SNP6 Copy number analysis (GISTIC2)
Prostate Adenocarcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1DJ5D3H
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/C1DJ5D3H
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 2.0.20 (Firehose task version: 126).

Summary

There were 278 tumor samples used in this analysis: 20 significant arm-level results, 24 significant focal amplifications, and 30 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 24 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
Xq27.1 | 2.3397e-12 | 3.5035e-12 | chrX:138564705-138580758 | 0 [F9]
Xq21.1 | 4.3522e-06 | 0.00055344 | chrX:79251708-79255479 | 0 [TBX22]
Xq25 | 0.0011431 | 0.0067923 | chrX:126306276-126315813 | 0 [CXorf64]
Xp22.11 | 0.0022268 | 0.0081661 | chrX:23975644-23983593 | 0 [CXorf58]
Xp22.11 | 0.0022268 | 0.010529 | chrX:24515774-24522924 | 1
3q26.2 | 0.010742 | 0.040612 | chr3:169415894-170116437 | 13
14q21.1 | 0.040612 | 0.040612 | chr14:38008682-38049106 | 1
Xq21.1 | 0.036484 | 0.040612 | chrX:80829747-80833679 | 0 [SH3BGRL]
3q21.3 | 0.040612 | 0.076994 | chr3:124084975-145458185 | 164
Xp21.1 | 0.044587 | 0.076994 | chrX:35651236-35660210 | 0 [MAGEB16]
Xq25 | 0.076994 | 0.095358 | chrX:122399494-122410812 | 1
11q13.3 | 0.10708 | 0.10708 | chr11:64592727-70349012 | 167
1q21.3 | 0.11771 | 0.11771 | chr1:120523956-155699117 | 288
8p11.22 | 0.067141 | 0.11771 | chr8:39051902-39137830 | 1
Xq21.31 | 0.040612 | 0.13138 | chrX:87704771-87710744 | 0 [CPXCR1]
8q21.3 | 0.10708 | 0.18571 | chr8:60883302-146364022 | 472
7p15.3 | 0.18936 | 0.18936 | chr7:1-42267570 | 281
4q13.3 | 0.19902 | 0.19902 | chr4:68039230-101971450 | 218
12q24.32 | 0.19999 | 0.19999 | chr12:59359201-133851895 | 516
20q13.33 | 0.19999 | 0.19999 | chr20:41749332-63025520 | 290
8p12 | 0.10617 | 0.20055 | chr8:33930573-38781039 | 25
8q24.21 | 0.040612 | 0.22 | chr8:76720721-146364022 | 388
15q11.2 | 0.229 | 0.229 | chr15:1-43062654 | 283
9q34.3 | 0.24561 | 0.24561 | chr9:95361064-141213431 | 565

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.11.

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

Genes
PDK3

Genes in Wide Peak

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

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

Genes
PRKCI
SKIL
TERC
SEC62
GPR160
MYNN
LRRC31
PHC3
ARPM1
LRRC34
LRRIQ4
SAMD7
LOC100128164

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.1.

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

Genes
MIPOL1

Genes in Wide Peak

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

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

Genes
FOXL2
GATA2
RPN1
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
ACPP
ATP1B3
ATR
EPHB1
GP9
ITGB5
MCM2
NCK1
PCCB
PIK3CB
PLS1
PLXNA1
PPP2R3A
RASA2
RBP1
RBP2
RHO
RYK
SLCO2A1
TF
TFDP2
TRH
TRPC1
UMPS
CNBP
ZNF148
RAB7A
SOX14
BFSP2
RUVBL1
SNX4
MBD4
H1FX
KALRN
COPB2
CHST2
RNF7
STAG1
ALDH1L1
TOPBP1
MRPL3
MGLL
MRAS
COPG
TMCC1
PLXND1
DNAJC13
U2SURP
C3orf27
ANAPC13
ARMC8
PCOLCE2
NPHP3
ATP2C1
ACAD9
ASTE1
KLF15
SEC61A1
PIK3R4
PODXL2
A4GNT
DBR1
CLDN18
AMOTL2
CCRL1
RAB6B
IL20RB
XRN1
SLC41A3
MSL2
FAIM
SLC25A36
CDV3
IFT122
MUC13
C3orf37
MRPS22
ISY1
HEG1
KIAA1257
SRPRB
BPESC1
EEFSEC
CLSTN2
TMEM108
ZXDC
CCDC48
NEK11
UBA5
C3orf36
CEP63
CEP70
ABTB1
TMEM22
ESYT3
ACAD11
CHCHD6
SLC12A8
LOC90246
C3orf25
SPSB4
ACPL2
TXNRD3
OSBPL11
CPNE4
TPRA1
UROC1
NUDT16
COL6A6
GRK7
RPL32P3
H1FOO
PISRT1
ROPN1B
C3orf22
NUDT16P1
DNAJB8
CHST13
KBTBD12
DZIP1L
ALG1L
C3orf58
ZBTB38
NUP210P1
COL6A5
GK5
SLC9A9
DNAJB8-AS1
TRIM42
RAB43
KY
LOC339874
H1FX-AS1
PAQR9
NME9
CCDC37
NPHP3-AS1
NMNAT3
PRR23B
PRR23C
C3orf72
ALG1L2
TXNRD3NB
COL6A4P2
LOC653712
SNORA7B
SNORA58
FAM86HP
PRR23A
LOC100125556
LOC100289361
MIR1280
MIR548I1
LOC100507032
LOC100507389
NPHP3-ACAD11
ISY1-RAB43
MIR4788

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq25.

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

Genes
GRIA3

Genes in Wide Peak

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

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

Genes
CCND1
hsa-mir-548k
hsa-mir-3164
hsa-mir-3163
hsa-mir-612
hsa-mir-194-2
ACTN3
ADRBK1
ALDH3B1
ALDH3B2
ARL2
BBS1
C11orf2
MRPL49
ZNHIT2
CAPN1
CFL1
CHKA
CPT1A
CST6
CTSW
CTTN
FAU
FGF3
FGF4
GSTP1
SLC29A2
IGHMBP2
LRP5
LTBP3
MAP3K11
NDUFV1
NDUFS8
OVOL1
PC
PPP1CA
PPP2R5B
PTPRCAP
RAD9A
RBM4
RELA
DPF2
RPS6KB2
SIPA1
SPTBN2
TM7SF2
ZFPL1
FOSL1
PPFIA1
CTSF
FADD
BANF1
AIP
SART1
FIBP
PITPNM1
RIN1
MTL5
FGF19
CCS
RCE1
NAALADL1
DPP3
KCNK7
CDK2AP2
TCIRG1
RBM14
CDC42EP2
KAT5
SSSCA1
DRAP1
YIF1A
EHD1
SF3B2
CCDC85B
B3GNT1
SHANK2
KDM2A
ATG2A
CLCF1
FAM89B
POLA2
BRMS1
MYEOV
SAC3D1
SNX15
RHOD
EFEMP2
GAL
SUV420H1
CABP2
C11orf24
SSH3
ANO1
CCDC87
PPP6R3
CDC42BPG
PACS1
CABP4
CD248
CORO1B
SCYL1
CARNS1
POLD4
KLC2
MRPL11
LRFN4
C11orf80
TMEM134
MUS81
UNC93B1
RAB1B
C11orf68
RBM4B
FRMD8
RNASEH2C
EIF1AD
SYVN1
GAL3ST3
DKFZp761E198
SYT12
ACY3
CDCA5
BATF2
MRGPRD
MRGPRF
CATSPER1
GPHA2
MRPL21
TPCN2
ORAOV1
TIGD3
PELI3
LOC254100
EHBP1L1
SNX32
TSGA10IP
CNIH2
ZDHHC24
C11orf86
NUDT8
TMEM151A
NPAS4
C11orf85
SLC25A45
NEAT1
ANKRD13D
TBX10
TBC1D10C
MALAT1
SPDYC
GPR152
DOC2GP
PCNXL3
MIR192
MIR194-2
SLC22A20
FAM86C2P
MIR612
LOC100130348
LOC100130987
MIR548K
RBM14-RBM4
ARL2-SNX15
MIR4489
MIR4690
MIR4691

Genes in Wide Peak

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

Table S7. Genes in bold are cancer genes as defined by The Sanger Institute's 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
DAP3
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
MSTO1
GOLPH3L
YY1AP1
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
LOC645676
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 8p11.22.

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

Genes
ADAM32

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q21.3.

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

Genes
COX6C
EXT1
MYC
RECQL4
NCOA2
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
hsa-mir-1273
hsa-mir-875
hsa-mir-3150
hsa-mir-3149
hsa-mir-2052
hsa-mir-124-2
ADCY8
ANGPT1
ANXA13
ASPH
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CA8
CALB1
RUNX1T1
CDH17
CRH
CYC1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
GEM
GLI4
GML
GPR20
GPT
GRINA
HAS2
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LY6E
LY6H
MATN2
MMP16
MYBL1
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
PDE7A
ENPP2
PLEC
PMP2
POLR2K
POU5F1B
PKIA
PTK2
PVT1
PEX2
RAB2A
RAD21
RPL7
RPL8
RPL30
SDC2
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
LY6D
JRK
EIF3H
DGAT1
GPAA1
RIPK2
GGH
WISP1
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
LRRC14
TTC35
RIMS2
MTSS1
PTDSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
ARFGEF1
COLEC10
KHDRBS3
POP1
COPS5
WWP1
STMN2
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
RRS1
SULF1
ARC
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
PTTG3P
SNORA72
OPLAH
PABPC1
KCNV1
STAU2
MTBP
EIF2C2
BHLHE22
MRPS28
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
FAM82B
ZNF706
VPS28
FAM203A
KCNK9
C8orf55
UBR5
FAM49B
AZIN1
OTUD6B
CHRAC1
GDAP1
EXOSC4
PDP1
CNGB3
LY6K
ESRP1
TMEM70
TRMT12
OXR1
WDYHV1
ARMC1
UBE2W
LAPTM4B
C8orf39
TMEM55A
SLC39A4
CHD7
SYBU
INTS8
PAG1
GSDMC
C8orf44
JPH1
ENY2
CPA6
SLURP1
SLC45A4
ZFAT
ZNF250
PRDM14
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
PLEKHF2
ZFAND1
ZFHX4
GSDMD
NIPAL2
CSPP1
BAALC
ZNF696
GRHL2
VCPIP1
PREX2
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SLCO5A1
SHARPIN
EPPK1
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NACAP1
NCALD
MAF1
UTP23
TRIM55
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
DNAJC5B
PSKH2
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
WDR67
HPYR1
TP53INP1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
C8orf34
TOP1MT
ZNF572
FAM92A1
C8orf38
ABRA
LYPD2
TMEM71
ADHFE1
DCAF4L2
RALYL
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
TMEM74
FAM91A1
C8orf45
CLVS1
C8orf84
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
C8orf83
DPY19L4
FBXO43
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
SLC10A5
SPATC1
CA13
XKR9
LOC389676
RBM12B
FLJ43860
MAFA
LOC392232
GDF6
LOC401463
C8orf59
SAMD12
MIR124-2
MIR30B
MIR30D
C8orf82
FER1L6-AS1
FLJ39080
FLJ46284
FLJ42969
C8orf85
LRRC24
LINC00251
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
ZNF704
C8orf69
LINC00051
SNHG6
SNORD87
C8orf73
SCXB
LINC00535
UG0898H09
RAD21-AS1
FABP9
FABP12
FER1L6
MIR599
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR875
MIR937
MIR939
LOC100127983
LOC100128126
LOC100128338
TCF24
SCXA
LOC100130155
LOC100130231
CCDC166
LOC100130298
LOC100130301
LRRC69
LOC100131726
LOC100132891
LOC100133669
LOC100192378
LOC100288181
REXO1L2P
LOC100288748
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR2052
MIR1208
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3150B
MIR3610
LOC100505659
LOC100505676
LOC100505718
LOC100507117
C8orf44-SGK3
ZHX1-C8ORF76
MIR378D2
MIR4661
MIR4663
MIR4472-1
MIR4664
MIR4471
MIR4470
LOC100616530
PCAT1
LINC00536
FSBP

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p15.3.

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

Genes
ETV1
HNRNPA2B1
HOXA9
HOXA11
HOXA13
PMS2
CARD11
JAZF1
hsa-mir-1200
hsa-mir-548n
hsa-mir-550-2
hsa-mir-550-1
hsa-mir-196b
hsa-mir-148a
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ACTB
ADCYAP1R1
AHR
AMPH
AOAH
AQP1
SEPT7
CHN2
CLK2P
CRHR2
DGKB
DFNA5
EVX1
GARS
GHRHR
GLI3
GNA12
GPER
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
ICA1
IL6
INHBA
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
NPY
PDE1C
PDGFA
PRKAR1B
RAC1
RALA
RP9
RPA3
SFRP4
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
CDK13
EIF3B
DNAH11
TAX1BP1
SKAP2
CYTH3
CREB5
NFE2L3
PHF14
HDAC9
RAPGEF5
SCRN1
KIAA0087
ELMO1
TRIL
KIAA0415
ARL4A
NOD1
GPNMB
AGR2
IGF2BP3
PPP1R17
KDELR2
ADAP1
NUPL2
HIBADH
INMT
POU6F2
FKBP9
CBX3
AVL9
SNX13
IQCE
DPY19L1
SUN1
KIAA0895
LSM5
SOSTDC1
KBTBD2
OSBPL3
WIPI2
INTS1
VPS41
TSPAN13
EIF2AK1
BBS9
BZW2
SNX8
SNX10
TRA2A
FTSJ2
NXPH1
NT5C3
TXNDC3
GET4
CCZ1
MPP6
CYCS
ANLN
MIOS
RNF216
CPVL
TOMM7
TMEM106B
EPDR1
ZNF853
CYP2W1
HEATR2
FKBP14
ZDHHC4
CHST12
CDCA7L
RADIL
KLHL7
STK31
PAPOLB
C1GALT1
FAM20C
YAE1D1
ANKMY2
TBX20
RBAK
NEUROD6
NPVF
HERPUD2
GGCT
C7orf26
MICALL2
C7orf10
FBXL18
TTYH3
EEPD1
STARD3NL
USP42
FAM188B
PSMG3
C7orf50
TNRC18
FAM126A
PLEKHA8
C7orf70
SCIN
ZFAND2A
COX19
CCDC126
GLCCI1
KIAA1908
GPR146
C7orf30
C7orf11
C7orf31
AMZ1
AGR3
BMPER
PER4
TMEM184A
VWDE
PRPS1L1
TWISTNB
SP8
HOXA11-AS1
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
DKFZP586I1420
C7orf41
PRR15
FERD3L
RPL23P8
SLC29A4
RSPH10B
CCDC129
ZNRF2
TMEM196
STEAP1B
RPS2P32
TFAMP1
C7orf71
LOC285954
UNCX
COL28A1
ABCB5
C7orf46
FAM183B
MACC1
LINC00265
GPR141
NPSR1
LOC389458
ELFN1
AGMO
GRID2IP
ZNF815
LOC401320
LOC401321
LOC401324
AAA1
MIR148A
RNF216P1
PMS2CL
LOC441204
ZNRF2P1
RP9P
FLJ44511
LOC442497
DPY19L2P3
MIR339
MIR196B
TARP
DPY19L2P1
WIPF3
ZNF890P
LOC646762
LOC646999
OCM
SNORD93
MIR550A1
MIR550A2
MIR589
RSPH10B2
LOC729852
ISPD
JAZF1-AS1
DPY19L1P1
LOC100130673
LOC100131257
LOC100133311
ZNRF2P2
LOC100288524
MIR1200
HOTTIP
MIR3146
MIR550B2
MIR550B1
LOC100506025
LRRC72
LOC100506178
HOTAIRM1
LOC100506497
LOC100506776
INMT-FAM188B
RBAK-LOC389458
HOXA10-HOXA9
MIR4648
MIR4655
MIR550A3
MIR4656
KLHL7-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
RAP1GDS1
hsa-mir-575
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
ALB
AMBN
ANXA3
AREG
ART3
ATOH1
BMP3
BMPR1B
BTC
CCNG2
SCARB2
CDS1
CENPC1
CSN1S1
CSN2
CSN3
DCK
DMP1
DSPP
EIF4E
EREG
FGF5
GC
GK2
GNRHR
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
H2AFZ
HNRNPD
HSP90AB3P
HTN1
HTN3
IBSP
IGJ
IL8
CXCL10
CXCL9
AFF1
MTTP
MUC7
NKX6-1
PDHA2
PF4
PF4V1
PKD2
PPEF2
PPBP
PPP3CA
PRKG2
MAPK10
PTPN13
CXCL6
CXCL11
CXCL5
SNCA
SPP1
STATH
SULT1E1
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
SPARCL1
USO1
UNC5C
LAMTOR3
SLC4A4
HERC3
STBD1
CDKL2
TMPRSS11D
ABCG2
ADAMTS3
G3BP2
HNRPDL
TSPAN5
ENAM
FAM13A
CXCL13
PDLIM5
UGT2B11
HPSE
SMR3B
NPFFR2
PPBPL2
UGT2A1
CCNI
SEC31A
RUFY3
MMRN1
WDFY3
METAP1
PARM1
RCHY1
ANKRD17
STAP1
SMR3A
DAPP1
NAAA
COQ2
SULT1B1
HPGDS
TMPRSS11E
MRPS18C
COPS4
HSD17B11
HERC5
PLAC8
EMCN
NUDT9
NUP54
UGT2B28
ODAM
HERC6
SDAD1
UBA6
BMP2K
SEPT11
SMARCAD1
MEPE
PRDM8
UTP3
KLHL8
SHROOM3
ENOPH1
PROL1
MRPL1
THAP9
UGT2A3
SCD5
DNAJB14
FRAS1
ARHGAP24
C4orf17
FAM175A
NAA11
AGPAT9
PIGY
CABS1
YTHDC1
MOB1B
RG9MTD2
HELQ
DDIT4L
GDEP
ANTXR2
LIN54
TMPRSS11B
C4orf36
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
TIGD2
RASSF6
CNOT6L
C4orf22
EPGN
LOC256880
FDCSP
NAP1L5
FAM13A-AS1
GPRIN3
COX18
C4orf37
CSN1S2AP
CCDC158
TMPRSS11A
SOWAHB
SLC10A6
HSD17B13
PCNAP1
TMPRSS11F
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
WDFY3-AS2
C4orf11
MTHFD2L
LOC441025
TMEM150C
LOC550112
LOC550113
UGT2A2
LOC644248
TMPRSS11GP
MIR575
FAM47E
FTLP10
CSN1S2BP
LOC100499177
MIR3684
LOC100505702
LOC100505875
LOC100506035
LOC100506746
LOC100507053
MIR4450
MIR4451
FAM47E-STBD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q24.32.

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

Genes
ALDH2
BCL7A
BTG1
MDM2
PTPN11
HMGA2
WIF1
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
AVPR1A
SCARB1
CMKLR1
COX6A1
CPM
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GNS
GOLGA3
GTF2H3
HAL
HPD
IFNG
IGF1
KCNC2
LTA4H
LUM
LYZ
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
CNOT2
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PTPRB
PTPRR
PXMP2
PXN
RAN
RAP1B
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
YEATS4
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
DYRK2
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
SLC16A7
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
USP15
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
TMEM5
CCT2
CAMKK2
ZNF268
FRS2
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
IRAK3
XPOT
PHLDA1
MLXIP
RPH3A
P2RX2
RAB21
FBXO21
MON2
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
TBC1D30
MED13L
ZDHHC17
SIRT4
GRIP1
ABCB9
ISCU
RIMBP2
ATP6V0A2
LEMD3
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
KCNMB4
MRPL42
IFT81
CCDC59
TBK1
FAM216A
HCFC2
TRHDE
SYCP3
CHST11
GALNT9
IL22
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
TMBIM4
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
IL26
CAND1
WSB2
NDUFA12
DIABLO
MDM1
ANKS1B
CHPT1
NUP107
TMCC3
PPM1H
SRGAP1
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
LLPH
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
HELB
SDSL
TMEM132B
OSBPL8
C12orf56
IQCD
LOC116437
RAB3IP
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
TPH2
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
C12orf66
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
RPSAP52
SLC17A8
GNN
MSRB3
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
RASSF3
GPR133
MORN3
LOC283392
C12orf61
DPY19L2
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
FAM19A2
EP400NL
RILPL1
PTPRQ
C12orf42
LRRC10
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
FLJ41278
MKRN9P
C12orf76
LOC400084
FLJ37505
MIRLET7I
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR548C
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
MRS2P2
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1279
MIR1827
MIR1178
MIR1251
SNORA70G
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507250
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
GNAS
SS18L1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-3194
ADA
ATP5E
BMP7
CD40
CDH4
CEBPB
CHRNA4
COL9A3
CSE1L
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
EYA2
NPBWR2
HNF4A
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
MC3R
MMP9
MYBL2
MYT1
NFATC2
NTSR1
OPRL1
PCK1
PFDN4
PI3
PLTP
CTSA
PPP1R3D
PSMA7
PTGIS
PTK6
PTPN1
RPS21
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SRMS
STAU1
STK4
AURKA
TAF4
TCEA2
TFAP2C
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF217
NCOA3
RAE1
BCAS1
STX16
TNFRSF6B
MATN4
DPM1
WISP2
VAPB
B4GALT5
SPATA2
OSBPL2
ACOT8
ATP9A
SGK2
ARFRP1
RGS19
SYCP2
WFDC2
ARFGEF2
TCFL5
SPINT3
TOMM34
SERINC3
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
HRH3
RBPJL
SLC9A8
ADNP
ZMYND8
SPO11
PRPF6
L3MBTL1
GTPBP5
GMEB2
SNORD12C
TP53TG5
MOCS3
SLCO4A1
STMN3
SLC35C2
SLMO2
IFT52
TH1L
C20orf43
C20orf111
PIGT
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
C20orf20
PPP4R1L
RBM38
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
DOK5
DBNDD2
RNF114
SULF2
SLC2A4RG
PMEPA1
CASS4
SPINLW1
JPH2
SALL4
ZNFX1
RAB22A
SLC12A5
ZNF512B
PREX1
COL20A1
NCOA5
CDH26
KCNK15
SLC17A9
ELMO2
ZNF335
LOC63930
PCIF1
FAM217B
CDH22
SLC13A3
GDAP1L1
LOC79015
C20orf195
PPDPF
TTPAL
BIRC7
NPEPL1
DNAJC5
PABPC1L
TUBB1
ZBP1
SLC2A10
CABLES2
PARD6B
ZGPAT
TOX2
PRIC285
SYS1
WFDC8
SNX21
ZSWIM1
TP53RK
DNTTIP1
FAM210B
PHACTR3
BHLHE23
NKAIN4
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
WFDC3
GCNT7
CBLN4
CTCFL
SAMD10
ABHD16B
RIMS4
NEURL2
ZSWIM3
WFDC10A
LINC00266-1
WFDC6
FAM65C
C20orf151
R3HDML
GTSF1L
WFDC5
LOC149773
GNAS-AS1
LSM14B
WFDC13
APCDD1L
C20orf201
FAM209A
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
TMEM189
TMEM189-UBE2V1
FAM209B
SPINT4
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
ZNFX1-AS1
SNORD12
MIR645
MIR647
SYS1-DBNDD2
HAR1A
HAR1B
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
ZNF663
LOC100131496
DPH3P1
LINC00029
LOC100144597
FLJ16779
MIR1914
MIR1257
MIR4325
MIR3194
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505783
LOC100505815
LOC100505826
LOC100506384
SPINLW1-WFDC6
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4758
MIR4532
MIR4533
MIR5095
LOC100652730

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p12.

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

Genes
FGFR1
WHSC1L1
ADRB3
EIF4EBP1
STAR
TACC1
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
BRF2
PLEKHA2
ZNF703
RAB11FIP1
PPAPDC1B
GOT1L1
UNC5D
LETM2
KCNU1
RNF5P1
C8orf86
LOC728024

Genes in Wide Peak

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

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

Genes
COX6C
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
hsa-mir-1273
hsa-mir-875
hsa-mir-3150
hsa-mir-3149
ADCY8
ANGPT1
ANXA13
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CYC1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
FABP4
FABP5
GEM
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LY6E
LY6H
MATN2
MMP16
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PLEC
PMP2
POLR2K
POU5F1B
PKIA
PTK2
PVT1
PEX2
RAD21
RPL8
RPL30
SDC2
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
LY6D
JRK
EIF3H
DGAT1
GPAA1
RIPK2
WISP1
CPNE3
FOXH1
CCNE2
EBAG9
LRRC14
TTC35
RIMS2
MTSS1
PTDSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
COLEC10
KHDRBS3
POP1
WWP1
STMN2
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
ZFPM2
HEY1
SCRIB
LRRC6
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
SNORA72
OPLAH
PABPC1
KCNV1
MTBP
EIF2C2
MRPS28
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
FAM135B
ZC2HC1A
PHF20L1
FAM82B
ZNF706
VPS28
FAM203A
KCNK9
C8orf55
UBR5
FAM49B
AZIN1
OTUD6B
CHRAC1
EXOSC4
PDP1
CNGB3
LY6K
ESRP1
TRMT12
OXR1
WDYHV1
LAPTM4B
C8orf39
TMEM55A
SLC39A4
SYBU
INTS8
PAG1
GSDMC
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
PLEKHF2
ZFAND1
ZFHX4
GSDMD
NIPAL2
BAALC
ZNF696
GRHL2
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
NACAP1
NCALD
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
PSKH2
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
WDR67
HPYR1
TP53INP1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
TOP1MT
ZNF572
FAM92A1
C8orf38
ABRA
LYPD2
TMEM71
DCAF4L2
RALYL
TMEM65
LOC157381
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
TMEM74
FAM91A1
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
REXO1L1
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
C8orf83
DPY19L4
FBXO43
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
SLC10A5
SPATC1
CA13
LOC389676
RBM12B
FLJ43860
MAFA
GDF6
C8orf59
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
FLJ46284
FLJ42969
C8orf85
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
ZNF704
C8orf69
LINC00051
C8orf73
SCXB
LINC00535
RAD21-AS1
FABP9
FABP12
FER1L6
MIR599
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR875
MIR937
MIR939
LOC100127983
LOC100128338
SCXA
LOC100130231
CCDC166
LRRC69
LOC100131726
LOC100133669
LOC100192378
LOC100288181
REXO1L2P
LOC100288748
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR1208
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3150B
MIR3610
LOC100507117
ZHX1-C8ORF76
MIR378D2
MIR4661
MIR4663
MIR4472-1
MIR4664
MIR4471
LOC100616530
PCAT1
LINC00536
FSBP

Genes in Wide Peak

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

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

Genes
BUB1B
C15orf55
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
APBA2
NBEAP1
CAPN3
CHRM5
CHRNA7
GABRA5
GABRB3
GABRG3
GANC
GCHFR
IPW
ITPKA
IVD
LTK
MEIS2
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SPINT1
SRP14
THBS1
TJP1
TYRO3
UBE3A
MKRN3
PAR5
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
AQR
ARHGAP11A
SLC12A6
RASGRP1
GPR176
CHP
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
C15orf2
TMEM87A
RPAP1
DKFZP434L187
GREM1
RPUSD2
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
KLF13
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
ZFP106
CHAC1
C15orf29
NIPA2
C15orf41
ZFYVE19
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
TUBGCP5
NIPA1
PLA2G4E
PAR1
LOC145845
TMCO5A
TTBK2
CDAN1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
EXD1
FSIP1
RHOV
LPCAT4
PLA2G4F
LRRC57
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
LOC503519
C15orf62
C15orf56
PHGR1
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
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
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
ABL1
FANCC
NOTCH1
RALGDS
SET
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
BAAT
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL2
CYLC2
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSD17B3
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NINJ1
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PHF2
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
ANP32B
AGPAT2
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
FAM120A
PMPCA
ASTN2
BICD2
FKBP15
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
FAM22F
BSPRY
C9orf167
TEX10
LPPR1
EXD3
FAM206A
STX17
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
C9orf86
CDK5RAP2
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
BDAG1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
IPPK
DDX31
FAM129B
MRPL41
WNK2
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
MIR600HG
URM1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
GARNL3
HSDL2
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
LOC158257
FAM120AOS
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
C9orf96
OLFML2A
QSOX2
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC340508
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR32
C9orf106
LCN10
LOC441454
LOC441455
FAM22G
LOC441461
C9orf173
NRARP
C9orf129
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
NRON
FAM163B
FLJ40292
TUBBP5
RNF224
C9orf29
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
LOC100129722
LOC100130954
LOC100131193
LOC100132077
FAM157B
LOC100132781
RNU6ATAC
LINC00092
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3154
MIR2861
MIR4291
MIR3134
C9orf174
LOC100499484
MIR3621
MIR3689A
MIR3911
MIR3689B
LOC100505478
LOC100506100
LOC100506190
LOC100506599
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4672
MIR3689E
MIR4479

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 - 30 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
--- | --- | --- | --- | ---
10q23.31 | 8.7058e-54 | 8.7058e-54 | chr10:89617158-90034038 | 2
6q14.3 | 3.3067e-38 | 3.3067e-38 | chr6:86202470-96030383 | 39
13q14.13 | 1.0102e-41 | 9.1948e-36 | chr13:44451821-48516844 | 26
21q22.3 | 1.0078e-51 | 1.647e-31 | chr21:42827479-43100702 | 1
3p13 | 2.2432e-16 | 2.2432e-16 | chr3:71832385-72798945 | 2
8p21.3 | 1.0493e-16 | 8.3612e-14 | chr8:18870505-27169834 | 72
16q23.3 | 2.1733e-22 | 2.0649e-13 | chr16:83845270-88516170 | 49
17p13.1 | 4.6639e-13 | 4.3337e-13 | chr17:7505228-7591760 | 4
5q15 | 2.3966e-16 | 6.6733e-13 | chr5:96515472-99722097 | 4
17q21.31 | 8.3564e-13 | 7.9777e-13 | chr17:42085973-42651945 | 18
12p13.1 | 2.698e-12 | 2.698e-12 | chr12:12418624-12952430 | 10
2q22.1 | 3.2806e-09 | 3.2806e-09 | chr2:120437949-148782464 | 108
21q22.2 | 8.4911e-34 | 6.5606e-08 | chr21:39665722-40715131 | 6
5q11.2 | 1.2309e-14 | 1.6079e-06 | chr5:54597198-57789060 | 14
11q23.2 | 2.7048e-06 | 2.7153e-06 | chr11:113148800-115045236 | 19
1p31.3 | 6.4175e-06 | 3.2081e-05 | chr1:64643278-65957095 | 11
16q22.2 | 8.0165e-15 | 0.00014911 | chr16:72146667-74472459 | 7
1q42.2 | 0.00376 | 0.0037818 | chr1:215791006-240939420 | 172
4q27 | 0.0045156 | 0.0045459 | chr4:115598111-134070791 | 57
9p24.1 | 0.0068212 | 0.0066864 | chr9:7175612-12693402 | 2
3q29 | 0.024056 | 0.025198 | chr3:195144439-198022430 | 47
18q22.1 | 0.0066864 | 0.054939 | chr18:51876581-78077248 | 102
13q22.1 | 4.9189e-21 | 0.062879 | chr13:36702526-93883732 | 200
8p11.21 | 7.0307e-06 | 0.068418 | chr8:39586389-42701313 | 25
1p13.3 | 0.0074585 | 0.072199 | chr1:75009100-119913683 | 310
2p22.1 | 0.076099 | 0.078527 | chr2:32263161-54957415 | 118
7q36.1 | 0.16203 | 0.16667 | chr7:151817415-152457802 | 4
15q21.3 | 0.20396 | 0.2002 | chr15:26104243-59175227 | 292
1q23.1 | 0.22413 | 0.21642 | chr1:155300781-179053050 | 325
18q23 | 0.00091139 | 0.77298 | chr18:67995567-78077248 | 36

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.3.

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

Genes
CGA
CNR1
EPHA7
GABRR1
GABRR2
HTR1E
MAP3K7
RNGTT
CASP8AP2
SYNCRIP
SLC35A1
PNRC1
ANKRD6
ZNF292
MDN1
ORC3
SNORD50A
UBE2J1
AKIRIN2
AKIRIN2-AS1
RARS2
C6orf162
LYRM2
SNX14
RRAGD
BACH2
C6orf164
SPACA1
GJA10
PM20D2
SRSF12
C6orf165
C6orf163
GJB7
SNHG5
TSG1
SNORD50B
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
LCP1
CPB2
ESD
GTF2F2
HTR2A
TPT1
TSC22D1
ZC3H13
LRCH1
NUFIP1
KIAA1704
KIAA0226L
COG3
LINC00284
LACC1
LINC00330
FAM194B
SPERT
SLC25A30
SIAH3
KCTD4
SERP2
TSC22D1-AS1
SNORA31
TPT1-AS1
LOC100509894

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
TMPRSS2

Genes in Wide Peak

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

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

Genes
RYBP
LOC201617

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

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

Genes
hsa-mir-548h-4
hsa-mir-320a
ADRA1A
ATP6V1B2
BMP1
POLR3D
BNIP3L
DPYSL2
EGR3
EPB49
GFRA2
GNRH1
LOXL2
LPL
NEFM
NEFL
NKX3-1
PPP2R2A
PPP3CC
SFTPC
SLC18A1
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
SLC39A14
ADAMDEC1
SLC25A37
KCTD9
PIWIL2
INTS10
CSGALNACT1
HR
BIN3
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
CHMP7
NKX2-6
PEBP4
CDCA2
R3HCC1
LGI3
LOC254896
LOC286059
LOC286114
LOC389641
MIR320A
C8orf58
LOC100128993
LOC100507156

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
hsa-mir-1910
CA5A
COX4I1
FOXF1
FOXL1
FOXC2
IRF8
SLC7A5
MBTPS1
TAF1C
USP10
KIAA0513
ATP2C2
COX4NB
ZCCHC14
KIAA0182
COTL1
MLYCD
OSGIN1
GINS2
NECAB2
KLHDC4
BANP
ZDHHC7
JPH3
KIAA1609
WFDC1
MTHFSD
KLHL36
FBXO31
MAP1LC3B
HSDL1
CRISPLD2
ZNF469
KCNG4
DNAAF1
SLC38A8
FLJ30679
LOC146513
ADAD2
LINC00311
FAM92B
LOC400548
LOC400550
C16orf74
LOC727710
LOC732275
MIR1910
C16orf95

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

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

Genes
TP53
ATP1B2
SHBG
SAT2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
CHD1
RGMB
FLJ35946
LOC100289230

Genes in Wide Peak

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

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

Genes
FZD2
GRN
ITGA2B
SLC4A1
UBTF
HDAC5
RUNDC3A
GPATCH8
SLC25A39
ATXN7L3
C17orf53
TMUB2
TMEM101
G6PC3
ASB16
LSM12
FAM171A2
C17orf65

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
hsa-mir-613
CDKN1B
CREBL2
GPR19
MANSC1
DUSP16
APOLD1
LOH12CR1
LOH12CR2
MIR613

Genes in Wide Peak

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

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

Genes
ERCC3
hsa-mir-128-1
hsa-mir-663b
ACVR2A
BIN1
CCNT2
DARS
GLI2
GPR17
GPR39
GYPC
HNMT
INHBB
LCT
MCM6
MGAT5
MYO7B
ORC4
POLR2D
PROC
PTPN4
RALB
TSN
CXCR4
KYNU
HS6ST1
ZEB2
MAP3K2
NXPH2
RAB3GAP1
UBXN4
CLASP1
R3HDM1
PTPN18
C2orf27A
TFCP2L1
ARHGEF4
LRP1B
PLEKHB2
WDR33
SMPD4
IWS1
LIMS2
ARHGAP15
CFC1
UGGT1
EPB41L5
TMEM185B
SAP130
GTDC1
MZT2B
YSK4
THSD7B
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
MKI67IP
SFT2D3
LOC84931
CCDC74A
CCDC74B
IMP4
TUBA3E
TUBA3D
LYPD1
CNTNAP5
ACMSD
FAM168B
LOC150527
LOC150776
WTH3DI
FAM123C
LOC254128
LOC285103
SPOPL
CYP27C1
NCKAP5
GPR148
LOC389033
LOC389043
LOC401010
DKFZp686O1327
MIR128-1
C2orf27B
LOC440905
LOC440910
POTEKP
POTEE
ANKRD30BL
LOC646743
LOC647012
CFC1B
MZT2A
POTEF
PABPC1P2
LOC100129961
LOC100131320
CYP4F30P
RNU4ATAC
LOC100216479
ZEB2-AS1
MIR663B
MIR3679
LOC100507600
MIR4783
MIR4784

Genes in Wide Peak

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

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

Genes
ERG
ETS2
PSMG1
BRWD1
BRWD1-IT2
LINC00114

Genes in Wide Peak

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

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

Genes
IL6ST
MAP3K1
PPAP2A
PLK2
SKIV2L2
DDX4
GPBP1
ANKRD55
C5orf35
IL31RA
SLC38A9
MIER3
ACTBL2
RNF138P1

Genes in Wide Peak

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

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

Genes
hsa-mir-4301
DRD2
HTR3A
NNMT
ZBTB16
HTR3B
ZW10
RBM7
REXO2
C11orf71
FAM55D
TTC12
USP28
TMPRSS5
FAM55A
FAM55B
ANKK1
CLDN25
MIR4301

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.3.

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

Genes
JAK1
hsa-mir-101-1
AK4
DNAJC6
LEPROT
RAVER2
CACHD1
UBE2U
MIR101-1
MIR3671
MIR4794

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.2.

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

Genes
ZFHX3
PSMD7
PMFBP1
HTA
LOC283922
CLEC18B
LOC100506172

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.2.

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

Genes
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
ACTA1
ACTN2
PARP1
AGT
ARF1
CAPN2
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
ITPKB
KCNK1
LBR
LGALS8
MARK1
MTR
NID1
NVL
PSEN2
RAB4A
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TSNAX
USH2A
WNT9A
HIST3H3
GNPAT
CDC42BPA
DEGS1
TAF1A
GGPS1
TMEM63A
TOMM20
URB2
BPNT1
LEFTY1
SPHAR
CAPN9
DUSP10
COG2
RBM34
FBXO28
ABCB10
RAB3GAP2
RNU5F-1
TAF5L
DISC2
DISC1
CNIH4
PYCR2
RRP15
TRIM17
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
GPATCH2
HEATR1
SLC30A10
IARS2
ENAH
NUP133
ERO1LB
FMN2
ADCK3
GJC2
SIPA1L2
ZP4
RHOU
GREM2
ACBD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
PCNXL2
WDR26
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
KIAA1804
C1orf198
DISP1
WNT3A
HIST3H2A
SNAP47
C1orf96
LYPLAL1
DNAH14
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
BROX
SLC35F3
B3GALNT2
CNIH3
EXOC8
RNF187
C1orf55
C1orf65
IBA57
LIN9
ZNF678
PRSS38
LOC339535
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf140
FAM177B
ZNF847P
MIR194-1
MIR215
TRIM67
H3F3AP4
DUSP5P
LOC643723
SNRPD2P2
RPS7P5
SNORA14B
SNORA36B
LOC728463
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3620
LOC100506795
LOC100506810
MIR4753
MIR4666A
MIR4671
MIR4427
MIR4742

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q27.

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

Genes
IL2
hsa-mir-2054
hsa-mir-1973
ANXA5
CCNA2
FABP2
FGF2
MAD2L1
EXOSC9
TRPC3
PRSS12
PDE5A
NDST3
SEC24D
SPRY1
PGRMC2
PLK4
PRDM5
NUDT6
HSPA4L
INTU
MYOZ2
USP53
LARP1B
BBS7
ANKRD50
METTL14
IL21
NDST4
NDNF
FAT4
TNIP3
PHF17
C4orf29
SLC25A31
QRFPR
KIAA1109
SCLT1
C4orf33
TMEM155
ADAD1
TRAM1L1
SPATA5
BBS12
SYNPO2
MFSD8
LOC285419
FLJ14186
C4orf3
CEP170P1
LOC645513
SNORA24
CETN4P
SNHG8
PP12613
MIR2054
MIR1973

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.1.

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

Genes
PTPRD
C9orf123

Genes in Wide Peak

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

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

Genes
TFRC
hsa-mir-922
hsa-mir-570
APOD
BDH1
DLG1
MFI2
MUC4
PAK2
PCYT1A
PPP1R2
RPL35A
KIAA0226
TNK2
NCBP2
UBXN7
PIGX
PIGZ
IQCG
FYTTD1
LRCH3
CEP19
LMLN
TM4SF19
ZDHHC19
LOC152217
RNF168
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
TCTEX1D2
C3orf43
SDHAP1
WDR53
ANKRD18DP
LRRC33
LOC401109
MIR570
SDHAP2
FAM157A
MIR922
MFI2-AS1
LOC100507086
TM4SF19-TCTEX1D2
MIR4797

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
CYB5A
FECH
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
ST8SIA3
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
CCBE1
CBLN2
C18orf54
FBXO15
DOK6
RNF152
LINC00305
C18orf26
BOD1P
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505474
LOC100505549
LOC100505776
LOC100505817
MIR4529
MIR3591

Genes in Wide Peak

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

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

Genes
LCP1
RB1
LHFP
TTL
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
ATP7B
KLF5
BTF3P11
RCBTB2
CLN5
CPB2
DACH1
EDNRB
ELF1
ESD
GPC5
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
LMO7
SMAD9
NEK3
PCDH8
PCDH9
POU4F1
RFXAP
ATXN8OS
TPT1
TRPC4
UCHL3
TNFSF11
SCEL
SUCLA2
DLEU2
TSC22D1
CCNA1
ITM2B
MTRF1
UTP14C
TBC1D4
LPAR6
SLC25A15
TRIM13
MRPS31
SPRY2
DLEU1
PIBF1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
SLITRK5
FBXL3
INTS6
CKAP2
NUFIP1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
NDFIP2
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
PCDH20
RNF219
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
SLITRK6
EBPL
KBTBD6
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
LINC00284
CSNK1A1L
SLAIN1
PRR20A
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
COMMD6
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
LINC00550
LINC00347
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ALG11
MZT1
TSC22D1-AS1
MIR4500HG
SERPINE3
CTAGE11P
SNORA31
MIR621
MIR622
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR759
MIR320D1
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
OR7E37P
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4500
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
CHRNB3
ADAM2
IKBKB
IDO1
PLAT
POLB
SFRP1
SLC20A2
VDAC3
KAT6A
CHRNA6
AP3M2
DKK4
GOLGA7
THAP1
C8orf4
ZMAT4
GINS4
C8orf40
AGPAT6
NKX6-3
IDO2
MIR486

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.3.

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

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ACADM
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FUBP1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
AK5
SNORA66
SNORD45B
SNORD45A
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
ST6GALNAC5
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
LHX8
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
SNORD45C
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p22.1.

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

Genes
MSH6
MSH2
EML4
hsa-mir-559
hsa-mir-558
ACYP2
ZFP36L2
CALM2
CYP1B1
EPAS1
FSHR
FOXN2
LHCGR
LTBP1
EPCAM
VIT
PIGF
PPM1B
PRKCE
EIF2AK2
SRSF7
SIX3
SLC3A1
SLC8A1
SOS1
SPAST
SPTBN1
STRN
MAP4K3
COX7A2L
NRXN1
CRIPT
PREPL
FEZ2
SOCS5
LRPPRC
CEBPZ
CDC42EP3
SIX2
GPR75
GTF2A1L
STON1
PSME4
RHOQ
HAAO
PRKD3
RASGRP3
QPCT
FAM98A
ERLEC1
ASB3
CRIM1
DYNC2LI1
HEATR5B
SRBD1
C2orf56
TTC27
SLC30A6
KCNK12
RPL23AP32
TTC7A
BIRC6
MTA3
NLRC4
THADA
ATL2
ABCG5
ABCG8
CAMKMT
GEMIN6
FBXO11
THUMPD2
YIPF4
MCFD2
ATP6V1E2
DHX57
PKDCC
HNRPLL
PPP1R21
C2orf73
PLEKHH2
GALM
TMEM178
MYADML
FAM82A1
OXER1
KCNG3
CCDC75
LINC00486
C2orf61
CYP1B1-AS1
STON1-GTF2A1L
CDKL4
LOC375196
LOC388942
LOC388946
LOC388948
TSPYL6
SULT6B1
LOC400950
UNQ6975
CHAC2
MIR558
MIR559
LOC728730
LOC728819
MORN2
LOC100128590
LOC100129726
LOC100134259
ARHGEF33
LOC100271832
LOC100288911
GPR75-ASB3
MIR3682
LOC100505876
MIR4765
MIR548AD

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.1.

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

Genes
MLL3
XRCC2
FABP5P3
LOC100128822

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.3.

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

Genes
BUB1B
TCF12
FLJ27352
C15orf55
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
ACTC1
ADAM10
APBA2
AQP9
B2M
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
USP8
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
FAM63B
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145663
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
LOC283710
FAM98B
PLA2G4D
GOLGA8G
GLDN
FMN1
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
MIR211
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC646278
LOC653075
HSP90AB4P
MIR626
MIR627
MIR628
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
GOLGA8F
LOC100132724
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
TMCO5B
MYZAP

Genes in Wide Peak

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

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

Genes
FCGR2B
NTRK1
PBX1
PRCC
SDHC
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
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
COPA
CRABP2
CRP
DPT
ETV3
F5
FCER1A
FCER1G
FCGR2A
FCGR3A
FCGR3B
FMO1
FMO2
FMO3
FMO4
DARC
HDGF
HSPA6
HSPA7
IFI16
INSRR
KCNJ9
KCNJ10
LMNA
LMX1A
LY9
MEF2D
MGST3
MNDA
MPZ
MYOC
NDUFS2
NHLH1
NIT1
DDR2
PFDN2
PIGC
PRRX1
POU2F1
PPOX
PEX19
RGS4
RIT1
RXRG
XCL1
SELE
SELL
SELP
SLAMF1
UAP1
SPTA1
SSR2
XCL2
TNR
TOP1P1
CCT3
TNFSF4
UCK2
USF1
DAP3
TAGLN2
RGS5
BLZF1
VAMP4
PEA15
B4GALT3
CREG1
CD84
TNFSF18
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
ARHGEF2
DEDD
GPR52
AIM2
RASAL2
ADAMTS4
PRDX6
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
RABGAP1L
FAM20B
NR1I3
GPA33
C1orf61
SLC19A2
NES
PMF1
DUSP12
KIAA0907
KIFAP3
ATF6
SYT11
PRRC2C
SMG5
NCSTN
GPR161
CCDC19
BRP44
OLFML2B
DNM3
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
USP21
CACYBP
KLHL20
LAMTOR2
NME7
DCAF8
F11R
RRNAD1
C1orf9
HSD17B7
UFC1
METTL13
CD244
TMCO1
GON4L
GPATCH4
DUSP23
RALGPS2
MSTO1
DARS2
KIRREL
YY1AP1
ITLN1
C1orf112
ADCY10
DCAF6
ASH1L
SLAMF8
UBQLN4
RAB25
RHBG
SCYL3
VANGL2
IGSF9
POGK
FAM5B
C1orf114
SLAMF7
CADM3
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
RFWD2
MGC4473
FCRL2
MRPL24
PAQR6
C1orf129
OR6N2
OR6K2
PVRL4
ISG20L2
FCRL5
FCRL4
NUF2
C1orf49
TOMM40L
TMEM79
ZBTB37
FCRLA
ANKRD36BP1
MAEL
SEC16B
SLAMF9
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
PIGM
IGSF8
C1orf85
SLAMF6
FCRL1
FCRL3
FMO9P
TADA1
SH2D1B
KLHDC9
OR10J5
UHMK1
FCRLB
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
ITLN2
RC3H1
METTL11B
FAM78B
LRRC71
PYHIN1
TTC24
ARHGAP30
C1orf192
TIPRL
SLC9A11
C1orf204
C1orf111
LOC284688
RXFP4
ANKRD45
C1orf110
OR10R2
FCRL6
CYCSP52
PEAR1
SFT2D2
ILDR2
FMO6P
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
C1orf220
MIR199A2
MIR214
MIR9-1
ETV3L
LRRC52
LOC440700
OR10J3
SUMO1P3
MIR488
SNORD74
RPL31P11
LOC645676
POU5F1P4
LOC646268
PCP4L1
SCARNA3
SCARNA4
SNORA42
SNORD75
SNORD76
SNORD77
SNORD78
MIR555
MIR556
MIR557
LOC730102
LOC730159
MIR765
MIR921
MSTO2P
TSTD1
LOC100131825
MIR1295A
LOC100302401
MIR3119-1
MIR3120
MIR3119-2
MIR3658
LOC100505633
LOC100505795
LOC100505918
LOC100506023
LOC100506046
PMF1-BGLAP
MIR4424
MIR4654
DNM3OS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TSHZ1
TXNL4A
ADNP2
KCNG2
SALL3
TIMM21
ZNF407
CNDP2
RBFA
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 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 | 0.02 | 0.208 | 0.999 | 0.04 | 2.51 | 0.0242
1q | 1955 | 0.03 | 1.47 | 0.354 | 0.01 | -1.06 | 1
2p | 924 | 0.01 | -2.17 | 0.999 | 0.01 | -2.47 | 1
2q | 1556 | 0.01 | -1.71 | 0.999 | 0.01 | -1.35 | 1
3p | 1062 | 0.07 | 2.76 | 0.0167 | 0.02 | -1.88 | 1
3q | 1139 | 0.09 | 4.85 | 6.31e-06 | 0.01 | -2.41 | 1
4p | 489 | 0.01 | -2.86 | 0.999 | 0.04 | -0.957 | 1
4q | 1049 | 0.01 | -2.32 | 0.999 | 0.02 | -1.4 | 1
5p | 270 | 0.02 | -2.3 | 0.999 | 0.01 | -2.82 | 1
5q | 1427 | 0.01 | -1.85 | 0.999 | 0.03 | -0.139 | 1
6p | 1173 | 0.01 | -2.49 | 0.999 | 0.03 | -0.258 | 1
6q | 839 | 0.01 | -2.77 | 0.999 | 0.06 | 1.32 | 0.247
7p | 641 | 0.17 | 9.54 | 0 | 0.00 | -3.34 | 1
7q | 1277 | 0.15 | 11.2 | 0 | 0.00 | -2.85 | 1
8p | 580 | 0.11 | 4.09 | 0.000173 | 0.38 | 25.5 | 0
8q | 859 | 0.21 | 13.3 | 0 | 0.07 | 2.24 | 0.039
9p | 422 | 0.03 | -1.47 | 0.999 | 0.05 | 0.131 | 0.895
9q | 1113 | 0.07 | 3.22 | 0.00428 | 0.02 | -1.48 | 1
10p | 409 | 0.03 | -1.73 | 0.999 | 0.07 | 1.21 | 0.283
10q | 1268 | 0.03 | -0.211 | 0.999 | 0.08 | 4.36 | 3.69e-05
11p | 862 | 0.03 | -1.05 | 0.999 | 0.01 | -2.81 | 1
11q | 1515 | 0.03 | 0.365 | 0.999 | 0.00 | -2.46 | 1
12p | 575 | 0.01 | -2.94 | 0.999 | 0.09 | 3.69 | 0.000559
12q | 1447 | 0.02 | -1.09 | 0.999 | 0.04 | 0.981 | 0.384
13q | 654 | 0.01 | -2.76 | 0.999 | 0.14 | 7.62 | 1.23e-13
14q | 1341 | 0.02 | -1.26 | 0.999 | 0.04 | 0.414 | 0.715
15q | 1355 | 0.01 | -1.89 | 0.999 | 0.06 | 2.48 | 0.0242
16p | 872 | 0.05 | 0.983 | 0.723 | 0.06 | 1.57 | 0.166
16q | 702 | 0.02 | -1.63 | 0.999 | 0.19 | 12 | 0
17p | 683 | 0.01 | -2.74 | 0.999 | 0.14 | 7.42 | 4.55e-13
17q | 1592 | 0.01 | -1.27 | 0.999 | 0.03 | -0.18 | 1
18p | 143 | 0.04 | -1.27 | 0.999 | 0.13 | 5.07 | 1.3e-06
18q | 446 | 0.02 | -2.23 | 0.999 | 0.18 | 10.1 | 0
19p | 995 | 0.01 | -2.36 | 0.999 | 0.03 | -0.533 | 1
19q | 1709 | 0.01 | -1.07 | 0.999 | 0.03 | 0.827 | 0.453
20p | 355 | 0.02 | -2.15 | 0.999 | 0.04 | -1.09 | 1
20q | 753 | 0.03 | -1.15 | 0.999 | 0.02 | -1.72 | 1
21q | 509 | 0.02 | -1.99 | 0.999 | 0.03 | -1.18 | 1
22q | 921 | 0.00 | -2.99 | 0.999 | 0.07 | 2.38 | 0.0285
Xq | 1312 | 0.00 | -2.96 | 0.999 | 0.07 | 3.33 | 0.00192

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/PRAD-TP/5950177/GDAC_MergeDataFiles_5954924/PRAD-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 278 Input Tumor Samples.

Tumor Sample Names
TCGA-CH-5737-01A-11D-1574-01
TCGA-CH-5738-01A-11D-1574-01
TCGA-CH-5739-01A-11D-1574-01
TCGA-CH-5740-01A-11D-1574-01
TCGA-CH-5741-01A-11D-1574-01
TCGA-CH-5743-01A-21D-1574-01
TCGA-CH-5744-01A-11D-1574-01
TCGA-CH-5746-01A-11D-1574-01
TCGA-CH-5748-01A-11D-1574-01
TCGA-CH-5750-01A-11D-1574-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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