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 303 tumor samples used in this analysis: 26 significant arm-level results, 28 significant focal amplifications, and 42 significant focal deletions were found.

Results
Focal results

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

Table 1. Get Full Table Amplifications Table - 28 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
14q13.3 | 5.6041e-35 | 5.6041e-35 | chr14:36854137-37023019 | 2
5p15.33 | 1.7619e-19 | 1.2663e-18 | chr5:1288616-1300024 | 1
8q24.21 | 3.3081e-18 | 3.6042e-18 | chr8:129157821-129195260 | 2
1q21.3 | 4.6343e-14 | 4.6343e-14 | chr1:120523956-155329412 | 283
12q15 | 9.7918e-18 | 2.3034e-12 | chr12:69212011-69485451 | 2
12p12.1 | 4.0686e-07 | 4.4888e-07 | chr12:24875364-26433911 | 13
19q12 | 1.9779e-06 | 1.9779e-06 | chr19:30022749-30605958 | 6
3q26.2 | 2.7949e-06 | 2.7949e-06 | chr3:168804384-170787300 | 20
Xq28 | 5.4673e-06 | 5.4673e-06 | chrX:151841230-155270560 | 104
11q13.3 | 1.4197e-05 | 1.4197e-05 | chr11:68652566-69531424 | 10
7p11.2 | 3.4884e-05 | 3.4884e-05 | chr7:54535672-55741100 | 6
7q31.2 | 9.9069e-05 | 9.9069e-05 | chr7:116301206-116449049 | 1
8p11.21 | 1.6629e-05 | 0.00021867 | chr8:41418164-42644874 | 16
12q14.1 | 2.6486e-09 | 0.0015279 | chr12:58038861-58560425 | 16
18q11.2 | 0.0026585 | 0.0026585 | chr18:21383413-21711032 | 2
20q13.33 | 1.3939e-06 | 0.003041 | chr20:62090554-63025520 | 43
20q13.2 | 3.9056e-07 | 0.0062864 | chr20:52040634-53196537 | 8
17q25.3 | 0.0022435 | 0.01632 | chr17:58350015-81195210 | 342
17q12 | 0.0025669 | 0.017234 | chr17:37804811-38011853 | 9
6p21.1 | 0.017234 | 0.03588 | chr6:40209663-42692619 | 37
1p34.3 | 0.030832 | 0.038485 | chr1:39367667-43987058 | 73
1p22.3 | 0.026564 | 0.065027 | chr1:85979933-86006008 | 1
5p12 | 2.1825e-05 | 0.085091 | chr5:33498056-50133468 | 75
6p25.3 | 0.11831 | 0.1837 | chr6:1-27229264 | 197
13q32.1 | 0.18688 | 0.18688 | chr13:72596997-115169878 | 152
20p11.21 | 0.19077 | 0.19077 | chr20:21783368-24784775 | 25
8q11.1 | 0.0040505 | 0.22393 | chr8:42804260-65580654 | 72
3p11.1 | 0.23457 | 0.23457 | chr3:89447444-90455161 | 1

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 5p15.33.

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

Genes
TERT

Genes in Wide Peak

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

Table S3. 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 1q21.3.

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

Genes
ARNT
BCL9
MUC1
NOTCH2
TPM3
PDE4DIP
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
CHRNB2
CKS1B
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
S100A7L2
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
MIR555
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR190B
C1orf68
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505666
TNFAIP8L2-SCNM1

Genes in Wide Peak

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

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

Genes
MDM2
CPM

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 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
BCAT1
LRMP
SSPN
RASSF8
CASC1
BHLHE41
LYRM5
IFLTD1
C12orf77
MIR4302
LOC100506451

Genes in Wide Peak

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

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

Genes
CCNE1
URI1
POP4
PLEKHF1
C19orf12
VSTM2B

Genes in Wide Peak

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

Table S8. 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 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
hsa-mir-718
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CETN2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
OPN1MW
GDI1
HCFC1
IDH3G
IL9R
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SPRY3
ZNF275
TREX2
SRPK3
SNORA70
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
PDZD4
FAM3A
FUNDC2
BRCC3
H2AFB3
PNMA6A
FAM58A
PNMA5
RAB39B
GAB3
PNCK
ZFP92
CSAG1
CTAG1A
MAGEA2B
LINC00204B
CSAG3
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CSAG2
CXorf68
LINC00204A
MTCP1NB
PNMA6C
PNMA6D
MIR1184-1
MIR718
MIR3202-2
MIR1184-3
MIR1184-2
MIR3202-1
LOC100507404

Genes in Wide Peak

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

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

Genes
CCND1
hsa-mir-3164
IGHMBP2
FGF19
MYEOV
MRGPRD
MRGPRF
MRPL21
TPCN2
ORAOV1

Genes in Wide Peak

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

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute'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 7q31.2.

Table S12. 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 8p11.21.

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

Genes
hsa-mir-486
ANK1
CHRNB3
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
CHRNA6
AP3M2
DKK4
C8orf40
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

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

Table S14. 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 18q11.2.

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

Genes
LAMA3
TTC39C

Genes in Wide Peak

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

Table S16. 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 20q13.2.

Table S17. 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 17q25.3.

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

Genes
CD79B
DDX5
PRKAR1A
ASPSCR1
BRIP1
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
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CACNG1
CD7
CDK3
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
MAFG
MAP3K3
NPTX1
P4HB
PDE6G
PECAM1
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RFNG
RPL38
MRPL12
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
TBCD
TBX2
TIMP2
TK1
AXIN2
PPM1D
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
RAB40B
TLK2
POLG2
CD300A
TMC6
DDX42
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
HN1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
SDK2
FAM20A
BCAS3
TMEM104
C17orf80
CCDC40
WIPI1
NPLOC4
ST6GALNAC1
TEX2
GPRC5C
WDR45L
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
SLC25A19
UBE2O
DUS1L
FN3K
DNAI2
SMURF2
ENGASE
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
C17orf70
LIMD2
KCNH6
TSPAN10
QRICH2
USP32
CBX2
FAM104A
MGC16275
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
NOTUM
TMC8
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
SLC26A11
ENDOV
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
FAM195B
GPR142
ZACN
LRRC37A3
C17orf82
BTBD17
AATK-AS1
FLJ43681
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LINC00338
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR634
MIR635
MIR636
MIR657
LOC729683
PRCD
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3678
MIR3615
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515

Genes in Wide Peak

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

Table S19. 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 6p21.1.

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

Genes
CCND3
TFEB
BYSL
GUCA1A
GUCA1B
MDFI
NFYA
PGC
PRPH2
NCR2
MED20
FRS3
APOBEC2
UBR2
USP49
PRICKLE4
TREM2
TREM1
MRPS10
TRERF1
LRFN2
TREML2
FOXP4
TAF8
TREML2P1
LOC221442
C6orf130
TSPO2
UNC5CL
TREML4
TREML1
TREML3
FLJ41649
C6orf132
TDRG1
TOMM6
MIR4641

Genes in Wide Peak

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

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

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

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 5p12.

Table S23. 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 6p25.3.

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

Genes
IRF4
DEK
HIST1H4I
hsa-mir-3143
hsa-mir-548a-1
BMP6
BPHL
BTN1A1
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
GPLD1
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
ID4
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SLC17A1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
ALDH5A1
HIST1H2AC
HIST1H2AB
HIST1H2BG
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3G
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4G
CMAHP
RIPK1
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
GCM2
CD83
CDYL
LY86
EEF1E1
FAM65B
KIAA0319
NUP153
RANBP9
SLC17A4
SLC17A2
PRSS16
BTN3A3
BTN2A2
ECI2
HMGN4
TRIM38
CAP2
SCGN
FARS2
SLC17A3
RPP40
BTN3A2
BTN3A1
BTN2A1
SIRT5
FAM50B
MYLIP
ABT1
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
GFOD1
BTN2A3P
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
MUTED
CCDC90A
KIF13A
ZNF322
TXNDC5
C6orf62
TMEM14B
RIOK1
DTNBP1
ADTRP
HIST1H2AH
HIST1H2BK
FOXQ1
HUS1B
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
PIP5K1P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
RNF144B
HIST1H2BA
LOC285768
LY86-AS1
CAGE1
LOC285819
MYLK4
TUBB2B
C6orf52
KAAG1
NHLRC1
GUSBP2
HIST1H2APS1
PSMG4
DKFZP686I15217
FLJ23152
LINC00340
C6orf201
ERVFRD-1
HCG11
PPP1R3G
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
LOC100130275
LOC100130357
LINC00240
LOC100270746
MIR3143
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q32.1.

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
ATP4B
KLF5
BTF3P11
CLN5
COL4A1
COL4A2
DCT
GPR183
EDNRB
EFNB2
F7
F10
FGF14
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
LMO7
PCCA
POU4F1
DNAJC3
RAP2A
GRK1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
UCHL3
ZIC2
STK24
CUL4A
IRS2
SCEL
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
TBC1D4
GPC6
MBNL2
FARP1
SPRY2
ABCC4
TUBGCP3
PIBF1
TNFSF13B
SOX21
KLF12
RASA3
DZIP1
DIS3
MYO16
MYCBP2
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
FBXL3
OXGR1
NDFIP2
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
RBM26
UPF3A
KDELC1
CARS2
RNF219
GRTP1
BORA
SLITRK6
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
SLITRK1
KCTD12
TEX29
METTL21CP1
SLAIN1
SPACA7
RNF113B
LINC00410
GPR180
COMMD6
CLYBL
METTL21C
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
LINC00347
FAM70B
C13orf35
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
MZT1
MIR4500HG
FLJ44054
CCDC168
CTAGE11P
FLJ41484
MIR622
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
MIR3170
MIR3665
RBM26-AS1
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.21.

Table S26. 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
SYNDIG1
GGTLC1
CSTL1
CST9L
CST9
LINC00261
CST11
CSTT
LOC200261
LOC284788
FLJ33581
LOC100270679

Genes in Wide Peak

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

Table S27. 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
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
OPRK1
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
ST18
TOX
RB1CC1
LYPLA1
KIAA0146
C8orf71
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
CHD7
SOX17
EFCAB1
SGK196
FAM110B
TGS1
XKR4
PCMTD1
TMEM68
UBXN2B
PXDNL
HGSNAT
CLVS1
SDR16C5
YTHDF3
LOC286177
NKAIN3
LOC286184
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
UG0898H09
LOC100130155
LOC100130298
SBF1P1
LOC100287846
LOC100507632
LOC100507651
MIR4470

Genes in Wide Peak

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

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

Genes
EPHA3

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 1.6108e-96 | 6.7594e-84 | chr9:21865498-21997722 | 2
13q12.11 | 6.7816e-13 | 6.7816e-13 | chr13:1-20714074 | 11
4q35.2 | 4.3665e-08 | 4.3665e-08 | chr4:177189490-191154276 | 69
22q13.32 | 7.228e-08 | 7.1642e-08 | chr22:47571204-51304566 | 48
9p24.1 | 1.5527e-20 | 1.4165e-07 | chr9:8310705-12693402 | 1
1p13.1 | 3.2806e-08 | 1.7349e-07 | chr1:95939768-149881397 | 281
18q21.32 | 1.0146e-05 | 1.0493e-05 | chr18:54696384-65185445 | 50
12p13.2 | 1.7398e-05 | 1.7923e-05 | chr12:7480129-20169548 | 151
6q26 | 3.9346e-05 | 0.00027401 | chr6:161693099-163153207 | 1
11q24.1 | 0.00029891 | 0.00030934 | chr11:104032904-135006516 | 288
15q11.2 | 3.8281e-07 | 0.00051494 | chr15:1-32929863 | 168
10p15.3 | 0.00051816 | 0.00054202 | chr10:1-4872250 | 21
16q23.1 | 0.001472 | 0.00152 | chr16:78016120-79627770 | 2
9p13.1 | 1.4593e-06 | 0.0018817 | chr9:38619152-71152237 | 50
19p13.2 | 5.5666e-05 | 0.0018817 | chr19:11040707-11207540 | 1
6q22.31 | 9.3129e-05 | 0.0021147 | chr6:123955968-125232805 | 1
19p13.3 | 3.1316e-05 | 0.0045323 | chr19:1-437820 | 10
21q11.2 | 0.00018033 | 0.0045323 | chr21:1-17913227 | 27
2q22.1 | 0.0031672 | 0.0061202 | chr2:139655617-143637838 | 1
5q11.2 | 0.00013661 | 0.0061202 | chr5:44813655-83238517 | 190
8p23.2 | 0.0020195 | 0.0064281 | chr8:2079140-6262191 | 1
5q22.1 | 0.00063838 | 0.009468 | chr5:64314072-138092300 | 370
8p21.3 | 0.00023346 | 0.009468 | chr8:16050275-38653962 | 162
11p15.5 | 0.0097582 | 0.0098535 | chr11:1-18731484 | 337
19q13.33 | 0.01032 | 0.010509 | chr19:47174409-50374495 | 160
10q26.3 | 0.015433 | 0.015831 | chr10:127463972-135534747 | 66
Xp22.31 | 0.001151 | 0.018561 | chrX:8766413-9694455 | 2
3p21.31 | 0.0083289 | 0.021928 | chr3:1-84688247 | 585
14q32.13 | 0.025727 | 0.02649 | chr14:57397485-107349540 | 487
1p36.13 | 0.0037373 | 0.031525 | chr1:1-31735879 | 500
3q28 | 0.036036 | 0.037871 | chr3:179753793-198022430 | 172
12q24.33 | 0.044002 | 0.043227 | chr12:71977788-133851895 | 452
17p13.3 | 0.022022 | 0.051642 | chr17:1-8191216 | 245
15q15.3 | 9.6715e-05 | 0.053216 | chr15:1-50849590 | 366
6q12 | 0.026596 | 0.061352 | chr6:57206486-70388021 | 9
4p15.31 | 0.10712 | 0.10572 | chr4:1-52714468 | 275
3p11.1 | 0.016724 | 0.1208 | chr3:75363575-96534596 | 29
Xp21.3 | 0.01877 | 0.14453 | chrX:27763585-39914732 | 36
2q37.3 | 0.057149 | 0.17319 | chr2:200336780-243199373 | 382
19p12 | 0.055795 | 0.18698 | chr19:22527847-22818842 | 2
17p11.2 | 0.13115 | 0.18763 | chr17:15928223-25270516 | 95
21q21.3 | 0.024148 | 0.18763 | chr21:16436212-39739664 | 159

Genes in Wide Peak

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

Table S29. 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 S30. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 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
ZFP42
ENPP6
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 22q13.32.

Table S32. 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 9p24.1.

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
VCAM1
WNT2B
CSDE1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
TTF2
ITGA10
CDC14A
RTCD1
PEX11B
SLC16A4
CD101
SEC22B
CHD1L
LRIG2
LPPR4
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
CD160
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
NBPF14
PTPN22
PHGDH
CHIA
RNF115
GPSM2
SLC25A24
BOLA1
HAO2
ACP6
SNX7
GPR89B
DPH5
GPR88
CCDC76
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
FAM91A2
AMIGO1
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
DNAJA1P5
HENMT1
GNRHR2
OLFM3
MAB21L3
HIST2H3C
ATXN7L2
C1orf194
LRRC39
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
SLC30A7
RP11-165H20.1
DENND2C
LPPR5
FNDC7
SASS6
PPIAL4A
UBL4B
PDIA3P
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
MYBPHL
NBPF7
LOC375010
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
FRRS1
MIR137HG
NBPF9
MIR137
MIR197
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
LOC729987
PPIAL4E
PFN1P2
MIR942
LOC100128787
LOC100129138
LOC100129269
LOC100129620
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
MIR548AA1
LOC100506343
MIR2682

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
FECH
KDSR
GRP
LMAN1
MC4R
NARS
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
SERPINB3
SERPINB4
SERPINB7
TNFRSF11A
ONECUT2
VPS4B
PHLPP1
NEDD4L
PIGN
CDH20
CDH19
RAX
ST8SIA3
ZCCHC2
ZNF532
KIAA1468
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
CCBE1
RNF152
LINC00305
BOD1P
HMSD
LOC284294
CPLX4
LOC390858
LOC400654
MIR122
LOC100505549
MIR3591

Genes in Wide Peak

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

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C3AR1
CD69
CDKN1B
CREBL2
PHC1
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
PZP
SLC2A3
MFAP5
KLRC4
CSDA
GPRC5A
CD163
GDF3
CLEC2B
KLRG1
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
NECAP1
CLEC4E
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
PLEKHA5
MANSC1
MAGOHB
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
NANOG
DUSP16
APOLD1
GSG1
RERG
PLCZ1
HTR7P1
CAPZA3
CLEC6A
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
CD163L1
CLEC9A
C12orf36
CLEC4D
LOC338817
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
KLRC4-KLRK1
PRH1-PRR4
MIR3974

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.1.

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

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

Genes in Wide Peak

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

Table S39. 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 10p15.3.

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

Genes
ADARB2
KLF6
IDI1
PFKP
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
IDI2-AS1
IDI2
LOC282980
LOC338588
TUBB8
LINC00200
LOC399708
C10orf108
ADARB2-AS1
LOC100216001
LOC100507034

Genes in Wide Peak

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

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

Genes
CLEC3A
WWOX

Genes in Wide Peak

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

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

Genes
hsa-mir-1299
PGM5
ZNF658
FAM75A7
CNTNAP3
ANKRD20A1
FAM201A
CBWD5
LOC286297
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
FAM74A1
FAM74A4
ZNF658B
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

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

Genes
SMARCA4

Genes in Wide Peak

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

Table S44. 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 19p13.3.

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

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

Genes in Wide Peak

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

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

Genes
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
HSPA13
TPTE
NRIP1
USP25
RBM11
C21orf15
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
LIPI
ABCC13
POTED
LOC388813
ANKRD20A11P
MIRLET7C
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

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

Table S47. 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 5q11.2.

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

Genes
IL6ST
PIK3R1
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
BHMT
BTF3
CCNB1
CDK7
CKMT2
ERCC8
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HTR1A
ISL1
ITGA1
ITGA2
KIF2A
TNPO1
CD180
MAP1B
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
PDE4D
PMCHL2
RAD17
RASGRF2
RPS23
SMN1
SMN2
TAF9
TBCA
THBS4
XRCC4
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
HOMER1
SCAMP1
CARTPT
ZFYVE16
COL4A3BP
LHFPL2
CWC27
CCNO
NSA2
FST
PLK2
IQGAP2
SMA4
SMA5
ESM1
ADAMTS6
SV2C
MRPS27
PPWD1
OTP
SKIV2L2
SSBP2
BHMT2
PART1
FAM169A
RNU5E-1
RNU5D-1
DIMT1
DMGDH
IPO11
GCNT4
POLK
PELO
DHX29
DDX4
SGTB
ARL15
AGGF1
WDR41
DEPDC1B
BDP1
ERBB2IP
NLN
ZSWIM6
ANKRA2
MCCC2
CENPK
RGNEF
SLC30A5
CENPH
GPBP1
PARP8
ANKRD55
PTCD2
ELOVL7
C5orf44
ATG10
UTP15
ZCCHC9
ZBED3
GFM2
SPZ1
NDUFAF2
MRPS36
ATP6AP1L
SNX18
FCHO2
RAB3C
C5orf35
IL31RA
EMB
JMY
TMEM171
TMEM174
POC5
ACOT12
SREK1
SLC38A9
TMEM167A
MARVELD2
MIER3
CDC20B
PAPD4
ZNF366
FAM151B
S100Z
CCDC125
GAPT
CMYA5
ANKRD31
SERINC5
LOC257396
C5orf64
RNF180
SREK1IP1
ANKRD34B
IDAS
ACTBL2
MTX3
HCN1
MAST4
RNF138P1
RGS7BP
CRSP8P
GPX8
MIR449A
LOC642366
C5orf43
LOC644936
LOC647859
GUSBP3
GTF2H2B
SCARNA18
SNORA47
MIR449B
MIR581
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LRRC70
LOC100131067
FAM159B
LOC100170939
LOC100272216
NCRUPAR
LOC100303749
MIR449C
MTRNR2L2
OCLN
MIR4804
MIR3977
MIR4803

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

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

Table S50. 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
CDC25C
CDK7
CDO1
CETN3
CHD1
CKMT2
AP3S1
COX7C
CRHBP
HAPLN1
CSF2
CSNK1G3
VCAN
DMXL1
DHFR
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
FBN2
FER
FOXD1
GDF9
GFRA3
GLRX
GTF2H2
HEXB
HINT1
HMGCR
HSD17B4
HSPA4
HSPA9
IL3
IL4
IL5
IL9
IL13
IRF1
KCNN2
TNPO1
LECT2
LMNB1
LNPEP
LOX
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MSH3
NAIP
NEUROG1
NPY6R
PAM
PCSK1
PGGT1B
PITX1
PMCHL2
PPIC
PPP2CA
RAD17
RASA1
RASGRF2
RPS23
SKP1
SLC12A2
SLC22A4
SLC22A5
SMN1
SMN2
SNX2
SPOCK1
SRP19
TAF9
TBCA
TCF7
NR2F1
TGFBI
THBS4
UBE2B
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PDE8B
CDC23
P4HA2
ATG12
NREP
RAB9BP1
HOMER1
MYOT
SCAMP1
CXCL14
H2AFY
SMAD5-AS1
CARTPT
SNCAIP
TTC37
ZFYVE16
PJA2
DDX46
EDIL3
COL4A3BP
RAD50
KIF20A
LHFPL2
NSA2
POLR3G
IQGAP2
SEC24A
BRD8
HNRNPA0
SMA4
SMA5
KIF3A
ADAMTS6
RHOBTB3
ELL2
SV2C
FSTL4
MRPS27
SEPT8
PPIP5K2
ACSL6
PHF15
PPWD1
OTP
SSBP2
BHMT2
TNFAIP8
FAM169A
FBXL21
KLHL3
SNORD63
RNU5E-1
RNU5D-1
PKD2L2
UQCRQ
AFF4
SLC27A6
SNX24
DMGDH
TMED7
ISOC1
SAR1B
CDKL3
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
RAPGEF6
ERAP1
KDM3B
PHAX
FLJ11235
SGTB
ZCCHC10
GIN1
AGGF1
WDR41
TRIM36
RIOK2
BDP1
ERBB2IP
FEM1C
C5orf15
CDC42SE2
TRPC7
NLN
ZNF608
SEMA6A
ARRDC3
ANKRA2
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
TXNDC15
MCTP1
PTCD2
C5orf44
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
PCBD2
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
MEGF10
SPZ1
TSLP
C5orf30
LYRM7
SLC25A46
CDKN2AIPNL
MRPS36
ATP6AP1L
PRDM6
FTMT
FNIP1
EPB41L4A-AS1
MARCH3
FCHO2
LYSMD3
LEAP2
SLCO6A1
PRRC1
JMY
ZNF474
POU5F2
TMEM171
TMEM174
POC5
STARD4
WDR36
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
MARVELD2
ARSK
FAM81B
CCDC112
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
CCDC125
C5orf27
CMYA5
AQPEP
ANKRD31
SERINC5
KIAA0825
GPR150
DTWD2
NBPF22P
RGMB
RFESD
CHSY3
FAM170A
LOC340073
LOC340074
ANKRD34B
FAM174A
MTX3
CATSPER3
SLCO4C1
TICAM2
MAST4
C5orf48
LOC389332
C5orf63
MIR9-2
CRSP8P
FLJ42709
C5orf56
TIFAB
FLJ35946
LOC553103
CTXN3
TMEM232
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR583
GTF2H2C
LOC728342
SERF1B
LOC728723
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
MIR3660
MIR3936
MIR3661
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 8p21.3.

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

Genes
FGFR1
PCM1
WRN
WHSC1L1
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
NAT1
NAT2
ADRA1A
ADRB3
ASAH1
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
DUSP4
EGR3
EIF4EBP1
EPB49
EPHX2
EXTL3
PTK2B
FGL1
GFRA2
GNRH1
GSR
GTF2E2
NRG1
LOXL2
LPL
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STAR
STC1
FZD3
UBXN8
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ASH2L
MTMR7
BAG4
ENTPD4
PHYHIP
SORBS3
NPM2
DCTN6
PNMA2
ADAM28
RBPMS
ERLIN2
LZTS1
PROSC
XPO7
TRIM35
RHOBTB2
DDHD2
KIF13B
PSD3
LEPROTL1
SLC39A14
GPR124
FGF20
LSM1
ADAMDEC1
CNOT7
PURG
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
INTS10
CCDC25
BRF2
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
MTUS1
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
DUSP26
HMBOX1
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
TTI2
RAB11FIP1
REEP4
STMN4
PPAPDC1B
MAK16
FUT10
CHMP7
GOT1L1
VPS37A
NKX2-6
UNC5D
LETM2
PEBP4
CDCA2
ESCO2
FBXO16
KCNU1
R3HCC1
LGI3
LOC254896
LOC286059
EFHA2
LOC286114
SCARA5
LOC286135
RNF5P1
LOC389641
C8orf80
C8orf86
MIR320A
C8orf58
C8orf75
MBOAT4
LOC728024
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 11p15.5.

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC6
MYOD1
NAP1L4
NUCB2
SLC22A18
SLC22A18AS
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
IFITM2
TRIM3
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
SERGEF
OR5E1P
OR10A3
FXC1
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
USP47
TRIM68
UEVLD
PIDD
KCNQ1DN
SOX6
PARVA
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
FAM160A2
FAR1
BTBD10
MICALCL
TRIM5
SYT8
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX3
MRGPRX4
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
LDHAL6A
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
B7H6
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
LOC494141
MIR483
SNORA3
SNORA52
LOC644656
RASSF10
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
LOC729013
MIR675
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
MIR210HG
LOC100506305
LOC100506540
SAA2-SAA4
MIR4686
MIR4485
MIR4687

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

Table S54. 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 Xp22.31.

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

Genes
TBL1X
FAM9B

Genes in Wide Peak

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

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

Genes
CTNNB1
FANCD2
FHIT
MITF
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FBLN2
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
WNT7A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
BHLHE40
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
VPRBP
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
CXCR6
CSPG5
CHL1
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CAND2
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
RYBP
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LINC00312
LMCD1
ARHGEF3
VILL
C3orf32
TRNT1
ABHD5
DYNC1LI1
C3orf18
CRBN
SS18L2
C3orf19
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ARL8B
SETD5
TMEM40
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
TMEM111
BRK1
ZNF167
LMOD3
RAD18
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
LRRN1
SELK
PROK2
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
THOC7
WDR82
TSEN2
GRIP2
RTP3
C3orf20
ID2B
ATRIP
NICN1
MON1A
JAGN1
KBTBD8
GHRLOS2
IL17RC
ABHD14B
C3orf39
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
C3orf24
LRRC3B
GALNTL2
GPR62
KCNH8
FAM3D
LYZL4
KBTBD5
TRIM71
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
FGD5
CIDECP
CNTN4
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC285401
EIF4E3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
COL6A4P1
TPRXL
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VENTXP7
LOC401052
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
SNORA7A
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR563
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
MIR885
EGOT
GHRLOS
C3orf74
LOC100128640
NRADDP
LOC100129480
ZNF717
LOC100132146
LOC100132526
BSN-AS2
PRSS46
LOC100287879
LOC100288428
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
MIR3938
MIR3714
FGD5-AS1
LOC100505696
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4791
MIR4790
MIR548AC
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.13.

Table S57. 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
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
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
KIAA0586
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
TIMM9
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
C14orf105
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
ACTR10
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
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
C14orf149
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
C14orf37
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
SLC35F4
COX8C
ASPG
RAB15
FLJ31306
TOMM20L
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
C14orf38
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
BCL6
EIF4A2
ETV5
LPP
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
EHHADH
EIF4G1
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
OPA1
PAK2
PCYT1A
POLR2H
PPP1R2
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SST
THPO
FXR1
TP63
CHRD
EIF2B5
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
IGF2BP2
CLDN16
NCBP2
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
FETUB
LAMP3
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
YEATS2
MCCC1
HRASLS
SENP2
RTP4
MAGEF1
ATP13A3
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
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

Genes in Wide Peak

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

Table S60. 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
RAB21
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
TRHDE
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
TMEM19
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
TBC1D15
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
THAP2
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
TPH2
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
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
LOC283392
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
MRS2P2
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
LOC100507377
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 17p13.3.

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

Genes
PER1
TP53
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
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RPA1
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
GABARAP
NLRP1
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
KIAA0664
SMG6
WSCD1
CTDNEP1
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
C17orf59
GPR172B
WRAP53
RNMTL1
VPS53
C17orf85
TSR1
DHX33
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
CTC1
PITPNM3
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
LSMD1
NEURL4
ZNF594
HES7
SPATA22
TXNDC17
MIR22HG
TMEM88
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
DNAH2
RTN4RL1
KCTD11
TRPV3
SLC16A11
FBXO39
SLC16A13
C17orf74
SPNS3
C17orf61
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
OR3A4P
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
SNORA48
SNORD10
OR1D4
SCARNA21
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
C17orf107
LOC100130950
DBIL5P
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 15q15.3.

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

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

Genes in Wide Peak

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

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

Genes
hsa-mir-548u
BAI3
PTP4A1
PHF3
LGSN
KHDRBS2
EYS
GUSBP4
MCART3P

Genes in Wide Peak

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

Table S64. 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 3p11.1.

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

Genes
hsa-mir-4273
hsa-mir-1324
EPHA3
GBE1
HTR1F
POU1F1
PROS1
ROBO1
ROBO2
CGGBP1
CHMP2B
ZNF654
NSUN3
ARL13B
DHFRL1
CADM2
LOC255025
C3orf38
VGLL3
LOC401074
STX19
LOC440970
FLJ20518
FAM86DP
ZNF717
FRG2C
MIR1324
MIR4273
MIR4795

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.3.

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

Genes
hsa-mir-548f-5
NR0B1
CYBB
DMD
GK
MAGEB1
MAGEB2
MAGEB3
MAGEB4
OTC
PRRG1
RPGR
DYNLT3
TSPAN7
XK
SRPX
IL1RAPL1
CXorf27
FTHL17
MID1IP1
CXorf21
TMEM47
SYTL5
MAGEB10
DCAF8L1
MAGEB16
FAM47A
FAM47B
CXorf22
TAB3
LOC286442
CXorf59
LANCL3
DCAF8L2
FAM47C
CXorf30

Genes in Wide Peak

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

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

Genes
ATIC
CREB1
ACSL3
IDH1
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
AOX1
KIF1A
BARD1
BCS1L
BMPR2
BOK
CASP8
CASP10
CD28
CHRND
CHRNG
CLK1
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CYP27A1
DES
DTYMK
EEF1B2
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NPPC
ORC2
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
SUMO1
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
FZD7
CUL3
DGKD
STK16
KLF7
ADAM23
NRP2
CFLAR
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
BZW1
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
ABI2
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
FASTKD2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
SPATS2L
GIGYF2
TRAF3IP1
ABCA12
SNORD51
CNPPD1
STK36
CPS1-IT1
ICOS
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
NOP58
ASB1
CAB39
PRKAG3
PPIL3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
INO80D
PID1
ATG16L1
ANKZF1
USP40
HJURP
STRADB
HES6
ACCN4
DOCK10
MREG
WDR12
PECR
C2orf83
MFF
CXCR7
RNPEPL1
CYP20A1
MARCH4
WDFY1
NYAP2
ALS2
ZDBF2
USP37
CTDSP1
MPP4
NIF3L1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
TRAK2
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
C2orf47
SPAG16
CHPF
IQCA1
ALS2CR8
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
PARD3B
TYW5
DIS3L2
NEU4
ICA1L
AP1S3
SGPP2
KCTD18
ALS2CR12
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
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
CXXC11
FAM126B
UNC80
RUFY4
DUSP28
ESPNL
AOX2P
ECEL1P2
FONG
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
SNORA41
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
SNORD11
SNORD70
D2HGDH
LOC728323
DIRC3
SNORD11B
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
LOC100329109
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
LOC100507140
LOC100507443
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4775
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
ZNF98
LOC440518

Genes in Wide Peak

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

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

Genes
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
ALDH3A1
ALDH3A2
DRG2
FOXO3B
FLII
KCNJ12
LLGL1
MFAP4
MAPK7
MAP2K3
PRPSAP2
SHMT1
SREBF1
TOP3A
UBB
RNF112
COPS3
TMEM11
PIGL
NCOR1
ULK2
CCDC144A
PEMT
FBXW10
RAI1
GRAP
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
DHRS7B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
MED9
SLC47A1
NT5M
ZNF287
ZNF624
C17orf39
FAM106A
LRRC48
ATPAF2
SPECC1
C17orf76-AS1
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
TRIM16L
USP32P1
CENPV
FLCN
PLD6
USP32P2
TBC1D28
CDRT15L2
C17orf103
CCDC144B
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
CCDC144C
FAM211A
KRT16P2
GRAPL
FAM83G
KRT16P3
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
FAM106CP
KCNJ18
MIR1288
MIR1180
MTRNR2L1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.3.

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

Genes
RUNX1
OLIG2
hsa-mir-802
hsa-mir-4327
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
APP
ATP5J
ATP5O
BACH1
TMEM50B
CBR1
CBR3
CXADR
RCAN1
DYRK1A
GABPA
GART
GRIK1
HLCS
IFNAR1
IFNAR2
IFNGR2
IL10RB
KCNE1
KCNJ6
KCNJ15
NCAM2
TMPRSS15
ITSN1
SIM2
SLC5A3
SOD1
SON
TIAM1
TTC3
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
LINC00160
FAM165B
C21orf49
MIS18A
LINC00158
CHODL-AS1
LINC00113
SETD4
CLIC6
LINC00308
MRPL39
C21orf91
DNAJC28
C21orf62
MRAP
C21orf59
C21orf7
SCAF4
JAM2
C21orf63
MRPS6
RUNX1-IT1
DSCR8
C21orf119
GCFC1
LINC00310
MIR155HG
CYYR1
OLIG1
LINC00161
KRTAP13-1
TCP10L
CHODL
LINC00189
C21orf91-OT1
LINC00314
KRTAP15-1
DSCR9
DSCR10
D21S2088E
LINC00307
LINC00515
KRTAP13-4
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
LINC00478
KRTAP26-1
MIRLET7C
MIR125B2
MIR155
MIR99A
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
KRTAP19-8
C21orf54
MIR802
KRTAP25-1
LOC100133286
KRTAP20-4
KRTAP22-2
KRTAP21-3
LOC100288432
GRIK1-AS2
MIR4327
C21orf37
GCFC1-AS1
LOC100506334
LOC100506385
CBR3-AS1
LINC00159
MIR4759

Arm-level results

Table 3. Get Full Table Arm-level significance table - 26 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.32 | 2.98 | 0.00711 | 0.25 | 0.3 | 0.728
1q | 1955 | 0.62 | 13.7 | 0 | 0.29 | 0.891 | 0.373
2p | 924 | 0.34 | 0.847 | 0.722 | 0.11 | -6.54 | 1
2q | 1556 | 0.31 | 1.21 | 0.449 | 0.11 | -5.63 | 1
3p | 1062 | 0.12 | -5.34 | 1 | 0.48 | 6.1 | 2.64e-09
3q | 1139 | 0.22 | -2.76 | 1 | 0.37 | 2.22 | 0.0328
4p | 489 | 0.21 | -4.39 | 1 | 0.30 | -1.64 | 1
4q | 1049 | 0.12 | -6.04 | 1 | 0.30 | -0.471 | 1
5p | 270 | 0.53 | 5.72 | 5.47e-08 | 0.29 | -1.83 | 1
5q | 1427 | 0.28 | -0.0865 | 1 | 0.41 | 4.45 | 1.31e-05
6p | 1173 | 0.32 | 0.63 | 0.881 | 0.33 | 0.926 | 0.373
6q | 839 | 0.17 | -4.01 | 1 | 0.52 | 6.97 | 9.29e-12
7p | 641 | 0.55 | 7.5 | 6.55e-13 | 0.17 | -4.26 | 1
7q | 1277 | 0.45 | 5.57 | 1.03e-07 | 0.18 | -3.51 | 1
8p | 580 | 0.33 | -0.176 | 1 | 0.56 | 7.2 | 1.98e-12
8q | 859 | 0.49 | 5.97 | 1.57e-08 | 0.23 | -2.56 | 1
9p | 422 | 0.14 | -5.18 | 1 | 0.56 | 7.41 | 6.28e-13
9q | 1113 | 0.11 | -5.42 | 1 | 0.51 | 7.37 | 6.9e-13
10p | 409 | 0.27 | -2.7 | 1 | 0.29 | -1.96 | 1
10q | 1268 | 0.20 | -3.02 | 1 | 0.30 | 0.25 | 0.73
11p | 862 | 0.23 | -2.83 | 1 | 0.29 | -0.974 | 1
11q | 1515 | 0.26 | -0.823 | 1 | 0.24 | -1.35 | 1
12p | 575 | 0.35 | 0.275 | 1 | 0.28 | -1.78 | 1
12q | 1447 | 0.29 | 0.264 | 1 | 0.25 | -1.29 | 1
13q | 654 | 0.18 | -4.34 | 1 | 0.50 | 5.91 | 6.92e-09
14q | 1341 | 0.30 | 0.392 | 1 | 0.30 | 0.189 | 0.739
15q | 1355 | 0.15 | -4.02 | 1 | 0.52 | 8.36 | 0
16p | 872 | 0.29 | -0.912 | 1 | 0.29 | -1.01 | 1
16q | 702 | 0.23 | -3 | 1 | 0.37 | 1.28 | 0.221
17p | 683 | 0.21 | -3.18 | 1 | 0.58 | 8.73 | 0
17q | 1592 | 0.40 | 4.39 | 3.82e-05 | 0.25 | -0.903 | 1
18p | 143 | 0.26 | -2.98 | 1 | 0.45 | 2.61 | 0.0128
18q | 446 | 0.20 | -3.91 | 1 | 0.52 | 5.87 | 7.9e-09
19p | 995 | 0.09 | -5.81 | 1 | 0.54 | 8.49 | 0
19q | 1709 | 0.16 | -3.54 | 1 | 0.40 | 5.01 | 9.04e-07
20p | 355 | 0.43 | 2.24 | 0.0558 | 0.40 | 1.54 | 0.146
20q | 753 | 0.42 | 3.08 | 0.00587 | 0.28 | -1.43 | 1
21q | 509 | 0.29 | -1.72 | 1 | 0.42 | 2.59 | 0.0128
22q | 921 | 0.18 | -3.81 | 1 | 0.49 | 6.04 | 3.37e-09
Xq | 1312 | 0.19 | -3.8 | 1 | 0.19 | -3.59 | 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/1708691/2.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 303 Input Tumor Samples.

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

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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