Copy number analysis (GISTIC2)
Esophageal Carcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1R20ZC3
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1R20ZC3
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 50 tumor samples used in this analysis: 21 significant arm-level results, 21 significant focal amplifications, and 32 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 - 21 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 | 6.1399e-43 | 6.1399e-43 | chr11:69523550-70248899 | 8
8q24.21 | 1.1595e-11 | 1.1595e-11 | chr8:128022833-129051939 | 11
7p11.2 | 1.3551e-07 | 1.8091e-07 | chr7:54842550-55715052 | 3
7q21.3 | 6.9104e-06 | 7.6041e-06 | chr7:87180199-99142620 | 92
3q29 | 0.00034192 | 0.00034192 | chr3:153593438-198022430 | 284
18q11.2 | 0.0014244 | 0.0014244 | chr18:20863588-22012348 | 12
19p13.2 | 0.0032259 | 0.0032259 | chr19:7296453-7398264 | 0 [INSR]
18p11.32 | 0.011924 | 0.011924 | chr18:983189-2081265 | 1
8p11.21 | 0.014739 | 0.014739 | chr8:41578578-42518767 | 10
6p21.1 | 0.015362 | 0.016905 | chr6:43416343-44056584 | 15
10p11.21 | 0.018882 | 0.018882 | chr10:35335459-35408297 | 1
12p13.33 | 0.014126 | 0.022577 | chr12:1-1071814 | 12
11p13 | 0.046791 | 0.051238 | chr11:34435171-36024467 | 12
Xp11.4 | 0.057199 | 0.057199 | chrX:40732423-40742477 | 0 [LOC100132831]
17q24.3 | 0.076179 | 0.076179 | chr17:66364805-70596221 | 19
19q12 | 0.095684 | 0.095684 | chr19:29460241-35198907 | 45
1q25.2 | 0.12026 | 0.12026 | chr1:120522602-249250621 | 1158
12p12.1 | 0.099202 | 0.1647 | chr12:24880663-25784000 | 7
6q12 | 0.19465 | 0.20715 | chr6:65318771-65423033 | 1
2q14.2 | 0.22151 | 0.22151 | chr2:102883357-123680256 | 133
1p13.1 | 0.2376 | 0.2376 | chr1:116001985-116922852 | 6

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1206
hsa-mir-1205
hsa-mir-1204
POU5F1B
PVT1
LOC727677
MIR1205
MIR1206
MIR1204
PCAT1

Genes in Wide Peak

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

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

Genes
EGFR
LANCL2
VOPP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.3.

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

Genes
CDK6
AKAP9
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
ASNS
CALCR
KRIT1
COL1A2
CYP51A1
DLX5
DLX6
DYNC1I1
GNG11
GNGT1
NPTX2
OCM2
PDK4
PEX1
CDK14
ABCB1
PON1
PON2
PON3
SRI
TAC1
MTERF
SHFM1
TFPI2
TRRAP
FZD1
BUD31
SGCE
CLDN12
ATP5J2
ARPC1B
SLC25A13
BET1
ARPC1A
CPSF4
DBF4
PDAP1
LMTK2
PEG10
ZKSCAN5
BRI3
TECPR1
PTCD1
STEAP1
ASB4
ADAM22
ANKIB1
SAMD9
PPP1R9A
CCDC132
BAIAP2L1
SLC25A40
ACN9
SMURF1
GATAD1
CASD1
STEAP4
C7orf63
RBM48
ZNF394
MYH16
MGC16142
GTPBP10
RUNDC3B
BHLHA15
SAMD9L
C7orf62
ZNF804B
TMEM130
HEPACAM2
FAM133B
STEAP2
DLX6-AS1
ZNF789
MGC72080
LRRD1
FLJ42280
KPNA7
DPY19L2P4
MIR489
MIR591
MIR653
LOC728066
MIR3609
LOC100506136
ATP5J2-PTCD1
MIR4652

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q29.

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

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

Genes in Wide Peak

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

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

Genes
hsa-mir-320c-2
LAMA3
NPC1
RIOK3
CABYR
C18orf8
IMPACT
TMEM241
OSBPL1A
TTC39C
ANKRD29
MIR320C2

Genes in Wide Peak

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

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

Genes
LINC00470

Genes in Wide Peak

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

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

Genes
ANK1
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
AP3M2
DKK4
C8orf40

Genes in Wide Peak

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

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

Genes
POLH
VEGFA
POLR1C
MAD2L1BP
YIPF3
GTPBP2
MRPS18A
XPO5
DLK2
ABCC10
TJAP1
C6orf223
RSPH9
LRRC73
LOC100132354

Genes in Wide Peak

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

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

Genes
CUL2

Genes in Wide Peak

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

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute's 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 11p13.

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

Genes
CAT
CD44
ELF5
SLC1A2
PDHX
FJX1
PAMR1
EHF
APIP
TRIM44
LDLRAD3
MIR1343

Genes in Wide Peak

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

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

Genes
PRKAR1A
hsa-mir-635
KCNJ2
KCNJ16
MAP2K6
SOX9
ABCA10
ABCA9
ABCA8
ARSG
ABCA6
ABCA5
FAM20A
WIPI1
KCNJ2-AS1
LINC00511
MIR635
LOC100499467
MIR4524A

Genes in Wide Peak

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

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

Genes
CEBPA
CCNE1
CEBPG
GPI
LRP3
PEPD
UQCRFS1
URI1
PDCD5
KIAA0355
ZNF536
UBA2
POP4
SLC7A9
ZNF507
LSM14A
GPATCH1
ZNF302
SLC7A10
TSHZ3
CHST8
KCTD15
PLEKHF1
LOC80054
C19orf12
ANKRD27
PDCD2L
CEP89
RHPN2
C19orf40
TDRD12
DKFZp566F0947
WDR88
WTIP
DPY19L3
LOC284395
SCGB2B2
VSTM2B
RGS9BP
NUDT19
LOC400684
SCGB1B2P
SCGB2B3P
LOC100505835
THEG5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q25.2.

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

Genes
ABL2
ARNT
BCL9
ELK4
FCGR2B
FH
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
TPR
PDE4DIP
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ACTA1
ACTN2
ADAR
ADORA1
PARP1
ADSS
AGT
ALDH9A1
APCS
APOA2
FASLG
ARF1
ASTN1
SERPINC1
ATF3
ATP1A2
ATP1A4
ATP1B1
ATP2B4
AVPR1B
BGLAP
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD34
CD48
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CHRNB2
CKS1B
CLK2
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSRP1
CTSE
CTSK
CTSS
CD55
DHX9
DPT
ECM1
EIF2D
EFNA1
EFNA3
EFNA4
ELF3
ENSA
EPHX1
EPRS
ESRRG
ETV3
F5
F13B
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GALNT2
GBA
GBAP1
GJA5
GJA8
GLUL
GNG4
GPR25
GUK1
H3F3A
HDGF
CFH
CFHR1
CFHR2
MR1
HLX
HNRNPU
HSD11B1
HSPA6
HSPA7
IFI16
IL6R
IL10
ILF2
INSRR
IRF6
ITPKB
IVL
KCNH1
KCNJ9
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
LMNA
LMX1A
LOR
LY9
MARK1
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MPZ
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NEK2
NHLH1
NID1
NIT1
NPR1
DDR2
NVL
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PPP2R5A
PRELP
PRKAB2
PROX1
PSEN2
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PEX19
RAB4A
RAB13
RABIF
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
RYR2
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRP9
TROVE2
SSR2
AURKAPS1
XCL2
TARBP1
CNTN2
TBCE
VPS72
TGFB2
LEFTY2
THBS3
TCHH
TLR5
GPR137B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TRAF5
CCT3
TSNAX
TUFT1
TNFSF4
UCK2
USF1
USH2A
WNT9A
ZNF124
SLC30A1
DAP3
NPHS2
BTG2
HIST3H3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
GNPAT
DYRK3
CDC42BPA
RGS5
PPFIA4
ITGA10
BLZF1
DEGS1
KMO
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
TNFSF18
TAF1A
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
PRPF3
EXO1
ARHGEF2
DEDD
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
AIM2
GGPS1
RASAL2
ADAMTS4
SEC22B
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
TMEM63A
TOMM20
URB2
ARHGEF11
CEP350
CEP170
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
RBM8A
NR1I3
AKT3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
BPNT1
PIAS3
TIMM17A
LRRN2
HAX1
ZNF238
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
LEFTY1
SPHAR
PMVK
FAM189B
CAPN9
NES
KDM5B
SDCCAG8
CFHR4
CFHR3
OCLM
JTB
MTMR11
MLLT11
SLC27A3
IL24
TDRKH
CD160
CELF3
DUSP10
PMF1
DUSP12
VPS45
COG2
PLEKHA6
KIAA0907
KIFAP3
ATF6
RBM34
KIF21B
NMNAT2
NFASC
POGZ
GLT25D2
RGL1
SYT11
PRRC2C
FBXO28
RPRD2
CAMSAP2
SRGAP2
SMG5
NCSTN
CRB1
GPR161
ABCB10
ZNF281
SNAPIN
OPN3
PHLDA3
RUSC1
CA14
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
TRIM58
INTS7
OLFML2B
AHCTF1
C1orf43
NSL1
DNM3
TOR1AIP1
CHTOP
OR1C1
LCE2B
OR2M4
OR2L2
OR2L1P
OPTC
OR10J1
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
RNU5F-1
USP21
DIEXF
TAF5L
CACYBP
SLC39A1
DISC2
DISC1
RNF115
KLHL20
LAMTOR2
FLVCR1
UBE2T
CNIH4
TMOD4
PYCR2
NME7
NENF
IL19
CERS2
CRNN
G0S2
IL20
DCAF8
F11R
RRP15
GLRX2
BOLA1
PPPDE1
ZBTB7B
RRNAD1
ADIPOR1
SCCPDH
APH1A
TRIM17
KCTD3
PLEKHO1
ACP6
IER5
UCHL5
C1orf9
GPR89B
HSD17B7
UFC1
DTL
METTL13
OAZ3
CYB5R1
ARID4B
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
EGLN1
KIAA1383
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
MARC2
SUSD4
KIF26B
RALGPS2
GPATCH2
HEATR1
MSTO1
DARS2
GOLPH3L
KLHDC8A
ETNK2
KIRREL
TMEM206
YY1AP1
YOD1
BATF3
SLC30A10
UBE2Q1
ITLN1
ZNF692
IARS2
IPO9
C1orf112
HHAT
ENAH
NUP133
RCOR3
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SERTAD4
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
SMYD2
LHX9
OTUD7B
ADCK3
RAB25
PGLYRP4
ZNF695
RHBG
SCYL3
GJC2
CAMK1G
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
SIPA1L2
ZNF687
POGK
HCN3
KIAA1614
FAM5B
C1orf114
SLAMF7
ZP4
CADM3
RHOU
PRUNE
KLHL12
LGR6
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
TFB2M
SEMA4A
TOR3A
RFWD2
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
MRPL9
JMJD4
INTS3
SCNM1
C1orf116
MGC4473
C1orf35
FCRL2
TTC13
CDC73
MRPL24
PGBD5
TNFAIP8L2
C1orf54
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PAQR6
PCNXL2
TRIM46
C1orf129
TARS2
WDR26
EDEM3
FLAD1
TRAF3IP3
SH3BP5L
NPL
OR6N2
OR6K2
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
MIXL1
C1orf124
FCAMR
OBSCN
C1orf49
HORMAD1
TOMM40L
POLR3GL
TMEM79
NTPCR
EFCAB2
ACBD6
KIAA1804
ZBTB37
LCE3D
LINC00260
LINC00467
FCRLA
ANKRD36BP1
ZNF496
C1orf198
PPP1R15B
MAEL
DISP1
RGS8
WNT3A
NAV1
SEC16B
AQP10
LHX4
SLAMF9
PYGO2
ANGEL2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
LEMD1
ZNF670
C1orf85
NLRP3
PGLYRP3
GNRHR2
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
FAM36A
TSEN15
FAM129A
SNAP47
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
C1orf96
KLHDC9
AXDND1
HIST2H3C
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
OR10J5
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
SPATA17
EDARADD
C1orf182
IQGAP3
APOA1BP
MRPL55
HIST3H2BB
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ITLN2
C1orf74
CREB3L4
BROX
C1orf51
SLC35F3
LOC148696
LOC148709
PTPRVP
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
LELP1
RC3H1
DCST1
CNIH3
LOC149134
METTL11B
FAM78B
SHISA4
EXOC8
BNIPL
LRRC71
RNF187
PYHIN1
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
SPRR4
C1orf55
CNST
PPIAL4A
TTC24
C1orf65
PDIA3P
LCE4A
NBPF11
NUDT17
FLJ23867
PLD5
C1orf100
KRTCAP2
CRTC2
IBA57
TMEM9
SLC41A1
OR2T6
LCE5A
LOC255654
SYT14
C1orf101
ARHGAP30
C1orf192
ASPM
TIPRL
PGBD2
RIIAD1
THEM5
OR2L13
SLC9A11
OR14A16
NBPF15
LINC00303
LOC284576
LOC284578
LOC284581
ANKRD34A
RUSC1-AS1
LOC284648
DKFZP564C196
C1orf204
C1orf111
LOC284688
HNRNPU-AS1
LIN9
VN1R5
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
ANKRD45
FAM5C
ZNF678
PRSS38
C1orf110
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR10R2
FCRL6
KCNT2
OR2T29
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
IRF2BP2
ZBTB41
CYCSP52
LOC375010
PEAR1
SFT2D2
MIA3
C1orf95
FAM89A
RPS10P7
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf226
LOC400794
C1orf220
C1orf140
NBPF9
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR194-1
MIR199A2
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
MIR9-1
RGS21
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR10J3
OR2W5
OR13G1
MIR135B
KPRP
LCE6A
SUMO1P3
C1orf98
HIST2H4B
DUSP5P
C1orf133
PRR9
MIR488
SNORD74
RPL31P11
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
PPIAL4G
PPIAL4D
LOC645166
SNRPD2P2
LOC645676
POU5F1P4
RPS7P5
S100A7L2
LOC646268
LOC646627
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
TMEM183B
FAM72B
PCP4L1
SCARNA3
SCARNA4
SNORA14B
SNORA36B
SNORA42
SNORA77
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
LOC728463
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
FAM72A
LOC730102
LOC730159
LOC730227
PPIAL4E
LOC731275
PFN1P2
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
LOC100130000
LOC100130093
LOC100130331
TSTD1
LOC100131234
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100287814
LGALS8-AS1
GM140
LOC100288079
LOC100289211
MIR1182
MIR1537
MIR1231
MIR1278
MIR1295A
MIR548F1
MIR664
LOC100302401
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3119-1
MIR3123
MIR3124
MIR3120
MIR4260
MIR3122
MIR4257
MIR3119-2
MIR4258
MIR3121
MIR3620
MIR3658
MIR3916
LOC100505633
LOC100505666
LOC100505795
PROX1-AS1
LOC100505918
LOC100506023
LOC100506046
KDM5B-AS1
LOC100506795
LOC100506810
PMF1-BGLAP
LOC100527964
ZNF670-ZNF695
TNFAIP8L2-SCNM1
MIR4753
MIR4666A
MIR4424
MIR4677
MIR4735
MIR4671
MIR4654
MIR4427
MIR4742
DNM3OS
LINC00538

Genes in Wide Peak

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

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
EYS

Genes in Wide Peak

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

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

Genes
PAX8
TTL
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
BUB1
DBI
EN1
FHL2
GLI2
IL1A
IL1B
IL1RN
INHBB
LIMS1
NPHP1
POU3F3
PTPN4
RALB
RANBP2
SCTR
SLC9A2
SLC20A1
SULT1C2
TSN
MALL
NCK2
MARCO
IL18RAP
IL18R1
DDX18
IL1RL1
TGFBRAP1
GCC2
BCL2L11
ACTR3
MERTK
EDAR
RABL2A
GPR45
CLASP1
PSD4
IL36RN
IL36B
IL37
IL36A
SULT1C4
TFCP2L1
INSIG2
CCDC93
STEAP3
ACOXL
IL36G
DPP10
EPB41L5
SLC5A7
ANAPC1
MRPS9
SOWAHC
C2orf49
TMEM185B
UXS1
SLC35F5
TMEM177
POLR1B
RGPD5
CHCHD5
MKI67IP
C2orf40
ZC3H8
ST6GAL2
IL1F10
DDX11L2
MFSD9
TMEM87B
LOC84931
LIMS3
RPL23AP7
FBLN7
C2orf76
TMEM182
TMEM37
CKAP2L
CBWD2
LOC150568
LOC151009
SEPT10
SULT1C2P1
CCDC138
C1QL2
FOXD4L1
PCDP1
LINC00116
LOC254128
LOC284998
LOC285000
PLGLA
RGPD4
SH3RF3
WASH2P
ZC3H6
SLC9A4
LOC389023
FLJ42351
LOC440894
LOC440895
LOC440900
SULT1C3
LOC541471
RGPD3
FAM138B
LOC654433
RGPD8
LOC729121
RGPD6
RNU4ATAC
LIMS3-LOC440895
LOC100287010
LOC100287216
LOC100288570
LIMS3L
MIR4265
MIR4267
MIR4266
LOC100499194
LOC100506421
LOC100507334
MIR4436B1
MIR4772
MIR4782
MIR4435-2
MIR4435-1

Genes in Wide Peak

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

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

Genes
ATP1A1
CASQ2
NHLH2
SLC22A15
VANGL1
MAB21L3

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 - 32 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 2.2929e-48 | 2.2929e-48 | chr9:21865498-21997722 | 2
16q23.1 | 2.4425e-10 | 2.4425e-10 | chr16:78129058-79627770 | 1
7q31.1 | 1.1053e-06 | 1.1053e-06 | chr7:109599468-111366370 | 2
2q22.1 | 2.3877e-07 | 2.1318e-06 | chr2:139655617-143637838 | 1
3p14.2 | 1.1049e-05 | 1.2357e-05 | chr3:59034763-61547330 | 1
Xp21.2 | 1.3068e-05 | 1.7769e-05 | chrX:30870233-32661893 | 3
10q23.31 | 0.00016773 | 0.00016773 | chr10:89617158-90533234 | 6
4q22.1 | 0.00057432 | 0.00057432 | chr4:90844993-93240505 | 1
6p25.3 | 0.0015269 | 0.0015269 | chr6:1608837-2250882 | 2
5q11.2 | 0.00015226 | 0.0016797 | chr5:58260298-59787985 | 3
20p12.1 | 0.0035188 | 0.0035188 | chr20:14302876-16252980 | 3
10p11.21 | 0.0048136 | 0.0048136 | chr10:34059131-35328087 | 1
Xq21.33 | 0.017061 | 0.016785 | chrX:96134519-98718611 | 1
19q13.31 | 0.026815 | 0.026341 | chr19:44038462-46149617 | 79
11p15.4 | 0.036223 | 0.036223 | chr11:3872464-4115961 | 2
18q12.2 | 0.037051 | 0.036223 | chr18:35235531-39060470 | 4
3q26.31 | 0.043481 | 0.043213 | chr3:173999806-175760559 | 2
5q12.3 | 0.0057526 | 0.049849 | chr5:59884318-94417957 | 173
22q11.1 | 0.070922 | 0.075756 | chr22:1-18275090 | 22
Xp11.3 | 0.028351 | 0.087117 | chrX:44702452-45008304 | 2
17q24.3 | 0.1113 | 0.1166 | chr17:70116519-71163787 | 4
4p15.31 | 0.12884 | 0.1296 | chr4:1-31150140 | 203
8p23.2 | 0.13798 | 0.13798 | chr8:2079140-6262191 | 1
11q24.3 | 0.13798 | 0.13798 | chr11:111284730-135006516 | 250
1q44 | 0.15791 | 0.15791 | chr1:178641946-249250621 | 557
6q26 | 0.16543 | 0.16875 | chr6:64422985-171115067 | 511
2q37.2 | 0.075756 | 0.18982 | chr2:192813454-243199373 | 406
3p11.1 | 0.030052 | 0.18982 | chr3:70016017-93778057 | 41
21q22.2 | 0.18982 | 0.18982 | chr21:36154821-48129895 | 147
13q14.2 | 0.21234 | 0.21437 | chr13:1-115169878 | 414
15q12 | 0.23049 | 0.22621 | chr15:1-60692978 | 434
1p35.2 | 0.23807 | 0.23807 | chr1:1-249250621 | 2410

Genes in Wide Peak

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

Table S20. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S21. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S22. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LRRN3
IMMP2L

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.2.

Table S25. Genes in bold are cancer genes as defined by The Sanger Institute's 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 10q23.31.

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

Genes
PTEN
LIPF
RNLS
LIPJ
LIPK
KLLN

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

Table S29. Genes in bold are cancer genes as defined by The Sanger Institute's 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 20p12.1.

Table S30. Genes in bold are cancer genes as defined by The Sanger Institute's 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 10p11.21.

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

Genes
PARD3

Genes in Wide Peak

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

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

Genes
RPA4

Genes in Wide Peak

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

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

Genes
BCL3
ERCC2
CBLC
hsa-mir-330
APOC1
APOC1P1
APOC2
APOC4
APOE
CKM
CLPTM1
ERCC1
FOSB
GPR4
KCNN4
BCAM
PLAUR
PVR
PVRL2
RELB
RTN2
VASP
XRCC1
ZNF45
ZNF221
ZNF222
ZNF155
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
ZNF235
TOMM40
ZNF234
PPP1R13L
CD3EAP
CLASRP
EML2
ZNF285
SMG9
IRGC
CEACAM19
MARK4
TRAPPC6A
ZNF576
GEMIN7
OPA3
EXOC3L2
CEACAM20
IRGQ
ZNF428
PPM1N
KLC3
IGSF23
ZNF296
CADM4
LYPD5
ZNF283
PPP1R37
NKPD1
ZNF404
ZNF284
ZNF233
CEACAM22P
CEACAM16
BLOC1S3
LOC390940
MIR330
SRRM5
LOC100287177
LOC100379224
LOC100505715
APOC4-APOC2
MIR4531

Genes in Wide Peak

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

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

Genes
STIM1
MIR4687

Genes in Wide Peak

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

Table S35. Genes in bold are cancer genes as defined by The Sanger Institute's 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 3q26.31.

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.3.

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

Genes
PIK3R1
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
TRIM23
ARSB
BHMT
BTF3
CCNB1
CCNH
CDK7
CETN3
CKMT2
ERCC8
COX7C
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
HTR1A
KIF2A
TNPO1
CD180
MAP1B
MEF2C
MSH3
NAIP
PMCHL2
RAD17
RASA1
RASGRF2
RPS23
SMN1
SMN2
TAF9
TBCA
NR2F1
THBS4
XRCC4
SERF1A
ENC1
AP3B1
PDE8B
HOMER1
SCAMP1
CARTPT
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
CWC27
NSA2
POLR3G
IQGAP2
SMA4
SMA5
ADAMTS6
SV2C
MRPS27
PPWD1
OTP
SSBP2
BHMT2
FAM169A
RNU5E-1
RNU5D-1
DIMT1
DMGDH
IPO11
GCNT4
POLK
SGTB
AGGF1
WDR41
DEPDC1B
BDP1
ERBB2IP
NLN
ARRDC3
ZSWIM6
ANKRA2
MCCC2
CENPK
RGNEF
SLC30A5
CENPH
MCTP1
PTCD2
ELOVL7
C5orf44
ATG10
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
SPZ1
NDUFAF2
MRPS36
ATP6AP1L
FCHO2
LYSMD3
JMY
POU5F2
TMEM171
TMEM174
POC5
ACOT12
SREK1
TMEM167A
MBLAC2
TMEM161B
MARVELD2
PAPD4
ZNF366
FAM151B
S100Z
CCDC125
CMYA5
ANKRD31
SERINC5
KIAA0825
NBPF22P
C5orf64
RNF180
SREK1IP1
ANKRD34B
MTX3
MAST4
RGS7BP
MIR9-2
CRSP8P
FLJ42709
C5orf43
LOC644936
LINC00461
LOC647859
GUSBP3
GTF2H2B
SCARNA18
SNORA47
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
LRRC70
LOC100131067
FAM159B
LOC100170939
LOC100272216
NCRUPAR
LOC100303749
MIR2277
MIR4280
MTRNR2L2
MIR3607
MIR3660
LOC100505894
OCLN
MIR4804
MIR3977
MIR4803

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.1.

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

Genes
hsa-mir-3198
ATP6V1E1
BID
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
HSFY1P1
CECR6
CECR5
CECR3
CECR2
CECR1
OR11H1
SLC25A18
GAB4
CCT8L2
XKR3
TPTEP1
CECR7
CECR5-AS1
MIR3198-1

Genes in Wide Peak

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

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

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

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

Genes
SOX9
SLC39A11
LINC00511
LOC100499467

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

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

Genes
FGFR3
WHSC1
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
ATP5I
NKX3-2
BST1
CCKAR
CD38
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RGS12
RNF4
S100P
SH3BP2
SOD3
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
SLC34A2
MXD4
CPLX1
SLC26A1
PPARGC1A
SEL1L3
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
SEPSECS
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
DCAF16
LGI2
TBC1D19
PI4K2B
CNO
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
CC2D2A
STIM2
KIAA1530
ZFYVE28
GBA3
AFAP1
NCAPG
TNIP2
HAUS3
ABCA11P
GRPEL1
MED28
KCNIP4
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
CPEB2
EVC2
PACRGL
OTOP1
ZNF595
LOC152742
JAKMIP1
FAM53A
METTL19
GPR125
ZBTB49
ZNF721
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
KCNIP4-IT1
C4orf52
USP17L6P
USP17
HSP90AB2P
C4orf48
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ABL2
ELK4
FH
MDM4
TPR
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ARF1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
DHX9
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GLUL
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
MR1
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NCF2
NEK2
NID1
NVL
CDK18
PDC
PFKFB2
PIGR
PIK3C2B
PKP1
PLA2G4A
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS1
RGS2
RGS7
RGS13
RGS16
RNASEL
RNF2
RNPEP
RYR2
SNRPE
SOAT1
SRP9
TROVE2
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
NPHS2
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
B3GALT2
RAB7L1
TAF1A
ANGPTL1
EXO1
XPR1
FAIM3
MAPKAPK2
GPR37L1
GGPS1
SOX13
IKBKE
TMEM63A
TOMM20
URB2
CEP350
CEP170
ZC3H11A
SMG7
TMCC2
FAM20B
LPGAT1
KIF14
AKT3
ARPC5
PRG4
STX6
BPNT1
TIMM17A
LRRN2
ZNF238
IVNS1ABP
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
OCLM
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NMNAT2
NFASC
GLT25D2
RGL1
FBXO28
CAMSAP2
SRGAP2
CRB1
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
TOR1AIP1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
GLRX2
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
IER5
UCHL5
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
SWT1
LAX1
C1orf27
MARC2
SUSD4
KIF26B
RALGPS2
GPATCH2
HEATR1
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
KIAA1614
ZP4
RHOU
KLHL12
LGR6
TFB2M
TOR3A
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
EDEM3
TRAF3IP3
SH3BP5L
NPL
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
SHCBP1L
TRMT1L
NUAK2
DDX59
RASSF5
HMCN1
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
ACBD6
KIAA1804
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
RGS8
WNT3A
NAV1
LHX4
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
TSEN15
FAM129A
SNAP47
C1orf96
AXDND1
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
C1orf55
CNST
C1orf65
FLJ23867
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
ASPM
PGBD2
OR2L13
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
LOC284648
DKFZP564C196
HNRNPU-AS1
LIN9
VN1R5
FAM5C
ZNF678
PRSS38
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
RGSL1
IRF2BP2
ZBTB41
MIA3
C1orf95
FAM89A
RPS10P7
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR194-1
MIR205
MIR181A1
MIR215
MIR29B2
MIR29C
RGS21
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SNORA14B
SNORA36B
SNORA77
SNORA16B
LOC728463
FAM72A
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
GM140
LOC100288079
MIR1182
MIR1537
MIR1231
MIR1278
MIR548F1
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3121
MIR3620
MIR3916
PROX1-AS1
KDM5B-AS1
LOC100506795
LOC100506810
LOC100527964
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4424
MIR4677
MIR4735
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

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

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
ACAT2
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GPR31
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
ME1
MAP3K4
MAP3K5
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLG
PLN
POU3F2
PREP
PKIB
PSMB1
PTPRK
REV3L
RNY4
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
HEY2
HEBP2
ORC3
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
SENP6
TIAM2
FBXL4
C6orf123
FBXO5
SLC17A5
RGS17
SNORD50A
PDE7B
FILIP1
SESN1
DLL1
OSTM1
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
BRP44L
HECA
COQ3
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
PHF10
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
C6orf70
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
C6orf7
UBE2CBP
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
FAM54A
SFT2D1
KLHL32
TMEM200A
MB21D1
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SRSF12
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GJB7
HMGA1P7
SNHG5
SUMO4
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
MIR30A
MIR30C2
OOEP
FAM26F
FLJ46906
LOC441177
MCART3P
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
KHDC1L
LOC100129518
LOC100130890
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100288198
LOC100289495
NHEG1
MIR1913
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100506804
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
ATIC
CREB1
ACSL3
IDH1
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
AOX1
KIF1A
BARD1
BCS1L
BMPR2
BOK
CASP8
CASP10
CD28
CHRND
CHRNG
CLK1
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CYP27A1
DES
DTYMK
EEF1B2
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR1
GPR35
HDLBP
AGFG1
DNAJB2
HSPD1
HSPE1
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NPPC
ORC2
PDCD1
PDE6D
SERPINE2
PLCL1
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
SUMO1
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
FZD7
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
CFLAR
PER2
CDK5R2
RQCD1
LRRFIP1
STK17B
GPR55
TRIP12
GTF3C3
ECEL1
EIF4E2
TTLL4
BZW1
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
ABI2
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
FASTKD2
PASK
ATG4B
SATB2
OBSL1
SF3B1
DNPEP
TMEFF2
SH3BP4
KCNE4
NGEF
SNORD82
MOB4
PNKD
SNED1
SPATS2L
GIGYF2
TRAF3IP1
ABCA12
SNORD51
CNPPD1
STK36
CPS1-IT1
ICOS
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
NOP58
ASB1
CAB39
PRKAG3
PPIL3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
STRADB
HES6
ACCN4
DOCK10
MREG
WDR12
PECR
DNAH7
C2orf83
MFF
CXCR7
RNPEPL1
SLC39A10
CYP20A1
HECW2
MARCH4
WDFY1
NYAP2
ALS2
ZDBF2
USP37
CTDSP1
MPP4
NIF3L1
PCGEM1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
TRAK2
BOLL
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
C2orf47
SPAG16
CHPF
IQCA1
ALS2CR8
NHEJ1
FAM124B
TM4SF20
C2orf54
PGAP1
TUBA4B
ARMC9
COQ10B
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
ANKRD44
TMEM169
DNER
MARS2
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
PARD3B
TYW5
DIS3L2
NEU4
ICA1L
RFTN2
AP1S3
SGPP2
KCTD18
ALS2CR12
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
FLJ32063
OTOS
MYEOV2
OR6B3
FAM117B
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
METTL21A
CCNYL1
SGOL2
ALS2CR11
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
PIKFYVE
LOC200726
TIGD1
LOC200772
C2orf69
CCDC108
C2orf72
CCDC150
CXXC11
FAM126B
UNC80
RUFY4
DUSP28
ESPNL
AOX2P
ECEL1P2
FONG
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
C2orf66
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
SNORA41
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
SNORD11
SNORD70
D2HGDH
LOC728323
DIRC3
SNORD11B
LOC100129175
PP14571
LOC100130451
LOC100130452
LOC100286922
MIR1471
MIR1244-1
MIR548F2
LOC100329109
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
LOC100507140
LOC100507443
HSPE1-MOB4
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4775
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
FOXP1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
EPHA3
GBE1
GPR27
HTR1F
CNTN3
POU1F1
PROS1
ROBO1
ROBO2
CGGBP1
PDZRN3
RYBP
CHMP2B
EBLN2
SHQ1
ZNF654
PROK2
PPP4R2
ARL13B
LOC201617
CADM2
C3orf38
EIF4E3
VGLL3
LOC401074
STX19
LOC440970
FLJ20518
FAM86DP
GXYLT2
ZNF717
FRG2C
MIR1284
MIR1324
MIR4273
MIR4795
MIR4444-1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.2.

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

Genes
RUNX1
ERG
TMPRSS2
hsa-mir-3197
hsa-mir-802
ADARB1
AIRE
PTTG1IP
C21orf2
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
DYRK1A
ETS2
HLCS
HMGN1
PRMT2
ITGB2
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SIM2
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
TTC3
U2AF1
UBE2G2
WRB
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DOPEY2
DSCR4
DSCR3
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
DNMT3L
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
PCBP3
C21orf58
YBEY
TSPEAR
LINC00112
LINC00111
SETD4
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
RUNX1-IT1
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
FAM207A
RSPH1
UMODL1
LINC00313
C21orf88
C21orf90
MCM3AP-AS1
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00315
DSCR9
BRWD1-IT2
DSCR10
LINC00323
LINC00319
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00114
LOC642852
LINC00163
SSR4P1
MIR802
LOC100129027
LOC100133286
MIR3197
LOC100505746
CBR3-AS1
DSCAM-AS1
MIR4760

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

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

Genes
BUB1B
TCF12
FLJ27352
C15orf55
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
NBEAP1
BNIP2
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
SNURF
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LDHAL6B
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
FAM81A
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
HSP90AB4P
MIR626
MIR627
MIR628
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
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
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR2116
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B
MYZAP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p35.2.

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

Genes
ABL2
ARNT
BCL9
CDKN2C
ELK4
EPS15
FCGR2B
FH
JAK1
JUN
LCK
MDM4
MPL
MUC1
MUTYH
MYCL1
NOTCH2
NRAS
NTRK1
PAX7
PBX1
PRCC
RPL22
SDHB
SDHC
SFPQ
TAL1
TPM3
TPR
ARID1A
TNFRSF14
BCL10
PDE4DIP
THRAP3
TRIM33
PRDM16
RBM15
SLC45A3
MDS2
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
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
ABCA4
ACADM
ACTA1
ACTN2
ADAR
ADORA1
ADORA3
PARP1
ADSS
AGL
AGT
AK2
AK4
ALDH9A1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
ARF1
RHOC
ASTN1
SERPINC1
ATF3
RERE
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
ATP5F1
ATP6V0B
AVPR1B
BAI2
BGLAP
BMP8B
BRDT
C1QA
C1QB
C1QC
C4BPA
C4BPB
C8A
C8B
CA6
CACNA1E
CACNA1S
CAPN2
CAPZA1
CAPZB
CASP9
CASQ1
CASQ2
RUNX3
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
TNFRSF8
CD34
CD48
CD53
CD58
CDA
CDK11B
CDC20
CDC42
CD52
CENPF
RCC1
CHI3L1
CHI3L2
CHIT1
CHML
LYST
CHRM3
CHRNB2
CKS1B
CLCA1
CLCN6
CLCNKA
CLCNKB
CLK2
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
COPA
CORT
CPT2
CR1
CR1L
CR2
CRABP2
CRP
CRYZ
CSF1
CSF3R
CSRP1
CTBS
CTH
CTPS
CTSE
CTSK
CTSS
CYP2J2
CYP4A11
CYP4B1
DAB1
CD55
DBT
GADD45A
DDOST
DHX9
DFFA
DFFB
DHCR24
DIO1
DPH2
DPT
DPYD
DR1
DVL1
E2F2
ECE1
ECM1
S1PR1
EDN2
PHC2
EIF2D
EFNA1
EFNA3
EFNA4
CELSR2
MEGF6
EPHA2
ELAVL4
ELF3
ENO1
ENSA
EPB41
EPHA8
EPHB2
EPHX1
EPRS
ESRRG
ETV3
EXTL1
EXTL2
EYA3
F3
F5
F13B
FAAH
FABP3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FGR
FHL3
FOXE3
FOXD2
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
MTOR
NR5A2
FUCA1
DARC
IFI6
GABRD
GALE
GALNT2
GBA
GBAP1
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GLUL
GNAI3
GNAT2
GNB1
GNG4
GNG5
SFN
GPR3
GPR25
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
GUK1
H3F3A
HCRTR1
HDAC1
HDGF
CFH
CFHR1
CFHR2
ZBTB48
MR1
HLX
HMGN2
HMGCL
HMGCS2
HNRNPU
HPCA
HSD3B1
HSD3B2
HSD11B1
HSPA6
HSPA7
IGSF3
HSPG2
HTR1D
HTR6
ID3
IFI16
CYR61
IL6R
IL10
IL12RB2
TNFRSF9
ILF2
INPP5B
INSRR
IPP
IRF6
ITPKB
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNH1
KCNJ9
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
STMN1
LBR
LEPR
LGALS8
LMNA
LMX1A
LOR
LY9
TACSTD2
MAGOH
MARK1
MATN1
MCL1
CD46
SMCP
MEF2D
MFAP2
MGST3
MNDA
MOV10
MPZ
MSH4
MTF1
MTHFR
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NASP
NBL1
NCF2
NDUFS2
NDUFS5
NEK2
NFIA
NFYC
NGF
NHLH1
NHLH2
NID1
NIT1
NPPA
NPPB
NPR1
NRD1
YBX1
ROR1
DDR2
NVL
OPRD1
ORC1
OVGP1
PAFAH2
PRDX1
CDK18
PDC
PDE4B
PDZK1
PEX10
PEX14
PFDN2
PFKFB2
PGD
PGM1
PIGC
PIGR
PIK3C2B
PIK3CD
PI4KB
PIN1P1
PKLR
PKP1
PLA2G2A
PLA2G4A
PLA2G5
PLOD1
PLXNA2
EXOSC10
PRRX1
POU2F1
POU3F1
PPOX
PPP1R8
PPP2R5A
PPT1
PRELP
PRKAA2
PRKAB2
PRKACB
PKN2
PRKCZ
PROX1
PSEN2
PSMA5
PSMB2
PSMB4
PSMD4
PTAFR
PTGER3
PTGFR
PTGFRN
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PTPRF
PEX19
ABCD3
RAB3B
RAB4A
RAB13
RABGGTB
RABIF
RAP1A
RAP1GAP
RBBP4
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RHCE
RHD
RIT1
RLF
RNASEL
RNF2
RNPEP
SNORD21
RORC
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RPS27
RSC1A1
RXRG
RYR2
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
SCNN1D
SCP2
XCL1
SELE
SELL
SELP
SRSF4
SHC1
ST3GAL3
STIL
SKI
SLAMF1
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SLC16A1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRM
SRP9
TROVE2
SSR2
AURKAPS1
STXBP3
XCL2
SYCP1
TAF12
TAF13
TARBP1
CNTN2
TBCE
TBX15
TCEA3
TCEB3
VPS72
TGFB2
LEFTY2
TGFBR3
THBS3
TCHH
TIE1
TLR5
GPR137B
TNFRSF1B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TP73
TRAF5
CCT3
TSHB
TSNAX
TTC4
TUFT1
TNFSF4
TNFRSF4
UCK2
UQCRH
UROD
USF1
USP1
USH2A
VCAM1
WNT2B
WNT9A
ZSCAN20
ZNF124
ZBTB17
SLC30A1
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
DAP3
NPHS2
BTG2
PTP4A2
HIST3H3
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
SNHG3
NR0B2
RAD54L
GNPAT
DYRK3
TTF2
CDC42BPA
RGS5
PPFIA4
PIK3R3
MMP23B
MMP23A
KCNAB2
ITGA10
LMO4
FCN3
BLZF1
CDC14A
DEGS1
KMO
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
VAMP4
PEA15
B4GALT3
B4GALT2
B3GALT2
TNFRSF25
ADAM15
PABPC4
TNFRSF18
FPGT
PEX11B
CREG1
CD84
PER3
FUBP1
EIF2B3
RAB7L1
SELENBP1
TNFSF18
TAF1A
MPZL1
SH2D2A
ARTN
MAP3K6
ANGPTL1
DIRAS3
TBX19
FCGR2C
SLC16A4
PRPF3
KCNQ4
EXO1
ARHGEF2
DEDD
ZMYM4
ZMYM6
XPR1
FAIM3
DHRS3
MAPKAPK2
GPR37L1
GPR52
SRSF11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
AIM2
GGPS1
RASAL2
C1orf38
ADAMTS4
TMEM59
SEC22B
CHD1L
H6PD
SOX13
PRDX6
CLCA3P
CLCA2
ISG15
IKBKE
PLCH2
HS2ST1
IPO13
SDC3
SLC25A44
KIAA0040
KDM4A
CROCC
PUM1
NOS1AP
TMEM63A
CEP104
RIMS3
TOMM20
KIAA0494
URB2
ARHGEF11
DNAJC6
CEP350
CEP170
LRIG2
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
KLHL21
SLC35E2
DENND4B
RABGAP1L
TMCC2
FAM20B
ZBTB40
LPGAT1
MFN2
KIF14
RBM8A
NR1I3
AKT3
INSL5
PIGK
SCAMP3
PTPRU
ARPC5
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
PRG4
ANGPTL7
GPA33
STX6
HNRNPR
SRRM1
CNKSR1
SF3B4
ZMPSTE24
UBE4B
BCAS2
AKR1A1
WARS2
BPNT1
CEPT1
PIAS3
TESK2
TIMM17A
LRRN2
PPIE
VAV3
HAX1
MAD2L2
PPIH
ZNF238
C1orf61
CAP1
LRRC41
SEMA6C
HBXIP
SLC19A2
IFI44
POLR3C
IVNS1ABP
TXNIP
PDPN
LEFTY1
SPHAR
PMVK
KHDRBS1
GMEB1
FAM189B
AP4B1
NUDC
PHTF1
MASP2
CAPN9
NES
KDM5B
AHCYL1
SRSF10
SDCCAG8
CFHR4
CFHR3
WDR3
OCLM
JTB
MTMR11
MAN1A2
UTS2
SF3A3
MLLT11
IFI44L
EBNA1BP2
SLC27A3
KIF2C
IL24
TDRKH
RER1
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
CELF3
MST1P2
DDX20
DUSP10
MST1P9
PADI2
PMF1
DUSP12
VPS45
LYPLA2
PARK7
CTRC
ACOT7
COG2
CLCA4
MTF2
DNAJC8
NTNG1
PLEKHA6
CLSTN1
FOXJ3
KIAA0907
WDR47
KIFAP3
ATF6
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
RBM34
USP33
WDTC1
KIF21B
NMNAT2
KIAA0090
KIF1B
NFASC
POGZ
GLT25D2
MAST2
NCDN
CLCC1
SLC35D1
RGL1
PLEKHM2
SYT11
PRRC2C
FBXO28
RPRD2
OTUD3
KAZN
CAMTA1
LPHN2
CAMSAP2
KIAA1107
ZCCHC11
SZT2
DNAJC16
UBR4
USP24
SRGAP2
SMG5
NCSTN
ATP13A2
CRB1
ITGB3BP
GPR161
TARDBP
CELA3B
SLC35A3
ABCB10
ICMT
MACF1
LRRC8B
ZNF281
SNAPIN
LPAR3
PADI4
DDAH1
TMEM50A
OPN3
PHLDA3
RUSC1
CA14
KPNA6
SSBP3
STX12
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
TRIM58
INTS7
OLFML2B
AHCTF1
C1orf43
CLIC4
NSL1
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
DNM3
TOR1AIP1
CHTOP
C1orf144
LDLRAP1
SERBP1
NOC2L
OR1C1
PTPN22
PHGDH
FBXO2
LCE2B
OR2M4
OR2L2
OR2L1P
OPTC
FBXO6
PLA2G2D
AK5
MYCBP
OR10J1
HEYL
EIF2C1
OR4F3
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORA66
SNORD47
SNORD45B
SNORD45A
SNORD44
SNORD55
RNU11
RNU5F-1
RNF11
USP21
FOXD3
DIEXF
TRAPPC3
TAF5L
CACYBP
HSPB7
CHIA
SLC39A1
DISC2
DISC1
ARHGEF16
AHDC1
RNF115
KLHL20
TEKT2
SMPDL3B
ANGPTL3
LAMTOR2
FLVCR1
PRO0611
UBE2T
LINC00339
CNIH4
SSU72
TMOD4
GNL2
GPSM2
UBIAD1
PYCR2
NME7
ALG6
NENF
PADI1
IL19
CERS2
SLC25A24
PLA2G2E
DNTTIP2
WRAP73
CRNN
G0S2
IL20
SLC45A1
DCAF8
HP1BP3
F11R
TMED5
RRP15
GLRX2
BOLA1
PPPDE1
CELA2B
ZNF593
ZBTB7B
ZNF691
TXNDC12
TNNI3K
RRNAD1
ADIPOR1
SCCPDH
SH3GLB1
MECR
APH1A
UTP11L
TRIM17
KCTD3
SDF4
MRTO4
PLEKHO1
HAO2
ACP6
TMEM69
MRPL37
IER5
HOOK1
SNX7
UCHL5
C1orf9
HPCAL4
YTHDF2
GPR89B
HSD17B7
UFC1
DTL
ZCCHC17
METTL13
DPH5
HSPB11
OAZ3
PADI3
CYB5R1
CMPK1
ARID4B
CD244
GPR88
ERRFI1
DPM3
WNT4
YIPF1
FBXO42
MRPS21
CCDC76
TMCO1
ADAMTSL4
CRCT1
RNF186
SPATA6
EGLN1
MXRA8
L1TD1
HES2
KIAA1383
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
SWT1
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
PQLC2
CASZ1
LAX1
RHBDL2
DUSP23
ADPRHL2
TRNAU1AP
C1orf27
C1orf109
C1orf56
CPSF3L
C1orf123
C1orf159
MARC2
AURKAIP1
TTC22
MRPL20
AIM1L
SUSD4
KIF26B
TMEM51
RALGPS2
GPATCH2
BSDC1
XKR8
TMEM39B
PRPF38B
HEATR1
CDCA8
LRRC8D
MSTO1
DARS2
ARHGEF10L
PRMT6
RNF220
VPS13D
FAM176B
GOLPH3L
ATAD3A
TMEM57
KLHDC8A
TRIM62
ETNK2
RAVER2
PANK4
KIRREL
TMEM206
YY1AP1
ECHDC2
FGGY
MCOLN3
SLC22A15
YOD1
CAMK2N1
BATF3
SLC30A10
UBE2Q1
RNPC3
ITLN1
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
ZNF692
NBPF1
IARS2
MAP7D1
IPO9
TMEM48
NECAP2
IQCC
C1orf112
HHAT
DNAJC11
ENAH
NUP133
RCOR3
C1orf106
LRIF1
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
RCC2
FAM212B
DMAP1
AJAP1
GNG12
SLC50A1
TMEM234
FAM54B
SERTAD4
CCBL2
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
TMEM167B
OLFML3
SMYD2
LHX9
OTUD7B
ADCK3
CTNNBIP1
C1orf63
AGTRAP
PITHD1
RAB25
PGLYRP4
ZNF695
RHBG
MAN1C1
SCYL3
GJC2
CAMK1G
NIPAL3
SEPN1
ATP8B2
TP73-AS1
VANGL2
FAM91A2
PBXIP1
S100A14
PLEKHG5
GATAD2B
AMIGO1
LRRC47
ODF2L
CGN
KIAA1324
PTCHD2
IGSF9
LRRC7
SIPA1L2
KIF17
ZNF687
ZSWIM5
POGK
KIAA1522
HCN3
CACHD1
MIER1
KIAA1614
FAM5B
HES4
C1orf114
GRHL3
SLAMF7
ZP4
CADM3
PTBP2
RHOU
PRUNE
DNASE2B
DLGAP3
IL22RA1
HIVEP3
KLHL12
LGR6
GPBP1L1
HAPLN2
MIIP
GAS5
PAPPA2
CELA2A
BCAN
GPATCH3
TNN
MRPS14
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
TINAGL1
LEPRE1
TFB2M
SEMA4A
TOR3A
RFWD2
GREM2
RGS18
PLA2G2F
HIAT1
NUCKS1
SMAP2
ACBD3
SMYD3
ATPAF1
MARC1
S100PBP
MEAF6
DEM1
CEP85
ARV1
NMNAT1
ELOVL1
AIDA
VWA1
DCLRE1B
MRPS15
MRPL9
PINK1
JMJD4
MARCKSL1
PRAMEF1
PRAMEF2
INTS3
NADK
ZNF643
SELRC1
PHACTR4
C1orf135
SCNM1
ERI3
C1orf50
WDR77
C1orf116
MGC4473
CCDC28B
C1orf35
EFHD2
MMEL1
RSG1
FCRL2
DLEU2L
OR4F5
NKAIN1
TTC13
EPS8L3
CDC73
MRPL24
MUL1
PGBD5
TNFAIP8L2
C1orf54
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
NOL9
PPCS
LIN28A
SH3D21
TTLL7
SNIP1
C1orf115
HHIPL2
VASH2
AGMAT
WDR78
ZMYM1
LINC00115
ZNF669
RPAP2
ZNF672
MORN1
FAM110D
KIAA0319L
DHDDS
PAQR6
DENND2D
WLS
PCNXL2
GPR157
TRIM46
C1orf129
RPF1
SIKE1
ZC3H12A
SPSB1
TARS2
WDR26
TRIM45
EDEM3
FLAD1
TRAF3IP3
GLTPD1
ZNF436
TAS1R2
TAS1R1
SH3BP5L
NPL
GJA9
OR4F16
OR6N2
OR6K2
OR2G3
OR2G2
OR2C3
SYNC
CFHR5
TRIM11
C1orf21
ACTL8
ANKRD13C
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
TSSK3
CCNL2
NUAK2
VANGL1
ST6GALNAC5
ISG20L2
HYI
FCRL5
FCRL4
SH3BGRL3
DDX59
NUF2
RASSF5
SESN2
ESPN
TAS1R3
ATAD3B
HMCN1
GPR61
MIXL1
STK40
C1orf124
TM2D1
FCAMR
REG4
OBSCN
TMEM222
C1orf49
PLEKHN1
HORMAD1
TOMM40L
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
SLC25A33
TMEM79
NTPCR
EFCAB2
DDI2
ACBD6
LZIC
PROK1
KIAA1804
EFCAB7
ZBTB37
NT5C1A
LCE3D
TRIM63
LINC00260
PSRC1
FAM167B
LINC00467
MGC12982
C1orf170
CROCCP2
FCRLA
ANKRD36BP1
ZNF496
HPDL
ATP1A1OS
AGBL4
MFSD2A
C1orf198
PPP1R15B
ATG4C
MAEL
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
DISP1
SNHG12
FAM40A
RGS8
DOCK7
KIAA1751
WNT3A
NAV1
SEC16B
AQP10
LHX4
SLAMF9
KIAA2013
THAP3
C1orf201
PYGO2
ANGEL2
SPOCD1
ZNF697
IGFN1
NUP210L
BTF3L4
UBXN11
NEXN
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
C1orf158
LEMD1
ZNF670
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
C1orf85
MED8
KTI12
C1orf212
ADC
TMEM54
HENMT1
TOE1
NLRP3
ERMAP
PGLYRP3
CSMD2
MYSM1
GNRHR2
CROCCP3
FHAD1
SLAMF6
OSBPL9
SLC26A9
LOC115110
OMA1
RAB42
FCRL1
FCRL3
LRRC42
GBP4
GBP5
FAM46B
FMO9P
FAM36A
RBP7
TSEN15
FAM129A
SNAP47
ACAP3
TADA1
THEM4
SH2D1B
SSX2IP
UBE2J2
OLFM3
GABPB2
TCHHL1
RPTN
CCDC163P
TDRD10
SHE
C1orf172
C1orf96
LRRC38
AADACL3
PUSL1
B3GALT6
WDR63
KLHDC9
AXDND1
MAB21L3
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
ASB17
TYW3
C1orf173
LRRIQ3
TPRG1L
FAM213B
MYOM3
DMBX1
OR10J5
TMCO2
ZNF684
TCEANC2
PODN
LRRC39
GJB4
HMGB4
RNF19B
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
HSD3BP4
SPATA17
EDARADD
KLF17
TMEM125
C1orf182
IQGAP3
APOA1BP
ARHGEF19
MRPL55
HIST3H2BB
DRAM2
C1orf88
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ACTRT2
MIB2
ITLN2
SYT6
C1orf74
CREB3L4
C1orf127
BROX
SAMD11
LOC148413
SAMD13
C1orf52
PHF13
C1orf51
TMEM56
NBPF4
UBE2U
SLC35F3
LOC148696
LOC148709
PTPRVP
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
SLC30A7
CCDC27
C1orf213
KNCN
MOB3C
GLIS1
LELP1
RC3H1
MGC27382
DCDC2B
ZNF362
LOC149086
DCST1
CNIH3
LOC149134
MANEAL
IL23R
METTL11B
FAM78B
SHISA4
EXOC8
PDIK1L
BNIPL
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
LRRC71
C1orf64
RNF187
RP11-165H20.1
PYHIN1
C1orf227
FAM71A
SLC2A7
DENND2C
GBP6
LPPR5
FNDC7
DENND1B
TDRD5
TOR1AIP2
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
SPRR4
KANK4
SASS6
C1orf55
CNST
FAM43B
PPIAL4A
HFM1
PAQR7
TTC24
C1orf65
UBL4B
PDIA3P
EIF2C3
EIF2C4
LCE4A
ALG14
FAM76A
LINC00466
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
NBPF11
NUDT17
FLJ23867
TXLNA
TCTEX1D1
PLD5
C1orf100
SPAG17
SLFNL1
KRTCAP2
CRTC2
C1orf126
IBA57
HIPK1
SLC44A5
ATAD3C
AKR7L
AKR7A2P1
TMEM9
FNDC5
EPHX4
LOC254099
TTLL10
AKNAD1
SLC41A1
OR2T6
LCE5A
TMCO4
MCOLN2
COL24A1
LOC255654
PCSK9
SYT14
ST6GALNAC3
C1orf101
ZNF683
ARHGAP30
C1orf192
NEGR1
ASPM
CYP4X1
MAGI3
TIPRL
NPHP4
BEST4
PGBD2
FAM19A3
RIIAD1
THEM5
OR2L13
SLC9A11
OR14A16
CYP4A22
C1orf185
LOC284551
NBPF15
LINC00303
LOC284576
LOC284578
LOC284581
FAM41C
FAM102B
SYPL2
CYB561D1
ANKRD34A
RUSC1-AS1
LOC284632
LOC284648
DKFZP564C196
RSPO1
EPHA10
LOC284661
C1orf204
C1orf111
LOC284688
ZNF326
BTBD8
HNRNPU-AS1
RIMKLA
SLC25A34
ESPNP
LIN9
VN1R5
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
FAM151A
S100A7A
LINGO4
RXFP4
ANKRD45
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
FAM5C
MTMR9LP
ZBTB8OS
TFAP2E
ZNF678
PRSS38
LOC339505
C1orf110
FAM58BP
LOC339524
LOC339529
LOC339535
C1orf228
ZNF642
RD3
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
CCDC18
OR6F1
OR2W3
OR2T8
OR2T3
MYBPHL
OR10R2
FCRL6
KCNT2
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
OR2T29
SERINC2
FAM159A
FAM131C
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PADI6
RGSL1
BMP8A
IRF2BP2
ZBTB41
CYCSP52
C1orf187
SPATA21
CCDC23
ATPAF1-AS1
HEATR8
FAM73A
LOC375010
PEAR1
SFT2D2
MIA3
C1orf95
FAM89A
AGRN
RPS10P7
APITD1
CATSPER4
NSUN4
GPR153
ILDR2
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LOC388630
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
UOX
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
GBP1P1
FLJ27354
MIR137HG
C1orf226
LOC400794
C1orf220
C1orf140
NBPF9
FAM177B
RNF223
PRAMEF3
LDLRAD2
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
LOC402779
OR2T27
OR2T35
APOBEC4
MIR101-1
MIR137
MIR181B1
MIR186
MIR194-1
MIR197
MIR199A2
MIR200A
MIR200B
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
MIR30C1
MIR30E
MIR34A
MIR9-1
RGS21
LHX8
C1orf180
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
FLJ32224
FAM183A
ZYG11A
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
ANKRD65
PRAMEF7
PGCP1
OR10J3
OR2W5
OR13G1
MIR135B
KPRP
LCE6A
SUMO1P3
GEMIN8P4
RBMXL1
LURAP1
PEF1
MIR429
C1orf98
HIST2H4B
DUSP5P
C1orf133
PRR9
MIR488
CYB5RL
SNORD74
RPL31P11
LOC641515
FAM138F
MIR205HG
SRG7
FLVCR1-AS1
CYMP
KIAA0754
LOC643441
LOC643723
LOC643837
TMEM88B
C1orf233
LOC644242
PPIAL4G
LOC644961
C1orf200
PPIAL4D
LOC645166
SNRPD2P2
PRAMEF19
PRAMEF20
FAM138A
LOC645676
POU5F1P4
RPS7P5
S100A7L2
LOC646268
LOC646471
LOC646626
LOC646627
EMBP1
SRGAP2P2
LOC648740
LOC649330
ZBTB8A
NBPF6
LOC653160
PPIAL4B
LOC653513
GPR89A
LOC653566
PPIAL4C
HIST2H3D
PRAMEF22
PRAMEF15
WASH7P
TMEM183B
FAM72B
PRAMEF16
PCP4L1
SCARNA3
SCARNA2
SCARNA4
SCARNA1
SNORA14B
SNORA36B
SNORA42
SNORA44
SNORA55
SNORA61
SNORA77
SNORA59B
SNORA59A
SNORA16A
SNORD45C
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR548D1
MIR551A
MIR553
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
ZBTB8B
LOC728431
PPIEL
LOC728463
CCDC30
CDK11A
SLC35E2B
LOC728716
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729041
LOC729059
HSD52
PRAMEF14
FAM72A
FLJ37453
LOC729737
OR4F29
LOC729970
LOC729987
LOC730102
LOC730159
LOC730227
PPIAL4E
LOC731275
PFN1P2
MIR765
MIR942
MIR190B
MIR760
MIR921
LOC100128071
LOC100128787
LOC100129046
LOC100129138
LOC100129196
LOC100129269
C1orf68
MSTO2P
LOC100129534
LOC100129620
LOC100129924
LOC100130000
LOC100130093
LOC100130197
LOC100130331
LOC100130417
LOC100130557
LOC100131060
TSTD1
LOC100131234
LOC100131564
LOC100131825
LOC100132062
LOC100132111
LOC100132287
NBPF10
FCGR1C
ZRANB2-AS1
LOC100132774
LOC100133331
LOC100133445
LOC100133612
C2CD4D
LOC100286793
DDX11L1
LOC100287722
LOC100287814
TTC34
LGALS8-AS1
GM140
LOC100288069
LOC100288079
LOC100289178
LOC100289211
MIR320B1
MIR1182
MIR1537
MIR1231
MIR1278
MIR1295A
MIR1976
MIR548F1
MIR664
MIR1262
LOC100302401
LINC00184
TSNAX-DISC1
MIR320B2
MIR761
NPPA-AS1
ZBED6
MIR3119-1
MIR3123
MIR3115
MIR3117
MIR3124
MIR3120
MIR4260
MIR4255
MIR4253
MIR3122
MIR4251
MIR4252
MIR4256
MIR4257
MIR3119-2
MIR4258
MIR4254
MIR3121
MIR3659
MIR3917
MIR3620
MIR3658
MIR3916
MIR3605
MIR3671
MIR548AA1
MIR3675
LOC100505633
LOC100505666
LOC100505768
LOC100505795
PROX1-AS1
LOC100505918
ENO1-AS1
LOC100506023
LOC100506046
ZMYM6NB
LOC100506343
KDM5B-AS1
LOC100506730
LOC100506795
LOC100506801
LOC100506810
LOC100506963
LOC100507178
LOC100507423
LOC100507564
LOC100507634
APITD1-CORT
FPGT-TNNI3K
GJA9-MYCBP
HEATR8-TTC4
PMF1-BGLAP
LOC100527964
TMEM56-RWDD3
C1orf151-NBL1
ZNF670-ZNF695
TNFAIP8L2-SCNM1
MIR4695
MIR4420
MIR4753
MIR4422
MIR4666A
MIR4781
MIR4424
MIR4794
MIR4677
MIR4735
MIR4671
MIR4654
MIR4427
MIR4684
MIR4711
MIR4689
MIR4632
MIR2682
MIR4742
MIR4423
MIR4417
MIR378F
DNM3OS
RCAN3AS
NEGR1-IT1
ZRANB2-AS2
LINC00538

Arm-level results

Table 3. Get Full Table Arm-level significance table - 21 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 | -0.747 | 0.999 | 0.19 | -0.446 | 0.948
1q | 1955 | 0.40 | 2.51 | 0.0386 | 0.21 | -0.286 | 0.948
2p | 924 | 0.36 | 0.0386 | 0.999 | 0.15 | -2.51 | 0.999
2q | 1556 | 0.22 | -0.856 | 0.999 | 0.12 | -2.18 | 0.999
3p | 1062 | 0.25 | -0.735 | 0.999 | 0.74 | 5.77 | 1.55e-07
3q | 1139 | 0.50 | 2.14 | 0.0813 | 0.48 | 1.92 | 0.0995
4p | 489 | 0.22 | -1.82 | 0.999 | 0.60 | 2.69 | 0.0204
4q | 1049 | 0.13 | -2.37 | 0.999 | 0.43 | 1.38 | 0.238
5p | 270 | 0.49 | 0.682 | 0.892 | 0.45 | 0.3 | 0.764
5q | 1427 | 0.15 | -1.67 | 0.999 | 0.50 | 3.06 | 0.0117
6p | 1173 | 0.16 | -2.1 | 0.999 | 0.30 | -0.403 | 0.948
6q | 839 | 0.12 | -3.13 | 0.999 | 0.22 | -1.96 | 0.999
7p | 641 | 0.67 | 3.74 | 0.00183 | 0.36 | -0.212 | 0.948
7q | 1277 | 0.50 | 2.63 | 0.0339 | 0.28 | -0.418 | 0.948
8p | 580 | 0.63 | 2.7 | 0.0339 | 0.65 | 2.88 | 0.016
8q | 859 | 0.69 | 4.46 | 0.000167 | 0.38 | 0.197 | 0.767
9p | 422 | 0.10 | -2.94 | 0.999 | 0.60 | 2.72 | 0.0204
9q | 1113 | 0.23 | -1.24 | 0.999 | 0.44 | 1.55 | 0.188
10p | 409 | 0.23 | -2.21 | 0.999 | 0.36 | -0.73 | 0.948
10q | 1268 | 0.16 | -1.91 | 0.999 | 0.40 | 1.26 | 0.259
11p | 862 | 0.20 | -1.83 | 0.999 | 0.45 | 1.31 | 0.255
11q | 1515 | 0.18 | -1.24 | 0.999 | 0.49 | 3.04 | 0.0117
12p | 575 | 0.54 | 1.88 | 0.134 | 0.32 | -0.779 | 0.948
12q | 1447 | 0.24 | -0.77 | 0.999 | 0.20 | -1.28 | 0.999
13q | 654 | 0.31 | -0.801 | 0.999 | 0.57 | 2.5 | 0.0314
14q | 1341 | 0.35 | 0.62 | 0.892 | 0.35 | 0.62 | 0.563
15q | 1355 | 0.13 | -2.3 | 0.999 | 0.27 | -0.528 | 0.948
16p | 872 | 0.26 | -1.23 | 0.999 | 0.30 | -0.776 | 0.948
16q | 702 | 0.19 | -2.28 | 0.999 | 0.33 | -0.716 | 0.948
17p | 683 | 0.29 | -1.04 | 0.999 | 0.40 | 0.25 | 0.764
17q | 1592 | 0.30 | 0.299 | 0.999 | 0.16 | -1.54 | 0.999
18p | 143 | 0.42 | -0.27 | 0.999 | 0.51 | 0.858 | 0.434
18q | 446 | 0.17 | -2.41 | 0.999 | 0.57 | 2.17 | 0.0607
19p | 995 | 0.23 | -1.28 | 0.999 | 0.47 | 1.66 | 0.16
19q | 1709 | 0.30 | 0.54 | 0.907 | 0.42 | 2.35 | 0.0418
20p | 355 | 0.60 | 2.47 | 0.0386 | 0.29 | -1.26 | 0.999
20q | 753 | 0.61 | 3.47 | 0.00349 | 0.05 | -2.98 | 0.999
21q | 509 | 0.25 | -1.38 | 0.999 | 0.67 | 3.64 | 0.00276
22q | 921 | 0.35 | -0.0026 | 0.999 | 0.42 | 0.876 | 0.434
Xq | 1312 | 0.38 | 0.921 | 0.714 | 0.29 | -0.283 | 0.948

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/ESCA-TP/3348544/GDAC_MergeDataFiles_3202407/ESCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

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

Tumor Sample Names
TCGA-IG-A3I8-01A-11D-A246-01
TCGA-IG-A3QL-01A-11D-A246-01
TCGA-IG-A3Y9-01A-12D-A246-01
TCGA-IG-A3YA-01A-11D-A246-01
TCGA-IG-A3YB-01A-11D-A246-01
TCGA-IG-A3YC-01A-11D-A246-01
TCGA-IG-A4P3-01A-11D-A25X-01
TCGA-IG-A4QS-01A-11D-A25X-01
TCGA-IG-A4QT-01A-21D-A25X-01
TCGA-IG-A50L-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

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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