SNP6 Copy number analysis (GISTIC2)

Skin Cutaneous Melanoma (Metastatic)

16 April 2014 | analyses__2014_04_16

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1HQ3XMB

Overview

Introduction

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

Summary

There were 299 tumor samples used in this analysis: 22 significant arm-level results, 23 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 - 23 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
3p13	1.5845e-10	1.5845e-10	chr3:69742187-70115687	1
5p15.33	1.5845e-10	1.5845e-10	chr5:1288616-1300024	1
1p12	2.7472e-10	1.4102e-09	chr1:120024288-120523954	10
1q44	2.3615e-09	3.5472e-08	chr1:245627602-247116301	10
6p24.3	6.0838e-07	6.0838e-07	chr6:1-14532705	90
22q13.2	7.9185e-07	7.9185e-07	chr22:41468899-41845216	9
11q13.3	1.0471e-09	3.5982e-06	chr11:69326532-70221716	10
12q14.1	4.434e-08	3.772e-06	chr12:58135797-58215836	10
17q25.3	9.1141e-06	9.1141e-06	chr17:67159433-81195210	244
7q34	3.0237e-05	3.0237e-05	chr7:135929407-143664054	89
7p22.1	0.00097385	0.00097385	chr7:1-11104052	96
15q26.2	0.0010278	0.0010278	chr15:75714654-102531392	238
12q15	1.432e-07	0.0018846	chr12:69102070-69374775	4
4q12	0.0034055	0.0034055	chr4:55721956-55767814	0 [KIT]
8q24.21	0.00059331	0.0057892	chr8:103293857-146364022	259
6q12	0.019145	0.019145	chr6:63939939-64685844	4
8q11.21	0.018675	0.037531	chr8:51335506-52360895	2
1q21.3	2.0944e-05	0.051657	chr1:120523956-157519894	345
5q35.3	0.063186	0.063186	chr5:175337387-180915260	110
19p13.2	0.079371	0.079371	chr19:7300056-7398264	0 [INSR]
20q13.33	0.1148	0.1148	chr20:46638087-63025520	200
11q13.4	0.0001627	0.12002	chr11:67240318-81526572	152
13q12.3	0.24172	0.24172	chr13:19861818-42104868	146

Genes in Wide Peak

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

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

Genes
MITF

Genes in Wide Peak

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

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

Genes
TERT

Genes in Wide Peak

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

Table S3. Genes in bold are cancer genes as defined by The Sanger Institute: 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 S4. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
AHCTF1
SCCPDH
KIF26B
ZNF695
TFB2M
SMYD3
LOC149134
CNST
LOC255654
ZNF670-ZNF695

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.3.

Table S5. Genes in bold are cancer genes as defined by The Sanger Institute: 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
CD83
CDYL
LY86
EEF1E1
RANBP9
ECI2
FARS2
RPP40
SIRT5
FAM50B
SLC35B3
TBC1D7
NRN1
NOL7
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
CCDC90A
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
C6orf195
PIP5K1P1
RNF182
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 S6. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
EP300
hsa-mir-1281
RANGAP1
TEF
TOB2
ZC3H7B
L3MBTL2
CHADL
MIR1281

Genes in Wide Peak

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

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

Genes
CCND1
hsa-mir-548k
FGF3
FGF4
PPFIA1
FADD
FGF19
ANO1
ORAOV1
MIR548K

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
METTL21B
MARCH9
AGAP2

Genes in Wide Peak

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

Table S9. Genes in bold are cancer genes as defined by The Sanger Institute: 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
KCNJ2
KCNJ16
LGALS3BP
LLGL2
MAFG
NPTX1
P4HB
PDE6G
MAP2K6
PRPSAP1
PYCR1
PCYT2
RAC3
RFNG
RPL38
MRPL12
SEC14L1
SECTM1
SRSF2
SGSH
SUMO2
SOX9
SRP68
SSTR2
TBCD
TIMP2
TK1
CBX4
DNAH17
GALR2
SPHK1
SOCS3
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
AATK
KIAA0195
EIF4A3
ALYREF
ABCA10
BAIAP2
ATP5H
ST6GALNAC2
SEPT9
CD300C
RAB40B
CD300A
TMC6
AZI1
GGA3
JMJD6
EXOC7
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NAT9
NARF
SAP30BP
NT5C
CDR2L
MRPS7
HN1
DCXR
ANAPC11
SIRT7
SDK2
TMEM104
C17orf80
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
FAM104A
MGC16275
FBF1
UNK
TRIM47
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
METTL23
SLC38A10
USH1G
CD300LB
KIF19
TBC1D16
AFMID
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
NOTUM
TMC8
STRA13
LRRC45
SLC39A11
TRIM65
UNC13D
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
SLC26A11
ENDOV
C17orf89
LINC00482
TMEM105
METRNL
RAB37
ENPP7
C17orf90
CCDC137
ARL16
CD300E
OTOP3
FAM195B
GPR142
ZACN
BTBD17
AATK-AS1
FLJ43681
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
MXRA7
FLJ90757
MIR338
CPSF4L
C17orf109
LINC00338
SCARNA16
SNORD1A
SNORD1B
SNORD1C
MIR636
MIR657
PRCD
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR3186
LOC100499467
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 7q34.

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

Genes
BRAF
KIAA1549
CREB3L2
hsa-mir-490
CASP2
CHRM2
CLCN1
EPHA1
EPHB6
KEL
NDUFB2
PIP
PRSS1
PRSS2
TAS2R38
PTN
AKR1D1
SSBP1
TBXAS1
ZYX
TRIM24
MGAM
DGKI
FAM131B
FAM115A
CLEC5A
MKRN1
OR2F1
DENND2A
HIPK2
ATP6V0A4
TAS2R3
TAS2R4
LUC7L2
MRPS33
TAS2R5
TRPV6
AGK
TRPV5
ZC3HAV1
KIAA1147
PARP12
TTC26
JHDM1D
SLC37A3
OR6W1P
ADCK2
ZC3HAV1L
LOC93432
OR9A4
OR9A2
C7orf34
TMEM139
OR2F2
PRSS37
SVOPL
PRSS58
TRY6
LOC154761
CLEC2L
C7orf55
TMEM213
UBN2
TAS2R39
TAS2R40
TAS2R41
FLJ40852
LOC285965
FAM115C
TAS2R60
CTAGE6P
OR6V1
KLRG2
LOC349160
GSTK1
RAB19
CTAGE15P
WEE2
MIR490
LOC730441
LOC100124692
LOC100129148
LOC100130880
LOC100134229
LOC100134713
MOXD2P
MTRNR2L6
LOC100507421
MIR4468

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.1.

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

Genes
PMS2
CARD11
hsa-mir-589
hsa-mir-339
ACTB
GNA12
GPER
ICA1
LFNG
NUDT1
NDUFA4
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
PHF14
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
PER4
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 15q26.2.

Table S12. Genes in bold are cancer genes as defined by The Sanger Institute: 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 12q15.

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

Genes
MDM2
CPM
SLC35E3
NUP107

Genes in Wide Peak

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

Table S14. Genes in bold are cancer genes as defined by The Sanger Institute: 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
SQLE
TAF2
TG
KLF10
TRHR
TRPS1
TSTA3
COL14A1
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
FBXL6
OPLAH
KCNV1
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
CYHR1
ASAP1
FAM135B
PHF20L1
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
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
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
FAM84B
TMEM74
FAM91A1
SLC30A8
COL22A1
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
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
PCAT1
LINC00536

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: 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 8q11.21.

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

Genes
SNTG1
PXDNL

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
MUC1
NOTCH2
NTRK1
PRCC
TPM3
PDE4DIP
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
BGLAP
CHRNB2
CKS1B
CLK2
CRABP2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
HDGF
IL6R
ILF2
INSRR
IVL
KCNN3
LMNA
LOR
MCL1
SMCP
MEF2D
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
SH2D2A
PRPF3
ARHGEF2
SEC22B
CHD1L
SLC25A44
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
PMF1
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SMG5
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
C1orf56
MSTO1
GOLPH3L
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
SNX27
ANP32E
ISG20L2
FCRL5
HORMAD1
POLR3GL
TMEM79
LCE3D
AQP10
PYGO2
NUP210L
MEX3A
C1orf85
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
C1orf182
IQGAP3
APOA1BP
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
LRRC71
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
LOC375010
PEAR1
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
NBPF9
MIR9-1
HIST2H2BF
ETV3L
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA4
SNORA42
MIR554
MIR555
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR765
MIR190B
C1orf68
MSTO2P
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505666
PMF1-BGLAP
TNFAIP8L2-SCNM1

Genes in Wide Peak

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

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

Genes
NSD1
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
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 20q13.33.

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

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

Genes in Wide Peak

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

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

Genes
CCND1
NUMA1
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
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
RAB6A
SNORD15A
RPS3
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
USP35
KRTAP5-8
PLEKHB1
KCTD14
ALG8
NARS2
MOGAT2
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
DOC2GP
GUCY2E
FLJ42102
MIR139
KRTAP5-7
KRTAP5-11
MIR326
FAM86C2P
MIR708
LOC100129216
LOC100133315
MIR548K
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 13q12.3.

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

Genes
BRCA2
CDX2
FLT3
LHFP
TTL
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
CDK8
ELF1
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
GTF3A
HMGB1
PDX1
MAB21L1
SMAD9
MIPEP
PABPC3
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TRPC4
ZMYM2
IFT88
CCNA1
MTMR6
DCLK1
ZMYM5
KL
MTRF1
NUPL1
FRY
SLC25A15
USPL1
MRPS31
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
WBP4
EXOSC8
PDS5B
SPG20
MTUS2
SACS
LATS2
SNORD102
NBEA
C13orf15
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
PSPC1
TNFRSF19
FAM48A
CENPJ
RNF17
COG6
XPO4
MRP63
NAA16
PROSER1
KATNAL1
KBTBD7
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
CG030
CSNK1A1L
RXFP2
TEX26
B3GALTL
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
ZDHHC20
PAN3
SUGT1P3
SLC46A3
C1QTNF9
FREM2
TPTE2P6
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERTM1
LINC00547
LINC00548
ATP5EP2
LOC440131
C1QTNF9B-AS1
SNORA27
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
MIR621
CCDC169
ANKRD26P3
RPL21P28
LINC00426
LINC00421
PAN3-AS1
MIR548F5
MIR2276
MIR320D1
MIR4305
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
CCDC169-SOHLH2
MIR4499
LOC100616668

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	1.511e-170	4.7953e-166	chr9:21959052-21997722	2
11q23.3	3.2577e-24	3.2577e-24	chr11:119368304-119984534	1
10q23.31	2.1574e-23	8.0618e-23	chr10:89617158-90034038	2
4q34.3	5.6516e-10	5.6516e-10	chr4:178911874-183060693	1
2q37.3	2.2347e-09	2.2535e-09	chr2:239463774-242417807	40
1p36.31	3.5704e-09	1.264e-07	chr1:1-6847369	137
6q26	2.7265e-09	2.7656e-07	chr6:161693099-163153207	1
5q31.3	1.6372e-07	4.5426e-07	chr5:132435573-166712758	326
16p13.3	5.3963e-05	5.3963e-05	chr16:5144019-7771745	1
15q13.3	2.1342e-09	0.00028225	chr15:28560817-33605300	36
10p15.3	0.00034909	0.00034909	chr10:1-857150	4
1p22.1	0.00021544	0.00143	chr1:76393552-119426205	296
12q23.3	0.0029814	0.0028419	chr12:75603217-133851895	440
16q24.3	0.0081663	0.010887	chr16:78016120-90354753	123
5p15.31	0.022219	0.022289	chr5:1-31199922	100
10q26.3	0.00193	0.022289	chr10:134944852-135093385	6
6q22.31	3.0105e-06	0.041479	chr6:85471465-160392914	383
14q32.2	0.030067	0.047527	chr14:75323344-107349540	336
3p24.3	0.053863	0.054458	chr3:1-62249165	521
5q11.2	0.0099911	0.057703	chr5:58145167-59787985	3
19p13.3	0.064451	0.065632	chr19:1-2350207	99
8p23.3	0.070965	0.071567	chr8:1-30601804	257
15q15.2	1.2035e-10	0.071567	chr15:1-59064785	420
16q12.1	0.060617	0.082248	chr16:31772318-64981096	137
3q23	0.1092	0.11	chr3:105294270-198022430	625
9p23	9.7905e-12	0.11356	chr9:7799607-12693402	1
15q14	1.3584e-12	0.11701	chr15:1-54308486	391
13q34	0.084556	0.12151	chr13:95363003-115169878	103
11p11.2	0.17866	0.18006	chr11:30357966-56020824	171
14q23.3	0.15708	0.21795	chr14:50577078-80963098	251
13q12.11	0.17848	0.23056	chr13:1-90884270	296

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
PVRL1

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
LINC00290

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PPP1R7
HDAC4
CAPN10
PASK
SNED1
ANO7
ANKMY1
RNPEPL1
C2orf54
MGC16025
TWIST2
MTERFD2
OTOS
MYEOV2
OR6B3
LOC150935
LOC200772
DUSP28
AQP12A
OR6B2
FLJ43879
MIR149
PRR21
AQP12B
PP14571
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 S27. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

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

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
CD74
EBF1
ITK
PDGFRB
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
ADRA1B
ADRB2
ANXA6
ATOX1
CAMK2A
CAMLG
CCNG1
CD14
CDC25C
CDX1
CSF1R
CSNK1A1
CTNNA1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EGR1
ETF1
FABP6
FAT2
FGF1
GABRA1
GABRA6
GABRB2
GABRG2
GFRA3
GLRA1
GM2A
GPX3
GRIA1
NR3C1
HARS
HMMR
HSPA9
NDST1
HTR4
IK
IL9
IL12B
LECT2
SMAD5
MFAP3
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPP2CA
PPP2R2B
PURA
RPS14
SGCD
SKP1
SLC6A7
SPARC
SPINK1
SPOCK1
TAF7
TCF7
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
PTTG1
CNOT8
HAND1
MED7
MYOT
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
SLU7
SEC24A
C5orf4
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
SYNPO
ABLIM3
HMGXB3
ARHGAP26
FSTL4
ATP10B
PHF15
LARP1
HARS2
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
IL17B
MAT2B
MRPL22
PCDHB1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
LARS
CXXC5
KDM3B
RBM27
PCDHB18
PCDHB17
WDR55
ANKHD1
THG1L
TMCO6
GALNT10
RBM22
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
C5orf15
TRPC7
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
ARAP3
PCYOX1L
CCNJL
SH3TC2
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
C5orf32
SPINK7
HAVCR2
C5orf62
FCHSD1
CDKN2AIPNL
TIMD4
ZNF300
MYOZ3
SLC35A4
PWWP2A
C1QTNF2
SCGB3A2
PPARGC1B
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
C5orf24
C5orf20
SLC36A2
SPINK13
SLC25A48
LOC153469
ZMAT2
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
SPATA24
DNAJC18
STK32A
SLC36A1
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
TMEM173
LOC340073
LOC340074
ARSI
IRGM
CATSPER3
NIPAL4
DND1
FLJ38109
LOC389332
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
MIR146A
SPINK14
FNDC9
IGIP
TIFAB
ECSCR
GRXCR2
SPINK9
SNHG4
MIR143HG
LOC729080
VTRNA2-1
MIR874
C5orf52
MIR1289-2
MIR3142
MIR3141
MIR3655
MIR3661
LOC100505658
MIR4461

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

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

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

Genes
hsa-mir-211
APBA2
CHRNA7
TRPM1
SCG5
TJP1
ARHGAP11A
FAN1
FAM189A1
DKFZP434L187
GREM1
KLF13
MTMR10
NDNL2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
OTUD7A
LOC283710
GOLGA8G
FMN1
MIR211
HERC2P9
WHAMMP2
LOC646278
LOC653075
GOLGA8F
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4509-3
TMCO5B

Genes in Wide Peak

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

Table S32. Genes in bold are cancer genes as defined by The Sanger Institute: 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 1p22.1.

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

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FUBP1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
PIGK
TSPAN2
BCAS2
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
AK5
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
ST6GALNAC5
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423

Genes in Wide Peak

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

Table S34. Genes in bold are cancer genes as defined by The Sanger Institute: 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
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
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 16q24.3.

Table S35. Genes in bold are cancer genes as defined by The Sanger Institute: 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 5p15.31.

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

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

Genes in Wide Peak

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

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute: 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 6q22.31.

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
STL
GOPC
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
ACAT2
AIM1
AMD1
ARG1
CCNC
CGA
CNR1
COL10A1
CTGF
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1E
IFNGR1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
MAS1
MAP3K5
NMBR
NT5E
OPRM1
PCMT1
ENPP1
ENPP3
PEX7
PLAGL1
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
RPS12
SGK1
SIM1
SMPD2
SOD2
MAP3K7
TCF21
TCP1
DYNLT1
NR2E1
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
FHL5
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
CASP8AP2
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
ANKRD6
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
HEY2
HEBP2
ORC3
BRD7P3
ASF1A
CCDC28A
MTHFD1L
PNISR
MOXD1
IPCEF1
TIAM2
FBXL4
FBXO5
RGS17
SNORD50A
PDE7B
SESN1
OSTM1
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
HECA
COQ3
IL20RA
MTRF1L
AHI1
RMND1
SOBP
AKIRIN2
QRSL1
VNN3
AKIRIN2-AS1
ECHDC1
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
TMEM181
ZBTB2
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
C6orf164
PERP
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
MANEA
ADGB
C6orf97
MYCT1
ULBP2
ULBP1
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
RSPH3
ARMC2
FBXO30
RPF2
L3MBTL3
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
KIAA1919
ARHGAP18
SYTL3
GTF3C6
FAM54A
KLHL32
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
RAET1E
PM20D2
SRSF12
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
C6orf165
BVES-AS1
OLIG3
TXLNB
OSTCP1
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
MMS22L
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
GJB7
HMGA1P7
SNHG5
SUMO4
CENPW
C6orf174
LINC00222
CEP85L
THEMIS
LIN28B
SAMD5
IYD
GTF2H5
FAM26F
FLJ46906
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
SNORA20
SNORA29
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC100128176
BET3L
LOC100129518
LOC100130890
C6orf99
LINC00271
LOC100132735
LOC100287632
NHEG1
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR3918
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
MIR4464
MIR4466
MIR4643
MIR4465
LOC100652739

Genes in Wide Peak

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

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute: 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
ACYP1
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF5
ELK2AP
EML1
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
ALKBH1
EIF2B2
MTA1
RPS6KA5
NRXN3
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
BATF
SIVA1
AHSA1
CYP46A1
PAPOLA
TMED10
PTPN21
C14orf1
VASH1
SNW1
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
FLRT2
KIF26A
C14orf109
MLH3
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
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
SLIRP
RPS6KL1
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
FAM181A
BTBD6
EFCAB11
NEK9
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NOXRED1
JDP2
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
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
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 3p24.3.

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

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

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: 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 19p13.3.

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
BUB1B
TCF12
FLJ27352
C15orf55
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
APBA2
AQP9
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
SNURF
USP8
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
HSP90AB4P
MIR626
MIR627
MIR628
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B
MYZAP

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

Table S46. Genes in bold are cancer genes as defined by The Sanger Institute: 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 9p23.

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

Genes
PTPRD

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q14.

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

Genes
BUB1B
C15orf55
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
OCA2
PLCB2
MAPK6
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
USP50
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p11.2.

Table S50. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DDB2
EXT2
LMO2
WT1
CREB3L1
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
ACP2
ARHGAP1
MPPED2
CAT
CD44
CD59
CHRM4
CRY2
CSTF3
ELF5
F2
FOLH1
CD82
LRP4
CAPRIN1
MDK
MYBPC3
NDUFS3
PAX6
PSMC3
PTPRJ
RAG1
RAG2
RAPSN
RCN1
SLC1A2
SPI1
TRAF6
PDHX
DGKZ
CHST1
API5
MADD
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
NR1H3
HIPK3
EIF3M
CELF1
OR5I1
NUP160
FNBP4
MTCH2
FJX1
C11orf41
ABTB2
PAMR1
FBXO3
EHF
OR5L2
ELP4
COMMD9
PACSIN3
APIP
HSD17B12
PHF21A
WT1-AS
TRIM44
NAT10
SLC35C1
TCP11L1
AMBRA1
KBTBD4
TTC17
PRDM11
SYT13
LRRC4C
ALX4
PRRG4
C11orf49
TRIM48
ZNF408
QSER1
AGBL2
PRR5L
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
ARFGAP2
ACCS
SPRYD5
TSPAN18
SLC39A13
DEPDC7
C1QTNF4
PTPMT1
C11orf74
OR4C46
OR4X2
OR4B1
GYLTL1B
DNAJC24
OR8I2
LOC120824
LDLRAD3
C11orf94
IMMP1L
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
ALKBH3
LOC221122
OR4C3
OR4S1
OR10AG1
OR5J2
OR4C13
OR4C12
LOC283116
HARBI1
LINC00294
OR5F1
LOC338739
DCDC1
DKFZp779M0652
C11orf96
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
HNRNPKP3
FAM180B
OR4A47
OR4C45
MIR129-2
DKFZp686K1684
LOC440040
LOC440041
LOC441601
CCDC73
TRIM64C
LOC646813
SNORD67
LOC729799
C11orf91
MIR670
MIR3160-2
MIR3160-1
DCDC5
LOC100507205
LOC100507300
LOC100507401
MIR3973
MIR4688
MIR1343

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

Table S51. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
KTN1
GPHN
NIN
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
ACTN1
ACYP1
ARG2
BMP4
ZFP36L1
ENTPD5
CDKN3
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GCH1
GMFB
GPX2
GSTZ1
HIF1A
HSPA2
LGALS3
LTBP2
MAX
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SIX6
OTX2
PGF
PIGH
PPM1A
PPP2R5E
PRKCH
PSEN1
PSMA3
PSMC6
PTGDR
PTGER2
ABCD4
PYGL
RAD51B
ARID4A
RTN1
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
STYX
TGFB3
ZBTB25
DPF3
NUMB
ADAM21
ADAM20
CDKL1
DCAF5
ALKBH1
EIF2B2
PNMA1
NRXN3
AKAP5
SPTLC2
RGS6
KIAA0247
KIAA0586
DLGAP5
KIAA0317
MED6
CNIH
VTI1B
BATF
NPC2
AHSA1
EXOC5
CGRRF1
ACOT2
TMED10
FERMT2
C14orf1
WDHD1
MAP4K5
NID2
VASH1
ATG14
ZBTB1
SNW1
PCNX
DAAM1
SAMD4A
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
TIMM9
MLH3
ATP5S
KCNH5
POMT2
ERO1L
COQ6
ATL1
FCF1
RDH11
COX16
DACT1
ATP6V1D
JKAMP
DHRS7
C14orf166
SIX4
ZFYVE1
GNG2
C14orf101
FBXO34
C14orf105
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
MUDENG
ACTR10
YLPM1
C14orf162
ADCK1
TMEM63C
PELI2
RHOJ
GALNTL1
PLEKHH1
TXNDC16
TRMT5
ZNF410
NGB
RBM25
SAV1
C14orf133
SMOC1
IRF2BPL
MPP5
C14orf135
GPR135
GNPNAT1
ZC2HC1C
C14orf169
L2HGDH
C14orf45
DDHD1
SGPP1
TMX1
SLIRP
DNAL1
RPS6KL1
SYT16
KIAA1737
PAPLN
CHURC1
C14orf43
LIN52
NEK9
MAPK1IP1L
IFT43
WDR89
C14orf149
TRIM9
FRMD6
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
RDH12
ADAM21P1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
FAM71D
TMEM229B
TMEM30B
SAMD15
LOC283553
GPR137C
PROX2
ZDHHC22
TMED8
C14orf178
C14orf55
C14orf39
SNORD56B
VSX2
SLC35F4
RAB15
FLJ31306
TBPL2
TOMM20L
HEATR4
FLJ22447
PLEKHD1
LINC00238
TEX21P
ACOT1
ACOT6
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
C14orf38
LOC731223
KTN1-AS1
LOC100289511
MIR1260A
OTX2OS1
MIR4308
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

Table S52. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
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
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
CPB2
DACH1
EDNRB
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
POU4F1
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
UCHL3
ZMYM2
IFT88
TNFSF11
SCEL
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
SAP18
DLEU1
N4BP2L2
PIBF1
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
MRP63
RNF219
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
COMMD6
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
SNORA31
MIR621
MIR622
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4500
MIR4499
MIR4703
LOC100616668

Arm-level results

Table 3. Get Full Table Arm-level significance table - 22 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	2121	0.24	0.454	1	0.19	-1.21	1
1q	1955	0.47	9.44	0	0.16	-2.08	1
2p	924	0.21	-1.99	1	0.17	-3.32	1
2q	1556	0.21	-1.18	1	0.16	-2.91	1
3p	1062	0.19	-2.49	1	0.19	-2.49	1
3q	1139	0.21	-1.67	1	0.16	-3.35	1
4p	489	0.18	-3.26	1	0.25	-0.906	1
4q	1049	0.15	-3.78	1	0.26	-0.118	1
5p	270	0.23	-1.81	1	0.29	0.0707	0.993
5q	1427	0.16	-3.12	1	0.33	2.98	0.0053
6p	1173	0.42	5.69	3.68e-08	0.39	4.33	4.3e-05
6q	839	0.17	-2.49	1	0.59	11.9	0
7p	641	0.57	11	0	0.13	-3.86	1
7q	1277	0.55	11.6	0	0.13	-3.35	1
8p	580	0.38	3.71	0.000467	0.30	0.702	0.603
8q	859	0.49	8.46	0	0.17	-2.83	1
9p	422	0.14	-3.19	1	0.69	15.5	0
9q	1113	0.14	-3.32	1	0.55	11.2	0
10p	409	0.06	-5.59	1	0.58	11.3	0
10q	1268	0.02	-5.79	1	0.62	14.6	0
11p	862	0.15	-3.77	1	0.38	4.25	5.25e-05
11q	1515	0.14	-3.35	1	0.43	7.13	3.34e-12
12p	575	0.18	-3.24	1	0.20	-2.8	1
12q	1447	0.13	-4.15	1	0.20	-1.97	1
13q	654	0.32	1.5	0.269	0.29	0.655	0.603
14q	1341	0.16	-3.17	1	0.35	3.66	0.000497
15q	1355	0.27	0.661	0.925	0.18	-2.38	1
16p	872	0.16	-3.73	1	0.23	-1.2	1
16q	702	0.15	-3.87	1	0.34	2.38	0.0289
17p	683	0.16	-3.45	1	0.39	4.14	7.7e-05
17q	1592	0.21	-1.13	1	0.23	-0.326	1
18p	143	0.21	-2.56	1	0.35	2.19	0.0444
18q	446	0.17	-3.55	1	0.32	1.44	0.216
19p	995	0.17	-3.18	1	0.25	-0.424	1
19q	1709	0.17	-2.35	1	0.24	0.2	0.935
20p	355	0.44	5.69	3.68e-08	0.11	-5.04	1
20q	753	0.50	8.79	0	0.06	-5.93	1
21q	509	0.22	-1.89	1	0.24	-1.46	1
22q	921	0.40	5.03	1.25e-06	0.17	-3.09	1
Xq	1312	0.14	-3.92	1	0.28	1.05	0.392

Methods & Data

Input

Description

Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).
Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).
Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.
CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End
Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.
Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.
Confidence Level: Confidence level used to calculate the region containing a driver.
Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.
Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).
Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM-TM/8021720/GDAC_MergeDataFiles_8024611/SKCM-TM.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat
CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.7
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 299 Input Tumor Samples.

Tumor Sample Names
TCGA-D3-A1Q1-06A-21D-A194-01
TCGA-D3-A1Q3-06A-11D-A194-01
TCGA-D3-A1Q4-06A-11D-A194-01
TCGA-D3-A1Q5-06A-11D-A194-01
TCGA-D3-A1Q6-06A-11D-A194-01
TCGA-D3-A1Q7-06A-11D-A192-01
TCGA-D3-A1Q8-06A-11D-A192-01
TCGA-D3-A1Q9-06A-11D-A192-01
TCGA-D3-A1QA-06A-11D-A194-01
TCGA-D3-A1QB-06A-11D-A192-01

Figure 3. Segmented copy number profiles in the input data

Output

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

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

Region Data

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

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

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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