Sarcoma: 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 20 tumor samples used in this analysis: 11 significant arm-level results, 10 significant focal amplifications, and 11 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 - 10 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
12q15 5.2186e-15 5.2186e-15 chr12:69178021-69397111 2
6p21.1 0.01032 0.01032 chr6:41698135-42692619 17
5p14.2 0.0050316 0.14525 chr5:23446521-23595300 1
5p14.3 0.060767 0.17313 chr5:21898400-21952259 1
19p13.3 0.20837 0.20837 chr19:5278879-5450703 1
1p32.2 0.21352 0.21352 chr1:58400165-60781208 12
3q26.31 0.22271 0.22271 chr3:172461349-181441711 24
4p15.31 0.22491 0.22491 chr4:11163703-31372566 65
19q13.2 0.22984 0.22984 chr19:39008548-39063136 1
12p13.32 0.24802 0.24802 chr12:4550620-5351735 10
Genes in Wide Peak

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

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

Genes
MDM2
CPM
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
CCND3
TFEB
BYSL
GUCA1A
GUCA1B
PGC
PRPH2
MED20
FRS3
UBR2
USP49
PRICKLE4
MRPS10
TRERF1
TAF8
C6orf132
TOMM6
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p14.2.

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

Genes
PRDM9
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p14.3.

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

Genes
CDH12
Genes in Wide Peak

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

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

Genes
PTPRS
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p32.2.

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

Genes
JUN
CYP2J2
DAB1
TACSTD2
HOOK1
FGGY
MYSM1
OMA1
C1orf87
HSD52
LOC100131060
MIR4711
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.31.

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

Genes
PIK3CA
SOX2
ACTL6A
ECT2
NDUFB5
FXR1
USP13
KCNMB2
NLGN1
KCNMB3
ZNF639
PEX5L
MFN1
MRPL47
GNB4
ZMAT3
TBL1XR1
SPATA16
DNAJC19
TTC14
NAALADL2
CCDC39
SOX2-OT
MIR4789
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p15.31.

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

Genes
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
NKX3-2
BST1
CCKAR
CD38
DHX15
RBPJ
PCDH7
QDPR
SOD3
PROM1
LDB2
SLIT2
RAB28
HS3ST1
FGFBP1
SLC34A2
PPARGC1A
SEL1L3
FBXL5
FAM184B
ZCCHC4
ANAPC4
LAP3
SEPSECS
DCAF16
LGI2
TBC1D19
PI4K2B
CC2D2A
STIM2
GBA3
NCAPG
MED28
KCNIP4
FGFBP2
CCDC149
C1QTNF7
CPEB2
PACRGL
LOC152742
GPR125
TAPT1
FLJ39653
LCORL
BOD1L
LOC285540
LOC285547
LOC285548
FAM200B
KCNIP4-IT1
C4orf52
HSP90AB2P
MIR218-1
LOC441009
CLRN2
MIR572
MIR573
MIR4275
SLIT2-IT1
LOC100505912
MIR548AJ2
Genes in Wide Peak

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

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

Genes
RYR1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
FGF6
KCNA1
KCNA5
KCNA6
NDUFA9
DYRK4
AKAP3
RAD51AP1
GALNT8
C12orf4

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 - 11 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
2q37.3 0.015163 0.015163 chr2:234254888-243199373 99
13q14.2 0.015163 0.015163 chr13:48666829-51801435 29
9p21.3 0.18353 0.18353 chr9:4709005-30412529 107
12p13.1 0.18353 0.18353 chr12:1-31149662 321
2p23.3 0.22099 0.22099 chr2:1-55246422 329
4q35.1 0.22099 0.22099 chr4:54241403-191154276 616
Xq21.1 0.22099 0.22099 chrX:76710176-77102528 1
3q22.3 0.22099 0.22099 chr3:89150943-178792048 499
11q24.3 0.22099 0.22099 chr11:56750837-135006516 910
16p13.3 0.22428 0.24542 chr16:1-90354753 967
19p13.3 0.22428 0.24542 chr19:1-59128983 1653
Genes in Wide Peak

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

Table S11.  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
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
SPP2
DGKD
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
MSL3P1
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
LOC100286922
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441
Genes in Wide Peak

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

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

Genes
RB1
hsa-mir-15a
RCBTB2
MLNR
GUCY1B2
KPNA3
DLEU2
ITM2B
LPAR6
TRIM13
DLEU1
FNDC3A
PHF11
RCBTB1
CYSLTR2
SPRYD7
RNASEH2B
CDADC1
CAB39L
SETDB2
EBPL
ARL11
ST13P4
DLEU7
CTAGE10P
KCNRG
MIR15A
MIR16-1
MIR3613
Genes in Wide Peak

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

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

Genes
JAK2
MLLT3
NFIB
CD274
hsa-mir-873
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
SNAPC3
TEK
TYRP1
MPDZ
CER1
PLAA
RCL1
RRAGA
PSIP1
INSL6
KDM4C
SLC24A2
RANBP6
AK3
C9orf53
C9orf11
BNC2
HAUS6
CNTLN
KIAA1797
DENND4C
C9orf46
KLHL9
IFNK
KIAA1432
DMRTA1
LRRC19
MOB3B
C9orf82
ERMP1
IFT74
PDCD1LG2
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
LINC00032
LINGO2
TTC39B
FAM154A
FREM1
KIAA2026
C9orf72
C9orf93
TUSC1
LURAP1L
IFNE
ZDHHC21
ACER2
LOC389705
FLJ41200
PTPLAD2
LOC401497
MIR101-2
MIR31
FLJ35282
MIR31HG
MIR491
SCARNA8
CDKN2B-AS1
C9orf146
MIR876
MIR873
MIR3152
LOC100506422
MIR4473
MIR4665
MIR4474
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
CCND2
ETV6
KRAS
KDM5A
ZNF384
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
BCAT1
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
GYS2
IAPP
ITPR2
KCNA1
KCNA5
KCNA6
KCNJ8
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LDHB
LRMP
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NINJ2
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTHLH
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
RECQL
SCNN1A
ST8SIA1
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SOX5
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
SSPN
KLRC4
PPFIBP1
CSDA
DYRK4
GPRC5A
CD163
MED21
GDF3
CLSTN3
KIAA0528
NCAPD2
CLEC2B
ABCC9
LPCAT3
KLRG1
LRRC23
EMG1
IPO8
LEPREL2
AKAP3
SLCO1B1
RAD51AP1
KLRAP1
TSPAN9
STRAP
RASSF8
PRR4
PHB2
KLRK1
STK38L
ERC1
GABARAPL1
IFFO1
NECAP1
FGFR1OP2
CLEC4E
GALNT8
GPR162
SLCO1B3
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
GOLT1B
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
ERGIC2
KLRF1
WBP11
TM7SF3
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
CASC1
CCDC91
STYK1
ETNK1
GPRC5D
FAR2
ASUN
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
CMAS
PRMT8
ARNTL2
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KLHDC5
KIAA1467
MRPS35
CLEC7A
WNK1
CAPRIN2
BHLHE41
BCL2L14
ADIPOR2
RERGL
PLBD1
PYROXD1
NANOG
C12orf39
DUSP16
WNT5B
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
TMTC1
CCDC77
ACRBP
SPSB2
EFCAB4B
RERG
PLCZ1
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
SLC2A14
LINC00477
LYRM5
A2ML1
LOC144571
C12orf60
FBXL14
CLEC12A
CLECL1
IFLTD1
CLEC4C
DSTNP2
C12orf77
C12orf53
DCP1B
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
B4GALNT3
CLEC9A
C12orf36
LOC283440
CLEC4D
LOC338817
SLCO1B7
C12orf70
OVCH1
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
REP15
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
TSPAN11
LOH12CR2
LOC574538
POU5F1P3
LOC642846
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
C12orf71
SLC15A5
MIR920
LOC100129361
LOC100271702
MANSC4
LOC100287314
LOC100288778
LOC100292680
MIR1244-1
MIR1244-3
MIR1244-2
MIR4302
KLRF2
LOC100499405
MIR3649
LOC100506314
LOC100506393
LOC100506451
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846
Genes in Wide Peak

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

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

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

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

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

Genes
IL2
KDR
KIT
PDGFRA
RAP1GDS1
DUX4
CHIC2
TET2
FBXW7
FIP1L1
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
hsa-mir-1269
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA2P1
ANXA3
ANXA5
AREG
ART3
ATOH1
BMP3
BMPR1B
BTC
CAMK2D
CASP3
CASP6
CCNA2
CCNG2
SCARB2
LRBA
CDS1
CLGN
CENPC1
CENPE
CLCN3
CPE
CSN1S1
CSN2
CSN3
CTSO
DCK
DCTD
DMP1
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
EPHA5
EREG
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGF5
FGG
FRG1
GAB1
GC
GK2
GK3P
GLRB
GNRHR
GPM6A
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HMGB2
HNRNPD
HPGD
HSP90AA4P
HSP90AB3P
HTN1
HTN3
IBSP
CFI
IGFBP7
IGJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
MAD2L1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MTNR1A
MTTP
MUC7
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PDHA2
PET112
PF4
PF4V1
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPBP
PPID
PPP3CA
PRKG2
MAPK10
PTPN13
REST
ABCE1
RPL34
RPS3A
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SNCA
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
TDO2
TLL1
TLR2
TLR3
TRPC3
UBE2D3
UCP1
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
VEGFC
GLRA3
SPARCL1
SMARCA5
SORBS2
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
HERC3
SNORD73A
STBD1
CDKL2
PAPSS1
LRAT
AIMP1
NDST3
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
MFAP3L
SEC24D
G3BP2
HNRPDL
TSPAN5
ENAM
FAM13A
SPRY1
ANAPC10
PGRMC2
SEC24B
CXCL13
MAB21L2
PAICS
PDLIM5
RRH
UGT2B11
PLK4
HPSE
NMU
SMR3B
NPFFR2
PPBPL2
UGT2A1
CCNI
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
RUFY3
MMRN1
WDFY3
PALLD
TBC1D9
METAP1
KIAA0922
LPHN3
TRIM2
ANP32C
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXO8
DUX2
SMR3A
PPA2
DAPP1
DKK2
INTU
NAAA
COQ2
ARFIP1
SULT1B1
PDLIM3
HPGDS
ZNF330
TMPRSS11E
SPOCK3
MRPS18C
COPS4
AADAT
HSD17B11
LEF1
HERC5
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
NUDT9
NUP54
CLDN22
GAR1
UGT2B28
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
ODAM
C4orf27
HERC6
CCDC109B
MARCH1
BANK1
LARP1B
SDAD1
BBS7
UBA6
NEIL3
TMEM144
C4orf43
UFSP2
C4orf21
AP1AR
MAML3
BMP2K
DDX60
CDKN2AIP
ODZ3
TMEM184C
SEPT11
EXOC1
LRP2BP
TMEM165
PDGFC
FSTL5
BDH2
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
KIAA1211
RNF150
KLHL8
PCDH10
KIAA1430
FNIP2
SHROOM3
SH3RF1
METTL14
ENOPH1
PROL1
OSTC
IL21
RXFP1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
HHIP
NDST4
AGXT2L1
MRPL1
ELOVL6
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
MLF1IP
THAP9
UGT2A3
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
SCD5
DNAJB14
WWC2
FRAS1
NAA15
C4orf29
ALPK1
CXXC4
CEP44
SETD7
PLA2G12A
SLC25A31
RAB33B
ARHGAP24
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
NOA1
HOPX
COL25A1
USP38
LNX1
C4orf49
NAA11
AGPAT9
CBR4
PIGY
CABS1
FHDC1
FLJ20021
MGC45800
PRMT10
DDX60L
YTHDC1
NAF1
MOB1B
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
WDR17
GDEP
ANTXR2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
C4orf32
TMPRSS11B
SPATA4
ARL9
AASDH
PDCL2
C4orf36
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
PAQR3
C4orf38
C4orf39
THAP6
C4orf26
PPM1K
C4orf45
RASGEF1B
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
TIGD2
RASSF6
RBM46
SGMS2
GSX2
SYNPO2
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
CNOT6L
TECRL
C4orf22
LOC255130
EPGN
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
FDCSP
NAP1L5
LOC285419
CYP4V2
LOC285441
LOC285456
LOC285501
FAM13A-AS1
GPRIN3
COX18
RNF175
C4orf37
CSN1S2AP
CCDC158
TMPRSS11A
LOC339975
TRIML1
LOC340017
PRSS48
SOWAHB
LRIT3
SLC10A6
HSD17B13
ANKRD37
PCNAP1
TMPRSS11F
LOC389247
TRIM61
HELT
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
FLJ14186
C4orf3
LOC401164
RPL21P44
FAM92A3
WDFY3-AS2
MIR302A
C4orf11
MTHFD2L
LOC441025
TMEM150C
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC550112
LOC550113
UGT2A2
LOC641364
LOC641365
LOC641518
SLED1
LOC644145
LOC644248
TMPRSS11GP
CEP170P1
LOC645513
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
SNORA24
MIR575
MIR577
MIR578
LINC00290
LOC728175
DUX4L2
CETN4P
FAM160A1
LOC731424
SNHG8
FAM47E
LOC100129858
FTLP10
CLDN24
LOC100144602
PP12613
LOC100288255
MIR1243
MIR2054
MIR1305
MIR1973
CSN1S2BP
MIR3140
MIR4276
LOC100499177
MIR3945
MIR3684
MIR3688-1
LOC100505545
LOC100505702
LOC100505875
LOC100505989
LOC100506013
LOC100506035
LOC100506085
LOC100506122
LOC100506229
LOC100506462
LOC100506564
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4453
MIR4799
MIR4450
MIR3688-2
MIR4451
FAM47E-STBD1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.1.

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

Genes
ATRX
Genes in Wide Peak

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

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

Genes
FOXL2
CBLB
GATA2
MLF1
RPN1
GMPS
TFG
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
AADAC
ACPP
ADCY5
ADPRH
AGTR1
ALCAM
ATP1B3
ATP6V1A
ATR
BCHE
CASR
CD80
CD86
CD47
COL8A1
CP
CPA3
CPB1
CPOX
CSTA
DRD3
ECT2
EPHA3
EPHB1
MECOM
GAP43
GHSR
GOLGB1
GP9
GPR15
GSK3B
GTF2E1
GYG1
HCLS1
HGD
IL12A
ITGB5
KPNA1
KPNA4
LSAMP
TM4SF1
MBNL1
MCM2
MME
CD200
MYLK
NCK1
NDUFB4
CLDN11
P2RY1
PCCB
PFN2
SERPINI1
SERPINI2
PIK3CB
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
PPP2R3A
PRKCI
PROS1
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
RHO
RPL24
RYK
SHOX2
SI
SIAH2
SKIL
SLC2A2
SLC15A2
SLCO2A1
HLTF
SSR3
TERC
TF
TFDP2
SEC62
TM4SF4
TRH
TRPC1
UPK1B
UMPS
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
SOX14
BFSP2
RUVBL1
B4GALT4
B3GALNT1
SNX4
TNFSF10
NR1I2
MBD4
H1FX
KALRN
SLC33A1
COPB2
CHST2
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
TSC22D2
TOMM70A
P2RY14
SMC4
COX17
CD96
KCNMB2
STAG1
ST3GAL6
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
FSTL1
MRPL3
PDCD10
FILIP1L
RNF13
MGLL
MRAS
COPG
SLITRK3
NLGN1
MYH15
PLCH1
TMCC1
TNIK
PLXND1
DNAJC13
U2SURP
C3orf27
ANAPC13
ARMC8
C3orf17
ABI3BP
WWTR1
PVRL3
TIPARP
ARHGEF26
ZBTB20
OR5K1
OR5H1
FAM162A
PCOLCE2
SEC22A
GPR160
NPHP3
ATP2C1
ZBTB11
MORC1
SERP1
GOLIM4
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
SCHIP1
PIK3R4
PODXL2
TRAT1
IMPG2
NMD3
COMMD2
A4GNT
DBR1
CLDN18
TIMMDC1
RSRC1
PLA1A
AMOTL2
CCRL1
RAB6B
SELT
FBXO40
P2RY13
IL20RB
GPR87
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
RG9MTD1
SLC41A3
SLC35A5
TMEM45A
IFT57
MSL2
FAIM
SLC25A36
DPPA4
TMEM39A
ABHD10
CDV3
IFT122
TBC1D23
WDR52
EAF2
MYNN
EIF5A2
CLDND1
MUC13
SUCNR1
LXN
C3orf37
MRPS22
NIT2
POGLUT1
BBX
CCNL1
PLSCR2
PLSCR4
PCNP
SENP7
ISY1
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
KIAA1524
SLC7A14
SRPRB
BPESC1
EEFSEC
NSUN3
CLSTN2
POPDC2
NFKBIZ
ZMAT3
ATG3
MFSD1
CCDC14
FNDC3B
P2RY12
TMEM108
OR5H6
OR5H2
ZXDC
ZBED2
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
TBL1XR1
ZBBX
LRRC31
CCDC48
NEK11
UBA5
PHC3
C3orf36
ARL14
NAA50
CEP63
CEP70
ABTB1
TMEM22
OR5AC2
PARP9
ESYT3
SPATA16
EIF2A
ARL6
ZIC4
ACAD11
CHCHD6
C3orf26
HPS3
ARPM1
SLC12A8
RETNLB
CCDC54
MINA
GPR128
DIRC2
GFM1
C3orf15
PHLDB2
LOC90246
C3orf25
BOC
FAM55C
SPSB4
ACPL2
EGFEM1P
TXNRD3
OSBPL11
LRRC58
TM4SF18
MED12L
CLRN1-AS1
CPNE4
CCDC58
OTOL1
ZPLD1
CD200R1
DCBLD2
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
GRK7
FAM172BP
RPL32P3
H1FOO
PISRT1
DTX3L
LOC151658
PPM1L
WDR49
LRRC34
DPPA2
CCDC80
BTLA
ROPN1B
C3orf22
C3orf55
C3orf79
SPICE1
NUDT16P1
LOC152225
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
CHST13
KBTBD12
DHX36
DZIP1L
ALG1L
ARL13B
DHFRL1
RPL22L1
GABRR3
PTPLB
TIGIT
LOC201651
C3orf58
KIAA2018
ZBTB38
NAALADL2
ZDHHC23
LOC255025
NUP210P1
COL6A5
GK5
PLCXD2
GCET2
LSAMP-AS3
SLC9A9
LOC285205
EPHA6
DNAJB8-AS1
RABL3
IGSF10
C3orf33
SLC9A10
LOC285359
ILDR1
TRIM59
TRIM42
RAB43
KY
LOC339874
LOC339894
H1FX-AS1
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
NME9
LNP1
CCDC37
NPHP3-AS1
NMNAT3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIR15B
MIR16-2
MIR198
STX19
ARGFX
TMEM30C
ALG1L2
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
LOC646903
PA2G4P4
LOC647107
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
MIR548A3
MIR551B
MIR567
MIR568
MIR569
FAM86HP
PRR23A
LOC730091
LOC100009676
LOC100125556
WWTR1-AS1
LOC100128164
LOC100129550
ZBTB20-AS1
TIPARP-AS1
LOC100289361
MIR1280
MIR548I1
LOC100302640
MIR548H2
MIR548G
LOC100498859
MIR3919
MIR3921
IQCJ-SCHIP1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
LOC100507032
LOC100507389
ARHGEF26-AS1
LOC100507537
NPHP3-ACAD11
ISY1-RAB43
MIR4796
MIR4788
MIR4789
MIR4446
Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CCND1
CBL
DDX6
DDX10
FLI1
MEN1
MLL
NUMA1
PAFAH1B2
POU2AF1
SDHD
PICALM
PCSK7
ARHGEF12
MAML2
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
ACAT1
ACRV1
ACTN3
ADRBK1
APLNR
ALDH3B1
ALDH3B2
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
PHOX2A
ARL2
ARRB1
FXYD2
BAD
BBS1
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
C11orf9
C11orf10
DAGLA
CAPN1
CASP1
CASP4
CASP5
SERPINH1
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CFL1
CTSC
CHEK1
CHKA
CHRM1
CLNS1A
CNTF
COX8A
CPT1A
CRYAB
CST6
CTNND1
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
EEF1G
MARK2
CTTN
ESRRA
ETS1
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLR1
FOLR2
FOLR3
FTH1
FUT4
SLC37A4
LRRC32
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GUCY1A2
H2AFX
HMBS
SLC29A2
HSPA8
HSPB2
DNAJC4
HTR3A
IGHMBP2
IL10RA
IL18
INCENP
INPPL1
STT3A
KCNJ1
KCNJ5
KRTAP5-9
FADS1
FADS3
VWA5A
LRP5
LTBP3
MAP6
MCAM
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYO7A
NCAM1
NDUFC2
NDUFV1
NDUFS8
NFRKB
NNMT
NPAT
NRGN
OMP
OPCML
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PC
PDE2A
PGA5
PGR
PLCB3
POLR2G
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PTPRCAP
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RARRES3
RBM4
RDX
RELA
DPF2
SNORD15A
ROM1
RPS3
RPS6KB2
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SIPA1
SLC3A2
SLN
SORL1
SPTBN2
SRPR
SSRP1
ST14
STX3
STX5
TAGLN
TCN1
TECTA
THRSP
THY1
TM7SF2
TRPC6
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WNT11
SF1
ZFPL1
ZBTB16
ZNF202
FOSL1
CUL5
FZD4
PPFIA1
SLC43A1
BARX2
OR7E2P
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
AIP
SYT7
SART1
USP2
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
FADS2
MED17
EI24
PITPNM1
RIN1
MTL5
FEZ1
CEP57
ARHGAP32
SPCS2
ARHGEF17
GAB2
C2CD2L
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
IL18BP
DPP3
KCNK7
RBM7
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
PRG3
YAP1
RBM14
CDC42EP2
NXF1
KAT5
HYOU1
SSSCA1
DRAP1
TAF6L
ATP5L
SCGB1D2
SCGB1D1
POLD3
STARD10
NEU3
ME3
GPR83
YIF1A
SRSF8
EHD1
STIP1
CLP1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
PTGDR2
SLCO2B1
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
NCAPD3
SIK3
CLCF1
VSIG2
BACE1
FAM89B
SNHG1
POLA2
TRIM29
RAB38
CADM1
FLRT1
PANX1
PRDX5
POU2F3
BRMS1
C11orf20
CHRDL2
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
PPP1R14B
OR8G2
OR8B8
OR8G1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
CHORDC1
ACAD8
B3GAT1
RAB30
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
DDX25
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
KCNK4
NTM
CDON
UBXN1
TMX2
GAL
SIDT2
SUV420H1
TMEM216
CHCHD8
SLC15A3
MS4A4A
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
RSF1
SPA17
FXYD6
C11orf24
CNTN5
SIAE
C11orf71
ROBO4
WDR74
SLC35F2
RAB39A
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
VPS37C
ANO1
NADSYN1
FAM86C1
C11orf57
CCDC87
PPP6R3
RNF121
ACER3
ELMOD1
CDC42BPG
FOXRED1
OTUB1
PACS1
KDM4D
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
TMPRSS4
GPR137
IFT46
C11orf75
C11orf30
PRDM10
CABP4
TRIM49
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
CARNS1
USP28
POLD4
KRTAP5-8
PLEKHB1
MS4A7
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
PKNOX2
FAM111A
TP53AIP1
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
KLC2
TUT1
MRPL11
TMEM135
KCTD14
C11orf95
LRFN4
AHNAK
ALG8
TMEM223
TMEM109
CCDC86
C11orf48
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
CCDC82
ALG9
CLMP
NAA40
ZBTB3
PDZD3
C11orf63
CPSF7
CCDC15
ASRGL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR10W1
OR10V2P
GDPD5
CLPB
UNC93B1
RAB1B
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
RNASEH2C
TMEM126A
DCUN1D5
EIF1AD
NUDT22
KIAA1826
SYVN1
KIRREL3
DGAT2
MS4A14
BUD13
TMEM25
RPUSD4
TBRG1
RELT
UBASH3B
C11orf70
LGALS12
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
ATG16L2
GLB1L2
ESAM
DKFZp761E198
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
VPS26B
GLB1L3
CDCA5
RPLP0P2
SLC22A9
SNORD15B
TIRAP
CARD16
C1QTNF5
TMEM123
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRF
ARAP1
CATSPER1
HRASLS5
SLC36A4
FAT3
TRIM64
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
XRRA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
AMOTL1
CCDC67
PATE1
C11orf65
GPHA2
ADAMTS15
B3GNT6
MPZL3
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
MS4A6E
DEFB108B
PELI3
ANGPTL5
LOC254100
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
EML3
TMEM151A
RNF214
NPAS4
C11orf31
AQP11
C11orf85
SLC25A45
NEAT1
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
LOC283194
LINC00301
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
CCDC88B
TTC9C
SLC22A24
RCOR2
CCDC84
TMEM225
OR8D4
ANKRD13D
ANKRD42
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
TBX10
C11orf34
RTN4RL2
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
KRTAP5-10
SLC22A25
SLC22A10
SPDYC
LIPT2
VSTM5
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
PCNXL3
FLJ42102
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR130A
MIR139
MIR192
MIR194-2
MIR34B
MIR34C
DDI1
BLID
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
LINC00167
OR5B3
MIR326
MS4A13
SCARNA9
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
BTBD18
LOC643733
PGA3
PGA4
LOC643923
CLDN25
FAM86C2P
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
SNORA57
MIR611
MIR612
TRIM49L1
METTL12
C11orf83
MIR708
LOC100128239
LOC100129216
LOC100130348
LOC100130987
LOC100132078
LOC100133315
PATE3
LOC100288077
LOC100288346
MIR1304
MIR1908
MIR1237
MIR548K
SNORA70E
BACE1-AS
MIR4300
MIR4301
MIR3162
MIR3167
MIR3165
MIR1260B
LOC100499227
MIR3654
MIR3920
MIR3656
MIR3664
MIR3680-1
LOC100506233
LOC100506368
CASP12
LOC100507050
LOC100507392
RBM14-RBM4
LOC100526771
TMX2-CTNND1
ARL2-SNX15
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
HNRNPUL2-BSCL2
MIR4697
MIR4490
MIR4489
MIR4690
MIR4493
MIR4491
MIR4492
MIR4696
MIR4691
MIR4692
MIR4693
MIR4488
LOC100652768
Genes in Wide Peak

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

Table S20.  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
Genes in Wide Peak

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

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

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
GNA11
JAK3
KLK2
LYL1
MLLT1
PPP2R1A
SH3GL1
SMARCA4
STK11
TCF3
TPM4
ELL
FSTL3
CIC
BRD4
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
hsa-mir-1270-2
hsa-mir-1270-1
hsa-mir-640
hsa-mir-3189
hsa-mir-3188
hsa-mir-1470
hsa-mir-639
hsa-mir-181d
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
hsa-mir-4322
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
A1BG
ACP5
ACTN4
AP2A1
AES
AMH
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ASNA1
ATP1A3
ATP4A
ATP5D
AXL
AZU1
BAX
BCAT2
BCKDHA
HCN2
CEACAM1
BLVRB
BSG
BST2
C3
C5AR1
CA11
CACNA1A
CALM3
CALR
CAPNS1
CAPS
CCNE1
CD22
CD33
SIGLEC6
CD37
CD70
CD97
CDC34
CDKN2D
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CIRBP
TBCB
CKM
AP2S1
CLC
CLPTM1
CNN1
CNN2
COMP
COX6B1
COX7A1
CRX
CSNK1G2
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DAPK3
DBP
CFD
DHPS
DMPK
DMWD
DNASE2
DNM2
DNMT1
ARID3A
ECH1
EEF2
EFNA2
MEGF8
ELANE
ELAVL1
ELAVL3
EMP3
EMR1
EPOR
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FARSA
FCAR
FCER2
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
FUT3
FUT5
FUT6
GAMT
GCDH
GDF1
GIPR
GNA15
GNG7
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
MKNK2
GPX4
GRIK5
GRIN2D
ARHGAP35
GSK3A
GTF2F1
GYS1
GZMM
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
DNAJB1
ICAM1
ICAM3
ICAM4
IL11
IL12RB1
ILF3
INSL3
INSR
IRF3
JUNB
JUND
KCNA7
KCNC3
KCNJ14
KCNN1
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LDLR
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
CYP4F3
BCAM
MAG
MAN2B1
MATK
MEF2BNB-MEF2B
RAB8A
MAP3K10
MYO1F
MYBPC2
GADD45B
MYO9B
HNRNPM
CEACAM6
NDUFA3
NDUFA7
NDUFB7
NFIC
NFIX
NFKBIB
NKG7
CNOT3
NOTCH3
NOVA2
NPAS1
NPHS1
NRTN
NTF4
NUCB1
OAZ1
P2RY11
PAFAH1B3
PALM
PDE4A
PDE4C
PEG3
PEPD
PIK3R2
PIN1
PLAUR
FXYD1
FXYD3
POLD1
POLR2E
POLR2I
POLRMT
POU2F2
PPP5C
PRKACA
PRKCG
PKN1
PRKCSH
MAP2K2
MAP2K7
PSPN
PRRG2
KLK7
KLK6
KLK10
PRTN3
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTBP1
PTGER1
PTGIR
PTPRH
PTPRS
PVR
PVRL2
RAB3A
RAD23A
RELB
UPF1
RFX1
RFX2
RPL18
RPL18A
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS15
RPS16
RPS19
RPS28
RRAS
RTN2
RYR1
SAFB
CLEC11A
SCN1B
CCL25
SEPW1
SGTA
SLC1A5
SLC1A6
SLC5A5
SLC8A2
SNAPC2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
STXBP2
SULT2B1
SULT2A1
SUPT5H
SYT5
TBXA2R
PRDX2
TGFB1
THOP1
ICAM5
TLE2
TNNI3
TNNT1
TULP2
TYK2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
VAV1
XRCC1
ZFP36
ZNF8
ZNF14
ZNF708
ZNF17
ZNF20
ZNF28
MZF1
ZNF43
ZNF45
ZNF69
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF121
ZNF132
ZNF134
ZNF135
ZNF136
ZNF137P
ZNF146
ZNF154
ZNF155
ZNF175
ZNF177
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
MADCAM1
SF3A2
SYMPK
MIA
CLPP
DPF1
LTBP4
TEAD2
RANBP3
CYP4F2
PPFIA3
KHSRP
PLA2G4C
PPAP2C
RFXANK
EIF3G
STX10
S1PR4
URI1
TNFSF14
TNFSF9
NAPA
SIGLEC5
FCGBP
AP1M1
AP3D1
PGLYRP1
F2RL3
UBE2M
ARHGEF1
PDCD5
DYRK1B
LPAR2
RAB11B
CRLF1
NUMBL
CYTH2
S1PR2
ZNF235
TRIP10
LONP1
ZNF264
KCNK6
NCR1
MED26
HOMER3
IL27RA
NAPSA
GDF15
TECR
ZNF254
GMFG
RAB3D
APBA3
IER2
KLK4
SAFB2
ZNF432
DHX34
KIAA0355
ZNF536
MLL4
KEAP1
MED16
CHAF1A
SH2D3A
AP1M2
UBA2
SAE1
SUGP2
EBI3
TRIM28
ZNF256
DDX39A
ZNF443
PLIN3
AKAP8
LILRB2
APC2
PAK4
B3GNT3
CLEC4M
ABCA7
HMG20B
KLF2
TUBB4A
TMEM147
IFI30
TOMM40
TIMM44
CARM1
SEMA6B
ZNF211
CHERP
RNASEH2A
RABAC1
TRAPPC2P1
SPINT2
KLF1
DLL3
CERS1
GIPC1
POP4
ZNF234
ZNF266
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
PNPLA6
KDELR1
UQCR11
LILRB5
ILVBL
SLC27A5
LILRB4
KLK11
TMED1
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
CLASRP
KPTN
SLC7A9
CDC37
MAP4K1
KLK8
CYP4F8
PNKP
COPE
U2AF2
ATF5
ZFP30
ZNF507
LPHN1
PPP6R1
CARD8
SBNO2
SIRT2
CYP2G1P
MAST1
UNC13A
KDM4B
MAST3
SIPA1L3
FCHO1
ZC3H4
ZFR2
SIN3B
HAUS5
ARHGEF18
CRTC1
MAU2
PIP5K1C
FBXO46
ETHE1
RPL13A
HMHA1
SYNGR4
LILRA4
PRG1
CASP14
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
SHC2
TMEM59L
PGLS
ZNF324
LSM4
KLK5
ZNF345
PRKD2
RPL36
ZNF473
KANK2
CLIP3
FAM32A
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
OR7A17
TIMM13
TSPAN16
DAZAP1
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7A5
OR7C1
SNORA68
SNORD41
SNORD37
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
AKAP8L
FGF22
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
TJP3
CPAMD8
SIGLEC9
SIGLEC8
GPR77
ITGB1BP3
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
C19orf53
BABAM1
LGALS13
UHRF1
CYP2S1
STRN4
CCDC106
HOOK2
EPN1
SERTAD3
SERTAD1
SLC39A3
GLTSCR2
GLTSCR1
TNPO2
EMR2
CD209
EHD2
KLK14
KLK12
COL5A3
RDH8
SHANK1
NOSIP
MRPL4
NDUFA13
ANGPTL4
ZNF580
HSD17B14
GP6
VRK3
MARCH2
ZNF571
GMIP
CD320
ECSIT
THEG
ZBTB7A
FZR1
WDR83OS
ISYNA1
ZNF581
SIRT6
PIAS4
LSR
LSM7
ZNF44
TM6SF2
MBD3
PTOV1
S1PR5
FXYD7
FXYD5
RAB4B
MIER2
DDX49
PAF1
PCSK4
PPP1R12C
TRPM4
ZNF586
ZNF562
QPCTL
GATAD2A
BEST2
FBXL12
FAM83E
PGPEP1
CC2D1A
EPS8L1
RASIP1
TMEM161A
SARS2
TMEM160
C19orf24
PIH1D1
C19orf60
GPATCH1
SAMD4B
ATP5SL
PLEKHJ1
C19orf73
MAP1S
PNMAL1
TMEM143
KLHL26
ZNF444
C19orf66
FEM1A
ZNF823
KLK15
MED29
STAP2
TRMT1
BTBD2
NLRP2
RNF126
ZNF416
ZNF446
CCDC94
ASF1B
ZNF701
ZNF83
ZNF415
USE1
PSENEN
ZNF302
C19orf80
LIN37
C19orf10
SMG9
ZNF253
IRGC
SLC7A10
PPAN
CABP5
RETN
SPHK2
LGALS14
EXOSC5
MEIS3
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
CEACAM19
SLC17A7
NAT14
CD177
ATP13A1
RGL3
SLC44A2
VN1R1
MCOLN1
RCN3
ZNF304
TTYH1
WDR18
REXO1
PNMAL2
ZNF490
PRR12
DOCK6
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
CAMSAP3
USP29
PLEKHA4
ZFP14
ZNF317
ZNF529
PRX
ANO8
SPTBN4
MARK4
SUGP1
HAMP
CATSPERG
CYP4F11
ZNF71
ZNF77
SCAF1
C19orf29
PRODH2
EPS15L1
WIZ
CACNG8
CACNG7
CACNG6
UBL5
ZNF350
TSKS
CELF5
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
LPPR2
ZNF574
PLEKHG2
RASAL3
MRPL34
KRI1
ZSWIM4
ZNF649
ZSCAN18
MGC2752
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
TMEM38A
TSEN34
KCTD15
SLC25A23
C19orf42
ZNF426
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
C19orf57
ZNF576
FSD1
ZNF557
LRFN3
ABHD8
CERS4
OCEL1
ZNF329
GLT25D1
IGFLR1
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
TLE6
ZNF552
EPHX3
PODNL1
ZNF671
ZNF613
ADCK4
CNTD2
SLC35E1
LPPR3
DENND1C
ZNF442
ZNF702P
ZNF556
LOC80054
ZNF606
ZNF614
LRRC8E
FLJ22184
FUZ
OPA3
ZNF430
ITPKC
UBXN6
PBX4
KIAA1683
B9D2
OR4F17
RSPH6A
CCDC130
ACSBG2
ADAMTS10
ZNF611
MED25
QTRT1
FAM108A1
ZNF93
DOHH
PLVAP
RTBDN
BCL2L12
C19orf12
TEX101
GRWD1
ANGPTL6
KLF16
USHBP1
WDR87
TSSK6
CCDC8
KIRREL2
ANKRD27
PRAM1
C19orf44
ZNF541
MRI1
SYT3
FBXW9
ALKBH7
WDR83
PDCD2L
ZNF414
AKT1S1
ELOF1
ZNF528
DOT1L
BRSK1
ZNF333
FBN3
ZNF527
CNFN
ZNF559
SNORD35B
KISS1R
EMR3
ZNF347
CREB3L3
GTPBP3
HDGFRP2
ZNF577
MPV17L2
ZNF607
SUV420H2
C19orf48
NFKBID
LMNB2
RAX2
ZBTB45
CEP89
ZNF382
ZNF587
FIZ1
ZNF566
MUM1
HSH2D
MPND
ALKBH6
ATG4D
ATCAY
SYDE1
RHPN2
MBD3L1
GALP
SIGLEC10
SIGLEC12
ZNF628
MIDN
KIR3DX1
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
SAMD1
DCAF15
GADD45GIP1
ZNF835
YIF1B
ZNF799
C19orf52
ZNF625
ZNF700
ZNF439
ZNF486
DPP9
ZNF682
R3HDM4
C19orf6
C19orf40
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
TPGS1
ZNF461
ZNF585B
CRB3
TIMM50
SHKBP1
REEP6
PEX11G
DMKN
ZNF561
OLFM2
CCDC114
HAUS8
FAM125A
DKFZp434J0226
ARMC6
ACPT
CGB5
DKFZp566F0947
MUC16
CGB7
LRRC4B
ZNF101
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
FDX1L
NACC1
PTH2
IZUMO4
SCAMP4
ADAT3
LOC113230
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
PGLYRP2
LMTK3
LENG8
CCDC124
ZNF554
FBXO17
KIR3DL3
ARHGAP33
EVI5L
RASGRP4
NXNL1
CCDC151
ZNF653
ZNF526
ZNF837
GRIN3B
MRPL54
LRG1
CIB3
RLN3
CLDND2
ZNF816
ZNF543
CEACAM20
RAVER1
OR7D4
OR7G1
OR1M1
COX6B2
CALR3
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
OSCAR
ZNF813
ZNF441
ZNF491
ZNF440
SWSAP1
CCDC159
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
WDR88
TMIGD2
EID2B
TNFAIP8L1
ZNF57
IRGQ
ZNF428
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
C19orf21
LRRC25
OR1I1
WTIP
ZNF792
NR2C2AP
HSPB6
CCDC105
CYP4F22
RINL
FBXO27
PLK5
C19orf47
LOC126536
OR10H4
ANKLE1
C2CD4C
ZNF358
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
LOC147727
ZNF560
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
ZNF563
SPC24
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
LGALS16
TTC9B
TICAM1
CIRBP-AS1
ZNRF4
ZNF599
FAM187B
CILP2
C19orf55
LOC148145
ZNF558
CDC42EP5
LOC148189
ZNF98
ZNF738
ZNF714
ZNF681
C19orf25
ATP8B3
FLJ25328
DIRAS1
ZNF555
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF846
OR7D2
ZNF579
ZNF791
ZNF564
ZNF709
ZNF433
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
PRR22
LGI4
C19orf46
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
ANKRD24
SPACA4
ZNF675
C19orf59
ZNF627
DAND5
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
C19orf26
CSNK1G2-AS1
PRR24
C19orf38
ZNF549
SYCE2
NAPSB
KANK3
PLAC2
TMEM146
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
ACTL9
OR2Z1
LOC284385
ZNF763
ZNF844
LOC284395
SCGB2B2
WDR62
ZFP82
LOC284408
LOC284412
VSTM1
TMEM150B
FAM71E2
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
OR10H5
NWD1
SLC25A42
LOC284440
ZNF493
ODF3L2
LOC284454
HKR1
VN1R2
VN1R4
EMR4P
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
ADAMTSL5
CLEC4G
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
NANOS3
PALM3
SELV
ZNF530
C19orf51
ZNF429
ZNF233
LILRA5
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
TMEM205
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
WASH5P
SLC27A1
LOC386758
LOC388499
C3P1
ZNF788
CLEC17A
CYP4F24P
RPSAP58
RGS9BP
KRTDAP
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ONECUT3
OR7G2
OR7G3
OR7A10
NUDT19
ZNF793
PAPL
LOC390940
ZNF805
SPRED3
MEX3D
ZNF321P
FLJ45445
PRSS57
VMAC
LOC400680
LOC400684
LOC400685
LGALS17A
SIGLEC16
FLJ26850
ZNF880
ZNF772
ZNF833P
IGLON5
HAPLN4
CTXN1
C19orf29-AS1
MIRLET7E
MIR125A
MIR150
MIR181C
MIR199A1
MIR23A
MIR24-2
MIR27A
MIR7-3
MIR99B
PLIN5
CLEC4GP1
ZNF506
LOC440518
ZNF724P
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
FLJ25758
A1BG-AS1
DPRX
DUXA
ASPDH
MIR181D
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
LOC641367
TMEM91
FAM138F
LOC643669
SCGB1B2P
SDHAF1
LOC644189
LOC644554
LINGO3
ARRDC5
FAM138A
LOC646508
SBK2
LOC646862
UCA1
PSG10P
LGALS7B
PHLDB3
MBD3L4
MBD3L3
SEC1
ZNF826P
SNORD23
SNORD88A
SNORD88B
SNORD88C
SNORD105
PPAN-P2RY11
MIR637
MIR638
MIR639
MIR641
MIR642A
MIR643
RPL13AP5
LOC728752
PLIN4
CCDC61
ZNF812
ZNF878
CEACAM18
SHISA7
LOC729966
FLJ30403
MEF2BNB
ZNF814
ZNF726
MIR769
SIGLEC14
MIMT1
LOC100101266
SNORD105B
ZGLP1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
C19orf71
LOC100128573
LOC100128675
LOC100128682
LOC100129083
ZNF737
LOC100129935
SCGB2B3P
TMEM221
SGK110
LOC100131094
BSPH1
LOC100131691
C19orf79
LOC100134317
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
MEF2B
LOC100287177
ZNF729
LOC100288123
LOC100289650
ZNF587B
MIR1470
MIR1270-1
MIR1283-2
MIR1909
MIR1181
MIR1238
MIR1323
MIR1283-1
MIR1227
LOC100379224
MIR3191
MIR3188
MIR3187
MIR3190
MIR320E
MIR4322
MIR3189
MIR4324
MIR4323
MIR1270-2
MIR4321
MIR642B
MIR3940
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100505835
LOC100506012
LOC100506033
LOC100506068
LOC100506469
LOC100506930
LOC100507003
ZNF865
LOC100507373
LOC100507433
THEG5
LOC100507567
LOC100507588
ZNF559-ZNF177
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
ZNF625-ZNF20
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4747
MIR4531
MIR4746
MIR4748
MIR4745
MIR4751
LOC100631378
LOC100652909
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 11 significant results found.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 2121 0.13 -0.179 0.966 0.28 1.52 0.243
1q 1955 0.13 -0.192 0.966 0.28 1.5 0.243
2p 924 0.11 -0.56 0.966 0.11 -0.56 0.761
2q 1556 0.06 -1.16 0.966 0.11 -0.592 0.761
3p 1062 0.06 -1.12 0.966 0.16 -0.00472 0.718
3q 1139 0.06 -1.12 0.966 0.16 0.00266 0.718
4p 489 0.06 -1.16 0.966 0.16 -0.0589 0.722
4q 1049 0.06 -1.12 0.966 0.16 -0.00597 0.718
5p 270 0.00 -1.83 0.966 0.15 -0.177 0.76
5q 1427 0.11 -0.518 0.966 0.11 -0.518 0.761
6p 1173 0.24 0.882 0.966 0.19 0.331 0.706
6q 839 0.30 1.71 0.966 0.00 -1.63 0.949
7p 641 0.21 0.578 0.966 0.06 -1.08 0.881
7q 1277 0.11 -0.531 0.966 0.11 -0.531 0.761
8p 580 0.18 0.16 0.966 0.18 0.16 0.718
8q 859 0.11 -0.565 0.966 0.11 -0.565 0.761
9p 422 0.18 0.145 0.966 0.18 0.145 0.718
9q 1113 0.13 -0.261 0.966 0.28 1.4 0.251
10p 409 0.00 -1.71 0.966 0.25 1.05 0.348
10q 1268 0.00 -1.61 0.966 0.30 1.76 0.173
11p 862 0.08 -0.816 0.966 0.37 2.48 0.0657
11q 1515 0.00 -1.6 0.966 0.30 1.8 0.173
12p 575 0.06 -1.08 0.966 0.21 0.571 0.58
12q 1447 0.00 -1.71 0.966 0.20 0.553 0.58
13q 654 0.00 -1.58 0.966 0.35 2.29 0.0882
14q 1341 0.25 0.897 0.966 0.47 3.57 0.00352
15q 1355 0.13 -0.241 0.966 0.28 1.42 0.251
16p 872 0.17 0.0793 0.966 0.12 -0.474 0.761
16q 702 0.14 -0.186 0.966 0.33 1.99 0.157
17p 683 0.00 -1.7 0.966 0.25 1.08 0.348
17q 1592 0.06 -1.09 0.966 0.16 0.0466 0.718
18p 143 0.14 -0.23 0.966 0.33 1.91 0.159
18q 446 0.13 -0.313 0.966 0.28 1.31 0.251
19p 995 0.11 -0.554 0.966 0.11 -0.554 0.761
19q 1709 0.00 -1.7 0.966 0.20 0.582 0.58
20p 355 0.18 0.139 0.966 0.18 0.139 0.718
20q 753 0.28 1.35 0.966 0.13 -0.289 0.761
21q 509 0.13 -0.308 0.966 0.28 1.32 0.251
22q 921 0.09 -0.621 0.966 0.47 3.74 0.00352
Xq 1312 0.08 -0.696 0.966 0.42 3.18 0.00988
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/SARC/1709018/2.GDAC_MergeDataFiles.Finished/SARC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

Table 4.  Get Full Table First 10 out of 20 Input Tumor Samples.

Tumor Sample Names
TCGA-DX-A2IZ-01A-11D-A21P-01
TCGA-DX-A2J0-01A-11D-A21P-01
TCGA-DX-A2J1-01A-11D-A21P-01
TCGA-DX-A2J4-01A-32D-A21P-01
TCGA-DX-A3LS-01A-11D-A21P-01
TCGA-DX-A3LT-01A-12D-A21P-01
TCGA-DX-A3LU-01A-11D-A21P-01
TCGA-DX-A3LW-01A-21D-A21P-01
TCGA-FX-A3NJ-01A-11D-A21P-01
TCGA-FX-A3NK-01A-11D-A21P-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.

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