SNP6 Copy number analysis (GISTIC2)
Brain Lower Grade Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C12J6B7R
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 2.0.22 (Firehose task version: 140).

Summary

There were 513 tumor samples used in this analysis: 24 significant arm-level results, 20 significant focal amplifications, and 29 significant focal deletions were found.

Results
Focal results

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

Table 1.  Get Full Table Amplifications Table - 20 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
7p11.2 2.0024e-59 2.0024e-59 chr7:54942676-55107468 1
12q14.1 7.8643e-40 7.8643e-40 chr12:58125396-58158557 5
4q12 1.5873e-20 1.5873e-20 chr4:55138948-55190896 2
1q32.1 1.9242e-17 7.8662e-17 chr1:204283821-204614474 6
8q24.13 6.7949e-16 6.7949e-16 chr8:113044644-138577659 115
12p13.32 8.7611e-16 8.7611e-16 chr12:3978957-4110296 1
7q32.3 1.7512e-11 2.4555e-08 chr7:130150706-131420712 8
17q25.1 1.52e-05 1.52e-05 chr17:59969586-81195210 330
10p15.3 1.9574e-05 1.9574e-05 chr10:1-5762547 44
11q24.1 6.1002e-05 6.1002e-05 chr11:118703193-127178762 127
19p13.3 0.00012955 0.00012955 chr19:713557-827048 7
3q26.33 0.0013532 0.0013532 chr3:177831608-184510375 68
Xp11.22 5.8636e-05 0.0021684 chrX:53703571-54011926 3
13q34 0.0023276 0.0023276 chr13:108614305-111603996 19
7q31.2 1.5525e-07 0.013284 chr7:99827236-159138663 504
Xp11.22 0.00022256 0.013284 chrX:53705366-66746742 51
2p24.3 0.026282 0.026282 chr2:16009712-16358714 4
1q22 0.029503 0.039254 chr1:156063604-157059892 38
15q26.3 0.19963 0.19963 chr15:57515337-102531392 453
9q34.3 0.21332 0.21332 chr9:126542729-141213431 302
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: 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: Cancer Gene Census[7].

Genes
CDK4
CYP27B1
TSPAN31
MARCH9
AGAP2
Genes in Wide Peak

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

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

Genes
PDGFRA
FIP1L1
Genes in Wide Peak

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

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

Genes
MDM4
RNA5SP74
PIK3C2B
LRRN2
PLEKHA6
PPP1R15B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.13.

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

Genes
EXT1
MYC
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
ADCY8
ANXA13
KCNQ3
NDUFB9
NOV
TNFRSF11B
ENPP2
RAD21
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
COL14A1
MTSS1
KIAA0196
HHLA1
TRIB1
NDRG1
KHDRBS3
ZHX1
ZHX2
EFR3A
LRRC6
MTBP
MRPL13
ATAD2
ASAP1
PHF20L1
FAM49B
TRMT12
WDYHV1
GSDMC
ZFAT
DEPTOR
DSCC1
DERL1
TATDN1
UTP23
C8orf76
FAM83A
MED30
TBC1D31
MAL2
CSMD3
FBXO32
ZNF572
TMEM71
FAM84B
FAM91A1
SLC30A8
NSMCE2
KLHL38
SAMD12
MIR30B
MIR30D
FER1L6
OC90
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3610
MIR4662B
MIR4663
MIR5194
Genes in Wide Peak

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

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

Genes
PARP11
Genes in Wide Peak

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

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

Genes
MIR29B1
MIR29A
RNA5SP246
COPG2
MKLN1
PODXL
TSGA13
KLF14
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
CD79B
DDX5
PRKAR1A
ASPSCR1
CANT1
MIR4525
RAB40B
snoU13|ENSG00000238403.1
snoU13|ENSG00000238947.1
DUS1L
PCYT2
SLC25A10
LINC00482
MIR1250
MIR657
MIR4730
CBX8
snoU13|ENSG00000239173.1
ENGASE
DDC8
RN7SL454P
SNORA30|ENSG00000200063.1
RN7SL236P
FLJ45079
LINC00338
LINC00868
MIR636
SNORD1B
SNHG16
PRCD
snoU13|ENSG00000238418.1
MYO15B
RN7SL573P
MIR3615
CD300LD
GPRC5C
RNA5SP448
LINC00469
SSTR2
SCARNA24|ENSG00000252274.1
RN7SKP180
LINC00511
MAP2K6
SNORA40|ENSG00000252352.1
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
RN7SL622P
SNORA38B
MIR548D2
RN7SL756P
snoU13|ENSG00000238612.1
PSMD12
SNORA8|ENSG00000207410.1
RNA5SP447
RNA5SP446
MIR634
RNA5SP445
RN7SL735P
RNA5SP444
SLC16A6P1
RN7SL404P
RN7SL409P
PLEKHM1P
SMURF2
MIR5047
MIR3064
SNORD104
SNORA76|ENSG00000266402.2
TCAM1P
RN7SL805P
ACE
TLK2
TBC1D3P2
RN7SL800P
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CACNG1
CD7
CDK3
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
MAFG
MAP3K3
NPTX1
P4HB
PDE6G
PRKCA
PRPSAP1
PSMC5
PYCR1
RAC3
RFNG
RPL38
MRPL12
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
TBCD
TIMP2
TK1
AXIN2
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
ST6GALNAC2
GNA13
SEPT9
CD300C
POLG2
CD300A
TMC6
DDX42
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
HN1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
SDK2
TMEM104
C17orf80
CCDC40
WIPI1
NPLOC4
ST6GALNAC1
TEX2
WDR45B
CCDC47
MIF4GD
INTS2
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
SLC25A19
UBE2O
FN3K
DNAI2
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
FN3KRP
OGFOD3
ZNF750
NUP85
C17orf70
LIMD2
KCNH6
TSPAN10
QRICH2
CBX2
FAM104A
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
SLC38A10
USH1G
CD300LB
KIF19
TBC1D16
AFMID
MGAT5B
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
EFCAB3
NOTUM
TMC8
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MYADML2
NPB
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
SLC26A11
ENDOV
C17orf89
TMEM105
METRNL
RAB37
METTL2A
ENPP7
OXLD1
CCDC137
ARL16
CD300E
OTOP3
FAM195B
GPR142
ZACN
LRRC37A3
BTBD17
TEX19
MXRA7
CPSF4L
SMIM5
MIR633
SMIM6
TEN1
C17orf99
MIR4316
MIR338
MIR3186
MIR3678
MIR3615
MIR4739
MIR4738
MIR4740
MIR4524B
Genes in Wide Peak

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

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

Genes
RN7SL445P
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
CALML3
AKR1C4
KLF6
AKR1C2
IDI1
PFKP
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
CALML5
FAM208B
ASB13
TUBAL3
AKR1E2
IDI2
UCN3
LINC00200
PRR26
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q24.1.

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

Genes
CBL
ARHGEF12
MIR3167
snoU13|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
ACRV1
CHEK1
DPAGT1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
STT3A
VWA5A
MCAM
NRGN
PVRL1
ST3GAL4
SORL1
SRPR
TECTA
UPK2
ZNF202
USP2
EI24
FEZ1
HYOU1
VSIG2
TRIM29
POU2F3
OR8B8
OR8B2
DCPS
DDX25
CDON
TRAPPC4
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
GRAMD1B
PKNOX2
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
KIRREL3
RPUSD4
UBASH3B
ESAM
TIRAP
C1QTNF5
PANX3
PATE1
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
PATE2
PATE4
MIRLET7A2
MIR100
MIR125B1
BLID
HEPN1
PATE3
MIR4493
MIR4492
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.3.

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

Genes
MIR4745
AZU1
PALM
PTBP1
LPPR3
MISP
MIR3187
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
PIK3CA
SOX2
SNORD66|ENSG00000212158.1
MIR1224
CYP2AB1P
SNORA4|ENSG00000251730.1
SNORA63|ENSG00000199363.1
SNORA81|ENSG00000253092.1
SNORA63|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
RN7SL229P
U8|ENSG00000201810.1
RNA5SP149
snoU13|ENSG00000239096.1
GNB4
SNORA25|ENSG00000201957.1
RNA5SP148
ACTL6A
AP2M1
CLCN2
DVL3
EIF4G1
EPHB3
NDUFB5
POLR2H
PSMD2
THPO
FXR1
CHRD
EIF2B5
USP13
ECE2
ABCC5
ALG3
KCNMB2
MCF2L2
ATP11B
LAMP3
KCNMB3
ZNF639
PEX5L
KLHL24
ABCF3
PARL
MFN1
YEATS2
MCCC1
MRPL47
MAGEF1
ZMAT3
MAP6D1
B3GNT5
KLHL6
VWA5B2
CAMK2N2
DNAJC19
FAM131A
TTC14
HTR3C
HTR3D
HTR3E
CCDC39
MIR4448
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: Cancer Gene Census[7].

Genes
RNA5SP505
HUWE1
PHF8
Genes in Wide Peak

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

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

Genes
LINC00346
LINC00567
snoU13|ENSG00000238629.1
RN7SL783P
RN7SKP10
LINC00676
RNA5SP39
COL4A1
COL4A2
ING1
LIG4
IRS2
TNFSF13B
MYO16
ANKRD10
RAB20
CARKD
CARS2
ABHD13
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.2.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1|ENSG00000271739.1
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13|ENSG00000238922.1
FLJ00325
U3|ENSG00000238297.1
snoU109|ENSG00000238832.1
RNA5SP236
SNORD112|ENSG00000251911.1
RN7SL8P
LHFPL3
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
AOC1
ACHE
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CAV1
CAV2
CFTR
CHRM2
AP1S1
CLCN1
CPA1
CPA2
CUX1
DLD
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNB2
GPR22
GRM8
MNX1
AGFG2
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRCAM
NRF1
ORC5
SERPINE1
PAX4
PCOLCE
SLC26A4
PIK3CG
PIP
PODXL
POLR2J
PPP1R3A
PRKAR2B
PRSS1
RELN
PSMC2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
PLOD3
DGKI
ATP6V1F
ASIC3
PMPCB
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
MUC12
NAMPT
RASA4
LRRC17
POP7
FAM3C
COG5
ZNHIT1
FASTK
DUS4L
ZNF277
ABCB8
TFEC
LAMB4
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
CLDN15
POT1
CNTNAP2
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
HBP1
DNAJC2
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
MRPS33
NUB1
GPR85
TAS2R5
CHPF2
PUS7
ING3
LRRN3
ALKBH4
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
KMT2E
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
PRKRIP1
CBLL1
ZNF767
CPED1
TTC26
ORAI2
JHDM1D
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
MYL10
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
COL26A1
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
MUC17
RNF32
ASB15
C7orf60
CLEC2L
C7orf55
IQUB
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
PPP1R35
LRWD1
FBXL13
NAPEPLD
ATXN7L1
CDHR3
NYAP1
POLR2J2
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
LSMEM1
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
MOGAT3
FAM71F2
STRA8
WDR86
DPY19L2P2
GATS
GSTK1
NAT16
SLC26A5
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
C7orf61
UFSP1
MIR182
MIR183
MIR96
SPDYE3
SPDYE2
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
EFCAB10
UPK3BL
CTAGE8
RASA4B
SMKR1
ZNF783
SPDYE2B
MIR548O
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707
Genes in Wide Peak

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

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

Genes
MSN
RN7SL799P
SPIN3
SNORD112|ENSG00000252961.1
APEX2
SNORA11|ENSG00000221750.1
SNORA11|ENSG00000221716.1
GNL3L
U3|ENSG00000252175.1
RNA5SP505
ALAS2
FGD1
PFKFB1
TRO
ZXDA
HEPH
HUWE1
RRAGB
MAGED2
KLF8
VSIG4
PHF8
ARHGEF9
MAGEH1
UBQLN2
SPIN2A
FAM120C
MTMR8
ZC4H2
EDA2R
WNK3
LAS1L
TSR2
FAM104B
PAGE5
AMER1
FOXR2
PAGE3
SPIN4
ASB12
FAAH2
ZXDB
USP51
PAGE2
ZC3H12B
ITIH6
PAGE2B
MIR223
SPIN2B
MIR1468
MTRNR2L10
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.3.

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

Genes
MYCN
RN7SL104P
MYCNOS
snoU13|ENSG00000238371.1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q22.

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

Genes
NTRK1
PRCC
RN7SL612P
MIR765
snoU13|ENSG00000238843.1
BGLAP
SNORA26|ENSG00000252236.1
CRABP2
HDGF
INSRR
LMNA
MEF2D
CCT3
SH2D2A
SLC25A44
ARHGEF11
C1orf61
NES
PMF1
SMG5
RRNAD1
GPATCH4
RHBG
HAPLN2
BCAN
SEMA4A
MRPL24
PAQR6
ISG20L2
TMEM79
C1orf85
TSACC
IQGAP3
APOA1BP
LRRC71
TTC24
PEAR1
VHLL
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
BLM
IDH2
NTRK3
PML
TCF12
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109|ENSG00000239197.1
snoU13|ENSG00000238981.1
RN7SL363P
SNORD18|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
SNORD74|ENSG00000200206.1
RNA5SP400
RN7SL428P
CSPG4P12
SNORA25|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
HDGFRP3
SCARNA15|ENSG00000252690.2
GOLGA6L10|ENSG00000254374.2
RN7SL410P
GOLGA6L9|ENSG00000196648.6
UBE2Q2P3
RN7SL256P
RN7SL61P
CSPG4P8
UBE2Q2P2
TMC3
STARD5
LINC00927
SNORD112|ENSG00000251881.1
C15orf37
MTHFS
ANKRD34C
CTSH
ACSBG1
IDH3A
SNORA63|ENSG00000199633.1
SH2D7
MIR1827
RN7SL214P
RN7SL278P
RN7SKP217
NRG4
RN7SL510P
SNORD112|ENSG00000252372.1
RN7SL319P
DNM1P35
SNX33
ANP32BP1
DNM1P34
RN7SL327P
GOLGA6D
RN7SL489P
GOLGA6C
SCARNA20|ENSG00000252722.1
RPP25
COX5A
SCAMP2
SNORD77|ENSG00000212279.2
RN7SL429P
C15orf59
RN7SL853P
GOLGA6B
RN7SL485P
TMEM202
RNA5SP399
NR2E3
RPL29P30
MIR629
LINC00593
U3|ENSG00000207119.1
RNA5SP398
SNORA77|ENSG00000221376.1
RN7SL438P
MIR4312
FEM1B
CALML4
SNORD18A
SNORD16
SNORD18B
SNORD18C
MIR4512
MAP2K1
SCARNA14
TIPIN
MIR4511
snoU13|ENSG00000238311.1
snoU13|ENSG00000238715.1
SNORA24|ENSG00000206903.1
CLPX
MTFMT
RN7SL348P
MIR1272
RN7SL707P
RN7SL595P
SNORA48|ENSG00000252774.1
USP3
CA12
MIR190A
RN7SL613P
RNA5SP397
RNA5SP396
snoU13|ENSG00000238767.1
MIR2116
C15ORF31
U3|ENSG00000200318.1
RN7SKP95
snoU13|ENSG00000239100.1
MYZAP
LINC00926
snoU13|ENSG00000239035.1
ADAM10
ACAN
ALDH1A3
ANPEP
ANXA2
AQP9
BBS4
BCL2A1
BNC1
BNIP2
CHD2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
FES
GTF2A2
HEXA
IGF1R
IL16
IREB2
ISLR
LIPC
LOXL1
SMAD3
SMAD6
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
MYO1E
MYO9A
NEO1
NMB
OAZ2
FURIN
PCSK6
PDE8A
PKM
PLIN1
POLG
PPIB
MAP2K5
PSMA4
PTPN9
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
SH3GL3
SNRPA1
SNX1
NR2F2
TLE3
TPM1
AP3B2
ANP32A
ST8SIA2
SEMA7A
CILP
PIAS1
RAB11A
PEX11A
IQGAP1
ALDH1A2
HERC1
PSTPIP1
PRC1
CCNB2
SLC28A1
SLC24A1
GCNT3
TRIP4
STOML1
HOMER2
KIF23
IGDCC3
ZNF592
KIAA0101
SV2B
ARNT2
HCN4
SNUPN
PDCD7
TSPAN3
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
ARID3B
MORF4L1
ABHD2
ADAMTS7
AKAP13
ITGA11
CHSY1
ZNF609
TBC1D2B
MESDC2
KIAA1024
SYNM
TMED3
SEC11A
DAPK2
ARIH1
SIN3A
ULK3
GLCE
FBXO22
VPS33B
MRPL46
OR4F4
NPTN
FOXB1
SLCO3A1
SCAPER
RPS27L
RASL12
SPG21
NGRN
RHCG
PTPLAD1
RAB8B
BTBD1
TM6SF1
CSNK1G1
ZFAND6
SCAND2P
FAM63B
RNF111
VPS13C
LRRC49
PAQR5
DPP8
COMMD4
PARP16
CLN6
ZSCAN2
ZWILCH
DET1
UACA
FANCI
IMP3
LARP6
DNAJA4
MCTP2
VIMP
UNC45A
C15orf39
THAP10
RGMA
WDR93
PARP6
FAM219B
ADAMTSL3
KIAA1199
ALPK3
ISLR2
IGDCC4
ABHD17C
MESDC1
PPCDC
CELF6
STRA6
KLHL25
CPEB1
AEN
IQCH
ISL2
TTC23
MRPS11
NOX5
EFTUD1
NEIL1
NARG2
LRRK1
AAGAB
LMAN1L
SLTM
PEAK1
SNX22
THSD4
PIF1
CCDC33
EDC3
TM2D3
PLEKHO2
WDR61
CD276
POLR2M
VWA9
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
MEGF11
LINGO1
WDR73
CGNL1
UBL7
TICRR
RCCD1
ARRDC4
LINC00923
LDHAL6B
UBE2Q2
LACTB
DIS3L
C15orf40
SENP8
SLC51B
TARSL2
HIGD2B
LRRC28
C15orf27
AGBL1
HYKK
WHAMM
FSD2
ASB7
C2CD4A
LYSMD4
FAM81A
PGPEP1L
C15orf61
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
C15orf26
TBC1D21
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
CT62
GRAMD2
LCTL
CERS3
SPESP1
LINC00277
C15orf60
C15ORF37
FAM154B
FAM169B
FBXL22
GOLGA6A
RBPMS2
ANKDD1A
KIF7
ZNF710
HDDC3
C2CD4B
UBE2Q2P1
SPATA41
KBTBD13
UBAP1L
SKOR1
GDPGP1
OR4F6
OR4F15
ST20
FAM174B
MIR184
GOLGA6L9|ENSG00000197978.8
TTLL13
MIR422A
CPLX3
GOLGA6L10|ENSG00000205281.6
MIR549
MIR630
MIR631
MIR1276
MIR1179
MIR3174
MIR4311
MIR4313
MIR3713
RPS17L
MIR4514
MIR4513
MIR4515
GCOM1
MIR548AP
Genes in Wide Peak

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

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

Genes
ABL1
NOTCH1
RALGDS
SET
TSC1
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
ABCA2
AK1
ASS1
C8G
CACNA1B
CCBL1
ENTPD2
CDK9
CEL
COL5A1
CRAT
DBH
SARDH
DNM1
TOR1A
ENDOG
ENG
FCN1
FCN2
FPGS
NR5A1
FUT7
NR6A1
GLE1
GOLGA1
GOLGA2
RAPGEF1
GRIN1
HSPA5
LCN1
LCN2
LMX1B
ODF2
PAEP
PBX3
PPP2R4
PPP6C
PSMB7
PTGDS
RPL7A
RPL12
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
ZNF79
LHX3
GFI1B
SSNA1
EDF1
DPM2
FUBP3
GTF3C5
LHX2
MED27
PTGES
RALGPS1
ADAMTSL2
PPP1R26
SEC16A
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
NEK6
SDCCAG3
NOXA1
USP20
SLC27A4
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
RPL35
MAN1B1
DOLK
SETX
ZBTB43
PMPCA
EXOSC2
NCS1
ANGPTL2
NUP188
CIZ1
NELFB
NSMF
GPSM1
GAPVD1
GBGT1
TRUB2
ST6GALNAC4
NDOR1
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf78
FBXW5
TBC1D13
TOR4A
EXD3
RABL6
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
DENND1A
GPR107
PRDM12
DDX31
FAM129B
C9orf16
MAPKAP1
EHMT1
PTGES2
ARPC5L
AIF1L
UCK1
GARNL3
NTNG2
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
TMEM141
C9orf37
MVB12B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
ARRDC1
DPH7
TMEM203
SLC25A25
ZMYND19
NACC2
C9orf116
LCN8
PTRH1
PIP5KL1
SLC34A3
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
TTC16
C9orf96
OLFML2A
QSOX2
NAIF1
PHYHD1
SCAI
C9orf117
LCN12
C9orf142
TPRN
FAM78A
GPR144
QRFP
GLT6D1
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
LCN9
FAM102A
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR181A2
MIR181B2
MIR199B
C9orf173
NRARP
MIR602
RNF208
CARD9
MIR3154
MIR3689A
MIR3911
MIR3689B
MIR3689D1
MIR3689F
MIR3960
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR548AW

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 - 29 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 2.2203e-106 7.9386e-99 chr9:21931610-22448737 3
11p15.1 1.0683e-75 4.6495e-68 chr11:16623557-16799846 1
19q13.42 1.4433e-28 1.4433e-28 chr19:54037464-58050128 181
2q37.3 1.4015e-20 1.4015e-20 chr2:240317967-243199373 40
10q26.3 4.3789e-20 4.3789e-20 chr10:120512840-135534747 111
4q34.3 8.736e-18 8.736e-18 chr4:179280062-183067669 4
14q24.3 1.1681e-13 1.1594e-13 chr14:62199756-92796406 229
13q14.2 5.4722e-09 1.348e-08 chr13:47011303-66543128 100
11p15.5 1.5339e-13 3.3077e-08 chr11:2441018-2892511 2
Xq21.1 1.4358e-07 1.54e-07 chrX:76710176-77102528 1
5q34 1.86e-07 1.8408e-07 chr5:150946437-176309853 149
1p36.32 8.2887e-06 4.8598e-05 chr1:3814904-5625565 2
1p32.3 1.3986e-05 0.00015497 chr1:50879767-51529064 4
5p15.33 0.0003285 0.00034017 chr5:1-7397749 44
3q29 4.7283e-05 0.0005126 chr3:194406201-198022430 51
3p21.31 0.00089193 0.00086114 chr3:43727913-54667435 245
12q12 0.00097114 0.00097183 chr12:40011946-47477314 32
18q23 0.0021974 0.002178 chr18:75573485-78077248 13
6p25.3 0.0037769 0.0037769 chr6:1-2666040 11
22q13.31 0.0042376 0.0042897 chr22:42289318-51304566 121
8q24.3 0.014004 0.013639 chr8:144486368-146364022 75
9p23 2.8108e-14 0.019611 chr9:7887952-12687261 3
6q22.31 0.0054594 0.022587 chr6:108580209-163152562 329
7p22.3 0.077684 0.075771 chr7:1-4687172 40
3q13.31 0.04374 0.11305 chr3:90078624-137237176 326
1q43 0.11599 0.11599 chr1:211306170-249250621 340
13q34 0.025531 0.13068 chr13:114630958-115169878 6
12p13.1 0.13677 0.1406 chr12:12262379-14509803 26
6q26 0.0022414 0.4309 chr6:126359233-171115067 270
Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
Genes in Wide Peak

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

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

Genes
C11orf58
Genes in Wide Peak

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

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

Genes
TFPT
ZNF548
ZNF805
ZNF264
DUXA
U3|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13|ENSG00000239137.1
KIR3DX1
LILRA6
LENG1
NDUFA3
MIR935
MIR371B
RN7SL317P
FCAR
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR1
LAIR2
CNOT3
PEG3
PRKCG
PTPRH
RPL28
RPS9
AURKC
TNNI3
TNNT1
ZNF17
NCR1
LILRB2
TRAPPC2P1
ZNF460
LILRB1
LILRB5
LILRB4
LILRA1
LILRB3
LILRA3
LILRA2
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
PRPF31
UBE2S
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
EPS8L1
ZNF444
NLRP2
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
CACNG8
CACNG7
CACNG6
ZNF667
TSEN34
MBOAT7
ZSCAN5A
ZNF419
ISOC2
BRSK1
SUV420H2
FIZ1
GALP
ZNF628
ZNF835
NLRP12
MYADM
LENG9
RDH13
ZIM3
LENG8
KIR3DL3
ZNF543
COX6B2
OSCAR
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
TMEM190
TMC4
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF579
NLRP7
NLRP11
TMEM86B
SSC5D
ZNF547
VSTM1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
DNAAF3
LILRA5
ZNF773
ZNF470
ZNF749
ZNF772
TARM1
MIR371A
MIR372
MIR373
DPRX
MIR498
MIR520E
MIR519E
MIR520F
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
SHISA7
SGK110
MIR1323
ZNF865
MIR4752
Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
GAL3ST2
C2orf54
ING5
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
DUSP28
AQP12A
OR6B2
PRR21
AQP12B
D2HGDH
MIR4786
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
FGFR2
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19|ENSG00000222588.1
SNORA19|ENSG00000207468.1
U3|ENSG00000251836.1
ACADSB
ADAM8
CTBP2
CYP2E1
DMBT1
DOCK1
ECHS1
GRK5
HMX2
INPP5A
MKI67
OAT
HTRA1
PTPRE
RGS10
UROS
ADAM12
UTF1
EIF3A
BUB3
BAG3
FAM53B
GLRX3
DPYSL4
TACC2
PRDX3
ATE1
SEC23IP
INPP5F
FAM175B
C10orf137
VENTX
CUZD1
CALY
CHST15
ZRANB1
TTC40
NSMCE4A
WDR11
DHX32
BCCIP
PLEKHA1
LHPP
IKZF5
MCMBP
C10orf88
LRRC27
GPR123
KNDC1
MTG1
FANK1
SYCE1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
CLRN3
SFXN4
CPXM2
PWWP2B
PPAPDC1A
PAOX
FAM24B
EBF3
TCERG1L
FUOM
JAKMIP3
STK32C
NANOS1
HMX3
ARMS2
TEX36
C10orf120
FOXI2
C10orf85
FRG2B
SPRN
MIR202
FAM196A
MIR378C
MIR4682
MIR4484
LINC00601
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
Genes in Wide Peak

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

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

Genes
TSHR
TRIP11
GPHN
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3|ENSG00000200693.1
WDR89
SCARNA20|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
ACTN1
ACYP1
ARG2
ZFP36L1
CALM1
FOXN3
DIO2
DLST
EIF2S1
ESR2
ESRRB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
HSPA2
LTBP2
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
PGF
PIGH
PSEN1
PSMC1
ABCD4
RAD51B
SEL1L
SRSF5
SLC8A3
SNAPC1
SPTB
DPF3
GPR68
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
RPS6KA5
AKAP5
SPTLC2
RGS6
KIAA0247
AREL1
MED6
VTI1B
FBLN5
BATF
NPC2
AHSA1
ACOT2
TMED10
PTPN21
VASH1
ZBTB1
SNW1
PCNX
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
PLEK2
MLH3
KCNH5
POMT2
COQ6
FCF1
RDH11
COX16
ZFYVE1
CPSF2
NRDE2
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
TDP1
SPATA7
YLPM1
KCNK13
ADCK1
TMEM63C
RHOJ
GALNT16
PLEKHH1
ZNF410
NGB
RBM25
VIPAS39
SMOC1
IRF2BPL
MPP5
ZC2HC1C
CATSPERB
ZC3H14
C14orf159
CCDC176
SGPP1
SLIRP
DNAL1
RPS6KL1
SYT16
STON2
KIAA1737
PAPLN
EFCAB11
CHURC1
ELMSAN1
NEK9
IFT43
NOXRED1
JDP2
TTC8
TC2N
RDH12
PPP1R36
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
EML5
PROX2
ZDHHC22
C14orf178
VSX2
RAB15
HEATR4
PLEKHD1
LINC00238
CCDC88C
ACOT1
ACOT6
SYNDIG1L
MIR625
MIR1260A
MIR548H1
MIR4505
MIR4708
MIR5694
Genes in Wide Peak

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

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

Genes
RB1
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
ATP7B
RCBTB2
ESD
MLNR
GUCY1B2
HTR2A
KPNA3
NEK3
PCDH8
SUCLA2
ITM2B
UTP14C
LPAR6
TRIM13
DLEU1
OLFM4
LECT1
FNDC3A
LRCH1
INTS6
CKAP2
PCDH17
MED4
VPS36
PHF11
RCBTB1
NUDT15
THSD1
CYSLTR2
SPRYD7
PCDH20
RNASEH2B
DHRS12
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
SETDB2
EBPL
ARL11
WDFY2
PRR20A
HNRNPA1L2
FAM124A
KCNRG
NEK5
DLEU2
ALG11
SERPINE3
PRR20B
PRR20C
PRR20D
PRR20E
MIR759
MIR3169
MIR3613
MIR548X2
MIR4703
MIR5007
MIR5693
Genes in Wide Peak

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

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

Genes
KCNQ1OT1
KCNQ1
Genes in Wide Peak

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

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

Genes
ATRX
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q34.

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

Genes
EBF1
ITK
NPM1
TLX3
RANBP17
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
RN7SKP148
snoU13|ENSG00000239026.1
NSG2
RNA5SP200
SNORA74B
ATP6V0E1
MIR5003
SNORA57|ENSG00000212529.1
C5orf50
SNORA70|ENSG00000206909.1
RN7SL339P
snoU13|ENSG00000252387.1
RN7SL623P
MIR4454
KCNMB1
LCP2
C5orf58
MIR378E
MIR585
MIR103A1
PANK3
FBLL1
SNORA40|ENSG00000253065.1
RN7SKP60
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68|ENSG00000252458.1
LSM11
THG1L
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
RNA5SP198
RN7SKP232
ATOX1
BNIP1
CCNG1
CLTB
DOCK2
DRD1
DUSP1
FABP6
FOXI1
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GLRA1
GRIA1
HMMR
HRH2
IL12B
MFAP3
MSX2
RARS
SGCD
SLIT3
SNCB
SPARC
STK10
TTC1
STC2
ADAM19
FGF18
PTTG1
CNOT8
HAND1
MED7
CLINT1
G3BP1
SLU7
CPLX2
FAXDC2
FAM114A2
SOX30
RNF44
ATP10B
FAF2
WWC1
FBXW11
LARP1
GEMIN5
TSPAN17
HAVCR1
CYFIP2
MAT2B
MRPL22
KCNIP1
RPL26L1
NOP16
NEURL1B
CDHR2
SPDL1
GALNT10
NMUR2
KIAA1191
ERGIC1
TENM2
C5orf54
CCNJL
SAP30L
CPEB4
THOC3
HAVCR2
UNC5A
BOD1
TIMD4
UBTD2
SFXN1
GPRIN1
PWWP2A
C1QTNF2
C5orf47
UBLCP1
CREBRF
FAM71B
RNF145
HIGD2A
FAM153B
EFCAB9
SH3PXD2B
KIF4B
NIPAL4
SIMC1
MIR146A
FNDC9
FAM196B
C5orf52
MIR1303
MIR3141
MIR3912
MIR4634
MIR378H
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

Genes
AJAP1
MIR4417
Genes in Wide Peak

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

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

Genes
CDKN2C
MIR4421
FAF1
DMRTA2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p15.33.

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

Genes
RNA5SP176
RN7SKP79
UBE2QL1
RN7SKP73
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIP13
PDCD6
SLC12A7
PAPD7
TPPP
EXOC3
KIAA0947
IRX4
NSUN2
CEP72
AHRR
MRPL36
BRD9
IRX1
ZDHHC11
LPCAT1
CLPTM1L
MED10
NKD2
C5orf55
C5orf38
IRX2
ADAMTS16
SLC6A19
SLC6A18
MIR4277
MIR4457
MIR4456
Genes in Wide Peak

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

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

Genes
TFRC
FAM157A
FYTTD1
snoU13|ENSG00000238491.1
MIR4797
U4|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
RN7SL36P
MIR3137
APOD
BDH1
DLG1
MFI2
MUC4
PAK2
PCYT1A
PPP1R2
RPL35A
KIAA0226
TNK2
NCBP2
ACAP2
PIGX
PIGZ
IQCG
LRCH3
CEP19
LMLN
TM4SF19
ZDHHC19
FAM43A
XXYLT1
RNF168
SLC51A
FBXO45
MUC20
SENP5
TCTEX1D2
SMCO1
WDR53
ANKRD18DP
NRROS
LINC00885
MIR570
MIR922
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.31.

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

Genes
BAP1
SETD2
PBRM1
CHDH
SNORD63|ENSG00000251987.1
SNORA26|ENSG00000212608.1
SNORD38|ENSG00000207109.1
RN7SL821P
snoU13|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19|ENSG00000222345.1
SNORD19B|ENSG00000238862.1
SNORD19|ENSG00000212493.1
SNORD19B|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13|ENSG00000238350.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000251938.1
PRSS44
PRSS45
SNORD77|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
ALAS1
AMT
APEH
RHOA
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DOCK3
DUSP7
CELSR3
GNAI2
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
TGM4
TKT
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
ZNF35
IFRD2
MAPKAPK3
MANF
HYAL3
HYAL2
BSN
ACKR5
RRP9
CACNA2D2
IP6K1
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CCR9
USP19
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
EXOSC7
RAD54L2
STAB1
NBEAL2
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
PTPN23
DNAH1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
C3orf18
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
ELP6
QRICH1
DALRD3
IL17RB
DCP1A
GLT8D1
ZKSCAN7
SEMA3G
KIF15
PCBP4
KIAA1143
SELK
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
WDR82
ATRIP
NICN1
MON1A
ABHD14B
UCN2
ZNF502
RFT1
ACTR8
ZNF501
GPR62
TMEM42
IQCF1
GLYCTK
PPM1M
LSMEM2
CCDC12
KLHDC8B
ALS2CL
TMIE
FBXW12
TCAIM
CCDC36
PRSS42
ZNF445
TOPAZ1
TMEM110
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
MIR425
SPINK8
ARIH2OS
C3orf84
CCR2
PRSS46
MIR4271
MIR4787
MIR4443
Genes in Wide Peak

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

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

Genes
SCAF11
RN7SL246P
RNA5SP361
SNORA74|ENSG00000252917.1
RN7SL10P
RNA5SP360
MUC19
SNORA22|ENSG00000199571.1
CNTN1
NELL2
TWF1
YAF2
PDZRN4
PLEKHA8P1
IRAK4
PPHLN1
SLC38A2
SLC38A4
ADAMTS20
SLC38A1
PUS7L
TMEM117
ZCRB1
SLC2A13
LRRK2
PRICKLE1
ANO6
ARID2
C12orf40
GXYLT1
AMIGO2
DBX2
Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
NFATC1
CTDP1
TXNL4A
ADNP2
KCNG2
PQLC1
PARD6G
ATP9B
HSBP1L1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

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

Genes
IRF4
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
FOXF2
FOXC1
GMDS
EXOC2
DUSP22
FOXQ1
HUS1B
Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
LINC00229
SCUBE1
RNU12
RN7SKP80
RRP7B
RRP7A
snoU13|ENSG00000238498.1
LINC00634
SHISA8
MIR33A
ACR
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
NAGA
NDUFA6
PPARA
MAPK11
MAPK12
SBF1
TCF20
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
MCAT
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
MIOX
PRR5
TRMU
SEPT3
PANX2
PARVG
CERK
EFCAB6
CENPM
CRELD2
ADM2
TRABD
PNPLA3
HDAC10
LDOC1L
POLDIP3
KIAA1644
SHANK3
TUBGCP6
LMF2
SMDT1
SERHL
PHF21B
KLHDC7B
TNFRSF13C
FAM109B
NFAM1
PNPLA5
WBP2NL
SERHL2
ATP5L2
C22orf34
LINC00207
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR378I
MIR4535
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q24.3.

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

Genes
RECQL4
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
CYC1
EEF1D
GPT
GRINA
HSF1
TONSL
PLEC
RPL8
TSTA3
ZNF7
ZNF16
GPAA1
FOXH1
LRRC14
ZNF623
PUF60
ZC3H3
BOP1
SCRIB
FBXL6
OPLAH
COMMD5
CPSF1
CYHR1
VPS28
FAM203A
EXOSC4
SLC39A4
ZNF250
PYCRL
C8orf33
SLC52A2
GSDMD
ARHGAP39
ZNF34
SHARPIN
SCRT1
MAF1
PARP10
TIGD5
PPP1R16A
ZNF251
KIFC2
NAPRT1
MFSD3
ADCK5
MAPK15
ZNF707
FAM83H
NRBP2
ZNF517
KIAA1875
TMEM249
SPATC1
MAFA
LRRC24
MROH6
MROH1
FAM203B
MIR4664
Genes in Wide Peak

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

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

Genes
RN7SL5P
SNORD27|ENSG00000251699.1
PTPRD
Genes in Wide Peak

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

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

Genes
MYB
ROS1
TNFAIP3
GOPC
AIRN
SNORA29
SNORA20|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
ACAT2
AMD1
ARG1
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FUCA2
FYN
GJA1
GPR6
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PKIB
PTPRK
REV3L
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
TCF21
TCP1
DYNLT1
TPD52L1
UTRN
EZR
VIP
EPM2A
DDO
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
MED23
AKAP7
WTAP
AKAP12
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
SMPDL3A
RAB32
KATNA1
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
FBXO5
RGS17
PDE7B
SESN1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TUBE1
CDC40
RWDD1
AIG1
SNX9
HECA
IL20RA
MTRF1L
AHI1
RMND1
VNN3
ECHDC1
AGPAT4
TULP4
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
ABRACL
PBOV1
TRMT11
PERP
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
ARMC2
L3MBTL3
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
ARHGAP18
SYTL3
GTF3C6
MTFR2
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAGAP
TAAR9
TAAR1
NCOA7
HINT3
RAET1E
ZC2HC1B
RAET1L
SAMD3
PNLDC1
RNF217
NKAIN2
OLIG3
TXLNB
OSTCP1
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
MCM9
SHPRH
CEP57L1
PPIL6
DCBLD1
TAAR6
SLC35D3
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
SUMO4
CENPW
SOGA3
CEP85L
THEMIS
SAMD5
IYD
GTF2H5
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR588
METTL24
TMEM242
TRAPPC3L
MIR1202
MIR1273C
MIR3144
MIR3918
MIR3668
SMLR1
MIR4466
MIR4465
MIR548AJ1
MIR548H5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.3.

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

Genes
CARD11
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
EIF3B
ADAP1
IQCE
SUN1
INTS1
SNX8
FTSJ2
GET4
CYP2W1
HEATR2
CHST12
MICALL2
TTYH3
PSMG3
C7orf50
ZFAND2A
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
CBLB
GATA2
RPN1
TFG
RNA5SP142
RNY4P4
U8|ENSG00000253004.1
RNA5SP141
KY
RPL39P5
RNA5SP140
TFP1
SNORA33|ENSG00000201827.1
snoU13|ENSG00000238701.1
MIR5704
SNORA58|ENSG00000249020.1
RN7SKP212
COL6A4P2
FAM86HP
ALG1L2
RN7SL752P
SNORA7B
RPL32P3
snoU13|ENSG00000238874.1
snoU13|ENSG00000252435.1
RN7SL698P
SNORA24|ENSG00000207130.1
MIR1280
RNA5SP139
NUP210P1
TXNRD3NB
RNA5SP138
U1|ENSG00000272020.1
FAM86JP
snoU13|ENSG00000238992.1
MIR5092
RNA5SP137
MIR544B
UMPS
MIR5002
SNORA5
PTPLB
SEC22A
snoU13|ENSG00000238480.1
SNORD112|ENSG00000252170.1
RN7SL172P
snoU13|ENSG00000238670.1
ARGFX
MIR5682
FSTL1
RN7SL397P
RN7SL762P
COX17
TIMMDC1
LINC00901
TUSC7
RN7SL582P
LINC00903
RN7SL815P
RN7SL767P
MIR4446
SNORD112|ENSG00000253076.1
SLC35A5
MIR567
PVRL3
RNU6ATAC15P
LINC00488
U3|ENSG00000221633.1
SNORA70|ENSG00000202379.1
LINC00636
LINC00635
LINC00883
LINC00882
snoU13|ENSG00000238525.1
snoU13|ENSG00000238312.1
SNORA31|ENSG00000252989.1
NIT2
SNORD61|ENSG00000238377.1
TMEM30C
LINC00973
OR5H8P
OR5AC1
CRYBG3|ENSG00000080200.5
CRYBG3|ENSG00000233280.2
MTRNR2L12
MTHFD2P1
LINC00879
NSUN3
U3|ENSG00000212598.1
ACPP
ADCY5
ADPRH
ALCAM
ATP6V1A
CASR
CD80
CD86
CD47
COL8A1
CPOX
CSTA
DRD3
EPHB1
GAP43
GOLGB1
GP9
GPR15
GSK3B
GTF2E1
HCLS1
HGD
ITGB5
KPNA1
LSAMP
MCM2
CD200
MYLK
NCK1
NDUFB4
PCCB
PLXNA1
PPP2R3A
PROS1
RHO
RPL24
RYK
SLC15A2
SLCO2A1
TF
TRH
UPK1B
CNBP
ZNF80
ZNF148
RAB7A
BFSP2
RUVBL1
B4GALT4
SNX4
NR1I2
MBD4
H1FX
KALRN
STXBP5L
GUCA1C
IQCB1
DZIP3
TOMM70A
CD96
STAG1
ST3GAL6
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
MRPL3
FILIP1L
MGLL
COPG1
MYH15
TMCC1
PLXND1
DNAJC13
C3orf27
ANAPC13
C3orf17
ABI3BP
ZBTB20
OR5K1
OR5H1
FAM162A
NPHP3
ATP2C1
ZBTB11
MORC1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
SEC61A1
PIK3R4
PODXL2
TRAT1
IMPG2
PLA1A
AMOTL2
ACKR4
RAB6B
FBXO40
IL20RB
SEMA5B
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
TRMT10C
SLC41A3
TMEM45A
IFT57
MSL2
DPPA4
TMEM39A
ABHD10
CDV3
IFT122
TBC1D23
WDR52
EAF2
CLDND1
MUC13
C3orf37
POGLUT1
BBX
PCNP
SENP7
HEG1
KIAA1257
ARHGAP31
KIAA1407
KIAA1524
SRPRB
EEFSEC
POPDC2
NFKBIZ
ATG3
CCDC14
TMEM108
OR5H6
OR5H2
ZXDC
ZBED2
CEP97
HSPBAP1
C3orf52
QTRTD1
EFCC1
NEK11
UBA5
C3orf36
NAA50
CEP63
ABTB1
SLC35G2
OR5AC2
PARP9
ARL6
ACAD11
CHCHD6
CMSS1
SLC12A8
RETNLB
CCDC54
MINA
GPR128
DIRC2
MAATS1
PHLDB2
EFCAB12
BOC
NXPE3
TXNRD3
OSBPL11
LRRC58
CPNE4
CCDC58
ZPLD1
CD200R1
DCBLD2
TPRA1
UROC1
NUDT16
COL6A6
H1FOO
DTX3L
DPPA2
CCDC80
BTLA
ROPN1B
C3orf22
SPICE1
NUDT16P
IGSF11
C3orf30
PARP15
DNAJB8
GPR156
CHST13
KBTBD12
ALG1L
ARL13B
DHFRL1
GABRR3
TIGIT
KIAA2018
ZDHHC23
COL6A5
PLCXD2
GCSAM
EPHA6
RABL3
C3orf56
SLC9C1
ILDR1
RAB43
TMPRSS7
CD200R1L
LNP1
CCDC37
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
STX19
MIR568
MIR548I1
MIR3921
ISY1
MIR4445
MIR4796
MIR4788
MIR548AB
MIR4447
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

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

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13|ENSG00000239094.1
snoU13|ENSG00000238545.1
MIR4742
snoU13|ENSG00000238856.1
MIR320B2
SNORA72|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13|ENSG00000238576.1
snoU13|ENSG00000238798.1
U3|ENSG00000221673.1
RNA5SP76
SLC30A10
U3|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26|ENSG00000212187.1
RN7SL344P
SLC30A1
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
ZNF124
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
INTS7
AHCTF1
NSL1
OR2M4
OR2L2
OR2T1
RPS6KC1
TAF5L
DISC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
DESI2
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
ZNF692
IARS2
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
SIPA1L2
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
SPRTN
OBSCN
EFCAB2
MLK4
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
NLRP3
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
GCSAML
CNIH3
EXOC8
C1orf227
FAM71A
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
TRIM67
MAP1LC3C
OR13G1
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A
Genes in Wide Peak

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

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

Genes
MIR548AR
CDC16
RASA3
UPF3A
CHAMP1
MIR4502
Genes in Wide Peak

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

Table S48.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
CDKN1B
CREBL2
EMP1
GPR19
LRP6
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
APOLD1
GSG1
LOH12CR1
C12orf36
MIR614
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
FGFR1OP
MLLT4
MYB
TNFAIP3
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13|ENSG00000239136.1
AIRN
SNORA29
SNORA20|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
ACAT2
ARG1
CCR6
CTGF
EPB41L2
EYA4
ESR1
FUCA2
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LAMA2
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PSMB1
PTPRK
RPS6KA2
SGK1
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCF21
TCP1
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
RNASET2
SYNJ2
VNN2
VNN1
TAAR5
MAP7
LATS1
TAAR2
MED23
QKI
AKAP7
WTAP
AKAP12
PHACTR2
BCLAF1
UST
CITED2
HBS1L
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
DLL1
MRPL18
CLDN20
NOX3
AIG1
SNX9
MPC1
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
ABRACL
PBOV1
PERP
SMOC2
ALDH8A1
ULBP3
OR2A4
C6orf211
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
L3MBTL3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
ARHGAP18
SYTL3
MTFR2
TMEM200A
IL22RA2
SLC18B1
TAGAP
TAAR9
TAAR1
PACRG
RAET1E
ZC2HC1B
RAET1L
SAMD3
PNLDC1
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
TMEM244
WDR27
SHPRH
PRR18
TAAR6
SLC35D3
ECT2L
NUP43
C6orf58
RAET1G
SUMO4
CENPW
SOGA3
C6orf120
THEMIS
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
CTAGE9
MIR548A2
MIR588
TMEM242
MIR1202
MIR1273C
MIR3918
MIR3939
MIR3668
SMLR1
MIR4466
MIR4465
MIR548AJ1
MIR548H5
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 24 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 1300 0.04 -2.41 1 0.37 25 0
1q 1195 0.05 -2.31 1 0.05 -1.83 1
2p 624 0.03 -4.05 1 0.04 -2.93 1
2q 967 0.02 -4.48 1 0.04 -3.04 1
3p 644 0.02 -4.63 1 0.06 -1.3 1
3q 733 0.02 -4.98 1 0.06 -1.79 1
4p 289 0.03 -4.17 1 0.15 5.57 4.67e-08
4q 670 0.01 -4.98 1 0.19 9.48 0
5p 183 0.02 -4.54 1 0.07 -0.767 1
5q 905 0.02 -4.9 1 0.07 -0.9 1
6p 710 0.01 -5.14 1 0.06 -1.48 1
6q 556 0.00 -5.79 1 0.12 3.88 0.000142
7p 389 0.23 13 0 0.01 -4.85 1
7q 783 0.29 18.5 0 0.01 -4.69 1
8p 338 0.09 1.03 0.889 0.04 -3.38 1
8q 551 0.11 2.69 0.0241 0.02 -4.28 1
9p 301 0.03 -3.33 1 0.24 13.8 0
9q 700 0.05 -2.33 1 0.11 2.59 0.0109
10p 253 0.13 3.67 0.00125 0.19 8.65 0
10q 738 0.01 -4.91 1 0.20 10.7 0
11p 509 0.07 -0.867 1 0.13 4.34 2.25e-05
11q 975 0.12 3.54 0.00164 0.05 -2.38 1
12p 339 0.06 -1.17 1 0.06 -1.48 1
12q 904 0.03 -3.85 1 0.11 2.7 0.00827
13q 560 0.01 -4.83 1 0.23 12.7 0
14q 938 0.01 -5.23 1 0.16 7.1 2.84e-12
15q 810 0.02 -4.42 1 0.10 2.28 0.0242
16p 559 0.03 -4.11 1 0.03 -3.79 1
16q 455 0.04 -3.24 1 0.04 -2.76 1
17p 415 0.04 -3.32 1 0.03 -3.95 1
17q 972 0.04 -2.71 1 0.02 -4.63 1
18p 104 0.04 -3.21 1 0.14 4.77 3.21e-06
18q 275 0.03 -4.09 1 0.13 3.92 0.000127
19p 681 0.20 10.2 0 0.07 -0.734 1
19q 935 0.08 0.421 1 0.43 29.4 0
20p 234 0.09 0.851 1 0.01 -5.12 1
20q 448 0.08 0.558 1 0.01 -5.61 1
21q 258 0.05 -2.45 1 0.08 -0.0898 1
22q 564 0.05 -2.15 1 0.12 3.23 0.0016
Xp 418 0.04 -3.09 1 0.21 11.2 0
Xq 668 0.08 0.591 1 0.16 6.6 8.43e-11
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/LGG-TP/22224370/GDAC_MergeDataFiles_12185181/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_GENCODE_v18_20140127.mat

  • CNV Files = /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.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 513 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

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

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