SNP6 Copy number analysis (GISTIC2)
Thyroid Adenocarcinoma (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/C19S1QBB
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 499 tumor samples used in this analysis: 18 significant arm-level results, 65 significant focal amplifications, and 39 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 - 65 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
Xq22.3 4.2218e-16 4.2218e-16 chrX:108537285-108552899 0 [GUCY2F]
22q11.21 0.078196 0.078196 chr22:17960587-17985559 1
1q31.2 0.085467 0.085467 chr1:191271422-191299482 0 [FAM5C]
2q32.2 0.085467 0.085467 chr2:189895124-189907238 1
4q31.21 0.085467 0.085467 chr4:144726169-144744045 0 [GYPE]
12q23.1 0.085467 0.085467 chr12:98389912-98415444 0 [MIR4303]
13q14.2 0.085467 0.085467 chr13:48885811-48888508 1
Xp11.4 0.085467 0.085467 chrX:40732510-40742477 0 [MED14]
Xp11.22 0.085467 0.085467 chrX:50915432-50932081 0 [NUDT10]
5q33.1 0.085467 0.14987 chr5:151286920-151349489 1
1q43 0.12187 0.23707 chr1:238648104-238783395 0 [MTRNR2L11]
1p32.3 0.23707 0.23707 chr1:54576640-54594270 1
1p31.1 0.23707 0.23707 chr1:83207721-83360359 0 [LPHN2]
1p36.32 0.23707 0.23707 chr1:1-3222626 77
2p16.1 0.23707 0.23707 chr2:56284887-56404534 0 [CCDC85A]
2q37.2 0.23707 0.23707 chr2:235779263-235831924 0 [SH3BP4]
3p22.3 0.23707 0.23707 chr3:35092118-35113119 0 [ARPP21]
3p14.1 0.23707 0.23707 chr3:65448170-67336366 5
4q32.3 0.23707 0.23707 chr4:168102123-168131447 1
4p16.1 0.23707 0.23707 chr4:1-9781579 138
4q28.2 0.23707 0.23707 chr4:130772673-130817028 1
5q21.1 0.12187 0.23707 chr5:98476809-99605070 0 [CHD1]
5q35.2 0.23707 0.23707 chr5:153038282-180915260 226
5p14.3 0.23707 0.23707 chr5:12774958-50133468 123
5q21.1 0.23707 0.23707 chr5:99634672-99707870 0 [FAM174A]
6p21.2 0.23707 0.23707 chr6:37963309-37988312 1
6p21.31 0.23707 0.23707 chr6:34548538-34558119 1
6q27 0.23707 0.23707 chr6:165446060-171115067 41
6p22.2 0.23707 0.23707 chr6:25119271-25906453 10
6p22.3 0.23707 0.23707 chr6:22903020-22909916 0 [HDGFL1]
6p12.2 0.23707 0.23707 chr6:52219374-52240957 1
6q12 0.23707 0.23707 chr6:68819438-68837727 0 [BAI3]
7q21.11 0.23707 0.23707 chr7:79316893-79410493 0 [RNA5SP234]
7q31.1 0.23707 0.23707 chr7:108596015-108646888 0 [FLJ00325]
7q11.21 0.23707 0.23707 chr7:63518994-64060584 4
7q34 0.23707 0.23707 chr7:138751617-140495459 22
9q34.3 0.23707 0.23707 chr9:130546051-141213431 256
9q31.1 0.23707 0.23707 chr9:105118622-105131390 0 [LINC00587]
9q22.31 0.23707 0.23707 chr9:94663700-95361062 13
10q24.2 0.23707 0.23707 chr10:100610173-100628737 1
10q25.1 0.23707 0.23707 chr10:109131723-109132637 0 [RNA5SP326]
11p13 0.23707 0.23707 chr11:35242908-35263137 1
12p11.1 0.23707 0.23707 chr12:33288959-39545910 7
12q21.31 0.23707 0.23707 chr12:84029045-84460060 1
13q34 0.23707 0.23707 chr13:114945777-114970617 0 [CDC16]
14q12 0.23707 0.23707 chr14:27096743-27123413 0 [NOVA1]
14q32.31 0.23707 0.23707 chr14:95996559-107349540 203
15q21.3 0.23707 0.23707 chr15:53884342-54920849 2
15q21.1 0.23707 0.23707 chr15:1-102531392 810
18q22.1 0.23707 0.23707 chr18:65255907-65268519 0 [DSEL]
18q12.1 0.23707 0.23707 chr18:29638611-29679921 3
18q22.3 0.23707 0.23707 chr18:69047660-72373936 15
19p13.3 0.23707 0.23707 chr19:6851789-7112264 8
20q13.2 0.23707 0.23707 chr20:54365201-54377394 0 [CBLN4]
20p13 0.23707 0.23707 chr20:1-17320316 149
20q13.11 0.23707 0.23707 chr20:41693609-41827908 1
20q13.2 0.23707 0.23707 chr20:52027743-52375140 2
21q21.3 0.23707 0.23707 chr21:26964829-26969780 1
Xp22.12 0.23707 0.23707 chrX:13742632-26504358 83
Xq23 0.23707 0.23707 chrX:115825961-116171470 0 [CXorf61]
Xq28 0.23707 0.23707 chrX:150934680-150982524 0 [CNGA2]
Xq21.2 0.23707 0.23707 chrX:85668033-85712154 1
Xq24 0.23707 0.23707 chrX:118924009-118930928 1
Xp11.21 0.23707 0.23707 chrX:55807470-56824034 3
Xq24 0.23707 0.23707 chrX:116960817-117019870 0 [KLHL13]
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q11.21.

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

Genes
CECR2
Genes in Wide Peak

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

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

Genes
COL5A2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q14.2.

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

Genes
RB1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q33.1.

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

Genes
GLRA1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p32.3.

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

Genes
TCEANC2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.32.

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

Genes
TNFRSF14
PRDM16
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
CDK11B
DVL1
GABRD
GNB1
PEX10
PRKCZ
SCNN1D
SKI
TNFRSF4
MMP23B
TNFRSF18
ISG15
PLCH2
SLC35E2
RER1
NOC2L
SSU72
SDF4
MXRA8
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
HES4
VWA1
NADK
MMEL1
LINC00115
MORN1
GLTPD1
OR4F16
CCNL2
ATAD3B
PLEKHN1
C1orf170
ACAP3
UBE2J2
PUSL1
B3GALT6
FAM213B
ACTRT2
MIB2
SAMD11
CALML6
C1orf86
ATAD3C
TTLL10
KLHL17
TMEM52
AGRN
FAM132A
HES5
MIR200A
MIR200B
ANKRD65
MIR429
TMEM88B
C1orf233
CDK11A
SLC35E2B
OR4F29
Genes in Wide Peak

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

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

Genes
RN7SL482P
MAGI1
LRIG1
KBTBD8
SLC25A26
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q32.3.

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

Genes
SPOCK3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.1.

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

Genes
FGFR3
WHSC1
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
SH3BP2
WFS1
NELFA
SLBP
ACOX3
CPZ
NOP14
FAM193A
KIAA0232
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
NSG1
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
BLOC1S4
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
UVSSA
ZFYVE28
AFAP1
TNIP2
HAUS3
MFSD7
TMEM175
ABLIM2
TMEM128
TMEM129
MRFAP1
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
JAKMIP1
FAM53A
TRMT44
ZBTB49
CCDC96
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
DEFB131
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
USP17L30
PSAPL1
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR548I2
MIR378D1
MIR4800
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q28.2.

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

Genes
RNY5P4
Genes in Wide Peak

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

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

Genes
EBF1
ITK
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
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68|ENSG00000252458.1
LSM11
THG1L
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
BNIP1
CANX
CCNG1
CLTB
DBN1
DOCK2
DRD1
DUSP1
F12
FABP6
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GRK6
GRIA1
GRM6
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
IL12B
LTC4S
MFAP3
MGAT1
MSX2
MAPK9
PROP1
RARS
SGCD
SLC34A1
SLIT3
SNCB
STK10
ZNF354A
TTC1
STC2
ADAM19
FGF18
SQSTM1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
ADAMTS2
CLINT1
MAML1
GFPT2
GNB2L1
SLU7
RGS14
CPLX2
FAXDC2
FAM114A2
BTNL3
LMAN2
SOX30
MGAT4B
B4GALT7
RNF44
TBC1D9B
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
ZNF346
GEMIN5
TSPAN17
OR4F3
OR2V1
HAVCR1
CYFIP2
PRELID1
MAT2B
MRPL22
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
SPDL1
GALNT10
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
C5orf54
RMND5B
CCNJL
SAP30L
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
TRIM7
MXD3
THOC3
HAVCR2
PHYKPL
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
UBTD2
SCGB3A1
SFXN1
GPRIN1
PWWP2A
C1QTNF2
C5orf47
OR2Y1
UBLCP1
CREBRF
BTNL9
FAM71B
RNF145
HIGD2A
FAM153B
RASGEF1C
EFCAB9
SH3PXD2B
FAM153A
KIF4B
OR2V2
ZNF454
C5orf60
PFN3
NIPAL4
SIMC1
MIR146A
FNDC9
ZFP62
CBY3
FAM153C
FAM196B
C5orf52
MIR1303
MIR3141
MIR3912
MIR4634
MIR378H
MIR4638
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p14.3.

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

Genes
LIFR
HCN1
RN7SL383P
FGF10
CCL28
ANXA2R
SNORD72
RPL37
SNORA57|ENSG00000212567.1
SNORA63|ENSG00000199552.1
LINC00604
LINC00603
WDR70
RN7SL37P
RNA5SP181
LMBRD2
U3|ENSG00000201368.1
BRIX1
C1QTNF3
MIR579
snoU13|ENSG00000238864.1
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
C6
C7
C9
CDH6
CDH9
CDH10
CDH12
CDH18
DAB2
DNAH5
FYB
GDNF
GHR
HMGCS1
IL7R
MYO10
NPR3
OXCT1
PMCHL1
PRKAA1
PRLR
PTGER4
RAD1
SEPP1
SKP2
SLC1A3
TARS
TRIO
ZNF131
OSMR
NUP155
BASP1
PAIP1
MRPS30
SUB1
PDZD2
FBXL7
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
FAM134B
MTMR12
C5orf22
ANKH
PRDM9
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
FAM105B
ZNF622
EMB
MROH2B
EGFLAM
NADK2
UGT3A1
CAPSL
DNAJC21
TTC23L
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
C5orf34
MARCH11
MIR580
CCDC152
MIR4279
MIR3650
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.2.

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

Genes
ZFAND3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.31.

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

Genes
C6orf106
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q27.

Table S15.  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
CCR6
KIF25
PDCD2
PSMB1
RPS6KA2
T
TBP
TCTE3
THBS2
RNASET2
PDE10A
C6orf123
DLL1
MPC1
UNC93A
PHF10
C6orf70
SMOC2
FRMD1
LINC00574
FAM120B
DACT2
C6orf118
WDR27
PRR18
C6orf120
TCP10L2
LINC00242
MIR3939
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.2.

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

Genes
snoU13|ENSG00000238322.1
RNY5P5
CMAHP
SLC17A1
SLC17A4
SCGN
SLC17A3
LRRC16A
HIST1H2AA
HIST1H2BA
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p12.2.

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

Genes
PAQR8
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q11.21.

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

Genes
ZNF736
ZNF727
ZNF679
ZNF680
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q34.

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

Genes
BRAF
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
NDUFB2
TBXAS1
MKRN1
DENND2A
HIPK2
ZC3HAV1
PARP12
TTC26
JHDM1D
SLC37A3
ADCK2
CLEC2L
C7orf55
UBN2
RAB19
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
ABL1
NOTCH1
RALGDS
SET
TSC1
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
ABCA2
AK1
ASS1
C8G
CACNA1B
CCBL1
ENTPD2
CDK9
CEL
COL5A1
CRAT
DBH
SARDH
DNM1
TOR1A
ENDOG
ENG
FCN1
FCN2
FPGS
FUT7
GLE1
GOLGA2
RAPGEF1
GRIN1
LCN1
LCN2
ODF2
PAEP
PPP2R4
PTGDS
RPL7A
SNAPC4
SPTAN1
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
DPM2
FUBP3
GTF3C5
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
SDCCAG3
NOXA1
USP20
SLC27A4
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
MAN1B1
DOLK
SETX
PMPCA
EXOSC2
NCS1
NUP188
CIZ1
NELFB
NSMF
GPSM1
GBGT1
TRUB2
ST6GALNAC4
NDOR1
TOR1B
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
OBP2B
OBP2A
ST6GALNAC6
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf78
FBXW5
TBC1D13
TOR4A
EXD3
RABL6
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
GPR107
PRDM12
DDX31
C9orf16
EHMT1
PTGES2
AIF1L
UCK1
NTNG2
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
TMEM141
C9orf37
WDR34
SAPCD2
C9orf69
UAP1L1
ARRDC1
DPH7
TMEM203
SLC25A25
ZMYND19
NACC2
C9orf116
LCN8
PIP5KL1
SLC34A3
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
NAIF1
PHYHD1
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
LCN9
FAM102A
LCNL1
C9orf139
FAM166A
SOHLH1
MIR199B
C9orf173
NRARP
MIR602
RNF208
CARD9
MIR3154
MIR3689A
MIR3689B
MIR3689D1
MIR3689F
MIR3960
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR548AW
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q22.31.

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

Genes
OMD
CENPP
SNORA84
snoU13|ENSG00000238996.1
LINC00475
ECM2
IARS
ROR2
OGN
SPTLC1
ASPN
NOL8
MIR4670
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q24.2.

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

Genes
HPSE2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
CD44
Genes in Wide Peak

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

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

Genes
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112|ENSG00000251863.1
CPNE8
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q21.31.

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

Genes
[SNORA3|ENSG00000221148.1]
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.31.

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

Genes
AKT1
TCL1A
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
BDKRB1
BDKRB2
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
BRF1
HSP90AA1
JAG2
KLC1
MARK3
PPP2R5C
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DLK1
MTA1
BAG5
C14orf2
CDC42BPB
TCL1B
TECPR2
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
GPR132
EVL
GSKIP
CINP
CDCA4
ATG2B
ZNF839
BEGAIN
INF2
ZFYVE21
WDR25
TMEM121
AMN
SETD3
HHIPL1
BTBD6
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
PLD4
ADSSL1
SLC25A29
NUDT14
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
ASPG
C14orf64
RTL1
TMEM179
C14orf180
MIR127
MIR136
MIR154
MIR203
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1197
MIR1193
MIR4309
MIR151B
MIR4710
MIR2392
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q21.3.

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

Genes
WDR72
UNC13C
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q21.1.

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

Genes
BLM
BUB1B
IDH2
NTRK3
PML
TCF12
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109|ENSG00000239197.1
snoU13|ENSG00000238981.1
RN7SL363P
SNORD18|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
SNORD74|ENSG00000200206.1
RNA5SP400
RN7SL428P
CSPG4P12
SNORA25|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
HDGFRP3
SCARNA15|ENSG00000252690.2
GOLGA6L10|ENSG00000254374.2
RN7SL410P
GOLGA6L9|ENSG00000196648.6
UBE2Q2P3
RN7SL256P
RN7SL61P
CSPG4P8
UBE2Q2P2
TMC3
STARD5
LINC00927
SNORD112|ENSG00000251881.1
C15orf37
MTHFS
ANKRD34C
CTSH
ACSBG1
IDH3A
SNORA63|ENSG00000199633.1
SH2D7
MIR1827
RN7SL214P
RN7SL278P
RN7SKP217
NRG4
RN7SL510P
SNORD112|ENSG00000252372.1
RN7SL319P
DNM1P35
SNX33
ANP32BP1
DNM1P34
RN7SL327P
GOLGA6D
RN7SL489P
GOLGA6C
SCARNA20|ENSG00000252722.1
RPP25
COX5A
SCAMP2
SNORD77|ENSG00000212279.2
RN7SL429P
C15orf59
RN7SL853P
GOLGA6B
RN7SL485P
TMEM202
RNA5SP399
NR2E3
RPL29P30
MIR629
LINC00593
U3|ENSG00000207119.1
RNA5SP398
SNORA77|ENSG00000221376.1
RN7SL438P
MIR4312
FEM1B
CALML4
SNORD18A
SNORD16
SNORD18B
SNORD18C
MIR4512
MAP2K1
SCARNA14
TIPIN
MIR4511
snoU13|ENSG00000238311.1
snoU13|ENSG00000238715.1
SNORA24|ENSG00000206903.1
CLPX
MTFMT
RN7SL348P
MIR1272
RN7SL707P
RN7SL595P
SNORA48|ENSG00000252774.1
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
ACAN
ALDH1A3
ANPEP
ANXA2
APBA2
AQP9
BBS4
BCL2A1
BNC1
BNIP2
CAPN3
CHD2
CHRM5
CHRNA3
CHRNA5
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FES
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
IGF1R
IL16
IREB2
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2A2
MAN2C1
MAP1A
MEF2A
MEIS2
MFAP1
MFGE8
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
NMB
OAZ2
OCA2
FURIN
PCSK6
PDE8A
PKM
PLCB2
PLIN1
POLG
PPIB
MAPK6
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SH3GL3
SLC12A1
SNRPA1
SNRPN
SNX1
SPINT1
SRP14
NR2F2
TJP1
TLE3
TP53BP1
TPM1
TYRO3
UBE3A
MKRN3
AP3B2
ANP32A
ST8SIA2
SEMA7A
CILP
PIAS1
EIF3J
RAB11A
SNAP23
PEX11A
IQGAP1
ALDH1A2
HERC2
HERC1
PSTPIP1
PRC1
USP8
CCNB2
SLC28A2
SLC28A1
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
SV2B
ARNT2
BCL2L10
HCN4
SNUPN
PDCD7
TSPAN3
RASGRP1
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
ARID3B
GNB5
ARPP19
MORF4L1
SLC27A2
ABHD2
ADAMTS7
AKAP13
GPR176
CHP1
OIP5
ITGA11
CHSY1
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
CYFIP1
KIAA1024
MGA
DMXL2
SYNM
VPS39
FAM189A1
TMED3
AP4E1
SEC11A
DAPK2
EID1
NPAP1
SERF2
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
BLOC1S6
FBXO22
VPS33B
GREM1
MRPL46
OR4F4
NPTN
FOXB1
RPUSD2
TUBGCP4
SLCO3A1
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
RPS27L
NDUFAF1
NUSAP1
EMC4
RASL12
SPG21
SPTBN5
NGRN
RHCG
PTPLAD1
CTDSPL2
KLF13
RAB8B
BTBD1
TM6SF1
DUOX1
CSNK1G1
ZFAND6
DLL4
SCAND2P
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
COMMD4
PARP16
CLN6
ZNF770
ZSCAN2
ZWILCH
DET1
UACA
HAUS2
RMDN3
DNAJC17
FANCI
IMP3
LARP6
MNS1
DNAJA4
NOP10
MCTP2
VIMP
UNC45A
MYO5C
NDNL2
FAM214A
EMC7
C15orf39
THAP10
PAK6
RGMA
WDR93
PARP6
DTWD1
CASC5
AVEN
FAM219B
ADAMTSL3
KIAA1199
STARD9
ALPK3
ISLR2
VPS18
IGDCC4
SQRDL
ABHD17C
MESDC1
PPCDC
CELF6
STRA6
ZNF106
KLHL25
CPEB1
AEN
IQCH
ISL2
RFX7
TTC23
MRPS11
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
LRRK1
AAGAB
LMAN1L
KATNBL1
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
PIF1
CCDC33
EDC3
SPG11
TM2D3
ELL3
PLEKHO2
WDR61
CD276
POLR2M
VWA9
NIPA2
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
WDR73
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ARHGAP11B
DPH6
TICRR
C15orf57
KNSTRN
BMF
SHF
DUOXA1
RCCD1
ARRDC4
LINC00923
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
C15orf40
SENP8
SLC51B
TARSL2
HIGD2B
LRRC28
C15orf27
NIPA1
AGBL1
HYKK
WHAMM
FSD2
PLA2G4E
ASB7
TRIM69
C15orf43
C2CD4A
LYSMD4
FAM81A
C15orf65
PGPEP1L
C15orf61
C15orf32
HAPLN3
MESP2
TMCO5A
SPATA8
LINC00052
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
ADAMTS17
RHOV
SCAMP5
FAM227B
DNM1P46
CT62
GRAMD2
LCTL
UBR1
PATL2
CERS3
SPESP1
LPCAT4
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
SLC24A5
PRTG
LINC00277
C15orf60
GOLGA6L2
C15ORF37
FAM154B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
FAM169B
GOLGA8I
FBXL22
GLDN
GOLGA6A
FMN1
RBPMS2
ANKDD1A
USP50
TEX9
KIF7
ZNF710
HDDC3
C15orf52
TNFAIP8L3
C2CD4B
UBE2Q2P1
SPATA41
GOLGA8EP
OR4M2
KBTBD13
UBAP1L
SKOR1
GDPGP1
OR4F6
OR4F15
SHC4
CTXN2
C15orf53
C15orf54
ST20
FAM174B
DUOXA2
MIR184
HERC2P9
GOLGA8B
EIF2AK4
UNC13C
GOLGA6L9|ENSG00000197978.8
TTLL13
MIR422A
CKMT1A
CPLX3
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
GOLGA6L10|ENSG00000205281.6
MIR549
MIR630
MIR631
MIR147B
ANKRD63
JMJD7
PLA2G4B
POTEB2
MIR1276
MIR1179
MIR1282
MIR3174
MIR4311
MIR4313
MIR3713
RPS17L
MIR4514
MIR4513
MIR4508
MIR4510
MIR4716
MIR4713
MIR4712
MIR4515
GCOM1
MIR548AP
POTEB
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q12.1.

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

Genes
snoU13|ENSG00000238982.1
RNF138
RNF125
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q22.3.

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

Genes
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
CYB5A
TIMM21
ZNF407
CNDP2
NETO1
CNDP1
FAM69C
CBLN2
FBXO15
LINC00909
C18orf63
Genes in Wide Peak

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

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

Genes
EMR4P
EMR1
VAV1
ZNF557
MBD3L2
MBD3L5
MBD3L4
MBD3L3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p13.

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

Genes
U3|ENSG00000212165.1
RNA5SP475
RN7SL864P
RN7SKP111
LINC00687
C20orf187
JAG1
RNU105B
TMX4
RN7SL547P
snoR26
RN7SL498P
LINC00654
LINC00658
SNORA26|ENSG00000212517.1
RNA5SP474
RN7SL514P
snoU13|ENSG00000252058.1
SNORA31|ENSG00000252096.1
MIR103A2
MAVS
U3|ENSG00000201346.1
RN7SL839P
RN7SL555P
TMEM239
SNORD57
SNORD56|ENSG00000229686.1
SNORD86
SNORA51|ENSG00000271798.1
SNORD110
MIR1292
SNORD119
RN7SL561P
TCF15
CSNK2A1
DEFB128
DEFB127
DEFB126
DEFB125
ADRA1D
JAG1
AVP
BMP2
CDC25B
CENPB
CHGB
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PCNA
PCSK2
PDYN
PLCB4
PRNP
PTPRA
SIGLEC1
SNAP25
SNRPB
SNRPB2
SOX12
TGM3
MKKS
ATRN
CDS2
PSMF1
SNPH
LZTS3
RASSF2
SLC23A2
SIRPB1
NOP56
RBCK1
RNF24
UBOX5
BTBD3
PLCB1
PRND
FLRT3
LAMP5
SPEF1
C20orf194
SDCBP2
TMEM230
ANGPT4
ESF1
TRMT6
HAO1
SMOX
CRLS1
C20orf27
SPTLC3
AP5S1
TMEM74B
SIRPG
FERMT1
KIF16B
TASP1
NSFL1C
GPCPD1
CPXM1
OTOR
PAK7
EBF4
TRIB3
FASTKD5
ANKEF1
GFRA4
VPS16
PCED1A
MRPS26
DDRGK1
NDUFAF5
ZNF343
NRSN2
PANK2
ADAM33
SEL1L2
FAM110A
SLC4A11
MCM8
ZCCHC3
SCRT2
SLC52A3
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
PROKR2
SLX4IP
C20orf96
MACROD2
SRXN1
ISM1
DEFB129
SIRPA
STK35
PRNT
C20orf196
LRRN4
SIRPB2
RSPO4
TGM6
DEFB132
C20orf202
RAD21L1
TMEM239
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.11.

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

Genes
PTPRT
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
ZNF217
TSHZ2
Genes in Wide Peak

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

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

Genes
MRPL39
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.12.

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

Genes
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
BMX
S100G
EIF1AX
FANCB
FIGF
GLRA2
GPM6B
NHS
PDHA1
PDK3
PHEX
PHKA2
PIGA
POLA1
PPEF1
RBBP7
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SMS
CDKL5
ZFX
ZRSR2
OFD1
PIR
AP1S2
REPS2
PCYT1B
GPR64
SCML2
PRDX4
RAI2
CA5B
CNKSR2
ACOT9
SMPX
SH3KBP1
MBTPS2
GEMIN8
TXLNG
CTPS2
TMEM27
ACE2
APOO
KLHL15
BEND2
ASB11
ASB9
ZNF645
MOSPD2
MAGEB6
DDX53
ARX
CXorf58
CXorf23
MAP7D2
KLHL34
MAGEB18
MAGEB5
MAP3K15
YY2
MAGEB17
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq21.2.

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

Genes
DACH2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq24.

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

Genes
RPL39
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.21.

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

Genes
SNORD112|ENSG00000252961.1
KLF8
UBQLN2

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 - 39 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
13q12.13 3.073e-06 1.62e-05 chr13:25542273-25686096 2
14q21.2 0.010402 0.010402 chr14:45721095-47120973 1
Xq22.3 0.010402 0.010402 chrX:107872289-108781115 2
1q24.2 0.010949 0.010949 chr1:168044896-168149500 1
6q22.31 0.010949 0.010949 chr6:123535791-125417017 3
20p12.1 0.017773 0.015679 chr20:14301156-15274325 2
10q21.2 0.010949 0.019844 chr10:61122180-61715313 3
13q22.1 0.010949 0.025796 chr13:47400506-91579655 169
16q23.3 0.025592 0.025796 chr16:82658729-90354753 104
22q13.1 0.030859 0.03085 chr22:39712315-39797177 2
8p23.2 0.035138 0.035138 chr8:3548028-4251283 2
8q24.22 0.045721 0.04905 chr8:56679786-146364022 518
10q23.31 0.010949 0.04905 chr10:63660611-108925515 411
22q13.2 0.057079 0.052437 chr22:43536127-43814456 3
4q34.3 0.062945 0.074751 chr4:169416144-186879743 80
9p21.3 0.070601 0.074751 chr9:8310705-24554117 72
22q12.3 0.072828 0.074751 chr22:33832149-35486401 3
8p12 0.087689 0.087689 chr8:32046104-32118295 2
10p12.31 0.10419 0.11208 chr10:18427431-20580124 7
22q13.32 0.11336 0.11208 chr22:48668761-51304566 42
7q34 0.12133 0.12108 chr7:140415562-140586621 1
8p22 0.12133 0.12108 chr8:13416667-14713213 2
21q21.1 0.12393 0.12133 chr21:19188311-19650435 1
5q35.1 0.13245 0.13245 chr5:169799676-170174829 1
18q12.3 0.12799 0.13245 chr18:12945828-78077248 292
11p15.1 0.14011 0.13871 chr11:21022008-21437691 2
5p15.2 0.16149 0.16149 chr5:9026779-13956214 15
19p13.12 0.087689 0.16149 chr19:13008827-19627981 199
1q42.13 0.16829 0.16829 chr1:228880467-229407966 1
2q37.3 0.039675 0.16829 chr2:212238542-243199373 287
2q22.1 0.11208 0.16829 chr2:137146325-138273399 2
15q25.3 0.16829 0.16829 chr15:86711326-88151832 2
19p13.2 0.10673 0.18281 chr19:1-14253025 469
2p23.1 0.20121 0.20121 chr2:29280762-37387485 42
7q22.3 0.21011 0.20121 chr7:106673884-116972725 49
19q12 0.1914 0.20121 chr19:29722448-31207591 8
4q22.3 0.24033 0.24033 chr4:1-191154276 959
16p13.3 0.23531 0.24033 chr16:1-90354753 1014
17p13.1 0.23531 0.24033 chr17:1-81195210 1387
5p13.1 0.25138 0.25054 chr5:1-180915260 1088
9q22.33 0.25452 0.25054 chr9:1-141213431 1001
Xq23 0.29558 0.25054 chrX:1-155270560 1086
Genes in Wide Peak

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

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

Genes
PABPC3
LSP1|ENSG00000269099.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.2.

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

Genes
LINC00871
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
GUCY2F
IRS4
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q24.2.

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

Genes
GPR161
Genes in Wide Peak

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

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

Genes
TRDN
RNF217
NKAIN2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
RNA5SP475
FLRT3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.2.

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

Genes
LINC00948
CCDC6
SLC16A9
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q22.1.

Table S47.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RB1
LINC00410
RNA5SP34
LINC00559
SNORD38|ENSG00000200733.1
LINC00353
LINC00440
LINC00560
LINC00433
MIR4500HG
LINC00351
LINC00333
PTMAP5
LINC00564
RNA5SP33
LINC00331
RNY3P3
LINC00446
RN7SL810P
RNY3P7
CLN5
RN7SL571P
LINC00561
C13orf45
LINC00347
LINC00381
RNY1P5
LINC00402
LINC00392
LINC00393
RNY1P8
SNORA9|ENSG00000199282.1
SNORA68|ENSG00000251715.1
SNORD37|ENSG00000212377.1
RNA5SP32
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
ATP7B
KLF5
RCBTB2
DACH1
EDNRB
MLNR
GUCY1B2
HTR2A
KPNA3
LMO7
NEK3
PCDH8
PCDH9
POU4F1
UCHL3
SCEL
SUCLA2
ITM2B
UTP14C
TBC1D4
LPAR6
TRIM13
SPRY2
DLEU1
PIBF1
OLFM4
LECT1
KLF12
FNDC3A
DIS3
MYCBP2
SLITRK5
FBXL3
INTS6
CKAP2
PCDH17
MED4
VPS36
PHF11
NDFIP2
RCBTB1
NUDT15
THSD1
CYSLTR2
SPRYD7
KLHL1
RBM26
PCDH20
RNF219
RNASEH2B
DHRS12
BORA
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
SETDB2
SLITRK6
EBPL
SLITRK1
KCTD12
ARL11
WDFY2
SLAIN1
PRR20A
HNRNPA1L2
COMMD6
FAM124A
KCNRG
NEK5
DLEU2
ALG11
MZT1
SERPINE3
MIR622
PRR20B
PRR20C
PRR20D
PRR20E
IRG1
MIR759
MIR3169
MIR3665
MIR3613
MIR4500
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 S48.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CBFA2T3
FANCA
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
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
HSBP1
IRF8
MC1R
MVD
CHMP1A
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
EMC8
TUBB3
PRDM7
TCF25
ZCCHC14
GSE1
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
JPH3
WFDC1
MTHFSD
DBNDD1
KLHL36
CDT1
MAP1LC3B
HSDL1
CRISPLD2
SPIRE2
CENPBD1
ZNF276
RNF166
DNAAF1
SPATA2L
SPATA33
ZC3H18
SLC38A8
ADAD2
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
C16orf74
MIR1910
C16orf95
MIR5093
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.1.

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

Genes
SNORD43|ENSG00000263764.1
SYNGR1
Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251
Genes in Wide Peak

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

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

Genes
EXT1
COX6C
MYC
PLAG1
RECQL4
NCOA2
CHCHD7
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
PREX2
RNA5SP268
SNORD87
LINC00967
PDE7A
LINC00966
RN7SKP135
RN7SL135P
NKAIN3
RN7SKP97
CA8
RNA5SP267
SNORA51|ENSG00000206853.1
snoU13|ENSG00000238433.1
LINC00588
RNA5SP266
LINC00968
SDR16C6P
SNORA3|ENSG00000221093.1
SNORD54
RPS20
RN7SL323P
RN7SL798P
SNORA1|ENSG00000199405.1
ADCY8
ANGPT1
ANXA13
ASPH
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CRH
CYC1
CYP7A1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
GEM
GLI4
GML
GPR20
GPT
GRINA
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
LY6E
LY6H
LYN
MATN2
MOS
MYBL1
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PENK
PLEC
PMP2
POLR2K
PKIA
PTK2
PEX2
RAB2A
RAD21
RPL7
RPL8
RPL30
SDC2
SDCBP
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
NSMAF
LY6D
GPAA1
RIPK2
GGH
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
LRRC14
EMC2
TOX
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
CPQ
ARFGEF1
KHDRBS3
POP1
COPS5
WWP1
STMN2
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
RRS1
SULF1
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
OPLAH
PABPC1
KCNV1
STAU2
MTBP
AGO2
BHLHE22
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
IMPAD1
TMEM70
TRMT12
OXR1
WDYHV1
ARMC1
UBE2W
TMEM55A
SLC39A4
CHD7
SYBU
INTS8
PAG1
GSDMC
C8orf44
JPH1
ENY2
CPA6
SLURP1
SLC45A4
ZFAT
ZNF250
PRDM14
SNX16
NECAB1
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
DSCC1
DERL1
SLC52A2
PLEKHF2
ZFAND1
ZFHX4
GSDMD
CSPP1
BAALC
GRHL2
VCPIP1
ARHGAP39
ZNF34
SLC25A32
DCSTAMP
SLCO5A1
SHARPIN
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NCALD
MAF1
UTP23
TRIM55
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
TBC1D31
TP53INP1
TGS1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
CTHRC1
OSR2
C8orf34
TOP1MT
ZNF572
FAM92A1
NDUFAF6
ABRA
LYPD2
TMEM71
ADHFE1
UBXN2B
DCAF4L2
RALYL
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
FAM91A1
MCMDC2
CLVS1
SBSPON
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
SDR16C5
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
TRIQK
DPY19L4
FBXO43
PPP1R42
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
CA13
XKR9
C8orf87
RBM12B
MROH5
MAFA
GDF6
C8orf59
SAMD12
MIR30B
MIR30D
LRRC24
ZNF704
SNHG6
MROH6
FABP9
FABP12
FER1L6
MIR548A3
MIR599
MROH1
FAM203B
OC90
MIR875
TCF24
LRRC69
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3150B
MIR3610
MIR378D2
MIR4662B
MIR4663
MIR4664
MIR4471
MIR4470
MIR5680
MIR5194
MIR5708
MIR5681A
Genes in Wide Peak

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

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

Genes
PTEN
BMPR1A
TLX1
NFKB2
PRF1
SUFU
RNA5SP325
snoU13|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112|ENSG00000253068.1
FGF8
snoU13|ENSG00000239091.1
SNORD112|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12|ENSG00000212464.1
ERLIN1
snoU13|ENSG00000238472.1
COX15
ENTPD7
snoU13|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13|ENSG00000238991.1
ANKRD22
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
AGAP11
U3|ENSG00000252189.1
MIR346
RNA5SP322
RN7SKP238
RN7SKP84
LINC00858
RGR
LINC00857
PLAC9
MBL1P
NUTM2E
NUTM2B
SFTPA1
SNORA71|ENSG00000201393.1
LINC00595
LINC00856
RN7SL284P
RNA5SP321
SNORA31|ENSG00000252888.1
RN7SL518P
MIR606
AP3M1
RMRPP1
GLUD1P3
BMS1P4
RNA5SP320
snoU13|ENSG00000238983.1
DNAJC9
FAM149B1
SNORA11|ENSG00000221164.1
MIR4676
SNORA36|ENSG00000200294.1
ASCC1
snoU13|ENSG00000238918.1
NODAL
NPFFR1
NEUROG3
RN7SL373P
SNORD98
snoU13|ENSG00000251926.1
SLC25A16
LINC00849
RNA5SP319
RN7SKP202
RN7SL220P
RN7SL394P
LRRTM3
snoU13|ENSG00000239000.1
snoR442|ENSG00000252203.1
MIR1296
RN7SL591P
ACTA2
ADK
ANXA7
ANXA11
FAS
ARL3
CAMK2G
ENTPD1
CHUK
ABCC2
COL13A1
COL17A1
CPN1
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DNA2
DNTT
EGR2
EIF4EBP2
GLUD1
GOT1
GRID1
HELLS
HK1
HNRNPH3
HPS1
HTR7
IDE
IFIT2
IFIT3
KCNMA1
KIF11
LIPA
MAT1A
NDUFB8
P4HA1
PAX2
PCBD1
PDE6C
PGAM1
PITX3
PLAU
PPA1
PPP1R3C
PPP3CB
SRGN
PSAP
PSD
ALDH18A1
RBP4
RPS24
SCD
SFRP5
SFTPD
FBXW4
SLIT1
SNCG
SUPV3L1
TACR2
TAF5
TLL2
VCL
VDAC2
WNT8B
NDST2
LIPF
GBF1
LDB1
SGPL1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
NEURL
DDX21
LGI1
NOLC1
DLG5
GSTO1
CHST3
VPS26A
MINPP1
KIF20B
SEC24C
SH3PXD2A
SLK
SPOCK2
FRAT1
PPIF
ACTR1A
NPM3
MICU1
RPP30
SORBS1
NRG3
MGEA5
ADIRF
POLR3A
LDB3
ECD
CPEB3
ZNF365
NT5C2
PDCD11
SORCS3
ZSWIM8
WAPAL
PPRC1
RRP12
TBC1D12
DNMBP
FRAT2
SIRT1
KAT6B
TSPAN15
IFIT5
DPCD
SEC31B
NUDT13
HERC4
LRIT1
TCTN3
KIAA1279
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
GHITM
PALD1
R3HCC1L
POLL
CTNNA3
BLNK
NRBF2
KCNIP2
MRPS16
CALHM2
CUTC
PLCE1
DUSP13
PANK1
CCSER2
EXOC6
FAM35A
DDIT4
CCNJ
MARCH5
DNAJB12
CNNM2
WBP1L
CRTAC1
CEP55
LRRC20
CWF19L1
SLC29A3
RNLS
PI4K2A
H2AFY2
RUFY2
FAM178A
CCAR1
DNAJC12
C10orf2
SAR1A
TM9SF3
ZMIZ1
AS3MT
STAMBPL1
SEMA4G
MYOZ1
AVPI1
CDH23
PBLD
C10orf54
MMS19
NOC3L
CUEDC2
DDX50
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
SYNPO2L
C10orf95
PDZD7
UBTD1
TMEM254
HKDC1
WDR96
TET1
TNKS2
TRIM8
TSPAN14
SFXN3
SLC25A28
ELOVL3
MARVELD1
C10orf11
PCGF6
ARID5B
LOXL4
ZDHHC16
FAM213A
DYDC2
PCGF5
LZTS2
LCOR
MRPL43
PLA2G12B
MYPN
PYROXD2
USMG5
ZNF503
AIFM2
ADO
ATAD1
ARHGAP19
MCU
CDHR1
OPALIN
OPN4
HOGA1
SORCS1
CHCHD1
MSS51
TTC18
PIK3AP1
MORN4
ZFYVE27
COMTD1
FRA10AC1
C10orf32
GSTO2
SFR1
CALHM3
ANAPC16
ADAMTS14
C10orf129
SAMD8
LIPJ
DYDC1
EIF5AL1
HECTD2
FGFBP3
USP54
SLC35G1
CCDC147
FUT11
OIT3
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
TBATA
ATOH7
REEP3
JMJD1C
CALHM1
FFAR4
DUPD1
LIPM
CYP26C1
LRIT2
SH2D4B
C10orf99
SLC16A12
CC2D2B
GOLGA7B
C10orf105
C10orf62
C10orf55
IFIT1B
MIR146B
FAM25A
LIPK
LIPN
MIR607
NUTM2A
NUTM2D
AGAP5
SFTPA2
TLX1NB
C10orf131
KLLN
MIR1307
MIR3157
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.2.

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

Genes
SCUBE1
TSPO
TTLL12
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
AGA
SLC25A4
CASP3
CLCN3
DCTD
ACSL1
GPM6A
HPGD
ING2
IRF2
NEK1
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
PALLD
FBXO8
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
SH3RF1
SPCS3
TRAPPC11
MLF1IP
WWC2
CEP44
SNX25
CBR4
WDR17
SPATA4
ENPP6
ASB5
RWDD4
CCDC111
CCDC110
ANKRD37
HELT
C4orf47
GALNTL6
CLDN24
MIR1305
MIR4276
MIR3945
MIR4455
Genes in Wide Peak

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

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

Genes
MLLT3
NFIB
DMRTA1
RN7SL151P
SNORD39|ENSG00000264379.1
MIR31HG
IFNA6
KLHL9
PTPLAD2
SNORA30|ENSG00000202189.1
MIR491
MIR4474
MIR4473
ACER2
snoU13|ENSG00000238348.1
RN7SL158P
SCARNA8
RN7SKP258
MIR3152
RN7SL720P
RN7SL98P
RN7SL157P
LINC00583
LURAP1L
RN7SL849P
RN7SL5P
SNORD27|ENSG00000251699.1
PLIN2
CDKN2A
CDKN2B
ELAVL2
IFNA1
IFNA2
IFNA4
IFNA5
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
MTAP
PTPRD
RPS6
SH3GL2
SNAPC3
TYRP1
MPDZ
CER1
RRAGA
PSIP1
SLC24A2
C9orf53
BNC2
HAUS6
CNTLN
FOCAD
DENND4C
ADAMTSL1
TTC39B
FAM154A
FREM1
CCDC171
IFNE
ZDHHC21
MIR31
C9orf92
IZUMO3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.3.

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

Genes
SNORA76|ENSG00000253007.2
MIR4764
ISX
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p12.

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

Genes
RNA5SP263
RNA5SP262
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p12.31.

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

Genes
RNA5SP303
U3|ENSG00000200545.1
C10orf112
CACNB2
PLXDC2
NSUN6
ARL5B
Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
ACR
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
IL17REL
PIM3
ODF3B
SYCE3
MIR3201
MIR3667
MIR4535
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q34.

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

Genes
U6|ENSG00000271932.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p22.

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

Genes
MIR383
C8orf48
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

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

Genes
CHODL
Genes in Wide Peak

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

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

Genes
KCNMB1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.3.

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

Genes
BCL2
SS18
MALT1
ZNF521
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
snoU13|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8|ENSG00000199713.1
RN7SL112P
SNORD28|ENSG00000252284.1
FECH
U3|ENSG00000212539.1
TXNL1
SNORA73|ENSG00000201816.1
RNA5SP459
SNORA37
DCC
snoU13|ENSG00000238885.1
RN7SL695P
ME2
RNA5SP458
RN7SL310P
RNA5SP457
SCARNA18|ENSG00000252139.1
SCARNA17|ENSG00000251992.1
SCARNA17|ENSG00000267322.1
SNORD58B
SNORD58A
SNORD58C
C18orf32
MIR4744
MIR4743
RNA5SP456
IER3IP1
RNF165
RN7SKP26
RNA5SP455
RNA5SP454
LINC00907
PIK3C3
LINC00669
RN7SKP182
SNORD112|ENSG00000252078.1
MOCOS
WBP11P1
RNA5SP453
snoU13|ENSG00000238982.1
LRRC37A7P
RN7SKP44
snoU13|ENSG00000238376.1
U3|ENSG00000265369.2
U3|ENSG00000252921.1
RN7SL97P
RN7SL247P
RNA5SP452
RN7SL745P
snoU13|ENSG00000238537.1
snoU13|ENSG00000238907.1
RNU6ATAC20P
RNA5SP451
SNORA73|ENSG00000199977.1
RN7SL233P
SNORA81|ENSG00000252677.1
SNORD23|ENSG00000221139.1
ROCK1
RN7SL662P
POTEC
CXADRP3
CYP4F35P
ANKRD20A5P
ZNF519
RN7SL362P
MIR4526
MIR5190
AQP4
ATP5A1
LDLRAD4
CDH2
CDH7
CYB5A
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
KDSR
GALNT1
GATA6
GRP
LAMA3
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC2R
MC4R
MC5R
MEP1B
MYO5B
NARS
NFATC1
NPC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
RBBP8
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SNRPD1
SYT4
TAF4B
TCF4
TTR
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
RNMT
RIOK3
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
B4GALT6
LIPG
ONECUT2
VPS4B
CTIF
TSHZ1
ACAA2
CD226
ZNF271
TXNL4A
MAPRE2
POLI
ADNP2
TRAPPC8
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
CABYR
CDH20
CDH19
TIMM21
ST8SIA5
C18orf8
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
CEP192
RPRD1A
ZNF532
ELP2
IMPACT
ELAC1
ZNF407
CNDP2
CELF4
MIB1
KIAA1328
KLHL14
KIAA1468
EPG5
HRH4
CTAGE1
GAREM
CCDC102B
GREB1L
PQLC1
FHOD3
CCDC68
ASXL3
NETO1
SEH1L
KATNAL2
CHST9
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
TMEM241
SERPINB12
SERPINB11
SEC11C
CABLES1
DSEL
ESCO1
OSBPL1A
HAUS1
ALPK2
FAM210A
LOXHD1
INO80C
TTC39C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
SLC25A52
DSG4
ANKRD29
C18orf54
TCEB3C
ABHD3
FBXO15
ZBTB7C
SKA1
CCDC11
GTSCR1
DOK6
LINC00305
ZNF396
KCTD1
DYNAP
BOD1L2
SIGLEC15
LINC00908
HMSD
CPLX4
ANKRD30B
CCDC178
ATP9B
LINC00909
MIR122
MIR187
HSBP1L1
C18orf63
SKOR2
TCEB3CL
ZSCAN30
MIR320C1
MIR320C2
MIR1539
MIR4319
MIR4318
MIR3929
TCEB3CL2
MIR4741
MIR4527
MIR4529
MIR5011
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.1.

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

Genes
RNA5SP337
RNA5SP336
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p15.2.

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

Genes
CT49
ANKRD33B
CMBL
FAM173B
RNA5SP177
SNORD123
MIR4636
CTNND2
DAP
DNAH5
SEMA5A
MARCH6
CCT5
TAS2R1
ROPN1L
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.12.

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

Genes
JAK3
LYL1
TPM4
ELL
BRD4
MIR640
MEF2BNB
MEF2B
RN7SL70P
RN7SL155P
MIR3189
RN7SL513P
PIK3R2
RNA5SP468
SNORA68|ENSG00000207166.1
RN7SL823P
RN7SL835P
F2RL3
TMEM38A
RN7SL146P
RN7SL844P
RAB8A
LINC00661
UCA1
CYP4F24P
CYP4F8
CYP4F23P
OR7A5
RN7SL842P
RN7SL337P
RN7SL231P
LPHN1
SAMD1
RLN3
NANOS3
RN7SL619P
C19orf53
SYCE2
BST2
CACNA1A
CALR
CD97
COMP
NCAN
NR2F6
FARSA
GDF1
DNAJB1
IL12RB1
INSL3
JUND
CYP4F3
MYO9B
NDUFB7
NFIX
NOTCH3
PDE4C
PIK3R2
PRKACA
PKN1
PTGER1
RAB3A
RAD23A
UPF1
RFX1
RPL18A
SLC1A6
SLC5A5
UBA52
CYP4F2
RFXANK
STX10
AP1M1
CRLF1
MED26
HOMER3
IL27RA
GDF15
TECR
IER2
SUGP2
DDX39A
AKAP8
B3GNT3
KLF2
IFI30
CHERP
CERS1
GIPC1
ILVBL
COPE
UNC13A
MAST3
FCHO1
SIN3B
CRTC1
MAU2
CASP14
FKBP8
TMEM59L
PGLS
LSM4
FAM32A
OR7A17
OR10H3
OR10H2
OR10H1
OR7C2
OR7C1
AKAP8L
ARRDC2
CPAMD8
BABAM1
EMR2
ISYNA1
TM6SF2
DDX49
GATAD2A
PGPEP1
CC2D1A
TMEM161A
C19orf60
MAP1S
KLHL26
TRMT1
ASF1B
USE1
ANO8
SUGP1
CYP4F11
EPS15L1
WIZ
RASAL3
MRPL34
ZSWIM4
CYP4F12
DDA1
KXD1
SMIM7
C19orf57
ABHD8
OCEL1
COLGALT1
EPHX3
PODNL1
SLC35E1
KIAA1683
CCDC130
PLVAP
USHBP1
TSSK6
C19orf44
MRI1
ZNF333
EMR3
GTPBP3
MPV17L2
HSH2D
SYDE1
DCAF15
GADD45GIP1
HAUS8
MVB12A
ARMC6
NACC1
PGLYRP2
CCDC124
NXNL1
CIB3
CALR3
LRRC25
OR1I1
NR2C2AP
CCDC105
CYP4F22
OR10H4
ANKLE1
LINC00905
SSBP4
DAND5
FAM129C
OR10H5
NWD1
SLC25A42
PALM3
SLC27A1
CLEC17A
OR7A10
HAPLN4
MIR181C
MIR23A
MIR27A
MIR181D
C19orf67
MIR639
TMEM221
MIR1470
MIR3188
MIR5695
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.13.

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

Genes
TMEM78
Genes in Wide Peak

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

Table S69.  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
SNORA70|ENSG00000207274.1
VWC2L
MIR4438
MIR548F2
RNA5SP119
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
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
IKZF2
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
SPAG16
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 2q22.1.

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

Genes
RNA5SP105
RN7SKP141
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q25.3.

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

Genes
SNORD74|ENSG00000200206.1
LINC00052
Genes in Wide Peak

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

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

Genes
MLLT1
GNA11
LYL1
SH3GL1
SMARCA4
STK11
TCF3
FSTL3
SAMD1
RLN3
NANOS3
RN7SL619P
C19orf53
SYCE2
SNORD41|ENSG00000209702.1
WDR83OS
ZNF490
ZNF709
ZNF625
RNA5SP467
ZNF788
RNA5SP466
ZNF844
RNA5SP465
RNA5SP464
ZNF763
ZNF833P
RN7SL833P
RN7SL669P
snoU13|ENSG00000238349.1
DKFZP761J1410
CCDC159
RN7SL298P
SPC24
RN7SL192P
TMED1
MIR4748
MIR638
MIR1238
MIR1181
S1PR2
SNORD105B
SNORD105
RN7SL94P
SNORA70|ENSG00000200237.1
ZNF177
ZNF699
OR7E19P
RPS28
NDUFA7
RN7SL115P
RNA5SP463
C19orf59
PET100
EMR4P
MIR3940
ACER1
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
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
ACP5
AES
AMH
ASNA1
ATP5D
AZU1
HCN2
BSG
C3
CACNA1A
CALR
CD70
CDC34
CDKN2D
CIRBP
CNN1
CNN2
CSNK1G2
DAPK3
DHPS
DNASE2
DNM2
DNMT1
EEF2
EFNA2
ELANE
ELAVL1
ELAVL3
EMR1
EPOR
FARSA
FCER2
FUT3
FUT5
FUT6
GAMT
GCDH
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
ICAM1
ICAM3
ICAM4
ILF3
INSR
JUNB
LDLR
MAN2B1
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NFIX
NRTN
OAZ1
P2RY11
PALM
PDE4A
PIN1
POLRMT
PRKACA
PRKCSH
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RAD23A
RFX1
RFX2
RPS15
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
PRDX2
THOP1
ICAM5
TLE2
TYK2
VAV1
ZNF20
ZNF69
ZNF121
ZNF136
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
EIF3G
STX10
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
TRIP10
LONP1
IL27RA
RAB3D
APBA3
IER2
SAFB2
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
EBI3
ZNF443
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4A
TIMM44
CARM1
SEMA6B
RNASEH2A
KLF1
ZNF266
PNPLA6
UQCR11
CDC37
SBNO2
MAST1
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
KANK2
TIMM13
TSPAN16
DAZAP1
OR7E24
FGF22
TJP3
NMRK2
HOOK2
SLC39A3
TNPO2
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
ECSIT
THEG
ZBTB7A
SIRT6
LSM7
ZNF44
MBD3
S1PR5
MIER2
PCSK4
ZNF562
BEST2
FBXL12
CC2D1A
PLEKHJ1
C19orf66
FEM1A
ZNF823
STAP2
TRMT1
BTBD2
RNF126
CCDC94
ASF1B
C19orf80
C19orf10
PPAN
RETN
NCLN
GPR108
DUS3L
XAB2
SHD
RGL3
SLC44A2
MCOLN1
WDR18
REXO1
DOCK6
CAMSAP3
ZNF317
ZNF77
CACTIN
UBL5
CELF5
KRI1
ZSWIM4
YIPF2
C19orf43
SLC25A23
ZNF426
C19orf57
FSD1
ZNF557
CERS4
TLE6
PODNL1
LPPR3
DENND1C
ZNF442
ZNF556
LRRC8E
UBXN6
CCDC130
ACSBG2
ADAMTS10
QTRT1
ABHD17A
DOHH
RTBDN
ANGPTL6
KLF16
PRAM1
MRI1
FBXW9
ALKBH7
WDR83
ZNF414
ELOF1
DOT1L
FBN3
ZNF559
KISS1R
CREB3L3
LMNB2
RAX2
MUM1
MPND
ATG4D
ATCAY
MBD3L1
MIDN
DCAF15
GADD45GIP1
ZNF799
C19orf52
ZNF700
ZNF439
DPP9
R3HDM4
TMEM259
TPGS1
CRB3
REEP6
PEX11G
ZNF561
OLFM2
MUC16
FDX1L
NACC1
IZUMO4
SCAMP4
ADAT3
EVI5L
CCDC151
ZNF653
GRIN3B
MRPL54
RAVER1
OR7D4
OR7G1
OR1M1
C19orf70
MBD3L2
TRAPPC5
PCP2
ZNF441
ZNF491
ZNF440
SWSAP1
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
MISP
PLK5
C2CD4C
ZNF358
ZNF560
ZNF563
TICAM1
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
ZNF846
OR7D2
ZNF791
ZNF564
ZNF709
ZNF433
PRR22
ANKRD24
ZNF627
DAND5
C19orf26
C19orf38
KANK3
TINCR
CATSPERD
ACTL9
OR2Z1
C19orf82
ZNF763
C19orf77
SLC25A41
MBD3L5
ODF3L2
ADAMTSL5
CLEC4G
PALM3
TMPRSS9
C19orf35
HSD11B1L
C19orf45
TMEM205
C3P1
ZNF788
OR7G2
OR7G3
MEX3D
PRSS57
CTXN1
MIR181C
MIR199A1
MIR23A
MIR27A
PLIN5
MIR181D
ARRDC5
C19orf67
MBD3L4
MBD3L3
PLIN4
ZNF812
ZNF878
ZGLP1
C19orf71
MIR3187
MIR4322
TGFBR3L
ZNF177
MIR4746
MIR5695
MIR4999
MIR5684
MIR5589
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p23.1.

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

Genes
ALK
RN7SL602P
RNA5SP92
RNA5SP91
SNORD112|ENSG00000252502.1
LINC00486
MIR4765
MIR558
YIPF4
DPY30
SRD5A2
EHD3
RNA5SP90
SNORA64|ENSG00000207187.1
RN7SL516P
LTBP1
VIT
EIF2AK2
SPAST
STRN
XDH
FEZ2
RASGRP3
FAM98A
MEMO1
CRIM1
YPEL5
HEATR5B
TTC27
SLC30A6
BIRC6
NLRC4
GALNT14
CLIP4
LBH
CAPN13
MYADML
LCLAT1
GPATCH11
C2orf71
CAPN14
MIR548AD
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.3.

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

Genes
MET
RNA5SP239
CAPZA2
snoZ185
SNORA25|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13|ENSG00000238922.1
FLJ00325
U3|ENSG00000238297.1
snoU109|ENSG00000238832.1
CAV1
CAV2
DLD
SLC26A3
GPR22
LAMB1
DNAJB9
NRCAM
SLC26A4
PPP1R3A
PRKAR2B
WNT2
ST7
DOCK4
COG5
DUS4L
ZNF277
TFEC
LAMB4
TES
HBP1
MDFIC
PNPLA8
GPR85
LRRN3
BCAP29
CBLL1
IMMP2L
FOXP2
C7orf60
C7orf66
THAP5
LSMEM1
Genes in Wide Peak

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

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

Genes
C19orf12
POP4
RN7SL340P
CCNE1
URI1
ZNF536
PLEKHF1
VSTM2B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.3.

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

Genes
IL2
FGFR3
KDR
KIT
PDGFRA
RAP1GDS1
WHSC1
PHOX2B
DUX4
CHIC2
TET2
FBXW7
FIP1L1
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
C4orf45
U3|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
SNORD73A
SNORD73
RNA5SP168
RNA5SP167
RNA5SP166
RN7SL254P
MIR4799
RNA5SP165
TMEM184C
RN7SKP235
ANAPC10
HHIP
MIR3139
USP38
snoU13|ENSG00000238695.1
RN7SL152P
UCP1
SNORD112|ENSG00000252300.1
RN7SKP253
RN7SKP237
ACA64|ENSG00000239005.1
RN7SL311P
RN7SL382P
LINC00500
LINC00499
LINC00498
LINC00616
LINC00613
PCDH10
SNORA70|ENSG00000252014.1
RN7SL205P
RNY5P4
snoU13|ENSG00000238802.1
HSPA4L
INTU
RN7SL335P
QRFPR
RN7SKP137
MAD2L1
SNORA11|ENSG00000221245.1
C4orf3
CEP170P1
SNHG8
NT5C3AP1
MTRNR2L13
RN7SL808P
MIR577
RN7SL184P
TIFA
C4orf32
ENPEP
RN7SL275P
CCDC109B
MIR576
RN7SL55P
SNORD112|ENSG00000252566.1
GIMD1
RN7SL89P
SNORA31|ENSG00000252136.1
TACR3
BDH2
CISD2
snoU13|ENSG00000238948.1
RN7SL728P
MIR1255A
ADH1B
PCNAP1
MIR3684
EIF4E
RN7SKP28
RNA5SP164
RN7SKP248
GPRIN3
RN7SKP244
RNU6ATAC31P
IBSP
snoU13|ENSG00000238652.1
RN7SL681P
RN7SKP96
MIR4451
RN7SKP48
RN7SL552P
MRPS18C
snoR442|ENSG00000252834.1
MIR575
LINC00575
SNORD42|ENSG00000202440.1
HNRNPD
SNORA31|ENSG00000252762.1
SNORA75|ENSG00000212620.1
OR7E94P
LINC00989
NAA11
RN7SL127P
MIR5096
snoU13|ENSG00000238816.1
SNORD75|ENSG00000221711.1
MIR548AH
MIR4450
SNORD50|ENSG00000199857.1
CDKL2
BTC
PPBPP2
RN7SL218P
PPBP
PF4
PF4V1
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
RNA5SP163
snoU13|ENSG00000238318.1
CSN1S2AP
SULT1B1
UGT2A1
UGT2A2
UGT2B10
TMPRSS11BNL
FTLP10
TMPRSS11GP
SNORA62|ENSG00000202374.1
GNRHR
UBA6
TECRL
snoU13|ENSG00000238925.1
snoU13|ENSG00000238541.1
snoU13|ENSG00000238579.1
NOA1
RN7SL357P
RN7SL492P
ARL9
SRP72
RNA5SP162
KIAA1211
RNA5SP161
RN7SKP30
RN7SL822P
RN7SL424P
snoU13|ENSG00000238753.1
GSX2
SNORA26|ENSG00000212490.1
SNORA26|ENSG00000212588.1
DANCR
snoU13|ENSG00000239068.1
NIPAL1
RN7SKP215
snoU13|ENSG00000238301.1
RN7SKP199
RN7SL193P
RN7SL691P
RN7SKP82
SLC30A9
LINC00682
RNA5SP160
snoU13|ENSG00000238351.1
RHOH
SNORA51|ENSG00000201863.1
RNA5SP159
RN7SL558P
SMIM14
MIR5591
RNA5SP158
DTHD1
snoU13|ENSG00000238694.1
RN7SL101P
SNORD74|ENSG00000200999.1
RN7SL16P
snoU13|ENSG00000238383.1
RNA5SP157
FAM184B
MED28
RN7SL315P
snoU13|ENSG00000238536.1
SNORA75|ENSG00000206780.1
ZEB2P1
CD38
FAM200B
RN7SKP170
SNORA63|ENSG00000202449.1
LINC00504
HSP90AB2P
RNA5SP156
HS3ST1
CLNK
RNA5SP155
MIR3138
RNA5SP154
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADH1A
ADH1C
ADH4
ADH5
ADH6
ADH7
ADRA2C
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA3
ANXA5
APBB2
AREG
ART3
ATOH1
ATP5I
BMP3
BMPR1B
BST1
CAMK2D
CASP3
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
LRBA
CDS1
CLGN
CENPC
CENPE
CLCN3
CNGA1
CPE
CRMP1
CSN1S1
CSN2
CSN3
CTBP1
CTSO
DGKQ
DCK
DCTD
DHX15
DMP1
DRD5
DSPP
EDNRA
EGF
ELF2
EPHA5
EREG
ETFDH
EVC
F11
FABP2
ACSL1
FAT1
FGA
FGF2
FGF5
FGG
FRG1
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GC
GK2
GLRB
GPM6A
GRK4
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HTT
HGFAC
UBE2K
HMX1
HPGD
HTN1
HTN3
IDUA
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
LETM1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MSX1
MTNR1A
MTTP
MUC7
MYL5
NDUFC1
NEK1
NFKB1
NPY1R
NPY2R
NPY5R
PCDH7
PDE6B
PDHA2
PET112
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPID
PPP2R2C
PPP3CA
PRKG2
MAPK10
PTPN13
QDPR
REST
RFC1
RGS12
RNF4
ABCE1
RPL9
RPL34
RPS3A
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SH3BP2
SNCA
SOD3
SPINK2
SPP1
STATH
SULT1E1
TDO2
TEC
TLL1
TLR1
TRPC3
TXK
UBE2D3
UCHL1
UGDH
UGT2B4
UGT2B7
UGT2B15
UGT2B17
UGT8
VEGFC
WFS1
NELFA
SLBP
GLRA3
ACOX3
SPARCL1
SMARCA5
SORBS2
PRSS12
CPZ
NOP14
FAM193A
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
PROM1
HERC3
PAPSS1
LDB2
LRAT
AIMP1
NDST3
SLIT2
RAB28
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
KIAA0232
MFAP3L
SEC24D
G3BP2
WDR1
FGFBP1
HNRNPDL
TSPAN5
ENAM
C4orf6
FAM13A
MFSD10
SPRY1
MAEA
TLR6
PCGF3
ATP8A1
SPON2
PGRMC2
SEC24B
TACC3
CXCL13
SLC34A2
MAB21L2
PAICS
MXD4
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
CPLX1
HPSE
SLC26A1
NMU
SMR3B
NPFFR2
PPARGC1A
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
MAN2B2
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXL5
FBXO8
SMR3A
NSG1
PPA2
DAPP1
DKK2
NAAA
COQ2
ARFIP1
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
LAP3
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ASIC5
GALNT7
NUDT9
NUP54
STX18
FGFRL1
CLDN22
CYTL1
GAR1
SH3TC1
UGT2B28
RBM47
PCDH18
USP53
OTUD4
DCHS2
ARHGEF38
PIGG
DCAF16
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
TMA16
BLOC1S4
C4orf21
STK32B
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
CDKN2AIP
LYAR
TENM3
N4BP2
SEPT11
EXOC1
LRP2BP
TMEM165
SLC2A9
FSTL5
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
RNF150
KIAA1239
TBC1D14
SORCS2
CC2D2A
KLHL8
KIAA1430
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
UVSSA
METTL14
WDR19
ZFYVE28
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
AFAP1
GUF1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
NCAPG
NDST4
ETNPPL
USP46
MRPL1
RASL11B
ELOVL6
TNIP2
HAUS3
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
MLF1IP
THAP9
NSUN7
UGT2A3
GSTCD
MAP9
TNIP3
PHF17
SCD5
DNAJB14
TMEM156
WWC2
FRAS1
NAA15
CWH43
C4orf29
ALPK1
CXXC4
KCNIP4
CEP44
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
FGFBP2
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
FAM175A
KIAA1109
MFSD7
TMEM175
ABLIM2
HOPX
COL25A1
LNX1
MGARP
AGPAT9
CBR4
PIGY
TMEM128
CABS1
ZNF518B
FHDC1
PRMT10
CCDC149
DDX60L
YTHDC1
TMEM129
NAF1
MOB1B
FAM114A1
TRMT10A
MRFAP1
TADA2B
TBCK
HTRA3
HELQ
CYP2U1
C1QTNF7
MRFAP1L1
DDIT4L
WDR17
ARAP2
PCAT4
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
SPATA18
TMPRSS11B
GNPDA2
SPATA4
CPEB2
EVC2
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
OTOP1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
NFXL1
PAQR3
SHISA3
SCFD2
FAM218A
JAKMIP1
THAP6
C4orf26
KLB
FAM53A
PPM1K
TRMT44
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
FREM3
MMAA
ZBTB49
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
SYNPO2
C4orf46
SLC10A4
TIGD4
RWDD4
CCDC111
TAPT1
TRIML2
CNOT6L
LCORL
C4orf22
EPGN
ELMOD2
NPNT
CCDC110
MFSD8
CCDC96
BOD1L1
FDCSP
NAP1L5
DCAF4L1
CRIPAK
DOK7
RNF212
COX18
YIPF7
FRYL
RNF175
STPG2
ZAR1
CCDC158
TMPRSS11A
TRIML1
LRRC66
NAT8L
PRSS48
SOWAHB
LRIT3
SLC10A6
HSD17B13
ANKRD37
POLN
KCTD8
SMIM20
BEND4
GRXCR1
TMPRSS11F
TRIM61
HELT
C4orf48
C4orf40
AMTN
CCSER1
MIR302A
MTHFD2L
TMEM150C
GUSBP5
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
DEFB131
CLRN2
C4orf51
DUX4L7
DUX4L6
DUX4L5
DUX4L3
MIR572
MIR573
MIR574
AREGB
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
DUX4L2
USP17L30
FAM160A1
RELL1
PSAPL1
MIR297
FAM47E
CLDN24
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR1269A
MIR1305
MIR548I2
MIR548G
MIR3140
MIR4276
MIR3945
THEGL
MIR4455
MIR4453
MIR378D1
MIR4802
MIR4800
MIR4801
MIR4449
MIR548AG1
MIR4452
FAM47E
MIR5091
MIR5705
PYURF
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

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

Genes
CDH11
IL21R
TNFRSF17
CBFA2T3
CBFB
CDH1
CREBBP
CYLD
ERCC4
FANCA
FUS
MAF
CIITA
MYH11
TSC2
SOCS1
HERPUD1
PALB2
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
RN7SL520P
ADAT1
CHST6
SNORA76|ENSG00000252122.1
GLG1
NPIPB15
HCCAT5
PKD1L3
IST1
SNORD71
SNORA70D
TAT
SNORD112|ENSG00000251700.1
RNU6ATAC25P
FLJ00418
SNORD111|ENSG00000221066.1
SNORD111B
SF3B3
RN7SL279P
RN7SL407P
snoU13|ENSG00000238734.1
FKSG63
PDXDC2P
MIR140
SNORA62|ENSG00000252443.1
snoU13|ENSG00000238683.1
COG8
CHTF8
RPS2P45
RNA5SP429
snoU109|ENSG00000252640.1
snoU109|ENSG00000252040.1
snoU13|ENSG00000238343.1
SLC7A6OS
SNORA48|ENSG00000212445.1
CTRL
NUTF2
RN7SKP118
TRADD
RN7SL543P
LINC00920
RNA5SP428
LINC00922
snoU13|ENSG00000238507.1
RN7SKP76
RN7SL143P
SLC38A7
snoU13|ENSG00000239121.1
SNORA50|ENSG00000206952.2
SNORA46|ENSG00000207493.1
RN7SL645P
TEPP
MT1DP
MT1M
MT1E
MT1L
MT2A
OGFOD1
MIR3935
IRX6
RN7SL841P
CRNDE
FTO
RNA5SP427
snoU13|ENSG00000238645.1
CASC16
LINC00919
RN7SKP142
HNRNPA1P48
RNA5SP426
NKD1
SNORD112|ENSG00000252077.1
snoU13|ENSG00000238544.1
SNORA70|ENSG00000252526.1
RNY4P3
snoU13|ENSG00000239038.1
snoU13|ENSG00000239013.1
RN7SL54P
LONP2
RNA5SP425
RNA5SP424
ITFG1
snoU13|ENSG00000238834.1
MYLK3
VPS35
ANKRD26P1
RNA5SP423
RNA5SP422
RNA5SP421
RNA5SP420
RNA5SP419
RNA5SP418
RNA5SP417
RNA5SP416
RNA5SP415
RNA5SP413
RNA5SP410
RNA5SP409
RNA5SP408
RNA5SP407
RNA5SP406
LINC00273
ARHGAP23P1
HERC2P8
HERC2P5
TP53TG3
TP53TG3D
HERC2P4
CLUHP3
PYDC1
ZNF668
MIR4519
MIR4519
BCL7C
SNORA30|ENSG00000206755.1
ZNF747
ZNF747
MIR4518
SNORA42|ENSG00000199787.1
SEPT1
snoU13|ENSG00000239114.1
GDPD3
PAGR1
RN7SKP127
QPRT
snoU13|ENSG00000239193.1
snoU13|ENSG00000238639.1
SNX29P2
SNX29P2
RRN3P2
snoU13|ENSG00000238699.1
MIR4517
SNORA43|ENSG00000252461.1
MIR4721
snoU13|ENSG00000238352.1
NPIPB9
snoU13|ENSG00000238684.1
NPIPB8
CLN3
NPIPB7
snoU13|ENSG00000238703.1
SNORA25|ENSG00000200652.1
C16orf82
RNA5SP405
MIR548W
RN7SL557P
SNORA1|ENSG00000201541.1
DCTN5
SNORA75|ENSG00000212593.1
RN7SKP23
RN7SL245P
snoU13|ENSG00000239172.1
SMG1P1
RRN3P3
EEF2K
SDR42E2
snoU13|ENSG00000238712.1
NPIPB4
RRN3P1
SCARNA6|ENSG00000252798.1
snoU13|ENSG00000238954.1
NPIPB3
DCUN1D3
GPR139
KNOP1
CLEC19A
SYT17
snoU13|ENSG00000238329.1
ABCC6P1
PKD1P5
NPIPA8
RN7SL90P
MPV17L
PKD1P6
NPIPP1
RN7SL274P
SNORA27|ENSG00000199474.1
CPPED1
ACA64|ENSG00000238685.1
BCAR4
RN7SL522P
snoU13|ENSG00000272310.1
snoU13|ENSG00000238409.1
SNORA48|ENSG00000212228.1
RN7SL99P
RN7SL493P
RNA5SP404
RNA5SP403
C16orf72
RN7SL743P
SNORA40|ENSG00000252138.1
ALG1
RN7SL850P
DNASE1
CASP16
LINC00514
PRSS41
SNORA3|ENSG00000221719.1
PRSS27
PDPK2
ATP6C
ABCA17P
BRICD5
SNORD60|ENSG00000206630.1
MIR1225
RN7SL219P
NPW
SNHG9
SNORA64|ENSG00000207405.1
SNORA10
RPL3L
RN7SL367P
MIR3177
CCDC154
PRSS29P
C1QTNF8
MSLNL
METRN
MIR3176
MIR5587
ITFG3
HBZ
SNRNP25
POLR3K
WASIR2
WASH4P
DDX11L10
AARS
ABAT
ABCA3
ADCY7
ADCY9
AP1G1
AFG3L1P
AGRP
ALDOA
AMFR
AQP8
APRT
ABCC6
ARHGDIG
ZFHX3
ATP2A1
ATP6V0C
BBS2
C16orf3
CA5A
CA7
CALB2
CBLN1
CCNF
CD19
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CDR2
CES1
CETP
CLCN7
CLN3
CNGB1
COX4I1
COX6A2
CRYM
CSNK2A2
CTF1
CTRB1
CYBA
ECI1
DHODH
NQO1
SEPT1
DNASE1L2
DYNC1LI2
DPEP1
E2F4
E4F1
EMP2
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GFER
GNAO1
GOT2
GP2
GRIN2A
GSPT1
GTF3C1
HAGH
HAS3
HBA1
HBA2
HBM
HBQ1
HMOX2
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
IGFALS
IL4R
ITGAD
ITGAL
ITGAM
ITGAX
KARS
KIFC3
KIF22
LCAT
MAZ
MC1R
MEFV
MMP2
MMP15
MPG
ABCC1
MT1A
MT1B
MT1F
MT1G
MT1H
MT1JP
MT1X
MT3
MVD
NUBP1
NDUFAB1
NDUFB10
NFATC3
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PARN
CHMP1A
PDPK1
PHKB
PHKG2
PKD1
PLCG2
PLK1
PMM2
POLR2C
PPL
PPP4C
PRKCB
MAPK3
PRM1
PRM2
PRSS8
PSKH1
PSMB10
PSMD7
RBBP6
RBL2
RPL13
RPS2
RPS15A
RRAD
ACSM3
SALL1
SCNN1B
SCNN1G
SRL
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC5A2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
CAPN15
SPG7
SPN
SSTR5
SULT1A2
STX4
SULT1A1
SULT1A3
TBX6
TCEB2
TERF2
TFAP4
TGFB1I1
TK2
TNP2
TPSAB1
TUFM
UBE2I
UMOD
UQCRC2
ZNF19
ZNF23
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
ZP2
USP7
NPRL3
SLC7A5
SNN
AXIN1
PLA2G10
DOC2A
HIRIP3
CDK10
EIF3C
MBTPS1
RGS11
CES2
NAE1
CACNA1H
BAIAP3
NOL3
TAF1C
RHBDL1
SLC7A6
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
USP10
ATP6V0D1
SYNGR3
IL32
NPIPA1
GPR56
TAOK2
SLC9A3R2
LITAF
BCAR1
VPS9D1
KIAA0430
N4BP1
NUP93
SEC14L5
ZNF646
RAB11FIP3
CCP110
SETD1A
IFT140
KIAA0513
PIEZO1
DHX38
RNF40
TELO2
ATP2C2
HS3ST4
HS3ST2
MVP
NUBP2
ZNF263
TRAP1
CLEC3A
CHST4
MPHOSPH6
COQ7
MSLN
IGSF6
IRX5
STUB1
DNAJA2
BCKDK
KATNB1
ZNF267
EMC8
CACNG3
TUBB3
CD2BP2
CDIPT
CFDP1
MRPL28
ERN2
TBL3
CTCF
NFAT5
SRCAP
RNPS1
PRSS21
NUDT21
WWP2
PRDM7
CORO1A
DDX19B
ATXN2L
GABARAPL2
SEPHS2
TCF25
CNOT1
PHLPP2
PDXDC1
SMG1
CLUAP1
GGA2
ZNF423
MAPK8IP3
ZCCHC14
GSE1
ARL6IP1
XPO6
KIAA0556
CLEC16A
MGRN1
ATMIN
RPGRIP1L
ZNF629
COTL1
MLYCD
NOMO1
TPSD1
CES3
SRRM2
CHST5
ARL2BP
CARHSP1
ORC6
EDC4
PLA2G15
TPSG1
RAB26
COG4
TMEM186
PLEKHG4
SH2B1
TBC1D10B
ZNF500
DECR2
RSL1D1
LRRC29
SEZ6L2
NUPR1
LAT
CPNE7
VPS4A
IL17C
TOX3
TNRC6A
DEXI
NOB1
ZC3H7A
CCDC113
TMEM208
C16orf80
PYCARD
FHOD1
BRD7
ANKRD11
ZDHHC1
UBN1
MYLPF
OSGIN1
CDIP1
SOX8
PARD6A
AMDHD2
PAM16
TXNDC11
PLLP
METTL9
NAGPA
CKLF
BFAR
AHSP
TNFRSF12A
ZNF771
NIP7
LCMT1
GDE1
FAM96B
TPPP3
TRAPPC2L
GPRC5B
CES1P1
MSRB1
WWOX
GNG13
BCMO1
TERF2IP
KCTD5
PRMT7
NECAB2
FBXL19
RRN3
RBFOX1
KLHDC4
HYDIN
NDE1
DEF8
DUS2L
CHTF8
ZSCAN32
LPCAT2
TXNL4B
BANP
HCFC1R1
ACSM5
HEATR3
PDPR
ARHGAP17
RFWD3
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
DNAH3
THUMPD1
ZDHHC7
LUC7L
VAC14
DOK4
POLR3E
FTSJD1
DDX28
TSNAXIP1
CENPN
APOBR
UBFD1
COQ9
CIAPIN1
C16orf62
TMEM159
LYRM1
THAP11
JPH3
NMRAL1
TBC1D24
USP31
MKL2
CASKIN1
PDP2
ZNF319
CRAMP1L
RANBP10
VAT1L
RAB40C
WFDC1
PRM3
TMEM8A
CHTF18
CHP2
PRSS22
NOD2
XYLT1
PDF
DPEP2
DPEP3
MLST8
PAPD5
RHBDF1
FBRS
MMP25
AKTIP
NARFL
TPSB2
HS3ST6
PDIA2
UNKL
C16orf58
MTHFSD
GINS3
LMF1
NDRG4
ACD
FAM173A
MRPS34
PRR14
VKORC1
DBNDD1
SLX1B
DCTPP1
METTL22
FA2H
IRX3
THOC6
KREMEN2
FAM65A
TMEM231
CORO7
TANGO6
ROGDI
USB1
TMEM204
ZNF768
WDR59
ZNF668
ELMO3
KLHL36
ARMC5
SHCBP1
KDM8
TMC5
RABEP2
NAA60
TMC7
SETD6
ESRP2
FAM192A
ATF7IP2
CENPT
C16orf59
CHD9
C16orf70
HSD3B7
CYB5B
CMIP
GFOD2
CDT1
MAP1LC3B
NETO2
FAHD1
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
YPEL3
FAM57B
SPNS1
ITFG3
ENKD1
KAT8
NLRC5
WDR24
CCDC135
TRAF7
FLYWCH1
HAGHL
CAPNS2
NUDT16L1
C16orf13
FAM195A
SLX4
SPIRE2
MT4
GNPTG
GLYR1
GLIS2
GPT2
B3GNT9
ZSCAN10
NFATC2IP
CIRH1A
ZNRF1
ABCC11
CNTNAP4
C16orf45
RHOT2
RSPRY1
C16orf93
ZNF598
HN1L
SPSB3
TIGD7
MARVELD3
COG7
SNX29
MTSS1L
ZNF764
CENPBD1
ZNF276
CCDC102A
ORAI3
SDR42E1
ABCC12
PRRT2
ERI2
STX1B
CCDC101
RPUSD1
CMTM1
PKD1L2
FLYWCH2
VASN
ZNF689
SLC5A11
TSR3
RNF166
RMI2
ACSM1
WFIKKN1
EXOSC6
C16orf46
NTAN1
FOPNL
DNAAF1
ACSM2A
NRN1L
CMTM3
C16orf78
SPATA2L
SPATA33
NOXO1
CCDC78
IQCK
ZG16B
PRSS30P
PAQR4
ZC3H18
CDYL2
ANKS3
UBALD1
SEPT12
ZNF720
TMEM219
EARS2
SNX20
TMEM170A
SLC38A8
VWA3A
OTOA
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
TEKT5
RNF151
C16orf11
FBXL16
C16orf92
GSG1L
IL34
ZNF597
CCDC64B
TMED6
ZNF785
ZNF688
PRSS36
C16orf89
C16orf71
ADAD2
ITPRIPL2
ZFP1
ADAMTS18
FAM86A
LDHD
FUK
MLKL
ZNF778
ACSF3
WDR90
EME2
NLRC3
NSMCE1
ZNF48
PDILT
CPNE2
GPR114
PRSS54
CES5A
GPR97
IL27
KCTD13
ASPHD1
MEIOB
PDZD9
CNEP1R1
ANKS4B
PRSS33
NOMO2
CCDC79
CES4A
EXOC3L1
LINC00304
PGP
C16orf54
INO80E
NUDT7
ZNF843
NHLRC4
C16orf91
TMEM114
CLEC18C
SNAI3
PRSS53
JMJD8
FAM92B
C16orf96
ZKSCAN2
ATXN1L
ACSM2B
CLEC18A
CTU2
SLC6A10P
PRR25
SBK1
C16orf87
C16orf97
C16orf86
C16orf47
PTX4
PABPN1L
C16orf74
NOMO3
SMIM22
CTRB2
MIR328
SULT1A4
TRIM72
CLEC18B
SLX1A
BOLA2
MIR193B
MIR484
NPIPA3
NPIPA2
C16orf90
KIAA0895L
TP53TG3C
ZG16
BOLA2B
MIR662
EIF3CL
NPIPB6
NPIPB11
TP53TG3B
SHISA9
C16orf52
CEMP1
TVP23A
MIR940
MIR365A
SYCE1L
NPIPB5
NPIPA5
MIR1538
MIR1910
MIR548H2
MIR762
MIR3178
MTRNR2L4
MIR3677
C16orf95
MIR4719
MIR4718
MIR4717
MIR4516
C16orf98
MIR5093
NPIPA7
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

Table S78.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BRIP1
RARA
BRCA1
CD79B
CLTC
COL1A1
DDX5
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
PER1
PRKAR1A
MAP2K4
TP53
TAF15
GAS7
USP6
SUZ12
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
NXPH3
ZNF652
snoU13|ENSG00000238804.1
SNF8
SNORA68|ENSG00000212565.1
RN7SL125P
HOXB4
HOXB3
HOXB2
HOXB1
U3|ENSG00000200538.1
MIR1203
MIR152
PNPO
KPNB1
MRPL45P2
ITGB3
snoU13|ENSG00000252088.1
RN7SL270P
LRRC37A17P
RNU6ATAC3P
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
ZNF385C
TTC25
RN7SL871P
RN7SL399P
RNA5SP442
EIF1
KRT42P
LINC00974
KRT223P
KRT222
KRT222
RNA5SP441
GJD3
RNY4P8
SNORD124
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
ARL5C
LINC00672
SNORA21|ENSG00000199293.1
SNORA21|ENSG00000252699.1
RPL23
RNA5SP440
CISD3
MIR4726
RN7SL102P
RN7SL458P
SOCS7
HMGB1P24
MIR2909
RNA5SP439
CCL4L2
RN7SL301P
CCL4
CCL18
RN7SKP274
SNORD7
SLFN12L
SLFN5
Vault|ENSG00000252328.1
snoU13|ENSG00000238858.1
RNA5SP438
C17orf75
SH3GL1P1
RNA5SP437
UTP6
RNU6ATAC7P
RN7SL45P
RN7SL79P
EVI2A
RN7SL138P
TEFM
SUZ12P
RN7SL316P
LRRC37BP1
SMURF2P1
SNORD63|ENSG00000252112.1
MIR423
MIR3184
RNY4P13
RNY4P13
snoU13|ENSG00000239129.1
SNORA70|ENSG00000252657.1
MIR4523
TIAF1
NEK8
SNORD4B
SNORD42A
SNORD4A
SNORD42B
RPL23A
SGK494
VTN
SEBOX
MIR4723
TMEM199
Vault|ENSG00000252283.1
SNORA70|ENSG00000202389.1
SCARNA20|ENSG00000251818.1
RN7SL576P
LGALS9
KSR1
TBC1D3P5
MTND1P15
UBBP4
RN7SL426P
TMEM11
KRT16P3
NOS2P3
USP32P3
UPF3AP2
RN7SL17P
U6|ENSG00000266839.2
CCDC144CP
SNORA31|ENSG00000252349.1
SNORA59B
MIR1180
SNORD3C
SNORD3A
GRAPL
SNORD3D
GRAP
FAM83G
RN7SL627P
ZNF286B
TBC1D28
RN7SL639P
KRT16P1
KRT17P2
SMCR8
snoU13|ENSG00000238691.1
MIR33B
SMCR5
SMCR2
RN7SL775P
TBC1D27
KRT17P1
KRT16P2
USP32P1
RN7SL620P
ZNF287
MIR1288
RN7SL442P
RNA5SP436
ZNF286A
SNORA74|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
SNORA74|ENSG00000252305.1
MIR548H3
RN7SL550P
MIR744
RPL21P122
RN7SL601P
LINC00675
MAGOH2
ADPRM
RCVRN
GLP2R
STX8
RN7SL129P
SNORA69|ENSG00000212206.1
CTC1
MIR3676
SNORD118
TMEM107
snoU13|ENSG00000238676.1
SCARNA21|ENSG00000252835.1
RPL29P2
snoU13|ENSG00000251860.1
SNORD10
SNORA48|ENSG00000209582.1
SNORA67|ENSG00000264772.2
SLC35G6
GABARAP
ALOX12P2
TEKT1
C17orf100
RNA5SP435
DERL2
RN7SL784P
RN7SL171P
SPNS2
RN7SL774P
snoU13|ENSG00000238807.1
RNA5SP434
C17orf85
SHPK
ASPA
OR1E1
OR1D4
RN7SL605P
MIR1253
RN7SL608P
snoU13|ENSG00000239024.1
RN7SL33P
SNORD91A
SNORD91B
RN7SL624P
TLCD2
snoU13|ENSG00000238946.1
RN7SL105P
BHLHA9
MIR3183
TIMM22
DBIL5P
DOC2B
AANAT
ABR
ACACA
ACADVL
ASIC2
ACLY
ACOX1
ACTG1
ADORA2B
AP2B1
ALDH3A1
ALDH3A2
ALDOC
ALOX12
ALOX12B
ALOX15
ALOX15B
AOC2
BIRC5
APOH
ARL4D
ARHGDIA
ARRB2
ASGR1
ASGR2
ATP1B2
ATP2A3
ATP5G1
ATP6V0A1
BLMH
C1QBP
FMNL1
CA4
CACNB1
CACNG1
CD7
CD68
CDC6
CDC27
CDK3
CHAD
CHD3
CHRNB1
CHRNE
CCR7
CNP
COX10
COX11
CPD
CLDN7
CRHR1
CRK
CRYBA1
CSF3
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CTNS
CYB561
ACE
DHX8
DLG4
DLX3
DLX4
DNAH9
DPH1
DRG2
DUSP3
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
ERN1
EVI2B
EVPL
EZH1
BPTF
FASN
FDXR
FGF11
FOXJ1
FLII
FLOT2
GAST
GAA
GALK1
GCGR
KAT2A
GFAP
GH1
GH2
GIP
GNGT2
GP1BA
UTS2R
GPS1
GPS2
GRB2
GRB7
GRN
GRIN2C
GUCY2D
H3F3B
HCRT
HIC1
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
ICAM2
ICT1
IFI35
IGFBP4
FOXK2
ITGA2B
ITGA3
ITGAE
ITGB3
ITGB4
JUP
KCNJ2
KCNJ12
KCNJ16
KPNA2
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS3BP
LHX1
LIG3
LLGL2
LLGL1
LPO
NBR1
MAFG
MAPT
ADAM11
MAP3K3
MEOX1
MFAP4
MNT
MPO
MPP2
MPP3
TRIM37
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYL4
MYO1C
MYO1D
NAGLU
NFE2L1
NGFR
NME1
NMT1
NOS2
NPTX1
NSF
NUP88
OMG
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
P4HB
PAFAH1B1
PDE6G
PDK2
SERPINF1
PEX12
PFAS
PFN1
PHB
PITPNA
PLD2
SERPINF2
PMP22
SEPT4
POLR2A
MED1
PPY
PRKCA
MAPK7
MAP2K3
PRPSAP1
PRPSAP2
PSMB3
PSMB6
PYY
PSMC5
PSMD3
PSMD11
PYCR1
RAB5C
RAC3
RAD51C
RAD51D
RFNG
RPA1
RPL19
RPL26
RPL27
RPL38
MRPL12
RPS6KB1
SCN4A
SCO1
CCL1
CCL2
CCL3
CCL3L1
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL23
SDF2
SEC14L1
SECTM1
SRSF2
SGCA
SGSH
SHBG
SHMT1
SLC2A4
SLC4A1
SLC6A4
SMARCD2
SMARCE1
SUMO2
SOX9
SOX15
SP2
SREBF1
SRP68
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
VAMP2
TADA2A
TBCD
TBX2
HNF1B
MLX
THRA
TIMP2
TK1
TNFAIP1
TOP2A
TOP3A
DNAJC7
TUBG1
UBB
UBE2G1
UBTF
TRPV1
WNT3
WNT9B
YWHAE
ZNF18
PCGF2
TRIM25
RNF112
ZNF207
ZNF232
RND2
COIL
AKAP1
EPX
AXIN2
OR1A1
OR1D5
OR1E2
OR1G1
OR3A3
PIP4K2B
SLC25A11
SPOP
FOXN1
CNTNAP1
DGKE
COPS3
CBX4
SCARF1
SKAP1
DNAH17
AOC3
BECN1
KRT38
KRT37
KRT36
TNK1
ABCC3
MYH13
TNFSF13
RGS9
GALR2
CDK5R1
SPHK1
CACNA1G
HAP1
SOCS3
TM4SF5
SPAG9
SLC13A2
UNC119
MTMR4
SLC16A6
SLC16A5
SLC16A3
RABEP1
SYNGR2
HGS
KCNAB3
AURKB
NOG
BZRAP1
CYTH1
ZNHIT3
EFTUD2
SLC9A3R1
COG1
RECQL5
NTN1
PIGL
PGS1
TBX4
RPH3AL
FXR2
NPEPPS
MPDU1
GOSR1
SPAG7
CCL4L1
GOSR2
NR1D1
NCOR1
TRAF4
AATK
KIAA0100
ULK2
CCDC144A
ACAP1
TBKBP1
KIAA0195
EIF4A3
PLEKHM1
KIAA0753
MED24
LRRC37A
MRC2
SGSM2
ARHGAP44
HELZ
HS3ST3A1
MED13
HDAC5
TOM1L1
GJC1
TOB1
ALYREF
PSME3
NBR2
SLC35B1
DCAF7
CALCOCO2
RAMP2
ABCA10
ABCA9
ABCA8
PEMT
BAIAP2
CLEC10A
ATP5H
HOXB13
VAT1
APPBP2
MYBBP1A
FBXW10
PRPF8
LEPREL4
ST6GALNAC2
HEXIM1
SPAG5
TRIM16
IGF2BP1
GNA13
CCT6B
RAI1
KIF1C
SEPT9
CD300C
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
KAT7
AKAP10
POLG2
SYNRG
CD300A
TMC6
DDX42
CASC3
NLRP1
ARHGEF15
EPN2
AZI1
SARM1
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
GGA3
MPRIP
JMJD6
EXOC7
CLUH
SMG6
WSCD1
USP22
CTDNEP1
KCNH4
ABCA6
ABCA5
TNFRSF13B
KCTD2
MMD
PIK3R5
WBP2
CDC42EP4
ELP5
FAM215A
PPY2
PYY2
SHPK
AIPL1
FSCN2
NOL11
DHRS7B
KRT23
RNF167
TMEM98
POLDIP2
TBC1D29
TANC2
WSB1
NAT9
SENP3
OR1A2
PITPNC1
ERAL1
NARF
AATF
OR4D1
PELP1
B9D1
CACNG5
CACNG4
TUBG2
TMEM97
NKIRAS2
COA3
GIT1
RANGRF
SAP30BP
PSMC3IP
SNX11
TBX21
NT5C
CDR2L
TAX1BP3
MINK1
GEMIN4
SOST
MED31
TVP23B
GLOD4
MRPS7
YBX2
UTP18
RNFT1
HN1
MYO15A
TUBD1
DCXR
RAPGEFL1
TACO1
ABI3
COPZ2
MRPL27
PIPOX
AMZ2
ARL17A
CRLF3
TRPV2
ANKFY1
ANAPC11
SIRT7
SLC25A39
PTRH2
RASD1
NLK
LUC7L3
HIGD1B
CDK12
INPP5K
KRT20
NLE1
FAM64A
SDK2
XAF1
FNDC8
C17orf59
MBTD1
BCAS3
TMEM104
CWC25
ALKBH5
RNF43
TTC19
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
SLC52A1
MED9
SLFN12
WRAP53
KLHL11
RNMTL1
SMG8
SLC47A1
TMEM100
VPS53
RHOT1
RSAD1
COPRS
LRRC59
NPLOC4
TSR1
FAM222B
ADAP2
ST6GALNAC1
TEX2
GSDMB
TEX14
WDR45B
DHX33
CA10
NT5M
ATXN7L3
CCDC47
PLSCR3
PLXDC1
LYZL6
ZNF286A
MIF4GD
INTS2
CASKIN2
RPTOR
NUFIP2
ZNF624
TAOK1
NLGN2
USP36
ARHGAP23
PHF12
ZBTB4
RNF213
TNRC6C
CXCL16
TRAPPC1
PCTP
SCPEP1
ALOXE3
SLC25A19
ELAC2
FKBP10
SRR
UBE2O
HEATR6
FN3K
XYLT2
NXN
DNAI2
TEKT3
SPATA20
MRPL38
UBE2Z
WNK4
C17orf53
MIS12
GID4
METTL16
TMUB2
CARD14
DHX58
PHF23
MMP28
DHRS11
MFSD11
PRR15L
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
OGFOD3
ZNF750
ACBD4
FAM57A
DCAKD
GGNBP2
NUP85
ATAD5
MRM1
PLEKHH3
FAM106A
DBF4B
MYO19
ACSF2
C17orf70
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
LIMD2
KCNH6
FAM117A
NDEL1
VMP1
ACKR6
LRRC48
EMC6
RILP
RAB34
TSPAN10
GSG2
MYCBPAP
QRICH2
NSRP1
PPP1R1B
TBC1D3F
ZMYND15
CAMKK1
RPAIN
RNF135
MIEN1
MRPL45
VPS25
LSMD1
TMEM101
PRAC
RAB11FIP4
NEURL4
GHDC
ZNF594
KIF2B
HES7
PPP1R9B
SPATA22
CBX2
TXNDC17
FAM104A
CORO6
TNS4
FBXL20
FBF1
UNK
SSH2
TP53I13
IFT20
LRRC46
SCRN2
CEP95
TRIM47
ANKRD40
ZNF830
SLFN11
RASL10B
ATPAF2
TMEM88
STRADA
C17orf72
SPECC1
G6PC3
ASB16
OTOP2
PGAP3
MYOCD
PIGS
TTYH2
HSPB9
ORMDL3
SAT2
PLCD3
SLC46A1
TMEM106A
LRRC37B
CYGB
RNF157
SMYD4
OSBPL7
C1QTNF1
NT5C3B
ABHD15
TLCD1
PPP1R27
CNTROB
FTSJ3
RFFL
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
ZPBP2
CYB5D1
OVCA2
USP43
KRBA2
C17orf64
SPATA32
HEXIM2
LSM12
CCDC43
TMEM132E
WFIKKN2
B4GALNT2
SPACA3
SEZ6
ANKRD13B
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
EFCAB13
MRPL10
WDR81
TBC1D16
AFMID
KRT40
ZSWIM7
SMCR7
SLC5A10
MGAT5B
TOM1L2
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
DNAH2
RTN4RL1
EFCAB3
SLC47A2
WDR16
CCDC42
PIK3R6
ODF4
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
PROCA1
DHRS13
KCTD11
NOTUM
TMC8
TRIM16L
WIPF2
KRT25
TMEM99
ANKFN1
MARCH10
MFSD6L
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
TRPV3
SLC16A11
FBXO39
SPPL2C
KRT28
KRT24
CEP112
DHRS7C
TVP23C
CENPV
FLCN
PLD6
ARHGAP27
SAMD14
LYRM9
SLC16A13
C17orf74
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
RDM1
SPNS3
USP32P2
GAS2L2
STH
STXBP4
TMEM256
TAC4
MYADML2
BCL6B
CDRT15L2
C17orf103
NPB
C17orf66
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
VMO1
C17orf58
MILR1
LINC00324
LINC00670
CDRT4
CCDC144B
KANSL1
FAM171A2
C17orf104
TTLL6
C17orf47
KRT18P55
PIGW
C17orf78
GSDMA
SLC13A5
TMEM102
PTRF
FAM27L
SLC26A11
ENDOV
GDPD1
C17orf89
TMEM105
LGALS9B
METRNL
TUSC5
KLHL10
RAB37
TMEM95
METTL2A
CCDC144NL
C17orf67
ENPP7
OXLD1
CCDC137
ARL16
C17orf51
MSL1
CD300E
SMTNL2
NACA2
KRT27
SLFN14
LRRC37A11P
STAC2
OTOP3
SKA2
FAM195B
GPR142
TBC1D26
ZACN
KRT26
FAM101B
CDRT1
SPEM1
EFCAB5
LRRC37A3
GLTPD2
INCA1
SCIMP
SPDYE4
TMEM220
SHISA6
FAM211A
TMIGD1
C17orf98
LINC00671
RPRML
YPEL2
C17orf82
BTBD17
OR3A4P
KRT39
SLC25A35
MYO18A
C17orf97
MED11
C17orf102
TEX19
CUEDC1
MIR10A
MIR132
MIR142
MIR193A
MIR196A1
MIR21
MIR212
MIR22HG
TNFSF12
TBC1D3B
TBC1D3C
CCL3L3
MXRA7
RNASEK
GPR179
MIR324
LRRC37A2
FBXO47
MIR497HG
CPSF4L
SMIM5
RNF222
PIRT
EVPLL
TBC1D3G
LGALS9C
NME2
MIR632
MIR633
TBC1D3
TBC1D3H
MIR365B
C17orf107
SMIM6
TEN1
C17orf99
C17orf96
MIR2117
MIR4316
MIR338
MIR3186
MIR3185
MIR4314
MTRNR2L1
MIR3614
MIR3678
MIR3615
LRRC3C
ARL17B
C17orf112
MIR4523
MIR4739
MIR4734
MIR4737
MIR4736
MIR4724
MIR4733
MIR4522
MIR4738
MIR4740
MIR4732
MIR4520B
MIR4727
MIR4725
MIR1269B
MIR4524B
MIR5089
PTGES3L
Genes in Wide Peak

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

Table S79.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
NPM1
PDGFRB
PIK3R1
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
LUCAT1
SNORA70|ENSG00000206958.1
RNA5SP187
RN7SL629P
RN7SKP34
MIR3607
COX7C
NBPF22P
RN7SKP295
SCARNA18|ENSG00000238835.1
RN7SL378P
SSBP2
SNORA31|ENSG00000251828.1
snoU13|ENSG00000239159.1
MTX3
HOMER1
SNORA18|ENSG00000206592.1
RNY3P1
BHMT2
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13|ENSG00000238688.1
RNA5SP186
POLK
SNORA40|ENSG00000212363.1
RN7SL814P
MIR4804
RN7SL153P
MIR4803
snoU13|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13|ENSG00000238334.1
SNORA50|ENSG00000220986.1
RN7SL103P
7SK|ENSG00000249352.3
U8|ENSG00000212249.2
snoU13|ENSG00000238400.1
SNORA76|ENSG00000252904.1
RN7SL169P
HTR1A
CKS1B|ENSG00000268942.1
KIF2A
RN7SKP157
FKSG52
MIR582
GAPT
snoU13|ENSG00000238899.1
snoU13|ENSG00000238717.1
RNU6ATAC2P
RNA5SP185
RNA5SP184
snoU13|ENSG00000238326.1
RNA5SP183
MIR5687
MIR449C
MIR449B
MIR449A
GPX8
GZMK
MIR4459
RN7SL801P
MIR581
PELO
ITGA1
RNA5SP182
snoU13|ENSG00000238702.1
HCN1
RN7SL383P
FGF10
CCL28
ANXA2R
SNORD72
RPL37
SNORA57|ENSG00000212567.1
SNORA63|ENSG00000199552.1
LINC00604
LINC00603
WDR70
RN7SL37P
RNA5SP181
LMBRD2
U3|ENSG00000201368.1
BRIX1
C1QTNF3
MIR579
snoU13|ENSG00000238864.1
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
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
CLTB
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
HARS
HEXB
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA2
KCNN2
TNPO1
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NEUROG1
NPR3
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
NREP
TRIP13
CNOT8
HAND1
MED7
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
FAXDC2
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
PAPD7
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
SKIV2L2
NNT
TTC33
ZNF346
AMACR
NIPBL
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
KLHL3
TSPAN17
FBXO4
OR4F3
OR2V1
HAVCR1
CYFIP2
PKD2L2
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
DROSHA
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MZB1
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
RBM27
FAM134B
NEURL1B
DHX29
DDX4
FAM193B
MTMR12
SGTB
ARL15
TMED9
ZCCHC10
CDHR2
GIN1
NSUN2
SPDL1
AGGF1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
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
ANKH
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
NLN
AHRR
ZNF608
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
ARHGEF28
SIL1
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
CCNJL
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
TRAPPC13
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
GFM2
MEGF10
SPINK7
SPZ1
CARD6
HAVCR2
PHYKPL
SMIM3
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
SCGB3A2
SETD9
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
MROH2B
EGFLAM
PRRC1
NADK2
UGT3A1
CAPSL
JMY
ZNF474
OR2Y1
C5orf49
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
POC5
STARD4
WDR36
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC38A9
SLC36A2
CREBRF
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
CCDC112
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
NIM1
LIX1
ZNF366
FAM151B
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
CCDC125
C5orf27
CMYA5
STK32A
AQPEP
SLC36A1
RICTOR
RASGEF1C
ANKRD31
SERINC5
EFCAB9
SH3PXD2B
FAM153A
KIAA0825
RELL2
C5orf51
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
RGMB
RFESD
CHSY3
SLC6A19
FAM170A
ARSI
ANKRD34B
PFN3
PLCXD3
IRGM
MCIDAS
ACTBL2
FAM174A
CATSPER3
SLC6A18
NIPAL4
SLCO4C1
DND1
C5orf34
MAST4
SIMC1
C5orf48
PROB1
C5orf46
ARHGEF37
RGS7BP
SPINK6
ANKHD1
MIR143
MIR145
MIR146A
LINC00461
SPINK14
FNDC9
MARCH11
C5orf56
IGIP
CTXN3
SMIM15
GRXCR2
SPINK9
ZFP62
CCNI2
CBY3
FAM153C
MIR580
MIR583
GTF2H2C
SERF1B
ANKDD1B
CCDC152
LRRC70
FAM196B
FAM159B
C5orf52
MIR1303
TICAM2
MIR2277
MIR4279
MIR4280
MIR3141
MIR4277
MTRNR2L2
MIR3650
MIR3660
MIR3912
MIR3936
MIR3661
OCLN
MIR4458
MIR4634
MIR4457
MIR378H
MIR4460
MIR548AE2
MIR4638
MIR4456
MIR5197
MIR5692C1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.33.

Table S80.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GNAQ
ABL1
FANCC
FANCG
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13|ENSG00000238530.1
MIR455
COL27A1
FKBP15
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
snoU13|ENSG00000238746.1
RNA5SP288
MIR27B
MIR23B
MIR2278
PCAT7
ZNF169
snoU13|ENSG00000238792.1
MIRLET7DHG
CENPP
SNORA84
snoU13|ENSG00000238996.1
LINC00475
LINC00484
MIR3153
SHC3
U3|ENSG00000252299.1
U6|ENSG00000271923.1
SPATA31C1
SNORA26|ENSG00000212421.1
RN7SKP264
IDNK
SNORD112|ENSG00000252256.1
snoU13|ENSG00000238608.1
RN7SKP242
SPATA31D3
SPATA31D4
SPATA31D5P
SNORD95|ENSG00000200969.1
RNA5SP287
TLE4
RN7SKP59
PCA3
snoU13|ENSG00000238598.1
RNY4P1
RN7SKP47
RNA5SP286
snoU13|ENSG00000238402.1
RNA5SP285
MIR204
RN7SL570P
CBWD3
PGM5P2
RNA5SP284
SNORA70|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
SNX18P3
IGFBPL1
snoU13|ENSG00000238313.1
U8|ENSG00000200026.1
SHB
RN7SKP171
RN7SL463P
MIR4476
MIR4540
LINC00961
RGP1
RN7SL22P
RMRP
MIR4667
RN7SL338P
FLJ00273
FAM205CP
FAM205B
GALT
RN7SKP24
KIAA1161
RNA5SP282
RN7SKP114
SNORD121A
SNORD121B
RNU4ATAC11P
PTENP1
RNU4ATAC15P
TMEM215
GVQW1
RNA5SP281
snoU13|ENSG00000239155.1
LINC00032
RNA5SP280
RN7SL100P
SNORA31|ENSG00000252580.1
RN7SKP120
RMRPP5
DMRTA1
RN7SL151P
SNORD39|ENSG00000264379.1
MIR31HG
IFNA6
KLHL9
PTPLAD2
SNORA30|ENSG00000202189.1
MIR491
MIR4474
MIR4473
ACER2
snoU13|ENSG00000238348.1
RN7SL158P
SCARNA8
RN7SKP258
MIR3152
RN7SL720P
RN7SL98P
RN7SL157P
LINC00583
LURAP1L
RN7SL849P
RN7SL5P
SNORD27|ENSG00000251699.1
RN7SL123P
snoU13|ENSG00000252110.1
RN7SL25P
C9orf38
MLANA
snoU13|ENSG00000238654.1
INSL4
AK3
CDC37L1
CARM1P1
RN7SL592P
RNA5SP279
RN7SL412P
FAM138C
ABCA1
ABCA2
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
IL11RA
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RORB
RPL7A
RPL12
RPS6
CCL19
CCL21
SH3GL2
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
PRPF4
KLF4
GTF3C5
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
TRIM14
MELK
RUSC2
PPP1R26
SEC16A
ZBTB5
KIAA0020
TNFSF15
PTBP3
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
CACFD1
PSIP1
INSL6
SLC2A6
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
KIAA1045
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
DDX58
RABGAP1
TMEM2
TMEM245
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
NELFB
NIPSNAP3A
NSMF
GPSM1
GAPVD1
PHF19
ZNF658
SPATA31A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
EXOSC3
ABHD17B
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
EQTN
TBC1D13
NUTM2F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
TOR4A
CNTLN
TEX10
FOCAD
UBE2R2
EXD3
FAM206A
NMRK1
NOL8
SPATA6L
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
DENND4C
RABL6
CDK5RAP2
UBAP2
PLGRKT
CBWD1
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KCNT1
KIAA1432
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
ZNF462
DMRT3
PRDM12
NAA35
SLC28A3
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOB3B
CAAP1
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
FAM214B
GKAP1
PDCD1LG2
AKNA
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
NTNG2
HIATL1
HINT2
C9orf24
PIGO
PPAPDC3
ZDHHC12
FAM73B
ARHGEF39
C9orf3
FIBCD1
KIAA1984
TMEM141
C9orf37
FGD3
MVB12B
TPD52L3
WDR34
SAPCD2
C9orf69
LRSAM1
IL33
C9orf123
UAP1L1
SLC25A51
MRRF
ARRDC1
DPH7
ADAMTSL1
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19P
ARID3C
RPP25L
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf62
C9orf66
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC39B
TRMT10B
TTC16
FAM120AOS
FAM154A
FREM1
KIAA2026
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
PRUNE2
C9orf96
KCNV2
OLFML2A
TMEM252
QSOX2
GLIS3
ZNF367
C9orf91
C9orf72
CCDC171
NAIF1
FAM219A
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
FAM205A
CRB2
SCAI
C9orf117
C9orf47
SPATA31E1
LCN12
C9orf142
TPRN
TUSC1
FAM78A
OR13C9
OR13D1
FOXD4L3
IFNE
ZDHHC21
GPR144
QRFP
OR1J1
OR1B1
KIF24
MURC
FOXD4L4
GLT6D1
ENHO
PTAR1
ERCC6L2
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
SPATA31A6
SPATA31D1
C9orf153
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
FAM221B
OR13J1
CTSL3P
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
TOMM5
FAM74A4
C9orf170
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR31
ANKRD20A3
ANKRD20A2
NUTM2G
ANKRD18B
C9orf173
NRARP
FOXB2
C9orf129
FAM27A
DNAJC25
SPATA31A2
SPATA31A4
CBWD6
HRCT1
SPATA31A1
FOXD4L6
FOXD4L5
MSMP
MIR600HG
MIR602
FAM27D1
RNF208
SPATA31A3
SPATA31A5
CBWD7
CARD9
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
MIR876
MIR873
C9orf92
IZUMO3
FAM27E3
FAM27C
FAM27B
MIR1299
MIR3074
MIR3154
MIR4291
MIR4290
MIR4289
CCDC180
MIR3689A
MIR3911
MIR3927
MIR3689B
MIR3689D1
MIR4477A
MIR3689F
MIR3960
MIR4665
MIR4475
MIR4674
MIR4478
MIR3689C
MIR3689D2
MIR4670
MIR3689E
MIR548AW
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq23.

Table S81.  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 - 18 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 0.01 -0.999 0.995 0.01 -0.999 0.995
1q 1195 0.05 7.26 7.76e-12 0.01 -1.31 0.995
2p 624 0.00 -2.15 0.995 0.02 1.76 0.323
2q 967 0.00 -2.16 0.995 0.02 1.35 0.601
3p 644 0.01 -1.39 0.995 0.01 -1.39 0.995
3q 733 0.00 -1.78 0.995 0.01 -0.997 0.995
4p 289 0.01 -0.594 0.995 0.00 -1.77 0.995
4q 670 0.01 -0.601 0.995 0.00 -1.77 0.995
5p 183 0.04 5.72 1.12e-07 0.00 -2.11 0.995
5q 905 0.03 4.1 0.000142 0.00 -2.54 0.995
6p 710 0.00 -1.78 0.995 0.01 -0.996 0.995
6q 556 0.00 -2.16 0.995 0.01 0.184 0.995
7p 389 0.04 4.51 3.26e-05 0.00 -2.53 0.995
7q 783 0.04 5.28 8.69e-07 0.00 -2.53 0.995
8p 338 0.01 -0.19 0.995 0.01 -0.972 0.995
8q 551 0.01 0.2 0.908 0.01 -0.972 0.995
9p 301 0.01 -1.32 0.995 0.04 4.94 5.29e-06
9q 700 0.01 -0.898 0.995 0.05 7.3 2.89e-12
10p 253 0.00 -1.76 0.995 0.01 0.197 0.995
10q 738 0.00 -1.77 0.995 0.01 -0.209 0.995
11p 509 0.01 -0.179 0.995 0.01 0.212 0.995
11q 975 0.01 -0.575 0.995 0.02 0.985 0.951
12p 339 0.03 2.95 0.00698 0.00 -2.14 0.995
12q 904 0.03 2.93 0.00698 0.00 -2.14 0.995
13q 560 0.01 -0.544 0.995 0.03 2.97 0.0151
14q 938 0.02 1.75 0.118 0.00 -2.15 0.995
15q 810 0.00 -2.56 0.995 0.02 0.566 0.995
16p 559 0.03 3.33 0.00219 0.00 -2.14 0.995
16q 455 0.03 2.56 0.0196 0.00 -1.74 0.995
17p 415 0.03 3.8 0.000429 0.02 0.669 0.995
17q 972 0.03 4.14 0.000141 0.01 -0.538 0.995
18p 104 0.01 -0.185 0.995 0.01 -0.968 0.995
18q 275 0.01 -0.189 0.995 0.01 -0.971 0.995
19p 681 0.02 0.598 0.631 0.01 -0.574 0.995
19q 935 0.02 0.968 0.455 0.00 -1.76 0.995
20p 234 0.02 2.16 0.0498 0.00 -2.54 0.995
20q 448 0.02 2.15 0.0498 0.00 -2.54 0.995
21q 258 0.01 -0.565 0.995 0.02 0.609 0.995
22q 564 0.00 -1.47 0.995 0.18 32.5 0
Xp 418 0.02 0.599 0.631 0.01 -0.966 0.995
Xq 668 0.02 0.592 0.631 0.01 -0.97 0.995
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/THCA-TP/19080741/GDAC_MergeDataFiles_19085652/THCA-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 499 Input Tumor Samples.

Tumor Sample Names
TCGA-4C-A93U-01A-11D-A396-01
TCGA-BJ-A0YZ-01A-11D-A10T-01
TCGA-BJ-A0Z0-01A-11D-A10T-01
TCGA-BJ-A0Z2-01A-11D-A10T-01
TCGA-BJ-A0Z3-01A-11D-A13V-01
TCGA-BJ-A0Z5-01A-11D-A10T-01
TCGA-BJ-A0Z9-01A-11D-A10T-01
TCGA-BJ-A0ZA-01A-11D-A10T-01
TCGA-BJ-A0ZB-01A-11D-A10T-01
TCGA-BJ-A0ZC-01A-12D-A13V-01

Figure 3.  Segmented copy number profiles in the input data

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

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

Region Data

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

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

  2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

  1. Cytoband

  2. Q value

  3. Residual Q value

  4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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)
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)