SNP6 Copy number analysis (GISTIC2)
Pancreatic Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C10G3HT0
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C10G3HT0
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 91 tumor samples used in this analysis: 18 significant arm-level results, 16 significant focal amplifications, and 27 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 - 16 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 3.5313e-10 3.5313e-10 chr18:19826724-19972386 0 [CTAGE1]
8q24.21 0.00031648 0.00031648 chr8:127864635-128801947 4
12p13.33 0.00141 0.00141 chr12:1-5520802 50
7q22.1 0.0015564 0.0015564 chr7:97888086-99186825 22
12q15 0.0031822 0.0031822 chr12:68307608-70989876 26
Xq27.1 0.011103 0.011103 chrX:138564705-138580557 0 [F9]
12p11.21 0.012704 0.012704 chr12:31414318-31442221 1
19q13.2 0.0134 0.0134 chr19:38391473-41050262 82
Xp22.11 0.014247 0.014247 chrX:23975644-23983593 0 [CXorf58]
1p12 0.020497 0.020497 chr1:120204209-120523901 6
9p13.3 0.063088 0.063088 chr9:35029166-36332795 39
17p11.2 0.09063 0.09063 chr17:19277362-19895201 12
20q13.2 0.12898 0.12898 chr20:50935475-59107639 64
17q21.32 0.14198 0.14198 chr17:43500951-54883634 144
11p11.2 0.18508 0.18508 chr11:24893542-56013797 188
1p34.2 0.19025 0.19025 chr1:31385322-44557362 208
Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
LOC727677
PCAT1
Genes in Wide Peak

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

Table S2.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 7q22.1.

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

Genes
NPTX2
TRRAP
BUD31
ATP5J2
ARPC1B
ARPC1A
CPSF4
PDAP1
ZKSCAN5
BRI3
PTCD1
BAIAP2L1
SMURF1
ZNF655
ZNF394
MYH16
FAM200A
TMEM130
ZNF789
KPNA7
MIR3609
ATP5J2-PTCD1
Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
IFNG
LYZ
CNOT2
PTPRB
RAP1B
YEATS4
CCT2
FRS2
CPSF6
KCNMB4
IL22
SLC35E3
IL26
MDM1
NUP107
RAB3IP
BEST3
LRRC10
MIR1279
SNORA70G
MIR3913-2
MIR3913-1
LOC100507250
Genes in Wide Peak

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

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

Genes
FAM60A
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
AKT2
hsa-mir-641
ACTN4
BLVRB
CLC
ECH1
FBL
HNRNPL
LGALS4
LGALS7
MAP3K10
NFKBIB
PSMC4
PSMD8
MRPS12
RPS16
RYR1
SUPT5H
ZFP36
DPF1
FCGBP
DYRK1B
KCNK6
GMFG
PAK4
SPINT2
DLL3
MAP4K1
SIRT2
SIPA1L3
PLD3
EIF3K
LGALS13
SERTAD3
SERTAD1
PAF1
SARS2
SAMD4B
MED29
LGALS14
LRFN1
PRX
SPTBN4
CATSPERG
C19orf33
PLEKHG2
CNTD2
WDR87
YIF1B
TIMM50
PPP1R14A
FBXO17
RASGRP4
EID2B
RINL
FBXO27
C19orf47
HIPK4
FAM98C
CAPN12
LGALS16
TTC9B
EID2
ZNF780B
GGN
IL28A
IL28B
IL29
ZNF780A
ZNF546
NCCRP1
SYCN
LEUTX
SELV
PAPL
SPRED3
LGALS17A
LOC643669
LGALS7B
MIR641
LOC100129935
MIR4530
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: Cancer Gene Census[7].

Genes
NOTCH2
HMGCS2
ADAM30
PHGDH
REG4
NBPF7
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: Cancer Gene Census[7].

Genes
FANCG
CA9
CCIN
CD72
CLTA
NPR2
RMRP
TESK1
TLN1
TPM2
VCP
RECK
RGP1
RUSC2
GNE
CREB3
UNC13B
SPAG8
SIT1
STOML2
TMEM8B
OR2S2
GBA2
FAM214B
HINT2
PIGO
C9orf100
FP588
C9orf131
GLIPR2
LOC158376
ATP8B5P
CCDC107
C9orf128
OR13J1
HRCT1
MSMP
FAM166B
MIR4667
Genes in Wide Peak

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

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

Genes
ALDH3A1
ALDH3A2
MFAP4
MAPK7
RNF112
ULK2
AKAP10
B9D1
SLC47A1
SLC47A2
SNORA59B
SNORA59A
Genes in Wide Peak

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

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

Genes
GNAS
hsa-mir-646
hsa-mir-298
hsa-mir-4325
ATP5E
BMP7
CSTF1
CTSZ
CYP24A1
EDN3
MC3R
PCK1
PFDN4
PPP1R3D
AURKA
TFAP2C
ZNF217
RAE1
BCAS1
STX16
VAPB
SYCP2
SPO11
SLMO2
TH1L
C20orf43
PPP4R1L
RBM38
DOK5
PMEPA1
CASS4
RAB22A
CDH26
FAM217B
NPEPL1
TUBB1
ZBP1
FAM210B
PHACTR3
TSHZ2
C20orf85
ZNF831
GCNT7
CBLN4
CTCFL
LOC149773
GNAS-AS1
APCDD1L
FAM209A
C20orf197
LOC284757
FAM209B
SUMO1P1
MIR296
MIR298
MIR4325
MTRNR2L3
LOC100506384
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4532
MIR4533
MIR5095
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q21.32.

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

Genes
COL1A1
HLF
hsa-mir-3185
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
hsa-mir-4315-1
ATP5G1
CDC27
CHAD
COX11
CRHR1
DLX3
DLX4
GIP
GNGT2
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
ITGA3
ITGB3
KPNB1
MAPT
MYL4
NFE2L1
NGFR
NME1
NME2
NSF
PDK2
PHB
SGCA
SP2
WNT3
WNT9B
SPOP
SKAP1
ABCC3
CACNA1G
SPAG9
NOG
NPEPPS
GOSR2
TBKBP1
PLEKHM1
LRRC37A
TOM1L1
TOB1
SLC35B1
CALCOCO2
HOXB13
IGF2BP1
CBX1
KAT7
NXPH3
SNF8
ZNF652
MMD
SNX11
TBX21
UTP18
ABI3
COPZ2
MRPL27
ARL17A
LUC7L3
MBTD1
LINC00483
EPN3
LRRC37A4
PNPO
TMEM100
RSAD1
LRRC59
CA10
PCTP
XYLT2
SPATA20
UBE2Z
PRR15L
ACSF2
CDK5RAP3
SP6
FAM117A
MYCBPAP
PRAC
KIF2B
PPP1R9B
LRRC46
SCRN2
ANKRD40
OSBPL7
WFIKKN2
FLJ40194
B4GALNT2
C17orf57
MRPL10
EME1
C17orf69
ANKFN1
TMEM92
PHOSPHO1
IMP5
ARHGAP27
SAMD14
STH
STXBP4
LOC253962
TAC4
KIAA1267
TTLL6
LOC284080
C17orf67
HOXB13-AS1
HILS1
RPRML
LOC400604
MGC57346
LOC404266
MIR10A
MIR152
MIR196A1
LRRC37A2
LOC644172
LOC644246
MRPL45P2
NME1-NME2
NSFP1
FLJ45513
LOC100128977
LOC100130148
MIR1203
MIR4315-2
MIR3185
MIR4315-1
ARL17B
LOC100506650
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p11.2.

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

Genes
DDB2
EXT2
LMO2
WT1
CREB3L1
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
ACP2
ARHGAP1
BDNF
MPPED2
CAT
CD44
CD59
CHRM4
CRY2
CSTF3
ELF5
F2
FOLH1
FSHB
CD82
KCNA4
LRP4
CAPRIN1
MDK
MYBPC3
NDUFS3
PAX6
PSMC3
PTPRJ
RAG1
RAG2
RAPSN
RCN1
SLC1A2
SPI1
TRAF6
PDHX
BBOX1
DGKZ
CHST1
API5
MADD
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
NR1H3
HIPK3
EIF3M
CELF1
OR5I1
NUP160
FNBP4
MTCH2
FJX1
C11orf41
ABTB2
PAMR1
FBXO3
EHF
OR5L2
ELP4
COMMD9
PACSIN3
APIP
HSD17B12
PHF21A
WT1-AS
TRIM44
NAT10
LIN7C
SLC35C1
TCP11L1
LGR4
AMBRA1
KBTBD4
TTC17
PRDM11
SYT13
LRRC4C
ALX4
ANO3
PRRG4
C11orf49
TRIM48
ZNF408
QSER1
AGBL2
PRR5L
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
KIF18A
ARFGAP2
ACCS
SPRYD5
TSPAN18
CCDC34
SLC39A13
DEPDC7
C1QTNF4
PTPMT1
C11orf74
OR4C46
OR4X2
OR4B1
GYLTL1B
DNAJC24
C11orf46
OR8I2
LOC120824
LDLRAD3
MUC15
C11orf94
SLC5A12
METTL15
IMMP1L
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
ALKBH3
LOC221122
OR4C3
OR4S1
OR10AG1
OR5J2
OR4C13
OR4C12
LOC283116
HARBI1
LINC00294
LUZP2
OR5F1
LOC338739
DCDC1
DKFZp779M0652
FIBIN
C11orf96
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
HNRNPKP3
FAM180B
OR4A47
OR4C45
MIR129-2
DKFZp686K1684
LOC440040
LOC440041
LOC441601
CCDC73
BDNF-AS1
TRIM64C
LOC646813
SNORD67
MIR610
LOC729799
C11orf91
MIR670
MIR3160-2
MIR3160-1
DCDC5
LOC100507205
LOC100507300
LOC100507401
MIR3973
MIR4688
MIR1343
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
LCK
MPL
MYCL1
SFPQ
THRAP3
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
AK2
ATP6V0B
BAI2
BMP8B
CDC20
COL8A2
COL9A2
COL16A1
CSF3R
CTPS
DPH2
EDN2
PHC2
FABP3
FHL3
GJA4
GJB3
GJB5
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
HPCA
INPP5B
MTF1
NDUFS5
NFYC
YBX1
POU3F1
PPT1
PSMB2
PTPRF
RBBP4
RLF
ST3GAL3
SLC2A1
SLC6A9
TIE1
ZSCAN20
DNALI1
PTP4A2
YARS
EIF3I
B4GALT2
PABPC4
ARTN
KCNQ4
ZMYM4
ZMYM6
SNRNP40
IPO13
KDM4A
PUM1
RIMS3
ZMPSTE24
PPIE
PPIH
CAP1
KHDRBS1
SF3A3
EBNA1BP2
FOXJ3
SCMH1
NCDN
SZT2
MACF1
KPNA6
MYCBP
HEYL
EIF2C1
TRAPPC3
TEKT2
PRO0611
GNL2
ZNF691
UTP11L
HPCAL4
ZCCHC17
TRIT1
RHBDL2
ADPRHL2
C1orf109
BSDC1
TMEM39B
CDCA8
FAM176B
TRIM62
MAP7D1
IQCC
TMEM234
KIAA1522
DLGAP3
HIVEP3
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
SMAP2
S100PBP
MEAF6
DEM1
ELOVL1
MRPS15
MARCKSL1
ZNF643
C1orf50
CCDC28B
NKAIN1
AKIRIN1
YRDC
PPCS
SH3D21
SNIP1
ZMYM1
KIAA0319L
ZC3H12A
GJA9
SYNC
TSSK3
HYI
STK40
ZMYND12
NT5C1A
FAM167B
MFSD2A
LSM10
C1orf94
SPOCD1
MED8
C1orf212
ADC
TMEM54
ERMAP
CSMD2
TMCO2
ZNF684
GJB4
HMGB4
RNF19B
C1orf122
OSCP1
C1orf216
TMEM125
DCDC2B
ZNF362
LOC149086
MANEAL
CLDN19
WDR65
C1orf210
CCDC24
CITED4
EIF2C3
EIF2C4
TXLNA
SLFNL1
FNDC5
LOC284551
RSPO1
EPHA10
RIMKLA
LOC339442
MTMR9LP
ZBTB8OS
TFAP2E
ZNF642
SERINC2
BMP8A
CCDC23
LOC402779
MIR30C1
MIR30E
FLJ32224
FAM183A
PEF1
KIAA0754
ZBTB8A
LOC653160
SNORA55
SNORD85
SNORD103A
SNORD103B
ZBTB8B
LOC728431
PPIEL
CCDC30
LOC100128071
LOC100129924
LOC100130557
LOC100132774
MIR4255
MIR4254
MIR3659
MIR3605
ZMYM6NB
LOC100507178
GJA9-MYCBP

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

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
9p21.3 1.9599e-40 1.9599e-40 chr9:21865498-21996995 2
18q21.2 2.4725e-11 2.4725e-11 chr18:48472083-48920689 3
17q22 0.0044223 0.0044155 chr17:50947516-71090299 181
6p25.2 0.011132 0.011132 chr6:1-5774928 39
7q36.1 0.033889 0.033889 chr7:104756307-159138663 396
22q13.31 0.038578 0.039872 chr22:43805179-51304566 98
1p36.11 0.010407 0.044488 chr1:20685998-31265856 172
5q14.2 0.052096 0.052096 chr5:82134980-82936981 5
12p12.1 0.052096 0.052096 chr12:4374374-22798169 243
11p15.4 0.057864 0.057864 chr11:1-11644638 279
8p21.3 0.062135 0.062135 chr8:1-29215076 243
12q24.33 0.065848 0.065848 chr12:74931350-133851895 442
21q21.1 0.065848 0.066811 chr21:1-34407260 130
9q22.33 0.065848 0.078093 chr9:101468446-101979393 4
1p36.32 0.057691 0.10133 chr1:1-31412918 496
19q13.41 0.09815 0.10133 chr19:41395276-59128983 730
10q23.2 0.11542 0.11966 chr10:86084854-108925515 255
16q23.1 0.12111 0.11966 chr16:78129058-79627770 1
18p11.32 0.12355 0.12398 chr18:1-9144356 48
12q12 0.095416 0.13187 chr12:31809739-55796833 251
4q35.2 0.14467 0.14442 chr4:96759449-191154276 388
2p23.3 0.17347 0.18029 chr2:1-59292261 347
8q12.1 0.16863 0.18029 chr8:48647103-69264813 94
1q42.2 0.20108 0.20108 chr1:230200929-234444030 31
19p13.3 0.19077 0.20108 chr19:1-11268555 366
3p24.1 0.20645 0.20281 chr3:1-88046665 592
9q32 0.16689 0.23605 chr9:1-141213431 983
Genes in Wide Peak

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

Table S14.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 S15.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SMAD4
MEX3C
ELAC1
Genes in Wide Peak

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

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

Genes
CD79B
CLTC
DDX5
HLF
PRKAR1A
BRIP1
MSI2
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
APOH
CA4
CACNG1
COX11
CSH1
CSH2
CSHL1
CYB561
ACE
ERN1
BPTF
GH1
GH2
ICAM2
KCNJ2
KCNJ16
KPNA2
LPO
MAP3K3
MPO
TRIM37
PECAM1
SEPT4
PRKCA
MAP2K6
PSMC5
PSMD12
RAD51C
RPS6KB1
SCN4A
SRSF1
SMARCD2
SOX9
SUPT4H1
TBX2
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
PPM1D
DGKE
RGS9
MTMR4
SLC16A6
NOG
BZRAP1
TBX4
MRC2
HELZ
MED13
TOM1L1
DCAF7
ABCA10
ABCA9
ABCA8
APPBP2
GNA13
TLK2
POLG2
DDX42
PPM1E
ARSG
ABCA6
ABCA5
MMD
NOL11
TANC2
PITPNC1
OR4D1
CACNG5
CACNG4
RNFT1
TUBD1
TACO1
AMZ2
MRPS23
PTRH2
FAM20A
BCAS3
RNF43
MKS1
WIPI1
SMG8
TMEM100
MSX2P1
PRR11
TEX2
TEX14
CCDC47
INTS2
PCTP
SCPEP1
HEATR6
SMURF2
DHX40
LIMD2
KCNH6
VMP1
KIF2B
USP32
CEP95
STRADA
C17orf72
FTSJ3
HSF5
OR4D2
C17orf64
DYNLL2
TCAM1P
EFCAB3
LOC146880
ANKFN1
MARCH10
CEP112
SLC39A11
AMZ2P1
MTVR2
STXBP4
C17orf58
MILR1
C17orf47
GDPD1
METTL2A
C17orf67
NACA2
SKA2
LRRC37A3
RNF126P1
YPEL2
C17orf82
KCNJ2-AS1
LINC00511
CUEDC1
MIR142
MIR21
MIR301A
TBC1D3P2
PLEKHM1P
LOC440461
LOC645638
TBC1D3P1-DHX40P1
LOC653653
SCARNA20
SNORA76
SNORD104
MIR634
MIR635
LOC729683
MIR454
SNORA38B
MIR548W
MIR4315-2
MIR4315-1
LOC100499466
LOC100499467
MIR3614
LOC100506650
LOC100506779
MIR4729
MIR4737
MIR4736
MIR4524A
MIR3064
MIR5047
Genes in Wide Peak

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

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

Genes
IRF4
BPHL
SERPINB1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
TUBB2A
RIPK1
PRPF4B
CDYL
ECI2
FARS2
RPP40
FAM50B
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
FOXQ1
HUS1B
C6orf195
PXDC1
MGC39372
FAM217A
LOC285768
MYLK4
TUBB2B
PSMG4
DKFZP686I15217
C6orf201
PPP1R3G
MIR3691
LOC100507194
LOC100508120
MIR4645
Genes in Wide Peak

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

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

Genes
BRAF
EZH2
MET
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
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DLD
DPP6
SLC26A3
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR22
GPR37
GRM8
MNX1
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRCAM
NRF1
PAX4
SLC26A4
PIK3CG
PIP
PODXL
PPP1R3A
PRKAR2B
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
NAMPT
AASS
FAM3C
COG5
FASTK
DUS4L
ZNF277
ABCB8
TFEC
LAMB4
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
COPG2
HBP1
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
NAA38
GPR85
TAS2R5
CHPF2
PUS7
ING3
LRRN3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
BCAP29
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
CBLL1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
ATXN7L1
CDHR3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
EIF3IP1
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
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
MIR3666
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468
Genes in Wide Peak

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

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
MPPED1
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
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 1p36.11.

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

Genes
ARID1A
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
ALPL
C1QA
C1QB
C1QC
RUNX3
CDA
CDC42
CD52
RCC1
CNR2
DDOST
E2F2
ECE1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
FUCA1
IFI6
GALE
SFN
GPR3
HMGN2
HMGCL
HSPG2
HTR1D
ID3
STMN1
MATN1
OPRD1
PAFAH2
PPP1R8
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
SRSF4
SLC9A1
TAF12
TCEA3
TCEB3
SLC30A2
LUZP1
LAPTM5
SNHG3
NR0B2
FCN3
EIF4G3
MAP3K6
C1orf38
ZBTB40
PTPRU
CELA3A
WASF2
HNRNPR
SRRM1
CNKSR1
GMEB1
NUDC
SRSF10
RCAN3
LYPLA2
DNAJC8
KDM1A
WDTC1
CELA3B
TMEM50A
STX12
CLIC4
SYF2
LDLRAP1
RNU11
AHDC1
SMPDL3B
LINC00339
HP1BP3
ZNF593
MECR
YTHDF2
WNT4
GPN2
MED18
TRNAU1AP
AIM1L
XKR8
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
FAM54B
C1orf63
PITHD1
MAN1C1
NIPAL3
SEPN1
KIF17
GRHL3
IL22RA1
GPATCH3
CEP85
PINK1
PHACTR4
C1orf135
MUL1
LIN28A
FAM110D
DHDDS
ZNF436
SH3BGRL3
SESN2
TMEM222
USP48
NBPF3
ZDHHC18
TRIM63
SYTL1
SNHG12
C1orf201
UBXN11
ATPIF1
RAB42
FAM46B
C1orf172
MYOM3
C1orf213
PDIK1L
IL28RA
FAM43B
PAQR7
FAM76A
ZNF683
LOC284632
LOC339505
CATSPER4
TRNP1
CD164L2
TMEM200B
SH2D5
C1orf130
LDLRAD2
LOC644961
LOC646471
LOC653566
SCARNA1
SNORA44
SNORA61
SNORA16A
SNORD99
LOC729059
LOC100129196
MIR1976
MIR3115
MIR4253
MIR3917
LOC100506801
LOC100506963
MIR4420
MIR4684
MIR378F
RCAN3AS
Genes in Wide Peak

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

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

Genes
VCAN
XRCC4
TMEM167A
SCARNA18
MIR3977
Genes in Wide Peak

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

Table S22.  Genes in bold are cancer genes as defined by The Sanger Institute: 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
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 11p15.4.

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
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
OR7E12P
LYVE1
KCNQ1OT1
PKP3
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
AKIP1
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
MOB2
SBF2
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
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
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
TMEM41B
LOC440028
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC644656
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
LOC729013
MIR675
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MTRNR2L8
MIR210HG
MIR4686
MIR4485
MIR4687
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

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

Genes
PCM1
hsa-mir-4288
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
DUSP4
EGR3
EPB49
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
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
KIF13B
PSD3
SLC39A14
FBXO25
FGF20
ADAMDEC1
CNOT7
ZDHHC2
SLC25A37
SCARA3
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
AGPAT5
INTS9
CSGALNACT1
HR
PBK
ZNF395
DEFB103B
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
HMBOX1
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
FBXO16
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
MIR4288
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 12q24.33.

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

Genes
ALDH2
BCL7A
BTG1
PTPN11
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
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497
Genes in Wide Peak

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

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

Genes
OLIG2
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
BACH1
BAGE
CXADR
GABPA
GRIK1
NCAM2
TMPRSS15
SOD1
HSPA13
TIAM1
TPTE
NRIP1
SYNJ1
CLDN8
ADAMTS1
URB1
RWDD2B
USP16
CCT8
BTG3
ADAMTS5
LTN1
CLDN17
N6AMT1
USP25
HUNK
RBM11
C21orf49
MIS18A
LINC00158
CHODL-AS1
LINC00113
C21orf15
LINC00308
MRPL39
C21orf91
C21orf62
MRAP
C21orf59
C21orf7
SCAF4
JAM2
C21orf63
SAMSN1
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
GCFC1
MIR155HG
CYYR1
LINC00161
KRTAP13-1
TCP10L
CHODL
ANKRD30BP2
LIPI
ABCC13
LINC00189
C21orf91-OT1
LINC00314
KRTAP15-1
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
KRTAP25-1
TEKT4P2
KRTAP20-4
KRTAP22-2
KRTAP21-3
GRIK1-AS2
MIR4327
MIR3156-3
MIR3687
MIR3648
C21orf37
GCFC1-AS1
LINC00159
MIR4759
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.33.

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

Genes
COL15A1
TGFBR1
GALNT12
ANKS6
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
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
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
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
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
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
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
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
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
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
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
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
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
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
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD99
SNORD103A
SNORD103B
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
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 19q13.41.

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

Genes
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
A1BG
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLPTM1
CRX
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
MEGF8
EMP3
ERCC1
ERF
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
LIPE
BCAM
MYBPC2
CEACAM6
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
RPS5
RPS9
RPS11
RPS19
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
UBE2M
ARHGEF1
CYTH2
ZNF235
ZNF264
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
TOMM40
ZNF211
RABAC1
TRAPPC2P1
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
CYP2G1P
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
CYP2S1
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
ELSPBP1
LIN7B
HIF3A
ZNF574
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
IRGQ
ZNF428
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
CADM4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
ZNF233
LILRA5
B3GNT8
IGFL1
ZNF773
LOC386758
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
LOC390940
ZNF805
ZNF321P
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
LOC646508
SBK2
LOC646862
PSG10P
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
SGK110
BSPH1
LOC100131691
PEG3-AS1
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
ERVV-2
LOC100287177
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
APOC4-APOC2
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
Genes in Wide Peak

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

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

Genes
BMPR1A
TLX1
NFKB2
PTEN
SUFU
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
ACTA2
FAS
ARL3
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DNTT
FGF8
GLUD1
GOT1
GRID1
HELLS
HHEX
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
KIF11
LIPA
NDUFB8
PAX2
PDE6C
PGAM1
PITX3
PPP1R3C
PSD
ALDH18A1
RBP4
SCD
SFRP5
FBXW4
SLIT1
SNCG
TAF5
TLL2
WNT8B
LIPF
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
NEURL
LGI1
NOLC1
GSTO1
MINPP1
KIF20B
SH3PXD2A
SLK
ZNF518A
FRAT1
ACTR1A
NPM3
RPP30
SORBS1
ERLIN1
LBX1
MGEA5
C10orf116
LDB3
CPEB3
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
C10orf28
POLL
BLNK
KCNIP2
EXOSC1
CALHM2
CUTC
PLCE1
PANK1
FAM190B
EXOC6
FAM35A
CCNJ
MARCH5
CNNM2
C10orf26
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
FAM178A
C10orf2
TM9SF3
ENTPD7
AS3MT
STAMBPL1
SEMA4G
AVPI1
HPSE2
MMS19
NOC3L
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
C10orf95
PDZD7
OBFC1
UBTD1
WDR96
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
LZTS2
LCOR
MRPL43
PYROXD2
USMG5
ATAD1
ARHGAP19
ITPRIP
LINC00263
OPALIN
OPN4
HOGA1
SORCS1
PIK3AP1
MORN4
ZFYVE27
FRA10AC1
ANKRD22
SFXN2
C10orf32
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
C10orf129
LIPJ
CFL1P1
HECTD2
FGFBP3
NKX2-3
SLC35G1
CCDC147
CALHM1
PIPSL
BLOC1S2
FLJ37201
O3FAR1
LIPM
CYP26C1
SLC16A12
CC2D2B
FLJ41350
GOLGA7B
MIR107
C10orf62
LOC439994
IFIT1B
MIR346
MIR146B
FAM25A
LIPK
LIPN
LOC643529
SNORA12
MIR608
MIR609
FAM22A
FAM22D
LOC728190
LOC728218
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
KLLN
LOC100188947
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
FAS-AS1
MIR3157
MIR3158-1
MIR3158-2
LOC100505540
LOC100505761
LOC100505839
LOC100507470
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
MIR4679-1
MIR4679-2
MIR4678
MIR4482-1
MIR4685
Genes in Wide Peak

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

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

Genes
WWOX
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.32.

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

Genes
hsa-mir-4317
ADCYAP1
CETN1
NDUFV2
PTPRM
TGIF1
TYMS
YES1
ZFP161
MYOM1
USP14
DLGAP1
LPIN2
THOC1
NDC80
MYL12A
EPB41L3
CCDC165
SMCHD1
CLUL1
ENOSF1
LINC00470
METTL4
ARHGAP28
COLEC12
EMILIN2
L3MBTL4
MYL12B
LINC00526
RAB12
LOC201477
LOC284215
LAMA1
LOC339290
LRRC30
LOC400643
C18orf56
C18orf42
CBX3P2
LOC645355
TMEM200C
FLJ35776
ROCK1P1
LOC727896
LOC100130480
LOC100192426
MIR4317
MIR3976
Genes in Wide Peak

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

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

Genes
ATF1
HOXC11
HOXC13
MLL2
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
AQP2
AQP5
AQP6
ARF3
ATP5G2
BICD1
CACNB3
CCNT1
CNTN1
COL2A1
EIF4B
CELA1
GPD1
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IGFBP6
ITGA5
ITGB7
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
NELL2
NFE2
SLC11A2
PCBP2
PDE1B
PFDN5
PFKM
PKP2
POU6F1
PPP1R1A
PRKAG1
PRPH
TWF1
RARG
RNY5
SCN8A
SMARCD1
SP1
TARBP2
TMBIM6
TFCP2
VDR
WNT1
WNT10B
MAP3K12
TUBA1A
AAAS
SOAT2
NPFF
ENDOU
KRT75
SCAF11
DDX23
SLC4A8
ESPL1
DAZAP2
KIAA0748
TROAP
DNM1L
YAF2
TUBA1B
RAPGEF3
MCRS1
ATF7
GALNT6
COPZ1
FAIM2
DDN
TENC1
KCNH3
CBX5
ANP32D
SMUG1
PRPF40B
METTL7A
LETMD1
ZNF385A
RND1
RACGAP1
SENP1
PDZRN4
DHH
PLEKHA8P1
YARS2
IRAK4
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
HDAC7
GPR84
SLC38A2
PRR13
KANSL2
SLC38A4
C12orf35
KIF21A
SLC48A1
LMBR1L
SMAGP
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
C12orf10
C12orf44
SPATS2
TMEM106C
RPAP3
DNAJC22
ADAMTS20
SLC38A1
CSRNP2
PUS7L
RACGAP1P
FAM186B
TMEM117
TUBA1C
ALG10
SPRYD3
MFSD5
C12orf62
ZCRB1
CCDC65
LACRT
FMNL3
CERS5
FAM113B
KRT71
LARP4
SLC2A13
DCD
MUCL1
LRRK2
FAM186A
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
FGD4
ASB8
KRT72
PRICKLE1
BCDIN3D
ALG10B
CPNE8
KRT80
GRASP
KRT78
AMN1
ANO6
ARID2
METTL20
OR6C74
OR6C3
LOC255411
LOC283332
LOC283335
ZNF740
OR6C6
LOC283403
LOC283404
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
SYT10
ANKRD33
H1FNT
OR8S1
AMIGO2
KRT77
C12orf68
OR6C1
OR6C75
LOC400027
LOC400043
FIGNL2
OR6C65
MIR196A2
H3F3C
DBX2
FLJ12825
OR9K2
MIR148B
HIGD1C
GLYCAM1
HNRNPA1P10
SNORA2A
SNORA2B
SNORA34
MIR615
HOTAIR
LOC100233209
LOC100240734
LOC100240735
LOC100286844
MIR1293
MIR1291
LOC100335030
MIR4701
MIR3198-2
MIR4698
LOC100652999
Genes in Wide Peak

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

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

Genes
IL2
RAP1GDS1
DUX4
TET2
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AGA
ANK2
SLC25A4
ANXA2P1
ANXA5
CAMK2D
CASP3
CASP6
CCNA2
LRBA
CLGN
CENPE
CLCN3
CPE
CTSO
DCTD
EDNRA
EGF
EIF4E
ELF2
ENPEP
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGG
FRG1
GAB1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HMGB2
HPGD
HSP90AA4P
CFI
IL15
ING2
IRF2
KLKB1
MAD2L1
SMAD1
MANBA
MGST2
NR3C2
MTNR1A
MTTP
NDUFC1
NEK1
NFKB1
NPY1R
NPY2R
NPY5R
PDHA2
PET112
PITX2
PLRG1
EXOSC9
POU4F2
PPID
PPP3CA
ABCE1
RPL34
RPS3A
MSMO1
SFRP2
TACR3
TDO2
TLL1
TLR2
TLR3
TRPC3
UBE2D3
UCP1
UGT8
VEGFC
GLRA3
SMARCA5
SORBS2
PRSS12
LAMTOR3
PDE5A
SAP30
INPP4B
SNORD73A
PAPSS1
LRAT
AIMP1
NDST3
HAND2
RAPGEF2
MFAP3L
SEC24D
TSPAN5
SPRY1
ANAPC10
PGRMC2
SEC24B
MAB21L2
RRH
PLK4
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
PALLD
TBC1D9
METAP1
KIAA0922
TRIM2
ANP32C
SLC7A11
CCRN4L
FAM149A
FBXO8
DUX2
PPA2
DAPP1
DKK2
INTU
ARFIP1
PDLIM3
ZNF330
SPOCK3
AADAT
LEF1
FAM198B
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
CLDN22
GAR1
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
C4orf27
CCDC109B
MARCH1
BANK1
LARP1B
BBS7
NEIL3
TMEM144
C4orf43
UFSP2
C4orf21
AP1AR
MAML3
DDX60
CDKN2AIP
ODZ3
TMEM184C
LRP2BP
PDGFC
FSTL5
BDH2
STOX2
INTS12
ANKRD50
RNF150
PCDH10
KIAA1430
FNIP2
SH3RF1
METTL14
OSTC
IL21
RXFP1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
HHIP
NDST4
AGXT2L1
ELOVL6
NDNF
FAT4
ARSJ
ARHGAP10
MLF1IP
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
DNAJB14
WWC2
NAA15
C4orf29
ALPK1
CXXC4
CEP44
SETD7
PLA2G12A
SLC25A31
RAB33B
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
KIAA1109
COL25A1
USP38
C4orf49
CBR4
FHDC1
FLJ20021
MGC45800
PRMT10
DDX60L
NAF1
TIFA
RG9MTD2
TBCK
CYP2U1
DDIT4L
WDR17
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
C4orf32
SPATA4
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
C4orf38
C4orf39
C4orf45
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
RBM46
SGMS2
SYNPO2
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
LOC285419
CYP4V2
LOC285441
LOC285456
LOC285501
RNF175
C4orf37
LOC339975
TRIML1
LOC340017
PRSS48
LRIT3
ANKRD37
PCNAP1
LOC389247
TRIM61
HELT
FLJ14186
C4orf3
LOC401164
FAM92A3
MIR302A
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC641364
LOC641365
LOC641518
SLED1
CEP170P1
LOC645513
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
SNORA24
MIR577
MIR578
LINC00290
LOC728175
DUX4L2
CETN4P
FAM160A1
LOC731424
SNHG8
LOC100129858
CLDN24
PP12613
LOC100288255
MIR1243
MIR2054
MIR1305
MIR1973
MIR3140
MIR4276
MIR3945
MIR3684
MIR3688-1
LOC100505545
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4453
MIR4799
MIR3688-2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p23.3.

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

Genes
ALK
DNMT3A
MSH6
MSH2
MYCN
NCOA1
EML4
hsa-mir-216b
hsa-mir-559
hsa-mir-558
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ACYP2
ADCY3
APOB
RHOB
ZFP36L2
CAD
CALM2
CENPA
CYP1B1
DDX1
DTNB
E2F6
EPAS1
EFEMP1
FKBP1B
FOSL2
FSHR
FTH1P3
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
FOXN2
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
LHCGR
LTBP1
EPCAM
MATN3
MPV17
MTIF2
ODC1
VIT
PIGF
POMC
PPM1B
PPM1G
PPP1CB
PRKCE
EIF2AK2
RPS7
RPS27A
RRM2
SDC1
SRSF7
SIX3
SLC3A1
SLC8A1
SOS1
SOX11
SPAST
SPTBN1
SRD5A2
STRN
ADAM17
TPO
TSSC1
UCN
VRK2
VSNL1
XDH
SLC30A3
PXDN
KLF11
MAP4K3
ASAP2
SLC5A6
EIF2B4
TAF1B
COX7A2L
ITGB1BP1
NRXN1
OTOF
CRIPT
ROCK2
TP53I3
MRPL33
BRE
PREPL
FEZ2
SOCS5
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
LRPPRC
PDIA6
CEBPZ
MYCNOS
CDC42EP3
CGREF1
SIX2
RAB10
GPR75
YWHAQ
GTF2A1L
STON1
EMILIN1
GPN1
MAPRE3
SLC4A1AP
EFR3B
MYT1L
WDR43
LPIN1
PSME4
PUM2
RHOQ
HAAO
NTSR2
PRKD3
RASGRP3
QPCT
FAM98A
IFT172
SH3YL1
SNORD53
ERLEC1
TRIB2
GRHL1
NRBP1
EHD3
ITSN2
MEMO1
TRAPPC12
ASB3
CRIM1
DNAJC27
C2orf28
NBAS
DYNC2LI1
SF3B14
YPEL5
CPSF3
SNTG2
ATAD2B
HEATR5B
TMEM214
C2orf18
TRMT61B
FANCL
SRBD1
ASXL2
ADI1
C2orf56
TTC27
SLC30A6
CCDC88A
ALLC
KCNK12
DPYSL5
RPL23AP32
RTN4
TRIM54
TTC7A
SMEK2
BIRC6
KIDINS220
MTA3
WDR35
RDH14
NLRC4
AGBL5
C2orf43
THADA
RBKS
ATL2
ABCG5
ABCG8
HS1BP3
FNDC4
COLEC11
CENPO
GALNT14
CCDC121
SMC6
CLIP4
CAMKMT
GEMIN6
NOL10
FBXO11
C2orf44
THUMPD2
FAM49A
LBH
C2orf16
YIPF4
ZNF512
DPY30
ABHD1
EPT1
PNPT1
MCFD2
ATP6V1E2
DHX57
PKDCC
RSAD2
CAPN13
CCDC164
HNRPLL
NT5C1B
CCDC104
CCDC85A
KLHL29
PPP1R21
CMPK2
MBOAT2
TMEM18
C2orf73
CIB4
C2orf63
PLEKHH2
OSR1
TTC32
ZNF513
GALM
TMEM178
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
PLB1
MYADML
FAM84A
FAM82A1
GDF7
GPR113
OXER1
FAM179A
UBXN2A
KCNG3
CYS1
KRTCAP3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
FAM150B
LINC00486
C2orf61
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
STON1-GTF2A1L
C2orf70
C2orf53
LOC339788
LINC00299
LOC339822
MSGN1
CDKL4
PRORSD1P
GEN1
C2orf48
PFN4
LOC375190
LOC375196
LOC386597
MFSD2B
C2orf71
LOC388942
LOC388946
LOC388948
TSPYL6
PTRHD1
SULT6B1
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
EML6
FLJ30838
MIR216A
MIR217
CAPN14
CHAC2
FAM110C
LOC645949
C2orf84
SNORD92
MIR558
MIR559
LOC727982
LOC728730
LOC728819
RAD51AP2
DNAJC27-AS1
MORN2
LOC730811
MIR216B
LOC100128590
OST4
LOC100129726
LOC100134259
ARHGEF33
LOC100271832
LOC100288911
MIR1301
LOC100302650
GPR75-ASB3
SNORA80B
MIR4261
MIR4263
MIR3125
MIR4262
MIR3682
LOC100505624
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4765
MIR4757
MIR4426
MIR4429
MIR548AD
Genes in Wide Peak

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

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

Genes
PLAG1
TCEA1
CHCHD7
hsa-mir-124-2
ASPH
CA8
CEBPD
CRH
CYP7A1
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
TMEM68
ADHFE1
UBXN2B
PXDNL
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100505659
LOC100505676
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.2.

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

Genes
hsa-mir-1182
AGT
GALNT2
KCNK1
TSNAX
GNPAT
CAPN9
COG2
DISC2
DISC1
EGLN1
KIAA1383
SIPA1L2
ARV1
TTC13
PGBD5
PCNXL2
C1orf124
NTPCR
KIAA1804
C1orf198
C1orf131
EXOC8
FAM89A
TRIM67
SNRPD2P2
LOC100287814
MIR1182
TSNAX-DISC1
MIR4671
MIR4427
Genes in Wide Peak

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

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

Genes
GNA11
MLLT1
SH3GL1
SMARCA4
STK11
TCF3
FSTL3
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
hsa-mir-4322
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
C3
CAPS
CD70
CDC34
CDKN2D
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
DNM2
DNMT1
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
EMR1
FCER2
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
ICAM1
ICAM3
ICAM4
ILF3
INSR
LDLR
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NRTN
OAZ1
P2RY11
PALM
PDE4A
PIN1
POLR2E
POLRMT
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RFX2
RPS15
RPS28
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
THOP1
ICAM5
TLE2
TYK2
VAV1
ZNF121
ZNF177
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
EIF3G
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
S1PR2
TRIP10
LONP1
APBA3
SAFB2
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
EBI3
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4A
TIMM44
CARM1
SEMA6B
ZNF266
PNPLA6
UQCR11
TMED1
CDC37
SBNO2
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
TIMM13
DAZAP1
OR7E24
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
SLC39A3
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
S1PR5
MIER2
PCSK4
ZNF562
FBXL12
C19orf24
PLEKHJ1
C19orf66
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
SLC44A2
MCOLN1
WDR18
REXO1
CAMSAP3
ZNF317
ZNF77
C19orf29
UBL5
CELF5
KRI1
YIPF2
SLC25A23
ZNF426
FSD1
ZNF557
CERS4
TLE6
LPPR3
DENND1C
ZNF556
LRRC8E
FLJ22184
UBXN6
OR4F17
ACSBG2
ADAMTS10
QTRT1
FAM108A1
DOHH
ANGPTL6
KLF16
PRAM1
ALKBH7
ZNF414
DOT1L
FBN3
ZNF559
KISS1R
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATG4D
ATCAY
MBD3L1
MIDN
C19orf52
DPP9
R3HDM4
C19orf6
TPGS1
CRB3
REEP6
PEX11G
ZNF561
OLFM2
MUC16
FDX1L
IZUMO4
SCAMP4
ADAT3
ZNF554
EVI5L
GRIN3B
MRPL54
LRG1
RAVER1
OR7D4
OR7G1
OR1M1
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
C19orf21
PLK5
C2CD4C
ZNF358
LOC147727
ZNF560
SPC24
TICAM1
CIRBP-AS1
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
ZNF846
OR7D2
PRR22
ANKRD24
C19orf59
C19orf26
CSNK1G2-AS1
C19orf38
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
LOC284385
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
ODF3L2
EMR4P
ADAMTSL5
CLEC4G
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
WASH5P
LOC388499
C3P1
ONECUT3
OR7G2
OR7G3
MEX3D
FLJ45445
PRSS57
VMAC
CTXN1
C19orf29-AS1
MIR199A1
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
FAM138F
LINGO3
ARRDC5
FAM138A
MBD3L4
MBD3L3
SNORD105
PPAN-P2RY11
MIR637
MIR638
PLIN4
ZNF812
SNORD105B
ZGLP1
C19orf71
LOC100128573
LOC100131094
C19orf79
LOC100288123
MIR1909
MIR1181
MIR1238
MIR1227
MIR3187
MIR4322
MIR4321
MIR3940
LOC100507567
LOC100507588
ZNF559-ZNF177
MIR4747
MIR4746
MIR4748
MIR4745
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p24.1.

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

Genes
CTNNB1
FANCD2
FHIT
MITF
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FBLN2
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
GRM7
HRH1
HTR1F
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
POU1F1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
WNT7A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
BHLHE40
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
VPRBP
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
CXCR6
CSPG5
CHL1
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CAND2
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
RYBP
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LINC00312
LMCD1
ARHGEF3
VILL
C3orf32
TRNT1
ABHD5
DYNC1LI1
C3orf18
CRBN
SS18L2
C3orf19
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ARL8B
SETD5
TMEM40
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
TMEM111
BRK1
ZNF167
LMOD3
RAD18
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
LRRN1
SELK
PROK2
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
THOC7
WDR82
TSEN2
GRIP2
RTP3
C3orf20
ID2B
ATRIP
NICN1
MON1A
JAGN1
KBTBD8
GHRLOS2
IL17RC
ABHD14B
C3orf39
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
C3orf24
LRRC3B
GALNTL2
GPR62
KCNH8
FAM3D
LYZL4
KBTBD5
TRIM71
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
FGD5
CIDECP
CNTN4
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC285401
EIF4E3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
COL6A4P1
TPRXL
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
VENTXP7
LOC401052
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
SNORA6
SNORA7A
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR563
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
MIR885
EGOT
GHRLOS
C3orf74
LOC100128640
NRADDP
LOC100129480
ZNF717
LOC100132146
LOC100132526
BSN-AS2
PRSS46
LOC100287879
LOC100288428
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
MIR3938
MIR3714
FGD5-AS1
LOC100505696
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4791
MIR4790
MIR548AC
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q32.

Table S40.  Genes in bold are cancer genes as defined by The Sanger Institute: 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-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
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-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
hsa-mir-873
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
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
CTSL1P8
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
GGTA1P
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
IFNA22P
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
PPP1R26
SEC16A
ZBTB5
KIAA0020
TNFSF15
PTBP3
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB4B
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
CNTRL
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
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
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
FAM206A
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
BDAG1
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
DMRT3
PRDM12
NAA35
DMRTA1
SLC28A3
CARD9
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
MRPL41
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOB3B
C9orf82
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
FAM214B
GKAP1
PDCD1LG2
AKNA
MIR600HG
URM1
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
PRRC2B
PPAPDC3
GLIS3-AS1
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
TPD52L3
WDR34
SAPCD2
C9orf69
LRSAM1
IL33
C9orf123
C9orf30
UAP1L1
MCART1
MRRF
RBM18
ARRDC1
WDR85
ADAMTSL1
FP588
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19P
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf66
LINC00032
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC39B
FAM201A
RG9MTD3
TTC16
LOC158257
FAM120AOS
FAM154A
LINC00475
FREM1
KIAA2026
LOC158376
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
C9orf96
KCNV2
OLFML2A
C9orf71
QSOX2
GLIS3
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
C9orf93
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
FAM205A
LINC00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
TPRN
LOC286297
TUSC1
LINC00256A
FAM78A
LURAP1L
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
IFNE
ZDHHC21
ACER2
LOC340508
LOC340515
GPR144
FAM75D5
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
GLT6D1
ENHO
AQP7P1
PTAR1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
KGFLP1
LOC389705
FAM205B
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
C9orf128
OR13J1
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FLJ35024
FLJ41200
PTPLAD2
LOC401497
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR101-2
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR31
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC415056
LOC440173
LOC440896
FLJ35282
SUGT1P1
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
ANKRD18B
LOC441461
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
MIR31HG
LOC572558
MIR491
PGM5P2
MIR455
NRON
LOC642236
FAM75A2
FAM75A4
LOC642929
FAM163B
FLJ40292
TUBBP5
RNF224
LOC643648
CBWD6
FAM75C2
HRCT1
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM138C
SCARNA8
SNORA17
SNORA43
SNORD62B
MSMP
SNORD90
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
CDKN2B-AS1
SNORD121A
SNORD121B
C9orf146
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
UNQ6494
LOC100129250
LOC100129316
LOC100129722
LOC100130954
LOC100131193
LOC100132077
LOC100132352
FAM157B
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
LINC00092
LOC100272217
LOC100286938
WASH1
LOC100288842
LOC100289019
LOC100289341
MIR548H3
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3152
MIR3154
MIR2861
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3621
MIR3910-1
MIR3689A
MIR3911
MIR3910-2
MIR3689B
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506422
LOC100506599
LOC100506710
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4667
MIR4473
MIR4669
MIR4673
MIR3960
MIR4540
MIR4665
MIR4475
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4670
MIR4672
MIR4474
MIR4476
MIR3689E
MIR4479
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 18 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 0.08 -0.59 1 0.20 2.99 0.00612
1q 1955 0.26 4.59 9.01e-05 0.09 -0.509 0.976
2p 924 0.07 -1.61 1 0.08 -1.32 0.995
2q 1556 0.08 -1.05 1 0.04 -2.29 0.995
3p 1062 0.05 -1.95 1 0.17 1.26 0.296
3q 1139 0.11 -0.35 1 0.13 0.238 0.774
4p 489 0.03 -2.96 1 0.13 -0.17 0.873
4q 1049 0.00 -3.38 1 0.14 0.435 0.737
5p 270 0.14 -0.223 1 0.05 -2.41 0.995
5q 1427 0.06 -1.55 1 0.13 0.269 0.774
6p 1173 0.03 -2.11 1 0.36 6.71 6.52e-11
6q 839 0.00 -2.74 1 0.46 9.25 0
7p 641 0.27 3.62 0.00292 0.03 -2.56 0.995
7q 1277 0.24 3.34 0.00563 0.04 -2.03 0.995
8p 580 0.13 -0.14 1 0.20 1.53 0.197
8q 859 0.23 2.6 0.0464 0.11 -0.528 0.976
9p 422 0.05 -1.87 1 0.41 7.14 3.64e-12
9q 1113 0.04 -2 1 0.27 4.14 8.53e-05
10p 409 0.05 -2.25 1 0.17 0.783 0.542
10q 1268 0.08 -1.15 1 0.18 1.52 0.197
11p 862 0.10 -0.924 1 0.11 -0.637 0.984
11q 1515 0.07 -1.15 1 0.13 0.374 0.746
12p 575 0.11 -0.686 1 0.13 -0.128 0.873
12q 1447 0.09 -0.775 1 0.15 1.04 0.396
13q 654 0.11 -0.641 1 0.13 -0.0788 0.873
14q 1341 0.12 -0.0435 1 0.09 -0.944 0.995
15q 1355 0.09 -0.755 1 0.18 1.64 0.182
16p 872 0.11 -0.506 1 0.04 -2.52 0.995
16q 702 0.11 -0.573 1 0.05 -2.27 0.995
17p 683 0.00 -2.89 1 0.42 7.81 3.7e-14
17q 1592 0.05 -1.78 1 0.14 0.685 0.581
18p 143 0.16 0.295 1 0.44 7.35 9.55e-13
18q 446 0.05 -1.53 1 0.61 12.6 0
19p 995 0.05 -2.11 1 0.13 -0.0693 0.873
19q 1709 0.14 0.862 1 0.08 -1.01 0.995
20p 355 0.16 0.462 1 0.14 -0.0833 0.873
20q 753 0.22 2.23 0.103 0.04 -2.31 0.995
21q 509 0.02 -2.73 1 0.36 5.87 1.28e-08
22q 921 0.08 -1.15 1 0.24 2.86 0.00846
Xq 1312 0.04 -2.35 1 0.10 -0.546 0.976
Methods & Data
Input
Description

  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

  • Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

  • Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

  • CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

  • Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

  • Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

  • Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

  • Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

  • Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

  • Confidence Level: Confidence level used to calculate the region containing a driver.

  • Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

  • Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

  • Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

  • Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PAAD-TP/8017831/GDAC_MergeDataFiles_6754691/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

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 91 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-F2-A44G-01A-11D-A26H-01
TCGA-F2-A44H-01A-11D-A26H-01
TCGA-FB-A4P5-01A-11D-A26H-01
TCGA-FB-A545-01A-11D-A26H-01
TCGA-FB-A5VM-01A-11D-A32M-01
TCGA-FB-A78T-01A-12D-A32M-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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[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)
[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)
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