SNP6 Copy number analysis (GISTIC2)
Uveal Melanoma (Primary solid tumor)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1TX3DWK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1TX3DWK
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 2.0.22 (Firehose task version: 140).

Summary

There were 80 tumor samples used in this analysis: 24 significant arm-level results, 3 significant focal amplifications, and 18 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 - 3 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
--- | --- | --- | --- | ---
8q24.22 | 8.8879e-13 | 8.8879e-13 | chr8:107863152-146364022 | 247
6p24.3 | 2.0409e-06 | 2.0409e-06 | chr6:1-18226822 | 115
17q25.3 | 0.054583 | 0.054583 | chr17:52926827-81195210 | 411

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.22.

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

Genes
EXT1
MYC
RECQL4
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25|ENSG00000251744.1
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
SNORD112|ENSG00000252559.1
TMEM74
RNA5SP275
ADCY8
ANGPT1
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HSF1
EIF3E
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
PTK2
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRHR
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
GPAA1
FOXH1
EBAG9
LRRC14
EMC2
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
KHDRBS3
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
KCNV1
MTBP
AGO2
COMMD5
MRPL13
ATAD2
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
THEM6
FAM49B
CHRAC1
EXOSC4
TRMT12
WDYHV1
SLC39A4
SYBU
GSDMC
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
DSCC1
DERL1
SLC52A2
GSDMD
ARHGAP39
ZNF34
SHARPIN
SCRT1
TRAPPC9
TATDN1
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
PKHD1L1
NAPRT1
TBC1D31
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
FAM84B
FAM91A1
SLC30A8
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
MROH5
MAFA
SAMD12
MIR30B
MIR30D
LRRC24
MROH6
FER1L6
MROH1
FAM203B
OC90
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3610
MIR4662B
MIR4663
MIR4664
MIR5194

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.3.

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

Genes
IRF4
DEK
RNA5SP204
STMND1
U3|ENSG00000251793.1
MIR4639
RN7SL332P
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
FAM8A1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
MCUR1
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
KDM1B
RBM24
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
NHLRC1
PSMG4
C6orf201
PPP1R3G
TMEM170B
MIR4645
MIR5689
MIR5683

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

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

Genes
BRIP1
CD79B
CLTC
DDX5
HLF
PRKAR1A
ASPSCR1
MSI2
CANT1
MIR4525
RAB40B
snoU13|ENSG00000238403.1
snoU13|ENSG00000238947.1
DUS1L
PCYT2
SLC25A10
LINC00482
MIR1250
MIR657
MIR4730
CBX8
snoU13|ENSG00000239173.1
ENGASE
DDC8
RN7SL454P
SNORA30|ENSG00000200063.1
RN7SL236P
FLJ45079
LINC00338
LINC00868
MIR636
SNORD1B
SNHG16
PRCD
snoU13|ENSG00000238418.1
MYO15B
RN7SL573P
MIR3615
CD300LD
GPRC5C
RNA5SP448
LINC00469
SSTR2
SCARNA24|ENSG00000252274.1
RN7SKP180
LINC00511
MAP2K6
SNORA40|ENSG00000252352.1
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
RN7SL622P
SNORA38B
MIR548D2
RN7SL756P
snoU13|ENSG00000238612.1
PSMD12
SNORA8|ENSG00000207410.1
RNA5SP447
RNA5SP446
MIR634
RNA5SP445
RN7SL735P
RNA5SP444
SLC16A6P1
RN7SL404P
RN7SL409P
PLEKHM1P
SMURF2
MIR5047
MIR3064
SNORD104
SNORA76|ENSG00000266402.2
TCAM1P
RN7SL805P
ACE
TLK2
TBC1D3P2
RN7SL800P
snoU13|ENSG00000238799.1
RN7SL448P
RN7SL606P
PPM1D
RPL12P38
SCARNA20|ENSG00000252577.1
USP32
MIR4729
PRR11
MIR301A
MIR454
RN7SL716P
PPM1E
U3|ENSG00000212195.1
DYNLL2
SRSF1
VEZF1
MRPS23
RN7SKP94
RN7SL449P
RN7SL437P
RNF126P1
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NPTX1
P4HB
PDE6G
SEPT4
PRKCA
PRPSAP1
PSMC5
PYCR1
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
COIL
AKAP1
EPX
AXIN2
DGKE
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
POLG2
CD300A
TMC6
DDX42
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
PTRH2
SDK2
BCAS3
TMEM104
RNF43
MKS1
C17orf80
CCDC40
WIPI1
SMG8
TMEM100
NPLOC4
ST6GALNAC1
TEX2
TEX14
WDR45B
CCDC47
MIF4GD
INTS2
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
FN3K
DNAI2
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
OGFOD3
ZNF750
NUP85
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
CBX2
FAM104A
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
MGAT5B
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
EFCAB3
NOTUM
TMC8
ANKFN1
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
STXBP4
MYADML2
NPB
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
OXLD1
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
LRRC37A3
YPEL2
C17orf82
BTBD17
TEX19
CUEDC1
MIR142
MIR21
MXRA7
CPSF4L
SMIM5
MIR633
SMIM6
TEN1
C17orf99
MIR4316
MIR338
MIR3186
MIR3614
MIR3678
MIR3615
MIR4739
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524B

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 - 18 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
--- | --- | --- | --- | ---
11p15.1 | 4.661e-23 | 4.661e-23 | chr11:16623557-16799846 | 1
1p36.12 | 0.00034394 | 0.00034394 | chr1:19073360-24108626 | 85
3q24 | 0.0049422 | 0.0049422 | chr3:142896601-143694372 | 1
3p22.2 | 0.0051421 | 0.0050023 | chr3:38314751-38389497 | 1
3p25.1 | 0.013477 | 0.013477 | chr3:13545239-13692618 | 1
11q24.3 | 0.023516 | 0.023516 | chr11:114997555-133313263 | 198
3q29 | 0.023516 | 0.023516 | chr3:194238890-194369918 | 1
6q25.2 | 0.0054289 | 0.023516 | chr6:142365089-158863471 | 93
2q37.2 | 0.024639 | 0.024232 | chr2:225871674-243199373 | 173
16q12.1 | 0.016325 | 0.024232 | chr16:47735031-48202502 | 1
6q27 | 0.0049422 | 0.046377 | chr6:166922042-167347293 | 1
8p11.22 | 0.046377 | 0.046377 | chr8:38312793-38587017 | 1
1p12 | 0.061261 | 0.062985 | chr1:117308686-120151587 | 21
3p25.2 | 0.086468 | 0.086468 | chr3:12809221-12884390 | 2
16q23.3 | 0.058855 | 0.086468 | chr16:82873004-83542835 | 2
3p14.2 | 0.09134 | 0.090113 | chr3:58651854-67050202 | 24
16q24.3 | 0.12091 | 0.1095 | chr16:88525832-90354753 | 49
17q12 | 0.22482 | 0.22482 | chr17:27397975-51318309 | 506

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.1.

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

Genes
C11orf58

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.12.

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

Genes
MDS2
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
ALPL
C1QA
C1QB
C1QC
CAPZB
CDA
CDC42
DDOST
E2F2
ECE1
EPHA8
EPHB2
HSPG2
HTR1D
HTR6
ID3
NBL1
PLA2G2A
RAP1GAP
RPL11
TCEA3
TCEB3
LUZP1
ALDH4A1
EIF4G3
ZBTB40
CELA3A
HNRNPR
KDM1A
EMC1
OTUD3
UBR4
CELA3B
HP1BP3
MRTO4
WNT4
RNF186
PQLC2
CAMK2N1
ASAP3
KIF17
PLA2G2F
PINK1
MUL1
ZNF436
TAS1R2
USP48
NBPF3
IFFO2
VWA5B1
C1orf213
FAM43B
AKR7L
TMCO4
SH2D5
LDLRAD2
MINOS1
LACTBL1
C1orf234
MIR4253
MIR4419A
MIR4418

Genes in Wide Peak

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

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

Genes
SLC9A9

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p22.2.

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

Genes
SLC22A14

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.1.

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

Genes
FBLN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

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

Genes
DDX6
PCSK7
CBL
FLI1
PAFAH1B2
ARHGEF12
snoU13|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CD3D
CD3E
CHEK1
DPAGT1
ETS1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
IL10RA
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NFRKB
NRGN
PVRL1
SCN2B
SCN4B
ST3GAL4
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZNF202
BARX2
USP2
UBE4A
EI24
FEZ1
ARHGAP32
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
OR8B8
OR8B2
DCPS
ZBTB44
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
TMPRSS13
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
ESAM
TIRAP
C1QTNF5
PANX3
APOA5
TMEM45B
AMICA1
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
HEPN1
PATE3
MIR4493
MIR4492

Genes in Wide Peak

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

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

Genes
TMEM44

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.2.

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

Genes
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
ESR1
FUCA2
GRM1
HIVEP2
NMBR
OPRM1
PCMT1
PLAGL1
UTRN
VIP
EPM2A
SYNJ2
LATS1
AKAP12
PHACTR2
UST
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
MTHFD1L
IPCEF1
TIAM2
FBXO5
RGS17
CLDN20
NOX3
AIG1
SNX9
MTRF1L
RMND1
GPR126
PLEKHG1
ARID1B
ZBTB2
ULBP3
C6orf211
ZDHHC14
ADGB
CCDC170
MYCT1
ULBP2
ULBP1
PPP1R14C
SF3B5
LRP11
LTV1
SERAC1
PPIL4
RAET1E
ZC2HC1B
RAET1L
SHPRH
NUP43
RAET1G
SUMO4
SAMD5
IYD
GTF2H5
TMEM242
MIR1202
MIR1273C
MIR4466

Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SAG
CCL20
SP100
SPP2
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
CAPN10
SP140
PASK
ATG4B
SH3BP4
NGEF
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
PID1
ATG16L1
USP40
HJURP
HES6
C2orf83
MFF
ACKR3
NYAP2
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
DNER
B3GNT7
SP140L
AGAP1
TWIST2
DIS3L2
NEU4
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
C2orf72
DUSP28
MROH2A
ESPNL
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4269
MIR4786
MIR5001
MIR5702
MIR5703

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q12.1.

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

Genes
ABCC12

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MIR1913

Genes in Wide Peak

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

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

Genes
C8orf86

Genes in Wide Peak

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

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

Genes
LINC00622
snoU13|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
HSD3B1
HSD3B2
PTGFRN
TBX15
CD101
WARS2
HAO2
GDAP2
FAM46C
VTCN1
TRIM45
SPAG17

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.2.

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

Genes
SNORA7A
RPL32

Genes in Wide Peak

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

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

Genes
MIR3182
RN7SL134P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
FHIT
RN7SL482P
U3|ENSG00000200222.1
SNTN
RNA5SP134
LINC00698
RN7SL863P
PTPRG
U3|ENSG00000212211.1
NPCDR1
ATXN7
CADPS
MAGI1
PSMD6
LRIG1
FEZF2
ADAMTS9
C3orf14
THOC7
SLC25A26
C3orf49
SYNPR
PRICKLE2
C3orf67

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

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

Genes
CBFA2T3
FANCA
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
AFG3L1P
APRT
C16orf3
CDH15
CYBA
DPEP1
GALNS
GAS8
MC1R
MVD
CHMP1A
RPL13
SPG7
CDK10
VPS9D1
PIEZO1
TUBB3
PRDM7
TCF25
CPNE7
IL17C
ANKRD11
TRAPPC2L
DEF8
DBNDD1
CDT1
SPIRE2
CENPBD1
ZNF276
RNF166
SPATA2L
SPATA33
ZC3H18
ZNF778
ACSF3
LINC00304
SNAI3
CTU2
PABPN1L

Genes in Wide Peak

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

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

Genes
RARA
BRCA1
COL1A1
ERBB2
ETV4
LASP1
MLLT6
NF1
TAF15
SUZ12
snoZ178
RN7SL699P
snoU13|ENSG00000238815.1
snoU13|ENSG00000239135.1
HILS1
NXPH3
ZNF652
snoU13|ENSG00000238804.1
SNF8
SNORA68|ENSG00000212565.1
RN7SL125P
HOXB4
HOXB3
HOXB2
HOXB1
U3|ENSG00000200538.1
MIR1203
MIR152
PNPO
KPNB1
MRPL45P2
ITGB3
snoU13|ENSG00000252088.1
RN7SL270P
LRRC37A17P
RNU6ATAC3P
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
ZNF385C
TTC25
RN7SL871P
RN7SL399P
RNA5SP442
EIF1
KRT42P
LINC00974
KRT223P
KRT222
KRT222
RNA5SP441
GJD3
RNY4P8
SNORD124
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
ARL5C
LINC00672
SNORA21|ENSG00000199293.1
SNORA21|ENSG00000252699.1
RPL23
RNA5SP440
CISD3
MIR4726
RN7SL102P
RN7SL458P
SOCS7
HMGB1P24
MIR2909
RNA5SP439
CCL4L2
RN7SL301P
CCL4
CCL18
RN7SKP274
SNORD7
SLFN12L
SLFN5
Vault|ENSG00000252328.1
snoU13|ENSG00000238858.1
RNA5SP438
C17orf75
SH3GL1P1
RNA5SP437
UTP6
RNU6ATAC7P
RN7SL45P
RN7SL79P
EVI2A
RN7SL138P
TEFM
SUZ12P
RN7SL316P
LRRC37BP1
SMURF2P1
SNORD63|ENSG00000252112.1
MIR423
MIR3184
RNY4P13
RNY4P13
snoU13|ENSG00000239129.1
SNORA70|ENSG00000252657.1
MIR4523
TIAF1
ACACA
ASIC2
ACLY
AP2B1
AOC2
ARL4D
ATP5G1
ATP6V0A1
BLMH
FMNL1
CACNB1
CDC6
CDC27
CHAD
CCR7
CNP
CPD
CRHR1
CRYBA1
CSF3
DHX8
DLX3
DLX4
DUSP3
EVI2B
EZH1
GAST
KAT2A
GFAP
GIP
GNGT2
GRB7
GRN
HCRT
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
IFI35
IGFBP4
ITGA2B
ITGA3
ITGB3
JUP
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LHX1
LIG3
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
MYO1D
NAGLU
NFE2L1
NGFR
NME1
NMT1
NSF
OMG
PDK2
PEX12
PHB
MED1
PPY
PSMB3
PYY
PSMD3
PSMD11
RAB5C
RAD51D
RPL19
RPL27
CCL1
CCL2
CCL3
CCL3L1
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL23
SGCA
SLC4A1
SLC6A4
SMARCE1
SP2
STAT3
STAT5A
STAT5B
TADA2A
HNF1B
MLX
THRA
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
PCGF2
ZNF207
RND2
PIP4K2B
SPOP
CNTNAP1
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
ABCC3
CDK5R1
CACNA1G
HAP1
SPAG9
ZNHIT3
EFTUD2
NPEPPS
GOSR1
CCL4L1
GOSR2
NR1D1
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
GJC1
TOB1
PSME3
NBR2
SLC35B1
CALCOCO2
RAMP2
HOXB13
VAT1
LEPREL4
HEXIM1
IGF2BP1
CCT6B
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
KAT7
SYNRG
CASC3
KCNH4
FAM215A
KRT23
TMEM98
TBC1D29
AATF
TUBG2
NKIRAS2
COA3
GIT1
PSMC3IP
SNX11
TBX21
SOST
UTP18
RAPGEFL1
ABI3
COPZ2
MRPL27
ARL17A
CRLF3
SLC25A39
LUC7L3
HIGD1B
CDK12
KRT20
NLE1
FNDC8
MBTD1
CWC25
LINC00483
EPN3
SLFN12
KLHL11
RHOT1
RSAD1
COPRS
LRRC59
ADAP2
GSDMB
CA10
ATXN7L3
PLXDC1
LYZL6
NUFIP2
TAOK1
ARHGAP23
FKBP10
XYLT2
SPATA20
UBE2Z
WNK4
C17orf53
TMUB2
DHX58
MMP28
DHRS11
PRR15L
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
FAM117A
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
RNF135
MIEN1
MRPL45
VPS25
TMEM101
PRAC
RAB11FIP4
GHDC
PPP1R9B
CORO6
TNS4
FBXL20
SSH2
TP53I13
LRRC46
SCRN2
ANKRD40
ZNF830
SLFN11
RASL10B
G6PC3
ASB16
PGAP3
HSPB9
ORMDL3
PLCD3
TMEM106A
LRRC37B
OSBPL7
NT5C3B
ABHD15
RFFL
ZPBP2
SPATA32
HEXIM2
LSM12
CCDC43
TMEM132E
WFIKKN2
B4GALNT2
SPACA3
ANKRD13B
EFCAB13
MRPL10
KRT40
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
WIPF2
KRT25
TMEM99
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
SPPL2C
KRT28
KRT24
ARHGAP27
SAMD14
RDM1
GAS2L2
STH
TAC4
C17orf66
KANSL1
FAM171A2
C17orf104
TTLL6
PIGW
C17orf78
GSDMA
PTRF
KLHL10
MSL1
KRT27
SLFN14
LRRC37A11P
STAC2
KRT26
EFCAB5
TMIGD1
C17orf98
LINC00671
RPRML
KRT39
MYO18A
C17orf102
MIR10A
MIR193A
MIR196A1
TBC1D3B
TBC1D3C
CCL3L3
GPR179
LRRC37A2
FBXO47
TBC1D3G
NME2
MIR632
TBC1D3
TBC1D3H
MIR365B
C17orf96
MIR2117
MIR3185
LRRC3C
ARL17B
C17orf112
MIR4523
MIR4734
MIR4724
MIR4733
MIR4727
MIR4725
MIR5089
PTGES3L

Arm-level results

Table 3. Get Full Table Arm-level significance table - 24 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 | -1.5 | 0.983 | 0.25 | 6.85 | 2.99e-11
1q | 1195 | 0.10 | 1.49 | 0.147 | 0.04 | -0.736 | 0.984
2p | 624 | 0.12 | 2.77 | 0.0127 | 0.00 | -2.01 | 0.984
2q | 967 | 0.10 | 1.53 | 0.143 | 0.00 | -2.13 | 0.984
3p | 644 | 0.00 | -1.47 | 0.983 | 0.54 | 19 | 0
3q | 733 | 0.00 | -1.48 | 0.983 | 0.54 | 18.7 | 0
4p | 289 | 0.09 | 1.62 | 0.127 | 0.03 | -0.88 | 0.984
4q | 670 | 0.04 | -0.601 | 0.983 | 0.05 | -0.126 | 0.984
5p | 183 | 0.04 | -0.428 | 0.983 | 0.01 | -1.45 | 0.984
5q | 905 | 0.04 | -0.733 | 0.983 | 0.04 | -0.733 | 0.984
6p | 710 | 0.47 | 16.1 | 0 | 0.05 | -0.265 | 0.984
6q | 556 | 0.19 | 4.6 | 1.73e-05 | 0.32 | 9.78 | 0
7p | 389 | 0.11 | 2.49 | 0.0241 | 0.00 | -1.96 | 0.984
7q | 783 | 0.10 | 1.67 | 0.122 | 0.00 | -2.08 | 0.984
8p | 338 | 0.39 | 12.2 | 0 | 0.34 | 9.87 | 0
8q | 551 | 0.68 | 24.4 | 0 | 0.14 | 2.1 | 0.0733
9p | 301 | 0.07 | 0.758 | 0.438 | 0.11 | 2.25 | 0.0553
9q | 700 | 0.05 | -0.0323 | 0.899 | 0.09 | 1.39 | 0.309
10p | 253 | 0.00 | -2.02 | 0.985 | 0.01 | -1.52 | 0.984
10q | 738 | 0.00 | -2.17 | 0.985 | 0.01 | -1.7 | 0.984
11p | 509 | 0.13 | 2.97 | 0.00876 | 0.03 | -0.911 | 0.984
11q | 975 | 0.13 | 2.52 | 0.0241 | 0.01 | -1.6 | 0.984
12p | 339 | 0.04 | -0.463 | 0.983 | 0.04 | -0.463 | 0.984
12q | 904 | 0.04 | -0.756 | 0.983 | 0.03 | -1.22 | 0.984
13q | 560 | 0.08 | 0.944 | 0.354 | 0.04 | -0.501 | 0.984
14q | 938 | 0.04 | -0.795 | 0.983 | 0.01 | -1.71 | 0.984
15q | 810 | 0.03 | -1.16 | 0.983 | 0.05 | -0.226 | 0.984
16p | 559 | 0.05 | -0.0664 | 0.899 | 0.04 | -0.549 | 0.984
16q | 455 | 0.02 | -1.31 | 0.983 | 0.20 | 6.01 | 6.35e-09
17p | 415 | 0.10 | 2.03 | 0.0573 | 0.03 | -0.914 | 0.984
17q | 972 | 0.11 | 2.04 | 0.0573 | 0.01 | -1.62 | 0.984
18p | 104 | 0.01 | -1.45 | 0.983 | 0.01 | -1.45 | 0.984
18q | 275 | 0.01 | -1.51 | 0.983 | 0.01 | -1.51 | 0.984
19p | 681 | 0.03 | -1.13 | 0.983 | 0.04 | -0.654 | 0.984
19q | 935 | 0.03 | -1.23 | 0.983 | 0.04 | -0.77 | 0.984
20p | 234 | 0.10 | 2.15 | 0.0497 | 0.01 | -1.38 | 0.984
20q | 448 | 0.11 | 2.43 | 0.0256 | 0.00 | -1.97 | 0.984
21q | 258 | 0.18 | 5.3 | 5.78e-07 | 0.03 | -0.715 | 0.984
22q | 564 | 0.06 | 0.377 | 0.658 | 0.01 | -1.55 | 0.984
Xp | 418 | 0.15 | 3.56 | 0.00129 | 0.17 | 4.53 | 1.52e-05
Xq | 668 | 0.13 | 2.84 | 0.0117 | 0.18 | 4.72 | 6.95e-06

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/GDAC_MergeDataFilesPipeline/UVM-TP/22223186/GDAC_MergeDataFiles_12187690/UVM-TP.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_GENCODE_v18_20140127.mat

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 80 Input Tumor Samples.

Tumor Sample Names
TCGA-RZ-AB0B-01A-11D-A39V-01
TCGA-V3-A9ZX-01A-11D-A39V-01
TCGA-V3-A9ZY-01A-11D-A39V-01
TCGA-V4-A9E5-01A-11D-A39V-01
TCGA-V4-A9E7-01A-11D-A39V-01
TCGA-V4-A9E8-01A-11D-A39V-01
TCGA-V4-A9E9-01A-11D-A39V-01
TCGA-V4-A9EA-01A-11D-A39V-01
TCGA-V4-A9EC-01A-11D-A39V-01
TCGA-V4-A9ED-01A-11D-A39V-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

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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