Copy number analysis (GISTIC2)
Pancreatic Adenocarcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1DV1GXP
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1DV1GXP
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 50 tumor samples used in this analysis: 15 significant arm-level results, 11 significant focal amplifications, and 24 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 - 11 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
--- | --- | --- | --- | ---
18q11.2 | 0.0012298 | 0.0012298 | chr18:19638276-20097505 | 2
Xq27.1 | 0.0067925 | 0.0067925 | chrX:138564705-138580557 | 0 [F9]
Xp22.11 | 0.0067925 | 0.0067925 | chrX:23975644-23983593 | 0 [CXorf58]
12p12.1 | 0.051079 | 0.067433 | chr12:19610032-39228082 | 80
8q24.21 | 0.078555 | 0.078555 | chr8:127864635-128801947 | 4
20q13.2 | 0.11906 | 0.11906 | chr20:51093677-52298532 | 2
1p34.3 | 0.18989 | 0.18989 | chr1:37413199-43297807 | 86
12p13.33 | 0.18989 | 0.19157 | chr12:1-5520802 | 50
1p12 | 0.21402 | 0.21402 | chr1:120033150-120523901 | 10
9p13.3 | 0.21402 | 0.21402 | chr9:35244633-35825412 | 22
7q22.1 | 0.24884 | 0.24884 | chr7:97521506-100214486 | 77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
GATA6
CTAGE1

Genes in Wide Peak

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

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

Genes
KRAS
hsa-mir-4302
hsa-mir-920
BCAT1
BICD1
DDX11
GYS2
IAPP
ITPR2
KCNJ8
LDHB
LRMP
PDE3A
PKP2
PTHLH
RECQL
ST8SIA1
SLCO1A2
SOX5
SSPN
PPFIBP1
MED21
KIAA0528
DNM1L
ABCC9
IPO8
SLCO1B1
RASSF8
STK38L
FGFR1OP2
SLCO1B3
GOLT1B
YARS2
ERGIC2
TM7SF3
SLCO1C1
C12orf35
CASC1
CCDC91
ETNK1
FAR2
ASUN
CMAS
ARNTL2
KLHDC5
FAM60A
MRPS35
CAPRIN2
BHLHE41
FLJ13224
PYROXD1
C12orf39
TMTC1
ALG10
FGD4
AEBP2
ALG10B
LINC00477
LYRM5
CPNE8
IFLTD1
DENND5B
AMN1
C12orf77
METTL20
SLCO1B7
C12orf70
OVCH1
SYT10
REP15
H3F3C
TSPAN11
C12orf71
MIR920
MANSC4
LOC100287314
MIR4302
LOC100506393
LOC100506451
LOC100506660

Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
LOC727677
PCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
ZNF217
TSHZ2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.3.

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

Genes
MYCL1
hsa-mir-30c-1
hsa-mir-4255
BMP8B
COL9A2
CTPS
EDN2
FHL3
GRIK3
GUCA2A
GUCA2B
INPP5B
MTF1
NDUFS5
NFYC
YBX1
POU3F1
PPT1
RLF
DNALI1
PABPC4
KCNQ4
RIMS3
ZMPSTE24
PPIE
PPIH
CAP1
SF3A3
FOXJ3
SCMH1
MACF1
MYCBP
HEYL
GNL2
UTP11L
HPCAL4
TRIT1
RHBDL2
C1orf109
CDCA8
HIVEP3
OXCT2
RRAGC
LEPRE1
SMAP2
MEAF6
DEM1
ZNF643
C1orf50
AKIRIN1
YRDC
PPCS
SNIP1
ZC3H12A
GJA9
ZMYND12
NT5C1A
MFSD2A
ERMAP
TMCO2
ZNF684
C1orf122
MANEAL
CLDN19
CITED4
SLFNL1
RSPO1
EPHA10
RIMKLA
LOC339442
ZNF642
BMP8A
CCDC23
MIR30C1
MIR30E
KIAA0754
SNORA55
LOC728431
PPIEL
CCDC30
LOC100129924
LOC100130557
MIR4255
MIR3659
LOC100507178
GJA9-MYCBP

Genes in Wide Peak

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

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

Genes
CCND2
KDM5A
CACNA1C
FGF6
FKBP4
FOXM1
KCNA1
KCNA5
KCNA6
NDUFA9
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
FGF23
DYRK4
AKAP3
RAD51AP1
TSPAN9
ERC1
GALNT8
ITFG2
PRMT8
PARP11
C12orf4
C12orf5
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
EFCAB4B
CACNA2D4
FBXL14
DCP1B
B4GALNT3
LOC283440
IQSEC3
LOC574538
LRTM2
FAM138D
LOC100271702
LOC100288778
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

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

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

Genes
NOTCH2
HMGCS2
HSD3B1
ADAM30
PHGDH
REG4
ZNF697
HSD3BP4
NBPF7
LOC644242

Genes in Wide Peak

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

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

Genes
CA9
CD72
NPR2
RMRP
TESK1
TLN1
TPM2
RGP1
RUSC2
CREB3
UNC13B
SPAG8
SIT1
GBA2
HINT2
C9orf100
ATP8B5P
CCDC107
C9orf128
MSMP
FAM166B
MIR4667

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
hsa-mir-106b
AZGP1
CYP3A7
CYP3A4
CYP3A5
AGFG2
LRCH4
MCM7
NPTX2
OCM2
PCOLCE
PMS2P1
TAF6
ZNF3
ZKSCAN1
ZSCAN21
TRRAP
BUD31
AP4M1
ATP5J2
ARPC1B
ARPC1A
STAG3
CPSF4
COPS6
PDAP1
LMTK2
ZKSCAN5
BRI3
TECPR1
PTCD1
FBXO24
PILRB
PILRA
ZCWPW1
C7orf43
BAIAP2L1
MEPCE
SMURF1
MOSPD3
CYP3A43
ZNF655
PVRIG
GAL3ST4
OR2AE1
TSC22D4
ZNF394
MYH16
TRIM4
BHLHA15
ZNF498
FAM200A
PPP1R35
GPC2
TMEM130
NYAP1
CNPY4
MBLAC1
ZNF789
GJC3
GATS
MGC72080
C7orf59
KPNA7
C7orf61
MIR106B
MIR25
MIR93
SPDYE3
AZGP1P1
LOC100129845
LOC100289187
SAP25
MIR3609
ATP5J2-PTCD1
MIR4658
CYP3A7-CYP3AP1

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 - 24 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 | 3.7341e-14 | 3.7341e-14 | chr9:21865498-21996995 | 2
18q21.2 | 0.0013619 | 0.0013619 | chr18:47344726-51063597 | 15
8p23.1 | 0.074888 | 0.074888 | chr8:1-28204263 | 233
10q23.2 | 0.074888 | 0.074888 | chr10:87353730-88197748 | 3
11p15.4 | 0.074888 | 0.074888 | chr11:1-8129432 | 238
22q13.31 | 0.074888 | 0.074888 | chr22:43263433-51304566 | 105
5q14.2 | 0.082188 | 0.088047 | chr5:80619535-90466295 | 31
1p36.22 | 0.088047 | 0.10521 | chr1:1-36027453 | 569
6p25.2 | 0.091235 | 0.10521 | chr6:3104965-3272193 | 5
1p21.2 | 0.074888 | 0.12659 | chr1:99774425-100161103 | 1
17q22 | 0.14301 | 0.13682 | chr17:48204059-81195210 | 446
7q36.1 | 0.15505 | 0.15505 | chr7:120987351-159138663 | 331
15q15.1 | 0.15645 | 0.15505 | chr15:1-56211217 | 404
21q22.11 | 0.18885 | 0.18434 | chr21:1-39962795 | 183
Xp22.31 | 0.18434 | 0.18434 | chrX:1-149685409 | 917
6q22.33 | 0.18885 | 0.18885 | chr6:64353191-171115067 | 512
17p11.2 | 0.18885 | 0.18885 | chr17:17249330-17381763 | 1
4p12 | 0.20113 | 0.19755 | chr4:41741183-65288598 | 77
12p12.3 | 0.20795 | 0.19755 | chr12:4374374-23740960 | 244
6p22.3 | 0.18885 | 0.21379 | chr6:1-40324094 | 533
8q12.1 | 0.21379 | 0.21379 | chr8:57429517-59365429 | 7
9p13.2 | 0.21961 | 0.21379 | chr9:36213180-88357924 | 141
12q12 | 0.16551 | 0.22704 | chr12:1-133851895 | 1200
12q24.32 | 0.15505 | 0.28353 | chr12:1-133851895 | 1200

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
hsa-mir-4320
DCC
SMAD4
MBD1
ME2
MYO5B
MAPK4
CXXC1
MEX3C
ELAC1
MRO
SKA1
CCDC11
LOC100287225
MIR4320

Genes in Wide Peak

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

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

Genes
PCM1
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
EGR3
EPB49
EPHX2
CLN8
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
PSD3
SLC39A14
FBXO25
FGF20
ADAMDEC1
CNOT7
ZDHHC2
SLC25A37
SCARA3
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
AGPAT5
CSGALNACT1
HR
PBK
DEFB103B
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
MCPH1
PPP1R3B
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
NKX2-6
SGCZ
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
ESCO2
LOC157627
C8orf42
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FLJ10661
XKR6
LOC286059
LOC286083
EFHA2
LOC286114
SCARA5
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
C8orf80
LOC392196
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA1B
FAM90A20
FAM90A19
ZNF705D
FAM66B
LOC100128993
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR4287
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
MIR4659A
MIR4660
MIR4659B
LOC100652791

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.2.

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

Genes
hsa-mir-346
GRID1
MIR346

Genes in Wide Peak

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

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

Genes
CARS
HRAS
NUP98
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
SMPD1
TRIM21
STIM1
TAF10
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
TUB
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IFITM2
TRIM3
OR7E12P
KCNQ1OT1
PKP3
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
MRPL17
EPS8L2
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
FAM160A2
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
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
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TRIM6-TRIM34
MIR483
SNORA52
LOC650368
LOC653486
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686
MIR4687

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
BIK
TSPO
MPPED1
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
MCAT
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
SCUBE1
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
PNPLA5
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
LINC00229
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q14.2.

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

Genes
hsa-mir-9-2
hsa-mir-4280
CCNH
CETN3
COX7C
HAPLN1
VCAN
MEF2C
RASA1
RPS23
XRCC4
EDIL3
POLR3G
SSBP2
ATG10
GPR98
ATP6AP1L
LYSMD3
ACOT12
TMEM167A
MBLAC2
TMEM161B
NBPF22P
MIR9-2
LINC00461
SCARNA18
MIR4280
MIR3607
MIR3660
LOC100505894
MIR3977

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.22.

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

Genes
LCK
PAX7
RPL22
SDHB
SFPQ
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
AK2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
PHC2
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
YARS
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
S100PBP
CEP85
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCP2
SYTL1
IGSF21
C1orf94
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
C1orf212
ADC
TMEM54
CSMD2
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
GJB4
HMGB4
RNF19B
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
FNDC5
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
ZBTB8OS
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
LOC402779
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
ZBTB8A
LOC653160
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
ZBTB8B
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR4254
MIR3917
MIR3605
MIR3675
ENO1-AS1
ZMYM6NB
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
BPHL
TUBB2A
TUBB2B
PSMG4
LOC100507194

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p21.2.

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

Genes
PALMD

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q22.

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

Genes
CD79B
CLTC
COL1A1
DDX5
HLF
PRKAR1A
ASPSCR1
BRIP1
MSI2
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
CHAD
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NME1
NME2
NPTX1
P4HB
PDE6G
PECAM1
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGCA
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
PPM1D
DGKE
CBX4
DNAH17
ABCC3
RGS9
GALR2
SPHK1
CACNA1G
SOCS3
SPAG9
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
TOB1
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
RAB40B
TLK2
POLG2
CD300A
TMC6
DDX42
PPM1E
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
UTP18
RNFT1
HN1
TUBD1
DCXR
TACO1
MRPL27
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
LUC7L3
SDK2
FAM20A
MBTD1
BCAS3
TMEM104
RNF43
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
SMG8
TMEM100
RSAD1
LRRC59
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45L
CA10
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
XYLT2
DNAI2
SMURF2
ENGASE
SPATA20
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
ACSF2
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
MYCBPAP
QRICH2
KIF2B
USP32
PPP1R9B
CBX2
FAM104A
MGC16275
FBF1
UNK
CEP95
TRIM47
ANKRD40
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
WFIKKN2
TBC1D16
AFMID
DYNLL2
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
EME1
NOTUM
TMC8
ANKFN1
MARCH10
TMEM92
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MTVR2
STXBP4
LOC253962
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
HILS1
LRRC37A3
RNF126P1
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
LOC400604
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
MIR142
MIR21
MIR301A
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LOC645638
TBC1D3P1-DHX40P1
LOC653653
NME1-NME2
LINC00338
SCARNA20
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR634
MIR635
MIR636
MIR657
LOC729683
PRCD
MIR454
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3614
MIR3678
MIR3615
LOC100506650
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4729
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.1.

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

Genes
BRAF
EZH2
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CADPS2
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
BUB1B
FLJ27352
C15orf55
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
USP8
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
USP50
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
MIR628
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.11.

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

Genes
RUNX1
ERG
OLIG2
hsa-mir-802
hsa-mir-4327
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
APP
ATP5J
ATP5O
BACH1
BAGE
TMEM50B
CBR1
CBR3
CXADR
RCAN1
DYRK1A
GABPA
GART
GRIK1
HLCS
IFNAR1
IFNAR2
IFNGR2
IL10RB
KCNE1
KCNJ6
KCNJ15
NCAM2
TMPRSS15
ITSN1
SIM2
SLC5A3
SOD1
SON
HSPA13
TIAM1
TPTE
TTC3
NRIP1
CHAF1B
SYNJ1
CLDN8
ADAMTS1
URB1
CRYZL1
DOPEY2
KCNE2
RWDD2B
DSCR4
DSCR3
USP16
CCT8
BTG3
ADAMTS5
MORC3
CLDN14
LTN1
CLDN17
N6AMT1
USP25
DONSON
HUNK
PIGP
DSCR6
RBM11
LINC00160
FAM165B
C21orf49
MIS18A
LINC00158
CHODL-AS1
LINC00113
SETD4
C21orf15
CLIC6
LINC00308
MRPL39
C21orf91
DNAJC28
C21orf62
MRAP
C21orf59
C21orf7
SCAF4
JAM2
C21orf63
SAMSN1
MRPS6
RUNX1-IT1
DSCR8
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
GCFC1
LINC00310
MIR155HG
CYYR1
OLIG1
LINC00161
KRTAP13-1
TCP10L
CHODL
ANKRD30BP2
LIPI
ABCC13
LINC00189
C21orf91-OT1
LINC00314
KRTAP15-1
DSCR9
DSCR10
D21S2088E
LINC00307
LINC00515
KRTAP13-4
POTED
KRTAP7-1
KRTAP8-1
KRTAP11-1
KRTAP19-1
KRTAP13-2
KRTAP13-3
KRTAP23-1
KRTAP6-1
KRTAP6-2
KRTAP6-3
KRTAP19-2
KRTAP19-3
KRTAP19-4
KRTAP19-5
KRTAP19-6
KRTAP19-7
KRTAP20-1
KRTAP20-2
KRTAP21-1
KRTAP21-2
KRTAP22-1
KRTAP20-3
LOC339622
LINC00317
LINC00320
LOC388813
LINC00478
KRTAP26-1
ANKRD20A11P
MIRLET7C
MIR125B2
MIR155
MIR99A
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
KRTAP19-8
C21orf54
MIR802
KRTAP25-1
TEKT4P2
LOC100133286
KRTAP20-4
KRTAP22-2
KRTAP21-3
LOC100288432
GRIK1-AS2
MIR4327
MIR3156-3
MIR3687
MIR3648
C21orf37
GCFC1-AS1
LOC100506334
LOC100506385
CBR3-AS1
LINC00159
MIR4759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.31.

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

Genes
ATRX
ELF4
GATA1
GPC3
MSN
NONO
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
CRLF2
P2RY8
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
hsa-mir-448
hsa-mir-1911
hsa-mir-1264
hsa-mir-4329
hsa-mir-652
hsa-mir-548m
hsa-mir-361
hsa-mir-548i-4
hsa-mir-4328
hsa-mir-325
hsa-mir-384
hsa-mir-374a
hsa-mir-223
hsa-mir-1468
hsa-let-7f-2
hsa-mir-502
hsa-mir-222
hsa-mir-548f-5
hsa-mir-1308
hsa-mir-651
ABCB7
AGTR2
NR0B1
ALAS2
AMELX
SLC25A5
SLC25A6
XIAP
SHROOM2
AR
ARAF
ARHGAP6
ARR3
STS
ARSD
ARSE
ARSF
ASMT
ATP7A
BCYRN1
BMX
BRS3
BTK
CACNA1F
S100G
CAPN6
CD40LG
CDR1
CDX4
CHM
CLCN4
CLCN5
COL4A5
COL4A6
COX7B
CSF2RA
CSTF2
CYBB
CYLC1
DCX
DDX3X
TIMM8A
DIAPH2
DLG3
DMD
DRP2
TSC22D3
EDA
EFNB1
EIF1AX
EIF2S3
ELK1
F9
ACSL4
FANCB
GPC4
FGD1
FGF13
FHL1
FIGF
FMR1
AFF2
CENPI
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
GJB1
GK
GLA
GLRA2
GLUD2
GPM6B
CXCR3
LPAR4
GPR34
GRIA3
GRPR
GUCY2F
HSD17B10
HCCS
HNRNPH2
HPRT1
ERAS
HTR2C
IDS
IGBP1
IGSF1
IL2RG
IL3RA
IL13RA1
IL13RA2
KAL1
KCND1
LAMP2
PRICKLE3
SH2D1A
MAGEA8
MAGEA9
MAGEA11
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
MCF2
CD99
MID1
FOXO4
CITED1
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
POLA1
POU3F4
PPEF1
PRKX
PRPS1
PRPS2
PRRG1
PSMD10
RBBP7
RBM3
RP2
RPGR
RPL39
RPL36A
RPS4X
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SH3BGRL
SHOX
SLC16A2
SMARCA1
SMS
SOX3
SRD5A1P1
SSX5
CDKL5
SUV39H1
SYN1
SYP
TAF1
SERPINA7
TBL1X
DYNLT3
TDGF1P3
TIMP1
TSPAN7
TSPAN6
TMSB4X
TRO
TRPC5
UBA1
UBE2A
SLC35A2
XG
XIST
XK
XPNPEP2
ZFX
ZIC3
ZNF711
ZNF182
ZNF41
ZNF75D
ZNF157
RNF113A
ZXDA
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
SRPX
UXT
CUL4B
IRS4
OGT
OFD1
PIR
INE2
INE1
CASK
ASMTL
PAGE1
FGF16
AKAP4
APLN
AP1S2
GYG2
FAM127A
SLC25A14
CLDN2
RGN
AIFM1
CXorf1
REPS2
ZBED1
ZMYM3
BMP15
MED14
TCEAL1
RAB33A
RAB9A
TSIX
ITM2A
ARHGEF6
PCYT1B
MAGED1
XAGE2
XAGE1D
PAGE4
MORF4L2
GPRASP1
STARD8
FRMPD4
PHF16
ARMCX2
HEPH
MAGEC1
AMMECR1
MED12
ZBTB33
HDAC6
MAMLD1
HUWE1
PQBP1
GPR64
ATP6AP2
ODZ1
SSX3
TIMM17B
RRAGB
SCML2
SLC9A6
ENOX2
PRDX4
EBP
STAG2
RAI2
PLAC1
CYSLTR1
UTP14A
PGRMC1
MAGED2
MSL3
TMSB15A
PIM2
MID2
IL1RAPL1
WDR45
PRAF2
CA5B
SLC6A14
KLF8
VSIG4
CNKSR2
IQSEC2
PHF8
SEPT6
ARHGEF9
ATP1B4
ACOT9
KCNE1L
LDOC1
SMPX
GSPT2
KIF4A
FTSJ1
CXorf27
MXRA5
EGFL6
FAM127B
IL1RAPL2
ITGB1BP2
VCX
GAGE12I
GAGE2E
SNORA69
SNORD61
NGFRAP1
NOX1
FAM155B
INGX
GPR82
GPKOW
SRPX2
APEX2
RBMX
PCDH11X
RPS6KA6
P2RY10
HTATSF1
PCSK1N
PPP2R3B
CCDC22
MCTS1
MAGEH1
FAM156A
C1GALT1C1
SNX12
RPA4
UBQLN2
SH3KBP1
SPANXA1
FOXP3
TBX22
ZDHHC9
RLIM
WBP5
RAB9B
LUZP4
PDZD11
CXorf26
TFDP3
TLR7
ARMCX1
TLR8
MBTPS2
MAGEC2
VGLL1
VCX2
VCX3A
ARMCX3
TAF9B
RBMX2
MST4
CPXCR1
CHIC1
FTHL17
GPR173
NLGN3
SASH3
TAF7L
SPIN2A
ARMCX6
WDR44
NDUFB11
GNL3L
ERCC6L
NUP62CL
GDPD2
BCOR
TBC1D8B
FAM120C
GEMIN8
CXorf48
FAM70A
CXorf57
NUDT11
RBM41
PLCXD1
SAGE1
OTUD5
ZNF280C
MTMR8
ZNF673
TXLNG
MBNL3
WWC3
FAM45B
BEX1
HDAC8
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
LRCH2
MAGEE1
RAP2C
MID1IP1
ACE2
TMEM35
EDA2R
NYX
BCORL1
DUSP21
CXorf56
DMRTC1
TSPYL2
TNMD
PJA1
SPANXD
SPANXC
WDR13
PORCN
ARMCX5
UPF3B
WNK3
APOO
HMGN5
NKAP
RNF128
MAP7D3
MORC4
CXorf36
LONRF3
ALG13
MAGIX
TCEAL4
TRMT2B
POF1B
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
ESX1
BHLHB9
MAGED4B
LAS1L
GPR101
TMEM47
USP26
FRMD8P1
MAGT1
TMEM164
PHF6
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
SLC9A7
BEX2
MGC16121
SLC7A3
TCEAL3
CCNB3
PPP1R3F
CCDC120
TSR2
HS6ST2
FRMD7
KLHL13
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
CXorf40A
RIPPLY1
LOC92249
ATXN3L
SLC38A5
MMGT1
ACRC
SYAP1
SYTL4
SYTL5
GPRASP2
ATG4A
DACH2
SLITRK4
SPANXN3
MAGEC3
BEND2
DCAF12L1
DGKK
LOC139201
CXorf41
MUM1L1
FAM199X
FAM123B
APOOL
HDX
FUNDC1
GPR112
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
OTUD6A
UPRT
MAGEE2
MAGEB16
FOXR2
ACTRT1
GPR119
PAGE3
RBMXL3
DOCK11
SPIN4
ASB11
ASB9
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
ZNF645
FMR1NB
LOC158572
FAAH2
ZXDB
LOC158696
FAM47A
MOSPD2
ARHGAP36
RIBC1
AKAP14
RHOXF1
NKAPP1
MAGEB6
CXorf65
AWAT1
AWAT2
ZDHHC15
USP51
TCEAL6
H2BFWT
CXorf38
FAM122B
FAM122C
DDX53
FAM46D
SPIN3
FAM47B
CXorf22
FAM48B2
TCEANC
ZCCHC12
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
SPANXE
SPANXF1
CXorf61
SLC25A43
LINC00246A
ZCCHC5
NRK
DDX26B
ZNF449
TMEM31
PAGE2
DHRSX
BRWD3
CXorf58
CT47A11
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX8
RAB40AL
PPP2R3B-AS1
ATP11C
RP1-177G6.2
H2BFM
LOC286437
LOC286442
YIPF6
CXorf59
LOC286467
TTC3P1
FAM133A
MAGEB18
TMSB15B
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
LOC340544
VSIG1
ZC3H12B
SATL1
DCAF12L2
CA5BP1
ZCCHC16
LHFPL1
ZNF81
ITIH6
LANCL3
LOC347411
DCAF8L2
SOWAHD
OR13H1
CCDC160
CXorf66
DGAT2L6
RAB41
ARSH
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
PAGE2B
ZCCHC13
UBE2NL
LOC389906
CXXC1P1
GLOD5
FLJ44635
ARL13A
LINC00086
CD99P1
LOC401588
MCART6
DKFZp686D0853
XKRX
YY2
MIRLET7F2
MIR106A
MIR188
MIR19B2
MIR221
MIR222
MIR223
MIR92A2
MIR98
VCX3B
LOC441495
FLJ46446
RPS26P11
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
PGAM4
FAM47C
UQCRBP1
LOC442459
MIR374A
SPIN2B
SPANXN1
SPANXN2
SPANXN5
MIR384
MIR424
CT45A6
CT45A1
CXorf40B
SSX4B
LOC550643
JPX
MIR448
MIR450A1
MIR362
MIR363
MIR20B
MIR18B
MIR500A
MIR501
MIR502
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
ZNF674
CT47B1
LOC643486
GAGE10
ZCCHC18
CXorf69
LINC00087
GAGE2B
GAGE13
GAGE12G
CXorf30
PABPC1L2B
NAP1L6
XAGE1C
XAGE1E
XAGE1A
XAGE1B
CT47A7
LINC00246B
MIR545
MIR542
SCARNA23
SNORA11
SNORA35
SNORD96B
MIR421
MIR532
MIR651
MIR660
CXorf31
SSX2B
FAM156B
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGED4
XAGE2B
MAGEA9B
NXF2B
DMRTC1B
SPANXB1
SPANXA2
CT45A2
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
LOC729609
H2BFXP
MIR766
GAGE12F
LOC100093698
GAGE8
SNORA11C
SNORA11D
SNORA11E
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR374B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129407
CXorf28
LOC100129515
LOC100129520
LOC100129662
HSFX2
FAM48B1
CXorf49
CXorf64
LOC100131434
ARMCX4
UBE2DNL
LOC100132163
GAGE12D
XGPY2
LOC100132741
LOC100132831
CXorf49B
CXorf51B
LOC100133123
SPANXB2
LOC100133957
SCARNA9L
LOC100272228
LOC100287765
LOC100288814
MIR1468
MIR1912
MIR1298
MIR1256
MIR320D2
MIR1277
MIR1911
MIR1264
FTX
SLC25A5-AS1
MIR764
MIR2114
LOC100329135
LINC00102
MIR514B
MIR500B
MIR4328
MIR4329
MTRNR2L10
MIR374C
MIR23C
MIR676
MIR3690
HSFX1
LOC100506757
CT47A12
LOC100509575
ARMCX5-GPRASP2
RPL36A-HNRNPH2
PIR-FIGF
MIR4769
MIR4536-1
MIR4768
MIR4770
MIR4767
MIR3978

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.33.

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
ACAT2
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GPR31
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
ME1
MAP3K4
MAP3K5
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGM3
PLAGL1
PLG
PLN
POU3F2
PREP
PKIB
PSMB1
PTPRK
REV3L
RNY4
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
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
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
PHF3
HEY2
HEBP2
ORC3
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
SENP6
TIAM2
FBXL4
C6orf123
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
BRP44L
HECA
COQ3
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
PHF10
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
C6orf70
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
SMAP1
C6orf164
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
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
C6orf7
UBE2CBP
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
FAM54A
SFT2D1
KLHL32
TMEM200A
MB21D1
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SRSF12
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GJB7
HMGA1P7
SNHG5
SUMO4
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
MIR30A
MIR30C2
OOEP
FAM26F
FLJ46906
LOC441177
MCART3P
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
KHDC1L
LOC100129518
LOC100130890
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100288198
LOC100289495
NHEG1
MIR1913
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100506804
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
SMCR9

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p12.

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

Genes
KDR
KIT
PDGFRA
PHOX2B
CHIC2
FIP1L1
CNGA1
GABRA2
GABRA4
GABRB1
GABRG1
IGFBP7
POLR2B
PPAT
REST
SGCB
SPINK2
SRP72
TEC
TXK
CLOCK
CEP135
ATP8A1
SLC30A9
PAICS
CORIN
NMU
DCUN1D4
LPHN3
OCIAD1
COMMD8
TMEM33
EXOC1
TMEM165
ATP10D
DANCR
KIAA1211
SLAIN2
GUF1
USP46
RASL11B
SRD5A3
CWH43
NOA1
HOPX
LNX1
OCIAD2
SPATA18
GNPDA2
ARL9
AASDH
PDCL2
NFXL1
NIPAL1
SHISA3
LOC152578
SCFD2
COX7B2
GSX2
SLC10A4
TECRL
LOC255130
DCAF4L1
YIPF7
FRYL
ZAR1
LRRC66
KCTD8
BEND4
GRXCR1
RPL21P44
LOC644145
SNORA26
ERVMER34-1
LOC100506462
LOC100506564
MIR4449

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p12.3.

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

Genes
CCND2
ETV6
ZNF384
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
GYS2
IAPP
KCNA1
KCNA5
KCNA6
KCNJ8
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LDHB
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTMS
PTPN6
PTPRO
PEX5
PZP
RECQL
SCNN1A
ST8SIA1
SLC2A3
SLCO1A2
SOX5
VAMP1
TNFRSF1A
TPI1
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
CSDA
DYRK4
GPRC5A
CD163
GDF3
CLSTN3
KIAA0528
NCAPD2
CLEC2B
ABCC9
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
SLCO1B1
RAD51AP1
KLRAP1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
SLCO1B3
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
GOLT1B
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
ETNK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
CMAS
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
PYROXD1
NANOG
C12orf39
DUSP16
APOLD1
GSG1
CDCA3
RBP5
ACRBP
SPSB2
RERG
PLCZ1
HTR7P1
CAPZA3
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf53
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
CLEC9A
C12orf36
CLEC4D
LOC338817
SLCO1B7
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
SCARNA12
SCARNA11
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
LOC100506393
KLRC4-KLRK1
PRH1-PRR4
MIR3974

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p22.3.

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

Genes
DAXX
FANCE
HMGA1
IRF4
PIM1
POU5F1
TRIM27
DEK
HIST1H4I
hsa-mir-1275
hsa-mir-219-1
hsa-mir-1236
hsa-mir-877
hsa-mir-3143
hsa-mir-548a-1
ABCF1
AGER
AIF1
ATP6V1G2
BAK1
CFB
BMP6
BPHL
BTN1A1
C2
C4A
C4B
DDR1
CDKN1A
CDSN
CLIC1
CLPS
COL11A2
ATF6B
MAPK14
CSNK2B
CYP21A2
CYP21A1P
DNAH8
DOM3Z
DSP
E2F3
EDN1
SERPINB1
F13A1
FKBP5
FOXF2
FOXC1
GABBR1
GCNT2
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPX5
GRM4
GTF2H4
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
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
HSPA1A
HSPA1B
HSPA1L
ID4
ITPR3
JARID2
KIFC1
LTA
LTB
MAK
MICB
MLN
MOCS1
MOG
MSH5
RPL10A
NEDD9
NEU1
NFKBIL1
NQO2
NOTCH4
PBX2
PHF1
SERPINB6
SERPINB9
PPARD
PPP1R10
MAPK13
PRL
PSMB8
PSMB9
RGL2
RING1
BRD2
RNF5
RPS10
RPS18
RREB1
RXRB
VPS52
ATXN1
SRSF3
SKIV2L
SLC17A1
SNRPC
SOX4
SRPK1
SSR1
TAF11
TAP1
TAP2
TAPBP
TCF19
TCP11
PPP1R11
TEAD3
TFAP2A
TNF
TNXA
TNXB
TPMT
TUBB2A
TULP1
VARS
ZNF76
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204P
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
OR2H2
RDBP
LST1
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
CMAHP
DHX16
KCNK5
B3GALT4
RIPK1
SYNGAP1
STK19
IER3
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
GCM2
WDR46
ZBTB22
CD83
PPT2
CDYL
LY86
EEF1E1
MDC1
FAM65B
ZSCAN12
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
FLOT1
SLC17A2
HCG9
PRSS16
BTN3A3
BTN2A2
ECI2
PFDN6
HMGN4
TRIM38
CAP2
UBD
AGPAT1
SCGN
C6orf10
FARS2
SLC17A3
RPP40
HCP5
EHMT2
TRIM31
BTN3A2
BTN3A1
BTN2A1
NUDT3
NRM
STK38
FTSJD2
ANKS1A
SIRT5
DAAM2
DDAH2
MTCH1
SPDEF
OR2B6
FAM50B
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
SNORD52
SNORD48
BRPF3
MRPS18B
C6orf15
MYLIP
ABT1
PACSIN1
ZNRD1
DEF6
C6orf48
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
ETV7
TMEM14C
TDP2
CUTA
PPIL1
HCG4
GFOD1
CCHCR1
BTN2A3P
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
TBC1D22B
EXOC2
SAYSD1
ACOT13
APOM
BTNL2
TRIM39
WRNIP1
DUSP22
LYRM4
VARS2
MRS2
CPNE5
LSM2
C6orf47
LY6G5B
LY6G6D
ZFAND3
SLC22A23
MUTED
CCDC90A
GPSM3
FKBPL
KIF13A
ZNF323
C6orf106
LY6G6E
ZNF322
RPP21
ATAT1
ZKSCAN3
ZSCAN16
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRR3
ZNRD1-AS1
PRRT1
EGFL8
HCG4B
TXNDC5
C6orf62
OR5V1
OR2B2
OR12D3
TMEM14B
RIOK1
KCNK16
DTNBP1
MNF1
PGBD1
ADTRP
HIST1H2AH
HIST1H2BK
KCNK17
TRIM15
POM121L2
FOXQ1
BTBD9
SCAND3
SLC26A8
MAS1L
IP6K3
HUS1B
TRIM40
DPCR1
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
CCDC167
PSORS1C1
PSORS1C2
PPP1R18
TRIM39-RPP21
TUBB
PIP5K1P1
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
TOB2P1
FAM217A
HCG27
RNF144B
HIST1H2BA
GPX6
NCR3
LY6G6F
MDGA1
ZNF311
LOC285768
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
HCG22
LOC285847
PNPLA1
RNF5P1
MYLK4
IFITM4P
CLPSL1
ZNF391
ZFP57
TUBB2B
C6orf52
HCG26
KAAG1
NHLRC1
ZKSCAN4
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
SFTA2
CLPSL2
C6orf222
MUC21
DKFZP686I15217
FLJ23152
LINC00340
LOC401242
MCCD1
SAPCD1
LINC00336
FLJ41649
C6orf201
ERVFRD-1
MIR219-1
HCG23
HCG25
HCG18
OR2B3
OR2J3
OR14J1
OR10C1
GGNBP1
HCG11
LOC554223
PPP1R3G
SNORA38
SNORD32B
SNORD84
SNORD117
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
MIR877
LOC100129636
LOC100130275
LOC100130357
PSORS1C3
LOC100131047
LOC100131289
LINC00240
LOC100270746
LOC100293534
LOC100294145
MIR1275
MIR1236
MIR3143
MIR3925
MIR3691
LOC100506207
LOC100506409
LOC100507173
LOC100507194
LOC100507362
MICA
LOC100507463
LOC100507547
LOC100507584
MUC22
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
RPS10-NUDT3
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4646
MIR4640
MIR4639
MIR4645
MIR4462

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q12.1.

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

Genes
C8orf71
IMPAD1
FAM110B
UBXN2B
LOC286177
LOC100507632
LOC100507651

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p13.2.

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

Genes
GNAQ
PAX5
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
ALDH1A1
ALDH1B1
ANXA1
APBA1
KLF9
FXN
GCNT1
HNRNPK
NTRK2
PCSK5
PGM5
PRKACG
RORB
SHB
TLE1
TLE4
ZFAND5
PIP5K1B
GRHPR
FAM189A2
TJP2
GDA
GNA14
MELK
ZBTB5
GNE
FRMPD1
SMC5
VPS13A
AGTPBP1
TMEM2
ZNF658
FAM75A7
FBXO10
OSTF1
PSAT1
UBQLN1
PCA3
EXOSC3
FAM108B1
C9orf95
C9orf40
RFK
KIF27
SLC28A3
POLR1E
DCAF10
CNTNAP3
RMI1
TRPM3
GKAP1
CEP78
ZCCHC7
ANKRD20A1
C9orf64
MCART1
FAM122A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
TRPM6
RNF38
RASEF
FAM201A
RG9MTD3
PRUNE2
C9orf71
CBWD5
ANKRD18A
MAMDC2
FRMD3
LOC286297
FOXD4L3
FAM75D5
IGFBPL1
FOXD4L4
AQP7P1
PTAR1
KGFLP1
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
TOMM5
FAM74A1
FAM74A4
ZNF658B
MIR204
MIR7-1
C9orf103
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
FOXB2
CBWD3
LOC494558
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920
LOC100286938
MIR548H3
LOC100506710
LOC100507244
LOC100507299
MIR4540
MIR4475
MIR4476

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q12.

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

Genes
ALDH2
ATF1
BCL7A
BTG1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
MLL2
HMGA2
WIF1
ZNF384
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
ACACB
ACADS
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ARL1
ART4
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
SCARB1
CD63
CD69
CDK2
CDKN1B
CHD4
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CREBL2
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
DDX11
ATN1
EPYC
DTX1
DUSP6
PHC1
EIF2B1
EIF4B
CELA1
ELK3
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GRIN2B
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTA4H
LTBR
LUM
LYZ
M6PR
MARS
METTL1
KITLG
MGP
MGST1
MIP
MMP17
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NDUFA9
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
POU6F1
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAB1
PRKAG1
PRPH
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAN
RAP1B
RARG
RBMS2
RDH5
RECQL
RFC5
RFX4
RNY5
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SNRPF
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
SYT1
TAC3
TARBP2
TBX5
TBX3
HNF1A
TDG
TEAD4
TMBIM6
TFCP2
TSPAN8
TMPO
TNFRSF1A
TPI1
NR2C1
HSP90B1
TULP3
TXNRD1
UBC
UBE2N
UNG
VDR
VWF
WNT1
WNT10B
ZNF10
ZNF26
ZNF84
ZNF140
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
DYRK2
PPFIBP1
PPFIA2
CSDA
LGR5
MAPKAPK5
DENR
RDH16
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
GPRC5A
KRT75
SCAF11
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
KIAA0748
KIAA0528
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
CLEC2B
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
RNF41
MPHOSPH9
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
LEPREL2
DCTN2
AKAP3
CCT2
SLCO1B1
RAD51AP1
CAMKK2
AVIL
PTGES3
KLRAP1
ZNF268
FRS2
TSPAN9
TRAFD1
OS9
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
PHLDA1
R3HDM2
MLXIP
RPH3A
KLRK1
P2RX2
RAB21
STK38L
FBXO21
FAIM2
MON2
SETD1B
UHRF1BP1L
ERC1
DDN
ANKLE2
TMEM194A
CUX2
KIAA1033
TBC1D30
ESYT1
TENC1
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
ABCB9
CBX5
ISCU
RIMBP2
ANP32D
ATP6V0A2
SMUG1
LEMD3
CORO1C
GABARAPL1
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
FBXW8
GALNT8
HSPB8
SNORD59A
GLS2
HCAR1
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CCDC41
IRAK4
ING4
GPN3
DDX47
GLTP
MRPL51
CLEC1B
CLEC1A
C12orf47
C1RL
ERGIC2
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TM7SF3
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
MAGOHB
SLC6A15
FAM90A1
RIC8B
C12orf35
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
CAND1
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
ARNTL2
CHPT1
PARP11
ANO2
C12orf4
C12orf5
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHDC5
PITPNM2
DIP2B
KIAA1467
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
C12orf44
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
OBFC2B
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
RPAP3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
FLJ13224
TCTN2
PLBD1
PYROXD1
NANOG
DNAJC22
NAA25
SLC24A6
ADAMTS20
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
C12orf39
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
C12orf32
NRIP2
INHBE
RBP5
TMTC1
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
C12orf26
TMEM117
TCHP
COQ5
LLPH
WIBG
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
EFCAB4B
TUBA1C
ZC3H10
ORAI1
RNFT2
C12orf34
ALG10
SPRYD3
C12orf52
MFSD5
MGC14436
C12orf62
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
FAM113B
C12orf65
TMEM132C
CCDC64
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
TMEM132B
OSBPL8
ARHGEF25
C12orf56
IQCD
LOC116437
AGAP2
DCD
RAB3IP
LOH12CR1
MUCL1
DEPDC4
LRRK2
CCDC38
C12orf59
FAM186A
C12orf45
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
HIST4H4
ERP27
FGD4
AEBP2
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
BRI3BP
KRT72
PRICKLE1
AMDHD1
SLC2A14
BCDIN3D
ALG10B
GLIPR1L2
FAM101A
ZNF664
LINC00477
LYRM5
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
KRT80
A2ML1
LOC144571
C12orf66
C12orf60
FBXL14
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
IFLTD1
DENND5B
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
CLEC4C
DSTNP2
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
C12orf53
DCP1B
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
C12orf33
GNN
MSRB3
METTL20
LRRC43
OR6C74
OR6C3
TCP11L2
LOC255411
LOC255480
LOC256021
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
POC1B
OTOGL
MATL2963
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
GPR133
MORN3
LOC283392
LOC283403
LOC283404
C12orf61
DPY19L2
CLEC9A
C12orf36
GAS2L3
LINC00485
LOC283440
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
C12orf40
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
LOC338758
C1QL4
TMEM119
KRT79
LOC338799
C12orf74
FAM19A2
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
PTPRQ
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
RPL13AP20
REP15
C12orf68
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
LOC389634
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
MKRN9P
C12orf76
LOC400084
FLJ37505
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
MIR26A2
C12orf37
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
DBX2
FLJ12825
TMEM198B
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
TSPAN11
OR9K2
MIR148B
MIR331
EID3
LOH12CR2
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC574538
HIGD1C
POU5F1P3
LOC642846
MAP1LC3B2
LOC643339
LOC643770
GLYCAM1
LOC647589
FAM86FP
PRB2
LRTM2
HNRNPA1P10
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA34
SNORA49
SNORA53
LOC678655
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
MIR617
MIR618
MIR620
LOC728084
C12orf73
SKP1P2
LOC728739
C12orf71
SLC15A5
MRS2P2
HOTAIR
MIR920
LOC100128191
LOC100128554
LOC100129361
LOC100130238
LOC100130776
LOC100131138
LOC100131733
LOC100190940
LOC100233209
LOC100240734
LOC100240735
LOC100271702
LOC100286844
MANSC4
LOC100287314
LINC00173
LOC100287944
LOC100288778
ZNF605
LOC100292680
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1178
MIR1244-1
MIR1251
LOC100335030
SNORA70G
MIR1244-3
MIR1244-2
MIR4302
MIR4303
MIR4304
KLRF2
LOC100499405
MIR3685
MIR3649
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506314
LOC100506393
LOC100506451
LOC100506649
LOC100506660
LOC100506668
LOC100506844
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507250
LOC100507377
LOC100507424
BLOC1S1-RDH5
POC1B-GALNT4
KLRC4-KLRK1
ZNF664-FAM101A
PRH1-PRR4
MIR4699
MIR4498
MIR548AL
MIR4701
MIR3974
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4698
LOC100652846
LOC100652999

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.32.

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

Genes
ALDH2
ATF1
BCL7A
BTG1
CCND2
CDK4
DDIT3
ETV6
HOXC11
HOXC13
KRAS
MDM2
NACA
PTPN11
KDM5A
MLL2
HMGA2
WIF1
ZNF384
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
ACACB
ACADS
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APAF1
APOF
APOBEC1
AQP2
AQP5
AQP6
ARF3
ARHGDIB
ARL1
ART4
ASCL1
ATP2A2
ATP2B1
ATP5B
ATP5G2
AVPR1A
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CACNB3
CCNT1
CD4
CD9
CD27
SCARB1
CD63
CD69
CDK2
CDKN1B
CHD4
CMKLR1
CNTN1
COL2A1
COX6A1
CPM
CREBL2
CRY1
CS
CSRP2
CYP27B1
DGKA
DAO
DCN
DDX11
ATN1
EPYC
DTX1
DUSP6
PHC1
EIF2B1
EIF4B
CELA1
ELK3
EMP1
ENO2
STX2
EPS8
ERBB3
FGF6
FKBP4
FOXM1
B4GALNT1
GAPDH
BLOC1S1
GLI1
GNB3
GNS
GOLGA3
GPD1
GPR19
GRIN2B
GTF2H3
GUCY2C
GYS2
HAL
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
HPD
IAPP
IFNG
IGF1
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
ITPR2
KCNA1
KCNA5
KCNA6
KCNC2
KCNJ8
KIF5A
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LAG3
LALBA
LDHB
LRMP
LRP1
LRP6
LTA4H
LTBR
LUM
LYZ
M6PR
MARS
METTL1
KITLG
MGP
MGST1
MIP
MMP17
MMP19
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
NDUFA9
NELL2
NFE2
NFYB
NINJ2
NOP2
NOS1
CNOT2
SLC11A2
NTF3
NTS
OAS1
OAS2
OAS3
OLR1
P2RX4
P2RX7
PA2G4
PEBP1
PAH
PAWR
PCBP2
CDK17
PDE3A
PDE6H
PDE1B
PFDN5
PFKM
SLC25A3
PIK3C2G
PKP2
PLA2G1B
PMCH
POLE
POU6F1
PPP1CC
PPP1R1A
PRB1
PRB3
PRB4
PRH1
PRH2
PRIM1
PRKAB1
PRKAG1
PRPH
PSMD9
PTHLH
TWF1
PTMS
PTPN6
PTPRB
PTPRO
PTPRR
PXMP2
PXN
PEX5
PZP
RAB5B
RAD52
RAN
RAP1B
RARG
RBMS2
RDH5
RECQL
RFC5
RFX4
RNY5
RPL6
RPL41
RPLP0
RPS26
CLIP1
TSPAN31
ATXN2
SCN8A
SCNN1A
SELPLG
SFSWAP
SHMT2
ST8SIA1
PMEL
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SMARCC2
SMARCD1
SNRPF
SOX5
SP1
STAT2
STAT6
SUOX
VAMP1
SYT1
TAC3
TARBP2
TBX5
TBX3
HNF1A
TDG
TEAD4
TMBIM6
TFCP2
TSPAN8
TMPO
TNFRSF1A
TPI1
NR2C1
HSP90B1
TULP3
TXNRD1
UBC
UBE2N
UNG
VDR
VWF
WNT1
WNT10B
ZNF10
ZNF26
ZNF84
ZNF140
MAP3K12
TUBA1A
FGF23
MFAP5
USP5
MLF2
SSPN
AAAS
YEATS4
ALX1
CDK2AP1
KLRC4
BRAP
ULK1
EEA1
SOAT2
RASAL1
DYRK2
PPFIBP1
PPFIA2
CSDA
LGR5
MAPKAPK5
DENR
RDH16
NPFF
HSD17B6
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
DYRK4
LIN7A
SOCS2
HCAR3
ENDOU
TIMELESS
HIP1R
GPRC5A
KRT75
SCAF11
RASSF9
SLC16A7
PIWIL1
CD163
MED21
DDX23
CABP1
SLC4A8
GDF3
NCOR2
WSCD2
ESPL1
SART3
KNTC1
CLSTN3
MLEC
DAZAP2
GIT2
KIAA0748
KIAA0528
ZBTB39
NUAK1
RBM19
NCAPD2
RNF10
PAN2
USP15
NR1H4
CLEC2B
SH2B3
TROAP
DNM1L
ABCC9
ARPC3
TSFM
CTDSP2
YAF2
PLXNC1
LPCAT3
RNF41
MPHOSPH9
KLRG1
GDF11
LRRC23
TMEM5
CNPY2
TUBA1B
RAPGEF3
EMG1
MCRS1
IPO8
LEPREL2
DCTN2
AKAP3
CCT2
SLCO1B1
RAD51AP1
CAMKK2
AVIL
PTGES3
KLRAP1
ZNF268
FRS2
TSPAN9
TRAFD1
OS9
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
ATF7
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
STRAP
BAZ2A
FZD10
IRAK3
GALNT6
RASSF8
NXPH4
XPOT
PRR4
GPR182
PHB2
COPZ1
PHLDA1
R3HDM2
MLXIP
RPH3A
KLRK1
P2RX2
RAB21
STK38L
FBXO21
FAIM2
MON2
SETD1B
UHRF1BP1L
ERC1
DDN
ANKLE2
TMEM194A
CUX2
KIAA1033
TBC1D30
ESYT1
TENC1
MED13L
ZDHHC17
SIRT4
KCNH3
GRIP1
ABCB9
CBX5
ISCU
RIMBP2
ANP32D
ATP6V0A2
SMUG1
LEMD3
CORO1C
GABARAPL1
PRPF40B
MGAT4C
METTL7A
LETMD1
METTL21B
IFFO1
ZNF385A
NECAP1
FGFR1OP2
CLEC4E
FBXW8
GALNT8
HSPB8
SNORD59A
GLS2
HCAR1
GPR162
RND1
UTP20
KCNMB4
SLCO1B3
MRPL42
IFT81
CCDC59
ORMDL2
TBK1
CLEC2D
RACGAP1
SENP1
FAM216A
HCFC2
PDZRN4
TRHDE
SYCP3
CHST11
GALNT9
IL22
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
DHH
CLEC4A
HEBP1
CCDC53
GOLT1B
PLEKHA8P1
YARS2
DERA
CCDC41
IRAK4
ING4
GPN3
DDX47
GLTP
MRPL51
CLEC1B
CLEC1A
C12orf47
C1RL
ERGIC2
FKBP11
ARL6IP4
TAOK3
KLRF1
KRT76
POP5
CSAD
BIN2
ANAPC5
ANAPC7
LIMA1
TRIAP1
PPHLN1
NT5DC3
IL23A
HDAC7
TMBIM4
VPS29
WBP11
TM7SF3
TPCN1
GPR84
SLCO1C1
SLC38A2
SSH1
PRR13
PLEKHA5
RHOF
VSIG10
MANSC1
KANSL2
TESC
PARPBP
TAPBPL
SLC38A4
MAGOHB
SLC6A15
FAM90A1
RIC8B
C12orf35
APPL2
PLEKHG6
SBNO1
CASC1
TMEM19
CCDC91
DRAM1
STYK1
ETNK1
GPRC5D
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
KIF21A
SLC48A1
SCYL2
POLR3B
FAR2
LMBR1L
ASUN
ATF7IP
CHFR
H2AFJ
FGD6
IL26
FOXJ2
CAND1
ITFG2
WSB2
LMO3
CMAS
NDUFA12
PRMT8
DIABLO
MDM1
ANKS1B
NDUFA4L2
ARNTL2
CHPT1
PARP11
ANO2
C12orf4
C12orf5
LPAR5
NUP107
SMAGP
AICDA
TMCC3
PPM1H
RIMKLB
SRGAP1
KLHDC5
PITPNM2
DIP2B
KIAA1467
EP400
DHX37
CALCOCO1
FBRSL1
DDX55
NCKAP5L
NEUROD4
FAM60A
NTN4
TRPV4
C12orf10
MRPS35
C12orf44
LHX5
ARHGAP9
IKZF4
SUDS3
ACTR6
CLEC7A
TBC1D15
C12orf43
SLC26A10
VPS33A
RSRC2
WNK1
SPATS2
CAPRIN2
AACS
TMEM106C
NUP37
OBFC2B
DDX54
NOC4L
GNPTAB
BHLHE41
B3GNT4
BCL2L14
TCTN1
ADIPOR2
ACSS3
RPAP3
OGFOD2
VPS37B
BBS10
RERGL
C12orf49
PIP4K2C
FLJ13224
TCTN2
PLBD1
PYROXD1
NANOG
DNAJC22
NAA25
SLC24A6
ADAMTS20
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
C12orf39
DUSP16
WNT5B
SLC38A1
CSRNP2
APOLD1
GSG1
PUS7L
CDCA3
GLT8D2
THAP2
C12orf32
NRIP2
INHBE
RBP5
TMTC1
KCTD10
RACGAP1P
FAM186B
USP44
SLC41A2
LRRIQ1
C12orf26
TMEM117
TCHP
COQ5
LLPH
WIBG
CCDC77
SARNP
HVCN1
ACRBP
SRRM4
CCDC62
KDM2B
CAPS2
SPSB2
UNC119B
USP30
EFCAB4B
TUBA1C
ZC3H10
ORAI1
RNFT2
C12orf34
ALG10
SPRYD3
C12orf52
MFSD5
MGC14436
C12orf62
RERG
DNAJC14
ZCRB1
CCDC65
ANKRD13A
NAV3
PLCZ1
TMEM116
UBE3B
LACRT
C12orf23
FMNL3
CERS5
C12orf29
XRCC6BP1
FAM113B
C12orf65
TMEM132C
CCDC64
HELB
MARCH9
COQ10A
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
KRT71
C12orf57
LARP4
SDSL
SLC2A13
MBD6
TMEM132B
OSBPL8
ARHGEF25
C12orf56
IQCD
LOC116437
AGAP2
DCD
RAB3IP
LOH12CR1
MUCL1
DEPDC4
LRRK2
CCDC38
C12orf59
FAM186A
C12orf45
OR10P1
SDR9C7
LRIG3
TMEM132D
SLC15A4
RHEBL1
C12orf54
ZNF641
OR10AD1
TPH2
SP7
GTSF1
OR10A7
KRT74
NEDD1
SLC9A7P1
IKBIP
HIST4H4
ERP27
FGD4
AEBP2
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
ASB8
MYL6B
BRI3BP
KRT72
PRICKLE1
AMDHD1
SLC2A14
BCDIN3D
ALG10B
GLIPR1L2
FAM101A
ZNF664
LINC00477
LYRM5
CPNE8
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
KRT80
A2ML1
LOC144571
C12orf66
C12orf60
FBXL14
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
CLEC12A
CLECL1
TMTC3
C12orf50
ALDH1L2
IFLTD1
DENND5B
GRASP
SLC5A8
PPTC7
CCDC63
CCDC60
CLEC4C
DSTNP2
PGAM5
KRT78
RILPL2
DNAH10
AMN1
DTX3
METTL7B
C12orf77
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
C12orf53
DCP1B
ANO6
ARID2
RPSAP52
SLC17A8
STAC3
C12orf33
GNN
MSRB3
METTL20
LRRC43
OR6C74
OR6C3
TCP11L2
LOC255411
LOC255480
LOC256021
GLIPR1L1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
POC1B
OTOGL
MATL2963
CD163L1
LOC283332
LOC283335
ZNF740
RPL13P5
RASSF3
B4GALNT3
OR6C6
ANKRD52
SLC39A5
SPRYD4
GPR133
MORN3
LOC283392
LOC283403
LOC283404
C12orf61
DPY19L2
CLEC9A
C12orf36
GAS2L3
LINC00485
LOC283440
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
C12orf40
GXYLT1
TMPRSS12
KRT6C
DDX51
KRT73
MMAB
CLEC4D
HCAR2
LOC338758
C1QL4
TMEM119
KRT79
LOC338799
C12orf74
FAM19A2
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
EP400NL
RILPL1
TAS2R42
DPPA3
NANOGNB
LOC374443
KRT77
PTPRQ
C12orf42
LRRC10
IL31
CLEC2A
CLEC12B
RPL13AP20
REP15
C12orf68
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
LOC389634
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FLJ41278
MKRN9P
C12orf76
LOC400084
FLJ37505
FIGNL2
OR6C65
OR6C68
MIRLET7I
MIR135A2
MIR141
MIR196A2
MIR200C
MIR26A2
C12orf37
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
DBX2
FLJ12825
TMEM198B
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
TSPAN11
OR9K2
MIR148B
MIR331
EID3
LOH12CR2
ATXN7L3B
CLLU1OS
CLLU1
MIR492
LOC574538
HIGD1C
POU5F1P3
LOC642846
MAP1LC3B2
LOC643339
LOC643770
GLYCAM1
LOC647589
FAM86FP
PRB2
LRTM2
HNRNPA1P10
SCARNA12
SCARNA11
FAM138D
SNORA2A
SNORA2B
SNORA34
SNORA49
SNORA53
LOC678655
SNORD59B
SCARNA10
MIR548C
MIR613
MIR614
MIR615
MIR617
MIR618
MIR620
LOC728084
C12orf73
SKP1P2
LOC728739
C12orf71
SLC15A5
MRS2P2
HOTAIR
MIR920
LOC100128191
LOC100128554
LOC100129361
LOC100130238
LOC100130776
LOC100131138
LOC100131733
LOC100190940
LOC100233209
LOC100240734
LOC100240735
LOC100271702
LOC100286844
MANSC4
LOC100287314
LINC00173
LOC100287944
LOC100288778
ZNF605
LOC100292680
MIR1252
MIR1279
MIR1228
MIR1827
MIR1293
MIR1291
MIR1178
MIR1244-1
MIR1251
LOC100335030
SNORA70G
MIR1244-3
MIR1244-2
MIR4302
MIR4303
MIR4304
KLRF2
LOC100499405
MIR3685
MIR3649
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506314
LOC100506393
LOC100506451
LOC100506649
LOC100506660
LOC100506668
LOC100506844
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507250
LOC100507377
LOC100507424
BLOC1S1-RDH5
POC1B-GALNT4
KLRC4-KLRK1
ZNF664-FAM101A
PRH1-PRR4
MIR4699
MIR4498
MIR548AL
MIR4701
MIR3974
MIR4472-2
MIR4700
MIR3198-2
MIR4497
MIR4698
LOC100652846
LOC100652999

Arm-level results

Table 3. Get Full Table Arm-level significance table - 15 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.07 | -0.322 | 0.988 | 0.19 | 2.53 | 0.0255
1q | 1955 | 0.26 | 3.82 | 0.00266 | 0.08 | -0.303 | 0.952
2p | 924 | 0.07 | -1.21 | 0.988 | 0.13 | -0.0406 | 0.952
2q | 1556 | 0.06 | -0.964 | 0.988 | 0.06 | -0.964 | 0.995
3p | 1062 | 0.05 | -1.43 | 0.988 | 0.21 | 1.75 | 0.133
3q | 1139 | 0.11 | -0.171 | 0.988 | 0.13 | 0.231 | 0.86
4p | 489 | 0.07 | -1.49 | 0.988 | 0.11 | -0.752 | 0.995
4q | 1049 | 0.02 | -2.09 | 0.988 | 0.10 | -0.491 | 0.967
5p | 270 | 0.04 | -2.1 | 0.988 | 0.06 | -1.74 | 0.995
5q | 1427 | 0.02 | -1.91 | 0.988 | 0.10 | -0.219 | 0.952
6p | 1173 | 0.07 | -0.911 | 0.988 | 0.42 | 6.29 | 2.15e-09
6q | 839 | 0.04 | -1.37 | 0.988 | 0.51 | 7.79 | 1.33e-13
7p | 641 | 0.23 | 1.79 | 0.368 | 0.05 | -1.59 | 0.995
7q | 1277 | 0.21 | 2.04 | 0.277 | 0.07 | -0.83 | 0.995
8p | 580 | 0.15 | 0.149 | 0.988 | 0.23 | 1.63 | 0.16
8q | 859 | 0.24 | 2.23 | 0.258 | 0.13 | -0.069 | 0.952
9p | 422 | 0.07 | -1.19 | 0.988 | 0.44 | 5.67 | 7.12e-08
9q | 1113 | 0.05 | -1.32 | 0.988 | 0.25 | 2.68 | 0.0184
10p | 409 | 0.03 | -2.19 | 0.988 | 0.20 | 1.11 | 0.334
10q | 1268 | 0.05 | -1.33 | 0.988 | 0.21 | 1.95 | 0.101
11p | 862 | 0.06 | -1.38 | 0.988 | 0.06 | -1.38 | 0.995
11q | 1515 | 0.07 | -0.949 | 0.988 | 0.09 | -0.521 | 0.967
12p | 575 | 0.12 | -0.483 | 0.988 | 0.16 | 0.261 | 0.86
12q | 1447 | 0.10 | -0.277 | 0.988 | 0.20 | 1.82 | 0.124
13q | 654 | 0.10 | -0.823 | 0.988 | 0.17 | 0.681 | 0.584
14q | 1341 | 0.08 | -0.686 | 0.988 | 0.04 | -1.52 | 0.995
15q | 1355 | 0.09 | -0.538 | 0.988 | 0.11 | -0.122 | 0.952
16p | 872 | 0.10 | -0.659 | 0.988 | 0.00 | -2.61 | 0.995
16q | 702 | 0.06 | -1.55 | 0.988 | 0.02 | -2.31 | 0.995
17p | 683 | 0.00 | -2.26 | 0.988 | 0.36 | 4.55 | 1.82e-05
17q | 1592 | 0.05 | -1.23 | 0.988 | 0.17 | 1.36 | 0.247
18p | 143 | 0.17 | 0.156 | 0.988 | 0.32 | 2.93 | 0.00959
18q | 446 | 0.04 | -1.61 | 0.988 | 0.47 | 6.39 | 1.65e-09
19p | 995 | 0.02 | -2.11 | 0.988 | 0.10 | -0.527 | 0.967
19q | 1709 | 0.11 | 0.152 | 0.988 | 0.09 | -0.289 | 0.952
20p | 355 | 0.13 | -0.367 | 0.988 | 0.09 | -1.09 | 0.995
20q | 753 | 0.20 | 1.4 | 0.648 | 0.03 | -2.04 | 0.995
21q | 509 | 0.03 | -1.78 | 0.988 | 0.39 | 4.85 | 4.95e-06
22q | 921 | 0.07 | -1.08 | 0.988 | 0.19 | 1.26 | 0.277
Xq | 1312 | 0.04 | -1.5 | 0.988 | 0.10 | -0.255 | 0.952

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.

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PAAD-TP/3349599/GDAC_MergeDataFiles_3203509/PAAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 50 Input Tumor Samples.

Tumor Sample Names
TCGA-F2-6879-01A-11D-2153-01
TCGA-F2-6880-01A-11D-2153-01
TCGA-F2-7273-01A-11D-2153-01
TCGA-F2-7276-01A-11D-2153-01
TCGA-FZ-5919-01A-11D-1608-01
TCGA-FZ-5920-01A-11D-1608-01
TCGA-FZ-5921-01A-11D-1608-01
TCGA-FZ-5922-01A-11D-1608-01
TCGA-FZ-5923-01A-12D-1608-01
TCGA-FZ-5924-01A-13D-1608-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. 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.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. 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.

8. 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').

9. 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:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

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

CNV Description

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

Download Results

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
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