Prostate Adenocarcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.15 (cga svn revision 34144).

Summary

There were 82 tumor samples used in this analysis: 13 significant arm-level results, 0 significant focal amplifications, and 20 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.

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 1.  Get Full Table Deletions Table - 20 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 2.3591e-20 2.3591e-20 chr10:89607138-90339889 3
21q22.3 1.5795e-16 1.5795e-16 chr21:41139146-41973771 7
6q15 1.3731e-08 1.3731e-08 chr6:83657485-110255516 105
3p14.1 1.4667e-07 1.4667e-07 chr3:70098707-73023978 7
16q24.1 9.4228e-06 9.5268e-06 chr16:29336041-88827254 494
13q14.11 2.1091e-05 1.8861e-05 chr13:36573237-74956615 134
17q21.31 1.9473e-05 1.8861e-05 chr17:39607677-39995252 12
8p21.3 0.0021732 0.0021732 chr8:20154161-28007166 69
5q13.1 0.0023612 0.0023612 chr5:50711055-78852734 149
12p13.2 0.0090844 0.0081444 chr12:10266570-18127159 78
11q23.2 0.010773 0.011321 chr11:100824108-122361490 188
17p13.1 0.012647 0.012647 chr17:5340587-59583175 880
1q42.2 0.014337 0.014337 chr1:211288240-239871828 163
2q22.2 0.015061 0.014337 chr2:133116880-151839573 39
3q29 0.020289 0.020858 chr3:176057839-199501827 169
1p31.3 0.057181 0.057181 chr1:60112726-67547583 37
6p22.1 0.083681 0.083866 chr6:25018182-28579429 101
18q23 0.090281 0.090281 chr18:48119230-76117153 93
5q21.1 0.10497 0.10779 chr5:82789298-145198970 343
3q13.13 0.17714 0.1798 chr3:95260749-159894716 388
Genes in Wide Peak

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

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

Genes
PTEN
RNLS
KILLIN
Genes in Wide Peak

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

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

Genes
TMPRSS2
MX1
MX2
BACE2
FAM3B
PLAC4
C21orf130
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q15.

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
CCNC
CGA
CNR1
EPHA7
FOXO3
GABRR1
GABRR2
GRIK2
HTR1E
ME1
NT5E
PGM3
POU3F2
PREP
SIM1
SMPD2
MAP3K7
NR2E1
SNX3
RNGTT
CD164
TBX18
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
MDN1
KIAA0776
ORC3L
SFRS18
FBXL4
SNORD50A
SESN1
OSTM1
NDUFAF4
CYB5R4
C6orf203
UBE2J1
COQ3
SOBP
AKIRIN2
QRSL1
NCRNA00120
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
GPR63
SPACA1
ARMC2
MCHR2
C6orf168
GJA10
RTN4IP1
USP45
UBE2CBP
MRAP2
RWDD2A
KLHL32
RIPPLY2
PM20D2
SFRS13B
C6orf165
PRSS35
C6orf163
C6orf185
AKD1
LACE1
C6orf167
SCML4
C6orf182
PPIL6
GJB7
SNHG5
LIN28B
LOC553137
TSG1
SNORD50B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
FOXP1
hsa-mir-1284
GPR27
RYBP
SHQ1
PROK2
EIF4E3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.1.

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

Genes
CBFA2T3
CBFB
CDH1
CDH11
CYLD
FANCA
FUS
MAF
HERPUD1
hsa-mir-1910
hsa-mir-1972
hsa-mir-140
hsa-mir-1538
hsa-mir-328
hsa-mir-138-2
hsa-mir-1826
AARS
ADCY7
AP1G1
AFG3L1
AGRP
ALDOA
AMFR
APRT
ZFHX3
BBS2
C16orf3
CA5A
CA7
CALB2
CBLN1
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CES1
CETP
CNGB1
COX4I1
COX6A2
CSNK2A2
CTF1
CTRB1
CTRL
CYBA
DHODH
NQO1
SEPT1
DYNC1LI2
DPEP1
E2F4
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
GNAO1
GOT2
HAS3
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
ITGAD
ITGAL
ITGAM
ITGAX
KARS
KIFC3
LCAT
MAZ
MC1R
CHST6
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1M
MT1L
MT1X
MT2A
MT3
MVD
NFATC3
CHMP1A
PHKB
PHKG2
PLCG2
POLR2C
PPP4C
MAPK3
PRSS8
PSKH1
PSMB10
PSMD7
RBL2
RPL13
RRAD
SALL1
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC5A2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SPG7
SPN
STX4
SULT1A3
TAT
TBX6
TERF2
TGFB1I1
TK2
ZNF19
ZNF23
GAN
SLC7A5
DOC2A
HIRIP3
CDK10
TRADD
MBTPS1
CES2
NAE1
NOL3
TAF1C
SLC7A6
USP10
ATP6V0D1
BCL7C
GPR56
TAOK2
BCAR1
C16orf7
N4BP1
NUP93
ZNF646
SETD1A
KIAA0513
FAM38A
DHX38
KIAA0174
RNF40
ATP2C2
MVP
CLEC3A
CHST4
MPHOSPH6
NUTF2
IRX5
DNAJA2
BCKDK
KATNB1
ZNF267
COX4NB
TUBB3
CD2BP2
CDIPT
CFDP1
CTCF
NFAT5
SRCAP
NUDT21
WWP2
PRDM7
CORO1A
DDX19B
GABARAPL2
MON1B
SEPHS2
TCF25
CNOT1
PHLPP2
ZNF423
ZCCHC14
KIAA0182
ATMIN
RPGRIP1L
ZNF629
COTL1
MLYCD
SF3B3
QPRT
CES3
ADAT1
CHST5
ARL2BP
ORC6L
EDC4
PLA2G15
TP53TG3
COG4
PLEKHG4
TBC1D10B
DKFZP434H168
LRRC29
SEZ6L2
CPNE7
VPS4A
IL17C
TOX3
NOB1
CCDC113
TMEM208
C16orf80
PYCARD
FHOD1
BRD7
ANKRD11
ZDHHC1
MYLPF
OSGIN1
PARD6A
PLLP
CKLF
AHSP
ZNF771
NIP7
FAM96B
GINS2
TPPP3
TRAPPC2L
CES4
WWOX
BCMO1
TERF2IP
PRMT7
NECAB2
FBXL19
KLHDC4
HYDIN
DEF8
DUS2L
CHTF8
LPCAT2
TXNL4B
BANP
HEATR3
PDPR
RFWD3
SLC38A7
OGFOD1
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
ZDHHC7
VAC14
DOK4
VPS35
FTSJD1
DDX28
TSNAXIP1
CENPN
C16orf61
COQ9
CIAPIN1
THAP11
JPH3
PDP2
ZNF319
RANBP10
VAT1L
KIAA1609
WFDC1
NOD2
PDF
DPEP2
DPEP3
PAPD5
FBRS
AKTIP
C16orf58
MTHFSD
GINS3
NDRG4
ACD
ZNF747
PRR14
VKORC1
DBNDD1
GIYD2
FTO
DCTPP1
FA2H
GDPD3
IRX6
IRX3
C16orf53
FAM65A
TMEM231
TMCO7
C16orf57
ZNF768
WDR59
ZNF668
ELMO3
KLHL36
FBXO31
ARMC5
SHCBP1
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
HSD3B7
CYB5B
CMIP
ITFG1
GFOD2
CDT1
MAP1LC3B
NETO2
SLC7A5P1
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
YPEL3
FAM57B
LONP2
C16orf48
SLC7A6OS
MYST1
NLRC5
CCDC135
CAPNS2
COG8
SPIRE2
MT4
ZNF469
GPT2
B3GNT9
CIRH1A
ZNRF1
ABCC11
NKD1
CNTNAP4
RSPRY1
C16orf93
MYLK3
MARVELD3
MTSS1L
ZNF764
CENPBD1
ZNF276
CCDC102A
KCNG4
ORAI3
SDR42E1
ABCC12
PRRT2
STX1B
CMTM1
PKD1L2
ZNF689
RNF166
EXOSC6
C16orf46
LRRC50
NRN1L
CMTM3
C16orf78
SPATA2L
C16orf55
ANKRD26P1
ZC3H18
CDYL2
ZNF720
TMEM219
SNX20
TMEM170A
SLC38A8
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN
C16orf92
IL34
TMED6
LOC146481
FLJ30679
ZNF785
ZNF688
PRSS36
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LDHD
FUK
MLKL
ZNF778
ACSF3
ZNF48
CPNE2
GPR114
KLKBL4
CES7
GPR97
KCTD13
ASPHD1
TMEM188
PYDC1
CCDC79
CES8
EXOC3L
LOC283856
C16orf81
LOC283867
C16orf54
INO80E
HTA
LOC283914
LOC283922
NUDT7
NCRNA00095
ZNF843
PDXDC2
CLEC18C
MT1DP
SNAI3
POL3S
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
TEPP
SLC6A10P
LOC388242
C16orf87
C16orf86
LOC390748
C16orf74
MIR138-2
MIR140
LOC440354
LOC440356
CSDAP1
HERC2P4
CTRB2
MIR328
SULT1A4
TRIM72
CLEC18B
GIYD1
BOLA2
LOC595101
SNORD68
UBE2MP1
LOC606724
LOC613037
LOC613038
MT1IP
LOC644649
KIAA0895L
BOLA2B
SNORA30
SNORA46
SNORA50
SNORD71
SNORD111
TP53TG3B
LOC732275
SNORD111B
LOC100129637
LOC100130015
SYCE1L
C16orf67
LOC100271831
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.11.

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

Genes
LCP1
RB1
LHFP
hsa-mir-1297
hsa-mir-15a
hsa-mir-621
hsa-mir-320d-1
ATP7B
KLF5
RCBTB2
CPB2
DACH1
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
NEK3
PCDH8
PCDH9
ATXN8OS
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
ITM2B
MTRF1
UTP14C
TBC1D4
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
PIBF1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
KLF12
FNDC3A
DIS3
KIAA0564
ZC3H13
LRCH1
INTS6
CKAP2
OR7E37P
NUFIP1
PCDH17
C13orf15
MED4
DNAJC15
VPS36
PHF11
UFM1
ENOX1
RCBTB1
NUDT15
KIAA1704
THSD1
CYSLTR2
C13orf1
COG6
KLHL1
PCDH20
NARG1L
RNASEH2B
DHRS12
C13orf34
C13orf18
C13orf23
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
LOC121838
CSNK1A1L
PRR20A
C13orf30
C13orf31
HNRNPA1L2
FAM10A4
DGKH
CCDC122
STOML3
FAM194B
SPERT
DLEU7
FAM124A
LOC220115
LOC220429
SLC25A30
OR7E156P
SUGT1L1
SIAH3
KCNRG
FLJ37307
FREM2
NEK5
THSD1P
KCTD4
NHLRC3
SERP2
MIR15A
MIR16-1
ALG11
C13orf37
LOC646982
SERPINE3
LOC647288
SNORA31
MIR621
PRR20B
PRR20C
PRR20D
PRR20E
LOC100190939
Genes in Wide Peak

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

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

Genes
FZD2
GRN
ITGA2B
SLC4A1
UBTF
RUNDC3A
GPATCH8
SLC25A39
ATXN7L3
TMUB2
FAM171A2
C17orf65
Genes in Wide Peak

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

Table S8.  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
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
EGR3
EPB49
EPHX2
PTK2B
GFRA2
GNRH1
LOXL2
NEFM
NEFL
NKX3-1
PPP2R2A
PPP3CC
SFTPC
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
PNMA2
ADAM28
XPO7
TRIM35
RHOBTB2
SLC39A14
ADAMDEC1
SLC25A37
SCARA3
KCTD9
PIWIL2
CCDC25
HR
PBK
BIN3
KIAA1967
PDLIM2
EBF2
FAM160B2
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
CHMP7
NKX2-6
PEBP4
CDCA2
ESCO2
R3HCC1
LGI3
SCARA5
C8orf80
MIR320A
C8orf58
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.1.

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

Genes
IL6ST
PIK3R1
hsa-mir-582
hsa-mir-449b
hsa-mir-581
TRIM23
ARSB
BHMT
BTF3
CCNB1
CDK7
ERCC8
CRHBP
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HTR1A
ISL1
ITGA1
ITGA2
KIF2A
TNPO1
CD180
MAP1B
MAP3K1
MOCS2
NAIP
NDUFS4
OCLN
PDE4D
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
HOMER1
SCAMP1
CARTPT
COL4A3BP
LHFPL2
SDCCAG10
CCNO
NSA2
FST
PLK2
IQGAP2
ESM1
ADAMTS6
SV2C
MRPS27
PPWD1
OTP
SKIV2L2
BHMT2
PART1
FAM169A
DIMT1L
DMGDH
IPO11
GCNT4
POLK
PELO
DHX29
DDX4
SGTB
ARL15
AGGF1
WDR41
DEPDC1B
BDP1
ERBB2IP
NLN
ZSWIM6
ANKRA2
MCCC2
CENPK
RGNEF
SLC30A5
CENPH
GPBP1
ANKRD55
PTCD2
ELOVL7
C5orf44
UTP15
ZBED3
GFM2
NDUFAF2
MRPS36
SNX18
FCHO2
RAB3C
C5orf35
IL31RA
JMY
TMEM171
TMEM174
C5orf37
SFRS12
SLC38A9
MARVELD2
MIER3
CDC20B
ZNF366
S100Z
CCDC125
GAPT
ANKRD31
FLJ37543
RNF180
SFRS12IP1
ACTBL2
MAST4
RNF138P1
ISCA1L
RGS7BP
GPX8
MIR449A
C5orf43
LOC647859
GUSBP3
GTF2H2B
LOC653391
SNORA47
MIR449B
MIR581
GTF2H2C
SERF1B
LOC728723
GTF2H2D
LRRC70
FAM159B
LOC100170939
LOC100272216
NCRUPAR
LOC100303749
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
hsa-mir-1244
ARHGDIB
ART4
CDKN1B
CREBL2
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
MGP
MGST1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
KLRC4
CSDA
GPRC5A
KLRA1
STRAP
PRR4
KLRK1
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
HEBP1
DERA
DDX47
WBP11
MANSC1
MAGOHB
STYK1
GPRC5D
ATF7IP
H2AFJ
LMO3
KIAA1467
BCL2L14
PLBD1
DUSP16
APOLD1
GSG1
RERG
HTR7P
LOH12CR1
HIST4H4
ERP27
C12orf60
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
C12orf36
TAS2R42
RPL13AP20
C12orf69
LOH12CR2
PRB2
MIR613
MIR614
Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-100
hsa-mir-125b-1
hsa-mir-34c
ACAT1
BIRC2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPB2
HTR3A
IL10RA
IL18
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
NCAM1
NNMT
NPAT
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
SLN
SORL1
TAGLN
TECTA
THY1
TRPC6
UPK2
ZBTB16
CUL5
ZNF259
USP2
HTR3B
ZW10
MMP20
UBE4A
C2CD2L
RBM7
MPZL2
YAP1
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
TIMM8B
SIDT2
TRAPPC4
FXYD6
C11orf71
SLC35F2
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
VPS11
TEX12
CRTAM
TMPRSS4
C11orf60
DSCAML1
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
MMP27
ABCG4
C11orf1
RNF26
DYNC2H1
NLRX1
ALG9
PDZD3
C11orf63
PDGFD
TMPRSS5
MFRP
BCO2
TMPRSS13
DCUN1D5
KIAA1826
BUD13
TMEM25
UBASH3B
C11orf70
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
TMEM123
APOA5
CASP12
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf65
MPZL3
TBCEL
TMEM136
OAF
ANGPTL5
ANKK1
RNF214
BCL9L
FOXR1
CCDC153
CCDC84
C11orf53
C11orf34
BSX
C11orf87
C11orf92
C11orf88
LOC399959
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LOC643923
CLDN25
RPL23AP64
Genes in Wide Peak

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

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

Genes
BRCA1
CD79B
CLTC
COL1A1
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
PER1
RARA
MAP2K4
TP53
TAF15
GAS7
SUZ12
BRIP1
MSI2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
hsa-mir-632
hsa-mir-365-2
hsa-mir-423
hsa-mir-144
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
hsa-mir-324
hsa-mir-497
ACACA
ACADVL
ACCN1
ACLY
ADORA2B
AP2B1
ALDH3A1
ALDH3A2
ALDOC
ALOX12
ALOX12B
ALOX12P2
ALOX15B
AOC2
ARL4D
ASGR1
ASGR2
ATP1B2
ATP5G1
ATP6V0A1
BLMH
FMNL1
CA4
CACNB1
CD68
CDC6
CDC27
CHAD
CHD3
CHRNB1
CCR7
CNP
COX10
COX11
CPD
CLDN7
CRHR1
CRYBA1
CSF3
CSH1
CSH2
CSHL1
CYB561
ACE
DHX8
DLG4
DLX3
DLX4
DNAH9
DRG2
DUSP3
DVL2
EFNB3
EIF4A1
EIF5A
ERN1
EVI2A
EVI2B
EZH1
FGF11
FOXO3B
FLII
FLOT2
GAST
FZD2
G6PC
KAT2A
GFAP
GH1
GH2
GIP
GNGT2
CCR10
GPS2
GRB7
GRN
GUCY2D
HCRT
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HSD17B1
ICAM2
IFI35
IGFBP4
ITGA2B
ITGA3
ITGB3
JUP
KCNJ12
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS9
LHX1
LIG3
LLGL1
LPO
NBR1
MAPT
ADAM11
MEIS3P1
MAP3K3
MEOX1
MFAP4
MPO
MPP2
MPP3
TRIM37
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYL4
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NOS2
NSF
OMG
PDK2
PEX12
PFAS
PHB
PMP22
PNMT
SEPT4
POLR2A
MED1
PPY
MAPK7
MAP2K3
PRPSAP2
PSMB3
PYY
PSMC5
PSMD3
PSMD11
RAB5C
RAD51C
RAD51L3
RCVRN
RPL19
RPL23A
RPL26
RPL27
RPS6KB1
SCN4A
SCO1
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SFRS1
SGCA
SHBG
SHMT1
SLC2A4
SLC4A1
SLC6A4
SMARCD2
SMARCE1
SOX15
SP2
SREBF1
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
VAMP2
TADA2A
TBX2
HNF1B
MLX
THRA
TNFAIP1
TOP2A
TOP3A
DNAJC7
TUBG1
UBB
UBTF
VTN
WNT3
WNT9B
ZNF18
PCGF2
TRIM25
VEZF1
RNF112
ZNF207
RND2
COIL
AKAP1
EPX
PIP4K2B
SPOP
FOXN1
PPM1D
CNTNAP1
DGKE
COPS3
TCAP
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
TNK1
ABCC3
MYH13
TNFSF13
TNFSF12
TMEM11
KSR1
CDK5R1
CACNA1G
HAP1
MAP3K14
SPAG9
SLC13A2
UNC119
MTMR4
KCNAB3
AURKB
TIAF1
NOG
BZRAP1
ZNHIT3
GLP2R
EFTUD2
RPL23
NTN1
STX8
PIGL
TBX4
FXR2
NPEPPS
MPDU1
GOSR1
CCL4L1
GOSR2
NR1D1
NCOR1
TRAF4
KIAA0100
ULK2
CCDC144A
ACAP1
TBKBP1
PLEKHM1
KIAA0753
MED24
LRRC37A
MRC2
RICH2
HS3ST3B1
HS3ST3A1
MED13
HDAC5
TOM1L1
GJC1
TOB1
PSME3
EIF1
NBR2
SLC35B1
DCAF7
CALCOCO2
RAMP2
PEMT
CLEC10A
HOXB13
VAT1
APPBP2
FBXW10
SC65
HEXIM1
SPAG5
TRIM16
IGF2BP1
CCT6B
RAI1
GRAP
C1QL1
RUNDC3A
STARD3
CBX1
TLK2
DDX52
DUSP14
MYST2
AKAP10
NXPH3
SNF8
SYNRG
DDX42
GABARAP
CASC3
IKZF3
ZNF652
PPM1E
NLRP1
ARHGEF15
EPN2
SARM1
GPATCH8
KDM6B
MPRIP
WSCD1
USP22
DULLARD
KCNH4
TNFRSF13B
MMD
PIK3R5
C17orf81
C17orf88
PPY2
PYY2
AIPL1
DHRS7B
KRT23
TMEM98
POLDIP2
TBC1D29
TANC2
WSB1
SENP3
ERAL1
AATF
OR4D1
SNORD4B
SNORD4A
SNORA67
SNORD49A
SNORD42B
SNORD42A
B9D1
TUBG2
TMEM97
NKIRAS2
CCDC56
GIT1
RANGRF
PSMC3IP
SNX11
TBX21
SOCS7
SOST
MED31
FAM18B
YBX2
UTP18
RNFT1
MYO15A
TUBD1
RAPGEFL1
TACO1
ABI3
COPZ2
MRPL27
PIPOX
ARL17P1
CRLF3
TRPV2
SLC25A39
MRPS23
PTRH2
RASD1
NLK
LUC7L3
HIGD1B
CRKRS
KRT20
NLE1
FAM64A
XAF1
FNDC8
C17orf59
MBTD1
BCAS3
CCDC49
ALKBH5
RNF43
TTC19
MKS1
C17orf73
EPN3
LRRC37A4
MED9
SLFN12
WRAP53
PNPO
KLHL11
C17orf71
SLC47A1
TMEM100
RHOT1
RSAD1
C17orf79
LRRC59
MSX2P1
C17orf63
PRR11
ADAP2
UTP6
GSDMB
TEX14
CA10
NT5M
ATXN7L3
C17orf48
CCDC47
PLSCR3
PLXDC1
LYZL6
ZNF286A
ZNF287
INTS2
NUFIP2
ZNF624
TAOK1
NLGN2
ARHGAP23
PHF12
ZBTB4
TRAPPC1
PCTP
SCPEP1
ALOXE3
ELAC2
FKBP10
HEATR6
XYLT2
C17orf75
TEKT3
SPATA20
UBE2Z
WNK4
C17orf53
C17orf39
TMUB2
DHX58
PHF23
MMP28
DHRS11
PRR15L
DHX40
C17orf42
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
FAM106A
C17orf68
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SNIP
AARSD1
LIMD2
KCNH6
FAM117A
NDEL1
TMEM49
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP2-1
PITPNM3
LRRC48
TTC25
TEKT1
KRTAP4-12
RAB34
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
MYCBPAP
CCDC55
PPP1R1B
TBC1D3F
RNF135
C17orf37
MRPL45
VPS25
TMEM107
LSMD1
TMEM101
PRAC
RAB11FIP4
NEURL4
GHDC
KRTAP4-4
KIF2B
HES7
USP32
PPP1R9B
MGC12916
TXNDC17
CORO6
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
SSH2
LOC90110
TP53I13
IFT20
LRRC46
SCRN2
LOC90586
ANKRD40
ZNF830
SLFN11
RASL10B
ATPAF2
TMEM88
STRADA
C17orf72
CYTSB
G6PC3
ASB16
PGAP3
MYOCD
PIGS
HSPB9
ORMDL3
CDRT15P
SAT2
PLCD3
SLC46A1
TMEM106A
LRRC37B
OSBPL7
NT5C3L
ABHD15
TLCD1
CNTROB
FTSJ3
RFFL
RPL29P2
HSF5
OR4D2
ZPBP2
CYB5D1
USP43
KRBA2
C17orf64
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
B4GALNT2
SPACA3
FLJ25006
SEZ6
ANKRD13B
C17orf49
C17orf57
MRPL10
GJD3
KRT222
KRT40
NCRNA00188
ZSWIM7
SMCR7
SLC5A10
DYNLL2
SMCR5
SMCR8
TOM1L2
DNAH2
TCAM1
EFCAB3
SLC47A2
CDRT15
WDR16
CCDC42
PIK3R6
ODF4
C17orf50
SLFN13
AMAC1
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
TMEM199
PROCA1
DHRS13
KCTD11
C17orf69
TRIM16L
LRRC37B2
WIPF2
KRT25
TMEM99
ANKFN1
MARCH10
MFSD6L
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
SLC16A11
FBXO39
IMP5
KRT28
LOC162632
KRT24
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
SH3D20
ARHGAP27
SAMD14
C17orf108
SLC16A13
C17orf74
RDM1
LOC220594
GAS2L2
STH
MTVR2
STXBP4
TBC1D28
C17orf61
TAC4
BCL6B
C17orf103
C17orf66
LOC284023
C17orf44
CDRT4
CCDC144B
KIAA1267
C17orf105
FAM171A2
C17orf104
TTLL6
C17orf47
FLJ40504
NEK8
PIGW
C17orf78
LOC284100
CISD3
GSDMA
SLC13A5
TMEM102
PTRF
FAM27L
FLJ36000
GDPD1
LGALS9B
KLHL10
TMEM95
METTL2A
CCDC144NL
C17orf65
C17orf67
LOC339240
C17orf51
MSL1
NACA2
KRT27
SLFN12L
SLFN14
STAC2
SKA2
CCL14-CCL15
CCDC144C
TBC1D26
KRT26
C17orf93
HILS1
CDRT1
SPEM1
EFCAB5
RNF126P1
C17orf100
SPDYE4
TMEM220
SHISA6
C17orf76
TMIGD1
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
YPEL2
C17orf82
ARL5C
KRT39
SLC25A35
MYO18A
LOC400578
GRAPL
C17orf102
MGC57346
CUEDC1
MIR10A
MIR142
MIR144
MIR152
MIR193A
MIR195
MIR196A1
MIR21
MIR301A
TNFSF12-TNFSF13
TBC1D3B
TBC1D3C
CCL3L3
RNASEK
SUZ12P
GPR179
TBC1D3P2
MIR324
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451
MIR497
SNORA21
ARL17
AMAC1L3
RNF222
PIRT
LOC644172
FAM83G
MGC102966
EVPLL
LOC645638
SEBOX
LOC645851
SNORA48
SNORD10
KRTAP4-11
DHX40P
LOC653653
TBC1D3G
LGALS9C
NME1-NME2
SCARNA20
SCARNA21
SNORA76
SNORA59B
SNORA59A
SNORD7
SNORD49B
SNORD65
SNORD104
MIR33B
MIR632
KRTAP4-8
LOC728392
ZNF286B
TBC1D3
TBC1D3H
MIR454
SNORD124
MIR744
MIR365-2
LOC100128288
LOC100128977
LOC100129396
LOC100130148
LOC100130581
KRTAP4-9
KRTAP4-7
LOC100133991
C17orf96
LOC100190938
LOC100272146
Genes in Wide Peak

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

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

Genes
FH
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
ACTA1
ACTN2
PARP1
AGT
ARF1
CAPN2
CENPF
CHML
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NID1
NVL
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TSNAX
USH2A
WNT9A
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
GGPS1
TMEM63A
TOMM20
URB2
BPNT1
LEFTY1
SPHAR
CAPN9
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
RPS6KC1
TAF5L
DISC2
DISC1
CNIH4
PYCR2
RRP15
TRIM17
KCTD3
ARID4B
EGLN1
KIAA1383
MOSC2
SUSD4
GPATCH2
HEATR1
SLC30A10
IARS2
ENAH
NUP133
ERO1LB
FMN2
SMYD2
CABC1
GJC2
SIPA1L2
ZP4
RHOU
GREM2
ACBD3
MOSC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
PCNXL2
WDR26
TRIM11
MIXL1
C1orf124
OBSCN
C1orf57
KIAA1804
C1orf198
DISP1
WNT3A
HIST3H2A
SNAP47
C1orf96
LYPLAL1
DNAH14
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
C1orf58
SLC35F3
B3GALNT2
CNIH3
EXOC8
RNF187
C1orf55
C1orf65
C1orf69
LIN9
ZNF678
PRSS38
LOC339535
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
LOC400804
FAM177B
MIR194-1
MIR215
TRIM67
LOC440926
DUSP5P
SNORA14B
SNORA36B
LOC100130093
LOC100130331
TSNAX-DISC1
Genes in Wide Peak

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

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

Genes
hsa-mir-1978
hsa-mir-128-1
ACVR2A
RND3
CCNT2
DARS
HNMT
KIF5C
LCT
MCM6
MGAT5
ORC4L
CXCR4
KYNU
ZEB2
NXPH2
RAB3GAP1
UBXN4
R3HDM1
EPC2
MMADHC
LRP1B
MBD5
ARHGAP15
GTDC1
YSK4
THSD7B
TMEM163
ZRANB3
LYPD1
ACMSD
LYPD6
LYPD6B
LOC151162
SPOPL
NCKAP5
RBM43
MIR128-1
PABPCP2
Genes in Wide Peak

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

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
ACTL6A
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
EHHADH
EIF4G1
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
POLR2H
PPP1R2
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SST
THPO
FXR1
TP63
CHRD
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
NCBP2
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
FETUB
LAMP3
KCNMB3
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MCCC1
HRASLS
MRPL47
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
ATP13A3
TBL1XR1
MAP6D1
PIGZ
B3GNT5
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
C3orf34
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
C3orf59
C3orf21
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
NAALADL2
TCTEX1D2
C3orf43
SDHALP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
RTP2
OSTN
ATP13A5
SOX2OT
WDR53
LOC348840
LRRC33
FLJ42393
SNORD2
SNORA4
C3orf65
LOC647309
SNORA81
SNORD66
MIR570
SDHALP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
SNAR-I
MIR1224
Genes in Wide Peak

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

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

Genes
JAK1
hsa-mir-101-1
AK3L1
CYP2J2
LEPR
NFIA
ROR1
PDE4B
PGM1
USP1
DNAJC6
INSL5
INADL
SLC35D1
ITGB3BP
FOXD3
ANGPTL3
ALG6
L1TD1
LEPROT
RAVER2
CACHD1
MIER1
DLEU2L
WDR78
TM2D1
SGIP1
EFCAB7
ATG4C
DOCK7
C1orf87
UBE2U
IL23R
KANK4
TCTEX1D1
C1orf141
MIR101-1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p22.1.

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

Genes
HIST1H4I
BTN1A1
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
SLC17A1
ZNF165
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
CMAH
HIST1H3F
HIST1H2AG
HIST1H2BJ
ZSCAN12
SLC17A4
SLC17A2
PRSS16
BTN3A3
BTN2A2
HMGN4
TRIM38
SCGN
SLC17A3
BTN3A2
BTN3A1
BTN2A1
OR2B6
ABT1
BTN2A3
LRRC16A
ZNF323
ZNF322A
ZKSCAN3
ZSCAN16
OR2B2
FKSG83
PGBD1
HIST1H2AH
HIST1H2BK
POM121L2
ZSCAN12L1
HIST1H2AA
ZSCAN23
NKAPL
LOC222699
HIST1H2BA
ZNF391
ZKSCAN4
GUSBL1
HCG11
ZNF389
C6orf41
LOC100270746
Genes in Wide Peak

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

Table S18.  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
DCC
FECH
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
C18orf55
RAX
ST8SIA3
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
C18orf22
PQLC1
CCDC68
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
DOK6
RNF152
C18orf20
C18orf26
ZADH2
C18orf62
LOC284276
HMSD
CPLX4
ATP9B
LOC390858
LOC400657
MIR122
HSBP1L1
SNORA37
LOC100130522
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.1.

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

Genes
APC
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-1974
hsa-mir-9-2
ALDH7A1
CAMK4
CAMLG
CAST
CCNH
CD14
CDC25C
CDO1
CETN3
CHD1
AP3S1
COX7C
HAPLN1
CSF2
CSNK1G3
VCAN
CTNNA1
DMXL1
DIAPH1
HBEGF
EFNA5
EGR1
ETF1
FBN2
FER
FGF1
GDF9
GFRA3
GLRX
NR3C1
HARS
HINT1
HSD17B4
HSPA4
HSPA9
IK
IL3
IL4
IL5
IL9
IL13
IRF1
KCNN2
LECT2
LMNB1
LNPEP
LOX
SMAD5
MAN2A1
MCC
MEF2C
NDUFA2
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PFDN1
PGGT1B
PITX1
PPIC
PPP2CA
PURA
RASA1
SKP1
SLC12A2
SLC22A4
SLC22A5
SNX2
SPOCK1
SRP19
TAF7
TCF7
NR2F1
TGFBI
UBE2B
UBE2D2
VDAC1
WNT8A
ST8SIA4
REEP5
NME5
PDLIM4
EIF4EBP3
PCDHGB4
CDC23
HDAC3
P4HA2
ATG12
C5orf13
RAB9P1
MYOT
NRG2
CXCL14
H2AFY
SMAD5OS
RNF14
SNCAIP
TTC37
PCDHGA8
PCDHA9
MATR3
KIAA0141
PJA2
DDX46
SLC23A1
GNPDA1
SRA1
EDIL3
RAD50
KIF20A
APBB3
POLR3G
SEC24A
BRD8
HNRNPA0
KIF3A
RHOBTB3
ELL2
ARHGAP26
FSTL4
SEPT8
HISPPD1
ACSL6
PHF15
HARS2
TNFAIP8
PCDHGA12
LRRTM2
PCDHB5
FBXL21
KLHL3
SNORD63
SNORA74A
PKD2L2
UQCRQ
AFF4
SLC27A6
SNX24
PCDHB1
TMED7
ISOC1
SAR1B
MGC29506
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
CXXC5
RAPGEF6
ERAP1
KDM3B
PHAX
FLJ11235
PCDHB18
PCDHB17
ZCCHC10
GIN1
WDR55
ANKHD1
TMCO6
TRIM36
RIOK2
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
FEM1C
C5orf15
CDC42SE2
TRPC7
ZNF608
KCTD16
SEMA6A
ARRDC3
PCDHB16
HMHB1
EPB41L4A
ERAP2
SIL1
ARAP3
FBXL17
YTHDC2
GRAMD3
TXNDC15
MCTP1
NDFIP1
YIPF5
SPRY4
NUDT12
SLC4A9
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
PSD2
ANKRD32
C5orf32
MEGF10
TSLP
FCHSD1
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
PRDM6
FTMT
FNIP1
SLC35A4
C5orf26
MARCH3
LYSMD3
LEAP2
SLCO6A1
PRRC1
ZNF474
POU5F2
STARD4
WDR36
ANKRD43
SHROOM1
C5orf24
C5orf20
CEP120
LOC153328
MBLAC2
TMEM161B
SRFBP1
ZMAT2
ARSK
FAM81B
CCDC112
PRELID2
DCP2
LIX1
ADAMTS19
SPATA24
DNAJC18
C5orf27
LVRN
C5orf36
GPR150
DTWD2
RELL2
NBPF22P
RGMB
RFESD
CHSY3
TMEM173
FAM170A
LOC340074
FAM174A
CATSPER3
SLCO4C1
TICAM2
DND1
C5orf48
LOC389332
LOC389333
FLJ44606
ANKHD1-EIF4EBP3
FLJ42709
C5orf56
C5orf53
TIFAB
CTXN3
ECSCR
TMEM232
FLJ33630
CCNI2
LOC645323
SNORA13
MIR548C
MIR583
SNHG4
MIR886
MIR874
LOC100129716
LOC100133050
TMED7-TICAM2
Genes in Wide Peak

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

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

Genes
FOXL2
CBLB
GATA2
MLF1
RPN1
GMPS
TFG
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-198
hsa-mir-568
hsa-mir-567
AADAC
ACPP
ADCY5
ADPRH
AGTR1
ALCAM
ATP1B3
ATP6V1A
ATR
CASR
CD80
CD86
CD47
COL8A1
CP
CPA3
CPB1
CPOX
CSTA
DRD3
EPHB1
GAP43
GOLGB1
GP9
GPR15
GSK3B
GTF2E1
GYG1
HCLS1
HGD
ITGB5
KPNA1
LSAMP
TM4SF1
MBNL1
MCM2
MME
CD200
MYLK
NCK1
NDUFB4
P2RY1
PCCB
PFN2
PIK3CB
PLOD2
PLS1
PLSCR1
PLXNA1
PPP2R3A
PTX3
RAP2B
RASA2
RBP1
RBP2
RHO
RPL24
RYK
SHOX2
SIAH2
SLC15A2
SLCO2A1
HLTF
SSR3
TF
TFDP2
TM4SF4
TRH
TRPC1
UPK1B
UMPS
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
SOX14
BFSP2
RUVBL1
B4GALT4
SNX4
NR1I2
MBD4
H1FX
KALRN
SLC33A1
COPB2
CHST2
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
TSC22D2
TOMM70A
P2RY14
COX17
CD96
STAG1
ST3GAL6
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
FSTL1
MRPL3
FILIP1L
RNF13
MGLL
MRAS
COPG
MYH15
PLCH1
TMCC1
PLXND1
DNAJC13
SR140
C3orf27
ANAPC13
ARMC8
C3orf17
ABI3BP
WWTR1
PVRL3
TIPARP
SGEF
ZBTB20
OR5K1
OR5H1
FAM162A
PCOLCE2
SEC22A
NPHP3
ATP2C1
ZBTB11
MORC1
SERP1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
PIK3R4
PODXL2
TRAT1
IMPG2
COMMD2
A4GNT
DBR1
CLDN18
C3orf1
RSRC1
PLA1A
AMOTL2
CCRL1
RAB6B
SELT
FBXO40
P2RY13
IL20RB
GPR87
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
RG9MTD1
SLC41A3
SLC35A5
TMEM45A
IFT57
MSL2
FAIM
SLC25A36
DPPA4
TMEM39A
ABHD10
CDV3
IFT122
TBC1D23
WDR52
EAF2
CLDND1
MUC13
SUCNR1
LXN
C3orf37
MRPS22
NIT2
KTELC1
BBX
CCNL1
PLSCR2
PLSCR4
PCNP
SENP7
ISY1
HEG1
KIAA1257
CDGAP
KIAA1407
KIAA1524
SRPRB
BPESC1
EEFSEC
NSUN3
CLSTN2
POPDC2
NFKBIZ
ATG3
CCDC14
P2RY12
TMEM108
OR5H6
OR5H2
ZXDC
ZBED2
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC48
NEK11
UBA5
C3orf36
NAT13
CEP63
CEP70
ABTB1
TMEM22
OR5AC2
PARP9
ESYT3
EIF2A
ARL6
ZIC4
ACAD11
CHCHD6
C3orf26
HPS3
SLC12A8
RETNLB
CCDC54
MINA
GPR128
DIRC2
GFM1
C3orf15
PHLDB2
LOC90246
C3orf25
BOC
FAM55C
SPSB4
ACPL2
OSBPL11
LRRC58
TM4SF18
MED12L
CLRN1OS
CPNE4
CCDC58
ZPLD1
CD200R1
CRYBG3
DCBLD2
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
GRK7
RPL32P3
H1FOO
PISRT1
DTX3L
LOC151658
DPPA2
CCDC80
BTLA
ROPN1B
C3orf22
C3orf55
C3orf79
CCDC52
NUDT16P
LOC152225
IGSF11
C3orf30
PARP15
DNAJB8
GPR156
CHST13
KBTBD12
DHX36
DZIP1L
ALG1L
GABRR3
PTPLB
TIGIT
LOC201651
C3orf58
KIAA2018
ZBTB38
ZDHHC23
LOC255025
COL29A1
GK5
PLCXD2
GCET2
LOC285194
SLC9A9
LOC285205
EPHA6
RABL3
IGSF10
C3orf33
SLC9A10
LOC285359
ILDR1
TRIM42
RAB43
KY
C3orf47
LOC344595
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
TXNDC6
LNP1
CCDC37
NCRNA00119
NMNAT3
PRR23B
PRR23C
PLSCR5
C3orf16
LEKR1
FLJ25363
C3orf72
LOC401093
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIR198
ARGFX
TMEM30C
ALG1L2
TXNRD3IT1
TMEM14E
COL6A4P2
PA2G4P4
C3orf66
SNORA7B
SNORA58
MIR567
MIR568
LOC729375
PRR23A
LOC100009676
LOC100125556
LOC100129550
LOC100287227
LOC100302640
Arm-level results

Table 2.  Get Full Table Arm-level significance table - 13 significant results found.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 1731 0.01 3.92 0.000848 0.01 3.92 0.000242
1q 1572 0.02 2.82 0.0231 0.00 -0.581 0.915
2p 753 0.00 -1.36 0.955 0.00 -1.36 0.915
2q 1235 0.00 -0.981 0.955 0.00 -0.981 0.915
3p 853 0.01 -0.492 0.955 0.01 -0.492 0.915
3q 917 0.05 2.02 0.14 0.00 -1.22 0.915
4p 366 0.00 -1.59 0.955 0.02 -0.331 0.915
4q 865 0.00 -1.28 0.955 0.00 -1.28 0.915
5p 207 0.00 -1.69 0.955 0.01 -1.1 0.915
5q 1246 0.01 0.0832 0.955 0.01 0.0832 0.85
6p 937 0.01 -0.391 0.955 0.01 -0.391 0.915
6q 692 0.00 -1.39 0.955 0.02 0.0511 0.85
7p 508 0.07 2.56 0.0413 0.01 -0.768 0.915
7q 1071 0.07 4.33 0.000292 0.01 -0.146 0.915
8p 495 0.00 -1.2 0.955 0.39 19.9 0
8q 697 0.08 3.2 0.00892 0.08 3.2 0.00335
9p 343 0.03 -0.301 0.955 0.04 0.324 0.804
9q 916 0.04 1.23 0.613 0.01 -0.392 0.915
10p 312 0.00 -1.6 0.955 0.05 0.871 0.553
10q 1050 0.01 -0.228 0.955 0.02 0.654 0.626
11p 731 0.01 -0.638 0.955 0.00 -1.37 0.915
11q 1279 0.00 -0.939 0.955 0.00 -0.939 0.915
12p 484 0.00 -1.45 0.955 0.11 4.47 2.5e-05
12q 1162 0.03 0.924 0.867 0.03 0.924 0.553
13q 554 0.00 -1.36 0.955 0.17 8.12 4.33e-15
14q 1144 0.00 -1.06 0.955 0.00 -1.06 0.915
15q 1132 0.00 -1.07 0.955 0.00 -1.07 0.915
16p 719 0.01 -0.61 0.955 0.04 0.847 0.553
16q 562 0.01 -0.647 0.955 0.14 6.14 4.13e-09
17p 575 0.00 -1.38 0.955 0.13 6.14 4.13e-09
17q 1321 0.01 0.241 0.955 0.01 0.241 0.804
18p 117 0.00 -1.68 0.955 0.09 2.39 0.0369
18q 340 0.00 -1.52 0.955 0.12 4.72 9.27e-06
19p 870 0.00 -1.27 0.955 0.02 0.311 0.804
19q 1452 0.00 -0.752 0.955 0.00 -0.752 0.915
20p 295 0.00 -1.62 0.955 0.04 0.222 0.804
20q 627 0.00 -1.42 0.955 0.04 0.675 0.626
21q 422 0.00 -1.54 0.955 0.05 1.03 0.553
22q 764 0.00 -1.33 0.955 0.04 0.904 0.553
Methods & Data
Input

Table 3.  Get Full Table First 10 out of 82 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

GISTIC

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

CNV Description

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

Download Results

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

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)
[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)
[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)
Meta
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