SNP6 Copy number analysis (GISTIC2)
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1D21W7R
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1D21W7R
Overview
Introduction

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

Summary

There were 197 tumor samples used in this analysis: 17 significant arm-level results, 6 significant focal amplifications, and 22 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 - 6 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
--- | --- | --- | --- | ---
19p13.2 | 4.3413e-17 | 4.3413e-17 | chr19:7296453-7397014 | 0 [INSR]
2q32.1 | 0.0040865 | 0.0040865 | chr2:186297358-186918006 | 1
17q25.2 | 0.024702 | 0.024702 | chr17:64284385-81195210 | 273
7q22.1 | 0.085526 | 0.085526 | chr7:100418577-103862258 | 55
3q22.3 | 0.11418 | 0.11418 | chr3:137896121-138927964 | 13
2p23.2 | 0.22114 | 0.22114 | chr2:27910707-28747666 | 10

Genes in Wide Peak

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

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

Genes
FSIP2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.2.

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

Genes
PRKAR1A
ASPSCR1
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
AANAT
ACOX1
ACTG1
BIRC5
ARHGDIA
CACNG1
CD7
CDK3
CSNK1D
SLC25A10
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
MAFG
NPTX1
P4HB
PDE6G
PRKCA
MAP2K6
PRPSAP1
PSMD12
PYCR1
PCYT2
RAC3
RFNG
RPL38
MRPL12
SEC14L1
SECTM1
SRSF2
SGSH
SUMO2
SOX9
SRP68
SSTR2
TBCD
TIMP2
TK1
CBX4
DNAH17
GALR2
SPHK1
SOCS3
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
AATK
KIAA0195
EIF4A3
HELZ
ALYREF
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
ST6GALNAC2
SEPT9
CD300C
RAB40B
CD300A
TMC6
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NOL11
NAT9
PITPNC1
NARF
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
HN1
DCXR
AMZ2
ANAPC11
SIRT7
SDK2
FAM20A
TMEM104
C17orf80
CCDC40
WIPI1
NPLOC4
ST6GALNAC1
GPRC5C
WDR45L
CBX8
MIF4GD
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
SLC25A19
UBE2O
DUS1L
FN3K
DNAI2
ENGASE
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
C17orf70
TSPAN10
QRICH2
CBX2
FAM104A
MGC16275
FBF1
UNK
TRIM47
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
METTL23
SLC38A10
USH1G
CD300LB
KIF19
TBC1D16
AFMID
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
NOTUM
TMC8
STRA13
LRRC45
SLC39A11
TRIM65
UNC13D
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
SLC26A11
ENDOV
C17orf89
LINC00482
TMEM105
METRNL
RAB37
ENPP7
C17orf90
CCDC137
ARL16
CD300E
OTOP3
FAM195B
GPR142
ZACN
BTBD17
AATK-AS1
FLJ43681
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
MXRA7
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LINC00338
SCARNA16
SNORD1A
SNORD1B
SNORD1C
MIR634
MIR635
MIR636
MIR657
PRCD
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR3186
LOC100499466
LOC100499467
MIR3678
MIR3615
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4738
MIR4740
MIR4524A
MIR4730
LOC100653515

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
hsa-mir-548o
hsa-mir-4285
ACHE
AP1S1
CUX1
EPHB4
ORC5
SERPINE1
POLR2J
RELN
PSMC2
TRIP6
VGF
PLOD3
PMPCB
MUC12
RASA4
LRRC17
ZNHIT1
SH2B2
CLDN15
DNAJC2
FIS1
SRRT
ALKBH4
SLC12A9
RABL5
PRKRIP1
ORAI2
TRIM56
ARMC10
MYL10
EMID2
MUC17
LRWD1
FAM185A
FBXL13
NAPEPLD
POLR2J2
MOGAT3
DPY19L2P2
NAT16
SLC26A5
UFSP1
SPDYE2
POLR2J3
SPDYE6
RPL19P12
UPK3BL
LOC100289561
SPDYE2L
MIR4285
MIR4653
MIR4467
LOC100630923

Genes in Wide Peak

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

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

Genes
FOXL2
PIK3CB
MRAS
ARMC8
FAIM
BPESC1
CEP70
ESYT3
NME9
PRR23B
PRR23C
C3orf72
PRR23A

Genes in Wide Peak

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

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

Genes
hsa-mir-4263
FOSL2
MRPL33
BRE
SLC4A1AP
RBKS
PLB1
LOC100302650
MIR4263
LOC100505716

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 - 22 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
--- | --- | --- | --- | ---
9p21.3 | 5.0433e-18 | 5.0433e-18 | chr9:21865498-22448737 | 4
1p36.31 | 7.3578e-06 | 7.3578e-06 | chr1:1-15399945 | 238
2q37.3 | 8.0995e-05 | 8.0995e-05 | chr2:217491485-243199373 | 266
3p22.1 | 0.012052 | 0.012052 | chr3:41280645-42218893 | 1
19q13.42 | 0.015346 | 0.015959 | chr19:41244888-59128983 | 739
11q24.2 | 0.0016333 | 0.029516 | chr11:102916368-135006516 | 293
5q35.2 | 0.037718 | 0.048961 | chr5:170843678-180915260 | 139
14q11.2 | 0.022099 | 0.063167 | chr14:1-35185588 | 189
16q24.1 | 0.079877 | 0.084188 | chr16:21350204-90354753 | 628
6q22.31 | 0.085972 | 0.088899 | chr6:123955968-125232805 | 1
15q15.2 | 0.11392 | 0.1108 | chr15:1-56540308 | 405
Xq28 | 0.1103 | 0.1108 | chrX:151843350-152761709 | 21
11q22.3 | 0.0030222 | 0.12376 | chr11:81598795-135006516 | 411
19p13.3 | 0.12825 | 0.12376 | chr19:1033227-7112264 | 193
5p14.2 | 0.14701 | 0.14311 | chr5:1-31329532 | 101
6q21 | 0.16414 | 0.16031 | chr6:44235214-171115067 | 602
14q32.2 | 0.036549 | 0.16031 | chr14:62033251-107349540 | 455
Xp11.22 | 0.16268 | 0.16031 | chrX:48888917-56261603 | 114
10p11.21 | 0.16903 | 0.16903 | chr10:34059131-35128523 | 1
21q22.3 | 0.18915 | 0.18149 | chr21:46230687-46306160 | 1
4q34.3 | 0.20998 | 0.20949 | chr4:123643386-191154276 | 255
5q15 | 0.18254 | 0.24514 | chr5:1-180915260 | 1050

Genes in Wide Peak

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

Table S6. Genes in bold are cancer genes as defined by The Sanger Institute: 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 1p36.31.

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

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
RERE
CA6
TNFRSF8
CDK11B
CLCN6
CORT
DFFA
DFFB
DVL1
MEGF6
ENO1
MTOR
GABRD
GNB1
ZBTB48
TNFRSF9
MTHFR
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLOD1
EXOSC10
PRKCZ
SCNN1D
SKI
SLC2A5
SRM
TNFRSF1B
TP73
TNFRSF4
PRDM2
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
MFN2
ANGPTL7
UBE4B
MAD2L2
PDPN
MASP2
UTS2
RER1
PARK7
ACOT7
CLSTN1
KIF1B
KAZN
CAMTA1
TARDBP
ICMT
CHD5
NOC2L
FBXO2
FBXO6
OR4F3
ARHGEF16
SSU72
UBIAD1
WRAP73
SLC45A1
SDF4
ERRFI1
MXRA8
HES2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
VPS13D
ATAD3A
PANK4
DNAJC11
AJAP1
CTNNBIP1
AGTRAP
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
HES4
MIIP
NMNAT1
VWA1
PRAMEF1
PRAMEF2
NADK
MMEL1
OR4F5
NOL9
LINC00115
MORN1
GPR157
SPSB1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
SLC25A33
LZIC
C1orf170
KIAA1751
KIAA2013
THAP3
C1orf158
FBXO44
LOC115110
RBP7
ACAP3
UBE2J2
LRRC38
AADACL3
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
SLC2A7
CALML6
TMEM201
C1orf86
ATAD3C
LOC254099
TTLL10
NPHP4
FAM41C
LOC284661
C1orf174
KLHL17
TMEM240
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
C1orf187
AGRN
APITD1
GPR153
FAM132A
HES5
LOC388588
RNF207
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PRAMEF4
PRAMEF13
RNF223
PRAMEF3
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC649330
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
PRAMEF14
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
NPPA-AS1
MIR4251
MIR4252
ENO1-AS1
APITD1-CORT
MIR4689
MIR4632
MIR4417

Genes in Wide Peak

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

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

Genes
ACSL3
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
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
CNPPD1
STK36
GMPPA
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
C2orf83
MFF
CXCR7
RNPEPL1
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

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

Genes
ULK4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.42.

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

Genes
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
A1BG
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
MEGF8
EMP3
ERCC1
ERF
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
LIPE
BCAM
MYBPC2
CEACAM6
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
RPS5
RPS9
RPS11
RPS19
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
UBE2M
ARHGEF1
CYTH2
ZNF235
ZNF264
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
TOMM40
ZNF211
RABAC1
TRAPPC2P1
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
CYP2G1P
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
CYP2S1
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
RAB4B
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
ELSPBP1
LIN7B
HIF3A
ZNF574
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
IRGQ
ZNF428
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
CADM4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
ZNF233
LILRA5
B3GNT8
IGFL1
ZNF773
LOC386758
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
LOC390940
ZNF805
ZNF321P
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
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
TMEM91
LOC646508
SBK2
LOC646862
PSG10P
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
SGK110
BSPH1
LOC100131691
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
ERVV-2
LOC100287177
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.2.

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

Genes
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100128239
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
NSD1
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
BNIP1
CANX
CLTB
NKX2-5
DBN1
DRD1
DUSP1
F12
FGFR4
FLT4
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
SLC34A1
SNCB
STK10
ZNF354A
STC2
FGF18
SQSTM1
ATP6V0E1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
FBXW11
ZNF346
TSPAN17
OR4F3
PRELID1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
CNOT6
GMCL1P1
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
AGXT2L2
UNC5A
TRIM41
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
ZNF354B
C5orf47
OR2Y1
C5orf41
BTNL9
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
OR2V2
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
C5orf25
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
CBY3
FAM153C
SNORA74B
LOC728554
AACSP1
LOC729678
OR4F29
LOC100132062
LOC100132287
LOC100133331
LOC100268168
MIR1229
MIR4281
LOC100507387
MIR4634
MIR4638
LOC100859930

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GPR33
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
PNP
NRL
OXA1L
PCK2
PRKD1
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
AKAP6
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
AP4S1
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
ARHGEF40
EAPP
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
SNX6
C14orf93
ABHD4
NPAS3
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
JPH4
RNASE7
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
EGLN3
C14orf126
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
C14orf21
SPTSSA
ADCY4
LOC283624
TSSK4
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
CBLN3
SNORD9
MIR624
DHRS4L1
SNORD126
MIR208B
MIR4307
LOC100505967
LOC100506071
NEDD8-MDP1
BCL2L2-PABPN1
MIR548AI
MIR4707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.1.

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

Genes
CBFA2T3
CBFB
CDH1
CDH11
CYLD
FANCA
FUS
MAF
HERPUD1
IL21R
PALB2
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
hsa-mir-762
hsa-mir-548w
AARS
ADCY7
AP1G1
AFG3L1P
AGRP
ALDOA
AMFR
AQP8
APRT
ZFHX3
ATP2A1
BBS2
C16orf3
CA5A
CA7
CALB2
CBLN1
CD19
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CDR2
CES1
CETP
CLN3
CNGB1
COX4I1
COX6A2
CSNK2A2
CTF1
CTRB1
CTRL
CYBA
DHODH
NQO1
SEPT1
DYNC1LI2
DPEP1
E2F4
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
GNAO1
GOT2
GTF3C1
HAS3
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
IL4R
ITGAD
ITGAL
ITGAM
ITGAX
KARS
KIFC3
KIF22
LCAT
MAZ
MC1R
CHST6
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
MVD
NDUFAB1
NFATC3
CHMP1A
PHKB
PHKG2
PLCG2
PLK1
POLR2C
PPP4C
PRKCB
MAPK3
PRSS8
PSKH1
PSMB10
PSMD7
RBBP6
RBL2
RPL13
RRAD
SALL1
SCNN1B
SCNN1G
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC5A2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SPG7
SPN
SULT1A2
STX4
SULT1A1
SULT1A3
TAT
TBX6
TERF2
TGFB1I1
TK2
TUFM
UQCRC2
ZNF19
ZNF23
GAN
SLC7A5
DOC2A
HIRIP3
CDK10
EIF3C
TRADD
MBTPS1
CES2
NAE1
NOL3
TAF1C
SLC7A6
USP10
ATP6V0D1
BCL7C
GPR56
TAOK2
BCAR1
C16orf7
N4BP1
NUP93
ZNF646
SETD1A
KIAA0513
PIEZO1
DHX38
IST1
RNF40
ATP2C2
HS3ST4
HS3ST2
MVP
CLEC3A
CHST4
MPHOSPH6
NUTF2
IGSF6
IRX5
DNAJA2
BCKDK
KATNB1
ZNF267
COX4NB
CACNG3
TUBB3
CD2BP2
CDIPT
CFDP1
ERN2
CTCF
NFAT5
SRCAP
NUDT21
WWP2
PRDM7
CORO1A
DDX19B
ATXN2L
GABARAPL2
MON1B
SEPHS2
TCF25
CNOT1
PHLPP2
GGA2
ZNF423
NPIPL3
ZCCHC14
KIAA0182
XPO6
KIAA0556
ATMIN
RPGRIP1L
ZNF629
COTL1
MLYCD
SF3B3
QPRT
CES3
ADAT1
CHST5
ARL2BP
ORC6
EDC4
PLA2G15
TP53TG3
COG4
PLEKHG4
SH2B1
TBC1D10B
DKFZP434H168
LRRC29
SEZ6L2
NUPR1
LAT
CPNE7
VPS4A
IL17C
TOX3
TNRC6A
NOB1
CCDC113
TMEM208
C16orf80
PYCARD
FHOD1
BRD7
ANKRD11
ZDHHC1
MYLPF
EEF2K
OSGIN1
PARD6A
PLLP
METTL9
CKLF
AHSP
ZNF771
NIP7
LCMT1
FAM96B
GINS2
TPPP3
TRAPPC2L
CES1P1
WWOX
BCMO1
TERF2IP
PRMT7
NECAB2
FBXL19
KLHDC4
HYDIN
DEF8
DUS2L
CHTF8
LPCAT2
TXNL4B
BANP
HEATR3
PDPR
ARHGAP17
RFWD3
SLC38A7
OGFOD1
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
ZDHHC7
VAC14
DOK4
POLR3E
VPS35
FTSJD1
DDX28
TSNAXIP1
CENPN
APOBR
UBFD1
C16orf61
COQ9
CIAPIN1
THAP11
JPH3
USP31
PDP2
ZNF319
RANBP10
VAT1L
KIAA1609
WFDC1
CHP2
NOD2
PDF
DPEP2
DPEP3
PAPD5
FBRS
AKTIP
C16orf58
MTHFSD
GINS3
NDRG4
ACD
ZNF747
PRR14
VKORC1
DBNDD1
SLX1B
FTO
DCTPP1
FA2H
GDPD3
IRX6
IRX3
C16orf53
FAM65A
TMEM231
TMCO7
C16orf57
ZNF768
WDR59
ZNF668
ELMO3
KLHL36
FBXO31
ARMC5
SHCBP1
JMJD5
RABEP2
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
HSD3B7
CYB5B
CMIP
ITFG1
GFOD2
CDT1
MAP1LC3B
NETO2
SLC7A5P1
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
YPEL3
FAM57B
LONP2
SPNS1
C16orf48
SLC7A6OS
KAT8
NLRC5
CCDC135
CAPNS2
COG8
SPIRE2
DCTN5
MT4
ZNF469
GPT2
B3GNT9
NFATC2IP
CIRH1A
ZNRF1
ABCC11
NKD1
CNTNAP4
RSPRY1
C16orf93
MYLK3
MARVELD3
COG7
MTSS1L
ZNF764
CENPBD1
ZNF276
CCDC102A
KCNG4
ORAI3
SDR42E1
ABCC12
PRRT2
STX1B
CCDC101
CMTM1
PKD1L2
ZNF689
SLC5A11
RNF166
EXOSC6
C16orf46
DNAAF1
NRN1L
CMTM3
C16orf78
SPATA2L
C16orf55
ANKRD26P1
ZC3H18
CDYL2
ZNF720
TMEM219
EARS2
SNX20
TMEM170A
SLC38A8
VWA3A
OTOA
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
C16orf92
GSG1L
SLC22A31
IL34
TMED6
LOC146481
FLJ30679
LOC146513
ZNF785
ZNF688
PRSS36
ZFPM1
ADAD2
C16orf82
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
NSMCE1
ZNF48
CPNE2
GPR114
PRSS54
CES5A
GPR97
IL27
KCTD13
ASPHD1
PDZD9
CNEP1R1
PYDC1
CCDC79
CES4A
EXOC3L1
LOC283856
LINC00304
LOC283867
LOC283888
C16orf54
INO80E
HTA
LOC283914
LOC283922
NUDT7
FBXL19-AS1
ZNF843
PDXDC2P
CLEC18C
MT1DP
SNAI3
PRSS53
FAM92B
ZKSCAN2
ATXN1L
PKD1L3
CLEC18A
CTU2
TEPP
SLC6A10P
SLC7A5P2
SBK1
LOC388242
C16orf87
LOC388276
C16orf86
LOC390705
CES1P2
PABPN1L
FLJ21408
FLJ26245
LOC400548
LOC400550
LOC400558
C16orf74
MIR138-2
MIR140
SNX29P2
LOC440354
LOC440356
CSDAP1
HERC2P4
CTRB2
MIR328
SULT1A4
TRIM72
CLEC18B
SLX1A
BOLA2
LOC554206
LOC595101
SNORD68
UBE2MP1
LOC606724
LOC613037
LOC613038
LOC641298
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
LINC00273
KIAA0895L
RRN3P2
TP53TG3C
LOC653786
ZG16
BOLA2B
SNORA30
SNORA46
SNORA50
SNORD71
SNORD111
MIR548D2
LOC727710
EIF3CL
LOC729264
TP53TG3B
LOC729513
RRN3P1
C16orf52
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130700
LOC100130894
SYCE1L
RRN3P3
LOC100132247
KIAA0664L3
LOC100190986
LOC100271836
LOC100287036
LOC100289092
MIR1538
MIR1972-1
MIR1910
MIR762
SNORA70D
MIR3182
MIR1972-2
MIR3935
MIR548AA2
LOC100505619
LOC100505865
LOC100506083
LOC100506172
C16orf95
LOC100506655
LOC100507577
SLX1A-SULT1A3
SLX1B-SULT1A4
CKLF-CMTM1
MIR4720
MIR4722
MIR4719
MIR4519
MIR4721
MIR548AE2
MIR4518
MIR4517
SNX29P1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
NKAIN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.2.

Table S16. Genes in bold are cancer genes as defined by The Sanger Institute: 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
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
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
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
MIR628
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq28.

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

Genes
CETN2
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
ZNF185
ZNF275
TREX2
PNMA3
NSDHL
HAUS7
PNMA6A
PNMA5
ZFP92
CSAG1
MAGEA2B
CSAG3
CSAG2
PNMA6C
PNMA6D

Genes in Wide Peak

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

Table S18. Genes in bold are cancer genes as defined by The Sanger Institute: 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
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
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
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
KIAA1377
ARHGAP20
USP28
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TMEM135
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
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
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
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 19p13.3.

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

Genes
GNA11
MLLT1
SH3GL1
STK11
TCF3
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
AES
AMH
ATP5D
C3
CAPS
CD70
CIRBP
CSNK1G2
DAPK3
EEF2
EFNA2
EMR1
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
GTF2F1
MATK
GADD45B
NFIC
NRTN
OAZ1
POLR2E
MAP2K2
PSPN
PTPRS
RFX2
RPS15
SAFB
SGTA
TBXA2R
THOP1
TLE2
VAV1
SF3A2
CLPP
RANBP3
KHSRP
S1PR4
TNFSF14
TNFSF9
AP3D1
TRIP10
LONP1
APBA3
SAFB2
CHAF1A
SH2D3A
EBI3
PLIN3
APC2
ABCA7
HMG20B
TUBB4A
SEMA6B
UQCR11
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
RPL36
TIMM13
DAZAP1
SNORD37
TJP3
ITGB1BP3
UHRF1
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
CCDC94
C19orf10
NCLN
GPR108
SPPL2B
DUS3L
SHD
REXO1
ZNF77
C19orf29
CELF5
SLC25A23
FSD1
ZNF557
TLE6
DENND1C
ZNF556
UBXN6
ACSBG2
FAM108A1
DOHH
KLF16
ALKBH7
DOT1L
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
CRB3
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
MRPL54
LRG1
ACER1
C19orf70
MBD3L2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
PLK5
TICAM1
CIRBP-AS1
ZNRF4
C19orf25
ATP8B3
DIRAS1
ZNF555
PRR22
ANKRD24
C19orf26
CSNK1G2-AS1
PLAC2
TMEM146
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
EMR4P
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
ONECUT3
MEX3D
VMAC
C19orf29-AS1
MIR7-3
PLIN5
FLJ25758
LINGO3
ARRDC5
MBD3L4
MBD3L3
MIR637
PLIN4
C19orf71
LOC100131094
LOC100288123
MIR1909
MIR1227
MIR4321
MIR3940
MIR4747
MIR4746

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p14.2.

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

Genes
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
CDH6
CDH9
CDH10
CDH12
CDH18
CTNND2
DAP
DNAH5
MTRR
MYO10
NDUFS6
PMCHL1
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
BASP1
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
PP7080
IRX4
TAS2R1
FAM134B
FAM105A
NSUN2
CEP72
ANKH
PRDM9
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285577
LOC285692
LOC285696
SLC6A19
LOC340094
LOC340107
SLC6A18
LRRC14B
FLJ33360
LOC401177
TAG
MARCH11
LOC442132
LOC643401
ANKRD33B
GUSBP1
SDHAP3
LOC728613
LOC729506
LOC729862
SNORD123
LOC100130744
MIR4277
MIR4278
LOC100505738
LOC100505806
LOC100506688
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q21.

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
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
hsa-mir-133b
hsa-mir-586
ACAT2
CRISP1
AIM1
AMD1
ARG1
BAI3
BCKDHB
BMP5
DST
RUNX2
CCNC
CDC5L
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GCLC
GPR6
GPR31
GRIK2
GRM1
GSTA1
GSTA2
GSTA3
GSTA4
HCRTR2
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IL17A
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MCM3
ME1
MAP3K4
MAP3K5
MEP1A
MUT
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGK2
PGM3
PKHD1
PLAGL1
PLG
PLN
POU3F2
PREP
PRIM2
PKIB
PSMB1
PTPRK
REV3L
RHAG
RNY4
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
TFAP2B
THBS2
NR2E1
TPBG
TPD52L1
CRISP2
TSPYL1
TTK
UTRN
EZR
VIP
PTP4A1
PLA2G7
EPM2A
STX7
SUPT3H
PEX3
GCM1
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
SLC25A27
TBPL1
BAG2
WTAP
AKAP12
TRAM2
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
RCAN2
CRISP3
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
PHF3
HEY2
HEBP2
ORC3
CD2AP
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
TIAM2
FBXL4
C6orf123
FBXO9
FBXO5
SLC17A5
RGS17
SNORD50A
PDE7B
FILIP1
TNFRSF21
SESN1
TINAG
DLL1
OSTM1
TMEM14A
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CYP39A1
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
LGSN
BRP44L
HECA
RAB23
COQ3
CLIC5
IL20RA
UNC93A
HMGCLL1
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
LRRC1
PHF10
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
C6orf70
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
AARS2
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
C6orf115
RRAGD
ENPP5
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
C6orf164
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
COL21A1
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
TFAP2D
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
PAQR8
SLC22A16
C6orf7
UBE2CBP
MLIP
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
IL17F
FAM54A
SFT2D1
EFHC1
KLHL32
TMEM200A
MB21D1
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SRSF12
C6orf141
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
TCTE1
KHDRBS2
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
GPR111
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
C6orf191
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
GPR110
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GUSBP4
GJB7
HMGA1P7
SNHG5
SUMO4
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
GLYATL3
GFRAL
LIN28B
SAMD5
IYD
KLHL31
DKFZp451B082
TCP10L2
LINC00242
DEFB133
GTF2H5
MIR206
MIR30A
MIR30C2
TMEM151B
OOEP
FAM26F
FLJ46906
LOC441177
PTCHD4
MCART3P
GSTM2P1
RFPL4B
MIR133B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
RPS16P5
MLLT4-AS1
SNORA20
SNORA29
SNORD50B
MIR548B
MIR586
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
LOC730101
GSTA7P
HGC6.3
LOC100128176
BET3L
KHDC1L
LOC100129518
LOC100130890
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100287718
LOC100288198
LOC100289495
NHEG1
MIR1913
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100506804
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
MIR4642
MIR4644
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.2.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5C
PPP2R5E
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
SEL1L
SRSF5
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
ATP6V1D
EVL
C14orf129
CINP
ASB2
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
COX8C
ASPG
RAB15
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.22.

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

Genes
SSX2
KDM5C
hsa-let-7f-2
hsa-mir-502
ALAS2
CACNA1F
CLCN5
FGD1
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
HSD17B10
PRICKLE3
PFKFB1
PLP2
SYP
TRO
SMC1A
PAGE1
AKAP4
BMP15
MAGED1
XAGE2
XAGE1D
PAGE4
HUWE1
RRAGB
MAGED2
WDR45
PRAF2
IQSEC2
PHF8
GSPT2
GAGE12I
GAGE2E
GPKOW
APEX2
CCDC22
MAGEH1
FAM156A
FOXP3
GPR173
GNL3L
FAM120C
NUDT11
SHROOM4
TSPYL2
WNK3
MAGIX
MAGED4B
CCNB3
PPP1R3F
CCDC120
TSR2
FAM104B
PAGE5
DGKK
FOXR2
PAGE3
LOC158572
RIBC1
USP51
XAGE3
XAGE5
NUDT10
PAGE2
SSX7
SSX8
ITIH6
USP27X
CENPVL1
PAGE2B
MIRLET7F2
MIR188
MIR98
LOC441495
SPANXN5
MIR362
MIR500A
MIR501
MIR502
GAGE10
GAGE2B
GAGE13
GAGE12G
XAGE1C
XAGE1E
XAGE1A
XAGE1B
SNORA11
MIR532
MIR660
SSX2B
FAM156B
MAGED4
XAGE2B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
GAGE12F
GAGE8
SNORA11D
SNORA11E
GAGE12D
MIR500B
MTRNR2L10
MIR4536-1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

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

Genes
PARD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
PTTG1IP

Genes in Wide Peak

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

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
AGA
SLC25A4
ANXA2P1
CASP3
LRBA
CLGN
CLCN3
CPE
CTSO
DCTD
EDNRA
ELF2
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGF2
FGG
FRG1
GAB1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
HMGB2
HPGD
HSP90AA4P
IL15
ING2
IRF2
KLKB1
SMAD1
MGST2
NR3C2
MTNR1A
NDUFC1
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
POU4F2
PPID
ABCE1
RPS3A
MSMO1
SFRP2
TDO2
TLL1
TLR2
TLR3
UCP1
VEGFC
GLRA3
SMARCA5
SORBS2
SAP30
INPP4B
SNORD73A
LRAT
HAND2
RAPGEF2
MFAP3L
SPRY1
ANAPC10
PGRMC2
MAB21L2
PLK4
ADAM29
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
PALLD
TBC1D9
KIAA0922
TRIM2
ANP32C
SLC7A11
CCRN4L
FAM149A
FBXO8
DUX2
INTU
ARFIP1
PDLIM3
ZNF330
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
PCDH18
DKFZP434I0714
OTUD4
DCHS2
C4orf27
MARCH1
LARP1B
NEIL3
TMEM144
C4orf43
UFSP2
MAML3
DDX60
CDKN2AIP
ODZ3
TMEM184C
LRP2BP
PDGFC
FSTL5
STOX2
ANKRD50
RNF150
PCDH10
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
SCOC
TRAPPC11
HHIP
FAT4
ARHGAP10
MLF1IP
NBLA00301
MAP9
PHF17
WWC2
NAA15
C4orf29
CEP44
SETD7
SLC25A31
RAB33B
SNX25
TTC29
MND1
SLC10A7
TKTL2
USP38
C4orf49
CBR4
FHDC1
MGC45800
PRMT10
DDX60L
NAF1
WDR17
SCLT1
C4orf33
PABPC4L
ZFP42
SPATA4
ENPP6
ASB5
ZNF827
SH3D19
C4orf38
C4orf39
C4orf45
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
ELMOD2
CCDC110
MFSD8
LOC285419
CYP4V2
LOC285441
LOC285501
RNF175
LOC339975
TRIML1
LOC340017
PRSS48
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
LOC641364
LOC641365
SLED1
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
CETN4P
FAM160A1
LOC731424
LOC100129858
CLDN24
LOC100288255
MIR2054
MIR1305
MIR3140
MIR4276
MIR3945
MIR3688-1
LOC100505545
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR4453
MIR4799
MIR3688-2

Genes in Wide Peak

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

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

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
NPM1
PDGFRB
PIK3R1
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
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
hsa-mir-582
hsa-mir-449c
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGF10
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NDUFS6
NEUROG1
NPR3
NPY6R
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
PURA
RAD17
RARS
RASA1
RASGRF2
RPL37
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP1
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
SRP19
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
NREP
TRIP13
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
PAPD7
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
OTP
SKIV2L2
NNT
TTC33
ZNF346
AMACR
SSBP2
BHMT2
TNFAIP8
NIPBL
PP7080
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
FBXO4
OR4F3
HAVCR1
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
DROSHA
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MZB1
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
FAM134B
FAM105A
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
MTMR12
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
NSUN2
CCDC99
THG1L
WDR70
AGGF1
WDR41
BRIX1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
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
ANKH
CCL28
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
AHRR
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1P1
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
CARD6
TRIM52
HAVCR2
AGXT2L2
C5orf62
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
LMBRD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C1QTNF3
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
HEATR7B2
EGFLAM
PRRC1
NADKD1
UGT3A1
CAPSL
JMY
C5orf58
ZNF474
CCDC127
OR2Y1
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC38A9
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
LOC153469
PLEKHG4B
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
LOC153684
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
NIM1
LIX1
ZNF366
FAM151B
S100Z
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
AQPEP
SLC36A1
RICTOR
EIF4E1B
LOC255167
RASGEF1C
ANKRD31
SERINC5
LOC257358
LOC257396
LOC285577
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
C5orf51
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
LOC285692
LOC285696
RGMB
RFESD
CHSY3
SLC6A19
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
LOC340094
LOC340107
LOC340113
ANKRD34B
PFN3
ZNF879
PLCXD3
IRGM
FBLL1
IDAS
ACTBL2
FAM174A
MTX3
CATSPER3
SLC6A18
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
C5orf34
MAST4
C5orf25
RNF138P1
FLJ38109
LRRC14B
C5orf39
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
FLJ33360
LOC401177
RGS7BP
C5orf63
SPINK6
TAG
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
MARCH11
CRSP8P
FLJ42709
C5orf56
FLJ16171
LOC442132
MIR340
IGIP
GPX8
TIFAB
FLJ35946
LOC553103
MIR449A
CTXN3
SNORD72
SNORD95
SNORD96A
ECSCR
LOC642366
TMEM232
C5orf43
LOC643201
GRXCR2
SPINK9
LOC643401
ZFP62
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
CBY3
LOC646719
LOC647859
LOC648987
ANKRD33B
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR580
MIR581
MIR583
MIR585
SNHG4
MIR143HG
GTF2H2C
LOC728342
GUSBP1
SERF1B
LOC728554
SDHAP3
LOC728613
LOC728723
LOC729080
LOC729506
AACSP1
LOC729678
OR4F29
LOC729862
GTF2H2D
GUSBP9
SNORD123
VTRNA2-1
MIR874
LOC100129716
CCDC152
LRRC70
LOC100130744
LOC100131067
FAM196B
LOC100132062
LOC100132287
LOC100132356
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR4279
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MIR4277
MIR4278
MTRNR2L2
MIR3607
MIR3655
MIR3650
MIR3660
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505738
LOC100505806
LOC100505841
LOC100505894
LOC100506548
OCLN
LOC100506688
LOC100507387
C1QTNF3-AMACR
MIR4458
MIR4804
MIR4633
MIR4634
MIR4461
MIR4454
MIR4457
MIR4637
MIR3977
MIR4460
MIR4636
MIR4638
MIR4803
MIR4456
MIR4635
MIR378E
EGFLAM-AS4
LOC100859930

Arm-level results

Table 3. Get Full Table Arm-level significance table - 17 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 | 0.02 | -3.85 | 1 | 0.12 | 0.484 | 1
1q | 1955 | 0.07 | -1.9 | 1 | 0.08 | -1.26 | 1
2p | 924 | 0.18 | 2.41 | 0.0215 | 0.02 | -4.06 | 1
2q | 1556 | 0.20 | 3.67 | 0.000343 | 0.01 | -4.29 | 1
3p | 1062 | 0.30 | 7.4 | 2.12e-13 | 0.10 | -0.843 | 1
3q | 1139 | 0.34 | 9.21 | 0 | 0.03 | -3.19 | 1
4p | 489 | 0.03 | -3.82 | 1 | 0.09 | -1.44 | 1
4q | 1049 | 0.03 | -3.83 | 1 | 0.10 | -0.972 | 1
5p | 270 | 0.14 | 0.19 | 0.999 | 0.04 | -3.52 | 1
5q | 1427 | 0.13 | 0.657 | 0.639 | 0.05 | -2.87 | 1
6p | 1173 | 0.04 | -3.41 | 1 | 0.07 | -1.97 | 1
6q | 839 | 0.03 | -3.94 | 1 | 0.09 | -1.52 | 1
7p | 641 | 0.60 | 19.7 | 0 | 0.01 | -3.08 | 1
7q | 1277 | 0.60 | 20.9 | 0 | 0.01 | -2.92 | 1
8p | 580 | 0.07 | -2.24 | 1 | 0.04 | -3.64 | 1
8q | 859 | 0.09 | -1.53 | 1 | 0.02 | -4.15 | 1
9p | 422 | 0.02 | -4.44 | 1 | 0.11 | -0.694 | 1
9q | 1113 | 0.01 | -4.42 | 1 | 0.12 | 0.0865 | 1
10p | 409 | 0.03 | -4.17 | 1 | 0.06 | -2.79 | 1
10q | 1268 | 0.02 | -4.07 | 1 | 0.07 | -2.22 | 1
11p | 862 | 0.05 | -2.94 | 1 | 0.05 | -2.94 | 1
11q | 1515 | 0.04 | -3.05 | 1 | 0.07 | -1.79 | 1
12p | 575 | 0.41 | 11.7 | 0 | 0.01 | -3.87 | 1
12q | 1447 | 0.41 | 12.7 | 0 | 0.00 | -3.93 | 1
13q | 654 | 0.12 | -0.169 | 1 | 0.10 | -0.963 | 1
14q | 1341 | 0.02 | -3.93 | 1 | 0.18 | 2.69 | 0.0711
15q | 1355 | 0.03 | -3.71 | 1 | 0.10 | -0.813 | 1
16p | 872 | 0.54 | 17.5 | 0 | 0.05 | -2.06 | 1
16q | 702 | 0.53 | 16.7 | 0 | 0.05 | -2.19 | 1
17p | 683 | 0.62 | 20.4 | 0 | 0.11 | -0.382 | 1
17q | 1592 | 0.67 | 24.5 | 0 | 0.02 | -2.51 | 1
18p | 143 | 0.05 | -3.03 | 1 | 0.16 | 1.04 | 1
18q | 446 | 0.03 | -3.8 | 1 | 0.17 | 1.52 | 0.645
19p | 995 | 0.02 | -4.41 | 1 | 0.06 | -2.58 | 1
19q | 1709 | 0.02 | -4.18 | 1 | 0.06 | -2.48 | 1
20p | 355 | 0.34 | 8.53 | 0 | 0.01 | -4.19 | 1
20q | 753 | 0.35 | 9.28 | 0 | 0.00 | -4.31 | 1
21q | 509 | 0.07 | -2.16 | 1 | 0.17 | 1.78 | 0.497
22q | 921 | 0.02 | -3.91 | 1 | 0.23 | 4.37 | 0.000251
Xq | 1312 | 0.35 | 9.6 | 0 | 0.16 | 1.33 | 0.728

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRP-TP/8017186/GDAC_MergeDataFiles_8022997/KIRP-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 197 Input Tumor Samples.

Tumor Sample Names
TCGA-A4-7286-01A-11D-2135-01
TCGA-A4-7287-01A-11D-2135-01
TCGA-A4-7288-01A-11D-2135-01
TCGA-A4-7583-01A-11D-2135-01
TCGA-A4-7584-01A-11D-2135-01
TCGA-A4-7585-01A-11D-2135-01
TCGA-A4-7732-01A-11D-2135-01
TCGA-A4-7734-01A-11D-2135-01
TCGA-A4-7828-01A-11D-2135-01
TCGA-A4-7915-01A-11D-2200-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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