SNP6 Copy number analysis (GISTIC2)
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C15Q4TGK
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C15Q4TGK
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.19 (Firehose task version: 125).

Summary

There were 494 tumor samples used in this analysis: 18 significant arm-level results, 1 significant focal amplifications, and 32 significant focal deletions were found.

Results
Focal results

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

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
Xq22.3 | 2.6187e-16 | 2.6187e-16 | chrX:108537285-108552899 | 0 [GUCY2F]

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

Table 2. Get Full Table Deletions Table - 32 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
1q24.2 | 0.011519 | 0.011519 | chr1:168044896-168149500 | 1
6q22.31 | 0.011519 | 0.011519 | chr6:123955968-125232805 | 1
13q14.3 | 0.011519 | 0.011519 | chr13:43424188-88326176 | 137
Xq22.3 | 0.011519 | 0.011519 | chrX:107872289-108781115 | 2
20p12.1 | 0.016287 | 0.015414 | chr20:14302876-16555385 | 4
10q21.2 | 0.011519 | 0.019466 | chr10:61122180-61718254 | 3
16q23.3 | 0.025435 | 0.025209 | chr16:82658729-90354753 | 103
22q13.1 | 0.02785 | 0.03017 | chr22:39712315-39797177 | 3
22q13.31 | 0.030991 | 0.031604 | chr22:47571204-48018269 | 1
8p23.2 | 0.036801 | 0.035167 | chr8:1986591-6269441 | 3
8q24.22 | 0.04957 | 0.04957 | chr8:56679786-146364022 | 492
10q23.31 | 0.011519 | 0.04957 | chr10:63660611-108925515 | 407
2q35 | 0.055659 | 0.055659 | chr2:213861165-243199373 | 283
22q13.2 | 0.06321 | 0.059843 | chr22:43536127-43814456 | 3
16p13.3 | 0.083843 | 0.084842 | chr16:5129162-8624050 | 3
22q13.32 | 0.079435 | 0.084842 | chr22:48668761-51304566 | 46
8p12 | 0.091417 | 0.099341 | chr8:31031189-32605364 | 1
19p13.2 | 0.12163 | 0.12163 | chr19:1-19627981 | 626
7q34 | 0.13738 | 0.13738 | chr7:140405575-140706707 | 1
8p22 | 0.1371 | 0.13738 | chr8:13416667-14713213 | 3
21q21.1 | 0.13738 | 0.13738 | chr21:19257718-19640557 | 1
5q35.1 | 0.14618 | 0.14618 | chr5:169799676-170210996 | 2
11p15.1 | 0.15233 | 0.14618 | chr11:20676254-22216204 | 1
18p11.21 | 0.14508 | 0.14618 | chr18:12986917-13225199 | 1
5p15.2 | 0.18258 | 0.18258 | chr5:9639412-13956214 | 11
15q25.3 | 0.19064 | 0.19064 | chr15:86838498-88151657 | 2
Xq22.1 | 0.19064 | 0.19064 | chrX:96134519-100418234 | 14
13q12.3 | 0.011519 | 0.19687 | chr13:20792419-32875762 | 80
2p23.1 | 0.21743 | 0.21157 | chr2:29280792-37376313 | 37
7q22.3 | 0.22327 | 0.21157 | chr7:106673884-116850979 | 43
17p13.1 | 0.23067 | 0.21157 | chr17:1-9812234 | 267
19q12 | 0.21157 | 0.21157 | chr19:30202912-30414571 | 1
9p21.3 | 0.25536 | 0.2505 | chr9:1-141213431 | 983
18q22.2 | 0.25127 | 0.2505 | chr18:1-78077248 | 342

Genes in Wide Peak

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

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

Genes
GPR161

Genes in Wide Peak

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

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

Genes
NKAIN2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
GUCY2F
IRS4

Genes in Wide Peak

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

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

Genes
FLRT3
KIF16B
MACROD2
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
CCDC6
SLC16A9
M1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
SYNGR1
SNORD43
RNU86

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

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

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

Genes
MYOM2
CSMD1
LOC100287015

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.2.

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

Genes
TSPO
TTLL12
SCUBE1

Genes in Wide Peak

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

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

Genes
RBFOX1
FAM86A
TMEM114

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
NRG1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
BRAF

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p22.

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

Genes
hsa-mir-383
C8orf48
MIR383

Genes in Wide Peak

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

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

Genes
CHODL

Genes in Wide Peak

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

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

Genes
KCNMB1
KCNIP1

Genes in Wide Peak

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

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

Genes
NELL1

Genes in Wide Peak

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

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

Genes
CEP192

Genes in Wide Peak

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

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

Genes
CTNND2
DAP
DNAH5
MARCH6
CCT5
ROPN1L
FAM173B
CMBL
LOC285692
TAG
ANKRD33B

Genes in Wide Peak

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

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

Genes
LINC00052
LOC727915

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ALK
hsa-mir-558
LTBP1
VIT
EIF2AK2
SPAST
SRD5A2
STRN
XDH
FEZ2
RASGRP3
FAM98A
EHD3
MEMO1
CRIM1
YPEL5
HEATR5B
TTC27
SLC30A6
BIRC6
NLRC4
GALNT14
CLIP4
LBH
YIPF4
DPY30
CAPN13
MYADML
LCLAT1
CCDC75
LINC00486
C2orf71
CAPN14
MIR558
LOC100271832
LOC100288911
MIR4765

Genes in Wide Peak

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

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

Genes
MET
CAPZA2
CAV1
CAV2
DLD
SLC26A3
GPR22
IFRD1
LAMB1
DNAJB9
NRCAM
SLC26A4
PPP1R3A
PRKAR2B
DOCK4
COG5
DUS4L
ZNF277
TFEC
LAMB4
TES
HBP1
MDFIC
PNPLA8
GPR85
LRRN3
BCAP29
TMEM168
CBLL1
IMMP2L
ST7-AS1
ST7-AS2
ST7-OT3
FOXP2
C7orf60
C7orf66
THAP5
LOC286002
C7orf53
ST7-OT4
LOC401397
EIF3IP1
MIR3666

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

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

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

Genes
ABL1
FANCC
FANCG
GNAQ
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
hsa-mir-873
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
ABCA1
ABCA2
ABO
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
ANXA2P2
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
TNFSF8
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CELP
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
MLANA
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
GGTA1P
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
IL11RA
INSL4
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RMRP
RORB
RPL7A
RPL12
RPS6
RXRA
CCL19
CCL21
SH3GL2
SHB
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
UGCG
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
RGP1
TRIM14
MELK
RUSC2
PPP1R26
SEC16A
ZBTB5
KIAA0020
TNFSF15
PTBP3
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
PSIP1
INSL6
SLC2A6
PTENP1
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA1045
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
PCA3
AK3
EXOSC3
FAM108B1
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
C9orf11
TBC1D13
FAM22F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
C9orf167
CNTLN
TEX10
LPPR1
KIAA1797
UBE2R2
EXD3
FAM206A
C9orf95
STX17
NOL8
C9orf68
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDC37L1
DENND4C
C9orf86
CDK5RAP2
UBAP2
C9orf46
CBWD1
KLHL9
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KIAA1161
KCNT1
KIAA1432
BDAG1
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
DMRT3
PRDM12
NAA35
DMRTA1
SLC28A3
CARD9
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
MRPL41
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOB3B
C9orf82
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
FAM214B
GKAP1
PDCD1LG2
AKNA
MIR600HG
URM1
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
PRRC2B
PPAPDC3
GLIS3-AS1
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
TPD52L3
WDR34
SAPCD2
C9orf69
LRSAM1
IL33
C9orf123
C9orf30
UAP1L1
MCART1
MRRF
RBM18
ARRDC1
WDR85
ADAMTSL1
FP588
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19P
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf66
LINC00032
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC39B
FAM201A
RG9MTD3
TTC16
LOC158257
FAM120AOS
FAM154A
LINC00475
FREM1
KIAA2026
LOC158376
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
C9orf96
KCNV2
OLFML2A
C9orf71
QSOX2
GLIS3
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
C9orf93
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
FAM205A
LINC00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
TPRN
LOC286297
TUSC1
LINC00256A
FAM78A
LURAP1L
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
IFNE
ZDHHC21
ACER2
LOC340508
LOC340515
GPR144
FAM75D5
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
GLT6D1
ENHO
AQP7P1
PTAR1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
KGFLP1
LOC389705
FAM205B
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
C9orf128
OR13J1
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FLJ35024
FLJ41200
PTPLAD2
LOC401497
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR101-2
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR31
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC415056
LOC440173
LOC440896
FLJ35282
SUGT1P1
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
ANKRD18B
LOC441461
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
MIR31HG
LOC572558
MIR491
PGM5P2
MIR455
NRON
LOC642236
FAM75A2
FAM75A4
LOC642929
FAM163B
FLJ40292
TUBBP5
RNF224
LOC643648
CBWD6
FAM75C2
HRCT1
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM138C
SCARNA8
SNORA17
SNORA43
SNORD62B
MSMP
SNORD90
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
CDKN2B-AS1
SNORD121A
SNORD121B
C9orf146
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
UNQ6494
LOC100129250
LOC100129316
LOC100129722
LOC100130954
LOC100131193
LOC100132077
LOC100132352
FAM157B
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
LINC00092
LOC100272217
LOC100286938
WASH1
LOC100288842
LOC100289019
LOC100289341
MIR548H3
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3152
MIR3154
MIR2861
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3621
MIR3910-1
MIR3689A
MIR3911
MIR3910-2
MIR3689B
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506422
LOC100506599
LOC100506710
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4667
MIR4473
MIR4669
MIR4673
MIR3960
MIR4540
MIR4665
MIR4475
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4670
MIR4672
MIR4474
MIR4476
MIR3689E
MIR4479

Genes in Wide Peak

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

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

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

Arm-level results

Table 3. Get Full Table Arm-level significance table - 18 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.01 | -1.29 | 0.994 | 0.01 | -1.29 | 0.995
1q | 1955 | 0.05 | 7.15 | 1.71e-11 | 0.00 | -1.63 | 0.995
2p | 924 | 0.00 | -1.74 | 0.994 | 0.02 | 1.4 | 0.645
2q | 1556 | 0.00 | -2.11 | 0.994 | 0.02 | 1.06 | 0.822
3p | 1062 | 0.01 | -1.36 | 0.994 | 0.00 | -1.76 | 0.995
3q | 1139 | 0.00 | -1.75 | 0.994 | 0.01 | -1.36 | 0.995
4p | 489 | 0.01 | -0.616 | 0.994 | 0.00 | -2.18 | 0.995
4q | 1049 | 0.01 | -0.574 | 0.994 | 0.00 | -2.15 | 0.995
5p | 270 | 0.04 | 5.63 | 1.79e-07 | 0.00 | -2.14 | 0.995
5q | 1427 | 0.03 | 4.23 | 7.75e-05 | 0.00 | -2.5 | 0.995
6p | 1173 | 0.00 | -1.75 | 0.994 | 0.01 | -1.36 | 0.995
6q | 839 | 0.00 | -2.16 | 0.994 | 0.01 | -0.195 | 0.995
7p | 641 | 0.04 | 4.5 | 3.32e-05 | 0.00 | -2.53 | 0.995
7q | 1277 | 0.04 | 5.4 | 4.44e-07 | 0.00 | -2.5 | 0.995
8p | 580 | 0.01 | -0.201 | 0.994 | 0.01 | -0.982 | 0.995
8q | 859 | 0.01 | 0.218 | 0.919 | 0.01 | -0.958 | 0.995
9p | 422 | 0.01 | -1.34 | 0.994 | 0.04 | 4.5 | 4.53e-05
9q | 1113 | 0.01 | -0.872 | 0.994 | 0.05 | 6.61 | 3.88e-10
10p | 409 | 0.00 | -1.78 | 0.994 | 0.01 | -0.225 | 0.995
10q | 1268 | 0.00 | -1.74 | 0.994 | 0.01 | -0.553 | 0.995
11p | 862 | 0.01 | -0.163 | 0.994 | 0.01 | 0.229 | 0.995
11q | 1515 | 0.01 | -0.502 | 0.994 | 0.02 | 1.08 | 0.822
12p | 575 | 0.03 | 2.93 | 0.00677 | 0.00 | -2.14 | 0.995
12q | 1447 | 0.03 | 3.05 | 0.00514 | 0.00 | -2.1 | 0.995
13q | 654 | 0.01 | -0.548 | 0.994 | 0.03 | 2.58 | 0.0496
14q | 1341 | 0.02 | 1.84 | 0.0945 | 0.00 | -2.12 | 0.995
15q | 1355 | 0.00 | -2.53 | 0.994 | 0.01 | 0.24 | 0.995
16p | 872 | 0.03 | 3.36 | 0.00191 | 0.00 | -2.13 | 0.995
16q | 702 | 0.03 | 2.56 | 0.019 | 0.00 | -1.74 | 0.995
17p | 683 | 0.03 | 3.8 | 0.000419 | 0.02 | 0.669 | 0.995
17q | 1592 | 0.03 | 4.3 | 6.71e-05 | 0.01 | -0.458 | 0.995
18p | 143 | 0.01 | -0.236 | 0.994 | 0.01 | -1.01 | 0.995
18q | 446 | 0.01 | -0.212 | 0.994 | 0.01 | -0.991 | 0.995
19p | 995 | 0.02 | 0.627 | 0.624 | 0.01 | -0.945 | 0.995
19q | 1709 | 0.02 | 1.08 | 0.363 | 0.00 | -2.1 | 0.995
20p | 355 | 0.02 | 2.11 | 0.0535 | 0.00 | -2.56 | 0.995
20q | 753 | 0.02 | 2.16 | 0.0516 | 0.00 | -2.54 | 0.995
21q | 509 | 0.01 | -0.582 | 0.994 | 0.02 | 0.588 | 0.995
22q | 921 | 0.01 | -1.03 | 0.994 | 0.17 | 31.1 | 0
Xq | 1312 | 0.02 | 1.06 | 0.363 | 0.01 | -0.919 | 0.995

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/THCA-TP/4433856/GDAC_MergeDataFiles_3622375/THCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 494 Input Tumor Samples.

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

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle