Skin Cutaneous Melanoma: Copy number analysis (GISTIC2)
(WT 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 35 tumor samples used in this analysis: 16 significant arm-level results, 12 significant focal amplifications, and 8 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 - 12 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
--- | --- | --- | --- | ---
5p15.33 | 0.00036086 | 0.00036086 | chr5:1287541-1300024 | 1
11q13.3 | 0.00036086 | 0.00059908 | chr11:69150824-71070966 | 13
12q14.1 | 0.001442 | 0.001442 | chr12:58135797-58287201 | 12
1p12 | 0.0034191 | 0.0034191 | chr1:119929443-149882013 | 95
4q12 | 0.0088139 | 0.0088139 | chr4:54677084-55102558 | 4
22q13.1 | 0.018493 | 0.018493 | chr22:39065583-39085890 | 3
1q44 | 0.020124 | 0.020124 | chr1:245627602-247069231 | 8
Xq28 | 0.1179 | 0.1179 | chrX:149527988-151248667 | 17
8q11.21 | 0.13957 | 0.13957 | chr8:42932479-70954271 | 105
5q35.3 | 0.17895 | 0.17895 | chr5:177884788-179704902 | 29
17q25.3 | 0.21877 | 0.21877 | chr17:78484485-81195210 | 78
11q13.3 | 0.00036086 | 1 | chr11:1-135006516 | 1478

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

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

Genes
TERT

Genes in Wide Peak

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

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

Genes
CCND1
hsa-mir-548k
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
SHANK2
ANO1
ORAOV1
MIR548K
MIR3664

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
hsa-mir-26a-2
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
METTL21B
MARCH9
AGAP2
MIR26A2

Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
PDE4DIP
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
HMGCS2
HSD3B1
HSD3B2
PDZK1
PRKAB2
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
ITGA10
PEX11B
SEC22B
CHD1L
SV2A
RBM8A
PIAS3
POLR3C
TXNIP
ADAM30
CD160
NBPF14
PHGDH
RNF115
BOLA1
HAO2
ACP6
GPR89B
FAM91A2
REG4
POLR3GL
ZNF697
GNRHR2
HIST2H3C
LIX1L
HSD3BP4
HFE2
ANKRD35
PPIAL4A
PDIA3P
NBPF11
NUDT17
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
NBPF7
LOC375010
NOTCH2NL
FLJ39739
LOC388692
NBPF9
HIST2H2BF
HIST2H4B
LOC644242
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100289211

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
PDGFRA
CHIC2
GSX2
RPL21P44

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q13.1.

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

Genes
JOSD1
CBY1
TOMM22

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q44.

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

Genes
AHCTF1
SCCPDH
KIF26B
TFB2M
SMYD3
LOC149134
CNST
LOC255654

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

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

Genes
hsa-mir-452
hsa-mir-4330
CNGA2
GABRE
HMGB3
MAGEA4
MTM1
MTMR1
GPR50
MAMLD1
PRRG3
CD99L2
FATE1
PASD1
VMA21
MIR452
MIR4330

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.21.

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

Genes
PLAG1
TCEA1
CHCHD7
hsa-mir-124-2
ASPH
CA8
CEBPD
CRH
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SULF1
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
SLCO5A1
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100287846
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

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

Genes
hsa-mir-340
hsa-mir-1229
CANX
GRM6
HNRNPH1
LTC4S
MAPK9
ZNF354A
SQSTM1
ADAMTS2
MAML1
MGAT4B
TBC1D9B
ZNF354C
C5orf45
RNF130
CLK4
ZFP2
RUFY1
COL23A1
ZNF354B
RASGEF1C
ZNF454
C5orf60
ZNF879
MIR340
CBY3
AACSP1
MIR1229

Genes in Wide Peak

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

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

Genes
ASPSCR1
hsa-mir-3186
hsa-mir-1250
ACTG1
ARHGDIA
CD7
CSNK1D
SLC25A10
FASN
GCGR
UTS2R
GPS1
FOXK2
MAFG
P4HB
PDE6G
PYCR1
PCYT2
RAC3
RFNG
MRPL12
SECTM1
TBCD
SLC16A3
HGS
AATK
ALYREF
BAIAP2
RAB40B
AZI1
FSCN2
NARF
DCXR
ANAPC11
SIRT7
NPLOC4
WDR45L
RPTOR
BAHCC1
DUS1L
FN3K
C17orf62
CHMP6
FN3KRP
C17orf101
ZNF750
C17orf70
TSPAN10
MAFG-AS1
PPP1R27
SLC38A10
C17orf56
B3GNTL1
NOTUM
STRA13
LRRC45
MYADML2
NPB
CCDC57
HEXDC
C17orf89
LINC00482
TMEM105
METRNL
C17orf90
CCDC137
ARL16
FAM195B
AATK-AS1
FLJ43681
TEX19
FLJ90757
MIR338
MIR657
MIR1250
MIR3065
MIR3186
MIR4740

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CCND1
CARS
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
HRAS
LMO1
LMO2
MEN1
MLL
NUMA1
NUP98
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
hsa-mir-3163
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-3162
hsa-mir-130a
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ACAT1
ACP2
ACRV1
ACTN3
ADM
ADRBK1
AP2A2
APLNR
ALDH3B1
ALDH3B2
AMPD3
APBB1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
RHOG
ARHGAP1
PHOX2A
ARL2
ARNTL
ARRB1
ART1
ASCL2
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CCKBR
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
TPP1
CLNS1A
CNGA4
CNTF
COPB1
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSD
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GTF2H1
GUCY1A2
H2AFX
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HMBS
SLC29A2
HPX
HSPA8
HSPB2
DNAJC4
HTR3A
IGF2
IGHMBP2
IL10RA
IL18
ILK
INCENP
INS
INPPL1
IRF7
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KCNQ1
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LSP1
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MUC2
MUC6
MYBPC3
MYO7A
MYOD1
NAP1L4
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
NUCB2
OMP
OPCML
SLC22A18
SLC22A18AS
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PDE3B
PGA5
PGR
PIK3C2A
PLCB3
POLR2G
POLR2L
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PSMA1
PSMC3
PSMD13
PTH
PTPRCAP
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
RNH1
SNORD15A
ROM1
MRPL23
RPL27A
RPLP2
RPS3
RPS6KB2
RPS13
RPS25
RRM1
SAA1
SAA2
SAA3P
SAA4
SC5DL
SCN2B
SCN4B
SCT
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SMPD1
SORL1
SPI1
SPTBN2
SRPR
TRIM21
SSRP1
ST5
ST14
STIM1
STX3
STX5
ABCC8
TAGLN
TAF10
TALDO1
TCN1
TEAD1
TECTA
TH
THRSP
THY1
TSPAN4
TM7SF2
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TRPC6
TSG101
PHLDA2
TUB
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WEE1
WNT11
SF1
ZFPL1
ZNF143
ZBTB16
ZNF195
ZNF202
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIBP2
PPFIA1
SLC43A1
IFITM1
DGKZ
CHST1
BARX2
API5
MADD
OR7E2P
OR6A2
DCHS1
EIF3F
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
BRSK2
AIP
SYT7
SART1
USP2
SLC6A5
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MED17
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
MICAL2
CTR9
CEP57
ARHGAP32
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
TRIM66
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
TSPAN32
TSSC4
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
MRVI1
TRIM22
PRG3
IFITM3
YAP1
SPON1
RBM14
CDC42EP2
EIF3M
NXF1
DEAF1
KAT5
HYOU1
IPO7
SSSCA1
HTATIP2
IFITM2
DRAP1
TRIM3
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
OR7E14P
OR7E12P
NEU3
ME3
GPR83
LYVE1
YIF1A
SRSF8
EHD1
C11orf58
STIP1
CLP1
KCNQ1OT1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
PKP3
HPS5
PTGDR2
SLCO2B1
RRAS2
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
SWAP70
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
DENND5A
NUP160
NCAPD3
FNBP4
RRP8
SIK3
SIRT3
CLCF1
OR52A1
VSIG2
BACE1
FAM89B
SNHG1
ARFIP2
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
C11orf41
PRDX5
POU2F3
ABTB2
BRMS1
C11orf20
CHRDL2
PAMR1
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
PPP1R14B
OR8G2
OR8B8
OR8G1
OR10A3
FXC1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
ACAD8
B3GAT1
DKK3
RBMXL2
RAB30
PGAP2
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
COMMD9
DDX25
C11orf21
PACSIN3
TRPM5
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
UBQLN3
KCNK4
RNF141
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
IGF2-AS1
TMEM216
BET1L
CEND1
CHCHD8
SLC15A3
PHF21A
MS4A4A
WT1-AS
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
CYB5R2
RSF1
SPA17
FXYD6
C11orf24
TRIM34
CDHR5
CNTN5
SIAE
TOLLIP
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39A
TRIM44
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
USP47
VPS37C
ANO1
TRIM68
NADSYN1
FAM86C1
C11orf57
NAT10
CCDC87
PPP6R3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
PIDD
ELMOD1
KCNQ1DN
SOX6
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
PARVA
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
MMP26
TMPRSS4
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
GPR137
IFT46
C11orf75
C11orf30
PRDM10
PRDM11
CABP4
CHRNA10
SLC17A6
TRIM49
PNPLA2
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
CARNS1
SYT13
USP28
PHRF1
LRRC4C
SCUBE2
POLD4
KRTAP5-8
PLEKHB1
MS4A7
ZBED5
CREBZF
CARD18
SIGIRR
CCDC90B
CCDC81
AASDHPPT
ALX4
RIC8A
MRPL17
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
EPS8L2
KLC2
TUT1
MRPL11
TMEM135
STK33
KCTD14
C11orf95
CHID1
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
OR51G1
OR51B4
OR51B2
OR52N1
FAM118B
RIC3
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
E2F8
SLC25A22
CCDC82
ALG9
ZNF408
CLMP
NAA40
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
ATHL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
PTDSS2
MOB2
GDPD5
CLPB
UNC93B1
SBF2
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
FAM160A2
RNASEH2C
FAR1
TMEM126A
DCUN1D5
BTBD10
EIF1AD
NUDT22
ARFGAP2
KIAA1826
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
SPRYD5
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
MICALCL
RELT
UBASH3B
C11orf70
LGALS12
TRIM5
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
NAV2
ATG16L2
GLB1L2
SYT8
TSPAN18
ESAM
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
PRKCDBP
VPS26B
GLB1L3
CDCA5
RPLP0P2
SAAL1
ODF3
SLC22A9
SNORD15B
TIRAP
CARD16
OSBPL5
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
LRRC56
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRE
MRGPRF
ART5
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
SLC36A4
FAT3
TRIM64
TMEM45B
CYP2R1
DBX1
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
LOC120824
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
XRRA1
UBQLNL
MUC15
LOC143666
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
C11orf42
GPHA2
ADAMTS15
NLRP6
NS3BP
B3GNT6
METTL15
MPZL3
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
MRPL21
TPCN2
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
PPP1R32
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
LOC254100
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
TMEM151A
OR51F1
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
KRT8P41
LOC283104
CSNK2A1P
OR51V1
LOC283116
H19
C11orf85
SLC25A45
NEAT1
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
OR9G4
LOC283194
LINC00301
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
EFCAB4A
TMEM80
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
OR10A2
OVCH2
TBX10
PDDC1
C11orf34
RTN4RL2
GALNTL4
B7H6
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
KRTAP5-10
SLC22A25
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
SLC22A10
SPDYC
LIPT2
VSTM5
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
NAV2-AS4
HNRNPKP3
FAM180B
PCNXL3
FLJ42102
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
OR4C45
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR210
MIR34B
MIR34C
DDI1
BLID
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
LOC440040
LOC440041
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
LINC00167
LOC441601
OR5B3
MIR326
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
MS4A13
OR8U8
OR9G9
SCARNA9
MIR483
SNORA3
SNORA52
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
BTBD18
LOC643733
PGA3
PGA4
LOC643923
LOC644656
CLDN25
RASSF10
FAM86C2P
TRIM64C
LOC646813
LOC649133
RPL23AP64
LOC650368
LOC653486
SNORA8
SNORA1
SNORA18
SNORA23
SNORA40
SNORA45
SNORA54
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
SNORD97
MIR610
MIR611
MIR612
INS-IGF2
MUC5B
LOC729013
TRIM49L1
LOC729799
METTL12
C11orf83
MIR675
MIR708
LOC100126784
LOC100128239
LOC100129216
MRVI1-AS1
LOC100130348
LOC100130987
C11orf91
LOC100132078
FAM99B
LOC100133161
LOC100133315
MRPL23-AS1
PATE3
LOC100288077
LOC100288346
MIR1304
MIR1908
MIR1237
MIR548K
MIR670
SNORA70E
BACE1-AS
MIR4300
MIR3160-2
MIR3160-1
MIR4301
MIR3162
MIR3167
MIR3165
MIR1260B
MIR4298
MIR4299
MTRNR2L8
LOC100499227
MIR3654
MIR3920
MIR3656
MIR3664
MIR3680-1
LOC100500938
MIR210HG
LOC100506233
LOC100506305
LOC100506368
LOC100506540
DCDC5
CASP12
LOC100507050
LOC100507205
LOC100507300
LOC100507392
LOC100507401
RBM14-RBM4
LOC100526771
TMX2-CTNND1
SAA2-SAA4
ARL2-SNX15
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
HNRNPUL2-BSCL2
MIR4486
MIR4697
MIR4686
MIR4490
MIR4485
MIR4489
MIR4690
MIR3973
MIR4493
MIR4491
MIR4688
MIR4492
MIR4696
MIR4691
MIR4692
MIR4694
MIR1343
MIR4687
MIR4693
MIR4488
LOC100652768

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 - 8 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 | 4.7668e-08 | 4.7668e-08 | chr9:21959052-22448737 | 4
2q37.3 | 0.0030414 | 0.0030414 | chr2:239007902-243199373 | 64
15q14 | 0.0030414 | 0.0030414 | chr15:27109052-50795834 | 233
11q23.2 | 0.003312 | 0.003312 | chr11:102979829-135006516 | 292
10q26.3 | 0.021422 | 0.021531 | chr10:105229749-135534747 | 214
4q34.3 | 0.035785 | 0.038018 | chr4:156262946-183068969 | 83
16p13.3 | 0.11518 | 0.10894 | chr16:5144019-7771745 | 1
5p15.31 | 0.11816 | 0.11816 | chr5:1-43319646 | 179

Genes in Wide Peak

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

Table S13. 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 2q37.3.

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
HDAC4
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
TRAF3IP1
ANO7
THAP4
ANKMY1
ASB1
HES6
RNPEPL1
GAL3ST2
C2orf54
ILKAP
ING5
MGC16025
TWIST2
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LOC200772
CXXC11
DUSP28
ESPNL
AQP12A
KLHL30
OR6B2
FLJ43879
MIR149
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q14.

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

Genes
BUB1B
C15orf55
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
ACTC1
APBA2
B2M
CAPN3
CHRM5
CHRNA7
CKMT1B
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
OCA2
PLCB2
RAD51
RYR3
SCG5
SLC12A1
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
FAM189A1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
DTWD1
CASC5
AVEN
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
HMGN2P46
SLC24A5
LOC283710
FAM98B
PLA2G4D
GOLGA8G
FMN1
MRPL42P5
C15orf52
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
MIR211
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC646278
LOC653075
MIR626
MIR627
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100129387
LOC100131089
ANKRD63
GOLGA8F
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4510
MIR4716
MIR4509-3
MIR4712
TMCO5B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

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

Genes
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100128239
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
FGFR2
DUX4
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
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
BNIP3
CASP7
COL17A1
CTBP2
CYP2E1
DMBT1
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
PRLHR
GPR26
GRK5
HABP2
HMX2
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NRAP
OAT
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PTPRE
RGS10
SLC18A2
TCF7L2
TECTB
TIAL1
UROS
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
SMC3
NEURL
BUB3
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
DCLRE1A
SMNDC1
GLRX3
DPYSL4
TACC2
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
SORCS3
FAM175B
ATRNL1
C10orf137
DUX2
PDCD4
VENTX
CUZD1
CALY
CHST15
ACSL5
ZRANB1
TTC40
NSMCE4A
C10orf118
WDR11
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
GPAM
KIAA1598
FAM160B1
PLEKHA1
FAM204A
LHPP
IKZF5
ZDHHC6
MCMBP
C10orf81
OBFC1
C10orf88
WDR96
LRRC27
GPR123
NKX6-2
AFAP1L2
KNDC1
ITPRIP
MTG1
BBIP1
FANK1
SYCE1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
PDZD8
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CASC2
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
RBM20
LOC282997
LOC283038
LOC283089
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
FAM45A
FRG2B
SPRN
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
MIR609
DUX4L2
MIR936
LOC100169752
MIR2110
MIR378C
MIR4297
MIR4295
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505839
LOC100505933
FAM24B-CUZD1
MIR4680
MIR4483
MIR4682
MIR4482-1
MIR4484
MIR4681

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
AGA
CLCN3
CPE
CTSO
ETFDH
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
NEK1
NPY1R
NPY5R
PPID
MSMO1
TDO2
TLL1
VEGFC
GLRA3
SAP30
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
ANP32C
FBXO8
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
DDX60
PDGFC
FSTL5
FNIP2
SH3RF1
RXFP1
SPCS3
NBLA00301
MAP9
CEP44
TKTL2
CBR4
MGC45800
DDX60L
NAF1
WDR17
SPATA4
ASB5
C4orf39
C4orf45
TRIM60
C4orf46
TMEM192
LOC285501
LOC340017
TRIM61
HSP90AA6P
GALNTL6
MIR578
LINC00290
MIR4276
MIR3688-1
LOC100505989
LOC100506013
LOC100506085
LOC100506122
MIR3688-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

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

Genes
RBFOX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p15.31.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
C6
C7
C9
CDH6
CDH9
CDH10
CDH12
CDH18
CTNND2
DAB2
DAP
DNAH5
FYB
GDNF
GHR
HMGCS1
IL7R
MTRR
MYO10
NDUFS6
NPR3
OXCT1
PMCHL1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SDHA
SEPP1
SKP2
SLC1A3
SLC6A3
SLC9A3
SRD5A1
TARS
TERT
TRIO
ZNF131
SEMA5A
OSMR
TRIP13
NUP155
PDCD6
MARCH6
BASP1
SLC12A7
SUB1
PAPD7
TPPP
EXOC3
CCT5
PDZD2
FBXL7
KIAA0947
TTC33
AMACR
NIPBL
PP7080
RAI14
FBXO4
DROSHA
IRX4
TAS2R1
SLC45A2
RXFP3
ZFR
FAM134B
FAM105A
MTMR12
NSUN2
WDR70
BRIX1
C5orf22
CEP72
ANKH
PRDM9
AHRR
GOLPH3
AGXT2
MRPL36
C5orf42
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
SPEF2
CLPTM1L
ADAMTS12
ROPN1L
MED10
CARD6
NKD2
FAM105B
ZNF622
LMBRD2
C1QTNF3
C5orf55
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
DNAJC21
PLEKHG4B
C5orf38
IRX2
TTC23L
LOC153684
UGT3A2
NIM1
ADAMTS16
RANBP3L
RICTOR
LOC255167
LOC285577
C5orf51
LOC285692
LOC285696
SLC6A19
LOC340094
LOC340107
LOC340113
PLCXD3
SLC6A18
LRRC14B
C5orf39
FLJ33360
LOC401177
TAG
MARCH11
LOC442132
SNORD72
LOC643401
LOC646719
LOC648987
ANKRD33B
MIR580
GUSBP1
SDHAP3
LOC728613
LOC729506
LOC729862
SNORD123
CCDC152
LOC100130744
LOC100132356
MIR4279
MIR4277
MIR4278
MIR3650
LOC100505738
LOC100505806
LOC100506548
LOC100506688
C1QTNF3-AMACR
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635
EGFLAM-AS4

Arm-level results

Table 3. Get Full Table Arm-level significance table - 16 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 | 0.23 | 0.256 | 0.993 | 0.18 | -0.459 | 0.974
1q | 1955 | 0.50 | 3.87 | 0.00123 | 0.16 | -0.633 | 0.974
2p | 924 | 0.14 | -1.21 | 0.993 | 0.23 | -0.191 | 0.974
2q | 1556 | 0.14 | -1.14 | 0.993 | 0.19 | -0.439 | 0.974
3p | 1062 | 0.16 | -1.08 | 0.993 | 0.10 | -1.77 | 0.974
3q | 1139 | 0.19 | -0.643 | 0.993 | 0.10 | -1.68 | 0.974
4p | 489 | 0.31 | 0.679 | 0.904 | 0.33 | 1 | 0.635
4q | 1049 | 0.19 | -0.641 | 0.993 | 0.27 | 0.372 | 0.788
5p | 270 | 0.17 | -1.11 | 0.993 | 0.17 | -1.11 | 0.974
5q | 1427 | 0.17 | -0.817 | 0.993 | 0.17 | -0.817 | 0.974
6p | 1173 | 0.52 | 3.58 | 0.00173 | 0.30 | 0.686 | 0.704
6q | 839 | 0.16 | -0.859 | 0.993 | 0.50 | 3.4 | 0.0067
7p | 641 | 0.52 | 3.58 | 0.00173 | 0.11 | -1.33 | 0.974
7q | 1277 | 0.52 | 3.84 | 0.00123 | 0.11 | -1.22 | 0.974
8p | 580 | 0.39 | 1.77 | 0.19 | 0.29 | 0.495 | 0.754
8q | 859 | 0.45 | 2.85 | 0.0145 | 0.10 | -1.48 | 0.974
9p | 422 | 0.12 | -1.27 | 0.993 | 0.55 | 3.89 | 0.00199
9q | 1113 | 0.09 | -1.61 | 0.993 | 0.39 | 2.13 | 0.0944
10p | 409 | 0.00 | -2.46 | 0.993 | 0.49 | 3.19 | 0.00954
10q | 1268 | 0.00 | -2.46 | 0.993 | 0.43 | 2.74 | 0.0247
11p | 862 | 0.10 | -1.57 | 0.993 | 0.42 | 2.45 | 0.048
11q | 1515 | 0.05 | -1.89 | 0.993 | 0.44 | 2.97 | 0.0148
12p | 575 | 0.27 | 0.235 | 0.993 | 0.19 | -0.757 | 0.974
12q | 1447 | 0.17 | -0.812 | 0.993 | 0.17 | -0.812 | 0.974
13q | 654 | 0.23 | -0.185 | 0.993 | 0.31 | 0.799 | 0.704
14q | 1341 | 0.11 | -1.56 | 0.993 | 0.22 | -0.168 | 0.974
15q | 1355 | 0.24 | 0.133 | 0.993 | 0.21 | -0.21 | 0.974
16p | 872 | 0.04 | -2.35 | 0.993 | 0.29 | 0.715 | 0.704
16q | 702 | 0.05 | -2.18 | 0.993 | 0.38 | 1.86 | 0.158
17p | 683 | 0.24 | -0.067 | 0.993 | 0.34 | 1.24 | 0.479
17q | 1592 | 0.34 | 1.53 | 0.273 | 0.24 | 0.17 | 0.91
18p | 143 | 0.26 | 0.00539 | 0.993 | 0.15 | -1.3 | 0.974
18q | 446 | 0.17 | -1.07 | 0.993 | 0.17 | -1.07 | 0.974
19p | 995 | 0.07 | -2.08 | 0.993 | 0.21 | -0.361 | 0.974
19q | 1709 | 0.15 | -0.937 | 0.993 | 0.26 | 0.466 | 0.754
20p | 355 | 0.42 | 2.26 | 0.0675 | 0.10 | -1.66 | 0.974
20q | 753 | 0.47 | 3.07 | 0.0085 | 0.05 | -1.94 | 0.974
21q | 509 | 0.30 | 0.561 | 0.958 | 0.30 | 0.561 | 0.754
22q | 921 | 0.35 | 1.49 | 0.273 | 0.17 | -0.847 | 0.974
Xq | 1312 | 0.19 | -0.479 | 0.993 | 0.30 | 0.883 | 0.686

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/SKCM-WT/3154447/GDAC_MergeDataFiles_3154807/SKCM-WT.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 35 Input Tumor Samples.

Tumor Sample Names
TCGA-D3-A1Q3-06A-11D-A194-01
TCGA-D3-A2J6-06A-11D-A192-01
TCGA-D3-A2JB-06A-11D-A194-01
TCGA-D3-A2JC-06A-11D-A192-01
TCGA-D3-A3BZ-06A-12D-A194-01
TCGA-D3-A3C8-06A-12D-A192-01
TCGA-D3-A3CC-06A-11D-A192-01
TCGA-D3-A3CF-06A-11D-A194-01
TCGA-D9-A149-06A-11D-A194-01
TCGA-DA-A1IA-06A-11D-A194-01

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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