Esophageal Carcinoma: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 20 tumor samples used in this analysis: 9 significant arm-level results, 14 significant focal amplifications, and 16 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 - 14 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
--- | --- | --- | --- | ---
11q13.3 | 3.7199e-16 | 3.865e-16 | chr11:69523550-70248899 | 8
8q24.21 | 0.0071269 | 0.0071269 | chr8:124192181-133156466 | 54
11p13 | 0.038401 | 0.043857 | chr11:34794025-35756636 | 8
Xp21.1 | 0.058564 | 0.058564 | chrX:36176963-36179980 | 0 [CXorf59]
10p11.21 | 0.1082 | 0.1082 | chr10:35335459-35736943 | 3
7q31.1 | 0.11395 | 0.11395 | chr7:77734989-110704701 | 263
3q28 | 0.11848 | 0.11848 | chr3:140610629-198022430 | 356
7p11.2 | 0.11848 | 0.11848 | chr7:54942676-55793009 | 4
12p13.33 | 0.2172 | 0.2172 | chr12:1-2591028 | 23
14q21.3 | 0.23096 | 0.23096 | chr14:48730510-55343878 | 48
1q42.3 | 0.24466 | 0.24466 | chr1:200527575-249250621 | 449
2p15 | 0.24466 | 0.24466 | chr2:55425531-68349182 | 63
6p12.3 | 0.24466 | 0.24466 | chr6:41604078-62236966 | 152
18p11.31 | 0.24466 | 0.24466 | chr18:1-3702370 | 25

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
hsa-mir-548k
CTTN
FGF3
FGF4
PPFIA1
FADD
ANO1
MIR548K

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's Cancer Gene Census [7].

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
ADCY8
ANXA13
KCNQ3
NDUFB9
POU5F1B
PVT1
SQLE
MTSS1
KIAA0196
HHLA1
TRIB1
RNF139
ZHX1
EFR3A
ATAD2
ASAP1-IT1
ASAP1
FAM49B
TRMT12
WDYHV1
GSDMC
TATDN1
C8orf76
FAM83A
FBXO32
ZNF572
TMEM65
LOC157381
FAM84B
FAM91A1
NSMCE2
KLHL38
FER1L6-AS1
FER1L6
LOC727677
LOC728724
OC90
LOC100130231
LOC100131726
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
LOC100507117
ZHX1-C8ORF76
MIR4663
PCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
CD44
SLC1A2
PDHX
FJX1
PAMR1
APIP
TRIM44
MIR1343

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p11.21.

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

Genes
CREM
CUL2
CCNY

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.1.

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

Genes
CDK6
AKAP9
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
ACHE
ASNS
AZGP1
CACNA2D1
CALCR
KRIT1
CD36
AP1S1
COL1A2
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
SLC26A3
EPHB4
EPO
GNAI1
GNB2
GNG11
GNGT1
GPR22
GRM3
HGF
AGFG2
LAMB1
LRCH4
MCM7
DNAJB9
NPTX2
NRCAM
OCM2
ORC5
SERPINE1
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PMS2P1
POLR2J
PON1
PON2
PON3
PRKAR2B
RELN
PSMC2
SRI
SRPK2
SYPL1
TAC1
TAF6
TFR2
TRIP6
VGF
ZAN
ZNF3
ZKSCAN1
ZSCAN21
MTERF
SHFM1
TFPI2
TRRAP
FZD1
BUD31
SGCE
PLOD3
CLDN12
AP4M1
PMPCB
ATP5J2
SEMA3E
MAGI2
DMTF1
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
BET1
SEMA3A
COG5
ZNHIT1
SEMA3C
ARPC1A
SH2B2
STAG3
CPSF4
DBF4
COPS6
DUS4L
TP53TG1
PDAP1
LAMB4
LMTK2
PEG10
ZKSCAN5
CLDN15
BRI3
TECPR1
PTCD1
FBXO24
STEAP1
HBP1
DNAJC2
PCLO
PILRB
PILRA
PNPLA8
FIS1
ACTL6B
SRRT
ASB4
ADAM22
ANKIB1
PUS7
CROT
ALKBH4
SAMD9
ZCWPW1
C7orf43
PPP1R9A
CCDC132
MLL5
BAIAP2L1
SLC25A40
BCAP29
MEPCE
SLC12A9
ACN9
SMURF1
GATAD1
RINT1
MOSPD3
GIGYF1
RABL5
CYP3A43
CASD1
ZNF655
PVRIG
C7orf23
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ORAI2
OR2AE1
TSC22D4
TRIM56
ARMC10
IMMP2L
RBM48
ZNF394
MYH16
MGC16142
GTPBP10
TRIM4
MYL10
EMID2
MUC17
RUNDC3B
C7orf66
THAP5
CCDC71L
BHLHA15
SAMD9L
C7orf62
ZNF804B
ZNF498
FAM200A
PPP1R35
GPC2
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
MBLAC1
FAM133B
STEAP2
DLX6-AS1
ZNF789
LOC286002
GNAT3
MOGAT3
GJC3
DPY19L2P2
GATS
NAT16
SLC26A5
LHFPL3
MGC72080
C7orf59
RPL13AP17
LRRD1
FLJ42280
KPNA7
C7orf61
UFSP1
MIR106B
MIR25
MIR93
SPDYE3
SPDYE2
DPY19L2P4
EIF3IP1
POLR2J3
MIR489
LOC645591
AZGP1P1
MIR591
LOC723809
MIR653
LOC728066
SPDYE6
RPL19P12
LOC100129845
EFCAB10
UPK3BL
LOC100216545
LOC100216546
LOC100289187
LOC100289561
SPDYE2L
MIR548M
SAP25
MIR4285
MIR3609
MAGI2-AS3
LOC100506136
ATP5J2-PTCD1
MIR4653
MIR4652
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q28.

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

Genes
BCL6
EIF4A2
ETV5
LPP
MLF1
PIK3CA
SOX2
TFRC
GMPS
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
AADAC
ACTL6A
AGTR1
AHSG
APOD
ATP1B3
ATR
BCHE
BDH1
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
GYG1
HRG
HES1
IL1RAP
IL12A
KNG1
KPNA4
TM4SF1
MBNL1
MFI2
MME
MUC4
NDUFB5
OPA1
CLDN11
P2RY1
PAK2
PCYT1A
PFN2
SERPINI1
SERPINI2
PLD1
PLOD2
PLS1
PLSCR1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
PTX3
RAP2B
RARRES1
RASA2
RFC4
SNORA63
RPL35A
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
HLTF
SSR3
SST
TERC
TFDP2
THPO
SEC62
TM4SF4
TRPC1
CLRN1
ZIC1
KCNAB1
FXR1
TP63
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
SLC33A1
ADIPOQ
CHST2
RNF7
KIAA0226
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
RNF13
SLITRK3
NLGN1
NCBP2
PLCH1
TNIK
MCF2L2
ATP11B
U2SURP
VPS8
ACAP2
WWTR1
TIPARP
UBXN7
ARHGEF26
PCOLCE2
GPR160
FETUB
LAMP3
KCNMB3
SERP1
GOLIM4
GPR171
SCHIP1
NMD3
COMMD2
ZNF639
RSRC1
PEX5L
SELT
DNAJB11
P2RY13
GPR87
DCUN1D1
XRN1
KLHL24
PIGX
TBCCD1
SLC25A36
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
SUCNR1
MCCC1
LXN
CCNL1
PLSCR2
PLSCR4
HRASLS
MRPL47
NCEH1
IFT80
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
MFSD1
FNDC3B
P2RY12
ATP13A3
VEPH1
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
PIGZ
SPATA16
EIF2A
B3GNT5
ZIC4
IQCG
ATP13A4
FYTTD1
HPS3
ARPM1
MGC2889
LRCH3
CEP19
GFM1
LMLN
KLHL6
VWA5B2
TMEM41A
SPSB4
ACPL2
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
FAM194A
GRK7
TMEM207
RTP1
TTC14
PPM1L
WDR49
LRRC34
MB21D2
XXYLT1
C3orf55
C3orf79
CCDC50
PYDC2
LOC152217
SPTSSB
RNF168
DHX36
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
LOC201651
C3orf58
SENP5
LOC220729
ZBTB38
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
GK5
UTS2D
SLC9A9
HTR3E
IGSF10
C3orf33
C3orf70
TPRG1
TRIM59
CCDC39
LOC339894
LOC339926
LPP-AS2
LRRIQ4
SAMD7
AADACL2
GPR149
PAQR9
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
PLSCR5
ANKUB1
LEKR1
TMEM212
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
SNORD2
SNORA4
TMEM14E
LOC646168
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
IQCJ
SCARNA7
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
LOC730091
MIR922
MIR944
LOC100128023
WWTR1-AS1
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
TIPARP-AS1
LOC100289361
MIR1248
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100505687
MFI2-AS1
LOC100507086
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR
LANCL2
VOPP1
FKBP9L

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
KDM5A
CACNA1C
NINJ2
RAD52
SLC6A12
SLC6A13
ERC1
WNK1
ADIPOR2
WNT5B
CCDC77
CACNA2D4
FBXL14
DCP1B
B4GALNT3
IQSEC3
LOC574538
LRTM2
FAM138D
LOC100271702
LOC100288778
LOC100292680
MIR3649

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.3.

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

Genes
NIN
ARF6
BMP4
CDKN3
GCH1
GMFB
MGAT2
POLE2
PSMC6
PTGDR
PTGER2
PYGL
RPL36AL
RPS29
SOS2
STYX
CDKL1
NEMF
CNIH
CGRRF1
FERMT2
MAP4K5
NID2
SAMD4A
KLHDC2
ATP5S
ERO1L
ATL1
C14orf166
GNG2
DNAAF2
TXNDC16
SAV1
GNPNAT1
METTL21D
L2HGDH
DDHD1
TMX1
TRIM9
LRR1
KLHDC1
FRMD6
FRMD6-AS1
ABHD12B
C14orf183
C14orf182
LOC283553
GPR137C

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.3.

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

Genes
ELK4
FH
MDM4
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ARF1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
EIF2D
ELF3
EPHX1
EPRS
ESRRG
FMOD
GALNT2
GNG4
GPR25
GUK1
H3F3A
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PIK3C2B
PKP1
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTPN7
PTPN14
RAB4A
RABIF
RBBP5
REN
RGS7
RNPEP
RYR2
SNRPE
SRP9
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GPR37L1
GGPS1
SOX13
IKBKE
TMEM63A
TOMM20
URB2
CEP170
ZC3H11A
TMCC2
LPGAT1
KIF14
AKT3
BPNT1
TIMM17A
LRRN2
ZNF238
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NFASC
FBXO28
CAMSAP2
SRGAP2
ABCB10
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
LAX1
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
KLHL12
LGR6
TFB2M
GREM2
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
NUAK2
DDX59
RASSF5
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
WNT3A
NAV1
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
PGBD2
OR2L13
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
RPS10P7
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR194-1
MIR205
MIR215
MIR29B2
MIR29C
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
DUSP5P
C1orf133
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SNORA14B
SNORA36B
SNORA77
SNORA16B
LOC728463
FAM72A
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR1231
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
KDM5B-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p15.

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

Genes
REL
BCL11A
hsa-mir-216b
EFEMP1
MDH1
MEIS1
MTIF2
OTX1
PEX13
RAB1A
RPS27A
SLC1A4
UGP2
VRK2
XPO1
USP34
SERTAD2
ACTR2
C1D
CCT4
B3GNT2
CEP68
EHBP1
LGALSL
WDPCP
VPS54
ETAA1
AFTPH
FANCL
CCDC88A
PELI1
SMEK2
PAPOLG
FAM161A
KIAA1841
PNPT1
CCDC104
CCDC85A
C2orf63
AHSA2
COMMD1
PUS10
LINC00309
TMEM17
SPRED2
LOC339803
C2orf74
LOC339807
PRORSD1P
FLJ30838
FLJ16341
LOC400958
MIR216A
MIR217
LOC644838
SNORA70B
MIR216B
LOC100132215
DBIL5P2
MIR4426
MIR4434
MIR4778
MIR4432

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p12.3.

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

Genes
CCND3
TFEB
hsa-mir-548u
hsa-mir-133b
hsa-mir-586
CRISP1
BMP5
DST
BYSL
RUNX2
CDC5L
SLC29A1
GCLC
GSTA1
GSTA2
GSTA3
GSTA4
GUCA1A
GUCA1B
HCRTR2
HSP90AB1
IL17A
MCM3
MDFI
MEA1
MEP1A
MUT
NFKBIE
PEX6
PGC
PGK2
PKHD1
POLH
PPP2R5D
PRIM2
PTK7
PRPH2
RHAG
SRF
TBCC
TFAP2B
CRISP2
VEGFA
PLA2G7
SUPT3H
GCM1
MED20
SLC25A27
BAG2
POLR1C
MAD2L1BP
TRAM2
CUL7
RCAN2
CRISP3
C6orf108
CNPY3
FRS3
SLC22A7
CAPN11
ICK
ENPP4
CUL9
UBR2
KIAA0240
CD2AP
ZNF318
YIPF3
USP49
ZNF451
FBXO9
GNMT
TNFRSF21
TINAG
TMEM14A
PRICKLE4
MRPL2
CYP39A1
RAB23
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
TCTE1
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
RSPH9
LRRC73
FAM83B
GPR111
DEFB110
DEFB112
DEFB113
DEFB114
GPR110
RPL7L1
SLC35B2
GUSBP4
GLYATL3
GFRAL
CRIP3
KLHL31
DEFB133
MIR206
C6orf226
TMEM151B
ATP6V0CP3
PTCHD4
MIR133B
C6orf132
RPS16P5
MIR586
LOC730101
GSTA7P
LOC100132354
TOMM6
LOC100287718
MIR4647
MIR4642

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.31.

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

Genes
ADCYAP1
CETN1
TGIF1
TYMS
YES1
MYOM1
USP14
DLGAP1
LPIN2
THOC1
NDC80
MYL12A
SMCHD1
CLUL1
ENOSF1
LINC00470
METTL4
COLEC12
EMILIN2
MYL12B
C18orf56
CBX3P2
FLJ35776
ROCK1P1
LOC727896

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 - 16 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 | 2.6068e-14 | 2.6068e-14 | chr9:21865498-22448737 | 4
2q22.1 | 0.023373 | 0.023373 | chr2:139655617-143637838 | 1
3p14.2 | 0.023373 | 0.023373 | chr3:59034763-61547330 | 1
5q11.2 | 0.11429 | 0.11429 | chr5:44806004-101636216 | 250
Xp11.3 | 0.11429 | 0.11429 | chrX:44702452-45008304 | 2
3p11.1 | 0.058795 | 0.13697 | chr3:74568944-93778057 | 27
7q31.1 | 0.16881 | 0.16881 | chr7:109598162-159138663 | 368
13q14.2 | 0.18599 | 0.18599 | chr13:34386735-76123297 | 171
4q21.23 | 0.18599 | 0.18599 | chr4:76433725-140490090 | 278
6p25.3 | 0.18599 | 0.18599 | chr6:1-21668433 | 114
10p11.21 | 0.18599 | 0.18599 | chr10:34059131-35328087 | 1
17q24.3 | 0.18599 | 0.18599 | chr17:70116519-71163787 | 4
19q13.2 | 0.18599 | 0.18599 | chr19:24008375-46149617 | 399
16q23.1 | 0.20631 | 0.19837 | chr16:78016120-79627770 | 2
10q23.31 | 0.24157 | 0.23305 | chr10:1-135534747 | 945
15q22.2 | 0.24159 | 0.23305 | chr15:1-102531392 | 844

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
IL6ST
PIK3R1
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
BHMT
BTF3
CAST
CCNB1
CCNH
CDK7
CETN3
CHD1
CKMT2
ERCC8
COX7C
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
FOXD1
GLRX
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HTR1A
ISL1
ITGA1
ITGA2
KIF2A
TNPO1
LNPEP
CD180
MAP1B
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
PCSK1
PDE4D
PMCHL2
RAD17
RASA1
RASGRF2
RPS23
SMN1
SMN2
TAF9
TBCA
NR2F1
THBS4
XRCC4
ST8SIA4
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
HOMER1
SCAMP1
CARTPT
TTC37
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
CWC27
CCNO
NSA2
FST
POLR3G
PLK2
IQGAP2
MRPS30
SMA4
SMA5
ESM1
ADAMTS6
RHOBTB3
ELL2
SV2C
MRPS27
PPWD1
OTP
SKIV2L2
SSBP2
BHMT2
PART1
FAM169A
RNU5E-1
RNU5D-1
DIMT1
DMGDH
IPO11
GCNT4
POLK
ERAP1
PELO
DHX29
DDX4
SGTB
ARL15
AGGF1
WDR41
RIOK2
DEPDC1B
BDP1
ERBB2IP
NLN
ARRDC3
ZSWIM6
ANKRA2
MCCC2
CENPK
ERAP2
RGNEF
SLC30A5
CENPH
GPBP1
PARP8
ANKRD55
MCTP1
PTCD2
ELOVL7
C5orf44
ATG10
SPATA9
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
SPZ1
NDUFAF2
MRPS36
ATP6AP1L
SNX18
FCHO2
RAB3C
LYSMD3
C5orf35
IL31RA
EMB
JMY
POU5F2
TMEM171
TMEM174
POC5
ACOT12
SREK1
SLC38A9
TMEM167A
MBLAC2
TMEM161B
MARVELD2
ARSK
FAM81B
MIER3
CDC20B
PAPD4
LIX1
ZNF366
FAM151B
S100Z
CCDC125
C5orf27
GAPT
CMYA5
ANKRD31
SERINC5
LOC257396
KIAA0825
GPR150
NBPF22P
C5orf64
RNF180
SREK1IP1
RGMB
RFESD
ANKRD34B
IDAS
ACTBL2
FAM174A
MTX3
HCN1
SLCO4C1
MAST4
RNF138P1
RGS7BP
MIR9-2
CRSP8P
FLJ42709
GPX8
FLJ35946
MIR449A
LOC642366
C5orf43
LOC644936
LINC00461
LOC647859
GUSBP3
GTF2H2B
SCARNA18
SNORA47
MIR449B
MIR581
MIR583
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
LRRC70
LOC100131067
FAM159B
LOC100133050
LOC100170939
LOC100272216
LOC100289230
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR4280
MTRNR2L2
MIR3607
MIR3660
LOC100505894
OCLN
MIR4804
MIR3977
MIR4803

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.3.

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

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

Genes
hsa-mir-4273
hsa-mir-1324
EPHA3
GBE1
HTR1F
POU1F1
PROS1
ROBO1
ROBO2
CGGBP1
CHMP2B
ZNF654
ARL13B
CADM2
C3orf38
VGLL3
LOC401074
STX19
LOC440970
FLJ20518
FAM86DP
ZNF717
FRG2C
MIR1324
MIR4273
MIR4795
MIR4444-1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ZNF277
ABCB8
TFEC
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
NAA38
GPR85
TAS2R5
CHPF2
ING3
LRRN3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
MIR3666
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

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

Genes
LCP1
RB1
LHFP
TTL
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
ATP7B
KLF5
RCBTB2
CPB2
DACH1
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
PCDH9
RFC3
RFXAP
ATXN8OS
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
ITM2B
MTRF1
UTP14C
TBC1D4
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
PIBF1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
KIAA0564
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
PCDH20
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
LINC00284
CSNK1A1L
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
COMMD6
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
LINC00550
LINC00347
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ALG11
MZT1
TSC22D1-AS1
SERPINE3
CTAGE11P
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR548F5
MIR759
MIR320D1
MIR4305
MIR3169
MIR3613
OR7E37P
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.23.

Table S22. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IL2
RAP1GDS1
TET2
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ANK2
ANXA3
ANXA5
ART3
ATOH1
BMP3
BMPR1B
CAMK2D
CASP6
CCNA2
CCNG2
SCARB2
CDS1
CENPE
DMP1
DSPP
EGF
EIF4E
ELF2
ENPEP
FABP2
FGF2
FGF5
GK2
GRID2
H2AFZ
HADH
HNRNPD
HSP90AB3P
IBSP
CFI
CXCL10
MAD2L1
MANBA
CXCL9
AFF1
MTTP
NDUFC1
NFKB1
NKX6-1
PDHA2
PITX2
PKD2
EXOSC9
PPEF2
PPP3CA
PRKG2
MAPK10
PTPN13
RPL34
CXCL11
SNCA
SPP1
TACR3
TRPC3
UBE2D3
UGT8
SPARCL1
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
HERC3
STBD1
CDKL2
PAPSS1
AIMP1
NDST3
ABCG2
SEC24D
G3BP2
HNRPDL
TSPAN5
FAM13A
SPRY1
PGRMC2
SEC24B
CXCL13
PDLIM5
RRH
PLK4
HPSE
CCNI
PRDM5
NUDT6
HSPA4L
SEC31A
MMRN1
WDFY3
METAP1
SLC7A11
CCRN4L
PPA2
DAPP1
DKK2
INTU
NAAA
COQ2
HPGDS
MRPS18C
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
MYOZ2
NUDT9
NUP54
GAR1
PCDH18
USP53
ARHGEF38
HERC6
CCDC109B
BANK1
LARP1B
SDAD1
BBS7
C4orf21
AP1AR
BMP2K
SEPT11
BDH2
SMARCAD1
MEPE
PRDM8
INTS12
ANKRD50
KLHL8
PCDH10
SHROOM3
METTL14
ENOPH1
OSTC
IL21
NEUROG2
SLC39A8
NDST4
AGXT2L1
MRPL1
ELOVL6
NDNF
FAT4
ARSJ
THAP9
GSTCD
TNIP3
PHF17
SCD5
DNAJB14
FRAS1
NAA15
C4orf29
ALPK1
CXXC4
SETD7
PLA2G12A
SLC25A31
RAB33B
ARHGAP24
C4orf17
QRFPR
FAM175A
KIAA1109
COL25A1
C4orf49
NAA11
AGPAT9
PIGY
FLJ20021
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
GDEP
ANTXR2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
LIN54
C4orf32
C4orf36
TRAM1L1
SLC9B2
SLC9B1
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
SPATA5
BBS12
TIGD2
SGMS2
SYNPO2
CNOT6L
C4orf22
NPNT
MFSD8
LOC256880
NAP1L5
LOC285419
LOC285456
FAM13A-AS1
GPRIN3
C4orf37
CCDC158
SOWAHB
LRIT3
SLC10A6
HSD17B13
PCNAP1
FAM190A
FLJ14186
C4orf3
WDFY3-AS2
MIR302A
C4orf11
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641364
LOC641365
LOC641518
LOC644248
CEP170P1
LOC645513
SNORA24
MIR575
MIR577
CETN4P
SNHG8
FAM47E
PP12613
MIR1243
MIR2054
MIR1973
LOC100499177
MIR3684
LOC100505702
LOC100505875
LOC100506035
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4450
MIR4451
FAM47E-STBD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

Table S23. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IRF4
DEK
hsa-mir-548a-1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
ID4
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
NOL7
FAM8A1
TMEM14C
GFOD1
ELOVL2
CDKAL1
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
CCDC90A
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
MBOAT1
C6orf195
PIP5K1P1
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
RNF144B
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
NHLRC1
PSMG4
DKFZP686I15217
FLJ23152
C6orf201
ERVFRD-1
PPP1R3G
MIR548A1
HULC
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

Table S24. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PARD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

Table S25. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
SOX9
SLC39A11
LINC00511
LOC100499467

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.2.

Table S26. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
CIC
CBLC
hsa-mir-330
hsa-mir-4323
hsa-mir-641
ACTN4
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
ATP1A3
ATP4A
AXL
BCKDHA
CEACAM1
BLVRB
CAPNS1
CCNE1
CD22
CEACAM5
CEBPG
CEACAM3
CEACAM7
CEACAM8
CEACAM4
TBCB
CKM
CLC
CLPTM1
COX6B1
COX7A1
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
ECH1
MEGF8
ERCC1
ERF
FBL
ETV2
FOSB
GPI
GPR4
FFAR1
FFAR3
FFAR2
GRIK5
GSK3A
HNRNPL
HPN
KCNN4
LGALS4
LGALS7
LIPE
LRP3
BCAM
MAG
MAP3K10
CEACAM6
NFKBIB
NPHS1
PAFAH1B3
PEPD
PLAUR
FXYD1
FXYD3
POLR2I
POU2F2
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PVR
PVRL2
RELB
MRPS12
RPS16
RPS19
RTN2
RYR1
SCN1B
SNRPA
SUPT5H
TGFB1
TYROBP
UQCRFS1
USF2
VASP
XRCC1
ZFP36
ZNF45
ZNF221
ZNF222
ZNF146
ZNF155
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
MIA
DPF1
LTBP4
URI1
FCGBP
ARHGEF1
PDCD5
DYRK1B
NUMBL
ZNF235
KCNK6
ZNF254
GMFG
KIAA0355
ZNF536
MLL4
UBA2
PAK4
TMEM147
TOMM40
RABAC1
SPINT2
DLL3
POP4
ZNF234
PPP1R13L
CD3EAP
HCST
UPK1A
HNRNPUL1
CLASRP
SLC7A9
MAP4K1
ZFP30
ZNF507
SIRT2
CYP2G1P
SIPA1L3
HAUS5
ETHE1
PRG1
PLD3
EML2
ZNF345
CLIP3
LSM14A
GAPDHS
ZNF285
ZBTB32
LYPD3
EIF3K
LGALS13
CYP2S1
SERTAD3
SERTAD1
ZNF571
LSR
FXYD7
FXYD5
RAB4B
PAF1
SARS2
GPATCH1
SAMD4B
ATP5SL
MED29
PSENEN
ZNF302
LIN37
SMG9
IRGC
SLC7A10
LGALS14
EXOSC5
CEACAM19
CD177
TSHZ3
LRFN1
GRAMD1A
ZFP14
ZNF529
PRX
SPTBN4
MARK4
HAMP
CATSPERG
PRODH2
DMRTC2
C19orf33
CHST8
ZNF574
PLEKHG2
KCTD15
TRAPPC6A
PLEKHF1
RBM42
ZNF576
LRFN3
IGFLR1
GEMIN7
ADCK4
CNTD2
LOC80054
OPA3
ITPKC
B9D2
C19orf12
TEX101
WDR87
KIRREL2
ANKRD27
PDCD2L
ZNF527
CNFN
ZNF607
NFKBID
CEP89
ZNF382
ZNF566
ALKBH6
RHPN2
ZNF30
CEACAM21
CCDC97
EXOC3L2
YIF1B
C19orf40
TDRD12
ZNF461
ZNF585B
TIMM50
SHKBP1
DMKN
DKFZp566F0947
PPP1R14A
EGLN2
FBXO17
ARHGAP33
RASGRP4
ZNF526
CEACAM20
ZNF573
WDR88
EID2B
IRGQ
ZNF428
WTIP
ZNF792
HSPB6
RINL
FBXO27
C19orf47
PPM1N
KLC3
IGSF23
LYPD4
HIPK4
ZNF420
ZNF565
FAM98C
CAPN12
DPY19L3
LGALS16
TTC9B
ZNF599
FAM187B
C19orf55
LOC148145
LOC148189
ZNF569
ZNF570
ZNF296
DEDD2
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
LGI4
C19orf46
ZNF540
ZNF585A
GGN
CADM4
THAP8
U2AF1L4
IL28A
IL28B
IL29
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
LOC284395
SCGB2B2
WDR62
ZFP82
LOC284408
LOC284412
HKR1
ZNF181
ZNF260
ZNF546
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
SELV
ZNF233
SBSN
ZNF829
ZNF568
B3GNT8
RGS9BP
KRTDAP
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
NUDT19
ZNF793
PAPL
LOC390940
SPRED3
LOC400684
LOC400685
LGALS17A
PSG8
MIR330
TMEM91
LOC643669
SCGB1B2P
SDHAF1
LOC644189
LOC644554
PSG10P
LGALS7B
PHLDB3
MIR641
LOC728752
ZNF726
LOC100101266
LOC100128675
LOC100128682
LOC100129935
SCGB2B3P
LOC100134317
SRRM5
C19orf69
LOC100287177
LOC100289650
LOC100379224
MIR4323
LOC100505495
LOC100505622
LOC100505715
LOC100505835
LOC100506469
LOC100506930
LOC100507433
THEG5
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4531
LOC100631378
LOC100652909

Genes in Wide Peak

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

Table S27. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CLEC3A
WWOX

Genes in Wide Peak

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

Table S28. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BMPR1A
FGFR2
GATA3
TLX1
NFKB2
PRF1
PTEN
RET
MLLT10
NCOA4
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
hsa-mir-4294
hsa-mir-3156-1
hsa-mir-938
hsa-mir-604
hsa-mir-603
hsa-mir-1915
hsa-mir-511-2
hsa-mir-511-1
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ACADSB
ACTA2
ADAM8
ADARB2
ADD3
ADK
ADRA2A
ADRB1
ALOX5
ANXA8L2
ANK3
ANXA2P3
ANXA7
ANXA11
FAS
ARL3
ATP5C1
BMI1
BNIP3
CACNB2
CALML3
CAMK2G
CASP7
ENTPD1
CDK1
CHAT
AKR1C4
CHUK
ABCC2
COL13A1
COL17A1
KLF6
MAP3K8
COX15
CPN1
CREM
CTBP2
CTSL1P2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
AKR1C1
AKR1C2
DMBT1
DNA2
TRDMT1
DNTT
DOCK1
DUSP5
ECHS1
EGR2
EIF4EBP2
EMX2
ERCC6
FGF8
GAD2
GDF2
GDF10
GDI2
GFRA1
GLUD1
GOT1
PRLHR
GPR26
GRK5
GRID1
HABP2
HELLS
HHEX
HK1
HMX2
HNRNPF
HNRNPH3
HPS1
HTR7
IDE
IDI1
IFIT2
IFIT1
IFIT3
IL2RA
IL15RA
INPP5A
ITGB1
ITIH2
KCNMA1
KIF5B
KIF11
ABLIM1
LIPA
MAT1A
MBL2
MGMT
MKI67
MRC1
MSMB
MXI1
NDUFB8
NODAL
NRAP
OAT
P4HA1
PAX2
PCBD1
PDE6C
PFKFB3
PFKP
PGAM1
PHYH
PIP4K2A
PITX3
PLAU
PNLIP
PNLIPRP1
PNLIPRP2
PPA1
PPP1R3C
PPP3CB
PPYR1
SRGN
PRKCQ
PRKG1
MAPK8
HTRA1
PSAP
PSD
PTPRE
ALDH18A1
RBP3
RBP4
RGR
RGS10
RPS24
RSU1
SCD
CXCL12
SFRP5
SFTPD
FBXW4
SLC18A2
SLC18A3
SLIT1
SNCG
SUPV3L1
SVIL
TACR2
TAF5
TCF7L2
ZEB1
TECTB
TFAM
TIAL1
TLL2
UBE2D1
UROS
VCL
VDAC2
VIM
WNT8B
XPNPEP1
ZNF22
ZNF32
ZNF33A
ZNF33B
ZNF37A
STAM
CUBN
CCDC6
SLC25A16
SHOC2
ADAM12
ZNF239
FZD8
UTF1
CUL2
PARG
NDST2
MBL1P
LIPF
ITGA8
PRPF18
AKR1C3
EIF3A
GBF1
NRP1
LDB1
CDC123
SGPL1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
DDX21
PTPLA
LGI1
NOLC1
DLG5
PTER
NMT2
GSTO1
CHST3
BAG3
VPS26A
MINPP1
SPAG6
KIF20B
SEC24C
SH3PXD2A
FAM53B
USP6NL
GPRIN2
SLK
BMS1
SPOCK2
ZNF518A
RHOBTB1
DCLRE1A
ABI1
FRAT1
PPIF
ACTR1A
OPTN
HNRNPA3P1
NET1
SMNDC1
NPM3
MICU1
NEBL
PITRM1
GLRX3
RPP30
RPP38
DPYSL4
TACC2
SORBS1
ERLIN1
CELF2
LBX1
NRG3
MGEA5
YME1L1
ZMYND11
TUBGCP2
PRDX3
C10orf116
VAX1
C10orf10
ATE1
POLR3A
ZWINT
LDB3
NUDT5
SEC23IP
ECD
RAB11FIP2
CPEB3
ANKRD26
INPP5F
WDR37
ZNF365
MSRB2
SEPHS1
RAB18
DKK1
KIN
NT5C2
DIP2C
PDCD11
SORCS3
KIAA0913
WAPAL
PPRC1
FAM175B
LARP4B
RRP12
TBC1D12
DNAJC9
DNMBP
CSTF2T
FRAT2
SIRT1
COMMD3
KAT6B
TSPAN15
GTPBP4
PDSS1
IFIT5
BAMBI
DPCD
SEC31B
NUDT13
UPF2
ATRNL1
HERC4
PTPN20B
C10orf137
LRIT1
TCTN3
KIAA1279
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
AP3M1
ANKRD1
GHITM
KIAA1274
PDCD4
VENTX
C10orf28
POLL
CTNNA3
BLNK
A1CF
NRBF2
KCNIP2
CUZD1
CALY
NEUROG3
ASCC1
EXOSC1
MRPS16
CALHM2
CUTC
HSPA14
PLCE1
DUSP13
WAC
CHST15
ACSL5
CALML5
PANK1
FXYD4
MYO3A
FAM190B
APBB1IP
ANKRD16
EXOC6
FAM35A
DDIT4
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
DNAJB12
CNNM2
C10orf26
FAM208B
C10orf118
CRTAC1
ARMC4
MTPAP
CEP55
SEC61A2
LRRC20
CWF19L1
OLAH
SLC29A3
RNLS
PI4K2A
MCM10
CSGALNACT2
H2AFY2
DHTKD1
HIF1AN
RUFY2
FRMD4A
WDR11
FAM178A
FAM21B
CCAR1
OGDHL
DHX32
PPP2R2D
CISD1
IDI2-AS1
FAM45B
TDRD1
KIAA1217
PARD3
DNAJC12
ASAH2
BCCIP
C10orf2
SAR1A
TM9SF3
PRTFDC1
ENTPD7
CAMK1D
ZMIZ1
ZNF248
AS3MT
GPR158
STAMBPL1
ARHGAP21
KIAA1462
GPAM
KIAA1598
FAM160B1
WDFY4
SFMBT2
SEMA4G
ARHGAP22
MYOZ1
PLEKHA1
AVPI1
HPSE2
FAM204A
CDH23
LHPP
PBLD
NPFFR1
C10orf54
MMS19
DNAJC1
NOC3L
IKZF5
DCLRE1C
ZDHHC6
PCDH15
CUEDC2
DDX50
FBXL15
OR13A1
C10orf76
SUV39H2
C10orf68
ECHDC3
ASB13
HPS6
MMRN2
TMEM180
TUBAL3
MCMBP
THNSL1
SYNPO2L
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
FAM188A
UBTD1
BICC1
FAM213A
HKDC1
WDR96
TET1
LRRC27
EPC1
TNKS2
ITIH5
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
AKR1E2
FAM107B
CCDC3
MARVELD1
SYT15
TAF3
RASSF4
C10orf11
PCGF6
ARID5B
LOXL4
ZDHHC16
C10orf58
DYDC2
PCGF5
GPR123
LZTS2
PHYHIPL
LCOR
NKX6-2
MRPL43
LYZL1
AFAP1L2
PLA2G12B
MYPN
PYROXD2
USMG5
LOC84856
ZNF503
AIFM2
ADO
FBXO18
ATAD1
PLXDC2
MASTL
ARHGAP19
LOC84989
RBM17
KNDC1
ITPRIP
LINC00263
MCU
ANKRD30A
ACBD5
IDI2
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
ZFAND4
ARHGAP12
OPN4
HOGA1
UCN3
SORCS1
C10orf71
PRAP1
ZNF511
CHCHD1
ZMYND17
TTC18
C10orf90
BTBD16
FAM24A
PSTK
ZNF488
PIK3AP1
MORN4
ZFYVE27
MMP21
COMTD1
FRA10AC1
ANKRD22
SFXN2
PDZD8
AGAP4
C10orf32
LYZL2
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
ANAPC16
PNLIPRP3
SFXN4
CPXM2
ADAMTS14
C10orf129
SAMD8
LIPJ
CFL1P1
TRUB1
MPP7
FRMPD2
VTI1A
LOC143188
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
C10orf46
HSD17B7P2
USP54
NKX2-3
SLC35G1
CCDC147
FAM170B
C10orf128
FUT11
OIT3
C10orf91
PWWP2B
LOC170425
ANTXRL
EMX2OS
PPAPDC1A
VSTM4
PAOX
FAM24B
SFTA1P
LOC219347
PLAC9
C10orf107
TMEM26
ZCCHC24
ENKUR
ARMC3
UNC5B
LOC219731
STOX1
C10orf35
TYSND1
ZNF25
GJD4
CCNY
RTKN2
C10orf27
ATOH7
OTUD1
LOC220906
ZNF438
ZEB1-AS1
SLC16A9
FAM13C
MARCH8
C10orf25
TMEM72-AS1
ZNF485
RASGEF1A
CCDC7
REEP3
JMJD1C
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
ZNF503-AS1
IPMK
FAM21C
EBF3
LOC254312
C10orf47
CALHM1
CASC2
PTF1A
TCERG1L
C10orf67
HSPA12A
SGMS1
PIPSL
PGBD3
C10orf53
C10orf125
JAKMIP3
STK32C
LOC282980
BLOC1S2
RBM20
LOC282997
FLJ37201
C10orf40
LOC283033
LOC283038
LOC283050
LOC283070
MKX
LOC283089
SEPT7L
FAM149B1
FLJ31813
O3FAR1
KCNK18
LOC338579
LOC338588
ST8SIA6
DUPD1
LIPM
CYP26C1
VWA2
NANOS1
LRIT2
HMX3
AKR1CL1
EBLN1
TUBB8
LRRTM3
PTCHD3
NHLRC2
C10orf96
FLJ46361
C10orf113
C10orf140
LINC00202
LOC387646
LOC387647
FAM21A
SH2D4B
C10orf99
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
tAKR
C1QL3
GUCY2GP
NKX1-2
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf114
LOC399744
ACTR3BP5
LOC399753
BMS1P5
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
ACBD7
C10orf105
C10orf62
AGAP6
ZNF32-AS3
C10orf108
C10orf55
FAM35B
C10orf103
C10orf136
LOC439949
LOC439950
FAM35B2
LOC439990
LOC439994
IFIT1B
CDNF
FRG2B
LOC441666
MIR346
LRRC18
SPRN
MIR511-1
MIR511-2
MIR146B
MIR202
NPS
LOC619207
SNORA19
LOC642361
ADARB2-AS1
AGAP9
ZNF487P
LOC642826
FAM196A
FAM25A
TMEM72
LIPK
LIPN
LOC643529
LOC643650
FAM25C
DRGX
RPL13AP6
MEIG1
LINC00264
LOC650623
PTPN20A
ANXA8
AGAP7
ASAH2B
SFTPA1
DUX4L7
DUX4L6
DUX4L5
DUX4L3
TMEM236
SNORA12
SNORD98
MIR603
MIR604
MIR605
MIR608
MIR609
BMS1P1
ANXA8L1
FAM22A
FAM22D
LOC728190
LOC728218
AGAP8
LOC728407
DUX4L2
LOC728558
LOC728640
LOC728643
FRMPD2P1
LOC728978
LOC729020
AGAP5
BMS1P4
SFTPA2
LOC729668
LOC731789
TLX1NB
MIR936
MIR938
C10orf131
LOC100128054
LOC100128098
LOC100128292
LOC100128511
LOC100128811
LOC100129055
LOC100129213
ZNF37BP
LOC100130992
ZNF503-AS2
FAM25B
LOC100132987
FAM25G
LOC100133308
KLLN
PRINS
LOC100169752
LOC100188947
DNMBP-AS1
LOC100192204
LOC100216001
TIMM23
MTRNR2L7
LOC100288974
LOC100289509
MIR1265
MIR1915
MIR1287
MIR1296
MIR1256
MIR1307
MIR2110
FAS-AS1
MIR378C
MIR4297
MIR3157
MIR4294
MIR3158-1
MIR4295
MIR3156-1
MIR3155A
MIR3158-2
MIR4296
MTRNR2L5
LOC100499489
MIR3924
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505583
LOC100505761
LOC100505839
LOC100505933
LOC100506733
LOC100506835
LOC100506939
M1
LOC100507034
LOC100507127
LOC100507331
LOC100507470
LOC100507605
MARK2P9
C10orf32-AS3MT
COMMD3-BMI1
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4480
MIR4483
MIR4679-2
MIR4676
MIR4678
MIR4682
MIR4482-1
MIR4484
MIR4675
MIR4681
MIR4685
MIR4683
MIR3155B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q22.2.

Table S29. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BLM
BUB1B
IDH2
NTRK3
PML
TCF12
CRTC3
FLJ27352
C15orf55
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
ACAN
ALDH1A3
ANPEP
ANXA2
APBA2
AQP9
B2M
BBS4
BCL2A1
NBEAP1
BNC1
BNIP2
CA12
CAPN3
CHD2
CHRM5
CHRNA3
CHRNA5
CHRNA7
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FES
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IDH3A
IGF1R
IL16
IPW
IREB2
ISG20
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2A2
MAN2C1
MAP1A
MEF2A
MEIS2
MFAP1
MFGE8
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
NMB
OAZ2
OCA2
FURIN
PCSK6
PDE8A
PKM2
PLCB2
PLIN1
POLG
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SH3GL3
SLC12A1
SNRPA1
SNRPN
SNX1
SORD
SPINT1
SRP14
NR2F2
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
UBE3A
MKRN3
SLC30A4
AP3B2
PAR5
ANP32A
ST8SIA2
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
PEX11A
IQGAP1
ALDH1A2
HERC2
HERC1
SNURF
PSTPIP1
PRC1
USP8
CCNB2
SLC28A2
SLC28A1
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
SV2B
ARNT2
USP3
SLC12A6
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
RASGRP1
SERF2
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
SLC27A2
ABHD2
ADAMTS7
AKAP13
GPR176
CHP
OIP5
ITGA11
CHSY1
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
CYFIP1
ACSBG1
KIAA1024
MGA
DMXL2
SYNM
VPS39
FAM189A1
TMED3
AP4E1
SEC11A
CCNDBP1
DAPK2
EID1
C15orf2
GABARAPL3
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
VPS33B
GREM1
MRPL46
OR4F4
NPTN
FOXB1
RPUSD2
TUBGCP4
SLCO3A1
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
HDGFRP3
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
RASL12
SPG21
SPTBN5
NGRN
RHCG
PTPLAD1
CTDSPL2
KLF13
RAB8B
BTBD1
TM6SF1
DUOX1
CSNK1G1
ZFAND6
MAGEL2
DLL4
SCAND2
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZNF770
ZSCAN2
ZWILCH
FLJ10038
DET1
UACA
HAUS2
FAM82A2
LINS
DNAJC17
FANCI
IMP3
LARP6
MNS1
DNAJA4
NOP10
MCTP2
SELS
GOLGA6B
MESP1
UNC45A
MYO5C
NDNL2
FAM214A
C15orf24
C15orf39
THAP10
PAK6
RGMA
WDR93
PARP6
DTWD1
CASC5
AVEN
C15orf17
ADAMTSL3
ATP10A
KIAA1199
GJD2
STARD9
ALPK3
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
ZFP106
KLHL25
CPEB1
AEN
IQCH
ISL2
RFX7
TTC23
MRPS11
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
LRRK1
AAGAB
LMAN1L
C15orf29
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
AGSK1
SPG11
TM2D3
ELL3
PLEKHO2
WDR61
CD276
STARD5
POLR2M
C15orf44
NIPA2
C15orf5
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
WDR73
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf42
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
RCCD1
LOC91450
CALML4
ARRDC4
LOC91948
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
C15orf40
SENP8
MTFMT
OSTBETA
TARSL2
HIGD2B
LRRC28
C15orf27
NIPA1
AGBL1
AGPHD1
WHAMM
FSD2
PLA2G4E
ASB7
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
LYSMD4
FAM81A
GCOM1
LOC145783
PGPEP1L
LOC145820
LOC145837
LOC145845
C15orf61
C15orf32
HAPLN3
MESP2
TMCO5A
SPATA8
NRG4
LINC00052
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
ADAMTS17
RHOV
SCAMP5
C15orf33
DNM1P46
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
CERS3
SPESP1
LOC253044
LPCAT4
LOC254559
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
HMGN2P46
SLC24A5
PRTG
LOC283663
LINC00277
C15orf60
LOC283683
C15orf37
LOC283688
LOC283692
LOC283693
OR4N4
LOC283710
FAM154B
LOC283731
LOC283738
FAM98B
PLA2G4D
HERC2P3
LOC283761
GOLGA6L1
GOLGA8G
FAM169B
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
TMEM202
LOC338963
WHAMMP3
POTEB
GLDN
GOLGA6A
TMC3
ZNF774
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
C15orf38
LOC348120
MRPL42P5
USP50
TEX9
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
LOC388152
UBE2Q2P1
FLJ42289
GOLGA8E
OR4M2
OR4N3P
KBTBD13
UBAP1L
SKOR1
ANKRD34C
C15orf58
OR4F6
OR4F15
LOC390660
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
ST20
FAM174B
LOC400456
DUOXA2
MIR184
MIR190A
MIR211
MIR7-2
MIR9-3
C15orf50
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
LOC503519
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC645752
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
SH2D7
LOC646938
GOLGA6L10
LOC648809
LOC653061
LOC653075
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA15
SCARNA14
FBXO22-AS1
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727849
LOC727915
LOC727924
ASB9P1
LOC728758
OIP5-AS1
LOC729739
GOLGA8C
LOC729911
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
FAM138E
MIR147B
DNM1P35
LOC100128714
LOC100129387
LOC100130855
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
UBE2Q2P3
UBE2Q2P2
JMJD7
PLA2G4B
LOC100144604
GPCRLTM7
DDX11L1
LOC100287559
LOC100287616
ULK4P2
DDX11L9
LOC100288615
LOC100288637
LOC100289656
MIR1276
MIR1233-1
MIR1272
MIR1266
MIR1179
MIR1282
MIR1469
LOC100306975
MIR548H4
MIR2116
MIR1233-2
MIR4311
MIR4312
MIR3175
MIR4310
MIR4313
MIR3942
RPS17L
LOC100505648
LOC100505679
LOC100506686
LOC100506874
LOC100507217
LOC100507466
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4514
MIR4513
MIR4509-1
MIR4509-2
MIR3529
MIR4508
MIR4510
MIR4716
MIR4713
MIR4511
MIR4509-3
MIR4712
MIR4515
MIR4714
MIR4715
TMCO5B
MYZAP

Arm-level results

Table 3. Get Full Table Arm-level significance table - 9 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 | 2121 | 0.07 | -0.958 | 0.989 | 0.26 | 1.28 | 0.463
1q | 1955 | 0.35 | 1.75 | 0.232 | 0.21 | 0.261 | 0.802
2p | 924 | 0.24 | -1.21 | 0.989 | 0.19 | -1.56 | 0.945
2q | 1556 | 0.17 | -0.908 | 0.989 | 0.12 | -1.34 | 0.945
3p | 1062 | 0.25 | -0.425 | 0.989 | 0.84 | 4.48 | 0.000151
3q | 1139 | 0.64 | 2.1 | 0.206 | 0.69 | 2.71 | 0.0453
4p | 489 | 0.30 | -0.997 | 0.989 | 0.59 | 1.09 | 0.463
4q | 1049 | 0.17 | -1.36 | 0.989 | 0.44 | 0.803 | 0.603
5p | 270 | 0.64 | 1.09 | 0.511 | 0.55 | 0.318 | 0.802
5q | 1427 | 0.17 | -0.904 | 0.989 | 0.44 | 1.51 | 0.463
6p | 1173 | 0.25 | -0.597 | 0.989 | 0.47 | 1.22 | 0.463
6q | 839 | 0.27 | -0.999 | 0.989 | 0.31 | -0.656 | 0.945
7p | 641 | 0.56 | 1.08 | 0.511 | 0.36 | -0.439 | 0.945
7q | 1277 | 0.53 | 1.94 | 0.212 | 0.27 | -0.281 | 0.945
8p | 580 | 0.62 | 1.49 | 0.342 | 0.40 | -0.257 | 0.945
8q | 859 | 0.80 | 3.77 | 0.00326 | 0.00 | -1.6 | 0.945
9p | 422 | 0.15 | -2.28 | 0.989 | 0.39 | -0.685 | 0.945
9q | 1113 | 0.43 | 0.681 | 0.68 | 0.43 | 0.681 | 0.661
10p | 409 | 0.38 | -0.63 | 0.989 | 0.47 | -0.0402 | 0.897
10q | 1268 | 0.29 | -0.225 | 0.989 | 0.38 | 0.529 | 0.702
11p | 862 | 0.10 | -1.87 | 0.989 | 0.53 | 1.23 | 0.463
11q | 1515 | 0.00 | -2.18 | 0.989 | 0.35 | 0.826 | 0.603
12p | 575 | 0.59 | 1.22 | 0.494 | 0.30 | -0.9 | 0.945
12q | 1447 | 0.12 | -1.39 | 0.989 | 0.22 | -0.552 | 0.945
13q | 654 | 0.36 | -0.423 | 0.989 | 0.56 | 1.1 | 0.463
14q | 1341 | 0.50 | 1.74 | 0.232 | 0.33 | 0.251 | 0.802
15q | 1355 | 0.12 | -1.51 | 0.989 | 0.22 | -0.7 | 0.945
16p | 872 | 0.36 | -0.226 | 0.989 | 0.40 | 0.107 | 0.832
16q | 702 | 0.31 | -0.806 | 0.989 | 0.44 | 0.159 | 0.832
17p | 683 | 0.40 | -0.168 | 0.989 | 0.36 | -0.487 | 0.945
17q | 1592 | 0.33 | 0.774 | 0.675 | 0.14 | -0.955 | 0.945
18p | 143 | 0.44 | -0.459 | 0.989 | 0.69 | 1.33 | 0.463
18q | 446 | 0.12 | -1.93 | 0.989 | 0.63 | 1.46 | 0.463
19p | 995 | 0.27 | -0.783 | 0.989 | 0.31 | -0.427 | 0.945
19q | 1709 | 0.21 | -0.16 | 0.989 | 0.35 | 1.18 | 0.463
20p | 355 | 0.72 | 2.04 | 0.206 | 0.29 | -1.04 | 0.945
20q | 753 | 0.68 | 2.44 | 0.145 | 0.14 | -1.43 | 0.945
21q | 509 | 0.60 | 0.658 | 0.68 | 0.88 | 3.55 | 0.00382
22q | 921 | 0.50 | 0.945 | 0.574 | 0.46 | 0.625 | 0.665
Xq | 1312 | 0.33 | 0.256 | 0.989 | 0.14 | -1.32 | 0.945

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.

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/ESCA-TP/2841328/2.GDAC_MergeDataFiles.Finished/ESCA-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_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.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

Table 4. Get Full Table First 10 out of 20 Input Tumor Samples.

Tumor Sample Names
TCGA-IG-A3I8-01A-11D-A246-01
TCGA-IG-A3QL-01A-11D-A246-01
TCGA-IG-A3Y9-01A-12D-A246-01
TCGA-IG-A3YA-01A-11D-A246-01
TCGA-IG-A3YB-01A-11D-A246-01
TCGA-IG-A3YC-01A-11D-A246-01
TCGA-L5-A43C-01A-11D-A246-01
TCGA-L5-A43E-01A-11D-A246-01
TCGA-L5-A43H-01A-11D-A246-01
TCGA-L5-A43I-01A-11D-A246-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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