SKCM-TM: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16a (cga svn revision 43808).

Summary

There were 236 tumor samples used in this analysis: 23 significant arm-level results, 23 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 - 23 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
1p12 8.4636e-09 1.1978e-08 chr1:120039597-120523954 10
5p15.33 2.2909e-06 2.2909e-06 chr5:1019815-1288018 6
1q44 1.1475e-06 8.6854e-06 chr1:245627602-247069231 8
17q25.3 1.7733e-05 1.7733e-05 chr17:71814085-81195210 226
3p13 2.2241e-05 2.2241e-05 chr3:69742187-70094803 1
6p25.1 3.3653e-05 3.3653e-05 chr6:1-13321855 83
12q15 2.9894e-06 7.9315e-05 chr12:69120903-69374775 4
22q13.2 9.4833e-05 9.4833e-05 chr22:41362750-41845216 10
7q34 0.00012523 0.00012523 chr7:135929407-143628771 87
11q13.3 1.2156e-06 0.00014839 chr11:68871640-70221716 11
15q24.3 0.00047142 0.00047142 chr15:75714654-102531392 238
4q12 0.0058936 0.0058936 chr4:55750164-55761654 0 [KIT]
7p22.3 0.0083214 0.0083214 chr7:1-8532843 93
12q14.1 1.2156e-06 0.013582 chr12:58135797-58374945 14
6q12 0.016771 0.016771 chr6:63915276-66023503 4
1q21.3 9.7831e-05 0.041783 chr1:120523956-157519894 345
8q11.21 0.032651 0.045159 chr8:51911225-52360895 1
8q24.21 0.013582 0.047527 chr8:101236904-146364022 272
19p13.2 0.050508 0.050508 chr19:7300056-7398264 0 [INSR]
5q35.3 0.070023 0.070023 chr5:175728395-179840507 81
11q13.4 0.00036982 0.081271 chr11:68695898-81526572 126
9p24.1 0.095154 0.095154 chr9:4135839-5703393 18
20q13.2 0.17023 0.17023 chr20:46491743-63025520 200
Genes in Wide Peak

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

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

Genes
NOTCH2
HMGCS2
HSD3B1
ADAM30
PHGDH
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 S2.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
MIR4635
Genes in Wide Peak

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

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

Genes
AHCTF1
SCCPDH
KIF26B
TFB2M
SMYD3
LOC149134
CNST
LOC255654
Genes in Wide Peak

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

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

Genes
ASPSCR1
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
AANAT
ACOX1
ACTG1
BIRC5
ARHGDIA
CD7
CDK3
CSNK1D
SLC25A10
EVPL
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICT1
FOXK2
ITGB4
LGALS3BP
LLGL2
MAFG
NPTX1
P4HB
PDE6G
PRPSAP1
PYCR1
PCYT2
RAC3
RFNG
RPL38
MRPL12
SEC14L1
SECTM1
SRSF2
SGSH
SUMO2
SRP68
TBCD
TIMP2
TK1
CBX4
DNAH17
GALR2
SPHK1
SOCS3
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
RECQL5
PGS1
AATK
KIAA0195
EIF4A3
ALYREF
BAIAP2
ATP5H
ST6GALNAC2
SEPT9
CD300C
RAB40B
CD300A
TMC6
AZI1
GGA3
JMJD6
EXOC7
KCTD2
WBP2
FSCN2
NAT9
NARF
SAP30BP
NT5C
CDR2L
MRPS7
HN1
DCXR
ANAPC11
SIRT7
TMEM104
CCDC40
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
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
TRIM65
UNC13D
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
SLC26A11
ENDOV
C17orf89
LINC00482
TMEM105
METRNL
RAB37
ENPP7
C17orf90
CCDC137
ARL16
CD300E
OTOP3
FAM195B
GPR142
ZACN
BTBD17
AATK-AS1
FLJ43681
FLJ45079
TEX19
MXRA7
FLJ90757
MIR338
C17orf109
LINC00338
SCARNA16
SNORD1A
SNORD1B
SNORD1C
MIR636
MIR657
PRCD
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR3186
MIR3678
MIR3615
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4738
MIR4740
MIR4730
LOC100653515
Genes in Wide Peak

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

Table S5.  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 6p25.1.

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

Genes
IRF4
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CDYL
LY86
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
TBC1D7
NRN1
TMEM14C
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
C6orf195
PIP5K1P1
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
PSMG4
DKFZP686I15217
C6orf201
ERVFRD-1
PPP1R3G
HULC
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4645
Genes in Wide Peak

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

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

Genes
MDM2
CPM
SLC35E3
NUP107
Genes in Wide Peak

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

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

Genes
EP300
hsa-mir-1281
RANGAP1
TEF
RBX1
TOB2
ZC3H7B
L3MBTL2
CHADL
MIR1281
Genes in Wide Peak

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

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

Genes
BRAF
KIAA1549
CREB3L2
hsa-mir-490
CASP2
CHRM2
CLCN1
EPHA1
EPHB6
KEL
NDUFB2
PIP
PRSS1
PRSS2
TAS2R38
PTN
AKR1D1
SSBP1
TBXAS1
ZYX
TRIM24
MGAM
DGKI
FAM131B
FAM115A
CLEC5A
MKRN1
DENND2A
HIPK2
ATP6V0A4
TAS2R3
TAS2R4
LUC7L2
MRPS33
TAS2R5
TRPV6
AGK
TRPV5
ZC3HAV1
KIAA1147
PARP12
TTC26
JHDM1D
SLC37A3
OR6W1P
ADCK2
ZC3HAV1L
LOC93432
OR9A4
OR9A2
C7orf34
TMEM139
PRSS37
SVOPL
PRSS58
TRY6
LOC154761
CLEC2L
C7orf55
TMEM213
UBN2
TAS2R39
TAS2R40
TAS2R41
FLJ40852
LOC285965
FAM115C
TAS2R60
CTAGE6P
OR6V1
KLRG2
LOC349160
GSTK1
RAB19
CTAGE15P
WEE2
MIR490
LOC730441
LOC100124692
LOC100129148
LOC100130880
LOC100134229
LOC100134713
MOXD2P
MTRNR2L6
LOC100507421
MIR4468
Genes in Wide Peak

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

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

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

This is the comprehensive list of amplified genes in the wide peak for 15q24.3.

Table S11.  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
ACAN
ALDH1A3
ANPEP
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CRABP1
CSPG4
CTSH
ETFA
FAH
FES
IDH3A
IGF1R
IL16
IREB2
ISG20
MAN2A2
MEF2A
MFGE8
NMB
FURIN
PCSK6
PDE8A
PLIN1
POLG
PSMA4
PTPN9
RASGRF1
RCN2
RLBP1
RPS17
SH3GL3
SNRPA1
NR2F2
TYRO3P
AP3B2
ST8SIA2
PEX11A
IQGAP1
PSTPIP1
PRC1
SLC28A1
HOMER2
ZNF592
SV2B
ARNT2
SNUPN
TSPAN3
AP3S2
HMG20A
SEMA4B
CIB2
CIB1
MTHFS
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
SIN3A
FBXO22
VPS33B
MRPL46
OR4F4
SLCO3A1
SCAPER
HDGFRP3
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2
ZSCAN2
DET1
LINS
FANCI
IMP3
DNAJA4
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
ADAMTSL3
KIAA1199
ALPK3
FAM108C1
MESDC1
KLHL25
CPEB1
AEN
ISL2
TTC23
MRPS11
EFTUD1
LRRK1
PEAK1
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
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
LOC645752
SH2D7
LOC646938
GOLGA6L10
LOC648809
SCARNA15
FBXO22-AS1
MIR549
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
MIR3529
MIR4515
MIR4714
Genes in Wide Peak

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

Table S12.  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 12q14.1.

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

Genes
CDK4
hsa-mir-26a-2
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
METTL21B
XRCC6BP1
MARCH9
AGAP2
MIR26A2
LOC100506844
Genes in Wide Peak

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

Table S14.  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 1q21.3.

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

Genes
ARNT
BCL9
MUC1
NOTCH2
NTRK1
PRCC
TPM3
PDE4DIP
hsa-mir-765
hsa-mir-9-1
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
BGLAP
CHRNB2
CKS1B
CLK2
CRABP2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
HDGF
IL6R
ILF2
INSRR
IVL
KCNN3
LMNA
LOR
MCL1
SMCP
MEF2D
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
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
SH2D2A
PRPF3
ARHGEF2
SEC22B
CHD1L
SLC25A44
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
PMF1
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SMG5
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
C1orf56
MSTO1
GOLPH3L
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
SNX27
ANP32E
ISG20L2
FCRL5
HORMAD1
POLR3GL
TMEM79
LCE3D
AQP10
PYGO2
NUP210L
MEX3A
C1orf85
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
C1orf182
IQGAP3
APOA1BP
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
LRRC71
SPRR4
PPIAL4A
TTC24
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
CYCSP52
LOC375010
PEAR1
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
NBPF9
MIR9-1
HIST2H2BF
ETV3L
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
MIR765
MIR190B
C1orf68
MSTO2P
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505666
PMF1-BGLAP
TNFAIP8L2-SCNM1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.21.

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

Genes
PXDNL
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
ADCY8
ANGPT1
ANXA13
ATP6V1C1
BAI1
CYC1
CYP11B1
CYP11B2
DPYS
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
EIF3E
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PLEC
POU5F1B
PTK2
PVT1
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
TAF2
TG
KLF10
TRHR
TRPS1
TSTA3
COL14A1
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
LY6D
JRK
EIF3H
DGAT1
GPAA1
WISP1
FOXH1
EBAG9
LRRC14
TTC35
RIMS2
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
KHDRBS3
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
ZFPM2
SCRIB
LRRC6
DCAF13
RNF19A
FBXL6
OPLAH
PABPC1
KCNV1
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
FAM135B
PHF20L1
ZNF706
VPS28
FAM203A
KCNK9
C8orf55
UBR5
FAM49B
AZIN1
CHRAC1
EXOSC4
LY6K
TRMT12
OXR1
WDYHV1
SLC39A4
SYBU
GSDMC
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
GSDMD
BAALC
ZNF696
GRHL2
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
NACAP1
NCALD
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
PKHD1L1
NAPRT1
WDR67
HPYR1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
CTHRC1
TOP1MT
ZNF572
ABRA
LYPD2
TMEM71
TMEM65
LOC157381
C8orf56
ANKRD46
FAM84B
TMEM74
FAM91A1
SLC30A8
COL22A1
SNX31
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
SPATC1
FLJ43860
MAFA
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
FLJ42969
C8orf85
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
C8orf73
SCXB
RAD21-AS1
FER1L6
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR937
MIR939
LOC100128338
SCXA
LOC100130231
CCDC166
LOC100131726
LOC100133669
LOC100288181
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR1208
MIR3151
LOC100499183
MIR3610
LOC100507117
ZHX1-C8ORF76
MIR4663
MIR4472-1
MIR4664
MIR4471
PCAT1
LINC00536
Genes in Wide Peak

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

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

Genes
NSD1
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
CANX
CLTB
DBN1
F12
FGFR4
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
LTC4S
MAPK9
PROP1
SLC34A1
SNCB
ZNF354A
SQSTM1
PDLIM7
ADAMTS2
MAML1
GFPT2
RGS14
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
ZNF346
TSPAN17
PRELID1
ZNF354C
C5orf45
DDX41
NOP16
UIMC1
RAB24
FAM193B
TMED9
CDHR2
NHP2
RNF130
KIAA1191
CLK4
GMCL1P1
RMND5B
DOK3
ZFP2
RUFY1
PRR7
MXD3
AGXT2L2
UNC5A
COL23A1
GPRIN1
ZNF354B
HIGD2A
LOC202181
EIF4E1B
RASGEF1C
FAM153A
ARL10
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
C5orf25
MIR340
CBY3
FAM153C
LOC728554
AACSP1
MIR1229
MIR4281
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.4.

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

Genes
CCND1
NUMA1
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
PHOX2A
ARRB1
CAPN5
SERPINH1
CLNS1A
DHCR7
CTTN
FGF3
FGF4
FOLR1
FOLR2
FOLR3
LRRC32
IGHMBP2
INPPL1
KRTAP5-9
MAP6
MYO7A
NDUFC2
OMP
P2RY2
P2RY6
PAK1
PDE2A
PRKRIR
RAB6A
SNORD15A
RPS3
THRSP
UCP2
UCP3
UVRAG
WNT11
PPFIA1
FADD
SPCS2
ARHGEF17
GAB2
FCHSD2
FGF19
KCNE3
IL18BP
POLD3
STARD10
NEU3
SLCO2B1
SHANK2
FAM168A
CHRDL2
C11orf51
TSKU
C2CD3
ODZ4
MYEOV
C11orf67
CHCHD8
PPME1
MRPL48
RSF1
LAMTOR1
ANO1
NADSYN1
FAM86C1
RNF121
ACER3
C11orf30
USP35
KRTAP5-8
PLEKHB1
KCTD14
ALG8
NARS2
MOGAT2
PAAF1
GDPD5
CLPB
DGAT2
RELT
ATG16L2
INTS4
SNORD15B
MRGPRD
MRGPRF
ARAP1
XRRA1
B3GNT6
TPCN2
GDPD4
ORAOV1
LRTOMT
DEFB108B
RNF169
AQP11
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
OR2AT4
DNAJB13
KRTAP5-10
LIPT2
GUCY2E
FLJ42102
MIR139
KRTAP5-7
KRTAP5-11
MIR326
MIR708
LOC100129216
LOC100133315
MIR548K
MIR3165
MIR3664
LOC100507050
NDUFC2-KCTD14
MIR4696
MIR4692
Genes in Wide Peak

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

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

Genes
JAK2
CD274
hsa-mir-101-2
INSL4
RLN1
RLN2
SLC1A1
RCL1
INSL6
AK3
C9orf68
CDC37L1
C9orf46
KIAA1432
PDCD1LG2
GLIS3
PPAPDC2
MIR101-2
Genes in Wide Peak

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

Table S21.  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

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 3.4126e-158 1.4317e-153 chr9:21959052-21997722 2
11q23.3 1.7171e-20 1.7171e-20 chr11:106886059-126295275 236
10q23.31 3.6757e-11 1.5984e-10 chr10:89617158-90034038 2
4q34.3 6.7335e-10 6.7335e-10 chr4:178911874-183060693 1
2q37.3 8.8278e-08 8.8278e-08 chr2:239007902-243199373 64
6q26 1.2625e-07 1.2264e-07 chr6:160874064-165698161 12
1p36.31 7.319e-08 2.0147e-06 chr1:1-6847369 137
15q15.3 5.0813e-09 1.367e-05 chr15:36217164-50717067 167
5q31.3 1.8334e-05 5.4729e-05 chr5:132435573-166712758 326
10p15.3 0.00041036 0.00041036 chr10:1-857150 4
16p13.3 0.001605 0.0016644 chr16:5144019-7771745 1
1p22.1 0.0018479 0.0080162 chr1:74658330-120162151 318
16q24.3 0.0080323 0.0080323 chr16:78016120-90354753 123
15q13.3 1.052e-07 0.0088559 chr15:31280297-33605300 16
14q32.2 0.011339 0.011212 chr14:78397628-107349540 292
19p13.3 0.014968 0.014968 chr19:1-2350207 99
10q26.3 0.0023412 0.025786 chr10:134944852-135093385 6
9p24.1 6.2644e-11 0.051218 chr9:7799607-12693402 1
16q12.1 0.051208 0.051218 chr16:31772318-64981096 137
5q11.2 0.0177 0.080807 chr5:58145167-59787985 3
12q23.3 0.0080323 0.085254 chr12:73057951-133851895 443
3q23 0.087208 0.089575 chr3:107095936-198022430 622
13q34 0.13215 0.13342 chr13:1-115169878 414
8p23.3 0.17124 0.17654 chr8:1-31499098 262
12p13.31 0.18464 0.18617 chr12:1-18838946 256
22q13.31 0.22425 0.22312 chr22:43902280-51304566 97
7q31.1 0.24083 0.23217 chr7:1-159138663 1148
12q24.33 0.014218 0.23217 chr12:73057951-133851895 443
Genes in Wide Peak

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

Table S22.  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 S23.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
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
FDX1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
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
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
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
PKNOX2
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
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
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
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
LOC100499227
MIR3656
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 S24.  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 S25.  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 2q37.3.

Table S26.  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
PER2
HDAC4
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
TRAF3IP1
ANO7
THAP4
ANKMY1
ASB1
HES6
RNPEPL1
GAL3ST2
C2orf54
ILKAP
ING5
MGC16025
TWIST2
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LOC200772
CXXC11
DUSP28
ESPNL
AQP12A
KLHL30
OR6B2
FLJ43879
MIR149
LOC643387
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 6q26.

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

Genes
LPA
MAP3K4
PARK2
PLG
QKI
AGPAT4
AGPAT4-IT1
LPAL2
PACRG
LOC285796
DKFZp451B082
CAHM
Genes in Wide Peak

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

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

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

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

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

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

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

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

Genes
CD74
EBF1
ITK
PDGFRB
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
ADRA1B
ADRB2
ANXA6
ATOX1
CAMK2A
CAMLG
CCNG1
CD14
CDC25C
CDX1
CSF1R
CSNK1A1
CTNNA1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EGR1
ETF1
FABP6
FAT2
FGF1
GABRA1
GABRA6
GABRB2
GABRG2
GFRA3
GLRA1
GM2A
GPX3
GRIA1
NR3C1
HARS
HMMR
HSPA9
NDST1
HTR4
IK
IL9
IL12B
LECT2
SMAD5
MFAP3
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPP2CA
PPP2R2B
PURA
RPS14
SGCD
SKP1
SLC6A7
SPARC
SPINK1
SPOCK1
TAF7
TCF7
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
PTTG1
CNOT8
HAND1
MED7
MYOT
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
SLU7
SEC24A
C5orf4
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
SYNPO
ABLIM3
HMGXB3
ARHGAP26
FSTL4
ATP10B
PHF15
LARP1
HARS2
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
IL17B
MAT2B
MRPL22
PCDHB1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
LARS
CXXC5
KDM3B
RBM27
PCDHB18
PCDHB17
WDR55
ANKHD1
THG1L
TMCO6
GALNT10
RBM22
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
C5orf15
TRPC7
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
ARAP3
PCYOX1L
CCNJL
SH3TC2
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
C5orf32
SPINK7
HAVCR2
C5orf62
FCHSD1
CDKN2AIPNL
TIMD4
ZNF300
MYOZ3
SLC35A4
PWWP2A
C1QTNF2
SCGB3A2
PPARGC1B
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
C5orf24
C5orf20
SLC36A2
SPINK13
SLC25A48
LOC153469
ZMAT2
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
SPATA24
DNAJC18
STK32A
SLC36A1
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
TMEM173
LOC340073
LOC340074
ARSI
IRGM
CATSPER3
NIPAL4
DND1
FLJ38109
LOC389332
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
MIR146A
SPINK14
FNDC9
IGIP
TIFAB
ECSCR
GRXCR2
SPINK9
SNHG4
MIR143HG
LOC729080
VTRNA2-1
MIR874
C5orf52
MIR1289-2
MIR3142
MIR3141
MIR3655
MIR3661
LOC100505658
MIR4461
Genes in Wide Peak

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

Table S31.  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 16p13.3.

Table S32.  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 1p22.1.

Table S33.  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
ACADM
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FPGT
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
SNORD45B
SNORD45A
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
TNNI3K
SH3GLB1
HAO2
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
ST6GALNAC5
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRC39
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
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
LHX8
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC644242
LOC646626
LOC648740
NBPF6
SCARNA2
SNORD45C
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
FPGT-TNNI3K
TMEM56-RWDD3
MIR2682
MIR4423
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

Table S34.  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
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
C16orf7
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
PRDM7
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
C16orf61
JPH3
KIAA1609
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
MGC23284
LINC00311
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722
Genes in Wide Peak

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

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

Genes
hsa-mir-211
CHRNA7
TRPM1
SCG5
ARHGAP11A
GREM1
KLF13
ULK4P3
ULK4P1
OTUD7A
LOC283710
FMN1
MIR211
ULK4P2
LOC100288615
TMCO5B
Genes in Wide Peak

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

Table S36.  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
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 19p13.3.

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

Genes
STK11
TCF3
FSTL3
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
MKNK2
GPX4
GZMM
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
MADCAM1
SF3A2
PPAP2C
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
DAZAP1
FGF22
THEG
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
WDR18
REXO1
LPPR3
OR4F17
FAM108A1
KLF16
DOT1L
KISS1R
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
GRIN3B
JSRP1
MOB3A
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
CSNK1G2-AS1
ODF3L2
ADAMTSL5
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
FAM138F
LINGO3
FAM138A
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
hsa-mir-202
ADAM8
UTF1
VENTX
KNDC1
MIR202
Genes in Wide Peak

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

Table S39.  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 16q12.1.

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

Genes
CYLD
HERPUD1
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
ADCY7
AMFR
BBS2
CBLN1
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
SNX20
LOC146481
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
LOC283856
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 5q11.2.

Table S41.  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 12q23.3.

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

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497
Genes in Wide Peak

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

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

Genes
BCL6
FOXL2
EIF4A2
ETV5
GATA2
LPP
MLF1
PIK3CA
RPN1
SOX2
TFRC
GMPS
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
AADAC
ACPP
ACTL6A
ADCY5
ADPRH
AGTR1
AHSG
APOD
ATP1B3
ATP6V1A
ATR
BCHE
BDH1
CASR
CD80
CD86
CD47
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
CRYGS
CSTA
DGKG
DLG1
DRD3
DVL3
ECT2
EHHADH
EIF4G1
EPHB1
EPHB3
MECOM
FGF12
GAP43
GHSR
GOLGB1
GP5
GP9
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRG
HES1
IL1RAP
IL12A
ITGB5
KNG1
KPNA1
KPNA4
LSAMP
TM4SF1
MBNL1
MCM2
MFI2
MME
CD200
MUC4
MYLK
NCK1
NDUFB4
NDUFB5
OPA1
CLDN11
P2RY1
PAK2
PCCB
PCYT1A
PFN2
SERPINI1
SERPINI2
PIK3CB
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
POLR2H
PPP1R2
PPP2R3A
PRKCI
MASP1
PSMD2
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
RPL35A
RYK
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC15A2
SLCO2A1
HLTF
SSR3
SST
TERC
TF
TFDP2
THPO
SEC62
TM4SF4
TRH
TRPC1
UPK1B
UMPS
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
FXR1
SOX14
BFSP2
RUVBL1
TP63
CHRD
B4GALT4
B3GALNT1
SNX4
TNFSF10
NR1I2
EIF2B5
MBD4
H1FX
USP13
KALRN
CLDN1
MAP3K13
SLC33A1
COPB2
ADIPOQ
CHST2
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
KIAA0226
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
COX17
TNK2
ALG3
CD96
KCNMB2
STAG1
IGF2BP2
CLDN16
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
FSTL1
MRPL3
PDCD10
RNF13
MGLL
MRAS
COPG
SLITRK3
NLGN1
NCBP2
MYH15
PLCH1
TMCC1
TNIK
MCF2L2
PLXND1
ATP11B
DNAJC13
U2SURP
VPS8
C3orf27
ACAP2
ANAPC13
ARMC8
C3orf17
WWTR1
PVRL3
TIPARP
UBXN7
ARHGEF26
ZBTB20
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
MORC1
SERP1
GOLIM4
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
SCHIP1
PIK3R4
PODXL2
TRAT1
NMD3
COMMD2
A4GNT
DBR1
ZNF639
CLDN18
TIMMDC1
RSRC1
PLA1A
AMOTL2
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
P2RY13
IL20RB
GPR87
DCUN1D1
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
KLHL24
SIDT1
SLC41A3
PIGX
SLC35A5
IFT57
MSL2
TBCCD1
FAIM
SLC25A36
DPPA4
LEPREL1
TMEM39A
ABCF3
LSG1
ABHD10
PARL
CDV3
MFN1
YEATS2
IFT122
WDR52
EAF2
MYNN
EIF5A2
MUC13
SUCNR1
MCCC1
LXN
C3orf37
MRPS22
POGLUT1
BBX
CCNL1
PLSCR2
PLSCR4
HRASLS
MRPL47
ISY1
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
KIAA1524
SLC7A14
SRPRB
SENP2
GNB4
BPESC1
EEFSEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZMAT3
ATG3
MFSD1
CCDC14
FNDC3B
P2RY12
TMEM108
ZXDC
ZBED2
ATP13A3
HSPBAP1
C3orf52
VEPH1
QTRTD1
TBL1XR1
ZBBX
LRRC31
CCDC48
NEK11
UBA5
MAP6D1
PHC3
C3orf36
ARL14
NAA50
PIGZ
CEP63
CEP70
ABTB1
TMEM22
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
ZIC4
ACAD11
IQCG
ATP13A4
FYTTD1
CHCHD6
HPS3
ARPM1
SLC12A8
RETNLB
CCDC54
MGC2889
LRCH3
DIRC2
CEP19
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
LOC90246
C3orf25
TMEM41A
BOC
SPSB4
ACPL2
TMEM44
EGFEM1P
CAMK2N2
TXNRD3
OSBPL11
LRRC58
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
CPNE4
CCDC58
DNAJC19
OTOL1
FAM131A
CD200R1
ZDHHC19
LRRC15
FAM43A
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
GRK7
TMEM207
RTP1
RPL32P3
H1FOO
PISRT1
TTC14
DTX3L
LOC151658
PPM1L
WDR49
LRRC34
DPPA2
CCDC80
BTLA
MB21D2
XXYLT1
ROPN1B
C3orf22
C3orf55
C3orf79
CCDC50
PYDC2
SPICE1
NUDT16P1
LOC152217
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
RNF168
CHST13
KBTBD12
DHX36
HTR3C
DZIP1L
ALG1L
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
PTPLB
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
LOC253573
NAALADL2
ZDHHC23
NUP210P1
TCTEX1D2
C3orf43
SDHAP1
COL6A5
GK5
PLCXD2
GCET2
UTS2D
LSAMP-AS3
SLC9A9
LOC285205
DNAJB8-AS1
HTR3E
RABL3
IGSF10
C3orf33
SLC9A10
C3orf70
TPRG1
ILDR1
TRIM59
TRIM42
RAB43
CCDC39
KY
LOC339874
LOC339894
LOC339926
LPP-AS2
H1FX-AS1
LRRIQ4
SAMD7
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
CCDC37
NPHP3-AS1
ANKRD18DP
NMNAT3
LRRC33
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
MIR198
ARGFX
SNORD2
SNORA4
ALG1L2
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
SNORA81
SNORD66
MIR551B
MIR567
MIR568
MIR569
MIR570
SDHAP2
FAM157A
FAM86HP
PRR23A
LOC730091
LOC100125556
MIR922
MIR944
LOC100128023
WWTR1-AS1
LOC100128164
LOC100129550
ZBTB20-AS1
LOC100131551
LOC100131635
SNAR-I
MIR1224
TIPARP-AS1
LOC100289361
MIR1248
MIR1280
MIR548I1
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100505687
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
LOC100507032
MFI2-AS1
LOC100507086
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
NPHP3-ACAD11
ISY1-RAB43
TM4SF19-TCTEX1D2
MIR4796
MIR4797
MIR4788
MIR4789
MIR4446
Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
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
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

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

Genes
PCM1
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
GSR
GTF2E2
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
UBXN8
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
FBXO25
FGF20
ADAMDEC1
CNOT7
PURG
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
AGPAT5
INTS9
CSGALNACT1
HR
PBK
ZNF395
DEFB103B
BIN3
TEX15
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
HMBOX1
MCPH1
PPP1R3B
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
NKX2-6
SGCZ
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
ESCO2
FBXO16
LOC157627
C8orf42
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FLJ10661
XKR6
LOC286059
LOC286083
EFHA2
LOC286114
SCARA5
LOC286135
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
C8orf80
LOC392196
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
C8orf75
MBOAT4
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA1B
FAM90A20
FAM90A19
ZNF705D
LOC100128750
FAM66B
LOC100128993
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR4287
MIR3148
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
LOC100507341
MIR548O2
MIR4659A
MIR4660
MIR4659B
LOC100652791
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.31.

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

Genes
CCND2
ETV6
KDM5A
ZNF384
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
KCNA1
KCNA5
KCNA6
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NINJ2
NOP2
NTF3
OLR1
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
SCNN1A
SLC2A3
SLC6A12
SLC6A13
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
CSDA
DYRK4
GPRC5A
CD163
GDF3
CLSTN3
NCAPD2
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
RAD51AP1
KLRAP1
TSPAN9
STRAP
PRR4
PHB2
KLRK1
ERC1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
PRMT8
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
WNK1
BCL2L14
ADIPOR2
RERGL
PLBD1
NANOG
DUSP16
WNT5B
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
CCDC77
ACRBP
SPSB2
EFCAB4B
RERG
HTR7P1
CACNA2D4
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
FBXL14
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf53
DCP1B
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
B4GALNT3
CLEC9A
C12orf36
LOC283440
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
LOC574538
POU5F1P3
LOC642846
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
LOC100271702
LOC100288778
LOC100292680
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
MIR3649
LOC100506314
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846
Genes in Wide Peak

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

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
PNPLA5
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
LINC00229
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535
Genes in Wide Peak

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

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

Genes
BRAF
CDK6
EGFR
ELN
ETV1
EZH2
HIP1
HNRNPA2B1
HOXA9
HOXA11
HOXA13
MET
PMS2
SMO
AKAP9
IKZF1
SBDS
KIAA1549
MLL3
CREB3L2
CARD11
JAZF1
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
hsa-mir-590
hsa-mir-4284
hsa-mir-4283-2
hsa-mir-3147
hsa-mir-4283-1
hsa-mir-1200
hsa-mir-548n
hsa-mir-550-2
hsa-mir-550-1
hsa-mir-196b
hsa-mir-148a
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ABP1
ACHE
ACTB
ADCY1
ADCYAP1R1
AEBP1
AHR
AKR1B1
AMPH
AOAH
AQP1
ARF5
ASL
ASNS
AZGP1
OPN1SW
BLVRA
BPGM
CACNA2D1
CALCR
CALD1
CALU
CAMK2B
CAPZA2
CASP2
CAV1
CAV2
KRIT1
CCT6A
CD36
SEPT7
CDK5
CFTR
CHN2
CHRM2
AP1S1
CLCN1
CLK2P
COL1A2
CPA1
CPA2
CLDN4
CLDN3
CRHR2
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DGKB
DDC
DFNA5
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
ERV3-1
EVX1
FLNC
GARS
GBAS
GBX1
GCK
GHRHR
GLI3
GNA12
GNAI1
GNB2
GNG11
GNGT1
GPR22
GPER
GPR37
GRB10
GRM3
GRM8
GTF2I
GTF2IP1
GUSB
HGF
MNX1
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
HPVC1
AGFG2
HSPB1
HTR5A
HUS1
ICA1
IFRD1
IGFBP1
IGFBP3
IL6
IMPDH1
INHBA
INSIG1
IRF5
ITGB8
KCND2
KCNH2
KEL
LAMB1
LEP
LFNG
LIMK1
LRCH4
MCM7
DNAJB9
MDH2
MEOX2
MEST
MKLN1
NUDT1
NDUFA4
NDUFA5
NDUFB2
NOS3
CNOT4
NPY
NPTX2
NRCAM
NRF1
OCM2
OGDH
ORC5
SERPINE1
PAX4
PCOLCE
PDE1C
PDGFA
PDK4
SLC26A4
PEX1
CDK14
PGAM2
ABCB1
ABCB4
PHKG1
PIK3CG
PIP
PMS2P1
PMS2L2
PMS2P4
PMS2P5
PMS2P3
PODXL
POLD2
POLR2J
PON1
PON2
PON3
POR
PPIA
PPP1R3A
PRKAR1B
PRKAR2B
PRSS1
PRSS2
RELN
PSMA2
PSMC2
PSPH
TAS2R38
PTN
PTPN12
PTPRN2
PTPRZ1
PURB
RAC1
RALA
RARRES2
RFC2
RHEB
RP9
RPA3
CCL24
SFRP4
SHH
SLC4A2
SLC13A1
SMARCD3
FSCN1
SP4
SPAM1
SRI
AKR1D1
SRPK2
SSBP1
STX1A
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
TWIST1
UBE2H
UPP1
VGF
VIPR2
ZAN
EIF4H
CLIP2
LAT2
WNT2
XRCC2
YWHAG
ZNF3
ZNF12
ZKSCAN1
ZSCAN21
ZNF138
ZP3
ZYX
AIMP2
MAFK
MTERF
SHFM1
TFPI2
ST7
ARHGEF5
ZNF212
TRRAP
FZD1
FZD9
MAD1L1
ZNF282
CUL1
TPST1
FKBP6
CDK13
EIF3B
DNAH11
TRIM24
TAX1BP1
BUD31
SGCE
SKAP2
MGAM
WASL
PLOD3
BAZ1B
CLDN12
DGKI
AP4M1
TBRG4
STK17A
CYTH3
BCL7B
ATP6V1F
ACCN3
PMPCB
ATP5J2
GTF2IRD1
CREB5
PDIA4
NFE2L3
PHF14
UBE3C
FAM131B
SEMA3E
DOCK4
HDAC9
FAM115A
RAPGEF5
SCRN1
KIAA0087
ELMO1
MAGI2
TRIL
POM121
KIAA0415
DMTF1
DNAJB6
ABCF2
MUC12
ARPC1B
ARL4A
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
RAMP3
BET1
CCL26
SEMA3A
NOD1
FAM3C
GPNMB
COG5
ZNHIT1
SEMA3C
AGR2
ARPC1A
SH2B2
IGF2BP3
YKT6
STAG3
ZNF273
PPP1R17
FGL2
CPSF4
FASTK
DBF4
COPS6
KDELR2
ADAP1
ZPBP
DUS4L
NUPL2
HIBADH
ZNF277
INMT
ABCB8
TP53TG1
POU6F2
FKBP9
PDAP1
CBX3
TFEC
LAMB4
LMTK2
POMZP3
PAXIP1
KLHDC10
HECW1
AVL9
PEG10
SSPO
NACAD
SNX13
NUP205
COBL
IQCE
DPY19L1
SUN1
KIAA0895
AHCYL2
NUDCD3
SEC61G
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
LSM5
ZKSCAN5
CLDN15
BRI3
TECPR1
SUMF2
POT1
SOSTDC1
KBTBD2
PTCD1
OSBPL3
CNTNAP2
AUTS2
HYALP1
WIPI2
TES
GIMAP2
INTS1
OR2F1
FBXO24
SLC13A4
TBL2
STEAP1
COPG2
HBP1
DNAJC2
TPK1
SND1
VPS41
TSPAN13
SND1-IT1
EIF2AK1
DENND2A
ZNF777
BBS9
CRCP
RABGEF1
POLM
PCLO
TMEM176B
BZW2
DBNL
HIPK2
WDR91
REPIN1
NPC1L1
SNX8
SNX10
TRA2A
HILPDA
FTSJ2
MDFIC
PILRB
PILRA
FSCN3
NXPH1
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
MLXIPL
CHCHD2
CPA4
NT5C3
TXNDC3
ZNF117
MRPS17
WNT16
ACTL6B
PRKAG2
ZNF107
ZC3HC1
SRRT
GET4
UBE2D4
CCZ1
LUC7L2
MRPS33
STYXL1
ASB4
NUB1
MPP6
NAA38
ADAM22
PION
CYCS
GPR85
TAS2R5
STAG3L1
ANLN
ANKIB1
MIOS
RNF216
CHPF2
CPVL
PUS7
TOMM7
ING3
DDX56
TMEM106B
LRRN3
CROT
EPDR1
ZNF853
ALKBH4
SAMD9
NCAPG2
CYP2W1
HEATR2
CHCHD3
FKBP14
ZCWPW1
C7orf42
WDR60
RBM28
ZDHHC4
TYW1
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
CHST12
TRPV6
CDCA7L
PPP1R9A
CCDC132
URGCP
NSUN5
RADIL
C7orf44
AGK
METTL2B
MLL5
LANCL2
BAIAP2L1
SLC25A40
BCAP29
KLHL7
STK31
MEPCE
TRPV5
ANKRD7
ZC3HAV1
PAPOLB
C1GALT1
FAM20C
SLC12A9
ACN9
YAE1D1
AKR1B10
ANKMY2
TBX20
SMURF1
PHTF2
ACTR3B
KIAA1147
RHBDD2
FAM40B
ESYT2
ZNF398
CCDC146
RBAK
GATAD1
MYL7
EXOC4
RINT1
GALNT11
NEUROD6
FIGNL1
MYO1G
LRRC4
NPVF
HERPUD2
LMBR1
WBSCR17
TMEM168
LINC00244
NOM1
MOSPD3
GIGYF1
CCDC136
TNS3
PARP12
RABL5
CYP3A43
CASD1
STAG3L4
MRPS24
MRPL32
LRRC61
C7orf49
GGCT
C7orf25
ZNF655
C7orf26
PVRIG
C7orf23
GCC1
STEAP4
GAL3ST4
PRKRIP1
MICALL2
C7orf10
C7orf63
CBLL1
ZNF767
C7orf58
TTC26
FBXL18
C7orf69
ORAI2
TTYH3
UPK3B
EEPD1
JHDM1D
OR2AE1
VOPP1
WBSCR16
TSC22D4
TRIM56
ABHD11
TMUB1
CCM2
ZMIZ2
CALN1
ARMC10
TMEM120A
STARD3NL
IMMP2L
CTTNBP2
RBM48
ZNF394
USP42
GTF2IRD2
MYH16
FAM188B
SLC37A3
PSMG3
DNAJC30
C7orf50
KRBA1
TNRC18
FAM126A
FAM71F1
PLEKHA8
C7orf70
POLR2J4
LINC00525
MGC16142
SLC35B4
TMEM209
TMEM60
SCIN
GTPBP10
TRIM4
OR6W1P
ZFAND2A
COX19
CCDC126
ZNF479
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
H2AFV
CEP41
GLCCI1
C7orf29
DTX2
WBSCR22
KIAA1908
TSGA13
GPR146
C7orf30
AGAP3
C7orf13
OR9A4
WBSCR28
TRIM50
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
C7orf57
SVOPL
MTPN
LRGUK
ASB10
PRSS58
C7orf11
SRCRB4D
C7orf31
ASZ1
MUC17
RNF32
ASB15
RUNDC3B
ABCA13
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
VKORC1L1
LOC154822
LOC154860
IQUB
LOC154872
KCTD7
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
AMZ1
WBSCR27
SBDSP1
VPS37D
NSUN5P1
RBM33
AGR3
MGC27345
ZNF92
GALNTL5
ZNF679
RNF133
CDC14C
THAP5
CCDC71L
PKD1L1
GIMAP7
ZNF467
BHLHA15
BMPER
PER4
ZNF800
GIMAP1
ABHD11-AS1
LOC202781
C7orf33
TMEM184A
SAMD9L
C7orf62
ZNF804B
FABP5P3
ZNF498
FAM200A
VWDE
PRPS1L1
TWISTNB
SP8
HOXA11-AS1
PPP1R35
GPC2
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
VSTM2A
DKFZp434L192
TMED4
DKFZP586I1420
C7orf41
PRR15
SRRM3
RSBN1L
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
FERD3L
RPL23P8
NYAP1
SLC29A4
RSPH10B
CCDC129
ZNRF2
SEMA3D
CNPY4
POLR2J2
HEPACAM2
UBN2
FLJ35390
MBLAC1
TMEM196
STEAP1B
RPS2P32
SUN3
FAM133B
TAS2R39
TAS2R40
TAS2R41
NSUN5P2
TFAMP1
STEAP2
POM121L12
LOC285878
CNPY1
LOC285889
INTS4L1
LINC00174
C7orf71
LOC285954
SPDYE1
SNHG15
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
DLX6-AS1
ZNF789
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
ZNF680
UNCX
COL28A1
ABCB5
C7orf46
FAM183B
CTAGE6P
TSPAN33
AGBL3
SEPT14
MACC1
OR6V1
OR2A12
OR2A1
GNAT3
MOGAT3
FAM71F2
STRA8
KLRG2
ZNF713
LINC00265
WDR86
GJC3
DPY19L2P2
LOC349160
GATS
GPR141
FKBP9L
GSTK1
VWC2
TRIM73
NAT16
SLC26A5
LHFPL3
KCP
TRIM74
FLJ43663
RNF148
NPSR1
LOC389458
LOC389493
SPDYE8P
GATSL1
GTF2IRD2B
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
ELFN1
AGMO
GRID2IP
OR2A5
RPL13AP17
ZNF815
LOC401320
LOC401321
LOC401324
RASA4P
C7orf65
FLJ45974
GTF2IRD2P1
LRRD1
FLJ42280
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
UFSP1
AAA1
MIR106B
MIR129-1
MIR148A
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
RNF216P1
PMS2CL
LOC441204
ZNRF2P1
RP9P
ZNF716
LOC441242
TYW1B
SPDYE7P
DTX2P1-UPK3BP1-PMS2P11
SPDYE3
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
FLJ44511
ZNF727
OR2A2
LOC442497
DPY19L2P4
DPY19L2P3
STAG3L3
STAG3L2
SPDYE5
EIF3IP1
LMOD2
MIR335
MIR339
MIR196B
ARHGEF35
TARP
GIMAP6
LOC493754
WEE2
LOC541473
POLR2J3
DPY19L2P1
MIR489
MIR490
FDPSL2A
LOC641746
SEPT7P2
GUSBP10
CCT6P3
CCT6P1
ZNF862
LOC643955
WIPF3
INTS4L2
LOC645249
LOC645591
ZNF890P
AZGP1P1
LOC646329
LOC646762
LOC646999
C7orf73
LOC649395
LOC650226
NCF1
ACTR3C
OCM
SNORA5A
NCF1B
NCF1C
SNORA5B
SNORA5C
SNORA9
SNORA14A
SNORA15
SNORA22
SNORD93
MIR550A1
MIR550A2
MIR589
MIR590
MIR591
MIR592
MIR593
MIR595
LOC723809
MIR653
LOC728066
RSPH10B2
LOC728377
LOC728743
ZNF736
LOC729156
GATSL2
SPDYE6
LOC729852
ISPD
TMEM229A
ZNF735
LOC730441
LUZP6
MIR671
LOC100093631
POM121C
LOC100124692
JAZF1-AS1
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100129427
DPY19L1P1
LOC100129845
LOC100130673
LOC100130705
EFCAB10
LOC100130849
LOC100130880
C7orf72
LOC100131176
LOC100131257
LOC100132707
LOC100132832
LOC100133091
LOC100133311
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
ZNRF2P2
LOC100287482
LOC100287704
LOC100287834
LOC100288524
MOXD2P
LOC100289187
LOC100289561
ZNF783
MIR1200
MIR548F3
MIR548I4
SPDYE2L
MIR548M
MIR548F4
HOTTIP
SAP25
MIR4283-2
MIR548T
MIR4285
MIR4283-1
MIR3147
MIR4284
MIR3146
MTRNR2L6
MIR3609
MIR3943
MIR550B2
MIR3907
MIR3914-1
MIR550B1
MIR3666
MIR3914-2
LOC100505483
LOC100505854
MAGI2-AS3
LOC100506025
LRRC72
LOC100506050
LOC100506136
LOC100506178
HOTAIRM1
LOC100506497
LOC100506585
LOC100506776
LOC100506895
LOC100507421
ATP5J2-PTCD1
INMT-FAM188B
GIMAP1-GIMAP5
RBAK-LOC389458
HOXA10-HOXA9
URGCP-MRPS24
MIR4648
MIR4653
MIR4655
MIR4652
MIR4468
MIR4651
MIR4650-1
MIR4650-2
MIR4649
MIR550A3
MIR4467
MIR4657
MIR4658
MIR4656
LOC100630923
KLHL7-AS1
CYP3A7-CYP3AP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.33.

Table S49.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497
Arm-level results

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

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 2121 0.25 0.423 1 0.22 -0.494 1
1q 1955 0.46 7.56 1.98e-13 0.16 -2.16 1
2p 924 0.23 -1.23 1 0.18 -2.71 1
2q 1556 0.22 -0.89 1 0.17 -2.43 1
3p 1062 0.19 -2.13 1 0.21 -1.76 1
3q 1139 0.24 -0.804 1 0.17 -2.81 1
4p 489 0.18 -2.89 1 0.25 -0.955 1
4q 1049 0.16 -3.06 1 0.25 -0.326 1
5p 270 0.21 -2.2 1 0.30 0.405 0.722
5q 1427 0.14 -3.23 1 0.33 2.46 0.0233
6p 1173 0.46 5.85 1.68e-08 0.44 5.15 7.36e-07
6q 839 0.18 -2.11 1 0.59 10.9 0
7p 641 0.55 9.23 0 0.12 -3.61 1
7q 1277 0.56 10.2 0 0.13 -3.01 1
8p 580 0.37 2.86 0.00934 0.33 1.46 0.191
8q 859 0.47 6.56 2.17e-10 0.18 -2.44 1
9p 422 0.14 -2.88 1 0.69 13.7 0
9q 1113 0.13 -3.23 1 0.56 10.3 0
10p 409 0.04 -5.45 1 0.57 9.96 0
10q 1268 0.00 -5.69 1 0.60 12.1 0
11p 862 0.15 -3.17 1 0.38 3.77 0.000364
11q 1515 0.12 -3.46 1 0.42 5.87 1.41e-08
12p 575 0.18 -3.14 1 0.18 -2.89 1
12q 1447 0.11 -4.66 1 0.19 -2.22 1
13q 654 0.31 1.21 0.451 0.30 0.857 0.456
14q 1341 0.16 -2.86 1 0.34 2.78 0.0108
15q 1355 0.26 0.104 1 0.16 -2.8 1
16p 872 0.15 -3.53 1 0.25 -0.561 1
16q 702 0.16 -3.19 1 0.35 2.62 0.0158
17p 683 0.19 -2.27 1 0.42 4.88 2.61e-06
17q 1592 0.23 -0.57 1 0.27 0.823 0.456
18p 143 0.21 -2.21 1 0.36 2.34 0.0299
18q 446 0.17 -3.28 1 0.32 1.39 0.204
19p 995 0.19 -2.38 1 0.24 -0.647 1
19q 1709 0.21 -1.18 1 0.24 -0.028 1
20p 355 0.43 4.91 2.55e-06 0.11 -4.62 1
20q 753 0.50 7.84 3.11e-14 0.05 -5.47 1
21q 509 0.21 -1.97 1 0.24 -1.01 1
22q 921 0.39 4.19 6.94e-05 0.16 -2.87 1
Xq 1312 0.17 -2.57 1 0.31 1.94 0.0752
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM-TM/2172083/2.GDAC_MergeDataFiles.Finished/SKCM-TM.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

Table 4.  Get Full Table First 10 out of 236 Input Tumor Samples.

Tumor Sample Names
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
TCGA-D3-A1Q7-06A-11D-A192-01
TCGA-D3-A1Q8-06A-11D-A192-01
TCGA-D3-A1Q9-06A-11D-A192-01
TCGA-D3-A1QA-06A-11D-A194-01
TCGA-D3-A1QB-06A-11D-A192-01

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)