SNP6 Copy number analysis (GISTIC2)
Pheochromocytoma and Paraganglioma (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1BC3XBR
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1BC3XBR
Overview
Introduction

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

Summary

There were 160 tumor samples used in this analysis: 18 significant arm-level results, 7 significant focal amplifications, and 21 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 - 7 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
--- | --- | --- | --- | ---
1q21.3 | 0.0003485 | 0.0003485 | chr1:120523956-154950221 | 251
4q31.1 | 0.001235 | 0.001408 | chr4:140946021-141006734 | 1
17q21.31 | 0.0069658 | 0.0069658 | chr17:42282074-42389627 | 3
12q13.3 | 0.031228 | 0.031228 | chr12:55017371-58374945 | 119
14q24.3 | 0.056742 | 0.056742 | chr14:77411889-77529068 | 1
4q25 | 0.21293 | 0.23432 | chr4:55115761-118191881 | 325
11p15.2 | 0.23664 | 0.23664 | chr11:12145534-25296454 | 78

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
ARNT
BCL9
NOTCH2
TPM3
PDE4DIP
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
CHRNB2
CKS1B
CTSK
CTSS
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
NPR1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
SNAPIN
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
S100A7L2
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR190B
C1orf68
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
TNFAIP8L2-SCNM1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q31.1.

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

Genes
MAML3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q21.31.

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

Genes
SLC4A1
UBTF
RUNDC3A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.3.

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

Genes
CDK4
DDIT3
NACA
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
APOF
ATP5B
CD63
CDK2
CS
CYP27B1
DGKA
ERBB3
B4GALNT1
BLOC1S1
GLI1
INHBC
ITGA7
KIF5A
LRP1
MARS
METTL1
MIP
MMP19
MYL6
MYO1A
NAB2
PA2G4
PRIM1
RAB5B
RBMS2
RDH5
RPL41
RPS26
TSPAN31
SHMT2
PMEL
SMARCC2
STAT2
STAT6
SUOX
TAC3
RDH16
HSD17B6
TIMELESS
KIAA0748
ZBTB39
PAN2
TSFM
CTDSP2
RNF41
GDF11
CNPY2
DCTN2
AVIL
PTGES3
OS9
BAZ2A
NXPH4
GPR182
R3HDM2
TMEM194A
ESYT1
METTL21B
SNORD59A
GLS2
ORMDL2
IL23A
NDUFA4L2
NEUROD4
ARHGAP9
IKZF4
SLC26A10
OBFC2B
PIP4K2C
INHBE
WIBG
SARNP
ZC3H10
DNAJC14
LACRT
XRCC6BP1
MARCH9
COQ10A
MBD6
ARHGEF25
AGAP2
DCD
MUCL1
OR10P1
SDR9C7
OR10A7
MYL6B
DTX3
METTL7B
STAC3
OR6C74
OR6C3
OR6C6
ANKRD52
SLC39A5
SPRYD4
OR6C2
OR6C4
OR6C1
OR6C75
OR6C76
OR6C70
OR6C65
OR6C68
MIR26A2
TMEM198B
OR9K2
SNORD59B
LOC100130776
MIR1228
LOC100506844
BLOC1S1-RDH5

Genes in Wide Peak

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

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

Genes
IRF2BPL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q25.

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

Genes
KDR
KIT
PDGFRA
RAP1GDS1
TET2
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
hsa-mir-1269
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
ALB
AMBN
ANK2
ANXA3
AREG
ART3
ATOH1
BMP3
BMPR1B
BTC
CAMK2D
CASP6
CCNG2
SCARB2
CDS1
CENPC1
CENPE
CSN1S1
CSN2
CSN3
DCK
DMP1
DSPP
EGF
EIF4E
ENPEP
EPHA5
EREG
FGF5
GC
GK2
GNRHR
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
H2AFZ
HADH
HNRNPD
HSP90AB3P
HTN1
HTN3
IBSP
CFI
IGFBP7
IGJ
IL8
CXCL10
MANBA
CXCL9
AFF1
MTTP
MUC7
NFKB1
NKX6-1
PDHA2
PF4
PF4V1
PITX2
PKD2
POLR2B
PPEF2
PPAT
PPBP
PPP3CA
PRKG2
MAPK10
PTPN13
REST
RPL34
CXCL6
CXCL11
CXCL5
SNCA
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
UBE2D3
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
SPARCL1
USO1
UNC5C
LAMTOR3
SLC4A4
HERC3
STBD1
CDKL2
PAPSS1
AIMP1
TMPRSS11D
ABCG2
ADAMTS3
CLOCK
CEP135
G3BP2
HNRPDL
TSPAN5
ENAM
FAM13A
SEC24B
CXCL13
PAICS
PDLIM5
RRH
UGT2B11
HPSE
NMU
SMR3B
NPFFR2
PPBPL2
UGT2A1
CCNI
SEC31A
RUFY3
MMRN1
WDFY3
METAP1
LPHN3
PARM1
RCHY1
ANKRD17
STAP1
SMR3A
PPA2
DAPP1
DKK2
NAAA
COQ2
SULT1B1
HPGDS
TMPRSS11E
MRPS18C
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
NUDT9
NUP54
GAR1
UGT2B28
ARHGEF38
ODAM
HERC6
CCDC109B
BANK1
SDAD1
UBA6
C4orf21
AP1AR
BMP2K
SEPT11
EXOC1
TMEM165
BDH2
SMARCAD1
MEPE
PRDM8
UTP3
INTS12
KIAA1211
KLHL8
SHROOM3
ENOPH1
PROL1
OSTC
NEUROG2
SLC39A8
NDST4
AGXT2L1
MRPL1
ELOVL6
ARSJ
SRD5A3
THAP9
UGT2A3
GSTCD
SCD5
DNAJB14
FRAS1
ALPK1
CXXC4
PLA2G12A
ARHGAP24
C4orf17
FAM175A
NOA1
HOPX
COL25A1
NAA11
AGPAT9
PIGY
CABS1
FLJ20021
YTHDC1
MOB1B
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
GDEP
ANTXR2
LIN54
C4orf32
TMPRSS11B
ARL9
AASDH
PDCL2
C4orf36
TRAM1L1
SLC9B2
SLC9B1
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
TIGD2
RASSF6
SGMS2
CNOT6L
TECRL
C4orf22
LOC255130
EPGN
NPNT
LOC256880
FDCSP
NAP1L5
LOC285456
FAM13A-AS1
GPRIN3
COX18
C4orf37
CSN1S2AP
CCDC158
TMPRSS11A
SOWAHB
LRIT3
SLC10A6
HSD17B13
PCNAP1
TMPRSS11F
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
WDFY3-AS2
MIR302A
C4orf11
MTHFD2L
LOC441025
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC550112
LOC550113
UGT2A2
LOC641518
LOC644145
LOC644248
TMPRSS11GP
MIR575
MIR577
FAM47E
FTLP10
LOC100144602
MIR1243
MIR1973
CSN1S2BP
LOC100499177
MIR3684
LOC100505702
LOC100505875
LOC100506035
LOC100506462
LOC100506564
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4450
MIR4451
FAM47E-STBD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p15.2.

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

Genes
FANCF
hsa-mir-3159
ARNTL
CALCA
CALCB
COPB1
GAS2
GTF2H1
KCNC1
KCNJ11
LDHA
LDHC
MYOD1
NELL1
NUCB2
PDE3B
PIK3C2A
PSMA1
PTH
RPS13
SAA1
SAA2
SAA3P
SAA4
ABCC8
TEAD1
TPH1
TSG101
CSRP3
SLC6A5
MICAL2
USH1C
PRMT3
SPON1
HTATIP2
OR7E14P
C11orf58
HPS5
RRAS2
SERGEF
ZDHHC13
UEVLD
SOX6
PARVA
SLC17A6
E2F8
FAR1
BTBD10
PTPN5
MICALCL
NAV2
SAAL1
MRGPRX2
MRGPRX3
MRGPRX4
CYP2R1
DBX1
PLEKHA7
SPTY2D1
TMEM86A
LDHAL6A
ANO5
SVIP
MRGPRX1
IGSF22
LUZP2
B7H6
INSC
NAV2-AS4
LOC494141
RASSF10
LOC100126784
LOC100500938
LOC100506305
LOC100506540
SAA2-SAA4
MIR4486
MIR4694

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 - 21 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
--- | --- | --- | --- | ---
1p12 | 7.4452e-20 | 7.4452e-20 | chr1:117751737-118152240 | 1
17q11.2 | 3.2375e-10 | 3.2167e-10 | chr17:29326736-29622105 | 2
3p24.1 | 6.0163e-07 | 6.407e-07 | chr3:27762089-28433157 | 2
3q26.1 | 2.0735e-06 | 2.0735e-06 | chr3:161217822-163894013 | 2
11q22.1 | 1.462e-05 | 1.462e-05 | chr11:96126036-100558999 | 1
22q13.31 | 0.00016533 | 0.00016533 | chr22:47571204-48018269 | 1
11p15.4 | 0.00054378 | 0.00051791 | chr11:1-11293017 | 277
9p24.2 | 0.00078878 | 0.00077675 | chr9:2842384-3826080 | 1
6p12.3 | 0.00080576 | 0.00081059 | chr6:49915604-49978544 | 2
4q35.2 | 0.0034221 | 0.003186 | chr4:169747574-191154276 | 99
16q21 | 0.0033927 | 0.003186 | chr16:59786558-64981096 | 2
4q22.1 | 0.0035492 | 0.0035799 | chr4:90762789-91050179 | 1
6q16.1 | 0.0065852 | 0.006558 | chr6:92231219-94419827 | 2
5q15 | 0.010326 | 0.009912 | chr5:79949348-113842067 | 111
12q21.33 | 0.0099067 | 0.009912 | chr12:91383361-91498710 | 1
8p22 | 0.02387 | 0.02393 | chr8:14710032-16024383 | 3
17p13.2 | 0.031972 | 0.030814 | chr17:6344536-6547775 | 3
9q21.12 | 0.040575 | 0.039541 | chr9:73027614-74298719 | 3
1q44 | 0.10475 | 0.10508 | chr1:215791352-249250621 | 267
7q33 | 0.21002 | 0.20428 | chr7:57244042-159138663 | 769
Xp21.1 | 0.22956 | 0.23713 | chrX:1-155270560 | 1046
2q34 | 0.25493 | 0.25493 | chr2:1-243199373 | 1516
13q22.3 | 0.25493 | 0.25493 | chr13:1-115169878 | 414

Genes in Wide Peak

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

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

Genes
MAN1A2

Genes in Wide Peak

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

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

Genes
NF1
MIR4733

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p24.1.

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

Genes
AZI2
CMC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.1.

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

Genes
hsa-mir-1263
LOC647107

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.1.

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

Genes
CNTN5

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
CARS
HRAS
LMO1
NUP98
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
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
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
MTRNR2L8
MIR210HG
MIR4686
MIR4485
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.2.

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

Genes
RFX3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p12.3.

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

Genes
DEFB113
DEFB114

Genes in Wide Peak

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

Table S17. Genes in bold are cancer genes as defined by The Sanger Institute: 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
PALLD
FAM149A
FBXO8
DUX2
PDLIM3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SH3RF1
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
CBR4
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 16q21.

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

Genes
CDH8
LOC644649

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
MMRN1

Genes in Wide Peak

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

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

Genes
EPHA7
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
APC
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
CAMK4
CAST
CCNH
CETN3
CHD1
CKMT2
COX7C
HAPLN1
VCAN
EFNA5
FER
GLRX
KCNN2
LNPEP
MAN2A1
MCC
MEF2C
MSH3
PAM
PCSK1
RASA1
RASGRF2
RPS23
SRP19
NR2F1
XRCC4
ST8SIA4
REEP5
NREP
RAB9BP1
TTC37
PJA2
EDIL3
POLR3G
RHOBTB3
ELL2
PPIP5K2
SSBP2
RNU5E-1
RNU5D-1
ERAP1
FLJ11235
GIN1
RIOK2
ARRDC3
EPB41L4A
ERAP2
FBXL17
YTHDC2
MCTP1
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
ZCCHC9
ANKRD32
TSLP
C5orf30
SLC25A46
ATP6AP1L
EPB41L4A-AS1
LYSMD3
SLCO6A1
POU5F2
STARD4
WDR36
ACOT12
TMEM167A
MBLAC2
TMEM161B
ARSK
FAM81B
DCP2
LIX1
C5orf27
KIAA0825
GPR150
NBPF22P
RGMB
RFESD
FAM174A
SLCO4C1
MIR9-2
FLJ42709
FLJ35946
TMEM232
LINC00461
SNORA13
SCARNA18
MIR583
LOC100129716
LOC100131067
LOC100133050
LOC100289230
LOC100289673
MIR2277
MIR4280
MIR3607
MIR3660
LOC100505678
LOC100505894
MIR3977

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.33.

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

Genes
KERA

Genes in Wide Peak

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

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

Genes
hsa-mir-383
TUSC3
MIR383

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.2.

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

Genes
KIAA0753
FAM64A
PITPNM3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.12.

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

Genes
hsa-mir-204
TRPM3
MIR204

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q33.

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

Genes
BRAF
CDK6
ELN
EZH2
HIP1
MET
SMO
AKAP9
SBDS
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
hsa-mir-590
hsa-mir-4284
hsa-mir-4283-2
hsa-mir-3147
ABP1
ACHE
AKR1B1
ARF5
ASL
ASNS
AZGP1
OPN1SW
BPGM
CACNA2D1
CALCR
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
KRIT1
CD36
CDK5
CFTR
CHRM2
AP1S1
CLCN1
COL1A2
CPA1
CPA2
CLDN4
CLDN3
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
ERV3-1
FLNC
GBX1
GNAI1
GNB2
GNG11
GNGT1
GPR22
GPR37
GRM3
GRM8
GTF2I
GTF2IP1
GUSB
HGF
MNX1
AGFG2
HSPB1
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LIMK1
LRCH4
MCM7
DNAJB9
MDH2
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PIP
PMS2P1
PMS2L2
PMS2P4
PMS2P5
PMS2P3
PODXL
POLR2J
PON1
PON2
PON3
POR
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
PSMC2
TAS2R38
PTN
PTPN12
PTPRN2
PTPRZ1
RARRES2
RFC2
RHEB
CCL24
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
SRI
AKR1D1
SRPK2
SSBP1
STX1A
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
EIF4H
CLIP2
LAT2
WNT2
XRCC2
YWHAG
ZNF3
ZKSCAN1
ZSCAN21
ZNF138
ZP3
ZYX
MTERF
SHFM1
TFPI2
ST7
ARHGEF5
ZNF212
TRRAP
FZD1
FZD9
ZNF282
CUL1
TPST1
FKBP6
TRIM24
BUD31
SGCE
MGAM
WASL
PLOD3
BAZ1B
CLDN12
DGKI
AP4M1
BCL7B
ATP6V1F
ACCN3
PMPCB
ATP5J2
GTF2IRD1
PDIA4
UBE3C
FAM131B
SEMA3E
DOCK4
FAM115A
MAGI2
POM121
DMTF1
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
BET1
CCL26
SEMA3A
FAM3C
COG5
ZNHIT1
SEMA3C
ARPC1A
SH2B2
STAG3
ZNF273
FGL2
CPSF4
FASTK
DBF4
COPS6
DUS4L
ZNF277
ABCB8
TP53TG1
PDAP1
TFEC
LAMB4
LMTK2
POMZP3
PAXIP1
KLHDC10
PEG10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
AUTS2
HYALP1
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
TBL2
STEAP1
COPG2
HBP1
DNAJC2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
CRCP
RABGEF1
PCLO
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRB
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
MLXIPL
CPA4
ZNF117
WNT16
ACTL6B
PRKAG2
ZNF107
ZC3HC1
SRRT
LUC7L2
MRPS33
STYXL1
ASB4
NUB1
NAA38
ADAM22
PION
GPR85
TAS2R5
STAG3L1
ANKIB1
CHPF2
PUS7
ING3
LRRN3
CROT
ALKBH4
SAMD9
NCAPG2
CHCHD3
ZCWPW1
C7orf42
WDR60
RBM28
TYW1
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
PPP1R9A
CCDC132
NSUN5
AGK
METTL2B
MLL5
BAIAP2L1
SLC25A40
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
PHTF2
ACTR3B
KIAA1147
RHBDD2
FAM40B
ESYT2
ZNF398
CCDC146
GATAD1
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
WBSCR17
TMEM168
LINC00244
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
RABL5
CYP3A43
CASD1
STAG3L4
LRRC61
C7orf49
ZNF655
PVRIG
C7orf23
GCC1
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ZNF767
C7orf58
TTC26
ORAI2
UPK3B
JHDM1D
OR2AE1
WBSCR16
TSC22D4
TRIM56
ABHD11
TMUB1
CALN1
ARMC10
TMEM120A
IMMP2L
CTTNBP2
RBM48
ZNF394
GTF2IRD2
MYH16
SLC37A3
DNAJC30
KRBA1
FAM71F1
MGC16142
SLC35B4
TMEM209
TMEM60
GTPBP10
TRIM4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
DTX2
WBSCR22
TSGA13
AGAP3
C7orf13
OR9A4
WBSCR28
TRIM50
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
SRCRB4D
ASZ1
MUC17
RNF32
ASB15
RUNDC3B
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
VKORC1L1
LOC154822
LOC154860
IQUB
LOC154872
KCTD7
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
WBSCR27
SBDSP1
VPS37D
NSUN5P1
RBM33
MGC27345
ZNF92
GALNTL5
ZNF679
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
BHLHA15
ZNF800
GIMAP1
ABHD11-AS1
LOC202781
C7orf33
SAMD9L
C7orf62
ZNF804B
FABP5P3
ZNF498
FAM200A
PPP1R35
GPC2
SRRM3
RSBN1L
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
UBN2
MBLAC1
FAM133B
TAS2R39
TAS2R40
TAS2R41
NSUN5P2
STEAP2
CNPY1
LOC285889
INTS4L1
LINC00174
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
DLX6-AS1
ZNF789
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
ZNF680
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
GNAT3
MOGAT3
FAM71F2
STRA8
KLRG2
WDR86
GJC3
DPY19L2P2
LOC349160
GATS
GSTK1
TRIM73
NAT16
SLC26A5
LHFPL3
KCP
TRIM74
FLJ43663
RNF148
SPDYE8P
GATSL1
GTF2IRD2B
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
OR2A5
RPL13AP17
GTF2IRD2P1
LRRD1
FLJ42280
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
UFSP1
MIR106B
MIR129-1
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
ZNF716
LOC441242
TYW1B
SPDYE7P
DTX2P1-UPK3BP1-PMS2P11
SPDYE3
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
ZNF727
OR2A2
DPY19L2P4
STAG3L3
STAG3L2
SPDYE5
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
LOC493754
WEE2
LOC541473
POLR2J3
MIR489
MIR490
FDPSL2A
LOC641746
CCT6P3
CCT6P1
ZNF862
LOC643955
INTS4L2
LOC645249
LOC645591
AZGP1P1
LOC646329
C7orf73
LOC649395
NCF1
ACTR3C
NCF1B
NCF1C
SNORA14A
SNORA22
MIR590
MIR591
MIR592
MIR593
MIR595
LOC723809
MIR653
LOC728066
LOC728377
LOC728743
ZNF736
LOC729156
GATSL2
SPDYE6
TMEM229A
ZNF735
LOC730441
LUZP6
MIR671
LOC100093631
POM121C
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100129845
LOC100130705
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100132832
LOC100133091
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
LOC100287482
LOC100287704
LOC100287834
MOXD2P
LOC100289187
LOC100289561
ZNF783
MIR548F3
MIR548I4
SPDYE2L
MIR548M
MIR548F4
SAP25
MIR4283-2
MIR548T
MIR4285
MIR4283-1
MIR3147
MIR4284
MTRNR2L6
MIR3609
MIR3907
MIR3914-1
MIR3666
MIR3914-2
LOC100505483
LOC100505854
MAGI2-AS3
LOC100506050
LOC100506136
LOC100506585
LOC100507421
ATP5J2-PTCD1
GIMAP1-GIMAP5
MIR4653
MIR4652
MIR4468
MIR4651
MIR4650-1
MIR4650-2
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
ATRX
ELF4
GATA1
GPC3
MSN
MTCP1
NONO
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
CRLF2
P2RY8
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
hsa-mir-448
hsa-mir-1911
hsa-mir-1264
hsa-mir-4329
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
hsa-let-7f-2
hsa-mir-502
hsa-mir-222
hsa-mir-548f-5
hsa-mir-1308
hsa-mir-651
ABCB7
AGTR2
NR0B1
ALAS2
ABCD1
AMELX
SLC25A5
SLC25A6
XIAP
SHROOM2
AR
ARAF
ARHGAP4
ARHGAP6
ARR3
STS
ARSD
ARSE
ARSF
ASMT
ATP2B3
ATP6AP1
ATP7A
AVPR2
BCYRN1
BGN
BMX
BRS3
BTK
CACNA1F
S100G
CAPN6
CD40LG
CDR1
CDX4
CETN2
CHM
CLCN4
CLCN5
CLIC2
CNGA2
COL4A5
COL4A6
COX7B
CSF2RA
CSTF2
CTAG1B
TEX28
CYBB
CYLC1
DCX
DDX3X
TIMM8A
DIAPH2
DKC1
DLG3
DMD
DNASE1L1
DRP2
TSC22D3
DUSP9
EDA
EFNB1
EIF1AX
EIF2S3
ELK1
EMD
F8
F9
ACSL4
FANCB
GPC4
FGD1
FGF13
FHL1
FIGF
FLNA
FMR1
AFF2
CENPI
G6PD
GAGE1
GABRA3
GABRE
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
OPN1MW
GDI1
GJB1
GK
GLA
GLRA2
GLUD2
GPM6B
CXCR3
LPAR4
GPR34
GRIA3
GRPR
GUCY2F
HSD17B10
HCCS
HCFC1
HMGB3
HNRNPH2
HPRT1
ERAS
HTR2C
IDH3G
IDS
IGBP1
IGSF1
IL2RG
IL3RA
IL9R
IL13RA1
IL13RA2
IRAK1
KAL1
KCND1
L1CAM
LAMP2
PRICKLE3
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
MCF2
MECP2
CD99
MID1
FOXO4
MPP1
CITED1
MTM1
NAP1L2
NAP1L3
NDP
NDUFA1
NHS
GPR143
TBC1D25
OCRL
OPHN1
OTC
P2RY4
PAK3
CDK16
PDHA1
PDK3
CFP
PFKFB1
PGK1
PHEX
PHKA1
PHKA2
PIGA
PIN4
PLP1
PLP2
PLS3
PLXNB3
POLA1
POU3F4
PPEF1
PRKX
PRPS1
PRPS2
PRRG1
PSMD10
RBBP7
RBM3
OPN1LW
RENBP
RP2
RPGR
RPL10
RPL39
RPL36A
RPS4X
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SH3BGRL
SHOX
SLC6A8
SLC16A2
SMARCA1
SMS
SOX3
SRD5A1P1
SSR4
SSX5
CDKL5
SUV39H1
VAMP7
SYN1
SYP
TAF1
TAZ
SERPINA7
TBL1X
DYNLT3
TDGF1P3
TIMP1
TSPAN7
TSPAN6
TMSB4X
TRO
TRPC5
UBA1
UBE2A
SLC35A2
VBP1
XG
XIST
XK
XPNPEP2
ZFX
ZIC3
ZNF711
ZNF182
ZNF41
ZNF75D
ZNF157
RNF113A
ZNF185
ZXDA
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
SRPX
UXT
CUL4B
IRS4
OGT
OFD1
IKBKG
PIR
INE2
INE1
CASK
ASMTL
PAGE1
MTMR1
FGF16
AKAP4
APLN
AP1S2
GYG2
FAM127A
SLC25A14
CLDN2
RGN
FAM50A
AIFM1
CXorf1
REPS2
ZBED1
ZMYM3
BMP15
GPR50
MED14
TCEAL1
RAB33A
RAB9A
TSIX
ITM2A
ARHGEF6
PCYT1B
MAGED1
XAGE2
XAGE1D
PAGE4
MORF4L2
GPRASP1
STARD8
FRMPD4
PHF16
ARMCX2
HEPH
MAGEC1
AMMECR1
MED12
ZBTB33
HDAC6
MAMLD1
HUWE1
PQBP1
BCAP31
GPR64
ATP6AP2
ODZ1
SSX3
TIMM17B
SPRY3
RRAGB
SCML2
SLC9A6
ENOX2
PRDX4
EBP
STAG2
RAI2
PLAC1
CYSLTR1
UTP14A
ZNF275
PGRMC1
MAGED2
MSL3
TMSB15A
PIM2
MID2
IL1RAPL1
WDR45
TREX2
PRAF2
CA5B
SLC6A14
KLF8
VSIG4
CNKSR2
IQSEC2
PHF8
SEPT6
ARHGEF9
ATP1B4
ACOT9
KCNE1L
LDOC1
SMPX
GSPT2
KIF4A
FTSJ1
CXorf27
MXRA5
EGFL6
FAM127B
IL1RAPL2
ITGB1BP2
SRPK3
VCX
GAGE12I
GAGE2E
SNORA70
SNORA69
SNORD61
NGFRAP1
NOX1
FAM155B
INGX
GPR82
GPKOW
SRPX2
APEX2
RBMX
PCDH11X
RPS6KA6
P2RY10
HTATSF1
PCSK1N
PPP2R3B
CCDC22
MCTS1
MAGEH1
FAM156A
C1GALT1C1
SNX12
RPA4
PNMA3
UBQLN2
SH3KBP1
SPANXA1
CTAG2
NSDHL
FOXP3
TBX22
ZDHHC9
RLIM
WBP5
RAB9B
LUZP4
PDZD11
CXorf26
TFDP3
TLR7
ARMCX1
TLR8
MBTPS2
MAGEC2
VGLL1
VCX2
VCX3A
ARMCX3
TAF9B
RBMX2
MST4
CPXCR1
CHIC1
FTHL17
GPR173
NLGN3
SASH3
TAF7L
SPIN2A
ARMCX6
WDR44
NDUFB11
GNL3L
ERCC6L
NUP62CL
GDPD2
BCOR
TBC1D8B
FAM120C
GEMIN8
CXorf48
FAM70A
CXorf57
NUDT11
TMLHE
RBM41
PLCXD1
SAGE1
PLXNA3
HAUS7
OTUD5
ZNF280C
MTMR8
ZNF673
TXLNG
MBNL3
WWC3
FAM45B
BEX1
HDAC8
GABRQ
ZC4H2
NXT2
NKRF
NXF5
NXF4
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
MOSPD1
BEX4
CTPS2
CHST7
TCEAL7
GRIPAP1
THOC2
ZNF630
TMEM27
SHROOM4
KIAA1210
NLGN4X
PCDH19
RGAG1
PDZD4
LRCH2
MAGEE1
RAP2C
MID1IP1
ACE2
TMEM35
FAM3A
EDA2R
NYX
BCORL1
DUSP21
CXorf56
DMRTC1
TSPYL2
TNMD
PJA1
SPANXD
SPANXC
WDR13
PORCN
ARMCX5
UPF3B
WNK3
FUNDC2
PRRG3
APOO
BRCC3
HMGN5
NKAP
RNF128
MAP7D3
MORC4
CXorf36
LONRF3
ALG13
MAGIX
TCEAL4
TRMT2B
POF1B
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
ESX1
BHLHB9
MAGED4B
LAS1L
GPR101
TMEM47
CD99L2
H2AFB3
USP26
FRMD8P1
MAGT1
TMEM164
PHF6
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
SLC9A7
BEX2
MGC16121
SLC7A3
PNMA6A
TCEAL3
CCNB3
PPP1R3F
FATE1
CCDC120
TSR2
HS6ST2
FRMD7
KLHL13
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
CXorf40A
FAM58A
RIPPLY1
LOC92249
ATXN3L
SLC38A5
MMGT1
ACRC
SYAP1
SYTL4
SYTL5
PNMA5
GPRASP2
ATG4A
RAB39B
DACH2
SLITRK4
SPANXN3
MAGEC3
BEND2
PASD1
DCAF12L1
DGKK
LOC139201
CXorf41
MUM1L1
FAM199X
FAM123B
APOOL
HDX
FUNDC1
GPR112
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
OTUD6A
UPRT
MAGEE2
MAGEB16
FOXR2
GAB3
PNCK
ZFP92
ACTRT1
GPR119
PAGE3
RBMXL3
DOCK11
SPIN4
ASB11
ASB9
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
ZNF645
CSAG1
FMR1NB
LOC158572
FAAH2
ZXDB
LOC158696
FAM47A
MOSPD2
ARHGAP36
RIBC1
AKAP14
RHOXF1
NKAPP1
MAGEB6
CXorf65
AWAT1
AWAT2
ZDHHC15
USP51
TCEAL6
H2BFWT
CXorf38
FAM122B
FAM122C
DDX53
FAM46D
SPIN3
FAM47B
CXorf22
FAM48B2
TCEANC
ZCCHC12
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
SPANXE
SPANXF1
CXorf61
SLC25A43
LINC00246A
ZCCHC5
NRK
DDX26B
ZNF449
VMA21
TMEM31
PAGE2
DHRSX
CTAG1A
BRWD3
CXorf58
CT47A11
CXorf23
MAP7D2
KLHL34
TAB3
MAGEA2B
SSX6
SSX7
SSX8
RAB40AL
PPP2R3B-AS1
ATP11C
RP1-177G6.2
H2BFM
LOC286437
LOC286442
YIPF6
CXorf59
LOC286467
TTC3P1
FAM133A
MAGEB18
TMSB15B
LINC00204B
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
LOC340544
VSIG1
ZC3H12B
SATL1
DCAF12L2
CA5BP1
ZCCHC16
LHFPL1
ZNF81
ITIH6
LANCL3
LOC347411
DCAF8L2
SOWAHD
OR13H1
CCDC160
CXorf66
DGAT2L6
RAB41
ARSH
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
PAGE2B
ZCCHC13
UBE2NL
CSAG3
LOC389906
CXXC1P1
GLOD5
FLJ44635
ARL13A
LINC00086
CD99P1
LOC401588
MCART6
DKFZp686D0853
XKRX
YY2
MIRLET7F2
MIR105-1
MIR105-2
MIR106A
MIR188
MIR19B2
MIR221
MIR222
MIR223
MIR92A2
MIR98
VCX3B
LOC441495
FLJ46446
RPS26P11
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
PGAM4
FAM47C
UQCRBP1
LOC442459
MIR374A
SPIN2B
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
SPANXN5
MIR384
MIR424
CT45A6
CT45A1
CXorf40B
SSX4B
LOC550643
JPX
MIR448
MIR450A1
MIR362
MIR363
MIR20B
MIR18B
MIR452
MIR500A
MIR501
MIR502
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
ZNF674
CT47B1
LOC643486
GAGE10
ZCCHC18
CXorf69
LINC00087
GAGE2B
GAGE13
GAGE12G
CXorf30
PABPC1L2B
NAP1L6
XAGE1C
XAGE1E
XAGE1A
XAGE1B
CT47A7
LINC00246B
MIR545
MIR542
SCARNA23
SNORA11
SNORA35
SNORA36A
SNORA56
SNORD96B
MIR421
MIR532
MIR651
MIR660
CXorf31
SSX2B
FAM156B
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGED4
XAGE2B
MAGEA9B
NXF2B
OPN1MW2
CSAG2
DMRTC1B
SPANXB1
SPANXA2
CT45A2
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
LOC729609
H2BFXP
MIR767
MIR766
GAGE12F
LOC100093698
GAGE8
SNORA11C
SNORA11D
SNORA11E
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR374B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129407
CXorf28
LOC100129515
LOC100129520
LOC100129662
HSFX2
FAM48B1
CXorf49
CXorf64
LOC100131434
ARMCX4
UBE2DNL
LOC100132163
GAGE12D
XGPY2
LOC100132741
LOC100132831
CXorf68
LINC00204A
CXorf49B
CXorf51B
LOC100133123
SPANXB2
LOC100133957
SCARNA9L
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
LOC100287765
LOC100288814
MIR1184-1
MIR1468
MIR1912
MIR1298
MIR1256
MIR320D2
MIR1277
MIR1911
MIR1264
FTX
SLC25A5-AS1
MIR718
MIR764
MIR2114
LOC100329135
LINC00102
MIR514B
MIR3202-2
MIR500B
MIR4330
MIR4328
MIR1184-3
MIR1184-2
MIR3202-1
MIR4329
MTRNR2L10
MIR374C
MIR23C
MIR676
MIR3690
HSFX1
LOC100506757
CT47A12
LOC100507404
LOC100509575
ARMCX5-GPRASP2
RPL36A-HNRNPH2
PIR-FIGF
MAGEA10-MAGEA5
MIR4769
MIR4536-1
MIR4768
MIR4770
MIR4767
MIR3978

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q34.

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

Genes
ALK
ATIC
CHN1
CREB1
DNMT3A
ERCC3
ACSL3
MSH6
HOXD11
HOXD13
IDH1
MSH2
MYCN
NFE2L2
PAX3
PMS1
REL
PAX8
NCOA1
EML4
BCL11A
FEV
TTL
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
hsa-mir-3127
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
hsa-mir-216b
hsa-mir-559
hsa-mir-558
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
AAMP
ACADL
ACP1
ACTG2
ACVR1
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
AGXT
ALPI
ALPP
ALPPL2
BIN1
ANXA4
AOX1
APOB
RHOB
RND3
ATP5G3
ATP6V1B1
KIF1A
AUP1
BARD1
BCS1L
BMPR2
BOK
ZFP36L2
BUB1
CACNB4
CAD
CALM2
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CENPA
CHRNA1
CHRND
CHRNG
CLK1
CNGA3
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
COX5B
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CTNNA2
CYP1B1
CYP27A1
DARS
DBI
DCTN1
DDX1
DES
DGUOK
LOC1720
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DTNB
DTYMK
DUSP2
E2F6
EEF1B2
EGR4
EMX1
EN1
EPAS1
EPHA4
ERBB4
FABP1
FAP
EFEMP1
FHL2
FKBP1B
FN1
FOSL2
FRZB
FSHR
FTH1P3
GAD1
GALNT3
GBX2
GCG
GCKR
MSTN
GFPT1
GGCX
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GTF3C2
GYPC
HADHA
HADHB
HDLBP
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HPCAL1
AGFG1
DNAJB2
HSPD1
HSPE1
FOXN2
HTR2B
ID2
SP110
IGFBP2
IGFBP5
IHH
IL1A
IL1B
IL1R1
IL1RN
CXCR1
CXCR2
CXCR2P1
INHA
INHBB
INPP1
INPP4A
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNF1
KCNJ3
KCNJ13
KCNK3
KCNS3
KHK
KIF3C
KIF5C
AFF3
LCT
LHCGR
LIMS1
LRP2
LTBP1
LY75
EPCAM
MXD1
MAL
MAP2
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MYO1B
MTIF2
MYL1
MYO7B
NAB1
NCL
NEB
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPAS2
NPHP1
NPPC
NR4A2
ODC1
ORC2
ORC4
OTX1
REG3A
PCBP1
PDCD1
PDE1A
PDE6D
PDK1
PEX13
VIT
SERPINE2
PIGF
PLCL1
PLEK
PLGLB2
PLGLB1
POLR2D
POMC
POU3F3
PPM1B
PPM1G
PPP1CB
PPP1R7
PPP3R1
PRKCE
EIF2AK2
PROC
PSMD1
PTH2R
PTMA
PTPN4
PTPRN
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
REG1P
SNORD20
RPE
RPL31
RPL37A
RPS7
RPS27A
RRM2
RTKN
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
CCL20
SDC1
SRSF7
SFTPB
SIX3
SLC4A3
SLC1A4
SLC3A1
SLC8A1
SLC9A2
SLC11A1
SLC20A1
SNRPG
SOS1
SOX11
SP3
SP100
SPAST
SPP2
SPR
SPTBN1
SRD5A2
SSB
SSFA2
STAT1
STAT4
STRN
SULT1C2
ADAM17
TACR1
GCFC2
TFPI
TGFA
TIA1
TNFAIP6
TNP1
TNS1
TPO
TSN
TSSC1
TTN
TUBA4A
SUMO1
UCN
UGP2
VIL1
VRK2
VSNL1
WIPF1
WNT6
XDH
XPO1
XRCC5
ZAP70
ZNF2
ZNF142
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
FZD5
SCG2
DYSF
FZD7
SDPR
NCK2
DUSP11
CUL3
KLF11
MAP4K3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ASAP2
PER2
ST3GAL5
SLC5A6
DDX18
EIF2B4
CDK5R2
KYNU
TAF1B
NAT8
NMI
RQCD1
COX7A2L
TMSB10
IL1RL1
LRRFIP1
STK17B
ITGB1BP1
GPR55
TRIP12
GTF3C3
PPIG
NRXN1
OTOF
CIAO1
TGFBRAP1
HS6ST1
CRIPT
ECEL1
MAP4K4
EIF2AK3
EIF4E2
ROCK2
CHST10
TP53I3
CIR1
MRPL33
BRE
PREPL
CYTIP
FEZ2
GCC2
TTLL4
SOCS5
EIF5B
GREB1
BZW1
USP34
LAPTM4A
HDAC4
RNF144A
SNX17
SERTAD2
MRPL19
ZEB2
FARP2
TLK1
SUPT7L
CD302
ARHGAP25
TANK
BCL2L11
FARSB
ABCB6
ACTR3
ACTR2
ARPC2
PREB
ACTR1B
ARL4C
LRPPRC
PDIA6
ABI2
CEBPZ
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
SMYD5
KBTBD10
MYCNOS
C1D
MERTK
UBE2E3
STK25
SEMA4F
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
MTX2
CGREF1
B3GNT2
USP39
TBR1
SIX2
MAP3K2
NCKAP1
VAMP5
MTHFD2
ARID5A
PROKR1
RAB10
EDAR
COPS8
GPR75
YWHAQ
IMMT
SNRNP27
GTF2A1L
STON1
RAPGEF4
EMILIN1
CAPN10
TBC1D8
RABL2A
GALNT5
NXPH2
GPR45
SP140
MGAT4A
GPN1
IKZF2
COBLL1
AAK1
FASTKD2
MAPRE3
PLA2R1
RAB3GAP1
RPIA
SLC4A1AP
EFR3B
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
PASK
UBXN4
ATG4B
PSME4
EXOC6B
EHBP1
SATB2
CLASP1
OBSL1
PUM2
NCAPH
RHOQ
SF3B1
HAAO
TMEM131
R3HDM1
DNPEP
PSD4
WBP1
NTSR2
TMEFF2
SH3BP4
PRKD3
KCNE4
RASGRP3
NGEF
QPCT
GCA
VAX2
SNORD82
MOB4
POLR1A
CNRIP1
FAM98A
PNKD
UNC50
SNED1
GORASP2
SPATS2L
RAB11FIP5
GIGYF2
EPC2
TRAF3IP1
ABCA12
IFT172
ARL5A
HIBCH
PTPN18
CNNM4
CNNM3
IL36RN
SH3YL1
SNORD53
SNORD51
CNPPD1
STK36
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
MMADHC
BMP10
ZNF638
STK39
HTRA2
TRIB2
CPS1-IT1
METTL5
LGALSL
OLA1
C2orf27A
GRHL1
TFCP2L1
ICOS
GMPPA
NRBP1
BAZ2B
SLC40A1
KCNIP3
EHD3
SMARCAL1
CD207
ITSN2
ANO7
ARHGEF4
PDE11A
TPRKB
FAHD2A
PRLH
WDPCP
MEMO1
THAP4
TRAPPC12
ASB3
INSIG2
CRIM1
ANKRD39
FAM178B
RNF181
MRPL30
DNAJC27
ANKMY1
KRCC1
MRPL35
C2orf28
PCYOX1
GULP1
REV1
NAT8B
SCLY
VPS54
NBAS
LIPT1
NOP58
DYNC2LI1
SF3B14
YPEL5
CHMP3
FKBP7
ASB1
CPSF3
CAB39
ZAK
LRP1B
PRKAG3
PPIL3
SNTG2
DNAJC10
ATAD2B
ETAA1
HEATR5B
CCDC93
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
AFTPH
MFSD6
TMEM214
RETSAT
INO80D
SEMA4C
C2orf18
C2orf42
TRMT61B
PID1
PTCD3
PLEKHB2
ATG16L1
FANCL
SRBD1
FIGN
ANKZF1
RIF1
USP40
MOB1A
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
HJURP
STRADB
C2orf56
HES6
ACCN4
C2orf29
NAGK
DOCK10
TTC27
SMPD4
TMEM127
PRPF40A
SLC30A6
IWS1
LIMS2
KANSL3
MREG
CCDC88A
WDR12
MBD5
KDM3A
ALLC
PECR
ARHGAP15
ZC3H15
CFC1
DNAH7
GKN1
IL36G
RPRM
CYP26B1
POLE4
KCNK12
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
C2orf83
MFF
RPL23AP32
CXCR7
RNPEPL1
RTN4
TRIM54
PELI1
SLC39A10
TTC7A
SMEK2
SLC4A10
CYP20A1
SPC25
BIRC6
ERMN
KIDINS220
MTA3
HECW2
WDR35
MARCH4
WDFY1
NYAP2
DPP10
RDH14
EPB41L5
ALS2
ZDBF2
USP37
CWC22
ANKRD36B
G6PC2
SLC4A5
CTDSP1
NLRC4
MPP4
SLC5A7
NIF3L1
AGBL5
C2orf43
THADA
PCGEM1
RBKS
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
ATL2
ABCG5
ABCG8
RAB17
RNF25
HS1BP3
GMCL1
TTC31
ANAPC1
COPS7B
RMND5A
FNDC4
MARCH7
OBFC2A
PAPOLG
MRPS9
MRPS5
REEP1
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
SOWAHC
PLEKHA3
TRAK2
BOLL
COLEC11
PDCL3
TRPM8
ATG9A
C2orf49
MLPH
TMEM185B
FAM134A
CENPO
OR7E91P
GLB1L
C2orf47
SPAG16
CHPF
SAP130
GALNT14
SCRN3
CCDC121
FASTKD1
SMC6
GTDC1
CLIP4
IQCA1
ALS2CR8
TTC21B
CAMKMT
METTL8
GEMIN6
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
NOL10
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
TUBA4B
MZT2B
YSK4
UXS1
FBXO11
ARMC9
COQ10B
SLC35F5
EFHD1
C2orf44
SPHKAP
WNT10A
SLC19A3
TSGA10
THSD7B
THUMPD2
TMEM177
KIAA1715
ILKAP
FAM49A
LMAN2L
LBH
TMEM163
ITM2C
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
RHBDD1
CHCHD5
YIPF4
PRADC1
C2orf88
ING5
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
DPY30
MCEE
LOXL3
ABHD1
PCGF1
DDX11L2
MFSD9
PLCD4
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
MGC16025
TANC1
EPT1
LBX2
PNPT1
KCNH7
FER1L5
MCFD2
ATP6V1E2
LOC90499
CCDC74A
LOC90784
DHX57
LOC91149
SESTD1
CCDC74B
PKDCC
ANKRD44
RSAD2
ZNF804A
TTC30A
DAPL1
CAPN13
TMEM169
DNER
CCDC164
IMP4
HNRPLL
MARS2
B3GNT7
NT5C1B
NEURL3
SP140L
SFXN5
ORMDL1
LIMS3
LINC00152
TUBA3E
CCDC104
TEX261
TUBA3D
STK11IP
FMNL2
CCDC85A
GALNT13
KLHL29
OSBPL6
NOSTRIN
DIRC1
WDR92
MOGAT1
LYPD1
MRPL53
AGAP1
TWIST2
PARD3B
RPL23AP7
PPP1R21
C2orf89
TMEM150A
NUP35
XIRP2
TYW5
NMS
LYG1
MITD1
DIS3L2
CMPK2
MBOAT2
CNTNAP5
TMEM18
FBLN7
NEU4
RBM45
C2orf73
TRIM43
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
CIB4
REG3G
RFTN2
C2orf63
PLEKHH2
AP1S3
C2orf76
SGPP2
ACVR1C
OSR1
TTC32
UBR3
KCTD18
ALS2CR12
ZNF513
SPATA3
LYPD6
LYPD6B
GALM
TMEM198
ZFAND2B
TMEM178
CPO
MDH1B
C2orf50
PQLC3
TMEM182
AHSA2
FBXO36
MTERFD2
CCDC148
C2orf65
MYO3B
TMEM37
UBE2F
DUSP19
CKAP2L
CBWD2
TEKT4
LOC150527
FLJ32063
LOC150568
SMYD1
C2orf15
LOC150622
OTOS
MYEOV2
OR6B3
COMMD1
PROM2
ANKAR
FBXO41
TTC30B
GPAT2
ITPRIPL1
LOC150776
WTH3DI
FAM117B
TCF23
LOC150935
FAM59B
PUS10
PKI55
LINC00309
LOC151009
SEPT10
C2orf67
PLB1
ZSWIM2
ZNF385B
LOC151171
LOC151174
ARL6IP6
METTL21A
CCNYL1
KLHL23
SULT1C2P1
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
LOC151300
GPBAR1
FAHD2B
MYADML
FAM84A
FAM82A1
GDF7
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
ASPRV1
WDSUB1
UPP2
LOC151534
GPR155
WDR69
LONRF2
CCDC138
GPR113
C2orf57
OXER1
FAM179A
FAM171B
C1QL2
UBXN2A
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
PIKFYVE
KRTCAP3
LOC200726
TMEM17
SPRED2
TIGD1
LOC200772
FAM123C
LINC00116
C2orf69
HNRNPA3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
CERS6
METAP1D
LOC254128
LYG2
CCDC108
C2orf72
SH2D6
LOC284950
CCDC150
RNF149
LOC284998
LOC285000
FAM150B
CCDC141
LOC285033
LINC00486
C2orf61
LOC285074
LOC285084
CXXC11
LOC285103
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
FAM126B
UNC80
RUFY4
PLGLA
RGPD4
DUSP28
STON1-GTF2A1L
SPOPL
MLK7-AS1
CYP27C1
ESPNL
C2orf70
C2orf53
LOC339788
LINC00299
LOC339803
C2orf74
LOC339807
LOC339822
MSGN1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
EVX2
CDKL4
PRORSD1P
AOX2P
SH3RF3
GPR148
ECEL1P2
LRRTM1
GEN1
C2orf48
FONG
LOC348761
PFN4
LOC375190
LOC375196
ANKRD36
WASH2P
RBM43
LOC375295
CERKL
C2orf62
RBM44
AQP12A
ZC3H6
KLHL30
LOC386597
MFSD2B
C2orf71
LOC388942
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
SLC9A4
LOC389023
LOC389033
LOC389043
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
PTRHD1
SULT6B1
DYTN
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
FLJ42351
LOC401010
DKFZp686O1327
LOC401022
FSIP2
C2orf66
ASB18
FLJ43879
VWC2L
MIR10B
MIR128-1
MIR149
MIR153-1
MIR216A
MIR217
MIR26B
C2orf27B
DNAJB3
ASTL
CAPN14
ACTR3BP2
LOC440894
LOC440895
LOC440900
LOC440905
LOC440910
POTEKP
LOC440925
LOC442028
SULT1C3
POTEE
COA5
PHOSPHO2
CHAC2
MIR375
DFNB59
LOC541471
LOC554201
ANKRD30BL
FBXO48
SNORA41
FAM110C
LOC643387
PRR21
LOC644838
GGT8P
ANKRD36BP2
LOC645949
LOC646324
LOC646736
LOC646743
PRSS56
LOC647012
C2orf84
TRIM43B
CFC1B
AQP12B
RGPD3
MZT2A
SNORA75
LOC654342
FAM138B
LOC654433
SCARNA6
SCARNA5
SNORD11
SNORD70
SNORD89
SNORD92
SNORD94
MIR558
MIR559
MIR561
RGPD8
LOC727982
D2HGDH
LOC728323
POTEF
LOC728537
LOC728730
PABPC1P2
LOC728819
LOC729121
ANKRD20A8P
LOC729234
RAD51AP2
RGPD6
DIRC3
DNAJC27-AS1
RGPD2
MORN2
LOC730811
RFX8
SNORD11B
SNORA36C
SNORA70B
MIR216B
MIR933
LOC100128590
OST4
LOC100129175
LOC100129726
LOC100129961
PP14571
LOC100130451
LOC100130452
LOC100130691
TMEM194B
LOC100131320
SP9
LOC100132215
CYP4F30P
LOC100133985
LOC100134259
LOC100144595
RNU4ATAC
DBIL5P2
SNAR-H
LOC100189589
LOC100216479
ARHGEF33
LOC100271832
LIMS3-LOC440895
LOC100286922
LOC100286979
LOC100287010
LOC100287216
LOC100288570
LIMS3L
LOC100288911
MIR1471
MIR1246
MIR548N
MIR1258
MIR1245A
MIR1301
MIR1244-1
LOC100302650
GPR75-ASB3
SNORA80B
ZEB2-AS1
MIR548F2
MIR663B
LOC100329109
SNORA70F
BOK-AS1
MIR3128
MIR4265
MIR1244-3
MIR1244-2
MIR4264
MIR3129
MIR3127
MIR4261
MIR3131
MIR4268
MIR4263
MIR3125
MIR3130-1
MIR4267
MIR4262
MIR3130-2
MIR4266
MIR3126
MIR2355
MIR3132
MIR4269
LOC100499194
MIR3606
MIR3682
MIR3679
LOC100505624
LOC100505695
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506123
LOC100506124
LOC100506134
LOC100506274
LOC100506421
LOC100506474
LOC100506783
LOC100506866
LOC100507140
BOLA3-AS1
LOC100507334
LOC100507443
LOC100507600
LY75-CD302
RNF103-CHMP3
NT5C1B-RDH14
PHOSPHO2-KLHL23
HSPE1-MOB4
INO80B-WBP1
UBE2F-SCLY
MIR4436B1
MIR4772
MIR4779
MIR4783
MIR4439
MIR4782
MIR4437
MIR4765
MIR4776-1
MIR4757
MIR4777
MIR1245B
MIR4435-2
MIR4426
MIR4774
MIR2467
MIR4775
MIR4785
MIR4784
MIR4773-1
MIR4444-1
MIR4440
MIR4436A
MIR4786
MIR4773-2
MIR4434
MIR4780
MIR4778
MIR4429
MIR4776-2
MIR4432
MIR548AD
MIR4441
MIR4435-1
LOC100630918
LOC100861402

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q22.3.

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
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
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Arm-level results

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

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.06 | -0.67 | 0.998 | 0.63 | 23.7 | 0
1q | 1955 | 0.14 | 2.03 | 0.211 | 0.19 | 4.43 | 1.89e-05
2p | 924 | 0.04 | -1.39 | 0.998 | 0.06 | -0.188 | 1
2q | 1556 | 0.01 | -2.95 | 0.998 | 0.08 | 0.138 | 0.937
3p | 1062 | 0.01 | -2.36 | 0.998 | 0.38 | 15.3 | 0
3q | 1139 | 0.00 | -2.37 | 0.998 | 0.55 | 23.3 | 0
4p | 489 | 0.03 | -1.76 | 0.998 | 0.07 | 0.467 | 0.712
4q | 1049 | 0.02 | -2.43 | 0.998 | 0.06 | -0.35 | 1
5p | 270 | 0.07 | 0.698 | 0.998 | 0.03 | -1.27 | 1
5q | 1427 | 0.05 | -1.46 | 0.998 | 0.05 | -1.46 | 1
6p | 1173 | 0.08 | 0.192 | 0.998 | 0.03 | -2.15 | 1
6q | 839 | 0.06 | -0.503 | 0.998 | 0.12 | 2.84 | 0.00763
7p | 641 | 0.16 | 5.12 | 6.04e-06 | 0.01 | -2.68 | 1
7q | 1277 | 0.13 | 2.64 | 0.0556 | 0.05 | -1.11 | 1
8p | 580 | 0.07 | 0.385 | 0.998 | 0.13 | 3.21 | 0.00245
8q | 859 | 0.09 | 0.976 | 0.998 | 0.08 | 0.673 | 0.626
9p | 422 | 0.03 | -1.72 | 0.998 | 0.07 | 0.53 | 0.702
9q | 1113 | 0.02 | -2.45 | 0.998 | 0.07 | -0.0903 | 1
10p | 409 | 0.08 | 0.81 | 0.998 | 0.01 | -2.73 | 1
10q | 1268 | 0.06 | -0.558 | 0.998 | 0.01 | -3.16 | 1
11p | 862 | 0.03 | -1.62 | 0.998 | 0.34 | 13.8 | 0
11q | 1515 | 0.02 | -2.54 | 0.998 | 0.25 | 7.86 | 8.88e-15
12p | 575 | 0.07 | 0.323 | 0.998 | 0.01 | -2.83 | 1
12q | 1447 | 0.08 | 0.178 | 0.998 | 0.00 | -3.51 | 1
13q | 654 | 0.06 | -0.275 | 0.998 | 0.05 | -0.898 | 1
14q | 1341 | 0.03 | -2.11 | 0.998 | 0.13 | 2.48 | 0.0189
15q | 1355 | 0.08 | 0.348 | 0.998 | 0.03 | -2.23 | 1
16p | 872 | 0.04 | -1.39 | 0.998 | 0.05 | -0.787 | 1
16q | 702 | 0.04 | -1.35 | 0.998 | 0.03 | -1.97 | 1
17p | 683 | 0.00 | -2.6 | 0.998 | 0.39 | 16.6 | 0
17q | 1592 | 0.03 | -2.24 | 0.998 | 0.13 | 2.22 | 0.0348
18p | 143 | 0.06 | -0.0106 | 0.998 | 0.11 | 2.66 | 0.012
18q | 446 | 0.06 | 0.214 | 0.998 | 0.04 | -1.07 | 1
19p | 995 | 0.13 | 2.76 | 0.0556 | 0.01 | -2.91 | 1
19q | 1709 | 0.09 | 0.41 | 0.998 | 0.04 | -1.8 | 1
20p | 355 | 0.07 | 0.55 | 0.998 | 0.01 | -2.37 | 1
20q | 753 | 0.06 | -0.434 | 0.998 | 0.02 | -2.28 | 1
21q | 509 | 0.02 | -1.77 | 0.998 | 0.22 | 8.05 | 2.22e-15
22q | 921 | 0.03 | -1.59 | 0.998 | 0.36 | 14.6 | 0
Xq | 1312 | 0.05 | -1.21 | 0.998 | 0.32 | 11.4 | 0

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/PCPG-TP/9826496/GDAC_MergeDataFiles_9828626/PCPG-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 160 Input Tumor Samples.

Tumor Sample Names
TCGA-P7-A5NY-01A-12D-A35C-01
TCGA-P8-A5KC-01A-11D-A35C-01
TCGA-P8-A5KD-01A-11D-A35C-01
TCGA-P8-A6RX-01A-11D-A35C-01
TCGA-P8-A6RY-01A-12D-A35C-01
TCGA-PR-A5PG-01A-11D-A35C-01
TCGA-PR-A5PH-01A-11D-A35C-01
TCGA-QR-A6GO-01A-11D-A35C-01
TCGA-QR-A6GR-01A-11D-A35C-01
TCGA-QR-A6GS-01A-11D-A35C-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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