Kidney Renal Papillary Cell Carcinoma: 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 43 tumor samples used in this analysis: 15 significant arm-level results, 0 significant focal amplifications, and 9 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 - 9 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
--- | --- | --- | --- | ---
9p21.3 | 0.075334 | 0.075334 | chr9:21545227-22438737 | 5
1p36.33 | 0.12387 | 0.12387 | chr1:1-28297496 | 430
2q37.1 | 0.12387 | 0.12387 | chr2:217430650-242951149 | 232
1p31.1 | 0.12387 | 0.12662 | chr1:70675808-71304028 | 1
9q21.13 | 0.13175 | 0.13175 | chr9:76751178-77699761 | 4
13q21.31 | 0.13175 | 0.13175 | chr13:1-69613124 | 232
18q23 | 0.1382 | 0.1337 | chr18:72302240-72667805 | 1
5q35.2 | 0.19928 | 0.20652 | chr5:172937971-177517373 | 57
16q23.1 | 0.20652 | 0.20652 | chr16:75872277-88827254 | 111

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.3.

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

Genes
CDKN2A
CDKN2B
MTAP
C9orf53
CDKN2BAS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.33.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC2L1
CDC42
CD52
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
CROCC
KIAA0562
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
NUDC
MASP2
SFRS13A
UTS2
RER1
RCAN3
MSTP2
MSTP9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KIAA1026
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
AHDC1
SMPDL3B
HSPC157
SSU72
UBIAD1
PADI1
PLA2G2E
WDR8
SLC45A1
HP1BP3
CELA2B
ZNF593
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
C1orf128
MAN1C1
NIPAL3
SEPN1
KIAA0495
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CCDC21
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
C1orf135
EFHD2
MMEL1
C1orf89
OR4F5
MUL1
NOL9
LIN28
AGMAT
NCRNA00115
MORN1
GRRP1
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCL1
SYTL1
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
CROCCL2
FHAD1
LOC115110
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
C1orf93
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
C1orf70
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
LOC441869
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH5P
PRAMEF16
FAM138C
SCARNA1
SNORA59B
SNORA59A
MIR551A
CDC2L2
LOC728661
PRAMEF14
FLJ37453
OR4F29
LOC100128003
LOC100128842
LOC100129534
FLJ39609
LOC100132062
LOC100132287
LOC100133331
LOC100133612
LOC100288778

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.1.

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

Genes
ACSL3
PAX3
FEV
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
hsa-mir-153-1
hsa-mir-375
hsa-mir-26b
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IHH
IL8RA
IL8RB
IL8RBP
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
C2orf24
STK36
GMPPA
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
C2orf83
MFF
CXCR7
RNPEPL1
WDFY1
KIAA1486
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
TIGD1
CCDC108
C2orf72
C2orf85
RUFY4
DUSP28
ESPNL
ECEL1P2
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
PP14571

Genes in Wide Peak

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

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

Genes
PTGER3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.13.

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

Genes
OSTF1
C9orf95
C9orf40
C9orf41

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.31.

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
hsa-mir-1297
hsa-mir-15a
hsa-mir-621
hsa-mir-320d-1
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
OR7E37P
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
C13orf1
COG6
KLHL1
XPO4
PCDH20
MRP63
NARG1L
RNASEH2B
DHRS12
C13orf18
C13orf23
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LOC121838
CSNK1A1L
RXFP2
C13orf26
PRR20A
C13orf30
C13orf31
HNRNPA1L2
FAM10A4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
LOC220115
LOC220429
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
DKFZp686A1627
OR7E156P
SUGT1L1
SIAH3
KCNRG
FLJ37307
SLC46A3
LOC284232
C1QTNF9
FREM2
NEK5
LOC348021
LOC374491
THSD1P
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
C13orf36
MIR15A
MIR16-1
ATP5EP2
ALG11
PCOTH
SNORA27
LOC646405
PRHOXNB
ZAR1L
LOC646982
SERPINE3
SNORA31
MIR621
C13orf38
PRR20B
PRR20C
PRR20D
PRR20E
LOC100101938
RPL21P28
LOC100188949
LOC100190939
LOC100288730

Genes in Wide Peak

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

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

Genes
LOC284276

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

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

Genes
NSD1
hsa-mir-1271
CLTB
DBN1
DRD1
F12
FGFR4
GRK6
HK3
HRH2
MSX2
PROP1
SLC34A1
SNCB
PDLIM7
RGS14
CPLX2
LMAN2
B4GALT7
RNF44
N4BP3
FAF2
ZNF346
TSPAN17
PRELID1
DDX41
NOP16
HMP19
UIMC1
RAB24
FAM193B
TMED9
PCDH24
NHP2
KIAA1191
RMND5B
DOK3
CPEB4
PRR7
MXD3
THOC3
UNC5A
BOD1
SFXN1
GPRIN1
C5orf47
HIGD2A
FAM153B
LOC202181
EIF4E1B
LOC285593
FAM153A
ARL10
PFN3
C5orf25
FAM153C
LOC728554

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
AFG3L1
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
C16orf7
KIAA0513
FAM38A
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
PRDM7
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
LRRC50
SPATA2L
C16orf55
ZC3H18
CDYL2
SLC38A8
FLJ30679
ZFPM1
ADAD2
ADAMTS18
MGC23284
ZNF778
ACSF3
C16orf81
NUDT7
SNAI3
FAM92B
CTU2
LOC390748
C16orf74
SNORD68
LOC732275
LOC100129637
LOC100130015

Arm-level results

Table 2. Get Full Table Arm-level significance table - 15 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.03 | -0.916 | 0.985 | 0.07 | 0.337 | 0.975
1q | 1572 | 0.10 | 0.788 | 0.56 | 0.03 | -1 | 0.975
2p | 753 | 0.12 | 0.498 | 0.754 | 0.03 | -1.46 | 0.975
2q | 1235 | 0.14 | 1.5 | 0.185 | 0.00 | -1.77 | 0.975
3p | 853 | 0.30 | 4.53 | 1.46e-05 | 0.10 | 0.0809 | 0.975
3q | 917 | 0.29 | 4.53 | 1.46e-05 | 0.06 | -0.498 | 0.975
4p | 366 | 0.03 | -1.7 | 0.985 | 0.10 | -0.327 | 0.975
4q | 865 | 0.03 | -1.47 | 0.985 | 0.07 | -0.463 | 0.975
5p | 207 | 0.12 | 0.0383 | 0.985 | 0.03 | -1.74 | 0.975
5q | 1246 | 0.17 | 2.16 | 0.0465 | 0.03 | -1.12 | 0.975
6p | 937 | 0.08 | -0.272 | 0.985 | 0.10 | 0.236 | 0.975
6q | 692 | 0.08 | -0.408 | 0.985 | 0.12 | 0.558 | 0.975
7p | 508 | 0.47 | 7.67 | 8.66e-14 | 0.00 | -1.65 | 0.975
7q | 1071 | 0.48 | 9.14 | 0 | 0.04 | -0.704 | 0.975
8p | 495 | 0.05 | -1.15 | 0.985 | 0.07 | -0.686 | 0.975
8q | 697 | 0.07 | -0.544 | 0.985 | 0.05 | -1.03 | 0.975
9p | 343 | 0.00 | -2.16 | 0.985 | 0.14 | 0.573 | 0.975
9q | 916 | 0.00 | -1.94 | 0.985 | 0.12 | 0.598 | 0.975
10p | 312 | 0.07 | -0.808 | 0.985 | 0.05 | -1.26 | 0.975
10q | 1050 | 0.05 | -0.795 | 0.985 | 0.07 | -0.273 | 0.975
11p | 731 | 0.03 | -1.51 | 0.985 | 0.10 | -0.0431 | 0.975
11q | 1279 | 0.03 | -1.19 | 0.985 | 0.10 | 0.461 | 0.975
12p | 484 | 0.26 | 3.17 | 0.0027 | 0.00 | -1.95 | 0.975
12q | 1162 | 0.26 | 4.21 | 5.51e-05 | 0.00 | -1.68 | 0.975
13q | 554 | 0.12 | 0.436 | 0.76 | 0.08 | -0.505 | 0.975
14q | 1144 | 0.00 | -1.74 | 0.985 | 0.21 | 3.06 | 0.0427
15q | 1132 | 0.00 | -1.87 | 0.985 | 0.09 | 0.265 | 0.975
16p | 719 | 0.40 | 6.7 | 7.89e-11 | 0.04 | -1.02 | 0.975
16q | 562 | 0.33 | 4.88 | 3.38e-06 | 0.03 | -1.22 | 0.975
17p | 575 | 0.55 | 9.47 | 0 | 0.05 | -0.781 | 0.975
17q | 1321 | 0.60 | 12.8 | 0 | 0.06 | -0.31 | 0.975
18p | 117 | 0.13 | 0.208 | 0.904 | 0.13 | 0.208 | 0.975
18q | 340 | 0.08 | -0.648 | 0.985 | 0.12 | 0.259 | 0.975
19p | 870 | 0.00 | -2.06 | 0.985 | 0.02 | -1.56 | 0.975
19q | 1452 | 0.00 | -1.77 | 0.985 | 0.02 | -1.2 | 0.975
20p | 295 | 0.26 | 3.02 | 0.00407 | 0.03 | -1.47 | 0.975
20q | 627 | 0.29 | 4.07 | 9.3e-05 | 0.06 | -0.677 | 0.975
21q | 422 | 0.03 | -1.6 | 0.985 | 0.14 | 0.705 | 0.975
22q | 764 | 0.00 | -1.95 | 0.985 | 0.16 | 1.49 | 0.975

Methods & Data
Input

Table 3. Get Full Table First 10 out of 43 Input Tumor Samples.

Tumor Sample Names
TCGA-AL-3466-01A-01D-1190-01
TCGA-AL-3467-01A-01D-1190-01
TCGA-AL-3468-01A-02D-1348-01
TCGA-AL-3471-01A-02D-1348-01
TCGA-AL-3472-01A-01D-1190-01
TCGA-AL-3473-01A-01D-1190-01
TCGA-B1-5398-01A-02D-1588-01
TCGA-B3-3925-01A-02D-1348-01
TCGA-B3-3926-01A-02D-1348-01
TCGA-B3-4103-01A-02D-1348-01

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.

- 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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- Maintainer = Dan DiCara

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