Skin Cutaneous Melanoma: 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 219 tumor samples used in this analysis: 21 significant arm-level results, 17 significant focal amplifications, and 28 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 - 17 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
12q15 2.3148e-08 2.3148e-08 chr12:69177406-69287744 2
1p12 1.599e-07 2.2094e-07 chr1:119929443-120527360 12
5p15.33 3.1708e-06 3.1708e-06 chr5:1287541-1300024 1
3p13 1.2743e-05 1.2743e-05 chr3:69692935-70241684 1
11q13.3 0.00022879 0.00022879 chr11:68888380-70433980 13
22q13.2 0.00036712 0.00036712 chr22:41144918-41849552 15
7q34 0.015506 0.015506 chr7:138769073-140753365 22
6q12 0.020155 0.020155 chr6:63915276-66044939 4
7p22.3 0.035092 0.035092 chr7:1-8532843 93
1q21.3 0.011826 0.038521 chr1:120523956-155971691 297
8q11.21 0.038521 0.038521 chr8:52102620-52218326 0 [PXDNL]
1q44 0.017629 0.042536 chr1:245126660-247390174 16
15q25.1 0.044641 0.044641 chr15:74985920-102531392 261
1p36.11 0.15874 0.15874 chr1:22494628-25892802 55
12p12.1 0.20441 0.20441 chr12:24880663-26064718 9
20q13.33 0.20566 0.20566 chr20:46817357-63025520 200
4q12 0.23943 0.23943 chr4:48068784-59997811 52
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q15.

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

Genes
MDM2
CPM
Genes in Wide Peak

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

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

Genes
NOTCH2
HMGCS2
HSD3B1
HSD3B2
ADAM30
PHGDH
HAO2
REG4
ZNF697
HSD3BP4
NBPF7
LOC644242
Genes in Wide Peak

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

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

Genes
TERT
Genes in Wide Peak

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

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

Genes
MITF
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CCND1
hsa-mir-548k
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
SHANK2
MYEOV
ANO1
ORAOV1
MIR548K
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q13.2.

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

Genes
EP300
hsa-mir-1281
RANGAP1
ST13
TEF
RBX1
SLC25A17
TOB2
ZC3H7B
XPNPEP3
L3MBTL2
DNAJB7
CHADL
MIR1281
MIR4766
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q34.

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

Genes
BRAF
NDUFB2
TBXAS1
MKRN1
DENND2A
HIPK2
LUC7L2
MRPS33
ZC3HAV1
PARP12
TTC26
JHDM1D
SLC37A3
ADCK2
CLEC2L
C7orf55
UBN2
KLRG2
RAB19
LOC100129148
LOC100134229
LOC100134713
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
PTP4A1
PHF3
LGSN
EYS
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.3.

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

Genes
PMS2
CARD11
hsa-mir-589
hsa-mir-339
ACTB
GNA12
GPER
ICA1
LFNG
NUDT1
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KIAA0415
KDELR2
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
C1GALT1
FAM20C
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
C7orf70
ZFAND2A
COX19
GLCCI1
KIAA1908
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
SLC29A4
RSPH10B
TFAMP1
UNCX
COL28A1
LOC389458
ELFN1
GRID2IP
ZNF815
RNF216P1
PMS2CL
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
MIR589
RSPH10B2
LOC729852
LOC100131257
LOC100288524
RBAK-LOC389458
MIR4648
MIR4655
MIR4656
Genes in Wide Peak

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

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

Genes
ARNT
BCL9
MUC1
NOTCH2
TPM3
PDE4DIP
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
CHRNB2
CKS1B
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
PRPF3
ARHGEF2
SEC22B
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
C1orf56
MSTO1
GOLPH3L
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA4
SNORA42
MIR554
MIR555
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR190B
C1orf68
MSTO2P
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505666
TNFAIP8L2-SCNM1
Genes in Wide Peak

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

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

Genes
ZNF124
AHCTF1
SCCPDH
KIF26B
ZNF695
TFB2M
SMYD3
ZNF669
EFCAB2
ZNF670
LOC149134
CNST
LOC255654
C1orf229
MIR3916
ZNF670-ZNF695
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q25.1.

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

Genes
BLM
IDH2
NTRK3
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
ACAN
ALDH1A3
ANPEP
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
ETFA
FAH
FES
IDH3A
IGF1R
IL16
IREB2
ISG20
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
NMB
FURIN
PCSK6
PDE8A
PLIN1
POLG
PSMA4
PTPN9
RASGRF1
RCN2
RLBP1
RPS17
SH3GL3
SNRPA1
NR2F2
TYRO3P
AP3B2
ST8SIA2
PEX11A
IQGAP1
PSTPIP1
PRC1
SLC28A1
COX5A
HOMER2
ZNF592
SV2B
ARNT2
SCAMP2
SNUPN
TSPAN3
AP3S2
HMG20A
SEMA4B
CIB2
CIB1
MTHFS
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
SIN3A
ULK3
FBXO22
VPS33B
MRPL46
OR4F4
SLCO3A1
SCAPER
HDGFRP3
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2
RPP25
COMMD4
ZSCAN2
DET1
LINS
FANCI
IMP3
DNAJA4
MCTP2
SELS
MESP1
UNC45A
C15orf39
RGMA
WDR93
C15orf17
ADAMTSL3
KIAA1199
ALPK3
FAM108C1
MESDC1
PPCDC
KLHL25
CPEB1
AEN
ISL2
TTC23
MRPS11
EFTUD1
NEIL1
LRRK1
LMAN1L
PEAK1
EDC3
AGSK1
TM2D3
WDR61
STARD5
C15orf5
FAM103A1
MEX3B
LINGO1
WDR73
C15orf42
RCCD1
LOC91450
ARRDC4
LOC91948
UBE2Q2
C15orf40
TARSL2
LRRC28
C15orf27
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
NRG4
LINC00052
C15orf26
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
CERS3
LOC253044
LOC254559
SNX33
C15orf37
LOC283688
LOC283692
LOC283693
FAM154B
LOC283738
LOC283761
FAM169B
LOC338963
TMC3
ZNF774
C15orf38
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
LOC388152
UBE2Q2P1
FLJ42289
ANKRD34C
C15orf58
OR4F6
OR4F15
LOC390660
ST20
FAM174B
LOC400456
MIR184
MIR7-2
MIR9-3
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
CPLX3
LOC645752
SH2D7
LOC646938
GOLGA6L10
LOC648809
GOLGA6C
GOLGA6D
SCARNA15
FBXO22-AS1
MIR549
MIR631
LOC727849
LOC727915
ASB9P1
LOC729911
FAM138E
DNM1P35
UBE2Q2P3
UBE2Q2P2
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1276
MIR1179
MIR1469
MIR3175
MIR4313
RPS17L
LOC100505679
LOC100506874
LOC100507217
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
MIR4514
MIR4513
MIR3529
MIR4515
MIR4714
Genes in Wide Peak

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

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

Genes
MDS2
hsa-mir-3115
hsa-mir-4253
C1QA
C1QB
C1QC
RUNX3
CNR2
E2F2
EPHA8
EPHB2
FUCA1
GALE
HMGCL
HTR1D
ID3
RHCE
RHD
RPL11
TCEA3
TCEB3
LUZP1
ZBTB40
HNRNPR
SRRM1
SRSF10
RCAN3
LYPLA2
KDM1A
TMEM50A
CLIC4
SYF2
LDLRAP1
TMEM57
ASAP3
PNRC2
C1orf63
PITHD1
NIPAL3
GRHL3
IL22RA1
ZNF436
C1orf201
MYOM3
C1orf213
IL28RA
LOC284632
C1orf130
LOC729059
MIR3115
MIR4253
LOC100506963
MIR4684
MIR378F
RCAN3AS
Genes in Wide Peak

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

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

Genes
KRAS
hsa-mir-4302
BCAT1
LRMP
CASC1
LYRM5
IFLTD1
C12orf77
MIR4302
Genes in Wide Peak

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

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

Genes
GNAS
SS18L1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-3194
ATP5E
BMP7
CDH4
CEBPB
CHRNA4
COL9A3
CSE1L
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
NPBWR2
KCNB1
KCNG1
KCNQ2
LAMA5
MC3R
MYT1
NFATC2
NTSR1
OPRL1
PCK1
PFDN4
PPP1R3D
PSMA7
PTGIS
PTK6
PTPN1
RPS21
SNAI1
SRMS
STAU1
AURKA
TAF4
TCEA2
TFAP2C
TPD52L2
UBE2V1
ZNF217
RAE1
BCAS1
STX16
TNFRSF6B
DPM1
VAPB
B4GALT5
SPATA2
OSBPL2
ATP9A
ARFRP1
RGS19
SYCP2
ARFGEF2
TCFL5
ADRM1
OGFR
DIDO1
HRH3
SLC9A8
ADNP
SPO11
PRPF6
GTPBP5
GMEB2
SNORD12C
MOCS3
SLCO4A1
STMN3
SLMO2
TH1L
C20orf43
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
C20orf20
PPP4R1L
RBM38
BCAS4
DDX27
ZFP64
ARFGAP1
DOK5
RNF114
SLC2A4RG
PMEPA1
CASS4
SALL4
ZNFX1
RAB22A
ZNF512B
PREX1
COL20A1
CDH26
SLC17A9
LOC63930
FAM217B
C20orf195
PPDPF
BIRC7
NPEPL1
DNAJC5
TUBB1
ZBP1
CABLES2
PARD6B
ZGPAT
PRIC285
FAM210B
PHACTR3
BHLHE23
NKAIN4
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
GCNT7
CBLN4
CTCFL
SAMD10
ABHD16B
LINC00266-1
FAM65C
C20orf151
LOC149773
GNAS-AS1
LSM14B
APCDD1L
C20orf201
FAM209A
C20orf166-AS1
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
TMEM189
TMEM189-UBE2V1
FAM209B
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
ZNFX1-AS1
SNORD12
MIR645
MIR647
HAR1A
HAR1B
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
DPH3P1
LINC00029
LOC100144597
FLJ16779
MIR1914
MIR1257
MIR4325
MIR3194
MIR4326
MIR3196
MTRNR2L3
LOC100505815
LOC100506384
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4758
MIR4532
MIR4533
MIR5095
LOC100652730
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
KDR
KIT
PDGFRA
CHIC2
FIP1L1
IGFBP7
POLR2B
PPAT
REST
SGCB
SPINK2
SRP72
TEC
TXK
CLOCK
CEP135
PAICS
NMU
DCUN1D4
OCIAD1
EXOC1
TMEM165
DANCR
KIAA1211
SLAIN2
USP46
RASL11B
SRD5A3
CWH43
NOA1
HOPX
LNX1
OCIAD2
SPATA18
ARL9
AASDH
PDCL2
LOC152578
SCFD2
GSX2
SLC10A4
LOC255130
FRYL
ZAR1
LRRC66
RPL21P44
LOC644145
SNORA26
ERVMER34-1
LOC100506462
LOC100506564
MIR4449

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 - 28 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 9.1292e-151 7.4636e-150 chr9:21865498-21997722 2
11q23.3 8.7666e-12 8.7666e-12 chr11:105937045-129322249 251
10q23.31 9.7205e-10 9.7205e-10 chr10:89617158-90034038 2
4q34.3 2.7215e-08 2.7215e-08 chr4:178911874-183060693 1
1p36.31 4.5436e-07 2.7192e-06 chr1:4012234-6847369 26
16p13.3 3.2551e-05 3.2551e-05 chr16:5144019-7771745 1
15q15.3 1.6708e-06 0.00017783 chr15:36217164-52602505 189
10p15.3 0.00022232 0.0002155 chr10:1-857150 4
2q37.3 0.00050618 0.00050618 chr2:239463774-243199373 54
1p22.2 0.0017595 0.003288 chr1:77548519-119684843 296
5q31.3 0.0014188 0.003288 chr5:134570836-179501152 442
15q13.3 1.0732e-05 0.0069169 chr15:33023460-33528694 1
6q26 0.0022167 0.0090842 chr6:161693099-163153207 1
14q32.32 0.015029 0.01563 chr14:78263652-107349540 293
5q11.2 0.010338 0.024069 chr5:58145167-59787985 3
17q11.2 0.03202 0.03202 chr17:21191360-45976564 481
13q34 0.016084 0.040709 chr13:93874694-115169878 108
3q21.3 0.055499 0.054887 chr3:107091586-159617449 372
9p24.1 0.00020544 0.054887 chr9:7799607-12693402 1
6q21 0.028061 0.061131 chr6:72122590-116386192 182
16q12.1 0.027823 0.066812 chr16:31722415-66442405 141
6q27 0.003872 0.089565 chr6:169023880-170618145 10
16q23.3 0.01812 0.10792 chr16:73455019-90354753 153
3p25.1 0.13692 0.13717 chr3:1-79072066 584
12q13.13 0.14595 0.15092 chr12:25353958-65376637 418
13q12.11 0.058288 0.15183 chr13:1-73307526 263
19p13.3 0.19582 0.19917 chr19:1-4403016 161
21q21.1 0.25051 0.25051 chr21:1-48129895 303
16q24.2 0.0055424 0.43629 chr16:1-90354753 967
Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.3.

Table S18.  Genes in bold are cancer genes as defined by The Sanger Institute's 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
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
C1QTNF5
PANX3
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
HEPN1
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
LOC100652768
Genes in Wide Peak

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

Table S19.  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 4q34.3.

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

Genes
LINC00290
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
RPL22
hsa-mir-4252
ZBTB48
KCNAB2
TNFRSF25
KLHL21
ACOT7
ICMT
CHD5
HES2
DNAJC11
AJAP1
PLEKHG5
NOL9
TAS1R1
ESPN
THAP3
PHF13
NPHP4
LOC284661
GPR153
RNF207
HES3
MIR4252
MIR4689
MIR4417
Genes in Wide Peak

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

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

Genes
RBFOX1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.3.

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

Genes
BUB1B
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
B2M
CAPN3
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
MAPK6
RAD51
SLC12A1
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
SECISBP2L
LCMT2
BCL2L10
RASGRP1
SERF2
GNB5
SLC27A2
GPR176
CHP
OIP5
BAHD1
CEP152
MAPKBP1
RTF1
MGA
DMXL2
VPS39
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PLDN
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
TRPM7
PPP1R14D
FLJ10038
HAUS2
FAM82A2
DNAJC17
MYO5C
PAK6
DTWD1
CASC5
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
SPRED1
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
PLA2G4F
LRRC57
LYSMD2
HMGN2P46
SLC24A5
FAM98B
PLA2G4D
GLDN
MRPL42P5
USP50
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
MIR626
MIR627
LOC728758
OIP5-AS1
MIR147B
LOC100129387
LOC100131089
ANKRD63
LOC100132724
JMJD7
PLA2G4B
MIR1266
MIR1282
LOC100306975
MIR4310
LOC100505648
SERF2-C15ORF63
MIR4510
MIR4716
MIR4713
MIR4712
Genes in Wide Peak

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

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

Genes
ZMYND11
DIP2C
TUBB8
C10orf108
Genes in Wide Peak

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

Table S25.  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
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
HDAC4
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
RNPEPL1
GAL3ST2
C2orf54
ING5
MGC16025
TWIST2
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
LOC150935
LOC200772
CXXC11
DUSP28
AQP12A
OR6B2
FLJ43879
MIR149
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
MIR2467
MIR4440
MIR4786
MIR4441
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p22.2.

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

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FUBP1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
AK5
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q31.3.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
ADRA1B
ADRB2
ANXA6
ATOX1
BNIP1
CAMK2A
CANX
CCNG1
CD14
CDC25C
CDX1
CLTB
CSF1R
CSNK1A1
NKX2-5
CTNNA1
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FGF1
FGFR4
FOXI1
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSPA9
NDST1
HTR4
IK
IL9
IL12B
KCNMB1
LCP2
LECT2
LTC4S
SMAD5
MFAP3
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
POU4F3
PPP2R2B
PROP1
PURA
RARS
RPS14
SGCD
SLC6A7
SLC34A1
SLIT3
SNCB
SPARC
SPINK1
SPOCK1
STK10
TAF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2D2
WNT8A
NME5
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
SLU7
RGS14
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
HNRNPA0
LMAN2
SPINK5
SOX30
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
PRELID1
IL17B
MAT2B
MRPL22
PCDHB1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DCTN4
MZB1
PAIP2
PCDH12
FAM13B
FAM53C
REEP2
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
KDM3B
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PSD2
THOC3
C5orf32
SPINK7
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
BOD1
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SFXN1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
C5orf58
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
C5orf20
SLC36A2
SPINK13
C5orf41
SLC25A48
LOC153469
ZMAT2
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
ZNF454
C5orf60
LOC340037
TMEM173
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
NIPAL4
DND1
C5orf25
FLJ38109
LOC389332
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
FLJ16171
MIR340
IGIP
TIFAB
ECSCR
LOC643201
GRXCR2
SPINK9
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728554
LOC729080
AACSP1
VTRNA2-1
MIR874
FAM196B
C5orf52
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
LOC100505658
LOC100507387
MIR4634
MIR378E
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.3.

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

Genes
FMN1
Genes in Wide Peak

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

Table S29.  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 14q32.32.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
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
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
GALC
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
MTA1
RPS6KA5
NRXN3
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
PTPN21
RCOR1
PACS2
PPP1R13B
FLRT2
KIF26A
C14orf109
PRO1768
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
ADCK1
UNC79
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
CEP128
TTC7B
C14orf49
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
CCDC85C
ITPK1-AS1
SERPINA9
LINC00226
LINC00221
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
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
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
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
MIR1247
MIR1185-1
MIR1185-2
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392
LOC100628307
Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

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

Genes
BRCA1
ERBB2
ETV4
LASP1
MLLT6
NF1
RARA
TAF15
SUZ12
hsa-mir-4315-1
hsa-mir-2117
hsa-mir-2909
hsa-mir-632
hsa-mir-365-2
hsa-mir-3184
hsa-mir-144
ACACA
ACCN1
ACLY
AP2B1
ALDOC
AOC2
ARL4D
ATP6V0A1
BLMH
FMNL1
CACNB1
CDC6
CDC27
CCR7
CNP
CPD
CRHR1
CRYBA1
CSF3
DHX8
DUSP3
EVI2A
EVI2B
EZH1
FLOT2
GAST
FZD2
G6PC
KAT2A
GFAP
CCR10
GRB7
GRN
HCRT
HSD17B1
IFI35
IGFBP4
ITGA2B
ITGB3
JUP
KCNJ12
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS9
LHX1
LIG3
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
MYO1D
NAGLU
NEUROD2
NMT1
NOS2
NSF
OMG
PEX12
PNMT
MED1
PPY
PSMB3
PYY
PSMD3
PSMD11
RAB5C
RAD51D
RPL19
RPL23A
RPL27
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SH3GL1P1
SH3GL1P2
SLC4A1
SLC6A4
SMARCE1
STAT3
STAT5A
STAT5B
SUPT6H
TADA2A
HNF1B
MLX
THRA
TNFAIP1
TOP2A
DNAJC7
TUBG1
UBTF
VTN
WNT3
WNT9B
PCGF2
ZNF207
RND2
PIP4K2B
FOXN1
CNTNAP1
TCAP
AOC3
BECN1
KRT38
KRT37
KRT36
KSR1
CDK5R1
HAP1
MAP3K14
SLC13A2
UNC119
TIAF1
ZNHIT3
EFTUD2
RPL23
NPEPPS
GOSR1
CCL4L1
GOSR2
NR1D1
TRAF4
KIAA0100
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
GJC1
PSME3
EIF1
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
SPAG5
CCT6B
C1QL1
RUNDC3A
STARD3
DDX52
DUSP14
SYNRG
CASC3
IKZF3
SARM1
GPATCH8
KCNH4
FAM215A
PPY2
PYY2
KRT23
TMEM98
POLDIP2
TBC1D29
WSB1
ERAL1
AATF
SNORD4B
SNORD4A
SNORD42B
SNORD42A
TUBG2
TMEM97
NKIRAS2
CCDC56
GIT1
PSMC3IP
TBX21
SOCS7
SOST
RAPGEFL1
PIPOX
ARL17A
CRLF3
SLC25A39
NLK
HIGD1B
CDK12
KRT20
NLE1
FNDC8
CWC25
LRRC37A4
SLFN12
KLHL11
RHOT1
C17orf79
C17orf63
ADAP2
UTP6
GSDMB
ATXN7L3
PLXDC1
LYZL6
NUFIP2
TAOK1
ARHGAP23
PHF12
FKBP10
C17orf75
WNK4
C17orf53
TMUB2
DHX58
MMP28
DHRS11
TEFM
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
DBF4B
MYO19
SP6
COASY
SRCIN1
AARSD1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
TTC25
KRTAP4-12
RAB34
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
NSRP1
PPP1R1B
TBC1D3F
RNF135
MIEN1
MRPL45
VPS25
TMEM101
RAB11FIP4
GHDC
KRTAP4-4
CORO6
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
SSH2
TP53I13
IFT20
LRRC46
SCRN2
AOC4
ZNF830
SLFN11
RASL10B
G6PC3
ASB16
PGAP3
PIGS
HSPB9
ORMDL3
PLCD3
SLC46A1
TMEM106A
LRRC37B
OSBPL7
NT5C3L
ABHD15
TLCD1
RFFL
ZPBP2
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
SPACA3
SGK494
SEZ6
ANKRD13B
C17orf57
MRPL10
GJD3
KRT222
KRT40
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
TMEM199
PROCA1
DHRS13
C17orf69
LOC147093
LRRC37BP1
WIPF2
KRT25
TMEM99
SLFN5
NAGS
FAM134C
RHBDL3
IMP5
KRT28
KRT24
ARHGAP27
ZNF385C
C17orf108
RDM1
GAS2L2
STH
C17orf66
KIAA1267
C17orf105
FAM171A2
C17orf104
KRT18P55
NEK8
PIGW
C17orf78
LOC284100
CISD3
GSDMA
KRT42P
PTRF
FAM27L
FLJ36000
KLHL10
C17orf65
C17orf51
MSL1
KRT27
SLFN14
FLJ43826
STAC2
CCL14-CCL15
KRT26
EFCAB5
TMIGD1
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
ARL5C
KRT39
MYO18A
C17orf102
MGC57346
MIR144
MIR193A
TBC1D3B
TBC1D3C
CCL3L3
TBC1D3P5
SUZ12P
LOC440434
GPR179
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451A
SNORA21
LOC644172
LOC644246
SEBOX
KRTAP4-11
MRPL45P2
TBC1D3G
SNORD7
MIR632
KRTAP4-8
KRTAP2-2
KRTAP9-1
NSFP1
TBC1D3
TBC1D3H
LOC730755
SNORD124
MIR365B
LOC100128977
LOC100130148
LOC100130581
LOC100131347
KRTAP4-9
KRTAP4-7
LOC100133991
KCNJ18
C17orf96
LOC100190938
MIR2117
MIR4315-2
MIR2909
MIR3184
MIR4315-1
MTRNR2L1
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
SPAG5-AS1
AA06
SLFN12L
RAD51L3-RFFL
MIR4523
MIR4728
MIR4726
MIR4734
MIR4724
MIR4733
MIR451B
MIR4522
MIR4732
MIR4723
MIR4727
MIR4725
RAB34
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q34.

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
FGF14
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
RAP2A
GRK1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
OXGR1
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
TEX29
METTL21CP1
SPACA7
RNF113B
GPR180
CLYBL
METTL21C
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
FAM70B
C13orf35
FLJ44054
CCDC168
FLJ41484
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
MIR3170
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4705
Genes in Wide Peak

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

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

Genes
FOXL2
GATA2
MLF1
RPN1
GMPS
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
AADAC
ACPP
ADCY5
ADPRH
AGTR1
ATP1B3
ATP6V1A
ATR
CASR
CD80
CD86
CD47
CP
CPA3
CPB1
CSTA
DRD3
EPHB1
GAP43
GOLGB1
GP9
GSK3B
GTF2E1
GYG1
HCLS1
HGD
ITGB5
KPNA1
LSAMP
TM4SF1
MBNL1
MCM2
MME
CD200
MYLK
NCK1
NDUFB4
P2RY1
PCCB
PFN2
PIK3CB
PLOD2
PLS1
PLSCR1
PLXNA1
PPP2R3A
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
RHO
RYK
SHOX2
SIAH2
SLC15A2
SLCO2A1
HLTF
SSR3
TF
TFDP2
TM4SF4
TRH
TRPC1
UPK1B
UMPS
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
SOX14
BFSP2
RUVBL1
B4GALT4
SNX4
NR1I2
MBD4
H1FX
KALRN
SLC33A1
COPB2
CHST2
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
TSC22D2
P2RY14
COX17
CD96
STAG1
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
FSTL1
MRPL3
RNF13
MGLL
MRAS
COPG
MYH15
PLCH1
TMCC1
PLXND1
DNAJC13
U2SURP
C3orf27
ANAPC13
ARMC8
C3orf17
WWTR1
PVRL3
TIPARP
ARHGEF26
ZBTB20
FAM162A
PCOLCE2
SEC22A
NPHP3
ATP2C1
MORC1
SERP1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
SCHIP1
PIK3R4
PODXL2
TRAT1
COMMD2
A4GNT
DBR1
CLDN18
TIMMDC1
RSRC1
PLA1A
AMOTL2
CCRL1
RAB6B
SELT
FBXO40
P2RY13
IL20RB
GPR87
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
SLC41A3
SLC35A5
IFT57
MSL2
FAIM
SLC25A36
DPPA4
TMEM39A
ABHD10
CDV3
IFT122
WDR52
EAF2
MUC13
SUCNR1
LXN
C3orf37
MRPS22
POGLUT1
BBX
CCNL1
PLSCR2
PLSCR4
ISY1
HEG1
KIAA1257
ARHGAP31
KIAA1407
KIAA1524
SRPRB
BPESC1
EEFSEC
CLSTN2
POPDC2
ATG3
MFSD1
CCDC14
P2RY12
TMEM108
ZXDC
ZBED2
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC48
NEK11
UBA5
C3orf36
NAA50
CEP63
CEP70
ABTB1
TMEM22
PARP9
ESYT3
EIF2A
ZIC4
ACAD11
CHCHD6
HPS3
SLC12A8
RETNLB
CCDC54
DIRC2
GFM1
C3orf15
PHLDB2
LOC90246
C3orf25
BOC
SPSB4
ACPL2
TXNRD3
OSBPL11
LRRC58
TM4SF18
MED12L
CLRN1-AS1
CPNE4
CCDC58
CD200R1
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
GRK7
RPL32P3
H1FOO
PISRT1
DTX3L
LOC151658
DPPA2
CCDC80
BTLA
ROPN1B
C3orf22
C3orf55
C3orf79
SPICE1
NUDT16P1
IGSF11
C3orf30
PARP15
DNAJB8
GPR156
CHST13
KBTBD12
DHX36
DZIP1L
ALG1L
PTPLB
TIGIT
LOC201651
C3orf58
KIAA2018
ZBTB38
ZDHHC23
NUP210P1
COL6A5
GK5
PLCXD2
GCET2
LSAMP-AS3
SLC9A9
LOC285205
DNAJB8-AS1
RABL3
IGSF10
C3orf33
SLC9A10
ILDR1
TRIM42
RAB43
KY
LOC339874
LOC339894
H1FX-AS1
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
NME9
CCDC37
NPHP3-AS1
NMNAT3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
FLJ22763
FLJ25363
C3orf72
LOC401093
MIR198
ARGFX
ALG1L2
TXNRD3NB
TMEM14E
COL6A4P2
LOC646903
PA2G4P4
LOC653712
IQCJ
LINC00488
SNORA7B
SNORA58
MIR567
MIR568
FAM86HP
PRR23A
LOC730091
LOC100125556
WWTR1-AS1
LOC100129550
ZBTB20-AS1
TIPARP-AS1
LOC100289361
MIR1280
MIR548I1
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
LOC100507032
LOC100507389
ARHGEF26-AS1
LOC100507537
NPHP3-ACAD11
ISY1-RAB43
MIR4796
MIR4788
MIR4446
Genes in Wide Peak

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

Table S35.  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 6q21.

Table S36.  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
hsa-mir-4282
AIM1
AMD1
BCKDHB
CCNC
CGA
CNR1
COL12A1
COX7A2
EEF1A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1B
HTR1E
IMPG1
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
UFL1
ORC3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
CYB5R4
TUBE1
C6orf203
CDC40
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
MB21D1
SLC16A10
RIPPLY2
IRAK1BP1
CD109
PM20D2
SRSF12
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
HS3ST5
LACE1
MMS22L
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DPPA5
GJB7
SNHG5
C6orf147
LINC00222
LIN28B
OOEP
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
TPI1P3
C6orf186
KHDC1L
LOC100130890
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
MIR4464
MIR4643
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q12.1.

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

Genes
CDH11
CYLD
HERPUD1
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
ADCY7
AMFR
BBS2
CBLN1
CDH5
CDH8
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
PHKB
POLR2C
RBL2
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC12A3
GPR56
N4BP1
NUP93
IRX5
DNAJA2
KATNB1
ZNF267
NUDT21
CNOT1
ZNF423
RPGRIP1L
ARL2BP
ORC6
TP53TG3
DKFZP434H168
TOX3
CCDC113
C16orf80
BRD7
PLLP
CES1P1
LPCAT2
HEATR3
SLC38A7
OGFOD1
DOK4
VPS35
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
FTO
IRX6
IRX3
C16orf57
SHCBP1
SETD6
FAM192A
CHD9
ITFG1
NETO2
LONP2
NLRC5
CCDC135
CAPNS2
MT4
GPT2
ABCC11
NKD1
RSPRY1
MYLK3
CCDC102A
ABCC12
C16orf78
ANKRD26P1
ZNF720
SNX20
LOC146481
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
LOC283856
LOC283867
LOC283914
MT1DP
TEPP
SLC6A10P
C16orf87
LOC388276
LOC390705
CES1P2
FLJ26245
MIR138-2
HERC2P4
UBE2MP1
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
LINC00273
TP53TG3C
SNORA46
SNORA50
LOC729264
TP53TG3B
LOC100130700
MIR3935
LOC100505619
LOC100507577
MIR548AE2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
TCTE3
THBS2
DLL1
PHF10
C6orf70
C6orf208
LOC154449
WDR27
C6orf120
LINC00242
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
BANP
RFWD3
ZDHHC7
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
MLKL
ZNF778
ACSF3
LINC00304
LOC283922
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
CTRB2
CLEC18B
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
SYCE1L
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722
MIR4719
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.1.

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

Genes
CTNNB1
FANCD2
FHIT
MITF
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FBLN2
FLNB
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
WNT7A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
BHLHE40
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
VPRBP
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
CXCR6
CSPG5
CHL1
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CAND2
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
RYBP
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LINC00312
LMCD1
ARHGEF3
VILL
C3orf32
TRNT1
ABHD5
DYNC1LI1
C3orf18
CRBN
SS18L2
C3orf19
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ARL8B
SETD5
TMEM40
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
TMEM111
BRK1
ZNF167
LMOD3
RAD18
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
LRRN1
SELK
PROK2
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
THOC7
WDR82
TSEN2
GRIP2
RTP3
C3orf20
ID2B
ATRIP
NICN1
MON1A
JAGN1
KBTBD8
GHRLOS2
IL17RC
ABHD14B
C3orf39
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
C3orf24
LRRC3B
GALNTL2
GPR62
KCNH8
FAM3D
LYZL4
KBTBD5
TRIM71
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
FGD5
CIDECP
CNTN4
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC285401
EIF4E3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
COL6A4P1
TPRXL
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VENTXP7
LOC401052
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
SNORA7A
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR563
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
MIR885
EGOT
GHRLOS
C3orf74
LOC100128640
NRADDP
LOC100129480
ZNF717
LOC100132146
LOC100132526
BSN-AS2
PRSS46
LOC100287879
LOC100288428
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
MIR3938
MIR3714
FGD5-AS1
LOC100505696
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4791
MIR4790
MIR548AC
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q13.13.

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

Genes
ATF1
CDK4
DDIT3
HOXC11
HOXC13
KRAS
NACA
MLL2
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APOF
AQP2
AQP5
AQP6
ARF3
ATP5B
ATP5G2
AVPR1A
BICD1
CACNB3
CCNT1
CD63
CDK2
CNTN1
COL2A1
CS
CYP27B1
DGKA
DDX11
EIF4B
CELA1
ERBB3
B4GALNT1
BLOC1S1
GLI1
GNS
GPD1
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
LRP1
MARS
METTL1
MIP
MMP19
MYL6
MYO1A
NAB2
NELL2
NFE2
SLC11A2
PA2G4
PCBP2
PDE1B
PFDN5
PFKM
PKP2
POU6F1
PPP1R1A
PRIM1
PRKAG1
PRPH
PTHLH
TWF1
RAB5B
RARG
RBMS2
RDH5
RNY5
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
PMEL
SMARCC2
SMARCD1
SP1
STAT2
STAT6
SUOX
TAC3
TARBP2
TMBIM6
TFCP2
VDR
WNT1
WNT10B
MAP3K12
TUBA1A
SSPN
AAAS
SOAT2
PPFIBP1
RDH16
NPFF
HSD17B6
ENDOU
TIMELESS
KRT75
SCAF11
SLC16A7
MED21
DDX23
SLC4A8
ESPL1
DAZAP2
KIAA0748
ZBTB39
PAN2
USP15
TROAP
DNM1L
TSFM
CTDSP2
YAF2
RNF41
GDF11
TMEM5
CNPY2
TUBA1B
RAPGEF3
MCRS1
IPO8
DCTN2
AVIL
PTGES3
OS9
ATF7
BAZ2A
GALNT6
RASSF8
NXPH4
XPOT
GPR182
COPZ1
R3HDM2
STK38L
FAIM2
MON2
DDN
TMEM194A
TBC1D30
ESYT1
TENC1
KCNH3
CBX5
ANP32D
SMUG1
PRPF40B
METTL7A
LETMD1
METTL21B
ZNF385A
FGFR1OP2
SNORD59A
GLS2
RND1
ORMDL2
TBK1
RACGAP1
SENP1
PDZRN4
DHH
PLEKHA8P1
YARS2
IRAK4
ERGIC2
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
IL23A
HDAC7
TM7SF3
GPR84
SLC38A2
PRR13
KANSL2
SLC38A4
C12orf35
CCDC91
KIF21A
SLC48A1
FAR2
LMBR1L
ASUN
NDUFA4L2
ARNTL2
SMAGP
PPM1H
SRGAP1
KLHDC5
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
FAM60A
C12orf10
MRPS35
C12orf44
ARHGAP9
IKZF4
SLC26A10
SPATS2
CAPRIN2
TMEM106C
OBFC2B
BHLHE41
RPAP3
PIP4K2C
FLJ13224
DNAJC22
ADAMTS20
SLC38A1
CSRNP2
PUS7L
INHBE
TMTC1
RACGAP1P
FAM186B
TMEM117
WIBG
SARNP
TUBA1C
ZC3H10
ALG10
SPRYD3
MFSD5
C12orf62
DNAJC14
ZCRB1
CCDC65
LACRT
FMNL3
CERS5
XRCC6BP1
FAM113B
MARCH9
COQ10A
KRT71
LARP4
SLC2A13
MBD6
ARHGEF25
C12orf56
AGAP2
DCD
MUCL1
LRRK2
FAM186A
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
FGD4
ASB8
MYL6B
KRT72
PRICKLE1
BCDIN3D
ALG10B
CPNE8
KRT80
C12orf66
IFLTD1
DENND5B
GRASP
KRT78
AMN1
DTX3
METTL7B
ANO6
ARID2
STAC3
METTL20
OR6C74
OR6C3
LOC255411
LOC283332
LOC283335
ZNF740
RASSF3
OR6C6
ANKRD52
SLC39A5
SPRYD4
LOC283403
LOC283404
C12orf61
DPY19L2
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
FAM19A2
C12orf70
OVCH1
SYT10
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
KRT77
REP15
C12orf68
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR196A2
MIR26A2
H3F3C
DBX2
FLJ12825
TMEM198B
TSPAN11
OR9K2
MIR148B
HIGD1C
GLYCAM1
HNRNPA1P10
SNORA2A
SNORA2B
SNORA34
SNORD59B
MIR548C
MIR615
C12orf71
HOTAIR
LOC100130776
LOC100233209
LOC100240734
LOC100240735
LOC100286844
MANSC4
LOC100287314
MIR1228
MIR1293
MIR1291
LOC100335030
MIR4302
MIR548Z
LOC100506451
LOC100506660
LOC100506844
BLOC1S1-RDH5
MIR4701
MIR3198-2
MIR4698
LOC100652999
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

Table S42.  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-3169
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
DACH1
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
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
KLHL1
XPO4
PCDH20
MRP63
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
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
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
LINC00550
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
MZT1
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
MIR3169
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 19p13.3.

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

Genes
GNA11
SH3GL1
STK11
TCF3
FSTL3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
ARID3A
EEF2
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
MATK
GADD45B
NFIC
OAZ1
PALM
POLR2E
POLRMT
MAP2K2
PRTN3
PTBP1
RPS15
SGTA
TBXA2R
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
APBA3
MED16
EBI3
APC2
ABCA7
HMG20B
UQCR11
SBNO2
ZFR2
PIP5K1C
HMHA1
SHC2
TIMM13
DAZAP1
SNORD37
FGF22
TJP3
ITGB1BP3
SLC39A3
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
STAP2
BTBD2
RNF126
CCDC94
NCLN
SPPL2B
SHD
WDR18
REXO1
ZNF77
C19orf29
CELF5
FSD1
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
CREB3L3
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
TMIGD2
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
CSNK1G2-AS1
C19orf77
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
C19orf29-AS1
FAM138F
LINGO3
FAM138A
MIR637
C19orf71
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

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

Genes
RUNX1
ERG
TMPRSS2
OLIG2
hsa-mir-3197
hsa-mir-802
hsa-mir-4327
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
ADARB1
AIRE
APP
ATP5J
ATP5O
BACH1
BAGE
PTTG1IP
C21orf2
TMEM50B
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
CXADR
DSCAM
RCAN1
DYRK1A
ETS2
GABPA
GART
GRIK1
HLCS
HMGN1
PRMT2
IFNAR1
IFNAR2
IFNGR2
IL10RB
ITGB2
KCNE1
KCNJ6
KCNJ15
LSS
MX1
MX2
NCAM2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
TMPRSS15
PWP2
S100B
SH3BGR
ITSN1
SIM2
SLC5A3
SLC19A1
SUMO3
SOD1
SON
HSPA13
TFF1
TFF2
TFF3
TIAM1
TRAPPC10
TPTE
TRPM2
TTC3
U2AF1
UBE2G2
WRB
NRIP1
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
SYNJ1
MCM3AP
CLDN8
ADAMTS1
ABCG1
URB1
CRYZL1
DOPEY2
KCNE2
RWDD2B
DSCR4
DSCR3
B3GALT5
USP16
CCT8
WDR4
FTCD
BTG3
HSF2BP
ADAMTS5
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
LTN1
CLDN17
N6AMT1
USP25
DNMT3L
DONSON
HUNK
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
RBM11
PCBP3
C21orf58
YBEY
LINC00160
FAM165B
C21orf49
MIS18A
LINC00158
CHODL-AS1
TSPEAR
LINC00113
LINC00112
LINC00111
SETD4
C21orf15
FAM3B
RIPK4
CLIC6
LINC00308
MRPL39
C21orf91
DNAJC28
C21orf62
MRAP
C21orf59
AGPAT3
C21orf7
SCAF4
JAM2
C21orf63
PRDM15
SAMSN1
TMPRSS3
MRPS6
RUNX1-IT1
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
FAM207A
RSPH1
UMODL1
GCFC1
LINC00310
LINC00313
C21orf88
C21orf90
MCM3AP-AS1
MIR155HG
CYYR1
OLIG1
LINC00161
KRTAP13-1
TCP10L
CHODL
ANKRD30BP2
LIPI
ABCC13
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00189
C21orf91-OT1
LINC00315
LINC00314
KRTAP15-1
DSCR9
BRWD1-IT2
DSCR10
D21S2088E
LINC00307
LINC00515
KRTAP13-4
LINC00323
LINC00319
LOC284837
POTED
KRTAP7-1
KRTAP8-1
KRTAP11-1
KRTAP19-1
KRTAP13-2
KRTAP13-3
KRTAP23-1
KRTAP6-1
KRTAP6-2
KRTAP6-3
KRTAP19-2
KRTAP19-3
KRTAP19-4
KRTAP19-5
KRTAP19-6
KRTAP19-7
KRTAP20-1
KRTAP20-2
KRTAP21-1
KRTAP21-2
KRTAP22-1
KRTAP20-3
LOC339622
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
LINC00317
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00320
LOC388813
LINC00478
KRTAP26-1
ANKRD20A11P
LINC00114
MIRLET7C
MIR125B2
MIR155
MIR99A
LOC642852
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
LINC00163
SSR4P1
KRTAP19-8
C21orf54
MIR802
LOC100129027
KRTAP25-1
TEKT4P2
LOC100133286
KRTAP20-4
KRTAP22-2
KRTAP21-3
LOC100288432
GRIK1-AS2
MIR4327
MIR3156-3
MIR3197
MIR3687
MIR3648
LOC100505746
C21orf37
GCFC1-AS1
LOC100506334
LOC100506385
CBR3-AS1
DSCAM-AS1
LINC00159
MIR4760
MIR4759
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.2.

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

Genes
TNFRSF17
CBFA2T3
CBFB
CDH1
CDH11
CREBBP
CYLD
ERCC4
FANCA
FUS
MAF
CIITA
MYH11
TSC2
SOCS1
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
hsa-mir-3179-3
hsa-mir-3180-2
hsa-mir-484
hsa-mir-1972-1
hsa-mir-3180-1
hsa-mir-365-1
hsa-mir-548h-2
hsa-mir-3178
hsa-mir-940
hsa-mir-1225
hsa-mir-3177
hsa-mir-662
hsa-mir-3176
AARS
ABAT
ABCA3
ADCY7
ADCY9
AP1G1
AFG3L1P
AGRP
ALDOA
AMFR
AQP8
APRT
ABCC6
ARHGDIG
ZFHX3
ATP2A1
ATP6V0C
BBS2
C16orf3
CA5A
CA7
CALB2
CBLN1
CCNF
CD19
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CDR2
CES1
CETP
CLCN7
CLN3
CNGB1
COX4I1
COX6A2
CRYM
CSNK2A2
CTF1
CTRB1
CTRL
CYBA
ECI1
DHODH
NQO1
SEPT1
DNASE1
DNASE1L2
DYNC1LI2
DPEP1
E2F4
E4F1
EMP2
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GFER
GLG1
GNAO1
GOT2
GP2
GRIN2A
GSPT1
GTF3C1
HAGH
HAS3
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
IGFALS
IL4R
ITGAD
ITGAL
ITGAM
ITGAX
KARS
KIFC3
KIF22
LCAT
MAZ
MC1R
CHST6
MEFV
MMP2
MMP15
MPG
ABCC1
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
MVD
NUBP1
NDUFAB1
NDUFB10
NFATC3
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PARN
CHMP1A
PDPK1
PHKB
PHKG2
PKD1
PLCG2
PLK1
PMM2
POLR2C
PPL
PPP4C
PRKCB
MAPK3
PRM1
PRM2
PRSS8
PSKH1
PSMB10
PSMD7
RBBP6
RBL2
RPL3L
RPL13
RPS2
RPS15A
RRAD
ACSM3
SALL1
SCNN1B
SCNN1G
SRL
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC5A2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SOLH
SPG7
SPN
SSTR5
SULT1A2
STX4
SULT1A1
SULT1A3
TAT
TBX6
TCEB2
TERF2
TFAP4
TGFB1I1
TK2
TNP2
TPSAB1
TUFM
UBE2I
UMOD
UQCRC2
ZNF19
ZNF23
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
ZP2
USP7
NPRL3
GAN
SLC7A5
SNN
AXIN1
PLA2G10
DOC2A
HIRIP3
CDK10
EIF3C
TRADD
MBTPS1
RGS11
CES2
NAE1
CACNA1H
BAIAP3
NOL3
TAF1C
RHBDL1
SLC7A6
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
USP10
ATP6V0D1
SYNGR3
IL32
BCL7C
NPIP
GPR56
TAOK2
SLC9A3R2
LITAF
BCAR1
C16orf7
KIAA0430
N4BP1
NUP93
SEC14L5
ZNF646
RAB11FIP3
CCP110
SETD1A
IFT140
KIAA0513
PIEZO1
DHX38
IST1
RNF40
TELO2
ATP2C2
HS3ST4
HS3ST2
MVP
NUBP2
ZNF263
TRAP1
CLEC3A
CHST4
MPHOSPH6
NUTF2
COQ7
MSLN
IGSF6
IRX5
STUB1
DNAJA2
BCKDK
KATNB1
ZNF267
COX4NB
CACNG3
TUBB3
CD2BP2
CDIPT
CFDP1
MRPL28
ERN2
TBL3
CTCF
NFAT5
SRCAP
RNPS1
PRSS21
NUDT21
WWP2
PRDM7
CORO1A
DDX19B
ATXN2L
GABARAPL2
MON1B
SEPHS2
TCF25
CNOT1
PHLPP2
PDXDC1
SMG1
CLUAP1
GGA2
ZNF423
NPIPL3
MAPK8IP3
ZCCHC14
KIAA0182
ARL6IP1
XPO6
KIAA0556
CLEC16A
MGRN1
ATMIN
RPGRIP1L
ZNF629
COTL1
MLYCD
NOMO1
TPSD1
SF3B3
QPRT
CES3
SRRM2
ADAT1
CHST5
ARL2BP
CARHSP1
ORC6
EDC4
PLA2G15
TP53TG3
TPSG1
RAB26
COG4
TMEM186
PLEKHG4
SH2B1
TBC1D10B
ZNF500
DECR2
DKFZP434H168
RSL1D1
OR1F2P
LRRC29
SEZ6L2
NUPR1
SNORA64
SNORD60
LAT
CPNE7
VPS4A
IL17C
TOX3
TNRC6A
DEXI
NOB1
C16orf72
ZC3H7A
CCDC113
TMEM208
C16orf80
PYCARD
FHOD1
BRD7
ANKRD11
ZDHHC1
UBN1
MYLPF
EEF2K
OSGIN1
C16orf5
SOX8
PARD6A
AMDHD2
PAM16
TXNDC11
PLLP
METTL9
NAGPA
CKLF
BFAR
AHSP
TNFRSF12A
ZNF771
NIP7
LCMT1
GDE1
FAM96B
GINS2
TPPP3
TRAPPC2L
GPRC5B
CES1P1
POLR3K
SEPX1
WWOX
SYT17
GNG13
BCMO1
TERF2IP
KCTD5
PRMT7
NECAB2
FBXL19
RRN3
RBFOX1
KLHDC4
HYDIN
NDE1
DEF8
DUS2L
CHTF8
ZNF434
LPCAT2
TXNL4B
BANP
HCFC1R1
ACSM5
HEATR3
PDPR
ARHGAP17
RFWD3
SLC38A7
OGFOD1
LRRC36
DDX19A
CPPED1
FBXL8
SMPD3
ZNF821
DNAH3
THUMPD1
ZDHHC7
LUC7L
VAC14
DOK4
POLR3E
VPS35
FTSJD1
DDX28
TSNAXIP1
CENPN
APOBR
ALG1
UBFD1
C16orf61
COQ9
CIAPIN1
C16orf62
TMEM159
LYRM1
THAP11
JPH3
NMRAL1
TBC1D24
USP31
MKL2
CASKIN1
PDP2
ZNF319
CRAMP1L
RANBP10
VAT1L
KIAA1609
RAB40C
WFDC1
PRM3
TMEM8A
CHTF18
CHP2
PRSS22
NOD2
XYLT1
PDF
DPEP2
DPEP3
MLST8
PAPD5
RHBDF1
FBRS
MMP25
AKTIP
NARFL
LINC00235
TPSB2
HS3ST6
PDIA2
UNKL
LINC00254
C16orf58
MTHFSD
GINS3
LMF1
NDRG4
ACD
ZNF747
FAM173A
MRPS34
PRR14
VKORC1
METRN
DBNDD1
SLX1B
FTO
DCTPP1
METTL22
FA2H
GDPD3
IRX6
IRX3
THOC6
KREMEN2
C16orf53
FAM65A
TMEM231
CORO7
TMCO7
SNRNP25
ROGDI
C16orf57
TMEM204
ZNF768
WDR59
ZNF668
ELMO3
KLHL36
FBXO31
ARMC5
SHCBP1
JMJD5
TMC5
RABEP2
NAA60
TMC7
SETD6
ESRP2
FAM192A
ATF7IP2
CENPT
C16orf59
CHD9
C16orf70
HSD3B7
CYB5B
CMIP
ITFG1
GFOD2
CDT1
MAP1LC3B
LOC81691
NETO2
MGC3771
FAHD1
SLC7A5P1
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
YPEL3
FAM57B
LONP2
PRSS27
SPNS1
ITFG3
C16orf48
SLC7A6OS
KAT8
NLRC5
WDR24
CCDC135
TRAF7
FLYWCH1
HAGHL
CAPNS2
NUDT16L1
C16orf13
FAM195A
COG8
SLX4
SPIRE2
DCTN5
MT4
GNPTG
ZNF469
GLYR1
GLIS2
GPT2
B3GNT9
ZSCAN10
NFATC2IP
CIRH1A
ZNRF1
ABCC11
NKD1
CNTNAP4
C16orf45
RHOT2
RSPRY1
C16orf93
ZNF598
HN1L
SPSB3
TIGD7
MYLK3
MARVELD3
COG7
SNX29
MTSS1L
ZNF764
CENPBD1
ZNF276
CCDC102A
KCNG4
ORAI3
SDR42E1
ABCC12
PRRT2
ERI2
STX1B
CCDC101
RPUSD1
CMTM1
PKD1L2
FLYWCH2
VASN
ZNF689
SLC5A11
C16orf42
RNF166
RMI2
ACSM1
WFIKKN1
EXOSC6
C16orf46
NTAN1
FOPNL
DNAAF1
ACSM2A
DCUN1D3
NRN1L
CMTM3
C16orf78
SPATA2L
C16orf55
NOXO1
CCDC78
ANKRD26P1
IQCK
ZG16B
PRSS30P
PAQR4
ZC3H18
GPR139
CDYL2
ANKS3
FAM100A
SEPT12
ZNF720
TMEM219
EARS2
SNX20
TMEM170A
SLC38A8
VWA3A
OTOA
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
TEKT5
RNF151
C16orf11
FBXL16
LOC146336
C16orf92
GSG1L
SLC22A31
IL34
ZNF597
CCDC64B
TMED6
LOC146481
FLJ30679
LOC146513
ZNF785
ZNF688
PRSS36
C16orf89
C16orf71
ZFPM1
ADAD2
ITPRIPL2
C16orf82
ZFP1
ADAMTS18
FAM86A
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
WDR90
EME2
NLRC3
NSMCE1
ZNF48
PDILT
CPNE2
GPR114
PRSS54
CES5A
GPR97
IL27
KCTD13
ASPHD1
C16orf73
MPV17L
PDZD9
CNEP1R1
ANKS4B
PRSS33
PYDC1
NOMO2
CCDC79
CES4A
EXOC3L1
LOC283856
LINC00304
LOC283867
NPW
C16orf79
PGP
LINC00514
FLJ39639
LOC283888
C16orf54
INO80E
HTA
LOC283914
LOC283922
NUDT7
FBXL19-AS1
ZNF843
NHLRC4
C16orf91
TMEM114
PDXDC2P
CLEC18C
MT1DP
SNAI3
PKD1P1
PRSS53
JMJD8
FAM92B
C16orf96
ZKSCAN2
ATXN1L
PKD1L3
ACSM2B
CLEC18A
CTU2
PRSS41
TEPP
SLC6A10P
SLC7A5P2
PRR25
SBK1
LOC388242
C16orf87
LOC388276
C16orf86
C1QTNF8
PTX4
LOC390705
CES1P2
PABPN1L
BCAR4
C16orf88
CRYM-AS1
FLJ21408
FLJ26245
LOC400548
LOC400550
LOC400558
MSLNL
C16orf74
MIR138-2
MIR140
NOMO3
LOC440335
SNX29P2
LOC440354
LOC440356
CSDAP1
HERC2P4
CTRB2
MIR328
SULT1A4
TRIM72
CLEC18B
SLX1A
BOLA2
LOC554206
SNORA10
MIR193B
LOC595101
SNORD68
UBE2MP1
LOC606724
LOC613037
LOC613038
MIR484
LOC641298
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
FLJ42627
CCDC154
C16orf90
LINC00273
ABCA17P
LOC652276
ABCC6P1
KIAA0895L
RRN3P2
TP53TG3C
LOC653786
ZG16
BOLA2B
SNORA30
SNORA46
SNORA50
SNORA78
SNORD71
SNORD111
MIR548D2
MIR662
LOC727710
EIF3CL
LOC729264
TP53TG3B
LOC729513
SHISA9
ABCC6P2
RRN3P1
C16orf52
LOC732275
SNHG9
CEMP1
FAM18A
SNORD111B
MIR940
MIR365A
LOC100128788
LOC100128881
LOC100129617
LOC100130015
LOC100130700
LOC100130894
SYCE1L
RRN3P3
LOC100132247
KIAA0664L3
LOC100134368
MIR1225
LOC100190986
LOC100271836
DDX11L10
LOC100287036
LOC100289092
MIR1538
MIR1972-1
MIR1910
MIR762
SNORA70D
MIR3180-3
MIR3182
MIR3180-1
MIR3179-2
MIR548X
MIR1972-2
MIR3180-2
MIR3179-1
MIR3178
MIR3179-3
MIR3177
MIR3176
MTRNR2L4
MIR3677
MIR3180-4
MIR3935
MIR548AA2
MIR3180-5
LOC100505619
LOC100505865
LOC100506083
LOC100506172
C16orf95
LOC100506655
ERVK13-1
LOC100507501
LOC100507577
LOC100507589
SLX1A-SULT1A3
SLX1B-SULT1A4
CORO7-PAM16
CKLF-CMTM1
MIR4720
MIR4722
MIR4719
MIR4718
MIR4519
MIR4717
MIR4721
MIR4516
MIR548AE2
MIR4518
MIR4517
SNX29P1
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 21 significant results found.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 2121 0.17 0.443 1 0.15 -0.388 1
1q 1955 0.39 8.69 0 0.09 -2.45 1
2p 924 0.12 -2 1 0.12 -2.16 1
2q 1556 0.13 -1.5 1 0.12 -1.67 1
3p 1062 0.09 -3.1 1 0.14 -1.18 1
3q 1139 0.10 -2.61 1 0.13 -1.8 1
4p 489 0.11 -2.41 1 0.18 -0.215 1
4q 1049 0.09 -3.12 1 0.18 0.079 1
5p 270 0.14 -1.67 1 0.19 0.184 0.979
5q 1427 0.07 -3.36 1 0.26 3.29 0.0022
6p 1173 0.39 7.42 5.92e-13 0.34 5.59 6.37e-08
6q 839 0.10 -2.03 1 0.54 13.6 0
7p 641 0.46 10.5 0 0.09 -2.63 1
7q 1277 0.47 11.3 0 0.07 -2.85 1
8p 580 0.25 2.54 0.0242 0.22 1.3 0.289
8q 859 0.32 5.22 5.89e-07 0.09 -2.82 1
9p 422 0.09 -2.25 1 0.62 16.4 0
9q 1113 0.05 -3.45 1 0.49 12.1 0
10p 409 0.02 -4.75 1 0.45 10.2 0
10q 1268 0.00 -4.89 1 0.47 11.9 0
11p 862 0.05 -4.15 1 0.29 4.41 2.49e-05
11q 1515 0.07 -3.16 1 0.36 7.51 1.98e-13
12p 575 0.09 -3.34 1 0.13 -1.76 1
12q 1447 0.04 -4.61 1 0.16 -0.524 1
13q 654 0.18 -0.00534 1 0.19 0.463 0.836
14q 1341 0.07 -3.54 1 0.23 2.13 0.065
15q 1355 0.14 -1.07 1 0.08 -3.18 1
16p 872 0.09 -3.23 1 0.13 -1.63 1
16q 702 0.08 -3.46 1 0.21 1.12 0.369
17p 683 0.09 -2.94 1 0.24 2.09 0.065
17q 1592 0.24 2.61 0.022 0.12 -1.61 1
18p 143 0.13 -2.06 1 0.23 1.48 0.225
18q 446 0.10 -2.91 1 0.19 0.213 0.979
19p 995 0.09 -3.33 1 0.10 -2.69 1
19q 1709 0.09 -2.9 1 0.09 -2.74 1
20p 355 0.28 3.41 0.00179 0.08 -3.42 1
20q 753 0.35 6.4 5.93e-10 0.04 -4.33 1
21q 509 0.12 -2.32 1 0.16 -0.91 1
22q 921 0.23 1.97 0.0952 0.14 -1.35 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/SKCM/1551855/2.GDAC_MergeDataFiles.Finished/SKCM.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 219 Input Tumor Samples.

Tumor Sample Names
TCGA-BF-A1PU-01A-11D-A192-01
TCGA-BF-A1PV-01A-11D-A192-01
TCGA-BF-A1PX-01A-12D-A192-01
TCGA-BF-A1PZ-01A-11D-A192-01
TCGA-BF-A1Q0-01A-21D-A192-01
TCGA-D3-A1Q1-06A-21D-A194-01
TCGA-D3-A1Q3-06A-11D-A194-01
TCGA-D3-A1Q4-06A-11D-A194-01
TCGA-D3-A1Q5-06A-11D-A194-01
TCGA-D3-A1Q6-06A-11D-A194-01

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.

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)
[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)
[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)