SNP6 Copy number analysis (GISTIC2)
Sarcoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1MK6BJ3
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/C1MK6BJ3
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 150 tumor samples used in this analysis: 16 significant arm-level results, 20 significant focal amplifications, and 38 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 - 20 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 | 3.3985e-56 | 3.3985e-56 | chr12:69178021-69244387 | 1
1q24.3 | 4.4883e-16 | 4.4883e-16 | chr1:172019584-172206659 | 6
17p11.2 | 1.5968e-11 | 1.5968e-11 | chr17:11715684-20307058 | 112
1p32.1 | 2.9144e-08 | 2.9144e-08 | chr1:58611919-59952427 | 8
6q24.3 | 6.4834e-07 | 6.4834e-07 | chr6:148810209-149707665 | 4
19q12 | 0.00031201 | 0.00031201 | chr19:30245403-30326293 | 1
5p15.33 | 0.00034232 | 0.00034232 | chr5:1019815-1300024 | 6
6p21.1 | 0.0069043 | 0.0069043 | chr6:42316793-42577711 | 2
13q34 | 0.0074931 | 0.0074931 | chr13:113363456-114860943 | 23
19p13.2 | 0.0090243 | 0.0090243 | chr19:6882410-7309686 | 9
Xp21.1 | 0.020674 | 0.020674 | chrX:18774807-39883393 | 80
11q22.2 | 0.022684 | 0.022684 | chr11:101789694-102572619 | 9
3p11.2 | 0.033883 | 0.033883 | chr3:85487213-93736225 | 13
Xq21.2 | 0.050645 | 0.050645 | chrX:80178943-86473034 | 15
12p13.32 | 0.091471 | 0.091471 | chr12:4436678-5507248 | 12
8q21.12 | 0.11459 | 0.11459 | chr8:42932479-134030416 | 391
21q21.1 | 0.11459 | 0.11459 | chr21:16733940-17882027 | 2
7q31.1 | 0.18116 | 0.18116 | chr7:103951214-118059425 | 66
20q13.33 | 0.18861 | 0.18861 | chr20:51155482-63025520 | 160
17q24.3 | 0.23909 | 0.23909 | chr17:55638524-81195210 | 395

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 5p15.33.

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

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
MIR4635

Genes in Wide Peak

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

Table S8. 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 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 19p13.2.

Table S10. 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 Xp21.1.

Table S11. 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
CYBB
DMD
EIF1AX
EIF2S3
GK
MAGEB1
MAGEB2
MAGEB3
MAGEB4
OTC
PDHA1
PDK3
PHEX
PHKA2
POLA1
PPEF1
PRRG1
RPGR
RPS6KA3
SAT1
SMS
DYNLT3
TSPAN7
XK
ZFX
SRPX
PCYT1B
GPR64
PRDX4
IL1RAPL1
CNKSR2
ACOT9
SMPX
CXorf27
SH3KBP1
MBTPS2
FTHL17
MID1IP1
APOO
CXorf21
KLHL15
TMEM47
SYTL5
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
MAGEB16
ZNF645
FAM47A
MAGEB6
DDX53
FAM47B
CXorf22
FAM48B2
ARX
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
LOC286442
CXorf59
MAGEB18
LANCL3
DCAF8L2
MAP3K15
YY2
FAM47C
CXorf30
SCARNA23
LOC729609
FAM48B1
LOC100132163
SCARNA9L
MIR23C

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 3p11.2.

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

Genes
EPHA3
HTR1F
POU1F1
PROS1
CGGBP1
CHMP2B
ZNF654
ARL13B
CADM2
C3orf38
VGLL3
STX19
MIR4795

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 12p13.32.

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

Genes
FGF6
KCNA1
KCNA5
KCNA6
NDUFA9
FGF23
DYRK4
AKAP3
RAD51AP1
GALNT8
C12orf4
C12orf5

Genes in Wide Peak

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

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

Genes
COX6C
EXT1
MYC
PLAG1
TCEA1
NCOA2
CHCHD7
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
OSGIN2
CA1
CA2
CA3
CA8
CALB1
RUNX1T1
CDH17
CEBPD
CRH
CYP7A1
DECR1
DPYS
E2F5
EYA1
FABP4
FABP5
FNTA
GEM
NPBWR1
HAS2
HNF4G
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LYN
MATN2
MCM4
MMP16
MOS
MYBL1
NBN
NDUFB9
NOV
ODF1
TNFRSF11B
OPRK1
PDE7A
ENPP2
PENK
PMP2
POLR2K
POU5F1B
PKIA
PRKDC
PVT1
PEX2
RAB2A
RAD21
RP1
RPL7
RPL30
RPS20
SDC2
SDCBP
SNAI2
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TTPA
UBE2V2
COL14A1
UQCRB
YWHAZ
FZD6
NSMAF
RGS20
EIF3H
RIPK2
GGH
CPNE3
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
TTC35
RIMS2
ST18
TOX
MTSS1
PTDSS1
RB1CC1
KIAA0196
HHLA1
TRIB1
HRSP12
PGCP
LYPLA1
ARFGEF1
COLEC10
POP1
COPS5
WWP1
STMN2
RNF139
ZHX1
ZHX2
EFR3A
RRS1
SULF1
ZFPM2
HEY1
TRAM1
KIAA0146
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
C8orf71
RGS22
PTTG3P
SNORA72
SNORD54
PABPC1
KCNV1
STAU2
MTBP
BHLHE22
MRPS28
MRPL13
ATAD2
ASAP1-IT1
MRPL15
LRP12
RRM2B
ASAP1
MTERFD1
PI15
ZC2HC1A
PHF20L1
LACTB2
FAM82B
ZNF706
UBR5
FAM49B
AZIN1
ATP6V1H
OTUD6B
SNTG1
GDAP1
PDP1
CNGB3
ESRP1
IMPAD1
TMEM70
TRMT12
OXR1
WDYHV1
ARMC1
UBE2W
LAPTM4B
C8orf39
TMEM55A
CHD7
SYBU
INTS8
PAG1
GSDMC
C8orf44
JPH1
ENY2
CPA6
PRDM14
SNX16
NECAB1
SOX17
DEPTOR
ZBTB10
DSCC1
DERL1
EFCAB1
PLEKHF2
ZFAND1
ZFHX4
NIPAL2
CSPP1
BAALC
GRHL2
VCPIP1
PREX2
SLC25A32
TM7SF4
SLCO5A1
CRISPLD1
TATDN1
NACAP1
NCALD
SGK196
UTP23
TRIM55
C8orf76
NUDCD1
FAM83A
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
TMEM67
MTDH
CHMP4C
PKHD1L1
WDR67
HPYR1
TP53INP1
TGS1
MAL2
XKR4
CSMD3
FBXO32
SLC26A7
PCMTD1
CTHRC1
OSR2
C8orf34
ZNF572
FAM92A1
C8orf38
TMEM68
ABRA
TMEM71
ADHFE1
UBXN2B
PXDNL
DCAF4L2
RALYL
HGSNAT
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
TMEM74
FAM91A1
C8orf45
CLVS1
C8orf84
CNBD1
SLC30A8
SNX31
TMEM64
SDR16C5
C8orf47
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NSMCE2
C8orf83
DPY19L4
FBXO43
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
KLHL38
RSPO2
POTEA
SLC10A5
CA13
FAM150A
XKR9
LOC389676
RBM12B
LOC392232
GDF6
LOC401463
C8orf59
SAMD12
MIR124-2
FER1L6-AS1
FLJ39080
FLJ46284
FLJ42969
C8orf85
C8orf22
LINC00293
LINC00251
SAMD12-AS1
HAS2-AS1
ZNF704
C8orf69
SNHG6
SNORD87
LINC00535
UG0898H09
RAD21-AS1
FABP9
FABP12
FER1L6
MIR599
LOC727677
LOC728724
OC90
MIR875
LOC100127983
LOC100128126
TCF24
LOC100130155
LOC100130231
LOC100130298
LOC100130301
LRRC69
LOC100131726
LOC100132891
SBF1P1
LOC100192378
LOC100287846
REXO1L2P
LOC100288748
MIR1205
MIR1206
MIR1207
MIR1204
MIR2053
MIR2052
MIR1208
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3150B
MIR3610
LOC100505659
LOC100505676
LOC100505718
LOC100507117
LOC100507632
LOC100507651
C8orf44-SGK3
ZHX1-C8ORF76
MIR378D2
MIR4661
MIR4663
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 S17. 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 7q31.1.

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

Genes
MET
CAPZA2
CAV1
CAV2
CFTR
DLD
SLC26A3
GPR22
IFRD1
LAMB1
DNAJB9
NRCAM
SLC26A4
PIK3CG
PPP1R3A
PRKAR2B
SRPK2
SYPL1
WNT2
ST7
DOCK4
NAMPT
COG5
DUS4L
ZNF277
TFEC
LAMB4
TES
HBP1
MDFIC
PNPLA8
NAA38
GPR85
PUS7
LRRN3
MLL5
BCAP29
ANKRD7
RINT1
TMEM168
CBLL1
IMMP2L
CTTNBP2
ST7-AS1
ST7-AS2
ST7-OT3
FOXP2
ASZ1
C7orf60
C7orf66
THAP5
CCDC71L
ATXN7L1
CDHR3
LOC286002
C7orf53
ST7-OT4
LHFPL3
LOC401397
EIF3IP1
LOC645591
LOC723809
EFCAB10
LOC100216545
LOC100216546
MIR3666

Genes in Wide Peak

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

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

Genes
GNAS
SS18L1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
ATP5E
BMP7
CDH4
CHRNA4
COL9A3
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
NPBWR2
KCNQ2
LAMA5
MC3R
MYT1
NTSR1
OPRL1
PCK1
PFDN4
PPP1R3D
PSMA7
PTK6
RPS21
SRMS
AURKA
TAF4
TCEA2
TFAP2C
TPD52L2
ZNF217
RAE1
BCAS1
STX16
TNFRSF6B
VAPB
OSBPL2
ARFRP1
RGS19
SYCP2
TCFL5
ADRM1
OGFR
DIDO1
HRH3
SPO11
PRPF6
GTPBP5
GMEB2
SLCO4A1
STMN3
SLMO2
TH1L
C20orf43
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
C20orf20
PPP4R1L
RBM38
ARFGAP1
DOK5
SLC2A4RG
PMEPA1
CASS4
RAB22A
ZNF512B
COL20A1
CDH26
SLC17A9
LOC63930
FAM217B
C20orf195
PPDPF
BIRC7
NPEPL1
DNAJC5
TUBB1
ZBP1
CABLES2
ZGPAT
PRIC285
FAM210B
PHACTR3
BHLHE23
NKAIN4
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
GCNT7
CBLN4
CTCFL
SAMD10
ABHD16B
LINC00266-1
C20orf151
LOC149773
GNAS-AS1
LSM14B
APCDD1L
C20orf201
FAM209A
C20orf166-AS1
LINC00176
C20orf197
LOC284757
FAM209B
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
MIR647
HAR1A
HAR1B
UCKL1-AS1
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
DPH3P1
LINC00029
LOC100144597
FLJ16779
MIR1914
MIR1257
MIR4325
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 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
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
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
LPO
MAFG
MAP3K3
MPO
TRIM37
NPTX1
P4HB
PDE6G
PECAM1
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
VEZF1
EPX
AXIN2
PPM1D
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
BZRAP1
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
PPM1E
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
SDK2
FAM20A
BCAS3
TMEM104
RNF43
MKS1
C17orf80
CCDC40
WIPI1
SMG8
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
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
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
DYNLL2
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
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
LRRC37A3
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
MIR142
MIR21
MIR301A
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
MIR454
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3678
MIR3615
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4729
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515

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 - 38 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 | 8.4312e-37 | 8.4312e-37 | chr13:48833767-49064807 | 2
17p13.1 | 5.1685e-30 | 5.1685e-30 | chr17:7549751-7593565 | 2
Xq21.1 | 1.6484e-16 | 6.8567e-16 | chrX:76710176-77102528 | 1
9p21.3 | 6.3174e-16 | 2.342e-12 | chr9:21865498-22448737 | 4
1p36.32 | 2.8973e-11 | 5.5641e-11 | chr1:1-5923787 | 115
2q37.3 | 1.4645e-14 | 3.1392e-09 | chr2:242162274-243199373 | 17
19q13.43 | 3.1159e-09 | 3.1392e-09 | chr19:58400307-59128983 | 34
10p15.3 | 3.8849e-09 | 3.8451e-09 | chr10:1-857150 | 4
19p13.3 | 2.0518e-08 | 2.0518e-08 | chr19:1-390340 | 9
4q35.1 | 3.6539e-08 | 3.5686e-08 | chr4:178911874-191154276 | 64
11p15.5 | 5.1499e-08 | 4.8619e-08 | chr11:1-496996 | 19
11q24.3 | 1.5018e-07 | 1.4773e-07 | chr11:126870419-129248060 | 9
10q23.31 | 1.3708e-06 | 1.3708e-06 | chr10:89617158-90034038 | 2
1q44 | 1.2596e-05 | 1.3025e-05 | chr1:208416154-249250621 | 319
9q34.3 | 3.0019e-05 | 3.122e-05 | chr9:139435477-141213431 | 79
17q25.3 | 3.2104e-06 | 3.3039e-05 | chr17:80443432-80617015 | 2
17q11.2 | 2.0856e-05 | 0.0002187 | chr17:29326736-30180957 | 11
2p25.3 | 0.0011736 | 0.0011736 | chr2:1-27804113 | 173
12p13.1 | 0.0010528 | 0.001532 | chr12:1-18417317 | 255
8p23.3 | 0.0016437 | 0.0016437 | chr8:1-6262191 | 15
7q36.3 | 0.0027305 | 0.0027974 | chr7:154685874-159138663 | 31
6q14.1 | 0.011323 | 0.010993 | chr6:64422619-111983004 | 184
6p25.1 | 0.019738 | 0.020012 | chr6:1-24128888 | 118
14q24.1 | 0.020614 | 0.020786 | chr14:68198508-69288431 | 3
21q22.3 | 0.015855 | 0.022064 | chr21:47427840-47609222 | 3
22q13.31 | 0.040012 | 0.039943 | chr22:45095899-51304566 | 86
9p24.3 | 7.3359e-06 | 0.04141 | chr9:1-2018113 | 11
2q37.3 | 3.5145e-12 | 0.046302 | chr2:230575320-243199373 | 159
3p21.31 | 0.045936 | 0.046302 | chr3:44372147-65340907 | 281
16q12.1 | 0.052306 | 0.050431 | chr16:31772318-55368634 | 61
Xq27.1 | 0.021609 | 0.054915 | chrX:111697047-155270560 | 384
3q29 | 0.10533 | 0.10741 | chr3:135982636-198022430 | 386
Xp22.32 | 0.10913 | 0.10741 | chrX:1-9694455 | 47
12q12 | 0.093156 | 0.13202 | chr12:33046522-39688977 | 4
21q11.2 | 0.15977 | 0.16468 | chr21:1-23095995 | 41
18q23 | 0.2165 | 0.2165 | chr18:19449367-78077248 | 243
1p32.3 | 0.11852 | 0.23289 | chr1:50879767-51569162 | 3
15q11.2 | 0.23102 | 0.23289 | chr15:1-56120131 | 403

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

Table S22. 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 S23. 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 S24. 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 S25. 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 2q37.3.

Table S26. 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 19q13.43.

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

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

Genes in Wide Peak

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

Table S28. 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 19p13.3.

Table S29. 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 4q35.1.

Table S30. 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 11p15.5.

Table S31. 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 11q24.3.

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

Genes
FLI1
ETS1
KCNJ1
KCNJ5
ARHGAP32
TP53AIP1
C11orf45
KIRREL3-AS3
LOC100507392

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

Table S34. 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 S35. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-602
hsa-mir-4292
hsa-mir-126
ABCA2
C8G
CACNA1B
ENTPD2
FUT7
GRIN1
PTGDS
TRAF2
SSNA1
EDF1
CLIC3
TUBB4B
AGPAT2
NOXA1
MAN1B1
COBRA1
NELF
NDOR1
PHPT1
ANAPC2
DPP7
EGFL7
FBXW5
C9orf167
EXD3
C9orf86
NPDC1
MRPL41
EHMT1
KIAA1984
SNHG7
TMEM141
C9orf37
SAPCD2
UAP1L1
ARRDC1
WDR85
TMEM203
ZMYND19
LCN8
FAM69B
SLC34A3
MAMDC4
LCN6
LCN12
C9orf142
TPRN
PNPLA7
C9orf169
ENTPD8
LCN15
C9orf172
LRRC26
LCNL1
C9orf139
FAM166A
MIR126
LCN10
C9orf173
NRARP
FLJ40292
TUBBP5
RNF224
SNORA17
SNORA43
MIR602
RNF208
LOC100128593
LOC100129722
LOC100131193
FAM157B
LOC100289341
MIR4292
MIR3621
MIR4674
MIR4479

Genes in Wide Peak

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

Table S36. 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 17q11.2.

Table S37. 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 2p25.3.

Table S38. 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 S39. 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 8p23.3.

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

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53
MIR596

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
EN2
MNX1
HTR5A
INSIG1
PTPRN2
SHH
VIPR2
UBE3C
DNAJB6
PAXIP1
NCAPG2
WDR60
ESYT2
LMBR1
LINC00244
NOM1
C7orf13
RNF32
LOC154822
RBM33
LOC202781
CNPY1
LOC285889
MIR153-2
LOC645249
MIR595
LOC100128264
LOC100132707
LOC100506585

Genes in Wide Peak

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

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
FOXO3
GABRR1
GABRR2
GPR6
GRIK2
HTR1B
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
UFL1
ORC3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
CYB5R4
C6orf203
CDC40
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
MB21D1
SLC16A10
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
LACE1
MMS22L
SCML4
CEP57L1
PPIL6
DPPA5
EYS
GJB7
SNHG5
C6orf147
LINC00222
LIN28B
MIR30A
MIR30C2
OOEP
MCART3P
GSTM2P1
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
C6orf186
KHDC1L
LOC100130890
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

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

Table S43. 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
HIVEP1
ID4
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
NOL7
FAM8A1
TMEM14C
GFOD1
ELOVL2
CDKAL1
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
CCDC90A
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
MBOAT1
HDGFL1
C6orf195
PIP5K1P1
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
RNF144B
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
NHLRC1
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 14q24.1.

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

Genes
ZFP36L1
RAD51B
ZFYVE26

Genes in Wide Peak

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

Table S45. 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 22q13.31.

Table S46. 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 9p24.3.

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

Genes
hsa-mir-1302-9
DMRT1
FOXD4
DMRT2
KANK1
CBWD1
DMRT3
DOCK8
C9orf66
FAM138C
WASH1

Genes in Wide Peak

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

Table S48. 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
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
HTR2B
SP110
INPP5D
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SNORD20
SAG
SP100
SPP2
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
SH3BP4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
C2orf54
ARMC9
EFHD1
ILKAP
ITM2C
ING5
MGC16025
B3GNT7
SP140L
AGAP1
TWIST2
DIS3L2
NEU4
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
C2orf57
TIGD1
LOC200772
C2orf72
CXXC11
DUSP28
ESPNL
ECEL1P2
LOC348761
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR4269
UBE2F-SCLY
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

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
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
C3orf62
TMEM110
PRSS45
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
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 16q12.1.

Table S50. 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
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 Xq27.1.

Table S51. 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
CD40LG
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
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
PLS3
PLXNB3
OPN1LW
RENBP
RPL10
RPL39
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
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
GPR101
CD99L2
H2AFB3
USP26
PHF6
RHOXF2
TMEM185A
SLITRK2
MGC16121
PNMA6A
FATE1
HS6ST2
FRMD7
KLHL13
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
LHFPL1
SOWAHD
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
LINC00086
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
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 3q29.

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

Genes
BCL6
FOXL2
EIF4A2
ETV5
LPP
MLF1
PIK3CA
SOX2
TFRC
GMPS
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
AADAC
ACTL6A
AGTR1
AHSG
APOD
ATP1B3
ATR
BCHE
BDH1
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
GYG1
HRG
HES1
IL1RAP
IL12A
KNG1
KPNA4
TM4SF1
MBNL1
MFI2
MME
MUC4
NCK1
NDUFB5
OPA1
CLDN11
P2RY1
PAK2
PCYT1A
PFN2
SERPINI1
SERPINI2
PIK3CB
PLD1
PLOD2
PLS1
PLSCR1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
RFC4
SNORA63
RPL35A
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
HLTF
SSR3
SST
TERC
TFDP2
THPO
SEC62
TM4SF4
TRPC1
CLRN1
ZIC1
KCNAB1
FXR1
SOX14
TP63
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
SLC33A1
COPB2
ADIPOQ
CHST2
RNF7
KIAA0226
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
TNK2
ALG3
KCNMB2
STAG1
IGF2BP2
CLDN16
PDCD10
RNF13
MRAS
SLITRK3
NLGN1
NCBP2
PLCH1
TNIK
MCF2L2
ATP11B
U2SURP
VPS8
ACAP2
ARMC8
WWTR1
TIPARP
UBXN7
ARHGEF26
PCOLCE2
GPR160
FETUB
LAMP3
KCNMB3
SERP1
GOLIM4
GPR171
SCHIP1
NMD3
COMMD2
A4GNT
DBR1
ZNF639
CLDN18
RSRC1
PEX5L
SELT
DNAJB11
P2RY13
IL20RB
GPR87
DCUN1D1
XRN1
KLHL24
PIGX
TBCCD1
FAIM
SLC25A36
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
SUCNR1
MCCC1
LXN
MRPS22
CCNL1
PLSCR2
PLSCR4
HRASLS
MRPL47
NCEH1
IFT80
SLC7A14
SENP2
GNB4
BPESC1
CLSTN2
RTP4
MAGEF1
ZMAT3
MFSD1
FNDC3B
P2RY12
ATP13A3
VEPH1
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
PIGZ
CEP70
TMEM22
ESYT3
SPATA16
EIF2A
B3GNT5
ZIC4
IQCG
ATP13A4
FYTTD1
HPS3
ARPM1
MGC2889
LRCH3
CEP19
GFM1
LMLN
KLHL6
VWA5B2
TMEM41A
SPSB4
ACPL2
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
FAM194A
GRK7
TMEM207
RTP1
PISRT1
TTC14
PPM1L
WDR49
LRRC34
MB21D2
XXYLT1
C3orf55
C3orf79
CCDC50
PYDC2
LOC152217
SPTSSB
RNF168
DHX36
HTR3C
DZIP1L
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
LOC201651
C3orf58
SENP5
LOC220729
ZBTB38
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
GK5
UTS2D
SLC9A9
HTR3E
IGSF10
C3orf33
C3orf70
TPRG1
TRIM59
TRIM42
CCDC39
LOC339894
LOC339926
LPP-AS2
LRRIQ4
SAMD7
AADACL2
GPR149
PAQR9
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
ANKRD18DP
NMNAT3
LRRC33
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
SNORD2
SNORA4
TMEM14E
LOC646168
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
IQCJ
SCARNA7
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
PRR23A
LOC730091
MIR922
MIR944
LOC100128023
WWTR1-AS1
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
TIPARP-AS1
LOC100289361
MIR1248
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100505687
MFI2-AS1
LOC100507086
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.32.

Table S53. 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 12q12.

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

Genes
ALG10
ALG10B
CPNE8
SYT10

Genes in Wide Peak

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

Table S55. 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 18q23.

Table S56. Genes in bold are cancer genes as defined by The Sanger Institute: 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
AQP4
ATP5A1
CDH2
CDH7
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GATA6
GRP
LAMA3
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MEP1B
MYO5B
NARS
NFATC1
NPC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RBBP8
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TAF4B
TCF4
TTR
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
RIOK3
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
ZNF271
TXNL4A
MAPRE2
POLI
ADNP2
TRAPPC8
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
CABYR
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
C18orf8
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
RPRD1A
ZNF532
ELP2
IMPACT
ELAC1
ZNF407
CNDP2
CELF4
KIAA1328
KLHL14
KIAA1468
EPG5
HRH4
CTAGE1
FAM59A
CCDC102B
RBFA
PQLC1
FHOD3
CCDC68
ASXL3
NETO1
KATNAL2
CHST9
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
TMEM241
SERPINB12
SERPINB11
SEC11C
CABLES1
DSEL
OSBPL1A
HAUS1
ALPK2
LOXHD1
INO80C
TTC39C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
MCART2
DSG4
CHST9-AS1
ANKRD29
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
ZNF396
KCTD1
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
C18orf34
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
MIR187
HSBP1L1
WBP11P1
RNF165
C18orf32
KC6
LOC643542
C18orf63
LOC647946
SCARNA17
SNORA37
LOC728606
TCEB3CL
LOC729950
ZSCAN30
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR302F
MIR320C2
MIR1539
MIR4319
MIR4318
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4741
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744
LOC100652770

Genes in Wide Peak

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

Table S57. 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 S58. 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
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
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 | 0.352 | 0.853 | 0.21 | -0.484 | 1
1q | 1955 | 0.23 | 0.0502 | 0.96 | 0.21 | -0.445 | 1
2p | 924 | 0.15 | -2.68 | 1 | 0.36 | 2.41 | 0.0286
2q | 1556 | 0.10 | -3.45 | 1 | 0.30 | 1.59 | 0.173
3p | 1062 | 0.12 | -3.49 | 1 | 0.24 | -0.648 | 1
3q | 1139 | 0.13 | -3.15 | 1 | 0.25 | -0.144 | 0.969
4p | 489 | 0.25 | -0.576 | 1 | 0.24 | -1.03 | 1
4q | 1049 | 0.20 | -1.5 | 1 | 0.24 | -0.562 | 1
5p | 270 | 0.38 | 2.41 | 0.16 | 0.15 | -2.93 | 1
5q | 1427 | 0.30 | 1.48 | 0.467 | 0.20 | -1.22 | 1
6p | 1173 | 0.27 | 0.441 | 0.853 | 0.31 | 1.37 | 0.245
6q | 839 | 0.24 | -0.621 | 1 | 0.22 | -1.24 | 1
7p | 641 | 0.35 | 1.99 | 0.311 | 0.24 | -0.853 | 1
7q | 1277 | 0.28 | 0.829 | 0.71 | 0.18 | -1.86 | 1
8p | 580 | 0.28 | 0.123 | 0.96 | 0.27 | -0.027 | 0.929
8q | 859 | 0.29 | 0.502 | 0.853 | 0.21 | -1.34 | 1
9p | 422 | 0.25 | -0.704 | 1 | 0.42 | 3.53 | 0.00119
9q | 1113 | 0.30 | 0.921 | 0.71 | 0.30 | 1.07 | 0.353
10p | 409 | 0.14 | -2.84 | 1 | 0.50 | 5.87 | 2.13e-08
10q | 1268 | 0.06 | -3.82 | 1 | 0.54 | 8 | 2.66e-14
11p | 862 | 0.14 | -2.75 | 1 | 0.42 | 3.98 | 0.000231
11q | 1515 | 0.12 | -2.96 | 1 | 0.36 | 2.99 | 0.00626
12p | 575 | 0.17 | -2.52 | 1 | 0.32 | 1.12 | 0.352
12q | 1447 | 0.10 | -3.74 | 1 | 0.26 | 0.308 | 0.798
13q | 654 | 0.09 | -3.48 | 1 | 0.52 | 6.77 | 8.37e-11
14q | 1341 | 0.29 | 0.984 | 0.71 | 0.37 | 2.99 | 0.00626
15q | 1355 | 0.31 | 1.58 | 0.452 | 0.23 | -0.616 | 1
16p | 872 | 0.22 | -0.966 | 1 | 0.34 | 1.92 | 0.0905
16q | 702 | 0.11 | -3.15 | 1 | 0.54 | 7.09 | 1.35e-11
17p | 683 | 0.28 | 0.107 | 0.96 | 0.29 | 0.408 | 0.759
17q | 1592 | 0.26 | 0.386 | 0.853 | 0.25 | 0.226 | 0.822
18p | 143 | 0.23 | -1.42 | 1 | 0.29 | 0.0528 | 0.912
18q | 446 | 0.17 | -2.6 | 1 | 0.32 | 1.01 | 0.368
19p | 995 | 0.32 | 1.39 | 0.469 | 0.18 | -1.86 | 1
19q | 1709 | 0.26 | 0.639 | 0.804 | 0.21 | -0.657 | 1
20p | 355 | 0.32 | 1.01 | 0.71 | 0.24 | -1.05 | 1
20q | 753 | 0.37 | 2.6 | 0.16 | 0.11 | -3.55 | 1
21q | 509 | 0.31 | 0.796 | 0.71 | 0.24 | -0.846 | 1
22q | 921 | 0.34 | 1.77 | 0.388 | 0.39 | 2.95 | 0.00629
Xq | 1312 | 0.15 | -2.15 | 1 | 0.47 | 5.8 | 2.6e-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/8021658/GDAC_MergeDataFiles_8024521/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 150 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:

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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