SNP6 Copy number analysis (GISTIC2)
Adrenocortical Carcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1SF2TGN
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1SF2TGN
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 2.0.19 (Firehose task version: 125).

Summary

There were 77 tumor samples used in this analysis: 20 significant arm-level results, 15 significant focal amplifications, and 23 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 - 15 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
--- | --- | --- | --- | ---
5p15.33 | 6.8562e-08 | 6.8562e-08 | chr5:1-1287702 | 23
5q35.3 | 0.003988 | 0.003988 | chr5:176723780-176833588 | 9
12q14.1 | 0.017519 | 0.017519 | chr12:58080141-58481453 | 16
19p13.12 | 0.017914 | 0.017914 | chr19:15293986-16620503 | 35
16q22.1 | 0.027999 | 0.027999 | chr16:69246837-69648494 | 11
4p16.3 | 0.03803 | 0.03803 | chr4:1-2703856 | 52
14q11.2 | 0.048573 | 0.048573 | chr14:21010467-23970250 | 74
4q35.1 | 0.092928 | 0.092928 | chr4:143364465-191154276 | 209
Xq28 | 0.099184 | 0.099184 | chrX:151841230-152714951 | 21
1q22 | 0.10298 | 0.10298 | chr1:153665611-155302817 | 64
6q24.3 | 0.12011 | 0.12011 | chr6:147060843-148023227 | 5
19q13.33 | 0.089479 | 0.13 | chr19:37264335-59128983 | 850
17q25.3 | 0.20678 | 0.20678 | chr17:54329365-81195210 | 406
19q12 | 0.15543 | 0.20715 | chr19:30126537-30551696 | 4
9q34.3 | 0.21604 | 0.21604 | chr9:107993933-141213431 | 446

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

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

Genes
SDHA
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4456
MIR4635

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

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

Genes
NSD1
F12
SLC34A1
RGS14
LMAN2
PRELID1
RAB24
MXD3
PFN3

Genes in Wide Peak

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

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

Genes
CDK4
hsa-mir-26a-2
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
OS9
METTL21B
XRCC6BP1
MARCH9
AGAP2
MIR26A2
LOC100130776
LOC100506844

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
TPM4
BRD4
hsa-mir-1470
CYP4F3
RAB8A
NOTCH3
CYP4F2
AP1M1
AKAP8
KLF2
CYP4F8
FAM32A
OR10H3
OR10H2
OR10H1
AKAP8L
CYP4F11
EPS15L1
WIZ
RASAL3
CYP4F12
EPHX3
C19orf44
HSH2D
PGLYRP2
CIB3
CALR3
CYP4F22
LOC126536
OR10H4
FLJ25328
OR10H5
CYP4F24P
UCA1
MIR1470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q22.1.

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

Genes
hsa-mir-1538
SNTB2
TERF2
NFAT5
VPS4A
NIP7
PDF
CYB5B
COG8
TMED6
MIR1538

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
hsa-mir-943
hsa-mir-571
ATP5I
CTBP1
DGKQ
GAK
IDUA
LETM1
MYL5
PDE6B
RNF4
WHSC2
ZNF141
SLBP
FAM193A
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
FGFRL1
PIGG
KIAA1530
ZFYVE28
HAUS3
ABCA11P
MFSD7
TMEM175
C4orf42
TMEM129
ZNF595
FAM53A
ZNF721
ZNF718
CRIPAK
RNF212
NAT8L
POLN
C4orf48
LOC402160
ZNF876P
ZNF732
SCARNA22
MIR943
LOC100129917
LOC100130872
TMED11P
MIR4800

Genes in Wide Peak

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

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

Genes
hsa-mir-208b
ANG
BCL2L2
CEBPE
DAD1
HNRNPC
MMP14
MYH6
MYH7
OXA1L
PSMB5
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
PABPN1
SLC7A7
TOX4
EFS
PRMT5
EDDM3A
SUPT16H
ACIN1
SLC7A8
NGDN
LRP10
OR10G3
OR10G2
OR4E2
SLC39A2
ZNF219
SLC22A17
HAUS4
C14orf119
RBM23
ARHGEF40
METTL3
RPGRIP1
NDRG2
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
RNASE7
RAB2B
AJUBA
PPP1R3E
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
REM2
LOC283624
SNORD8
OR6S1
RNASE9
OR5AU1
MIR208A
RNASE13
RNASE12
ECRP
C14orf176
SNORD9
MIR208B
BCL2L2-PABPN1
MIR4707

Genes in Wide Peak

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

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
AGA
SLC25A4
ANXA2P1
CASP3
LRBA
CLCN3
CPE
CTSO
DCTD
EDNRA
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GAB1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
SMAD1
NR3C2
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
POU4F2
PPID
ABCE1
RPS3A
MSMO1
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SMARCA5
SORBS2
SAP30
INPP4B
SNORD73A
LRAT
HAND2
RAPGEF2
MFAP3L
ANAPC10
MAB21L2
ADAM29
LSM6
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
DUX2
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
DKFZP434I0714
OTUD4
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
TMEM184C
LRP2BP
PDGFC
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
HHIP
ARHGAP10
MLF1IP
NBLA00301
MAP9
WWC2
CEP44
SNX25
TTC29
MND1
SLC10A7
TKTL2
USP38
CBR4
FHDC1
MGC45800
PRMT10
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
ZNF827
SH3D19
C4orf38
C4orf39
C4orf45
DCLK2
TRIM60
FREM3
MMAA
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
RNF175
LOC339975
TRIML1
LOC340017
PRSS48
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
FAM160A1
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3140
MIR4276
MIR3945
MIR3688-1
LOC100505545
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR4453
MIR4799
MIR3688-2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

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

Genes
CETN2
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
ZNF185
ZNF275
TREX2
PNMA3
NSDHL
HAUS7
PNMA6A
PNMA5
ZFP92
CSAG1
MAGEA2B
CSAG3
CSAG2
PNMA6C
PNMA6D

Genes in Wide Peak

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

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

Genes
MUC1
TPM3
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
ADAR
CHRNB2
CKS1B
CLK2
EFNA1
EFNA3
EFNA4
FDPS
GBA
GBAP1
IL6R
KCNN3
MTX1
NPR1
PKLR
RAB13
RPS27
SHC1
THBS3
ADAM15
UBAP2L
DENND4B
SCAMP3
HAX1
PMVK
FAM189B
JTB
SLC27A3
RUSC1
C1orf43
SLC39A1
ZBTB7B
DPM3
UBE2Q1
LENEP
SLC50A1
ATP8B2
PBXIP1
GATAD2B
HCN3
INTS3
TRIM46
FLAD1
AQP10
PYGO2
NUP210L
TDRD10
SHE
DCST2
CREB3L4
DCST1
KRTCAP2
CRTC2
RUSC1-AS1
C1orf189
MIR92B
MIR190B
MIR4258
LOC100505666

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q24.3.

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

Genes
ADGB
STXBP5
SAMD5
LOC729176
LOC729178

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.33.

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

Genes
AKT2
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
hsa-mir-641
A1BG
ACTN4
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
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
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
PPP6R1
CARD8
SIRT2
CYP2G1P
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
ZNF345
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
PRX
SPTBN4
MARK4
CATSPERG
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
WDR87
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
SNORD35B
ZNF347
ZNF577
ZNF607
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
ZNF585B
TIMM50
SHKBP1
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF383
ZNF781
EID2
ZNF780B
ZNF540
ZNF525
SPACA4
ZNF585A
NLRP7
GGN
CADM4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
LOC284408
LOC284412
VSTM1
TMEM150B
FAM71E2
HKR1
VN1R2
VN1R4
NLRP9
ZNF546
MYPOP
NANOS2
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
C19orf51
ZNF233
LILRA5
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
LOC386758
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF793
PAPL
LOC390940
ZNF805
SPRED3
ZNF321P
LGALS17A
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
LOC643669
LOC644554
LOC646508
SBK2
LOC646862
PSG10P
LGALS7B
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
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
LOC100129935
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
LOC100507433
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
LOC100631378

Genes in Wide Peak

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

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

Genes
CD79B
CLTC
DDX5
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
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
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
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
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45L
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
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
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
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
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 amplified genes in the wide peak for 19q12.

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

Genes
CCNE1
URI1
PLEKHF1
C19orf12

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
ABL1
NOTCH1
RALGDS
SET
TAL2
TSC1
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
ABCA2
ABO
AK1
ALAD
AMBP
ASS1
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
SLC31A1
SLC31A2
CRAT
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP6C
PSMB7
PSMD5
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TLR4
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
ZFP37
ZNF79
LHX3
GFI1B
IKBKAP
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
RALGPS1
ADAMTSL2
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
SLC27A4
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
PTGR1
TRIM32
SETX
ZBTB43
PMPCA
ASTN2
FKBP15
KIAA0368
EXOSC2
NCS1
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
RAB14
C9orf78
POLE3
FBXW5
RC3H2
EPB41L4B
TBC1D13
BSPRY
C9orf167
EXD3
FAM206A
TMEM38B
STRBP
C9orf86
CDK5RAP2
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
EHMT1
SVEP1
PTGES2
AKNA
MIR600HG
URM1
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
NTNG2
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
C9orf96
OLFML2A
QSOX2
ZNF883
C9orf91
NAIF1
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
LINC00256A
FAM78A
GPR144
QRFP
OR1J1
OR1B1
GLT6D1
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR32
C9orf106
LCN10
C9orf173
NRARP
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
NRON
FAM163B
FLJ40292
TUBBP5
RNF224
C9orf29
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
LINC00256B
LOC100128505
LOC100128593
LOC100129034
LOC100129722
LOC100130954
LOC100131193
FAM157B
RNU6ATAC
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR548Q
MIR181A2HG
MIR4292
MIR3154
MIR2861
MIR3134
MIR3621
MIR3689A
MIR3911
MIR3689B
LOC100505478
LOC100506100
LOC100506190
LOC100506599
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4672
MIR3689E
MIR4479

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 - 23 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
--- | --- | --- | --- | ---
22q12.1 | 4.5487e-22 | 4.5487e-22 | chr22:29192671-29455701 | 1
4q35.1 | 1.5972e-15 | 1.4078e-11 | chr4:183089198-184213557 | 6
9p21.3 | 1.3823e-06 | 1.3782e-05 | chr9:21865498-21997722 | 2
4q34.3 | 1.3432e-08 | 3.6294e-05 | chr4:178911874-183060693 | 1
1p36.23 | 7.7138e-05 | 7.7138e-05 | chr1:8403012-8925111 | 1
13q14.2 | 0.00038834 | 0.00038834 | chr13:48833767-49064807 | 2
11p15.5 | 0.0052259 | 0.0052259 | chr11:1681026-1944201 | 10
3q13.31 | 0.001897 | 0.01311 | chr3:115440285-116429324 | 1
17q24.2 | 0.011389 | 0.016815 | chr17:66185305-66865465 | 9
2q37.3 | 0.04871 | 0.051599 | chr2:230133788-243199373 | 160
17q11.2 | 0.058258 | 0.058258 | chr17:29704122-29888119 | 4
6q26 | 0.061686 | 0.061686 | chr6:88753800-171115067 | 425
7q32.3 | 0.061686 | 0.061686 | chr7:95210837-159138663 | 555
17q21.31 | 0.02022 | 0.067724 | chr17:26570940-53405607 | 563
16p13.3 | 0.12548 | 0.12548 | chr16:5144019-8620694 | 1
9p24.1 | 0.037028 | 0.12548 | chr9:3824005-26894302 | 99
12q14.2 | 0.12548 | 0.12548 | chr12:56315051-92536825 | 225
10q26.3 | 0.15194 | 0.1466 | chr10:134118510-135534747 | 36
6p25.2 | 0.16784 | 0.1602 | chr6:1-21599699 | 114
3q13.31 | 0.018337 | 0.18763 | chr3:115440285-118620828 | 2
1q24.1 | 0.23173 | 0.23173 | chr1:163290474-225979711 | 477
11q24.3 | 0.2463 | 0.2463 | chr11:1-135006516 | 1478
16q23.1 | 0.2463 | 0.2463 | chr16:1-90354753 | 967

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.1.

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

Genes
ZNRF3

Genes in Wide Peak

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

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

Genes
hsa-mir-1305
DCTD
ODZ3
C4orf38
FAM92A3
MIR1305

Genes in Wide Peak

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

Table S18. 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 4q34.3.

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

Genes
LINC00290

Genes in Wide Peak

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

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

Genes
RERE

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

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

Genes
hsa-mir-4298
CTSD
LSP1
TNNI2
SYT8
FAM99A
IFITM10
KRTAP5-6
FAM99B
MIR4298

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
LSAMP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.2.

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

Genes
PRKAR1A
hsa-mir-635
SLC16A6
ARSG
AMZ2
FAM20A
WIPI1
LOC440461
MIR635

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
HTR2B
SP110
INPP5D
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SNORD20
SAG
SP100
SPP2
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
SH3BP4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
C2orf54
ARMC9
EFHD1
ILKAP
ITM2C
ING5
MGC16025
DNER
B3GNT7
SP140L
AGAP1
TWIST2
DIS3L2
NEU4
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
C2orf57
TIGD1
LOC200772
C2orf72
CXXC11
DUSP28
ESPNL
ECEL1P2
LOC348761
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR4269
UBE2F-SCLY
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

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

Genes
hsa-mir-193a
RAB11FIP4
MIR193A
MIR4724

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
ACAT2
AIM1
AMD1
ARG1
CCNC
CCR6
CNR1
COL10A1
CTGF
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GPR6
GPR31
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
POU3F2
PREP
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
MAP3K7
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
NR2E1
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
FHL5
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
CASP8AP2
UST
TRDN
CITED2
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
ANKRD6
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MTHFD1L
PNISR
MOXD1
IPCEF1
TIAM2
FBXL4
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
OSTM1
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
BRP44L
HECA
COQ3
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
SOBP
PHF10
QRSL1
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
HYMAI
PDSS2
GPR126
KIAA1244
NHSL1
LYRM2
PLEKHG1
ARID1B
SERINC1
HACE1
TMEM181
ZBTB2
BEND3
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
TRMT11
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
MANEA
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
GPR63
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
SLC22A16
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
FAM54A
SFT2D1
KLHL32
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
PM20D2
SRSF12
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
BVES-AS1
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FAM26F
FLJ46906
LOC441177
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
MIR548B
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
LOC100129518
LOC100130890
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100289495
NHEG1
MIR1913
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q32.3.

Table S28. 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
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
ABP1
ACHE
AKR1B1
ARF5
ASNS
AZGP1
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
AP1S1
CLCN1
CPA1
CPA2
CUX1
CYP3A7
CYP3A4
CYP3A5
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNB2
GPR22
GPR37
GRM8
MNX1
AGFG2
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PIK3CG
PIP
PMS2P1
PODXL
POLR2J
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
PSMC2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
ZNF3
ZKSCAN1
ZSCAN21
ZYX
SHFM1
ST7
ARHGEF5
ZNF212
TRRAP
ZNF282
CUL1
TRIM24
BUD31
MGAM
WASL
PLOD3
DGKI
AP4M1
ATP6V1F
ACCN3
PMPCB
ATP5J2
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
FAM3C
COG5
ZNHIT1
ARPC1A
SH2B2
STAG3
CPSF4
FASTK
COPS6
DUS4L
ZNF277
ABCB8
PDAP1
TFEC
LAMB4
LMTK2
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
COPG2
HBP1
DNAJC2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRB
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
LUC7L2
MRPS33
NUB1
NAA38
GPR85
TAS2R5
CHPF2
PUS7
ING3
LRRN3
ALKBH4
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
MLL5
BAIAP2L1
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
RABL5
CYP3A43
LRRC61
C7orf49
ZNF655
PVRIG
GCC1
GAL3ST4
PRKRIP1
CBLL1
ZNF767
C7orf58
TTC26
ORAI2
JHDM1D
OR2AE1
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
ZNF394
MYH16
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
TRIM4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
MUC17
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
BHLHA15
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
ZNF498
FAM200A
PPP1R35
GPC2
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
CNPY4
POLR2J2
UBN2
MBLAC1
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
DLX6-AS1
ZNF789
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
MOGAT3
FAM71F2
STRA8
KLRG2
WDR86
GJC3
DPY19L2P2
LOC349160
GATS
GSTK1
NAT16
SLC26A5
LHFPL3
KCP
FLJ43663
RNF148
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
OR2A5
FLJ42280
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
UFSP1
MIR106B
MIR129-1
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
SPDYE3
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR490
ZNF862
LOC645249
LOC645591
AZGP1P1
LOC646329
C7orf73
ACTR3C
MIR591
MIR592
MIR593
MIR595
LOC723809
LOC728377
LOC728743
SPDYE6
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100129845
LOC100130705
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
LOC100287482
MOXD2P
LOC100289187
LOC100289561
ZNF783
MIR548F3
MIR548I4
SPDYE2L
MIR548F4
SAP25
MIR548T
MIR4285
MTRNR2L6
MIR3609
MIR3907
MIR3666
LOC100505483
LOC100506136
LOC100506585
LOC100507421
ATP5J2-PTCD1
GIMAP1-GIMAP5
MIR4653
MIR4468
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

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

Genes
BRCA1
COL1A1
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
RARA
TAF15
SUZ12
hsa-mir-3185
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
hsa-mir-4315-1
hsa-mir-2117
hsa-mir-2909
hsa-mir-632
hsa-mir-365-2
hsa-mir-3184
hsa-mir-144
ACACA
ACCN1
ACLY
AP2B1
ALDOC
AOC2
ARL4D
ATP5G1
ATP6V0A1
BLMH
FMNL1
CACNB1
CDC6
CDC27
CHAD
CCR7
CNP
COX11
CPD
CRHR1
CRYBA1
CSF3
DHX8
DLX3
DLX4
DUSP3
EVI2A
EVI2B
EZH1
FLOT2
GAST
FZD2
G6PC
KAT2A
GFAP
GIP
GNGT2
CCR10
GRB7
GRN
HCRT
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HSD17B1
IFI35
IGFBP4
ITGA2B
ITGA3
ITGB3
JUP
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LHX1
LIG3
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NSF
OMG
PDK2
PEX12
PHB
PNMT
MED1
PPY
PSMB3
PYY
PSMD3
PSMD11
RAB5C
RAD51D
RPL19
RPL23A
RPL27
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SGCA
SH3GL1P1
SH3GL1P2
SLC4A1
SLC6A4
SMARCE1
SP2
STAT3
STAT5A
STAT5B
SUPT6H
TADA2A
HNF1B
MLX
THRA
TNFAIP1
TOP2A
DNAJC7
TUBG1
UBTF
VTN
WNT3
WNT9B
PCGF2
ZNF207
RND2
PIP4K2B
SPOP
FOXN1
CNTNAP1
TCAP
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
ABCC3
CDK5R1
CACNA1G
HAP1
MAP3K14
SPAG9
SLC13A2
UNC119
TIAF1
ZNHIT3
EFTUD2
RPL23
NPEPPS
GOSR1
CCL4L1
GOSR2
NR1D1
TRAF4
KIAA0100
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
TOM1L1
GJC1
TOB1
PSME3
EIF1
NBR2
SLC35B1
CALCOCO2
RAMP2
HOXB13
VAT1
LEPREL4
HEXIM1
SPAG5
IGF2BP1
CCT6B
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
KAT7
NXPH3
SNF8
SYNRG
CASC3
IKZF3
ZNF652
SARM1
GPATCH8
KCNH4
FAM215A
PPY2
KRT23
TMEM98
POLDIP2
TBC1D29
ERAL1
AATF
SNORD4B
SNORD4A
SNORD42B
SNORD42A
TUBG2
TMEM97
NKIRAS2
CCDC56
GIT1
PSMC3IP
SNX11
TBX21
SOCS7
SOST
UTP18
RAPGEFL1
ABI3
COPZ2
MRPL27
PIPOX
ARL17A
CRLF3
SLC25A39
LUC7L3
HIGD1B
CDK12
KRT20
NLE1
FNDC8
MBTD1
CWC25
LINC00483
EPN3
LRRC37A4
SLFN12
PNPO
KLHL11
RHOT1
RSAD1
C17orf79
LRRC59
C17orf63
ADAP2
UTP6
GSDMB
CA10
ATXN7L3
PLXDC1
LYZL6
NUFIP2
TAOK1
ARHGAP23
PHF12
FKBP10
XYLT2
C17orf75
SPATA20
UBE2Z
WNK4
C17orf53
TMUB2
DHX58
MMP28
DHRS11
PRR15L
TEFM
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
FAM117A
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
TTC25
KRTAP4-12
RAB34
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
RNF135
MIEN1
MRPL45
VPS25
TMEM101
PRAC
RAB11FIP4
GHDC
KRTAP4-4
KIF2B
PPP1R9B
CORO6
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
SSH2
TP53I13
IFT20
LRRC46
SCRN2
AOC4
ANKRD40
ZNF830
SLFN11
RASL10B
G6PC3
ASB16
PGAP3
PIGS
HSPB9
ORMDL3
PLCD3
SLC46A1
TMEM106A
LRRC37B
OSBPL7
NT5C3L
ABHD15
TLCD1
RFFL
ZPBP2
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
FLJ40194
B4GALNT2
SPACA3
SGK494
SEZ6
ANKRD13B
C17orf57
MRPL10
GJD3
KRT222
KRT40
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
TMEM199
PROCA1
DHRS13
C17orf69
LOC147093
LRRC37BP1
WIPF2
KRT25
TMEM99
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
IMP5
KRT28
KRT24
ARHGAP27
ZNF385C
SAMD14
RDM1
GAS2L2
STH
STXBP4
LOC253962
TAC4
C17orf66
KIAA1267
C17orf105
FAM171A2
C17orf104
TTLL6
LOC284080
KRT18P55
NEK8
PIGW
C17orf78
LOC284100
CISD3
GSDMA
KRT42P
PTRF
KLHL10
C17orf65
MSL1
KRT27
SLFN14
FLJ43826
STAC2
CCL14-CCL15
KRT26
HOXB13-AS1
HILS1
EFCAB5
TMIGD1
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
ARL5C
KRT39
MYO18A
C17orf102
LOC400604
MGC57346
LOC404266
MIR10A
MIR144
MIR152
MIR193A
MIR196A1
TBC1D3B
TBC1D3C
CCL3L3
SUZ12P
LOC440434
GPR179
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451A
SNORA21
LOC644172
LOC644246
SEBOX
KRTAP4-11
MRPL45P2
TBC1D3G
NME1-NME2
SNORD7
MIR632
KRTAP4-8
KRTAP2-2
KRTAP9-1
NSFP1
FLJ45513
TBC1D3
TBC1D3H
LOC730755
SNORD124
MIR365B
LOC100128977
LOC100130148
LOC100130581
LOC100131347
KRTAP4-9
KRTAP4-7
LOC100133991
C17orf96
LOC100190938
MIR1203
MIR2117
MIR4315-2
MIR2909
MIR3185
MIR3184
MIR4315-1
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
SPAG5-AS1
LOC100506650
AA06
SLFN12L
RAD51L3-RFFL
MIR4523
MIR4728
MIR4726
MIR4734
MIR4724
MIR4733
MIR451B
MIR4732
MIR4723
MIR4727
MIR4725
RAB34

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

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

Genes
RBFOX1

Genes in Wide Peak

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

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

Genes
JAK2
MLLT3
NFIB
CD274
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
PLIN2
CDKN2A
CDKN2B
ELAVL2
MLANA
GLDC
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
INSL4
MTAP
PTPRD
RLN1
RLN2
RPS6
SH3GL2
SLC1A1
SNAPC3
TYRP1
MPDZ
CER1
RCL1
RRAGA
PSIP1
INSL6
KDM4C
SLC24A2
RANBP6
AK3
C9orf53
BNC2
HAUS6
CNTLN
KIAA1797
C9orf68
CDC37L1
DENND4C
C9orf46
KLHL9
KIAA1432
DMRTA1
C9orf82
ERMP1
PDCD1LG2
GLIS3-AS1
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
TTC39B
FAM154A
FREM1
KIAA2026
GLIS3
C9orf93
TUSC1
LURAP1L
IFNE
ZDHHC21
ACER2
LOC389705
FLJ41200
PTPLAD2
PPAPDC2
MIR101-2
MIR31
FLJ35282
MIR31HG
MIR491
SCARNA8
CDKN2B-AS1
C9orf146
MIR3152
LOC100506422
MIR4473
MIR4665
MIR4474

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q14.2.

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

Genes
CDK4
DDIT3
MDM2
NACA
HMGA2
WIF1
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
APOF
ATP2B1
ATP5B
AVPR1A
CDK2
CPM
CS
CSRP2
CYP27B1
DGKA
DCN
EPYC
DUSP6
ERBB3
B4GALNT1
GLI1
GNS
IFNG
INHBC
KCNC2
KIF5A
LRP1
LUM
LYZ
MARS
METTL1
KITLG
MIP
MYF5
MYF6
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
CNOT2
NTS
PA2G4
PAWR
PRIM1
PTPRB
PTPRR
RAB5B
RAP1B
RBMS2
RPL41
RPS26
TSPAN31
SHMT2
PMEL
SMARCC2
STAT2
STAT6
SUOX
SYT1
TAC3
TSPAN8
YEATS4
ALX1
DYRK2
PPFIA2
LGR5
RDH16
HSD17B6
GALNT4
LIN7A
TIMELESS
RASSF9
SLC16A7
ZBTB39
PAN2
USP15
TSFM
CTDSP2
RNF41
TMEM5
CNPY2
DCTN2
CCT2
AVIL
PTGES3
FRS2
OS9
GLIPR1
CPSF6
KERA
KRR1
BAZ2A
IRAK3
NXPH4
XPOT
GPR182
PHLDA1
R3HDM2
RAB21
MON2
TMEM194A
TBC1D30
ESYT1
ZDHHC17
GRIP1
LEMD3
MGAT4C
METTL21B
SNORD59A
GLS2
KCNMB4
CCDC59
TBK1
TRHDE
IL22
IL23A
TMBIM4
SLC6A15
TMEM19
SLC35E3
IL26
CAND1
MDM1
NDUFA4L2
NUP107
PPM1H
SRGAP1
ARHGAP9
IKZF4
TBC1D15
SLC26A10
OBFC2B
ACSS3
BBS10
PIP4K2C
CEP290
THAP2
INHBE
LRRIQ1
C12orf26
LLPH
CAPS2
ZC3H10
NAV3
C12orf29
XRCC6BP1
HELB
MARCH9
COQ10A
MBD6
OSBPL8
ARHGEF25
C12orf56
AGAP2
RAB3IP
SDR9C7
LRIG3
TPH2
MYL6B
GLIPR1L2
TSPAN19
BEST3
E2F7
C12orf66
TMTC2
TMTC3
C12orf50
DTX3
ZFC3H1
C12orf12
RPSAP52
STAC3
MSRB3
LOC256021
GLIPR1L1
POC1B
OTOGL
RASSF3
ANKRD52
SLC39A5
SPRYD4
LOC283392
C12orf61
DPY19L2
LOC338758
FAM19A2
PTPRQ
LRRC10
FLJ41278
MKRN9P
MIRLET7I
MIR26A2
C12orf37
ATXN7L3B
SNORD59B
MIR548C
MIR617
MIR618
LOC728084
MRS2P2
LOC100130776
MIR1252
MIR1279
MIR1228
SNORA70G
MIR548Z
MIR3913-2
MIR3913-1
LOC100506844
LOC100507250
LOC100507377
POC1B-GALNT4
MIR4699
MIR548AL

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
DUX4
hsa-mir-202
ADAM8
CYP2E1
ECHS1
INPP5A
UTF1
TUBGCP2
DUX2
VENTX
CALY
TTC40
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
C10orf91
PWWP2B
PAOX
C10orf125
LOC399829
SPRNP1
FRG2B
SPRN
MIR202
LOC619207
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
MIR3944

Genes in Wide Peak

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

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

Genes
IRF4
DEK
hsa-mir-548a-1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
ID4
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
NOL7
FAM8A1
TMEM14C
GFOD1
ELOVL2
CDKAL1
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
CCDC90A
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
MBOAT1
C6orf195
PIP5K1P1
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
RNF144B
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
NHLRC1
PSMG4
DKFZP686I15217
FLJ23152
C6orf201
ERVFRD-1
PPP1R3G
MIR548A1
HULC
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
LSAMP
LSAMP-AS3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q24.1.

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

Genes
ABL2
ELK4
MDM4
PBX1
TPR
SLC45A3
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
ADORA1
ALDH9A1
FASLG
ASTN1
SERPINC1
ATF3
ATP1B1
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CD247
CD34
CENPF
CHI3L1
CHIT1
CR1
CR1L
CR2
CSRP1
CTSE
CD55
DHX9
DPT
EIF2D
ELF3
EPRS
ESRRG
F5
F13B
FMO1
FMO2
FMO3
FMO4
FMOD
NR5A2
GLUL
GPR25
CFH
CFHR1
CFHR2
MR1
HLX
HSD11B1
IL10
IRF6
KCNH1
KCNK2
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LMX1A
MARK1
CD46
MGST3
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NEK2
NVL
CDK18
PDC
PFKFB2
PIGC
PIGR
PIK3C2B
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPP2R5A
PRELP
PROX1
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
RABIF
RBBP5
REN
RGS1
RGS2
RGS13
RGS16
RNASEL
RNF2
RNPEP
RXRG
XCL1
SELE
SELL
SELP
SNRPE
SOAT1
SRP9
TROVE2
AURKAPS1
XCL2
CNTN2
TGFB2
TLR5
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TRAF5
TNFSF4
UCK2
USH2A
SLC30A1
NPHS2
BTG2
DYRK3
PPFIA4
BLZF1
DEGS1
VAMP4
B3GALT2
CREG1
RAB7L1
TNFSF18
TAF1A
MPZL1
ANGPTL1
TBX19
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
RASAL2
SOX13
PRDX6
IKBKE
KIAA0040
CEP350
ZC3H11A
SMG7
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
ARPC5
PRG4
GPA33
STX6
BPNT1
TIMM17A
LRRN2
SLC19A2
IVNS1ABP
KDM5B
CFHR4
CFHR3
OCLM
IL24
DUSP10
PLEKHA6
KIFAP3
KIF21B
NMNAT2
NFASC
GLT25D2
RGL1
PRRC2C
FBXO28
CAMSAP2
SRGAP2
CRB1
GPR161
ZNF281
PHLDA3
DSTYK
RAB3GAP2
LMOD1
BRP44
INTS7
NSL1
DNM3
TOR1AIP1
OPTC
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
RNU5F-1
DIEXF
CACYBP
KLHL20
FLVCR1
UBE2T
CNIH4
NME7
NENF
IL19
G0S2
IL20
RRP15
GLRX2
ADIPOR1
KCTD3
IER5
UCHL5
C1orf9
DTL
METTL13
CYB5R1
TMCO1
SWT1
LAX1
C1orf27
MARC2
SUSD4
RALGPS2
GPATCH2
DARS2
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
IARS2
IPO9
C1orf112
HHAT
ENAH
RCOR3
C1orf106
ADCY10
DCAF6
SERTAD4
SMYD2
LHX9
SCYL3
CAMK1G
POGK
KIAA1614
FAM5B
C1orf114
KLHL12
LGR6
GAS5
PAPPA2
TNN
MRPS14
TOR3A
RFWD2
RGS18
NUCKS1
MARC1
AIDA
C1orf116
MGC4473
CDC73
C1orf115
HHIPL2
VASH2
C1orf129
WDR26
EDEM3
TRAF3IP3
NPL
CFHR5
C1orf21
SHCBP1L
TRMT1L
NUAK2
DDX59
NUF2
RASSF5
HMCN1
FCAMR
C1orf49
ACBD6
ZBTB37
LINC00260
LINC00467
ANKRD36BP1
PPP1R15B
MAEL
DISP1
RGS8
NAV1
SEC16B
LHX4
ANGEL2
IGFN1
CENPL
DUSP27
RCSD1
METTL18
GORAB
C1orf105
TMEM183A
LEMD1
SLC26A9
FMO9P
TSEN15
FAM129A
TADA1
AXDND1
LYPLAL1
ATP6V1G3
DNAH14
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
SPATA17
TATDN3
NEK7
C1orf74
BROX
LOC148696
LOC148709
PTPRVP
FAM163A
MFSD4
PM20D1
RC3H1
CNIH3
METTL11B
FAM78B
SHISA4
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
C1orf65
FLJ23867
TMEM9
SLC41A1
SYT14
ASPM
TIPRL
SLC9A11
LINC00303
LOC284576
LOC284578
LOC284581
LOC284648
DKFZP564C196
LOC284688
ANKRD45
FAM5C
FAM58BP
RD3
KCNT2
RGSL1
ZBTB41
SFT2D2
MIA3
RPS10P7
ILDR2
FMO6P
LINC00272
C1orf53
TMEM81
CAPN8
LOC400794
C1orf220
C1orf140
FAM177B
LOC401980
APOBEC4
MIR181B1
MIR194-1
MIR199A2
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
RGS21
LRRC52
LOC440700
LOC440704
C1orf186
MIR135B
C1orf98
C1orf133
MIR488
SNORD74
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
TMEM183B
SCARNA3
SNORA36B
SNORA77
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
MIR557
LOC728463
FAM72A
LOC730102
LOC730159
LOC730227
MIR921
LOC100131234
GM140
LOC100288079
MIR1231
MIR1278
MIR1295A
MIR548F1
MIR664
LOC100302401
MIR320B2
ZBED6
MIR3119-1
MIR3120
MIR4260
MIR3122
MIR3119-2
MIR3121
MIR3658
LOC100505795
PROX1-AS1
LOC100505918
LOC100506023
LOC100506046
KDM5B-AS1
LOC100527964
MIR4424
MIR4735
MIR4742
DNM3OS
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

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

Genes
BIRC3
ATM
CCND1
CARS
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
HRAS
LMO1
LMO2
MEN1
MLL
NUMA1
NUP98
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
hsa-mir-3163
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-3162
hsa-mir-130a
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ACAT1
ACP2
ACRV1
ACTN3
ADM
ADRBK1
AP2A2
APLNR
ALDH3B1
ALDH3B2
AMPD3
APBB1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
RHOG
ARHGAP1
PHOX2A
ARL2
ARNTL
ARRB1
ART1
ASCL2
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CCKBR
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
TPP1
CLNS1A
CNGA4
CNTF
COPB1
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSD
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GTF2H1
GUCY1A2
H2AFX
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HMBS
SLC29A2
HPX
HSPA8
HSPB2
DNAJC4
HTR3A
IGF2
IGHMBP2
IL10RA
IL18
ILK
INCENP
INS
INPPL1
IRF7
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KCNQ1
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LSP1
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MUC2
MUC6
MYBPC3
MYO7A
MYOD1
NAP1L4
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
NUCB2
OMP
OPCML
SLC22A18
SLC22A18AS
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PDE3B
PGA5
PGR
PIK3C2A
PLCB3
POLR2G
POLR2L
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PSMA1
PSMC3
PSMD13
PTH
PTPRCAP
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
RNH1
SNORD15A
ROM1
MRPL23
RPL27A
RPLP2
RPS3
RPS6KB2
RPS13
RPS25
RRM1
SAA1
SAA2
SAA3P
SAA4
SC5DL
SCN2B
SCN4B
SCT
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SMPD1
SORL1
SPI1
SPTBN2
SRPR
TRIM21
SSRP1
ST5
ST14
STIM1
STX3
STX5
ABCC8
TAGLN
TAF10
TALDO1
TCN1
TEAD1
TECTA
TH
THRSP
THY1
TSPAN4
TM7SF2
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TRPC6
TSG101
PHLDA2
TUB
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WEE1
WNT11
SF1
ZFPL1
ZNF143
ZBTB16
ZNF195
ZNF202
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIBP2
PPFIA1
SLC43A1
IFITM1
DGKZ
CHST1
BARX2
API5
MADD
OR7E2P
OR6A2
DCHS1
EIF3F
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
BRSK2
AIP
SYT7
SART1
USP2
SLC6A5
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MED17
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
MICAL2
CTR9
CEP57
ARHGAP32
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
TRIM66
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
TSPAN32
TSSC4
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
MRVI1
TRIM22
PRG3
IFITM3
YAP1
SPON1
RBM14
CDC42EP2
EIF3M
NXF1
DEAF1
KAT5
HYOU1
IPO7
SSSCA1
HTATIP2
IFITM2
DRAP1
TRIM3
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
OR7E14P
OR7E12P
NEU3
ME3
GPR83
LYVE1
YIF1A
SRSF8
EHD1
C11orf58
STIP1
CLP1
KCNQ1OT1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
PKP3
HPS5
PTGDR2
SLCO2B1
RRAS2
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
SWAP70
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
DENND5A
NUP160
NCAPD3
FNBP4
RRP8
SIK3
SIRT3
CLCF1
OR52A1
VSIG2
BACE1
FAM89B
SNHG1
ARFIP2
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
C11orf41
PRDX5
POU2F3
ABTB2
BRMS1
C11orf20
CHRDL2
PAMR1
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
PPP1R14B
OR8G2
OR8B8
OR8G1
OR10A3
FXC1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
ACAD8
B3GAT1
DKK3
RBMXL2
RAB30
PGAP2
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
COMMD9
DDX25
C11orf21
PACSIN3
TRPM5
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
UBQLN3
KCNK4
RNF141
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
IGF2-AS1
TMEM216
BET1L
CEND1
CHCHD8
SLC15A3
PHF21A
MS4A4A
WT1-AS
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
CYB5R2
RSF1
SPA17
FXYD6
C11orf24
TRIM34
CDHR5
CNTN5
SIAE
TOLLIP
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39A
TRIM44
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
USP47
VPS37C
ANO1
TRIM68
NADSYN1
FAM86C1
C11orf57
NAT10
CCDC87
PPP6R3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
PIDD
ELMOD1
KCNQ1DN
SOX6
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
PARVA
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
MMP26
TMPRSS4
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
GPR137
IFT46
C11orf75
C11orf30
PRDM10
PRDM11
CABP4
CHRNA10
SLC17A6
TRIM49
PNPLA2
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
CARNS1
SYT13
USP28
PHRF1
LRRC4C
SCUBE2
POLD4
KRTAP5-8
PLEKHB1
MS4A7
ZBED5
CREBZF
CARD18
SIGIRR
CCDC90B
CCDC81
AASDHPPT
ALX4
RIC8A
MRPL17
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
EPS8L2
KLC2
TUT1
MRPL11
TMEM135
STK33
KCTD14
C11orf95
CHID1
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
OR51G1
OR51B4
OR51B2
OR52N1
FAM118B
RIC3
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
E2F8
SLC25A22
CCDC82
ALG9
ZNF408
CLMP
NAA40
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
ATHL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
PTDSS2
MOB2
GDPD5
CLPB
UNC93B1
SBF2
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
FAM160A2
RNASEH2C
FAR1
TMEM126A
DCUN1D5
BTBD10
EIF1AD
NUDT22
ARFGAP2
KIAA1826
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
SPRYD5
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
MICALCL
RELT
UBASH3B
C11orf70
LGALS12
TRIM5
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
NAV2
ATG16L2
GLB1L2
SYT8
TSPAN18
ESAM
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
PRKCDBP
VPS26B
GLB1L3
CDCA5
RPLP0P2
SAAL1
ODF3
SLC22A9
SNORD15B
TIRAP
CARD16
OSBPL5
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
LRRC56
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRE
MRGPRF
ART5
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
SLC36A4
FAT3
TRIM64
TMEM45B
CYP2R1
DBX1
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
LOC120824
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
XRRA1
UBQLNL
MUC15
LOC143666
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
C11orf42
GPHA2
ADAMTS15
NLRP6
NS3BP
B3GNT6
METTL15
MPZL3
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
MRPL21
TPCN2
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
PPP1R32
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
LOC254100
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
TMEM151A
OR51F1
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
KRT8P41
LOC283104
CSNK2A1P
OR51V1
LOC283116
H19
C11orf85
SLC25A45
NEAT1
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
OR9G4
LOC283194
LINC00301
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
EFCAB4A
TMEM80
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
OR10A2
OVCH2
TBX10
PDDC1
C11orf34
RTN4RL2
GALNTL4
B7H6
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
KRTAP5-10
SLC22A25
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
SLC22A10
SPDYC
LIPT2
VSTM5
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
NAV2-AS4
HNRNPKP3
FAM180B
PCNXL3
FLJ42102
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
OR4C45
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR210
MIR34B
MIR34C
DDI1
BLID
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
LOC440040
LOC440041
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
LINC00167
LOC441601
OR5B3
MIR326
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
MS4A13
OR8U8
OR9G9
SCARNA9
MIR483
SNORA3
SNORA52
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
BTBD18
LOC643733
PGA3
PGA4
LOC643923
LOC644656
CLDN25
RASSF10
FAM86C2P
TRIM64C
LOC646813
LOC649133
RPL23AP64
LOC650368
LOC653486
SNORA8
SNORA1
SNORA18
SNORA23
SNORA40
SNORA45
SNORA54
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
SNORD97
MIR610
MIR611
MIR612
INS-IGF2
MUC5B
LOC729013
TRIM49L1
LOC729799
METTL12
C11orf83
MIR675
MIR708
LOC100126784
LOC100128239
LOC100129216
MRVI1-AS1
LOC100130348
LOC100130987
C11orf91
LOC100132078
FAM99B
LOC100133161
LOC100133315
MRPL23-AS1
PATE3
LOC100288077
LOC100288346
MIR1304
MIR1908
MIR1237
MIR548K
MIR670
SNORA70E
BACE1-AS
MIR4300
MIR3160-2
MIR3160-1
MIR4301
MIR3162
MIR3167
MIR3165
MIR1260B
MIR4298
MIR4299
MTRNR2L8
LOC100499227
MIR3654
MIR3920
MIR3656
MIR3664
MIR3680-1
LOC100500938
MIR210HG
LOC100506233
LOC100506305
LOC100506368
LOC100506540
DCDC5
CASP12
LOC100507050
LOC100507205
LOC100507300
LOC100507392
LOC100507401
RBM14-RBM4
LOC100526771
TMX2-CTNND1
SAA2-SAA4
ARL2-SNX15
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
HNRNPUL2-BSCL2
MIR4486
MIR4697
MIR4686
MIR4490
MIR4485
MIR4489
MIR4690
MIR3973
MIR4493
MIR4491
MIR4688
MIR4492
MIR4696
MIR4691
MIR4692
MIR4694
MIR1343
MIR4687
MIR4693
MIR4488
LOC100652768

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
TNFRSF17
CBFA2T3
CBFB
CDH1
CDH11
CREBBP
CYLD
ERCC4
FANCA
FUS
MAF
CIITA
MYH11
TSC2
SOCS1
HERPUD1
IL21R
PALB2
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
hsa-mir-762
hsa-mir-548w
hsa-mir-3179-3
hsa-mir-3180-2
hsa-mir-484
hsa-mir-1972-1
hsa-mir-3180-1
hsa-mir-365-1
hsa-mir-548h-2
hsa-mir-3178
hsa-mir-940
hsa-mir-1225
hsa-mir-3177
hsa-mir-662
hsa-mir-3176
AARS
ABAT
ABCA3
ADCY7
ADCY9
AP1G1
AFG3L1P
AGRP
ALDOA
AMFR
AQP8
APRT
ABCC6
ARHGDIG
ZFHX3
ATP2A1
ATP6V0C
BBS2
C16orf3
CA5A
CA7
CALB2
CBLN1
CCNF
CD19
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CDR2
CES1
CETP
CLCN7
CLN3
CNGB1
COX4I1
COX6A2
CRYM
CSNK2A2
CTF1
CTRB1
CTRL
CYBA
ECI1
DHODH
NQO1
SEPT1
DNASE1
DNASE1L2
DYNC1LI2
DPEP1
E2F4
E4F1
EMP2
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GFER
GLG1
GNAO1
GOT2
GP2
GRIN2A
GSPT1
GTF3C1
HAGH
HAS3
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
IGFALS
IL4R
ITGAD
ITGAL
ITGAM
ITGAX
KARS
KIFC3
KIF22
LCAT
MAZ
MC1R
CHST6
MEFV
MMP2
MMP15
MPG
ABCC1
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
MVD
NUBP1
NDUFAB1
NDUFB10
NFATC3
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PARN
CHMP1A
PDPK1
PHKB
PHKG2
PKD1
PLCG2
PLK1
PMM2
POLR2C
PPL
PPP4C
PRKCB
MAPK3
PRM1
PRM2
PRSS8
PSKH1
PSMB10
PSMD7
RBBP6
RBL2
RPL3L
RPL13
RPS2
RPS15A
RRAD
ACSM3
SALL1
SCNN1B
SCNN1G
SRL
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC5A2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SOLH
SPG7
SPN
SSTR5
SULT1A2
STX4
SULT1A1
SULT1A3
TAT
TBX6
TCEB2
TERF2
TFAP4
TGFB1I1
TK2
TNP2
TPSAB1
TUFM
UBE2I
UMOD
UQCRC2
ZNF19
ZNF23
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
ZP2
USP7
NPRL3
GAN
SLC7A5
SNN
AXIN1
PLA2G10
DOC2A
HIRIP3
CDK10
EIF3C
TRADD
MBTPS1
RGS11
CES2
NAE1
CACNA1H
BAIAP3
NOL3
TAF1C
RHBDL1
SLC7A6
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
USP10
ATP6V0D1
SYNGR3
IL32
BCL7C
NPIP
GPR56
TAOK2
SLC9A3R2
LITAF
BCAR1
C16orf7
KIAA0430
N4BP1
NUP93
SEC14L5
ZNF646
RAB11FIP3
CCP110
SETD1A
IFT140
KIAA0513
PIEZO1
DHX38
IST1
RNF40
TELO2
ATP2C2
HS3ST4
HS3ST2
MVP
NUBP2
ZNF263
TRAP1
CLEC3A
CHST4
MPHOSPH6
NUTF2
COQ7
MSLN
IGSF6
IRX5
STUB1
DNAJA2
BCKDK
KATNB1
ZNF267
COX4NB
CACNG3
TUBB3
CD2BP2
CDIPT
CFDP1
MRPL28
ERN2
TBL3
CTCF
NFAT5
SRCAP
RNPS1
PRSS21
NUDT21
WWP2
PRDM7
CORO1A
DDX19B
ATXN2L
GABARAPL2
MON1B
SEPHS2
TCF25
CNOT1
PHLPP2
PDXDC1
SMG1
CLUAP1
GGA2
ZNF423
NPIPL3
MAPK8IP3
ZCCHC14
KIAA0182
ARL6IP1
XPO6
KIAA0556
CLEC16A
MGRN1
ATMIN
RPGRIP1L
ZNF629
COTL1
MLYCD
NOMO1
TPSD1
SF3B3
QPRT
CES3
SRRM2
ADAT1
CHST5
ARL2BP
CARHSP1
ORC6
EDC4
PLA2G15
TP53TG3
TPSG1
RAB26
COG4
TMEM186
PLEKHG4
SH2B1
TBC1D10B
ZNF500
DECR2
DKFZP434H168
RSL1D1
OR1F2P
LRRC29
SEZ6L2
NUPR1
SNORA64
SNORD60
LAT
CPNE7
VPS4A
IL17C
TOX3
TNRC6A
DEXI
NOB1
C16orf72
ZC3H7A
CCDC113
TMEM208
C16orf80
PYCARD
FHOD1
BRD7
ANKRD11
ZDHHC1
UBN1
MYLPF
EEF2K
OSGIN1
C16orf5
SOX8
PARD6A
AMDHD2
PAM16
TXNDC11
PLLP
METTL9
NAGPA
CKLF
BFAR
AHSP
TNFRSF12A
ZNF771
NIP7
LCMT1
GDE1
FAM96B
GINS2
TPPP3
TRAPPC2L
GPRC5B
CES1P1
POLR3K
SEPX1
WWOX
SYT17
GNG13
BCMO1
TERF2IP
KCTD5
PRMT7
NECAB2
FBXL19
RRN3
RBFOX1
KLHDC4
HYDIN
NDE1
DEF8
DUS2L
CHTF8
ZNF434
LPCAT2
TXNL4B
BANP
HCFC1R1
ACSM5
HEATR3
PDPR
ARHGAP17
RFWD3
SLC38A7
OGFOD1
LRRC36
DDX19A
CPPED1
FBXL8
SMPD3
ZNF821
DNAH3
THUMPD1
ZDHHC7
LUC7L
VAC14
DOK4
POLR3E
VPS35
FTSJD1
DDX28
TSNAXIP1
CENPN
APOBR
ALG1
UBFD1
C16orf61
COQ9
CIAPIN1
C16orf62
TMEM159
LYRM1
THAP11
JPH3
NMRAL1
TBC1D24
USP31
MKL2
CASKIN1
PDP2
ZNF319
CRAMP1L
RANBP10
VAT1L
KIAA1609
RAB40C
WFDC1
PRM3
TMEM8A
CHTF18
CHP2
PRSS22
NOD2
XYLT1
PDF
DPEP2
DPEP3
MLST8
PAPD5
RHBDF1
FBRS
MMP25
AKTIP
NARFL
LINC00235
TPSB2
HS3ST6
PDIA2
UNKL
LINC00254
C16orf58
MTHFSD
GINS3
LMF1
NDRG4
ACD
ZNF747
FAM173A
MRPS34
PRR14
VKORC1
METRN
DBNDD1
SLX1B
FTO
DCTPP1
METTL22
FA2H
GDPD3
IRX6
IRX3
THOC6
KREMEN2
C16orf53
FAM65A
TMEM231
CORO7
TMCO7
SNRNP25
ROGDI
C16orf57
TMEM204
ZNF768
WDR59
ZNF668
ELMO3
KLHL36
FBXO31
ARMC5
SHCBP1
JMJD5
TMC5
RABEP2
NAA60
TMC7
SETD6
ESRP2
FAM192A
ATF7IP2
CENPT
C16orf59
CHD9
C16orf70
HSD3B7
CYB5B
CMIP
ITFG1
GFOD2
CDT1
MAP1LC3B
LOC81691
NETO2
MGC3771
FAHD1
SLC7A5P1
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
YPEL3
FAM57B
LONP2
PRSS27
SPNS1
ITFG3
C16orf48
SLC7A6OS
KAT8
NLRC5
WDR24
CCDC135
TRAF7
FLYWCH1
HAGHL
CAPNS2
NUDT16L1
C16orf13
FAM195A
COG8
SLX4
SPIRE2
DCTN5
MT4
GNPTG
ZNF469
GLYR1
GLIS2
GPT2
B3GNT9
ZSCAN10
NFATC2IP
CIRH1A
ZNRF1
ABCC11
NKD1
CNTNAP4
C16orf45
RHOT2
RSPRY1
C16orf93
ZNF598
HN1L
SPSB3
TIGD7
MYLK3
MARVELD3
COG7
SNX29
MTSS1L
ZNF764
CENPBD1
ZNF276
CCDC102A
KCNG4
ORAI3
SDR42E1
ABCC12
PRRT2
ERI2
STX1B
CCDC101
RPUSD1
CMTM1
PKD1L2
FLYWCH2
VASN
ZNF689
SLC5A11
C16orf42
RNF166
RMI2
ACSM1
WFIKKN1
EXOSC6
C16orf46
NTAN1
FOPNL
DNAAF1
ACSM2A
DCUN1D3
NRN1L
CMTM3
C16orf78
SPATA2L
C16orf55
NOXO1
CCDC78
ANKRD26P1
IQCK
ZG16B
PRSS30P
PAQR4
ZC3H18
GPR139
CDYL2
ANKS3
FAM100A
SEPT12
ZNF720
TMEM219
EARS2
SNX20
TMEM170A
SLC38A8
VWA3A
OTOA
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
TEKT5
RNF151
C16orf11
FBXL16
LOC146336
C16orf92
GSG1L
SLC22A31
IL34
ZNF597
CCDC64B
TMED6
LOC146481
FLJ30679
LOC146513
ZNF785
ZNF688
PRSS36
C16orf89
C16orf71
ZFPM1
ADAD2
ITPRIPL2
C16orf82
ZFP1
ADAMTS18
FAM86A
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
WDR90
EME2
NLRC3
NSMCE1
ZNF48
PDILT
CPNE2
GPR114
PRSS54
CES5A
GPR97
IL27
KCTD13
ASPHD1
C16orf73
MPV17L
PDZD9
CNEP1R1
ANKS4B
PRSS33
PYDC1
NOMO2
CCDC79
CES4A
EXOC3L1
LOC283856
LINC00304
LOC283867
NPW
C16orf79
PGP
LINC00514
FLJ39639
LOC283888
C16orf54
INO80E
HTA
LOC283914
LOC283922
NUDT7
FBXL19-AS1
ZNF843
NHLRC4
C16orf91
TMEM114
PDXDC2P
CLEC18C
MT1DP
SNAI3
PKD1P1
PRSS53
JMJD8
FAM92B
C16orf96
ZKSCAN2
ATXN1L
PKD1L3
ACSM2B
CLEC18A
CTU2
PRSS41
TEPP
SLC6A10P
SLC7A5P2
PRR25
SBK1
LOC388242
C16orf87
LOC388276
C16orf86
C1QTNF8
PTX4
LOC390705
CES1P2
PABPN1L
BCAR4
C16orf88
CRYM-AS1
FLJ21408
FLJ26245
LOC400548
LOC400550
LOC400558
MSLNL
C16orf74
MIR138-2
MIR140
NOMO3
LOC440335
SNX29P2
LOC440354
LOC440356
CSDAP1
HERC2P4
CTRB2
MIR328
SULT1A4
TRIM72
CLEC18B
SLX1A
BOLA2
LOC554206
SNORA10
MIR193B
LOC595101
SNORD68
UBE2MP1
LOC606724
LOC613037
LOC613038
MIR484
LOC641298
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
FLJ42627
CCDC154
C16orf90
LINC00273
ABCA17P
LOC652276
ABCC6P1
KIAA0895L
RRN3P2
TP53TG3C
LOC653786
ZG16
BOLA2B
SNORA30
SNORA46
SNORA50
SNORA78
SNORD71
SNORD111
MIR548D2
MIR662
LOC727710
EIF3CL
LOC729264
TP53TG3B
LOC729513
SHISA9
ABCC6P2
RRN3P1
C16orf52
LOC732275
SNHG9
CEMP1
FAM18A
SNORD111B
MIR940
MIR365A
LOC100128788
LOC100128881
LOC100129617
LOC100130015
LOC100130700
LOC100130894
SYCE1L
RRN3P3
LOC100132247
KIAA0664L3
LOC100134368
MIR1225
LOC100190986
LOC100271836
DDX11L10
LOC100287036
LOC100289092
MIR1538
MIR1972-1
MIR1910
MIR762
SNORA70D
MIR3180-3
MIR3182
MIR3180-1
MIR3179-2
MIR548X
MIR1972-2
MIR3180-2
MIR3179-1
MIR3178
MIR3179-3
MIR3177
MIR3176
MTRNR2L4
MIR3677
MIR3180-4
MIR3935
MIR548AA2
MIR3180-5
LOC100505619
LOC100505865
LOC100506083
LOC100506172
C16orf95
LOC100506655
ERVK13-1
LOC100507501
LOC100507577
LOC100507589
SLX1A-SULT1A3
SLX1B-SULT1A4
CORO7-PAM16
CKLF-CMTM1
MIR4720
MIR4722
MIR4719
MIR4718
MIR4519
MIR4717
MIR4721
MIR4516
MIR548AE2
MIR4518
MIR4517
SNX29P1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 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 | 0.00 | -3.35 | 1 | 0.32 | 3.39 | 0.00462
1q | 1955 | 0.08 | -2.13 | 1 | 0.22 | 0.73 | 0.999
2p | 924 | 0.11 | -2.85 | 1 | 0.16 | -1.96 | 0.999
2q | 1556 | 0.07 | -2.81 | 1 | 0.14 | -1.59 | 0.999
3p | 1062 | 0.15 | -1.85 | 1 | 0.24 | -0.285 | 0.999
3q | 1139 | 0.18 | -1.11 | 1 | 0.26 | 0.238 | 0.999
4p | 489 | 0.39 | 1.86 | 0.0734 | 0.22 | -1.17 | 0.999
4q | 1049 | 0.38 | 2.28 | 0.028 | 0.25 | -0.099 | 0.999
5p | 270 | 0.70 | 7.05 | 5.16e-12 | 0.33 | 0.337 | 0.999
5q | 1427 | 0.68 | 9.07 | 0 | 0.27 | 0.546 | 0.999
6p | 1173 | 0.21 | -0.605 | 1 | 0.23 | -0.154 | 0.999
6q | 839 | 0.22 | -0.781 | 1 | 0.22 | -0.781 | 0.999
7p | 641 | 0.52 | 4.64 | 5.69e-06 | 0.05 | -3.12 | 0.999
7q | 1277 | 0.53 | 5.91 | 8.42e-09 | 0.08 | -2.27 | 0.999
8p | 580 | 0.42 | 2.54 | 0.015 | 0.22 | -0.918 | 0.999
8q | 859 | 0.46 | 3.76 | 0.000245 | 0.18 | -1.32 | 0.999
9p | 422 | 0.22 | -1.32 | 1 | 0.27 | -0.507 | 0.999
9q | 1113 | 0.26 | 0.272 | 0.714 | 0.14 | -1.98 | 0.999
10p | 409 | 0.31 | 0.323 | 0.711 | 0.18 | -1.92 | 0.999
10q | 1268 | 0.29 | 1.05 | 0.308 | 0.14 | -1.7 | 0.999
11p | 862 | 0.03 | -4.01 | 1 | 0.24 | -0.473 | 0.999
11q | 1515 | 0.05 | -3.16 | 1 | 0.23 | 0.224 | 0.999
12p | 575 | 0.71 | 8.12 | 1.78e-15 | 0.16 | -1.37 | 0.999
12q | 1447 | 0.72 | 10.2 | 0 | 0.12 | -1.16 | 0.999
13q | 654 | 0.10 | -2.82 | 1 | 0.38 | 1.83 | 0.338
14q | 1341 | 0.25 | 0.433 | 0.665 | 0.23 | -0.0276 | 0.999
15q | 1355 | 0.16 | -1.29 | 1 | 0.22 | -0.12 | 0.999
16p | 872 | 0.56 | 5.58 | 5.37e-08 | 0.18 | -1.11 | 0.999
16q | 702 | 0.56 | 5.33 | 1.81e-07 | 0.14 | -1.91 | 0.999
17p | 683 | 0.06 | -3.63 | 1 | 0.31 | 0.66 | 0.999
17q | 1592 | 0.05 | -3.01 | 1 | 0.26 | 0.905 | 0.999
18p | 143 | 0.04 | -4.06 | 1 | 0.39 | 1.36 | 0.695
18q | 446 | 0.02 | -4.24 | 1 | 0.36 | 1.2 | 0.773
19p | 995 | 0.63 | 7.39 | 4.99e-13 | 0.07 | -2.37 | 0.999
19q | 1709 | 0.59 | 8.17 | 1.11e-15 | 0.06 | -2.06 | 0.999
20p | 355 | 0.53 | 4.19 | 4.25e-05 | 0.17 | -1.71 | 0.999
20q | 753 | 0.55 | 5.35 | 1.71e-07 | 0.06 | -2.91 | 0.999
21q | 509 | 0.36 | 1.35 | 0.198 | 0.21 | -1.3 | 0.999
22q | 921 | 0.05 | -2.91 | 1 | 0.52 | 5.13 | 5.71e-06
Xq | 1312 | 0.69 | 8.23 | 1.11e-15 | 0.51 | 4.04 | 0.000543

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/ACC-TP/4391549/GDAC_MergeDataFiles_4305776/ACC-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 77 Input Tumor Samples.

Tumor Sample Names
TCGA-OR-A5J1-01A-11D-A29H-01
TCGA-OR-A5J2-01A-11D-A29H-01
TCGA-OR-A5J3-01A-11D-A29H-01
TCGA-OR-A5J4-01A-11D-A29H-01
TCGA-OR-A5J5-01A-11D-A29H-01
TCGA-OR-A5J6-01A-31D-A29H-01
TCGA-OR-A5J7-01A-11D-A29H-01
TCGA-OR-A5J8-01A-11D-A29H-01
TCGA-OR-A5J9-01A-11D-A29H-01
TCGA-OR-A5JA-01A-11D-A29H-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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