SNP6 Copy number analysis (GISTIC2)
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 2.0.23.

Summary

There were 122 tumor samples used in this analysis: 19 significant arm-level results, 25 significant focal amplifications, and 53 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 - 25 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
--- | --- | --- | --- | ---
17q12 | 1.9403e-22 | 3.2091e-18 | chr17:37677184-38032998 | 13
11q13.3 | 9.3191e-18 | 9.5491e-18 | chr11:69914979-70275188 | 5
8q24.21 | 5.1296e-14 | 5.1296e-14 | chr8:126448482-130771681 | 21
12p13.33 | 1.1773e-13 | 4.1601e-13 | chr12:1-92091 | 0 [FAM138D]
8p11.23 | 2.6381e-08 | 2.6381e-08 | chr8:37422222-37917437 | 10
1q23.2 | 2.6341e-11 | 1.2177e-06 | chr1:153265039-175066685 | 387
10p15.1 | 2.2074e-05 | 2.2074e-05 | chr10:2687843-13221943 | 75
11p13 | 0.00016723 | 0.00018287 | chr11:34064144-36669635 | 23
13q34 | 0.00073724 | 0.00073724 | chr13:111362010-115169878 | 42
20q13.31 | 0.0015232 | 0.0015232 | chr20:50775407-56740418 | 37
7q36.1 | 0.0018785 | 0.0018785 | chr7:149475189-149529933 | 1
1q42.13 | 9.1629e-09 | 0.002389 | chr1:154154497-237547920 | 862
3q26.32 | 0.0024062 | 0.0024062 | chr3:178552266-178969743 | 5
17q24.2 | 3.1992e-07 | 0.0035335 | chr17:64299057-67510890 | 39
19q13.13 | 0.004807 | 0.004807 | chr19:33639748-40881781 | 197
9p24.3 | 0.0087466 | 0.0087466 | chr9:1-35194 | 1
12p11.21 | 0.0028393 | 0.0090891 | chr12:29911327-32744825 | 21
14q11.2 | 0.011108 | 0.015772 | chr14:1-27065790 | 266
16p13.3 | 0.015772 | 0.015772 | chr16:1-2831549 | 143
2q11.1 | 0.027642 | 0.027642 | chr2:95471289-99976661 | 64
15q26.3 | 0.071981 | 0.071981 | chr15:88999049-102531392 | 113
1p34.2 | 0.012035 | 0.087521 | chr1:40820677-46134498 | 94
14q32.31 | 0.088008 | 0.13469 | chr14:101505145-101533099 | 25
1p35.2 | 0.056151 | 0.20111 | chr1:32042906-32101921 | 3
6p22.1 | 0.21301 | 0.21301 | chr6:1-64420472 | 716

Genes in Wide Peak

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

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

Genes
ERBB2
STARD3
PPP1R1B
GRB7
MIEN1
PNMT
PGAP3
IKZF3
CDK12
NEUROD2
TCAP
ZPBP2
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CTTN
ANO1
PPFIA1
FADD
MIR548K

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
GSDMC
FAM84B
TRIB1
RN7SKP226
POU5F1B
MIR1207
MIR1208
MIR1205
RN7SKP206
CCDC26
LINC00861
CASC8
CCAT1
PVT1
LINC00977
PCAT2
PCAT1
TMEM75
MIR3686
RN7SL590P

Genes in Wide Peak

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

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

Genes
GPR124
BRF2
PROSC
ERLIN2
RAB11FIP1
GOT1L1
ZNF703
EIF4EBP1
ADRB3
RN7SL709P

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q23.2.

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

Genes
FCGR2B
SDHC
PRCC
TPM3
MUC1
PBX1
NTRK1
SCYL3
C1orf112
SELE
FMO3
METTL13
FMO1
ATP1A2
SLAMF7
INSRR
SH2D2A
MYOC
CD84
CD5L
KIFAP3
FMO4
KLHL20
DUSP12
IGSF9
FMO2
SUCO
PRRX1
CACYBP
SCAMP3
ASH1L
GON4L
ARHGEF2
LAMTOR2
MEF2D
ETV3
SLAMF1
CD48
UAP1
RGS4
BLZF1
CCDC181
SLC19A2
MROH9
FMO6P
PRRC2C
VAMP4
FASLG
TNFSF4
PRDX6
DARS2
SERPINC1
ATF6
TNN
MRPS14
CENPL
TNFSF18
GORAB
COPA
CD244
LY9
MSTO1
C1orf61
FCRLA
HSD17B7
DAP3
RHBG
KIAA0907
ATP1A4
NES
BCAN
CRP
ARHGEF11
RAB25
HAPLN2
APCS
FCRL2
DCAF8
SYT11
PIGC
RC3H1
GPR161
ALDH9A1
ATP1B1
TIPRL
NME7
POGK
MPC2
CREG1
DCAF6
GPA33
RXRG
TBX19
UCK2
TMCO1
XCL1
XCL2
POU2F1
MAEL
ILDR2
DPT
MGST3
ADCY10
PVRL4
UFC1
PPOX
FCGR2A
NUF2
RGS5
PFDN2
NR1I3
USP21
FCRL5
RRNAD1
MRPL24
PIGM
CASQ1
ISG20L2
CRABP2
HDGF
ATP8B2
ADAM15
JTB
RAB13
S100A8
NUP210L
SNAPIN
SLC27A3
S100A7
UBAP2L
SLC39A1
HAX1
CREB3L4
EFNA3
AQP10
KCNN3
C1orf43
GATAD2B
ILF2
RIT1
INTS3
PKLR
HCN3
RABGAP1L
UHMK1
TADA1
CD1D
CD1A
CD1C
CD1B
CD1E
TAGLN2
SLAMF8
DUSP23
ITLN2
F11R
USF1
NIT1
DEDD
B4GALT3
ADAMTS4
NDUFS2
FCER1G
APOA2
TOMM40L
MPZ
PGLYRP3
S100A1
CHTOP
ZBTB7B
FLAD1
SHC1
ADAR
IL6R
UBE2Q1
CHRNB2
CRTC2
FDPS
RUSC1
GBAP1
FAM189B
PAQR6
PMF1
SLC25A44
LMNA
UBQLN4
GPATCH4
LRRC71
FCRL3
CADM3
SLAMF9
KCNJ9
IGSF8
DDR2
PEA15
PEX19
NCSTN
VANGL2
SLAMF6
OLFML2B
FCRLB
FCGR3B
SLC9C2
KLHDC9
LMX1A
LRRC52
PGLYRP4
S100A9
S100A12
TDRD10
C1orf189
PMVK
PBXIP1
PYGO2
LENEP
DCST2
DCST1
YY1AP1
APOA1BP
TRIM46
KRTCAP2
TSACC
CCT3
TMEM79
SSR2
FCRL4
FCRL1
SPTA1
MNDA
PYHIN1
IFI16
AIM2
THBS3
SLC50A1
EFNA1
SHE
NPR1
C1orf111
NHLH1
METTL18
RXFP4
HSPA6
MTX1
CKS1B|ENSG00000173207.8
OR10K1
SELP
CLK2
GBA
KCNJ10
RPS27
DPM3
FCER1A
ITLN1
OR6K6
OR10K2
C1orf105
FCRL6
ANKRD45
KIRREL
IQGAP3
OR10J5
S100A7A
ZBTB37
C1orf110
OR10T2
OR10X1
OR6P1
ARHGAP30
PEAR1
TTC24
C1orf204
S100A3
OR6N2
SELL
S100A16
FAM78B
C1orf192
VHLL
S100A13
S100A14
S100A4
OR6K2
OR10J1
SEMA4A
OR10J3
S100A5
S100A2
S100A7L2
OR6N1
OR6Y1
S100A6
DNM3
MPZL1
SH2D1B
C1orf85
F5
RCSD1
CD247
DENND4B
DUSP27
NOS1AP
SMG5
OR10R2
OR10Z1
RNA5SP65
RNA5SP62
RN7SKP160
RNA5SP68
SNORA58|ENSG00000201129.1
LINC00970
GPR52
METTL11B
FCGR3A
OR6K3
RNA5SP64
SNORA42|ENSG00000207475.1
MIR555
MIR556
MIR214
MIR557
MIR199A2
SNORD78|ENSG00000208317.1
MIR765
SNORD64|ENSG00000212161.1
RNA5SP63
U3|ENSG00000212538.1
SFT2D2
RPL31P11
CCDC19
DARC
ANKRD36BP1
FMO9P
TSTD1
MIR190B
MIR921
MIR1295A
MIR1255B2
RNA5SP60
LINC00626
DNM3OS
GAS5
snoU13|ENSG00000238325.1
snoU13|ENSG00000238430.1
snoU13|ENSG00000238511.1
snoU13|ENSG00000238805.1
snoU13|ENSG00000238843.1
snoU13|ENSG00000238859.1
snoU13|ENSG00000238872.1
ACA64|ENSG00000238934.1
RN7SL425P
RN7SL333P
C1orf226
RN7SL466P
BGLAP
RN7SL372P
RN7SL269P
RN7SL861P
VSIG8
EFNA4
FCGR2C
PCP4L1
OR10J4
EFNA3
snoU13|ENSG00000251817.1
RNA5SP67
SNORA26|ENSG00000252236.1
RNA5SP61
SNORD112|ENSG00000252354.1
SNORD112|ENSG00000252359.1
U3|ENSG00000252669.1
SNORD59|ENSG00000252682.1
SNORD112|ENSG00000252740.1
SCARNA4|ENSG00000252808.1
RNA5SP66
SCARNA20|ENSG00000253060.1
ETV3L
MEX3A
DCAF8
MIR5187
RN7SL44P
MIR5698
MIR4258
RN7SL431P
MIR4654
RN7SL612P
F11R
MIR92B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.1.

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

Genes
GATA3
CELF2
GDI2
MCM10
SEC61A2
PRKCQ
PFKP
KLF6
PITRM1
FAM208B
OPTN
ITIH5
FBXO18
RBM17
IL2RA
ANKRD16
ECHDC3
IL15RA
PROSER2
USP6NL
UPF2
CDC123
CCDC3
AKR1C2
ITIH2
KIN
AKR1E2
NUDT5
ATP5C1
TAF3
PFKFB3
NET1
CALML3
CALML5
TUBAL3
UCN3
DHTKD1
CAMK1D
AKR1C1
AKR1C3
AKR1CL1
ASB13
AKR1C4
SFMBT2
RN7SKP78
RNA5SP300
RNA5SP299
DKFZP667F0711
AKR1C7P
MIR548Q
LINC00703
LINC00705
SFTA1P
LINC00710
LINC00709
LINC00704
LINC00708
LINC00702
LINC00707
U8|ENSG00000238840.1
snoU13|ENSG00000238900.1
U8|ENSG00000239142.1
U8|ENSG00000239148.1
RN7SL445P
U8|ENSG00000251740.1
U8|ENSG00000251909.1
SNORA14
RNU6ATAC39P
SNORD45|ENSG00000252438.1
MIR4480
MIR3155A
RN7SL198P
MIR548AK
RN7SL232P
U6|ENSG00000272507.1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
CD44
PDHX
SLC1A2
COMMD9
CAT
PRR5L
NAT10
EHF
ELF5
CAPRIN1
APIP
PAMR1
ABTB2
TRIM44
RAG1
C11orf74
RAG2
TRAF6
LDLRAD3
FJX1
LINC00610
MIR1343
MIR3973

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q34.

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

Genes
F7
ATP11A
ANKRD10
ARHGEF7
TUBGCP3
MCF2L
F10
PCID2
PROZ
CDC16
CARS2
GRTP1
CUL4A
DCUN1D2
TMCO3
ING1
TEX29
SPACA7
ADPRHL1
UPF3A
SOX1
GAS6
TMEM255B
LAMP1
GRK1
RASA3
ATP4B
C13orf35
TFDP1
CHAMP1
SNORD44
LINC00403
LINC00354
LINC00454
LINC00452
LINC00404
LINC00453
LINC00346
LINC00567
LINC00565
MIR548AR
MIR4502

Genes in Wide Peak

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

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

Genes
CYP24A1
ZFP64
RTFDC1
SPO11
CBLN4
BCAS1
TFAP2C
AURKA
CASS4
PFDN4
DOK5
CSTF1
BMP7
RAE1
MC3R
GCNT7
CTCFL
FAM210B
FAM209A
PMEPA1
C20orf85
PCK1
ZBP1
RBM38
ZNF217
TSHZ2
RN7SKP184
FAM209B
RNA5SP487
snoU13|ENSG00000238294.1
RN7SL170P
RNU4ATAC7P
U3|ENSG00000252536.1
MTRNR2L3
MIR4532
MIR4756
MIR4325

Genes in Wide Peak

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

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

Genes
SSPO

Genes in Wide Peak

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

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

Genes
TPR
FCGR2B
SDHC
PRCC
ABL2
TPM3
ELK4
SLC45A3
MUC1
PBX1
NTRK1
MDM4
SCYL3
C1orf112
CFH
SELE
FMO3
CAMK1G
TRAF3IP3
SPRTN
METTL13
FMO1
ATP1A2
GLRX2
SLAMF7
INSRR
SH2D2A
MYOC
USH2A
ARID4B
HHAT
SOAT1
LAMC2
ATP2B4
ZC3H11A
TARBP1
TMEM206
PPP2R5A
ASPM
CD84
RRP15
IARS2
NUP133
NUCKS1
CD5L
PTGS2
RASAL2
KIFAP3
FMO4
KLHL20
PLXNA2
UBE2T
PPP1R12B
ACTN2
GPR137B
CFHR2
PTPRC
CACNA1S
PKP1
JMJD4
DUSP12
KCNK2
SERTAD4
TRAF5
IGSF9
ERO1LB
RGS1
TGFB2
GPATCH2
FMO2
SUCO
PRRX1
MARK1
TNR
CACYBP
PAPPA2
RALGPS2
ANGPTL1
FAM20B
NPHS2
QSOX1
EDEM3
SCAMP3
ASH1L
RHOU
GON4L
ARHGEF2
LAMTOR2
MEF2D
C1orf21
SWT1
IVNS1ABP
PRG4
SMG7
NCF2
PDC
PLA2G4A
RGS2
TROVE2
UCHL5
CFHR3
NR5A2
KIF21B
TMEM9
EXOC8
GNPAT
TSNAX
TBCE
NID1
LGALS8
MTR
SIPA1L2
ETV3
SLAMF1
CD48
KDM5B
UAP1
RGS4
KLHL12
RBBP5
CDK18
RAB7L1
CR2
CD46
BLZF1
CCDC181
SLC19A2
MROH9
FMO6P
PRRC2C
VAMP4
FASLG
TNFSF4
PRDX6
DARS2
HSD11B1
IRF6
DIEXF
SERPINC1
RCOR3
NEK2
NENF
NSL1
PROX1
CENPF
MARC2
KIF14
TNNT2
DDX59
CAMSAP2
ATF6
RAB3GAP2
C1orf198
TRIM67
HEATR1
TNN
MRPS14
CENPL
TNFSF18
SEC16B
GORAB
RGSL1
LHX4
RNF2
TRMT1L
FMOD
MYOG
LAX1
COPA
CD244
LY9
LPGAT1
BATF3
G0S2
PFKFB2
C4BPA
C4BPB
MSTO1
C1orf61
RGS13
FCRLA
HSD17B7
DAP3
RHBG
KIAA0907
ATP1A4
NES
BCAN
CRP
ARHGEF11
RAB25
HAPLN2
APCS
FCRL2
DCAF8
SYT11
CHI3L1
MYBPH
PIK3C2B
DSTYK
CHIT1
SLC41A1
LGR6
TMCC2
CFHR4
NAV1
CDC73
TIMM17A
CRB1
CFHR5
AGT
PCNXL2
KCNK1
URB2
EGLN1
CAPN9
COG2
ABCB10
NTPCR
TAF5L
GLUL
STX6
RGS8
RNASEL
DHX9
KIAA1614
CEP350
NPL
FAM129A
PIGC
ACBD6
LAMC1
RC3H1
EPRS
HLX
IL10
KCTD3
RPS6KC1
RASSF5
IL19
GPR161
ALDH9A1
ATP1B1
TIPRL
NME7
POGK
MPC2
CREG1
DCAF6
GPA33
RXRG
TBX19
UCK2
TMCO1
XCL1
XCL2
POU2F1
MAEL
ILDR2
DPT
MGST3
ADCY10
RFWD2
PVRL4
UFC1
PPOX
FCGR2A
NUF2
RGS5
PFDN2
NR1I3
USP21
F13B
FCRL5
RRNAD1
MRPL24
PIGM
CASQ1
ISG20L2
CRABP2
HDGF
XPR1
RGS16
TOR1AIP1
FAM163A
HMCN1
RGL1
LYPLAL1
LHX9
IKBKE
SYT14
KCNH1
DTL
DYRK3
EIF2D
INTS7
VASH2
TAF1A
SMYD2
SUSD4
DUSP10
HHIPL2
TP53BP2
ATP8B2
ADAM15
UBAP2L
HAX1
EFNA3
AQP10
KCNN3
C1orf43
RIT1
PKLR
HCN3
ACTA1
C1orf131
GALNT2
TTC13
LYST
MLK4
SNAP47
SRP9
NVL
SDE2
DEGS1
FBXO28
ARF1
LEFTY2
CNIH4
ITPKB
GUK1
CDC42BPA
CNIH3
C1orf35
PARP1
PSEN2
PYCR2
LBR
WNT9A
EPHX1
REN
SOX13
ETNK2
PPFIA4
PLEKHA6
PTPN7
SYT2
ARL8A
RGS18
NEK7
ATP6V1G3
RABGAP1L
ASTN1
PTPN14
UHMK1
TADA1
GGPS1
MR1
LINC00467
MIA3
DISP1
WNT3A
OBSCN
TRIM11
ENAH
CCSAP
SHCBP1L
NMNAT2
C1orf27
CD1D
CD1A
CD1C
CD1B
CD1E
PPP1R15B
TAGLN2
SLAMF8
DUSP23
ITLN2
F11R
USF1
NIT1
DEDD
B4GALT3
ADAMTS4
NDUFS2
FCER1G
APOA2
TOMM40L
MPZ
LAD1
TNNI1
CSRP1
ADIPOR1
CYB5R1
BTG2
ZBTB7B
FLAD1
SHC1
ADAR
IL6R
UBE2Q1
CHRNB2
FDPS
RUSC1
GBAP1
FAM189B
PAQR6
PMF1
SLC25A44
LMNA
UBQLN4
GPATCH4
LRRC71
FCRL3
B3GALT2
FAM5C
KCNT2
ZNF281
ARPC5
CADM3
SLAMF9
KCNJ9
IGSF8
DDR2
PEA15
PEX19
NCSTN
VANGL2
SLAMF6
OLFML2B
FCRLB
FCGR3B
SLC9C2
KLHDC9
C1orf74
LMX1A
LRRC52
FLVCR1
FAM71A
ATF3
AXDND1
TDRD5
IER5
BPNT1
SPATA17
C1orf115
BROX
KLHDC8A
PM20D1
B3GALNT2
C1orf147
MAPKAPK2
IL20
IL24
FAIM3
PIGR
FCAMR
CAPN2
MRPL55
C1orf145
WDR26
TRIM17
DISC1
H3F3A
ADCK3
TDRD10
C1orf189
PMVK
PBXIP1
PYGO2
LENEP
DCST2
DCST1
C1orf106
YY1AP1
APOA1BP
IGFN1
LMOD1
ELF3
TMEM183A
TRIM46
KRTCAP2
TSACC
CCT3
TMEM79
SSR2
ADORA1
SRGAP2
FCRL4
NFASC
FCRL1
NUAK2
SPTA1
MNDA
PYHIN1
IFI16
AIM2
RAB4A
HIST3H3
RNF187
GNG4
IRF2BP2
COA6
THBS3
SLC50A1
EFNA1
SHE
TOR1AIP2
GPR37L1
GPR25
LRRN2
SLC30A1
KISS1
C1orf111
NHLH1
METTL18
RXFP4
HSPA6
MTX1
CKS1B|ENSG00000173207.8
OR10K1
ARV1
APOBEC4
TOMM20
CD34
SELP
PHLDA3
SLC26A9
MFSD4
TMEM81
GOLT1A
ANGEL2
RNPEP
CLK2
LINC00303
PGBD5
GBA
TMEM78
KCNJ10
ZBTB41
C1orf65
DPM3
FCER1A
ITLN1
ZNF648
OR6K6
YOD1
OR10K2
C1orf105
FCRL6
HIST3H2A
ZNF678
IBA57
SNRPE
FAM89A
C1orf116
ACBD3
RABIF
SLC35F3
LIN9
ANKRD45
KIRREL
IQGAP3
CNTN2
OR10J5
C1ORF220
MIXL1
ZBTB37
C1orf227
DNAH14
C1orf110
PRSS38
LEMD1
AIDA
EDARADD
MARC1
TOR3A
OR10T2
OR10X1
OR6P1
ARHGAP30
TLR5
PEAR1
TTC24
C1orf204
OR6N2
SELL
LINC00083
RBM34
OPTC
PRELP
FAM78B
C1orf192
VHLL
OR6K2
OR10J1
TMEM63A
CTSE
SEMA4A
OR10J3
CD55
ESRRG
C1orf186
FAM72A
SLC30A10
LAMB3
HIST3H2BB
OR6N1
FAM177B
OR6Y1
CR1L
DNM3
MPZL1
AVPR1B
CACNA1E
RD3
SH2D1B
RYR2
IPO9
C1orf85
F5
COLGALT2
RCSD1
FAM5B
CD247
GJC2
DUSP27
TSEN15
SHISA4
NOS1AP
SMG5
OR10R2
OR10Z1
MIR135B
RNA5S12
RNA5S11
RNA5S3
RNA5S1
RNA5S5
RNA5SP71
RNA5S10
RNA5SP65
RNA5SP62
RNA5S8
RNA5S17
RNA5S4
RNA5SP74
RNA5S6
RN7SKP160
RNA5SP68
SNORA58|ENSG00000201129.1
RNA5SP72
RNA5S9
RNA5SP69
RNA5S14
RNA5SP78
SNORA16B
RNA5S2
SNORA67|ENSG00000201619.1
RNY4P16
SNORA63|ENSG00000201791.1
SNORA72|ENSG00000201898.1
RNA5S15
SNORA72|ENSG00000201944.1
RNA5SP19
RNA5SP79
RNA5S16
RNA5SP77
SNORD116|ENSG00000202498.1
RNA5S7
RNA5S13
MIR488
LINC00970
C1orf148
C1orf95
CAPN8
TATDN3
C1orf132
CR1
LINC00862
C1orf53
LINC00272
TEDDM1
GPR52
METTL11B
FCGR3A
OR6K3
SNORA70|ENSG00000206637.1
SNORA51|ENSG00000206878.1
SNORA14B
RNA5SP64
SNORA42|ENSG00000207475.1
MIR215
MIR555
MIR556
MIR181A1
MIR29B2
MIR214
MIR29C
MIR557
MIR181B1
MIR199A2
SNORD78|ENSG00000208317.1
MIR765
U8|ENSG00000212144.1
SNORD64|ENSG00000212161.1
SNORA26|ENSG00000212187.1
RNA5SP18
SNORA67|ENSG00000212338.1
RNA5SP63
U3|ENSG00000212538.1
U3|ENSG00000212610.1
MAP10
SPHAR
DENND1B
C1orf220
SFT2D2
RPL31P11
CCDC19
DARC
ANKRD36BP1
BTNL10
FMO9P
TSTD1
MIR190B
MIR921
MIR1231
MIR1182
MIR1295A
MIR320B2
MIR1255B2
RNU6ATAC35P
SNORA77|ENSG00000221643.1
U3|ENSG00000221673.1
MIR1278
RN7SKP156
SNORA36B
RN7SKP229
RNA5SP80
RNA5SP60
MIR1537
RN7SKP126
RN7SKP165
RPS10P7
LINC00184
LINC00626
C1orf143
PCAT6
LINC00582
MIR181A1HG
DNM3OS
MIR205HG
LINC00210
ASCL5
HDAC1P2
GAS5
KIAA0040
snoU13|ENSG00000238325.1
snoU13|ENSG00000238401.1
snoU13|ENSG00000238430.1
snoU13|ENSG00000238545.1
snoU13|ENSG00000238571.1
snoU13|ENSG00000238576.1
snoU109|ENSG00000238754.1
snoU13|ENSG00000238798.1
snoU13|ENSG00000238805.1
snoU13|ENSG00000238843.1
snoU13|ENSG00000238856.1
snoU13|ENSG00000238859.1
snoU13|ENSG00000238872.1
ACA64|ENSG00000238934.1
snoU13|ENSG00000238985.1
snoU13|ENSG00000239046.1
snoU13|ENSG00000239054.1
snoU13|ENSG00000239094.1
RN7SL425P
RN7SL333P
RN7SL668P
C1orf226
TEX35
RN7SL837P
RN7SL466P
RN7SL344P
BGLAP
RN7SL299P
RN7SL269P
RN7SL861P
VSIG8
PTPRVP
EFNA4
LEFTY1
RN7SL464P
MT1HL1
CFHR1
RN7SL654P
FCGR2C
PCP4L1
OR10J4
EFNA3
snoU13|ENSG00000251817.1
SCARNA20|ENSG00000251861.1
RN7SKP276
RNA5SP76
RNA5SP67
SNORA26|ENSG00000252236.1
U3|ENSG00000252241.1
RNA5SP61
SNORD112|ENSG00000252354.1
SNORD112|ENSG00000252359.1
RN7SKP195
RN7SKP49
RNA5SP73
snoU13|ENSG00000252638.1
RNA5SP75
SNORD59|ENSG00000252682.1
SNORD60|ENSG00000252692.1
SNORD112|ENSG00000252740.1
SNORD112|ENSG00000252790.1
SCARNA4|ENSG00000252808.1
SNORD112|ENSG00000252853.1
RN7SKP98
SCARNA3
SNORD112|ENSG00000252946.1
RNA5SP70
RNA5SP66
SNORA70|ENSG00000253042.1
SCARNA20|ENSG00000253060.1
RGS21
ETV3L
MEX3A
ZBED6
DCAF8
IFRG15
OCLM
MIR4753
MIR5187
RN7SL374P
RN7SL467P
RN7SL276P
MIR4258
MIR3122
MIR4671
MIR5008
RN7SL512P
MIR5191
MIR4260
RN7SL230P
MIR3620
MIR3121
MIR4427
MIR4735
MIR4654
RN7SL612P
MIR4666A
MIR4424
MIR4742
TRAX
F11R
MIR92B
U6|ENSG00000272262.1
U6|ENSG00000272292.1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

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

Genes
PIK3CA
KCNMB3
ZMAT3
KCNMB2
SNORA25|ENSG00000201957.1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.2.

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

Genes
PRKAR1A
WIPI1
CACNG5
CACNG4
CACNG1
SLC16A6
FAM20A
MAP2K6
NOL11
ARSG
ABCA8
PITPNC1
PRKCA
ABCA9
ABCA6
ABCA10
ABCA5
BPTF
KPNA2
C17orf58
AMZ2
PSMD12
HELZ
SNORA38B
RNA5SP447
SNORA8|ENSG00000207410.1
MIR635
MIR548D2
MIR634
LINC00674
snoU13|ENSG00000238612.1
RN7SL735P
RN7SL756P
RNA5SP445
RNA5SP446
SNORA40|ENSG00000252352.1
RN7SL622P
MIR4524B
LRRC37A16P

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.13.

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

Genes
AKT2
CEBPA
HSPB6
ARHGAP33
LGALS14
PAF1
DPF1
ZBTB32
TYROBP
CD22
PSMC4
MED29
SIRT2
WDR62
FXYD5
ZNF302
GRAMD1A
FXYD3
FCGBP
PLEKHG2
DLL3
KCNK6
CATSPERG
PSMD8
MAP4K1
ECH1
HNRNPL
NFKBIB
SARS2
RPS16
TIMM50
LGALS13
FBL
DYRK1B
CLC
CNTD2
GPI
PLD3
TBCB
POLR2I
OVOL3
CLIP3
APLP1
KMT2B
UPK1A
ETV2
ATP4A
TMEM147
GAPDHS
MAG
HAMP
USF2
LSR
HPN
SCN1B
SIPA1L3
ZFP30
PEPD
CHST8
LRFN3
IGFLR1
CAPNS1
PDCD2L
GPR42
RBM42
KIRREL2
UBA2
FFAR2
HCST
FFAR1
COX6B1
ZNF780B
LRFN1
ZFP36
MRPS12
FAM98C
ACTN4
PAK4
GMFG
MAP3K10
SLC7A10
LRP3
ZFP14
WTIP
CEBPG
KCTD15
ZNF599
LGI4
C19orf47
FBXO27
DMKN
U2AF1L4
NPHS1
THAP8
COX7A1
ZNF382
WDR88
KIAA0355
C19orf55
NFKBID
ZNF146
PPP1R14A
SPINT2
C19orf33
YIF1B
ZNF30
LGALS4
RASGRP4
WDR87
ZNF540
ZNF570
TTC9B
EID2
EID2B
FAM187B
LGALS7B
EIF3K
SAMD4B
GGN
SYCN
ZNF571
ZNF792
ZFP82
SYNE4
HKR1
IFNL1
CAPN12
IFNL2
PAPL
ZNF829
FFAR3
ZNF566
ZNF529
SELV
ZNF546
RINL
ZNF793
ZNF383
NCCRP1
KRTDAP
SPRED3
SBSN
ZNF567
ZNF573
ZNF527
RYR1
SUPT5H
ZNF565
ZNF781
ZNF569
ZNF585A
ZNF420
IFNL3
ZNF780A
ZNF461
ZNF181
ZNF790
ZNF607
ZNF568
LGALS7
SDHAF1
PSENEN
SCGB2B2
MIR641
LEUTX
FXYD7
LGALS17A
LINC00665
snoU13|ENSG00000238838.1
ALKBH6
RN7SL150P
RN7SL566P
RN7SL402P
ZNF585B
HAUS5
LGALS16
PRODH2
ZNF345
snoU13|ENSG00000251709.1
SNORD111|ENSG00000252230.1
ZNF260
LSM14A
MIR5196
RN7SL287P
RN7SL154P
RN7SL491P
RN7SL663P
RN7SL765P
MIR4530
FXYD1
ZNF850
LIN37
SCGB1B2P
FBXO17
LINC00904
WBP7
IFNL4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.3.

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

Genes
FAM138C

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p11.21.

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

Genes
DDX11
CAPRIN2
TSPAN11
TMTC1
IPO8
FGD4
FAM60A
METTL20
AMN1
BICD1
DENND5B
KIAA1551
H3F3C
SNORA75|ENSG00000212533.1
LINC00941
snoU13|ENSG00000238661.1
snoU13|ENSG00000239033.1
RNA5SP356
SNORA25|ENSG00000252204.1
U3|ENSG00000253052.1
STMN1P1

Genes in Wide Peak

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

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

Genes
CCNB1IP1
CMA1
PSME1
HAUS4
JPH4
MYH7
CEBPE
SLC7A8
OSGEP
SLC22A17
RNF31
HNRNPC
RPGRIP1
SUPT16H
TOX4
TGM1
TINF2
ABHD4
KHNYN
SDR39U1
CTSG
GZMH
GZMB
RBM23
PRMT5
C14orf93
PSMB5
ACIN1
APEX1
PABPN1
EFS
DHRS2
CPNE6
CHD8
PCK2
DCAF11
EMC9
PSME2
REC8
TM9SF1
GMPR2
RABGGTA
NFATC4
NGDN
RIPK3
ADCY4
RAB2B
BCL2L2
AJUBA
PARP2
NRL
RNASE1
NEDD8
DAD1
TEP1
CIDEB
TTC5
ZFHX2
CDH24
REM2
CBLN3
TSSK4
NOVA1
FITM1
OR4K1
OXA1L
SLC7A7
MMP14
DHRS4
DHRS1
OR4K2
TMEM55B
METTL17
SLC39A2
NDRG2
RNASE7
ARHGEF40
ZNF219
METTL3
SALL2
IL25
CMTM5
STXBP6
OR10G3
OR5AU1
RNASE2
RNASE3
RNASE6
OR4K14
OR4K15
MRPL52
RNASE8
RNASE11
OR11H4
OR11H6
OR4K17
OR4L1
OR4K13
OR4K5
OR4N2
OR4M1
TPPP2
C14orf119
EDDM3B
EDDM3A
OR6S1
RNASE10
OR4Q3
OR4N5
KLHL33
LRRC16B
POTEM
DHRS4L2
RNASE9
OR4Q2
IPO4
OR11G2
NOP9
LRP10
MYH6
PNP
MIR208A
SNORD9
RNA5SP383
RNA5SP382
SNORD8
NYNRIN
RNASE13
TRAV2
TRAV3
TRAV4
TRAV5
TRAV6
TRAV7
TRAV10
TRAV14DV4
TRAV16
TRAV17
TRAV18
TRAV19
TRAV20
TRAV21
TRAV22
TRAV23DV6
TRDV1
TRAV24
TRAV25
TRAV27
TRAV29DV5
TRAV34
TRAV35
TRAV36DV7
TRAV39
TRAV40
TRAV41
TRDV2
TRDJ1
TRDJ4
TRDJ2
TRDJ3
TRDC
TRAJ61
TRAJ59
TRAJ58
TRAJ57
TRAJ56
TRAJ54
TRAJ53
TRAJ52
TRAJ50
TRAJ49
TRAJ48
TRAJ47
TRAJ46
TRAJ45
TRAJ44
TRAJ43
TRAJ42
TRAJ41
TRAJ40
TRAJ39
TRAJ38
TRAJ37
TRAJ36
TRAJ35
TRAJ34
TRAJ33
TRAJ32
TRAJ31
TRAJ30
TRAJ29
TRAJ28
TRAJ27
TRAJ26
TRAJ25
TRAJ24
TRAJ23
TRAJ22
TRAJ21
TRAJ20
TRAJ19
TRAJ18
TRAJ17
TRAJ16
TRAJ14
TRAJ13
TRAJ12
TRAJ11
TRAJ10
TRAJ9
TRAJ8
TRAJ7
TRAJ6
TRAJ5
TRAJ4
TRAJ3
TRAJ2
TRAJ1
SNORD37|ENSG00000212270.1
SNORD41|ENSG00000212302.1
LTB4R
LTB4R2
MDP1
IRF9
AP1G2
ANG
HOMEZ
C14orf164
LINC00516
MIR208B
OR4E2
PSMB11
POTEG
SNORA79|ENSG00000222489.1
RN7SKP205
TRDD1
DHRS4L1
TRDD3
TRAC
TMEM253
PPP1R3E
TRDD2
SNORD126
snoU13|ENSG00000238492.1
RN7SL189P
RNA5SP381
SNORA73|ENSG00000252114.1
RNA5SP380
CHMP4A
TM9SF1
OR10G2
OR6J1
TRDV3
OR11H12
MED15P6
MED15P1
RNASE12
LINC00641
OR11H7
RNASE4
RPPH1
TRAV30
LINC00596
THTPA
RN7SL650P
MIR4707

Genes in Wide Peak

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

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

Genes
TSC2
SOX8
RPUSD1
RHBDF1
LUC7L
BAIAP3
TSR3
PIGQ
CRAMP1L
PKD1
UNKL
HAGH
SLC9A3R2
NTHL1
MRPS34
RGS11
MRPL28
HBQ1
RAB11FIP3
GNPTG
NUBP2
TPSD1
IGFALS
TELO2
MSLN
NME3
AXIN1
NPRL3
MPG
NME4
LMF1
NARFL
CLCN7
HAGHL
FAM173A
METRN
STUB1
RHBDL1
UBE2I
CAPN15
TCEB2
TPSG1
GFER
SYNGR3
WFIKKN1
WDR24
FBXL16
CHTF18
GNG13
TMEM8A
HBZ
C16orf13
TMEM204
TRAF7
MAPK8IP3
RHOT2
RPL3L
RPS2
NDUFB10
PDPK1
POLR3K
SNRNP25
C16orf11
WDR90
JMJD8
CCDC78
MSLNL
SSTR5
SPSB3
MEIOB
HS3ST6
C16orf59
CCNF
TBC1D24
AMDHD2
NTN3
ITFG3
PRR25
ZNF598
RAB26
MLST8
E4F1
DNASE1L2
ECI1
CASKIN1
ABCA3
KCTD5
SRRM2
TPSAB1
FAM195A
PRSS27
C16orf91
RNF151
FAHD1
BRICD5
TBL3
NPW
PGP
C1QTNF8
PDIA2
ATP6V0C
IFT140
HBA2
PRSS29P
NOXO1
CACNA1H
TPSB2
RAB40C
CCDC154
EME2
MSRB1
PDPK2
CEMP1
RNPS1
HN1L
HBA1
HBM
SNORD60|ENSG00000206630.1
SNORA10
SNORA64|ENSG00000207405.1
MIR662
MIR1225
WASIR2
DDX11L10
WASH4P
ABCA17P
ARHGDIG
DECR2
PTX4
SNHG9
NHLRC4
ATP6C
MIR940
RN7SL367P
MIR4717
RN7SL219P
MIR3177
MIR4516
MIR5587
MIR3178
MIR3176
MIR3677
ITFG3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q11.1.

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

Genes
INPP4A
MGAT4A
TMEM131
STARD7
KANSL3
LMAN2L
KCNIP3
FAHD2A
ACTR1B
ZAP70
UNC50
TXNDC9
NCAPH
COX5B
TSGA10
TMEM127
ANKRD36
TRIM43
CIAO1
ZNF514
SNRNP200
MRPS5
LIPT1
CNGA3
FAHD2B
LYG1
PROM2
DUSP2
CNNM4
MITD1
EIF5B
TEKT4
ZNF2
NEURL3
ANKRD23
VWA3B
FAM178B
SEMA4C
CNNM3
MAL
ANKRD36C
COA5
MRPL30
LYG2
GPAT2
ASTL
ARID5A
KIAA1211L
ANKRD36B
ITPRIPL1
ANKRD39
ADRA2B
ANKRD20A8P
FLJ14082
FAHD2CP
LINC00342
snoU13|ENSG00000238760.1
C2orf15
RN7SL313P
RN7SL575P
RN7SL210P
FER1L5
RNA5SP101
MIR3127

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
CRTC3
IDH2
BLM
MEF2A
TTC23
VIMP
CHSY1
SNRPA1
IGF1R
ARRDC4
ADAMTS17
LINS
PCSK6
HAPLN3
RHCG
POLG
RLBP1
FANCI
ABHD2
WDR93
TICRR
DET1
MFGE8
ZNF710
UNC45A
ST8SIA2
MCTP2
FURIN
IQGAP1
CERS3
LRRK1
ACAN
AP3S2
KIF7
PLIN1
PEX11A
MESP1
ANPEP
RCCD1
LRRC28
ISG20
CHD2
SLCO3A1
OR4F4
AEN
MRPS11
RGMA
SYNM
DNM1P46
FES
NGRN
OR4F15
LYSMD4
GDPGP1
ASB7
PGPEP1L
C15orf32
VPS33B
OR4F6
ALDH1A3
TM2D3
HDDC3
SEMA4B
CIB1
FAM169B
TARSL2
FAM174B
SV2B
NR2F2
SPATA8
WASH3P
MESP2
SPATA41
ZNF774
MAN2A2
PRC1
SNORD18|ENSG00000200677.1
TTLL13
OR4F13P
DKFZP779J2370
MIR1179
RN7SKP254
MIR1469
RN7SKP181
GABARAPL3
snoU13|ENSG00000238502.1
snoU13|ENSG00000238981.1
snoU109|ENSG00000239197.1
RN7SL346P
RN7SL209P
RN7SL484P
RN7SL363P
C15orf38
RN7SL736P
RN7SL677P
DDX11L9
FAM138E
LINC00923
RNA5SP401
RNA5SP402
LINC00925
LINC00930
LINC00924
LINC00928
MRPL46
DNM1P47
RN7SL755P
RN7SL599P
MIR3175
MIR4714
MIR5009
MIR5094
MIR3174

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MPL
MUTYH
SCMH1
GUCA2B
YBX1
TIE1
KDM4A
NFYC
ZMYND12
ELOVL1
TESK2
EIF2B3
SMAP2
ZNF684
KCNQ4
RIMS3
LEPRE1
SLC2A1
EBNA1BP2
CDC20
ARTN
IPO13
ATP6V0B
B4GALT2
ERI3
PTCH2
AKR1A1
PRDX1
UROD
ST3GAL3
TMEM53
HECTD3
HIVEP3
PPCS
EDN2
MMACHC
DPH2
TOE1
NASP
RPS8
KIF2C
PTPRF
BEST4
CCDC24
MED8
CCDC17
GPBP1L1
ZSWIM5
EXO5
CLDN19
C1orf50
ERMAP
ZNF691
SLFNL1
CTPS1
KLF17
PPIH
PLK3
RIMKLA
CCDC23
DMAP1
HYI
TMEM125
CITED4
CCDC30
HPDL
FAM183A
RNF220
ZFP69B
ZFP69
TCTEX1D4
SLC6A9
GUCA2A
SZT2
C1orf228
FOXJ3
MIR30E
RNA5SP46
SNORD46|ENSG00000200913.1
SNORD38A
FOXO6
SNORD38B
MIR30C1
BTBD19
CCDC163P
snoU13|ENSG00000238945.1
RN7SL479P
WDR65
RNA5SP45
RNA5SP47
C1orf210
MIR5584
SNORD55
RN7SL326P

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.31.

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

Genes
MIR412
MIR377
MIR381
MIR369
MIR410
MIR409
MIR539
MIR487A
MIR544A
MIR655
MIR382
MIR487B
MIR654
MIR656
MIR496
MIR154
MIR134
MIR323B
MIR485
MIR300
MIR889
MIR541
MIR381HG
MIR376A1
MIR376C

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p35.2.

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

Genes
HCRTR1
TINAGL1
PEF1

Genes in Wide Peak

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

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

Genes
FANCE
TFEB
CCND3
DEK
PIM1
IRF4
HMGA1
HIST1H4I
DAXX
POU5F1
TRIM27
GCLC
NFYA
ENPP4
TEAD3
MYLIP
JARID2
TFAP2B
TFAP2D
RANBP9
ETV7
HFE
ELOVL5
SERPINB1
DEF6
UBR2
BTN3A1
BAK1
CENPQ
CUL7
DTNBP1
MRPS10
GUCA1A
MCUR1
FOXC1
TAF11
ANKS1A
ZNF76
UHRF1BP1
TRAM2
TBC1D22B
ZNRD1
GPR116
EDN1
SCGN
LRRC16A
HIVEP1
TREM2
KCNK16
CRISP3
FKBP5
SRPK1
BRPF3
MRPS18A
PGC
TMEM14A
EFHC1
NCR2
HSP90AB1
MLN
CDC5L
ITPR3
ZNF184
DSP
BTN3A3
TDP2
MAK
TMEM14C
PAK1IP1
GCNT2
NEDD9
ADTRP
FAM65B
PPARD
TULP1
SLC26A8
MAPK14
RHAG
KCTD20
STK38
SRSF3
IL17A
IL17F
MCM3
RNF8
PHACTR1
MDGA1
ICK
FBXO9
CD83
GLP1R
SAYSD1
BMP5
RBM24
CAP2
TREML2
ZNF451
BAG2
RAB23
TSPO2
KHDRBS2
E2F3
PTP4A1
HDGFL1
GPLD1
ALDH5A1
ACOT13
C6orf62
GMNN
SLC17A2
TRIM38
OR12D3
SLC39A7
PHF1
CUTA
MDFI
BYSL
GUCA1B
PRPH2
GLTSCR1L
PPP2R5D
MRPL2
PTK7
SRF
CUL9
DNPH1
DUSP22
EXOC2
GMDS
VEGFA
PRPF4B
SLC29A1
BTN2A1
CLIC5
ENPP5
LY86
PRSS16
MEP1A
PHF3
CRISP2
F13A1
GRM4
TRERF1
PACSIN1
BTN2A2
SIRT5
HIST1H4B
MRS2
WRNIP1
RRP36
BTN2A3P
BTN1A1
SNRPC
SLC17A3
SLC17A1
SERPINB6
XPO5
ABCC10
HIST1H1D
HIST1H4G
PEX6
NQO2
PRICKLE4
OARD1
UNC5CL
AARS2
HIST1H1A
ZNF391
RPS10
MOCS1
HIST1H2BJ
MED20
OR2B6
TBCC
SPDEF
TCP11
MAD2L1BP
HIST1H3B
APOBEC2
KLHDC3
GNMT
DNAH8
TREM1
MEA1
KLHL31
COL21A1
CDKN1A
SOX4
GLO1
CPNE5
KCNK17
RREB1
SSR1
RIOK1
NRN1
SLC35B3
RPP40
ATXN1
NUP153
EEF1E1
CRISP1
RUNX2
OPN5
GCM2
CNPY3
FOXP4
PPIL1
KLC4
KIF13A
ZSCAN9
GMPR
FTSJD2
TFAP2A
SLC22A7
YIPF3
TMEM14B
TMEM63B
FRS3
TJAP1
CAPN11
TINAG
HCRTR2
HIST1H2AB
KIAA0319
SLC22A23
TUBB2A
LRRC1
GCM1
FOXF2
BPHL
RIPK1
TUBB2B
MNF1
TCF19
FLOT1
IER3
MDC1
PGBD1
ATAT1
TPMT
CLPS
RNF144B
NRM
MTCH1
VARS2
TAF8
FAM8A1
C6orf52
FAM50B
MYLK4
C6ORF50
FAM217A
TBC1D7
FARS2
GFOD1
CDKAL1
DCDC2
SLC17A4
HIST1H2BA
KAAG1
PLA2G7
TNFRSF21
MUT
ABT1
PPP1R18
DAAM2
PRIM2
MLIP
HMGCLL1
LGSN
FGD2
SCUBE3
CRIP3
TTBK1
TCTE1
RPL7L1
NFKBIE
CYP39A1
DST
BEND6
NRSN1
CDYL
SYCP2L
BMP6
SLC25A27
GPR110
GPR115
LRFN2
ZFAND3
MAPK13
ARMC12
SLC35B2
HIST1H2BD
HIST1H4H
POM121L2
ZSCAN12
IP6K3
LEMD2
TREML1
ADCY10P1
CAGE1
FOXQ1
C6orf195
GPR111
HIST1H2AA
PI16
KCNK5
KIF6
USP49
KDM1B
C2
KIAA1586
OR2B2
FAM83B
HIST1H2BI
HIST1H2AE
HIST1H1E
TAP1
CMAHP
TNXB
SNRNP48
DPCR1
OR12D2
PXDC1
SERPINB9
POLH
GSTA4
PAQR8
PKHD1
PGK2
POLR1C
DLK2
ZNF318
PTCRA
PRL
MBOAT1
ID4
RCAN2
RSPH9
GTPBP2
TMEM217
GSTA3
DEFB114
TMEM151B
PXT1
TDRD6
PNPLA1
RNF182
HIST1H2AC
HIST1H2BC
PSMG4
DEFB112
MRPL14
ZNF322
OFCC1
C6orf223
HIST1H3I
HIST1H2AJ
GSTA5
HMGN4
LINC00518
BTBD9
TREML3P
HIST1H2AK
HIST1H1B
HIST1H2AH
HIST1H2BL
C6orf201
BTN3A2
C6orf1
HIST1H1T
NHLRC1
ZKSCAN4
HIST1H1C
GFRAL
ZSCAN23
HIST1H2BG
TREML4
C6orf132
BLOC1S5
HIST1H4D
HUS1B
NKAPL
ZKSCAN3
C6orf222
HIST1H4A
HIST1H2BB
TUBB
SFTA2
SUPT3H
HIST1H2BO
HIST1H2BM
HIST1H3C
HIST1H2AI
CLPSL2
HIST1H2AG
ZSCAN16
C6orf106
HIST1H2AD
HIST1H3E
HIST1H4C
HIST1H3J
HIST1H4J
LINC00336
C6orf141
ZNF165
SYNGAP1
HIST1H3D
HIST1H2BH
HIST1H2BE
LHFPL5
HIST1H2BF
HIST1H2BK
HIST1H4K
ZNF311
ELOVL2
CD2AP
FKBP1C
ZKSCAN8
HIST1H4F
HIST1H3A
HIST1H2AL
HIST1H4E
HIST1H4L
DDX39B
C6orf89
GPX6
ECI2
RPL10A
CCDC167
MIR133B
U3|ENSG00000199851.1
SNORD45|ENSG00000200706.1
SNORA38|ENSG00000200816.1
RNA5SP202
SNORD32B
RNA5SP204
RNA5SP205
SNORD52
SNORD117
SNORD48
RN7SK
RN7SKP186
RN7SKP204
RNY4P10
HIST1H3H
DEFB110
GLYATL3
LRRC73
TDRG1
LINC00951
CLPSL1
GGNBP1
PFDN6
RING1
HSD17B8
RXRB
COL11A2
BRD2
PSMB8
TAP2
BTNL2
C6orf10
NOTCH4
PBX2
AGER
RNF5
AGPAT1
PRRT1
FKBPL
CYP21A1P
STK19
DOM3Z
SKIV2L
NELFE
ZBTB12
EHMT2
SLC44A4
NEU1
C6orf48
HSPA1B
HSPA1A
HSPA1L
LSM2
VARS
VWA7
MSH5
C6orf25
LY6G6C
LY6G6F
ABHD16A
LY6G5C
CSNK2B
GPANK1
C6orf47
APOM
BAG6
PRRC2A
AIF1
NCR3
LST1
NFKBIL1
MCCD1
MICB
MICA
PSORS1C3
CCHCR1
PSORS1C2
CDSN
PSORS1C1
C6orf15
MUC21
DHX16
C6orf136
MRPS18B
PPP1R10
ABCF1
PRR3
DDR1
GNL1
TRIM39
TRIM15
TRIM10
TRIM40
TRIM31
RNF39
PPP1R11
HCG9
ZFP57
MOG
OR2H2
GABBR1
MAS1L
OR2H1
OR11A1
OR14J1
OR2J2
OR2J3
OR2J1
OR2B3
OR2W1
C6orf100
TMEM170B
GCNT6
HCP5
HCG27
OR10C1
SNORA8|ENSG00000206977.1
SNORA67|ENSG00000207419.1
MIR206
MIR586
MIR548A1
MIR548U
RNA5SP207
SNORD66|ENSG00000212532.1
SNORA40|ENSG00000212579.1
SNORA8|ENSG00000212586.1
ZBTB9
GPSM3
ATF6B
CLIC1
DDAH2
ATP6V1G2
GTF2H4
UBD
LYRM4
DEFB113
DEFB133
TOMM6
LINC00243
LINC00680
MIR877
PPP1R3G
ZSCAN12P1
U3|ENSG00000221252.1
MIR1236
RNU6ATAC21P
MIR1275
C6orf226
PPT2
RNA5SP201
RNY5P5
RNA5SP203
RN7SKP240
RN7SKP293
VPS52
HCG14
C4B
SMIM13
GPX5
LINC00240
NOL7
ZNF192P1
COX6A1P2
LTA
WDR46
HCG15
LTB
HCG20
HCG11
SAPCD1
HCG22
HCG23
ANKRD66
HCG24
STMND1
HCG18
RPS18
CYP21A2
TAPBP
SCAND3
TNF
HCG25
HIST1H2AM
HCG21
HIST1H2BN
TRIM26
PPP1R2P1
ZSCAN31
LINC00533
B3GALT4
ZBTB22
RGL2
KIFC1
snoU13|ENSG00000238322.1
snoU13|ENSG00000238375.1
snoU13|ENSG00000238438.1
snoU13|ENSG00000238458.1
snoU13|ENSG00000238484.1
snoU13|ENSG00000238611.1
TRNAI2
TRNAI6
snoU13|ENSG00000238801.1
snoU13|ENSG00000238896.1
snoU13|ENSG00000239059.1
TXNDC5
RN7SL221P
RN7SL273P
RN7SL748P
LY6G5B
PSMB9
RN7SL403P
RN7SL580P
RN7SL502P
RN7SL128P
RN7SL554P
RPP21
EGFL8
GUSBP2
RN7SL26P
RN7SL244P
RN7SL332P
RN7SL285P
RN7SL352P
CFB
OR5V1
GSTA1
GSTA2
CFB
RN7SL465P
HCG16
LY6G6D
RN7SL334P
PTCHD4
C4A
SPATS1
TAP2
MEGT1
HULC
OR12D1P
snoU13|ENSG00000251762.1
U3|ENSG00000251793.1
SNORD46|ENSG00000251830.1
U3|ENSG00000251930.1
SCARNA15|ENSG00000252218.1
SNORA48|ENSG00000252228.1
RMRPP2
RNA5SP206
snoU13|ENSG00000252668.1
SNORD112|ENSG00000252687.1
RN7SKP116
RN7SKP256
LY6G6E
RAB44
MTRNR2L9
HIST1H3G
HIST1H3F
MUC22
RN7SL471P
MIR5683
RN7SL353P
MIR3135B
MIR5689
MIR4639
MIR3925
MIR4462
MIR5685
MIR5004
MIR4640
RN7SL175P
MIR3691
RN7SL200P
SNORD84
MIR5690
MIR3143
MIR4647
MIR4641
MIR3934
MIR4642
MIR4645
MIR4646
SBP1
HCG17
LINC00340
NUDT3
TMEM151B

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 - 53 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
--- | --- | --- | --- | ---
2q11.2 | 2.5799e-58 | 2.9385e-56 | chr2:99815771-100022927 | 4
19q13.11 | 1.9087e-69 | 2.9314e-53 | chr19:33445752-33635793 | 3
7q11.23 | 6.6878e-33 | 3.5841e-31 | chr7:74867286-75038052 | 1
15q12 | 8.1146e-55 | 7.7715e-30 | chr15:27044063-27233912 | 1
15q11.2 | 4.5518e-46 | 1.3215e-27 | chr15:25342050-25543337 | 2
11q13.3 | 4.533e-39 | 3.7655e-26 | chr11:69589684-70049708 | 2
16q22.1 | 5.3502e-23 | 6.4928e-22 | chr16:67002965-67144110 | 3
4q25 | 3.8865e-18 | 2.2061e-16 | chr4:113435945-113970926 | 7
6p22.1 | 1.6717e-14 | 1.6717e-14 | chr6:27370258-27925489 | 19
19p13.2 | 1.3832e-18 | 8.8797e-14 | chr19:8940927-9214221 | 4
1p36.21 | 1.8666e-11 | 1.8666e-11 | chr1:12677257-17346451 | 78
8p23.1 | 6.8189e-18 | 1.4637e-10 | chr8:1-8650017 | 57
11q22.3 | 7.8663e-13 | 6.6939e-10 | chr11:100837270-126300387 | 288
6q26 | 1.8676e-09 | 1.9081e-09 | chr6:160931352-161127530 | 1
17p13.1 | 2.6957e-09 | 2.6957e-09 | chr17:10101617-11502159 | 14
19q13.42 | 1.5188e-12 | 2.9854e-09 | chr19:53885534-54385653 | 51
11p15.5 | 2.3976e-07 | 3.5611e-07 | chr11:1-470166 | 17
8p21.2 | 1.1138e-14 | 4.5414e-05 | chr8:24350073-25111178 | 3
5q13.2 | 5.8426e-05 | 5.8426e-05 | chr5:68721792-70888563 | 17
11q13.4 | 5.7596e-08 | 5.8426e-05 | chr11:70858270-71432906 | 3
12q24.21 | 1.9469e-07 | 7.9926e-05 | chr12:116280850-117002527 | 4
19p12 | 5.8793e-13 | 9.0561e-05 | chr19:19788737-23494464 | 35
3p14.3 | 0.00046358 | 0.00046358 | chr3:49934011-78174118 | 203
9p21.3 | 0.00051218 | 0.00048739 | chr9:20613198-26806001 | 36
12p13.31 | 1.1734e-05 | 0.00057864 | chr12:7857368-8224886 | 9
4q33 | 2.3986e-05 | 0.00081881 | chr4:170191694-170549655 | 1
1q25.1 | 4.1592e-05 | 0.0010767 | chr1:174985330-175134711 | 1
17q21.2 | 0.0017976 | 0.0018162 | chr17:39140303-45286757 | 176
4p15.32 | 0.0060174 | 0.0057187 | chr4:1-41263759 | 248
12p13.2 | 0.00020333 | 0.010977 | chr12:11144954-12232453 | 13
7q22.1 | 2.8656e-06 | 0.013587 | chr7:99801692-99974170 | 4
16q11.2 | 2.9267e-06 | 0.014153 | chr16:46806531-46992839 | 2
9q22.32 | 0.011689 | 0.015349 | chr9:99060722-99219443 | 2
18q21.33 | 0.015094 | 0.015349 | chr18:59559987-59994420 | 2
19p13.2 | 6.055e-07 | 0.019426 | chr19:11836080-12126569 | 9
3q29 | 0.021155 | 0.020638 | chr3:194071059-198022430 | 57
14q31.3 | 0.023754 | 0.023828 | chr14:52734136-104559790 | 495
2q22.3 | 8.6777e-07 | 0.025679 | chr2:145088480-148693935 | 6
20p11.1 | 0.030003 | 0.029455 | chr20:25834498-29900943 | 6
13q12.11 | 0.0021068 | 0.04294 | chr13:1-21720943 | 31
12q24.11 | 9.0561e-05 | 0.048944 | chr12:111323829-111783681 | 2
10p13 | 0.055863 | 0.058713 | chr10:11375582-32740709 | 157
19q13.2 | 0.0001329 | 0.08149 | chr19:40513357-40704370 | 2
1q42.13 | 0.013587 | 0.096339 | chr1:228346121-228806043 | 32
10q21.3 | 0.10905 | 0.11098 | chr10:54053539-135534747 | 623
11p11.12 | 0.050944 | 0.11802 | chr11:48371312-56043604 | 39
13q14.3 | 0.00015279 | 0.13182 | chr13:40343187-70682555 | 172
13q21.32 | 0.00057864 | 0.15975 | chr13:31703605-110386848 | 390
18p11.31 | 0.19624 | 0.19648 | chr18:2893532-5145656 | 11
19p13.3 | 0.00055785 | 0.19648 | chr19:1-3366920 | 117
22q11.1 | 0.19624 | 0.19648 | chr22:1-18264873 | 23
16p13.12 | 0.1621 | 0.21594 | chr16:11749102-30366810 | 217
9q34.13 | 0.16518 | 0.23266 | chr9:130904022-141213431 | 241

Genes in Wide Peak

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

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

Genes
TXNDC9
LYG1
EIF5B
LYG2

Genes in Wide Peak

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

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

Genes
GPATCH1
RHPN2
C19orf40

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.23.

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

Genes
STAG3L1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

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

Genes
GABRA5

Genes in Wide Peak

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

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

Genes
SNORD115|ENSG00000212428.1
SNORD109B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q13.3.

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

Genes
ANO1
FGF3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.1.

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

Genes
CBFB
CES4A
RN7SL543P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q25.

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

Genes
C4orf21
LARP7
MIR302C
MIR302D
MIR367
MIR302A
MIR302B

Genes in Wide Peak

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

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

Genes
ZNF184
OR2B2
HIST1H3I
HIST1H2AJ
HIST1H2AK
HIST1H1B
HIST1H2BL
HIST1H2BO
HIST1H2BM
HIST1H2AI
HIST1H3J
HIST1H4J
HIST1H4K
HIST1H2AL
HIST1H4L
HIST1H3H
HIST1H2AM
HIST1H2BN
TRNAI6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

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

Genes
OR7G2
OR1M1
MBD3L1
MUC16

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.21.

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

Genes
FBXO42
SZRD1
CROCC
SPEN
CROCCP3
DNAJC16
PRAMEF1
PRAMEF12
PRDM2
AGMAT
PLEKHM2
ZBTB17
MFAP2
PRAMEF2
RSG1
CASP9
CELA2A
FHAD1
EPHA2
ARHGEF19
EFHD2
NECAP2
C1orf158
PRAMEF15
ATP13A2
CTRC
FBLIM1
TMEM82
SLC25A34
PDPN
LRRC38
TMEM51
HSPB7
HNRNPCL1
PRAMEF8
C1orf64
CLCNKB
FAM131C
CLCNKA
MST1L
SPATA21
PRAMEF10
AADACL3
KAZN
DDI2
C1orf134
C1orf195
PRAMEF20
PRAMEF17
PRAMEF19
PRAMEF14
PRAMEF21
PRAMEF16
PRAMEF18
PRAMEF13
PRAMEF9
PRAMEF5
PRAMEF3
PRAMEF22
PRAMEF7
PRAMEF11
AADACL4
RSC1A1
CELA2B
CROCCP2
NBPF1
RNA5SP41
U1|ENSG00000228549.2
PRAMEF6
U1|ENSG00000233421.3
ANO7P1
snoU13|ENSG00000238771.1
snoU13|ENSG00000238818.1
PRAMEF4
SCARNA21|ENSG00000251866.1
SCARNA11|ENSG00000253085.1
MIR3675
ESPNP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.1.

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

Genes
MYOM2
ANGPT2
ERICH1
ARHGEF10
MCPH1
FBXO25
AGPAT5
DEFA5
DEFA4
DEFA6
DEFB1
SPAG11B
DEFB4A
ZNF596
FAM86B3P
OR4F21
KBTBD11
DEFB104A
DEFB103A
DEFB104B
DEFB103B
DEFB4B
SPAG11A
TDRP
SGK223
CLN8
CSMD1
XKR5
DEFB105A
DEFB107A
DEFB106A
DEFB105B
DEFB106B
DLGAP2
DEFB107B
DEFA1
SNORA70|ENSG00000206661.1
MIR596
FAM90A24P
ZNF705B
ZNF705G
FAM66B
MIR548I3
RNA5SP251
RN7SKP159
RPL23AP53
FAM66E
DEFA3
DEFA1B
RN7SL318P
FAM85B
CLDN23
ALG1L13P
RN7SL178P
RN7SL872P
MIR4659A
LRLE1

Genes in Wide Peak

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

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

Genes
BIRC3
DDX6
CBL
POU2AF1
ATM
PCSK7
PAFAH1B2
DDX10
ARHGEF12
SDHD
SDHD
VSIG2
PHLDB1
GRAMD1B
USP2
USP28
SPA17
CDON
ACAT1
REXO2
RBM7
MCAM
PGR
ZW10
ALG9
NXPE1
ARCN1
DDX25
CRYAB
ZBTB16
ZNF259
TECTA
SC5D
CRTAM
C11orf63
HSPA8
VWA5A
SIAE
PUS3
DCPS
FOXRED1
APOA5
APOA4
APOC3
CEP164
KIAA1377
IL10RA
BIRC2
UBE4A
MMP12
UPK2
PVRL1
SLC35F2
ELMOD1
EXPH5
KMT2A
TREH
IFT46
MMP8
APOA1
RPS25
MSANTD2
STT3A
ACRV1
SLC37A2
NXPE4
SORL1
TMPRSS4
BUD13
TRPC6
MMP7
MMP20
MMP27
C11orf70
DCUN1D5
YAP1
TRIM29
SLC37A4
BTG4
POU2F3
RDX
PPP2R1B
FDX1
C11orf1
FXYD6
ARHGAP20
FXYD2
MMP13
TMPRSS13
CASP1
CASP5
ALKBH8
ZC3H12C
TTC12
NCAM1
DRD2
C11orf52
HTR3B
NPAT
AASDHPPT
GRIK4
HYOU1
EI24
CCDC15
CHEK1
FEZ1
ESAM
MPZL2
SCN2B
SIDT2
TMEM25
TAGLN
MMP3
TMEM218
TIRAP
C11orf53
DIXDC1
DLAT
PIH1D2
C11orf57
TIMM8B
IL18
TEX12
PTS
GUCY1A2
CWF19L2
TMEM123
GRIA4
THY1
TBCEL
UBASH3B
ROBO4
ROBO3
PANX3
TBRG1
NRGN
SIK3
MPZL3
AMICA1
CD3G
CXCR5
VPS11
NLRX1
HEPACAM
PKNOX2
RPUSD4
CLMP
SCN3B
ZNF202
CUL5
C11orf65
MMP10
TMPRSS5
HTR3A
NNMT
RNF214
ATP5L
CD3D
SIK2
ANKK1
HSPB2
SLN
TMEM133
MSANTD4
OR8B12
PDGFD
DDI1
OR4D5
PATE1
DPAGT1
HINFP
ABCG4
PDZD3
C2CD2L
TTC36
RNF26
FOXR1
SCN4B
DSCAML1
KDELC2
RAB39A
C11orf71
TMEM136
OR6T1
OR8D4
KBTBD3
OR10G7
SRPR
CADM1
C11orf88
OAF
C11orf87
CCDC84
BCL9L
BACE1
ANGPTL5
DYNC2H1
KRT18P59
H2AFX
C11orf34
BSX
OR6M1
OR8A1
C11orf92
OR10S1
OR8D1
MMP1
TRAPPC4
OR8B3
PATE2
CASP4
OR8B8
OR8D2
OR10D3
BCO2
FAM118B
HYLS1
OR8B4
CD3E
MIRLET7A2
RNA5SP350
RNA5SP352
U8|ENSG00000200496.1
RNY4P6
RNA5SP349
SNORD14E
SNORD14C
OR8B2
TMEM225
NXPE2
LAYN
CARD16
CASP12
SNORD14D
MIR34C
MIR34B
MIR125B1
MIR100
snosnR66
C11orf93
OR6X1
HEPN1
RN7SKP273
C1QTNF5
CLDN25
OR10G8
MFRP
PATE3
OR10G9
PATE4
snoU13|ENSG00000238625.1
snoU13|ENSG00000238724.1
snoU13|ENSG00000238855.1
RNA5SP351
snoU13|ENSG00000239079.1
snoU13|ENSG00000239153.1
snoU13|ENSG00000239154.1
RN7SL688P
RN7SL351P
RN7SL529P
LINC00900
CCDC153
ACA64|ENSG00000252119.1
RNA5SP348
snoU13|ENSG00000252679.1
RNU4ATAC10P
ACA59|ENSG00000252870.1
SCARNA11|ENSG00000252992.1
RNU4ATAC5P
OR10G4
CARD17
WTAPP1
CARD18
FDXACB1
ATF4P4
HMBS
ALG9
MFRP
BLID
MIR3920
RN7SL86P
MIR4491
MIR4693
MIR4492
SNORD39|ENSG00000264997.1
MIR4301
MIR4493
MIR3656

Genes in Wide Peak

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

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

Genes
LPA

Genes in Wide Peak

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

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

Genes
MYH13
MYH1
MYH3
MYH2
MYH8
SCO1
ADPRM
TMEM220
SHISA6
PIRT
RN7SL601P
LINC00675
MAGOH2
MYH4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.42.

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

Genes
ZNF331
NLRP12
ZNF761
MYADM
ZNF765
ZNF813
MIR371A
MIR372
MIR373
DPRX
MIR518C
MIR520F
MIR526B
MIR520A
MIR520E
MIR516A2
MIR526A1
MIR518A2
MIR518F
MIR525
MIR520B
MIR517A
MIR520D
MIR520C
MIR518D
MIR516A1
MIR519C
MIR520G
MIR518A1
MIR522
MIR519E
MIR519B
MIR517B
MIR517C
MIR520H
MIR518B
MIR498
MIR516B2
MIR516B1
MIR524
MIR527
MIR519D
MIR518E
MIR519A1
MIR523
MIR526A2
MIR1323
TPM3P9
RN7SL317P
MIR519A2
MIR371B

Genes in Wide Peak

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

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

Genes
SIRT3
IFITM3
ATHL1
NLRP6
ODF3
BET1L
RIC8A
B4GALNT4
PKP3
ANO9
SIGIRR
IFITM2
PSMD13
IFITM1
SCGB1C1
IFITM5
RN7SL838P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

Genes
NEFM
NEFL
RN7SL651P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.2.

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

Genes
BDP1
GTF2H2
PMCHL2
SERF1A
SMN1
GTF2H2C
OCLN
SMN2
SERF1B
GTF2H2B
snoU13|ENSG00000238451.1
snoU13|ENSG00000238740.1
NAIP
GUSBP3
RN7SL476P
RN7SL9P
RN7SL616P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q13.4.

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

Genes
NADSYN1
DHCR7
UNC93B6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.21.

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

Genes
MED13L
LINC00173
SNORD56|ENSG00000200112.1
MIR620

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p12.

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

Genes
ZNF506
ZNF14
ZNF85
ZNF430
ZNF66
ZNF208
ZNF714
ZNF738
ZNF708
ZNF730
ZNF93
ZNF626
ZNF724P
ZNF676
ZNF493
ZNF729
ZNF431
ZNF429
ZNF100
ZNF682
ZNF257
ZNF98
ZNF43
RNA5SP469
ZNF99
ZNF90
ZNF492
ZNF826P
ZNF737
RN7SL860P
ZNF486
ZNF253
LINC00663
LINC00664
ZNF728

Genes in Wide Peak

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

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

Genes
FOXP1
BAP1
PBRM1
MITF
FHIT
SEMA3F
RBM5
RBM6
ZMYND10
CACNA2D2
PHF7
SEMA3G
NISCH
STAB1
SEMA3B
CHDH
GLT8D1
ALAS1
PARP3
ITIH4
ITIH1
IL17RB
HYAL2
RASSF1
DOCK3
C3orf18
PCBP4
CNTN3
SELK
ACTR8
WNT5A
GNAT1
GNAI2
HYAL1
TUSC2
NPRL2
CYB561D2
C3orf14
FRMD4B
HEMK1
CISH
MAPKAPK3
RRP9
ABHD14B
DNAH1
TNNC1
SPCS1
NEK4
PDZRN3
TMEM115
FLNB
PTPRG
IL17RD
SHQ1
SLC25A26
UBA3
ARL6IP5
TMF1
LRIG1
LRTM1
VPRBP
MANF
MAGI1
FEZF2
CACNA1D
CACNA2D3
APPL1
RPL29
ITIH3
DCP1A
KBTBD8
FAM19A4
EOGT
LMOD3
EIF4E3
PROK2
RYBP
PPP4R2
CADPS
SYNPR
C3orf49
THOC7
ATXN7
PSMD6
PRICKLE2
ADAMTS9
HESX1
SLMAP
RPP14
ABHD6
DNASE1L3
C3orf67
TKT
PRKCD
RFT1
SFMBT1
GNL3
FAM208A
ARHGEF3
MON1A
RAD54L2
TEX264
GRM2
DUSP7
POC1A
PPM1M
WDR82
GLYCTK
NT5DC2
SMIM4
PDHB
PXK
KCTD6
ACOX2
FAM107A
ARF4
GPR27
SUCLG2
FRG2C
GXYLT2
TLR9
IQCF1
DENND6A
PDE12
DNAH12
LSMEM2
RBM15B
CCDC66
GPR62
FAM19A1
IQCF2
ROBO2
SPATA12
HYAL3
ERC2
SLC38A3
SNTN
FAM3D
MIRLET7G
U3|ENSG00000200222.1
RNA5SP133
RN7SKP45
RNA5SP132
RNA5SP131
SNORD38|ENSG00000207109.1
MIR566
MIR135A1
RNU6ATAC26P
U3|ENSG00000212211.1
SNORD69
SNORD19|ENSG00000212493.1
SNORA26|ENSG00000212608.1
TMEM110
IQCF5
IQCF6
IFRD2
RNU6ATAC29P
MIR1284
RNU6ATAC16P
MIR1324
SNORD19|ENSG00000222345.1
RNA5SP136
ZNF717
IQCF3
snoU13|ENSG00000238416.1
snoU13|ENSG00000238565.1
snoU13|ENSG00000238568.1
SNORD19B|ENSG00000238862.1
snoU13|ENSG00000238905.1
RN7SL271P
ASB14
TLR9
LINC00877
RN7SL482P
RN7SL418P
RN7SL504P
LINC00960
RN7SL294P
LINC00870
NAT6
MUSTN1
RN7SL647P
ACY1
FAM86DP
LINC00698
RN7SL863P
TWF2
ABHD14A
SNORD63|ENSG00000251987.1
RNA5SP134
SNORD19B|ENSG00000252787.1
RNA5SP135
RPP14
EBLN2
LINC00696
RN7SL821P
MIR3938
MIR3136
RN7SL92P
ESRG
MIR4273
NPCDR1
MIR4787

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.3.

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

Genes
MTAP
ELAVL2
IFNA6
IFNA8
IFNA21
IFNA5
CDKN2B
IFNA16
CDKN2A
IFNB1
MIR31HG
DMRTA1
IFNW1
IFNE
IFNA10
FOCAD
IFNA2
PTPLAD2
IFNA1
KLHL9
TUSC1
MIR31
SNORA30|ENSG00000202189.1
IZUMO3
MIR491
IFNA7
RN7SKP120
RMRPP5
C9orf53
IFNA14
IFNA13
IFNA17
IFNA4
RN7SL151P
SNORA31|ENSG00000252580.1
SNORD39|ENSG00000264379.1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.31.

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

Genes
SLC2A3
FOXJ2
NANOG
C3AR1
SLC2A14
NANOGP1
DPPA3
CLEC4C
NANOGNB

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q33.

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

Genes
NEK1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q25.1.

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

Genes
TNN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.2.

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

Genes
BRCA1
ETV4
CDC27
SLC4A1
MEOX1
ITGA2B
KRT33A
MAP3K14
SLC25A39
GRN
ATP6V0A1
TUBG2
DHX8
IFI35
COASY
PLEKHH3
ADAM11
NSF
ATXN7L3
KCNH4
TMEM101
KRT31
RUNDC3A
UBTF
WNT3
KRT37
GOSR2
KRT32
DHX58
KAT2A
RAB5C
NAGLU
HSD17B1
MLX
CNTNAP1
EZH1
VAT1
RND2
HDAC5
PPY
MPP2
DUSP3
EFTUD2
KANSL1
CRHR1
C17orf53
KRT36
STAT5A
WNK4
BECN1
KRT17
C1QL1
GFAP
PYY
HIGD1B
TUBG1
PSME3
RPL27
PSMC3IP
AOC3
ACLY
VPS25
RAMP2
AOC2
G6PC
KRT34
KRT33B
NMT1
G6PC3
LEPREL4
NT5C3B
FAM134C
FKBP10
WNT9B
ARHGAP27
KLHL10
HCRT
MPP3
CD300LG
NAGS
LSM12
ASB16
FAM171A2
DBF4B
PLCD3
CCDC103
GHDC
SOST
NKIRAS2
DNAJC7
HEXIM2
TMUB2
STAT3
KRT19
KRT15
KRT38
KRT13
KRT9
DCAKD
STAT5B
CNP
JUP
HAP1
EIF1
ARL4D
CNTD1
LRRC37A
PTRF
KLHL11
RPRML
CCDC43
C17orf104
FZD2
ACBD4
GJC1
COA3
SPATA32
CCR10
GAST
FMNL1
TMEM106A
SPPL2C
ARL17A
KIF18B
GPATCH8
KRT16
HEXIM1
KRT14
MAPT
ZNF385C
NBR1
LINC00910
KRT35
HSPB9
NBR2
RUNDC1
RNA5SP443
RNY4P2
RNA5SP442
TTC25
RNU6ATAC3P
SNORA40|ENSG00000212149.1
LINC00671
LRRC37A4P
FAM187A
KRT42P
U3|ENSG00000221044.1
U3|ENSG00000221496.1
PLEKHM1
LINC00974
ARL17B
C17orf105
FAM215B
LINC00854
LRRC37A2
RN7SL399P
RN7SL507P
RN7SL258P
STH
AOC4P
LRRC37A17P
RN7SL270P
RN7SL871P
RN7SL730P
RN7SL819P
MIR548AT
RN7SL405P
MIR5089
RN7SL199P
RN7SL656P
MIR5010
RN7SL739P
AARSD1
PTGES3L
MIR2117
FAM215A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.32.

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

Genes
FGFR3
WHSC1
LAP3
HS3ST1
CD38
PROM1
MAN2B2
TACC3
RFC1
PI4K2B
BOD1L1
ARAP2
FAM184B
CC2D2A
ANAPC4
RNF4
TBC1D1
WDR1
CRMP1
EVC
PPP2R2C
UBE2K
N4BP2
C4orf6
ACOX3
SH3BP2
NOP14
ADD1
MAEA
SEL1L3
WFS1
GRPEL1
DHX15
SOD3
SEPSECS
CPZ
SLC2A9
TBC1D19
CLNK
STIM2
MFSD10
BST1
HGFAC
KLF3
KLHL5
NCAPG
UGDH
PPARGC1A
FBXL5
MED28
PDS5A
TMEM156
LIAS
MXD4
SH3TC1
FAM193A
GRK4
IDUA
FGFRL1
TMEM175
POLN
ZNF141
TBC1D14
TMEM128
PDE6B
KLB
FGFBP1
FGFBP2
CPEB2
SLIT2
DGKQ
SLC26A1
LYAR
QDPR
STK32B
JAKMIP1
GPR125
LGI2
C4orf19
GPR78
TRMT44
SLC34A2
WDR19
RAB28
SPON2
CTBP1
ZFYVE28
RGS12
MSX1
PACRGL
C1QTNF7
DCAF16
CCKAR
RPL9
SMIM14
RBM47
APBB2
UVSSA
SLBP
LRPAP1
OTOP1
S100P
ABLIM2
RBPJ
ZCCHC4
RHOH
STX18
NSG1
ZBTB49
TNIP2
LETM1
TMEM129
CPLX1
ATP5I
MFSD7
PGM2
DRD5
LDB2
TAPT1
PCDH7
HTRA3
KIAA0232
CYTL1
TADA2B
CCDC96
EVC2
TLR10
TLR1
TLR6
FAM53A
KIAA1239
PIGG
CHRNA9
DOK7
ZNF518B
LCORL
RNF212
PSAPL1
GAK
MRFAP1L1
MRFAP1
NSUN7
CRIPAK
C4orf50
RELL1
CCDC149
ZNF721
ADRA2C
SORCS2
NELFA
PCGF3
KCNIP4
NAT8L
DEFB131
BLOC1S4
ZNF732
MSANTD1
AFAP1
DTHD1
HTT
ZNF595
FAM114A1
ZNF876P
RN7SKP170
RN7SKP113
RN7SKP36
SNORD74|ENSG00000200999.1
RN7SKP275
RNA5SP160
SNORA51|ENSG00000201863.1
RNA5SP152
RN7SKP292
SNORA63|ENSG00000202449.1
HSP90AB2P
SNORA75|ENSG00000206780.1
MIR571
MIR573
MIR572
MIR95
MIR574
SNORA48|ENSG00000212458.1
HAUS3
TMED11P
MYL5
HMX1
MIR943
LINC00955
MIR548I2
RNA5SP156
RNA5SP158
RNA5SP155
USP17L15
USP17L5
USP17L12
USP17L30
USP17L26
FAM90A26
USP17L25
USP17L28
USP17L10
USP17L29
USP17L24
USP17L13
USP17L11
USP17L27
FAM200B
snoU13|ENSG00000238351.1
snoU13|ENSG00000238383.1
snoU13|ENSG00000238536.1
snoU13|ENSG00000238694.1
RN7SL589P
RN7SL671P
RN7SL16P
RN7SL558P
C4orf48
RN7SL101P
LINC00504
USP17L19
USP17L22
USP17L17
ZEB2P1
CLRN2
SCARNA22
USP17L21
GBA3
PTTG2
ZNF718
SMIM20
USP17L20
USP17L18
USP17L23
ABCA11P
FAM86EP
RNA5SP157
RNA5SP154
RNA5SP153
RNA5SP159
RN7SL358P
MIR378D1
MIR4802
MIR4801
MIR5591
MIR4798
MIR3138
RN7SL315P
MIR4800
MIR5091
MIR4274

Genes in Wide Peak

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

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

Genes
ETV6
PRB2
TAS2R42
PRB3
TAS2R19
TAS2R46
PRB4
PRB1
TAS2R43
TAS2R20
TAS2R30
TAS2R64P
TAS2R31

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.1.

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

Genes
PILRB
PVRIG
SPDYE3
STAG3L5P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q11.2.

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

Genes
C16orf87
GPT2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.32.

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

Genes
SLC35D2
ZNF367

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.33.

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

Genes
KIAA1468
PIGN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

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

Genes
ZNF439
ZNF440
ZNF491
ZNF700
ZNF441
ZNF763
ZNF69
RNA5SP464
ZNF763

Genes in Wide Peak

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

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

Genes
TFRC
LSG1
TNK2
DLG1
ACAP2
IQCG
NCBP2
PIGZ
SENP5
FYTTD1
ATP13A3
TMEM44
KIAA0226
TM4SF19
MUC4
PCYT1A
BDH1
ZDHHC19
SLC51A
UBXN7
RNF168
PIGX
MFI2
LRRC15
XXYLT1
NRROS
CEP19
FBXO45
MUC20
GP5
PAK2
RPL35A
PPP1R2
FAM43A
SDHAP1
LMLN
WDR53
LRCH3
APOD
MIR570
TCTEX1D2
SMCO1
MIR922
LINC00885
ANKRD18DP
LINC00884
FAM157A
snoU13|ENSG00000238491.1
RN7SL434P
LINC00969
RN7SL738P
RN7SL36P
RNU6ATAC24P
MIR3137
MIR4797
RN7SL773P
U4|ENSG00000272359.1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.3.

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

Genes
GOLGA5
DICER1
TCL1A
TRIP11
KTN1
BCL11B
TSHR
GPHN
TCL6
MAP3K9
POMT2
BTBD7
UBR7
ANGEL1
CCDC88C
MNAT1
SAMD4A
NRXN3
ZNF839
SNAPC1
PRKCH
SLC39A9
ARID4A
FUT8
CYP46A1
TDP1
SPATA7
JKAMP
FOXN3
AP5M1
SYNE2
PLEKHH1
GALC
ADCK1
ATXN3
EML1
ATG2B
SPTB
TMEM260
EXOC5
PTPN21
VASH1
SEL1L
RDH11
ACTN1
ZFYVE26
MPP5
FERMT2
MARK3
PPP2R5C
PSEN1
MOK
HSP90AA1
EXD2
ARG2
TXNDC16
PPP1R13B
OTUB2
DDX24
ZBTB25
RCOR1
GPATCH2L
PAPOLA
CCNK
KCNK10
PSMC6
GNPNAT1
DDHD1
CDKN3
CNIH
CGRRF1
ATP6V1D
C14orf105
PLEK2
PIGH
C14orf166B
PSMA3
VTI1B
TIMM9
GSTZ1
KIAA0586
TMED8
SAMD15
AHSA1
DAAM1
ISM2
SPTLC2
RIN3
LGMN
ALKBH1
SNW1
CHGA
ITPK1
DHRS7
PPM1A
SIX4
GALNT16
ASB2
CEP128
ERH
HIF1A
KIAA0247
SRSF5
SLC10A1
EIF5
SERPINA4
SLC8A3
ZFYVE21
MTHFD1
ZC3H14
PCNX
BDKRB1
GSKIP
VRK1
PSMC1
PAPLN
RPS6KA5
SMEK1
YY1
CINP
YLPM1
DCAF4
PROX2
VSX2
FCF1
PGF
IFI27L2
CCDC176
NEK9
ACYP1
IFT43
NPC2
DNAL1
IRF2BPL
ACOT2
LTBP2
AREL1
MLH3
TTLL5
FLVCR2
ABCD4
DLST
PPP4R4
TGFB3
ZC2HC1C
SLIRP
RBM25
ALDH6A1
GPR68
ESRRB
EIF2B2
NRDE2
COQ6
ZNF410
BMP4
PTGER2
MAX
KLC1
XRCC3
PCNXL4
ATG14
SIX1
RHOJ
DLGAP5
L3HYPDH
HSPA2
ZBTB1
TRMT5
SGPP1
PLEKHG3
TRAF3
LRRC9
ACTR10
GCH1
LGALS3
C14orf1
GSC
C14orf159
UNC79
NUMB
CATSPERB
VRTN
COX16
TTC9
MED6
EIF2S1
ADAM20
PELI2
RTN1
C14orf37
SYT16
SLC38A6
NAA30
ADAM21
RDH12
DCAF5
RAB15
WDR89
ESR2
KCNH5
STON2
EFCAB11
GPR65
PTGR2
JDP2
AK7
FAM181A
SLC24A4
FBLN5
SERPINA10
WARS
SLC25A47
WDR20
VIPAS39
SLC35F4
CCDC175
KCNK13
TMEM251
PPP2R5E
ELMSAN1
FAM161B
BATF
ANKRD9
C14orf2
TDRD9
GTF2A1
EML5
TTC8
TMEM63C
NGB
NOXRED1
OTX2
DACT1
PPP1R36
ZFYVE1
ISCA2
TTC7B
TC2N
CPSF2
MOAP1
IFI27L1
IFI27
SERPINA12
CLMN
AMN
CKB
TRMT61A
BAG5
MAPK1IP1L
PTGDR
DEGS2
BDKRB2
SERPINA9
SERPINA6
C14orf142
FOS
TMED10
FAM71D
LINC00521
PRIMA1
PLEKHD1
GPX2
SYNE3
WDR25
C14orf177
PNMA1
ZDHHC22
RPL13AP3
ACOT4
FBXO34
C14orf39
GPHB5
AKAP5
SOCS4
GPR137C
GPR135
TMEM30B
RAD51B
HHIPL1
GLRX5
TBPL2
RGS6
BEGAIN
SYNDIG1L
SETD3
NDUFB1
ACOT1
SIX6
FLRT2
TNFAIP2
DLK1
ZFP36L1
LINC00643
SERPINA11
ENTPD5
HEATR4
SERPINA13P
COX8C
SERPINA5
MIR494
SERPINA3
LINC00523
EVL
LINC00238
TECPR2
TOMM20L
GMFB
DYNC1H1
SLC25A29
SERPINA1
DIO3
SIPA1L1
C14orf178
ERO1L
TMEM229B
RPS6KL1
STYX
WDHD1
CALM1
SMOC1
CDC42BPB
KIAA1737
MIR380
MIR345
MIR370
MIR412
MIR377
MIR381
MIR369
MIR323A
MIR342
MIR379
MIR410
MIR409
MIR411
MIR337
RNA5SP388
U3|ENSG00000200042.1
SNORD113|ENSG00000200150.1
RN7SKP255
U3|ENSG00000200693.1
RN7SKP107
SNORD113|ENSG00000201036.1
RNA5SP387
SNORA32|ENSG00000201384.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000201710.1
SNORD51|ENSG00000202275.1
MIR539
EXOC3L4
CCDC85C
LIN52
ACOT6
DPF3
U3|ENSG00000206761.1
SNORD56B
MIR487A
MIR433
MIR544A
MIR127
MIR655
MIR382
MIR495
MIR299
MIR487B
MIR625
MIR654
MIR136
MIR656
MIR496
MIR154
MIR493
MIR134
MIR431
MIR323B
MIR485
DIO2
MIR770
MIR758
MIR543
SNORA46|ENSG00000212371.1
TCL1B
SYNJ2BP
MEG3
MIR300
MIR889
MIR541
MIR1193
SNORA11|ENSG00000221060.1
SNORA11B
SNORA79|ENSG00000221303.1
MIR548H1
MIR1197
MIR1260A
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000222185.1
SNORA7|ENSG00000222604.1
RN7SKP17
RN7SKP108
MEG9
LINC00618
C14orf132
RD3L
LINC00341
LINC00642
ADAM21P1
snoU13|ENSG00000238330.1
RNU6ATAC28P
snoU13|ENSG00000238776.1
snoU13|ENSG00000238853.1
snoU13|ENSG00000238972.1
snoU13|ENSG00000238978.1
snoU13|ENSG00000239061.1
RN7SL546P
RN7SL213P
RN7SL530P
RN7SL587P
RN7SL472P
RN7SL710P
RN7SL77P
RN7SL586P
RN7SL369P
RN7SL714P
RN7SL683P
RN7SL634P
RN7SL108P
RN7SL598P
RN7SL461P
RN7SL523P
RN7SL706P
C14orf64
SNHG10
LINC00617
LINC00605
SNORD112|ENSG00000251769.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252009.1
RNU4ATAC14P
RNU6ATAC9P
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000252380.1
SCARNA13
RNU3P3
U3|ENSG00000252792.1
SCARNA20|ENSG00000252800.1
RN7SKP99
SNORD112|ENSG00000252873.1
U3|ENSG00000253014.1
RN7SKP92
RTL1
C14orf169
CCDC177|ENSG00000255994.1
APOPT1
FNTB
CHURC1
MEG8
DIO3OS
DKFZP434O1614
LINC00637
LINC00520
MIR381HG
LINC00524
LINC00911
LINC00644
ADAM20P1
LINC00677
MIR5586
RN7SL224P
RN7SL747P
MIR3173
RN7SL588P
MIR4505
MIR376A1
RN7SL540P
MIR151B
MIR4308
MIR4709
MIR4506
MIR5694
MIR4309
RN7SL506P
MIR5580
MIR2392
MIR4706
RN7SL356P
RN7SL137P
MIR4708
CCDC177|ENSG00000267909.1
FKSG61
MIR376C
MIR665
U6|ENSG00000272439.1
MIR432
SNORA28

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.3.

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

Genes
ACVR2A
ZEB2
TEX41
snoU13|ENSG00000238860.1
snR65|ENSG00000253036.1
RNA5SP106

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p11.1.

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

Genes
FAM182A
FRG1B
DEFB116
DEFB115
MIR663A
NCOR1P1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

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

Genes
IFT88
PSPC1
ZMYM2
GJB6
GJA3
ZMYM5
XPO4
TPTE2
N6AMT2
LATS2
GJB2
CRYL1
IL17D
MPHOSPH8
TUBA3C
LINC00350
PHF2P2
LINC00388
LINC00349
LINC00387
LINC00442
HNRNPA1P30
LINC00421
snoU13|ENSG00000238665.1
snoU13|ENSG00000238893.1
SNORD27|ENSG00000252128.1
RNA5SP24
LINC00556
RN7SL80P
MIR4499
RN7SL166P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.11.

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

Genes
MYL2
RNA5SP373

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p13.

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

Genes
MLLT10
VIM
MCM10
SEC61A2
FAM107B
SPAG6
APBB1IP
ITGA8
NEBL
SEPHS1
BAMBI
MYO3A
WAC
RAB18
PRTFDC1
PHYH
CUBN
TRDMT1
ARHGAP21
ANKRD26
ACBD5
MTPAP
MAP3K8
MASTL
KIAA1217
LYZL1
MRC1
PLXDC2
EPC1
OPTN
ECHDC3
STAM
GAD2
ABI1
YME1L1
DNAJC1
PROSER2
USP6NL
COMMD3
MSRB2
PDSS1
FAM171A1
FAM188A
SLC39A12
TMEM236|ENSG00000148483.7
RSU1
ST8SIA6
ZEB1
MKX
MPP7
PIP4K2A
ENKUR
GPR158
LYZL2
UPF2
CDC123
CCDC3
FRMD4A
SUV39H2
DCLRE1C
OLAH
RPP38
NMT2
ARMC3
OTUD1
ARHGAP12
NUDT5
UCMA
BEND7
PRPF18
KIAA1462
PTER
C1QL3
CACNB2
PTPLA
ARL5B
PTF1A
BMI1
ARMC4
KIF5B
C10orf111
ACBD7
C10orf67
SKIDA1
DHTKD1
PTCHD3
CAMK1D
ZNF438
MRC1L1
TMEM236|ENSG00000184040.7
CDNF
THNSL1
HSPA14
SVIL
MEIG1
RNA5SP308
RNA5SP301
RNA5SP305
RNA5SP307
U3|ENSG00000200545.1
RN7SKP37
RNA5SP302
C10orf126
C10orf115
CASC10
C10orf113
C10orf112
MIR604
MIR603
SNORD115|ENSG00000212411.1
RNA5SP300
MIR938
MIR548Q
MIR1265
MIR1915
RN7SKP220
U3|ENSG00000222666.1
RN7SKP39
RNA5SP306
SNORA57|ENSG00000223027.1
RNA5SP304
EBLN1
PTCHD3P1
LRRC37A6P
LINC00264
SVILP1
LINC00837
LINC00614
ARMC4P1
snoU13|ENSG00000238414.1
snoU13|ENSG00000238515.1
snoU13|ENSG00000238552.1
snoU13|ENSG00000238900.1
snoU13|ENSG00000239130.1
RN7SL241P
RN7SL825P
RN7SL63P
RN7SKP241
NSUN6
U3|ENSG00000251749.1
RN7SKP132
snoR442|ENSG00000251959.1
RNA5SP303
SNORA40|ENSG00000252049.1
RNU6ATAC39P
RNU4ATAC6P
SNORD45|ENSG00000252438.1
RNA5SP309
SNORA31|ENSG00000252537.1
RN7SKP219
MIR4480
RN7SL198P
MIR4675
MIR548AK
RN7SL232P
MIR4293
U6|ENSG00000272507.1

Genes in Wide Peak

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

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

Genes
ZNF780B
ZNF780A

Genes in Wide Peak

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

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

Genes
OBSCN
TRIM11
C1orf145
TRIM17
HIST3H3
RNF187
HIST3H2A
IBA57
HIST3H2BB
RNA5S12
RNA5S11
RNA5S3
RNA5S1
RNA5S5
RNA5S10
RNA5S8
RNA5S17
RNA5S4
RNA5S6
RNA5S9
RNA5S14
RNA5S2
RNA5S15
RNA5SP19
RNA5S16
RNA5S7
RNA5S13
C1orf148
SNORA51|ENSG00000206878.1
RNA5SP18
BTNL10
MIR4666A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.3.

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

Genes
FGFR2
NFKB2
BMPR1A
TLX1
SUFU
PTEN
PRF1
COX15
ZRANB1
ZDHHC6
ABCC2
FAS
VCL
AIFM2
ADRB1
RRP12
MRPL43
ALDH18A1
PSD
CCAR1
WAPAL
OAT
SLK
COL17A1
GSTO2
INPP5A
UBE2D1
RHOBTB1
TACR2
WNT8B
SEC31B
PAX2
NT5C2
TM9SF3
SAR1A
DUSP13
DHX32
PDE6C
CWF19L1
SEMA4G
BTAF1
IKZF5
BLNK
TLL2
CYP26A1
TDRD1
SORBS1
CRTAC1
SIRT1
HNRNPH3
SCD
ABLIM1
TSPAN15
H2AFY2
PDLIM1
CCNJ
DNTT
ATRNL1
HPS1
DNMBP
RAB11FIP2
ERLIN1
EIF3A
PKD2L1
DDX50
SEC23IP
ATE1
NSMCE4A
PLEKHA1
PALD1
UNC5B
CDH23
C10orf54
SPOCK2
MICU1
PPP3CB
CCSER2
MINPP1
ACTA2
LIPA
C10orf2
LZTS2
SFXN3
KAZALD1
FBXW4
FGF8
NPM3
TNKS2
PITX3
GBF1
CPEB3
FBXL15
CUEDC2
LHPP
C10orf137
BCCIP
NEURL
SH3PXD2A
OBFC1
DKK1
EBF3
GLRX3
SORCS1
XPNPEP1
SMC3
SHOC2
TFAM
CCDC6
ZMIZ1
DNAJC12
PPIF
PBLD
TSPAN14
LGI1
TBC1D12
CYP2C18
FAM178A
IDE
TECTB
ELOVL3
IFIT3
IFIT2
GPAM
CUTC
PPP1R3C
PYROXD2
CNNM1
MXI1
SMNDC1
C10orf88
HELLS
PRLHR
TCTN3
FAM45A
AVPI1
WDR11
C10orf76
KCNIP2
CCDC147
GOT1
CPN1
C10orf95
SFRP5
CPXM2
ANXA11
LDB3
OPN4
FAM35A
FAM213A
SFTPA1
NEUROG3
PLAU
SRGN
CHST3
BICC1
CISD1
EGR2
ECD
P4HA1
SLC25A16
ZWINT
VPS26A
ECHS1
TUBGCP2
CALY
CYP2E1
PTPRE
SFTPD
DYDC2
TMEM254
ACTR1A
CYP2C9
TMEM180
CYP2C8
MYOF
LOXL4
STAMBPL1
CH25H
LBX1
ATAD1
BTBD16
KIF11
CUZD1
TACC2
DUSP5
CALHM2
ARL3
CEP55
KIF20B
ENTPD1
EXOC6
PLCE1
RBP4
ANXA7
FAM149B1
ASCC1
PLA2G12B
ZNF365
OIT3
ADAMTS14
RPS24
TET1
DNA2
MYPN
FAM13C
NRBF2
CDHR1
LRIT1
RGR
POLR3A
HERC4
C10orf11
CAMK2G
ADIRF
GLUD1
ANKRD1
HTR7
RPP30
FRA10AC1
ADD3
HABP2
VAX1
DNAJB12
EIF4EBP2
NPFFR1
PLEKHS1
TCF7L2
MKI67
CYP17A1
INA
FUOM
LRRC27
MTG1
PAOX
GSTO1
TAF5
PPRC1
ITPRIP
CNNM2
PDCD11
ADAM12
RGS10
PCDH15
ARID5B
PDCD4
ADRA2A
DOCK1
ANK3
IPMK
DLG5
MAT1A
AGAP11
VTI1A
FAM160B1
DPYSL4
VENTX
ADAM8
GFRA1
CACUL1
TIAL1
BAG3
ANKRD22
IFIT5
SLC16A12
PANK1
HHEX
BUB3
GPR26
MMP21
C10orf90
MMS19
PI4K2A
MARVELD1
ZFYVE27
GOLGA7B
SLC25A28
PIK3AP1
C10orf12
MCU
TTC18
ADK
KCNMA1
PCGF6
SFR1
SORCS3
SFXN2
SUPV3L1
HKDC1
HK1
TYSND1
NODAL
KAT6B
SAMD8
HECTD2
ZCCHC24
PHYHIPL
SLC16A9
MBL2
REEP3
VDAC2
COMTD1
SLC18A2
PDZD8
ZNF503
FAM175B
FAM204A
PRDX3
GHITM
STOX1
DDX21
STK32C
CASP7
C10orf118
VWA2
PRAP1
TRUB1
CYP2C19
PNLIPRP2
C10orf82
HSPA12A
FRAT1
UBTD1
ANKRD2
R3HCC1L
HTRA1
HIF1AN
NDUFB8
BTRC
POLL
DPCD
HPS6
NOLC1
TBATA
SGPL1
PCBD1
WBP1L
C10orf32
ANAPC16
SYNPO2L
NUDT13
MSS51
USP54
NDST2
MIR202
DDIT4
AFAP1L2
CDK1
EMX2
MGMT
DYDC1
MORN4
TRIM8
C10orf35
ZDHHC16
EXOSC1
PGAM1
SYCE1
UTF1
KNDC1
TTC40
PWWP2B
JMJD1C
CHCHD1
AGAP5
LRRC20
HPSE2
C10orf131
C10orf129
NOC3L
LIPM
SNCG
MMRN2
USMG5
FGFBP3
TEX36
CTBP2
PPP2R2D
PNLIP
BNIP3
SLC35G1
TCERG1L
SEC24C
C10orf85
CASC2
MYOZ1
ZNF518A
SH2D4B
ATOH7
PSTK
C10orf91
PCGF5
CLRN3
PIPSL
PPA1
FRAT2
ADO
RTKN2
CHST15
MRPS16
LIPF
CCDC172
GRID1
CALHM3
CTNNA3
C10orf107
C10orf120
SFXN4
RNLS
NUTM2A
AP3M1
SFTPA2
NRG3
IFIT1
CALHM1
FFAR4
FOXI2
KCNK18
PDZD7
PNLIPRP1
SLIT1
KIAA1598
CYP26C1
DMBT1
FAM25A
NUTM2B
ENO4
C10orf99
JAKMIP3
NANOS1
HMX3
CC2D2B
UROS
DUPD1
HMX2
FAM196A
PLAC9
FAM53B
BLOC1S2
ACADSB
LCOR
NHLRC2
TMEM26
FUT11
ACSL5
GPR123
OPALIN
COL13A1
PSAP
WDR96
MCMBP
NRAP
ENTPD7
MARCH5
SLC29A3
MGEA5
ZNF511
PAPSS2
LDB1
LRRTM3
INPP5F
GRK5
DCLRE1A
KIAA1279
MIR107
MIR346
SNORD60|ENSG00000199321.1
RNA5SP327
RNA5SP321
RNA5SP319
RNA5SP326
SNORA36|ENSG00000200294.1
RNA5SP322
RNA5SP325
SNORD74|ENSG00000200891.1
SNORA71|ENSG00000201393.1
RNA5SP324
MIR146B
SPRN
FANK1
METTL10
FAM24A
PPAPDC1A
PNLIPRP3
RBM20
C10orf62
IFIT1B
LIPN
LIPK
LIPJ
LRIT2
RUFY2
SNORA19|ENSG00000207468.1
MIR608
MIR606
MIR607
MIR609
RNA5SP323
SNORA12|ENSG00000212464.1
SNORA17|ENSG00000212589.1
FAM24B
CHUK
ARHGAP19
DNAJC9
NPS
BBIP1
AS3MT
NUTM2D
ZSWIM8
C10orf105
MIR936
MIR1296
SNORA11|ENSG00000221164.1
SNORD98
MIR548E
MIR1287
MIR548F1
MIR1307
C10orf55
RN7SKP202
RN7SKP278
RN7SKP143
SNORA19|ENSG00000222588.1
RNA5SP328
RN7SKP167
CFL1P1
LINC00502
LINC00863
FRG2B
LINC00595
LINC00845
KLLN
LINC00866
LINC00948
LINC00864
NUTM2E
LINC00858
EMX2OS
LINC00856
LINC00867
LINC00865
LINC00849
LINC00601
LINC00263
C10orf40
TLX1NB
LINC00959
LINC00857
LINC00844
snoU13|ENSG00000238355.1
snoU13|ENSG00000238472.1
snoU13|ENSG00000238577.1
snoU13|ENSG00000238588.1
snoU13|ENSG00000238620.1
SNORD2|ENSG00000238707.1
MIR2110
snoU13|ENSG00000238918.1
snoU13|ENSG00000238970.1
snoU13|ENSG00000238983.1
snoU13|ENSG00000238991.1
snoU13|ENSG00000239000.1
snoU13|ENSG00000239091.1
snoU13|ENSG00000239125.1
RN7SL394P
RN7SL591P
HOGA1
RN7SL21P
BMS1P4
MBL1P
RN7SL846P
RN7SL749P
RN7SL384P
GUCY2GP
RN7SL284P
RN7SL78P
MTRNR2L5
PI4K2A
GLUD1P3
U3|ENSG00000251836.1
snoU13|ENSG00000251926.1
RN7SKP288
RNA5SP320
RN7SKP196
RNA5SP318
U3|ENSG00000252189.1
snoR442|ENSG00000252203.1
RN7SKP238
RN7SKP84
SNORD112|ENSG00000252844.1
SNORA31|ENSG00000252888.1
RNY4P26
SNORA25|ENSG00000252993.1
RMRPP1
SNORD112|ENSG00000253068.1
EIF5AL1
ARMS2
NDUFB8
RN7SL450P
RN7SL686P
RN7SL644P
MIR4296
MIR4685
MIR3924
MIR4295
MIR378C
MIR4484
MIR4682
MIR3944
MIR3941
RN7SL518P
MIR4681
MIR4680
RN7SL373P
RN7SL733P
MIR3157
RN7SL220P
MIR4297
MIR4676
RN7SL524P
MIR3663
HUG1
GOLGA7B
C10ORF32
U4|ENSG00000272160.1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p11.12.

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

Genes
FOLH1
TRIM51
OR5F1
TRIM48
TRIM51HP
OR8J3
OR5I1
OR8I2
OR4C11
OR5T3
OR5J2
OR10AG1
OR4S2
OR4C5
OR5T2
OR8K5
OR8H3
OR8H2
OR5AS1
OR4C6
OR4P4
OR4C16
OR4C15
OR4A15
OR4A16
TRIM49B
OR4C46
OR5D14
OR5L1
OR5D18
OR5W2
OR5D13
OR5D16
OR5L2
TRIM64C
OR4A5
OR4C12
OR4A47
OR4C13

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.3.

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

Genes
LCP1
RB1
AKAP11
CPB2
TDRD3
NUFIP1
KIAA0226L
HTR2A
FNDC3A
MLNR
CDADC1
CAB39L
MRPS31
SLC25A15
KPNA3
RGCC
VWA8
DGKH
INTS6
DHRS12
TSC22D1
OLFM4
PCDH17
ENOX1
TNFSF11
MTRF1
DNAJC15
WBP4
ELF1
KBTBD7
CCDC70
SPRYD7
EBPL
ATP7B
ZC3H13
GUCY1B2
EPSTI1
TPT1
KIAA1704
NEK3
PCDH8
VPS36
RNASEH2B
CKAP2
LECT1
THSD1
LRCH1
SUCLA2
RCBTB1
MED4
PHF11
COG3
ITM2B
NUDT15
RCBTB2
SETDB2
SMIM2
WDFY2
HNRNPA1L2
LPAR6
ESD
DIAPH3
FAM124A
FOXO1
CCDC122
SERP2
CYSLTR2
ARL11
SUGT1
KBTBD6
FAM194B
TPTE2P5
NAA16
LRRC63
SPERT
SLC25A30
DLEU1
LACC1
FAM216B
KCTD4
PCDH9
DLEU7
GTF2F2
NEK5
PCDH20
KCNRG
SNORA31|ENSG00000199477.1
RNY4P24
RNY3P2
RNY4P9
RNY4P14
RNA5SP27
RNA5SP28
RN7SKP6
RNY4P28
RNA5SP30
PRR20B
PRR20A
TRIM13
RNY3P5
RNY1P6
RNY3P9
RNY3P10
MIR621
MIR320D1
MIR759
SNORD116|ENSG00000212553.1
SIAH3
LINC00598
RNY4P30
RNY4P29
RNA5SP29
RNA5SP31
RN7SKP3
RPS4XP16
LINC00378
LINC00371
PRR20D
LINC00434
LINC00355
LINC00448
LINC00459
LINC00358
PRR20C
LINC00400
LINC00364
LINC00332
LINC00395
LINC00441
DLEU2
LINC00462
LINC00284
PRR20E
LINC00444
LINC00458
LINC00330
LINC00345
snoU13|ENSG00000238455.1
snoU13|ENSG00000238483.1
snoU13|ENSG00000238651.1
snoU13|ENSG00000238932.1
SUGT1P3
RN7SL288P
RN7SL515P
RN7SL618P
RN7SL413P
RN7SL761P
RN7SL320P
RN7SL597P
RN7SL700P
RN7SKP2
RN7SKP5
RNY4P31
SNORA31|ENSG00000253051.1
SERPINE3
ALG11
UTP14C
LINC00562
LINC00563
LINC00558
MIR4704
MIR548X2
MIR5006
MIR3168
MIR5007
MIR3613
RN7SL375P
RN7SL49P
MIR5693
MIR4703
MIR3169
7SK|ENSG00000271818.1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.32.

Table S72. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ERCC5
LCP1
BRCA2
RB1
LHFP
MYCBP2
FBXL3
AKAP11
MYO16
ZIC2
IPO5
FRY
DCT
CPB2
DIS3
PIBF1
TDRD3
NUFIP1
PDS5B
SLC15A1
DOCK9
TGDS
KIAA0226L
NALCN
FGF14
HTR2A
NDFIP2
TNFSF13B
FNDC3A
MLNR
CDADC1
CAB39L
KLF5
STK24
DNAJC3
UGGT2
SUPT20H
MRPS31
SLC25A15
KPNA3
RGCC
VWA8
DGKH
INTS6
IRG1
DHRS12
TSC22D1
CLN5
OLFM4
KLF12
UCHL3
PCDH17
ENOX1
TNFSF11
MTRF1
SPG20OS
SOHLH2
DNAJC15
PROSER1
UFM1
WBP4
ELF1
SMAD9
HSPH1
KBTBD7
ALG5
EXOSC8
CCDC70
SPRYD7
EBPL
ATP7B
ZC3H13
GUCY1B2
GPR18
CLYBL
TMTC4
RAP2A
SLC10A2
ABCC4
EFNB2
SOX21
TM9SF2
DCLK1
CCNA1
COG6
SPG20
RXFP2
EPSTI1
TRPC4
POSTN
RFXAP
TPT1
KIAA1704
STOML3
KL
RFC3
STARD13
GGACT
CLDN10
DZIP1
UBAC2
ARGLU1
BIVM
TPP2
KDELC1
NEK3
PCDH8
VPS36
RNASEH2B
CKAP2
LECT1
TBC1D4
THSD1
BORA
LRCH1
SUCLA2
RCBTB1
MED4
PHF11
COG3
LMO7
SCEL
ITM2B
SPRY2
NUDT15
EDNRB
RCBTB2
SETDB2
N4BP2L1
SMIM2
WDFY2
HNRNPA1L2
LPAR6
ESD
DIAPH3
SLAIN1
RBM26
METTL21C
MBNL2
RNF113B
ZIC5
ABHD13
KLHL1
FAM124A
FREM2
FOXO1
TEX30
CCDC122
SERP2
POU4F1
RNF219
CYSLTR2
ARL11
GPR180
FARP1
SLITRK5
SUGT1
KBTBD6
OXGR1
DACH1
FAM194B
TPTE2P5
GPR183
NAA16
NBEA
LRRC63
SPERT
SLC25A30
LIG4
PCCA
CCDC168
DLEU1
SLITRK1
KCTD12
C13orf45
GPC5
LACC1
FAM216B
CSNK1A1L
KCTD4
SERTM1
MAB21L1
DAOA
GPC6
PCDH9
SLITRK6
HS6ST3
DLEU7
B3GALTL
COMMD6
GTF2F2
NHLRC3
ZAR1L
NEK5
PCDH20
ITGBL1
KCNRG
SNORA25|ENSG00000199196.1
RNA5SP26
SNORA9|ENSG00000199282.1
SNORA31|ENSG00000199477.1
RNY4P24
RNY3P2
RNA5SP32
RNY4P9
RNY4P27
RNY4P14
RNY3P3
RNA5SP27
RNA5SP28
SNORD38|ENSG00000200733.1
SNORA25|ENSG00000201245.1
RN7SKP6
RNY1P2
RN7SKP9
SNORD31
RNY4P28
RNA5SP37
RN7SKP1
RNA5SP30
LINC00449
FAM155A
MZT1
PRR20B
PRR20A
TRIM13
RNY1P5
RNY1P8
RNY3P7
RNY3P5
RNY1P6
RNY1P4
RNY3P9
RNY3P10
MIR621
MIR623
MIR622
MIR320D1
MIR759
RNY3P6
SNORA16|ENSG00000212293.1
SNORD37|ENSG00000212377.1
SNORD116|ENSG00000212553.1
RNA5SP35
PTMAP5
MIR17HG
SIAH3
LINC00598
ARL2BPP3
MIR1267
RNA5SP36
RNY4P30
RNY5P8
RN7SKP7
RNA5SP38
RNY4P29
RNA5SP29
RN7SKP8
RNA5SP31
RNA5SP39
RNY3P8
RN7SKP3
LINC00571
LINC00393
RPS4XP16
LINC00457
LINC00378
LINC00331
LINC00344
LINC00381
LINC00351
LINC00343
LINC00371
LINC00348
LINC00423
PRR20D
LINC00434
LINC00355
LINC00392
LINC00448
MIR4500HG
LINC00446
LINC00459
LINC00366
LINC00433
LINC00379
LINC00358
LINC00411
PRR20C
EEF1DP3
LINC00400
LINC00364
LINC00443
ATXN8OS
LINC00332
LINC00395
LINC00441
DLEU2
LINC00283
LINC00410
LINC00333
LINC00460
LINC00462
LINC00284
PRR20E
LINC00440
LINC00444
LINC00458
LINC00676
LINC00330
LINC00402
LINC00345
LINC00445
LINC00353
LINC00347
LINC00391
snoU13|ENSG00000238305.1
snoU13|ENSG00000238407.1
snoU13|ENSG00000238408.1
snoU13|ENSG00000238455.1
snoU13|ENSG00000238463.1
snoU13|ENSG00000238483.1
snoU13|ENSG00000238522.1
snoU13|ENSG00000238651.1
snoU13|ENSG00000238869.1
snoU13|ENSG00000238932.1
SUGT1P3
RN7SL288P
RN7SL515P
RN7SL618P
RN7SL585P
RN7SL164P
CCDC169
RN7SL413P
RN7SL810P
RN7SL571P
LINC00359
RN7SL60P
RN7SL761P
RN7SL320P
RN7SL597P
RN7SL700P
N4BP2L2
METTL21EP
SNORA68|ENSG00000251715.1
snR65|ENSG00000251901.1
SNORD112|ENSG00000252154.1
SNORD22
RNA5SP33
RNU4ATAC3P
SNORA25|ENSG00000252550.1
RNA5SP34
RN7SKP2
RN7SKP5
RNY4P31
SNORA31|ENSG00000253051.1
SERPINE3
ALG11
UTP14C
LINC00564
LINC00562
LINC00554
LINC00557
LINC00555
LINC00563
LINC00561
LINC00559
LINC00558
LINC00560
MIR3170
MIR4704
MIR548X2
MIR4306
MIR548AS
MIR4305
MIR5006
MIR3168
MIR5007
MIR4705
MIR3613
MIR2681
RN7SL375P
RN7SL49P
MIR4500
MIR5693
MIR3665
MIR4703
MIR3169
7SK|ENSG00000271818.1
LINC00551

Genes in Wide Peak

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

Table S73. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LPIN2
MYOM1
MYL12A
MYL12B
DLGAP1
TGIF1
snoU13|ENSG00000238445.1
snoU13|ENSG00000238790.1
snoU13|ENSG00000238863.1
RN7SL39P
SNORA70|ENSG00000252258.1

Genes in Wide Peak

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

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FSTL3
TCF3
GNA11
STK11
SPPL2B
PTBP1
GNA15
CNN2
ABCA7
SBNO2
AP3D1
WDR18
TLE2
FGF22
RNF126
DAZAP1
MBD3
REXO1
EFNA2
CIRBP
ATP5D
C19orf26
TIMM13
CDC34
MISP
POLR2E
POLRMT
HCN2
IZUMO4
GADD45B
PALM
MADCAM1
MKNK2
DOT1L
PLEKHJ1
SF3A2
AMH
OAZ1
TLE6
AES
SGTA
THEG
MIER2
REEP6
PCSK4
APC2
RPS15
NDUFS7
KISS1R
ARID3A
GRIN3B
C19orf25
S1PR4
NCLN
UQCR11
KLF16
SHC2
LPPR3
ABHD17A
GAMT
ATP8B3
LSM7
BTBD2
CSNK1G2
SLC39A3
TPGS1
PPAP2C
MUM1
CELF5
GPX4
MIDN
JSRP1
ZNF57
ZNF556
ZNF554
THOP1
MOB3A
AZU1
BSG
MED16
ZNF77
DIRAS1
GNG7
LMNB2
OR4F17
TMPRSS9
HMHA1
MEX3D
ODF3L2
TMEM259
C2CD4C
PRSS57
ADAMTSL5
PLK5
ZNF555
C19orf35
PRTN3
GZMM
ELANE
CFD
R3HDM4
ONECUT3
ADAT3
LINGO3
MIR1227
MIR1909
WASH5P
SCAMP4
C19orf24
FAM138F
RN7SL477P
RNA5SP462
MIR3187
MIR4745
RN7SL226P
MIR4321
UQCR11

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.1.

Table S75. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BID
CECR5
CECR1
CECR2
BCL2L13
TPTEP1
OR11H1
ATP6V1E1
XKR3
IL17RA
SLC25A18
CECR6
POTEH
CCT8L2
GAB4
HSFY1P1
CECR9
CECR7
KCNMB3P1
RN7SL843P
CECR3
snoU13|ENSG00000251737.1
LINC00528

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.12.

Table S76. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TNFRSF17
PALB2
IL21R
MYH11
ERCC4
NDUFAB1
ACSM3
GDE1
CACNG3
TMEM159
MVP
KIAA0556
SNX29
POLR3E
THUMPD1
ACSM2B
PLA2G10
NDE1
GTF3C1
IL4R
KIF22
RRN3
YPEL3
TNRC6A
ABCC6
CORO1A
MAPK3
GDPD3
LYRM1
ABCC1
NOMO3
ZP2
CRYM
EEF2K
GSPT1
UBFD1
EARS2
GGA2
AQP8
CPPED1
USP31
BFAR
RRN3P2
QPRT
XYLT1
MAZ
CDIPT
NOMO1
SYT17
TMC5
CCP110
C16orf62
KNOP1
HS3ST2
RBBP6
ZC3H7A
SLX1A
FOPNL
ERN2
RPS15A
PARN
UQCRC2
CDR2
IGSF6
ARHGAP17
TBX6
PPP4C
ALDOA
FAM57B
DOC2A
HIRIP3
TAOK2
TMEM219
TXNDC11
ZKSCAN2
KDM8
PDZD9
OTOA
MPV17L
NTAN1
SMG1
DNAH3
SLC5A11
PRKCB
ACSM1
C16orf45
KIAA0430
SCNN1G
DCTN5
PLK1
CHP2
COQ7
GPRC5B
C16orf92
PRRT2
COG7
SCNN1B
ATXN2L
XPO6
GSG1L
NSMCE1
CD2BP2
NPIPB3
PDILT
UMOD
GP2
INO80E
BOLA2B
SPNS1
TMC7
ARL6IP1
RSL1D1
IQCK
SEZ6L2
ASPHD1
KCTD13
ZG16
VWA3A
ANKS4B
NUPR1
CCDC101
NFATC2IP
CD19
RABEP2
SH2B1
TUFM
PDXDC1
GPR139
SLX1B
HS3ST4
BOLA2
NPIPA1
ACSM5
ACSM2A
NPIPA5
SDR42E2
EIF3C
SNN
APOBR
NOMO2
C16orf52
NPIPB4
C16orf54
PAGR1
MKL2
DCUN1D3
SBK1
NPIPP1
CLN3
ATP2A1
SULT1A1
ERI2
NPIPB9
METTL9
SULT1A2
IL27
SPN
SNX29P2
NPIPB6
MIR365A
SNORA27|ENSG00000199474.1
RNA5SP405
SNORA25|ENSG00000200652.1
SNORA1|ENSG00000201541.1
EIF3CL
LCMT1
ITPRIPL2
MIR193B
SNORA75|ENSG00000212593.1
SULT1A4
LAT
NPIPA8
NPIPA7
RN7SKP127
NPIPA3
NPIPB7
C16orf82
SMG1P1
SHISA9
snoU13|ENSG00000238329.1
snoU13|ENSG00000238352.1
snoU13|ENSG00000238639.1
snoU13|ENSG00000238684.1
ACA64|ENSG00000238685.1
snoU13|ENSG00000238699.1
snoU13|ENSG00000238703.1
snoU13|ENSG00000238712.1
snoU13|ENSG00000238954.1
snoU13|ENSG00000239114.1
snoU13|ENSG00000239172.1
snoU13|ENSG00000239193.1
RN7SL274P
NPIPB5
RRN3P1
PKD1P6
SNORA43|ENSG00000252461.1
SCARNA6|ENSG00000252798.1
RN7SKP23
NPIPB11
PKD1P5
NPIPA2
NPIPB8
ABCC6P1
RRN3P3
SULT1A3
CLEC19A
CLN3
BCAR4
MIR4721
MIR4718
RN7SL90P
MIR548W
RN7SL245P
RN7SL557P
MIR4517
SNX29P2
MIR484

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.13.

Table S77. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ABL1
SET
NUP214
NOTCH1
RALGDS
TSC1
BRD3
FNBP1
LAMC3
PHPT1
ENTPD2
FCN1
NUP188
CRAT
DNM1
TBC1D13
NCS1
KCNT1
FUBP3
LHX3
EDF1
RAPGEF1
NPDC1
SETX
PTGDS
ABCA2
WDR34
PPP2R4
GLE1
PAEP
OBP2A
MRPS2
SARDH
DBH
TTF1
GTF3C4
DDX31
BARHL1
AIF1L
FAM78A
TRAF2
OLFM1
CAMSAP1
UBAC1
COL5A1
PNPLA7
ASS1
PRDM12
EXOSC2
POMT1
UCK1
FIBCD1
PRRC2B
LRRC8A
ODF2
TOR1B
C9orf78
TOR1A
USP20
SURF4
GBGT1
SURF1
SURF2
SURF6
MED22
REXO4
RPL7A
GTF3C5
ASB6
NTMT1
CIZ1
SH3GLB2
FAM73B
PTGES
LCN2
HMCN2
GPR107
C9orf142
INPP5E
LCN9
SEC16A
DPH7
CACNA1B
NACC2
FBXW5
TUBBP5
VAV2
ADAMTS13
CACFD1
SLC2A6
FCN2
C9orf116
LCN1
GPSM1
ZER1
ZDHHC12
PKN3
PPAPDC3
MED27
SOHLH1
QSOX2
SNAPC4
PMPCA
SDCCAG3
AK8
C9orf9
GFI1B
FAM69B
ZMYND19
NSMF
GOLGA2
TRUB2
COQ4
SLC27A4
URM1
CERCAM
DOLPP1
ENDOG
PRRX2
CLIC3
AGPAT2
CELP
CEL
CCBL1
OBP2B
C9orf16
EGFL7
ABO
DOLK
PHYHD1
SWI5
TPRN
SSNA1
ANAPC2
GRIN1
C8G
DPP7
MAN1B1
MAMDC4
LCN15
C9orf62
C9orf50
C9orf106
C9orf139
FUT7
EHMT1
MRPL41
LRRC26
LCN12
TMEM210
SAPCD2
RXRA
EXD3
TMEM8C
TMEM203
CARD9
LCN10
FAM166A
TUBB4B
IER5L
C9orf171
NDOR1
QRFP
NOXA1
ENTPD8
NELFB
NTNG2
WDR5
C9orf163
PPP1R26
RABL6
FAM163B
ARRDC1
C9orf169
UAP1L1
SPTAN1
C9orf173
ADAMTSL2
TOR4A
NRARP
C9orf141
SLC34A3
C9orf96
C9orf114
MIR126
SNORD62
SNORD36A
SNORD36B
C9orf37
LCN8
LCN6
GLT6D1
LINC00963
SNORD24
MIR199B
MIR602
SNORA67|ENSG00000212395.1
RNF208
KIAA1984
DNLZ
LCNL1
RNU6ATAC
SNORD62B
C9orf172
FAM157B
SNHG7
RNF224
HMGA1P4
LINC00094
SNORD62A
C9orf69
snoU13|ENSG00000238298.1
snoU13|ENSG00000238657.1
snoU13|ENSG00000238824.1
snoU13|ENSG00000239055.1
RN7SL328P
RN7SL159P
TMEM141
U3|ENSG00000252440.1
SNORD36C
SNORA31|ENSG00000252582.1
MIR4673
MIR3621
MIR548AW
MIR4669
MIR3689D2
MIR3689B
RN7SL665P
RN7SL560P
MIR3689C
MIR3154
MIR4674
MIR4292
MIR3689D1
MIR3689A
MIR4479
MIR3689F
MIR3689E
LCN6
DKFZP434A062
snoU13|ENSG00000272272.1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 19 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Frequency Score | Amp Z score | Amp Q value | Del Frequency | Del Frequency Score | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1p | 1300 | 0.17 | 0.20 | 0.487 | 0.94 | 0.15 | 0.18 | -0.136 | 1
1q | 1195 | 0.48 | 0.49 | 8.37 | 0 | 0.03 | 0.06 | -2.59 | 1
2p | 624 | 0.12 | 0.14 | -1.98 | 1 | 0.14 | 0.16 | -1.6 | 1
2q | 967 | 0.10 | 0.12 | -2.22 | 1 | 0.15 | 0.16 | -1.03 | 1
3p | 644 | 0.23 | 0.25 | 0.821 | 0.729 | 0.10 | 0.13 | -2.2 | 1
3q | 733 | 0.29 | 0.31 | 2.46 | 0.0453 | 0.08 | 0.11 | -2.31 | 1
4p | 289 | 0.02 | 0.03 | -4.53 | 1 | 0.29 | 0.29 | 1.3 | 0.25
4q | 670 | 0.02 | 0.03 | -4.25 | 1 | 0.27 | 0.28 | 1.5 | 0.202
5p | 183 | 0.17 | 0.19 | -1.36 | 1 | 0.11 | 0.13 | -2.8 | 1
5q | 905 | 0.12 | 0.15 | -1.44 | 1 | 0.17 | 0.20 | -0.266 | 1
6p | 710 | 0.19 | 0.21 | -0.13 | 1 | 0.11 | 0.14 | -1.85 | 1
6q | 556 | 0.16 | 0.20 | -0.749 | 1 | 0.16 | 0.20 | -0.749 | 1
7p | 389 | 0.27 | 0.29 | 1.43 | 0.369 | 0.08 | 0.11 | -2.76 | 1
7q | 783 | 0.23 | 0.25 | 0.987 | 0.631 | 0.09 | 0.12 | -2.29 | 1
8p | 338 | 0.34 | 0.43 | 4.45 | 4.17e-05 | 0.20 | 0.31 | 1.52 | 0.202
8q | 551 | 0.48 | 0.52 | 7.33 | 2.22e-12 | 0.08 | 0.16 | -1.36 | 1
9p | 301 | 0.12 | 0.16 | -1.87 | 1 | 0.23 | 0.26 | 0.471 | 0.731
9q | 700 | 0.09 | 0.12 | -2.43 | 1 | 0.22 | 0.24 | 0.625 | 0.648
10p | 253 | 0.19 | 0.24 | -0.18 | 1 | 0.20 | 0.25 | 0.175 | 0.933
10q | 738 | 0.11 | 0.12 | -2.27 | 1 | 0.15 | 0.17 | -1.3 | 1
11p | 509 | 0.12 | 0.14 | -2.16 | 1 | 0.13 | 0.15 | -1.98 | 1
11q | 975 | 0.10 | 0.11 | -2.33 | 1 | 0.12 | 0.14 | -1.73 | 1
12p | 339 | 0.15 | 0.17 | -1.83 | 1 | 0.11 | 0.12 | -2.74 | 1
12q | 904 | 0.15 | 0.17 | -1.03 | 1 | 0.11 | 0.13 | -1.82 | 1
13q | 560 | 0.11 | 0.18 | -1 | 1 | 0.36 | 0.41 | 4.48 | 2.45e-05
14q | 938 | 0.12 | 0.17 | -0.846 | 1 | 0.27 | 0.31 | 2.66 | 0.0153
15q | 810 | 0.03 | 0.04 | -3.89 | 1 | 0.26 | 0.27 | 1.57 | 0.202
16p | 559 | 0.24 | 0.31 | 1.82 | 0.191 | 0.22 | 0.29 | 1.46 | 0.202
16q | 455 | 0.14 | 0.25 | 0.399 | 0.961 | 0.45 | 0.52 | 7.05 | 1.8e-11
17p | 415 | 0.12 | 0.27 | 0.651 | 0.836 | 0.55 | 0.63 | 9.53 | 0
17q | 972 | 0.16 | 0.25 | 1.12 | 0.574 | 0.35 | 0.42 | 5.5 | 1.88e-07
18p | 104 | 0.13 | 0.21 | -0.804 | 1 | 0.39 | 0.44 | 4.49 | 2.45e-05
18q | 275 | 0.08 | 0.14 | -1.91 | 1 | 0.43 | 0.47 | 5.66 | 9.94e-08
19p | 681 | 0.10 | 0.15 | -1.46 | 1 | 0.35 | 0.39 | 4.33 | 3.59e-05
19q | 935 | 0.11 | 0.16 | -0.99 | 1 | 0.34 | 0.38 | 4.43 | 2.63e-05
20p | 234 | 0.39 | 0.41 | 4.12 | 0.000146 | 0.04 | 0.07 | -3.57 | 1
20q | 448 | 0.43 | 0.45 | 5.46 | 3.05e-07 | 0.02 | 0.04 | -3.73 | 1
21q | 258 | 0.13 | 0.16 | -1.97 | 1 | 0.18 | 0.21 | -0.889 | 1
22q | 564 | 0.09 | 0.14 | -1.95 | 1 | 0.34 | 0.37 | 3.59 | 0.000717

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 = /cromwell_root/fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7cb711fc-2bbf-4c6b-ad57-cd8836a24fa7/allelic_capseg_combine_seg/959b0092-a8d3-4eb2-8216-f63d88932383/call-allelic_capseg_combine_seg_task_1/BRCA-freeze-v5.allelic_capseg.seg.txt

- Markers File = ./this_file_does_not_exist.txt

- Reference Genome = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg19_GENCODE_v18_20140127.mat

- CNV Files = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/SNP6.merged.151117.hg19.CNV.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.98

- 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 122 Input Tumor Samples.

Tumor Sample Names
01BR001
01BR008
01BR009
01BR010
01BR015
01BR017
01BR018
01BR020
01BR023
01BR025

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.

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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