SNP6 Copy number analysis (GISTIC2)
Rectum Adenocarcinoma (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1PC315V
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1PC315V
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 162 tumor samples used in this analysis: 20 significant arm-level results, 25 significant focal amplifications, and 35 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
--- | --- | --- | --- | ---
20q11.23 | 3.84e-21 | 1.7738e-12 | chr20:35722356-40357006 | 41
13q12.2 | 5.3056e-18 | 1.8447e-12 | chr13:28385587-28773237 | 7
20q11.21 | 3.84e-21 | 1.8483e-09 | chr20:26196264-35696561 | 119
8q24.21 | 3.438e-08 | 3.438e-08 | chr8:128204396-128652497 | 2
17q12 | 1.2463e-06 | 1.3147e-05 | chr17:37837542-37876018 | 2
13q12.13 | 4.489e-16 | 0.00057744 | chr13:27521847-27539800 | 0 [USP12]
8p11.23 | 0.0001102 | 0.0006459 | chr8:38170522-38469302 | 5
11p15.5 | 0.0014114 | 0.0014114 | chr11:2157956-2241214 | 6
8p11.21 | 0.0027233 | 0.0072253 | chr8:41352076-41641623 | 7
6p21.1 | 0.029019 | 0.029019 | chr6:42366336-45044523 | 57
1q21.3 | 0.018549 | 0.034946 | chr1:120523956-163100192 | 468
13q22.1 | 3.1011e-06 | 0.035057 | chr13:73577729-74250466 | 2
5q22.3 | 0.035839 | 0.035839 | chr5:114756122-114759166 | 0 [FEM1C]
1q32.2 | 0.038807 | 0.058512 | chr1:202853626-209439928 | 93
19p13.2 | 0.060064 | 0.060064 | chr19:7296453-7398264 | 0 [INSR]
12p12.1 | 0.002938 | 0.13512 | chr12:24753749-26629748 | 14
16p11.2 | 0.13821 | 0.13821 | chr16:30581939-30943981 | 18
12p13.33 | 0.025405 | 0.14269 | chr12:1-4369146 | 37
10q22.2 | 0.14732 | 0.14732 | chr10:73426159-83489711 | 84
Xp22.2 | 0.14732 | 0.14732 | chrX:1-28634031 | 154
17q24.1 | 0.066494 | 0.1498 | chr17:49230309-71116693 | 187
20q13.33 | 0.04835 | 0.1498 | chr20:50227949-63025520 | 163
Xq27.3 | 0.16087 | 0.16087 | chrX:129318302-155270560 | 287
11q13.3 | 0.21402 | 0.21402 | chr11:69661335-69806082 | 0 [FGF3]
15q26.1 | 0.21402 | 0.21402 | chr15:86200762-102531392 | 116

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.23.

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

Genes
TOP1
MAFB
BPI
GHRH
LBP
NNAT
PLCG1
RBL1
RPN2
SRC
TGM2
TTI1
BLCAP
ZHX3
PPP1R16B
SNORA71B
SNORA71A
CTNNBL1
RALGAPB
RPRD1B
DHX35
MANBAL
LPIN3
ACTR5
FAM83D
CHD6
KIAA1755
EMILIN3
VSTM2L
SNHG11
SLC32A1
C20orf132
ADIG
LOC339568
ARHGAP40
LOC388796
SNORA39
SNORA60
SNORA71C
SNORA71D
LOC100287792

Genes in Wide Peak

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

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

Genes
CDX2
FLT3
PDX1
PAN3
ATP5EP2
PRHOXNB
PAN3-AS1

Genes in Wide Peak

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

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

Genes
ASXL1
hsa-mir-1289-1
hsa-mir-499
hsa-mir-644
hsa-mir-1825
hsa-mir-3193
AHCY
ASIP
BCL2L1
DNMT3B
E2F1
EPB41L1
FOXS1
GGT7
GSS
HCK
ID1
EIF6
PLAGL2
RBL1
SNTA1
SPAG4
GDF5
EIF2S2
CPNE1
NFS1
CBFA2T2
KIF3B
RBM39
TM9SF4
RBM12
MYL9
PROCR
MMP24
CEP250
PXMP4
DLGAP4
RALY
MAPRE1
TPX2
NCOA6
POFUT1
SAMHD1
C20orf4
TRPC4AP
REM1
PHF20
SCAND1
BPIFA1
ERGIC3
CDK5RAP1
UQCC
EDEM2
ACSS2
C20orf24
NDRG3
MYH7B
TP53INP2
TGIF2
NECAB3
DSN1
FER1L4
BPIFB2
HM13
PDRG1
DYNLRB1
ITCH
SLA2
MAP1LC3A
COX4I2
ZNF341
MYLK2
BPIFB1
DEFB118
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
MLLT10P1
BPIFA2
C20orf112
C20orf160
KIAA0889
C20orf118
SUN5
ROMO1
C20orf173
LINC00028
C20orf152
LOC149950
COMMD7
BPIFB4
TTLL9
ACTL10
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
C20orf203
BPIFA4P
XKR7
BPIFB3
MIR499A
LOC647979
MIR644A
PSIMCT-1
MIR3193
TGIF2-C20ORF24
MIR499B
MIR4755

Genes in Wide Peak

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

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

Genes
POU5F1B
LOC727677

Genes in Wide Peak

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

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

Genes
ERBB2
PGAP3

Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
LETM2
RNF5P1
C8orf86

Genes in Wide Peak

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

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

Genes
IGF2
INS
TH
IGF2-AS1
INS-IGF2
MIR4686

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
GOLGA7
GINS4
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

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

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

Genes
CDC5L
SLC29A1
HSP90AB1
MEA1
NFKBIE
PEX6
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
SUPT3H
POLR1C
MAD2L1BP
CUL7
C6orf108
CNPY3
SLC22A7
CAPN11
CUL9
UBR2
KIAA0240
ZNF318
YIPF3
GNMT
MRPL2
GTPBP2
MRPS18A
TMEM63B
TRERF1
AARS2
XPO5
MRPL14
DLK2
TTBK1
RRP36
ABCC10
KLC4
TJAP1
KLHDC3
PTCRA
TCTE1
SPATS1
C6orf223
RSPH9
LRRC73
RPL7L1
SLC35B2
CRIP3
C6orf226
TMEM151B
ATP6V0CP3
LOC100132354
MIR4647
MIR4642

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PRCC
SDHC
TPM3
PDE4DIP
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
APCS
APOA2
ATP1A2
ATP1A4
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO5
DARC
GBA
GBAP1
GJA5
GJA8
HDGF
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LMNA
LOR
LY9
MCL1
SMCP
MEF2D
MNDA
MPZ
MTX1
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PI4KB
PKLR
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
USF1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
ITGA10
PEA15
B4GALT3
ADAM15
PEX11B
CD84
SELENBP1
SH2D2A
FCGR2C
PRPF3
ARHGEF2
DEDD
AIM2
ADAMTS4
SEC22B
CHD1L
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
PMF1
DUSP12
VPS45
KIAA0907
ATF6
POGZ
SYT11
RPRD2
SMG5
NCSTN
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
OLFML2B
C1orf43
CHTOP
LCE2B
OR10J1
USP21
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
ACP6
GPR89B
HSD17B7
UFC1
OAZ3
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
FAM63A
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
AQP10
SLAMF9
PYGO2
NUP210L
MEX3A
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
HIST2H3C
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
LRRC71
PYHIN1
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
C1orf204
C1orf111
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
C1orf110
OR10R2
FCRL6
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
LOC375010
PEAR1
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
NBPF9
MIR9-1
HIST2H2BF
ETV3L
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
PRR9
RPL31P11
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA4
SNORA42
MIR554
MIR555
MIR556
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR765
MIR190B
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505633
LOC100505666
PMF1-BGLAP
TNFAIP8L2-SCNM1
MIR4654

Genes in Wide Peak

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

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

Genes
KLF5
PIBF1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q32.2.

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

Genes
ELK4
MDM4
SLC45A3
hsa-mir-29b-2
hsa-mir-135b
ADORA1
ATP2B4
AVPR1B
C4BPA
C4BPB
CD34
CHI3L1
CHIT1
CR1
CR1L
CR2
CTSE
CD55
EIF2D
FMOD
IL10
KISS1
CD46
MYBPH
MYOG
CDK18
PFKFB2
PIGR
PIK3C2B
PLXNA2
PRELP
RABIF
RBBP5
REN
SNRPE
CNTN2
BTG2
DYRK3
PPFIA4
RAB7L1
FAIM3
MAPKAPK2
SOX13
IKBKE
ZC3H11A
TMCC2
LRRN2
IL24
PLEKHA6
NFASC
SRGAP2
DSTYK
OPTC
IL19
IL20
ADIPOR1
CYB5R1
LAX1
KLHDC8A
ETNK2
YOD1
KLHL12
NUCKS1
C1orf116
NUAK2
RASSF5
FCAMR
LINC00260
PPP1R15B
TMEM183A
LEMD1
SLC26A9
LOC127841
GOLT1A
LOC148696
MFSD4
PM20D1
SLC41A1
LINC00303
LOC284576
LOC284578
LOC284581
TMEM81
LOC401980
MIR29B2
MIR29C
C1orf186
MIR135B
TMEM183B
SNORA77
FAM72A
LOC730227
ZBED6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
hsa-mir-4302
BCAT1
ITPR2
LRMP
SSPN
RASSF8
CASC1
BHLHE41
LYRM5
IFLTD1
C12orf77
MIR4302
LOC100506451

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
KDM5A
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
PARP11
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
EFCAB4B
CACNA2D4
FBXL14
DCP1B
B4GALNT3
LOC283440
IQSEC3
LOC574538
LRTM2
FAM138D
LOC100271702
LOC100288778
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.2.

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

Genes
hsa-mir-606
ADK
ANXA7
ANXA11
CAMK2G
KCNMA1
MAT1A
P4HA1
PLAU
PPP3CB
PSAP
RPS24
SFTPD
VCL
VDAC2
NDST2
MBL1P
DLG5
CHST3
SEC24C
SPOCK2
PPIF
MICU1
POLR3A
ECD
KIAA0913
DNAJC9
KAT6B
NUDT13
AP3M1
ASCC1
MRPS16
DUSP13
DDIT4
DNAJB12
ZMIZ1
MYOZ1
CDH23
C10orf54
SYNPO2L
FAM213A
TSPAN14
C10orf11
C10orf58
DYDC2
PLA2G12B
ZNF503
MCU
CHCHD1
ZMYND17
TTC18
COMTD1
ANAPC16
SAMD8
DYDC1
EIF5AL1
USP54
FUT11
OIT3
LOC219347
PLAC9
ZCCHC24
ZNF503-AS1
LOC283050
FAM149B1
DUPD1
SH2D4B
C10orf105
C10orf55
C10orf103
LOC439990
LOC642361
LOC650623
SFTPA1
AGAP5
BMS1P4
SFTPA2
LOC100128292
ZNF503-AS2
LOC100132987
LOC100288974
MIR1256
LOC100507331
MIR4676

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.2.

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

Genes
CRLF2
P2RY8
hsa-mir-1308
hsa-mir-651
AMELX
SLC25A6
SHROOM2
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT
BMX
S100G
CLCN4
CSF2RA
EIF1AX
EIF2S3
FANCB
FIGF
GLRA2
GPM6B
GRPR
HCCS
IL3RA
KAL1
CD99
MID1
NHS
GPR143
PDHA1
PDK3
PHEX
PHKA2
PIGA
POLA1
PPEF1
PRKX
PRPS2
RBBP7
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SHOX
SMS
CDKL5
TBL1X
TMSB4X
XG
ZFX
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
OFD1
PIR
INE2
ASMTL
AP1S2
GYG2
REPS2
ZBED1
RAB9A
PCYT1B
FRMPD4
GPR64
SCML2
PRDX4
RAI2
MSL3
IL1RAPL1
CA5B
CNKSR2
ACOT9
SMPX
MXRA5
EGFL6
VCX
PPP2R3B
SH3KBP1
TLR7
TLR8
MBTPS2
VCX2
VCX3A
GEMIN8
PLCXD1
TXLNG
WWC3
CTPS2
TMEM27
NLGN4X
ACE2
APOO
ASMTL-AS1
KLHL15
ATXN3L
SYAP1
BEND2
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
ASB11
ASB9
ZNF645
MOSPD2
MAGEB6
DDX53
FAM48B2
TCEANC
ARX
FAM9A
FAM9B
FAM9C
DHRSX
CXorf58
CXorf23
MAP7D2
KLHL34
PPP2R3B-AS1
MAGEB18
CA5BP1
DCAF8L2
ARSH
TLR8-AS1
MAP3K15
LOC389906
CD99P1
YY2
VCX3B
SCARNA23
MIR651
LOC729609
LOC100093698
CXorf28
FAM48B1
LOC100132163
XGPY2
LOC100133123
SCARNA9L
LOC100288814
LINC00102
MIR23C
MIR3690
PIR-FIGF
MIR4768
MIR4770
MIR4767

Genes in Wide Peak

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

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

Genes
CD79B
CLTC
DDX5
HLF
PRKAR1A
BRIP1
MSI2
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
APOH
CA4
CACNG1
COX11
CSH1
CSH2
CSHL1
CYB561
ACE
ERN1
BPTF
GH1
GH2
ICAM2
KCNJ2
KCNJ16
KPNA2
LPO
MAP3K3
MPO
TRIM37
NME1
NME2
PECAM1
SEPT4
PRKCA
MAP2K6
PSMC5
PSMD12
RAD51C
RPS6KB1
SCN4A
SRSF1
SMARCD2
SOX9
SUPT4H1
TBX2
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
PPM1D
DGKE
RGS9
MTMR4
SLC16A6
NOG
BZRAP1
TBX4
MRC2
HELZ
MED13
TOM1L1
DCAF7
ABCA10
ABCA9
ABCA8
APPBP2
GNA13
TLK2
POLG2
DDX42
PPM1E
ARSG
ABCA6
ABCA5
MMD
NOL11
TANC2
PITPNC1
OR4D1
CACNG5
CACNG4
UTP18
RNFT1
TUBD1
TACO1
AMZ2
MRPS23
PTRH2
FAM20A
MBTD1
BCAS3
RNF43
MKS1
WIPI1
SMG8
TMEM100
MSX2P1
PRR11
TEX2
TEX14
CA10
CCDC47
INTS2
PCTP
SCPEP1
HEATR6
SMURF2
DHX40
LIMD2
KCNH6
VMP1
KIF2B
USP32
CEP95
STRADA
C17orf72
FTSJ3
HSF5
OR4D2
C17orf64
DYNLL2
TCAM1P
EFCAB3
LOC146880
ANKFN1
MARCH10
CEP112
SLC39A11
AMZ2P1
MTVR2
STXBP4
C17orf58
MILR1
C17orf47
GDPD1
METTL2A
C17orf67
NACA2
SKA2
LRRC37A3
RNF126P1
YPEL2
C17orf82
KCNJ2-AS1
LINC00511
CUEDC1
MIR142
MIR21
MIR301A
TBC1D3P2
PLEKHM1P
LOC440461
LOC645638
TBC1D3P1-DHX40P1
LOC653653
NME1-NME2
SCARNA20
SNORA76
SNORD104
MIR634
MIR635
LOC729683
MIR454
SNORA38B
MIR548W
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3614
LOC100506650
LOC100506779
MIR4729
MIR4737
MIR4736
MIR4524A
MIR3064
MIR5047

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
GNAS
SS18L1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
ATP5E
BMP7
CDH4
CHRNA4
COL9A3
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
NPBWR2
KCNQ2
LAMA5
MC3R
MYT1
NTSR1
OPRL1
PCK1
PFDN4
PPP1R3D
PSMA7
PTK6
RPS21
SRMS
AURKA
TAF4
TCEA2
TFAP2C
TPD52L2
ZNF217
RAE1
BCAS1
STX16
TNFRSF6B
VAPB
OSBPL2
ATP9A
ARFRP1
RGS19
SYCP2
TCFL5
ADRM1
OGFR
DIDO1
HRH3
SPO11
PRPF6
GTPBP5
GMEB2
SLCO4A1
STMN3
SLMO2
TH1L
C20orf43
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
C20orf20
PPP4R1L
RBM38
ZFP64
ARFGAP1
DOK5
SLC2A4RG
PMEPA1
CASS4
SALL4
RAB22A
ZNF512B
COL20A1
CDH26
SLC17A9
LOC63930
FAM217B
C20orf195
PPDPF
BIRC7
NPEPL1
DNAJC5
TUBB1
ZBP1
CABLES2
ZGPAT
PRIC285
FAM210B
PHACTR3
BHLHE23
NKAIN4
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
GCNT7
CBLN4
CTCFL
SAMD10
ABHD16B
LINC00266-1
C20orf151
LOC149773
GNAS-AS1
LSM14B
APCDD1L
C20orf201
FAM209A
C20orf166-AS1
LINC00176
C20orf197
LOC284757
FAM209B
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
MIR647
HAR1A
HAR1B
UCKL1-AS1
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
DPH3P1
LINC00029
LOC100144597
FLJ16779
MIR1914
MIR1257
MIR4325
MIR4326
MIR3196
MTRNR2L3
LOC100505815
LOC100506384
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4758
MIR4532
MIR4533
MIR5095
LOC100652730

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq27.3.

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

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

Genes in Wide Peak

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

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

Genes
BLM
IDH2
NTRK3
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
ACAN
ALDH1A3
ANPEP
CHD2
FES
IGF1R
ISG20
MAN2A2
MEF2A
MFGE8
FURIN
PCSK6
PLIN1
POLG
RLBP1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
ABHD2
AKAP13
CHSY1
SYNM
GABARAPL3
VPS33B
MRPL46
OR4F4
SLCO3A1
NGRN
RHCG
DET1
LINS
FANCI
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
KLHL25
AEN
TTC23
MRPS11
LRRK1
TM2D3
C15orf42
RCCD1
ARRDC4
LOC91948
TARSL2
LRRC28
AGBL1
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
ADAMTS17
DNM1P46
CERS3
LOC254559
LOC283738
LOC283761
FAM169B
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
WASH3P
FLJ42289
C15orf58
OR4F6
OR4F15
FAM174B
LOC400456
MIR7-2
MIR9-3
TTLL13
LOC727915
ASB9P1
FAM138E
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1276
MIR1179
MIR1469
MIR3175
LOC100507217
LOC100507472
C15orf38-AP3S2
MIR3529
MIR4714

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 - 35 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
16p13.3 | 1.551e-35 | 1.551e-35 | chr16:5144019-7771745 | 1
20p12.1 | 8.5511e-25 | 8.5511e-25 | chr20:14690293-15165995 | 1
4q22.1 | 5.8455e-23 | 1.5175e-22 | chr4:91148280-93240505 | 1
8p23.2 | 6.0971e-16 | 6.0971e-16 | chr8:2079140-6262191 | 1
6q26 | 2.0404e-13 | 2.0404e-13 | chr6:161693099-163153207 | 1
5q11.2 | 8.5532e-11 | 2.1973e-10 | chr5:58260298-59787985 | 3
1p36.11 | 2.1973e-10 | 6.6262e-10 | chr1:3596990-31841618 | 401
3q26.31 | 1.9187e-08 | 1.9187e-08 | chr3:173999806-175760559 | 2
3p14.2 | 3.4035e-08 | 3.2176e-08 | chr3:59034763-61547330 | 1
18q21.2 | 2.7047e-09 | 3.6808e-08 | chr18:48472083-48705371 | 2
21q11.2 | 4.5572e-07 | 4.5572e-07 | chr21:1-15482604 | 16
15q22.33 | 8.805e-06 | 8.805e-06 | chr15:67067796-67494822 | 1
16q23.1 | 3.7607e-05 | 3.7607e-05 | chr16:78129058-79627770 | 1
18q22.1 | 6.2987e-06 | 0.00017643 | chr18:65565142-66383463 | 1
5q22.2 | 3.6055e-06 | 0.00053802 | chr5:102895125-114460579 | 28
22q13.31 | 0.00073821 | 0.0007082 | chr22:44391372-51304566 | 92
1p33 | 7.8375e-05 | 0.00086376 | chr1:49193395-50514967 | 1
10q21.1 | 0.0027448 | 0.0034503 | chr10:53057593-54061437 | 3
14q11.2 | 0.0039317 | 0.0039336 | chr14:1-24510208 | 116
4q35.1 | 3.6113e-05 | 0.0045253 | chr4:178911874-191154276 | 64
6p25.3 | 0.0053105 | 0.0053319 | chr6:1608837-2250882 | 2
1p13.2 | 0.012715 | 0.02594 | chr1:94146122-120255125 | 208
10q25.2 | 0.012978 | 0.031127 | chr10:86084854-135534747 | 449
7q31.1 | 0.038978 | 0.039682 | chr7:109599468-111366370 | 2
11q22.3 | 0.050272 | 0.05149 | chr11:96117839-126871638 | 281
12p13.1 | 0.05976 | 0.060616 | chr12:7945385-20853661 | 145
14q31.1 | 0.065675 | 0.068715 | chr14:61441176-107349540 | 458
17p11.2 | 0.071466 | 0.068715 | chr17:8300098-25626166 | 155
Xp22.33 | 0.065675 | 0.068715 | chrX:1-150846785 | 926
12q22 | 0.12719 | 0.12126 | chr12:51815787-108914595 | 481
4p13 | 0.13085 | 0.13424 | chr4:31148303-52714468 | 72
19p13.3 | 0.17014 | 0.17024 | chr19:1-59128983 | 1653
2p12 | 0.18574 | 0.1821 | chr2:56408180-96881977 | 250
8p11.21 | 0.1864 | 0.1821 | chr8:11648790-90944738 | 411
20p12.1 | 8.5511e-25 | 1 | chr20:1-63025520 | 672

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

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

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

Genes
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
E2F2
ECE1
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GALE
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
SDC3
CROCC
PUM1
CEP104
KLHL21
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
FBXO2
FBXO6
PLA2G2D
RNU11
HSPB7
AHDC1
SMPDL3B
PRO0611
LINC00339
UBIAD1
PADI1
PLA2G2E
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
PINK1
PRAMEF1
PRAMEF2
PHACTR4
C1orf135
EFHD2
RSG1
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
FAM110D
DHDDS
GPR157
SPSB1
ZNF436
TAS1R2
TAS1R1
ACTL8
SH3BGRL3
SESN2
ESPN
TMEM222
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
RAB42
FAM46B
RBP7
C1orf172
LRRC38
AADACL3
IFFO2
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf127
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf126
AKR7L
TMCO4
ZNF683
NPHP4
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
APITD1
CATSPER4
GPR153
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
MIR34A
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
PRAMEF7
LOC644961
C1orf200
PRAMEF19
PRAMEF20
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC100129196
LOC100133612
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
SMAD4
ELAC1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
SMAD3

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

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

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

Genes
TMX3

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
LINC00229
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

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

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

Genes
BEND5

Genes in Wide Peak

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

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

Genes
hsa-mir-605
CSTF2T
MIR605

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
BCL2L2
CEBPE
DAD1
HNRNPC
MMP14
MYH6
MYH7
PNP
OXA1L
PSMB5
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
PABPN1
AP1G2
SLC7A7
TOX4
PARP2
DHRS2
EFS
PRMT5
EDDM3A
DHRS4
SUPT16H
ACIN1
SLC7A8
NGDN
LRP10
OR10G3
OR10G2
OR4E2
SLC39A2
ZNF219
SLC22A17
HAUS4
C14orf119
RBM23
C14orf167
OSGEP
ARHGEF40
METTL3
RPGRIP1
NDRG2
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
OR4K15
JPH4
RNASE7
RAB2B
AJUBA
ZFHX2
RPPH1
PPP1R3E
TMEM55B
TTC5
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
REM2
LOC283624
DHRS4L2
SNORD8
RNASE10
OR6S1
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
SNORD9
SNORD126
MIR208B
BCL2L2-PABPN1
MIR4707

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ZFP42
ENPP6
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CNN3
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
F3
GCLM
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
ABCD3
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
VCAM1
WNT2B
CSDE1
TTF2
CDC14A
RTCD1
SLC16A4
CD101
ARHGAP29
LRIG2
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
RWDD3
PTPN22
CHIA
GPSM2
SLC25A24
DNTTIP2
HAO2
SNX7
DPH5
GPR88
CCDC76
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
AMIGO1
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
DNAJA1P5
HENMT1
OLFM3
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
TMEM56
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
LPPR5
FNDC7
SASS6
UBL4B
ALG14
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
FRRS1
MIR137HG
MIR137
MIR197
FLJ31662
LOC440600
BCL2L15
PGCP1
SRG7
CYMP
LOC643441
LOC644242
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129138
LOC100129269
LOC100129620
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100506343
TMEM56-RWDD3
MIR2682

Genes in Wide Peak

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

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

Genes
BMPR1A
FGFR2
TLX1
NFKB2
PTEN
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
FAS
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GLUD1
GOT1
PRLHR
GPR26
GRK5
GRID1
HABP2
HELLS
HHEX
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
C10orf116
VAX1
ATE1
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
ANKRD1
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
FAM190B
EXOC6
FAM35A
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ATAD1
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
OPALIN
SYCE1
OPN4
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
ANKRD22
SFXN2
PDZD8
C10orf32
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
CFL1P1
TRUB1
VTI1A
LOC143188
HECTD2
FGFBP3
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
FLJ37201
LOC283038
LOC283089
O3FAR1
KCNK18
LIPM
CYP26C1
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
C10orf62
LOC439994
IFIT1B
FRG2B
MIR346
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
FAM25A
LIPK
LIPN
LOC643529
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
FAM22A
FAM22D
LOC728190
LOC728218
DUX4L2
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
KLLN
LOC100169752
LOC100188947
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
FAS-AS1
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
LOC100507470
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4678
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

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

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

Genes
LRRN3
IMMP2L

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
BIRC2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
NCAM1
NNMT
NPAT
NRGN
PGR
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
TAGLN
TECTA
THY1
TRPC6
UPK2
ZBTB16
ZNF202
CUL5
JRKL
ZNF259
USP2
HTR3B
ZW10
MMP20
UBE4A
EI24
FEZ1
C2CD2L
RBM7
MPZL2
YAP1
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
MMP27
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
BCO2
TMEM133
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
MPZL3
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANGPTL5
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
PATE3
LOC100288077
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3920
MIR3656
CASP12
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
A2M
A2MP1
ARHGDIB
ART4
C3AR1
CD69
CDKN1B
CREBL2
PHC1
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
PZP
SLC2A3
MFAP5
KLRC4
CSDA
GPRC5A
CLEC2B
KLRG1
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
NECAP1
CLEC4E
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
PLEKHA5
MANSC1
MAGOHB
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
DUSP16
APOLD1
GSG1
RERG
PLCZ1
HTR7P1
CAPZA3
CLEC6A
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
CLEC9A
C12orf36
CLEC4D
LOC338817
TAS2R42
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
LOC100506393
KLRC4-KLRK1
PRH1-PRR4
MIR3974

Genes in Wide Peak

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

Table S48. 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
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
SEL1L
SRSF5
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
ATP6V1D
EVL
C14orf129
CINP
ASB2
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
COX8C
ASPG
RAB15
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p11.2.

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

Genes
MAP2K4
GAS7
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FOXO3B
FLII
KCNJ12
LLGL1
MEIS3P1
MFAP4
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
PMP22
MAPK7
MAP2K3
PRPSAP2
RCVRN
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
MYH13
TMEM11
GLP2R
NTN1
STX8
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
GRAP
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
PIK3R5
DHRS7B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
C17orf48
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
FAM106A
NDEL1
LRRC48
MGC12916
ATPAF2
SPECC1
MYOCD
CDRT7
CDRT15P1
USP43
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
CDRT15
WDR16
CCDC42
PIK3R6
TRIM16L
MFSD6L
USP32P1
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
USP32P2
TBC1D28
CDRT15L2
C17orf103
FLJ34690
CDRT4
CCDC144B
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
CCDC144C
TBC1D26
CDRT1
SPDYE4
TMEM220
SHISA6
FAM211A
KRT16P2
GRAPL
PIRT
CDRT15P2
FAM83G
KRT16P3
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
MIR744
FAM106CP
KCNJ18
LOC100289255
MIR1288
MIR1180
MTRNR2L1
FAM18B2-CDRT4
MIR4731
MIR4522

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.33.

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

Genes
ATRX
ELF4
GATA1
GPC3
MSN
NONO
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
CRLF2
P2RY8
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
hsa-mir-448
hsa-mir-1911
hsa-mir-1264
hsa-mir-4329
hsa-mir-652
hsa-mir-548m
hsa-mir-361
hsa-mir-548i-4
hsa-mir-4328
hsa-mir-325
hsa-mir-384
hsa-mir-374a
hsa-mir-223
hsa-mir-1468
hsa-let-7f-2
hsa-mir-502
hsa-mir-222
hsa-mir-548f-5
hsa-mir-1308
hsa-mir-651
ABCB7
AGTR2
NR0B1
ALAS2
AMELX
SLC25A5
SLC25A6
XIAP
SHROOM2
AR
ARAF
ARHGAP6
ARR3
STS
ARSD
ARSE
ARSF
ASMT
ATP7A
BCYRN1
BMX
BRS3
BTK
CACNA1F
S100G
CAPN6
CD40LG
CDR1
CDX4
CHM
CLCN4
CLCN5
COL4A5
COL4A6
COX7B
CSF2RA
CSTF2
CYBB
CYLC1
DCX
DDX3X
TIMM8A
DIAPH2
DLG3
DMD
DRP2
TSC22D3
EDA
EFNB1
EIF1AX
EIF2S3
ELK1
F9
ACSL4
FANCB
GPC4
FGD1
FGF13
FHL1
FIGF
FMR1
AFF2
CENPI
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
GJB1
GK
GLA
GLRA2
GLUD2
GPM6B
CXCR3
LPAR4
GPR34
GRIA3
GRPR
GUCY2F
HSD17B10
HCCS
HMGB3
HNRNPH2
HPRT1
ERAS
HTR2C
IDS
IGBP1
IGSF1
IL2RG
IL3RA
IL13RA1
IL13RA2
KAL1
KCND1
LAMP2
PRICKLE3
SH2D1A
MAGEA8
MAGEA9
MAGEA11
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
MCF2
CD99
MID1
FOXO4
CITED1
MTM1
NAP1L2
NAP1L3
NDP
NDUFA1
NHS
GPR143
TBC1D25
OCRL
OPHN1
OTC
P2RY4
PAK3
CDK16
PDHA1
PDK3
CFP
PFKFB1
PGK1
PHEX
PHKA1
PHKA2
PIGA
PIN4
PLP1
PLP2
PLS3
POLA1
POU3F4
PPEF1
PRKX
PRPS1
PRPS2
PRRG1
PSMD10
RBBP7
RBM3
RP2
RPGR
RPL39
RPL36A
RPS4X
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SH3BGRL
SHOX
SLC16A2
SMARCA1
SMS
SOX3
SRD5A1P1
SSX5
CDKL5
SUV39H1
SYN1
SYP
TAF1
SERPINA7
TBL1X
DYNLT3
TDGF1P3
TIMP1
TSPAN7
TSPAN6
TMSB4X
TRO
TRPC5
UBA1
UBE2A
SLC35A2
XG
XIST
XK
XPNPEP2
ZFX
ZIC3
ZNF711
ZNF182
ZNF41
ZNF75D
ZNF157
RNF113A
ZXDA
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
SRPX
UXT
CUL4B
IRS4
OGT
OFD1
PIR
INE2
INE1
CASK
ASMTL
PAGE1
MTMR1
FGF16
AKAP4
APLN
AP1S2
GYG2
FAM127A
SLC25A14
CLDN2
RGN
AIFM1
CXorf1
REPS2
ZBED1
ZMYM3
BMP15
GPR50
MED14
TCEAL1
RAB33A
RAB9A
TSIX
ITM2A
ARHGEF6
PCYT1B
MAGED1
XAGE2
XAGE1D
PAGE4
MORF4L2
GPRASP1
STARD8
FRMPD4
PHF16
ARMCX2
HEPH
MAGEC1
AMMECR1
MED12
ZBTB33
HDAC6
MAMLD1
HUWE1
PQBP1
GPR64
ATP6AP2
ODZ1
SSX3
TIMM17B
RRAGB
SCML2
SLC9A6
ENOX2
PRDX4
EBP
STAG2
RAI2
PLAC1
CYSLTR1
UTP14A
PGRMC1
MAGED2
MSL3
TMSB15A
PIM2
MID2
IL1RAPL1
WDR45
PRAF2
CA5B
SLC6A14
KLF8
VSIG4
CNKSR2
IQSEC2
PHF8
SEPT6
ARHGEF9
ATP1B4
ACOT9
KCNE1L
LDOC1
SMPX
GSPT2
KIF4A
FTSJ1
CXorf27
MXRA5
EGFL6
FAM127B
IL1RAPL2
ITGB1BP2
VCX
GAGE12I
GAGE2E
SNORA69
SNORD61
NGFRAP1
NOX1
FAM155B
INGX
GPR82
GPKOW
SRPX2
APEX2
RBMX
PCDH11X
RPS6KA6
P2RY10
HTATSF1
PCSK1N
PPP2R3B
CCDC22
MCTS1
MAGEH1
FAM156A
C1GALT1C1
SNX12
RPA4
UBQLN2
SH3KBP1
SPANXA1
FOXP3
TBX22
ZDHHC9
RLIM
WBP5
RAB9B
LUZP4
PDZD11
CXorf26
TFDP3
TLR7
ARMCX1
TLR8
MBTPS2
MAGEC2
VGLL1
VCX2
VCX3A
ARMCX3
TAF9B
RBMX2
MST4
CPXCR1
CHIC1
FTHL17
GPR173
NLGN3
SASH3
TAF7L
SPIN2A
ARMCX6
WDR44
NDUFB11
GNL3L
ERCC6L
NUP62CL
GDPD2
BCOR
TBC1D8B
FAM120C
GEMIN8
CXorf48
FAM70A
CXorf57
NUDT11
RBM41
PLCXD1
SAGE1
OTUD5
ZNF280C
MTMR8
ZNF673
TXLNG
MBNL3
WWC3
FAM45B
BEX1
HDAC8
ZC4H2
NXT2
NKRF
NXF5
NXF4
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
MOSPD1
BEX4
CTPS2
CHST7
TCEAL7
GRIPAP1
THOC2
ZNF630
TMEM27
SHROOM4
KIAA1210
NLGN4X
PCDH19
RGAG1
LRCH2
MAGEE1
RAP2C
MID1IP1
ACE2
TMEM35
EDA2R
NYX
BCORL1
DUSP21
CXorf56
DMRTC1
TSPYL2
TNMD
PJA1
SPANXD
SPANXC
WDR13
PORCN
ARMCX5
UPF3B
WNK3
APOO
HMGN5
NKAP
RNF128
MAP7D3
MORC4
CXorf36
LONRF3
ALG13
MAGIX
TCEAL4
TRMT2B
POF1B
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
ESX1
BHLHB9
MAGED4B
LAS1L
GPR101
TMEM47
CD99L2
USP26
FRMD8P1
MAGT1
TMEM164
PHF6
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
SLC9A7
BEX2
MGC16121
SLC7A3
TCEAL3
CCNB3
PPP1R3F
CCDC120
TSR2
HS6ST2
FRMD7
KLHL13
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
CXorf40A
RIPPLY1
LOC92249
ATXN3L
SLC38A5
MMGT1
ACRC
SYAP1
SYTL4
SYTL5
GPRASP2
ATG4A
DACH2
SLITRK4
SPANXN3
MAGEC3
BEND2
PASD1
DCAF12L1
DGKK
LOC139201
CXorf41
MUM1L1
FAM199X
FAM123B
APOOL
HDX
FUNDC1
GPR112
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
OTUD6A
UPRT
MAGEE2
MAGEB16
FOXR2
ACTRT1
GPR119
PAGE3
RBMXL3
DOCK11
SPIN4
ASB11
ASB9
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
ZNF645
FMR1NB
LOC158572
FAAH2
ZXDB
LOC158696
FAM47A
MOSPD2
ARHGAP36
RIBC1
AKAP14
RHOXF1
NKAPP1
MAGEB6
CXorf65
AWAT1
AWAT2
ZDHHC15
USP51
TCEAL6
H2BFWT
CXorf38
FAM122B
FAM122C
DDX53
FAM46D
SPIN3
FAM47B
CXorf22
FAM48B2
TCEANC
ZCCHC12
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
SPANXE
SPANXF1
CXorf61
SLC25A43
LINC00246A
ZCCHC5
NRK
DDX26B
ZNF449
VMA21
TMEM31
PAGE2
DHRSX
BRWD3
CXorf58
CT47A11
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX8
RAB40AL
PPP2R3B-AS1
ATP11C
RP1-177G6.2
H2BFM
LOC286437
LOC286442
YIPF6
CXorf59
LOC286467
TTC3P1
FAM133A
MAGEB18
TMSB15B
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
LOC340544
VSIG1
ZC3H12B
SATL1
DCAF12L2
CA5BP1
ZCCHC16
LHFPL1
ZNF81
ITIH6
LANCL3
LOC347411
DCAF8L2
SOWAHD
OR13H1
CCDC160
CXorf66
DGAT2L6
RAB41
ARSH
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
PAGE2B
ZCCHC13
UBE2NL
LOC389906
CXXC1P1
GLOD5
FLJ44635
ARL13A
LINC00086
CD99P1
LOC401588
MCART6
DKFZp686D0853
XKRX
YY2
MIRLET7F2
MIR106A
MIR188
MIR19B2
MIR221
MIR222
MIR223
MIR92A2
MIR98
VCX3B
LOC441495
FLJ46446
RPS26P11
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
PGAM4
FAM47C
UQCRBP1
LOC442459
MIR374A
SPIN2B
SPANXN1
SPANXN2
SPANXN5
MIR384
MIR424
CT45A6
CT45A1
CXorf40B
SSX4B
LOC550643
JPX
MIR448
MIR450A1
MIR362
MIR363
MIR20B
MIR18B
MIR500A
MIR501
MIR502
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
ZNF674
CT47B1
LOC643486
GAGE10
ZCCHC18
CXorf69
LINC00087
GAGE2B
GAGE13
GAGE12G
CXorf30
PABPC1L2B
NAP1L6
XAGE1C
XAGE1E
XAGE1A
XAGE1B
CT47A7
LINC00246B
MIR545
MIR542
SCARNA23
SNORA11
SNORA35
SNORD96B
MIR421
MIR532
MIR651
MIR660
CXorf31
SSX2B
FAM156B
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGED4
XAGE2B
MAGEA9B
NXF2B
DMRTC1B
SPANXB1
SPANXA2
CT45A2
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
LOC729609
H2BFXP
MIR766
GAGE12F
LOC100093698
GAGE8
SNORA11C
SNORA11D
SNORA11E
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR374B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129407
CXorf28
LOC100129515
LOC100129520
LOC100129662
HSFX2
FAM48B1
CXorf49
CXorf64
LOC100131434
ARMCX4
UBE2DNL
LOC100132163
GAGE12D
XGPY2
LOC100132741
LOC100132831
CXorf49B
CXorf51B
LOC100133123
SPANXB2
LOC100133957
SCARNA9L
LOC100272228
LOC100287765
LOC100288814
MIR1468
MIR1912
MIR1298
MIR1256
MIR320D2
MIR1277
MIR1911
MIR1264
FTX
SLC25A5-AS1
MIR764
MIR2114
LOC100329135
LINC00102
MIR514B
MIR500B
MIR4330
MIR4328
MIR4329
MTRNR2L10
MIR374C
MIR23C
MIR676
MIR3690
HSFX1
LOC100506757
CT47A12
LOC100509575
ARMCX5-GPRASP2
RPL36A-HNRNPH2
PIR-FIGF
MIR4769
MIR4536-1
MIR4768
MIR4770
MIR4767
MIR3978

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q22.

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

Genes
BTG1
CDK4
DDIT3
HOXC11
HOXC13
MDM2
NACA
HMGA2
WIF1
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
ACVR1B
ACVRL1
AMHR2
APAF1
APOF
ARL1
ASCL1
ATP2B1
ATP5B
ATP5G2
AVPR1A
CD63
CDK2
CMKLR1
CPM
CRY1
CS
CSRP2
CYP27B1
DGKA
DCN
EPYC
DUSP6
EIF4B
ELK3
ERBB3
B4GALNT1
BLOC1S1
GLI1
GNS
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
KCNC2
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LRP1
LTA4H
LUM
LYZ
MARS
METTL1
KITLG
MIP
MMP19
MYBPC1
MYF5
MYF6
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NFE2
NFYB
CNOT2
NTS
PA2G4
PAH
PAWR
PCBP2
CDK17
PDE1B
PFDN5
SLC25A3
PMCH
PPP1R1A
PRIM1
PTPRB
PTPRR
RAB5B
RAP1B
RARG
RBMS2
RDH5
RFX4
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
PMEL
SMARCC2
SNRPF
SP1
STAT2
STAT6
SUOX
SYT1
TAC3
TARBP2
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBE2N
MAP3K12
AAAS
YEATS4
ALX1
EEA1
SOAT2
DYRK2
PPFIA2
LGR5
RDH16
NPFF
HSD17B6
GALNT4
CRADD
LIN7A
SOCS2
TIMELESS
KRT75
RASSF9
SLC16A7
SLC4A8
WSCD2
ESPL1
KIAA0748
ZBTB39
NUAK1
PAN2
USP15
NR1H4
TSFM
CTDSP2
PLXNC1
RNF41
GDF11
TMEM5
CNPY2
DCTN2
CCT2
AVIL
PTGES3
FRS2
OS9
CKAP4
METAP2
GLIPR1
ATF7
CPSF6
KERA
KRR1
PRDM4
PWP1
FICD
NUDT4
BAZ2A
IRAK3
NXPH4
XPOT
GPR182
COPZ1
PHLDA1
R3HDM2
RAB21
MON2
UHRF1BP1L
TMEM194A
KIAA1033
TBC1D30
ESYT1
TENC1
ZDHHC17
GRIP1
CBX5
SMUG1
LEMD3
MGAT4C
METTL21B
ZNF385A
SNORD59A
GLS2
UTP20
KCNMB4
MRPL42
CCDC59
ORMDL2
TBK1
HCFC2
TRHDE
SYCP3
CHST11
IL22
CCDC53
CCDC41
KRT76
CSAD
NT5DC3
IL23A
TMBIM4
GPR84
PRR13
PARPBP
SLC6A15
RIC8B
APPL2
TMEM19
DRAM1
SLC35E3
STAB2
VEZT
GOLGA2P5
SCYL2
POLR3B
FGD6
IL26
CAND1
NDUFA12
MDM1
ANKS1B
NDUFA4L2
CHPT1
NUP107
TMCC3
PPM1H
SRGAP1
CALCOCO1
NEUROD4
NTN4
C12orf10
C12orf44
ARHGAP9
IKZF4
ACTR6
TBC1D15
SLC26A10
NUP37
OBFC2B
GNPTAB
ACSS3
BBS10
PIP4K2C
CEP290
MTERFD3
GLT8D2
THAP2
INHBE
USP44
SLC41A2
LRRIQ1
C12orf26
LLPH
WIBG
SARNP
CAPS2
ZC3H10
SPRYD3
MFSD5
DNAJC14
NAV3
LACRT
C12orf23
C12orf29
XRCC6BP1
HELB
MARCH9
COQ10A
KRT71
MBD6
OSBPL8
ARHGEF25
C12orf56
AGAP2
DCD
RAB3IP
MUCL1
DEPDC4
CCDC38
C12orf45
OR10P1
SDR9C7
LRIG3
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
MYL6B
KRT72
AMDHD1
GLIPR1L2
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
KRT80
C12orf66
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
GRASP
SLC5A8
KRT78
DTX3
METTL7B
ZFC3H1
FAM71C
RMST
C12orf12
RPSAP52
SLC17A8
STAC3
GNN
MSRB3
OR6C74
OR6C3
TCP11L2
LOC256021
GLIPR1L1
POC1B
OTOGL
LOC283335
ZNF740
RASSF3
OR6C6
ANKRD52
SLC39A5
SPRYD4
LOC283392
LOC283403
LOC283404
C12orf61
DPY19L2
GAS2L3
LINC00485
KRT6C
KRT73
LOC338758
KRT79
C12orf74
FAM19A2
ANKRD33
OR6C2
OR6C4
KRT77
PTPRQ
C12orf42
LRRC10
C12orf75
OR6C1
OR6C75
OR6C76
OR6C70
LOC400043
FLJ41278
MKRN9P
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR196A2
MIR26A2
C12orf37
FLJ12825
TMEM198B
PLEKHG7
NUDT4P1
OR9K2
MIR148B
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC643339
LOC643770
GLYCAM1
HNRNPA1P10
SNORA53
SNORD59B
MIR548C
MIR615
MIR617
MIR618
LOC728084
C12orf73
LOC728739
MRS2P2
HOTAIR
LOC100128191
LOC100130776
LOC100240734
LOC100240735
LOC100287944
MIR1252
MIR1279
MIR1228
MIR1827
MIR1251
SNORA70G
MIR4303
MIR3685
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
LOC100505978
LOC100506844
LOC100507250
LOC100507377
BLOC1S1-RDH5
POC1B-GALNT4
MIR4699
MIR548AL
MIR3198-2
LOC100652999

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p13.

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

Genes
PHOX2B
hsa-mir-574
hsa-mir-1255b-1
APBB2
RHOH
CNGA1
GABRA2
GABRA4
GABRB1
GABRG1
UBE2K
RFC1
RPL9
TEC
TLR1
TXK
UCHL1
UGDH
TLR6
ATP8A1
SLC30A9
CORIN
PTTG2
LIAS
LIMCH1
TBC1D1
PDS5A
KLHL5
KLF3
RBM47
OCIAD1
COMMD8
TMEM33
PGM2
C4orf19
CHRNA9
N4BP2
ATP10D
KIAA1239
SLAIN2
WDR19
GUF1
FLJ13197
NSUN7
TMEM156
CWH43
TLR10
FAM114A1
ARAP2
OCIAD2
GNPDA2
NFXL1
NIPAL1
SHISA3
KLB
COX7B2
SLC10A4
C4orf34
DCAF4L1
YIPF7
FRYL
ZAR1
LOC344967
KCTD8
BEND4
GRXCR1
DTHD1
LOC401127
MIR574
RELL1
MIR4802
MIR4801

Genes in Wide Peak

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

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

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
GNA11
JAK3
KLK2
LYL1
MLLT1
PPP2R1A
SH3GL1
SMARCA4
STK11
TCF3
TPM4
ELL
FSTL3
CIC
BRD4
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
hsa-mir-641
hsa-mir-1270-2
hsa-mir-1270-1
hsa-mir-640
hsa-mir-3189
hsa-mir-3188
hsa-mir-1470
hsa-mir-639
hsa-mir-181d
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
hsa-mir-4322
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
A1BG
ACP5
ACTN4
AP2A1
AES
AMH
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ASNA1
ATP1A3
ATP4A
ATP5D
AXL
AZU1
BAX
BCAT2
BCKDHA
HCN2
CEACAM1
BLVRB
BSG
BST2
C3
C5AR1
CA11
CACNA1A
CALM3
CALR
CAPNS1
CAPS
CCNE1
CD22
CD33
SIGLEC6
CD37
CD70
CD97
CDC34
CDKN2D
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CIRBP
TBCB
CKM
AP2S1
CLC
CLPTM1
CNN1
CNN2
COMP
COX6B1
COX7A1
CRX
CSNK1G2
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DAPK3
DBP
CFD
DHPS
DMPK
DMWD
DNASE2
DNM2
DNMT1
ARID3A
ECH1
EEF2
EFNA2
MEGF8
ELANE
ELAVL1
ELAVL3
EMP3
EMR1
EPOR
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FARSA
FCAR
FCER2
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
FUT3
FUT5
FUT6
GAMT
GCDH
GDF1
GIPR
GNA15
GNG7
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
MKNK2
GPX4
GRIK5
GRIN2D
ARHGAP35
GSK3A
GTF2F1
GYS1
GZMM
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
DNAJB1
ICAM1
ICAM3
ICAM4
IL11
IL12RB1
ILF3
INSL3
INSR
IRF3
JUNB
JUND
KCNA7
KCNC3
KCNJ14
KCNN1
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LDLR
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
CYP4F3
BCAM
MAG
MAN2B1
MATK
MEF2BNB-MEF2B
RAB8A
MAP3K10
MYO1F
MYBPC2
GADD45B
MYO9B
HNRNPM
CEACAM6
NDUFA3
NDUFA7
NDUFB7
NFIC
NFIX
NFKBIB
NKG7
CNOT3
NOTCH3
NOVA2
NPAS1
NPHS1
NRTN
NTF4
NUCB1
OAZ1
P2RY11
PAFAH1B3
PALM
PDE4A
PDE4C
PEG3
PEPD
PIK3R2
PIN1
PLAUR
FXYD1
FXYD3
POLD1
POLR2E
POLR2I
POLRMT
POU2F2
PPP5C
PRKACA
PRKCG
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRRG2
KLK7
KLK6
KLK10
PRTN3
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTBP1
PTGER1
PTGIR
PTPRH
PTPRS
PVR
PVRL2
RAB3A
RAD23A
RELB
UPF1
RFX1
RFX2
RPL18
RPL18A
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS15
RPS16
RPS19
RPS28
RRAS
RTN2
RYR1
SAFB
CLEC11A
SCN1B
CCL25
SEPW1
SGTA
SLC1A5
SLC1A6
SLC5A5
SLC8A2
SNAPC2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
STXBP2
SULT2B1
SULT2A1
SUPT5H
SYT5
TBXA2R
PRDX2
TGFB1
THOP1
ICAM5
TLE2
TNNI3
TNNT1
TULP2
TYK2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
VAV1
XRCC1
ZFP36
ZNF8
ZNF14
ZNF708
ZNF17
ZNF20
ZNF28
MZF1
ZNF43
ZNF45
ZNF69
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF121
ZNF132
ZNF134
ZNF135
ZNF136
ZNF137P
ZNF146
ZNF154
ZNF155
ZNF175
ZNF177
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
MADCAM1
SF3A2
SYMPK
MIA
CLPP
DPF1
LTBP4
TEAD2
RANBP3
CYP4F2
PPFIA3
KHSRP
PLA2G4C
PPAP2C
RFXANK
EIF3G
STX10
S1PR4
URI1
TNFSF14
TNFSF9
NAPA
SIGLEC5
FCGBP
AP1M1
AP3D1
PGLYRP1
F2RL3
UBE2M
ARHGEF1
PDCD5
DYRK1B
LPAR2
RAB11B
CRLF1
NUMBL
CYTH2
S1PR2
ZNF235
TRIP10
LONP1
ZNF264
KCNK6
NCR1
MED26
HOMER3
IL27RA
NAPSA
GDF15
TECR
ZNF254
GMFG
RAB3D
APBA3
IER2
KLK4
SAFB2
ZNF432
DHX34
KIAA0355
ZNF536
MLL4
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
UBA2
SAE1
SUGP2
EBI3
TRIM28
ZNF256
DDX39A
ZNF443
PLIN3
AKAP8
LILRB2
APC2
PAK4
B3GNT3
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4A
TMEM147
IFI30
TOMM40
TIMM44
CARM1
SEMA6B
ZNF211
CHERP
RNASEH2A
RABAC1
TRAPPC2P1
SPINT2
KLF1
DLL3
CERS1
GIPC1
POP4
ZNF234
ZNF266
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
PNPLA6
KDELR1
UQCR11
LILRB5
ILVBL
SLC27A5
LILRB4
KLK11
TMED1
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
CLASRP
KPTN
SLC7A9
CDC37
MAP4K1
KLK8
CYP4F8
PNKP
COPE
U2AF2
ATF5
ZFP30
ZNF507
LPHN1
PPP6R1
CARD8
SBNO2
SIRT2
CYP2G1P
MAST1
UNC13A
KDM4B
MAST3
SIPA1L3
FCHO1
ZC3H4
ZFR2
SIN3B
HAUS5
ARHGEF18
CRTC1
MAU2
PIP5K1C
FBXO46
ETHE1
RPL13A
HMHA1
SYNGR4
LILRA4
PRG1
CASP14
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
SHC2
TMEM59L
PGLS
ZNF324
LSM4
KLK5
ZNF345
PRKD2
RPL36
ZNF473
KANK2
CLIP3
FAM32A
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
SNORD37
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
AKAP8L
FGF22
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
TJP3
CPAMD8
SIGLEC9
SIGLEC8
GPR77
ITGB1BP3
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
C19orf53
BABAM1
LGALS13
UHRF1
CYP2S1
STRN4
CCDC106
HOOK2
EPN1
SERTAD3
SERTAD1
SLC39A3
GLTSCR2
GLTSCR1
TNPO2
EMR2
CD209
EHD2
KLK14
KLK12
COL5A3
RDH8
SHANK1
NOSIP
MRPL4
NDUFA13
ANGPTL4
ZNF580
HSD17B14
GP6
VRK3
MARCH2
ZNF571
GMIP
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
ISYNA1
ZNF581
SIRT6
PIAS4
LSR
LSM7
ZNF44
TM6SF2
MBD3
PTOV1
S1PR5
FXYD7
FXYD5
RAB4B
MIER2
DDX49
PAF1
PCSK4
PPP1R12C
TRPM4
ZNF586
ZNF562
QPCTL
GATAD2A
BEST2
FBXL12
FAM83E
PGPEP1
CC2D1A
EPS8L1
RASIP1
TMEM161A
SARS2
TMEM160
C19orf24
PIH1D1
C19orf60
GPATCH1
SAMD4B
ATP5SL
PLEKHJ1
C19orf73
MAP1S
PNMAL1
TMEM143
KLHL26
ZNF444
C19orf66
FEM1A
ZNF823
KLK15
MED29
STAP2
TRMT1
BTBD2
NLRP2
RNF126
ZNF416
ZNF446
CCDC94
ASF1B
ZNF701
ZNF83
ZNF415
USE1
PSENEN
ZNF302
C19orf80
LIN37
C19orf10
SMG9
ZNF253
IRGC
SLC7A10
PPAN
CABP5
RETN
SPHK2
LGALS14
EXOSC5
MEIS3
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
CEACAM19
SLC17A7
NAT14
CD177
ATP13A1
RGL3
SLC44A2
VN1R1
MCOLN1
RCN3
ZNF304
TTYH1
WDR18
REXO1
PNMAL2
ZNF490
PRR12
DOCK6
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
CAMSAP3
USP29
PLEKHA4
ZFP14
ZNF317
ZNF529
PRX
ANO8
SPTBN4
MARK4
SUGP1
HAMP
CATSPERG
CYP4F11
ZNF71
ZNF77
SCAF1
C19orf29
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
UBL5
ZNF350
TSKS
CELF5
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
LPPR2
ZNF574
PLEKHG2
RASAL3
MRPL34
KRI1
ZSWIM4
ZNF649
ZSCAN18
MGC2752
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
TMEM38A
TSEN34
KCTD15
SLC25A23
C19orf42
ZNF426
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
C19orf57
ZNF576
FSD1
ZNF557
LRFN3
ABHD8
CERS4
OCEL1
ZNF329
GLT25D1
IGFLR1
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
TLE6
ZNF552
EPHX3
PODNL1
ZNF671
ZNF613
ADCK4
CNTD2
SLC35E1
LPPR3
DENND1C
ZNF442
ZNF702P
ZNF556
LOC80054
ZNF606
ZNF614
LRRC8E
FLJ22184
FUZ
OPA3
ZNF430
ITPKC
UBXN6
PBX4
KIAA1683
B9D2
OR4F17
RSPH6A
CCDC130
ACSBG2
ADAMTS10
ZNF611
MED25
QTRT1
FAM108A1
ZNF93
DOHH
PLVAP
RTBDN
BCL2L12
C19orf12
TEX101
GRWD1
ANGPTL6
KLF16
USHBP1
WDR87
TSSK6
CCDC8
KIRREL2
ANKRD27
PRAM1
C19orf44
ZNF541
MRI1
SYT3
FBXW9
ALKBH7
WDR83
PDCD2L
ZNF414
AKT1S1
ELOF1
ZNF528
DOT1L
BRSK1
ZNF333
FBN3
ZNF527
CNFN
ZNF559
SNORD35B
KISS1R
EMR3
ZNF347
CREB3L3
GTPBP3
HDGFRP2
ZNF577
MPV17L2
ZNF607
SUV420H2
C19orf48
NFKBID
LMNB2
RAX2
ZBTB45
CEP89
ZNF382
ZNF587
FIZ1
ZNF566
MUM1
HSH2D
MPND
ALKBH6
ATG4D
ATCAY
SYDE1
RHPN2
MBD3L1
GALP
SIGLEC10
SIGLEC12
ZNF628
MIDN
KIR3DX1
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
SAMD1
DCAF15
GADD45GIP1
ZNF835
YIF1B
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
ZNF486
DPP9
ZNF682
R3HDM4
C19orf6
C19orf40
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
TPGS1
ZNF461
ZNF585B
CRB3
TIMM50
SHKBP1
REEP6
PEX11G
DMKN
ZNF561
OLFM2
CCDC114
HAUS8
FAM125A
DKFZp434J0226
ARMC6
ACPT
CGB5
DKFZp566F0947
MUC16
CGB7
LRRC4B
ZNF101
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
FDX1L
NACC1
PTH2
IZUMO4
SCAMP4
ADAT3
LOC113230
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
LENG8
CCDC124
ZNF554
FBXO17
KIR3DL3
ARHGAP33
EVI5L
RASGRP4
NXNL1
CCDC151
ZNF653
ZNF526
ZNF837
GRIN3B
MRPL54
LRG1
CIB3
RLN3
CLDND2
ZNF816
ZNF543
CEACAM20
RAVER1
OR7D4
OR7G1
OR1M1
COX6B2
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
OSCAR
ZNF813
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
WDR88
TMIGD2
EID2B
TNFAIP8L1
ZNF57
IRGQ
ZNF428
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
C19orf21
LRRC25
OR1I1
WTIP
ZNF792
NR2C2AP
HSPB6
CCDC105
CYP4F22
RINL
FBXO27
PLK5
C19orf47
LOC126536
OR10H4
ANKLE1
C2CD4C
ZNF358
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
LOC147727
ZNF560
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
ZNF563
SPC24
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
LGALS16
TTC9B
TICAM1
CIRBP-AS1
ZNRF4
ZNF599
FAM187B
CILP2
C19orf55
LOC148145
ZNF558
CDC42EP5
LOC148189
ZNF98
ZNF738
ZNF714
ZNF681
C19orf25
ATP8B3
FLJ25328
DIRAS1
ZNF555
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF846
OR7D2
ZNF579
ZNF791
ZNF564
ZNF709
ZNF433
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
PRR22
LGI4
C19orf46
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
ANKRD24
SPACA4
ZNF675
C19orf59
ZNF627
DAND5
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
C19orf26
CSNK1G2-AS1
PRR24
C19orf38
ZNF549
SYCE2
NAPSB
KANK3
PLAC2
TMEM146
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
ACTL9
OR2Z1
LOC284385
ZNF763
ZNF844
LOC284395
SCGB2B2
WDR62
ZFP82
LOC284408
LOC284412
VSTM1
TMEM150B
FAM71E2
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
OR10H5
NWD1
SLC25A42
LOC284440
ZNF493
ODF3L2
LOC284454
HKR1
VN1R2
VN1R4
EMR4P
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
ADAMTSL5
CLEC4G
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
NANOS3
PALM3
SELV
ZNF530
C19orf51
ZNF429
ZNF233
LILRA5
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
WASH5P
SLC27A1
LOC386758
LOC388499
C3P1
ZNF788
CLEC17A
CYP4F24P
RPSAP58
RGS9BP
KRTDAP
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ONECUT3
OR7G2
OR7G3
OR7A10
NUDT19
ZNF793
PAPL
LOC390940
ZNF805
SPRED3
MEX3D
ZNF321P
FLJ45445
PRSS57
VMAC
LOC400680
LOC400684
LOC400685
LGALS17A
SIGLEC16
FLJ26850
ZNF880
ZNF772
ZNF833P
IGLON5
HAPLN4
CTXN1
C19orf29-AS1
MIRLET7E
MIR125A
MIR150
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR7-3
MIR99B
PLIN5
CLEC4GP1
ZNF506
LOC440518
ZNF724P
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
FLJ25758
A1BG-AS1
DPRX
DUXA
ASPDH
MIR181D
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC641367
TMEM91
FAM138F
LOC643669
SCGB1B2P
SDHAF1
LOC644189
LOC644554
LINGO3
ARRDC5
FAM138A
LOC646508
SBK2
LOC646862
UCA1
PSG10P
LGALS7B
PHLDB3
MBD3L4
MBD3L3
SEC1
ZNF826P
SNORD23
SNORD88A
SNORD88B
SNORD88C
SNORD105
PPAN-P2RY11
MIR637
MIR638
MIR639
MIR641
MIR642A
MIR643
RPL13AP5
LOC728752
PLIN4
CCDC61
ZNF812
ZNF878
CEACAM18
SHISA7
LOC729966
FLJ30403
MEF2BNB
ZNF814
ZNF726
MIR769
SIGLEC14
MIMT1
LOC100101266
SNORD105B
ZGLP1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
C19orf71
LOC100128573
LOC100128675
LOC100128682
LOC100129083
ZNF737
LOC100129935
SCGB2B3P
TMEM221
SGK110
LOC100131094
BSPH1
LOC100131691
C19orf79
LOC100134317
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
ERVV-2
MEF2B
LOC100287177
ZNF729
LOC100288123
LOC100289650
ZNF587B
MIR1470
MIR1270-1
MIR1283-2
MIR1909
MIR1181
MIR1238
MIR1323
MIR1283-1
MIR1227
LOC100379224
MIR3191
MIR3188
MIR3187
MIR3190
MIR320E
MIR4322
MIR3189
MIR4324
MIR4323
MIR1270-2
MIR4321
MIR642B
MIR3940
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100505835
LOC100506012
LOC100506033
LOC100506068
LOC100506469
LOC100506930
LOC100507003
ZNF865
LOC100507373
LOC100507433
THEG5
LOC100507567
LOC100507588
ZNF559-ZNF177
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
ZNF625-ZNF20
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4747
MIR4531
MIR4746
MIR4748
MIR4745
MIR4751
LOC100631378
LOC100652909

Genes in Wide Peak

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

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

Genes
REL
BCL11A
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
ACTG2
ADD2
ADRA2B
ANXA4
ATP6V1B1
AUP1
CAPG
CD8A
CD8B
CTNNA2
DCTN1
DGUOK
LOC1720
DNAH6
DOK1
DUSP2
EGR4
EMX1
FABP1
GFPT1
GGCX
HK2
TLX2
MXD1
MAL
MAT2A
MDH1
MEIS1
OTX1
REG3A
PCBP1
PEX13
PLEK
PLGLB2
PLGLB1
PPP3R1
RAB1A
REG1A
REG1B
REG1P
RTKN
SFTPB
SLC1A4
SNRPG
SPR
TACR1
GCFC2
TGFA
TIA1
UGP2
VRK2
XPO1
ZNF2
ALMS1
MOGS
RNF103
DYSF
DUSP11
VAMP8
SUCLG1
ST3GAL5
NAT8
TMSB10
EIF2AK3
USP34
SERTAD2
MRPL19
ARHGAP25
ACTR2
MPHOSPH10
SMYD5
C1D
SEMA4F
CCT7
CCT4
GNLY
STAMBP
TGOLN2
B3GNT2
USP39
VAMP5
MTHFD2
PROKR1
IMMT
SNRNP27
AAK1
RPIA
CEP68
EXOC6B
EHBP1
WBP1
VAX2
POLR1A
CNRIP1
RAB11FIP5
NFU1
BMP10
ZNF638
HTRA2
LGALSL
KCNIP3
CD207
TPRKB
FAHD2A
WDPCP
RNF181
KRCC1
MRPL35
PCYOX1
NAT8B
VPS54
CHMP3
ETAA1
AFTPH
RETSAT
C2orf42
PTCD3
FANCL
MOB1A
THNSL2
NAGK
KDM3A
GKN1
CYP26B1
POLE4
KCMF1
PNO1
STARD7
PELI1
SLC4A5
GMCL1
TTC31
RMND5A
PAPOLG
MRPS5
REEP1
OR7E91P
ANKRD53
LRRTM4
TCF7L1
INO80B
WDR54
FAM161A
FAM176A
ANTXR1
ELMOD3
PRADC1
KIAA1841
MCEE
LOXL3
PCGF1
CCDC142
ZNF514
FAM136A
ATOH8
LBX2
LOC90499
LOC90784
SFXN5
LINC00152
TEX261
CCDC85A
WDR92
MRPL53
C2orf89
TMEM150A
TRIM43
REG3G
AHSA2
C2orf65
TEKT4
SMYD1
COMMD1
PROM2
FBXO41
GPAT2
PUS10
LINC00309
ASPRV1
LOC151534
CLEC4F
DQX1
ALMS1P
TET3
GKN2
C2orf51
APLF
TMEM17
SPRED2
SH2D6
LOC284950
LOC285074
LOC339803
C2orf74
LOC339807
FIGLA
NOTO
FOXI3
LRRTM1
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
ASTL
ACTR3BP2
LOC442028
FBXO48
LOC644838
GGT8P
ANKRD36BP2
TRIM43B
LOC654342
SNORD94
ANKRD20A8P
LOC729234
RGPD2
SNORA36C
SNORA70B
LOC100132215
LOC100133985
DBIL5P2
SNAR-H
LOC100189589
LOC100286979
MIR4264
MIR3126
BOLA3-AS1
RNF103-CHMP3
INO80B-WBP1
MIR4779
MIR4435-2
MIR4436A
MIR4434
MIR4780
MIR4778
MIR4432
MIR4435-1
LOC100630918

Genes in Wide Peak

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

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

Genes
FGFR1
PCM1
PLAG1
TCEA1
WRN
NCOA2
WHSC1L1
CHCHD7
HOOK3
hsa-mir-3149
hsa-mir-2052
hsa-mir-124-2
hsa-mir-486
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
NAT1
NAT2
ADRA1A
ADRB3
ANK1
ASAH1
ASPH
ATP6V1B2
BMP1
POLR3D
BNIP3L
OSGIN2
CA1
CA2
CA3
CA8
CEBPD
CHRNA2
CHRNB3
CLU
CRH
CTSB
CYP7A1
ADAM3A
DPYSL2
DUSP4
E2F5
EGR3
EIF4EBP1
EPB49
EPHX2
EXTL3
EYA1
FABP4
FABP5
PTK2B
FDFT1
FGL1
FNTA
ADAM2
GFRA2
GNRH1
NPBWR1
GSR
GTF2E2
NRG1
HNF4G
IKBKB
IL7
IMPA1
IDO1
LOXL2
LPL
LYN
MCM4
MMP16
MOS
MSR1
MYBL1
NEFM
NEFL
NKX3-1
OPRK1
PDE7A
PDGFRL
PENK
PLAT
PNOC
PMP2
POLB
PPP2CB
PPP2R2A
PPP3CC
PKIA
PRKDC
PEX2
RAB2A
RP1
RPL7
RPS20
SDCBP
SFRP1
SFTPC
SLC7A2
SLC18A1
SLC20A2
SNAI2
STAR
STC1
TACC1
TCEB1
TERF1
TPD52
TTPA
UBE2V2
VDAC3
FZD3
TUSC3
UBXN8
KAT6A
NSMAF
RGS20
ADAM18
ADAM9
ADAM7
RIPK2
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
GGH
CPNE3
CHRNA6
TRPA1
DOK2
ASH2L
MTMR7
MSC
KCNB2
CYP7B1
BAG4
ENTPD4
MTFR1
ST18
TOX
PHYHIP
RB1CC1
SORBS3
NPM2
DLC1
LYPLA1
ARFGEF1
DCTN6
PNMA2
ADAM28
AP3M2
COPS5
RBPMS
WWP1
STMN2
ERLIN2
LZTS1
PROSC
XPO7
TRIM35
RRS1
SULF1
RHOBTB2
DDHD2
KIF13B
PSD3
HEY1
TRAM1
LEPROTL1
KIAA0146
SLC39A14
LY96
SGK3
GPR124
C8orf71
PTTG3P
FGF20
SNORD54
STAU2
DKK4
LSM1
ADAMDEC1
BHLHE22
MRPS28
MRPL15
CNOT7
PURG
PI15
ZC2HC1A
LACTB2
FAM82B
GOLGA7
ZDHHC2
SLC25A37
SCARA3
ATP6V1H
TMEM66
SNTG1
GDAP1
CNGB3
KCTD9
IMPAD1
TMEM70
PIWIL2
ELP3
THAP1
ARMC1
INTS10
CCDC25
UBE2W
BRF2
CHD7
INTS9
CSGALNACT1
HR
PAG1
PBK
ZNF395
BIN3
TEX15
C8orf44
JPH1
C8orf4
CPA6
MTUS1
KIAA1456
KIAA1967
PLEKHA2
SH2D4A
PRDM14
SNX16
PDLIM2
SOX17
EBF2
FAM160B2
ZBTB10
DUSP26
HMBOX1
EFCAB1
ZMAT4
ZFAND1
ZFHX4
RNF122
CSPP1
NUDT18
DOCK5
FLJ14107
VCPIP1
ZNF703
TTI2
RAB11FIP1
PREX2
REEP4
STMN4
RNF170
SLCO5A1
CRISPLD1
TM2D2
SGK196
GINS4
PPAPDC1B
MAK16
TRIM55
FUT10
FAM86B1
LRRCC1
DNAJC5B
PSKH2
FAM110B
LONRF1
CHMP7
CHMP4C
TGS1
XKR4
C8orf40
PCMTD1
C8orf34
GOT1L1
VPS37A
TMEM68
NKX2-6
SGCZ
ADHFE1
UBXN2B
PXDNL
AGPAT6
UNC5D
LETM2
DCAF4L2
RALYL
HGSNAT
PEBP4
CDCA2
RDH10
ESCO2
FBXO16
SLC7A13
C8orf48
C8orf45
CLVS1
NKX6-3
KCNU1
C8orf84
CNBD1
IDO2
SDR16C5
R3HCC1
HTRA4
ADAM32
LGI3
DEFB109P1
DEFB130
ATP6V0D2
YTHDF3
C8orf46
LOC254896
REXO1L1
ADAM5P
LOC286059
EFHA2
LOC286114
SCARA5
LOC286135
RNF5P1
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
LOC340357
POTEA
SLC10A5
USP17L2
CA13
FAM90A25P
LOC389641
C8orf80
C8orf86
FAM150A
XKR9
LOC392196
LOC392232
LOC401463
C8orf59
MIR124-2
MIR320A
FLJ39080
C8orf22
MIR383
LINC00293
C8orf58
LINC00251
DEFB135
DEFB136
DEFB134
ZNF704
C8orf75
MBOAT4
MIR486
SNHG6
SNORD87
UG0898H09
FABP9
FABP12
FAM86B2
LOC728024
ZNF705D
LOC100128126
LOC100128750
LOC100128993
TCF24
LOC100130155
LOC100130298
LOC100130301
LOC100130964
LOC100132891
FAM66D
FAM66A
SBF1P1
LOC100133267
LOC100192378
LOC100287846
REXO1L2P
MIR2052
MIR4287
MIR3148
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100505659
LOC100505676
LOC100505718
LOC100506990
LOC100507156
LOC100507341
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4469
MIR548O2
MIR4470

Genes in Wide Peak

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

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

Genes
GNAS
TOP1
MAFB
SS18L1
ASXL1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-1289-1
hsa-mir-499
hsa-mir-644
hsa-mir-1825
hsa-mir-3193
hsa-mir-663
hsa-mir-3192
hsa-mir-103-2-as
hsa-mir-1292
hsa-mir-3194
ADA
ADRA1D
JAG1
AHCY
ASIP
ATP5E
AVP
BCL2L1
BFSP1
BMP2
BMP7
BPI
ENTPD6
CD40
CDC25B
CDH4
CEBPB
CENPB
CHGB
CHRNA4
COL9A3
CSE1L
CSNK2A1
CST1
CST2
CST3
CST4
CST5
CSTF1
CTSZ
CYP24A1
DNMT3B
E2F1
EDN3
EEF1A2
EPB41L1
EYA2
FKBP1A
FOXS1
GGT7
GHRH
GNRH2
NPBWR2
GSS
HCK
FOXA2
HNF4A
ID1
IDH3B
INSM1
EIF6
ITPA
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
LBP
MC3R
MMP9
MYBL2
MYT1
NFATC2
NKX2-2
NNAT
NTSR1
OPRL1
OXT
PAX1
PCK1
PCNA
PCSK2
PDYN
PFDN4
PI3
PLAGL2
PLCB4
PLCG1
PLTP
CTSA
PPP1R3D
PRNP
PSMA7
PTGIS
PTK6
PTPN1
PTPRA
PYGB
RBL1
RPN2
RPS21
RRBP1
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SIGLEC1
SNAI1
SNAP25
SNRPB
SNRPB2
SNTA1
SOX12
SPAG4
SRC
SRMS
SSTR4
STAU1
STK4
AURKA
TAF4
TCEA2
TCF15
TFAP2C
TGM2
TGM3
THBD
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF133
ZNF217
MKKS
GDF5
NCOA3
ATRN
RAE1
CST7
BCAS1
STX16
CDS2
TNFRSF6B
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
VAPB
B4GALT5
KIF3B
PSMF1
RBM39
TTI1
SNPH
ProSAPiP1
RASSF2
TM9SF4
SPATA2
GINS1
OSBPL2
SLC23A2
ACOT8
CST8
ATP9A
SGK2
RBM12
ARFRP1
RGS19
SIRPB1
SYCP2
MYL9
WFDC2
SEC23B
NOP56
PROCR
ARFGEF2
RBCK1
POLR3F
TCFL5
RBBP9
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
DSTN
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
CEP250
RNF24
HRH3
PXMP4
RBPJL
XRN2
DLGAP4
UBOX5
BTBD3
RALY
CD93
MAPRE1
TPX2
NINL
ZHX3
NCOA6
PLCB1
SLC9A8
ADNP
POFUT1
ZMYND8
SPO11
PRND
FLRT3
LAMP5
PRPF6
SPEF1
SAMHD1
C20orf194
C20orf4
L3MBTL1
PPP1R16B
C20orf26
ABHD12
TRPC4AP
ZNF337
GTPBP5
GMEB2
SNORD12C
SNORA71B
SNORA71A
SNORD57
SNORD56
SDCBP2
SNX5
TP53TG5
MOCS3
SLCO4A1
REM1
C20orf30
HSPC072
NXT1
VSX1
STMN3
SLC35C2
SLMO2
IFT52
NAA20
PHF20
SCAND1
BPIFA1
CRNKL1
ANGPT4
TH1L
C20orf43
C20orf111
ESF1
PIGT
TRMT6
ERGIC3
CDK5RAP1
RTEL1
SOX18
HAO1
RIN2
SMOX
CRLS1
YTHDF1
LIME1
UCKL1
C20orf27
C20orf11
DZANK1
UQCC
PCMTD2
C20orf20
SPTLC3
C20orf29
TMEM74B
PPP4R1L
SIRPG
RBM38
FERMT1
KIF16B
TASP1
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
EDEM2
DOK5
PLK1S1
DBNDD2
ACSS2
RNF114
SULF2
NSFL1C
C20orf24
TMX4
CTNNBL1
GPCPD1
CPXM1
SLC2A4RG
OTOR
PMEPA1
CASS4
SPINLW1
C20orf3
PAK7
RALGAPB
JPH2
SALL4
ZNFX1
RALGAPA2
CSRP2BP
RAB22A
SLC24A3
NDRG3
SLC12A5
ZNF512B
MAVS
PREX1
EBF4
COL20A1
MYH7B
NCOA5
TRIB3
TP53INP2
RPRD1B
OVOL2
TGIF2
CDH26
FASTKD5
KCNK15
DHX35
MANBAL
NAPB
SLC17A9
ELMO2
ZNF335
ANKRD5
LOC63930
PCIF1
FAM217B
NECAB3
GFRA4
CDH22
GZF1
VPS16
FAM113A
SLC13A3
LPIN3
MRPS26
DDRGK1
GDAP1L1
LOC79015
C20orf195
C20orf7
PPDPF
ZNF343
TTPAL
BIRC7
NPEPL1
ACTR5
SYNDIG1
DSN1
NRSN2
PANK2
FER1L4
DNAJC5
ADAM33
PABPC1L
BPIFB2
SEL1L2
TUBB1
ZBP1
SLC2A10
HM13
PDRG1
FAM83D
DEFB126
CABLES2
FAM110A
DYNLRB1
ITCH
SLC4A11
SLA2
CHD6
MCM8
ACSS1
MAP1LC3A
PARD6B
ZGPAT
COX4I2
ZNF341
TOX2
ZCCHC3
MYLK2
PRIC285
KIAA1755
SCRT2
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
GGTLC1
C20orf72
DTD1
BPIFB1
TP53RK
C20orf54
DNTTIP1
FAM210B
PHACTR3
HSPA12B
DEFB118
TMC2
BHLHE23
NKAIN4
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
TBC1D20
SIRPD
C20orf141
PROKR2
C20orf94
CSTL1
CST9L
CST9
C20orf166
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
GATA5
MLLT10P1
SLC32A1
C20orf96
BPIFA2
ZBTB46
WFDC3
GCNT7
C20orf112
CBLN4
CTCFL
C20orf132
SAMD10
ABHD16B
C20orf160
KIAA0889
C20orf118
RIMS4
SUN5
MACROD2
SRXN1
ROMO1
NEURL2
LINC00261
ZSWIM3
WFDC10A
BANF2
NANP
LINC00266-1
DEFB127
C20orf79
ISM1
WFDC6
C20orf173
LINC00028
FAM65C
CST11
DEFB129
SIRPA
C20orf151
C20orf152
STK35
R3HDML
ADIG
GTSF1L
WFDC5
LOC149773
GNAS-AS1
PRNT
LOC149837
C20orf196
NCOR1P1
LOC149950
COMMD7
BPIFB4
LSM14B
WFDC13
APCDD1L
LRRN4
CSTT
TTLL9
ACTL10
C20orf201
FAM209A
LOC200261
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
DEFB125
DEFB128
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
SIRPB2
LOC284788
LOC284798
FAM182A
LOC284801
FRG1B
C20orf203
BPIFA4P
LOC339568
LOC339593
ARHGAP40
RSPO4
TGM6
XKR7
BPIFB3
TMEM189
TMEM189-UBE2V1
LINC00493
LOC388796
FAM209B
SPINT4
SUMO1P1
DEFB132
C20orf202
FLJ33581
MIR103A2
MIR1-1
MIR124-3
MIR133A2
MIR296
DZANK1-AS1
ZNFX1-AS1
MIR499A
RAD21L1
LOC643406
NKX2-4
LOC647979
SNORA39
SNORA51
SNORA60
SNORA71C
SNORA71D
SNORD12
SNORD17
SNORD86
SNORD110
MIR644A
MIR645
MIR647
MIR663A
LOC728228
FAM182B
SYS1-DBNDD2
HAR1A
HAR1B
PSIMCT-1
SNORD119
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
LOC100128496
LOC100130264
ZNF663
LOC100131208
LOC100131496
DPH3P1
LOC100134015
LOC100134868
LINC00029
LOC100144597
FLJ16779
LOC100270679
LOC100270804
LOC100287792
TMEM239
LOC100289473
MIR1914
MIR1292
MIR1257
MIR103B2
PCNA-AS1
PET117
MACROD2-AS1
MIR3192
MIR4325
MIR3194
MIR3193
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505536
LOC100505783
LOC100505815
LOC100505826
LOC100506384
LOC100507495
LOC100507629
SPINLW1-WFDC6
TGIF2-C20ORF24
FKBP1A-SDCBP2
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR499B
MIR4756
MIR4758
MIR4532
MIR4533
MIR4755
MIR5095
LOC100652730

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.08 | -1.95 | 1 | 0.31 | 5.87 | 1.22e-08
1q | 1955 | 0.21 | 1.76 | 0.195 | 0.22 | 2.15 | 0.045
2p | 924 | 0.25 | 0.15 | 1 | 0.10 | -3.9 | 1
2q | 1556 | 0.26 | 2.25 | 0.0697 | 0.05 | -3.97 | 1
3p | 1062 | 0.18 | -1.49 | 1 | 0.11 | -3.41 | 1
3q | 1139 | 0.22 | -0.303 | 1 | 0.09 | -3.88 | 1
4p | 489 | 0.08 | -4.69 | 1 | 0.38 | 2.65 | 0.0125
4q | 1049 | 0.05 | -4.29 | 1 | 0.41 | 5.22 | 4.5e-07
5p | 270 | 0.23 | -1.97 | 1 | 0.23 | -1.97 | 1
5q | 1427 | 0.16 | -1.18 | 1 | 0.30 | 2.89 | 0.00635
6p | 1173 | 0.24 | 0.492 | 1 | 0.14 | -2.27 | 1
6q | 839 | 0.24 | -0.443 | 1 | 0.19 | -1.81 | 1
7p | 641 | 0.62 | 9.89 | 0 | 0.05 | -4.02 | 1
7q | 1277 | 0.52 | 9.35 | 0 | 0.04 | -3.85 | 1
8p | 580 | 0.34 | 1.22 | 0.497 | 0.65 | 9.69 | 0
8q | 859 | 0.55 | 7.94 | 6.66e-15 | 0.27 | 0.291 | 0.857
9p | 422 | 0.29 | 0.06 | 1 | 0.19 | -2.48 | 1
9q | 1113 | 0.24 | 0.126 | 1 | 0.17 | -1.63 | 1
10p | 409 | 0.09 | -5.04 | 1 | 0.21 | -2.16 | 1
10q | 1268 | 0.04 | -4.78 | 1 | 0.24 | 0.747 | 0.535
11p | 862 | 0.21 | -1.13 | 1 | 0.19 | -1.74 | 1
11q | 1515 | 0.18 | -0.534 | 1 | 0.23 | 1.03 | 0.377
12p | 575 | 0.22 | -1.43 | 1 | 0.18 | -2.45 | 1
12q | 1447 | 0.15 | -1.52 | 1 | 0.16 | -1.35 | 1
13q | 654 | 0.71 | 12.3 | 0 | 0.15 | -1.92 | 1
14q | 1341 | 0.08 | -3.1 | 1 | 0.42 | 6.42 | 4.5e-10
15q | 1355 | 0.03 | -4.11 | 1 | 0.45 | 7.53 | 2.03e-13
16p | 872 | 0.25 | 0.0641 | 1 | 0.07 | -4.58 | 1
16q | 702 | 0.25 | -0.391 | 1 | 0.13 | -3.53 | 1
17p | 683 | 0.07 | -3.24 | 1 | 0.68 | 11.7 | 0
17q | 1592 | 0.21 | 0.733 | 0.843 | 0.20 | 0.202 | 0.885
18p | 143 | 0.19 | -1.59 | 1 | 0.81 | 13.3 | 0
18q | 446 | 0.12 | -1.79 | 1 | 0.87 | 16 | 0
19p | 995 | 0.18 | -1.65 | 1 | 0.21 | -0.866 | 1
19q | 1709 | 0.21 | 0.893 | 0.744 | 0.17 | -0.387 | 1
20p | 355 | 0.74 | 10.7 | 0 | 0.53 | 4.2 | 5.82e-05
20q | 753 | 0.87 | 17 | 0 | 0.39 | 1.57 | 0.156
21q | 509 | 0.10 | -3.92 | 1 | 0.43 | 4.08 | 9.09e-05
22q | 921 | 0.09 | -3.86 | 1 | 0.37 | 3.56 | 0.000681
Xq | 1312 | 0.23 | 0.41 | 1 | 0.20 | -0.421 | 1

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/READ-TP/9826731/GDAC_MergeDataFiles_3127248/READ-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 162 Input Tumor Samples.

Tumor Sample Names
TCGA-AF-2687-01A-02D-1732-01
TCGA-AF-2689-01A-01D-1549-01
TCGA-AF-2690-01A-02D-1732-01
TCGA-AF-2691-01A-01D-1549-01
TCGA-AF-2692-01A-01D-0819-01
TCGA-AF-2693-01A-02D-1732-01
TCGA-AF-3400-01A-01D-1549-01
TCGA-AF-3911-01A-01D-1732-01
TCGA-AF-3913-01A-02D-1428-01
TCGA-AF-4110-01A-02D-1732-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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