Kidney Renal Clear Cell 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 2.0.16 (cga svn revision 38839).

Summary

There were 489 tumor samples used in this analysis: 25 significant arm-level results, 12 significant focal amplifications, and 31 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 - 12 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
--- | --- | --- | --- | ---
5q35.2 | 1.7405e-08 | 1.7405e-08 | chr5:164111667-180915260 | 167
4q32.1 | 0.014021 | 0.014021 | chr4:159611309-161508640 | 7
6p21.1 | 0.022294 | 0.022294 | chr6:41780756-41822198 | 1
3q26.32 | 0.023765 | 0.023765 | chr3:177793108-179141923 | 7
1q32.1 | 0.029049 | 0.029049 | chr1:203851275-205049065 | 14
14q13.2 | 0.066124 | 0.066124 | chr14:35048643-37404863 | 19
7q36.1 | 0.091871 | 0.091871 | chr7:150696504-150732811 | 3
6q12 | 0.12555 | 0.12555 | chr6:63199732-63667923 | 0 [KHDRBS2]
9p24.1 | 0.14325 | 0.14325 | chr9:5037462-5234141 | 3
13q14.2 | 0.15429 | 0.15429 | chr13:49279242-50232489 | 9
15q26.1 | 0.16159 | 0.16159 | chr15:90218948-90997428 | 20
5q15 | 0.15429 | 0.21672 | chr5:93535136-95852768 | 16

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.2.

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

Genes
NPM1
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
BNIP1
CANX
CLTB
NKX2-5
DBN1
DOCK2
DRD1
DUSP1
F12
FGFR4
FOXI1
FLT4
GABRP
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
KCNMB1
LCP2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
RARS
SLC34A1
SLIT3
SNCB
STK10
ZNF354A
STC2
FGF18
SQSTM1
ATP6V0E1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
WWC1
FBXW11
ZNF346
TSPAN17
OR4F3
PRELID1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
CCDC99
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
GMCL1P1
RMND5B
PANK3
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
AGXT2L2
UNC5A
TRIM41
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
ZNF354B
C5orf47
C5orf58
OR2Y1
C5orf41
BTNL9
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
OR2V2
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
FBLL1
C5orf25
MIR103A1
MIR218-2
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
LOC728554
AACSP1
LOC729678
OR4F29
FAM196B
LOC100132062
LOC100132287
LOC100133331
LOC100268168
MIR1229
MIR103B1
MIR4281
MIR3912
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q32.1.

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

Genes
ETFDH
PPID
RAPGEF2
FNIP2
C4orf45
MIR3688-1
MIR3688-2

Genes in Wide Peak

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

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

Genes
USP49

Genes in Wide Peak

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

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

Genes
PIK3CA
KCNMB2
KCNMB3
ZNF639
MFN1
GNB4
ZMAT3

Genes in Wide Peak

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

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

Genes
MDM4
KISS1
PIK3C2B
REN
CNTN2
SOX13
LRRN2
PLEKHA6
NFASC
ETNK2
PPP1R15B
LOC127841
GOLT1A
LINC00303

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.2.

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

Genes
NKX2-1
CFL2
NFKBIA
PAX9
PSMA6
SRP54
KIAA0391
BAZ1A
NKX2-8
MBIP
PPP2R3C
SNX6
BRMS1L
INSM2
SLC25A21
RALGAPA1
SFTA3
IGBP1P1
FAM177A1

Genes in Wide Peak

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

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

Genes
NOS3
ABCB8
ATG9B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.1.

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

Genes
JAK2
INSL4
INSL6

Genes in Wide Peak

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

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

Genes
MLNR
FNDC3A
PHF11
RCBTB1
CYSLTR2
CDADC1
CAB39L
SETDB2
ARL11

Genes in Wide Peak

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

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

Genes
IDH2
hsa-mir-3174
ANPEP
PLIN1
PEX11A
IQGAP1
AP3S2
SEMA4B
CIB1
GABARAPL3
NGRN
MESP1
WDR93
MESP2
ZNF774
C15orf38
ZNF710
C15orf58
TTLL13
C15orf38-AP3S2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q15.

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

Genes
hsa-mir-583
GLRX
PCSK1
TTC37
RHOBTB3
ELL2
MCTP1
SPATA9
ANKRD32
ARSK
FAM81B
C5orf27
KIAA0825
GPR150
RFESD
MIR583

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 - 31 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
--- | --- | --- | --- | ---
2q37.3 | 8.6402e-17 | 8.6402e-17 | chr2:237410659-243199373 | 76
9p21.3 | 1.8078e-17 | 7.3224e-16 | chr9:21865498-22448737 | 4
9p24.1 | 2.3671e-13 | 2.9272e-11 | chr9:8310705-12693402 | 1
1p36.11 | 4.0593e-08 | 8.8795e-08 | chr1:1-29655655 | 489
6q26 | 2.4405e-07 | 3.918e-07 | chr6:161693099-163153207 | 1
1p31.1 | 1.1306e-06 | 5.2573e-06 | chr1:71699756-74522473 | 2
3p21.1 | 1.1043e-07 | 8.236e-06 | chr3:52572448-52727256 | 4
14q24.3 | 6.2919e-05 | 6.2919e-05 | chr14:78397628-80334035 | 1
10q23.31 | 0.00024858 | 0.00024858 | chr10:89617158-90034038 | 2
3p12.2 | 4.7485e-07 | 0.0002685 | chr3:78644877-84688247 | 2
3p12.3 | 1.1788e-06 | 0.00052165 | chr3:75363575-81540112 | 11
3p14.1 | 0.00014482 | 0.0039467 | chr3:63601963-66121046 | 13
4q34.3 | 0.012186 | 0.012335 | chr4:159684871-191154276 | 129
13q13.3 | 0.012973 | 0.012335 | chr13:1-60739304 | 252
1q44 | 0.015332 | 0.015332 | chr1:211555476-249250621 | 299
3p11.1 | 0.0014788 | 0.016736 | chr3:86120087-93777876 | 12
3p26.3 | 0.00095086 | 0.02098 | chr3:1-25645262 | 146
7q31.1 | 0.029897 | 0.029654 | chr7:109599468-111857057 | 3
3p14.2 | 0.00088079 | 0.03537 | chr3:54960968-63429540 | 36
3p14.1 | 0.0048272 | 0.062874 | chr3:67061380-71592506 | 17
3p12.1 | 0.00016696 | 0.069562 | chr3:81807544-88101421 | 7
4q24 | 0.069581 | 0.069562 | chr4:88752879-120222882 | 139
8p12 | 0.069747 | 0.069562 | chr8:27531942-35110688 | 46
3q13.13 | 0.062874 | 0.085748 | chr3:98297058-120117359 | 122
18q12.3 | 0.098169 | 0.098169 | chr18:39619677-40325227 | 1
5p15.33 | 0.12648 | 0.12544 | chr5:1015064-2759249 | 18
6q15 | 0.090065 | 0.15688 | chr6:86384292-117598960 | 144
19p13.3 | 0.15688 | 0.15688 | chr19:1-56092972 | 1545
10q11.23 | 0.16563 | 0.17393 | chr10:38636764-85915936 | 276
8p11.21 | 0.1821 | 0.18703 | chr8:35650656-50825088 | 74
3q11.2 | 0.11899 | 0.21057 | chr3:81537865-124784420 | 200

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
COL6A3
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
MLPH
C2orf54
ILKAP
ING5
MGC16025
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
FLJ43879
MIR149
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

Table S13. 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 9p24.1.

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD99
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.1.

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

Genes
NEGR1
NEGR1-IT1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.1.

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

Genes
PBRM1
SNORD19
SNORD69
SNORD19B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.3.

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

Genes
NRXN3

Genes in Wide Peak

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

Table S20. 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 3p12.2.

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

Genes
GBE1
ROBO1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.3.

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

Genes
hsa-mir-4273
hsa-mir-1324
ROBO1
ROBO2
LOC401074
FLJ20518
FAM86DP
ZNF717
FRG2C
MIR1324
MIR4273

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
ATXN7
MAGI1
PSMD6
ADAMTS9
THOC7
C3orf49
SNTN
PRICKLE2
MIR548A2
LOC100287879
LOC100507062
ADAMTS9-AS2
LOC100652759

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
AGA
SLC25A4
CASP3
CLCN3
CPE
DCTD
F11
ACSL1
FAT1
FRG1
GK3P
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY5R
MSMO1
TLL1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
ANP32C
FAM149A
FBXO8
DUX2
PDLIM3
SPOCK3
AADAT
GALNT7
CLDN22
C4orf27
MARCH1
NEIL3
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
TKTL2
CBR4
MGC45800
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
C4orf45
TRIM60
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
MIR3688-1
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR3688-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.3.

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
XPO4
MRP63
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3613
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q44.

Table S26. 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
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
HNRNPU
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
RPS6KC1
RNU5F-1
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
PPPDE1
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
SLC30A10
ZNF692
IARS2
ENAH
NUP133
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR194-1
MIR215
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
DUSP5P
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
SNORA36B
SNORA16B
LOC728463
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3124
MIR3122
MIR3620
MIR3916
PROX1-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

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

Genes
EPHA3
HTR1F
POU1F1
PROS1
CGGBP1
CHMP2B
ZNF654
ARL13B
C3orf38
VGLL3
STX19
MIR4795

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.3.

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

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RARB
RPL15
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
THRB
TIMP4
NR2C2
UBE2E1
UBE2E2
WNT7A
BRPF1
COLQ
CAMK1
BHLHE40
KAT2B
SH3BP5
VGLL4
EDEM1
TBC1D5
TATDN2
IQSEC1
NR1D2
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LSM3
NKIRAS1
LINC00312
LMCD1
C3orf32
TRNT1
CRBN
C3orf19
GHRL
ARL8B
SETD5
TMEM40
TMEM111
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
ZNF385D
HDAC11
TSEN2
GRIP2
C3orf20
JAGN1
GHRLOS2
IL17RC
EAF1
OXNAD1
C3orf24
GALNTL2
KCNH8
CHCHD4
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
LOC152024
FGD5
CIDECP
CNTN4
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC339862
COL6A4P1
TPRXL
LHFPL4
VENTXP7
LOC401052
LOC440944
SNORA7A
LOC644990
MIR563
MIR885
EGOT
GHRLOS
LOC100129480
LOC100132526
LOC100288428
MIR4270
MIR3714
FGD5-AS1
LOC100505696
LOC100507582
ARPC4-TTLL3
MIR4791
MIR4790
MIR548AC
MIR4792

Genes in Wide Peak

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

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

Genes
DOCK4
LRRN3
IMMP2L

Genes in Wide Peak

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

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

Genes
FHIT
ARF4
C3orf51
DNASE1L3
FLNB
PDHB
PTPRG
WNT5A
SLMAP
ACOX2
CADPS
HESX1
RPP14
FAM107A
FAM208A
ERC2
APPL1
ARHGEF3
IL17RD
PXK
FEZF2
ABHD6
C3orf14
ID2B
FAM3D
ASB14
C3orf67
KCTD6
DNAH12
PDE12
FAM116A
CCDC66
LOC285401
SPATA12
MIR3938
LOC100506994

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
MITF
FOXP1
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
TMF1
SUCLG2
UBA3
ARL6IP5
FRMD4B
LMOD3
FAM19A4
C3orf64
FAM19A1
MIR1284
MIR3136
MIR4272

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.1.

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

Genes
HTR1F
POU1F1
CHMP2B
CADM2
VGLL3
LOC440970
MIR4795

Genes in Wide Peak

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

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

Genes
RAP1GDS1
TET2
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ANK2
ATOH1
BMPR1B
CAMK2D
CASP6
CENPE
EGF
EIF4E
ENPEP
GRID2
H2AFZ
HADH
HSP90AB3P
CFI
MANBA
MTTP
NFKB1
PDHA2
PITX2
PKD2
PPP3CA
RPL34
SNCA
SPP1
TACR3
UBE2D3
UGT8
PRSS12
UNC5C
LAMTOR3
HERC3
PAPSS1
AIMP1
NDST3
ABCG2
SEC24D
TSPAN5
FAM13A
SEC24B
PDLIM5
RRH
MMRN1
METAP1
PPA2
DAPP1
DKK2
HPGDS
LEF1
HERC5
LARP7
EMCN
MYOZ2
GAR1
USP53
ARHGEF38
HERC6
CCDC109B
BANK1
C4orf21
AP1AR
BDH2
SMARCAD1
MEPE
INTS12
METTL14
OSTC
NEUROG2
SLC39A8
NDST4
AGXT2L1
ELOVL6
ARSJ
GSTCD
DNAJB14
ALPK1
CXXC4
PLA2G12A
C4orf17
COL25A1
PIGY
FLJ20021
TIFA
RG9MTD2
TBCK
CYP2U1
DDIT4L
C4orf32
TRAM1L1
SLC9B2
SLC9B1
PPM1K
TIGD2
SGMS2
SYNPO2
NPNT
LOC256880
NAP1L5
LOC285456
FAM13A-AS1
GPRIN3
C4orf37
LRIT3
PCNAP1
FAM190A
C4orf3
MIR302A
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641518
LOC644248
CEP170P1
SNORA24
MIR577
SNHG8
MIR1243
MIR1973
MIR3684
LOC100507053
LOC100507096
1/2-SBSRNA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p12.

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

Genes
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
DUSP4
EXTL3
GSR
GTF2E2
NRG1
PNOC
PPP2CB
FZD3
UBXN8
DCTN6
RBPMS
KIF13B
LEPROTL1
PURG
TMEM66
ELP3
CCDC25
INTS9
PBK
ZNF395
TEX15
DUSP26
HMBOX1
RNF122
TTI2
MAK16
FUT10
ESCO2
FBXO16
SCARA5
LOC286135
C8orf80
C8orf75
MBOAT4
LOC100128750
MIR4287
MIR3148
MIR4288
MIR3622A
MIR3622B
LOC100507341
MIR548O2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.13.

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

Genes
CBLB
TFG
hsa-mir-198
hsa-mir-568
hsa-mir-567
ADPRH
ALCAM
ATP6V1A
CD80
CD47
COL8A1
CPOX
DRD3
GAP43
GSK3B
LSAMP
CD200
RPL24
UPK1B
ZNF80
B4GALT4
NR1I2
GUCA1C
DZIP3
TOMM70A
COX17
CD96
ST3GAL6
HHLA2
FILIP1L
MYH15
C3orf17
ABI3BP
PVRL3
ZBTB20
ZBTB11
MORC1
GTPBP8
TAGLN3
TRAT1
IMPG2
TIMMDC1
PLA1A
GRAMD1C
SIDT1
RG9MTD1
SLC35A5
TMEM45A
IFT57
DPPA4
TMEM39A
ABHD10
TBC1D23
WDR52
NIT2
POGLUT1
BBX
PCNP
SENP7
ARHGAP31
KIAA1407
KIAA1524
POPDC2
NFKBIZ
ATG3
ZBED2
CEP97
C3orf52
QTRTD1
NAA50
C3orf26
RETNLB
CCDC54
GPR128
C3orf15
PHLDB2
BOC
FAM55C
LRRC58
ZPLD1
CD200R1
DCBLD2
FAM172BP
LOC151658
DPPA2
CCDC80
BTLA
SPICE1
LOC152225
IGSF11
C3orf30
GPR156
TIGIT
KIAA2018
ZDHHC23
PLCXD2
GCET2
LSAMP-AS3
LOC285205
SLC9A10
LOC285359
LOC344595
TMPRSS7
CD200R1L
LNP1
FLJ22763
FLJ25363
MIR198
TMEM30C
LINC00488
MIR548A3
MIR567
MIR568
LOC100009676
ZBTB20-AS1
LOC100302640
MIR548G
MIR3921
PVRL3-AS1
IGSF11-AS1
MIR4796
MIR4446

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.3.

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

Genes
LOC284260

Genes in Wide Peak

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

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

Genes
hsa-mir-4277
NDUFS6
SLC6A3
TERT
SLC12A7
IRX4
MRPL36
LPCAT1
CLPTM1L
C5orf38
IRX2
SLC6A19
SLC6A18
SDHAP3
LOC728613
MIR4277
MIR4457
MIR4635

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q15.

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
CCNC
CGA
CNR1
COL10A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1E
KPNA5
LAMA4
MARCKS
POU3F2
PREP
REV3L
SIM1
SMPD2
MAP3K7
NR2E1
TSPYL1
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
CASP8AP2
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
ANKRD6
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
PNISR
FBXL4
SNORD50A
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
RARS2
PDSS2
C6orf162
LYRM2
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
GPR63
SPACA1
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
KIAA1919
GTF3C6
KLHL32
SLC16A10
PM20D2
SRSF12
C6orf165
BVES-AS1
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
VGLL2
LACE1
MMS22L
FAM26E
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
RSPH4A
GJB7
SNHG5
LINC00222
LIN28B
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
TPI1P3
C6orf186
BET3L
LOC100130890
MIR2113
MIR548H3
LOC100422737
MIR4464
MIR4643

Genes in Wide Peak

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

Table S39. 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-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
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
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
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
RPS9
RPS11
RPS15
RPS16
RPS19
RPS28
RRAS
RTN2
RYR1
SAFB
CLEC11A
SCN1B
CCL25
SEPW1
SGTA
SLC1A5
SLC1A6
SLC5A5
SLC8A2
SNAPC2
SNRNP70
SNRPA
SNRPD2
SPIB
STXBP2
SULT2B1
SULT2A1
SUPT5H
SYT5
TBXA2R
PRDX2
TGFB1
THOP1
ICAM5
TLE2
TNNI3
TNNT1
TULP2
TYK2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
VAV1
XRCC1
ZFP36
ZNF14
ZNF708
ZNF20
ZNF28
ZNF43
ZNF45
ZNF69
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF121
ZNF136
ZNF137P
ZNF146
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
ARHGEF1
PDCD5
DYRK1B
LPAR2
RAB11B
CRLF1
NUMBL
CYTH2
S1PR2
ZNF235
TRIP10
LONP1
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
DDX39A
ZNF443
PLIN3
AKAP8
LILRB2
APC2
PAK4
B3GNT3
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4A
TMEM147
IFI30
TOMM40
TIMM44
CARM1
SEMA6B
CHERP
RNASEH2A
RABAC1
SPINT2
KLF1
DLL3
CERS1
GIPC1
POP4
ZNF234
ZNF266
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
PNPLA6
KDELR1
UQCR11
LILRB5
ILVBL
LILRB4
KLK11
TMED1
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
CLASRP
KPTN
SLC7A9
CDC37
MAP4K1
KLK8
CYP4F8
PNKP
COPE
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
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
SHC2
TMEM59L
PGLS
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
DHDH
EIF3K
UBE2S
SLC6A16
C19orf53
BABAM1
LGALS13
UHRF1
CYP2S1
STRN4
HOOK2
SERTAD3
SERTAD1
SLC39A3
GLTSCR2
GLTSCR1
TNPO2
EMR2
CD209
EHD2
KLK14
KLK12
COL5A3
RDH8
SHANK1
NOSIP
MRPL4
NDUFA13
ANGPTL4
HSD17B14
GP6
VRK3
MARCH2
ZNF571
GMIP
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
ISYNA1
SIRT6
PIAS4
LSR
LSM7
ZNF44
TM6SF2
MBD3
PTOV1
S1PR5
FXYD7
FXYD5
RAB4B
MIER2
DDX49
PAF1
PCSK4
PPP1R12C
TRPM4
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
C19orf66
FEM1A
ZNF823
KLK15
MED29
STAP2
TRMT1
BTBD2
NLRP2
RNF126
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
MCOLN1
RCN3
TTYH1
WDR18
REXO1
PNMAL2
ZNF490
PRR12
DOCK6
ZNF492
TSHZ3
LRFN1
GRAMD1A
CAMSAP3
PLEKHA4
ZFP14
ZNF317
ZNF529
PRX
ANO8
SPTBN4
MARK4
SUGP1
HAMP
CATSPERG
CYP4F11
ZNF77
SCAF1
C19orf29
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
UBL5
ZNF350
TSKS
CELF5
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
LPPR2
ZNF574
PLEKHG2
RASAL3
MRPL34
KRI1
ZSWIM4
ZNF649
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
TMEM38A
TSEN34
KCTD15
SLC25A23
C19orf42
ZNF426
TRAPPC6A
MBOAT7
FKRP
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
C19orf57
ZNF576
FSD1
ZNF557
LRFN3
ABHD8
CERS4
OCEL1
GLT25D1
IGFLR1
TBC1D17
GEMIN7
ISOC2
MYH14
ZNF665
TLE6
EPHX3
PODNL1
ZNF613
ADCK4
CNTD2
SLC35E1
LPPR3
DENND1C
ZNF442
ZNF702P
ZNF556
LOC80054
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
CEP89
ZNF382
ZNF566
MUM1
HSH2D
MPND
ALKBH6
ATG4D
ATCAY
SYDE1
RHPN2
MBD3L1
SIGLEC10
SIGLEC12
ZNF628
MIDN
KIR3DX1
ZNF30
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
SAMD1
DCAF15
GADD45GIP1
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
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
LENG8
CCDC124
ZNF554
FBXO17
KIR3DL3
ARHGAP33
EVI5L
RASGRP4
NXNL1
CCDC151
ZNF653
ZNF526
GRIN3B
MRPL54
LRG1
CIB3
RLN3
CLDND2
ZNF816
CEACAM20
RAVER1
OR7D4
OR7G1
OR1M1
COX6B2
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
OSCAR
ZNF813
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
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
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
PPM1N
KLC3
IGSF23
LYPD4
LOC147727
ZNF560
TMEM190
HIPK4
TMC4
LOC147804
ZNF563
SPC24
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
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
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
TMEM86B
C19orf26
CSNK1G2-AS1
PRR24
C19orf38
SYCE2
NAPSB
KANK3
PLAC2
TMEM146
IL4I1
IL28A
IL28B
IL29
SSC5D
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
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
ADAMTSL5
CLEC4G
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
NANOS3
PALM3
SELV
C19orf51
ZNF429
ZNF233
LILRA5
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
WASH5P
SLC27A1
LOC388499
C3P1
ZNF788
CLEC17A
CYP4F24P
RPSAP58
RGS9BP
KRTDAP
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ONECUT3
OR7G2
OR7G3
OR7A10
NUDT19
ZNF793
PAPL
LOC390940
SPRED3
MEX3D
ZNF321P
FLJ45445
PRSS57
VMAC
LOC400680
LOC400684
LOC400685
LGALS17A
SIGLEC16
FLJ26850
ZNF880
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
DPRX
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
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
ZNF726
MIR769
SIGLEC14
LOC100101266
SNORD105B
ZGLP1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
C19orf71
LOC100128573
LOC100128675
LOC100128682
LOC100129083
ZNF737
LOC100129935
SCGB2B3P
TMEM221
SGK110
LOC100131094
BSPH1
C19orf79
LOC100134317
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
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
LOC100507373
LOC100507433
THEG5
LOC100507567
LOC100507588
ZNF559-ZNF177
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
ZNF625-ZNF20
APOC4-APOC2
MIR4530
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 10q11.23.

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

Genes
PRF1
RET
NCOA4
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
hsa-mir-4294
hsa-mir-3156-1
ADK
ALOX5
ANXA8L2
ANK3
ANXA2P3
ANXA7
ANXA11
CAMK2G
CDK1
CHAT
COL13A1
CTSL1P2
DNA2
EGR2
EIF4EBP2
ERCC6
GDF2
GDF10
HK1
HNRNPF
HNRNPH3
KCNMA1
MAT1A
MBL2
MSMB
NODAL
P4HA1
PCBD1
PLAU
PPA1
PPP3CB
PPYR1
SRGN
PRKG1
MAPK8
PSAP
RBP3
RPS24
CXCL12
SFTPD
SLC18A3
SUPV3L1
TACR2
TFAM
UBE2D1
VCL
VDAC2
ZNF22
ZNF32
ZNF33B
CCDC6
SLC25A16
ZNF239
PARG
NDST2
MBL1P
SGPL1
DDX21
DLG5
CHST3
VPS26A
SEC24C
GPRIN2
BMS1
SPOCK2
RHOBTB1
PPIF
HNRNPA3P1
MICU1
NRG3
C10orf10
POLR3A
ZWINT
ECD
ZNF365
DKK1
KIAA0913
DNAJC9
CSTF2T
SIRT1
KAT6B
TSPAN15
NUDT13
HERC4
PTPN20B
KIAA1279
AP3M1
GHITM
KIAA1274
CTNNA3
A1CF
NRBF2
NEUROG3
ASCC1
MRPS16
DUSP13
FXYD4
DDIT4
DNAJB12
LRRC20
SLC29A3
CSGALNACT2
H2AFY2
RUFY2
FAM21B
CCAR1
OGDHL
CISD1
DNAJC12
ASAH2
SAR1A
ZMIZ1
WDFY4
ARHGAP22
MYOZ1
CDH23
PBLD
NPFFR1
C10orf54
PCDH15
DDX50
OR13A1
SYNPO2L
BICC1
FAM213A
HKDC1
TET1
TSPAN14
SYT15
RASSF4
C10orf11
ARID5B
C10orf58
DYDC2
PHYHIPL
PLA2G12B
MYPN
LOC84856
ZNF503
AIFM2
ADO
LOC84989
MCU
ZFAND4
C10orf71
CHCHD1
ZMYND17
TTC18
ZNF488
COMTD1
AGAP4
ANAPC16
ADAMTS14
SAMD8
FRMPD2
DYDC1
EIF5AL1
HSD17B7P2
USP54
FAM170B
C10orf128
FUT11
OIT3
ANTXRL
VSTM4
LOC219347
PLAC9
C10orf107
TMEM26
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
C10orf27
ATOH7
SLC16A9
FAM13C
MARCH8
C10orf25
TMEM72-AS1
ZNF485
RASGEF1A
REEP3
JMJD1C
ZNF503-AS1
IPMK
FAM21C
SGMS1
PGBD3
C10orf53
C10orf40
LOC283033
LOC283050
SEPT7L
FAM149B1
FLJ31813
LOC338579
DUPD1
LRRTM3
FAM21A
SH2D4B
LOC399744
ACTR3BP5
LOC399753
BMS1P5
C10orf105
AGAP6
ZNF32-AS3
C10orf55
FAM35B
C10orf103
C10orf136
FAM35B2
LOC439990
LOC441666
LRRC18
LOC642361
AGAP9
ZNF487P
LOC642826
TMEM72
LOC643650
FAM25C
DRGX
LOC650623
PTPN20A
ANXA8
AGAP7
ASAH2B
SFTPA1
SNORD98
MIR605
BMS1P1
ANXA8L1
AGAP8
LOC728407
LOC728640
LOC728643
FRMPD2P1
LOC728978
AGAP5
BMS1P4
SFTPA2
LOC100128292
ZNF37BP
ZNF503-AS2
FAM25B
LOC100132987
FAM25G
LOC100133308
TIMM23
LOC100288974
MIR1296
MIR1256
MIR4294
MIR3156-1
MTRNR2L5
MIR3924
LOC100506733
LOC100506835
LOC100506939
M1
LOC100507331
MIR4676

Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
HOOK3
hsa-mir-486
ADRB3
ANK1
CEBPD
CHRNB3
ADAM3A
EIF4EBP1
FNTA
ADAM2
IKBKB
IDO1
MCM4
PLAT
POLB
PRKDC
SFRP1
SLC20A2
SNAI2
STAR
TACC1
UBE2V2
VDAC3
KAT6A
ADAM18
ADAM9
CHRNA6
ASH2L
BAG4
AP3M2
ERLIN2
PROSC
DDHD2
KIAA0146
GPR124
DKK4
LSM1
GOLGA7
THAP1
BRF2
C8orf4
PLEKHA2
EFCAB1
ZMAT4
ZNF703
RAB11FIP1
RNF170
TM2D2
SGK196
GINS4
PPAPDC1B
C8orf40
GOT1L1
AGPAT6
LETM2
HGSNAT
NKX6-3
KCNU1
IDO2
HTRA4
ADAM32
ADAM5P
RNF5P1
POTEA
C8orf86
C8orf22
LINC00293
MIR486
LOC728024
LOC100130964
LOC100287846
MIR4469

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.2.

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

Genes
CBLB
TFG
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
ADCY5
ADPRH
ALCAM
ATP6V1A
CASR
CD80
CD86
CD47
COL8A1
CPOX
CSTA
DRD3
EPHA3
GAP43
GBE1
GOLGB1
GPR15
GSK3B
GTF2E1
HCLS1
HGD
HTR1F
ITGB5
KPNA1
LSAMP
CD200
MYLK
NDUFB4
POU1F1
PROS1
RPL24
SLC15A2
UPK1B
UMPS
ZNF80
CGGBP1
B4GALT4
NR1I2
KALRN
STXBP5L
GUCA1C
IQCB1
DZIP3
TOMM70A
COX17
CD96
ST3GAL6
POLQ
PDIA5
HHLA2
FSTL1
FILIP1L
MYH15
C3orf17
ABI3BP
PVRL3
CHMP2B
ZBTB20
OR5K1
OR5H1
FAM162A
SEC22A
ZBTB11
MORC1
GTPBP8
TAGLN3
TRAT1
IMPG2
TIMMDC1
PLA1A
FBXO40
SEMA5B
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
RG9MTD1
SLC35A5
TMEM45A
IFT57
DPPA4
TMEM39A
ZNF654
ABHD10
TBC1D23
WDR52
EAF2
CLDND1
MUC13
NIT2
POGLUT1
BBX
PCNP
SENP7
HEG1
ARHGAP31
KIAA1407
KIAA1524
NSUN3
POPDC2
NFKBIZ
ATG3
CCDC14
OR5H6
OR5H2
ZBED2
CEP97
HSPBAP1
C3orf52
QTRTD1
NAA50
OR5AC2
PARP9
ARL6
C3orf26
RETNLB
CCDC54
MINA
GPR128
DIRC2
C3orf15
PHLDB2
BOC
FAM55C
LRRC58
CCDC58
ZPLD1
CD200R1
DCBLD2
FAM172BP
DTX3L
LOC151658
DPPA2
CCDC80
BTLA
SPICE1
LOC152225
IGSF11
C3orf30
PARP15
GPR156
ARL13B
DHFRL1
GABRR3
PTPLB
TIGIT
KIAA2018
CADM2
ZDHHC23
LOC255025
PLCXD2
GCET2
LSAMP-AS3
LOC285205
EPHA6
C3orf38
RABL3
SLC9A10
LOC285359
ILDR1
LOC344595
TMPRSS7
CD200R1L
LNP1
VGLL3
FLJ22763
FLJ25363
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIR198
STX19
LOC440970
ARGFX
TMEM30C
LINC00488
MIR548A3
MIR567
MIR568
LOC100009676
LOC100129550
ZBTB20-AS1
LOC100302640
MIR548G
MIR3921
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
MIR4795
MIR4796
MIR4446

Arm-level results

Table 3. Get Full Table Arm-level significance table - 25 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.02 | -3.04 | 1 | 0.08 | 3.11 | 0.00364
1q | 1955 | 0.08 | 2.44 | 0.026 | 0.06 | 0.309 | 1
2p | 924 | 0.09 | 2.2 | 0.0446 | 0.03 | -3.3 | 1
2q | 1556 | 0.11 | 4.16 | 6.86e-05 | 0.03 | -2.48 | 1
3p | 1062 | 0.02 | -1.98 | 1 | 0.79 | 63.5 | 0
3q | 1139 | 0.06 | -0.322 | 1 | 0.22 | 13.1 | 0
4p | 489 | 0.02 | -4.5 | 1 | 0.07 | -0.71 | 1
4q | 1049 | 0.02 | -4.06 | 1 | 0.06 | -0.229 | 1
5p | 270 | 0.31 | 19.2 | 0 | 0.00 | -5.15 | 1
5q | 1427 | 0.47 | 37.7 | 0 | 0.01 | -3.36 | 1
6p | 1173 | 0.01 | -4.5 | 1 | 0.12 | 5.21 | 4.64e-07
6q | 839 | 0.01 | -4.67 | 1 | 0.20 | 10.8 | 0
7p | 641 | 0.26 | 15.5 | 0 | 0.00 | -5.15 | 1
7q | 1277 | 0.26 | 17.6 | 0 | 0.01 | -4.55 | 1
8p | 580 | 0.04 | -2.42 | 1 | 0.22 | 12.3 | 0
8q | 859 | 0.08 | 0.75 | 0.631 | 0.10 | 2.62 | 0.0141
9p | 422 | 0.02 | -4.09 | 1 | 0.17 | 8.16 | 6.19e-16
9q | 1113 | 0.02 | -3.96 | 1 | 0.17 | 9.53 | 0
10p | 409 | 0.01 | -5.24 | 1 | 0.07 | -0.335 | 1
10q | 1268 | 0.01 | -4.86 | 1 | 0.11 | 4.42 | 2.13e-05
11p | 862 | 0.03 | -3.19 | 1 | 0.01 | -5.24 | 1
11q | 1515 | 0.03 | -2.7 | 1 | 0.02 | -3.99 | 1
12p | 575 | 0.15 | 6.25 | 1.37e-09 | 0.01 | -5.21 | 1
12q | 1447 | 0.15 | 8.35 | 0 | 0.01 | -4.4 | 1
13q | 654 | 0.04 | -3.08 | 1 | 0.07 | 0.0956 | 1
14q | 1341 | 0.02 | -3.6 | 1 | 0.32 | 23.7 | 0
15q | 1355 | 0.03 | -3.02 | 1 | 0.02 | -3.56 | 1
16p | 872 | 0.14 | 5.7 | 3.33e-08 | 0.00 | -5.25 | 1
16q | 702 | 0.12 | 4.25 | 5.32e-05 | 0.01 | -4.66 | 1
17p | 683 | 0.04 | -2.94 | 1 | 0.06 | -0.922 | 1
17q | 1592 | 0.04 | -1.4 | 1 | 0.03 | -2.7 | 1
18p | 143 | 0.04 | -3.42 | 1 | 0.10 | 1.2 | 0.346
18q | 446 | 0.04 | -3.11 | 1 | 0.11 | 2.63 | 0.0141
19p | 995 | 0.05 | -1.61 | 1 | 0.01 | -4.9 | 1
19q | 1709 | 0.06 | -0.0242 | 1 | 0.00 | -4.92 | 1
20p | 355 | 0.10 | 2.17 | 0.0446 | 0.01 | -4.98 | 1
20q | 753 | 0.10 | 2.71 | 0.0132 | 0.01 | -5.07 | 1
21q | 509 | 0.07 | -0.234 | 1 | 0.07 | -0.563 | 1
22q | 921 | 0.05 | -1.8 | 1 | 0.02 | -3.87 | 1

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

- 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/KIRC/1551486/2.GDAC_MergeDataFiles.Finished/KIRC.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 = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 489 Input Tumor Samples.

Tumor Sample Names
TCGA-A3-3306-01A-01D-0858-01
TCGA-A3-3307-01A-01D-0858-01
TCGA-A3-3308-01A-02D-1322-01
TCGA-A3-3311-01A-02D-1322-01
TCGA-A3-3313-01A-02D-1322-01
TCGA-A3-3316-01A-01D-0858-01
TCGA-A3-3317-01A-02D-1322-01
TCGA-A3-3319-01A-02D-1322-01
TCGA-A3-3320-01A-02D-1322-01
TCGA-A3-3322-01A-02D-1322-01

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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