SNP6 Copy number analysis (GISTIC2)
Liver Hepatocellular Carcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C10R9MRC
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C10R9MRC
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 2.0.19 (Firehose task version: 125).

Summary

There were 139 tumor samples used in this analysis: 25 significant arm-level results, 25 significant focal amplifications, and 28 significant focal deletions were found.

Results
Focal results

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

Table 1. Get Full Table Amplifications Table - 25 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 | 2.7543e-10 | 3.5727e-10 | chr1:154936704-155045171 | 12
11q13.3 | 3.9051e-10 | 3.9051e-10 | chr11:69051077-69434302 | 1
6p21.1 | 1.0153e-09 | 9.7875e-08 | chr6:43733839-43828640 | 1
8q24.13 | 2.5072e-07 | 1.7025e-06 | chr8:104711573-146364022 | 245
3q26.31 | 3.9281e-05 | 3.9281e-05 | chr3:172254454-172319444 | 0 [TNFSF10]
17q25.3 | 5.0325e-06 | 0.00054605 | chr17:80072050-80639238 | 14
7q21.2 | 0.0010171 | 0.0010171 | chr7:88138350-92715262 | 24
5p15.33 | 0.0020744 | 0.0020744 | chr5:977487-1300024 | 7
13q32.3 | 0.0046254 | 0.0046254 | chr13:98177518-101664730 | 25
17q23.1 | 6.3184e-05 | 0.0095569 | chr17:57648506-58857125 | 21
6p25.2 | 0.00021421 | 0.010827 | chr6:1-27825666 | 213
17p11.2 | 0.011332 | 0.011332 | chr17:18860536-19473519 | 14
8q13.1 | 0.0052691 | 0.012548 | chr8:42932479-70207915 | 103
15q26.3 | 0.023213 | 0.023213 | chr15:98401298-102531392 | 35
1q42.3 | 0.000276 | 0.024009 | chr1:224458469-249250621 | 221
2p24.1 | 0.039166 | 0.039166 | chr2:20215545-20478870 | 3
20q13.33 | 0.046795 | 0.046795 | chr20:60328006-63025520 | 96
2q31.2 | 0.074329 | 0.074329 | chr2:163221508-214993996 | 299
1p22.3 | 0.080311 | 0.080311 | chr1:85974031-86006008 | 1
19q13.11 | 0.083652 | 0.083652 | chr19:33712163-33837231 | 3
19p13.12 | 0.088758 | 0.088758 | chr19:15338574-15670894 | 10
10p15.1 | 0.10063 | 0.10063 | chr10:5008384-5043327 | 2
12q23.1 | 0.10063 | 0.10063 | chr12:100720086-100979511 | 4
5q35.3 | 0.14553 | 0.14553 | chr5:102690634-180915260 | 610
9q34.2 | 0.19137 | 0.19137 | chr9:137109246-137225102 | 1

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
hsa-mir-4258
CKS1B
EFNA4
SHC1
ADAM15
ZBTB7B
LENEP
FLAD1
DCST2
DCST1
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 6p21.1.

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

Genes
VEGFA

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.13.

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

Genes
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
ADCY8
ANGPT1
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
DPYS
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
EIF3E
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
POU5F1B
PTK2
PVT1
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRHR
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
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
FBXL6
OPLAH
KCNV1
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
C8orf55
FAM49B
CHRAC1
EXOSC4
LY6K
TRMT12
OXR1
WDYHV1
SLC39A4
SYBU
GSDMC
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
GSDMD
ZNF696
ARHGAP39
ZNF34
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
TOP1MT
ZNF572
ABRA
LYPD2
TMEM71
TMEM65
LOC157381
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
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 17q25.3.

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

Genes
CD7
CSNK1D
UTS2R
FOXK2
SECTM1
SLC16A3
RAB40B
NARF
WDR45L
C17orf62
C17orf101
CCDC57
HEXDC
TEX19

Genes in Wide Peak

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

Table S6. 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
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 5p15.33.

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

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
LOC100506688
MIR4635

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q32.3.

Table S8. 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
GPR18
IPO5
PCCA
SLC15A1
ZIC2
STK24
TM9SF2
FARP1
DOCK9
TMTC4
ZIC5
A2LD1
RNF113B
CLYBL
UBAC2
MIR623
FKSG29
UBAC2-AS1
MIR4306
MIR3170
MIR548AN

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
CLTC
hsa-mir-21
CA4
RPS6KB1
PPM1D
APPBP2
RNFT1
TUBD1
PTRH2
BCAS3
HEATR6
DHX40
VMP1
USP32
C17orf64
MIR21
LOC645638
TBC1D3P1-DHX40P1
LOC653653
SCARNA20
MIR4737

Genes in Wide Peak

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

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

Genes
IRF4
DEK
HIST1H4I
hsa-mir-3143
hsa-mir-548a-1
BMP6
BPHL
BTN1A1
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
ZNF184
ZNF204P
ALDH5A1
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AC
HIST1H2AB
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3G
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4G
CMAHP
RIPK1
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
GCM2
CD83
CDYL
LY86
EEF1E1
FAM65B
KIAA0319
NUP153
RANBP9
SLC17A4
SLC17A2
PRSS16
BTN3A3
BTN2A2
ECI2
HMGN4
TRIM38
CAP2
SCGN
FARS2
SLC17A3
RPP40
BTN3A2
BTN3A1
BTN2A1
SIRT5
FAM50B
MYLIP
ABT1
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
GFOD1
BTN2A3P
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
MUTED
CCDC90A
KIF13A
ZNF322
TXNDC5
C6orf62
TMEM14B
RIOK1
DTNBP1
ADTRP
HIST1H2AH
HIST1H2BK
POM121L2
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
LOC285819
MYLK4
ZNF391
TUBB2B
C6orf52
KAAG1
NHLRC1
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
DKFZP686I15217
FLJ23152
LINC00340
C6orf201
ERVFRD-1
HCG11
PPP1R3G
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
LOC100130275
LOC100130357
LOC100131289
LINC00240
LOC100270746
MIR3143
MIR3691
LOC100506207
LOC100506409
LOC100507173
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 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 8q13.1.

Table S12. 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
CEBPD
CRH
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100287846
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 15q26.3.

Table S13. 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 1q42.3.

Table S14. 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
PARP1
ADSS
AGT
ARF1
CHML
LYST
CHRM3
EPHX1
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
LBR
LGALS8
MTR
NID1
NVL
PSEN2
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
LEFTY2
GPR137B
TSNAX
WNT9A
ZNF124
HIST3H3
GNPAT
CDC42BPA
KMO
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
AKT3
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
COG2
RBM34
ABCB10
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
TAF5L
DISC2
DISC1
CNIH4
PYCR2
PPPDE1
SCCPDH
TRIM17
ARID4B
EGLN1
KIAA1383
KIF26B
HEATR1
ZNF692
ENAH
NUP133
ERO1LB
FMN2
ADCK3
ZNF695
GJC2
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
ACBD3
SMYD3
ARV1
JMJD4
C1orf35
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
ZNF496
C1orf198
WNT3A
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf55
CNST
PLD5
C1orf100
IBA57
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf95
FAM89A
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
DUSP5P
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
MIR3123
MIR3124
MIR3620
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742

Genes in Wide Peak

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

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

Genes
SDC1
LAPTM4A
PUM2

Genes in Wide Peak

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

Table S16. 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 2q31.2.

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

Genes
CHN1
CREB1
HOXD11
HOXD13
IDH1
NFE2L2
PMS1
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
ACADL
AOX1
ATP5G3
BMPR2
CASP8
CASP10
CD28
CHRNA1
CLK1
COL3A1
COL5A2
CPS1
ATF2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
DLX1
DLX2
DYNC1I2
EEF1B2
ERBB4
FRZB
GAD1
GALNT3
MSTN
GLS
GPR1
GRB14
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HSPD1
HSPE1
INPP1
ITGA6
ITGA4
ITGAV
LRP2
MAP2
MYO1B
MYL1
NAB1
NDUFB3
NDUFS1
NEUROD1
ORC2
PDE1A
PDK1
PLCL1
PTH2R
RPE
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SP3
SSB
SSFA2
STAT1
STAT4
TFPI
TTN
SUMO1
WIPF1
FZD5
FZD7
SDPR
HAT1
AGPS
PRKRA
SLC25A12
KLF7
ABCB11
B3GALT1
ADAM23
NRP2
CFLAR
STK17B
GTF3C3
PPIG
CIR1
BZW1
TLK1
ABI2
DHRS9
CALCRL
LANCL1
KBTBD10
UBE2E3
MTX2
NCKAP1
RAPGEF4
IKZF2
COBLL1
FASTKD2
SATB2
SF3B1
TMEFF2
MOB4
GORASP2
SPATS2L
HIBCH
SNORD51
STK39
CPS1-IT1
METTL5
OLA1
ICOS
SLC40A1
PDE11A
GULP1
NOP58
FKBP7
ZAK
PPIL3
DNAJC10
ASNSD1
MFSD6
INO80D
FIGN
STRADB
WDR12
ZC3H15
DNAH7
SLC39A10
CYP20A1
SPC25
HECW2
ALS2
ZDBF2
CWC22
G6PC2
MPP4
NIF3L1
PCGEM1
OSGEPL1
OBFC2A
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
PLEKHA3
TRAK2
BOLL
C2orf47
SPAG16
SCRN3
FASTKD1
ALS2CR8
TTC21B
METTL8
CYBRD1
CSRNP3
PGAP1
DCAF17
COQ10B
KIAA1715
CDCA7
WDR75
C2orf88
KCNH7
LOC91149
SESTD1
ANKRD44
ZNF804A
TTC30A
MARS2
ORMDL1
OSBPL6
NOSTRIN
DIRC1
PARD3B
NUP35
XIRP2
TYW5
RBM45
BBS5
C2orf77
ICA1L
RFTN2
UBR3
KCTD18
ALS2CR12
CPO
MDH1B
MYO3B
DUSP19
FLJ32063
ANKAR
TTC30B
FAM117B
C2orf67
ZSWIM2
ZNF385B
METTL21A
CCNYL1
KLHL23
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
GPR155
FAM171B
PIKFYVE
LOC200726
C2orf69
HNRNPA3
CERS6
METAP1D
CCDC150
CCDC141
LOC285084
FAM126B
UNC80
MLK7-AS1
EVX2
AOX2P
FONG
LOC375295
CERKL
SP5
PLEKHM3
C2orf80
DYTN
LOC401022
FSIP2
C2orf66
MIR10B
LOC440925
PHOSPHO2
DFNB59
SNORA41
SNORD11
SNORD70
MIR561
SNORD11B
MIR933
LOC100130451
LOC100130452
LOC100130691
TMEM194B
SP9
MIR1246
MIR548N
MIR1258
MIR1245A
MIR548F2
LOC100329109
SNORA70F
MIR3128
MIR3129
MIR3130-1
MIR3130-2
MIR2355
MIR3606
LOC100505695
LOC100506124
LOC100506134
LOC100506783
LOC100506866
LOC100507140
LOC100507443
PHOSPHO2-KLHL23
HSPE1-MOB4
MIR4437
MIR4776-1
MIR1245B
MIR4774
MIR4775
MIR4444-1
MIR4776-2
LOC100861402

Genes in Wide Peak

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

Table S18. 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 19q13.11.

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

Genes
CEBPA
SLC7A10
LOC80054

Genes in Wide Peak

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

Table S20. 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 10p15.1.

Table S21. 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 12q23.1.

Table S22. 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 5q35.3.

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

Genes
APC
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK4
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDO1
CDX1
AP3S1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
NKX2-5
CTNNA1
DBN1
DMXL1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FER
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HINT1
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
KCNN2
LCP2
LECT2
LMNB1
LOX
LTC4S
SMAD5
MAN2A1
MCC
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
REEP5
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
ATG12
PTTG1
PDLIM7
NREP
CNOT8
RAB9BP1
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FLJ11235
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
TRIM36
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
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
C5orf54
EPB41L4A
SIL1
GMCL1P1
ARAP3
RMND5B
FBXL17
YTHDC2
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
SLC25A2
TSSK1B
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
TSLP
FCHSD1
UNC5A
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
ZNF474
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
SRFBP1
LOC153469
ZMAT2
BTNL9
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
DCP2
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
AQPEP
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
DTWD2
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
TICAM2
DND1
C5orf25
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
TMEM232
LOC643201
GRXCR2
SPINK9
ZFP62
LOC644100
FLJ33630
CCNI2
CBY3
FAM153C
SNORA13
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728342
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
VTRNA2-1
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505841
LOC100507387
MIR4633
MIR4634
MIR4461
MIR4460
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.2.

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

Genes
RXRA

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

Table 2. Get Full Table Deletions Table - 28 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
1p36.32 | 3.0567e-15 | 9.802e-14 | chr1:1-6688857 | 135
4q35.1 | 6.343e-11 | 7.3178e-09 | chr4:178360197-191154276 | 65
8p23.2 | 3.9374e-06 | 4.3462e-06 | chr8:2079140-6262191 | 1
13q14.2 | 3.5585e-10 | 4.7029e-06 | chr13:48666829-49281290 | 4
10q23.31 | 5.0174e-05 | 5.2826e-05 | chr10:89604733-90034038 | 2
4q25 | 1.0277e-06 | 6.6643e-05 | chr4:96467504-109732655 | 61
9p21.3 | 9.0269e-05 | 8.8017e-05 | chr9:21865498-22448737 | 4
19p13.3 | 0.00010756 | 0.00010087 | chr19:761790-4159100 | 125
22q13.31 | 0.00074468 | 0.00072339 | chr22:44599673-51304566 | 90
17p12 | 0.00057773 | 0.0010316 | chr17:15891757-16185399 | 2
12q24.33 | 0.0012218 | 0.0012334 | chr12:123447929-133851895 | 80
2q37.3 | 0.0051053 | 0.0089656 | chr2:218803330-243199373 | 261
6q26 | 0.011667 | 0.021105 | chr6:159237726-171115067 | 76
3p13 | 0.026209 | 0.026209 | chr3:51419867-84688247 | 163
4p16.1 | 0.032602 | 0.032602 | chr4:1-8585988 | 115
11q23.3 | 0.036439 | 0.0367 | chr11:96126036-135006516 | 316
12p12.1 | 0.045179 | 0.046687 | chr12:22837283-25209763 | 6
13q22.2 | 0.00011826 | 0.05706 | chr13:1-95258224 | 309
18q21.2 | 0.067439 | 0.065658 | chr18:47717577-51678342 | 12
14q23.3 | 0.070781 | 0.069003 | chr14:50554333-107349540 | 541
16q23.1 | 0.092285 | 0.093792 | chr16:58764031-90354753 | 305
9q34.3 | 0.11587 | 0.12144 | chr9:38619152-141213431 | 741
17p13.3 | 0.054068 | 0.13045 | chr17:1-10429076 | 272
2q22.1 | 0.04906 | 0.17429 | chr2:136875713-165765533 | 76
5q23.1 | 0.17449 | 0.17429 | chr5:45365060-180915260 | 863
8p11.22 | 0.11562 | 0.20967 | chr8:15623808-47753079 | 205
6q16.3 | 0.10977 | 0.2289 | chr6:57206486-165741428 | 474
1p35.2 | 2.8098e-05 | 0.25074 | chr1:1-68300612 | 905

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
CDK11B
DFFB
DVL1
MEGF6
GABRD
GNB1
ZBTB48
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
RER1
ACOT7
ICMT
CHD5
NOC2L
OR4F3
ARHGEF16
SSU72
WRAP73
SDF4
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
AJAP1
TP73-AS1
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
OR4F5
NOL9
LINC00115
MORN1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
C1orf170
KIAA1751
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 4q35.1.

Table S26. 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 8p23.2.

Table S27. 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 13q14.2.

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

Genes
RB1
RCBTB2
ITM2B
LPAR6

Genes in Wide Peak

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

Table S29. 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 4q25.

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

Genes
RAP1GDS1
TET2
hsa-mir-1255a
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
CENPE
EIF4E
H2AFZ
HADH
MANBA
MTTP
NFKB1
PDHA2
PPP3CA
RPL34
TACR3
UBE2D3
LAMTOR3
PAPSS1
AIMP1
TSPAN5
METAP1
PPA2
DAPP1
DKK2
LEF1
EMCN
ARHGEF38
BANK1
BDH2
INTS12
OSTC
SLC39A8
AGXT2L1
GSTCD
DNAJB14
CXXC4
C4orf17
FLJ20021
RG9MTD2
TBCK
CYP2U1
DDIT4L
SLC9B2
SLC9B1
SGMS2
NPNT
LOC256880
LOC285456
C4orf37
PCNAP1
CISD2
LOC641518
MIR3684
LOC100507053
LOC100507096

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

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
STK11
TCF3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
AES
AMH
ATP5D
AZU1
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
ARID3A
EEF2
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
MATK
GADD45B
NFIC
OAZ1
POLR2E
MAP2K2
PRTN3
PTBP1
RPS15
SGTA
TBXA2R
THOP1
TLE2
SF3A2
S1PR4
AP3D1
APBA3
MED16
APC2
ABCA7
HMG20B
UQCR11
SBNO2
ZFR2
PIP5K1C
HMHA1
TIMM13
DAZAP1
SNORD37
TJP3
ITGB1BP3
SLC39A3
ZBTB7A
FZR1
PIAS4
LSM7
MBD3
PCSK4
C19orf24
PLEKHJ1
BTBD2
NCLN
SPPL2B
WDR18
REXO1
ZNF77
C19orf29
CELF5
TLE6
LPPR3
ZNF556
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
LMNB2
RAX2
MUM1
ATCAY
MIDN
R3HDM4
C19orf6
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
PLK5
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
C19orf26
CSNK1G2-AS1
C19orf77
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
ONECUT3
MEX3D
C19orf29-AS1
LINGO3
MIR637
C19orf71
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745

Genes in Wide Peak

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

Table S33. 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
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
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 17p12.

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

Genes
NCOR1
TTC19

Genes in Wide Peak

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

Table S35. 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
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 2q37.3.

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

Genes
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TUBA4A
VIL1
WNT6
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
CNPPD1
STK36
GMPPA
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
C2orf83
MFF
CXCR7
RNPEPL1
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
LOC100129175
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

Table S37. 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
RSPH3
TTLL2
FAM120B
FNDC1
LINC00473
SFT2D1
TAGAP
PACRG
PNLDC1
LOC154449
DACT2
C6orf118
OSTCP1
WDR27
LOC285796
PRR18
C6orf120
DKFZp451B082
TCP10L2
LINC00242
LOC441177
MLLT4-AS1
SNORA20
SNORA29
LOC729603
HGC6.3
LOC100129518
C6orf99
LOC100289495
MIR1913
MIR3939
CAHM
MIR4644

Genes in Wide Peak

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

Table S38. 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
DNASE1L3
DUSP7
FLNB
GBE1
GPR27
GRM2
ITIH1
ITIH3
ITIH4
CNTN3
PDHB
PRKCD
PTPRG
ROBO1
ROBO2
RPL29
ATXN7
NEK4
TKT
TMF1
TNNC1
WNT5A
SLMAP
MANF
ACOX2
CADPS
SUCLG2
HESX1
UBA3
RRP9
MAGI1
VPRBP
PSMD6
PARP3
ARL6IP5
RPP14
FAM107A
NISCH
TWF2
PDZRN3
RAD54L2
FRMD4B
STAB1
FAM208A
RYBP
ABHD14A
POC1A
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
RBM15B
ARHGEF3
TEX264
SFMBT1
PHF7
TLR9
IL17RD
PXK
FEZF2
EBLN2
SHQ1
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
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
LOC201617
DNAH12
PDE12
FAM116A
C3orf64
CCDC66
LOC285401
EIF4E3
SPATA12
TMEM110
IQCF2
IQCF5
MUSTN1
IQCF3
LOC401074
MIRLET7G
MIR135A1
FAM19A1
IQCF6
C3orf78
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
MIR4444-1
LOC100652759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.1.

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

Genes
FGFR3
WHSC1
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
EVC
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
ACOX3
NOP14
FAM193A
KIAA0232
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
D4S234E
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
CNO
STK32B
LYAR
TBC1D14
SORCS2
KIAA1530
ZFYVE28
AFAP1
TNIP2
HAUS3
ABCA11P
GRPEL1
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
ZNF595
JAKMIP1
FAM53A
METTL19
ZBTB49
ZNF721
ZNF718
CCDC96
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
C4orf48
LOC402160
ZNF876P
ZNF732
SCARNA22
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
TMED11P
MIR4274
LOC100507266
MIR378D1
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

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

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

Genes
BIRC3
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
BIRC2
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
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
TRPC6
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
MMP20
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
YAP1
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
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
ARHGAP42
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
ANGPTL5
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
LOC100288077
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3920
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 12p12.1.

Table S41. 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 13q22.2.

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
CPB2
DACH1
DCT
EDNRB
ELF1
ESD
FGF9
GPC5
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
GPC6
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
TGDS
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
LINC00410
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
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
DCC
SMAD4
MBD1
ME2
MAPK4
CXXC1
MEX3C
ELAC1
MRO
SKA1
CCDC11
LOC100287225

Genes in Wide Peak

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

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

Genes
AKT1
KTN1
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
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
ENTPD5
CDKN3
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GCH1
GMFB
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
NDUFB1
SIX6
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
PSMC6
PTGDR
PTGER2
ABCD4
PYGL
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
STYX
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
CDKL1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
DLGAP5
KIAA0125
KIAA0317
TECPR2
MED6
CNIH
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
PAPOLA
ACOT2
TMED10
FERMT2
PTPN21
C14orf1
WDHD1
MAP4K5
NID2
VASH1
ATG14
ZBTB1
SNW1
PCNX
DAAM1
SAMD4A
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
TIMM9
MLH3
ATP5S
KCNH5
PRO1768
GPR132
POMT2
ERO1L
COQ6
ATL1
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
GNG2
C14orf101
FBXO34
CDCA4
C14orf102
ATG2B
UBR7
C14orf105
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
ACTR10
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNTL1
PLEKHH1
TXNDC16
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
SAV1
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
GNPNAT1
OTUB2
ZFYVE21
MEG8
WDR25
METTL21D
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
L2HGDH
C14orf159
C14orf45
TMEM121
DDHD1
SGPP1
TMX1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
MAPK1IP1L
IFT43
WDR89
C14orf149
AHNAK2
TRIM9
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
FRMD6
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
LOC283553
GPR137C
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
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
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
KTN1-AS1
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR4309
MIR3173
MIR4308
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

Table S45. 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 9q34.3.

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

Genes
ABL1
FANCC
GNAQ
NOTCH1
OMD
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
ABCA1
ABCA2
ABO
AK1
ALAD
ALDH1A1
ALDOB
AMBP
ANXA1
APBA1
ASS1
AUH
BAAT
KLF9
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
CKS2
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXE1
FPGS
FXN
NR5A1
FUT7
GAS1
NR6A1
GCNT1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
HSPA5
TNC
IARS
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RORB
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLE1
TLE4
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
SMC5
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
RABGAP1
TMEM2
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
PCA3
FAM108B1
MRPS2
COQ4
CERCAM
EGFL7
GOLM1
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
FAM22F
DIRAS2
ASPN
BSPRY
C9orf167
TEX10
LPPR1
EXD3
FAM206A
C9orf95
STX17
NOL8
C9orf40
TMEM38B
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
C9orf86
CDK5RAP2
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
BDAG1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
NAA35
SLC28A3
CARD9
SUSD1
IPPK
DDX31
FAM129B
MRPL41
WNK2
SECISBP2
C9orf16
MAPKAP1
ZCCHC6
GALNT12
EHMT1
CNTNAP3
SVEP1
RMI1
TRPM3
PTGES2
GKAP1
AKNA
MIR600HG
URM1
ISCA1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
DAB2IP
CAMSAP1
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
FAM201A
TTC16
LOC158257
FAM120AOS
LINC00475
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
C9orf96
OLFML2A
C9orf71
QSOX2
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
LINC00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
TPRN
LOC286297
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
LOC340508
LOC340515
GPR144
FAM75D5
QRFP
OR1J1
OR1B1
MURC
FOXD4L4
GLT6D1
AQP7P1
PTAR1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
KGFLP1
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC440173
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
LOC441461
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
LOC572558
PGM5P2
MIR455
NRON
LOC642236
FAM75A2
FAM75A4
LOC642929
FAM163B
FLJ40292
TUBBP5
RNF224
LOC643648
CBWD6
FAM75C2
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
SNORA84
SNORA70C
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
UNQ6494
LOC100129316
LOC100129722
LOC100130954
LOC100131193
LOC100132077
LOC100132352
FAM157B
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
LINC00092
LOC100272217
LOC100286938
LOC100288842
LOC100289019
LOC100289341
MIR548H3
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3154
MIR2861
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3621
MIR3910-1
MIR3689A
MIR3911
MIR3910-2
MIR3689B
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506599
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4670
MIR4672
MIR3689E
MIR4479

Genes in Wide Peak

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

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

Genes
PER1
TP53
GAS7
USP6
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
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MNT
MYH1
MYH4
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RCVRN
RPA1
RPL26
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
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
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
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
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
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
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
SNORA48
SNORD10
OR1D4
SCARNA21
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
LOC100128288
C17orf107
LOC100130950
DBIL5P
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 2q22.1.

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

Genes
ACVR1
ACVR2A
RND3
CACNB4
DPP4
FAP
GCG
GPD2
GRB14
HNMT
ITGB6
KCNJ3
KIF5C
LY75
NEB
NR4A2
ORC4
RBMS1
TNFAIP6
PKP4
KYNU
NMI
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
TBR1
GALNT5
NXPH2
COBLL1
PLA2R1
GCA
EPC2
ARL5A
MMADHC
BAZ2B
LRP1B
FIGN
RIF1
PRPF40A
MBD5
ARHGAP15
RPRM
SLC4A10
ERMN
IFIH1
MARCH7
GTDC1
THSD7B
TANC1
KCNH7
DAPL1
FMNL2
GALNT13
ACVR1C
LYPD6
LYPD6B
CCDC148
ARL6IP6
WDSUB1
UPP2
SPOPL
RBM43
DKFZp686O1327
LOC554201
LOC647012
PABPC1P2
LOC100144595
ZEB2-AS1
SNORA70F
LY75-CD302
MIR4785
MIR4773-1
MIR4773-2

Genes in Wide Peak

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

Table S49. 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
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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.22.

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

Genes
FGFR1
PCM1
WRN
WHSC1L1
HOOK3
hsa-mir-486
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
NAT1
NAT2
ADRA1A
ADRB3
ANK1
ASAH1
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CHRNB3
CLU
ADAM3A
DPYSL2
DUSP4
EGR3
EIF4EBP1
EPB49
EPHX2
EXTL3
PTK2B
FGL1
FNTA
ADAM2
GFRA2
GNRH1
GSR
GTF2E2
NRG1
IKBKB
IDO1
LOXL2
LPL
MSR1
NEFM
NEFL
NKX3-1
PDGFRL
PLAT
PNOC
POLB
PPP2CB
PPP2R2A
PPP3CC
SFRP1
SFTPC
SLC7A2
SLC18A1
SLC20A2
STAR
STC1
TACC1
VDAC3
FZD3
UBXN8
KAT6A
ADAM18
ADAM9
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
CHRNA6
DOK2
ASH2L
MTMR7
BAG4
ENTPD4
PHYHIP
SORBS3
NPM2
DCTN6
PNMA2
ADAM28
AP3M2
RBPMS
ERLIN2
LZTS1
PROSC
XPO7
TRIM35
RHOBTB2
DDHD2
KIF13B
PSD3
LEPROTL1
SLC39A14
GPR124
FGF20
DKK4
LSM1
ADAMDEC1
CNOT7
PURG
GOLGA7
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
THAP1
INTS10
CCDC25
BRF2
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
C8orf4
MTUS1
KIAA1967
PLEKHA2
SH2D4A
PDLIM2
EBF2
FAM160B2
DUSP26
HMBOX1
ZMAT4
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
TTI2
RAB11FIP1
REEP4
STMN4
RNF170
TM2D2
SGK196
GINS4
PPAPDC1B
MAK16
FUT10
CHMP7
C8orf40
GOT1L1
VPS37A
NKX2-6
AGPAT6
UNC5D
LETM2
HGSNAT
PEBP4
CDCA2
ESCO2
FBXO16
NKX6-3
KCNU1
IDO2
R3HCC1
HTRA4
ADAM32
LGI3
LOC254896
ADAM5P
LOC286059
EFHA2
LOC286114
SCARA5
LOC286135
RNF5P1
POTEA
LOC389641
C8orf80
C8orf86
MIR320A
C8orf58
C8orf75
MBOAT4
MIR486
LOC728024
LOC100128750
LOC100128993
LOC100130964
MIR4287
MIR3148
MIR4288
MIR3622A
MIR3622B
LOC100507156
LOC100507341
MIR4469
MIR548O2

Genes in Wide Peak

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

Table S51. 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
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 S52. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CDKN2C
EPS15
JAK1
JUN
LCK
MPL
MUTYH
MYCL1
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
AK2
AK4
ALPL
RERE
ATP6V0B
BAI2
BMP8B
C1QA
C1QB
C1QC
C8A
C8B
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
PLK3
CNR2
COL8A2
COL9A2
COL16A1
CORT
CPT2
CSF3R
CTPS
CYP2J2
CYP4A11
CYP4B1
DAB1
GADD45A
DDOST
DFFA
DFFB
DHCR24
DIO1
DPH2
DVL1
E2F2
ECE1
EDN2
PHC2
MEGF6
EPHA2
ELAVL4
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FAAH
FABP3
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GPX7
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
IL12RB2
TNFRSF9
INPP5B
IPP
STMN1
LEPR
TACSTD2
MAGOH
MATN1
MFAP2
MTF1
MTHFR
NASP
NBL1
NDUFS5
NFIA
NFYC
NPPA
NPPB
NRD1
YBX1
ROR1
OPRD1
ORC1
PAFAH2
PRDX1
PDE4B
PEX10
PEX14
PGD
PGM1
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKAA2
PRKCZ
PSMB2
PTAFR
PTPRF
RAB3B
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RPS8
RSC1A1
SCNN1D
SCP2
SRSF4
ST3GAL3
STIL
SKI
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TIE1
TNFRSF1B
TP73
TTC4
TNFRSF4
UQCRH
UROD
USP1
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
PTP4A2
SNHG3
NR0B2
RAD54L
PIK3R3
MMP23B
MMP23A
KCNAB2
FCN3
YARS
MKNK1
AKR7A2
PPAP2B
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
PER3
EIF2B3
ARTN
MAP3K6
KCNQ4
ZMYM4
ZMYM6
DHRS3
VAMP3
ZFYVE9
SNRNP40
C1orf38
TMEM59
H6PD
ISG15
PLCH2
IPO13
SDC3
KDM4A
CROCC
PUM1
CEP104
RIMS3
KIAA0494
DNAJC6
KLHL21
SLC35E2
ZBTB40
MFN2
INSL5
PTPRU
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
AKR1A1
TESK2
PPIE
MAD2L2
PPIH
CAP1
LRRC41
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
EBNA1BP2
KIF2C
RER1
RCAN3
FAF1
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
FOXJ3
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
MAST2
NCDN
SLC35D1
PLEKHM2
OTUD3
KAZN
CAMTA1
ZCCHC11
SZT2
DNAJC16
UBR4
USP24
ATP13A2
ITGB3BP
TARDBP
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
SSBP3
STX12
CLIC4
SYF2
PARS2
MMACHC
ACOT11
CHD5
C1orf144
LDLRAP1
SERBP1
NOC2L
FBXO2
FBXO6
PLA2G2D
MYCBP
HEYL
EIF2C1
OR4F3
SNORD55
RNU11
RNF11
FOXD3
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
ANGPTL3
PRO0611
LINC00339
SSU72
GNL2
UBIAD1
ALG6
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
ZNF691
TXNDC12
MECR
UTP11L
SDF4
MRTO4
TMEM69
MRPL37
HOOK1
HPCAL4
YTHDF2
ZCCHC17
HSPB11
PADI3
CMPK1
ERRFI1
WNT4
YIPF1
FBXO42
RNF186
SPATA6
MXRA8
L1TD1
HES2
GPN2
LEPROT
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf123
C1orf159
AURKAIP1
TTC22
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
RNF220
VPS13D
FAM176B
ATAD3A
TMEM57
TRIM62
RAVER2
PANK4
ECHDC2
FGGY
CAMK2N1
ASAP3
POMGNT1
PNRC2
PIGV
NBPF1
MAP7D1
TMEM48
NECAP2
IQCC
DNAJC11
RCC2
DMAP1
AJAP1
GNG12
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
ZSWIM5
KIAA1522
CACHD1
MIER1
HES4
GRHL3
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
PLA2G2F
SMAP2
ATPAF1
S100PBP
MEAF6
DEM1
CEP85
NMNAT1
ELOVL1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZNF643
SELRC1
PHACTR4
C1orf135
ERI3
C1orf50
CCDC28B
EFHD2
MMEL1
RSG1
DLEU2L
OR4F5
NKAIN1
MUL1
TMEM53
AKIRIN1
HECTD3
BEND5
YRDC
ZYG11B
NOL9
PPCS
LIN28A
SH3D21
SNIP1
AGMAT
WDR78
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
GPR157
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
HYI
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
STK40
TM2D1
TMEM222
PLEKHN1
USP48
ZMYND12
NBPF3
ZDHHC18
SGIP1
SLC25A33
DDI2
LZIC
EFCAB7
NT5C1A
TRIM63
FAM167B
MGC12982
C1orf170
CROCCP2
HPDL
AGBL4
MFSD2A
ATG4C
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
DOCK7
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
BTF3L4
UBXN11
C1orf158
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
MED8
KTI12
C1orf212
ADC
TMEM54
TOE1
ERMAP
CSMD2
MYSM1
CROCCP3
FHAD1
OSBPL9
LOC115110
OMA1
RAB42
LRRC42
FAM46B
RBP7
ACAP3
UBE2J2
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
TCEANC2
PODN
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
KLF17
TMEM125
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
UBE2U
CCDC27
C1orf213
KNCN
MOB3C
GLIS1
DCDC2B
ZNF362
LOC149086
MANEAL
IL23R
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
C1orf64
SLC2A7
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
KANK4
FAM43B
PAQR7
EIF2C3
EIF2C4
FAM76A
LINC00466
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
TXLNA
TCTEX1D1
SLFNL1
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
PCSK9
ZNF683
CYP4X1
NPHP4
BEST4
CYP4A22
C1orf185
LOC284551
FAM41C
LOC284632
RSPO1
EPHA10
LOC284661
RIMKLA
SLC25A34
ESPNP
FAM151A
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
C1orf228
ZNF642
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
TCTEX1D4
SERINC2
FAM159A
FAM131C
PADI6
BMP8A
C1orf187
SPATA21
CCDC23
ATPAF1-AS1
HEATR8
AGRN
APITD1
CATSPER4
NSUN4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LOC388630
LDLRAD1
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR101-1
MIR200A
MIR200B
MIR30C1
MIR30E
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
FLJ32224
FAM183A
ZYG11A
ANKRD65
PRAMEF7
LURAP1
PEF1
MIR429
CYB5RL
FAM138F
KIAA0754
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA55
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
LOC728431
PPIEL
CCDC30
CDK11A
SLC35E2B
LOC728716
RPS15AP10
LOC729041
LOC729059
HSD52
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100129924
LOC100130197
LOC100130417
LOC100130557
LOC100131060
LOC100132062
LOC100132287
LOC100132774
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
MIR761
NPPA-AS1
MIR3115
MIR3117
MIR4255
MIR4253
MIR4251
MIR4252
MIR4254
MIR3659
MIR3917
MIR3605
MIR3671
MIR3675
ENO1-AS1
ZMYM6NB
LOC100506730
LOC100506801
LOC100506963
LOC100507178
LOC100507423
LOC100507564
LOC100507634
APITD1-CORT
GJA9-MYCBP
HEATR8-TTC4
C1orf151-NBL1
MIR4695
MIR4420
MIR4422
MIR4781
MIR4794
MIR4684
MIR4711
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Arm-level results

Table 3. Get Full Table Arm-level significance table - 25 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 | 0.20 | 0.275 | 1 | 0.28 | 2.56 | 0.0168
1q | 1955 | 0.57 | 10.6 | 0 | 0.31 | 2.54 | 0.0168
2p | 924 | 0.16 | -1.07 | 1 | 0.08 | -2.99 | 1
2q | 1556 | 0.13 | -1.83 | 1 | 0.10 | -2.61 | 1
3p | 1062 | 0.08 | -3.11 | 1 | 0.12 | -1.95 | 1
3q | 1139 | 0.08 | -3.32 | 1 | 0.07 | -3.51 | 1
4p | 489 | 0.07 | -3.3 | 1 | 0.26 | 1.85 | 0.0795
4q | 1049 | 0.02 | -4.14 | 1 | 0.34 | 4.5 | 2.25e-05
5p | 270 | 0.40 | 5.87 | 2.92e-08 | 0.17 | -0.621 | 1
5q | 1427 | 0.31 | 3.35 | 0.00227 | 0.16 | -0.816 | 1
6p | 1173 | 0.26 | 1.92 | 0.103 | 0.19 | -0.16 | 0.98
6q | 839 | 0.18 | -0.334 | 1 | 0.36 | 4.71 | 9.8e-06
7p | 641 | 0.31 | 3.25 | 0.00256 | 0.12 | -1.85 | 1
7q | 1277 | 0.35 | 4.59 | 2.27e-05 | 0.15 | -1.08 | 1
8p | 580 | 0.19 | -0.0593 | 1 | 0.60 | 11.6 | 0
8q | 859 | 0.48 | 7.78 | 7.33e-14 | 0.29 | 2.17 | 0.04
9p | 422 | 0.05 | -3.58 | 1 | 0.31 | 3.28 | 0.0021
9q | 1113 | 0.05 | -3.53 | 1 | 0.31 | 3.37 | 0.00167
10p | 409 | 0.13 | -1.69 | 1 | 0.20 | 0.213 | 0.792
10q | 1268 | 0.12 | -1.96 | 1 | 0.28 | 2.43 | 0.0216
11p | 862 | 0.06 | -3.64 | 1 | 0.17 | -0.749 | 1
11q | 1515 | 0.05 | -3.74 | 1 | 0.19 | -0.0583 | 0.951
12p | 575 | 0.08 | -3.03 | 1 | 0.21 | 0.411 | 0.681
12q | 1447 | 0.11 | -2.16 | 1 | 0.13 | -1.77 | 1
13q | 654 | 0.13 | -1.52 | 1 | 0.37 | 5.05 | 2.2e-06
14q | 1341 | 0.11 | -2.12 | 1 | 0.34 | 4.35 | 3.86e-05
15q | 1355 | 0.10 | -2.49 | 1 | 0.21 | 0.587 | 0.586
16p | 872 | 0.09 | -2.52 | 1 | 0.32 | 3.56 | 0.000929
16q | 702 | 0.05 | -3.51 | 1 | 0.38 | 5.44 | 3.53e-07
17p | 683 | 0.09 | -2.01 | 1 | 0.56 | 10.8 | 0
17q | 1592 | 0.31 | 3.32 | 0.00227 | 0.15 | -1.05 | 1
18p | 143 | 0.09 | -2.96 | 1 | 0.18 | -0.48 | 1
18q | 446 | 0.09 | -2.7 | 1 | 0.18 | -0.407 | 1
19p | 995 | 0.24 | 1.38 | 0.277 | 0.17 | -0.51 | 1
19q | 1709 | 0.26 | 1.91 | 0.103 | 0.13 | -1.54 | 1
20p | 355 | 0.32 | 3.66 | 0.000857 | 0.08 | -2.78 | 1
20q | 753 | 0.32 | 3.76 | 0.000682 | 0.05 | -3.49 | 1
21q | 509 | 0.13 | -1.73 | 1 | 0.29 | 2.61 | 0.0163
22q | 921 | 0.15 | -1.04 | 1 | 0.23 | 1.05 | 0.347
Xq | 1312 | 0.19 | 0.0618 | 1 | 0.21 | 0.632 | 0.586

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/4393269/GDAC_MergeDataFiles_4311825/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 139 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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