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

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

Summary

There were 230 tumor samples used in this analysis: 28 significant arm-level results, 27 significant focal amplifications, and 40 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 - 27 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 2.2653e-26 2.2653e-26 chr14:36854137-37023019 2
8q24.21 1.7015e-17 1.8767e-17 chr8:129157821-129195260 2
5p15.33 8.8939e-16 4.6947e-14 chr5:1288616-1300024 1
12q15 2.7778e-16 7.4235e-13 chr12:69212011-69485451 2
1q21.3 7.2055e-10 7.2055e-10 chr1:120523956-152743148 173
12p12.1 1.3322e-05 1.5056e-05 chr12:25402469-26433911 8
20q13.33 1.5774e-07 1.9978e-05 chr20:62090554-63025520 43
7p11.2 1.5173e-05 7.0892e-05 chr7:54535672-55737616 6
Xq28 0.00031917 0.00031917 chrX:153306080-155270560 58
7q31.2 0.00059128 0.00059128 chr7:116283302-116449049 1
3q26.2 0.00068905 0.00068905 chr3:168804384-170787300 20
19q13.11 0.0024887 0.0024887 chr19:29099880-38092168 143
11q13.3 0.0026573 0.0026573 chr11:68745684-69587582 8
6p21.1 0.011819 0.011819 chr6:37381636-42861797 59
12q14.1 6.6171e-09 0.017674 chr12:58038861-58369932 16
17q12 0.005914 0.019017 chr17:37804811-38011853 9
5p13.2 5.0471e-05 0.04864 chr5:33498056-50133375 75
17q25.3 0.039508 0.073911 chr17:47675684-81195210 458
8p11.21 7.4585e-05 0.079818 chr8:39869009-40368804 2
20p11.21 0.087505 0.087505 chr20:21919726-24012524 23
8p11.21 6.4231e-05 0.089784 chr8:41181422-42823083 22
1p22.3 0.099142 0.099142 chr1:85979933-86006008 1
20q13.2 8.3843e-06 0.11033 chr20:51999924-53234727 8
18q11.2 0.11639 0.11639 chr18:20332270-21711032 10
8q11.1 0.012177 0.14847 chr8:42729980-70207915 106
3p11.1 0.16985 0.16985 chr3:88467818-89017633 0 [EPHA3]
7p21.1 0.1786 0.19204 chr7:1-28267875 193
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
NKX2-1
SFTA3
Genes in Wide Peak

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

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

Genes
hsa-mir-1208
MIR1208
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 12q15.

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

Genes
MDM2
CPM
Genes in Wide Peak

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

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

Genes
ARNT
BCL9
NOTCH2
PDE4DIP
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
CTSK
CTSS
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
MCL1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A10
S100A11
VPS72
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
SV2A
RBM8A
SF3B4
PIAS3
SEMA6C
POLR3C
TXNIP
MTMR11
MLLT11
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
CA14
NBPF14
LCE2B
RNF115
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
FAM63A
CDC42SE1
OTUD7B
FAM91A2
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
HIST2H3C
LIX1L
C1orf51
HFE2
ANKRD35
BNIPL
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
LINGO4
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
NBPF9
HIST2H2BF
KPRP
HIST2H4B
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
C1orf68
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
TNFAIP8L2-SCNM1
Genes in Wide Peak

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

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

Genes
KRAS
hsa-mir-4302
SSPN
RASSF8
BHLHE41
IFLTD1
MIR4302
LOC100506451
Genes in Wide Peak

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

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

Genes
hsa-mir-647
EEF1A2
NPBWR2
KCNQ2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
PCMTD2
SLC2A4RG
ZNF512B
C20orf195
PPDPF
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 7p11.2.

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

Genes
EGFR
SEC61G
LANCL2
VOPP1
VSTM2A
LOC285878
Genes in Wide Peak

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

Table S9.  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
ATP6AP1
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
EMD
F8
FLNA
G6PD
OPN1MW
GDI1
IL9R
MECP2
MPP1
OPN1LW
RPL10
VAMP7
TAZ
VBP1
F8A1
UBL4A
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
SPRY3
SNORA70
CTAG2
TMLHE
PLXNA3
FAM3A
FUNDC2
BRCC3
H2AFB3
RAB39B
GAB3
CTAG1A
LINC00204B
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CXorf68
LINC00204A
MTCP1NB
MIR1184-1
MIR1184-3
MIR1184-2
LOC100507404
Genes in Wide Peak

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

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

Genes
MET
Genes in Wide Peak

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

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

Genes
MECOM
CLDN11
PRKCI
SKIL
SLC2A2
TERC
SEC62
TNIK
GPR160
MYNN
EIF5A2
SLC7A14
LRRC31
PHC3
ARPM1
LRRC34
RPL22L1
LRRIQ4
SAMD7
LOC100128164
Genes in Wide Peak

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

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

Genes
CEBPA
APLP1
ATP4A
CAPNS1
CCNE1
CD22
CEBPG
TBCB
COX6B1
COX7A1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
LRP3
MAG
NPHS1
PEPD
FXYD1
FXYD3
POLR2I
SCN1B
TYROBP
UQCRFS1
USF2
ZNF146
URI1
PDCD5
KIAA0355
ZNF536
MLL4
UBA2
TMEM147
POP4
HCST
UPK1A
SLC7A9
ZNF507
HAUS5
ZNF345
CLIP3
LSM14A
GAPDHS
ZBTB32
ZNF571
LSR
FXYD7
FXYD5
GPATCH1
PSENEN
ZNF302
LIN37
SLC7A10
TSHZ3
GRAMD1A
ZFP14
ZNF529
HAMP
PRODH2
CHST8
KCTD15
PLEKHF1
RBM42
LRFN3
IGFLR1
LOC80054
C19orf12
KIRREL2
ANKRD27
PDCD2L
ZNF527
NFKBID
CEP89
ZNF382
ZNF566
ALKBH6
RHPN2
ZNF30
C19orf40
TDRD12
ZNF461
ZNF585B
DMKN
DKFZp566F0947
ARHGAP33
WDR88
WTIP
ZNF792
HSPB6
ZNF420
ZNF565
DPY19L3
ZNF599
FAM187B
C19orf55
LOC148145
ZNF569
ZNF570
ZNF567
ZNF383
LGI4
C19orf46
ZNF540
ZNF585A
THAP8
U2AF1L4
LOC284395
SCGB2B2
WDR62
ZFP82
LOC284408
LOC284412
HKR1
ZNF181
ZNF260
VSTM2B
ZNF850
SBSN
ZNF829
ZNF568
RGS9BP
KRTDAP
ZNF790
NUDT19
ZNF793
LOC400684
LOC400685
SCGB1B2P
SDHAF1
LOC644189
LOC728752
LOC100128675
LOC100128682
SCGB2B3P
LOC100134317
LOC100505835
LOC100506469
LOC100506930
LOC100507433
THEG5
LOC100652909
Genes in Wide Peak

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

Table S13.  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 6p21.1.

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

Genes
CCND3
TFEB
BYSL
DNAH8
GLO1
GLP1R
GUCA1A
GUCA1B
MDFI
MOCS1
NFYA
PGC
PRPH2
TBCC
KCNK5
NCR2
MED20
FRS3
APOBEC2
FTSJD2
UBR2
DAAM2
KIAA0240
USP49
PRICKLE4
TREM2
TREM1
MRPS10
SAYSD1
TRERF1
LRFN2
ZFAND3
TREML2
KCNK16
KCNK17
BTBD9
FOXP4
TAF8
CCDC167
TREML2P1
LOC221442
C6orf130
KIF6
TSPO2
UNC5CL
MDGA1
TREML4
RPL7L1
TREML1
TREML3
FLJ41649
C6orf226
ATP6V0CP3
C6orf132
TDRG1
LOC100131047
TOMM6
MIR4641
MIR4462
Genes in Wide Peak

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

Table S15.  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 17q12.

Table S16.  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 5p13.2.

Table S17.  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
RAD1
RPL37
SEPP1
SKP2
SLC1A3
ZNF131
OSMR
NUP155
PAIP1
MRPS30
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
SLC45A2
RXFP3
WDR70
BRIX1
CCL28
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

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

Genes
CD79B
CLTC
COL1A1
DDX5
HLF
PRKAR1A
ASPSCR1
BRIP1
MSI2
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
CHAD
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
DLX3
DLX4
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGA3
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NME1
NME2
NPTX1
P4HB
PDE6G
PDK2
PECAM1
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGCA
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
SPOP
PPM1D
DGKE
CBX4
DNAH17
ABCC3
RGS9
GALR2
SPHK1
CACNA1G
SOCS3
SPAG9
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
TOB1
ALYREF
SLC35B1
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
RAB40B
TLK2
KAT7
POLG2
CD300A
TMC6
DDX42
PPM1E
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
UTP18
RNFT1
HN1
TUBD1
DCXR
TACO1
MRPL27
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
LUC7L3
SDK2
FAM20A
MBTD1
BCAS3
TMEM104
RNF43
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
SMG8
TMEM100
RSAD1
LRRC59
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45L
CA10
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
XYLT2
DNAI2
SMURF2
ENGASE
SPATA20
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
ACSF2
C17orf70
LIMD2
KCNH6
FAM117A
VMP1
TSPAN10
MYCBPAP
QRICH2
KIF2B
USP32
PPP1R9B
CBX2
FAM104A
MGC16275
FBF1
UNK
CEP95
TRIM47
ANKRD40
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
WFIKKN2
TBC1D16
AFMID
DYNLL2
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
EME1
NOTUM
TMC8
ANKFN1
MARCH10
TMEM92
CEP112
SAMD14
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MTVR2
STXBP4
LOC253962
TAC4
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
LOC284080
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
HILS1
LRRC37A3
RNF126P1
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
LOC400604
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
MIR142
MIR21
MIR301A
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LOC645638
TBC1D3P1-DHX40P1
LOC653653
NME1-NME2
LINC00338
SCARNA20
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR634
MIR635
MIR636
MIR657
FLJ45513
LOC729683
PRCD
MIR454
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3614
MIR3678
MIR3615
LOC100506650
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4729
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515
Genes in Wide Peak

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

Table S19.  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 20p11.21.

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

Genes
CST1
CST2
CST3
CST4
CST5
FOXA2
SSTR4
THBD
CST8
CD93
NXT1
NAPB
GZF1
GGTLC1
CSTL1
CST9L
CST9
LINC00261
CST11
CSTT
LOC200261
LOC284788
LOC100270679
Genes in Wide Peak

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

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

Genes
HOOK3
hsa-mir-486
ANK1
CHRNB3
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
CHRNA6
AP3M2
DKK4
GOLGA7
THAP1
RNF170
GINS4
C8orf40
AGPAT6
NKX6-3
MIR486
MIR4469
Genes in Wide Peak

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

Table S22.  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 20q13.2.

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

Genes
CYP24A1
PFDN4
ZNF217
BCAS1
DOK5
TSHZ2
SUMO1P1
MIR4756
Genes in Wide Peak

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

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

Genes
LAMA3
NPC1
RBBP8
RIOK3
C18orf8
TMEM241
CABLES1
TTC39C
ANKRD29
MIR4741
Genes in Wide Peak

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

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

Genes
PLAG1
TCEA1
CHCHD7
HOOK3
hsa-mir-124-2
ASPH
CA8
CEBPD
CRH
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
RNF170
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100287846
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4469
MIR4470
Genes in Wide Peak

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

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

Genes
ETV1
HNRNPA2B1
HOXA9
HOXA11
HOXA13
PMS2
CARD11
JAZF1
hsa-mir-196b
hsa-mir-148a
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ACTB
AHR
CLK2P
DGKB
DFNA5
EVX1
GNA12
GPER
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
ICA1
IL6
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
NPY
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
DNAH11
TAX1BP1
SKAP2
CYTH3
NFE2L3
PHF14
HDAC9
RAPGEF5
KIAA0087
KIAA0415
ARL4A
GPNMB
AGR2
IGF2BP3
KDELR2
ADAP1
NUPL2
HIBADH
CBX3
SNX13
IQCE
SUN1
SOSTDC1
OSBPL3
WIPI2
INTS1
TSPAN13
EIF2AK1
BZW2
SNX8
SNX10
TRA2A
FTSJ2
NXPH1
GET4
CCZ1
MPP6
CYCS
MIOS
RNF216
TOMM7
TMEM106B
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
CDCA7L
RADIL
KLHL7
STK31
PAPOLB
C1GALT1
FAM20C
ANKMY2
RBAK
NPVF
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM126A
C7orf70
SCIN
ZFAND2A
COX19
CCDC126
GLCCI1
KIAA1908
GPR146
C7orf30
C7orf31
AMZ1
AGR3
PER4
TMEM184A
VWDE
PRPS1L1
TWISTNB
SP8
HOXA11-AS1
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
FERD3L
RPL23P8
SLC29A4
RSPH10B
TMEM196
STEAP1B
RPS2P32
TFAMP1
C7orf71
UNCX
COL28A1
ABCB5
C7orf46
MACC1
LOC389458
ELFN1
AGMO
GRID2IP
ZNF815
MIR148A
RNF216P1
PMS2CL
LOC441204
FLJ44511
LOC442497
MIR339
MIR196B
ZNF890P
OCM
SNORD93
MIR589
RSPH10B2
LOC729852
ISPD
JAZF1-AS1
LOC100131257
LOC100133311
LOC100288524
HOTTIP
MIR3146
LOC100506025
LRRC72
LOC100506178
HOTAIRM1
RBAK-LOC389458
HOXA10-HOXA9
MIR4648
MIR4655
MIR4656
KLHL7-AS1

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 - 40 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 2.1933e-73 1.1033e-61 chr9:21865498-21997722 2
13q12.11 3.5257e-13 3.5257e-13 chr13:19586755-19748348 1
9p24.1 6.8145e-18 1.2254e-06 chr9:8310705-12693402 1
22q13.32 6.5775e-06 6.5775e-06 chr22:47571204-51304566 48
4q35.2 3.596e-05 3.5232e-05 chr4:176920228-191154276 72
1p12 1.8212e-05 4.276e-05 chr1:92947252-149898950 310
11q25 0.00049364 0.00047789 chr11:105969102-135006516 276
15q11.2 1.8212e-05 0.0010587 chr15:1-32929863 168
12p12.3 0.001168 0.0011307 chr12:2778972-20169548 237
6q22.31 6.0422e-05 0.001529 chr6:123955968-125232805 1
10p15.3 0.0017657 0.0018429 chr10:1-2048902 13
6q26 0.0011095 0.0052315 chr6:161538251-171115067 52
19q13.33 0.0059385 0.0060231 chr19:48401496-48533611 21
19p13.3 0.0063178 0.0061922 chr19:807593-1563471 39
8p21.3 0.00016694 0.0067043 chr8:15092726-37561346 144
12q24.33 0.0067043 0.0067043 chr12:74674746-133851895 442
18q21.32 0.0011307 0.0098065 chr18:47089955-78077248 123
9p13.1 4.7192e-05 0.018307 chr9:36169188-99793095 260
5q31.1 0.00083091 0.019862 chr5:64314072-145972092 501
10q26.3 0.020219 0.02079 chr10:127463972-135534747 66
3p11.1 0.024995 0.028071 chr3:24144707-97168582 460
21q11.2 0.0018975 0.031243 chr21:1-26218513 44
Xp22.31 0.037037 0.037506 chrX:8766413-9757524 3
8p23.2 0.017395 0.043919 chr8:1-8256585 67
1p36.13 0.023615 0.062035 chr1:6759472-31345223 356
14q32.33 0.064665 0.063511 chr14:60755985-107349540 464
5q11.2 0.0019282 0.090618 chr5:44813655-134185314 388
16q23.1 0.093626 0.093793 chr16:68479657-90354753 224
8p11.21 0.023237 0.11012 chr8:42883855-47753079 4
4p15.31 0.1358 0.13798 chr4:1-52714468 275
6q11.1 0.083513 0.1489 chr6:52773709-105177050 162
3q28 0.14286 0.15719 chr3:173999806-198022430 187
17p11.2 0.088157 0.17262 chr17:17136414-25270516 73
2q22.1 0.080477 0.17634 chr2:139655617-143637838 1
21q21.3 0.020342 0.18666 chr21:1-40181765 184
15q15.2 0.00041043 0.2099 chr15:1-62930242 439
2q37.3 0.074874 0.22127 chr2:188414913-243199373 438
17p13.3 0.031243 0.23815 chr17:1-11147539 279
18q21.1 0.00073306 0.23815 chr18:18689748-78077248 253
5p12 0.019862 0.36915 chr5:1-180915260 1050
Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53
Genes in Wide Peak

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

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

Genes
PHF2P1
Genes in Wide Peak

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

Table S29.  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 22q13.32.

Table S30.  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
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
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 4q35.2.

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

Genes
DUX4
hsa-mir-1305
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3945
LOC100506229
Genes in Wide Peak

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

Table S32.  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
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CNN3
COL11A1
CSF1
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
GCLM
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
VCAM1
WNT2B
CSDE1
EVI5
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
TTF2
ITGA10
CDC14A
RTCD1
PEX11B
SLC16A4
CD101
ARHGAP29
SEC22B
CHD1L
LRIG2
LPPR4
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
CD160
DDX20
MTF2
NTNG1
WDR47
CLCC1
SLC35A3
NBPF14
RWDD3
PTPN22
PHGDH
SNORA66
CHIA
RNF115
GPSM2
SLC25A24
DNTTIP2
TMED5
BOLA1
HAO2
ACP6
SNX7
GPR89B
DPH5
GPR88
CCDC76
RSBN1
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
FAM91A2
AMIGO1
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
DNAJA1P5
HENMT1
GNRHR2
OLFM3
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LRRC39
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
TMEM56
NBPF4
HFE2
ANKRD35
SLC30A7
RP11-165H20.1
DENND2C
LPPR5
FNDC7
SASS6
PPIAL4A
UBL4B
PDIA3P
ALG14
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
CCDC18
MYBPHL
NBPF7
LOC375010
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
FRRS1
MIR137HG
NBPF9
MIR137
MIR197
FLJ31662
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
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130000
LOC100131564
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
MIR548AA1
LOC100506343
TMEM56-RWDD3
MIR2682
Genes in Wide Peak

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

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

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

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

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

Genes
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
APBA2
NBEAP1
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
NDN
OCA2
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
ARHGAP11A
FAN1
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
KLF13
MAGEL2
MTMR10
NDNL2
ATP10A
NIPA2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
OTUD7A
LOC283683
OR4N4
LOC283710
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
MIR211
NF1P2
HERC2P9
WHAMMP2
LOC503519
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p12.3.

Table S35.  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
PIK3C2G
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
PLEKHA5
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
PRMT8
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
NANOG
DUSP16
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
ACRBP
SPSB2
EFCAB4B
RERG
PLCZ1
HTR7P1
CAPZA3
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
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 6q22.31.

Table S36.  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 10p15.3.

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

Genes
ADARB2
IDI1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
IDI2-AS1
IDI2
TUBB8
LINC00200
C10orf108
ADARB2-AS1
Genes in Wide Peak

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

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
CCR6
GPR31
KIF25
PARK2
PDCD2
PSMB1
RPS6KA2
T
TBP
TCP10
TCTE3
THBS2
RNASET2
QKI
PDE10A
C6orf123
DLL1
BRP44L
UNC93A
PHF10
C6orf70
AGPAT4
SMOC2
FRMD1
AGPAT4-IT1
C6orf208
TTLL2
FAM120B
LINC00473
SFT2D1
PACRG
LOC154449
DACT2
C6orf118
WDR27
LOC285796
PRR18
C6orf120
DKFZp451B082
TCP10L2
LINC00242
LOC441177
MLLT4-AS1
HGC6.3
LOC100289495
MIR1913
MIR3939
CAHM
MIR4644
Genes in Wide Peak

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

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

Genes
ELSPBP1
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-C5
SNAR-C1
SNAR-C3
SNAR-A14
Genes in Wide Peak

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

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

Genes
STK11
hsa-mir-3187
ATP5D
AZU1
CIRBP
CNN2
CFD
ARID3A
EFNA2
ELANE
GAMT
GPX4
POLR2E
PRTN3
RPS15
MED16
APC2
ABCA7
SBNO2
HMHA1
DAZAP1
PCSK4
C19orf24
WDR18
LPPR3
KISS1R
MUM1
MIDN
R3HDM4
C19orf6
REEP6
GRIN3B
PLK5
CIRBP-AS1
C19orf25
C19orf26
ADAMTSL5
NDUFS7
MIR3187
Genes in Wide Peak

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

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

Genes
PCM1
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
NAT1
NAT2
ADRA1A
ASAH1
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
EXTL3
PTK2B
FGL1
GFRA2
GNRH1
GSR
GTF2E2
NRG1
LOXL2
LPL
MSR1
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
UBXN8
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
ENTPD4
PHYHIP
SORBS3
NPM2
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
FGF20
ADAMDEC1
CNOT7
PURG
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
MTUS1
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
DUSP26
HMBOX1
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
TTI2
REEP4
STMN4
MAK16
FUT10
CHMP7
VPS37A
NKX2-6
UNC5D
PEBP4
CDCA2
ESCO2
FBXO16
KCNU1
R3HCC1
LGI3
LOC254896
LOC286059
EFHA2
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 12q24.33.

Table S42.  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 18q21.32.

Table S43.  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
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD4
MBD1
MBP
MC4R
ME2
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
CXXC1
ST8SIA3
MEX3C
TMX3
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
MRO
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
SKA1
CCDC11
DOK6
RNF152
LINC00305
C18orf26
BOD1P
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
SCARNA17
SNORA37
LOC100130522
LOC100131655
LOC100287225
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
MIR4529
MIR3591
Genes in Wide Peak

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

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

Genes
FANCC
GNAQ
OMD
PAX5
SYK
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
ALDH1A1
ALDH1B1
ANXA1
APBA1
AUH
KLF9
CCIN
CKS2
CLTA
CTSL1
CTSL1P8
DAPK1
ECM2
S1PR3
FBP1
FXN
GAS1
GCNT1
HNRNPK
HSD17B3
IARS
NFIL3
NINJ1
NTRK2
ROR2
OGN
PCSK5
PGM5
PHF2
PRKACG
PTCH1
RORB
SHB
TLE1
TLE4
ZFAND5
PIP5K1B
CDC14B
FBP2
GRHPR
FAM189A2
TJP2
GDA
GNA14
MELK
ZBTB5
GNE
SEMA4D
SPTLC1
GADD45G
SPIN1
SLC35D2
FRMPD1
ZNF510
HABP4
SMC5
FAM120A
VPS13A
AGTPBP1
BICD2
CDK20
TMEM2
ZNF658
FAM75A7
FBXO10
OSTF1
PSAT1
UBQLN1
PCA3
EXOSC3
FAM108B1
GOLM1
SHC3
FAM22F
DIRAS2
ASPN
C9orf95
NOL8
C9orf40
RFK
KIF27
BARX1
NAA35
SLC28A3
POLR1E
IPPK
WNK2
SECISBP2
DCAF10
ZCCHC6
CNTNAP3
RMI1
TRPM3
GKAP1
ISCA1
ZNF484
CEP78
ZCCHC7
ANKRD20A1
C9orf64
C9orf89
HIATL2
HIATL1
C9orf3
FGD3
MCART1
FAM122A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
PTPDC1
ANKRD19P
TRPM6
RNF38
NXNL2
RASEF
FAM201A
RG9MTD3
LOC158257
FAM120AOS
LINC00475
ZNF782
LOC158434
LOC158435
PRUNE2
C9orf71
ZNF169
C9orf21
ZNF367
SUSD3
CBWD5
ANKRD18A
MAMDC2
FRMD3
C9orf47
C9orf79
LOC286238
LOC286297
LOC286370
FOXD4L3
LOC340515
FAM75D5
IGFBPL1
FOXD4L4
AQP7P1
PTAR1
C9orf102
KGFLP1
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
CTSL3
LOC392364
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR204
MIR23B
MIR24-1
MIR27B
MIR7-1
C9orf103
LOC440173
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
LOC442421
FOXB2
CBWD3
C9orf129
LOC494127
LOC494558
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75C2
FAM75A1
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
SNORA84
LOC100128076
LOC100128361
LINC00476
UNQ6494
LOC100129316
LOC100132077
LOC100132352
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
LINC00092
LOC100286938
MIR548H3
MIR2278
MIR3074
MIR4291
MIR3153
MIR4290
MIR4289
MIR3910-1
MIR3910-2
MIR3651
LOC100506710
LOC100507244
LOC100507299
LOC100507346
MIR4540
MIR4475
MIR4670
MIR4476
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q31.1.

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

Genes
APC
PIK3R1
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
TRIM23
ARSB
ALDH7A1
BHMT
BTF3
CAMK4
CAMLG
CAST
CCNB1
CCNH
CD14
CDC25C
CDK7
CDO1
CETN3
CHD1
CKMT2
AP3S1
COX7C
CRHBP
HAPLN1
CSF2
CSNK1G3
VCAN
CTNNA1
DMXL1
DHFR
DIAPH1
HBEGF
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
FBN2
FER
FGF1
FOXD1
GDF9
GFRA3
GLRX
NR3C1
GTF2H2
HARS
HEXB
HINT1
HMGCR
HSD17B4
HSPA4
HSPA9
IK
IL3
IL4
IL5
IL9
IL13
IRF1
KCNN2
TNPO1
LECT2
LMNB1
LNPEP
LOX
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MSH3
NAIP
NDUFA2
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2CA
PURA
RAD17
RASA1
RASGRF2
RPS23
SKP1
SLC12A2
SLC22A4
SLC22A5
SMN1
SMN2
SNX2
SPOCK1
SRP19
TAF7
TAF9
TBCA
TCF7
NR2F1
TGFBI
THBS4
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PDE8B
EIF4EBP3
PCDHGB4
CDC23
HDAC3
P4HA2
ATG12
NREP
RAB9BP1
HOMER1
MYOT
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
TTC37
PCDHGA8
PCDHA9
ZFYVE16
MATR3
KIAA0141
PJA2
DDX46
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
LHFPL2
APBB3
NSA2
POLR3G
IQGAP2
SEC24A
BRD8
TCERG1
HNRNPA0
SMA4
SMA5
KIF3A
ADAMTS6
RHOBTB3
ELL2
SV2C
ARHGAP26
FSTL4
MRPS27
SEPT8
PPIP5K2
ACSL6
PHF15
PPWD1
HARS2
OTP
SSBP2
BHMT2
TNFAIP8
PCDHGA12
LRRTM2
FAM169A
PCDHB5
FBXL21
KLHL3
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
PKD2L2
UQCRQ
AFF4
SLC27A6
SNX24
PCDHB1
DMGDH
TMED7
ISOC1
SAR1B
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
LARS
CXXC5
RAPGEF6
ERAP1
KDM3B
PHAX
RBM27
FLJ11235
SGTB
PCDHB18
PCDHB17
ZCCHC10
GIN1
WDR55
ANKHD1
AGGF1
WDR41
TMCO6
TRIM36
RIOK2
BDP1
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
FEM1C
C5orf15
CDC42SE2
TRPC7
NLN
ZNF608
KCTD16
SEMA6A
ARRDC3
PCDHB16
ANKRA2
HMHB1
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
ARAP3
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
TXNDC15
MCTP1
PTCD2
C5orf44
NDFIP1
YIPF5
SPRY4
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
PSD2
ANKRD32
ZBED3
GFM2
C5orf32
MEGF10
SPZ1
TSLP
FCHSD1
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
MRPS36
ATP6AP1L
PRDM6
FTMT
FNIP1
SLC35A4
EPB41L4A-AS1
MARCH3
FCHO2
LYSMD3
LEAP2
SLCO6A1
PRRC1
JMY
ZNF474
POU5F2
TMEM171
TMEM174
POC5
GPR151
STARD4
WDR36
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
ZMAT2
MARVELD2
ARSK
FAM81B
CCDC112
PRELID2
SH3RF2
PLAC8L1
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
SPATA24
DNAJC18
CCDC125
C5orf27
CMYA5
AQPEP
ANKRD31
SERINC5
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
RGMB
RFESD
CHSY3
TMEM173
FAM170A
LOC340073
LOC340074
ANKRD34B
FAM174A
MTX3
CATSPER3
SLCO4C1
TICAM2
DND1
MAST4
C5orf48
LOC389332
C5orf65
C5orf63
ANKHD1-EIF4EBP3
MIR9-2
CRSP8P
FLJ42709
C5orf56
IGIP
TIFAB
FLJ35946
LOC553103
CTXN3
ECSCR
TMEM232
GRXCR2
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR583
SNHG4
GTF2H2C
LOC728342
SERF1B
LOC728723
LOC729080
GTF2H2D
GUSBP9
VTRNA2-1
MIR874
LOC100129716
LOC100131067
LOC100133050
LOC100170939
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR1244-3
MIR1244-2
MIR4280
MTRNR2L2
MIR3607
MIR3655
MIR3660
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505841
LOC100505894
OCLN
MIR4804
MIR4633
MIR4461
MIR3977
MIR4460
MIR4803
Genes in Wide Peak

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

Table S46.  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
UROS
ADAM12
UTF1
GLRX3
DPYSL4
TUBGCP2
DUX2
VENTX
CALY
TTC40
DHX32
PPP2R2D
BCCIP
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
FANK1
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
MIR4484
Genes in Wide Peak

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

Table S47.  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
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
EPHA3
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
HTR1F
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
POU1F1
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
RARB
SNORA62
ROBO1
ROBO2
RPL29
ATXN7
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
THRB
TKT
TMF1
CLEC3B
TNNC1
TOP2B
UBA7
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
EOMES
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SLC4A7
VPRBP
IP6K1
EPM2AIP1
PSMD6
TRANK1
DLEC1
EXOG
XYLB
OXSR1
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
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
GNL3
RBMS3
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
ZNF654
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
NSUN3
KIF9
AZI2
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
LRRC3B
GPR62
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
ARL13B
DHFRL1
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ZNF620
LOC255025
ALS2CL
TMIE
C3orf64
FBXW12
C3orf38
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
STX19
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
SNORA6
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
LOC100128640
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST
Genes in Wide Peak

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

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

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
LINC00308
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
D21S2088E
POTED
LINC00317
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37
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
GPR143
TBL1X
FAM9B
Genes in Wide Peak

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

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

Genes
hsa-mir-548i-3
hsa-mir-596
ANGPT2
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
SPAG11B
FBXO25
AGPAT5
DEFB103B
CSMD1
MCPH1
DEFB104A
SGK223
C8orf42
ERICH1
ZNF596
DEFT1P
DEFB105A
DEFB106A
DEFB107A
FLJ10661
LOC286083
LOC349196
XKR5
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
DEFB107B
DEFB104B
DEFB106B
DEFB105B
DEFB109P1B
RPL23AP53
FAM90A14
SPAG11A
MIR596
DEFA1B
FAM90A20
FAM90A19
FAM66B
ZNF705G
FAM66E
LOC100132396
LOC100287015
DEFT1P2
DEFB4B
MIR548I3
MIR4659A
MIR4659B
LOC100652791
Genes in Wide Peak

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

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

Genes
PAX7
SDHB
ARID1A
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
E2F2
ECE1
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GALE
SFN
GPR3
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
FCN3
AKR7A2
ALDH4A1
EIF4G3
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
CROCC
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
PADI4
TMEM50A
STX12
CLIC4
SYF2
C1orf144
LDLRAP1
FBXO2
FBXO6
PLA2G2D
RNU11
HSPB7
AHDC1
SMPDL3B
LINC00339
UBIAD1
PADI1
PLA2G2E
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
RCC2
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
PTCHD2
KIF17
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
PINK1
PRAMEF1
PRAMEF2
PHACTR4
C1orf135
EFHD2
RSG1
MUL1
LIN28A
AGMAT
FAM110D
DHDDS
GPR157
SPSB1
ZNF436
TAS1R2
ACTL8
SH3BGRL3
SESN2
TMEM222
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA2013
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
RAB42
FAM46B
RBP7
C1orf172
LRRC38
AADACL3
IFFO2
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf127
C1orf213
PDIK1L
C1orf64
SLC2A7
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf126
AKR7L
TMCO4
ZNF683
LOC284632
SLC25A34
ESPNP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
APITD1
CATSPER4
TMEM82
TRNP1
CD164L2
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
MIR34A
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
PRAMEF7
LOC644961
C1orf200
PRAMEF19
PRAMEF20
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD99
LOC729059
PRAMEF14
FLJ37453
LOC100129196
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4632
MIR378F
RCAN3AS
Genes in Wide Peak

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

Table S52.  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
MNAT1
MTHFD1
NDUFB1
SIX6
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
SEL1L
SRSF5
SIX1
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
SIX4
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
TRMT5
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
C14orf39
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 5q11.2.

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

Genes
APC
IL6ST
PIK3R1
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
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
ALDH7A1
BHMT
BTF3
CAMK4
CAMLG
CAST
CCNB1
CCNH
CDK7
CDO1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
COX7C
CRHBP
HAPLN1
CSF2
CSNK1G3
VCAN
DMXL1
DHFR
EFNA5
F2R
F2RL1
F2RL2
FBN2
FER
FOXD1
GDF9
GLRX
GTF2H2
GZMA
GZMK
HEXB
HINT1
HMGCR
HSD17B4
HSPA4
HTR1A
IL3
IL4
IL5
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNN2
KIF2A
TNPO1
LMNB1
LNPEP
LOX
CD180
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
PAM
PCSK1
PDE4D
PGGT1B
PMCHL2
PPIC
PPP2CA
RAD17
RASA1
RASGRF2
RPS23
SKP1
SLC12A2
SLC22A4
SLC22A5
SMN1
SMN2
SNX2
SRP19
TAF9
TBCA
TCF7
NR2F1
THBS4
UBE2B
VDAC1
XRCC4
ST8SIA4
REEP5
SERF1A
ENC1
AP3B1
PDLIM4
PPAP2A
PDE8B
P4HA2
HSPB3
ATG12
NREP
RAB9BP1
HOMER1
SCAMP1
CARTPT
SNCAIP
TTC37
ZFYVE16
PJA2
DDX46
EDIL3
COL4A3BP
RAD50
LHFPL2
CWC27
CCNO
NSA2
FST
POLR3G
PLK2
IQGAP2
SEC24A
SMA4
SMA5
ESM1
KIF3A
ADAMTS6
RHOBTB3
ELL2
SV2C
FSTL4
MRPS27
SEPT8
PPIP5K2
ACSL6
PHF15
PPWD1
OTP
SKIV2L2
SSBP2
BHMT2
TNFAIP8
PART1
FAM169A
RNU5E-1
RNU5D-1
UQCRQ
AFF4
DIMT1
SLC27A6
SNX24
DMGDH
TMED7
ISOC1
SAR1B
IPO11
CDKL3
GCNT4
PRR16
COMMD10
POLK
RAPGEF6
ERAP1
PHAX
PELO
DHX29
FLJ11235
DDX4
SGTB
ARL15
ZCCHC10
GIN1
AGGF1
WDR41
TRIM36
RIOK2
DEPDC1B
BDP1
ERBB2IP
FEM1C
C5orf15
CDC42SE2
NLN
ZNF608
SEMA6A
ARRDC3
ZSWIM6
ANKRA2
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PARP8
ANKRD55
MCTP1
PTCD2
ELOVL7
C5orf44
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
MEGF10
SPZ1
TSLP
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
NDUFAF2
MRPS36
ATP6AP1L
PRDM6
FTMT
FNIP1
SNX18
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
LEAP2
C5orf35
IL31RA
EMB
SLCO6A1
PRRC1
JMY
ZNF474
POU5F2
TMEM171
TMEM174
POC5
STARD4
WDR36
ACOT12
SOWAHA
SHROOM1
SREK1
SLC38A9
CEP120
TMEM167A
MBLAC2
TMEM161B
SRFBP1
MARVELD2
ARSK
FAM81B
CCDC112
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
CCDC125
C5orf27
GAPT
CMYA5
AQPEP
ANKRD31
SERINC5
LOC257396
KIAA0825
GPR150
DTWD2
NBPF22P
C5orf64
RNF180
SREK1IP1
RGMB
RFESD
CHSY3
FAM170A
ANKRD34B
IDAS
ACTBL2
FAM174A
MTX3
HCN1
SLCO4C1
TICAM2
MAST4
RNF138P1
C5orf48
RGS7BP
C5orf63
MIR9-2
CRSP8P
FLJ42709
C5orf56
GPX8
FLJ35946
LOC553103
MIR449A
CTXN3
LOC642366
TMEM232
C5orf43
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR449B
MIR581
MIR583
GTF2H2C
LOC728342
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
LRRC70
LOC100131067
FAM159B
LOC100133050
LOC100170939
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR1244-2
MIR4280
MTRNR2L2
MIR3607
MIR3660
MIR3936
MIR3661
LOC100505678
LOC100505841
LOC100505894
OCLN
MIR4804
MIR4633
MIR3977
MIR4460
MIR4803
Genes in Wide Peak

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

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

Genes
CBFA2T3
CDH1
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
AARS
AP1G1
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH3
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
NQO1
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HAS3
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
ST3GAL2
SNTB2
SPG7
TAT
TERF2
ZNF19
ZNF23
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
COX4NB
TUBB3
CFDP1
NFAT5
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
ADAT1
CHST5
COG4
CPNE7
VPS4A
IL17C
NOB1
ANKRD11
OSGIN1
NIP7
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
CHTF8
TXNL4B
BANP
PDPR
RFWD3
DDX19A
ZNF821
ZDHHC7
VAC14
FTSJD1
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
PDF
MTHFSD
DBNDD1
FA2H
TMEM231
TMCO7
WDR59
KLHL36
FBXO31
CYB5B
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
COG8
SPIRE2
ZNF469
CIRH1A
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
ZFP90
SLC22A31
IL34
TMED6
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
MIR140
CTRB2
CLEC18B
SNORD68
SNORD71
SNORD111
LOC727710
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130894
SYCE1L
LOC100287036
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
LOC100506083
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719
Genes in Wide Peak

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

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

Genes
FNTA
SGK196
HGSNAT
POTEA
Genes in Wide Peak

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

Table S56.  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 6q11.1.

Table S57.  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
CCNC
CGA
CNR1
COL9A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
GABRR1
GABRR2
GCLC
GRIK2
GSTA4
HCRTR2
HTR1B
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
POU3F2
PRIM2
RNY4
SIM1
ELOVL4
MAP3K7
TPBG
TTK
PTP4A1
GCM1
RNGTT
TBX18
HMGN3
FHL5
BAG2
SNAP91
CASP8AP2
SYNCRIP
SLC35A1
FUT9
PNRC1
ASCC3
KIAA1009
ICK
ANKRD6
RIMS1
DOPEY1
ZNF292
MDN1
UFL1
PHF3
ORC3
MTO1
PNISR
IBTK
ZNF451
SENP6
FBXL4
FBXO9
SLC17A5
SNORD50A
FILIP1
TINAG
NDUFAF4
CYB5R4
UBE2J1
LGSN
RAB23
COQ3
HMGCLL1
PHIP
AKIRIN2
LRRC1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
C6orf162
LYRM2
SNX14
FAM135A
KIAA1586
RRAGD
PRDM13
BACH2
ELOVL5
SMAP1
C6orf164
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
COL21A1
SPACA1
SH3BGRL2
MCHR2
FAXC
GJA10
USP45
C6orf7
UBE2CBP
MLIP
MRAP2
RWDD2A
KLHL32
MB21D1
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
PRSS35
LCA5
KHDRBS2
C6orf163
BEND6
FAM83B
MMS22L
DPPA5
EYS
GUSBP4
GJB7
SNHG5
C6orf147
GFRAL
KLHL31
MIR30A
MIR30C2
OOEP
MCART3P
TSG1
RPS16P5
SNORD50B
LOC728012
KHDC1L
LOC100130890
LOC100288198
MIR2113
MIR548H3
MIR4282
LOC100506804
MIR4464
MIR4643
Genes in Wide Peak

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

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
ACTL6A
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
EHHADH
EIF4G1
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
POLR2H
PPP1R2
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SST
THPO
FXR1
TP63
CHRD
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
NCBP2
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
FETUB
LAMP3
KCNMB3
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MCCC1
HRASLS
MRPL47
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
ATP13A3
TBL1XR1
MAP6D1
PIGZ
B3GNT5
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LOC339926
LPP-AS2
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
FLJ46066
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
C3orf65
GMNC
LOC647323
SNORA81
SNORD66
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p11.2.

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

Genes
hsa-mir-1180
hsa-mir-33b
ALDH3A1
ALDH3A2
DRG2
FOXO3B
FLII
KCNJ12
LLGL1
MFAP4
MAPK7
MAP2K3
PRPSAP2
SHMT1
SREBF1
TOP3A
RNF112
COPS3
TMEM11
ULK2
PEMT
FBXW10
RAI1
GRAP
AKAP10
EPN2
USP22
DHRS7B
B9D1
FAM18B1
MYO15A
RASD1
ALKBH5
MED9
SLC47A1
NT5M
C17orf39
FAM106A
LRRC48
ATPAF2
SPECC1
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
TRIM16L
USP32P2
TBC1D28
CDRT15L2
C17orf103
CCDC144B
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
CCDC144C
GRAPL
FAM83G
KRT16P3
EVPLL
LGALS9C
SNORA59B
SNORA59A
MIR33B
ZNF286B
KCNJ18
MIR1180
MTRNR2L1
Genes in Wide Peak

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

Table S60.  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 21q21.3.

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

Genes
RUNX1
ERG
OLIG2
hsa-mir-802
hsa-mir-4327
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
APP
ATP5J
ATP5O
BACH1
BAGE
TMEM50B
CBR1
CBR3
CXADR
RCAN1
DYRK1A
GABPA
GART
GRIK1
HLCS
IFNAR1
IFNAR2
IFNGR2
IL10RB
KCNE1
KCNJ6
KCNJ15
NCAM2
TMPRSS15
ITSN1
SIM2
SLC5A3
SOD1
SON
HSPA13
TIAM1
TPTE
TTC3
NRIP1
CHAF1B
SYNJ1
CLDN8
ADAMTS1
URB1
CRYZL1
DOPEY2
KCNE2
RWDD2B
DSCR4
DSCR3
USP16
CCT8
BTG3
ADAMTS5
MORC3
CLDN14
LTN1
CLDN17
N6AMT1
USP25
DONSON
HUNK
PIGP
DSCR6
RBM11
LINC00160
FAM165B
C21orf49
MIS18A
LINC00158
CHODL-AS1
LINC00113
SETD4
C21orf15
CLIC6
LINC00308
MRPL39
C21orf91
DNAJC28
C21orf62
MRAP
C21orf59
C21orf7
SCAF4
JAM2
C21orf63
SAMSN1
MRPS6
RUNX1-IT1
DSCR8
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
GCFC1
LINC00310
MIR155HG
CYYR1
OLIG1
LINC00161
KRTAP13-1
TCP10L
CHODL
ANKRD30BP2
LIPI
ABCC13
LINC00189
C21orf91-OT1
LINC00314
KRTAP15-1
DSCR9
DSCR10
D21S2088E
LINC00307
LINC00515
KRTAP13-4
POTED
KRTAP7-1
KRTAP8-1
KRTAP11-1
KRTAP19-1
KRTAP13-2
KRTAP13-3
KRTAP23-1
KRTAP6-1
KRTAP6-2
KRTAP6-3
KRTAP19-2
KRTAP19-3
KRTAP19-4
KRTAP19-5
KRTAP19-6
KRTAP19-7
KRTAP20-1
KRTAP20-2
KRTAP21-1
KRTAP21-2
KRTAP22-1
KRTAP20-3
LOC339622
LINC00317
LINC00320
LOC388813
LINC00478
KRTAP26-1
ANKRD20A11P
LINC00114
MIRLET7C
MIR125B2
MIR155
MIR99A
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
KRTAP19-8
C21orf54
MIR802
KRTAP25-1
TEKT4P2
LOC100133286
KRTAP20-4
KRTAP22-2
KRTAP21-3
LOC100288432
GRIK1-AS2
MIR4327
MIR3156-3
MIR3687
MIR3648
C21orf37
GCFC1-AS1
LOC100506334
LOC100506385
CBR3-AS1
LINC00159
MIR4759
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.2.

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

Genes
BUB1B
TCF12
FLJ27352
C15orf55
hsa-mir-2116
hsa-mir-628
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
ADAM10
ANXA2
APBA2
AQP9
B2M
NBEAP1
BNIP2
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RORA
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
SNURF
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TGM5
PIGB
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
PYGO1
PLDN
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
NARG2
C15orf29
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LDHAL6B
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
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
TEX9
C15orf52
TNFAIP8L3
C2CD4B
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
HSP90AB4P
MIR626
MIR627
MIR628
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
MIR2116
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B
MYZAP
Genes in Wide Peak

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

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

Genes
ATIC
CREB1
ACSL3
IDH1
PAX3
PMS1
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
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
AOX1
KIF1A
BARD1
BCS1L
BMPR2
BOK
CASP8
CASP10
CD28
CHRND
CHRNG
CLK1
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CYP27A1
DES
DTYMK
EEF1B2
EPHA4
ERBB4
FN1
GBX2
MSTN
GLS
GPC1
GPR1
GPR35
HDLBP
AGFG1
DNAJB2
HSPD1
HSPE1
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP1
INPP5D
IRS1
KCNJ13
MAP2
MYO1B
MYL1
NAB1
NCL
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NPPC
ORC2
PDCD1
PDE6D
SERPINE2
PLCL1
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
STAT1
STAT4
TNP1
TNS1
TUBA4A
SUMO1
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
FZD7
SDPR
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
CFLAR
PER2
CDK5R2
RQCD1
LRRFIP1
STK17B
GPR55
TRIP12
GTF3C3
ECEL1
EIF4E2
TTLL4
BZW1
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
ABI2
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
FASTKD2
PASK
ATG4B
SATB2
OBSL1
SF3B1
DNPEP
TMEFF2
SH3BP4
KCNE4
NGEF
SNORD82
MOB4
PNKD
SNED1
SPATS2L
GIGYF2
TRAF3IP1
ABCA12
HIBCH
SNORD51
CNPPD1
STK36
CPS1-IT1
ICOS
GMPPA
SLC40A1
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
GULP1
SCLY
NOP58
ASB1
CAB39
PRKAG3
PPIL3
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
MFSD6
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
STRADB
HES6
ACCN4
DOCK10
MREG
WDR12
PECR
DNAH7
C2orf83
MFF
CXCR7
RNPEPL1
SLC39A10
CYP20A1
HECW2
MARCH4
WDFY1
NYAP2
ALS2
ZDBF2
USP37
CTDSP1
MPP4
NIF3L1
PCGEM1
GAL3ST2
TMBIM1
OSGEPL1
RAB17
RNF25
COPS7B
OBFC2A
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
TRAK2
BOLL
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
C2orf47
SPAG16
CHPF
IQCA1
ALS2CR8
NHEJ1
FAM124B
TM4SF20
C2orf54
PGAP1
TUBA4B
ARMC9
COQ10B
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
WDR75
RHBDD1
C2orf88
ING5
PLCD4
MGC16025
ANKRD44
TMEM169
DNER
MARS2
B3GNT7
SP140L
ORMDL1
STK11IP
DIRC1
MOGAT1
AGAP1
TWIST2
PARD3B
TYW5
DIS3L2
NEU4
ICA1L
RFTN2
AP1S3
SGPP2
KCTD18
ALS2CR12
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
FLJ32063
OTOS
MYEOV2
OR6B3
ANKAR
FAM117B
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
METTL21A
CCNYL1
SGOL2
ALS2CR11
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
PIKFYVE
LOC200726
TIGD1
LOC200772
C2orf69
CCDC108
C2orf72
CCDC150
CXXC11
FAM126B
UNC80
RUFY4
DUSP28
ESPNL
AOX2P
ECEL1P2
FONG
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
C2orf66
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
SNORA41
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
SNORD11
SNORD70
MIR561
D2HGDH
LOC728323
DIRC3
SNORD11B
LOC100129175
PP14571
LOC100130451
LOC100130452
TMEM194B
LOC100286922
MIR1471
MIR1245A
MIR1244-1
MIR548F2
LOC100329109
BOK-AS1
MIR1244-3
MIR1244-2
MIR3129
MIR3131
MIR4268
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
MIR3606
LOC100507140
LOC100507443
HSPE1-MOB4
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR1245B
MIR2467
MIR4775
MIR4440
MIR4786
MIR4776-2
MIR4441
Genes in Wide Peak

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

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

Genes
PER1
TP53
GAS7
USP6
hsa-mir-4314
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ACADVL
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MNT
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RCVRN
RPA1
RPL26
SCO1
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
MYH13
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
GLP2R
NTN1
STX8
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
GABARAP
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
KIAA0664
SMG6
WSCD1
CTDNEP1
PIK3R5
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
C17orf59
GPR172B
WRAP53
RNMTL1
VPS53
C17orf85
TSR1
DHX33
C17orf48
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
CTC1
NDEL1
PITPNM3
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
LSMD1
NEURL4
ZNF594
HES7
SPATA22
TXNDC17
MIR22HG
TMEM88
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
DNAH2
RTN4RL1
WDR16
CCDC42
PIK3R6
ODF4
KCTD11
MFSD6L
TRPV3
SLC16A11
FBXO39
DHRS7C
SLC16A13
C17orf74
SPNS3
C17orf61
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
PIRT
SNORA48
SNORD10
OR1D4
SCARNA21
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
LOC100128288
C17orf107
LOC100130950
DBIL5P
LOC100289255
MIR1253
LOC100306951
MIR3183
MIR4314
MIR3676
LOC100506388
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4520A
MIR4521
MIR4520B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.1.

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

Genes
BCL2
SS18
MALT1
ZNF521
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
hsa-mir-187
hsa-mir-302f
hsa-mir-320c-2
hsa-mir-1-2
hsa-mir-320c-1
AQP4
ATP5A1
CDH2
CDH7
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GATA6
GRP
LAMA3
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MEP1B
MYO5B
NARS
NFATC1
NPC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RBBP8
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SNRPD1
SYT4
TAF4B
TCF4
TTR
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
RIOK3
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
ZNF271
TXNL4A
MAPRE2
POLI
ADNP2
TRAPPC8
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
CABYR
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
C18orf8
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
RPRD1A
ZNF532
ELP2
IMPACT
ELAC1
ZNF407
CNDP2
CELF4
MIB1
KIAA1328
KLHL14
KIAA1468
EPG5
HRH4
CTAGE1
FAM59A
CCDC102B
RBFA
GREB1L
PQLC1
FHOD3
CCDC68
ASXL3
NETO1
KATNAL2
CHST9
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
TMEM241
SERPINB12
SERPINB11
SEC11C
CABLES1
DSEL
ESCO1
OSBPL1A
HAUS1
ALPK2
LOXHD1
INO80C
TTC39C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
MCART2
DSG4
CHST9-AS1
ANKRD29
C18orf54
TCEB3C
ABHD3
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
ZNF396
KCTD1
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
C18orf34
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR1-2
MIR122
MIR133A1
MIR187
HSBP1L1
WBP11P1
RNF165
C18orf32
KC6
LOC643542
C18orf63
LOC647946
SCARNA17
SNORA37
LOC728606
TCEB3CL
LOC729950
ZSCAN30
SNORD58C
LOC100130522
LOC100131655
LOC100287225
MIR302F
MIR320C1
MIR320C2
MIR1539
MIR4319
MIR4318
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4741
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744
LOC100652770
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p12.

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

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
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
hsa-mir-582
hsa-mir-449c
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGF10
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NDUFS6
NEUROG1
NPR3
NPY6R
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
PURA
RAD17
RARS
RASA1
RASGRF2
RPL37
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP1
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
SRP19
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
NREP
TRIP13
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
PAPD7
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
OTP
SKIV2L2
NNT
TTC33
ZNF346
AMACR
SSBP2
BHMT2
TNFAIP8
NIPBL
PP7080
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
FBXO4
OR4F3
HAVCR1
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
DROSHA
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MZB1
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
FAM134B
FAM105A
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
MTMR12
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
NSUN2
CCDC99
THG1L
WDR70
AGGF1
WDR41
BRIX1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
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
ANKH
CCL28
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
AHRR
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1P1
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
CARD6
TRIM52
HAVCR2
AGXT2L2
C5orf62
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
LMBRD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C1QTNF3
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
HEATR7B2
EGFLAM
PRRC1
NADKD1
UGT3A1
CAPSL
JMY
C5orf58
ZNF474
CCDC127
OR2Y1
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC38A9
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
LOC153469
PLEKHG4B
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
LOC153684
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
NIM1
LIX1
ZNF366
FAM151B
S100Z
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
AQPEP
SLC36A1
RICTOR
EIF4E1B
LOC255167
RASGEF1C
ANKRD31
SERINC5
LOC257358
LOC257396
LOC285577
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
C5orf51
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
LOC285692
LOC285696
RGMB
RFESD
CHSY3
SLC6A19
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
LOC340094
LOC340107
LOC340113
ANKRD34B
PFN3
ZNF879
PLCXD3
IRGM
FBLL1
IDAS
ACTBL2
FAM174A
MTX3
CATSPER3
SLC6A18
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
C5orf34
MAST4
C5orf25
RNF138P1
FLJ38109
LRRC14B
C5orf39
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
FLJ33360
LOC401177
RGS7BP
C5orf63
SPINK6
TAG
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
MARCH11
CRSP8P
FLJ42709
C5orf56
FLJ16171
LOC442132
MIR340
IGIP
GPX8
TIFAB
FLJ35946
LOC553103
MIR449A
CTXN3
SNORD72
SNORD95
SNORD96A
ECSCR
LOC642366
TMEM232
C5orf43
LOC643201
GRXCR2
SPINK9
LOC643401
ZFP62
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
CBY3
LOC646719
LOC647859
LOC648987
ANKRD33B
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR580
MIR581
MIR583
MIR585
SNHG4
MIR143HG
GTF2H2C
LOC728342
GUSBP1
SERF1B
LOC728554
SDHAP3
LOC728613
LOC728723
LOC729080
LOC729506
AACSP1
LOC729678
OR4F29
LOC729862
GTF2H2D
GUSBP9
SNORD123
VTRNA2-1
MIR874
LOC100129716
CCDC152
LRRC70
LOC100130744
LOC100131067
FAM196B
LOC100132062
LOC100132287
LOC100132356
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR4279
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MIR4277
MIR4278
MTRNR2L2
MIR3607
MIR3655
MIR3650
MIR3660
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505738
LOC100505806
LOC100505841
LOC100505894
LOC100506548
OCLN
LOC100506688
LOC100507387
C1QTNF3-AMACR
MIR4458
MIR4804
MIR4633
MIR4634
MIR4461
MIR4454
MIR4457
MIR4637
MIR3977
MIR4460
MIR4636
MIR4638
MIR4803
MIR4456
MIR4635
MIR378E
EGFLAM-AS4
LOC100859930
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 28 significant results found.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 2121 0.35 4.06 0.000164 0.26 0.889 0.356
1q 1955 0.65 13.7 0 0.29 1.27 0.228
2p 924 0.34 0.902 0.623 0.10 -5.83 1
2q 1556 0.33 2.11 0.0878 0.09 -4.91 1
3p 1062 0.11 -4.73 1 0.47 5.47 9.87e-08
3q 1139 0.19 -2.98 1 0.39 2.96 0.00437
4p 489 0.20 -4.12 1 0.26 -2.36 1
4q 1049 0.11 -5.58 1 0.28 -0.611 1
5p 270 0.54 5.44 2.83e-07 0.28 -1.74 1
5q 1427 0.32 1.32 0.372 0.40 3.79 0.000254
6p 1173 0.31 0.572 0.873 0.34 1.49 0.16
6q 839 0.15 -3.95 1 0.54 6.84 3.87e-11
7p 641 0.54 6.44 1.16e-09 0.18 -3.48 1
7q 1277 0.44 4.84 5.24e-06 0.18 -2.82 1
8p 580 0.31 -0.483 1 0.54 6.04 4.37e-09
8q 859 0.49 5.43 2.83e-07 0.24 -1.81 1
9p 422 0.14 -4.43 1 0.58 7.1 8.21e-12
9q 1113 0.08 -5.14 1 0.50 6.56 2.17e-10
10p 409 0.27 -2.19 1 0.30 -1.33 1
10q 1268 0.20 -2.55 1 0.30 0.437 0.602
11p 862 0.24 -2.25 1 0.26 -1.57 1
11q 1515 0.25 -0.647 1 0.22 -1.39 1
12p 575 0.32 -0.381 1 0.31 -0.813 1
12q 1447 0.27 -0.155 1 0.27 -0.276 1
13q 654 0.17 -3.99 1 0.47 4.33 2.72e-05
14q 1341 0.27 -0.376 1 0.27 -0.496 1
15q 1355 0.16 -3.07 1 0.51 7.47 1.06e-12
16p 872 0.31 -0.164 1 0.30 -0.5 1
16q 702 0.26 -1.78 1 0.37 1.18 0.238
17p 683 0.19 -3.11 1 0.57 7.43 1.06e-12
17q 1592 0.39 3.92 0.000252 0.24 -0.719 1
18p 143 0.27 -2.37 1 0.45 2.42 0.0206
18q 446 0.18 -3.86 1 0.53 5.67 3.51e-08
19p 995 0.07 -5.69 1 0.50 6.12 3.04e-09
19q 1709 0.13 -3.66 1 0.35 3.2 0.0021
20p 355 0.38 0.889 0.623 0.40 1.2 0.238
20q 753 0.39 1.82 0.152 0.29 -0.91 1
21q 509 0.31 -0.747 1 0.42 2.2 0.0344
22q 921 0.18 -3.35 1 0.46 4.65 6.75e-06
Xq 1312 0.18 -3.34 1 0.16 -3.71 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/2044042/2.GDAC_MergeDataFiles.Finished/LUAD.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 230 Input Tumor Samples.

Tumor Sample Names
TCGA-05-4249-01A-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-05-4398-01A-01D-1204-01
TCGA-05-4402-01A-01D-1204-01
TCGA-05-4403-01A-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.

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)
[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)
[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)