SNP6 Copy number analysis (GISTIC2) - Liver Hepatocellular Carcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Liver Hepatocellular Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1474990

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 370 tumor samples used in this analysis: 30 significant arm-level results, 27 significant focal amplifications, and 34 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 - 27 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	3.4149e-29	3.4149e-29	chr11:69448576-69490737	2
1q21.3	2.0728e-24	4.8471e-22	chr1:150637495-150740723	3
8q24.21	1.1795e-21	1.1795e-21	chr8:113630879-139984811	116
17q25.3	1.3152e-14	1.3152e-14	chr17:79191727-79389250	7
3q26.31	6.7256e-11	6.7256e-11	chr3:172266022-172285491	0 [TNFSF10]
5p15.33	1.099e-10	1.099e-10	chr5:981020-1300024	6
6p21.1	9.4799e-15	1.6932e-10	chr6:43733839-43828640	1
13q32.3	6.8193e-10	2.9564e-06	chr13:98177502-104617917	48
7q31.2	0.00018251	0.00018251	chr7:116229470-116662814	4
5q35.3	0.00031067	0.00031067	chr5:178716390-178940592	2
6p25.2	1.013e-05	0.00054152	chr6:1-14122151	96
2p24.1	0.00067861	0.00067861	chr2:20342502-20365874	0 [RN7SL140P]
1q42.2	4.3428e-09	0.00095159	chr1:228801039-249250621	180
19p13.12	0.0089034	0.0089034	chr19:15361827-15600481	7
15q26.3	0.010217	0.010217	chr15:100146665-102531392	29
Xq28	0.011319	0.011319	chrX:151745184-154883395	102
19q13.11	0.012082	0.012082	chr19:33723706-33837231	1
9q34.2	0.01251	0.01251	chr9:137137096-137208596	0 [RXRA]
2q33.1	0.016453	0.016453	chr2:201547244-201576134	1
4p14	0.0362	0.0362	chr4:39327941-39571500	7
20q13.13	0.0037169	0.078654	chr20:49017144-49057135	1
6q12	0.029807	0.1108	chr6:66991835-68057504	1
17p11.2	0.1412	0.1412	chr17:18859019-20253412	25
20q13.33	0.013414	0.17296	chr20:60328006-63025520	76
10p15.1	0.22261	0.22261	chr10:5008384-5101925	5
6q12	0.00019738	0.29214	chr6:64045972-64315938	1
13q33.3	2.2054e-10	0.32561	chr13:89392414-115169878	159

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
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
CTSS
GOLPH3L
HORMAD1

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
EXT1
MYC
SNORA40\|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72\|ENSG00000252158.1
SNORA12\|ENSG00000212342.1
SNORA25\|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13\|ENSG00000238422.1
U3\|ENSG00000221461.1
RNY4P5
snoU13\|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32\|ENSG00000206776.1
COLEC10
SNORA31\|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
ADCY8
ANXA13
KCNQ3
NDUFB9
NOV
TNFRSF11B
ENPP2
RAD21
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
COL14A1
MTSS1
KIAA0196
HHLA1
TRIB1
NDRG1
KHDRBS3
ZHX1
ZHX2
EFR3A
LRRC6
MTBP
MRPL13
ATAD2
ASAP1
FAM135B
PHF20L1
FAM49B
TRMT12
WDYHV1
GSDMC
ZFAT
DEPTOR
DSCC1
DERL1
TATDN1
UTP23
C8orf76
FAM83A
MED30
TBC1D31
MAL2
CSMD3
FBXO32
ZNF572
TMEM71
FAM84B
FAM91A1
SLC30A8
COL22A1
NSMCE2
KLHL38
SAMD12
MIR30B
MIR30D
FER1L6
OC90
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3610
MIR4662B
MIR4663
MIR5194

Genes in Wide Peak

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

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

Genes
LINC00482
AZI1
SLC38A10
ENTHD2
C17orf89
TMEM105
MIR4740

Genes in Wide Peak

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

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

Genes
MIR4635
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
VEGFA

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q32.3.

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

Genes
ERCC5
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
GPR183
GPR18
IPO5
PCCA
SLC10A2
SLC15A1
TPP2
ZIC2
STK24
ITGBL1
TM9SF2
FARP1
DOCK9
BIVM
KDELC1
TMTC4
ZIC5
TEX30
RNF113B
CLYBL
METTL21C
NALCN
UBAC2
MIR3170

Genes in Wide Peak

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

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

Genes
MET
RNA5SP239
CAPZA2
ST7

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

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

Genes
RN7SL71P
ADAMTS2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p25.2.

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

Genes
IRF4
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67\|ENSG00000207419.1
snoU13\|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
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
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
RANBP9
ECI2
FARS2
RPP40
SIRT5
FAM50B
SLC35B3
TBC1D7
NRN1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
MCUR1
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
PSMG4
C6orf201
PPP1R3G
TMEM170B
MIR4645
MIR5689
MIR5683

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.2.

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

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25\|ENSG00000252011.1
SNORD112\|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25\|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13\|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8\|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13\|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
ACTA1
ACTN2
ADSS
AGT
CHML
LYST
GALNT2
GNG4
HNRNPU
KCNK1
LGALS8
MTR
NID1
RAB4A
RGS7
RYR2
TARBP1
TBCE
GPR137B
TSNAX
ZNF124
GNPAT
KMO
EXO1
GGPS1
TOMM20
URB2
CEP170
AKT3
ZBTB18
SPHAR
CAPN9
SDCCAG8
COG2
RBM34
ABCB10
OPN3
AHCTF1
OR2M4
OR2L2
OR2T1
TAF5L
DISC1
DESI2
SCCPDH
ARID4B
EGLN1
MAP10
KIF26B
HEATR1
ZNF692
NUP133
ERO1LB
FMN2
ZNF695
SIPA1L2
RHOU
TFB2M
GREM2
SMYD3
ARV1
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
SPRTN
EFCAB2
MLK4
ZNF496
C1orf198
NLRP3
COX20
CCSAP
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
C1orf131
EDARADD
SLC35F3
B3GALNT2
GCSAML
EXOC8
CNST
PLD5
C1orf100
OR2T6
C1orf101
OR2L13
OR14A16
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
OR13G1
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916

Genes in Wide Peak

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

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

Genes
BRD4
AKAP8
AKAP8L
WIZ
RASAL3
PGLYRP2
MIR1470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13\|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
ALDH1A3
MEF2A
PCSK6
SNRPA1
CHSY1
OR4F4
VIMP
LRRK1
TM2D3
TARSL2
ASB7
LYSMD4
ADAMTS17
DNM1P46
CERS3
SPATA41
OR4F6
OR4F15

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

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

Genes
MTCP1
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70\|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36\|ENSG00000251846.1
RN7SL687P
RN7SL667P
snoU13\|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
GDI1
HCFC1
IDH3G
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
TAZ
VBP1
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
ZNF275
TREX2
SRPK3
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
PDZD4
FAM3A
BRCC3
H2AFB3
FAM58A
PNMA5
RAB39B
GAB3
PNCK
ZFP92
CSAG1
CTAG1A
H2AFB2
H2AFB1
OPN1MW2
SMIM9
CMC4
PNMA6C
MIR718

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
CEBPA

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q33.1.

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

Genes
AOX2P

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p14.

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

Genes
SMIM14
MIR5591
RFC1
RPL9
UGDH
LIAS
KLB

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.13.

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

Genes
RN7SL636P

Genes in Wide Peak

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

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

Genes
SNORD65\|ENSG00000212229.1

Genes in Wide Peak

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

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

Genes
RN7SL17P
U6\|ENSG00000266839.2
CCDC144CP
SNORA31\|ENSG00000252349.1
SNORA59B
MIR1180
SNORD3C
SNORD3A
GRAPL
SNORD3D
GRAP
FAM83G
ALDH3A1
ALDH3A2
MFAP4
MAPK7
RNF112
ULK2
AKAP10
EPN2
B9D1
SLC47A1
SPECC1
SLC5A10
SLC47A2

Genes in Wide Peak

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

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

Genes
SS18L1
NPBWR2
MIR647
MIR1914
C20ORF135
SLC2A4RG
MIR4326
MIR3196
HAR1A
HAR1B
LINC00029
GID8
LINC00659
LINC00686
MIR133A2
MIR4758
CDH4
CHRNA4
COL9A3
EEF1A2
KCNQ2
LAMA5
MYT1
NTSR1
OPRL1
PSMA7
PTK6
RPS21
SRMS
TAF4
TCEA2
TPD52L2
TNFRSF6B
OSBPL2
ARFRP1
RGS19
TCFL5
ADRM1
OGFR
DIDO1
HRH3
PRPF6
MTG2
GMEB2
SLCO4A1
STMN3
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
PCMTD2
MRGBP
ARFGAP1
ZNF512B
COL20A1
SLC17A9
C20orf195
PPDPF
BIRC7
DNAJC5
CABLES2
ZGPAT
HELZ2
BHLHE23
NKAIN4
C20orf166
GATA5
ZBTB46
SAMD10
ABHD16B
RBBP8NL
LSM14B
C20orf201
LINC00176
MIR1257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.1.

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

Genes
U8\|ENSG00000251740.1
U8\|ENSG00000239148.1
AKR1C1
AKR1C2
AKR1C3

Genes in Wide Peak

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

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

Genes
PTP4A1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q33.3.

Table S24. 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
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
OXGR1
BIVM
TMCO3
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
TEX30
ADPRHL1
TEX29
SPACA7
RNF113B
GPR180
CLYBL
METTL21C
NALCN
DAOA
CHAMP1
UBAC2
TMEM255B
C13orf35
MIR17HG
MIR622
FAM155A
MIR3170
MIR4502

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 - 34 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
13q14.2	2.2515e-37	2.2515e-37	chr13:48875329-49064807	2
1p36.31	1.1606e-33	5.8593e-25	chr1:1-6847369	116
9p21.3	3.0821e-22	3.0821e-22	chr9:21931610-22003135	2
4q35.1	1.8058e-23	8.3673e-21	chr4:185200319-185674312	5
8p23.2	2.1187e-19	1.3308e-17	chr8:3548028-4251283	2
6q27	3.4191e-15	3.5424e-15	chr6:169649200-170153593	4
19p13.3	4.7028e-08	4.7028e-08	chr19:1-5455610	180
17p13.1	3.9592e-10	1.1033e-07	chr17:1-10358937	262
10q23.31	2.1093e-09	1.8833e-07	chr10:89617158-89755074	3
16q23.1	7.8009e-06	7.7482e-06	chr16:78098006-79299841	3
2q22.1	7.7465e-07	8.242e-06	chr2:140708948-143637838	2
12q24.33	2.3723e-05	2.3615e-05	chr12:122439370-133851895	109
14q23.3	9.195e-08	4.5372e-05	chr14:66963153-67658112	1
3p13	6.4295e-05	6.2497e-05	chr3:70016017-71729299	2
1p36.11	1.6679e-20	0.0004787	chr1:16785565-33285595	284
14q32.33	8.4799e-08	0.0007843	chr14:95113281-107349540	209
12p12.1	0.0008113	0.0008113	chr12:22837283-24365820	2
10q26.13	5.7505e-06	0.0019901	chr10:105613884-135534747	198
4q21.3	3.0903e-07	0.0073441	chr4:66534835-95376252	205
11q23.3	0.00030497	0.0073441	chr11:102825636-135006516	305
17p11.2	0.0001026	0.0077403	chr17:15923099-16246015	3
2q37.3	0.0022356	0.0085087	chr2:234985548-243199373	73
11q14.1	0.0030474	0.013032	chr11:82995735-85348794	2
18q21.2	0.019373	0.019595	chr18:40857296-78077248	175
8p12	0.00033726	0.033891	chr8:31454518-33231036	4
20p12.1	0.051716	0.05124	chr20:13964029-16252980	4
15q26.3	0.056724	0.056577	chr15:87570102-102531392	115
4q24	7.0927e-07	0.081694	chr4:87847398-115525698	135
22q13.32	0.05307	0.10696	chr22:44205320-51304566	84
Xq26.2	0.12335	0.12214	chrX:132542482-133309860	7
9q31.3	0.12467	0.12903	chr9:93403988-141213431	577
4p16.3	0.14149	0.13968	chr4:1-30734965	206
22q12.1	0.095859	0.15584	chr22:28314430-29085838	4
7q36.3	0.24831	0.25529	chr7:99583749-159138663	523

Genes in Wide Peak

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

Table S25. 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 1p36.31.

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

Genes
RPL22
TNFRSF14
PRDM16
snoU13\|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
CDK11B
DFFB
DVL1
GABRD
GNB1
ZBTB48
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
KCNAB2
TNFRSF25
TNFRSF18
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
RER1
ACOT7
ICMT
CHD5
NOC2L
ARHGEF16
SSU72
WRAP73
SDF4
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
DNAJC11
AJAP1
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
NOL9
LINC00115
MORN1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
ATAD3B
PLEKHN1
C1orf170
THAP3
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
PHF13
CCDC27
CALML6
C1orf86
ATAD3C
TTLL10
NPHP4
C1orf174
KLHL17
TMEM52
AGRN
GPR153
FAM132A
HES5
SMIM1
RNF207
HES3
MIR200A
MIR200B
ANKRD65
MIR429
TMEM88B
C1orf233
CDK11A
SLC35E2B
OR4F29
MIR4252
MIR4689
MIR4417

Genes in Wide Peak

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

Table S27. 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 4q35.1.

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

Genes
SNORD79
CASP3
IRF2
MLF1IP
CCDC111

Genes in Wide Peak

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

Table S29. 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 6q27.

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

Genes
TCTE3
PHF10
WDR27
C6orf120

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
STK11
TCF3
FSTL3
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
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
EEF2
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
MATK
GADD45B
NFIC
OAZ1
PALM
POLRMT
MAP2K2
PRTN3
PTBP1
PTPRS
RPS15
SGTA
TBXA2R
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
APBA3
MED16
CHAF1A
EBI3
PLIN3
APC2
ABCA7
HMG20B
SEMA6B
UQCR11
SBNO2
KDM4B
ZFR2
PIP5K1C
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
TJP3
NMRK2
SLC39A3
THEG
ZBTB7A
SIRT6
LSM7
MBD3
MIER2
PCSK4
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
NCLN
SHD
WDR18
REXO1
ZNF77
CACTIN
CELF5
FSD1
TLE6
LPPR3
ZNF556
UBXN6
ABHD17A
DOHH
KLF16
DOT1L
KISS1R
CREB3L3
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
R3HDM4
TMEM259
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
GRIN3B
MRPL54
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
MISP
PLK5
C2CD4C
TICAM1
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
C19orf77
ODF3L2
ADAMTSL5
TMPRSS9
C19orf35
MEX3D
PRSS57
PLIN5
ARRDC5
PLIN4
C19orf71
MIR3187
MIR4746

Genes in Wide Peak

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

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

Genes
PER1
TP53
GAS7
USP6
RCVRN
GLP2R
STX8
RN7SL129P
SNORA69\|ENSG00000212206.1
CTC1
MIR3676
SNORD118
TMEM107
snoU13\|ENSG00000238676.1
SCARNA21\|ENSG00000252835.1
RPL29P2
snoU13\|ENSG00000251860.1
SNORD10
SNORA48\|ENSG00000209582.1
SNORA67\|ENSG00000264772.2
SLC35G6
GABARAP
ALOX12P2
TEKT1
C17orf100
RNA5SP435
DERL2
RN7SL784P
RN7SL171P
SPNS2
RN7SL774P
snoU13\|ENSG00000238807.1
RNA5SP434
C17orf85
SHPK
ASPA
OR1E1
OR1D4
RN7SL605P
MIR1253
RN7SL608P
snoU13\|ENSG00000239024.1
RN7SL33P
SNORD91A
SNORD91B
RN7SL624P
TLCD2
snoU13\|ENSG00000238946.1
RN7SL105P
BHLHA9
MIR3183
TIMM22
DBIL5P
DOC2B
ABR
ACADVL
ALOX12
ALOX12B
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MNT
MYH8
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RPA1
RPL26
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E2
OR1G1
OR3A3
SLC25A11
SCARF1
TNK1
MYH13
TNFSF13
TM4SF5
RABEP1
KCNAB3
AURKB
NTN1
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
CLUH
SMG6
WSCD1
CTDNEP1
PIK3R5
ELP5
SHPK
AIPL1
RNF167
SENP3
OR1A2
PELP1
RANGRF
TAX1BP3
MINK1
GEMIN4
MED31
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
C17orf59
SLC52A1
WRAP53
RNMTL1
VPS53
TSR1
DHX33
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
NDEL1
ACKR6
EMC6
RILP
GSG2
ZMYND15
CAMKK1
RPAIN
LSMD1
NEURL4
ZNF594
HES7
SPATA22
TXNDC17
TMEM88
SAT2
SMYD4
CNTROB
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
WDR81
DNAH2
RTN4RL1
WDR16
CCDC42
PIK3R6
ODF4
KCTD11
MFSD6L
TRPV3
SLC16A11
FBXO39
DHRS7C
SLC16A13
C17orf74
SPNS3
TMEM256
BCL6B
VMO1
LINC00324
SLC13A5
TMEM102
TUSC5
TMEM95
SMTNL2
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
SPDYE4
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR212
MIR22HG
TNFSF12
RNASEK
MIR324
MIR497HG
RNF222
C17orf107
MIR4314
MIR4520B

Genes in Wide Peak

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

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

Genes
PTEN
SNORD74\|ENSG00000200891.1
KLLN

Genes in Wide Peak

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

Table S34. 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 2q22.1.

Table S35. 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 12q24.33.

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

Genes
BCL7A
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
SCARB1
STX2
GOLGA3
GTF2H3
MMP17
POLE
PXMP2
CLIP1
SFSWAP
UBC
ZNF10
ZNF26
ZNF84
CDK2AP1
ULK1
DENR
HCAR3
HIP1R
PIWIL1
NCOR2
KNTC1
MPHOSPH9
ZNF268
TMED2
FZD10
P2RX2
ANKLE2
ABCB9
RIMBP2
ATP6V0A2
GALNT9
ARL6IP4
SBNO1
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
CCDC92
PUS1
CCDC62
C12orf65
TMEM132D
SLC15A4
FAM101A
ZNF664
GLT1D1
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
DDX51
HCAR2
EP400NL
RILPL1
IL31
SETD8
ZNF605
MIR3908
MIR4419B
MIR5188

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
GPHN

Genes in Wide Peak

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

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

Genes
FOXP1
MIR1284

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
LCK
PAX7
SDHB
ARID1A
MDS2
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
ALPL
BAI2
C1QA
C1QB
C1QC
CAPZB
RUNX3
CDA
CDC42
CD52
RCC1
CNR2
COL16A1
DDOST
E2F2
ECE1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
FUCA1
IFI6
GALE
SFN
GPR3
HCRTR1
HDAC1
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
NBL1
OPRD1
PAFAH2
PLA2G2A
PPP1R8
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
SRSF4
SLC9A1
TAF12
TCEA3
TCEB3
SLC30A2
LUZP1
LAPTM5
PTP4A2
SNHG3
NR0B2
FCN3
YARS
ALDH4A1
EIF3I
EIF4G3
MAP3K6
SNRNP40
THEMIS2
CROCC
PUM1
ZBTB40
PTPRU
CELA3A
WASF2
HNRNPR
SRRM1
CNKSR1
KHDRBS1
GMEB1
NUDC
SRSF10
RCAN3
PADI2
LYPLA2
DNAJC8
KDM1A
WDTC1
EMC1
OTUD3
UBR4
ATP13A2
CELA3B
PADI4
TMEM50A
KPNA6
STX12
CLIC4
LDLRAP1
AHDC1
SMPDL3B
PADI1
HP1BP3
MECR
MRTO4
YTHDF2
ZCCHC17
PADI3
WNT4
RNF186
MED18
PQLC2
TRNAU1AP
BSDC1
XKR8
TMEM39B
ARHGEF10L
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
IQCC
RCC2
TMEM234
MTFR1L
C1orf63
PITHD1
NIPAL3
SEPN1
KIF17
KIAA1522
GRHL3
IL22RA1
GPATCH3
TINAGL1
PLA2G2F
CEP85
PINK1
MARCKSL1
PHACTR4
AUNIP
CCDC28B
NKAIN1
MUL1
LIN28A
FAM110D
DHDDS
ZNF436
TAS1R2
SYNC
ACTL8
TSSK3
SESN2
TMEM222
USP48
NBPF3
TRIM63
FAM167B
SYTL1
IGSF21
STPG1
SPOCD1
UBXN11
ATPIF1
FAM46B
C1orf172
IFFO2
MYOM3
KLHDC7A
VWA5B1
C1orf213
DCDC2B
PDIK1L
IFNLR1
FAM43B
PAQR7
FAM76A
TXLNA
AKR7L
TMCO4
ZNF683
SERINC2
CATSPER4
TRNP1
CD164L2
TMEM200B
SH2D5
NCMAP
LDLRAD2
MINOS1
PEF1
LACTBL1
ZBTB8A
C1orf234
FAM229A
MIR4253
MIR3917
MIR3675
MIR4419A
MIR4425
MIR4418
MIR378F

Genes in Wide Peak

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

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

Genes
AKT1
TCL1A
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
BDKRB1
BDKRB2
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
BRF1
HSP90AA1
JAG2
KLC1
MARK3
PPP2R5C
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DLK1
MTA1
BAG5
C14orf2
CDC42BPB
TCL1B
TECPR2
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
GPR132
EVL
GSKIP
CINP
CDCA4
ATG2B
ZNF839
BEGAIN
INF2
ZFYVE21
WDR25
LINC00341
CLMN
TMEM121
AMN
SETD3
HHIPL1
BTBD6
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
PLD4
ADSSL1
SLC25A29
GSC
SYNE3
NUDT14
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
ASPG
C14orf64
RTL1
TMEM179
C14orf180
MIR127
MIR136
MIR154
MIR203
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1197
MIR1193
MIR4309
MIR3173
MIR151B
MIR4710
MIR2392

Genes in Wide Peak

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

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

Genes
SOX5
MIR920

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.13.

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

Genes
FGFR2
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60\|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19\|ENSG00000222588.1
SNORA19\|ENSG00000207468.1
U3\|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13\|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17\|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13\|ENSG00000239125.1
SMNDC1
RN7SL450P
U4\|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13\|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
CASP7
COL17A1
CTBP2
CYP2E1
DMBT1
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
PRLHR
GRK5
HABP2
HMX2
INPP5A
ABLIM1
MKI67
MXI1
NRAP
OAT
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PTPRE
RGS10
SLC18A2
TCF7L2
TECTB
UROS
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
SMC3
BUB3
GSTO1
BAG3
FAM53B
SLK
DCLRE1A
GLRX3
DPYSL4
TACC2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
SORCS3
FAM175B
ATRNL1
C10orf137
PDCD4
VENTX
CUZD1
CALY
CHST15
ACSL5
ZRANB1
TTC40
NSMCE4A
C10orf118
WDR11
DHX32
TDRD1
BCCIP
GPAM
KIAA1598
FAM160B1
PLEKHA1
FAM204A
LHPP
IKZF5
ZDHHC6
MCMBP
PLEKHS1
C10orf88
WDR96
LRRC27
GPR123
AFAP1L2
KNDC1
MTG1
BBIP1
FANK1
SYCE1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
GSTO2
SFR1
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
C10orf82
CACUL1
CCDC147
PWWP2B
PPAPDC1A
PAOX
FAM24B
EBF3
CASC2
TCERG1L
HSPA12A
FUOM
JAKMIP3
STK32C
RBM20
KCNK18
NANOS1
HMX3
CCDC172
ARMS2
TEX36
C10orf120
FOXI2
C10orf85
FRG2B
SPRN
MIR202
FAM196A
MIR2110
MIR378C
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.3.

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

Genes
RNA5SP164
RN7SKP248
GPRIN3
RN7SKP244
RNU6ATAC31P
IBSP
snoU13\|ENSG00000238652.1
RN7SL681P
RN7SKP96
MIR4451
RN7SKP48
RN7SL552P
MRPS18C
snoR442\|ENSG00000252834.1
MIR575
LINC00575
SNORD42\|ENSG00000202440.1
HNRNPD
SNORA31\|ENSG00000252762.1
SNORA75\|ENSG00000212620.1
OR7E94P
LINC00989
NAA11
RN7SL127P
MIR5096
snoU13\|ENSG00000238816.1
SNORD75\|ENSG00000221711.1
MIR548AH
MIR4450
SNORD50\|ENSG00000199857.1
CDKL2
BTC
PPBPP2
RN7SL218P
PPBP
PF4
PF4V1
SNORA3\|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
RNA5SP163
snoU13\|ENSG00000238318.1
CSN1S2AP
SULT1B1
UGT2A1
UGT2A2
UGT2B10
TMPRSS11BNL
FTLP10
TMPRSS11GP
SNORA62\|ENSG00000202374.1
GNRHR
UBA6
AFM
AFP
ALB
AMBN
ANXA3
AREG
ART3
ATOH1
BMP3
CCNG2
SCARB2
CDS1
CENPC
CSN1S1
CSN2
CSN3
DCK
DMP1
DSPP
EREG
FGF5
GC
GK2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
HTN1
HTN3
IGJ
IL8
CXCL10
CXCL9
AFF1
MUC7
PKD2
PPEF2
PRKG2
MAPK10
PTPN13
CXCL6
CXCL11
CXCL5
SNCA
SPP1
STATH
SULT1E1
UGT2B4
UGT2B7
UGT2B15
UGT2B17
SPARCL1
USO1
SLC4A4
HERC3
TMPRSS11D
ABCG2
ADAMTS3
G3BP2
HNRNPDL
ENAM
FAM13A
CXCL13
UGT2B11
HPSE
SMR3B
NPFFR2
UGT2A1
CCNI
SEC31A
RUFY3
MMRN1
WDFY3
PARM1
RCHY1
ANKRD17
STAP1
SMR3A
NAAA
COQ2
HPGDS
TMPRSS11E
COPS4
HSD17B11
HERC5
PLAC8
NUDT9
NUP54
UGT2B28
ODAM
HERC6
SDAD1
BMP2K
SEPT11
SMARCAD1
MEPE
PRDM8
UTP3
KLHL8
SHROOM3
ENOPH1
PROL1
MRPL1
THAP9
UGT2A3
SCD5
FRAS1
ARHGAP24
FAM175A
AGPAT9
PIGY
CABS1
YTHDC1
MOB1B
HELQ
PCAT4
ANTXR2
LIN54
TMPRSS11B
C4orf36
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
TIGD2
RASSF6
CNOT6L
C4orf22
EPGN
FDCSP
NAP1L5
COX18
CCDC158
TMPRSS11A
SOWAHB
SLC10A6
HSD17B13
TMPRSS11F
C4orf40
AMTN
CCSER1
MTHFD2L
TMEM150C
AREGB
FAM47E
MIR1269A
MIR4452
FAM47E
MIR5705
PYURF

Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
snoU13\|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13\|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8\|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13\|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64\|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11\|ENSG00000252992.1
RNY4P6
ZNF259
snoU13\|ENSG00000238625.1
LINC00900
snoU13\|ENSG00000239153.1
ACA59\|ENSG00000252870.1
snoU13\|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39\|ENSG00000264997.1
RNA5SP349
RNA5SP348
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
BARX2
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
DCUN1D5
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
SPATA19
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR4301
CASP12
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693

Genes in Wide Peak

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

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

Genes
MIR1288
RN7SL442P
NCOR1

Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39\|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
ACKR3
GAL3ST2
RAB17
MLPH
IQCA1
C2orf54
ILKAP
ING5
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
DUSP28
ESPNL
AQP12A
KLHL30
OR6B2
ASB18
PRR21
AQP12B
D2HGDH
MIR4269
MIR4786

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.1.

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

Genes
DLG2
TMEM126B

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25\|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
snoU13\|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8\|ENSG00000199713.1
RN7SL112P
SNORD28\|ENSG00000252284.1
FECH
U3\|ENSG00000212539.1
TXNL1
SNORA73\|ENSG00000201816.1
RNA5SP459
SNORA37
DCC
snoU13\|ENSG00000238885.1
RN7SL695P
ME2
RNA5SP458
RN7SL310P
RNA5SP457
SCARNA18\|ENSG00000252139.1
SCARNA17\|ENSG00000251992.1
SCARNA17\|ENSG00000267322.1
SNORD58B
SNORD58A
SNORD58C
C18orf32
MIR4744
MIR4743
RNA5SP456
IER3IP1
RNF165
RN7SKP26
RNA5SP455
ATP5A1
CDH7
CYB5A
KDSR
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
RPL17
SERPINB3
SERPINB4
SLC14A1
TCF4
ZNF236
SLC14A2
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
LIPG
ONECUT2
VPS4B
CTIF
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
SETBP1
KCNG2
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
EPG5
CCDC102B
PQLC1
CCDC68
NETO1
KATNAL2
MRO
HDHD2
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
GTSCR1
DOK6
LINC00305
DYNAP
BOD1L2
SIGLEC15
LINC00908
HMSD
CPLX4
ATP9B
LINC00909
MIR122
HSBP1L1
C18orf63
SKOR2
TCEB3CL
MIR1539
MIR4319
TCEB3CL2
MIR4527
MIR4529
MIR5011

Genes in Wide Peak

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

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

Genes
RNA5SP263
RNA5SP262
RNA5SP261
NRG1

Genes in Wide Peak

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

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

Genes
RNA5SP475
RN7SL864P
FLRT3
MACROD2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q26.3.

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

Genes
BLM
IDH2
NTRK3
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13\|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109\|ENSG00000239197.1
snoU13\|ENSG00000238981.1
RN7SL363P
SNORD18\|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
ACAN
ALDH1A3
ANPEP
CHD2
FES
IGF1R
MAN2A2
MEF2A
MFGE8
FURIN
PCSK6
PLIN1
POLG
RLBP1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
ABHD2
CHSY1
SYNM
VPS33B
MRPL46
OR4F4
SLCO3A1
NGRN
RHCG
DET1
FANCI
MCTP2
VIMP
UNC45A
RGMA
WDR93
AEN
TTC23
MRPS11
LRRK1
TM2D3
TICRR
RCCD1
ARRDC4
LINC00923
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
ADAMTS17
DNM1P46
CERS3
FAM169B
KIF7
ZNF710
HDDC3
SPATA41
GDPGP1
OR4F6
OR4F15
FAM174B
TTLL13
MIR1179
MIR3174

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q24.

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

Genes
RAP1GDS1
TET2
RN7SL184P
TIFA
C4orf32
ENPEP
RN7SL275P
CCDC109B
MIR576
RN7SL55P
SNORD112\|ENSG00000252566.1
GIMD1
RN7SL89P
SNORA31\|ENSG00000252136.1
TACR3
BDH2
CISD2
snoU13\|ENSG00000238948.1
RN7SL728P
MIR1255A
ADH1B
PCNAP1
MIR3684
EIF4E
RN7SKP28
RNA5SP164
RN7SKP248
GPRIN3
RN7SKP244
RNU6ATAC31P
IBSP
snoU13\|ENSG00000238652.1
RN7SL681P
ADH1A
ADH1C
ADH4
ADH5
ADH6
ADH7
ANK2
ATOH1
BMPR1B
CAMK2D
CASP6
CENPE
DMP1
DSPP
EGF
GRID2
H2AFZ
HADH
CFI
MANBA
AFF1
MTTP
NFKB1
PDHA2
PITX2
PKD2
PPP3CA
RPL34
SNCA
SPP1
UBE2D3
SPARCL1
UNC5C
LAMTOR3
HERC3
PAPSS1
AIMP1
ABCG2
TSPAN5
FAM13A
SEC24B
PDLIM5
RRH
MMRN1
METAP1
PPA2
DAPP1
DKK2
HPGDS
HSD17B11
LEF1
HERC5
LARP7
EMCN
NUDT9
GAR1
ARHGEF38
HERC6
BANK1
C4orf21
AP1AR
SMARCAD1
MEPE
INTS12
KLHL8
OSTC
NEUROG2
SLC39A8
ETNPPL
ELOVL6
ARSJ
GSTCD
DNAJB14
ALPK1
CXXC4
PLA2G12A
C4orf17
COL25A1
PIGY
TRMT10A
TBCK
CYP2U1
DDIT4L
SLC9B2
SLC9B1
PPM1K
TIGD2
SGMS2
NPNT
NAP1L5
STPG2
LRIT3
HSD17B13
CCSER1
MIR302A
MIR302B
MIR302C
MIR302D
MIR367
MIR297
MIR5705
PYURF

Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
LINC00229
ACR
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
CRELD2
ADM2
TRABD
PNPLA3
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LMF2
PHF21B
KLHDC7B
PNPLA5
C22orf34
LINC00207
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq26.2.

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

Genes
GPC3
MIR106A
MIR19B2
MIR92A2
MIR363
MIR20B
MIR18B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q31.3.

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

Genes
ABL1
FANCC
NOTCH1
OMD
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13\|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13\|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3\|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13\|ENSG00000238657.1
CELP
GTF3C4
SNORA67\|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31\|ENSG00000252582.1
snoU13\|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13\|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116\|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13\|ENSG00000238530.1
MIR455
COL27A1
FKBP15
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31\|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
snoU13\|ENSG00000238746.1
RNA5SP288
MIR27B
MIR23B
MIR2278
PCAT7
ZNF169
snoU13\|ENSG00000238792.1
MIRLET7DHG
CENPP
SNORA84
snoU13\|ENSG00000238996.1
LINC00475
LINC00484
ABCA1
ABCA2
AK1
ALAD
ALDOB
AMBP
ASS1
AUH
BAAT
C5
C8G
CACNA1B
CCBL1
ENTPD2
CDK9
CEL
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CYLC2
DBC1
DBH
SARDH
DNM1
ECM2
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
NR6A1
GLE1
GNG10
GOLGA1
GOLGA2
RAPGEF1
GRIN1
GSN
HSD17B3
HSPA5
TNC
IARS
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PHF2
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
FBP2
DPM2
FUBP3
PRPF4
KLF4
GTF3C5
LHX2
MED27
PTGES
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7A
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
FAM120A
PMPCA
ASTN2
BICD2
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
RABGAP1
TMEM245
CIZ1
DFNB31
NELFB
NIPSNAP3A
NSMF
GPSM1
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
NUTM2F
ASPN
BSPRY
TOR4A
TEX10
EXD3
FAM206A
NOL8
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
RABL6
CDK5RAP2
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
SLC46A2
ZNF462
PRDM12
SUSD1
IPPK
DDX31
FAM129B
WNK2
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
GARNL3
HSDL2
C9orf89
HIATL2
NTNG2
HIATL1
PPAPDC3
ZDHHC12
FAM73B
C9orf3
FIBCD1
KIAA1984
TMEM141
C9orf37
FGD3
MVB12B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
MRRF
ARRDC1
DPH7
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
SLC34A3
DAB2IP
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
FAM120AOS
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
C9orf96
OLFML2A
QSOX2
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CDC26
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
FAM78A
OR13C9
OR13D1
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
ERCC6L2
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
NUTM2G
C9orf173
NRARP
C9orf129
DNAJC25
MIR600HG
MIR602
RNF208
CARD9
MIR3074
MIR3154
MIR4291
CCDC180
MIR3689A
MIR3911
MIR3927
MIR3689B
MIR3689D1
MIR3689F
MIR3960
MIR4674
MIR4478
MIR3689C
MIR3689D2
MIR4670
MIR3689E
MIR548AW

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.3.

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

Genes
FGFR3
WHSC1
RN7SL101P
SNORD74\|ENSG00000200999.1
RN7SL16P
snoU13\|ENSG00000238383.1
RNA5SP157
FAM184B
MED28
RN7SL315P
snoU13\|ENSG00000238536.1
SNORA75\|ENSG00000206780.1
ZEB2P1
CD38
FAM200B
RN7SKP170
SNORA63\|ENSG00000202449.1
LINC00504
HSP90AB2P
RNA5SP156
HS3ST1
CLNK
RNA5SP155
MIR3138
RNA5SP154
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48\|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
BST1
CCKAR
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
RBPJ
LETM1
MSX1
MYL5
PDE6B
PPP2R2C
QDPR
RGS12
RNF4
SH3BP2
SOD3
WFS1
NELFA
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
FGFBP1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
SLC34A2
MXD4
CPLX1
SLC26A1
PPARGC1A
SEL1L3
MAN2B2
FBXL5
NSG1
ZCCHC4
ANAPC4
LAP3
SEPSECS
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
DCAF16
LGI2
TBC1D19
PI4K2B
BLOC1S4
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
CC2D2A
STIM2
UVSSA
ZFYVE28
GBA3
AFAP1
NCAPG
TNIP2
HAUS3
KCNIP4
FGFBP2
MFSD7
TMEM175
ABLIM2
TMEM128
ZNF518B
CCDC149
TMEM129
MRFAP1
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CPEB2
EVC2
PACRGL
OTOP1
JAKMIP1
FAM53A
TRMT44
GPR125
ZBTB49
TAPT1
LCORL
CCDC96
BOD1L1
CRIPAK
DOK7
RNF212
NAT8L
POLN
SMIM20
C4orf48
DEFB131
CLRN2
MIR572
MIR573
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
USP17L30
PSAPL1
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR548I2
MIR378D1
MIR4800
MIR5091

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.1.

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

Genes
RN7SL162P
SNORD42\|ENSG00000201209.1
RN7SL757P
TTC28

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
BRAF
EZH2
MET
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
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25\|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13\|ENSG00000238922.1
FLJ00325
U3\|ENSG00000238297.1
snoU109\|ENSG00000238832.1
RNA5SP236
SNORD112\|ENSG00000251911.1
RN7SL8P
LHFPL3
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48\|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
MIR4658
MIR106B
MIR93
MIR25
AOC1
ACHE
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CAV1
CAV2
CFTR
CHRM2
AP1S1
CLCN1
CPA1
CPA2
CUX1
DLD
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNB2
GPR22
GRM8
MNX1
AGFG2
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRCAM
NRF1
ORC5
SERPINE1
PAX4
PCOLCE
SLC26A4
PIK3CG
PIP
PODXL
POLR2J
PPP1R3A
PRKAR2B
PRSS1
RELN
PSMC2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
ZNF3
ZKSCAN1
ZSCAN21
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
PLOD3
DGKI
AP4M1
ATP6V1F
ASIC3
PMPCB
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
MUC12
NAMPT
RASA4
LRRC17
POP7
FAM3C
COG5
ZNHIT1
STAG3
FASTK
COPS6
DUS4L
ZNF277
ABCB8
TFEC
LAMB4
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
CLDN15
POT1
CNTNAP2
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
HBP1
DNAJC2
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
MRPS33
NUB1
GPR85
TAS2R5
CHPF2
PUS7
ING3
LRRN3
ALKBH4
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
KMT2E
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
LRRC61
C7orf49
PVRIG
GCC1
GAL3ST4
PRKRIP1
CBLL1
ZNF767
CPED1
TTC26
ORAI2
JHDM1D
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
MYL10
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
COL26A1
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
MUC17
RNF32
ASB15
C7orf60
CLEC2L
C7orf55
IQUB
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
PPP1R35
GPC2
LRWD1
FBXL13
NAPEPLD
ATXN7L1
CDHR3
NYAP1
CNPY4
POLR2J2
UBN2
MBLAC1
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
LSMEM1
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
MOGAT3
FAM71F2
STRA8
WDR86
DPY19L2P2
GATS
GSTK1
NAT16
SLC26A5
RNF148
LAMTOR4
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
C7orf61
UFSP1
MIR182
MIR183
MIR96
SPDYE3
SPDYE2
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
EFCAB10
UPK3BL
CTAGE8
RASA4B
SMKR1
ZNF783
SPDYE2B
MIR548O
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Arm-level results

Table 3. Get Full Table Arm-level significance table - 30 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	0.17	-0.0491	1	0.29	5.3	1.69e-07
1q	1195	0.61	20.2	0	0.30	4.3	2.19e-05
2p	624	0.12	-3.15	1	0.11	-3.86	1
2q	967	0.12	-2.89	1	0.12	-3.13	1
3p	644	0.10	-3.98	1	0.16	-1.25	1
3q	733	0.10	-4.06	1	0.14	-2.27	1
4p	289	0.08	-4.58	1	0.32	5.54	4.76e-08
4q	670	0.02	-6.33	1	0.41	10.6	0
5p	183	0.38	8.22	1.52e-15	0.15	-2.03	1
5q	905	0.32	6.63	1.77e-10	0.15	-1.3	1
6p	710	0.31	5.61	6.08e-08	0.17	-0.577	1
6q	556	0.20	0.32	1	0.34	6.86	2.38e-11
7p	389	0.30	4.83	3.06e-06	0.08	-4.79	1
7q	783	0.31	6.1	4.46e-09	0.08	-4.22	1
8p	338	0.23	1.1	0.502	0.70	23.4	0
8q	551	0.52	14	0	0.36	6.31	6.19e-10
9p	301	0.08	-4.85	1	0.34	6.66	8.01e-11
9q	700	0.07	-4.88	1	0.32	6.11	1.82e-09
10p	253	0.15	-2.13	1	0.18	-0.859	1
10q	738	0.12	-2.92	1	0.24	2.29	0.0254
11p	509	0.06	-5.95	1	0.18	-0.646	1
11q	975	0.06	-5.25	1	0.21	1.29	0.203
12p	339	0.13	-2.97	1	0.20	0.266	0.675
12q	904	0.14	-2.01	1	0.11	-3.33	1
13q	560	0.09	-4.09	1	0.35	7.69	6.19e-14
14q	938	0.08	-4.1	1	0.31	6.32	6.19e-10
15q	810	0.11	-3.43	1	0.20	0.633	0.47
16p	559	0.12	-3.11	1	0.32	6.19	1.2e-09
16q	455	0.07	-4.78	1	0.41	10.5	0
17p	415	0.11	-2.69	1	0.56	17.1	0
17q	972	0.27	3.95	0.000161	0.17	-0.703	1
18p	104	0.11	-3.82	1	0.23	1.2	0.217
18q	275	0.10	-4.36	1	0.23	1.53	0.137
19p	681	0.17	-0.8	1	0.17	-0.8	1
19q	935	0.20	0.819	0.705	0.15	-1.58	1
20p	234	0.31	5.2	5.11e-07	0.10	-4.07	1
20q	448	0.31	5.62	6.08e-08	0.05	-5.7	1
21q	258	0.10	-3.98	1	0.32	5.64	2.95e-08
22q	564	0.16	-1.38	1	0.22	1.19	0.217
Xp	418	0.12	-3.07	1	0.31	5.24	2.14e-07
Xq	668	0.18	-0.48	1	0.26	3.26	0.00135

Methods & Data

Input

Description

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

Values

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

Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC-TP/22227692/GDAC_MergeDataFiles_12185307/LIHC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat
CNV Files = /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.7
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 370 Input Tumor Samples.

Tumor Sample Names
TCGA-2V-A95S-01A-11D-A36W-01
TCGA-2Y-A9GS-01A-12D-A381-01
TCGA-2Y-A9GT-01A-11D-A381-01
TCGA-2Y-A9GU-01A-11D-A381-01
TCGA-2Y-A9GV-01A-11D-A381-01
TCGA-2Y-A9GW-01A-11D-A381-01
TCGA-2Y-A9GX-01A-11D-A381-01
TCGA-2Y-A9GY-01A-11D-A381-01
TCGA-2Y-A9GZ-01A-11D-A38W-01
TCGA-2Y-A9H0-01A-11D-A381-01

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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