Colon/Rectal Adenocarcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16 (cga svn revision 38839).

Summary

There were 574 tumor samples used in this analysis: 21 significant arm-level results, 30 significant focal amplifications, and 48 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 - 30 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
--- | --- | --- | --- | ---
17q12 | 2.0877e-27 | 2.5797e-26 | chr17:37837542-37876018 | 2
13q12.2 | 3.8784e-25 | 1.1075e-20 | chr13:28385587-28562900 | 4
8p11.23 | 4.6715e-16 | 3.6149e-14 | chr8:38170522-38260814 | 2
8q24.21 | 1.2291e-13 | 1.7639e-13 | chr8:128198180-128754562 | 3
12p13.32 | 8.2262e-13 | 8.2262e-13 | chr12:4385384-4436676 | 2
20q11.21 | 5.8916e-13 | 2.2187e-11 | chr20:30153887-30232288 | 5
11p15.5 | 1.7857e-10 | 1.7857e-10 | chr11:2157956-2241214 | 6
8p11.21 | 2.0801e-10 | 4.7572e-08 | chr8:41614677-41632229 | 1
6p21.1 | 6.1242e-07 | 6.1242e-07 | chr6:41609221-44234813 | 65
20q13.32 | 5.2074e-08 | 2.5024e-05 | chr20:54054666-58960760 | 55
20q13.12 | 5.0776e-08 | 0.00013948 | chr20:42167237-43278693 | 18
13q22.1 | 1.9821e-05 | 0.00035377 | chr13:73614731-74042620 | 1
13q12.13 | 2.5216e-20 | 0.00037452 | chr13:27521847-27539800 | 0 [USP12]
10q23.1 | 0.00077274 | 0.00077274 | chr10:79553562-82903467 | 28
16p11.2 | 0.0021057 | 0.002527 | chr16:30581939-30780910 | 10
20p11.21 | 0.001715 | 0.0063055 | chr20:25355954-25483163 | 3
17q24.1 | 0.00025802 | 0.010626 | chr17:63368617-65979140 | 16
2q33.1 | 0.020459 | 0.020459 | chr2:199627908-199644614 | 0 [SATB2]
20p12.1 | 0.023595 | 0.047176 | chr20:14244972-14479372 | 2
16q12.1 | 0.065529 | 0.078014 | chr16:51098275-52648730 | 5
7p11.2 | 0.079658 | 0.079658 | chr7:54260926-55790603 | 8
15q26.1 | 0.086802 | 0.086802 | chr15:78288793-102531392 | 209
1q21.3 | 0.088694 | 0.088694 | chr1:119875522-163100192 | 479
19q12 | 0.086802 | 0.09269 | chr19:24052831-31395995 | 15
8q11.23 | 0.042791 | 0.094274 | chr8:42928658-78839758 | 140
9p13.3 | 0.096732 | 0.096732 | chr9:35654479-35767752 | 10
5p13.2 | 0.099221 | 0.099221 | chr5:33432238-44942400 | 73
20p11.23 | 0.031989 | 0.11707 | chr20:20185875-20680922 | 3
19q13.12 | 0.21543 | 0.23953 | chr19:37075197-38140991 | 24
4q28.3 | 0.24983 | 0.24983 | chr4:131167467-131171934 | 0 [C4orf33]

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
PGAP3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.2.

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

Genes
CDX2
PDX1
ATP5EP2
PRHOXNB

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
WHSC1L1
LETM2

Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
LOC727677

Genes in Wide Peak

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

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

Genes
CCND2
C12orf5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-3193
ID1
HM13
COX4I2
MIR3193

Genes in Wide Peak

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

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

Genes
IGF2
INS
TH
IGF2-AS1
INS-IGF2
MIR4686

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
ANK1

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
BYSL
SLC29A1
GUCA1A
GUCA1B
HSP90AB1
MDFI
MEA1
NFKBIE
PEX6
PGC
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
MED20
POLR1C
MAD2L1BP
CUL7
C6orf108
CNPY3
FRS3
SLC22A7
CAPN11
CUL9
UBR2
KIAA0240
ZNF318
YIPF3
USP49
GNMT
PRICKLE4
MRPL2
GTPBP2
MRPS18A
MRPS10
TMEM63B
TRERF1
XPO5
MRPL14
DLK2
TTBK1
RRP36
ABCC10
KLC4
TJAP1
KLHDC3
TAF8
PTCRA
C6orf223
RSPH9
LRRC73
RPL7L1
SLC35B2
CRIP3
C6orf226
ATP6V0CP3
C6orf132
LOC100132354
TOMM6
MIR4647

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.32.

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

Genes
GNAS
hsa-mir-646
hsa-mir-298
hsa-mir-4325
ATP5E
BMP7
CSTF1
CTSZ
EDN3
MC3R
PCK1
PPP1R3D
AURKA
TFAP2C
RAE1
STX16
VAPB
SYCP2
SPO11
SLMO2
TH1L
C20orf43
PPP4R1L
RBM38
PMEPA1
CASS4
RAB22A
CDH26
FAM217B
NPEPL1
TUBB1
ZBP1
FAM210B
PHACTR3
C20orf85
ZNF831
GCNT7
CBLN4
CTCFL
LOC149773
GNAS-AS1
APCDD1L
FAM209A
C20orf197
LOC284757
FAM209B
MIR296
MIR298
MIR4325
MTRNR2L3
LOC100506384
SLMO2-ATP5E
STX16-NPEPL1
MIR4532
MIR5095

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.12.

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

Genes
ADA
HNF4A
MYBL2
SGK2
SERINC3
PKIG
L3MBTL1
IFT52
C20orf111
JPH2
GDAP1L1
TTPAL
TOX2
FITM2
R3HDML
GTSF1L
MIR3646
LOC100505783

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q22.1.

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

Genes
KLF5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q23.1.

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

Genes
ANXA11
MAT1A
RPS24
SFTPD
MBL1P
DLG5
PPIF
POLR3A
ZMIZ1
FAM213A
TSPAN14
C10orf58
DYDC2
DYDC1
EIF5AL1
LOC219347
PLAC9
ZCCHC24
LOC283050
SH2D4B
LOC439990
LOC642361
LOC650623
SFTPA1
SFTPA2
LOC100128292
LOC100132987
LOC100288974

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

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

Genes
PHKG2
RNF40
SRCAP
FBRS
PRR14
C16orf93
ZNF689
ZNF785
ZNF688
SNORA30

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.21.

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

Genes
GINS1
NINL
ABHD12

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.1.

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

Genes
hsa-mir-548d-2
hsa-mir-634
APOH
CACNG1
BPTF
PRKCA
PSMD12
AXIN2
HELZ
NOL11
PITPNC1
CACNG5
CACNG4
CEP112
MIR634
SNORA38B

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q12.1.

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

Genes
SALL1
TOX3
LOC388276
LOC643714
LOC100505619

Genes in Wide Peak

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

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

Genes
EGFR
HPVC1
SEC61G
LANCL2
VOPP1
VSTM2A
LOC285878
FKBP9L

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
IDH2
NTRK3
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
ACAN
ALDH1A3
ANPEP
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CRABP1
CTSH
FAH
FES
IDH3A
IGF1R
IL16
IREB2
ISG20
MAN2A2
MEF2A
MFGE8
NMB
FURIN
PCSK6
PDE8A
PLIN1
POLG
PSMA4
RASGRF1
RLBP1
RPS17
SH3GL3
SNRPA1
NR2F2
AP3B2
ST8SIA2
PEX11A
IQGAP1
PRC1
SLC28A1
HOMER2
ZNF592
SV2B
ARNT2
AP3S2
SEMA4B
CIB2
CIB1
MTHFS
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
VPS33B
MRPL46
OR4F4
SLCO3A1
HDGFRP3
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2
ZSCAN2
DET1
LINS
FANCI
DNAJA4
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
ADAMTSL3
KIAA1199
ALPK3
FAM108C1
MESDC1
KLHL25
CPEB1
AEN
TTC23
MRPS11
EFTUD1
LRRK1
AGSK1
TM2D3
WDR61
STARD5
FAM103A1
MEX3B
WDR73
C15orf42
RCCD1
ARRDC4
LOC91948
C15orf40
TARSL2
LRRC28
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
C15orf26
ADAMTS17
DNM1P46
CERS3
LOC254559
C15orf37
LOC283688
LOC283692
LOC283693
FAM154B
LOC283738
LOC283761
FAM169B
LOC338963
TMC3
ZNF774
C15orf38
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
LOC388152
UBE2Q2P1
FLJ42289
ANKRD34C
C15orf58
OR4F6
OR4F15
LOC390660
ST20
FAM174B
LOC400456
MIR184
MIR7-2
MIR9-3
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
SH2D7
LOC646938
GOLGA6L10
LOC648809
SCARNA15
MIR549
LOC727849
LOC727915
ASB9P1
LOC729911
FAM138E
UBE2Q2P3
UBE2Q2P2
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1276
MIR1179
MIR1469
MIR3175
RPS17L
LOC100505679
LOC100506874
LOC100507217
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
MIR4514
MIR3529
MIR4515
MIR4714

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PRCC
SDHC
TPM3
PDE4DIP
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
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
APCS
APOA2
ATP1A2
ATP1A4
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO5
DARC
GBA
GBAP1
GJA5
GJA8
HDGF
HMGCS2
HSD3B1
HSD3B2
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LMNA
LOR
LY9
MCL1
SMCP
MEF2D
MNDA
MPZ
MTX1
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PI4KB
PKLR
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
USF1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
ITGA10
PEA15
B4GALT3
ADAM15
PEX11B
CD84
SELENBP1
SH2D2A
FCGR2C
PRPF3
ARHGEF2
DEDD
AIM2
ADAMTS4
SEC22B
CHD1L
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
CELF3
PMF1
DUSP12
VPS45
KIAA0907
ATF6
POGZ
SYT11
RPRD2
SMG5
NCSTN
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
OLFML2B
C1orf43
CHTOP
PHGDH
LCE2B
OR10J1
USP21
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
HAO2
ACP6
GPR89B
HSD17B7
UFC1
OAZ3
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
FAM63A
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
REG4
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
AQP10
SLAMF9
PYGO2
ZNF697
NUP210L
MEX3A
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
HIST2H3C
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
HSD3BP4
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
LRRC71
PYHIN1
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
C1orf204
C1orf111
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
C1orf110
OR10R2
FCRL6
NBPF7
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
LOC375010
PEAR1
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
NBPF9
MIR9-1
HIST2H2BF
ETV3L
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
PRR9
RPL31P11
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA4
SNORA42
MIR554
MIR555
MIR556
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR765
MIR190B
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505633
LOC100505666
PMF1-BGLAP
TNFAIP8L2-SCNM1
MIR4654

Genes in Wide Peak

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

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

Genes
CCNE1
UQCRFS1
URI1
ZNF254
ZNF536
POP4
PLEKHF1
C19orf12
LOC148145
LOC148189
LOC284395
VSTM2B
ZNF726
LOC100101266
LOC100505835

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.23.

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

Genes
PLAG1
TCEA1
NCOA2
CHCHD7
hsa-mir-3149
hsa-mir-2052
hsa-mir-124-2
ASPH
CA8
CEBPD
CRH
CYP7A1
EYA1
FNTA
NPBWR1
HNF4G
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
PEX2
RAB2A
RP1
RPL7
RPS20
SDCBP
SNAI2
TCEB1
TERF1
TTPA
UBE2V2
NSMAF
RGS20
GGH
TRPA1
MSC
KCNB2
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SULF1
TRAM1
KIAA0146
LY96
SGK3
C8orf71
PTTG3P
SNORD54
STAU2
BHLHE22
MRPL15
PI15
LACTB2
ATP6V1H
SNTG1
GDAP1
IMPAD1
TMEM70
ARMC1
UBE2W
CHD7
C8orf44
JPH1
CPA6
PRDM14
SOX17
EFCAB1
ZFHX4
CSPP1
VCPIP1
PREX2
SLCO5A1
CRISPLD1
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
RDH10
C8orf45
CLVS1
C8orf84
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
POTEA
FAM150A
XKR9
LOC392232
LOC401463
MIR124-2
FLJ39080
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
LOC100128126
TCF24
LOC100130155
LOC100130298
LOC100130301
LOC100132891
SBF1P1
LOC100192378
LOC100287846
MIR2052
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
CA9
RMRP
TLN1
TPM2
RGP1
CREB3
GBA2
C9orf100
CCDC107
MSMP

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.2.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
C6
C7
C9
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
SLC45A2
RXFP3
WDR70
BRIX1
CCL28
C5orf28
AGXT2
C5orf42
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.23.

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

Genes
INSM1
C20orf26
RALGAPA2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.12.

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

Genes
ZFP30
ZNF345
ZNF571
ZNF529
ZNF527
ZNF382
ZNF461
ZNF585B
ZNF420
ZNF569
ZNF570
ZNF567
ZNF383
ZNF540
ZNF585A
LOC284408
LOC284412
HKR1
ZNF850
ZNF829
ZNF568
ZNF790
ZNF793
LOC100507433

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 - 48 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
--- | --- | --- | --- | ---
16p13.3 | 2.5969e-156 | 2.5969e-156 | chr16:5144019-7771745 | 1
20p12.1 | 1.7449e-64 | 1.7449e-64 | chr20:14302876-16036135 | 3
6q26 | 8.1337e-61 | 8.1337e-61 | chr6:161693099-163153207 | 1
4q22.1 | 4.0624e-61 | 1.0619e-58 | chr4:91148280-93240505 | 1
3p14.2 | 3.6855e-42 | 5.6949e-42 | chr3:59034763-61547330 | 1
5q11.2 | 1.7833e-42 | 6.7053e-41 | chr5:58260298-59787985 | 3
16q23.1 | 6.7053e-41 | 6.7053e-41 | chr16:78129058-79627770 | 1
1p33 | 7.0307e-35 | 2.2734e-32 | chr1:49193395-50514967 | 1
3q26.31 | 1.8253e-25 | 1.7008e-25 | chr3:173999806-175760559 | 2
18q21.2 | 3.2615e-28 | 1.5664e-23 | chr18:48514396-48705371 | 1
1p36.11 | 2.8268e-35 | 2.406e-21 | chr1:26527443-27708281 | 30
6p25.3 | 2.5238e-18 | 2.5238e-18 | chr6:1608837-2252425 | 2
10q11.23 | 9.8855e-17 | 5.6419e-15 | chr10:53057593-53461574 | 3
4q35.1 | 1.5657e-18 | 1.4384e-13 | chr4:178911874-191154276 | 64
5q22.2 | 1.4269e-18 | 2.1122e-12 | chr5:111061638-112357921 | 9
8p23.2 | 8.9149e-14 | 4.9443e-12 | chr8:1-6262191 | 15
15q22.33 | 3.3787e-11 | 1.4602e-10 | chr15:67067796-67494822 | 1
10q23.31 | 7.8724e-13 | 8.7797e-10 | chr10:89313008-90034038 | 5
18q12.2 | 3.6644e-16 | 1.0046e-09 | chr18:35235531-37213012 | 3
7q31.1 | 3.5384e-08 | 3.5384e-08 | chr7:110725672-111366370 | 1
21q11.2 | 4.5097e-06 | 8.1025e-06 | chr21:1-23095995 | 41
17p12 | 3.4721e-05 | 3.6026e-05 | chr17:11467196-12456081 | 5
1p13.2 | 3.6527e-06 | 0.0001925 | chr1:95939768-119426205 | 185
19p13.3 | 0.00027316 | 0.00028367 | chr19:1-5210544 | 183
10q25.2 | 1.3977e-06 | 0.00077339 | chr10:114205094-115311046 | 5
15q21.1 | 7.7336e-07 | 0.00077339 | chr15:44851245-45299932 | 5
1p36.21 | 1.4677e-25 | 0.0013847 | chr1:1-32049393 | 506
15q11.2 | 1.7832e-06 | 0.0015613 | chr15:1-32934882 | 168
22q13.31 | 0.0041339 | 0.0043163 | chr22:44706815-51304566 | 89
11q22.3 | 0.0091987 | 0.0089638 | chr11:104939777-115045236 | 80
12p13.1 | 0.0097404 | 0.0096567 | chr12:9393289-15714898 | 99
8p11.21 | 0.00053624 | 0.012826 | chr8:38457106-41119553 | 16
2p21 | 0.01119 | 0.022271 | chr2:42559257-44007392 | 10
2p12 | 0.014902 | 0.023217 | chr2:75935002-78188396 | 2
18q22.1 | 3.9671e-09 | 0.026581 | chr18:61232169-66383463 | 17
8p11.21 | 0.013266 | 0.027375 | chr8:42883855-49633244 | 11
3p26.3 | 0.010542 | 0.036067 | chr3:1-14530661 | 92
18p11.31 | 0.035988 | 0.036067 | chr18:3277692-4299545 | 5
17q24.3 | 0.037669 | 0.037654 | chr17:68173089-70595192 | 2
1q42.3 | 0.054587 | 0.056168 | chr1:229792777-249250621 | 162
2q22.1 | 0.040109 | 0.056168 | chr2:122525427-168815541 | 169
4p16.2 | 0.063657 | 0.065006 | chr4:1-14912145 | 148
5q21.1 | 1.1098e-08 | 0.07814 | chr5:82649160-112357921 | 91
2q37.2 | 0.065014 | 0.11005 | chr2:220355530-243199373 | 204
12q21.2 | 0.14517 | 0.14298 | chr12:72320595-100431272 | 123
21q22.2 | 0.082228 | 0.15442 | chr21:35560690-48129895 | 154
14q11.2 | 0.16701 | 0.16975 | chr14:1-34909469 | 185
8p22 | 0.000204 | 0.19657 | chr8:4847659-28924857 | 226

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p33.

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

Genes
BEND5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
SMAD4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
ARID1A
hsa-mir-1976
CD52
SFN
HMGN2
RPS6KA1
SLC9A1
NR0B2
FCN3
MAP3K6
NUDC
WDTC1
GPN2
AIM1L
PIGV
GPATCH3
CEP85
LIN28A
DHDDS
SH3BGRL3
TMEM222
ZDHHC18
SYTL1
UBXN11
FAM46B
C1orf172
ZNF683
TRNP1
LOC644961
MIR1976

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's Cancer Gene Census [7].

Genes
FOXC1
GMDS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.23.

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

Genes
hsa-mir-605
CSTF2T
MIR605

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
DUX4
hsa-mir-1305
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ZFP42
ENPP6
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q22.2.

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

Genes
APC
SRP19
REEP5
NREP
FLJ11235
EPB41L4A
EPB41L4A-AS1
DCP2
SNORA13

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q22.33.

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

Genes
SMAD3

Genes in Wide Peak

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

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

Genes
PTEN
PAPSS2
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

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

Genes
hsa-mir-924
hsa-mir-4318
MIR4318

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
LRRN3

Genes in Wide Peak

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

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

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
POTED
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

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

Genes
MAP2K4
hsa-mir-744
DNAH9
ZNF18
MIR744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

Table S50. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NRAS
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TSHB
VCAM1
WNT2B
CSDE1
TTF2
CDC14A
RTCD1
SLC16A4
CD101
LRIG2
LPPR4
TSPAN2
BCAS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
PTPN22
CHIA
GPSM2
SLC25A24
SNX7
DPH5
GPR88
CCDC76
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
AMIGO1
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1OS
FAM40A
DNAJA1P5
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
LPPR5
FNDC7
SASS6
UBL4B
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
FRRS1
MIR137HG
MIR137
MIR197
FLJ31662
LOC440600
BCL2L15
PGCP1
SRG7
CYMP
LOC643441
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729987
MIR942
LOC100128787
LOC100129138
LOC100129269
LOC100129620
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100506343
MIR2682

Genes in Wide Peak

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

Table S51. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GNA11
SH3GL1
STK11
TCF3
FSTL3
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
ARID3A
EEF2
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
MATK
GADD45B
NFIC
OAZ1
PALM
POLR2E
POLRMT
MAP2K2
PRTN3
PTBP1
RPS15
SGTA
TBXA2R
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
APBA3
MED16
CHAF1A
EBI3
PLIN3
APC2
ABCA7
HMG20B
SEMA6B
UQCR11
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
SHC2
TIMM13
DAZAP1
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
SLC39A3
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
NCLN
SPPL2B
SHD
WDR18
REXO1
ZNF77
C19orf29
CELF5
FSD1
TLE6
LPPR3
ZNF556
UBXN6
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
C19orf21
PLK5
C2CD4C
TICAM1
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
CSNK1G2-AS1
C19orf77
MIR7-3HG
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
C19orf29-AS1
MIR7-3
PLIN5
FAM138F
LINGO3
ARRDC5
FAM138A
MIR637
PLIN4
C19orf71
LOC100131094
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4747
MIR4746
MIR4745

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.2.

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

Genes
hsa-mir-4295
TCF7L2
VTI1A
LOC143188
MIR4295

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

Table S53. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
B2M
SPG11
TRIM69
C15orf43
PATL2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.21.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

Table S55. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
APBA2
NBEAP1
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
NDN
OCA2
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
ARHGAP11A
FAN1
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
KLF13
MAGEL2
MTMR10
NDNL2
ATP10A
NIPA2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
OTUD7A
LOC283683
OR4N4
LOC283710
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
MIR211
NF1P2
HERC2P9
WHAMMP2
LOC503519
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715

Genes in Wide Peak

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

Table S56. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
LDOC1L
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
LINC00229
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

Table S57. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATM
DDX10
POU2AF1
SDHD
hsa-mir-4301
hsa-mir-34c
ACAT1
CRYAB
DLAT
DRD2
FDX1
GRIA4
GUCY1A2
HSPB2
HTR3A
IL18
NCAM1
NNMT
NPAT
PPP2R1B
PTS
RDX
SLN
ZBTB16
CUL5
HTR3B
ZW10
RBM7
EXPH5
SIK2
REXO2
TIMM8B
C11orf71
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
TEX12
ARHGAP20
USP28
CARD18
AASDHPPT
C11orf1
ALG9
TMPRSS5
BCO2
KIAA1826
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
C11orf93
PIH1D2
FAM55A
FAM55B
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
ANKK1
C11orf53
C11orf34
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CARD17
LOC643923
CLDN25
LOC100132078
LOC100288346
MIR4301
HSPB2-C11orf52
MIR4491

Genes in Wide Peak

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

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ETV6
hsa-mir-614
hsa-mir-613
ARHGDIB
ART4
CD69
CDKN1B
CREBL2
EMP1
GPR19
GRIN2B
GUCY2C
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
MGP
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
KLRC4
CSDA
GPRC5A
CLEC2B
KLRAP1
PRR4
KLRK1
GABARAPL1
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
HEBP1
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
MANSC1
MAGOHB
STYK1
GPRC5D
ATF7IP
H2AFJ
KIAA1467
CLEC7A
BCL2L14
PLBD1
DUSP16
APOLD1
GSG1
RERG
HTR7P1
LOH12CR1
C12orf59
HIST4H4
ERP27
C12orf60
CLEC12A
CLECL1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
CLEC9A
C12orf36
LOC338817
TAS2R42
LOC374443
CLEC2A
CLEC12B
RPL13AP20
DDX12P
C12orf69
LOH12CR2
LOC642846
PRB2
MIR613
MIR614
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100506314
KLRC4-KLRK1
PRH1-PRR4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.21.

Table S59. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ADAM3A
ADAM2
IDO1
TACC1
ADAM18
ADAM9
C8orf4
PLEKHA2
ZMAT4
TM2D2
IDO2
HTRA4
ADAM32
ADAM5P
RNF5P1
LOC100130964

Genes in Wide Peak

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

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZFP36L2
COX7A2L
HAAO
MTA3
THADA
PLEKHH2
OXER1
KCNG3
LOC728819
LOC100129726

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p12.

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LRRTM4
SNAR-H

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

Table S62. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CDH7
SERPINB2
SERPINB8
SERPINB10
SERPINB13
SERPINB3
SERPINB4
SERPINB7
CDH19
TMX3
SERPINB11
DSEL
LINC00305
HMSD
LOC284294
LOC400654
LOC643542

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.21.

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CEBPD
FNTA
MCM4
PRKDC
UBE2V2
KIAA0146
SGK196
HGSNAT
POTEA
LINC00293
LOC100287846

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.3.

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-885
ATP2B2
CAV3
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RPL32
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
TIMP4
WNT7A
BRPF1
CAMK1
BHLHE40
VGLL4
EDEM1
TATDN2
IQSEC1
ARPC4
TADA3
ATG7
CHL1
CAND2
NUP210
MKRN2
THUMPD3
TTLL3
CNTN6
LSM3
LINC00312
LMCD1
C3orf32
TRNT1
CRBN
GHRL
ARL8B
SETD5
TMEM40
TMEM111
BRK1
RAD18
LRRN1
CIDEC
MTMR14
CRELD1
TMEM43
HDAC11
TSEN2
JAGN1
GHRLOS2
IL17RC
C3orf24
CHCHD4
TAMM41
IL17RE
CPNE9
CIDECP
CNTN4
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
TPRXL
LHFPL4
LOC401052
LOC440944
SNORA7A
MIR885
EGOT
GHRLOS
LOC100129480
LOC100132526
LOC100288428
LOC100507582
ARPC4-TTLL3
MIR4790

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.31.

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TGIF1
DLGAP1
LOC201477
LOC284215
FLJ35776

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
SOX9
LOC100499467

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.3.

Table S67. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
ACTN2
ADSS
AGT
CHML
LYST
CHRM3
GALNT2
GNG4
HNRNPU
KCNK1
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
TSNAX
ZNF124
GNPAT
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZNF238
CAPN9
SDCCAG8
COG2
RBM34
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
DISC2
DISC1
PPPDE1
SCCPDH
ARID4B
EGLN1
KIAA1383
KIF26B
HEATR1
ZNF692
ERO1LB
FMN2
ZNF695
SIPA1L2
ZP4
TFB2M
GREM2
SMYD3
ARV1
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2G3
OR2G2
OR2C3
C1orf124
NTPCR
EFCAB2
KIAA1804
ZNF496
C1orf198
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
C1orf131
EDARADD
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
EXOC8
CNST
PLD5
C1orf100
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
FAM89A
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
OR2W5
OR13G1
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
MIR3123
MIR3124
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4677
MIR4671
MIR4427

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

Table S68. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERCC3
hsa-mir-128-1
hsa-mir-663b
ACVR1
ACVR2A
BIN1
RND3
CACNB4
CCNT2
DARS
DPP4
FAP
GALNT3
GCG
GPD2
GPR17
GPR39
GRB14
GYPC
HNMT
ITGB6
KCNJ3
KIF5C
LCT
LY75
MCM6
MGAT5
MYO7B
NEB
NR4A2
ORC4
POLR2D
PROC
RBMS1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
TNFAIP6
CXCR4
PKP4
B3GALT1
KYNU
NMI
HS6ST1
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
TBR1
MAP3K2
GALNT5
NXPH2
COBLL1
PLA2R1
RAB3GAP1
UBXN4
R3HDM1
GCA
EPC2
ARL5A
PTPN18
MMADHC
C2orf27A
BAZ2B
ARHGEF4
LRP1B
PLEKHB2
FIGN
RIF1
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
CFC1
RPRM
UGGT1
SLC4A10
ERMN
IFIH1
MARCH7
SAP130
GTDC1
TTC21B
CSRNP3
MZT2B
YSK4
THSD7B
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
SFT2D3
TANC1
KCNH7
CCDC74A
CCDC74B
DAPL1
IMP4
TUBA3E
TUBA3D
FMNL2
GALNT13
LYPD1
XIRP2
CNTNAP5
ACMSD
FAM168B
ACVR1C
LYPD6
LYPD6B
CCDC148
LOC150527
LOC150776
WTH3DI
ARL6IP6
SLC38A11
WDSUB1
UPP2
FAM123C
LOC285103
SPOPL
CYP27C1
NCKAP5
GPR148
RBM43
LOC389033
LOC389043
LOC401010
DKFZp686O1327
MIR128-1
C2orf27B
LOC440905
LOC440910
POTEKP
POTEE
LOC554201
ANKRD30BL
LOC646743
LOC647012
CFC1B
MZT2A
POTEF
PABPC1P2
LOC100129961
LOC100131320
CYP4F30P
LOC100144595
LOC100216479
ZEB2-AS1
MIR663B
SNORA70F
MIR3679
LOC100506124
LOC100506134
LOC100507600
LY75-CD302
MIR4783
MIR4785
MIR4784
MIR4773-1
MIR4773-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.2.

Table S69. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FGFR3
WHSC1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
NKX3-2
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
RAB28
KIAA0232
WDR1
HS3ST1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
D4S234E
GPR78
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
CNO
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
KIAA1530
ZFYVE28
AFAP1
TNIP2
HAUS3
ABCA11P
GRPEL1
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
MRFAP1L1
CLNK
EVC2
OTOP1
ZNF595
LOC152742
JAKMIP1
FAM53A
METTL19
ZBTB49
ZNF721
ZNF718
CCDC96
BOD1L
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285547
LOC285548
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
USP17L6P
USP17
HSP90AB2P
C4orf48
LOC402160
ZNF876P
DEFB131
LOC650293
ZNF732
SCARNA22
MIR572
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR3138
LOC100507266
MIR378D1
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.1.

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute's 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
COX7C
HAPLN1
VCAN
EFNA5
FER
GLRX
LNPEP
MAN2A1
MEF2C
PAM
PCSK1
RASA1
SRP19
NR2F1
ST8SIA4
REEP5
NREP
RAB9BP1
TTC37
PJA2
EDIL3
POLR3G
RHOBTB3
ELL2
PPIP5K2
ERAP1
FLJ11235
GIN1
RIOK2
ARRDC3
EPB41L4A
ERAP2
FBXL17
MCTP1
NUDT12
SPATA9
FAM172A
GPR98
ANKRD32
TSLP
C5orf30
SLC25A46
EPB41L4A-AS1
LYSMD3
SLCO6A1
POU5F2
STARD4
WDR36
MBLAC2
TMEM161B
ARSK
FAM81B
DCP2
LIX1
C5orf27
KIAA0825
GPR150
NBPF22P
RGMB
RFESD
FAM174A
SLCO4C1
MIR9-2
FLJ42709
FLJ35946
TMEM232
LINC00461
SNORA13
MIR583
LOC100129716
LOC100133050
LOC100289230
LOC100289673
MIR2277
MIR4280
MIR3607
MIR3660
LOC100505678
LOC100505894

Genes in Wide Peak

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

Table S71. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ACSL3
PAX3
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
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
SNORD20
SAG
CCL20
SLC4A3
SP100
SPP2
SCG2
CUL3
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
FARSB
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
OBSL1
SH3BP4
KCNE4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
GMPPA
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
USP40
HJURP
HES6
ACCN4
DOCK10
C2orf83
MFF
CXCR7
RNPEPL1
WDFY1
NYAP2
GAL3ST2
RAB17
COPS7B
MRPL44
TRPM8
MLPH
CHPF
IQCA1
FAM124B
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
MGC16025
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
CCDC140
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
C2orf72
CXXC11
DUSP28
ESPNL
ECEL1P2
LOC348761
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.2.

Table S72. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BTG1
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
APAF1
ATP2B1
CSRP2
DCN
EPYC
DUSP6
ELK3
HAL
KCNC2
LTA4H
LUM
KITLG
MYF5
MYF6
PPP1R12A
NAP1L1
NTS
PAWR
CDK17
SLC25A3
SNRPF
SYT1
TMPO
NR2C1
UBE2N
ALX1
EEA1
PPFIA2
GALNT4
CRADD
LIN7A
SOCS2
RASSF9
PLXNC1
METAP2
GLIPR1
KERA
KRR1
NUDT4
PHLDA1
ZDHHC17
MGAT4C
MRPL42
CCDC59
TRHDE
CCDC41
SLC6A15
VEZT
FGD6
NDUFA12
ANKS1B
TMCC3
NTN4
ACSS3
BBS10
CEP290
USP44
LRRIQ1
C12orf26
CAPS2
NAV3
C12orf29
OSBPL8
CCDC38
TPH2
NEDD1
SLC9A7P1
IKBIP
AMDHD1
GLIPR1L2
TSPAN19
E2F7
LOC144481
LOC144486
KRT19P2
TMTC2
TMTC3
C12orf50
FAM71C
RMST
C12orf12
LOC256021
GLIPR1L1
POC1B
OTOGL
LOC283392
LOC338758
C12orf74
PTPRQ
MKRN9P
MIR135A2
C12orf37
PLEKHG7
NUDT4P1
MIR331
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC643339
LOC643770
SNORA53
MIR617
MIR618
LOC728084
LOC100128191
MIR1252
MIR1251
MIR4303
MIR3685
LOC100507377
POC1B-GALNT4
MIR4699
MIR548AL

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.2.

Table S73. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RUNX1
ERG
TMPRSS2
hsa-mir-3197
hsa-mir-802
ADARB1
AIRE
PTTG1IP
C21orf2
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
RCAN1
DYRK1A
ETS2
HLCS
HMGN1
PRMT2
ITGB2
KCNE1
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SIM2
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
TTC3
U2AF1
UBE2G2
WRB
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DOPEY2
KCNE2
DSCR4
DSCR3
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
DNMT3L
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
PCBP3
C21orf58
YBEY
LINC00160
FAM165B
TSPEAR
LINC00112
LINC00111
SETD4
FAM3B
RIPK4
CLIC6
AGPAT3
PRDM15
TMPRSS3
RUNX1-IT1
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
FAM207A
RSPH1
UMODL1
LINC00313
C21orf88
C21orf90
MCM3AP-AS1
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00315
DSCR9
BRWD1-IT2
DSCR10
LINC00323
LINC00319
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00114
LOC642852
LINC00163
SSR4P1
MIR802
LOC100129027
LOC100133286
MIR3197
LOC100505746
LOC100506385
CBR3-AS1
DSCAM-AS1
MIR4760

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q11.2.

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CCNB1IP1
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GPR33
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
PNP
NRL
OXA1L
PCK2
PRKD1
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
AKAP6
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
AP4S1
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
NPAS3
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
JPH4
RNASE7
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
EGLN3
C14orf126
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
C14orf21
ADCY4
LOC283624
TSSK4
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
CBLN3
SNORD9
MIR624
DHRS4L1
SNORD126
MIR208B
MIR4307
LOC100505967
LOC100506071
NEDD8-MDP1
BCL2L2-PABPN1
MIR548AI
MIR4707

Genes in Wide Peak

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

Table S75. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PCM1
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
EGR3
EPB49
EPHX2
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
MFHAS1
ENTPD4
PHYHIP
SORBS3
NPM2
DLC1
SPAG11B
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
PSD3
SLC39A14
FGF20
ADAMDEC1
CNOT7
ZDHHC2
SLC25A37
SCARA3
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
AGPAT5
INTS9
CSGALNACT1
HR
PBK
ZNF395
DEFB103B
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
MTMR9
HMBOX1
MCPH1
PPP1R3B
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
NKX2-6
SGCZ
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
ESCO2
FBXO16
LOC157627
TDH
C8orf48
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FLJ10661
XKR6
LOC286059
EFHA2
LOC286114
SCARA5
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
C8orf80
LOC392196
MIR124-1
MIR320A
DEFB103A
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
DEFB109P1B
FAM90A14
FAM86B2
SPAG11A
MIR597
MIR598
DEFA1B
FAM90A20
FAM90A19
ZNF705D
FAM66B
LOC100128993
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR4287
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
MIR4659A
MIR4660
MIR4659B
LOC100652791

Arm-level results

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

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.04 | -1.22 | 1 | 0.16 | 12.8 | 0
1q | 1955 | 0.14 | 7.7 | 3.77e-14 | 0.08 | 1.87 | 0.0921
2p | 924 | 0.10 | -3.56 | 1 | 0.02 | -8.72 | 1
2q | 1556 | 0.11 | 0.537 | 0.824 | 0.01 | -6.62 | 1
3p | 1062 | 0.07 | -4.89 | 1 | 0.08 | -4.12 | 1
3q | 1139 | 0.10 | -2.4 | 1 | 0.03 | -6.9 | 1
4p | 489 | 0.02 | -9.55 | 1 | 0.24 | 2.44 | 0.024
4q | 1049 | 0.01 | -7.98 | 1 | 0.21 | 4.67 | 6.56e-06
5p | 270 | 0.12 | -5.58 | 1 | 0.10 | -6.38 | 1
5q | 1427 | 0.06 | -3.51 | 1 | 0.13 | 1.48 | 0.193
6p | 1173 | 0.15 | 0.751 | 0.679 | 0.06 | -4.81 | 1
6q | 839 | 0.13 | -2.1 | 1 | 0.08 | -5.06 | 1
7p | 641 | 0.50 | 19.6 | 0 | 0.01 | -7.74 | 1
7q | 1277 | 0.44 | 22.7 | 0 | 0.02 | -5.95 | 1
8p | 580 | 0.25 | 2.89 | 0.00802 | 0.49 | 16.9 | 0
8q | 859 | 0.44 | 17.5 | 0 | 0.13 | -1.52 | 1
9p | 422 | 0.15 | -2.79 | 1 | 0.09 | -6.29 | 1
9q | 1113 | 0.12 | -1.2 | 1 | 0.08 | -3.98 | 1
10p | 409 | 0.04 | -9.45 | 1 | 0.09 | -6.68 | 1
10q | 1268 | 0.02 | -7.3 | 1 | 0.10 | -2 | 1
11p | 862 | 0.08 | -5.16 | 1 | 0.08 | -5.47 | 1
11q | 1515 | 0.08 | -1.8 | 1 | 0.10 | -0.247 | 1
12p | 575 | 0.17 | -0.869 | 1 | 0.07 | -6.4 | 1
12q | 1447 | 0.15 | 2.87 | 0.00802 | 0.06 | -3.3 | 1
13q | 654 | 0.57 | 24 | 0 | 0.04 | -5.84 | 1
14q | 1341 | 0.05 | -4.48 | 1 | 0.28 | 11.8 | 0
15q | 1355 | 0.02 | -5.94 | 1 | 0.28 | 11.7 | 0
16p | 872 | 0.18 | 1.01 | 0.51 | 0.04 | -7.47 | 1
16q | 702 | 0.18 | -0.101 | 1 | 0.05 | -7.4 | 1
17p | 683 | 0.06 | -5.31 | 1 | 0.53 | 21.5 | 0
17q | 1592 | 0.12 | 1.67 | 0.17 | 0.16 | 4.74 | 5.14e-06
18p | 143 | 0.08 | -5.53 | 1 | 0.60 | 20.9 | 0
18q | 446 | 0.05 | -5.49 | 1 | 0.64 | 25.8 | 0
19p | 995 | 0.09 | -3.84 | 1 | 0.06 | -6.1 | 1
19q | 1709 | 0.12 | 3.1 | 0.0047 | 0.05 | -3.19 | 1
20p | 355 | 0.54 | 17.5 | 0 | 0.31 | 4.18 | 5.78e-05
20q | 753 | 0.70 | 32.8 | 0 | 0.15 | -0.933 | 1
21q | 509 | 0.04 | -8.49 | 1 | 0.22 | 1.19 | 0.306
22q | 921 | 0.02 | -8.02 | 1 | 0.22 | 3.93 | 0.000151

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.

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD/1444584/2.GDAC_MergeDataFiles.Finished/COADREAD.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 = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 574 Input Tumor Samples.

Tumor Sample Names
TCGA-A6-2670-01A-02D-0819-01
TCGA-A6-2671-01A-01D-1549-01
TCGA-A6-2672-01A-01D-1549-01
TCGA-A6-2674-01A-02D-1549-01
TCGA-A6-2675-01A-02D-1717-01
TCGA-A6-2676-01A-01D-1549-01
TCGA-A6-2677-01A-01D-1549-01
TCGA-A6-2678-01A-01D-1549-01
TCGA-A6-2679-01A-02D-1549-01
TCGA-A6-2680-01A-01D-1549-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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