SNP6 Copy number analysis (GISTIC2)
Pancreatic Adenocarcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C19W0CZX
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/C19W0CZX
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 2.0.20 (Firehose task version: 126).

Summary

There were 81 tumor samples used in this analysis: 15 significant arm-level results, 20 significant focal amplifications, and 26 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 20 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 | 9.8196e-09 | 9.8196e-09 | chr18:19826724-19972386 | 0 [CTAGE1]
8q24.21 | 0.00019884 | 0.00019884 | chr8:127864635-128801947 | 4
12q15 | 0.00028106 | 0.00028106 | chr12:68392819-68422028 | 0 [IFNG]
Xq27.1 | 0.0058367 | 0.0058367 | chrX:138564705-138580557 | 0 [F9]
Xp22.11 | 0.0069272 | 0.0069272 | chrX:23975644-23983593 | 0 [CXorf58]
1p12 | 0.0079905 | 0.0079905 | chr1:120204209-120523901 | 6
12p11.21 | 0.0018712 | 0.010272 | chr12:31414318-31442221 | 1
19q13.2 | 0.019649 | 0.019649 | chr19:38513399-40880126 | 75
9p13.3 | 0.040692 | 0.040692 | chr9:35244633-35825412 | 22
7q22.1 | 0.0024545 | 0.086834 | chr7:97568629-99240073 | 29
20q13.2 | 0.094951 | 0.094951 | chr20:51093677-52298532 | 2
12p13.33 | 0.0031749 | 0.097316 | chr12:1-5520802 | 50
12p12.1 | 0.00039743 | 0.10281 | chr12:19727978-39228082 | 79
17q21.32 | 0.10281 | 0.10281 | chr17:46157853-46187564 | 2
17p11.2 | 0.11287 | 0.11287 | chr17:18097231-18598782 | 16
1p34.2 | 0.13937 | 0.13937 | chr1:37413199-44557362 | 112
11p11.2 | 0.13937 | 0.13937 | chr11:24893542-49993292 | 153
6p21.31 | 0.21174 | 0.21174 | chr6:33564413-65927345 | 254
7q21.13 | 0.10281 | 0.21174 | chr7:88138350-89983651 | 7
4q31.3 | 0.22678 | 0.22678 | chr4:153247953-154465993 | 13

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'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 1p12.

Table S2. Genes in bold are cancer genes as defined by The Sanger Institute's 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 12p11.21.

Table S3. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S4. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
AKT2
hsa-mir-641
ACTN4
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
PAF1
SARS2
SAMD4B
MED29
LGALS14
LRFN1
CATSPERG
C19orf33
PLEKHG2
CNTD2
YIF1B
TIMM50
PPP1R14A
FBXO17
RASGRP4
EID2B
RINL
FBXO27
C19orf47
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 9p13.3.

Table S5. 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 S6. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NPTX2
OCM2
TRRAP
BUD31
ATP5J2
ARPC1B
ARPC1A
CPSF4
PDAP1
LMTK2
ZKSCAN5
BRI3
TECPR1
PTCD1
BAIAP2L1
SMURF1
ZNF655
ZNF394
MYH16
BHLHA15
ZNF498
FAM200A
TMEM130
ZNF789
MGC72080
KPNA7
LOC100289187
MIR3609
ATP5J2-PTCD1

Genes in Wide Peak

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

Table S7. 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 12p13.33.

Table S8. 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 12p12.1.

Table S9. 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
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 17q21.32.

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

Genes
CBX1
SNX11

Genes in Wide Peak

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

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

Genes
FOXO3B
FLII
LLGL1
SHMT1
TOP3A
ALKBH5
FAM106A
SMCR7
SMCR8
USP32P2
TBC1D28
CCDC144B
LOC339240
EVPLL
LGALS9C
ZNF286B

Genes in Wide Peak

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

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

Genes
MPL
MYCL1
hsa-mir-30c-1
hsa-mir-4255
ATP6V0B
BMP8B
CDC20
COL9A2
CTPS
DPH2
EDN2
FHL3
GRIK3
GUCA2A
GUCA2B
INPP5B
MTF1
NDUFS5
NFYC
YBX1
POU3F1
PPT1
PTPRF
RLF
ST3GAL3
SLC2A1
SLC6A9
TIE1
DNALI1
B4GALT2
PABPC4
ARTN
KCNQ4
IPO13
KDM4A
RIMS3
ZMPSTE24
PPIE
PPIH
CAP1
SF3A3
EBNA1BP2
FOXJ3
SCMH1
SZT2
MACF1
MYCBP
HEYL
GNL2
ZNF691
UTP11L
HPCAL4
TRIT1
RHBDL2
C1orf109
CDCA8
HIVEP3
OXCT2
RRAGC
LEPRE1
SMAP2
MEAF6
DEM1
ELOVL1
ZNF643
C1orf50
AKIRIN1
YRDC
PPCS
SNIP1
ZC3H12A
GJA9
HYI
ZMYND12
NT5C1A
MFSD2A
MED8
ERMAP
TMCO2
ZNF684
C1orf122
TMEM125
MANEAL
CLDN19
WDR65
C1orf210
CCDC24
CITED4
SLFNL1
RSPO1
EPHA10
RIMKLA
LOC339442
ZNF642
BMP8A
CCDC23
MIR30C1
MIR30E
FLJ32224
FAM183A
KIAA0754
SNORA55
LOC728431
PPIEL
CCDC30
LOC100129924
LOC100130557
LOC100132774
MIR4255
MIR3659
LOC100507178
GJA9-MYCBP

Genes in Wide Peak

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

Table S13. Genes in bold are cancer genes as defined by The Sanger Institute's 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
NUP160
FNBP4
MTCH2
FJX1
C11orf41
ABTB2
PAMR1
FBXO3
EHF
ELP4
COMMD9
PACSIN3
APIP
HSD17B12
PHF21A
WT1-AS
TRIM44
NAT10
LIN7C
SLC35C1
TCP11L1
LGR4
AMBRA1
KBTBD4
TTC17
PRDM11
SYT13
LRRC4C
ALX4
ANO3
PRRG4
C11orf49
ZNF408
QSER1
AGBL2
PRR5L
KIF18A
ARFGAP2
ACCS
TSPAN18
CCDC34
SLC39A13
DEPDC7
C1QTNF4
PTPMT1
C11orf74
OR4X2
OR4B1
GYLTL1B
DNAJC24
C11orf46
LOC120824
LDLRAD3
MUC15
C11orf94
SLC5A12
METTL15
IMMP1L
ALKBH3
LOC221122
OR4C3
OR4S1
OR4C13
LOC283116
HARBI1
LINC00294
LUZP2
LOC338739
DCDC1
DKFZp779M0652
FIBIN
C11orf96
ACCSL
OR4X1
HNRNPKP3
FAM180B
OR4A47
OR4C45
MIR129-2
DKFZp686K1684
LOC440040
CCDC73
BDNF-AS1
TRIM64C
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 6p21.31.

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

Genes
CCND3
FANCE
HMGA1
PIM1
TFEB
hsa-mir-548u
hsa-mir-133b
hsa-mir-586
hsa-mir-1275
CRISP1
BMP5
DST
BYSL
RUNX2
CDC5L
CDKN1A
CLPS
MAPK14
DNAH8
SLC29A1
FKBP5
GCLC
GLO1
GLP1R
GRM4
GSTA1
GSTA2
GSTA3
GSTA4
GUCA1A
GUCA1B
HCRTR2
HSP90AB1
IL17A
ITPR3
MCM3
MDFI
MEA1
MEP1A
MLN
MOCS1
MUT
RPL10A
NFKBIE
NFYA
PEX6
PGC
PGK2
PKHD1
POLH
PPARD
PPP2R5D
PRIM2
MAPK13
PTK7
PRPH2
RHAG
RPS10
SRSF3
SNRPC
SRF
SRPK1
TAF11
TBCC
TCP11
TEAD3
TFAP2B
CRISP2
TULP1
VEGFA
ZNF76
PTP4A1
PLA2G7
SUPT3H
GCM1
KCNK5
RNF8
NCR2
MED20
SLC25A27
BAG2
POLR1C
MAD2L1BP
TRAM2
CUL7
RCAN2
CRISP3
C6orf108
CNPY3
FRS3
SLC22A7
APOBEC2
CAPN11
NUDT3
STK38
ICK
ENPP4
FTSJD2
CUL9
ANKS1A
UBR2
PHF3
DAAM2
KIAA0240
CD2AP
MTCH1
ZNF318
SPDEF
YIPF3
USP49
ZNF451
FBXO9
BRPF3
GNMT
TNFRSF21
TINAG
TMEM14A
PRICKLE4
PACSIN1
DEF6
MRPL2
CYP39A1
ETV7
LGSN
PPIL1
RAB23
CLIC5
TREM2
TREM1
HMGCLL1
GTPBP2
UHRF1BP1
CENPQ
MRPS18A
MRPS10
LRRC1
TMEM63B
TBC1D22B
SAYSD1
TRERF1
LRFN2
AARS2
XPO5
KIAA1586
CPNE5
ENPP5
ELOVL5
ZFAND3
C6orf106
MRPL14
DLK2
TREML2
COL21A1
TFAP2D
KCNK16
MNF1
TTBK1
PAQR8
RRP36
KCNK17
ABCC10
KLC4
MLIP
TJAP1
IL17F
EFHC1
BTBD9
FOXP4
KLHDC3
SLC26A8
IP6K3
TAF8
C6orf141
CCDC167
PTCRA
TCTE1
KHDRBS2
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
RSPH9
LRRC73
TREML2P1
LOC221442
C6orf130
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
FAM83B
GPR111
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
DEFB110
DEFB112
DEFB113
DEFB114
MDGA1
GPR110
LOC285847
PNPLA1
TREML4
RPL7L1
CLPSL1
TREML1
TREML3
EYS
SLC35B2
GUSBP4
CLPSL2
C6orf222
GLYATL3
GFRAL
FLJ41649
CRIP3
KLHL31
DEFB133
MIR206
C6orf226
TMEM151B
ATP6V0CP3
PTCHD4
MIR133B
C6orf132
RPS16P5
MIR586
LOC730101
GSTA7P
TDRG1
LOC100131047
LOC100132354
TOMM6
LOC100287718
MIR1275
MIR3925
LOC100507584
RPS10-NUDT3
MIR4647
MIR4641
MIR4642
MIR4462

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.13.

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

Genes
STEAP1
C7orf63
GTPBP10
C7orf62
ZNF804B
STEAP2
DPY19L2P4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q31.3.

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

Genes
FBXW7
hsa-mir-3140
ANXA2P1
KIAA0922
TRIM2
ARFIP1
DKFZP434I0714
MND1
FHDC1
TIGD4
TMEM154
MIR3140
MIR4453

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 26 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 5.8064e-35 | 5.8064e-35 | chr9:21865498-21996995 | 2
18q21.2 | 2.4816e-10 | 9.1846e-10 | chr18:48514396-48920689 | 2
17q22 | 0.010556 | 0.010556 | chr17:50947516-81195210 | 415
6p25.2 | 0.038648 | 0.038648 | chr6:1-13288668 | 81
5q14.2 | 0.038648 | 0.040193 | chr5:82134980-82936981 | 5
8p21.3 | 0.046739 | 0.046739 | chr8:1-29215076 | 243
11p15.4 | 0.046739 | 0.046739 | chr11:1-10330819 | 265
22q13.31 | 0.046739 | 0.046739 | chr22:43805179-51304566 | 98
12p12.1 | 0.052451 | 0.05194 | chr12:4374374-22798169 | 243
12q23.3 | 0.047355 | 0.056261 | chr12:72664047-133851895 | 444
7q36.1 | 0.068409 | 0.068566 | chr7:102041680-159138663 | 427
9q22.33 | 0.069707 | 0.068566 | chr9:101468446-101979393 | 4
19q13.42 | 0.094492 | 0.090416 | chr19:41676972-59128983 | 725
10q23.2 | 0.10183 | 0.10526 | chr10:86084854-108925515 | 255
1p36.11 | 0.046739 | 0.10831 | chr1:18079813-173579494 | 1525
12q12 | 0.079096 | 0.12922 | chr12:31809739-55796833 | 251
4q35.2 | 0.13935 | 0.1352 | chr4:96759449-191154276 | 388
2p23.3 | 0.16421 | 0.15992 | chr2:1-59292261 | 347
8q12.1 | 0.1588 | 0.15992 | chr8:48647103-69264813 | 94
18q12.1 | 0.019629 | 0.15992 | chr18:22038543-59223753 | 157
3p24.1 | 0.17224 | 0.17923 | chr3:1-88046665 | 592
16q23.1 | 0.17174 | 0.17923 | chr16:72148304-90354753 | 157
1p36.22 | 0.090416 | 0.18527 | chr1:1-36196866 | 573
4p16.1 | 0.2067 | 0.21496 | chr4:1-24523325 | 184
1p21.2 | 0.090416 | 0.2412 | chr1:44455614-117583297 | 529
15q15.1 | 0.24947 | 0.25689 | chr15:1-102531392 | 844
21q22.11 | 0.25457 | 0.25689 | chr21:1-48129895 | 303
Xp22.31 | 0.25689 | 0.25689 | chrX:1-155270560 | 1046
21q22.11 | 0.25457 | 1 | chr21:1-48129895 | 303

Genes in Wide Peak

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

Table S17. 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 S18. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
SMAD4
MEX3C

Genes in Wide Peak

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

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

Genes
CD79B
CLTC
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
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
NPTX1
P4HB
PDE6G
PECAM1
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
PPM1D
DGKE
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
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
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
SDK2
FAM20A
BCAS3
TMEM104
RNF43
MKS1
C17orf80
CCDC40
WIPI1
SMG8
TMEM100
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45L
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
DNAI2
SMURF2
ENGASE
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
KIF2B
USP32
CBX2
FAM104A
MGC16275
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
DYNLL2
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
NOTUM
TMC8
ANKFN1
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MTVR2
STXBP4
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
LRRC37A3
RNF126P1
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
MIR142
MIR21
MIR301A
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LOC645638
TBC1D3P1-DHX40P1
LOC653653
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 6p25.2.

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

Genes
IRF4
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CDYL
LY86
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
NRN1
TMEM14C
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
C6orf195
PIP5K1P1
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
PSMG4
DKFZP686I15217
C6orf201
ERVFRD-1
PPP1R3G
HULC
TMEM170B
SCARNA27
LOC100130275
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4645

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's 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 8p21.3.

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
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
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
TRIM66
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
OR7E12P
KCNQ1OT1
PKP3
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
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
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
TMEM41B
LOC440028
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC644656
LOC650368
LOC653486
SNORA23
SNORA45
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 S24. 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
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 12p12.1.

Table S25. 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
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 12q23.3.

Table S26. Genes in bold are cancer genes as defined by The Sanger Institute's 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
TRHDE
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
LOC100507377
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 7q36.1.

Table S27. Genes in bold are cancer genes as defined by The Sanger Institute's 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
hsa-mir-548o
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
ORC5
PAX4
SLC26A4
PIK3CG
PIP
PODXL
POLR2J
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
PSMC2
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
PMPCB
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
NAMPT
RASA4
AASS
LRRC17
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
DNAJC2
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
ALKBH4
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
MLL5
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
ORAI2
JHDM1D
TMUB1
ARMC10
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
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
POLR2J2
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
DPY19L2P2
LOC349160
GSTK1
SLC26A5
LHFPL3
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
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR490
ZNF862
LOC645249
LOC645591
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC723809
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100130705
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
SPDYE2L
MIR548F4
MIR548T
MTRNR2L6
MIR3907
MIR3666
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468
MIR4467

Genes in Wide Peak

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

Table S28. Genes in bold are cancer genes as defined by The Sanger Institute's 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 19q13.42.

Table S29. Genes in bold are cancer genes as defined by The Sanger Institute's 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
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
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's 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 1p36.11.

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

Genes
ARNT
BCL9
CDKN2C
EPS15
FCGR2B
JAK1
JUN
LCK
MPL
MUC1
MUTYH
MYCL1
NOTCH2
NRAS
NTRK1
PAX7
PBX1
PRCC
SDHC
SFPQ
TAL1
TPM3
ARID1A
BCL10
PDE4DIP
THRAP3
TRIM33
RBM15
MDS2
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
ABCA4
ACADM
ADAR
ADORA3
AGL
AK2
AK4
ALDH9A1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
RHOC
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP5F1
ATP6V0B
BAI2
BGLAP
BMP8B
BRDT
C1QA
C1QB
C1QC
C8A
C8B
CAPZA1
CAPZB
CASQ1
CASQ2
RUNX3
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
CD48
CD53
CD58
CDA
CDC20
CDC42
CD52
RCC1
CHI3L2
CHRNB2
CKS1B
CLCA1
CLK2
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
COPA
CPT2
CRABP2
CRP
CRYZ
CSF1
CSF3R
CTBS
CTH
CTPS
CTSK
CTSS
CYP2J2
CYP4A11
CYP4B1
DAB1
DBT
GADD45A
DDOST
DHCR24
DIO1
DPH2
DPT
DPYD
DR1
E2F2
ECE1
ECM1
S1PR1
EDN2
PHC2
EFNA1
EFNA3
EFNA4
CELSR2
ELAVL4
ENSA
EPB41
EPHA8
EPHB2
ETV3
EXTL1
EXTL2
EYA3
F3
F5
FAAH
FABP3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FGR
FHL3
FOXE3
FOXD2
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FUCA1
DARC
IFI6
GALE
GBA
GBAP1
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GNAI3
GNAT2
GNG5
SFN
GPR3
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
HCRTR1
HDAC1
HDGF
HMGN2
HMGCL
HMGCS2
HPCA
HSD3B1
HSD3B2
HSPA6
HSPA7
IGSF3
HSPG2
HTR1D
HTR6
ID3
IFI16
CYR61
IL6R
IL12RB2
ILF2
INPP5B
INSRR
IPP
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNJ9
KCNJ10
KCNN3
STMN1
LEPR
LMNA
LMX1A
LOR
LY9
TACSTD2
MAGOH
MATN1
MCL1
SMCP
MEF2D
MGST3
MNDA
MOV10
MPZ
MSH4
MTF1
MTX1
MYOC
NASP
NBL1
NDUFS2
NDUFS5
NFIA
NFYC
NGF
NHLH1
NHLH2
NIT1
NPR1
NRD1
YBX1
ROR1
DDR2
OPRD1
ORC1
OVGP1
PAFAH2
PRDX1
PDE4B
PDZK1
PFDN2
PGM1
PIGC
PI4KB
PIN1P1
PKLR
PLA2G2A
PLA2G5
PRRX1
POU2F1
POU3F1
PPOX
PPP1R8
PPT1
PRKAA2
PRKAB2
PRKACB
PKN2
PSMA5
PSMB2
PSMB4
PSMD4
PTAFR
PTGER3
PTGFR
PTGFRN
PTPRF
PEX19
ABCD3
RAB3B
RAB13
RABGGTB
RAP1A
RAP1GAP
RBBP4
RFX5
RGS4
RHCE
RHD
RIT1
RLF
SNORD21
RORC
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RPS27
RXRG
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
SCP2
XCL1
SELE
SELL
SELP
SRSF4
SHC1
ST3GAL3
STIL
SLAMF1
SLC1A7
SLC2A1
SLC6A9
SLC9A1
SLC16A1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
STXBP3
XCL2
SYCP1
TAF12
TAF13
TBX15
TCEA3
TCEB3
VPS72
TGFBR3
THBS3
TCHH
TIE1
TOP1P1
CCT3
TSHB
TTC4
TUFT1
TNFSF4
UCK2
UQCRH
UROD
USF1
USP1
VCAM1
WNT2B
ZSCAN20
SLC30A2
LUZP1
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
DAP3
PTP4A2
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
SNHG3
NR0B2
RAD54L
TTF2
RGS5
PIK3R3
ITGA10
LMO4
FCN3
BLZF1
CDC14A
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
VAMP4
PEA15
B4GALT3
B4GALT2
ADAM15
PABPC4
FPGT
PEX11B
CREG1
CD84
FUBP1
EIF2B3
SELENBP1
TNFSF18
MPZL1
SH2D2A
ARTN
MAP3K6
DIRAS3
TBX19
FCGR2C
SLC16A4
PRPF3
KCNQ4
ARHGEF2
DEDD
ZMYM4
ZMYM6
SRSF11
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
AIM2
C1orf38
ADAMTS4
TMEM59
SEC22B
CHD1L
PRDX6
CLCA3P
CLCA2
HS2ST1
IPO13
SDC3
SLC25A44
KDM4A
PUM1
NOS1AP
RIMS3
KIAA0494
ARHGEF11
DNAJC6
LRIG2
SETDB1
LPPR4
UBAP2L
SV2A
DENND4B
ZBTB40
RBM8A
NR1I3
INSL5
PIGK
SCAMP3
PTPRU
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
GPA33
HNRNPR
SRRM1
CNKSR1
SF3B4
ZMPSTE24
BCAS2
AKR1A1
WARS2
CEPT1
PIAS3
TESK2
PPIE
VAV3
HAX1
PPIH
C1orf61
CAP1
LRRC41
SEMA6C
HBXIP
SLC19A2
IFI44
POLR3C
TXNIP
PMVK
KHDRBS1
GMEB1
FAM189B
AP4B1
NUDC
PHTF1
NES
AHCYL1
SRSF10
WDR3
JTB
MTMR11
MAN1A2
SF3A3
MLLT11
IFI44L
EBNA1BP2
SLC27A3
KIF2C
TDRKH
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
CELF3
DDX20
PMF1
DUSP12
VPS45
LYPLA2
CLCA4
MTF2
DNAJC8
NTNG1
FOXJ3
KIAA0907
WDR47
KIFAP3
ATF6
SCMH1
AKR7A3
TTC39A
KDM1A
USP33
WDTC1
KIAA0090
POGZ
MAST2
NCDN
CLCC1
SLC35D1
SYT11
PRRC2C
RPRD2
OTUD3
LPHN2
KIAA1107
ZCCHC11
SZT2
UBR4
USP24
SMG5
NCSTN
ITGB3BP
GPR161
CELA3B
SLC35A3
MACF1
LRRC8B
SNAPIN
LPAR3
DDAH1
TMEM50A
RUSC1
CA14
KPNA6
SSBP3
STX12
CCDC19
NBPF14
BRP44
OLFML2B
C1orf43
CLIC4
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
DNM3
CHTOP
LDLRAP1
SERBP1
PTPN22
PHGDH
LCE2B
PLA2G2D
AK5
MYCBP
OR10J1
HEYL
EIF2C1
SNORA66
SNORD45B
SNORD45A
SNORD55
RNU11
RNF11
USP21
FOXD3
TRAPPC3
CHIA
SLC39A1
AHDC1
RNF115
TEKT2
SMPDL3B
ANGPTL3
LAMTOR2
PRO0611
LINC00339
TMOD4
GNL2
GPSM2
NME7
ALG6
CERS2
SLC25A24
PLA2G2E
DNTTIP2
CRNN
DCAF8
HP1BP3
F11R
TMED5
BOLA1
ZNF593
ZBTB7B
ZNF691
TXNDC12
TNNI3K
RRNAD1
SH3GLB1
MECR
APH1A
UTP11L
MRTO4
PLEKHO1
HAO2
ACP6
TMEM69
MRPL37
HOOK1
SNX7
C1orf9
HPCAL4
YTHDF2
GPR89B
HSD17B7
UFC1
ZCCHC17
METTL13
DPH5
HSPB11
OAZ3
CMPK1
CD244
GPR88
DPM3
WNT4
YIPF1
MRPS21
CCDC76
TMCO1
ADAMTSL4
CRCT1
RNF186
SPATA6
L1TD1
RSBN1
ZNHIT6
GPN2
LEPROT
MED18
TRIT1
GIPC2
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
PQLC2
RHBDL2
DUSP23
ADPRHL2
TRNAU1AP
C1orf109
C1orf56
C1orf123
TTC22
AIM1L
BSDC1
XKR8
TMEM39B
PRPF38B
CDCA8
LRRC8D
MSTO1
PRMT6
RNF220
FAM176B
GOLPH3L
TMEM57
TRIM62
RAVER2
KIRREL
YY1AP1
ECHDC2
FGGY
MCOLN3
SLC22A15
CAMK2N1
UBE2Q1
RNPC3
ITLN1
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
MAP7D1
TMEM48
IQCC
C1orf112
LRIF1
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
FAM212B
DMAP1
GNG12
SLC50A1
TMEM234
FAM54B
CCBL2
SLAMF8
CDC42SE1
UBQLN4
TMEM167B
OLFML3
OTUD7B
C1orf63
PITHD1
RAB25
PGLYRP4
RHBG
MAN1C1
SCYL3
NIPAL3
SEPN1
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
AMIGO1
ODF2L
CGN
KIAA1324
IGSF9
LRRC7
KIF17
ZNF687
ZSWIM5
POGK
KIAA1522
HCN3
CACHD1
MIER1
C1orf114
GRHL3
SLAMF7
CADM3
PTBP2
PRUNE
DNASE2B
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
HAPLN2
BCAN
GPATCH3
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
TINAGL1
LEPRE1
SEMA4A
PLA2G2F
HIAT1
SMAP2
ATPAF1
S100PBP
MEAF6
DEM1
CEP85
ELOVL1
DCLRE1B
MRPS15
MRPL9
PINK1
MARCKSL1
INTS3
ZNF643
SELRC1
PHACTR4
C1orf135
SCNM1
ERI3
C1orf50
WDR77
MGC4473
CCDC28B
FCRL2
DLEU2L
NKAIN1
EPS8L3
MRPL24
MUL1
TNFAIP8L2
C1orf54
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
PPCS
LIN28A
SH3D21
TTLL7
SNIP1
WDR78
ZMYM1
RPAP2
FAM110D
KIAA0319L
DHDDS
PAQR6
DENND2D
WLS
TRIM46
C1orf129
RPF1
SIKE1
ZC3H12A
TARS2
TRIM45
FLAD1
ZNF436
TAS1R2
GJA9
OR6N2
OR6K2
SYNC
ACTL8
ANKRD13C
PVRL4
SNX27
ANP32E
TSSK3
VANGL1
ST6GALNAC5
ISG20L2
HYI
FCRL5
FCRL4
SH3BGRL3
NUF2
SESN2
GPR61
STK40
TM2D1
REG4
TMEM222
HORMAD1
TOMM40L
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
TMEM79
PROK1
EFCAB7
NT5C1A
LCE3D
TRIM63
PSRC1
FAM167B
MGC12982
FCRLA
ANKRD36BP1
HPDL
ATP1A1OS
AGBL4
MFSD2A
ATG4C
MAEL
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
SNHG12
FAM40A
DOCK7
AQP10
SLAMF9
C1orf201
PYGO2
SPOCD1
ZNF697
NUP210L
BTF3L4
UBXN11
NEXN
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
PIGM
IGSF8
ATPIF1
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
C1orf85
MED8
KTI12
C1orf212
ADC
TMEM54
HENMT1
TOE1
ERMAP
PGLYRP3
CSMD2
MYSM1
GNRHR2
SLAMF6
OSBPL9
OMA1
RAB42
FCRL1
FCRL3
LRRC42
GBP4
GBP5
FAM46B
FMO9P
TADA1
THEM4
SH2D1B
SSX2IP
OLFM3
GABPB2
TCHHL1
RPTN
CCDC163P
TDRD10
SHE
C1orf172
WDR63
KLHDC9
MAB21L3
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
MYOM3
DMBX1
OR10J5
TMCO2
ZNF684
TCEANC2
PODN
LRRC39
GJB4
HMGB4
RNF19B
DCST2
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
UHMK1
FCRLB
LIX1L
HSD3BP4
KLF17
TMEM125
C1orf182
IQGAP3
APOA1BP
DRAM2
C1orf88
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
SYT6
CREB3L4
SAMD13
C1orf52
C1orf51
TMEM56
NBPF4
UBE2U
HFE2
ANKRD35
SLC30A7
C1orf213
KNCN
MOB3C
GLIS1
LELP1
MGC27382
DCDC2B
ZNF362
LOC149086
DCST1
MANEAL
IL23R
METTL11B
FAM78B
PDIK1L
BNIPL
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
LRRC71
RP11-165H20.1
PYHIN1
DENND2C
GBP6
LPPR5
FNDC7
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
SPRR4
KANK4
SASS6
FAM43B
PPIAL4A
HFM1
PAQR7
TTC24
UBL4B
PDIA3P
EIF2C3
EIF2C4
LCE4A
ALG14
FAM76A
LINC00466
C1orf168
TMEM61
CYP4Z1
CDCP2
SLC5A9
CC2D1B
NBPF11
NUDT17
TXLNA
TCTEX1D1
SPAG17
SLFNL1
KRTCAP2
CRTC2
HIPK1
SLC44A5
AKR7L
AKR7A2P1
FNDC5
EPHX4
AKNAD1
LCE5A
TMCO4
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
ZNF683
ARHGAP30
C1orf192
NEGR1
CYP4X1
MAGI3
TIPRL
BEST4
FAM19A3
RIIAD1
THEM5
SLC9A11
CYP4A22
C1orf185
LOC284551
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
RUSC1-AS1
LOC284632
RSPO1
EPHA10
C1orf204
C1orf111
LOC284688
ZNF326
BTBD8
RIMKLA
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
FAM151A
S100A7A
LINGO4
RXFP4
LOC339442
MTMR9LP
ZBTB8OS
TFAP2E
LOC339505
C1orf110
LOC339524
C1orf228
ZNF642
CCDC18
MYBPHL
OR10R2
FCRL6
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
SERINC2
FAM159A
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
BMP8A
CYCSP52
CCDC23
ATPAF1-AS1
HEATR8
FAM73A
LOC375010
PEAR1
SFT2D2
CATSPER4
NSUN4
ILDR2
TRNP1
CD164L2
LOC388630
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
PLA2G2C
SKINTL
UOX
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
TMEM200B
SH2D5
C1orf130
LOC400752
C1orf141
GBP1P1
FLJ27354
MIR137HG
C1orf226
LOC400794
NBPF9
LDLRAD2
LOC402779
MIR101-1
MIR137
MIR186
MIR197
MIR199A2
MIR214
MIR30C1
MIR30E
MIR9-1
LHX8
C1orf180
MINOS1
FLJ32224
FAM183A
ZYG11A
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
ETV3L
LRRC52
LOC440700
PGCP1
OR10J3
KPRP
LCE6A
SUMO1P3
GEMIN8P4
RBMXL1
LURAP1
PEF1
HIST2H4B
PRR9
CYB5RL
RPL31P11
SRG7
CYMP
KIAA0754
LOC643441
LOC644242
PPIAL4G
LOC644961
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
LOC646471
LOC646626
EMBP1
SRGAP2P2
LOC648740
ZBTB8A
NBPF6
LOC653160
PPIAL4B
LOC653513
GPR89A
LOC653566
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA2
SCARNA4
SCARNA1
SNORA42
SNORA44
SNORA55
SNORA61
SNORA16A
SNORD45C
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR548D1
MIR553
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
ZBTB8B
LOC728431
PPIEL
CCDC30
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729041
LOC729059
HSD52
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR765
MIR942
MIR190B
MIR760
MIR921
LOC100128071
LOC100128787
LOC100129046
LOC100129138
LOC100129196
LOC100129269
C1orf68
MSTO2P
LOC100129620
LOC100129924
LOC100130000
LOC100130197
LOC100130557
LOC100131060
TSTD1
LOC100131564
LOC100131825
LOC100132111
NBPF10
FCGR1C
ZRANB2-AS1
LOC100132774
C2CD4D
LOC100286793
LOC100287722
LOC100289178
LOC100289211
MIR320B1
MIR1295A
MIR1976
MIR1262
MIR761
MIR3119-1
MIR3115
MIR3117
MIR3120
MIR4255
MIR4253
MIR4256
MIR4257
MIR3119-2
MIR4258
MIR4254
MIR3659
MIR3917
MIR3658
MIR3605
MIR3671
MIR548AA1
LOC100505633
LOC100505666
LOC100505768
LOC100505795
LOC100505918
LOC100506023
ZMYM6NB
LOC100506343
LOC100506730
LOC100506801
LOC100506963
LOC100507178
LOC100507423
LOC100507564
LOC100507634
FPGT-TNNI3K
GJA9-MYCBP
HEATR8-TTC4
PMF1-BGLAP
TMEM56-RWDD3
C1orf151-NBL1
TNFAIP8L2-SCNM1
MIR4695
MIR4420
MIR4422
MIR4781
MIR4794
MIR4654
MIR4684
MIR4711
MIR2682
MIR4423
MIR378F
DNM3OS
RCAN3AS
NEGR1-IT1
ZRANB2-AS2

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
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 S33. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S34. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S35. Genes in bold are cancer genes as defined by The Sanger Institute's 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 18q12.1.

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

Genes
SS18
MALT1
ZNF521
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
hsa-mir-187
hsa-mir-302f
AQP4
ATP5A1
CDH2
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
GALNT1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MC4R
ME2
MEP1B
MYO5B
NARS
ATP8B1
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SLC14A1
SYT4
TAF4B
TCF4
TTR
ZNF24
SLC14A2
NOL4
MBD2
PSTPIP2
PIAS2
B4GALT6
TXNL1
LIPG
ONECUT2
CTIF
ACAA2
ZNF271
MAPRE2
POLI
TRAPPC8
NEDD4L
WDR7
SLC39A6
TPGS2
SETBP1
SNORD58B
SNORD58A
CDH20
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
DYM
RNF125
MOCOS
RPRD1A
ZNF532
ELP2
ELAC1
CELF4
KIAA1328
KLHL14
EPG5
HRH4
FAM59A
FHOD3
CCDC68
ASXL3
KATNAL2
CHST9
C18orf21
MRO
HDHD2
ZNF397
SEC11C
HAUS1
ALPK2
LOXHD1
INO80C
PSMA8
STARD6
C18orf25
CCBE1
MCART2
DSG4
CHST9-AS1
C18orf54
TCEB3C
ZBTB7C
SKA1
CCDC11
ZNF396
KCTD1
C18orf26
BOD1P
LOC284260
SIGLEC15
CPLX4
C18orf34
LOC390858
MIR122
MIR187
WBP11P1
RNF165
C18orf32
KC6
LOC647946
SCARNA17
SNORA37
LOC728606
TCEB3CL
LOC729950
ZSCAN30
SNORD58C
LOC100287225
MIR302F
MIR1539
MIR4319
MIR4318
MIR4320
LOC100505474
LOC100505549
LOC100506888
RPL17-C18ORF32
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744
LOC100652770

Genes in Wide Peak

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

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute's 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 16q23.1.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
BANP
RFWD3
ZDHHC7
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
CTRB2
CLEC18B
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
SYCE1L
LOC100287036
MIR1910
MIR3182
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

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

Table S39. 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
PSMB2
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
NCDN
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
C1orf216
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
TFAP2E
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 4p16.1.

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

Genes
FGFR3
WHSC1
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
NKX3-2
BST1
CD38
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
QDPR
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
PPARGC1A
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
LAP3
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
DCAF16
CNO
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
CC2D2A
KIAA1530
ZFYVE28
GBA3
AFAP1
NCAPG
TNIP2
HAUS3
ABCA11P
GRPEL1
MED28
KCNIP4
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
CPEB2
EVC2
PACRGL
OTOP1
ZNF595
LOC152742
JAKMIP1
FAM53A
METTL19
GPR125
ZBTB49
ZNF721
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285547
LOC285548
FAM200B
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
KCNIP4-IT1
USP17L6P
USP17
HSP90AB2P
C4orf48
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

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

Table S41. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CDKN2C
EPS15
JAK1
JUN
MUTYH
NRAS
TAL1
BCL10
TRIM33
RBM15
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
ABCA4
ACADM
ADORA3
AGL
AK4
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
C8A
C8B
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
PLK3
CNN3
COL11A1
CPT2
CRYZ
CSF1
CTBS
CTH
CYP2J2
CYP4A11
CYP4B1
DAB1
DBT
GADD45A
DHCR24
DIO1
DPYD
DR1
S1PR1
CELSR2
ELAVL4
EXTL2
F3
FAAH
FOXE3
FOXD2
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GPX7
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
IL12RB2
IPP
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
LEPR
TACSTD2
MAGOH
MOV10
MSH4
NASP
NFIA
NGF
NHLH2
NRD1
ROR1
ORC1
OVGP1
PRDX1
PDE4B
PGM1
PIN1P1
PRKAA2
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RAB3B
RABGGTB
RAP1A
SNORD21
RPE65
RPL5
RPS8
SORT1
SARS
SCP2
STIL
SLC1A7
SLC6A9
SLC16A1
STXBP3
SYCP1
TAF13
TGFBR3
TSHB
TTC4
UQCRH
UROD
USP1
VCAM1
WNT2B
LRP8
BSND
CSDE1
EVI5
CDC7
BCAR3
RAD54L
PIK3R3
LMO4
CDC14A
MKNK1
PPAP2B
RTCD1
PTCH2
FPGT
FUBP1
EIF2B3
DIRAS3
SLC16A4
SRSF11
ZFYVE9
CD101
SEP15
ZRANB2
ARHGAP29
TMEM59
CLCA3P
CLCA2
HS2ST1
KIAA0494
DNAJC6
LRIG2
LPPR4
INSL5
PIGK
TSPAN2
TSPAN1
PDZK1IP1
INADL
BCAS2
AKR1A1
CEPT1
TESK2
VAV3
LRRC41
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
IFI44L
KIF2C
DNAJB4
FAF1
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
TTC39A
USP33
MAST2
CLCC1
SLC35D1
LPHN2
KIAA1107
ZCCHC11
USP24
ITGB3BP
SLC35A3
LRRC8B
LPAR3
DDAH1
SSBP3
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
SERBP1
PTPN22
AK5
SNORA66
SNORD45B
SNORD45A
SNORD55
RNF11
FOXD3
CHIA
ANGPTL3
GPSM2
ALG6
SLC25A24
DNTTIP2
TMED5
TXNDC12
TNNI3K
SH3GLB1
TMEM69
MRPL37
HOOK1
SNX7
DPH5
HSPB11
CMPK1
GPR88
YIPF1
CCDC76
SPATA6
L1TD1
RSBN1
ZNHIT6
LEPROT
GIPC2
PALMD
FNBP1L
ST7L
C1orf123
TTC22
PRPF38B
LRRC8D
PRMT6
RNF220
RAVER2
ECHDC2
FGGY
MCOLN3
SLC22A15
RNPC3
POMGNT1
LRRC40
DEPDC1
TMEM48
LRIF1
CTTNBP2NL
FAM212B
DMAP1
GNG12
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
LRRC7
ZSWIM5
CACHD1
MIER1
PTBP2
DNASE2B
GPBP1L1
DMRTB1
DMRTA2
ELTD1
HIAT1
ATPAF1
DCLRE1B
SELRC1
ERI3
WDR77
DLEU2L
EPS8L3
TMEM53
HECTD3
BEND5
ZYG11B
TTLL7
WDR78
RPAP2
DENND2D
WLS
RPF1
SIKE1
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
TM2D1
SYDE2
ZNF644
LRRC8C
SGIP1
PROK1
EFCAB7
PSRC1
MGC12982
HPDL
ATP1A1OS
AGBL4
ATG4C
PRPF38A
FAM40A
DOCK7
BTF3L4
NEXN
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
KTI12
HENMT1
TOE1
MYSM1
OSBPL9
OMA1
LRRC42
GBP4
GBP5
SSX2IP
OLFM3
CCDC163P
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
DMBX1
TCEANC2
PODN
LRRC39
C1orf87
KLF17
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
UBE2U
SLC30A7
KNCN
MOB3C
GLIS1
MGC27382
IL23R
CCDC24
BTBD19
CCDC17
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
CYP4Z2P
FLJ40434
C1orf177
KANK4
SASS6
HFM1
UBL4B
ALG14
LINC00466
C1orf168
TMEM61
CYP4Z1
CDCP2
SLC5A9
CC2D1B
TCTEX1D1
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
NEGR1
CYP4X1
MAGI3
BEST4
FAM19A3
CYP4A22
C1orf185
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
FAM151A
LOC339524
C1orf228
CCDC18
MYBPHL
BARHL2
HSP90B3P
TCTEX1D4
FAM159A
ATPAF1-AS1
HEATR8
FAM73A
NSUN4
LOC388630
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
SKINTL
UOX
FRRS1
LOC400752
C1orf141
GBP1P1
FLJ27354
MIR137HG
MIR101-1
MIR137
MIR186
MIR197
LHX8
C1orf180
ZYG11A
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
LURAP1
CYB5RL
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
SNORD45C
MIR548D1
MIR553
RPS15AP10
LOC729041
HSD52
LOC729970
LOC729987
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130197
LOC100131060
LOC100131564
ZRANB2-AS1
LOC100287722
LOC100289178
MIR320B1
MIR1262
MIR761
MIR3117
MIR4256
MIR3671
MIR548AA1
LOC100505768
LOC100506343
LOC100507423
LOC100507564
LOC100507634
FPGT-TNNI3K
HEATR8-TTC4
TMEM56-RWDD3
MIR4422
MIR4781
MIR4794
MIR4711
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2

Genes in Wide Peak

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

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

Genes
BLM
BUB1B
IDH2
NTRK3
PML
TCF12
CRTC3
FLJ27352
C15orf55
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
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
ADAM10
ACAN
ALDH1A3
ANPEP
ANXA2
APBA2
AQP9
B2M
BBS4
BCL2A1
NBEAP1
BNC1
BNIP2
CA12
CAPN3
CHD2
CHRM5
CHRNA3
CHRNA5
CHRNA7
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FES
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IDH3A
IGF1R
IL16
IPW
IREB2
ISG20
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2A2
MAN2C1
MAP1A
MEF2A
MEIS2
MFAP1
MFGE8
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
NMB
OAZ2
OCA2
FURIN
PCSK6
PDE8A
PKM2
PLCB2
PLIN1
POLG
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SH3GL3
SLC12A1
SNRPA1
SNRPN
SNX1
SORD
SPINT1
SRP14
NR2F2
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
UBE3A
MKRN3
SLC30A4
AP3B2
PAR5
ANP32A
ST8SIA2
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
PEX11A
IQGAP1
ALDH1A2
HERC2
HERC1
SNURF
PSTPIP1
PRC1
USP8
CCNB2
SLC28A2
SLC28A1
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
SV2B
ARNT2
USP3
SLC12A6
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
RASGRP1
SERF2
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
SLC27A2
ABHD2
ADAMTS7
AKAP13
GPR176
CHP
OIP5
ITGA11
CHSY1
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
CYFIP1
ACSBG1
KIAA1024
MGA
DMXL2
SYNM
VPS39
FAM189A1
TMED3
AP4E1
SEC11A
CCNDBP1
DAPK2
EID1
C15orf2
GABARAPL3
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
VPS33B
GREM1
MRPL46
OR4F4
NPTN
FOXB1
RPUSD2
TUBGCP4
SLCO3A1
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
HDGFRP3
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
RASL12
SPG21
SPTBN5
NGRN
RHCG
PTPLAD1
CTDSPL2
KLF13
RAB8B
BTBD1
TM6SF1
DUOX1
CSNK1G1
ZFAND6
MAGEL2
DLL4
SCAND2
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZNF770
ZSCAN2
ZWILCH
FLJ10038
DET1
UACA
HAUS2
FAM82A2
LINS
DNAJC17
FANCI
IMP3
LARP6
MNS1
DNAJA4
NOP10
MCTP2
SELS
GOLGA6B
MESP1
UNC45A
MYO5C
NDNL2
FAM214A
C15orf24
C15orf39
THAP10
PAK6
RGMA
WDR93
PARP6
DTWD1
CASC5
AVEN
C15orf17
ADAMTSL3
ATP10A
KIAA1199
GJD2
STARD9
ALPK3
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
ZFP106
KLHL25
CPEB1
AEN
IQCH
ISL2
RFX7
TTC23
MRPS11
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
LRRK1
AAGAB
LMAN1L
C15orf29
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
AGSK1
SPG11
TM2D3
ELL3
PLEKHO2
WDR61
CD276
STARD5
POLR2M
C15orf44
NIPA2
C15orf5
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
WDR73
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf42
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
RCCD1
LOC91450
CALML4
ARRDC4
LOC91948
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
C15orf40
SENP8
MTFMT
OSTBETA
TARSL2
HIGD2B
LRRC28
C15orf27
NIPA1
AGBL1
AGPHD1
WHAMM
FSD2
PLA2G4E
ASB7
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
LYSMD4
FAM81A
GCOM1
LOC145783
PGPEP1L
LOC145820
LOC145837
LOC145845
C15orf61
C15orf32
HAPLN3
MESP2
TMCO5A
SPATA8
NRG4
LINC00052
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
ADAMTS17
RHOV
SCAMP5
C15orf33
DNM1P46
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
CERS3
SPESP1
LOC253044
LPCAT4
LOC254559
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
HMGN2P46
SLC24A5
PRTG
LOC283663
LINC00277
C15orf60
LOC283683
C15orf37
LOC283688
LOC283692
LOC283693
OR4N4
LOC283710
FAM154B
LOC283731
LOC283738
FAM98B
PLA2G4D
HERC2P3
LOC283761
GOLGA6L1
GOLGA8G
FAM169B
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
TMEM202
LOC338963
WHAMMP3
POTEB
GLDN
GOLGA6A
TMC3
ZNF774
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
C15orf38
LOC348120
MRPL42P5
USP50
TEX9
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
LOC388152
UBE2Q2P1
FLJ42289
GOLGA8E
OR4M2
OR4N3P
KBTBD13
UBAP1L
SKOR1
ANKRD34C
C15orf58
OR4F6
OR4F15
LOC390660
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
ST20
FAM174B
LOC400456
DUOXA2
MIR184
MIR190A
MIR211
MIR7-2
MIR9-3
C15orf50
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
LOC503519
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC645752
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
SH2D7
LOC646938
GOLGA6L10
LOC648809
LOC653061
LOC653075
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA15
SCARNA14
FBXO22-AS1
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727849
LOC727915
LOC727924
ASB9P1
LOC728758
OIP5-AS1
LOC729739
GOLGA8C
LOC729911
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
FAM138E
MIR147B
DNM1P35
LOC100128714
LOC100129387
LOC100130855
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
UBE2Q2P3
UBE2Q2P2
JMJD7
PLA2G4B
LOC100144604
GPCRLTM7
DDX11L1
LOC100287559
LOC100287616
ULK4P2
DDX11L9
LOC100288615
LOC100288637
LOC100289656
MIR1276
MIR1233-1
MIR1272
MIR1266
MIR1179
MIR1282
MIR1469
LOC100306975
MIR548H4
MIR2116
MIR1233-2
MIR4311
MIR4312
MIR3175
MIR4310
MIR4313
MIR3942
RPS17L
LOC100505648
LOC100505679
LOC100506686
LOC100506874
LOC100507217
LOC100507466
LOC100507472
C15orf38-AP3S2
ST20-MTHFS
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4514
MIR4513
MIR4509-1
MIR4509-2
MIR3529
MIR4508
MIR4510
MIR4716
MIR4713
MIR4511
MIR4509-3
MIR4712
MIR4515
MIR4714
MIR4715
TMCO5B
MYZAP

Genes in Wide Peak

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

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

Genes
RUNX1
ERG
TMPRSS2
OLIG2
hsa-mir-3197
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
ADARB1
AIRE
APP
ATP5J
ATP5O
BACH1
BAGE
PTTG1IP
C21orf2
TMEM50B
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
CXADR
DSCAM
RCAN1
DYRK1A
ETS2
GABPA
GART
GRIK1
HLCS
HMGN1
PRMT2
IFNAR1
IFNAR2
IFNGR2
IL10RB
ITGB2
KCNE1
KCNJ6
KCNJ15
LSS
MX1
MX2
NCAM2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
TMPRSS15
PWP2
S100B
SH3BGR
ITSN1
SIM2
SLC5A3
SLC19A1
SUMO3
SOD1
SON
HSPA13
TFF1
TFF2
TFF3
TIAM1
TRAPPC10
TPTE
TRPM2
TTC3
U2AF1
UBE2G2
WRB
NRIP1
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
SYNJ1
MCM3AP
CLDN8
ADAMTS1
ABCG1
URB1
CRYZL1
DOPEY2
KCNE2
RWDD2B
DSCR4
DSCR3
B3GALT5
USP16
CCT8
WDR4
FTCD
BTG3
HSF2BP
ADAMTS5
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
LTN1
CLDN17
N6AMT1
USP25
DNMT3L
DONSON
HUNK
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
RBM11
PCBP3
C21orf58
YBEY
LINC00160
FAM165B
C21orf49
MIS18A
LINC00158
CHODL-AS1
TSPEAR
LINC00113
LINC00112
LINC00111
SETD4
C21orf15
FAM3B
RIPK4
CLIC6
LINC00308
MRPL39
C21orf91
DNAJC28
C21orf62
MRAP
C21orf59
AGPAT3
C21orf7
SCAF4
JAM2
C21orf63
PRDM15
SAMSN1
TMPRSS3
MRPS6
RUNX1-IT1
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
FAM207A
RSPH1
UMODL1
GCFC1
LINC00310
LINC00313
C21orf88
C21orf90
MCM3AP-AS1
MIR155HG
CYYR1
OLIG1
LINC00161
KRTAP13-1
TCP10L
CHODL
ANKRD30BP2
LIPI
ABCC13
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00189
C21orf91-OT1
LINC00315
LINC00314
KRTAP15-1
DSCR9
BRWD1-IT2
DSCR10
D21S2088E
LINC00307
LINC00515
KRTAP13-4
LINC00323
LINC00319
LOC284837
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
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
LINC00317
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00320
LOC388813
LINC00478
KRTAP26-1
ANKRD20A11P
LINC00114
MIRLET7C
MIR125B2
MIR155
MIR99A
LOC642852
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
LINC00163
SSR4P1
KRTAP19-8
C21orf54
MIR802
LOC100129027
KRTAP25-1
TEKT4P2
LOC100133286
KRTAP20-4
KRTAP22-2
KRTAP21-3
LOC100288432
GRIK1-AS2
MIR4327
MIR3156-3
MIR3197
MIR3687
MIR3648
LOC100505746
C21orf37
GCFC1-AS1
LOC100506334
LOC100506385
CBR3-AS1
DSCAM-AS1
LINC00159
MIR4760
MIR4759

Genes in Wide Peak

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

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

Genes
ATRX
ELF4
GATA1
GPC3
MSN
MTCP1
NONO
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
CRLF2
P2RY8
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
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
ABCD1
AMELX
SLC25A5
SLC25A6
XIAP
SHROOM2
AR
ARAF
ARHGAP4
ARHGAP6
ARR3
STS
ARSD
ARSE
ARSF
ASMT
ATP2B3
ATP6AP1
ATP7A
AVPR2
BCYRN1
BGN
BMX
BRS3
BTK
CACNA1F
S100G
CAPN6
CD40LG
CDR1
CDX4
CETN2
CHM
CLCN4
CLCN5
CLIC2
CNGA2
COL4A5
COL4A6
COX7B
CSF2RA
CSTF2
CTAG1B
TEX28
CYBB
CYLC1
DCX
DDX3X
TIMM8A
DIAPH2
DKC1
DLG3
DMD
DNASE1L1
DRP2
TSC22D3
DUSP9
EDA
EFNB1
EIF1AX
EIF2S3
ELK1
EMD
F8
F9
ACSL4
FANCB
GPC4
FGD1
FGF13
FHL1
FIGF
FLNA
FMR1
AFF2
CENPI
G6PD
GAGE1
GABRA3
GABRE
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
OPN1MW
GDI1
GJB1
GK
GLA
GLRA2
GLUD2
GPM6B
CXCR3
LPAR4
GPR34
GRIA3
GRPR
GUCY2F
HSD17B10
HCCS
HCFC1
HMGB3
HNRNPH2
HPRT1
ERAS
HTR2C
IDH3G
IDS
IGBP1
IGSF1
IL2RG
IL3RA
IL9R
IL13RA1
IL13RA2
IRAK1
KAL1
KCND1
L1CAM
LAMP2
PRICKLE3
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
MCF2
MECP2
CD99
MID1
FOXO4
MPP1
CITED1
MTM1
NAP1L2
NAP1L3
NDP
NDUFA1
NHS
GPR143
TBC1D25
OCRL
OPHN1
OTC
P2RY4
PAK3
CDK16
PDHA1
PDK3
CFP
PFKFB1
PGK1
PHEX
PHKA1
PHKA2
PIGA
PIN4
PLP1
PLP2
PLS3
PLXNB3
POLA1
POU3F4
PPEF1
PRKX
PRPS1
PRPS2
PRRG1
PSMD10
RBBP7
RBM3
OPN1LW
RENBP
RP2
RPGR
RPL10
RPL39
RPL36A
RPS4X
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SH3BGRL
SHOX
SLC6A8
SLC16A2
SMARCA1
SMS
SOX3
SRD5A1P1
SSR4
SSX5
CDKL5
SUV39H1
VAMP7
SYN1
SYP
TAF1
TAZ
SERPINA7
TBL1X
DYNLT3
TDGF1P3
TIMP1
TSPAN7
TSPAN6
TMSB4X
TRO
TRPC5
UBA1
UBE2A
SLC35A2
VBP1
XG
XIST
XK
XPNPEP2
ZFX
ZIC3
ZNF711
ZNF182
ZNF41
ZNF75D
ZNF157
RNF113A
ZNF185
ZXDA
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
SRPX
UXT
CUL4B
IRS4
OGT
OFD1
IKBKG
PIR
INE2
INE1
CASK
ASMTL
PAGE1
MTMR1
FGF16
AKAP4
APLN
AP1S2
GYG2
FAM127A
SLC25A14
CLDN2
RGN
FAM50A
AIFM1
CXorf1
REPS2
ZBED1
ZMYM3
BMP15
GPR50
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
BCAP31
GPR64
ATP6AP2
ODZ1
SSX3
TIMM17B
SPRY3
RRAGB
SCML2
SLC9A6
ENOX2
PRDX4
EBP
STAG2
RAI2
PLAC1
CYSLTR1
UTP14A
ZNF275
PGRMC1
MAGED2
MSL3
TMSB15A
PIM2
MID2
IL1RAPL1
WDR45
TREX2
PRAF2
CA5B
SLC6A14
KLF8
VSIG4
CNKSR2
IQSEC2
PHF8
SEPT6
ARHGEF9
ATP1B4
ACOT9
KCNE1L
LDOC1
SMPX
GSPT2
KIF4A
FTSJ1
CXorf27
MXRA5
EGFL6
FAM127B
IL1RAPL2
ITGB1BP2
SRPK3
VCX
GAGE12I
GAGE2E
SNORA70
SNORA69
SNORD61
NGFRAP1
NOX1
FAM155B
INGX
GPR82
GPKOW
SRPX2
APEX2
RBMX
PCDH11X
RPS6KA6
P2RY10
HTATSF1
PCSK1N
PPP2R3B
CCDC22
MCTS1
MAGEH1
FAM156A
C1GALT1C1
SNX12
RPA4
PNMA3
UBQLN2
SH3KBP1
SPANXA1
CTAG2
NSDHL
FOXP3
TBX22
ZDHHC9
RLIM
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
TMLHE
RBM41
PLCXD1
SAGE1
PLXNA3
HAUS7
OTUD5
ZNF280C
MTMR8
ZNF673
TXLNG
MBNL3
WWC3
FAM45B
BEX1
HDAC8
GABRQ
ZC4H2
NXT2
NKRF
NXF5
NXF4
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
MOSPD1
BEX4
CTPS2
CHST7
TCEAL7
GRIPAP1
THOC2
ZNF630
TMEM27
SHROOM4
KIAA1210
NLGN4X
PCDH19
RGAG1
PDZD4
LRCH2
MAGEE1
RAP2C
MID1IP1
ACE2
TMEM35
FAM3A
EDA2R
NYX
BCORL1
DUSP21
CXorf56
DMRTC1
TSPYL2
TNMD
PJA1
SPANXD
SPANXC
WDR13
PORCN
ARMCX5
UPF3B
WNK3
FUNDC2
PRRG3
APOO
BRCC3
HMGN5
NKAP
RNF128
MAP7D3
MORC4
CXorf36
LONRF3
ALG13
MAGIX
TCEAL4
TRMT2B
POF1B
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
ESX1
BHLHB9
MAGED4B
LAS1L
GPR101
TMEM47
CD99L2
H2AFB3
USP26
FRMD8P1
MAGT1
TMEM164
PHF6
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
SLC9A7
BEX2
MGC16121
SLC7A3
PNMA6A
TCEAL3
CCNB3
PPP1R3F
FATE1
CCDC120
TSR2
HS6ST2
FRMD7
KLHL13
TGIF2LX
FAM104B
PAGE5
TCEAL8
CHRDL1
CXorf40A
FAM58A
RIPPLY1
LOC92249
ATXN3L
SLC38A5
MMGT1
ACRC
SYAP1
SYTL4
SYTL5
PNMA5
GPRASP2
ATG4A
RAB39B
DACH2
SLITRK4
SPANXN3
MAGEC3
BEND2
PASD1
DCAF12L1
DGKK
LOC139201
CXorf41
MUM1L1
FAM199X
FAM123B
APOOL
HDX
FUNDC1
GPR112
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
OTUD6A
UPRT
MAGEE2
MAGEB16
FOXR2
GAB3
PNCK
ZFP92
ACTRT1
GPR119
PAGE3
RBMXL3
DOCK11
SPIN4
ASB11
ASB9
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
ZNF645
CSAG1
FMR1NB
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
VMA21
TMEM31
PAGE2
DHRSX
CTAG1A
BRWD3
CXorf58
CT47A11
CXorf23
MAP7D2
KLHL34
TAB3
MAGEA2B
SSX6
SSX7
SSX8
RAB40AL
PPP2R3B-AS1
ATP11C
RP1-177G6.2
H2BFM
LOC286437
LOC286442
YIPF6
CXorf59
LOC286467
TTC3P1
FAM133A
MAGEB18
TMSB15B
LINC00204B
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
CSAG3
LOC389906
CXXC1P1
GLOD5
FLJ44635
ARL13A
LINC00086
CD99P1
LOC401588
MCART6
DKFZp686D0853
XKRX
YY2
MIRLET7F2
MIR105-1
MIR105-2
MIR106A
MIR188
MIR19B2
MIR221
MIR222
MIR223
MIR92A2
MIR98
VCX3B
LOC441495
FLJ46446
RPS26P11
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
PGAM4
FAM47C
UQCRBP1
LOC442459
MIR374A
SPIN2B
H2AFB2
H2AFB1
F8A2
F8A3
SPANXN1
SPANXN2
SPANXN5
MIR384
MIR424
CT45A6
CT45A1
CXorf40B
SSX4B
LOC550643
JPX
MIR448
MIR450A1
MIR362
MIR363
MIR20B
MIR18B
MIR452
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
SNORA36A
SNORA56
SNORD96B
MIR421
MIR532
MIR651
MIR660
CXorf31
SSX2B
FAM156B
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGED4
XAGE2B
MAGEA9B
NXF2B
OPN1MW2
CSAG2
DMRTC1B
SPANXB1
SPANXA2
CT45A2
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
LOC729609
H2BFXP
MIR767
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
CXorf68
LINC00204A
CXorf49B
CXorf51B
LOC100133123
SPANXB2
LOC100133957
SCARNA9L
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
LOC100287765
LOC100288814
MIR1184-1
MIR1468
MIR1912
MIR1298
MIR1256
MIR320D2
MIR1277
MIR1911
MIR1264
FTX
SLC25A5-AS1
MIR718
MIR764
MIR2114
LOC100329135
LINC00102
MIR514B
MIR3202-2
MIR500B
MIR4330
MIR4328
MIR1184-3
MIR1184-2
MIR3202-1
MIR4329
MTRNR2L10
MIR374C
MIR23C
MIR676
MIR3690
HSFX1
LOC100506757
CT47A12
LOC100507404
LOC100509575
ARMCX5-GPRASP2
RPL36A-HNRNPH2
PIR-FIGF
MAGEA10-MAGEA5
MIR4769
MIR4536-1
MIR4768
MIR4770
MIR4767
MIR3978

Genes in Wide Peak

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

Table S45. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RUNX1
ERG
TMPRSS2
OLIG2
hsa-mir-3197
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
ADARB1
AIRE
APP
ATP5J
ATP5O
BACH1
BAGE
PTTG1IP
C21orf2
TMEM50B
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
CXADR
DSCAM
RCAN1
DYRK1A
ETS2
GABPA
GART
GRIK1
HLCS
HMGN1
PRMT2
IFNAR1
IFNAR2
IFNGR2
IL10RB
ITGB2
KCNE1
KCNJ6
KCNJ15
LSS
MX1
MX2
NCAM2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
TMPRSS15
PWP2
S100B
SH3BGR
ITSN1
SIM2
SLC5A3
SLC19A1
SUMO3
SOD1
SON
HSPA13
TFF1
TFF2
TFF3
TIAM1
TRAPPC10
TPTE
TRPM2
TTC3
U2AF1
UBE2G2
WRB
NRIP1
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
SYNJ1
MCM3AP
CLDN8
ADAMTS1
ABCG1
URB1
CRYZL1
DOPEY2
KCNE2
RWDD2B
DSCR4
DSCR3
B3GALT5
USP16
CCT8
WDR4
FTCD
BTG3
HSF2BP
ADAMTS5
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
LTN1
CLDN17
N6AMT1
USP25
DNMT3L
DONSON
HUNK
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
RBM11
PCBP3
C21orf58
YBEY
LINC00160
FAM165B
C21orf49
MIS18A
LINC00158
CHODL-AS1
TSPEAR
LINC00113
LINC00112
LINC00111
SETD4
C21orf15
FAM3B
RIPK4
CLIC6
LINC00308
MRPL39
C21orf91
DNAJC28
C21orf62
MRAP
C21orf59
AGPAT3
C21orf7
SCAF4
JAM2
C21orf63
PRDM15
SAMSN1
TMPRSS3
MRPS6
RUNX1-IT1
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
FAM207A
RSPH1
UMODL1
GCFC1
LINC00310
LINC00313
C21orf88
C21orf90
MCM3AP-AS1
MIR155HG
CYYR1
OLIG1
LINC00161
KRTAP13-1
TCP10L
CHODL
ANKRD30BP2
LIPI
ABCC13
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00189
C21orf91-OT1
LINC00315
LINC00314
KRTAP15-1
DSCR9
BRWD1-IT2
DSCR10
D21S2088E
LINC00307
LINC00515
KRTAP13-4
LINC00323
LINC00319
LOC284837
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
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
LINC00317
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00320
LOC388813
LINC00478
KRTAP26-1
ANKRD20A11P
LINC00114
MIRLET7C
MIR125B2
MIR155
MIR99A
LOC642852
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
LINC00163
SSR4P1
KRTAP19-8
C21orf54
MIR802
LOC100129027
KRTAP25-1
TEKT4P2
LOC100133286
KRTAP20-4
KRTAP22-2
KRTAP21-3
LOC100288432
GRIK1-AS2
MIR4327
MIR3156-3
MIR3197
MIR3687
MIR3648
LOC100505746
C21orf37
GCFC1-AS1
LOC100506334
LOC100506385
CBR3-AS1
DSCAM-AS1
LINC00159
MIR4760
MIR4759

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 | 0.06 | -0.556 | 0.997 | 0.17 | 3.03 | 0.00538
1q | 1955 | 0.24 | 5.13 | 5.76e-06 | 0.05 | -0.992 | 0.997
2p | 924 | 0.08 | -1.13 | 0.997 | 0.08 | -1.13 | 0.997
2q | 1556 | 0.08 | -0.672 | 0.997 | 0.03 | -2.09 | 0.997
3p | 1062 | 0.04 | -1.88 | 0.997 | 0.17 | 1.35 | 0.294
3q | 1139 | 0.11 | -0.172 | 0.997 | 0.10 | -0.498 | 0.997
4p | 489 | 0.04 | -2.39 | 0.997 | 0.12 | -0.612 | 0.997
4q | 1049 | 0.01 | -2.71 | 0.997 | 0.12 | 0.196 | 0.938
5p | 270 | 0.09 | -1.37 | 0.997 | 0.07 | -1.94 | 0.997
5q | 1427 | 0.05 | -1.36 | 0.997 | 0.10 | 0.0138 | 0.995
6p | 1173 | 0.02 | -2.17 | 0.997 | 0.35 | 6.69 | 9.12e-11
6q | 839 | 0.00 | -2.57 | 0.997 | 0.43 | 8.3 | 0
7p | 641 | 0.24 | 2.79 | 0.0438 | 0.03 | -2.34 | 0.997
7q | 1277 | 0.21 | 2.72 | 0.0438 | 0.05 | -1.63 | 0.997
8p | 580 | 0.13 | -0.133 | 0.997 | 0.17 | 0.762 | 0.558
8q | 859 | 0.22 | 2.59 | 0.0474 | 0.08 | -1.14 | 0.997
9p | 422 | 0.06 | -1.53 | 0.997 | 0.44 | 7.44 | 5.13e-13
9q | 1113 | 0.07 | -1.22 | 0.997 | 0.26 | 3.96 | 0.000186
10p | 409 | 0.03 | -2.67 | 0.997 | 0.16 | 0.562 | 0.676
10q | 1268 | 0.06 | -1.37 | 0.997 | 0.16 | 1.3 | 0.297
11p | 862 | 0.09 | -0.831 | 0.997 | 0.08 | -1.14 | 0.997
11q | 1515 | 0.08 | -0.544 | 0.997 | 0.09 | -0.194 | 0.997
12p | 575 | 0.10 | -0.962 | 0.997 | 0.12 | -0.363 | 0.997
12q | 1447 | 0.08 | -0.504 | 0.997 | 0.13 | 0.876 | 0.508
13q | 654 | 0.08 | -1.2 | 0.997 | 0.13 | 0.00667 | 0.995
14q | 1341 | 0.12 | 0.289 | 0.997 | 0.06 | -1.41 | 0.997
15q | 1355 | 0.09 | -0.556 | 0.997 | 0.15 | 1.14 | 0.364
16p | 872 | 0.10 | -0.631 | 0.997 | 0.03 | -2.52 | 0.997
16q | 702 | 0.10 | -0.75 | 0.997 | 0.04 | -2.28 | 0.997
17p | 683 | 0.00 | -2.67 | 0.997 | 0.42 | 7.65 | 1.3e-13
17q | 1592 | 0.06 | -1.13 | 0.997 | 0.14 | 1.36 | 0.294
18p | 143 | 0.18 | 0.472 | 0.997 | 0.42 | 6.23 | 1.58e-09
18q | 446 | 0.06 | -1.47 | 0.997 | 0.57 | 10.9 | 0
19p | 995 | 0.05 | -1.75 | 0.997 | 0.09 | -0.785 | 0.997
19q | 1709 | 0.12 | 0.777 | 0.997 | 0.07 | -0.678 | 0.997
20p | 355 | 0.15 | 0.199 | 0.997 | 0.13 | -0.38 | 0.997
20q | 753 | 0.21 | 2.22 | 0.106 | 0.02 | -2.71 | 0.997
21q | 509 | 0.02 | -2.52 | 0.997 | 0.35 | 5.47 | 1.28e-07
22q | 921 | 0.06 | -1.51 | 0.997 | 0.21 | 2.27 | 0.0463
Xq | 1312 | 0.04 | -1.92 | 0.997 | 0.06 | -1.25 | 0.997

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/5950849/GDAC_MergeDataFiles_5955463/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 81 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.

- 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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