Thyroid Adenocarcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16a (cga svn revision 43808).

Summary

There were 330 tumor samples used in this analysis: 18 significant arm-level results, 0 significant focal amplifications, and 17 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.

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 1. Get Full Table Deletions Table - 17 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
--- | --- | --- | --- | ---
10q23.31 | 0.0019105 | 0.0019105 | chr10:87353899-93631303 | 62
Xq22.3 | 0.0019105 | 0.0019105 | chrX:107872289-108781115 | 2
22q13.31 | 0.024988 | 0.0225 | chr22:47571204-48018269 | 1
8q24.22 | 0.031596 | 0.031596 | chr8:56679786-139512990 | 371
13q14.2 | 0.040453 | 0.03963 | chr13:23346769-95061168 | 280
17p13.1 | 0.039414 | 0.03963 | chr17:1-9793321 | 266
22q13.2 | 0.044923 | 0.044126 | chr22:43577625-43814456 | 1
1q24.2 | 0.051746 | 0.050936 | chr1:168044896-168149500 | 1
2q37.1 | 0.048556 | 0.050936 | chr2:212238542-243199373 | 288
6q22.31 | 0.22021 | 0.21954 | chr6:123955968-125232805 | 1
9p21.3 | 0.22566 | 0.22566 | chr9:8310705-26118857 | 68
16q23.3 | 0.020668 | 0.22566 | chr16:78129058-90354753 | 122
16p13.3 | 0.22934 | 0.22566 | chr16:5129162-8624050 | 3
19q12 | 0.23298 | 0.2347 | chr19:30202912-30414571 | 1
7q22.3 | 0.23958 | 0.23958 | chr7:66576035-116850979 | 384
9q22.32 | 0.23668 | 0.23958 | chr9:97571319-140735289 | 531
2p22.3 | 0.25762 | 0.25214 | chr2:1-243199373 | 1516
16q22.1 | 0.13711 | 0.25214 | chr16:1-90354753 | 967

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.31.

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

Genes
BMPR1A
PTEN
hsa-mir-107
hsa-mir-346
ACTA2
FAS
GLUD1
GRID1
HTR7
IFIT2
IFIT1
IFIT3
LIPA
PPP1R3C
SNCG
LIPF
CH25H
PAPSS2
MINPP1
KIF20B
RPP30
C10orf116
LDB3
WAPAL
IFIT5
ANKRD1
PANK1
FAM35A
RNLS
STAMBPL1
MMRN2
TNKS2
PCGF5
ATAD1
OPN4
ANKRD22
NUDT9P1
AGAP11
LIPJ
CFL1P1
HECTD2
FLJ37201
LIPM
SLC16A12
MIR107
LOC439994
IFIT1B
MIR346
FAM25A
LIPK
LIPN
LOC643529
FAM22A
FAM22D
LOC728190
LOC728218
KLLN
LOC100188947
FAS-AS1
MIR4679-1
MIR4679-2
MIR4678

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
GUCY2F
IRS4

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q24.22.

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

Genes
COX6C
EXT1
MYC
PLAG1
NCOA2
CHCHD7
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
hsa-mir-1273
hsa-mir-875
hsa-mir-3150
hsa-mir-3149
hsa-mir-2052
hsa-mir-124-2
ADCY8
ANGPT1
ANXA13
ASPH
ATP6V1C1
OSGIN2
CA1
CA2
CA3
CA8
CALB1
RUNX1T1
CDH17
CRH
CYP7A1
DECR1
DPYS
E2F5
EYA1
FABP4
FABP5
GEM
HAS2
HNF4G
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LYN
MATN2
MMP16
MOS
MYBL1
NBN
NDUFB9
NOV
ODF1
TNFRSF11B
PDE7A
ENPP2
PENK
PMP2
POLR2K
POU5F1B
PKIA
PVT1
PEX2
RAB2A
RAD21
RPL7
RPL30
RPS20
SDC2
SDCBP
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TTPA
COL14A1
UQCRB
YWHAZ
FZD6
NSMAF
EIF3H
RIPK2
GGH
WISP1
CPNE3
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
TTC35
RIMS2
TOX
MTSS1
PTDSS1
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
ARFGEF1
COLEC10
KHDRBS3
POP1
COPS5
WWP1
STMN2
RNF139
ZHX1
ZHX2
EFR3A
RRS1
SULF1
ZFPM2
HEY1
TRAM1
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
C8orf71
RGS22
PTTG3P
SNORA72
SNORD54
PABPC1
KCNV1
STAU2
MTBP
BHLHE22
MRPS28
MRPL13
ATAD2
ASAP1-IT1
LRP12
RRM2B
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
FAM82B
ZNF706
UBR5
FAM49B
AZIN1
OTUD6B
GDAP1
PDP1
CNGB3
ESRP1
IMPAD1
TMEM70
TRMT12
OXR1
WDYHV1
ARMC1
UBE2W
LAPTM4B
C8orf39
TMEM55A
CHD7
SYBU
INTS8
PAG1
GSDMC
C8orf44
JPH1
ENY2
CPA6
ZFAT
PRDM14
SNX16
NECAB1
DEPTOR
ZBTB10
DSCC1
DERL1
PLEKHF2
ZFAND1
ZFHX4
NIPAL2
CSPP1
BAALC
GRHL2
VCPIP1
PREX2
SLC25A32
TM7SF4
SLCO5A1
CRISPLD1
TATDN1
NACAP1
NCALD
UTP23
TRIM55
C8orf76
NUDCD1
FAM83A
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
TMEM67
MTDH
CHMP4C
PKHD1L1
WDR67
HPYR1
TP53INP1
TGS1
MAL2
CSMD3
FBXO32
SLC26A7
CTHRC1
OSR2
C8orf34
ZNF572
FAM92A1
C8orf38
ABRA
TMEM71
ADHFE1
UBXN2B
DCAF4L2
RALYL
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
TMEM74
FAM91A1
C8orf45
CLVS1
C8orf84
CNBD1
SLC30A8
SNX31
TMEM64
SDR16C5
C8orf47
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NSMCE2
LOC286094
C8orf83
DPY19L4
FBXO43
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
KLHL38
RSPO2
SLC10A5
CA13
XKR9
LOC389676
RBM12B
LOC392232
GDF6
LOC401463
C8orf59
SAMD12
MIR124-2
MIR30B
MIR30D
FER1L6-AS1
FLJ39080
FLJ46284
FLJ42969
C8orf85
LINC00251
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
ZNF704
C8orf69
SNHG6
SNORD87
LINC00535
UG0898H09
RAD21-AS1
FABP9
FABP12
FER1L6
MIR599
LOC727677
LOC728724
OC90
MIR875
LOC100127983
LOC100128126
TCF24
LOC100130155
LOC100130231
LOC100130298
LOC100130301
LRRC69
LOC100131726
LOC100132891
LOC100192378
REXO1L2P
LOC100288748
MIR1205
MIR1206
MIR1207
MIR1204
MIR2053
MIR2052
MIR1208
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3150B
MIR3610
LOC100505659
LOC100505676
LOC100505718
LOC100507117
LOC100507632
LOC100507651
C8orf44-SGK3
ZHX1-C8ORF76
MIR378D2
MIR4661
MIR4663
MIR4471
MIR4470
LOC100616530
PCAT1
LINC00536
FSBP

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
CPB2
DACH1
EDNRB
ELF1
ESD
GPC5
FOXO1
FLT1
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
PCDH9
UBL3
POU4F1
RFC3
RFXAP
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
TPT1
TRPC4
UCHL3
TNFSF11
SCEL
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
KL
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
DLEU1
N4BP2L2
PIBF1
OLFM4
POSTN
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SLITRK5
FBXL3
SACS
INTS6
CKAP2
NUFIP1
SNORD102
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
PHF11
POMP
UFM1
ATP8A2
NDFIP2
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
PCDH20
RNF219
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
COMMD6
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SPATA13
LNX2
SLC25A30
PAN3
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
SNORA31
MIR621
MIR622
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
RPL21P28
LINC00426
TPT1-AS1
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4500
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

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

Genes
PER1
TP53
USP6
hsa-mir-4314
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ACADVL
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MNT
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RPA1
RPL26
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
GLP2R
NTN1
STX8
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
GABARAP
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
KIAA0664
SMG6
WSCD1
CTDNEP1
PIK3R5
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
C17orf59
GPR172B
WRAP53
RNMTL1
VPS53
C17orf85
TSR1
DHX33
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
CTC1
NDEL1
PITPNM3
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
LSMD1
NEURL4
ZNF594
HES7
SPATA22
TXNDC17
MIR22HG
TMEM88
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
DNAH2
RTN4RL1
WDR16
CCDC42
PIK3R6
ODF4
KCTD11
MFSD6L
TRPV3
SLC16A11
FBXO39
DHRS7C
SLC16A13
C17orf74
SPNS3
C17orf61
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
SNORA48
SNORD10
OR1D4
SCARNA21
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
LOC100128288
C17orf107
LOC100130950
DBIL5P
MIR1253
LOC100306951
MIR3183
MIR4314
MIR3676
LOC100506388
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4520A
MIR4521
MIR4520B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.2.

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

Genes
SCUBE1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q24.2.

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

Genes
GPR161

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.1.

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
NKAIN2

Genes in Wide Peak

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

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

Genes
MLLT3
NFIB
hsa-mir-31
hsa-mir-491
hsa-mir-3152
PLIN2
CDKN2A
CDKN2B
ELAVL2
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
MTAP
PTPRD
RPS6
SH3GL2
SNAPC3
TYRP1
MPDZ
CER1
RRAGA
PSIP1
SLC24A2
C9orf53
BNC2
HAUS6
CNTLN
KIAA1797
DENND4C
KLHL9
DMRTA1
ADAMTSL1
TTC39B
FAM154A
FREM1
C9orf93
TUSC1
LURAP1L
IFNE
ZDHHC21
ACER2
LOC389705
FLJ41200
PTPLAD2
MIR31
FLJ35282
MIR31HG
MIR491
SCARNA8
CDKN2B-AS1
C9orf146
MIR3152
LOC100506422
MIR4473
MIR4474

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

Table S12. 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
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
C16orf7
KIAA0513
PIEZO1
ATP2C2
MPHOSPH6
COX4NB
TUBB3
PRDM7
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
C16orf61
JPH3
KIAA1609
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
MGC23284
LINC00311
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722

Genes in Wide Peak

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

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

Genes
RBFOX1
FAM86A
TMEM114

Genes in Wide Peak

This is the comprehensive list of deleted 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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.3.

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

Genes
CDK6
ELN
HIP1
MET
AKAP9
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
hsa-mir-590
hsa-mir-4284
ACHE
ASNS
AZGP1
CACNA2D1
CALCR
CAPZA2
CAV1
CAV2
KRIT1
CD36
AP1S1
COL1A2
CLDN4
CLDN3
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
SLC26A3
EPHB4
EPO
GNAI1
GNB2
GNG11
GNGT1
GPR22
GRM3
GTF2I
GTF2IP1
HGF
AGFG2
HSPB1
IFRD1
LAMB1
LIMK1
LRCH4
MCM7
DNAJB9
MDH2
NPTX2
NRCAM
OCM2
ORC5
SERPINE1
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PMS2P1
PMS2L2
PMS2P4
PMS2P5
PMS2P3
POLR2J
PON1
PON2
PON3
POR
PPP1R3A
PRKAR2B
RELN
PSMC2
PTPN12
RFC2
CCL24
SRI
SRPK2
STX1A
SYPL1
TAC1
TAF6
TFR2
TRIP6
VGF
ZAN
EIF4H
CLIP2
LAT2
YWHAG
ZNF3
ZKSCAN1
ZSCAN21
ZP3
MTERF
SHFM1
TFPI2
TRRAP
FZD1
FZD9
FKBP6
BUD31
SGCE
PLOD3
BAZ1B
CLDN12
AP4M1
BCL7B
PMPCB
ATP5J2
GTF2IRD1
SEMA3E
DOCK4
MAGI2
POM121
DMTF1
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
BET1
CCL26
SEMA3A
COG5
ZNHIT1
SEMA3C
ARPC1A
SH2B2
STAG3
FGL2
CPSF4
DBF4
COPS6
DUS4L
ZNF277
TP53TG1
PDAP1
TFEC
LAMB4
LMTK2
POMZP3
PEG10
ZKSCAN5
CLDN15
BRI3
TECPR1
PTCD1
AUTS2
TES
FBXO24
TBL2
STEAP1
HBP1
DNAJC2
PCLO
MDFIC
PILRB
PILRA
PNPLA8
FIS1
MLXIPL
ACTL6B
SRRT
STYXL1
ASB4
ADAM22
PION
GPR85
STAG3L1
ANKIB1
PUS7
LRRN3
CROT
ALKBH4
SAMD9
ZCWPW1
C7orf43
PPP1R9A
CCDC132
NSUN5
MLL5
BAIAP2L1
SLC25A40
BCAP29
MEPCE
SLC12A9
ACN9
SMURF1
PHTF2
RHBDD2
CCDC146
GATAD1
RINT1
WBSCR17
TMEM168
MOSPD3
GIGYF1
RABL5
CYP3A43
CASD1
STAG3L4
ZNF655
PVRIG
C7orf23
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ORAI2
UPK3B
OR2AE1
WBSCR16
TSC22D4
TRIM56
ABHD11
CALN1
ARMC10
TMEM120A
IMMP2L
RBM48
ZNF394
GTF2IRD2
MYH16
DNAJC30
MGC16142
TMEM60
GTPBP10
TRIM4
MYL10
ST7-AS1
ST7-AS2
ST7-OT3
FOXP2
DTX2
WBSCR22
WBSCR28
TRIM50
EMID2
SRCRB4D
MUC17
RUNDC3B
C7orf60
C7orf66
WBSCR27
SBDSP1
VPS37D
NSUN5P1
THAP5
CCDC71L
BHLHA15
ABHD11-AS1
SAMD9L
C7orf62
ZNF804B
ZNF498
FAM200A
PPP1R35
GPC2
SRRM3
RSBN1L
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
MBLAC1
FAM133B
NSUN5P2
STEAP2
DLX6-AS1
ZNF789
LOC286002
C7orf53
ST7-OT4
GNAT3
MOGAT3
GJC3
DPY19L2P2
GATS
TRIM73
NAT16
SLC26A5
LHFPL3
TRIM74
SPDYE8P
GATSL1
GTF2IRD2B
MGC72080
C7orf59
RPL13AP17
GTF2IRD2P1
LRRD1
FLJ42280
LOC401397
KPNA7
C7orf61
UFSP1
MIR106B
MIR25
MIR93
TYW1B
SPDYE7P
DTX2P1-UPK3BP1-PMS2P11
SPDYE3
SPDYE2
DPY19L2P4
STAG3L3
STAG3L2
SPDYE5
EIF3IP1
LOC541473
POLR2J3
MIR489
FDPSL2A
LOC645591
AZGP1P1
NCF1
NCF1B
NCF1C
SNORA14A
MIR590
MIR591
LOC723809
MIR653
LOC728066
GATSL2
SPDYE6
LOC100093631
POM121C
RPL19P12
LOC100129845
EFCAB10
LOC100132832
LOC100133091
UPK3BL
LOC100216545
LOC100216546
LOC100289187
LOC100289561
SPDYE2L
MIR548M
SAP25
MIR4285
MIR4284
MIR3609
MIR3914-1
MIR3666
MIR3914-2
LOC100505854
MAGI2-AS3
LOC100506136
ATP5J2-PTCD1
MIR4653
MIR4652
MIR4651
MIR4650-1
MIR4650-2
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.32.

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

Genes
ABL1
FANCC
NOTCH1
RALGDS
SET
TAL2
TSC1
XPA
NR4A3
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
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
BAAT
C5
C8G
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL2
CYLC2
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSD17B3
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
ANP32B
AGPAT2
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
PMPCA
ASTN2
FKBP15
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
BSPRY
C9orf167
TEX10
LPPR1
EXD3
FAM206A
STX17
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
C9orf86
CDK5RAP2
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
BDAG1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
MIR600HG
URM1
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
HIATL2
C9orf125
NTNG2
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
C9orf96
OLFML2A
QSOX2
ZNF883
C9orf21
ZNF367
C9orf91
NAIF1
ANKS6
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC340508
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR32
C9orf106
LCN10
LOC441454
LOC441455
FAM22G
LOC441461
C9orf173
NRARP
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
NRON
FAM163B
FLJ40292
RNF224
C9orf29
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
LOC100129722
LOC100130954
LOC100131193
LOC100132781
RNU6ATAC
LINC00092
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3154
MIR2861
MIR3134
C9orf174
LOC100499484
MIR3621
MIR3689A
MIR3911
MIR3689B
LOC100505478
LOC100506100
LOC100506190
LOC100506599
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4672
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p22.3.

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

Genes
ALK
ATIC
CHN1
CREB1
DNMT3A
ERCC3
ACSL3
MSH6
HOXD11
HOXD13
IDH1
MSH2
MYCN
NFE2L2
PAX3
PMS1
REL
PAX8
NCOA1
EML4
BCL11A
FEV
TTL
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
hsa-mir-3127
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
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
AAMP
ACADL
ACP1
ACTG2
ACVR1
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
AGXT
ALPI
ALPP
ALPPL2
BIN1
ANXA4
AOX1
APOB
RHOB
RND3
ATP5G3
ATP6V1B1
KIF1A
AUP1
BARD1
BCS1L
BMPR2
BOK
ZFP36L2
BUB1
CACNB4
CAD
CALM2
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CENPA
CHRNA1
CHRND
CHRNG
CLK1
CNGA3
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
COX5B
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CTNNA2
CYP1B1
CYP27A1
DARS
DBI
DCTN1
DDX1
DES
DGUOK
LOC1720
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DTNB
DTYMK
DUSP2
E2F6
EEF1B2
EGR4
EMX1
EN1
EPAS1
EPHA4
ERBB4
FABP1
FAP
EFEMP1
FHL2
FKBP1B
FN1
FOSL2
FRZB
FSHR
FTH1P3
GAD1
GALNT3
GBX2
GCG
GCKR
MSTN
GFPT1
GGCX
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GTF3C2
GYPC
HADHA
HADHB
HDLBP
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HPCAL1
AGFG1
DNAJB2
HSPD1
HSPE1
FOXN2
HTR2B
ID2
SP110
IGFBP2
IGFBP5
IHH
IL1A
IL1B
IL1R1
IL1RN
CXCR1
CXCR2
CXCR2P1
INHA
INHBB
INPP1
INPP4A
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNF1
KCNJ3
KCNJ13
KCNK3
KCNS3
KHK
KIF3C
KIF5C
AFF3
LCT
LHCGR
LIMS1
LRP2
LTBP1
LY75
EPCAM
MXD1
MAL
MAP2
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MYO1B
MTIF2
MYL1
MYO7B
NAB1
NCL
NEB
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPAS2
NPHP1
NPPC
NR4A2
ODC1
ORC2
ORC4
OTX1
REG3A
PCBP1
PDCD1
PDE1A
PDE6D
PDK1
PEX13
VIT
SERPINE2
PIGF
PLCL1
PLEK
PLGLB2
PLGLB1
POLR2D
POMC
POU3F3
PPM1B
PPM1G
PPP1CB
PPP1R7
PPP3R1
PRKCE
EIF2AK2
PROC
PSMD1
PTH2R
PTMA
PTPN4
PTPRN
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
REG1P
SNORD20
RPE
RPL31
RPL37A
RPS7
RPS27A
RRM2
RTKN
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
CCL20
SDC1
SRSF7
SFTPB
SIX3
SLC4A3
SLC1A4
SLC3A1
SLC8A1
SLC9A2
SLC11A1
SLC20A1
SNRPG
SOS1
SOX11
SP3
SP100
SPAST
SPP2
SPR
SPTBN1
SRD5A2
SSB
SSFA2
STAT1
STAT4
STRN
SULT1C2
ADAM17
TACR1
GCFC2
TFPI
TGFA
TIA1
TNFAIP6
TNP1
TNS1
TPO
TSN
TSSC1
TTN
TUBA4A
SUMO1
UCN
UGP2
VIL1
VRK2
VSNL1
WIPF1
WNT6
XDH
XPO1
XRCC5
ZAP70
ZNF2
ZNF142
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
FZD5
SCG2
DYSF
FZD7
SDPR
NCK2
DUSP11
CUL3
KLF11
MAP4K3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ASAP2
PER2
ST3GAL5
SLC5A6
DDX18
EIF2B4
CDK5R2
KYNU
TAF1B
NAT8
NMI
RQCD1
COX7A2L
TMSB10
IL1RL1
LRRFIP1
STK17B
ITGB1BP1
GPR55
TRIP12
GTF3C3
PPIG
NRXN1
OTOF
CIAO1
TGFBRAP1
HS6ST1
CRIPT
ECEL1
MAP4K4
EIF2AK3
EIF4E2
ROCK2
CHST10
TP53I3
CIR1
MRPL33
BRE
PREPL
CYTIP
FEZ2
GCC2
TTLL4
SOCS5
EIF5B
GREB1
BZW1
USP34
LAPTM4A
HDAC4
RNF144A
SNX17
SERTAD2
MRPL19
ZEB2
FARP2
TLK1
SUPT7L
CD302
ARHGAP25
TANK
BCL2L11
FARSB
ABCB6
ACTR3
ACTR2
ARPC2
PREB
ACTR1B
ARL4C
LRPPRC
PDIA6
ABI2
CEBPZ
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
SMYD5
KBTBD10
MYCNOS
C1D
MERTK
UBE2E3
STK25
SEMA4F
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
MTX2
CGREF1
B3GNT2
USP39
TBR1
SIX2
MAP3K2
NCKAP1
VAMP5
MTHFD2
ARID5A
PROKR1
RAB10
EDAR
COPS8
GPR75
YWHAQ
IMMT
SNRNP27
GTF2A1L
STON1
RAPGEF4
EMILIN1
CAPN10
TBC1D8
RABL2A
GALNT5
NXPH2
GPR45
SP140
MGAT4A
GPN1
IKZF2
COBLL1
AAK1
FASTKD2
MAPRE3
PLA2R1
RAB3GAP1
RPIA
SLC4A1AP
EFR3B
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
PASK
UBXN4
ATG4B
PSME4
EXOC6B
EHBP1
SATB2
CLASP1
OBSL1
PUM2
NCAPH
RHOQ
SF3B1
HAAO
TMEM131
R3HDM1
DNPEP
PSD4
WBP1
NTSR2
TMEFF2
SH3BP4
PRKD3
KCNE4
RASGRP3
NGEF
QPCT
GCA
VAX2
SNORD82
MOB4
POLR1A
CNRIP1
FAM98A
PNKD
UNC50
SNED1
GORASP2
SPATS2L
RAB11FIP5
GIGYF2
EPC2
TRAF3IP1
ABCA12
IFT172
ARL5A
HIBCH
PTPN18
CNNM4
CNNM3
IL36RN
SH3YL1
SNORD53
SNORD51
CNPPD1
STK36
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
MMADHC
BMP10
ZNF638
STK39
HTRA2
TRIB2
CPS1-IT1
METTL5
LGALSL
OLA1
C2orf27A
GRHL1
TFCP2L1
ICOS
GMPPA
NRBP1
BAZ2B
SLC40A1
KCNIP3
EHD3
SMARCAL1
CD207
ITSN2
ANO7
ARHGEF4
PDE11A
TPRKB
FAHD2A
PRLH
WDPCP
MEMO1
THAP4
TRAPPC12
ASB3
INSIG2
CRIM1
ANKRD39
FAM178B
RNF181
MRPL30
DNAJC27
ANKMY1
KRCC1
MRPL35
C2orf28
PCYOX1
GULP1
REV1
NAT8B
SCLY
VPS54
NBAS
LIPT1
NOP58
DYNC2LI1
SF3B14
YPEL5
CHMP3
FKBP7
ASB1
CPSF3
CAB39
ZAK
LRP1B
PRKAG3
PPIL3
SNTG2
DNAJC10
ATAD2B
ETAA1
HEATR5B
CCDC93
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
AFTPH
MFSD6
TMEM214
RETSAT
INO80D
SEMA4C
C2orf18
C2orf42
TRMT61B
PID1
PTCD3
PLEKHB2
ATG16L1
FANCL
SRBD1
FIGN
ANKZF1
RIF1
USP40
MOB1A
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
HJURP
STRADB
C2orf56
HES6
ACCN4
C2orf29
NAGK
DOCK10
TTC27
SMPD4
TMEM127
PRPF40A
SLC30A6
IWS1
LIMS2
KANSL3
MREG
CCDC88A
WDR12
MBD5
KDM3A
ALLC
PECR
ARHGAP15
ZC3H15
CFC1
DNAH7
GKN1
IL36G
RPRM
CYP26B1
POLE4
KCNK12
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
C2orf83
MFF
RPL23AP32
CXCR7
RNPEPL1
RTN4
TRIM54
PELI1
SLC39A10
TTC7A
SMEK2
SLC4A10
CYP20A1
SPC25
BIRC6
ERMN
KIDINS220
MTA3
HECW2
WDR35
MARCH4
WDFY1
NYAP2
DPP10
RDH14
EPB41L5
ALS2
ZDBF2
USP37
CWC22
ANKRD36B
G6PC2
SLC4A5
CTDSP1
NLRC4
MPP4
SLC5A7
NIF3L1
AGBL5
C2orf43
THADA
PCGEM1
RBKS
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
ATL2
ABCG5
ABCG8
RAB17
RNF25
HS1BP3
GMCL1
TTC31
ANAPC1
COPS7B
RMND5A
FNDC4
MARCH7
OBFC2A
PAPOLG
MRPS9
MRPS5
REEP1
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
SOWAHC
PLEKHA3
TRAK2
BOLL
COLEC11
PDCL3
TRPM8
ATG9A
C2orf49
MLPH
TMEM185B
FAM134A
CENPO
OR7E91P
GLB1L
C2orf47
SPAG16
CHPF
SAP130
GALNT14
SCRN3
CCDC121
FASTKD1
SMC6
GTDC1
CLIP4
IQCA1
ALS2CR8
TTC21B
CAMKMT
METTL8
GEMIN6
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
NOL10
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
TUBA4B
MZT2B
YSK4
UXS1
FBXO11
ARMC9
COQ10B
SLC35F5
EFHD1
C2orf44
SPHKAP
WNT10A
SLC19A3
TSGA10
THSD7B
THUMPD2
TMEM177
KIAA1715
ILKAP
FAM49A
LMAN2L
LBH
TMEM163
ITM2C
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
RHBDD1
CHCHD5
YIPF4
PRADC1
C2orf88
ING5
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
DPY30
MCEE
LOXL3
ABHD1
PCGF1
DDX11L2
MFSD9
PLCD4
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
MGC16025
TANC1
EPT1
LBX2
PNPT1
KCNH7
FER1L5
MCFD2
ATP6V1E2
LOC90499
CCDC74A
LOC90784
DHX57
LOC91149
SESTD1
CCDC74B
PKDCC
ANKRD44
RSAD2
ZNF804A
TTC30A
DAPL1
CAPN13
TMEM169
DNER
CCDC164
IMP4
HNRPLL
MARS2
B3GNT7
NT5C1B
NEURL3
SP140L
SFXN5
ORMDL1
LIMS3
LINC00152
TUBA3E
CCDC104
TEX261
TUBA3D
STK11IP
FMNL2
CCDC85A
GALNT13
KLHL29
OSBPL6
NOSTRIN
DIRC1
WDR92
MOGAT1
LYPD1
MRPL53
AGAP1
TWIST2
PARD3B
RPL23AP7
PPP1R21
C2orf89
TMEM150A
NUP35
XIRP2
TYW5
NMS
LYG1
MITD1
DIS3L2
CMPK2
MBOAT2
CNTNAP5
TMEM18
FBLN7
NEU4
RBM45
C2orf73
TRIM43
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
CIB4
REG3G
RFTN2
C2orf63
PLEKHH2
AP1S3
C2orf76
SGPP2
ACVR1C
OSR1
TTC32
UBR3
KCTD18
ALS2CR12
ZNF513
SPATA3
LYPD6
LYPD6B
GALM
TMEM198
ZFAND2B
TMEM178
CPO
MDH1B
C2orf50
PQLC3
TMEM182
AHSA2
FBXO36
MTERFD2
CCDC148
C2orf65
MYO3B
TMEM37
UBE2F
DUSP19
CKAP2L
CBWD2
TEKT4
LOC150527
FLJ32063
LOC150568
SMYD1
C2orf15
LOC150622
OTOS
MYEOV2
OR6B3
COMMD1
PROM2
ANKAR
FBXO41
TTC30B
GPAT2
ITPRIPL1
LOC150776
WTH3DI
FAM117B
TCF23
LOC150935
FAM59B
PUS10
PKI55
LINC00309
LOC151009
SEPT10
C2orf67
PLB1
ZSWIM2
ZNF385B
LOC151171
LOC151174
ARL6IP6
METTL21A
CCNYL1
KLHL23
SULT1C2P1
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
LOC151300
GPBAR1
FAHD2B
MYADML
FAM84A
FAM82A1
GDF7
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
ASPRV1
WDSUB1
UPP2
LOC151534
GPR155
WDR69
LONRF2
CCDC138
GPR113
C2orf57
OXER1
FAM179A
FAM171B
C1QL2
UBXN2A
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
PIKFYVE
KRTCAP3
LOC200726
TMEM17
SPRED2
TIGD1
LOC200772
FAM123C
LINC00116
C2orf69
HNRNPA3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
CERS6
METAP1D
LOC254128
LYG2
CCDC108
C2orf72
SH2D6
LOC284950
CCDC150
RNF149
LOC284998
LOC285000
FAM150B
CCDC141
LOC285033
LINC00486
C2orf61
LOC285074
LOC285084
CXXC11
LOC285103
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
FAM126B
UNC80
RUFY4
PLGLA
RGPD4
DUSP28
STON1-GTF2A1L
SPOPL
MLK7-AS1
CYP27C1
ESPNL
C2orf70
C2orf53
LOC339788
LINC00299
LOC339803
C2orf74
LOC339807
LOC339822
MSGN1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
EVX2
CDKL4
PRORSD1P
AOX2P
SH3RF3
GPR148
ECEL1P2
LRRTM1
GEN1
C2orf48
FONG
LOC348761
PFN4
LOC375190
LOC375196
ANKRD36
WASH2P
RBM43
LOC375295
CERKL
C2orf62
RBM44
AQP12A
ZC3H6
KLHL30
LOC386597
MFSD2B
C2orf71
LOC388942
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
SLC9A4
LOC389023
LOC389033
LOC389043
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
PTRHD1
SULT6B1
DYTN
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
FLJ42351
LOC401010
DKFZp686O1327
LOC401022
FSIP2
C2orf66
ASB18
FLJ43879
VWC2L
MIR10B
MIR128-1
MIR149
MIR153-1
MIR216A
MIR217
MIR26B
C2orf27B
DNAJB3
ASTL
CAPN14
ACTR3BP2
LOC440894
LOC440895
LOC440900
LOC440905
LOC440910
POTEKP
LOC440925
LOC442028
SULT1C3
POTEE
COA5
PHOSPHO2
CHAC2
MIR375
DFNB59
LOC541471
LOC554201
ANKRD30BL
FBXO48
SNORA41
FAM110C
LOC643387
PRR21
LOC644838
GGT8P
ANKRD36BP2
LOC645949
LOC646324
LOC646736
LOC646743
PRSS56
LOC647012
C2orf84
TRIM43B
CFC1B
AQP12B
RGPD3
MZT2A
SNORA75
LOC654342
FAM138B
LOC654433
SCARNA6
SCARNA5
SNORD11
SNORD70
SNORD89
SNORD92
SNORD94
MIR558
MIR559
MIR561
RGPD8
LOC727982
D2HGDH
LOC728323
POTEF
LOC728537
LOC728730
PABPC1P2
LOC728819
LOC729121
ANKRD20A8P
LOC729234
RAD51AP2
RGPD6
DIRC3
DNAJC27-AS1
RGPD2
MORN2
LOC730811
RFX8
SNORD11B
SNORA36C
SNORA70B
MIR216B
MIR933
LOC100128590
OST4
LOC100129175
LOC100129726
LOC100129961
PP14571
LOC100130451
LOC100130452
LOC100130691
TMEM194B
LOC100131320
SP9
LOC100132215
CYP4F30P
LOC100133985
LOC100134259
LOC100144595
RNU4ATAC
DBIL5P2
SNAR-H
LOC100189589
LOC100216479
ARHGEF33
LOC100271832
LIMS3-LOC440895
LOC100286922
LOC100286979
LOC100287010
LOC100287216
LOC100288570
LIMS3L
LOC100288911
MIR1471
MIR1246
MIR548N
MIR1258
MIR1245A
MIR1301
MIR1244-1
LOC100302650
GPR75-ASB3
SNORA80B
ZEB2-AS1
MIR548F2
MIR663B
LOC100329109
SNORA70F
BOK-AS1
MIR3128
MIR4265
MIR1244-3
MIR1244-2
MIR4264
MIR3129
MIR3127
MIR4261
MIR3131
MIR4268
MIR4263
MIR3125
MIR3130-1
MIR4267
MIR4262
MIR3130-2
MIR4266
MIR3126
MIR2355
MIR3132
MIR4269
LOC100499194
MIR3606
MIR3682
MIR3679
LOC100505624
LOC100505695
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506123
LOC100506124
LOC100506134
LOC100506274
LOC100506421
LOC100506474
LOC100506783
LOC100506866
LOC100507140
BOLA3-AS1
LOC100507334
LOC100507443
LOC100507600
LY75-CD302
RNF103-CHMP3
NT5C1B-RDH14
PHOSPHO2-KLHL23
HSPE1-MOB4
INO80B-WBP1
UBE2F-SCLY
MIR4436B1
MIR4772
MIR4779
MIR4783
MIR4439
MIR4782
MIR4437
MIR4765
MIR4776-1
MIR4757
MIR4777
MIR1245B
MIR4435-2
MIR4426
MIR4774
MIR2467
MIR4775
MIR4785
MIR4784
MIR4773-1
MIR4444-1
MIR4440
MIR4436A
MIR4786
MIR4773-2
MIR4434
MIR4780
MIR4778
MIR4429
MIR4776-2
MIR4432
MIR548AD
MIR4441
MIR4435-1
LOC100630918
LOC100861402

Genes in Wide Peak

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

Table S18. 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 2. Get Full Table Arm-level significance table - 18 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.01 | -0.931 | 0.988 | 0.01 | -1.37 | 0.988
1q | 1955 | 0.05 | 4.44 | 4.53e-05 | 0.01 | -1.31 | 0.988
2p | 924 | 0.01 | -1.33 | 0.988 | 0.03 | 1.78 | 0.301
2q | 1556 | 0.00 | -1.79 | 0.988 | 0.02 | 1.31 | 0.637
3p | 1062 | 0.01 | -0.917 | 0.988 | 0.01 | -1.36 | 0.988
3q | 1139 | 0.01 | -1.36 | 0.988 | 0.01 | -0.918 | 0.988
4p | 489 | 0.02 | -0.0158 | 0.972 | 0.00 | -1.8 | 0.988
4q | 1049 | 0.02 | -0.0256 | 0.972 | 0.00 | -1.8 | 0.988
5p | 270 | 0.05 | 5.37 | 9.91e-07 | 0.00 | -2.2 | 0.988
5q | 1427 | 0.04 | 3.98 | 0.000171 | 0.00 | -2.22 | 0.988
6p | 1173 | 0.01 | -1.37 | 0.988 | 0.01 | -1.37 | 0.988
6q | 839 | 0.00 | -1.8 | 0.988 | 0.02 | -0.022 | 0.988
7p | 641 | 0.05 | 4.46 | 4.53e-05 | 0.00 | -2.21 | 0.988
7q | 1277 | 0.05 | 5.33 | 9.91e-07 | 0.00 | -2.21 | 0.988
8p | 580 | 0.02 | -0.0037 | 0.972 | 0.01 | -0.893 | 0.988
8q | 859 | 0.02 | 0.441 | 0.802 | 0.01 | -0.892 | 0.988
9p | 422 | 0.01 | -1.32 | 0.988 | 0.03 | 2.24 | 0.125
9q | 1113 | 0.01 | -0.85 | 0.988 | 0.04 | 4.03 | 0.000554
10p | 409 | 0.01 | -1.35 | 0.988 | 0.01 | -0.907 | 0.988
10q | 1268 | 0.01 | -1.36 | 0.988 | 0.01 | -0.919 | 0.988
11p | 862 | 0.01 | -0.446 | 0.988 | 0.02 | -0.00171 | 0.988
11q | 1515 | 0.01 | -0.901 | 0.988 | 0.02 | 0.429 | 0.988
12p | 575 | 0.04 | 4.01 | 0.000171 | 0.00 | -2.22 | 0.988
12q | 1447 | 0.04 | 3.98 | 0.000171 | 0.00 | -2.22 | 0.988
13q | 654 | 0.01 | -0.861 | 0.988 | 0.03 | 2.7 | 0.0468
14q | 1341 | 0.02 | 1.3 | 0.257 | 0.00 | -2.24 | 0.988
15q | 1355 | 0.00 | -2.25 | 0.988 | 0.02 | 0.409 | 0.988
16p | 872 | 0.04 | 4.01 | 0.000171 | 0.00 | -1.76 | 0.988
16q | 702 | 0.04 | 3.13 | 0.00314 | 0.01 | -1.31 | 0.988
17p | 683 | 0.04 | 3.17 | 0.00306 | 0.02 | 0.0574 | 0.988
17q | 1592 | 0.04 | 3.55 | 0.00084 | 0.01 | -1.32 | 0.988
18p | 143 | 0.01 | -0.898 | 0.988 | 0.01 | -0.898 | 0.988
18q | 446 | 0.01 | -0.902 | 0.988 | 0.01 | -0.902 | 0.988
19p | 995 | 0.02 | -0.00403 | 0.972 | 0.01 | -0.448 | 0.988
19q | 1709 | 0.02 | 0.41 | 0.802 | 0.00 | -1.8 | 0.988
20p | 355 | 0.03 | 2.22 | 0.0414 | 0.00 | -2.23 | 0.988
20q | 753 | 0.03 | 2.21 | 0.0414 | 0.00 | -2.23 | 0.988
21q | 509 | 0.01 | -1.34 | 0.988 | 0.02 | -0.00934 | 0.988
22q | 921 | 0.01 | -1.08 | 0.988 | 0.17 | 22.9 | 0
Xq | 1312 | 0.03 | 1.78 | 0.107 | 0.01 | -0.881 | 0.988

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/THCA/1971765/2.GDAC_MergeDataFiles.Finished/THCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 3. Get Full Table First 10 out of 330 Input Tumor Samples.

Tumor Sample Names
TCGA-BJ-A0YZ-01A-11D-A10T-01
TCGA-BJ-A0Z0-01A-11D-A10T-01
TCGA-BJ-A0Z2-01A-11D-A10T-01
TCGA-BJ-A0Z3-01A-11D-A13V-01
TCGA-BJ-A0Z5-01A-11D-A10T-01
TCGA-BJ-A0Z9-01A-11D-A10T-01
TCGA-BJ-A0ZA-01A-11D-A10T-01
TCGA-BJ-A0ZB-01A-11D-A10T-01
TCGA-BJ-A0ZC-01A-12D-A13V-01
TCGA-BJ-A0ZE-01A-11D-A10T-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

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

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

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

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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