SNP6 Copy number analysis (GISTIC2)
Esophageal Carcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1W094JC
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1W094JC
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 103 tumor samples used in this analysis: 22 significant arm-level results, 24 significant focal amplifications, and 47 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 - 24 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 | 3.3985e-52 | 3.3985e-52 | chr11:69388908-70248899 | 11
8q24.21 | 7.0885e-22 | 7.0885e-22 | chr8:128140368-128582312 | 2
3q26.2 | 1.3876e-10 | 1.3876e-10 | chr3:160686437-198022430 | 239
17q12 | 5.7509e-09 | 5.7509e-09 | chr17:37737138-37930169 | 11
7q21.2 | 1.6295e-08 | 1.7549e-08 | chr7:91356821-95072746 | 35
6p21.1 | 1.0298e-06 | 1.0298e-06 | chr6:43582177-43989449 | 8
7p11.2 | 1.7571e-07 | 1.0071e-05 | chr7:54815172-55715052 | 4
18q11.2 | 0.00010896 | 0.00010896 | chr18:21245909-21940792 | 6
12p12.1 | 3.078e-05 | 0.00012943 | chr12:24880663-25593511 | 6
8p11.21 | 0.00031362 | 0.00031362 | chr8:42155813-42504952 | 6
1q21.3 | 0.0010923 | 0.0010923 | chr1:151439860-152096507 | 20
19q12 | 0.0015007 | 0.0015007 | chr19:29758040-30711180 | 7
19p13.2 | 0.0029514 | 0.0029514 | chr19:7296453-7398264 | 0 [INSR]
5p15.33 | 0.004831 | 0.004831 | chr5:1287541-1348797 | 3
11p13 | 0.015693 | 0.0172 | chr11:33546488-36024467 | 20
2q14.2 | 0.033221 | 0.033221 | chr2:122266853-122371509 | 2
1p34.2 | 0.046464 | 0.046464 | chr1:39565350-42557010 | 40
13q22.1 | 0.072261 | 0.072261 | chr13:73630621-74281406 | 2
9p13.3 | 0.086668 | 0.086668 | chr9:32240404-37795391 | 106
10p11.21 | 0.0996 | 0.0996 | chr10:34794460-35736943 | 4
12p13.33 | 0.042453 | 0.13564 | chr12:1-1071814 | 12
15q26.3 | 0.14801 | 0.14801 | chr15:88072718-102531392 | 110
18p11.32 | 0.15201 | 0.15201 | chr18:1-2916037 | 17
7p22.3 | 0.051148 | 0.23398 | chr7:1-22165420 | 135

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: Cancer Gene Census[7].

Genes
CCND1
hsa-mir-548k
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
ANO1
ORAOV1
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: Cancer Gene Census[7].

Genes
POU5F1B
LOC727677

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
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
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
CLDN11
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
SI
ST6GAL1
SKIL
SLC2A2
SST
TERC
THPO
SEC62
FXR1
TP63
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
NMD3
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
FYTTD1
ARPM1
MGC2889
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
RPL39L
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
PPM1L
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
SPTSSB
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LOC339926
LPP-AS2
LRRIQ4
SAMD7
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
TMEM212
FLJ46066
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
LOC646168
C3orf65
LOC647107
GMNC
LOC647323
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
GRB7
NEUROD2
PNMT
TCAP
STARD3
IKZF3
PPP1R1B
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
hsa-mir-489
hsa-mir-1285-1
CALCR
KRIT1
COL1A2
CYP51A1
GNG11
GNGT1
PEX1
PON1
PON2
PON3
MTERF
TFPI2
SGCE
BET1
PEG10
ANKIB1
SAMD9
PPP1R9A
CCDC132
GATAD1
CASD1
RBM48
MGC16142
SAMD9L
HEPACAM2
FAM133B
LRRD1
MIR489
MIR653
LOC728066
MIR4652

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
POLH
VEGFA
MAD2L1BP
GTPBP2
MRPS18A
C6orf223
RSPH9
LOC100132354

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: Cancer Gene Census[7].

Genes
EGFR
SEC61G
LANCL2
VOPP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
hsa-mir-320c-2
LAMA3
CABYR
OSBPL1A
TTC39C
MIR320C2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
C12orf77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
IKBKB
POLB
SLC20A2
VDAC3
DKK4
C8orf40

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
hsa-mir-554
RORC
S100A10
S100A11
TCHH
TUFT1
TDRKH
CELF3
OAZ3
CGN
MRPL9
SNX27
THEM4
TCHHL1
RIIAD1
THEM5
LINGO4
MIR554
LOC100132111
C2CD4D

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q12.

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

Genes
CCNE1
URI1
POP4
PLEKHF1
C19orf12
LOC284395
VSTM2B

Genes in Wide Peak

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

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

Genes
TERT
CLPTM1L
MIR4457

Genes in Wide Peak

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

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

Genes
LMO2
CAT
CD44
CD59
ELF5
CAPRIN1
SLC1A2
PDHX
FJX1
C11orf41
ABTB2
PAMR1
FBXO3
EHF
APIP
TRIM44
NAT10
LDLRAD3
C11orf91
MIR1343

Genes in Wide Peak

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

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

Genes
CLASP1
RNU4ATAC

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MYCL1
hsa-mir-30c-1
BMP8B
COL9A2
CTPS
EDN2
NFYC
PPT1
RLF
PABPC4
KCNQ4
RIMS3
ZMPSTE24
PPIE
CAP1
SCMH1
MACF1
HEYL
HPCAL4
TRIT1
HIVEP3
OXCT2
SMAP2
DEM1
ZNF643
NT5C1A
MFSD2A
TMCO2
ZNF684
CITED4
SLFNL1
ZNF642
BMP8A
MIR30C1
MIR30E
KIAA0754
SNORA55
PPIEL
LOC100130557
LOC100507178

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q22.1.

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

Genes
KLF5
KLF12

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
FANCG
PAX5
ACO1
ANXA2P2
NUDT2
AQP3
AQP7
BAG1
CA9
CCIN
CD72
CLTA
CNTFR
GALT
B4GALT1
DNAJA1
IL11RA
NDUFB6
NFX1
NPR2
PRSS3
RMRP
CCL19
CCL21
TESK1
TLN1
TPM2
VCP
RECK
GRHPR
RGP1
MELK
RUSC2
ZBTB5
GNE
TOPORS
SIGMAR1
CREB3
UNC13B
CCL27
PTENP1
DCTN3
FRMPD1
KIAA1045
DDX58
DNAJB5
DCAF12
SPAG8
FBXO10
DNAI1
SIT1
SPINK4
STOML2
EXOSC3
UBAP1
CHMP5
TMEM8B
APTX
UBE2R2
SMU1
UBAP2
OR2S2
KIAA1161
GBA2
POLR1E
NOL6
FAM214B
ZCCHC7
HINT2
C9orf24
PIGO
C9orf100
FP588
TAF1L
ARID3C
C9orf23
C9orf131
RNF38
GLIPR2
RG9MTD3
LOC158376
ATP8B5P
C9orf25
CCDC107
FAM205A
KIF24
ENHO
FAM205B
C9orf128
OR13J1
TMEM215
TOMM5
LOC415056
SUGT1P1
ANKRD18B
HRCT1
MSMP
FAM166B
SNORD121A
SNORD121B
LOC100129250
LOC100506710
MIR4667
MIR4540
MIR4475
MIR4476

Genes in Wide Peak

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

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

Genes
CREM
CUL2
PARD3
CCNY

Genes in Wide Peak

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

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

Genes
KDM5A
NINJ2
RAD52
SLC6A12
SLC6A13
WNK1
CCDC77
B4GALNT3
IQSEC3
LOC574538
FAM138D
LOC100288778

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
BLM
IDH2
NTRK3
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
ACAN
ALDH1A3
ANPEP
CHD2
FES
IGF1R
ISG20
MAN2A2
MEF2A
MFGE8
FURIN
PCSK6
PLIN1
POLG
RLBP1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
ABHD2
CHSY1
SYNM
GABARAPL3
VPS33B
MRPL46
OR4F4
SLCO3A1
NGRN
RHCG
DET1
LINS
FANCI
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
AEN
TTC23
MRPS11
LRRK1
TM2D3
C15orf42
RCCD1
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
ADAMTS17
DNM1P46
CERS3
LOC254559
LOC283738
LOC283761
FAM169B
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
WASH3P
FLJ42289
C15orf58
OR4F6
OR4F15
FAM174B
LOC400456
MIR7-2
MIR9-3
TTLL13
ASB9P1
FAM138E
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1179
MIR1469
MIR3175
LOC100507217
LOC100507472
C15orf38-AP3S2
MIR3529
MIR4714

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.32.

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

Genes
ADCYAP1
CETN1
TYMS
YES1
USP14
THOC1
NDC80
SMCHD1
CLUL1
ENOSF1
LINC00470
METTL4
COLEC12
EMILIN2
C18orf56
CBX3P2
ROCK1P1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.3.

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

Genes
ETV1
PMS2
CARD11
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ACTB
AHR
DGKB
GNA12
GPER
ICA1
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
DNAH11
CYTH3
PHF14
HDAC9
RAPGEF5
KIAA0415
ARL4A
AGR2
KDELR2
ADAP1
SNX13
IQCE
SUN1
SOSTDC1
WIPI2
INTS1
TSPAN13
EIF2AK1
BZW2
SNX8
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
TMEM106B
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
CDCA7L
RADIL
PAPOLB
C1GALT1
FAM20C
ANKMY2
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
C7orf70
SCIN
ZFAND2A
COX19
GLCCI1
KIAA1908
GPR146
AMZ1
AGR3
PER4
TMEM184A
VWDE
PRPS1L1
TWISTNB
SP8
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
FERD3L
RPL23P8
SLC29A4
RSPH10B
TMEM196
TFAMP1
UNCX
COL28A1
ABCB5
MACC1
LOC389458
ELFN1
AGMO
GRID2IP
ZNF815
RNF216P1
PMS2CL
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
MIR589
RSPH10B2
LOC729852
ISPD
LOC100131257
LOC100288524
MIR3146
LOC100506025
LRRC72
RBAK-LOC389458
MIR4648
MIR4655
MIR4656

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 - 47 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 | 6.7453e-79 | 6.7453e-79 | chr9:21865498-21997722 | 2
16q23.1 | 6.7059e-40 | 6.7059e-40 | chr16:78129058-79627770 | 1
7q31.1 | 8.2191e-19 | 4.6253e-16 | chr7:110725672-111366370 | 1
2q22.1 | 9.2681e-17 | 6.8983e-16 | chr2:139655617-143637838 | 1
Xp21.1 | 6.5274e-16 | 1.0097e-15 | chrX:30870233-32665140 | 3
4q22.1 | 6.8983e-16 | 5.9749e-15 | chr4:90844993-93240505 | 1
5q11.2 | 2.1271e-11 | 2.1271e-11 | chr5:58260298-59787985 | 3
6p25.3 | 7.102e-09 | 7.102e-09 | chr6:1608837-2252425 | 2
3p14.2 | 5.6948e-12 | 9.4765e-09 | chr3:59034763-61547330 | 1
18q21.2 | 4.6613e-08 | 4.9824e-07 | chr18:48351671-48705371 | 3
8p23.2 | 4.5433e-06 | 4.5433e-06 | chr8:2079140-6262191 | 1
10p11.21 | 7.546e-05 | 0.00025549 | chr10:34059131-35328087 | 1
1q44 | 0.00027447 | 0.00027447 | chr1:245864790-247052144 | 6
20p12.1 | 0.00036906 | 0.00036906 | chr20:14302876-16252980 | 3
11q24.3 | 0.00058395 | 0.00058395 | chr11:130014370-135006516 | 21
10q23.31 | 0.00051002 | 0.0012811 | chr10:89506488-92501260 | 31
18q12.2 | 1.7813e-05 | 0.0017895 | chr18:35235531-39060470 | 4
4p15.2 | 0.00049298 | 0.0023318 | chr4:20727465-22330985 | 2
19p13.3 | 0.0034003 | 0.0034003 | chr19:1-3363200 | 122
13q14.2 | 0.00089965 | 0.0039709 | chr13:48833767-49064807 | 2
1p13.2 | 0.0019368 | 0.0045158 | chr1:108505744-119913683 | 139
Xp11.3 | 0.0011218 | 0.005937 | chrX:44702452-45008304 | 2
3q26.31 | 0.010285 | 0.010285 | chr3:173999806-175760559 | 2
3p14.3 | 1.8081e-05 | 0.012458 | chr3:53923579-55500153 | 3
11p15.4 | 0.012525 | 0.012671 | chr11:3861173-4115961 | 2
7q36.2 | 1.6567e-07 | 0.013864 | chr7:148117946-159138663 | 104
2q33.3 | 0.0024351 | 0.016479 | chr2:204826225-206558638 | 1
Xq21.33 | 0.02636 | 0.02636 | chrX:96134519-98718611 | 1
3q11.1 | 0.0016423 | 0.038905 | chr3:77699023-93777876 | 16
17q25.3 | 0.014054 | 0.041749 | chr17:79820675-81195210 | 41
6q16.1 | 0.026403 | 0.048336 | chr6:66488949-119138282 | 222
6q26 | 0.012844 | 0.051922 | chr6:161693099-163153207 | 1
15q11.2 | 0.053601 | 0.051922 | chr15:1-31198928 | 157
1p36.13 | 0.033774 | 0.06023 | chr1:1-32831542 | 531
13q21.2 | 0.031577 | 0.083418 | chr13:54886106-69439763 | 15
21q11.2 | 0.081578 | 0.084738 | chr21:1-26218513 | 44
21q22.12 | 0.086636 | 0.093413 | chr21:36154821-36413738 | 2
4q21.23 | 0.008626 | 0.12197 | chr4:85927963-87517209 | 3
10q22.3 | 0.041235 | 0.12197 | chr10:77312101-78629541 | 2
22q12.3 | 0.13235 | 0.13235 | chr22:33448268-35462146 | 3
12q23.1 | 0.13454 | 0.13444 | chr12:71510065-133851895 | 454
19q13.31 | 0.13613 | 0.13444 | chr19:15310246-54948464 | 998
17p11.2 | 0.16385 | 0.16312 | chr17:11896630-25626166 | 126
17q24.3 | 0.03047 | 0.16698 | chr17:70116519-71163787 | 4
4p16.3 | 0.045115 | 0.18307 | chr4:1-47849465 | 263
16p13.3 | 0.19544 | 0.19641 | chr16:1-8772380 | 230
10p15.1 | 0.097016 | 0.23112 | chr10:1-20866709 | 123

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

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

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

Genes
LRRN3

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
hsa-mir-548f-5
DMD
FTHL17

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
FAM190A

Genes in Wide Peak

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

Table S30. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

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

Table S31. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FOXC1
GMDS

Genes in Wide Peak

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

Table S32. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

Table S33. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SMAD4
ME2
ELAC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

Table S34. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CSMD1

Genes in Wide Peak

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

Table S35. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PARD3

Genes in Wide Peak

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

Table S36. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SCCPDH
TFB2M
SMYD3
LOC149134
CNST
LOC255654

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FLRT3
MACROD2
MACROD2-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

Table S38. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
OPCML
ST14
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
JAM3
GLB1L2
VPS26B
GLB1L3
ADAMTS15
SPATA19
LOC283174
LOC283177
SNX19
LOC100128239
MIR4697

Genes in Wide Peak

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

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PTEN
hsa-mir-107
ACTA2
FAS
IFIT2
IFIT1
IFIT3
LIPA
LIPF
CH25H
KIF20B
IFIT5
PANK1
RNLS
STAMBPL1
ATAD1
ANKRD22
LIPJ
CFL1P1
FLJ37201
LIPM
SLC16A12
MIR107
IFIT1B
LIPK
LIPN
LOC643529
KLLN
FAS-AS1
MIR4679-1
MIR4679-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

Table S40. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-924
hsa-mir-4318
LOC647946
MIR4318

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.2.

Table S41. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
KCNIP4
KCNIP4-IT1

Genes in Wide Peak

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

Table S42. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GNA11
STK11
TCF3
FSTL3
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
GADD45B
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
SGTA
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
SLC39A3
THEG
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
NCLN
SPPL2B
WDR18
REXO1
ZNF77
CELF5
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
KLF16
DOT1L
KISS1R
LMNB2
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
ZNF57
JSRP1
MOB3A
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
C19orf26
CSNK1G2-AS1
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
FAM138F
LINGO3
FAM138A
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745

Genes in Wide Peak

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

Table S43. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

Table S44. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
NRAS
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
ADORA3
ALX3
AMPD1
AMPD2
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CSF1
CELSR2
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
TTF2
SLC16A4
CD101
LRIG2
TSPAN2
BCAS2
WARS2
CEPT1
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
WDR47
CLCC1
PTPN22
CHIA
GPSM2
SLC25A24
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
SLC22A15
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1OS
FAM40A
HENMT1
MAB21L3
ATXN7L2
C1orf194
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
RP11-165H20.1
DENND2C
FNDC7
UBL4B
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
MIR197
LOC440600
BCL2L15
PGCP1
SRG7
CYMP
LOC643441
NBPF6
SCARNA2
MIR942
LOC100129269
LOC100287722
MIR320B1
MIR4256
LOC100506343

Genes in Wide Peak

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

Table S45. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

Table S46. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
NAALADL2
MIR4789

Genes in Wide Peak

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

Table S47. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CACNA2D3
LRTM1
ESRG

Genes in Wide Peak

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

Table S48. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
STIM1
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.2.

Table S49. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
EZH2
MLL3
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
ABP1
CDK5
DPP6
EN2
GBX1
MNX1
HTR5A
INSIG1
KCNH2
NOS3
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
VIPR2
XRCC2
ZNF212
ZNF282
CUL1
ACCN3
PDIA4
UBE3C
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
GIMAP2
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ESYT2
ZNF398
GALNT11
LMBR1
LINC00244
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
C7orf29
AGAP3
C7orf13
ZNF786
ASB10
RNF32
LOC154822
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5P3
CNPY1
LOC285889
ZNF775
LOC285972
ATG9B
WDR86
LOC401431
MIR153-2
GIMAP6
ZNF862
LOC645249
ACTR3C
MIR595
LOC728743
MIR671
LOC100128264
LOC100128822
LOC100131176
LOC100132707
ZNF783
MIR3907
LOC100505483
LOC100506585
GIMAP1-GIMAP5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q33.3.

Table S50. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PARD3B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

Table S51. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RPA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.1.

Table S52. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
EPHA3
GBE1
HTR1F
POU1F1
PROS1
ROBO1
CGGBP1
CHMP2B
ZNF654
ARL13B
CADM2
C3orf38
VGLL3
STX19
LOC440970
MIR4795

Genes in Wide Peak

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

Table S53. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ASPSCR1
ARHGDIA
CD7
CSNK1D
FASN
UTS2R
GPS1
FOXK2
MAFG
PYCR1
PCYT2
RAC3
RFNG
SECTM1
TBCD
SLC16A3
ALYREF
RAB40B
NARF
DCXR
ANAPC11
SIRT7
WDR45L
DUS1L
FN3K
C17orf62
FN3KRP
C17orf101
ZNF750
MAFG-AS1
B3GNTL1
NOTUM
STRA13
LRRC45
MYADML2
NPB
CCDC57
HEXDC
METRNL
FLJ43681
TEX19

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.1.

Table S54. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PRDM1
ROS1
GOPC
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
BRD7P3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
MB21D1
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
DPPA5
RSPH4A
GJB7
SNHG5
C6orf147
LINC00222
CEP85L
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

Table S55. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

Table S56. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
APBA2
NBEAP1
GABRA5
GABRB3
GABRG3
IPW
NDN
OCA2
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
MAGEL2
NDNL2
ATP10A
NIPA2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
HERC2P9
WHAMMP2
LOC503519
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
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
LOC100128714
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.13.

Table S57. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LCK
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR4254
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.2.

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-3169
hsa-mir-1297
PCDH9
PCDH17
PCDH20
TDRD3
DIAPH3
PRR20A
OR7E156P
PRR20B
PRR20C
PRR20D
PRR20E
MIR1297
MIR3169

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

Table S59. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
LINC00308
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
D21S2088E
POTED
LINC00317
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.12.

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RUNX1
RUNX1-IT1

Genes in Wide Peak

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

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MAPK10
ARHGAP24
MIR4451

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q22.3.

Table S62. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-606
C10orf11

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.3.

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LARGE
LOC100506195
MIR4764

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
RAB21
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
TRHDE
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
TPH2
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
LOC283392
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
MRS2P2
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

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

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
JAK3
KLK2
PPP2R1A
TPM4
ELL
CIC
BRD4
CBLC
TFPT
ZNF331
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
hsa-mir-641
hsa-mir-1270-2
hsa-mir-1270-1
hsa-mir-640
hsa-mir-3189
hsa-mir-3188
hsa-mir-1470
ACTN4
AP2A1
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
ATP4A
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
BST2
C5AR1
CA11
CALM3
CAPNS1
CCNE1
CD22
CD33
SIGLEC6
CD37
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
TBCB
CKM
AP2S1
CLC
CLPTM1
COMP
COX6B1
COX7A1
CRX
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FCGRT
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GDF1
GIPR
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
IL12RB1
INSL3
IRF3
JUND
KCNA7
KCNC3
KCNJ14
KCNN1
KCNN4
KLK1
LAIR1
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
CYP4F3
BCAM
MAG
MEF2BNB-MEF2B
RAB8A
MAP3K10
MYBPC2
MYO9B
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NPHS1
NTF4
NUCB1
PAFAH1B3
PDE4C
PEPD
PIK3R2
PLAUR
FXYD1
FXYD3
POLD1
POLR2I
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PVR
PVRL2
RAB3A
RELB
UPF1
RPL18
RPL18A
MRPS12
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SCN1B
SEPW1
SLC1A5
SLC5A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
SULT2B1
SULT2A1
SUPT5H
TGFB1
TULP2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
XRCC1
ZFP36
ZNF14
ZNF708
ZNF28
ZNF43
ZNF45
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF137P
ZNF146
ZNF155
ZNF175
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
CYP4F2
PPFIA3
PLA2G4C
RFXANK
URI1
NAPA
SIGLEC5
FCGBP
AP1M1
PGLYRP1
F2RL3
ARHGEF1
PDCD5
DYRK1B
LPAR2
CRLF1
NUMBL
CYTH2
ZNF235
KCNK6
MED26
HOMER3
NAPSA
GDF15
ZNF254
GMFG
KLK4
ZNF432
DHX34
KIAA0355
ZNF536
MLL4
UBA2
SAE1
SUGP2
AKAP8
LILRB2
PAK4
B3GNT3
KLF2
TMEM147
IFI30
TOMM40
CHERP
RABAC1
SPINT2
DLL3
CERS1
POP4
ZNF234
PPP1R13L
CD3EAP
RUVBL2
HCST
KDELR1
LILRB5
KLK11
LILRB3
LILRA3
UPK1A
HNRNPUL1
CLASRP
KPTN
SLC7A9
MAP4K1
KLK8
CYP4F8
PNKP
COPE
ATF5
ZFP30
ZNF507
CARD8
SIRT2
CYP2G1P
UNC13A
MAST3
SIPA1L3
FCHO1
ZC3H4
SIN3B
HAUS5
CRTC1
MAU2
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
NUP62
PPP1R15A
PLD3
FKBP8
EML2
TMEM59L
PGLS
LSM4
KLK5
ZNF345
PRKD2
ZNF473
CLIP3
FAM32A
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
OR10H3
OR10H2
OR10H1
SNORA68
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
AKAP8L
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
CPAMD8
SIGLEC9
SIGLEC8
GPR77
DHDH
EIF3K
SLC6A16
BABAM1
LGALS13
CYP2S1
STRN4
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
NDUFA13
HSD17B14
VRK3
ZNF571
GMIP
ISYNA1
LSR
TM6SF2
PTOV1
FXYD7
FXYD5
RAB4B
DDX49
PAF1
TRPM4
QPCTL
GATAD2A
FAM83E
PGPEP1
RASIP1
TMEM161A
SARS2
TMEM160
PIH1D1
C19orf60
GPATCH1
SAMD4B
ATP5SL
C19orf73
MAP1S
PNMAL1
TMEM143
KLHL26
KLK15
MED29
ZNF701
ZNF83
ZNF415
USE1
PSENEN
ZNF302
LIN37
SMG9
ZNF253
IRGC
SLC7A10
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
CD177
ATP13A1
RCN3
TTYH1
PNMAL2
PRR12
ZNF492
TSHZ3
LRFN1
GRAMD1A
PLEKHA4
ZFP14
ZNF529
PRX
ANO8
SPTBN4
MARK4
SUGP1
HAMP
CATSPERG
CYP4F11
SCAF1
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
ZNF574
PLEKHG2
RASAL3
MRPL34
ZNF649
CYP4F12
DDA1
KXD1
TMEM38A
TSEN34
KCTD15
C19orf42
TRAPPC6A
MBOAT7
FKRP
PLEKHF1
LENG1
LILRA6
RBM42
ZNF576
LRFN3
ABHD8
OCEL1
GLT25D1
IGFLR1
TBC1D17
GEMIN7
MYH14
ZNF665
EPHX3
ZNF613
ADCK4
CNTD2
SLC35E1
ZNF702P
LOC80054
ZNF614
FUZ
OPA3
ZNF430
ITPKC
PBX4
KIAA1683
B9D2
RSPH6A
ZNF611
MED25
ZNF93
PLVAP
BCL2L12
C19orf12
TEX101
GRWD1
USHBP1
WDR87
TSSK6
CCDC8
KIRREL2
ANKRD27
C19orf44
ZNF541
SYT3
PDCD2L
AKT1S1
ZNF528
ZNF527
CNFN
SNORD35B
ZNF347
GTPBP3
ZNF577
MPV17L2
ZNF607
C19orf48
NFKBID
CEP89
ZNF382
ZNF566
HSH2D
ALKBH6
RHPN2
SIGLEC10
SIGLEC12
ZNF30
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
YIF1B
ZNF486
ZNF682
C19orf40
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
ZNF461
ZNF585B
TIMM50
SHKBP1
DMKN
CCDC114
HAUS8
FAM125A
DKFZp434J0226
ARMC6
ACPT
CGB5
DKFZp566F0947
CGB7
LRRC4B
ZNF101
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
PTH2
ZNF257
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
CCDC124
FBXO17
ARHGAP33
RASGRP4
NXNL1
ZNF526
CIB3
CLDND2
ZNF816
CEACAM20
CALR3
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
ZNF573
WDR88
EID2B
IRGQ
ZNF428
LRRC25
WTIP
ZNF792
NR2C2AP
HSPB6
CYP4F22
RINL
FBXO27
C19orf47
LOC126536
OR10H4
ANKLE1
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
PPM1N
KLC3
IGSF23
LYPD4
HIPK4
TMC4
LOC147804
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
FAM98C
CAPN12
DPY19L3
LGALS16
TTC9B
ZNF599
FAM187B
CILP2
C19orf55
LOC148145
LOC148189
ZNF98
ZNF738
ZNF714
ZNF681
FLJ25328
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF296
DEDD2
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
LGI4
C19orf46
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
SPACA4
ZNF675
ZNF585A
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
C19orf76
PRR24
NAPSB
IL4I1
IL28A
IL28B
IL29
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
LOC284395
SCGB2B2
WDR62
ZFP82
LOC284408
LOC284412
VSTM1
OR10H5
NWD1
SLC25A42
LOC284440
ZNF493
HKR1
VN1R2
VN1R4
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
SELV
ZNF429
ZNF233
LILRA5
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
SLC27A1
CYP4F24P
RPSAP58
RGS9BP
KRTDAP
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
NUDT19
ZNF793
PAPL
LOC390940
SPRED3
ZNF321P
LOC400680
LOC400684
LOC400685
LGALS17A
SIGLEC16
FLJ26850
ZNF880
IGLON5
HAPLN4
MIRLET7E
MIR125A
MIR150
MIR99B
ZNF506
LOC440518
ZNF724P
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
DPRX
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC641367
TMEM91
LOC643669
SCGB1B2P
SDHAF1
LOC644189
LOC644554
LOC646508
UCA1
PSG10P
LGALS7B
PHLDB3
SEC1
ZNF826P
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
RPL13AP5
LOC728752
CCDC61
CEACAM18
LOC729966
FLJ30403
MEF2BNB
ZNF726
MIR769
SIGLEC14
LOC100101266
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128675
LOC100128682
LOC100129083
ZNF737
LOC100129935
SCGB2B3P
TMEM221
BSPH1
LOC100134317
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
ERVV-2
MEF2B
LOC100287177
ZNF729
LOC100289650
MIR1470
MIR1270-1
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3188
MIR3190
MIR320E
MIR3189
MIR4324
MIR4323
MIR1270-2
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100505835
LOC100506012
LOC100506033
LOC100506068
LOC100506469
LOC100506930
LOC100507003
LOC100507433
THEG5
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
LOC100631378
LOC100652909

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p11.2.

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MAP2K4
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
ALDH3A1
ALDH3A2
COX10
DRG2
FOXO3B
FLII
KCNJ12
LLGL1
MEIS3P1
MFAP4
PMP22
MAPK7
MAP2K3
PRPSAP2
SHMT1
SREBF1
TOP3A
UBB
RNF112
COPS3
TMEM11
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
GRAP
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
DHRS7B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
FAM106A
LRRC48
MGC12916
ATPAF2
SPECC1
MYOCD
CDRT7
CDRT15P1
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
CDRT15
TRIM16L
USP32P1
FAM18B2
CENPV
FLCN
PLD6
USP32P2
TBC1D28
CDRT15L2
C17orf103
FLJ34690
CDRT4
CCDC144B
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
CCDC144C
TBC1D26
CDRT1
FAM211A
KRT16P2
GRAPL
CDRT15P2
FAM83G
KRT16P3
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
MIR744
FAM106CP
KCNJ18
MIR1288
MIR1180
MTRNR2L1
FAM18B2-CDRT4
MIR4731
MIR4522

Genes in Wide Peak

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

Table S67. Genes in bold are cancer genes as defined by The Sanger Institute: 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 4p16.3.

Table S68. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR3
WHSC1
PHOX2B
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
APBB2
RHOH
ATP5I
NKX3-2
BST1
CCKAR
CD38
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GRK4
HTT
HGFAC
UBE2K
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RFC1
RGS12
RNF4
RPL9
S100P
SH3BP2
SOD3
TLR1
UCHL1
UGDH
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
TLR6
PCGF3
ATP8A1
SPON2
TACC3
SLC30A9
SLC34A2
MXD4
CORIN
PTTG2
CPLX1
SLC26A1
PPARGC1A
LIAS
LIMCH1
TBC1D1
SEL1L3
PDS5A
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
KLHL5
SEPSECS
KLF3
STX18
FGFRL1
CYTL1
SH3TC1
RBM47
PIGG
DCAF16
COMMD8
TMEM33
LGI2
PGM2
C4orf19
TBC1D19
PI4K2B
CNO
STK32B
CHRNA9
LYAR
N4BP2
SLC2A9
ATP10D
KIAA1239
TBC1D14
SORCS2
CC2D2A
STIM2
KIAA1530
WDR19
ZFYVE28
GBA3
AFAP1
GUF1
NCAPG
TNIP2
HAUS3
FLJ13197
NSUN7
ABCA11P
TMEM156
GRPEL1
MED28
KCNIP4
TLR10
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
FAM114A1
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
ARAP2
GNPDA2
CPEB2
EVC2
PACRGL
OTOP1
SHISA3
ZNF595
LOC152742
JAKMIP1
KLB
FAM53A
METTL19
GPR125
ZBTB49
COX7B2
ZNF721
C4orf34
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
DCAF4L1
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
YIPF7
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
NAT8L
LOC344967
C4orf44
FAM86EP
POLN
KCNIP4-IT1
KCTD8
C4orf52
BEND4
GRXCR1
USP17L6P
USP17
HSP90AB2P
C4orf48
DTHD1
LOC401127
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
MIR574
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
RELL1
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4802
MIR4800
MIR4801
MIR4798
HTT-AS1

Genes in Wide Peak

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

Table S69. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CREBBP
TSC2
hsa-mir-3178
hsa-mir-940
hsa-mir-1225
hsa-mir-3177
hsa-mir-662
hsa-mir-3176
ABCA3
ADCY9
ARHGDIG
ATP6V0C
CCNF
CLCN7
ECI1
DNASE1
DNASE1L2
E4F1
GFER
HAGH
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
IGFALS
MEFV
MPG
NDUFB10
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PDPK1
PKD1
PPL
RPL3L
RPS2
SRL
SOLH
SSTR5
TCEB2
TFAP4
TPSAB1
UBE2I
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
NPRL3
AXIN1
RGS11
CACNA1H
BAIAP3
RHBDL1
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
SYNGR3
IL32
SLC9A3R2
SEC14L5
RAB11FIP3
IFT140
TELO2
NUBP2
ZNF263
TRAP1
MSLN
STUB1
MRPL28
TBL3
RNPS1
PRSS21
CLUAP1
MAPK8IP3
MGRN1
TPSD1
SRRM2
TPSG1
RAB26
ZNF500
DECR2
OR1F2P
SNORA64
SNORD60
UBN1
C16orf5
SOX8
AMDHD2
PAM16
NAGPA
TNFRSF12A
POLR3K
SEPX1
GNG13
KCTD5
RBFOX1
ZNF434
HCFC1R1
LUC7L
ALG1
NMRAL1
TBC1D24
CASKIN1
CRAMP1L
RAB40C
TMEM8A
CHTF18
PRSS22
MLST8
RHBDF1
MMP25
NARFL
LINC00235
TPSB2
HS3ST6
PDIA2
UNKL
LINC00254
LMF1
FAM173A
MRPS34
METRN
METTL22
THOC6
KREMEN2
CORO7
SNRNP25
ROGDI
TMEM204
NAA60
C16orf59
MGC3771
FAHD1
PRSS27
ITFG3
WDR24
TRAF7
FLYWCH1
HAGHL
NUDT16L1
C16orf13
FAM195A
SLX4
GNPTG
GLYR1
GLIS2
ZSCAN10
RHOT2
ZNF598
HN1L
SPSB3
TIGD7
RPUSD1
FLYWCH2
VASN
C16orf42
WFIKKN1
NOXO1
CCDC78
ZG16B
PRSS30P
PAQR4
ANKS3
FAM100A
SEPT12
RNF151
C16orf11
FBXL16
LOC146336
ZNF597
CCDC64B
C16orf89
C16orf71
FAM86A
WDR90
EME2
NLRC3
C16orf73
PRSS33
NPW
C16orf79
PGP
LINC00514
FLJ39639
NHLRC4
C16orf91
TMEM114
JMJD8
C16orf96
PRSS41
PRR25
C1QTNF8
PTX4
MSLNL
LOC440335
SNORA10
FLJ42627
CCDC154
C16orf90
ABCA17P
LOC652276
SNORA78
MIR662
SNHG9
CEMP1
MIR940
LOC100128788
LOC100134368
MIR1225
DDX11L10
MIR3178
MIR3177
MIR3176
MTRNR2L4
MIR3677
MIR3180-5
ERVK13-1
LOC100507501
LOC100507589
CORO7-PAM16
MIR4717
MIR4516

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.1.

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GATA3
hsa-mir-511-2
hsa-mir-511-1
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
CACNB2
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
TRDMT1
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PRKCQ
RSU1
VIM
STAM
CUBN
ITGA8
PRPF18
AKR1C3
CDC123
PTPLA
PTER
NMT2
USP6NL
OPTN
NET1
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
SEPHS1
KIN
DIP2C
LARP4B
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
CAMK1D
SFMBT2
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
FBXO18
PLXDC2
RBM17
IDI2
UCN3
SFTA1P
LOC219731
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
LOC254312
C10orf47
LOC282980
LOC283070
LOC338588
ST8SIA6
AKR1CL1
TUBB8
tAKR
C1QL3
LINC00200
LOC399708
LOC399715
FLJ45983
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
MIR511-1
MIR511-2
ADARB2-AS1
MEIG1
TMEM236
LOC100128098
LOC100129213
LOC100192204
LOC100216001
MIR1265
MIR3155A
LOC100507034
LOC100507127
MIR4480
MIR4675
MIR3155B

Arm-level results

Table 3. Get Full Table Arm-level significance table - 22 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 | 0.17 | -0.713 | 1 | 0.25 | 0.991 | 0.339
1q | 1955 | 0.34 | 2.61 | 0.0302 | 0.21 | -0.395 | 1
2p | 924 | 0.40 | 0.969 | 0.605 | 0.11 | -4.08 | 1
2q | 1556 | 0.33 | 1.15 | 0.501 | 0.15 | -2.34 | 1
3p | 1062 | 0.20 | -1.88 | 1 | 0.62 | 5.86 | 8.99e-08
3q | 1139 | 0.39 | 1.24 | 0.481 | 0.32 | -0.0621 | 0.875
4p | 489 | 0.20 | -2.84 | 1 | 0.61 | 4.06 | 0.000194
4q | 1049 | 0.17 | -2.6 | 1 | 0.52 | 3.86 | 0.000328
5p | 270 | 0.54 | 1.84 | 0.165 | 0.49 | 1.06 | 0.339
5q | 1427 | 0.19 | -1.59 | 1 | 0.50 | 4.48 | 7.32e-05
6p | 1173 | 0.20 | -2.23 | 1 | 0.23 | -1.72 | 1
6q | 839 | 0.17 | -3.61 | 1 | 0.22 | -2.64 | 1
7p | 641 | 0.62 | 4.57 | 2.81e-05 | 0.29 | -1.3 | 1
7q | 1277 | 0.53 | 4.54 | 2.81e-05 | 0.25 | -0.914 | 1
8p | 580 | 0.54 | 2.45 | 0.0405 | 0.56 | 2.85 | 0.0108
8q | 859 | 0.60 | 4.71 | 2.51e-05 | 0.28 | -1.13 | 1
9p | 422 | 0.18 | -3.16 | 1 | 0.61 | 3.99 | 0.000217
9q | 1113 | 0.28 | -0.844 | 1 | 0.45 | 2.38 | 0.0314
10p | 409 | 0.24 | -2.93 | 1 | 0.34 | -1.3 | 1
10q | 1268 | 0.21 | -1.75 | 1 | 0.36 | 1.14 | 0.316
11p | 862 | 0.26 | -1.71 | 1 | 0.36 | 0.0187 | 0.86
11q | 1515 | 0.24 | -0.78 | 1 | 0.40 | 2.6 | 0.021
12p | 575 | 0.41 | 0.354 | 1 | 0.29 | -1.72 | 1
12q | 1447 | 0.23 | -1.21 | 1 | 0.23 | -1.21 | 1
13q | 654 | 0.39 | 0.0961 | 1 | 0.52 | 2.52 | 0.0233
14q | 1341 | 0.34 | 0.749 | 0.756 | 0.34 | 0.749 | 0.454
15q | 1355 | 0.24 | -1.03 | 1 | 0.30 | 0.0145 | 0.86
16p | 872 | 0.24 | -2.01 | 1 | 0.34 | -0.266 | 0.968
16q | 702 | 0.21 | -3 | 1 | 0.34 | -0.668 | 1
17p | 683 | 0.24 | -2.2 | 1 | 0.47 | 1.71 | 0.125
17q | 1592 | 0.24 | -0.574 | 1 | 0.15 | -2.44 | 1
18p | 143 | 0.39 | -0.837 | 1 | 0.50 | 1.02 | 0.339
18q | 446 | 0.26 | -2.11 | 1 | 0.62 | 4.06 | 0.000194
19p | 995 | 0.15 | -3.17 | 1 | 0.41 | 1.39 | 0.218
19q | 1709 | 0.23 | -0.486 | 1 | 0.34 | 1.76 | 0.121
20p | 355 | 0.59 | 3.2 | 0.00552 | 0.31 | -1.6 | 1
20q | 753 | 0.60 | 4.77 | 2.51e-05 | 0.16 | -2.97 | 1
21q | 509 | 0.18 | -3.03 | 1 | 0.61 | 4.22 | 0.000164
22q | 921 | 0.29 | -1.04 | 1 | 0.44 | 1.76 | 0.121
Xq | 1312 | 0.24 | -1.24 | 1 | 0.32 | 0.313 | 0.718

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/ESCA-TP/8016680/GDAC_MergeDataFiles_8022461/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

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 103 Input Tumor Samples.

Tumor Sample Names
TCGA-IC-A6RE-01A-11D-A33D-01
TCGA-IC-A6RF-01A-13D-A33D-01
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-IG-A4P3-01A-11D-A25X-01
TCGA-IG-A4QS-01A-11D-A25X-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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- 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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