Thyroid Adenocarcinoma: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 470 tumor samples used in this analysis: 18 significant arm-level results, 1 significant focal amplifications, and 32 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 - 1 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
--- | --- | --- | --- | ---
Xq22.3 | 2.4964e-16 | 2.4964e-16 | chrX:108537285-108552899 | 0 [GUCY2F]

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 - 32 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
--- | --- | --- | --- | ---
1q24.2 | 0.011139 | 0.011139 | chr1:168044896-168149500 | 1
6q22.31 | 0.011139 | 0.011139 | chr6:123955968-125232805 | 1
Xq22.3 | 0.011139 | 0.011139 | chrX:107872289-108781115 | 2
13q14.3 | 0.011139 | 0.011326 | chr13:43424188-88326176 | 137
10q21.2 | 0.011139 | 0.020179 | chr10:61122180-61718254 | 3
16q23.3 | 0.025051 | 0.025051 | chr16:78129058-90354753 | 122
22q13.1 | 0.027184 | 0.029517 | chr22:39712315-39797177 | 3
22q13.31 | 0.029874 | 0.029874 | chr22:47571204-48018269 | 1
15q25.3 | 0.033928 | 0.033153 | chr15:86838498-88151657 | 2
20p12.1 | 0.039272 | 0.04043 | chr20:14302876-16555385 | 4
8q24.22 | 0.045054 | 0.045054 | chr8:56679786-146364022 | 492
10q23.31 | 0.011139 | 0.045054 | chr10:63660611-108925515 | 407
2q35 | 0.054374 | 0.054374 | chr2:213861165-243199373 | 283
22q13.2 | 0.059418 | 0.058548 | chr22:43536127-43814456 | 3
8p12 | 0.077663 | 0.081494 | chr8:31031189-32605364 | 1
16p13.3 | 0.077724 | 0.081494 | chr16:5129162-8624050 | 3
22q13.32 | 0.07375 | 0.081494 | chr22:48668761-51304566 | 46
19p13.2 | 0.1179 | 0.1179 | chr19:1-19627981 | 626
7q34 | 0.13452 | 0.13542 | chr7:140405575-140706707 | 1
21q21.1 | 0.13542 | 0.13542 | chr21:19257718-19640557 | 1
5q35.1 | 0.13607 | 0.13607 | chr5:169799676-170167404 | 2
11p15.1 | 0.13542 | 0.13607 | chr11:20676254-22216204 | 1
18p11.21 | 0.13816 | 0.13607 | chr18:12986917-13225199 | 1
13q12.3 | 0.011139 | 0.15048 | chr13:20792419-32982005 | 82
5p15.2 | 0.17427 | 0.17427 | chr5:10968873-13956214 | 3
Xq22.1 | 0.18246 | 0.17427 | chrX:96134519-100418234 | 14
19q12 | 0.20815 | 0.20265 | chr19:30202912-30414571 | 1
2p23.1 | 0.20815 | 0.20815 | chr2:1-243199373 | 1516
7q22.3 | 0.21753 | 0.20815 | chr7:1-159138663 | 1148
17p13.1 | 0.22379 | 0.20815 | chr17:1-81195210 | 1386
9p21.3 | 0.23685 | 0.24323 | chr9:1-141213431 | 983
18q22.2 | 0.24475 | 0.24323 | chr18:1-78077248 | 342

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q24.2.

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

Genes
GPR161

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
NKAIN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
GUCY2F
IRS4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.3.

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

Genes
LCP1
RB1
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
ATP7B
KLF5
BTF3P11
RCBTB2
CLN5
CPB2
DACH1
EDNRB
ESD
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
LMO7
NEK3
PCDH8
PCDH9
POU4F1
ATXN8OS
TPT1
UCHL3
SCEL
SUCLA2
DLEU2
TSC22D1
ITM2B
UTP14C
TBC1D4
LPAR6
TRIM13
SPRY2
DLEU1
PIBF1
OLFM4
SUGT1
LECT1
KLF12
FNDC3A
DIS3
MYCBP2
ZC3H13
LRCH1
FBXL3
INTS6
CKAP2
NUFIP1
PCDH17
MED4
DNAJC15
VPS36
PHF11
NDFIP2
ENOX1
RCBTB1
NUDT15
KIAA1704
THSD1
CYSLTR2
SPRYD7
KLHL1
RBM26
PCDH20
RNF219
RNASEH2B
DHRS12
BORA
KIAA0226L
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
SLITRK6
EBPL
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
LINC00284
SLAIN1
PRR20A
LACC1
LINC00330
HNRNPA1L2
ST13P4
CCDC122
COMMD6
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SIAH3
KCNRG
LINC00282
LINC00550
LINC00347
NEK5
THSD1P1
KCTD4
SERP2
MIR15A
MIR16-1
ALG11
MZT1
TSC22D1-AS1
MIR4500HG
SERPINE3
CTAGE11P
SNORA31
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR759
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100509894
MIR4500
MIR4703

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.2.

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

Genes
CCDC6
SLC16A9
M1

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
C16orf7
KIAA0513
PIEZO1
ATP2C2
MPHOSPH6
COX4NB
TUBB3
PRDM7
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
C16orf61
JPH3
KIAA1609
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
MGC23284
LINC00311
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722

Genes in Wide Peak

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

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

Genes
SYNGR1
SNORD43
RNU86

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q25.3.

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

Genes
LINC00052
LOC727915

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
FLRT3
KIF16B
MACROD2
MACROD2-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q24.22.

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

Genes
COX6C
EXT1
MYC
PLAG1
RECQL4
NCOA2
CHCHD7
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
hsa-mir-1273
hsa-mir-875
hsa-mir-3150
hsa-mir-3149
hsa-mir-2052
hsa-mir-124-2
ADCY8
ANGPT1
ANXA13
ASPH
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CA8
CALB1
RUNX1T1
CDH17
CRH
CYC1
CYP7A1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
GEM
GLI4
GML
GPR20
GPT
GRINA
HAS2
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LY6E
LY6H
LYN
MATN2
MMP16
MOS
MYBL1
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
PDE7A
ENPP2
PENK
PLEC
PMP2
POLR2K
POU5F1B
PKIA
PTK2
PVT1
PEX2
RAB2A
RAD21
RPL7
RPL8
RPL30
RPS20
SDC2
SDCBP
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
NSMAF
LY6D
JRK
EIF3H
DGAT1
GPAA1
RIPK2
GGH
WISP1
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
LRRC14
TTC35
RIMS2
TOX
MTSS1
PTDSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
ARFGEF1
COLEC10
KHDRBS3
POP1
COPS5
WWP1
STMN2
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
RRS1
SULF1
ARC
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
C8orf71
RGS22
FBXL6
PTTG3P
SNORA72
SNORD54
OPLAH
PABPC1
KCNV1
STAU2
MTBP
EIF2C2
BHLHE22
MRPS28
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
FAM82B
ZNF706
VPS28
FAM203A
KCNK9
C8orf55
UBR5
FAM49B
AZIN1
OTUD6B
CHRAC1
GDAP1
EXOSC4
PDP1
CNGB3
LY6K
ESRP1
IMPAD1
TMEM70
TRMT12
OXR1
WDYHV1
ARMC1
UBE2W
LAPTM4B
C8orf39
TMEM55A
SLC39A4
CHD7
SYBU
INTS8
PAG1
GSDMC
C8orf44
JPH1
ENY2
CPA6
SLURP1
SLC45A4
ZFAT
ZNF250
PRDM14
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
PLEKHF2
ZFAND1
ZFHX4
GSDMD
NIPAL2
CSPP1
BAALC
ZNF696
GRHL2
VCPIP1
PREX2
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SLCO5A1
SHARPIN
EPPK1
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NACAP1
NCALD
MAF1
UTP23
TRIM55
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
WDR67
HPYR1
TP53INP1
TGS1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
C8orf34
TOP1MT
ZNF572
FAM92A1
C8orf38
ABRA
LYPD2
TMEM71
ADHFE1
UBXN2B
DCAF4L2
RALYL
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
TMEM74
FAM91A1
C8orf45
CLVS1
C8orf84
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
SDR16C5
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
C8orf83
DPY19L4
FBXO43
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
SLC10A5
SPATC1
CA13
XKR9
LOC389676
RBM12B
FLJ43860
MAFA
LOC392232
GDF6
LOC401463
C8orf59
SAMD12
MIR124-2
MIR30B
MIR30D
C8orf82
FER1L6-AS1
FLJ39080
FLJ46284
FLJ42969
C8orf85
LRRC24
LINC00251
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
ZNF704
C8orf69
LINC00051
SNHG6
SNORD87
C8orf73
SCXB
LINC00535
UG0898H09
RAD21-AS1
FABP9
FABP12
FER1L6
MIR599
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR875
MIR937
MIR939
LOC100127983
LOC100128126
LOC100128338
TCF24
SCXA
LOC100130155
LOC100130231
CCDC166
LOC100130298
LOC100130301
LRRC69
LOC100131726
LOC100132891
LOC100133669
LOC100192378
LOC100288181
REXO1L2P
LOC100288748
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR2052
MIR1208
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3150B
MIR3610
LOC100505659
LOC100505676
LOC100505718
LOC100507117
LOC100507632
LOC100507651
C8orf44-SGK3
ZHX1-C8ORF76
MIR378D2
MIR4661
MIR4663
MIR4472-1
MIR4664
MIR4471
MIR4470
LOC100616530
PCAT1
LINC00536
FSBP

Genes in Wide Peak

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

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

Genes
BMPR1A
TLX1
NFKB2
PRF1
PTEN
SUFU
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
ACTA2
ADK
ANXA2P3
ANXA7
ANXA11
FAS
ARL3
CAMK2G
ENTPD1
CHUK
ABCC2
COL13A1
COL17A1
COX15
CPN1
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DNA2
DNTT
EGR2
EIF4EBP2
FGF8
GLUD1
GOT1
GRID1
HELLS
HHEX
HK1
HNRNPH3
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
KCNMA1
KIF11
LIPA
MAT1A
NDUFB8
NODAL
P4HA1
PAX2
PCBD1
PDE6C
PGAM1
PITX3
PLAU
PPA1
PPP1R3C
PPP3CB
SRGN
PSAP
PSD
ALDH18A1
RBP4
RGR
RPS24
SCD
SFRP5
SFTPD
FBXW4
SLIT1
SNCG
SUPV3L1
TACR2
TAF5
TLL2
VCL
VDAC2
WNT8B
SLC25A16
NDST2
MBL1P
LIPF
GBF1
LDB1
SGPL1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
NEURL
DDX21
LGI1
NOLC1
DLG5
GSTO1
CHST3
VPS26A
MINPP1
KIF20B
SEC24C
SH3PXD2A
SLK
SPOCK2
ZNF518A
FRAT1
PPIF
ACTR1A
NPM3
MICU1
RPP30
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
C10orf116
POLR3A
LDB3
ECD
CPEB3
ZNF365
NT5C2
PDCD11
SORCS3
KIAA0913
WAPAL
PPRC1
RRP12
TBC1D12
DNAJC9
DNMBP
FRAT2
SIRT1
KAT6B
TSPAN15
IFIT5
DPCD
SEC31B
NUDT13
HERC4
LRIT1
TCTN3
KIAA1279
C10orf12
ANKRD2
CNNM1
MYOF
AP3M1
ANKRD1
GHITM
KIAA1274
C10orf28
POLL
CTNNA3
BLNK
NRBF2
KCNIP2
NEUROG3
ASCC1
EXOSC1
MRPS16
CALHM2
CUTC
PLCE1
DUSP13
PANK1
FAM190B
EXOC6
FAM35A
DDIT4
CCNJ
MARCH5
DNAJB12
CNNM2
C10orf26
CRTAC1
CEP55
LRRC20
CWF19L1
SLC29A3
RNLS
PI4K2A
H2AFY2
HIF1AN
RUFY2
FAM178A
CCAR1
DNAJC12
C10orf2
SAR1A
TM9SF3
ENTPD7
ZMIZ1
AS3MT
STAMBPL1
SEMA4G
MYOZ1
AVPI1
HPSE2
CDH23
PBLD
NPFFR1
C10orf54
MMS19
NOC3L
CUEDC2
DDX50
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
SYNPO2L
C10orf95
PDZD7
OBFC1
UBTD1
FAM213A
HKDC1
WDR96
TET1
TNKS2
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
C10orf11
PCGF6
ARID5B
LOXL4
ZDHHC16
C10orf58
DYDC2
PCGF5
LZTS2
LCOR
MRPL43
PLA2G12B
MYPN
PYROXD2
USMG5
ZNF503
AIFM2
ADO
ATAD1
ARHGAP19
LOC84989
ITPRIP
LINC00263
MCU
CDHR1
OPALIN
OPN4
HOGA1
SORCS1
CHCHD1
ZMYND17
TTC18
PIK3AP1
MORN4
ZFYVE27
COMTD1
FRA10AC1
ANKRD22
SFXN2
C10orf32
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
ANAPC16
ADAMTS14
C10orf129
SAMD8
LIPJ
CFL1P1
DYDC1
EIF5AL1
HECTD2
FGFBP3
USP54
NKX2-3
SLC35G1
CCDC147
FUT11
OIT3
LOC170425
LOC219347
PLAC9
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
C10orf27
ATOH7
REEP3
JMJD1C
ZNF503-AS1
CALHM1
PIPSL
BLOC1S2
FLJ37201
LOC283050
FAM149B1
O3FAR1
DUPD1
LIPM
CYP26C1
LRIT2
LRRTM3
SH2D4B
C10orf99
SLC16A12
CC2D2B
FLJ41350
GOLGA7B
MIR107
C10orf105
C10orf62
C10orf55
C10orf103
LOC439990
LOC439994
IFIT1B
MIR346
MIR146B
LOC642361
FAM25A
LIPK
LIPN
LOC643529
LOC650623
SFTPA1
SNORA12
SNORD98
MIR608
MIR609
FAM22A
FAM22D
LOC728190
LOC728218
LOC728558
LOC728978
LOC729020
AGAP5
BMS1P4
SFTPA2
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100128292
ZNF503-AS2
LOC100132987
KLLN
LOC100188947
DNMBP-AS1
LOC100288974
LOC100289509
MIR1287
MIR1296
MIR1256
MIR1307
FAS-AS1
MIR3157
MIR3158-1
MIR3158-2
LOC100505540
LOC100505761
LOC100505839
LOC100507331
LOC100507470
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
MIR4679-1
MIR4679-2
MIR4676
MIR4678
MIR4482-1
MIR4685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q35.

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

Genes
ATIC
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
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
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
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
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
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
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
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
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 22q13.2.

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

Genes
TSPO
TTLL12
SCUBE1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p12.

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

Genes
NRG1

Genes in Wide Peak

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

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

Genes
RBFOX1
FAM86A
TMEM114

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

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

Genes
hsa-mir-3201
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC284933
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR3201
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

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

Genes
GNA11
JAK3
LYL1
MLLT1
SH3GL1
SMARCA4
STK11
TCF3
TPM4
ELL
FSTL3
BRD4
hsa-mir-640
hsa-mir-3189
hsa-mir-3188
hsa-mir-1470
hsa-mir-639
hsa-mir-181d
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
hsa-mir-4322
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
ACP5
AES
AMH
ASNA1
ATP5D
AZU1
HCN2
BSG
BST2
C3
CACNA1A
CALR
CAPS
CD70
CD97
CDC34
CDKN2D
CIRBP
CNN1
CNN2
COMP
CSNK1G2
NCAN
DAPK3
CFD
DHPS
DNASE2
DNM2
DNMT1
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
ELAVL3
EMR1
EPOR
NR2F6
FARSA
FCER2
FUT3
FUT5
FUT6
GAMT
GCDH
GDF1
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
DNAJB1
ICAM1
ICAM3
ICAM4
IL12RB1
ILF3
INSL3
INSR
JUNB
JUND
KCNN1
LDLR
CYP4F3
MAN2B1
MATK
MEF2BNB-MEF2B
RAB8A
MYO1F
GADD45B
MYO9B
HNRNPM
NDUFA7
NDUFB7
NFIC
NFIX
NOTCH3
NRTN
OAZ1
P2RY11
PALM
PDE4A
PDE4C
PIK3R2
PIN1
POLR2E
POLRMT
PRKACA
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTGER1
PTPRS
RAB3A
RAD23A
UPF1
RFX1
RFX2
RPL18A
RPS15
RPS28
SAFB
CCL25
SGTA
SLC1A6
SLC5A5
SNAPC2
STXBP2
TBXA2R
PRDX2
THOP1
ICAM5
TLE2
TYK2
UBA52
VAV1
ZNF20
ZNF69
ZNF121
ZNF136
ZNF177
MADCAM1
SF3A2
CLPP
RANBP3
CYP4F2
KHSRP
PPAP2C
RFXANK
EIF3G
STX10
S1PR4
TNFSF14
TNFSF9
AP1M1
AP3D1
F2RL3
RAB11B
CRLF1
S1PR2
TRIP10
LONP1
MED26
HOMER3
IL27RA
GDF15
TECR
RAB3D
APBA3
IER2
SAFB2
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
SUGP2
EBI3
DDX39A
ZNF443
PLIN3
AKAP8
APC2
B3GNT3
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4A
IFI30
TIMM44
CARM1
SEMA6B
CHERP
RNASEH2A
KLF1
CERS1
GIPC1
ZNF266
PNPLA6
UQCR11
ILVBL
TMED1
CDC37
CYP4F8
COPE
LPHN1
SBNO2
MAST1
UNC13A
KDM4B
MAST3
FCHO1
ZFR2
SIN3B
ARHGEF18
CRTC1
MAU2
PIP5K1C
HMHA1
CASP14
FKBP8
SHC2
TMEM59L
PGLS
LSM4
RPL36
KANK2
FAM32A
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
SNORD37
AKAP8L
FGF22
ARRDC2
TJP3
CPAMD8
ITGB1BP3
C19orf53
BABAM1
UHRF1
HOOK2
SLC39A3
TNPO2
EMR2
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
ISYNA1
SIRT6
PIAS4
LSM7
ZNF44
TM6SF2
MBD3
S1PR5
MIER2
DDX49
PCSK4
ZNF562
GATAD2A
BEST2
FBXL12
PGPEP1
CC2D1A
TMEM161A
C19orf24
C19orf60
PLEKHJ1
MAP1S
KLHL26
C19orf66
FEM1A
ZNF823
STAP2
TRMT1
BTBD2
RNF126
CCDC94
ASF1B
USE1
C19orf80
C19orf10
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
RGL3
SLC44A2
MCOLN1
WDR18
REXO1
ZNF490
DOCK6
CAMSAP3
ZNF317
ANO8
SUGP1
CYP4F11
ZNF77
C19orf29
EPS15L1
WIZ
UBL5
CELF5
LPPR2
RASAL3
MRPL34
KRI1
ZSWIM4
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
TMEM38A
SLC25A23
C19orf42
ZNF426
C19orf57
FSD1
ZNF557
ABHD8
CERS4
OCEL1
GLT25D1
TLE6
EPHX3
PODNL1
SLC35E1
LPPR3
DENND1C
ZNF442
ZNF556
LRRC8E
FLJ22184
UBXN6
KIAA1683
OR4F17
CCDC130
ACSBG2
ADAMTS10
QTRT1
FAM108A1
DOHH
PLVAP
RTBDN
ANGPTL6
KLF16
USHBP1
TSSK6
PRAM1
C19orf44
MRI1
FBXW9
ALKBH7
WDR83
ZNF414
ELOF1
DOT1L
ZNF333
FBN3
ZNF559
KISS1R
EMR3
CREB3L3
GTPBP3
HDGFRP2
MPV17L2
LMNB2
RAX2
MUM1
HSH2D
MPND
ATG4D
ATCAY
SYDE1
MBD3L1
MIDN
SAMD1
DCAF15
GADD45GIP1
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
DPP9
R3HDM4
C19orf6
TPGS1
CRB3
REEP6
PEX11G
ZNF561
OLFM2
HAUS8
FAM125A
ARMC6
MUC16
FDX1L
NACC1
IZUMO4
SCAMP4
ADAT3
LOC113230
PGLYRP2
CCDC124
ZNF554
EVI5L
NXNL1
CCDC151
ZNF653
GRIN3B
MRPL54
LRG1
CIB3
RLN3
RAVER1
OR7D4
OR7G1
OR1M1
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
C19orf21
LRRC25
OR1I1
NR2C2AP
CCDC105
CYP4F22
PLK5
LOC126536
OR10H4
ANKLE1
C2CD4C
ZNF358
LOC147727
ZNF560
ZNF563
SPC24
TICAM1
CIRBP-AS1
ZNRF4
ZNF558
C19orf25
ATP8B3
FLJ25328
DIRAS1
ZNF555
ZNF846
OR7D2
ZNF791
ZNF564
ZNF709
ZNF433
PRR22
SSBP4
ANKRD24
C19orf59
ZNF627
DAND5
FAM129C
C19orf26
CSNK1G2-AS1
C19orf38
SYCE2
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
LOC284385
ZNF763
ZNF844
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
OR10H5
NWD1
SLC25A42
ODF3L2
LOC284454
EMR4P
ADAMTSL5
CLEC4G
NANOS3
PALM3
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
WASH5P
SLC27A1
LOC388499
C3P1
ZNF788
CLEC17A
CYP4F24P
ONECUT3
OR7G2
OR7G3
OR7A10
MEX3D
FLJ45445
PRSS57
VMAC
ZNF833P
HAPLN4
CTXN1
C19orf29-AS1
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
MIR181D
FAM138F
LINGO3
ARRDC5
FAM138A
UCA1
MBD3L4
MBD3L3
SNORD105
PPAN-P2RY11
MIR637
MIR638
MIR639
PLIN4
ZNF812
ZNF878
LOC729966
MEF2BNB
SNORD105B
ZGLP1
C19orf71
LOC100128573
TMEM221
LOC100131094
C19orf79
MEF2B
LOC100288123
MIR1470
MIR1909
MIR1181
MIR1238
MIR1227
MIR3188
MIR3187
MIR4322
MIR3189
MIR4321
MIR3940
LOC100507373
LOC100507567
LOC100507588
ZNF559-ZNF177
ZNF625-ZNF20
MIR4747
MIR4746
MIR4748
MIR4745

Genes in Wide Peak

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

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

Genes
BRAF

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

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

Genes
CHODL

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.1.

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

Genes
KCNMB1
KCNIP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.1.

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

Genes
NELL1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.21.

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

Genes
CEP192

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.3.

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

Genes
BRCA2
CDX2
FLT3
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
CDK8
FGF9
FLT1
GPR12
GTF3A
HMGB1
PDX1
MIPEP
PABPC3
UBL3
RNF6
RPL21
SGCG
SLC7A1
IFT88
MTMR6
NUPL1
FRY
USPL1
SAP18
GJB6
HSPH1
WASF3
MTUS2
SACS
LATS2
SNORD102
POLR1D
CRYL1
POMP
ATP8A2
IL17D
TNFRSF19
CENPJ
RNF17
XPO4
MRP63
KATNAL1
C13orf33
RXFP2
TEX26
B3GALTL
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
ZDHHC20
PAN3
SLC46A3
C1QTNF9
TPTE2P6
RASL11A
C1QTNF9B
SHISA2
ATP5EP2
LOC440131
C1QTNF9B-AS1
SNORA27
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
RPL21P28
LINC00426
PAN3-AS1
MIR2276
LINC00327
TEX26-AS1
MIR4499

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p15.2.

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

Genes
CTNND2
DNAH5
TAG

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.1.

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

Genes
CSTF2
CENPI
TSPAN6
NOX1
SRPX2
RPA4
PCDH19
TMEM35
TNMD
TRMT2B
SYTL4
ARL13A
XKRX
LOC442459

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q12.

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

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p23.1.

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

Genes
ALK
ATIC
CHN1
CREB1
DNMT3A
ERCC3
ACSL3
MSH6
HOXD11
HOXD13
IDH1
MSH2
MYCN
NFE2L2
PAX3
PMS1
REL
PAX8
NCOA1
EML4
BCL11A
FEV
TTL
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
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
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
hsa-mir-3127
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
hsa-mir-216b
hsa-mir-559
hsa-mir-558
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
AAMP
ACADL
ACP1
ACTG2
ACVR1
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
AGXT
ALPI
ALPP
ALPPL2
BIN1
ANXA4
AOX1
APOB
RHOB
RND3
ATP5G3
ATP6V1B1
KIF1A
AUP1
BARD1
BCS1L
BMPR2
BOK
ZFP36L2
BUB1
CACNB4
CAD
CALM2
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CENPA
CHRNA1
CHRND
CHRNG
CLK1
CNGA3
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
COX5B
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CTNNA2
CYP1B1
CYP27A1
DARS
DBI
DCTN1
DDX1
DES
DGUOK
LOC1720
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DTNB
DTYMK
DUSP2
E2F6
EEF1B2
EGR4
EMX1
EN1
EPAS1
EPHA4
ERBB4
FABP1
FAP
EFEMP1
FHL2
FKBP1B
FN1
FOSL2
FRZB
FSHR
FTH1P3
GAD1
GALNT3
GBX2
GCG
GCKR
MSTN
GFPT1
GGCX
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GTF3C2
GYPC
HADHA
HADHB
HDLBP
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HPCAL1
AGFG1
DNAJB2
HSPD1
HSPE1
FOXN2
HTR2B
ID2
SP110
IGFBP2
IGFBP5
IHH
IL1A
IL1B
IL1R1
IL1RN
CXCR1
CXCR2
CXCR2P1
INHA
INHBB
INPP1
INPP4A
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNF1
KCNJ3
KCNJ13
KCNK3
KCNS3
KHK
KIF3C
KIF5C
AFF3
LCT
LHCGR
LIMS1
LRP2
LTBP1
LY75
EPCAM
MXD1
MAL
MAP2
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MYO1B
MTIF2
MYL1
MYO7B
NAB1
NCL
NEB
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPAS2
NPHP1
NPPC
NR4A2
ODC1
ORC2
ORC4
OTX1
REG3A
PCBP1
PDCD1
PDE1A
PDE6D
PDK1
PEX13
VIT
SERPINE2
PIGF
PLCL1
PLEK
PLGLB2
PLGLB1
POLR2D
POMC
POU3F3
PPM1B
PPM1G
PPP1CB
PPP1R7
PPP3R1
PRKCE
EIF2AK2
PROC
PSMD1
PTH2R
PTMA
PTPN4
PTPRN
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
REG1P
SNORD20
RPE
RPL31
RPL37A
RPS7
RPS27A
RRM2
RTKN
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
CCL20
SDC1
SRSF7
SFTPB
SIX3
SLC4A3
SLC1A4
SLC3A1
SLC8A1
SLC9A2
SLC11A1
SLC20A1
SNRPG
SOS1
SOX11
SP3
SP100
SPAST
SPP2
SPR
SPTBN1
SRD5A2
SSB
SSFA2
STAT1
STAT4
STRN
SULT1C2
ADAM17
TACR1
GCFC2
TFPI
TGFA
TIA1
TNFAIP6
TNP1
TNS1
TPO
TSN
TSSC1
TTN
TUBA4A
SUMO1
UCN
UGP2
VIL1
VRK2
VSNL1
WIPF1
WNT6
XDH
XPO1
XRCC5
ZAP70
ZNF2
ZNF142
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
FZD5
SCG2
DYSF
FZD7
SDPR
NCK2
DUSP11
CUL3
KLF11
MAP4K3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ASAP2
PER2
ST3GAL5
SLC5A6
DDX18
EIF2B4
CDK5R2
KYNU
TAF1B
NAT8
NMI
RQCD1
COX7A2L
TMSB10
IL1RL1
LRRFIP1
STK17B
ITGB1BP1
GPR55
TRIP12
GTF3C3
PPIG
NRXN1
OTOF
CIAO1
TGFBRAP1
HS6ST1
CRIPT
ECEL1
MAP4K4
EIF2AK3
EIF4E2
ROCK2
CHST10
TP53I3
CIR1
MRPL33
BRE
PREPL
CYTIP
FEZ2
GCC2
TTLL4
SOCS5
EIF5B
GREB1
BZW1
USP34
LAPTM4A
HDAC4
RNF144A
SNX17
SERTAD2
MRPL19
ZEB2
FARP2
TLK1
SUPT7L
CD302
ARHGAP25
TANK
BCL2L11
FARSB
ABCB6
ACTR3
ACTR2
ARPC2
PREB
ACTR1B
ARL4C
LRPPRC
PDIA6
ABI2
CEBPZ
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
SMYD5
KBTBD10
MYCNOS
C1D
MERTK
UBE2E3
STK25
SEMA4F
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
MTX2
CGREF1
B3GNT2
USP39
TBR1
SIX2
MAP3K2
NCKAP1
VAMP5
MTHFD2
ARID5A
PROKR1
RAB10
EDAR
COPS8
GPR75
YWHAQ
IMMT
SNRNP27
GTF2A1L
STON1
RAPGEF4
EMILIN1
CAPN10
TBC1D8
RABL2A
GALNT5
NXPH2
GPR45
SP140
MGAT4A
GPN1
IKZF2
COBLL1
AAK1
FASTKD2
MAPRE3
PLA2R1
RAB3GAP1
RPIA
SLC4A1AP
EFR3B
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
PASK
UBXN4
ATG4B
PSME4
EXOC6B
EHBP1
SATB2
CLASP1
OBSL1
PUM2
NCAPH
RHOQ
SF3B1
HAAO
TMEM131
R3HDM1
DNPEP
PSD4
WBP1
NTSR2
TMEFF2
SH3BP4
PRKD3
KCNE4
RASGRP3
NGEF
QPCT
GCA
VAX2
SNORD82
MOB4
POLR1A
CNRIP1
FAM98A
PNKD
UNC50
SNED1
GORASP2
SPATS2L
RAB11FIP5
GIGYF2
EPC2
TRAF3IP1
ABCA12
IFT172
ARL5A
HIBCH
PTPN18
CNNM4
CNNM3
IL36RN
SH3YL1
SNORD53
SNORD51
CNPPD1
STK36
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
MMADHC
BMP10
ZNF638
STK39
HTRA2
TRIB2
CPS1-IT1
METTL5
LGALSL
OLA1
C2orf27A
GRHL1
TFCP2L1
ICOS
GMPPA
NRBP1
BAZ2B
SLC40A1
KCNIP3
EHD3
SMARCAL1
CD207
ITSN2
ANO7
ARHGEF4
PDE11A
TPRKB
FAHD2A
PRLH
WDPCP
MEMO1
THAP4
TRAPPC12
ASB3
INSIG2
CRIM1
ANKRD39
FAM178B
RNF181
MRPL30
DNAJC27
ANKMY1
KRCC1
MRPL35
C2orf28
PCYOX1
GULP1
REV1
NAT8B
SCLY
VPS54
NBAS
LIPT1
NOP58
DYNC2LI1
SF3B14
YPEL5
CHMP3
FKBP7
ASB1
CPSF3
CAB39
ZAK
LRP1B
PRKAG3
PPIL3
SNTG2
DNAJC10
ATAD2B
ETAA1
HEATR5B
CCDC93
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
AFTPH
MFSD6
TMEM214
RETSAT
INO80D
SEMA4C
C2orf18
C2orf42
TRMT61B
PID1
PTCD3
PLEKHB2
ATG16L1
FANCL
SRBD1
FIGN
ANKZF1
RIF1
USP40
MOB1A
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
HJURP
STRADB
C2orf56
HES6
ACCN4
C2orf29
NAGK
DOCK10
TTC27
SMPD4
TMEM127
PRPF40A
SLC30A6
IWS1
LIMS2
KANSL3
MREG
CCDC88A
WDR12
MBD5
KDM3A
ALLC
PECR
ARHGAP15
ZC3H15
CFC1
DNAH7
GKN1
IL36G
RPRM
CYP26B1
POLE4
KCNK12
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
C2orf83
MFF
RPL23AP32
CXCR7
RNPEPL1
RTN4
TRIM54
PELI1
SLC39A10
TTC7A
SMEK2
SLC4A10
CYP20A1
SPC25
BIRC6
ERMN
KIDINS220
MTA3
HECW2
WDR35
MARCH4
WDFY1
NYAP2
DPP10
RDH14
EPB41L5
ALS2
ZDBF2
USP37
CWC22
ANKRD36B
G6PC2
SLC4A5
CTDSP1
NLRC4
MPP4
SLC5A7
NIF3L1
AGBL5
C2orf43
THADA
PCGEM1
RBKS
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
ATL2
ABCG5
ABCG8
RAB17
RNF25
HS1BP3
GMCL1
TTC31
ANAPC1
COPS7B
RMND5A
FNDC4
MARCH7
OBFC2A
PAPOLG
MRPS9
MRPS5
REEP1
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
SOWAHC
PLEKHA3
TRAK2
BOLL
COLEC11
PDCL3
TRPM8
ATG9A
C2orf49
MLPH
TMEM185B
FAM134A
CENPO
OR7E91P
GLB1L
C2orf47
SPAG16
CHPF
SAP130
GALNT14
SCRN3
CCDC121
FASTKD1
SMC6
GTDC1
CLIP4
IQCA1
ALS2CR8
TTC21B
CAMKMT
METTL8
GEMIN6
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
NOL10
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
TUBA4B
MZT2B
YSK4
UXS1
FBXO11
ARMC9
COQ10B
SLC35F5
EFHD1
C2orf44
SPHKAP
WNT10A
SLC19A3
TSGA10
THSD7B
THUMPD2
TMEM177
KIAA1715
ILKAP
FAM49A
LMAN2L
LBH
TMEM163
ITM2C
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
RHBDD1
CHCHD5
YIPF4
PRADC1
C2orf88
ING5
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
DPY30
MCEE
LOXL3
ABHD1
PCGF1
DDX11L2
MFSD9
PLCD4
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
MGC16025
TANC1
EPT1
LBX2
PNPT1
KCNH7
FER1L5
MCFD2
ATP6V1E2
LOC90499
CCDC74A
LOC90784
DHX57
LOC91149
SESTD1
CCDC74B
PKDCC
ANKRD44
RSAD2
ZNF804A
TTC30A
DAPL1
CAPN13
TMEM169
DNER
CCDC164
IMP4
HNRPLL
MARS2
B3GNT7
NT5C1B
NEURL3
SP140L
SFXN5
ORMDL1
LIMS3
LINC00152
TUBA3E
CCDC104
TEX261
TUBA3D
STK11IP
FMNL2
CCDC85A
GALNT13
KLHL29
OSBPL6
NOSTRIN
DIRC1
WDR92
MOGAT1
LYPD1
MRPL53
AGAP1
TWIST2
PARD3B
RPL23AP7
PPP1R21
C2orf89
TMEM150A
NUP35
XIRP2
TYW5
NMS
LYG1
MITD1
DIS3L2
CMPK2
MBOAT2
CNTNAP5
TMEM18
FBLN7
NEU4
RBM45
C2orf73
TRIM43
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
CIB4
REG3G
RFTN2
C2orf63
PLEKHH2
AP1S3
C2orf76
SGPP2
ACVR1C
OSR1
TTC32
UBR3
KCTD18
ALS2CR12
ZNF513
SPATA3
LYPD6
LYPD6B
GALM
TMEM198
ZFAND2B
TMEM178
CPO
MDH1B
C2orf50
PQLC3
TMEM182
AHSA2
FBXO36
MTERFD2
CCDC148
C2orf65
MYO3B
TMEM37
UBE2F
DUSP19
CKAP2L
CBWD2
TEKT4
LOC150527
FLJ32063
LOC150568
SMYD1
C2orf15
LOC150622
OTOS
MYEOV2
OR6B3
COMMD1
PROM2
ANKAR
FBXO41
TTC30B
GPAT2
ITPRIPL1
LOC150776
WTH3DI
FAM117B
TCF23
LOC150935
FAM59B
PUS10
PKI55
LINC00309
LOC151009
SEPT10
C2orf67
PLB1
ZSWIM2
ZNF385B
LOC151171
LOC151174
ARL6IP6
METTL21A
CCNYL1
KLHL23
SULT1C2P1
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
LOC151300
GPBAR1
FAHD2B
MYADML
FAM84A
FAM82A1
GDF7
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
ASPRV1
WDSUB1
UPP2
LOC151534
GPR155
WDR69
LONRF2
CCDC138
GPR113
C2orf57
OXER1
FAM179A
FAM171B
C1QL2
UBXN2A
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
PIKFYVE
KRTCAP3
LOC200726
TMEM17
SPRED2
TIGD1
LOC200772
FAM123C
LINC00116
C2orf69
HNRNPA3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
CERS6
METAP1D
LOC254128
LYG2
CCDC108
C2orf72
SH2D6
LOC284950
CCDC150
RNF149
LOC284998
LOC285000
FAM150B
CCDC141
LOC285033
LINC00486
C2orf61
LOC285074
LOC285084
CXXC11
LOC285103
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
FAM126B
UNC80
RUFY4
PLGLA
RGPD4
DUSP28
STON1-GTF2A1L
SPOPL
MLK7-AS1
CYP27C1
ESPNL
C2orf70
C2orf53
LOC339788
LINC00299
LOC339803
C2orf74
LOC339807
LOC339822
MSGN1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
EVX2
CDKL4
PRORSD1P
AOX2P
SH3RF3
GPR148
ECEL1P2
LRRTM1
GEN1
C2orf48
FONG
LOC348761
PFN4
LOC375190
LOC375196
ANKRD36
WASH2P
RBM43
LOC375295
CERKL
C2orf62
RBM44
AQP12A
ZC3H6
KLHL30
LOC386597
MFSD2B
C2orf71
LOC388942
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
SLC9A4
LOC389023
LOC389033
LOC389043
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
PTRHD1
SULT6B1
DYTN
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
FLJ42351
LOC401010
DKFZp686O1327
LOC401022
FSIP2
C2orf66
ASB18
FLJ43879
VWC2L
MIR10B
MIR128-1
MIR149
MIR153-1
MIR216A
MIR217
MIR26B
C2orf27B
DNAJB3
ASTL
CAPN14
ACTR3BP2
LOC440894
LOC440895
LOC440900
LOC440905
LOC440910
POTEKP
LOC440925
LOC442028
SULT1C3
POTEE
COA5
PHOSPHO2
CHAC2
MIR375
DFNB59
LOC541471
LOC554201
ANKRD30BL
FBXO48
SNORA41
FAM110C
LOC643387
PRR21
LOC644838
GGT8P
ANKRD36BP2
LOC645949
LOC646324
LOC646736
LOC646743
PRSS56
LOC647012
C2orf84
TRIM43B
CFC1B
AQP12B
RGPD3
MZT2A
SNORA75
LOC654342
FAM138B
LOC654433
SCARNA6
SCARNA5
SNORD11
SNORD70
SNORD89
SNORD92
SNORD94
MIR558
MIR559
MIR561
RGPD8
LOC727982
D2HGDH
LOC728323
POTEF
LOC728537
LOC728730
PABPC1P2
LOC728819
LOC729121
ANKRD20A8P
LOC729234
RAD51AP2
RGPD6
DIRC3
DNAJC27-AS1
RGPD2
MORN2
LOC730811
RFX8
SNORD11B
SNORA36C
SNORA70B
MIR216B
MIR933
LOC100128590
OST4
LOC100129175
LOC100129726
LOC100129961
PP14571
LOC100130451
LOC100130452
LOC100130691
TMEM194B
LOC100131320
SP9
LOC100132215
CYP4F30P
LOC100133985
LOC100134259
LOC100144595
RNU4ATAC
DBIL5P2
SNAR-H
LOC100189589
LOC100216479
ARHGEF33
LOC100271832
LIMS3-LOC440895
LOC100286922
LOC100286979
LOC100287010
LOC100287216
LOC100288570
LIMS3L
LOC100288911
MIR1471
MIR1246
MIR548N
MIR1258
MIR1245A
MIR1301
MIR1244-1
LOC100302650
GPR75-ASB3
SNORA80B
ZEB2-AS1
MIR548F2
MIR663B
LOC100329109
SNORA70F
BOK-AS1
MIR3128
MIR4265
MIR1244-3
MIR1244-2
MIR4264
MIR3129
MIR3127
MIR4261
MIR3131
MIR4268
MIR4263
MIR3125
MIR3130-1
MIR4267
MIR4262
MIR3130-2
MIR4266
MIR3126
MIR2355
MIR3132
MIR4269
LOC100499194
MIR3606
MIR3682
MIR3679
LOC100505624
LOC100505695
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506123
LOC100506124
LOC100506134
LOC100506274
LOC100506421
LOC100506474
LOC100506783
LOC100506866
LOC100507140
BOLA3-AS1
LOC100507334
LOC100507443
LOC100507600
LY75-CD302
RNF103-CHMP3
NT5C1B-RDH14
PHOSPHO2-KLHL23
HSPE1-MOB4
INO80B-WBP1
UBE2F-SCLY
MIR4436B1
MIR4772
MIR4779
MIR4783
MIR4439
MIR4782
MIR4437
MIR4765
MIR4776-1
MIR4757
MIR4777
MIR1245B
MIR4435-2
MIR4426
MIR4774
MIR2467
MIR4775
MIR4785
MIR4784
MIR4773-1
MIR4444-1
MIR4440
MIR4436A
MIR4786
MIR4773-2
MIR4434
MIR4780
MIR4778
MIR4429
MIR4776-2
MIR4432
MIR548AD
MIR4441
MIR4435-1
LOC100630918
LOC100861402

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.3.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

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

Genes
BRCA1
CD79B
CLTC
COL1A1
DDX5
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
PER1
PRKAR1A
RARA
MAP2K4
TP53
TAF15
GAS7
USP6
SUZ12
ASPSCR1
BRIP1
MSI2
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
hsa-mir-3185
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
hsa-mir-4315-1
hsa-mir-2117
hsa-mir-2909
hsa-mir-632
hsa-mir-365-2
hsa-mir-3184
hsa-mir-144
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
hsa-mir-4314
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
AANAT
ABR
ACACA
ACADVL
ACCN1
ACLY
ACOX1
ACTG1
ADORA2B
AP2B1
ALDH3A1
ALDH3A2
ALDOC
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
AOC2
BIRC5
APOH
ARL4D
ARHGDIA
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
ATP5G1
ATP6V0A1
BLMH
C1QBP
FMNL1
CA4
CACNB1
CACNG1
CD7
CD68
CDC6
CDC27
CDK3
CHAD
CHD3
CHRNB1
CHRNE
CCR7
CNP
COX10
COX11
CPD
CLDN7
CRHR1
CRK
CRYBA1
CSF3
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CTNS
CYB561
ACE
DHX8
DLG4
DLX3
DLX4
DNAH9
DPH1
DRG2
DUSP3
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
ERN1
EVI2A
EVI2B
EVPL
EZH1
BPTF
FASN
FDXR
FGF11
FOXJ1
FOXO3B
FLII
FLOT2
GAST
FZD2
G6PC
GAA
GALK1
GCGR
KAT2A
GFAP
GH1
GH2
GIP
GNGT2
GP1BA
CCR10
UTS2R
GPS1
GPS2
GRB2
GRB7
GRN
GRIN2C
GUCY2D
H3F3B
HCRT
HIC1
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HSD17B1
ICAM2
ICT1
IFI35
IGFBP4
FOXK2
ITGA2B
ITGA3
ITGAE
ITGB3
ITGB4
JUP
KCNJ2
KCNJ12
KCNJ16
KPNB1
KPNA2
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS3BP
LGALS9
LHX1
LIG3
LLGL2
LLGL1
LPO
NBR1
MAFG
MAPT
ADAM11
MEIS3P1
MAP3K3
MEOX1
MFAP4
MNT
MPO
MPP2
MPP3
TRIM37
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYL4
MYO1C
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NOS2
NPTX1
NSF
NUP88
OMG
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
P4HB
PAFAH1B1
PDE6G
PDK2
PECAM1
SERPINF1
PEX12
PFAS
PFN1
PHB
PITPNA
PLD2
SERPINF2
PMP22
PNMT
SEPT4
POLR2A
MED1
PPY
PRKCA
MAPK7
MAP2K3
MAP2K6
PRPSAP1
PRPSAP2
PSMB3
PSMB6
PYY
PSMC5
PSMD3
PSMD11
PSMD12
PYCR1
PCYT2
RAB5C
RAC3
RAD51C
RAD51D
RCVRN
RFNG
RPA1
RPL19
RPL23A
RPL26
RPL27
RPL38
MRPL12
RPS6KB1
SCN4A
SCO1
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SEC14L1
SECTM1
SRSF1
SRSF2
SGCA
SGSH
SH3GL1P1
SH3GL1P2
SHBG
SHMT1
SLC2A4
SLC4A1
SLC6A4
SMARCD2
SMARCE1
SUMO2
SOX9
SOX15
SP2
SREBF1
SRP68
SSTR2
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
VAMP2
TADA2A
TBCD
TBX2
HNF1B
MLX
THRA
TIMP2
TK1
TNFAIP1
TOP2A
TOP3A
DNAJC7
TUBG1
UBB
UBE2G1
UBTF
TRPV1
VTN
WNT3
WNT9B
YWHAE
ZNF18
PCGF2
TRIM25
VEZF1
RNF112
ZNF207
ZNF232
RND2
COIL
AKAP1
EPX
AXIN2
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
PIP4K2B
SLC25A11
SPOP
DOC2B
FOXN1
PPM1D
CNTNAP1
DGKE
COPS3
CBX4
TCAP
SCARF1
SKAP1
DNAH17
AOC3
BECN1
KRT38
KRT37
KRT36
TNK1
ABCC3
MYH13
TNFSF13
TNFSF12
RGS9
GALR2
TMEM11
KSR1
CDK5R1
SPHK1
CACNA1G
HAP1
MAP3K14
SOCS3
TM4SF5
SPAG9
SLC13A2
UNC119
MTMR4
SLC16A6
SLC16A5
SLC16A3
RABEP1
SYNGR2
HGS
KCNAB3
AURKB
TIAF1
NOG
BZRAP1
CYTH1
ZNHIT3
GLP2R
EFTUD2
RPL23
SLC9A3R1
COG1
RECQL5
NTN1
STX8
PIGL
PGS1
TBX4
RPH3AL
FXR2
NPEPPS
MPDU1
GOSR1
SPAG7
CCL4L1
GOSR2
NR1D1
NCOR1
TRAF4
AATK
KIAA0100
ULK2
CCDC144A
ACAP1
TBKBP1
KIAA0195
EIF4A3
PLEKHM1
KIAA0753
MED24
LRRC37A
MRC2
SGSM2
ARHGAP44
HELZ
HS3ST3B1
HS3ST3A1
MED13
HDAC5
TOM1L1
GJC1
TOB1
ALYREF
PSME3
EIF1
NBR2
SLC35B1
DCAF7
CALCOCO2
RAMP2
ABCA10
ABCA9
ABCA8
PEMT
BAIAP2
CLEC10A
ATP5H
HOXB13
VAT1
APPBP2
MYBBP1A
FBXW10
PRPF8
LEPREL4
ST6GALNAC2
HEXIM1
SPAG5
TRIM16
IGF2BP1
GNA13
CCT6B
RAI1
KIF1C
GRAP
SEPT9
CD300C
C1QL1
RUNDC3A
STARD3
CBX1
RAB40B
TLK2
DDX52
DUSP14
KAT7
AKAP10
POLG2
NXPH3
SNF8
SYNRG
CD300A
TMC6
DDX42
GABARAP
CASC3
IKZF3
ZNF652
PPM1E
NLRP1
ARHGEF15
ARSG
EPN2
AZI1
SARM1
RAP1GAP2
CAMTA2
GPATCH8
KDM6B
ZZEF1
GGA3
MPRIP
JMJD6
EXOC7
KIAA0664
SMG6
WSCD1
USP22
CTDNEP1
KCNH4
ABCA6
ABCA5
TNFRSF13B
KCTD2
MMD
PIK3R5
WBP2
CDC42EP4
C17orf81
FAM215A
PPY2
PYY2
SHPK
AIPL1
FSCN2
NOL11
DHRS7B
KRT23
RNF167
TMEM98
POLDIP2
TBC1D29
TANC2
WSB1
NAT9
SENP3
OR1A2
PITPNC1
ERAL1
NARF
AATF
OR4D1
SNORD4B
SNORD4A
SNORA67
SNORD49A
SNORD42B
SNORD42A
PELP1
B9D1
CACNG5
CACNG4
TUBG2
TMEM97
NKIRAS2
CCDC56
GIT1
RANGRF
SAP30BP
PSMC3IP
SNX11
TIMM22
TBX21
NT5C
SOCS7
CDR2L
TAX1BP3
MINK1
GEMIN4
SOST
MED31
DERL2
FAM18B1
GLOD4
MRPS7
YBX2
UTP18
RNFT1
HN1
MYO15A
TUBD1
DCXR
RAPGEFL1
TACO1
ABI3
COPZ2
MRPL27
PIPOX
AMZ2
ARL17A
CRLF3
TRPV2
ANKFY1
ANAPC11
SIRT7
SLC25A39
MRPS23
PTRH2
RASD1
NLK
LUC7L3
HIGD1B
CDK12
INPP5K
KRT20
NLE1
FAM64A
SDK2
XAF1
FNDC8
FAM20A
C17orf59
MBTD1
BCAS3
TMEM104
CWC25
ALKBH5
RNF43
TTC19
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
GPR172B
LRRC37A4
MED9
SLFN12
WRAP53
PNPO
KLHL11
RNMTL1
SMG8
SLC47A1
TMEM100
VPS53
RHOT1
RSAD1
C17orf79
LRRC59
C17orf85
MSX2P1
NPLOC4
TSR1
C17orf63
PRR11
ADAP2
ST6GALNAC1
UTP6
TEX2
GSDMB
GPRC5C
TEX14
WDR45L
DHX33
CA10
NT5M
ATXN7L3
C17orf48
CCDC47
PLSCR3
PLXDC1
LYZL6
CBX8
ZNF286A
ZNF287
MIF4GD
INTS2
CASKIN2
RPTOR
NUFIP2
ZNF624
TAOK1
NLGN2
BAHCC1
USP36
ARHGAP23
PHF12
ZBTB4
RNF213
TNRC6C
CXCL16
TRAPPC1
PCTP
SCPEP1
ALOXE3
SLC25A19
ELAC2
FKBP10
SRR
UBE2O
HEATR6
DUS1L
FN3K
XYLT2
C17orf75
NXN
DNAI2
TEKT3
SMURF2
ENGASE
SPATA20
MRPL38
UBE2Z
WNK4
C17orf53
MIS12
C17orf39
METTL16
TMUB2
CARD14
DHX58
PHF23
MMP28
DHRS11
MFSD11
PRR15L
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
TEFM
ZNF750
ACBD4
FAM57A
DCAKD
GGNBP2
NUP85
ATAD5
MRM1
PLEKHH3
MYO15B
FAM106A
CTC1
DBF4B
MYO19
ACSF2
C17orf70
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
LIMD2
KCNH6
FAM117A
NDEL1
VMP1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
PITPNM3
LRRC48
TMEM93
TTC25
RILP
TEKT1
KRTAP4-12
RAB34
TSPAN10
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
GSG2
MYCBPAP
QRICH2
NSRP1
PPP1R1B
TBC1D3F
ZMYND15
CAMKK1
RPAIN
RNF135
MIEN1
MRPL45
VPS25
TMEM107
LSMD1
TMEM101
PRAC
RAB11FIP4
NEURL4
GHDC
KRTAP4-4
ZNF594
KIF2B
HES7
USP32
PPP1R9B
SPATA22
CBX2
MGC12916
TXNDC17
FAM104A
CORO6
TNS4
FBXL20
MIR22HG
MGC16275
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
FBF1
UNK
SSH2
TP53I13
IFT20
LRRC46
SCRN2
AOC4
CEP95
TRIM47
ANKRD40
ZNF830
SLFN11
RASL10B
ATPAF2
TMEM88
STRADA
C17orf72
SPECC1
G6PC3
ASB16
MAFG-AS1
OTOP2
PGAP3
MYOCD
PIGS
TTYH2
HSPB9
ORMDL3
CDRT7
CDRT15P1
SAT2
PLCD3
SLC46A1
TMEM106A
LRRC37B
CYGB
RNF157
SMYD4
OSBPL7
C1QTNF1
NT5C3L
ABHD15
TLCD1
PPP1R27
CNTROB
FTSJ3
RFFL
RPL29P2
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
ZPBP2
CYB5D1
OVCA2
USP43
KRBA2
C17orf64
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
FLJ40194
B4GALNT2
SPACA3
SGK494
SEZ6
ANKRD13B
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
C17orf57
MRPL10
WDR81
TBC1D16
AFMID
GJD3
KRT222
KRT40
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
DYNLL2
SMCR5
SMCR8
SMCR9
MGAT5B
TOM1L2
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
DNAH2
RTN4RL1
TCAM1P
EFCAB3
SLC47A2
CDRT15
WDR16
CCDC42
PIK3R6
ODF4
C17orf50
SLFN13
SLC35G3
UNC45B
LOC146880
CD300LG
KIF18B
RUNDC1
EME1
TMEM199
PROCA1
DHRS13
KCTD11
C17orf69
LOC147093
NOTUM
TMC8
TRIM16L
LRRC37BP1
WIPF2
KRT25
TMEM99
ANKFN1
MARCH10
MFSD6L
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
TRPV3
SLC16A11
FBXO39
IMP5
KRT28
USP32P1
KRT24
CEP112
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
ARHGAP27
ZNF385C
SAMD14
C17orf108
SLC16A13
C17orf74
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
RDM1
SPNS3
USP32P2
GAS2L2
STH
MTVR2
STXBP4
LOC253962
TBC1D28
C17orf61
TAC4
MYADML2
BCL6B
CDRT15L2
C17orf103
NPB
C17orf66
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
LOC284009
VMO1
C17orf58
MILR1
LOC284023
LINC00324
FLJ34690
CDRT4
CCDC144B
KIAA1267
C17orf105
FAM171A2
C17orf104
TTLL6
LOC284080
C17orf47
KRT18P55
NEK8
PIGW
C17orf78
LOC284100
CISD3
GSDMA
SLC13A5
TMEM102
KRT42P
PTRF
FAM27L
FLJ36000
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
LGALS9B
METRNL
TUSC5
KLHL10
RAB37
LOC339166
TMEM95
METTL2A
CCDC144NL
C17orf65
C17orf67
ENPP7
C17orf90
CCDC137
ARL16
LOC339240
C17orf51
MSL1
CD300E
SMTNL2
ALOX15P1
NACA2
KRT27
SLFN14
FLJ43826
STAC2
OTOP3
SKA2
CCL14-CCL15
CCDC144C
FAM195B
GPR142
TBC1D26
ZACN
KRT26
FAM101B
HOXB13-AS1
HILS1
CDRT1
SPEM1
EFCAB5
LRRC37A3
RNF126P1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
SHISA6
FAM211A
TMIGD1
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
OR3A4P
ARL5C
KRT39
SLC25A35
MYO18A
C17orf97
MED11
KRT16P2
GRAPL
C17orf102
LOC400604
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
MGC57346
CUEDC1
LOC404266
MIR10A
MIR132
MIR142
MIR144
MIR152
MIR193A
MIR195
MIR196A1
MIR21
MIR212
MIR22
MIR301A
TNFSF12-TNFSF13
TBC1D3B
TBC1D3C
CCL3L3
MXRA7
RNASEK
TBC1D3P5
SUZ12P
LOC440434
GPR179
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR324
MIR338
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451A
MIR497
SNORA21
CPSF4L
C17orf109
SLC35G6
RNF222
PIRT
LOC644172
LOC644246
CDRT15P2
FAM83G
KRT16P3
EVPLL
LOC645638
SEBOX
SNORA48
SNORD10
OR1D4
KRTAP4-11
MRPL45P2
TBC1D3P1-DHX40P1
LOC653653
TBC1D3G
LGALS9C
NME1-NME2
LINC00338
SCARNA20
SCARNA21
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORA59B
SNORA59A
SNORD7
SNORD49B
SNORD65
SNORD91A
SNORD91B
SNORD104
MIR33B
MIR632
MIR634
MIR635
MIR636
MIR657
BHLHA9
TLCD2
KRTAP4-8
KRTAP2-2
KRTAP9-1
LOC728392
NSFP1
FLJ45513
ZNF286B
LOC729683
TBC1D3
TBC1D3H
LOC730755
PRCD
MIR454
SNORD124
SNORA38B
MIR744
MIR365B
LOC100128288
LOC100128977
FAM106CP
LOC100130148
C17orf107
LOC100130581
C17orf110
LOC100130950
LOC100131096
LOC100131347
CD300LD
DBIL5P
KRTAP4-9
KRTAP4-7
LOC100133991
KCNJ18
TEN1
C17orf99
C17orf96
LOC100190938
LOC100287042
LOC100289255
LOC100294362
MIR1288
MIR1253
MIR1203
MIR1250
MIR1180
LOC100306951
MIR2117
MIR3183
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR2909
MIR3185
MIR4314
MIR3184
MIR4315-1
MTRNR2L1
LOC100499466
LOC100499467
MIR3614
MIR3678
MIR3615
MIR3676
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
LOC100506388
SPAG5-AS1
LOC100506650
AA06
LOC100506713
SLFN12L
MIR497HG
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
RAD51L3-RFFL
RNASEK-C17ORF49
C17orf61-PLSCR3
FAM18B2-CDRT4
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4523
MIR4731
MIR4728
MIR4726
MIR4739
MIR4734
MIR4729
MIR4737
MIR4736
MIR4724
MIR4733
MIR451B
MIR4522
MIR4738
MIR4740
MIR4524A
MIR4730
MIR4732
MIR3064
MIR4723
MIR4520A
MIR4521
MIR5047
MIR4727
MIR4725
MIR4520B
LOC100653515
RAB34

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
ABL1
FANCC
FANCG
GNAQ
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
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
hsa-mir-873
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
ABCA1
ABCA2
ABO
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
ANXA2P2
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
TNFSF8
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CELP
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
MLANA
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
GGTA1P
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
IL11RA
INSL4
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RMRP
RORB
RPL7A
RPL12
RPS6
RXRA
CCL19
CCL21
SH3GL2
SHB
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
UGCG
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
RGP1
TRIM14
MELK
RUSC2
PPP1R26
SEC16A
ZBTB5
KIAA0020
TNFSF15
PTBP3
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
PSIP1
INSL6
SLC2A6
PTENP1
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA1045
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
PCA3
AK3
EXOSC3
FAM108B1
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
C9orf11
TBC1D13
FAM22F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
C9orf167
CNTLN
TEX10
LPPR1
KIAA1797
UBE2R2
EXD3
FAM206A
C9orf95
STX17
NOL8
C9orf68
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDC37L1
DENND4C
C9orf86
CDK5RAP2
UBAP2
C9orf46
CBWD1
KLHL9
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KIAA1161
KCNT1
KIAA1432
BDAG1
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
DMRT3
PRDM12
NAA35
DMRTA1
SLC28A3
CARD9
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
MRPL41
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOB3B
C9orf82
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
FAM214B
GKAP1
PDCD1LG2
AKNA
MIR600HG
URM1
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
PRRC2B
PPAPDC3
GLIS3-AS1
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
TPD52L3
WDR34
SAPCD2
C9orf69
LRSAM1
IL33
C9orf123
C9orf30
UAP1L1
MCART1
MRRF
RBM18
ARRDC1
WDR85
ADAMTSL1
FP588
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19P
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf66
LINC00032
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC39B
FAM201A
RG9MTD3
TTC16
LOC158257
FAM120AOS
FAM154A
LINC00475
FREM1
KIAA2026
LOC158376
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
C9orf96
KCNV2
OLFML2A
C9orf71
QSOX2
GLIS3
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
C9orf93
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
FAM205A
LINC00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
TPRN
LOC286297
TUSC1
LINC00256A
FAM78A
LURAP1L
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
IFNE
ZDHHC21
ACER2
LOC340508
LOC340515
GPR144
FAM75D5
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
GLT6D1
ENHO
AQP7P1
PTAR1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
KGFLP1
LOC389705
FAM205B
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
C9orf128
OR13J1
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FLJ35024
FLJ41200
PTPLAD2
LOC401497
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR101-2
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR31
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC415056
LOC440173
LOC440896
FLJ35282
SUGT1P1
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
ANKRD18B
LOC441461
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
MIR31HG
LOC572558
MIR491
PGM5P2
MIR455
NRON
LOC642236
FAM75A2
FAM75A4
LOC642929
FAM163B
FLJ40292
TUBBP5
RNF224
LOC643648
CBWD6
FAM75C2
HRCT1
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM138C
SCARNA8
SNORA17
SNORA43
SNORD62B
MSMP
SNORD90
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
CDKN2B-AS1
SNORD121A
SNORD121B
C9orf146
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
UNQ6494
LOC100129250
LOC100129316
LOC100129722
LOC100130954
LOC100131193
LOC100132077
LOC100132352
FAM157B
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
LINC00092
LOC100272217
LOC100286938
WASH1
LOC100288842
LOC100289019
LOC100289341
MIR548H3
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3152
MIR3154
MIR2861
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3621
MIR3910-1
MIR3689A
MIR3911
MIR3910-2
MIR3689B
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506422
LOC100506599
LOC100506710
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4667
MIR4473
MIR4669
MIR4673
MIR3960
MIR4540
MIR4665
MIR4475
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4670
MIR4672
MIR4474
MIR4476
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.2.

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

Genes
BCL2
SS18
MALT1
ZNF521
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
hsa-mir-187
hsa-mir-302f
hsa-mir-320c-2
hsa-mir-1-2
hsa-mir-320c-1
hsa-mir-3156-2
hsa-mir-4317
ADCYAP1
AQP4
ATP5A1
C18orf1
CDH2
CDH7
CETN1
CIDEA
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GATA6
GNAL
GRP
IMPA2
LAMA3
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC2R
MC4R
MC5R
ME2
MEP1B
MYO5B
NARS
NDUFV2
NFATC1
NPC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
PTPN2
PTPRM
RAB27B
RBBP8
RIT2
ROCK1
RPL17
SERPINB3
SERPINB4
SLC14A1
SNRPD1
SYT4
TAF4B
TCF4
TGIF1
TTR
TYMS
YES1
ZFP161
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
RNMT
MYOM1
NAPG
RIOK3
TNFRSF11A
MBD2
PSTPIP2
PIAS2
USP14
CTDP1
VAPA
DLGAP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
LPIN2
CTIF
THOC1
PPP4R1
TSHZ1
NDC80
ACAA2
MYL12A
SLMO1
CD226
ZNF271
TXNL4A
RALBP1
AFG3L2
MAPRE2
RAB31
POLI
ADNP2
TRAPPC8
EPB41L3
PHLPP1
ANKRD12
CCDC165
NEDD4L
WDR7
SMCHD1
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
CABYR
SNORD58B
SNORD58A
CLUL1
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
C18orf8
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
CEP192
RPRD1A
ZNF532
ELP2
IMPACT
ELAC1
ENOSF1
ZNF407
CNDP2
LINC00470
CELF4
SPIRE1
PSMG2
TWSG1
CHMP1B
MIB1
KIAA1328
KLHL14
KIAA1468
EPG5
HRH4
PIEZO2
CTAGE1
FAM59A
METTL4
MPPE1
ARHGAP28
CCDC102B
RBFA
CEP76
GREB1L
PQLC1
FHOD3
CCDC68
ASXL3
COLEC12
NETO1
SEH1L
KATNAL2
CHST9
C18orf21
MRO
EMILIN2
HDHD2
TXNDC2
ZNF397
PARD6G
TUBB6
CNDP1
TMEM241
SERPINB12
SERPINB11
SEC11C
L3MBTL4
CABLES1
DSEL
MYL12B
ESCO1
OSBPL1A
HAUS1
ALPK2
FAM210A
LOXHD1
INO80C
TTC39C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
MCART2
DSG4
CHST9-AS1
ANKRD29
APCDD1
LINC00526
ZNF519
C18orf54
TCEB3C
ABHD3
FBXO15
RAB12
LOC201477
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
ZNF396
LOC284215
LAMA1
CYP4F35P
KCTD1
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339290
LRRC30
LOC339298
CPLX4
ANKRD30B
C18orf34
ATP9B
POTEC
LOC390858
LOC400643
LOC400654
LOC400655
LOC400657
MIR1-2
MIR122
MIR133A1
MIR187
CXADRP3
ANKRD20A5P
HSBP1L1
WBP11P1
RNF165
C18orf56
C18orf32
KC6
C18orf42
LOC643542
C18orf63
LOC644669
CBX3P2
LOC645355
TMEM200C
LOC647946
FLJ35776
SCARNA17
SNORA37
ROCK1P1
LOC727896
LOC728606
TCEB3CL
LOC729950
ZSCAN30
SNORD58C
LOC100130480
LOC100130522
LOC100131655
LOC100192426
LOC100287225
LOC100288122
MIR302F
MIR320C1
MIR320C2
MIR1539
MIR4319
MIR4317
MIR4318
MIR4320
MIR3156-2
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4526
MIR4741
MIR3976
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744
LOC100652770

Arm-level results

Table 3. Get Full Table Arm-level significance table - 18 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 | 0.01 | -0.898 | 0.994 | 0.01 | -1.3 | 0.994
1q | 1955 | 0.05 | 7.54 | 9.19e-13 | 0.00 | -1.63 | 0.994
2p | 924 | 0.00 | -1.71 | 0.994 | 0.02 | 1.45 | 0.59
2q | 1556 | 0.00 | -2.1 | 0.994 | 0.02 | 1.08 | 0.94
3p | 1062 | 0.01 | -1.34 | 0.994 | 0.00 | -1.74 | 0.994
3q | 1139 | 0.00 | -1.73 | 0.994 | 0.01 | -1.34 | 0.994
4p | 489 | 0.01 | -0.171 | 0.987 | 0.00 | -2.14 | 0.994
4q | 1049 | 0.01 | -0.147 | 0.987 | 0.00 | -2.13 | 0.994
5p | 270 | 0.04 | 5.75 | 8.71e-08 | 0.00 | -2.5 | 0.994
5q | 1427 | 0.04 | 4.26 | 8.13e-05 | 0.00 | -2.49 | 0.994
6p | 1173 | 0.00 | -1.73 | 0.994 | 0.01 | -1.34 | 0.994
6q | 839 | 0.00 | -2.13 | 0.994 | 0.01 | -0.156 | 0.994
7p | 641 | 0.04 | 4.6 | 2.15e-05 | 0.00 | -2.5 | 0.994
7q | 1277 | 0.04 | 5.45 | 3.41e-07 | 0.00 | -2.48 | 0.994
8p | 580 | 0.01 | -0.55 | 0.994 | 0.01 | -0.944 | 0.994
8q | 859 | 0.01 | -0.139 | 0.987 | 0.01 | -0.93 | 0.994
9p | 422 | 0.01 | -1.3 | 0.994 | 0.04 | 4.21 | 0.000169
9q | 1113 | 0.01 | -0.848 | 0.994 | 0.05 | 6.28 | 3.42e-09
10p | 409 | 0.00 | -1.74 | 0.994 | 0.01 | -0.169 | 0.994
10q | 1268 | 0.00 | -1.72 | 0.994 | 0.01 | -0.533 | 0.994
11p | 862 | 0.01 | -0.129 | 0.987 | 0.01 | -0.129 | 0.994
11q | 1515 | 0.01 | -0.494 | 0.994 | 0.02 | 0.698 | 0.994
12p | 575 | 0.03 | 3.01 | 0.00519 | 0.00 | -2.11 | 0.994
12q | 1447 | 0.03 | 3.07 | 0.00473 | 0.00 | -2.09 | 0.994
13q | 654 | 0.01 | -0.503 | 0.994 | 0.03 | 2.65 | 0.0399
14q | 1341 | 0.02 | 1.86 | 0.0889 | 0.00 | -2.1 | 0.994
15q | 1355 | 0.00 | -2.52 | 0.994 | 0.01 | -0.14 | 0.994
16p | 872 | 0.03 | 3.43 | 0.00151 | 0.00 | -2.1 | 0.994
16q | 702 | 0.03 | 2.63 | 0.0155 | 0.00 | -1.71 | 0.994
17p | 683 | 0.03 | 3.48 | 0.00143 | 0.02 | 0.72 | 0.994
17q | 1592 | 0.03 | 3.92 | 0.000293 | 0.01 | -0.452 | 0.994
18p | 143 | 0.01 | -0.169 | 0.987 | 0.01 | -0.955 | 0.994
18q | 446 | 0.01 | -0.157 | 0.987 | 0.01 | -0.944 | 0.994
19p | 995 | 0.02 | 0.666 | 0.594 | 0.01 | -0.916 | 0.994
19q | 1709 | 0.02 | 1.08 | 0.349 | 0.00 | -2.1 | 0.994
20p | 355 | 0.03 | 2.2 | 0.0432 | 0.00 | -2.53 | 0.994
20q | 753 | 0.03 | 2.22 | 0.0432 | 0.00 | -2.52 | 0.994
21q | 509 | 0.01 | -0.538 | 0.994 | 0.02 | 0.25 | 0.994
22q | 921 | 0.01 | -1 | 0.994 | 0.17 | 29.8 | 0
Xq | 1312 | 0.02 | 1.08 | 0.349 | 0.01 | -0.9 | 0.994

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/THCA-TP/2842979/2.GDAC_MergeDataFiles.Finished/THCA-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

Table 4. Get Full Table First 10 out of 470 Input Tumor Samples.

Tumor Sample Names
TCGA-BJ-A0YZ-01A-11D-A10T-01
TCGA-BJ-A0Z0-01A-11D-A10T-01
TCGA-BJ-A0Z2-01A-11D-A10T-01
TCGA-BJ-A0Z3-01A-11D-A13V-01
TCGA-BJ-A0Z5-01A-11D-A10T-01
TCGA-BJ-A0Z9-01A-11D-A10T-01
TCGA-BJ-A0ZA-01A-11D-A10T-01
TCGA-BJ-A0ZB-01A-11D-A10T-01
TCGA-BJ-A0ZC-01A-12D-A13V-01
TCGA-BJ-A0ZE-01A-11D-A10T-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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