Brain Lower Grade Glioma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16a (cga svn revision 43808).

Summary

There were 180 tumor samples used in this analysis: 21 significant arm-level results, 13 significant focal amplifications, and 23 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 - 13 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
--- | --- | --- | --- | ---
7p11.2 | 9.2087e-22 | 9.2087e-22 | chr7:54942676-55107468 | 1
12q14.1 | 1.5805e-10 | 1.5805e-10 | chr12:58125396-58163019 | 6
1q32.1 | 6.0215e-07 | 6.0215e-07 | chr1:203710591-204630921 | 17
8q24.21 | 6.0215e-07 | 6.0215e-07 | chr8:113044644-146364022 | 225
12p13.32 | 6.0215e-07 | 6.0215e-07 | chr12:3496687-4659158 | 9
7q32.3 | 1.1515e-05 | 1.1515e-05 | chr7:129888335-131942568 | 20
4q12 | 0.00064413 | 0.00064413 | chr4:55115761-56491855 | 9
10p15.1 | 0.011048 | 0.011048 | chr10:1-21356591 | 124
19q13.2 | 0.03695 | 0.03695 | chr19:40246077-40291097 | 1
11q23.3 | 0.054529 | 0.054529 | chr11:114585126-135006516 | 202
Xp22.33 | 0.061281 | 0.061281 | chrX:1-4472533 | 31
Xq11.2 | 0.05779 | 0.10953 | chrX:53705366-115822129 | 325
Xp11.22 | 0.10605 | 0.19369 | chrX:53659048-54011926 | 2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
MARCH9
AGAP2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q32.1.

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

Genes
MDM4
ATP2B4
KISS1
PIK3C2B
REN
SNRPE
SOX13
ZC3H11A
LRRN2
PLEKHA6
LAX1
ETNK2
PPP1R15B
LOC127841
GOLT1A
LINC00303
ZBED6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
ADCY8
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
POU5F1B
PTK2
PVT1
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
JRK
EIF3H
DGAT1
GPAA1
WISP1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
KHDRBS3
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
C8orf55
FAM49B
CHRAC1
EXOSC4
LY6K
TRMT12
WDYHV1
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
GSDMD
ZNF696
ARHGAP39
ZNF34
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
MAF1
UTP23
PARP10
C8orf76
TIGD5
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
NAPRT1
WDR67
HPYR1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
TMEM65
LOC157381
FAM84B
FAM91A1
SLC30A8
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
SPATC1
FLJ43860
MAFA
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
C8orf85
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
C8orf73
SCXB
RAD21-AS1
FER1L6
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR937
MIR939
LOC100128338
SCXA
LOC100130231
CCDC166
LOC100131726
LOC100133669
LOC100288181
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR1208
MIR3610
LOC100507117
ZHX1-C8ORF76
MIR4663
MIR4472-1
MIR4664
PCAT1
LINC00536

Genes in Wide Peak

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

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

Genes
CCND2
FGF6
FGF23
RAD51AP1
PRMT8
PARP11
C12orf4
C12orf5
EFCAB4B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q32.3.

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

Genes
hsa-mir-29b-1
hsa-mir-335
CPA1
CPA2
MEST
MKLN1
PODXL
COPG2
CPA4
PLXNA4
CPA5
CEP41
TSGA13
KLF14
MESTIT1
FLJ43663
MIR29A
MIR29B1
MIR335
LOC646329

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
KDR
KIT
PDGFRA
CLOCK
NMU
TMEM165
SRD5A3
PDCL2
LOC100506462

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.1.

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

Genes
GATA3
hsa-mir-511-2
hsa-mir-511-1
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
CACNB2
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
TRDMT1
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PRKCQ
RSU1
VIM
STAM
CUBN
ITGA8
PRPF18
AKR1C3
CDC123
PTPLA
PTER
NMT2
USP6NL
OPTN
NET1
NEBL
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
SEPHS1
KIN
DIP2C
LARP4B
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
CAMK1D
SFMBT2
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
FBXO18
PLXDC2
RBM17
IDI2
UCN3
SFTA1P
LOC219731
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
LOC254312
C10orf47
LOC282980
LOC283070
LOC338588
ST8SIA6
AKR1CL1
TUBB8
tAKR
C1QL3
LINC00200
LOC399708
LOC399715
FLJ45983
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
MIR511-1
MIR511-2
ADARB2-AS1
MEIG1
TMEM236
LOC100128098
LOC100129213
LOC100192204
LOC100216001
MIR1265
MIR3155A
LOC100507034
LOC100507127
MIR4480
MIR4675
MIR3155B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
LEUTX

Genes in Wide Peak

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

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

Genes
CBL
DDX6
FLI1
MLL
PAFAH1B2
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CD3D
CD3E
CD3G
CHEK1
DPAGT1
ETS1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
IL10RA
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NFRKB
NRGN
OPCML
PVRL1
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZNF202
BARX2
ZNF259
USP2
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
PHLDB1
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
OR8G2
OR8B8
OR8G1
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
C11orf61
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
JAM3
TMPRSS13
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
APOA5
TMEM45B
AMICA1
TTC36
PATE1
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
LINC00167
HEPN1
LOC649133
RPL23AP64
LOC100128239
PATE3
BACE1-AS
MIR3167
LOC100499227
MIR3656
LOC100507392
LOC100526771
FXYD6-FXYD2
MIR4697
MIR4493
MIR4492
LOC100652768

Genes in Wide Peak

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

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

Genes
CRLF2
P2RY8
SLC25A6
ARSD
ARSE
ARSF
ASMT
CSF2RA
IL3RA
CD99
PRKX
SHOX
XG
GTPBP6
AKAP17A
ASMTL
GYG2
ZBED1
MXRA5
PPP2R3B
PLCXD1
ASMTL-AS1
DHRSX
PPP2R3B-AS1
ARSH
LOC389906
CD99P1
CXorf28
XGPY2
LINC00102
MIR3690

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq11.2.

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

Genes
ATRX
MSN
NONO
hsa-mir-448
hsa-mir-1911
hsa-mir-1264
hsa-mir-4329
hsa-mir-652
hsa-mir-548m
hsa-mir-361
hsa-mir-548i-4
hsa-mir-4328
hsa-mir-325
hsa-mir-384
hsa-mir-374a
hsa-mir-223
hsa-mir-1468
ABCB7
AGTR2
ALAS2
AR
ARR3
ATP7A
BCYRN1
BTK
CAPN6
CDX4
CHM
COL4A5
COL4A6
COX7B
CSTF2
CYLC1
DCX
TIMM8A
DIAPH2
DLG3
DRP2
TSC22D3
EDA
EFNB1
ACSL4
FGD1
CENPI
GJB1
GLA
CXCR3
LPAR4
GUCY2F
HNRNPH2
HTR2C
IGBP1
IL2RG
IL13RA2
FOXO4
CITED1
NAP1L2
NAP1L3
OPHN1
P2RY4
PAK3
PFKFB1
PGK1
PHKA1
PIN4
PLP1
PLS3
POU3F4
PRPS1
PSMD10
RPL36A
RPS4X
SH3BGRL
SLC16A2
TAF1
SERPINA7
TDGF1P3
TSPAN6
TRO
TRPC5
XIST
ZNF711
ZXDA
IRS4
OGT
FGF16
CLDN2
ZMYM3
TCEAL1
TSIX
ITM2A
MORF4L2
GPRASP1
STARD8
ARMCX2
HEPH
AMMECR1
MED12
HUWE1
RRAGB
CYSLTR1
MAGED2
TMSB15A
MID2
SLC6A14
KLF8
VSIG4
PHF8
ARHGEF9
KCNE1L
KIF4A
IL1RAPL2
ITGB1BP2
NGFRAP1
NOX1
FAM155B
INGX
SRPX2
APEX2
PCDH11X
RPS6KA6
P2RY10
MAGEH1
SNX12
RPA4
UBQLN2
TBX22
RLIM
WBP5
RAB9B
LUZP4
PDZD11
CXorf26
ARMCX1
ARMCX3
TAF9B
CPXCR1
CHIC1
NLGN3
TAF7L
SPIN2A
ARMCX6
GNL3L
ERCC6L
NUP62CL
GDPD2
TBC1D8B
FAM120C
CXorf57
RBM41
MTMR8
BEX1
HDAC8
ZC4H2
NXT2
NXF5
NXF4
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
BEX4
TCEAL7
PCDH19
RGAG1
LRCH2
MAGEE1
TMEM35
EDA2R
DMRTC1
TNMD
PJA1
ARMCX5
WNK3
HMGN5
RNF128
MORC4
ALG13
TCEAL4
TRMT2B
POF1B
ESX1
BHLHB9
LAS1L
FRMD8P1
MAGT1
TMEM164
ZMAT1
GPR174
BEX2
SLC7A3
TCEAL3
TSR2
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
RIPPLY1
LOC92249
ACRC
SYTL4
GPRASP2
ATG4A
DACH2
LOC139201
CXorf41
MUM1L1
FAM199X
FAM123B
APOOL
HDX
OTUD6A
UPRT
MAGEE2
FOXR2
PAGE3
RBMXL3
SPIN4
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
FAAH2
ZXDB
CXorf65
AWAT1
AWAT2
ZDHHC15
USP51
TCEAL6
H2BFWT
FAM46D
SPIN3
CXorf61
LINC00246A
ZCCHC5
NRK
TMEM31
PAGE2
BRWD3
RAB40AL
H2BFM
LOC286437
YIPF6
TTC3P1
FAM133A
TMSB15B
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
LOC340544
VSIG1
ZC3H12B
SATL1
ZCCHC16
LHFPL1
ITIH6
DGAT2L6
RAB41
PAGE2B
ZCCHC13
FLJ44635
ARL13A
MCART6
DKFZp686D0853
XKRX
MIR223
FLJ46446
RPS26P11
GLRA4
PGAM4
UQCRBP1
LOC442459
MIR374A
SPIN2B
MIR384
LOC550643
JPX
MIR448
LOC643486
ZCCHC18
PABPC1L2B
NAP1L6
LINC00246B
MIR545
SNORA11
SNORA35
SNORD96B
MIR421
NXF2B
DMRTC1B
H2BFXP
MIR374B
LOC100129407
CXorf49
ARMCX4
UBE2DNL
LOC100132741
CXorf49B
LOC100287765
MIR1468
MIR1912
MIR1298
MIR1256
MIR1911
MIR1264
FTX
MIR764
LOC100329135
MIR4328
MIR4329
MTRNR2L10
MIR374C
MIR676
ARMCX5-GPRASP2
RPL36A-HNRNPH2
MIR4536-1
MIR3978

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.22.

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

Genes
HUWE1
PHF8

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 - 23 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
--- | --- | --- | --- | ---
9p21.3 | 4.995e-33 | 4.995e-33 | chr9:21865498-22448737 | 4
19q13.42 | 7.0142e-13 | 7.0142e-13 | chr19:53856554-59128983 | 249
2q37.3 | 2.5857e-10 | 2.5002e-10 | chr2:233736245-243199373 | 106
10q26.2 | 1.7803e-06 | 1.746e-06 | chr10:112773179-135534747 | 179
14q24.3 | 0.00010926 | 0.00010742 | chr14:62120768-95873844 | 247
4q32.3 | 1.0897e-08 | 0.00016612 | chr4:144615493-191154276 | 202
11p15.5 | 0.00046203 | 0.00044157 | chr11:1-11679116 | 281
4q35.2 | 5.816e-11 | 0.00066965 | chr4:170189485-191154276 | 96
13q34 | 0.0011979 | 0.0024576 | chr13:114620052-115169878 | 4
3p21.2 | 0.0028818 | 0.0028818 | chr3:45837066-54957121 | 206
18q23 | 0.0040535 | 0.0038954 | chr18:74979706-78077248 | 12
1p36.31 | 0.0099316 | 0.0097383 | chr1:3353950-10272008 | 71
6q24.3 | 0.011009 | 0.011098 | chr6:108580209-171115067 | 357
13q14.2 | 0.0090512 | 0.013598 | chr13:24115748-90884270 | 265
22q13.31 | 0.042154 | 0.04292 | chr22:41368022-51304566 | 154
5q35.2 | 0.045496 | 0.045887 | chr5:112819861-180915260 | 583
Xp22.31 | 0.073777 | 0.073744 | chrX:3474210-11137490 | 24
3q29 | 0.094884 | 0.094884 | chr3:194502405-198022430 | 50
17q25.3 | 0.10319 | 0.10517 | chr17:80379333-81195210 | 12
1q44 | 0.17063 | 0.17063 | chr1:181775464-249250621 | 529
6p24.1 | 0.18083 | 0.183 | chr6:1-30260981 | 283
Xq21.1 | 0.183 | 0.183 | chrX:76710176-77360723 | 5
12p13.1 | 0.24274 | 0.24231 | chr12:12048002-18235892 | 52

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.42.

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

Genes
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
A1BG
FCAR
FKBP1AP1
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR1
LAIR2
NDUFA3
CNOT3
PEG3
PRKCG
PTPRH
RPL28
RPS5
RPS9
AURKC
SYT5
TNNI3
TNNT1
ZNF8
ZNF17
MZF1
ZNF132
ZNF134
ZNF135
ZNF154
UBE2M
ZNF264
NCR1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
LILRB1
LILRB5
SLC27A5
LILRB4
LILRA1
LILRB3
LILRA3
LILRA2
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
ZNF324
PRPF31
CHMP2A
ZNF544
UBE2S
CCDC106
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
NLRP2
ZNF416
ZNF446
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
ZNF71
CACNG8
CACNG7
CACNG6
ZNF667
ZSCAN18
MGC2752
TSEN34
MBOAT7
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
ZNF419
ISOC2
ZNF552
ZNF671
ZNF606
BRSK1
SUV420H2
ZBTB45
ZNF587
FIZ1
GALP
ZNF628
KIR3DX1
ZNF551
ZNF835
ZNF765
NLRP12
MYADM
LENG9
RDH13
ZIM3
LENG8
KIR3DL3
ZNF837
ZNF543
COX6B2
OSCAR
ZNF813
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF497
ZNF550
ZNF579
ZNF525
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
LOC284379
VSTM1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
ZNF773
LOC386758
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF772
TARM1
MIR371A
MIR372
MIR373
A1BG-AS1
DPRX
DUXA
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
LOC646862
SHISA7
ZNF814
MIMT1
MIR935
LOC100128252
LOC100128398
SGK110
LOC100131691
PEG3-AS1
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
ZNF865
MIR4754
MIR4752
MIR371B

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.2.

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

Genes
FGFR2
DUX4
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
ACADSB
ADAM8
ADRA2A
ADRB1
BNIP3
CASP7
CTBP2
CYP2E1
DMBT1
DOCK1
ECHS1
EMX2
GFRA1
PRLHR
GPR26
GRK5
HABP2
HMX2
INPP5A
ABLIM1
MGMT
MKI67
NRAP
OAT
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PTPRE
RGS10
SLC18A2
TCF7L2
TECTB
TIAL1
UROS
ADAM12
UTF1
EIF3A
BUB3
BAG3
FAM53B
DCLRE1A
GLRX3
DPYSL4
TACC2
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
FAM175B
ATRNL1
C10orf137
DUX2
VENTX
CUZD1
CALY
CHST15
ACSL5
ZRANB1
TTC40
NSMCE4A
C10orf118
WDR11
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
GPAM
KIAA1598
FAM160B1
PLEKHA1
FAM204A
LHPP
IKZF5
ZDHHC6
MCMBP
C10orf81
C10orf88
LRRC27
GPR123
NKX6-2
AFAP1L2
KNDC1
MTG1
FANK1
SYCE1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
PDZD8
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CASC2
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
LOC283038
LOC283089
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
FAM45A
FRG2B
SPRN
MIR202
NPS
LOC619207
SNORA19
FAM196A
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
LOC100169752
MIR2110
MIR378C
MIR4297
MIR4295
MIR4296
MIR3941
MIR3663
MIR3944
FAM24B-CUZD1
MIR4483
MIR4682
MIR4484
MIR4681

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.3.

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

Genes
TSHR
TRIP11
GOLGA5
GPHN
DICER1
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
HIF1A
HSPA2
IFI27
ITPK1
LTBP2
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5E
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
SEL1L
SRSF5
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
RGS6
KIAA0247
KIAA0317
MED6
VTI1B
FBLN5
BATF
NPC2
AHSA1
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
C14orf109
PLEK2
MLH3
KCNH5
PRO1768
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
ATP6V1D
ASB2
ZFYVE1
CPSF2
KCNK10
C14orf102
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
SPATA7
YLPM1
KCNK13
C14orf162
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
UNC79
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
IRF2BPL
MPP5
OTUB2
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
SGPP1
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
IFT43
WDR89
IFI27L1
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SAMD15
EML5
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
C14orf55
ITPK1-AS1
SNORD56B
SERPINA9
VSX2
COX8C
RAB15
SERPINA13
HEATR4
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
LINC00238
CCDC88C
TEX21P
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
SNORA79
LOC731223
SNORA11B
LOC100289511
MIR1260A
MIR3173
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.3.

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
AGA
SLC25A4
ANXA2P1
CASP3
LRBA
CLCN3
CPE
CTSO
DCTD
EDNRA
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
SMAD1
NR3C2
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
POU4F2
PPID
ABCE1
RPS3A
MSMO1
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SORBS2
SAP30
SNORD73A
LRAT
HAND2
RAPGEF2
MFAP3L
ANAPC10
MAB21L2
ADAM29
LSM6
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
DUX2
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
DKFZP434I0714
OTUD4
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
TMEM184C
LRP2BP
PDGFC
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
HHIP
ARHGAP10
MLF1IP
NBLA00301
MAP9
WWC2
CEP44
SNX25
TTC29
MND1
SLC10A7
TKTL2
CBR4
FHDC1
MGC45800
PRMT10
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
ZNF827
SH3D19
C4orf38
C4orf39
C4orf45
DCLK2
TRIM60
MMAA
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
RNF175
LOC339975
TRIML1
LOC340017
PRSS48
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
FAM160A1
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3140
MIR4276
MIR3945
MIR3688-1
LOC100505545
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR4453
MIR4799
MIR3688-2

Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
EIF4G2
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPL27A
RPLP2
RRM1
SCT
SMPD1
TRIM21
ST5
STIM1
TAF10
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
CTR9
TRIM66
TSPAN32
TSSC4
MRVI1
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
OR7E12P
LYVE1
KCNQ1OT1
PKP3
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
FAM160A2
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC644656
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
LOC729013
MIR675
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
MIR210HG
MIR4686
MIR4485
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
SCRG1
FAM149A
FBXO8
DUX2
PDLIM3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
LOC100506085
LOC100506122
LOC100506229

Genes in Wide Peak

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

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

Genes
CDC16
RASA3
UPF3A
CHAMP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.2.

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

Genes
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
ACY1
ALAS1
AMT
APEH
RHOA
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DOCK3
DUSP7
CELSR3
GNAI2
GNAT1
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TKT
TNNC1
UBA7
USP4
UQCRC1
IFRD2
MAPKAPK3
SEMA3B
MANF
HYAL3
HYAL2
BSN
CCRL2
RRP9
CACNA2D2
VPRBP
IP6K1
PARP3
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SCAP
LAMB2P1
RAD54L2
STAB1
NBEAL2
KLHL18
NAT6
ABHD14A
POC1A
NDUFAF3
PTPN23
DNAH1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
C3orf18
SHISA5
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
C3orf75
QRICH1
DALRD3
CHDH
IL17RB
DCP1A
GLT8D1
SEMA3G
PCBP4
SELK
RNF123
KIF9
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
WDR82
RTP3
ATRIP
NICN1
MON1A
ABHD14B
UCN2
RFT1
ACTR8
GPR62
IQCF1
GLYCTK
PPM1M
C3orf45
CCDC12
KLHDC8B
ALS2CL
TMIE
FBXW12
FLJ39534
CCDC36
PRSS42
C3orf62
TMEM110
PRSS45
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR191
TMEM89
IQCF6
C3orf78
MIR425
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
LOC100132146
BSN-AS2
PRSS46
MIR1226
MIR711
MIR4271
IQCF4
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4443
LUST

Genes in Wide Peak

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

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

Genes
NFATC1
CTDP1
TXNL4A
ADNP2
KCNG2
SALL3
RBFA
PQLC1
PARD6G
ATP9B
HSBP1L1
LOC100130522

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
RPL22
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
RERE
CA6
DFFB
MEGF6
ENO1
ZBTB48
TNFRSF9
PIK3CD
SLC2A5
TP73
KCNAB2
TNFRSF25
PER3
VAMP3
H6PD
CEP104
KLHL21
UBE4B
UTS2
PARK7
ACOT7
CLSTN1
CAMTA1
ICMT
CHD5
ARHGEF16
WRAP73
SLC45A1
ERRFI1
HES2
DNAJC11
AJAP1
CTNNBIP1
TP73-AS1
PLEKHG5
LRRC47
NMNAT1
NOL9
GPR157
SPSB1
TAS1R1
ESPN
SLC25A33
LZIC
THAP3
RBP7
TPRG1L
PHF13
CCDC27
SLC2A7
TMEM201
NPHP4
LOC284661
C1orf174
GPR153
LOC388588
RNF207
HES3
MIR34A
C1orf200
MIR551A
LOC728716
LOC100133612
MIR4252
ENO1-AS1
MIR4689
MIR4417

Genes in Wide Peak

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

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

Genes
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
ACAT2
AMD1
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GJA1
GPR6
GPR31
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
RPS12
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
AKAP7
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TFB1M
TUBE1
CDC40
RWDD1
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
C6orf115
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
FNDC1
RSPO3
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
FAM54A
SFT2D1
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
WDR27
FAM26E
MCM9
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FAM26F
FLJ46906
LOC441177
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
MIR548B
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
CPB2
DACH1
EDNRB
ELF1
ESD
FOXO1
FLT1
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
POU4F1
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SLC7A1
TPT1
TRPC4
UCHL3
TNFSF11
SCEL
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
KL
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
DLEU1
N4BP2L2
PIBF1
OLFM4
POSTN
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SLITRK5
FBXL3
INTS6
CKAP2
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
PHF11
POMP
UFM1
ATP8A2
NDFIP2
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
PCDH20
RNF219
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
COMMD6
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SPATA13
LNX2
SLC25A30
PAN3
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
SNORA31
MIR621
MIR622
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
RPL21P28
LINC00426
TPT1-AS1
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4500
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
EP300
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
hsa-mir-33a
hsa-mir-1281
ACR
ACO2
ARSA
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
NAGA
NDUFA6
NHP2L1
PMM1
PPARA
MAPK11
RANGAP1
MAPK12
SBF1
SREBF2
TCF20
TEF
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
TOB2
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
ZC3H7B
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
CSDC2
RRP7A
MCAT
PPPDE2
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
SEPT3
PANX2
PARVG
CERK
EFCAB6
CENPM
ALG12
CRELD2
C22orf46
CCDC134
ADM2
SCUBE1
TRABD
PNPLA3
SELO
L3MBTL2
HDAC10
LDOC1L
POLDIP3
PHF5A
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
TNFRSF13C
CHADL
MEI1
FAM109B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
WBP2NL
POLR3H
SERHL2
RNU12
ATP5L2
LOC284933
RPL23AP82
BK250D10.8
LOC339685
C22orf34
CHKB-CPT1B
LOC388906
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
MIR33A
LINC00229
FAM116B
PIM3
SHISA8
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100132273
LOC100144603
LOC100271722
MIR1249
MIR1281
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDO1
CDX1
AP3S1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
NKX2-5
CTNNA1
DBN1
DMXL1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HINT1
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
KCNN2
LCP2
LECT2
LMNB1
LOX
LTC4S
SMAD5
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SNX2
SPARC
SPINK1
SPOCK1
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
ATG12
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
YTHDC2
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
LYRM7
TRIM41
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
ZNF474
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
SRFBP1
LOC153469
ZMAT2
BTNL9
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
AQPEP
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
DTWD2
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
TICAM2
DND1
C5orf25
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
LOC644100
FLJ33630
CCNI2
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728342
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
VTRNA2-1
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505841
LOC100507387
MIR4633
MIR4634
MIR4461
MIR4460
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.31.

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

Genes
hsa-mir-651
SHROOM2
STS
CLCN4
KAL1
MID1
GPR143
PRKX
TBL1X
HDHD1
PNPLA4
VCX
VCX2
VCX3A
WWC3
NLGN4X
FAM9A
FAM9B
LOC389906
VCX3B
MIR651
LOC100288814
MIR4770
MIR4767

Genes in Wide Peak

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

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

Genes
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
APOD
BDH1
DLG1
MFI2
MUC4
PAK2
PCYT1A
PPP1R2
RPL35A
KIAA0226
TNK2
NCBP2
ACAP2
UBXN7
PIGX
PIGZ
IQCG
FYTTD1
LRCH3
CEP19
LMLN
TM4SF19
ZDHHC19
XXYLT1
LOC152217
RNF168
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
TCTEX1D2
C3orf43
SDHAP1
WDR53
ANKRD18DP
LRRC33
LOC401109
MIR570
SDHAP2
FAM157A
MIR922
MFI2-AS1
LOC100507086
TM4SF19-TCTEX1D2
MIR4797

Genes in Wide Peak

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

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

Genes
FOXK2
TBCD
RAB40B
NARF
WDR45L
FN3K
C17orf62
FN3KRP
ZNF750
B3GNTL1
METRNL
FLJ43681

Genes in Wide Peak

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

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

Genes
ELK4
FH
MDM4
TPR
SLC45A3
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
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ARF1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
DHX9
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GLUL
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NCF2
NEK2
NID1
NVL
CDK18
PDC
PFKFB2
PIGR
PIK3C2B
PKP1
PLA2G4A
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTGS2
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS1
RGS2
RGS7
RGS13
RGS16
RNASEL
RNF2
RNPEP
RYR2
SNRPE
SRP9
TROVE2
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
B3GALT2
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GPR37L1
GGPS1
SOX13
IKBKE
TMEM63A
TOMM20
URB2
CEP170
ZC3H11A
SMG7
TMCC2
LPGAT1
KIF14
AKT3
ARPC5
PRG4
BPNT1
TIMM17A
LRRN2
ZNF238
IVNS1ABP
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
OCLM
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NMNAT2
NFASC
GLT25D2
RGL1
FBXO28
CAMSAP2
SRGAP2
CRB1
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
GLRX2
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
UCHL5
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
SWT1
LAX1
C1orf27
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
KLHL12
LGR6
TFB2M
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
EDEM3
TRAF3IP3
SH3BP5L
NPL
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
SHCBP1L
TRMT1L
NUAK2
DDX59
RASSF5
HMCN1
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
RGS8
WNT3A
NAV1
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
TSEN15
FAM129A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
ASPM
PGBD2
OR2L13
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
LOC284648
DKFZP564C196
HNRNPU-AS1
LIN9
VN1R5
FAM5C
ZNF678
PRSS38
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
RGSL1
IRF2BP2
ZBTB41
MIA3
C1orf95
FAM89A
RPS10P7
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR194-1
MIR205
MIR181A1
MIR215
MIR29B2
MIR29C
RGS21
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SNORA14B
SNORA36B
SNORA77
SNORA16B
LOC728463
FAM72A
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
LOC100288079
MIR1182
MIR1537
MIR1231
MIR1278
MIR548F1
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
KDM5B-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4735
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.1.

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

Genes
IRF4
TRIM27
DEK
HIST1H4I
hsa-mir-3143
hsa-mir-548a-1
BMP6
BPHL
BTN1A1
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GABBR1
GCNT2
GMDS
GMPR
GPLD1
GPX5
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
HLA-A
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
ID4
JARID2
MAK
MOG
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SLC17A1
SOX4
SSR1
PPP1R11
TFAP2A
TPMT
TUBB2A
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204P
ALDH5A1
OR2H2
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
CMAHP
RIPK1
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
GCM2
CD83
CDYL
LY86
EEF1E1
FAM65B
ZSCAN12
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
SLC17A2
HCG9
PRSS16
BTN3A3
BTN2A2
ECI2
HMGN4
TRIM38
CAP2
UBD
SCGN
FARS2
SLC17A3
RPP40
TRIM31
BTN3A2
BTN3A1
BTN2A1
SIRT5
OR2B6
FAM50B
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
MYLIP
ABT1
ZNRD1
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
HCG4
GFOD1
BTN2A3P
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
MUTED
CCDC90A
KIF13A
ZNF323
ZNF322
ZKSCAN3
ZSCAN16
RNF39
ZNRD1-AS1
HCG4B
TXNDC5
C6orf62
OR5V1
OR2B2
OR12D3
TMEM14B
RIOK1
DTNBP1
PGBD1
ADTRP
HIST1H2AH
HIST1H2BK
TRIM15
POM121L2
FOXQ1
SCAND3
MAS1L
HUS1B
TRIM40
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
PIP5K1P1
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
ZSCAN23
NKAPL
TOB2P1
FAM217A
RNF144B
HIST1H2BA
GPX6
ZNF311
LOC285768
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
MYLK4
IFITM4P
ZNF391
ZFP57
TUBB2B
C6orf52
KAAG1
NHLRC1
ZKSCAN4
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
DKFZP686I15217
FLJ23152
LINC00340
LOC401242
C6orf201
ERVFRD-1
OR2B3
OR2J3
OR14J1
OR10C1
HCG11
LOC554223
PPP1R3G
SNORD32B
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
LOC100129636
LOC100130275
LOC100130357
LOC100131289
LINC00240
LOC100270746
MIR3143
MIR3691
LOC100506207
LOC100506409
LOC100507173
LOC100507194
LOC100507362
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

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

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

Genes
ATRX
ATP7A
COX7B
MAGT1
PGAM4

Genes in Wide Peak

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

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

Genes
hsa-mir-614
hsa-mir-613
ARHGDIB
ART4
CDKN1B
CREBL2
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
LRP6
MGP
MGST1
PDE6H
PTPRO
GPRC5A
STRAP
HEBP1
DERA
DDX47
WBP11
MANSC1
GPRC5D
ATF7IP
H2AFJ
LMO3
KIAA1467
BCL2L14
PLBD1
DUSP16
APOLD1
GSG1
RERG
HTR7P1
LOH12CR1
HIST4H4
ERP27
C12orf60
C12orf36
RPL13AP20
C12orf69
LOH12CR2
MIR613
MIR614
SKP1P2
SLC15A5
MIR1244-1
MIR1244-3
MIR1244-2
LOC100506314
MIR3974

Arm-level results

Table 3. Get Full Table Arm-level significance table - 21 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.06 | -0.956 | 1 | 0.34 | 12.5 | 0
1q | 1955 | 0.06 | -0.8 | 1 | 0.06 | -1.06 | 1
2p | 924 | 0.02 | -3.02 | 1 | 0.05 | -1.45 | 1
2q | 1556 | 0.02 | -3.06 | 1 | 0.05 | -1.75 | 1
3p | 1062 | 0.03 | -2.48 | 1 | 0.05 | -1.69 | 1
3q | 1139 | 0.04 | -2.12 | 1 | 0.07 | -0.287 | 1
4p | 489 | 0.01 | -2.98 | 1 | 0.18 | 4.91 | 2.03e-06
4q | 1049 | 0.00 | -3.5 | 1 | 0.22 | 6.98 | 1.14e-11
5p | 270 | 0.01 | -3.18 | 1 | 0.10 | 0.777 | 0.486
5q | 1427 | 0.01 | -3.54 | 1 | 0.08 | -0.134 | 1
6p | 1173 | 0.02 | -2.74 | 1 | 0.06 | -1.16 | 1
6q | 839 | 0.02 | -2.81 | 1 | 0.14 | 2.71 | 0.0105
7p | 641 | 0.23 | 7.34 | 2.14e-12 | 0.01 | -3.17 | 1
7q | 1277 | 0.30 | 10.8 | 0 | 0.00 | -3.33 | 1
8p | 580 | 0.09 | 0.578 | 1 | 0.04 | -2.05 | 1
8q | 859 | 0.12 | 1.9 | 0.218 | 0.03 | -2.56 | 1
9p | 422 | 0.05 | -1.44 | 1 | 0.28 | 9.81 | 0
9q | 1113 | 0.05 | -1.44 | 1 | 0.11 | 1.44 | 0.188
10p | 409 | 0.12 | 1.84 | 0.218 | 0.19 | 5.23 | 4.75e-07
10q | 1268 | 0.01 | -2.92 | 1 | 0.21 | 6.5 | 2.71e-10
11p | 862 | 0.09 | 0.407 | 1 | 0.14 | 2.76 | 0.0105
11q | 1515 | 0.13 | 2.47 | 0.067 | 0.04 | -1.97 | 1
12p | 575 | 0.08 | 0.065 | 1 | 0.05 | -1.51 | 1
12q | 1447 | 0.03 | -2.34 | 1 | 0.10 | 1.06 | 0.339
13q | 654 | 0.00 | -3.35 | 1 | 0.28 | 10 | 0
14q | 1341 | 0.01 | -3 | 1 | 0.18 | 4.84 | 2.57e-06
15q | 1355 | 0.03 | -2.37 | 1 | 0.09 | 0.513 | 0.64
16p | 872 | 0.03 | -2.23 | 1 | 0.03 | -2.23 | 1
16q | 702 | 0.05 | -1.59 | 1 | 0.06 | -1.06 | 1
17p | 683 | 0.03 | -2.5 | 1 | 0.03 | -2.23 | 1
17q | 1592 | 0.03 | -2.56 | 1 | 0.02 | -2.82 | 1
18p | 143 | 0.03 | -2.21 | 1 | 0.13 | 2.53 | 0.0162
18q | 446 | 0.02 | -2.8 | 1 | 0.14 | 2.73 | 0.0105
19p | 995 | 0.17 | 4.14 | 0.00023 | 0.09 | 0.228 | 0.819
19q | 1709 | 0.06 | -0.624 | 1 | 0.42 | 16.1 | 0
20p | 355 | 0.10 | 1.05 | 0.841 | 0.01 | -3.17 | 1
20q | 753 | 0.09 | 0.702 | 1 | 0.00 | -3.77 | 1
21q | 509 | 0.06 | -0.978 | 1 | 0.07 | -0.452 | 1
22q | 921 | 0.04 | -1.96 | 1 | 0.13 | 2.23 | 0.0341
Xq | 1312 | 0.07 | -0.591 | 1 | 0.19 | 5.14 | 6.92e-07

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LGG-TP/2170145/2.GDAC_MergeDataFiles.Finished/LGG-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 180 Input Tumor Samples.

Tumor Sample Names
TCGA-CS-4938-01B-11D-1892-01
TCGA-CS-4941-01A-01D-1466-01
TCGA-CS-4942-01A-01D-1466-01
TCGA-CS-4943-01A-01D-1466-01
TCGA-CS-4944-01A-01D-1466-01
TCGA-CS-5390-01A-02D-1466-01
TCGA-CS-5393-01A-01D-1466-01
TCGA-CS-5394-01A-01D-1466-01
TCGA-CS-5395-01A-01D-1466-01
TCGA-CS-5396-01A-02D-1466-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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