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

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

Summary

There were 205 tumor samples used in this analysis: 23 significant arm-level results, 19 significant focal amplifications, and 32 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 - 19 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
--- | --- | --- | --- | ---
12q15 | 7.9079e-18 | 7.9079e-18 | chr12:67498278-67771718 | 2
14q13.2 | 4.6042e-15 | 4.6042e-15 | chr14:35018284-35136635 | 2
8q24.21 | 3.8438e-08 | 3.8438e-08 | chr8:129180026-129264442 | 2
5p15.33 | 4.6988e-07 | 1.1316e-06 | chr5:395459-936341 | 10
7p11.2 | 2.982e-05 | 2.982e-05 | chr7:54518543-56361153 | 18
12p12.1 | 5.3045e-05 | 5.3045e-05 | chr12:25040817-27318064 | 16
1q21.2 | 8.9762e-05 | 8.9762e-05 | chr1:121045320-151061583 | 159
8p11.21 | 0.00037067 | 0.00037067 | chr8:41456216-42942240 | 21
11q13.2 | 0.0025514 | 0.0025514 | chr11:68044196-69240961 | 13
19q13.11 | 0.0031756 | 0.0031756 | chr19:34177358-41264403 | 96
20q13.2 | 0.0019273 | 0.0069342 | chr20:51607233-52062233 | 3
5p13.1 | 0.027132 | 0.043166 | chr5:35865449-39716203 | 23
18q11.2 | 0.053135 | 0.053135 | chr18:20619167-20769643 | 0 [ZNF521]
7p21.1 | 0.074377 | 0.074377 | chr7:16579935-20585121 | 16
7q31.2 | 0.10229 | 0.10229 | chr7:114918544-116912844 | 14
17q12 | 0.10229 | 0.10229 | chr17:33006698-36953339 | 113
3q26.31 | 0.13318 | 0.13318 | chr3:168271226-199501827 | 209
20q13.33 | 0.011393 | 0.16269 | chr20:60955896-62435964 | 55
1p31.3 | 0.2393 | 0.2393 | chr1:58357075-63203974 | 19

Genes in Wide Peak

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

Table S1. 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 14q13.2.

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

Genes
INSM2
RALGAPA1

Genes in Wide Peak

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

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

Genes
hsa-mir-1208
PVT1

Genes in Wide Peak

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

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

Genes
SLC9A3
TPPP
EXOC3
LOC25845
CEP72
AHRR
BRD9
ZDHHC11
C5orf55
LOC100310782

Genes in Wide Peak

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

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

Genes
EGFR
CCT6A
GBAS
PHKG1
PSPH
SEC61G
SUMF2
CHCHD2
MRPS17
LANCL2
VOPP1
VSTM2A
SEPT14
ZNF713
FKBP9L
LOC389493
LOC442308
SNORA15

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
ITPR2
LRMP
SSPN
MED21
RASSF8
STK38L
FGFR1OP2
TM7SF3
CASC1
C12orf11
BHLHE41
LYRM5
IFLTD1
C12orf77
C12orf71

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
ARNT
BCL9
PDE4DIP
hsa-mir-554
CTSK
CTSS
ECM1
ENSA
FCGR1A
FLG
FMO5
GJA5
GJA8
MCL1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A10
S100A11
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
TNRC4
VPS45
POGZ
RPRD2
CA14
NBPF14
LCE2B
RNF115
TMOD4
LASS2
CRNN
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
FAM63A
CDC42SE1
OTUD7B
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
HIST2H3C
LIX1L
C1orf51
HFE2
ANKRD35
BNIPL
PPIAL4A
PDIA3P
LCE4A
LOC200030
NUDT17
LCE5A
C1orf230
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
LINGO4
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
NBPF20
HIST2H2BF
KPRP
HIST2H4B
PPIAL4G
PPIAL4D
LOC645166
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
MIR554
HIST2H2AA4
LOC728855
LOC728875
NBPF11
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
C1orf152
C1orf68
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793

Genes in Wide Peak

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

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

Genes
HOOK3
hsa-mir-486
ANK1
CHRNB3
IKBKB
PLAT
POLB
SLC20A2
VDAC3
MYST3
CHRNA6
AP3M2
DKK4
GOLGA7
THAP1
RNF170
GINS4
C8orf40
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
CCND1
CPT1A
IGHMBP2
MTL5
FGF19
MYEOV
GAL
SAPS3
MRGPRD
MRGPRF
MRPL21
TPCN2
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
CEBPA
APLP1
ATP4A
CCNE1
CD22
CEBPG
COX6B1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
LRP3
MAG
NPHS1
PEPD
FXYD1
FXYD3
SCN1B
TYROBP
UQCRFS1
USF2
C19orf2
PDCD5
KIAA0355
ZNF536
MLL4
UBA2
TMEM147
POP4
HCST
UPK1A
SLC7A9
ZNF507
HAUS5
CLIP3
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
GPATCH1
PSENEN
ZNF302
LIN37
SLC7A10
TSHZ3
GRAMD1A
HAMP
PRODH2
CHST8
KCTD15
PLEKHF1
RBM42
LRFN3
TMEM149
LOC80054
C19orf12
KIRREL2
ANKRD27
PDCD2L
NFKBID
CCDC123
ALKBH6
RHPN2
ZNF30
C19orf40
TDRD12
DMKN
DKFZp566F0947
SNX26
WDR88
WTIP
ZNF792
HSPB6
DPY19L3
ZNF599
FAM187B
C19orf55
LGI4
C19orf46
THAP8
U2AF1L4
SCGBL
WDR62
ZNF181
VSTM2B
SBSN
RGS9BP
KRTDAP
NUDT19
LOC643719
SDHAF1
LOC100128675

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
ZNF217
BCAS1
SUMO1P1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.1.

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

Genes
LIFR
hsa-mir-580
C9
DAB2
FYB
GDNF
IL7R
SKP2
SLC1A3
OSMR
NUP155
NIPBL
WDR70
C5orf42
LMBRD2
EGFLAM
C5orf33
UGT3A1
CAPSL
UGT3A2
RANBP3L
RICTOR
MIR580

Genes in Wide Peak

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

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

Genes
hsa-mir-1302-6
AHR
ITGB8
TWIST1
HDAC9
AGR2
SNX13
TSPAN13
BZW2
ANKMY2
AGR3
PRPS1L1
TWISTNB
FERD3L
TMEM196
MACC1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.2.

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

Genes
MET
CAPZA2
CAV1
CAV2
CFTR
WNT2
ST7
TFEC
TES
ST7OT1
ST7OT2
ST7OT3
ASZ1
ST7OT4

Genes in Wide Peak

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

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

Genes
ERBB2
LASP1
MLLT6
RARA
CACNB1
CDC6
CCR7
CSF3
GRB7
IGFBP4
KRT10
KRT12
KRT13
KRT15
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
NEUROD2
PNMT
MED1
PSMB3
PSMD3
RPL19
SMARCE1
HNF1B
THRA
TOP2A
PCGF2
PIP4K2B
TCAP
KRT38
KRT37
KRT36
RPL23
NR1D1
MED24
STARD3
DDX52
SYNRG
CASC3
IKZF3
KRT23
SOCS7
RAPGEFL1
CRKRS
KRT20
CCDC49
GSDMB
PLXDC1
ARHGAP23
SNIP
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP2-1
KRTAP4-12
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
PPP1R1B
TBC1D3F
C17orf37
MRPL45
KRTAP4-4
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
LOC90110
PGAP3
ORMDL3
ZPBP2
GJD3
KRT222
KRT40
WIPF2
KRT25
TMEM99
KRT28
KRT24
LOC284100
CISD3
GSDMA
MSL1
KRT27
STAC2
KRT26
C17orf98
ARL5C
KRT39
GPR179
FBXO47
SNORA21
KRTAP4-11
KRTAP4-8
TBC1D3
SNORD124
KRTAP4-9
KRTAP4-7
C17orf96

Genes in Wide Peak

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

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
ACTL6A
AHSG
APOD
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
ST6GAL1
SKIL
SLC2A2
SST
TERC
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
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
C3orf34
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
C3orf50
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
C3orf59
C3orf21
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
NAALADL2
TCTEX1D2
C3orf43
SDHALP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
SOX2OT
WDR53
LOC348840
LRRC33
TMEM212
FLJ42393
SNORD2
SNORA4
C3orf65
LOC647309
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHALP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
SNAR-I
MIR1224

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
hsa-mir-647
hsa-mir-124-3
CHRNA4
EEF1A2
NPBWR2
KCNQ2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
TCFL5
DIDO1
PRPF6
GMEB2
STMN3
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
ARFGAP1
SLC2A4RG
ZNF512B
COL20A1
SLC17A9
C20orf195
PPDPF
BIRC7
DNAJC5
ZGPAT
PRIC285
BHLHE23
NKAIN4
ZBTB46
SAMD10
C20orf135
C20orf201
NCRNA00176
MIR124-3
MIR647
HAR1A
HAR1B
UCKL1AS
MIR941-1
MIR941-2
MIR941-3
NCRNA00029
FLJ16779

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p31.3.

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

Genes
JUN
CYP2J2
DAB1
TACSTD2
NFIA
USP1
INADL
ANGPTL3
HOOK1
L1TD1
FGGY
TM2D1
ATG4C
DOCK7
MYSM1
OMA1
C1orf87
KANK4
LOC729467

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 - 32 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 | 1.5297e-61 | 1.5751e-56 | chr9:21855498-21986995 | 2
5q11.2 | 0.00033614 | 0.0004421 | chr5:58180924-59823214 | 3
22q13.31 | 0.0004421 | 0.0004421 | chr22:42067547-49691432 | 86
11q23.1 | 0.0090527 | 0.0089549 | chr11:106062351-132908299 | 242
9p24.1 | 8.4936e-09 | 0.014296 | chr9:7786330-12683402 | 2
12q12 | 0.02099 | 0.020235 | chr12:44119408-46344541 | 9
10p15.3 | 0.024629 | 0.025358 | chr10:1-3948118 | 15
11q12.1 | 0.026185 | 0.027429 | chr11:57962698-58104340 | 3
5q22.1 | 0.0023765 | 0.030907 | chr5:110493857-111527630 | 5
13q12.11 | 0.0038058 | 0.030907 | chr13:1-48687164 | 174
9p13.1 | 0.0012667 | 0.036028 | chr9:38609152-70342057 | 46
3q28 | 0.045052 | 0.043004 | chr3:180998810-199501827 | 156
11p15.5 | 0.043025 | 0.043004 | chr11:1-63090793 | 695
1p36.13 | 0.043004 | 0.047143 | chr1:1-31157907 | 459
17p13.3 | 0.050752 | 0.050713 | chr17:639271-1126772 | 4
15q14 | 0.0024053 | 0.0528 | chr15:1-58674404 | 389
6q26 | 0.047143 | 0.059733 | chr6:133177501-170899992 | 191
1p13.3 | 0.056665 | 0.077006 | chr1:71299209-144141104 | 320
6q12 | 0.077006 | 0.11711 | chr6:58337167-116893854 | 191
16q23.1 | 0.030064 | 0.13051 | chr16:76686559-78185271 | 1
15q25.3 | 0.064452 | 0.13814 | chr15:83052718-83164351 | 1
21q11.2 | 0.14178 | 0.14178 | chr21:1-30889615 | 76
16q24.2 | 0.059798 | 0.16464 | chr16:68336157-88827254 | 181
2q37.2 | 0.17767 | 0.17767 | chr2:208838538-242951149 | 261
10q26.3 | 0.1815 | 0.1815 | chr10:99065617-135374737 | 290
18q12.2 | 0.1815 | 0.1815 | chr18:33055423-35467010 | 2
19p13.3 | 0.18556 | 0.18466 | chr19:1-10370364 | 315
3p14.1 | 0.20611 | 0.20611 | chr3:1-117649079 | 647
13q31.1 | 0.11083 | 0.20611 | chr13:63205516-87134644 | 33
13q14.2 | 0.015254 | 0.21297 | chr13:1-63322365 | 229
8p23.1 | 0.2157 | 0.2223 | chr8:8275090-11180681 | 20
15q14 | 0.0029376 | 0.23587 | chr15:1-58674404 | 389

Genes in Wide Peak

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

Table S19. 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 5q11.2.

Table S20. 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 22q13.31.

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

Genes
hsa-let-7b
hsa-mir-1249
ACR
ARSA
MPPED1
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
C22orf9
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
PNPLA5
LOC150381
C22orf40
CN5H6.4
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
NCRNA00207
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.1.

Table S22. 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-100
hsa-mir-125b-1
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
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
RICS
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
ZBTB44
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
C11orf60
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
C11orf61
ALG9
ASAM
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
LOC399959
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
NCRNA00167
HEPN1
LOC643923
CLDN25
RPL23AP64
PATE3

Genes in Wide Peak

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

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

Genes
PTPRD
C9orf123

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q12.

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

Genes
SFRS2IP
SLC38A2
SLC38A4
SLC38A1
FAM113B
ARID2
AMIGO2
LOC400027
LOC100233209

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

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

Genes
ADARB2
KLF6
IDI1
PFKP
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
C10orf110
IDI2
TUBB8
NCRNA00200
C10orf108

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q12.1.

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

Genes
LPXN
OR5B21
OR5B12

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q22.1.

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

Genes
CAMK4
C5orf13
C5orf26
STARD4
SNORA13

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
hsa-mir-621
hsa-mir-320d-1
PARP4
ALOX5AP
ATP12A
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
GTF2F2
GTF3A
HMGB1
HTR2A
PDX1
MAB21L1
SMAD9
MIPEP
PABPC3
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
NUPL1
FRY
LPAR6
SLC25A15
USPL1
MRPS31
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
LATS2
OR7E37P
NUFIP1
SNORD102
NBEA
C13orf15
MED4
DNAJC15
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
RNF17
CYSLTR2
COG6
XPO4
MRP63
NARG1L
C13orf18
C13orf23
COG3
KATNAL1
KBTBD7
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
CG030
LOC121838
CSNK1A1L
RXFP2
C13orf26
C13orf30
C13orf31
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
DKFZp686A1627
SUGT1L1
SIAH3
SLC46A3
LOC284232
C1QTNF9
FREM2
LOC348021
LOC374491
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
C13orf36
ATP5EP2
PCOTH
SNORA27
LOC646405
PRHOXNB
ZAR1L
LOC646982
SNORA31
MIR621
C13orf38
LOC100101938
RPL21P28
LOC100188949
LOC100190939
LOC100288730

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p13.1.

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

Genes
hsa-mir-1299
PGM5
ZNF658
FAM75A7
CNTNAP3
ANKRD20A1
C9orf122
CBWD5
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
AQP7P2
FAM74A1
FAM74A4
ZNF658B
LOC440839
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
FAM75A2
LOC642929
CBWD6
FAM75A1
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
ANKRD20A4
CCDC29
FOXD4L2
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q28.

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

Genes
BCL6
EIF4A2
ETV5
LPP
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
EHHADH
EIF4G1
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
OPA1
PAK2
PCYT1A
POLR2H
PPP1R2
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SST
THPO
FXR1
TP63
CHRD
EIF2B5
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
IGF2BP2
CLDN16
NCBP2
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
FETUB
LAMP3
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
YEATS2
MCCC1
HRASLS
SENP2
RTP4
MAGEF1
ATP13A3
MAP6D1
PIGZ
B3GNT5
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
C3orf34
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
C3orf59
C3orf21
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
TCTEX1D2
C3orf43
SDHALP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
RTP2
OSTN
ATP13A5
SOX2OT
WDR53
LOC348840
LRRC33
FLJ42393
SNORD2
SNORA4
C3orf65
LOC647309
SNORA81
SNORD66
MIR570
SDHALP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
SNAR-I
MIR1224

Genes in Wide Peak

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

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

Genes
CARS
DDB2
EXT2
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
CREB3L1
hsa-mir-1908
hsa-mir-130a
hsa-mir-129-2
hsa-mir-610
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-210
ACP2
ADM
AP2A2
APLNR
AMPD3
APBB1
RHOG
ARHGAP1
ARNTL
ART1
ASCL2
BDNF
SERPING1
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAT
CCKBR
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CHRM1
CHRM4
TPP1
CNGA4
CNTF
COPB1
CRY2
CSTF3
CTNND1
CTSD
DDB1
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
F2
MS4A2
FEN1
FOLH1
FSHB
FTH1
GAS2
GIF
GNG3
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INCENP
INS
IRF7
CD82
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
FADS1
FADS3
LRP4
LSP1
CAPRIN1
MDK
SCGB2A1
SCGB2A2
MUC2
MUC6
MYBPC3
MYOD1
NAP1L4
NDUFS3
NELL1
NUCB2
SLC22A18
SLC22A18AS
OSBP
P2RX3
PAX6
PDE3B
PGA5
PIK3C2A
POLR2G
POLR2L
PRG2
PSMA1
PSMC3
PSMD13
PTH
PTPRJ
RAB3IL1
RAG1
RAG2
RAPSN
RARRES3
RCN1
RNH1
ROM1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SLC1A2
SLC3A2
SMPD1
SPI1
TRIM21
SSRP1
ST5
STIM1
STX3
STX5
ABCC8
TAF10
TALDO1
TCN1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TSG101
PHLDA2
TUB
SCGB1A1
BEST1
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
BBOX1
PPFIBP2
SLC43A1
IFITM1
DGKZ
CHST1
API5
MADD
OR6A2
DCHS1
EIF3F
BRSK2
SYT7
SLC6A5
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
SLC22A6
SLC22A8
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
MICAL2
CTR9
KIAA0652
CKAP5
TRIM66
NR1H3
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
GLYAT
MRVI1
TRIM22
PRG3
IFITM3
SPON1
EIF3M
NXF1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
TAF6L
SCGB1D2
SCGB1D1
CUGBP1
OR5I1
LYVE1
C11orf58
CLP1
KCNQ1OT1
PKP3
HPS5
GPR44
RRAS2
ZP1
SWAP70
GANAB
DTX4
DENND5A
NUP160
FNBP4
RRP8
SIRT3
OR52A1
SNHG1
ARFIP2
MTCH2
FJX1
C11orf41
ABTB2
PAMR1
ZDHHC5
DAK
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
OR10A3
FXC1
TIMM10
BSCL2
ELP4
DKK3
RBMXL2
PGAP2
PRPF19
SLC43A3
COMMD9
C11orf21
PACSIN3
TRPM5
UBQLN3
RNF141
UBXN1
APIP
TMX2
HSD17B12
IGF2AS
TMEM216
BET1L
CEND1
SLC15A3
PHF21A
MS4A4A
WIT1
TMEM138
CYB5R2
TRIM34
MUPCDH
TOLLIP
ZDHHC13
WDR74
TRIM44
MS4A12
MRPL16
SDHAF2
TMEM132A
HRASLS2
USP47
VPS37C
TRIM68
NAT10
UEVLD
LIN7C
SLC35C1
TCP11L1
LGR4
LRDD
KCNQ1DN
SOX6
AMBRA1
KBTBD4
PARVA
TTC17
MMP26
C11orf17
C11orf16
TMEM9B
NRIP3
ASCL3
PRDM11
CHRNA10
SLC17A6
PNPLA2
SYT13
PHRF1
LRRC4C
SCUBE2
MS4A7
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
FAM111A
ANO3
MS4A6A
MS4A5
EPS8L2
TUT1
STK33
CHID1
AHNAK
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ZNF408
QSER1
AGBL2
ZBTB3
CPSF7
PRR5L
ASRGL1
ATHL1
INTS5
ZFP91
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
PTDSS2
HCCA2
SBF2
KIF18A
MS4A8B
FAM160A2
FAR1
BTBD10
ARFGAP2
ACCS
MS4A14
SPRYD5
PTPN5
MICALCL
LGALS12
TRIM5
TNKS1BP1
NAV2
SYT8
TSPAN18
CCDC34
SLC39A13
DEPDC7
GLYATL1
PRKCDBP
RPLP0P2
SAAL1
ODF3
SLC22A9
OSBPL5
C1QTNF4
PTPMT1
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIMP1
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
CYP2R1
DBX1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
C11orf94
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
METT5D1
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
C11orf66
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
OR51F1
SVIP
MRGPRX1
C11orf31
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
FLJ46111
CSNK2A1P
OR51V1
H19
OR9G4
C11orf64
EFCAB4A
TMEM80
TTC9C
SLC22A24
HARBI1
LOC283267
IGSF22
OR10A4
OLFML1
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
OR5F1
OR5AP2
B4GALNT4
OR52L1
OR2AG2
OR52B6
DCDC1
MS4A10
OR10A2
OVCH2
PDDC1
RTN4RL2
GALNTL4
DKFZp686O24166
DKFZp779M0652
FAM111B
TMEM179B
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
SLC22A25
IFITM5
FAM99A
OR56B1
GVIN1
INSC
FIBIN
LOC387763
SLC22A10
OR52K1
OR52I1
OR51D1
OR52A4
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
FAM180B
OR51T1
OR51A4
OR51A2
OR4A47
OR4C45
SCGB1D4
MIR129-2
MIR130A
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440040
LOC441601
OR5B3
TRIM6-TRIM34
CCDC73
LOC494141
BDNFOS
MS4A13
OR8U8
OR9G9
MIR483
SNORA3
SNORA52
BTBD18
PGA3
PGA4
RASSF10
LOC646813
LOC650368
SNORA23
SNORA45
SNORA54
SNORD67
SNORA57
SNORD97
MIR610
MIR611
INS-IGF2
MUC5B
LOC729799
METTL12
C11orf83
MIR675
LOC100126784
C11orf91
FAM99B
LOC100133161
LOC100133545

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.13.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC2L1
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SFRS4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
KIAA0562
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SFRS13A
UTS2
RER1
RCAN3
MSTP2
MSTP9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KIAA1026
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
HSPC157
SSU72
UBIAD1
PADI1
PLA2G2E
WDR8
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
C1orf128
MAN1C1
NIPAL3
SEPN1
KIAA0495
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CCDC21
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
C1orf89
OR4F5
MUL1
NOL9
LIN28
AGMAT
NCRNA00115
MORN1
GRRP1
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCL1
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCL2
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
C1orf93
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
C1orf70
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
LOC441869
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH5P
PRAMEF16
FAM138C
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD99
MIR551A
CDC2L2
LOC728661
PRAMEF14
FLJ37453
OR4F29
SNHG3-RCC1
LOC100128003
LOC100128842
LOC100129534
FLJ39609
LOC100132062
LOC100132287
LOC100133331
LOC100133612
LOC100288778

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.3.

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

Genes
ABR
TIMM22
NXN
BHLHA9

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q14.

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

Genes
BUB1B
TCF12
C15orf55
C15orf21
hsa-mir-628
hsa-mir-1300
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
hsa-mir-211
hsa-mir-1268
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
BCL8
BNIP2
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RORA
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
SNURF
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TGM5
PIGB
HISPPD2A
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
MTMR15
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
KIAA1370
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
NARG2
C15orf29
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
GRINL1A
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LDHAL6B
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
FAM81A
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SLC24A5
PRTG
LOC283663
OR4N4
FAM98B
PLA2G4D
GOLGA6L1
GOLGA8G
GOLGA9P
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMML1
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P1
WHAMML2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC646214
CXADRP2
HSP90AB4P
MIR548A3
MIR626
MIR627
MIR628
LOC723972
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
LOC729082
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
HBII-52-24
HBII-52-27
HBII-52-28
HBII-52-45
HBII-52-46
MIR147B
LOC100129387
GOLGA8F
LOC100132724
GOLGA8D
JMJD7
PLA2G4B
FAM7A2

Genes in Wide Peak

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

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

Genes
MLLT4
MYB
TNFAIP3
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-548a-2
ACAT2
CCR6
EYA4
ESR1
FUCA2
GPR31
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
PEX7
PLAGL1
PLG
PSMB1
RPS6KA2
SGK1
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
PEX3
RNASET2
STX11
SYNJ2
MAP7
LATS1
QKI
TBPL1
WTAP
AKAP12
PHACTR2
BCLAF1
UST
CITED2
HBS1L
PDE10A
RAB32
KATNA1
RBM16
MAP3K7IP2
SASH1
SYNE1
HEBP2
CCDC28A
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
DLL1
MRPL18
CLDN20
NOX3
TFB1M
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
C6orf70
AGPAT4
TULP4
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
C6orf115
PBOV1
PERP
SMOC2
ALDH8A1
ULBP3
C6orf211
ZDHHC14
C6orf103
FRMD1
C6orf59
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
RSPH3
TTLL2
FBXO30
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
C6orf176
SYTL3
FAM54A
SFT2D1
C6orf72
IL22RA2
TAGAP
ADAT2
STXBP5
PACRG
RAET1E
LOC153910
C6orf94
CNKSR3
RAET1L
MGC34034
SLC2A12
PNLDC1
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCL
WDR27
SHPRH
LOC285735
LOC285740
LOC285796
PRR18
SLC35D3
ZC3H12D
ECT2L
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
TCP10L2
C6orf122
GTF2H5
LOC441177
SNORD101
SNORD100
SNORA33
RAET1K
C6orf124
SNORA20
SNORA29
LOC729176
LOC729603
HGC6.3
C6orf217
NHEG1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.3.

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

Genes
NOTCH2
NRAS
BCL10
PDE4DIP
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
ABCA4
ACADM
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1B
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FPGT
FUBP1
SLC16A4
CD101
SEP15
ZRANB2
ARHGAP29
SEC22B
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
TNNI3K
SH3GLB1
HAO2
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
C1orf103
CTTNBP2NL
C1orf183
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
SPATA1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
ST6GALNAC5
GPR61
REG4
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
C1orf203
FAM40A
ZNF697
NEXN
C1orf59
GBP4
GBP5
SSX2IP
OLFM3
WDR63
C1orf161
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
HFE2
SLC30A7
MGC27382
LOC149620
DENND2C
GBP6
LPPR5
FNDC7
SASS6
PPIAL4A
HFM1
UBL4B
ALG14
SPAG17
HIPK1
SLC44A5
AFARP1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
NEGR1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
HIST2H2BA
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
UOX
FRRS1
LOC400759
NBPF20
MIR137
MIR186
MIR197
LHX8
C1orf180
BCL2L15
LOC441897
LOC492303
RBMXL1
CYMP
PPIAL4G
LOC647121
LOC648740
NBPF6
PPIAL4B
PPIAL4C
FAM72B
SCARNA2
SNORD45C
MIR553
LOC728855
LOC728875
C1orf152
MIR942
MIR760
NBPF10
LOC100286793

Genes in Wide Peak

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

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
hsa-mir-30a
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1B
HTR1E
IMPG1
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
REV3L
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
PTP4A1
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDC2L6
MDN1
TSPYL4
KIAA0776
PHF3
ORC3L
MTO1
SFRS18
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
UBE2J1
LGSN
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
NCRNA00120
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
MANEA
C6orf155
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
C6orf168
GJA10
RTN4IP1
USP45
SLC22A16
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
C6orf150
SLC16A10
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SFRS13B
C6orf221
C6orf165
PRSS35
LCA5
KHDRBS2
C6orf163
C6orf185
AKD1
NT5DC1
HS3ST5
LACE1
C6orf167
SCML4
C6orf182
PPIL6
FLJ34503
DPPA5
EYS
GUSBL2
GJB7
SNHG5
C6orf147
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
LOC442245
RFPL4B
LOC553137
C6orf225
TSG1
SNORD50B
LOC728402
C6orf186
KHDC1L

Genes in Wide Peak

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

Table S38. 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 15q25.3.

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

Genes
ZNF592

Genes in Wide Peak

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

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

Genes
hsa-mir-155
hsa-mir-125b-2
APP
ATP5J
BACH1
BAGE
CXADR
GABPA
GRIK1
NCAM2
PRSS7
HSPA13
TPTE
NRIP1
CLDN8
ADAMTS1
RWDD2B
USP16
CCT8
BTG3
ADAMTS5
RNF160
CLDN17
N6AMT1
USP25
RBM11
NCRNA00158
NCRNA00157
NCRNA00113
C21orf15
MRPL39
C21orf91
C21orf7
JAM2
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
MIR155HG
CYYR1
NCRNA00161
KRTAP13-1
CHODL
C21orf99
LIPI
ABCC13
NCRNA00189
C21orf94
KRTAP15-1
C21orf71
KRTAP13-4
POTED
KRTAP19-1
KRTAP13-2
KRTAP13-3
KRTAP23-1
KRTAP6-3
KRTAP19-2
KRTAP19-3
KRTAP19-4
KRTAP19-5
KRTAP19-6
KRTAP19-7
C21orf131
C21orf34
KRTAP26-1
C21orf81
MIRLET7C
MIR125B2
MIR99A
NCRNA00110
KRTAP24-1
KRTAP27-1
KRTAP25-1
KRTAP22-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.2.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-1972
hsa-mir-140
AARS
AP1G1
AFG3L1
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
ST3GAL2
SPG7
TAT
ZNF19
ZNF23
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
FAM38A
DHX38
KIAA0174
ATP2C2
CLEC3A
CHST4
MPHOSPH6
COX4NB
TUBB3
CFDP1
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
ADAT1
CHST5
COG4
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
TXNL4B
BANP
PDPR
RFWD3
DDX19A
ZNF821
ZDHHC7
VAC14
FTSJD1
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
EXOSC6
C16orf46
LRRC50
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
IL34
FLJ30679
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LDHD
FUK
MLKL
ZNF778
ACSF3
C16orf81
HTA
LOC283922
NUDT7
PDXDC2
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
LOC390748
C16orf74
MIR140
CTRB2
CLEC18B
SNORD68
SNORD71
SNORD111
LOC732275
SNORD111B
LOC100129637
LOC100130015
SYCE1L

Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
hsa-mir-153-1
hsa-mir-375
hsa-mir-26b
hsa-mir-548f-2
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
IL8RA
IL8RB
IL8RBP
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
C2orf24
STK36
LOC29034
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
KIAA1486
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
C2orf67
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
PIKFYVE
TIGD1
CCDC108
C2orf72
C2orf85
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
PP14571

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-2110
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-608
hsa-mir-1287
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2E1
CYP17A1
DMBT1
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HMX2
HPS1
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
RGS10
SCD
SFRP5
FBXW4
SLC18A2
TAF5
TCF7L2
TECTB
TIAL1
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
DNMBP
FRAT2
RP11-529I10.4
SEC31B
ATRNL1
C10orf137
ANKRD2
CNNM1
PDCD4
VENTX
C10orf28
POLL
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
CHST15
ACSL5
ZRANB1
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CWF19L1
PI4K2A
HIF1AN
BRWD2
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
C10orf84
LHPP
MMS19
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
C10orf119
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
C10orf79
LRRC27
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
GPR123
LZTS2
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
KNDC1
ITPRIP
C10orf75
MTG1
NCRNA00081
FANK1
SYCE1
DHDPSL
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MORN4
ZFYVE27
MMP21
SFXN2
PDZD8
C10orf32
GSTO2
C10orf78
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
NKX2-3
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
C10orf93
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
ARMS2
C10orf122
GUCY2G
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FOXI2
GOLGA7B
FAM45A
C10orf62
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
LOC653543
LOC653544
LOC653545
LOC653548
SNORA12
MIR608
MIR609
LOC728410
LOC729020
TLX1NB
LOC100169752
NCRNA00093
LOC100270710

Genes in Wide Peak

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

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

Genes
hsa-mir-924
BRUNOL4

Genes in Wide Peak

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

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

Genes
GNA11
MLLT1
SH3GL1
STK11
TCF3
FSTL3
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-1227
hsa-mir-1909
hsa-mir-1302-2
AES
AMH
ATP5D
AZU1
HCN2
BSG
C3
CAPS
CD70
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
DNMT1
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
EMR1
FCER2
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
ICAM1
ICAM3
ICAM4
INSR
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NRTN
OAZ1
P2RY11
PALM
PIN1
POLR2E
POLRMT
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RFX2
RPS15
RPS28
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
THOP1
ICAM5
TLE2
TYK2
VAV1
ZNF121
ZNF177
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
EIF3G
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
S1PR2
TRIP10
LONP1
APBA3
SAFB2
MED16
CHAF1A
SH2D3A
EBI3
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4
TIMM44
SEMA6B
ZNF266
PNPLA6
UQCR
SBNO2
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
TIMM13
DAZAP1
OR7E24
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
SLC39A3
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
ZNF562
FBXL12
C19orf24
PLEKHJ1
C19orf66
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
MCOLN1
WDR18
REXO1
KIAA1543
ZNF317
ZNF77
C19orf29
UBL5
BRUNOL5
SLC25A23
ZNF426
FSD1
ZNF557
LASS4
TLE6
LPPR3
DENND1C
ZNF556
LRRC8E
UBXN6
OR4F17
ACSBG2
ADAMTS10
FAM108A1
DOHH
ANGPTL6
KLF16
PRAM1
ALKBH7
ZNF414
DOT1L
FBN3
ZNF559
KISS1R
CREB3L3
HDGF2
LMNB2
RAX2
MUM1
MPND
ATCAY
MBD3L1
MIDN
DPP9
C19orf22
C19orf6
C19orf20
CRB3
REEP6
PEX11G
ZNF561
OLFM2
MUC16
FDX1L
C19orf36
SCAMP4
ADAT3
ZNF554
EVI5L
GRIN3B
MRPL54
LRG1
RAVER1
OR7D4
OR7G1
OR1M1
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOBKL2A
C19orf28
GIPC3
NDUFA11
C19orf21
PLK5P
C2CD4C
ZNF358
ZNF560
TICAM1
C19orf23
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
ZNF846
OR7D2
PRR22
ANKRD24
C19orf59
C19orf26
C19orf34
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
C19orf77
C19orf30
SLC25A41
MBD3L5
ODF3L2
EMR4P
ADAMTSL5
CLEC4G
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
C3P1
ONECUT3
OR7G2
OR7G3
MEX3D
FLJ45445
PRSSL1
VMAC
CTXN1
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
FAM138F
LINGO3
ARRDC5
FAM138A
MBD3L4
MBD3L3
FAM138C
SNORD105
PPAN-P2RY11
MIR637
PLIN4
SNORD105B
ZGLP1
MIR220B
C19orf71
LOC100128573

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
CBLB
CTNNB1
FANCD2
FHIT
MITF
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
TFG
FOXP1
SETD2
PBRM1
hsa-mir-568
hsa-mir-567
hsa-mir-1324
hsa-mir-1284
hsa-mir-135a-1
hsa-let-7g
hsa-mir-566
hsa-mir-191
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-563
hsa-mir-885
ACAA1
ACVR2B
ACY1
ALAS1
ALCAM
AMT
APEH
ARF4
RHOA
ATP2B2
ATP6V1A
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CD47
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CPOX
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DRD3
DUSP7
CELSR3
EPHA3
FBLN2
FLNB
GAP43
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR15
GPR27
GPX1
GRM2
GRM7
HRH1
HTR1F
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LSAMP
LTF
MAP4
MOBP
CD200
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
POU1F1
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL24
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
WNT7A
ZNF35
ZNF80
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
CGGBP1
BHLHE40
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
GUCA1C
DZIP3
VGLL4
EDEM1
VPRBP
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
TOMM70A
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
CD96
EIF1B
TRAIP
ST3GAL6
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
TUSC4
CXCR6
CSPG5
CHL1
ARPP-21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
HHLA2
FAM107A
WDR6
RASSF1
NISCH
FILIP1L
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2L
MYH15
EXOSC7
PDZRN3
CAND2
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
C3orf63
KLHL18
LARS2
RYBP
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
C3orf17
WDR51A
ABI3BP
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
PVRL3
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
HACL1
ZBTB20
TTLL3
OR5K1
OR5H1
GNL3
ZBTB11
MORC1
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
GTPBP8
TAGLN3
PRSS50
RBM15B
GMPPB
LOH3CR2A
LMCD1
ARHGEF3
TRAT1
VILL
IMPG2
C3orf32
TRNT1
ABHD5
DYNC1LI1
C3orf18
CRBN
SS18L2
C3orf19
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
GRAMD1C
SIDT1
C3orf75
SNRK
QRICH1
PXK
CMTM6
RG9MTD1
SLC25A38
ULK4
OXSM
SLC35A5
TMEM45A
FEZF2
IFT57
FLJ10213
ANO10
DALRD3
SHQ1
ARL8B
SETD5
DPPA4
ZNF654
TMEM40
ABHD10
CHDH
IL17RB
NGLY1
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
TMEM111
C3orf10
ZNF167
LMOD3
CLDND1
RAD18
SEMA3G
NIT2
BBX
KIF15
ADAMTS9
PCBP4
PCNP
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
KIAA1407
WDR48
LRRN1
KIAA1524
SELK
PROK2
RNF123
NSUN3
CIDEC
ZFYVE20
KIF9
NFKBIZ
AZI2
MTMR14
ATG3
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
OR5H6
OR5H2
ZBED2
LRRC2
FYCO1
CEP97
C3orf52
QTRTD1
CCDC51
ZNF385D
HDAC11
THOC7
NAT13
WDR82
TSEN2
GRIP2
OR5AC2
RTP3
C3orf20
ID2B
ARL6
ATRIP
NICN1
MON1A
C3orf26
JAGN1
KBTBD8
C3orf42
RETNLB
CCDC54
IL17RC
ABHD14B
MINA
GPR128
C3orf39
EAF1
DCLK3
PHLDB2
UCN2
ZNF502
BOC
FAM55C
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
C3orf24
LRRC3B
GALNTL2
GPR62
KCNH8
FAM3D
ZPLD1
LYZL4
KBTBD5
TRIM71
CD200R1
CHCHD4
CRYBG3
DCBLD2
TMEM42
METTL6
C3orf31
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
SGOL1
C3orf48
EFHB
LOC151658
CPNE9
DPPA2
CCDC80
BTLA
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CCDC52
CMTM8
CCDC13
LOC152225
FGD5
CIDECP
CNTN4
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
ARL13B
DHFRL1
KLHDC8B
GABRR3
STT3B
DNAH12
PDE12
FAM116A
TIGIT
KIAA2018
CADM2
ZNF620
ZDHHC23
LOC255025
PLCXD2
GCET2
ALS2CL
TMIE
C3orf64
LOC285205
EPHA6
FBXW12
C3orf38
ZNF619
ZNF621
CCDC66
SLC9A10
C3orf23
ZNF660
LOC285359
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC285401
EIF4E3
CCDC36
C3orf35
GADL1
PRSS42
LOC344595
ZNF860
TMPRSS7
CD200R1L
DVWA
LNP1
TPRXL
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDH29
C3orf54
IQCF2
IQCF5
MUSTN1
VGLL3
VENTXP7
LOC401052
IQCF3
FLJ25363
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
STX19
LOC440944
TMEM89
IQCF6
LOC440957
MIR425
SNORA6
SNORA7A
TMPPE
TMEM30C
SPINK8
C3orf71
LOC646498
C3orf66
SNORD19
FAM86D
SNORD69
MIR563
MIR564
MIR567
MIR568
GLT8D4
FAM198A
CCR2
HESRG
LOC100009676
SNORD19B
MIR885
EGOT
GHRLOS
C3orf74
LOC100128640
LOC100129354
ZNF717
FRG2C
LOC100302640

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q31.1.

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

Genes
KLF5
BTF3L1
CLN5
DACH1
EDNRB
LMO7
PCDH9
POU4F1
ATXN8OS
UCHL3
SCEL
TBC1D4
SPRY2
PIBF1
KLF12
DIS3
MYCBP2
SLITRK5
FBXL3
NDFIP2
KLHL1
RBM26
RNF219
C13orf34
SLITRK6
SLITRK1
KCTD12
SLAIN1
COMMD6
OR7E156P
C13orf37
LOC647288
MIR548A2

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
hsa-mir-1297
hsa-mir-15a
hsa-mir-621
hsa-mir-320d-1
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
OR7E37P
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
C13orf1
COG6
XPO4
PCDH20
MRP63
NARG1L
RNASEH2B
DHRS12
C13orf18
C13orf23
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LOC121838
CSNK1A1L
RXFP2
C13orf26
PRR20A
C13orf30
C13orf31
HNRNPA1L2
FAM10A4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
LOC220115
LOC220429
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
DKFZp686A1627
OR7E156P
SUGT1L1
SIAH3
KCNRG
FLJ37307
SLC46A3
LOC284232
C1QTNF9
FREM2
NEK5
LOC348021
LOC374491
THSD1P
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
C13orf36
MIR15A
MIR16-1
ATP5EP2
ALG11
PCOTH
SNORA27
LOC646405
PRHOXNB
ZAR1L
LOC646982
SERPINE3
SNORA31
MIR621
C13orf38
PRR20B
PRR20C
PRR20D
PRR20E
LOC100101938
RPL21P28
LOC100188949
LOC100190939
LOC100288730

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.1.

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

Genes
hsa-mir-598
hsa-mir-1322
hsa-mir-124-1
hsa-mir-597
MSRA
TNKS
MFHAS1
PINX1
PPP1R3B
SOX7
ERI1
RP1L1
CLDN23
LOC157627
T-SP1
C8orf74
XKR6
MIR124-1
MIR597
MIR598

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q14.

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

Genes
BUB1B
TCF12
C15orf55
C15orf21
hsa-mir-628
hsa-mir-1300
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
hsa-mir-211
hsa-mir-1268
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
BCL8
BNIP2
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RORA
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
SNURF
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TGM5
PIGB
HISPPD2A
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
MTMR15
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
KIAA1370
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
NARG2
C15orf29
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
GRINL1A
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LDHAL6B
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
FAM81A
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SLC24A5
PRTG
LOC283663
OR4N4
FAM98B
PLA2G4D
GOLGA6L1
GOLGA8G
GOLGA9P
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMML1
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P1
WHAMML2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC646214
CXADRP2
HSP90AB4P
MIR548A3
MIR626
MIR627
MIR628
LOC723972
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
LOC729082
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
HBII-52-24
HBII-52-27
HBII-52-28
HBII-52-45
HBII-52-46
MIR147B
LOC100129387
GOLGA8F
LOC100132724
GOLGA8D
JMJD7
PLA2G4B
FAM7A2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.16 | 2.32 | 0.0663 | 0.13 | 0.653 | 0.626
1q | 1572 | 0.38 | 11.5 | 0 | 0.07 | -1.68 | 1
2p | 753 | 0.12 | -1 | 1 | 0.01 | -5.07 | 1
2q | 1235 | 0.09 | -1.47 | 1 | 0.00 | -5.2 | 1
3p | 853 | 0.04 | -3.62 | 1 | 0.20 | 2.33 | 0.0274
3q | 917 | 0.10 | -1.6 | 1 | 0.15 | 0.459 | 0.7
4p | 366 | 0.06 | -3.66 | 1 | 0.14 | -0.667 | 1
4q | 865 | 0.04 | -3.65 | 1 | 0.13 | -0.29 | 1
5p | 207 | 0.43 | 9.95 | 0 | 0.12 | -1.22 | 1
5q | 1246 | 0.15 | 1.01 | 0.611 | 0.19 | 2.56 | 0.0158
6p | 937 | 0.16 | 0.888 | 0.664 | 0.13 | -0.234 | 1
6q | 692 | 0.05 | -3.37 | 1 | 0.24 | 3.74 | 0.000457
7p | 508 | 0.37 | 8.51 | 0 | 0.08 | -2.44 | 1
7q | 1071 | 0.26 | 5.16 | 9.71e-07 | 0.07 | -2.25 | 1
8p | 495 | 0.14 | -0.284 | 1 | 0.35 | 7.58 | 6.58e-13
8q | 697 | 0.30 | 5.9 | 1.8e-08 | 0.13 | -0.397 | 1
9p | 343 | 0.03 | -4.09 | 1 | 0.29 | 5.19 | 1e-06
9q | 916 | 0.03 | -3.84 | 1 | 0.24 | 4.21 | 7.03e-05
10p | 312 | 0.10 | -1.94 | 1 | 0.13 | -1.07 | 1
10q | 1050 | 0.07 | -2.51 | 1 | 0.10 | -1.18 | 1
11p | 731 | 0.08 | -2.36 | 1 | 0.07 | -2.73 | 1
11q | 1279 | 0.11 | -0.81 | 1 | 0.09 | -1.6 | 1
12p | 484 | 0.14 | -0.542 | 1 | 0.17 | 0.521 | 0.691
12q | 1162 | 0.10 | -1.08 | 1 | 0.11 | -0.882 | 1
13q | 554 | 0.05 | -3.51 | 1 | 0.23 | 3.31 | 0.00184
14q | 1144 | 0.15 | 0.682 | 0.804 | 0.12 | -0.47 | 1
15q | 1132 | 0.04 | -3.54 | 1 | 0.21 | 3.39 | 0.00153
16p | 719 | 0.12 | -0.861 | 1 | 0.13 | -0.495 | 1
16q | 562 | 0.08 | -2.64 | 1 | 0.14 | -0.306 | 1
17p | 575 | 0.08 | -2.29 | 1 | 0.30 | 5.92 | 2.07e-08
17q | 1321 | 0.17 | 1.95 | 0.124 | 0.06 | -2.39 | 1
18p | 117 | 0.07 | -3.21 | 1 | 0.24 | 2.94 | 0.00533
18q | 340 | 0.05 | -3.53 | 1 | 0.27 | 4.34 | 4.63e-05
19p | 870 | 0.01 | -4.62 | 1 | 0.29 | 6.2 | 5.38e-09
19q | 1452 | 0.06 | -2.38 | 1 | 0.19 | 3.24 | 0.00211
20p | 295 | 0.19 | 1.29 | 0.43 | 0.20 | 1.63 | 0.134
20q | 627 | 0.21 | 2.22 | 0.0745 | 0.15 | 0.0635 | 0.974
21q | 422 | 0.12 | -1.36 | 1 | 0.14 | -0.474 | 1
22q | 764 | 0.06 | -3.01 | 1 | 0.26 | 4.51 | 2.53e-05

Methods & Data
Input

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/LUAD/1216565/2.GDAC_MergeDataFiles.Finished/LUAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

- Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

- CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt

- Amplification Threshold = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 205 Input Tumor Samples.

Tumor Sample Names
TCGA-05-4244-01A-01D-1877-01
TCGA-05-4249-01A-01D-1877-01
TCGA-05-4250-01A-01D-1877-01
TCGA-05-4382-01A-01D-1204-01
TCGA-05-4384-01A-01D-1752-01
TCGA-05-4389-01A-01D-1204-01
TCGA-05-4390-01A-02D-1752-01
TCGA-05-4395-01A-01D-1204-01
TCGA-05-4396-01A-21D-1854-01
TCGA-05-4397-01A-01D-1204-01

Figure 3. Segmented copy number profiles in the input data

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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

- Maintainer = Dan DiCara

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