SNP6 Copy number analysis (GISTIC2) - Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1FF3RRP

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 2.0.22 (Firehose task version: 140).

Summary

There were 528 tumor samples used in this analysis: 28 significant arm-level results, 10 significant focal amplifications, and 19 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 - 10 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
5q35.1	2.1944e-60	2.1944e-60	chr5:157747359-180359088	178
3q26.32	2.0306e-05	2.0306e-05	chr3:161783309-198022430	256
Xq11.2	0.001208	0.001208	chrX:64003371-64052730	0 [ZC4H2]
7q31.2	0.075418	0.075418	chr7:110663086-159138663	381
1q32.1	0.016713	0.10278	chr1:203699717-205218424	26
1q24.1	0.059566	0.1093	chr1:120522602-208770337	845
Xq28	0.12739	0.12739	chrX:93621281-155270560	515
8q24.22	0.15559	0.15559	chr8:69506698-146364022	450
10p14	0.17403	0.17403	chr10:1-16776063	122
4q32.1	0.18358	0.18358	chr4:159611309-162008604	7

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.1.

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

Genes
EBF1
NPM1
TLX3
NSD1
RANBP17
LINC00847
MIR340
RN7SKP150
MIR1229
HMGB3P22
RN7SL71P
ZNF879
ZNF354B
AACSP1
RN7SKP70
RN7SL646P
RN7SL562P
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
RN7SKP148
snoU13\|ENSG00000239026.1
NSG2
RNA5SP200
SNORA74B
ATP6V0E1
MIR5003
SNORA57\|ENSG00000212529.1
C5orf50
SNORA70\|ENSG00000206909.1
RN7SL339P
snoU13\|ENSG00000252387.1
RN7SL623P
MIR4454
KCNMB1
LCP2
C5orf58
MIR378E
MIR585
MIR103A1
PANK3
FBLL1
SNORA40\|ENSG00000253065.1
RN7SKP60
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68\|ENSG00000252458.1
BNIP1
CANX
CCNG1
CLTB
DBN1
DOCK2
DRD1
DUSP1
F12
FABP6
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GRK6
GRM6
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
IL12B
LTC4S
MGAT1
MSX2
MAPK9
PROP1
RARS
SLC34A1
SLIT3
SNCB
STK10
ZNF354A
TTC1
STC2
FGF18
SQSTM1
PTTG1
PDLIM7
ADAMTS2
MAML1
GFPT2
SLU7
RGS14
CPLX2
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
ATP10B
N4BP3
FAF2
WWC1
FBXW11
ZNF346
TSPAN17
PRELID1
MAT2B
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
SPDL1
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
C5orf54
RMND5B
CCNJL
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
MXD3
THOC3
PHYKPL
UNC5A
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
PWWP2A
C1QTNF2
C5orf47
OR2Y1
UBLCP1
CREBRF
RNF145
HIGD2A
FAM153B
RASGEF1C
EFCAB9
SH3PXD2B
FAM153A
ZNF454
C5orf60
PFN3
SIMC1
MIR146A
ZFP62
CBY3
FAM153C
FAM196B
MIR3912
MIR4634

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

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

Genes
PIK3CA
BCL6
EIF4A2
ETV5
LPP
SOX2
TFRC
FAM157A
FYTTD1
snoU13\|ENSG00000238491.1
MIR4797
U4\|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
RN7SL36P
MIR3137
LINC00884
LINC00887
RN7SL215P
RN7SL447P
snoU13\|ENSG00000238902.1
RN7SKP222
RN7SKP296
RN7SL486P
MIR944
MIR28
snoU13\|ENSG00000239093.1
RTP4
SNORA4\|ENSG00000263776.1
SNORA63\|ENSG00000200320.1
SNORA81\|ENSG00000221420.2
SNORA63\|ENSG00000200418.1
SNORD2\|ENSG00000238942.1
KNG1
CRYGS
RN7SL637P
TRA2B
MIR548AQ
SENP2
snoU13\|ENSG00000239146.1
SNORD66\|ENSG00000212158.1
MIR1224
CYP2AB1P
SNORA4\|ENSG00000251730.1
SNORA63\|ENSG00000199363.1
SNORA81\|ENSG00000253092.1
SNORA63\|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
RN7SL229P
U8\|ENSG00000201810.1
RNA5SP149
snoU13\|ENSG00000239096.1
GNB4
SNORA25\|ENSG00000201957.1
RNA5SP148
SNORA18\|ENSG00000200288.1
RN7SKP52
LINC00578
LINC00501
RNA5SP147
snoU13\|ENSG00000271842.1
MIR4789
RN7SKP40
RN7SKP234
snoU13\|ENSG00000239141.1
SNORA72\|ENSG00000200355.1
RN7SL141P
PP13439
snoU13\|ENSG00000238359.1
MIR569
RNY5P3
CLDN11
TERC
EGFEM1P
RN7SKP298
MIR720
snoU13\|ENSG00000238398.1
CT64
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
RPL35A
SI
ST6GAL1
SKIL
SLC2A2
SST
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
ACTRT3
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
SLC51A
FBXO45
MUC20
SENP5
NAALADL2
TCTEX1D2
SMCO1
UTS2B
HTR3E
C3orf70
TPRG1
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
WDR53
ANKRD18DP
NRROS
TMEM212
LINC00885
C3orf65
GMNC
MIR551B
MIR570
MIR922
MIR1263
MIR4448

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.2.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26\|ENSG00000212590.1
snoU13\|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13\|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112\|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3\|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6\|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13\|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40\|ENSG00000252188.1
snoU13\|ENSG00000239123.1
SNORA51\|ENSG00000201465.1
snoU13\|ENSG00000238984.1
snoU13\|ENSG00000239145.1
RN7SKP223
SNORD81\|ENSG00000202023.1
snoU13\|ENSG00000238488.1
LUZP6
C7orf73
U6\|ENSG00000272393.1
SNORD46\|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13\|ENSG00000239044.1
snoU13\|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13\|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1\|ENSG00000271739.1
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25\|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13\|ENSG00000238922.1
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CAV1
CAV2
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
FAM3C
FASTK
ZNF277
ABCB8
TFEC
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
TES
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
GPR85
TAS2R5
CHPF2
ING3
LRRN3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
CPED1
TTC26
JHDM1D
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
C7orf60
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
LSMEM1
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q32.1.

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

Genes
MDM4
SNORD112\|ENSG00000252946.1
SCARNA20\|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
ATP2B4
KISS1
PIK3C2B
RBBP5
REN
CNTN2
SOX13
ZC3H11A
TMCC2
LRRN2
PLEKHA6
NFASC
DSTYK
LAX1
ETNK2
PPP1R15B
GOLT1A
LINC00303
TMEM81

Genes in Wide Peak

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

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

Genes
SDHC
ABL2
ARNT
BCL9
ELK4
FCGR2B
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
TPM3
TPR
PDE4DIP
SLC45A3
MIR29B2
MIR29C
snoU13\|ENSG00000238401.1
FAIM3
IL20
SNORD112\|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60\|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72\|ENSG00000201944.1
SNORD112\|ENSG00000252946.1
SCARNA20\|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77\|ENSG00000221643.1
RABIF
PCAT6
SNORA70\|ENSG00000253042.1
U6\|ENSG00000272262.1
snoU13\|ENSG00000239046.1
snoU13\|ENSG00000238571.1
PTPRVP
GPR37L1
SNORA70\|ENSG00000206637.1
MIR1231
MIR5191
RPS10P7
ASCL5
LINC00862
MIR181A1HG
MIR4735
U3\|ENSG00000252241.1
MIR1278
snoU109\|ENSG00000238754.1
RN7SKP126
RNA5SP73
RN7SKP156
RNA5SP72
SNORD112\|ENSG00000252790.1
RN7SL654P
RNA5SP71
RN7SKP229
RNA5SP70
KIAA1614
U6\|ENSG00000272292.1
MIR3121
LHX4
RN7SL230P
IFRG15
RN7SL374P
SNORA67\|ENSG00000201619.1
SNORA67\|ENSG00000212338.1
TOR3A
SNORA63\|ENSG00000201791.1
RNA5SP69
C1orf220
LINC00083
MIR488
SCARNA3
snoU13\|ENSG00000238872.1
RNA5SP68
RNA5SP67
SNORD78\|ENSG00000208317.1
GAS5
RN7SKP160
snoU13\|ENSG00000238430.1
ANKRD45
snoU13\|ENSG00000251817.1
TNFSF18
SNORD112\|ENSG00000252354.1
DNM3OS
SCARNA20\|ENSG00000253060.1
RN7SL425P
snoU13\|ENSG00000238859.1
RN7SL269P
RN7SL333P
C1orf112
F5
RNA5SP66
LINC00970
LINC00626
ANKRD36BP1
SFT2D2
MIR1255B2
snoU13\|ENSG00000238325.1
RNA5SP65
POGK
MIR921
RNA5SP64
UCK2
TMCO1
SNORD112\|ENSG00000252359.1
U3\|ENSG00000212538.1
RNA5SP63
RNA5SP62
SNORD112\|ENSG00000252740.1
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64\|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64\|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13\|ENSG00000238843.1
BGLAP
SNORA26\|ENSG00000252236.1
SCARNA4\|ENSG00000252808.1
SNORA42\|ENSG00000207475.1
snoU13\|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59\|ENSG00000252682.1
SNORA58\|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3\|ENSG00000252669.1
snoU13\|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31\|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13\|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
ADORA1
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
C4BPA
C4BPB
CACNA1E
CACNA1S
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD34
CD48
CHI3L1
CHIT1
CHRNB2
CKS1B\|ENSG00000173207.8
CLK2
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSRP1
CTSE
CTSK
CTSS
CD55
DHX9
DPT
ECM1
EIF2D
EFNA1
EFNA3
EFNA4
ELF3
ENSA
ETV3
F13B
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GBA
GJA5
GJA8
GLUL
GPR25
HDGF
CFH
CFHR1
CFHR2
MR1
HSPA6
IFI16
IL6R
IL10
ILF2
INSRR
IVL
KCNJ10
KCNN3
KISS1
LAD1
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NHLH1
NIT1
NPR1
DDR2
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PRELP
PRKAB2
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPRC
PEX19
RAB13
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
CNTN2
VPS72
THBS3
TCHH
TNNI1
TNNT2
TNR
CCT3
TUFT1
TNFSF4
USF1
DAP3
NPHS2
BTG2
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
DYRK3
RGS5
PPFIA4
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
MPZL1
SH2D2A
ANGPTL1
TBX19
PRPF3
ARHGEF2
DEDD
XPR1
MAPKAPK2
GPR52
AIM2
RASAL2
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
KIF14
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
PIAS3
TIMM17A
LRRN2
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
KDM5B
CFHR4
CFHR3
OCLM
JTB
MTMR11
SLC27A3
IL24
TDRKH
CD160
PMF1
DUSP12
VPS45
PLEKHA6
KIAA0907
KIFAP3
ATF6
KIF21B
NMNAT2
NFASC
POGZ
COLGALT2
RGL1
SYT11
PRRC2C
RPRD2
CAMSAP2
SMG5
NCSTN
CRB1
GPR161
ZNF281
SNAPIN
PHLDA3
RUSC1
CA14
DSTYK
CCDC19
LMOD1
NBPF14
MPC2
OLFML2B
C1orf43
DNM3
TOR1AIP1
CHTOP
LCE2B
OPTC
OR10J1
USP21
CACYBP
SLC39A1
KLHL20
LAMTOR2
UBE2T
TMOD4
NME7
IL19
CERS2
CRNN
DCAF8
F11R
GLRX2
BOLA1
ZBTB7B
RRNAD1
ADIPOR1
APH1A
PLEKHO1
IER5
UCHL5
SUCO
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CYB5R1
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
RALGPS2
MSTO1
DARS2
GOLPH3L
KLHDC8A
ETNK2
KIRREL
YY1AP1
YOD1
UBE2Q1
ITLN1
IPO9
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
LHX9
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
FAM5B
CCDC181
SLAMF7
CADM3
PRUNE
KLHL12
LGR6
HAPLN2
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
RFWD2
RGS18
NUCKS1
MRPL9
INTS3
SCNM1
C1orf116
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
MROH9
TARS2
EDEM3
FLAD1
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
FCAMR
TEX35
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
FCRLA
PPP1R15B
MAEL
RGS8
NAV1
SEC16B
AQP10
SLAMF9
PYGO2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
PIGM
IGSF8
LEMD1
C1orf85
PGLYRP3
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
AXDND1
ATP6V1G3
OR10J5
DCST2
ZNF648
TEDDM1
ARL8A
SYT2
GOLT1A
UHMK1
FCRLB
LIX1L
TSACC
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
NEK7
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
FAM163A
MFSD4
PM20D1
NBPF12
LELP1
RC3H1
DCST1
METTL11B
FAM78B
SHISA4
BNIPL
LRRC71
PYHIN1
DENND1B
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
LCE4A
NBPF11
KRTCAP2
CRTC2
TMEM9
SLC41A1
LCE5A
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
SLC9C2
NBPF16
LINC00303
ANKRD34A
C1orf204
HIST2H2AB
S100A7A
RXFP4
FAM5C
C1orf110
OR10R2
FCRL6
KCNT2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
PEAR1
ILDR2
NOTCH2NL
LYSMD1
HRNR
FLG2
FMO6P
LINC00272
C1orf53
TMEM81
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
C1ORF220
NBPF9
APOBEC4
MIR181B1
MIR199A2
MIR181A1
MIR214
C1orf132
RGS21
HIST2H2BF
ETV3L
LRRC52
OR10J3
MIR135B
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR557
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
TSTD1
C2CD4D
NBPF20
MIR1295A
MIR4257
MIR4424

Genes in Wide Peak

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

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

Genes
ELF4
GPC3
MTCP1
WASH6P\|ENSG00000182484.10
WASIR1\|ENSG00000185203.7
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70\|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36\|ENSG00000251846.1
RN7SL687P
RN7SL667P
snoU13\|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
MIR452
MIR224
U3\|ENSG00000253009.1
LINC00894
LINC00893
RN7SKP267
CXorf51A
CXorf51B
RNA5SP517
SPANXN1
RN7SKP189
RN7SKP149
RN7SKP81
snoU13\|ENSG00000239188.1
RNA5SP516
SPANXD
SPANXA2
SPANXA1
RN7SL727P
MIR505
SNORA18\|ENSG00000252719.1
RNU6ATAC23P
snoU13\|ENSG00000238485.1
MIR504
RN7SKP31
RN7SL325P
SNORD61\|ENSG00000206979.1
MIR934
snoU13\|ENSG00000239080.1
RNA5SP515
LINC00086
LINC00633
LINC00087
SMIM10
LINC00629
GPC4
SNORA8\|ENSG00000207100.1
RNA5SP514
RN7SL191P
FAM45B
RNA5SP513
DCAF12L2
snoU13\|ENSG00000238626.1
SNORA40\|ENSG00000252693.1
snoU13\|ENSG00000239058.1
RN7SL29P
U3\|ENSG00000212321.1
CT47A12
MCTS1
snoU13\|ENSG00000272179.1
RHOXF2B
NDUFA1
SNORA69\|ENSG00000206622.1
MIR766
RN7SL118P
SNORA35\|ENSG00000239182.1
MIR1277
RN7SL712P
SNORA64\|ENSG00000252441.1
SNORA35\|ENSG00000271907.1
MIR448
MIR1911
SNORA35\|ENSG00000208839.1
SNORD30
RN7SL93P
U3\|ENSG00000201674.1
snoU13\|ENSG00000238811.1
RN7SL266P
MIR4329
ZCCHC16
TRPC5OS
RNA5SP512
RN7SL661P
LINC00890
TDGF1P3
GNG5P2
SNORD96B
MIR3978
MIR652
MID2
NCBP2L
RBM41
MIR548AN
ZCCHC18
RNA5SP511
LINC00630
NXF4
TCP11X1
TCP11X3P
TCEAL6
SNORA9\|ENSG00000202231.1
TSPAN6
SNORA25\|ENSG00000252296.1
RN7SL74P
RN7SKP194
RN7SL379P
RNA5SP510
AGTR2
ABCD1
SLC25A5
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
BTK
CAPN6
CD40LG
CDR1
CLIC2
CNGA2
COL4A5
COL4A6
CSTF2
CTAG1B
TEX28
DCX
TIMM8A
DIAPH2
DKC1
DNASE1L1
DRP2
TSC22D3
DUSP9
EMD
F8
F9
ACSL4
FGF13
FHL1
FLNA
FMR1
AFF2
CENPI
G6PD
GABRA3
GABRE
GDI1
GLA
GLUD2
GRIA3
GUCY2F
HCFC1
HMGB3
HNRNPH2
HPRT1
HTR2C
IDH3G
IDS
IGSF1
IL9R\|ENSG00000124334.12
IL13RA1
IL13RA2
IRAK1
L1CAM
LAMP2
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
OCRL
PAK3
PLP1
PLS3
PLXNB3
PRPS1
PSMD10
OPN1LW
RENBP
RPL10
RPL39
RPL36A
SLC6A8
SMARCA1
SOX3
SSR4
VAMP7\|ENSG00000124333.10
TAZ
SERPINA7
TRPC5
UBE2A
VBP1
XPNPEP2
ZIC3
ZNF75D
RNF113A
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
CUL4B
IRS4
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
CLDN2
FAM50A
AIFM1
TMEM257
GPR50
TCEAL1
RAB33A
ARHGEF6
MORF4L2
GPRASP1
ARMCX2
MAGEC1
AMMECR1
ZBTB33
MAMLD1
BCAP31
TENM1
SPRY3\|ENSG00000168939.6
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
PGRMC1
TMSB15A
TREX2
SLC6A14
SEPT6
ATP1B4
KCNE1L
LDOC1
FAM127B
IL1RAPL2
SRPK3
NGFRAP1
NOX1
SRPX2
RBMX
HTATSF1
C1GALT1C1
RPA4
PNMA3
CTAG2
NSDHL
ZDHHC9
WBP5
RAB9B
LUZP4
TFDP3
ARMCX1
MAGEC2
VGLL1
ARMCX3
RBMX2
MST4
SASH3
TAF7L
ARMCX6
WDR44
NUP62CL
TBC1D8B
CXorf48
TMEM255A
CXorf57
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
BEX1
NXT2
NKRF
NXF5
NXF3
NXF2
TEX13B
TEX13A
MOSPD1
BEX4
TCEAL7
THOC2
KIAA1210
PCDH19
RGAG1
PDZD4
LRCH2
RAP2C
TMEM35
FAM3A
BCORL1
CXorf56
TNMD
SPANXC
ARMCX5
UPF3B
PRRG3
BRCC3
NKAP
RNF128
MAP7D3
MORC4
LONRF3
ALG13
TCEAL4
TRMT2B
ESX1
BHLHB9
GPR101
CD99L2
H2AFB3
USP26
TMEM164
PHF6
FRMPD3
ZMAT1
RHOXF2
TMEM185A
SLITRK2
BEX2
TCEAL3
FATE1
HS6ST2
FRMD7
KLHL13
TCEAL8
CHRDL1
CXorf40A
FAM58A
RIPPLY1
MMGT1
SYTL4
PNMA5
GPRASP2
ATG4A
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
PIH1D3
MUM1L1
FAM199X
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
RBMXL3
DOCK11
TCEAL2
RAB40A
AMOT
CSAG1
FMR1NB
ARHGAP36
AKAP14
RHOXF1
NKAPP1
H2BFWT
FAM122B
FAM122C
ZCCHC12
CXorf61
SLC25A43
NRK
DDX26B
ZNF449
VMA21
TMEM31
CTAG1A
CT47A11
RAB40AL
ATP11C
LINC00632
H2BFM
TMSB15B
BEX5
TCEAL5
VSIG1
LHFPL1
SOWAHD
OR13H1
CCDC160
CXorf66
UBE2NL
ARL13A
SLC25A53
XKRX
MIR106A
MIR19B2
MIR92A2
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
SPANXN2
MIR503HG
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR450A2
MIR503
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR510
MIR514A1
MIR514A2
MIR514A3
CT47B1
CT47A7
MIR542
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
NXF2B
OPN1MW2
SPANXB1
CT45A2
MIR767
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR891A
MIR892A
LINC00892
HSFX2
CXorf64
ARMCX4
SMIM9
SPANXB2
CMC4
PNMA6C
MIR513C
MIR1912
MIR1298
MIR320D2
MIR548M
MIR718
MIR513B
MIR764
MIR2114
MIR514B
MIR4330
MIR3672
HSFX1
TCP11X2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.22.

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

Genes
EXT1
COX6C
MYC
RECQL4
NCOA2
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK\|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5\|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25\|ENSG00000251744.1
SNORA40\|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72\|ENSG00000252158.1
SNORA12\|ENSG00000212342.1
SNORA25\|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13\|ENSG00000238422.1
U3\|ENSG00000221461.1
RNY4P5
snoU13\|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32\|ENSG00000206776.1
COLEC10
SNORA31\|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13\|ENSG00000238656.1
SNORD112\|ENSG00000252559.1
TMEM74
RNA5SP275
snoU13\|ENSG00000238687.1
RIMS2
MIR3151
RNU6ATAC8P
snoU13\|ENSG00000238533.1
snoU13\|ENSG00000238372.1
RN7SL563P
NACAP1
RN7SKP249
RN7SL685P
RNU6ATAC41P
MIR1273A
SNORD77\|ENSG00000212414.1
RN7SL350P
RN7SKP85
KCNS2
NIPAL2
SNORA72\|ENSG00000207067.1
LAPTM4B
U3\|ENSG00000207215.1
PTDSS1
snoU13\|ENSG00000238791.1
FSBP
RNA5SP274
LINC00535
RN7SKP231
snoU13\|ENSG00000239134.1
MIR4661
RN7SL777P
RNA5SP273
LINC00534
RNA5SP272
MMP16
REXO1L10P\|ENSG00000255940.1
REXO1L11P
REXO1L10P\|ENSG00000270416.1
snoU13\|ENSG00000238566.1
SLC10A5
IMPA1P
RN7SL308P
RN7SL107P
SNORA20\|ENSG00000206649.1
RN7SL41P
snoU13\|ENSG00000238595.1
CASC9
RNA5SP271
U8\|ENSG00000200191.1
RN7SL19P
snoU13\|ENSG00000238450.1
RNA5SP270
RN7SL675P
RN7SKP29
RNA5SP269
ADCY8
ANGPT1
ANXA13
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CYC1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
GEM
GLI4
GML
GPR20
GPT
GRINA
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
LY6E
LY6H
MATN2
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PLEC
PMP2
POLR2K
PKIA
PTK2
PEX2
RAD21
RPL7
RPL8
RPL30
SDC2
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
LY6D
GPAA1
RIPK2
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
LRRC14
EMC2
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
CPQ
KHDRBS3
POP1
WWP1
STMN2
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
SULF1
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
LRRC6
LY96
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
OPLAH
PABPC1
KCNV1
STAU2
MTBP
AGO2
MRPS28
COMMD5
MRPL13
ATAD2
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
RMDN1
ZNF706
VPS28
FAM203A
KCNK9
THEM6
UBR5
FAM49B
AZIN1
OTUD6B
CHRAC1
GDAP1
EXOSC4
PDP1
CNGB3
ESRP1
TMEM70
TRMT12
OXR1
WDYHV1
UBE2W
TMEM55A
SLC39A4
SYBU
INTS8
PAG1
GSDMC
JPH1
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
PRDM14
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
DSCC1
DERL1
SLC52A2
PLEKHF2
ZFAND1
ZFHX4
GSDMD
BAALC
GRHL2
ARHGAP39
ZNF34
SLC25A32
DCSTAMP
SLCO5A1
SHARPIN
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NCALD
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
PSKH2
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
TBC1D31
TP53INP1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
C8orf34
TOP1MT
ZNF572
FAM92A1
NDUFAF6
ABRA
LYPD2
TMEM71
DCAF4L2
RALYL
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
FAM91A1
SBSPON
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
REXO1L1
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
TRIQK
DPY19L4
FBXO43
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
CA13
XKR9
C8orf87
RBM12B
MROH5
MAFA
GDF6
C8orf59
SAMD12
MIR30B
MIR30D
LRRC24
ZNF704
MROH6
FABP9
FABP12
FER1L6
MIR548A3
MIR599
MROH1
FAM203B
OC90
MIR875
LRRC69
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3150B
MIR3610
MIR378D2
MIR4662B
MIR4663
MIR4664
MIR4471
MIR5680
MIR5194
MIR5708
MIR5681A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p14.

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

Genes
GATA3
snoU13\|ENSG00000238552.1
SNORA31\|ENSG00000252537.1
snoU13\|ENSG00000239130.1
ITGA8
NMT2
ACBD7
MEIG1
CDNF
RNA5SP302
RNA5SP301
RNA5SP300
MIR4480
RNU6ATAC39P
SNORD45\|ENSG00000252438.1
RN7SL198P
RN7SL232P
snoU13\|ENSG00000238900.1
U6\|ENSG00000272507.1
LINC00710
SFTA1P
LINC00709
RNA5SP299
LINC00708
TAF3
LINC00707
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8\|ENSG00000251909.1
AKR1CL1
U8\|ENSG00000239142.1
U8\|ENSG00000251740.1
U8\|ENSG00000239148.1
U8\|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PHYH
PRKCQ
RSU1
PRPF18
AKR1C3
CDC123
PTER
USP6NL
OPTN
NET1
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
SEPHS1
KIN
DIP2C
LARP4B
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
CAMK1D
SFMBT2
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
FBXO18
RBM17
IDI2
UCN3
UCMA
C10orf111
FAM171A1
BEND7
PROSER2
C1QL3
LINC00200
PRR26
MIR1265
MIR548Q
MIR4293
MIR548AK

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q32.1.

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

Genes
U3\|ENSG00000251979.1
C4orf45
U3\|ENSG00000271817.1
ETFDH
PPID
RAPGEF2
FNIP2

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 - 19 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
3p22.2	2.908e-53	7.5762e-22	chr3:32098168-37495009	33
3p25.3	2.8873e-53	4.811e-18	chr3:1-17201156	130
9p21.3	1.7881e-20	8.9341e-17	chr9:21931610-22448737	3
2q37.3	5.6049e-16	5.6049e-16	chr2:237410659-243199373	66
1p36.13	2.3538e-09	1.1188e-08	chr1:1-31345223	502
8p23.2	2.0039e-08	1.9947e-08	chr8:3548028-4251283	2
9p23	4.2573e-09	1.9041e-07	chr9:8885227-12687261	2
6q26	9.4796e-10	0.00018131	chr6:107778359-171115067	384
6q26	7.439e-11	0.00048708	chr6:107778359-171115067	384
4q34.3	0.0008848	0.0008848	chr4:147442955-191154276	199
3p12.3	9.3546e-06	0.0016801	chr3:75363575-78166985	9
1p31.1	1.6781e-05	0.0031597	chr1:71540450-73657665	2
14q31.1	0.0074281	0.0079453	chr14:56181301-107349540	516
10q23.31	0.014509	0.014509	chr10:89506488-90034038	6
1q44	0.018371	0.018371	chr1:211306170-249250621	340
3p12.2	3.8452e-05	0.022318	chr3:78209676-86177974	9
13q13.3	0.031318	0.029358	chr13:1-72013697	345
3q11.2	0.11092	0.1728	chr3:93845715-162849334	472
3p11.1	0.011312	0.20268	chr3:81811225-93767487	18

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p22.2.

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

Genes
MLH1
RNA5SP129
snoU13\|ENSG00000238929.1
RNU6ATAC4P
TRANK1
HSPD1P6
RN7SKP227
RNA5SP128
RN7SL296P
TMPPE
CCR4
TRIM71
snoU13\|ENSG00000238646.1
GOLGA4
STAC
UBP1
LRRFIP2
EPM2AIP1
PDCD6IP
CRTAP
ARPP21
CLASP2
GPD1L
FBXL2
CNOT10
SUSD5
DYNC1LI1
CMTM6
DCLK3
CMTM7
CMTM8
C3orf35
GLB1

Genes in Wide Peak

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

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

Genes
VHL
FANCD2
PPARG
RAF1
XPC
SRGAP3
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13\|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13\|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13\|ENSG00000238345.1
snoU13\|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43\|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13\|ENSG00000239126.1
EGOT
SNORA43\|ENSG00000253049.1
RN7SKP144
RN7SL120P
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RPL32
SEC13
SETMAR
SLC6A1
SLC6A6
TIMP4
BRPF1
COLQ
CAMK1
BHLHE40
SH3BP5
VGLL4
EDEM1
TATDN2
IQSEC1
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LMCD1
SSUH2
TRNT1
CRBN
CCDC174
GHRL
ARL8B
SETD5
TMEM40
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
HDAC11
TSEN2
C3orf20
JAGN1
IL17RC
EAF1
OXNAD1
FANCD2OS
GALNT15
CHCHD4
METTL6
TAMM41
IL17RE
CPNE9
FGD5
CNTN4
SUMF1
RPUSD3
PRRT3
TPRXL
MIR563
MIR378B
MIR3714
MIR4790

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39\|ENSG00000263723.1
RBM44
COPS8
AGXT
KIF1A
BOK
COL6A3
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
RAMP1
STK25
CAPN10
PASK
ATG4B
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
ACKR3
GAL3ST2
RAB17
MLPH
C2orf54
ILKAP
ING5
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
DUSP28
ESPNL
AQP12A
KLHL30
OR6B2
PRR21
AQP12B
D2HGDH
MIR4269
MIR4786

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
RN7SL5P
SNORD27\|ENSG00000251699.1

Genes in Wide Peak

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

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

Genes
FGFR1OP
MLLT4
MYB
ROS1
TNFAIP3
GOPC
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45\|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13\|ENSG00000239136.1
AIRN
SNORA29
SNORA20\|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13\|ENSG00000252609.1
SNORD28\|ENSG00000212295.1
TFB1M
U8\|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13\|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13\|ENSG00000238594.1
RAET1K
SNORA2\|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112\|ENSG00000252476.1
SNORA27\|ENSG00000201807.1
RNA5SP219
7SK\|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13\|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33\|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13\|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13\|ENSG00000238563.1
U3\|ENSG00000253091.1
snoU13\|ENSG00000239095.1
snoU13\|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13\|ENSG00000238775.1
SNORA40\|ENSG00000212587.1
RN7SL617P
snoU13\|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13\|ENSG00000238974.1
SNORA73\|ENSG00000253090.1
SCML4
ACAT2
AMD1
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FUCA2
FYN
GJA1
GPR6
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
TBP
TCF21
TCP1
TCTE3
DYNLT1
THBS2
NR2E1
TPD52L1
UTRN
EZR
VIP
EPM2A
DDO
RNASET2
SNX3
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
MED23
QKI
AKAP7
WTAP
AKAP12
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
SEC63
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
OSTM1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TUBE1
CDC40
RWDD1
AIG1
SNX9
MPC1
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
SOBP
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
ABRACL
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
ARMC2
L3MBTL3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
ARHGAP18
SYTL3
GTF3C6
MTFR2
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAGAP
TAAR9
TAAR1
NCOA7
HINT3
PACRG
RAET1E
ZC2HC1B
RAET1L
SAMD3
PNLDC1
RNF217
NKAIN2
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
WDR27
MCM9
SHPRH
CEP57L1
PPIL6
DCBLD1
PRR18
TAAR6
SLC35D3
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
SUMO4
CENPW
SOGA3
CEP85L
C6orf120
THEMIS
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR588
METTL24
TMEM242
TRAPPC3L
MIR1202
MIR1273C
MIR3144
MIR3918
MIR3939
MIR3668
SMLR1
MIR4466
MIR4465
MIR548AJ1
MIR548H5

Genes in Wide Peak

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

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

Genes
FGFR1OP
MLLT4
MYB
ROS1
TNFAIP3
GOPC
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45\|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13\|ENSG00000239136.1
AIRN
SNORA29
SNORA20\|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13\|ENSG00000252609.1
SNORD28\|ENSG00000212295.1
TFB1M
U8\|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13\|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13\|ENSG00000238594.1
RAET1K
SNORA2\|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112\|ENSG00000252476.1
SNORA27\|ENSG00000201807.1
RNA5SP219
7SK\|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13\|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33\|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13\|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13\|ENSG00000238563.1
U3\|ENSG00000253091.1
snoU13\|ENSG00000239095.1
snoU13\|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13\|ENSG00000238775.1
SNORA40\|ENSG00000212587.1
RN7SL617P
snoU13\|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13\|ENSG00000238974.1
SNORA73\|ENSG00000253090.1
SCML4
ACAT2
AMD1
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FUCA2
FYN
GJA1
GPR6
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
TBP
TCF21
TCP1
TCTE3
DYNLT1
THBS2
NR2E1
TPD52L1
UTRN
EZR
VIP
EPM2A
DDO
RNASET2
SNX3
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
MED23
QKI
AKAP7
WTAP
AKAP12
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
SEC63
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
OSTM1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TUBE1
CDC40
RWDD1
AIG1
SNX9
MPC1
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
SOBP
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
ABRACL
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
ARMC2
L3MBTL3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
ARHGAP18
SYTL3
GTF3C6
MTFR2
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAGAP
TAAR9
TAAR1
NCOA7
HINT3
PACRG
RAET1E
ZC2HC1B
RAET1L
SAMD3
PNLDC1
RNF217
NKAIN2
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
WDR27
MCM9
SHPRH
CEP57L1
PPIL6
DCBLD1
PRR18
TAAR6
SLC35D3
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
SUMO4
CENPW
SOGA3
CEP85L
C6orf120
THEMIS
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR588
METTL24
TMEM242
TRAPPC3L
MIR1202
MIR1273C
MIR3144
MIR3918
MIR3939
MIR3668
SMLR1
MIR4466
MIR4465
MIR548AJ1
MIR548H5

Genes in Wide Peak

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

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

Genes
DUX4
FBXW7
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31\|ENSG00000253013.1
TLR3
snoU13\|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13\|ENSG00000239116.1
snoU13\|ENSG00000238596.1
snoU13\|ENSG00000238319.1
U3\|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173
snoU13\|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51\|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51\|ENSG00000207171.1
snoU13\|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3\|ENSG00000251979.1
C4orf45
U3\|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
SNORD73A
SNORD73
RNA5SP168
RNA5SP167
RNA5SP166
RN7SL254P
MIR4799
RNA5SP165
TMEM184C
AGA
SLC25A4
CASP3
LRBA
CLCN3
CPE
CTSO
DCTD
EDNRA
ETFDH
F11
ACSL1
FAT1
FGA
FGG
FRG1
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HPGD
ING2
IRF2
KLKB1
NR3C2
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
POU4F2
PPID
RPS3A
MSMO1
SFRP2
TDO2
TLL1
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
MAB21L2
ADAM29
ANXA10
KLHL2
PALLD
KIAA0922
TRIM2
FAM149A
FBXO8
ARFIP1
SPOCK3
AADAT
FAM198B
ASIC5
GALNT7
CLDN22
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
TMA16
DDX60
CDKN2AIP
TENM3
LRP2BP
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
ARHGAP10
MLF1IP
MAP9
WWC2
CEP44
SNX25
TTC29
MND1
TKTL2
CBR4
FHDC1
PRMT10
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
SH3D19
FAM218A
DCLK2
TRIM60
RBM46
C4orf46
TIGD4
RWDD4
CCDC111
TRIML2
CCDC110
RNF175
TRIML1
PRSS48
ANKRD37
TRIM61
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
FAM160A1
CLDN24
MIR1305
MIR548G
MIR3140
MIR4276
MIR3945
MIR4455
MIR4453

Genes in Wide Peak

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

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

Genes
RN7SL647P
RN7SL92P
ZNF717
LINC00960
FAM86DP
ROBO2
FRG2C
MIR1324
MIR4273

Genes in Wide Peak

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

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

Genes
RN7SKP19
NEGR1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.1.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51\|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13\|ENSG00000238853.1
RN7SL546P
snoU13\|ENSG00000239061.1
RN7SL472P
LINC00524
U3\|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113\|ENSG00000222185.1
SNORD112\|ENSG00000252009.1
SNORD113\|ENSG00000222095.1
SNORD113\|ENSG00000201710.1
SNORD113\|ENSG00000201036.1
SNORD113\|ENSG00000201500.1
SNORD113\|ENSG00000200150.1
SNORD112\|ENSG00000251918.1
SNORD112\|ENSG00000252144.1
SNORD112\|ENSG00000251949.1
SNORD112\|ENSG00000252873.1
SNORD112\|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6\|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13\|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3\|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13\|ENSG00000238978.1
SNORA79\|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46\|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32\|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7\|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13\|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13\|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11\|ENSG00000221060.1
SLC10A1
CCDC177\|ENSG00000267909.1
CCDC177\|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3\|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3\|ENSG00000200693.1
WDR89
SCARNA20\|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112\|ENSG00000252380.1
SIX1
U3\|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
RN7SKP99
NAA30
RN7SL461P
LINC00520
RPL13AP3
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SLC8A3
SNAPC1
SPTB
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
AREL1
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
TIMM9
MLH3
KCNH5
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
DACT1
EVL
GSKIP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
TMEM260
CDCA4
NRDE2
ATG2B
UBR7
C14orf105
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
AP5M1
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNT16
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
SMOC1
MOAP1
IRF2BPL
MPP5
INF2
PCNXL4
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
IFT43
L3HYPDH
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
RDH12
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SYNE3
TMEM30B
EML5
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
C14orf39
CCDC85C
SERPINA9
VSX2
SLC35F4
LRRC9
COX8C
ASPG
RAB15
TOMM20L
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
LINC00238
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4505
MIR4708
MIR151B
MIR4710
MIR2392
MIR5694

Genes in Wide Peak

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

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

Genes
PTEN
SNORD74\|ENSG00000200891.1
RN7SL78P
CFL1P1
ATAD1
KLLN

Genes in Wide Peak

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

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

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25\|ENSG00000252011.1
SNORD112\|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25\|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13\|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8\|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13\|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51\|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13\|ENSG00000239094.1
snoU13\|ENSG00000238545.1
MIR4742
snoU13\|ENSG00000238856.1
MIR320B2
SNORA72\|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13\|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13\|ENSG00000238576.1
snoU13\|ENSG00000238798.1
U3\|ENSG00000221673.1
RNA5SP76
SLC30A10
U3\|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116\|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26\|ENSG00000212187.1
RN7SL344P
SLC30A1
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
ZNF124
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
INTS7
AHCTF1
NSL1
OR2M4
OR2L2
OR2T1
RPS6KC1
TAF5L
DISC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
DESI2
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
ZNF692
IARS2
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
SIPA1L2
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
SPRTN
OBSCN
EFCAB2
MLK4
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
NLRP3
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
GCSAML
CNIH3
EXOC8
C1orf227
FAM71A
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
TRIM67
MAP1LC3C
OR13G1
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.2.

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

Genes
snoZ40
MIR5688
LINC00971
RN7SL751P
RN7SKP61
GBE1
ROBO1
CADM2
MIR3923

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.3.

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

Genes
CDX2
BRCA2
FLT3
LCP1
RB1
LHFP
LINC00348
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13\|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13\|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31\|ENSG00000199477.1
SNORA31\|ENSG00000253051.1
7SK\|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13\|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13\|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116\|ENSG00000212553.1
RNY4P14
snoU13\|ENSG00000238408.1
LINC00366
LINC00571
RNA5SP26
RN7SKP1
ARL2BPP3
DCLK1
LINC00445
LINC00457
SNORA25\|ENSG00000199196.1
LINC00423
RNY1P4
SNORA16\|ENSG00000212293.1
ZAR1L
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
LINC00365
LINC00544
LINC00572
LINC00297
MTUS2
RN7SL272P
URAD
LINC00543
GSX1
RNY1P1
SNORA27\|ENSG00000207051.1
SNORD102
LINC00415
RNY1P3
RN7SL741P
RN7SL289P
PABPC3
LSP1\|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
MIR2276
ANKRD20A19P
LINC00352
LINC00327
LINC00362
RNY3P4
LINC00621
SNORD36\|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13\|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27\|ENSG00000252128.1
snoU13\|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13\|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
ZMYM2
IFT88
TNFSF11
SUCLA2
CCNA1
MTMR6
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
VWA8
ZC3H13
SPG20
LRCH1
SACS
INTS6
LATS2
CKAP2
NUFIP1
NBEA
PCDH17
RGCC
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
ENOX1
RCBTB1
NUDT15
KIAA1704
TNFRSF19
SUPT20H
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
XPO4
PCDH20
MRP63
SMIM2
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
EBPL
MEDAG
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
HNRNPA1L2
B3GALTL
DGKH
CCDC122
STOML3
AMER2
USP12
MTIF3
FAM194B
SPERT
FAM124A
LRRC63
N6AMT2
SKA3
MICU2
SPATA13
LNX2
SLC25A30
PAN3
SIAH3
KCNRG
SLC46A3
C1QTNF9
FREM2
NEK5
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
DLEU2
ATP5EP2
ALG11
SERPINE3
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
MIR759
MIR320D1
MIR3168
MIR4305
MIR3169
MIR3613
SPG20OS
SOHLH2
MIR4704
MIR548X2
MIR4703
MIR5007
MIR5693

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.2.

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

Genes
FOXL2
CBLB
GATA2
MLF1
RPN1
GMPS
TFG
SPTSSB
PPM1L
SNORA72\|ENSG00000207084.1
KRT8P12
SCARNA7
MIR15B
C3orf80
MIR3919
SHOX2
RN7SKP46
RNA5SP146
CCNL1
LINC00881
LINC00880
RN7SKP177
LINC00886
snoU13\|ENSG00000271922.1
U8\|ENSG00000201398.1
RN7SL300P
RAP2B
SUCNR1
IGSF10
P2RY12
RNA5SP145
FAM188B2
snoU13\|ENSG00000243321.2
ANKUB1
TM4SF4
CPHL1P
U3\|ENSG00000251800.1
RNA5SP144
PBX2P1
CHST2
RN7SKP25
RNA5SP143
GRK7
RNF7
CLSTN2
RN7SL724P
RN7SKP124
PIK3CB
SOX14
RNA5SP142
RNY4P4
U8\|ENSG00000253004.1
RNA5SP141
KY
RPL39P5
RNA5SP140
TFP1
SNORA33\|ENSG00000201827.1
snoU13\|ENSG00000238701.1
MIR5704
SNORA58\|ENSG00000249020.1
RN7SKP212
COL6A4P2
FAM86HP
ALG1L2
RN7SL752P
SNORA7B
RPL32P3
snoU13\|ENSG00000238874.1
snoU13\|ENSG00000252435.1
RN7SL698P
SNORA24\|ENSG00000207130.1
MIR1280
RNA5SP139
NUP210P1
TXNRD3NB
RNA5SP138
U1\|ENSG00000272020.1
FAM86JP
snoU13\|ENSG00000238992.1
MIR5092
RNA5SP137
MIR544B
UMPS
MIR5002
SNORA5
PTPLB
SEC22A
snoU13\|ENSG00000238480.1
SNORD112\|ENSG00000252170.1
RN7SL172P
snoU13\|ENSG00000238670.1
ARGFX
MIR5682
FSTL1
RN7SL397P
RN7SL762P
COX17
TIMMDC1
LINC00901
TUSC7
RN7SL582P
LINC00903
RN7SL815P
RN7SL767P
MIR4446
SNORD112\|ENSG00000253076.1
SLC35A5
MIR567
PVRL3
RNU6ATAC15P
LINC00488
U3\|ENSG00000221633.1
SNORA70\|ENSG00000202379.1
LINC00636
LINC00635
LINC00883
LINC00882
snoU13\|ENSG00000238525.1
snoU13\|ENSG00000238312.1
SNORA31\|ENSG00000252989.1
NIT2
SNORD61\|ENSG00000238377.1
TMEM30C
LINC00973
OR5H8P
OR5AC1
CRYBG3\|ENSG00000080200.5
CRYBG3\|ENSG00000233280.2
MTRNR2L12
MTHFD2P1
LINC00879
AADAC
ACPP
ADCY5
ADPRH
AGTR1
ALCAM
ATP1B3
ATP6V1A
ATR
CASR
CD80
CD86
CD47
COL8A1
CP
CPA3
CPB1
CPOX
CSTA
DRD3
EPHB1
GAP43
GOLGB1
GP9
GPR15
GSK3B
GTF2E1
GYG1
HCLS1
HGD
IL12A
ITGB5
KPNA1
KPNA4
LSAMP
TM4SF1
MBNL1
MCM2
MME
CD200
MYLK
NCK1
NDUFB4
P2RY1
PCCB
PFN2
PLOD2
PLS1
PLSCR1
PLXNA1
PPP2R3A
PTX3
RARRES1
RASA2
RBP1
RBP2
RHO
RPL24
RYK
SIAH2
SLC15A2
SLCO2A1
HLTF
SSR3
TF
TFDP2
TRH
TRPC1
UPK1B
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
BFSP2
RUVBL1
B4GALT4
B3GALNT1
SNX4
NR1I2
MBD4
H1FX
KALRN
SLC33A1
COPB2
STXBP5L
GUCA1C
IQCB1
DZIP3
TSC22D2
TOMM70A
P2RY14
SMC4
CD96
STAG1
ST3GAL6
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
MRPL3
FILIP1L
RNF13
MGLL
MRAS
COPG1
MYH15
PLCH1
TMCC1
PLXND1
DNAJC13
U2SURP
C3orf27
ANAPC13
ARMC8
C3orf17
ABI3BP
WWTR1
TIPARP
ARHGEF26
ZBTB20
OR5K1
OR5H1
FAM162A
PCOLCE2
NPHP3
ATP2C1
ZBTB11
MORC1
SERP1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
SCHIP1
PIK3R4
PODXL2
TRAT1
IMPG2
NMD3
COMMD2
A4GNT
DBR1
CLDN18
RSRC1
PLA1A
AMOTL2
ACKR4
RAB6B
SELT
FBXO40
P2RY13
IL20RB
GPR87
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
TRMT10C
SLC41A3
TMEM45A
IFT57
MSL2
FAIM
SLC25A36
DPPA4
TMEM39A
ABHD10
CDV3
IFT122
TBC1D23
WDR52
EAF2
CLDND1
MUC13
LXN
C3orf37
MRPS22
POGLUT1
BBX
PLSCR2
PLSCR4
PCNP
SENP7
HEG1
KIAA1257
ARHGAP31
IFT80
KIAA1407
KIAA1524
SRPRB
BPESC1
EEFSEC
POPDC2
NFKBIZ
ATG3
MFSD1
CCDC14
TMEM108
OR5H6
OR5H2
ZXDC
ZBED2
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
EFCC1
NEK11
UBA5
C3orf36
ARL14
NAA50
CEP63
CEP70
ABTB1
SLC35G2
OR5AC2
PARP9
ESYT3
EIF2A
ARL6
ZIC4
ACAD11
CHCHD6
CMSS1
HPS3
SLC12A8
RETNLB
CCDC54
MINA
GPR128
DIRC2
GFM1
MAATS1
PHLDB2
EFCAB12
BOC
NXPE3
SPSB4
ACPL2
TXNRD3
OSBPL11
LRRC58
TM4SF18
MED12L
CPNE4
CCDC58
OTOL1
ZPLD1
CD200R1
DCBLD2
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
H1FOO
DTX3L
DPPA2
CCDC80
BTLA
ROPN1B
C3orf22
C3orf55
C3orf79
SPICE1
NUDT16P
IGSF11
C3orf30
PARP15
DNAJB8
GPR156
CHST13
KBTBD12
DHX36
DZIP1L
ALG1L
GABRR3
TIGIT
C3orf58
KIAA2018
ZBTB38
ZDHHC23
COL6A5
GK5
PLCXD2
GCSAM
SLC9A9
EPHA6
RABL3
C3orf56
C3orf33
SLC9C1
ILDR1
TRIM59
TRIM42
RAB43
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
NME9
LNP1
CCDC37
NMNAT3
PRR23B
PRR23C
PLSCR5
LEKR1
C3orf72
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
TMEM14E
IQCJ
MIR568
PRR23A
MIR548I1
MIR3921
ISY1
MIR4445
MIR4796
MIR4788
MIR548AB
MIR4447
MIR5186

Genes in Wide Peak

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

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

Genes
U3\|ENSG00000212598.1
HTR1F
RNU6ATAC6P
RN7SKP284
snoZ40
MIR5688
LINC00971
EPHA3
POU1F1
PROS1
CGGBP1
CHMP2B
ZNF654
CADM2
C3orf38
VGLL3
STX19
MIR4795

Arm-level results

Table 3. Get Full Table Arm-level significance table - 28 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	1300	0.04	-3.43	1	0.12	3.11	0.00322
1q	1195	0.10	0.727	0.684	0.08	-0.435	1
2p	624	0.15	3.11	0.00322	0.03	-5.3	1
2q	967	0.15	4.34	2.61e-05	0.03	-4.71	1
3p	644	0.09	-0.643	1	0.75	46.8	0
3q	733	0.14	2.12	0.0536	0.22	8.2	6.5e-16
4p	289	0.03	-6.18	1	0.14	1.44	0.191
4q	670	0.03	-5.65	1	0.13	1.5	0.181
5p	183	0.37	16.8	0	0.02	-5.6	1
5q	905	0.40	23.2	0	0.02	-4.6	1
6p	710	0.03	-5.4	1	0.19	6.46	2.75e-10
6q	556	0.02	-5.8	1	0.25	9.9	0
7p	389	0.33	14.9	0	0.01	-6.55	1
7q	783	0.33	17	0	0.01	-6.05	1
8p	338	0.06	-3.7	1	0.29	11.9	0
8q	551	0.12	0.594	0.755	0.15	2.66	0.0123
9p	301	0.03	-5.14	1	0.29	11.9	0
9q	700	0.03	-4.68	1	0.29	13.9	0
10p	253	0.03	-5.72	1	0.13	0.744	0.551
10q	738	0.03	-5.31	1	0.17	5	1.32e-06
11p	509	0.06	-3.73	1	0.04	-5.41	1
11q	975	0.06	-2.99	1	0.05	-3.83	1
12p	339	0.23	7.8	2.2e-14	0.01	-6.66	1
12q	904	0.23	10.2	0	0.01	-6.02	1
13q	560	0.05	-4.3	1	0.14	1.94	0.0775
14q	938	0.05	-2.78	1	0.42	24.6	0
15q	810	0.05	-3.64	1	0.07	-2.42	1
16p	559	0.21	6.89	1.4e-11	0.02	-5.71	1
16q	455	0.19	5.44	1.07e-07	0.04	-4.9	1
17p	415	0.05	-4.4	1	0.09	-1.6	1
17q	972	0.06	-2.47	1	0.06	-2.89	1
18p	104	0.06	-4.37	1	0.18	3.88	0.000198
18q	275	0.06	-4.18	1	0.19	4.76	4e-06
19p	681	0.10	-0.744	1	0.03	-5.79	1
19q	935	0.10	0.425	0.86	0.01	-6.1	1
20p	234	0.21	6.33	5.64e-10	0.02	-6.29	1
20q	448	0.21	7.11	3.41e-12	0.01	-6.44	1
21q	258	0.11	-1.08	1	0.12	-0.456	1
22q	564	0.08	-2.06	1	0.08	-2.19	1
Xp	418	0.05	-4.21	1	0.10	-1.03	1
Xq	668	0.06	-3.61	1	0.10	-0.7	1

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/KIRC-TP/22232852/GDAC_MergeDataFiles_20405487/KIRC-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_GENCODE_v18_20140127.mat
CNV Files = /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.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 528 Input Tumor Samples.

Tumor Sample Names
TCGA-3Z-A93Z-01A-11D-A36W-01
TCGA-6D-AA2E-01A-11D-A36W-01
TCGA-A3-3306-01A-01D-0858-01
TCGA-A3-3307-01A-01D-0858-01
TCGA-A3-3308-01A-02D-1322-01
TCGA-A3-3311-01A-02D-1322-01
TCGA-A3-3313-01A-02D-1322-01
TCGA-A3-3316-01A-01D-0858-01
TCGA-A3-3317-01A-02D-1322-01
TCGA-A3-3319-01A-02D-1322-01

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:

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)

[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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