Brain Lower Grade Glioma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16 (cga svn revision 38839).

Summary

There were 80 tumor samples used in this analysis: 17 significant arm-level results, 5 significant focal amplifications, and 18 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 - 5 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
--- | --- | --- | --- | ---
7p11.2 | 5.3906e-21 | 5.3906e-21 | chr7:54910170-55074962 | 1
1q32.1 | 2.462e-05 | 2.462e-05 | chr1:201977214-202897544 | 16
12p13.32 | 0.0025135 | 0.0025135 | chr12:4400387-4472821 | 2
12q14.1 | 0.0031783 | 0.0031783 | chr12:56370368-56546867 | 14
4q12 | 0.037424 | 0.037424 | chr4:54050264-56186612 | 12

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

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

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

Genes
MDM4
ATP2B4
KISS1
PIK3C2B
REN
SNRPE
SOX13
ZC3H11A
LRRN2
PLEKHA6
LAX1
ETNK2
PPP1R15B
LOC127841
GOLT1A
C1orf157

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
FGF6
C12orf4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
hsa-mir-26a-2
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
OS9
FAM119B
MARCH9
AGAP2
MIR26A2
LOC100130776

Genes in Wide Peak

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

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

Genes
KDR
KIT
PDGFRA
CHIC2
CLOCK
NMU
TMEM165
SRD5A3
LNX1
PDCL2
GSX2
RPL21P44

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 2.6497e-22 | 7.9106e-21 | chr9:21981753-22438737 | 2
2q37.3 | 0.0019765 | 0.0019765 | chr2:232493600-242951149 | 107
19q13.42 | 0.0019765 | 0.0019765 | chr19:21055359-63811651 | 920
4q35.1 | 0.0032038 | 0.0032038 | chr4:167012652-191273063 | 85
22q13.31 | 0.0066855 | 0.0066855 | chr22:42722705-49691432 | 80
18q23 | 0.020502 | 0.020502 | chr18:75847612-76117153 | 4
3p21.1 | 0.02704 | 0.02704 | chr3:49545887-53099552 | 95
2p25.3 | 0.055711 | 0.055711 | chr2:1-9464621 | 29
14q32.12 | 0.028444 | 0.055711 | chr14:68406386-106368585 | 379
11p15.4 | 0.067246 | 0.073038 | chr11:1-11941429 | 264
14q23.2 | 0.025167 | 0.073038 | chr14:57939329-79751635 | 175
1p36.23 | 0.12196 | 0.12196 | chr1:1-28712888 | 437
10p12.1 | 0.13538 | 0.13403 | chr10:22746393-26919698 | 19
5q35.2 | 0.14392 | 0.14392 | chr5:104437660-180857866 | 572
1q44 | 0.16964 | 0.17801 | chr1:235015260-247249719 | 94
10q23.1 | 0.1833 | 0.17801 | chr10:63621438-90529962 | 170
6p24.1 | 0.22994 | 0.22953 | chr6:1-170899992 | 1120
9p24.1 | 0.014044 | 0.25244 | chr9:1-140273252 | 890

Genes in Wide Peak

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

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

Genes
CDKN2B
CDKN2BAS

Genes in Wide Peak

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

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

Genes
hsa-mir-149
hsa-mir-562
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
KCNJ13
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PPP1R7
SAG
SPP2
DGKD
PER2
LRRFIP1
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
NGEF
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
EFHD1
ILKAP
ING5
MGC16025
AGAP1
DIS3L2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC151174
MSL3L2
TIGD1
C2orf85
DUSP28
ESPNL
ECEL1P2
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
MIR149
DNAJB3
LOC643387
PRR21
AQP12B
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.42.

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

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-519a-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-220c
hsa-mir-769
hsa-mir-642
hsa-mir-330
hsa-mir-641
A1BG
ACTN4
AP2A1
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
ATP4A
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CAPNS1
CCNE1
CD22
CD33
SIGLEC6
CD37
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
TBCB
CKM
AP2S1
CLC
CLPTM1
COX6B1
COX7A1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
ETV2
FCAR
FCGRT
FKBP1P1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
GRIK5
GRIN2D
GRLF1
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
BCAM
MAG
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NPHS1
NTF4
NUCB1
PAFAH1B3
PEG3
PEPD
PLAUR
FXYD1
FXYD3
POLD1
POLR2I
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SCN1B
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
TYROBP
NR1H2
UQCRFS1
USF2
VASP
XRCC1
ZFP36
ZNF8
ZNF708
ZNF17
ZNF28
MZF1
ZNF43
ZNF45
ZNF221
ZNF91
ZNF99
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137
ZNF146
ZNF154
ZNF155
ZNF175
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
C19orf2
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
PDCD5
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
NAPSA
ZNF254
GMFG
KLK4
ZNF432
DHX34
KIAA0355
ZNF536
MLL4
UBA2
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TMEM147
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
POP4
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
SFRS16
KPTN
SLC7A9
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
ZNF507
SAPS1
CARD8
SIRT2
SIPA1L3
ZC3H4
HAUS5
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
ZNF345
PRKD2
ZNF473
CLIP3
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285A
ZBTB32
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
LSR
PTOV1
FXYD7
FXYD5
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
GPATCH1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
PSENEN
ZNF302
LIN37
C19orf61
IRGC
SLC7A10
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
USP29
PLEKHA4
ZFP14
ZNF529
PRX
SPTBN4
MARK4
HAMP
CATSPERG
ZNF71
SCAF1
PRODH2
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
ZNF574
PLEKHG2
ZNF649
ZSCAN18
MGC2752
TSEN34
KCTD15
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
ZNF576
LRFN3
ZNF329
TMEM149
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
LOC80054
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSHL1
ZNF611
MED25
BCL2L12
C19orf12
TEX101
GRWD1
WDR87
CCDC8
KIRREL2
ANKRD27
ZNF541
SYT3
PDCD2L
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
SNORD35B
ZNF347
ZNF577
ZNF607
SUV420H2
C19orf48
NFKBID
ZBTB45
CCDC123
ZNF382
ZNF587
FIZ1
ZNF566
ALKBH6
RHPN2
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
C19orf40
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
ZNF461
ZNF585B
TIMM50
SHKBP1
DMKN
CCDC114
DKFZp434J0226
ACPT
CGB5
DKFZp566F0947
CGB7
LRRC4B
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
SNX26
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816A
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
C19orf41
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
WDR88
EID2B
IRGQ
ZNF428
WTIP
ZNF792
HSPB6
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
NCRNA00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
ZNF417
ZNF548
FLJ40125
KLC3
LYPD4
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
TTC9B
ZNF599
FAM187B
C19orf55
LOC148145
CDC42EP5
LOC148189
ZNF98
ZNF738
ZNF714
ZNF681
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
LGI4
C19orf46
ZNF676
ZNF100
ZNF540
ZNF525
ZNF431
SPACA4
ZNF675
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
ZNF575
LYPD5
ZNF283
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
SCGBL
WDR62
ZFP82
LOC284412
VSTM1
TMEM150B
FAM71E2
ZNF493
HKR1
VN1R2
VN1R4
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
VSTM2B
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
C19orf51
ZNF429
ZNF233
LILRA5
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
RPSAP58
RGS9BP
KRTDAP
ZNF790
FLJ41856
CEACAM16
BLOC1S3
IGFL3
ZNF808
ZNF761
ZNF470
ZNF749
ZNF324B
NUDT19
ZNF793
PAPL
ZNF805
SPRED3
ZNF321
LOC400696
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
OLT-2
MIR330
MIR371
MIR372
MIR373
IGFL4
NCRNA00181
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC641367
TMEM91
LOC643719
SDHAF1
SBK2
PSG10
LGALS7B
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
ZNF814
MIR769
KIR3DP1
SIGLEC14
MIMT1
LOC100101266
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128675
LOC100129935
BSPH1
LOC100131691
LOC100134317
PEG3AS
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
TLL1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
MORF4
ADAM29
ANXA10
SCRG1
PALLD
FAM149A
FBXO8
PDLIM3
SPOCK3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
TUBB4Q
STOX2
KIAA1430
SH3RF1
SPCS3
C4orf41
MLF1IP
NBLA00301
WWC2
KIAA1712
SNX25
CBR4
MGC45800
DDX60L
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
TRIML1
ANKRD37
HELT
FAM92A3
C4orf47
GALNTL6
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

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

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

Genes
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
C22orf9
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
LOC150381
C22orf40
CN5H6.4
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
NCRNA00207
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
ADNP2
C18orf22
PARD6G
LOC100130522

Genes in Wide Peak

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

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

Genes
BAP1
PBRM1
hsa-mir-135a-1
hsa-let-7g
hsa-mir-566
ACY1
ALAS1
APEH
CISH
DOCK3
DUSP7
GNAI2
GNAT1
GRM2
HYAL1
ITIH1
ITIH3
ITIH4
MST1
MST1R
RPL29
SEMA3F
NEK4
TNNC1
UBA7
IFRD2
MAPKAPK3
SEMA3B
MANF
HYAL3
HYAL2
BSN
RRP9
CACNA2D2
VPRBP
IP6K1
PARP3
RBM6
RBM5
TRAIP
TUSC4
SLC38A3
CYB561D2
TMEM115
RASSF1
NISCH
TUSC2
TWF2
RAD54L2
STAB1
NAT6
ABHD14A
WDR51A
DNAH1
GNL3
SPCS1
RBM15B
GMPPB
C3orf18
ZMYND10
TEX264
HEMK1
SFMBT1
PHF7
TLR9
GLT8D1
SEMA3G
PCBP4
RNF123
NT5DC2
CAMKV
WDR82
MON1A
ABHD14B
GPR62
IQCF1
GLYCTK
PPM1M
C3orf45
TMEM110
AMIGO3
CDH29
C3orf54
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
IQCF6
LOC440957
SNORD19
SNORD69
SNORD19B
C3orf74

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.3.

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

Genes
ACP1
ID2
RPS7
SOX11
TPO
TSSC1
PXDN
ASAP2
RNF144A
MYT1L
SH3YL1
TTC15
SNTG2
ADI1
ALLC
KIDINS220
COLEC11
RSAD2
CMPK2
MBOAT2
TMEM18
LOC150622
RNASEH1
FAM150B
LOC339788
C2orf90
LOC400940
FAM110C
LOC730811

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.12.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-770
hsa-mir-345
hsa-mir-342
hsa-mir-1260
SERPINA3
ACTN1
ACYP1
BCYRN1
BDKRB1
BDKRB2
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF5
EML1
ERH
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
ATXN3
MAP3K9
ALDH6A1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSEN1
PSMC1
ABCD4
RAGE
SEL1L
SFRS5
SLC8A3
SLC10A1
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
SNW1
PCNX
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
TTC9
FLRT2
SIPA1L1
DCAF4
KIF26A
C14orf109
MLH3
PRO1768
GPR132
POMT2
COQ6
FCF1
SERPINA10
GLRX5
COX16
EVL
C14orf129
CINP
ASB2
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
C14orf115
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
GALNTL1
KIAA1409
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
C14orf4
INF2
OTUB2
ZFYVE21
MEG8
WDR25
C14orf139
FAM164C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
AMN
C14orf156
DNAL1
RPS6KL1
IFI27L2
SETD3
C14orf153
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
C14orf143
C14orf43
LIN52
NEK9
C14orf73
WDR20
C14orf179
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
C14orf148
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
C14orf72
ADAM21P
GSC
SERPINA12
PRIMA1
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
C14orf145
TTC7B
C14orf49
C14orf174
EML5
MGC23270
NUDT14
C14orf48
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
C14orf86
SNHG10
C14orf177
C14orf68
C14orf70
KIAA0284
C14orf80
CCDC85C
NCRNA00203
SNORD56B
SERPINA9
VSX2
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ44817
FLJ45244
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323
MIR337
MIR342
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR453
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
TMEM90A
C14orf184
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
SNORD112
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-3
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-8
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100133469
LOC100289511

Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
EIF4G2
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPL27A
RPLP2
RRM1
SCT
SMPD1
TRIM21
ST5
STIM1
TAF10
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
CTR9
TRIM66
TSPAN32
TSSC4
MRVI1
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
LYVE1
KCNQ1OT1
PKP3
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2AS
BET1L
CEND1
CYB5R2
TRIM34
MUPCDH
TOLLIP
USP47
TRIM68
LRDD
KCNQ1DN
MMP26
C11orf17
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
HCCA2
SBF2
FAM160A2
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIMP1
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
FLJ46111
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVIN1
OR52K1
OR52I1
OR51D1
OR52A4
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC650368
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
LOC100133545

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.2.

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

Genes
RAD51L1
GPHN
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
ACTN1
ACYP1
ARG2
BCYRN1
ZFP36L1
ENTPD5
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GPX2
GSTZ1
HIF1A
HSPA2
LTBP2
MAX
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SIX6
PGF
PIGH
PPM1A
PPP2R5E
PRKCH
PSEN1
ABCD4
RTN1
SFRS5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
ZBTB25
DPF3
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
NRXN3
AKAP5
SPTLC2
RGS6
KIAA0247
KIAA0586
KIAA0317
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
TIMM9
MLH3
KCNH5
POMT2
COQ6
FCF1
RDH11
COX16
DACT1
ATP6V1D
JKAMP
DHRS7
SIX4
ZFYVE1
EXD2
C14orf115
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
YLPM1
C14orf162
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
TRMT5
ZNF410
NGB
RBM25
C14orf133
SMOC1
C14orf4
MPP5
C14orf135
GPR135
FAM164C
C14orf169
C14orf45
SGPP1
C14orf156
DNAL1
RPS6KL1
SYT16
KIAA1737
PAPLN
CHURC1
C14orf43
LIN52
NEK9
C14orf179
WDR89
C14orf149
GPHB5
C14orf148
JDP2
ISCA2
ACOT4
RDH12
ADAM21P
C14orf50
SLC38A6
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
FAM71D
TMEM229B
TMEM30B
C14orf174
PROX2
ZDHHC22
TMED8
C14orf178
C14orf39
SNORD56B
VSX2
RAB15
HEATR4
C14orf181
FLJ44817
C14orf53
ACOT1
ACOT6
LOC645431
FLJ43390
TMEM90A
C14orf38
LOC100289511

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDC2L1
CDC42
CD52
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
CROCC
KIAA0562
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
NUDC
MASP2
SFRS13A
UTS2
RER1
RCAN3
MSTP2
MSTP9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KIAA1026
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
AHDC1
SMPDL3B
HSPC157
SSU72
UBIAD1
PADI1
PLA2G2E
WDR8
SLC45A1
HP1BP3
CELA2B
ZNF593
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
C1orf128
MAN1C1
NIPAL3
SEPN1
KIAA0495
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CCDC21
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
C1orf89
OR4F5
MUL1
NOL9
LIN28
AGMAT
NCRNA00115
MORN1
GRRP1
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCL1
SYTL1
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCL2
FHAD1
LOC115110
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
C1orf93
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
C1orf70
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
C1orf130
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
LOC441869
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH5P
PRAMEF16
FAM138C
SCARNA1
SNORA59B
SNORA59A
MIR551A
CDC2L2
LOC728661
PRAMEF14
FLJ37453
OR4F29
LOC100128003
LOC100128842
LOC100129534
FLJ39609
LOC100132062
LOC100132287
LOC100133331
LOC100133612
LOC100288778

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p12.1.

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

Genes
hsa-mir-603
GAD2
PIP4K2A
MSRB2
MYO3A
APBB1IP
KIAA1217
PRTFDC1
GPR158
ARHGAP21
THNSL1
ENKUR
ARMC3
OTUD1
PTF1A
C10orf67
MIR603
LOC100128811
PRINS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

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

Genes
APC
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-1303
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244
hsa-mir-548f-3
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK4
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDO1
CDX1
AP3S1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
NKX2-5
CTNNA1
DBN1
DMXL1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FER
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HINT1
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
KCNN2
LCP2
LECT2
LMNB1
LOX
LTC4S
SMAD5
MAN2A1
MCC
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
REEP5
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
ATG12
PTTG1
PDLIM7
C5orf13
CNOT8
RAB9P1
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5OS
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MGC29506
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FLJ11235
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
PCDH24
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
C5orf54
EPB41L4A
SIL1
GMCL1L
ARAP3
RMND5B
FBXL17
YTHDC2
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
TSSK1B
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
TSLP
FCHSD1
UNC5A
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C5orf26
MARCH3
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
ZNF474
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
STARD4
WDR36
LOC134466
NUDCD2
UBLCP1
ANKRD43
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK5L3
C5orf41
CEP120
LOC153328
SRFBP1
ZMAT2
BTNL9
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
DCP2
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
LVRN
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
SH3PXD2B
LOC285593
FAM153A
ARL10
DTWD2
RELL2
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
TMEM173
FAM170A
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
TICAM2
DND1
C5orf25
C5orf48
LOC389332
LOC389333
C5orf46
FLJ41603
FLJ44606
SPINK6
ANKHD1-EIF4EBP3
MIR103-1
MIR143
MIR145
MIR146A
MIR218-2
SPINK5L2
C5orf40
C5orf56
MIR340
C5orf53
TIFAB
CTXN3
SNORD95
SNORD96A
ECSCR
TMEM232
GRXCR2
SPINK9
ZFP62
FLJ33630
CCNI2
CBY3
FAM153C
SNORA13
SNORA74B
MIR548C
MIR548D2
MIR585
SNHG4
LOC728264
LOC728554
AACSL
LOC729678
OR4F29
MIR886
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
LOC100286948
TMED7-TICAM2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q44.

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

Genes
FH
ADSS
CHML
CHRM3
HNRNPU
MTR
RGS7
RYR2
ZNF124
KMO
EXO1
CEP170
AKT3
ZNF238
SDCCAG8
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
PPPDE1
SCCPDH
KIF26B
ZNF692
FMN2
ZNF695
ZP4
TFB2M
GREM2
SMYD3
ZNF669
ZNF672
SH3BP5L
OR2G3
OR2G2
OR2C3
EFCAB2
ZNF496
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
OR2T6
C1orf101
PGBD2
OR2L13
OR14A16
NCRNA00201
VN1R5
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR2W5
OR13G1
LOC646627
LOC731275
LOC100130331

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.1.

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

Genes
BMPR1A
PRF1
PTEN
MYST4
hsa-mir-346
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
ADK
ANXA2P3
ANXA7
ANXA11
CAMK2G
COL13A1
DNA2
EGR2
EIF4EBP2
GLUD1
GRID1
HK1
HNRNPH3
KCNMA1
MAT1A
NODAL
P4HA1
PCBD1
PLAU
PPA1
PPP3CB
SRGN
PSAP
RGR
RPS24
SFTPD
SNCG
SUPV3L1
TACR2
VCL
VDAC2
SLC25A16
NDST2
MBL1P1
LIPF
SGPL1
PAPSS2
DDX21
DLG5
CHST3
VPS26A
MINPP1
SEC24C
SPOCK2
PPIF
CBARA1
NRG3
C10orf116
POLR3A
LDB3
ECD
ZNF365
KIAA0913
WAPAL
DNAJC9
SIRT1
TSPAN15
NUDT13
HERC4
LRIT1
KIAA1279
AP3M1
GHITM
KIAA1274
CTNNA3
NRBF2
NEUROG3
ASCC1
MRPS16
DUSP13
FAM190B
FAM35A
DDIT4
DNAJB12
LRRC20
SLC29A3
RNLS
H2AFY2
RUFY2
CCAR1
DNAJC12
SAR1A
ZMIZ1
MYOZ1
CDH23
PBLD
NPFFR1
C10orf54
DDX50
MMRN2
SYNPO2L
C10orf57
HKDC1
TET1
TSPAN14
C10orf11
C10orf58
DYDC2
PLA2G12B
MYPN
ZNF503
AIFM2
ADO
ATAD1
LOC84989
CCDC109A
PCDH21
OPN4
CHCHD1
ZMYND17
TTC18
COMTD1
AGAP11
C10orf104
ADAMTS14
SAMD8
LIPJ
CFLP1
DYDC1
EIF5AL1
USP54
FUT11
OIT3
LOC219347
PLAC9
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
C10orf27
ATOH7
REEP3
JMJD1C
LOC283050
FAM149B1
DUPD1
LRIT2
LRRTM3
SH2D4B
C10orf99
C10orf105
C10orf55
LOC439994
MIR346
LOC642361
FAM25A
LIPK
LIPN
LOC650623
SFTPA1
SNORD98
FAM22A
FAM22D
LOC728190
AGAP5
BMS1P4
SFTPA2
LOC100128292
C10orf41
KILLIN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.1.

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

Genes
PRDM1
CCND3
DAXX
FANCE
HMGA1
IRF4
MLLT4
MYB
PIM1
POU5F1
TRIM27
ROS1
SFRS3
TNFAIP3
DEK
TFEB
STL
HIST1H4I
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-548a-2
hsa-mir-588
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-30a
hsa-mir-133b
hsa-mir-586
hsa-mir-1275
hsa-mir-219-1
hsa-mir-1236
hsa-mir-877
hsa-mir-548a-1
ABCF1
ACAT2
CRISP1
AGER
AIF1
AIM1
AMD1
ARG1
ATP6V1G2
BAI3
BAK1
BCKDHB
CFB
BMP5
BMP6
DST
BPHL
BTN1A1
BYSL
C2
C4A
C4B
DDR1
RUNX2
CCNC
CDC5L
CDKN1A
CDSN
CGA
CLIC1
CLPS
CCR6
CNR1
COL9A1
COL10A1
COL11A2
COL12A1
COL19A1
COX7A2
ATF6B
MAPK14
CSNK2B
CTGF
CYP21A2
DNAH8
DOM3Z
DSP
E2F3
EDN1
EEF1A1
SERPINB1
SLC29A1
EPB41L2
EPHA7
EYA4
ESR1
F13A1
FABP7
FKBP5
FOXF2
FOXC1
FOXO3
FRK
FUCA2
FYN
GABBR1
GABRR1
GABRR2
GCNT2
GJA1
GCLC
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPR6
GPR31
GPX5
GRIK2
GRM1
GRM4
GSTA1
GSTA2
GSTA3
GSTA4
GTF2H4
GUCA1A
GUCA1B
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HCRTR2
HDAC2
HFE
HIVEP1
HIVEP2
HLA-A
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSF2
HSPA1A
HSPA1B
HSPA1L
HSP90AB1
HTR1B
HTR1E
ID4
IFNGR1
IGF2R
IL17A
IMPG1
ITPR3
JARID2
KIFC1
KIF25
KPNA5
LAMA2
LAMA4
LPA
LTA
LTB
MARCKS
MAK
MAN1A1
MAS1
MCM3
MDFI
ME1
MEA1
MAP3K4
MAP3K5
MEP1A
MICA
MICB
MLN
MOCS1
MOG
MSH5
MUT
MYO6
RPL10A
NEDD9
NEU1
NFKBIE
NFKBIL1
NFYA
NMBR
NQO2
NOTCH4
NT5E
OPRM1
PARK2
PBX2
PCMT1
PDCD2
ENPP1
ENPP3
PEX6
PEX7
PGC
PGK2
PGM3
PHF1
SERPINB6
SERPINB9
PKHD1
PLAGL1
PLG
PLN
POLH
POU3F2
PPARD
PPP1R2P1
PPP1R10
PPP2R5D
PREP
PRIM2
PKIB
MAPK13
PRL
PSMB1
PSMB8
PSMB9
PTK7
PTPRK
RGL2
PRPH2
REV3L
RHAG
RING1
BRD2
RNF5
RPS6KA2
RPS10
RPS12
RPS18
RREB1
RXRB
VPS52
ATXN1
SGK1
SIM1
SKIV2L
SLC17A1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SNRPC
SOD2
SOX4
SRF
SRPK1
SSR1
ELOVL4
T
TAF11
MAP3K7
TAP1
TAP2
TAPBP
TBCC
TBP
TCF19
TCF21
TCP1
TCP10
TCP11
TCTE3
PPP1R11
DYNLT1
TEAD3
TFAP2A
TFAP2B
THBS2
NR2E1
TNF
TNXA
TNXB
TPBG
TPD52L1
TPMT
CRISP2
TSPYL1
TTK
TUBB2A
TULP1
UTRN
VARS
VEGFA
EZR
VIP
ZNF76
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204
PTP4A1
ALDH5A1
BAT2
BAT3
BAT4
BAT1
BAT5
SLC39A7
HSD17B8
OR2H2
RDBP
LST1
PLA2G7
EPM2A
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
STX7
CMAH
DHX16
SUPT3H
PEX3
GCM1
DDO
RNASET2
KCNK5
STX11
B3GALT4
SNX3
RNGTT
RIPK1
CD164
SYNGAP1
WISP3
STK19
IER3
SYNJ2
VNN2
VNN1
PRPF4B
WASF1
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
TAAR5
MAP7
TBX18
LATS1
GCM2
WDR46
ZBTB22
TAAR2
TAAR3
CD83
HMGN3
PPT2
CDYL
NCR2
MED23
QKI
LY86
FHL5
AKAP7
ATG5
MED20
SLC25A27
TBPL1
EEF1E1
BAG2
POLR1C
MAD2L1BP
WTAP
AKAP12
MDC1
TRAM2
KIAA0408
PHACTR2
FAM65B
ZSCAN12
BCLAF1
CUL7
ZBTB24
KIAA0319
SNAP91
FIG4
NUP153
CASP8AP2
RANBP9
SLC17A4
UST
TRIM10
FLOT1
RCAN2
SLC17A2
HCG9
PRSS16
CRISP3
TRDN
CITED2
BTN3A3
BTN2A2
PECI
PFDN6
HMGN4
TRIM38
CAP2
SYNCRIP
UBD
AGPAT1
SLC35A1
SCGN
C6orf108
C6orf10
FARS2
FUT9
CNPY3
TRAF3IP2
HBS1L
SLC17A3
RPP40
FRS3
PDE10A
SLC22A7
HCP5
EHMT2
SMPDL3A
APOBEC2
PNRC1
ASCC3
RAB32
TRIM31
KATNA1
BTN3A2
BTN3A1
BTN2A1
CAPN11
BVES
NUDT3
SEC63
NRM
STK38
RBM16
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
FTSJD2
CDC2L6
CUL9
MAP3K7IP2
MDN1
TSPYL4
ANKS1A
UBR2
SASH1
SYNE1
KIAA0776
SIRT5
PHF3
HEY2
DAAM2
KIAA0240
DDAH2
HEBP2
ORC3L
CD2AP
BRD7P3
MTCH1
ZNF318
SPDEF
MTO1
ASF1A
YIPF3
USP49
CCDC28A
MTHFD1L
SFRS18
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
OR2B6
TIAM2
FBXL4
C6orf123
FAM50B
FBXO9
FBXO5
SLC17A5
OR12D2
OR11A1
RGS17
OR2W1
OR2J2
OR2H1
SNORD52
SNORD50A
SNORD48
PDE7B
FILIP1
BRPF3
GNMT
TNFRSF21
SESN1
TINAG
DLL1
OSTM1
MRPS18B
TMEM14A
MRPL18
NDUFAF4
C6orf15
MYLIP
ABT1
DSE
PRICKLE4
PACSIN1
ZNRD1
CLDN20
NOX3
DEF6
C6orf48
SLC35B3
HDDC2
GMNN
MRPL2
TFB1M
CYB5R4
TUBE1
C6orf203
TBC1D7
NRN1
CYP39A1
CDC40
RWDD1
AIG1
NOL7
SNX9
FAM8A1
UBE2J1
DCDC2
ETV7
TMEM14C
VTA1
LGSN
TTRAP
CUTA
PPIL1
BRP44L
HECA
RAB23
COQ3
CLIC5
IL20RA
TREM2
TREM1
UNC93A
HCG4
GFOD1
HMGCLL1
MTRF1L
CCHCR1
GTPBP2
BTN2A3
AHI1
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
MRPS18A
MRPS10
LRRC1
PHF10
QRSL1
VNN3
TMEM63B
NCRNA00120
DDX43
FAM46A
LRRC16A
TBC1D22B
TMEM30A
EXOC2
C6orf64
C6orf70
LMBRD1
TRERF1
ACOT13
ECHDC1
APOM
BTNL2
KCNQ5
TRIM39
AGPAT4
WRNIP1
DUSP22
TULP4
RARS2
HYMAI
PDSS2
LYRM4
C6orf162
VARS2
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
MRS2
PLEKHG1
ARID1B
LRFN2
AARS2
XPO5
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
CPNE5
LSM2
C6orf47
LY6G5B
C6orf115
RRAGD
LY6G6D
ENPP5
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
ZFAND3
SLC22A23
C6orf164
MUTED
CCDC90A
GPSM3
FKBPL
KIF13A
PERP
SMOC2
POPDC3
ZNF323
ALDH8A1
C6orf106
MICAL1
MRPL14
DLK2
LY6G6E
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
ZNF322A
MANEA
C6orf103
TREML2
RPP21
C6orf155
C6orf134
FRMD1
C6orf59
C6orf208
C6orf97
MYCT1
ZKSCAN3
ULBP2
ULBP1
ZSCAN16
LPAL2
RNF39
SLC44A4
C6orf27
C6orf25
LY6G6C
LY6G5C
PRR3
KHDC1
NCRNA00171
PRRT1
EGFL8
HCG2P7
HCG4P6
GPR63
TXNDC5
COL21A1
C6orf62
OR5V1
OR2B2
PPP1R14C
OR12D3
SPACA1
RNF146
TMEM14B
SF3B5
TAAR8
SH3BGRL2
RIOK1
TFAP2D
KCNK16
RSPH3
TTLL2
FKSG83
DTNBP1
ARMC2
FBXO30
RPF2
C6orf125
L3MBTL3
FAM120B
MCHR2
PGBD1
C6orf168
FNDC1
TTBK1
GJA10
RTN4IP1
C6orf105
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
HIST1H2AH
HIST1H2BK
PPIL4
PAQR8
C6orf114
SLC22A16
C6orf153
KCNK17
ABCC10
TRIM15
KLC4
UBE2CBP
C6orf142
C6orf176
KIAA1919
TJAP1
ARHGAP18
POM121L2
SYTL3
FOXQ1
GTF3C6
MRAP2
RWDD2A
IL17F
FAM54A
SFT2D1
EFHC1
BTBD9
KLHL32
TMEM200A
SCAND3
C6orf150
FOXP4
KLHDC3
NUS1
C6orf72
SLC26A8
IL22RA2
MAS1L
C6orf192
SLC16A10
IP6K3
TAGAP
TAF8
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SFRS13B
C6orf141
HUS1B
TRIM40
DPCR1
NRSN1
LOC153910
C6orf94
SNRNP48
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
MBOAT1
HDGFL1
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
C6orf195
LOC154449
C6orf129
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
PSORS1C1
PSORS1C2
KIAA1949
PTCRA
OSTCL
TCTE1
KHDRBS2
TUBB
C6orf163
MGC26597
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
RSPH9
C6orf154
TREML2P
LOC221442
C6orf130
KIF6
TMEM217
FGD2
PI16
C6orf89
C6orf81
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12L1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
LOC221710
SYCP2L
C6orf218
C6orf145
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
GPR111
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
LOC222699
C6orf146
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
HCG27
C6orf191
C6orf167
WDR27
FAM26E
MCM9
RNF144B
HIST1H2BA
SCML4
GPX6
SHPRH
NCR3
LY6G6F
MDGA1
GPR110
ZNF311
LOC285733
LOC285735
LOC285740
C6orf182
PPIL6
FLJ34503
DCBLD1
LOC285768
LOC285780
CAGE1
LOC285796
PRR18
LOC285830
HCG22
LOC285847
PNPLA1
TREML4
RPL7L1
RNF5P1
TAAR6
SLC35D3
ZC3H12D
MYLK4
DPPA5
IFITM4P
C6orf127
TREML1
TREML3
RSPH4A
ECT2L
EYS
ZNF391
ZFP57
TUBB2B
SLC35B2
C6orf52
NUP43
HCG26
C6orf58
RAET1G
KAAG1
GUSBL2
GJB7
NHLRC1
ZKSCAN4
GUSBL1
SNHG5
FAM136B
SUMO4
C6orf147
C6orf173
C6orf174
C6orf204
C6orf120
THEMIS
PSMG4
SFTA2
C6orf126
C6orf222
C6orf140
GFRAL
LIN28B
SAMD5
IYD
MUC21
DKFZP686I15217
FLJ22536
MCCD1
C6orf26
C6orf227
CRIP3
KLHL31
TCP10L2
C6orf122
DEFB133
C6orf201
GTF2H5
HERV-FRD
MIR206
MIR219-1
MIR30A
MIR30C2
HCG18
C6orf226
TMEM151B
OOEP
FAM26F
LOC441177
OR2B3
OR2J3
OR14J1
OR10C1
C6orf138
MCART3P
LOC442245
RFPL4B
MIR133B
GGNBP1
HCG11
LOC553137
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
CTAGE9
RAET1K
C6orf132
PPP1R3G
ZNF389
C6orf124
LYPLA2P1
SNORA20
SNORA29
SNORA38
SNORD50B
SNORD32B
SNORD84
SNORD117
MIR548A1
MIR548B
MIR586
LOC728402
C6orf186
HULC
LOC729176
LOC729603
LOC730101
TDRG1
TMEM170B
SCARNA27
MIR877
HGC6.3
BET3L
KHDC1L
PSORS1C3
C6orf217
LOC100132354
C6orf41
TOMM6
LOC100270746
LOC100287718
NHEG1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.1.

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

Genes
ABL1
FANCC
FANCG
GNAQ
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
hsa-mir-602
hsa-mir-126
hsa-mir-219-2
hsa-mir-199b
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-let-7d
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
hsa-mir-873
hsa-mir-31
hsa-mir-491
hsa-mir-101-2
hsa-mir-1302-2
ABCA1
ABCA2
ABO
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
ANXA2P2
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
TNFSF8
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CELP
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
MLANA
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
GGTA1
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
IL11RA
INSL4
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RMRP
RORB
RPL7A
RPL12
RPS6
RXRA
CCL19
CCL21
SH3GL2
SHB
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
UGCG
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
RGP1
TRIM14
MELK
RUSC2
KIAA0649
SEC16A
ZBTB5
KIAA0020
TNFSF15
ROD1
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB2C
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CEP110
WDR5
C9orf9
ADAMTS13
C9orf7
PSIP1
INSL6
SLC2A6
PTENP1
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA1045
KIAA0368
EXOSC2
FREQ
TDRD7
SLC44A1
ANGPTL2
NUP188
CCRK
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
LOC26102
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
PCA3
AK3
EXOSC3
FAM108B1
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
C9orf11
TBC1D13
FAM22F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
C9orf167
CNTLN
TEX10
LPPR1
KIAA1797
UBE2R2
EXD3
C9orf6
C9orf95
STX17
NOL8
C9orf68
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDC37L1
DENND4C
C9orf86
CDK5RAP2
UBAP2
C9orf46
CBWD1
KLHL9
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KIAA1161
KCNT1
KIAA1432
KIAA1529
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
C9orf27
C9orf80
ZNF462
DMRT3
PRDM12
MAK10
DMRTA1
SLC28A3
CARD9
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
MRPL41
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOBKL2B
C9orf82
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
KIAA1539
GKAP1
PDCD1LG2
AKNA
C9orf45
URM1
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
BAT2L
PPAPDC3
C9orf70
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
TPD52L3
WDR34
C9orf140
C9orf69
LRSAM1
IL33
C9orf123
C9orf30
UAP1L1
MCART1
MRRF
RBM18
ARRDC1
WDR85
ADAMTSL1
LOC92973
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf66
NCRNA00032
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
C9orf98
OR1Q1
TTLL11
RASEF
TTC39B
C9orf122
RG9MTD3
TTC16
FAM120AOS
FAM154A
C9orf44
FREM1
KIAA2026
LOC158376
LOC158381
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
PRUNE2
C9orf96
KCNV2
OLFML2A
C9orf71
QSOX2
GLIS3
LOC169834
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
C9orf93
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
C9orf144B
NCRNA00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
C9orf75
TUSC1
C9orf109
FAM78A
C9orf150
LOC286359
OR13C9
OR13D1
LOC286367
FOXD4L3
IFNE
ZDHHC21
ACER2
LOC340508
GPR144
FLJ43950
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
GLT6D1
ENHO
AQP7P1
PTAR1
C9orf102
C9orf119
C9orf50
PNPLA7
C9orf169
ENTPD8
ZNF322B
KGFLP1
LOC389705
C9orf144
FAM75A6
MGC21881
AQP7P2
FLJ43859
FLJ44082
FLJ46321
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
C9orf128
OR13J1
CTSL3
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FLJ35024
PTPLAD2
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
LOC402377
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR101-2
MIR126
MIR147
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR31
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC415056
LOC440173
LOC440839
LOC440896
SUGT1P
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
FAM27A
DNAJC25
DNAJC25-GNG10
LOC554202
LOC572558
MIR491
PGM5P2
MIR455
FAM138F
FAM75A2
LOC642313
LOC642929
FAM163B
FLJ40292
TUBBP5
CBWD6
FAM138A
LOC645961
HRCT1
FAM75A1
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM138C
SCARNA8
SNORA17
SNORA43
SNORD62B
MSMP
SNORD90
MIR548D1
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
ANKRD20A4
CCDC29
FAM166B
FOXD4L2
CDKN2BAS
SNORD121A
SNORD121B
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
C9orf110
C9orf130
LOC100129034
LOC100129066
LOC100130426
LOC100131193
FAM157B
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
NCRNA00092
LOC100272217
WASH1
LOC100289341

Arm-level results

Table 3. Get Full Table Arm-level significance table - 17 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.05 | 1.09 | 0.596 | 0.30 | 14.2 | 0
1q | 1572 | 0.04 | 0.305 | 0.991 | 0.05 | 0.918 | 0.411
2p | 753 | 0.03 | -1.24 | 0.991 | 0.00 | -2.17 | 0.989
2q | 1235 | 0.01 | -1.33 | 0.991 | 0.01 | -1.33 | 0.989
3p | 853 | 0.01 | -1.58 | 0.991 | 0.05 | -0.14 | 0.942
3q | 917 | 0.00 | -2.04 | 0.991 | 0.06 | 0.408 | 0.666
4p | 366 | 0.01 | -1.87 | 0.991 | 0.08 | 0.265 | 0.735
4q | 865 | 0.01 | -1.45 | 0.991 | 0.14 | 3.36 | 0.00167
5p | 207 | 0.00 | -2.38 | 0.991 | 0.10 | 0.926 | 0.411
5q | 1246 | 0.00 | -1.83 | 0.991 | 0.06 | 0.875 | 0.414
6p | 937 | 0.03 | -1.04 | 0.991 | 0.03 | -1.04 | 0.989
6q | 692 | 0.01 | -1.55 | 0.991 | 0.15 | 3.51 | 0.00109
7p | 508 | 0.29 | 8.14 | 4.33e-15 | 0.00 | -1.98 | 0.989
7q | 1071 | 0.36 | 13.2 | 0 | 0.00 | -1.6 | 0.989
8p | 495 | 0.05 | -0.453 | 0.991 | 0.04 | -0.893 | 0.989
8q | 697 | 0.15 | 3.52 | 0.0028 | 0.01 | -1.54 | 0.989
9p | 343 | 0.02 | -1.58 | 0.991 | 0.27 | 6.89 | 2.63e-11
9q | 916 | 0.03 | -1.06 | 0.991 | 0.03 | -1.06 | 0.989
10p | 312 | 0.11 | 1.23 | 0.529 | 0.22 | 5 | 1.91e-06
10q | 1050 | 0.00 | -1.78 | 0.991 | 0.23 | 7.35 | 1.24e-12
11p | 731 | 0.03 | -1.05 | 0.991 | 0.13 | 2.67 | 0.0136
11q | 1279 | 0.05 | 0.447 | 0.991 | 0.04 | -0.0996 | 0.942
12p | 484 | 0.07 | 0.0288 | 0.991 | 0.05 | -0.409 | 0.989
12q | 1162 | 0.01 | -1.31 | 0.991 | 0.08 | 1.32 | 0.251
13q | 554 | 0.01 | -1.64 | 0.991 | 0.15 | 3.26 | 0.0022
14q | 1144 | 0.00 | -1.79 | 0.991 | 0.16 | 5 | 1.91e-06
15q | 1132 | 0.03 | -0.781 | 0.991 | 0.08 | 1.3 | 0.251
16p | 719 | 0.00 | -2.18 | 0.991 | 0.04 | -0.788 | 0.989
16q | 562 | 0.01 | -1.82 | 0.991 | 0.03 | -1.37 | 0.989
17p | 575 | 0.01 | -1.84 | 0.991 | 0.00 | -2.29 | 0.989
17q | 1321 | 0.03 | -0.704 | 0.991 | 0.00 | -1.82 | 0.989
18p | 117 | 0.03 | -1.47 | 0.991 | 0.14 | 2.18 | 0.0437
18q | 340 | 0.00 | -2.26 | 0.991 | 0.14 | 2.41 | 0.0261
19p | 870 | 0.10 | 1.84 | 0.212 | 0.18 | 4.71 | 6.76e-06
19q | 1452 | 0.10 | 2.38 | 0.0675 | 0.40 | 16.7 | 0
20p | 295 | 0.11 | 1.51 | 0.367 | 0.01 | -1.86 | 0.989
20q | 627 | 0.12 | 2.4 | 0.0675 | 0.00 | -2.13 | 0.989
21q | 422 | 0.03 | -1.41 | 0.991 | 0.05 | -0.548 | 0.989
22q | 764 | 0.01 | -1.61 | 0.991 | 0.08 | 0.735 | 0.474

Methods & Data
Input

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LGG/1216617/2.GDAC_MergeDataFiles.Finished/LGG.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

- Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

- CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt

- Amplification Threshold = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 80 Input Tumor Samples.

Tumor Sample Names
TCGA-CS-4938-01B-11D-1892-01
TCGA-CS-4941-01A-01D-1466-01
TCGA-CS-4942-01A-01D-1466-01
TCGA-CS-4943-01A-01D-1466-01
TCGA-CS-4944-01A-01D-1466-01
TCGA-CS-5390-01A-02D-1466-01
TCGA-CS-5393-01A-01D-1466-01
TCGA-CS-5394-01A-01D-1466-01
TCGA-CS-5395-01A-01D-1466-01
TCGA-CS-5396-01A-02D-1466-01

Figure 3. Segmented copy number profiles in the input data

GISTIC

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

CNV Description

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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
Meta

- Maintainer = Dan DiCara

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