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

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

Summary

There were 403 tumor samples used in this analysis: 27 significant arm-level results, 32 significant focal amplifications, and 45 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 32 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
14q13.3 | 6.7912e-55 | 6.7912e-55 | chr14:36648432-36782887 | 1
1q21.3 | 2.5583e-22 | 2.6246e-22 | chr1:150570986-151056062 | 16
5p15.33 | 1.0348e-23 | 3.9682e-21 | chr5:1288616-1300024 | 1
8q24.21 | 9.4204e-21 | 1.2017e-20 | chr8:128708285-128801947 | 1
12q15 | 1.2405e-18 | 4.3383e-13 | chr12:69212011-69244387 | 1
20q13.33 | 7.4601e-11 | 2.9311e-10 | chr20:62160482-63025520 | 40
12p12.1 | 3.0264e-09 | 3.3007e-09 | chr12:24880663-25401622 | 6
19q12 | 1.9777e-08 | 1.9777e-08 | chr19:30029296-30605958 | 6
3q26.2 | 9.9207e-08 | 9.9207e-08 | chr3:168745175-170832921 | 22
8p11.21 | 6.053e-08 | 4.0454e-07 | chr8:39869009-40197508 | 2
Xq28 | 6.7895e-07 | 6.7895e-07 | chrX:151841230-155270560 | 104
7p11.2 | 7.3324e-07 | 2.2869e-06 | chr7:54773427-55741100 | 4
7q31.2 | 6.9793e-06 | 6.9793e-06 | chr7:116283302-116609814 | 5
11q13.3 | 3.0311e-05 | 3.0311e-05 | chr11:68745684-69531424 | 8
17q23.1 | 4.7423e-05 | 0.00016072 | chr17:57921224-57958614 | 1
18q11.2 | 0.00098048 | 0.00098048 | chr18:21383413-21711032 | 2
12q14.1 | 2.5362e-09 | 0.00235 | chr12:58038861-58516999 | 16
6p21.1 | 0.0060968 | 0.012275 | chr6:40728123-42692619 | 34
1p22.3 | 0.0026512 | 0.014415 | chr1:85979933-86006008 | 1
17q12 | 0.005767 | 0.022602 | chr17:37804811-38011853 | 9
8q11.1 | 0.00023795 | 0.036128 | chr8:42932479-48685880 | 9
5p13.1 | 1.9701e-06 | 0.037264 | chr5:34993216-50133343 | 64
1p34.3 | 0.023175 | 0.040978 | chr1:39332033-44105169 | 77
4q12 | 0.05337 | 0.05337 | chr4:55115761-59188078 | 26
13q33.3 | 0.059902 | 0.059902 | chr13:88417803-115169878 | 120
5q35.1 | 0.1028 | 0.1028 | chr5:168407937-180915260 | 157
20q11.21 | 0.017793 | 0.14587 | chr20:30083473-30404273 | 8
7p21.1 | 0.14587 | 0.15766 | chr7:1-24965995 | 157
22q11.22 | 0.18233 | 0.18233 | chr22:18613558-23816427 | 110
18p11.32 | 0.18996 | 0.18996 | chr18:2536178-2785067 | 4
6p25.3 | 0.12697 | 0.19776 | chr6:1-17708051 | 101
10p15.1 | 0.20641 | 0.20641 | chr10:5027949-5217176 | 3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.3.

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

Genes
MBIP

Genes in Wide Peak

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

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

Genes
ARNT
CTSK
CTSS
ENSA
ANXA9
SETDB1
MLLT11
CERS2
C1orf56
GOLPH3L
FAM63A
CDC42SE1
PRUNE
HORMAD1
GABPB2
BNIPL

Genes in Wide Peak

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

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

Genes
TERT

Genes in Wide Peak

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

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

Genes
MYC

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

Genes in Wide Peak

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

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

Genes
hsa-mir-647
NPBWR2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
PCMTD2
SLC2A4RG
ZNF512B
C20orf195
DNAJC5
ZGPAT
PRIC285
ZBTB46
SAMD10
ABHD16B
LINC00266-1
C20orf201
LINC00176
MIR647
UCKL1-AS1
MIR941-1
MIR941-4
MIR941-2
MIR941-3
MIR1914
LOC100505815
RTEL1-TNFRSF6B

Genes in Wide Peak

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

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
C12orf77

Genes in Wide Peak

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

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

Genes
CCNE1
URI1
POP4
PLEKHF1
C19orf12
VSTM2B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
hsa-mir-569
MECOM
CLDN11
PRKCI
SKIL
SLC2A2
TERC
SEC62
TNIK
GPR160
MYNN
EIF5A2
SLC7A14
LRRC31
PHC3
ARPM1
LRRC34
RPL22L1
LRRIQ4
SAMD7
MIR569
LOC100128164

Genes in Wide Peak

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

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

Genes
C8orf4
IDO2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

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

Genes
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CETN2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
OPN1MW
GDI1
HCFC1
IDH3G
IL9R
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SPRY3
ZNF275
TREX2
SRPK3
SNORA70
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
PDZD4
FAM3A
FUNDC2
BRCC3
H2AFB3
PNMA6A
FAM58A
PNMA5
RAB39B
GAB3
PNCK
ZFP92
CSAG1
CTAG1A
MAGEA2B
LINC00204B
CSAG3
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CSAG2
CXorf68
LINC00204A
MTCP1NB
PNMA6C
PNMA6D
MIR1184-1
MIR718
MIR3202-2
MIR1184-3
MIR1184-2
MIR3202-1
LOC100507404

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2
VOPP1

Genes in Wide Peak

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

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

Genes
MET
CAPZA2
ST7
ST7-AS1
ST7-OT4

Genes in Wide Peak

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

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

Genes
CCND1
hsa-mir-3164
FGF19
MYEOV
MRGPRD
MRGPRF
TPCN2
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
TUBD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
LAMA3
TTC39C

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
hsa-mir-26a-2
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
OS9
METTL21B
XRCC6BP1
MARCH9
AGAP2
MIR26A2
LOC100130776
LOC100506844

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
BYSL
GUCA1A
GUCA1B
MDFI
NFYA
PGC
PRPH2
NCR2
MED20
FRS3
APOBEC2
UBR2
USP49
PRICKLE4
TREM2
TREM1
MRPS10
TRERF1
TREML2
FOXP4
TAF8
TREML2P1
LOC221442
C6orf130
TSPO2
UNC5CL
TREML4
TREML1
TREML3
C6orf132
TOMM6
MIR4641

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p22.3.

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

Genes
DDAH1

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
PNMT
TCAP
STARD3
IKZF3
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.1.

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

Genes
CEBPD
FNTA
PRKDC
KIAA0146
SGK196
HGSNAT
POTEA
LINC00293
LOC100287846

Genes in Wide Peak

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

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
C6
C7
C9
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
OXCT1
PRKAA1
PRLR
PTGER4
RPL37
SEPP1
SKP2
SLC1A3
ZNF131
OSMR
NUP155
PAIP1
MRPS30
NNT
TTC33
NIPBL
FBXO4
WDR70
CCL28
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
CARD6
LMBRD2
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR3650
LOC100506548
EGFLAM-AS4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.3.

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

Genes
MPL
MYCL1
hsa-mir-30c-1
BMP8B
CDC20
COL9A2
CTPS
EDN2
GUCA2A
GUCA2B
NDUFS5
NFYC
YBX1
PPT1
PTPRF
RLF
SLC2A1
TIE1
PABPC4
KCNQ4
RIMS3
ZMPSTE24
PPIE
PPIH
CAP1
EBNA1BP2
FOXJ3
SCMH1
SZT2
MACF1
MYCBP
HEYL
ZNF691
HPCAL4
TRIT1
RHBDL2
HIVEP3
OXCT2
LEPRE1
SMAP2
DEM1
ELOVL1
ZNF643
C1orf50
AKIRIN1
PPCS
GJA9
HYI
ZMYND12
NT5C1A
MFSD2A
MED8
ERMAP
TMCO2
ZNF684
TMEM125
CLDN19
WDR65
C1orf210
CITED4
SLFNL1
RIMKLA
ZNF642
BMP8A
CCDC23
MIR30C1
MIR30E
FLJ32224
FAM183A
KIAA0754
SNORA55
PPIEL
CCDC30
LOC100129924
LOC100130557
LOC100507178
GJA9-MYCBP

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
KDR
KIT
PDGFRA
IGFBP7
POLR2B
PPAT
REST
SPINK2
SRP72
CLOCK
CEP135
PAICS
NMU
EXOC1
TMEM165
KIAA1211
SRD5A3
NOA1
HOPX
ARL9
AASDH
PDCL2
LOC255130
LOC644145
LOC100506462
LOC100506564

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q33.3.

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
FGF14
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
RAP2A
GRK1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
OXGR1
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
TEX29
METTL21CP1
SPACA7
RNF113B
LINC00410
GPR180
CLYBL
METTL21C
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
FAM70B
C13orf35
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
FLJ44054
CCDC168
FLJ41484
MIR622
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
MIR3170
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4705

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.1.

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

Genes
NPM1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
BNIP1
CANX
CLTB
NKX2-5
DBN1
DOCK2
DRD1
DUSP1
F12
FGFR4
FOXI1
FLT4
GABRP
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
KCNMB1
LCP2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
SLC34A1
SLIT3
SNCB
STK10
ZNF354A
STC2
FGF18
SQSTM1
ATP6V0E1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
FBXW11
ZNF346
TSPAN17
OR4F3
PRELID1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
CCDC99
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
CNOT6
GMCL1P1
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
AGXT2L2
UNC5A
TRIM41
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
ZNF354B
C5orf47
C5orf58
OR2Y1
C5orf41
BTNL9
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
OR2V2
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
C5orf25
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
LOC728554
AACSP1
LOC729678
OR4F29
FAM196B
LOC100132062
LOC100132287
LOC100133331
LOC100268168
MIR1229
MIR4281
MIR3912
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ETV1
PMS2
CARD11
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ACTB
AHR
CLK2P
DGKB
DFNA5
GNA12
GPER
ICA1
IL6
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
NPY
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
DNAH11
CYTH3
PHF14
HDAC9
RAPGEF5
KIAA0415
ARL4A
GPNMB
AGR2
IGF2BP3
KDELR2
ADAP1
NUPL2
SNX13
IQCE
SUN1
SOSTDC1
OSBPL3
WIPI2
INTS1
TSPAN13
EIF2AK1
BZW2
SNX8
TRA2A
FTSJ2
NXPH1
GET4
CCZ1
MPP6
MIOS
RNF216
TOMM7
TMEM106B
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
CDCA7L
RADIL
KLHL7
STK31
PAPOLB
C1GALT1
FAM20C
ANKMY2
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM126A
C7orf70
SCIN
ZFAND2A
COX19
CCDC126
GLCCI1
KIAA1908
GPR146
C7orf30
AMZ1
AGR3
PER4
TMEM184A
VWDE
PRPS1L1
TWISTNB
SP8
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
FERD3L
RPL23P8
SLC29A4
RSPH10B
TMEM196
STEAP1B
RPS2P32
TFAMP1
UNCX
COL28A1
ABCB5
C7orf46
MACC1
LOC389458
ELFN1
AGMO
GRID2IP
ZNF815
RNF216P1
PMS2CL
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
SNORD93
MIR589
RSPH10B2
LOC729852
ISPD
LOC100131257
LOC100288524
MIR3146
LOC100506025
LRRC72
LOC100506178
RBAK-LOC389458
MIR4648
MIR4655
MIR4656
KLHL7-AS1

Genes in Wide Peak

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

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

Genes
BCR
CLTCL1
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
ARVCF
COMT
CRKL
GGT3P
GNAZ
GP1BB
GSC2
SERPIND1
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
VPREB1
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
TOP3B
P2RX6
SNAP29
RAB36
PPM1F
DGCR2
TXNRD2
USP18
HIC2
PRAME
TSSK2
SDF2L1
PPIL2
DGCR11
DGCR9
POM121L1P
DGCR5
DGCR10
FBXW4P1
TRMT2A
RTDR1
POM121L8P
YPEL1
ZDHHC8
MED15
TUBA8
DGCR8
GNB1L
MRPL40
RTN4R
C22orf29
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
GGTLC2
LOC96610
MGC16703
C22orf39
C22orf25
ZNF280A
ZNF280B
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
CCDC116
POM121L4P
LOC284865
PI4KAP2
LOC388849
LOC400891
BCRP2
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
TMEM191C
LOC648691
CES5AP1
MIR650
TMEM191B
PI4KAP1
LOC729444
MIR301B
MIR1286
MIR1306
IGLL5
MIR3618
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.32.

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

Genes
NDC80
SMCHD1
METTL4
CBX3P2

Genes in Wide Peak

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

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

Genes
IRF4
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
NOL7
FAM8A1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
CCDC90A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
C6orf195
PIP5K1P1
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
PSMG4
DKFZP686I15217
FLJ23152
C6orf201
ERVFRD-1
PPP1R3G
HULC
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

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

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

Genes
AKR1C2
AKR1C3
AKR1CL1

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 2.9988e-120 | 5.0716e-104 | chr9:21865498-21997722 | 2
22q13.32 | 8.089e-10 | 8.089e-10 | chr22:46748947-51304566 | 52
9p24.1 | 2.3405e-24 | 1.9318e-09 | chr9:8310705-12693402 | 1
1p13.1 | 3.9519e-10 | 5.2775e-09 | chr1:97280314-149881397 | 279
4q35.1 | 1.3799e-08 | 1.354e-07 | chr4:171523712-191154276 | 89
16q23.1 | 5.9098e-07 | 5.9893e-07 | chr16:78016120-90354753 | 123
13q12.11 | 1.4119e-17 | 2.503e-06 | chr13:1-20714074 | 11
11q25 | 2.6005e-06 | 2.5439e-06 | chr11:126870419-135006516 | 36
21q11.2 | 3.2547e-06 | 3.4196e-06 | chr21:1-16335988 | 22
9p13.1 | 2.5604e-09 | 8.8633e-06 | chr9:38619152-71152237 | 50
6q26 | 8.307e-07 | 1.4034e-05 | chr6:161693099-163153207 | 1
15q11.2 | 1.4871e-08 | 2.7324e-05 | chr15:1-27218028 | 136
8p23.2 | 3.5805e-06 | 4.8429e-05 | chr8:1897569-6262191 | 3
12p13.2 | 2.2248e-05 | 5.4881e-05 | chr12:2778972-18235892 | 231
18q21.32 | 4.6692e-08 | 6.0728e-05 | chr18:47335542-65185445 | 79
5q11.2 | 5.2819e-05 | 7.4742e-05 | chr5:58145167-60047770 | 4
Xp22.31 | 0.00017176 | 0.00017176 | chrX:6446594-9757524 | 15
13q12.13 | 2.1855e-11 | 0.00023246 | chr13:20795889-26788113 | 38
19p13.3 | 6.0871e-07 | 0.00033142 | chr19:1-437820 | 10
17p13.3 | 0.00063452 | 0.00065949 | chr17:1-3469852 | 73
10p15.3 | 0.0006954 | 0.00067179 | chr10:1-3183746 | 16
11p15.5 | 0.0013855 | 0.0013912 | chr11:1-10597049 | 270
19q13.33 | 0.0012696 | 0.0018716 | chr19:47174409-50374495 | 160
2q22.1 | 0.0015013 | 0.0034697 | chr2:139655617-143637838 | 1
19p13.2 | 3.0437e-05 | 0.0040041 | chr19:11040707-11207540 | 1
3q29 | 0.005249 | 0.0064609 | chr3:184081589-198022430 | 133
14q32.33 | 0.007576 | 0.0075399 | chr14:61440184-107349540 | 458
1p36.13 | 0.0018537 | 0.0079489 | chr1:1-31262836 | 493
12q24.33 | 0.011004 | 0.013073 | chr12:74674746-133851895 | 442
8p21.3 | 1.698e-05 | 0.014176 | chr8:18870505-31499098 | 117
10q26.3 | 0.013723 | 0.014176 | chr10:127698010-135534747 | 61
6q22.31 | 0.0002758 | 0.018081 | chr6:123955968-125232805 | 1
13q34 | 0.00086611 | 0.024764 | chr13:114086783-115169878 | 15
3p11.1 | 0.012347 | 0.073731 | chr3:86120087-96534596 | 15
18q23 | 8.7373e-07 | 0.098047 | chr18:54696384-78077248 | 93
3p26.3 | 0.017701 | 0.10377 | chr3:1-64082002 | 535
4q22.1 | 0.021602 | 0.10907 | chr4:58049079-139085918 | 356
6q12 | 0.035976 | 0.10907 | chr6:55266626-99284305 | 134
12p11.1 | 0.028245 | 0.11377 | chr12:33046522-42476143 | 11
2q37.3 | 0.026459 | 0.1227 | chr2:209359189-243199373 | 297
4p15.31 | 0.13332 | 0.13111 | chr4:1-52714468 | 275
15q15.3 | 0.00012576 | 0.14527 | chr15:1-53050428 | 389
3p21.31 | 0.0035399 | 0.17566 | chr3:15535703-84688247 | 478
5q34 | 0.12691 | 0.18771 | chr5:64314072-180915260 | 799
19p12 | 0.038667 | 0.23482 | chr19:23939307-28281863 | 4

Genes in Wide Peak

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

Table S33. 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 22q13.32.

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

Genes
hsa-mir-3201
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
CELSR1
PPP6R2
ZBED4
SCO2
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
FLJ46257
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR3201
MIR4535

Genes in Wide Peak

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

Table S35. 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 1p13.1.

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
VCAM1
WNT2B
CSDE1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
TTF2
ITGA10
CDC14A
RTCD1
PEX11B
SLC16A4
CD101
SEC22B
CHD1L
LRIG2
LPPR4
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
CD160
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
NBPF14
PTPN22
PHGDH
CHIA
RNF115
GPSM2
SLC25A24
BOLA1
HAO2
ACP6
SNX7
GPR89B
DPH5
GPR88
CCDC76
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
FAM91A2
AMIGO1
KIAA1324
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
DNAJA1P5
HENMT1
GNRHR2
OLFM3
MAB21L3
HIST2H3C
ATXN7L2
C1orf194
LRRC39
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
SLC30A7
RP11-165H20.1
DENND2C
LPPR5
FNDC7
SASS6
PPIAL4A
UBL4B
PDIA3P
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
MYBPHL
NBPF7
LOC375010
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
FRRS1
MIR137HG
NBPF9
MIR137
MIR197
LOC440600
BCL2L15
HIST2H2BF
PGCP1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
LOC648740
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
MIR548D1
MIR553
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
LOC729987
PPIAL4E
PFN1P2
MIR942
LOC100128787
LOC100129138
LOC100129269
LOC100129620
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
MIR548AA1
LOC100506343
MIR2682

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
ADAM29
SCRG1
FAM149A
FBXO8
DUX2
PDLIM3
GALNT7
CLDN22
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
LOC100506122
LOC100506229

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
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
C16orf7
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
PRDM7
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
C16orf61
JPH3
KIAA1609
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
MGC23284
LINC00311
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722

Genes in Wide Peak

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

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

Genes
TUBA3C
ZMYM2
ZMYM5
MPHOSPH8
PSPC1
TPTE2
PHF2P1
ANKRD20A9P
LINC00442
ANKRD26P3
LINC00421

Genes in Wide Peak

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

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

Genes
FLI1
APLP2
ETS1
KCNJ1
KCNJ5
NFRKB
OPCML
ST14
BARX2
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
PRDM10
TP53AIP1
JAM3
GLB1L2
VPS26B
GLB1L3
TMEM45B
ADAMTS15
C11orf45
SPATA19
KIRREL3-AS3
LOC283174
LOC283177
SNX19
LINC00167
LOC100128239
LOC100507392
MIR4697

Genes in Wide Peak

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

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

Genes
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
HSPA13
TPTE
RBM11
C21orf15
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
LIPI
ABCC13
POTED
LOC388813
ANKRD20A11P
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

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

Table S42. 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
FAM201A
CBWD5
LOC286297
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
FAM74A1
FAM74A4
ZNF658B
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
NBEAP1
GABRA5
GABRB3
IPW
NDN
SNRPN
UBE3A
MKRN3
PAR5
SNURF
CYFIP1
C15orf2
MAGEL2
ATP10A
NIPA2
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
LOC503519
CHEK2P2
LOC646214
CXADRP2
REREP3
LOC653061
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8DP
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715

Genes in Wide Peak

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

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

Genes
MYOM2
KBTBD11
CSMD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

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

Genes
CCND2
ETV6
ZNF384
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
KCNA1
KCNA5
KCNA6
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NOP2
NTF3
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTMS
PTPN6
PTPRO
PEX5
PZP
SCNN1A
SLC2A3
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
CSDA
DYRK4
GPRC5A
CD163
GDF3
CLSTN3
NCAPD2
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
RAD51AP1
KLRAP1
TSPAN9
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
PRMT8
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
PLBD1
NANOG
DUSP16
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
ACRBP
SPSB2
EFCAB4B
RERG
HTR7P1
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf53
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
CLEC9A
C12orf36
LOC283440
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
SCARNA12
SCARNA11
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.32.

Table S47. 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
CDH7
DCC
FECH
KDSR
GRP
LMAN1
SMAD4
MBD1
MC4R
ME2
MYO5B
NARS
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
SERPINB3
SERPINB4
TCF4
SERPINB7
TNFRSF11A
MBD2
TXNL1
ONECUT2
VPS4B
POLI
PHLPP1
NEDD4L
WDR7
PIGN
CDH20
CDH19
RAX
CXXC1
ST8SIA3
MEX3C
ZCCHC2
ZNF532
ELAC1
KIAA1468
CCDC68
MRO
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
STARD6
CCBE1
C18orf54
SKA1
CCDC11
RNF152
LINC00305
C18orf26
BOD1P
HMSD
LOC284294
CPLX4
LOC390858
LOC400654
MIR122
SCARNA17
SNORA37
LOC100287225
MIR4320
LOC100505474
LOC100505549
MIR4529
MIR3591

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1
DEPDC1B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.31.

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

Genes
hsa-mir-651
STS
KAL1
GPR143
TBL1X
HDHD1
PNPLA4
VCX
VCX2
VCX3A
FAM9A
FAM9B
VCX3B
MIR651
MIR4767

Genes in Wide Peak

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

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

Genes
hsa-mir-2276
PARP4
ATP12A
FGF9
MIPEP
PABPC3
SGCG
IFT88
MTMR6
NUPL1
SAP18
GJB6
SACS
LATS2
CRYL1
ATP8A2
IL17D
TNFRSF19
CENPJ
RNF17
XPO4
MRP63
FAM123A
N6AMT2
SKA3
EFHA1
SPATA13
ZDHHC20
C1QTNF9
TPTE2P6
C1QTNF9B
SHISA2
C1QTNF9B-AS1
BASP1P1
TPTE2P1
MIR2276
LINC00327
MIR4499

Genes in Wide Peak

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

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

Genes
hsa-mir-1302-11
PPAP2C
THEG
MIER2
OR4F17
C2CD4C
WASH5P
FLJ45445
FAM138F
FAM138A

Genes in Wide Peak

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

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

Genes
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ASPA
CRK
DPH1
HIC1
MNT
MYO1C
OR1D2
OR3A1
OR3A2
PAFAH1B1
SERPINF1
PITPNA
SERPINF2
RPA1
YWHAE
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
DOC2B
SCARF1
RPH3AL
SGSM2
PRPF8
RAP1GAP2
KIAA0664
SMG6
OR1A2
TIMM22
GEMIN4
GLOD4
INPP5K
RNMTL1
VPS53
TSR1
SRR
NXN
METTL16
FAM57A
RILP
SPATA22
MIR22HG
SMYD4
OVCA2
SLC43A2
WDR81
RTN4RL1
TRPV3
LOC284009
TUSC5
FAM101B
OR3A4P
C17orf97
MIR132
MIR212
MIR22
OR1D4
SNORD91A
SNORD91B
BHLHA9
TLCD2
DBIL5P
MIR1253
LOC100306951
MIR3183
LOC100506388

Genes in Wide Peak

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

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

Genes
ADARB2
IDI1
PFKP
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
IDI2-AS1
IDI2
LOC282980
TUBB8
LINC00200
LOC399708
C10orf108
ADARB2-AS1

Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPL27A
RPLP2
RRM1
SCT
SMPD1
TRIM21
ST5
STIM1
TAF10
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
TRIM66
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
OR7E12P
LYVE1
KCNQ1OT1
PKP3
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
FAM160A2
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
KRT8P41
LOC283104
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC644656
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MTRNR2L8
MIR210HG
MIR4686
MIR4485
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
AP2A1
BAX
BCAT2
C5AR1
CA11
CD37
CGB
AP2S1
CRX
DBP
EMP3
FCGRT
FLT3LG
FTL
FUT1
FUT2
GRIN2D
ARHGAP35
GYS1
HRC
PRMT1
IRF3
KCNA7
KCNJ14
LHB
LIG1
NPAS1
NTF4
NUCB1
PRRG2
RPL18
RPS11
RRAS
SEPW1
SLC1A5
SLC8A2
SNRNP70
SULT2B1
SULT2A1
TULP2
TEAD2
PPFIA3
PLA2G4C
NAPA
CYTH2
DHX34
SAE1
RUVBL2
KDELR1
KPTN
PNKP
CARD8
ZC3H4
RPL13A
SYNGR4
PPP1R15A
PRKD2
CCDC9
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
BBC3
DKKL1
GPR77
DHDH
SLC6A16
STRN4
GLTSCR2
GLTSCR1
EHD2
NOSIP
HSD17B14
PTOV1
TRPM4
FAM83E
RASIP1
TMEM160
PIH1D1
C19orf73
TMEM143
CABP5
SPHK2
MEIS3
SLC17A7
RCN3
PRR12
PLEKHA4
SCAF1
TSKS
ELSPBP1
LIN7B
FKRP
FUZ
MED25
BCL2L12
GRWD1
ZNF541
SNORD35B
CCDC114
CGB5
CGB7
CGB8
PTH2
CGB1
CGB2
LMTK3
CPT1C
ALDH16A1
NTN5
CCDC155
ZNF114
SPACA4
C19orf76
PRR24
TPRX1
MAMSTR
IZUMO1
MIR150
SEC1
SNORD23
RPL13AP5
SNAR-G1
SNAR-A1
SNAR-A2
SNAR-A12
BSPH1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-C1
SNAR-C3
SNAR-G2
SNAR-A14
MIR3191
MIR3190
MIR320E
MIR4324
LOC100505681
LOC100505812
LOC100506033
LOC100507003
MIR4749

Genes in Wide Peak

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

Table S56. 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 19p13.2.

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

Genes
SMARCA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

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

Genes
BCL6
EIF4A2
ETV5
LPP
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
AHSG
APOD
BDH1
CPN2
CRYGS
DGKG
DLG1
EHHADH
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
OPA1
PAK2
PCYT1A
PPP1R2
MASP1
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SST
THPO
TP63
CHRD
CLDN1
MAP3K13
ADIPOQ
KIAA0226
TNK2
IGF2BP2
CLDN16
NCBP2
VPS8
ACAP2
UBXN7
FETUB
DNAJB11
PIGX
TBCCD1
LEPREL1
LSG1
HRASLS
SENP2
RTP4
MAGEF1
ATP13A3
PIGZ
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
CEP19
LMLN
TMEM41A
TMEM44
TM4SF19
RPL39L
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
LIPH
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
TCTEX1D2
C3orf43
SDHAP1
UTS2D
C3orf70
TPRG1
LOC339926
LPP-AS2
LOC344887
RTP2
OSTN
ATP13A5
WDR53
ANKRD18DP
LRRC33
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
C3orf65
GMNC
LOC647323
SNORA81
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
LOC100131635
SNAR-I
MIR1248
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.33.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
SEL1L
SRSF5
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
ATP6V1D
EVL
C14orf129
CINP
ASB2
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
COX8C
ASPG
RAB15
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.33.

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

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

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

Genes
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
ADRA1A
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
EXTL3
PTK2B
GFRA2
GNRH1
GSR
GTF2E2
LOXL2
LPL
NEFM
NEFL
NKX3-1
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC18A1
STC1
FZD3
UBXN8
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
LEPROTL1
SLC39A14
ADAMDEC1
PURG
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
HMBOX1
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
CHMP7
NKX2-6
PEBP4
CDCA2
ESCO2
FBXO16
R3HCC1
LGI3
LOC254896
LOC286059
LOC286114
SCARA5
LOC286135
LOC389641
C8orf80
MIR320A
C8orf58
C8orf75
MBOAT4
LOC100128750
LOC100128993
MIR4287
MIR3148
MIR4288
MIR3622A
MIR3622B
LOC100507156
LOC100507341
MIR548O2

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
ADAM8
BNIP3
CYP2E1
DOCK1
ECHS1
INPP5A
MGMT
MKI67
PTPRE
ADAM12
UTF1
GLRX3
DPYSL4
TUBGCP2
DUX2
VENTX
CALY
TTC40
PPP2R2D
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
C10orf90
CTAGE7P
CLRN3
C10orf91
PWWP2B
PAOX
EBF3
TCERG1L
C10orf125
JAKMIP3
STK32C
LOC387723
FOXI2
FLJ46300
LOC399829
SPRNP1
FRG2B
SPRN
MIR202
NPS
LOC619207
FAM196A
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
MIR378C
MIR4297
MIR3944

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
NKAIN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q34.

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

Genes
ATP4B
GAS6
GRK1
TFDP1
CDC16
RASA3
TMCO3
DCUN1D2
UPF3A
CHAMP1
FAM70B
FLJ44054
FLJ41484
LINC00552
LOC100506394

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

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

Genes
EPHA3
HTR1F
POU1F1
PROS1
CGGBP1
CHMP2B
ZNF654
NSUN3
ARL13B
DHFRL1
LOC255025
C3orf38
VGLL3
STX19
MIR4795

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
CYB5A
FECH
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
SERPINB3
SERPINB4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
NEDD4L
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
ST8SIA3
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
CCBE1
CBLN2
FBXO15
DOK6
RNF152
LINC00305
BOD1P
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505549
LOC100505776
LOC100505817
MIR3591

Genes in Wide Peak

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

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

Genes
CTNNB1
FANCD2
FHIT
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
SETD2
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FBLN2
FLNB
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPX1
GRM2
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
RPL15
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
WNT7A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
BHLHE40
CADPS
HYAL2
HESX1
KAT2B
BSN
LIMD1
CCRL2
RPL14
SEC22C
RRP9
LRRFIP2
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
VPRBP
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
NPRL2
CXCR6
CSPG5
CHL1
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
CAND2
CLASP2
RAD54L2
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
DNAH1
HIGD1A
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LINC00312
LMCD1
ARHGEF3
VILL
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
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
ANO10
DALRD3
ARL8B
SETD5
TMEM40
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
TMEM111
BRK1
ZNF167
RAD18
SEMA3G
KIF15
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
LRRN1
SELK
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
THOC7
WDR82
TSEN2
GRIP2
RTP3
C3orf20
ID2B
ATRIP
NICN1
MON1A
JAGN1
GHRLOS2
IL17RC
ABHD14B
C3orf39
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
ZNF501
C3orf24
LRRC3B
GALNTL2
GPR62
KCNH8
FAM3D
LYZL4
KBTBD5
TRIM71
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
FGD5
CIDECP
CNTN4
XIRP1
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC285401
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
COL6A4P1
TPRXL
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VENTXP7
LOC401052
IQCF3
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
SNORA7A
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
MIR563
MIR564
FAM198A
CCR2
ESRG
SNORD19B
MIR885
EGOT
GHRLOS
C3orf74
LOC100128640
NRADDP
LOC100129480
LOC100132146
LOC100132526
BSN-AS2
PRSS46
LOC100287879
LOC100288428
MIR1226
MIR711
MIR4270
MIR4271
MIR3938
MIR3714
FGD5-AS1
LOC100505696
KRBOX1
IQCF4
LOC100506994
LOC100507062
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4791
MIR4790
MIR548AC
MIR4443
MIR4792
MIR4442
LUST

Genes in Wide Peak

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

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

Genes
IL2
RAP1GDS1
TET2
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
hsa-mir-1269
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
ALB
AMBN
ANK2
ANXA3
ANXA5
AREG
ART3
ATOH1
BMP3
BMPR1B
BTC
CAMK2D
CASP6
CCNA2
CCNG2
SCARB2
CDS1
CENPC1
CENPE
CSN1S1
CSN2
CSN3
DCK
DMP1
DSPP
EGF
EIF4E
ENPEP
EPHA5
EREG
FABP2
FGF2
FGF5
GC
GK2
GNRHR
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
H2AFZ
HADH
HNRNPD
HSP90AB3P
HTN1
HTN3
IBSP
CFI
IGJ
IL8
CXCL10
MAD2L1
MANBA
CXCL9
AFF1
MTTP
MUC7
NFKB1
NKX6-1
PDHA2
PF4
PF4V1
PITX2
PKD2
EXOSC9
PPEF2
PPBP
PPP3CA
PRKG2
MAPK10
PTPN13
RPL34
CXCL6
CXCL11
CXCL5
SNCA
SPP1
STATH
SULT1E1
TACR3
TRPC3
UBE2D3
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
SPARCL1
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
HERC3
STBD1
CDKL2
PAPSS1
AIMP1
NDST3
TMPRSS11D
ABCG2
ADAMTS3
SEC24D
G3BP2
HNRPDL
TSPAN5
ENAM
FAM13A
SPRY1
PGRMC2
SEC24B
CXCL13
PDLIM5
RRH
UGT2B11
PLK4
HPSE
SMR3B
NPFFR2
PPBPL2
UGT2A1
CCNI
PRDM5
NUDT6
HSPA4L
SEC31A
RUFY3
MMRN1
WDFY3
METAP1
LPHN3
PARM1
RCHY1
ANKRD17
STAP1
SMR3A
PPA2
DAPP1
DKK2
INTU
NAAA
COQ2
SULT1B1
HPGDS
TMPRSS11E
MRPS18C
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
MYOZ2
NUDT9
NUP54
GAR1
UGT2B28
PCDH18
USP53
ARHGEF38
ODAM
HERC6
CCDC109B
BANK1
LARP1B
SDAD1
BBS7
UBA6
C4orf21
AP1AR
BMP2K
SEPT11
BDH2
SMARCAD1
MEPE
PRDM8
UTP3
INTS12
ANKRD50
KLHL8
PCDH10
SHROOM3
METTL14
ENOPH1
PROL1
OSTC
IL21
NEUROG2
SLC39A8
NDST4
AGXT2L1
MRPL1
ELOVL6
NDNF
FAT4
ARSJ
THAP9
UGT2A3
GSTCD
TNIP3
PHF17
SCD5
DNAJB14
FRAS1
C4orf29
ALPK1
CXXC4
PLA2G12A
SLC25A31
ARHGAP24
C4orf17
QRFPR
FAM175A
KIAA1109
COL25A1
NAA11
AGPAT9
PIGY
CABS1
FLJ20021
YTHDC1
MOB1B
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
GDEP
ANTXR2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
LIN54
C4orf32
TMPRSS11B
C4orf36
TRAM1L1
SLC9B2
SLC9B1
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
SPATA5
BBS12
TIGD2
RASSF6
SGMS2
SYNPO2
CNOT6L
TECRL
C4orf22
EPGN
NPNT
MFSD8
LOC256880
FDCSP
NAP1L5
LOC285419
LOC285456
FAM13A-AS1
GPRIN3
COX18
C4orf37
CSN1S2AP
CCDC158
TMPRSS11A
SOWAHB
LRIT3
SLC10A6
HSD17B13
PCNAP1
TMPRSS11F
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
FLJ14186
C4orf3
WDFY3-AS2
MIR302A
C4orf11
MTHFD2L
LOC441025
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC550112
LOC550113
UGT2A2
LOC641365
LOC641518
LOC644248
TMPRSS11GP
CEP170P1
LOC645513
SNORA24
MIR575
MIR577
CETN4P
SNHG8
FAM47E
FTLP10
LOC100144602
PP12613
MIR1243
MIR2054
MIR1973
CSN1S2BP
LOC100499177
MIR3684
LOC100505702
LOC100505875
LOC100506035
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4450
MIR4451
FAM47E-STBD1

Genes in Wide Peak

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

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
BAI3
BCKDHB
BMP5
DST
CGA
CNR1
COL9A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
GABRR1
GABRR2
HTR1B
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
PRIM2
RNY4
ELOVL4
MAP3K7
TPBG
TTK
PTP4A1
RNGTT
TBX18
HMGN3
FHL5
BAG2
SNAP91
CASP8AP2
SYNCRIP
SLC35A1
FUT9
PNRC1
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
MDN1
UFL1
PHF3
ORC3
MTO1
IBTK
ZNF451
SENP6
SLC17A5
SNORD50A
FILIP1
NDUFAF4
CYB5R4
UBE2J1
LGSN
RAB23
HMGCLL1
PHIP
AKIRIN2
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
C6orf162
LYRM2
SNX14
FAM135A
KIAA1586
RRAGD
BACH2
SMAP1
C6orf164
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
COL21A1
SPACA1
SH3BGRL2
GJA10
C6orf7
UBE2CBP
MRAP2
RWDD2A
KLHL32
MB21D1
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
PRSS35
LCA5
KHDRBS2
C6orf163
BEND6
MMS22L
DPPA5
EYS
GUSBP4
GJB7
SNHG5
C6orf147
MIR30A
MIR30C2
OOEP
MCART3P
TSG1
SNORD50B
KHDC1L
LOC100288198
MIR2113
MIR548H3
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p11.1.

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

Genes
ABCD2
CNTN1
PDZRN4
KIF21A
ALG10
SLC2A13
LRRK2
ALG10B
CPNE8
C12orf40
SYT10

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
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
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
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
CNPPD1
STK36
CPS1-IT1
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
NYAP2
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
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

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

Genes
FGFR3
WHSC1
PHOX2B
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
APBB2
RHOH
ATP5I
NKX3-2
BST1
CCKAR
CD38
CNGA1
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GRK4
HTT
HGFAC
UBE2K
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RFC1
RGS12
RNF4
RPL9
S100P
SH3BP2
SOD3
TEC
TLR1
TXK
UCHL1
UGDH
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
TLR6
PCGF3
ATP8A1
SPON2
TACC3
SLC30A9
SLC34A2
MXD4
CORIN
PTTG2
CPLX1
SLC26A1
PPARGC1A
LIAS
LIMCH1
TBC1D1
SEL1L3
PDS5A
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
KLHL5
SEPSECS
KLF3
STX18
FGFRL1
CYTL1
SH3TC1
RBM47
PIGG
DCAF16
OCIAD1
COMMD8
TMEM33
LGI2
PGM2
C4orf19
TBC1D19
PI4K2B
CNO
STK32B
CHRNA9
LYAR
N4BP2
SLC2A9
ATP10D
KIAA1239
TBC1D14
SORCS2
CC2D2A
SLAIN2
STIM2
KIAA1530
WDR19
ZFYVE28
GBA3
AFAP1
GUF1
NCAPG
TNIP2
HAUS3
FLJ13197
NSUN7
ABCA11P
TMEM156
CWH43
GRPEL1
MED28
KCNIP4
TLR10
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
FAM114A1
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
ARAP2
OCIAD2
GNPDA2
CPEB2
EVC2
PACRGL
OTOP1
NFXL1
NIPAL1
SHISA3
ZNF595
LOC152742
JAKMIP1
KLB
FAM53A
METTL19
GPR125
ZBTB49
COX7B2
ZNF721
SLC10A4
C4orf34
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
DCAF4L1
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
YIPF7
FRYL
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
ZAR1
NAT8L
LOC344967
C4orf44
FAM86EP
POLN
KCNIP4-IT1
KCTD8
C4orf52
BEND4
GRXCR1
USP17L6P
USP17
HSP90AB2P
C4orf48
DTHD1
LOC401127
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
MIR574
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
RELL1
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4802
MIR4800
MIR4801
MIR4798
HTT-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.3.

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

Genes
BUB1B
C15orf55
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
OCA2
PLCB2
MAPK6
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
HMGN2P46
SLC24A5
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
USP50
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B

Genes in Wide Peak

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

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

Genes
CTNNB1
FHIT
MITF
MLH1
MYD88
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
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
SATB1
ATXN7
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
THRB
TKT
TMF1
CLEC3B
TNNC1
TOP2B
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
EOMES
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SLC4A7
VPRBP
TBC1D5
IP6K1
EPM2AIP1
PSMD6
TRANK1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
CRTAP
ARL6IP5
NPRL2
CXCR6
CSPG5
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
RYBP
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
HACL1
GNL3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
VILL
ABHD5
DYNC1LI1
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
KIF9
AZI2
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
ZNF385D
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
LRRC3B
GALNTL2
GPR62
KCNH8
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
SGOL1
PP2D1
EFHB
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
DPH3
LOC285401
EIF4E3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VENTXP7
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR563
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
LOC100128640
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
MIR3938
MIR3714
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4791
MIR548AC
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q34.

Table S76. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
APC
CD74
EBF1
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
HARS
HEXB
HINT1
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
KCNN2
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MFAP3
MGAT1
MSH3
MSX2
NAIP
NDUFA2
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
ATG12
PTTG1
PDLIM7
NREP
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
APBB3
TNIP1
GNB2L1
NSA2
SLU7
POLR3G
RGS14
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
SOX30
KIF3A
ADAMTS6
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
PPWD1
HARS2
OTP
ZNF346
SSBP2
BHMT2
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FLJ11235
FAM193B
SGTB
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
CCDC99
THG1L
AGGF1
WDR41
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
ZNF608
KCTD16
SEMA6A
ARRDC3
PCDHB16
ANKRA2
HMHB1
C5orf54
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1P1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
TRIM52
HAVCR2
AGXT2L2
C5orf62
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
FCHO2
LYSMD3
LEAP2
SCGB3A2
ZNF354B
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
C5orf58
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
LOC153469
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
CCDC125
C5orf27
CMYA5
STK32A
AQPEP
SLC36A1
EIF4E1B
RASGEF1C
ANKRD31
SERINC5
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
RGMB
RFESD
CHSY3
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
ANKRD34B
PFN3
ZNF879
IRGM
FBLL1
FAM174A
MTX3
CATSPER3
NIPAL4
SLCO4C1
TICAM2
DND1
MAST4
C5orf25
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
CRSP8P
FLJ42709
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
FLJ35946
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
TMEM232
LOC643201
GRXCR2
SPINK9
ZFP62
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
CBY3
LOC647859
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR583
MIR585
SNHG4
MIR143HG
GTF2H2C
LOC728342
SERF1B
LOC728554
LOC728723
LOC729080
AACSP1
LOC729678
OR4F29
GTF2H2D
GUSBP9
VTRNA2-1
MIR874
LOC100129716
LOC100131067
FAM196B
LOC100132062
LOC100132287
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR1244-3
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MTRNR2L2
MIR3607
MIR3655
MIR3660
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505841
LOC100505894
OCLN
LOC100507387
MIR4804
MIR4633
MIR4634
MIR4461
MIR3977
MIR4460
MIR4638
MIR4803
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p12.

Table S77. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZNF254
RPSAP58
ZNF726
LOC100101266

Arm-level results

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

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.32 | 3.23 | 0.00304 | 0.24 | -0.0866 | 0.93
1q | 1955 | 0.61 | 15.4 | 0 | 0.26 | 0.438 | 0.654
2p | 924 | 0.33 | 0.505 | 0.943 | 0.10 | -7.87 | 1
2q | 1556 | 0.30 | 1.01 | 0.547 | 0.09 | -7.22 | 1
3p | 1062 | 0.11 | -6.44 | 1 | 0.46 | 6.6 | 8.11e-11
3q | 1139 | 0.20 | -3.64 | 1 | 0.37 | 2.81 | 0.00713
4p | 489 | 0.18 | -6.01 | 1 | 0.29 | -2.19 | 1
4q | 1049 | 0.11 | -7.5 | 1 | 0.29 | -0.594 | 1
5p | 270 | 0.54 | 6.83 | 4.34e-11 | 0.34 | -0.57 | 1
5q | 1427 | 0.28 | -0.258 | 1 | 0.42 | 5.54 | 4.95e-08
6p | 1173 | 0.35 | 1.91 | 0.111 | 0.34 | 1.4 | 0.18
6q | 839 | 0.18 | -4.47 | 1 | 0.51 | 7.68 | 4.38e-14
7p | 641 | 0.55 | 8.69 | 0 | 0.17 | -4.81 | 1
7q | 1277 | 0.45 | 6.53 | 2.61e-10 | 0.17 | -4.3 | 1
8p | 580 | 0.31 | -0.717 | 1 | 0.55 | 8.18 | 7.4e-16
8q | 859 | 0.50 | 7.17 | 4.89e-12 | 0.24 | -2.46 | 1
9p | 422 | 0.14 | -5.92 | 1 | 0.57 | 8.97 | 0
9q | 1113 | 0.11 | -5.93 | 1 | 0.51 | 8.84 | 0
10p | 409 | 0.25 | -3.45 | 1 | 0.28 | -2.39 | 1
10q | 1268 | 0.19 | -3.88 | 1 | 0.30 | 0.404 | 0.654
11p | 862 | 0.23 | -3.57 | 1 | 0.25 | -2.54 | 1
11q | 1515 | 0.25 | -1.14 | 1 | 0.23 | -1.78 | 1
12p | 575 | 0.33 | -0.288 | 1 | 0.28 | -2.01 | 1
12q | 1447 | 0.29 | 0.22 | 1 | 0.24 | -1.77 | 1
13q | 654 | 0.16 | -5.19 | 1 | 0.52 | 7.51 | 1.43e-13
14q | 1341 | 0.31 | 0.977 | 0.547 | 0.30 | 0.36 | 0.654
15q | 1355 | 0.14 | -4.85 | 1 | 0.49 | 8.56 | 0
16p | 872 | 0.31 | -0.454 | 1 | 0.31 | -0.286 | 1
16q | 702 | 0.26 | -2.63 | 1 | 0.37 | 1.42 | 0.18
17p | 683 | 0.22 | -3.34 | 1 | 0.55 | 8.69 | 0
17q | 1592 | 0.40 | 5.2 | 6.69e-07 | 0.24 | -1.13 | 1
18p | 143 | 0.27 | -3.21 | 1 | 0.43 | 2.68 | 0.00995
18q | 446 | 0.20 | -4.65 | 1 | 0.49 | 5.84 | 9.27e-09
19p | 995 | 0.11 | -6.29 | 1 | 0.52 | 8.82 | 0
19q | 1709 | 0.18 | -3.15 | 1 | 0.38 | 4.67 | 4.69e-06
20p | 355 | 0.42 | 2.38 | 0.038 | 0.36 | 0.367 | 0.654
20q | 753 | 0.43 | 3.88 | 0.000299 | 0.26 | -2.11 | 1
21q | 509 | 0.28 | -2.06 | 1 | 0.41 | 2.51 | 0.015
22q | 921 | 0.20 | -3.76 | 1 | 0.48 | 6.89 | 1.25e-11
Xq | 1312 | 0.16 | -5.22 | 1 | 0.19 | -3.95 | 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.

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/LUAD-TP/2328537/2.GDAC_MergeDataFiles.Finished/LUAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 403 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

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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