Kidney Renal Papillary Cell Carcinoma: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
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 103 tumor samples used in this analysis: 16 significant arm-level results, 1 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.

Table 1. Get Full Table Amplifications Table - 1 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
--- | --- | --- | --- | ---
19p13.2 | 3.6023e-08 | 3.6023e-08 | chr19:7296453-7397014 | 0 [INSR]

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 - 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
--- | --- | --- | --- | ---
9p21.3 | 7.1005e-13 | 7.1005e-13 | chr9:21865498-22448737 | 4
1p36.31 | 0.0012987 | 0.0012987 | chr1:1-8932353 | 147
2q37.3 | 0.012894 | 0.013108 | chr2:217722405-243199373 | 264
6q22.31 | 0.024579 | 0.024296 | chr6:123955968-125232805 | 1
Xq28 | 0.028528 | 0.028528 | chrX:151843350-152761709 | 21
14q11.2 | 0.018087 | 0.051601 | chr14:1-33303273 | 183
5q35.2 | 0.058882 | 0.098615 | chr5:174422375-177410415 | 51
3p22.1 | 0.11483 | 0.1217 | chr3:1-55115508 | 491
14q23.3 | 0.032983 | 0.13376 | chr14:58869576-81577655 | 189
Xq21.31 | 0.1799 | 0.16298 | chrX:91074436-92938656 | 2
4q32.1 | 0.18103 | 0.1799 | chr4:14992411-183068969 | 692
14q32.2 | 0.029968 | 0.1799 | chr14:95634861-100072998 | 25
19q13.42 | 0.19368 | 0.19368 | chr19:36149017-59128983 | 893
2p11.2 | 0.20171 | 0.20171 | chr2:1-148698455 | 880
5p15.33 | 0.22356 | 0.24024 | chr5:1-93956985 | 405
5q15 | 0.19368 | 0.24024 | chr5:1-180915260 | 1050
12q24.33 | 0.24024 | 0.24024 | chr12:124452696-133851895 | 57

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
RERE
CDK11B
DFFB
DVL1
MEGF6
ENO1
GABRD
GNB1
ZBTB48
TNFRSF9
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
PER3
VAMP3
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
UTS2
RER1
PARK7
ACOT7
CAMTA1
ICMT
CHD5
NOC2L
OR4F3
ARHGEF16
SSU72
WRAP73
SLC45A1
SDF4
ERRFI1
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
DNAJC11
AJAP1
TP73-AS1
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
OR4F5
NOL9
LINC00115
MORN1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
C1orf170
KIAA1751
THAP3
LOC115110
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
LOC148413
PHF13
CCDC27
CALML6
C1orf86
ATAD3C
LOC254099
TTLL10
NPHP4
FAM41C
LOC284661
C1orf174
KLHL17
TMEM240
TMEM52
AGRN
GPR153
FAM132A
HES5
LOC388588
RNF207
HES3
RNF223
MIR200A
MIR200B
FLJ42875
ANKRD65
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
FAM138A
WASH7P
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR4251
MIR4252
MIR4689
MIR4417

Genes in Wide Peak

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

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

Genes
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
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
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
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
CNPPD1
STK36
GMPPA
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
C2orf83
MFF
CXCR7
RNPEPL1
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
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
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

Table S4. 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 Xq28.

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

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

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GPR33
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
PNP
NRL
OXA1L
PCK2
PRKD1
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
AKAP6
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
AP4S1
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
JPH4
RNASE7
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
C14orf126
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
C14orf21
ADCY4
LOC283624
TSSK4
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
CBLN3
SNORD9
MIR624
DHRS4L1
SNORD126
MIR208B
MIR4307
LOC100505967
LOC100506071
NEDD8-MDP1
BCL2L2-PABPN1
MIR548AI
MIR4707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

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

Genes
NSD1
hsa-mir-4281
hsa-mir-1271
CLTB
DBN1
DRD1
F12
FGFR4
GRK6
HK3
HRH2
SLC34A1
SNCB
PDLIM7
RGS14
CPLX2
LMAN2
B4GALT7
RNF44
FAF2
ZNF346
TSPAN17
PRELID1
DDX41
NOP16
UIMC1
RAB24
FAM193B
TMED9
CDHR2
KIAA1191
DOK3
PRR7
MXD3
THOC3
UNC5A
SFXN1
GPRIN1
HIGD2A
FAM153B
LOC202181
EIF4E1B
FAM153A
ARL10
LOC340037
PFN3
C5orf25
LOC643201
LOC728554
MIR4281
LOC100507387

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p22.1.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
TSHR
GPHN
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
ACTN1
ACYP1
ARG2
ZFP36L1
ENTPD5
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GPX2
GSTZ1
HIF1A
HSPA2
LTBP2
MAX
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SIX6
PGF
PIGH
PPM1A
PPP2R5E
PRKCH
PSEN1
ABCD4
RAD51B
RTN1
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
ZBTB25
DPF3
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
NRXN3
AKAP5
SPTLC2
RGS6
KIAA0247
KIAA0586
KIAA0317
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
TIMM9
MLH3
KCNH5
POMT2
COQ6
FCF1
RDH11
COX16
DACT1
ATP6V1D
JKAMP
DHRS7
SIX4
ZFYVE1
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
YLPM1
C14orf162
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
TRMT5
ZNF410
NGB
RBM25
C14orf133
SMOC1
IRF2BPL
MPP5
C14orf135
GPR135
ZC2HC1C
C14orf169
C14orf45
SGPP1
SLIRP
DNAL1
RPS6KL1
SYT16
KIAA1737
PAPLN
CHURC1
C14orf43
LIN52
NEK9
IFT43
WDR89
C14orf149
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
RDH12
ADAM21P1
PPP1R36
SLC38A6
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
FAM71D
TMEM229B
TMEM30B
SAMD15
PROX2
ZDHHC22
TMED8
C14orf178
C14orf55
C14orf39
SNORD56B
VSX2
RAB15
HEATR4
FLJ22447
PLEKHD1
LINC00238
TEX21P
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
C14orf38
LOC731223
LOC100289511
MIR1260A
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.31.

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

Genes
NAP1L3
PCDH11X

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.1.

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

Genes
IL2
KDR
KIT
PDGFRA
RAP1GDS1
PHOX2B
CHIC2
TET2
FBXW7
FIP1L1
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
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
AGA
ALB
AMBN
ANK2
ANXA2P1
ANXA3
ANXA5
APBB2
AREG
RHOH
ART3
ATOH1
BMP3
BMPR1B
BST1
BTC
CAMK2D
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
CD38
LRBA
CDS1
CLGN
CENPC1
CENPE
CLCN3
CNGA1
CPE
CSN1S1
CSN2
CSN3
CTSO
DCK
DHX15
DMP1
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
EPHA5
EREG
ETFDH
FABP2
FGA
FGB
FGF2
FGF5
FGG
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GC
GK2
GK3P
GLRB
GNRHR
GPM6A
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
UBE2K
HMGB2
HNRNPD
HPGD
HSP90AB3P
HTN1
HTN3
IBSP
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
CXCL10
MAD2L1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MTTP
MUC7
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PCDH7
PDHA2
PET112
PF4
PF4V1
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPBP
PPID
PPP3CA
PRKG2
MAPK10
PTPN13
QDPR
REST
RFC1
ABCE1
RPL9
RPL34
RPS3A
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SNCA
SOD3
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
TDO2
TEC
TLL1
TLR1
TLR2
TRPC3
TXK
UBE2D3
UCHL1
UCP1
UGDH
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
VEGFC
GLRA3
SPARCL1
SMARCA5
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
PROM1
HERC3
SNORD73A
STBD1
CDKL2
PAPSS1
LDB2
LRAT
AIMP1
NDST3
SLIT2
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
MFAP3L
SEC24D
G3BP2
FGFBP1
HNRPDL
TSPAN5
ENAM
FAM13A
SPRY1
TLR6
ANAPC10
ATP8A1
PGRMC2
SEC24B
SLC30A9
CXCL13
SLC34A2
MAB21L2
PAICS
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
HPSE
NMU
SMR3B
NPFFR2
PPARGC1A
PPBPL2
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
ANP32C
SLC7A11
CCRN4L
PARM1
RCHY1
ANKRD17
STAP1
FBXL5
FBXO8
SMR3A
PPA2
DAPP1
DKK2
FAM184B
INTU
NAAA
COQ2
ARFIP1
SULT1B1
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
MRPS18C
LAP3
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
NUDT9
NUP54
GAR1
UGT2B28
RBM47
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
DCAF16
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
CCDC109B
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
UBA6
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
C4orf43
C4orf21
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
N4BP2
TMEM184C
SEPT11
EXOC1
TMEM165
PDGFC
FSTL5
BDH2
SMARCAD1
MEPE
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
DANCR
KIAA1211
RNF150
KIAA1239
CC2D2A
KLHL8
PCDH10
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
METTL14
WDR19
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
GUF1
SPCS3
SCOC
NEUROG2
SLC39A8
NCAPG
HHIP
NDST4
AGXT2L1
USP46
MRPL1
RASL11B
ELOVL6
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
FLJ13197
THAP9
NSUN7
UGT2A3
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
SCD5
DNAJB14
TMEM156
FRAS1
NAA15
CWH43
C4orf29
ALPK1
MED28
CXXC4
KCNIP4
CEP44
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
FGFBP2
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
NOA1
HOPX
COL25A1
USP38
LNX1
C4orf49
NAA11
AGPAT9
CBR4
PIGY
CABS1
FHDC1
FLJ20021
MGC45800
PRMT10
CCDC149
DDX60L
YTHDC1
NAF1
MOB1B
TIFA
FAM114A1
RG9MTD2
TBCK
HELQ
CYP2U1
C1QTNF7
DDIT4L
WDR17
ARAP2
GDEP
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
LIN54
SPATA18
C4orf32
TMPRSS11B
GNPDA2
SPATA4
CPEB2
ARL9
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
NFXL1
NIPAL1
PAQR3
SHISA3
LOC152578
SCFD2
C4orf39
THAP6
C4orf26
KLB
PPM1K
C4orf45
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
FREM3
MMAA
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
GSX2
SYNPO2
C4orf46
SLC10A4
TIGD4
TMEM154
C4orf34
TMEM192
TAPT1
FLJ39653
CNOT6L
TECRL
LCORL
C4orf22
LOC255130
EPGN
ELMOD2
NPNT
MFSD8
LOC256880
FDCSP
NAP1L5
LOC285419
DCAF4L1
LOC285456
LOC285501
FAM13A-AS1
GPRIN3
COX18
YIPF7
FRYL
RNF175
LOC285540
FAM200B
C4orf37
CSN1S2AP
ZAR1
CCDC158
TMPRSS11A
LRRC66
LOC340017
LOC344967
PRSS48
SOWAHB
LRIT3
SLC10A6
HSD17B13
PCNAP1
KCNIP4-IT1
KCTD8
C4orf52
BEND4
GRXCR1
TMPRSS11F
TRIM61
DTHD1
LOC401127
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
FLJ14186
C4orf3
RPL21P44
WDFY3-AS2
MIR218-1
MIR302A
C4orf11
MTHFD2L
LOC441025
TMEM150C
GUSBP5
HSP90AA6P
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC550112
LOC550113
UGT2A2
LOC641364
LOC641365
LOC641518
LOC644145
LOC644248
TMPRSS11GP
CLRN2
CEP170P1
LOC645513
LOC646576
C4orf51
SNORA24
SNORA26
MIR573
MIR574
MIR575
MIR577
MIR578
LINC00290
CETN4P
FAM160A1
RELL1
SNHG8
FAM47E
LOC100129858
FTLP10
LOC100144602
PP12613
ERVMER34-1
MIR1243
MIR2054
MIR1973
CSN1S2BP
MIR3140
MIR4275
MIR4276
LOC100499177
MIR3684
MIR3688-1
LOC100505545
LOC100505702
LOC100505875
SLIT2-IT1
LOC100505912
LOC100505989
LOC100506013
LOC100506035
LOC100506085
LOC100506122
LOC100506462
LOC100506564
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4453
MIR4799
MIR548AJ2
MIR4802
MIR4450
MIR3688-2
MIR4451
MIR4801
MIR4449
FAM47E-STBD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.2.

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

Genes
TCL1A
TCL6
BCL11B
BDKRB1
BDKRB2
VRK1
CCNK
TCL1B
PAPOLA
GLRX5
C14orf129
ATG2B
C14orf132
LINC00341
CLMN
SETD3
AK7
C14orf49
SNHG10
C14orf177
CCDC85C
C14orf64
SCARNA13
LOC100129345
LOC100507043

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.42.

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

Genes
AKT2
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
hsa-mir-641
A1BG
ACTN4
AP2A1
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CAPNS1
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
TBCB
CKM
AP2S1
CLC
CLPTM1
COX7A1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NPHS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POLR2I
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
TYROBP
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF146
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
MLL4
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
CLASRP
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
PPP6R1
CARD8
SIRT2
CYP2G1P
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
ZNF345
PRKD2
ZNF473
CLIP3
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
ZBTB32
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
PSENEN
LIN37
SMG9
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
ZFP14
ZNF529
PRX
SPTBN4
MARK4
CATSPERG
ZNF71
SCAF1
PRODH2
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
LRFN3
ZNF329
IGFLR1
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
WDR87
CCDC8
KIRREL2
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
SNORD35B
ZNF347
ZNF577
ZNF607
SUV420H2
C19orf48
NFKBID
ZBTB45
ZNF382
ZNF587
FIZ1
ZNF566
ALKBH6
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
ZNF461
ZNF585B
TIMM50
SHKBP1
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
ARHGAP33
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
HSPB6
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
LGALS16
TTC9B
C19orf55
CDC42EP5
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
C19orf46
ZNF540
ZNF525
SPACA4
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
WDR62
ZFP82
LOC284408
LOC284412
VSTM1
TMEM150B
FAM71E2
HKR1
VN1R2
VN1R4
NLRP9
ZNF260
ZNF546
MYPOP
NANOS2
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
C19orf51
ZNF233
LILRA5
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
LOC386758
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF793
PAPL
LOC390940
ZNF805
SPRED3
ZNF321P
LGALS17A
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
LOC643669
SDHAF1
LOC644189
LOC644554
LOC646508
SBK2
LOC646862
PSG10P
LGALS7B
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
RPL13AP5
LOC728752
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
LOC100129935
SGK110
BSPH1
LOC100131691
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
LOC100287177
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100506930
LOC100507003
ZNF865
LOC100507433
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
LOC100631378

Genes in Wide Peak

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

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

Genes
ALK
DNMT3A
ERCC3
MSH6
MSH2
MYCN
REL
PAX8
NCOA1
EML4
BCL11A
TTL
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
ACP1
ACTG2
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
BIN1
ANXA4
APOB
RHOB
ATP6V1B1
AUP1
ZFP36L2
BUB1
CAD
CALM2
CAPG
CCNT2
CD8A
CD8B
CENPA
CNGA3
COX5B
CTNNA2
CYP1B1
DARS
DBI
DCTN1
DDX1
DGUOK
LOC1720
DNAH6
DOK1
DTNB
DUSP2
E2F6
EGR4
EMX1
EN1
EPAS1
FABP1
EFEMP1
FHL2
FKBP1B
FOSL2
FSHR
FTH1P3
GCKR
GFPT1
GGCX
GLI2
GPR17
GPR39
GTF3C2
GYPC
HADHA
HADHB
HK2
HNMT
TLX2
HPCAL1
FOXN2
ID2
IL1A
IL1B
IL1R1
IL1RN
INHBB
INPP4A
KCNF1
KCNK3
KCNS3
KHK
KIF3C
AFF3
LCT
LHCGR
LIMS1
LTBP1
EPCAM
MXD1
MAL
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MTIF2
MYO7B
NPAS2
NPHP1
ODC1
OTX1
REG3A
PCBP1
PEX13
VIT
PIGF
PLEK
PLGLB2
PLGLB1
POLR2D
POMC
POU3F3
PPM1B
PPM1G
PPP1CB
PPP3R1
PRKCE
EIF2AK2
PROC
PTPN4
RAB1A
RALB
RANBP2
REG1A
REG1B
REG1P
RPL31
RPS7
RPS27A
RRM2
RTKN
SCTR
SDC1
SRSF7
SFTPB
SIX3
SLC1A4
SLC3A1
SLC8A1
SLC9A2
SLC20A1
SNRPG
SOS1
SOX11
SPAST
SPR
SPTBN1
SRD5A2
STRN
SULT1C2
ADAM17
TACR1
GCFC2
TGFA
TIA1
TPO
TSN
TSSC1
UCN
UGP2
VRK2
VSNL1
XDH
XPO1
ZAP70
ZNF2
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
DYSF
NCK2
DUSP11
KLF11
MAP4K3
VAMP8
MARCO
SUCLG1
IL18RAP
IL1RL2
IL18R1
ASAP2
ST3GAL5
SLC5A6
DDX18
EIF2B4
KYNU
TAF1B
NAT8
COX7A2L
TMSB10
IL1RL1
ITGB1BP1
NRXN1
OTOF
CIAO1
TGFBRAP1
HS6ST1
CRIPT
MAP4K4
EIF2AK3
ROCK2
CHST10
TP53I3
MRPL33
BRE
PREPL
FEZ2
GCC2
SOCS5
EIF5B
GREB1
USP34
LAPTM4A
RNF144A
SNX17
SERTAD2
MRPL19
ZEB2
SUPT7L
ARHGAP25
BCL2L11
ACTR3
ACTR2
PREB
ACTR1B
LRPPRC
PDIA6
CEBPZ
TXNDC9
MPHOSPH10
SMYD5
MYCNOS
C1D
MERTK
SEMA4F
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
CGREF1
B3GNT2
USP39
SIX2
MAP3K2
VAMP5
MTHFD2
ARID5A
PROKR1
RAB10
EDAR
GPR75
YWHAQ
IMMT
SNRNP27
GTF2A1L
STON1
EMILIN1
TBC1D8
RABL2A
NXPH2
GPR45
MGAT4A
GPN1
AAK1
MAPRE3
RAB3GAP1
RPIA
SLC4A1AP
EFR3B
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
UBXN4
PSME4
EXOC6B
EHBP1
CLASP1
PUM2
NCAPH
RHOQ
HAAO
TMEM131
R3HDM1
PSD4
WBP1
NTSR2
PRKD3
RASGRP3
QPCT
VAX2
POLR1A
CNRIP1
FAM98A
UNC50
RAB11FIP5
IFT172
PTPN18
CNNM4
CNNM3
IL36RN
SH3YL1
SNORD53
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
BMP10
ZNF638
HTRA2
TRIB2
LGALSL
C2orf27A
GRHL1
TFCP2L1
NRBP1
KCNIP3
EHD3
CD207
ITSN2
ARHGEF4
TPRKB
FAHD2A
WDPCP
MEMO1
TRAPPC12
ASB3
INSIG2
CRIM1
ANKRD39
FAM178B
RNF181
MRPL30
DNAJC27
KRCC1
MRPL35
C2orf28
PCYOX1
REV1
NAT8B
VPS54
NBAS
LIPT1
DYNC2LI1
SF3B14
YPEL5
CHMP3
CPSF3
LRP1B
SNTG2
ATAD2B
ETAA1
HEATR5B
CCDC93
AFTPH
TMEM214
RETSAT
SEMA4C
C2orf18
C2orf42
TRMT61B
PTCD3
PLEKHB2
FANCL
SRBD1
MOB1A
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
C2orf56
C2orf29
NAGK
TTC27
SMPD4
TMEM127
SLC30A6
IWS1
LIMS2
KANSL3
CCDC88A
KDM3A
ALLC
ARHGAP15
CFC1
GKN1
IL36G
CYP26B1
POLE4
KCNK12
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
RPL23AP32
RTN4
TRIM54
PELI1
TTC7A
SMEK2
BIRC6
KIDINS220
MTA3
WDR35
DPP10
RDH14
EPB41L5
ANKRD36B
SLC4A5
NLRC4
SLC5A7
AGBL5
C2orf43
THADA
RBKS
ATL2
ABCG5
ABCG8
HS1BP3
GMCL1
TTC31
ANAPC1
RMND5A
FNDC4
PAPOLG
MRPS9
MRPS5
REEP1
SOWAHC
COLEC11
PDCL3
C2orf49
TMEM185B
CENPO
OR7E91P
SAP130
GALNT14
CCDC121
SMC6
GTDC1
CLIP4
CAMKMT
GEMIN6
NOL10
ANKRD53
LRRTM4
MZT2B
YSK4
UXS1
FBXO11
SLC35F5
C2orf44
TSGA10
THSD7B
THUMPD2
TMEM177
FAM49A
LMAN2L
LBH
TMEM163
TCF7L1
INO80B
AMMECR1L
WDR54
ZRANB3
RAB6C
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
CHCHD5
YIPF4
PRADC1
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
DPY30
MCEE
LOXL3
ABHD1
PCGF1
DDX11L2
MFSD9
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
EPT1
LBX2
PNPT1
FER1L5
MCFD2
ATP6V1E2
LOC90499
CCDC74A
LOC90784
DHX57
CCDC74B
PKDCC
RSAD2
CAPN13
CCDC164
IMP4
HNRPLL
NT5C1B
NEURL3
SFXN5
LIMS3
LINC00152
TUBA3E
CCDC104
TEX261
TUBA3D
CCDC85A
KLHL29
WDR92
LYPD1
MRPL53
RPL23AP7
PPP1R21
C2orf89
TMEM150A
NMS
LYG1
MITD1
CMPK2
MBOAT2
CNTNAP5
TMEM18
FBLN7
C2orf73
TRIM43
ACMSD
FAM168B
CIB4
REG3G
C2orf63
PLEKHH2
C2orf76
OSR1
TTC32
ZNF513
GALM
TMEM178
C2orf50
PQLC3
TMEM182
AHSA2
C2orf65
TMEM37
CKAP2L
CBWD2
TEKT4
LOC150527
LOC150568
SMYD1
C2orf15
LOC150622
COMMD1
PROM2
FBXO41
GPAT2
ITPRIPL1
LOC150776
WTH3DI
TCF23
FAM59B
PUS10
LINC00309
LOC151009
SEPT10
PLB1
SULT1C2P1
FAHD2B
MYADML
FAM84A
FAM82A1
GDF7
ASPRV1
LOC151534
LONRF2
CCDC138
GPR113
OXER1
FAM179A
C1QL2
UBXN2A
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
KRTCAP3
TMEM17
SPRED2
FAM123C
LINC00116
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
LOC254128
LYG2
SH2D6
LOC284950
RNF149
LOC284998
LOC285000
FAM150B
LOC285033
LINC00486
C2orf61
LOC285074
LOC285103
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
PLGLA
RGPD4
STON1-GTF2A1L
SPOPL
CYP27C1
C2orf70
C2orf53
LOC339788
LINC00299
LOC339803
C2orf74
LOC339807
LOC339822
MSGN1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
CDKL4
PRORSD1P
SH3RF3
GPR148
LRRTM1
GEN1
C2orf48
PFN4
LOC375190
LOC375196
ANKRD36
WASH2P
ZC3H6
LOC386597
MFSD2B
C2orf71
LOC388942
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
SLC9A4
LOC389023
LOC389033
LOC389043
PTRHD1
SULT6B1
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
FLJ42351
LOC401010
DKFZp686O1327
MIR128-1
MIR216A
MIR217
C2orf27B
ASTL
CAPN14
ACTR3BP2
LOC440894
LOC440895
LOC440900
LOC440905
LOC440910
POTEKP
LOC442028
SULT1C3
POTEE
COA5
CHAC2
LOC541471
ANKRD30BL
FBXO48
FAM110C
LOC644838
GGT8P
ANKRD36BP2
LOC645949
LOC646743
LOC647012
C2orf84
TRIM43B
CFC1B
RGPD3
MZT2A
LOC654342
FAM138B
LOC654433
SNORD89
SNORD92
SNORD94
MIR558
MIR559
RGPD8
LOC727982
POTEF
LOC728537
LOC728730
PABPC1P2
LOC728819
LOC729121
ANKRD20A8P
LOC729234
RAD51AP2
RGPD6
DNAJC27-AS1
RGPD2
MORN2
LOC730811
RFX8
SNORA36C
SNORA70B
MIR216B
LOC100128590
OST4
LOC100129726
LOC100129961
LOC100131320
LOC100132215
CYP4F30P
LOC100133985
LOC100134259
RNU4ATAC
DBIL5P2
SNAR-H
LOC100189589
LOC100216479
ARHGEF33
LOC100271832
LIMS3-LOC440895
LOC100286979
LOC100287010
LOC100287216
LOC100288570
LIMS3L
LOC100288911
MIR1301
LOC100302650
GPR75-ASB3
SNORA80B
ZEB2-AS1
MIR663B
MIR4265
MIR4264
MIR3127
MIR4261
MIR4263
MIR3125
MIR4267
MIR4262
MIR4266
MIR3126
LOC100499194
MIR3682
MIR3679
LOC100505624
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506123
LOC100506274
LOC100506421
LOC100506474
BOLA3-AS1
LOC100507334
LOC100507600
RNF103-CHMP3
NT5C1B-RDH14
INO80B-WBP1
MIR4436B1
MIR4772
MIR4779
MIR4783
MIR4782
MIR4765
MIR4757
MIR4435-2
MIR4426
MIR4784
MIR4436A
MIR4434
MIR4780
MIR4778
MIR4429
MIR4432
MIR548AD
MIR4435-1
LOC100630918

Genes in Wide Peak

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

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

Genes
IL6ST
LIFR
PIK3R1
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
TRIM23
ARSB
BHMT
BTF3
C6
C7
C9
CCNB1
CCNH
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CETN3
CKMT2
ERCC8
COX7C
CRHBP
HAPLN1
VCAN
CTNND2
DAB2
DAP
DHFR
DNAH5
F2R
F2RL1
F2RL2
FGF10
FOXD1
FYB
GDNF
GHR
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HMGCS1
HTR1A
IL7R
ISL1
ITGA1
ITGA2
KIF2A
TNPO1
CD180
MAP1B
MEF2C
MAP3K1
MOCS2
MSH3
MTRR
MYO10
NAIP
NDUFS4
NDUFS6
NPR3
OXCT1
PDE4D
PMCHL1
PMCHL2
PRKAA1
PRLR
PTGER4
RAD1
RAD17
RASA1
RASGRF2
RPL37
RPS23
SDHA
SEPP1
SKP2
SLC1A3
SLC6A3
SLC9A3
SMN1
SMN2
SRD5A1
TAF9
TARS
TBCA
TERT
NR2F1
THBS4
TRIO
XRCC4
ZNF131
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
SEMA5A
OSMR
TRIP13
HOMER1
SCAMP1
CARTPT
NUP155
ZFYVE16
PDCD6
EDIL3
COL4A3BP
LHFPL2
CWC27
MARCH6
CCNO
BASP1
NSA2
FST
PAIP1
POLR3G
SLC12A7
PLK2
IQGAP2
MRPS30
SUB1
SMA4
SMA5
PAPD7
TPPP
ESM1
ADAMTS6
EXOC3
CCT5
SV2C
PDZD2
MRPS27
FBXL7
KIAA0947
PPWD1
OTP
SKIV2L2
NNT
TTC33
AMACR
SSBP2
BHMT2
NIPBL
PP7080
PART1
FAM169A
RAI14
FBXO4
RNU5E-1
RNU5D-1
DIMT1
DROSHA
DMGDH
IRX4
TAS2R1
SLC45A2
IPO11
RXFP3
GCNT4
POLK
ZFR
PELO
FAM134B
FAM105A
DHX29
DDX4
MTMR12
SGTB
ARL15
NSUN2
WDR70
AGGF1
WDR41
BRIX1
C5orf22
CEP72
DEPDC1B
BDP1
ERBB2IP
ANKH
CCL28
PRDM9
NLN
AHRR
ARRDC3
ZSWIM6
ANKRA2
GOLPH3
MCCC2
CENPK
RGNEF
C5orf28
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
FASTKD3
IRX1
PARP8
ANKRD55
PTCD2
ZDHHC11
LPCAT1
SPEF2
ELOVL7
C5orf44
CLPTM1L
ADAMTS12
ATG10
ROPN1L
FAM172A
GPR98
UTP15
ZCCHC9
MED10
ZBED3
GFM2
SPZ1
CARD6
NKD2
FAM105B
ZNF622
NDUFAF2
LMBRD2
MRPS36
ATP6AP1L
SNX18
C1QTNF3
FCHO2
RAB3C
LYSMD3
C5orf55
C5orf35
IL31RA
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
JMY
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
TMEM171
TMEM174
POC5
ACOT12
SREK1
SLC38A9
TMEM167A
MBLAC2
TMEM161B
PLEKHG4B
MARVELD2
C5orf38
IRX2
TTC23L
LOC153684
MIER3
CDC20B
UGT3A2
PAPD4
NIM1
ZNF366
FAM151B
S100Z
ADAMTS16
RANBP3L
CCDC125
GAPT
CMYA5
RICTOR
LOC255167
ANKRD31
SERINC5
LOC257396
LOC285577
KIAA0825
NBPF22P
C5orf51
C5orf64
RNF180
SREK1IP1
LOC285692
LOC285696
SLC6A19
LOC340094
LOC340107
LOC340113
ANKRD34B
PLCXD3
IDAS
ACTBL2
MTX3
SLC6A18
HCN1
C5orf34
MAST4
RNF138P1
LRRC14B
C5orf39
FLJ33360
LOC401177
RGS7BP
TAG
MIR9-2
MARCH11
CRSP8P
FLJ42709
LOC442132
GPX8
MIR449A
SNORD72
LOC642366
C5orf43
LOC643401
LOC644936
LINC00461
LOC646719
LOC647859
LOC648987
ANKRD33B
GUSBP3
GTF2H2B
SCARNA18
SNORA47
MIR449B
MIR580
MIR581
GTF2H2C
GUSBP1
SERF1B
SDHAP3
LOC728613
LOC728723
LOC729506
LOC729862
GTF2H2D
GUSBP9
SNORD123
LOC100129716
CCDC152
LRRC70
LOC100130744
LOC100131067
LOC100132356
FAM159B
LOC100170939
LOC100272216
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR4279
MIR4280
MIR4277
MIR4278
MTRNR2L2
MIR3607
MIR3650
MIR3660
LOC100505738
LOC100505806
LOC100505894
LOC100506548
OCLN
LOC100506688
C1QTNF3-AMACR
MIR4458
MIR4804
MIR4454
MIR4457
MIR4637
MIR3977
MIR4636
MIR4803
MIR4456
MIR4635
EGFLAM-AS4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGF10
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NDUFS6
NEUROG1
NPR3
NPY6R
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
PURA
RAD17
RARS
RASA1
RASGRF2
RPL37
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP1
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
SRP19
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
NREP
TRIP13
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
PAPD7
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
OTP
SKIV2L2
NNT
TTC33
ZNF346
AMACR
SSBP2
BHMT2
TNFAIP8
NIPBL
PP7080
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
FBXO4
OR4F3
HAVCR1
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
DROSHA
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MZB1
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
FAM134B
FAM105A
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
MTMR12
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
NSUN2
CCDC99
THG1L
WDR70
AGGF1
WDR41
BRIX1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
ANKH
CCL28
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
AHRR
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1P1
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
CARD6
TRIM52
HAVCR2
AGXT2L2
C5orf62
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
LMBRD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C1QTNF3
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
HEATR7B2
EGFLAM
PRRC1
NADKD1
UGT3A1
CAPSL
JMY
C5orf58
ZNF474
CCDC127
OR2Y1
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC38A9
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
LOC153469
PLEKHG4B
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
LOC153684
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
NIM1
LIX1
ZNF366
FAM151B
S100Z
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
AQPEP
SLC36A1
RICTOR
EIF4E1B
LOC255167
RASGEF1C
ANKRD31
SERINC5
LOC257358
LOC257396
LOC285577
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
C5orf51
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
LOC285692
LOC285696
RGMB
RFESD
CHSY3
SLC6A19
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
LOC340094
LOC340107
LOC340113
ANKRD34B
PFN3
ZNF879
PLCXD3
IRGM
FBLL1
IDAS
ACTBL2
FAM174A
MTX3
CATSPER3
SLC6A18
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
C5orf34
MAST4
C5orf25
RNF138P1
FLJ38109
LRRC14B
C5orf39
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
FLJ33360
LOC401177
RGS7BP
C5orf63
SPINK6
TAG
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
MARCH11
CRSP8P
FLJ42709
C5orf56
FLJ16171
LOC442132
MIR340
IGIP
GPX8
TIFAB
FLJ35946
LOC553103
MIR449A
CTXN3
SNORD72
SNORD95
SNORD96A
ECSCR
LOC642366
TMEM232
C5orf43
LOC643201
GRXCR2
SPINK9
LOC643401
ZFP62
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
CBY3
LOC646719
LOC647859
LOC648987
ANKRD33B
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR580
MIR581
MIR583
MIR585
SNHG4
MIR143HG
GTF2H2C
LOC728342
GUSBP1
SERF1B
LOC728554
SDHAP3
LOC728613
LOC728723
LOC729080
LOC729506
AACSP1
LOC729678
OR4F29
LOC729862
GTF2H2D
GUSBP9
SNORD123
VTRNA2-1
MIR874
LOC100129716
CCDC152
LRRC70
LOC100130744
LOC100131067
FAM196B
LOC100132062
LOC100132287
LOC100132356
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR4279
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MIR4277
MIR4278
MTRNR2L2
MIR3607
MIR3655
MIR3650
MIR3660
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505738
LOC100505806
LOC100505841
LOC100505894
LOC100506548
OCLN
LOC100506688
LOC100507387
C1QTNF3-AMACR
MIR4458
MIR4804
MIR4633
MIR4634
MIR4461
MIR4454
MIR4457
MIR4637
MIR3977
MIR4460
MIR4636
MIR4638
MIR4803
MIR4456
MIR4635
MIR378E
EGFLAM-AS4
LOC100859930

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.33.

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

Genes
SCARB1
STX2
GOLGA3
MMP17
POLE
PXMP2
RAN
SFSWAP
UBC
ZNF10
ZNF26
ZNF84
ZNF140
ULK1
PIWIL1
NCOR2
ZNF268
FZD10
P2RX2
ANKLE2
RIMBP2
GALNT9
CHFR
EP400
DHX37
FBRSL1
AACS
NOC4L
PUS1
TMEM132C
TMEM132B
LOC116437
TMEM132D
SLC15A4
BRI3BP
FAM101A
ZNF664
GLT1D1
PGAM5
GPR133
DDX51
EP400NL
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
LOC647589
SNORA49
LOC100128554
LOC100130238
LOC100190940
ZNF605
MIR3612
LOC100507055
LOC100507206
ZNF664-FAM101A

Arm-level results

Table 3. Get Full Table Arm-level significance table - 16 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.02 | -2.41 | 0.999 | 0.12 | 0.748 | 0.999
1q | 1955 | 0.10 | 0.132 | 0.999 | 0.08 | -0.799 | 0.999
2p | 924 | 0.14 | 0.509 | 0.815 | 0.01 | -3.17 | 0.999
2q | 1556 | 0.16 | 1.54 | 0.176 | 0.00 | -3.25 | 0.999
3p | 1062 | 0.28 | 4.89 | 1.53e-06 | 0.08 | -1.06 | 0.999
3q | 1139 | 0.31 | 6.03 | 3.27e-09 | 0.04 | -1.98 | 0.999
4p | 489 | 0.05 | -2.18 | 0.999 | 0.10 | -0.811 | 0.999
4q | 1049 | 0.04 | -2.25 | 0.999 | 0.10 | -0.533 | 0.999
5p | 270 | 0.14 | 0.0417 | 0.999 | 0.08 | -1.56 | 0.999
5q | 1427 | 0.11 | 0.12 | 0.999 | 0.08 | -1.06 | 0.999
6p | 1173 | 0.04 | -2.19 | 0.999 | 0.10 | -0.461 | 0.999
6q | 839 | 0.03 | -2.63 | 0.999 | 0.11 | -0.382 | 0.999
7p | 641 | 0.54 | 12.7 | 0 | 0.00 | -2.61 | 0.999
7q | 1277 | 0.56 | 14.4 | 0 | 0.00 | -2.4 | 0.999
8p | 580 | 0.06 | -1.97 | 0.999 | 0.05 | -2.25 | 0.999
8q | 859 | 0.08 | -1.29 | 0.999 | 0.03 | -2.7 | 0.999
9p | 422 | 0.02 | -3.01 | 0.999 | 0.15 | 0.524 | 0.999
9q | 1113 | 0.01 | -3.06 | 0.999 | 0.16 | 1.25 | 0.703
10p | 409 | 0.03 | -2.88 | 0.999 | 0.08 | -1.52 | 0.999
10q | 1268 | 0.02 | -2.87 | 0.999 | 0.07 | -1.41 | 0.999
11p | 862 | 0.04 | -2.38 | 0.999 | 0.08 | -1.25 | 0.999
11q | 1515 | 0.03 | -2.37 | 0.999 | 0.10 | -0.288 | 0.999
12p | 575 | 0.34 | 6.44 | 2.61e-10 | 0.00 | -3.16 | 0.999
12q | 1447 | 0.34 | 7.43 | 3.03e-13 | 0.00 | -2.9 | 0.999
13q | 654 | 0.12 | -0.232 | 0.999 | 0.11 | -0.507 | 0.999
14q | 1341 | 0.04 | -2.2 | 0.999 | 0.20 | 2.77 | 0.0373
15q | 1355 | 0.02 | -2.73 | 0.999 | 0.12 | 0.211 | 0.999
16p | 872 | 0.46 | 10.4 | 0 | 0.07 | -1.19 | 0.999
16q | 702 | 0.43 | 9.29 | 0 | 0.07 | -1.37 | 0.999
17p | 683 | 0.54 | 12.2 | 0 | 0.12 | -0.173 | 0.999
17q | 1592 | 0.61 | 16.5 | 0 | 0.00 | -2.19 | 0.999
18p | 143 | 0.08 | -1.45 | 0.999 | 0.19 | 1.45 | 0.583
18q | 446 | 0.06 | -1.93 | 0.999 | 0.19 | 1.86 | 0.311
19p | 995 | 0.02 | -3.02 | 0.999 | 0.05 | -2.17 | 0.999
19q | 1709 | 0.02 | -2.75 | 0.999 | 0.04 | -2.15 | 0.999
20p | 355 | 0.33 | 5.77 | 1.45e-08 | 0.03 | -2.56 | 0.999
20q | 753 | 0.36 | 7.23 | 1.22e-12 | 0.00 | -3.06 | 0.999
21q | 509 | 0.03 | -2.66 | 0.999 | 0.15 | 0.621 | 0.999
22q | 921 | 0.01 | -2.88 | 0.999 | 0.26 | 4.46 | 0.000168
Xq | 1312 | 0.29 | 5.27 | 2.25e-07 | 0.23 | 3.28 | 0.0103

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/KIRP-TP/2328341/2.GDAC_MergeDataFiles.Finished/KIRP-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 103 Input Tumor Samples.

Tumor Sample Names
TCGA-A4-7286-01A-11D-2135-01
TCGA-A4-7287-01A-11D-2135-01
TCGA-A4-7288-01A-11D-2135-01
TCGA-A4-7583-01A-11D-2135-01
TCGA-A4-7584-01A-11D-2135-01
TCGA-A4-7585-01A-11D-2135-01
TCGA-A4-7732-01A-11D-2135-01
TCGA-A4-7734-01A-11D-2135-01
TCGA-A4-7828-01A-11D-2135-01
TCGA-A4-7915-01A-11D-2200-01

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
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle