SNP6 Copy number analysis (GISTIC2)
Colorectal Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C17W6B2H
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 2.0.21 (Firehose task version: 127).

Summary

There were 615 tumor samples used in this analysis: 23 significant arm-level results, 27 significant focal amplifications, and 46 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 - 27 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 6.7874e-58 1.0716e-30 chr20:40103192-40360022 2
20q11.21 4.6129e-65 2.9819e-30 chr20:26197900-30339275 20
8q24.21 2.6513e-27 2.7977e-26 chr8:128204396-128754688 4
17q12 4.1848e-22 2.7123e-21 chr17:37837542-37876018 2
13q12.2 4.507e-40 3.9936e-15 chr13:28192985-28773237 11
8p11.23 4.5551e-17 7.8176e-14 chr8:38170522-38237581 1
11p15.5 7.4477e-13 7.4477e-13 chr11:2157522-2241214 4
13q12.13 2.824e-42 9.5381e-12 chr13:27521847-27533641 0 [USP12]
13q22.1 3.6372e-18 1.0911e-09 chr13:73642492-73711006 1
12p13.32 1.3921e-09 1.3921e-09 chr12:2989031-4627057 12
5q22.3 1.1974e-08 1.1974e-08 chr5:114756122-114759166 0 [FEM1C]
8p11.21 8.3037e-13 5.6764e-08 chr8:41579827-41591273 1
6p21.1 1.3943e-05 1.3943e-05 chr6:41612585-44353667 73
20q13.31 1.2311e-07 0.00016777 chr20:51458068-59479339 63
19p13.2 0.0018376 0.0018376 chr19:7300056-7398264 0 [INSR]
16p11.2 0.002984 0.002984 chr16:30611431-30780910 8
10q22.3 0.0064322 0.0064322 chr10:79267544-82903467 29
20p11.21 2.8582e-21 0.0070914 chr20:25355954-25483163 3
1q31.1 0.034422 0.034422 chr1:120523956-249250621 1199
17q24.1 0.008044 0.047309 chr17:63179119-66603035 36
2q33.1 0.078614 0.078614 chr2:199627908-199644614 0 [PLCL1]
7p21.3 0.101 0.101 chr7:1-34204682 233
8q12.1 2.395e-05 0.10384 chr8:42922991-70211670 109
19q12 0.12968 0.12968 chr19:24052831-36847803 126
15q26.1 0.12968 0.12968 chr15:83367349-102531392 156
5p12 0.1526 0.1526 chr5:27726309-50133343 89
20p12.1 0.14853 0.21781 chr20:14244972-14353100 2
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: Cancer Gene Census[7].

Genes
SNORA26|ENSG00000212224.1
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: Cancer Gene Census[7].

Genes
LINC00028
DEFB122
SNORA40|ENSG00000212134.1
RNA5SP480
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
DEFB118
DEFB115
DEFB116
DEFB119
DEFB121
DEFB123
DEFB124
FRG1B
MIR663A
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: Cancer Gene Census[7].

Genes
MYC
POU5F1B
CASC8
CCAT1
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: 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: Cancer Gene Census[7].

Genes
CDX2
FLT3
RN7SL272P
URAD
LINC00543
GSX1
PDX1
POLR1D
LNX2
PAN3
ATP5EP2
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: 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: Cancer Gene Census[7].

Genes
IGF2
INS
TH
MIR4686
Genes in Wide Peak

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

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

Genes
KLF5
Genes in Wide Peak

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

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

Genes
CCND2
C12orf5
FGF6
TEAD4
TULP3
FGF23
TSPAN9
PRMT8
PARP11
C12orf4
RHNO1
EFCAB4B
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: 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: Cancer Gene Census[7].

Genes
CCND3
TFEB
TCTE1
TMEM151B
RSPH9
SCARNA15|ENSG00000252218.1
RN7SL403P
MEA1
snoU13|ENSG00000238611.1
U3|ENSG00000221252.1
GUCA1B
SNORA8|ENSG00000206977.1
TOMM6
BYSL
SLC29A1
GUCA1A
HSP90AB1
MDFI
NFKBIE
PEX6
PGC
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
MED20
POLR1C
MAD2L1BP
CUL7
DNPH1
CNPY3
FRS3
SLC22A7
CAPN11
CUL9
UBR2
GLTSCR1L
ZNF318
YIPF3
USP49
GNMT
PRICKLE4
MRPL2
GTPBP2
MRPS18A
MRPS10
TMEM63B
TRERF1
AARS2
XPO5
MRPL14
DLK2
TTBK1
RRP36
ABCC10
KLC4
TJAP1
KLHDC3
TAF8
PTCRA
SPATS1
C6orf223
LRRC73
RPL7L1
SLC35B2
CRIP3
C6orf226
TMEM151B
C6orf132
MIR4647
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.31.

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

Genes
GNAS
ATP5E
MGC4294
ANKRD60
RAE1
RN7SL170P
U3|ENSG00000252536.1
FAM209A
GCNT7
snoU13|ENSG00000238294.1
RNA5SP487
RNU4ATAC7P
RN7SKP184
BMP7
CSTF1
CTSZ
CYP24A1
EDN3
MC3R
PCK1
PFDN4
PPP1R3D
AURKA
TFAP2C
ZNF217
BCAS1
STX16
VAPB
SYCP2
SPO11
SLMO2
NELFCD
RTFDC1
PPP4R1L
RBM38
DOK5
PMEPA1
CASS4
RAB22A
CDH26
FAM217B
NPEPL1
TUBB1
ZBP1
FAM210B
PHACTR3
TSHZ2
C20orf85
ZNF831
CBLN4
CTCFL
APCDD1L
C20orf197
FAM209B
MIR296
MIR646
MIR298
MIR4325
MTRNR2L3
MIR4756
MIR4532
MIR4533
MIR548AG2
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: Cancer Gene Census[7].

Genes
SNORA30|ENSG00000206755.1
PHKG2
RNF40
SRCAP
FBRS
PRR14
C16orf93
ZNF689
Genes in Wide Peak

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

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

Genes
LINC00857
PLAC9
MBL1P
NUTM2E
NUTM2B
SFTPA1
SNORA71|ENSG00000201393.1
LINC00595
LINC00856
RN7SL284P
RNA5SP321
ANXA11
KCNMA1
MAT1A
RPS24
SFTPD
DLG5
PPIF
POLR3A
ZMIZ1
TMEM254
TSPAN14
FAM213A
DYDC2
DYDC1
EIF5AL1
ZCCHC24
SH2D4B
SFTPA2
Genes in Wide Peak

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

Table S15.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 1q31.1.

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

Genes
SDHC
ABL2
ARNT
BCL9
ELK4
FCGR2B
FH
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
TPM3
TPR
PDE4DIP
SLC45A3
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13|ENSG00000239094.1
snoU13|ENSG00000238545.1
MIR4742
snoU13|ENSG00000238856.1
MIR320B2
SNORA72|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13|ENSG00000238576.1
snoU13|ENSG00000238798.1
U3|ENSG00000221673.1
RNA5SP76
SLC30A10
U3|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
SERTAD4
MIR4260
MIR205HG
MIR29B2
MIR29C
snoU13|ENSG00000238401.1
FAIM3
IL20
SNORD112|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72|ENSG00000201944.1
SNORD112|ENSG00000252946.1
SCARNA20|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77|ENSG00000221643.1
RABIF
PCAT6
SNORA70|ENSG00000253042.1
U6|ENSG00000272262.1
snoU13|ENSG00000239046.1
snoU13|ENSG00000238571.1
PTPRVP
GPR37L1
SNORA70|ENSG00000206637.1
MIR1231
MIR5191
RPS10P7
ASCL5
LINC00862
MIR181A1HG
MIR4735
U3|ENSG00000252241.1
MIR1278
snoU109|ENSG00000238754.1
RN7SKP126
RNA5SP73
RN7SKP156
RNA5SP72
SNORD112|ENSG00000252790.1
RN7SL654P
RNA5SP71
RN7SKP229
RNA5SP70
KIAA1614
U6|ENSG00000272292.1
MIR3121
LHX4
RN7SL230P
IFRG15
RN7SL374P
SNORA67|ENSG00000201619.1
SNORA67|ENSG00000212338.1
TOR3A
SNORA63|ENSG00000201791.1
RNA5SP69
C1orf220
LINC00083
MIR488
SCARNA3
snoU13|ENSG00000238872.1
RNA5SP68
RNA5SP67
SNORD78|ENSG00000208317.1
GAS5
RN7SKP160
snoU13|ENSG00000238430.1
ANKRD45
snoU13|ENSG00000251817.1
TNFSF18
SNORD112|ENSG00000252354.1
DNM3OS
SCARNA20|ENSG00000253060.1
RN7SL425P
snoU13|ENSG00000238859.1
RN7SL269P
RN7SL333P
C1orf112
F5
RNA5SP66
LINC00970
LINC00626
ANKRD36BP1
SFT2D2
MIR1255B2
snoU13|ENSG00000238325.1
RNA5SP65
POGK
MIR921
RNA5SP64
UCK2
TMCO1
SNORD112|ENSG00000252359.1
U3|ENSG00000212538.1
RNA5SP63
RNA5SP62
SNORD112|ENSG00000252740.1
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13|ENSG00000238843.1
BGLAP
SNORA26|ENSG00000252236.1
SCARNA4|ENSG00000252808.1
SNORA42|ENSG00000207475.1
snoU13|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ACTA1
ACTN2
ADAR
ADORA1
PARP1
ADSS
AGT
ALDH9A1
APCS
APOA2
FASLG
ARF1
ASTN1
SERPINC1
ATF3
ATP1A2
ATP1A4
ATP1B1
ATP2B4
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD34
CD48
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRNB2
CKS1B|ENSG00000173207.8
CLK2
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSRP1
CTSE
CTSK
CTSS
CD55
DHX9
DPT
ECM1
EIF2D
EFNA1
EFNA3
EFNA4
ELF3
ENSA
EPHX1
EPRS
ESRRG
ETV3
F13B
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GALNT2
GBA
GJA5
GJA8
GLUL
GNG4
GPR25
GUK1
H3F3A
HDGF
CFH
CFHR1
CFHR2
MR1
HNRNPU
HSD11B1
HSPA6
IFI16
IL6R
IL10
ILF2
INSRR
IRF6
ITPKB
IVL
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
LMNA
LMX1A
LOR
LY9
MARK1
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MPZ
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NEK2
NHLH1
NID1
NIT1
NPR1
DDR2
NVL
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PPP2R5A
PRELP
PRKAB2
PROX1
PSEN2
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PEX19
RAB4A
RAB13
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
RYR2
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRP9
TROVE2
SSR2
XCL2
TARBP1
CNTN2
TBCE
VPS72
TGFB2
LEFTY2
THBS3
TCHH
TLR5
GPR137B
TNNI1
TNNT2
TNR
TP53BP2
TRAF5
CCT3
TSNAX
TUFT1
TNFSF4
USF1
USH2A
ZNF124
DAP3
NPHS2
BTG2
HIST3H3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
GNPAT
DYRK3
CDC42BPA
RGS5
PPFIA4
ITGA10
BLZF1
DEGS1
KMO
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
TAF1A
MPZL1
SH2D2A
ANGPTL1
TBX19
PRPF3
EXO1
ARHGEF2
DEDD
XPR1
MAPKAPK2
GPR52
AIM2
GGPS1
RASAL2
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
TMEM63A
TOMM20
URB2
ARHGEF11
CEP350
CEP170
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
RBM8A
NR1I3
AKT3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
BPNT1
PIAS3
TIMM17A
LRRN2
HAX1
ZBTB18
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
LEFTY1
SPHAR
PMVK
FAM189B
CAPN9
NES
KDM5B
SDCCAG8
CFHR4
CFHR3
OCLM
JTB
MTMR11
SLC27A3
IL24
TDRKH
CD160
DUSP10
PMF1
DUSP12
VPS45
COG2
PLEKHA6
KIAA0907
KIFAP3
ATF6
RBM34
KIF21B
NMNAT2
NFASC
POGZ
COLGALT2
RGL1
SYT11
PRRC2C
FBXO28
RPRD2
CAMSAP2
SMG5
NCSTN
CRB1
GPR161
ABCB10
ZNF281
SNAPIN
OPN3
PHLDA3
RUSC1
CA14
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
MPC2
INTS7
OLFML2B
AHCTF1
C1orf43
NSL1
DNM3
TOR1AIP1
CHTOP
LCE2B
OR2M4
OR2L2
OPTC
OR10J1
OR2T1
RPS6KC1
USP21
DIEXF
TAF5L
CACYBP
SLC39A1
DISC1
KLHL20
LAMTOR2
FLVCR1
UBE2T
CNIH4
TMOD4
PYCR2
NME7
NENF
IL19
CERS2
CRNN
G0S2
DCAF8
F11R
RRP15
GLRX2
BOLA1
DESI2
ZBTB7B
RRNAD1
ADIPOR1
SCCPDH
APH1A
TRIM17
KCTD3
PLEKHO1
IER5
UCHL5
SUCO
GPR89B
HSD17B7
UFC1
DTL
METTL13
OAZ3
CYB5R1
ARID4B
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
EGLN1
MAP10
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
MARC2
SUSD4
KIF26B
RALGPS2
GPATCH2
HEATR1
MSTO1
DARS2
GOLPH3L
KLHDC8A
ETNK2
KIRREL
TMEM206
YY1AP1
YOD1
BATF3
UBE2Q1
ITLN1
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
SMYD2
LHX9
ADCK3
RAB25
PGLYRP4
ZNF695
RHBG
SCYL3
GJC2
CAMK1G
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
SIPA1L2
ZNF687
HCN3
FAM5B
CCDC181
SLAMF7
CADM3
RHOU
PRUNE
KLHL12
LGR6
HAPLN2
PAPPA2
BCAN
TNN
MRPS14
TFB2M
SEMA4A
RFWD2
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
MRPL9
JMJD4
INTS3
SCNM1
C1orf116
C1orf35
FCRL2
TTC13
CDC73
MRPL24
PGBD5
TNFAIP8L2
C1orf54
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PAQR6
PCNXL2
TRIM46
MROH9
TARS2
WDR26
EDEM3
FLAD1
TRAF3IP3
SH3BP5L
NPL
OR6N2
OR6K2
OR2L5
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
MIXL1
SPRTN
FCAMR
OBSCN
TEX35
HORMAD1
TOMM40L
POLR3GL
TMEM79
EFCAB2
ACBD6
MLK4
ZBTB37
LCE3D
LINC00467
FCRLA
ZNF496
C1orf198
PPP1R15B
MAEL
DISP1
RGS8
WNT3A
NAV1
SEC16B
AQP10
SLAMF9
PYGO2
ANGEL2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
LEMD1
C1orf85
NLRP3
PGLYRP3
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
COX20
TSEN15
FAM129A
SNAP47
TADA1
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
CCSAP
KLHDC9
AXDND1
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
OR10J5
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
EDARADD
TSACC
IQGAP3
APOA1BP
MRPL55
HIST3H2BB
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ITLN2
C1orf74
CREB3L4
BROX
C1orf51
SLC35F3
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
GCSAML
NBPF12
LELP1
RC3H1
DCST1
CNIH3
METTL11B
FAM78B
SHISA4
EXOC8
BNIPL
LRRC71
PYHIN1
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
SPRR4
SDE2
CNST
PPIAL4A
TTC24
C1orf65
LCE4A
NBPF11
PLD5
C1orf100
KRTCAP2
CRTC2
IBA57
TMEM9
SLC41A1
OR2T6
LCE5A
SYT14
C1orf101
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
OR2L13
SLC9C2
OR14A16
NBPF16
LINC00303
ANKRD34A
C1orf204
LIN9
HIST2H2AB
S100A7A
RXFP4
FAM5C
PRSS38
C1orf110
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR10R2
FCRL6
KCNT2
OR2T29
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
IRF2BP2
ZBTB41
PEAR1
MIA3
C1orf95
FAM89A
ILDR2
NOTCH2NL
LYSMD1
HRNR
FLG2
FMO6P
LINC00272
C1orf53
TMEM81
COA6
C1orf229
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf226
C1ORF220
NBPF9
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR199A2
MIR181A1
MIR214
MIR215
C1orf132
RGS21
HIST2H2BF
ETV3L
LRRC52
TRIM67
MAP1LC3C
OR10J3
OR13G1
MIR135B
KPRP
LCE6A
HIST2H4B
C1orf145
PRR9
C1orf148
PPIAL4G
PPIAL4D
MT1HL1
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR557
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
TSTD1
C2CD4D
NBPF20
MIR1537
MIR1295A
MIR3123
MIR3124
MIR4257
MIR3916
MIR4666A
MIR4424
Genes in Wide Peak

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

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

Genes
PRKAR1A
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
RN7SL622P
SNORA38B
MIR548D2
RN7SL756P
snoU13|ENSG00000238612.1
PSMD12
SNORA8|ENSG00000207410.1
RNA5SP447
RNA5SP446
MIR634
RNA5SP445
RN7SL735P
RNA5SP444
APOH
CACNG1
BPTF
KPNA2
PRKCA
AXIN2
RGS9
SLC16A6
HELZ
NOL11
PITPNC1
CACNG5
CACNG4
AMZ2
WIPI1
CEP112
C17orf58
Genes in Wide Peak

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

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

Genes
HOXA13
ETV1
HNRNPA2B1
HOXA9
HOXA11
PMS2
CARD11
JAZF1
RNA5SP229
snoU13|ENSG00000252706.1
RN7SL505P
RP9P
SNORA31|ENSG00000251999.1
AQP1
CRHR2
MIR550A1
snoU13|ENSG00000238906.1
TRIL
RN7SL365P
EVX1
HOTTIP
HOTAIRM1
U3|ENSG00000202233.1
CYCS
snoU13|ENSG00000239098.1
RNA5SP228
snoU13|ENSG00000238849.1
SNORD65|ENSG00000212264.1
MALSU1
SNORD93
RNA5SP227
MIR1183
RN7SL542P
SP8
SNORD56|ENSG00000200753.1
MIR3146
RN7SKP266
SNORA63|ENSG00000199473.1
ISPD
RN7SKP228
SNORA64|ENSG00000199470.1
TMEM106B
U3|ENSG00000212422.1
RPA3
PMS2CL
GRID2IP
FLJ20306
RN7SL851P
SNORA42|ENSG00000207217.1
RN7SL556P
ZNF815P
MIR589
snoU13|ENSG00000238394.1
ZNF890P
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
ACTB
ADCYAP1R1
AHR
AQP1
CHN2
DGKB
DFNA5
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
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
DNAH11
TAX1BP1
SKAP2
CYTH3
CREB5
NFE2L3
PHF14
HDAC9
RAPGEF5
SCRN1
KIAA0087
ARL4A
NOD1
GPNMB
AGR2
IGF2BP3
PPP1R17
KDELR2
ADAP1
NUPL2
HIBADH
INMT
FKBP9
CBX3
AVL9
SNX13
IQCE
SUN1
LSM5
SOSTDC1
KBTBD2
OSBPL3
WIPI2
INTS1
TSPAN13
EIF2AK1
BBS9
BZW2
SNX8
SNX10
TRA2A
FTSJ2
NXPH1
NT5C3A
GET4
CCZ1
MPP6
MIOS
RNF216
CPVL
TOMM7
ZNF853
CYP2W1
HEATR2
FKBP14
ZDHHC4
CHST12
CDCA7L
RADIL
KLHL7
STK31
PAPOLB
C1GALT1
ANKMY2
RBAK
NEUROD6
NPVF
GGCT
C7orf26
MICALL2
FBXL18
TTYH3
USP42
FAM188B
PSMG3
C7orf50
TNRC18
FAM126A
PLEKHA8
FAM220A
SCIN
ZFAND2A
CCDC126
GLCCI1
GPR146
C7orf31
AMZ1
AGR3
BMPER
TMEM184A
VWDE
PRPS1L1
TWISTNB
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
C7orf41
PRR15
FERD3L
SLC29A4
RSPH10B
CCDC129
ZNRF2
TMEM196
STEAP1B
C7orf71
COL28A1
ABCB5
FAM221A
MACC1
AGMO
MIR148A
MIR196B
WIPF3
OCM
MIR550A2
RSPH10B2
ANKRD61
MIR3683
LRRC72
MIR550A3
MIR4656
Genes in Wide Peak

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

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

Genes
PLAG1
TCEA1
CHCHD7
RNA5SP269
PREX2
RNA5SP268
SNORD87
LINC00967
PDE7A
LINC00966
RN7SKP135
RN7SL135P
NKAIN3
RN7SKP97
CA8
RNA5SP267
SNORA51|ENSG00000206853.1
snoU13|ENSG00000238433.1
LINC00588
RNA5SP266
LINC00968
SDR16C6P
SNORA3|ENSG00000221093.1
SNORD54
RPS20
RN7SL323P
RN7SL798P
SNORA1|ENSG00000199405.1
RNA5SP265
XKR4
RN7SL250P
RNU105C
RNU6ATAC32P
MRPL15
NPBWR1
SNORA7|ENSG00000201316.1
RN7SKP294
UBE2V2
CEBPD
RN7SKP32
LINC00293
RN7SKP41
U3|ENSG00000201329.1
POTEA
ASPH
CRH
CYP7A1
FNTA
LYN
MCM4
MOS
MYBL1
OPRK1
PENK
PRKDC
RAB2A
RP1
SDCBP
SNAI2
TTPA
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SPIDR
SGK3
BHLHE22
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
MCMDC2
CLVS1
SDR16C5
YTHDF3
C8orf46
PPP1R42
FAM150A
C8orf22
SNHG6
TCF24
MIR4470
Genes in Wide Peak

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

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

Genes
CEBPA
ZFP14
LINC00665
RN7SL287P
OVOL3
RN7SL402P
PSENEN
KMT2B
RN7SL765P
RN7SL491P
GPR42
MIR5196
HAMP
LINC00904
SNORD111|ENSG00000252230.1
SCGB1B2P
WTIP
RN7SL154P
RN7SL150P
LRP3
C19orf40
RN7SKP22
RN7SL789P
SNORA68|ENSG00000201388.1
RNA5SP472
RNA5SP471
THEG5
C19orf12
POP4
RN7SL340P
UQCRFS1
RNA5SP470
LINC00906
snoU13|ENSG00000238514.1
LINC00662
ZNF726
APLP1
ATP4A
CAPNS1
CCNE1
CD22
CEBPG
TBCB
COX6B1
COX7A1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
MAG
NPHS1
PEPD
FXYD1
FXYD3
POLR2I
SCN1B
TYROBP
USF2
ZNF146
URI1
PDCD5
ZNF254
KIAA0355
ZNF536
WBP7
UBA2
TMEM147
HCST
UPK1A
SLC7A9
ZNF507
HAUS5
CLIP3
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
GPATCH1
ZNF302
LIN37
SLC7A10
TSHZ3
GRAMD1A
PRODH2
CHST8
KCTD15
PLEKHF1
RBM42
LRFN3
IGFLR1
KIRREL2
ANKRD27
PDCD2L
NFKBID
CEP89
ALKBH6
RHPN2
ZNF30
TDRD12
DMKN
ARHGAP33
WDR88
ZNF792
HSPB6
ZNF565
DPY19L3
ZNF599
FAM187B
C19orf55
LGI4
SYNE4
THAP8
U2AF1L4
SCGB2B2
WDR62
ZNF181
VSTM2B
SBSN
RGS9BP
KRTDAP
NUDT19
SDHAF1
Genes in Wide Peak

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

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

Genes
BLM
IDH2
NTRK3
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109|ENSG00000239197.1
snoU13|ENSG00000238981.1
RN7SL363P
SNORD18|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
SNORD74|ENSG00000200206.1
RNA5SP400
RN7SL428P
CSPG4P12
SNORA25|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
HDGFRP3
SCARNA15|ENSG00000252690.2
ACAN
ALDH1A3
ANPEP
BNC1
CHD2
FES
IGF1R
MAN2A2
MEF2A
MFGE8
NMB
FURIN
PCSK6
PDE8A
PLIN1
POLG
RLBP1
SH3GL3
SNRPA1
NR2F2
AP3B2
ST8SIA2
PEX11A
IQGAP1
PRC1
SLC28A1
HOMER2
ZNF592
SV2B
AP3S2
SEMA4B
ABHD2
AKAP13
CHSY1
SYNM
SEC11A
VPS33B
MRPL46
OR4F4
SLCO3A1
NGRN
RHCG
BTBD1
TM6SF1
SCAND2P
ZSCAN2
DET1
FANCI
MCTP2
VIMP
UNC45A
RGMA
WDR93
ADAMTSL3
ALPK3
KLHL25
AEN
TTC23
MRPS11
LRRK1
TM2D3
FAM103A1
WDR73
TICRR
RCCD1
ARRDC4
LINC00923
C15orf40
TARSL2
LRRC28
AGBL1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
ADAMTS17
DNM1P46
CERS3
FAM169B
KIF7
ZNF710
HDDC3
UBE2Q2P1
SPATA41
GDPGP1
OR4F6
OR4F15
FAM174B
TTLL13
MIR1276
MIR1179
MIR3174
MIR4515
MIR548AP
Genes in Wide Peak

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

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

Genes
LIFR
HCN1
RN7SL383P
FGF10
CCL28
ANXA2R
SNORD72
RPL37
SNORA57|ENSG00000212567.1
SNORA63|ENSG00000199552.1
LINC00604
LINC00603
WDR70
RN7SL37P
RNA5SP181
LMBRD2
U3|ENSG00000201368.1
BRIX1
C1QTNF3
MIR579
snoU13|ENSG00000238864.1
RN7SKP207
SNORA18|ENSG00000252601.1
C6
C7
C9
CDH6
DAB2
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
C5orf22
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
EMB
MROH2B
EGFLAM
NADK2
UGT3A1
CAPSL
DNAJC21
TTC23L
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
C5orf34
MIR580
CCDC152
MIR4279
MIR3650
Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2

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 - 46 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 4.0632e-157 4.0632e-157 chr16:5144019-7780235 2
20p12.1 8.8353e-69 8.8353e-69 chr20:14301156-15274325 2
4q22.1 6.6202e-69 3.3216e-66 chr4:91271445-93240505 1
6q26 9.194e-57 9.194e-57 chr6:161693099-163153207 1
3p14.2 1.5184e-40 4.287e-39 chr3:59701447-61547330 3
16q23.1 8.6652e-36 8.6652e-36 chr16:78098006-79031486 1
5q12.1 1.5729e-36 2.0648e-34 chr5:58998410-59780946 2
1p33 5.0909e-38 5.1925e-33 chr1:49615826-50514967 1
3q26.31 1.4473e-32 1.4196e-32 chr3:174345545-175760559 3
1p36.11 6.5118e-34 2.8375e-29 chr1:26527443-27708281 33
18q21.2 1.0365e-34 5.6665e-27 chr18:48472083-48650073 3
6p25.3 5.5565e-21 5.5568e-21 chr6:1608837-2624052 2
10q21.1 2.1528e-19 2.6122e-17 chr10:53057593-53461574 2
8p23.2 2.2479e-22 4.2572e-16 chr8:2112968-4985851 3
4q35.1 1.2829e-20 1.2364e-15 chr4:179280062-186507186 41
21q11.2 5.2203e-10 5.1525e-10 chr21:1-15447211 12
8p22 5.744e-20 1.0415e-09 chr8:15092726-17157258 7
10q23.31 4.6928e-16 1.4265e-09 chr10:89313008-90034038 7
15q22.33 2.5887e-09 3.328e-08 chr15:67067796-67494822 1
18q22.1 2.3502e-20 6.1079e-08 chr18:65181982-66383463 1
7q31.1 3.9132e-07 4.0239e-07 chr7:110746146-111366370 1
5q22.2 2.1248e-22 7.5589e-07 chr5:110097863-113699666 19
19p13.3 1.8555e-06 1.7779e-06 chr19:1033227-1907478 35
22q13.32 3.4295e-06 3.3345e-06 chr22:48668761-51304566 42
17p12 1.1645e-05 1.1262e-05 chr17:11060240-12456081 7
5q21.2 1.8215e-18 4.7491e-05 chr5:98261106-107071504 21
15q21.1 3.3339e-09 0.0039977 chr15:44994070-45026122 1
1p13.2 4.8172e-06 0.0047743 chr1:95709569-119802060 186
15q11.2 7.6982e-08 0.0049329 chr15:1-28001323 58
8q11.1 0.006962 0.0069189 chr8:42883855-47750537 6
10q25.2 1.0553e-08 0.0085994 chr10:108922700-116193166 43
18p11.31 0.010852 0.0105 chr18:3277692-5145388 6
12p13.1 0.014509 0.014297 chr12:9360276-18235892 106
17q24.3 0.018325 0.017893 chr17:68173089-70642789 2
18q12.2 8.1914e-12 0.035066 chr18:36593175-39537209 2
3p26.3 0.0019975 0.040649 chr3:1-21472074 142
14q11.2 0.065518 0.066285 chr14:1-48291746 349
14q31.1 0.07097 0.068727 chr14:59835305-107349540 494
2p12 0.079713 0.079713 chr2:76821134-79697981 8
2q22.1 0.085447 0.085447 chr2:140708948-143637838 2
4p16.2 0.10012 0.097058 chr4:1-14496314 152
9p24.2 0.10306 0.10482 chr9:1-24553396 122
11q22.3 0.12376 0.12026 chr11:102494467-126859156 275
12q21.33 0.157 0.15351 chr12:72068874-101115327 146
15q15.2 1.1226e-08 0.21178 chr15:37383162-44164004 111
10p15.3 0.22146 0.22146 chr10:1-3183746 18
Genes in Wide Peak

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

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

Genes
SNORA40|ENSG00000252138.1
RBFOX1
Genes in Wide Peak

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

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

Genes
RNA5SP475
FLRT3
Genes in Wide Peak

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

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

Genes
RN7SKP248
Genes in Wide Peak

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

Table S27.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 S28.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FHIT
U3|ENSG00000212211.1
NPCDR1
Genes in Wide Peak

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

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

Genes
PIH1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

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

Genes
FKSG52
MIR582
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000239144.1
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000271842.1
MIR4789
RN7SKP40
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: Cancer Gene Census[7].

Genes
ARID1A
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
CD52
SFN
RPS6KA1
SLC9A1
NR0B2
FCN3
MAP3K6
NUDC
WDTC1
PIGV
GPATCH3
CEP85
LIN28A
DHDDS
TMEM222
SYTL1
UBXN11
FAM46B
C1orf172
ZNF683
TRNP1
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: Cancer Gene Census[7].

Genes
RN7SL695P
SMAD4
ELAC1
Genes in Wide Peak

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

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

Genes
FOXC1
GMDS
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.1.

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

Genes
MIR605
CSTF2T
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: Cancer Gene Census[7].

Genes
RN7SL872P
RNA5SP251
CSMD1
Genes in Wide Peak

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

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

Genes
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
ENPP6
RWDD4
CCDC111
CCDC110
ANKRD37
HELT
C4orf47
CLDN24
MIR1305
MIR3945
MIR4455
Genes in Wide Peak

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

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

Genes
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
TPTE
POTED
MIR3687
Genes in Wide Peak

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

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

Genes
ZDHHC2
FGF20
RN7SL474P
MSR1
TUSC3
CNOT7
MICU3
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
PAPSS2
ATAD1
KLLN
Genes in Wide Peak

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

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

Genes
SMAD3
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: Cancer Gene Census[7].

Genes
TMX3
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238922.1
Genes in Wide Peak

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

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

Genes
APC
RN7SKP89
RNU4ATAC13P
ZRSR1
SRP19
FLJ11235
SNORA13
RN7SKP57
CAMK4
MCC
REEP5
NREP
EPB41L4A
YTHDC2
TSSK1B
TSLP
STARD4
WDR36
DCP2
Genes in Wide Peak

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

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

Genes
STK11
TCF3
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
ATP5D
CIRBP
EFNA2
GAMT
GPX4
RPS15
APC2
ABCA7
UQCR11
SBNO2
HMHA1
DAZAP1
MBD3
PCSK4
REXO1
ABHD17A
KLF16
MUM1
MIDN
REEP6
PLK5
C19orf25
ATP8B3
C19orf26
ADAMTSL5
MEX3D
Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
ACR
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
IL17REL
PIM3
ODF3B
SYCE3
MIR3201
MIR3667
MIR4535
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: Cancer Gene Census[7].

Genes
MAP2K4
MIR744
RPL21P122
RN7SL601P
DNAH9
ZNF18
SHISA6
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.2.

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

Genes
RN7SL782P
SNORA31|ENSG00000252337.1
RNA5SP189
RN7SL255P
LINC00491
LINC00492
RN7SKP68
RNA5SP188
RN7SL802P
MIR548P
RN7SKP62
EFNA5
PAM
ST8SIA4
PPIP5K2
GIN1
NUDT12
C5orf30
SLCO6A1
FAM174A
SLCO4C1
Genes in Wide Peak

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

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

Genes
B2M
Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RBM15
snoU13|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ADORA3
AGL
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TBX15
TSHB
VCAM1
CSDE1
CDC14A
RTCA
SLC16A4
CD101
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
LAMTOR5
AP4B1
PHTF1
AHCYL1
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
PTPN22
CHIA
GPSM2
SLC25A24
SNX7
GPR88
TRMT13
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
OLFML3
AMIGO1
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
STRIP1
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
LRRC39
DRAM2
PIFO
C1orf162
SYT6
NBPF4
SLC30A7
CHIAP2
FNDC7
SASS6
UBL4B
SPAG17
HIPK1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
C1orf137
FRRS1
MIR197
NBPF6
MIR320B1
MIR137HG
Genes in Wide Peak

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

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

Genes
RNA5SP391
LINC00929
SNORA48|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64|ENSG00000270704.2
SNHG14
SNURF
snoU13|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13|ENSG00000239083.1
CHEK2P2
RN7SL584P
GABRA5
GABRB3
GABRG3
NDN
SNRPN
UBE3A
MKRN3
CYFIP1
NPAP1
NIPA2
TUBGCP5
NIPA1
GOLGA6L2
HERC2P3
GOLGA6L1
GOLGA8I
GOLGA8EP
OR4M2
POTEB2
MIR4508
POTEB
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q11.1.

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

Genes
RN7SKP41
U3|ENSG00000201329.1
POTEA
FNTA
SGK196
HGSNAT
Genes in Wide Peak

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

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

Genes
RN7SL384P
VWA2
NHLRC2
SNORA17|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13|ENSG00000239125.1
SMNDC1
RN7SL450P
U4|ENSG00000272160.1
RN7SKP278
RNA5SP326
ADD3
ADRA2A
ADRB1
CASP7
DUSP5
HABP2
MXI1
NRAP
TCF7L2
TECTB
XPNPEP1
SHOC2
SMC3
DCLRE1A
PDCD4
ACSL5
C10orf118
TDRD1
GPAM
ZDHHC6
PLEKHS1
AFAP1L2
BBIP1
VTI1A
RBM20
MIR2110
MIR4680
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.31.

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

Genes
snoU13|ENSG00000238790.1
snoU13|ENSG00000238445.1
RN7SL39P
snoU13|ENSG00000238863.1
TGIF1
DLGAP1
Genes in Wide Peak

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

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

Genes
ETV6
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
ARHGDIB
CD69
CDKN1B
CREBL2
EMP1
EPS8
GPR19
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
MGP
MGST1
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PTPRO
KLRC4
YBX3
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
TAS2R9
TAS2R7
TAS2R13
TAS2R10
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
MANSC1
STYK1
GPRC5D
ATF7IP
H2AFJ
LMO3
KIAA1467
CLEC7A
BCL2L14
APOLD1
GSG1
RERG
LOH12CR1
TMEM52B
HIST4H4
CLEC12A
CLECL1
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CLEC9A
C12orf36
TAS2R42
CLEC2A
CLEC12B
SMCO3
PRB2
MIR614
SLC15A5
Genes in Wide Peak

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

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

Genes
LINC00511
SOX9
Genes in Wide Peak

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

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

Genes
LINC00669
RN7SKP182
Genes in Wide Peak

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

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

Genes
VHL
FANCD2
PPARG
RAF1
XPC
SRGAP3
RNY4P22
MIR3135A
U7|ENSG00000271841.1
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13|ENSG00000238345.1
snoU13|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13|ENSG00000239126.1
EGOT
SNORA43|ENSG00000253049.1
RN7SKP144
RN7SL120P
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
TIMP4
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
LMCD1
SSUH2
TRNT1
CRBN
CCDC174
GHRL
ARL8B
SETD5
TMEM40
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
HDAC11
TSEN2
C3orf20
JAGN1
IL17RC
EAF1
OXNAD1
FANCD2OS
GALNT15
KCNH8
CHCHD4
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
FGD5
CNTN4
SUMF1
RPUSD3
PRRT3
TPRXL
MIR563
MIR378B
MIR3714
MIR4791
MIR4790
Genes in Wide Peak

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

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

Genes
CCNB1IP1
LINC00648
SNORA25|ENSG00000251735.1
LINC00871
SNORD127
SNORD58
snoU13|ENSG00000238501.1
SNORA31|ENSG00000251858.1
FBXO33
LINC00639
LINC00517
SNORA42|ENSG00000200385.1
TTC6
MIR4503
SLC25A21
RN7SKP257
DPPA3P2
RN7SKP21
PTCSC3
snoU13|ENSG00000238718.1
SNORA31|ENSG00000253059.1
KIAA0391
RN7SL660P
GPR33
MIR624
BNIP3P1
LINC00645
SNORD37|ENSG00000212270.1
TM9SF1
RNA5SP383
DHRS4L1
LINC00596
RN7SKP205
MIR208B
MIR208A
PABPN1
C14orf164
SNORA73|ENSG00000252114.1
SNORD41|ENSG00000212302.1
OR6J1
TRAC
TRAJ1
TRAJ2
TRAJ3
TRAJ4
TRAJ5
TRAJ6
TRAJ7
TRAJ8
TRAJ9
TRAJ10
TRAJ11
TRAJ12
TRAJ13
TRAJ14
TRAJ16
TRAJ17
TRAJ18
TRAJ19
TRAJ20
TRAJ21
TRAJ22
TRAJ23
TRAJ24
TRAJ25
TRAJ26
TRAJ27
TRAJ28
TRAJ29
TRAJ30
TRAJ31
TRAJ32
TRAJ33
TRAJ34
TRAJ35
TRAJ36
TRAJ37
TRAJ38
TRAJ39
TRAJ40
TRAJ41
TRAJ42
TRAJ43
TRAJ44
TRAJ45
TRAJ46
TRAJ47
TRAJ48
TRAJ49
TRAJ50
TRAJ52
TRAJ53
TRAJ54
TRAJ56
TRAJ57
TRAJ58
TRAJ59
TRAJ61
TRDV3
TRDC
TRDJ3
TRDJ2
TRDJ4
TRDJ1
TRDD3
TRDD2
TRDD1
TRDV2
TRAV41
TRAV40
TRAV39
TRAV36DV7
TRAV35
TRAV34
TRAV30
TRAV29DV5
TRAV27
TRAV25
TRAV24
TRDV1
TRAV23DV6
TRAV22
TRAV21
TRAV20
TRAV19
TRAV18
TRAV17
TRAV16
TRAV14DV4
TRAV10
TRAV7
TRAV6
TRAV5
TRAV4
TRAV3
TRAV2
RN7SL650P
SNORD8
SNORD9
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
OR4Q2
snoU13|ENSG00000238492.1
MED15P6
LINC00516
MED15P1
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
FKBP3
FOXG1
GZMH
GZMB
FOXA1
HNRNPC
CTAGE5
MMP14
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
NRL
OXA1L
PAX9
PCK2
PNN
PRKD1
PSMA6
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
SRP54
SSTR1
TEP1
TGM1
GEMIN2
AP1G2
SLC7A7
CPNE6
AKAP6
KIAA0391
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
SEC23A
TM9SF1
EDDM3A
DHRS4
RIPK3
AP4S1
BAZ1A
SUPT16H
ACIN1
FAM179B
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
EMC9
ZNF219
GMPR2
SLC22A17
MBIP
KLHL28
HAUS4
PPP2R3C
PRPF39
C14orf119
RNF31
RBM23
MIS18BP1
G2E3
OSGEP
ARHGEF40
EAPP
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
FANCM
SNX6
C14orf93
ABHD4
NPAS3
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
FSCB
BRMS1L
JPH4
RNASE7
INSM2
RAB2B
AJUBA
ZFHX2
LRRC16B
PPP1R3E
TMEM55B
EGLN3
DTD2
DHRS1
CMTM5
MIA2
C14orf28
TRAPPC6B
RNASE11
TPPP2
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
RPL10L
MIPOL1
MDP1
LRFN5
CLEC14A
FITM1
REM2
MDGA2
NOP9
SPTSSA
ADCY4
RALGAPA1
SFTA3
TSSK4
FAM177A1
DHRS4L2
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
TMEM253
CBLN3
MIR4307
MIR548Y
MIR4707
LINC00609
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.1.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3|ENSG00000200693.1
WDR89
SCARNA20|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112|ENSG00000252380.1
SIX1
U3|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PRKCH
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
RTN1
SEL1L
SRSF5
SLC8A3
SNAPC1
SPTB
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
AREL1
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
MLH3
KCNH5
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
EVL
GSKIP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
RHOJ
GALNT16
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
SMOC1
MOAP1
IRF2BPL
MPP5
INF2
PCNXL4
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
IFT43
L3HYPDH
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
RDH12
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SYNE3
TMEM30B
EML5
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
C14orf39
CCDC85C
SERPINA9
VSX2
LRRC9
COX8C
ASPG
RAB15
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
LINC00238
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4505
MIR4708
MIR151B
MIR4710
MIR2392
MIR5694
Genes in Wide Peak

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

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

Genes
REG1P
RNA5SP98
RN7SKP164
REG3A
REG1A
REG1B
LRRTM4
REG3G
Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B
Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
HSP90AB2P
RNA5SP156
HS3ST1
CLNK
RNA5SP155
MIR3138
RNA5SP154
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
SH3BP2
WFS1
NELFA
SLBP
ACOX3
CPZ
NOP14
FAM193A
RAB28
KIAA0232
WDR1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
NSG1
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
BLOC1S4
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
UVSSA
ZFYVE28
AFAP1
TNIP2
HAUS3
MFSD7
TMEM175
ABLIM2
TMEM128
ZNF518B
TMEM129
MRFAP1
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
JAKMIP1
FAM53A
TRMT44
ZBTB49
CCDC96
BOD1L1
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
DEFB131
MIR572
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
USP17L30
PSAPL1
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR548I2
MIR378D1
MIR4800
MIR5091
Genes in Wide Peak

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

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

Genes
JAK2
MLLT3
NFIB
CD274
DMRTA1
RN7SL151P
SNORD39|ENSG00000264379.1
MIR31HG
IFNA6
KLHL9
PTPLAD2
SNORA30|ENSG00000202189.1
MIR491
MIR4474
MIR4473
ACER2
snoU13|ENSG00000238348.1
RN7SL158P
SCARNA8
RN7SKP258
MIR3152
RN7SL720P
RN7SL98P
RN7SL157P
LINC00583
LURAP1L
RN7SL849P
RN7SL5P
SNORD27|ENSG00000251699.1
RN7SL123P
snoU13|ENSG00000252110.1
RN7SL25P
C9orf38
MLANA
snoU13|ENSG00000238654.1
INSL4
AK3
CDC37L1
CARM1P1
RN7SL592P
RNA5SP279
RN7SL412P
FAM138C
PLIN2
CDKN2A
CDKN2B
DMRT1
ELAVL2
FOXD4
GLDC
IFNA1
IFNA2
IFNA4
IFNA5
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
MTAP
PTPRD
RFX3
RLN1
RLN2
RPS6
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TYRP1
VLDLR
MPDZ
CER1
KIAA0020
RCL1
DMRT2
RRAGA
PSIP1
INSL6
KDM4C
KANK1
SLC24A2
RANBP6
C9orf53
BNC2
HAUS6
CNTLN
FOCAD
SPATA6L
DENND4C
PLGRKT
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
C9orf66
TTC39B
FAM154A
FREM1
KIAA2026
KCNV2
GLIS3
CCDC171
IFNE
ZDHHC21
PPAPDC2
MIR31
C9orf92
IZUMO3
MIR4665
Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
MIR3167
snoU13|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
RNA5SP348
MMP12
WTAPP1
ACAT1
ACRV1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
VWA5A
MCAM
KMT2A
MMP1
MMP3
MMP8
MMP10
MMP13
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
DCPS
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
MMP27
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
DCUN1D5
MSANTD4
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR4301
CASP12
MIR4493
MIR4491
MIR4492
MIR4693
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.33.

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

Genes
BTG1
snoU13|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13|ENSG00000239073.1
SNORD74|ENSG00000201502.1
snoU13|ENSG00000238361.1
snoU13|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
U8|ENSG00000201809.1
RAB21
APAF1
ATP2B1
CSRP2
DCN
EPYC
DUSP6
HAL
KCNC2
LTA4H
MYF5
MYF6
PPP1R12A
NAP1L1
NTS
CDK17
SLC25A3
SYT1
TMPO
NR2C1
ALX1
EEA1
PPFIA2
GALNT4
CRADD
LIN7A
SOCS2
RASSF9
NR1H4
PLXNC1
METAP2
KERA
KRR1
NUDT4
UHRF1BP1L
ZDHHC17
MGAT4C
MRPL42
CCDC59
TRHDE
CCDC41
SLC6A15
TMEM19
VEZT
GOLGA2B
SCYL2
FGD6
NDUFA12
ANKS1B
TMCC3
NTN4
ACTR6
TBC1D15
ACSS3
BBS10
CEP290
USP44
LRRIQ1
METTL25
CAPS2
NAV3
C12orf29
OSBPL8
DEPDC4
CCDC38
TPH2
NEDD1
IKBIP
AMDHD1
GLIPR1L2
TSPAN19
E2F7
TMTC2
TMTC3
C12orf50
FAM71C
CCER1
SLC17A8
C12orf79
GLIPR1L1
POC1B
OTOGL
GAS2L3
C12orf74
MIR135A2
PLEKHG7
MIR331
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MIR1251
MIR4303
MIR3685
MIR4495
MIR5700
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.2.

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

Genes
BUB1B
HYPK
CATSPER2P1
snoU13|ENSG00000238494.1
snoU13|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13|ENSG00000238564.1
THBS1
FAM98B
CAPN3
CKMT1B
EPB42
GANC
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MFAP1
PLCB2
RAD51
SPINT1
SRP14
TP53BP1
TYRO3
SNAP23
TGM5
PPIP5K1
LCMT2
RASGRP1
GPR176
CHP1
OIP5
BAHD1
MAPKBP1
RTF1
MGA
VPS39
SERF2
TMEM87A
RPAP1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
SPTBN5
DLL4
INO80
PPP1R14D
HAUS2
RMDN3
DNAJC17
PAK6
CASC5
STARD9
VPS18
ZNF106
CHAC1
WDR76
TMEM62
ELL3
ZFYVE19
DISP2
C15orf57
KNSTRN
BMF
CHST14
TGM7
CATSPER2
PLA2G4E
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
SPRED1
ADAL
EXD1
FSIP1
RHOV
UBR1
PLA2G4F
LRRC57
PLA2G4D
C15orf52
C15orf53
C15orf54
EIF2AK4
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
ANKRD63
JMJD7
PLA2G4B
MIR1282
Genes in Wide Peak

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

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

Genes
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
IDI1
PFKP
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
IDI2
LINC00200
PRR26
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 23 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 1300 0.07 -3.65 1 0.27 10.3 0
1q 1195 0.20 4.16 7.8e-05 0.18 2.57 0.0144
2p 624 0.20 -0.385 1 0.04 -9.34 1
2q 967 0.20 2.24 0.0508 0.03 -8.27 1
3p 644 0.13 -4.3 1 0.13 -4.38 1
3q 733 0.17 -1.67 1 0.10 -5.74 1
4p 289 0.04 -9.85 1 0.33 4.73 4.44e-06
4q 670 0.04 -8.2 1 0.32 7.35 4.41e-13
5p 183 0.18 -4.34 1 0.19 -4.03 1
5q 905 0.11 -3.55 1 0.23 3.68 0.000372
6p 710 0.21 0.553 0.774 0.11 -5.17 1
6q 556 0.20 -1.15 1 0.14 -4.05 1
7p 389 0.57 19.2 0 0.02 -8.44 1
7q 783 0.51 20.1 0 0.02 -7.43 1
8p 338 0.35 4.39 3.27e-05 0.54 15.4 0
8q 551 0.52 17 0 0.21 -0.571 1
9p 301 0.22 -1.4 1 0.16 -4.42 1
9q 700 0.19 -0.783 1 0.15 -2.65 1
10p 253 0.09 -8.62 1 0.19 -3.78 1
10q 738 0.05 -8.1 1 0.19 -0.115 1
11p 509 0.15 -4.11 1 0.15 -4.11 1
11q 975 0.14 -1.55 1 0.18 0.791 0.536
12p 339 0.23 -0.749 1 0.15 -4.92 1
12q 904 0.20 1.51 0.221 0.15 -1.72 1
13q 560 0.62 23.7 0 0.08 -5.06 1
14q 938 0.11 -3.51 1 0.36 12.1 0
15q 810 0.04 -7.45 1 0.38 12.3 0
16p 559 0.25 2.09 0.0663 0.09 -6.62 1
16q 455 0.25 1.12 0.375 0.10 -6.76 1
17p 415 0.08 -5.8 1 0.60 21.1 0
17q 972 0.21 2.79 0.0118 0.19 1.53 0.168
18p 104 0.11 -5.43 1 0.66 20.8 0
18q 275 0.08 -5.69 1 0.69 24.5 0
19p 681 0.17 -1.83 1 0.15 -3.25 1
19q 935 0.19 1.2 0.351 0.13 -2.74 1
20p 234 0.62 18.6 0 0.35 3.67 0.000372
20q 448 0.75 29.9 0 0.18 -1.55 1
21q 258 0.08 -8.18 1 0.33 4.4 1.96e-05
22q 564 0.05 -8.03 1 0.34 7.52 1.4e-13
Xq 668 0.19 -1.03 1 0.17 -1.91 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.

  • Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD-TP/11446789/GDAC_MergeDataFiles_11448847/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_GENCODE_v18_20140127.mat

  • CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 615 Input Tumor Samples.

Tumor Sample Names
TCGA-3L-AA1B-01A-11D-A36W-01
TCGA-4N-A93T-01A-11D-A36W-01
TCGA-4T-AA8H-01A-11D-A40O-01
TCGA-5M-AAT4-01A-11D-A40O-01
TCGA-5M-AAT5-01A-21D-A40O-01
TCGA-5M-AAT6-01A-11D-A40O-01
TCGA-5M-AATA-01A-31D-A40O-01
TCGA-5M-AATE-01A-11D-A40O-01
TCGA-A6-2671-01A-01D-1549-01
TCGA-A6-2672-01A-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

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

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