SNP6 Copy number analysis (GISTIC2)

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 2.0.23.

Summary

There were 38 tumor samples used in this analysis: 21 significant arm-level results, 23 significant focal amplifications, and 15 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 - 23 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
8q24.21	3.7753e-09	4.6953e-09	chr8:128140001-128220000	1
7p11.2	1.354e-05	1.4269e-05	chr7:54430001-55769999	10
14q13.3	8.1206e-08	8.7269e-05	chr14:36600002-36640000	0 [NKX2-8]
12q15	1.9704e-06	0.0006131	chr12:69110002-69210000	0 [CPSF6]
5p15.33	0.0041394	0.0041394	chr5:1020002-1310000	8
20q13.31	0.00021234	0.0068959	chr20:57230001-59040000	35
20q13.33	0.00026442	0.017225	chr20:62820001-64444167	68
Xq27.3	0.0052183	0.031966	chrX:108150001-156040895	424
Yq11.223	0.040752	0.040752	chrY:20120001-20180000	0 [TTTY10]
1q32.1	0.044469	0.044469	chr1:192140001-210790000	199
19q12	0.05747	0.05747	chr19:29020001-29880000	7
5q35.1	0.059783	0.059783	chr5:169550001-181380000	169
7q11.21	0.056998	0.065107	chr7:65770001-65840000	1
8q24.3	0.00029234	0.069715	chr8:144170002-145138636	46
21p12	0.069715	0.069715	chr21:6780001-6950000	1
11q13.3	0.083912	0.083912	chr11:68860001-70350000	22
14q13.3	8.1206e-08	0.086375	chr14:35980002-37170000	10
Xq21.31	0.056998	0.095057	chrX:90320001-96379999	8
14q32.33	0.10086	0.11264	chr14:105520002-107043718	14
17q12	0.11728	0.11728	chr17:38700001-39870000	39
6p21.1	0.1476	0.1476	chr6:41530001-42000000	13
12p11.21	0.16574	0.16574	chr12:32300001-32639999	2
12q15	1.9704e-06	0.19654	chr12:67130002-70860000	37

Genes in Wide Peak

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

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

Genes
MIR1208

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2
VOPP1
VSTM2A
VSTM2A-OT1
FKBP9P1
EGFR-AS1
LOC100996654
ELDR

Genes in Wide Peak

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

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

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
MIR4457
MIR4635
CTD-3080P12.3

Genes in Wide Peak

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

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

Genes
GNAS
ATP5E
BMP7
CTSZ
PCK1
RAE1
STX16
VAPB
SPO11
PRELID3B
NELFCD
PPP4R1L
RBM38
PMEPA1
RAB22A
LOC79160
NPEPL1
TUBB1
ZBP1
C20orf85
CTCFL
ANKRD60
APCDD1L-AS1
GNAS-AS1
APCDD1L
MIR296
MIR298
MIR4325
MTRNR2L3
SLMO2-ATP5E
STX16-NPEPL1
MIR4532
LOC101927932
LOC105372695
NKILA

Genes in Wide Peak

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

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

Genes
hsa-mir-941-3
CHRNA4
COL9A3
EEF1A2
NPBWR2
KCNQ2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
TCFL5
DIDO1
PRPF6
GMEB2
STMN3
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
GID8
PCMTD2
ARFGAP1
SLC2A4RG
ZNF512B
COL20A1
SLC17A9
LOC63930
FNDC11
PPDPF
BIRC7
DNAJC5
ZGPAT
HELZ2
BHLHE23
NKAIN4
ZBTB46
SAMD10
ABHD16B
LINC00266-1
LKAAEAR1
LINC00176
MIR124-3
MIR647
HAR1A
HAR1B
UCKL1-AS1
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100130587
DPH3P1
LINC00029
LINC01056
FLJ16779
MIR1914
MIR4326
MIR3196
LOC100505771
RTEL1-TNFRSF6B
ZBTB46-AS1
MIR6813

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq27.3.

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-220a
AGTR2
ABCD1
SLC25A5
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CAPN6
CD40LG
CDR1
CETN2
CLIC2
CNGA2
COL4A5
COL4A6
TEX28
DCX
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
ACSL4
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
GLUD2
GRIA3
GUCY2F
HCFC1
HMGB3
HPRT1
HTR2C
IDH3G
IDS
IGSF1
IL9R
IL13RA1
IL13RA2
IRAK1
L1CAM
LAMP2
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
NDUFA1
OCRL
PAK3
PLS3
PLXNB3
OPN1LW
RENBP
RPL10
RPL39
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
TDGF1P3
TRPC5
UBE2A
VBP1
XPNPEP2
ZIC3
ZNF75D
RNF113A
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
CUL4B
IRS4
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
TMEM257
GPR50
RAB33A
ARHGEF6
MAGEC1
AMMECR1
ZBTB33
MAMLD1
BCAP31
TENM1
SPRY3
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
PGRMC1
TREX2
SLC6A14
SEPT6
ATP1B4
KCNE5
LDOC1
FAM127B
SRPK3
SNORA70
SNORA69
SNORD61
RNU6-1
RBMX
HTATSF1
MCTS1
C1GALT1C1
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
LUZP4
TFDP3
MAGEC2
VGLL1
RBMX2
STK26
SASH3
WDR44
CT55
TMEM255A
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45BP
GABRQ
NXT2
NKRF
MOSPD1
THOC2
KIAA1210
RGAG1
PDZD4
LRCH2
RAP2C
FAM3A
BCORL1
CXorf56
SPANXD
SPANXC
UPF3B
FUNDC2
PRRG3
BRCC3
NKAP
MAP7D3
LONRF3
ALG13
GPR101
CD99L2
USP26
TMEM164
PHF6
RHOXF2
TMEM185A
SLITRK2
MIR503HG
PNMA6A
FATE1
HS6ST2
FRMD7
KLHL13
CHRDL1
CXorf40A
FAM58A
MMGT1
PNMA5
ATG4A
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
ADGRG4
GAB3
PNCK
ZFP92
ACTRT1
GPR119
RBMXL3
DOCK11
AMOT
CSAG1
FMR1NB
LINC00889
ARHGAP36
AKAP14
RHOXF1
NKAPP1
CH17-340M24.3
FAM122B
FAM122C
ZCCHC12
CT83
SLC25A43
INTS6L
ZNF449
VMA21
CTAG1A
CT47A11
MAGEA2B
ATP11C
LINC00632
FIRRE
DCAF12L2
LOC340581
ZCCHC16
LHFPL1
SOWAHD
OR13H1
CCDC160
CXorf66
LOC389895
UBE2NL
CSAG3
SMIM10L2A
LINC00890
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR224
MIR92A2
FAM127C
CT45A3
CT45A5
SPANXN4
H2AFB2
H2AFB1
F8A2
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR448
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
DANT2
CT47B1
SMIM10
SMIM10L2B
LOC645188
CT47A7
MIR542
SNORA35
SNORA36A
SNORA56
SNORD96B
MIR652
DDX11L16
CT47A10
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
OPN1MW2
SPANXB1
CT45A2
MIR767
MIR766
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100126447
WASIR1
LINC00892
GPR50-AS1
CXorf51A
LINC00633
TEX13C
FGF13-AS1
HSFX2
PRR32
CSAG4
LINC00893
SMIM9
FAM223A
CMC4
LINC00894
LOC100287728
MIR1184-1
MIR513C
MIR1912
MIR1298
MIR320D2
MIR1277
MIR1911
MIR1264
SLC25A5-AS1
MIR718
MIR513B
MIR764
MIR2114
TRPC5OS
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
MIR4329
MIR3672
HSFX1
LINC00629
LOC100506790
CT47A12
MAGEA10-MAGEA5
MIR4454
MIR3978
MIR664B
HCFC1-AS1
HS6ST2-AS1
DDX26B-AS1
LCA10
CT45A7
OPN1MW3
LINC00850
MAGEA8-AS1
PLS3-AS1
LOC101927830
LINC01285
LOC101928336
LOC101928358
LOC101928402
LOC101928437
LOC101928495
RAP2C-AS1
LOC101928917
RHOXF1P1
RHOXF1-AS1
RNU6-7
MIR6087
MIR6858
MIR892C
CT45A10
CT45A9
RNU6-2
LINC01201
LINC01402
LOC105373338
LOC105373368
LOC105373378
LOC105373383
LOC105377213
XACT

Genes in Wide Peak

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

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

Genes
ELK4
MDM4
SLC45A3
ADORA1
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1S
CD34
CHI3L1
CHIT1
CR1
CR1L
CR2
CSRP1
CTSE
CD55
EIF2D
ELF3
F13B
FMOD
NR5A2
GPR25
CFH
CFHR1
CFHR2
HSD11B1
IL10
IRF6
KCNH1
KISS1
LAD1
LAMB3
CD46
MYBPH
MYOG
PPP1R12B
CDK18
PFKFB2
PIGR
PIK3C2B
PKP1
PLXNA2
PRELP
PTPN7
PTPRC
RABIF
RBBP5
REN
RGS1
RGS2
RGS13
RNPEP
SNRPE
TROVE2
CNTN2
TNNI1
TNNT2
BTG2
DYRK3
PPFIA4
B3GALT2
RAB29
FCMR
MAPKAPK2
GPR37L1
SOX13
IKBKE
ZC3H11A
TMCC2
KIF14
TIMM17A
LRRN2
KDM5B
CFHR4
CFHR3
IL24
PLEKHA6
KIF21B
NFASC
CAMSAP2
SRGAP2
CRB1
ZNF281
PHLDA3
DSTYK
LMOD1
OPTC
DIEXF
UBE2T
IL19
G0S2
IL20
GLRX2
ADIPOR1
UCHL5
CYB5R1
LAX1
KLHDC8A
ETNK2
YOD1
IPO9
HHAT
C1orf106
SERTAD4
LHX9
CAMK1G
KLHL12
LGR6
RGS18
NUCKS1
C1orf116
CDC73
TRAF3IP3
CFHR5
NUAK2
DDX59
RASSF5
FCAMR
LINC00260
PPP1R15B
NAV1
IGFN1
TMEM183A
LEMD1
SLC26A9
ATP6V1G3
ARL8A
SYT2
LINC00628
GOLT1A
NEK7
C1orf74
LOC148696
LOC148709
PTPRVP
MFSD4A
PM20D1
SHISA4
DENND1B
TMEM9
SLC41A1
SYT14
ASPM
LINC00303
LEMD1-AS1
LOC284578
LOC284581
RAB7B
KCNT2
ZBTB41
RPS10P7
C1orf53
TMEM81
MIR181B1
MIR205
MIR181A1
MIR29B2
MIR29C
RGS21
C1orf186
MIR135B
LINC00862
SERTAD4-AS1
MGAT4EP
MIR205HG
ASCL5
SNORA77
FAM72A
LINC01136
C1orf132
MIR181A1HG
MIR1231
MIR1278
ZBED6
MIR4260
PCAT6
LOC100506747
LINC01353
MIR4426
MIR4735
MIR5191
IPO9-AS1
BLACAT1
LINC01031
LOC101929224
LOC101929441
LOC101930114
MIR6740
MIR6769B
MIR6739
LINC01032
LINC01222
LOC103021295
LOC103021296
LINC01221
LOC105372897
SCARNA18B

Genes in Wide Peak

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

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

Genes
CCNE1
UQCRFS1
POP4
PLEKHF1
C19orf12
LOC284395
VSTM2B

Genes in Wide Peak

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

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

Genes
NPM1
TLX3
NSD1
RANBP17
BNIP1
CANX
CLTB
NKX2-5
DBN1
DOCK2
DRD1
DUSP1
F12
FGFR4
FOXI1
FLT4
GABRP
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
KCNMB1
LCP2
LTC4S
MGAT1
MSX2
MAPK9
PROP1
SLC34A1
SNCB
STK10
ZNF354A
STC2
FGF18
SQSTM1
ATP6V0E1
PDLIM7
ADAMTS2
MAML1
GFPT2
RACK1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
FBXW11
ZNF346
TSPAN17
OR2V1
PRELID1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
SPDL1
NHP2
RNF130
KIAA1191
ERGIC1
CLK4
CNOT6
GMCL1P1
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
PHYKPL
UNC5A
TRIM41
BOD1
COL23A1
UBTD2
SCGB3A1
SFXN1
GPRIN1
ZNF354B
C5orf47
C5orf58
OR2Y1
CREBRF
BTNL9
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
LINC01366
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
OR2V2
ZNF454
C5orf60
PRR7-AS1
PFN3
ZNF879
SIMC1
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
SMIM23
CBY3
FAM153C
SNORA74B
LOC728554
AACSP1
LINC00847
OR4F29
FAM196B
LOC100132062
LOC100268168
LOC100288254
MIR1229
MIR1271
MIR4281
MIR3912
LINC01187
LOC100507387
TRIM52-AS1
MIR4634
MIR4638
MIR378E
MIR5003
HEIH
LOC100996385
LOC100996419
CTD-2270F17.1
LOC101928093
LINC01484
LINC01485
LINC01411
LOC101928445
CTC-338M12.4
MIR8056
MIR8089
LINC01574
LOC102577426
LOC105377716
LOC105377763

Genes in Wide Peak

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

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

Genes
LOC441242

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.3.

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

Genes
RECQL4
GPT
HSF1
TONSL
RPL8
ZNF7
ZNF16
DGAT1
FOXH1
LRRC14
BOP1
FBXL6
COMMD5
CPSF1
CYHR1
VPS28
SLC39A4
ZNF250
C8orf33
SLC52A2
ARHGAP39
ZNF34
SCRT1
PPP1R16A
ZNF251
KIFC2
MFSD3
ADCK5
ZNF252P
TMED10P1
ZNF252P-AS1
ZNF517
TMEM249
C8orf82
LRRC24
SCX
MROH1
MIR939
TONSL-AS1
MIR1234
LOC101928902
MIR6848
MIR7112
MIR6850
MIR6893
MIR6849

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21p12.

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

Genes
MIR8069-1

Genes in Wide Peak

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

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

Genes
CCND1
FGF3
FGF4
IGHMBP2
PPFIA1
FADD
FGF19
MYEOV
ANO1
MRGPRD
MRGPRF
MRPL21
TPCN2
ORAOV1
LOC338694
ANO1-AS2
MIR548K
MIR3164
MRGPRF-AS1
LINC01488
LOC101928443
LOC102724265

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.3.

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

Genes
NKX2-1
PAX9
NKX2-8
MBIP
SLC25A21
SFTA3
NKX2-1-AS1
MIR4503
PTCSC3
LINC00609

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq21.31.

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

Genes
NAP1L3
PCDH11X
PABPC5
FAM133A
BRDTP1
MIR548M
MIR4454
PABPC5-AS1

Genes in Wide Peak

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

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

Genes
ELK2AP
ADAM6
FAM30A
TMEM121
LINC00226
LINC00221
MIR4507
MIR4538
MIR4539
MIR4537
MIR5195
MIR7641-2
MIR8071-1
LOC105370697

Genes in Wide Peak

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

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

Genes
ERBB2
LASP1
MLLT6
CACNB1
GRB7
NEUROD2
PNMT
MED1
PSMB3
RPL19
PCGF2
PIP4K2B
TCAP
RPL23
STARD3
IKZF3
CDK12
CWC25
PLXDC1
PPP1R1B
MIEN1
FBXL20
PGAP3
ZPBP2
CISD3
LRRC37A11P
STAC2
C17orf98
ARL5C
FBXO47
SNORA21
LOC100131347
LINC00672
MIR4728
MIR4726
MIR4734
MIR4727
MIR6779
LOC105371766

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
BYSL
MDFI
PGC
MED20
FRS3
USP49
PRICKLE4
FOXP4
TOMM6
MIR4641
FOXP4-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p11.21.

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

Genes
BICD1
FGD4

Genes in Wide Peak

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

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

Genes
MDM2
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
YEATS4
DYRK2
CCT2
FRS2
CPSF6
KCNMB4
IL22
SLC35E3
IL26
CAND1
MDM1
NUP107
RAB3IP
BEST3
MYRFL
LRRC10
LOC100130075
MIR1279
SNORA70G
MIR3913-2
MIR3913-1
LOC100507175
LOC100507195
LOC100507250
IFNG-AS1
LOC101927901
LINC01479
LOC101928002
LINC01481

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

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
9p21.3	1.2537e-16	1.2537e-16	chr9:21550002-22450000	5
17p13.1	2.1705e-07	2.1705e-07	chr17:130001-64159999	1190
21q11.2	4.8143e-07	4.8143e-07	chr21:9820002-14110000	13
8p23.1	2.2851e-05	2.2851e-05	chr8:1-17159999	144
22p11.2	7.4032e-05	7.4032e-05	chr22:10960001-16939999	14
13q11	0.00061291	0.00065333	chr13:1-24170000	51
1p21.3	0.0037072	0.0037072	chr1:73290002-119910000	380
Yq11.223	0.0024868	0.0037072	chrY:14780001-56979030	49
10q25.1	0.044653	0.042571	chr10:78020001-133797422	521
Xp21.1	0.068113	0.076567	chrX:1-43239999	232
19q13.33	0.11377	0.11128	chr19:38620002-58617616	850
20p12.3	0.11128	0.11128	chr20:1-25619999	246
6q25.3	0.13845	0.13845	chr6:57300001-170805979	609
12p13.1	0.19573	0.19351	chr12:1-133275309	1341
Yq12	0.07892	0.22698	chrY:1-57227415	117

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
MTAP
CDKN2A-AS1
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
BRCA1
CD79B
CLTC
COL1A1
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
PER1
RARA
MAP2K4
TP53
TAF15
GAS7
USP6
SUZ12
BRIP1
MSI2
ABR
ACACA
ACADVL
ASIC2
ACLY
ADORA2B
AP2B1
ALDH3A1
ALDH3A2
ALDOC
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
AOC2
ARL4D
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
ATP5G1
ATP6V0A1
BLMH
C1QBP
FMNL1
CA4
CACNB1
CD68
CDC6
CDC27
CHAD
CHD3
CHRNB1
CHRNE
CCR7
CNP
COX10
COX11
CPD
CLDN7
CRHR1
CRK
CRYBA1
CSF3
CSH1
CSH2
CSHL1
CTNS
CYB561
ACE
DHX8
DLG4
DLX3
DLX4
DNAH9
DPH1
DRG2
DUSP3
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
ERN1
EVI2A
EVI2B
EZH1
FGF11
FOXO3B
FLII
FLOT2
GAST
FZD2
G6PC
KAT2A
GFAP
GH1
GH2
GIP
GNGT2
GP1BA
CCR10
GPS2
GRB7
GRN
GUCY2D
HCRT
HIC1
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HSD17B1
ICAM2
IFI35
IGFBP4
ITGA2B
ITGA3
ITGAE
ITGB3
JUP
KCNJ12
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS9
LHX1
LIG3
LLGL1
LPO
NBR1
MAPT
ADAM11
MEIS3P1
MAP3K3
MEOX1
MFAP4
MNT
MPO
MPP2
MPP3
TRIM37
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYL4
MYO1C
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NOS2
NSF
NUP88
OMG
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
PDK2
SERPINF1
PEX12
PFAS
PFN1
PHB
PITPNA
PLD2
SERPINF2
PMP22
PNMT
SEPT4
POLR2A
MED1
PPY
MAPK7
MAP2K3
PRPSAP2
PSMB3
PSMB6
PYY
PSMC5
PSMD3
PSMD11
RAB5C
RAD51C
RAD51D
RCVRN
RNU2-1
RPA1
RPL19
RPL23A
RPL26
RPL27
RPS6KB1
SCN4A
SCO1
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SRSF1
SGCA
SH3GL1P1
SH3GL1P2
SHBG
SHMT1
SLC2A4
SLC4A1
SLC6A4
SMARCD2
SMARCE1
SOX15
SP2
SREBF1
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
VAMP2
TADA2A
TBX2
HNF1B
MLX
THRA
TNFAIP1
TOP2A
TOP3A
DNAJC7
TUBG1
UBB
UBE2G1
UBTF
TRPV1
VTN
WNT3
WNT9B
YWHAE
ZNF18
PCGF2
TRIM25
VEZF1
RNF112
ZNF207
ZNF232
RND2
COIL
AKAP1
EPX
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
PIP4K2B
SLC25A11
SPOP
DOC2B
FOXN1
PPM1D
CNTNAP1
DGKE
COPS3
TCAP
SCARF1
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
TNK1
ABCC3
MYH13
TNFSF13
TNFSF12
TMEM11
KSR1
CDK5R1
CACNA1G
HAP1
MAP3K14
TM4SF5
SPAG9
SLC13A2
UNC119
MTMR4
RABEP1
KCNAB3
AURKB
TIAF1
NOG
TSPOAP1
ZNHIT3
GLP2R
EFTUD2
RPL23
NTN1
STX8
PIGL
TBX4
RPH3AL
FXR2
NPEPPS
MPDU1
GOSR1
SPAG7
CCL4L2
GOSR2
NR1D1
NCOR1
TRAF4
KIAA0100
ULK2
CCDC144A
ACAP1
TBKBP1
PLEKHM1
KIAA0753
MED24
LRRC37A
MRC2
SGSM2
ARHGAP44
HS3ST3B1
HS3ST3A1
MED13
HDAC5
TOM1L1
GJC1
TOB1
PSME3
EIF1
NBR2
SLC35B1
DCAF7
CALCOCO2
RAMP2
PEMT
CLEC10A
HOXB13
VAT1
APPBP2
MYBBP1A
FBXW10
PRPF8
P3H4
HEXIM1
SPAG5
TRIM16
IGF2BP1
CCT6B
RAI1
KIF1C
GRAP
C1QL1
RUNDC3A
STARD3
CBX1
TLK2
DDX52
DUSP14
KAT7
AKAP10
NXPH3
SNF8
SYNRG
DDX42
GABARAP
CASC3
IKZF3
ZNF652
PPM1E
NLRP1
ARHGEF15
EPN2
SARM1
RAP1GAP2
CAMTA2
GPATCH8
KDM6B
ZZEF1
MPRIP
CLUH
SMG6
WSCD1
USP22
CTDNEP1
KCNH4
TNFRSF13B
MMD
PIK3R5
ELP5
FAM215A
PPY2P
PYY2
SHPK
AIPL1
DHRS7B
KRT23
RNF167
TMEM98
POLDIP2
TBC1D29
TANC2
WSB1
SENP3
OR1A2
ERAL1
AATF
OR4D1
SNORD4B
SNORD4A
SNORA67
SNORD49A
SNORD42B
SNORD42A
SNORD3B-1
PELP1
B9D1
TUBG2
TMEM97
NKIRAS2
COA3
GIT1
RANGRF
PSMC3IP
SNX11
TIMM22
TBX21
SOCS7
TAX1BP3
MINK1
GEMIN4
SOST
MED31
DERL2
TVP23B
GLOD4
YBX2
UTP18
RNFT1
MYO15A
TUBD1
RAPGEFL1
TACO1
ABI3
COPZ2
MRPL27
PIPOX
ARL17A
CRLF3
TRPV2
ANKFY1
SLC25A39
MRPS23
PTRH2
RASD1
NLK
LUC7L3
HIGD1B
CDK12
INPP5K
KRT20
NLE1
FAM64A
XAF1
FNDC8
BORCS6
MBTD1
BCAS3
CWC25
ALKBH5
RNF43
TTC19
MKS1
LINC00483
EPN3
SLC52A1
LRRC37A4P
MED9
SLFN12
WRAP53
PNPO
KLHL11
MRM3
SMG8
SLC47A1
TMEM100
VPS53
RHOT1
RSAD1
COPRS
LRRC59
NCBP3
MSX2P1
TSR1
FAM222B
PRR11
ADAP2
UTP6
GSDMB
TEX14
DHX33
CA10
NT5M
ATXN7L3
ADPRM
CCDC47
PLSCR3
PLXDC1
LYZL6
ZNF286A
ZNF287
INTS2
NUFIP2
ZNF624
TAOK1
NLGN2
ARHGAP23
PHF12
ZBTB4
CXCL16
TRAPPC1
PCTP
SCPEP1
ALOXE3
ELAC2
FKBP10
SRR
HEATR6
XYLT2
C17orf75
NXN
TEKT3
SPATA20
UBE2Z
WNK4
C17orf53
MIS12
GID4
METTL16
TMUB2
DHX58
PHF23
MMP28
DHRS11
PRR15L
DHX40
TEFM
ACBD4
FAM57A
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
FAM106A
CTC1
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
LIMD2
KCNH6
FAM117A
NDEL1
VMP1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
PITPNM3
DRC3
EMC6
TTC25
RILP
TEKT1
KRTAP4-12
RAB34
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
GSG2
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
ZMYND15
CAMKK1
RPAIN
RNF135
MIEN1
MRPL45
VPS25
TMEM107
NAA38
TMEM101
PRAC1
RAB11FIP4
NEURL4
GHDC
KRTAP4-4
ZNF594
KIF2B
HES7
USP32
PPP1R9B
SPATA22
MGC12916
TXNDC17
CORO6
TNS4
FBXL20
MIR22HG
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
SSH2
TP53I13
IFT20
LRRC46
SCRN2
AOC4P
ANKRD40
ZNF830
SLFN11
RASL10B
ATPAF2
TMEM88
STRADA
PRR29
SPECC1
G6PC3
ASB16
PGAP3
MYOCD
PIGS
HSPB9
ORMDL3
CDRT7
CDRT8
CDRT15P1
SAT2
PLCD3
SLC46A1
TMEM106A
LRRC37B
SMYD4
OSBPL7
NT5C3B
ABHD15
TLCD1
CNTROB
FTSJ3
RFFL
RPL29P2
HSF5
OR4D2
ZPBP2
CYB5D1
OVCA2
USP43
KRBA2
C17orf64
SPATA32
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
FLJ40194
B4GALNT2
SPACA3
SGK494
SEZ6
ANKRD13B
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
EFCAB13
MRPL10
WDR81
GJD3
KRT222
KRT40
LRRC75A-AS1
ZSWIM7
MIEF2
SLC5A10
DYNLL2
SMCR5
SMCR8
TOM1L2
DNAH2
RTN4RL1
TCAM1P
EFCAB3
SLC47A2
CDRT15
CFAP52
CCDC42
PIK3R6
ODF4
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
TMEM199
PROCA1
DHRS13
KCTD11
CRHR1-IT1
LINC00974
TRIM16L
WIPF2
KRT25
TMEM99
ANKFN1
MARCH10
MFSD6L
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
TRPV3
SLC16A11
FBXO39
SPPL2C
KRT28
USP32P1
KRT24
DHRS7C
TVP23C
CENPV
FLCN
PLD6
ARHGAP27
ZNF385C
SAMD14
LYRM9
SLC16A13
C17orf74
RDM1
SPNS3
USP32P2
GAS2L2
STH
MTVR2
STXBP4
CACNA1G-AS1
TBC1D28
TMEM256
TAC4
BCL6B
CDRT15L2
NATD1
HEATR9
LOC284009
VMO1
LOC284023
LINC00324
LINC00670
CDRT4
CCDC144B
KANSL1
C17orf105
FAM171A2
MEIOC
TTLL6
LOC284080
C17orf47
KRT18P55
NEK8
PIGW
C17orf78
YWHAEP7
CISD3
GSDMA
SLC13A5
TMEM102
KRT42P
PTRF
FAM27E5
FLJ36000
GDPD1
LGALS9B
TUSC5
KLHL10
LOC339166
TMEM95
METTL2A
CCDC144NL
ASB16-AS1
C17orf67
KRT17P5
LOC339260
C17orf51
MSL1
SMTNL2
NACA2
KRT27
SLFN14
LRRC37A11P
STAC2
SKA2
CCL15-CCL14
CCDC144CP
TBC1D26
KRT26
RFLNB
PRAC2
HILS1
CDRT1
SPEM1
EFCAB5
RNF126P1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
SHISA6
LRRC75A
TMIGD1
CCL4L1
C17orf98
LINC00671
CCDC103
RPRML
YPEL2
LOC388406
C17orf82
LOC388436
OR3A4P
ARL5C
KRT39
SLC25A35
MYO18A
C17orf97
MED11
KRT16P2
FLJ35934
GRAPL
C17orf102
TOB1-AS1
PRR29-AS1
CUEDC1
HOXB-AS3
MIR10A
MIR132
MIR142
MIR144
MIR152
MIR193A
MIR195
MIR196A1
MIR21
MIR212
MIR22
MIR301A
TNFSF12-TNFSF13
TBC1D3B
TBC1D3C
CCL3L3
RNASEK
CCDC144NL-AS1
TBC1D3P5
SUZ12P1
LOC440434
GPR179
LOC440446
TBC1D3P2
MIR324
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451A
MIR497
SNORA21
SLC35G6
RNF222
GSG1L2
PIRT
LOC644172
KANSL1-AS1
CDRT15P2
FAM83G
KRT16P3
EVPLL
WFDC21P
SEBOX
SNORA48
SNORD10
OR1D4
KRTAP4-11
MRPL45P2
SCGB1C2
TBC1D3P1-DHX40P1
LOC653653
LGALS9C
NME1-NME2
SCARNA20
SCARNA21
SNORA50C
SNORA59A
SNORD7
SNORD49B
SNORD65
SNORD91A
SNORD91B
SNORD104
MIR33B
MIR632
MIR633
SNORD118
BHLHA9
TLCD2
KRTAP4-8
KRTAP1-4
KRTAP2-2
KRTAP9-1
LOC728392
NSFP1
FLJ45513
KRT16P1
ZNF286B
LOC729683
TBC1D3
TBC1D3H
KRTAP2-3
MIR454
SNORD3A
SNORD3C
SNORD3D
MIR744
MIR365B
LOC100128006
LOC100128288
MYHAS
MAPT-AS1
FAM106CP
MAPT-IT1
C17orf107
LINC00910
LOC100130950
LOC100131347
DBIL5P
KRTAP4-9
KRTAP4-7
MAP3K14-AS1
KCNJ18
C17orf96
RAMP2-AS1
LOC100287072
LOC100288866
LINC00675
MIR1288
MIR1253
MIR1203
MIR1180
MIR548H3
PITPNA-AS1
MIR2117
MIR3183
MIR4315-2
MIR2909
MIR3185
MIR4314
MIR3184
MIR4315-1
MTRNR2L1
MIR3614
LINC00672
LRRC3C
KRTAP9-7
KRTAP16-1
LOC100505782
ARL17B
SP2-AS1
LOC100506371
LOC100506388
SPAG5-AS1
C17orf112
AA06
ALOX12-AS1
SLFN12L
MIR497HG
TSPOAP1-AS1
MAGOH2P
KRTAP9-6
RAD51L3-RFFL
RNASEK-C17orf49
TMEM256-PLSCR3
KRTAP29-1
TVP23C-CDRT4
LRRC37A8P
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4523
MIR4731
MIR4728
MIR4726
MIR4734
MIR4729
MIR4737
MIR4736
MIR4724
MIR4733
MIR451B
MIR4522
MIR4732
MIR4723
MIR4520-1
MIR4521
MIR4727
MIR5096
MIR4725
MIR4520-2
MIR1269B
ALOX15P1
MIR548AT
MIR5010
MIR5089
NARR
RAI1-AS1
EPN2-AS1
COX10-AS1
LINC00854
EPN2-IT1
HOXB-AS1
PTGES3L
PTGES3L-AARSD1
FAM106B
LOC100996842
TBC1D3G
TBC1D3K
TBC1D3L
LOC101060389
LINC01563
TMEM220-AS1
SNORD124
LOC101559451
RUNDC3A-AS1
LINC01180
LOC101927018
LOC101927166
LOC101927207
LOC101927230
LOC101927239
LOC101927274
LOC101927539
LOC101927557
CCDC182
LOC101927666
SEPT4-AS1
LOC101927727
LINC01476
LOC101927755
LOC101927839
LOC101927855
LOC101927877
LOC101927911
LOC101928000
LOC101928266
LOC101928418
LOC101928475
LOC101928567
RARA-AS1
LOC101929767
MIR378J
MIR6129
MIR6165
MIR6776
MIR6777
MIR6779
MIR6781
MIR6782
MIR6784
MIR6864
MIR6865
MIR6867
MIR6883
MIR6780A
MIR6510
MIR6778
MIR6783
MIR6884
MIR8059
MIR6866
LOC102723471
TBC1D3E
LOC102724009
THCAT158
LOC102724532
LOC102724596
TBC1D3I
LOC103021295
TBX2-AS1
TMEM92-AS1
CRHR1-IT1-CRHR1
LOC105371430
LOC105371485
LOC105371506
SMCR2
LOC105371592
LOC105371703
LOC105371730
LOC105371743
LOC105371766
LOC105371789
LOC105371795
THRA1/BTR
LOC105371814
LOC105371824
LOC105371849
SNHG25
SNORA90
LOC107133515
LOC107546764
LOC107985033

Genes in Wide Peak

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

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

Genes
BAGE
TPTE
CYP4F29P
BAGE4
BAGE3
BAGE2
ANKRD30BP2
POTED
ANKRD20A11P
MIR3118-1
MIR3156-3
MIR8069-1
LOC102724188

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.1.

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

Genes
ANGPT2
BLK
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
CLN8
FDFT1
GATA4
MSR1
MSRA
TUSC3
TNKS
MYOM2
DLGAP2
MFHAS1
ARHGEF10
KBTBD11
DLC1
SPAG11B
FBXO25
FGF20
PINX1
AGPAT5
KIAA1456
CSMD1
MTMR9
MCPH1
PPP1R3B
SOX7
FAM167A
SLC35G5
LINC00208
FAM167A-AS1
FAM86B1
ERI1
LONRF1
RP1L1
CLDN23
SGCZ
DEFB104A
LOC157273
SGK223
LINC00599
FAM87A
TDRP
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
PRSS55
C8orf74
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
FAM86B3P
XKR6
LOC286083
MICU3
LOC340357
LINC00965
USP17L2
XKR5
FAM90A25P
USP17L8
LOC392196
USP17L7
LOC401442
USP17L1
MIR124-1
DEFB103A
OR4F21
FAM90A7P
FAM90A10P
DEFA8P
DEFA9P
DEFA10P
MIR383
C8orf49
DEFB135
DEFB136
DEFB134
ERICH1-AS1
DEFB109P1B
RPL23AP53
USP17L4
USP17L3
LOC649352
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA11P
DEFA1B
ZNF705D
FAM90A2P
LOC729732
FAM66B
PRR23D1
ZNF705G
FAM66E
ZNF705B
FAM66D
FAM66A
PRR23D2
LOC100287015
DEFB4B
MIR1322
MIR548I3
MIR4286
MIR3926-2
MIR3926-1
MIR3674
LOC100506990
DLGAP2-AS1
MCPH1-AS1
MIR4659A
MIR4660
MIR4659B
GS1-24F4.2
MIR5692A2
MIR5692A1
LINC00681
LOC101927752
LOC101927815
LOC101928058
LOC101929128
LINCR-0001
LOC101929229
LOC101929269
MIR7160
MIR8055
LOC102725080
KBTBD11-OT1
SNORA99

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22p11.2.

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

Genes
ANKRD62P1-PARP4P3
POTEH
HSFY1P1
OR11H1
CCT8L2
XKR3
TPTEP1
DUXAP8
POTEH-AS1
BMS1P17
LOC101929350
LOC102723769
LINC01297
BMS1P22

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q11.

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

Genes
FGF9
GJA3
GJB2
MIPEP
SGCG
TUBA3C
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
FAM230C
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
PSPC1
TNFRSF19
XPO4
MRPL57
TPTE2
EEF1AKMT1
SKA3
MICU2
SPATA13
ZDHHC20
ANKRD20A9P
LINC00442
C1QTNF9B
ANKRD20A19P
C1QTNF9B-AS1
BASP1P1
MIPEPP3
ANKRD26P3
LINC00421
MIR2276
LINC00540
SACS-AS1
LINC00327
MIR4499
LINC00408
LINC00539
LINC00350
LINC00417
LINC00424
LINC00621
LOC101928697
LINC00367
LINC01046
LINC01072

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p21.3.

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

Genes
NRAS
BCL10
TRIM33
RBM15
ABCA4
ACADM
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
DBT
DLSTP1
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCA
FPGT
FUBP1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
PLPPR4
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
LAMTOR5
IFI44
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
ADGRL2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
TNNI3K
SH3GLB1
HAO2
SNX7
DPH5
GPR88
TRMT13
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
KYAT3
TMEM167B
OLFML3
TMIGD3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ADGRL4
MFSD14A
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
ST6GALNAC5
GPR61
REG4
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1-AS1
STRIP1
ZNF697
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
ERICH3
LRRIQ3
LRRC39
HSD3BP4
DRAM2
PIFO
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
CHIAP2
DENND2C
GBP6
PLPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LINC01140
CCDC18
MYBPHL
BARHL2
NBPF7
MIGA1
NEXN-AS1
GBP7
C1orf146
FAM69A
SLC6A17
C1orf137
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
LHX8
LINC01555
FLJ31662
LOC440600
LOC440602
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SPATA42
CYMP
LOC643355
LOC643441
LINC00622
LOC646626
SETSIP
ACTG1P4
NBPF6
SCARNA2
SNORD45C
MIR553
LOC729930
LOC729970
LOC729987
MIR942
MIR760
LINC01349
LOC100129046
LOC100129138
LINC01160
LOC100129620
CCDC18-AS1
AP4B1-AS1
MIR320B1
MIR548N
MIR4256
SPATA1
LINC01364
RTCA-AS1
FAM212B-AS1
SLC16A1-AS1
FPGT-TNNI3K
TMEM56-RWDD3
MIR378G
MIR548AC
MIR2682
MIR4423
DPYD-AS1
DPYD-AS2
VAV3-AS1
KCNC4-AS1
KCND3-AS1
HAO2-IT1
KCND3-IT1
LOC100996251
LOC100996263
LOC100996630
LOC100996635
LINC01356
LAMTOR5-AS1
LINC01360
ERICH3-AS1
LOC101927342
LOC101927412
LOC101927434
LINC01361
LOC101927560
LOC101927587
LOC101927844
PKN2-AS1
LINC01057
LOC101928098
LOC101928118
LOC101928241
LOC101928270
LOC101928370
LOC101928436
LOC101928476
LOC101928718
HIPK1-AS1
LOC101928977
LOC101928995
LOC101929023
LOC101929099
LOC101929147
MIR7852
MIR7856
MIR7156
LOC102606465
LOC102723661
LINC01461
LINC01397
LINC01307
LINC01525
WARS2-IT1
LOC105378828
LOC105378853
LOC105378933

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Yq11.223.

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

Genes
DAZ1
RBMY1A1
KDM5D
PRY
XKRY
BPY2
CDY1
EIF1AY
CDY2A
SPRY3
DAZ3
DAZ2
DAZ4
TTTY5
TTTY9A
TTTY13
TTTY14
GOLGA2P2Y
TTTY6
HSFY1
CSPG4P1Y
TTTY3
TTTY4
RPS4Y2
HSFY2
RBMY2EP
RBMY2FP
RBMY1F
CDY2B
TTTY10
TXLNGY
TTTY17A
BCORP1
FAM41AY1
RBMY1B
RBMY1D
RBMY1E
RBMY1J
FAM224B
FAM224A
TTTY6B
BPY2B
TTTY3B
TTTY4B
TTTY17B
PRORY
LOC100652931
NLGN4Y-AS1
LOC101929148

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.1.

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

Genes
BMPR1A
FGFR2
TLX1
NFKB2
PTEN
SUFU
DUX4
hsa-mir-3158-1
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
ANXA11
FAS
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GLUD1
GOT1
PRLHR
GPR26
GRK5
GRID1
HABP2
HELLS
HHEX
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MAT1A
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGR
RGS10
RPL21
RPS24
SCD
SFRP5
SFTPD
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
MBL1P
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL1
BUB3
LGI1
NOLC1
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
PPIF
ACTR1A
SMNDC1
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
TUBGCP2
PRDX3
ADIRF
VAX1
ATE1
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
EDRF1
LRIT1
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
GHITM
PDCD4
VENTX
R3HCC1L
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
CCSER2
EXOC6
FAM35A
CCNJ
MARCH5
ZRANB1
CFAP46
NSMCE4A
CNNM2
WBP1L
CCDC186
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
WDR11
SLF2
DHX32
PPP2R2D
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
ZMIZ1
AS3MT
STAMBPL1
GPAM
SHTN1
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
MFSD13A
MCMBP
C10orf95
PLEKHS1
PDZD7
OBFC1
C10orf88
UBTD1
TMEM254
CFAP43
LRRC27
TNKS2
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
FAM213A
DYDC2
PCGF5
ADGRA1
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ATAD1
ARHGAP19
KNDC1
ITPRIP
OLMALINC
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
OPN4
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
ANKRD22
SFXN2
PDZD8
BORCS7
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
ACSM6
LIPJ
CFL1P1
TRUB1
VTI1A
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
CACUL1
NKX2-3
SLC35G1
CFAP58
C10orf91
PWWP2B
LINC00858
EMX2OS
PLPP4
PAOX
FAM24B
TMEM254-AS1
PLAC9
ZCCHC24
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
FUOM
JAKMIP3
STK32C
BLOC1S2
RBM20
PDCD4-AS1
FLJ37201
LOC283038
ZMIZ1-AS1
WDR11-AS1
FFAR4
KCNK18
LIPM
CYP26C1
VWA2
NANOS1
LRIT2
HMX3
NHLRC2
CCDC172
DMBT1P1
SH2D4B
C10orf99
SLC16A12
CC2D2B
ENO4
ARMS2
TEX36
LINC00959
GUCY2GP
NKX1-2
LBX1-AS1
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
LINC01164
LINC01168
SPRNP1
GOLGA7B
LINC01561
FAM45A
MIR107
C10orf62
LINC00595
LINC00857
LINC00863
IFIT1B
FRG2B
MIR346
SPRN
MIR146B
MIR202
NPS
SCART1
SNORA19
LOC642361
HOST2
FAM196A
FAM25A
LIPK
LIPN
LINC00865
RPL13AP6
BEND3P3
SFTPA1
SNORA12
MIR607
MIR608
MIR609
NUTM2A
NUTM2D
NUTM2A-AS1
LINC00864
ENTPD1-AS1
RPL13AP5
RPEL1
SFTPA2
NUTM2B
LOC729815
TLX1NB
MIR936
C10orf131
PLCE1-AS1
ADGRA1-AS1
LOC100130698
ATE1-AS1
ACTA2-AS1
LINC00856
KLLN
TEX36-AS1
HECTD2-AS1
DNMBP-AS1
BMS1P21
KCNIP2-AS1
MIR1287
MIR1307
MIR2110
FAS-AS1
MIR548E
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
SLIT1-AS1
LINC00866
RPARP-AS1
SH3PXD2A-AS1
CFAP58-AS1
SORCS3-AS1
ADD3-AS1
LINC00867
GRID1-AS1
TNKS2-AS1
MARK2P9
BORCS7-ASMT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4678
MIR4682
MIR4482
MIR4484
MIR4681
MIR4685
LINC00502
NUTM2B-AS1
LINC00601
FANK1-AS1
SLC16A12-AS1
LINC01375
LOC101926942
PLCE1-AS2
LOC101927278
LINC01475
LINC01163
LINC01514
LOC101927419
LOC101927472
TCERG1L-AS1
LOC101927523
LOC101927549
LINC01166
MIR202HG
LOC101927692
MIR3663HG
FAM53B-AS1
EDRF1-AS1
LOC101929574
NRG3-AS1
LINC01519
LOC101929646
LOC101929662
LINC01520
MIR6507
MIR6715B
MIR6715A
LOC102723665
LOC102723703
NEURL1-AS1
LOC102724589
LOC103344931
LINC01435
LINC01167
LOC105378385
LOC105378397
XLOC_008559
LOC105378430
LOC105378470
AS-PTPRE
SNORA87

Genes in Wide Peak

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

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

Genes
CRLF2
P2RY8
hsa-mir-1308
NR0B1
AMELX
SLC25A6
SHROOM2
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT
BMX
S100G
CLCN4
CSF2RA
CYBB
DDX3X
DMD
EIF1AX
EIF2S3
FANCB
VEGFD
GK
GLRA2
GPM6B
GPR34
GRPR
HCCS
IL3RA
ANOS1
MAGEB1
MAGEB2
MAGEB3
MAGEB4
CD99
MID1
NHS
GPR143
OTC
PDHA1
PDK3
PHEX
PHKA2
PIGA
POLA1
PPEF1
PRKX
PRPS2
PRRG1
RBBP7
RPGR
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SHOX
SMS
CDKL5
TBL1X
DYNLT3
TSPAN7
TMSB4X
XG
XK
ZFX
GTPBP6
PUDP
AKAP17A
PNPLA4
ZRSR2
USP9X
SRPX
OFD1
PIR
INE2
CASK
ASMTL
AP1S2
GYG2
REPS2
ZBED1
MED14
RAB9A
PCYT1B
FRMPD4
ADGRG2
ATP6AP2
SCML2
PRDX4
RAI2
MSL3
IL1RAPL1
CA5B
CNKSR2
ACOT9
SMPX
HYPM
MXRA5
EGFL6
VCX
GPR82
PPP2R3B
SH3KBP1
TLR7
TLR8
MBTPS2
VCX2
VCX3A
FTHL17
BCOR
GEMIN8
PLCXD1
TXLNG
WWC3
CTPS2
TMEM27
NLGN4X
MID1IP1
ACE2
NYX
APOO
ASMTL-AS1
CXorf21
KLHL15
PPP1R2P9
TMEM47
ATXN3L
SYAP1
SYTL5
BEND2
PTCHD1
PPP4R3CP
MAGEB10
DCAF8L1
VENTXP1
MAGEB16
ASB11
ASB9
ZNF645
FAM47A
MOSPD2
MAGEB6
CXorf38
DDX53
FAM47B
SUPT20HL2
TCEANC
ARX
FAM9A
FAM9B
FAM9C
DHRSX
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
LINC00685
LINC01281
CFAP47
UBE2E4P
MAGEB18
CA5BP1
LANCL3
MPC1L
DCAF8L2
ARSH
MAGEB5
TLR8-AS1
MAP3K15
LOC389906
CD99P1
YY2
VCX3B
FTH1P18
FAM47C
MAGEB17
SCARNA23
MIR651
LOC729609
LINC00106
GS1-600G8.3
LINC01546
SUPT20HL1
PHKA2-AS1
XGY2
LOC100132831
LINC01203
SCARNA9L
CLDN34
MIR548F5
LINC00102
MIR23C
MIR3937
MIR3690
MIR3915
PIR-FIGF
MIR4768
MIR1587
MIR548AJ2
MIR4770
MIR548AM
MIR4767
MIR4666B
MIR548AX
PTCHD1-AS
NHS-AS1
ZFX-AS1
PHEX-AS1
PRKX-AS1
MED14OS
PPEF1-AS1
EIF1AX-AS1
PCYT1B-AS1
MID1IP1-AS1
LINC01282
LOC101927476
LOC101927501
LOC101928201
LOC101928389
LOC101928627
MIR6089
MIR6134
MIR7641-2
MIR6086
GS1-594A7.3
LINC01456
LOC105373156
LOC105373185

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
AKT2
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-643
hsa-mir-220c
A1BG
ACTN4
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB3
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL2
KIR2DL3
KIR2DL4
KIR2DS1
KIR2DS3
KIR2DS4
KIR2DS5
KIR3DL1
KIR3DL2
KIR3DS1
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PTGIR
PTPRH
PVR
NECTIN2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
SYMPK
MIA
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2B
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA2
HNRNPUL1
CLASRP
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
SIRT2
CYP2G1P
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
C5AR2
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
PRX
SPTBN4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
CENPBD1P1
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
COQ8B
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
KMT5C
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
TIMM50
SHKBP1
CCDC114
LOC93429
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
C19orf84
SPACA6
ZNF480
ZNF534
ZNF578
ERVV-1
SMIM17
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542P
ZNF582
ZNF583
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
EID2
ZNF780B
ZNF525
SPACA4
NLRP7
CADM4
ADM5
ZNF584
ZSCAN4
NLRP11
TMEM86B
INAFM1
ZNF549
NAPSB
IL4I1
IFNL2
IFNL3
IFNL1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
EMC10
MGC45922
KLK9
SIGLEC17P
SIGLECL1
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
ZNF546
MYPOP
NANOS2
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
DNAAF3
ZNF233
LILRA5
B3GNT8
IGFL1
C19orf68
ZNF773
ZNF582-AS1
CEACAM22P
CEACAM16
BLOC1S3
BHMG1
IGFL3
ZNF808
ZNF888
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ACP7
PINLYP
ZNF818P
ZNF805
ZNF321P
LGALS17A
LOC400706
SIGLEC16
LOC400710
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
CCER2
LOC645553
FAM90A27P
SBK2
RNF225
PSG10P
LGALS7B
PHLDB3
SEC1P
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
CCDC61
CEACAM18
SHISA7
RFPL4AL1
LINC01530
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A12
ZNF667-AS1
LOC100128398
LOC100129083
LOC100129935
SBK3
BSPH1
MZF1-AS1
KIR2DS2
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A10
SNAR-C2
SNAR-C4
SNAR-E
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
ERICH4
SNAR-A14
ERVV-2
EML2-AS1
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
PCAT19
LOC100505585
LOC100505622
NAPA-AS1
LOC100505715
CARD8-AS1
PPP5D1
PTOV1-AS1
DACT3-AS1
GFY
ZNF865
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
MIR5088
NUCB1-AS1
LIPE-AS1
LOC101059948
IFNL4
ZNF350-AS1
LINC01480
LOC101928063
LOC101928295
PTOV1-AS2
LOC101928517
ZNF649-AS1
LOC101928804
LOC101928886
ZIM2-AS1
LOC101930071
SPACA6P-AS
MIR6088
MIR6796
MIR6797
MIR6799
MIR6800
MIR6802
MIR6804
MIR6805
MIR6806
MIR8074
MIR8077
MIR8085
MIR6719
MIR6807
MIR8061
MIR6798
MIR6803
MIR7975
MIR6801
ZNF528-AS1
LENG8-AS1
LOC105372419
LOC105372440
LOC105372441
LOC105372444
LOC105372476
LOC105372483
LOC105447645
PLA2G4C-AS1
GLTSCR2-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.3.

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

Genes
ADRA1D
JAG1
AVP
BFSP1
BMP2
ENTPD6
CDC25B
CENPB
CHGB
CSNK2A1
CST1
CST2
CST3
CST4
CST5
FKBP1A
GNRH2
FOXA2
IDH3B
INSM1
ITPA
NKX2-2
OXT
PAX1
PCNA
PCSK2
PDYN
PLCB4
PRNP
PTPRA
PYGB
RRBP1
SIGLEC1
SNAP25
SNRPB
SNRPB2
SOX12
SSTR4
TCF15
TGM3
THBD
ZNF133
MKKS
ATRN
CST7
CDS2
PSMF1
SNPH
LZTS3
RASSF2
GINS1
SLC23A2
CST8
SIRPB1
SEC23B
NOP56
RBCK1
POLR3F
RBBP9
DSTN
RNF24
XRN2
UBOX5
BTBD3
CD93
NINL
PLCB1
PRND
FLRT3
LAMP5
SPEF1
C20orf194
CFAP61
ABHD12
RNU105B
SNORD57
SNORD56
SDCBP2
SNX5
TMEM230
LINC00652
NXT1
VSX1
NAA20
CRNKL1
ANGPT4
ESF1
TRMT6
HAO1
RIN2
SMOX
CRLS1
C20orf27
DZANK1
SPTLC3
AP5S1
TMEM74B
SIRPG
FERMT1
KIF16B
TASP1
KIZ
NSFL1C
TMX4
GPCPD1
CPXM1
OTOR
APMAP
PAK5
RALGAPA2
KAT14
SLC24A3
MAVS
EBF4
TRIB3
OVOL2
FASTKD5
NAPB
ANKEF1
GFRA4
GZF1
VPS16
PCED1A
MRPS26
DDRGK1
NDUFAF5
ZNF343
SYNDIG1
NRSN2
PANK2
ADAM33
SEL1L2
DEFB126
FAM110A
SLC4A11
MCM8
ACSS1
ZCCHC3
SCRT2
GGTLC1
MGME1
DTD1
SLC52A3
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
PROKR2
SLX4IP
CSTL1
CST9L
CST9
C20orf96
MACROD2
SRXN1
LINC00261
BANF2
MACROD2-IT1
DEFB127
SCP2D1
ISM1
CST11
DEFB129
SIRPA
STK35
PRNT
LINC00654
C20orf196
LRRN4
CST13P
LINC00656
DEFB125
DEFB128
SIRPB2
LOC284788
LOC284798
LOC339593
RSPO4
TGM6
LOC388780
LINC00493
DEFB132
C20orf202
FLJ33581
MIR103A2
LINC00851
LOC613266
RAD21L1
LOC643406
NKX2-4
SNORA51
SNORD17
SNORD86
SNORD110
LOC727993
LINC01433
LINC00687
SNORD119
C20orf78
LOC100130264
SNAP25-AS1
UBOX5-AS1
LINC01432
LOC100270804
TMEM239
LOC100289473
MIR1292
MIR103B2
PCNA-AS1
PET117
MACROD2-AS1
MIR3192
LOC100505515
ISM1-AS1
LINC01431
NRSN2-AS1
SDCBP2-AS1
LINC00658
FKBP1A-SDCBP2
PLCB1-IT1
LOC101926889
SIRPG-AS1
LOC101929125
LOC101929207
MCM8-AS1
CASC20
LINC01428
LOC101929288
LOC101929312
LAMP5-AS1
LOC101929371
LOC101929395
LOC101929413
LOC101929486
LOC101929526
KIZ-AS1
LOC101929608
LOC101929625
LINC01427
LINC01384
MIR6869
MIR6870
MIR8062
LOC102606466
LOC105372493

Genes in Wide Peak

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

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
FGFR1OP
GOPC
hsa-mir-2113
ACAT2
AIM1
AMD1
ARG1
ADGRB3
BCKDHB
CCNC
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GPR31
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
ME1
MAP3K4
MAP3K5
AFDN
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLG
PLN
POU3F2
PREP
PRIM2
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
UTRN
EZR
VIP
PTP4A1
RNF217-AS1
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
CEP162
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
PHF3
HEY2
HEBP2
ORC3
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
SENP6
TIAM2
FBXL4
LINC01558
FBXO5
SLC17A5
RGS17
SNORD50A
PDE7B
FILIP1
SESN1
DLL1
OSTM1
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
LGSN
MPC1
HECA
COQ3
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
PHF10
QRSL1
VNN3
DDX43
FAM46A
TMEM30A
ERMARD
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
SMIM8
ADGRG6
ARFGEF3
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
ABRACL
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
SMAP1
LINC01590
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
ARMT1
OGFRL1
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
FRMD1
AGPAT4-IT1
LINC00574
LCAL1
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
LINC01621
UBE3D
LINC00473
MFSD4B
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
MTFR2
SFT2D1
KLHL32
TMEM200A
MB21D1
NUS1
GINM1
IL22RA2
SLC18B1
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
SDHAF4
CD109
RAET1E
PM20D2
SRSF12
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
LINC01312
SLC2A12
LINC01010
PNLDC1
RNF217
NKAIN2
KHDC3L
CFAP206
BVES-AS1
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
KHDRBS2
C6orf163
CCDC162P
AK9
NT5DC1
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
PHACTR2-AS1
CEP57L1
PPIL6
LINC01268
FLJ34503
DCBLD1
LOC285762
PACRG-AS1
PRR18
LOC285804
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GUSBP4
GJB7
HMGA1P7
SNHG5
SUMO4
CENPW
SOGA3
LINC00222
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
TCP10L2
LOC401286
LINC00242
LINC01624
GTF2H5
MIR30A
MIR30C2
LOC441155
OOEP
FAM26F
FLJ46906
LINC00602
LOC441178
SLC25A51P1
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
FAM229B
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LINC01625
RPS18P9
LOC645967
RAET1K
AFDN-AS1
SNORA20
SNORA29
SNORD50B
MIR548A2
MIR548B
MIR587
MIR588
MCHR2-AS1
TPI1P3
METTL24
KATNBL1P6
STXBP5-AS1
TMEM242
LOC729603
PACRG-AS3
LIN28B-AS1
HGC6.3
UST-AS1
TRAPPC3L
KHDC1L
LOC100129518
LOC100130476
TSTD3
C6orf99
LOC100131532
LINC00271
LOC100132735
CD24
AIRN
LOC100287632
HMGN3-AS1
LOC100289495
NHEG1
MIR1913
MIR2113
MIR1202
LOC100422737
MIR1273C
MIR548U
MIR3144
MIR3145
MIR4282
MTRNR2L9
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
SYNE1-AS1
KIF25-AS1
LOC100506804
SMLR1
LINC01013
TARID
KCNQ5-IT1
LOC100507406
GVQW2
LOC100507477
LINC01277
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
MIR548AJ1
MIR4459
MIR548AI
MIR4463
MIR4644
MIR548H5
RAET1E-AS1
RPS6KA2-AS1
KCNQ5-AS1
SYNJ2-IT1
RPS6KA2-IT1
LOC100996634
EZR-AS1
MANEA-AS1
LOC101927314
LOC101927365
LOC101927640
LOC101927686
LOC101927768
LOC101927919
HRAT13
LOC101928140
LOC101928231
LOC101928280
LOC101928304
LOC101928307
EVADR
LOC101928429
LOC101928461
LOC101928489
LOC101928516
LOC101928540
MEI4
LOC101928661
LINC01526
LOC101928820
LOC101928911
LOC101928936
LOC101929057
CASC6
LOC101929122
PACRG-AS2
LOC101929297
LOC101929420
LOC101929460
LINC01615
LOC101929504
LOC101929523
ARMC2-AS1
MIR7161
MIR7641-2
LOC102723649
LOC102723831
LOC102723883
LINC01626
LOC102724053
LOC102724152
TBX18-AS1
LOC102724357
LOC102724511
LOC103352541
NCOA7-AS1
LOC105377879
LINC01611
LOC105377924
LOC105377962
LOC105377967
LOC105377975
LOC105378047
LOC105378052
LOC105378068
LOC105378098
MEAT6
LOC105378123
LOC105378127
LOC105378137
LOC105378146
LUADT1
SNORA98
SNORD141A
LINC00680
LINC00680-GUSBP4

Genes in Wide Peak

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

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

Genes
ALDH2
ATF1
BCL7A
BTG1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
HMGA2
WIF1
ZNF384
hsa-mir-616
hsa-mir-1244-3
A2M
A2MP1
ACACB
ACADS
ASIC1
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ARL1
ART4
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
SCARB1
CD63
CD69
CDK2
CDKN1B
CHD4
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CREBL2
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
DDX11
ATN1
EPYC
DTX1
DUSP6
PHC1
EIF2B1
EIF4B
CELA1
ELK3
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GRIN2B
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTA4H
LTBR
LUM
LYZ
M6PR
MARS
METTL1
KITLG
MGP
MGST1
MIP
MMP17
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NDUFA9
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
POU6F1
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAB1
PRKAG1
PRPH
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAN
RAP1B
RARG
RBMS2
RDH5
RECQL
RFC5
RFX4
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SNRPF
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
SYT1
TAC3
TARBP2
TBX5
TBX3
HNF1A
TDG
TEAD4
TMBIM6
TFCP2
TSPAN8
TMPO
TNFRSF1A
TPI1
NR2C1
HSP90B1
TULP3
TXNRD1
UBC
UBE2N
UNG
VDR
VWF
WNT1
WNT10B
ZNF10
ZNF26
ZNF84
ZNF140
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
KMT2D
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
DYRK2
PPFIBP1
PPFIA2
YBX3
LGR5
MAPKAPK5
DENR
RDH16
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1A
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
GPRC5A
KRT75
SCAF11
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
TESPA1
C2CD5
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
CLEC2B
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
RNF41
MPHOSPH9
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
P3H3
DCTN2
AKAP3
CCT2
SLCO1B1
RAD51AP1
CAMKK2
AVIL
PTGES3
KLRA1P
ZNF268
FRS2
TSPAN9
TRAFD1
OS9
TMED2
ERP29
CKAP4
GCN1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
PHLDA1
R3HDM2
MLXIP
RPH3A
KLRK1
P2RX2
RAB21
STK38L
FBXO21
FAIM2
MON2
SETD1B
UHRF1BP1L
ERC1
DDN
ANKLE2
NEMP1
CUX2
KIAA1033
TBC1D30
ESYT1
TNS2
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
ABCB9
CBX5
ISCU
RIMBP2
ANP32D
ATP6V0A2
SMUG1
LEMD3
CORO1C
GABARAPL1
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
FBXW8
GALNT8
HSPB8
OR7E47P
SNORD59A
RNU4-2
RNU4-1
GLS2
HCAR1
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CEP83
IRAK4
ING4
GPN3
DDX47
GLTP
MRPL51
CLEC1B
CLEC1A
MAPKAPK5-AS1
C1RL
ERGIC2
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TM7SF3
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
MAGOHB
SLC6A15
FAM90A1
RIC8B
KIAA1551
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
CAND1
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
ARNTL2
CHPT1
PARP11
ANO2
C12orf4
TIGAR
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHL42
PITPNM2
DIP2B
FAM234B
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
ATG101
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
NABP2
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
RPAP3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
FLJ13224
TCTN2
PLBD1
PYROXD1
NANOG
DNAJC22
NAA25
SLC8B1
ADAMTS20
CEP290
RNF34
CCDC92
MTERF2
PUS1
ACAD10
SPX
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
RHNO1
NRIP2
INHBE
RBP5
TMTC1
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
METTL25
TMEM117
TCHP
COQ5
LLPH
PYM1
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
CRACR2A
TUBA1C
ZC3H10
ORAI1
RNFT2
FAM222A
ALG10
SPRYD3
RITA1
MFSD5
FAM222A-AS1
COX14
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
TMEM263
FMNL3
CERS5
C12orf29
ATP23
PCED1B
C12orf65
TMEM132C
BICDL1
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
TMEM132B
OSBPL8
ARHGEF25
C12orf56
IQCD
LINC01257
AGAP2
DCD
RAB3IP
BORCS5
MUCL1
DEPDC4
LRRK2
CCDC38
TMEM52B
FAM186A
C12orf45
OR2AP1
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
HIST4H4
ERP27
FGD4
AEBP2
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
BRI3BP
KRT72
PRICKLE1
AMDHD1
SLC2A14
BCDIN3D
ALG10B
GLIPR1L2
RFLNA
ZNF664
LINC00477
ETFRF1
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
SOCS2-AS1
CEP83-AS1
KRT80
CFAP54
A2ML1
A2M-AS1
C12orf66
C12orf60
FBXL14
RAD9B
FAM109A
LINC00934
KRT19P2
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
LMNTD1
DENND5B
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
CLEC4C
DSTNP2
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
MYRFL
PLBD2
FAM71C
RMST
CCER1
PIANP
DCP1B
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
LINC00612
TTC41P
MSRB3
ETFBKMT
LRRC43
OR6C74
OR6C3
TCP11L2
LINC00935
TBX5-AS1
LINC01619
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
POC1B
OTOGL
C1RL-AS1
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
LOC283352
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
ADGRD1
MORN3
TRHDE-AS1
C12orf80
LINC00592
LINC01465
DPY19L2
CLEC9A
LINC01559
GAS2L3
LINC00485
LOC283440
MYO1H
HECTD4
KSR2
GATC
HNF1A-AS1
C12orf40
MUC19
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
LINC00936
C1QL4
TMEM119
KRT79
LOC338797
LINC01089
C12orf74
FAM19A2
LINC01252
SLCO1B7
SMCO2
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
PTPRQ
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
RPL13AP20
REP15
CCDC184
C12orf75
CFAP73
TMEM233
KMT5A
LINC00944
LINC00937
OR6C1
OR6C75
OR6C76
OR6C70
LOC400002
LINC00938
LOC400043
FLJ41278
MKRN9P
C12orf76
LINC00939
FLJ37505
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
MIR26A2
LOC414300
LINC00615
IQSEC3
ZNF705A
FAM66C
DDX12P
SMCO3
H3F3C
DBX2
FLJ12825
TMEM198B
PLEKHG7
LOC440117
FZD10-AS1
TSPAN11
OR9K2
MIR148B
MIR331
EID3
LOH12CR2
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC574538
HIGD1C
POU5F1P3
LOC642846
MAP1LC3B2
LOC643339
LOC643711
LOC643770
GLYCAM1
LOC645177
LOC645485
ANHX
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA2C
SNORA49
SNORA53
CD27-AS1
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
MIR616
MIR617
MIR618
MIR619
MIR620
LOC728084
C12orf73
SKP1P2
LOC728739
C12orf71
SLC15A5
MRS2P2
LOC100049716
HOTAIR
MIR920
KRT73-AS1
TMPO-AS1
LOC100128554
THCAT155
SMIM10L1
LOC100129940
LOC100130075
LOC100130238
AGAP2-AS1
LINC01405
USP30-AS1
PGAM1P5
RNU7-1
LOC100190940
PCED1B-AS1
LOC100240734
LOC100240735
LINC00940
BCDIN3D-AS1
MANSC4
LINC00941
LINC00173
LOC100287944
LOC100288778
LOC100288798
ZNF605
LINC00942
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1302-1
MIR1178
MIR1244-1
MIR1251
LOC100335030
SNORA70G
MIR1244-3
MIR1244-2
MIR4302
MIR4303
MIR4304
KLRF2
LINC00987
MIR3685
MIR3649
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3657
MIR3913-1
MIR3908
LOC100505978
LOC100506125
LOC100506159
LOC100506314
LOC100506393
RASSF8-AS1
LINC01234
LOC100506551
LOC100506606
PXN-AS1
DDX11-AS1
NRAV
LOC100506691
LOC100506844
LOC100506869
LRCOL1
LOC100507065
CLIP1-AS1
LOC100507091
LOC100507175
LOC100507195
LINC00943
LOC100507250
LOC100507377
LOC100507424
BLOC1S1-RDH5
POC1B-GALNT4
KLRC4-KLRK1
ZNF664-FAM101A
PRH1-PRR4
MIR4699
MIR4498
MIR4496
MIR4701
MIR3974
MIR4495
MIR4419B
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4494
MIR4698
CACNA1C-AS1
LOC100652999
MIR5188
MIR5700
MIR548AQ
LINC00507
RERG-AS1
CACNA1C-AS4
CACNA1C-AS2
DENND5B-AS1
HOXC-AS1
HOXC-AS2
HOXC-AS3
HOXC13-AS
CACNA1C-IT2
CACNA1C-IT3
IFNG-AS1
LOC100996671
LOC100996679
OVCH1-AS1
ZNF891
LOC101593348
LOC101927038
LOC101927058
LOC101927267
LOC101927292
LOC101927318
LOC101927415
LOC101927464
LOC101927583
LOC101927592
LOC101927616
LOC101927637
LOC101927653
LOC101927694
LOC101927735
LOC101927901
LOC101927905
LINC01479
LOC101928002
LOC101928030
LINC01481
LOC101928100
LOC101928137
LINC01486
LOC101928162
TESC-AS1
PLBD1-AS1
LINC01489
LOC101928416
LINC01490
LOC101928441
LOC101928449
LOC101928471
LOC101928530
LOC101928597
LOC101928617
ARNTL2-AS1
LOC101928731
LOC101928937
LOC101929058
LOC101929084
CASC18
LOC101929162
LOC101929384
LOC101929549
LOC101929584
LOC101930452
PCBP2-OT1
CISTR
MIR6074
MIR6125
MIR6502
MIR6758
MIR6760
MIR6761
MIR6762
MIR6861
MIR7107
MIR7641-2
MIR7844
MIR6763
MIR6757
MIR6880
MIR7106
MIR6505
MIR6759
MIR8072
MIR7851
THRIL
LOC102723544
LINC01498
LOC102724020
LOC102724050
LOC102724421
LOC102724663
LOC102724933
LLPH-AS1
CCND2-AS1
TMEM5-AS1
LHX5-AS1
LINC00508
LOC105369187
LOC105369595
LOC105369632
LOC105369635
LOC105369691
LOC105369723
LOC105369738
LOC105369739
LOC105369747
LOC105369781
LOC105369785
LOC105369860
LOC105369879
LOC105369891
LOC105369893
LOC105369911
LOC105369920
LOC105369921
LOC105369945
KCCAT198
LOC105369971
LOC105369980
LOC105370014
LOC105370016
LOC105370024
LOC105370068
CRAT8
XLOC_009911
LRP1-AS
LACAT8
SNORD133
SNORA105C
PRH1-TAS2R14
LOC107161159

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Yq12.

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

Genes
CRLF2
P2RY8
AMELY
SLC25A6
ASMT
CSF2RA
DAZ1
IL3RA
IL9R
CD99
PRKY
RBMY1A1
RPS4Y1
SHOX
SRY
VAMP7
TSPY1
UTY
ZFY
GTPBP6
AKAP17A
KDM5D
USP9Y
ASMTL
DDX3Y
PRY
XKRY
BPY2
VCY
CDY1
EIF1AY
TMSB4Y
ZBED1
CDY2A
SPRY3
NLGN4Y
PPP2R3B
TTTY1
PLCXD1
DAZ3
DAZ2
DAZ4
TTTY2
TSPY2
RBMY3AP
TTTY15
ASMTL-AS1
PCDH11Y
TTTY5
TTTY9A
TTTY11
TTTY12
TTTY13
TTTY14
GOLGA2P2Y
TTTY6
TTTY8
HSFY1
TGIF2LY
TBL1Y
CSPG4P1Y
TTTY3
TTTY4
RPS4Y2
HSFY2
RBMY2EP
RBMY2FP
RBMY1F
CDY2B
DHRSX
TTTY10
TTTY7
TXLNGY
FAM197Y2P
TTTY16
TTTY17A
TTTY18
TTTY20
TTTY19
TTTY21
TTTY22
TTTY23
LINC00685
BCORP1
RBMY1A3P
FAM41AY1
GYG2P1
VCY1B
RBMY1B
RBMY1D
RBMY1E
RBMY1J
CD99P1
FAM224B
FAM224A
TTTY6B
BPY2B
TTTY3B
TTTY4B
TTTY17B
DDX11L16
TSPY4
TSPY8
LINC00106
WASIR1
XGY2
TSPY10
LINC00102
MIR3690
PRORY
LOC100652931
LINC00278
LINC00279
LINC00280
NLGN4Y-AS1
LOC101929148
MIR6089

Arm-level results

Table 3. Get Full Table Arm-level significance table - 21 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Frequency Score	Amp Z score	Amp Q value	Del Frequency	Del Frequency Score	Del Z score	Del Q value
1p	3092	0.39	0.42	2.69	0.0242	0.05	0.09	-1.61	0.999
1q	2863	0.63	0.65	5.84	1.25e-07	0.03	0.07	-1.47	0.999
2p	1500	0.08	0.09	-2.66	1	0.13	0.14	-2.07	0.999
2q	2495	0.08	0.09	-2.18	1	0.13	0.14	-1.54	0.999
3p	1531	0.05	0.09	-2.25	1	0.39	0.42	1.49	0.253
3q	1708	0.11	0.15	-1.67	1	0.29	0.32	0.376	0.679
4p	693	0.05	0.06	-3.56	1	0.08	0.08	-3.28	0.999
4q	1467	0.05	0.06	-3.19	1	0.08	0.08	-2.9	0.999
5p	456	0.58	0.61	3.23	0.00597	0.05	0.12	-1.91	0.999
5q	2185	0.39	0.44	2.23	0.0694	0.11	0.17	-1.05	0.999
6p	1664	0.32	0.40	1.24	0.366	0.21	0.31	0.128	0.799
6q	1304	0.16	0.23	-0.908	1	0.32	0.38	0.751	0.517
7p	926	0.74	0.78	5.69	1.53e-07	0.05	0.20	-0.883	0.999
7q	1717	0.58	0.65	4.52	4.87e-05	0.11	0.25	-0.384	0.999
8p	795	0.18	0.32	-0.193	1	0.42	0.52	2.1	0.107
8q	1249	0.29	0.39	0.874	0.573	0.26	0.37	0.607	0.567
9p	621	0.08	0.20	-1.19	1	0.61	0.66	3.87	0.00087
9q	1610	0.05	0.13	-1.4	1	0.61	0.64	4.46	0.000199
10p	767	0.03	0.04	-3.16	1	0.34	0.35	0.159	0.799
10q	1968	0.03	0.04	-2.69	1	0.34	0.35	0.941	0.442
11p	1162	0.24	0.29	-0.356	1	0.18	0.24	-0.91	0.999
11q	2133	0.18	0.23	-0.601	1	0.18	0.23	-0.601	0.999
12p	804	0.21	0.32	-0.182	1	0.34	0.43	1.11	0.398
12q	2055	0.16	0.24	-0.42	1	0.34	0.41	1.62	0.227
13p	0	0.11	0.25	-1.04	1	0.58	0.65	3.27	0.00518
13q	1092	0.05	0.12	-1.7	1	0.58	0.61	3.69	0.00135
14p	0	0.32	0.48	1.08	0.449	0.34	0.50	1.31	0.326
14q	1829	0.34	0.39	1.34	0.334	0.13	0.20	-0.976	0.999
15p	0	0.08	0.17	-1.83	1	0.53	0.57	2.39	0.0573
15q	2082	0.00	0.00	-2.47	1	0.58	0.58	4.17	0.000363
16p	1378	0.55	0.58	3.55	0.00233	0.05	0.12	-1.71	0.999
16q	1070	0.37	0.44	1.36	0.334	0.16	0.25	-0.78	0.999
17p	937	0.26	0.30	-0.34	1	0.13	0.18	-1.71	0.999
17q	2298	0.37	0.40	1.79	0.175	0.08	0.12	-1.56	0.999
18p	212	0.05	0.11	-2.36	1	0.50	0.53	2.02	0.115
18q	644	0.08	0.18	-1.46	1	0.55	0.60	3.18	0.00598
19p	1331	0.08	0.12	-2.17	1	0.32	0.34	0.392	0.679
19q	2402	0.08	0.12	-1.61	1	0.34	0.37	1.49	0.253
20p	583	0.26	0.33	-0.166	1	0.21	0.29	-0.689	0.999
20q	1092	0.29	0.33	0.121	1	0.13	0.19	-1.54	0.999
21p	92	0.03	0.05	-3.16	1	0.42	0.43	0.771	0.517
21q	750	0.18	0.28	-0.631	1	0.34	0.42	0.935	0.442
22p	2	0.03	0.05	-3.2	1	0.42	0.43	0.716	0.517
22q	1258	0.05	0.09	-2.27	1	0.42	0.44	1.66	0.227
Xp	945	0.47	0.53	2.47	0.0411	0.11	0.20	-1.24	0.999
Xq	1533	0.50	0.54	3.1	0.00786	0.08	0.16	-1.37	0.999
Yp	113	0.34	0.50	1.37	0.334	0.32	0.48	1.14	0.398
Yq	245	0.18	0.29	-0.735	1	0.37	0.45	1.02	0.438

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 = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/cptac3_luad_cnv.v3.EGFR.seg.txt
Markers File = ./this_file_does_not_exist.txt
Reference Genome = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/gistic2.refgene.hg38.UCSC.add_miR.160920.mat
CNV Files = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg38_GDC_SNP6_CNV_list.161107.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.98
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 38 Input Tumor Samples.

Tumor Sample Names
11LU013_TP
11LU016_TP
C3L-00093_TP
C3L-00368_TP
C3L-00510_TP
C3L-00604_TP
C3L-00893_TP
C3L-01330_TP
C3L-02219_TP
C3N-00167_TP

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.

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

Made with Nozzle