SNP6 Copy number analysis (GISTIC2) - Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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 (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C13T9GF9

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 288 tumor samples used in this analysis: 17 significant arm-level results, 7 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 - 7 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
19p13.2	1.18e-29	1.18e-29	chr19:7296453-7397014	0 [INSR]
7q31.2	0.0004729	0.0004729	chr7:115065872-116807349	10
2q32.1	0.0024188	0.0024188	chr2:185805454-186960953	2
17q25.2	0.060201	0.060201	chr17:47857704-81195210	454
3q27.1	0.12495	0.12495	chr3:162477826-198022430	256
5q35.2	0.12495	0.12495	chr5:93157567-180915260	669
2p23.2	0.14716	0.14716	chr2:27910707-28747666	7

Genes in Wide Peak

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

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

Genes
MET
RNA5SP239
CAPZA2
snoZ185
SNORA25\|ENSG00000202377.1
CAV1
CAV2
ST7
TFEC
TES

Genes in Wide Peak

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

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

Genes
U8\|ENSG00000212581.1
FSIP2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.2.

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

Genes
BRIP1
CD79B
CLTC
COL1A1
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
snoU13\|ENSG00000239135.1
HILS1
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
CHAD
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
DLX3
DLX4
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGA3
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NME1
NPTX1
P4HB
PDE6G
PDK2
SEPT4
PRKCA
PRPSAP1
PSMC5
PYCR1
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF2
SGCA
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
KAT7
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
MRPL27
AMZ2
ANAPC11
SIRT7
PTRH2
LUC7L3
SDK2
MBTD1
BCAS3
TMEM104
RNF43
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
SMG8
TMEM100
RSAD1
LRRC59
NPLOC4
ST6GALNAC1
TEX2
TEX14
WDR45B
CA10
CCDC47
MIF4GD
INTS2
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
FN3K
XYLT2
DNAI2
SPATA20
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
OGFOD3
ZNF750
NUP85
ACSF2
C17orf70
LIMD2
KCNH6
FAM117A
VMP1
TSPAN10
MYCBPAP
QRICH2
KIF2B
PPP1R9B
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
EME1
NOTUM
TMC8
ANKFN1
MARCH10
TMEM92
CEP112
SAMD14
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
STXBP4
TAC4
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 3q27.1.

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 5q35.2.

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

Genes
APC
CD74
EBF1
ITK
NPM1
PDGFRB
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
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68\|ENSG00000252458.1
LSM11
THG1L
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
RNA5SP198
RN7SKP232
RNA5SP197
ZNF300P1
snoU13\|ENSG00000239191.1
snoU13\|ENSG00000238369.1
MIR378A
RN7SL868P
U3\|ENSG00000221043.1
MIR143HG
RN7SKP145
MIR584
SH3TC2
SPINK13
RN7SL791P
RNA5SP196
GPR151
RN7SKP246
KCTD16
RN7SL87P
RN7SL68P
PCDHGB8P
PCDHB18
PCDHB17
PCDHA14
WDR55
MIR3655
SNORA27\|ENSG00000200235.1
SNORD45\|ENSG00000200051.1
CYSTM1
PURA
TMEM173
ECSCR
RN7SKP64
RNA5SP195
SNORA74A
SNORA74\|ENSG00000252213.1
RNA5SP194
RN7SL867P
snoU13\|ENSG00000238745.1
SNORD63\|ENSG00000206989.1
SNORD63\|ENSG00000222937.1
RN7SL682P
snoU13\|ENSG00000238605.1
NPY6R
MIR874
RNA5SP193
FBXL21
TIFAB
MIR4461
MIR4461
PCBD2
RN7SL541P
PPP2CA
SKP1
snoU13\|ENSG00000238796.1
HSPA4
LEAP2
UQCRQ
RNA5SP192
snoZ6\|ENSG00000253067.1
HINT1
RNA5SP191
RNU6ATAC10P
KIAA1024L
MIR4633
C5orf63
RN7SKP117
RN7SL711P
RN7SL689P
snoU13\|ENSG00000239103.1
snoU13\|ENSG00000252295.1
snoU13\|ENSG00000239067.1
snoU13\|ENSG00000239084.1
RNA5SP190
RN7SL174P
TNFAIP8
MIR5706
snoU13\|ENSG00000239011.1
DTWD2
ARL14EPL
AP3S1
RN7SKP89
RNU4ATAC13P
ZRSR1
SRP19
FLJ11235
SNORA13
RN7SKP57
CAMK4
SNORA51\|ENSG00000207177.1
MIR548F3
TMEM232
RN7SKP230
FER
RN7SKP122
RN7SL782P
SNORA31\|ENSG00000252337.1
RNA5SP189
RN7SL255P
LINC00491
LINC00492
RN7SKP68
RNA5SP188
RN7SL802P
MIR548P
RN7SKP62
GPR150
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK2A
CAMLG
CANX
CAST
CCNG1
CD14
CDC25C
CDO1
CDX1
CHD1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
CTNNA1
DBN1
DMXL1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNN2
LECT2
LMNB1
LNPEP
LOX
LTC4S
SMAD5
MAN2A1
MCC
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
PAM
PCDH1
PCDHGC3
PCSK1
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2R2B
MAPK9
PROP1
RARS
RPS14
SGCD
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SNX2
SPARC
SPINK1
SPOCK1
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
ST8SIA4
REEP5
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATG12
PTTG1
PDLIM7
NREP
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
RNF14
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
FAXDC2
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
TSPAN17
OR4F3
OR2V1
HAVCR1
CYFIP2
PKD2L2
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
TMED9
ZCCHC10
CDHR2
GIN1
SPDL1
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
ZNF608
SEMA6A
PCDHB16
HMHB1
C5orf54
EPB41L4A
ERAP2
SIL1
ARAP3
RMND5B
FBXL17
YTHDC2
GRAMD3
PCYOX1L
CCNJL
SAP30L
TXNDC15
MCTP1
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
SLC25A2
SPATA9
TSSK1B
FAM172A
PSD2
ANKRD32
THOC3
MEGF10
SPINK7
HAVCR2
PHYKPL
SMIM3
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
SCGB3A2
SLCO6A1
C5orf47
PPARGC1B
PRRC1
ZNF474
OR2Y1
AFAP1L1
GRPEL2
STARD4
WDR36
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
CREBRF
CEP120
SLC25A48
SRFBP1
ZMAT2
BTNL9
ARSK
FAM81B
CCDC112
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
DCP2
LIX1
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
C5orf27
STK32A
AQPEP
SLC36A1
RASGEF1C
EFCAB9
SH3PXD2B
FAM153A
KIAA0825
RELL2
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
RGMB
RFESD
CHSY3
FAM170A
ARSI
PFN3
IRGM
FAM174A
CATSPER3
NIPAL4
SLCO4C1
DND1
SIMC1
C5orf48
PROB1
C5orf46
ARHGEF37
SPINK6
ANKHD1
MIR143
MIR145
MIR146A
SPINK14
FNDC9
C5orf56
IGIP
CTXN3
GRXCR2
SPINK9
ZFP62
CCNI2
CBY3
FAM153C
MIR583
FAM196B
C5orf52
MIR1303
TICAM2
MIR3141
MIR3912
MIR3936
MIR3661
MIR4634
MIR378H
MIR4460
MIR4638
MIR5197
MIR5692C1

Genes in Wide Peak

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

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

Genes
FOSL2
MIR4263
RBKS
MRPL33
BRE
SLC4A1AP
PLB1

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	2.1842e-17	2.1842e-17	chr9:21626574-22448737	5
1p36.31	1.2361e-09	1.2361e-09	chr1:1-28829388	479
4q34.3	0.00012059	0.00012059	chr4:179280062-183067669	4
11q22.3	1.1705e-06	0.00030165	chr11:98886288-117696649	146
2q37.3	4.8391e-05	0.00034855	chr2:215795572-243199373	278
3p22.1	0.0028226	0.0029714	chr3:41280645-41732267	1
16q24.1	0.0040102	0.0040983	chr16:76501328-90354753	136
14q11.2	0.0045498	0.0074964	chr14:20501369-21855250	52
11q23.3	2.7651e-05	0.014056	chr11:101318898-135006516	326
19p13.3	0.044691	0.044895	chr19:1171151-4230222	106
19q13.42	0.049458	0.047975	chr19:36699035-59128983	814
6q25.3	0.052947	0.05325	chr6:144604464-171115067	155
22q12.2	0.053841	0.05325	chr22:29969457-30128393	2
6q22.31	0.072869	0.072869	chr6:123955968-125285408	1
2p12	0.07946	0.07946	chr2:1-95526163	625
5p15.33	0.087669	0.085366	chr5:1-31329532	99
2q22.1	0.022429	0.094495	chr2:140708297-157203369	38
5q35.2	0.10514	0.10219	chr5:168726087-180915260	153
6p12.3	0.10374	0.10219	chr6:44235214-70508162	102
10q21.1	0.18041	0.18092	chr10:49889860-69836432	87
15q13.3	0.20078	0.19485	chr15:1-64450037	410
Xp11.4	0.19688	0.19485	chrX:37777370-38012754	3
14q24.2	0.078482	0.21732	chr14:60381448-107349540	488
Xq28	0.2527	0.25645	chrX:1-155270560	1086

Genes in Wide Peak

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

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

Genes
RN7SL151P
CDKN2A
CDKN2B
MTAP
C9orf53

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
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
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
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
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
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
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
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 4q34.3.

Table S9. 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 11q22.3.

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

Genes
PCSK7
SDHD
BIRC3
ATM
DDX10
PAFAH1B2
POU2AF1
SDHD
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
RN7SKP53
ACAT1
BIRC2
APOA1
APOA4
APOC3
CASP1
CASP4
CASP5
CRYAB
DLAT
DRD2
FDX1
GRIA4
GUCY1A2
HTR3A
IL18
MMP1
MMP3
MMP7
MMP8
MMP10
MMP13
NCAM1
NNMT
NPAT
PGR
PPP2R1B
PTS
RDX
SLN
TAGLN
TRPC6
ZBTB16
CUL5
HTR3B
ZW10
MMP20
RBM7
YAP1
CEP164
EXPH5
SIK3
BACE1
CADM1
REXO2
TIMM8B
SIDT2
CNTN5
C11orf71
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
TEX12
DSCAML1
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
MMP27
C11orf1
DYNC2H1
PDGFD
TMPRSS5
BCO2
TMEM133
DCUN1D5
MSANTD4
BUD13
C11orf70
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
TMEM123
APOA5
C11orf93
PIH1D2
NXPE1
NXPE2
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
ANGPTL5
ANKK1
RNF214
C11orf53
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
DDI1
CARD17
CLDN25
MIR4301
CASP12
MIR4491
MIR4693

Genes in Wide Peak

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

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

Genes
ACSL3
ATIC
PAX3
FEV
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39\|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6\|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13\|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75\|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112\|ENSG00000251801.1
SNORA25\|ENSG00000272237.1
RNA5SP121
SNORA48\|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13\|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3\|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
snoU13\|ENSG00000238736.1
snoU13\|ENSG00000238428.1
CXCR2P1
DIRC3
RN7SKP43
RNA5SP120
RPL37A
MREG
LINC00607
snoU13\|ENSG00000238663.1
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BCS1L
BOK
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
INHA
INPP5D
IRS1
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ASIC4
DOCK10
PECR
C2orf83
MFF
ACKR3
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
CCDC140
SLC23A3
GPBAR1
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
CCDC108
C2orf72
RUFY4
DUSP28
MROH2A
ESPNL
C2orf62
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
MIR375
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4268
MIR3132
MIR4269
MIR4786
MIR5001
MIR5702
MIR5703

Genes in Wide Peak

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

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

Genes
SCARNA21\|ENSG00000252409.1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.1.

Table S13. 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
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
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 14q11.2.

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

Genes
CCNB1IP1
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79\|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
ANG
APEX1
HNRNPC
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
TEP1
PARP2
EDDM3A
SUPT16H
SLC39A2
ZNF219
OSGEP
ARHGEF40
RPGRIP1
NDRG2
EDDM3B
METTL17
RNASE7
TMEM55B
RNASE11
TPPP2
OR4L1
OR11H6
KLHL33
RNASE10
OR6S1
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
RNASE13
RNASE12
TMEM253

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.3.

Table S15. 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
snoU13\|ENSG00000238693.1
RNU6ATAC12P
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
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
OPCML
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
IGSF9B
EXPH5
PHLDB1
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
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
JAM3
BCO2
TMPRSS13
DCUN1D5
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
C11orf70
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
SPATA19
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
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693

Genes in Wide Peak

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

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

Genes
GNA11
STK11
TCF3
RN7SL84P
PIAS4
SNORD37\|ENSG00000206775.1
MIR637
RN7SL202P
SNORD38\|ENSG00000252408.1
FZR1
RN7SL866P
ZNF554
SPPL2B
LINGO3
MIR4321
MIR1227
RN7SL226P
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
AES
AMH
ATP5D
CIRBP
CSNK1G2
DAPK3
EEF2
EFNA2
GAMT
GNA15
GNG7
MKNK2
MATK
GADD45B
NFIC
OAZ1
MAP2K2
RPS15
SGTA
TBXA2R
THOP1
TLE2
SF3A2
S1PR4
AP3D1
APBA3
APC2
HMG20B
UQCR11
ZFR2
PIP5K1C
TIMM13
DAZAP1
TJP3
NMRK2
SLC39A3
ZBTB7A
SIRT6
LSM7
MBD3
PCSK4
PLEKHJ1
BTBD2
NCLN
REXO1
ZNF77
CACTIN
CELF5
TLE6
ZNF556
ABHD17A
DOHH
KLF16
DOT1L
CREB3L3
LMNB2
RAX2
MUM1
ATCAY
MIDN
REEP6
IZUMO4
SCAMP4
ADAT3
MRPL54
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
PLK5
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
C19orf77
ADAMTSL5
TMPRSS9
C19orf35
MEX3D
C19orf71

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.42.

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

Genes
PPP2R1A
AKT2
BCL3
CD79A
ERCC2
KLK2
CIC
CBLC
TFPT
ZNF331
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3\|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13\|ENSG00000239137.1
KIR3DX1
LILRA6
LENG1
NDUFA3
MIR935
MIR371B
RN7SL317P
ZNF813
ZNF761
FAM90A28P
FAM90A27P
ZNF321P
ZNF888
ZNF600
ZNF137P
MIR643
snoU13\|ENSG00000238630.1
HCCAT3
FPR1
snoU13\|ENSG00000238486.1
SIGLEC5
CEACAM18
SIGLEC22P
SIGLEC17P
KLK13
KLK9
KLKP1
SNORD88C
SNORD88A
SNORD88B
LRRC4B
SPIB
RN7SL324P
NAPSB
SIGLEC16
U3\|ENSG00000221125.1
MIR4751
MIR4750
MIR4749
ADM5
MIR5088
BCL2L12
SNORD35B
SNORD35A
SNORD34
SNORD33\|ENSG00000199631.1
SNORD32A
MIR4324
RN7SL708P
RN7SL345P
SEC1P
DBP
GRWD1
C19orf68
CABP5
TPRX2P
SNORD23\|ENSG00000221803.1
RN7SL322P
RN7SL533P
snoU13\|ENSG00000252071.1
MIR320E
RN7SL364P
PGLYRP1
NOVA2
MIR642A
RN7SL836P
MIR330
PPM1N
APOC1P1
SNORA70\|ENSG00000253027.1
snoZ6\|ENSG00000252200.1
CEACAM22P
CEACAM20
ZNF180
ZNF234
RN7SL53P
ZNF284
ZNF223
RN7SL368P
ZNF576
ZNF575
CEACAMP10
PSG7
PSG10P
CXCL17
SNORD112\|ENSG00000252356.1
CEA
CEACAMP3
C19orf69
TGFB1
RN7SL34P
RN7SL718P
CYP2B7P1
CYP2G1P
NUMBL
RN7SL758P
SERTAD1
LGALS17A
EID2
RN7SL566P
IFNL4
snoU13\|ENSG00000251709.1
ACTN4
SPRED3
snoU13\|ENSG00000238838.1
RN7SL663P
ZNF790
ZFP14
LINC00665
A1BG
AP2A1
APOC1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2F1
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FLT3LG
FOSB
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NFKBIB
NKG7
CNOT3
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF135
ZNF146
ZNF154
ZNF155
ZNF175
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
UBE2M
ARHGEF1
DYRK1B
CYTH2
ZNF235
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
PPP6R1
CARD8
SIRT2
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
ZNF345
PRKD2
ZNF473
CCDC9
PRPF31
IRF2BP1
FGF21
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
C5AR2
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
EPN1
SERTAD3
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
ZNF529
PRX
SPTBN4
MARK4
CATSPERG
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
RPL23AP79
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
TEX101
WDR87
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
ZNF347
ZNF577
ZNF607
SUV420H2
C19orf48
ZBTB45
ZNF382
ZNF587
FIZ1
ZNF566
GALP
SIGLEC10
SIGLEC12
ZNF628
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
ZNF461
ZNF585B
TIMM50
SHKBP1
CCDC114
ACPT
CGB5
CGB7
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
LINC00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF569
ZNF570
ZNF836
ZNF610
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF567
ZNF383
ZNF781
ZNF780B
ZNF540
ZNF525
SPACA4
ZNF585A
NLRP7
GGN
CADM4
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
IL4I1
IFNL2
IFNL3
IFNL1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
EMC10
KLK9
SIGLECL1
ZNF615
ZNF841
ZFP82
VSTM1
TMEM150B
FAM71E2
HKR1
VN1R2
VN1R4
NLRP9
ZNF260
ZNF546
MYPOP
NANOS2
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
DNAAF3
ZNF233
LILRA5
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
CEACAM16
BLOC1S3
IGFL3
ZNF808
ZNF470
ZNF749
ZNF324B
ZNF793
PAPL
PINLYP
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR371A
MIR372
MIR373
IGFL4
DPRX
ASPDH
MIR498
MIR520E
MIR519E
MIR520F
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
TMEM91
SBK2
LGALS7B
PHLDB3
MIR641
CCDC61
SHISA7
MIR769
SIGLEC14
SGK110
BSPH1
SRRM5
ZNF587B
MIR1323
MIR3191
MIR4323
PPP5D1
ZNF865
MIR4530
MIR4754
MIR4752

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.3.

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

Genes
FGFR1OP
MLLT4
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
ACAT2
CCR6
ESR1
GRM1
IGF2R
KIF25
LPA
MAS1
MAP3K4
OPRM1
PARK2
PCMT1
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
RNASET2
SYNJ2
LATS1
QKI
WTAP
AKAP12
UST
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
SNX9
MPC1
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
PLEKHG1
ARID1B
TMEM181
ZBTB2
SMOC2
ULBP3
C6orf211
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RSPH3
FAM120B
FNDC1
LRP11
SERAC1
PPIL4
SYTL3
TAGAP
PACRG
RAET1E
RAET1L
PNLDC1
DACT2
C6orf118
OSTCP1
WDR27
SHPRH
PRR18
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
TMEM242
MIR1202
MIR1273C
MIR3918
MIR3939
MIR4466

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.2.

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

Genes
NF2
CABP7

Genes in Wide Peak

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

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

Genes
NKAIN2

Genes in Wide Peak

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

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

Genes
ALK
DNMT3A
MSH6
MSH2
MYCN
REL
NCOA1
EML4
BCL11A
ANKRD20A8P
SLC9B1P2
RNA5SP100
IGKJ1
IGKJ2
IGKJ3
IGKJ4
IGKJ5
IGKC
ANKRD36BP2
FOXI3
snoU13\|ENSG00000239049.1
RNY4P15
snoU13\|ENSG00000238979.1
RGPD2
PLGLB2
PLGLB1
SNORA19\|ENSG00000251974.1
U8\|ENSG00000202537.1
MIR4779
SNORD94
RN7SKP83
ATOH8
C2orf68
RNF181
RN7SL126P
RN7SL830P
RN7SL251P
RN7SL113P
SNORD112\|ENSG00000252298.1
RN7SL201P
RNA5SP99
REG1P
RNA5SP98
RN7SKP164
RN7SKP203
MRPL19
snoU13\|ENSG00000239018.1
U3\|ENSG00000221638.1
snoU109\|ENSG00000238410.1
snoU13\|ENSG00000238521.1
POLE4
SEMA4F
PCGF1
CCDC142
MRPL53
C2orf81
MTHFD2
MOB1A
MGC10955
RNA5SP97
NOTO
SNORD78\|ENSG00000212378.1
RN7SL160P
snoU13\|ENSG00000239064.1
RN7SL470P
snoU13\|ENSG00000239072.1
snoU13\|ENSG00000238465.1
SNRNP27
GMCL1
snoU13\|ENSG00000238708.1
SNORA36C
RN7SL604P
AAK1
RNA5SP96
MIR3126
FBXO48
C1D
Vault\|ENSG00000251900.1
RN7SL635P
SNORA74\|ENSG00000272025.1
snoU13\|ENSG00000238696.1
RN7SL211P
RN7SL341P
LINC00309
ACA59\|ENSG00000251775.1
RPS4XP5
DBIL5P2
RN7SL18P
snoU13\|ENSG00000238809.1
RN7SL51P
COMMD1
SNORA70B
C2orf74
RNA5SP95
RN7SL632P
RN7SL361P
RNA5SP94
SNORD78\|ENSG00000212168.1
snoU13\|ENSG00000238690.1
RNA5SP93
RN7SKP208
SNORA12\|ENSG00000212175.1
PRORSD1P
MIR3682
snoU13\|ENSG00000238756.1
ASB3
SCARNA16\|ENSG00000251942.1
SNORA75\|ENSG00000212580.1
RN7SKP224
KCNK12
MIR559
RN7SKP119
BCYRN1
RHOQ
RN7SL817P
RN7SL414P
SLC3A1
snoU13\|ENSG00000239052.1
RN7SKP66
SNORD75\|ENSG00000221300.1
snoZ247
HNRNPA1P57
SNORA67\|ENSG00000252473.1
RN7SL96P
GEMIN6
LINC00211
RN7SL602P
RNA5SP92
RNA5SP91
SNORD112\|ENSG00000252502.1
LINC00486
MIR4765
MIR558
YIPF4
DPY30
SRD5A2
EHD3
RNA5SP90
SNORA64\|ENSG00000207187.1
RN7SL516P
SNORD53
SNORD92
RNA5SP89
FOSL2
MIR4263
RBKS
SNORA36\|ENSG00000206731.1
UCN
TCF23
KCNK3
RN7SL856P
EFR3B
SNORD14
PTRHD1
RNA5SP88
SCARNA21\|ENSG00000251805.1
PFN4
RN7SL610P
UBXN2A
RN7SKP27
RNA5SP87
RN7SL117P
TDRD15
GDF7
RNA5SP86
RN7SL140P
LINC00954
SNORA40\|ENSG00000212455.1
RN7SKP168
SNORA40\|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13\|ENSG00000238371.1
LINC00276
MIR3125
SNORD18\|ENSG00000238503.1
MIR548S
RN7SL674P
RNA5SP85
RNA5SP84
LINC00570
RN7SL832P
SNORA80B
SNORA51\|ENSG00000206898.1
RN7SL66P
SNORA2\|ENSG00000206647.1
SNORA26\|ENSG00000212558.1
snoU13\|ENSG00000238462.1
IAH1
snoU13\|ENSG00000238888.1
MBOAT2
RNU6ATAC37P
RN7SKP112
FLJ30594
SNORA31\|ENSG00000252238.1
RN7SL531P
DCDC2C
SNORA73\|ENSG00000252531.1
snoU13\|ENSG00000238722.1
TMEM18
FAM110C
ACP1
ACTG2
ACYP2
ADCY3
ADD2
ANXA4
APOB
RHOB
ATP6V1B1
AUP1
ZFP36L2
CAD
CALM2
CAPG
CD8A
CD8B
CENPA
CTNNA2
CYP1B1
DCTN1
DDX1
DGUOK
DNAH6
DOK1
DTNB
E2F6
EGR4
EMX1
EPAS1
FABP1
EFEMP1
FKBP1B
FSHR
GCKR
GFPT1
GGCX
GTF3C2
HADHA
HADHB
HK2
TLX2
HPCAL1
FOXN2
ID2
KCNF1
KCNS3
KHK
KIF3C
LHCGR
LTBP1
EPCAM
MXD1
MAT2A
MATN3
MDH1
MEIS1
MPV17
MTIF2
ODC1
OTX1
REG3A
PCBP1
PEX13
VIT
PIGF
PLEK
POMC
PPM1B
PPM1G
PPP1CB
PPP3R1
PRKCE
EIF2AK2
RAB1A
REG1A
REG1B
RPS7
RPS27A
RRM2
RTKN
SDC1
SRSF7
SFTPB
SIX3
SLC1A4
SLC8A1
SNRPG
SOS1
SOX11
SPAST
SPR
SPTBN1
STRN
ADAM17
TACR1
GCFC2
TGFA
TIA1
TPO
TSSC1
UGP2
VRK2
VSNL1
XDH
XPO1
SLC30A3
PXDN
ALMS1
MOGS
RNF103
DYSF
DUSP11
KLF11
MAP4K3
VAMP8
SUCLG1
ASAP2
ST3GAL5
SLC5A6
EIF2B4
TAF1B
NAT8
COX7A2L
TMSB10
ITGB1BP1
NRXN1
OTOF
CRIPT
EIF2AK3
ROCK2
TP53I3
MRPL33
BRE
PREPL
FEZ2
SOCS5
GREB1
USP34
LAPTM4A
RNF144A
SNX17
SERTAD2
SUPT7L
ARHGAP25
ACTR2
PREB
LRPPRC
PDIA6
CEBPZ
MPHOSPH10
SMYD5
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
CGREF1
B3GNT2
USP39
SIX2
VAMP5
PROKR1
RAB10
GPR75
YWHAQ
IMMT
GTF2A1L
STON1
EMILIN1
GPN1
MAPRE3
RPIA
SLC4A1AP
MYT1L
WDR43
LPIN1
CEP68
PSME4
EXOC6B
EHBP1
PUM2
HAAO
WBP1
NTSR2
PRKD3
RASGRP3
QPCT
VAX2
POLR1A
CNRIP1
FAM98A
RAB11FIP5
IFT172
SH3YL1
NFU1
ERLEC1
BMP10
ZNF638
HTRA2
TRIB2
LGALSL
GRHL1
NRBP1
CD207
ITSN2
TPRKB
WDPCP
MEMO1
TRAPPC12
CRIM1
DNAJC27
KRCC1
MRPL35
ATRAID
PCYOX1
VPS54
NBAS
DYNC2LI1
SF3B14
YPEL5
CPSF3
SNTG2
ATAD2B
ETAA1
HEATR5B
AFTPH
TMEM214
RETSAT
SLC35F6
C2orf42
TRMT61B
PTCD3
FANCL
SRBD1
ASXL2
ADI1
THNSL2
NDUFAF7
NAGK
TTC27
SLC30A6
CCDC88A
KDM3A
ALLC
GKN1
CYP26B1
KCMF1
DPYSL5
PNO1
RTN4
TRIM54
PELI1
TTC7A
SMEK2
BIRC6
KIDINS220
MTA3
WDR35
RDH14
SLC4A5
NLRC4
AGBL5
C2orf43
THADA
ATL2
ABCG5
ABCG8
HS1BP3
TTC31
RMND5A
FNDC4
PAPOLG
REEP1
COLEC11
CENPO
GALNT14
CCDC121
SMC6
CLIP4
CAMKMT
NOL10
ANKRD53
LRRTM4
FBXO11
C2orf44
THUMPD2
FAM49A
LBH
TCF7L1
INO80B
WDR54
FAM161A
EVA1A
ANTXR1
ELMOD3
C2orf16
PRADC1
ZNF512
KIAA1841
MCEE
LOXL3
ABHD1
FAM136A
EPT1
LBX2
PNPT1
MCFD2
ATP6V1E2
DHX57
PKDCC
RSAD2
CAPN13
DRC1
HNRNPLL
NT5C1B
SFXN5
LINC00152
CCDC104
TEX261
CCDC85A
KLHL29
WDR92
PPP1R21
TRABD2A
TMEM150A
CMPK2
C2orf73
CIB4
REG3G
CLHC1
PLEKHH2
OSR1
TTC32
ZNF513
GALM
TMEM178A
C2orf50
PQLC3
AHSA2
M1AP
SMYD1
FBXO41
GAREML
PUS10
PLB1
MYADML
FAM84A
RMDN2
ASPRV1
GPR113
OXER1
FAM179A
CLEC4F
DQX1
KCNG3
CYS1
ALMS1P
TET3
GKN2
TEX37
APLF
KRTCAP3
TMEM17
SPRED2
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
GPATCH11
SH2D6
FAM150B
C2orf61
DNAJC5G
C2orf70
C2orf53
LINC00299
MSGN1
FIGLA
CDKL4
LRRTM1
GEN1
C2orf48
FAM228B
MFSD2B
C2orf71
TMEM247
TSPYL6
C2orf78
BOLA3
FUNDC2P2
SULT6B1
LINC00487
C2orf91
EML6
PAIP2B
RGPD1
MIR216A
MIR217
CAPN14
CHAC2
FAM228A
RAD51AP2
MORN2
MIR216B
OST4
ARHGEF33
MIR1301
MIR4264
MIR4261
MIR4262
MIR3681
CHMP3
MIR4433
MIR4757
MIR4436A
MIR4431
MIR4780
MIR4778
MIR4429
MIR4432
MIR548AD
MIR5000
MIR5192

Genes in Wide Peak

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

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

Genes
RN7SKP207
SNORA18\|ENSG00000252601.1
SNORD29
SNORA40\|ENSG00000252083.1
C5orf17
RN7SL572P
GUSBP1
snoU13\|ENSG00000238674.1
RN7SL58P
SNORD81\|ENSG00000212278.1
FTH1P10
RN7SKP133
RNA5SP180
RNA5SP179
RNA5SP178
MIR887
U8\|ENSG00000202269.1
MIR4637
FAM105A
CT49
ANKRD33B
CMBL
FAM173B
RNA5SP177
SNORD123
MIR4636
RNA5SP176
RN7SKP79
UBE2QL1
RN7SKP73
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
ADCY2
CDH6
CDH9
CDH10
CDH12
CDH18
CTNND2
DAP
DNAH5
MTRR
MYO10
PMCHL1
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
BASP1
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
IRX4
TAS2R1
FAM134B
NSUN2
CEP72
ANKH
PRDM9
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
C5orf49
C5orf38
IRX2
ADAMTS16
SLC6A19
SLC6A18
MARCH11
MIR4277
MIR4458
MIR4457
MIR4456

Genes in Wide Peak

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

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

Genes
RNA5SP107
SNORD56\|ENSG00000200377.1
ARL5A
RN7SL124P
SNORA48\|ENSG00000212181.1
RNA5SP106
snoU13\|ENSG00000238860.1
snR65\|ENSG00000253036.1
TEX41
RN7SL283P
ACVR2A
RND3
CACNB4
KCNJ3
KIF5C
NEB
NR4A2
ORC4
TNFAIP6
KYNU
NMI
ZEB2
STAM2
EPC2
MMADHC
LRP1B
RIF1
PRPF40A
MBD5
ARHGAP15
RPRM
GTDC1
FMNL2
GALNT13
LYPD6
LYPD6B
ARL6IP6
RBM43

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

Table S24. 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
BNIP1
CANX
CLTB
DBN1
DOCK2
DRD1
DUSP1
F12
FGFR4
FOXI1
FLT4
GABRP
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
SLC34A1
SNCB
STK10
ZNF354A
STC2
FGF18
SQSTM1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
FBXW11
ZNF346
TSPAN17
OR4F3
OR2V1
PRELID1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
SPDL1
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
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 deleted genes in the wide peak for 6p12.3.

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

Genes
RNA5SP208
SNORD65\|ENSG00000212229.1
FKBP1C
LINC00680
PRIM2
RAB23
BAG2
FAM83B
RN7SKP256
U3\|ENSG00000251930.1
RN7SL244P
RN7SK
GSTA1
RN7SL580P
SNORD66\|ENSG00000212532.1
DEFB133
GLYATL3
OPN5
RN7SKP116
ANKRD66
MIR586
MIR4642
TCTE1
TMEM151B
CRISP1
BAI3
BMP5
DST
RUNX2
CDC5L
GCLC
GSTA2
GSTA3
GSTA4
HCRTR2
IL17A
MCM3
MEP1A
MUT
PGK2
PKHD1
RHAG
TFAP2B
CRISP2
PTP4A1
PLA2G7
SUPT3H
GCM1
SLC25A27
TRAM2
RCAN2
CRISP3
ICK
ENPP4
PHF3
CD2AP
ZNF451
FBXO9
TNFRSF21
TINAG
TMEM14A
CYP39A1
LGSN
CLIC5
HMGCLL1
CENPQ
LRRC1
LMBRD1
AARS2
KIAA1586
ENPP5
ELOVL5
COL21A1
TFAP2D
PAQR8
MLIP
IL17F
EFHC1
C6orf141
KHDRBS2
BEND6
GSTA5
GPR115
GPR116
TDRD6
SPATS1
GPR111
DEFB110
DEFB112
DEFB113
DEFB114
GPR110
EYS
GFRAL
KLHL31
MIR206
TMEM151B
PTCHD4
MIR133B
MIR548U
MTRNR2L9
MIR5685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.1.

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

Genes
NCOA4
RN7SL220P
RN7SL394P
LRRTM3
snoU13\|ENSG00000239000.1
snoR442\|ENSG00000252203.1
MIR1296
RN7SL591P
LINC00845
LINC00948
LINC00844
RN7SKP196
snoU13\|ENSG00000238970.1
SNORD2\|ENSG00000238707.1
snoU13\|ENSG00000238355.1
MIR548F1
RNA5SP318
MIR605
RMRPP4
RNA5SP317
LINC00843
SNORA74\|ENSG00000223111.1
SNORA74\|ENSG00000223182.1
RNA5SP316
FAM25D
FAM21D
PARG
C10orf53
DRGX
C10orf128
WDFY4
ANK3
CDK1
CHAT
EGR2
ERCC6
MBL2
MSMB
PRKG1
SLC18A3
TFAM
UBE2D1
CCDC6
RHOBTB1
ZWINT
ZNF365
DKK1
CSTF2T
SIRT1
HERC4
CTNNA3
A1CF
NRBF2
OGDHL
CISD1
DNAJC12
ASAH2
PCDH15
BICC1
ARID5B
PHYHIPL
ADO
C10orf71
FAM170B
VSTM4
C10orf107
TMEM26
RTKN2
SLC16A9
FAM13C
REEP3
JMJD1C
IPMK
SGMS1
C10orf40
FAM21A
AGAP6
LRRC18
TIMM23B
AGAP7
ASAH2B
AGAP8
TIMM23
MIR4294
MTRNR2L5
MIR3924
PGBD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.3.

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

Genes
BUB1B
TCF12
USP3
CA12
MIR190A
RN7SL613P
RNA5SP397
RNA5SP396
snoU13\|ENSG00000238767.1
MIR2116
C15ORF31
U3\|ENSG00000200318.1
RN7SKP95
snoU13\|ENSG00000239100.1
MYZAP
LINC00926
snoU13\|ENSG00000239035.1
RN7SL568P
snoU13\|ENSG00000238513.1
PYGO1
MIR628
RSL24D1
ONECUT1
MIR1266
U6\|ENSG00000272337.1
RN7SL354P
RNA5SP395
U6\|ENSG00000271819.1
RN7SL494P
RNA5SP394
FGF7
RN7SL307P
RN7SL577P
RN7SKP139
FKSG62
RN7SKP101
SNORD11\|ENSG00000238819.1
SNORA41\|ENSG00000207516.1
HMGN2P46
snoU13\|ENSG00000238583.1
SLC30A4
SNORA11\|ENSG00000261709.2
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13\|ENSG00000238494.1
snoU13\|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13\|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13\|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13\|ENSG00000238564.1
THBS1
FAM98B
U3\|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18\|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77\|ENSG00000212415.1
snoU13\|ENSG00000238342.1
RN7SL286P
RN7SL539P
GOLGA8O
U8\|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18\|ENSG00000206849.1
MIR211
RN7SL82P
U8\|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8\|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8\|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8\|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
RNA5SP391
LINC00929
SNORA48\|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115\|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64\|ENSG00000270704.2
SNHG14
SNURF
snoU13\|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13\|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13\|ENSG00000239083.1
CHEK2P2
RN7SL584P
ACTC1
ADAM10
ANXA2
APBA2
AQP9
BNIP2
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RORA
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SPINT1
SRP14
TJP1
TP53BP1
TPM1
TYRO3
UBE3A
MKRN3
EIF3J
SNAP23
ALDH1A2
HERC2
HERC1
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
BCL2L10
RASGRP1
GNB5
ARPP19
SLC27A2
GPR176
CHP1
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
DAPK2
EID1
NPAP1
SERF2
TMEM87A
RPAP1
BLOC1S6
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
RPS27L
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
KLF13
RAB8B
DUOX1
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
PPP1R14D
MTMR10
ZNF770
HAUS2
RMDN3
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
EMC7
PAK6
DTWD1
CASC5
AVEN
STARD9
VPS18
SQRDL
ZNF106
RFX7
SPATA5L1
CHAC1
NARG2
KATNBL1
SLTM
SNX22
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
NIPA2
APH1B
TLN2
FAM96A
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
LDHAL6B
CHST14
CASC4
LACTB
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
C15orf43
C2CD4A
FAM81A
C15orf65
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
FAM227B
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
SLC24A5
PRTG
GOLGA6L2
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
FBXL22
GLDN
FMN1
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
GOLGA8EP
OR4M2
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
HERC2P9
GOLGA8B
EIF2AK4
UNC13C
MIR422A
CKMT1A
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
POTEB2
MIR1282
MIR4508
MIR4510
MIR4716
MIR4713
MIR4712
GCOM1
POTEB

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.4.

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

Genes
CXorf27
SYTL5
MIR548AJ2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.2.

Table S29. 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
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
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PRKCH
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
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
AREL1
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
MLH3
KCNH5
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
EVL
GSKIP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
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
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
LRRC9
COX8C
ASPG
RAB15
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
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 Xq28.

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

Genes
ATRX
ELF4
GATA1
GPC3
MSN
MTCP1
NONO
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
WASH6P\|ENSG00000182484.10
WASIR1\|ENSG00000185203.7
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70\|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36\|ENSG00000251846.1
RN7SL687P
RN7SL667P
snoU13\|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
MIR452
MIR224
U3\|ENSG00000253009.1
LINC00894
LINC00893
RN7SKP267
CXorf51A
CXorf51B
RNA5SP517
SPANXN1
RN7SKP189
RN7SKP149
RN7SKP81
snoU13\|ENSG00000239188.1
RNA5SP516
SPANXD
SPANXA2
SPANXA1
RN7SL727P
MIR505
SNORA18\|ENSG00000252719.1
RNU6ATAC23P
snoU13\|ENSG00000238485.1
MIR504
RN7SKP31
RN7SL325P
SNORD61\|ENSG00000206979.1
MIR934
snoU13\|ENSG00000239080.1
RNA5SP515
LINC00086
LINC00633
LINC00087
SMIM10
LINC00629
GPC4
SNORA8\|ENSG00000207100.1
RNA5SP514
RN7SL191P
FAM45B
RNA5SP513
DCAF12L2
snoU13\|ENSG00000238626.1
SNORA40\|ENSG00000252693.1
snoU13\|ENSG00000239058.1
RN7SL29P
U3\|ENSG00000212321.1
CT47A12
MCTS1
snoU13\|ENSG00000272179.1
RHOXF2B
NDUFA1
SNORA69\|ENSG00000206622.1
MIR766
RN7SL118P
SNORA35\|ENSG00000239182.1
MIR1277
RN7SL712P
SNORA64\|ENSG00000252441.1
SNORA35\|ENSG00000271907.1
MIR448
MIR1911
SNORA35\|ENSG00000208839.1
SNORD30
RN7SL93P
U3\|ENSG00000201674.1
snoU13\|ENSG00000238811.1
RN7SL266P
MIR4329
ZCCHC16
TRPC5OS
RNA5SP512
RN7SL661P
LINC00890
TDGF1P3
GNG5P2
SNORD96B
MIR3978
MIR652
MID2
NCBP2L
RBM41
MIR548AN
ZCCHC18
RNA5SP511
LINC00630
NXF4
TCP11X1
TCP11X3P
TCEAL6
SNORA9\|ENSG00000202231.1
TSPAN6
SNORA25\|ENSG00000252296.1
RN7SL74P
RN7SKP194
RN7SL379P
RNA5SP510
ACA64\|ENSG00000252016.1
SNORD45\|ENSG00000200422.1
MIR361
APOOL
UBE2DNL
RPS6KA6
SNORA4\|ENSG00000202183.1
ACA64\|ENSG00000239008.1
CYSLTR1
COX7B
RN7SL460P
FGF16
RNA5SP509
RNA5SP508
RN7SL641P
RN7SL790P
RN7SL648P
FTX
JPX
XIST
TSIX
MAP2K4P1
CDX4
LINC00684
FAM226A
U3\|ENSG00000202482.1
RPS4X
RN7SL264P
RN7SL388P
CXorf49B
CXorf49
INGX
snoU13\|ENSG00000252525.1
CXorf65
RN7SL746P
U3\|ENSG00000199769.1
RNY4P23
RNA5SP507
RN7SL581P
MIR676
U3\|ENSG00000212434.1
LINC00269
RN7SL799P
SPIN3
SNORD112\|ENSG00000252961.1
APEX2
SNORA11\|ENSG00000221750.1
SNORA11\|ENSG00000221716.1
GNL3L
U3\|ENSG00000252175.1
RNA5SP505
MIRLET7F2
MIR98
SPANXN5
RNA5SP504
XAGE2
SNORA11D
SNORA11E
CENPVP1
DGKK
MIR502
MIR660
MIR500B
MIR501
MIR362
MIR500A
MIR188
MIR532
GAGE1
MAGIX
RN7SL262P
GPKOW
WDR45
RN7SL139P
ERAS
GLOD5
RBM3
snoU13\|ENSG00000239017.1
RNA5SP503
snoU13\|ENSG00000238473.1
CXXC1P1
CXorf24
SNORA11C
ZNF157
RN7SL785P
snoU13\|ENSG00000238729.1
INE1
SLC9A7
SNORD77\|ENSG00000212347.2
RN7SL291P
EFHC2
MAOA
RN7SL144P
RN7SL406P
RN7SL15P
RNA5SP502
CXorf38
snoU13\|ENSG00000238920.1
MIR1587
RN7SL732P
SNORA31\|ENSG00000252050.1
TM4SF2
CXorf30
snoU13\|ENSG00000238969.1
MIR548F5
MIR3915
RNA5SP501
NR0B1
MIR4666B
RNA5SP500
SNORD74\|ENSG00000201666.1
IL1RAPL1
DCAF8L2
VENTXP1
RN7SL91P
SCARNA23
SNORA68\|ENSG00000201407.1
EIF2S3
snoU13\|ENSG00000238327.1
PTCHD1
RN7SL436P
RN7SKP183
MIR23C
RN7SL48P
MIR4768
snoU13\|ENSG00000238764.1
SNORA16\|ENSG00000201467.1
SYAP1
MIR548AM
RN7SL658P
GRPR
SNORA7\|ENSG00000200620.1
CA5BP1
RAB9A
TCEANC
RN7SKP20
7SK\|ENSG00000271814.1
MIR548AX
RNA5SP499
SNORA31\|ENSG00000252291.1
SNORA20\|ENSG00000201660.1
SNORA48\|ENSG00000212214.1
RN7SL578P
snoU13\|ENSG00000251848.1
LINC00102\|ENSG00000230542.1
CD99P1\|ENSG00000223773.2
LINC00106\|ENSG00000236871.2
SLC25A6\|ENSG00000169100.8
RN7SL355P\|ENSG00000265350.1
RNA5SP498\|ENSG00000223274.1
MIR3690\|ENSG00000265658.1
LINC00685\|ENSG00000226179.1
PLCXD1\|ENSG00000182378.8
ABCB7
AGTR2
ALAS2
ABCD1
AMELX
SLC25A5
XIAP
SHROOM2
AR
ARAF
ARHGAP4
ARHGAP6
ARR3
STS
ARSD
ARSE
ARSF
ASMT\|ENSG00000196433.6
ATP2B3
ATP6AP1
ATP7A
AVPR2
BGN
BMX
BRS3
BTK
CACNA1F
S100G
CAPN6
CD40LG
CDR1
CHM
CLCN4
CLCN5
CLIC2
CNGA2
COL4A5
COL4A6
CSF2RA\|ENSG00000198223.9
CSTF2
CTAG1B
TEX28
CYBB
CYLC1
DCX
DDX3X
TIMM8A
DIAPH2
DKC1
DLG3
DMD
DNASE1L1
DRP2
TSC22D3
DUSP9
EDA
EFNB1
EIF1AX
ELK1
EMD
F8
F9
ACSL4
FANCB
FGD1
FGF13
FHL1
FIGF
FLNA
FMR1
AFF2
CENPI
G6PD
GABRA3
GABRE
GAGE2C
GDI1
GJB1
GK
GLA
GLRA2
GLUD2
GPM6B
CXCR3
LPAR4
GPR34
GRIA3
GUCY2F
HSD17B10
HCCS
HCFC1
HMGB3
HNRNPH2
HPRT1
HTR2C
IDH3G
IDS
IGBP1
IGSF1
IL2RG
IL3RA\|ENSG00000185291.6
IL9R\|ENSG00000124334.12
IL13RA1
IL13RA2
IRAK1
KAL1
KCND1
L1CAM
LAMP2
PRICKLE3
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOB
MCF2
MECP2
CD99\|ENSG00000002586.13
MID1
FOXO4
MPP1
CITED1
MTM1
NAP1L2
NAP1L3
NDP
NHS
GPR143
TBC1D25
OCRL
OPHN1
OTC
P2RY4
PAK3
CDK16
PDHA1
PDK3
CFP
PFKFB1
PGK1
PHEX
PHKA1
PHKA2
PIGA
PIN4
PLP1
PLP2
PLS3
PLXNB3
POLA1
POU3F4
PPEF1
PRKX
PRPS1
PRPS2
PRRG1
PSMD10
RBBP7
OPN1LW
RENBP
RP2
RPGR
RPL10
RPL39
RPL36A
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SH3BGRL
SHOX\|ENSG00000185960.8
SLC6A8
SLC16A2
SMARCA1
SMS
SOX3
SSR4
SSX5
CDKL5
SUV39H1
VAMP7\|ENSG00000124333.10
SYN1
SYP
TAF1
TAZ
SERPINA7
TBL1X
DYNLT3
TIMP1
TSPAN7
TMSB4X
TRO
TRPC5
UBA1
UBE2A
SLC35A2
VBP1
XG
XK
XPNPEP2
ZFX
ZIC3
ZNF711
ZNF182
ZNF41
ZNF75D
RNF113A
ZNF185
ZXDA
GTPBP6\|ENSG00000178605.8
HDHD1
AKAP17A\|ENSG00000197976.6
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
SRPX
UXT
CUL4B
IRS4
OGT
OFD1
IKBKG
PIR
CASK
ASMTL\|ENSG00000169093.10
PAGE1
MTMR1
AKAP4
APLN
AP1S2
GYG2
FAM127A
SLC25A14
CLDN2
RGN
FAM50A
AIFM1
TMEM257
REPS2
ZBED1\|ENSG00000214717.4
ZMYM3
BMP15
GPR50
MED14
TCEAL1
RAB33A
ITM2A
ARHGEF6
PCYT1B
MAGED1
XAGE2B
XAGE1D
PAGE4
MORF4L2
GPRASP1
STARD8
FRMPD4
PHF16
ARMCX2
HEPH
MAGEC1
AMMECR1
MED12
ZBTB33
HDAC6
MAMLD1
HUWE1
PQBP1
BCAP31
GPR64
ATP6AP2
TENM1
SSX3
TIMM17B
SPRY3\|ENSG00000168939.6
RRAGB
SCML2
SLC9A6
ENOX2
PRDX4
EBP
STAG2
RAI2
PLAC1
UTP14A
ZNF275
PGRMC1
MAGED2
MSL3
TMSB15A
PIM2
WDR45
TREX2
PRAF2
CA5B
SLC6A14
KLF8
VSIG4
CNKSR2
IQSEC2
PHF8
SEPT6
ARHGEF9
ATP1B4
ACOT9
KCNE1L
LDOC1
SMPX
GSPT2
KIF4A
FTSJ1
CXorf27
MXRA5
EGFL6
FAM127B
IL1RAPL2
ITGB1BP2
SRPK3
VCX
GAGE12I
GAGE2E
NGFRAP1
NOX1
FAM155B
GPR82
SRPX2
RBMX
PCDH11X
P2RY10
HTATSF1
PCSK1N
PPP2R3B\|ENSG00000167393.12
CCDC22
MAGEH1
FAM156A
C1GALT1C1
SNX12
RPA4
PNMA3
UBQLN2
SH3KBP1
CTAG2
NSDHL
FOXP3
TBX22
ZDHHC9
RLIM
WBP5
RAB9B
LUZP4
PDZD11
PBDC1
TFDP3
TLR7
ARMCX1
TLR8
MBTPS2
MAGEC2
VGLL1
VCX2
VCX3A
ARMCX3
TAF9B
RBMX2
MST4
CPXCR1
CHIC1
FTHL17
GPR173
NLGN3
SASH3
TAF7L
SPIN2A
ARMCX6
WDR44
NDUFB11
ERCC6L
NUP62CL
GDPD2
BCOR
TBC1D8B
FAM120C
GEMIN8
CXorf48
TMEM255A
CXorf57
NUDT11
TMLHE
SAGE1
PLXNA3
HAUS7
OTUD5
ZNF280C
MTMR8
KRBOX4
TXLNG
MBNL3
WWC3
BEX1
HDAC8
ZC4H2
NXT2
NKRF
NXF5
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
MOSPD1
BEX4
CTPS2
CHST7
TCEAL7
GRIPAP1
THOC2
ZNF630
TMEM27
SHROOM4
KIAA1210
NLGN4X
PCDH19
RGAG1
PDZD4
LRCH2
MAGEE1
RAP2C
MID1IP1
ACE2
TMEM35
FAM3A
EDA2R
NYX
BCORL1
DUSP21
CXorf56
DMRTC1
TSPYL2
TNMD
CRLF2\|ENSG00000205755.6
PJA1
SPANXC
WDR13
PORCN
ARMCX5
UPF3B
WNK3
PRRG3
APOO
BRCC3
HMGN5
NKAP
RNF128
MAP7D3
MORC4
CXorf36
LONRF3
ALG13
TCEAL4
TRMT2B
POF1B
CXorf21
KLHL15
ESX1
BHLHB9
MAGED4B
LAS1L
GPR101
TMEM47
CD99L2
H2AFB3
USP26
MAGT1
TMEM164
PHF6
FRMPD3
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
BEX2
SLC7A3
TCEAL3
CCNB3
PPP1R3F
FATE1
CCDC120
TSR2
HS6ST2
FRMD7
KLHL13
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
CXorf40A
FAM58A
RIPPLY1
ATXN3L
SLC38A5
MMGT1
ACRC
SYTL4
SYTL5
PNMA5
GPRASP2
ATG4A
RAB39B
DACH2
SLITRK4
SPANXN3
MAGEC3
BEND2
PASD1
DCAF12L1
PIH1D3
MUM1L1
FAM199X
AMER1
HDX
FUNDC1
GPR112
MAGEB10
DCAF8L1
OTUD6A
UPRT
MAGEE2
MAGEB16
FOXR2
GAB3
PNCK
ZFP92
ACTRT1
GPR119
PAGE3
RBMXL3
DOCK11
SPIN4
ASB11
ASB9
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
ZNF645
CSAG1
FMR1NB
FAAH2
ZXDB
FAM47A
MOSPD2
ARHGAP36
RIBC1
AKAP14
RHOXF1
NKAPP1
MAGEB6
AWAT1
AWAT2
ZDHHC15
USP51
H2BFWT
FAM122B
FAM122C
DDX53
FAM46D
FAM47B
CXorf22
ZCCHC12
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
CXorf61
SLC25A43
ZCCHC5
NRK
DDX26B
ZNF449
VMA21
TMEM31
PAGE2
DHRSX\|ENSG00000169084.8
CTAG1A
BRWD3
CXorf58
CT47A11
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX9
RAB40AL
ATP11C
LINC00632
H2BFM
YIPF6
CHDC2
FAM133A
MAGEB18
TMSB15B
P2RY8\|ENSG00000182162.5
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
VSIG1
ZC3H12B
SATL1
LHFPL1
CXorf67
ZNF81
ITIH6
LANCL3
SOWAHD
OR13H1
CCDC160
CXorf66
DGAT2L6
RAB41
ARSH
MAGEB5
MAP3K15
SPACA5
USP27X
PAGE2B
ZCCHC13
UBE2NL
ARL13A
SLC25A53
XKRX
YY2
MIR106A
MIR19B2
MIR221
MIR222
MIR223
MIR92A2
VCX3B
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
PGAM4
FAM47C
MIR325
MIR374A
SPIN2B
H2AFB2
H2AFB1
SPANXN2
MIR503HG
CT45A6
CT45A1
CXorf40B
SSX4B
MIR450A1
MIR363
MIR20B
MIR18B
MIR450A2
MIR503
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR510
MIR514A1
MIR514A2
MIR514A3
ZNF674
CT47B1
GAGE10
GAGE2B
GAGE13
GAGE12G
MAGEB17
PABPC1L2B
NAP1L6
XAGE1C
XAGE1E
XAGE1A
XAGE1B
CT47A7
MIR545
MIR542
MIR421
MIR651
CXorf31
SSX2B
FAM156B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGED4
MAGEA9B
NXF2B
OPN1MW2
DMRTC1B
SPANXB1
CT45A2
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
MIR767
GAGE12F
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR374B
MIR891A
MIR892A
LINC00892
CXorf28
HSFX2
CXorf64
ARMCX4
GAGE12D
SMIM9
SPANXB2
CMC4
PNMA6C
MIR513C
MIR1468
MIR1912
MIR1298
MIR320D2
MIR548I4
MIR548M
MIR718
MIR513B
MIR764
MIR2114
MIR514B
MIR4330
MTRNR2L10
MIR3937
MIR3672
HSFX1
MIR4769
MIR1587
MIR548AJ2
MIR4770
MIR4767
TCP11X2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 17 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	0.02	-4.13	1	0.12	1.37	0.702
1q	1195	0.06	-1.99	1	0.08	-1.25	1
2p	624	0.15	1.19	0.301	0.02	-4.7	1
2q	967	0.16	3.03	0.00336	0.01	-4.81	1
3p	644	0.28	7.83	7.48e-15	0.10	-0.835	1
3q	733	0.33	11.2	0	0.04	-3.54	1
4p	289	0.04	-4.61	1	0.09	-2.21	1
4q	670	0.03	-4.28	1	0.09	-1.4	1
5p	183	0.12	-1.03	1	0.03	-4.98	1
5q	905	0.11	-0.205	1	0.03	-3.91	1
6p	710	0.03	-4.46	1	0.08	-1.9	1
6q	556	0.02	-4.96	1	0.10	-1.3	1
7p	389	0.60	23.5	0	0.01	-3.91	1
7q	783	0.60	25.7	0	0.01	-3.6	1
8p	338	0.07	-2.9	1	0.06	-3.54	1
8q	551	0.09	-1.79	1	0.03	-4.45	1
9p	301	0.01	-5.75	1	0.12	-0.934	1
9q	700	0.01	-5.48	1	0.12	-0.0217	1
10p	253	0.03	-4.97	1	0.06	-3.85	1
10q	738	0.03	-4.5	1	0.06	-2.78	1
11p	509	0.04	-4.24	1	0.06	-3.09	1
11q	975	0.04	-3.74	1	0.08	-1.78	1
12p	339	0.39	12.8	0	0.01	-4.98	1
12q	904	0.39	15	0	0.00	-4.7	1
13q	560	0.11	-0.916	1	0.09	-1.58	1
14q	938	0.01	-4.84	1	0.16	2.95	0.0321
15q	810	0.02	-4.8	1	0.11	-0.291	1
16p	559	0.54	21	0	0.04	-3.1	1
16q	455	0.53	19.9	0	0.05	-2.78	1
17p	415	0.63	24.4	0	0.13	-0.0668	1
17q	972	0.67	30.4	0	0.02	-2.79	1
18p	104	0.05	-4.2	1	0.15	0.471	1
18q	275	0.04	-4.49	1	0.16	1.25	0.723
19p	681	0.01	-5.33	1	0.06	-3.12	1
19q	935	0.01	-5.03	1	0.06	-2.9	1
20p	234	0.34	10.2	0	0.01	-5.27	1
20q	448	0.35	11.2	0	0.00	-5.26	1
21q	258	0.08	-2.68	1	0.16	1.12	0.765
22q	564	0.02	-4.69	1	0.21	4.46	0.000171
Xp	418	0.34	9.92	0	0.17	1.82	0.352
Xq	668	0.35	11	0	0.17	1.93	0.352

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/KIRP-TP/19077684/GDAC_MergeDataFiles_12184996/KIRP-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/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
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 288 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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