Copy number analysis (GISTIC2)
Colon/Rectal Adenocarcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1736NT5
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon/Rectal Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1736NT5
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 575 tumor samples used in this analysis: 24 significant arm-level results, 28 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 - 28 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
--- | --- | --- | --- | ---
20q12 | 2.4179e-55 | 7.4429e-31 | chr20:40103192-40360022 | 1
20q11.21 | 5.0406e-61 | 5.2013e-29 | chr20:26197900-30339275 | 20
8q24.21 | 1.266e-27 | 1.5074e-26 | chr8:128204396-128754688 | 3
17q12 | 1.1511e-21 | 8.5882e-21 | chr17:37837542-37876018 | 2
13q12.2 | 9.0067e-32 | 3.4377e-14 | chr13:28192985-28773237 | 10
8p11.23 | 2.0727e-16 | 1.232e-13 | chr8:38170522-38237581 | 1
11p15.5 | 1.9026e-12 | 1.9026e-12 | chr11:2157522-2241214 | 6
12p13.32 | 3.141e-10 | 3.141e-10 | chr12:893819-4699385 | 34
13q12.13 | 6.9215e-32 | 1.5719e-08 | chr13:27521847-27539800 | 0 [USP12]
13q22.1 | 2.1833e-13 | 2.3824e-08 | chr13:73616064-74055302 | 1
5q22.3 | 7.4008e-08 | 7.4008e-08 | chr5:114756122-114759166 | 0 [FEM1C]
8p11.21 | 7.7078e-13 | 9.2414e-08 | chr8:41579827-41591273 | 1
6p21.1 | 2.3194e-06 | 2.3194e-06 | chr6:41612585-44353667 | 69
19p13.2 | 0.00039375 | 0.00039375 | chr19:7300056-7398264 | 0 [INSR]
20q13.32 | 1.4202e-06 | 0.0007731 | chr20:51458068-59479339 | 64
16p11.2 | 0.003029 | 0.003029 | chr16:30581939-30943981 | 18
8q12.1 | 2.127e-06 | 0.021279 | chr8:42922991-70211670 | 103
10q22.3 | 0.021279 | 0.021279 | chr10:75818971-83489711 | 43
17q24.1 | 0.0040013 | 0.026335 | chr17:63189688-66603035 | 29
2q33.1 | 0.027586 | 0.027586 | chr2:199627908-199644614 | 0 [SATB2]
1q31.1 | 0.036851 | 0.036851 | chr1:120523956-211479538 | 858
19q12 | 0.050626 | 0.050626 | chr19:24052831-36656105 | 114
20p11.21 | 1.3015e-21 | 0.064365 | chr20:25355954-25483163 | 3
20p11.23 | 0.00034009 | 0.064438 | chr20:19045837-20817413 | 8
5p12 | 0.067105 | 0.067105 | chr5:27726309-50133343 | 90
15q26.1 | 0.098523 | 0.098523 | chr15:78506186-102531392 | 205
Xq28 | 0.14876 | 0.14876 | chrX:121228345-155270560 | 309
7p21.3 | 0.24947 | 0.24947 | chr7:1-37043421 | 260

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q12.

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

Genes
CHD6

Genes in Wide Peak

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

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

Genes
hsa-mir-3193
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
DEFB118
MLLT10P1
LINC00028
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
PSIMCT-1
MIR3193

Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
LOC727677

Genes in Wide Peak

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

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

Genes
ERBB2
PGAP3

Genes in Wide Peak

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

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

Genes
CDX2
FLT3
PDX1
POLR1D
GSX1
LNX2
PAN3
ATP5EP2
PRHOXNB
PAN3-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
WHSC1L1

Genes in Wide Peak

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

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

Genes
IGF2
INS
TH
IGF2-AS1
INS-IGF2
MIR4686

Genes in Wide Peak

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

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

Genes
CCND2
CACNA1C
FGF6
FKBP4
FOXM1
RAD52
TEAD4
TULP3
FGF23
DYRK4
RAD51AP1
TSPAN9
ERC1
ITFG2
PRMT8
PARP11
C12orf4
C12orf5
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
EFCAB4B
CACNA2D4
FBXL14
DCP1B
LOC283440
LRTM2
LOC100271702
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

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

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

Genes
KLF5

Genes in Wide Peak

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

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

Genes
ANK1

Genes in Wide Peak

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

Table S11. 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
NFKBIE
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
AARS2
XPO5
MRPL14
DLK2
TTBK1
RRP36
ABCC10
KLC4
TJAP1
KLHDC3
TAF8
PTCRA
TCTE1
SPATS1
C6orf223
RSPH9
LRRC73
RPL7L1
SLC35B2
CRIP3
C6orf226
TMEM151B
ATP6V0CP3
C6orf132
LOC100132354
TOMM6
MIR4647

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.32.

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

Genes
GNAS
hsa-mir-646
hsa-mir-298
hsa-mir-4325
ATP5E
BMP7
CSTF1
CTSZ
CYP24A1
EDN3
MC3R
PCK1
PFDN4
PPP1R3D
AURKA
TFAP2C
ZNF217
RAE1
BCAS1
STX16
VAPB
SYCP2
SPO11
SLMO2
TH1L
C20orf43
PPP4R1L
RBM38
DOK5
PMEPA1
CASS4
RAB22A
CDH26
FAM217B
NPEPL1
TUBB1
ZBP1
FAM210B
PHACTR3
TSHZ2
C20orf85
ZNF831
GCNT7
CBLN4
CTCFL
LOC149773
GNAS-AS1
APCDD1L
FAM209A
C20orf197
LOC284757
FAM209B
SUMO1P1
MIR296
MIR298
MIR4325
MTRNR2L3
LOC100506384
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4532
MIR4533
MIR5095

Genes in Wide Peak

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

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

Genes
hsa-mir-762
CTF1
PHKG2
BCL7C
RNF40
SRCAP
ZNF629
FBXL19
FBRS
PRR14
C16orf93
ZNF689
ZNF785
ZNF688
FBXL19-AS1
SNORA30
MIR762
MIR4519

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q12.1.

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

Genes
PLAG1
TCEA1
CHCHD7
hsa-mir-124-2
ASPH
CA8
CEBPD
CRH
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100287846
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

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

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

Genes
hsa-mir-606
ADK
ANXA11
KCNMA1
MAT1A
RPS24
SFTPD
VCL
VDAC2
MBL1P
DLG5
PPIF
POLR3A
KAT6B
AP3M1
DUSP13
ZMIZ1
FAM213A
TSPAN14
C10orf11
C10orf58
DYDC2
ZNF503
COMTD1
SAMD8
DYDC1
EIF5AL1
LOC219347
PLAC9
ZCCHC24
ZNF503-AS1
LOC283050
DUPD1
SH2D4B
LOC439990
LOC642361
LOC650623
SFTPA1
SFTPA2
LOC100128292
ZNF503-AS2
LOC100132987
LOC100288974

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
KPNA2
PRKCA
PSMD12
AXIN2
RGS9
SLC16A6
HELZ
ARSG
NOL11
PITPNC1
CACNG5
CACNG4
AMZ2
FAM20A
WIPI1
CEP112
C17orf58
LOC440461
MIR634
MIR635
SNORA38B
LOC100499466

Genes in Wide Peak

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

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

Genes
ABL2
ARNT
BCL9
ELK4
FCGR2B
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
TPR
PDE4DIP
SLC45A3
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
ADORA1
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
AVPR1B
BGLAP
C4BPA
C4BPB
CACNA1E
CACNA1S
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD34
CD48
CHI3L1
CHIT1
CHRNB2
CKS1B
CLK2
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSRP1
CTSE
CTSK
CTSS
CD55
DHX9
DPT
ECM1
EIF2D
EFNA1
EFNA3
EFNA4
ELF3
ENSA
ETV3
F5
F13B
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GBA
GBAP1
GJA5
GJA8
GLUL
GPR25
HDGF
CFH
CFHR1
CFHR2
MR1
HSD11B1
HSPA6
HSPA7
IFI16
IL6R
IL10
ILF2
INSRR
IRF6
IVL
KCNH1
KCNJ9
KCNJ10
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NHLH1
NIT1
NPR1
DDR2
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PRELP
PRKAB2
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPRC
PEX19
RAB13
RABIF
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
CNTN2
VPS72
THBS3
TCHH
TNNI1
TNNT2
TNR
TOP1P1
CCT3
TUFT1
TNFSF4
UCK2
USF1
DAP3
NPHS2
BTG2
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
DYRK3
RGS5
PPFIA4
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
TNFSF18
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
AIM2
RASAL2
ADAMTS4
SEC22B
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
KIF14
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
PIAS3
TIMM17A
LRRN2
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
KDM5B
CFHR4
CFHR3
OCLM
JTB
MTMR11
MLLT11
SLC27A3
IL24
TDRKH
CD160
CELF3
PMF1
DUSP12
VPS45
PLEKHA6
KIAA0907
KIFAP3
ATF6
KIF21B
NMNAT2
NFASC
POGZ
GLT25D2
RGL1
SYT11
PRRC2C
RPRD2
CAMSAP2
SRGAP2
SMG5
NCSTN
CRB1
GPR161
ZNF281
SNAPIN
PHLDA3
RUSC1
CA14
DSTYK
CCDC19
LMOD1
NBPF14
BRP44
OLFML2B
C1orf43
DNM3
TOR1AIP1
CHTOP
LCE2B
OPTC
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
USP21
DIEXF
CACYBP
SLC39A1
RNF115
KLHL20
LAMTOR2
UBE2T
TMOD4
NME7
IL19
CERS2
CRNN
G0S2
IL20
DCAF8
F11R
GLRX2
BOLA1
ZBTB7B
RRNAD1
ADIPOR1
APH1A
PLEKHO1
ACP6
IER5
UCHL5
C1orf9
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CYB5R1
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
RALGPS2
MSTO1
DARS2
GOLPH3L
KLHDC8A
ETNK2
KIRREL
YY1AP1
YOD1
UBE2Q1
ITLN1
IPO9
C1orf112
HHAT
RCOR3
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SERTAD4
SLAMF8
CDC42SE1
UBQLN4
LHX9
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
CAMK1G
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
KIAA1614
FAM5B
C1orf114
SLAMF7
CADM3
PRUNE
KLHL12
LGR6
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
TOR3A
RFWD2
RGS18
NUCKS1
MRPL9
INTS3
SCNM1
C1orf116
MGC4473
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
C1orf129
TARS2
EDEM3
FLAD1
TRAF3IP3
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
FCAMR
C1orf49
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
LINC00260
FCRLA
ANKRD36BP1
PPP1R15B
MAEL
RGS8
NAV1
SEC16B
AQP10
LHX4
SLAMF9
PYGO2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
PIGM
IGSF8
LEMD1
C1orf85
PGLYRP3
GNRHR2
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
AXDND1
HIST2H3C
ATP6V1G3
OR10J5
DCST2
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
NEK7
ITLN2
C1orf74
CREB3L4
C1orf51
LOC148696
LOC148709
PTPRVP
HFE2
ANKRD35
FAM163A
MFSD4
PM20D1
LELP1
RC3H1
DCST1
METTL11B
FAM78B
SHISA4
BNIPL
LRRC71
PYHIN1
DENND1B
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
FLJ23867
KRTCAP2
CRTC2
TMEM9
SLC41A1
LCE5A
SYT14
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
SLC9A11
NBPF15
LINC00303
LOC284576
LOC284578
LOC284581
ANKRD34A
RUSC1-AS1
LOC284648
DKFZP564C196
C1orf204
C1orf111
LOC284688
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
ANKRD45
FAM5C
C1orf110
FAM58BP
OR10R2
FCRL6
KCNT2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
CYCSP52
LOC375010
PEAR1
SFT2D2
RPS10P7
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
TMEM81
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
C1orf220
NBPF9
LOC401980
APOBEC4
MIR181B1
MIR199A2
MIR205
MIR181A1
MIR214
MIR29B2
MIR29C
MIR9-1
RGS21
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
C1orf186
OR10J3
MIR135B
KPRP
LCE6A
SUMO1P3
C1orf98
HIST2H4B
C1orf133
PRR9
MIR488
SNORD74
RPL31P11
LOC641515
MIR205HG
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
TMEM183B
FAM72B
PCP4L1
SCARNA3
SCARNA4
SNORA42
SNORA77
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
FAM72A
LOC730102
LOC730159
LOC730227
PPIAL4E
PFN1P2
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131234
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
GM140
LOC100288079
LOC100289211
MIR1231
MIR1278
MIR1295A
MIR548F1
LOC100302401
ZBED6
MIR3119-1
MIR3120
MIR4260
MIR4257
MIR3119-2
MIR4258
MIR3121
MIR3658
LOC100505633
LOC100505666
LOC100505795
LOC100505918
LOC100506023
LOC100506046
KDM5B-AS1
PMF1-BGLAP
LOC100527964
TNFAIP8L2-SCNM1
MIR4424
MIR4735
MIR4654
DNM3OS

Genes in Wide Peak

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

Table S18. 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
URI1
PDCD5
ZNF254
KIAA0355
ZNF536
MLL4
UBA2
TMEM147
POP4
HCST
UPK1A
SLC7A9
ZNF507
HAUS5
CLIP3
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
GPATCH1
PSENEN
ZNF302
LIN37
SLC7A10
TSHZ3
GRAMD1A
HAMP
PRODH2
CHST8
KCTD15
PLEKHF1
RBM42
LRFN3
IGFLR1
LOC80054
C19orf12
KIRREL2
ANKRD27
PDCD2L
NFKBID
CEP89
ALKBH6
RHPN2
ZNF30
C19orf40
TDRD12
DMKN
DKFZp566F0947
ARHGAP33
WDR88
WTIP
ZNF792
HSPB6
DPY19L3
ZNF599
FAM187B
C19orf55
LOC148145
LOC148189
LGI4
C19orf46
THAP8
U2AF1L4
LOC284395
SCGB2B2
WDR62
ZNF181
VSTM2B
SBSN
RGS9BP
KRTDAP
NUDT19
LOC400684
LOC400685
SCGB1B2P
SDHAF1
ZNF726
LOC100101266
LOC100128675
LOC100128682
SCGB2B3P
LOC100505835
LOC100506469
THEG5
LOC100652909

Genes in Wide Peak

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

Table S19. 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 20p11.23.

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

Genes
INSM1
C20orf26
NAA20
CRNKL1
RIN2
RALGAPA2
SLC24A3
LOC100130264

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p12.

Table S21. 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
hsa-mir-579
hsa-mir-4279
C6
C7
C9
CDH6
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
WDR70
BRIX1
C5orf22
CCL28
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
LOC340113
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
LOC729862
CCDC152
LOC100132356
MIR4279
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4

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-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
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
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
CIB1
MTHFS
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
VPS33B
MRPL46
OR4F4
SLCO3A1
HDGFRP3
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2
ZSCAN2
DET1
LINS
FANCI
DNAJA4
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
ADAMTSL3
KIAA1199
ALPK3
FAM108C1
MESDC1
KLHL25
CPEB1
AEN
TTC23
MRPS11
EFTUD1
LRRK1
AGSK1
TM2D3
WDR61
STARD5
FAM103A1
MEX3B
WDR73
C15orf42
RCCD1
ARRDC4
LOC91948
C15orf40
TARSL2
LRRC28
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
C15orf26
ADAMTS17
DNM1P46
CERS3
LOC254559
C15orf37
LOC283688
LOC283692
LOC283693
FAM154B
LOC283738
LOC283761
FAM169B
LOC338963
TMC3
ZNF774
C15orf38
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
LOC388152
UBE2Q2P1
FLJ42289
ANKRD34C
C15orf58
OR4F6
OR4F15
LOC390660
ST20
FAM174B
LOC400456
MIR184
MIR7-2
MIR9-3
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
LOC646938
GOLGA6L10
LOC648809
SCARNA15
MIR549
LOC727849
LOC727915
ASB9P1
LOC729911
FAM138E
UBE2Q2P3
UBE2Q2P2
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1276
MIR1179
MIR1469
MIR3175
RPS17L
LOC100505679
LOC100506874
LOC100507217
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
MIR4514
MIR3529
MIR4515
MIR4714

Genes in Wide Peak

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

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
ABCD1
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CD40LG
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
GRIA3
HCFC1
HMGB3
HPRT1
IDH3G
IDS
IGSF1
IL9R
IRAK1
L1CAM
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
OCRL
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
VBP1
XPNPEP2
ZIC3
ZNF75D
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
CXorf1
GPR50
RAB33A
ARHGEF6
MAGEC1
MAMLD1
BCAP31
ODZ1
SPRY3
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
TREX2
LDOC1
FAM127B
SRPK3
SNORA70
SNORD61
RBMX
HTATSF1
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
CXorf48
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45B
GABRQ
MOSPD1
THOC2
PDZD4
RAP2C
FAM3A
BCORL1
SPANXD
SPANXC
FUNDC2
PRRG3
BRCC3
MAP7D3
GPR101
CD99L2
H2AFB3
USP26
PHF6
TMEM185A
SLITRK2
MGC16121
PNMA6A
FATE1
HS6ST2
FRMD7
CXorf40A
FAM58A
MMGT1
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
CSAG1
FMR1NB
LOC158696
ARHGAP36
FAM122B
FAM122C
SPANXE
SPANXF1
DDX26B
ZNF449
VMA21
CTAG1A
MAGEA2B
ATP11C
RP1-177G6.2
LOC286467
LINC00204B
DCAF12L2
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
LINC00086
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
CXorf69
LINC00087
MIR542
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
CT45A2
MIR767
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129520
LOC100129662
HSFX2
CXorf64
LOC100131434
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR320D2
MIR718
MIR2114
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
LOC100506757
LOC100507404
MAGEA10-MAGEA5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p21.3.

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

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

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 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 | 1.2751e-147 | 1.2751e-147 | chr16:5144019-7771745 | 1
20p12.1 | 3.0857e-65 | 3.0857e-65 | chr20:14302876-15179819 | 2
4q22.1 | 3.8017e-58 | 3.1485e-55 | chr4:91148280-93240505 | 1
6q26 | 5.7694e-53 | 5.7694e-53 | chr6:161693099-163153207 | 1
3p14.2 | 8.9301e-38 | 3.6144e-36 | chr3:59034763-61547330 | 1
5q11.2 | 3.0133e-38 | 7.7325e-36 | chr5:58260298-59787985 | 3
16q23.1 | 3.8912e-34 | 3.8912e-34 | chr16:78129058-79627770 | 1
1p33 | 6.8413e-36 | 6.5717e-31 | chr1:49193395-50514967 | 1
1p36.11 | 6.3702e-34 | 1.9993e-29 | chr1:26527443-27708281 | 30
18q21.2 | 4.4384e-32 | 1.6571e-24 | chr18:48514396-48705371 | 1
3q26.31 | 3.876e-21 | 3.876e-21 | chr3:173999806-175760559 | 2
6p25.3 | 6.6326e-21 | 6.6326e-21 | chr6:1608837-2252425 | 2
4q35.1 | 5.5734e-22 | 3.4698e-17 | chr4:178911874-186507186 | 38
10q11.23 | 3.2848e-17 | 1.7215e-15 | chr10:53057593-53461574 | 3
8p23.2 | 2.0726e-21 | 4.2349e-15 | chr8:2079140-6262191 | 1
5q22.2 | 1.0943e-19 | 1.1674e-13 | chr5:101832498-114508587 | 33
21q11.2 | 9.0507e-11 | 8.9892e-11 | chr21:1-15482604 | 16
8p22 | 2.8582e-20 | 1.4674e-09 | chr8:15092726-16024383 | 1
18q22.1 | 9.4504e-20 | 2.1229e-08 | chr18:65565142-66383463 | 1
10q23.31 | 2.139e-13 | 1.6217e-07 | chr10:89313008-90348818 | 6
15q22.33 | 1.6016e-08 | 3.6826e-07 | chr15:67067796-67494822 | 1
7q31.1 | 9.5031e-07 | 9.3743e-07 | chr7:110725672-111366370 | 1
19p13.3 | 1.244e-05 | 1.2357e-05 | chr19:1033227-1989866 | 40
17p12 | 3.8e-05 | 3.6825e-05 | chr17:10740609-12456081 | 6
15q21.1 | 4.9533e-09 | 5.5632e-05 | chr15:44964334-45036916 | 1
22q13.32 | 0.0026911 | 0.0026863 | chr22:48668761-51304566 | 46
15q11.2 | 4.1145e-08 | 0.0031469 | chr15:1-28001323 | 137
1p13.2 | 5.1344e-06 | 0.0060002 | chr1:95939768-119913683 | 187
10q25.2 | 1.44e-07 | 0.011574 | chr10:102123044-122217470 | 173
8p11.21 | 0.004367 | 0.015717 | chr8:42883855-47753079 | 4
17q24.3 | 0.022425 | 0.022177 | chr17:68173089-70595192 | 2
8p11.21 | 0.0015636 | 0.03739 | chr8:38850253-40388317 | 10
14q11.2 | 0.038849 | 0.03739 | chr14:1-107349540 | 788
12p13.1 | 0.04213 | 0.041406 | chr12:10978771-15808677 | 65
18p11.31 | 0.041977 | 0.041406 | chr18:3277692-5144550 | 5
4p16.1 | 0.06074 | 0.060824 | chr4:1-14912145 | 148
9p24.2 | 0.058915 | 0.060824 | chr9:1-26841183 | 115
3p26.3 | 0.0035059 | 0.066686 | chr3:1-23245949 | 135
11q22.3 | 0.07078 | 0.070317 | chr11:104939777-115045236 | 80
12q21.2 | 0.14587 | 0.14407 | chr12:71029284-100872466 | 140
2p12 | 0.16995 | 0.16685 | chr2:75935002-79697981 | 7
2q22.1 | 0.13757 | 0.17785 | chr2:122525427-168815541 | 169
18q12.2 | 1.5199e-10 | 0.18228 | chr18:35235531-39060470 | 4
2q37.2 | 0.10684 | 0.19819 | chr2:220439344-243199373 | 196
19q13.43 | 0.21541 | 0.21254 | chr19:46099297-59128983 | 584
10p15.3 | 0.23076 | 0.23076 | chr10:1-3183746 | 16
20p12.1 | 3.0857e-65 | 1 | chr20:1-63025520 | 672

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
RBFOX1

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
FAM190A

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 3p14.2.

Table S29. 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 5q11.2.

Table S30. 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 16q23.1.

Table S31. 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 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 1p36.11.

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

Genes
ARID1A
hsa-mir-1976
CD52
SFN
HMGN2
RPS6KA1
SLC9A1
NR0B2
FCN3
MAP3K6
NUDC
WDTC1
GPN2
AIM1L
PIGV
GPATCH3
CEP85
LIN28A
DHDDS
SH3BGRL3
TMEM222
ZDHHC18
SYTL1
UBXN11
FAM46B
C1orf172
ZNF683
TRNP1
LOC644961
MIR1976

Genes in Wide Peak

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

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

Genes
SMAD4

Genes in Wide Peak

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

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

Genes
NAALADL2
MIR4789

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 4q35.1.

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

Genes
hsa-mir-1305
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ENPP6
C4orf38
RWDD4
CCDC111
CCDC110
ANKRD37
LOC389247
HELT
FAM92A3
C4orf47
SLED1
LINC00290
LOC728175
LOC731424
CLDN24
MIR1305
MIR3945
LOC100506229

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 8p23.2.

Table S39. 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 5q22.2.

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

Genes
APC
hsa-mir-548f-3
CAMK4
EFNA5
FER
KCNN2
MAN2A1
MCC
PAM
SRP19
REEP5
NREP
RAB9BP1
PJA2
PPIP5K2
FLJ11235
GIN1
EPB41L4A
FBXL17
YTHDC2
NUDT12
TSSK1B
TSLP
C5orf30
SLC25A46
EPB41L4A-AS1
STARD4
WDR36
DCP2
TMEM232
SNORA13
LOC100289673
LOC100505678

Genes in Wide Peak

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

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

Genes
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
TPTE
C21orf15
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
POTED
ANKRD20A11P
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p22.

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

Genes
TUSC3

Genes in Wide Peak

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

Table S43. 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 10q23.31.

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

Genes
PTEN
PAPSS2
RNLS
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

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

Table S45. 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 7q31.1.

Table S46. 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 19p13.3.

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

Genes
STK11
TCF3
hsa-mir-1909
ATP5D
CIRBP
CSNK1G2
EFNA2
GAMT
GPX4
POLR2E
RPS15
APC2
ABCA7
UQCR11
SBNO2
HMHA1
DAZAP1
MBD3
PCSK4
C19orf24
REXO1
FAM108A1
KLF16
MUM1
MIDN
REEP6
SCAMP4
ADAT3
PLK5
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
CSNK1G2-AS1
ADAMTSL5
NDUFS7
ONECUT3
MEX3D
LOC100288123
MIR1909

Genes in Wide Peak

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

Table S48. 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 15q21.1.

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

Genes
B2M

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

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

Genes
hsa-mir-3201
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC284933
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR3201
MIR4535

Genes in Wide Peak

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

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

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
NBEAP1
GABRA5
GABRB3
GABRG3
IPW
NDN
SNRPN
UBE3A
MKRN3
PAR5
SNURF
CYFIP1
C15orf2
MAGEL2
ATP10A
NIPA2
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
LOC503519
CHEK2P2
LOC646214
CXADRP2
REREP3
LOC653061
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8DP
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

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

Genes
NRAS
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
VCAM1
WNT2B
CSDE1
TTF2
CDC14A
RTCD1
SLC16A4
CD101
LRIG2
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
PTPN22
CHIA
GPSM2
SLC25A24
SNX7
DPH5
GPR88
CCDC76
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
AMIGO1
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1OS
FAM40A
DNAJA1P5
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
LPPR5
FNDC7
SASS6
UBL4B
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
FRRS1
MIR137HG
MIR137
MIR197
FLJ31662
LOC440600
BCL2L15
PGCP1
SRG7
CYMP
LOC643441
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729987
MIR942
LOC100128787
LOC100129138
LOC100129269
LOC100129620
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100506343
MIR2682

Genes in Wide Peak

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

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

Genes
TLX1
NFKB2
SUFU
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
ADD3
ADRA2A
ADRB1
ARL3
CASP7
COL17A1
CYP17A1
DUSP5
EMX2
FGF8
GFRA1
PRLHR
GRK5
HABP2
ABLIM1
MXI1
NDUFB8
NRAP
PAX2
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PSD
RGS10
FBXW4
SLC18A2
TAF5
TCF7L2
TECTB
TIAL1
WNT8B
XPNPEP1
SHOC2
EIF3A
GBF1
LDB1
BTRC
INA
SMC3
NEURL
NOLC1
GSTO1
BAG3
SH3PXD2A
SLK
DCLRE1A
ACTR1A
SMNDC1
NPM3
LBX1
MGEA5
PRDX3
VAX1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
DPCD
SEC31B
ATRNL1
PDCD4
POLL
KCNIP2
CALHM2
ACSL5
CNNM2
C10orf26
C10orf118
HIF1AN
FAM178A
FAM45B
TDRD1
C10orf2
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
FAM204A
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
WDR96
TRIM8
KAZALD1
SFXN3
ELOVL3
PCGF6
LZTS2
MRPL43
AFAP1L2
USMG5
ITPRIP
LINC00263
BBIP1
SORCS1
SFXN2
PDZD8
C10orf32
GSTO2
SFR1
CALHM3
PNLIPRP3
SFXN4
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
CCDC147
EMX2OS
CALHM1
CASC2
HSPA12A
RBM20
LOC282997
KCNK18
VWA2
NANOS1
NHLRC2
C10orf96
ENO4
GUCY2GP
FLJ41350
FAM45A
MIR146B
SNORA19
RPL13AP6
MIR608
MIR609
LOC729020
TLX1NB
MIR936
LOC100289509
MIR1307
MIR2110
MIR3158-1
MIR4295
MIR3158-2
MIR3663
LOC100505761
LOC100505839
LOC100505933
C10orf32-AS3MT
MIR4680
MIR4483
MIR4682
MIR4482-1
MIR4681

Genes in Wide Peak

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

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

Genes
FNTA
SGK196
HGSNAT
POTEA

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

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

Genes
SOX9
LOC100499467

Genes in Wide Peak

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

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

Genes
ADAM3A
ADAM2
IDO1
ADAM18
ADAM9
C8orf4
IDO2
ADAM32
ADAM5P
LOC100130964

Genes in Wide Peak

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

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

Genes
AKT1
KTN1
NKX2-1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
NIN
CCNB1IP1
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
SERPINA3
ACTN1
ACYP1
ANG
APEX1
ARF6
ARG2
ARHGAP5
BCL2L2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
ENTPD5
CDKN3
CEBPE
CFL2
FOXN3
CHGA
CKB
CMA1
LTB4R
CRIP1
CRIP2
CTSG
DAD1
COCH
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FKBP3
FOXG1
FNTB
FOS
FUT8
GALC
GCH1
GMFB
GPR33
GPX2
GSTZ1
GTF2A1
BRF1
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
MGAT2
CTAGE5
ATXN3
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NDUFB1
NEDD8
NFATC4
NFKBIA
NOVA1
PNP
NRL
SIX6
OTX2
OXA1L
PAX9
SERPINA5
PCK2
PGF
SERPINA1
SERPINA4
PIGH
PNN
POLE2
PPM1A
PPP2R5C
PPP2R5E
PRKCH
PRKD1
LGMN
PSEN1
PSMA3
PSMA6
PSMB5
PSMC1
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
MOK
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPL36AL
RPS29
RTN1
SALL2
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGFB3
TGM1
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
PABPN1
DPF3
GPR68
GPR65
GEMIN2
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
CDKL1
DCAF5
ALKBH1
EIF2B2
AP1G2
SLC7A7
MTA1
NEMF
PNMA1
RPS6KA5
CPNE6
NRXN3
AKAP6
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
KIAA0125
KIAA0317
TOX4
TECPR2
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
FBLN5
BATF
TM9SF1
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
EDDM3A
DHRS4
PAPOLA
ACOT2
TMED10
FERMT2
RIPK3
PTPN21
AP4S1
C14orf1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
VASH1
ATG14
ZBTB1
SNW1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
RCOR1
SYNE2
PACS2
SCFD1
KHNYN
ANGEL1
PPP1R13B
SLC7A8
ZFYVE26
TTC9
KLHDC2
FLRT2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
NKX2-8
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
PRO1768
CHMP4A
STXBP6
GPR132
POMT2
STRN3
SLC39A2
ERO1L
COQ6
FAM158A
ATL1
FCF1
RDH11
SERPINA10
GLRX5
ZNF219
COX16
GMPR2
SLC22A17
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
MBIP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
GNG2
KLHL28
C14orf101
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
CDCA4
C14orf102
RNF31
ATG2B
RBM23
UBR7
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SYNJ2BP
SLC39A9
MEG3
C14orf167
G2E3
FLVCR2
OSGEP
C14orf118
SMEK1
ARHGEF40
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
EAPP
ACTR10
YLPM1
METTL3
LTB4R2
KCNK13
C14orf162
SDR39U1
C14orf132
DDX24
RPGRIP1
ADCK1
TMEM63C
PELI2
RHOJ
NDRG2
GALNTL1
PLEKHH1
NYNRIN
TXNDC16
TRMT5
UNC79
HOMEZ
BEGAIN
CHD8
FANCM
PPP4R4
ZNF410
NGB
RBM25
SNX6
SAV1
C14orf93
ABHD4
C14orf133
NPAS3
SMOC1
MOAP1
DIO3OS
EDDM3B
IRF2BPL
MPP5
CDH24
INF2
C14orf135
GPR135
METTL17
IL25
GNPNAT1
OTUB2
ZFYVE21
MEG8
THTPA
OR4K5
OR11H2
WDR25
OR4K1
METTL21D
LINC00341
ZC2HC1C
C14orf169
IPO4
CLMN
CATSPERB
ZC3H14
RIN3
L2HGDH
C14orf159
C14orf45
NUBPL
DCAF11
TMEM121
DDHD1
OR4K15
SGPP1
TMX1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
FSCB
SETD3
BRMS1L
APOPT1
HHIPL1
JPH4
C14orf142
RNASE7
INSM2
ARHGAP5-AS1
RAB2B
AJUBA
STON2
ZFHX2
KIAA1737
RPPH1
SLC25A21
PAPLN
FAM181A
BTBD6
EFCAB11
LRRC16B
PPP1R3E
TMEM55B
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
TTC5
MAPK1IP1L
EGLN3
C14orf126
IFT43
WDR89
C14orf149
AHNAK2
TRIM9
TRMT61A
DHRS1
CMTM5
MIA2
TDRD9
ANKRD9
AK7
IFI27L1
C14orf28
TRAPPC6B
C14orf79
PLD4
ADSSL1
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
KLHL33
RPL10L
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
MIPOL1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
MDP1
TTC7B
LRFN5
FAM71D
TMEM229B
C14orf49
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
SAMD15
C14orf21
EML5
SPTSSA
MGC23270
ADCY4
C14orf183
RALGAPA1
SFTA3
FBXO33
NUDT14
LINC00521
SERPINA11
IGBP1P1
LOC283547
C14orf182
LOC283553
GPR137C
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
LOC283624
TSSK4
FAM177A1
KIAA0284
C14orf80
DHRS4L2
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD8
SNORD56B
SERPINA9
LINC00226
LINC00221
RNASE10
VSX2
OR6S1
SLC35F4
COX8C
ASPG
RAB15
FLJ31306
TBPL2
C14orf23
TOMM20L
SERPINA13
C14orf64
RTL1
TMEM179
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
POTEG
MIR127
MIR134
MIR136
MIR154
MIR203
MIR208A
MIR299
C14orf165
OR11H12
RNASE13
LINC00238
CCDC88C
OR4Q3
OR4M1
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
RNASE12
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
POTEM
LOC642426
ECRP
C14orf176
CBLN3
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
SNORD9
MIR411
MIR624
MIR654
MIR655
MIR656
DHRS4L1
C14orf38
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
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
SNORD127
SNORD126
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR208B
MIR889
ZBTB42
KTN1-AS1
LOC100129345
LOC100129794
LOC100131366
LOC100288846
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR4309
MIR3173
MIR4308
MIR4307
MIR548Y
LOC100505967
LOC100506071
LOC100506321
LOC100506433
LOC100507043
NEDD8-MDP1
BCL2L2-PABPN1
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4503
MIR4710
MIR548AI
MIR4707
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

Table S58. 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
ARHGDIB
ART4
CDKN1B
CREBL2
EMP1
GPR19
GRIN2B
GUCY2C
LRP6
MGP
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
GPRC5A
PRR4
TAS2R13
TAS2R14
HEBP1
DDX47
WBP11
MANSC1
GPRC5D
ATF7IP
H2AFJ
KIAA1467
BCL2L14
PLBD1
DUSP16
APOLD1
GSG1
RERG
HTR7P1
LOH12CR1
HIST4H4
ERP27
C12orf60
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
C12orf36
LOC338817
TAS2R42
RPL13AP20
C12orf69
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 18p11.31.

Table S59. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TGIF1
DLGAP1
LOC201477
LOC284215
FLJ35776

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.1.

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

Genes
FGFR3
WHSC1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
NKX3-2
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
RAB28
KIAA0232
WDR1
HS3ST1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
D4S234E
GPR78
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
CNO
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
KIAA1530
ZFYVE28
AFAP1
TNIP2
HAUS3
ABCA11P
GRPEL1
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
MRFAP1L1
CLNK
EVC2
OTOP1
ZNF595
LOC152742
JAKMIP1
FAM53A
METTL19
ZBTB49
ZNF721
ZNF718
CCDC96
BOD1L
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285547
LOC285548
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
USP17L6P
USP17
HSP90AB2P
C4orf48
LOC402160
ZNF876P
DEFB131
LOC650293
ZNF732
SCARNA22
MIR572
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR3138
LOC100507266
MIR378D1
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.2.

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

Genes
JAK2
MLLT3
NFIB
CD274
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
PLIN2
CDKN2A
CDKN2B
DMRT1
ELAVL2
FOXD4
MLANA
GLDC
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
INSL4
MTAP
PTPRD
RFX3
RLN1
RLN2
RPS6
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TYRP1
VLDLR
MPDZ
CER1
KIAA0020
RCL1
DMRT2
RRAGA
PSIP1
INSL6
KDM4C
KANK1
SLC24A2
RANBP6
AK3
C9orf53
BNC2
HAUS6
CNTLN
KIAA1797
C9orf68
CDC37L1
DENND4C
C9orf46
CBWD1
KLHL9
KIAA1432
DMRT3
DMRTA1
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
C9orf66
TTC39B
FAM154A
FREM1
KIAA2026
KCNV2
GLIS3
C9orf93
TUSC1
LURAP1L
IFNE
ZDHHC21
ACER2
LOC389705
FLJ35024
FLJ41200
PTPLAD2
PPAPDC2
MIR101-2
MIR31
FLJ35282
MIR31HG
MIR491
FAM138C
SCARNA8
CDKN2B-AS1
C9orf146
WASH1
MIR3152
LOC100506422
MIR4473
MIR4665
MIR4474

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.3.

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

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
TIMP4
NR2C2
WNT7A
BRPF1
COLQ
CAMK1
BHLHE40
KAT2B
SH3BP5
VGLL4
EDEM1
TBC1D5
TATDN2
IQSEC1
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LSM3
LINC00312
LMCD1
C3orf32
TRNT1
CRBN
C3orf19
GHRL
ARL8B
SETD5
TMEM40
TMEM111
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
ZNF385D
HDAC11
TSEN2
GRIP2
C3orf20
JAGN1
GHRLOS2
IL17RC
EAF1
OXNAD1
C3orf24
GALNTL2
KCNH8
CHCHD4
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
FGD5
CIDECP
CNTN4
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC339862
COL6A4P1
TPRXL
LHFPL4
VENTXP7
LOC401052
LOC440944
SNORA7A
MIR563
MIR885
EGOT
GHRLOS
LOC100129480
LOC100132526
LOC100288428
MIR4270
MIR3714
FGD5-AS1
LOC100505696
LOC100507582
ARPC4-TTLL3
MIR4791
MIR4790

Genes in Wide Peak

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

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

Genes
ATM
DDX10
POU2AF1
SDHD
hsa-mir-4301
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
RAB39A
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
LOC100132078
LOC100288346
MIR4301
HSPB2-C11orf52
MIR4491

Genes in Wide Peak

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

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

Genes
BTG1
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
APAF1
ATP2B1
CSRP2
DCN
EPYC
DUSP6
ELK3
HAL
KCNC2
LTA4H
LUM
KITLG
MYF5
MYF6
PPP1R12A
NAP1L1
NTS
PAWR
CDK17
SLC25A3
PTPRR
SNRPF
SYT1
TSPAN8
TMPO
NR2C1
UBE2N
ALX1
EEA1
PPFIA2
LGR5
GALNT4
CRADD
LIN7A
SOCS2
RASSF9
PLXNC1
METAP2
GLIPR1
KERA
KRR1
NUDT4
PHLDA1
RAB21
UHRF1BP1L
ZDHHC17
MGAT4C
MRPL42
CCDC59
TRHDE
CCDC41
SLC6A15
TMEM19
VEZT
GOLGA2P5
SCYL2
FGD6
NDUFA12
ANKS1B
TMCC3
NTN4
ACTR6
TBC1D15
ACSS3
BBS10
CEP290
THAP2
USP44
LRRIQ1
C12orf26
CAPS2
NAV3
C12orf29
OSBPL8
DEPDC4
CCDC38
TPH2
NEDD1
SLC9A7P1
IKBIP
AMDHD1
GLIPR1L2
TSPAN19
E2F7
LOC144481
LOC144486
KRT19P2
TMTC2
TMTC3
C12orf50
ZFC3H1
FAM71C
RMST
C12orf12
SLC17A8
LOC256021
GLIPR1L1
POC1B
OTOGL
LOC283392
LOC338758
C12orf74
PTPRQ
MKRN9P
MIR135A2
C12orf37
PLEKHG7
NUDT4P1
MIR331
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC643339
LOC643770
SNORA53
MIR617
MIR618
LOC728084
MRS2P2
LOC100128191
MIR1252
MIR1827
MIR1251
MIR4303
MIR3685
LOC100507377
POC1B-GALNT4
MIR4699
MIR548AL

Genes in Wide Peak

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

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

Genes
REG3A
REG1A
REG1B
REG1P
LRRTM4
REG3G
SNAR-H

Genes in Wide Peak

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

Table S66. 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
ACVR1
ACVR2A
BIN1
RND3
CACNB4
CCNT2
DARS
DPP4
FAP
GALNT3
GCG
GPD2
GPR17
GPR39
GRB14
GYPC
HNMT
ITGB6
KCNJ3
KIF5C
LCT
LY75
MCM6
MGAT5
MYO7B
NEB
NR4A2
ORC4
POLR2D
PROC
RBMS1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
TNFAIP6
CXCR4
PKP4
B3GALT1
KYNU
NMI
HS6ST1
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
TBR1
MAP3K2
GALNT5
NXPH2
COBLL1
PLA2R1
RAB3GAP1
UBXN4
R3HDM1
GCA
EPC2
ARL5A
PTPN18
MMADHC
C2orf27A
BAZ2B
ARHGEF4
LRP1B
PLEKHB2
FIGN
RIF1
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
CFC1
RPRM
UGGT1
SLC4A10
ERMN
IFIH1
MARCH7
SAP130
GTDC1
TTC21B
CSRNP3
MZT2B
YSK4
THSD7B
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
SFT2D3
TANC1
KCNH7
CCDC74A
CCDC74B
DAPL1
IMP4
TUBA3E
TUBA3D
FMNL2
GALNT13
LYPD1
XIRP2
CNTNAP5
ACMSD
FAM168B
ACVR1C
LYPD6
LYPD6B
CCDC148
LOC150527
LOC150776
WTH3DI
ARL6IP6
SLC38A11
WDSUB1
UPP2
FAM123C
LOC285103
SPOPL
CYP27C1
NCKAP5
GPR148
RBM43
LOC389033
LOC389043
LOC401010
DKFZp686O1327
MIR128-1
C2orf27B
LOC440905
LOC440910
POTEKP
POTEE
LOC554201
ANKRD30BL
LOC646743
LOC647012
CFC1B
MZT2A
POTEF
PABPC1P2
LOC100129961
LOC100131320
CYP4F30P
LOC100144595
LOC100216479
ZEB2-AS1
MIR663B
SNORA70F
MIR3679
LOC100506124
LOC100506134
LOC100507600
LY75-CD302
MIR4783
MIR4785
MIR4784
MIR4773-1
MIR4773-2

Genes in Wide Peak

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

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

Genes
hsa-mir-924
hsa-mir-4318
LOC647946
MIR4318

Genes in Wide Peak

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

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

Genes
ACSL3
PAX3
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
SNORD20
SAG
CCL20
SLC4A3
SP100
SPP2
SCG2
CUL3
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
FARSB
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
SH3BP4
KCNE4
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
WDFY1
NYAP2
GAL3ST2
RAB17
COPS7B
MRPL44
TRPM8
MLPH
IQCA1
FAM124B
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
MGC16025
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
CCDC140
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
C2orf72
CXXC11
DUSP28
ESPNL
ECEL1P2
LOC348761
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR4268
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.43.

Table S69. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
KLK2
PPP2R1A
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
A1BG
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
DBP
DMPK
DMWD
EMP3
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
MYBPC2
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PEG3
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTGIR
PTPRH
RPL18
RPL28
RPS5
RPS9
RPS11
RRAS
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SYT5
TNNI3
TNNT1
TULP2
NR1H2
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF175
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
UBE2M
CYTH2
ZNF264
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
FBXO46
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
CABP5
SPHK2
MEIS3
SLC17A7
NAT14
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
ZSCAN18
MGC2752
TSEN34
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
TBC1D17
ZNF419
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
RSPH6A
ZNF611
MED25
BCL2L12
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
IGFL1
ZNF773
LOC386758
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF321P
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC646508
SBK2
LOC646862
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
SGK110
BSPH1
LOC100131691
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SNAR-A14
ERVV-2
LOC100287177
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
MIR3191
MIR3190
MIR320E
MIR4324
MIR642B
LOC100505681
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4751

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

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

Genes
ADARB2
IDI1
PFKP
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
IDI2-AS1
IDI2
LOC282980
TUBB8
LINC00200
LOC399708
C10orf108
ADARB2-AS1

Genes in Wide Peak

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

Table S71. 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-663
hsa-mir-3192
hsa-mir-103-2-as
hsa-mir-1292
hsa-mir-3194
ADA
ADRA1D
JAG1
AHCY
ASIP
ATP5E
AVP
BCL2L1
BFSP1
BMP2
BMP7
BPI
ENTPD6
CD40
CDC25B
CDH4
CEBPB
CENPB
CHGB
CHRNA4
COL9A3
CSE1L
CSNK2A1
CST1
CST2
CST3
CST4
CST5
CSTF1
CTSZ
CYP24A1
DNMT3B
E2F1
EDN3
EEF1A2
EPB41L1
EYA2
FKBP1A
FOXS1
GGT7
GHRH
GNRH2
NPBWR2
GSS
HCK
FOXA2
HNF4A
ID1
IDH3B
INSM1
EIF6
ITPA
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
LBP
MC3R
MMP9
MYBL2
MYT1
NFATC2
NKX2-2
NNAT
NTSR1
OPRL1
OXT
PAX1
PCK1
PCNA
PCSK2
PDYN
PFDN4
PI3
PLAGL2
PLCB4
PLCG1
PLTP
CTSA
PPP1R3D
PRNP
PSMA7
PTGIS
PTK6
PTPN1
PTPRA
PYGB
RBL1
RPN2
RPS21
RRBP1
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SIGLEC1
SNAI1
SNAP25
SNRPB
SNRPB2
SNTA1
SOX12
SPAG4
SRC
SRMS
SSTR4
STAU1
STK4
AURKA
TAF4
TCEA2
TCF15
TFAP2C
TGM2
TGM3
THBD
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF133
ZNF217
MKKS
GDF5
NCOA3
ATRN
RAE1
CST7
BCAS1
STX16
CDS2
TNFRSF6B
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
VAPB
B4GALT5
KIF3B
PSMF1
RBM39
TTI1
SNPH
ProSAPiP1
RASSF2
TM9SF4
SPATA2
GINS1
OSBPL2
SLC23A2
ACOT8
CST8
ATP9A
SGK2
RBM12
ARFRP1
RGS19
SIRPB1
SYCP2
MYL9
WFDC2
SEC23B
NOP56
PROCR
ARFGEF2
RBCK1
POLR3F
TCFL5
RBBP9
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
DSTN
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
CEP250
RNF24
HRH3
PXMP4
RBPJL
XRN2
DLGAP4
UBOX5
BTBD3
RALY
CD93
MAPRE1
TPX2
NINL
ZHX3
NCOA6
PLCB1
SLC9A8
ADNP
POFUT1
ZMYND8
SPO11
PRND
FLRT3
LAMP5
PRPF6
SPEF1
SAMHD1
C20orf194
C20orf4
L3MBTL1
PPP1R16B
C20orf26
ABHD12
TRPC4AP
ZNF337
GTPBP5
GMEB2
SNORD12C
SNORA71B
SNORA71A
SNORD57
SNORD56
SDCBP2
SNX5
TP53TG5
MOCS3
SLCO4A1
REM1
C20orf30
HSPC072
NXT1
VSX1
STMN3
SLC35C2
SLMO2
IFT52
NAA20
PHF20
SCAND1
BPIFA1
CRNKL1
ANGPT4
TH1L
C20orf43
C20orf111
ESF1
PIGT
TRMT6
ERGIC3
CDK5RAP1
RTEL1
SOX18
HAO1
RIN2
SMOX
CRLS1
YTHDF1
LIME1
UCKL1
C20orf27
C20orf11
DZANK1
UQCC
PCMTD2
C20orf20
SPTLC3
C20orf29
TMEM74B
PPP4R1L
SIRPG
RBM38
FERMT1
KIF16B
TASP1
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
EDEM2
DOK5
PLK1S1
DBNDD2
ACSS2
RNF114
SULF2
NSFL1C
C20orf24
TMX4
CTNNBL1
GPCPD1
CPXM1
SLC2A4RG
OTOR
PMEPA1
CASS4
SPINLW1
C20orf3
PAK7
RALGAPB
JPH2
SALL4
ZNFX1
RALGAPA2
CSRP2BP
RAB22A
SLC24A3
NDRG3
SLC12A5
ZNF512B
MAVS
PREX1
EBF4
COL20A1
MYH7B
NCOA5
TRIB3
TP53INP2
RPRD1B
OVOL2
TGIF2
CDH26
FASTKD5
KCNK15
DHX35
MANBAL
NAPB
SLC17A9
ELMO2
ZNF335
ANKRD5
LOC63930
PCIF1
FAM217B
NECAB3
GFRA4
CDH22
GZF1
VPS16
FAM113A
SLC13A3
LPIN3
MRPS26
DDRGK1
GDAP1L1
LOC79015
C20orf195
C20orf7
PPDPF
ZNF343
TTPAL
BIRC7
NPEPL1
ACTR5
SYNDIG1
DSN1
NRSN2
PANK2
FER1L4
DNAJC5
ADAM33
PABPC1L
BPIFB2
SEL1L2
TUBB1
ZBP1
SLC2A10
HM13
PDRG1
FAM83D
DEFB126
CABLES2
FAM110A
DYNLRB1
ITCH
SLC4A11
SLA2
CHD6
MCM8
ACSS1
MAP1LC3A
PARD6B
ZGPAT
COX4I2
ZNF341
TOX2
ZCCHC3
MYLK2
PRIC285
KIAA1755
SCRT2
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
GGTLC1
C20orf72
DTD1
BPIFB1
TP53RK
C20orf54
DNTTIP1
FAM210B
PHACTR3
HSPA12B
DEFB118
TMC2
BHLHE23
NKAIN4
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
TBC1D20
SIRPD
C20orf141
PROKR2
C20orf94
CSTL1
CST9L
CST9
C20orf166
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
GATA5
MLLT10P1
SLC32A1
C20orf96
BPIFA2
ZBTB46
WFDC3
GCNT7
C20orf112
CBLN4
CTCFL
C20orf132
SAMD10
ABHD16B
C20orf160
KIAA0889
C20orf118
RIMS4
SUN5
MACROD2
SRXN1
ROMO1
NEURL2
LINC00261
ZSWIM3
WFDC10A
BANF2
NANP
LINC00266-1
DEFB127
C20orf79
ISM1
WFDC6
C20orf173
LINC00028
FAM65C
CST11
DEFB129
SIRPA
C20orf151
C20orf152
STK35
R3HDML
ADIG
GTSF1L
WFDC5
LOC149773
GNAS-AS1
PRNT
LOC149837
C20orf196
NCOR1P1
LOC149950
COMMD7
BPIFB4
LSM14B
WFDC13
APCDD1L
LRRN4
CSTT
TTLL9
ACTL10
C20orf201
FAM209A
LOC200261
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
DEFB125
DEFB128
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
SIRPB2
LOC284788
LOC284798
FAM182A
LOC284801
FRG1B
C20orf203
BPIFA4P
LOC339568
LOC339593
ARHGAP40
RSPO4
TGM6
XKR7
BPIFB3
TMEM189
TMEM189-UBE2V1
LINC00493
LOC388796
FAM209B
SPINT4
SUMO1P1
DEFB132
C20orf202
FLJ33581
MIR103A2
MIR1-1
MIR124-3
MIR133A2
MIR296
DZANK1-AS1
ZNFX1-AS1
MIR499A
RAD21L1
LOC643406
NKX2-4
LOC647979
SNORA39
SNORA51
SNORA60
SNORA71C
SNORA71D
SNORD12
SNORD17
SNORD86
SNORD110
MIR644A
MIR645
MIR647
MIR663A
LOC728228
FAM182B
SYS1-DBNDD2
HAR1A
HAR1B
PSIMCT-1
SNORD119
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
LOC100128496
LOC100130264
ZNF663
LOC100131208
LOC100131496
DPH3P1
LOC100134015
LOC100134868
LINC00029
LOC100144597
FLJ16779
LOC100270679
LOC100270804
LOC100287792
TMEM239
LOC100289473
MIR1914
MIR1292
MIR1257
MIR103B2
PCNA-AS1
PET117
MACROD2-AS1
MIR3192
MIR4325
MIR3194
MIR3193
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505536
LOC100505783
LOC100505815
LOC100505826
LOC100506384
LOC100507495
LOC100507629
SPINLW1-WFDC6
TGIF2-C20ORF24
FKBP1A-SDCBP2
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR499B
MIR4756
MIR4758
MIR4532
MIR4533
MIR4755
MIR5095
LOC100652730

Arm-level results

Table 3. Get Full Table Arm-level significance table - 24 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 | 0.06 | -3.26 | 1 | 0.25 | 10.2 | 0
1q | 1955 | 0.20 | 4.82 | 4.08e-06 | 0.16 | 2.4 | 0.0231
2p | 924 | 0.18 | -1.54 | 1 | 0.04 | -9.22 | 1
2q | 1556 | 0.18 | 1.4 | 0.247 | 0.03 | -7.85 | 1
3p | 1062 | 0.12 | -4.4 | 1 | 0.12 | -4.58 | 1
3q | 1139 | 0.16 | -2.03 | 1 | 0.08 | -6.17 | 1
4p | 489 | 0.03 | -10 | 1 | 0.32 | 3.9 | 0.000178
4q | 1049 | 0.04 | -8.24 | 1 | 0.30 | 6.04 | 3.5e-09
5p | 270 | 0.17 | -4.84 | 1 | 0.17 | -4.84 | 1
5q | 1427 | 0.11 | -3.5 | 1 | 0.22 | 3.08 | 0.00315
6p | 1173 | 0.21 | 1.09 | 0.366 | 0.11 | -4.47 | 1
6q | 839 | 0.20 | -1.09 | 1 | 0.15 | -3.64 | 1
7p | 641 | 0.57 | 18.9 | 0 | 0.02 | -8.01 | 1
7q | 1277 | 0.52 | 20.6 | 0 | 0.02 | -6.86 | 1
8p | 580 | 0.34 | 4.39 | 2.78e-05 | 0.54 | 15 | 0
8q | 859 | 0.52 | 16.6 | 0 | 0.19 | -0.938 | 1
9p | 422 | 0.21 | -2.11 | 1 | 0.16 | -4.73 | 1
9q | 1113 | 0.18 | -0.897 | 1 | 0.14 | -2.85 | 1
10p | 409 | 0.08 | -8.58 | 1 | 0.18 | -4.04 | 1
10q | 1268 | 0.04 | -7.8 | 1 | 0.19 | 0.155 | 1
11p | 862 | 0.15 | -3.87 | 1 | 0.15 | -3.87 | 1
11q | 1515 | 0.14 | -1.42 | 1 | 0.17 | 0.514 | 0.759
12p | 575 | 0.23 | -0.454 | 1 | 0.13 | -5.31 | 1
12q | 1447 | 0.19 | 1.59 | 0.188 | 0.13 | -2.22 | 1
13q | 654 | 0.62 | 21.5 | 0 | 0.09 | -5.28 | 1
14q | 1341 | 0.11 | -3.6 | 1 | 0.35 | 10.3 | 0
15q | 1355 | 0.05 | -6.53 | 1 | 0.37 | 12.2 | 0
16p | 872 | 0.25 | 1.78 | 0.136 | 0.07 | -7.2 | 1
16q | 702 | 0.24 | 0.683 | 0.618 | 0.09 | -7.24 | 1
17p | 683 | 0.07 | -6.01 | 1 | 0.59 | 20.2 | 0
17q | 1592 | 0.20 | 2.91 | 0.00806 | 0.17 | 0.84 | 0.535
18p | 143 | 0.11 | -5.44 | 1 | 0.65 | 19.7 | 0
18q | 446 | 0.07 | -5.66 | 1 | 0.68 | 23.7 | 0
19p | 995 | 0.16 | -2.59 | 1 | 0.15 | -3.32 | 1
19q | 1709 | 0.18 | 1.92 | 0.109 | 0.13 | -1.19 | 1
20p | 355 | 0.62 | 18 | 0 | 0.35 | 3.65 | 0.000434
20q | 753 | 0.75 | 29.4 | 0 | 0.20 | -0.863 | 1
21q | 509 | 0.08 | -7.81 | 1 | 0.32 | 4.13 | 7.24e-05
22q | 921 | 0.05 | -7.68 | 1 | 0.33 | 6.73 | 4.34e-11
Xq | 1312 | 0.20 | 1.13 | 0.366 | 0.16 | -0.903 | 1

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.

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/COADREAD-TP/3023505/2.GDAC_MergeDataFiles.Finished/COADREAD-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

Table 4. Get Full Table First 10 out of 575 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

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

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
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