Liver Hepatocellular Carcinoma: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 97 tumor samples used in this analysis: 23 significant arm-level results, 26 significant focal amplifications, and 27 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 - 26 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 | 3.4174e-10 | 3.8428e-10 | chr1:154971163-155045171 | 6
11q13.3 | 1.2968e-07 | 1.2968e-07 | chr11:69261268-69434302 | 0 [CCND1]
6p21.1 | 6.8343e-09 | 3.2254e-07 | chr6:43768831-43778390 | 0 [VEGFA]
8q24.13 | 2.3645e-06 | 6.9581e-06 | chr8:117662812-135367259 | 91
3q26.31 | 9.3716e-05 | 9.3716e-05 | chr3:172254454-172319444 | 0 [TNFSF10]
17q25.3 | 1.3615e-05 | 0.00024784 | chr17:80079436-80527577 | 12
13q32.3 | 0.0013996 | 0.0013996 | chr13:96213209-104617917 | 50
7q21.2 | 0.0027514 | 0.0027514 | chr7:90450977-92715262 | 16
1q42.3 | 0.00031889 | 0.024354 | chr1:231581586-249250621 | 145
17p11.2 | 0.026877 | 0.026877 | chr17:18035312-18289209 | 9
2p24.1 | 0.035106 | 0.035106 | chr2:20750368-20775316 | 0 [HS1BP3]
5q35.3 | 0.038516 | 0.038516 | chr5:136221300-180915260 | 452
5p15.33 | 0.065814 | 0.065814 | chr5:1-1300024 | 23
6p25.2 | 0.0086713 | 0.086276 | chr6:1-31051552 | 313
1p22.3 | 0.088183 | 0.088183 | chr1:85974031-86006008 | 1
12q23.1 | 0.088183 | 0.088183 | chr12:100720086-100979511 | 4
2q33.1 | 0.094507 | 0.094507 | chr2:163221508-214993996 | 299
17q23.1 | 0.0058952 | 0.094507 | chr17:57648506-58857125 | 21
8q13.1 | 0.079385 | 0.10737 | chr8:42932479-70954271 | 105
10p15.1 | 0.11059 | 0.11059 | chr10:5008384-5043327 | 2
19q13.11 | 0.12163 | 0.12163 | chr19:33711641-33762256 | 1
20q13.13 | 0.16362 | 0.16362 | chr20:48959085-49075529 | 0 [LOC284751]
4q31.3 | 0.18514 | 0.18514 | chr4:154206362-158836019 | 25
15q21.3 | 0.13707 | 0.20495 | chr15:53689045-53797742 | 0 [WDR72]
6q12 | 0.18514 | 0.21276 | chr6:64031846-64078184 | 0 [LGSN]
15q26.3 | 0.040276 | 0.40839 | chr15:55682757-102531392 | 447

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 8q24.13.

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

Genes
EXT1
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
ADCY8
ANXA13
HAS2
KCNQ3
NDUFB9
NOV
TNFRSF11B
ENPP2
POU5F1B
PVT1
RAD21
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
COL14A1
EIF3H
WISP1
MTSS1
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
RNF139
ZHX1
ZHX2
EFR3A
LRRC6
MTBP
MRPL13
ATAD2
ASAP1-IT1
ASAP1
PHF20L1
FAM49B
TRMT12
WDYHV1
GSDMC
DEPTOR
DSCC1
DERL1
TATDN1
UTP23
C8orf76
FAM83A
MED30
WDR67
HPYR1
MAL2
FBXO32
ZNF572
TMEM71
TMEM65
LOC157381
FAM84B
FAM91A1
SLC30A8
NSMCE2
KLHL38
SAMD12
FER1L6-AS1
C8orf85
SAMD12-AS1
HAS2-AS1
RAD21-AS1
FER1L6
LOC727677
LOC728724
OC90
LOC100130231
LOC100131726
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
MIR3610
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 1q42.3.

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
ACTN2
ADSS
CHML
LYST
CHRM3
GNG4
HNRNPU
KCNK1
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
TSNAX
ZNF124
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZNF238
SDCCAG8
RBM34
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
DISC2
DISC1
PPPDE1
SCCPDH
ARID4B
KIAA1383
KIF26B
HEATR1
ZNF692
ERO1LB
FMN2
ZNF695
SIPA1L2
ZP4
TFB2M
GREM2
SMYD3
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2G3
OR2G2
OR2C3
NTPCR
EFCAB2
KIAA1804
ZNF496
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
EDARADD
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR2W5
OR13G1
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LOC100287814
LGALS8-AS1
MIR1537
LINC00184
TSNAX-DISC1
MIR3123
MIR3124
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4677
MIR4671
MIR4427

Genes in Wide Peak

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

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

Genes
FLII
LLGL1
SHMT1
TOP3A
MYO15A
ALKBH5
SMCR7
SMCR8
EVPLL

Genes in Wide Peak

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

Table S8. 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 5p15.33.

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

Genes
SDHA
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
IRF4
TRIM27
DEK
HIST1H4I
hsa-mir-877
hsa-mir-3143
hsa-mir-548a-1
ABCF1
BMP6
BPHL
BTN1A1
DDR1
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-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
ID4
JARID2
MAK
MOG
NEDD9
NQO2
SERPINB6
SERPINB9
PPP1R10
PRL
RREB1
ATXN1
SLC17A1
SOX4
SSR1
PPP1R11
TFAP2A
TPMT
TUBB2A
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204P
ALDH5A1
OR2H2
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
IER3
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
GCM2
CD83
CDYL
LY86
EEF1E1
MDC1
FAM65B
ZSCAN12
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
FLOT1
SLC17A2
HCG9
PRSS16
BTN3A3
BTN2A2
ECI2
HMGN4
TRIM38
CAP2
UBD
SCGN
FARS2
SLC17A3
RPP40
TRIM31
BTN3A2
BTN3A1
BTN2A1
NRM
SIRT5
OR2B6
FAM50B
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
MRPS18B
MYLIP
ABT1
ZNRD1
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
HCG4
GFOD1
BTN2A3P
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
TRIM39
WRNIP1
DUSP22
LYRM4
VARS2
MRS2
SLC22A23
MUTED
CCDC90A
KIF13A
ZNF323
ZNF322
RPP21
ATAT1
ZKSCAN3
ZSCAN16
RNF39
PRR3
ZNRD1-AS1
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
PPP1R18
TRIM39-RPP21
TUBB
PIP5K1P1
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
ZSCAN23
NKAPL
TOB2P1
FAM217A
RNF144B
HIST1H2BA
GPX6
ZNF311
LOC285768
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
HCG22
MYLK4
IFITM4P
ZNF391
ZFP57
TUBB2B
C6orf52
KAAG1
NHLRC1
ZKSCAN4
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
SFTA2
MUC21
DKFZP686I15217
FLJ23152
LINC00340
LOC401242
C6orf201
ERVFRD-1
HCG18
OR2B3
OR2J3
OR14J1
OR10C1
HCG11
LOC554223
PPP1R3G
SNORD32B
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
MIR877
LOC100129636
LOC100130275
LOC100130357
LOC100131289
LINC00240
LOC100270746
MIR3143
MIR3691
LOC100506207
LOC100506409
LOC100507173
LOC100507194
LOC100507362
MUC22
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4640
MIR4639
MIR4645

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 12q23.1.

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

Genes
NR1H4
SCYL2
SLC17A8
GAS2L3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q33.1.

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

Genes
CHN1
CREB1
HOXD11
HOXD13
IDH1
NFE2L2
PMS1
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
ACADL
AOX1
ATP5G3
BMPR2
CASP8
CASP10
CD28
CHRNA1
CLK1
COL3A1
COL5A2
CPS1
ATF2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
DLX1
DLX2
DYNC1I2
EEF1B2
ERBB4
FRZB
GAD1
GALNT3
MSTN
GLS
GPR1
GRB14
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HSPD1
HSPE1
INPP1
ITGA6
ITGA4
ITGAV
LRP2
MAP2
MYO1B
MYL1
NAB1
NDUFB3
NDUFS1
NEUROD1
ORC2
PDE1A
PDK1
PLCL1
PTH2R
RPE
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SP3
SSB
SSFA2
STAT1
STAT4
TFPI
TTN
SUMO1
WIPF1
FZD5
FZD7
SDPR
HAT1
AGPS
PRKRA
SLC25A12
KLF7
ABCB11
B3GALT1
ADAM23
NRP2
CFLAR
STK17B
GTF3C3
PPIG
CIR1
BZW1
TLK1
ABI2
DHRS9
CALCRL
LANCL1
KBTBD10
UBE2E3
MTX2
NCKAP1
RAPGEF4
IKZF2
COBLL1
FASTKD2
SATB2
SF3B1
TMEFF2
MOB4
GORASP2
SPATS2L
HIBCH
SNORD51
STK39
CPS1-IT1
METTL5
OLA1
ICOS
SLC40A1
PDE11A
GULP1
NOP58
FKBP7
ZAK
PPIL3
DNAJC10
ASNSD1
MFSD6
INO80D
FIGN
STRADB
WDR12
ZC3H15
DNAH7
SLC39A10
CYP20A1
SPC25
HECW2
ALS2
ZDBF2
CWC22
G6PC2
MPP4
NIF3L1
PCGEM1
OSGEPL1
OBFC2A
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
PLEKHA3
TRAK2
BOLL
C2orf47
SPAG16
SCRN3
FASTKD1
ALS2CR8
TTC21B
METTL8
CYBRD1
CSRNP3
PGAP1
DCAF17
COQ10B
KIAA1715
CDCA7
WDR75
C2orf88
KCNH7
LOC91149
SESTD1
ANKRD44
ZNF804A
TTC30A
MARS2
ORMDL1
OSBPL6
NOSTRIN
DIRC1
PARD3B
NUP35
XIRP2
TYW5
RBM45
BBS5
C2orf77
ICA1L
RFTN2
UBR3
KCTD18
ALS2CR12
CPO
MDH1B
MYO3B
DUSP19
FLJ32063
ANKAR
TTC30B
FAM117B
C2orf67
ZSWIM2
ZNF385B
METTL21A
CCNYL1
KLHL23
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
GPR155
FAM171B
PIKFYVE
LOC200726
C2orf69
HNRNPA3
CERS6
METAP1D
CCDC150
CCDC141
LOC285084
FAM126B
UNC80
MLK7-AS1
EVX2
AOX2P
FONG
LOC375295
CERKL
SP5
PLEKHM3
C2orf80
DYTN
LOC401022
FSIP2
C2orf66
MIR10B
LOC440925
PHOSPHO2
DFNB59
SNORA41
SNORD11
SNORD70
MIR561
SNORD11B
MIR933
LOC100130451
LOC100130452
LOC100130691
TMEM194B
SP9
MIR1246
MIR548N
MIR1258
MIR1245A
MIR548F2
LOC100329109
SNORA70F
MIR3128
MIR3129
MIR3130-1
MIR3130-2
MIR2355
MIR3606
LOC100505695
LOC100506124
LOC100506134
LOC100506783
LOC100506866
LOC100507140
LOC100507443
PHOSPHO2-KLHL23
HSPE1-MOB4
MIR4437
MIR4776-1
MIR1245B
MIR4774
MIR4775
MIR4444-1
MIR4776-2
LOC100861402

Genes in Wide Peak

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

Table S14. 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 8q13.1.

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

Genes
PLAG1
TCEA1
CHCHD7
hsa-mir-124-2
ASPH
CA8
CEBPD
CRH
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SULF1
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
SLCO5A1
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100287846
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

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

Table S16. 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 19q13.11.

Table S17. 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 4q31.3.

Table S18. 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 15q26.3.

Table S19. 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
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
IDH3A
IGF1R
IL16
IREB2
ISG20
ISLR
LIPC
LOXL1
SMAD3
SMAD6
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
MYO1E
MYO9A
NEDD4
NEO1
NMB
OAZ2
FURIN
PCSK6
PDE8A
PKM2
PLIN1
POLG
PPIB
MAP2K1
MAP2K5
PSMA4
PTPN9
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
KIF23
IGDCC3
ZNF592
KIAA0101
SV2B
ARNT2
USP3
NR2E3
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
CLPX
MORF4L1
ABHD2
ADAMTS7
AKAP13
ITGA11
CHSY1
ZNF609
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
DAPK2
GABARAPL3
ARIH1
SIN3A
ULK3
GLCE
PYGO1
FBXO22
VPS33B
MRPL46
OR4F4
NPTN
FOXB1
SLCO3A1
SCAPER
HDGFRP3
RPS27L
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
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
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
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
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
LOC645752
SH2D7
LOC646938
GOLGA6L10
LOC648809
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA15
SCARNA14
FBXO22-AS1
MIR549
MIR629
MIR630
MIR631
LOC727849
LOC727915
ASB9P1
LOC729739
LOC729911
FAM138E
DNM1P35
LOC100130855
UBE2Q2P3
UBE2Q2P2
LOC100144604
GPCRLTM7
DDX11L1
LOC100287559
LOC100287616
DDX11L9
MIR1276
MIR1272
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

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 - 27 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 | 4.7605e-13 | 4.7605e-13 | chr1:1-9612196 | 156
13q14.2 | 1.9101e-08 | 1.9101e-08 | chr13:48833767-49281290 | 3
4q35.1 | 4.6182e-07 | 8.3412e-06 | chr4:176920228-191154276 | 72
10q23.31 | 2.1063e-05 | 5.3993e-05 | chr10:89604733-90034038 | 2
8p23.2 | 6.9993e-05 | 7.0017e-05 | chr8:2079140-6262191 | 1
9p21.3 | 0.00011517 | 0.00011456 | chr9:21865498-22448737 | 4
17p12 | 0.0015476 | 0.0014479 | chr17:15891757-16121163 | 2
22q13.31 | 0.0016389 | 0.0028776 | chr22:42482229-51304566 | 121
4q24 | 0.00041669 | 0.0068301 | chr4:77323420-115525698 | 187
12q24.32 | 0.01589 | 0.01589 | chr12:111019710-133851895 | 217
19p13.3 | 0.015534 | 0.01589 | chr19:1-13218317 | 439
14q23.3 | 0.023299 | 0.02266 | chr14:62600712-77496618 | 137
12p12.1 | 0.046993 | 0.04568 | chr12:22837283-24720370 | 3
16q23.1 | 0.047224 | 0.04568 | chr16:59786558-90354753 | 305
5q23.1 | 0.053208 | 0.053208 | chr5:83016344-136312786 | 222
6q26 | 0.045407 | 0.078277 | chr6:136514673-171115067 | 200
2q37.3 | 0.07172 | 0.095492 | chr2:207637054-243199373 | 320
2q22.1 | 0.039193 | 0.11429 | chr2:139655617-143637838 | 1
10q24.33 | 0.025007 | 0.13012 | chr10:97452644-135534747 | 351
11q14.1 | 0.14471 | 0.15174 | chr11:77848950-135006516 | 418
3p13 | 0.16241 | 0.16241 | chr3:20227198-93777876 | 466
22q12.1 | 0.12045 | 0.18945 | chr22:1-31006003 | 247
6q16.3 | 0.099389 | 0.20279 | chr6:57206486-124125707 | 246
10p15.3 | 0.21979 | 0.21649 | chr10:1-7746594 | 51
18q21.2 | 0.22084 | 0.21649 | chr18:23970718-78077248 | 220
Xq27.3 | 0.2113 | 0.21649 | chrX:115591648-155270560 | 362
15q15.1 | 0.22484 | 0.22699 | chr15:1-57178683 | 408

Genes in Wide Peak

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

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

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
RERE
CA6
CDK11B
DFFB
DVL1
MEGF6
ENO1
GABRD
GNB1
ZBTB48
TNFRSF9
PEX10
PRKCZ
SCNN1D
SKI
SLC2A5
TP73
TNFRSF4
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
PER3
VAMP3
H6PD
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
UTS2
RER1
PARK7
ACOT7
CAMTA1
ICMT
CHD5
NOC2L
OR4F3
ARHGEF16
SSU72
WRAP73
SLC45A1
SDF4
ERRFI1
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
DNAJC11
AJAP1
TP73-AS1
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
OR4F5
NOL9
LINC00115
MORN1
GPR157
SPSB1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
C1orf170
KIAA1751
THAP3
LOC115110
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
LOC148413
PHF13
CCDC27
SLC2A7
CALML6
C1orf86
ATAD3C
LOC254099
TTLL10
NPHP4
FAM41C
LOC284661
C1orf174
KLHL17
TMEM240
TMEM52
AGRN
GPR153
FAM132A
HES5
LOC388588
RNF207
HES3
RNF223
MIR200A
MIR200B
MIR34A
FLJ42875
ANKRD65
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
FAM138A
WASH7P
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR4251
MIR4252
ENO1-AS1
MIR4689
MIR4417

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

Table S21. 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 S22. 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 10q23.31.

Table S23. 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 8p23.2.

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

Table S26. 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 22q13.31.

Table S27. 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
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
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 4q24.

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

Genes
RAP1GDS1
TET2
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
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
SOWAHB
LRIT3
SLC10A6
HSD17B13
PCNAP1
FAM190A
WDFY3-AS2
MIR302A
C4orf11
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641518
LOC644248
MIR575
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 12q24.32.

Table S29. 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
ACADS
SCARB1
COX6A1
DTX1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
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
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
BRAP
ULK1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
HRK
ADAM1
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RBM19
RNF10
SH2B3
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
GALNT9
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
TRIAP1
TPCN1
RHOF
VSIG10
TESC
SBNO1
ZCCHC8
CHFR
WSB2
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
LHX5
SUDS3
C12orf43
VPS33A
RSRC2
AACS
DDX54
NOC4L
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
RNF34
CCDC92
PUS1
ACAD10
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
ORAI1
RNFT2
C12orf52
TMEM116
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
TMEM132D
SLC15A4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
FAM109A
LOC144742
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
LRRC43
LOC255480
GPR133
MORN3
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
HCAR2
LOC338799
EP400NL
RILPL1
IL31
CCDC42B
TMEM233
SETD8
LOC387895
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

Genes in Wide Peak

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

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

Genes
GNA11
LYL1
MLLT1
SH3GL1
SMARCA4
STK11
TCF3
FSTL3
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
ACP5
AES
AMH
ASNA1
ATP5D
AZU1
HCN2
BSG
C3
CALR
CAPS
CD70
CDC34
CDKN2D
CIRBP
CNN1
CNN2
CSNK1G2
DAPK3
CFD
DHPS
DNASE2
DNM2
DNMT1
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
ELAVL3
EMR1
EPOR
FARSA
FCER2
FUT3
FUT5
FUT6
GAMT
GCDH
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
ICAM1
ICAM3
ICAM4
ILF3
INSR
JUNB
LDLR
MAN2B1
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NFIX
NRTN
OAZ1
P2RY11
PALM
PDE4A
PIN1
POLR2E
POLRMT
PRKCSH
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RAD23A
RFX2
RPS15
RPS28
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
PRDX2
THOP1
ICAM5
TLE2
TYK2
VAV1
ZNF20
ZNF69
ZNF121
ZNF136
ZNF177
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
EIF3G
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
S1PR2
TRIP10
LONP1
RAB3D
APBA3
SAFB2
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
EBI3
ZNF443
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4A
TIMM44
CARM1
SEMA6B
RNASEH2A
KLF1
ZNF266
PNPLA6
UQCR11
TMED1
CDC37
SBNO2
MAST1
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
KANK2
TIMM13
TSPAN16
DAZAP1
OR7E24
SNORD41
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
HOOK2
SLC39A3
TNPO2
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
SIRT6
PIAS4
LSM7
ZNF44
MBD3
S1PR5
MIER2
PCSK4
ZNF562
BEST2
FBXL12
C19orf24
PLEKHJ1
C19orf66
FEM1A
ZNF823
STAP2
BTBD2
RNF126
CCDC94
C19orf80
C19orf10
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
RGL3
SLC44A2
MCOLN1
WDR18
REXO1
ZNF490
DOCK6
CAMSAP3
ZNF317
ZNF77
C19orf29
UBL5
CELF5
LPPR2
KRI1
YIPF2
C19orf43
SLC25A23
ZNF426
FSD1
ZNF557
CERS4
TLE6
LPPR3
DENND1C
ZNF442
ZNF556
LRRC8E
FLJ22184
UBXN6
OR4F17
ACSBG2
ADAMTS10
QTRT1
FAM108A1
DOHH
RTBDN
ANGPTL6
KLF16
PRAM1
FBXW9
ALKBH7
WDR83
ZNF414
ELOF1
DOT1L
FBN3
ZNF559
KISS1R
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATG4D
ATCAY
MBD3L1
MIDN
GADD45GIP1
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
DPP9
R3HDM4
C19orf6
TPGS1
CRB3
REEP6
PEX11G
ZNF561
OLFM2
MUC16
FDX1L
IZUMO4
SCAMP4
ADAT3
ZNF554
EVI5L
CCDC151
ZNF653
GRIN3B
MRPL54
LRG1
RAVER1
OR7D4
OR7G1
OR1M1
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
C19orf21
PLK5
C2CD4C
ZNF358
LOC147727
ZNF560
ZNF563
SPC24
TICAM1
CIRBP-AS1
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
ZNF846
OR7D2
ZNF791
ZNF564
ZNF709
ZNF433
PRR22
ANKRD24
C19orf59
ZNF627
DAND5
C19orf26
CSNK1G2-AS1
C19orf38
SYCE2
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
LOC284385
ZNF763
ZNF844
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
ODF3L2
EMR4P
ADAMTSL5
CLEC4G
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
WASH5P
LOC388499
C3P1
ZNF788
ONECUT3
OR7G2
OR7G3
MEX3D
FLJ45445
PRSS57
VMAC
ZNF833P
CTXN1
C19orf29-AS1
MIR199A1
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
FAM138F
LINGO3
ARRDC5
FAM138A
MBD3L4
MBD3L3
SNORD105
PPAN-P2RY11
MIR637
MIR638
PLIN4
ZNF812
ZNF878
SNORD105B
ZGLP1
C19orf71
LOC100128573
LOC100131094
C19orf79
LOC100288123
MIR1909
MIR1181
MIR1238
MIR1227
MIR3187
MIR4322
MIR4321
MIR3940
LOC100507567
LOC100507588
ZNF559-ZNF177
ZNF625-ZNF20
MIR4747
MIR4746
MIR4748
MIR4745

Genes in Wide Peak

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

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

Genes
GPHN
hsa-mir-625
hsa-mir-548h-1
ACTN1
ACYP1
ARG2
ZFP36L1
ENTPD5
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GPX2
HSPA2
LTBP2
MAX
MAP3K9
ALDH6A1
MTHFD1
PGF
PIGH
PPP2R5E
PSEN1
ABCD4
RAD51B
SRSF5
SLC8A3
SLC10A1
SPTB
TGFB3
ZBTB25
DPF3
NUMB
ADAM21
ADAM20
DCAF5
EIF2B2
PNMA1
AKAP5
RGS6
KIAA0247
KIAA0317
MED6
VTI1B
BATF
NPC2
ACOT2
TMED10
C14orf1
VASH1
ZBTB1
PCNX
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
MLH3
KCNH5
COQ6
FCF1
RDH11
COX16
ATP6V1D
ZFYVE1
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
YLPM1
C14orf162
RHOJ
GALNTL1
PLEKHH1
ZNF410
RBM25
SMOC1
IRF2BPL
MPP5
ZC2HC1C
C14orf169
C14orf45
SGPP1
DNAL1
RPS6KL1
PAPLN
CHURC1
C14orf43
LIN52
NEK9
IFT43
WDR89
GPHB5
JDP2
ISCA2
ACOT4
RDH12
ADAM21P1
PPP1R36
LOC145474
PTGR2
FAM161B
C14orf166B
FAM71D
TMEM229B
PROX2
C14orf55
SNORD56B
VSX2
RAB15
HEATR4
PLEKHD1
LINC00238
TEX21P
ACOT1
ACOT6
LOC645431
SYNDIG1L
LOC731223
LOC100289511
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706

Genes in Wide Peak

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

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

Genes
hsa-mir-920
SOX5
MIR920

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 5q23.1.

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

Genes
APC
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
ALDH7A1
CAMK4
CAMLG
CAST
CCNH
CDO1
CETN3
CHD1
AP3S1
COX7C
CSF2
CSNK1G3
DMXL1
EFNA5
FBN2
FER
GDF9
GLRX
HINT1
HSD17B4
HSPA4
IL3
IL4
IL5
IL9
IL13
IRF1
KCNN2
LECT2
LMNB1
LNPEP
LOX
SMAD5
MAN2A1
MCC
MEF2C
NEUROG1
PAM
PCSK1
PGGT1B
PITX1
PPIC
PPP2CA
RASA1
SKP1
SLC12A2
SLC22A4
SLC22A5
SNX2
SRP19
TCF7
NR2F1
TGFBI
UBE2B
VDAC1
ST8SIA4
REEP5
PDLIM4
P4HA2
ATG12
NREP
RAB9BP1
CXCL14
H2AFY
SMAD5-AS1
SNCAIP
TTC37
PJA2
DDX46
EDIL3
RAD50
POLR3G
SEC24A
KIF3A
RHOBTB3
ELL2
FSTL4
SEPT8
PPIP5K2
ACSL6
PHF15
TNFAIP8
FBXL21
UQCRQ
AFF4
SLC27A6
SNX24
TMED7
ISOC1
SAR1B
CDKL3
PRR16
COMMD10
RAPGEF6
ERAP1
PHAX
FLJ11235
ZCCHC10
GIN1
TRIM36
RIOK2
FEM1C
C5orf15
CDC42SE2
TRPC7
ZNF608
SEMA6A
ARRDC3
EPB41L4A
ERAP2
FBXL17
YTHDC2
GRAMD3
TXNDC15
MCTP1
NUDT12
SPATA9
TSSK1B
FAM172A
GPR98
PCBD2
ANKRD32
MEGF10
TSLP
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
PRDM6
FTMT
FNIP1
EPB41L4A-AS1
MARCH3
LYSMD3
LEAP2
SLCO6A1
PRRC1
ZNF474
POU5F2
STARD4
WDR36
SOWAHA
SHROOM1
C5orf24
C5orf20
CEP120
SLC25A48
MBLAC2
TMEM161B
SRFBP1
ARSK
FAM81B
CCDC112
DCP2
LIX1
ADAMTS19
C5orf27
AQPEP
KIAA0825
GPR150
DTWD2
NBPF22P
RGMB
RFESD
CHSY3
FAM170A
LOC340073
LOC340074
FAM174A
CATSPER3
SLCO4C1
TICAM2
C5orf48
LOC389332
C5orf63
MIR9-2
FLJ42709
C5orf56
TIFAB
FLJ35946
LOC553103
CTXN3
TMEM232
LOC644100
FLJ33630
CCNI2
LINC00461
SNORA13
MIR583
LOC728342
VTRNA2-1
LOC100129716
LOC100133050
LOC100289230
LOC100289673
MIR1289-2
MIR1244-1
TMED7-TICAM2
MIR2277
MIR1244-3
MIR1244-2
MIR4280
MIR3607
MIR3660
MIR3936
MIR3661
LOC100505678
LOC100505841
LOC100505894
MIR4633
MIR4461
MIR4460

Genes in Wide Peak

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

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

Genes
MLLT4
TNFAIP3
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
ACAT2
CCR6
ESR1
FUCA2
GPR31
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
PEX7
PLAGL1
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
PEX3
RNASET2
STX11
SYNJ2
MAP7
LATS1
QKI
WTAP
AKAP12
PHACTR2
BCLAF1
UST
CITED2
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
HEBP2
CCDC28A
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
TFB1M
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
C6orf115
PBOV1
PERP
SMOC2
ULBP3
C6orf211
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
RSPH3
TTLL2
FBXO30
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
LINC00473
SYTL3
FAM54A
SFT2D1
C6orf72
IL22RA2
TAGAP
ADAT2
STXBP5
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
PNLDC1
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
WDR27
SHPRH
LOC285740
LOC285796
PRR18
SLC35D3
ZC3H12D
ECT2L
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FLJ46906
LOC441177
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LOC100132735
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3692
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 2q37.3.

Table S36. 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 2q22.1.

Table S37. 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 10q24.33.

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

Genes
FGFR2
TLX1
NFKB2
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
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2E1
CYP17A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HMX2
HPS1
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
DNMBP
FRAT2
DPCD
SEC31B
ATRNL1
C10orf137
C10orf12
ANKRD2
CNNM1
DUX2
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
CHST15
ACSL5
CCNJ
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CWF19L1
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
WDR96
LRRC27
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
OPALIN
SYCE1
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
SFXN2
PDZD8
C10orf32
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
NKX2-3
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
LOC283038
LOC283089
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
C10orf62
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
DUX4L2
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100169752
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4483
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PICALM
PCSK7
ARHGEF12
MAML2
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CTSC
CHEK1
CRYAB
DLAT
DLG2
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
GRIA4
GRIK4
GRM5
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PRCP
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
TRPC6
TYR
UPK2
ZBTB16
ZNF202
CUL5
FZD4
BARX2
OR7E2P
JRKL
EED
ZNF259
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
GAB2
C2CD2L
NAALAD2
RBM7
MPZL2
YAP1
HYOU1
ATP5L
ME3
GPR83
SRSF8
ADAMTS8
PRSS23
TREH
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
RAB38
CADM1
PANX1
POU2F3
HINFP
REXO2
ODZ4
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
CHORDC1
ACAD8
B3GAT1
RAB30
DCPS
C11orf54
ZBTB44
THYN1
DDX25
NOX4
NTM
CDON
SIDT2
TRAPPC4
C11orf73
CWC15
PCF11
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
SYTL2
ANKRD49
TTC12
C11orf57
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TMEM126B
TEX12
CRTAM
TMPRSS4
IFT46
C11orf75
PRDM10
TRIM49
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
USP28
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TMEM135
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
NARS2
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
TMEM126A
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
KIAA1731
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
SLC36A4
FAT3
TRIM64
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
CCDC67
PATE1
C11orf65
ADAMTS15
MPZL3
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
C11orf82
CCDC83
HEPACAM
OAF
FAM181B
CCDC89
ANGPTL5
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
KCTD21
CCDC84
TMEM225
OR8D4
ANKRD42
C11orf53
LOC341056
HEPHL1
C11orf34
VSTM5
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
SCARNA9
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49L1
MIR708
LOC100128239
LOC100132078
PATE3
LOC100288077
LOC100288346
MIR1304
SNORA70E
BACE1-AS
MIR4300
MIR4301
MIR3167
MIR1260B
LOC100499227
MIR3920
MIR3656
LOC100506233
LOC100506368
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

Table S40. 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
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
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
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
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SLC4A7
VPRBP
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
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
ARL13B
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
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
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 22q12.1.

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

Genes
BCR
EWSR1
MN1
NF2
SMARCB1
CLTCL1
CHEK2
hsa-mir-3199-2
hsa-mir-548j
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ADORA2A
ADRBK2
AP1B1
ARVCF
ATP6V1E1
BID
COMT
CRKL
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
DDT
GGT1
GGT3P
GGT5
GNAZ
GP1BB
GSC2
GSTT1
GSTT2
SERPIND1
IGLL1
LIF
MIF
MMP11
NEFH
OSM
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
RFPL1
SLC7A4
SLC25A1
SNRPD3
TBX1
CLDN5
TOP1P2
HIRA
UBE2L3
UFD1L
VPREB1
XBP1
ZNF70
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
TPST2
NIPSNAP1
THOC5
MTMR3
TOP3B
P2RX6
SNAP29
GAL3ST1
RAB36
PPM1F
DGCR2
SF3A1
TXNRD2
RASL10A
GAS2L1
RFPL1-AS1
USP18
HIC2
TTC28
SPECC1L
PES1
CABIN1
PRAME
SEC14L2
SEZ6L
TSSK2
SDF2L1
PPIL2
PITPNB
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
TFIP11
C22orf31
GSTTP1
DGCR11
DGCR9
RHBDD3
POM121L1P
DGCR5
DGCR10
FBXW4P1
TRMT2A
RTDR1
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L9P
UQCR10
POM121L8P
YPEL1
ZDHHC8
VPREB3
C22orf43
MTFP1
MED15
UPB1
TUBA8
CECR1
DGCR8
GNB1L
PEX26
ZMAT5
SUSD2
ASPHD2
MICAL3
MRPL40
RTN4R
SLC2A11
C22orf29
THAP7
OR11H1
C22orf13
SLC25A18
TBC1D10A
KREMEN1
ZNRF3
ASCC2
TMEM191A
MYO18B
KLHL22
DGCR6L
KIAA1656
RIMBP3
KIAA1671
HPS4
SCARF2
GGTLC2
GUSBP11
DERL3
IGLL3P
LRP5L
LOC96610
MGC16703
GAB4
C22orf39
C22orf25
ZNF280A
SGSM1
EMID1
ZNF280B
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
C22orf15
HSCB
CCDC117
HORMAD2
CCDC116
CABP7
RNF215
TMEM211
SEC14L3
POM121L4P
RGL4
LOC284865
LOC284889
TTC28-AS1
SEC14L4
PI4KAP2
SDC4P
TPTEP1
LOC388849
FAM211B
LOC391322
LOC400891
BCRP2
CHCHD10
SRRD
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
PIWIL3
MIAT
CCDC157
BCRP3
TMEM191C
C22orf45
POM121L10P
LOC648691
CES5AP1
GATSL3
GSTTP2
GSTT2B
MIR648
MIR650
TMEM191B
PI4KAP1
LOC729444
SEC14L6
DDTL
SNORD125
MIR301B
LOC100128531
CECR7
CECR5-AS1
FLJ41941
MIR1286
MIR1306
MIR548J
MIR3199-2
MIR3198-1
MIR3199-1
IGLL5
MIR3653
MIR3618
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.3.

Table S42. 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
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
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
PTP4A1
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
PHF3
ORC3
BRD7P3
MTO1
ASF1A
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
LGSN
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
SERINC1
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
FAM184A
MANEA
LINC00472
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
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
KHDRBS2
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
EYS
GUSBP4
GJB7
SNHG5
C6orf147
LINC00222
CEP85L
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
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 10p15.3.

Table S43. 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 18q21.2.

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

Genes
BCL2
MALT1
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
hsa-mir-187
hsa-mir-302f
AQP4
ATP5A1
CDH2
CDH7
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MEP1B
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TCF4
TTR
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
ZNF271
TXNL4A
MAPRE2
POLI
ADNP2
TRAPPC8
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
RPRD1A
ZNF532
ELP2
ELAC1
ZNF407
CNDP2
CELF4
KIAA1328
KLHL14
KIAA1468
EPG5
FAM59A
CCDC102B
RBFA
PQLC1
FHOD3
CCDC68
ASXL3
NETO1
KATNAL2
CHST9
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
INO80C
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
MCART2
DSG4
CHST9-AS1
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
ZNF396
KCTD1
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
C18orf34
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
MIR187
HSBP1L1
WBP11P1
RNF165
C18orf32
KC6
LOC643542
C18orf63
LOC647946
SCARNA17
SNORA37
LOC728606
TCEB3CL
ZSCAN30
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR302F
MIR1539
MIR4319
MIR4318
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744
LOC100652770

Genes in Wide Peak

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

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
ABCD1
SLC25A5
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CD40LG
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
GLUD2
GRIA3
HCFC1
HMGB3
HPRT1
IDH3G
IDS
IGSF1
IL9R
IL13RA1
IRAK1
L1CAM
LAMP2
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
NDUFA1
OCRL
PLXNB3
OPN1LW
RENBP
RPL10
RPL39
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
UBE2A
VBP1
XPNPEP2
ZIC3
ZNF75D
RNF113A
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
CUL4B
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
CXorf1
GPR50
RAB33A
ARHGEF6
MAGEC1
ZBTB33
MAMLD1
BCAP31
ODZ1
SPRY3
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
PGRMC1
TREX2
SEPT6
ATP1B4
LDOC1
FAM127B
SRPK3
SNORA70
SNORA69
SNORD61
RBMX
HTATSF1
MCTS1
C1GALT1C1
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
WDR44
CXorf48
FAM70A
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45B
GABRQ
NKRF
MOSPD1
THOC2
KIAA1210
PDZD4
RAP2C
FAM3A
BCORL1
CXorf56
SPANXD
SPANXC
UPF3B
FUNDC2
PRRG3
BRCC3
NKAP
MAP7D3
LONRF3
GPR101
CD99L2
H2AFB3
USP26
PHF6
RHOXF2
TMEM185A
SLITRK2
MGC16121
PNMA6A
FATE1
HS6ST2
FRMD7
KLHL13
CXorf40A
FAM58A
MMGT1
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
DOCK11
CSAG1
FMR1NB
LOC158696
ARHGAP36
AKAP14
RHOXF1
NKAPP1
FAM122B
FAM122C
ZCCHC12
SPANXE
SPANXF1
CXorf61
SLC25A43
DDX26B
ZNF449
VMA21
CTAG1A
CT47A11
MAGEA2B
ATP11C
RP1-177G6.2
LOC286467
LINC00204B
DCAF12L2
SOWAHD
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
LINC00086
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
CT47B1
CXorf69
LINC00087
CT47A7
MIR542
SNORA36A
SNORA56
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
CT45A2
MIR767
MIR766
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129520
LOC100129662
HSFX2
CXorf64
LOC100131434
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR320D2
MIR1277
SLC25A5-AS1
MIR718
MIR2114
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
LOC100506757
CT47A12
LOC100507404
MAGEA10-MAGEA5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

Table S46. 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
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

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.14 | -0.928 | 1 | 0.30 | 2.78 | 0.00905
1q | 1955 | 0.58 | 8.9 | 0 | 0.37 | 3.34 | 0.00184
2p | 924 | 0.16 | -0.974 | 1 | 0.08 | -2.57 | 0.999
2q | 1556 | 0.13 | -1.32 | 1 | 0.09 | -2.24 | 0.999
3p | 1062 | 0.09 | -2.38 | 1 | 0.12 | -1.7 | 0.999
3q | 1139 | 0.09 | -2.6 | 1 | 0.06 | -3.29 | 0.999
4p | 489 | 0.11 | -2.04 | 1 | 0.25 | 1.09 | 0.346
4q | 1049 | 0.03 | -3.38 | 1 | 0.33 | 3.23 | 0.00247
5p | 270 | 0.42 | 4.96 | 4.71e-06 | 0.18 | -0.447 | 0.999
5q | 1427 | 0.32 | 2.97 | 0.00985 | 0.17 | -0.415 | 0.999
6p | 1173 | 0.27 | 1.86 | 0.126 | 0.18 | -0.391 | 0.999
6q | 839 | 0.19 | -0.196 | 1 | 0.39 | 4.43 | 4.81e-05
7p | 641 | 0.34 | 3.32 | 0.00356 | 0.13 | -1.33 | 0.999
7q | 1277 | 0.36 | 4.07 | 0.000234 | 0.14 | -1.11 | 0.999
8p | 580 | 0.17 | -0.396 | 1 | 0.63 | 10.3 | 0
8q | 859 | 0.50 | 6.73 | 1.73e-10 | 0.33 | 2.5 | 0.0191
9p | 422 | 0.06 | -2.82 | 1 | 0.34 | 3.42 | 0.00156
9q | 1113 | 0.06 | -2.62 | 1 | 0.37 | 4.18 | 0.000119
10p | 409 | 0.08 | -2.79 | 1 | 0.20 | -0.0963 | 0.999
10q | 1268 | 0.07 | -2.69 | 1 | 0.26 | 1.66 | 0.129
11p | 862 | 0.06 | -3.1 | 1 | 0.16 | -0.819 | 0.999
11q | 1515 | 0.06 | -2.91 | 1 | 0.18 | -0.127 | 0.999
12p | 575 | 0.09 | -2.48 | 1 | 0.20 | -0.00169 | 0.999
12q | 1447 | 0.12 | -1.76 | 1 | 0.13 | -1.53 | 0.999
13q | 654 | 0.14 | -1.23 | 1 | 0.36 | 3.86 | 0.000322
14q | 1341 | 0.14 | -1.09 | 1 | 0.36 | 4.09 | 0.000142
15q | 1355 | 0.09 | -2.45 | 1 | 0.17 | -0.603 | 0.999
16p | 872 | 0.12 | -1.69 | 1 | 0.31 | 2.79 | 0.00905
16q | 702 | 0.05 | -2.93 | 1 | 0.38 | 4.48 | 4.81e-05
17p | 683 | 0.10 | -1.63 | 1 | 0.60 | 9.74 | 0
17q | 1592 | 0.29 | 2.47 | 0.0299 | 0.17 | -0.487 | 0.999
18p | 143 | 0.07 | -2.95 | 1 | 0.16 | -0.943 | 0.999
18q | 446 | 0.08 | -2.66 | 1 | 0.16 | -1.09 | 0.999
19p | 995 | 0.25 | 1.2 | 0.386 | 0.16 | -0.828 | 0.999
19q | 1709 | 0.24 | 1.28 | 0.367 | 0.13 | -1.26 | 0.999
20p | 355 | 0.32 | 2.76 | 0.0165 | 0.09 | -2.34 | 0.999
20q | 753 | 0.31 | 2.68 | 0.0182 | 0.04 | -3.19 | 0.999
21q | 509 | 0.14 | -1.26 | 1 | 0.30 | 2.28 | 0.032
22q | 921 | 0.17 | -0.533 | 1 | 0.19 | -0.0823 | 0.999
Xq | 1312 | 0.16 | -0.723 | 1 | 0.19 | -0.0392 | 0.999

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-TP/2841849/2.GDAC_MergeDataFiles.Finished/LIHC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 97 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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