SNP6 Copy number analysis (GISTIC2)
Liver Hepatocellular Carcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C18P5XXM
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/C18P5XXM
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 2.0.20 (Firehose task version: 126).

Summary

There were 165 tumor samples used in this analysis: 27 significant arm-level results, 28 significant focal amplifications, and 29 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 - 28 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
--- | --- | --- | --- | ---
1q22 | 1.2425e-11 | 1.6269e-11 | chr1:154884596-155218792 | 29
11q13.3 | 4.3898e-10 | 4.3898e-10 | chr11:69051077-69434302 | 1
17q25.3 | 2.4474e-08 | 2.4474e-08 | chr17:79923868-80004927 | 5
6p21.1 | 2.5193e-10 | 4.0207e-08 | chr6:43768831-43778390 | 0 [VEGFA]
8q24.21 | 1.0067e-07 | 2.9254e-06 | chr8:100134841-146364022 | 281
3q26.31 | 1.2623e-05 | 1.2623e-05 | chr3:172254454-172319444 | 0 [TNFSF10]
5p15.33 | 0.00055344 | 0.00055344 | chr5:1019815-1300024 | 6
13q32.3 | 0.0041394 | 0.0041394 | chr13:98177518-102989109 | 31
1q42.3 | 1.7429e-05 | 0.0051048 | chr1:227931561-249250621 | 191
6p25.2 | 0.00013768 | 0.0051048 | chr6:1-26355282 | 174
7q31.2 | 3.4684e-05 | 0.0079613 | chr7:116339425-116349050 | 1
20q13.33 | 0.0095098 | 0.0095098 | chr20:60328006-63025520 | 96
17p11.2 | 0.010587 | 0.010587 | chr17:18860536-19475969 | 14
19q13.11 | 0.013313 | 0.013313 | chr19:33723706-33837231 | 2
1p22.3 | 0.017998 | 0.017998 | chr1:85979933-85998035 | 1
10p15.1 | 0.019323 | 0.019323 | chr10:5013075-5043327 | 2
7q21.2 | 0.00037017 | 0.021453 | chr7:88138350-92743496 | 25
15q26.3 | 0.0223 | 0.0223 | chr15:98107154-102531392 | 35
2q31.2 | 0.033061 | 0.033061 | chr2:178083264-178286705 | 6
5q35.3 | 0.055714 | 0.055714 | chr5:136221300-180915260 | 452
2p24.1 | 0.057573 | 0.057573 | chr2:20253732-20467928 | 2
9q34.2 | 0.12865 | 0.12865 | chr9:137109246-137216407 | 0 [RXRA]
8q13.3 | 0.0055769 | 0.13355 | chr8:51236883-70954271 | 91
12q23.1 | 0.17014 | 0.17014 | chr12:100720086-100979511 | 4
19p13.12 | 0.17014 | 0.17014 | chr19:15338574-15701101 | 10
22q13.1 | 0.18128 | 0.18128 | chr22:37951995-38293658 | 16
4q32.3 | 0.17014 | 0.2013 | chr4:140006212-191154276 | 226
4q13.3 | 0.10227 | 0.2454 | chr4:74285336-74320109 | 2

Genes in Wide Peak

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

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

Genes
MUC1
hsa-mir-92b
hsa-mir-4258
CKS1B
EFNA1
EFNA3
EFNA4
GBA
GBAP1
MTX1
SHC1
THBS3
ADAM15
PMVK
FAM189B
ZBTB7B
DPM3
LENEP
SLC50A1
PBXIP1
TRIM46
FLAD1
PYGO2
DCST2
DCST1
KRTCAP2
MIR92B
MIR4258
LOC100505666

Genes in Wide Peak

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

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

Genes
MYEOV

Genes in Wide Peak

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

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

Genes
ASPSCR1
RAC3
DCXR
STRA13
LRRC45

Genes in Wide Peak

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

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

Genes
COX6C
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
hsa-mir-1273
hsa-mir-875
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
POLR2K
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
RGS22
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
VPS13B
TMEM74
FAM91A1
SLC30A8
COL22A1
SNX31
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
FBXO43
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
MIR599
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR875
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 5p15.33.

Table S5. 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 13q32.3.

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

Genes
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
GPR183
FGF14
GPR18
IPO5
PCCA
SLC15A1
ZIC2
STK24
ITGBL1
TM9SF2
FARP1
DOCK9
TMTC4
ZIC5
A2LD1
RNF113B
CLYBL
NALCN
FGF14-IT1
UBAC2
MIR623
FKSG29
UBAC2-AS1
MIR4306
MIR3170
MIR2681
MIR548AN
MIR4705

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.3.

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
ACTA1
ACTN2
ADSS
AGT
ARF1
CHML
LYST
CHRM3
GALNT2
GNG4
GUK1
HNRNPU
KCNK1
LGALS8
MTR
NID1
RAB4A
RGS7
RYR2
TARBP1
TBCE
GPR137B
TSNAX
WNT9A
ZNF124
HIST3H3
GNPAT
KMO
EXO1
GGPS1
TOMM20
URB2
CEP170
AKT3
ZNF238
SPHAR
CAPN9
SDCCAG8
COG2
RBM34
ABCB10
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
TAF5L
DISC2
DISC1
PPPDE1
SCCPDH
TRIM17
ARID4B
EGLN1
KIAA1383
KIF26B
HEATR1
ZNF692
NUP133
ERO1LB
FMN2
ZNF695
GJC2
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
SMYD3
ARV1
C1orf35
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
ZNF496
C1orf198
WNT3A
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
EXOC8
RNF187
CNST
PLD5
C1orf100
IBA57
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
PRSS38
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
FAM89A
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
OR2W5
OR13G1
DUSP5P
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
MIR3123
MIR3124
MIR3620
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p25.2.

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

Genes
IRF4
DEK
hsa-mir-548a-1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
GPLD1
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
ID4
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SLC17A1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
ALDH5A1
HIST1H2AC
HIST1H2AB
HIST1H2BG
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3G
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4G
CMAHP
RIPK1
PRPF4B
HIST1H3F
GCM2
CD83
CDYL
LY86
EEF1E1
FAM65B
KIAA0319
NUP153
RANBP9
SLC17A4
SLC17A2
ECI2
TRIM38
CAP2
SCGN
FARS2
SLC17A3
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
GFOD1
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
MUTED
CCDC90A
KIF13A
TXNDC5
C6orf62
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
PIP5K1P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
RNF144B
HIST1H2BA
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
KAAG1
NHLRC1
HIST1H2APS1
PSMG4
DKFZP686I15217
FLJ23152
LINC00340
C6orf201
ERVFRD-1
PPP1R3G
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.2.

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

Genes
MET

Genes in Wide Peak

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

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

Genes
SS18L1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
CDH4
CHRNA4
COL9A3
EEF1A2
NPBWR2
KCNQ2
LAMA5
MYT1
NTSR1
OPRL1
PSMA7
PTK6
RPS21
SRMS
TAF4
TCEA2
TPD52L2
TNFRSF6B
OSBPL2
ARFRP1
RGS19
TCFL5
ADRM1
OGFR
DIDO1
HRH3
PRPF6
GTPBP5
GMEB2
SLCO4A1
STMN3
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
C20orf20
ARFGAP1
SLC2A4RG
ZNF512B
COL20A1
SLC17A9
LOC63930
C20orf195
PPDPF
BIRC7
DNAJC5
CABLES2
ZGPAT
PRIC285
BHLHE23
NKAIN4
C20orf166
GATA5
ZBTB46
SAMD10
ABHD16B
LINC00266-1
C20orf151
LSM14B
C20orf201
C20orf166-AS1
LINC00176
MIR1-1
MIR124-3
MIR133A2
MIR647
HAR1A
HAR1B
UCKL1-AS1
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
DPH3P1
LINC00029
LOC100144597
FLJ16779
MIR1914
MIR1257
MIR4326
MIR3196
LOC100505815
RTEL1-TNFRSF6B
MIR4758
LOC100652730

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p11.2.

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

Genes
hsa-mir-1180
MFAP4
MAPK7
RNF112
GRAP
EPN2
B9D1
SLC47A1
SLC5A10
GRAPL
FAM83G
SNORA59B
SNORA59A
MIR1180

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
CEBPA
LOC80054

Genes in Wide Peak

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

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

Genes
DDAH1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.1.

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

Genes
AKR1C1
AKR1C2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
hsa-mir-1285-1
KRIT1
CYP51A1
PEX1
CDK14
MTERF
FZD1
CLDN12
STEAP1
ANKIB1
SAMD9
GATAD1
C7orf63
RBM48
MGC16142
GTPBP10
C7orf62
ZNF804B
FAM133B
STEAP2
LRRD1
DPY19L2P4
LOC728066

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
hsa-mir-1302-10
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
LINS
SELS
TTC23
LRRK1
TM2D3
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
ADAMTS17
DNM1P46
CERS3
FAM169B
WASH3P
FLJ42289
OR4F6
OR4F15
FAM138E
GPCRLTM7
DDX11L1
DDX11L9
LOC100507472
MIR4714

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q31.2.

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

Genes
NFE2L2
hsa-mir-3128
AGPS
HNRNPA3
LOC100130691
MIR3128

Genes in Wide Peak

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

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
ADRA1B
ADRB2
ANXA6
ATOX1
BNIP1
CAMK2A
CANX
CCNG1
CD14
CDC25C
CDX1
CLTB
CSF1R
CSNK1A1
NKX2-5
CTNNA1
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSPA9
NDST1
HTR4
IK
IL12B
KCNMB1
LCP2
LTC4S
MFAP3
MGAT1
MSX2
NDUFA2
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
POU4F3
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SLC6A7
SLC34A1
SLIT3
SNCB
SPARC
SPINK1
SPOCK1
STK10
TAF7
ZNF354A
TCOF1
TTC1
UBE2D2
WNT8A
NME5
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
GFPT2
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
PRELID1
IL17B
MAT2B
MRPL22
PCDHB1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DCTN4
MZB1
PAIP2
PCDH12
FAM13B
FAM53C
REEP2
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
KDM3B
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PSD2
THOC3
C5orf32
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
SFXN1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
C5orf58
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SLC36A2
SPINK13
C5orf41
LOC153469
ZMAT2
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
LOC340037
TMEM173
ARSI
PFN3
ZNF879
IRGM
FBLL1
NIPAL4
DND1
C5orf25
FLJ38109
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
FLJ16171
MIR340
IGIP
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
LOC100505658
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.1.

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

Genes
SDC1
PUM2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q13.3.

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

Genes
PLAG1
TCEA1
CHCHD7
hsa-mir-124-2
ASPH
CA8
CRH
CYP7A1
NPBWR1
LYN
MOS
MYBL1
OPRK1
PDE7A
PENK
RAB2A
RP1
RPS20
SDCBP
TTPA
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SULF1
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
CSPP1
VCPIP1
PREX2
SLCO5A1
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
FAM150A
LOC401463
MIR124-2
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q23.1.

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

Genes
NR1H4
SCYL2
SLC17A8
GAS2L3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
BRD4
hsa-mir-1470
AKAP8
AKAP8L
WIZ
RASAL3
EPHX3
PGLYRP2
CYP4F22
MIR1470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q13.1.

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

Genes
hsa-mir-659
H1F0
LGALS1
LGALS2
GALR3
TRIOBP
CDC42EP1
GCAT
SH3BP1
GGA1
EIF3L
PDXP
NOL12
ANKRD54
MIR658
MIR659

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q32.3.

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
AFP
ALB

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 - 29 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
--- | --- | --- | --- | ---
1p36.23 | 6.4964e-16 | 5.1687e-15 | chr1:1-9212782 | 154
13q14.2 | 2.1392e-11 | 2.6573e-09 | chr13:48833767-49064807 | 2
8p23.2 | 3.221e-06 | 3.2927e-06 | chr8:2079140-6262191 | 1
9p21.3 | 5.8539e-06 | 5.9267e-06 | chr9:21865498-21997722 | 2
4q35.1 | 3.2662e-09 | 1.0788e-05 | chr4:178360197-191154276 | 65
17p12 | 4.4094e-06 | 1.0788e-05 | chr17:15928223-16185399 | 1
19p13.3 | 3.3174e-05 | 3.4564e-05 | chr19:1-5455610 | 184
10q23.31 | 2.8383e-05 | 0.00016677 | chr10:89604733-90034038 | 2
12q24.33 | 0.00053759 | 0.00056645 | chr12:123377266-133851895 | 81
22q13.31 | 0.001251 | 0.0011927 | chr22:44205320-51304566 | 96
6q27 | 0.0027741 | 0.0045465 | chr6:159692597-171115067 | 71
2q34 | 0.0054045 | 0.0070836 | chr2:211340599-212243533 | 2
11q23.3 | 0.0076418 | 0.0079697 | chr11:102825636-135006516 | 293
4q24 | 1.8968e-06 | 0.0085669 | chr4:87734262-115525698 | 133
13q22.2 | 1.4369e-05 | 0.017615 | chr13:53623915-95094384 | 64
3p13 | 0.024023 | 0.024023 | chr3:50228522-89162506 | 196
16q23.1 | 0.034846 | 0.035592 | chr16:59786558-90354753 | 305
14q23.3 | 0.013048 | 0.03722 | chr14:66963153-67658112 | 1
4q21.23 | 9.5339e-05 | 0.054246 | chr4:57971870-135199164 | 355
10q24.32 | 0.0016167 | 0.060031 | chr10:89728127-135534747 | 421
12p12.1 | 0.064316 | 0.062579 | chr12:22837283-25209763 | 6
2q22.1 | 0.020949 | 0.074664 | chr2:139655617-143637838 | 1
18q12.2 | 0.10029 | 0.09892 | chr18:35235531-78077248 | 170
6q16.3 | 0.094472 | 0.1346 | chr6:57206295-166080093 | 475
1p35.2 | 4.2073e-05 | 0.15048 | chr1:1-37921042 | 593
14q32.33 | 0.016997 | 0.17599 | chr14:31949447-107349540 | 611
4p16.3 | 0.21035 | 0.21035 | chr4:1-36070348 | 203
17p13.3 | 0.04353 | 0.22016 | chr17:1-13933317 | 292
5q23.1 | 0.23785 | 0.23261 | chr5:44813655-180915260 | 864

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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
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
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 13q14.2.

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

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

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

Genes
CSMD1

Genes in Wide Peak

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

Table S29. 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 4q35.1.

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

Genes
DUX4
hsa-mir-1305
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ZFP42
ENPP6
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

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

Genes
NCOR1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.3.

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

Genes
GNA11
SH3GL1
STK11
TCF3
FSTL3
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
ARID3A
EEF2
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
MATK
GADD45B
NFIC
OAZ1
PALM
POLR2E
POLRMT
MAP2K2
PRTN3
PTBP1
PTPRS
RPS15
SGTA
TBXA2R
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
APBA3
MED16
CHAF1A
EBI3
PLIN3
APC2
ABCA7
HMG20B
SEMA6B
UQCR11
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
SHC2
TIMM13
DAZAP1
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
SLC39A3
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
NCLN
SPPL2B
SHD
WDR18
REXO1
ZNF77
C19orf29
CELF5
FSD1
TLE6
LPPR3
ZNF556
UBXN6
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
C19orf21
PLK5
C2CD4C
TICAM1
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
CSNK1G2-AS1
C19orf77
MIR7-3HG
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
C19orf29-AS1
MIR7-3
PLIN5
FAM138F
LINGO3
ARRDC5
FAM138A
MIR637
PLIN4
C19orf71
LOC100131094
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4747
MIR4746
MIR4745

Genes in Wide Peak

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

Table S33. 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 12q24.33.

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

Genes
hsa-mir-4304
SCARB1
EIF2B1
STX2
GOLGA3
GTF2H3
MMP17
POLE
PXMP2
RAN
SFSWAP
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
ULK1
PIWIL1
NCOR2
MPHOSPH9
ZNF268
TMED2
SNRNP35
FZD10
P2RX2
ANKLE2
ABCB9
RIMBP2
ATP6V0A2
GALNT9
ARL6IP4
SBNO1
CHFR
PITPNM2
EP400
DHX37
FBRSL1
DDX55
AACS
NOC4L
OGFOD2
TCTN2
CCDC92
PUS1
C12orf65
TMEM132C
TMEM132B
LOC116437
TMEM132D
SLC15A4
BRI3BP
FAM101A
ZNF664
GLT1D1
PGAM5
RILPL2
DNAH10
GPR133
DDX51
EP400NL
RILPL1
SETD8
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
LOC647589
SNORA49
LOC100128554
LOC100130238
LOC100190940
ZNF605
MIR4304
MIR3612
MIR3908
LOC100507055
LOC100507091
LOC100507206
ZNF664-FAM101A

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
ACAT2
CCR6
GPR31
IGF2R
KIF25
LPA
MAS1
MAP3K4
PARK2
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
THBS2
RNASET2
QKI
WTAP
PDE10A
C6orf123
DLL1
MRPL18
BRP44L
UNC93A
PHF10
C6orf70
AGPAT4
SMOC2
FRMD1
AGPAT4-IT1
C6orf208
LPAL2
TTLL2
FAM120B
LINC00473
SFT2D1
PACRG
PNLDC1
LOC154449
DACT2
C6orf118
WDR27
LOC285796
PRR18
C6orf120
DKFZp451B082
TCP10L2
LINC00242
LOC441177
MLLT4-AS1
SNORA20
SNORA29
LOC729603
HGC6.3
LOC100129518
LOC100289495
MIR1913
MIR3939
CAHM
MIR4644

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q34.

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

Genes
CPS1
CPS1-IT1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q24.

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

Genes
RAP1GDS1
TET2
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ANK2
ATOH1
BMPR1B
CAMK2D
CASP6
CENPE
DMP1
DSPP
EGF
EIF4E
ENPEP
GRID2
H2AFZ
HADH
HSP90AB3P
IBSP
CFI
MANBA
AFF1
MTTP
NFKB1
PDHA2
PITX2
PKD2
PPP3CA
RPL34
SNCA
SPP1
TACR3
UBE2D3
SPARCL1
UNC5C
LAMTOR3
HERC3
PAPSS1
AIMP1
ABCG2
TSPAN5
FAM13A
SEC24B
PDLIM5
RRH
MMRN1
METAP1
PPA2
DAPP1
DKK2
HPGDS
HSD17B11
LEF1
HERC5
LARP7
EMCN
NUDT9
GAR1
ARHGEF38
HERC6
CCDC109B
BANK1
C4orf21
AP1AR
BDH2
SMARCAD1
MEPE
INTS12
KLHL8
OSTC
NEUROG2
SLC39A8
AGXT2L1
ELOVL6
ARSJ
GSTCD
DNAJB14
ALPK1
CXXC4
PLA2G12A
C4orf17
COL25A1
PIGY
FLJ20021
TIFA
RG9MTD2
TBCK
CYP2U1
DDIT4L
C4orf32
C4orf36
SLC9B2
SLC9B1
PPM1K
TIGD2
SGMS2
NPNT
LOC256880
NAP1L5
LOC285456
FAM13A-AS1
GPRIN3
C4orf37
LRIT3
SLC10A6
HSD17B13
PCNAP1
FAM190A
MIR302A
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641518
LOC644248
MIR1243
MIR3684
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q22.2.

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

Genes
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
KLF5
BTF3P11
CLN5
DACH1
EDNRB
GPC5
LMO7
PCDH9
POU4F1
ATXN8OS
UCHL3
SCEL
TBC1D4
GPC6
SPRY2
PIBF1
KLF12
DIS3
MYCBP2
SLITRK5
FBXL3
PCDH17
NDFIP2
KLHL1
RBM26
PCDH20
RNF219
BORA
TDRD3
DIAPH3
SLITRK6
SLITRK1
KCTD12
SLAIN1
PRR20A
LINC00410
COMMD6
OR7E156P
LINC00550
LINC00347
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
MZT1
MIR4500HG
CTAGE11P
MIR622
PRR20B
PRR20C
PRR20D
PRR20E
MIR1297
MIR3169
MIR3665
RBM26-AS1
MIR4500

Genes in Wide Peak

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

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

Genes
FHIT
MITF
BAP1
FOXP1
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
ACY1
ALAS1
ARF4
C3orf51
CACNA1D
CISH
DNASE1L3
DOCK3
DUSP7
FLNB
GBE1
GNAI2
GNAT1
GPR27
GRM2
HTR1F
HYAL1
ITIH1
ITIH3
ITIH4
CNTN3
PDHB
POU1F1
PRKCD
PTPRG
ROBO1
ROBO2
RPL29
ATXN7
NEK4
TKT
TMF1
TNNC1
WNT5A
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
UBA3
RRP9
MAGI1
CACNA2D2
VPRBP
PSMD6
PARP3
ARL6IP5
NPRL2
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
RASSF1
NISCH
TUSC2
TWF2
PDZRN3
RAD54L2
FRMD4B
STAB1
FAM208A
RYBP
NAT6
ABHD14A
POC1A
CHMP2B
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
RBM15B
ARHGEF3
C3orf18
ZMYND10
TEX264
HEMK1
SFMBT1
PHF7
TLR9
IL17RD
PXK
FEZF2
EBLN2
SHQ1
ZNF654
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
LMOD3
SEMA3G
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
SELK
PROK2
NT5DC2
THOC7
WDR82
ID2B
KBTBD8
ABHD14B
RFT1
ACTR8
SLC25A26
GPR62
FAM3D
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
LOC201617
DNAH12
PDE12
FAM116A
CADM2
C3orf64
C3orf38
CCDC66
LOC285401
EIF4E3
SPATA12
TMEM110
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LOC401074
MIRLET7G
MIR135A1
FAM19A1
IQCF6
C3orf78
LOC440970
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
GXYLT2
ESRG
SNORD19B
C3orf74
ZNF717
LOC100287879
FRG2C
MIR1284
MIR1324
MIR3136
MIR4272
MIR4273
MIR3938
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4787
MIR4795
MIR4444-1
LOC100652759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
CBFA2T3
CBFB
CDH1
CDH11
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
AARS
AP1G1
AFG3L1P
AGRP
APRT
ZFHX3
C16orf3
CA5A
CA7
CALB2
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
COX4I1
CTRB1
CTRL
CYBA
DHODH
NQO1
DYNC1LI2
DPEP1
E2F4
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HAS3
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
KARS
LCAT
MC1R
CHST6
MVD
NFATC3
CHMP1A
PLCG2
PSKH1
PSMB10
PSMD7
RPL13
RRAD
ST3GAL2
SLC9A5
SLC12A4
SNTB2
SPG7
TAT
TERF2
TK2
ZNF19
ZNF23
GAN
SLC7A5
CDK10
TRADD
MBTPS1
CES2
NAE1
NOL3
TAF1C
SLC7A6
USP10
ATP6V0D1
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
NUTF2
COX4NB
TUBB3
CFDP1
CTCF
NFAT5
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
CES3
ADAT1
CHST5
EDC4
PLA2G15
COG4
PLEKHG4
LRRC29
CPNE7
VPS4A
IL17C
NOB1
TMEM208
FHOD1
ANKRD11
ZDHHC1
OSGIN1
PARD6A
CKLF
NIP7
FAM96B
GINS2
TPPP3
TRAPPC2L
WWOX
BCMO1
TERF2IP
PRMT7
NECAB2
KLHDC4
HYDIN
DEF8
DUS2L
CHTF8
TXNL4B
BANP
PDPR
RFWD3
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
ZDHHC7
VAC14
FTSJD1
DDX28
TSNAXIP1
CENPN
C16orf61
THAP11
JPH3
PDP2
RANBP10
VAT1L
KIAA1609
WFDC1
PDF
DPEP2
DPEP3
MTHFSD
ACD
DBNDD1
FA2H
FAM65A
TMEM231
TMCO7
WDR59
ELMO3
KLHL36
FBXO31
ESRP2
CENPT
C16orf70
CYB5B
CMIP
GFOD2
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
C16orf48
SLC7A6OS
COG8
SPIRE2
ZNF469
B3GNT9
CIRH1A
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
CMTM1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
NRN1L
CMTM3
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
SLC22A31
IL34
TMED6
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
CCDC79
CES4A
EXOC3L1
LINC00304
LOC283867
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
C16orf86
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
MIR140
CTRB2
MIR328
CLEC18B
SNORD68
LOC644649
KIAA0895L
SNORD71
SNORD111
LOC727710
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130894
SYCE1L
LOC100287036
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
LOC100505865
LOC100506083
LOC100506172
C16orf95
CKLF-CMTM1
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

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

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

Genes
GPHN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.23.

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

Genes
IL2
RAP1GDS1
TET2
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
hsa-mir-1269
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
ALB
AMBN
ANK2
ANXA3
ANXA5
AREG
ART3
ATOH1
BMP3
BMPR1B
BTC
CAMK2D
CASP6
CCNA2
CCNG2
SCARB2
CDS1
CENPC1
CENPE
CSN1S1
CSN2
CSN3
DCK
DMP1
DSPP
EGF
EIF4E
ENPEP
EPHA5
EREG
FABP2
FGF2
FGF5
GC
GK2
GNRHR
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
H2AFZ
HADH
HNRNPD
HSP90AB3P
HTN1
HTN3
IBSP
CFI
IGJ
IL8
CXCL10
MAD2L1
MANBA
CXCL9
AFF1
MTTP
MUC7
NFKB1
NKX6-1
PDHA2
PF4
PF4V1
PITX2
PKD2
EXOSC9
PPEF2
PPBP
PPP3CA
PRKG2
MAPK10
PTPN13
RPL34
CXCL6
CXCL11
CXCL5
SNCA
SPP1
STATH
SULT1E1
TACR3
TRPC3
UBE2D3
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
SPARCL1
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
HERC3
STBD1
CDKL2
PAPSS1
AIMP1
NDST3
TMPRSS11D
ABCG2
ADAMTS3
SEC24D
G3BP2
HNRPDL
TSPAN5
ENAM
FAM13A
SPRY1
PGRMC2
SEC24B
CXCL13
PDLIM5
RRH
UGT2B11
PLK4
HPSE
SMR3B
NPFFR2
PPBPL2
UGT2A1
CCNI
PRDM5
NUDT6
HSPA4L
SEC31A
RUFY3
MMRN1
WDFY3
METAP1
LPHN3
PARM1
RCHY1
ANKRD17
STAP1
SMR3A
PPA2
DAPP1
DKK2
INTU
NAAA
COQ2
SULT1B1
HPGDS
TMPRSS11E
MRPS18C
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
MYOZ2
NUDT9
NUP54
GAR1
UGT2B28
USP53
ARHGEF38
ODAM
HERC6
CCDC109B
BANK1
LARP1B
SDAD1
BBS7
UBA6
C4orf21
AP1AR
BMP2K
SEPT11
BDH2
SMARCAD1
MEPE
PRDM8
UTP3
INTS12
ANKRD50
KLHL8
PCDH10
SHROOM3
METTL14
ENOPH1
PROL1
OSTC
IL21
NEUROG2
SLC39A8
NDST4
AGXT2L1
MRPL1
ELOVL6
NDNF
FAT4
ARSJ
THAP9
UGT2A3
GSTCD
TNIP3
PHF17
SCD5
DNAJB14
FRAS1
C4orf29
ALPK1
CXXC4
PLA2G12A
SLC25A31
ARHGAP24
C4orf17
QRFPR
FAM175A
KIAA1109
COL25A1
NAA11
AGPAT9
PIGY
CABS1
FLJ20021
YTHDC1
MOB1B
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
GDEP
ANTXR2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
LIN54
C4orf32
TMPRSS11B
C4orf36
TRAM1L1
SLC9B2
SLC9B1
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
SPATA5
BBS12
TIGD2
RASSF6
SGMS2
SYNPO2
CNOT6L
TECRL
C4orf22
LOC255130
EPGN
NPNT
MFSD8
LOC256880
FDCSP
NAP1L5
LOC285419
LOC285456
FAM13A-AS1
GPRIN3
COX18
C4orf37
CSN1S2AP
CCDC158
TMPRSS11A
SOWAHB
LRIT3
SLC10A6
HSD17B13
PCNAP1
TMPRSS11F
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
FLJ14186
C4orf3
WDFY3-AS2
MIR302A
C4orf11
MTHFD2L
LOC441025
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC550112
LOC550113
UGT2A2
LOC641518
LOC644248
TMPRSS11GP
CEP170P1
LOC645513
SNORA24
MIR575
MIR577
CETN4P
SNHG8
FAM47E
FTLP10
LOC100144602
PP12613
MIR1243
MIR2054
MIR1973
CSN1S2BP
LOC100499177
MIR3684
LOC100505702
LOC100505875
LOC100506035
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4450
MIR4451
FAM47E-STBD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q24.32.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
FAS
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HELLS
HHEX
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
KIF20B
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
ANKRD1
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
EXOC6
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
OPALIN
SYCE1
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
ANKRD22
SFXN2
PDZD8
C10orf32
NUDT9P1
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
TRUB1
VTI1A
LOC143188
HECTD2
FGFBP3
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
FLJ37201
LOC283038
LOC283089
O3FAR1
KCNK18
LIPM
CYP26C1
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
C10orf62
IFIT1B
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
LIPK
LIPN
LOC643529
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
DUX4L2
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100169752
LOC100188947
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
FAS-AS1
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

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

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

Genes
hsa-mir-920
BCAT1
SOX5
LINC00477
C12orf77
MIR920

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

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

Genes
LRP1B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

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

Genes
BCL2
MALT1
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
ATP5A1
CDH7
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TCF4
ZNF236
SLC14A2
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
EPG5
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
KATNAL2
MRO
HDHD2
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
RNF165
C18orf32
KC6
LOC643542
C18orf63
LOC647946
SCARNA17
SNORA37
TCEB3CL
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR1539
MIR4319
MIR4318
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4529
MIR3591
MIR4743
MIR4744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.3.

Table S49. 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-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
ACAT2
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IMPG1
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
ME1
MAP3K4
MAP3K5
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLG
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
RNY4
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
MAP3K7
TCF21
TCP1
DYNLT1
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
UTRN
EZR
VIP
PTP4A1
EPM2A
STX7
PEX3
DDO
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
PHF3
HEY2
HEBP2
ORC3
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
SENP6
TIAM2
FBXL4
FBXO5
SLC17A5
RGS17
SNORD50A
PDE7B
FILIP1
SESN1
OSTM1
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
LGSN
HECA
COQ3
IL20RA
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
AGPAT4-IT1
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
RSPH3
ARMC2
FBXO30
RPF2
L3MBTL3
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
C6orf7
UBE2CBP
KIAA1919
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
FAM54A
KLHL32
TMEM200A
MB21D1
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SRSF12
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
OLIG3
TXLNB
C6orf118
OSTCP1
KHDRBS2
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
LOC285796
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GUSBP4
GJB7
HMGA1P7
SNHG5
SUMO4
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
GTF2H5
MIR30A
MIR30C2
OOEP
FAM26F
FLJ46906
MCART3P
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
SNORA20
SNORA29
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
LOC100128176
BET3L
KHDC1L
LOC100129518
LOC100130890
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100288198
NHEG1
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3918
MIR3668
MIR3662
MIR3692
LOC100506804
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p35.2.

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

Genes
LCK
PAX7
RPL22
SDHB
SFPQ
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
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
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL8A2
COL16A1
CORT
CSF3R
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PSMB2
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
YARS
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
EIF2C1
OR4F3
RNU11
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
ADPRHL2
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
FAM176B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
MIIP
CELA2A
GPATCH3
CLSPN
TINAGL1
PLA2G2F
S100PBP
CEP85
NMNAT1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
SH3D21
AGMAT
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCP2
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
C1orf212
ADC
TMEM54
CSMD2
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
GJB4
HMGB4
RNF19B
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
EIF2C3
EIF2C4
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4255
MIR4253
MIR4251
MIR4252
MIR4254
MIR3917
MIR3605
MIR3675
ENO1-AS1
ZMYM6NB
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.33.

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

Genes
AKT1
KTN1
NKX2-1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
NIN
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
hsa-mir-3172
SERPINA3
ACTN1
ACYP1
ARF6
ARG2
ARHGAP5
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
ENTPD5
CDKN3
CFL2
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FKBP3
FNTB
FOS
FUT8
GALC
GCH1
GMFB
GPR33
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
FOXA1
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
MGAT2
CTAGE5
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
NDUFB1
NFKBIA
SIX6
OTX2
PAX9
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PNN
POLE2
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMA3
PSMA6
PSMC1
PSMC6
PTGDR
PTGER2
ABCD4
PYGL
RAD51B
MOK
ARID4A
RPL36AL
RPS29
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
GEMIN2
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
CDKL1
DCAF5
ALKBH1
EIF2B2
MTA1
NEMF
PNMA1
RPS6KA5
NRXN3
AKAP6
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
KIAA0125
KIAA0317
TECPR2
MED6
CNIH
SEC23A
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
PAPOLA
ACOT2
TMED10
FERMT2
PTPN21
C14orf1
WDHD1
BAZ1A
MAP4K5
NID2
VASH1
ATG14
ZBTB1
SNW1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
KLHDC2
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
NKX2-8
PLEK2
TIMM9
MLH3
ATP5S
KCNH5
PRO1768
GPR132
POMT2
ERO1L
COQ6
ATL1
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
MBIP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
GNG2
KLHL28
C14orf101
PPP2R3C
PRPF39
FBXO34
CDCA4
C14orf102
ATG2B
UBR7
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
EAPP
ACTR10
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNTL1
PLEKHH1
TXNDC16
TRMT5
UNC79
BEGAIN
FANCM
PPP4R4
ZNF410
NGB
RBM25
SNX6
SAV1
C14orf133
NPAS3
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
GNPNAT1
OTUB2
ZFYVE21
MEG8
WDR25
METTL21D
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
L2HGDH
C14orf159
C14orf45
NUBPL
TMEM121
DDHD1
SGPP1
TMX1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
FSCB
SETD3
BRMS1L
APOPT1
HHIPL1
C14orf142
INSM2
ARHGAP5-AS1
STON2
KIAA1737
SLC25A21
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
MAPK1IP1L
EGLN3
IFT43
WDR89
C14orf149
AHNAK2
TRIM9
TRMT61A
MIA2
TDRD9
ANKRD9
AK7
IFI27L1
C14orf28
TRAPPC6B
C14orf79
PLD4
ADSSL1
LRR1
KLHDC1
FRMD6
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
RPL10L
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
MIPOL1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
LRFN5
FAM71D
TMEM229B
C14orf49
CLEC14A
TMEM30B
MDGA2
SAMD15
EML5
SPTSSA
MGC23270
C14orf183
RALGAPA1
SFTA3
FBXO33
NUDT14
LINC00521
SERPINA11
IGBP1P1
LOC283547
C14orf182
LOC283553
GPR137C
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
FAM177A1
KIAA0284
C14orf80
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
SLC35F4
COX8C
ASPG
RAB15
FLJ31306
TBPL2
TOMM20L
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
C14orf38
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
SNORD127
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
KTN1-AS1
LOC100129345
LOC100129794
LOC100131366
LOC100288846
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR4309
MIR3173
MIR4308
MIR548Y
LOC100506321
LOC100506433
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4503
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
NKX3-2
BST1
CCKAR
CD38
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RGS12
RNF4
S100P
SH3BP2
SOD3
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
SLC34A2
MXD4
CPLX1
SLC26A1
PPARGC1A
SEL1L3
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
SEPSECS
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
DCAF16
LGI2
TBC1D19
PI4K2B
CNO
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
CC2D2A
STIM2
KIAA1530
ZFYVE28
GBA3
AFAP1
NCAPG
TNIP2
HAUS3
ABCA11P
GRPEL1
MED28
KCNIP4
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
CPEB2
EVC2
PACRGL
OTOP1
ZNF595
LOC152742
JAKMIP1
FAM53A
METTL19
GPR125
ZBTB49
ZNF721
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
KCNIP4-IT1
C4orf52
USP17L6P
USP17
HSP90AB2P
C4orf48
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.3.

Table S53. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PER1
MAP2K4
TP53
GAS7
USP6
hsa-mir-548h-3
hsa-mir-744
hsa-mir-4314
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ACADVL
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DNAH9
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MNT
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RCVRN
RPA1
RPL26
SCO1
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF18
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
MYH13
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
GLP2R
NTN1
STX8
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
ARHGAP44
HS3ST3A1
CLEC10A
MYBBP1A
PRPF8
KIF1C
GABARAP
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
KIAA0664
SMG6
WSCD1
CTDNEP1
PIK3R5
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
C17orf59
GPR172B
WRAP53
RNMTL1
VPS53
C17orf85
TSR1
DHX33
C17orf48
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
ELAC2
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
CTC1
NDEL1
PITPNM3
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
LSMD1
NEURL4
ZNF594
HES7
SPATA22
TXNDC17
MIR22HG
TMEM88
MYOCD
CDRT15P1
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
DNAH2
RTN4RL1
WDR16
CCDC42
PIK3R6
ODF4
KCTD11
MFSD6L
TRPV3
SLC16A11
FBXO39
DHRS7C
SLC16A13
C17orf74
SPNS3
C17orf61
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
FLJ34690
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
SHISA6
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
PIRT
SNORA48
SNORD10
OR1D4
SCARNA21
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
MIR744
LOC100128288
C17orf107
LOC100130950
DBIL5P
LOC100289255
MIR1253
LOC100306951
MIR3183
MIR4314
MIR3676
LOC100506388
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4520A
MIR4521
MIR4520B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q23.1.

Table S54. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
APC
CD74
EBF1
IL6ST
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
NAIP
NDUFA2
NDUFS4
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
ATG12
PTTG1
PDLIM7
NREP
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
APBB3
CCNO
TNIP1
GNB2L1
NSA2
FST
SLU7
POLR3G
RGS14
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
SOX30
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
PPWD1
HARS2
OTP
SKIV2L2
ZNF346
SSBP2
BHMT2
TNFAIP8
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
IPO11
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
CCDC99
THG1L
AGGF1
WDR41
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1P1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
TRIM52
HAVCR2
AGXT2L2
C5orf62
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
C5orf58
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC38A9
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
LOC153469
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
AQPEP
SLC36A1
EIF4E1B
RASGEF1C
ANKRD31
SERINC5
LOC257358
LOC257396
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
RGMB
RFESD
CHSY3
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
ANKRD34B
PFN3
ZNF879
IRGM
FBLL1
IDAS
ACTBL2
FAM174A
MTX3
CATSPER3
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
MAST4
C5orf25
RNF138P1
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
RGS7BP
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
CRSP8P
FLJ42709
C5orf56
FLJ16171
MIR340
IGIP
GPX8
TIFAB
FLJ35946
LOC553103
MIR449A
CTXN3
SNORD95
SNORD96A
ECSCR
LOC642366
TMEM232
C5orf43
LOC643201
GRXCR2
SPINK9
ZFP62
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
CBY3
LOC647859
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR581
MIR583
MIR585
SNHG4
MIR143HG
GTF2H2C
LOC728342
SERF1B
LOC728554
LOC728723
LOC729080
AACSP1
LOC729678
OR4F29
GTF2H2D
GUSBP9
VTRNA2-1
MIR874
LOC100129716
LRRC70
LOC100131067
FAM196B
LOC100132062
LOC100132287
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MTRNR2L2
MIR3607
MIR3655
MIR3660
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505841
LOC100505894
OCLN
LOC100507387
MIR4804
MIR4633
MIR4634
MIR4461
MIR3977
MIR4460
MIR4638
MIR4803
MIR378E
LOC100859930

Arm-level results

Table 3. Get Full Table Arm-level significance table - 27 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 | 0.16 | -0.564 | 1 | 0.30 | 3.51 | 0.00082
1q | 1955 | 0.56 | 11.4 | 0 | 0.32 | 3.23 | 0.0019
2p | 924 | 0.15 | -1.14 | 1 | 0.11 | -2.56 | 1
2q | 1556 | 0.13 | -1.85 | 1 | 0.11 | -2.39 | 1
3p | 1062 | 0.11 | -2.45 | 1 | 0.13 | -1.92 | 1
3q | 1139 | 0.10 | -2.84 | 1 | 0.09 | -3.19 | 1
4p | 489 | 0.07 | -3.41 | 1 | 0.26 | 2.04 | 0.0514
4q | 1049 | 0.02 | -4.55 | 1 | 0.34 | 5.03 | 1.61e-06
5p | 270 | 0.39 | 6 | 1.28e-08 | 0.14 | -1.39 | 1
5q | 1427 | 0.31 | 3.8 | 0.00048 | 0.13 | -1.48 | 1
6p | 1173 | 0.27 | 2.46 | 0.0279 | 0.19 | 0.0126 | 0.761
6q | 839 | 0.19 | -0.0281 | 1 | 0.38 | 5.65 | 8.07e-08
7p | 641 | 0.31 | 3.85 | 0.000468 | 0.10 | -2.44 | 1
7q | 1277 | 0.34 | 4.71 | 1.24e-05 | 0.12 | -1.78 | 1
8p | 580 | 0.19 | 0.0516 | 1 | 0.64 | 14.2 | 0
8q | 859 | 0.51 | 9.5 | 0 | 0.31 | 3.06 | 0.00321
9p | 422 | 0.07 | -3.31 | 1 | 0.32 | 4.21 | 5.81e-05
9q | 1113 | 0.07 | -3.24 | 1 | 0.32 | 4.35 | 3.82e-05
10p | 409 | 0.12 | -2.03 | 1 | 0.19 | -0.0997 | 0.8
10q | 1268 | 0.09 | -2.7 | 1 | 0.25 | 1.91 | 0.0662
11p | 862 | 0.07 | -3.44 | 1 | 0.19 | 0.109 | 0.731
11q | 1515 | 0.08 | -3.05 | 1 | 0.21 | 0.875 | 0.382
12p | 575 | 0.10 | -2.59 | 1 | 0.24 | 1.62 | 0.116
12q | 1447 | 0.13 | -1.7 | 1 | 0.14 | -1.34 | 1
13q | 654 | 0.09 | -2.61 | 1 | 0.37 | 5.59 | 9.07e-08
14q | 1341 | 0.08 | -2.86 | 1 | 0.30 | 3.68 | 0.000459
15q | 1355 | 0.11 | -2.43 | 1 | 0.21 | 0.765 | 0.42
16p | 872 | 0.09 | -2.82 | 1 | 0.32 | 4.2 | 5.81e-05
16q | 702 | 0.05 | -3.71 | 1 | 0.38 | 6.13 | 6.04e-09
17p | 683 | 0.13 | -1.27 | 1 | 0.58 | 12.3 | 0
17q | 1592 | 0.29 | 3.02 | 0.00567 | 0.20 | 0.39 | 0.58
18p | 143 | 0.08 | -3.24 | 1 | 0.21 | 0.44 | 0.574
18q | 446 | 0.09 | -2.95 | 1 | 0.22 | 0.736 | 0.42
19p | 995 | 0.22 | 1.05 | 0.491 | 0.17 | -0.707 | 1
19q | 1709 | 0.24 | 1.58 | 0.205 | 0.13 | -1.61 | 1
20p | 355 | 0.30 | 3.49 | 0.00121 | 0.08 | -2.97 | 1
20q | 753 | 0.30 | 3.62 | 0.000842 | 0.06 | -3.6 | 1
21q | 509 | 0.12 | -1.86 | 1 | 0.30 | 3.36 | 0.00129
22q | 921 | 0.15 | -1.08 | 1 | 0.27 | 2.59 | 0.0127
Xq | 1312 | 0.17 | -0.48 | 1 | 0.22 | 0.93 | 0.371

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/LIHC-TP/5950057/GDAC_MergeDataFiles_5954830/LIHC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 165 Input Tumor Samples.

Tumor Sample Names
TCGA-BC-4072-01B-11D-A151-01
TCGA-BC-4073-01B-02D-A12Y-01
TCGA-BC-A10Q-01A-11D-A12Y-01
TCGA-BC-A10R-01A-11D-A12Y-01
TCGA-BC-A10S-01A-22D-A12Y-01
TCGA-BC-A10T-01A-11D-A12Y-01
TCGA-BC-A10U-01A-11D-A12Y-01
TCGA-BC-A10W-01A-11D-A12Y-01
TCGA-BC-A10X-01A-11D-A12Y-01
TCGA-BC-A10Y-01A-11D-A12Y-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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