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