SNP6 Copy number analysis (GISTIC2)

Esophageal Carcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

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/C1XP73XB

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 92 tumor samples used in this analysis: 25 significant arm-level results, 22 significant focal amplifications, and 45 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 - 22 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
11q13.3	8.9598e-107	8.9598e-107	chr11:69388908-69531780	3
7p11.2	3.7416e-10	4.1384e-10	chr7:54815172-55390810	3
8q24.21	7.1345e-09	7.1345e-09	chr8:128153806-128376800	2
7q21.2	9.4497e-07	9.6958e-07	chr7:87312937-95072746	53
3q26.2	1.762e-09	2.0233e-06	chr3:169415894-171079179	20
12q15	0.0001746	0.0001746	chr12:69108273-70106834	12
1p34.2	0.0002276	0.0002276	chr1:40264205-40747321	8
8p11.21	1.5665e-05	0.0012183	chr8:41721029-42518767	12
14q13.2	0.0023562	0.0023562	chr14:35795996-36687053	8
3q26.33	1.1065e-10	0.0026358	chr3:180680795-183901191	32
2q14.2	0.003413	0.003413	chr2:117933951-122777652	30
12p12.1	0.0049199	0.0049199	chr12:24656657-26372477	13
11p13	0.01098	0.01098	chr11:35244045-35263137	1
5p15.33	0.013046	0.013046	chr5:1288020-1348797	3
19p13.2	0.014693	0.014693	chr19:7300056-7398264	0 [INSR]
8p11.22	0.0040913	0.027062	chr8:36235571-39123689	30
4q13.3	0.038927	0.038927	chr4:73519324-74161890	5
1q42.3	0.078749	0.078749	chr1:205149968-249250621	406
13q34	0.099015	0.099015	chr13:112353826-114313493	22
4p13	0.1133	0.1133	chr4:44274104-44775014	4
9p13.3	0.2098	0.2098	chr9:23771264-71039939	202
19q13.43	0.2098	0.2098	chr19:58573560-59128983	28

Genes in Wide Peak

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

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

Genes
CCND1
FGF19
ORAOV1

Genes in Wide Peak

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

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

Genes
EGFR
SNORA73\|ENSG00000252054.1
SEC61G

Genes in Wide Peak

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

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

Genes
CASC8
CCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
PON1
snoU13\|ENSG00000238384.1
RN7SKP129
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
snoU13\|ENSG00000238739.1
DPY19L2P4
SNORA67\|ENSG00000207094.1
CALCR
KRIT1
COL1A2
CYP51A1
GNGT1
PEX1
CDK14
ABCB1
PON2
PON3
SRI
MTERF
TFPI2
FZD1
SGCE
CLDN12
BET1
DBF4
PEG10
STEAP1
ADAM22
ANKIB1
SAMD9
PPP1R9A
CCDC132
SLC25A40
CASD1
STEAP4
C7orf63
RBM48
GTPBP10
RUNDC3B
SAMD9L
C7orf62
ZNF804B
HEPACAM2
FAM133B
STEAP2
LRRD1
MIR4652

Genes in Wide Peak

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

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

Genes
MIR569
RNY5P3
CLDN11
TERC
PRKCI
SKIL
SLC2A2
SEC62
TNIK
GPR160
MYNN
EIF5A2
SLC7A14
LRRC31
PHC3
ACTRT3
LRRC34
RPL22L1
LRRIQ4
SAMD7

Genes in Wide Peak

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

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

Genes
MDM2
RN7SL804P
SLC35E3
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
NUP107
BEST3
LRRC10

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MYCL
PPT1
RLF
ZMPSTE24
CAP1
TRIT1
MFSD2A
TMCO2

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238714.1
SNORD112\|ENSG00000238966.1
ANK1
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
AP3M2
DKK4
SMIM19

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.2.

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

Genes
PTCSC3
snoU13\|ENSG00000238718.1
SNORA31\|ENSG00000253059.1
NFKBIA
BRMS1L
INSM2
RALGAPA1
LINC00609

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
SOX2
CYP2AB1P
SNORA4\|ENSG00000251730.1
SNORA63\|ENSG00000199363.1
SNORA81\|ENSG00000253092.1
SNORA63\|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
AP2M1
DVL3
FXR1
EIF2B5
ABCC5
MCF2L2
ATP11B
LAMP3
KLHL24
PARL
YEATS2
MCCC1
MAP6D1
B3GNT5
KLHL6
DNAJC19
HTR3C
HTR3D
HTR3E
MIR4448

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238341.1
RNU4ATAC
TMEM185B
snoU13\|ENSG00000238368.1
PCDP1
RN7SL468P
RN7SL111P
HTR5BP
DBI
EN1
GLI2
INHBB
PTPN4
RALB
SCTR
TSN
MARCO
DDX18
CLASP1
TFCP2L1
INSIG2
CCDC93
STEAP3
EPB41L5
TMEM177
MKI67IP
FLJ14816
C2orf76
TMEM37
C1QL2

Genes in Wide Peak

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

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

Genes
KRAS
SSPN
RN7SKP262
RN7SL38P
BCAT1
LRMP
RASSF8
CASC1
BHLHE41
LINC00477
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

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

Table S13. 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 5p15.33.

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

Genes
TERT
CLPTM1L
MIR4457

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.22.

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

Genes
FGFR1
WHSC1L1
SNORD38\|ENSG00000207199.1
PLEKHA2
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
RNA5SP264
ADRB3
EIF4EBP1
TACC1
ADAM9
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
RAB11FIP1
TM2D2
PPAPDC1B
GOT1L1
LETM2
KCNU1
HTRA4
ADAM32
C8orf86

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
SNORA3\|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
ANKRD17
COX18

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.3.

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

Genes
ELK4
FH
SLC45A3
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25\|ENSG00000252011.1
SNORD112\|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25\|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13\|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8\|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13\|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51\|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13\|ENSG00000239094.1
snoU13\|ENSG00000238545.1
MIR4742
snoU13\|ENSG00000238856.1
MIR320B2
SNORA72\|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13\|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13\|ENSG00000238576.1
snoU13\|ENSG00000238798.1
U3\|ENSG00000221673.1
RNA5SP76
SLC30A10
U3\|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116\|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26\|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
SERTAD4
MIR4260
MIR205HG
MIR29B2
MIR29C
snoU13\|ENSG00000238401.1
FAIM3
IL20
SNORD112\|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60\|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72\|ENSG00000201944.1
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
C4BPA
C4BPB
CAPN2
CD34
CENPF
CHML
LYST
CR1
CR1L
CR2
CTSE
CD55
EIF2D
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PLXNA2
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
ZNF124
HIST3H3
GNPAT
DYRK3
CDC42BPA
DEGS1
KMO
RAB7L1
TAF1A
EXO1
MAPKAPK2
GGPS1
IKBKE
TMEM63A
TOMM20
URB2
CEP170
TMCC2
LPGAT1
AKT3
BPNT1
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
IL24
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
DSTYK
RAB3GAP2
INTS7
AHCTF1
NSL1
OR2M4
OR2L2
OR2T1
RPS6KC1
DIEXF
TAF5L
DISC1
FLVCR1
CNIH4
PYCR2
NENF
IL19
G0S2
RRP15
DESI2
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
TMEM206
YOD1
BATF3
ZNF692
IARS2
HHAT
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
RHOU
TFB2M
GREM2
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
NUAK2
RASSF5
MIXL1
SPRTN
FCAMR
OBSCN
EFCAB2
MLK4
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
LEMD1
NLRP3
SLC26A9
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
B3GALNT2
MFSD4
PM20D1
GCSAML
CNIH3
EXOC8
C1orf227
FAM71A
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
SLC41A1
OR2T6
SYT14
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
C1orf132
TRIM67
MAP1LC3C
OR13G1
MIR135B
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q34.

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

Genes
DCUN1D2
LINC00403
LINC00404
SNORD44
LINC00354
ATP4B
F7
F10
LAMP1
SOX1
TFDP1
CUL4A
PROZ
TUBGCP3
ATP11A
MCF2L
TMCO3
PCID2
GRTP1
ADPRHL1
SPACA7
C13orf35

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p13.

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

Genes
GUF1
GNPDA2
YIPF7
KCTD8

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
FANCG
PAX5
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
ACO1
ALDH1B1
NUDT2
AQP3
AQP7
BAG1
CA9
CCIN
CD72
CLTA
CNTFR
ELAVL2
GALT
B4GALT1
DNAJA1
IL11RA
NDUFB6
NFX1
NPR2
PGM5
PRSS3
CCL19
CCL21
TEK
TESK1
TLN1
TPM2
VCP
RECK
PLAA
GRHPR
MELK
RUSC2
ZBTB5
GNE
TOPORS
SIGMAR1
CREB3
UNC13B
CCL27
DCTN3
FRMPD1
KIAA1045
DDX58
DNAJB5
DCAF12
ZNF658
SPATA31A7
SPAG8
FBXO10
DNAI1
SIT1
SPINK4
STOML2
EXOSC3
UBAP1
CHMP5
TMEM8B
EQTN
APTX
UBE2R2
SMU1
UBAP2
OR2S2
IFNK
GBA2
POLR1E
LRRC19
NOL6
DCAF10
MOB3B
CAAP1
CNTNAP3
IFT74
FAM214B
ZCCHC7
ANKRD20A1
HINT2
C9orf24
PIGO
ARHGEF39
SLC25A51
TAF1L
ARID3C
RPP25L
C9orf131
RNF38
GLIPR2
LINGO2
TRMT10B
ATP8B5P
C9orf72
FAM219A
CCDC107
CBWD5
ANKRD18A
FAM205A
TUSC1
FOXD4L3
KIF24
FOXD4L4
ENHO
SPATA31A6
FAM221B
OR13J1
TOMM5
FAM74A4
ANKRD20A3
ANKRD20A2
ANKRD18B
FAM27A
SPATA31A2
SPATA31A4
CBWD6
HRCT1
SPATA31A1
FOXD4L6
FOXD4L5
MSMP
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
MIR876
MIR873
IZUMO3
FAM27E3
FAM27C
FAM27B
MIR1299
MIR4477A
MIR4475

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.43.

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

Genes
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
ZSCAN18
RPL23AP79
ZNF329
ZBTB45
ZNF837
ZNF497
ZNF584
ZSCAN22
ZNF324B
MIR4754

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

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
9p21.3	2.1415e-138	2.1415e-138	chr9:21931610-22003135	2
2q22.1	3.8359e-30	1.9854e-27	chr2:140708948-143637838	2
8p23.2	4.1263e-17	4.1263e-17	chr8:3548028-4251283	2
Xp11.3	1.1705e-12	2.138e-12	chrX:44702452-45008304	2
10p11.21	5.1715e-09	4.8905e-09	chr10:34059131-35328087	1
3p14.3	4.4688e-08	9.1821e-07	chr3:53923579-54677190	1
4q22.1	1.9653e-06	1.162e-05	chr4:91271445-93240505	1
4p15.2	1.1684e-05	1.162e-05	chr4:20726855-22351071	1
5q12.1	7.8738e-06	3.6762e-05	chr5:58998410-59780946	2
11q24.3	0.00065071	0.00065071	chr11:130014370-130275019	2
19p13.3	0.00081048	0.00081048	chr19:1-3363200	117
7q31.1	0.00089342	0.00096869	chr7:108535383-111366370	4
3q11.1	2.1355e-05	0.0021765	chr3:90078624-93767487	3
17q25.3	0.0027185	0.0029216	chr17:80604514-80902410	6
1p13.2	0.0024662	0.0032025	chr1:112530734-149898950	153
3p25.3	0.00027861	0.0037476	chr3:11303687-11833472	2
13q14.2	0.00070055	0.0044375	chr13:48875329-49064807	2
3p14.2	5.5415e-08	0.005244	chr3:59702822-61026498	2
4q21.23	0.00056019	0.0053469	chr4:86021783-87259005	3
2q37.2	1.162e-05	0.010456	chr2:209223020-243199373	298
3p26.2	0.00089342	0.011965	chr3:3220635-4535479	3
11p15.4	0.013942	0.014344	chr11:3861173-7045657	107
6q24.3	0.020138	0.025662	chr6:146134165-146352589	1
6p25.1	0.00062013	0.032045	chr6:5259170-5919145	2
6q22.1	0.027857	0.036937	chr6:91220796-119138282	138
6p25.3	0.00089589	0.041028	chr6:1-9597208	61
16q23.1	0.052987	0.05327	chr16:78098006-79299841	3
10q21.1	0.045824	0.056846	chr10:38661947-69600646	162
18q12.2	0.047176	0.074214	chr18:36593175-39537209	2
Xq21.33	0.073573	0.074214	chrX:96134519-99356556	3
Xp21.1	0.02725	0.086812	chrX:32117084-34644819	5
7q32.1	0.057092	0.08756	chr7:117853365-159138663	348
10q23.31	0.071704	0.08756	chr10:89506488-92501260	30
18q21.2	0.085772	0.09927	chr18:48472083-48650073	3
13q32.2	0.091819	0.11322	chr13:76185235-115169878	194
4q32.1	0.079071	0.11829	chr4:156726176-165912961	27
12q23.1	0.12197	0.11829	chr12:71510065-133851895	488
22q11.1	0.12979	0.12979	chr22:1-18463817	24
1p36.13	0.11023	0.15032	chr1:1-37504669	609
15q22.2	0.16482	0.15889	chr15:58427451-84796159	304
21q11.2	0.17156	0.1738	chr21:1-26760449	41
13q12.11	0.0085793	0.18342	chr13:1-57136640	311
5q15	0.0042051	0.18882	chr5:42799832-132364450	419
15q13.3	0.19286	0.18882	chr15:1-54921359	341
14q32.33	0.23487	0.22747	chr14:68165488-107349540	425
19q13.31	0.25347	0.25533	chr19:1-59128983	1616

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B

Genes in Wide Peak

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

Table S24. 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 Xp11.3.

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

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

Genes
PARD3

Genes in Wide Peak

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

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

Genes
ESRG

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
RN7SKP248

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.2.

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

Genes
KCNIP4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

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

Genes
FKSG52
MIR582

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

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

Genes
ST14
ZBTB44

Genes in Wide Peak

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

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

Genes
GNA11
STK11
TCF3
FSTL3
ZNF554
SPPL2B
LINGO3
MIR4321
MIR1227
RN7SL226P
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
GADD45B
OAZ1
PALM
POLRMT
PRTN3
PTBP1
RPS15
SGTA
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
SLC39A3
THEG
LSM7
MBD3
MIER2
PCSK4
PLEKHJ1
BTBD2
RNF126
NCLN
WDR18
REXO1
ZNF77
CELF5
TLE6
LPPR3
ZNF556
ABHD17A
KLF16
DOT1L
KISS1R
LMNB2
MUM1
MIDN
R3HDM4
TMEM259
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
GRIN3B
ZNF57
JSRP1
MOB3A
MISP
PLK5
C2CD4C
C19orf25
ATP8B3
DIRAS1
ZNF555
C19orf26
ODF3L2
ADAMTSL5
TMPRSS9
C19orf35
MEX3D
PRSS57
MIR3187

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
snoU13\|ENSG00000238922.1
FLJ00325
LRRN3
IMMP2L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.1.

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

Genes
U3\|ENSG00000212598.1
PROS1
STX19

Genes in Wide Peak

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

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

Genes
MIR4525
RAB40B
TBCD
FN3K
FN3KRP
ZNF750

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
LINC00622
snoU13\|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40\|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3\|ENSG00000221040.1
SNORA42\|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13\|ENSG00000238975.1
WNT2B
snoU13\|ENSG00000238761.1
snoU13\|ENSG00000239111.1
AMPD1
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD58
FCGR1A
FMO5
GJA5
GJA8
HMGCS2
HSD3B1
HSD3B2
IGSF3
MOV10
NGF
NHLH2
PDZK1
PRKAB2
PTGFRN
SLC16A1
SYCP1
TBX15
TSHB
CSDE1
HIST2H2AC
HIST2H2BE
HIST2H4A
ITGA10
PEX11B
CD101
CHD1L
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
PIAS3
POLR3C
TXNIP
AP4B1
PHTF1
ADAM30
CD160
NBPF14
PTPN22
PHGDH
BOLA1
HAO2
GPR89B
RSBN1
GDAP2
FAM46C
ST7L
SLC22A15
CTTNBP2NL
OLFML3
DCLRE1B
VTCN1
SIKE1
TRIM45
VANGL1
REG4
POLR3GL
ZNF697
MAB21L3
LIX1L
SYT6
HFE2
ANKRD35
NBPF12
PPIAL4A
NBPF11
SPAG17
HIPK1
MAGI3
FAM19A3
NBPF16
ANKRD34A
HIST2H2AB
PPM1J
C1orf137
NOTCH2NL
NBPF9
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
NBPF20
MIR320B1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.3.

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

Genes
VGLL4
ATG7

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
U3\|ENSG00000212211.1
NPCDR1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.23.

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

Genes
RN7SKP96
MIR4451
ARHGAP24

Genes in Wide Peak

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

Table S41. 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
RPE
RNA5SP118
RNA5SP117
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
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
LANCL1
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
KANSL1L
CCDC140
SLC23A3
GPBAR1
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
CCDC108
C2orf72
UNC80
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 3p26.2.

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

Genes
SETMAR
LRRN1
SUMF1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
GVINP1
TAF10
RRP8
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62\|ENSG00000201980.1
OR51C1P
SNORA7\|ENSG00000206976.1
APBB1
CCKBR
TPP1
CNGA4
HBB
HBD
HBE1
HBG2
HPX
ILK
RRM1
SMPD1
TRIM21
STIM1
ZNF214
ZNF215
OR6A2
DCHS1
TRIM22
TRIM3
OR52A1
ARFIP2
TIMM10B
UBQLN3
TRIM68
MMP26
MRPL17
OR51G1
OR51B4
OR51B2
OR52N1
OR51G2
OR51E2
FAM160A2
TRIM5
PRKCDBP
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
OR10A5
OR2AG1
DNHD1
C11orf42
OR56B4
OR52B2
OR51F1
OR51V1
OR10A4
OR52L1
OR2AG2
OR52B6
OR10A2
OR56B1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR51T1
OR51A4
OR51A2
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q24.3.

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

Genes
SHPRH

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.1.

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

Genes
RN7SL221P
FARS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.1.

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

Genes
PRDM1
ROS1
GOPC
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13\|ENSG00000238563.1
U3\|ENSG00000253091.1
snoU13\|ENSG00000239095.1
snoU13\|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13\|ENSG00000238775.1
SNORA40\|ENSG00000212587.1
RN7SL617P
snoU13\|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13\|ENSG00000238974.1
SNORA73\|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33\|ENSG00000202283.1
snoU13\|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18\|ENSG00000252249.1
U3\|ENSG00000221455.1
U3\|ENSG00000200492.1
RN7SL415P
AIM1
AMD1
CCNC
COL10A1
EPHA7
FOXO3
FYN
GPR6
GRIK2
HDAC2
KPNA5
LAMA4
MARCKS
PLN
POU3F2
PREP
REV3L
SIM1
SMPD2
MAP3K7
NR2E1
DDO
SNX3
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
FUT9
TRAF3IP2
ASCC3
BVES
SEC63
CDK19
TSPYL4
UFL1
PNISR
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
COQ3
SOBP
QRSL1
PDSS2
HACE1
BEND3
MICAL1
MANEA
GPR63
ARMC2
MCHR2
FAXC
USP45
SLC22A16
GTF3C6
KLHL32
NUS1
SLC16A10
AK9
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
CEP57L1
PPIL6
DCBLD1
RSPH4A
CEP85L
LIN28B
FAM26F
RFPL4B
FAM229B
MIR587
METTL24
TRAPPC3L
MIR2113
MIR4643
MIR548AI

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

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

Genes
IRF4
HULC
snoU13\|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13\|ENSG00000238801.1
RNA5SP202
snoU13\|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13\|ENSG00000238438.1
BMP6
BPHL
DSP
SERPINB1
F13A1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TUBB2A
RIPK1
PRPF4B
CDYL
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
NRN1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
TXNDC5
RIOK1
FOXQ1
HUS1B
SNRNP48
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
PSMG4
C6orf201
PPP1R3G
MIR4645
MIR5683

Genes in Wide Peak

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

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

Genes
RNA5SP431
PIH1
WWOX

Genes in Wide Peak

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

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

Genes
RET
NCOA4
RN7SL394P
LRRTM3
snoU13\|ENSG00000239000.1
snoR442\|ENSG00000252203.1
MIR1296
RN7SL591P
LINC00845
LINC00948
LINC00844
RN7SKP196
snoU13\|ENSG00000238970.1
SNORD2\|ENSG00000238707.1
snoU13\|ENSG00000238355.1
MIR548F1
RNA5SP318
MIR605
RMRPP4
RNA5SP317
LINC00843
SNORA74\|ENSG00000223111.1
SNORA74\|ENSG00000223182.1
RNA5SP316
FAM25D
FAM21D
PARG
C10orf53
DRGX
C10orf128
WDFY4
RNA5SP315
RN7SL527P
GLUD1P2
RNA5SP314
RNA5SP313
ASAH2C
C10orf43
ANTXRLP1
RN7SL453P
BMS1P2
RNA5SP312
AGAP10
LINC00842
GPRIN2
RN7SL248P
FAM35BP
RNA5SP311
RNA5SP310
FAM25E
RSU1P2
CEP164P1
TMEM72
LINC00841
LINC00840
LINC00619
ZNF487
U3\|ENSG00000221400.1
RNU6ATAC11P
snoU13\|ENSG00000238732.1
ZNF33B
ZNF37BP
CCNYL2
SEPT7P9
ALOX5
ANXA8L2
ANK3
CDK1
CHAT
EGR2
ERCC6
GDF2
GDF10
HNRNPF
MBL2
MSMB
NPY4R
PRKG1
MAPK8
RBP3
CXCL12
SLC18A3
TFAM
UBE2D1
ZNF22
ZNF32
ZNF33B
CCDC6
ZNF239
BMS1
RHOBTB1
C10orf10
ZWINT
ZNF365
DKK1
CSTF2T
PTPN20B
CTNNA3
A1CF
NRBF2
FXYD4
CSGALNACT2
FAM21B
OGDHL
CISD1
DNAJC12
ASAH2
ARHGAP22
PCDH15
OR13A1
BICC1
SYT15
RASSF4
ARID5B
PHYHIPL
LINC00839
ADO
ZFAND4
C10orf71
ZNF488
AGAP4
FRMPD2
FAM170B
ANTXRL
VSTM4
C10orf107
TMEM26
RTKN2
SLC16A9
FAM13C
MARCH8
C10orf25
ZNF485
RASGEF1A
REEP3
JMJD1C
IPMK
FAM21C
SGMS1
C10orf40
FAM21A
BMS1P5
AGAP6
LRRC18
AGAP9
FAM25C
PTPN20A
ANXA8
TIMM23B
AGAP7
ASAH2B
BMS1P1
ANXA8L1
AGAP8
FAM25B
FAM25G
TIMM23
MIR4294
MTRNR2L5
MIR3924
MIR5100
PGBD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

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

Genes
LINC00669
RN7SKP182

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
SNORA25\|ENSG00000252296.1
RN7SL74P
RPA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
snoU13\|ENSG00000238969.1
MIR548F5
MIR3915
RNA5SP501
FAM47A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q32.1.

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

Genes
BRAF
EZH2
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26\|ENSG00000212590.1
snoU13\|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13\|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112\|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3\|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6\|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13\|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40\|ENSG00000252188.1
snoU13\|ENSG00000239123.1
SNORA51\|ENSG00000201465.1
snoU13\|ENSG00000238984.1
snoU13\|ENSG00000239145.1
RN7SKP223
SNORD81\|ENSG00000202023.1
snoU13\|ENSG00000238488.1
LUZP6
C7orf73
U6\|ENSG00000272393.1
SNORD46\|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13\|ENSG00000239044.1
snoU13\|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13\|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1\|ENSG00000271739.1
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
CPED1
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

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

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

Genes
PTEN
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13\|ENSG00000238991.1
ANKRD22
SNORD74\|ENSG00000200891.1
RN7SL78P
CFL1P1
ACTA2
FAS
IFIT2
IFIT3
LIPA
LIPF
CH25H
KIF20B
IFIT5
PANK1
RNLS
STAMBPL1
ATAD1
LIPJ
LIPM
SLC16A12
IFIT1B
LIPK
LIPN
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
RN7SL695P
SMAD4
ELAC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q32.2.

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

Genes
ERCC5
MIR548AR
LINC00565
LINC00452
LINC00453
LINC00454
GRK1
DCUN1D2
LINC00403
LINC00404
SNORD44
LINC00354
LINC00346
LINC00567
snoU13\|ENSG00000238629.1
RN7SL783P
RN7SKP10
LINC00676
RNA5SP39
MIR1267
SNORD31
LINC00443
LINC00551
ARGLU1
LINC00460
RNA5SP38
SNORA25\|ENSG00000252550.1
LINC00344
LINC00343
METTL21EP
RNY5P8
LINC00283
CCDC168
snoU13\|ENSG00000238869.1
LINC00555
MIR4705
RNY1P2
MIR2681
FGF14
LINC00411
GGACT
LINC00554
snoU13\|ENSG00000238305.1
SNORA25\|ENSG00000201245.1
MIR4306
RNY3P6
LINC00449
MIR623
RN7SKP9
RN7SL60P
RN7SKP8
snoU13\|ENSG00000238407.1
RAP2A
RNA5SP37
snoU13\|ENSG00000238522.1
SNORD112\|ENSG00000252154.1
RN7SKP7
LINC00359
RN7SL164P
HS6ST3
snR65\|ENSG00000251901.1
RNY4P27
RNY3P8
snoU13\|ENSG00000238463.1
LINC00557
LINC00391
RN7SL585P
RNA5SP36
RNA5SP35
SNORD22
MIR548AS
RNU4ATAC3P
LINC00379
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
ATP4B
COL4A1
COL4A2
DCT
GPR183
EDNRB
EFNB2
F7
F10
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
LMO7
PCCA
POU4F1
DNAJC3
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
SCEL
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
SPRY2
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
MYCBP2
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
FBXL3
OXGR1
NDFIP2
BIVM
TMCO3
ANKRD10
RAB20
CARKD
UGGT2
PCID2
RBM26
UPF3A
KDELC1
CARS2
RNF219
GRTP1
SLITRK6
TMTC4
ABHD13
ZIC5
TEX30
ADPRHL1
SLITRK1
KCTD12
TEX29
SLAIN1
SPACA7
RNF113B
GPR180
CLYBL
METTL21C
NALCN
DAOA
CHAMP1
UBAC2
TMEM255B
C13orf35
MIR17HG
MIR622
FAM155A
IRG1
MIR3170
MIR3665
MIR4500
MIR4502

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.1.

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

Genes
RN7SKP105
U3\|ENSG00000251979.1
C4orf45
U3\|ENSG00000271817.1
PDGFC
CTSO
ETFDH
GLRB
GRIA2
NPY1R
NPY5R
PPID
TDO2
RAPGEF2
FAM198B
ASIC5
MARCH1
TMEM144
TMA16
FSTL5
FNIP2
RXFP1
TKTL2
NAF1
FAM218A
C4orf46
TRIM61

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

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

Genes
BCL7A
BTG1
ALDH2
PTPN11
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13\|ENSG00000238822.1
RN7SL534P
snoU13\|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9\|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9\|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70\|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13\|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38\|ENSG00000201042.1
RNA5SP374
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56\|ENSG00000200112.1
RN7SL865P
SNORA27\|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7\|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50\|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40\|ENSG00000264043.2
FICD
RNA5SP371
SNORD74\|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13\|ENSG00000238914.1
U8\|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13\|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13\|ENSG00000238800.1
SLC5A8
snoU13\|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13\|ENSG00000239073.1
SNORD74\|ENSG00000201502.1
snoU13\|ENSG00000238361.1
snoU13\|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3\|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13\|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70\|ENSG00000251893.2
GLIPR1
U8\|ENSG00000201809.1
RAB21
SNORA17\|ENSG00000212461.1
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
KERA
KRR1
PRDM4
CIT
PWP1
NUDT4
FZD10
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
UTP20
MRPL42
IFT81
CCDC59
FAM216A
TRHDE
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
METTL25
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
CCDC64
SDSL
OSBPL8
IQCD
DEPDC4
CCDC38
TMEM132D
SLC15A4
TPH2
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
RAD9B
FAM109A
TMTC2
TMTC3
C12orf50
ALDH1L2
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
CCER1
SLC17A8
LRRC43
TCP11L2
C12orf79
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
DDX51
MMAB
HCAR2
TMEM119
C12orf74
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
C12orf73
ZNF605
MIR1251
MIR4303
MIR3685
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR5188
MIR5700

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.1.

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

Genes
LINC00528
snoU13\|ENSG00000251737.1
RN7SL843P
CECR9
CECR3
CECR7
HSFY1P1
TPTEP1
KCNMB3P1
OR11H1
POTEH
ATP6V1E1
BID
IL17RA
BCL2L13
CECR6
CECR5
CECR2
CECR1
SLC25A18
GAB4
CCT8L2
XKR3
MIR648

Genes in Wide Peak

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

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

Genes
LCK
PAX7
RPL22
SDHB
SFPQ
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
SNORA63\|ENSG00000201448.1
RN7SL131P
RN7SL281P
PSMB2
RNY5P1
SNORA62\|ENSG00000201542.1
RN7SL503P
RN7SL136P
ZMYM6
SNORD112\|ENSG00000252728.1
SMIM12
RNA5SP42
RN7SKP16
MIR3605
FKSG48
ZBTB8OS
ZBTB8B
RN7SL122P
MTMR9LP
MIR5585
MIR4254
FABP3
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24\|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13\|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18\|ENSG00000252691.1
SCARNA17\|ENSG00000252190.1
MAN1C1
snoU13\|ENSG00000238889.1
SYF2
snoU13\|ENSG00000238986.1
RN7SL857P
snoU13\|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13\|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13\|ENSG00000239020.1
PADI6
MIR3972
U1\|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1\|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13\|ENSG00000238818.1
DDI2
AGMAT
SCARNA21\|ENSG00000251866.1
C1orf195
SCARNA11\|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13\|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70\|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13\|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16\|ENSG00000252404.1
RN7SL451P
SNORA77\|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13\|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
AK2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL8A2
COL16A1
CORT
CSF3R
DDOST
DFFB
DVL1
E2F2
ECE1
PHC2
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
HCRTR1
HDAC1
ZBTB48
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
KCNAB2
FCN3
YARS
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
THEMIS2
H6PD
ISG15
PLCH2
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
AGO1
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
ADPRHL2
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
EVA1B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
MIIP
CELA2A
GPATCH3
CLSPN
TINAGL1
PLA2G2F
S100PBP
CEP85
NMNAT1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
AUNIP
CCDC28B
EFHD2
MMEL1
RSG1
NKAIN1
MUL1
NOL9
LIN28A
SH3D21
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SESN2
ESPN
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
FAM167B
C1orf170
SYTL1
IGSF21
LSM10
C1orf94
KIAA2013
THAP3
STPG1
SPOCD1
UBXN11
FBXO44
ATPIF1
ADC
TMEM54
CSMD2
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
GJB4
HMGB4
RNF19B
A3GALT2
OSCP1
C1orf216
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
AGO3
AGO4
FAM76A
TMEM201
C1orf86
TXLNA
ATAD3C
AKR7L
FNDC5
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
TFAP2E
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
ZBTB8A
PRAMEF22
PRAMEF15
PRAMEF16
MIR552
CDK11A
SLC35E2B
C1orf234
OR4F29
FAM229A
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
ZMYM6NB
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q22.2.

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

Genes
PML
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
ADAM10
ANXA2
AQP9
BBS4
BCL2A1
BNC1
BNIP2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
GTF2A2
HEXA
IL16
IREB2
ISLR
LIPC
LOXL1
SMAD3
SMAD6
MAN2C1
MPI
MYO1E
MYO9A
NEO1
OAZ2
PKM
PPIB
MAP2K5
PSMA4
PTPN9
RASGRF1
RCN2
RORA
RPL4
RPLP1
RPS17
SH3GL3
SNX1
TLE3
TPM1
AP3B2
ANP32A
SEMA7A
CILP
PIAS1
RAB11A
HERC1
PSTPIP1
CCNB2
SLC24A1
GCNT3
TRIP4
STOML1
HOMER2
KIF23
IGDCC3
KIAA0101
ARNT2
HCN4
SNUPN
PDCD7
TSPAN3
DENND4A
SNAPC5
HMG20A
CORO2B
CIB2
ARID3B
MORF4L1
ADAMTS7
ITGA11
ZNF609
TBC1D2B
MESDC2
KIAA1024
TMED3
DAPK2
ARIH1
SIN3A
ULK3
GLCE
FBXO22
NPTN
FOXB1
SCAPER
RPS27L
RASL12
SPG21
PTPLAD1
RAB8B
BTBD1
TM6SF1
CSNK1G1
ZFAND6
FAM63B
RNF111
VPS13C
LRRC49
PAQR5
DPP8
COMMD4
PARP16
CLN6
ZWILCH
UACA
IMP3
LARP6
DNAJA4
C15orf39
THAP10
PARP6
FAM219B
ADAMTSL3
KIAA1199
ISLR2
IGDCC4
ABHD17C
MESDC1
PPCDC
CELF6
STRA6
CPEB1
IQCH
ISL2
NOX5
EFTUD1
NEIL1
NARG2
AAGAB
LMAN1L
SLTM
PEAK1
SNX22
THSD4
PIF1
CCDC33
EDC3
PLEKHO2
WDR61
CD276
VWA9
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
MEGF11
LINGO1
UBL7
LDHAL6B
UBE2Q2
LACTB
DIS3L
C15orf40
SENP8
SLC51B
HIGD2B
C15orf27
HYKK
WHAMM
FSD2
C2CD4A
FAM81A
C15orf61
C15orf26
TBC1D21
ODF3L1
SCAMP5
CT62
GRAMD2
LCTL
SPESP1
LINC00277
C15orf60
C15ORF37
FAM154B
FBXL22
GOLGA6A
RBPMS2
ANKDD1A
C2CD4B
KBTBD13
UBAP1L
SKOR1
ST20
MIR184
GOLGA6L9\|ENSG00000197978.8
MIR422A
CPLX3
GOLGA6L10\|ENSG00000205281.6
MIR549
MIR630
MIR631
MIR4311
MIR4313
MIR3713
RPS17L
MIR4514
MIR4513
MIR4515

Genes in Wide Peak

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

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

Genes
RNA5SP489
7SK\|ENSG00000232512.2
RN7SL609P
LINC00308
LINC00317
LINC00320
RN7SKP147
RN7SL163P
SNORD74\|ENSG00000201025.1
snoU13\|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70\|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
C21orf91
SAMSN1
CHODL
LIPI
ABCC13
POTED
LINC00478
MIRLET7C
MIR125B2
MIR99A
MIR548X
MIR3687
C21orf37

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
APC
IL6ST
PIK3R1
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
TRIM23
ARSB
ALDH7A1
BHMT
BTF3
CAST
CCNB1
CCNH
CDK7
CDO1
CETN3
CHD1
CKMT2
ERCC8
CRHBP
HAPLN1
CSF2
CSNK1G3
VCAN
DMXL1
DHFR
EFNA5
F2R
F2RL1
F2RL2
FBN2
FOXD1
GDF9
GLRX
GTF2H2
GZMA
HEXB
HMGCR
HMGCS1
HSD17B4
IL3
IL4
IL5
IL13
IRF1
ISL1
ITGA2
KCNN2
TNPO1
LMNB1
LNPEP
LOX
CD180
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
PAM
PCSK1
PDE4D
PGGT1B
PMCHL2
PPIC
RAD17
RASA1
RASGRF2
RPS23
SEPP1
SLC12A2
SLC22A4
SLC22A5
SMN1
SMN2
SNX2
TAF9
TBCA
NR2F1
THBS4
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
ENC1
AP3B1
PDLIM4
PPAP2A
PDE8B
P4HA2
HSPB3
ATG12
NREP
SCAMP1
CARTPT
SNCAIP
TTC37
ZFYVE16
PJA2
EDIL3
COL4A3BP
RAD50
LHFPL2
CWC27
CCNO
NSA2
FST
PAIP1
POLR3G
PLK2
IQGAP2
MRPS30
ESM1
KIF3A
ADAMTS6
RHOBTB3
ELL2
SV2C
MRPS27
SEPT8
PPIP5K2
ACSL6
PPWD1
SKIV2L2
NNT
PART1
FAM169A
AFF4
DIMT1
SLC27A6
SNX24
DMGDH
TMED7
ISOC1
IPO11
GCNT4
PRR16
COMMD10
RAPGEF6
ERAP1
PHAX
DHX29
DDX4
SGTB
ARL15
ZCCHC10
GIN1
AGGF1
TRIM36
RIOK2
DEPDC1B
BDP1
ERBB2IP
FEM1C
CDC42SE2
NLN
ZNF608
SEMA6A
ARRDC3
ZSWIM6
ANKRA2
MCCC2
EPB41L4A
CENPK
ERAP2
ARHGEF28
C5orf28
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
GRAMD3
PARP8
ANKRD55
MCTP1
PTCD2
ELOVL7
TRAPPC13
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
GFM2
MEGF10
SPZ1
TSLP
C5orf30
LYRM7
SLC25A46
NDUFAF2
MRPS36
ATP6AP1L
PRDM6
FTMT
FNIP1
SNX18
MARCH3
FCHO2
RAB3C
LYSMD3
SETD9
IL31RA
EMB
SLCO6A1
PRRC1
JMY
ZNF474
POU5F2
TMEM171
TMEM174
POC5
STARD4
WDR36
ACOT12
SOWAHA
SHROOM1
SREK1
SLC38A9
CEP120
TMEM167A
MBLAC2
TMEM161B
SRFBP1
MARVELD2
ARSK
FAM81B
CCDC112
MIER3
CDC20B
PAPD4
DCP2
NIM1
LIX1
ZNF366
FAM151B
ADAMTS19
CCDC125
C5orf27
CMYA5
AQPEP
ANKRD31
SERINC5
KIAA0825
C5orf64
RNF180
SREK1IP1
RGMB
RFESD
CHSY3
FAM170A
ANKRD34B
MCIDAS
ACTBL2
FAM174A
SLCO4C1
C5orf34
MAST4
C5orf48
RGS7BP
LINC00461
C5orf56
CTXN3
SMIM15
CCNI2
MIR583
GTF2H2C
SERF1B
ANKDD1B
LRRC70
FAM159B
TICAM2
MIR2277
MIR4280
MTRNR2L2
MIR3660
MIR3936
OCLN
MIR4460
MIR548AE2

Genes in Wide Peak

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

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

Genes
BUB1B
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
APBA2
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
OCA2
PLCB2
MAPK6
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SPINT1
SRP14
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
EIF3J
SNAP23
HERC2
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
BCL2L10
RASGRP1
GNB5
ARPP19
SLC27A2
GPR176
CHP1
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
EID1
NPAP1
SERF2
TMEM87A
RPAP1
BLOC1S6
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
TRPM7
PPP1R14D
MTMR10
ZNF770
HAUS2
RMDN3
DNAJC17
NOP10
MYO5C
NDNL2
FAM214A
EMC7
PAK6
DTWD1
CASC5
AVEN
STARD9
VPS18
SQRDL
ZNF106
SPATA5L1
CHAC1
KATNBL1
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
C15orf43
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
FAM227B
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
SLC24A5
GOLGA6L2
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
GLDN
FMN1
USP50
C15orf52
TNFAIP8L3
GOLGA8EP
OR4M2
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
HERC2P9
GOLGA8B
EIF2AK4
UNC13C
CKMT1A
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
POTEB2
MIR1282
MIR4508
MIR4510
MIR4716
MIR4713
MIR4712
POTEB

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.31.

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

Genes
PPP2R1A
MLLT1
GNA11
AKT2
BCL3
CD79A
CEBPA
ERCC2
JAK3
KLK2
LYL1
SH3GL1
SMARCA4
STK11
TCF3
TPM4
ELL
FSTL3
CIC
BRD4
CBLC
TFPT
ZNF331
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3\|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13\|ENSG00000239137.1
KIR3DX1
LILRA6
LENG1
NDUFA3
MIR935
MIR371B
RN7SL317P
ZNF813
ZNF761
FAM90A28P
FAM90A27P
ZNF321P
ZNF888
ZNF600
ZNF137P
MIR643
snoU13\|ENSG00000238630.1
HCCAT3
FPR1
snoU13\|ENSG00000238486.1
SIGLEC5
CEACAM18
SIGLEC22P
SIGLEC17P
KLK13
KLK9
KLKP1
SNORD88C
SNORD88A
SNORD88B
LRRC4B
SPIB
RN7SL324P
NAPSB
SIGLEC16
U3\|ENSG00000221125.1
MIR4751
MIR4750
MIR4749
ADM5
MIR5088
BCL2L12
SNORD35B
SNORD35A
SNORD34
SNORD33\|ENSG00000199631.1
SNORD32A
MIR4324
RN7SL708P
RN7SL345P
SEC1P
DBP
GRWD1
C19orf68
CABP5
TPRX2P
SNORD23\|ENSG00000221803.1
RN7SL322P
RN7SL533P
snoU13\|ENSG00000252071.1
MIR320E
RN7SL364P
PGLYRP1
NOVA2
MIR642A
RN7SL836P
MIR330
PPM1N
APOC1P1
SNORA70\|ENSG00000253027.1
snoZ6\|ENSG00000252200.1
CEACAM22P
CEACAM20
ZNF180
ZNF234
RN7SL53P
ZNF284
ZNF223
RN7SL368P
ZNF576
ZNF575
CEACAMP10
PSG7
PSG10P
CXCL17
SNORD112\|ENSG00000252356.1
CEA
CEACAMP3
C19orf69
TGFB1
RN7SL34P
RN7SL718P
CYP2B7P1
CYP2G1P
NUMBL
RN7SL758P
SERTAD1
LGALS17A
EID2
RN7SL566P
IFNL4
snoU13\|ENSG00000251709.1
ACTN4
SPRED3
snoU13\|ENSG00000238838.1
RN7SL663P
ZNF790
ZFP14
LINC00665
RN7SL287P
OVOL3
RN7SL402P
PSENEN
KMT2B
RN7SL765P
RN7SL491P
GPR42
MIR5196
HAMP
LINC00904
SNORD111\|ENSG00000252230.1
SCGB1B2P
WTIP
RN7SL154P
RN7SL150P
LRP3
C19orf40
RN7SKP22
RN7SL789P
SNORA68\|ENSG00000201388.1
RNA5SP472
RNA5SP471
THEG5
C19orf12
POP4
RN7SL340P
UQCRFS1
RNA5SP470
LINC00906
snoU13\|ENSG00000238514.1
LINC00662
ZNF726
ZNF724P
ZNF728
ZNF99
RN7SL860P
ZNF208
LINC00664
ZNF738
RNA5SP469
ZNF66
ZNF737
ZNF826P
ZNF90
ZNF253
ZNF506
LINC00663
ZNF101
NDUFA13
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
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
A1BG
ACP5
AP2A1
AES
AMH
APLP1
APOC1
APOC2
APOC4
APOE
KLK3
ASNA1
ATP1A3
ATP4A
ATP5D
AXL
AZU1
BAX
BCAT2
BCKDHA
HCN2
CEACAM1
BLVRB
BSG
BST2
C3
C5AR1
CA11
CACNA1A
CALM3
CALR
CAPNS1
CCNE1
CD22
CD33
SIGLEC6
CD37
CD70
CD97
CDC34
CDKN2D
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CIRBP
TBCB
CKM
AP2S1
CLC
CLPTM1
CNN1
CNN2
COMP
COX6B1
COX7A1
CRX
CSNK1G2
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2F1
DAPK3
DHPS
DMPK
DMWD
DNASE2
DNM2
DNMT1
ECH1
EEF2
EFNA2
MEGF8
ELANE
ELAVL1
ELAVL3
EMP3
EMR1
EPOR
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FARSA
FCAR
FCER2
FCGRT
FLT3LG
FOSB
FPR2
FPR3
FTL
FUT1
FUT2
FUT3
FUT5
FUT6
GAMT
GCDH
GDF1
GIPR
GNA15
GNG7
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
MKNK2
GPX4
GRIK5
GRIN2D
ARHGAP35
GSK3A
GTF2F1
GYS1
GZMM
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
DNAJB1
ICAM1
ICAM3
ICAM4
IL11
IL12RB1
ILF3
INSL3
INSR
IRF3
JUNB
JUND
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LDLR
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
CYP4F3
BCAM
MAG
MAN2B1
MATK
MAP3K10
MYO1F
MYBPC2
GADD45B
MYO9B
HNRNPM
CEACAM6
NDUFA7
NDUFB7
NFIC
NFIX
NFKBIB
NKG7
CNOT3
NOTCH3
NPAS1
NPHS1
NRTN
NTF4
NUCB1
OAZ1
P2RY11
PAFAH1B3
PALM
PDE4A
PDE4C
PEG3
PEPD
PIK3R2
PIN1
PLAUR
FXYD1
FXYD3
POLD1
POLR2I
POLRMT
POU2F2
PPP5C
PRKACA
PRKCG
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRRG2
KLK7
KLK6
KLK10
PRTN3
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG9
PSG11
PSMC4
PSMD8
PTBP1
PTGER1
PTGIR
PTPRH
PTPRS
PVR
PVRL2
RAB3A
RAD23A
RELB
UPF1
RFX1
RFX2
RPL18
RPL18A
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS15
RPS16
RPS19
RRAS
RTN2
RYR1
SAFB
CLEC11A
SCN1B
CCL25
SEPW1
SGTA
SLC1A5
SLC1A6
SLC5A5
SLC8A2
SNAPC2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
STXBP2
SULT2B1
SULT2A1
SUPT5H
TBXA2R
PRDX2
THOP1
ICAM5
TLE2
TNNI3
TNNT1
TULP2
TYK2
TYROBP
UBA52
NR1H2
USF2
VASP
VAV1
XRCC1
ZFP36
ZNF8
ZNF14
ZNF708
ZNF17
ZNF20
ZNF28
MZF1
ZNF43
ZNF45
ZNF69
ZNF221
ZNF85
ZNF91
ZNF222
ZNF121
ZNF132
ZNF135
ZNF136
ZNF146
ZNF154
ZNF155
ZNF175
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
MADCAM1
SF3A2
SYMPK
MIA
CLPP
DPF1
LTBP4
TEAD2
RANBP3
CYP4F2
PPFIA3
KHSRP
PLA2G4C
PPAP2C
RFXANK
EIF3G
STX10
S1PR4
URI1
TNFSF14
TNFSF9
NAPA
SIGLEC5
FCGBP
AP1M1
AP3D1
UBE2M
ARHGEF1
PDCD5
DYRK1B
LPAR2
RAB11B
CRLF1
CYTH2
ZNF235
TRIP10
LONP1
KCNK6
NCR1
MED26
HOMER3
IL27RA
NAPSA
GDF15
TECR
ZNF254
GMFG
RAB3D
APBA3
IER2
KLK4
SAFB2
ZNF432
DHX34
KIAA0355
ZNF536
WBP7
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
UBA2
SAE1
SUGP2
EBI3
TRIM28
ZNF256
DDX39A
ZNF443
PLIN3
AKAP8
LILRB2
APC2
PAK4
B3GNT3
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4A
TMEM147
IFI30
TOMM40
TIMM44
CARM1
SEMA6B
ZNF211
CHERP
RNASEH2A
RABAC1
TRAPPC2P1
SPINT2
KLF1
DLL3
CERS1
GIPC1
ZNF266
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
PNPLA6
KDELR1
UQCR11
LILRB5
ILVBL
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
CLASRP
KPTN
SLC7A9
CDC37
MAP4K1
KLK8
PNKP
COPE
U2AF2
ATF5
ZFP30
ZNF507
PPP6R1
CARD8
SBNO2
SIRT2
MAST1
UNC13A
KDM4B
MAST3
SIPA1L3
FCHO1
ZC3H4
ZFR2
SIN3B
HAUS5
ARHGEF18
CRTC1
MAU2
PIP5K1C
FBXO46
ETHE1
RPL13A
HMHA1
SYNGR4
LILRA4
CASP14
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
SHC2
TMEM59L
PGLS
ZNF324
LSM4
KLK5
ZNF345
PRKD2
RPL36
ZNF473
KANK2
CLIP3
FAM32A
LSM14A
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7C1
ZNF285
AKAP8L
FGF22
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
TJP3
CPAMD8
SIGLEC9
SIGLEC8
C5AR2
NMRK2
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
BABAM1
LGALS13
CYP2S1
STRN4
HOOK2
EPN1
SERTAD3
SLC39A3
GLTSCR2
GLTSCR1
TNPO2
EMR2
CD209
EHD2
KLK14
KLK12
COL5A3
RDH8
SHANK1
NOSIP
MRPL4
ANGPTL4
ZNF580
HSD17B14
GP6
VRK3
MARCH2
ZNF571
GMIP
CD320
ECSIT
THEG
ZBTB7A
ISYNA1
ZNF581
SIRT6
LSR
LSM7
ZNF44
TM6SF2
MBD3
PTOV1
S1PR5
FXYD7
FXYD5
RAB4B
MIER2
DDX49
PAF1
PCSK4
PPP1R12C
TRPM4
ZNF586
ZNF562
QPCTL
GATAD2A
BEST2
FBXL12
FAM83E
PGPEP1
CC2D1A
EPS8L1
RASIP1
TMEM161A
SARS2
TMEM160
PIH1D1
C19orf60
GPATCH1
SAMD4B
ATP5SL
PLEKHJ1
C19orf73
MAP1S
PNMAL1
TMEM143
KLHL26
ZNF444
C19orf66
FEM1A
ZNF823
KLK15
MED29
STAP2
TRMT1
BTBD2
NLRP2
RNF126
ZNF416
ZNF446
CCDC94
ASF1B
ZNF701
ZNF83
ZNF415
USE1
ZNF302
C19orf80
LIN37
C19orf10
SMG9
IRGC
SLC7A10
PPAN
RETN
SPHK2
LGALS14
EXOSC5
MEIS3
NCLN
GPR108
DUS3L
XAB2
SHD
CEACAM19
SLC17A7
NAT14
CD177
ATP13A1
RGL3
SLC44A2
VN1R1
MCOLN1
RCN3
ZNF304
TTYH1
WDR18
REXO1
PNMAL2
PRR12
DOCK6
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
CAMSAP3
USP29
PLEKHA4
ZNF317
ZNF529
PRX
ANO8
SPTBN4
MARK4
SUGP1
CATSPERG
CYP4F11
ZNF77
SCAF1
CACTIN
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
UBL5
ZNF350
TSKS
CELF5
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
ZNF574
PLEKHG2
RASAL3
MRPL34
KRI1
ZSWIM4
ZNF649
ZSCAN18
RPL23AP79
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
TSEN34
KCTD15
SLC25A23
SMIM7
ZNF426
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
RBM42
C19orf57
FSD1
ZNF557
LRFN3
ABHD8
CERS4
OCEL1
ZNF329
COLGALT1
IGFLR1
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
TLE6
ZNF552
EPHX3
PODNL1
ZNF671
ZNF613
ADCK4
CNTD2
SLC35E1
LPPR3
DENND1C
ZNF442
ZNF702P
ZNF556
ZNF606
ZNF614
LRRC8E
FUZ
OPA3
ZNF430
ITPKC
UBXN6
PBX4
KIAA1683
B9D2
RSPH6A
CCDC130
ACSBG2
ADAMTS10
ZNF611
MED25
QTRT1
ABHD17A
ZNF93
DOHH
PLVAP
RTBDN
TEX101
ANGPTL6
KLF16
USHBP1
WDR87
TSSK6
CCDC8
KIRREL2
ANKRD27
PRAM1
C19orf44
ZNF541
MRI1
SYT3
FBXW9
ALKBH7
WDR83
PDCD2L
ZNF414
AKT1S1
ELOF1
ZNF528
DOT1L
BRSK1
ZNF333
FBN3
ZNF527
CNFN
ZNF559
KISS1R
EMR3
ZNF347
CREB3L3
GTPBP3
ZNF577
MPV17L2
ZNF607
SUV420H2
C19orf48
NFKBID
LMNB2
RAX2
ZBTB45
CEP89
ZNF382
ZNF587
FIZ1
ZNF566
MUM1
HSH2D
MPND
ALKBH6
ATG4D
ATCAY
SYDE1
RHPN2
MBD3L1
GALP
SIGLEC10
SIGLEC12
ZNF628
MIDN
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
DCAF15
GADD45GIP1
ZNF835
YIF1B
ZNF799
C19orf52
ZNF700
ZNF439
ZNF486
DPP9
ZNF682
R3HDM4
TMEM259
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
TPGS1
ZNF461
ZNF585B
CRB3
TIMM50
SHKBP1
REEP6
PEX11G
DMKN
ZNF561
OLFM2
CCDC114
HAUS8
MVB12A
ARMC6
ACPT
CGB5
MUC16
CGB7
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
FDX1L
NACC1
PTH2
IZUMO4
SCAMP4
ADAT3
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
LENG8
CCDC124
FBXO17
KIR3DL3
ARHGAP33
EVI5L
RASGRP4
NXNL1
CCDC151
ZNF653
ZNF526
ZNF837
GRIN3B
MRPL54
CIB3
CLDND2
ZNF816
ZNF543
RAVER1
OR7D4
OR7G1
OR1M1
COX6B2
CALR3
C19orf70
MBD3L2
TRAPPC5
PCP2
OSCAR
ZNF441
ZNF491
ZNF440
SWSAP1
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
WDR88
TMIGD2
EID2B
TNFAIP8L1
ZNF57
IRGQ
ZNF428
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
MISP
LRRC25
OR1I1
ZNF792
NR2C2AP
HSPB6
CCDC105
CYP4F22
RINL
FBXO27
PLK5
C19orf47
OR10H4
ANKLE1
C2CD4C
ZNF358
ZFP28
VSIG10L
LINC00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
KLC3
IGSF23
LYPD4
ZNF560
TMEM190
HIPK4
TMC4
TPM3P9
ZNF524
ZNF784
ZNF563
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
LGALS16
TTC9B
TICAM1
ZNRF4
ZNF599
FAM187B
CILP2
C19orf55
ZNF558
CDC42EP5
ZNF98
ZNF714
ZNF681
C19orf25
ATP8B3
LINC00905
DIRAS1
ZNF555
ZNF569
ZNF570
ZNF836
ZNF610
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF846
OR7D2
ZNF579
ZNF791
ZNF564
ZNF709
ZNF433
ZNF114
ZNF567
ZNF383
ZNF781
ZNF780B
PRR22
LGI4
SYNE4
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
ANKRD24
SPACA4
ZNF675
ZNF627
DAND5
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
ZNF584
ZSCAN4
NLRP11
TMEM86B
C19orf26
PRR24
C19orf38
ZNF549
KANK3
TINCR
CATSPERD
IL4I1
IFNL2
IFNL3
IFNL1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
EMC10
KLK9
SIGLECL1
ZNF615
ZNF841
ACTL9
OR2Z1
C19orf82
ZNF763
SCGB2B2
WDR62
ZFP82
VSTM1
TMEM150B
FAM71E2
C19orf77
SLC25A41
MBD3L5
OR10H5
NWD1
SLC25A42
ZNF493
ODF3L2
HKR1
VN1R2
VN1R4
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
ADAMTSL5
CLEC4G
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
PALM3
SELV
ZNF530
DNAAF3
ZNF429
ZNF233
LILRA5
TMPRSS9
C19orf35
HSD11B1L
C19orf45
TMEM205
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
SLC27A1
C3P1
ZNF788
CLEC17A
RPSAP58
RGS9BP
KRTDAP
CEACAM16
BLOC1S3
IGFL3
ZNF808
ZNF470
ZNF749
ZNF324B
OR7G2
OR7G3
OR7A10
NUDT19
ZNF793
PAPL
PINLYP
MEX3D
PRSS57
ZNF880
ZNF772
IGLON5
HAPLN4
CTXN1
MIRLET7E
MIR125A
MIR150
MIR181C
MIR199A1
MIR23A
MIR27A
MIR99B
PLIN5
PSG8
TARM1
MIR371A
MIR372
MIR373
IGFL4
DPRX
ASPDH
MIR181D
MIR498
MIR520E
MIR519E
MIR520F
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
TMEM91
SDHAF1
ARRDC5
C19orf67
SBK2
LGALS7B
PHLDB3
MBD3L4
MBD3L3
MIR639
MIR641
PLIN4
CCDC61
ZNF812
ZNF878
SHISA7
MIR769
SIGLEC14
ZGLP1
C19orf71
ZNF730
TMEM221
SGK110
BSPH1
SRRM5
ZNF729
ZNF587B
MIR1470
MIR1323
MIR3188
MIR3187
MIR3191
MIR4322
MIR4323
PPP5D1
ZNF865
TGFBR3L
ZNF177
MIR4530
MIR4754
MIR4752
MIR4746
MIR5695
MIR4999
MIR5684
MIR5589

Arm-level results

Table 3. Get Full Table Arm-level significance table - 25 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	0.21	-0.807	1	0.26	0.208	0.778
1q	1195	0.45	3.77	0.000843	0.18	-1.43	1
2p	624	0.41	0.974	0.564	0.17	-3.02	1
2q	967	0.29	-0.374	1	0.21	-1.65	1
3p	644	0.12	-1.96	1	0.84	9.59	0
3q	733	0.62	4.72	2.42e-05	0.54	2.94	0.00735
4p	289	0.29	-1.6	1	0.70	5.07	4.18e-06
4q	670	0.18	-2.67	1	0.49	2.64	0.0141
5p	183	0.62	3.09	0.00678	0.40	-0.451	1
5q	905	0.14	-2.6	1	0.51	3.77	0.000667
6p	710	0.26	-1.47	1	0.36	0.209	0.778
6q	556	0.18	-3.37	1	0.30	-1.37	1
7p	389	0.63	4.07	0.000324	0.33	-1.03	1
7q	783	0.51	3.12	0.00678	0.42	1.36	0.211
8p	338	0.51	1.39	0.307	0.66	4.2	0.000134
8q	551	0.69	5.77	1.63e-07	0.32	-0.639	1
9p	301	0.32	-1.14	1	0.69	4.9	6.39e-06
9q	700	0.36	0.209	1	0.51	2.91	0.00735
10p	253	0.24	-2.74	1	0.48	1	0.359
10q	738	0.13	-3.31	1	0.45	2	0.0615
11p	509	0.27	-1.76	1	0.47	1.54	0.158
11q	975	0.17	-2.05	1	0.48	3.52	0.00134
12p	339	0.51	1.75	0.166	0.22	-2.83	1
12q	904	0.28	-0.788	1	0.17	-2.6	1
13q	560	0.20	-2.62	1	0.50	2.36	0.0284
14q	938	0.45	2.58	0.025	0.28	-0.566	1
15q	810	0.19	-2.39	1	0.32	-0.288	1
16p	559	0.39	0.321	0.972	0.29	-1.45	1
16q	455	0.39	-0.0817	1	0.27	-1.97	1
17p	415	0.32	-1.23	1	0.38	-0.305	1
17q	972	0.32	0.307	0.972	0.21	-1.7	1
18p	104	0.42	-0.522	1	0.48	0.452	0.668
18q	275	0.17	-3.25	1	0.60	3.33	0.0022
19p	681	0.24	-1.82	1	0.47	2.14	0.0476
19q	935	0.28	-0.49	1	0.46	2.82	0.0089
20p	234	0.59	2.99	0.00825	0.25	-2.39	1
20q	448	0.52	2.5	0.0281	0.09	-4.24	1
21q	258	0.22	-2.65	1	0.61	3.5	0.00134
22q	564	0.43	0.912	0.57	0.38	0.131	0.799
Xp	418	0.16	-3.62	1	0.43	0.675	0.539
Xq	668	0.40	0.773	0.643	0.23	-2.06	1

Methods & Data

Input

Description

Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).
Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).
Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.
CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End
Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.
Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.
Confidence Level: Confidence level used to calculate the region containing a driver.
Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.
Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).
Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
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_home/cherniack/seg_files/stad_may2015/SCC_U.seg
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 = 2.0
Broad Length Cutoff = 0.5
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 92 Input Tumor Samples.

Tumor Sample Names
TCGA-IG-A3I8-01A-11D-A246-01
TCGA-IG-A3QL-01A-11D-A246-01
TCGA-IG-A3Y9-01A-12D-A246-01
TCGA-IG-A3YA-01A-11D-A246-01
TCGA-IG-A3YB-01A-11D-A246-01
TCGA-IG-A3YC-01A-11D-A246-01
TCGA-IG-A4P3-01A-11D-A25X-01
TCGA-IG-A4QT-01A-21D-A25X-01
TCGA-IG-A50L-01A-11D-A25X-01
TCGA-IG-A51D-01A-11D-A25X-01

Figure 3. Segmented copy number profiles in the input data

Output

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

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

Region Data

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

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.
Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').
Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

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

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

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

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

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

[2] GISTIC version 1

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

[4] GISTIC version 2

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

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

[7] The Sanger Institute: Cancer Gene Census

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