SNP6 Copy number analysis (GISTIC2) - Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1CR5SSS

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 2.0.22 (Firehose task version: 140).

Summary

There were 882 tumor samples used in this analysis: 32 significant arm-level results, 9 significant focal amplifications, and 23 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 - 9 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
5q35.1	5.8456e-42	5.8456e-42	chr5:163593195-180915260	163
7q31.2	3.2009e-07	3.2009e-07	chr7:116382828-116391555	1
2q32.1	0.00010935	0.00010935	chr2:172809655-212709797	251
3q26.32	0.0001149	0.0001149	chr3:162477826-198022430	256
17q24.3	0.017894	0.017894	chr17:48641966-81195210	430
Xq11.2	0.036599	0.036599	chrX:64003371-64052730	0 [ZC4H2]
10p14	0.11691	0.11691	chr10:1-22423301	152
1q32.1	0.19244	0.19244	chr1:120522602-216075493	895
8q24.22	0.2129	0.2129	chr8:69506698-146364022	450

Genes in Wide Peak

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

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

Genes
NPM1
TLX3
NSD1
RANBP17
TRIM52
SNORD95\|ENSG00000264549.1
SNORD96A
LINC00847
MIR340
RN7SKP150
MIR1229
HMGB3P22
RN7SL71P
ZNF879
ZNF354B
AACSP1
RN7SKP70
RN7SL646P
RN7SL562P
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
RN7SKP148
snoU13\|ENSG00000239026.1
NSG2
RNA5SP200
SNORA74B
ATP6V0E1
MIR5003
SNORA57\|ENSG00000212529.1
C5orf50
SNORA70\|ENSG00000206909.1
RN7SL339P
snoU13\|ENSG00000252387.1
RN7SL623P
MIR4454
KCNMB1
LCP2
C5orf58
MIR378E
MIR585
MIR103A1
PANK3
FBLL1
SNORA40\|ENSG00000253065.1
RN7SKP60
BNIP1
CANX
CLTB
DBN1
DOCK2
DRD1
DUSP1
F12
FGFR4
FOXI1
FLT4
GABRP
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
RARS
SLC34A1
SLIT3
SNCB
STK10
ZNF354A
STC2
FGF18
SQSTM1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
WWC1
FBXW11
ZNF346
TSPAN17
OR4F3
OR2V1
PRELID1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
SPDL1
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
TRIM7
MXD3
THOC3
PHYKPL
UNC5A
TRIM41
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
C5orf47
OR2Y1
CREBRF
BTNL9
HIGD2A
FAM153B
RASGEF1C
EFCAB9
SH3PXD2B
FAM153A
OR2V2
ZNF454
C5orf60
PFN3
SIMC1
ZFP62
CBY3
FAM153C
FAM196B
MIR3912
MIR4634
MIR4638

Genes in Wide Peak

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

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

Genes
MET

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q32.1.

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

Genes
HOXD11
CHN1
CREB1
HOXD13
IDH1
NFE2L2
PMS1
RNA5SP119
RPE
RNA5SP118
RNA5SP117
CRYGEP
snoU13\|ENSG00000238582.1
RNA5SP116
MIR2355
FASTKD2
RN7SKP260
RN7SKP200
SNORA41\|ENSG00000207406.1
SNORD51\|ENSG00000207047.2
NDUFS1
Vault\|ENSG00000252485.1
RN7SKP178
RN7SL670P
SNORA1\|ENSG00000202059.1
WDR12
RN7SL40P
RN7SL753P
SNORD11\|ENSG00000238317.1
SNORD11B
SNORD70\|ENSG00000212309.1
SNORD70\|ENSG00000212534.1
snoU13\|ENSG00000238770.1
RN7SL694P
ORC2
RNA5SP115
AOX2P
RN7SL717P
PLCL1
RFTN2
MOB4
SNORA4\|ENSG00000202434.1
C2orf66
SCARNA16\|ENSG00000252923.1
RN7SL820P
snoU13\|ENSG00000239161.1
SNORD59\|ENSG00000252517.1
PCGEM1
NABP1
RN7SKP179
TMEM194B
MIR3129
MIR1245A
DIRC1
GULP1
RNA5SP114
RN7SKP42
U8\|ENSG00000212581.1
snoU13\|ENSG00000238306.1
SNORA77\|ENSG00000221498.1
DNAJC10
RN7SL267P
RNA5SP113
RNU6ATAC19P
SNORA43\|ENSG00000202216.1
snoU13\|ENSG00000238339.1
ACA59\|ENSG00000252000.1
PLEKHA3
TTC30A
TTC30B
snoU13\|ENSG00000238295.1
MIR3128
RNA5SP112
RNU6ATAC14P
HOXD9
EVX2
KIAA1715
ATP5G3
SP9
RN7SL65P
snoU13\|ENSG00000239041.1
PDK1
snoU13\|ENSG00000238572.1
METAP1D
ACADL
AOX1
BMPR2
CASP8
CASP10
CD28
CHRNA1
CLK1
COL3A1
COL5A2
CPS1
ATF2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
DLX1
DLX2
EEF1B2
ERBB4
FRZB
MSTN
GLS
GPR1
HOXD1
HOXD3
HOXD4
HOXD8
HOXD10
HOXD12
HSPD1
HSPE1
INPP1
ITGA6
ITGA4
ITGAV
MAP2
MYO1B
MYL1
NAB1
NDUFB3
NEUROD1
PDE1A
PTH2R
SP3
SSFA2
STAT1
STAT4
TFPI
TTN
SUMO1
WIPF1
FZD5
FZD7
SDPR
HAT1
AGPS
PRKRA
SLC25A12
KLF7
ADAM23
NRP2
CFLAR
STK17B
GTF3C3
CIR1
BZW1
ABI2
CALCRL
LANCL1
UBE2E3
MTX2
NCKAP1
RAPGEF4
SATB2
SF3B1
TMEFF2
MOB4
SPATS2L
HIBCH
OLA1
ICOS
SLC40A1
PDE11A
NOP58
FKBP7
MLTK
PPIL3
ASNSD1
MFSD6
INO80D
STRADB
ZC3H15
DNAH7
SLC39A10
CYP20A1
HECW2
ALS2
ZDBF2
CWC22
MPP4
NIF3L1
OSGEPL1
RAPH1
CDK15
TMEM237
NBEAL1
TRAK2
BOLL
C2orf47
SCRN3
CARF
PGAP1
COQ10B
CDCA7
WDR75
C2orf88
SESTD1
ANKRD44
ZNF804A
MARS2
ORMDL1
OSBPL6
PARD3B
NUP35
TYW5
RBM45
ICA1L
KCTD18
ALS2CR12
CPO
MDH1B
DUSP19
ANKAR
FAM117B
KANSL1L
ZSWIM2
ZNF385B
METTL21A
CCNYL1
PPP1R1C
SGOL2
ALS2CR11
GPR155
FAM171B
PIKFYVE
C2orf69
HNRNPA3
CCDC150
CCDC141
FAM126B
UNC80
FTCDNL1
CERKL
PLEKHM3
C2orf80
DYTN
FSIP2
MIR10B
DFNB59
MIR561
MIR933
MIR1258
MIR4437
MIR548AE1
MIR4775

Genes in Wide Peak

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

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

Genes
PIK3CA
BCL6
EIF4A2
ETV5
LPP
SOX2
TFRC
FAM157A
FYTTD1
snoU13\|ENSG00000238491.1
MIR4797
U4\|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
RN7SL36P
MIR3137
LINC00884
LINC00887
RN7SL215P
RN7SL447P
snoU13\|ENSG00000238902.1
RN7SKP222
RN7SKP296
RN7SL486P
MIR944
MIR28
snoU13\|ENSG00000239093.1
RTP4
SNORA4\|ENSG00000263776.1
SNORA63\|ENSG00000200320.1
SNORA81\|ENSG00000221420.2
SNORA63\|ENSG00000200418.1
SNORD2\|ENSG00000238942.1
KNG1
CRYGS
RN7SL637P
TRA2B
MIR548AQ
SENP2
snoU13\|ENSG00000239146.1
SNORD66\|ENSG00000212158.1
MIR1224
CYP2AB1P
SNORA4\|ENSG00000251730.1
SNORA63\|ENSG00000199363.1
SNORA81\|ENSG00000253092.1
SNORA63\|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
RN7SL229P
U8\|ENSG00000201810.1
RNA5SP149
snoU13\|ENSG00000239096.1
GNB4
SNORA25\|ENSG00000201957.1
RNA5SP148
SNORA18\|ENSG00000200288.1
RN7SKP52
LINC00578
LINC00501
RNA5SP147
snoU13\|ENSG00000271842.1
MIR4789
RN7SKP40
RN7SKP234
snoU13\|ENSG00000239141.1
SNORA72\|ENSG00000200355.1
RN7SL141P
PP13439
snoU13\|ENSG00000238359.1
MIR569
RNY5P3
CLDN11
TERC
EGFEM1P
RN7SKP298
MIR720
snoU13\|ENSG00000238398.1
CT64
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
RPL35A
SI
ST6GAL1
SKIL
SLC2A2
SST
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
ACTRT3
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
SLC51A
FBXO45
MUC20
SENP5
NAALADL2
TCTEX1D2
SMCO1
UTS2B
HTR3E
C3orf70
TPRG1
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
WDR53
ANKRD18DP
NRROS
TMEM212
LINC00885
C3orf65
GMNC
MIR551B
MIR570
MIR922
MIR1263
MIR4448

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.3.

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

Genes
BRIP1
CD79B
CLTC
DDX5
HLF
PRKAR1A
ASPSCR1
MSI2
CANT1
MIR4525
RAB40B
snoU13\|ENSG00000238403.1
snoU13\|ENSG00000238947.1
DUS1L
PCYT2
SLC25A10
LINC00482
MIR1250
MIR657
MIR4730
CBX8
snoU13\|ENSG00000239173.1
ENGASE
DDC8
RN7SL454P
SNORA30\|ENSG00000200063.1
RN7SL236P
FLJ45079
LINC00338
LINC00868
MIR636
SNORD1B
SNHG16
PRCD
snoU13\|ENSG00000238418.1
MYO15B
RN7SL573P
MIR3615
CD300LD
GPRC5C
RNA5SP448
LINC00469
SSTR2
SCARNA24\|ENSG00000252274.1
RN7SKP180
LINC00511
MAP2K6
SNORA40\|ENSG00000252352.1
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
RN7SL622P
SNORA38B
MIR548D2
RN7SL756P
snoU13\|ENSG00000238612.1
PSMD12
SNORA8\|ENSG00000207410.1
RNA5SP447
RNA5SP446
MIR634
RNA5SP445
RN7SL735P
RNA5SP444
SLC16A6P1
RN7SL404P
RN7SL409P
PLEKHM1P
SMURF2
MIR5047
MIR3064
SNORD104
SNORA76\|ENSG00000266402.2
TCAM1P
RN7SL805P
ACE
TLK2
TBC1D3P2
RN7SL800P
snoU13\|ENSG00000238799.1
RN7SL448P
RN7SL606P
PPM1D
RPL12P38
SCARNA20\|ENSG00000252577.1
USP32
MIR4729
PRR11
MIR301A
MIR454
RN7SL716P
PPM1E
U3\|ENSG00000212195.1
DYNLL2
SRSF1
VEZF1
MRPS23
RN7SKP94
RN7SL449P
RN7SL437P
RNF126P1
RN7SKP14
snoZ178
RN7SL699P
snoU13\|ENSG00000238815.1
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
COX11
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
LPO
MAFG
MAP3K3
MPO
TRIM37
NME1
NPTX1
P4HB
PDE6G
SEPT4
PRKCA
PRPSAP1
PSMC5
PYCR1
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
COIL
AKAP1
EPX
AXIN2
DGKE
CBX4
DNAH17
ABCC3
RGS9
GALR2
SPHK1
CACNA1G
SOCS3
SPAG9
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
TOB1
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
POLG2
CD300A
TMC6
DDX42
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
UTP18
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
PTRH2
LUC7L3
SDK2
MBTD1
BCAS3
TMEM104
RNF43
MKS1
LINC00483
C17orf80
CCDC40
WIPI1
SMG8
TMEM100
NPLOC4
ST6GALNAC1
TEX2
TEX14
WDR45B
CA10
CCDC47
MIF4GD
INTS2
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
FN3K
DNAI2
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
OGFOD3
ZNF750
NUP85
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
KIF2B
CBX2
FAM104A
FBF1
UNK
CEP95
TRIM47
ANKRD40
STRADA
C17orf72
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
WFIKKN2
TBC1D16
AFMID
MGAT5B
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
EFCAB3
NOTUM
TMC8
ANKFN1
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
STXBP4
MYADML2
NPB
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
OXLD1
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
LRRC37A3
YPEL2
C17orf82
BTBD17
TEX19
CUEDC1
MIR142
MIR21
MXRA7
CPSF4L
SMIM5
NME2
MIR633
SMIM6
TEN1
C17orf99
MIR4316
MIR338
MIR3186
MIR3614
MIR3678
MIR3615
C17orf112
MIR4739
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p14.

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

Genes
GATA3
MLLT10
RN7SKP37
RN7SKP219
MIR1915
CASC10
U3\|ENSG00000251749.1
RNA5SP303
U3\|ENSG00000200545.1
C10orf112
TMEM236\|ENSG00000184040.7
MRC1L1
snoR442\|ENSG00000251959.1
ST8SIA6
snoU13\|ENSG00000238552.1
SNORA31\|ENSG00000252537.1
snoU13\|ENSG00000239130.1
ITGA8
NMT2
ACBD7
MEIG1
CDNF
RNA5SP302
RNA5SP301
RNA5SP300
MIR4480
RNU6ATAC39P
SNORD45\|ENSG00000252438.1
RN7SL198P
RN7SL232P
snoU13\|ENSG00000238900.1
U6\|ENSG00000272507.1
LINC00710
SFTA1P
LINC00709
RNA5SP299
LINC00708
TAF3
LINC00707
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8\|ENSG00000251909.1
AKR1CL1
U8\|ENSG00000239142.1
U8\|ENSG00000251740.1
U8\|ENSG00000239148.1
U8\|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ATP5C1
CACNB2
CALML3
AKR1C4
KLF6
AKR1C2
TRDMT1
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PRKCQ
RSU1
VIM
STAM
CUBN
PRPF18
AKR1C3
CDC123
PTPLA
PTER
USP6NL
OPTN
NET1
NEBL
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
SEPHS1
KIN
DIP2C
LARP4B
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
CAMK1D
SFMBT2
DNAJC1
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
FBXO18
PLXDC2
RBM17
IDI2
UCN3
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
PROSER2
C10orf113
SKIDA1
C1QL3
LINC00200
PRR26
TMEM236\|ENSG00000148483.7
MIR1265
MIR548Q
MIR4293
MIR4675
MIR548AK

Genes in Wide Peak

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

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

Genes
SDHC
ABL2
ARNT
BCL9
ELK4
FCGR2B
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
TPM3
TPR
PDE4DIP
SLC45A3
SNORD116\|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26\|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
SERTAD4
MIR4260
MIR205HG
MIR29B2
MIR29C
snoU13\|ENSG00000238401.1
FAIM3
IL20
SNORD112\|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60\|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72\|ENSG00000201944.1
SNORD112\|ENSG00000252946.1
SCARNA20\|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77\|ENSG00000221643.1
RABIF
PCAT6
SNORA70\|ENSG00000253042.1
U6\|ENSG00000272262.1
snoU13\|ENSG00000239046.1
snoU13\|ENSG00000238571.1
PTPRVP
GPR37L1
SNORA70\|ENSG00000206637.1
MIR1231
MIR5191
RPS10P7
ASCL5
LINC00862
MIR181A1HG
MIR4735
U3\|ENSG00000252241.1
MIR1278
snoU109\|ENSG00000238754.1
RN7SKP126
RNA5SP73
RN7SKP156
RNA5SP72
SNORD112\|ENSG00000252790.1
RN7SL654P
RNA5SP71
RN7SKP229
RNA5SP70
KIAA1614
U6\|ENSG00000272292.1
MIR3121
LHX4
RN7SL230P
IFRG15
RN7SL374P
SNORA67\|ENSG00000201619.1
SNORA67\|ENSG00000212338.1
TOR3A
SNORA63\|ENSG00000201791.1
RNA5SP69
C1orf220
LINC00083
MIR488
SCARNA3
snoU13\|ENSG00000238872.1
RNA5SP68
RNA5SP67
SNORD78\|ENSG00000208317.1
GAS5
RN7SKP160
snoU13\|ENSG00000238430.1
ANKRD45
snoU13\|ENSG00000251817.1
TNFSF18
SNORD112\|ENSG00000252354.1
DNM3OS
SCARNA20\|ENSG00000253060.1
RN7SL425P
snoU13\|ENSG00000238859.1
RN7SL269P
RN7SL333P
C1orf112
F5
RNA5SP66
LINC00970
LINC00626
ANKRD36BP1
SFT2D2
MIR1255B2
snoU13\|ENSG00000238325.1
RNA5SP65
POGK
MIR921
RNA5SP64
UCK2
TMCO1
SNORD112\|ENSG00000252359.1
U3\|ENSG00000212538.1
RNA5SP63
RNA5SP62
SNORD112\|ENSG00000252740.1
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64\|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64\|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13\|ENSG00000238843.1
BGLAP
SNORA26\|ENSG00000252236.1
SCARNA4\|ENSG00000252808.1
SNORA42\|ENSG00000207475.1
snoU13\|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59\|ENSG00000252682.1
SNORA58\|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3\|ENSG00000252669.1
snoU13\|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31\|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13\|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
ADORA1
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATF3
ATP1A2
ATP1A4
ATP1B1
ATP2B4
C4BPA
C4BPB
CACNA1E
CACNA1S
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD34
CD48
CENPF
CHI3L1
CHIT1
CHRNB2
CKS1B\|ENSG00000173207.8
CLK2
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSRP1
CTSE
CTSK
CTSS
CD55
DHX9
DPT
ECM1
EIF2D
EFNA1
EFNA3
EFNA4
ELF3
ENSA
ETV3
F13B
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GBA
GJA5
GJA8
GLUL
GPR25
HDGF
CFH
CFHR1
CFHR2
MR1
HSD11B1
HSPA6
IFI16
IL6R
IL10
ILF2
INSRR
IRF6
IVL
KCNJ10
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NEK2
NHLH1
NIT1
NPR1
DDR2
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PPP2R5A
PRELP
PRKAB2
PROX1
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PEX19
RAB13
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
CNTN2
VPS72
THBS3
TCHH
TNNI1
TNNT2
TNR
TRAF5
CCT3
TUFT1
TNFSF4
USF1
USH2A
DAP3
NPHS2
BTG2
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
DYRK3
RGS5
PPFIA4
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
MPZL1
SH2D2A
ANGPTL1
TBX19
PRPF3
ARHGEF2
DEDD
XPR1
MAPKAPK2
GPR52
AIM2
RASAL2
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
PIAS3
TIMM17A
LRRN2
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
KDM5B
CFHR4
CFHR3
OCLM
JTB
MTMR11
SLC27A3
IL24
TDRKH
CD160
PMF1
DUSP12
VPS45
PLEKHA6
KIAA0907
KIFAP3
ATF6
KIF21B
NMNAT2
NFASC
POGZ
COLGALT2
RGL1
SYT11
PRRC2C
RPRD2
CAMSAP2
SMG5
NCSTN
CRB1
GPR161
ZNF281
SNAPIN
PHLDA3
RUSC1
CA14
DSTYK
CCDC19
LMOD1
NBPF14
MPC2
INTS7
OLFML2B
C1orf43
NSL1
DNM3
TOR1AIP1
CHTOP
LCE2B
OPTC
OR10J1
RPS6KC1
USP21
DIEXF
CACYBP
SLC39A1
KLHL20
LAMTOR2
FLVCR1
UBE2T
TMOD4
NME7
NENF
IL19
CERS2
CRNN
G0S2
DCAF8
F11R
GLRX2
BOLA1
ZBTB7B
RRNAD1
ADIPOR1
APH1A
KCTD3
PLEKHO1
IER5
UCHL5
SUCO
GPR89B
HSD17B7
UFC1
DTL
METTL13
OAZ3
CYB5R1
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
RALGPS2
MSTO1
DARS2
GOLPH3L
KLHDC8A
ETNK2
KIRREL
TMEM206
YY1AP1
YOD1
BATF3
UBE2Q1
ITLN1
IPO9
HHAT
RCOR3
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
SMYD2
LHX9
RAB25
PGLYRP4
RHBG
SCYL3
CAMK1G
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
FAM5B
CCDC181
SLAMF7
CADM3
PRUNE
KLHL12
LGR6
HAPLN2
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
RFWD2
RGS18
NUCKS1
MRPL9
INTS3
SCNM1
C1orf116
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
VASH2
PAQR6
TRIM46
MROH9
TARS2
EDEM3
FLAD1
TRAF3IP3
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
FCAMR
TEX35
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
LINC00467
FCRLA
PPP1R15B
MAEL
RGS8
NAV1
SEC16B
AQP10
SLAMF9
PYGO2
ANGEL2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
PIGM
IGSF8
LEMD1
C1orf85
PGLYRP3
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
AXDND1
ATP6V1G3
OR10J5
DCST2
ZNF648
TEDDM1
ARL8A
SYT2
GOLT1A
UHMK1
FCRLB
LIX1L
TSACC
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ITLN2
C1orf74
CREB3L4
C1orf51
HFE2
ANKRD35
FAM163A
MFSD4
PM20D1
NBPF12
LELP1
RC3H1
DCST1
METTL11B
FAM78B
SHISA4
BNIPL
LRRC71
PYHIN1
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
LCE4A
NBPF11
KRTCAP2
CRTC2
TMEM9
SLC41A1
LCE5A
SYT14
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
SLC9C2
NBPF16
LINC00303
ANKRD34A
C1orf204
HIST2H2AB
S100A7A
RXFP4
FAM5C
C1orf110
RD3
OR10R2
FCRL6
KCNT2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
PEAR1
ILDR2
NOTCH2NL
LYSMD1
HRNR
FLG2
FMO6P
LINC00272
C1orf53
TMEM81
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
C1ORF220
NBPF9
APOBEC4
MIR181B1
MIR199A2
MIR181A1
MIR214
C1orf132
RGS21
HIST2H2BF
ETV3L
LRRC52
OR10J3
MIR135B
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR557
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
TSTD1
C2CD4D
NBPF20
MIR1295A
MIR4257
MIR4424

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.22.

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

Genes
EXT1
COX6C
MYC
RECQL4
NCOA2
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK\|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5\|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25\|ENSG00000251744.1
SNORA40\|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72\|ENSG00000252158.1
SNORA12\|ENSG00000212342.1
SNORA25\|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13\|ENSG00000238422.1
U3\|ENSG00000221461.1
RNY4P5
snoU13\|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32\|ENSG00000206776.1
COLEC10
SNORA31\|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13\|ENSG00000238656.1
SNORD112\|ENSG00000252559.1
TMEM74
RNA5SP275
snoU13\|ENSG00000238687.1
RIMS2
MIR3151
RNU6ATAC8P
snoU13\|ENSG00000238533.1
snoU13\|ENSG00000238372.1
RN7SL563P
NACAP1
RN7SKP249
RN7SL685P
RNU6ATAC41P
MIR1273A
SNORD77\|ENSG00000212414.1
RN7SL350P
RN7SKP85
KCNS2
NIPAL2
SNORA72\|ENSG00000207067.1
LAPTM4B
U3\|ENSG00000207215.1
PTDSS1
snoU13\|ENSG00000238791.1
FSBP
RNA5SP274
LINC00535
RN7SKP231
snoU13\|ENSG00000239134.1
MIR4661
RN7SL777P
RNA5SP273
LINC00534
RNA5SP272
MMP16
REXO1L10P\|ENSG00000255940.1
REXO1L11P
REXO1L10P\|ENSG00000270416.1
snoU13\|ENSG00000238566.1
SLC10A5
IMPA1P
RN7SL308P
RN7SL107P
SNORA20\|ENSG00000206649.1
RN7SL41P
snoU13\|ENSG00000238595.1
CASC9
RNA5SP271
U8\|ENSG00000200191.1
RN7SL19P
snoU13\|ENSG00000238450.1
RNA5SP270
RN7SL675P
RN7SKP29
RNA5SP269
ADCY8
ANGPT1
ANXA13
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CYC1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
GEM
GLI4
GML
GPR20
GPT
GRINA
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
LY6E
LY6H
MATN2
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PLEC
PMP2
POLR2K
PKIA
PTK2
PEX2
RAD21
RPL7
RPL8
RPL30
SDC2
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
LY6D
GPAA1
RIPK2
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
LRRC14
EMC2
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
CPQ
KHDRBS3
POP1
WWP1
STMN2
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
SULF1
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
LRRC6
LY96
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
OPLAH
PABPC1
KCNV1
STAU2
MTBP
AGO2
MRPS28
COMMD5
MRPL13
ATAD2
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
RMDN1
ZNF706
VPS28
FAM203A
KCNK9
THEM6
UBR5
FAM49B
AZIN1
OTUD6B
CHRAC1
GDAP1
EXOSC4
PDP1
CNGB3
ESRP1
TMEM70
TRMT12
OXR1
WDYHV1
UBE2W
TMEM55A
SLC39A4
SYBU
INTS8
PAG1
GSDMC
JPH1
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
PRDM14
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
DSCC1
DERL1
SLC52A2
PLEKHF2
ZFAND1
ZFHX4
GSDMD
BAALC
GRHL2
ARHGAP39
ZNF34
SLC25A32
DCSTAMP
SLCO5A1
SHARPIN
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NCALD
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
PSKH2
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
TBC1D31
TP53INP1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
C8orf34
TOP1MT
ZNF572
FAM92A1
NDUFAF6
ABRA
LYPD2
TMEM71
DCAF4L2
RALYL
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
FAM91A1
SBSPON
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
REXO1L1
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
TRIQK
DPY19L4
FBXO43
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
CA13
XKR9
C8orf87
RBM12B
MROH5
MAFA
GDF6
C8orf59
SAMD12
MIR30B
MIR30D
LRRC24
ZNF704
MROH6
FABP9
FABP12
FER1L6
MIR548A3
MIR599
MROH1
FAM203B
OC90
MIR875
LRRC69
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3150B
MIR3610
MIR378D2
MIR4662B
MIR4663
MIR4664
MIR4471
MIR5680
MIR5194
MIR5708
MIR5681A

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 - 23 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	7.8605e-40	7.3617e-36	chr9:21931610-22448737	3
2q37.3	8.2662e-22	6.3015e-21	chr2:240317967-243199373	40
1p36.31	1.2096e-17	1.4636e-16	chr1:1-29140747	492
3p26.3	7.93e-38	7.8444e-16	chr3:1-17201156	130
3p21.2	6.3629e-41	2.2245e-15	chr3:37864412-53529383	303
4q34.3	1.2094e-08	1.2094e-08	chr4:179280062-182757119	4
8p23.2	1.2054e-07	1.1831e-07	chr8:3548028-4251283	2
9p23	2.11e-10	2.0853e-07	chr9:8885227-12687261	2
6q26	2.2959e-10	3.4392e-05	chr6:128840740-171115067	257
11q23.1	0.00048907	0.00048633	chr11:100228730-131242853	317
1p31.1	5.6659e-06	0.0011493	chr1:71540450-73657665	2
10q23.31	0.0019119	0.0019157	chr10:89617158-90034038	3
6q26	9.4611e-11	0.0053042	chr6:119669222-171115067	293
14q31.1	0.0069069	0.0070101	chr14:56181301-107349540	516
3p12.2	0.00035682	0.014293	chr3:78209676-88044123	16
13q13.2	0.023682	0.024613	chr13:1-72013697	345
16q23.3	0.028988	0.028707	chr16:75893345-90354753	139
1q44	0.033316	0.033615	chr1:210848345-249250621	341
3p14.1	0.00020384	0.06656	chr3:67061380-69791737	11
19p13.3	0.14251	0.13736	chr19:1033227-6228216	162
5p15.33	0.14875	0.14445	chr5:1015064-5129938	18
2q22.1	0.053858	0.23769	chr2:140708948-143637838	2
Xp22.2	0.23516	0.23769	chrX:11792056-12870927	3

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53

Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
GAL3ST2
C2orf54
ING5
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
DUSP28
AQP12A
OR6B2
PRR21
AQP12B
D2HGDH
MIR4786

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
SCARNA24\|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13\|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18\|ENSG00000252691.1
SCARNA17\|ENSG00000252190.1
MAN1C1
snoU13\|ENSG00000238889.1
SYF2
snoU13\|ENSG00000238986.1
RN7SL857P
snoU13\|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13\|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13\|ENSG00000239020.1
PADI6
MIR3972
U1\|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1\|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13\|ENSG00000238818.1
DDI2
AGMAT
SCARNA21\|ENSG00000251866.1
C1orf195
SCARNA11\|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13\|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70\|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13\|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16\|ENSG00000252404.1
RN7SL451P
SNORA77\|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13\|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
KCNAB2
FCN3
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
THEMIS2
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
AHDC1
SMPDL3B
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
AUNIP
EFHD2
MMEL1
RSG1
MUL1
NOL9
LIN28A
LINC00115
MORN1
FAM110D
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SESN2
ESPN
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
C1orf170
SYTL1
IGSF21
KIAA2013
THAP3
STPG1
UBXN11
FBXO44
ATPIF1
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
C1orf234
OR4F29
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

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

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

Genes
VHL
FANCD2
PPARG
RAF1
XPC
SRGAP3
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13\|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13\|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13\|ENSG00000238345.1
snoU13\|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43\|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13\|ENSG00000239126.1
EGOT
SNORA43\|ENSG00000253049.1
RN7SKP144
RN7SL120P
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RPL32
SEC13
SETMAR
SLC6A1
SLC6A6
TIMP4
BRPF1
COLQ
CAMK1
BHLHE40
SH3BP5
VGLL4
EDEM1
TATDN2
IQSEC1
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LMCD1
SSUH2
TRNT1
CRBN
CCDC174
GHRL
ARL8B
SETD5
TMEM40
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
HDAC11
TSEN2
C3orf20
JAGN1
IL17RC
EAF1
OXNAD1
FANCD2OS
GALNT15
CHCHD4
METTL6
TAMM41
IL17RE
CPNE9
FGD5
CNTN4
SUMF1
RPUSD3
PRRT3
TPRXL
MIR563
MIR378B
MIR3714
MIR4790

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.2.

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

Genes
CTNNB1
MYD88
BAP1
SETD2
PBRM1
SNORA26\|ENSG00000212608.1
SNORD38\|ENSG00000207109.1
RN7SL821P
snoU13\|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19\|ENSG00000222345.1
SNORD19B\|ENSG00000238862.1
SNORD19\|ENSG00000212493.1
SNORD19B\|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13\|ENSG00000238350.1
snoU13\|ENSG00000239128.1
snoU13\|ENSG00000251938.1
PRSS44
PRSS45
SNORD77\|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3\|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
U8\|ENSG00000212145.2
RN7SKP58
SCARNA21\|ENSG00000252409.1
ZNF621
SNORA64\|ENSG00000202517.1
RN7SL411P
SNORA62\|ENSG00000202363.1
SNORA6
MIR26A1
ACAA1
ACVR2B
ALAS1
AMT
APEH
RHOA
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR5
CCR8
ACKR2
COL7A1
CX3CR1
CYP8B1
DAG1
DOCK3
DUSP7
CELSR3
GNAI2
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
SCN5A
SCN10A
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
VIPR1
ZNF35
IFRD2
MAPKAPK3
MANF
HYAL3
HYAL2
BSN
ACKR5
RPL14
SEC22C
RRP9
CACNA2D2
SLC22A14
SLC22A13
IP6K1
DLEC1
EXOG
XYLB
OXSR1
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
NPRL2
CXCR6
CCR9
USP19
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
EXOSC7
RAD54L2
STAB1
NBEAL2
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
MYRIP
PTPN23
DNAH1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
VILL
C3orf18
SS18L2
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
ELP6
SNRK
QRICH1
SLC25A38
ULK4
ANO10
DALRD3
DCP1A
GLT8D1
ZKSCAN7
SEMA3G
KIF15
PCBP4
KIAA1143
HHATL
WDR48
RNF123
KIF9
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
WDR82
ATRIP
NICN1
MON1A
ABHD14B
GTDC2
UCN2
ZNF502
RFT1
ZNF501
GPR62
LYZL4
KLHL40
TMEM42
IQCF1
GLYCTK
PPM1M
LSMEM2
CCDC12
CCDC13
XIRP1
TTC21A
KLHDC8B
ZNF620
ALS2CL
TMIE
FBXW12
ZNF619
TCAIM
CCDC36
PRSS42
ZNF445
TOPAZ1
TMEM110
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
MIR425
SPINK8
ARIH2OS
C3orf84
FAM198A
CCR2
PRSS46
MIR4271
KRBOX1
MIR4787
MIR4443

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173

Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
RN7SL5P
SNORD27\|ENSG00000251699.1

Genes in Wide Peak

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

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

Genes
FGFR1OP
MLLT4
MYB
TNFAIP3
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45\|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13\|ENSG00000239136.1
AIRN
SNORA29
SNORA20\|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13\|ENSG00000252609.1
SNORD28\|ENSG00000212295.1
TFB1M
U8\|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13\|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13\|ENSG00000238594.1
RAET1K
SNORA2\|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112\|ENSG00000252476.1
SNORA27\|ENSG00000201807.1
RNA5SP219
7SK\|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13\|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33\|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13\|ENSG00000238938.1
ACAT2
ARG1
CCR6
CTGF
EPB41L2
EYA4
ESR1
FUCA2
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LAMA2
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PSMB1
RPS6KA2
SGK1
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCF21
TCP1
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
RNASET2
SYNJ2
VNN2
VNN1
TAAR5
MAP7
LATS1
TAAR2
MED23
QKI
AKAP7
WTAP
AKAP12
PHACTR2
BCLAF1
UST
CITED2
HBS1L
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
DLL1
MRPL18
CLDN20
NOX3
AIG1
SNX9
MPC1
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
VNN3
C6orf70
AGPAT4
TULP4
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
ABRACL
PBOV1
PERP
SMOC2
ALDH8A1
ULBP3
OR2A4
C6orf211
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
TAAR8
RSPH3
L3MBTL3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
ARHGAP18
SYTL3
MTFR2
TMEM200A
IL22RA2
SLC18B1
TAGAP
TAAR9
TAAR1
PACRG
RAET1E
ZC2HC1B
RAET1L
SAMD3
PNLDC1
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
TMEM244
WDR27
SHPRH
PRR18
TAAR6
SLC35D3
ECT2L
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
CTAGE9
MIR548A2
TMEM242
MIR1202
MIR1273C
MIR3918
MIR3939
MIR3668
SMLR1
MIR4466
MIR4465
MIR548AJ1
MIR548H5

Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
BIRC3
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13\|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8\|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13\|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64\|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11\|ENSG00000252992.1
RNY4P6
ZNF259
snoU13\|ENSG00000238625.1
LINC00900
snoU13\|ENSG00000239153.1
ACA59\|ENSG00000252870.1
snoU13\|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39\|ENSG00000264997.1
RNA5SP349
RNA5SP348
MMP12
WTAPP1
snoU13\|ENSG00000239154.1
snoU13\|ENSG00000252679.1
MIR3920
snoU13\|ENSG00000238388.1
RN7SKP115
RN7SL222P
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
MMP1
MMP3
MMP7
MMP8
MMP10
MMP13
NCAM1
NFRKB
NNMT
NPAT
NRGN
PGR
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
TRPC6
UPK2
ZBTB16
ZNF202
CUL5
BARX2
USP2
HTR3B
ZW10
MMP20
UBE4A
EI24
FEZ1
ARHGAP32
RBM7
MPZL2
YAP1
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
EXPH5
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
DCPS
ZBTB44
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
BCO2
TMEM133
TMPRSS13
DCUN1D5
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
C11orf70
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
ANGPTL5
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR4301
CASP12
MIR4493
MIR4491
MIR4492
MIR4693

Genes in Wide Peak

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

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

Genes
RN7SKP19
NEGR1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.31.

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

Genes
PTEN
SNORD74\|ENSG00000200891.1
KLLN

Genes in Wide Peak

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

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

Genes
FGFR1OP
MLLT4
MYB
TNFAIP3
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45\|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13\|ENSG00000239136.1
AIRN
SNORA29
SNORA20\|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13\|ENSG00000252609.1
SNORD28\|ENSG00000212295.1
TFB1M
U8\|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13\|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13\|ENSG00000238594.1
RAET1K
SNORA2\|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112\|ENSG00000252476.1
SNORA27\|ENSG00000201807.1
RNA5SP219
7SK\|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13\|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33\|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13\|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
ACAT2
ARG1
CCR6
CTGF
EPB41L2
EYA4
ESR1
FABP7
FUCA2
GJA1
GRM1
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
LAMA2
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PKIB
PSMB1
PTPRK
RPS6KA2
SGK1
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCF21
TCP1
TCTE3
DYNLT1
THBS2
TPD52L1
UTRN
EZR
VIP
EPM2A
RNASET2
SYNJ2
VNN2
VNN1
TAAR5
MAP7
LATS1
TAAR2
MED23
QKI
AKAP7
WTAP
AKAP12
PHACTR2
BCLAF1
UST
TRDN
CITED2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
HEY2
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
DLL1
MRPL18
CLDN20
NOX3
HDDC2
AIG1
SNX9
MPC1
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
TMEM181
ZBTB2
ABRACL
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
ULBP3
OR2A4
C6orf211
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
L3MBTL3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
ARHGAP18
SYTL3
MTFR2
TMEM200A
IL22RA2
SLC18B1
TAGAP
TAAR9
TAAR1
NCOA7
HINT3
PACRG
RAET1E
ZC2HC1B
RAET1L
SAMD3
PNLDC1
RNF217
NKAIN2
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
TBC1D32
TMEM244
WDR27
SHPRH
PRR18
TAAR6
SLC35D3
ECT2L
NUP43
C6orf58
RAET1G
SUMO4
CENPW
SOGA3
C6orf120
THEMIS
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
CTAGE9
MIR548A2
MIR588
TMEM242
MIR1202
MIR1273C
MIR3144
MIR3918
MIR3939
MIR3668
SMLR1
MIR4466
MIR4465
MIR548AJ1
MIR548H5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.1.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51\|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13\|ENSG00000238853.1
RN7SL546P
snoU13\|ENSG00000239061.1
RN7SL472P
LINC00524
U3\|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113\|ENSG00000222185.1
SNORD112\|ENSG00000252009.1
SNORD113\|ENSG00000222095.1
SNORD113\|ENSG00000201710.1
SNORD113\|ENSG00000201036.1
SNORD113\|ENSG00000201500.1
SNORD113\|ENSG00000200150.1
SNORD112\|ENSG00000251918.1
SNORD112\|ENSG00000252144.1
SNORD112\|ENSG00000251949.1
SNORD112\|ENSG00000252873.1
SNORD112\|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6\|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13\|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3\|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13\|ENSG00000238978.1
SNORA79\|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46\|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32\|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7\|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13\|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13\|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11\|ENSG00000221060.1
SLC10A1
CCDC177\|ENSG00000267909.1
CCDC177\|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3\|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3\|ENSG00000200693.1
WDR89
SCARNA20\|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112\|ENSG00000252380.1
SIX1
U3\|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
RN7SKP99
NAA30
RN7SL461P
LINC00520
RPL13AP3
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SLC8A3
SNAPC1
SPTB
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
AREL1
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
TIMM9
MLH3
KCNH5
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
DACT1
EVL
GSKIP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
TMEM260
CDCA4
NRDE2
ATG2B
UBR7
C14orf105
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
AP5M1
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNT16
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
SMOC1
MOAP1
IRF2BPL
MPP5
INF2
PCNXL4
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
IFT43
L3HYPDH
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
RDH12
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SYNE3
TMEM30B
EML5
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
C14orf39
CCDC85C
SERPINA9
VSX2
SLC35F4
LRRC9
COX8C
ASPG
RAB15
TOMM20L
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
LINC00238
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4505
MIR4708
MIR151B
MIR4710
MIR2392
MIR5694

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.2.

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

Genes
HTR1F
RNU6ATAC6P
RN7SKP284
snoZ40
MIR5688
LINC00971
RN7SL751P
RN7SKP61
GBE1
POU1F1
ROBO1
CHMP2B
CADM2
VGLL3
MIR3923
MIR4795

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.2.

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

Genes
CDX2
BRCA2
FLT3
LCP1
RB1
LHFP
LINC00348
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13\|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13\|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31\|ENSG00000199477.1
SNORA31\|ENSG00000253051.1
7SK\|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13\|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13\|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116\|ENSG00000212553.1
RNY4P14
snoU13\|ENSG00000238408.1
LINC00366
LINC00571
RNA5SP26
RN7SKP1
ARL2BPP3
DCLK1
LINC00445
LINC00457
SNORA25\|ENSG00000199196.1
LINC00423
RNY1P4
SNORA16\|ENSG00000212293.1
ZAR1L
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
LINC00365
LINC00544
LINC00572
LINC00297
MTUS2
RN7SL272P
URAD
LINC00543
GSX1
RNY1P1
SNORA27\|ENSG00000207051.1
SNORD102
LINC00415
RNY1P3
RN7SL741P
RN7SL289P
PABPC3
LSP1\|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
MIR2276
ANKRD20A19P
LINC00352
LINC00327
LINC00362
RNY3P4
LINC00621
SNORD36\|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13\|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27\|ENSG00000252128.1
snoU13\|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13\|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
ZMYM2
IFT88
TNFSF11
SUCLA2
CCNA1
MTMR6
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
VWA8
ZC3H13
SPG20
LRCH1
SACS
INTS6
LATS2
CKAP2
NUFIP1
NBEA
PCDH17
RGCC
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
ENOX1
RCBTB1
NUDT15
KIAA1704
TNFRSF19
SUPT20H
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
XPO4
PCDH20
MRP63
SMIM2
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
EBPL
MEDAG
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
HNRNPA1L2
B3GALTL
DGKH
CCDC122
STOML3
AMER2
USP12
MTIF3
FAM194B
SPERT
FAM124A
LRRC63
N6AMT2
SKA3
MICU2
SPATA13
LNX2
SLC25A30
PAN3
SIAH3
KCNRG
SLC46A3
C1QTNF9
FREM2
NEK5
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
DLEU2
ATP5EP2
ALG11
SERPINE3
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
MIR759
MIR320D1
MIR3168
MIR4305
MIR3169
MIR3613
SPG20OS
SOHLH2
MIR4704
MIR548X2
MIR4703
MIR5007
MIR5693

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
CBFA2T3
FANCA
MAF
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13\|ENSG00000239186.1
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
MIR3182
RN7SL134P
snoU13\|ENSG00000238321.1
RN7SKP190
7SK\|ENSG00000260682.2
MIR4720
GAN
PKD1L2
CMC2
RNA5SP431
PIH1
MON1B
SNORD33\|ENSG00000252022.1
RN7SKP233
RNA5SP430
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
PRDM7
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
JPH3
VAT1L
WFDC1
MTHFSD
DBNDD1
KLHL36
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
CNTNAP4
CENPBD1
ZNF276
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
SLC38A8
ADAD2
ADAMTS18
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
C16orf74
SYCE1L
MIR1910
C16orf95
MIR4719
MIR5093

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q44.

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

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25\|ENSG00000252011.1
SNORD112\|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25\|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13\|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8\|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13\|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51\|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13\|ENSG00000239094.1
snoU13\|ENSG00000238545.1
MIR4742
snoU13\|ENSG00000238856.1
MIR320B2
SNORA72\|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13\|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13\|ENSG00000238576.1
snoU13\|ENSG00000238798.1
U3\|ENSG00000221673.1
RNA5SP76
SLC30A10
U3\|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116\|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26\|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
ZNF124
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
INTS7
AHCTF1
NSL1
OR2M4
OR2L2
OR2T1
RPS6KC1
TAF5L
DISC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
DESI2
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
ZNF692
IARS2
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
SIPA1L2
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
SPRTN
OBSCN
EFCAB2
MLK4
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
NLRP3
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
GCSAML
CNIH3
EXOC8
C1orf227
FAM71A
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
TRIM67
MAP1LC3C
OR13G1
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

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

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

Genes
MIR3136
RNA5SP135
TMF1
SUCLG2
UBA3
ARL6IP5
FRMD4B
LMOD3
FAM19A4
EOGT
FAM19A1

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
STK11
TCF3
CAPS
VMAC
RN7SL626P
MIR4747
UHRF1
RN7SL121P
LRG1
HDGFRP2
RN7SL528P
RN7SL84P
PIAS4
SNORD37\|ENSG00000206775.1
MIR637
RN7SL202P
SNORD38\|ENSG00000252408.1
FZR1
RN7SL866P
ZNF554
SPPL2B
LINGO3
MIR4321
MIR1227
RN7SL226P
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
AES
AMH
ATP5D
CIRBP
CSNK1G2
DAPK3
EEF2
EFNA2
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
MATK
GADD45B
NFIC
NRTN
OAZ1
MAP2K2
PTPRS
RFX2
RPS15
SAFB
SGTA
TBXA2R
THOP1
TLE2
SF3A2
RANBP3
S1PR4
AP3D1
LONP1
APBA3
SAFB2
CHAF1A
EBI3
PLIN3
APC2
ABCA7
HMG20B
SEMA6B
UQCR11
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
RPL36
TIMM13
DAZAP1
TJP3
NMRK2
SLC39A3
ZBTB7A
SIRT6
LSM7
MBD3
PCSK4
PLEKHJ1
FEM1A
STAP2
BTBD2
CCDC94
C19orf10
NCLN
DUS3L
SHD
REXO1
ZNF77
CACTIN
CELF5
FSD1
TLE6
ZNF556
UBXN6
ACSBG2
ABHD17A
DOHH
KLF16
DOT1L
CREB3L3
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
REEP6
IZUMO4
SCAMP4
ADAT3
MRPL54
C19orf70
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
PLK5
TICAM1
ZNRF4
C19orf25
ATP8B3
DIRAS1
ZNF555
PRR22
ANKRD24
C19orf26
TINCR
CATSPERD
C19orf77
ADAMTSL5
TMPRSS9
C19orf35
HSD11B1L
MEX3D
PLIN5
ARRDC5
PLIN4
C19orf71
MIR4746

Genes in Wide Peak

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

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

Genes
RN7SKP73
NDUFS6
SDHAP3
MIR4635
SLC6A3
TERT
SLC12A7
IRX4
MRPL36
IRX1
LPCAT1
CLPTM1L
C5orf38
IRX2
SLC6A19
SLC6A18
MIR4277
MIR4457

Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.2.

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

Genes
7SK\|ENSG00000271814.1
PRPS2
FRMPD4

Arm-level results

Table 3. Get Full Table Arm-level significance table - 32 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	1300	0.04	-6.96	1	0.18	5.1	8.62e-07
1q	1195	0.08	-3.18	1	0.14	1.64	0.115
2p	624	0.15	1.26	0.238	0.09	-3.64	1
2q	967	0.16	2.62	0.0113	0.08	-3.44	1
3p	644	0.21	4.76	2.84e-06	0.53	33.4	0
3q	733	0.21	6.48	1.4e-10	0.17	3.17	0.00286
4p	289	0.06	-6.37	1	0.12	-1.57	1
4q	670	0.06	-6.11	1	0.11	-1.64	1
5p	183	0.28	11.7	0	0.04	-7.46	1
5q	905	0.29	14.8	0	0.04	-6.65	1
6p	710	0.03	-8.03	1	0.20	6.23	1.58e-09
6q	556	0.02	-8.54	1	0.24	9.34	0
7p	389	0.42	24.7	0	0.01	-8.44	1
7q	783	0.42	26.1	0	0.01	-8.14	1
8p	338	0.08	-4.22	1	0.21	6.18	1.92e-09
8q	551	0.12	-0.831	1	0.11	-1.57	1
9p	301	0.04	-7.68	1	0.23	7.53	2.11e-13
9q	700	0.03	-7.49	1	0.23	8.6	0
10p	253	0.04	-8.06	1	0.16	1.62	0.115
10q	738	0.03	-7.92	1	0.18	4.69	6.19e-06
11p	509	0.07	-5.46	1	0.05	-6.94	1
11q	975	0.07	-5.09	1	0.06	-5.38	1
12p	339	0.29	13.1	0	0.01	-9.15	1
12q	904	0.29	14.8	0	0.01	-9.02	1
13q	560	0.07	-5.03	1	0.17	2.8	0.00875
14q	938	0.06	-4.66	1	0.31	16.6	0
15q	810	0.06	-5.45	1	0.08	-3.95	1
16p	559	0.32	16.7	0	0.03	-7.29	1
16q	455	0.31	15.3	0	0.05	-6.32	1
17p	415	0.25	9.63	0	0.16	2.17	0.0396
17q	972	0.27	12.8	0	0.13	0.271	0.806
18p	104	0.07	-5.29	1	0.17	2.48	0.0209
18q	275	0.07	-5.54	1	0.18	3.49	0.001
19p	681	0.09	-3.75	1	0.04	-7.95	1
19q	935	0.09	-3.25	1	0.03	-8.09	1
20p	234	0.27	10.9	0	0.02	-8.52	1
20q	448	0.27	11.7	0	0.01	-9.09	1
21q	258	0.10	-3.29	1	0.16	2.2	0.0396
22q	564	0.08	-4.07	1	0.13	-0.108	1
Xp	418	0.16	1.89	0.0713	0.16	2.16	0.0396
Xq	668	0.16	2.84	0.00626	0.15	2.01	0.0541

Methods & Data

Input

Description

Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).
Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).
Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.
CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End
Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.
Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.
Confidence Level: Confidence level used to calculate the region containing a driver.
Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.
Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).
Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIPAN-TP/22223507/GDAC_MergeDataFiles_20407734/KIPAN-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat
CNV Files = /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.7
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 882 Input Tumor Samples.

Tumor Sample Names
TCGA-2K-A9WE-01A-11D-A381-01
TCGA-2Z-A9J1-01A-11D-A381-01
TCGA-2Z-A9J2-01A-11D-A381-01
TCGA-2Z-A9J3-01A-12D-A381-01
TCGA-2Z-A9J5-01A-21D-A381-01
TCGA-2Z-A9J6-01A-11D-A381-01
TCGA-2Z-A9J7-01A-11D-A381-01
TCGA-2Z-A9J8-01A-11D-A42I-01
TCGA-2Z-A9J9-01A-11D-A42I-01
TCGA-2Z-A9JD-01A-11D-A42I-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:

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)

[2] GISTIC version 1

[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)

[4] GISTIC version 2

[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)

[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)

[7] The Sanger Institute: Cancer Gene Census

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