SNP6 Copy number analysis (GISTIC2)

Cholangiocarcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1610ZG4

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 2.0.22 (Firehose task version: 140).

Summary

There were 36 tumor samples used in this analysis: 13 significant arm-level results, 4 significant focal amplifications, and 19 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 - 4 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
11q13.3	0.001436	0.001436	chr11:68720012-69603036	9
1q22	0.013374	0.013374	chr1:120527362-158514225	359
1p22.3	0.076904	0.076904	chr1:85974031-86006008	1
12q13.2	0.22872	0.22872	chr12:54953957-54972298	2

Genes in Wide Peak

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

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

Genes
CCND1
MIR3164
TPCN2
FGF4
FGF19
MYEOV
MRGPRD
MRGPRF
ORAOV1

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
MUC1
NOTCH2
NTRK1
PRCC
TPM3
PDE4DIP
RN7SL612P
MIR765
snoU13\|ENSG00000238843.1
BGLAP
SNORA26\|ENSG00000252236.1
SCARNA4\|ENSG00000252808.1
SNORA42\|ENSG00000207475.1
snoU13\|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59\|ENSG00000252682.1
SNORA58\|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3\|ENSG00000252669.1
snoU13\|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31\|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13\|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
CD1A
CD1B
CD1C
CD1D
CD1E
CD5L
CHRNB2
CKS1B\|ENSG00000173207.8
CLK2
CRABP2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCGR1A
FDPS
FLG
FMO5
GBA
GJA5
GJA8
HDGF
IL6R
ILF2
INSRR
IVL
KCNN3
LMNA
LOR
MCL1
SMCP
MEF2D
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
DAP3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
SH2D2A
PRPF3
ARHGEF2
CHD1L
SLC25A44
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
SLC27A3
TDRKH
CD160
PMF1
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SMG5
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
LAMTOR2
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
UBQLN4
RAB25
PGLYRP4
RHBG
ATP8B2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
HORMAD1
POLR3GL
TMEM79
LCE3D
AQP10
PYGO2
NUP210L
MEX3A
C1orf85
PGLYRP3
FCRL1
FCRL3
GABPB2
TCHHL1
RPTN
TDRD10
SHE
DCST2
LIX1L
TSACC
IQGAP3
APOA1BP
OR10T2
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
NBPF12
LELP1
DCST1
BNIPL
LRRC71
SPRR4
PPIAL4A
TTC24
LCE4A
NBPF11
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF16
ANKRD34A
HIST2H2AB
S100A7A
RXFP4
OR10R2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PEAR1
NOTCH2NL
LYSMD1
HRNR
FLG2
VHLL
OR10K2
OR10K1
NBPF9
HIST2H2BF
ETV3L
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
C2CD4D
NBPF20
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p22.3.

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

Genes
DDAH1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.2.

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

Genes
PDE1B
PPP1R1A

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 - 19 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
1p36.21	4.7888e-22	4.7888e-22	chr1:7829287-29140747	375
4q34.3	5.9932e-06	5.9932e-06	chr4:178100730-182757119	9
9p21.3	2.1537e-05	4.7036e-05	chr9:21626574-22448737	5
14q22.1	0.032552	0.032552	chr14:50993752-51312472	5
3p13	0.016158	0.033075	chr3:44449563-78650559	343
14q32.11	2.1537e-05	0.033075	chr14:60106279-107349540	489
3p25.3	0.021694	0.045413	chr3:1-50126729	421
10q26.12	0.04873	0.048612	chr10:97318150-135534747	335
12q24.13	0.067933	0.064106	chr12:83527712-133851895	438
6q13	0.021943	0.075759	chr6:57084910-87648565	85
13q21.32	0.08229	0.081712	chr13:63305697-78275817	44
11q25	0.13909	0.13909	chr11:90288262-135006516	387
9q21.11	0.06273	0.14944	chr9:38614979-131009466	500
5q13.3	0.16937	0.17683	chr5:44817857-94730339	241
14q32.33	1.2155e-05	0.21614	chr14:52289590-107349540	549
8p23.1	0.23608	0.22894	chr8:10891960-11105303	1
16q23.1	0.23608	0.22894	chr16:78098006-79299841	3
6q25.3	0.039656	0.26142	chr6:1-171115067	1266
14q32.12	2.1537e-05	0.29584	chr14:1-107349540	938

Genes in Wide Peak

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

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

Genes
PAX7
SDHB
ARID1A
MDS2
SCARNA24\|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13\|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18\|ENSG00000252691.1
SCARNA17\|ENSG00000252190.1
MAN1C1
snoU13\|ENSG00000238889.1
SYF2
snoU13\|ENSG00000238986.1
RN7SL857P
snoU13\|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13\|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13\|ENSG00000239020.1
PADI6
MIR3972
U1\|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1\|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13\|ENSG00000238818.1
DDI2
AGMAT
SCARNA21\|ENSG00000251866.1
C1orf195
SCARNA11\|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13\|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70\|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13\|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16\|ENSG00000252404.1
RN7SL451P
SNORA77\|ENSG00000221083.1
RN7SL729P
TNFRSF9
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
E2F2
ECE1
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GALE
SFN
GPR3
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
FCN3
ALDH4A1
EIF4G3
PER3
MAP3K6
DHRS3
VAMP3
THEMIS2
H6PD
CROCC
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RCAN3
PADI2
LYPLA2
PARK7
CTRC
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
CELA3B
PADI4
TMEM50A
STX12
CLIC4
SZRD1
LDLRAP1
FBXO2
FBXO6
HSPB7
AHDC1
SMPDL3B
UBIAD1
PADI1
SLC45A1
HP1BP3
CELA2B
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
TMEM51
XKR8
ARHGEF10L
VPS13D
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
RCC2
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PTCHD2
KIF17
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
PINK1
PRAMEF1
PRAMEF2
PHACTR4
AUNIP
EFHD2
RSG1
MUL1
LIN28A
FAM110D
DHDDS
SPSB1
ZNF436
TAS1R2
ACTL8
SESN2
TMEM222
USP48
NBPF3
LZIC
TRIM63
SYTL1
IGSF21
KIAA2013
STPG1
UBXN11
FBXO44
ATPIF1
FHAD1
FAM46B
RBP7
C1orf172
LRRC38
AADACL3
IFFO2
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
C1orf127
C1orf213
PDIK1L
SLC2A7
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
AKR7L
TMCO4
ZNF683
SLC25A34
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
CATSPER4
TMEM82
TRNP1
CD164L2
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR34A
PRAMEF11
PRAMEF6
MINOS1
PRAMEF7
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
C1orf234
MIR4253
MIR1273D
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4418
MIR378F
MIR5697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173
snoU13\|ENSG00000252388.1
RNA5SP172
RN7SKP136
AGA
NEIL3

Genes in Wide Peak

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

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

Genes
RN7SL151P
CDKN2A
CDKN2B
MTAP
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q22.1.

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

Genes
NIN
snoU83B
RN7SL452P
ATL1
SAV1

Genes in Wide Peak

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

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

Genes
FHIT
MITF
BAP1
FOXP1
SETD2
PBRM1
RN7SKP61
RN7SL647P
RN7SL92P
ZNF717
LINC00960
FAM86DP
RN7SL294P
snoU13\|ENSG00000238416.1
GXYLT2
RNA5SP136
snoU13\|ENSG00000238568.1
RYBP
LINC00870
LINC00877
RN7SL271P
GPR27
RN7SL418P
MIR3136
RNA5SP135
RN7SL482P
U3\|ENSG00000200222.1
SNTN
RNA5SP134
LINC00698
RN7SL863P
PTPRG
U3\|ENSG00000212211.1
NPCDR1
RPP14
RNU6ATAC26P
PDE12
snoU13\|ENSG00000238905.1
HESX1
RNA5SP133
RN7SKP45
MIR3938
ESRG
CHDH
SNORD63\|ENSG00000251987.1
SNORA26\|ENSG00000212608.1
SNORD38\|ENSG00000207109.1
RN7SL821P
snoU13\|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19\|ENSG00000222345.1
SNORD19B\|ENSG00000238862.1
SNORD19\|ENSG00000212493.1
SNORD19B\|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13\|ENSG00000238350.1
snoU13\|ENSG00000239128.1
snoU13\|ENSG00000251938.1
PRSS44
PRSS45
SNORD77\|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3\|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ALAS1
AMT
APEH
ARF4
RHOA
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
CNTN3
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
ROBO2
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
TMF1
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
SUCLG2
BSN
ACKR5
UBA3
RRP9
MAGI1
CACNA2D2
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CCR9
USP19
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
EXOSC7
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
PTPN23
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
ELP6
QRICH1
PXK
FEZF2
EBLN2
DALRD3
SHQ1
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZKSCAN7
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
SELK
PROK2
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
UCN2
ZNF502
RFT1
ACTR8
SLC25A26
ZNF501
GPR62
FAM3D
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SYNPR
LSMEM2
ASB14
FAM19A4
CCDC12
PPP4R2
PRICKLE2
C3orf67
KCTD6
KLHDC8B
DNAH12
DENND6A
ALS2CL
TMIE
EOGT
FBXW12
CCDC66
EIF4E3
CCDC36
PRSS42
ZNF445
SPATA12
TMEM110
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
FAM19A1
MIR425
SPINK8
ARIH2OS
C3orf84
CCR2
PRSS46
FRG2C
MIR1284
MIR1324
MIR4271
MIR4273
MIR4787
MIR4443

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.11.

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

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

Genes in Wide Peak

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

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

Genes
VHL
CTNNB1
FANCD2
MLH1
MYD88
PPARG
RAF1
XPC
SRGAP3
SETD2
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13\|ENSG00000238350.1
snoU13\|ENSG00000239128.1
snoU13\|ENSG00000251938.1
PRSS44
PRSS45
SNORD77\|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3\|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
U8\|ENSG00000212145.2
RN7SKP58
SCARNA21\|ENSG00000252409.1
ZNF621
SNORA64\|ENSG00000202517.1
RN7SL411P
SNORA62\|ENSG00000202363.1
SNORA6
MIR26A1
ITGA9
RNA5SP129
snoU13\|ENSG00000238929.1
RNU6ATAC4P
TRANK1
HSPD1P6
RN7SKP227
RNA5SP128
RN7SL296P
TMPPE
CCR4
TRIM71
snoU13\|ENSG00000238646.1
SNORA25\|ENSG00000201701.1
OSBPL10
STT3B
RNA5SP127
U3\|ENSG00000199927.1
LINC00693
CMC1
RN7SL859P
SNORD5\|ENSG00000272166.1
RNA5SP126
RNA5SP125
RN7SL216P
LINC00691
UBE2E2
HMGB1P5
RNY4P22
MIR3135A
U7\|ENSG00000271841.1
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13\|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13\|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13\|ENSG00000238345.1
snoU13\|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43\|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13\|ENSG00000239126.1
EGOT
SNORA43\|ENSG00000253049.1
RN7SKP144
RN7SL120P
ACAA1
ACVR2B
AMT
APEH
RHOA
ATP2B2
BTD
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CCR1
CCR3
CCR5
CCR8
ACKR2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
CELSR3
FBLN2
GOLGA4
XCR1
GPX1
GRM7
HRH1
IL5RA
IMPDH2
IRAK2
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PTH1R
QARS
RAB5A
RARB
RPL15
RPL32
SATB1
SCN5A
SCN10A
SEC13
SETMAR
SLC6A1
SLC6A6
SMARCC1
STAC
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
CLEC3B
TOP2B
UBA7
UBE2E1
UBP1
USP4
UQCRC1
VIPR1
ZNF35
BRPF1
COLQ
EOMES
CAMK1
BHLHE40
KAT2B
BSN
ACKR5
RPL14
SEC22C
LRRFIP2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
TBC1D5
TATDN2
IP6K1
EPM2AIP1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
ARPC4
ZNF197
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
CXCR6
CHL1
ARPP21
CCR9
USP19
WDR6
TREX1
SCN11A
TRAK1
DHX30
SACM1L
SCAP
EXOSC7
CAND2
CLASP2
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
KLHL18
LARS2
CAPN7
MKRN2
FBXL2
CNOT10
TMEM158
THUMPD3
MYRIP
PTPN23
SUSD5
HACL1
TTLL3
CNTN6
RBMS3
NKIRAS1
PRSS50
GMPPB
LMCD1
VILL
SSUH2
TRNT1
DYNC1LI1
CRBN
SS18L2
CCDC174
SHISA5
TMA7
ZNF589
IP6K2
NCKIPSD
GHRL
LZTFL1
P4HTM
SLC6A20
ELP6
SNRK
QRICH1
CMTM6
SLC25A38
ULK4
OXSM
ANO10
DALRD3
ARL8B
SETD5
TMEM40
NGLY1
BRK1
ZKSCAN7
RAD18
KIF15
KIAA1143
HHATL
WDR48
LRRN1
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
TSEN2
C3orf20
ATRIP
NICN1
MON1A
JAGN1
IL17RC
GTDC2
EAF1
DCLK3
UCN2
ZNF502
OXNAD1
CMTM7
ZNF501
FANCD2OS
LRRC3B
GALNT15
KCNH8
LYZL4
KLHL40
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
ZCWPW2
NEK10
CMTM8
CCDC13
FGD5
CNTN4
XIRP1
TTC21A
KLHDC8B
ZNF620
ALS2CL
TMIE
FBXW12
ZNF619
LINC00692
TCAIM
SUMF1
RPUSD3
PRRT3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
TPRXL
ZNF445
TOPAZ1
AMIGO3
ZNF662
CDHR4
FAM212A
MIR191
MIR425
GLB1
SPINK8
ARIH2OS
C3orf84
MIR563
FAM198A
CCR2
PRSS46
MIR378B
MIR4271
MIR3714
KRBOX1
MIR4791
MIR4790
MIR4443
MIR4792
MIR4442

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.12.

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

Genes
FGFR2
TLX1
NFKB2
SUFU
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60\|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19\|ENSG00000222588.1
SNORA19\|ENSG00000207468.1
U3\|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13\|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17\|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13\|ENSG00000239125.1
SMNDC1
RN7SL450P
U4\|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13\|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112\|ENSG00000253068.1
FGF8
snoU13\|ENSG00000239091.1
SNORD112\|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12\|ENSG00000212464.1
ERLIN1
snoU13\|ENSG00000238472.1
COX15
ENTPD7
snoU13\|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
CPN1
CTBP2
CYP2E1
CYP17A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
GOT1
PRLHR
GRK5
HABP2
HMX2
HPS1
INPP5A
ABLIM1
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
ALDH18A1
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
DCLRE1A
FRAT1
ACTR1A
NPM3
GLRX3
DPYSL4
TACC2
MGEA5
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
DNMBP
FRAT2
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
PDCD4
VENTX
R3HCC1L
POLL
BLNK
KCNIP2
CUZD1
CALY
CALHM2
CUTC
CHST15
ACSL5
CCNJ
ZRANB1
TTC40
NSMCE4A
CNNM2
WBP1L
C10orf118
CRTAC1
CWF19L1
PI4K2A
WDR11
FAM178A
DHX32
TDRD1
BCCIP
C10orf2
TM9SF3
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
FAM204A
LHPP
MMS19
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
PLEKHS1
PDZD7
C10orf88
UBTD1
WDR96
LRRC27
TRIM8
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
GPR123
LZTS2
LCOR
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
MTG1
BBIP1
FANK1
OPALIN
SYCE1
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
C10orf32
GSTO2
SFR1
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
C10orf82
CACUL1
CCDC147
PWWP2B
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
FUOM
JAKMIP3
STK32C
RBM20
KCNK18
NANOS1
HMX3
CCDC172
CC2D2B
ARMS2
TEX36
C10orf120
FOXI2
GOLGA7B
C10orf85
C10orf62
FRG2B
SPRN
MIR146B
MIR202
FAM196A
MIR607
TLX1NB
C10orf131
MIR1307
MIR2110
MIR378C
MIR3157
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.13.

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

Genes
BCL7A
BTG1
ALDH2
PTPN11
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13\|ENSG00000238822.1
RN7SL534P
snoU13\|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9\|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9\|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70\|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13\|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38\|ENSG00000201042.1
RNA5SP374
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56\|ENSG00000200112.1
RN7SL865P
SNORA27\|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7\|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50\|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40\|ENSG00000264043.2
FICD
RNA5SP371
SNORD74\|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13\|ENSG00000238914.1
U8\|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13\|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13\|ENSG00000238800.1
SLC5A8
snoU13\|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13\|ENSG00000239073.1
SNORD74\|ENSG00000201502.1
snoU13\|ENSG00000238361.1
snoU13\|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3\|ENSG00000221148.1
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DCN
EPYC
DTX1
DUSP6
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
LTA4H
MMP17
MSI1
MVK
MYBPC1
MYL2
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
KERA
PRDM4
CIT
PWP1
NUDT4
FZD10
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
UTP20
MRPL42
IFT81
FAM216A
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
CCDC64
SDSL
IQCD
DEPDC4
CCDC38
TMEM132D
SLC15A4
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
RAD9B
FAM109A
TMTC3
C12orf50
ALDH1L2
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
CCER1
SLC17A8
LRRC43
TCP11L2
C12orf79
POC1B
GPR133
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
DDX51
MMAB
HCAR2
TMEM119
C12orf74
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
CLLU1OS
CLLU1
MIR492
C12orf73
ZNF605
MIR1251
MIR4303
MIR3685
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR5188
MIR5700

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q13.

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

Genes
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70\|ENSG00000206886.1
RNA5SP210
SNORD112\|ENSG00000252932.1
HTR1B
U6\|ENSG00000272445.1
snoU13\|ENSG00000239132.1
RNA5SP209
RN7SKP163
U3\|ENSG00000221332.1
MB21D1
snoU13\|ENSG00000238464.1
OOEP
OGFRL1
U3\|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65\|ENSG00000212229.1
FKBP1C
LINC00680
PRIM2
BAI3
BCKDHB
COL9A1
COL12A1
COX7A2
EEF1A1
IMPG1
ME1
MYO6
NT5E
PGM3
ELOVL4
TPBG
TTK
PTP4A1
TBX18
HMGN3
SNAP91
SYNCRIP
KIAA1009
RIMS1
DOPEY1
PHF3
MTO1
IBTK
SENP6
SLC17A5
FILIP1
LGSN
PHIP
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
SNX14
FAM135A
SMAP1
LINC00472
KHDC1
SH3BGRL2
UBE3D
MRAP2
RIPPLY2
IRAK1BP1
CD109
KHDC3L
PRSS35
LCA5
KHDRBS2
DPPA5
EYS
MIR30A
MIR30C2
KHDC1L
MIR548U
MIR4282
MTRNR2L9
MIR4463

Genes in Wide Peak

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

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

Genes
RNY3P7
CLN5
RN7SL571P
LINC00561
C13orf45
LINC00347
LINC00381
RNY1P5
LINC00402
LINC00392
LINC00393
RNY1P8
SNORA9\|ENSG00000199282.1
SNORA68\|ENSG00000251715.1
SNORD37\|ENSG00000212377.1
RNA5SP32
LINC00348
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
LINC00355
LINC00395
KLF5
DACH1
LMO7
PCDH9
UCHL3
SCEL
TBC1D4
PIBF1
KLF12
DIS3
MYCBP2
FBXL3
KLHL1
BORA
KCTD12
COMMD6
MZT1
IRG1
MIR3665
MIR4704
MIR548X2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

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

Genes
DDX6
PCSK7
SDHD
MAML2
BIRC3
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
snoU13\|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13\|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8\|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13\|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64\|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11\|ENSG00000252992.1
RNY4P6
ZNF259
snoU13\|ENSG00000238625.1
LINC00900
snoU13\|ENSG00000239153.1
ACA59\|ENSG00000252870.1
snoU13\|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39\|ENSG00000264997.1
RNA5SP349
RNA5SP348
MMP12
WTAPP1
snoU13\|ENSG00000239154.1
snoU13\|ENSG00000252679.1
MIR3920
snoU13\|ENSG00000238388.1
RN7SKP115
RN7SL222P
RN7SKP53
RNA5SP347
RNA5SP346
RNA5SP345
SRSF8
SRSF8
MIR548L
VSTM5
RN7SL195P
snoU13\|ENSG00000238437.1
MED17
SNORA40\|ENSG00000210825.1
SNORA18\|ENSG00000207145.1
SNORD5\|ENSG00000239195.1
SNORA8\|ENSG00000207304.1
SNORA1\|ENSG00000206834.1
SNORD6
SNORA32\|ENSG00000206799.1
SNORA25\|ENSG00000207112.1
SCARNA9
RN7SL223P
SLC36A4
snoU13\|ENSG00000239086.1
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
MMP1
MMP3
MMP7
MMP8
MMP10
MMP13
MRE11A
MTNR1B
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
TRPC6
UPK2
ZBTB16
ZNF202
CUL5
BARX2
JRKL
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
EI24
FEZ1
CEP57
ARHGAP32
RBM7
MPZL2
YAP1
HYOU1
ATP5L
GPR83
ADAMTS8
TREH
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
PANX1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
C11orf54
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
CWC15
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
ANKRD49
TTC12
C11orf57
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TEX12
CRTAM
IFT46
SMCO4
PRDM10
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
CCDC82
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
DCUN1D5
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
C11orf70
DIXDC1
KIAA1731
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
FAT3
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
AMOTL1
CCDC67
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
SPATA19
HEPACAM
ANGPTL5
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
HEPHL1
FOLR4
KDM4E
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR1261
MIR1304
MIR4301
MIR1260B
CASP12
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4693

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.11.

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

Genes
GNAQ
FANCC
OMD
SYK
TAL2
XPA
NR4A3
MIR4672
RNA5SP296
SNORA65
SNORD116\|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13\|ENSG00000238530.1
MIR455
COL27A1
FKBP15
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31\|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
snoU13\|ENSG00000238746.1
RNA5SP288
MIR27B
MIR23B
MIR2278
PCAT7
ZNF169
snoU13\|ENSG00000238792.1
MIRLET7DHG
CENPP
SNORA84
snoU13\|ENSG00000238996.1
LINC00475
LINC00484
MIR3153
SHC3
U3\|ENSG00000252299.1
U6\|ENSG00000271923.1
SPATA31C1
SNORA26\|ENSG00000212421.1
RN7SKP264
IDNK
SNORD112\|ENSG00000252256.1
snoU13\|ENSG00000238608.1
RN7SKP242
SPATA31D3
SPATA31D4
SPATA31D5P
SNORD95\|ENSG00000200969.1
RNA5SP287
TLE4
RN7SKP59
PCA3
snoU13\|ENSG00000238598.1
RNY4P1
RN7SKP47
RNA5SP286
snoU13\|ENSG00000238402.1
RNA5SP285
MIR204
RN7SL570P
CBWD3
PGM5P2
RNA5SP284
SNORA70\|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70\|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70\|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70\|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
ABCA1
AK1
ALAD
ALDH1A1
ALDOB
AMBP
ANXA1
APBA1
AUH
BAAT
KLF9
C5
CDK9
CKS2
COL15A1
SLC31A1
SLC31A2
CTSL
CYLC2
DAPK1
DBC1
ECM2
LPAR1
S1PR3
MEGF9
ENG
STOM
FBP1
FKTN
FOXE1
FPGS
FXN
NR5A1
GAS1
NR6A1
GCNT1
GNG10
GOLGA1
GSN
HNRNPK
HSD17B3
HSPA5
TNC
IARS
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
NTRK2
ROR2
OGN
ORM1
ORM2
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP3R2
PPP6C
PRKACG
PSMB7
PSMD5
PTCH1
PTGS1
PTPN3
RAD23B
RGS3
RORB
RPL12
STXBP1
TGFBR1
TLE1
TLR4
TMOD1
TRAF1
TXN
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
PIP5K1B
IKBKAP
CDC14B
TMEFF1
CTNNAL1
FBP2
DPM2
PRPF4
KLF4
LHX2
FAM189A2
TJP2
GABBR2
GDA
GNA14
RALGPS1
TRIM14
TNFSF15
PTBP3
SH2D3C
RABEPK
SEMA4D
ANP32B
SPTLC1
SMC2
ZBTB6
NEK6
ACTL7A
GADD45G
SPIN1
SEC61B
SLC35D2
CNTRL
AKAP2
RPL35
ZNF510
HABP4
PTGR1
TRIM32
ERP44
ZBTB43
SMC5
FAM120A
VPS13A
ASTN2
AGTPBP1
BICD2
KIAA0368
TDRD7
SLC44A1
ANGPTL2
CDK20
RABGAP1
TMEM2
TMEM245
CIZ1
DFNB31
NIPSNAP3A
GAPVD1
PHF19
ZNF658
SPATA31A7
FBXW2
OR1J4
OR2K2
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
ST6GALNAC4
INVS
TOR2A
PSAT1
UBQLN1
SLC2A8
ST6GALNAC6
DEC1
ABHD17B
GOLM1
C9orf156
RAB14
POLE3
NANS
MRPL50
RC3H2
EPB41L4B
NUTM2F
DIRAS2
ASPN
BSPRY
TEX10
FAM206A
NMRK1
NOL8
C9orf40
TMEM38B
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDK5RAP2
BARX1
RNF20
ZBTB26
DENND1A
SLC46A2
ZNF462
NAA35
SLC28A3
SUSD1
IPPK
FAM129B
WNK2
SECISBP2
C9orf16
MAPKAP1
ZCCHC6
GALNT12
CNTNAP3
SVEP1
RMI1
TRPM3
PTGES2
GKAP1
AKNA
ISCA1
ARPC5L
HDHD3
ZNF484
FSD1L
CEP78
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
HIATL1
C9orf3
FGD3
MVB12B
LRSAM1
MRRF
KIF12
PALM2
SLC25A25
WDR31
ZNF618
FAM122A
GRIN3A
TMC1
RNF183
C9orf41
C9orf57
C9orf85
C9orf135
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
TRPM6
DAB2IP
NXNL2
OR1Q1
TTLL11
RASEF
TTC16
FAM120AOS
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
PRUNE2
OLFML2A
TMEM252
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CBWD5
CDC26
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
CRB2
SCAI
C9orf117
C9orf47
SPATA31E1
OR13C9
OR13D1
FOXD4L3
GPR144
OR1J1
OR1B1
MURC
FOXD4L4
PTAR1
ERCC6L2
SPATA31A6
SPATA31D1
C9orf153
CTSL3P
OR13C2
OR1L6
OR5C1
OR1K1
FAM102A
FAM74A4
C9orf170
C9orf152
SNX30
WDR38
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
ANKRD20A3
ANKRD20A2
NUTM2G
FOXB2
C9orf129
FAM27A
DNAJC25
SPATA31A2
SPATA31A4
CBWD6
SPATA31A1
FOXD4L6
FOXD4L5
MIR600HG
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR3074
MIR3154
MIR4291
MIR4290
MIR4289
CCDC180
MIR3911
MIR3927
MIR4477A
MIR3960
MIR4478
MIR4670

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.3.

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

Genes
IL6ST
PIK3R1
LUCAT1
SNORA70\|ENSG00000206958.1
RNA5SP187
RN7SL629P
RN7SKP34
MIR3607
COX7C
NBPF22P
RN7SKP295
SCARNA18\|ENSG00000238835.1
RN7SL378P
SSBP2
SNORA31\|ENSG00000251828.1
snoU13\|ENSG00000239159.1
MTX3
HOMER1
SNORA18\|ENSG00000206592.1
RNY3P1
BHMT2
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13\|ENSG00000238688.1
RNA5SP186
POLK
SNORA40\|ENSG00000212363.1
RN7SL814P
MIR4804
RN7SL153P
MIR4803
snoU13\|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13\|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13\|ENSG00000238334.1
SNORA50\|ENSG00000220986.1
RN7SL103P
7SK\|ENSG00000249352.3
U8\|ENSG00000212249.2
snoU13\|ENSG00000238400.1
SNORA76\|ENSG00000252904.1
RN7SL169P
HTR1A
CKS1B\|ENSG00000268942.1
KIF2A
RN7SKP157
FKSG52
MIR582
GAPT
snoU13\|ENSG00000238899.1
snoU13\|ENSG00000238717.1
RNU6ATAC2P
RNA5SP185
RNA5SP184
snoU13\|ENSG00000238326.1
RNA5SP183
MIR5687
MIR449C
MIR449B
MIR449A
GPX8
GZMK
MIR4459
RN7SL801P
MIR581
PELO
ITGA1
RNA5SP182
snoU13\|ENSG00000238702.1
HCN1
TRIM23
ARSB
BHMT
BTF3
CCNB1
CCNH
CDK7
CETN3
CKMT2
ERCC8
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
GZMA
HEXB
HMGCR
ISL1
ITGA2
TNPO1
CD180
MAP1B
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
PDE4D
PMCHL2
RAD17
RASA1
RASGRF2
RPS23
SMN1
SMN2
TAF9
TBCA
NR2F1
THBS4
XRCC4
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
SCAMP1
CARTPT
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
CWC27
CCNO
NSA2
FST
POLR3G
PLK2
IQGAP2
ESM1
ADAMTS6
SV2C
MRPS27
PPWD1
SKIV2L2
PART1
FAM169A
DIMT1
DMGDH
IPO11
GCNT4
DHX29
DDX4
SGTB
ARL15
AGGF1
DEPDC1B
BDP1
ERBB2IP
NLN
ARRDC3
ZSWIM6
ANKRA2
MCCC2
CENPK
ARHGEF28
SLC30A5
CENPH
GPBP1
PARP8
ANKRD55
MCTP1
PTCD2
ELOVL7
TRAPPC13
ATG10
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
GFM2
SPZ1
NDUFAF2
MRPS36
ATP6AP1L
SNX18
FCHO2
RAB3C
LYSMD3
SETD9
IL31RA
EMB
JMY
POU5F2
TMEM171
TMEM174
POC5
ACOT12
SREK1
SLC38A9
TMEM167A
MBLAC2
TMEM161B
MARVELD2
MIER3
CDC20B
PAPD4
ZNF366
FAM151B
CCDC125
CMYA5
ANKRD31
SERINC5
KIAA0825
C5orf64
RNF180
SREK1IP1
ANKRD34B
MCIDAS
ACTBL2
MAST4
RGS7BP
LINC00461
SMIM15
GTF2H2C
SERF1B
ANKDD1B
LRRC70
FAM159B
MIR2277
MIR4280
MTRNR2L2
MIR3660
OCLN
MIR548AE2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.33.

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

Genes
AKT1
KTN1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51\|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13\|ENSG00000238853.1
RN7SL546P
snoU13\|ENSG00000239061.1
RN7SL472P
LINC00524
U3\|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113\|ENSG00000222185.1
SNORD112\|ENSG00000252009.1
SNORD113\|ENSG00000222095.1
SNORD113\|ENSG00000201710.1
SNORD113\|ENSG00000201036.1
SNORD113\|ENSG00000201500.1
SNORD113\|ENSG00000200150.1
SNORD112\|ENSG00000251918.1
SNORD112\|ENSG00000252144.1
SNORD112\|ENSG00000251949.1
SNORD112\|ENSG00000252873.1
SNORD112\|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6\|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13\|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3\|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13\|ENSG00000238978.1
SNORA79\|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46\|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32\|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7\|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13\|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13\|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11\|ENSG00000221060.1
SLC10A1
CCDC177\|ENSG00000267909.1
CCDC177\|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3\|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3\|ENSG00000200693.1
WDR89
SCARNA20\|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112\|ENSG00000252380.1
SIX1
U3\|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
RN7SKP99
NAA30
RN7SL461P
LINC00520
RPL13AP3
TBPL2
MIR4308
RNU6ATAC9P
RN7SL588P
ERO1L
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
CDKN3
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FOS
FUT8
GALC
GCH1
GMFB
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
PSMC6
PTGDR
PTGER2
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SLC8A3
SNAPC1
SPTB
STYX
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
DLGAP5
AREL1
TECPR2
MED6
CNIH
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
PAPOLA
ACOT2
TMED10
FERMT2
PTPN21
WDHD1
NID2
VASH1
ATG14
ZBTB1
SNW1
PCNX
DAAM1
SAMD4A
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
TIMM9
MLH3
KCNH5
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
DACT1
EVL
GSKIP
CINP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
GNG2
TMEM260
FBXO34
CDCA4
NRDE2
ATG2B
UBR7
C14orf105
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
AP5M1
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNT16
PLEKHH1
TXNDC16
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
SMOC1
MOAP1
IRF2BPL
MPP5
INF2
PCNXL4
GNPNAT1
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
DDHD1
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
MAPK1IP1L
IFT43
L3HYPDH
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
SOCS4
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
RDH12
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SYNE3
TMEM30B
EML5
NUDT14
LINC00521
SERPINA11
GPR137C
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
C14orf39
CCDC85C
SERPINA9
VSX2
SLC35F4
LRRC9
COX8C
ASPG
RAB15
TOMM20L
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
LINC00238
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4505
MIR4708
MIR151B
MIR4710
MIR2392
MIR5694
MIR5580

Genes in Wide Peak

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

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

Genes
MIR598

Genes in Wide Peak

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

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

Genes
RNA5SP431
PIH1
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.3.

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

Genes
FGFR1OP
HIST1H4I
PRDM1
CCND3
DAXX
FANCE
HMGA1
IRF4
MLLT4
MYB
PIM1
POU5F1
TRIM27
ROS1
TNFAIP3
DEK
TFEB
GOPC
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45\|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13\|ENSG00000239136.1
AIRN
SNORA29
SNORA20\|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13\|ENSG00000252609.1
SNORD28\|ENSG00000212295.1
TFB1M
U8\|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13\|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13\|ENSG00000238594.1
RAET1K
SNORA2\|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112\|ENSG00000252476.1
SNORA27\|ENSG00000201807.1
RNA5SP219
7SK\|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13\|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33\|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13\|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13\|ENSG00000238563.1
U3\|ENSG00000253091.1
snoU13\|ENSG00000239095.1
snoU13\|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13\|ENSG00000238775.1
SNORA40\|ENSG00000212587.1
RN7SL617P
snoU13\|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13\|ENSG00000238974.1
SNORA73\|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33\|ENSG00000202283.1
snoU13\|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18\|ENSG00000252249.1
U3\|ENSG00000221455.1
U3\|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13\|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73\|ENSG00000222145.1
RN7SL183P
snoU13\|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70\|ENSG00000206886.1
RNA5SP210
SNORD112\|ENSG00000252932.1
HTR1B
U6\|ENSG00000272445.1
snoU13\|ENSG00000239132.1
RNA5SP209
RN7SKP163
U3\|ENSG00000221332.1
MB21D1
snoU13\|ENSG00000238464.1
OOEP
OGFRL1
U3\|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65\|ENSG00000212229.1
FKBP1C
LINC00680
PRIM2
RAB23
BAG2
FAM83B
RN7SKP256
U3\|ENSG00000251930.1
RN7SL244P
RN7SK
GSTA1
RN7SL580P
SNORD66\|ENSG00000212532.1
DEFB133
GLYATL3
OPN5
RN7SKP116
ANKRD66
MIR586
MIR4642
TCTE1
TMEM151B
RSPH9
SCARNA15\|ENSG00000252218.1
RN7SL403P
MEA1
snoU13\|ENSG00000238611.1
U3\|ENSG00000221252.1
GUCA1B
SNORA8\|ENSG00000206977.1
TOMM6
MIR4641
RNA5SP207
TREML3P
NFYA
APOBEC2
LINC00951
TDRG1
SNORA8\|ENSG00000212586.1
RN7SL465P
SNORD45\|ENSG00000200706.1
RN7SL285P
RN7SL273P
snoU13\|ENSG00000238375.1
SNORD112\|ENSG00000252687.1
COX6A1P2
RAB44
SRSF3
RN7SL748P
RN7SL502P
SNORA40\|ENSG00000212579.1
SNRPC
snoU13\|ENSG00000238484.1
RN7SL200P
snoU13\|ENSG00000239059.1
NUDT3
SBP1
GGNBP1
RN7SL26P
MIR5004
HCG25
RNY4P10
HCG24
PPP1R2P1
TAP2
HCG23
RNA5SP206
CYP21A1P
MIR1236
CFB
SNORD52
SNORD48
LY6G6E
MEGT1
MIR4646
LY6G5B
SNORA38\|ENSG00000200816.1
SNORD84
SNORD117
MCCD1
HCP5
PSORS1C3
HCG22
HCG21
RN7SL175P
MIR4640
RN7SKP186
LINC00243
HCG20
RN7SL353P
MIR877
PRR3
HCG18
HCG17
SNORA48\|ENSG00000252228.1
SNORD32B
OR10C1
OR12D1P
OR2J1
HCG16
HCG15
RN7SL471P
C6orf100
HCG14
LINC00533
ZSCAN12
ZNF192P1
ZSCAN12P1
U3\|ENSG00000199851.1
HIST1H2AJ
TRNAI6
HIST1H2AG
HIST1H2BJ
TRNAI2
LINC00240
GUSBP2
ZNF322
HMGN4
HCG11
HIST1H4G
HIST1H4F
HIST1H4E
HIST1H2BF
HIST1H2AD
HIST1H2BC
HIST1H4C
snoU13\|ENSG00000238322.1
RNY5P5
CMAHP
RN7SL334P
C6orf62
SNORD46\|ENSG00000251830.1
RN7SKP240
LINC00340
RN7SL128P
MBOAT1
ID4
RNA5SP205
snoU13\|ENSG00000238458.1
RNA5SP204
STMND1
U3\|ENSG00000251793.1
MIR4639
RN7SL332P
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67\|ENSG00000207419.1
snoU13\|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13\|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13\|ENSG00000238801.1
RNA5SP202
snoU13\|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13\|ENSG00000238438.1
ABCF1
ACAT2
CRISP1
AGER
AIF1
AIM1
AMD1
ARG1
ATP6V1G2
BAI3
BAK1
BCKDHB
CFB
BMP5
BMP6
DST
BPHL
BTN1A1
BYSL
C2
C4A
C4B
DDR1
RUNX2
CCNC
CDC5L
CDKN1A
CDSN
CGA
CLIC1
CLPS
CCR6
CNR1
COL9A1
COL10A1
COL11A2
COL12A1
COX7A2
ATF6B
MAPK14
CSNK2B
CTGF
CYP21A2
DNAH8
DOM3Z
DSP
E2F3
EDN1
EEF1A1
SERPINB1
SLC29A1
EPB41L2
EPHA7
EYA4
ESR1
F13A1
FABP7
FKBP5
FOXF2
FOXC1
FOXO3
FUCA2
FYN
GABBR1
GABRR1
GABRR2
GCNT2
GJA1
GCLC
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPR6
GPX5
GRIK2
GRM1
GRM4
GSTA2
GSTA3
GSTA4
GTF2H4
GUCA1A
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2BD
HIST1H2BB
HIST1H1A
HCRTR2
HDAC2
HFE
HIVEP1
HIVEP2
HSF2
HSPA1A
HSPA1B
HSPA1L
HSP90AB1
HTR1E
IFNGR1
IGF2R
IL17A
IMPG1
ITPR3
JARID2
KIFC1
KIF25
KPNA5
LAMA2
LAMA4
LPA
LTA
LTB
MARCKS
MAK
MAN1A1
MAS1
MCM3
MDFI
ME1
MAP3K4
MAP3K5
MEP1A
MICB
MLN
MOCS1
MOG
MSH5
MUT
MYO6
RPL10A
NEDD9
NEU1
NFKBIE
NFKBIL1
NMBR
NQO2
NOTCH4
NT5E
OPRM1
PARK2
PBX2
PCMT1
PDCD2
ENPP1
ENPP3
PEX6
PEX7
PGC
PGK2
PGM3
PHF1
SERPINB6
SERPINB9
PKHD1
PLAGL1
PLG
PLN
POLH
POU3F2
PPARD
PPP1R10
PPP2R5D
PREP
PKIB
MAPK13
PRL
PSMB1
PSMB8
PSMB9
PTK7
PTPRK
RGL2
PRPH2
REV3L
RHAG
RING1
BRD2
RNF5
RPS6KA2
RPS10
RPS18
RREB1
RXRB
VPS52
ATXN1
SGK1
SIM1
SKIV2L
SLC17A1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
SOX4
SRF
SRPK1
SSR1
ELOVL4
T
TAF11
MAP3K7
TAP1
TAP2
TAPBP
TBCC
TBP
TCF19
TCF21
TCP1
TCP11
TCTE3
PPP1R11
DYNLT1
TEAD3
TFAP2A
TFAP2B
THBS2
NR2E1
TNF
TNXB
TPBG
TPD52L1
TPMT
CRISP2
TTK
TUBB2A
TULP1
UTRN
VARS
VEGFA
EZR
VIP
ZNF76
ZNF165
TRIM26
ZNF184
ZKSCAN8
ZSCAN9
PTP4A1
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
OR2H2
NELFE
LST1
PLA2G7
EPM2A
HIST1H2AI
HIST1H2AK
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4K
HIST1H4J
HIST1H4H
HIST1H4B
HIST1H4L
DHX16
SUPT3H
GCM1
DDO
RNASET2
KCNK5
B3GALT4
SNX3
RNGTT
RIPK1
CD164
SYNGAP1
WISP3
STK19
IER3
SYNJ2
VNN2
VNN1
PRPF4B
WASF1
HIST1H3F
RNF8
TAAR5
MAP7
TBX18
LATS1
GCM2
WDR46
ZBTB22
TAAR2
CD83
HMGN3
PPT2
CDYL
NCR2
MED23
QKI
FHL5
AKAP7
ATG5
MED20
SLC25A27
EEF1E1
POLR1C
MAD2L1BP
WTAP
AKAP12
MDC1
TRAM2
PHACTR2
FAM65B
BCLAF1
CUL7
ZBTB24
KIAA0319
SNAP91
FIG4
NUP153
RANBP9
SLC17A4
UST
TRIM10
FLOT1
RCAN2
SLC17A2
HCG9
PRSS16
CRISP3
TRDN
CITED2
BTN3A3
BTN2A2
ECI2
PFDN6
TRIM38
CAP2
SYNCRIP
UBD
AGPAT1
SLC35A1
SCGN
DNPH1
C6orf10
FARS2
FUT9
CNPY3
TRAF3IP2
HBS1L
SLC17A3
RPP40
FRS3
PDE10A
SLC22A7
EHMT2
SMPDL3A
PNRC1
ASCC3
RAB32
TRIM31
KATNA1
BTN3A2
BTN3A1
BTN2A1
CAPN11
BVES
SEC63
NRM
STK38
SCAF8
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
FTSJD2
CDK19
CUL9
TAB2
MDN1
TSPYL4
ANKS1A
UBR2
SASH1
SYNE1
UFL1
SIRT5
PHF3
HEY2
DAAM2
GLTSCR1L
DDAH2
ORC3
CD2AP
MTCH1
ZNF318
SPDEF
MTO1
ASF1A
YIPF3
USP49
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
OR2B6
TIAM2
FBXL4
C6orf123
FAM50B
FBXO9
FBXO5
SLC17A5
OR12D2
OR11A1
RGS17
OR2W1
OR2J2
OR2H1
PDE7B
FILIP1
BRPF3
GNMT
TNFRSF21
SESN1
TINAG
DLL1
OSTM1
MRPS18B
TMEM14A
MRPL18
NDUFAF4
C6orf15
MYLIP
ABT1
DSE
PRICKLE4
PACSIN1
ZNRD1
CLDN20
NOX3
DEF6
C6orf48
SLC35B3
HDDC2
GMNN
MRPL2
TUBE1
C6orf203
TBC1D7
NRN1
CYP39A1
CDC40
RWDD1
AIG1
SNX9
FAM8A1
UBE2J1
DCDC2
ETV7
TMEM14C
LGSN
TDP2
CUTA
PPIL1
MPC1
HECA
COQ3
CLIC5
IL20RA
TREM2
TREM1
UNC93A
GFOD1
HMGCLL1
MTRF1L
CCHCR1
GTPBP2
BTN2A3P
AHI1
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
MRPS18A
MRPS10
LRRC1
PHF10
QRSL1
VNN3
TMEM63B
DDX43
FAM46A
LRRC16A
TBC1D22B
TMEM30A
EXOC2
SAYSD1
C6orf70
LMBRD1
TRERF1
ACOT13
ECHDC1
APOM
BTNL2
KCNQ5
TRIM39
AGPAT4
WRNIP1
DUSP22
TULP4
RARS2
PDSS2
LYRM4
SMIM8
VARS2
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
MRS2
PLEKHG1
ARID1B
LRFN2
AARS2
XPO5
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
CPNE5
LSM2
C6orf47
ABRACL
RRAGD
LY6G6D
ENPP5
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
ZFAND3
SLC22A23
C6orf164
BLOC1S5
MCUR1
GPSM3
FKBPL
KIF13A
PERP
SMOC2
ZSCAN31
ALDH8A1
C6orf106
MICAL1
MRPL14
DLK2
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
MANEA
ADGB
TREML2
RPP21
LINC00472
ATAT1
FRMD1
LINC00574
CCDC170
MYCT1
ZKSCAN3
ULBP2
ULBP1
ZSCAN16
LPAL2
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
KHDC1
PRRT1
EGFL8
GPR63
TXNDC5
COL21A1
OR5V1
OR2B2
PPP1R14C
OR12D3
SPACA1
RNF146
TMEM14B
SF3B5
TAAR8
SH3BGRL2
RIOK1
TFAP2D
KCNK16
RSPH3
DTNBP1
ARMC2
MNF1
L3MBTL3
FAM120B
MCHR2
PGBD1
FAXC
FNDC1
TTBK1
GJA10
ADTRP
LRP11
LTV1
SERAC1
USP45
REPS1
HIST1H2AH
HIST1H2BK
PPIL4
PAQR8
SLC22A16
RRP36
KCNK17
ABCC10
TRIM15
KLC4
UBE3D
MLIP
TJAP1
ARHGAP18
POM121L2
SYTL3
FOXQ1
GTF3C6
MRAP2
IL17F
MTFR2
EFHC1
BTBD9
KLHL32
TMEM200A
SCAND3
FOXP4
KLHDC3
NUS1
SLC26A8
IL22RA2
MAS1L
SLC18B1
SLC16A10
IP6K3
TAGAP
TAF8
RIPPLY2
IRAK1BP1
TAAR9
TAAR1
NCOA7
HINT3
PACRG
CD109
RAET1E
PM20D2
SRSF12
C6orf141
HUS1B
TRIM40
DPCR1
NRSN1
ZC2HC1B
SNRNP48
RAET1L
SAMD3
HDGFL1
PNLDC1
RNF217
NKAIN2
KHDC3L
C6orf165
CCDC167
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
PSORS1C1
PSORS1C2
PPP1R18
PTCRA
OSTCP1
KHDRBS2
TUBB
C6orf163
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
BEND6
GSTA5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
LRRC73
ADCY10P1
OARD1
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
HIST1H2AA
KDM1B
RBM24
RNF182
SMIM13
SYCP2L
PXDC1
HS3ST5
GPRC6A
RFX6
SLC35F1
GPR111
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
FAM217A
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
HCG27
TMEM244
MMS22L
WDR27
MCM9
RNF144B
HIST1H2BA
GPX6
SHPRH
NCR3
LY6G6F
MDGA1
GPR110
ZNF311
CEP57L1
PPIL6
DCBLD1
CAGE1
PRR18
PNPLA1
TREML4
RPL7L1
TAAR6
SLC35D3
MYLK4
DPPA5
CLPSL1
TREML1
RSPH4A
ECT2L
EYS
ZNF391
ZFP57
TUBB2B
SLC35B2
NUP43
C6orf58
RAET1G
KAAG1
GJB7
NHLRC1
ZKSCAN4
SUMO4
CENPW
SOGA3
CEP85L
C6orf120
THEMIS
PSMG4
SFTA2
CLPSL2
C6orf222
GFRAL
LIN28B
SAMD5
IYD
MUC21
SAPCD1
LINC00336
CRIP3
KLHL31
TCP10L2
LINC00242
C6orf201
GTF2H5
MIR206
MIR30A
MIR30C2
C6orf226
TMEM151B
FAM26F
OR2B3
OR2J3
OR14J1
PTCHD4
RFPL4B
MIR133B
FAM229B
CTAGE9
C6orf132
PPP1R3G
MIR548A1
MIR548A2
MIR587
MIR588
METTL24
TMEM242
TMEM170B
TRAPPC3L
KHDC1L
MIR1275
MIR2113
MIR1202
MIR1273C
MIR548U
MIR3143
MIR3144
MIR4282
MTRNR2L9
MIR3918
MIR3939
MIR3934
MIR3668
MIR3925
SMLR1
MICA
MUC22
MIR4464
MIR4647
MIR4466
MIR4643
MIR4465
MIR548AJ1
MIR3135B
MIR4645
MIR548AI
MIR4463
MIR4462
MIR548H5
MIR5689
MIR5683
MIR5690
MIR5685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.12.

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

Genes
AKT1
KTN1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
NIN
CCNB1IP1
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51\|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13\|ENSG00000238853.1
RN7SL546P
snoU13\|ENSG00000239061.1
RN7SL472P
LINC00524
U3\|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113\|ENSG00000222185.1
SNORD112\|ENSG00000252009.1
SNORD113\|ENSG00000222095.1
SNORD113\|ENSG00000201710.1
SNORD113\|ENSG00000201036.1
SNORD113\|ENSG00000201500.1
SNORD113\|ENSG00000200150.1
SNORD112\|ENSG00000251918.1
SNORD112\|ENSG00000252144.1
SNORD112\|ENSG00000251949.1
SNORD112\|ENSG00000252873.1
SNORD112\|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6\|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13\|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3\|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13\|ENSG00000238978.1
SNORA79\|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46\|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32\|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7\|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13\|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13\|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11\|ENSG00000221060.1
SLC10A1
CCDC177\|ENSG00000267909.1
CCDC177\|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3\|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3\|ENSG00000200693.1
WDR89
SCARNA20\|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112\|ENSG00000252380.1
SIX1
U3\|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
RN7SKP99
NAA30
RN7SL461P
LINC00520
RPL13AP3
TBPL2
MIR4308
RNU6ATAC9P
RN7SL588P
ERO1L
RNA5SP385
LINC00640
LINC00519
SNORA70\|ENSG00000201376.1
TMX1
snoU83B
RN7SL452P
CDKL1
MIR4504
RN7SKP193
ARF6
RN7SL2
RN7SL3
RNU6ATAC30P
RPL36AL
RN7SL1
RNA5SP384
SNORD112\|ENSG00000251824.1
LINC00648
SNORA25\|ENSG00000251735.1
LINC00871
SNORD127
SNORD58
snoU13\|ENSG00000238501.1
SNORA31\|ENSG00000251858.1
FBXO33
LINC00639
LINC00517
SNORA42\|ENSG00000200385.1
TTC6
MIR4503
SLC25A21
RN7SKP257
DPPA3P2
RN7SKP21
PTCSC3
snoU13\|ENSG00000238718.1
SNORA31\|ENSG00000253059.1
KIAA0391
RN7SL660P
GPR33
MIR624
BNIP3P1
LINC00645
SNORD37\|ENSG00000212270.1
TM9SF1
RNA5SP383
DHRS4L1
LINC00596
RN7SKP205
MIR208B
MIR208A
PABPN1
C14orf164
SNORA73\|ENSG00000252114.1
SNORD41\|ENSG00000212302.1
OR6J1
TRAC
TRAJ1
TRAJ2
TRAJ3
TRAJ4
TRAJ5
TRAJ6
TRAJ7
TRAJ8
TRAJ9
TRAJ10
TRAJ11
TRAJ12
TRAJ13
TRAJ14
TRAJ16
TRAJ17
TRAJ18
TRAJ19
TRAJ20
TRAJ21
TRAJ22
TRAJ23
TRAJ24
TRAJ25
TRAJ26
TRAJ27
TRAJ28
TRAJ29
TRAJ30
TRAJ31
TRAJ32
TRAJ33
TRAJ34
TRAJ35
TRAJ36
TRAJ37
TRAJ38
TRAJ39
TRAJ40
TRAJ41
TRAJ42
TRAJ43
TRAJ44
TRAJ45
TRAJ46
TRAJ47
TRAJ48
TRAJ49
TRAJ50
TRAJ52
TRAJ53
TRAJ54
TRAJ56
TRAJ57
TRAJ58
TRAJ59
TRAJ61
TRDV3
TRDC
TRDJ3
TRDJ2
TRDJ4
TRDJ1
TRDD3
TRDD2
TRDD1
TRDV2
TRAV41
TRAV40
TRAV39
TRAV36DV7
TRAV35
TRAV34
TRAV30
TRAV29DV5
TRAV27
TRAV25
TRAV24
TRDV1
TRAV23DV6
TRAV22
TRAV21
TRAV20
TRAV19
TRAV18
TRAV17
TRAV16
TRAV14DV4
TRAV10
TRAV7
TRAV6
TRAV5
TRAV4
TRAV3
TRAV2
RN7SL650P
SNORD8
SNORD9
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79\|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
OR4Q2
snoU13\|ENSG00000238492.1
MED15P6
LINC00516
MED15P1
SERPINA3
ACTN1
ACYP1
ANG
APEX1
ARG2
ARHGAP5
BCL2L2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
CDKN3
CEBPE
CFL2
FOXN3
CHGA
CKB
CMA1
LTB4R
CRIP1
CRIP2
CTSG
DAD1
COCH
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FKBP3
FOXG1
FOS
FUT8
GALC
GCH1
GMFB
GPX2
GSTZ1
GTF2A1
BRF1
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
MGAT2
CTAGE5
ATXN3
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
NRL
OTX2
OXA1L
PAX9
SERPINA5
PCK2
PGF
SERPINA1
SERPINA4
PIGH
PNN
POLE2
PPM1A
PPP2R5C
PRKCH
PRKD1
LGMN
PSEN1
PSMA3
PSMA6
PSMB5
PSMC1
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
MOK
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPS29
RTN1
SALL2
SEL1L
SRSF5
SLC8A3
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGM1
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
GEMIN2
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
AP1G2
SLC7A7
MTA1
NEMF
PNMA1
RPS6KA5
CPNE6
AKAP6
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
AREL1
TOX4
TECPR2
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
FBLN5
BATF
TM9SF1
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
EDDM3A
DHRS4
PAPOLA
ACOT2
TMED10
FERMT2
RIPK3
PTPN21
AP4S1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
VASH1
ATG14
ZBTB1
SNW1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
RCOR1
SYNE2
PACS2
SCFD1
KHNYN
ANGEL1
PPP1R13B
SLC7A8
ZFYVE26
TTC9
KLHDC2
FLRT2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
CHMP4A
STXBP6
GPR132
POMT2
STRN3
SLC39A2
COQ6
EMC9
ATL1
FCF1
RDH11
SERPINA10
ZNF219
COX16
GMPR2
SLC22A17
DACT1
EVL
GSKIP
CINP
MBIP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
GNG2
KLHL28
TMEM260
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
CDCA4
NRDE2
RNF31
ATG2B
RBM23
UBR7
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SLC39A9
G2E3
FLVCR2
OSGEP
GPATCH2L
SMEK1
ARHGEF40
BTBD7
AP5M1
TDP1
ZNF839
SPATA7
EAPP
YLPM1
METTL3
LTB4R2
KCNK13
SDR39U1
DDX24
RPGRIP1
ADCK1
TMEM63C
PELI2
RHOJ
NDRG2
GALNT16
PLEKHH1
NYNRIN
TXNDC16
TRMT5
UNC79
HOMEZ
BEGAIN
CHD8
FANCM
PPP4R4
ZNF410
NGB
RBM25
SNX6
SAV1
C14orf93
ABHD4
VIPAS39
NPAS3
SMOC1
MOAP1
EDDM3B
IRF2BPL
MPP5
CDH24
INF2
PCNXL4
METTL17
IL25
GNPNAT1
OTUB2
ZFYVE21
THTPA
OR4K5
WDR25
OR4K1
METTL21D
LINC00341
ZC2HC1C
IPO4
CLMN
CATSPERB
ZC3H14
RIN3
L2HGDH
C14orf159
CCDC176
NUBPL
DCAF11
TMEM121
DDHD1
OR4K15
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
FSCB
SETD3
BRMS1L
HHIPL1
JPH4
C14orf142
RNASE7
INSM2
RAB2B
AJUBA
STON2
ZFHX2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
LRRC16B
PPP1R3E
TMEM55B
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
MAPK1IP1L
EGLN3
DTD2
IFT43
L3HYPDH
AHNAK2
TRIM9
TRMT61A
DHRS1
CMTM5
MIA2
TDRD9
ANKRD9
AK7
IFI27L1
C14orf28
TRAPPC6B
PLD4
ADSSL1
RNASE11
TPPP2
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
KLHL33
RPL10L
RDH12
GSC
SERPINA12
PRIMA1
MIPOL1
PPP1R36
SLC38A6
ABHD12B
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
MDP1
TTC7B
LRFN5
FAM71D
TMEM229B
SYNE3
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
NOP9
EML5
SPTSSA
ADCY4
C14orf183
RALGAPA1
SFTA3
NUDT14
LINC00521
SERPINA11
C14orf182
GPR137C
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
TSSK4
FAM177A1
CEP170B
C14orf80
DHRS4L2
C14orf39
CCDC85C
SERPINA9
RNASE10
VSX2
OR6S1
SLC35F4
LRRC9
COX8C
ASPG
RAB15
C14orf23
TOMM20L
SERPINA13P
C14orf64
RTL1
TMEM179
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
PLEKHD1
C14orf180
POTEG
MIR127
MIR136
MIR154
MIR203
OR11H12
RNASE13
LINC00238
CCDC88C
OR4Q3
OR4M1
MIR323A
MIR337
MIR345
MIR370
RNASE12
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
POTEM
TMEM253
CBLN3
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4307
MIR548Y
MIR4505
MIR4708
MIR151B
MIR4710
MIR4707
MIR2392
MIR5694
MIR5580
LINC00609

Arm-level results

Table 3. Get Full Table Arm-level significance table - 13 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	1300	0.31	2.17	0.256	0.15	-0.201	0.982
1q	1195	0.58	6.07	2.6e-08	0.18	0.0207	0.982
2p	624	0.17	-0.518	0.989	0.03	-2.35	0.991
2q	967	0.18	-0.165	0.989	0.07	-1.7	0.982
3p	644	0.08	-1.05	0.989	0.69	7.02	4.46e-11
3q	733	0.22	0.254	0.989	0.14	-0.845	0.982
4p	289	0.12	-1.35	0.989	0.30	1.06	0.424
4q	670	0.09	-1.4	0.989	0.38	2.57	0.0206
5p	183	0.35	1.67	0.28	0.08	-1.72	0.982
5q	905	0.33	2.08	0.256	0.12	-0.903	0.982
6p	710	0.23	0.329	0.989	0.17	-0.398	0.982
6q	556	0.12	-0.841	0.989	0.59	5.4	6.98e-07
7p	389	0.22	-0.0205	0.989	0.14	-1.07	0.982
7q	783	0.19	-0.148	0.989	0.13	-0.888	0.982
8p	338	0.17	-0.665	0.989	0.38	2.06	0.0729
8q	551	0.34	1.84	0.27	0.16	-0.626	0.982
9p	301	0.00	-2.29	0.989	0.50	3.95	0.000407
9q	700	0.00	-2.08	0.989	0.53	4.85	8.28e-06
10p	253	0.17	-0.8	0.989	0.19	-0.457	0.982
10q	738	0.06	-1.89	0.989	0.15	-0.778	0.982
11p	509	0.14	-0.912	0.989	0.25	0.505	0.786
11q	975	0.12	-0.937	0.989	0.30	1.71	0.149
12p	339	0.24	0.267	0.989	0.11	-1.47	0.982
12q	904	0.24	0.751	0.989	0.11	-1.13	0.982
13q	560	0.14	-0.761	0.989	0.45	3.44	0.0024
14q	938	0.04	-1.78	0.989	0.37	2.75	0.0134
15q	810	0.19	-0.0398	0.989	0.17	-0.41	0.982
16p	559	0.22	0.113	0.989	0.14	-0.96	0.982
16q	455	0.17	-0.577	0.989	0.23	0.126	0.982
17p	415	0.12	-1.28	0.989	0.30	1.17	0.381
17q	972	0.18	-0.0793	0.989	0.10	-1.22	0.982
18p	104	0.23	-0.0396	0.989	0.21	-0.374	0.982
18q	275	0.19	-0.515	0.989	0.29	0.846	0.543
19p	681	0.16	-0.586	0.989	0.16	-0.586	0.982
19q	935	0.18	-0.11	0.989	0.10	-1.25	0.982
20p	234	0.35	1.67	0.28	0.20	-0.346	0.982
20q	448	0.35	1.92	0.27	0.08	-1.59	0.982
21q	258	0.14	-0.927	0.989	0.45	3.11	0.00552
22q	564	0.16	-0.67	0.989	0.16	-0.67	0.982
Xp	418	0.05	-1.9	0.989	0.43	3.01	0.0068
Xq	668	0.05	-1.78	0.989	0.43	3.29	0.00345

Methods & Data

Input

Description

Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).
Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).
Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.
CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End
Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.
Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.
Confidence Level: Confidence level used to calculate the region containing a driver.
Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.
Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).
Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/CHOL-TP/19075976/GDAC_MergeDataFiles_11499526/CHOL-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat
CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.7
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 36 Input Tumor Samples.

Tumor Sample Names
TCGA-3X-AAV9-01A-72D-A416-01
TCGA-3X-AAVA-01A-11D-A416-01
TCGA-3X-AAVB-01A-31D-A416-01
TCGA-3X-AAVC-01A-21D-A416-01
TCGA-3X-AAVE-01A-11D-A416-01
TCGA-4G-AAZO-01A-12D-A416-01
TCGA-4G-AAZT-01A-11D-A416-01
TCGA-W5-AA2G-01A-11D-A416-01
TCGA-W5-AA2H-01A-31D-A416-01
TCGA-W5-AA2I-01A-32D-A416-01

Figure 3. Segmented copy number profiles in the input data

Output

All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

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

References

[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)

[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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