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 2.0.16a (cga svn revision 43808).

Summary

There were 253 tumor samples used in this analysis: 23 significant arm-level results, 21 significant focal amplifications, and 31 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 21 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 | 1.8118e-07 | 1.8118e-07 | chr12:69589834-69670720 | 3
1p12 | 2.8369e-07 | 2.8369e-07 | chr1:120024288-120523954 | 10
1q44 | 2.8369e-07 | 2.8369e-07 | chr1:245627602-247069231 | 8
5p15.33 | 2.8369e-07 | 2.8369e-07 | chr5:1019815-1288018 | 6
3p13 | 9.4723e-06 | 9.4723e-06 | chr3:69692982-70094803 | 1
17q25.3 | 1.3245e-05 | 1.3245e-05 | chr17:71814085-81195210 | 226
6p25.1 | 2.3472e-05 | 2.3472e-05 | chr6:1-13321855 | 83
22q13.2 | 5.6425e-05 | 5.6425e-05 | chr22:41362750-41835107 | 10
7q34 | 5.9934e-05 | 5.9934e-05 | chr7:138769073-141734393 | 36
15q24.3 | 0.00092592 | 0.00092592 | chr15:75714654-102531392 | 238
11q13.3 | 1.2139e-05 | 0.0026085 | chr11:68871795-70221716 | 11
7p22.3 | 0.010098 | 0.010098 | chr7:1-8532843 | 93
4q12 | 0.013969 | 0.013969 | chr4:55120558-56011315 | 3
8q11.22 | 0.013587 | 0.019289 | chr8:52233277-52360895 | 1
6q12 | 0.01979 | 0.01979 | chr6:63915276-66023503 | 4
8q24.3 | 0.0022146 | 0.028629 | chr8:101236904-146364022 | 272
19p13.2 | 0.070313 | 0.070313 | chr19:7296453-7398264 | 0 [INSR]
5q35.3 | 0.086046 | 0.086046 | chr5:175337387-180915260 | 110
20q13.2 | 0.095169 | 0.095169 | chr20:47460696-51138698 | 38
11q13.4 | 0.0015926 | 0.1365 | chr11:67196584-81786966 | 160
1p36.11 | 0.19419 | 0.24396 | chr1:1-66991559 | 891

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
hsa-mir-1279
CPSF6
MIR1279

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
ADAM30
PHGDH
REG4
ZNF697
HSD3BP4
NBPF7
LOC644242

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 5p15.33.

Table S4. 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 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 17q25.3.

Table S6. 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 6p25.1.

Table S7. 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 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
NDUFB2
TAS2R38
SSBP1
TBXAS1
MGAM
CLEC5A
MKRN1
DENND2A
HIPK2
TAS2R3
TAS2R4
LUC7L2
MRPS33
TAS2R5
AGK
ZC3HAV1
KIAA1147
PARP12
TTC26
JHDM1D
SLC37A3
ADCK2
OR9A4
PRSS37
CLEC2L
C7orf55
UBN2
FLJ40852
KLRG2
RAB19
WEE2
LOC100129148
LOC100134229
LOC100134713
LOC100507421

Genes in Wide Peak

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

Table S10. 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 11q13.3.

Table S11. 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 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 4q12.

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

Genes
KDR
KIT
PDGFRA

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.22.

Table S14. 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 6q12.

Table S15. 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 8q24.3.

Table S16. 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 S17. 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
FLT4
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
LTC4S
MGAT1
MAPK9
PROP1
SLC34A1
SNCB
ZNF354A
SQSTM1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
ZNF346
TSPAN17
OR4F3
PRELID1
ZNF354C
C5orf45
DDX41
NOP16
UIMC1
RAB24
FAM193B
TMED9
CDHR2
NHP2
RNF130
KIAA1191
CLK4
CNOT6
GMCL1P1
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
AGXT2L2
UNC5A
TRIM41
COL23A1
SCGB3A1
GPRIN1
ZNF354B
OR2Y1
BTNL9
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
FAM153A
ARL10
OR2V2
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
C5orf25
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
CBY3
FAM153C
LOC728554
AACSP1
LOC729678
OR4F29
LOC100132062
LOC100132287
LOC100133331
MIR1229
MIR4281
LOC100507387
MIR4638
LOC100859930

Genes in Wide Peak

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

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

Genes
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-3194
CEBPB
CSE1L
KCNB1
KCNG1
NFATC2
PTGIS
PTPN1
SNAI1
STAU1
UBE2V1
DPM1
B4GALT5
SPATA2
ATP9A
ARFGEF2
SLC9A8
ADNP
SNORD12C
MOCS3
BCAS4
DDX27
ZFP64
RNF114
SALL4
ZNFX1
PARD6B
FAM65C
LOC284751
TMEM189
TMEM189-UBE2V1
ZNFX1-AS1
SNORD12
MIR645
SNORD12B
MIR3194

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-4300
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
ALDH3B1
ALDH3B2
PHOX2A
ARRB1
CAPN5
SERPINH1
CHKA
CLNS1A
CPT1A
DHCR7
CTTN
FGF3
FGF4
FOLR1
FOLR2
FOLR3
LRRC32
GSTP1
IGHMBP2
INPPL1
KRTAP5-9
LRP5
MAP6
MYO7A
NDUFC2
NDUFV1
NDUFS8
OMP
P2RY2
P2RY6
PAK1
PDE2A
PRKRIR
PTPRCAP
RAB6A
SNORD15A
RPS3
RPS6KB2
THRSP
UCP2
UCP3
UVRAG
WNT11
PPFIA1
FADD
AIP
PITPNM1
MTL5
SPCS2
ARHGEF17
GAB2
FCHSD2
FGF19
KCNE3
IL18BP
CDK2AP2
TCIRG1
POLD3
STARD10
NEU3
SLCO2B1
SHANK2
FAM168A
CHRDL2
C11orf51
TSKU
C2CD3
ODZ4
MYEOV
C11orf67
GAL
SUV420H1
CHCHD8
PPME1
CABP2
MRPL48
RSF1
C11orf24
LAMTOR1
ANO1
NADSYN1
FAM86C1
PPP6R3
RNF121
ACER3
C11orf30
CABP4
CORO1B
USP35
KRTAP5-8
PLEKHB1
KCTD14
ALG8
NARS2
MOGAT2
TMEM134
PAAF1
GDPD5
CLPB
UNC93B1
DGAT2
RELT
ATG16L2
ACY3
INTS4
SNORD15B
MRGPRD
MRGPRF
ARAP1
XRRA1
B3GNT6
MRPL21
TPCN2
GDPD4
ORAOV1
LRTOMT
DEFB108B
RNF169
NUDT8
AQP11
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
OR2AT4
TBX10
DNAJB13
KRTAP5-10
LIPT2
GPR152
DOC2GP
GUCY2E
FLJ42102
MIR139
KRTAP5-7
KRTAP5-11
MIR326
FAM86C2P
MIR708
LOC100129216
LOC100133315
MIR548K
MIR4300
MIR3165
MIR3664
LOC100507050
NDUFC2-KCTD14
MIR4696
MIR4691
MIR4692

Genes in Wide Peak

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

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

Genes
CDKN2C
EPS15
JAK1
JUN
LCK
MPL
MUTYH
MYCL1
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
AK2
AK4
ALPL
RERE
ATP6V0B
BAI2
BMP8B
C1QA
C1QB
C1QC
C8A
C8B
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
PLK3
CNR2
COL8A2
COL9A2
COL16A1
CORT
CPT2
CSF3R
CTPS
CYP2J2
CYP4A11
CYP4B1
DAB1
DDOST
DFFA
DFFB
DHCR24
DIO1
DPH2
DVL1
E2F2
ECE1
EDN2
PHC2
MEGF6
EPHA2
ELAVL4
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FAAH
FABP3
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GPX7
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
INPP5B
IPP
STMN1
LEPR
TACSTD2
MAGOH
MATN1
MFAP2
MTF1
MTHFR
NASP
NBL1
NDUFS5
NFIA
NFYC
NPPA
NPPB
NRD1
YBX1
ROR1
OPRD1
ORC1
PAFAH2
PRDX1
PDE4B
PEX10
PEX14
PGD
PGM1
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKAA2
PRKCZ
PSMB2
PTAFR
PTPRF
RAB3B
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RPS8
RSC1A1
SCNN1D
SCP2
SRSF4
ST3GAL3
STIL
SKI
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TIE1
TNFRSF1B
TP73
TTC4
TNFRSF4
UQCRH
UROD
USP1
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
PTP4A2
SNHG3
NR0B2
RAD54L
PIK3R3
MMP23B
MMP23A
KCNAB2
FCN3
YARS
MKNK1
AKR7A2
PPAP2B
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
PER3
EIF2B3
ARTN
MAP3K6
KCNQ4
ZMYM4
ZMYM6
DHRS3
VAMP3
ZFYVE9
SNRNP40
C1orf38
TMEM59
H6PD
ISG15
PLCH2
IPO13
SDC3
KDM4A
CROCC
PUM1
CEP104
RIMS3
KIAA0494
DNAJC6
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
AKR1A1
TESK2
PPIE
MAD2L2
PPIH
CAP1
LRRC41
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
EBNA1BP2
KIF2C
RER1
RCAN3
FAF1
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
FOXJ3
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
MAST2
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
ZCCHC11
SZT2
DNAJC16
UBR4
USP24
ATP13A2
ITGB3BP
TARDBP
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
SSBP3
STX12
CLIC4
SYF2
PARS2
MMACHC
ACOT11
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
MYCBP
HEYL
EIF2C1
OR4F3
SNORD55
RNU11
RNF11
FOXD3
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
ANGPTL3
PRO0611
LINC00339
SSU72
GNL2
UBIAD1
ALG6
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
ZNF691
TXNDC12
MECR
UTP11L
SDF4
MRTO4
TMEM69
MRPL37
HOOK1
HPCAL4
YTHDF2
ZCCHC17
HSPB11
PADI3
CMPK1
ERRFI1
WNT4
YIPF1
FBXO42
RNF186
SPATA6
MXRA8
L1TD1
HES2
GPN2
LEPROT
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf123
C1orf159
AURKAIP1
TTC22
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
RNF220
VPS13D
FAM176B
ATAD3A
TMEM57
TRIM62
RAVER2
PANK4
ECHDC2
FGGY
CAMK2N1
ASAP3
POMGNT1
PNRC2
PIGV
NBPF1
MAP7D1
TMEM48
NECAP2
IQCC
DNAJC11
RCC2
DMAP1
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
ZSWIM5
KIAA1522
CACHD1
HES4
GRHL3
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
PLA2G2F
SMAP2
ATPAF1
S100PBP
MEAF6
DEM1
CEP85
NMNAT1
ELOVL1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZNF643
SELRC1
PHACTR4
C1orf135
ERI3
C1orf50
CCDC28B
EFHD2
MMEL1
RSG1
DLEU2L
OR4F5
NKAIN1
MUL1
TMEM53
AKIRIN1
HECTD3
BEND5
YRDC
ZYG11B
NOL9
PPCS
LIN28A
SH3D21
SNIP1
AGMAT
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
GPR157
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
HYI
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
STK40
TM2D1
TMEM222
PLEKHN1
USP48
ZMYND12
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
EFCAB7
NT5C1A
TRIM63
FAM167B
MGC12982
C1orf170
CROCCP2
HPDL
AGBL4
MFSD2A
ATG4C
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
DOCK7
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
BTF3L4
UBXN11
C1orf158
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
MED8
KTI12
C1orf212
ADC
TMEM54
TOE1
ERMAP
CSMD2
MYSM1
CROCCP3
FHAD1
OSBPL9
LOC115110
OMA1
RAB42
LRRC42
FAM46B
RBP7
ACAP3
UBE2J2
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
TCEANC2
PODN
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
KLF17
TMEM125
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
UBE2U
CCDC27
C1orf213
KNCN
MOB3C
GLIS1
DCDC2B
ZNF362
LOC149086
MANEAL
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
C1orf64
SLC2A7
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
KANK4
FAM43B
PAQR7
EIF2C3
EIF2C4
FAM76A
LINC00466
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
TXLNA
SLFNL1
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
PCSK9
ZNF683
CYP4X1
NPHP4
BEST4
CYP4A22
C1orf185
LOC284551
FAM41C
LOC284632
RSPO1
EPHA10
LOC284661
RIMKLA
SLC25A34
ESPNP
FAM151A
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
C1orf228
ZNF642
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
TCTEX1D4
SERINC2
FAM159A
FAM131C
PADI6
BMP8A
C1orf187
SPATA21
CCDC23
ATPAF1-AS1
HEATR8
AGRN
APITD1
CATSPER4
NSUN4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LOC388630
LDLRAD1
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR101-1
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
FLJ32224
FAM183A
ZYG11A
ANKRD65
PRAMEF7
LURAP1
PEF1
MIR429
CYB5RL
FAM138F
KIAA0754
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA55
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
LOC728431
PPIEL
CCDC30
CDK11A
SLC35E2B
LOC728716
RPS15AP10
LOC729041
LOC729059
HSD52
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100129924
LOC100130197
LOC100130417
LOC100130557
LOC100131060
LOC100132062
LOC100132287
LOC100132774
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
MIR761
NPPA-AS1
MIR3115
MIR4255
MIR4253
MIR4251
MIR4252
MIR4254
MIR3659
MIR3917
MIR3605
MIR3671
MIR3675
ENO1-AS1
ZMYM6NB
LOC100506730
LOC100506801
LOC100506963
LOC100507178
LOC100507423
LOC100507564
LOC100507634
APITD1-CORT
GJA9-MYCBP
HEATR8-TTC4
C1orf151-NBL1
MIR4695
MIR4420
MIR4422
MIR4781
MIR4794
MIR4684
MIR4711
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 31 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 8.5247e-173 | 7.9891e-169 | chr9:21959052-21997722 | 2
11q23.3 | 1.603e-21 | 1.603e-21 | chr11:105969102-126295275 | 237
10q23.31 | 1.7328e-16 | 4.867e-16 | chr10:89617158-90034038 | 2
4q34.3 | 4.5542e-10 | 4.5542e-10 | chr4:178911874-183060693 | 1
2q37.3 | 1.2364e-06 | 1.2364e-06 | chr2:239007902-243199373 | 64
1p36.31 | 5.0904e-08 | 2.3642e-06 | chr1:1-9612196 | 156
5q31.3 | 2.9262e-06 | 8.2931e-06 | chr5:136833361-166712758 | 284
10p15.3 | 2.251e-05 | 2.3102e-05 | chr10:1-857150 | 4
15q15.1 | 2.1948e-08 | 2.7301e-05 | chr15:36149095-50717067 | 167
6q26 | 1.7429e-08 | 0.00013195 | chr6:161693099-163153207 | 1
16p13.3 | 0.0011851 | 0.0011809 | chr16:5144019-7771745 | 1
1p22.1 | 0.0011718 | 0.006627 | chr1:71699756-120162151 | 321
16q23.3 | 0.019173 | 0.018793 | chr16:78016120-90354753 | 123
14q32.32 | 0.022206 | 0.021334 | chr14:75939040-107349540 | 324
15q13.3 | 1.0326e-06 | 0.031205 | chr15:1-44070690 | 303
10q26.3 | 0.0054044 | 0.032379 | chr10:134944852-135093385 | 6
6q27 | 1.4662e-08 | 0.035597 | chr6:169023880-170618145 | 10
6q16.3 | 0.00085326 | 0.039354 | chr6:64422619-143930767 | 354
12q23.3 | 0.0041265 | 0.044773 | chr12:74674746-133851895 | 442
16q12.1 | 0.046573 | 0.047489 | chr16:31772318-61686142 | 136
5q11.2 | 0.015 | 0.062022 | chr5:58145167-59787985 | 3
9p24.1 | 5.5693e-09 | 0.09412 | chr9:7799607-12693402 | 1
3q23 | 0.1148 | 0.11538 | chr3:105294270-198022430 | 625
12q24.33 | 0.0047683 | 0.13388 | chr12:74674746-133851895 | 442
19p13.3 | 0.14015 | 0.13845 | chr19:1-3814391 | 139
4p16.3 | 0.16758 | 0.16758 | chr4:1-6203066 | 86
13q34 | 0.17073 | 0.17263 | chr13:1-115169878 | 414
17q11.2 | 0.18642 | 0.18751 | chr17:19651612-59760122 | 667
8p23.3 | 0.22175 | 0.22963 | chr8:1-35110688 | 268
7q31.1 | 0.23742 | 0.23821 | chr7:1-159138663 | 1148
12p13.31 | 0.23818 | 0.23821 | chr12:1-18838946 | 256

Genes in Wide Peak

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

Table S21. 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 S22. 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
GUCY1A2
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 S23. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PTEN
KLLN

Genes in Wide Peak

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

Table S24. 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 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
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 1p36.31.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 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
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
ADRA1B
ADRB2
ANXA6
ATOX1
CAMK2A
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
IL12B
MFAP3
NDUFA2
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
POU4F3
PPP2R2B
PURA
RPS14
SGCD
SLC6A7
SPARC
SPINK1
TAF7
TCOF1
TTC1
UBE2D2
WNT8A
NME5
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
PTTG1
CNOT8
HAND1
MED7
MYOT
NRG2
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
SLU7
C5orf4
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
SYNPO
ABLIM3
HMGXB3
ARHGAP26
ATP10B
LARP1
HARS2
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
IL17B
MAT2B
MRPL22
PCDHB1
DCTN4
MZB1
PAIP2
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
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
ARAP3
PCYOX1L
CCNJL
SH3TC2
SAP30L
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PCDHB19P
PSD2
C5orf32
SPINK7
HAVCR2
C5orf62
FCHSD1
TIMD4
ZNF300
MYOZ3
SLC35A4
PWWP2A
C1QTNF2
SCGB3A2
PPARGC1B
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SLC36A2
SPINK13
LOC153469
ZMAT2
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
SPATA24
DNAJC18
STK32A
SLC36A1
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
TMEM173
ARSI
IRGM
NIPAL4
DND1
FLJ38109
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
MIR146A
SPINK14
FNDC9
IGIP
ECSCR
GRXCR2
SPINK9
SNHG4
MIR143HG
LOC729080
MIR874
C5orf52
MIR3142
MIR3141
MIR3655
LOC100505658

Genes in Wide Peak

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

Table S28. 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 15q15.1.

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 6q26.

Table S30. 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 16p13.3.

Table S31. 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 S32. 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
LRRIQ3
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
NEGR1
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
NEGR1-IT1

Genes in Wide Peak

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

Table S33. 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 14q32.32.

Table S34. 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
hsa-mir-1260
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
ESRRB
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
ALKBH1
MTA1
RPS6KA5
NRXN3
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
BATF
SIVA1
AHSA1
CYP46A1
PAPOLA
PTPN21
C14orf1
VASH1
SNW1
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
FLRT2
KIF26A
C14orf109
PRO1768
GPR132
POMT2
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
ADCK1
TMEM63C
UNC79
BEGAIN
PPP4R4
NGB
C14orf133
MOAP1
DIO3OS
IRF2BPL
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
SLIRP
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NOXRED1
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
C14orf166B
ISM2
CEP128
TTC7B
C14orf49
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
ZDHHC22
TMED8
C14orf178
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
MIR1260A
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 15q13.3.

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

Genes
BUB1B
C15orf55
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
EPB42
GABRA5
GABRB3
GABRG3
GANC
GCHFR
PDIA3
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
PAR5
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
TGM5
PPIP5K1
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
GPR176
CHP
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
C15orf2
TMEM87A
RPAP1
DKFZP434L187
GREM1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
KLF13
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
ZFP106
CHAC1
C15orf29
TMEM62
ELL3
NIPA2
C15orf41
ZFYVE19
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
PAR1
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
LPCAT4
PLA2G4F
LRRC57
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
C15orf62
C15orf56
PHGR1
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

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

Table S36. 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 6q27.

Table S37. 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 6q16.3.

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
STL
GOPC
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IMPG1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
ME1
MAP3K5
MYO6
NMBR
NT5E
ENPP1
ENPP3
PEX7
PGM3
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
RNY4
RPS12
SGK1
SIM1
SMPD2
ELOVL4
MAP3K7
TCF21
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
STX7
PEX3
DDO
SNX3
RNGTT
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
TAAR2
TAAR3
HMGN3
MED23
FHL5
AKAP7
ATG5
TBPL1
KIAA0408
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
SMPDL3A
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
HEY2
HEBP2
ORC3
BRD7P3
MTO1
ASF1A
CCDC28A
PNISR
IBTK
MOXD1
SENP6
FBXL4
SLC17A5
SNORD50A
PDE7B
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
HDDC2
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
UBE2J1
VTA1
HECA
COQ3
IL20RA
AHI1
PHIP
SOBP
AKIRIN2
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
ECHDC1
KCNQ5
RARS2
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
SERINC1
HACE1
FAM135A
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
POPDC3
ALDH8A1
MICAL1
OR2A4
OGFRL1
FAM184A
MANEA
LINC00472
KHDC1
GPR63
SPACA1
RNF146
TAAR8
SH3BGRL2
ARMC2
RPF2
L3MBTL3
MCHR2
FAXC
GJA10
RTN4IP1
RSPO3
USP45
REPS1
SLC22A16
C6orf7
UBE2CBP
KIAA1919
ARHGAP18
GTF3C6
MRAP2
RWDD2A
FAM54A
KLHL32
TMEM200A
MB21D1
NUS1
IL22RA2
C6orf192
SLC16A10
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
NCOA7
HINT3
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
LOC153910
SAMD3
MGC34034
SLC2A12
LOC154092
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
OLIG3
TXLNB
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
MMS22L
FAM26E
MCM9
SCML4
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
TAAR6
SLC35D3
DPPA5
RSPH4A
ECT2L
EYS
C6orf58
GJB7
HMGA1P7
SNHG5
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
THEMIS
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
FLJ46906
MCART3P
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LINC00271
LOC100132735
LOC100287632
LOC100288198
NHEG1
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3668
MIR3662
LOC100506804
LOC100507203
LOC100507254
LOC100507462
LOC100507489
MIR4464
MIR4643
MIR4465

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.3.

Table S39. 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
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 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
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 9p24.1.

Table S42. 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 3q23.

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

Genes
BCL6
FOXL2
CBLB
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
LOC344595
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
LOC100302640
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 12q24.33.

Table S44. 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
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 19p13.3.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.3.

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

Genes
FGFR3
WHSC1
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
EVC
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
RGS12
RNF4
SH3BP2
WHSC2
ZNF141
SLBP
NOP14
FAM193A
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
D4S234E
STX18
FGFRL1
CYTL1
PIGG
STK32B
LYAR
KIAA1530
ZFYVE28
TNIP2
HAUS3
ABCA11P
MFSD7
TMEM175
TMEM128
C4orf42
TMEM129
EVC2
OTOP1
ZNF595
JAKMIP1
FAM53A
ZBTB49
ZNF721
ZNF718
CRIPAK
DOK7
FLJ35424
RNF212
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
C4orf48
LOC402160
ZNF876P
ZNF732
SCARNA22
MIR943
LOC100129917
LOC100130872
LOC100133461
TMED11P
LOC100507266
MIR378D1
MIR4800
HTT-AS1

Genes in Wide Peak

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

Table S47. 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 17q11.2.

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

Genes
BRCA1
CLTC
COL1A1
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
RARA
TAF15
SUZ12
MSI2
hsa-mir-21
hsa-mir-301a
hsa-mir-142
hsa-mir-3185
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
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
ATP5G1
ATP6V0A1
BLMH
FMNL1
CA4
CACNB1
CDC6
CDC27
CHAD
CCR7
CNP
COX11
CPD
CRHR1
CRYBA1
CSF3
DHX8
DLX3
DLX4
DUSP3
EVI2A
EVI2B
EZH1
FLOT2
GAST
FZD2
G6PC
KAT2A
GFAP
GIP
GNGT2
CCR10
GRB7
GRN
HCRT
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HSD17B1
IFI35
IGFBP4
ITGA2B
ITGA3
ITGB3
JUP
KCNJ12
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS9
LHX1
LIG3
LPO
NBR1
MAPT
ADAM11
MEOX1
MPO
MPP2
MPP3
TRIM37
MYL4
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NOS2
NSF
OMG
PDK2
PEX12
PHB
PNMT
SEPT4
MED1
PPY
MAP2K3
PSMB3
PYY
PSMD3
PSMD11
RAB5C
RAD51C
RAD51D
RPL19
RPL23A
RPL27
RPS6KB1
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SRSF1
SGCA
SH3GL1P1
SH3GL1P2
SLC4A1
SLC6A4
SMARCE1
SP2
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
TADA2A
TBX2
HNF1B
MLX
THRA
TNFAIP1
TOP2A
DNAJC7
TUBG1
UBTF
VTN
WNT3
WNT9B
PCGF2
TRIM25
VEZF1
ZNF207
RND2
COIL
AKAP1
EPX
PIP4K2B
SPOP
FOXN1
PPM1D
CNTNAP1
DGKE
TCAP
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
ABCC3
TMEM11
KSR1
CDK5R1
CACNA1G
HAP1
MAP3K14
SPAG9
SLC13A2
UNC119
MTMR4
TIAF1
NOG
BZRAP1
ZNHIT3
EFTUD2
RPL23
TBX4
NPEPPS
GOSR1
CCL4L1
GOSR2
NR1D1
TRAF4
KIAA0100
ULK2
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
TOM1L1
GJC1
TOB1
PSME3
EIF1
NBR2
SLC35B1
CALCOCO2
RAMP2
HOXB13
VAT1
APPBP2
LEPREL4
HEXIM1
SPAG5
IGF2BP1
CCT6B
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
KAT7
AKAP10
NXPH3
SNF8
SYNRG
CASC3
IKZF3
ZNF652
PPM1E
SARM1
GPATCH8
USP22
KCNH4
MMD
FAM215A
PPY2
PYY2
DHRS7B
KRT23
TMEM98
POLDIP2
TBC1D29
WSB1
ERAL1
AATF
OR4D1
SNORD4B
SNORD4A
SNORD42B
SNORD42A
TUBG2
TMEM97
NKIRAS2
CCDC56
GIT1
PSMC3IP
SNX11
TBX21
SOCS7
SOST
UTP18
RNFT1
TUBD1
RAPGEFL1
ABI3
COPZ2
MRPL27
PIPOX
ARL17A
CRLF3
SLC25A39
MRPS23
PTRH2
NLK
LUC7L3
HIGD1B
CDK12
KRT20
NLE1
FNDC8
MBTD1
BCAS3
CWC25
RNF43
MKS1
LINC00483
EPN3
LRRC37A4
SLFN12
PNPO
KLHL11
SMG8
TMEM100
RHOT1
RSAD1
C17orf79
LRRC59
MSX2P1
C17orf63
PRR11
ADAP2
UTP6
GSDMB
TEX14
CA10
ATXN7L3
PLXDC1
LYZL6
NUFIP2
TAOK1
ARHGAP23
PHF12
PCTP
SCPEP1
FKBP10
HEATR6
XYLT2
C17orf75
SPATA20
UBE2Z
WNK4
C17orf53
TMUB2
DHX58
MMP28
DHRS11
PRR15L
DHX40
TEFM
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
FAM117A
VMP1
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
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
RNF135
MIEN1
MRPL45
VPS25
TMEM101
PRAC
RAB11FIP4
GHDC
KRTAP4-4
KIF2B
USP32
PPP1R9B
CORO6
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
SSH2
TP53I13
IFT20
LRRC46
SCRN2
AOC4
ANKRD40
ZNF830
SLFN11
RASL10B
SPECC1
G6PC3
ASB16
PGAP3
PIGS
HSPB9
ORMDL3
PLCD3
SLC46A1
TMEM106A
LRRC37B
OSBPL7
NT5C3L
ABHD15
TLCD1
RFFL
HSF5
OR4D2
ZPBP2
C17orf64
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
FLJ40194
B4GALNT2
SPACA3
SGK494
SEZ6
ANKRD13B
C17orf57
MRPL10
GJD3
KRT222
KRT40
DYNLL2
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
TMEM199
PROCA1
DHRS13
C17orf69
LOC147093
LRRC37BP1
WIPF2
KRT25
TMEM99
ANKFN1
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
IMP5
KRT28
KRT24
ARHGAP27
ZNF385C
SAMD14
C17orf108
RDM1
GAS2L2
STH
MTVR2
STXBP4
LOC253962
TAC4
CDRT15L2
C17orf103
C17orf66
KIAA1267
C17orf105
FAM171A2
C17orf104
TTLL6
LOC284080
C17orf47
KRT18P55
NEK8
PIGW
C17orf78
LOC284100
CISD3
GSDMA
KRT42P
PTRF
FAM27L
FLJ36000
GDPD1
LGALS9B
KLHL10
CCDC144NL
C17orf65
C17orf67
C17orf51
MSL1
NACA2
KRT27
SLFN14
FLJ43826
STAC2
SKA2
CCL14-CCL15
CCDC144C
KRT26
HOXB13-AS1
HILS1
EFCAB5
RNF126P1
TMIGD1
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
YPEL2
C17orf82
ARL5C
KRT39
MYO18A
C17orf102
LOC400604
MGC57346
CUEDC1
LOC404266
MIR10A
MIR142
MIR144
MIR152
MIR193A
MIR196A1
MIR21
MIR301A
TBC1D3B
TBC1D3C
CCL3L3
TBC1D3P5
SUZ12P
LOC440434
GPR179
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451A
SNORA21
LOC644172
LOC644246
KRT16P3
LOC645638
SEBOX
KRTAP4-11
MRPL45P2
TBC1D3P1-DHX40P1
LOC653653
TBC1D3G
NME1-NME2
SCARNA20
SNORD7
MIR632
KRTAP4-8
KRTAP2-2
KRTAP9-1
NSFP1
FLJ45513
TBC1D3
TBC1D3H
LOC730755
MIR454
SNORD124
MIR365B
LOC100128977
LOC100130148
LOC100130581
LOC100131347
KRTAP4-9
KRTAP4-7
LOC100133991
KCNJ18
C17orf96
LOC100190938
MIR1203
MIR2117
MIR4315-2
MIR2909
MIR3185
MIR3184
MIR4315-1
MTRNR2L1
MIR3614
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
SPAG5-AS1
LOC100506650
AA06
SLFN12L
LOC100506779
RAD51L3-RFFL
MIR4523
MIR4728
MIR4726
MIR4734
MIR4729
MIR4737
MIR4736
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 8p23.3.

Table S49. 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
NRG1
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
DUSP26
HMBOX1
MCPH1
PPP1R3B
RNF122
NUDT18
DOCK5
FLJ14107
TTI2
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
MAK16
FUT10
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 7q31.1.

Table S50. 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 12p13.31.

Table S51. 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

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 | 0.64 | 0.95 | 0.22 | -0.249 | 1
1q | 1955 | 0.45 | 7.7 | 6.99e-14 | 0.17 | -1.99 | 1
2p | 924 | 0.22 | -1.51 | 1 | 0.19 | -2.23 | 1
2q | 1556 | 0.22 | -1 | 1 | 0.19 | -1.75 | 1
3p | 1062 | 0.19 | -2.15 | 1 | 0.19 | -2.15 | 1
3q | 1139 | 0.22 | -1.13 | 1 | 0.16 | -3.08 | 1
4p | 489 | 0.17 | -3.16 | 1 | 0.23 | -1.27 | 1
4q | 1049 | 0.15 | -3.56 | 1 | 0.25 | -0.282 | 1
5p | 270 | 0.21 | -2.23 | 1 | 0.28 | -0.0281 | 1
5q | 1427 | 0.14 | -3.34 | 1 | 0.33 | 2.8 | 0.0102
6p | 1173 | 0.46 | 6.22 | 1.69e-09 | 0.42 | 4.86 | 3.35e-06
6q | 839 | 0.17 | -2.36 | 1 | 0.58 | 10.8 | 0
7p | 641 | 0.56 | 10 | 0 | 0.12 | -3.75 | 1
7q | 1277 | 0.56 | 11 | 0 | 0.12 | -3.39 | 1
8p | 580 | 0.36 | 2.74 | 0.0138 | 0.33 | 1.71 | 0.116
8q | 859 | 0.46 | 6.63 | 1.3e-10 | 0.19 | -2.12 | 1
9p | 422 | 0.12 | -3.18 | 1 | 0.68 | 14.1 | 0
9q | 1113 | 0.12 | -3.51 | 1 | 0.56 | 10.6 | 0
10p | 409 | 0.04 | -5.63 | 1 | 0.57 | 10.5 | 0
10q | 1268 | 0.03 | -5.13 | 1 | 0.61 | 13.1 | 0
11p | 862 | 0.15 | -3.36 | 1 | 0.37 | 3.77 | 0.000367
11q | 1515 | 0.11 | -3.87 | 1 | 0.40 | 5.61 | 6.75e-08
12p | 575 | 0.17 | -3.38 | 1 | 0.20 | -2.43 | 1
12q | 1447 | 0.10 | -4.89 | 1 | 0.20 | -1.76 | 1
13q | 654 | 0.30 | 1.06 | 0.578 | 0.28 | 0.364 | 0.843
14q | 1341 | 0.14 | -3.47 | 1 | 0.32 | 2.41 | 0.0273
15q | 1355 | 0.24 | -0.29 | 1 | 0.15 | -3.25 | 1
16p | 872 | 0.15 | -3.65 | 1 | 0.23 | -1 | 1
16q | 702 | 0.16 | -3.27 | 1 | 0.34 | 2.4 | 0.0273
17p | 683 | 0.17 | -2.72 | 1 | 0.40 | 4.64 | 8.63e-06
17q | 1592 | 0.21 | -1.14 | 1 | 0.25 | 0.223 | 0.867
18p | 143 | 0.21 | -1.96 | 1 | 0.35 | 2.36 | 0.0279
18q | 446 | 0.18 | -2.86 | 1 | 0.31 | 1.34 | 0.226
19p | 995 | 0.19 | -2.33 | 1 | 0.25 | -0.167 | 1
19q | 1709 | 0.20 | -1.21 | 1 | 0.25 | 0.284 | 0.863
20p | 355 | 0.44 | 5.71 | 3.19e-08 | 0.10 | -4.75 | 1
20q | 753 | 0.50 | 8.18 | 1.48e-15 | 0.05 | -5.5 | 1
21q | 509 | 0.19 | -2.64 | 1 | 0.24 | -0.988 | 1
22q | 921 | 0.37 | 3.61 | 0.000765 | 0.18 | -2.56 | 1
Xq | 1312 | 0.15 | -3.04 | 1 | 0.32 | 2.21 | 0.0388

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/1971732/2.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 = 0.1

- 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 253 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-BF-A3DJ-01A-11D-A20B-01
TCGA-BF-A3DL-01A-11D-A20B-01
TCGA-BF-A3DM-01A-11D-A20B-01
TCGA-BF-A3DN-01A-11D-A20B-01
TCGA-D3-A1Q1-06A-21D-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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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