SNP6 Copy number analysis (GISTIC2)
Bladder Urothelial Carcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1GF0RX3
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/C1GF0RX3
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 2.0.20 (Firehose task version: 126).

Summary

There were 221 tumor samples used in this analysis: 27 significant arm-level results, 28 significant focal amplifications, and 34 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 - 28 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 | 2.4295e-48 | 2.4295e-48 | chr6:21084998-21757620 | 3
1q23.3 | 4.1289e-28 | 7.1264e-25 | chr1:161001146-161109018 | 8
11q13.3 | 3.0945e-25 | 8.0695e-24 | chr11:69464719-69503929 | 2
3p25.2 | 1.5579e-20 | 1.5579e-20 | chr3:12481505-12491536 | 0 [PPARG]
8q22.3 | 4.1239e-25 | 2.0551e-20 | chr8:101180651-102532637 | 11
12q15 | 2.4363e-13 | 2.4363e-13 | chr12:69183279-69570351 | 2
19q12 | 8.3691e-11 | 8.3691e-11 | chr19:30243979-30537755 | 2
8p11.23 | 6.0755e-11 | 6.6739e-09 | chr8:37387916-37645465 | 4
10p15.1 | 3.2771e-08 | 3.2771e-08 | chr10:5411035-5844627 | 8
7p11.2 | 6.3819e-09 | 2.9314e-06 | chr7:54752424-55428978 | 2
1p34.2 | 2.7214e-05 | 2.7214e-05 | chr1:39531274-40539227 | 17
17q12 | 2.196e-06 | 6.546e-05 | chr17:37820993-37905815 | 7
20q11.21 | 0.00043619 | 0.00043619 | chr20:30064458-30332464 | 10
17q11.2 | 7.6493e-06 | 0.00051086 | chr17:27386448-27864389 | 6
5p15.33 | 0.00064506 | 0.00064506 | chr5:1-2732677 | 34
4p16.3 | 0.00070471 | 0.00070471 | chr4:1738268-1817427 | 3
16p12.1 | 0.0025663 | 0.0025663 | chr16:23877230-25068585 | 7
7p21.1 | 2.1059e-05 | 0.0029933 | chr7:16811809-20592448 | 16
6q21 | 0.0065325 | 0.0065325 | chr6:107098934-107514789 | 6
13q22.1 | 0.0069171 | 0.0069171 | chr13:73652305-74157164 | 0 [KLF5]
4q13.3 | 0.0077358 | 0.0077358 | chr4:72385235-74854651 | 16
3q26.32 | 0.009926 | 0.009926 | chr3:160803527-198022430 | 238
1q21.3 | 2.8918e-10 | 0.015816 | chr1:120523956-153385355 | 201
22q11.23 | 0.016278 | 0.016278 | chr22:25205720-26820434 | 12
11q22.2 | 5.2961e-05 | 0.055992 | chr11:101879571-102676263 | 12
8q24.21 | 1.8011e-10 | 0.15233 | chr8:127333214-129789133 | 15
8p11.21 | 0.0021002 | 0.15593 | chr8:41413019-42133127 | 9
9p24.1 | 0.21016 | 0.21016 | chr9:1-11069852 | 48

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 1q23.3.

Table S2. Genes in bold are cancer genes as defined by The Sanger Institute's 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 11q13.3.

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

Genes
CCND1
ORAOV1

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's Cancer Gene Census [7].

Genes
SPAG1
YWHAZ
RNF19A
PABPC1
ZNF706
GRHL2
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's Cancer Gene Census [7].

Genes
MDM2
CPM

Genes in Wide Peak

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

Table S6. 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 8p11.23.

Table S7. Genes in bold are cancer genes as defined by The Sanger Institute's 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 10p15.1.

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

Genes
CALML3
GDI2
NET1
CALML5
FAM208B
ASB13
TUBAL3
UCN3

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G

Genes in Wide Peak

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

Table S10. 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 17q12.

Table S11. 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 S12. 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 17q11.2.

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

Genes
CRYBA1
TIAF1
NUFIP2
TAOK1
MYO18A
MIR4523

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-4277
NDUFS6
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
IRX4
CEP72
AHRR
MRPL36
BRD9
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
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 4p16.3.

Table S15. 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 16p12.1.

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

Genes
PRKCB
RBBP6
CACNG3
TNRC6A
ARHGAP17
SLC5A11
LOC554206

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p21.1.

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

Genes
hsa-mir-3146
hsa-mir-1302-6
AHR
ITGB8
TWIST1
HDAC9
AGR2
SNX13
TSPAN13
AGR3
PRPS1L1
TWISTNB
FERD3L
TMEM196
MACC1
MIR3146

Genes in Wide Peak

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

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

Genes
hsa-mir-587
C6orf203
QRSL1
PDSS2
BEND3
LOC100422737

Genes in Wide Peak

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

Table S19. 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
SLC4A4
ADAMTS3
NPFFR2
ANKRD17
RASSF6
COX18

Genes in Wide Peak

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

Table S20. 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
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 1q21.3.

Table S21. 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
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
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 22q11.23.

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.2.

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

Genes
BIRC3
BIRC2
MMP1
MMP7
MMP8
MMP10
MMP20
YAP1
MMP27
C11orf70
TMEM123
LOC100288077

Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
POU5F1B
PVT1
FAM84B
LOC727677
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
PCAT1

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
IKBKB
PLAT
KAT6A
AP3M2
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

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

Table S26. Genes in bold are cancer genes as defined by The Sanger Institute's 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

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 - 34 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 | 9.4964e-120 | 2.2781e-115 | chr9:21865498-21997722 | 2
13q14.2 | 1.2829e-19 | 1.2829e-19 | chr13:48833767-49281290 | 3
5q11.2 | 6.6604e-19 | 6.6604e-19 | chr5:58260298-59787985 | 3
2q37.1 | 7.9925e-20 | 9.937e-18 | chr2:233180351-234554813 | 23
16p13.3 | 9.2964e-12 | 9.1753e-12 | chr16:3586231-4013466 | 5
2q22.1 | 1.1224e-13 | 1.9349e-11 | chr2:139655617-143637838 | 1
4q22.1 | 2.1541e-10 | 3.0665e-09 | chr4:90844993-93240505 | 1
19p13.3 | 6.6918e-07 | 6.9734e-07 | chr19:1-1882761 | 77
8p23.3 | 5.3911e-07 | 1.405e-06 | chr8:1-2793575 | 14
4q34.2 | 8.6003e-08 | 2.2283e-06 | chr4:175749016-178651942 | 9
16q23.1 | 5.3007e-06 | 5.5996e-06 | chr16:78129058-79627770 | 1
17p12 | 1.0861e-05 | 1.0987e-05 | chr17:14111288-15999789 | 19
11q25 | 0.00010292 | 0.0001021 | chr11:102825636-135006516 | 293
15q12 | 0.00014526 | 0.00014059 | chr15:24328498-33605300 | 137
22q13.31 | 0.00014059 | 0.00014059 | chr22:47571204-48018269 | 1
11p15.5 | 0.00023791 | 0.00023791 | chr11:1-748945 | 36
6p25.3 | 0.00025654 | 0.00026292 | chr6:1-2250882 | 9
10q23.31 | 0.0015785 | 0.0015785 | chr10:89313008-135534747 | 426
1p36.11 | 0.0019006 | 0.0019006 | chr1:15431382-32195069 | 272
6q21 | 6.9232e-05 | 0.0056379 | chr6:74537761-123104204 | 204
9p24.1 | 5.5922e-08 | 0.027861 | chr9:7799607-12693402 | 1
14q24.1 | 0.0065643 | 0.028685 | chr14:68275375-69288431 | 2
3p21.31 | 6.1687e-06 | 0.031252 | chr3:40346105-78650559 | 357
3p13 | 4.6769e-06 | 0.045085 | chr3:44372147-93777876 | 340
Xq21.33 | 0.011537 | 0.048739 | chrX:94288568-98718611 | 4
7q36.3 | 0.050456 | 0.050907 | chr7:144531050-159138663 | 110
14q12 | 0.014577 | 0.053968 | chr14:25517973-29896922 | 7
Xp11.3 | 0.053968 | 0.053968 | chrX:44702452-45607189 | 6
18q23 | 0.064519 | 0.064519 | chr18:31801431-78077248 | 191
6q27 | 0.00083069 | 0.08218 | chr6:31167499-171115067 | 896
8p11.21 | 0.023542 | 0.08218 | chr8:11384842-64090683 | 295
1q32.1 | 0.11036 | 0.11036 | chr1:181775464-249250621 | 529
3p14.2 | 2.5965e-07 | 0.12436 | chr3:40531137-93777876 | 368
Xq23 | 0.060123 | 0.12436 | chrX:108973842-110489519 | 9

Genes in Wide Peak

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

Table S27. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S28. 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 S29. 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 2q37.1.

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

Genes
ALPI
ALPP
ALPPL2
CHRND
CHRNG
INPP5D
KCNJ13
NEU2
SAG
DGKD
ECEL1
EIF4E2
NGEF
GIGYF2
ATG16L1
USP40
EFHD1
TIGD1
ECEL1P2
C2orf82
PRSS56
SCARNA6
SCARNA5

Genes in Wide Peak

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

Table S31. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S32. 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 4q22.1.

Table S33. 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 19p13.3.

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

Genes
STK11
TCF3
FSTL3
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CFD
ARID3A
EFNA2
ELANE
GAMT
GPX4
GZMM
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
MADCAM1
PPAP2C
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
DAZAP1
FGF22
THEG
MBD3
MIER2
PCSK4
C19orf24
RNF126
WDR18
REXO1
LPPR3
OR4F17
KLF16
KISS1R
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
GRIN3B
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
ODF3L2
ADAMTSL5
NDUFS7
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
FAM138F
FAM138A
LOC100288123
MIR1909
MIR3187
MIR4745

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

Table S36. Genes in bold are cancer genes as defined by The Sanger Institute's 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 16q23.1.

Table S37. 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 17p12.

Table S38. 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 11q25.

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute's 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
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 15q12.

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

Genes
hsa-mir-211
APBA2
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
OCA2
SCG5
SNRPN
TJP1
UBE3A
PAR5
HERC2
SNURF
ARHGAP11A
FAN1
FAM189A1
C15orf2
DKFZP434L187
GREM1
KLF13
MTMR10
NDNL2
ATP10A
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
PAR1
OTUD7A
LOC283710
GOLGA8G
SNORD108
SNORD109A
SNORD109B
SNORD115-1
FMN1
SNORD64
PAR4
PAR-SN
MIR211
HERC2P9
WHAMMP2
LOC503519
LOC646278
LOC653075
SNORD116-19
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
GOLGA8F
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

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

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

Genes
HRAS
hsa-mir-210
DRD4
IRF7
PSMD13
RNH1
SCT
RASSF7
IFITM1
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
BET1L
CDHR5
PHRF1
SIGIRR
RIC8A
EPS8L2
ATHL1
PTDSS2
ODF3
LRRC56
LOC143666
SCGB1C1
NLRP6
C11orf35
TMEM80
ANO9
B4GALNT4
IFITM5
MIR210
LOC653486
LOC100133161
MIR210HG

Genes in Wide Peak

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

Table S43. 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 10q23.31.

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

Genes
FGFR2
TLX1
NFKB2
PTEN
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
FAS
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HELLS
HHEX
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
KIF20B
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
ANKRD1
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
EXOC6
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ATAD1
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
OPALIN
SYCE1
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
ANKRD22
SFXN2
PDZD8
C10orf32
NUDT9P1
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
CFL1P1
TRUB1
VTI1A
LOC143188
HECTD2
FGFBP3
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
FLJ37201
LOC283038
LOC283089
O3FAR1
KCNK18
LIPM
CYP26C1
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
C10orf62
IFIT1B
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
LIPK
LIPN
LOC643529
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
DUX4L2
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
KLLN
LOC100169752
LOC100188947
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
FAS-AS1
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

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

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

Genes
PAX7
SDHB
ARID1A
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
ALPL
C1QA
C1QB
C1QC
CAPZB
CASP9
RUNX3
CDA
CDC42
CD52
RCC1
CLCNKA
CLCNKB
CNR2
COL16A1
DDOST
E2F2
ECE1
EPHA2
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
FUCA1
IFI6
GALE
SFN
GPR3
HCRTR1
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
NBL1
OPRD1
PAFAH2
PLA2G2A
PLA2G5
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC9A1
TAF12
TCEA3
TCEB3
ZBTB17
SLC30A2
LUZP1
LAPTM5
SNHG3
NR0B2
FCN3
AKR7A2
ALDH4A1
EIF4G3
MAP3K6
SNRNP40
C1orf38
SDC3
CROCC
PUM1
ZBTB40
PTPRU
CELA3A
WASF2
HNRNPR
SRRM1
CNKSR1
GMEB1
NUDC
SRSF10
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
CTRC
DNAJC8
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
PLEKHM2
OTUD3
DNAJC16
UBR4
ATP13A2
CELA3B
PADI4
TMEM50A
STX12
CLIC4
SYF2
C1orf144
LDLRAP1
PLA2G2D
RNU11
HSPB7
AHDC1
SMPDL3B
PRO0611
LINC00339
PADI1
PLA2G2E
HP1BP3
CELA2B
ZNF593
MECR
MRTO4
YTHDF2
ZCCHC17
PADI3
WNT4
FBXO42
RNF186
GPN2
FBLIM1
MED18
PQLC2
TRNAU1AP
AIM1L
TMEM51
XKR8
ARHGEF10L
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
RCC2
FAM54B
C1orf63
PITHD1
MAN1C1
NIPAL3
SEPN1
KIF17
GRHL3
IL22RA1
CELA2A
GPATCH3
TINAGL1
PLA2G2F
CEP85
PINK1
PHACTR4
C1orf135
EFHD2
RSG1
NKAIN1
MUL1
LIN28A
AGMAT
FAM110D
DHDDS
ZNF436
TAS1R2
ACTL8
SH3BGRL3
SESN2
TMEM222
USP48
NBPF3
ZDHHC18
DDI2
TRIM63
CROCCP2
SYTL1
IGSF21
SNHG12
C1orf201
UBXN11
ATPIF1
CROCCP3
FHAD1
RAB42
FAM46B
C1orf172
IFFO2
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf213
LOC149086
PDIK1L
C1orf64
IL28RA
FAM43B
PAQR7
FAM76A
C1orf126
AKR7L
TMCO4
ZNF683
LOC284551
LOC284632
SLC25A34
ESPNP
LOC339505
SERINC2
FAM131C
PADI6
SPATA21
CATSPER4
TMEM82
TRNP1
CD164L2
PLA2G2C
TMEM200B
SH2D5
C1orf130
LDLRAD2
UQCRHL
MINOS1
PEF1
LOC644961
LOC646471
LOC653566
SCARNA1
SNORA44
SNORA61
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
LOC729059
FLJ37453
LOC100129196
MIR1976
MIR3115
MIR4253
MIR3917
MIR3675
LOC100506730
LOC100506801
LOC100506963
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR378F
RCAN3AS

Genes in Wide Peak

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

Table S46. 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
BCKDHB
CCNC
CGA
CNR1
COL10A1
COL12A1
COX7A2
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
HSF2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
MAN1A1
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
PKIB
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
BRD7P3
ASF1A
PNISR
IBTK
SENP6
FBXL4
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
FAM46A
TMEM30A
RARS2
PDSS2
C6orf162
LYRM2
SNX14
SERINC1
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
FAM184A
MANEA
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
PM20D2
SRSF12
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
RSPH4A
GJB7
SNHG5
LINC00222
CEP85L
LIN28B
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
ZFP36L1
RAD51B

Genes in Wide Peak

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

Table S49. 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
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
EIF1B
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
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
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 3p13.

Table S50. 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 Xq21.33.

Table S51. 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 7q36.3.

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

Genes
EZH2
MLL3
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
ABP1
CDK5
DPP6
EN2
GBX1
MNX1
HTR5A
INSIG1
KCNH2
NOS3
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
VIPR2
XRCC2
ZNF212
ZNF282
CUL1
ACCN3
PDIA4
UBE3C
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
CNTNAP2
GIMAP2
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ESYT2
ZNF398
GALNT11
LMBR1
LINC00244
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
C7orf29
AGAP3
C7orf13
ZNF786
ASB10
RNF32
LOC154822
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5P3
CNPY1
LOC285889
ZNF775
LOC285972
ATG9B
WDR86
LOC401431
MIR153-2
GIMAP6
ZNF862
LOC645249
ACTR3C
MIR595
LOC728743
MIR671
LOC100128264
LOC100128822
LOC100131176
LOC100132707
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MIR3907
LOC100505483
LOC100506585
GIMAP1-GIMAP5

Genes in Wide Peak

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

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

Genes
hsa-mir-3171
hsa-mir-4307
FOXG1
NOVA1
C14orf23
MIR4307
LOC100505967

Genes in Wide Peak

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

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

Genes
KDM6A
hsa-mir-222
DUSP21
CXorf36
MIR221
MIR222

Genes in Wide Peak

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

Table S55. Genes in bold are cancer genes as defined by The Sanger Institute's 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
hsa-mir-187
ATP5A1
CDH7
CYB5A
DCC
DTNA
FECH
KDSR
GALR1
GALNT1
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
ZNF24
ZNF236
SLC14A2
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
ZNF271
TXNL4A
MAPRE2
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
MOCOS
RPRD1A
ZNF532
ELP2
ELAC1
ZNF407
CNDP2
CELF4
KIAA1328
KIAA1468
EPG5
CCDC102B
RBFA
PQLC1
FHOD3
CCDC68
NETO1
KATNAL2
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
INO80C
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
ZNF396
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
MIR187
HSBP1L1
RNF165
C18orf32
KC6
LOC643542
C18orf63
LOC647946
SCARNA17
SNORA37
TCEB3CL
ZSCAN30
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR1539
MIR4319
MIR4318
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744

Genes in Wide Peak

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

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

Genes
PRDM1
CCND3
DAXX
FANCE
HMGA1
MLLT4
MYB
PIM1
ROS1
TNFAIP3
TFEB
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
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
hsa-mir-133b
hsa-mir-586
hsa-mir-1275
hsa-mir-219-1
hsa-mir-1236
ACAT2
CRISP1
AGER
AIF1
AIM1
AMD1
ARG1
ATP6V1G2
BAI3
BAK1
BCKDHB
CFB
BMP5
DST
BYSL
C2
C4A
C4B
RUNX2
CCNC
CDC5L
CDKN1A
CGA
CLIC1
CLPS
CCR6
CNR1
COL9A1
COL10A1
COL11A2
COL12A1
COL19A1
COX7A2
ATF6B
MAPK14
CSNK2B
CTGF
CYP21A2
CYP21A1P
DNAH8
DOM3Z
EEF1A1
SLC29A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FKBP5
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GCLC
GLO1
GLP1R
GPR6
GPR31
GRIK2
GRM1
GRM4
GSTA1
GSTA2
GSTA3
GSTA4
GUCA1A
GUCA1B
HCRTR2
HDAC2
HIVEP2
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HSF2
HSPA1A
HSPA1B
HSPA1L
HSP90AB1
HTR1B
HTR1E
IFNGR1
IGF2R
IL17A
IMPG1
ITPR3
KIFC1
KIF25
KPNA5
LAMA2
LAMA4
LPA
LTA
LTB
MARCKS
MAN1A1
MAS1
MCM3
MDFI
ME1
MEA1
MAP3K4
MAP3K5
MEP1A
MICB
MLN
MOCS1
MSH5
MUT
MYO6
RPL10A
NEU1
NFKBIE
NFKBIL1
NFYA
NMBR
NOTCH4
NT5E
OPRM1
PARK2
PBX2
PCMT1
PDCD2
ENPP1
ENPP3
PEX6
PEX7
PGC
PGK2
PGM3
PHF1
PKHD1
PLAGL1
PLG
PLN
POLH
POU3F2
PPARD
PPP2R5D
PREP
PRIM2
PKIB
MAPK13
PSMB1
PSMB8
PSMB9
PTK7
PTPRK
RGL2
PRPH2
REV3L
RHAG
RING1
BRD2
RNF5
RNY4
RPS6KA2
RPS10
RPS12
RPS18
RXRB
VPS52
SRSF3
SGK1
SIM1
SKIV2L
SLC22A1
SLC22A3
SLC22A2
SMPD2
SNRPC
SOD2
SRF
SRPK1
ELOVL4
T
TAF11
MAP3K7
TAP1
TAP2
TAPBP
TBCC
TBP
TCF21
TCP1
TCP10
TCP11
TCTE3
DYNLT1
TEAD3
TFAP2B
THBS2
NR2E1
TNF
TNXA
TNXB
TPBG
TPD52L1
CRISP2
TSPYL1
TTK
TULP1
UTRN
VARS
VEGFA
EZR
VIP
ZNF76
PTP4A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
RDBP
LST1
PLA2G7
EPM2A
STX7
SUPT3H
PEX3
GCM1
DDO
RNASET2
KCNK5
STX11
B3GALT4
SNX3
RNGTT
CD164
SYNGAP1
WISP3
STK19
SYNJ2
VNN2
VNN1
WASF1
RNF8
TAAR5
MAP7
TBX18
LATS1
WDR46
ZBTB22
TAAR2
TAAR3
HMGN3
PPT2
NCR2
MED23
QKI
FHL5
AKAP7
ATG5
MED20
SLC25A27
TBPL1
BAG2
POLR1C
MAD2L1BP
WTAP
AKAP12
TRAM2
KIAA0408
PHACTR2
BCLAF1
CUL7
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
RCAN2
CRISP3
TRDN
CITED2
PFDN6
SYNCRIP
AGPAT1
SLC35A1
C6orf108
C6orf10
FUT9
CNPY3
TRAF3IP2
HBS1L
FRS3
PDE10A
SLC22A7
HCP5
EHMT2
SMPDL3A
APOBEC2
PNRC1
ASCC3
RAB32
KATNA1
CAPN11
BVES
NUDT3
SEC63
STK38
SCAF8
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
FTSJD2
CDK19
CUL9
TAB2
MDN1
TSPYL4
ANKS1A
UBR2
SASH1
SYNE1
UFL1
PHF3
HEY2
DAAM2
KIAA0240
DDAH2
HEBP2
ORC3
CD2AP
BRD7P3
MTCH1
ZNF318
SPDEF
MTO1
ASF1A
YIPF3
USP49
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
TIAM2
FBXL4
C6orf123
FBXO9
FBXO5
SLC17A5
RGS17
SNORD52
SNORD50A
SNORD48
PDE7B
FILIP1
BRPF3
GNMT
TNFRSF21
SESN1
TINAG
DLL1
OSTM1
TMEM14A
MRPL18
NDUFAF4
DSE
PRICKLE4
PACSIN1
CLDN20
NOX3
DEF6
C6orf48
HDDC2
MRPL2
TFB1M
CYB5R4
TUBE1
C6orf203
CYP39A1
CDC40
RWDD1
AIG1
SNX9
UBE2J1
ETV7
VTA1
LGSN
CUTA
PPIL1
BRP44L
HECA
RAB23
COQ3
CLIC5
IL20RA
TREM2
TREM1
UNC93A
HMGCLL1
MTRF1L
GTPBP2
AHI1
UHRF1BP1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
MRPS18A
MRPS10
LRRC1
PHF10
QRSL1
VNN3
TMEM63B
AKIRIN2-AS1
DDX43
FAM46A
TBC1D22B
TMEM30A
SAYSD1
C6orf70
LMBRD1
TRERF1
ECHDC1
APOM
BTNL2
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
LRFN2
AARS2
XPO5
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
CPNE5
LSM2
C6orf47
LY6G5B
C6orf115
RRAGD
LY6G6D
ENPP5
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
ZFAND3
C6orf164
GPSM3
FKBPL
PERP
SMOC2
POPDC3
ALDH8A1
C6orf106
MICAL1
MRPL14
DLK2
LY6G6E
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
ADGB
TREML2
LINC00472
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
KHDC1
PRRT1
EGFL8
GPR63
COL21A1
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
TFAP2D
KCNK16
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
MNF1
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
TTBK1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
PAQR8
SLC22A16
RRP36
C6orf7
KCNK17
ABCC10
KLC4
UBE2CBP
MLIP
LINC00473
KIAA1919
TJAP1
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
IL17F
FAM54A
SFT2D1
EFHC1
BTBD9
KLHL32
TMEM200A
MB21D1
FOXP4
KLHDC3
NUS1
C6orf72
SLC26A8
IL22RA2
C6orf192
SLC16A10
IP6K3
TAGAP
TAF8
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SRSF12
C6orf141
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
LOC154449
CCDC167
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
PTCRA
OSTCP1
TCTE1
KHDRBS2
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
RSPH9
LRRC73
TREML2P1
LOC221442
C6orf130
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
GPR111
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
C6orf191
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
NCR3
LY6G6F
MDGA1
GPR110
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
LOC285847
PNPLA1
TREML4
RPL7L1
RNF5P1
TAAR6
SLC35D3
ZC3H12D
DPPA5
CLPSL1
TREML1
TREML3
RSPH4A
ECT2L
EYS
SLC35B2
NUP43
HCG26
C6orf58
RAET1G
GUSBP4
GJB7
HMGA1P7
SNHG5
SUMO4
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
CLPSL2
C6orf222
GLYATL3
GFRAL
LIN28B
SAMD5
IYD
MCCD1
SAPCD1
LINC00336
FLJ41649
CRIP3
KLHL31
DKFZp451B082
TCP10L2
LINC00242
DEFB133
GTF2H5
MIR206
MIR219-1
MIR30A
MIR30C2
HCG23
HCG25
C6orf226
TMEM151B
OOEP
FAM26F
FLJ46906
LOC441177
ATP6V0CP3
PTCHD4
MCART3P
GSTM2P1
RFPL4B
MIR133B
GGNBP1
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
C6orf132
RPS16P5
MLLT4-AS1
SNORA20
SNORA29
SNORA38
SNORD50B
SNORD84
SNORD117
MIR548B
MIR586
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
LOC730101
GSTA7P
TDRG1
HGC6.3
LOC100128176
BET3L
KHDC1L
LOC100129518
LOC100130890
C6orf99
LOC100131047
LINC00271
LOC100132354
LOC100132735
TOMM6
LOC100287632
LOC100287718
LOC100288198
LOC100289495
LOC100293534
LOC100294145
NHEG1
MIR1275
MIR1913
MIR2113
MIR1236
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3918
MIR3939
MIR3668
MIR3662
MIR3925
MIR3692
LOC100506804
LOC100507203
LOC100507254
MICA
LOC100507462
LOC100507463
LOC100507489
LOC100507547
LOC100507557
LOC100507584
CAHM
RPS10-NUDT3
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4464
MIR4647
MIR4466
MIR4643
MIR4641
MIR4465
MIR4646
MIR4642
MIR4462
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
FGFR1
PCM1
PLAG1
TCEA1
WRN
WHSC1L1
CHCHD7
HOOK3
hsa-mir-486
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
ADRB3
ANK1
ASAH1
ASPH
ATP6V1B2
BMP1
POLR3D
BNIP3L
CA8
CEBPD
CHRNA2
CHRNB3
CLU
CTSB
CYP7A1
ADAM3A
DPYSL2
DUSP4
EGR3
EIF4EBP1
EPB49
EPHX2
EXTL3
PTK2B
FDFT1
FGL1
FNTA
ADAM2
GATA4
GFRA2
GNRH1
NPBWR1
GSR
GTF2E2
NRG1
IKBKB
IDO1
LOXL2
LPL
LYN
MCM4
MOS
MSR1
NEFM
NEFL
NKX3-1
OPRK1
PDGFRL
PENK
PLAT
PNOC
POLB
PPP2CB
PPP2R2A
PPP3CC
PRKDC
RAB2A
RP1
RPS20
SDCBP
SFRP1
SFTPC
SLC7A2
SLC18A1
SLC20A2
SNAI2
STAR
STC1
TACC1
TTPA
UBE2V2
VDAC3
FZD3
TUSC3
UBXN8
KAT6A
NSMAF
RGS20
ADAM18
ADAM9
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
GGH
CHRNA6
DOK2
ASH2L
MTMR7
BAG4
ENTPD4
ST18
TOX
PHYHIP
RB1CC1
SORBS3
NPM2
DLC1
LYPLA1
DCTN6
PNMA2
ADAM28
AP3M2
RBPMS
ERLIN2
LZTS1
PROSC
XPO7
TRIM35
RHOBTB2
DDHD2
KIF13B
PSD3
LEPROTL1
KIAA0146
SLC39A14
GPR124
C8orf71
FGF20
SNORD54
DKK4
LSM1
ADAMDEC1
MRPL15
CNOT7
PURG
GOLGA7
ZDHHC2
SLC25A37
SCARA3
ATP6V1H
TMEM66
SNTG1
KCTD9
IMPAD1
PIWIL2
ELP3
THAP1
INTS10
CCDC25
BRF2
CHD7
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
C8orf4
MTUS1
KIAA1456
KIAA1967
PLEKHA2
SH2D4A
PDLIM2
SOX17
EBF2
FAM160B2
DUSP26
HMBOX1
EFCAB1
ZMAT4
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
TTI2
RAB11FIP1
REEP4
STMN4
RNF170
LINC00208
TM2D2
SGK196
GINS4
PPAPDC1B
MAK16
FUT10
FAM86B1
FAM110B
LONRF1
CHMP7
TGS1
XKR4
C8orf40
PCMTD1
GOT1L1
VPS37A
TMEM68
NKX2-6
SGCZ
UBXN2B
PXDNL
AGPAT6
UNC5D
LETM2
HGSNAT
PEBP4
CDCA2
ESCO2
FBXO16
C8orf48
CLVS1
NKX6-3
KCNU1
IDO2
SDR16C5
R3HCC1
HTRA4
ADAM32
LGI3
DEFB109P1
DEFB130
NEIL2
LOC254896
ADAM5P
LOC286059
EFHA2
LOC286114
SCARA5
LOC286135
RNF5P1
LOC286177
NKAIN3
LOC340357
POTEA
USP17L2
FAM90A25P
LOC389641
C8orf80
C8orf86
FAM150A
LOC392196
MIR320A
C8orf22
MIR383
LINC00293
C8orf58
DEFB135
DEFB136
DEFB134
C8orf75
MBOAT4
MIR486
UG0898H09
FAM86B2
LOC728024
ZNF705D
LOC100128750
LOC100128993
LOC100130298
LOC100130964
FAM66D
FAM66A
SBF1P1
LOC100133267
LOC100287846
MIR4287
MIR3148
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
LOC100507341
LOC100507632
LOC100507651
MIR4469
MIR548O2
MIR4470

Genes in Wide Peak

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

Table S58. Genes in bold are cancer genes as defined by The Sanger Institute's 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 3p14.2.

Table S59. 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
CDC25A
CISH
CCR1
CCR3
CCR5
CCBP2
COL7A1
CYP8B1
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
NKTR
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
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
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
CHMP2B
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
ZNF654
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
ARL13B
KLHDC8B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
C3orf38
ZNF621
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
PRSS42
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LOC401074
MIRLET7G
MIR135A1
MIR138-1
MIR191
FAM19A1
STX19
TMEM89
IQCF6
C3orf78
LOC440970
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
MIR4795
MIR4444-1
MIR4443
LOC100652759
LUST

Genes in Wide Peak

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

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

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

Arm-level results

Table 3. Get Full Table Arm-level significance table - 27 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 | 0.24 | 0.967 | 0.513 | 0.12 | -2.92 | 1
1q | 1955 | 0.34 | 4 | 0.00021 | 0.14 | -2.37 | 1
2p | 924 | 0.30 | 0.2 | 1 | 0.20 | -2.8 | 1
2q | 1556 | 0.17 | -2.53 | 1 | 0.27 | 0.751 | 0.477
3p | 1062 | 0.37 | 2.58 | 0.0195 | 0.23 | -1.51 | 1
3q | 1139 | 0.45 | 5.54 | 1.92e-07 | 0.12 | -3.91 | 1
4p | 489 | 0.14 | -4.78 | 1 | 0.40 | 2.3 | 0.0304
4q | 1049 | 0.09 | -5.06 | 1 | 0.39 | 3.29 | 0.00182
5p | 270 | 0.39 | 1.38 | 0.303 | 0.40 | 1.49 | 0.17
5q | 1427 | 0.16 | -2.59 | 1 | 0.47 | 6.87 | 6.51e-11
6p | 1173 | 0.19 | -2.58 | 1 | 0.29 | 0.524 | 0.572
6q | 839 | 0.13 | -4.44 | 1 | 0.40 | 3.05 | 0.00381
7p | 641 | 0.43 | 3.71 | 0.000564 | 0.08 | -5.65 | 1
7q | 1277 | 0.38 | 3.6 | 0.000717 | 0.12 | -4.08 | 1
8p | 580 | 0.29 | -0.708 | 1 | 0.59 | 8.16 | 4.44e-15
8q | 859 | 0.48 | 5.5 | 1.92e-07 | 0.23 | -1.66 | 1
9p | 422 | 0.24 | -2.16 | 1 | 0.52 | 5.48 | 2.13e-07
9q | 1113 | 0.22 | -1.68 | 1 | 0.45 | 5.27 | 5.32e-07
10p | 409 | 0.31 | -0.693 | 1 | 0.32 | -0.36 | 1
10q | 1268 | 0.10 | -4.47 | 1 | 0.38 | 3.47 | 0.00115
11p | 862 | 0.14 | -3.96 | 1 | 0.45 | 4.79 | 5.56e-06
11q | 1515 | 0.18 | -2.08 | 1 | 0.37 | 3.58 | 0.000851
12p | 575 | 0.32 | -0.0352 | 1 | 0.16 | -4.21 | 1
12q | 1447 | 0.25 | -0.154 | 1 | 0.16 | -2.87 | 1
13q | 654 | 0.33 | 0.396 | 0.989 | 0.29 | -0.747 | 1
14q | 1341 | 0.23 | -0.952 | 1 | 0.34 | 2.18 | 0.0394
15q | 1355 | 0.15 | -3.17 | 1 | 0.37 | 3.41 | 0.00129
16p | 872 | 0.21 | -2.33 | 1 | 0.33 | 0.986 | 0.36
16q | 702 | 0.26 | -1.45 | 1 | 0.32 | 0.396 | 0.629
17p | 683 | 0.22 | -2.14 | 1 | 0.53 | 6.53 | 4.41e-10
17q | 1592 | 0.37 | 3.69 | 0.000564 | 0.23 | -0.57 | 1
18p | 143 | 0.35 | 0.0254 | 1 | 0.37 | 0.557 | 0.572
18q | 446 | 0.20 | -3.18 | 1 | 0.42 | 2.86 | 0.00642
19p | 995 | 0.25 | -0.989 | 1 | 0.33 | 1.28 | 0.236
19q | 1709 | 0.38 | 4.49 | 2.82e-05 | 0.25 | 0.318 | 0.652
20p | 355 | 0.55 | 6.43 | 1.25e-09 | 0.15 | -4.15 | 1
20q | 753 | 0.58 | 8.61 | 0 | 0.11 | -4.22 | 1
21q | 509 | 0.36 | 1.06 | 0.479 | 0.23 | -2.56 | 1
22q | 921 | 0.23 | -1.58 | 1 | 0.44 | 4.5 | 1.95e-05
Xq | 1312 | 0.12 | -4.43 | 1 | 0.25 | -0.459 | 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/5947871/GDAC_MergeDataFiles_5950456/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 221 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:

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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