Bladder Urothelial Carcinoma: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

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

Summary

There were 135 tumor samples used in this analysis: 27 significant arm-level results, 24 significant focal amplifications, and 31 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 - 24 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
--- | --- | --- | --- | ---
6p22.3 | 7.184e-36 | 7.184e-36 | chr6:20781286-21757620 | 3
8q22.3 | 1.8628e-17 | 1.8628e-17 | chr8:101193622-102458148 | 10
1q23.3 | 2.8387e-18 | 1.681e-16 | chr1:160979061-161109018 | 9
11q13.3 | 5.119e-16 | 5.119e-16 | chr11:70216472-70360458 | 3
3p25.2 | 3.6162e-15 | 3.6162e-15 | chr3:12481505-12491536 | 0 [PPARG]
19q12 | 3.3069e-10 | 2.8183e-09 | chr19:30243979-30529931 | 2
7p11.2 | 1.82e-08 | 1.82e-08 | chr7:54993065-55397917 | 1
12q15 | 1.0308e-07 | 1.0308e-07 | chr12:69183279-70280714 | 14
8p11.23 | 1.4923e-07 | 1.4923e-07 | chr8:37387916-37701929 | 6
10p15.1 | 2.2916e-05 | 2.2916e-05 | chr10:4197255-6398978 | 27
17q12 | 5.8976e-05 | 0.0001007 | chr17:37820993-37905815 | 7
20q11.21 | 0.00057115 | 0.00057115 | chr20:30064458-30332464 | 10
1p34.2 | 0.001929 | 0.001929 | chr1:39531274-40539227 | 17
4p16.3 | 0.0062492 | 0.0062492 | chr4:1738268-1817427 | 3
5p15.33 | 0.0064826 | 0.0064826 | chr5:1-15332573 | 81
17q11.2 | 0.0036764 | 0.018866 | chr17:27386448-28058968 | 12
3q26.32 | 0.020052 | 0.020052 | chr3:159091642-198022430 | 252
16p12.1 | 0.04561 | 0.04561 | chr16:23463203-25858475 | 22
1q21.3 | 4.7195e-07 | 0.06338 | chr1:120523956-153421408 | 203
13q22.1 | 0.076105 | 0.076105 | chr13:73642878-74157164 | 1
22q11.23 | 0.080049 | 0.080049 | chr22:1-27277261 | 197
4q13.3 | 0.1248 | 0.1248 | chr4:72453602-74875451 | 16
6q12 | 0.12717 | 0.12717 | chr6:63883156-64133661 | 1
19q13.43 | 0.077928 | 0.16056 | chr19:51155789-59128983 | 352

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

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

Genes
SOX4
CDKAL1
LINC00340

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q22.3.

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

Genes
SPAG1
YWHAZ
RNF19A
PABPC1
ZNF706
NACAP1
ANKRD46
SNX31
FLJ42969
MIR4471

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q23.3.

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

Genes
NIT1
PFDN2
USF1
DEDD
F11R
PVRL4
KLHDC9
ARHGAP30
TSTD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CTTN
PPFIA1
SHANK2

Genes in Wide Peak

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

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

Genes
CCNE1
URI1

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q15.

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

Genes
MDM2
hsa-mir-1279
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
RAB3IP
BEST3
LRRC10
MIR1279
MIR3913-2
MIR3913-1

Genes in Wide Peak

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

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

Genes
ERLIN2
PROSC
GPR124
BRF2
ZNF703
LOC728024

Genes in Wide Peak

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

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

Genes
hsa-mir-3155
CALML3
AKR1C4
AKR1C1
AKR1C2
GDI2
IL2RA
IL15RA
PFKFB3
AKR1C3
NET1
CALML5
ANKRD16
FAM208B
ASB13
TUBAL3
AKR1E2
FBXO18
RBM17
UCN3
LOC338588
AKR1CL1
tAKR
LOC399715
LOC100216001
MIR3155A
MIR3155B

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
PNMT
TCAP
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

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

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

Genes
hsa-mir-3193
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
LINC00028
PSIMCT-1
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MYCL1
BMP8B
PPT1
PABPC4
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
OXCT2
NT5C1A
MFSD2A
BMP8A
KIAA0754
SNORA55
PPIEL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

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

Genes
FGFR3
LETM1
TACC3

Genes in Wide Peak

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

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

Genes
hsa-mir-4278
hsa-mir-4277
ADCY2
CTNND2
DAP
DNAH5
MTRR
NDUFS6
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
KIAA0947
PP7080
IRX4
TAS2R1
FAM105A
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285577
LOC285692
SLC6A19
LOC340094
SLC6A18
LRRC14B
FLJ33360
TAG
LOC442132
ANKRD33B
SDHAP3
LOC728613
LOC729506
SNORD123
LOC100130744
MIR4277
MIR4278
LOC100505738
LOC100505806
LOC100506688
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
CRYBA1
TIAF1
GIT1
NUFIP2
TAOK1
CORO6
SSH2
TP53I13
ABHD15
ANKRD13B
MYO18A
MIR4523

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
IL12A
KNG1
KPNA4
MFI2
MUC4
NDUFB5
OPA1
CLDN11
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
SI
ST6GAL1
SKIL
SLC2A2
SST
TERC
THPO
SEC62
FXR1
TP63
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
SMC4
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
SCHIP1
NMD3
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
IFT80
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
FYTTD1
ARPM1
MGC2889
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
RPL39L
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
PPM1L
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
SPTSSB
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
TRIM59
CCDC39
LOC339926
LPP-AS2
LRRIQ4
SAMD7
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
TMEM212
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
SNORD2
SNORA4
LOC646168
C3orf65
LOC647107
GMNC
LOC647323
SCARNA7
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
IQCJ-SCHIP1
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p12.1.

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

Genes
PALB2
AQP8
NDUFAB1
PLK1
PRKCB
RBBP6
HS3ST4
CACNG3
ERN2
GGA2
TNRC6A
LCMT1
ARHGAP17
UBFD1
CHP2
DCTN5
COG7
SLC5A11
EARS2
ZKSCAN2
LOC554206
LOC100506655

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
NOTCH2
PDE4DIP
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
CTSK
CTSS
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
IVL
LOR
MCL1
SMCP
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A8
S100A9
S100A10
S100A11
S100A12
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
SV2A
RBM8A
SF3B4
PIAS3
SEMA6C
POLR3C
TXNIP
MTMR11
MLLT11
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
CA14
NBPF14
LCE2B
RNF115
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
FAM63A
CDC42SE1
OTUD7B
PGLYRP4
FAM91A2
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
HIST2H3C
LIX1L
C1orf51
HFE2
ANKRD35
LELP1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
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
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
C1orf68
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
TNFAIP8L2-SCNM1

Genes in Wide Peak

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

Table S19. 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 22q11.23.

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

Genes
BCR
SMARCB1
CLTCL1
hsa-mir-548j
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ADORA2A
ADRBK2
ARVCF
ATP6V1E1
BID
COMT
CRKL
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
DDT
GGT1
GGT3P
GGT5
GNAZ
GP1BB
GSC2
GSTT1
GSTT2
SERPIND1
IGLL1
MIF
MMP11
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
SNRPD3
TBX1
CLDN5
TOP1P2
HIRA
UBE2L3
UFD1L
VPREB1
ZNF70
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
TPST2
TOP3B
P2RX6
SNAP29
RAB36
PPM1F
DGCR2
TXNRD2
USP18
HIC2
SPECC1L
CABIN1
PRAME
SEZ6L
TSSK2
SDF2L1
PPIL2
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
TFIP11
GSTTP1
DGCR11
DGCR9
POM121L1P
DGCR5
DGCR10
FBXW4P1
TRMT2A
RTDR1
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L9P
POM121L8P
YPEL1
ZDHHC8
VPREB3
C22orf43
MED15
UPB1
TUBA8
CECR1
DGCR8
GNB1L
PEX26
SUSD2
ASPHD2
MICAL3
MRPL40
RTN4R
SLC2A11
C22orf29
THAP7
OR11H1
C22orf13
SLC25A18
TMEM191A
MYO18B
KLHL22
DGCR6L
RIMBP3
KIAA1671
HPS4
SCARF2
GGTLC2
GUSBP11
DERL3
IGLL3P
LRP5L
LOC96610
MGC16703
GAB4
C22orf39
C22orf25
ZNF280A
SGSM1
ZNF280B
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
C22orf15
CCDC116
TMEM211
POM121L4P
RGL4
LOC284865
LOC284889
PI4KAP2
TPTEP1
LOC388849
FAM211B
LOC391322
LOC400891
BCRP2
CHCHD10
SRRD
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
PIWIL3
MIAT
BCRP3
TMEM191C
C22orf45
POM121L10P
LOC648691
CES5AP1
GSTTP2
GSTT2B
MIR648
MIR650
TMEM191B
PI4KAP1
LOC729444
DDTL
MIR301B
LOC100128531
CECR7
CECR5-AS1
FLJ41941
MIR1286
MIR1306
MIR548J
MIR3198-1
IGLL5
MIR3618
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
AFM
AFP
ALB
GC
CXCL1
IL8
PF4
PF4V1
PPBP
CXCL6
CXCL5
ADAMTS3
NPFFR2
ANKRD17
RASSF6
COX18

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
LGSN

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.43.

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

Genes
KLK2
PPP2R1A
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
A1BG
KLK3
CD33
SIGLEC6
ETFB
FCAR
FKBP1AP1
FPR1
FPR2
FPR3
GPR32
HAS1
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LIM2
NDUFA3
NKG7
CNOT3
PEG3
PRKCG
KLK7
KLK6
KLK10
PTPRH
RPL28
RPS5
RPS9
CLEC11A
AURKC
SYT5
TNNI3
TNNT1
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF175
SIGLEC5
UBE2M
ZNF264
NCR1
KLK4
ZNF432
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
LILRB1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KLK8
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
ZNF324
KLK5
KLK13
PRPF31
SIGLEC7
SIGLEC9
SIGLEC8
CHMP2A
ZNF544
UBE2S
CCDC106
EPN1
KLK14
KLK12
SHANK1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
ZNF71
CACNG8
CACNG7
CACNG6
ZNF350
ZNF667
ZNF649
ZSCAN18
MGC2752
TSEN34
MBOAT7
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
ZNF419
ISOC2
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
ZNF611
ZNF528
BRSK1
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
ACPT
LENG9
BIRC8
RDH13
ZIM3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
ZNF813
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF579
ZNF525
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
ZNF773
LOC386758
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF321P
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR99B
TARM1
MIR371A
MIR372
MIR373
A1BG-AS1
DPRX
DUXA
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC646508
SBK2
LOC646862
SNORD88A
SNORD88B
SNORD88C
MIR643
CEACAM18
SHISA7
FLJ30403
ZNF814
SIGLEC14
MIMT1
MIR935
LOC100128252
LOC100128398
LOC100129083
SGK110
LOC100131691
PEG3-AS1
ERVV-2
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
ZNF865
ZNF816-ZNF321P
MIR4754
MIR4752
MIR371B

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 6.9953e-76 | 6.9953e-76 | chr9:21865498-22448737 | 4
13q14.2 | 2.7533e-12 | 2.7533e-12 | chr13:48833767-49281290 | 3
5q11.2 | 3.1135e-11 | 3.1135e-11 | chr5:58260298-59787985 | 3
2q22.1 | 1.3544e-08 | 1.4089e-07 | chr2:139655617-143637838 | 1
16p13.3 | 3.1452e-07 | 3.2832e-07 | chr16:3764793-4013466 | 1
4q22.1 | 7.6191e-08 | 5.3121e-07 | chr4:90844993-93240505 | 1
17p12 | 1.0947e-05 | 1.1576e-05 | chr17:14131834-15999789 | 19
2q37.1 | 3.2206e-10 | 2.0081e-05 | chr2:219457039-243199373 | 244
19p13.3 | 3.2197e-05 | 3.2197e-05 | chr19:1-4375161 | 160
2q34 | 1.5606e-10 | 0.00059117 | chr2:213290536-214143899 | 5
6p25.3 | 0.0024927 | 0.0024993 | chr6:1-2250882 | 9
4q34.2 | 0.00072762 | 0.003281 | chr4:174241076-184209734 | 29
15q12 | 0.0049128 | 0.0048703 | chr15:1-33605300 | 172
10q23.31 | 0.0052336 | 0.0052368 | chr10:89617158-91063177 | 17
8p23.3 | 0.00078894 | 0.010812 | chr8:1-29592015 | 243
6q21 | 0.00051295 | 0.012483 | chr6:89672136-123104204 | 147
8p21.1 | 2.0109e-05 | 0.012835 | chr8:11644822-32409995 | 162
11q25 | 0.014243 | 0.014489 | chr11:86133030-135006516 | 389
1p36.11 | 0.020922 | 0.02084 | chr1:1-33981017 | 551
22q13.31 | 0.02084 | 0.02084 | chr22:39186413-51304566 | 193
3p12.3 | 0.0002397 | 0.037956 | chr3:55108056-93777876 | 108
16q23.1 | 0.038675 | 0.039277 | chr16:78129058-79627770 | 1
11p15.4 | 0.05817 | 0.060275 | chr11:1-34077944 | 404
Xq21.33 | 0.059241 | 0.060275 | chrX:94288568-98718611 | 4
6q27 | 0.0012478 | 0.069622 | chr6:152422456-171115067 | 107
3p14.2 | 1.2373e-05 | 0.073242 | chr3:44372147-93777876 | 340
14q12 | 0.020304 | 0.077483 | chr14:1-31030869 | 166
3p21.31 | 5.6143e-05 | 0.087098 | chr3:38829152-77091215 | 371
10p12.1 | 0.14074 | 0.14304 | chr10:14911595-38300099 | 123
1q32.1 | 0.18728 | 0.18728 | chr1:172381781-249250621 | 606
14q32.31 | 0.091008 | 0.2085 | chr14:64679299-107349540 | 442

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
RB1
RCBTB2
LPAR6

Genes in Wide Peak

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

Table S26. 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 2q22.1.

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

Genes
LRP1B

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
CREBBP

Genes in Wide Peak

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

Table S29. 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 17p12.

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

Genes
ADORA2B
MEIS3P1
PMP22
HS3ST3B1
TRIM16
TTC19
ZNF286A
TEKT3
MGC12916
CDRT7
ZSWIM7
CDRT15
FAM18B2
CDRT4
TBC1D26
CDRT1
CDRT15P2
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.1.

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

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

Genes in Wide Peak

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

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

Genes
GNA11
STK11
TCF3
FSTL3
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
EBI3
APC2
ABCA7
HMG20B
UQCR11
SBNO2
ZFR2
PIP5K1C
HMHA1
SHC2
TIMM13
DAZAP1
SNORD37
FGF22
TJP3
ITGB1BP3
SLC39A3
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
STAP2
BTBD2
RNF126
CCDC94
NCLN
SPPL2B
SHD
WDR18
REXO1
ZNF77
C19orf29
CELF5
FSD1
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
CREB3L3
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
TMIGD2
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
CSNK1G2-AS1
C19orf77
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
C19orf29-AS1
FAM138F
LINGO3
FAM138A
MIR637
C19orf71
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745

Genes in Wide Peak

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

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

Genes
hsa-mir-548f-2
IKZF2
MIR548F2
MIR4776-1
MIR4776-2

Genes in Wide Peak

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

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

Genes
IRF4
FOXF2
FOXC1
GMDS
EXOC2
DUSP22
FOXQ1
HUS1B
LOC285768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.2.

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

Genes
hsa-mir-1305
hsa-mir-4276
AGA
DCTD
GPM6A
HMGB2
HPGD
VEGFC
GLRA3
SAP30
HAND2
ADAM29
SCRG1
FBXO8
NEIL3
ODZ3
SPCS3
NBLA00301
CEP44
MGC45800
WDR17
SPATA4
ASB5
C4orf38
LOC285501
FAM92A3
LINC00290
MIR1305
MIR4276

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

Table S36. 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
SCG5
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
ARHGAP11A
FAN1
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
GREM1
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
FMN1
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
TMCO5B

Genes in Wide Peak

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

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

Genes
PTEN
ACTA2
FAS
LIPA
LIPF
CH25H
RNLS
STAMBPL1
ANKRD22
LIPJ
LIPM
LIPK
LIPN
KLLN
FAS-AS1
MIR4679-1
MIR4679-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

Table S38. 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
hsa-mir-596
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
CLN8
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
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
SLC39A14
FBXO25
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
CSMD1
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
C8orf42
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FLJ10661
XKR6
LOC286059
LOC286083
EFHA2
LOC286114
SCARA5
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
C8orf80
LOC392196
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q21.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
CCNC
COL10A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
HSF2
KPNA5
LAMA4
MARCKS
MAN1A1
PLN
POU3F2
PREP
PKIB
REV3L
SIM1
SMPD2
MAP3K7
NR2E1
TSPYL1
DDO
SNX3
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
CASP8AP2
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
ANKRD6
CDK19
MDN1
TSPYL4
UFL1
BRD7P3
ASF1A
PNISR
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
SOBP
QRSL1
PDSS2
LYRM2
SERINC1
HACE1
BEND3
RRAGD
PRDM13
BACH2
POPDC3
MICAL1
FAM184A
MANEA
GPR63
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
KIAA1919
GTF3C6
KLHL32
NUS1
SLC16A10
PM20D2
SRSF12
BVES-AS1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
RSPH4A
LINC00222
CEP85L
LIN28B
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
LOC100130890
LOC100287632
MIR2113
MIR548H3
LOC100422737
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.1.

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

Genes
PCM1
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
NAT1
NAT2
ADRA1A
ASAH1
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
EXTL3
PTK2B
FDFT1
FGL1
GFRA2
GNRH1
GSR
GTF2E2
LOXL2
LPL
MSR1
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
UBXN8
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
ENTPD4
PHYHIP
SORBS3
NPM2
DLC1
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
FGF20
ADAMDEC1
CNOT7
PURG
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
HMBOX1
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
FAM86B1
LONRF1
CHMP7
VPS37A
NKX2-6
SGCZ
PEBP4
CDCA2
ESCO2
FBXO16
C8orf48
R3HCC1
LGI3
DEFB109P1
DEFB130
LOC254896
LOC286059
EFHA2
LOC286114
SCARA5
LOC286135
LOC340357
USP17L2
FAM90A25P
LOC389641
C8orf80
LOC392196
MIR320A
MIR383
C8orf58
DEFB135
DEFB136
DEFB134
C8orf75
MBOAT4
FAM86B2
ZNF705D
LOC100128750
LOC100128993
FAM66D
FAM66A
LOC100133267
MIR4287
MIR3148
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
LOC100507341
MIR548O2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
MAML2
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CTSC
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
GRIA4
GRIK4
GRM5
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
TRPC6
TYR
UPK2
ZBTB16
ZNF202
CUL5
FZD4
BARX2
OR7E2P
JRKL
ZNF259
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
C2CD2L
NAALAD2
RBM7
MPZL2
YAP1
HYOU1
ATP5L
ME3
GPR83
SRSF8
ADAMTS8
PRSS23
TREH
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
RAB38
CADM1
PANX1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
CHORDC1
ACAD8
B3GAT1
DCPS
C11orf54
ZBTB44
THYN1
DDX25
NOX4
NTM
CDON
SIDT2
TRAPPC4
CWC15
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
ANKRD49
TTC12
C11orf57
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
C11orf75
PRDM10
TRIM49
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TMEM135
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
KIAA1731
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
SLC36A4
FAT3
TRIM64
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
CCDC67
PATE1
C11orf65
ADAMTS15
MPZL3
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANGPTL5
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
HEPHL1
C11orf34
VSTM5
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
SCARNA9
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49L1
LOC100128239
LOC100132078
PATE3
LOC100288077
LOC100288346
MIR1304
BACE1-AS
MIR4301
MIR3167
MIR1260B
LOC100499227
MIR3920
MIR3656
LOC100506368
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
LCK
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-4254
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
AK2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
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
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
YARS
AKR7A2
ALDH4A1
EIF3I
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
KHDRBS1
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
KPNA6
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
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
S100PBP
CEP85
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
ADC
TMEM54
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
RNF19B
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
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
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR4254
MIR3917
MIR3605
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 22q13.31.

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

Genes
EP300
PDGFB
MKL1
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
hsa-mir-33a
hsa-mir-1281
ACR
ACO2
ADSL
ARSA
ATF4
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
MCHR1
MGAT3
NAGA
NDUFA6
NHP2L1
PMM1
PPARA
MAPK11
RANGAP1
RPL3
MAPK12
SBF1
SREBF2
ST13
TCF20
TEF
UPK3A
WNT7B
CACNA1I
SYNGR1
GRAP2
APOBEC3B
CELSR1
PPP6R2
ZBED4
RBX1
SCO2
PKDREJ
TAB1
SLC25A17
NUP50
TOB2
RABL2B
PACSIN2
TNRC6B
GRAMD4
TTLL12
MLC1
ZC3H7B
KIAA0930
CBX6
NPTXR
CBX7
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SNORD43
SMC1B
CSDC2
RRP7A
MCAT
APOBEC3C
PPPDE2
SGSM3
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
SMCR7L
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
SEPT3
PANX2
APOBEC3G
XPNPEP3
PARVG
CERK
EFCAB6
CENPM
ALG12
CRELD2
C22orf46
CCDC134
ADM2
SCUBE1
TRABD
PNPLA3
SELO
L3MBTL2
HDAC10
LDOC1L
POLDIP3
PHF5A
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
RPS19BP1
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
FAM83F
TNFRSF13C
RNU86
SNORD83A
SNORD83B
APOBEC3D
ENTHD1
DNAJB7
CHADL
MEI1
FAM109B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
APOBEC3H
WBP2NL
POLR3H
APOBEC3A
APOBEC3F
SERHL2
RNU12
ATP5L2
LOC284933
RPL23AP82
BK250D10.8
LOC339685
C22orf34
CHKB-CPT1B
LOC388906
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
MIR33A
LINC00229
FAM116B
PIM3
SHISA8
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100130899
LOC100132273
LOC100144603
LOC100271722
MIR1249
MIR1281
MIR3201
MIR3619
LOC100506472
LOC100506714
MIR4763
MIR4762
MIR4766
MIR4535

Genes in Wide Peak

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

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

Genes
FHIT
MITF
FOXP1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
ARF4
C3orf51
DNASE1L3
EPHA3
FLNB
GBE1
GPR27
HTR1F
CNTN3
PDHB
POU1F1
PROS1
PTPRG
ROBO1
ROBO2
ATXN7
TMF1
WNT5A
SLMAP
ACOX2
CGGBP1
CADPS
SUCLG2
HESX1
UBA3
MAGI1
PSMD6
ARL6IP5
RPP14
FAM107A
PDZRN3
FRMD4B
FAM208A
RYBP
CHMP2B
LRIG1
ERC2
APPL1
ARHGEF3
IL17RD
PXK
FEZF2
EBLN2
SHQ1
ZNF654
LMOD3
ADAMTS9
ABHD6
C3orf14
PROK2
THOC7
ID2B
KBTBD8
SLC25A26
FAM3D
C3orf49
SNTN
SYNPR
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
ARL13B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
C3orf64
C3orf38
CCDC66
LOC285401
EIF4E3
SPATA12
VGLL3
LOC401074
FAM19A1
STX19
LOC440970
FLJ20518
FAM86DP
MIR548A2
GXYLT2
ZNF717
LOC100287879
FRG2C
MIR1284
MIR1324
MIR3136
MIR4272
MIR4273
MIR3938
LOC100506994
LOC100507062
ADAMTS9-AS2
MIR4795
MIR4444-1
LOC100652759

Genes in Wide Peak

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

Table S45. 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 11p15.4.

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

Genes
CARS
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
MPPED2
CALCA
CALCB
CCKBR
CD59
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CSTF3
CTSD
DRD4
DUSP8
EIF4G2
FSHB
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PAX6
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RCN1
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
EIF3M
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
C11orf41
FBXO3
SERGEF
OR5E1P
OR10A3
FXC1
ELP4
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
WT1-AS
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
LIN7C
TCP11L1
LGR4
PIDD
KCNQ1DN
SOX6
PARVA
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
PRRG4
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
QSER1
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
NAV2
SYT8
CCDC34
DEPDC7
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
DNAJC24
C11orf46
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
NS3BP
METTL15
IMMP1L
OR56B4
ANO5
LOC255512
OR52B2
C11orf35
OR51F1
SVIP
MRGPRX1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
OR10A2
OVCH2
PDDC1
GALNTL4
B7H6
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
NAV2-AS4
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
MIR483
SNORA3
SNORA52
LOC644656
RASSF10
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
MIR610
INS-IGF2
MUC5B
LOC729013
MIR675
LOC100126784
MRVI1-AS1
C11orf91
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
LOC100500938
MIR210HG
LOC100506305
LOC100506540
DCDC5
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR4694
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
hsa-mir-548m
DIAPH2
RPA4
LOC643486

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
ACAT2
CCR6
GPR31
IGF2R
KIF25
LPA
MAS1
MAP3K4
OPRM1
PARK2
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
EZR
VIP
RNASET2
SYNJ2
QKI
WTAP
PDE10A
SCAF8
SYNE1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
TFB1M
SNX9
BRP44L
UNC93A
MTRF1L
PHF10
C6orf70
AGPAT4
TULP4
ARID1B
TMEM181
SMOC2
ZDHHC14
FRMD1
AGPAT4-IT1
C6orf208
MYCT1
LPAL2
RSPH3
TTLL2
FAM120B
FNDC1
SERAC1
LINC00473
SYTL3
SFT2D1
TAGAP
PACRG
CNKSR3
PNLDC1
LOC154449
DACT2
C6orf118
OSTCP1
WDR27
LOC285796
PRR18
C6orf120
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
LOC441177
MLLT4-AS1
SNORA20
SNORA29
TMEM242
LOC729603
HGC6.3
LOC100129518
C6orf99
LOC100289495
MIR1913
MIR3918
MIR3939
MIR3692
CAHM
MIR4466
MIR4644

Genes in Wide Peak

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

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

Genes
FHIT
MITF
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
EPHA3
FLNB
GBE1
GNAI2
GNAT1
XCR1
GPR27
GPX1
GRM2
HTR1F
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
CNTN3
PDHB
PFKFB4
PLXNB1
POU1F1
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
ROBO1
ROBO2
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
TMF1
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RRP9
MAGI1
CACNA2D2
VPRBP
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
PTPN23
CHMP2B
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
QRICH1
PXK
FEZF2
EBLN2
DALRD3
SHQ1
ZNF654
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
SELK
PROK2
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
UCN2
ZNF502
RFT1
ACTR8
SLC25A26
ZNF501
GPR62
FAM3D
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
PRICKLE2
C3orf67
KCTD6
ARL13B
KLHDC8B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ALS2CL
TMIE
C3orf64
FBXW12
C3orf38
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
PRSS42
ZNF445
SPATA12
C3orf62
TMEM110
PRSS45
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LOC401074
MIRLET7G
MIR135A1
MIR191
FAM19A1
STX19
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
LOC644714
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4444-1
MIR4443
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q12.

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

Genes
CCNB1IP1
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
FOXG1
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
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
SUPT16H
ACIN1
KHNYN
SLC7A8
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
C14orf167
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
DCAF11
OR4K15
JPH4
RNASE7
RAB2B
AJUBA
ZFHX2
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
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
DHRS4L1
SNORD126
MIR208B
MIR4307
LOC100505967
NEDD8-MDP1
BCL2L2-PABPN1
MIR548AI
MIR4707

Genes in Wide Peak

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

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

Genes
CTNNB1
FHIT
MITF
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
SNORA62
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
TMF1
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
MAGI1
CACNA2D2
VPRBP
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
EIF1B
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
MYRIP
PTPN23
DNAH1
HIGD1A
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
ABHD5
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
SLC25A38
ULK4
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
KIF9
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
SLC25A26
ZNF501
GPR62
FAM3D
LYZL4
KBTBD5
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
PRSS42
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
LOC401074
MIRLET7G
MIR135A1
MIR138-1
MIR191
FAM19A1
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
LOC644714
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4444-1
MIR4443
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p12.1.

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

Genes
MLLT10
hsa-mir-938
hsa-mir-604
hsa-mir-603
hsa-mir-1915
hsa-mir-511-2
hsa-mir-511-1
BMI1
CACNB2
MAP3K8
CREM
TRDMT1
GAD2
ITGB1
KIF5B
MRC1
PIP4K2A
RSU1
SVIL
ZEB1
VIM
STAM
CUBN
FZD8
CUL2
ITGA8
NRP1
PTPLA
PTER
NMT2
SPAG6
ABI1
NEBL
RPP38
YME1L1
ANKRD26
MSRB2
RAB18
COMMD3
PDSS1
BAMBI
WAC
MYO3A
APBB1IP
ARMC4
MTPAP
OLAH
KIAA1217
PARD3
PRTFDC1
ZNF248
GPR158
ARHGAP21
KIAA1462
DNAJC1
DCLRE1C
SUV39H2
C10orf68
THNSL1
FAM188A
EPC1
LYZL1
PLXDC2
MASTL
ANKRD30A
ACBD5
ARHGAP12
LYZL2
MPP7
ENKUR
ARMC3
ZNF25
GJD4
CCNY
OTUD1
LOC220906
ZNF438
ZEB1-AS1
CCDC7
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
PTF1A
C10orf67
MKX
ST8SIA6
EBLN1
PTCHD3
C10orf113
C10orf140
LINC00202
LOC387646
LOC387647
C1QL3
C10orf114
ACBD7
MIR511-1
MIR511-2
MEIG1
LINC00264
TMEM236
MIR603
MIR604
LOC729668
LOC731789
MIR938
LOC100128098
LOC100128511
LOC100128811
LOC100129213
LOC100130992
PRINS
LOC100192204
MTRNR2L7
MIR1915
LOC100499489
LOC100505583
LOC100507605
COMMD3-BMI1
MIR4675
MIR4683

Genes in Wide Peak

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

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

Genes
ABL2
ELK4
FH
MDM4
TPR
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
FASLG
ARF1
ASTN1
SERPINC1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
DHX9
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GLUL
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
MR1
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NCF2
NEK2
NID1
NVL
CDK18
PDC
PFKFB2
PIGC
PIGR
PIK3C2B
PKP1
PLA2G4A
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS1
RGS2
RGS7
RGS13
RGS16
RNASEL
RNF2
RNPEP
RYR2
SNRPE
SOAT1
SRP9
TROVE2
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TNR
TP53BP2
TRAF5
TSNAX
TNFSF4
USH2A
WNT9A
ZNF124
SLC30A1
NPHS2
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
B3GALT2
RAB7L1
TNFSF18
TAF1A
ANGPTL1
EXO1
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
GGPS1
RASAL2
SOX13
PRDX6
IKBKE
KIAA0040
TMEM63A
TOMM20
URB2
CEP350
CEP170
ZC3H11A
SMG7
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
AKT3
ARPC5
PRG4
STX6
BPNT1
TIMM17A
LRRN2
ZNF238
IVNS1ABP
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
OCLM
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NMNAT2
NFASC
GLT25D2
RGL1
FBXO28
CAMSAP2
SRGAP2
CRB1
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
TOR1AIP1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
RNU5F-1
DIEXF
TAF5L
CACYBP
DISC2
DISC1
KLHL20
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
GLRX2
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
IER5
UCHL5
C1orf9
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
SWT1
LAX1
C1orf27
MARC2
SUSD4
KIF26B
RALGPS2
GPATCH2
HEATR1
DARS2
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
KIAA1614
FAM5B
ZP4
RHOU
KLHL12
LGR6
GAS5
PAPPA2
TNN
MRPS14
TFB2M
TOR3A
RFWD2
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
EDEM3
TRAF3IP3
SH3BP5L
NPL
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
SHCBP1L
TRMT1L
NUAK2
DDX59
RASSF5
HMCN1
MIXL1
C1orf124
FCAMR
OBSCN
C1orf49
NTPCR
EFCAB2
ACBD6
KIAA1804
ZBTB37
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
RGS8
WNT3A
NAV1
SEC16B
LHX4
ANGEL2
IGFN1
CENPL
C1orf105
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
TSEN15
FAM129A
SNAP47
C1orf96
AXDND1
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
RC3H1
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
C1orf55
CNST
C1orf65
FLJ23867
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
ASPM
PGBD2
OR2L13
SLC9A11
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
LOC284648
DKFZP564C196
HNRNPU-AS1
LIN9
VN1R5
ANKRD45
FAM5C
ZNF678
PRSS38
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
RGSL1
IRF2BP2
ZBTB41
MIA3
C1orf95
FAM89A
RPS10P7
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf220
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR194-1
MIR205
MIR181A1
MIR215
MIR29B2
MIR29C
RGS21
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
MIR488
SNORD74
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SCARNA3
SNORA14B
SNORA36B
SNORA77
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
LOC728463
FAM72A
LOC730102
LOC730159
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
GM140
LOC100288079
MIR1182
MIR1537
MIR1231
MIR1278
MIR548F1
MIR664
LOC100302401
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3121
MIR3620
MIR3916
PROX1-AS1
LOC100506023
LOC100506046
KDM5B-AS1
LOC100506795
LOC100506810
LOC100527964
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4424
MIR4677
MIR4735
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.31.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5C
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
SEL1L
SRSF5
SLC8A3
SLC10A1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
MLH3
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
ATP6V1D
EVL
C14orf129
CINP
ASB2
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
GALNTL1
PLEKHH1
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
AMN
SLIRP
DNAL1
RPS6KL1
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
COX8C
ASPG
RAB15
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307

Arm-level results

Table 3. Get Full Table Arm-level significance table - 27 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.26 | 1.65 | 0.182 | 0.10 | -2.67 | 1
1q | 1955 | 0.37 | 3.98 | 0.000344 | 0.13 | -1.94 | 1
2p | 924 | 0.33 | 0.734 | 0.618 | 0.21 | -2 | 1
2q | 1556 | 0.19 | -1.34 | 1 | 0.27 | 0.504 | 0.627
3p | 1062 | 0.45 | 3.64 | 0.000906 | 0.29 | 0.0507 | 0.872
3q | 1139 | 0.50 | 5.35 | 5.97e-07 | 0.18 | -2.04 | 1
4p | 489 | 0.11 | -4.4 | 1 | 0.40 | 1.7 | 0.138
4q | 1049 | 0.04 | -5.12 | 1 | 0.34 | 1.37 | 0.244
5p | 270 | 0.41 | 1.14 | 0.391 | 0.41 | 1.14 | 0.309
5q | 1427 | 0.17 | -1.7 | 1 | 0.49 | 5.86 | 9.47e-08
6p | 1173 | 0.14 | -3.06 | 1 | 0.30 | 0.443 | 0.627
6q | 839 | 0.11 | -3.86 | 1 | 0.38 | 1.9 | 0.0964
7p | 641 | 0.42 | 2.48 | 0.0262 | 0.06 | -4.96 | 1
7q | 1277 | 0.40 | 3.17 | 0.00381 | 0.11 | -3.43 | 1
8p | 580 | 0.27 | -0.979 | 1 | 0.56 | 5.38 | 7.56e-07
8q | 859 | 0.43 | 2.95 | 0.00711 | 0.19 | -2.27 | 1
9p | 422 | 0.29 | -0.983 | 1 | 0.51 | 3.92 | 0.000354
9q | 1113 | 0.24 | -0.937 | 1 | 0.44 | 3.79 | 0.000508
10p | 409 | 0.31 | -0.697 | 1 | 0.33 | -0.276 | 0.974
10q | 1268 | 0.10 | -3.49 | 1 | 0.39 | 2.95 | 0.00795
11p | 862 | 0.12 | -3.52 | 1 | 0.47 | 4.01 | 0.000306
11q | 1515 | 0.14 | -2.45 | 1 | 0.35 | 2.54 | 0.0245
12p | 575 | 0.34 | 0.286 | 0.912 | 0.15 | -3.67 | 1
12q | 1447 | 0.28 | 0.639 | 0.654 | 0.15 | -2.51 | 1
13q | 654 | 0.36 | 0.911 | 0.518 | 0.31 | -0.235 | 0.974
14q | 1341 | 0.23 | -0.763 | 1 | 0.32 | 1.32 | 0.248
15q | 1355 | 0.14 | -2.74 | 1 | 0.34 | 1.98 | 0.0865
16p | 872 | 0.22 | -1.87 | 1 | 0.30 | -0.0539 | 0.907
16q | 702 | 0.25 | -1.49 | 1 | 0.25 | -1.49 | 1
17p | 683 | 0.25 | -1.28 | 1 | 0.51 | 4.4 | 7.05e-05
17q | 1592 | 0.37 | 3.19 | 0.00381 | 0.19 | -1.32 | 1
18p | 143 | 0.34 | -0.475 | 1 | 0.41 | 1.12 | 0.309
18q | 446 | 0.19 | -2.7 | 1 | 0.47 | 3.2 | 0.0039
19p | 995 | 0.22 | -1.56 | 1 | 0.32 | 0.585 | 0.62
19q | 1709 | 0.39 | 3.82 | 0.000538 | 0.21 | -0.581 | 1
20p | 355 | 0.61 | 6.3 | 2.92e-09 | 0.19 | -2.55 | 1
20q | 753 | 0.62 | 7.51 | 1.18e-12 | 0.18 | -2.23 | 1
21q | 509 | 0.40 | 1.53 | 0.209 | 0.19 | -2.76 | 1
22q | 921 | 0.29 | -0.123 | 1 | 0.40 | 2.24 | 0.0499
Xq | 1312 | 0.17 | -2.27 | 1 | 0.29 | 0.482 | 0.627

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BLCA-TP/2327633/2.GDAC_MergeDataFiles.Finished/BLCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 135 Input Tumor Samples.

Tumor Sample Names
TCGA-BL-A0C8-01A-11D-A10T-01
TCGA-BL-A13I-01A-11D-A13V-01
TCGA-BL-A13J-01A-11D-A10T-01
TCGA-BL-A3JM-01A-12D-A219-01
TCGA-BT-A0S7-01A-11D-A10T-01
TCGA-BT-A0YX-01A-11D-A10T-01
TCGA-BT-A20J-01A-11D-A14V-01
TCGA-BT-A20N-01A-11D-A14V-01
TCGA-BT-A20O-01A-21D-A14V-01
TCGA-BT-A20P-01A-11D-A14V-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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