LowPass Copy number analysis (GISTIC2)
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by Spring Yingchun Liu (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): LowPass Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1KK9B33
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 2.0.21 (Firehose task version: 127).

Summary

There were 50 tumor samples used in this analysis: 18 significant arm-level results, 4 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.

Table 1.  Get Full Table Amplifications Table - 4 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
11q22.1 0.00050687 0.00050687 chr11:101299139-102362044 11
8q24.21 0.0040232 0.044734 chr8:128860926-129059003 3
19q13.31 0.058226 0.058226 chr19:43208675-45519241 73
8q24.21 0.0079597 0.11538 chr8:128639628-128894353 2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.1.

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

Genes
BIRC3
snoU13|ENSG00000239154.1
snoU13|ENSG00000252679.1
MIR3920
BIRC2
TRPC6
YAP1
KIAA1377
C11orf70
TMEM123
ANGPTL5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
TMEM75
MIR1205
PVT1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.31.

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

Genes
BCL3
CBLC
APOC1P1
SNORA70|ENSG00000253027.1
snoZ6|ENSG00000252200.1
CEACAM22P
CEACAM20
ZNF180
ZNF234
RN7SL53P
ZNF284
ZNF223
RN7SL368P
ZNF576
ZNF575
CEACAMP10
PSG7
PSG10P
APOC1
APOC2
APOC4
APOE
CLPTM1
KCNN4
BCAM
PLAUR
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG9
PSG11
PVR
PVRL2
RELB
XRCC1
ZNF45
ZNF221
ZNF222
ZNF155
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
ZNF235
TOMM40
ETHE1
ZNF285
LYPD3
SMG9
IRGC
CEACAM19
CD177
TEX101
IRGQ
ZNF428
IGSF23
CADM4
LYPD5
ZNF283
ZNF404
ZNF233
CEACAM16
PINLYP
PSG8
PHLDB3
SRRM5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
MYC
PVT1

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 - 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
2q36.2 0.0012842 0.0012842 chr2:202020655-243199373 369
11q24.1 0.0012842 0.0012842 chr11:103987375-135006516 301
13q13.2 0.0012842 0.0012842 chr13:28869370-59699592 221
2q22.1 0.0012842 0.002379 chr2:141742653-141854673 1
4q35.2 0.012584 0.012584 chr4:174935592-191154276 84
14q32.32 0.043188 0.043188 chr14:75600050-107349540 335
19p13.3 0.073418 0.073418 chr19:1-9508245 293
6p12.1 0.097895 0.097895 chr6:41754827-62388977 156
1p36.23 0.23409 0.23409 chr1:1-31732721 509
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q36.2.

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

Genes
ACSL3
ATIC
CREB1
IDH1
PAX3
FEV
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
RN7SL807P
snoU13|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
snoU13|ENSG00000238736.1
snoU13|ENSG00000238428.1
CXCR2P1
DIRC3
RN7SKP43
RNA5SP120
RPL37A
MREG
LINC00607
snoU13|ENSG00000238663.1
SNORA70|ENSG00000207274.1
VWC2L
MIR4438
MIR548F2
RNA5SP119
RPE
RNA5SP118
RNA5SP117
CRYGEP
snoU13|ENSG00000238582.1
RNA5SP116
MIR2355
FASTKD2
RN7SKP260
RN7SKP200
SNORA41|ENSG00000207406.1
SNORD51|ENSG00000207047.2
NDUFS1
Vault|ENSG00000252485.1
RN7SKP178
RN7SL670P
SNORA1|ENSG00000202059.1
WDR12
RN7SL40P
RN7SL753P
SNORD11|ENSG00000238317.1
SNORD11B
SNORD70|ENSG00000212309.1
SNORD70|ENSG00000212534.1
snoU13|ENSG00000238770.1
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BMPR2
BOK
CASP8
CASP10
CD28
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CYP27A1
DES
DTYMK
EEF1B2
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
SUMO1
WNT6
XRCC5
ZNF142
FZD5
SCG2
FZD7
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
CFLAR
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
ABI2
RAMP1
SPEG
LANCL1
NMUR1
STK25
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
ICOS
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
NOP58
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
STRADB
HES6
ASIC4
DOCK10
PECR
C2orf83
MFF
ACKR3
CYP20A1
MARCH4
WDFY1
NYAP2
ALS2
ZDBF2
USP37
CTDSP1
MPP4
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
RAPH1
CDK15
TMEM237
NBEAL1
MRPL44
TRAK2
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
CARF
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
PARD3B
DIS3L2
NEU4
ICA1L
AP1S3
ALS2CR12
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
FAM117B
KANSL1L
METTL21A
CCNYL1
ALS2CR11
CCDC140
SLC23A3
GPBAR1
SLC16A14
LINC00471
DAW1
C2orf57
PIKFYVE
TIGD1
CCDC108
C2orf72
UNC80
RUFY4
DUSP28
MROH2A
ESPNL
C2orf62
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
ASB18
MIR375
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4268
MIR3132
MIR4269
MIR4775
MIR4786
MIR5001
MIR5702
MIR5703
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.1.

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
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
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
RNA5SP348
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
BARX2
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
SPATA19
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR4301
CASP12
MIR4697
MIR4493
MIR4491
MIR4492
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.2.

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

Genes
BRCA2
LCP1
RB1
LHFP
RNY4P29
RNA5SP30
RN7SKP6
snoU13|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31|ENSG00000199477.1
SNORA31|ENSG00000253051.1
7SK|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116|ENSG00000212553.1
RNY4P14
snoU13|ENSG00000238408.1
LINC00366
LINC00571
RNA5SP26
RN7SKP1
ARL2BPP3
DCLK1
LINC00445
LINC00457
SNORA25|ENSG00000199196.1
LINC00423
RNY1P4
SNORA16|ENSG00000212293.1
ZAR1L
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
LINC00365
LINC00544
LINC00572
LINC00297
MTUS2
ALOX5AP
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
FLT1
MLNR
GTF2F2
GUCY1B2
HMGB1
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
UBL3
RFC3
RFXAP
SLC7A1
TPT1
TRPC4
TNFSF11
SUCLA2
CCNA1
KL
ITM2B
MTRF1
UTP14C
FRY
LPAR6
TRIM13
USPL1
MRPS31
DLEU1
N4BP2L2
OLFM4
POSTN
HSPH1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
VWA8
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
RGCC
MED4
DNAJC15
ALG5
VPS36
PHF11
POMP
UFM1
ENOX1
RCBTB1
NUDT15
KIAA1704
SUPT20H
THSD1
CYSLTR2
SPRYD7
COG6
SMIM2
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
CDADC1
CAB39L
CCDC70
COG3
SETDB2
KATNAL1
EBPL
MEDAG
KBTBD6
STARD13
N4BP2L1
EPSTI1
ARL11
WDFY2
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
HNRNPA1L2
B3GALTL
DGKH
CCDC122
STOML3
FAM194B
SPERT
FAM124A
LRRC63
SLC25A30
PAN3
SIAH3
KCNRG
SLC46A3
FREM2
NEK5
KCTD4
NHLRC3
SERP2
SERTM1
DLEU2
ALG11
SERPINE3
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
MIR759
MIR320D1
MIR3168
MIR4305
MIR3613
SPG20OS
SOHLH2
MIR4703
MIR5007
MIR5693
Genes in Wide Peak

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

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

Genes
LRP1B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HPGD
ING2
IRF2
KLKB1
MTNR1A
VEGFC
GLRA3
SORBS2
ADAM29
FAM149A
FBXO8
CLDN22
NEIL3
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
WWC2
CEP44
SNX25
WDR17
ZFP42
SPATA4
ENPP6
ASB5
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR4276
MIR3945
MIR4455
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.32.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DYNC1H1
EIF5
EML1
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
GPR68
DLK1
ALKBH1
MTA1
RPS6KA5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
TECPR2
FBLN5
BATF
SIVA1
AHSA1
CYP46A1
PAPOLA
TMED10
PTPN21
VASH1
SNW1
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
FLRT2
KIF26A
TMEM251
GPR132
POMT2
SERPINA10
EVL
GSKIP
CINP
ASB2
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
FLVCR2
GPATCH2L
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
DDX24
ADCK1
TMEM63C
UNC79
BEGAIN
PPP4R4
NGB
VIPAS39
MOAP1
IRF2BPL
INF2
OTUB2
ZFYVE21
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
SLIRP
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
GSC
SERPINA12
PRIMA1
C14orf166B
ISM2
CEP128
TTC7B
SYNE3
EML5
NUDT14
LINC00521
SERPINA11
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
SERPINA9
COX8C
ASPG
SERPINA13P
C14orf64
RTL1
TMEM179
C14orf180
MIR127
MIR136
MIR154
MIR203
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
MIR151B
MIR4710
MIR2392
Genes in Wide Peak

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

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

Genes
MLLT1
GNA11
SH3GL1
STK11
TCF3
FSTL3
ZNF177
ZNF699
OR7E19P
RPS28
NDUFA7
RN7SL115P
RNA5SP463
C19orf59
PET100
EMR4P
MIR3940
ACER1
CAPS
VMAC
RN7SL626P
MIR4747
UHRF1
RN7SL121P
LRG1
HDGFRP2
RN7SL528P
RN7SL84P
PIAS4
SNORD37|ENSG00000206775.1
MIR637
RN7SL202P
SNORD38|ENSG00000252408.1
FZR1
RN7SL866P
ZNF554
SPPL2B
LINGO3
MIR4321
MIR1227
RN7SL226P
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
AES
AMH
ATP5D
AZU1
HCN2
BSG
C3
CD70
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
EEF2
EFNA2
ELANE
ELAVL1
EMR1
FCER2
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
INSR
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NRTN
OAZ1
PALM
POLRMT
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RFX2
RPS15
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
THOP1
TLE2
VAV1
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
TRIP10
LONP1
APBA3
SAFB2
MED16
CHAF1A
SH2D3A
EBI3
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4A
TIMM44
SEMA6B
PNPLA6
UQCR11
SBNO2
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
TIMM13
DAZAP1
OR7E24
FGF22
TJP3
NMRK2
SLC39A3
CD209
ANGPTL4
MARCH2
CD320
THEG
ZBTB7A
SIRT6
LSM7
MBD3
MIER2
PCSK4
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
RETN
NCLN
GPR108
DUS3L
XAB2
SHD
MCOLN1
WDR18
REXO1
CAMSAP3
ZNF317
ZNF77
CACTIN
CELF5
SLC25A23
FSD1
ZNF557
CERS4
TLE6
LPPR3
DENND1C
ZNF556
LRRC8E
UBXN6
ACSBG2
ADAMTS10
ABHD17A
DOHH
KLF16
PRAM1
ALKBH7
ZNF414
DOT1L
FBN3
ZNF559
KISS1R
CREB3L3
LMNB2
RAX2
MUM1
MPND
ATCAY
MBD3L1
MIDN
DPP9
R3HDM4
TMEM259
TPGS1
CRB3
REEP6
PEX11G
MUC16
IZUMO4
SCAMP4
ADAT3
EVI5L
GRIN3B
MRPL54
OR7D4
OR7G1
OR1M1
C19orf70
MBD3L2
TRAPPC5
PCP2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
MISP
PLK5
C2CD4C
ZNF358
TICAM1
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
OR7D2
PRR22
ANKRD24
C19orf26
KANK3
TINCR
CATSPERD
ACTL9
OR2Z1
C19orf77
SLC25A41
MBD3L5
ODF3L2
ADAMTSL5
CLEC4G
TMPRSS9
C19orf35
HSD11B1L
C19orf45
OR7G2
OR7G3
MEX3D
PRSS57
CTXN1
PLIN5
ARRDC5
MBD3L4
MBD3L3
PLIN4
C19orf71
MIR3187
TGFBR3L
ZNF177
MIR4746
MIR4999
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p12.1.

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

Genes
CCND3
LINC00680
PRIM2
RAB23
BAG2
FAM83B
RN7SKP256
U3|ENSG00000251930.1
RN7SL244P
RN7SK
GSTA1
RN7SL580P
SNORD66|ENSG00000212532.1
DEFB133
GLYATL3
OPN5
RN7SKP116
ANKRD66
MIR586
MIR4642
TCTE1
TMEM151B
RSPH9
SCARNA15|ENSG00000252218.1
RN7SL403P
MEA1
snoU13|ENSG00000238611.1
U3|ENSG00000221252.1
GUCA1B
SNORA8|ENSG00000206977.1
TOMM6
CRISP1
BMP5
DST
BYSL
RUNX2
CDC5L
SLC29A1
GCLC
GSTA2
GSTA3
GSTA4
GUCA1A
HCRTR2
HSP90AB1
IL17A
MCM3
MEP1A
MUT
NFKBIE
PEX6
PGK2
PKHD1
POLH
PPP2R5D
PTK7
PRPH2
RHAG
SRF
TBCC
TFAP2B
CRISP2
VEGFA
PLA2G7
SUPT3H
GCM1
MED20
SLC25A27
POLR1C
MAD2L1BP
TRAM2
CUL7
RCAN2
CRISP3
DNPH1
CNPY3
SLC22A7
CAPN11
ICK
ENPP4
CUL9
UBR2
GLTSCR1L
CD2AP
ZNF318
YIPF3
USP49
ZNF451
FBXO9
GNMT
TNFRSF21
TINAG
TMEM14A
PRICKLE4
MRPL2
CYP39A1
CLIC5
HMGCLL1
GTPBP2
CENPQ
MRPS18A
MRPS10
LRRC1
TMEM63B
TRERF1
AARS2
XPO5
KIAA1586
ENPP5
ELOVL5
MRPL14
DLK2
COL21A1
TFAP2D
TTBK1
PAQR8
RRP36
ABCC10
KLC4
MLIP
TJAP1
IL17F
EFHC1
KLHDC3
TAF8
C6orf141
PTCRA
BEND6
GSTA5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
LRRC73
GPR111
DEFB110
DEFB112
DEFB113
DEFB114
GPR110
RPL7L1
SLC35B2
GFRAL
CRIP3
KLHL31
MIR206
C6orf226
TMEM151B
PTCHD4
MIR133B
C6orf132
MIR548U
MTRNR2L9
MIR4647
MIR5685
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18|ENSG00000252691.1
SCARNA17|ENSG00000252190.1
MAN1C1
snoU13|ENSG00000238889.1
SYF2
snoU13|ENSG00000238986.1
RN7SL857P
snoU13|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16|ENSG00000252404.1
RN7SL451P
SNORA77|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
MMP23B
KCNAB2
FCN3
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
THEMIS2
H6PD
ISG15
PLCH2
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
AHDC1
SMPDL3B
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
MECR
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
AUNIP
EFHD2
MMEL1
RSG1
NKAIN1
MUL1
NOL9
LIN28A
LINC00115
MORN1
FAM110D
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SESN2
ESPN
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
C1orf170
SYTL1
IGSF21
KIAA2013
THAP3
STPG1
UBXN11
FBXO44
ATPIF1
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
C1orf234
OR4F29
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 18 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 0.29 3.27 0.00302 0.03 -1.81 0.986
1q 1195 0.40 5.71 1.16e-07 0.00 -2.11 0.986
2p 624 0.08 -1.03 0.995 0.02 -2.2 0.986
2q 967 0.04 -1.78 0.995 0.06 -1.39 0.986
3p 644 0.18 0.785 0.665 0.36 4.57 9.65e-05
3q 733 0.65 10.5 0 0.20 0.919 0.597
4p 289 0.00 -2.34 0.995 0.28 3.09 0.0203
4q 670 0.03 -1.95 0.995 0.22 1.94 0.134
5p 183 0.32 3.77 0.000644 0.09 -0.817 0.986
5q 905 0.07 -1.31 0.995 0.09 -0.919 0.986
6p 710 0.12 -0.226 0.995 0.18 0.934 0.597
6q 556 0.03 -1.95 0.995 0.22 1.93 0.134
7p 389 0.08 -0.994 0.995 0.04 -1.77 0.986
7q 783 0.04 -1.75 0.995 0.08 -0.972 0.986
8p 338 0.10 -0.704 0.995 0.17 0.839 0.617
8q 551 0.32 3.81 0.000644 0.09 -0.799 0.986
9p 301 0.09 -0.758 0.995 0.15 0.401 0.81
9q 700 0.07 -1.23 0.995 0.13 -0.0651 0.956
10p 253 0.05 -1.58 0.995 0.19 1.13 0.518
10q 738 0.00 -2.39 0.995 0.24 2.29 0.0877
11p 509 0.00 -2.55 0.995 0.14 0.178 0.913
11q 975 0.02 -2.05 0.995 0.16 0.693 0.695
12p 339 0.11 -0.36 0.995 0.13 0.026 0.933
12q 904 0.09 -0.919 0.995 0.07 -1.31 0.986
13q 560 0.20 1.29 0.361 0.24 2.05 0.134
14q 938 0.11 -0.325 0.995 0.13 0.0646 0.933
15q 810 0.12 -0.277 0.995 0.16 0.499 0.772
16p 559 0.23 2.09 0.0741 0.08 -1.01 0.986
16q 455 0.08 -0.961 0.995 0.26 2.51 0.0608
17p 415 0.03 -1.88 0.995 0.27 2.76 0.0381
17q 972 0.17 0.82 0.665 0.07 -1.13 0.986
18p 104 0.07 -1.31 0.995 0.11 -0.533 0.986
18q 275 0.02 -2.07 0.995 0.16 0.641 0.695
19p 681 0.16 0.554 0.828 0.14 0.167 0.913
19q 935 0.26 2.64 0.021 0.11 -0.455 0.986
20p 234 0.26 2.57 0.0225 0.11 -0.493 0.986
20q 448 0.31 3.71 0.000704 0.06 -1.3 0.986
21q 258 0.11 -0.472 0.995 0.09 -0.859 0.986
22q 564 0.07 -1.28 0.995 0.11 -0.506 0.986
Xq 668 0.33 3.89 0.000644 0.22 1.62 0.232
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

  • Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

  • Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

  • CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

  • Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

  • Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

  • Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

  • Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

  • Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

  • Confidence Level: Confidence level used to calculate the region containing a driver.

  • Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

  • Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

  • Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

  • Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/CESC-TP/22506466/segmentationfile.txt

  • Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/CESC-TP/22506466/markersfile.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 = 0.3

  • Deletion Threshold = 0.3

  • Cap Values = 2

  • Broad Length Cutoff = 0.5

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 10

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 10000

  • Gene GISTIC = 0

Table 4.  Get Full Table First 10 out of 50 Input Tumor Samples.

Tumor Sample Names
TCGA-C5-A1BQ-01C-11D-A20X-26
TCGA-C5-A2LS-01A-22D-A232-26
TCGA-C5-A2LX-01A-11D-A18I-02
TCGA-C5-A2LZ-01A-11D-A20X-26
TCGA-C5-A2M1-01A-11D-A18I-02
TCGA-C5-A3HD-01B-11D-A20X-26
TCGA-C5-A3HE-01A-21D-A232-26
TCGA-C5-A3HF-01A-11D-A20X-26
TCGA-C5-A3HL-01A-11D-A20X-26
TCGA-EA-A1QS-01A-61D-A232-26

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.

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)