Colon/Rectal 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 2.0.16 (cga svn revision 38839).

Summary

There were 564 tumor samples used in this analysis: 22 significant arm-level results, 29 significant focal amplifications, and 47 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 - 29 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
--- | --- | --- | --- | ---
2q21.2 | 1.2258e-39 | 1.2537e-39 | chr2:132789458-132831108 | 0 [NCRNA00164]
17q12 | 9.2502e-27 | 9.0549e-26 | chr17:35058337-35129544 | 5
13q12.2 | 3.7336e-21 | 1.3142e-17 | chr13:27283758-27484219 | 5
8p12 | 3.7842e-16 | 1.5641e-14 | chr8:38289679-38379971 | 2
12p13.32 | 3.0573e-12 | 3.0573e-12 | chr12:3647022-4569646 | 9
8q24.21 | 1.9227e-10 | 7.7825e-10 | chr8:128198852-129039208 | 5
11p15.5 | 9.0134e-09 | 9.0134e-09 | chr11:2113727-2197847 | 5
6p21.1 | 4.372e-08 | 4.372e-08 | chr6:41642900-44325631 | 62
20q13.12 | 1.0956e-09 | 5.5689e-07 | chr20:41908074-42726669 | 11
8p11.21 | 1.4108e-08 | 1.0732e-06 | chr8:41567261-41657573 | 5
20q11.21 | 1.493e-07 | 4.3182e-05 | chr20:26020583-30046390 | 26
13q22.1 | 5.4126e-05 | 0.00015251 | chr13:72640919-72940621 | 0 [KLF5]
17p11.2 | 0.00020531 | 0.00043995 | chr17:22069634-22326436 | 0 [FLJ36000]
13q12.13 | 9.0886e-16 | 0.0012006 | chr13:26419847-26437800 | 0 [USP12]
10q22.3 | 0.0020238 | 0.0020238 | chr10:79631229-82887959 | 21
16p11.2 | 0.0020238 | 0.0028433 | chr16:30489440-30688411 | 10
7q34 | 0.0050528 | 0.0050528 | chr7:141944541-142213402 | 3
20p11.21 | 0.0024159 | 0.0089259 | chr20:25298224-25431163 | 3
20p12.1 | 0.012238 | 0.015943 | chr20:14192972-14455908 | 2
17q24.1 | 0.0014825 | 0.025973 | chr17:60613808-66161993 | 37
20q13.2 | 1.3847e-05 | 0.040784 | chr20:50977664-57403067 | 46
20p11.23 | 0.021431 | 0.065846 | chr20:20208315-20629134 | 3
19q13.11 | 0.079319 | 0.079319 | chr19:24161929-42832831 | 130
16q12.1 | 0.063352 | 0.08871 | chr16:49501489-51520789 | 2
1q21.1 | 0.11571 | 0.11571 | chr1:118353921-194714435 | 646
15q26.1 | 0.12142 | 0.12142 | chr15:75597790-100338915 | 177
5p13.2 | 0.12794 | 0.12794 | chr5:32910521-44978157 | 66
2q33.1 | 0.14956 | 0.18325 | chr2:199336153-199352859 | 0 [SATB2]
8q21.13 | 0.077095 | 0.21146 | chr8:52669246-87594542 | 138

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
PNMT
TCAP
STARD3
PGAP3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.2.

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

Genes
CDX2
FLT3
PDX1
ATP5EP2
PRHOXNB

Genes in Wide Peak

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

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

Genes
WHSC1L1
LETM2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
CCND2
FGF6
FGF23
DYRK4
RAD51AP1
PARP11
C12orf4
C12orf5
EFCAB4B

Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1204
POU5F1B
PVT1
LOC727677

Genes in Wide Peak

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

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

Genes
IGF2
INS
TH
IGF2AS
INS-IGF2

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
BYSL
SLC29A1
GUCA1A
GUCA1B
HSP90AB1
MDFI
MEA1
PEX6
PGC
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
MED20
POLR1C
MAD2L1BP
CUL7
C6orf108
CNPY3
FRS3
SLC22A7
CAPN11
CUL9
UBR2
KIAA0240
ZNF318
YIPF3
USP49
GNMT
PRICKLE4
MRPL2
GTPBP2
MRPS18A
MRPS10
TMEM63B
TRERF1
XPO5
MRPL14
DLK2
TTBK1
C6orf153
ABCC10
KLC4
TJAP1
FOXP4
KLHDC3
TAF8
PTCRA
C6orf223
RSPH9
C6orf154
RPL7L1
CRIP3
C6orf226
C6orf132
LOC100132354
TOMM6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.12.

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

Genes
ADA
HNF4A
SERINC3
PKIG
C20orf111
JPH2
GDAP1L1
TTPAL
TOX2
FITM2
R3HDML

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-663
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
NCRNA00028
C20orf191
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
MIR663
PSIMCT-1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.3.

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

Genes
ANXA11
MAT1A
SFTPD
MBL1P1
PPIF
ZMIZ1
C10orf57
TSPAN14
C10orf58
DYDC2
DYDC1
EIF5AL1
LOC219347
PLAC9
ZCCHC24
LOC283050
SH2D4B
LOC642361
LOC650623
SFTPA1
SFTPA2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

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

Genes
PHKG2
RNF40
SRCAP
FBRS
PRR14
C16orf93
ZNF689
ZNF785
ZNF688
SNORA30

Genes in Wide Peak

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

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

Genes
PRSS1
PRSS2
TRY6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.21.

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

Genes
GINS1
NINL
ABHD12

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.1.

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

Genes
PRKAR1A
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
APOH
CACNG1
BPTF
KCNJ2
KCNJ16
KPNA2
PRKCA
MAP2K6
PSMD12
AXIN2
RGS9
SLC16A6
HELZ
ABCA10
ABCA9
ABCA8
ARSG
ABCA6
ABCA5
NOL11
PITPNC1
CACNG5
CACNG4
AMZ2
FAM20A
WIPI1
CCDC46
C17orf58
LOC440461
LOC651250
MIR634
MIR635
SNORA38B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
GNAS
hsa-mir-298
ATP5E
BMP7
CSTF1
CTSZ
CYP24A1
EDN3
MC3R
PCK1
PFDN4
AURKA
TFAP2C
ZNF217
RAE1
BCAS1
STX16
VAPB
HMGB1L1
SPO11
SLMO2
TH1L
C20orf43
PPP4R1L
RBM38
DOK5
PMEPA1
CASS4
RAB22A
NPEPL1
TUBB1
ZBP1
C20orf108
TSHZ2
C20orf85
ZNF831
GCNT7
CBLN4
CTCFL
GNASAS
APCDD1L
C20orf106
C20orf107
SUMO1P1
MIR296
MIR298

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.23.

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

Genes
INSM1
C20orf26
RALGAPA2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
CEBPA
APLP1
ATP4A
CAPNS1
CCNE1
CD22
CEBPG
TBCB
COX6B1
COX7A1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
LRP3
MAG
NPHS1
PEPD
FXYD1
FXYD3
POLR2I
SCN1B
TYROBP
UQCRFS1
USF2
ZNF146
C19orf2
PDCD5
KIAA0355
ZNF536
MLL4
UBA2
TMEM147
POP4
HCST
UPK1A
SLC7A9
ZFP30
ZNF507
HAUS5
ZNF345
CLIP3
LSM14A
GAPDHS
ZBTB32
ZNF571
LSR
FXYD7
FXYD5
GPATCH1
PSENEN
ZNF302
LIN37
SLC7A10
TSHZ3
GRAMD1A
ZFP14
ZNF529
HAMP
PRODH2
CHST8
KCTD15
PLEKHF1
RBM42
LRFN3
TMEM149
LOC80054
C19orf12
KIRREL2
ANKRD27
PDCD2L
ZNF527
NFKBID
CCDC123
ZNF382
ZNF566
ALKBH6
RHPN2
ZNF30
C19orf40
TDRD12
ZNF461
ZNF585B
DMKN
DKFZp566F0947
SNX26
WDR88
WTIP
ZNF792
HSPB6
ZNF420
ZNF565
DPY19L3
ZNF599
FAM187B
C19orf55
LOC148145
LOC148189
ZNF569
ZNF570
ZNF567
ZNF383
LGI4
C19orf46
ZNF540
ZNF585A
THAP8
U2AF1L4
SCGBL
WDR62
ZFP82
LOC284412
HKR1
ZNF181
ZNF260
VSTM2B
SBSN
ZNF829
ZNF568
RGS9BP
KRTDAP
ZNF790
NUDT19
ZNF793
LOC643719
SDHAF1
LOC100128675
LOC100134317

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q12.1.

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

Genes
SALL1
TOX3

Genes in Wide Peak

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

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

Genes
ABL2
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
TPR
PDE4DIP
hsa-mir-1278
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-190b
hsa-mir-554
ADAR
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
BGLAP
CACNA1E
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
DHX9
DPT
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
F5
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
DARC
GBA
GBAP
GJA5
GJA8
GLUL
HDGF
MR1
HMGCS2
HSD3B1
HSD3B2
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYOC
NCF2
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDC
PDZK1
PFDN2
PIGC
PI4KB
PKLR
PLA2G4A
PRRX1
POU2F1
PPOX
PRKAB2
PSMB4
PSMD4
PTGS2
QSOX1
PEX19
RAB13
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
TBX15
VPS72
THBS3
TCHH
TNR
TOP1P1
CCT3
TUFT1
TNFSF4
UCK2
USF1
DAP3
NPHS2
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
SELENBP1
TNFSF18
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
XPR1
GPR52
AIM2
RASAL2
ADAMTS4
SEC22B
CHD1L
PRDX6
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
FAM20B
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
WARS2
PIAS3
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
OCLM
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
TNRC4
PMF1
DUSP12
VPS45
KIAA0907
KIFAP3
ATF6
NMNAT2
POGZ
GLT25D2
RGL1
SYT11
BAT2D1
RPRD2
SMG5
NCSTN
GPR161
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
BRP44
OLFML2B
C1orf43
DNM3
TOR1AIP1
C1orf77
PHGDH
LCE2B
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
USP21
CACYBP
SLC39A1
RNF115
KLHL20
ROBLD3
TMOD4
NME7
LASS2
CRNN
DCAF8
F11R
GLRX2
BOLA1
ZBTB7B
C1orf66
APH1A
PLEKHO1
HAO2
ACP6
IER5
UCHL5
C1orf9
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
C1orf26
GON4L
GPATCH4
DUSP23
C1orf27
C1orf56
RALGPS2
MSTO1
DARS2
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
C1orf112
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
RAG1AP1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
KIAA1614
FAM5B
C1orf114
SLAMF7
CADM3
PRUNE
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
TOR3A
RFWD2
RGS18
MRPL9
INTS3
SCNM1
MGC4473
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
C1orf129
TARS2
EDEM3
FLAD1
NPL
OR6N2
OR6K2
C1orf21
PVRL4
SNX27
ANP32E
C1orf14
C1orf25
ISG20L2
FCRL5
FCRL4
NUF2
HMCN1
REG4
C1orf49
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
FCRLA
ANKRD36BL1
MAEL
RGS8
SEC16B
AQP10
LHX4
SLAMF9
PYGO2
ZNF697
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
C1orf156
GORAB
C1orf105
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
C1orf125
HIST2H3C
OR10J5
DCST2
ZNF648
TEDDM1
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
FAM163A
LELP1
RC3H1
DCST1
METTL11B
FAM78B
BNIPL
C1orf92
PYHIN1
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
LOC200030
NUDT17
FLJ23867
SPAG17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
TIPRL
C1orf230
THEM5
SLC9A11
NBPF15
ANKRD34A
C1orf104
C1orf204
C1orf111
LOC284688
HIST2H2AB
HIST2H3A
HIST2H2BA
S100A7A
LINGO4
RXFP4
ANKRD45
FAM5C
C1orf110
OR10R2
FCRL6
KCNT2
NBPF7
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
CYCSP52
PEAR1
SFT2D2
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
C1orf220
NBPF20
APOBEC4
MIR199A2
MIR214
MIR9-1
RGS21
HIST2H2BF
ETV3L
LRRC52
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
MIR488
SNORD74
RPL31P11
LOC642502
PPIAL4G
PPIAL4D
LOC645166
LOC645676
S100A7L2
LOC647121
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA3
SCARNA4
SNORA42
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
LOC728855
LOC728875
NBPF11
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
C1orf152
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
TSTD1
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100302401

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
IDH2
NTRK3
CRTC3
hsa-mir-1302-2
hsa-mir-1469
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
ACAN
ALDH1A3
ANPEP
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CRABP1
CTSH
FAH
FES
IDH3A
IGF1R
IL16
IREB2
ISG20
MAN2A2
MEF2A
MFGE8
NMB
FURIN
PCSK6
PDE8A
PLIN1
POLG
PSMA4
RASGRF1
RLBP1
RPS17
SH3GL3
SNRPA1
NR2F2
AP3B2
ST8SIA2
PEX11A
IQGAP1
PRC1
SLC28A1
HOMER2
ZNF592
SV2B
ARNT2
AP3S2
SEMA4B
CIB2
CIB1
MTHFS
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
VPS33B
MRPL46
OR4F4
SLCO3A1
HDGFRP3
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2
ZSCAN2
DET1
LINS1
FANCI
DNAJA4
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
ADAMTSL3
KIAA1199
ALPK3
FAM108C1
MESDC1
KLHL25
CPEB1
AEN
TTC23
MRPS11
EFTUD1
LRRK1
LOC80154
TM2D3
WDR61
STARD5
FAM103A1
MEX3B
LINGO1
WDR73
C15orf42
RCCD1
LOC91450
ARRDC4
LOC91948
C15orf40
TARSL2
LRRC28
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
LYSMD4
LOC145814
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
NCRNA00052
C15orf26
ADAMTS17
C15orf51
LASS3
LOC254559
C15orf37
FAM154B
LOC283761
FAM169B
TMC3
ZNF774
C15orf38
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
LOC388152
UBE2QP1
FLJ42289
ANKRD34C
C15orf58
OR4F6
OR4F15
ST20
FAM174B
MIR184
MIR7-2
MIR9-3
GOLGA6L9
TTLL13
LOC645752
SH2D7
GOLGA6L10
SCARNA15
MIR549
FAM138E
LOC100133144
UBE2QP2
LOC100144604
LOC100288778

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.2.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
C6
C7
C9
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
SLC45A2
RXFP3
WDR70
BRIX1
CCL28
C5orf28
AGXT2
C5orf42
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
HEATR7B2
EGFLAM
C5orf33
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
MGC42105
RANBP3L
RICTOR
C5orf51
PLCXD3
C5orf34
C5orf39
SNORD72
MIR580
CCDC152

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q21.13.

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

Genes
PLAG1
TCEA1
NCOA2
CHCHD7
hsa-mir-2052
hsa-mir-124-2
ASPH
CA1
CA2
CA3
CA8
CRH
CYP7A1
E2F5
EYA1
FABP4
FABP5
NPBWR1
HNF4G
IL7
IMPA1
LYN
MOS
MYBL1
OPRK1
PDE7A
PENK
PMP2
PKIA
PXMP3
RAB2A
RP1
RPL7
RPS20
SDCBP
TCEB1
TERF1
TPD52
TTPA
NSMAF
RGS20
GGH
TRPA1
MSC
KCNB2
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
WWP1
STMN2
RRS1
SULF1
HEY1
TRAM1
LY96
SGK3
C8orf71
PTTG3P
SNORD54
STAU2
BHLHE22
MRPS28
MRPL15
PI15
FAM164A
LACTB2
FAM82B
ATP6V1H
GDAP1
IMPAD1
TMEM70
ARMC1
UBE2W
CHD7
PAG1
C8orf44
JPH1
CPA6
PRDM14
SNX16
SOX17
ZBTB10
ZFAND1
ZFHX4
CSPP1
VCPIP1
PREX2
SLCO5A1
CRISPLD1
TRIM55
LRRCC1
DNAJC5B
PSKH2
FAM110B
CHMP4C
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
RALYL
RDH10
SLC7A13
C8orf45
CLVS1
C8orf84
SDR16C5
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NKAIN3
LRRC67
SLC10A5
CA13
FAM150A
XKR9
LOC401463
C8orf59
MIR124-2
REXO1L2P
SDR16C6
ZNF704
SNHG6
SNORD87
LOC643763
FABP9
FABP12
SBF1P1
LOC100192378

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 - 47 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
--- | --- | --- | --- | ---
16p13.3 | 2.9027e-185 | 2.9027e-185 | chr16:5085718-7704198 | 1
3p14.2 | 7.2461e-179 | 7.2461e-179 | chr3:59009803-61522370 | 1
20p12.1 | 4.0674e-123 | 4.0674e-123 | chr20:14250876-15984135 | 2
6q26 | 3.101e-81 | 3.101e-81 | chr6:161613089-163073197 | 1
4q22.1 | 1.4023e-52 | 2.1432e-49 | chr4:91367303-93459528 | 2
16q23.1 | 1.4137e-36 | 1.4137e-36 | chr16:76686559-78185271 | 1
5q11.2 | 3.9239e-34 | 5.2931e-32 | chr5:58296055-59823742 | 3
1p33 | 2.1521e-28 | 2.1718e-26 | chr1:48965982-50287554 | 1
3q26.31 | 1.7903e-25 | 1.7903e-25 | chr3:175482500-178221491 | 1
1p36.11 | 1.7915e-23 | 4.4439e-21 | chr1:26195436-27736842 | 39
4q35.1 | 2.0932e-19 | 9.0124e-16 | chr4:183957313-186744180 | 27
6p25.3 | 1.604e-13 | 1.604e-13 | chr6:1553836-2569051 | 2
8p23.2 | 1.2113e-13 | 3.4249e-13 | chr8:2080589-6255647 | 1
10q11.23 | 4.6453e-14 | 6.0706e-13 | chr10:52727599-53131580 | 3
5q22.2 | 4.4272e-18 | 3.9564e-12 | chr5:110848461-112385820 | 10
18q21.2 | 3.9274e-14 | 7.138e-12 | chr18:46726081-46959369 | 2
10q23.2 | 6.0519e-14 | 1.7303e-10 | chr10:89302988-90024018 | 5
7q31.1 | 2.2707e-09 | 2.326e-09 | chr7:110512908-111163100 | 1
18q12.2 | 3.9564e-12 | 3.4692e-08 | chr18:33055423-35467010 | 2
15q22.33 | 6.6581e-08 | 6.5092e-08 | chr15:64854850-65281876 | 1
15q21.1 | 3.9412e-07 | 3.7409e-07 | chr15:42638537-43083404 | 5
21q11.2 | 1.1569e-06 | 5.0834e-06 | chr21:1-21293802 | 29
17p12 | 2.0266e-06 | 4.7815e-05 | chr17:15405082-15555845 | 2
14q13.1 | 0.00025866 | 0.00025923 | chr14:32371600-33463751 | 1
19p13.3 | 0.00033967 | 0.00032877 | chr19:1-5161544 | 172
17p12 | 0.00010628 | 0.0005334 | chr17:10681334-12512565 | 6
11q22.3 | 0.0045499 | 0.0045596 | chr11:104448941-114550446 | 74
10q25.2 | 1.1893e-05 | 0.0087657 | chr10:103442976-123739741 | 134
18q22.1 | 0.0011426 | 0.0087657 | chr18:63332962-64534443 | 1
8p21.3 | 7.7228e-05 | 0.0098438 | chr8:13468291-28980776 | 105
1p21.3 | 0.00073133 | 0.010606 | chr1:64415866-120966132 | 340
22q13.2 | 0.016704 | 0.01688 | chr22:41851347-49691432 | 90
2q37.3 | 0.018488 | 0.018765 | chr2:225156666-242951149 | 151
4p16.2 | 0.020677 | 0.020539 | chr4:1-9439317 | 110
13q14.12 | 0.021204 | 0.021204 | chr13:33437992-56893713 | 130
12q21.2 | 0.034275 | 0.033665 | chr12:70467048-97656242 | 105
8p12 | 0.0026869 | 0.039809 | chr8:30823925-37835459 | 16
2p21 | 0.028004 | 0.044785 | chr2:42412761-43968670 | 13
5q35.2 | 0.0011665 | 0.047517 | chr5:174888191-175157510 | 1
2p12 | 0.044455 | 0.074215 | chr2:75788510-79106457 | 2
5q21.1 | 4.5886e-08 | 0.091286 | chr5:83713017-112385820 | 78
14q32.32 | 0.097615 | 0.10105 | chr14:67345128-106368585 | 382
17q22 | 0.18328 | 0.18329 | chr17:52553420-53272917 | 1
21q22.2 | 0.0049875 | 0.18329 | chr21:35331842-46944323 | 135
12p13.1 | 0.19514 | 0.19817 | chr12:6795018-18127159 | 158
1q42.3 | 0.20221 | 0.20486 | chr1:226099583-238324535 | 78
8q11.21 | 0.20003 | 0.20486 | chr8:41519793-73613253 | 117

Genes in Wide Peak

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

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

Genes
A2BP1

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p33.

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

Genes
BEND5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

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

Genes
NAALADL2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
ARID1A
hsa-mir-1976
CD52
EXTL1
SFN
GPR3
HMGN2
RPS6KA1
SLC9A1
SLC30A2
NR0B2
FCN3
MAP3K6
WASF2
CNKSR1
NUDC
WDTC1
ZNF593
GPN2
AIM1L
PIGV
GPATCH3
CCDC21
LIN28
GRRP1
DHDDS
SH3BGRL3
TMEM222
ZDHHC18
TRIM63
SYTL1
UBXN11
FAM46B
C1orf172
PDIK1L
ZNF683
CATSPER4
TRNP1
CD164L2

Genes in Wide Peak

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

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

Genes
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
LRP2BP
STOX2
KIAA1430
C4orf41
MLF1IP
WWC2
SNX25
ENPP6
C4orf38
RWDD4A
CCDC111
CCDC110
ANKRD37
HELT
FAM92A3
C4orf47
SLED1

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.23.

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

Genes
hsa-mir-605
CSTF2T
MIR605

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q22.2.

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

Genes
APC
SRP19
REEP5
C5orf13
FLJ11235
EPB41L4A
C5orf26
STARD4
DCP2
SNORA13

Genes in Wide Peak

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

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

Genes
SMAD4
ELAC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.2.

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

Genes
PTEN
PAPSS2
ATAD1
CFLP1
KILLIN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
LRRN3

Genes in Wide Peak

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

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

Genes
hsa-mir-924
BRUNOL4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q22.33.

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

Genes
SMAD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

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

Genes
B2M
SPG11
TRIM69
C15orf43
PATL2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

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

Genes
hsa-mir-125b-2
BAGE
CXADR
PRSS7
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
NCRNA00157
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
C21orf99
LIPI
ABCC13
POTED
C21orf131
C21orf34
C21orf81
MIRLET7C
MIR125B2
MIR99A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

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

Genes
TRIM16
CDRT1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q13.1.

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

Genes
NPAS3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.3.

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

Genes
GNA11
SH3GL1
STK11
TCF3
FSTL3
hsa-mir-7-3
hsa-mir-637
hsa-mir-1227
hsa-mir-1909
hsa-mir-1302-2
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
ARID3A
EEF2
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
MATK
GADD45B
NFIC
OAZ1
PALM
POLR2E
POLRMT
MAP2K2
PRTN3
PTBP1
RPS15
SGTA
TBXA2R
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
APBA3
MED16
CHAF1A
EBI3
PLIN3
APC2
ABCA7
HMG20B
SEMA6B
UQCR
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
SHC2
TIMM13
DAZAP1
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
SLC39A3
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
NCLN
SPPL2B
SHD
WDR18
REXO1
ZNF77
C19orf29
BRUNOL5
FSD1
TLE6
LPPR3
ZNF556
UBXN6
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
CREB3L3
HDGF2
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
C19orf22
C19orf6
C19orf20
REEP6
C19orf36
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOBKL2A
C19orf28
GIPC3
C19orf21
PLK5P
C2CD4C
TICAM1
C19orf23
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
C19orf34
C19orf77
C19orf30
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
ONECUT3
MEX3D
FLJ45445
PRSSL1
MIR7-3
PLIN5
FAM138F
LINGO3
ARRDC5
FAM138A
FAM138C
MIR637
PLIN4
C19orf71

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

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

Genes
MAP2K4
hsa-mir-744
DNAH9
ZNF18
SHISA6
MIR744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

Genes
ATM
DDX10
POU2AF1
SDHD
hsa-mir-34c
ACAT1
CRYAB
DLAT
DRD2
FDX1
GRIA4
GUCY1A2
HSPB2
HTR3A
IL18
NCAM1
NNMT
NPAT
PPP2R1B
PTS
RDX
SLN
ZBTB16
CUL5
HTR3B
ZW10
RBM7
EXPH5
SIK2
REXO2
TIMM8B
C11orf71
SLC35F2
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
TEX12
ARHGAP20
USP28
CARD18
AASDHPPT
C11orf1
ALG9
TMPRSS5
BCO2
KIAA1826
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
C11orf93
PIH1D2
FAM55A
FAM55B
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
ANKK1
C11orf53
C11orf34
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CARD17
LOC643923
CLDN25

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.2.

Table S52. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FGFR2
NFKB2
SUFU
hsa-mir-2110
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
ADD3
ADRA2A
ADRB1
ARL3
CASP7
COL17A1
CYP17A1
DUSP5
EMX2
FGF8
GFRA1
PRLHR
GRK5
HABP2
ABLIM1
MXI1
NRAP
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PSD
RGS10
SLC18A2
TAF5
TCF7L2
TECTB
TIAL1
XPNPEP1
SHOC2
EIF3A
GBF1
LDB1
INA
SMC3
NEURL
NOLC1
GSTO1
BAG3
SH3PXD2A
SLK
DCLRE1A
ACTR1A
SMNDC1
NPM3
MGEA5
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
ATRNL1
PDCD4
KCNIP2
CALHM2
ACSL5
NSMCE4A
CNNM2
C10orf26
C10orf118
BRWD2
FAM45B
TDRD1
AS3MT
GPAM
KIAA1598
FAM160B1
C10orf84
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
C10orf119
C10orf95
C10orf81
OBFC1
C10orf79
TRIM8
ELOVL3
PCGF6
AFAP1L2
USMG5
ITPRIP
NCRNA00081
SORCS1
SFXN2
PDZD8
C10orf32
GSTO2
C10orf78
CALHM3
PNLIPRP3
SFXN4
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
CCDC147
EMX2OS
PPAPDC1A
CALHM1
CASC2
HSPA12A
RBM20
LOC282997
KCNK18
VWA2
NANOS1
NHLRC2
C10orf96
GUCY2G
FAM45A
MIR146B
SNORA19
RPL13AP6
MIR609
LOC729020

Genes in Wide Peak

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

Table S53. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TMX3

Genes in Wide Peak

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

Table S54. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PCM1
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-383
NAT1
NAT2
ADRA1A
ASAH1
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
EGR3
EPB49
EPHX2
EXTL3
PTK2B
FGL1
GFRA2
GNRH1
LOXL2
LPL
MSR1
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
ENTPD4
PHYHIP
SORBS3
NPM2
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
PSD3
SLC39A14
FGF20
ADAMDEC1
CNOT7
ZDHHC2
SLC25A37
SCARA3
KCTD9
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
MTUS1
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
HMBOX1
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
CHMP7
VPS37A
NKX2-6
SGCZ
PEBP4
CDCA2
ESCO2
FBXO16
C8orf48
R3HCC1
LGI3
EFHA2
SCARA5
C8orf80
MIR320A
MIR383
C8orf58

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p21.3.

Table S55. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
JAK1
NOTCH2
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-101-1
ABCA4
ACADM
ADORA3
AGL
AK3L1
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
CTH
DBT
GADD45A
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1B
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
IL12RB2
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
LEPR
MOV10
MSH4
NGF
NHLH2
OVGP1
PDE4B
PIN1L
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPE65
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FPGT
FUBP1
DIRAS3
SLC16A4
SFRS11
CD101
SEP15
ZRANB2
ARHGAP29
CLCA3P
CLCA2
HS2ST1
DNAJC6
LRIG2
LPPR4
INSL5
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
SLC35D1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
SERBP1
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
TNNI3K
SH3GLB1
HAO2
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
LEPROT
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RAVER2
MCOLN3
SLC22A15
RNPC3
LRRC40
DEPDC1
C1orf103
CTTNBP2NL
C1orf183
GNG12
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
LRRC7
CACHD1
MIER1
PTBP2
DNASE2B
ELTD1
SPATA1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
WDR78
RPAP2
DENND2D
GPR177
RPF1
SIKE1
TRIM45
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
REG4
SYDE2
ZNF644
LRRC8C
SGIP1
PROK1
PSRC1
C1orf203
FAM40A
ZNF697
NEXN
C1orf59
GBP4
GBP5
SSX2IP
OLFM3
WDR63
C1orf161
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
UBE2U
SLC30A7
MGC27382
IL23R
LOC149620
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
TCTEX1D1
SPAG17
HIPK1
SLC44A5
AFARP1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
NEGR1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
HIST2H2BA
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
C1orf141
LOC400759
MIR101-1
MIR137
MIR186
MIR197
LHX8
C1orf180
BCL2L15
LOC441897
LOC492303
RBMXL1
CYMP
LOC648740
NBPF6
FAM72B
SCARNA2
SNORD45C
MIR553
MIR942
MIR760

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.2.

Table S56. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-let-7b
hsa-mir-1249
ACR
ARSA
TSPO
MPPED1
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
TTLL12
MLC1
C22orf9
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
MCAT
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
SCUBE1
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
PNPLA5
LOC150381
C22orf40
CN5H6.4
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
NCRNA00207
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

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

Table S57. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SNORD20
SAG
CCL20
SP100
SPP2
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
SH3BP4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
USP40
HJURP
HES6
DOCK10
C2orf83
MFF
CXCR7
RNPEPL1
KIAA1486
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
MGC16025
DNER
B3GNT7
SP140L
AGAP1
DIS3L2
NEU4
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC151174
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
TIGD1
C2orf72
C2orf85
DUSP28
ESPNL
ECEL1P2
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
MIR149
DNAJB3
LOC643387
PRR21
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.2.

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FGFR3
WHSC1
hsa-mir-548i-2
hsa-mir-95
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
KIAA0232
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
D4S234E
GPR78
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
CNO
STK32B
LYAR
TBC1D14
SORCS2
KIAA1530
ZFYVE28
AFAP1
TNIP2
HAUS3
ABCA11P
GRPEL1
MFSD7
TMEM175
ABLIM2
LOC84740
TMEM128
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
ZNF595
JAKMIP1
FAM53A
C4orf23
ZNF509
ZNF721
ZNF718
CCDC96
CRIPAK
DOK7
RNF212
C4orf10
NAT8L
C4orf44
LOC348926
POLN
C4orf50
USP17L6P
USP17
C4orf48
ZNF876P
DEFB131
LOC650293
ZNF732
SCARNA22
FLJ36777
PSAPL1
MIR943
LOC100130872

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.12.

Table S59. 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
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
RFXAP
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
ITM2B
MTRF1
UTP14C
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
KIAA0564
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
OR7E37P
NUFIP1
NBEA
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
C13orf1
COG6
NARG1L
RNASEH2B
DHRS12
C13orf18
C13orf23
CDADC1
CAB39L
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
SUGT1L1
SIAH3
KCNRG
FLJ37307
FREM2
NEK5
THSD1P
KCTD4
NHLRC3
SERP2
C13orf36
MIR15A
MIR16-1
ALG11
LOC646982
SERPINE3
SNORA31
MIR621
C13orf38
PRR20B
PRR20C
PRR20D
PRR20E
LOC100190939

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.2.

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BTG1
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
APAF1
ATP2B1
CSRP2
DCN
EPYC
DUSP6
ELK3
HAL
KCNC2
LTA4H
LUM
KITLG
MYF5
MYF6
PPP1R12A
NAP1L1
NTS
PAWR
PCTK2
SLC25A3
SNRPF
SYT1
TMPO
NR2C1
UBE2N
ALX1
EEA1
PPFIA2
GALNT4
CRADD
LIN7A
SOCS2
RASSF9
PLXNC1
METAP2
GLIPR1
KERA
KRR1
NUDT4
PHLDA1
ZDHHC17
MGAT4C
MRPL42
CCDC59
TRHDE
CCDC41
SLC6A15
VEZT
FGD6
NDUFA12
TMCC3
NTN4
TBC1D15
ACSS3
BBS10
CEP290
USP44
LRRIQ1
C12orf26
CAPS2
NAV3
C12orf29
OSBPL8
CCDC38
TPH2
NEDD1
IKBIP
AMDHD1
GLIPR1L2
TSPAN19
E2F7
LOC144486
TMTC2
TMTC3
C12orf50
RMST
C12orf12
GLIPR1L1
WDR51B
LOC283392
LOC338758
C12orf74
PTPRQ
C12orf63
MIR135A2
PLEKHG7
NUDT4P1
MIR331
LOC552889
CLLU1OS
CLLU1
MIR492
SNORA53
MIR617
MIR618
MRS2P2
LOC100128191

Genes in Wide Peak

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

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
WRN
NRG1
ERLIN2
PROSC
GPR124
PURG
BRF2
DUSP26
RNF122
ZNF703
C8orf41
MAK16
FUT10
UNC5D
KCNU1
LOC728024

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p21.

Table S62. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZFP36L2
COX7A2L
HAAO
DYNC2LI1
MTA3
THADA
ABCG5
ABCG8
PLEKHH2
OXER1
KCNG3
LOC728819
LOC100129726

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
HRH2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p12.

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LRRTM4
SNAR-H

Genes in Wide Peak

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

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
APC
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-1974
hsa-mir-9-2
CAMK4
CAST
CCNH
CETN3
CHD1
COX7C
EFNA5
FER
GLRX
LNPEP
MAN2A1
MEF2C
PAM
PCSK1
RASA1
SRP19
NR2F1
ST8SIA4
REEP5
C5orf13
RAB9P1
TTC37
PJA2
POLR3G
RHOBTB3
ELL2
HISPPD1
ERAP1
FLJ11235
GIN1
RIOK2
ARRDC3
EPB41L4A
ERAP2
FBXL17
MCTP1
NUDT12
SPATA9
FAM172A
GPR98
ANKRD32
TSLP
C5orf30
SLC25A46
C5orf26
LYSMD3
SLCO6A1
POU5F2
STARD4
WDR36
MBLAC2
TMEM161B
ARSK
FAM81B
DCP2
LIX1
C5orf27
C5orf36
GPR150
NBPF22P
RGMB
RFESD
FAM174A
SLCO4C1
FLJ42709
TMEM232
LOC645323
SNORA13
MIR548C
MIR583
LOC100129716
LOC100133050

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.32.

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
AKT1
RAD51L1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-770
hsa-mir-345
hsa-mir-342
hsa-mir-1260
SERPINA3
ACTN1
ACYP1
BCYRN1
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF5
EML1
ERH
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
ATXN3
MAP3K9
ALDH6A1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSEN1
PSMC1
ABCD4
RAGE
SEL1L
SFRS5
SLC8A3
SLC10A1
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
SNW1
PCNX
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
TTC9
FLRT2
SIPA1L1
DCAF4
KIF26A
C14orf109
MLH3
PRO1768
GPR132
POMT2
COQ6
FCF1
SERPINA10
GLRX5
COX16
EVL
C14orf129
CINP
ASB2
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
C14orf115
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
GALNTL1
KIAA1409
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
C14orf4
INF2
OTUB2
ZFYVE21
MEG8
WDR25
C14orf139
FAM164C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
AMN
C14orf156
DNAL1
RPS6KL1
IFI27L2
SETD3
C14orf153
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
C14orf143
C14orf43
LIN52
NEK9
C14orf73
WDR20
C14orf179
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
C14orf148
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
C14orf72
ADAM21P
GSC
SERPINA12
PRIMA1
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
C14orf145
TTC7B
C14orf49
C14orf174
EML5
MGC23270
NUDT14
C14orf48
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
C14orf86
SNHG10
C14orf177
C14orf68
C14orf70
KIAA0284
C14orf80
CCDC85C
NCRNA00203
SNORD56B
SERPINA9
VSX2
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
C14orf181
FLJ44817
FLJ45244
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323
MIR337
MIR342
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR453
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
TMEM90A
C14orf184
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
SNORD112
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-3
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-8
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100133469
LOC100289511

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q22.

Table S67. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MSI2

Genes in Wide Peak

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

Table S68. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERG
TMPRSS2
hsa-mir-802
ADARB1
AIRE
PTTG1IP
C21orf2
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
DYRK1A
ETS2
HLCS
HMGN1
PRMT2
ITGB2
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SIM2
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
TTC3
U2AF1
UBE2G2
WRB
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DOPEY2
DSCR4
DSCR3
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
DNMT3L
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
PCBP3
C21orf58
C21orf57
C21orf29
NCRNA00112
NCRNA00111
SETD4
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
C21orf96
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
C21orf70
RSPH1
UMODL1
C21orf84
C21orf88
C21orf90
MCM3APAS
LCA5L
IGSF5
SIK1
C21orf129
C21orf121
C21orf128
PLAC4
DSCR9
DSCR10
C21orf130
C21orf125
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
NCRNA00162
NCRNA00175
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
NCRNA00114
LOC642852
C21orf122
MIR802

Genes in Wide Peak

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

Table S69. 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
hsa-mir-1244
hsa-mir-141
A2M
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CD69
CDKN1B
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
GNB3
GPR19
GRIN2B
GUCY2C
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTPN6
PTPRO
PEX5
PZP
SLC2A3
TPI1
MFAP5
USP5
KLRC4
CSDA
GPRC5A
CD163
GDF3
CLSTN3
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
KLRA1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
NECAP1
CLEC4E
GPR162
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
MAGOHB
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
PLBD1
NANOG
DUSP16
APOLD1
GSG1
CDCA3
RBP5
SPSB2
RERG
HTR7P
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
LOC283314
CD163L1
RPL13P5
CLEC9A
C12orf36
CLEC4D
ACSM4
TAS2R42
DPPA3
LOC360030
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
ZNF705A
FAM66C
DDX12
C12orf69
LOH12CR2
LOC642846
LOC653113
PRB2
SCARNA12
MIR613
MIR614

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.3.

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-1537
hsa-mir-1182
ACTA1
ACTN2
AGT
ARF1
LYST
CHRM3
GALNT2
GNG4
GUK1
KCNK1
LGALS8
MTR
NID1
RAB4A
RYR2
TARBP1
TBCE
GPR137B
TSNAX
WNT9A
HIST3H3
GNPAT
GGPS1
TOMM20
URB2
SPHAR
CAPN9
COG2
RBM34
ABCB10
TAF5L
DISC2
DISC1
TRIM17
ARID4B
EGLN1
KIAA1383
HEATR1
NUP133
ERO1LB
GJC2
SIPA1L2
ZP4
RHOU
ARV1
C1orf35
TTC13
PGBD5
PCNXL2
TRIM11
C1orf124
OBSCN
C1orf57
KIAA1804
C1orf198
WNT3A
HIST3H2A
C1orf96
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
EXOC8
RNF187
C1orf69
LOC339535
IRF2BP2
FAM89A
C1orf31
TRIM67
DUSP5P
SNORA14B
LOC100130331
TSNAX-DISC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q11.21.

Table S71. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PLAG1
TCEA1
NCOA2
CHCHD7
HOOK3
hsa-mir-124-2
hsa-mir-486
ANK1
ASPH
CA8
CEBPD
CHRNB3
CRH
CYP7A1
EYA1
FNTA
NPBWR1
IKBKB
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PLAT
POLB
PRKDC
RAB2A
RP1
RPS20
SDCBP
SLC20A2
SNAI2
TTPA
UBE2V2
VDAC3
MYST3
NSMAF
RGS20
GGH
CHRNA6
TRPA1
MSC
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
AP3M2
COPS5
RRS1
SULF1
TRAM1
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
DKK4
BHLHE22
MRPL15
LACTB2
ATP6V1H
SNTG1
IMPAD1
THAP1
ARMC1
CHD7
C8orf44
CPA6
PRDM14
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
RNF170
SLCO5A1
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
C8orf40
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
AGPAT6
HGSNAT
C8orf45
CLVS1
NKX6-3
SDR16C5
YTHDF3
C8orf46
NKAIN3
LRRC67
POTEA
FAM150A
XKR9
LOC401463
MIR124-2
SDR16C6
C8orf22
BEYLA
MIR486
SNHG6
SNORD87
LOC643763
SBF1P1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 22 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.06 | 0.839 | 0.65 | 0.16 | 10.2 | 0
1q | 1572 | 0.18 | 9.17 | 0 | 0.07 | -0.0081 | 1
2p | 753 | 0.11 | -2.93 | 1 | 0.02 | -8.45 | 1
2q | 1235 | 0.11 | 0.449 | 0.91 | 0.01 | -6.75 | 1
3p | 853 | 0.07 | -5.01 | 1 | 0.08 | -4.25 | 1
3q | 917 | 0.09 | -3.13 | 1 | 0.04 | -6.73 | 1
4p | 366 | 0.02 | -9.18 | 1 | 0.23 | 1.78 | 0.104
4q | 865 | 0.03 | -7.19 | 1 | 0.20 | 3.7 | 0.000386
5p | 207 | 0.11 | -5.7 | 1 | 0.12 | -5.06 | 1
5q | 1246 | 0.06 | -3 | 1 | 0.15 | 3.3 | 0.00157
6p | 937 | 0.15 | 0.783 | 0.65 | 0.06 | -4.85 | 1
6q | 692 | 0.13 | -2.07 | 1 | 0.07 | -5.71 | 1
7p | 508 | 0.49 | 19 | 0 | 0.01 | -7.41 | 1
7q | 1071 | 0.42 | 21.1 | 0 | 0.02 | -6.01 | 1
8p | 495 | 0.25 | 3.2 | 0.00293 | 0.47 | 16.3 | 0
8q | 697 | 0.45 | 17.4 | 0 | 0.14 | -0.954 | 1
9p | 343 | 0.16 | -2.03 | 1 | 0.10 | -5.68 | 1
9q | 916 | 0.14 | 0.0255 | 1 | 0.08 | -4 | 1
10p | 312 | 0.04 | -9.04 | 1 | 0.08 | -7.35 | 1
10q | 1050 | 0.03 | -6.61 | 1 | 0.09 | -2.23 | 1
11p | 731 | 0.09 | -4.56 | 1 | 0.07 | -5.71 | 1
11q | 1279 | 0.07 | -2.32 | 1 | 0.09 | -0.876 | 1
12p | 484 | 0.18 | -0.458 | 1 | 0.07 | -6.29 | 1
12q | 1162 | 0.16 | 3.11 | 0.00369 | 0.05 | -4.44 | 1
13q | 554 | 0.58 | 24.6 | 0 | 0.04 | -5.76 | 1
14q | 1144 | 0.04 | -4.69 | 1 | 0.27 | 11 | 0
15q | 1132 | 0.02 | -6.15 | 1 | 0.28 | 12 | 0
16p | 719 | 0.16 | 0.107 | 1 | 0.03 | -7.54 | 1
16q | 562 | 0.16 | -0.912 | 1 | 0.04 | -7.6 | 1
17p | 575 | 0.03 | -6.47 | 1 | 0.51 | 20.8 | 0
17q | 1321 | 0.12 | 1.62 | 0.185 | 0.16 | 4.82 | 3.56e-06
18p | 117 | 0.07 | -5.5 | 1 | 0.63 | 22.8 | 0
18q | 340 | 0.04 | -5.72 | 1 | 0.65 | 26.5 | 0
19p | 870 | 0.10 | -3.22 | 1 | 0.05 | -6.31 | 1
19q | 1452 | 0.13 | 3.58 | 0.00085 | 0.05 | -3.06 | 1
20p | 295 | 0.52 | 16.8 | 0 | 0.30 | 4.29 | 3.79e-05
20q | 627 | 0.69 | 31.3 | 0 | 0.25 | 3.13 | 0.00265
21q | 422 | 0.04 | -8.37 | 1 | 0.21 | 1.31 | 0.248
22q | 764 | 0.02 | -8.03 | 1 | 0.21 | 3.77 | 0.000323

Methods & Data
Input

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/COADREAD/1216776/2.GDAC_MergeDataFiles.Finished/COADREAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

- Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

- CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt

- Amplification Threshold = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 564 Input Tumor Samples.

Tumor Sample Names
TCGA-A6-2670-01A-02D-0819-01
TCGA-A6-2671-01A-01D-1549-01
TCGA-A6-2672-01A-01D-1549-01
TCGA-A6-2674-01A-02D-1549-01
TCGA-A6-2675-01A-02D-1717-01
TCGA-A6-2676-01A-01D-1549-01
TCGA-A6-2677-01A-01D-1549-01
TCGA-A6-2678-01A-01D-1549-01
TCGA-A6-2679-01A-02D-1549-01
TCGA-A6-2680-01A-01D-1549-01

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.

- 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
Meta

- Maintainer = Dan DiCara

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