SNP6 Copy number analysis (GISTIC2)

Sarcoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1CR5S5Q

Overview

Introduction

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

Summary

There were 169 tumor samples used in this analysis: 16 significant arm-level results, 21 significant focal amplifications, and 40 significant focal deletions were found.

Results

Focal results

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

Table 1. Get Full Table Amplifications Table - 21 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
12q15	6.3942e-55	6.6219e-55	chr12:69178021-69244387	1
1q24.3	1.9502e-18	1.9502e-18	chr1:172019584-172206659	6
17p11.2	3.9597e-13	3.9597e-13	chr17:11702856-20307058	112
1p32.1	6.0642e-08	6.0642e-08	chr1:58611919-59952427	8
6q24.3	8.1086e-07	8.1086e-07	chr6:148810209-149707665	4
19q12	3.7975e-06	3.7975e-06	chr19:30245403-30326293	1
5p15.2	0.00038702	0.00038702	chr5:12762532-15331399	8
19p13.2	0.0065442	0.0065442	chr19:6882410-7309686	9
13q34	0.007254	0.007254	chr13:113363456-114860943	23
3p11.2	0.010161	0.010161	chr3:85487213-90485635	10
6p21.1	0.014487	0.014487	chr6:42316793-42577711	2
11q22.2	0.02433	0.02433	chr11:101789694-102572619	9
Xp21.2	0.043953	0.043953	chrX:15659116-39969460	102
Xq21.2	0.080431	0.080431	chrX:80178943-86538209	15
8q21.12	0.12137	0.12137	chr8:42929311-146364022	524
21q21.1	0.14837	0.14837	chr21:16733940-17882027	2
12p12.1	0.12794	0.18871	chr12:26202486-26227683	1
20q13.33	0.21269	0.21269	chr20:47744948-63025520	196
7q31.1	0.22472	0.22472	chr7:103581627-150319289	332
17q24.3	0.24776	0.24776	chr17:57292827-81195210	361
12p13.32	0.10727	1	chr12:1-133851895	1200

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q15.

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

Genes
MDM2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q24.3.

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

Genes
hsa-mir-199a-2
DNM3
MIR199A2
MIR214
MIR3120
DNM3OS

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FOXO3B
FLII
LLGL1
MEIS3P1
MFAP4
PMP22
MAPK7
PRPSAP2
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
GRAP
AKAP10
EPN2
MPRIP
TNFRSF13B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
FAM106A
LRRC48
MGC12916
ATPAF2
SPECC1
MYOCD
CDRT7
CDRT15P1
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
CDRT15
TRIM16L
USP32P1
FAM18B2
CENPV
FLCN
PLD6
USP32P2
TBC1D28
FLJ34690
CDRT4
CCDC144B
LOC339240
CCDC144C
TBC1D26
CDRT1
FAM211A
KRT16P2
GRAPL
CDRT15P2
FAM83G
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
MIR744
FAM106CP
MIR1288
MIR1180
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p32.1.

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

Genes
JUN
DAB1
TACSTD2
FGGY
MYSM1
OMA1
HSD52
LOC100131060

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q24.3.

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

Genes
UST
TAB2
SASH1
LOC100128176

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

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

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

Genes
DNAH5
TRIO
FAM105A
ANKH
FAM105B
TAG
LOC100130744
MIR4637

Genes in Wide Peak

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

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

Genes
EMR1
INSR
ZNF557
MBD3L2
MBD3L5
EMR4P
FLJ25758
MBD3L4
MBD3L3

Genes in Wide Peak

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

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

Genes
ATP4B
F7
F10
GAS6
LAMP1
GRK1
TFDP1
CUL4A
PROZ
RASA3
ATP11A
MCF2L
TMCO3
DCUN1D2
PCID2
GRTP1
ADPRHL1
FAM70B
FLJ44054
FLJ41484
LINC00552
MCF2L-AS1
LOC100506394

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p11.2.

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

Genes
EPHA3
HTR1F
POU1F1
CGGBP1
CHMP2B
ZNF654
CADM2
C3orf38
VGLL3
MIR4795

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
UBR2
TRERF1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.2.

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

Genes
BIRC3
BIRC2
MMP7
MMP20
YAP1
KIAA1377
MMP27
C11orf70
TMEM123

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp21.2.

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

Genes
hsa-mir-548f-5
hsa-mir-1308
NR0B1
S100G
CYBB
DMD
EIF1AX
EIF2S3
GK
GRPR
MAGEB1
MAGEB2
MAGEB3
MAGEB4
NHS
OTC
PDHA1
PDK3
PHEX
PHKA2
POLA1
PPEF1
PRRG1
RBBP7
RPGR
RPS6KA3
RS1
SAT1
SCML1
SMS
CDKL5
DYNLT3
TSPAN7
XK
ZFX
ZRSR2
SRPX
INE2
AP1S2
REPS2
PCYT1B
GPR64
SCML2
PRDX4
RAI2
IL1RAPL1
CA5B
CNKSR2
ACOT9
SMPX
CXorf27
SH3KBP1
MBTPS2
FTHL17
BCOR
TXLNG
CTPS2
TMEM27
MID1IP1
APOO
CXorf21
KLHL15
TMEM47
SYAP1
SYTL5
BEND2
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
MAGEB16
ZNF645
FAM47A
MAGEB6
DDX53
FAM47B
CXorf22
FAM48B2
ARX
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
LOC286442
CXorf59
MAGEB18
CA5BP1
LANCL3
DCAF8L2
MAP3K15
YY2
FAM47C
CXorf30
SCARNA23
LOC729609
FAM48B1
LOC100132163
SCARNA9L
MIR23C
MIR4768

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq21.2.

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

Genes
hsa-mir-361
hsa-mir-548i-4
CHM
CYLC1
POU3F4
SH3BGRL
ZNF711
RPS6KA6
HMGN5
POF1B
DACH2
APOOL
HDX
SATL1
UBE2DNL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q21.12.

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

Genes
COX6C
EXT1
MYC
PLAG1
TCEA1
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
CEBPD
CRH
CYC1
CYP7A1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
FNTA
GEM
GLI4
GML
NPBWR1
GPR20
GPT
GRINA
HAS2
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LY6E
LY6H
LYN
MATN2
MCM4
MMP16
MOS
MYBL1
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
OPRK1
PDE7A
ENPP2
PENK
PLEC
PMP2
POLR2K
POU5F1B
PKIA
PRKDC
PTK2
PVT1
PEX2
RAB2A
RAD21
RP1
RPL7
RPL8
RPL30
RPS20
SDC2
SDCBP
ST3GAL1
SLA
SNAI2
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
UBE2V2
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
NSMAF
LY6D
RGS20
JRK
EIF3H
DGAT1
GPAA1
RIPK2
GGH
WISP1
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
LRRC14
TTC35
RIMS2
ST18
TOX
MTSS1
PTDSS1
RB1CC1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
LYPLA1
ARFGEF1
COLEC10
KHDRBS3
POP1
COPS5
WWP1
STMN2
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
RRS1
SULF1
ARC
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
KIAA0146
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
MRPL15
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
FAM82B
ZNF706
VPS28
FAM203A
KCNK9
C8orf55
UBR5
FAM49B
AZIN1
ATP6V1H
OTUD6B
CHRAC1
SNTG1
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
SOX17
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
EFCAB1
PLEKHF2
ZFAND1
ZFHX4
GSDMD
NIPAL2
CSPP1
BAALC
ZNF696
GRHL2
VCPIP1
PREX2
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SLCO5A1
SHARPIN
EPPK1
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NACAP1
NCALD
SGK196
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
XKR4
CSMD3
RHPN1
FBXO32
SLC26A7
PCMTD1
CTHRC1
OSR2
C8orf34
TOP1MT
ZNF572
FAM92A1
C8orf38
TMEM68
ABRA
LYPD2
TMEM71
ADHFE1
UBXN2B
PXDNL
DCAF4L2
RALYL
HGSNAT
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
POTEA
SLC10A5
SPATC1
CA13
FAM150A
XKR9
LOC389676
RBM12B
FLJ43860
MAFA
LOC392232
GDF6
LOC401463
C8orf59
SAMD12
MIR124-2
MIR30B
MIR30D
C8orf82
FER1L6-AS1
FLJ39080
FLJ46284
FLJ42969
C8orf85
LRRC24
C8orf22
LINC00293
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
SBF1P1
LOC100133669
LOC100192378
LOC100287846
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 amplified genes in the wide peak for 21q21.1.

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

Genes
USP25
LINC00478

Genes in Wide Peak

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

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

Genes
RASSF8

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.1.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
CREB3L2
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
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CFTR
CHRM2
CLCN1
CPA1
CPA2
DLD
SLC26A3
EPHA1
EPHB6
FLNC
GPR22
GPR37
GRM8
IFRD1
IMPDH1
IRF5
KCND2
KEL
LAMB1
LEP
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
CNOT4
NRCAM
NRF1
ORC5
PAX4
SLC26A4
PIK3CG
PIP
PODXL
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
TAS2R38
PTN
PTPRZ1
RARRES2
SLC13A1
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TBXAS1
UBE2H
WNT2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
PDIA4
FAM131B
DOCK4
FAM115A
NAMPT
AASS
FAM3C
COG5
DUS4L
ZNF277
TFEC
LAMB4
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
OR2F1
SLC13A4
COPG2
HBP1
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
ZC3HC1
LUC7L2
MRPS33
NAA38
GPR85
TAS2R5
PUS7
ING3
LRRN3
CHCHD3
RBM28
TMEM140
GIMAP4
TRPV6
AGK
METTL2B
MLL5
BCAP29
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
KIAA1147
FAM40B
ZNF398
EXOC4
RINT1
LRRC4
TMEM168
CCDC136
PARP12
LRRC61
C7orf49
GCC1
CBLL1
ZNF767
C7orf58
TTC26
JHDM1D
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
PRSS58
ASZ1
ASB15
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154860
IQUB
LOC154872
C7orf66
TMEM213
GIMAP8
ZNF425
LOC155060
ZNF746
ATP6V0E2
MGC27345
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
ZNF800
C7orf33
ATXN7L1
CDHR3
UBN2
TAS2R39
TAS2R40
TAS2R41
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
LOC349160
GSTK1
LHFPL3
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF35
WEE2
MIR490
ZNF862
LOC645591
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
LOC723809
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
LOC100124692
CTAGE4
LOC100129148
LOC100130705
EFCAB10
LOC100130880
LOC100134229
LOC100134713
LOC100216545
LOC100216546
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3666
LOC100507421
MIR4468

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.3.

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

Genes
CD79B
CLTC
DDX5
PRKAR1A
ASPSCR1
BRIP1
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
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
MAFG
MAP3K3
NPTX1
P4HB
PDE6G
PECAM1
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
TBCD
TBX2
TIMP2
TK1
AXIN2
PPM1D
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
RAB40B
TLK2
POLG2
CD300A
TMC6
DDX42
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
PTRH2
SDK2
FAM20A
BCAS3
TMEM104
C17orf80
CCDC40
WIPI1
NPLOC4
ST6GALNAC1
TEX2
GPRC5C
WDR45L
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
DNAI2
SMURF2
ENGASE
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
USP32
CBX2
FAM104A
MGC16275
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
NOTUM
TMC8
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
FAM195B
GPR142
ZACN
LRRC37A3
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
MIR21
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LOC645638
TBC1D3P1-DHX40P1
LOC653653
LINC00338
SCARNA20
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR634
MIR635
MIR636
MIR657
LOC729683
PRCD
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3678
MIR3615
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4729
MIR4737
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
ALDH2
ATF1
BCL7A
BTG1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
MLL2
HMGA2
WIF1
ZNF384
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
ACACB
ACADS
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ARL1
ART4
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
SCARB1
CD63
CD69
CDK2
CDKN1B
CHD4
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CREBL2
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
DDX11
ATN1
EPYC
DTX1
DUSP6
PHC1
EIF2B1
EIF4B
CELA1
ELK3
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GRIN2B
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTA4H
LTBR
LUM
LYZ
M6PR
MARS
METTL1
KITLG
MGP
MGST1
MIP
MMP17
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NDUFA9
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
POU6F1
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAB1
PRKAG1
PRPH
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAN
RAP1B
RARG
RBMS2
RDH5
RECQL
RFC5
RFX4
RNY5
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SNRPF
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
SYT1
TAC3
TARBP2
TBX5
TBX3
HNF1A
TDG
TEAD4
TMBIM6
TFCP2
TSPAN8
TMPO
TNFRSF1A
TPI1
NR2C1
HSP90B1
TULP3
TXNRD1
UBC
UBE2N
UNG
VDR
VWF
WNT1
WNT10B
ZNF10
ZNF26
ZNF84
ZNF140
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
DYRK2
PPFIBP1
PPFIA2
CSDA
LGR5
MAPKAPK5
DENR
RDH16
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
GPRC5A
KRT75
SCAF11
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
KIAA0748
KIAA0528
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
CLEC2B
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
RNF41
MPHOSPH9
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
LEPREL2
DCTN2
AKAP3
CCT2
SLCO1B1
RAD51AP1
CAMKK2
AVIL
PTGES3
KLRAP1
ZNF268
FRS2
TSPAN9
TRAFD1
OS9
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
PHLDA1
R3HDM2
MLXIP
RPH3A
KLRK1
P2RX2
RAB21
STK38L
FBXO21
FAIM2
MON2
SETD1B
UHRF1BP1L
ERC1
DDN
ANKLE2
TMEM194A
CUX2
KIAA1033
TBC1D30
ESYT1
TENC1
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
ABCB9
CBX5
ISCU
RIMBP2
ANP32D
ATP6V0A2
SMUG1
LEMD3
CORO1C
GABARAPL1
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
FBXW8
GALNT8
HSPB8
SNORD59A
GLS2
HCAR1
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CCDC41
IRAK4
ING4
GPN3
DDX47
GLTP
MRPL51
CLEC1B
CLEC1A
C12orf47
C1RL
ERGIC2
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TM7SF3
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
MAGOHB
SLC6A15
FAM90A1
RIC8B
C12orf35
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
CAND1
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
ARNTL2
CHPT1
PARP11
ANO2
C12orf4
C12orf5
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHDC5
PITPNM2
DIP2B
KIAA1467
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
C12orf44
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
OBFC2B
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
RPAP3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
FLJ13224
TCTN2
PLBD1
PYROXD1
NANOG
DNAJC22
NAA25
SLC24A6
ADAMTS20
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
C12orf39
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
C12orf32
NRIP2
INHBE
RBP5
TMTC1
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
C12orf26
TMEM117
TCHP
COQ5
LLPH
WIBG
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
EFCAB4B
TUBA1C
ZC3H10
ORAI1
RNFT2
C12orf34
ALG10
SPRYD3
C12orf52
MFSD5
MGC14436
C12orf62
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
FAM113B
C12orf65
TMEM132C
CCDC64
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
TMEM132B
OSBPL8
ARHGEF25
C12orf56
IQCD
LOC116437
AGAP2
DCD
RAB3IP
LOH12CR1
MUCL1
DEPDC4
LRRK2
CCDC38
C12orf59
FAM186A
C12orf45
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
HIST4H4
ERP27
FGD4
AEBP2
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
BRI3BP
KRT72
PRICKLE1
AMDHD1
SLC2A14
BCDIN3D
ALG10B
GLIPR1L2
FAM101A
ZNF664
LINC00477
LYRM5
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
KRT80
A2ML1
LOC144571
C12orf66
C12orf60
FBXL14
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
IFLTD1
DENND5B
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
CLEC4C
DSTNP2
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
C12orf53
DCP1B
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
C12orf33
GNN
MSRB3
METTL20
LRRC43
OR6C74
OR6C3
TCP11L2
LOC255411
LOC255480
LOC256021
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
POC1B
OTOGL
MATL2963
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
GPR133
MORN3
LOC283392
LOC283403
LOC283404
C12orf61
DPY19L2
CLEC9A
C12orf36
GAS2L3
LINC00485
LOC283440
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
C12orf40
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
LOC338758
C1QL4
TMEM119
KRT79
LOC338799
C12orf74
FAM19A2
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
PTPRQ
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
RPL13AP20
REP15
C12orf68
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
LOC389634
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
MKRN9P
C12orf76
LOC400084
FLJ37505
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
MIR26A2
C12orf37
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
DBX2
FLJ12825
TMEM198B
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
TSPAN11
OR9K2
MIR148B
MIR331
EID3
LOH12CR2
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC574538
HIGD1C
POU5F1P3
LOC642846
MAP1LC3B2
LOC643339
LOC643770
GLYCAM1
LOC647589
FAM86FP
PRB2
LRTM2
HNRNPA1P10
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA34
SNORA49
SNORA53
LOC678655
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
MIR617
MIR618
MIR620
LOC728084
C12orf73
SKP1P2
LOC728739
C12orf71
SLC15A5
MRS2P2
HOTAIR
MIR920
LOC100128191
LOC100128554
LOC100129361
LOC100130238
LOC100130776
LOC100131138
LOC100131733
LOC100190940
LOC100233209
LOC100240734
LOC100240735
LOC100271702
LOC100286844
MANSC4
LOC100287314
LINC00173
LOC100287944
LOC100288778
ZNF605
LOC100292680
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1178
MIR1244-1
MIR1251
LOC100335030
SNORA70G
MIR1244-3
MIR1244-2
MIR4302
MIR4303
MIR4304
KLRF2
LOC100499405
MIR3685
MIR3649
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506314
LOC100506393
LOC100506451
LOC100506649
LOC100506660
LOC100506668
LOC100506844
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507250
LOC100507377
LOC100507424
BLOC1S1-RDH5
POC1B-GALNT4
KLRC4-KLRK1
ZNF664-FAM101A
PRH1-PRR4
MIR4699
MIR4498
MIR548AL
MIR4701
MIR3974
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4698
LOC100652846
LOC100652999

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 - 40 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
13q14.2	1.0733e-40	1.0733e-40	chr13:48833767-48992809	1
17p13.1	2.5169e-32	2.5169e-32	chr17:7549751-7593565	2
Xq21.1	7.625e-17	4.6541e-16	chrX:76710176-77102528	1
9p21.3	3.0418e-16	2.2657e-13	chr9:21865498-22448737	4
1p36.32	4.1813e-11	7.9086e-11	chr1:1-5923787	115
10p15.3	1.2852e-10	1.2366e-10	chr10:1-857150	4
19q13.43	7.2337e-10	7.2213e-10	chr19:58264000-59128983	40
4q35.1	5.587e-09	5.587e-09	chr4:178911874-191154276	64
19p13.3	1.3714e-08	1.4064e-08	chr19:1-390340	9
10q23.31	9.5464e-08	9.5464e-08	chr10:89574877-90034038	3
11q24.3	2.1787e-07	2.1752e-07	chr11:118094649-135006516	173
2q37.3	3.7707e-16	3.5649e-07	chr2:242162274-243199373	17
11p15.5	4.177e-07	4.177e-07	chr11:1-496996	19
1q44	9.7928e-06	9.6026e-06	chr1:208416154-249250621	319
9q34.3	6.0535e-05	5.8936e-05	chr9:139885821-141213431	48
17q25.3	3.9749e-06	6.5451e-05	chr17:80443432-80617015	2
8p23.3	0.00014874	0.00014874	chr8:1-1713973	8
2q37.3	9.3795e-15	0.00017667	chr2:233877222-243199373	105
17q11.2	1.7798e-05	0.00022429	chr17:29326736-30180957	11
7q36.3	0.00077337	0.00077337	chr7:157210222-159138663	11
2p25.3	0.001431	0.0014814	chr2:1-27804113	173
12p13.1	0.0019953	0.0029393	chr12:1-18417317	255
3q29	0.010397	0.010165	chr3:165509351-198022430	228
14q24.1	0.010342	0.010165	chr14:68275375-69288431	2
21q22.3	0.020244	0.028352	chr21:47427840-47609222	3
18q23	0.032104	0.0321	chr18:47717577-78077248	118
22q13.31	0.046143	0.046704	chr22:45095899-51304566	86
3p21.31	0.061407	0.061407	chr3:43761442-65340907	284
Xq27.1	0.015015	0.063578	chrX:109698760-155270560	394
Xp22.33	0.073269	0.075291	chrX:1-9694455	47
6p25.1	0.080128	0.079819	chr6:1-26019211	142
9p23	0.0011937	0.10431	chr9:5568722-12693402	13
21q11.2	0.10958	0.11455	chr21:1-23095995	41
16q12.1	0.088873	0.13096	chr16:31772318-55548321	62
6q14.1	0.0013547	0.15021	chr6:53210826-97373584	137
6q16.1	0.0097262	0.17652	chr6:64422619-145950272	362
16q23.1	0.11032	0.18633	chr16:78016120-79627770	2
12q12	0.16798	0.22214	chr12:16188286-69204948	479
1p32.3	0.14043	0.24922	chr1:50879767-51569162	3
15q11.2	0.24563	0.24922	chr15:1-56723369	405

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

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

Genes
LPAR6

Genes in Wide Peak

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

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

Genes
TP53
ATP1B2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.1.

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

Genes
ATRX

Genes in Wide Peak

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

Table S25. Genes in bold are cancer genes as defined by The Sanger Institute: 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 1p36.32.

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

Genes
TNFRSF14
PRDM16
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
CDK11B
DFFB
DVL1
MEGF6
GABRD
GNB1
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
MMP23A
TNFRSF18
ISG15
PLCH2
CEP104
SLC35E2
RER1
NOC2L
OR4F3
ARHGEF16
SSU72
WRAP73
SDF4
MXRA8
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
AJAP1
TP73-AS1
LRRC47
HES4
VWA1
NADK
MMEL1
OR4F5
LINC00115
MORN1
GLTPD1
OR4F16
CCNL2
TAS1R3
ATAD3B
PLEKHN1
C1orf170
KIAA1751
LOC115110
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
LOC148413
CCDC27
CALML6
C1orf86
ATAD3C
LOC254099
TTLL10
FAM41C
LOC284661
C1orf174
KLHL17
TMEM240
TMEM52
AGRN
FAM132A
HES5
LOC388588
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
MIR4689
MIR4417

Genes in Wide Peak

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

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

Genes
ZMYND11
DIP2C
TUBB8
C10orf108

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.43.

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

Genes
A1BG
FKBP1AP1
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF256
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF586
ZNF446
ZSCAN18
MGC2752
ZNF329
ZNF552
ZNF606
ZBTB45
ZNF587
ZNF837
C19orf18
ZNF418
ZNF417
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
A1BG-AS1
LOC646862
ZNF814
LOC100128398
LOC100131691
ZNF587B
MIR4754

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

Table S29. Genes in bold are cancer genes as defined by The Sanger Institute: 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
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 19p13.3.

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

Genes
hsa-mir-1302-11
PPAP2C
THEG
MIER2
OR4F17
WASH5P
FLJ45445
FAM138F
FAM138A

Genes in Wide Peak

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

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

Genes
PTEN
CFL1P1
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

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

Genes
CBL
DDX6
FLI1
MLL
ARHGEF12
hsa-mir-3167
hsa-mir-100
ACRV1
APLP2
ARCN1
CXCR5
CD3D
CD3E
CD3G
CHEK1
DPAGT1
ETS1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NFRKB
NRGN
OPCML
PVRL1
RPS25
SC5DL
ST3GAL4
SORL1
SRPR
ST14
TECTA
THY1
UPK2
ZNF202
BARX2
USP2
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
IGSF9B
PHLDB1
NCAPD3
VSIG2
TRIM29
POU2F3
HINFP
OR8G2
OR8B8
OR8G1
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
TRAPPC4
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
IFT46
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
C11orf61
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
JAM3
KIRREL3
TMEM25
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
TMEM45B
TTC36
PATE1
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
LINC00167
HEPN1
LOC649133
RPL23AP64
LOC100128239
PATE3
MIR3167
LOC100499227
MIR3656
LOC100507392
MIR4697
MIR4493
MIR4492

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
BOK
DTYMK
HDLBP
SEPT2
PDCD1
FARP2
STK25
ATG4B
THAP4
GAL3ST2
ING5
NEU4
CXXC11
D2HGDH
LOC728323
BOK-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

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

Genes
PSMD13
IFITM1
IFITM3
IFITM2
PKP3
SIRT3
BET1L
SIGIRR
RIC8A
ATHL1
PTDSS2
ODF3
SCGB1C1
NLRP6
ANO9
B4GALNT4
IFITM5
LOC653486
LOC100133161

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q44.

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
HNRNPU
HSD11B1
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
G0S2
RRP15
PPPDE1
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
SLC30A10
ZNF692
IARS2
HHAT
ENAH
NUP133
RCOR3
SERTAD4
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
B3GALNT2
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
LOC255654
SYT14
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR194-1
MIR205
MIR215
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
DUSP5P
C1orf133
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
SNORA36B
SNORA16B
LOC728463
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.3.

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

Genes
hsa-mir-602
ABCA2
CACNA1B
ENTPD2
FUT7
GRIN1
SSNA1
CLIC3
TUBB4B
NOXA1
MAN1B1
COBRA1
NELF
NDOR1
ANAPC2
DPP7
C9orf167
EXD3
NPDC1
MRPL41
EHMT1
C9orf37
SAPCD2
UAP1L1
ARRDC1
WDR85
TMEM203
ZMYND19
SLC34A3
C9orf142
TPRN
PNPLA7
C9orf169
ENTPD8
LRRC26
C9orf139
FAM166A
C9orf173
NRARP
FLJ40292
TUBBP5
RNF224
MIR602
RNF208
LOC100129722
FAM157B
LOC100289341
MIR3621

Genes in Wide Peak

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

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

Genes
FOXK2
WDR45L

Genes in Wide Peak

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

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

Genes
DLGAP2
FBXO25
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
NDUFA10
SEPT2
NEU2
PDCD1
PPP1R7
SAG
SPP2
DGKD
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
MSL3P1
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
AQP12B
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

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

Genes
NF1
hsa-mir-365-2
EVI2A
EVI2B
OMG
RAB11FIP4
MIR193A
MIR365B
MIR4724
MIR4733
MIR4725

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
hsa-mir-595
hsa-mir-153-2
PTPRN2
VIPR2
NCAPG2
WDR60
ESYT2
LOC154822
MIR153-2
MIR595
LOC100506585

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.3.

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

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ADCY3
APOB
RHOB
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
FTH1P3
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
SNX17
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
MAPRE3
EFR3B
MYT1L
LPIN1
PUM2
NTSR2
IFT172
SH3YL1
TRIB2
GRHL1
NRBP1
ITSN2
TRAPPC12
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
HS1BP3
FNDC4
COLEC11
CENPO
SMC6
NOL10
C2orf44
FAM49A
ABHD1
EPT1
RSAD2
CCDC164
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
FAM84A
GDF7
GPR113
UBXN2A
CYS1
KRTCAP3
ATP6V1C2
RNASEH1
FAM150B
DNAJC5G
IAH1
FLJ33534
C2orf70
C2orf53
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
PFN4
LOC375190
LOC386597
MFSD2B
PTRHD1
LOC400940
LINC00487
FLJ12334
FAM110C
LOC645949
C2orf84
LOC727982
RAD51AP2
DNAJC27-AS1
LOC730811
OST4
MIR1301
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505624
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
CCND2
ETV6
KDM5A
ZNF384
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
KCNA1
KCNA5
KCNA6
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NINJ2
NOP2
NTF3
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
SCNN1A
SLC2A3
SLC6A12
SLC6A13
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
CSDA
DYRK4
GPRC5A
CD163
GDF3
CLSTN3
NCAPD2
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
RAD51AP1
KLRAP1
TSPAN9
STRAP
PRR4
PHB2
KLRK1
ERC1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
PRMT8
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
WNK1
BCL2L14
ADIPOR2
RERGL
PLBD1
NANOG
DUSP16
WNT5B
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
CCDC77
ACRBP
SPSB2
EFCAB4B
RERG
HTR7P1
CACNA2D4
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
FBXL14
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf53
DCP1B
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
B4GALNT3
CLEC9A
C12orf36
LOC283440
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
LOC574538
POU5F1P3
LOC642846
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
LOC100271702
LOC100288778
LOC100292680
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
MIR3649
LOC100506314
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
ACTL6A
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
CLDN11
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SKIL
SLC2A2
SST
TERC
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
FYTTD1
ARPM1
MGC2889
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LOC339926
LPP-AS2
LRRIQ4
SAMD7
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
TMEM212
FLJ46066
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
LOC646168
C3orf65
GMNC
LOC647323
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.1.

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

Genes
ZFP36L1
RAD51B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
COL6A2
FTCD
C21orf56

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD4
MBD1
MBP
MC4R
ME2
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
CXXC1
ST8SIA3
MEX3C
TMX3
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
MRO
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
SKA1
CCDC11
DOK6
RNF152
LINC00305
C18orf26
BOD1P
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
SNORA37
LOC100130522
LOC100131655
LOC100287225
LOC100505474
LOC100505549
LOC100505776
LOC100505817
MIR4529
MIR3591

Genes in Wide Peak

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

Table S48. Genes in bold are cancer genes as defined by The Sanger Institute: 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
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
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 3p21.31.

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

Genes
FHIT
BAP1
SETD2
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
HESX1
BSN
LIMD1
CCRL2
RRP9
CACNA2D2
VPRBP
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
RAD54L2
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
PTPN23
DNAH1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
QRICH1
PXK
FEZF2
DALRD3
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
SELK
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
ABHD14B
UCN2
ZNF502
RFT1
ACTR8
ZNF501
GPR62
FAM3D
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
CCDC12
PRICKLE2
C3orf67
KCTD6
KLHDC8B
DNAH12
PDE12
FAM116A
ALS2CL
TMIE
FBXW12
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
CCDC36
PRSS42
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR138-1
MIR191
TMEM89
IQCF6
C3orf78
MIR425
LOC644714
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
MIR548A2
MIR564
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
LOC100132146
BSN-AS2
PRSS46
LOC100287879
MIR1226
MIR711
MIR4271
MIR3938
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4443
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq27.1.

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
hsa-mir-448
hsa-mir-1911
hsa-mir-1264
hsa-mir-4329
AGTR2
ABCD1
SLC25A5
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CAPN6
CD40LG
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DCX
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
GLUD2
GRIA3
HCFC1
HMGB3
HPRT1
HTR2C
IDH3G
IDS
IGSF1
IL9R
IL13RA1
IL13RA2
IRAK1
L1CAM
LAMP2
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
NDUFA1
OCRL
PAK3
PLS3
PLXNB3
OPN1LW
RENBP
RPL10
RPL39
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
TDGF1P3
TRPC5
UBE2A
VBP1
XPNPEP2
ZIC3
ZNF75D
RNF113A
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
CUL4B
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
CXorf1
GPR50
RAB33A
ARHGEF6
MAGEC1
ZBTB33
MAMLD1
BCAP31
ODZ1
SPRY3
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
PGRMC1
TREX2
SLC6A14
SEPT6
ATP1B4
LDOC1
FAM127B
SRPK3
SNORA70
SNORA69
SNORD61
RBMX
HTATSF1
MCTS1
C1GALT1C1
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
LUZP4
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
WDR44
CXorf48
FAM70A
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45B
GABRQ
NKRF
MOSPD1
THOC2
KIAA1210
PDZD4
LRCH2
RAP2C
FAM3A
BCORL1
CXorf56
SPANXD
SPANXC
UPF3B
FUNDC2
PRRG3
BRCC3
NKAP
MAP7D3
LONRF3
ALG13
GPR101
CD99L2
H2AFB3
USP26
PHF6
RHOXF2
TMEM185A
SLITRK2
MGC16121
PNMA6A
FATE1
HS6ST2
FRMD7
KLHL13
CHRDL1
CXorf40A
FAM58A
MMGT1
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
RBMXL3
DOCK11
AMOT
CSAG1
FMR1NB
LOC158696
ARHGAP36
AKAP14
RHOXF1
NKAPP1
FAM122B
FAM122C
ZCCHC12
SPANXE
SPANXF1
CXorf61
SLC25A43
DDX26B
ZNF449
VMA21
CTAG1A
CT47A11
MAGEA2B
ATP11C
RP1-177G6.2
LOC286467
LINC00204B
DCAF12L2
ZCCHC16
LHFPL1
SOWAHD
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
LINC00086
DKFZp686D0853
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR448
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
CT47B1
CXorf69
LINC00087
CT47A7
MIR542
SNORA35
SNORA36A
SNORA56
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
CT45A2
MIR767
MIR766
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129520
LOC100129662
HSFX2
CXorf64
LOC100131434
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR1912
MIR1298
MIR320D2
MIR1277
MIR1911
MIR1264
SLC25A5-AS1
MIR718
MIR764
MIR2114
LOC100329135
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
MIR4329
HSFX1
LOC100506757
CT47A12
LOC100507404
MAGEA10-MAGEA5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.33.

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

Genes
CRLF2
P2RY8
hsa-mir-651
SLC25A6
STS
ARSD
ARSE
ARSF
ASMT
CSF2RA
IL3RA
KAL1
CD99
PRKX
SHOX
TBL1X
XG
GTPBP6
HDHD1
AKAP17A
PNPLA4
ASMTL
GYG2
ZBED1
MXRA5
VCX
PPP2R3B
VCX2
VCX3A
PLCXD1
NLGN4X
ASMTL-AS1
FAM9A
FAM9B
DHRSX
PPP2R3B-AS1
ARSH
LOC389906
CD99P1
VCX3B
MIR651
CXorf28
XGPY2
LINC00102
MIR3690
MIR4770
MIR4767

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.1.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
MLANA
GLDC
PTPRD
KDM4C
RANBP6
KIAA1432
ERMP1
TPD52L3
IL33
C9orf123
UHRF2
KIAA2026
MIR4665

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

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

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
POTED
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37

Genes in Wide Peak

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

Table S55. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CYLD
hsa-mir-3181
hsa-mir-1826
ADCY7
CBLN1
MMP2
PHKB
RBL2
SALL1
SIAH1
N4BP1
IRX5
DNAJA2
ZNF267
ZNF423
RPGRIP1L
ORC6
TP53TG3
TOX3
BRD7
HEATR3
VPS35
NOD2
PAPD5
AKTIP
FTO
IRX6
IRX3
SHCBP1
CHD9
ITFG1
NETO2
LONP2
GPT2
ABCC11
NKD1
MYLK3
ABCC12
C16orf78
ANKRD26P1
SNX20
LOC146481
CNEP1R1
LOC283914
SLC6A10P
C16orf87
LOC388276
LOC390705
FLJ26245
HERC2P4
UBE2MP1
LOC643714
LOC643802
CRNDE
LINC00273
TP53TG3C
LOC729264
TP53TG3B
LOC100130700
LOC100505619
LOC100507577
MIR548AE2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.1.

Table S56. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
BAI3
BCKDHB
BMP5
DST
CGA
CNR1
COL9A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
GABRR1
GABRR2
GCLC
HCRTR2
HTR1B
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
PRIM2
RNY4
ELOVL4
MAP3K7
TPBG
TTK
PTP4A1
RNGTT
TBX18
HMGN3
FHL5
BAG2
SNAP91
CASP8AP2
SYNCRIP
SLC35A1
FUT9
PNRC1
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
MDN1
UFL1
PHF3
ORC3
MTO1
IBTK
ZNF451
SENP6
SLC17A5
SNORD50A
FILIP1
TINAG
NDUFAF4
CYB5R4
UBE2J1
LGSN
RAB23
HMGCLL1
PHIP
AKIRIN2
LRRC1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
C6orf162
LYRM2
SNX14
FAM135A
KIAA1586
RRAGD
BACH2
SMAP1
C6orf164
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
COL21A1
SPACA1
SH3BGRL2
GJA10
C6orf7
UBE2CBP
MLIP
MRAP2
RWDD2A
MB21D1
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
PRSS35
LCA5
KHDRBS2
C6orf163
BEND6
FAM83B
DPPA5
EYS
GUSBP4
GJB7
SNHG5
C6orf147
GFRAL
KLHL31
MIR30A
MIR30C2
OOEP
MCART3P
TSG1
SNORD50B
KHDC1L
LOC100288198
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.1.

Table S57. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PRDM1
MYB
ROS1
TNFAIP3
STL
GOPC
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IMPG1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
ME1
MAP3K5
MYO6
NMBR
NT5E
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
RNY4
RPS12
SGK1
SIM1
SMPD2
ELOVL4
MAP3K7
TCF21
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
UTRN
STX7
PEX3
DDO
STX11
SNX3
RNGTT
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
TAAR2
TAAR3
HMGN3
MED23
FHL5
AKAP7
ATG5
TBPL1
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
SMPDL3A
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
HEY2
HEBP2
ORC3
BRD7P3
MTO1
ASF1A
CCDC28A
PNISR
IBTK
MOXD1
SENP6
FBXL4
SLC17A5
SNORD50A
PDE7B
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
HDDC2
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
UBE2J1
VTA1
HECA
COQ3
IL20RA
AHI1
PHIP
SOBP
AKIRIN2
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
ECHDC1
KCNQ5
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
SERINC1
HACE1
FAM135A
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
POPDC3
ALDH8A1
MICAL1
OR2A4
OGFRL1
FAM184A
MANEA
LINC00472
KHDC1
GPR63
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
ARMC2
RPF2
L3MBTL3
MCHR2
FAXC
GJA10
RTN4IP1
RSPO3
LTV1
USP45
REPS1
SLC22A16
C6orf7
UBE2CBP
KIAA1919
ARHGAP18
GTF3C6
MRAP2
RWDD2A
FAM54A
KLHL32
TMEM200A
MB21D1
NUS1
IL22RA2
C6orf192
SLC16A10
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
NCOA7
HINT3
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
LOC153910
ZC2HC1B
SAMD3
MGC34034
SLC2A12
LOC154092
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
OLIG3
TXLNB
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
MMS22L
FAM26E
MCM9
SCML4
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
TAAR6
SLC35D3
DPPA5
RSPH4A
ECT2L
EYS
C6orf58
GJB7
HMGA1P7
SNHG5
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
THEMIS
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
FLJ46906
MCART3P
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LINC00271
LOC100132735
LOC100287632
LOC100288198
NHEG1
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3668
MIR3662
LOC100506804
LOC100507203
LOC100507254
LOC100507462
LOC100507489
MIR4464
MIR4643
MIR4465

Genes in Wide Peak

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

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CLEC3A
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q12.

Table S59. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ATF1
CDK4
DDIT3
HOXC11
HOXC13
KRAS
NACA
MLL2
HMGA2
WIF1
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
hsa-mir-920
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APOF
AQP2
AQP5
AQP6
ARF3
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
CACNB3
CCNT1
CD63
CDK2
CNTN1
COL2A1
CS
CYP27B1
DGKA
DDX11
EIF4B
CELA1
ERBB3
B4GALNT1
BLOC1S1
GLI1
GNS
GPD1
GYS2
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IAPP
IFNG
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNJ8
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
LDHB
LRMP
LRP1
MARS
METTL1
MGST1
MIP
MMP19
MYL6
MYO1A
NAB2
NELL2
NFE2
SLC11A2
PA2G4
PCBP2
PDE3A
PDE1B
PFDN5
PFKM
PIK3C2G
PKP2
POU6F1
PPP1R1A
PRIM1
PRKAG1
PRPH
PTHLH
TWF1
RAB5B
RAP1B
RARG
RBMS2
RDH5
RECQL
RNY5
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
ST8SIA1
PMEL
SLCO1A2
SMARCC2
SMARCD1
SOX5
SP1
STAT2
STAT6
SUOX
TAC3
TARBP2
TMBIM6
TFCP2
VDR
WNT1
WNT10B
MAP3K12
TUBA1A
SSPN
AAAS
SOAT2
DYRK2
PPFIBP1
RDH16
NPFF
HSD17B6
ENDOU
TIMELESS
KRT75
SCAF11
SLC16A7
MED21
DDX23
SLC4A8
ESPL1
DAZAP2
KIAA0748
KIAA0528
ZBTB39
PAN2
USP15
TROAP
DNM1L
ABCC9
TSFM
CTDSP2
YAF2
RNF41
GDF11
TMEM5
CNPY2
TUBA1B
RAPGEF3
MCRS1
IPO8
DCTN2
SLCO1B1
AVIL
PTGES3
OS9
ATF7
BAZ2A
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
GPR182
COPZ1
R3HDM2
STK38L
FAIM2
MON2
DDN
TMEM194A
TBC1D30
ESYT1
TENC1
KCNH3
GRIP1
CBX5
ANP32D
SMUG1
LEMD3
PRPF40B
METTL7A
LETMD1
METTL21B
ZNF385A
FGFR1OP2
SNORD59A
GLS2
RND1
SLCO1B3
ORMDL2
TBK1
RACGAP1
SENP1
PDZRN4
IL22
DHH
GOLT1B
PLEKHA8P1
YARS2
IRAK4
ERGIC2
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
IL23A
HDAC7
TMBIM4
TM7SF3
GPR84
SLCO1C1
SLC38A2
PRR13
PLEKHA5
KANSL2
SLC38A4
C12orf35
CASC1
CCDC91
ETNK1
SLC35E3
KIF21A
SLC48A1
FAR2
LMBR1L
ASUN
IL26
CAND1
LMO3
CMAS
MDM1
NDUFA4L2
ARNTL2
NUP107
SMAGP
PPM1H
SRGAP1
KLHDC5
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
FAM60A
C12orf10
MRPS35
C12orf44
ARHGAP9
IKZF4
SLC26A10
SPATS2
CAPRIN2
TMEM106C
OBFC2B
BHLHE41
RPAP3
RERGL
PIP4K2C
FLJ13224
PYROXD1
DNAJC22
ADAMTS20
C12orf39
SLC38A1
CSRNP2
PUS7L
INHBE
TMTC1
RACGAP1P
FAM186B
TMEM117
LLPH
WIBG
SARNP
TUBA1C
ZC3H10
ALG10
SPRYD3
MFSD5
C12orf62
DNAJC14
ZCRB1
CCDC65
PLCZ1
LACRT
FMNL3
CERS5
XRCC6BP1
FAM113B
HELB
MARCH9
COQ10A
CAPZA3
KRT71
LARP4
SLC2A13
MBD6
ARHGEF25
C12orf56
AGAP2
DCD
MUCL1
LRRK2
FAM186A
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
FGD4
AEBP2
ASB8
MYL6B
KRT72
PRICKLE1
BCDIN3D
ALG10B
LINC00477
LYRM5
CPNE8
KRT80
C12orf66
IFLTD1
DENND5B
GRASP
KRT78
AMN1
DTX3
METTL7B
C12orf77
ANO6
ARID2
RPSAP52
STAC3
MSRB3
METTL20
OR6C74
OR6C3
LOC255411
LOC283332
LOC283335
ZNF740
RASSF3
OR6C6
ANKRD52
SLC39A5
SPRYD4
LOC283403
LOC283404
C12orf61
DPY19L2
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
FAM19A2
SLCO1B7
C12orf70
OVCH1
SYT10
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
KRT77
REP15
C12orf68
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR196A2
MIR26A2
H3F3C
DBX2
FLJ12825
TMEM198B
TSPAN11
OR9K2
MIR148B
HIGD1C
GLYCAM1
HNRNPA1P10
SNORA2A
SNORA2B
SNORA34
SNORD59B
MIR548C
MIR615
SKP1P2
C12orf71
SLC15A5
HOTAIR
MIR920
LOC100130776
LOC100233209
LOC100240734
LOC100240735
LOC100286844
MANSC4
LOC100287314
MIR1228
MIR1293
MIR1291
LOC100335030
SNORA70G
MIR4302
MIR548Z
LOC100506393
LOC100506451
LOC100506660
LOC100506844
LOC100507250
BLOC1S1-RDH5
MIR4701
MIR3974
MIR3198-2
MIR4698
LOC100652999

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p32.3.

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CDKN2C
FAF1
DMRTA2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

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

Arm-level results

Table 3. Get Full Table Arm-level significance table - 16 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	2121	0.24	0.646	0.739	0.19	-0.787	0.998
1q	1955	0.22	-0.182	1	0.21	-0.497	0.998
2p	924	0.12	-3.52	1	0.34	2.06	0.0657
2q	1556	0.09	-3.94	1	0.29	1.46	0.205
3p	1062	0.14	-3.23	1	0.24	-0.551	0.998
3q	1139	0.15	-2.9	1	0.25	-0.0588	0.872
4p	489	0.27	-0.243	1	0.23	-1.09	1
4q	1049	0.21	-1.25	1	0.23	-0.808	0.998
5p	270	0.36	1.98	0.256	0.18	-2.48	1
5q	1427	0.30	1.49	0.539	0.23	-0.454	0.998
6p	1173	0.28	0.715	0.73	0.34	2.17	0.0549
6q	839	0.24	-0.605	1	0.24	-0.605	0.998
7p	641	0.35	1.95	0.256	0.23	-1.16	1
7q	1277	0.28	0.838	0.73	0.18	-1.86	1
8p	580	0.28	0.264	0.932	0.30	0.545	0.574
8q	859	0.30	1.02	0.71	0.21	-1.29	1
9p	422	0.25	-0.686	1	0.43	3.98	0.000228
9q	1113	0.29	0.996	0.71	0.31	1.29	0.248
10p	409	0.12	-3.33	1	0.53	6.97	1.57e-11
10q	1268	0.05	-4.03	1	0.56	9.08	0
11p	862	0.12	-3.32	1	0.40	3.94	0.000236
11q	1515	0.10	-3.57	1	0.36	3.46	0.00135
12p	575	0.19	-2.13	1	0.32	1.29	0.248
12q	1447	0.12	-3.36	1	0.27	0.612	0.569
13q	654	0.10	-3.5	1	0.55	7.84	3.11e-14
14q	1341	0.30	1.4	0.539	0.36	2.86	0.00952
15q	1355	0.30	1.31	0.539	0.21	-0.927	0.998
16p	872	0.20	-1.6	1	0.34	2.01	0.0689
16q	702	0.11	-3.22	1	0.55	7.97	1.55e-14
17p	683	0.26	-0.383	1	0.29	0.612	0.569
17q	1592	0.23	-0.394	1	0.26	0.52	0.574
18p	143	0.20	-2.1	1	0.29	0.123	0.82
18q	446	0.14	-3.39	1	0.32	1.02	0.364
19p	995	0.29	0.858	0.73	0.20	-1.63	1
19q	1709	0.26	0.531	0.744	0.24	0.0712	0.82
20p	355	0.31	0.776	0.73	0.25	-0.894	0.998
20q	753	0.36	2.49	0.252	0.11	-3.89	1
21q	509	0.30	0.591	0.739	0.25	-0.675	0.998
22q	921	0.35	2.19	0.256	0.37	2.61	0.0182
Xq	1312	0.14	-2.49	1	0.45	5.81	2.47e-08

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/SARC-TP/9826883/GDAC_MergeDataFiles_9828975/SARC-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 169 Input Tumor Samples.

Tumor Sample Names
TCGA-DX-A1KU-01A-32D-A24M-01
TCGA-DX-A1KW-01A-22D-A24M-01
TCGA-DX-A1KX-01A-22D-A24M-01
TCGA-DX-A1KY-01A-11D-A24M-01
TCGA-DX-A1KZ-01A-11D-A24M-01
TCGA-DX-A1L0-01A-11D-A24M-01
TCGA-DX-A1L1-01A-11D-A24M-01
TCGA-DX-A1L2-01A-22D-A24M-01
TCGA-DX-A1L3-01A-11D-A24M-01
TCGA-DX-A1L4-01A-12D-A26F-01

Figure 3. Segmented copy number profiles in the input data

Output

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

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

Region Data

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

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.
Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').
Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

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

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

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

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)

[2] GISTIC version 1

[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)

[4] GISTIC version 2

[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)

[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)

[7] The Sanger Institute: Cancer Gene Census

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