SNP6 Copy number analysis (GISTIC2)
Prostate Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1ZW1J9R
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1ZW1J9R
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 2.0.19 (Firehose task version: 125).

Summary

There were 197 tumor samples used in this analysis: 17 significant arm-level results, 21 significant focal amplifications, and 25 significant focal deletions were found.

Results
Focal results

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

Table 1. Get Full Table Amplifications Table - 21 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
Xq27.1 | 2.1209e-13 | 2.7018e-13 | chrX:138564705-138580758 | 0 [F9]
Xq21.1 | 1.3079e-06 | 0.00018581 | chrX:79251708-79255479 | 0 [TBX22]
3q26.2 | 0.0031901 | 0.0031901 | chr3:169415894-170071693 | 12
Xq25 | 0.00046716 | 0.0031901 | chrX:126306276-126315813 | 0 [CXorf64]
Xp22.11 | 0.0031901 | 0.0057275 | chrX:23975644-23983593 | 0 [CXorf58]
Xp22.11 | 0.0031901 | 0.0080505 | chrX:24515774-24522924 | 1
Xq21.1 | 0.018188 | 0.018188 | chrX:80829747-80833679 | 0 [SH3BGRL]
7p15.3 | 0.082611 | 0.082611 | chr7:13415791-38453654 | 167
8q24.21 | 0.082611 | 0.082611 | chr8:124497797-129665763 | 34
8p11.22 | 0.082611 | 0.082611 | chr8:39051902-39137830 | 1
14q21.1 | 0.082611 | 0.082611 | chr14:38008682-38049106 | 1
11q13.2 | 0.085069 | 0.085069 | chr11:65674264-70349012 | 105
Xp21.1 | 0.085069 | 0.085069 | chrX:35651236-35660210 | 0 [MAGEB16]
Xq25 | 0.085069 | 0.085069 | chrX:122399494-122410812 | 1
Xq21.31 | 0.082611 | 0.11582 | chrX:87704771-87710744 | 0 [CPXCR1]
1q21.3 | 0.13119 | 0.13119 | chr1:119666095-155699117 | 300
12q24.32 | 0.23359 | 0.23359 | chr12:59359201-133851895 | 516
Xq12 | 0.23359 | 0.23359 | chrX:64162405-67316938 | 12
7q34 | 0.2372 | 0.2372 | chr7:84755421-159138663 | 615
9q34.3 | 0.2372 | 0.2372 | chr9:95361064-141213431 | 565
20q13.33 | 0.2372 | 0.2372 | chr20:26196264-63025520 | 449

Genes in Wide Peak

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

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

Genes
PRKCI
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 Xp22.11.

Table S2. 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 7p15.3.

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

Genes
ETV1
HNRNPA2B1
HOXA9
HOXA11
HOXA13
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
ADCYAP1R1
AHR
AMPH
AOAH
AQP1
SEPT7
CHN2
CLK2P
CRHR2
DGKB
DFNA5
EVX1
GARS
GHRHR
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
IL6
ITGB8
MEOX2
NPY
PDE1C
RP9
SFRP4
SP4
TWIST1
DNAH11
TAX1BP1
SKAP2
CREB5
NFE2L3
HDAC9
RAPGEF5
SCRN1
KIAA0087
ELMO1
TRIL
NOD1
GPNMB
AGR2
IGF2BP3
PPP1R17
NUPL2
HIBADH
INMT
FKBP9
CBX3
AVL9
SNX13
DPY19L1
KIAA0895
LSM5
SOSTDC1
KBTBD2
OSBPL3
TSPAN13
BBS9
BZW2
SNX10
TRA2A
NT5C3
TXNDC3
MPP6
CYCS
ANLN
CPVL
TOMM7
EPDR1
FKBP14
CDCA7L
KLHL7
STK31
ANKMY2
TBX20
NEUROD6
NPVF
HERPUD2
GGCT
EEPD1
STARD3NL
FAM188B
FAM126A
PLEKHA8
CCDC126
C7orf30
C7orf31
AGR3
BMPER
PRPS1L1
TWISTNB
SP8
HOXA11-AS1
DKFZP586I1420
C7orf41
PRR15
FERD3L
RPL23P8
CCDC129
ZNRF2
TMEM196
STEAP1B
RPS2P32
C7orf71
ABCB5
C7orf46
MACC1
GPR141
NPSR1
AGMO
LOC401320
LOC401321
LOC401324
AAA1
MIR148A
LOC441204
ZNRF2P1
RP9P
DPY19L2P3
MIR196B
TARP
DPY19L2P1
WIPF3
LOC646762
SNORD93
MIR550A1
MIR550A2
ISPD
JAZF1-AS1
DPY19L1P1
LOC100130673
LOC100133311
ZNRF2P2
MIR1200
HOTTIP
MIR3146
MIR550B2
MIR550B1
LOC100506025
LRRC72
LOC100506178
HOTAIRM1
LOC100506497
LOC100506776
INMT-FAM188B
HOXA10-HOXA9
MIR550A3
KLHL7-AS1

Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
ANXA13
NDUFB9
POU5F1B
PVT1
SQLE
MTSS1
KIAA0196
TRIB1
RNF139
TRMT12
TATDN1
FBXO32
ZNF572
TMEM65
LOC157381
FAM84B
FAM91A1
NSMCE2
KLHL38
FER1L6-AS1
FER1L6
LOC727677
LOC100130231
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
PCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.22.

Table S5. 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 14q21.1.

Table S6. 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 11q13.2.

Table S7. 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
ACTN3
ADRBK1
ALDH3B1
ALDH3B2
BBS1
CHKA
CPT1A
CST6
CTTN
FGF3
FGF4
GSTP1
SLC29A2
IGHMBP2
LRP5
NDUFV1
NDUFS8
PC
PPP1CA
PTPRCAP
RAD9A
RBM4
RPS6KB2
SPTBN2
PPFIA1
CTSF
FADD
BANF1
AIP
SART1
PITPNM1
RIN1
MTL5
FGF19
CCS
RCE1
DPP3
CDK2AP2
TCIRG1
RBM14
DRAP1
YIF1A
SF3B2
B3GNT1
SHANK2
KDM2A
CLCF1
BRMS1
MYEOV
RHOD
GAL
SUV420H1
CABP2
C11orf24
SSH3
ANO1
CCDC87
PPP6R3
PACS1
CABP4
CD248
CORO1B
CARNS1
POLD4
KLC2
MRPL11
LRFN4
C11orf80
TMEM134
UNC93B1
RAB1B
C11orf68
RBM4B
EIF1AD
GAL3ST3
SYT12
ACY3
MRGPRD
MRGPRF
CATSPER1
MRPL21
TPCN2
ORAOV1
PELI3
TSGA10IP
CNIH2
ZDHHC24
C11orf86
NUDT8
TMEM151A
NPAS4
ANKRD13D
TBX10
TBC1D10C
GPR152
DOC2GP
FAM86C2P
LOC100130987
MIR548K
RBM14-RBM4
MIR4691

Genes in Wide Peak

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

Table S8. 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 1q21.3.

Table S9. 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
HMGCS2
HSD3B1
HSD3B2
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
WARS2
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
CELF3
VPS45
POGZ
RPRD2
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
PHGDH
LCE2B
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
HAO2
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
REG4
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
ZNF697
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
HSD3BP4
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
NBPF7
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
LOC644242
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 12q24.32.

Table S10. 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 Xq12.

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

Genes
MSN
hsa-mir-223
AR
OPHN1
HEPH
VSIG4
ZC4H2
EDA2R
LAS1L
FRMD8P1
ZC3H12B
MIR223

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q34.

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

Genes
BRAF
CDK6
EZH2
MET
SMO
AKAP9
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
ABP1
ACHE
AKR1B1
ARF5
ASNS
AZGP1
OPN1SW
BPGM
CALCR
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
KRIT1
CDK5
CFTR
CHRM2
AP1S1
CLCN1
COL1A2
CPA1
CPA2
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNB2
GNG11
GNGT1
GPR22
GPR37
GRM3
GRM8
MNX1
AGFG2
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PIP
PMS2P1
PODXL
POLR2J
PON1
PON2
PON3
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
PSMC2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
SRI
AKR1D1
SRPK2
SSBP1
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
ZNF3
ZKSCAN1
ZSCAN21
ZYX
MTERF
SHFM1
TFPI2
ST7
ARHGEF5
ZNF212
TRRAP
FZD1
ZNF282
CUL1
TRIM24
BUD31
SGCE
MGAM
WASL
PLOD3
CLDN12
DGKI
AP4M1
ATP6V1F
ACCN3
PMPCB
ATP5J2
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DMTF1
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
BET1
FAM3C
COG5
ZNHIT1
ARPC1A
SH2B2
STAG3
CPSF4
FASTK
DBF4
COPS6
DUS4L
ZNF277
ABCB8
TP53TG1
PDAP1
TFEC
LAMB4
LMTK2
PAXIP1
KLHDC10
PEG10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
STEAP1
COPG2
HBP1
DNAJC2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRB
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
LUC7L2
MRPS33
ASB4
NUB1
NAA38
ADAM22
GPR85
TAS2R5
ANKIB1
CHPF2
PUS7
ING3
LRRN3
CROT
ALKBH4
SAMD9
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
PPP1R9A
CCDC132
AGK
METTL2B
MLL5
BAIAP2L1
SLC25A40
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
GATAD1
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
RABL5
CYP3A43
CASD1
LRRC61
C7orf49
ZNF655
PVRIG
C7orf23
GCC1
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ZNF767
C7orf58
TTC26
ORAI2
JHDM1D
OR2AE1
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
RBM48
ZNF394
MYH16
SLC37A3
KRBA1
FAM71F1
MGC16142
SLC35B4
TMEM209
GTPBP10
TRIM4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
MUC17
RNF32
ASB15
RUNDC3B
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
BHLHA15
ZNF800
GIMAP1
LOC202781
C7orf33
SAMD9L
C7orf62
ZNF804B
FABP5P3
ZNF498
FAM200A
PPP1R35
GPC2
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
CNPY4
POLR2J2
HEPACAM2
UBN2
MBLAC1
FAM133B
TAS2R39
TAS2R40
TAS2R41
STEAP2
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
DLX6-AS1
ZNF789
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
MOGAT3
FAM71F2
STRA8
KLRG2
WDR86
GJC3
DPY19L2P2
LOC349160
GATS
GSTK1
NAT16
SLC26A5
LHFPL3
KCP
FLJ43663
RNF148
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
OR2A5
LRRD1
FLJ42280
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
UFSP1
MIR106B
MIR129-1
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
SPDYE3
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
OR2A2
DPY19L2P4
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR489
MIR490
ZNF862
LOC645249
LOC645591
AZGP1P1
LOC646329
C7orf73
ACTR3C
MIR591
MIR592
MIR593
MIR595
LOC723809
MIR653
LOC728066
LOC728377
LOC728743
SPDYE6
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100129845
LOC100130705
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
LOC100287482
MOXD2P
LOC100289187
LOC100289561
ZNF783
MIR548F3
MIR548I4
SPDYE2L
MIR548F4
SAP25
MIR548T
MIR4285
MTRNR2L6
MIR3609
MIR3907
MIR3666
LOC100505483
LOC100506136
LOC100506585
LOC100507421
ATP5J2-PTCD1
GIMAP1-GIMAP5
MIR4653
MIR4652
MIR4468
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

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

Table S13. 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

Genes in Wide Peak

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

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

Genes
GNAS
TOP1
MAFB
SS18L1
ASXL1
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-1289-1
hsa-mir-499
hsa-mir-644
hsa-mir-1825
hsa-mir-3193
hsa-mir-3194
ADA
AHCY
ASIP
ATP5E
BCL2L1
BMP7
BPI
CD40
CDH4
CEBPB
CHRNA4
COL9A3
CSE1L
CSTF1
CTSZ
CYP24A1
DNMT3B
E2F1
EDN3
EEF1A2
EPB41L1
EYA2
FOXS1
GGT7
GHRH
NPBWR2
GSS
HCK
HNF4A
ID1
EIF6
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
LBP
MC3R
MMP9
MYBL2
MYT1
NFATC2
NNAT
NTSR1
OPRL1
PCK1
PFDN4
PI3
PLAGL2
PLCG1
PLTP
CTSA
PPP1R3D
PSMA7
PTGIS
PTK6
PTPN1
RBL1
RPN2
RPS21
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SNTA1
SPAG4
SRC
SRMS
STAU1
STK4
AURKA
TAF4
TCEA2
TFAP2C
TGM2
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF217
GDF5
NCOA3
RAE1
BCAS1
STX16
TNFRSF6B
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
VAPB
B4GALT5
KIF3B
RBM39
TTI1
TM9SF4
SPATA2
OSBPL2
ACOT8
ATP9A
SGK2
RBM12
ARFRP1
RGS19
SYCP2
MYL9
WFDC2
PROCR
ARFGEF2
TCFL5
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
CEP250
HRH3
PXMP4
RBPJL
DLGAP4
RALY
MAPRE1
TPX2
ZHX3
NCOA6
SLC9A8
ADNP
POFUT1
ZMYND8
SPO11
PRPF6
SAMHD1
C20orf4
L3MBTL1
PPP1R16B
TRPC4AP
GTPBP5
GMEB2
SNORD12C
SNORA71B
SNORA71A
TP53TG5
MOCS3
SLCO4A1
REM1
STMN3
SLC35C2
SLMO2
IFT52
PHF20
SCAND1
BPIFA1
TH1L
C20orf43
C20orf111
PIGT
ERGIC3
CDK5RAP1
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
UQCC
PCMTD2
C20orf20
PPP4R1L
RBM38
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
EDEM2
DOK5
DBNDD2
ACSS2
RNF114
SULF2
C20orf24
CTNNBL1
SLC2A4RG
PMEPA1
CASS4
SPINLW1
RALGAPB
JPH2
SALL4
ZNFX1
RAB22A
NDRG3
SLC12A5
ZNF512B
PREX1
COL20A1
MYH7B
NCOA5
TP53INP2
RPRD1B
TGIF2
CDH26
KCNK15
DHX35
MANBAL
SLC17A9
ELMO2
ZNF335
LOC63930
PCIF1
FAM217B
NECAB3
CDH22
SLC13A3
LPIN3
GDAP1L1
LOC79015
C20orf195
PPDPF
TTPAL
BIRC7
NPEPL1
ACTR5
DSN1
FER1L4
DNAJC5
PABPC1L
BPIFB2
TUBB1
ZBP1
SLC2A10
HM13
PDRG1
FAM83D
CABLES2
DYNLRB1
ITCH
SLA2
CHD6
MAP1LC3A
PARD6B
ZGPAT
COX4I2
ZNF341
TOX2
MYLK2
PRIC285
KIAA1755
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
BPIFB1
TP53RK
DNTTIP1
FAM210B
PHACTR3
DEFB118
BHLHE23
NKAIN4
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
C20orf166
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
GATA5
MLLT10P1
SLC32A1
BPIFA2
ZBTB46
WFDC3
GCNT7
C20orf112
CBLN4
CTCFL
C20orf132
SAMD10
ABHD16B
C20orf160
KIAA0889
C20orf118
RIMS4
SUN5
ROMO1
NEURL2
ZSWIM3
WFDC10A
LINC00266-1
WFDC6
C20orf173
LINC00028
FAM65C
C20orf151
C20orf152
R3HDML
ADIG
GTSF1L
WFDC5
LOC149773
GNAS-AS1
LOC149950
COMMD7
BPIFB4
LSM14B
WFDC13
APCDD1L
TTLL9
ACTL10
C20orf201
FAM209A
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
FRG1B
C20orf203
BPIFA4P
LOC339568
ARHGAP40
XKR7
BPIFB3
TMEM189
TMEM189-UBE2V1
LOC388796
FAM209B
SPINT4
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
ZNFX1-AS1
MIR499A
LOC647979
SNORA39
SNORA60
SNORA71C
SNORA71D
SNORD12
MIR644A
MIR645
MIR647
SYS1-DBNDD2
HAR1A
HAR1B
PSIMCT-1
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
ZNF663
LOC100131496
DPH3P1
LINC00029
LOC100144597
FLJ16779
LOC100287792
MIR1914
MIR1257
MIR4325
MIR3194
MIR3193
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505783
LOC100505815
LOC100505826
LOC100506384
SPINLW1-WFDC6
TGIF2-C20ORF24
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR499B
MIR4756
MIR4758
MIR4532
MIR4533
MIR4755
MIR5095
LOC100652730

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 - 25 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 | 2.1684e-43 | 2.1684e-43 | chr10:89617158-90348818 | 3
13q14.13 | 9.1779e-30 | 9.1779e-30 | chr13:44358188-48879660 | 31
6q15 | 1.435e-21 | 1.435e-21 | chr6:84936364-96464413 | 42
21q22.3 | 3.1086e-34 | 1.356e-18 | chr21:42827479-43100702 | 1
8p21.3 | 2.1552e-14 | 2.4754e-12 | chr8:18870505-27496079 | 76
17q21.31 | 1.1871e-10 | 1.0768e-10 | chr17:42019495-42651945 | 20
5q15 | 4.2621e-11 | 3.6093e-09 | chr5:96515472-101571689 | 8
3p13 | 1.5764e-08 | 1.5764e-08 | chr3:70016017-72941288 | 9
16q23.3 | 5.748e-13 | 1.5764e-08 | chr16:83845270-87440428 | 42
12p13.2 | 3.1411e-08 | 3.1318e-08 | chr12:10978771-13523791 | 48
17p13.1 | 6.9629e-08 | 7.2709e-08 | chr17:6982445-7591760 | 50
5q11.2 | 4.8085e-11 | 3.8928e-07 | chr5:54597198-57879426 | 15
21q22.2 | 1.9713e-23 | 5.0975e-07 | chr21:39665722-41385442 | 14
1p31.3 | 6.6293e-07 | 6.6293e-07 | chr1:64709461-65526658 | 7
2q22.1 | 1.5012e-06 | 1.5012e-06 | chr2:120123049-152105710 | 120
11q23.2 | 2.9935e-06 | 2.9692e-06 | chr11:113636184-115045236 | 12
4q28.1 | 0.0060381 | 0.0061979 | chr4:117218129-134070791 | 56
18q23 | 0.0084868 | 0.00901 | chr18:55467646-78077248 | 86
3q29 | 0.011461 | 0.012227 | chr3:189614459-198022430 | 81
1q42.13 | 0.061136 | 0.061714 | chr1:208416154-245913707 | 251
8p11.21 | 0.00020507 | 0.15332 | chr8:20109881-56016467 | 205
16q22.2 | 7.169e-06 | 0.16086 | chr16:69411141-90354753 | 210
7q36.1 | 0.17126 | 0.16519 | chr7:142753718-159138663 | 148
9p23 | 0.17268 | 0.16519 | chr9:1-19116021 | 72
19q13.2 | 0.21443 | 0.21909 | chr19:42569414-43963642 | 35

Genes in Wide Peak

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

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

Genes
PTEN
RNLS
KLLN

Genes in Wide Peak

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

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

Genes
LCP1
CPB2
ESD
GTF2F2
HTR2A
TPT1
SUCLA2
TSC22D1
ITM2B
ZC3H13
LRCH1
NUFIP1
MED4
NUDT15
KIAA1704
KIAA0226L
COG3
LINC00284
LACC1
LINC00330
CCDC122
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 6q15.

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

Genes
CGA
CNR1
EPHA7
GABRR1
GABRR2
HTR1E
NT5E
MAP3K7
RNGTT
TBX18
CASP8AP2
SYNCRIP
SLC35A1
PNRC1
ANKRD6
ZNF292
MDN1
ORC3
SNORD50A
UBE2J1
AKIRIN2
AKIRIN2-AS1
RARS2
C6orf162
LYRM2
SNX14
RRAGD
BACH2
C6orf164
MANEA
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 21q22.3.

Table S18. 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 8p21.3.

Table S19. 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
CHRNA2
CLU
DPYSL2
EGR3
EPB49
EPHX2
PTK2B
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 17q21.31.

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

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

Genes in Wide Peak

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

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

Genes
hsa-mir-548p
CHD1
ST8SIA4
RGMB
FAM174A
FLJ35946
LOC100133050
LOC100289230

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
FOXP1
hsa-mir-1284
GPR27
RYBP
SHQ1
PROK2
LOC201617
EIF4E3
MIR1284

Genes in Wide Peak

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

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

Genes
hsa-mir-1910
COX4I1
FOXF1
FOXL1
FOXC2
IRF8
MBTPS1
TAF1C
USP10
KIAA0513
ATP2C2
COX4NB
KIAA0182
COTL1
MLYCD
OSGIN1
GINS2
NECAB2
ZDHHC7
KIAA1609
WFDC1
MTHFSD
KLHL36
FBXO31
MAP1LC3B
HSDL1
CRISPLD2
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 12p13.2.

Table S24. 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
CDKN1B
CREBL2
EMP1
GPR19
LRP6
PRB1
PRB3
PRB4
PRH1
PRH2
GPRC5A
PRR4
TAS2R13
TAS2R14
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
DUSP16
APOLD1
GSG1
HTR7P1
LOH12CR1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
LOC338817
TAS2R42
RPL13AP20
LOH12CR2
PRB2
MIR613
MIR614
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
LOC100506314
PRH1-PRR4

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
hsa-mir-324
ACADVL
ASGR1
ASGR2
ATP1B2
CD68
CHRNB1
CLDN7
DLG4
DVL2
EIF4A1
EIF5A
FGF11
GPS2
POLR2A
SHBG
SLC2A4
SOX15
TNK1
TNFSF13
TNFSF12
FXR2
MPDU1
ACAP1
GABARAP
CTDNEP1
C17orf81
SENP3
SNORA67
YBX2
PLSCR3
NLGN2
ZBTB4
PHF23
NEURL4
SAT2
KCTD11
C17orf74
C17orf61
TMEM102
TMEM95
SPEM1
TNFSF12-TNFSF13
MIR324
SLC35G6
SNORA48
SNORD10
C17orf61-PLSCR3
SENP3-EIF4A1

Genes in Wide Peak

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

Table S26. 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
GAPT
ACTBL2
RNF138P1

Genes in Wide Peak

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

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

Genes
ERG
ETS2
HMGN1
PCP4
SH3BGR
WRB
PSMG1
B3GALT5
BRWD1
C21orf88
LCA5L
IGSF5
BRWD1-IT2
LINC00114

Genes in Wide Peak

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

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

Genes
JAK1
hsa-mir-101-1
RAVER2
CACHD1
MIR101-1
MIR3671
MIR4794

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
RND3
CCNT2
DARS
DBI
GLI2
GPR17
GPR39
GYPC
HNMT
INHBB
KIF5C
LCT
MCM6
MGAT5
MYO7B
ORC4
POLR2D
PROC
PTPN4
RALB
SCTR
TSN
CXCR4
KYNU
HS6ST1
ZEB2
MAP3K2
NXPH2
RAB3GAP1
UBXN4
CLASP1
R3HDM1
EPC2
PTPN18
MMADHC
C2orf27A
TFCP2L1
ARHGEF4
LRP1B
PLEKHB2
WDR33
SMPD4
IWS1
LIMS2
MBD5
ARHGAP15
CFC1
UGGT1
EPB41L5
TMEM185B
SAP130
GTDC1
MZT2B
YSK4
THSD7B
TMEM177
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
MKI67IP
SFT2D3
LOC84931
CCDC74A
CCDC74B
IMP4
TUBA3E
TUBA3D
LYPD1
CNTNAP5
ACMSD
FAM168B
LYPD6
LYPD6B
TMEM37
LOC150527
LOC150776
WTH3DI
PCDP1
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 11q23.2.

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

Genes
HTR3A
NNMT
ZBTB16
HTR3B
RBM7
REXO2
C11orf71
FAM55D
USP28
FAM55A
FAM55B
CLDN25

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q28.1.

Table S31. 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
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 18q23.

Table S32. 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
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NFATC1
SERPINB2
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
SERPINB3
SERPINB4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
NEDD4L
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
CCBE1
CBLN2
FBXO15
DOK6
RNF152
LINC00305
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817
MIR3591

Genes in Wide Peak

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

Table S33. 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
hsa-mir-3137
APOD
BDH1
CPN2
DLG1
FGF12
GP5
HES1
IL1RAP
MFI2
MUC4
OPA1
PAK2
PCYT1A
PPP1R2
RPL35A
CLDN1
KIAA0226
TNK2
CLDN16
NCBP2
ACAP2
UBXN7
PIGX
LEPREL1
LSG1
HRASLS
ATP13A3
PIGZ
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
CEP19
LMLN
TMEM44
TM4SF19
ZDHHC19
LRRC15
FAM43A
TMEM207
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
TCTEX1D2
C3orf43
SDHAP1
UTS2D
OSTN
ATP13A5
WDR53
ANKRD18DP
LRRC33
FLJ34208
LOC401109
GMNC
LOC647323
MIR570
SDHAP2
FAM157A
MIR922
LOC100128023
LOC100131551
SNAR-I
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.13.

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

Genes
FH
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
HNRNPU
HSD11B1
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
INTS7
NSL1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
G0S2
RRP15
PPPDE1
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
SLC30A10
IARS2
HHAT
ENAH
NUP133
RCOR3
SERTAD4
ERO1LB
FMN2
SMYD2
ADCK3
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
GREM2
ACBD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
PCNXL2
WDR26
TRAF3IP3
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00467
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
FAM36A
SNAP47
C1orf96
LYPLAL1
DNAH14
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
B3GALNT2
CNIH3
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
C1orf65
PLD5
C1orf100
IBA57
SYT14
C1orf101
HNRNPU-AS1
LIN9
ZNF678
PRSS38
LOC339529
LOC339535
RD3
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf140
FAM177B
ZNF847P
MIR194-1
MIR205
MIR215
TRIM67
MAP1LC3C
H3F3AP4
DUSP5P
C1orf133
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
SNORA14B
SNORA36B
SNORA16B
LOC728463
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR4260
MIR3122
MIR3620
PROX1-AS1
LOC100506795
LOC100506810
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

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

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

Genes
FGFR1
TCEA1
WRN
WHSC1L1
HOOK3
hsa-mir-486
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
ADRA1A
ADRB3
ANK1
BMP1
POLR3D
BNIP3L
CEBPD
CHRNA2
CHRNB3
CLU
ADAM3A
DPYSL2
DUSP4
EGR3
EIF4EBP1
EPB49
EPHX2
EXTL3
PTK2B
FNTA
ADAM2
GFRA2
GNRH1
NPBWR1
GSR
GTF2E2
NRG1
IKBKB
IDO1
LOXL2
MCM4
NEFM
NEFL
NKX3-1
OPRK1
PLAT
PNOC
POLB
PPP2CB
PPP2R2A
PPP3CC
PRKDC
RP1
SFRP1
SFTPC
SLC20A2
SNAI2
STAR
STC1
TACC1
UBE2V2
VDAC3
FZD3
UBXN8
KAT6A
RGS20
ADAM18
ADAM9
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
CHRNA6
DOK2
ASH2L
BAG4
ENTPD4
ST18
PHYHIP
RB1CC1
SORBS3
NPM2
LYPLA1
DCTN6
PNMA2
ADAM28
AP3M2
RBPMS
ERLIN2
PROSC
XPO7
TRIM35
RHOBTB2
DDHD2
KIF13B
LEPROTL1
KIAA0146
SLC39A14
GPR124
DKK4
LSM1
ADAMDEC1
MRPL15
PURG
GOLGA7
SLC25A37
SCARA3
ATP6V1H
TMEM66
SNTG1
KCTD9
PIWIL2
ELP3
THAP1
CCDC25
BRF2
INTS9
HR
PBK
ZNF395
BIN3
TEX15
C8orf4
KIAA1967
PLEKHA2
PDLIM2
SOX17
EBF2
FAM160B2
DUSP26
HMBOX1
EFCAB1
ZMAT4
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
TTI2
RAB11FIP1
REEP4
STMN4
RNF170
TM2D2
SGK196
GINS4
PPAPDC1B
MAK16
FUT10
CHMP7
C8orf40
PCMTD1
GOT1L1
NKX2-6
PXDNL
AGPAT6
UNC5D
LETM2
HGSNAT
PEBP4
CDCA2
ESCO2
FBXO16
NKX6-3
KCNU1
IDO2
R3HCC1
HTRA4
ADAM32
LGI3
LOC254896
ADAM5P
LOC286059
LOC286114
SCARA5
LOC286135
RNF5P1
POTEA
LOC389641
C8orf80
C8orf86
FAM150A
MIR320A
C8orf22
LINC00293
C8orf58
C8orf75
MBOAT4
MIR486
LOC728024
LOC100128750
LOC100130964
LOC100287846
MIR4287
MIR3148
MIR4288
MIR3622A
MIR3622B
LOC100507156
LOC100507341
MIR4469
MIR548O2

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
AARS
AP1G1
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
NQO1
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
ST3GAL2
SPG7
TAT
ZNF19
ZNF23
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
COX4NB
TUBB3
CFDP1
NFAT5
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
ADAT1
CHST5
COG4
CPNE7
IL17C
NOB1
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
TXNL4B
BANP
PDPR
RFWD3
DDX19A
ZNF821
ZDHHC7
VAC14
FTSJD1
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CYB5B
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
IL34
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
MIR140
CTRB2
CLEC18B
SNORD68
SNORD71
SNORD111
LOC727710
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130894
SYCE1L
LOC100287036
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
LOC100506083
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

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

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

Genes
EZH2
MLL3
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
ABP1
CASP2
CDK5
CLCN1
DPP6
EN2
EPHA1
GBX1
MNX1
HTR5A
INSIG1
KCNH2
NOS3
PIP
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
CNTNAP2
GIMAP2
OR2F1
TPK1
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ESYT2
ZNF398
GALNT11
LMBR1
LINC00244
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
OR6W1P
C7orf29
AGAP3
C7orf13
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
ASB10
RNF32
LOC154761
LOC154822
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5P3
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TAS2R60
CTAGE6P
OR2A12
OR2A1
WDR86
GSTK1
OR2A25
OR2A5
OR2A7
OR2A20P
LOC401431
OR2A42
MIR153-2
CTAGE15P
OR2A9P
OR2A2
ARHGEF35
GIMAP6
ZNF862
LOC645249
ACTR3C
MIR595
LOC728377
LOC728743
MIR671
LOC100128264
CTAGE4
LOC100128822
LOC100131176
LOC100132707
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MIR3907
LOC100505483
LOC100506585
GIMAP1-GIMAP5

Genes in Wide Peak

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

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

Genes
JAK2
NFIB
CD274
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
DMRT1
FOXD4
MLANA
GLDC
INSL4
PTPRD
RFX3
RLN1
RLN2
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TYRP1
VLDLR
MPDZ
CER1
KIAA0020
RCL1
DMRT2
RRAGA
PSIP1
INSL6
KDM4C
KANK1
RANBP6
AK3
BNC2
HAUS6
CNTLN
C9orf68
CDC37L1
C9orf46
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
C9orf66
TTC39B
FAM154A
FREM1
KIAA2026
KCNV2
GLIS3
C9orf93
LURAP1L
ZDHHC21
LOC389705
FLJ35024
FLJ41200
PPAPDC2
MIR101-2
FAM138C
SCARNA8
C9orf146
WASH1
MIR3152
MIR4665

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.2.

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

Genes
CIC
hsa-mir-4323
CEACAM1
CEACAM8
MEGF8
ERF
GSK3A
LIPE
PAFAH1B3
POU2F2
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PRG1
CD177
ZNF574
TEX101
CNFN
ZNF526
DEDD2
PRR19
TMEM145
CXCL17
LOC284344
PSG8
PSG10P
LOC100289650
MIR4323
LOC100505622

Arm-level results

Table 3. Get Full Table Arm-level significance table - 17 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.03 | 1.16 | 0.549 | 0.03 | 1.16 | 0.309
1q | 1955 | 0.04 | 2.15 | 0.0906 | 0.01 | -0.9 | 0.998
2p | 924 | 0.01 | -2.32 | 0.996 | 0.01 | -2.32 | 0.998
2q | 1556 | 0.01 | -1.99 | 0.996 | 0.02 | -1.16 | 0.998
3p | 1062 | 0.06 | 1.45 | 0.369 | 0.02 | -1.71 | 0.998
3q | 1139 | 0.08 | 3.07 | 0.0083 | 0.01 | -1.96 | 0.998
4p | 489 | 0.02 | -2.38 | 0.996 | 0.03 | -1.47 | 0.998
4q | 1049 | 0.02 | -1.81 | 0.996 | 0.02 | -1.46 | 0.998
5p | 270 | 0.02 | -2.28 | 0.996 | 0.03 | -1.7 | 0.998
5q | 1427 | 0.01 | -1.69 | 0.996 | 0.05 | 1.08 | 0.327
6p | 1173 | 0.01 | -2.38 | 0.996 | 0.04 | -0.204 | 0.998
6q | 839 | 0.01 | -2.65 | 0.996 | 0.07 | 1.31 | 0.292
7p | 641 | 0.18 | 8.36 | 0 | 0.00 | -2.95 | 0.998
7q | 1277 | 0.17 | 9.91 | 0 | 0.00 | -2.48 | 0.998
8p | 580 | 0.11 | 3.02 | 0.0083 | 0.40 | 21.3 | 0
8q | 859 | 0.19 | 9.41 | 0 | 0.09 | 2.82 | 0.0119
9p | 422 | 0.04 | -0.851 | 0.996 | 0.04 | -0.851 | 0.998
9q | 1113 | 0.09 | 3.41 | 0.00322 | 0.02 | -1.22 | 0.998
10p | 409 | 0.03 | -1.41 | 0.996 | 0.07 | 0.975 | 0.366
10q | 1268 | 0.04 | 0.191 | 0.996 | 0.09 | 3.93 | 0.000246
11p | 862 | 0.03 | -1.37 | 0.996 | 0.01 | -2.7 | 0.998
11q | 1515 | 0.03 | 0.0401 | 0.996 | 0.01 | -1.6 | 0.998
12p | 575 | 0.01 | -2.5 | 0.996 | 0.09 | 2.45 | 0.0256
12q | 1447 | 0.02 | -0.83 | 0.996 | 0.05 | 1.16 | 0.309
13q | 654 | 0.01 | -2.3 | 0.996 | 0.15 | 6.2 | 2.29e-09
14q | 1341 | 0.02 | -1.4 | 0.996 | 0.04 | 0.516 | 0.606
15q | 1355 | 0.02 | -1.33 | 0.996 | 0.07 | 2.52 | 0.024
16p | 872 | 0.05 | 0.574 | 0.996 | 0.07 | 1.9 | 0.0951
16q | 702 | 0.03 | -1.42 | 0.996 | 0.20 | 9.71 | 0
17p | 683 | 0.01 | -2.59 | 0.996 | 0.17 | 7.56 | 2.05e-13
17q | 1592 | 0.01 | -1.92 | 0.996 | 0.04 | 0.615 | 0.567
18p | 143 | 0.05 | -0.872 | 0.996 | 0.14 | 4.49 | 2.42e-05
18q | 446 | 0.02 | -2.05 | 0.996 | 0.19 | 8.15 | 2.96e-15
19p | 995 | 0.01 | -2.57 | 0.996 | 0.03 | -0.844 | 0.998
19q | 1709 | 0.01 | -1.78 | 0.996 | 0.03 | 0.444 | 0.625
20p | 355 | 0.02 | -2.5 | 0.996 | 0.04 | -1.32 | 0.998
20q | 753 | 0.03 | -1.13 | 0.996 | 0.02 | -1.78 | 0.998
21q | 509 | 0.03 | -1.69 | 0.996 | 0.05 | -0.467 | 0.998
22q | 921 | 0.01 | -2.55 | 0.996 | 0.08 | 2.51 | 0.024
Xq | 1312 | 0.00 | -2.61 | 0.996 | 0.05 | 1.19 | 0.309

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/4394838/GDAC_MergeDataFiles_4313215/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 197 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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