Liver Hepatocellular Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16a (cga svn revision 43808).

Summary

There were 82 tumor samples used in this analysis: 23 significant arm-level results, 27 significant focal amplifications, and 26 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 27 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
1q22 | 1.3055e-08 | 1.3055e-08 | chr1:154971163-155045171 | 6
11q13.3 | 7.8754e-08 | 7.8754e-08 | chr11:69261268-69434302 | 0 [CCND1]
6p21.1 | 1.185e-07 | 1.3282e-06 | chr6:43768831-43778390 | 0 [VEGFA]
8q24.22 | 7.8625e-05 | 7.8625e-05 | chr8:122477740-135367259 | 68
17q25.3 | 1.1647e-05 | 0.00040873 | chr17:80079436-80527577 | 12
3q26.31 | 0.00058644 | 0.00058644 | chr3:172254454-172319444 | 0 [TNFSF10]
13q32.3 | 0.0014838 | 0.0014838 | chr13:96213209-104617917 | 50
7q21.2 | 0.0053008 | 0.0053008 | chr7:90450977-92715262 | 16
2p24.1 | 0.035331 | 0.035331 | chr2:9349056-27703965 | 136
5p15.33 | 0.035331 | 0.035331 | chr5:953901-1300024 | 7
17q23.1 | 0.0049879 | 0.050489 | chr17:57648506-58857125 | 21
5q35.3 | 0.058808 | 0.058808 | chr5:136221300-180915260 | 452
4q31.3 | 0.089675 | 0.089675 | chr4:154206362-158836019 | 25
1p22.3 | 0.099658 | 0.099658 | chr1:85974031-86006008 | 1
7p21.3 | 0.099658 | 0.099658 | chr7:1-34013580 | 244
10p15.1 | 0.099658 | 0.099658 | chr10:5008384-5043327 | 2
1q42.3 | 0.0059548 | 0.10324 | chr1:193594795-249250621 | 475
19q13.11 | 0.10324 | 0.10324 | chr19:33711641-33762256 | 1
6p25.2 | 0.016894 | 0.14505 | chr6:1-32870056 | 422
16q11.2 | 0.15211 | 0.15211 | chr16:31845698-47608671 | 26
15q21.3 | 0.10324 | 0.15972 | chr15:53689045-53797742 | 0 [WDR72]
6q12 | 0.15211 | 0.16776 | chr6:67148820-67995170 | 0 [MCART3P]
20q13.2 | 0.18314 | 0.18314 | chr20:47874006-63025520 | 194
12q23.1 | 0.15972 | 0.2083 | chr12:90785550-133851895 | 386
12p13.2 | 0.24941 | 0.24941 | chr12:12435873-12486704 | 1
15q26.3 | 0.033697 | 0.38609 | chr15:51701205-102531392 | 470
12q13.3 | 0.12586 | 0.43128 | chr12:1-133851895 | 1200

Genes in Wide Peak

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

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

Genes
EFNA4
ADAM15
ZBTB7B
DCST2
DCST1
LOC100505666

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.22.

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

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
ADCY8
ANXA13
HAS2
KCNQ3
NDUFB9
POU5F1B
PVT1
ST3GAL1
SLA
SQLE
TG
WISP1
MTSS1
KIAA0196
HHLA1
TRIB1
NDRG1
RNF139
ZHX1
ZHX2
EFR3A
LRRC6
ATAD2
ASAP1-IT1
ASAP1
PHF20L1
FAM49B
TRMT12
WDYHV1
GSDMC
DERL1
TATDN1
C8orf76
FAM83A
WDR67
HPYR1
FBXO32
ZNF572
TMEM71
TMEM65
LOC157381
FAM84B
FAM91A1
NSMCE2
KLHL38
FER1L6-AS1
HAS2-AS1
FER1L6
LOC727677
LOC728724
OC90
LOC100130231
LOC100131726
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
LOC100507117
ZHX1-C8ORF76
MIR4663
PCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

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

Genes
CD7
CSNK1D
UTS2R
FOXK2
SECTM1
SLC16A3
NARF
C17orf62
C17orf101
CCDC57
HEXDC
TEX19

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q32.3.

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

Genes
ERCC5
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
GPR183
FGF14
GPR18
IPO5
PCCA
DNAJC3
RAP2A
SLC10A2
SLC15A1
TPP2
ZIC2
STK24
CLDN10
ITGBL1
TM9SF2
MBNL2
FARP1
DZIP1
DOCK9
OXGR1
BIVM
UGGT2
KDELC1
TMTC4
ZIC5
A2LD1
TEX30
METTL21CP1
RNF113B
CLYBL
METTL21C
NALCN
HS6ST3
FGF14-IT1
LOC283481
UBAC2
CCDC168
MIR623
FKSG29
UBAC2-AS1
MIR4306
MIR3170
BIVM-ERCC5
MIR2681
MIR548AN
MIR4705

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
hsa-mir-1285-1
KRIT1
CYP51A1
PEX1
CDK14
MTERF
FZD1
ANKIB1
GATAD1
RBM48
MGC16142
FAM133B
LRRD1
LOC728066

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.1.

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

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ADCY3
APOB
RHOB
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
FTH1P3
GTF3C2
HADHA
HADHB
HPCAL1
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
RRM2
SDC1
ADAM17
UCN
VSNL1
SLC30A3
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
SNX17
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
MAPRE3
EFR3B
LPIN1
PUM2
NTSR2
IFT172
TRIB2
GRHL1
NRBP1
ITSN2
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
ATAD2B
TMEM214
C2orf18
ASXL2
DPYSL5
TRIM54
WDR35
RDH14
AGBL5
C2orf43
HS1BP3
CENPO
SMC6
NOL10
C2orf44
FAM49A
ABHD1
EPT1
CCDC164
NT5C1B
KLHL29
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
TCF23
FAM59B
FAM84A
GDF7
GPR113
UBXN2A
CYS1
KRTCAP3
ATP6V1C2
DNAJC5G
IAH1
FLJ33534
C2orf70
C2orf53
MSGN1
GEN1
C2orf48
PFN4
LOC375190
MFSD2B
PTRHD1
FLJ12334
LOC645949
C2orf84
RAD51AP2
DNAJC27-AS1
OST4
MIR1301
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505624
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

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

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
LOC100506688
MIR4635

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
CLTC
hsa-mir-21
CA4
RPS6KB1
PPM1D
APPBP2
RNFT1
TUBD1
PTRH2
BCAS3
HEATR6
DHX40
VMP1
USP32
C17orf64
MIR21
LOC645638
TBC1D3P1-DHX40P1
LOC653653
SCARNA20
MIR4737

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
ADRA1B
ADRB2
ANXA6
ATOX1
BNIP1
CAMK2A
CANX
CCNG1
CD14
CDC25C
CDX1
CLTB
CSF1R
CSNK1A1
NKX2-5
CTNNA1
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSPA9
NDST1
HTR4
IK
IL12B
KCNMB1
LCP2
LTC4S
MFAP3
MGAT1
MSX2
NDUFA2
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
POU4F3
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SLC6A7
SLC34A1
SLIT3
SNCB
SPARC
SPINK1
SPOCK1
STK10
TAF7
ZNF354A
TCOF1
TTC1
UBE2D2
WNT8A
NME5
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
GFPT2
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
PRELID1
IL17B
MAT2B
MRPL22
PCDHB1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DCTN4
MZB1
PAIP2
PCDH12
FAM13B
FAM53C
REEP2
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
KDM3B
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PSD2
THOC3
C5orf32
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
SFXN1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
C5orf58
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SLC36A2
SPINK13
C5orf41
LOC153469
ZMAT2
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
LOC340037
TMEM173
ARSI
PFN3
ZNF879
IRGM
FBLL1
NIPAL4
DND1
C5orf25
FLJ38109
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
FLJ16171
MIR340
IGIP
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
LOC100505658
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q31.3.

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

Genes
ANXA2P1
CTSO
FGA
FGB
FGG
GLRB
GRIA2
GUCY1A3
GUCY1B3
NPY2R
PLRG1
SFRP2
TDO2
TLR2
LRAT
KIAA0922
TRIM2
ACCN5
DCHS2
PDGFC
MAP9
MND1
RBM46
RNF175
LOC340017

Genes in Wide Peak

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

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

Genes
DDAH1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
AKR1C1
AKR1C2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.3.

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

Genes
ELK4
FH
MDM4
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ARF1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PIK3C2B
PKP1
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS7
RNPEP
RYR2
SNRPE
SRP9
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GPR37L1
GGPS1
SOX13
IKBKE
TMEM63A
TOMM20
URB2
CEP170
ZC3H11A
TMCC2
LPGAT1
KIF14
AKT3
BPNT1
TIMM17A
LRRN2
ZNF238
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NFASC
FBXO28
CAMSAP2
SRGAP2
CRB1
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
LAX1
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
KLHL12
LGR6
TFB2M
GREM2
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
NUAK2
DDX59
RASSF5
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
WNT3A
NAV1
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
ASPM
PGBD2
OR2L13
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
IRF2BP2
ZBTB41
MIA3
C1orf95
FAM89A
RPS10P7
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR181B1
MIR194-1
MIR205
MIR181A1
MIR215
MIR29B2
MIR29C
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SNORA14B
SNORA36B
SNORA77
SNORA16B
LOC728463
FAM72A
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR1231
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
KDM5B-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4735
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

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

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

Genes
SLC7A10

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p25.2.

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

Genes
IRF4
POU5F1
TRIM27
DEK
HIST1H4I
hsa-mir-1236
hsa-mir-877
hsa-mir-3143
hsa-mir-548a-1
ABCF1
AGER
AIF1
ATP6V1G2
CFB
BMP6
BPHL
BTN1A1
C2
C4A
C4B
DDR1
CDSN
CLIC1
ATF6B
CSNK2B
CYP21A2
CYP21A1P
DOM3Z
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GABBR1
GCNT2
GMDS
GMPR
GNL1
GPLD1
GPX5
GTF2H4
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
HLA-A
HLA-B
HLA-C
HLA-DOB
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSPA1A
HSPA1B
HSPA1L
ID4
JARID2
LTA
LTB
MAK
MICB
MOG
MSH5
NEDD9
NEU1
NFKBIL1
NQO2
NOTCH4
PBX2
SERPINB6
SERPINB9
PPP1R10
PRL
PSMB8
PSMB9
RNF5
RREB1
ATXN1
SKIV2L
SLC17A1
SOX4
SSR1
TAP1
TAP2
TCF19
PPP1R11
TFAP2A
TNF
TNXA
TNXB
TPMT
TUBB2A
VARS
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204P
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
OR2H2
RDBP
LST1
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
CMAHP
DHX16
RIPK1
STK19
IER3
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
GCM2
CD83
PPT2
CDYL
LY86
EEF1E1
MDC1
FAM65B
ZSCAN12
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
FLOT1
SLC17A2
HCG9
PRSS16
BTN3A3
BTN2A2
ECI2
HMGN4
TRIM38
CAP2
UBD
AGPAT1
SCGN
C6orf10
FARS2
SLC17A3
RPP40
HCP5
EHMT2
TRIM31
BTN3A2
BTN3A1
BTN2A1
NRM
SIRT5
DDAH2
OR2B6
FAM50B
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
SNORD52
SNORD48
MRPS18B
C6orf15
MYLIP
ABT1
ZNRD1
C6orf48
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
HCG4
GFOD1
CCHCR1
BTN2A3P
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
APOM
BTNL2
TRIM39
WRNIP1
DUSP22
LYRM4
VARS2
MRS2
LSM2
C6orf47
LY6G5B
LY6G6D
SLC22A23
MUTED
CCDC90A
GPSM3
FKBPL
KIF13A
ZNF323
LY6G6E
ZNF322
RPP21
ATAT1
ZKSCAN3
ZSCAN16
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRR3
ZNRD1-AS1
PRRT1
EGFL8
HCG4B
TXNDC5
C6orf62
OR5V1
OR2B2
OR12D3
TMEM14B
RIOK1
DTNBP1
PGBD1
ADTRP
HIST1H2AH
HIST1H2BK
TRIM15
POM121L2
FOXQ1
SCAND3
MAS1L
HUS1B
TRIM40
DPCR1
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
PSORS1C1
PSORS1C2
PPP1R18
TRIM39-RPP21
TUBB
PIP5K1P1
ZBTB12
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
ZSCAN23
NKAPL
TOB2P1
FAM217A
HCG27
RNF144B
HIST1H2BA
GPX6
NCR3
LY6G6F
ZNF311
LOC285768
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
HCG22
RNF5P1
MYLK4
IFITM4P
ZNF391
ZFP57
TUBB2B
C6orf52
HCG26
KAAG1
NHLRC1
ZKSCAN4
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
SFTA2
MUC21
DKFZP686I15217
FLJ23152
LINC00340
LOC401242
MCCD1
SAPCD1
C6orf201
ERVFRD-1
HCG23
HCG18
OR2B3
OR2J3
OR14J1
OR10C1
HCG11
LOC554223
PPP1R3G
SNORA38
SNORD32B
SNORD84
SNORD117
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
MIR877
LOC100129636
LOC100130275
LOC100130357
PSORS1C3
LOC100131289
LINC00240
LOC100270746
LOC100293534
LOC100294145
MIR1236
MIR3143
MIR3691
LOC100506207
LOC100506409
LOC100507173
LOC100507194
LOC100507362
MICA
LOC100507463
LOC100507547
MUC22
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4646
MIR4640
MIR4639
MIR4645

Genes in Wide Peak

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

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

Genes
hsa-mir-1826
PHKB
DNAJA2
ZNF267
ORC6
TP53TG3
VPS35
SHCBP1
ITFG1
NETO2
GPT2
MYLK3
ANKRD26P1
LOC146481
LOC283914
SLC6A10P
C16orf87
LOC390705
FLJ26245
HERC2P4
UBE2MP1
LINC00273
TP53TG3C
LOC729264
TP53TG3B
LOC100130700

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

Table S18. Genes in bold are cancer genes as defined by The Sanger Institute's 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
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-3194
ATP5E
BMP7
CDH4
CEBPB
CHRNA4
COL9A3
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
NPBWR2
KCNB1
KCNG1
KCNQ2
LAMA5
MC3R
MYT1
NFATC2
NTSR1
OPRL1
PCK1
PFDN4
PPP1R3D
PSMA7
PTGIS
PTK6
PTPN1
RPS21
SNAI1
SRMS
AURKA
TAF4
TCEA2
TFAP2C
TPD52L2
UBE2V1
ZNF217
RAE1
BCAS1
STX16
TNFRSF6B
DPM1
VAPB
B4GALT5
SPATA2
OSBPL2
ATP9A
ARFRP1
RGS19
SYCP2
TCFL5
ADRM1
OGFR
DIDO1
HRH3
SLC9A8
ADNP
SPO11
PRPF6
GTPBP5
GMEB2
SNORD12C
MOCS3
SLCO4A1
STMN3
SLMO2
TH1L
C20orf43
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
C20orf20
PPP4R1L
RBM38
BCAS4
ZFP64
ARFGAP1
DOK5
RNF114
SLC2A4RG
PMEPA1
CASS4
SALL4
ZNFX1
RAB22A
ZNF512B
COL20A1
CDH26
SLC17A9
LOC63930
FAM217B
C20orf195
PPDPF
BIRC7
NPEPL1
DNAJC5
TUBB1
ZBP1
CABLES2
PARD6B
ZGPAT
PRIC285
FAM210B
PHACTR3
BHLHE23
NKAIN4
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
GCNT7
CBLN4
CTCFL
SAMD10
ABHD16B
LINC00266-1
FAM65C
C20orf151
LOC149773
GNAS-AS1
LSM14B
APCDD1L
C20orf201
FAM209A
C20orf166-AS1
LINC00176
LOC284751
C20orf197
LOC284757
TMEM189
TMEM189-UBE2V1
FAM209B
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
ZNFX1-AS1
SNORD12
MIR645
MIR647
HAR1A
HAR1B
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
DPH3P1
LINC00029
LOC100144597
FLJ16779
MIR1914
MIR1257
MIR4325
MIR3194
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 12q23.1.

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

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DCN
EPYC
DTX1
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
LTA4H
LUM
MMP17
MSI1
MVK
MYBPC1
MYL2
NFYB
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
CRADD
HRK
ADAM1
SOCS2
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
SNRNP35
KERA
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
FAM216A
HCFC2
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GPR133
MORN3
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR620
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4498
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

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

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

Genes
MANSC1

Genes in Wide Peak

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

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

Genes
BLM
IDH2
NTRK3
PML
TCF12
CRTC3
FLJ27352
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
ADAM10
ACAN
ALDH1A3
ANPEP
ANXA2
AQP9
BBS4
BCL2A1
BNC1
BNIP2
CA12
CHD2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
FES
GTF2A2
HEXA
ONECUT1
IDH3A
IGF1R
IL16
IREB2
ISG20
ISLR
LIPC
LOXL1
SMAD3
SMAD6
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
MYO1E
MYO5A
MYO9A
NEDD4
NEO1
NMB
OAZ2
FURIN
PCSK6
PDE8A
PKM2
PLIN1
POLG
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
SH3GL3
SNRPA1
SNX1
NR2F2
TLE3
TPM1
TYRO3P
AP3B2
ANP32A
ST8SIA2
SEMA7A
CILP
PIAS1
RAB11A
PEX11A
IQGAP1
ALDH1A2
HERC1
PSTPIP1
PRC1
CCNB2
SLC28A1
SLC24A1
CCPG1
GCNT3
TRIP4
COX5A
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
KIAA0101
SV2B
ARNT2
USP3
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
ABHD2
ADAMTS7
AKAP13
ITGA11
CHSY1
ZNF609
TBC1D2B
MESDC2
ACSBG1
KIAA1024
DMXL2
SYNM
TMED3
SEC11A
DAPK2
GABARAPL3
ARIH1
SIN3A
ULK3
GLCE
PYGO1
FBXO22
VPS33B
MRPL46
OR4F4
NPTN
FOXB1
SLCO3A1
SCG3
TMOD3
TMOD2
SCAPER
HDGFRP3
RPS27L
RSL24D1
RASL12
SPG21
NGRN
RHCG
PTPLAD1
RAB8B
BTBD1
TM6SF1
CSNK1G1
ZFAND6
SCAND2
FAM63B
RNF111
ZNF280D
VPS13C
LRRC49
PAQR5
DPP8
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZSCAN2
ZWILCH
DET1
UACA
LINS
FANCI
IMP3
LARP6
MNS1
DNAJA4
MCTP2
SELS
GOLGA6B
MESP1
UNC45A
MYO5C
FAM214A
C15orf39
THAP10
RGMA
WDR93
PARP6
C15orf17
ADAMTSL3
KIAA1199
ALPK3
ISLR2
IGDCC4
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
KLHL25
CPEB1
AEN
IQCH
ISL2
RFX7
TTC23
MRPS11
NOX5
EFTUD1
NEIL1
NARG2
LRRK1
AAGAB
LMAN1L
SLTM
PEAK1
SNX22
THSD4
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
AGSK1
TM2D3
PLEKHO2
WDR61
CD276
STARD5
POLR2M
C15orf44
C15orf5
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
MEGF11
LINGO1
WDR73
CGNL1
UBL7
C15orf42
RCCD1
LOC91450
CALML4
ARRDC4
LOC91948
LDHAL6B
UBE2Q2
LACTB
DIS3L
LEO1
C15orf40
SENP8
MTFMT
OSTBETA
TARSL2
HIGD2B
LRRC28
C15orf27
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
C2CD4A
LYSMD4
FAM81A
GCOM1
LOC145783
PGPEP1L
LOC145820
LOC145837
C15orf61
C15orf32
HAPLN3
MESP2
SPATA8
NRG4
LINC00052
C15orf26
TBC1D21
DYX1C1
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
CT62
GRAMD2
MGC15885
LCTL
CERS3
SPESP1
LOC253044
LOC254559
LYSMD2
WDR72
SNX33
PRTG
LOC283663
LINC00277
C15orf60
C15orf37
LOC283688
LOC283692
LOC283693
FAM154B
LOC283731
LOC283738
LOC283761
FAM169B
FBXL22
TMEM202
LOC338963
GOLGA6A
TMC3
ZNF774
RBPMS2
ANKDD1A
C15orf38
TEX9
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
C2CD4B
C15orf59
LOC388152
UBE2Q2P1
FLJ42289
KBTBD13
UBAP1L
SKOR1
ANKRD34C
C15orf58
OR4F6
OR4F15
LOC390660
ST20
FAM174B
LOC400456
MIR184
MIR190A
MIR7-2
MIR9-3
C15orf50
UNC13C
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
LOC645752
SH2D7
LOC646938
GOLGA6L10
LOC648809
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA15
SCARNA14
FBXO22-AS1
MIR549
MIR628
MIR629
MIR630
MIR631
LOC727849
LOC727915
ASB9P1
LOC729739
LOC729911
FAM138E
DNM1P35
LOC100130855
UBE2Q2P3
UBE2Q2P2
LOC100144604
GPCRLTM7
DDX11L1
LOC100287559
LOC100287616
DDX11L9
MIR1276
MIR1272
MIR1266
MIR1179
MIR1469
MIR548H4
MIR2116
MIR4311
MIR4312
MIR3175
MIR4313
RPS17L
LOC100505679
LOC100506686
LOC100506874
LOC100507217
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
DYX1C1-CCPG1
MIR4514
MIR4513
MIR3529
MIR4511
MIR4515
MIR4714
MYZAP

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.3.

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

Genes
ALDH2
ATF1
BCL7A
BTG1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
MLL2
HMGA2
WIF1
ZNF384
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
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
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
ACACB
ACADS
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ARL1
ART4
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
SCARB1
CD63
CD69
CDK2
CDKN1B
CHD4
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CREBL2
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
DDX11
ATN1
EPYC
DTX1
DUSP6
PHC1
EIF2B1
EIF4B
CELA1
ELK3
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GRIN2B
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTA4H
LTBR
LUM
LYZ
M6PR
MARS
METTL1
KITLG
MGP
MGST1
MIP
MMP17
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NDUFA9
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
POU6F1
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAB1
PRKAG1
PRPH
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAN
RAP1B
RARG
RBMS2
RDH5
RECQL
RFC5
RFX4
RNY5
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SNRPF
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
SYT1
TAC3
TARBP2
TBX5
TBX3
HNF1A
TDG
TEAD4
TMBIM6
TFCP2
TSPAN8
TMPO
TNFRSF1A
TPI1
NR2C1
HSP90B1
TULP3
TXNRD1
UBC
UBE2N
UNG
VDR
VWF
WNT1
WNT10B
ZNF10
ZNF26
ZNF84
ZNF140
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
DYRK2
PPFIBP1
PPFIA2
CSDA
LGR5
MAPKAPK5
DENR
RDH16
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
GPRC5A
KRT75
SCAF11
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
KIAA0748
KIAA0528
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
CLEC2B
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
RNF41
MPHOSPH9
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
LEPREL2
DCTN2
AKAP3
CCT2
SLCO1B1
RAD51AP1
CAMKK2
AVIL
PTGES3
KLRAP1
ZNF268
FRS2
TSPAN9
TRAFD1
OS9
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
PHLDA1
R3HDM2
MLXIP
RPH3A
KLRK1
P2RX2
RAB21
STK38L
FBXO21
FAIM2
MON2
SETD1B
UHRF1BP1L
ERC1
DDN
ANKLE2
TMEM194A
CUX2
KIAA1033
TBC1D30
ESYT1
TENC1
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
ABCB9
CBX5
ISCU
RIMBP2
ANP32D
ATP6V0A2
SMUG1
LEMD3
CORO1C
GABARAPL1
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
FBXW8
GALNT8
HSPB8
SNORD59A
GLS2
HCAR1
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CCDC41
IRAK4
ING4
GPN3
DDX47
GLTP
MRPL51
CLEC1B
CLEC1A
C12orf47
C1RL
ERGIC2
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TM7SF3
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
MAGOHB
SLC6A15
FAM90A1
RIC8B
C12orf35
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
CAND1
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
ARNTL2
CHPT1
PARP11
ANO2
C12orf4
C12orf5
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHDC5
PITPNM2
DIP2B
KIAA1467
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
C12orf44
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
OBFC2B
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
RPAP3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
FLJ13224
TCTN2
PLBD1
PYROXD1
NANOG
DNAJC22
NAA25
SLC24A6
ADAMTS20
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
C12orf39
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
C12orf32
NRIP2
INHBE
RBP5
TMTC1
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
C12orf26
TMEM117
TCHP
COQ5
LLPH
WIBG
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
EFCAB4B
TUBA1C
ZC3H10
ORAI1
RNFT2
C12orf34
ALG10
SPRYD3
C12orf52
MFSD5
MGC14436
C12orf62
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
FAM113B
C12orf65
TMEM132C
CCDC64
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
TMEM132B
OSBPL8
ARHGEF25
C12orf56
IQCD
LOC116437
AGAP2
DCD
RAB3IP
LOH12CR1
MUCL1
DEPDC4
LRRK2
CCDC38
C12orf59
FAM186A
C12orf45
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
HIST4H4
ERP27
FGD4
AEBP2
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
BRI3BP
KRT72
PRICKLE1
AMDHD1
SLC2A14
BCDIN3D
ALG10B
GLIPR1L2
FAM101A
ZNF664
LINC00477
LYRM5
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
KRT80
A2ML1
LOC144571
C12orf66
C12orf60
FBXL14
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
IFLTD1
DENND5B
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
CLEC4C
DSTNP2
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
C12orf53
DCP1B
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
C12orf33
GNN
MSRB3
METTL20
LRRC43
OR6C74
OR6C3
TCP11L2
LOC255411
LOC255480
LOC256021
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
POC1B
OTOGL
MATL2963
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
GPR133
MORN3
LOC283392
LOC283403
LOC283404
C12orf61
DPY19L2
CLEC9A
C12orf36
GAS2L3
LINC00485
LOC283440
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
C12orf40
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
LOC338758
C1QL4
TMEM119
KRT79
LOC338799
C12orf74
FAM19A2
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
PTPRQ
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
RPL13AP20
REP15
C12orf68
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
LOC389634
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
MKRN9P
C12orf76
LOC400084
FLJ37505
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
MIR26A2
C12orf37
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
DBX2
FLJ12825
TMEM198B
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
TSPAN11
OR9K2
MIR148B
MIR331
EID3
LOH12CR2
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC574538
HIGD1C
POU5F1P3
LOC642846
MAP1LC3B2
LOC643339
LOC643770
GLYCAM1
LOC647589
FAM86FP
PRB2
LRTM2
HNRNPA1P10
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA34
SNORA49
SNORA53
LOC678655
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
MIR617
MIR618
MIR620
LOC728084
C12orf73
SKP1P2
LOC728739
C12orf71
SLC15A5
MRS2P2
HOTAIR
MIR920
LOC100128191
LOC100128554
LOC100129361
LOC100130238
LOC100130776
LOC100131138
LOC100131733
LOC100190940
LOC100233209
LOC100240734
LOC100240735
LOC100271702
LOC100286844
MANSC4
LOC100287314
LINC00173
LOC100287944
LOC100288778
ZNF605
LOC100292680
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1178
MIR1244-1
MIR1251
LOC100335030
SNORA70G
MIR1244-3
MIR1244-2
MIR4302
MIR4303
MIR4304
KLRF2
LOC100499405
MIR3685
MIR3649
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506314
LOC100506393
LOC100506451
LOC100506649
LOC100506660
LOC100506668
LOC100506844
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507250
LOC100507377
LOC100507424
BLOC1S1-RDH5
POC1B-GALNT4
KLRC4-KLRK1
ZNF664-FAM101A
PRH1-PRR4
MIR4699
MIR4498
MIR548AL
MIR4701
MIR3974
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4698
LOC100652846
LOC100652999

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
1p36.32 | 4.1878e-11 | 4.8485e-10 | chr1:1-48649489 | 773
13q14.2 | 4.675e-08 | 4.5598e-08 | chr13:48833767-49281290 | 3
4q35.1 | 6.2475e-08 | 1.0642e-06 | chr4:176920228-191154276 | 72
8p23.2 | 3.1932e-05 | 3.1932e-05 | chr8:1953486-6262191 | 2
10q23.31 | 4.2453e-06 | 4.9315e-05 | chr10:89604733-90034038 | 2
22q13.31 | 0.0052457 | 0.0052217 | chr22:42474454-51304566 | 123
17p12 | 0.0070653 | 0.006758 | chr17:15891757-16121163 | 2
12q24.32 | 0.0080999 | 0.0081101 | chr12:109528819-133851895 | 243
4q24 | 0.00051487 | 0.014118 | chr4:77232044-115601010 | 191
9p21.3 | 0.013742 | 0.014118 | chr9:21410163-26068229 | 14
16q23.1 | 0.022201 | 0.022201 | chr16:59786347-90354753 | 305
14q23.3 | 0.067778 | 0.068575 | chr14:37121924-90515109 | 317
2q22.1 | 0.019568 | 0.082089 | chr2:139655617-143637838 | 1
11q14.1 | 0.091209 | 0.088525 | chr11:77811864-102719729 | 124
6q26 | 0.049474 | 0.095221 | chr6:126802823-171115067 | 260
19p13.3 | 0.10016 | 0.10644 | chr19:1-59128983 | 1653
10q26.13 | 0.0027295 | 0.12017 | chr10:77160683-135534747 | 489
6q16.3 | 0.058402 | 0.13487 | chr6:72593884-125149024 | 225
12p12.1 | 0.1416 | 0.13487 | chr12:1-68058246 | 719
10p15.3 | 0.15506 | 0.15474 | chr10:1-7746594 | 51
15q21.1 | 0.17341 | 0.16633 | chr15:1-57219891 | 409
2q37.3 | 0.044235 | 0.18016 | chr2:207636660-243199373 | 320
3p13 | 0.1833 | 0.18016 | chr3:17195937-93784545 | 478
1p35.2 | 0.00010901 | 0.20048 | chr1:1-48465382 | 772
2q23.1 | 0.021412 | 0.22062 | chr2:136870324-166062106 | 79
2p15 | 0.22938 | 0.23682 | chr2:1-243199373 | 1516

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

Genes
LCK
MPL
MUTYH
MYCL1
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
AK2
ALPL
RERE
ATP6V0B
BAI2
BMP8B
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
PLK3
CNR2
COL8A2
COL9A2
COL16A1
CORT
CSF3R
CTPS
CYP4A11
CYP4B1
DDOST
DFFA
DFFB
DPH2
DVL1
E2F2
ECE1
EDN2
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FAAH
FABP3
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
INPP5B
IPP
STMN1
MATN1
MFAP2
MTF1
MTHFR
NASP
NBL1
NDUFS5
NFYC
NPPA
NPPB
YBX1
OPRD1
PAFAH2
PRDX1
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKCZ
PSMB2
PTAFR
PTPRF
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RPS8
RSC1A1
SCNN1D
SRSF4
ST3GAL3
STIL
SKI
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TIE1
TNFRSF1B
TP73
TNFRSF4
UQCRH
UROD
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LAPTM5
PTP4A2
SNHG3
NR0B2
RAD54L
PIK3R3
MMP23B
MMP23A
KCNAB2
FCN3
YARS
MKNK1
AKR7A2
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
PER3
EIF2B3
ARTN
MAP3K6
KCNQ4
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
IPO13
SDC3
KDM4A
CROCC
PUM1
CEP104
RIMS3
KIAA0494
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
TSPAN1
CELA3A
PDZK1IP1
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
AKR1A1
TESK2
PPIE
MAD2L2
PPIH
CAP1
LRRC41
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
EBNA1BP2
KIF2C
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
FOXJ3
SCMH1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
MAST2
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
SZT2
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
MMACHC
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
MYCBP
HEYL
EIF2C1
OR4F3
SNORD55
RNU11
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
PRO0611
LINC00339
SSU72
GNL2
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
ZNF691
MECR
UTP11L
SDF4
MRTO4
TMEM69
HPCAL4
YTHDF2
ZCCHC17
PADI3
CMPK1
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
RNF220
VPS13D
FAM176B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
POMGNT1
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
DMAP1
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
ZSWIM5
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
PLA2G2F
SMAP2
ATPAF1
S100PBP
MEAF6
DEM1
CEP85
NMNAT1
ELOVL1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZNF643
PHACTR4
C1orf135
ERI3
C1orf50
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
TMEM53
AKIRIN1
HECTD3
YRDC
NOL9
PPCS
LIN28A
SH3D21
SNIP1
AGMAT
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
GPR157
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
HYI
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
ZMYND12
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
NT5C1A
TRIM63
FAM167B
MGC12982
C1orf170
CROCCP2
HPDL
MFSD2A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
MED8
C1orf212
ADC
TMEM54
TOE1
ERMAP
CSMD2
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
KLF17
TMEM125
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
KNCN
MOB3C
DCDC2B
ZNF362
LOC149086
MANEAL
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
C1orf64
SLC2A7
CALML6
IL28RA
CYP4Z2P
CITED4
FAM43B
PAQR7
EIF2C3
EIF2C4
FAM76A
TMEM201
CYP4Z1
C1orf86
TXLNA
SLFNL1
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
ZNF683
CYP4X1
NPHP4
BEST4
CYP4A22
LOC284551
FAM41C
LOC284632
RSPO1
EPHA10
LOC284661
RIMKLA
SLC25A34
ESPNP
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
C1orf228
ZNF642
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
TCTEX1D4
SERINC2
FAM131C
PADI6
BMP8A
C1orf187
SPATA21
CCDC23
ATPAF1-AS1
AGRN
APITD1
CATSPER4
NSUN4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LOC388630
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
FLJ32224
FAM183A
ANKRD65
PRAMEF7
LURAP1
PEF1
MIR429
FAM138F
KIAA0754
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA55
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
LOC728431
PPIEL
CCDC30
CDK11A
SLC35E2B
LOC728716
RPS15AP10
LOC729041
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100129924
LOC100130197
LOC100130417
LOC100130557
LOC100132062
LOC100132287
LOC100132774
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4255
MIR4253
MIR4251
MIR4252
MIR4254
MIR3659
MIR3917
MIR3605
MIR3675
ENO1-AS1
ZMYM6NB
LOC100506730
LOC100506801
LOC100506963
LOC100507178
LOC100507423
APITD1-CORT
GJA9-MYCBP
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 13q14.2.

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

Genes
RB1
RCBTB2
LPAR6

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
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 8p23.2.

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

Genes
MYOM2
CSMD1

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
NDUFA6
PPARA
MAPK11
MAPK12
SBF1
TCF20
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
RRP7A
MCAT
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
SCUBE1
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
POLDIP3
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
SERHL2
RNU12
ATP5L2
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
LOC388906
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
LINC00229
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100132273
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 17p12.

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

Genes
NCOR1
TTC19

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.32.

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

Genes
ALDH2
BCL7A
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
ACACB
ACADS
ATP2A2
SCARB1
COX6A1
DTX1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
MVK
MYL2
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PLA2G1B
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RPL6
RPLP0
CLIP1
ATXN2
SFSWAP
TBX5
TBX3
HNF1A
UBC
UNG
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
BRAP
ULK1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
HRK
ADAM1
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
GIT2
RBM19
RNF10
SH2B3
ARPC3
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
GCN1L1
SDS
RAB35
SNRNP35
CIT
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
ANKLE2
CUX2
MED13L
SIRT4
ABCB9
RIMBP2
ATP6V0A2
FBXW8
HSPB8
HCAR1
IFT81
FAM216A
GALNT9
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
VPS29
TPCN1
RHOF
VSIG10
TESC
SBNO1
ZCCHC8
CHFR
WSB2
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
TRPV4
LHX5
SUDS3
C12orf43
VPS33A
RSRC2
AACS
DDX54
NOC4L
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
RNF34
CCDC92
PUS1
ACAD10
KCTD10
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
TMEM116
UBE3B
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
TMEM132D
SLC15A4
FOXN4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
RAD9B
FAM109A
LOC144742
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
LRRC43
LOC255480
GPR133
MORN3
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338799
EP400NL
RILPL1
IL31
CCDC42B
TMEM233
SETD8
LOC387895
C12orf76
LOC400084
FLJ37505
LOC440117
FLJ31485
MAP1LC3B2
LOC647589
SNORA49
MIR620
LOC100128554
LOC100130238
LOC100131138
LOC100190940
LINC00173
ZNF605
MIR1178
MIR4304
MIR3612
MIR3908
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4498
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q24.

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

Genes
RAP1GDS1
TET2
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ANK2
ANXA3
ATOH1
BMP3
BMPR1B
CAMK2D
CASP6
CCNG2
CDS1
CENPE
DMP1
DSPP
EGF
EIF4E
ENPEP
FGF5
GK2
GRID2
H2AFZ
HADH
HNRNPD
HSP90AB3P
IBSP
CFI
MANBA
AFF1
MTTP
NFKB1
NKX6-1
PDHA2
PITX2
PKD2
PPP3CA
PRKG2
MAPK10
PTPN13
RPL34
SNCA
SPP1
TACR3
UBE2D3
UGT8
SPARCL1
UNC5C
LAMTOR3
HERC3
PAPSS1
AIMP1
ABCG2
HNRPDL
TSPAN5
FAM13A
SEC24B
CXCL13
PDLIM5
RRH
HPSE
CCNI
SEC31A
MMRN1
WDFY3
METAP1
PPA2
DAPP1
DKK2
COQ2
HPGDS
MRPS18C
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
NUDT9
GAR1
ARHGEF38
HERC6
CCDC109B
BANK1
C4orf21
AP1AR
BMP2K
SEPT11
BDH2
SMARCAD1
MEPE
PRDM8
INTS12
KLHL8
SHROOM3
ENOPH1
OSTC
NEUROG2
SLC39A8
AGXT2L1
MRPL1
ELOVL6
ARSJ
THAP9
GSTCD
SCD5
DNAJB14
FRAS1
ALPK1
CXXC4
PLA2G12A
ARHGAP24
C4orf17
FAM175A
COL25A1
NAA11
AGPAT9
PIGY
FLJ20021
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
GDEP
ANTXR2
LIN54
C4orf32
C4orf36
SLC9B2
SLC9B1
PAQR3
PPM1K
RASGEF1B
TIGD2
SGMS2
CNOT6L
C4orf22
NPNT
LOC256880
NAP1L5
LOC285456
FAM13A-AS1
GPRIN3
C4orf37
CCDC158
SOWAHB
LRIT3
SLC10A6
HSD17B13
PCNAP1
FAM190A
WDFY3-AS2
MIR302A
C4orf11
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641518
LOC644248
MIR575
MIR577
MIR1243
LOC100499177
MIR3684
LOC100505702
LOC100505875
LOC100506035
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4450
MIR4451

Genes in Wide Peak

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

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

Genes
hsa-mir-31
CDKN2A
CDKN2B
ELAVL2
IFNA1
MTAP
C9orf53
DMRTA1
TUSC1
IFNE
MIR31
FLJ35282
MIR31HG
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
CBFA2T3
CBFB
CDH1
CDH11
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
AARS
AP1G1
AFG3L1P
AGRP
APRT
ZFHX3
C16orf3
CA5A
CA7
CALB2
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
COX4I1
CTRB1
CTRL
CYBA
DHODH
NQO1
DYNC1LI2
DPEP1
E2F4
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HAS3
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
KARS
LCAT
MC1R
CHST6
MVD
NFATC3
CHMP1A
PLCG2
PSKH1
PSMB10
PSMD7
RPL13
RRAD
ST3GAL2
SLC9A5
SLC12A4
SNTB2
SPG7
TAT
TERF2
TK2
ZNF19
ZNF23
GAN
SLC7A5
CDK10
TRADD
MBTPS1
CES2
NAE1
NOL3
TAF1C
SLC7A6
USP10
ATP6V0D1
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
NUTF2
COX4NB
TUBB3
CFDP1
CTCF
NFAT5
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
CES3
ADAT1
CHST5
EDC4
PLA2G15
COG4
PLEKHG4
LRRC29
CPNE7
VPS4A
IL17C
NOB1
TMEM208
FHOD1
ANKRD11
ZDHHC1
OSGIN1
PARD6A
CKLF
NIP7
FAM96B
GINS2
TPPP3
TRAPPC2L
WWOX
BCMO1
TERF2IP
PRMT7
NECAB2
KLHDC4
HYDIN
DEF8
DUS2L
CHTF8
TXNL4B
BANP
PDPR
RFWD3
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
ZDHHC7
VAC14
FTSJD1
DDX28
TSNAXIP1
CENPN
C16orf61
THAP11
JPH3
PDP2
RANBP10
VAT1L
KIAA1609
WFDC1
PDF
DPEP2
DPEP3
MTHFSD
ACD
DBNDD1
FA2H
FAM65A
TMEM231
TMCO7
WDR59
ELMO3
KLHL36
FBXO31
ESRP2
CENPT
C16orf70
CYB5B
CMIP
GFOD2
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
C16orf48
SLC7A6OS
COG8
SPIRE2
ZNF469
B3GNT9
CIRH1A
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
CMTM1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
NRN1L
CMTM3
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
SLC22A31
IL34
TMED6
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
CCDC79
CES4A
EXOC3L1
LINC00304
LOC283867
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
C16orf86
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
MIR140
CTRB2
MIR328
CLEC18B
SNORD68
LOC644649
KIAA0895L
SNORD71
SNORD111
LOC727710
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130894
SYCE1L
LOC100287036
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
LOC100505865
LOC100506083
LOC100506172
C16orf95
CKLF-CMTM1
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
KTN1
TSHR
GPHN
NIN
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
ACTN1
ACYP1
ARF6
ARG2
BMP4
ZFP36L1
ENTPD5
CDKN3
FOXN3
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FKBP3
FNTB
FOS
FUT8
GALC
GCH1
GMFB
GPX2
GSTZ1
GTF2A1
HIF1A
FOXA1
HSPA2
LGALS3
LTBP2
MAX
MGAT2
CTAGE5
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SIX6
OTX2
PAX9
PGF
PIGH
PNN
POLE2
PPM1A
PPP2R5E
PRKCH
PSEN1
PSMA3
PSMC6
PTGDR
PTGER2
ABCD4
PYGL
RAD51B
ARID4A
RPL36AL
RPS29
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
SSTR1
STYX
TGFB3
ZBTB25
DPF3
GPR65
GEMIN2
NUMB
ADAM21
ADAM20
CDKL1
DCAF5
ALKBH1
EIF2B2
NEMF
PNMA1
NRXN3
AKAP5
SPTLC2
RGS6
KIAA0247
KIAA0586
DLGAP5
KIAA0317
MED6
CNIH
SEC23A
VTI1B
BATF
NPC2
AHSA1
EXOC5
CGRRF1
ACOT2
TMED10
FERMT2
PTPN21
C14orf1
WDHD1
MAP4K5
NID2
VASH1
ATG14
ZBTB1
SNW1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
SYNE2
ANGEL1
ZFYVE26
TTC9
KLHDC2
FLRT2
PLEKHG3
SIPA1L1
DCAF4
PLEK2
TIMM9
MLH3
ATP5S
KCNH5
PRO1768
POMT2
ERO1L
COQ6
ATL1
FCF1
RDH11
COX16
DACT1
ATP6V1D
JKAMP
DHRS7
C14orf166
SIX4
ZFYVE1
KCNK10
GNG2
KLHL28
C14orf101
PRPF39
FBXO34
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
MUDENG
TDP1
SPATA7
ACTR10
YLPM1
C14orf162
ADCK1
TMEM63C
PELI2
RHOJ
GALNTL1
PLEKHH1
TXNDC16
TRMT5
FANCM
ZNF410
NGB
RBM25
SAV1
C14orf133
SMOC1
IRF2BPL
MPP5
C14orf135
GPR135
GNPNAT1
METTL21D
ZC2HC1C
C14orf169
ZC3H14
L2HGDH
C14orf45
DDHD1
SGPP1
TMX1
SLIRP
DNAL1
RPS6KL1
SYT16
FSCB
STON2
KIAA1737
SLC25A21
PAPLN
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
MAPK1IP1L
IFT43
WDR89
C14orf149
TRIM9
MIA2
C14orf28
TRAPPC6B
LRR1
KLHDC1
FRMD6
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
RPL10L
RDH12
ADAM21P1
MIPOL1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
LRFN5
FAM71D
TMEM229B
CLEC14A
TMEM30B
MDGA2
SAMD15
EML5
C14orf183
FBXO33
LOC283547
C14orf182
LOC283553
GPR137C
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
C14orf55
C14orf39
SNORD56B
VSX2
SLC35F4
RAB15
FLJ31306
TBPL2
TOMM20L
HEATR4
FLJ22447
PLEKHD1
LOC400236
LINC00238
TEX21P
ACOT1
ACOT6
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
SNORA79
C14orf38
LOC731223
SNORD127
KTN1-AS1
LOC100129794
LOC100288846
LOC100289511
MIR1260A
OTX2OS1
MIR4308
MIR548Y
LOC100506321
LOC100506433
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4503
MIR4706
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.1.

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

Genes
BIRC3
PICALM
MAML2
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
BIRC2
CTSC
DLG2
FUT4
GRM5
MMP1
MMP3
MMP7
MMP8
MMP10
MRE11A
MTNR1B
PGR
PRCP
TRPC6
TYR
FZD4
OR7E2P
JRKL
EED
MTMR2
MMP20
MED17
CEP57
GAB2
NAALAD2
YAP1
ME3
GPR83
SRSF8
PRSS23
ENDOD1
RAB38
PANX1
ODZ4
CHORDC1
RAB30
C11orf54
NOX4
C11orf73
CWC15
PCF11
CNTN5
SYTL2
ANKRD49
KDM4D
TMEM126B
C11orf75
TRIM49
USP35
KIAA1377
CREBZF
CCDC90B
CCDC81
MMP27
TMEM135
ALG8
TAF1D
NARS2
CCDC82
TMEM133
TMEM126A
C11orf70
KIAA1731
TMEM123
SLC36A4
FAT3
TRIM64
FAM76B
SESN3
PIWIL4
ARHGAP42
AMOTL1
CCDC67
FOLH1B
C11orf82
CCDC83
FAM181B
CCDC89
ANGPTL5
KCTD21
ANKRD42
HEPHL1
VSTM5
TRIM77P
FOLR4
KDM4DL
LOC399939
LOC399940
SCARNA9
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49L1
MIR708
LOC100288077
MIR1304
SNORA70E
MIR4300
MIR1260B
MIR3920
LOC100506233
LOC100506368
MIR4490

Genes in Wide Peak

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

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

Genes
MLLT4
MYB
TNFAIP3
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
ACAT2
ARG1
CCR6
CTGF
EPB41L2
EYA4
ESR1
FUCA2
GPR31
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LAMA2
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PSMB1
PTPRK
RPS6KA2
RPS12
SGK1
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
STX7
PEX3
RNASET2
STX11
SYNJ2
VNN2
VNN1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
AKAP7
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
UST
CITED2
HBS1L
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
HEBP2
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
DLL1
MRPL18
CLDN20
NOX3
TFB1M
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
C6orf115
PBOV1
PERP
SMOC2
ALDH8A1
ULBP3
OR2A4
C6orf211
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
TTLL2
FBXO30
L3MBTL3
FAM120B
FNDC1
RSPO3
LRP11
LTV1
SERAC1
REPS1
PPIL4
LINC00473
ARHGAP18
SYTL3
FAM54A
SFT2D1
TMEM200A
C6orf72
IL22RA2
C6orf192
TAGAP
ADAT2
TAAR9
TAAR1
STXBP5
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
C6orf191
WDR27
SHPRH
LINC00326
LOC285740
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
C6orf174
C6orf120
THEMIS
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FLJ46906
LOC441177
SNORD101
SNORD100
SNORA33
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

Table S38. Genes in bold are cancer genes as defined by The Sanger Institute's 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 10q26.13.

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute's 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
hsa-mir-606
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
ANXA11
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
KCNMA1
KIF11
ABLIM1
LIPA
MAT1A
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGR
RGS10
RPS24
SCD
SFRP5
SFTPD
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
MBL1P
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
DLG5
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
PPIF
ACTR1A
SMNDC1
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
TUBGCP2
PRDX3
C10orf116
VAX1
ATE1
POLR3A
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
LRIT1
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
ANKRD1
GHITM
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
ZMIZ1
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
FAM213A
WDR96
LRRC27
TNKS2
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
C10orf11
PCGF6
LOXL4
ZDHHC16
C10orf58
DYDC2
PCGF5
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ATAD1
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
CDHR1
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
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
LOC170425
EMX2OS
PPAPDC1A
PAOX
FAM24B
LOC219347
PLAC9
ZCCHC24
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
FLJ37201
LOC283038
LOC283050
LOC283089
O3FAR1
KCNK18
LIPM
CYP26C1
VWA2
NANOS1
LRIT2
HMX3
NHLRC2
C10orf96
FLJ46361
SH2D4B
C10orf99
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
C10orf62
LOC439990
LOC439994
IFIT1B
FRG2B
MIR346
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
LOC642361
FAM196A
FAM25A
LIPK
LIPN
LOC643529
RPL13AP6
LOC650623
SFTPA1
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
FAM22A
FAM22D
LOC728190
LOC728218
DUX4L2
LOC728558
LOC729020
SFTPA2
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100128292
ZNF503-AS2
LOC100132987
KLLN
LOC100169752
LOC100188947
DNMBP-AS1
LOC100288974
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 6q16.3.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
AIM1
AMD1
BCKDHB
CCNC
CGA
CNR1
COL10A1
COL12A1
COX7A2
EEF1A1
EPHA7
FABP7
FOXO3
FRK
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
HSF2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
MAN1A1
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
PKIB
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
TRDN
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
SMPDL3A
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
BRD7P3
MTO1
ASF1A
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
SERINC1
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
FAM184A
MANEA
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
MB21D1
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
CLVS2
CD109
PM20D2
SRSF12
NKAIN2
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
DPPA5
RSPH4A
GJB7
SNHG5
C6orf147
LINC00222
CEP85L
LIN28B
OOEP
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
ATF1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
NACA
KDM5A
MLL2
HMGA2
WIF1
ZNF384
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
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ART4
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
CD63
CD69
CDK2
CDKN1B
CHD4
CNTN1
COL2A1
CREBL2
CS
CYP27B1
DGKA
DDX11
ATN1
PHC1
EIF4B
CELA1
EMP1
ENO2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GPD1
GPR19
GRIN2B
GUCY2C
GYS2
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IAPP
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTBR
M6PR
MARS
METTL1
MGP
MGST1
MIP
MMP19
MYL6
MYO1A
NAB2
NDUFA9
NELL2
NFE2
NINJ2
NOP2
SLC11A2
NTF3
OLR1
PA2G4
PCBP2
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
PIK3C2G
PKP2
POU6F1
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAG1
PRPH
PTHLH
TWF1
PTMS
PTPN6
PTPRO
PEX5
PZP
RAB5B
RAD52
RARG
RBMS2
RDH5
RECQL
RNY5
RPL41
RPS26
TSPAN31
SCN8A
SCNN1A
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
TAC3
TARBP2
TEAD4
TMBIM6
TFCP2
TNFRSF1A
TPI1
TULP3
VDR
VWF
WNT1
WNT10B
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
AAAS
KLRC4
SOAT2
DYRK2
PPFIBP1
CSDA
RDH16
NPFF
HSD17B6
DYRK4
ENDOU
TIMELESS
GPRC5A
KRT75
SCAF11
SLC16A7
CD163
MED21
DDX23
SLC4A8
GDF3
ESPL1
CLSTN3
DAZAP2
KIAA0748
KIAA0528
ZBTB39
NCAPD2
PAN2
USP15
CLEC2B
TROAP
DNM1L
ABCC9
TSFM
CTDSP2
YAF2
LPCAT3
RNF41
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
LEPREL2
DCTN2
AKAP3
SLCO1B1
RAD51AP1
AVIL
PTGES3
KLRAP1
TSPAN9
OS9
ATF7
STRAP
BAZ2A
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
R3HDM2
KLRK1
STK38L
FAIM2
MON2
ERC1
DDN
TMEM194A
TBC1D30
ESYT1
TENC1
KCNH3
GRIP1
CBX5
ANP32D
SMUG1
LEMD3
GABARAPL1
PRPF40B
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
GALNT8
SNORD59A
GLS2
GPR162
RND1
SLCO1B3
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
PDZRN4
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
GOLT1B
PLEKHA8P1
YARS2
DERA
IRAK4
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
ERGIC2
FKBP11
KLRF1
KRT76
CSAD
BIN2
LIMA1
PPHLN1
IL23A
HDAC7
TMBIM4
WBP11
TM7SF3
GPR84
SLCO1C1
SLC38A2
PRR13
PLEKHA5
MANSC1
KANSL2
TAPBPL
SLC38A4
MAGOHB
FAM90A1
C12orf35
PLEKHG6
CASC1
CCDC91
STYK1
ETNK1
GPRC5D
KIF21A
SLC48A1
FAR2
LMBR1L
ASUN
ATF7IP
H2AFJ
FOXJ2
CAND1
ITFG2
LMO3
CMAS
PRMT8
NDUFA4L2
ARNTL2
PARP11
ANO2
C12orf4
C12orf5
LPAR5
SMAGP
AICDA
PPM1H
RIMKLB
SRGAP1
KLHDC5
DIP2B
KIAA1467
CALCOCO1
NCKAP5L
NEUROD4
FAM60A
C12orf10
MRPS35
C12orf44
ARHGAP9
IKZF4
CLEC7A
SLC26A10
WNK1
SPATS2
CAPRIN2
TMEM106C
OBFC2B
BHLHE41
BCL2L14
ADIPOR2
RPAP3
RERGL
PIP4K2C
FLJ13224
PLBD1
PYROXD1
NANOG
DNAJC22
ADAMTS20
C12orf39
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
C12orf32
NRIP2
INHBE
RBP5
TMTC1
RACGAP1P
FAM186B
TMEM117
LLPH
WIBG
CCDC77
SARNP
ACRBP
SPSB2
EFCAB4B
TUBA1C
ZC3H10
ALG10
SPRYD3
MFSD5
C12orf62
RERG
DNAJC14
ZCRB1
CCDC65
PLCZ1
LACRT
FMNL3
CERS5
XRCC6BP1
FAM113B
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SLC2A13
MBD6
ARHGEF25
C12orf56
AGAP2
DCD
LOH12CR1
MUCL1
LRRK2
C12orf59
FAM186A
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
HIST4H4
ERP27
FGD4
AEBP2
ASB8
MYL6B
KRT72
PRICKLE1
SLC2A14
BCDIN3D
ALG10B
LINC00477
LYRM5
CPNE8
KRT80
A2ML1
LOC144571
C12orf66
C12orf60
FBXL14
CLEC12A
CLECL1
IFLTD1
DENND5B
GRASP
CLEC4C
DSTNP2
KRT78
AMN1
DTX3
METTL7B
C12orf77
C12orf53
DCP1B
ANO6
ARID2
RPSAP52
STAC3
C12orf33
MSRB3
METTL20
OR6C74
OR6C3
LOC255411
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
LOC283403
LOC283404
C12orf61
DPY19L2
CLEC9A
C12orf36
LOC283440
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
CLEC4D
C1QL4
KRT79
FAM19A2
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
CLEC2A
CLEC12B
RPL13AP20
REP15
C12orf68
LOC389634
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR141
MIR196A2
MIR200C
MIR26A2
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
DBX2
FLJ12825
TMEM198B
TSPAN11
OR9K2
MIR148B
LOH12CR2
LOC574538
HIGD1C
POU5F1P3
LOC642846
GLYCAM1
FAM86FP
PRB2
LRTM2
HNRNPA1P10
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA34
LOC678655
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
SKP1P2
C12orf71
SLC15A5
HOTAIR
MIR920
LOC100129361
LOC100130776
LOC100233209
LOC100240734
LOC100240735
LOC100271702
LOC100286844
MANSC4
LOC100287314
LOC100288778
LOC100292680
MIR1228
MIR1293
MIR1291
MIR1244-1
LOC100335030
MIR1244-3
MIR1244-2
MIR4302
KLRF2
LOC100499405
MIR3649
MIR548Z
LOC100506314
LOC100506393
LOC100506451
LOC100506660
LOC100506844
LOC100507424
BLOC1S1-RDH5
KLRC4-KLRK1
PRH1-PRR4
MIR4701
MIR3974
MIR3198-2
MIR4698
LOC100652846
LOC100652999

Genes in Wide Peak

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

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

Genes
hsa-mir-3155
ADARB2
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
PFKFB3
PFKP
PRKCQ
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
IDI2-AS1
SFMBT2
ASB13
TUBAL3
ITIH5
AKR1E2
FBXO18
RBM17
IDI2
UCN3
LOC282980
LOC338588
AKR1CL1
TUBB8
tAKR
LINC00200
LOC399708
LOC399715
C10orf108
LOC439949
ADARB2-AS1
LOC100216001
MIR3155A
LOC100507034
LOC100507127
MIR3155B

Genes in Wide Peak

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

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

Genes
BUB1B
FLJ27352
C15orf55
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
USP8
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
MIR628
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

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

Genes
ATIC
CREB1
ACSL3
IDH1
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
CUL3
DGKD
STK16
KLF7
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
CPO
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
METTL21A
CCNYL1
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
PIKFYVE
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
LOC100507443
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4775
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
CTNNB1
FHIT
MITF
MLH1
MYD88
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
EPHA3
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
HTR1F
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
POU1F1
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
SATB1
ATXN7
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
THRB
TKT
TMF1
CLEC3B
TNNC1
TOP2B
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
EOMES
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SLC4A7
VPRBP
TBC1D5
IP6K1
EPM2AIP1
PSMD6
TRANK1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
CRTAP
ARL6IP5
NPRL2
CXCR6
CSPG5
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
GNL3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
VILL
ABHD5
DYNC1LI1
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ZNF654
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
KIF9
AZI2
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
ZNF385D
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
LRRC3B
GPR62
KCNH8
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
SGOL1
PP2D1
EFHB
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
ARL13B
DHFRL1
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
C3orf38
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
VENTXP7
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
STX19
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
SNORA6
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
LOC100128640
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4791
MIR548AC
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST

Genes in Wide Peak

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

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

Genes
LCK
MPL
MUTYH
MYCL1
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
AK2
ALPL
RERE
ATP6V0B
BAI2
BMP8B
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
PLK3
CNR2
COL8A2
COL9A2
COL16A1
CORT
CSF3R
CTPS
CYP4A11
CYP4B1
DDOST
DFFA
DFFB
DPH2
DVL1
E2F2
ECE1
EDN2
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FAAH
FABP3
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
INPP5B
IPP
STMN1
MATN1
MFAP2
MTF1
MTHFR
NASP
NBL1
NDUFS5
NFYC
NPPA
NPPB
YBX1
OPRD1
PAFAH2
PRDX1
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKCZ
PSMB2
PTAFR
PTPRF
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RPS8
RSC1A1
SCNN1D
SRSF4
ST3GAL3
STIL
SKI
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TIE1
TNFRSF1B
TP73
TNFRSF4
UQCRH
UROD
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LAPTM5
PTP4A2
SNHG3
NR0B2
RAD54L
PIK3R3
MMP23B
MMP23A
KCNAB2
FCN3
YARS
MKNK1
AKR7A2
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
PER3
EIF2B3
ARTN
MAP3K6
KCNQ4
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
IPO13
SDC3
KDM4A
CROCC
PUM1
CEP104
RIMS3
KIAA0494
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
TSPAN1
CELA3A
PDZK1IP1
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
AKR1A1
TESK2
PPIE
MAD2L2
PPIH
CAP1
LRRC41
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
EBNA1BP2
KIF2C
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
FOXJ3
SCMH1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
MAST2
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
SZT2
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
MMACHC
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
MYCBP
HEYL
EIF2C1
OR4F3
SNORD55
RNU11
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
PRO0611
LINC00339
SSU72
GNL2
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
ZNF691
MECR
UTP11L
SDF4
MRTO4
TMEM69
HPCAL4
YTHDF2
ZCCHC17
PADI3
CMPK1
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
RNF220
VPS13D
FAM176B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
POMGNT1
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
DMAP1
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
ZSWIM5
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
PLA2G2F
SMAP2
ATPAF1
S100PBP
MEAF6
DEM1
CEP85
NMNAT1
ELOVL1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZNF643
PHACTR4
C1orf135
ERI3
C1orf50
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
TMEM53
AKIRIN1
HECTD3
YRDC
NOL9
PPCS
LIN28A
SH3D21
SNIP1
AGMAT
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
GPR157
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
HYI
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
ZMYND12
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
NT5C1A
TRIM63
FAM167B
MGC12982
C1orf170
CROCCP2
HPDL
MFSD2A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
MED8
C1orf212
ADC
TMEM54
TOE1
ERMAP
CSMD2
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
KLF17
TMEM125
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
KNCN
MOB3C
DCDC2B
ZNF362
LOC149086
MANEAL
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
C1orf64
SLC2A7
CALML6
IL28RA
CYP4Z2P
CITED4
FAM43B
PAQR7
EIF2C3
EIF2C4
FAM76A
TMEM201
CYP4Z1
C1orf86
TXLNA
SLFNL1
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
ZNF683
CYP4X1
NPHP4
BEST4
CYP4A22
LOC284551
FAM41C
LOC284632
RSPO1
EPHA10
LOC284661
RIMKLA
SLC25A34
ESPNP
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
C1orf228
ZNF642
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
TCTEX1D4
SERINC2
FAM131C
PADI6
BMP8A
C1orf187
SPATA21
CCDC23
ATPAF1-AS1
AGRN
APITD1
CATSPER4
NSUN4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LOC388630
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
FLJ32224
FAM183A
ANKRD65
PRAMEF7
LURAP1
PEF1
MIR429
FAM138F
KIAA0754
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA55
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
LOC728431
PPIEL
CCDC30
CDK11A
SLC35E2B
LOC728716
RPS15AP10
LOC729041
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100129924
LOC100130197
LOC100130417
LOC100130557
LOC100132062
LOC100132287
LOC100132774
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4255
MIR4253
MIR4251
MIR4252
MIR4254
MIR3659
MIR3917
MIR3605
MIR3675
ENO1-AS1
ZMYM6NB
LOC100506730
LOC100506801
LOC100506963
LOC100507178
LOC100507423
APITD1-CORT
GJA9-MYCBP
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 2q23.1.

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

Genes
ACVR1
ACVR2A
RND3
CACNB4
DPP4
FAP
GCG
GPD2
GRB14
HNMT
ITGB6
KCNJ3
KIF5C
LY75
NEB
NR4A2
ORC4
RBMS1
SCN3A
TNFAIP6
CXCR4
PKP4
KYNU
NMI
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
TBR1
GALNT5
NXPH2
COBLL1
PLA2R1
GCA
EPC2
ARL5A
MMADHC
BAZ2B
LRP1B
FIGN
RIF1
PRPF40A
MBD5
ARHGAP15
RPRM
SLC4A10
ERMN
IFIH1
MARCH7
GTDC1
THSD7B
TANC1
KCNH7
DAPL1
FMNL2
GALNT13
ACVR1C
LYPD6
LYPD6B
CCDC148
ARL6IP6
SLC38A11
WDSUB1
UPP2
SPOPL
RBM43
DKFZp686O1327
LOC554201
LOC647012
PABPC1P2
LOC100144595
ZEB2-AS1
SNORA70F
LY75-CD302
MIR4785
MIR4773-1
MIR4773-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p15.

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

Genes
ALK
ATIC
CHN1
CREB1
DNMT3A
ERCC3
ACSL3
MSH6
HOXD11
HOXD13
IDH1
MSH2
MYCN
NFE2L2
PAX3
PMS1
REL
PAX8
NCOA1
EML4
BCL11A
FEV
TTL
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
hsa-mir-3127
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
hsa-mir-216b
hsa-mir-559
hsa-mir-558
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
AAMP
ACADL
ACP1
ACTG2
ACVR1
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
AGXT
ALPI
ALPP
ALPPL2
BIN1
ANXA4
AOX1
APOB
RHOB
RND3
ATP5G3
ATP6V1B1
KIF1A
AUP1
BARD1
BCS1L
BMPR2
BOK
ZFP36L2
BUB1
CACNB4
CAD
CALM2
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CENPA
CHRNA1
CHRND
CHRNG
CLK1
CNGA3
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
COX5B
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CTNNA2
CYP1B1
CYP27A1
DARS
DBI
DCTN1
DDX1
DES
DGUOK
LOC1720
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DTNB
DTYMK
DUSP2
E2F6
EEF1B2
EGR4
EMX1
EN1
EPAS1
EPHA4
ERBB4
FABP1
FAP
EFEMP1
FHL2
FKBP1B
FN1
FOSL2
FRZB
FSHR
FTH1P3
GAD1
GALNT3
GBX2
GCG
GCKR
MSTN
GFPT1
GGCX
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GTF3C2
GYPC
HADHA
HADHB
HDLBP
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HPCAL1
AGFG1
DNAJB2
HSPD1
HSPE1
FOXN2
HTR2B
ID2
SP110
IGFBP2
IGFBP5
IHH
IL1A
IL1B
IL1R1
IL1RN
CXCR1
CXCR2
CXCR2P1
INHA
INHBB
INPP1
INPP4A
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNF1
KCNJ3
KCNJ13
KCNK3
KCNS3
KHK
KIF3C
KIF5C
AFF3
LCT
LHCGR
LIMS1
LRP2
LTBP1
LY75
EPCAM
MXD1
MAL
MAP2
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MYO1B
MTIF2
MYL1
MYO7B
NAB1
NCL
NEB
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPAS2
NPHP1
NPPC
NR4A2
ODC1
ORC2
ORC4
OTX1
REG3A
PCBP1
PDCD1
PDE1A
PDE6D
PDK1
PEX13
VIT
SERPINE2
PIGF
PLCL1
PLEK
PLGLB2
PLGLB1
POLR2D
POMC
POU3F3
PPM1B
PPM1G
PPP1CB
PPP1R7
PPP3R1
PRKCE
EIF2AK2
PROC
PSMD1
PTH2R
PTMA
PTPN4
PTPRN
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
REG1P
SNORD20
RPE
RPL31
RPL37A
RPS7
RPS27A
RRM2
RTKN
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
CCL20
SDC1
SRSF7
SFTPB
SIX3
SLC4A3
SLC1A4
SLC3A1
SLC8A1
SLC9A2
SLC11A1
SLC20A1
SNRPG
SOS1
SOX11
SP3
SP100
SPAST
SPP2
SPR
SPTBN1
SRD5A2
SSB
SSFA2
STAT1
STAT4
STRN
SULT1C2
ADAM17
TACR1
GCFC2
TFPI
TGFA
TIA1
TNFAIP6
TNP1
TNS1
TPO
TSN
TSSC1
TTN
TUBA4A
SUMO1
UCN
UGP2
VIL1
VRK2
VSNL1
WIPF1
WNT6
XDH
XPO1
XRCC5
ZAP70
ZNF2
ZNF142
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
FZD5
SCG2
DYSF
FZD7
SDPR
NCK2
DUSP11
CUL3
KLF11
MAP4K3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ASAP2
PER2
ST3GAL5
SLC5A6
DDX18
EIF2B4
CDK5R2
KYNU
TAF1B
NAT8
NMI
RQCD1
COX7A2L
TMSB10
IL1RL1
LRRFIP1
STK17B
ITGB1BP1
GPR55
TRIP12
GTF3C3
PPIG
NRXN1
OTOF
CIAO1
TGFBRAP1
HS6ST1
CRIPT
ECEL1
MAP4K4
EIF2AK3
EIF4E2
ROCK2
CHST10
TP53I3
CIR1
MRPL33
BRE
PREPL
CYTIP
FEZ2
GCC2
TTLL4
SOCS5
EIF5B
GREB1
BZW1
USP34
LAPTM4A
HDAC4
RNF144A
SNX17
SERTAD2
MRPL19
ZEB2
FARP2
TLK1
SUPT7L
CD302
ARHGAP25
TANK
BCL2L11
FARSB
ABCB6
ACTR3
ACTR2
ARPC2
PREB
ACTR1B
ARL4C
LRPPRC
PDIA6
ABI2
CEBPZ
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
SMYD5
KBTBD10
MYCNOS
C1D
MERTK
UBE2E3
STK25
SEMA4F
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
MTX2
CGREF1
B3GNT2
USP39
TBR1
SIX2
MAP3K2
NCKAP1
VAMP5
MTHFD2
ARID5A
PROKR1
RAB10
EDAR
COPS8
GPR75
YWHAQ
IMMT
SNRNP27
GTF2A1L
STON1
RAPGEF4
EMILIN1
CAPN10
TBC1D8
RABL2A
GALNT5
NXPH2
GPR45
SP140
MGAT4A
GPN1
IKZF2
COBLL1
AAK1
FASTKD2
MAPRE3
PLA2R1
RAB3GAP1
RPIA
SLC4A1AP
EFR3B
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
PASK
UBXN4
ATG4B
PSME4
EXOC6B
EHBP1
SATB2
CLASP1
OBSL1
PUM2
NCAPH
RHOQ
SF3B1
HAAO
TMEM131
R3HDM1
DNPEP
PSD4
WBP1
NTSR2
TMEFF2
SH3BP4
PRKD3
KCNE4
RASGRP3
NGEF
QPCT
GCA
VAX2
SNORD82
MOB4
POLR1A
CNRIP1
FAM98A
PNKD
UNC50
SNED1
GORASP2
SPATS2L
RAB11FIP5
GIGYF2
EPC2
TRAF3IP1
ABCA12
IFT172
ARL5A
HIBCH
PTPN18
CNNM4
CNNM3
IL36RN
SH3YL1
SNORD53
SNORD51
CNPPD1
STK36
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
MMADHC
BMP10
ZNF638
STK39
HTRA2
TRIB2
CPS1-IT1
METTL5
LGALSL
OLA1
C2orf27A
GRHL1
TFCP2L1
ICOS
GMPPA
NRBP1
BAZ2B
SLC40A1
KCNIP3
EHD3
SMARCAL1
CD207
ITSN2
ANO7
ARHGEF4
PDE11A
TPRKB
FAHD2A
PRLH
WDPCP
MEMO1
THAP4
TRAPPC12
ASB3
INSIG2
CRIM1
ANKRD39
FAM178B
RNF181
MRPL30
DNAJC27
ANKMY1
KRCC1
MRPL35
C2orf28
PCYOX1
GULP1
REV1
NAT8B
SCLY
VPS54
NBAS
LIPT1
NOP58
DYNC2LI1
SF3B14
YPEL5
CHMP3
FKBP7
ASB1
CPSF3
CAB39
ZAK
LRP1B
PRKAG3
PPIL3
SNTG2
DNAJC10
ATAD2B
ETAA1
HEATR5B
CCDC93
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
AFTPH
MFSD6
TMEM214
RETSAT
INO80D
SEMA4C
C2orf18
C2orf42
TRMT61B
PID1
PTCD3
PLEKHB2
ATG16L1
FANCL
SRBD1
FIGN
ANKZF1
RIF1
USP40
MOB1A
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
HJURP
STRADB
C2orf56
HES6
ACCN4
C2orf29
NAGK
DOCK10
TTC27
SMPD4
TMEM127
PRPF40A
SLC30A6
IWS1
LIMS2
KANSL3
MREG
CCDC88A
WDR12
MBD5
KDM3A
ALLC
PECR
ARHGAP15
ZC3H15
CFC1
DNAH7
GKN1
IL36G
RPRM
CYP26B1
POLE4
KCNK12
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
C2orf83
MFF
RPL23AP32
CXCR7
RNPEPL1
RTN4
TRIM54
PELI1
SLC39A10
TTC7A
SMEK2
SLC4A10
CYP20A1
SPC25
BIRC6
ERMN
KIDINS220
MTA3
HECW2
WDR35
MARCH4
WDFY1
NYAP2
DPP10
RDH14
EPB41L5
ALS2
ZDBF2
USP37
CWC22
ANKRD36B
G6PC2
SLC4A5
CTDSP1
NLRC4
MPP4
SLC5A7
NIF3L1
AGBL5
C2orf43
THADA
PCGEM1
RBKS
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
ATL2
ABCG5
ABCG8
RAB17
RNF25
HS1BP3
GMCL1
TTC31
ANAPC1
COPS7B
RMND5A
FNDC4
MARCH7
OBFC2A
PAPOLG
MRPS9
MRPS5
REEP1
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
SOWAHC
PLEKHA3
TRAK2
BOLL
COLEC11
PDCL3
TRPM8
ATG9A
C2orf49
MLPH
TMEM185B
FAM134A
CENPO
OR7E91P
GLB1L
C2orf47
SPAG16
CHPF
SAP130
GALNT14
SCRN3
CCDC121
FASTKD1
SMC6
GTDC1
CLIP4
IQCA1
ALS2CR8
TTC21B
CAMKMT
METTL8
GEMIN6
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
NOL10
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
TUBA4B
MZT2B
YSK4
UXS1
FBXO11
ARMC9
COQ10B
SLC35F5
EFHD1
C2orf44
SPHKAP
WNT10A
SLC19A3
TSGA10
THSD7B
THUMPD2
TMEM177
KIAA1715
ILKAP
FAM49A
LMAN2L
LBH
TMEM163
ITM2C
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
RHBDD1
CHCHD5
YIPF4
PRADC1
C2orf88
ING5
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
DPY30
MCEE
LOXL3
ABHD1
PCGF1
DDX11L2
MFSD9
PLCD4
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
MGC16025
TANC1
EPT1
LBX2
PNPT1
KCNH7
FER1L5
MCFD2
ATP6V1E2
LOC90499
CCDC74A
LOC90784
DHX57
LOC91149
SESTD1
CCDC74B
PKDCC
ANKRD44
RSAD2
ZNF804A
TTC30A
DAPL1
CAPN13
TMEM169
DNER
CCDC164
IMP4
HNRPLL
MARS2
B3GNT7
NT5C1B
NEURL3
SP140L
SFXN5
ORMDL1
LIMS3
LINC00152
TUBA3E
CCDC104
TEX261
TUBA3D
STK11IP
FMNL2
CCDC85A
GALNT13
KLHL29
OSBPL6
NOSTRIN
DIRC1
WDR92
MOGAT1
LYPD1
MRPL53
AGAP1
TWIST2
PARD3B
RPL23AP7
PPP1R21
C2orf89
TMEM150A
NUP35
XIRP2
TYW5
NMS
LYG1
MITD1
DIS3L2
CMPK2
MBOAT2
CNTNAP5
TMEM18
FBLN7
NEU4
RBM45
C2orf73
TRIM43
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
CIB4
REG3G
RFTN2
C2orf63
PLEKHH2
AP1S3
C2orf76
SGPP2
ACVR1C
OSR1
TTC32
UBR3
KCTD18
ALS2CR12
ZNF513
SPATA3
LYPD6
LYPD6B
GALM
TMEM198
ZFAND2B
TMEM178
CPO
MDH1B
C2orf50
PQLC3
TMEM182
AHSA2
FBXO36
MTERFD2
CCDC148
C2orf65
MYO3B
TMEM37
UBE2F
DUSP19
CKAP2L
CBWD2
TEKT4
LOC150527
FLJ32063
LOC150568
SMYD1
C2orf15
LOC150622
OTOS
MYEOV2
OR6B3
COMMD1
PROM2
ANKAR
FBXO41
TTC30B
GPAT2
ITPRIPL1
LOC150776
WTH3DI
FAM117B
TCF23
LOC150935
FAM59B
PUS10
PKI55
LINC00309
LOC151009
SEPT10
C2orf67
PLB1
ZSWIM2
ZNF385B
LOC151171
LOC151174
ARL6IP6
METTL21A
CCNYL1
KLHL23
SULT1C2P1
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
LOC151300
GPBAR1
FAHD2B
MYADML
FAM84A
FAM82A1
GDF7
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
ASPRV1
WDSUB1
UPP2
LOC151534
GPR155
WDR69
LONRF2
CCDC138
GPR113
C2orf57
OXER1
FAM179A
FAM171B
C1QL2
UBXN2A
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
PIKFYVE
KRTCAP3
LOC200726
TMEM17
SPRED2
TIGD1
LOC200772
FAM123C
LINC00116
C2orf69
HNRNPA3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
CERS6
METAP1D
LOC254128
LYG2
CCDC108
C2orf72
SH2D6
LOC284950
CCDC150
RNF149
LOC284998
LOC285000
FAM150B
CCDC141
LOC285033
LINC00486
C2orf61
LOC285074
LOC285084
CXXC11
LOC285103
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
FAM126B
UNC80
RUFY4
PLGLA
RGPD4
DUSP28
STON1-GTF2A1L
SPOPL
MLK7-AS1
CYP27C1
ESPNL
C2orf70
C2orf53
LOC339788
LINC00299
LOC339803
C2orf74
LOC339807
LOC339822
MSGN1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
EVX2
CDKL4
PRORSD1P
AOX2P
SH3RF3
GPR148
ECEL1P2
LRRTM1
GEN1
C2orf48
FONG
LOC348761
PFN4
LOC375190
LOC375196
ANKRD36
WASH2P
RBM43
LOC375295
CERKL
C2orf62
RBM44
AQP12A
ZC3H6
KLHL30
LOC386597
MFSD2B
C2orf71
LOC388942
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
SLC9A4
LOC389023
LOC389033
LOC389043
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
PTRHD1
SULT6B1
DYTN
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
FLJ42351
LOC401010
DKFZp686O1327
LOC401022
FSIP2
C2orf66
ASB18
FLJ43879
VWC2L
MIR10B
MIR128-1
MIR149
MIR153-1
MIR216A
MIR217
MIR26B
C2orf27B
DNAJB3
ASTL
CAPN14
ACTR3BP2
LOC440894
LOC440895
LOC440900
LOC440905
LOC440910
POTEKP
LOC440925
LOC442028
SULT1C3
POTEE
COA5
PHOSPHO2
CHAC2
MIR375
DFNB59
LOC541471
LOC554201
ANKRD30BL
FBXO48
SNORA41
FAM110C
LOC643387
PRR21
LOC644838
GGT8P
ANKRD36BP2
LOC645949
LOC646324
LOC646736
LOC646743
PRSS56
LOC647012
C2orf84
TRIM43B
CFC1B
AQP12B
RGPD3
MZT2A
SNORA75
LOC654342
FAM138B
LOC654433
SCARNA6
SCARNA5
SNORD11
SNORD70
SNORD89
SNORD92
SNORD94
MIR558
MIR559
MIR561
RGPD8
LOC727982
D2HGDH
LOC728323
POTEF
LOC728537
LOC728730
PABPC1P2
LOC728819
LOC729121
ANKRD20A8P
LOC729234
RAD51AP2
RGPD6
DIRC3
DNAJC27-AS1
RGPD2
MORN2
LOC730811
RFX8
SNORD11B
SNORA36C
SNORA70B
MIR216B
MIR933
LOC100128590
OST4
LOC100129175
LOC100129726
LOC100129961
PP14571
LOC100130451
LOC100130452
LOC100130691
TMEM194B
LOC100131320
SP9
LOC100132215
CYP4F30P
LOC100133985
LOC100134259
LOC100144595
RNU4ATAC
DBIL5P2
SNAR-H
LOC100189589
LOC100216479
ARHGEF33
LOC100271832
LIMS3-LOC440895
LOC100286922
LOC100286979
LOC100287010
LOC100287216
LOC100288570
LIMS3L
LOC100288911
MIR1471
MIR1246
MIR548N
MIR1258
MIR1245A
MIR1301
MIR1244-1
LOC100302650
GPR75-ASB3
SNORA80B
ZEB2-AS1
MIR548F2
MIR663B
LOC100329109
SNORA70F
BOK-AS1
MIR3128
MIR4265
MIR1244-3
MIR1244-2
MIR4264
MIR3129
MIR3127
MIR4261
MIR3131
MIR4268
MIR4263
MIR3125
MIR3130-1
MIR4267
MIR4262
MIR3130-2
MIR4266
MIR3126
MIR2355
MIR3132
MIR4269
LOC100499194
MIR3606
MIR3682
MIR3679
LOC100505624
LOC100505695
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506123
LOC100506124
LOC100506134
LOC100506274
LOC100506421
LOC100506474
LOC100506783
LOC100506866
LOC100507140
BOLA3-AS1
LOC100507334
LOC100507443
LOC100507600
LY75-CD302
RNF103-CHMP3
NT5C1B-RDH14
PHOSPHO2-KLHL23
HSPE1-MOB4
INO80B-WBP1
UBE2F-SCLY
MIR4436B1
MIR4772
MIR4779
MIR4783
MIR4439
MIR4782
MIR4437
MIR4765
MIR4776-1
MIR4757
MIR4777
MIR1245B
MIR4435-2
MIR4426
MIR4774
MIR2467
MIR4775
MIR4785
MIR4784
MIR4773-1
MIR4444-1
MIR4440
MIR4436A
MIR4786
MIR4773-2
MIR4434
MIR4780
MIR4778
MIR4429
MIR4776-2
MIR4432
MIR548AD
MIR4441
MIR4435-1
LOC100630918
LOC100861402

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.18 | -0.231 | 0.999 | 0.31 | 2.44 | 0.0246
1q | 1955 | 0.62 | 8.71 | 0 | 0.39 | 3.14 | 0.00378
2p | 924 | 0.19 | -0.105 | 0.999 | 0.07 | -2.56 | 1
2q | 1556 | 0.17 | -0.574 | 0.999 | 0.09 | -2.3 | 1
3p | 1062 | 0.10 | -2.16 | 0.999 | 0.13 | -1.43 | 1
3q | 1139 | 0.09 | -2.37 | 0.999 | 0.07 | -2.87 | 1
4p | 489 | 0.13 | -1.47 | 0.999 | 0.26 | 1.19 | 0.291
4q | 1049 | 0.04 | -3.02 | 0.999 | 0.34 | 3.1 | 0.00387
5p | 270 | 0.42 | 4.54 | 2.84e-05 | 0.19 | -0.174 | 1
5q | 1427 | 0.31 | 2.37 | 0.0393 | 0.18 | -0.28 | 1
6p | 1173 | 0.30 | 2.13 | 0.0671 | 0.20 | -0.0378 | 1
6q | 839 | 0.19 | -0.204 | 0.999 | 0.40 | 4.31 | 0.000111
7p | 641 | 0.38 | 3.82 | 0.000537 | 0.15 | -0.963 | 1
7q | 1277 | 0.41 | 4.56 | 2.84e-05 | 0.17 | -0.456 | 1
8p | 580 | 0.21 | 0.0735 | 0.999 | 0.64 | 9.49 | 0
8q | 859 | 0.55 | 6.94 | 3.81e-11 | 0.38 | 3.14 | 0.00378
9p | 422 | 0.06 | -2.67 | 0.999 | 0.35 | 3.39 | 0.00199
9q | 1113 | 0.05 | -2.72 | 0.999 | 0.33 | 2.9 | 0.00678
10p | 409 | 0.09 | -2.33 | 0.999 | 0.18 | -0.375 | 1
10q | 1268 | 0.08 | -2.32 | 0.999 | 0.26 | 1.35 | 0.235
11p | 862 | 0.06 | -2.95 | 0.999 | 0.17 | -0.732 | 1
11q | 1515 | 0.06 | -2.83 | 0.999 | 0.19 | -0.113 | 1
12p | 575 | 0.09 | -2.27 | 0.999 | 0.20 | -0.0758 | 1
12q | 1447 | 0.11 | -1.84 | 0.999 | 0.14 | -1.35 | 1
13q | 654 | 0.13 | -1.36 | 0.999 | 0.36 | 3.45 | 0.00188
14q | 1341 | 0.13 | -1.26 | 0.999 | 0.37 | 3.81 | 0.000696
15q | 1355 | 0.10 | -1.97 | 0.999 | 0.19 | -0.246 | 1
16p | 872 | 0.12 | -1.61 | 0.999 | 0.29 | 2.03 | 0.061
16q | 702 | 0.06 | -2.61 | 0.999 | 0.37 | 3.7 | 0.000857
17p | 683 | 0.11 | -1.27 | 0.999 | 0.60 | 8.87 | 0
17q | 1592 | 0.31 | 2.46 | 0.0349 | 0.14 | -1.19 | 1
18p | 143 | 0.07 | -2.69 | 0.999 | 0.17 | -0.734 | 1
18q | 446 | 0.09 | -2.37 | 0.999 | 0.17 | -0.658 | 1
19p | 995 | 0.24 | 0.846 | 0.662 | 0.17 | -0.607 | 1
19q | 1709 | 0.25 | 1.14 | 0.464 | 0.16 | -0.814 | 1
20p | 355 | 0.33 | 2.82 | 0.0158 | 0.05 | -2.76 | 1
20q | 753 | 0.32 | 2.72 | 0.0188 | 0.02 | -3.41 | 1
21q | 509 | 0.13 | -1.31 | 0.999 | 0.30 | 2.06 | 0.0599
22q | 921 | 0.19 | -0.173 | 0.999 | 0.20 | 0.069 | 1
Xq | 1312 | 0.16 | -0.697 | 0.999 | 0.21 | 0.278 | 0.919

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC/1708663/2.GDAC_MergeDataFiles.Finished/LIHC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 82 Input Tumor Samples.

Tumor Sample Names
TCGA-BC-4072-01B-11D-A151-01
TCGA-BC-4073-01B-02D-A12Y-01
TCGA-BC-A10Q-01A-11D-A12Y-01
TCGA-BC-A10R-01A-11D-A12Y-01
TCGA-BC-A10S-01A-22D-A12Y-01
TCGA-BC-A10T-01A-11D-A12Y-01
TCGA-BC-A10U-01A-11D-A12Y-01
TCGA-BC-A10W-01A-11D-A12Y-01
TCGA-BC-A10X-01A-11D-A12Y-01
TCGA-BC-A10Y-01A-11D-A12Y-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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