SNP6 Copy number analysis (GISTIC2)

Rectum Adenocarcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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 (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1TB15VM

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 2.0.21 (Firehose task version: 127).

Summary

There were 165 tumor samples used in this analysis: 20 significant arm-level results, 24 significant focal amplifications, and 35 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 - 24 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
20q11.21	5.0663e-23	1.0333e-15	chr20:26196264-31620534	46
13q12.2	2.1659e-18	9.7611e-13	chr13:28385587-28773237	8
8q24.21	8.334e-09	8.334e-09	chr8:128204396-128652497	3
17q12	1.6108e-08	1.1834e-07	chr17:37837542-37876018	2
20q11.23	1.5535e-22	1.0334e-06	chr20:35722356-40360023	52
13q12.13	1.8242e-16	0.00047924	chr13:27521847-27539800	0 [USP12]
8p11.23	0.00011678	0.00055234	chr8:38170522-38469302	5
11p15.5	0.0013072	0.0013072	chr11:2157956-2241214	4
8p11.21	0.0026067	0.0069542	chr8:41352076-41641623	5
6p21.1	0.026518	0.026518	chr6:42366336-45044523	60
5q22.3	0.033759	0.033759	chr5:114756122-114759166	0 [FEM1C]
13q22.1	3.2651e-06	0.033759	chr13:73577729-74250466	5
1q21.3	0.022085	0.037393	chr1:120523956-163100192	471
20q13.31	0.0057237	0.051395	chr20:50227949-63025520	143
1q32.2	0.0476	0.067486	chr1:202853626-209439928	92
19p13.2	0.075983	0.075983	chr19:7296453-7398264	0 [INSR]
12p12.1	0.002811	0.13557	chr12:24753749-26629748	14
16p11.2	0.13785	0.13785	chr16:30581939-30943981	17
12p13.33	0.023749	0.14365	chr12:1-4369146	35
10q22.2	0.14858	0.14858	chr10:73426159-83489711	87
Xp22.2	0.14858	0.14858	chrX:1-28634031	162
17q24.1	0.065121	0.16403	chr17:49230309-71116693	196
11q13.3	0.21247	0.21247	chr11:69661335-69806082	0 [FGF3]
15q26.1	0.21247	0.21247	chr15:88163369-102531392	114

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
ASXL1
EFCAB8
C20orf203
RNA5SP482
RNA5SP481
XKR7
LINC00028
DEFB122
SNORA40\|ENSG00000212134.1
RNA5SP480
BCL2L1
DNMT3B
FOXS1
HCK
ID1
PLAGL2
KIF3B
TM9SF4
MAPRE1
TPX2
POFUT1
REM1
BPIFB2
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TSPY26P
BPIFB6
C20orf112
CCM2L
SUN5
COMMD7
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB123
DEFB124
FRG1B
MIR663A
MIR1825
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.2.

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

Genes
CDX2
FLT3
RN7SL272P
URAD
LINC00543
PDX1
PAN3
ATP5EP2

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
POU5F1B
CASC8
CCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
PGAP3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.23.

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

Genes
TOP1
MAFB
SNORA26\|ENSG00000212224.1
RN7SL615P
RNA5SP484
SNORD112\|ENSG00000252434.1
RN7SL194P
RN7SL680P
RN7SL116P
RN7SKP173
ARHGAP40
MIR548O2
SNORA60
SNORA71\|ENSG00000201811.1
SNORA71D
SNORA71C
SNORA71A
SNORA71B
SNHG17
RN7SL237P
RN7SKP185
LINC00489
RBL1
BPI
GHRH
LBP
NNAT
PLCG1
RBL1
RPN2
SRC
TGM2
TTI1
BLCAP
ZHX3
PPP1R16B
CTNNBL1
RALGAPB
RPRD1B
DHX35
MANBAL
LPIN3
ACTR5
FAM83D
CHD6
KIAA1755
EMILIN3
VSTM2L
SNHG11
SLC32A1
MROH8
ADIG

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
FGFR1
WHSC1L1
RPS20P22
LETM2
C8orf86

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p15.5.

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

Genes
IGF2
INS
TH
MIR4686

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
MIR486
ANK1
GOLGA7
GINS4
AGPAT6

Genes in Wide Peak

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

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

Genes
MIR4642
TCTE1
TMEM151B
RSPH9
SCARNA15\|ENSG00000252218.1
RN7SL403P
MEA1
snoU13\|ENSG00000238611.1
U3\|ENSG00000221252.1
CDC5L
SLC29A1
HSP90AB1
NFKBIE
PEX6
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
SUPT3H
POLR1C
MAD2L1BP
CUL7
DNPH1
CNPY3
SLC22A7
CAPN11
CUL9
UBR2
GLTSCR1L
ZNF318
YIPF3
GNMT
MRPL2
GTPBP2
MRPS18A
TMEM63B
TRERF1
AARS2
XPO5
MRPL14
DLK2
TTBK1
RRP36
ABCC10
KLC4
TJAP1
KLHDC3
PTCRA
SPATS1
C6orf223
LRRC73
RPL7L1
SLC35B2
CRIP3
C6orf226
TMEM151B
MIR4647

Genes in Wide Peak

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

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

Genes
LINC00392
LINC00393
RNY1P8
KLF5
PIBF1

Genes in Wide Peak

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

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

Genes
SDHC
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PRCC
TPM3
PDE4DIP
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64\|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64\|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13\|ENSG00000238843.1
BGLAP
SNORA26\|ENSG00000252236.1
SCARNA4\|ENSG00000252808.1
SNORA42\|ENSG00000207475.1
snoU13\|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59\|ENSG00000252682.1
SNORA58\|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3\|ENSG00000252669.1
snoU13\|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31\|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13\|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
APCS
APOA2
ATP1A2
ATP1A4
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD5L
CD48
CHRNB2
CKS1B\|ENSG00000173207.8
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO5
DARC
GBA
GJA5
GJA8
HDGF
HSPA6
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ10
KCNN3
LMNA
LOR
LY9
MCL1
SMCP
MEF2D
MNDA
MPZ
MTX1
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PI4KB
PKLR
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
USF1
DAP3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
PEA15
B4GALT3
ADAM15
PEX11B
CD84
SELENBP1
SH2D2A
PRPF3
ARHGEF2
DEDD
AIM2
CHD1L
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
SLC27A3
TDRKH
CD160
PMF1
DUSP12
VPS45
KIAA0907
ATF6
POGZ
SYT11
RPRD2
SMG5
NCSTN
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
OLFML2B
C1orf43
CHTOP
LCE2B
OR10J1
USP21
SLC39A1
LAMTOR2
TMOD4
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
GPR89B
HSD17B7
UFC1
OAZ3
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
FAM63A
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
RAB25
PGLYRP4
RHBG
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
AQP10
SLAMF9
PYGO2
NUP210L
MEX3A
PIGM
IGSF8
C1orf85
PGLYRP3
SLAMF6
FCRL1
FCRL3
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
TSACC
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
NBPF12
LELP1
DCST1
BNIPL
LRRC71
PYHIN1
SPRR4
PPIAL4A
TTC24
LCE4A
NBPF11
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
RIIAD1
THEM5
NBPF16
ANKRD34A
C1orf204
HIST2H2AB
S100A7A
RXFP4
C1orf110
OR10R2
FCRL6
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PEAR1
NOTCH2NL
LYSMD1
HRNR
FLG2
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
NBPF9
HIST2H2BF
ETV3L
OR10J3
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
TSTD1
C2CD4D
NBPF20
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.31.

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

Genes
GNAS
SS18L1
NPBWR2
MIR647
MIR1914
C20ORF135
SLC2A4RG
MIR4326
MIR3196
HAR1A
HAR1B
LINC00029
GID8
LINC00659
LINC00686
MIR133A2
MIR4758
ATP5E
MGC4294
ANKRD60
RAE1
RN7SL170P
U3\|ENSG00000252536.1
FAM209A
GCNT7
snoU13\|ENSG00000238294.1
RNA5SP487
RNU4ATAC7P
RN7SKP184
RN7SL603P
BMP7
CDH4
CHRNA4
COL9A3
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
KCNQ2
LAMA5
MC3R
MYT1
NTSR1
OPRL1
PCK1
PFDN4
PPP1R3D
PSMA7
PTK6
RPS21
SRMS
AURKA
TAF4
TCEA2
TFAP2C
TPD52L2
ZNF217
BCAS1
STX16
TNFRSF6B
VAPB
OSBPL2
ATP9A
ARFRP1
RGS19
SYCP2
TCFL5
ADRM1
OGFR
DIDO1
HRH3
SPO11
PRPF6
MTG2
GMEB2
SLCO4A1
STMN3
SLMO2
NELFCD
RTFDC1
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
PCMTD2
MRGBP
PPP4R1L
RBM38
ZFP64
ARFGAP1
DOK5
PMEPA1
CASS4
SALL4
RAB22A
ZNF512B
COL20A1
CDH26
SLC17A9
FAM217B
C20orf195
PPDPF
BIRC7
NPEPL1
DNAJC5
TUBB1
ZBP1
CABLES2
ZGPAT
HELZ2
FAM210B
PHACTR3
BHLHE23
NKAIN4
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
CBLN4
CTCFL
SAMD10
ABHD16B
RBBP8NL
LSM14B
APCDD1L
C20orf201
LINC00176
C20orf197
FAM209B
MIR296
MIR646
MIR298
MIR1257
MIR4325
MTRNR2L3
MIR4756
MIR4532
MIR4533
MIR548AG2

Genes in Wide Peak

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

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

Genes
ELK4
MDM4
SLC45A3
MIR29B2
MIR29C
snoU13\|ENSG00000238401.1
FAIM3
IL20
SNORD112\|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60\|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72\|ENSG00000201944.1
SNORD112\|ENSG00000252946.1
SCARNA20\|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77\|ENSG00000221643.1
RABIF
ADORA1
ATP2B4
C4BPA
C4BPB
CD34
CHI3L1
CHIT1
CR1
CR1L
CR2
CTSE
CD55
EIF2D
FMOD
IL10
KISS1
CD46
MYBPH
MYOG
CDK18
PFKFB2
PIGR
PIK3C2B
PLXNA2
PRELP
RBBP5
REN
CNTN2
BTG2
DYRK3
PPFIA4
RAB7L1
MAPKAPK2
SOX13
IKBKE
ZC3H11A
TMCC2
LRRN2
IL24
PLEKHA6
NFASC
DSTYK
OPTC
IL19
ADIPOR1
CYB5R1
LAX1
KLHDC8A
ETNK2
YOD1
KLHL12
NUCKS1
C1orf116
NUAK2
RASSF5
FCAMR
PPP1R15B
TMEM183A
LEMD1
SLC26A9
GOLT1A
MFSD4
PM20D1
SLC41A1
LINC00303
TMEM81
C1orf132
MIR135B

Genes in Wide Peak

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

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

Genes
KRAS
RNA5SP354
SSPN
RN7SKP262
RN7SL38P
BCAT1
ITPR2
LRMP
RASSF8
CASC1
BHLHE41
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

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

Genes
MIR4519
MIR4519
BCL7C
SNORA30\|ENSG00000206755.1
CTF1
PHKG2
RNF40
SRCAP
ZNF629
FBXL19
FBRS
PRR14
C16orf93
ZNF689
ZNF785
ZNF688
MIR762

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
KDM5A
FKBP4
CBX3P4
CACNA1C
LINC00940
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
PARP11
WNK1
ADIPOR2
WNT5B
RHNO1
NRIP2
CCDC77
EFCAB4B
CACNA2D4
FBXL14
DCP1B
B4GALNT3
IQSEC3
LRTM2
MIR3649

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.2.

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

Genes
LINC00857
PLAC9
MBL1P
NUTM2E
NUTM2B
SFTPA1
SNORA71\|ENSG00000201393.1
LINC00595
LINC00856
RN7SL284P
RNA5SP321
SNORA31\|ENSG00000252888.1
RN7SL518P
MIR606
AP3M1
RMRPP1
GLUD1P3
BMS1P4
RNA5SP320
snoU13\|ENSG00000238983.1
DNAJC9
FAM149B1
SNORA11\|ENSG00000221164.1
MIR4676
SNORA36\|ENSG00000200294.1
ASCC1
ADK
ANXA7
ANXA11
CAMK2G
KCNMA1
MAT1A
P4HA1
PLAU
PPP3CB
PSAP
RPS24
SFTPD
VCL
VDAC2
NDST2
DLG5
CHST3
SEC24C
SPOCK2
PPIF
MICU1
POLR3A
ECD
ZSWIM8
KAT6B
NUDT13
MRPS16
DUSP13
DDIT4
DNAJB12
ZMIZ1
MYOZ1
CDH23
C10orf54
SYNPO2L
TMEM254
TSPAN14
C10orf11
FAM213A
DYDC2
PLA2G12B
ZNF503
MCU
CHCHD1
MSS51
TTC18
COMTD1
ANAPC16
SAMD8
DYDC1
EIF5AL1
USP54
FUT11
OIT3
ZCCHC24
DUPD1
SH2D4B
C10orf105
C10orf55
AGAP5
SFTPA2

Genes in Wide Peak

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

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

Genes
IL1RAPL1
DCAF8L2
VENTXP1
RN7SL91P
SCARNA23
SNORA68\|ENSG00000201407.1
EIF2S3
snoU13\|ENSG00000238327.1
PTCHD1
RN7SL436P
RN7SKP183
MIR23C
RN7SL48P
MIR4768
snoU13\|ENSG00000238764.1
SNORA16\|ENSG00000201467.1
SYAP1
MIR548AM
RN7SL658P
GRPR
SNORA7\|ENSG00000200620.1
CA5BP1
RAB9A
TCEANC
RN7SKP20
7SK\|ENSG00000271814.1
MIR548AX
RNA5SP499
SNORA31\|ENSG00000252291.1
SNORA20\|ENSG00000201660.1
SNORA48\|ENSG00000212214.1
RN7SL578P
snoU13\|ENSG00000251848.1
LINC00102\|ENSG00000230542.1
CD99P1\|ENSG00000223773.2
LINC00106\|ENSG00000236871.2
SLC25A6\|ENSG00000169100.8
RN7SL355P\|ENSG00000265350.1
RNA5SP498\|ENSG00000223274.1
MIR3690\|ENSG00000265658.1
LINC00685\|ENSG00000226179.1
PLCXD1\|ENSG00000182378.8
AMELX
SHROOM2
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT\|ENSG00000196433.6
BMX
S100G
CLCN4
CSF2RA\|ENSG00000198223.9
EIF1AX
FANCB
FIGF
GLRA2
GPM6B
HCCS
IL3RA\|ENSG00000185291.6
KAL1
CD99\|ENSG00000002586.13
MID1
NHS
GPR143
PDHA1
PDK3
PHEX
PHKA2
PIGA
POLA1
PPEF1
PRKX
PRPS2
RBBP7
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SHOX\|ENSG00000185960.8
SMS
CDKL5
TBL1X
TMSB4X
XG
ZFX
GTPBP6\|ENSG00000178605.8
HDHD1
AKAP17A\|ENSG00000197976.6
PNPLA4
ZRSR2
OFD1
PIR
ASMTL\|ENSG00000169093.10
AP1S2
GYG2
REPS2
ZBED1\|ENSG00000214717.4
PCYT1B
FRMPD4
GPR64
SCML2
PRDX4
RAI2
MSL3
CA5B
CNKSR2
ACOT9
SMPX
MXRA5
EGFL6
VCX
PPP2R3B\|ENSG00000167393.12
SH3KBP1
TLR7
TLR8
MBTPS2
VCX2
VCX3A
GEMIN8
TXLNG
WWC3
CTPS2
TMEM27
NLGN4X
ACE2
CRLF2\|ENSG00000205755.6
APOO
KLHL15
ATXN3L
BEND2
MAGEB10
DCAF8L1
ASB11
ASB9
ZNF645
MOSPD2
MAGEB6
DDX53
ARX
FAM9A
FAM9B
FAM9C
DHRSX\|ENSG00000169084.8
CXorf58
CXorf23
MAP7D2
KLHL34
MAGEB18
P2RY8\|ENSG00000182162.5
ARSH
MAGEB5
MAP3K15
YY2
VCX3B
MAGEB17
MIR651
CXorf28
MIR4770
MIR4767

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.1.

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

Genes
BRIP1
CD79B
CLTC
DDX5
HLF
PRKAR1A
MSI2
SCARNA24\|ENSG00000252274.1
RN7SKP180
LINC00511
MAP2K6
SNORA40\|ENSG00000252352.1
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
RN7SL622P
SNORA38B
MIR548D2
RN7SL756P
snoU13\|ENSG00000238612.1
PSMD12
SNORA8\|ENSG00000207410.1
RNA5SP447
RNA5SP446
MIR634
RNA5SP445
RN7SL735P
RNA5SP444
SLC16A6P1
RN7SL404P
RN7SL409P
PLEKHM1P
SMURF2
MIR5047
MIR3064
SNORD104
SNORA76\|ENSG00000266402.2
TCAM1P
RN7SL805P
ACE
TLK2
TBC1D3P2
RN7SL800P
snoU13\|ENSG00000238799.1
RN7SL448P
RN7SL606P
PPM1D
RPL12P38
SCARNA20\|ENSG00000252577.1
USP32
MIR4729
PRR11
MIR301A
MIR454
RN7SL716P
PPM1E
U3\|ENSG00000212195.1
DYNLL2
SRSF1
VEZF1
MRPS23
RN7SKP94
RN7SL449P
RN7SL437P
RNF126P1
RN7SKP14
snoZ178
RN7SL699P
APOH
CA4
CACNG1
COX11
CSH1
CSH2
CSHL1
CYB561
ACE
ERN1
BPTF
GH1
GH2
ICAM2
KCNJ2
KCNJ16
KPNA2
LPO
MAP3K3
MPO
TRIM37
NME1
SEPT4
PRKCA
PSMC5
RAD51C
RPS6KB1
SCN4A
SMARCD2
SOX9
SUPT4H1
TBX2
TRIM25
COIL
AKAP1
EPX
AXIN2
DGKE
RGS9
MTMR4
SLC16A6
NOG
BZRAP1
TBX4
MRC2
HELZ
MED13
TOM1L1
DCAF7
ABCA10
ABCA9
ABCA8
APPBP2
GNA13
POLG2
DDX42
ABCA6
ABCA5
MMD
NOL11
TANC2
PITPNC1
OR4D1
CACNG5
CACNG4
UTP18
RNFT1
TUBD1
TACO1
AMZ2
PTRH2
MBTD1
BCAS3
RNF43
MKS1
WIPI1
SMG8
TMEM100
TEX2
TEX14
CA10
CCDC47
INTS2
PCTP
SCPEP1
HEATR6
DHX40
LIMD2
KCNH6
VMP1
KIF2B
CEP95
STRADA
C17orf72
FTSJ3
HSF5
OR4D2
C17orf64
EFCAB3
ANKFN1
MARCH10
CEP112
SLC39A11
AMZ2P1
STXBP4
C17orf58
MILR1
C17orf47
GDPD1
METTL2A
C17orf67
NACA2
SKA2
LRRC37A3
YPEL2
C17orf82
CUEDC1
MIR142
MIR21
NME2
MIR633
MIR3614
C17orf112
MIR4737
MIR4736
MIR4524B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

Table S20. 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
ADAMTS17
DNM1P46
CERS3
FAM169B
KIF7
ZNF710
HDDC3
SPATA41
GDPGP1
OR4F6
OR4F15
FAM174B
TTLL13
MIR1179
MIR3174

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 - 35 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
16p13.3	1.1226e-35	1.1226e-35	chr16:5144019-7780235	2
20p12.1	1.1956e-26	1.1956e-26	chr20:14301156-15274325	2
4q22.1	1.228e-22	2.8716e-22	chr4:91271445-93240505	1
8p23.2	1.4477e-15	1.6444e-15	chr8:3548028-4985851	2
6q26	4.4834e-13	4.4834e-13	chr6:161693099-163153207	1
1p36.11	1.5121e-10	4.2035e-10	chr1:3814904-31841618	420
5q12.1	1.5121e-10	4.2035e-10	chr5:58998410-59780946	2
3q26.31	1.4203e-09	1.4203e-09	chr3:174345545-175760559	3
3p14.2	5.6392e-09	5.4105e-09	chr3:59702822-61026498	2
18q21.2	2.5437e-09	7.8208e-08	chr18:48472083-48705371	3
21q11.2	5.8552e-07	5.8552e-07	chr21:1-15447211	12
15q22.33	1.1276e-05	2.0124e-05	chr15:67067796-67494822	1
16q23.1	6.3197e-05	6.3197e-05	chr16:78098006-79299841	3
18q22.1	8.0486e-06	0.00021517	chr18:65181982-66383463	1
5q22.2	4.031e-06	0.00057564	chr5:102895125-114460579	35
1p33	5.067e-05	0.00086419	chr1:49615826-50514967	1
22q13.31	0.00090422	0.00094224	chr22:44391372-51304566	80
10q21.1	0.0017152	0.0023391	chr10:53057593-54077929	3
14q11.2	0.0046396	0.0047081	chr14:1-21820453	67
4q35.1	4.5651e-05	0.0053208	chr4:178100730-191154276	71
6p25.3	0.0079887	0.0078062	chr6:1608837-2624052	2
7q31.1	0.011406	0.011518	chr7:110746146-111366370	1
1p13.2	0.014935	0.028903	chr1:94019529-120204207	207
10q25.2	0.015389	0.036181	chr10:86084854-135534747	432
11q22.3	0.054507	0.055817	chr11:101742851-126293284	284
12p13.1	0.064995	0.067242	chr12:7945385-20853661	141
14q31.1	0.071679	0.071939	chr14:58462393-107349540	504
Xp22.33	0.071679	0.071939	chrX:1-10420184	56
17p11.2	0.079742	0.079256	chr17:8300098-25626166	172
8p11.21	0.054113	0.096165	chr8:12938527-52729481	240
19p13.3	0.095877	0.096165	chr19:1-59128983	1616
12q22	0.13043	0.131	chr12:32257220-108922982	640
4p13	0.14028	0.14457	chr4:31148303-52714468	82
15q21.1	0.074807	0.14457	chr15:1-66338646	448
2p12	0.18649	0.1861	chr2:56603652-96852542	277

Genes in Wide Peak

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

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

Genes
SNORA40\|ENSG00000252138.1
RBFOX1

Genes in Wide Peak

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

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

Genes
RNA5SP475
FLRT3

Genes in Wide Peak

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

Table S23. 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 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 6q26.

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
MDS2
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
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
E2F2
ECE1
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GALE
SFN
GPR3
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SRSF4
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
KCNAB2
FCN3
ALDH4A1
EIF4G3
TNFRSF25
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
THEMIS2
H6PD
CROCC
PUM1
KLHL21
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
FBXO2
FBXO6
HSPB7
AHDC1
SMPDL3B
UBIAD1
PADI1
SLC45A1
HP1BP3
CELA2B
MECR
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
HES2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
TMEM51
XKR8
ARHGEF10L
VPS13D
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
PTCHD2
KIF17
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
PINK1
PRAMEF1
PRAMEF2
PHACTR4
AUNIP
EFHD2
RSG1
NKAIN1
MUL1
NOL9
LIN28A
FAM110D
DHDDS
SPSB1
ZNF436
TAS1R2
TAS1R1
ACTL8
SESN2
ESPN
TMEM222
USP48
NBPF3
LZIC
TRIM63
SYTL1
IGSF21
KIAA2013
THAP3
STPG1
UBXN11
FBXO44
ATPIF1
FHAD1
FAM46B
RBP7
C1orf172
LRRC38
AADACL3
IFFO2
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
C1orf127
PHF13
C1orf213
PDIK1L
SLC2A7
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
AKR7L
TMCO4
ZNF683
NPHP4
SLC25A34
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
CATSPER4
GPR153
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR34A
PRAMEF11
PRAMEF6
MINOS1
PRAMEF7
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
C1orf234
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

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

Table S27. 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 3q26.31.

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

Genes
snoU13\|ENSG00000271842.1
MIR4789
RN7SKP40

Genes in Wide Peak

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

Table S29. 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 18q21.2.

Table S30. 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 21q11.2.

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

Genes
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70\|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
TPTE
POTED
MIR3687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q22.33.

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

Genes
SMAD3

Genes in Wide Peak

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

Table S33. 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 18q22.1.

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

Genes
TMX3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q22.2.

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

Genes
APC
RN7SKP89
RNU4ATAC13P
ZRSR1
SRP19
FLJ11235
SNORA13
RN7SKP57
CAMK4
SNORA51\|ENSG00000207177.1
MIR548F3
TMEM232
RN7SKP230
FER
RN7SKP122
RN7SL782P
SNORA31\|ENSG00000252337.1
RNA5SP189
RN7SL255P
EFNA5
KCNN2
MAN2A1
MCC
REEP5
NREP
PJA2
EPB41L4A
FBXL17
YTHDC2
TSSK1B
TSLP
SLC25A46
STARD4
WDR36
DCP2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p33.

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

Genes
snoU13\|ENSG00000239144.1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

Table S37. 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
ATXN10
FAM19A5
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
CRELD2
ADM2
TRABD
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LMF2
PHF21B
KLHDC7B
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 10q21.1.

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

Genes
MIR605
DKK1
CSTF2T

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q11.2.

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

Genes
CCNB1IP1
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79\|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
OR4Q2
snoU13\|ENSG00000238492.1
MED15P6
LINC00516
MED15P1
ANG
APEX1
HNRNPC
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
TEP1
PARP2
EDDM3A
SLC39A2
ZNF219
OSGEP
ARHGEF40
RPGRIP1
NDRG2
EDDM3B
METTL17
OR4K5
OR4K1
OR4K15
RNASE7
TMEM55B
RNASE11
TPPP2
OR4K14
OR4L1
OR11H6
KLHL33
RNASE10
OR6S1
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
TMEM253

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31\|ENSG00000253013.1
TLR3
snoU13\|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13\|ENSG00000239116.1
snoU13\|ENSG00000238596.1
snoU13\|ENSG00000238319.1
U3\|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173
snoU13\|ENSG00000252388.1
RNA5SP172
RN7SKP136
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
ING2
IRF2
KLKB1
MTNR1A
SORBS2
FAM149A
CLDN22
NEIL3
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
ZFP42
ENPP6
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR3945
MIR4455

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238922.1

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RBM15
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
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25\|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13\|ENSG00000238296.1
SCARNA16\|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13\|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
ABCA4
ADORA3
AGL
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CNN3
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
F3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
ABCD3
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TBX15
TSHB
VCAM1
CSDE1
BCAR3
CDC14A
RTCA
SLC16A4
CD101
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
LAMTOR5
AP4B1
PHTF1
AHCYL1
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
RWDD3
PTPN22
CHIA
GPSM2
SLC25A24
HAO2
SNX7
GPR88
TRMT13
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
OLFML3
AMIGO1
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
STRIP1
ZNF697
HENMT1
OLFM3
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
PIFO
C1orf162
SYT6
TMEM56
NBPF4
SLC30A7
CHIAP2
FNDC7
SASS6
UBL4B
SPAG17
HIPK1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
C1orf137
FRRS1
MIR197
NBPF6
MIR760
MIR320B1
MIR378G
MIR137HG

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.2.

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

Genes
PTEN
BMPR1A
FGFR2
TLX1
NFKB2
SUFU
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
C10ORF32
SFXN2
RN7SL21P
SNORD112\|ENSG00000253068.1
FGF8
snoU13\|ENSG00000239091.1
SNORD112\|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12\|ENSG00000212464.1
ERLIN1
snoU13\|ENSG00000238472.1
COX15
ENTPD7
snoU13\|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25\|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13\|ENSG00000238991.1
ANKRD22
SNORD74\|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
AGAP11
U3\|ENSG00000252189.1
MIR346
RNA5SP322
RN7SKP238
RN7SKP84
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
FAS
ARL3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
CPN1
CTBP2
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
GLUD1
GOT1
PRLHR
GRK5
GRID1
HABP2
HELLS
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
DCLRE1A
FRAT1
ACTR1A
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
MGEA5
PRDX3
ADIRF
VAX1
ATE1
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
PDCD4
VENTX
R3HCC1L
POLL
BLNK
KCNIP2
CUZD1
CALY
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
CCSER2
EXOC6
FAM35A
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
WBP1L
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
WDR11
FAM178A
DHX32
TDRD1
BCCIP
C10orf2
TM9SF3
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
MCMBP
C10orf95
PLEKHS1
PDZD7
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
GPR123
LZTS2
LCOR
MRPL43
AFAP1L2
PYROXD2
USMG5
ATAD1
ARHGAP19
KNDC1
MTG1
BBIP1
FANK1
OPALIN
SYCE1
OPN4
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
C10orf32
GSTO2
SFR1
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
TRUB1
VTI1A
HECTD2
FGFBP3
C10orf82
CACUL1
SLC35G1
CCDC147
PWWP2B
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
FUOM
JAKMIP3
STK32C
RBM20
FFAR4
KCNK18
LIPM
CYP26C1
NANOS1
HMX3
CCDC172
SLC16A12
CC2D2B
ARMS2
TEX36
C10orf120
FOXI2
GOLGA7B
C10orf85
C10orf62
IFIT1B
FRG2B
SPRN
MIR146B
MIR202
FAM196A
FAM25A
LIPK
LIPN
MIR607
NUTM2A
NUTM2D
TLX1NB
C10orf131
KLLN
MIR1307
MIR2110
MIR378C
MIR3157
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
ETV6
AEBP2
RN7SL67P
RN7SL459P
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75\|ENSG00000212432.1
SNORA75\|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11\|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
A2M
ARHGDIB
C3AR1
CD69
CDKN1B
CREBL2
PHC1
EMP1
EPS8
GPR19
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PTPRO
PZP
SLC2A3
MFAP5
KLRC4
YBX3
KLRG1
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
NECAP1
CLEC4E
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
PLEKHA5
MANSC1
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
APOLD1
GSG1
RERG
PLCZ1
CAPZA3
CLEC6A
LOH12CR1
TMEM52B
HIST4H4
SLC2A14
A2ML1
CLEC12A
CLECL1
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CLEC9A
C12orf36
CLEC4D
TAS2R42
CLEC2A
CLEC12B
LINC00937
ZNF705A
SMCO3
PRB2
MIR614
SLC15A5

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.33.

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

Genes
RNA5SP499
SNORA31\|ENSG00000252291.1
SNORA20\|ENSG00000201660.1
SNORA48\|ENSG00000212214.1
RN7SL578P
snoU13\|ENSG00000251848.1
LINC00102\|ENSG00000230542.1
CD99P1\|ENSG00000223773.2
LINC00106\|ENSG00000236871.2
SLC25A6\|ENSG00000169100.8
RN7SL355P\|ENSG00000265350.1
RNA5SP498\|ENSG00000223274.1
MIR3690\|ENSG00000265658.1
LINC00685\|ENSG00000226179.1
PLCXD1\|ENSG00000182378.8
SHROOM2
STS
ARSD
ARSE
ARSF
ASMT\|ENSG00000196433.6
CLCN4
CSF2RA\|ENSG00000198223.9
IL3RA\|ENSG00000185291.6
KAL1
CD99\|ENSG00000002586.13
GPR143
PRKX
SHOX\|ENSG00000185960.8
TBL1X
XG
GTPBP6\|ENSG00000178605.8
HDHD1
AKAP17A\|ENSG00000197976.6
PNPLA4
ASMTL\|ENSG00000169093.10
GYG2
ZBED1\|ENSG00000214717.4
MXRA5
VCX
PPP2R3B\|ENSG00000167393.12
VCX2
VCX3A
WWC3
NLGN4X
CRLF2\|ENSG00000205755.6
FAM9A
FAM9B
DHRSX\|ENSG00000169084.8
P2RY8\|ENSG00000182162.5
ARSH
VCX3B
MIR651
CXorf28
MIR4770
MIR4767

Genes in Wide Peak

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

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

Genes
MAP2K4
GAS7
MTND1P15
UBBP4
RN7SL426P
TMEM11
KRT16P3
NOS2P3
USP32P3
UPF3AP2
RN7SL17P
U6\|ENSG00000266839.2
CCDC144CP
SNORA31\|ENSG00000252349.1
SNORA59B
MIR1180
SNORD3C
SNORD3A
GRAPL
SNORD3D
GRAP
FAM83G
RN7SL627P
ZNF286B
TBC1D28
RN7SL639P
KRT16P1
KRT17P2
SMCR8
snoU13\|ENSG00000238691.1
MIR33B
SMCR5
SMCR2
RN7SL775P
TBC1D27
KRT17P1
KRT16P2
USP32P1
RN7SL620P
ZNF287
MIR1288
RN7SL442P
RNA5SP436
ZNF286A
SNORA74\|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13\|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
SNORA74\|ENSG00000252305.1
MIR548H3
RN7SL550P
MIR744
RPL21P122
RN7SL601P
LINC00675
MAGOH2
ADPRM
RCVRN
GLP2R
STX8
RN7SL129P
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FLII
KCNJ12
LLGL1
MFAP4
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
PMP22
MAPK7
MAP2K3
PRPSAP2
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
MYH13
NTN1
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
PIK3R5
DHRS7B
B9D1
TVP23B
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
ZNF286A
ZNF624
ELAC2
TEKT3
GID4
FAM106A
NDEL1
LRRC48
ATPAF2
SPECC1
MYOCD
USP43
ZSWIM7
SMCR7
SLC5A10
TOM1L2
SLC47A2
WDR16
CCDC42
PIK3R6
TRIM16L
MFSD6L
DHRS7C
TVP23C
CENPV
FLCN
PLD6
USP32P2
CDRT15L2
C17orf103
LINC00670
CDRT4
CCDC144B
FAM27L
LGALS9B
CCDC144NL
C17orf51
TBC1D26
CDRT1
SPDYE4
TMEM220
SHISA6
FAM211A
PIRT
EVPLL
LGALS9C
MTRNR2L1
MIR4522
MIR1269B

Genes in Wide Peak

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

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

Genes
FGFR1
PCM1
WRN
WHSC1L1
HOOK3
SNORA7\|ENSG00000201316.1
RN7SKP294
UBE2V2
CEBPD
RN7SKP32
LINC00293
RN7SKP41
U3\|ENSG00000201329.1
POTEA
RN7SL806P
snoU13\|ENSG00000238714.1
SNORD112\|ENSG00000238966.1
RN7SL149P
MIR486
SNORD65\|ENSG00000238936.1
MIR548AO
IDO1
ADAM3A
ADAM5
SNORD38\|ENSG00000207199.1
PLEKHA2
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
RNA5SP264
RN7SKP201
RN7SL457P
RN7SL621P
SNORA70\|ENSG00000252505.1
SNORD13
RNA5SP263
RNA5SP262
RNA5SP261
UBXN8
TUBBP1
FAM183CP
LINC00589
RN7SL781P
RNA5SP260
RNA5SP259
MIR4287
snoU13\|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67\|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13\|ENSG00000238466.1
U3\|ENSG00000251944.1
SNORA62\|ENSG00000201157.1
RNA5SP256
MIR548V
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
NAT1
NAT2
ADRA1A
ADRB3
ANK1
ASAH1
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CHRNB3
CLU
DPYSL2
DUSP4
EGR3
EIF4EBP1
DMTN
EPHX2
EXTL3
PTK2B
FGL1
FNTA
ADAM2
GFRA2
GNRH1
GSR
GTF2E2
NRG1
IKBKB
LOXL2
LPL
MCM4
MSR1
NEFM
PDGFRL
PLAT
PNOC
POLB
PPP2CB
PPP2R2A
PPP3CC
PRKDC
SFRP1
SFTPC
SLC7A2
SLC18A1
SLC20A2
SNAI2
STC1
TACC1
VDAC3
FZD3
TUSC3
KAT6A
ADAM18
ADAM9
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
CHRNA6
DOK2
ASH2L
BAG4
ENTPD4
PHYHIP
SORBS3
NPM2
DLC1
DCTN6
PNMA2
ADAM28
AP3M2
RBPMS
ERLIN2
LZTS1
PROSC
XPO7
TRIM35
RHOBTB2
DDHD2
KIF13B
PSD3
LEPROTL1
SPIDR
SLC39A14
GPR124
DKK4
LSM1
ADAMDEC1
CNOT7
PURG
GOLGA7
SCARA3
TMEM66
SNTG1
KCTD9
PIWIL2
ELP3
THAP1
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
C8orf4
MTUS1
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
DUSP26
HMBOX1
EFCAB1
ZMAT4
RNF122
DOCK5
TTI2
RAB11FIP1
REEP4
STMN4
RNF170
TM2D2
SGK196
GINS4
PPAPDC1B
MAK16
FUT10
CHMP7
SMIM19
GOT1L1
VPS37A
SGCZ
PXDNL
AGPAT6
UNC5D
LETM2
HGSNAT
PEBP4
CDCA2
ESCO2
FBXO16
C8orf48
KCNU1
IDO2
R3HCC1
HTRA4
ADAM32
LGI3
MICU3
SCARA5
NUGGC
C8orf86
MIR320A
C8orf22
C8orf58
MBOAT4
MIR548H4
MIR3148
MIR4288
MIR3622B
SMIM18
MIR4469

Genes in Wide Peak

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

Table S51. 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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q22.

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

Genes
BTG1
ATF1
CDK4
DDIT3
HOXC11
HOXC13
MDM2
NACA
HMGA2
WIF1
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
MYRFL
RN7SL804P
SLC35E3
SNORA70G
DYRK2
CAND1
snoU13\|ENSG00000238528.1
RN7SKP166
TMBIM4
RNA5SP362
RPSAP52
RNU6ATAC42P
snoU13\|ENSG00000238592.1
MIR548C
SNORD83
XPOT
snoU13\|ENSG00000238440.1
RPS11P6
AVPR1A
LDHAL6CP
snoU13\|ENSG00000238475.1
SNORD112\|ENSG00000252883.1
SNORA19\|ENSG00000251822.1
RN7SKP65
MIR26A2
snoU13\|ENSG00000238436.1
RN7SL312P
MIR1228
HBCBP
RDH16
SNORA48\|ENSG00000212383.1
RN7SL809P
SNORD59A
RBMS2
RNF41
RN7SL770P
MMP19
TMEM198B
ORMDL2
GLYCAM1
RN7SL744P
MIR148B
RN7SL390P
MIR615
HOXC8
HOTAIR
HOXC12
RN7SKP289
SNORD81\|ENSG00000223213.1
KRT121P
LINC00592
C12orf80
OR7E47P
POU6F1
U6\|ENSG00000272028.1
HIGD1C
RN7SL519P
MIR1293
AQP6
AQP5
BCDIN3D
PRPH
WNT1
snoU13\|ENSG00000238395.1
MIR4701
SNORA2B
SNORA2A
SNORA34
DKFZP779L1853
RPAP3
SNORA64\|ENSG00000199566.1
SCAF11
RN7SL246P
RNA5SP361
SNORA74\|ENSG00000252917.1
RN7SL10P
RNA5SP360
MUC19
SNORA22\|ENSG00000199571.1
ABCD2
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112\|ENSG00000251863.1
ASIC1
ACVR1B
ACVRL1
ADCY6
AMHR2
APAF1
APOF
AQP2
ARF3
ARL1
ASCL1
ATP2B1
ATP5B
ATP5G2
BICD1
CACNB3
CCNT1
CD63
CDK2
CMKLR1
CNTN1
COL2A1
CPM
CRY1
CS
CSRP2
CYP27B1
DGKA
DCN
EPYC
DUSP6
EIF4B
CELA1
ERBB3
B4GALNT1
BLOC1S1
GLI1
GNS
GPD1
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC9
HOXC10
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
KCNC2
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
LRP1
LTA4H
LYZ
MARS
METTL1
MIP
MYBPC1
MYF5
MYF6
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NELL2
NFE2
NFYB
CNOT2
SLC11A2
NTS
PA2G4
PAH
PCBP2
CDK17
PDE1B
PFDN5
PFKM
SLC25A3
PKP2
PMCH
PPP1R1A
PRIM1
PRKAG1
TWF1
PTPRB
PTPRR
RAB5B
RAP1B
RARG
RDH5
RFX4
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
PMEL
SMARCC2
SMARCD1
SP1
STAT2
STAT6
SUOX
SYT1
TAC3
TARBP2
TDG
TMBIM6
TFCP2
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
VDR
WNT10B
MAP3K12
TUBA1A
KMT2D
AAAS
YEATS4
ALX1
EEA1
SOAT2
PPFIA2
LGR5
NPFF
HSD17B6
GALNT4
CRADD
LIN7A
SOCS2
ENDOU
TIMELESS
KRT75
RASSF9
SLC16A7
DDX23
SLC4A8
WSCD2
ESPL1
DAZAP2
TESPA1
ZBTB39
NUAK1
PAN2
USP15
NR1H4
TROAP
DNM1L
TSFM
CTDSP2
YAF2
PLXNC1
GDF11
TMEM5
CNPY2
TUBA1B
RAPGEF3
MCRS1
DCTN2
CCT2
AVIL
PTGES3
FRS2
OS9
CKAP4
METAP2
ATF7
CPSF6
KERA
KRR1
PRDM4
PWP1
NUDT4
BAZ2A
IRAK3
GALNT6
NXPH4
GPR182
COPZ1
R3HDM2
FAIM2
MON2
UHRF1BP1L
DDN
TMEM194A
KIAA1033
TBC1D30
ESYT1
TENC1
ZDHHC17
KCNH3
GRIP1
CBX5
ANP32D
SMUG1
LEMD3
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
ZNF385A
GLS2
RND1
UTP20
KCNMB4
MRPL42
CCDC59
TBK1
RACGAP1
SENP1
PDZRN4
TRHDE
SYCP3
CHST11
IL22
DHH
CCDC53
PLEKHA8P1
YARS2
CCDC41
IRAK4
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
GPR84
SLC38A2
PRR13
KANSL2
PARPBP
SLC38A4
SLC6A15
RIC8B
APPL2
TMEM19
DRAM1
STAB2
VEZT
GOLGA2B
KIF21A
SLC48A1
SCYL2
POLR3B
LMBR1L
FGD6
IL26
NDUFA12
MDM1
ANKS1B
NDUFA4L2
CHPT1
NUP107
SMAGP
TMCC3
PPM1H
SRGAP1
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
NTN4
C12orf10
C12orf44
ARHGAP9
IKZF4
ACTR6
TBC1D15
SLC26A10
SPATS2
TMEM106C
NUP37
NABP2
GNPTAB
ACSS3
BBS10
PIP4K2C
DNAJC22
ADAMTS20
CEP290
MTERFD3
SLC38A1
CSRNP2
PUS7L
GLT8D2
THAP2
INHBE
FAM186B
USP44
SLC41A2
LRRIQ1
METTL25
TMEM117
LLPH
WIBG
SARNP
CAPS2
TUBA1C
ZC3H10
SPRYD3
MFSD5
COX14
DNAJC14
ZCRB1
CCDC65
NAV3
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
PCED1B
HELB
MARCH9
COQ10A
KRT71
LARP4
SLC2A13
MBD6
OSBPL8
ARHGEF25
C12orf56
AGAP2
DCD
RAB3IP
MUCL1
DEPDC4
LRRK2
CCDC38
FAM186A
OR2AP1
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
IKBIP
FGD4
ASCL4
BTBD11
SPIC
ANO4
ASB8
MYL6B
KRT72
PRICKLE1
AMDHD1
GLIPR1L2
CPNE8
TSPAN19
BEST3
E2F7
KRT80
C12orf66
TMTC2
TMTC3
C12orf50
ALDH1L2
GRASP
KRT78
DTX3
METTL7B
ZFC3H1
FAM71C
CCER1
ANO6
ARID2
SLC17A8
STAC3
MSRB3
OR6C74
OR6C3
TCP11L2
LINC00935
C12orf79
GLIPR1L1
POC1B
OTOGL
ZNF740
RASSF3
OR6C6
ANKRD52
SLC39A5
SPRYD4
C12orf61
DPY19L2
GAS2L3
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
C12orf74
FAM19A2
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
KRT77
C12orf42
LRRC10
C12orf68
C12orf75
OR6C1
OR6C75
OR6C76
OR6C70
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR196A2
DBX2
PLEKHG7
OR9K2
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MIR616
C12orf73
MIR1251
MIR4303
MIR3685
MIR4495
MIR4494
MIR4698
MIR5700

Genes in Wide Peak

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

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

Genes
PHOX2B
NIPAL1
RN7SKP215
snoU13\|ENSG00000238301.1
RN7SKP199
RN7SL193P
RN7SL691P
RN7SKP82
SLC30A9
LINC00682
RNA5SP160
snoU13\|ENSG00000238351.1
RHOH
SNORA51\|ENSG00000201863.1
RNA5SP159
RN7SL558P
SMIM14
MIR5591
RNA5SP158
DTHD1
snoU13\|ENSG00000238694.1
APBB2
CNGA1
GABRA2
GABRA4
GABRB1
GABRG1
UBE2K
RFC1
RPL9
TEC
TLR1
TXK
UCHL1
UGDH
TLR6
ATP8A1
CORIN
PTTG2
LIAS
LIMCH1
TBC1D1
PDS5A
KLHL5
KLF3
RBM47
OCIAD1
COMMD8
TMEM33
PGM2
C4orf19
CHRNA9
N4BP2
ATP10D
KIAA1239
SLAIN2
WDR19
GUF1
NSUN7
TMEM156
CWH43
TLR10
FAM114A1
ARAP2
OCIAD2
GNPDA2
NFXL1
SHISA3
KLB
COX7B2
SLC10A4
DCAF4L1
YIPF7
FRYL
ZAR1
KCTD8
BEND4
GRXCR1
MIR574
RELL1
MIR4802
MIR4801

Genes in Wide Peak

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

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

Genes
BUB1B
TCF12
MIR4511
snoU13\|ENSG00000238311.1
snoU13\|ENSG00000238715.1
SNORA24\|ENSG00000206903.1
CLPX
MTFMT
RN7SL348P
MIR1272
RN7SL707P
RN7SL595P
SNORA48\|ENSG00000252774.1
USP3
CA12
MIR190A
RN7SL613P
RNA5SP397
RNA5SP396
snoU13\|ENSG00000238767.1
MIR2116
C15ORF31
U3\|ENSG00000200318.1
RN7SKP95
snoU13\|ENSG00000239100.1
MYZAP
LINC00926
snoU13\|ENSG00000239035.1
RN7SL568P
snoU13\|ENSG00000238513.1
PYGO1
MIR628
RSL24D1
ONECUT1
MIR1266
U6\|ENSG00000272337.1
RN7SL354P
RNA5SP395
U6\|ENSG00000271819.1
RN7SL494P
RNA5SP394
FGF7
RN7SL307P
RN7SL577P
RN7SKP139
FKSG62
RN7SKP101
SNORD11\|ENSG00000238819.1
SNORA41\|ENSG00000207516.1
HMGN2P46
snoU13\|ENSG00000238583.1
SLC30A4
SNORA11\|ENSG00000261709.2
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13\|ENSG00000238494.1
snoU13\|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13\|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13\|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13\|ENSG00000238564.1
THBS1
FAM98B
U3\|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18\|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77\|ENSG00000212415.1
snoU13\|ENSG00000238342.1
RN7SL286P
RN7SL539P
GOLGA8O
U8\|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18\|ENSG00000206849.1
MIR211
RN7SL82P
U8\|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8\|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8\|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8\|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
RNA5SP391
LINC00929
SNORA48\|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115\|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64\|ENSG00000270704.2
SNHG14
SNURF
snoU13\|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13\|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13\|ENSG00000239083.1
CHEK2P2
RN7SL584P
ACTC1
ADAM10
ANXA2
APBA2
AQP9
BNIP2
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OAZ2
OCA2
PLCB2
PPIB
MAPK6
RAB27A
RAD51
RORA
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SPINT1
SRP14
TJP1
TP53BP1
TPM1
TYRO3
UBE3A
MKRN3
CILP
EIF3J
RAB11A
SNAP23
ALDH1A2
HERC2
HERC1
USP8
CCNB2
SLC28A2
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
PIGB
IGDCC3
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
BCL2L10
PDCD7
RASGRP1
DENND4A
GNB5
ARPP19
SLC27A2
GPR176
CHP1
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
DAPK2
EID1
NPAP1
SERF2
TMEM87A
RPAP1
BLOC1S6
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
RPS27L
NDUFAF1
NUSAP1
EMC4
RASL12
SPG21
SPTBN5
PTPLAD1
CTDSPL2
KLF13
RAB8B
DUOX1
CSNK1G1
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
PPP1R14D
DPP8
MTMR10
PARP16
ZNF770
HAUS2
RMDN3
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
EMC7
PAK6
DTWD1
CASC5
AVEN
STARD9
VPS18
IGDCC4
SQRDL
ZNF106
RFX7
SPATA5L1
CHAC1
NARG2
KATNBL1
SLTM
SNX22
ATP8B4
WDR76
TMEM62
SEMA6D
PIF1
SPG11
ELL3
PLEKHO2
POLR2M
VWA9
NIPA2
APH1B
TLN2
FAM96A
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
LDHAL6B
CHST14
CASC4
LACTB
TUBGCP5
TGM7
CATSPER2
LEO1
SLC51B
NIPA1
PLA2G4E
TRIM69
C15orf43
C2CD4A
FAM81A
C15orf65
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
FAM227B
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
SLC24A5
PRTG
GOLGA6L2
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
FBXL22
GLDN
FMN1
RBPMS2
ANKDD1A
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
GOLGA8EP
OR4M2
KBTBD13
UBAP1L
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
HERC2P9
GOLGA8B
EIF2AK4
UNC13C
MIR422A
CKMT1A
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
POTEB2
MIR1282
MIR4311
MIR4508
MIR4510
MIR4716
MIR4713
MIR4712
GCOM1
POTEB

Genes in Wide Peak

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

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

Genes
REL
BCL11A
FAHD2CP
RN7SL210P
ANKRD36C
LINC00342
FLJ14082
RN7SL575P
ANKRD20A8P
SLC9B1P2
RNA5SP100
IGKJ1
IGKJ2
IGKJ3
IGKJ4
IGKJ5
IGKC
ANKRD36BP2
FOXI3
snoU13\|ENSG00000239049.1
RNY4P15
snoU13\|ENSG00000238979.1
RGPD2
PLGLB2
PLGLB1
SNORA19\|ENSG00000251974.1
U8\|ENSG00000202537.1
MIR4779
SNORD94
RN7SKP83
ATOH8
C2orf68
RNF181
RN7SL126P
RN7SL830P
RN7SL251P
RN7SL113P
SNORD112\|ENSG00000252298.1
RN7SL201P
RNA5SP99
REG1P
RNA5SP98
RN7SKP164
RN7SKP203
MRPL19
snoU13\|ENSG00000239018.1
U3\|ENSG00000221638.1
snoU109\|ENSG00000238410.1
snoU13\|ENSG00000238521.1
POLE4
SEMA4F
PCGF1
CCDC142
MRPL53
C2orf81
MTHFD2
MOB1A
MGC10955
RNA5SP97
NOTO
SNORD78\|ENSG00000212378.1
RN7SL160P
snoU13\|ENSG00000239064.1
RN7SL470P
snoU13\|ENSG00000239072.1
snoU13\|ENSG00000238465.1
SNRNP27
GMCL1
snoU13\|ENSG00000238708.1
SNORA36C
RN7SL604P
AAK1
RNA5SP96
MIR3126
FBXO48
C1D
Vault\|ENSG00000251900.1
RN7SL635P
SNORA74\|ENSG00000272025.1
snoU13\|ENSG00000238696.1
RN7SL211P
RN7SL341P
LINC00309
ACA59\|ENSG00000251775.1
RPS4XP5
DBIL5P2
RN7SL18P
snoU13\|ENSG00000238809.1
RN7SL51P
COMMD1
SNORA70B
C2orf74
RNA5SP95
RN7SL632P
RN7SL361P
RNA5SP94
SNORD78\|ENSG00000212168.1
snoU13\|ENSG00000238690.1
ACTG2
ADD2
ADRA2B
ANXA4
ATP6V1B1
AUP1
CAPG
CD8A
CD8B
CTNNA2
DCTN1
DGUOK
DNAH6
DOK1
DUSP2
EGR4
EMX1
FABP1
GFPT1
GGCX
HK2
TLX2
MXD1
MAL
MAT2A
MDH1
MEIS1
OTX1
REG3A
PCBP1
PEX13
PLEK
PPP3R1
RAB1A
REG1A
REG1B
RTKN
SFTPB
SLC1A4
SNRPG
SPR
TACR1
GCFC2
TGFA
TIA1
UGP2
VRK2
XPO1
ZNF2
ALMS1
MOGS
RNF103
DYSF
DUSP11
VAMP8
SUCLG1
ST3GAL5
NAT8
TMSB10
EIF2AK3
USP34
SERTAD2
ARHGAP25
ACTR2
MPHOSPH10
SMYD5
CCT7
CCT4
GNLY
STAMBP
TGOLN2
B3GNT2
USP39
VAMP5
PROKR1
IMMT
RPIA
CEP68
EXOC6B
EHBP1
WBP1
VAX2
POLR1A
CNRIP1
RAB11FIP5
NFU1
BMP10
ZNF638
HTRA2
LGALSL
KCNIP3
CD207
TPRKB
FAHD2A
WDPCP
KRCC1
MRPL35
PCYOX1
VPS54
ETAA1
AFTPH
RETSAT
C2orf42
PTCD3
FANCL
THNSL2
NAGK
KDM3A
GKN1
CYP26B1
KCMF1
PNO1
PELI1
SLC4A5
TTC31
RMND5A
PAPOLG
MRPS5
REEP1
ANKRD53
LRRTM4
TCF7L1
INO80B
WDR54
FAM161A
EVA1A
ANTXR1
ELMOD3
PRADC1
KIAA1841
MCEE
LOXL3
ZNF514
FAM136A
LBX2
SFXN5
LINC00152
TEX261
WDR92
TRABD2A
TMEM150A
TRIM43
REG3G
AHSA2
M1AP
TEKT4
SMYD1
PROM2
FBXO41
GPAT2
PUS10
ASPRV1
CLEC4F
DQX1
ALMS1P
TET3
GKN2
TEX37
APLF
TMEM17
SPRED2
SH2D6
FIGLA
LRRTM1
C2orf78
BOLA3
FUNDC2P2
PAIP2B
RGPD1
ASTL
MIR4264
CHMP3
MIR4433
MIR4436A
MIR4780
MIR4778
MIR4432
MIR5000
MIR5192

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 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	0.08	-2.21	1	0.31	5.68	3.83e-08
1q	1195	0.22	1.83	0.168	0.23	2.02	0.0622
2p	624	0.26	0.59	1	0.10	-3.79	1
2q	967	0.27	2.38	0.0488	0.05	-4.07	1
3p	644	0.18	-1.68	1	0.11	-3.58	1
3q	733	0.21	-0.363	1	0.08	-3.93	1
4p	289	0.08	-4.75	1	0.38	2.68	0.0113
4q	670	0.05	-4.33	1	0.41	5.3	2.92e-07
5p	183	0.24	-1.45	1	0.22	-2.01	1
5q	905	0.17	-1.05	1	0.30	2.98	0.00476
6p	710	0.24	0.441	1	0.14	-2.43	1
6q	556	0.24	-0.245	1	0.18	-1.77	1
7p	389	0.62	10	0	0.05	-4.05	1
7q	783	0.52	9.37	0	0.04	-3.94	1
8p	338	0.33	1.05	0.655	0.64	9.6	0
8q	551	0.55	8.13	1.48e-15	0.25	0.0461	1
9p	301	0.29	0.18	1	0.19	-2.23	1
9q	700	0.23	0.0415	1	0.17	-1.55	1
10p	253	0.10	-4.86	1	0.22	-1.99	1
10q	738	0.05	-4.79	1	0.25	0.585	0.657
11p	509	0.22	-0.992	1	0.18	-2.05	1
11q	975	0.18	-0.406	1	0.23	0.977	0.438
12p	339	0.23	-1.42	1	0.17	-2.73	1
12q	904	0.15	-1.69	1	0.15	-1.52	1
13q	560	0.72	13.6	0	0.15	-1.59	1
14q	938	0.08	-2.92	1	0.43	7.13	3.24e-12
15q	810	0.03	-4.28	1	0.45	7.24	1.75e-12
16p	559	0.26	0.38	1	0.07	-4.56	1
16q	455	0.26	0.000578	1	0.13	-3.28	1
17p	415	0.07	-3.23	1	0.69	12	0
17q	972	0.22	0.886	0.751	0.20	0.196	0.938
18p	104	0.19	-1.5	1	0.82	13.8	0
18q	275	0.12	-1.76	1	0.87	16.4	0
19p	681	0.19	-1.21	1	0.20	-0.892	1
19q	935	0.22	0.468	1	0.16	-1.24	1
20p	234	0.74	11	0	0.54	4.64	7.78e-06
20q	448	0.88	17.4	0	0.32	0.684	0.617
21q	258	0.10	-4.05	1	0.44	4.09	8.61e-05
22q	564	0.08	-3.94	1	0.37	3.55	0.00071
Xq	668	0.23	-0.0913	1	0.20	-0.875	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/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/READ-TP/11448905/GDAC_MergeDataFiles_11451441/READ-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat
CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.7
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 165 Input Tumor Samples.

Tumor Sample Names
TCGA-AF-2687-01A-02D-1732-01
TCGA-AF-2689-01A-01D-1549-01
TCGA-AF-2690-01A-02D-1732-01
TCGA-AF-2691-01A-01D-1549-01
TCGA-AF-2692-01A-01D-0819-01
TCGA-AF-2693-01A-02D-1732-01
TCGA-AF-3400-01A-01D-1549-01
TCGA-AF-3911-01A-01D-1732-01
TCGA-AF-3913-01A-02D-1428-01
TCGA-AF-4110-01A-02D-1732-01

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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