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 108 tumor samples used in this analysis: 33 significant arm-level results, 28 significant focal amplifications, and 26 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 - 28 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
3q26.33	1.6828e-49	1.1375e-37	chr3:181680002-182310000	3
8p11.23	2.7299e-26	2.7299e-26	chr8:38280002-38430000	3
11q13.3	3.9769e-18	3.9769e-18	chr11:69700001-69820000	3
8q24.21	1.6582e-08	1.6582e-08	chr8:127290002-127490000	4
19q13.11	3.627e-05	3.627e-05	chr19:33190001-33390000	6
3q26.31	5.6928e-40	0.00088862	chr3:141990002-186660000	299
7p11.2	0.0025739	0.0031777	chr7:54410001-55370000	8
4q12	0.0047104	0.0047104	chr4:53490002-56719999	29
20q11.21	0.0079438	0.0079438	chr20:31300002-32360000	33
15q26.3	0.019099	0.019099	chr15:101940002-101991189	10
Xq22.3	0.024841	0.024841	chrX:108110002-108340000	2
12p12.1	0.025483	0.025483	chr12:24720002-25349999	7
13q34	0.031886	0.031886	chr13:112570001-114080000	32
5p15.2	0.034723	0.034723	chr5:1-16059999	107
1q21.2	0.044612	0.044612	chr1:119990001-154760000	281
17q25.3	0.045839	0.045839	chr17:81880002-82099999	20
7q21.3	0.04327	0.047362	chr7:93400001-97300000	29
21q21.1	0.056707	0.056707	chr21:14570001-18980000	19
19p13.3	0.067054	0.067054	chr19:1-280000	9
Yq11.223	0.067054	0.067054	chrY:20160002-20190000	0 [TTTY10]
9q34.3	0.10445	0.10445	chr9:138250002-138394717	0 [FAM157B]
Xp22.33	0.12667	0.12667	chrX:1-139999	0 [PLCXD1]
9p24.3	0.059934	0.14884	chr9:1-789999	14
6p12.2	0.16126	0.16126	chr6:52450001-53509999	19
14q13.3	0.16403	0.16403	chr14:36420001-38070000	12
22q11.22	0.16403	0.16403	chr22:18120001-24500000	151
19q13.43	0.17337	0.17337	chr19:58360002-58617616	20
9p13.3	0.0035397	0.33049	chr9:33280002-37070000	92

Genes in Wide Peak

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

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

Genes
SOX2
SOX2-OT
LINC01206

Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
LETM2

Genes in Wide Peak

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

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

Genes
FGF3
FGF4
FGF19

Genes in Wide Peak

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

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

Genes
POU5F1B
CASC8
CCAT2
CASC21

Genes in Wide Peak

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

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

Genes
CEBPA
CEBPG
LRP3
PEPD
SLC7A10
CEBPA-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.31.

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

Genes
ETV5
MLF1
PIK3CA
SOX2
GMPS
hsa-mir-720
AADAC
ACTL6A
AGTR1
AHSG
ATR
BCHE
AP2M1
CLCN2
CP
CPA3
CPB1
CRYGS
DGKG
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
GHSR
GYG1
IL12A
KPNA4
TM4SF1
MBNL1
MME
NDUFB5
CLDN11
P2RY1
PFN2
SERPINI1
SERPINI2
PLD1
PLOD2
PLS1
PLSCR1
POLR2H
PRKCI
PSMD2
PTX3
RAP2B
RARRES1
TRA2B
SHOX2
SI
SIAH2
SKIL
SLC2A2
HLTF
SSR3
TERC
TFDP2
THPO
SEC62
TM4SF4
TRPC1
CLRN1
ZIC1
KCNAB1
FXR1
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
MAP3K13
SLC33A1
CHST2
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
ALG3
KCNMB2
IGF2BP2
PDCD10
RNF13
SLITRK3
NLGN1
PLCH1
TNIK
MCF2L2
ATP11B
U2SURP
VPS8
WWTR1
TIPARP
ARHGEF26
PCOLCE2
RNU6-1
GPR160
FETUB
LAMP3
KCNMB3
SERP1
GOLIM4
GPR171
SCHIP1
NMD3
COMMD2
ZNF639
RSRC1
PEX5L
SELT
DNAJB11
P2RY13
GPR87
DCUN1D1
XRN1
KLHL24
TBCCD1
ABCF3
PARL
MFN1
YEATS2
MYNN
EIF5A2
SUCNR1
MCCC1
LXN
CCNL1
PLSCR2
PLSCR4
MRPL47
NCEH1
IFT80
SLC7A14
SENP2
GNB4
MAGEF1
ZMAT3
MFSD1
FNDC3B
P2RY12
VEPH1
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
SPATA16
EIF2A
B3GNT5
ZIC4
HPS3
ACTRT3
GFM1
KLHL6
VWA5B2
TMEM41A
EGFEM1P
CAMK2N2
TM4SF18
MED12L
CLRN1-AS1
DNAJC19
OTOL1
FAM131A
ERICH6
TTC14
PPM1L
WDR49
LRRC34
PQLC2L
C3orf79
SPTSSB
DHX36
HTR3C
LIPH
HTR3D
RPL22L1
AADACP1
C3orf58
LOC253573
NAALADL2
GK5
SLC9A9
HTR3E
IGSF10
C3orf33
C3orf70
TRIM59
CCDC39
LINC00880
EHHADH-AS1
LRRIQ4
SAMD7
AADACL2
GPR149
PAQR9
NMRAL1P1
SOX2-OT
PLSCR5
ANKUB1
LEKR1
TMEM212
MBNL1-AS1
C3orf80
FLJ46066
MIR15B
MIR16-2
LOC440982
TMEM14EP
LINC01330
IGF2BP2-AS1
LOC646903
PA2G4P4
LINC01192
TMEM183B
IQCJ
SCARNA7
SNORD66
MIR551B
MIR569
LINC00886
LINC01100
WWTR1-AS1
LOC100128164
MIR1224
TIPARP-AS1
LOC100289361
MIR1263
LINC00881
MIR3919
IQCJ-SCHIP1
LINC01208
LINC00578
LOC100505609
LINC00888
LOC100507389
LOC100507461
ARHGEF26-AS1
LOC100507537
LOC100507661
MIR4448
MIR4789
LINC00501
MIR5186
MIR5588
MIR548AQ
NAALADL2-AS3
HLTF-AS1
ABCC5-AS1
NLGN1-AS1
KLHL6-AS1
EIF2B5-AS1
KCNAB1-AS2
KCNAB1-AS1
TM4SF1-AS1
TMEM212-AS1
NAALADL2-AS2
NAALADL2-AS1
LINC01014
IQCJ-SCHIP1-AS1
SLC9A9-AS1
LOC100996447
LINC01206
LOC101243545
PAQR9-AS1
LOC101927866
LINC01213
LINC01214
ERICH6-AS1
LOC101928105
AADACL2-AS1
LOC101928166
LINC01487
IL12A-AS1
LOC101928583
LINC01209
LOC101928739
PEX5L-AS2
LOC101928882
LOC101928992
RNU6-7
MIR6828
MIR7977
KCCAT211
LOC102724604
RNU6-2
LINC01322
LINC01327
LINC01324
KCNMB2-AS1
LOC105374177
LOC105374194
LOC105374205
LOC105374244
LOC105374250
LOC105374313
HTR3E-AS1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
KDR
KIT
PDGFRA
CHIC2
PPAT
SRP72
CLOCK
CEP135
PAICS
NMU
EXOC1
TMEM165
KIAA1211
SRD5A3
HOPX
LNX1
ARL9
AASDH
PDCL2
GSX2
LOC339978
RPL21P44
LOC644145
LOC100506444
SRD5A3-AS1
THEGL
LNX1-AS1
LNX1-AS2
MIR7641-2

Genes in Wide Peak

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

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

Genes
ASXL1
BCL2L1
FOXS1
HCK
ID1
PLAGL2
KIF3B
TM9SF4
TPX2
POFUT1
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TSPY26P
CCM2L
LINC00028
TTLL9
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
XKR7
MIR1825
MIR3193
HM13-AS1
MIR7641-2
ABALON

Genes in Wide Peak

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

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

Genes
WASH3P
FAM138E
DDX11L9
MIR1302-2
MIR1302-9
MIR1302-10
MIR1302-11
MIR6859-2
MIR6859-3
MIR6859-1

Genes in Wide Peak

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

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

Genes
COL4A6
ATG4A

Genes in Wide Peak

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

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

Genes
KRAS
BCAT1
LRMP
CASC1
ETFRF1
C12orf77
LOC645177

Genes in Wide Peak

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

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

Genes
ATP4B
F7
F10
GAS6
LAMP1
GRK1
TFDP1
CUL4A
PROZ
TUBGCP3
RASA3
ATP11A
MCF2L
TMCO3
DCUN1D2
PCID2
GRTP1
ADPRHL1
TMEM255B
ATP11AUN
LINC00452
GAS6-AS1
LINC00552
MCF2L-AS1
GAS6-AS2
LINC00565
GRTP1-AS1
LINC00454
ATP11A-AS1
LOC101928841
MIR8075
F10-AS1

Genes in Wide Peak

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

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

Genes
ADCY2
CTNND2
DAP
DNAH5
MTRR
NDUFS6
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
ICE1
PP7080
IRX4
TAS2R1
FAM105A
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
OTULIN
EXOC3-AS1
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LINC01018
LINC01019
LOC285692
SLC6A19
LINC01020
SLC6A18
LRRC14B
LOC389273
FLJ33360
LINC01194
LOC442132
ANKRD33B
SDHAP3
LOC728613
LOC729506
SNORD123
MIR887
LOC100130744
LOC100288152
MIR4277
MIR4278
LOC100505625
MIR4458HG
SNHG18
ROPN1L-AS1
LOC100506688
LINC01511
LOC100506858
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635
LOC100996325
CTD-3080P12.3
LOC101929034
CTD-2194D22.4
LOC101929153
CTD-2297D10.2
LOC101929261
LOC101929284
CTD-2201E9.1
LOC101929412
LOC101929454
CTD-2350J17.1
MIR6131
MIR6075
HRAT5
LINC01377
LINC01017
LOC105374620
LOC105374631
SNORD141A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
ARNT
BCL9
NOTCH2
TPM3
PDE4DIP
ADAR
CHRNB2
CTSK
CTSS
DRD5P2
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
NPR1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RNU1-4
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
SNAPIN
CA14
NBPF14
C1orf43
CHTOP
LCE2B
RNVU1-7
RNU1-3
RNU1-2
RNU1-1
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
LINC00869
S100A14
GATAD2B
CGN
ZNF687
PRUNE1
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
LIX1L
S100A16
CREB3L4
CIART
HFE2
ANKRD35
NBPF12
LELP1
BNIPL
SPRR4
NUDT4P2
PDIA3P1
LCE4A
NBPF11
NUDT17
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
FLG-AS1
LOC343052
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
NOTCH2NL
LINC01138
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
NUDT4P1
HIST2H2BF
NBPF18P
KPRP
LCE6A
FAM72C
ADAMTSL4-AS1
PRR9
PPIAL4G
FAM231D
NBPF13P
PPIAL4D
LOC645166
S100A7L2
EMBP1
SRGAP2B
SRGAP2C
PPIAL4A
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
FAM72D
NBPF8
LINC00623
LOC728989
PPIAL4E
PFN1P2
PDZK1P1
MIR190B
C1orf68
LOC100131107
LOC100132057
LOC100132111
NBPF10
FCGR1CP
C2CD4D
NBPF20
HYDIN2
LINC00624
MIR4257
LOC100505824
LOC100507670
TNFAIP8L2-SCNM1
MIR5698
MIR5087
SRGAP2-AS1
FALEC
UBE2Q1-AS1
SRGAP2D
RNVU1-8
LOC101927429
LOC101927468
GBAT2
LOC101928009
LOC101928034
LOC101928979
NBPF25P
LOC101929798
RNVU1-4
RNVU1-14
RNVU1-15
RNVU1-20
RNVU1-17
RNVU1-3
RNVU1-1
RNVU1-6
RNVU1-19
MIR6737
MIR6878
MIR6736
MIR6077
MIR8083
CH17-408M7.1
LOC103091866
LOC105371433

Genes in Wide Peak

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

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

Genes
ASPSCR1
FASN
GPS1
MAFG
PYCR1
PCYT2
RAC3
RFNG
ALYREF
DCXR
ANAPC11
SIRT7
DUS1L
MAFG-AS1
NOTUM
CENPX
LRRC45
MYADML2
NPB
SNORD134

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.3.

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

Genes
CALCR
COL1A2
DLX5
DLX6
DYNC1I1
GNG11
GNGT1
PDK4
PON1
PON2
PON3
SHFM1
TFPI2
SGCE
SLC25A13
BET1
PEG10
ASB4
PPP1R9A
SDHAF3
CASD1
DLX6-AS1
C7orf76
MIR489
MIR591
MIR653
LOC100506136
MIR4652
LOC105375401

Genes in Wide Peak

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

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

Genes
CXADR
TMPRSS15
NRIP1
BTG3
USP25
CHODL-AS1
C21orf91
SAMSN1
CHODL
C21orf91-OT1
LOC388813
MIR99AHG
MIRLET7C
MIR125B2
MIR99A
MIR548X
LINC01549
SAMSN1-AS1
MIR548XHG

Genes in Wide Peak

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

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

Genes
OR4F17
WASH5P
LINC01002
FAM138A
FAM138C
MIR1302-2
MIR1302-9
MIR1302-10
MIR1302-11

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.3.

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

Genes
FOXD4
KANK1
CBWD1
DOCK8
C9orf66
FAM138A
FAM138C
WASH1
DDX11L5
MIR1302-2
MIR1302-9
MIR1302-10
MIR1302-11
PGM5P3-AS1

Genes in Wide Peak

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

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

Genes
GCLC
GSTA1
GSTA2
GSTA3
GSTA4
GCM1
TRAM2
ICK
FBXO9
TMEM14A
ELOVL5
EFHC1
RN7SK
GSTA5
TRAM2-AS1
RPS16P5
LOC730101
GSTA7P
MIR5685

Genes in Wide Peak

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

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

Genes
NKX2-1
FOXA1
PAX9
NKX2-8
SLC25A21
MIPOL1
SFTA3
TTC6
LINC00517
SLC25A21-AS1
NKX2-1-AS1
MIR4503

Genes in Wide Peak

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

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

Genes
BCR
SMARCB1
CLTCL1
ADORA2A
ARVCF
COMT
CRKL
DDT
GGT3P
GGT5
GNAZ
GP1BB
GSC2
GSTT2
SERPIND1
IGLL1
MIF
MMP11
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
VPREB1
ZNF70
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
TOP3B
P2RX6
SNAP29
RAB36
PPM1F
DGCR2
TXNRD2
USP18
HIC2
SPECC1L
CABIN1
PRAME
TSSK2
SDF2L1
PPIL2
GSTTP1
DGCR11
DGCR9
POM121L1P
DGCR5
DGCR10
FBXW4P1
TRMT2A
RSPH14
POM121L9P
POM121L8P
YPEL1
ZDHHC8
VPREB3
DRICH1
MED15
UPB1
TUBA8
DGCR8
GNB1L
SUSD2
MRPL40
RTN4R
SLC2A11
C22orf29
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
GGTLC2
GUSBP11
DERL3
BMS1P20
TUBA3FP
C22orf39
TANGO2
ZNF280A
ZNF280B
LINC00895
LINC00896
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
C22orf15
CCDC116
POM121L4P
RGL4
LOC284865
MIF-AS1
PI4KAP2
CCDC188
LOC388882
LOC391322
LRRC74B
BCRP2
CHCHD10
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
FAM230B
LOC642643
TMEM191C
ADORA2A-AS1
LL22NC03-63E9.3
PRAMENP
CES5AP1
FAM230A
GSTTP2
GSTT2B
MIR649
MIR650
TMEM191B
PI4KAP1
LOC729461
DDTL
MIR301B
MIR1286
MIR1306
IGLL5
MIR3618
SEPT5-GP1BB
MIR4761
LINC01311
MIR5571
LOC100996335
LOC100996415
LOC100996432
SPECC1L-ADORA2A
LOC101927859
LOC101928891
LOC101929374
PCAT14
MIR6816
LOC102725072

Genes in Wide Peak

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

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

Genes
RPS5
MZF1
ZNF132
UBE2M
TRIM28
SLC27A5
ZNF324
CHMP2A
ZNF446
CENPBD1P1
ZBTB45
ZNF837
ZNF497
ZNF584
ZNF324B
RNF225
MZF1-AS1
MIR4754
MIR6807
LOC105372483

Genes in Wide Peak

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

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

Genes
FANCG
PAX5
ANXA2P2
NUDT2
AQP3
AQP7
CA9
CCIN
CD72
CLTA
CNTFR
GALT
IL11RA
NFX1
NPR2
PRSS3
RMRP
CCL19
CCL21
TESK1
TLN1
TPM2
VCP
RECK
RGP1
MELK
RUSC2
GNE
SIGMAR1
CREB3
UNC13B
CCL27
PTENP1
DCTN3
PHF24
DNAJB5
DCAF12
SPAG8
DNAI1
SIT1
STOML2
UBAP1
CHMP5
TMEM8B
UBE2R2
UBAP2
OR2S2
KIAA1161
GBA2
NOL6
FAM214B
HINT2
C9orf24
PIGO
ARHGEF39
LINC00950
ARID3C
RPP25L
C9orf131
RNF38
GLIPR2
LINC00961
ATP8B5P
FAM219A
CCDC107
FAM205A
KIF24
ENHO
FAM205BP
FAM221B
OR13J1
CNTFR-AS1
SUGT1P1
ANKRD18B
HRCT1
MSMP
LOC730098
FAM166B
SNORD121A
FAM205C
MIR4667
MIR4540
MIR4475
MIR4476
PTENP1-AS
SNORD121B
DNAJB5-AS1
LOC101926948
LINC01251
MIR6851
MIR6852
MIR6853

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 - 26 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	3.342e-35	3.342e-35	chr9:21860002-22449999	4
8p23.2	1.5115e-15	1.5115e-15	chr8:2130002-6410000	3
17p11.1	2.8668e-11	2.8824e-11	chr17:21290002-27129999	7
Yq11.23	3.6755e-09	3.4739e-09	chrY:14050001-56959204	51
10q23.31	1.1666e-07	1.1666e-07	chr10:87850002-88280000	2
14q11.2	3.2018e-07	3.2976e-07	chr14:1-20069999	22
21p11.2	3.9897e-07	3.906e-07	chr21:7820002-8439999	10
1p21.1	9.2609e-06	9.2609e-06	chr1:100730002-118889999	179
13q11	4.3658e-06	0.00010721	chr13:1-18870000	2
5q12.1	0.00013501	0.00013501	chr5:58950002-60490000	2
4q35.2	0.00030542	0.00030528	chr4:153780001-190179999	167
Xq21.1	0.00029273	0.00030528	chrX:1-156040895	1112
3p13	5.3355e-05	0.00065358	chr3:44620001-87989999	368
2q22.1	0.00031701	0.001434	chr2:140570002-142879999	1
18q22.1	0.0015562	0.0015921	chr18:40090002-80373285	196
22p11.2	0.0017517	0.0016842	chr22:10960001-16940000	14
13q14.2	0.00029273	0.0019411	chr13:35450001-69709999	214
4p16.3	0.0045054	0.0046896	chr4:1-44630000	285
2q37.3	0.0033518	0.027601	chr2:207760001-242193529	337
6q22.1	0.02892	0.027601	chr6:72210001-170805979	579
3p11.1	0.0016725	0.03693	chr3:81090001-94010000	18
21q22.3	0.041296	0.041732	chr21:36040002-46709983	177
11p15.5	0.099293	0.096313	chr11:1-45099999	497
Xq22.3	0.051228	0.10605	chrX:108140002-108790000	4
11q22.3	0.14148	0.13804	chr11:70460001-135086622	593
19q11	0.22668	0.22903	chr19:1-58617616	1750

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
CDKN2A-AS1
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
CSMD1
LOC100287015
LOC101927815

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p11.1.

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

Genes
KCNJ12
FAM27E5
FLJ36000
C17orf51
KCNJ18
MTRNR2L1
LOC105371703

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Yq11.23.

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

Genes
DAZ1
RBMY1A1
KDM5D
PRY
XKRY
BPY2
VCY
CDY1
EIF1AY
CDY2A
NLGN4Y
DAZ3
DAZ2
DAZ4
TTTY5
TTTY9A
TTTY13
TTTY14
GOLGA2P2Y
TTTY6
HSFY1
CSPG4P1Y
TTTY3
TTTY4
RPS4Y2
HSFY2
RBMY2EP
RBMY2FP
RBMY1F
CDY2B
TTTY10
TXLNGY
TTTY17A
BCORP1
FAM41AY1
VCY1B
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 10q23.31.

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
OR4K5
OR11H2
OR4K1
OR4K15
OR4K14
OR4L1
OR4N2
OR4K2
OR4K13
POTEG
OR11H12
OR4Q3
OR4M1
DUXAP10
POTEM
LOC642426
LINC01296
LOC100508046
POTEH-AS1
BMS1P17
LOC101929572
BMS1P22

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21p11.2.

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

Genes
MIR663A
RNA5-8S5
RNA18S5
RNA28S5
MIR3687-1
MIR3648-1
LOC100507412
MIR6724-1
MIR6724-2
MIR6724-3

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RBM15
ADORA3
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
S1PR1
CELSR2
EXTL2
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TSHB
WNT2B
CSDE1
TTF2
SLC16A4
CD101
LRIG2
TSPAN2
BCAS2
CEPT1
VAV3
LAMTOR5
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
NTNG1
WDR47
CLCC1
PTPN22
CHIA
GPSM2
SLC25A24
DPH5
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
TMIGD3
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1-AS1
STRIP1
DNAJA1P5
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
DRAM2
PIFO
C1orf162
SYT6
NBPF4
SLC30A7
CHIAP2
DENND2C
FNDC7
UBL4B
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
C1orf137
MIR197
LOC440600
LOC440602
BCL2L15
PGCP1
SPATA42
CYMP
LOC643355
LOC643441
ACTG1P4
NBPF6
SCARNA2
MIR942
LOC100129138
LINC01160
AP4B1-AS1
MIR320B1
MIR4256
FAM212B-AS1
SLC16A1-AS1
MIR548AC
VAV3-AS1
KCNC4-AS1
KCND3-AS1
KCND3-IT1
LOC100996251
LOC100996263
LINC01356
LAMTOR5-AS1
LOC101928370
LOC101928436
LOC101928476
LOC101928718
HIPK1-AS1
LOC101928977
LOC101928995
LOC101929023
LOC101929099
MIR7852
LOC102606465
LINC01397
LINC01307
LINC01525

Genes in Wide Peak

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

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

Genes
FAM230C
LINC00417

Genes in Wide Peak

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

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

Genes
PDE4D
MIR582

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

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

Genes
DUX4
hsa-mir-1979
AGA
SLC25A4
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PLRG1
PPID
MSMO1
SFRP2
TDO2
TLL1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
ANP32C
FAM149A
FBXO8
PDLIM3
SPOCK3
AADAT
FAM198B
ASIC5
GALNT7
CLDN22
DCHS2
HPF1
MARCH1
NEIL3
TMEM144
TMA16
UFSP2
DDX60
CDKN2AIP
TENM3
LRP2BP
PDGFC
FSTL5
STOX2
CFAP97
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
CENPU
HAND2-AS1
MAP9
WWC2
CEP44
SNX25
TKTL2
CBR4
LOC90768
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
WWC2-AS2
FAM218A
C4orf45
TRIM60
RBM46
C4orf46
TMEM192
RWDD4
PRIMPOL
TRIML2
CCDC110
CYP4V2
F11-AS1
LINC01098
LOC339975
TRIML1
LOC340017
ANKRD37
LOC389247
TRIM61
HELT
LINC01060
FAM92A1P2
LOC441052
C4orf47
GALNTL6
FRG2
SLED1
FLJ38576
MIR578
LINC00290
LOC728175
MIR3945HG
CLDN24
MIR1305
DBET
MIR548T
MIR4276
MIR3945
MIR3688-1
LINC01207
APELA
LOC100506085
LOC100506107
LOC100506122
LINC01093
LOC100506272
MIR4455
MIR4454
MIR3688-2
LOC101928052
LOC101928131
LINC01179
LINC01612
LOC101928314
LOC101928509
LOC101928551
LOC101928590
LINC01099
WWC2-AS1
LINC01262
LOC101930370
MIR6082
LOC102723766
LOC102724776
LVCAT8
LOC105377590
LINC01596

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.1.

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

Genes
ATRX
ELF4
GATA1
GPC3
MSN
MTCP1
NONO
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
CRLF2
P2RY8
hsa-mir-220a
hsa-mir-362
hsa-mir-1308
ABCB7
AGTR2
NR0B1
ALAS2
ABCD1
AMELX
SLC25A5
SLC25A6
XIAP
SHROOM2
AR
ARAF
ARHGAP4
ARHGAP6
ARR3
STS
ARSD
ARSE
ARSF
ASMT
ATP2B3
ATP6AP1
ATP7A
AVPR2
BGN
BMX
BRS3
BTK
CACNA1F
S100G
CAPN6
CD40LG
CDR1
CDX4
CETN2
CHM
CLCN4
CLCN5
CLIC2
CNGA2
COL4A5
COL4A6
COX7B
CSF2RA
CSTF2
TEX28
CYBB
CYLC1
DCX
DDX3X
TIMM8A
DIAPH2
DKC1
DLG3
DMD
DNASE1L1
DRP2
TSC22D3
DUSP9
EDA
EFNB1
EIF1AX
EIF2S3
ELK1
EMD
F8
F9
ACSL4
FANCB
GPC4
FGD1
FGF13
FHL1
VEGFD
FLNA
FMR1
AFF2
CENPI
G6PD
GAGE1
GABRA3
GABRE
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
OPN1MW
GDI1
GJB1
GK
GLA
GLRA2
GLUD2
GPM6B
CXCR3
LPAR4
GPR34
GRIA3
GRPR
GUCY2F
HSD17B10
HCCS
HCFC1
HMGB3
HNRNPH2
HPRT1
ERAS
HTR2C
IDH3G
IDS
IGBP1
IGSF1
IL2RG
IL3RA
IL9R
IL13RA1
IL13RA2
IRAK1
ANOS1
KCND1
L1CAM
LAMP2
PRICKLE3
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
MCF2
MECP2
CD99
MID1
FOXO4
MPP1
CITED1
MTM1
NAP1L2
NAP1L3
NDP
NDUFA1
NHS
GPR143
TBC1D25
OCRL
OPHN1
OTC
P2RY4
PAK3
CDK16
PDHA1
PDK3
CFP
PFKFB1
PGK1
PHEX
PHKA1
PHKA2
PIGA
PIN4
PLP1
PLP2
PLS3
PLXNB3
POLA1
POU3F4
PPEF1
PRKX
PRPS1
PRPS2
PRRG1
PSMD10
RBBP7
RBM3
OPN1LW
RENBP
RP2
RPGR
RPL10
RPL39
RPL36A
RPS4X
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SH3BGRL
SHOX
SLC6A8
SLC16A2
SMARCA1
SMS
SOX3
SRD5A1P1
SSR4
SSX5
CDKL5
SUV39H1
VAMP7
SYN1
SYP
TAF1
TAZ
SERPINA7
TBL1X
DYNLT3
TDGF1P3
TIMP1
TSPAN7
TSPAN6
TMSB4X
TRO
TRPC5
UBA1
UBE2A
SLC35A2
VBP1
XG
XIST
XK
XPNPEP2
ZFX
ZIC3
ZNF711
ZNF182
ZNF41
ZNF75D
ZNF157
RNF113A
ZNF185
ZXDA
GTPBP6
PUDP
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
SRPX
UXT
CUL4B
IRS4
OGT
OFD1
IKBKG
PIR
INE2
INE1
CASK
ASMTL
PAGE1
MTMR1
FGF16
AKAP4
APLN
AP1S2
GYG2
FAM127A
SLC25A14
CLDN2
RGN
FAM50A
AIFM1
TMEM257
REPS2
ZBED1
ZMYM3
BMP15
GPR50
MED14
TCEAL1
RAB33A
RAB9A
TSIX
ITM2A
ARHGEF6
PCYT1B
MAGED1
XAGE2
PAGE4
MORF4L2
GPRASP1
STARD8
FRMPD4
JADE3
ARMCX2
HEPH
MAGEC1
AMMECR1
MED12
ZBTB33
HDAC6
MAMLD1
HUWE1
PQBP1
BCAP31
ADGRG2
ATP6AP2
TENM1
SSX3
TIMM17B
SPRY3
RRAGB
SCML2
SLC9A6
ENOX2
PRDX4
EBP
STAG2
RAI2
PLAC1
CYSLTR1
UTP14A
DIAPH2-AS1
ZNF275
PGRMC1
MAGED2
MSL3
TMSB15A
PIM2
MID2
IL1RAPL1
WDR45
TREX2
PRAF2
CA5B
SLC6A14
KLF8
VSIG4
CNKSR2
IQSEC2
PHF8
SEPT6
ARHGEF9
ATP1B4
ACOT9
KCNE5
LDOC1
SMPX
GSPT2
KIF4A
FTSJ1
HYPM
MXRA5
EGFL6
FAM127B
IL1RAPL2
ITGB1BP2
SRPK3
VCX
GAGE12I
GAGE2E
SNORA70
SNORA69
SNORD61
RNU6-1
BEX3
NOX1
FAM155B
INGX
GPR82
GPKOW
SRPX2
APEX2
RBMX
PCDH11X
RPS6KA6
P2RY10
HTATSF1
PCSK1N
PPP2R3B
CCDC22
MCTS1
MAGEH1
FAM156A
C1GALT1C1
SNX12
RPA4
PNMA3
UBQLN2
SH3KBP1
SPANXA1
CTAG2
NSDHL
FOXP3
TBX22
ZDHHC9
RLIM
TCEAL9
RAB9B
LUZP4
PDZD11
PBDC1
TFDP3
TLR7
ARMCX1
TLR8
MBTPS2
MAGEC2
VGLL1
VCX2
VCX3A
ARMCX3
TAF9B
RBMX2
STK26
CPXCR1
CHIC1
FTHL17
GPR173
NLGN3
SASH3
TAF7L
SPIN2A
ARMCX6
WDR44
NDUFB11
GNL3L
ERCC6L
NUP62CL
GDPD2
BCOR
TBC1D8B
FAM120C
GEMIN8
CT55
TMEM255A
CXorf57
NUDT11
TMLHE
RBM41
PLCXD1
SAGE1
PLXNA3
HAUS7
OTUD5
ZNF280C
MTMR8
KRBOX4
TXLNG
MBNL3
WWC3
FAM45BP
BEX1
HDAC8
GABRQ
ZC4H2
NXT2
NKRF
NXF5
NXF4
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
MOSPD1
BEX4
CTPS2
CHST7
TCEAL7
GRIPAP1
THOC2
ZNF630
TMEM27
SHROOM4
KIAA1210
NLGN4X
PCDH19
RGAG1
PDZD4
LRCH2
MAGEE1
RAP2C
MID1IP1
ACE2
TMEM35A
FAM3A
EDA2R
NYX
BCORL1
DUSP21
CXorf56
DMRTC1
TSPYL2
TNMD
PJA1
SPANXD
SPANXC
WDR13
PORCN
ARMCX5
UPF3B
WNK3
FUNDC2
PRRG3
APOO
BRCC3
HMGN5
NKAP
RNF128
MAP7D3
MORC4
CXorf36
LONRF3
ALG13
MAGIX
TCEAL4
TRMT2B
POF1B
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
ESX1
BHLHB9
MAGED4B
LAS1L
GPR101
TMEM47
CD99L2
USP26
FRMD8P1
MAGT1
TMEM164
PHF6
FRMPD3
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
SLC9A7
BEX2
MIR503HG
SLC7A3
PNMA6A
TCEAL3
CCNB3
PPP1R3F
FATE1
CCDC120
TSR2
HS6ST2
FRMD7
KLHL13
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
CXorf40A
FAM58A
RIPPLY1
LINC01278
ATXN3L
SLC38A5
MMGT1
ACRC
SYAP1
SYTL4
SYTL5
PNMA5
GPRASP2
ATG4A
RAB39B
DACH2
SLITRK4
SPANXN3
MAGEC3
BEND2
PASD1
DCAF12L1
DGKK
MAP2K4P1
PIH1D3
MUM1L1
FAM199X
AMER1
APOOL
HDX
FUNDC1
ADGRG4
PTCHD1
PPP4R3CP
MAGEB10
DCAF8L1
VENTXP1
OTUD6A
UPRT
MAGEE2
MAGEB16
FOXR2
GAB3
PNCK
ZFP92
ACTRT1
GPR119
PAGE3
RBMXL3
DOCK11
SPIN4
ASB11
ASB9
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
ZNF645
CSAG1
FMR1NB
USP27X-AS1
FAAH2
ZXDB
LINC00889
FAM47A
MOSPD2
ARHGAP36
RIBC1
AKAP14
RHOXF1
NKAPP1
MAGEB6
CXorf65
AWAT1
AWAT2
ZDHHC15
USP51
TCEAL6
CH17-340M24.3
H2BFWT
CXorf38
FAM122B
FAM122C
DDX53
FAM46D
SPIN3
FAM47B
SUPT20HL2
TCEANC
ZCCHC12
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
CT83
LINC01560
SLC25A43
FAM226A
ZCCHC5
NRK
INTS6L
ZNF449
VMA21
TMEM31
PAGE2
DHRSX
CTAG1A
BRWD3
CXorf58
CT47A11
CXorf23
MAP7D2
KLHL34
TAB3
MAGEA2B
SSX6
SSX7
SSX8
SSX9
RAB40AL
LINC00685
ATP11C
LINC00632
NLRP2B
H2BFM
LOC286437
LINC01281
YIPF6
CFAP47
FIRRE
UBE2E4P
TTC3P1
FAM133A
MAGEB18
TMSB15B
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
MORF4L2-AS1
VSIG1
ZC3H12B
SATL1
DCAF12L2
LOC340581
CA5BP1
ZCCHC16
LHFPL1
CXorf67
ZNF81
ITIH6
LANCL3
MPC1L
DCAF8L2
SOWAHD
OR13H1
CCDC160
CXorf66
DGAT2L6
RAB41
ARSH
MAGEB5
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
PAGE2B
ZCCHC13
LOC389895
UBE2NL
CSAG3
LOC389906
LOC392452
CXXC1P1
GLOD5
FLJ44635
ARL13A
SMIM10L2A
CD99P1
LOC401585
ZNF674-AS1
SLC25A53
LINC00890
XKRX
YY2
MIRLET7F2
MIR105-1
MIR105-2
MIR106A
MIR188
MIR19B2
MIR221
MIR222
MIR223
MIR224
MIR92A2
MIR98
VCX3B
FTH1P18
LINC00891
RPS26P11
GLRA4
FAM127C
CT45A3
CT45A5
SPANXN4
PGAM4
FAM47C
UQCRBP1
XRCC6P5
MIR325
MIR374A
SPIN2B
H2AFB2
H2AFB1
F8A2
SPANXN1
SPANXN2
SPANXN5
MIR361
MIR384
MIR424
CT45A6
CT45A1
CXorf40B
SSX4B
LINC01420
JPX
MIR448
MIR450A1
MIR362
MIR363
MIR20B
MIR18B
MIR452
MIR500A
MIR501
MIR502
MIR450A2
MIR503
MIR504
MIR505
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
ZNF674
DANT2
CT47B1
BRDTP1
ZCCHC18
SMIM10
SMIM10L2B
GAGE2B
GAGE13
GAGE12G
LOC645188
MAGEB17
PABPC1L2B
NAP1L6
XAGE1B
CT47A7
MIR545
MIR542
SCARNA23
SNORA11
SNORA35
SNORA36A
SNORA56
SNORD96B
MIR421
MIR532
MIR651
MIR652
MIR660
LINC01545
SSX2B
DDX11L16
FAM156B
CT47A10
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGED4
MAGEA9B
OPN1MW2
SPANXB1
CT45A2
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE2A
LOC729609
LINC00106
H2BFXP
MIR767
MIR766
GAGE12F
GS1-600G8.3
GAGE8
SNORA11C
SNORA11D
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR374B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100126447
WASIR1
LINC00892
GPR50-AS1
CXorf51A
LOC100129291
LINC00684
LINC01546
LINC00633
TEX13C
FGF13-AS1
HSFX2
SUPT20HL1
CXorf49
PRR32
CSAG4
LINC00893
ARMCX4
UBE2DNL
PHKA2-AS1
LOC100132304
GAGE12D
XGY2
LOC100132831
SMIM9
FAM223A
LINC01203
UXT-AS1
SCARNA9L
CMC4
LINC00894
LOC100287728
LINC00630
CLDN34
MIR1184-1
MIR513C
MIR1468
MIR1912
MIR1298
MIR320D2
MIR1321
MIR548I4
MIR1277
MIR1911
MIR548F5
MIR1264
FTX
SLC25A5-AS1
MIR548M
MIR718
MIR513B
MIR764
MIR2114
TRPC5OS
LINC00102
LOC100421746
MIR514B
MIR3202-2
MIR500B
MIR4330
MIR4328
MIR1184-3
MIR1184-2
MIR3202-1
MIR4329
MTRNR2L10
MIR374C
MIR23C
MIR3937
MIR3672
MIR676
MIR3690
MIR3915
HSFX1
LINC00629
LOC100506790
CT47A12
ARMCX5-GPRASP2
RPL36A-HNRNPH2
PIR-FIGF
MAGEA10-MAGEA5
MIR548AN
MIR4769
MIR4536-1
MIR4454
MIR4768
MIR1587
MIR548AJ2
MIR4770
MIR548AM
MIR4767
MIR3978
MIR4666B
MIR664B
MIR548AX
PTCHD1-AS
NHS-AS1
SYP-AS1
ZFX-AS1
DLG3-AS1
PHEX-AS1
PRKX-AS1
MED14OS
HCFC1-AS1
PPEF1-AS1
EIF1AX-AS1
PCYT1B-AS1
HS6ST2-AS1
DDX26B-AS1
ZNF630-AS1
FRMPD3-AS1
MID1IP1-AS1
ARHGEF9-IT1
LINC00269
LCA10
TCP11X2
LOC101059915
CHMP1B2P
CT45A7
OPN1MW3
LINC00850
MAGEA8-AS1
LINC01284
PLS3-AS1
LINC01282
LOC101927476
LOC101927501
LINC01204
LINC01186
LOC101927635
LOC101927830
LOC101928128
LOC101928201
LOC101928259
LINC01285
LOC101928335
LOC101928336
PABPC1L2B-AS1
LOC101928358
LOC101928389
LOC101928402
LOC101928437
MIR325HG
LOC101928495
RAP2C-AS1
LOC101928627
LOC101928917
RHOXF1P1
RHOXF1-AS1
RNU6-7
MIR6087
MIR6089
MIR6134
MIR6857
MIR6858
MIR6895
MIR7641-2
MIR6086
MIR892C
MIR6894
MIR8088
LINC01496
KANTR
CT45A10
CT45A9
PABPC5-AS1
GAGE10
RNU6-2
LINC01201
LINC01402
GS1-594A7.3
LINC01456
LOC105373156
LOC105373185
LOC105373300
LOC105373338
LOC105373368
LOC105373378
LOC105373383
LOC105377213
XACT
SNORA109

Genes in Wide Peak

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

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

Genes
FHIT
MITF
BAP1
FOXP1
SETD2
PBRM1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ERC2-IT1
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GBE1
GNAI2
GNAT1
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
CNTN3
PDHB
PFKFB4
PLXNB1
POU1F1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
ROBO1
ROBO2
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
TMF1
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RRP9
MAGI1
CACNA2D2
DCAF1
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
ARL6IP5
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
RAD54L2
FRMD4B
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
PTPN23
CHMP2B
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZDHHC3
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
ELP6
QRICH1
PXK
FEZF2
EBLN2
DALRD3
SHQ1
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
SELK
PROK2
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
LRRC2-AS1
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
UCN2
ZNF502
RFT1
ACTR8
SLC25A26
ZNF501
GPR62
FAM3D
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
LSMEM2
ASB14
FAM19A4
CCDC12
PPP4R2
PRICKLE2
C3orf67
KCTD6
KLHDC8B
LINC00870
DNAH12
PDE12
DENND6A
CADM2
ALS2CL
TMIE
EOGT
FBXW12
LINC00877
CCDC66
KIF9-AS1
LINC00698
EIF4E3
CCDC36
PRSS42
SPATA12
C3orf62
TMEM110
PRSS45
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LINC00960
MIRLET7G
MIR135A1
MIR191
FAM19A1
TMEM89
IQCF6
SMIM4
LINC00971
MIR425
LIMD1-AS1
SPINK8
ARIH2OS
C3orf84
SNORD19
FAM86DP
SNORD69
MIR564
MIR566
GXYLT2
LOC728290
CCR2
ESRG
SNORD19B
LINC00696
SEMA3F-AS1
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LINC00994
FRG2C
MIR1284
MIR1324
MIR1226
MIR2115
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
MIR3923
PRKAR2A-AS1
IQCF4
PTPRG-AS1
PSMD6-AS2
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4444-1
MIR4443
PRICKLE2-AS1
RBM5-AS1
LINC00506
MIR5688
MIR5193
MAGI1-AS1
ITIH4-AS1
SYNPR-AS1
CADM2-AS2
THOC7-AS1
GLYCTK-AS1
ARHGEF3-AS1
CACNA2D3-AS1
PRICKLE2-AS2
PRICKLE2-AS3
LARS2-AS1
FCF1P2
SUCLG2-AS1
SAMMSON
PDZRN3-AS1
LOC101927296
LOC101927374
LOC101927494
SEMA3B-AS1
IQCF5-AS1
LOC101929054
LOC101929159
C3orf67-AS1
ADAMTS9-AS1
RASSF1-AS1
MIR5787
MIR6823
MIR6824
MIR6872
MIR6890
MIR8064
LOC102724297
CELSR3-AS1
MIR548BB
FOXP1-AS1
LOC105377102
LOC105377105
FAM3D-AS1
LOC105377143
LOC105377146
LOC105377162
ARF4-AS1
SNORD136
SNORA94
SNORA95

Genes in Wide Peak

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

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

Genes
MIR7157

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

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

Genes
BCL2
MALT1
ATP5A1
CDH7
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TCF4
ZNF236
SLC14A2
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
CTIF
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
EPG5
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
KATNAL2
MRO
HDHD2
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CFAP53
GTSCR1
DOK6
RNF152
LINC00305
LOC284241
DYNAP
BOD1L2
LINC00907
SIGLEC15
ZADH2
SMIM21
LINC00908
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
OACYLP
LINC01538
LOC400655
LINC00909
C18orf65
LINC00683
LOC400661
MIR122
HSBP1L1
RNF165
C18orf32
KC6
LOC643542
C18orf63
SKOR2
SCARNA17
SNORA37
TCEB3CL
SNORD58C
PARD6G-AS1
LOC100131655
LINC01630
MIR1539
MIR4319
MIR4320
LINC01539
LOC100505549
LINC01541
LOC100505797
LOC100505817
LOC100505853
RBFADN
TCEB3CL2
RPL17-C18orf32
MIR4528
MIR4527
MIR4529
MIR3591
MIR4743
MIR4744
MIR5011
MIR548AV
LINC-ROR
LINC01544
LOC101060542
LOC101927229
LINC01416
LOC101927322
LOC101927481
LOC101927606
LOC101927651
LINC01029
LINC01478
SLC14A2-AS1
LOC101927989
LOC101928167
LOC102724651
LOC102724913
SNHG22
TCF4-AS1
LOC105372179
LOC105667213
SNORA108

Genes in Wide Peak

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

Table S41. 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 13q14.2.

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

Genes
LCP1
RB1
LHFP
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
PCDH9
RFXAP
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
ITM2B
MTRF1
UTP14C
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
VWA8
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
RGCC
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
GPALPP1
SUPT20H
THSD1
CYSLTR2
SPRYD7
COG6
PCDH20
SMIM2
NAA16
RNASEH2B
DHRS12
RUBCNL
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
LINC00284
CSNK1A1L
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
ERICH6B
SPERT
DLEU7
FAM124A
TPTE2P3
LRRC63
CTAGE10P
SLC25A30
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
LINC00550
FREM2
NEK5
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
TUSC8
MIR15A
MIR16-1
ALG11
TSC22D1-AS1
LINC00598
LINC00371
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
LINC00462
TPT1-AS1
MIR1297
MIR759
MIR320D1
MIR3168
MIR4305
MIR3169
MIR3613
OR7E37P
LINC00445
SPG20-AS1
VWA8-AS1
INTS6-AS1
LINC00458
CPB2-AS1
CCDC169-SOHLH2
MIR4704
MIR548X2
MIR4703
TPTE2P5
MIR5007
MIR5693
MIR5006
LINC00562
LINC00558
LINC00563
LINC00441
MED4-AS1
PCDH9-AS2
DLEU7-AS1
HTR2A-AS1
PCDH9-AS3
PCDH9-AS4
LINC00332
ENOX1-AS2
LINC00358
LINC00364
LINC00366
LINC00395
LINC00400
LINC00434
LINC00448
LINC00571
DIAPH3-AS1
DIAPH3-AS2
RNASEH2B-AS1
SLC25A30-AS1
SMIM2-IT1
MRPS31P5
LOC101926897
LINC00378
LOC101926951
LINC00437
LOC101929140
SMIM2-AS1
LOC101929259
LINC01198
LOC101929657
MIR8079
LINC01065
LOC102723968
LOC103191607
LINC01050
LINC00383
DLEU1-AS1
LINC01048
LINC01055
LINC01075
LINC00428
LINC00376
LOC105370177
LINC00390
LOC105370203
LINC01052
LINC00374
SETDB2-PHF11

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
PHOX2B
ADD1
ADRA2C
APBB2
RHOH
ATP5I
NKX3-2
BST1
CCKAR
CD38
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GAK
GRK4
HTT
HGFAC
UBE2K
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RFC1
RGS12
RNF4
RPL9
S100P
SH3BP2
SOD3
TLR1
UCHL1
UGDH
WFS1
NELFA
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
LINC01587
MFSD10
MAEA
TLR6
PCGF3
ATP8A1
SPON2
TACC3
SLC30A9
SLC34A2
MXD4
PTTG2
CPLX1
SLC26A1
PPARGC1A
LIAS
LIMCH1
TBC1D1
SEL1L3
PDS5A
MAN2B2
FBXL5
NSG1
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
KLHL5
SEPSECS
KLF3
STX18
FGFRL1
CYTL1
SH3TC1
RBM47
NKX1-1
PIGG
DCAF16
TMEM33
LGI2
PGM2
C4orf19
TBC1D19
PI4K2B
BLOC1S4
STK32B
CHRNA9
LYAR
N4BP2
SLC2A9
NWD2
TBC1D14
SORCS2
CC2D2A
STIM2
UVSSA
WDR19
ZFYVE28
GBA3
AFAP1
NCAPG
TNIP2
HAUS3
KLF3-AS1
NSUN7
ABCA11P
TMEM156
GRPEL1
MED28
KCNIP4
TLR10
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
CTBP1-AS2
TMEM129
FAM114A1
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
ARAP2
CPEB2
EVC2
PACRGL
OTOP1
SHISA3
ZNF595
LINC01085
JAKMIP1
KLB
FAM53A
TRMT44
ADGRA3
ZBTB49
ZNF721
LINC00504
SMIM14
TAPT1
TAPT1-AS1
LCORL
ZNF718
CCDC96
BOD1L1
DCAF4L1
CTBP1-AS
CRIPAK
LOC285484
DOK7
LINC00955
RNF212
SEPSECS-AS1
LINC01097
LINC01096
FAM200B
NOP14-AS1
NAT8L
LOC344967
MSANTD1
FAM86EP
POLN
KCNIP4-IT1
KCTD8
LOC389199
SMIM20
BEND4
GRXCR1
USP17L6P
USP17L9P
C4orf48
DTHD1
LOC401127
CFAP99
MIR218-1
MIR95
LOC439933
CPEB2-AS1
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR571
MIR572
MIR573
MIR574
USP17L24
USP17L25
USP17L26
USP17L27
USP17L28
USP17L29
USP17L30
FLJ36777
RELL1
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L15
MIR548I2
MIR1255B1
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LVCAT1
STX18-AS1
LOC100508631
MIR378D1
MIR4802
MIR4800
MIR4801
MIR4798
HTT-AS
MIR5091
MIR5591
UGDH-AS1
LOC101060498
UCHL1-AS1
LINC00682
LOC101927363
LOC101928279
LOC101928306
LOC101928622
LINC01258
LOC101929019
LINC01182
LOC101929095
LOC101929123
LOC101929161
LOC101929199
MIR7978
LOC102723778
LOC102723828
LINC01396
STX18-IT1
LOC105374344
LOC105374366
LOC105374428
LOC105374516
LOC105374546
LOC105377651

Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
IDH1
PAX3
FEV
hsa-mir-1244-1
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
CNOT9
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ASIC4
DOCK10
MREG
PECR
C2orf83
MFF
ACKR3
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
LOC93463
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERF4
UBE2F
OTOS
COPS9
OR6B3
LOC150935
PKI55
KANSL1L
LINC01107
LOC151174
ERFE
CCDC140
SLC23A3
LINC00608
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
DAW1
C2orf57
PIKFYVE
TIGD1
LOC200772
CFAP65
C2orf72
RTP5
LOC285095
UNC80
RUFY4
DUSP28
MROH2A
ESPNL
ECEL1P2
SPATA3-AS1
CATIP
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
LOC440934
MIR375
LOC643387
LINC00607
LOC646736
PRSS56
AQP12B
SNORA75
LOC654841
SCARNA6
SCARNA5
MIR562
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3133
MIR3131
MIR4268
MIR3132
MIR4269
AGAP1-IT1
LOC100507443
IDH1-AS1
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4438
MIR4440
MIR4786
MIR4441
MIR5001
MIR5702
MIR5703
VWC2L-IT1
LOC100996693
CAPN10-AS1
LINC01237
LOC101927960
LOC101928020
LOC101928103
LOC101928111
LINC01280
LOC101928327
CATIP-AS1
LINC01494
LOC101928881
MIR6513
MIR6809
MIR6811
MIR6810
LOC102723927
LANCL1-AS1
LOC102724849
LOC102725079
MIR9500
CATIP-AS2
LINC01614
LOC105373876
DIRC3-AS1
LOC105373878
LINC01173

Genes in Wide Peak

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

Table S45. 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
BCKDHB
CCNC
CGA
CCR6
CNR1
COL10A1
COL12A1
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
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
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
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
MPC1
HECA
COQ3
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
PHF10
QRSL1
VNN3
DDX43
FAM46A
TMEM30A
ERMARD
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
SMIM8
ADGRG6
ARFGEF3
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
TMEM181
ZBTB2
BEND3
ABRACL
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
LINC01590
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
ARMT1
FAM184A
ZDHHC14
MANEA
ADGB
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
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
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
NUP43
C6orf58
RAET1G
GJB7
HMGA1P7
SNHG5
SUMO4
CENPW
SOGA3
LINC00222
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
TCP10L2
LOC401286
LINC00242
LINC01624
GTF2H5
OOEP
FAM26F
FLJ46906
LINC00602
LOC441178
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
MIR3144
MIR3145
MIR4282
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
LOC101928304
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
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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

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

Genes
EPHA3
GBE1
HTR1F
POU1F1
PROS1
CGGBP1
CHMP2B
ZNF654
CADM2
C3orf38
VGLL3
LINC00971
MIR4795
LINC00506
MIR5688
CADM2-AS2
LOC101927494
SNORA95

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
ERG
TMPRSS2
ADARB1
AIRE
PTTG1IP
C21orf2
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
DYRK1A
ETS2
HLCS
HMGN1
PRMT2
ITGB2
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SIM2
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
TTC3
U2AF1
UBE2G2
WRB
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DOPEY2
DSCR4
DSCR3
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
DNMT3L
ZBTB21
PIGP
UBASH3A
RIPPLY3
BRWD1
SLC37A1
PCBP3
C21orf58
YBEY
TSPEAR-AS1
TSPEAR
LINC00112
LINC00111
SETD4
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
COL18A1
LRRC3
SPATC1L
LINC01547
DSCR8
FAM207A
RSPH1
UMODL1
ERVH48-1
LINC00313
B3GALT5-AS1
LINC00334
TSPEAR-AS2
MCM3AP-AS1
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
UMODL1-AS1
PLAC4
DSCR9
DSCR10
LINC00323
LINC00319
AATBC
KRTAP12-2
KRTAP12-1
KRTAP10-10
PICSAR
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00316
LINC00114
LOC400867
LOC642852
LINC00163
SSR4P1
LINC00322
LOC100129027
LOC100133286
MIR3197
ITGB2-AS1
CBR3-AS1
DSCAM-AS1
MIR4760
MIR5692B
LRRC3-AS1
DIP2A-IT1
TTC3-AS1
BRWD1-AS1
COL18A1-AS2
DSCAM-IT1
LOC101928233
LOC101928311
LOC101928398
TCONS_00029157
LOC101928435
TRPM2-AS
LINC01424
LOC101928796
LOC101930094
MIR6070
MIR6814
MIR6815
MIR6508
LOC102724354
LOC102724428
U2AF1L5
LOC102724652
LINC01423
BRWD1-IT2
LOC105372795
LOC105372833
FRGCA
SNORA91
WRB-SH3BGR

Genes in Wide Peak

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

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

Genes
CARS
EXT2
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
MPPED2
CALCA
CALCB
CAT
CCKBR
CD44
CD59
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CSTF3
CTSD
DRD4
DUSP8
EIF4G2
ELF5
FSHB
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
CD82
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
CAPRIN1
MUC2
MUC5AC
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PAX6
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RAG1
RAG2
RCN1
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SLC1A2
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
BBOX1
PPFIBP2
IFITM1
API5
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
TP53I11
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
EIF3M
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
FJX1
KIAA1549L
ABTB2
PAMR1
FBXO3
SERGEF
EHF
OR5E1P
OR10A3
TIMM10B
ELP4
SNORD14A
DKK3
RBMXL2
PGAP2
COMMD9
C11orf21
TRPM5
UBQLN3
RNF141
APIP
HSD17B12
IGF2-AS
BET1L
CEND1
WT1-AS
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
TRIM44
USP47
TRIM68
NAT10
UEVLD
LIN7C
TCP11L1
LGR4
PIDD1
KCNQ1DN
SOX6
PARVA
TTC17
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
LRRC4C
SCUBE2
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
PRRG4
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
QSER1
PRR5L
PGGHG
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
ACCS
PTPN5
MICALCL
TRIM5
SNORD14B
NAV2
SYT8
TSPAN18
CCDC34
DEPDC7
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
DNAJC24
ARL14EP
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
LOC171391
METTL15
IMMP1L
OR56B4
ANO5
ALKBH3
LOC221122
TOLLIP-AS1
OR52B2
LMNTD2
OR51F1
SVIP
MRGPRX1
OR51B5
KRT8P41
SBF2-AS1
CSNK2A3
OR51V1
H19
CRACR2B
TMEM80
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
MRGPRG-AS1
NLRP10
NLRP14
ANO9
LUZP2
KRTAP5-AS1
KCNQ1-AS1
B4GALNT4
CSTF3-AS1
OR52L1
OR2AG2
OR52B6
OTOG
DCDC1
OR10A2
OVCH2
PDDC1
GALNT18
NCR3LG1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
NAV2-AS4
HNRNPKP3
OR51T1
OR51A4
OR51A2
IFITM10
MIR129-2
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
TRIM6-TRIM34
CCDC73
TMEM9B-AS1
LOC494141
BDNF-AS
MIR483
SNORA3A
SNORA52
LOC644656
RASSF10
TSSC2
SNORA23
SNORA3B
SNORA54
SNORD97
MIR610
INS-IGF2
MUC5B
ZBED5-AS1
SEC14L1P1
MIR675
LOC100126784
MRVI1-AS1
CAND1.11
C11orf91
FAM99B
LINC01001
MRPL23-AS1
MIR302E
MIR670
MIR3159
MIR4298
MIR4299
MTRNR2L8
CCDC179
LOC100506082
MIR210HG
LOC100506258
LINC00958
SPTY2D1-AS1
DCDC5
LOC100506675
LOC100507144
LOC100507205
MIR670HG
ALKBH3-AS1
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR3973
MIR4694
MIR1343
MIR4687
MIR5691
NAV2-AS5
NAV2-AS2
LINC00678
PANO1
LOC101927503
LINC01150
CD81-AS1
LOC101927708
OLFM5P
TUB-AS1
LOC101928008
LOC101928053
LOC101928132
FBXO3-AS1
LOC101928510
LINC01493
LOC101928591
MIR6073
MIR6743
MIR8054
MIR8070
MIR8087
MIR7847
MIR6744
MIR8068
MIR6124
LOC102723330
LINC01495
LINC01499
LOC102724784
LOC102724957
PAUPAR
LOC103312105
HOTS
BGLT3
CASC23
BBOX1-AS1
LINC01219
LOC105376554
LOC105376575
LOC105376599
LOC105376633
LOC105376671
LINC01616
SNORA88
SNORD131

Genes in Wide Peak

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

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

Genes
COL4A5
COL4A6
IRS4
LOC101928358

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
NUMA1
PAFAH1B2
POU2AF1
SDHD
PICALM
PCSK7
ARHGEF12
MAML2
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
PHOX2A
ARRB1
FXYD2
CXCR5
CAPN5
CASP1
CASP4
CASP5
SERPINH1
CD3D
CD3E
CD3G
CTSC
CHEK1
CLNS1A
CRYAB
DHCR7
DLAT
DLG2
DPAGT1
DRD2
ETS1
FDX1
FOLR1
FOLR2
FOLR3
FUT4
SLC37A4
LRRC32
GRIA4
GRIK4
GRM5
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
INPPL1
STT3A
KCNJ1
KCNJ5
KRTAP5-9
VWA5A
MAP6
MCAM
KMT2A
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYO7A
NCAM1
NDUFC2
NFRKB
NNMT
NPAT
NRGN
OMP
OPCML
P2RY2
P2RY6
PAK1
PDE2A
PGR
PPP2R1B
PRCP
THAP12
PTS
NECTIN1
RAB6A
RDX
SNORD15A
RPS3
RPS25
SC5D
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPRA
ST14
TAGLN
TECTA
THRSP
THY1
TRPC6
TYR
UCP2
UCP3
UPK2
UVRAG
WNT11
ZBTB16
ZNF202
CUL5
FZD4
BARX2
OR7E2P
JRKL
EED
ZPR1
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
SPCS2
ARHGEF17
GAB2
C2CD2L
FCHSD2
NAALAD2
KCNE3
IL18BP
RBM7
MPZL2
YAP1
HYOU1
ATP5L
POLD3
STARD10
NEU3
ME3
GPR83
SRSF8
ADAMTS8
PRSS23
TREH
SLCO2B1
CEP164
SHANK2
IGSF9B
ENDOD1
EXPH5
PHLDB1
FAM168A
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
RAB38
CADM1
PANX1
POU2F3
CHRDL2
ANAPC15
TSKU
HINFP
REXO2
C2CD3
TENM4
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
CHORDC1
ACAD8
B3GAT1
RAB30
DCPS
C11orf54
AAMDC
ZBTB44
THYN1
DDX25
NOX4
NTM
CDON
SIDT2
COA4
TRAPPC4
PPME1
HIKESHI
CWC15
PCF11
MRPL48
RSF1
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
SYTL2
ANKRD49
TTC12
LAMTOR1
NADSYN1
FAM86C1
C11orf57
RNF121
ACER3
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TMEM126B
TEX12
CRTAM
TMPRSS4
IFT46
SMCO4
EMSY
PRDM10
TRIM49
DSCAML1
GRAMD1B
USP35
CEP126
ARHGAP20
USP28
KRTAP5-8
PLEKHB1
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TMEM135
KCTD14
ALG8
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
NARS2
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
MOGAT2
PAAF1
PDGFD
TMPRSS5
GDPD5
CLPB
PUS3
JAM3
BCO2
TMEM133
TMPRSS13
TMEM126A
DCUN1D5
MSANTD4
KIRREL3
DGAT2
BUD13
TMEM25
RPUSD4
TBRG1
RELT
UBASH3B
C11orf70
SNORD14C
SNORD14D
SNORD14E
DIXDC1
CEP295
ZC3H12C
ATG16L2
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
INTS4
VPS26B
GLB1L3
SNORD15B
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
ARAP1
SLC36A4
FAT3
TRIM64
TMEM45B
COLCA2
PIH1D2
NXPE1
NXPE2
JAML
XRRA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
DEUP1
PATE1
C11orf65
ADAMTS15
B3GNT6
MPZL3
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
GDPD4
DDIAS
CCDC83
SHANK2-AS3
LRTOMT
HEPACAM
OAF
FAM181B
CCDC89
DEFB108B
ANGPTL5
RNF169
ANKK1
RNF214
AQP11
LOC283140
LINC00900
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
C11orf44
MIR4697HG
LOC283177
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
ALG1L9P
CCDC84
TMEM225
OR8D4
ANKRD42
C11orf53
LOC341056
OR2AT4
HEPHL1
PLET1
DNAJB13
KRTAP5-10
LIPT2
VSTM5
LOC387810
GUCY2EP
TRIM77
IZUMO1R
KDM4E
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
FLJ42102
TRIM49D1
C11orf87
COLCA1
C11orf88
MIR100HG
PATE2
PATE4
ST3GAL4-AS1
SNX19
LOC403312
MIRLET7A2
MIR100
MIR125B1
MIR139
MIR34B
MIR34C
DDI1
BLID
KRTAP5-7
KRTAP5-11
CASP1P2
CARD17
LINC00167
MIR326
SCARNA9
HEPN1
TRIM64B
TRIM53AP
TRIM49C
UBTFL1
C11orf97
LOC643733
LOC643923
CLDN25
LOC646029
LOC646522
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49D2
MIR708
LOC100128239
LOC100128386
LOC100128494
LOC100129203
LOC100129216
ZNF705E
LOC100131626
LOC100132078
LOC100132686
LOC100133315
PATE3
LOC100287896
WTAPP1
NCAM1-AS1
KCTD21-AS1
MIR1261
MIR1304
MIR548L
SNORA70E
BACE1-AS
MIR4300
MIR4301
MIR3167
MIR3165
MIR1260B
MIR3166
USP2-AS1
MIR3920
MIR3656
MIR3664
LOC100506127
RAB30-AS1
LOC100506368
CASP12
TPBGL
LOC100507283
SENCR
LOC100507431
LOC100507548
TMPRSS4-AS1
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
MIR4697
MIR4490
MIR548AL
MIR4459
MIR4493
MIR4491
MIR4492
MIR4696
MIR4692
MIR4693
LOC100652768
MIR5579
GRM5-AS1
JRKL-AS1
SHANK2-AS1
KIRREL3-AS2
NTM-IT
LOC101054525
LOC101928424
LOC101928535
LINC01537
LOC101928580
LOC101928823
LOC101928837
LOC101928847
LOC101928865
LOC101928896
LOC101928940
LOC101928944
LOC101928985
MIR4300HG
LOC101929011
LOC101929089
LOC101929208
DISC1FP1
LOC101929227
LOC101929295
LOC101929340
LOC101929427
LOC101929473
LOC101929497
LOC101929517
LOC101929538
LINC01395
NTM-AS1
LOC101929653
MIR6755
MIR6756
MIR7641-1
MIR7641-2
MIR6090
MIR6716
MIR6754
MIR8052
LOC102723838
LOC102723895
LOC102724301
LOC103611081
PKNOX2-AS1
APOA1-AS
LOC105369423
LOC105369431
LOC105369438
LOC105369443
LOC105369473
LOC105369486
LOC105369507
LOC105369509
LOC105369532
STT3A-AS1
PCF11-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q11.

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

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
GNA11
JAK3
KLK2
LYL1
MLLT1
PPP2R1A
SH3GL1
SMARCA4
STK11
TCF3
TPM4
ELL
FSTL3
CIC
BRD4
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-643
hsa-mir-220c
hsa-mir-1270-1
hsa-mir-220b
A1BG
ACP5
ACTN4
AP2A1
AES
AMH
APLP1
APOC1
APOC1P1
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
CAPS
CCNE1
CD22
CD33
SIGLEC6
CD37
CD70
ADGRE5
CDC34
CDKN2D
CEACAM5
CEBPG
CGB3
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CIRBP
TBCB
CKM
AP2S1
CLC
CLPTM1
CNN1
CNN2
COMP
COX6B1
COX7A1
CRX
CSNK1G2
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P
CYP2F1
DAPK3
DBP
CFD
DHPS
DMPK
DMWD
DNASE2
DNM2
DNMT1
ARID3A
ECH1
EEF2
EFNA2
MEGF8
ELANE
ELAVL1
ELAVL3
EMP3
ADGRE1
EPOR
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FARSA
FCAR
FCER2
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
FUT3
FUT5
FUT6
GAMT
GCDH
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
KCNN1
KCNN4
KIR2DL1
KIR2DL2
KIR2DL3
KIR2DL4
KIR2DS1
KIR2DS3
KIR2DS4
KIR2DS5
KIR3DL1
KIR3DL2
KIR3DS1
KLK1
LAIR1
LAIR2
LDLR
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
CYP4F3
BCAM
MAG
MAN2B1
MATK
BORCS8-MEF2B
RAB8A
MAP3K10
MYO1F
MYBPC2
GADD45B
MYO9B
HNRNPM
CEACAM6
NDUFA3
NDUFA7
NDUFB7
NFIC
NFIX
NFKBIB
NKG7
CNOT3
NOTCH3
NOVA2
NPAS1
NPHS1
NRTN
NTF4
NUCB1
OAZ1
P2RY11
PAFAH1B3
PALM
PDE4A
PDE4C
PEG3
PEPD
PIK3R2
PIN1
PLAUR
FXYD1
FXYD3
POLD1
POLR2E
POLR2I
POLRMT
POU2F2
PPP5C
PRKACA
PRKCG
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRRG2
KLK7
KLK6
KLK10
PRTN3
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTBP1
PTGER1
PTGIR
PTPRH
PTPRS
PVR
NECTIN2
RAB3A
RAD23A
RELB
UPF1
RFX1
RFX2
RPL18
RPL18A
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS15
RPS16
RPS19
RPS28
RRAS
RTN2
RYR1
SAFB
CLEC11A
SCN1B
CCL25
SEPW1
SGTA
SLC1A5
SLC1A6
SLC5A5
SLC8A2
SNAPC2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
STXBP2
SULT2B1
SULT2A1
SUPT5H
SYT5
TBXA2R
PRDX2
TGFB1
THOP1
ICAM5
TLE2
TNNI3
TNNT1
TULP2
TYK2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
VAV1
XRCC1
ZFP36
ZNF8
ZNF14
ZNF708
ZNF17
ZNF20
ZNF28
MZF1
ZNF43
ZNF45
ZNF69
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF121
ZNF132
ZNF134
ZNF135
ZNF136
ZNF137P
ZNF146
ZNF154
ZNF155
ZNF175
ZNF177
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
MADCAM1
SF3A2
SYMPK
MIA
CLPP
DPF1
LTBP4
TEAD2
RANBP3
CYP4F2
PPFIA3
KHSRP
PLA2G4C
PLPP2
RFXANK
EIF3G
STX10
S1PR4
URI1
TNFSF14
TNFSF9
NAPA
SIGLEC5
FCGBP
AP1M1
AP3D1
PGLYRP1
F2RL3
UBE2M
ARHGEF1
PDCD5
DYRK1B
LPAR2
RAB11B
CRLF1
NUMBL
CYTH2
S1PR2
ZNF235
TRIP10
LONP1
ZNF264
KCNK6
NCR1
MED26
HOMER3
IL27RA
NAPSA
GDF15
TECR
ZNF254
GMFG
RAB3D
APBA3
IER2
KLK4
SAFB2
ZNF432
DHX34
KIAA0355
ZNF536
KMT2B
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
TRAPPC2B
SPINT2
KLF1
DLL3
CERS1
GIPC1
POP4
ZNF234
ZNF266
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
PNPLA6
KDELR1
UQCR11
LILRB5
ILVBL
SLC27A5
LILRB4
KLK11
TMED1
LILRA1
LILRB3
LILRA2
UPK1A
HNRNPUL1
CLASRP
KPTN
SLC7A9
CDC37
MAP4K1
KLK8
CYP4F8
PNKP
COPE
U2AF2
ATF5
ZFP30
ZNF507
ADGRL1
PPP6R1
CARD8
SBNO2
SIRT2
CYP2G1P
MAST1
UNC13A
KDM4B
MAST3
SIPA1L3
FCHO1
ZC3H4
ZFR2
SIN3B
HAUS5
ARHGEF18
CRTC1
MAU2
PIP5K1C
FBXO46
ETHE1
RPL13A
ARHGAP45
SYNGR4
LILRA4
PRG1
CASP14
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
SHC2
TMEM59L
PGLS
ZNF324
LSM4
KLK5
ZNF345
PRKD2
RPL36
ZNF473
KANK2
CLIP3
FAM32A
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
SNORD37
SNORD35A
SNORD34
SNORD33
SNORD32A
RNU6-1
ZNF285
AKAP8L
FGF22
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
TJP3
CPAMD8
SIGLEC9
SIGLEC8
C5AR2
NMRK2
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
C19orf53
BABAM1
LGALS13
UHRF1
CYP2S1
STRN4
CCDC106
HOOK2
EPN1
SERTAD3
SERTAD1
SLC39A3
GLTSCR2
GLTSCR1
TNPO2
ADGRE2
CD209
EHD2
KLK14
KLK12
COL5A3
RDH8
SHANK1
NOSIP
MRPL4
NDUFA13
ANGPTL4
ZNF580
HSD17B14
GP6
VRK3
MARCH2
ZNF571
GMIP
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
ISYNA1
ZNF581
SIRT6
PIAS4
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
C19orf24
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
PSENEN
ZNF302
ANGPTL8
LIN37
MYDGF
SMG9
ZNF253
IRGC
SLC7A10
PPAN
CABP5
RETN
SPHK2
LGALS14
EXOSC5
MEIS3
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
CEACAM19
SLC17A7
NAT14
CD177
ATP13A1
RGL3
SLC44A2
VN1R1
MCOLN1
RCN3
ZNF304
TTYH1
WDR18
REXO1
PNMAL2
ZNF490
PRR12
DOCK6
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
CAMSAP3
USP29
PLEKHA4
ZFP14
ZNF317
ZNF529
PRX
ANO8
SPTBN4
MARK4
SUGP1
HAMP
CATSPERG
CYP4F11
ZNF71
ZNF77
SCAF1
CACTIN
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
UBL5
ZNF350
TSKS
CELF5
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
PLPPR2
ZNF574
PLEKHG2
RASAL3
MRPL34
KRI1
ZSWIM4
ZNF649
ZSCAN18
CENPBD1P1
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
TMEM38A
TSEN34
KCTD15
SLC25A23
SMIM7
ZNF426
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
C19orf57
ZNF576
FSD1
ZNF557
LRFN3
ABHD8
CERS4
OCEL1
ZNF329
COLGALT1
IGFLR1
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
TLE6
ZNF552
EPHX3
PODNL1
ZNF671
ZNF613
COQ8B
CNTD2
SLC35E1
PLPPR3
DENND1C
ZNF442
ZNF702P
ZNF556
CEBPA-AS1
ZNF606
ZNF614
LRRC8E
PRR36
FUZ
OPA3
ZNF430
ITPKC
UBXN6
PBX4
KIAA1683
B9D2
OR4F17
RSPH6A
CCDC130
ACSBG2
ADAMTS10
ZNF611
MED25
QTRT1
ABHD17A
ZNF93
DOHH
PLVAP
RTBDN
BCL2L12
C19orf12
TEX101
GRWD1
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
SNORD35B
KISS1R
ADGRE3
ZNF347
CREB3L3
GTPBP3
HDGFRP2
ZNF577
MPV17L2
ZNF607
KMT5C
C19orf48
NFKBID
LMNB2
RAX2
ZBTB45
CEP89
ZNF382
ZNF587
FIZ1
ZNF566
MUM1
HSH2D
MPND
ALKBH6
ATG4D
ATCAY
SYDE1
RHPN2
MBD3L1
GALP
SIGLEC10
SIGLEC12
ZNF628
MIDN
KIR3DX1
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
SAMD1
DCAF15
GADD45GIP1
ZNF835
YIF1B
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
ZNF486
DPP9
ZNF682
R3HDM4
TMEM259
FAAP24
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
TPGS1
ZNF461
ZNF585B
CRB3
TIMM50
SHKBP1
REEP6
PEX11G
DMKN
ZNF561
OLFM2
CCDC114
HAUS8
MVB12A
LOC93429
ARMC6
ACPT
CGB5
MUC16
CGB7
LRRC4B
ZNF101
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
FDX1L
NACC1
PTH2
IZUMO4
SCAMP4
ADAT3
MISP3
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
LENG8
CCDC124
ZNF554
FBXO17
KIR3DL3
ARHGAP33
EVI5L
RASGRP4
NXNL1
CCDC151
ZNF653
ZNF526
ZNF837
GRIN3B
MRPL54
LRG1
CIB3
RLN3
CLDND2
ZNF816
ZNF543
CEACAM20
RAVER1
OR7D4
OR7G1
OR1M1
COX6B2
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
OSCAR
ZNF813
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
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
WTIP
ZNF792
NR2C2AP
HSPB6
CCDC105
CYP4F22
RINL
FBXO27
PLK5
C19orf47
LINC00661
OR10H4
ANKLE1
C2CD4C
ZNF358
ZFP28
VSIG10L
C19orf84
SPACA6
ZNF480
ZNF534
ZNF578
ERVV-1
SMIM17
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
ILF3-AS1
ZNF560
TMEM190
HIPK4
TMC4
TPM3P9
ZNF524
ZNF784
ZNF563
SPC24
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542P
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
LGALS16
TTC9B
TICAM1
CIRBP-AS1
ZNRF4
ZNF599
FAM187B
CILP2
PROSER3
LINC00906
ZNF558
CDC42EP5
LINC00662
ZNF98
ZNF738
ZNF714
ZNF681
C19orf25
ATP8B3
LINC00905
DIRAS1
ZNF555
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF846
OR7D2
ZNF579
ZNF791
ZNF564
ZNF709
ZNF433
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
PRR22
LGI4
SYNE4
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
ANKRD24
SPACA4
ZNF675
MCEMP1
ZNF627
DAND5
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
ADM5
ZNF584
ZSCAN4
NLRP11
TMEM86B
CBARP
CSNK1G2-AS1
INAFM1
C19orf38
ZNF549
SYCE2
NAPSB
KANK3
TINCR
CATSPERD
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
ACTL9
OR2Z1
ZNF561-AS1
ZNF763
ZNF844
LOC284395
SCGB2B2
WDR62
ZFP82
ZNF790-AS1
LOC284412
VSTM1
TMEM150B
FAM71E2
SMIM24
MIR7-3HG
SLC25A41
MBD3L5
OR10H5
NWD1
SLC25A42
LINC00663
ZNF493
ODF3L2
LOC284454
HKR1
VN1R2
VN1R4
ADGRE4P
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
ADAMTSL5
CLEC4G
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
NANOS3
PALM3
SELV
ZNF530
DNAAF3
ZNF429
ZNF233
LILRA5
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
YJEFN3
LOC374890
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
C19orf68
ZNF773
WASH5P
SLC27A1
ZNF582-AS1
LYPLA2P2
C3P1
ZNF788
CLEC17A
CYP4F24P
ZNF728
RPSAP58
RGS9BP
KRTDAP
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
BHMG1
IGFL3
ZNF808
ZNF888
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ONECUT3
LOC390877
OR7G2
OR7G3
OR7A10
NUDT19
ZNF793
ACP7
PINLYP
ZNF818P
ZNF805
SPRED3
MEX3D
ZNF321P
LINC01002
PRSS57
VMAC
LINC00664
LOC400684
LOC400685
LGALS17A
LOC400706
SIGLEC16
LOC400710
ZNF880
ZNF772
ZNF833P
IGLON5
HAPLN4
CTXN1
CACTIN-AS1
MIRLET7E
MIR125A
MIR150
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR7-3
MIR99B
PLIN5
CLEC4GP1
ZNF506
GOLGA2P9
ZNF724
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
FLJ25758
A1BG-AS1
DPRX
DUXA
ASPDH
MIR181D
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
LOC641367
TMEM91
CCER2
SCGB1B2P
LINC01529
SDHAF1
LOC644189
LOC644554
LINGO3
ARRDC5
FAM138A
LOC645553
C19orf67
FAM90A27P
SBK2
RNF225
UCA1
PSG10P
LGALS7B
PHLDB3
MBD3L4
MBD3L3
SEC1P
FAM138C
ZNF826P
HNRNPA1P10
SNORD23
SNORD88A
SNORD88B
SNORD88C
SNORD105
PPAN-P2RY11
MIR637
MIR638
MIR639
MIR640
MIR641
MIR642A
MIR643
OVOL3
LOC728485
LOC728752
PLIN4
CCDC61
ZNF878
CEACAM18
SHISA7
LOC729966
RFPL4AL1
LINC01530
BORCS8
ZNF814
ZNF726
MIR769
SIGLEC14
MIMT1
HAVCR1P1
SNORD105B
ZGLP1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A12
LINC01233
ZNF667-AS1
LOC100128398
LOC100128568
C19orf71
LOC100128573
HPN-AS1
LINC01531
LOC100129083
ZNF730
ZNF737
LOC100129935
SCGB2B3P
TMEM221
SBK3
DPP9-AS1
BSPH1
MZF1-AS1
PET100
KIR2DS2
IPO5P1
LOC100134317
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
MEF2B
EML2-AS1
ZNF729
LOC100288123
LOC100289333
LOC100289650
ZNF587B
MIR1470
MIR1270
MIR1283-2
MIR1909
MIR1181
MIR1238
MIR1268A
MIR1323
MIR1283-1
MIR1302-2
MIR1227
LOC100379224
LOC100420587
MIR1302-9
MIR3191
MIR3188
MIR1302-10
MIR3187
MIR3190
MIR320E
MIR1302-11
MIR4322
MIR3189
MIR4324
MIR4323
MIR4321
MIR642B
MIR3940
PCAT19
LOC100505585
LOC100505622
NAPA-AS1
LOC100505715
CARD8-AS1
LINC01532
PPP5D1
PTOV1-AS1
DACT3-AS1
TMEM147-AS1
LINC00665
GFY
ZNF865
LOC100507373
ZNF571-AS1
THEG5
RAB11B-AS1
TGFBR3L
ZNF559-ZNF177
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
ZNF625-ZNF20
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4747
MIR4531
MIR4746
MIR4748
MIR4745
MIR4751
LOC100631378
LINC00904
MIR5695
MIR4999
MIR5196
MIR5684
MIR5088
MIR5589
UPK1A-AS1
NUCB1-AS1
LIPE-AS1
LOC100996349
LOC100996351
LINC01533
LOC101059948
IFNL4
ZNF350-AS1
LOC101927151
LOC101927411
LOC101927572
ZNF529-AS1
LINC01534
LINC01535
ZNF793-AS1
LINC01480
LOC101928063
LOC101928238
LOC101928295
PTOV1-AS2
LOC101928464
LOC101928517
ZNF649-AS1
LOC101928602
LOC101928804
LOC101928844
LOC101928845
LOC101928886
ZIM2-AS1
LOC101929124
LOC101929144
LOC101929164
LOC101930071
RNU6-7
SPACA6P-AS
MIR6088
MIR6790
MIR6791
MIR6792
MIR6795
MIR6796
MIR6797
MIR6799
MIR6800
MIR6802
MIR6804
MIR6805
MIR6806
MIR6885
MIR6886
MIR7850
MIR7974
MIR8074
MIR8077
MIR8085
MIR6719
MIR6807
MIR6794
MIR6887
MIR8061
MIR1199
MIR6515
MIR6789
MIR6793
MIR6798
MIR6803
MIR7108
MIR7975
MIR6801
ZNF30-AS1
LOC102723617
ZNF528-AS1
LOC102724279
LOC102724360
LOC102724908
LOC102724958
LOC102725254
RNU6-2
LENG8-AS1
LINC01224
BISPR
LOC105372273
LOC105372280
LOC105372288
LOC105372383
LOC105372397
LOC105372419
LOC105372440
LOC105372441
LOC105372444
LOC105372476
LOC105372483
LOC105447645
PLA2G4C-AS1
GLTSCR2-AS1
SNORD135
SNORA104

Arm-level results

Table 3. Get Full Table Arm-level significance table - 33 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	0.10	0.13	-1.69	1	0.23	0.26	1.21	0.303
1q	2863	0.36	0.41	4.43	0.000113	0.11	0.17	-0.91	1
2p	1500	0.42	0.42	3.07	0.00632	0.01	0.02	-4.75	1
2q	2495	0.29	0.29	1.33	0.243	0.02	0.03	-4.36	1
3p	1531	0.20	0.38	1.6	0.189	0.46	0.58	6.1	6.46e-09
3q	1708	0.42	0.47	4.31	0.00013	0.12	0.21	-1.24	1
4p	693	0.01	0.02	-4.29	1	0.59	0.60	6.01	8.96e-09
4q	1467	0.01	0.02	-4.18	1	0.54	0.54	5.81	2.52e-08
5p	456	0.63	0.73	8.03	2.13e-14	0.14	0.38	0.501	0.704
5q	2185	0.14	0.32	1.05	0.342	0.56	0.66	8.95	0
6p	1664	0.22	0.27	-0.113	1	0.19	0.24	-0.819	1
6q	1304	0.19	0.22	-1.47	1	0.18	0.22	-1.64	1
7p	926	0.35	0.40	1.88	0.121	0.13	0.20	-2.06	1
7q	1717	0.30	0.34	1.34	0.243	0.12	0.17	-2.04	1
8p	795	0.31	0.39	1.41	0.243	0.22	0.32	-0.0158	0.993
8q	1249	0.41	0.46	3.51	0.00156	0.12	0.20	-1.67	1
9p	621	0.10	0.22	-1.65	1	0.54	0.60	5.63	6.28e-08
9q	1610	0.14	0.26	-0.376	1	0.46	0.54	5.51	1.07e-07
10p	767	0.14	0.22	-1.79	1	0.37	0.43	2.23	0.039
10q	1968	0.08	0.13	-2.45	1	0.37	0.40	3.18	0.00292
11p	1162	0.09	0.13	-3.41	1	0.27	0.30	-0.149	0.997
11q	2133	0.13	0.16	-2.02	1	0.19	0.22	-0.705	1
12p	804	0.44	0.45	2.87	0.00979	0.04	0.07	-4.27	1
12q	2055	0.29	0.30	1.04	0.342	0.06	0.08	-3.63	1
13p	0	0.07	0.16	-3.02	1	0.53	0.57	4.38	2.75e-05
13q	1092	0.03	0.06	-3.83	1	0.53	0.54	5.26	3.84e-07
14p	0	0.20	0.35	-0.177	1	0.42	0.52	3.16	0.00295
14q	1829	0.18	0.26	-0.257	1	0.31	0.38	2.38	0.0277
15p	0	0.17	0.26	-1.71	1	0.36	0.43	1.45	0.207
15q	2082	0.13	0.17	-1.85	1	0.23	0.27	0.185	0.922
16p	1378	0.10	0.14	-2.99	1	0.27	0.30	0.147	0.922
16q	1070	0.10	0.15	-2.96	1	0.31	0.35	0.922	0.451
17p	937	0.19	0.26	-1.13	1	0.24	0.30	-0.302	1
17q	2298	0.26	0.29	1.08	0.342	0.12	0.16	-1.75	1
18p	212	0.29	0.37	0.376	0.738	0.22	0.31	-0.696	1
18q	644	0.18	0.22	-2.06	1	0.21	0.26	-1.4	1
19p	1331	0.18	0.22	-1.44	1	0.21	0.26	-0.747	1
19q	2402	0.25	0.30	1.35	0.243	0.18	0.23	-0.154	0.997
20p	583	0.47	0.50	3.71	0.0011	0.06	0.12	-3.34	1
20q	1092	0.44	0.47	3.64	0.0011	0.08	0.15	-2.69	1
21p	92	0.04	0.07	-4.44	1	0.48	0.50	3.08	0.00354
21q	750	0.05	0.09	-3.62	1	0.50	0.52	4.37	2.75e-05
22p	2	0.12	0.19	-3.04	1	0.35	0.40	0.816	0.497
22q	1258	0.34	0.43	2.59	0.0207	0.19	0.30	-0.0428	0.993
Xp	945	0.32	0.39	1.62	0.189	0.18	0.26	-0.98	1
Xq	1533	0.39	0.46	3.66	0.0011	0.15	0.24	-0.759	1
Yp	113	0.19	0.58	2.87	0.00979	0.67	0.83	9.23	0
Yq	245	0.14	0.39	0.606	0.594	0.65	0.75	8.2	1.78e-15

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-fa05c490-b7c1-4ddd-ba57-cfae0646dc55/4dde7c3e-0266-46b3-ac0f-35fd23a094aa/aggregate_data_workflow/38cc3283-45ff-4a2f-a994-131b2dd3eaba/call-aggregate_data/CPTAC3-LSCC-v3beta.CNV__wgs_wxs_pool.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 108 Input Tumor Samples.

Tumor Sample Names
C3L-00081
C3L-00415
C3L-00445
C3L-00568
C3L-00603
C3L-00904
C3L-00923
C3L-00927
C3L-00965
C3L-00993

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

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