SNP6 Copy number analysis (GISTIC2)

Adrenocortical Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C11Z430S

Overview

Introduction

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

Summary

There were 90 tumor samples used in this analysis: 22 significant arm-level results, 19 significant focal amplifications, and 26 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 - 19 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
5p15.33	2.1179e-08	2.1179e-08	chr5:1288616-1300024	1
5q35.3	0.00020364	0.00020364	chr5:176723780-176833588	9
12q14.1	0.0043919	0.0043919	chr12:58080141-58481453	16
16q22.1	0.004052	0.0051993	chr16:69367997-69491844	5
Xq28	0.0114	0.0114	chrX:151841230-152714951	21
17q25.3	0.014283	0.014283	chr17:79999378-80024315	3
19p13.12	0.020068	0.020068	chr19:15293986-16628163	35
4p16.3	0.022386	0.022386	chr4:1-2496016	51
14q11.2	0.032075	0.032075	chr14:21010467-23970250	74
19q12	0.04544	0.04544	chr19:30245583-30385544	1
Xp11.22	0.075299	0.075299	chrX:53242630-53465013	5
1q22	0.077256	0.077256	chr1:120523956-155499256	284
6q24.3	0.10369	0.10369	chr6:147060843-148023227	5
9q31.3	0.12028	0.12028	chr9:114596042-114618032	0 [UGCG]
16q24.2	0.075299	0.12028	chr16:87736713-88204631	4
6p21.31	0.19557	0.19557	chr6:36197374-36214490	2
4q35.1	0.22208	0.22208	chr4:19216059-191154276	733
16p13.3	0.22723	0.22723	chr16:1-5327725	227
7p22.1	0.2356	0.2356	chr7:1-24087697	153

Genes in Wide Peak

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

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

Genes
TERT

Genes in Wide Peak

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

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

Genes
NSD1
F12
SLC34A1
RGS14
LMAN2
PRELID1
RAB24
MXD3
PFN3

Genes in Wide Peak

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

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

Genes
CDK4
hsa-mir-26a-2
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
OS9
METTL21B
XRCC6BP1
MARCH9
AGAP2
MIR26A2
LOC100130776
LOC100506844

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q22.1.

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

Genes
TERF2
NIP7
CYB5B
COG8
TMED6

Genes in Wide Peak

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

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

Genes
CETN2
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
ZNF185
ZNF275
TREX2
PNMA3
NSDHL
HAUS7
PNMA6A
PNMA5
ZFP92
CSAG1
MAGEA2B
CSAG3
CSAG2
PNMA6C
PNMA6D

Genes in Wide Peak

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

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

Genes
GPS1
RFNG
DUS1L

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
TPM4
BRD4
hsa-mir-1470
CYP4F3
RAB8A
NOTCH3
CYP4F2
AP1M1
AKAP8
KLF2
CYP4F8
FAM32A
OR10H3
OR10H2
OR10H1
AKAP8L
CYP4F11
EPS15L1
WIZ
RASAL3
CYP4F12
EPHX3
C19orf44
HSH2D
PGLYRP2
CIB3
CALR3
CYP4F22
LOC126536
OR10H4
FLJ25328
OR10H5
CYP4F24P
UCA1
MIR1470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

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

Genes
FGFR3
WHSC1
hsa-mir-943
hsa-mir-571
ATP5I
CTBP1
DGKQ
GAK
IDUA
LETM1
MYL5
PDE6B
RNF4
WHSC2
ZNF141
SLBP
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
FGFRL1
PIGG
KIAA1530
ZFYVE28
HAUS3
ABCA11P
MFSD7
TMEM175
C4orf42
TMEM129
ZNF595
FAM53A
ZNF721
ZNF718
CRIPAK
RNF212
NAT8L
POLN
C4orf48
LOC402160
ZNF876P
ZNF732
SCARNA22
MIR943
LOC100129917
LOC100130872
TMED11P
MIR4800

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q11.2.

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

Genes
hsa-mir-208b
ANG
BCL2L2
CEBPE
DAD1
HNRNPC
MMP14
MYH6
MYH7
OXA1L
PSMB5
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
PABPN1
SLC7A7
TOX4
EFS
PRMT5
EDDM3A
SUPT16H
ACIN1
SLC7A8
NGDN
LRP10
OR10G3
OR10G2
OR4E2
SLC39A2
ZNF219
SLC22A17
HAUS4
C14orf119
RBM23
ARHGEF40
METTL3
RPGRIP1
NDRG2
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
RNASE7
RAB2B
AJUBA
PPP1R3E
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
REM2
LOC283624
SNORD8
OR6S1
RNASE9
OR5AU1
MIR208A
RNASE13
RNASE12
ECRP
C14orf176
SNORD9
MIR208B
BCL2L2-PABPN1
MIR4707

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.22.

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

Genes
KDM5C
HSD17B10
SMC1A
IQSEC2
RIBC1

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
MUC1
NOTCH2
TPM3
PDE4DIP
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
ADAR
CHRNB2
CKS1B
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
POU5F1P4
S100A7L2
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
MIR555
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR190B
C1orf68
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505666
TNFAIP8L2-SCNM1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q24.3.

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

Genes
ADGB
STXBP5
SAMD5
LOC729176
LOC729178

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q24.2.

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

Genes
CA5A
SLC7A5
KLHDC4
BANP

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.31.

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

Genes
BRPF3
PNPLA1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q35.1.

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

Genes
IL2
KDR
KIT
PDGFRA
RAP1GDS1
PHOX2B
DUX4
CHIC2
TET2
FBXW7
FIP1L1
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
hsa-mir-1269
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA2P1
ANXA3
ANXA5
APBB2
AREG
RHOH
ART3
ATOH1
BMP3
BMPR1B
BTC
CAMK2D
CASP3
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
LRBA
CDS1
CLGN
CENPC1
CENPE
CLCN3
CNGA1
CPE
CSN1S1
CSN2
CSN3
CTSO
DCK
DCTD
DHX15
DMP1
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
EPHA5
EREG
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGF5
FGG
FRG1
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GC
GK2
GK3P
GLRB
GNRHR
GPM6A
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
UBE2K
HMGB2
HNRNPD
HPGD
HSP90AA4P
HSP90AB3P
HTN1
HTN3
IBSP
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
MAD2L1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MTNR1A
MTTP
MUC7
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PCDH7
PDHA2
PET112
PF4
PF4V1
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPBP
PPID
PPP3CA
PRKG2
MAPK10
PTPN13
REST
RFC1
ABCE1
RPL9
RPL34
RPS3A
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SNCA
SOD3
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
TDO2
TEC
TLL1
TLR1
TLR2
TLR3
TRPC3
TXK
UBE2D3
UCHL1
UCP1
UGDH
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
VEGFC
GLRA3
SPARCL1
SMARCA5
SORBS2
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
HERC3
SNORD73A
STBD1
CDKL2
PAPSS1
LRAT
AIMP1
NDST3
SLIT2
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
MFAP3L
SEC24D
G3BP2
HNRPDL
TSPAN5
ENAM
FAM13A
SPRY1
TLR6
ANAPC10
ATP8A1
PGRMC2
SEC24B
SLC30A9
CXCL13
SLC34A2
MAB21L2
PAICS
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
HPSE
NMU
SMR3B
NPFFR2
PPARGC1A
PPBPL2
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
ANP32C
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXO8
DUX2
SMR3A
PPA2
DAPP1
DKK2
INTU
NAAA
COQ2
ARFIP1
SULT1B1
PDLIM3
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
MRPS18C
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
NUDT9
NUP54
CLDN22
GAR1
UGT2B28
RBM47
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
CCDC109B
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
UBA6
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
C4orf43
UFSP2
C4orf21
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
CDKN2AIP
ODZ3
N4BP2
TMEM184C
SEPT11
EXOC1
LRP2BP
TMEM165
PDGFC
FSTL5
BDH2
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
DANCR
KIAA1211
RNF150
KIAA1239
KLHL8
PCDH10
KIAA1430
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
METTL14
WDR19
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
GUF1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
HHIP
NDST4
AGXT2L1
USP46
MRPL1
RASL11B
ELOVL6
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
FLJ13197
MLF1IP
THAP9
NSUN7
UGT2A3
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
SCD5
DNAJB14
TMEM156
WWC2
FRAS1
NAA15
CWH43
C4orf29
ALPK1
CXXC4
KCNIP4
CEP44
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
NOA1
HOPX
COL25A1
USP38
LNX1
C4orf49
NAA11
AGPAT9
CBR4
PIGY
CABS1
FHDC1
FLJ20021
MGC45800
PRMT10
CCDC149
DDX60L
YTHDC1
NAF1
MOB1B
TIFA
FAM114A1
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
WDR17
ARAP2
GDEP
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
SPATA18
C4orf32
TMPRSS11B
GNPDA2
SPATA4
ARL9
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
NFXL1
NIPAL1
PAQR3
SHISA3
LOC152578
SCFD2
C4orf38
C4orf39
THAP6
C4orf26
KLB
PPM1K
C4orf45
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
FREM3
MMAA
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
GSX2
SYNPO2
C4orf46
SLC10A4
TIGD4
TMEM154
C4orf34
TMEM192
RWDD4
CCDC111
TRIML2
CNOT6L
TECRL
C4orf22
LOC255130
EPGN
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
FDCSP
NAP1L5
LOC285419
DCAF4L1
CYP4V2
LOC285441
LOC285456
LOC285501
FAM13A-AS1
GPRIN3
COX18
YIPF7
FRYL
RNF175
LOC285540
C4orf37
CSN1S2AP
ZAR1
CCDC158
TMPRSS11A
LOC339975
TRIML1
LRRC66
LOC340017
LOC344967
PRSS48
SOWAHB
LRIT3
SLC10A6
HSD17B13
ANKRD37
PCNAP1
KCNIP4-IT1
KCTD8
C4orf52
BEND4
GRXCR1
TMPRSS11F
LOC389247
TRIM61
HELT
DTHD1
LOC401127
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
FLJ14186
C4orf3
LOC401164
RPL21P44
FAM92A3
WDFY3-AS2
MIR218-1
MIR302A
C4orf11
MTHFD2L
LOC441025
TMEM150C
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC550112
LOC550113
UGT2A2
LOC641364
LOC641365
LOC641518
SLED1
LOC644145
LOC644248
TMPRSS11GP
CEP170P1
LOC645513
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
SNORA24
SNORA26
MIR573
MIR574
MIR575
MIR577
MIR578
LINC00290
LOC728175
DUX4L2
CETN4P
FAM160A1
LOC731424
RELL1
SNHG8
FAM47E
LOC100129858
FTLP10
CLDN24
LOC100144602
PP12613
LOC100288255
ERVMER34-1
MIR1243
MIR2054
MIR1305
MIR1973
CSN1S2BP
MIR3140
MIR4275
MIR4276
LOC100499177
MIR3945
MIR3684
MIR3688-1
LOC100505545
LOC100505702
LOC100505875
SLIT2-IT1
LOC100505912
LOC100505989
LOC100506013
LOC100506035
LOC100506085
LOC100506122
LOC100506229
LOC100506462
LOC100506564
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4453
MIR4799
MIR548AJ2
MIR4802
MIR4450
MIR3688-2
MIR4451
MIR4801
MIR4449
FAM47E-STBD1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.1.

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

Genes
ETV1
PMS2
CARD11
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ACTB
AHR
CLK2P
DGKB
GNA12
GPER
ICA1
IL6
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
DNAH11
CYTH3
PHF14
HDAC9
RAPGEF5
KIAA0415
ARL4A
GPNMB
AGR2
IGF2BP3
KDELR2
ADAP1
NUPL2
SNX13
IQCE
SUN1
SOSTDC1
WIPI2
INTS1
TSPAN13
EIF2AK1
BZW2
SNX8
TRA2A
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
TOMM7
TMEM106B
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
CDCA7L
RADIL
KLHL7
STK31
PAPOLB
C1GALT1
FAM20C
ANKMY2
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM126A
C7orf70
SCIN
ZFAND2A
COX19
CCDC126
GLCCI1
KIAA1908
GPR146
C7orf30
AMZ1
AGR3
PER4
TMEM184A
VWDE
PRPS1L1
TWISTNB
SP8
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
FERD3L
RPL23P8
SLC29A4
RSPH10B
TMEM196
STEAP1B
RPS2P32
TFAMP1
UNCX
COL28A1
ABCB5
C7orf46
MACC1
LOC389458
ELFN1
AGMO
GRID2IP
ZNF815
RNF216P1
PMS2CL
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
SNORD93
MIR589
RSPH10B2
LOC729852
ISPD
LOC100131257
LOC100288524
MIR3146
LOC100506025
LRRC72
LOC100506178
RBAK-LOC389458
MIR4648
MIR4655
MIR4656
KLHL7-AS1

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 - 26 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
22q12.1	2.4521e-26	2.4521e-26	chr22:29192671-29455701	1
4q35.1	1.2106e-16	3.6867e-11	chr4:183089198-184213557	6
1p36.23	1.4404e-08	1.4404e-08	chr1:8403012-8925111	1
4q34.3	1.239e-11	2.5947e-06	chr4:178911874-183060693	1
3q13.31	4.5637e-05	4.5637e-05	chr3:115440285-116429324	1
9p21.3	4.2848e-06	4.5637e-05	chr9:21865498-21997722	2
13q14.2	0.00030797	0.00030797	chr13:48833767-49064807	2
9p23	0.0014418	0.0021427	chr9:8310705-12693402	1
17q24.2	0.0014418	0.0088214	chr17:66185305-66865465	9
11p15.5	0.011772	0.011772	chr11:1637882-1944201	12
2q37.3	0.026388	0.025279	chr2:239359581-243199373	55
17q21.31	0.0038046	0.025279	chr17:35750456-45001206	278
20p12.1	0.025279	0.025279	chr20:1-19269544	167
16p13.3	0.036104	0.036104	chr16:5144019-8620694	1
6q26	0.039484	0.039484	chr6:161693099-169617013	35
11q14.1	0.04244	0.042397	chr11:83165646-85567968	6
17q11.2	0.041287	0.042397	chr17:29704122-29888119	4
16q23.1	0.083467	0.086184	chr16:72148304-90354753	157
7q32.3	0.090311	0.088012	chr7:95210837-159138663	555
18q21.2	0.092052	0.088012	chr18:48514396-48705371	1
2q22.1	0.16439	0.16439	chr2:101177744-144529063	234
6p24.3	0.17655	0.18353	chr6:1-21599699	114
10q23.1	0.18244	0.18353	chr10:1-135534747	945
14q21.2	0.17841	0.18353	chr14:1-76969289	472
12q14.2	0.18877	0.18993	chr12:56315051-92536825	225
1q43	0.23388	0.23388	chr1:1-249250621	2410

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.1.

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

Genes
ZNRF3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
hsa-mir-1305
DCTD
ODZ3
C4orf38
FAM92A3
MIR1305

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
RERE

Genes in Wide Peak

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

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

Genes
LINC00290

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
LSAMP

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

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

Genes
PTPRD

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.2.

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

Genes
PRKAR1A
hsa-mir-635
SLC16A6
ARSG
AMZ2
FAM20A
WIPI1
LOC440461
MIR635

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

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

Genes
hsa-mir-4298
CTSD
LSP1
TNNI2
SYT8
KRTAP5-4
FAM99A
IFITM10
KRTAP5-5
KRTAP5-6
FAM99B
MIR4298

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

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

Genes
BRCA1
ERBB2
ETV4
LASP1
MLLT6
RARA
hsa-mir-4315-1
hsa-mir-2117
ACLY
AOC2
ARL4D
ATP6V0A1
FMNL1
CACNB1
CDC6
CCR7
CNP
CRHR1
CSF3
DHX8
DUSP3
EZH1
GAST
FZD2
G6PC
KAT2A
GFAP
CCR10
GRB7
GRN
HCRT
HSD17B1
IFI35
IGFBP4
ITGA2B
JUP
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
NAGLU
NEUROD2
NMT1
NSF
PNMT
MED1
PPY
PSMB3
PYY
PSMD3
RAB5C
RPL19
RPL27
SLC4A1
SMARCE1
STAT3
STAT5A
STAT5B
TADA2A
HNF1B
MLX
THRA
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
PCGF2
RND2
PIP4K2B
CNTNAP1
TCAP
AOC3
BECN1
KRT38
KRT37
KRT36
HAP1
MAP3K14
EFTUD2
RPL23
NR1D1
PLEKHM1
MED24
LRRC37A
HDAC5
GJC1
PSME3
EIF1
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
C1QL1
RUNDC3A
STARD3
DDX52
DUSP14
SYNRG
CASC3
IKZF3
GPATCH8
KCNH4
FAM215A
KRT23
TUBG2
NKIRAS2
CCDC56
PSMC3IP
SOCS7
SOST
RAPGEFL1
ARL17A
SLC25A39
HIGD1B
CDK12
KRT20
CWC25
LRRC37A4
KLHL11
GSDMB
ATXN7L3
PLXDC1
ARHGAP23
FKBP10
WNK4
C17orf53
TMUB2
DHX58
ACBD4
DCAKD
PLEKHH3
DBF4B
COASY
SRCIN1
AARSD1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
TTC25
KRTAP4-12
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
PPP1R1B
TBC1D3F
MIEN1
MRPL45
VPS25
TMEM101
GHDC
KRTAP4-4
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
AOC4
G6PC3
ASB16
PGAP3
HSPB9
ORMDL3
PLCD3
TMEM106A
NT5C3L
ZPBP2
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
GJD3
KRT222
KRT40
CD300LG
KIF18B
RUNDC1
C17orf69
LOC147093
WIPF2
KRT25
TMEM99
NAGS
FAM134C
IMP5
KRT28
KRT24
ARHGAP27
ZNF385C
STH
KIAA1267
C17orf105
FAM171A2
C17orf104
LOC284100
CISD3
GSDMA
KRT42P
PTRF
KLHL10
C17orf65
MSL1
KRT27
FLJ43826
STAC2
KRT26
C17orf98
LOC388387
CCDC103
ARL5C
KRT39
MGC57346
LOC440434
GPR179
LRRC37A2
FBXO47
SNORA21
LOC644172
LOC644246
KRTAP4-11
KRTAP4-8
KRTAP2-2
KRTAP9-1
NSFP1
TBC1D3
LOC730755
SNORD124
LOC100128977
LOC100130148
LOC100130581
LOC100131347
KRTAP4-9
KRTAP4-7
LOC100133991
C17orf96
LOC100190938
MIR2117
MIR4315-2
MIR4315-1
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
MIR4728
MIR4726
MIR4734
MIR4727

Genes in Wide Peak

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

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

Genes
hsa-mir-3192
hsa-mir-103-2-as
hsa-mir-1292
ADRA1D
JAG1
AVP
BFSP1
BMP2
CDC25B
CENPB
CHGB
CSNK2A1
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PCNA
PCSK2
PDYN
PLCB4
PRNP
PTPRA
RRBP1
SIGLEC1
SNAP25
SNRPB
SNRPB2
SOX12
TCF15
TGM3
ZNF133
MKKS
ATRN
CDS2
PSMF1
SNPH
ProSAPiP1
RASSF2
SLC23A2
SIRPB1
SEC23B
NOP56
RBCK1
POLR3F
RBBP9
DSTN
RNF24
UBOX5
BTBD3
PLCB1
PRND
FLRT3
LAMP5
SPEF1
C20orf194
SNORD57
SNORD56
SDCBP2
SNX5
C20orf30
HSPC072
ANGPT4
ESF1
TRMT6
HAO1
SMOX
CRLS1
C20orf27
DZANK1
SPTLC3
C20orf29
TMEM74B
SIRPG
FERMT1
KIF16B
TASP1
NSFL1C
TMX4
GPCPD1
CPXM1
OTOR
PAK7
CSRP2BP
MAVS
EBF4
TRIB3
OVOL2
FASTKD5
ANKRD5
GFRA4
VPS16
FAM113A
MRPS26
DDRGK1
C20orf7
ZNF343
NRSN2
PANK2
ADAM33
SEL1L2
DEFB126
FAM110A
SLC4A11
MCM8
ZCCHC3
SCRT2
C20orf72
DTD1
C20orf54
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
PROKR2
C20orf94
C20orf96
MACROD2
SRXN1
BANF2
DEFB127
C20orf79
ISM1
DEFB129
SIRPA
STK35
PRNT
LOC149837
C20orf196
LRRN4
DEFB125
DEFB128
SIRPB2
LOC339593
RSPO4
TGM6
LINC00493
DEFB132
C20orf202
MIR103A2
DZANK1-AS1
RAD21L1
LOC643406
SNORA51
SNORD17
SNORD86
SNORD110
LOC728228
SNORD119
LOC100128496
LOC100130264
LOC100131208
LOC100134015
LOC100270804
TMEM239
LOC100289473
MIR1292
MIR103B2
PCNA-AS1
PET117
MACROD2-AS1
MIR3192
LOC100505536
LOC100507495
LOC100507629
FKBP1A-SDCBP2

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

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

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
CCR6
GPR31
KIF25
PARK2
RPS6KA2
T
TCP10
RNASET2
QKI
PDE10A
C6orf123
BRP44L
UNC93A
SMOC2
FRMD1
TTLL2
LINC00473
SFT2D1
PACRG
DACT2
C6orf118
LOC285796
PRR18
DKFZp451B082
TCP10L2
LOC441177
MLLT4-AS1
HGC6.3
LOC100289495
MIR1913
MIR3939
CAHM

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.1.

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

Genes
DLG2
SYTL2
TMEM126B
CREBZF
TMEM126A
CCDC89

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

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

Genes
hsa-mir-193a
RAB11FIP4
MIR193A
MIR4724

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
BANP
RFWD3
ZDHHC7
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
CTRB2
CLEC18B
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
SYCE1L
LOC100287036
MIR1910
MIR3182
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q32.3.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
ABP1
ACHE
AKR1B1
ARF5
ASNS
AZGP1
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
AP1S1
CLCN1
CPA1
CPA2
CUX1
CYP3A7
CYP3A4
CYP3A5
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNB2
GPR22
GPR37
GRM8
MNX1
AGFG2
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PIK3CG
PIP
PMS2P1
PODXL
POLR2J
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
PSMC2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
ZNF3
ZKSCAN1
ZSCAN21
ZYX
SHFM1
ST7
ARHGEF5
ZNF212
TRRAP
ZNF282
CUL1
TRIM24
BUD31
MGAM
WASL
PLOD3
DGKI
AP4M1
ATP6V1F
ACCN3
PMPCB
ATP5J2
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
FAM3C
COG5
ZNHIT1
ARPC1A
SH2B2
STAG3
CPSF4
FASTK
COPS6
DUS4L
ZNF277
ABCB8
PDAP1
TFEC
LAMB4
LMTK2
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
COPG2
HBP1
DNAJC2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRB
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
LUC7L2
MRPS33
NUB1
NAA38
GPR85
TAS2R5
CHPF2
PUS7
ING3
LRRN3
ALKBH4
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
MLL5
BAIAP2L1
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
RABL5
CYP3A43
LRRC61
C7orf49
ZNF655
PVRIG
GCC1
GAL3ST4
PRKRIP1
CBLL1
ZNF767
C7orf58
TTC26
ORAI2
JHDM1D
OR2AE1
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
ZNF394
MYH16
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
TRIM4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
MUC17
RNF32
ASB15
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
BHLHA15
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
ZNF498
FAM200A
PPP1R35
GPC2
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
CNPY4
POLR2J2
UBN2
MBLAC1
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
DLX6-AS1
ZNF789
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
MOGAT3
FAM71F2
STRA8
KLRG2
WDR86
GJC3
DPY19L2P2
LOC349160
GATS
GSTK1
NAT16
SLC26A5
LHFPL3
KCP
FLJ43663
RNF148
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
OR2A5
FLJ42280
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
UFSP1
MIR106B
MIR129-1
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
SPDYE3
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR490
ZNF862
LOC645249
LOC645591
AZGP1P1
LOC646329
C7orf73
ACTR3C
MIR591
MIR592
MIR593
MIR595
LOC723809
LOC728377
LOC728743
SPDYE6
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100129845
LOC100130705
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
LOC100287482
MOXD2P
LOC100289187
LOC100289561
ZNF783
MIR548F3
MIR548I4
SPDYE2L
MIR548F4
SAP25
MIR548T
MIR4285
MTRNR2L6
MIR3609
MIR3907
MIR3666
LOC100505483
LOC100506136
LOC100506585
LOC100507421
ATP5J2-PTCD1
GIMAP1-GIMAP5
MIR4653
MIR4468
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

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

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

Genes
SMAD4

Genes in Wide Peak

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

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

Genes
ERCC3
PAX8
TTL
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
BIN1
BUB1
CCNT2
DARS
DBI
EN1
FHL2
GLI2
GPR17
GPR39
GYPC
HNMT
IL1A
IL1B
IL1R1
IL1RN
INHBB
LCT
LIMS1
MCM6
MGAT5
MYO7B
NPAS2
NPHP1
POLR2D
POU3F3
PROC
PTPN4
RALB
RANBP2
RPL31
SCTR
SLC9A2
SLC20A1
SULT1C2
TSN
IL1R2
MALL
CXCR4
NCK2
MARCO
IL18RAP
IL1RL2
IL18R1
DDX18
KYNU
IL1RL1
TGFBRAP1
HS6ST1
MAP4K4
GCC2
BCL2L11
ACTR3
MERTK
MAP3K2
EDAR
TBC1D8
RABL2A
NXPH2
GPR45
RAB3GAP1
UBXN4
CLASP1
R3HDM1
PSD4
PTPN18
IL36RN
IL36B
IL37
IL36A
SULT1C4
C2orf27A
TFCP2L1
ARHGEF4
INSIG2
LRP1B
CCDC93
PLEKHB2
STEAP3
ACOXL
WDR33
C2orf29
SMPD4
IWS1
LIMS2
ARHGAP15
CFC1
IL36G
UGGT1
DPP10
EPB41L5
SLC5A7
ANAPC1
MRPS9
SOWAHC
PDCL3
C2orf49
TMEM185B
SAP130
MZT2B
YSK4
UXS1
SLC35F5
THSD7B
TMEM177
TMEM163
AMMECR1L
ZRANB3
RAB6C
POLR1B
RGPD5
CHCHD5
CCDC115
MKI67IP
C2orf40
ZC3H8
ST6GAL2
IL1F10
DDX11L2
MFSD9
SFT2D3
TMEM87B
LOC84931
CCDC74A
CCDC74B
IMP4
LIMS3
TUBA3E
TUBA3D
LYPD1
RPL23AP7
CNTNAP5
FBLN7
ACMSD
FAM168B
C2orf76
TMEM182
TMEM37
CKAP2L
CBWD2
LOC150527
LOC150568
LOC150776
WTH3DI
LOC151009
SEPT10
SULT1C2P1
CCDC138
C1QL2
FOXD4L1
PCDP1
CREG2
FAM123C
LINC00116
LOC254128
RNF149
LOC284998
LOC285000
LOC285103
PLGLA
RGPD4
SPOPL
CYP27C1
NCKAP5
SH3RF3
GPR148
WASH2P
ZC3H6
SLC9A4
LOC389023
LOC389033
LOC389043
FLJ42351
LOC401010
MIR128-1
C2orf27B
LOC440894
LOC440895
LOC440900
LOC440905
LOC440910
POTEKP
SULT1C3
POTEE
LOC541471
ANKRD30BL
LOC646743
LOC647012
CFC1B
RGPD3
MZT2A
FAM138B
LOC654433
SNORD89
RGPD8
POTEF
LOC729121
RGPD6
RFX8
LOC100129961
LOC100131320
CYP4F30P
RNU4ATAC
LOC100216479
LIMS3-LOC440895
LOC100287010
LOC100287216
LOC100288570
LIMS3L
MIR663B
MIR4265
MIR4267
MIR4266
LOC100499194
MIR3679
LOC100506421
LOC100507334
LOC100507600
MIR4436B1
MIR4772
MIR4783
MIR4782
MIR4435-2
MIR4784
MIR4435-1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.3.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.1.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.2.

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

Genes
KTN1
NKX2-1
GPHN
NIN
CCNB1IP1
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ACTN1
ACYP1
ANG
APEX1
ARF6
ARG2
ARHGAP5
BCL2L2
BMP4
ZFP36L1
ENTPD5
CDKN3
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
DLST
EIF2S1
ERH
ESR2
ESRRB
FKBP3
FOXG1
FNTB
FOS
FUT8
GCH1
GMFB
GPR33
GPX2
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
LGALS3
LTBP2
MAX
MGAT2
CTAGE5
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
PNP
NRL
SIX6
OTX2
OXA1L
PAX9
PCK2
PGF
PIGH
PNN
POLE2
PPM1A
PPP2R5E
PRKCH
PRKD1
PSEN1
PSMA3
PSMA6
PSMB5
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPL36AL
RPS29
RTN1
SALL2
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGFB3
TGM1
ZBTB25
PABPN1
DPF3
GEMIN2
NUMB
ADAM21
ADAM20
CDKL1
DCAF5
EIF2B2
AP1G2
SLC7A7
NEMF
PNMA1
CPNE6
AKAP6
AKAP5
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
KIAA0317
TOX4
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
BATF
TM9SF1
NPC2
EXOC5
CGRRF1
EDDM3A
DHRS4
ACOT2
TMED10
FERMT2
RIPK3
AP4S1
C14orf1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
ATG14
ZBTB1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
SYNE2
SCFD1
KHNYN
SLC7A8
ZFYVE26
TTC9
KLHDC2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
NKX2-8
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
ERO1L
COQ6
FAM158A
ATL1
FCF1
RDH11
ZNF219
COX16
GMPR2
SLC22A17
DACT1
ATP6V1D
JKAMP
MBIP
DHRS7
C14orf166
SIX4
ZFYVE1
GNG2
KLHL28
C14orf101
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
RNF31
RBM23
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SYNJ2BP
SLC39A9
C14orf167
G2E3
FLVCR2
OSGEP
C14orf118
ARHGEF40
MUDENG
EAPP
ACTR10
YLPM1
METTL3
LTB4R2
C14orf162
SDR39U1
RPGRIP1
PELI2
RHOJ
NDRG2
GALNTL1
PLEKHH1
NYNRIN
TXNDC16
TRMT5
HOMEZ
CHD8
FANCM
ZNF410
RBM25
SNX6
SAV1
C14orf93
ABHD4
NPAS3
SMOC1
EDDM3B
MPP5
CDH24
C14orf135
GPR135
METTL17
IL25
GNPNAT1
THTPA
OR4K5
OR11H2
OR4K1
METTL21D
ZC2HC1C
C14orf169
IPO4
L2HGDH
C14orf45
NUBPL
DCAF11
DDHD1
OR4K15
SGPP1
TMX1
DNAL1
RPS6KL1
SYT16
FSCB
BRMS1L
JPH4
RNASE7
INSM2
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
SLC25A21
PAPLN
LRRC16B
PPP1R3E
TMEM55B
CHURC1
C14orf43
LIN52
NEK9
TTC5
MAPK1IP1L
EGLN3
C14orf126
IFT43
WDR89
C14orf149
TRIM9
DHRS1
CMTM5
MIA2
C14orf28
TRAPPC6B
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
NAA30
GPHB5
JDP2
ISCA2
ACOT4
KLHL33
RPL10L
RDH12
ADAM21P1
MIPOL1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
MDP1
LRFN5
FAM71D
TMEM229B
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
C14orf21
SPTSSA
ADCY4
C14orf183
RALGAPA1
SFTA3
FBXO33
IGBP1P1
LOC283547
C14orf182
LOC283553
GPR137C
PROX2
LOC283624
TSSK4
FAM177A1
DHRS4L2
C14orf55
C14orf39
SNORD8
SNORD56B
RNASE10
VSX2
OR6S1
SLC35F4
RAB15
FLJ31306
TBPL2
C14orf23
TOMM20L
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
FLJ22447
PLEKHD1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
LINC00238
OR4Q3
OR4M1
TEX21P
RNASE12
ACOT1
ACOT6
POTEM
LOC642426
ECRP
C14orf176
CBLN3
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
SNORD9
MIR624
DHRS4L1
C14orf38
LOC731223
SNORD127
SNORD126
MIR208B
KTN1-AS1
LOC100129794
LOC100288846
LOC100289511
OTX2OS1
MIR4308
MIR4307
MIR548Y
LOC100505967
LOC100506071
LOC100506321
LOC100506433
NEDD8-MDP1
BCL2L2-PABPN1
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4503
MIR548AI
MIR4707
MIR4706
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q14.2.

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

Genes
CDK4
DDIT3
MDM2
NACA
HMGA2
WIF1
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
APOF
ATP2B1
ATP5B
AVPR1A
CDK2
CPM
CS
CSRP2
CYP27B1
DGKA
DCN
EPYC
DUSP6
ERBB3
B4GALNT1
GLI1
GNS
IFNG
INHBC
KCNC2
KIF5A
LRP1
LUM
LYZ
MARS
METTL1
KITLG
MIP
MYF5
MYF6
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
CNOT2
NTS
PA2G4
PAWR
PRIM1
PTPRB
PTPRR
RAB5B
RAP1B
RBMS2
RPL41
RPS26
TSPAN31
SHMT2
PMEL
SMARCC2
STAT2
STAT6
SUOX
SYT1
TAC3
TSPAN8
YEATS4
ALX1
DYRK2
PPFIA2
LGR5
RDH16
HSD17B6
GALNT4
LIN7A
TIMELESS
RASSF9
SLC16A7
ZBTB39
PAN2
USP15
TSFM
CTDSP2
RNF41
TMEM5
CNPY2
DCTN2
CCT2
AVIL
PTGES3
FRS2
OS9
GLIPR1
CPSF6
KERA
KRR1
BAZ2A
IRAK3
NXPH4
XPOT
GPR182
PHLDA1
R3HDM2
RAB21
MON2
TMEM194A
TBC1D30
ESYT1
ZDHHC17
GRIP1
LEMD3
MGAT4C
METTL21B
SNORD59A
GLS2
KCNMB4
CCDC59
TBK1
TRHDE
IL22
IL23A
TMBIM4
SLC6A15
TMEM19
SLC35E3
IL26
CAND1
MDM1
NDUFA4L2
NUP107
PPM1H
SRGAP1
ARHGAP9
IKZF4
TBC1D15
SLC26A10
OBFC2B
ACSS3
BBS10
PIP4K2C
CEP290
THAP2
INHBE
LRRIQ1
C12orf26
LLPH
CAPS2
ZC3H10
NAV3
C12orf29
XRCC6BP1
HELB
MARCH9
COQ10A
MBD6
OSBPL8
ARHGEF25
C12orf56
AGAP2
RAB3IP
SDR9C7
LRIG3
TPH2
MYL6B
GLIPR1L2
TSPAN19
BEST3
E2F7
C12orf66
TMTC2
TMTC3
C12orf50
DTX3
ZFC3H1
C12orf12
RPSAP52
STAC3
MSRB3
LOC256021
GLIPR1L1
POC1B
OTOGL
RASSF3
ANKRD52
SLC39A5
SPRYD4
LOC283392
C12orf61
DPY19L2
LOC338758
FAM19A2
PTPRQ
LRRC10
FLJ41278
MKRN9P
MIRLET7I
MIR26A2
C12orf37
ATXN7L3B
SNORD59B
MIR548C
MIR617
MIR618
LOC728084
MRS2P2
LOC100130776
MIR1252
MIR1279
MIR1228
SNORA70G
MIR548Z
MIR3913-2
MIR3913-1
LOC100506844
LOC100507250
LOC100507377
POC1B-GALNT4
MIR4699
MIR548AL

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

Table S44. Genes in bold are cancer genes as defined by The Sanger Institute: 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 - 22 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	2121	0.03	-3.47	1	0.35	2.95	0.0269
1q	1955	0.09	-2.82	1	0.26	0.634	0.999
2p	924	0.18	-2.28	1	0.22	-1.52	0.999
2q	1556	0.15	-2.17	1	0.20	-1.14	0.999
3p	1062	0.17	-2.15	1	0.27	-0.43	0.999
3q	1139	0.20	-1.53	1	0.28	-0.193	0.999
4p	489	0.45	2.25	0.0306	0.22	-1.75	0.999
4q	1049	0.41	2.29	0.0292	0.21	-1.43	0.999
5p	270	0.69	6.59	1.42e-10	0.26	-0.967	0.999
5q	1427	0.64	7.64	1.44e-13	0.19	-1.07	0.999
6p	1173	0.23	-0.961	1	0.28	-0.00541	0.999
6q	839	0.24	-1.27	1	0.30	-0.163	0.999
7p	641	0.56	4.73	3.89e-06	0.14	-2.53	0.999
7q	1277	0.57	6.02	4.87e-09	0.14	-1.95	0.999
8p	580	0.43	2.01	0.052	0.28	-0.768	0.999
8q	859	0.49	3.5	0.000662	0.23	-1.16	0.999
9p	422	0.28	-1.02	1	0.30	-0.673	0.999
9q	1113	0.36	1.38	0.175	0.19	-1.64	0.999
10p	409	0.32	-0.258	1	0.18	-2.56	0.999
10q	1268	0.33	0.942	0.346	0.16	-2.17	0.999
11p	862	0.08	-4.04	1	0.28	-0.444	0.999
11q	1515	0.08	-3.43	1	0.28	0.436	0.999
12p	575	0.75	8.47	0	0.19	-1.43	0.999
12q	1447	0.74	10	0	0.15	-1.29	0.999
13q	654	0.12	-3.07	1	0.46	2.87	0.0269
14q	1341	0.29	0.355	0.688	0.26	-0.227	0.999
15q	1355	0.16	-2.1	1	0.27	-0.125	0.999
16p	872	0.58	5.44	1.36e-07	0.17	-1.93	0.999
16q	702	0.55	4.72	3.89e-06	0.12	-2.81	0.999
17p	683	0.09	-3.77	1	0.38	1.19	0.665
17q	1592	0.08	-3.27	1	0.31	1.04	0.744
18p	143	0.11	-3.64	1	0.44	1.7	0.443
18q	446	0.09	-3.79	1	0.41	1.56	0.471
19p	995	0.66	7.33	8.93e-13	0.15	-1.9	0.999
19q	1709	0.60	7.49	3.47e-13	0.13	-1.74	0.999
20p	355	0.56	4.25	3.31e-05	0.22	-1.64	0.999
20q	753	0.56	4.93	1.61e-06	0.10	-3.03	0.999
21q	509	0.41	1.58	0.127	0.25	-1.2	0.999
22q	921	0.07	-3.24	1	0.55	5.11	6.52e-06
Xq	1312	0.54	5.07	8.87e-07	0.35	1.25	0.665

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/ACC-TP/8015986/GDAC_MergeDataFiles_4926855/ACC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat
CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.7
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 90 Input Tumor Samples.

Tumor Sample Names
TCGA-OR-A5J1-01A-11D-A29H-01
TCGA-OR-A5J2-01A-11D-A29H-01
TCGA-OR-A5J3-01A-11D-A29H-01
TCGA-OR-A5J4-01A-11D-A29H-01
TCGA-OR-A5J5-01A-11D-A29H-01
TCGA-OR-A5J6-01A-31D-A29H-01
TCGA-OR-A5J7-01A-11D-A29H-01
TCGA-OR-A5J8-01A-11D-A29H-01
TCGA-OR-A5J9-01A-11D-A29H-01
TCGA-OR-A5JA-01A-11D-A29H-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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