SNP6 Copy number analysis (GISTIC2) - Bladder Urothelial Carcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Bladder Urothelial Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1833QQT

Overview

Introduction

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

Summary

There were 264 tumor samples used in this analysis: 26 significant arm-level results, 32 significant focal amplifications, and 38 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 - 32 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	1.3958e-59	1.3958e-59	chr6:21084998-21455824	1
11q13.3	1.1657e-33	8.3024e-32	chr11:69464719-69503929	2
1q23.3	2.5903e-34	6.9615e-31	chr1:161001146-161109018	8
8q22.3	2.4991e-28	2.4991e-28	chr8:101242758-102458148	10
3p25.2	6.5382e-26	6.5382e-26	chr3:12481505-12491536	0 [PPARG]
12q15	9.5891e-15	9.5891e-15	chr12:69183279-69570351	2
8p11.23	1.4046e-13	1.4053e-11	chr8:37449639-37645465	4
10p14	3.8972e-11	3.8972e-11	chr10:7924008-8345608	3
19q12	3.142e-11	6.3191e-10	chr19:30092578-30537755	5
20q11.21	9.7452e-08	9.7452e-08	chr20:30109883-30332464	8
17q12	1.8371e-08	1.1184e-06	chr17:37820993-37905815	7
7p11.2	3.4161e-09	1.1738e-06	chr7:54752424-55428978	2
5p15.33	2.2688e-05	2.2688e-05	chr5:1-2801756	36
1p34.2	6.4953e-05	6.4953e-05	chr1:39531274-40980627	25
17q11.2	4.0356e-05	0.0020991	chr17:27201061-27933231	15
13q22.1	0.0022662	0.0022662	chr13:73652305-74157164	0 [KLF5]
4p16.3	0.0024633	0.0024633	chr4:1738268-1817427	3
7p21.1	2.6788e-05	0.002471	chr7:16811809-18477009	8
6q21	0.0036507	0.0036507	chr6:107215849-107457456	4
4q13.3	0.0036507	0.0039932	chr4:73675242-74478903	6
1q21.3	5.1607e-13	0.011057	chr1:120523956-152982053	185
11q22.2	1.3729e-05	0.018584	chr11:101984719-102676263	11
22q11.23	0.020614	0.020614	chr22:25145754-26820434	14
3q26.32	0.023416	0.023416	chr3:160803527-198022430	238
16p13.13	0.004092	0.031515	chr16:10732356-12245460	22
16p11.2	0.017188	0.065726	chr16:28605319-30320319	61
19q13.43	0.020066	0.12193	chr19:51278590-59128983	348
8p11.21	0.00037617	0.17805	chr8:41491141-42133127	8
9p24.1	0.18747	0.18747	chr9:1-10506027	48
16q22.1	0.18747	0.18747	chr16:65817387-78391279	180
14q11.2	0.20107	0.20107	chr14:23432392-24115472	29
4q31.21	0.22082	0.24149	chr4:144726169-150474715	24

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: Cancer Gene Census[7].

Genes
CDKAL1

Genes in Wide Peak

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

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

Genes
CCND1
ORAOV1

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: Cancer Gene Census[7].

Genes
NIT1
PFDN2
USF1
DEDD
PVRL4
KLHDC9
ARHGAP30
TSTD1

Genes in Wide Peak

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

Table S4. Genes in bold are cancer genes as defined by The Sanger Institute: 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 12q15.

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

Genes
MDM2
CPM

Genes in Wide Peak

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

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

Genes
ERLIN2
PROSC
ZNF703
LOC728024

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p14.

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

Genes
GATA3
TAF3
FLJ45983

Genes in Wide Peak

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

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

Genes
CCNE1
URI1
POP4
PLEKHF1
C19orf12

Genes in Wide Peak

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

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

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

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: 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 7p11.2.

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

Genes
EGFR
SEC61G

Genes in Wide Peak

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

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

Genes
hsa-mir-4277
NDUFS6
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
IRX4
CEP72
AHRR
MRPL36
BRD9
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
C5orf38
IRX2
SLC6A19
SLC6A18
LRRC14B
SDHAP3
LOC728613
MIR4277
LOC100506688
MIR4457
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
MYCL1
BMP8B
COL9A2
PPT1
RLF
PABPC4
ZMPSTE24
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
OXCT2
SMAP2
DEM1
ZNF643
NT5C1A
MFSD2A
TMCO2
ZNF642
BMP8A
KIAA0754
SNORA55
PPIEL

Genes in Wide Peak

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

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

Genes
CRYBA1
FLOT2
TIAF1
GIT1
PIPOX
NUFIP2
TAOK1
PHF12
TP53I13
ABHD15
SEZ6
ANKRD13B
DHRS13
MYO18A
MIR4523

Genes in Wide Peak

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

Table S15. Genes in bold are cancer genes as defined by The Sanger Institute: 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 7p21.1.

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

Genes
hsa-mir-1302-6
AHR
HDAC9
AGR2
SNX13
TSPAN13
AGR3
PRPS1L1

Genes in Wide Peak

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

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

Genes
hsa-mir-587
C6orf203
BEND3
LOC100422737

Genes in Wide Peak

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

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

Genes
AFM
AFP
ALB
ANKRD17
RASSF6
COX18

Genes in Wide Peak

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

Table S19. Genes in bold are cancer genes as defined by The Sanger Institute: 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
MCL1
SMCP
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A10
S100A11
SPRR1A
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
FAM91A2
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
HIST2H3C
LIX1L
C1orf51
HFE2
ANKRD35
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
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
PPIAL4G
PPIAL4D
LOC645166
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 11q22.2.

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

Genes
BIRC3
BIRC2
MMP1
MMP7
MMP8
MMP10
MMP20
YAP1
MMP27
TMEM123
LOC100288077

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q11.23.

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

Genes
ADRBK2
CRYBB2
CRYBB2P1
CRYBB3
TOP1P2
SEZ6L
MYO18B
KIAA1671
IGLL3P
LRP5L
SGSM1
TMEM211
PIWIL3
LOC100128531

Genes in Wide Peak

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

Table S22. Genes in bold are cancer genes as defined by The Sanger Institute: 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
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
KNG1
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
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
NMD3
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
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
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
CCDC39
LOC339926
LPP-AS2
LRRIQ4
SAMD7
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
TMEM212
FLJ46066
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
LOC646168
C3orf65
LOC647107
GMNC
LOC647323
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
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 16p13.13.

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

Genes
TNFRSF17
CIITA
SOCS1
hsa-mir-548h-2
GSPT1
NUBP1
PRM1
PRM2
TNP2
SNN
LITAF
CLEC16A
RSL1D1
DEXI
ZC3H7A
TXNDC11
PRM3
SNX29
RMI2
TEKT5
BCAR4
FAM18A

Genes in Wide Peak

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

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

Genes
ALDOA
ATP2A1
CD19
KIF22
MAZ
PPP4C
MAPK3
SPN
SULT1A2
SULT1A1
SULT1A3
TBX6
TUFM
DOC2A
HIRIP3
EIF3C
TAOK2
MVP
CDIPT
CORO1A
ATXN2L
QPRT
SH2B1
SEZ6L2
LAT
SLX1B
GDPD3
C16orf53
RABEP2
SLC7A5P1
YPEL3
FAM57B
SPNS1
NFATC2IP
PRRT2
TMEM219
C16orf92
KCTD13
ASPHD1
C16orf54
INO80E
LOC388242
SNX29P2
LOC440354
LOC440356
SULT1A4
SLX1A
BOLA2
LOC595101
LOC606724
LOC613037
LOC613038
RRN3P2
ZG16
BOLA2B
EIF3CL
LOC100289092
SLX1A-SULT1A3
SLX1B-SULT1A4
MIR4721
MIR4517

Genes in Wide Peak

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

Table S25. Genes in bold are cancer genes as defined by The Sanger Institute: 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
HAS1
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LIM2
NDUFA3
NKG7
CNOT3
PEG3
PRKCG
KLK7
KLK6
KLK10
PTPRH
RPL28
RPS5
RPS9
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
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
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

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
IKBKB
PLAT
KAT6A
AP3M2
NKX6-3
MIR486

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.1.

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

Genes
JAK2
CD274
hsa-mir-101-2
hsa-mir-1302-9
DMRT1
FOXD4
MLANA
GLDC
INSL4
PTPRD
RFX3
RLN1
RLN2
SLC1A1
SMARCA2
VLDLR
KIAA0020
RCL1
DMRT2
INSL6
KDM4C
KANK1
RANBP6
AK3
C9orf68
CDC37L1
C9orf46
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
UHRF2
C9orf66
KIAA2026
KCNV2
GLIS3
FLJ35024
PPAPDC2
MIR101-2
FAM138C
WASH1
MIR4665

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q22.1.

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

Genes
CBFB
CDH1
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
AARS
AP1G1
AGRP
ZFHX3
CA7
CALB2
CDH3
CDH5
CDH16
CTRB1
CTRL
DHODH
NQO1
DYNC1LI2
E2F4
GLG1
HAS3
HP
HPR
HSD11B2
HSF4
KARS
LCAT
CHST6
NFATC3
PSKH1
PSMB10
PSMD7
RRAD
ST3GAL2
SLC9A5
SLC12A4
SNTB2
TAT
TERF2
TK2
ZNF19
ZNF23
TRADD
CES2
NAE1
NOL3
SLC7A6
ATP6V0D1
BCAR1
DHX38
IST1
CLEC3A
CHST4
NUTF2
CFDP1
CTCF
NFAT5
WWP2
DDX19B
GABARAPL2
MON1B
PHLPP2
SF3B3
CES3
ADAT1
CHST5
EDC4
PLA2G15
COG4
PLEKHG4
LRRC29
VPS4A
NOB1
TMEM208
FHOD1
ZDHHC1
PARD6A
CKLF
NIP7
FAM96B
TPPP3
WWOX
TERF2IP
PRMT7
HYDIN
DUS2L
CHTF8
TXNL4B
PDPR
RFWD3
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
VAC14
FTSJD1
DDX28
TSNAXIP1
THAP11
PDP2
RANBP10
VAT1L
PDF
DPEP2
DPEP3
ACD
FA2H
FAM65A
TMEM231
TMCO7
WDR59
ELMO3
ESRP2
CENPT
C16orf70
CYB5B
GFOD2
PMFBP1
C16orf48
SLC7A6OS
COG8
B3GNT9
CIRH1A
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CMTM1
EXOSC6
NRN1L
CMTM3
TMEM170A
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
IL34
TMED6
ZFP1
ADAMTS18
LDHD
FUK
MLKL
CCDC79
CES4A
EXOC3L1
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
ATXN1L
PKD1L3
CLEC18A
C16orf86
MIR140
CTRB2
MIR328
CLEC18B
KIAA0895L
SNORD71
SNORD111
LOC729513
SNORD111B
LOC100130894
SYCE1L
MIR1538
MIR1972-1
SNORA70D
MIR1972-2
LOC100505865
LOC100506083
LOC100506172
CKLF-CMTM1
MIR4719

Genes in Wide Peak

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

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

Genes
hsa-mir-208b
BCL2L2
CEBPE
MYH6
MYH7
PSMB5
PABPN1
AP1G2
DHRS2
EFS
ACIN1
SLC7A8
NGDN
SLC22A17
C14orf119
HOMEZ
C14orf93
CDH24
IL25
THTPA
JPH4
AJUBA
ZFHX2
PPP1R3E
CMTM5
PSMB11
MIR208A
MIR208B
BCL2L2-PABPN1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q31.21.

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

Genes
hsa-mir-548g
EDNRA
GYPA
GYPB
GYPE
SMAD1
NR3C2
POU4F2
ABCE1
ANAPC10
LSM6
OTUD4
TMEM184C
HHIP
ARHGAP10
TTC29
SLC10A7
PRMT10
ZNF827
MMAA
LOC646576
C4orf51
LOC100505545
MIR4799

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

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
9p21.3	2.4341e-137	1.1064e-132	chr9:21865498-21997722	2
13q14.2	2.1615e-23	2.1615e-23	chr13:48833767-49281290	3
2q37.1	2.9075e-25	5.9482e-23	chr2:231683850-238537581	80
5q11.2	5.4588e-23	1.0342e-22	chr5:58260298-59787985	3
4q22.1	7.256e-13	1.7631e-11	chr4:90844993-93240505	1
16p13.3	2.1096e-11	2.1033e-11	chr16:3586231-4013466	5
2q22.1	9.9658e-12	4.4738e-09	chr2:139655617-143637838	1
4q34.2	1.6754e-09	5.7633e-08	chr4:175749016-178651942	9
19p13.3	4.9798e-07	5.0444e-07	chr19:1-4230222	153
16q23.1	1.9631e-06	1.8959e-06	chr16:78129058-79627770	1
10q23.31	7.8122e-06	7.5849e-06	chr10:89617158-90429035	4
22q13.31	2.6872e-05	2.6878e-05	chr22:47571204-48018269	1
15q13.1	2.7502e-05	2.7446e-05	chr15:25197754-32934882	130
6p25.3	2.984e-05	3.0791e-05	chr6:1-2250882	9
17p12	3.3704e-05	3.4132e-05	chr17:14111288-16121163	20
11q23.3	0.00026907	0.00025594	chr11:102700695-135006516	296
8p23.3	4.2007e-06	0.00027029	chr8:1-13947514	124
11p15.5	0.00036602	0.00036602	chr11:516521-748945	16
1p36.11	0.0053018	0.0053018	chr1:7829287-32195069	372
Xp11.3	0.0056725	0.0058471	chrX:44702452-45021933	2
14q24.1	0.0019752	0.0079456	chr14:68275375-69288431	2
3p13	9.4034e-07	0.0087644	chr3:57110241-84688247	86
18q21.2	0.018387	0.018189	chr18:35235531-78077248	170
Xq21.33	0.009522	0.030279	chrX:94288568-98718611	4
9q33.2	0.042572	0.04237	chr9:125560281-125680546	5
9p23	8.1342e-08	0.048469	chr9:7799607-12693402	1
6q21	0.00047014	0.053591	chr6:53527000-124125707	262
8p12	0.0011762	0.063776	chr8:11644822-36642339	169
6q27	0.0019548	0.09619	chr6:142957980-171115067	164
3p21.31	9.2901e-07	0.10442	chr3:40493219-78650559	354
7q36.3	0.11348	0.11734	chr7:120389649-159138663	335
8p11.21	0.021915	0.14471	chr8:42883855-47753079	4
10p12.1	0.17191	0.1708	chr10:14478619-38300099	126
1q32.1	0.18914	0.1935	chr1:181775464-249250621	529
14q12	0.064081	0.1935	chr14:1-31030869	166
5q35.1	0.0082178	0.2247	chr5:138721165-180915260	421
Xq23	0.11322	0.24906	chrX:108973842-110489519	9
3p14.2	1.055e-07	0.375	chr3:33910270-150810544	792

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

Table S32. Genes in bold are cancer genes as defined by The Sanger Institute: 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 2q37.1.

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

Genes
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
ALPI
ALPP
ALPPL2
CHRND
CHRNG
COL6A3
GBX2
HTR2B
INPP5D
KCNJ13
NCL
NEU2
NPPC
PDE6D
PSMD1
PTMA
SNORD20
SAG
SPP2
DGKD
GPR55
ECEL1
EIF4E2
ARL4C
NMUR1
COPS8
SH3BP4
NGEF
SNORD82
GIGYF2
PRLH
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
CXCR7
RAB17
COPS7B
TRPM8
MLPH
IQCA1
ARMC9
EFHD1
ITM2C
B3GNT7
AGAP1
DIS3L2
SPATA3
LINC00471
LOC151484
MSL3P1
C2orf57
TIGD1
C2orf72
ECEL1P2
LOC348761
C2orf82
ASB18
DNAJB3
PRSS56
SNORA75
SCARNA6
SCARNA5
LOC100286922
MIR1471
MIR1244-1
MIR1244-3
MIR1244-2
MIR4777

Genes in Wide Peak

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

Table S34. Genes in bold are cancer genes as defined by The Sanger Institute: 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 4q22.1.

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
CREBBP
DNASE1
TRAP1
SLX4
NLRC3

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
AGA
GPM6A
VEGFC
ADAM29
NEIL3
SPCS3
WDR17
SPATA4
ASB5

Genes in Wide Peak

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

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute: 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
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
BTBD2
RNF126
NCLN
SPPL2B
WDR18
REXO1
ZNF77
C19orf29
CELF5
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
CREB3L3
LMNB2
RAX2
MUM1
ATCAY
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
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 16q23.1.

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

Genes
WWOX

Genes in Wide Peak

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

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

Genes
PTEN
RNLS
LIPJ
KLLN

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.1.

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

Genes
hsa-mir-211
APBA2
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
OCA2
SNRPN
TJP1
UBE3A
PAR5
HERC2
SNURF
ARHGAP11A
FAN1
FAM189A1
DKFZP434L187
KLF13
MTMR10
NDNL2
ATP10A
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
PAR1
OTUD7A
LOC283710
GOLGA8G
SNORD108
SNORD109A
SNORD109B
SNORD115-1
SNORD64
PAR4
PAR-SN
MIR211
HERC2P9
WHAMMP2
LOC503519
LOC646278
LOC653075
SNORD116-19
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
GOLGA8F
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4509-3
MIR4715

Genes in Wide Peak

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

Table S44. Genes in bold are cancer genes as defined by The Sanger Institute: 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 17p12.

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

Genes
ADORA2B
MEIS3P1
PMP22
NCOR1
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 11q23.3.

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

Genes
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP3
MMP12
MMP13
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100128239
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
ANGPT2
BLK
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
CLN8
FDFT1
GATA4
MSRA
TNKS
MYOM2
DLGAP2
MFHAS1
ARHGEF10
KBTBD11
DLC1
SPAG11B
FBXO25
PINX1
AGPAT5
DEFB103B
KIAA1456
CSMD1
MTMR9
MCPH1
PPP1R3B
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
FAM86B1
ERI1
LONRF1
RP1L1
CLDN23
DEFB104A
LOC157273
SGK223
LOC157627
C8orf42
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
PRSS55
C8orf74
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
FLJ10661
XKR6
LOC286083
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC392196
MIR124-1
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
DEFB107B
DEFB104B
DEFB106B
DEFB105B
DEFB135
DEFB136
DEFB134
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA1B
FAM90A20
FAM90A19
ZNF705D
FAM66B
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR3926-2
MIR3926-1
LOC100506990
MIR4659A
MIR4660
MIR4659B
LOC100652791

Genes in Wide Peak

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

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

Genes
HRAS
hsa-mir-210
DRD4
IRF7
SCT
RASSF7
DEAF1
CDHR5
PHRF1
EPS8L2
LRRC56
LOC143666
C11orf35
TMEM80
MIR210
MIR210HG

Genes in Wide Peak

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

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

Genes
PAX7
SDHB
ARID1A
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
E2F2
ECE1
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GALE
SFN
GPR3
HCRTR1
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
FCN3
AKR7A2
ALDH4A1
EIF4G3
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
SDC3
CROCC
PUM1
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
PADI4
TMEM50A
STX12
CLIC4
SYF2
C1orf144
LDLRAP1
FBXO2
FBXO6
PLA2G2D
RNU11
HSPB7
AHDC1
SMPDL3B
PRO0611
LINC00339
UBIAD1
PADI1
PLA2G2E
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
RCC2
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
PTCHD2
KIF17
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
CEP85
NMNAT1
PINK1
PRAMEF1
PRAMEF2
PHACTR4
C1orf135
EFHD2
RSG1
NKAIN1
MUL1
LIN28A
AGMAT
FAM110D
DHDDS
GPR157
SPSB1
ZNF436
TAS1R2
ACTL8
SH3BGRL3
SESN2
TMEM222
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA2013
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
RAB42
FAM46B
RBP7
C1orf172
LRRC38
AADACL3
IFFO2
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf127
C1orf213
LOC149086
PDIK1L
C1orf64
SLC2A7
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf126
AKR7L
TMCO4
ZNF683
LOC284551
LOC284632
SLC25A34
ESPNP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
APITD1
CATSPER4
TMEM82
TRNP1
CD164L2
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
MIR34A
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
PRAMEF7
PEF1
LOC644961
C1orf200
PRAMEF19
PRAMEF20
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
LOC729059
PRAMEF14
FLJ37453
LOC100129196
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4632
MIR378F
RCAN3AS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.3.

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.1.

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

Genes
ZFP36L1
RAD51B

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
ATP5A1
CDH7
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TCF4
ZNF236
SLC14A2
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
EPG5
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
KATNAL2
MRO
HDHD2
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
RNF165
C18orf32
KC6
LOC643542
C18orf63
LOC647946
SCARNA17
SNORA37
TCEB3CL
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR1539
MIR4319
MIR4318
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4529
MIR3591
MIR4743
MIR4744

Genes in Wide Peak

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

Table S54. Genes in bold are cancer genes as defined by The Sanger Institute: 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 9q33.2.

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

Genes
PDCL
ZBTB6
RC3H2
OR1K1
SNORD90

Genes in Wide Peak

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

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
AIM1
AMD1
BAI3
BCKDHB
BMP5
DST
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
FABP7
FOXO3
FRK
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HCRTR2
HDAC2
HSF2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
MAN1A1
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
PRIM2
PKIB
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
PTP4A1
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
BAG2
ZBTB24
SNAP91
FIG4
CASP8AP2
TRDN
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
SMPDL3A
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
PHF3
ORC3
BRD7P3
MTO1
ASF1A
PNISR
IBTK
ZNF451
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
TINAG
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
LGSN
RAB23
COQ3
HMGCLL1
PHIP
SOBP
AKIRIN2
LRRC1
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
SERINC1
HACE1
FAM135A
BEND3
KIAA1586
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
FAM184A
MANEA
LINC00472
KHDC1
GPR63
COL21A1
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
MLIP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
MB21D1
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
CLVS2
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
KHDRBS2
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
DPPA5
RSPH4A
EYS
GUSBP4
GJB7
SNHG5
C6orf147
LINC00222
CEP85L
GFRAL
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p12.

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute: 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
NRG1
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
DUSP26
HMBOX1
RNF122
NUDT18
DOCK5
FLJ14107
TTI2
REEP4
STMN4
MAK16
FUT10
FAM86B1
LONRF1
CHMP7
VPS37A
NKX2-6
SGCZ
UNC5D
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 6q27.

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
ACAT2
CCR6
ESR1
FUCA2
GPR31
GRM1
HIVEP2
IGF2R
KIF25
LPA
MAS1
MAP3K4
OPRM1
PARK2
PCMT1
PDCD2
PLAGL1
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
PEX3
RNASET2
STX11
SYNJ2
LATS1
QKI
WTAP
AKAP12
PHACTR2
UST
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
TFB1M
AIG1
SNX9
BRP44L
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
HYMAI
PLEKHG1
ARID1B
TMEM181
ZBTB2
SMOC2
ULBP3
C6orf211
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
RSPH3
TTLL2
FBXO30
FAM120B
FNDC1
LRP11
LTV1
SERAC1
PPIL4
LINC00473
SYTL3
SFT2D1
C6orf72
TAGAP
ADAT2
STXBP5
PACRG
RAET1E
ZC2HC1B
CNKSR3
RAET1L
PNLDC1
LOC154449
DACT2
C6orf118
OSTCP1
WDR27
SHPRH
LOC285740
LOC285796
PRR18
ZC3H12D
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
LOC441177
RAET1K
MLLT4-AS1
SNORA20
SNORA29
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LOC100289495
MIR1913
MIR3918
MIR3939
MIR3692
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4644
LOC100652739

Genes in Wide Peak

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

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute: 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
CDC25A
CISH
CCR1
CCR3
CCR5
CCBP2
COL7A1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
ROBO2
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
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
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
ULK4
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
SELK
PROK2
RNF123
KIF9
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
PRICKLE2
C3orf67
KCTD6
KLHDC8B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
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
TMEM89
IQCF6
C3orf78
MIR425
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 7q36.3.

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

Genes
BRAF
EZH2
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CADPS2
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

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

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

Genes
FNTA
SGK196
HGSNAT
POTEA

Genes in Wide Peak

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

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute: 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
HSPA14
WAC
MYO3A
APBB1IP
ARMC4
MTPAP
OLAH
KIAA1217
PARD3
PRTFDC1
ZNF248
GPR158
ARHGAP21
KIAA1462
DNAJC1
DCLRE1C
SUV39H2
C10orf68
THNSL1
FAM188A
EPC1
FAM107B
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
CDNF
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 S64. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

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

Genes in Wide Peak

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

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute: 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 5q35.1.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
ADRA1B
ADRB2
ANXA6
ATOX1
BNIP1
CAMK2A
CANX
CCNG1
CD14
CDX1
CLTB
CSF1R
CSNK1A1
NKX2-5
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
F12
FABP6
FAT2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
NDST1
HTR4
IK
IL12B
KCNMB1
LCP2
LTC4S
MFAP3
MGAT1
MSX2
NDUFA2
PCDH1
PCDHGC3
PDE6A
PFDN1
POU4F3
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SLC6A7
SLC34A1
SLIT3
SNCB
SPARC
SPINK1
STK10
TAF7
ZNF354A
TCOF1
TTC1
UBE2D2
STC2
EIF4EBP3
PCDHGB4
ADAM19
FGF18
HDAC3
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
ADAMTS2
NRG2
RNF14
CLINT1
PCDHGA8
PCDHA9
MAML1
KIAA0141
JAKMIP2
GFPT2
GNPDA1
SRA1
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
CPLX2
C5orf4
FAM114A2
TCERG1
BTNL3
LMAN2
SPINK5
SOX30
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
CCDC69
PCDHB5
TSPAN17
OR4F3
HAVCR1
CYFIP2
PRELID1
IL17B
MAT2B
MRPL22
PCDHB1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DCTN4
MZB1
PCDH12
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
KCTD16
PCDHB16
HMHB1
C5orf54
GMCL1P1
ARAP3
RMND5B
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PSD2
THOC3
C5orf32
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
SFXN1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
C5orf58
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SLC36A2
SPINK13
C5orf41
LOC153469
ZMAT2
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
LOC340037
TMEM173
ARSI
PFN3
ZNF879
IRGM
FBLL1
NIPAL4
DND1
C5orf25
FLJ38109
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
FLJ16171
MIR340
IGIP
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
MIR143HG
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
LOC100505658
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq23.

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

Genes
hsa-mir-652
PAK3
TDGF1P3
AMMECR1
RGAG1
TMEM164
CHRDL1
SNORD96B
MIR3978

Genes in Wide Peak

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

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

Genes
FOXL2
CBLB
CTNNB1
FHIT
GATA2
MITF
MLH1
MYD88
RPN1
BAP1
TFG
FOXP1
SETD2
PBRM1
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
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
hsa-mir-26a-1
hsa-mir-128-2
ACAA1
ACPP
ACVR2B
ACY1
ADCY5
ADPRH
AGTR1
ALAS1
ALCAM
AMT
APEH
ARF4
RHOA
ATP1B3
ATP6V1A
ATR
C3orf51
CACNA1D
SLC25A20
CAMP
CASR
CCK
CD80
CD86
ENTPD3
CD47
CDC25A
CISH
CCR1
CCR3
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CP
CPA3
CPB1
CPOX
CSTA
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DRD3
DUSP7
CELSR3
EPHA3
EPHB1
FLNB
GAP43
GBE1
GNAI2
GNAT1
GOLGA4
GOLGB1
GP9
XCR1
GPR15
GPR27
GPX1
GRM2
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HTR1F
HYAL1
IMPDH2
ITGA9
ITGB5
ITIH1
ITIH3
ITIH4
KPNA1
LAMB2
RPSA
LSAMP
LTF
TM4SF1
MAP4
MCM2
MOBP
CD200
MST1
MST1R
MYL3
MYLK
NCK1
NDUFB4
NKTR
CNTN3
PCCB
PDHB
PFKFB4
PFN2
PIK3CB
PLCD1
PLOD2
PLS1
PLSCR1
PLXNA1
PLXNB1
POU1F1
PPP2R3A
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
RASA2
RBP1
RBP2
RHO
SNORA62
ROBO1
ROBO2
RPL24
RPL29
RYK
ATXN7
SCN5A
SCN10A
SEMA3F
SIAH2
SLC15A2
SLCO2A1
HLTF
SMARCC1
STAC
NEK4
TCTA
TDGF1
TF
TFDP2
TGM4
TKT
TM4SF4
TMF1
CLEC3B
TNNC1
TRH
TRPC1
UBA7
UPK1B
UMPS
USP4
UQCRC1
CLRN1
VIPR1
WNT5A
ZIC1
CNBP
ZNF35
ZNF80
ZNF148
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
RAB7A
ACOX2
HYAL3
SOX14
BFSP2
CGGBP1
RUVBL1
CADPS
HYAL2
B4GALT4
SNX4
SUCLG2
HESX1
NR1I2
BSN
MBD4
H1FX
LIMD1
KALRN
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
COPB2
SLC22A14
SLC22A13
CHST2
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
VPRBP
IP6K1
TSC22D2
EPM2AIP1
PSMD6
TOMM70A
TRANK1
DLEC1
EXOG
XYLB
OXSR1
PARP3
COX17
ZNF197
RBM6
RBM5
NME6
CTDSPL
CD96
STAG1
EIF1B
TRAIP
ST3GAL6
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
POLQ
ARPP21
CCR9
ALDH1L1
USP19
PDIA5
SLC38A3
CYB561D2
TMEM115
TOPBP1
RPP14
HHLA2
FSTL1
FAM107A
WDR6
RASSF1
NISCH
MRPL3
FILIP1L
TREX1
SCN11A
TUSC2
RNF13
MGLL
TWF2
MRAS
COPG
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
MYH15
EXOSC7
TMCC1
PDZRN3
PLXND1
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
DNAJC13
U2SURP
LARS2
RYBP
C3orf27
NAT6
ANAPC13
ARMC8
ABHD14A
C3orf17
POC1A
ABI3BP
TMEM158
NDUFAF3
MYRIP
PTPN23
WWTR1
PVRL3
CHMP2B
DNAH1
HIGD1A
LRIG1
ERC2
APPL1
ZBTB20
OR5K1
OR5H1
GNL3
FAM162A
PCOLCE2
SEC22A
NPHP3
ATP2C1
ZBTB11
MORC1
SERP1
SPCS1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
PRSS50
RBM15B
GMPPB
SEC61A1
PIK3R4
PODXL2
ARHGEF3
TRAT1
VILL
IMPG2
ABHD5
COMMD2
A4GNT
C3orf18
DBR1
SS18L2
CLDN18
SHISA5
TIMMDC1
ZDHHC3
ZMYND10
PLA1A
TEX264
CCDC72
ZNF589
HEMK1
AMOTL2
IP6K2
SFMBT1
NCKIPSD
PHF7
CCRL1
RAB6B
SELT
FBXO40
IL20RB
TLR9
SEMA5B
XRN1
WDR5B
LZTFL1
PARP14
P4HTM
SLC6A20
IL17RD
GRAMD1C
ROPN1
SIDT1
C3orf75
SNRK
QRICH1
PXK
RG9MTD1
SLC41A3
SLC25A38
ULK4
SLC35A5
TMEM45A
FEZF2
IFT57
EBLN2
ANO10
DALRD3
SHQ1
MSL2
FAIM
SLC25A36
DPPA4
TMEM39A
ZNF654
ABHD10
CHDH
IL17RB
CDV3
IFT122
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
EAF2
ZNF167
LMOD3
CLDND1
MUC13
SEMA3G
C3orf37
MRPS22
NIT2
POGLUT1
BBX
KIF15
ADAMTS9
PLSCR2
PCBP4
PLSCR4
PCNP
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
ISY1
HHATL
HEG1
KIAA1257
ARHGAP31
KIAA1407
WDR48
KIAA1524
SRPRB
SELK
BPESC1
PROK2
EEFSEC
RNF123
NSUN3
CLSTN2
POPDC2
KIF9
NFKBIZ
ATG3
CSRNP1
GORASP1
CCDC14
CDCP1
CCDC71
NT5DC2
SLC26A6
TMEM108
CAMKV
OR5H6
OR5H2
ZXDC
ZBED2
LRRC2
FYCO1
CEP97
HSPBAP1
C3orf52
QTRTD1
CCDC51
CCDC48
NEK11
UBA5
C3orf36
THOC7
NAA50
CEP63
CEP70
ABTB1
WDR82
TMEM22
OR5AC2
RTP3
PARP9
ESYT3
EIF2A
ID2B
ARL6
ZIC4
ATRIP
ACAD11
NICN1
CHCHD6
MON1A
C3orf26
HPS3
KBTBD8
SLC12A8
RETNLB
CCDC54
ABHD14B
MINA
GPR128
C3orf39
DIRC2
DCLK3
C3orf15
PHLDB2
UCN2
LOC90246
C3orf25
ZNF502
BOC
FAM55C
RFT1
SPSB4
ACPL2
ZBTB47
ACTR8
TXNRD3
OSBPL11
SLC25A26
ZNF501
LRRC58
TM4SF18
CLRN1-AS1
GPR62
CPNE4
CCDC58
FAM3D
ZPLD1
LYZL4
KBTBD5
CD200R1
DCBLD2
TPRA1
TMEM42
UROC1
FAM194A
NUDT16
COL6A6
GRK7
FAM172BP
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
RPL32P3
H1FOO
PISRT1
ASB14
DTX3L
FAM19A4
LOC151658
DPPA2
CCDC80
BTLA
CCDC12
PPP4R2
ROPN1B
C3orf22
SPICE1
NUDT16P1
CCDC13
LOC152225
IGSF11
C3orf30
PARP15
DNAJB8
GPR156
XIRP1
CHST13
PRICKLE2
KBTBD12
DZIP1L
TTC21A
ALG1L
C3orf67
KCTD6
ARL13B
DHFRL1
KLHDC8B
GABRR3
PTPLB
LOC201617
DNAH12
PDE12
FAM116A
TIGIT
C3orf58
KIAA2018
ZBTB38
CADM2
ZNF620
ZDHHC23
LOC255025
NUP210P1
COL6A5
GK5
PLCXD2
GCET2
ALS2CL
TMIE
LSAMP-AS3
SLC9A9
C3orf64
LOC285205
EPHA6
DNAJB8-AS1
FBXW12
C3orf38
ENTPD3-AS1
ZNF619
ZNF621
RABL3
CCDC66
SLC9A10
C3orf23
ZNF660
FLJ39534
LOC285359
LOC285401
ILDR1
TRIM42
EIF4E3
RAB43
CCDC36
KY
LOC339874
C3orf35
PRSS42
H1FX-AS1
LOC344595
TMPRSS7
CD200R1L
PAQR9
NME9
LNP1
CCDC37
NPHP3-AS1
NMNAT3
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
PRR23B
PRR23C
PLSCR5
ANKUB1
IQCF3
LOC401074
FLJ22763
FLJ25363
C3orf72
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR198
MIR26A1
FAM19A1
STX19
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
ARGFX
SNORA6
TMEM30C
LOC644714
ALG1L2
TXNRD3NB
COL6A4P2
SPINK8
C3orf71
LOC646498
LOC646903
FLJ20518
LOC653712
LINC00488
SNORA7B
SNORA58
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR548A3
MIR564
MIR567
MIR568
GXYLT2
FAM198A
CCR2
FAM86HP
PRR23A
ESRG
LOC100009676
SNORD19B
LOC100125556
WWTR1-AS1
C3orf74
LOC100128640
NRADDP
LOC100129550
ZBTB20-AS1
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
LOC100289361
MIR1284
MIR1280
MIR548I1
MIR1324
MIR1226
LOC100302640
MIR711
MIR548G
MIR3136
MIR4272
MIR4271
MIR4273
MIR3921
MIR3938
KRBOX1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
IQCF4
LOC100506994
LOC100507032
LOC100507062
ADAMTS9-AS2
LOC100507389
ABHD14A-ACY1
TMEM110-MUSTN1
NPHP3-ACAD11
ISY1-RAB43
MIR4793
MIR4787
MIR4795
MIR4796
MIR4788
MIR4444-1
MIR4443
MIR4446
LOC100652759
LUST

Arm-level results

Table 3. Get Full Table Arm-level significance table - 26 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	2121	0.23	0.594	0.84	0.12	-3.1	1
1q	1955	0.34	4.3	4.84e-05	0.15	-2.29	1
2p	924	0.29	-0.112	1	0.18	-3.43	1
2q	1556	0.16	-2.84	1	0.27	0.656	0.488
3p	1062	0.38	3.09	0.00398	0.21	-2.11	1
3q	1139	0.46	6.43	6.34e-10	0.11	-4.51	1
4p	489	0.17	-4.4	1	0.38	1.98	0.0632
4q	1049	0.09	-5.5	1	0.38	3.31	0.00157
5p	270	0.37	0.848	0.66	0.38	1.14	0.297
5q	1427	0.17	-2.49	1	0.49	8.01	1.11e-14
6p	1173	0.20	-2.41	1	0.30	0.885	0.376
6q	839	0.12	-4.91	1	0.41	3.93	0.000208
7p	641	0.43	4	0.000156	0.10	-5.86	1
7q	1277	0.40	4.54	1.9e-05	0.12	-4.34	1
8p	580	0.30	-0.429	1	0.62	9.73	0
8q	859	0.50	6.58	3.14e-10	0.26	-1.1	1
9p	422	0.24	-2.2	1	0.52	6.21	2.63e-09
9q	1113	0.22	-1.81	1	0.46	6.11	3.96e-09
10p	409	0.29	-1.14	1	0.31	-0.529	1
10q	1268	0.11	-4.73	1	0.37	3.6	0.000577
11p	862	0.14	-4.29	1	0.46	5.59	7.63e-08
11q	1515	0.19	-1.83	1	0.36	3.83	0.000286
12p	575	0.31	-0.251	1	0.16	-4.62	1
12q	1447	0.24	-0.475	1	0.16	-3.09	1
13q	654	0.33	0.542	0.84	0.28	-1.04	1
14q	1341	0.23	-0.985	1	0.34	2.57	0.0144
15q	1355	0.14	-3.83	1	0.37	3.63	0.000566
16p	872	0.19	-3.23	1	0.32	0.931	0.37
16q	702	0.24	-2	1	0.31	-0.0775	0.923
17p	683	0.20	-2.71	1	0.52	6.96	2.26e-11
17q	1592	0.36	3.89	0.000226	0.19	-1.72	1
18p	143	0.35	0.181	1	0.36	0.474	0.578
18q	446	0.21	-3.08	1	0.42	3.08	0.00318
19p	995	0.26	-0.96	1	0.34	1.67	0.119
19q	1709	0.38	4.88	4.16e-06	0.27	0.947	0.37
20p	355	0.54	6.91	4.84e-11	0.18	-3.75	1
20q	753	0.57	9.05	0	0.11	-4.55	1
21q	509	0.36	1.2	0.415	0.24	-2.43	1
22q	921	0.22	-1.98	1	0.45	5.12	8.76e-07
Xq	1312	0.13	-4.33	1	0.23	-1.16	1

Methods & Data

Input

Description

Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).
Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).
Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.
CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End
Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.
Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.
Confidence Level: Confidence level used to calculate the region containing a driver.
Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.
Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).
Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BLCA-TP/9824260/GDAC_MergeDataFiles_9824726/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
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 264 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-BL-A5ZZ-01A-31D-A30D-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

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:

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

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

[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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