Thyroid 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 2.0.15 (cga svn revision 34144).

Summary

There were 85 tumor samples used in this analysis: 10 significant arm-level results, 2 significant focal amplifications, and 6 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 - 2 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
13q14.11 0.0091372 0.0091372 chr13:42429589-42688912 3
11p15.4 0.15982 0.15982 chr11:3376079-3481387 1
Genes in Wide Peak

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

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

Genes
DNAJC15
ENOX1
EPSTI1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p15.4.

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

Genes
LOC650368

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 - 6 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
7q22.3 0.21628 0.21628 chr7:106587765-116611362 40
10q23.1 0.21628 0.21628 chr10:82289828-94825202 74
10q21.2 0.21628 0.21628 chr10:42596299-93781320 304
13q12.12 0.21628 0.21628 chr13:23794594-24082673 2
19p13.3 0.21628 0.21628 chr19:5774904-5865624 5
9q33.1 0.22496 0.22496 chr9:1-140273252 890
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.3.

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

Genes
MET
CAPZA2
CAV1
CAV2
DLD
SLC26A3
GPR22
IFRD1
LAMB1
DNAJB9
NRCAM
SLC26A4
PPP1R3A
DOCK4
COG5
DUS4L
ZNF277
TFEC
LAMB4
TES
HBP1
MDFIC
PNPLA8
GPR85
LRRN3
BCAP29
TMEM168
CBLL1
IMMP2L
ST7OT1
ST7OT2
FOXP2
C7orf60
C7orf66
THAP5
LOC286002
C7orf53
ST7OT4
LOC401397
EIF3IP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.1.

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

Genes
BMPR1A
PTEN
hsa-mir-107
hsa-mir-346
ACTA2
FAS
GLUD1
GRID1
HHEX
HTR7
IDE
IFIT2
IFIT1
IFIT3
KIF11
LIPA
PPP1R3C
RGR
SNCG
LIPF
CH25H
BTAF1
PAPSS2
MINPP1
KIF20B
RPP30
NRG3
C10orf116
LDB3
CPEB3
WAPAL
IFIT5
LRIT1
ANKRD1
GHITM
PANK1
FAM190B
EXOC6
FAM35A
MARCH5
RNLS
STAMBPL1
MMRN2
TNKS2
PCGF5
ATAD1
PCDH21
OPN4
ANKRD22
NUDT9P1
AGAP11
LIPJ
CFLP1
HECTD2
FGFBP3
FLJ37201
LIPM
CYP26C1
LRIT2
SH2D4B
C10orf99
SLC16A12
MIR107
LOC439994
IFIT1L
MIR346
FAM25A
LIPK
LIPN
FAM22A
FAM22D
LOC728190
KILLIN
LOC100188947
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.2.

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

Genes
BMPR1A
PRF1
PTEN
RET
NCOA4
MYST4
hsa-mir-107
hsa-mir-346
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
ACTA2
ADK
ALOX5
ANXA8L2
ANK3
ANXA2P3
ANXA7
ANXA11
FAS
CAMK2G
CDC2
CHAT
COL13A1
DNA2
EGR2
EIF4EBP2
ERCC6
GDF2
GDF10
GLUD1
GRID1
HK1
HNRNPF
HNRNPH3
HTR7
IFIT2
IFIT1
IFIT3
KCNMA1
LIPA
MAT1A
MBL2
MSMB
NODAL
P4HA1
PCBD1
PLAU
PPA1
PPP1R3C
PPP3CB
PPYR1
SRGN
PRKG1
MAPK8
PSAP
RBP3
RGR
RPS24
CXCL12
SFTPD
SLC18A3
SNCG
SUPV3L1
TACR2
TFAM
UBE2D1
VCL
VDAC2
ZNF22
ZNF32
CCDC6
SLC25A16
ZNF239
PARG
NDST2
MBL1P1
LIPF
SGPL1
CH25H
BTAF1
PAPSS2
DDX21
DLG5
CHST3
VPS26A
MINPP1
KIF20B
SEC24C
GPRIN2
BMS1
SPOCK2
RHOBTB1
PPIF
HNRNPA3P1
CBARA1
TIMM23
RPP30
NRG3
C10orf116
C10orf10
POLR3A
ZWINT
LDB3
ECD
ZNF365
DKK1
KIAA0913
WAPAL
DNAJC9
CSTF2T
SIRT1
TSPAN15
IFIT5
NUDT13
HERC4
PTPN20B
LRIT1
KIAA1279
AP3M1
ANKRD1
GHITM
KIAA1274
CTNNA3
A1CF
NRBF2
NEUROG3
ASCC1
MRPS16
DUSP13
PANK1
FXYD4
FAM190B
FAM35A
DDIT4
DNAJB12
LRRC20
SLC29A3
RNLS
CSGALNACT2
H2AFY2
RUFY2
FAM21B
CCAR1
OGDHL
CISD1
DNAJC12
ASAH2
SAR1A
ZMIZ1
STAMBPL1
WDFY4
ARHGAP22
MYOZ1
CDH23
PBLD
NPFFR1
C10orf54
PCDH15
DDX50
OR13A1
MMRN2
SYNPO2L
BICC1
C10orf57
HKDC1
TET1
TNKS2
TSPAN14
SYT15
RASSF4
C10orf11
ARID5B
C10orf58
DYDC2
PCGF5
PHYHIPL
PLA2G12B
MYPN
ZNF503
AIFM2
ADO
ATAD1
LOC84989
CCDC109A
PCDH21
ANUBL1
OPN4
C10orf71
CHCHD1
ZMYND17
TTC18
ZNF488
COMTD1
ANKRD22
AGAP4
NUDT9P1
AGAP11
C10orf104
ADAMTS14
SAMD8
LIPJ
CFLP1
FRMPD2
DYDC1
EIF5AL1
HECTD2
FGFBP3
USP54
FAM170B
C10orf128
FUT11
OIT3
ANTXRL
C10orf72
LOC219347
PLAC9
C10orf107
TMEM26
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
C10orf27
ATOH7
SLC16A9
FAM13C
MARCH8
C10orf25
ZNF485
RASGEF1A
REEP3
JMJD1C
IPMK
FAM21C
SGMS1
PGBD3
C10orf53
FLJ37201
C10orf40
LOC283050
FAM149B1
DUPD1
LIPM
LRIT2
LRRTM3
FAM21A
SH2D4B
C10orf99
SLC16A12
LOC399753
BMS1P5
MIR107
C10orf105
AGAP6
C10orf55
FAM35B
FAM35B2
LOC439994
IFIT1L
MIR346
LRRC18
LOC642361
ZNF487
LOC642826
FAM25A
TMEM72
LIPK
LIPN
FAM25C
DRGX
LOC650623
PTPN20A
ANXA8
AGAP7
ASAH2B
SFTPA1
SNORD98
MIR605
BMS1P1
ANXA8L1
FAM22A
FAM22D
LOC728190
AGAP8
LOC728407
FRMPD2L2
LOC728640
LOC728643
FRMPD2L1
AGAP5
BMS1P4
SFTPA2
LOC100128292
C10orf41
FAM25B
FAM25G
LOC100133308
KILLIN
LOC100188947
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.12.

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

Genes
PARP4
LOC374491
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.3.

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

Genes
FUT3
FUT5
FUT6
NDUFA11
VMAC
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q33.1.

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

Genes
ABL1
FANCC
FANCG
GNAQ
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
hsa-mir-602
hsa-mir-126
hsa-mir-219-2
hsa-mir-199b
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-let-7d
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
hsa-mir-873
hsa-mir-31
hsa-mir-491
hsa-mir-101-2
hsa-mir-1302-2
ABCA1
ABCA2
ABO
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
ANXA2P2
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
TNFSF8
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CELP
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
MLANA
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
GGTA1
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
IL11RA
INSL4
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RMRP
RORB
RPL7A
RPL12
RPS6
RXRA
CCL19
CCL21
SH3GL2
SHB
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
UGCG
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
RGP1
TRIM14
MELK
RUSC2
KIAA0649
SEC16A
ZBTB5
KIAA0020
TNFSF15
ROD1
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB2C
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CEP110
WDR5
C9orf9
ADAMTS13
C9orf7
PSIP1
INSL6
SLC2A6
PTENP1
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA1045
KIAA0368
EXOSC2
FREQ
TDRD7
SLC44A1
ANGPTL2
NUP188
CCRK
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
LOC26102
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
PCA3
AK3
EXOSC3
FAM108B1
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
C9orf11
TBC1D13
FAM22F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
C9orf167
CNTLN
TEX10
LPPR1
KIAA1797
UBE2R2
EXD3
C9orf6
C9orf95
STX17
NOL8
C9orf68
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDC37L1
DENND4C
C9orf86
CDK5RAP2
UBAP2
C9orf46
CBWD1
KLHL9
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KIAA1161
KCNT1
KIAA1432
KIAA1529
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
C9orf27
C9orf80
ZNF462
DMRT3
PRDM12
MAK10
DMRTA1
SLC28A3
CARD9
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
MRPL41
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOBKL2B
C9orf82
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
KIAA1539
GKAP1
PDCD1LG2
AKNA
C9orf45
URM1
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
BAT2L
PPAPDC3
C9orf70
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
TPD52L3
WDR34
C9orf140
C9orf69
LRSAM1
IL33
C9orf123
C9orf30
UAP1L1
MCART1
MRRF
RBM18
ARRDC1
WDR85
ADAMTSL1
LOC92973
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf66
NCRNA00032
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
C9orf98
OR1Q1
TTLL11
RASEF
TTC39B
C9orf122
RG9MTD3
TTC16
FAM120AOS
FAM154A
C9orf44
FREM1
KIAA2026
LOC158376
LOC158381
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
PRUNE2
C9orf96
KCNV2
OLFML2A
C9orf71
QSOX2
GLIS3
LOC169834
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
C9orf93
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
C9orf144B
NCRNA00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
C9orf75
TUSC1
C9orf109
FAM78A
C9orf150
LOC286359
OR13C9
OR13D1
LOC286367
FOXD4L3
IFNE
ZDHHC21
ACER2
LOC340508
GPR144
FLJ43950
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
GLT6D1
ENHO
AQP7P1
PTAR1
C9orf102
C9orf119
C9orf50
PNPLA7
C9orf169
ENTPD8
ZNF322B
KGFLP1
LOC389705
C9orf144
FAM75A6
MGC21881
AQP7P2
FLJ43859
FLJ44082
FLJ46321
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
C9orf128
OR13J1
CTSL3
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FLJ35024
PTPLAD2
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
LOC402377
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR101-2
MIR126
MIR147
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR31
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC415056
LOC440173
LOC440839
LOC440896
SUGT1P
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
FAM27A
DNAJC25
DNAJC25-GNG10
LOC554202
LOC572558
MIR491
PGM5P2
MIR455
FAM138F
FAM75A2
LOC642313
LOC642929
FAM163B
FLJ40292
TUBBP5
CBWD6
FAM138A
LOC645961
HRCT1
FAM75A1
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM138C
SCARNA8
SNORA17
SNORA43
SNORD62B
MSMP
SNORD90
MIR548D1
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
ANKRD20A4
CCDC29
FAM166B
FOXD4L2
CDKN2BAS
SNORD121A
SNORD121B
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
C9orf110
C9orf130
LOC100129034
LOC100129066
LOC100130426
LOC100131193
FAM157B
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
NCRNA00092
LOC100272217
WASH1
LOC100289341
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 10 significant results found.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 1731 0.01 -0.408 0.879 0.01 -0.408 0.884
1q 1572 0.04 1.3 0.38 0.01 -0.354 0.884
2p 753 0.00 -1.11 0.879 0.02 0.675 0.884
2q 1235 0.00 -1.17 0.879 0.02 0.533 0.884
3p 853 0.00 -1.13 0.879 0.01 -0.247 0.884
3q 917 0.00 -1.13 0.879 0.02 0.625 0.884
4p 366 0.02 0.82 0.711 0.01 -0.114 0.884
4q 865 0.02 0.658 0.711 0.01 -0.225 0.884
5p 207 0.05 2.77 0.0843 0.00 -1.03 0.884
5q 1246 0.05 2.24 0.0981 0.00 -1.16 0.884
6p 937 0.01 -0.253 0.879 0.01 -0.253 0.884
6q 692 0.00 -1.11 0.879 0.02 0.695 0.884
7p 508 0.04 1.68 0.227 0.00 -1.08 0.884
7q 1071 0.05 2.32 0.0981 0.00 -1.14 0.884
8p 495 0.00 -1.09 0.879 0.01 -0.168 0.884
8q 697 0.00 -1.11 0.879 0.01 -0.213 0.884
9p 343 0.01 -0.109 0.879 0.02 0.828 0.884
9q 916 0.01 -0.224 0.879 0.04 1.53 0.791
10p 312 0.01 -0.113 0.879 0.01 -0.113 0.884
10q 1050 0.01 -0.264 0.879 0.02 0.603 0.884
11p 731 0.01 -0.197 0.879 0.02 0.7 0.884
11q 1279 0.01 -0.298 0.879 0.04 1.4 0.791
12p 484 0.04 1.69 0.227 0.00 -1.07 0.884
12q 1162 0.04 1.42 0.338 0.00 -1.15 0.884
13q 554 0.01 -0.133 0.879 0.05 2.61 0.0887
14q 1144 0.01 -0.307 0.879 0.00 -1.17 0.884
15q 1132 0.00 -1.17 0.879 0.01 -0.305 0.884
16p 719 0.02 0.686 0.711 0.00 -1.11 0.884
16q 562 0.01 -0.183 0.879 0.00 -1.1 0.884
17p 575 0.05 2.63 0.0843 0.02 0.803 0.884
17q 1321 0.05 2.24 0.0981 0.01 -0.293 0.884
18p 117 0.00 -1.04 0.879 0.01 -0.0777 0.884
18q 340 0.00 -1.07 0.879 0.01 -0.132 0.884
19p 870 0.01 -0.251 0.879 0.00 -1.13 0.884
19q 1452 0.02 0.473 0.827 0.00 -1.19 0.884
20p 295 0.04 1.77 0.227 0.00 -1.05 0.884
20q 627 0.02 0.715 0.711 0.00 -1.1 0.884
21q 422 0.00 -1.08 0.879 0.01 -0.151 0.884
22q 764 0.00 -1.05 0.879 0.14 9.67 0
Methods & Data
Input

Table 4.  Get Full Table First 10 out of 85 Input Tumor Samples.

Tumor Sample Names
TCGA-BJ-A0YZ-01A-11D-A10T-01
TCGA-BJ-A0Z0-01A-11D-A10T-01
TCGA-BJ-A0Z2-01A-11D-A10T-01
TCGA-BJ-A0Z3-01A-11D-A13V-01
TCGA-BJ-A0Z5-01A-11D-A10T-01
TCGA-BJ-A0Z9-01A-11D-A10T-01
TCGA-BJ-A0ZA-01A-11D-A10T-01
TCGA-BJ-A0ZB-01A-11D-A10T-01
TCGA-BJ-A0ZC-01A-12D-A13V-01
TCGA-BJ-A0ZE-01A-11D-A10T-01

Figure 3.  Segmented copy number profiles in the input data

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.

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