SNP6 Copy number analysis (GISTIC2)
Prostate Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C16H4G63
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 2.0.21 (Firehose task version: 127).

Summary

There were 419 tumor samples used in this analysis: 22 significant arm-level results, 29 significant focal amplifications, and 33 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 - 29 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
Xq27.1 1.3606e-08 3.1671e-08 chrX:138564705-138580758 0 [F9]
8q24.21 0.00012328 0.00012328 chr8:124967994-129665763 30
11q13.2 0.00026591 0.00026591 chr11:65910130-69888893 88
3q26.2 0.00012507 0.00065173 chr3:169415894-170116437 13
Xq21.1 0.00012507 0.001662 chrX:79251708-79255479 0 [TBX22]
8p11.23 0.0028673 0.0028673 chr8:36721020-39443168 32
Xq25 0.00051201 0.0037818 chrX:126306276-126315813 0 [CXorf64]
Xp22.11 0.0003346 0.0037866 chrX:23975644-23983593 0 [CXorf58]
Xp22.11 0.0003346 0.0046379 chrX:24515774-24522924 1
3q21.3 0.0010959 0.007502 chr3:127875022-128424455 9
14q21.1 0.0093228 0.0093228 chr14:38008682-38049106 1
1q21.3 0.010357 0.010357 chr1:149881399-155306670 198
7p14.3 0.012474 0.012474 chr7:13797002-34477089 144
16q11.2 0.012474 0.012474 chr16:46638910-47387972 9
4q13.3 0.01719 0.01719 chr4:73892436-74219241 2
17q23.2 0.01719 0.01719 chr17:59788818-60189565 3
15q11.2 0.019458 0.019458 chr15:1-26017542 131
Xq21.1 0.016497 0.019458 chrX:80829747-80833679 0 [SH3BGRL]
Xp22.2 0.0014222 0.032771 chrX:15692440-17727237 14
13q12.11 0.03905 0.03905 chr13:1-24578109 35
20q13.2 0.044525 0.044525 chr20:41749332-63025520 290
Xp21.1 0.0028673 0.069079 chrX:35651236-35660210 0 [MAGEB16]
Xq21.31 0.020342 0.069276 chrX:87704771-87710744 0 [CPXCR1]
19q13.43 0.090494 0.090494 chr19:54378674-58255438 147
12q23.1 0.094875 0.094875 chr12:62872750-133014685 497
5q33.3 0.15356 0.15356 chr5:120671010-180915260 556
9q34.11 0.15818 0.15818 chr9:97960858-141213431 527
18q21.31 0.21737 0.21737 chr18:55901999-56446055 6
Xq25 0.2019 0.24449 chrX:122399494-122410812 1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
NDUFB9
POU5F1B
PVT1
SQLE
MTSS1
KIAA0196
TRIB1
RNF139
TRMT12
TATDN1
ZNF572
TMEM65
LOC157381
FAM84B
NSMCE2
FER1L6-AS1
FER1L6
LOC727677
LOC100130231
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
PCAT1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
CCND1
hsa-mir-3164
hsa-mir-3163
ACTN3
ADRBK1
ALDH3B1
ALDH3B2
BBS1
CHKA
CPT1A
FGF3
FGF4
GSTP1
SLC29A2
IGHMBP2
LRP5
NDUFV1
NDUFS8
PC
PPP1CA
PTPRCAP
RAD9A
RBM4
RPS6KB2
SPTBN2
CTSF
AIP
PITPNM1
RIN1
MTL5
FGF19
CCS
RCE1
DPP3
CDK2AP2
TCIRG1
RBM14
YIF1A
B3GNT1
KDM2A
CLCF1
BRMS1
MYEOV
RHOD
GAL
SUV420H1
CABP2
C11orf24
SSH3
CCDC87
PPP6R3
PACS1
CABP4
CD248
CORO1B
CARNS1
POLD4
KLC2
MRPL11
LRFN4
C11orf80
TMEM134
UNC93B1
RAB1B
RBM4B
SYT12
ACY3
MRGPRD
MRGPRF
MRPL21
TPCN2
ORAOV1
PELI3
CNIH2
ZDHHC24
C11orf86
NUDT8
TMEM151A
NPAS4
ANKRD13D
TBX10
TBC1D10C
GPR152
DOC2GP
FAM86C2P
LOC100130987
RBM14-RBM4
MIR4691
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
PRKCI
SKIL
TERC
SEC62
GPR160
MYNN
LRRC31
PHC3
ARPM1
LRRC34
LRRIQ4
SAMD7
LOC100128164
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
FGFR1
WHSC1L1
ADRB3
ADAM3A
EIF4EBP1
STAR
TACC1
ADAM18
ADAM9
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
BRF2
PLEKHA2
ZNF703
RAB11FIP1
TM2D2
PPAPDC1B
GOT1L1
LETM2
KCNU1
HTRA4
ADAM32
ADAM5P
RNF5P1
C8orf86
LOC728024
LOC100130964
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.11.

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

Genes
PDK3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q21.3.

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

Genes
GATA2
RPN1
hsa-mir-1280
C3orf27
EEFSEC
LOC90246
DNAJB8
DNAJB8-AS1
MIR1280
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.1.

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

Genes
MIPOL1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
ARNT
MUC1
TPM3
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
ADAR
CHRNB2
CKS1B
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FDPS
FLG
GBA
GBAP1
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PI4KB
PKLR
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
PIP5K1A
ANXA9
ADAM15
SELENBP1
PRPF3
SETDB1
UBAP2L
SV2A
DENND4B
SCAMP3
SF3B4
HAX1
SEMA6C
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CELF3
VPS45
POGZ
RPRD2
SNAPIN
RUSC1
CA14
C1orf43
CHTOP
LCE2B
SLC39A1
TMOD4
CERS2
CRNN
ZBTB7B
APH1A
PLEKHO1
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
DCST2
S100A16
CREB3L4
C1orf51
LELP1
DCST1
BNIPL
SPRR4
LCE4A
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
RUSC1-AS1
S100A7A
LINGO4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LYSMD1
HRNR
FLG2
C1orf189
KPRP
LCE6A
PRR9
S100A7L2
MIR554
MIR92B
MIR190B
C1orf68
LOC100132111
C2CD4D
MIR4257
MIR4258
LOC100505666
TNFAIP8L2-SCNM1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p14.3.

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

Genes
ETV1
HNRNPA2B1
HOXA9
HOXA11
HOXA13
JAZF1
hsa-mir-550-2
hsa-mir-550-1
hsa-mir-196b
hsa-mir-148a
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
ADCYAP1R1
AHR
AQP1
CHN2
CLK2P
CRHR2
DGKB
DFNA5
EVX1
GARS
GHRHR
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
IL6
ITGB8
MEOX2
NPY
PDE1C
RP9
SP4
TWIST1
DNAH11
TAX1BP1
SKAP2
CREB5
NFE2L3
HDAC9
RAPGEF5
SCRN1
KIAA0087
TRIL
NOD1
GPNMB
AGR2
IGF2BP3
PPP1R17
NUPL2
HIBADH
INMT
FKBP9
CBX3
AVL9
SNX13
LSM5
SOSTDC1
KBTBD2
OSBPL3
TSPAN13
BBS9
BZW2
SNX10
TRA2A
NT5C3
MPP6
CYCS
CPVL
TOMM7
FKBP14
CDCA7L
KLHL7
STK31
ANKMY2
NEUROD6
NPVF
GGCT
FAM188B
FAM126A
PLEKHA8
CCDC126
C7orf30
C7orf31
AGR3
BMPER
PRPS1L1
TWISTNB
SP8
HOXA11-AS1
DKFZP586I1420
C7orf41
PRR15
FERD3L
RPL23P8
CCDC129
ZNRF2
TMEM196
STEAP1B
RPS2P32
C7orf71
ABCB5
C7orf46
MACC1
AGMO
LOC401320
LOC401321
AAA1
MIR148A
LOC441204
ZNRF2P1
RP9P
DPY19L2P3
MIR196B
WIPF3
LOC646762
SNORD93
MIR550A1
MIR550A2
ISPD
JAZF1-AS1
DPY19L1P1
LOC100130673
LOC100133311
ZNRF2P2
HOTTIP
MIR3146
MIR550B2
MIR550B1
LOC100506025
LRRC72
LOC100506178
HOTAIRM1
LOC100506497
INMT-FAM188B
HOXA10-HOXA9
MIR550A3
KLHL7-AS1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q11.2.

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

Genes
DNAJA2
ORC6
VPS35
SHCBP1
ITFG1
NETO2
GPT2
MYLK3
C16orf87
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
ANKRD17
COX18
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.2.

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

Genes
BRIP1
MED13
INTS2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q11.2.

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

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
NBEAP1
IPW
NDN
SNRPN
UBE3A
MKRN3
PAR5
SNURF
CYFIP1
C15orf2
MAGEL2
ATP10A
NIPA2
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
CHEK2P2
LOC646214
CXADRP2
REREP3
LOC653061
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
HERC2P7
GOLGA8DP
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.2.

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

Genes
S100G
GRPR
NHS
RBBP7
ZRSR2
INE2
AP1S2
REPS2
CA5B
TXLNG
CTPS2
SYAP1
CA5BP1
MIR4768
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.11.

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

Genes
FGF9
GJA3
GJB2
MIPEP
SGCG
TUBA3C
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
PSPC1
TNFRSF19
XPO4
MRP63
TPTE2
N6AMT2
SKA3
EFHA1
ZDHHC20
PHF2P1
ANKRD20A9P
LINC00442
C1QTNF9B
C1QTNF9B-AS1
BASP1P1
ANKRD26P3
LINC00421
LINC00327
MIR4499
Genes in Wide Peak

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

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

Genes
GNAS
SS18L1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-3194
ADA
ATP5E
BMP7
CD40
CDH4
CEBPB
CHRNA4
COL9A3
CSE1L
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
EYA2
NPBWR2
HNF4A
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
MC3R
MMP9
MYBL2
MYT1
NFATC2
NTSR1
OPRL1
PCK1
PFDN4
PI3
PLTP
CTSA
PPP1R3D
PSMA7
PTGIS
PTK6
PTPN1
RPS21
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SRMS
STAU1
STK4
AURKA
TAF4
TCEA2
TFAP2C
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF217
NCOA3
RAE1
BCAS1
STX16
TNFRSF6B
MATN4
DPM1
WISP2
VAPB
B4GALT5
SPATA2
OSBPL2
ACOT8
ATP9A
SGK2
ARFRP1
RGS19
SYCP2
WFDC2
ARFGEF2
TCFL5
SPINT3
TOMM34
SERINC3
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
HRH3
RBPJL
SLC9A8
ADNP
ZMYND8
SPO11
PRPF6
L3MBTL1
GTPBP5
GMEB2
SNORD12C
TP53TG5
MOCS3
SLCO4A1
STMN3
SLC35C2
SLMO2
IFT52
TH1L
C20orf43
C20orf111
PIGT
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
C20orf11
PCMTD2
C20orf20
PPP4R1L
RBM38
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
DOK5
DBNDD2
RNF114
SULF2
SLC2A4RG
PMEPA1
CASS4
SPINLW1
JPH2
SALL4
ZNFX1
RAB22A
SLC12A5
ZNF512B
PREX1
COL20A1
NCOA5
CDH26
KCNK15
SLC17A9
ELMO2
ZNF335
LOC63930
PCIF1
FAM217B
CDH22
SLC13A3
GDAP1L1
LOC79015
C20orf195
PPDPF
TTPAL
BIRC7
NPEPL1
DNAJC5
PABPC1L
TUBB1
ZBP1
SLC2A10
CABLES2
PARD6B
ZGPAT
TOX2
PRIC285
SYS1
WFDC8
SNX21
ZSWIM1
TP53RK
DNTTIP1
FAM210B
PHACTR3
BHLHE23
NKAIN4
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
WFDC3
GCNT7
CBLN4
CTCFL
SAMD10
ABHD16B
RIMS4
NEURL2
ZSWIM3
WFDC10A
LINC00266-1
WFDC6
FAM65C
C20orf151
R3HDML
GTSF1L
WFDC5
LOC149773
GNAS-AS1
LSM14B
WFDC13
APCDD1L
C20orf201
FAM209A
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
TMEM189
TMEM189-UBE2V1
FAM209B
SPINT4
SUMO1P1
MIR1-1
MIR124-3
MIR133A2
MIR296
ZNFX1-AS1
SNORD12
MIR645
MIR647
SYS1-DBNDD2
HAR1A
HAR1B
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
ZNF663
LOC100131496
DPH3P1
LINC00029
LOC100144597
FLJ16779
MIR1914
MIR1257
MIR4325
MIR3194
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505783
LOC100505815
LOC100505826
LOC100506384
SPINLW1-WFDC6
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4758
MIR4532
MIR4533
MIR5095
LOC100652730
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.43.

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

Genes
TFPT
hsa-mir-1274b
hsa-mir-935
FCAR
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR1
LAIR2
NDUFA3
CNOT3
PEG3
PRKCG
PTPRH
RPL28
RPS9
AURKC
SYT5
TNNI3
TNNT1
ZNF17
ZNF134
ZNF154
ZNF264
NCR1
LILRB2
ZNF211
TRAPPC2P1
ZNF460
LILRB1
LILRB5
LILRB4
LILRA1
LILRB3
LILRA3
LILRA2
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
PRPF31
UBE2S
CCDC106
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
EPS8L1
ZNF444
NLRP2
ZNF416
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
ZNF71
CACNG8
CACNG7
CACNG6
ZNF667
TSEN34
MBOAT7
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF419
ISOC2
ZNF671
BRSK1
SUV420H2
FIZ1
GALP
ZNF628
KIR3DX1
ZNF551
ZNF835
MYADM
LENG9
RDH13
ZIM3
LENG8
KIR3DL3
ZNF543
COX6B2
OSCAR
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
LOC147670
ZNF548
TMEM190
TMC4
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF550
ZNF579
NLRP7
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
VSTM1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZNF530
C19orf51
LILRA5
ZNF773
LOC386758
TMEM238
ZNF470
ZNF749
ZNF805
ZNF772
TARM1
DUXA
SBK2
SHISA7
MIMT1
MIR935
LOC100128252
SGK110
PEG3-AS1
ZNF865
MIR4752
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q23.1.

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

Genes
ALDH2
BCL7A
BTG1
MDM2
PTPN11
HMGA2
WIF1
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
hsa-mir-1279
hsa-mir-548c
hsa-let-7i
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
AVPR1A
SCARB1
CMKLR1
COX6A1
CPM
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GNS
GTF2H3
HAL
HPD
IFNG
IGF1
KCNC2
LTA4H
LUM
LYZ
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
CNOT2
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
PPP1CC
PRKAB1
PSMD9
PTPRB
PTPRR
PXN
RAN
RAP1B
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
YEATS4
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
DYRK2
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
TMEM5
CCT2
CAMKK2
FRS2
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
CPSF6
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
IRAK3
XPOT
PHLDA1
MLXIP
RPH3A
RAB21
FBXO21
MON2
SETD1B
UHRF1BP1L
CUX2
KIAA1033
TBC1D30
MED13L
ZDHHC17
SIRT4
GRIP1
ABCB9
ISCU
RIMBP2
ATP6V0A2
LEMD3
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
KCNMB4
MRPL42
IFT81
CCDC59
TBK1
FAM216A
HCFC2
TRHDE
SYCP3
CHST11
GALNT9
IL22
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
TMBIM4
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SLC35E3
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
FGD6
IL26
CAND1
WSB2
NDUFA12
DIABLO
MDM1
ANKS1B
CHPT1
NUP107
TMCC3
PPM1H
SRGAP1
PITPNM2
EP400
DHX37
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
LLPH
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
HELB
SDSL
TMEM132B
OSBPL8
C12orf56
IQCD
LOC116437
RAB3IP
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
TPH2
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
C12orf66
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
RPSAP52
SLC17A8
GNN
MSRB3
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
RASSF3
GPR133
MORN3
LOC283392
C12orf61
DPY19L2
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
LRRC10
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
FLJ41278
MKRN9P
C12orf76
LOC400084
FLJ37505
MIRLET7I
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
SNORA49
SNORA53
MIR548C
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
MRS2P2
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
MIR1252
MIR1279
MIR1827
MIR1178
MIR1251
SNORA70G
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR548Z
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507066
LOC100507091
LOC100507206
LOC100507250
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q33.3.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
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
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDX1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
NKX2-5
CTNNA1
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HINT1
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
LCP2
LECT2
LMNB1
LOX
LTC4S
SMAD5
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SNX2
SPARC
SPINK1
SPOCK1
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
GALNT10
NHP2
RBM22
RNF130
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
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
ZNF608
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
LYRM7
TRIM41
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
ZNF474
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
SRFBP1
LOC153469
ZMAT2
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
LOC340037
TMEM173
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
DND1
C5orf25
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
FLJ33630
CCNI2
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
VTRNA2-1
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1289-2
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505841
LOC100507387
MIR4633
MIR4634
MIR4461
MIR4460
MIR4638
MIR378E
LOC100859930
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.11.

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

Genes
ABL1
FANCC
NOTCH1
RALGDS
SET
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
BAAT
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL2
CYLC2
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSD17B3
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
ANP32B
AGPAT2
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
PMPCA
ASTN2
FKBP15
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
BSPRY
C9orf167
TEX10
LPPR1
EXD3
FAM206A
STX17
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
C9orf86
CDK5RAP2
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
BDAG1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
MIR600HG
URM1
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
HIATL2
C9orf125
NTNG2
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
C9orf96
OLFML2A
QSOX2
ZNF883
C9orf21
ZNF367
C9orf91
NAIF1
ANKS6
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC340508
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR32
C9orf106
LCN10
LOC441454
LOC441455
FAM22G
LOC441461
C9orf173
NRARP
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
NRON
FAM163B
FLJ40292
TUBBP5
RNF224
C9orf29
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
LOC100129722
LOC100130954
LOC100131193
FAM157B
LOC100132781
RNU6ATAC
LINC00092
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR548Q
MIR181A2HG
MIR4292
MIR3154
MIR2861
MIR3134
C9orf174
LOC100499484
MIR3621
MIR3689A
MIR3911
MIR3689B
LOC100505478
LOC100506100
LOC100506190
LOC100506599
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4672
MIR3689E
MIR4479
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q21.31.

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

Genes
MALT1
hsa-mir-122
NEDD4L
ALPK2
MIR122
MIR3591
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq25.

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

Genes
GRIA3

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

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
10q23.31 3.0293e-71 3.0293e-71 chr10:89617158-90034038 2
6q14.3 7.9558e-64 7.9558e-64 chr6:87800060-88001063 1
21q22.3 2.1837e-71 3.6487e-50 chr21:42827479-43100702 1
13q14.13 1.8078e-58 4.0069e-47 chr13:44451821-48879660 30
17p13.1 2.1698e-30 2.1365e-30 chr17:7523775-7591760 4
8p21.3 1.647e-27 1.4228e-25 chr8:20109881-24773185 49
5q21.1 5.3012e-27 3.5707e-22 chr5:98131506-98270263 2
3p13 6.0368e-20 6.0368e-20 chr3:71832385-72798945 2
12p13.1 7.432e-20 7.432e-20 chr12:12844234-12921132 3
16q24.1 1.2036e-34 3.5644e-17 chr16:83845270-89304310 72
17q21.31 1.28e-16 1.28e-16 chr17:42086616-42651945 18
2q22.1 1.4136e-18 4.131e-12 chr2:132506741-141000702 30
16q22.3 6.9466e-29 1.9039e-10 chr16:72110941-74472459 9
11q23.2 2.2216e-06 2.1796e-06 chr11:113148800-115045236 19
21q22.2 2.2049e-40 2.0903e-05 chr21:39665722-40669897 4
18q22.1 2.5133e-05 2.5133e-05 chr18:55467646-78077248 86
1q42.2 0.00023279 0.00023279 chr1:220444926-241297899 152
9p23 0.00042221 0.00041943 chr9:7799607-12693402 1
4q28.1 0.0062489 0.0064537 chr4:115598111-134070791 57
12q24.31 0.011105 0.011053 chr12:123752264-133851895 71
13q22.1 1.19e-25 0.01457 chr13:36341323-86367939 185
5q11.2 5.9532e-21 0.015381 chr5:53838110-59787457 31
1p31.3 0.0012598 0.015789 chr1:63986866-66261758 16
19q13.2 0.015789 0.015789 chr19:42733289-42891571 7
1p22.1 0.0026351 0.019545 chr1:76260273-107685756 159
5q13.2 1.3409e-18 0.024815 chr5:60238443-74970901 82
2q22.3 1.1535e-11 0.032661 chr2:139532192-152975659 27
11p11.2 0.048199 0.047444 chr11:36679363-49580689 85
7q31.33 0.060753 0.05984 chr7:124429419-127293962 9
15q21.3 0.081489 0.079338 chr15:26104243-59175227 292
8p11.21 3.1335e-06 0.090737 chr8:40752244-42608198 18
3q29 0.16443 0.16668 chr3:189504492-198022430 84
2p22.1 0.24438 0.24438 chr2:30482436-84519662 311
Genes in Wide Peak

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

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

Genes
PTEN
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.3.

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

Genes
ZNF292
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
TMPRSS2
Genes in Wide Peak

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

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

Genes
LCP1
CPB2
ESD
GTF2F2
HTR2A
TPT1
SUCLA2
TSC22D1
ITM2B
ZC3H13
LRCH1
NUFIP1
MED4
NUDT15
KIAA1704
KIAA0226L
COG3
LINC00284
LACC1
LINC00330
FAM194B
SPERT
SLC25A30
SIAH3
KCTD4
SERP2
TSC22D1-AS1
SNORA31
TPT1-AS1
LOC100509894
Genes in Wide Peak

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

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

Genes
TP53
ATP1B2
SHBG
SAT2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

Table S28.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-320a
BMP1
POLR3D
EGR3
EPB49
GFRA2
LOXL2
NKX3-1
PPP3CC
SFTPC
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
ADAM28
XPO7
RHOBTB2
SLC39A14
ADAMDEC1
SLC25A37
PIWIL2
HR
BIN3
KIAA1967
PDLIM2
FAM160B2
NUDT18
FLJ14107
REEP4
CHMP7
NKX2-6
PEBP4
R3HCC1
LGI3
LOC254896
LOC286059
LOC286114
LOC389641
MIR320A
C8orf58
LOC100507156
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.1.

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

Genes
CHD1
LOC100289230
Genes in Wide Peak

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

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

Genes
RYBP
LOC201617
Genes in Wide Peak

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

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

Genes
hsa-mir-613
CDKN1B
MIR613
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.1.

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

Genes
CBFA2T3
hsa-mir-1910
APRT
CA5A
CDH15
COX4I1
CYBA
FOXF1
FOXL1
FOXC2
GALNS
IRF8
MVD
SLC7A5
MBTPS1
TAF1C
USP10
KIAA0513
PIEZO1
ATP2C2
COX4NB
ZCCHC14
KIAA0182
COTL1
MLYCD
IL17C
OSGIN1
GINS2
TRAPPC2L
NECAB2
KLHDC4
BANP
ZDHHC7
JPH3
KIAA1609
WFDC1
MTHFSD
KLHL36
FBXO31
CDT1
MAP1LC3B
HSDL1
CRISPLD2
ZNF469
KCNG4
RNF166
DNAAF1
ZC3H18
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
MGC23284
LINC00311
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
LOC727710
LOC732275
MIR1910
C16orf95
MIR4722
Genes in Wide Peak

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

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

Genes
FZD2
GRN
ITGA2B
SLC4A1
UBTF
HDAC5
RUNDC3A
GPATCH8
SLC25A39
ATXN7L3
C17orf53
TMUB2
TMEM101
G6PC3
ASB16
LSM12
FAM171A2
C17orf65
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

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

Genes
hsa-mir-128-1
hsa-mir-663b
CCNT2
DARS
GPR39
HNMT
LCT
MCM6
MGAT5
CXCR4
NXPH2
RAB3GAP1
UBXN4
R3HDM1
YSK4
THSD7B
TMEM163
ZRANB3
LYPD1
ACMSD
SPOPL
NCKAP5
MIR128-1
C2orf27B
ANKRD30BL
LOC647012
LOC100129961
MIR663B
MIR3679
LOC100507600
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.3.

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

Genes
ZFHX3
PSMD7
DHX38
TXNL4B
PMFBP1
HTA
LOC283922
CLEC18B
LOC100506172
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

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

Genes
hsa-mir-4301
DRD2
HTR3A
NNMT
ZBTB16
HTR3B
ZW10
RBM7
REXO2
C11orf71
FAM55D
TTC12
USP28
TMPRSS5
FAM55A
FAM55B
ANKK1
CLDN25
MIR4301
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.2.

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

Genes
ERG
ETS2
PSMG1
LINC00114
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
CYB5A
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NFATC1
SERPINB2
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
SERPINB3
SERPINB4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
NEDD4L
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
CCBE1
CBLN2
FBXO15
DOK6
RNF152
LINC00305
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817
MIR3591
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.2.

Table S39.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
ACTA1
ACTN2
PARP1
AGT
ARF1
CAPN2
LYST
CHRM3
EPHX1
GALNT2
GNG4
GUK1
H3F3A
HLX
ITPKB
KCNK1
LBR
LGALS8
MARK1
MTR
NID1
NVL
PSEN2
RAB4A
RYR2
SRP9
TARBP1
TBCE
LEFTY2
TLR5
GPR137B
TP53BP2
TSNAX
WNT9A
HIST3H3
GNPAT
CDC42BPA
DEGS1
TAF1A
GGPS1
TMEM63A
TOMM20
URB2
LEFTY1
SPHAR
CAPN9
DUSP10
COG2
RBM34
FBXO28
ABCB10
TAF5L
DISC2
DISC1
CNIH4
PYCR2
TRIM17
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
HEATR1
ENAH
NUP133
ERO1LB
FMN2
ADCK3
GJC2
SIPA1L2
ZP4
RHOU
GREM2
ACBD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
PCNXL2
WDR26
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
KIAA1804
C1orf198
DISP1
WNT3A
HIST3H2A
SNAP47
C1orf96
DNAH14
C1orf131
EDARADD
MRPL55
HIST3H2BB
BROX
SLC35F3
B3GALNT2
CNIH3
EXOC8
RNF187
C1orf55
C1orf65
IBA57
LIN9
ZNF678
PRSS38
LOC339535
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf140
FAM177B
ZNF847P
TRIM67
H3F3AP4
DUSP5P
SNRPD2P2
RPS7P5
SNORA14B
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3620
LOC100506795
LOC100506810
MIR4753
MIR4666A
MIR4671
MIR4427
MIR4742
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
PTPRD
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q28.1.

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

Genes
IL2
hsa-mir-2054
hsa-mir-1973
ANXA5
CCNA2
FABP2
FGF2
MAD2L1
EXOSC9
TRPC3
PRSS12
PDE5A
NDST3
SEC24D
SPRY1
PGRMC2
PLK4
PRDM5
NUDT6
HSPA4L
INTU
MYOZ2
USP53
LARP1B
BBS7
ANKRD50
METTL14
IL21
NDST4
NDNF
FAT4
TNIP3
PHF17
C4orf29
SLC25A31
QRFPR
KIAA1109
SCLT1
C4orf33
TMEM155
ADAD1
TRAM1L1
SPATA5
BBS12
SYNPO2
MFSD8
LOC285419
FLJ14186
C4orf3
CEP170P1
LOC645513
SNORA24
CETN4P
SNHG8
PP12613
MIR2054
MIR1973
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.31.

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

Genes
SCARB1
EIF2B1
STX2
GOLGA3
GTF2H3
MMP17
POLE
PXMP2
RAN
SFSWAP
UBC
ZNF10
ZNF26
ZNF84
ZNF140
ULK1
PIWIL1
NCOR2
ZNF268
TMED2
SNRNP35
FZD10
P2RX2
ANKLE2
RIMBP2
ATP6V0A2
GALNT9
SBNO1
CHFR
EP400
DHX37
FBRSL1
DDX55
AACS
NOC4L
TCTN2
CCDC92
PUS1
TMEM132C
TMEM132B
LOC116437
TMEM132D
SLC15A4
BRI3BP
FAM101A
ZNF664
GLT1D1
PGAM5
RILPL2
DNAH10
GPR133
DDX51
EP400NL
RILPL1
SETD8
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
LOC647589
SNORA49
LOC100128554
LOC100130238
LOC100190940
ZNF605
MIR3612
MIR3908
LOC100507055
LOC100507206
ZNF664-FAM101A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q22.1.

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

Genes
LCP1
RB1
LHFP
TTL
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
ATP7B
KLF5
BTF3P11
RCBTB2
CLN5
CPB2
DACH1
EDNRB
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
LMO7
SMAD9
NEK3
PCDH8
PCDH9
POU4F1
RFXAP
ATXN8OS
TPT1
TRPC4
UCHL3
TNFSF11
SCEL
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
ITM2B
MTRF1
UTP14C
TBC1D4
LPAR6
SLC25A15
TRIM13
MRPS31
SPRY2
DLEU1
PIBF1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
KLF12
EXOSC8
FNDC3A
DIS3
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
FBXL3
INTS6
CKAP2
NUFIP1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
NDFIP2
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
PCDH20
RNF219
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
LINC00284
CSNK1A1L
SLAIN1
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
COMMD6
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
LINC00550
LINC00347
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ALG11
MZT1
TSC22D1-AS1
SERPINE3
CTAGE11P
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR759
MIR320D1
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
OR7E37P
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4703
LOC100616668
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
IL6ST
hsa-mir-582
hsa-mir-449c
GZMA
GZMK
MAP3K1
PDE4D
PPAP2A
CCNO
PLK2
ESM1
SKIV2L2
PART1
DHX29
DDX4
GPBP1
ANKRD55
RAB3C
C5orf35
IL31RA
SLC38A9
MIER3
CDC20B
GAPT
IDAS
ACTBL2
RNF138P1
GPX8
MIR449A
MIR449B
MIR449C
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.3.

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

Genes
JAK1
hsa-mir-101-1
AK4
LEPR
ROR1
PGM1
DNAJC6
LEPROT
RAVER2
CACHD1
DLEU2L
EFCAB7
UBE2U
MIR101-1
MIR3671
MIR4794
Genes in Wide Peak

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

Table S46.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CIC
MEGF8
ERF
GSK3A
PAFAH1B3
PRR19
TMEM145
Genes in Wide Peak

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

Table S47.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BCL10
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
AGL
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
BRDT
CLCA1
CNN3
COL11A1
CTBS
DBT
DPYD
DR1
S1PR1
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNG5
GTF2B
CYR61
MSH4
PRKACB
PKN2
PTGFR
ABCD3
SNORD21
RPL5
TGFBR3
VCAM1
EVI5
CDC7
BCAR3
LMO4
CDC14A
RTCD1
FUBP1
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LPPR4
PIGK
IFI44
IFI44L
DNAJB4
GLMN
CLCA4
MTF2
USP33
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
AK5
SNORA66
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
ZNHIT6
GIPC2
PALMD
FNBP1L
LRRC8D
PRMT6
MCOLN3
RNPC3
CCBL2
ODF2L
PTBP2
DNASE2B
ELTD1
HIAT1
TTLL7
RPAP2
RPF1
ST6GALNAC5
SYDE2
ZNF644
LRRC8C
NEXN
DNAJA1P5
GBP4
GBP5
SSX2IP
OLFM3
WDR63
SLC44A3
ASB17
LRRC39
SAMD13
C1orf52
TMEM56
SLC30A7
MGC27382
GBP6
LPPR5
SASS6
HFM1
ALG14
EPHX4
MCOLN2
COL24A1
ST6GALNAC3
ZNF326
BTBD8
LOC339524
CCDC18
BARHL2
HSP90B3P
FAM73A
GBP7
C1orf146
FAM69A
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
C1orf180
FLJ31662
GEMIN8P4
RBMXL1
LOC646626
LOC648740
MIR548D1
MIR553
LOC729970
LOC729987
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129620
LOC100131564
MIR548AA1
LOC100505768
TMEM56-RWDD3
MIR2682
MIR4423
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.2.

Table S48.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PIK3R1
TRIM23
BTF3
CCNB1
CDK7
FOXD1
GTF2H2
HEXB
HMGCR
HTR1A
KIF2A
TNPO1
CD180
MAP1B
NAIP
PMCHL2
RAD17
SMN1
SMN2
TAF9
SERF1A
ENC1
CARTPT
COL4A3BP
CWC27
NSA2
SMA4
SMA5
ADAMTS6
MRPS27
PPWD1
FAM169A
DIMT1
IPO11
GCNT4
POLK
SGTB
BDP1
ERBB2IP
NLN
ZSWIM6
ANKRA2
MCCC2
CENPK
RGNEF
SLC30A5
CENPH
PTCD2
C5orf44
UTP15
GFM2
NDUFAF2
MRPS36
FCHO2
TMEM171
TMEM174
SREK1
MARVELD2
ZNF366
CCDC125
ANKRD31
C5orf64
RNF180
SREK1IP1
MAST4
RGS7BP
C5orf43
LOC647859
GUSBP3
GTF2H2B
GTF2H2C
SERF1B
GTF2H2D
GUSBP9
LRRC70
FAM159B
LOC100170939
LOC100272216
LOC100303749
OCLN
MIR4804
MIR4803
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.3.

Table S49.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ACVR2A
RND3
CACNB4
KIF5C
NEB
ORC4
TNFAIP6
KYNU
NMI
ZEB2
EPC2
ARL5A
MMADHC
LRP1B
RIF1
MBD5
ARHGAP15
GTDC1
LYPD6
LYPD6B
RBM43
DKFZp686O1327
LOC647012
PABPC1P2
ZEB2-AS1
MIR4773-1
MIR4773-2
Genes in Wide Peak

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

Table S50.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DDB2
EXT2
CREB3L1
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
ACP2
ARHGAP1
CHRM4
CRY2
F2
FOLH1
CD82
LRP4
MDK
MYBPC3
NDUFS3
PSMC3
PTPRJ
RAPSN
SPI1
DGKZ
CHST1
API5
MADD
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
NR1H3
CELF1
NUP160
FNBP4
MTCH2
PACSIN3
HSD17B12
PHF21A
SLC35C1
AMBRA1
KBTBD4
TTC17
PRDM11
SYT13
LRRC4C
ALX4
C11orf49
ZNF408
AGBL2
ARFGAP2
ACCS
TSPAN18
SLC39A13
C1QTNF4
PTPMT1
OR4X2
OR4B1
GYLTL1B
LOC120824
C11orf94
ALKBH3
LOC221122
OR4C3
OR4S1
LOC283116
HARBI1
DKFZp779M0652
C11orf96
ACCSL
OR4X1
HNRNPKP3
FAM180B
OR4A47
OR4C45
MIR129-2
TRIM64C
SNORD67
LOC729799
MIR670
MIR3160-2
MIR3160-1
LOC100507205
LOC100507300
LOC100507401
MIR4688
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.33.

Table S51.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-592
ARF5
GRM8
PAX4
POT1
FSCN3
GCC1
ZNF800
MIR592
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.3.

Table S52.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BUB1B
TCF12
FLJ27352
C15orf55
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
ACTC1
ADAM10
APBA2
AQP9
B2M
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
USP8
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
FAM63B
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145663
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
LOC283710
FAM98B
PLA2G4D
GOLGA8G
GLDN
FMN1
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
MIR211
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC646278
LOC653075
HSP90AB4P
MIR626
MIR627
MIR628
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
GOLGA8F
LOC100132724
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
TMCO5B
MYZAP
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.21.

Table S53.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-486
ANK1
CHRNB3
IKBKB
PLAT
POLB
SFRP1
SLC20A2
VDAC3
KAT6A
AP3M2
DKK4
GOLGA7
GINS4
C8orf40
AGPAT6
NKX6-3
MIR486
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

Table S54.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
APOD
BDH1
CPN2
DLG1
FGF12
GP5
HES1
IL1RAP
MFI2
MUC4
OPA1
PAK2
PCYT1A
PPP1R2
RPL35A
TP63
CLDN1
KIAA0226
TNK2
CLDN16
NCBP2
ACAP2
UBXN7
PIGX
LEPREL1
LSG1
HRASLS
ATP13A3
PIGZ
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
CEP19
LMLN
TMEM44
TM4SF19
ZDHHC19
LRRC15
FAM43A
TMEM207
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
TCTEX1D2
C3orf43
SDHAP1
UTS2D
OSTN
ATP13A5
WDR53
ANKRD18DP
LRRC33
FLJ34208
LOC401109
GMNC
LOC647323
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
SNAR-I
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p22.1.

Table S55.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MSH6
MSH2
REL
EML4
BCL11A
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
hsa-mir-216b
hsa-mir-559
hsa-mir-558
ACTG2
ACYP2
ADD2
ANXA4
ATP6V1B1
AUP1
ZFP36L2
CALM2
CTNNA2
CYP1B1
DCTN1
DGUOK
LOC1720
DOK1
EGR4
EMX1
EPAS1
EFEMP1
FSHR
GFPT1
HK2
TLX2
FOXN2
LHCGR
LTBP1
EPCAM
MXD1
MDH1
MEIS1
MTIF2
OTX1
REG3A
PCBP1
PEX13
VIT
PIGF
PLEK
PPM1B
PPP3R1
PRKCE
EIF2AK2
RAB1A
REG1A
REG1B
REG1P
RPS27A
RTKN
SRSF7
SIX3
SLC1A4
SLC3A1
SLC8A1
SNRPG
SOS1
SPAST
SPR
SPTBN1
SRD5A2
STRN
TACR1
GCFC2
TGFA
TIA1
UGP2
VRK2
XDH
XPO1
ALMS1
MOGS
DYSF
DUSP11
MAP4K3
NAT8
COX7A2L
NRXN1
CRIPT
PREPL
FEZ2
SOCS5
USP34
SERTAD2
MRPL19
ARHGAP25
ACTR2
LRPPRC
CEBPZ
MPHOSPH10
SMYD5
C1D
SEMA4F
CCT7
CCT4
CDC42EP3
STAMBP
B3GNT2
SIX2
MTHFD2
PROKR1
GPR75
SNRNP27
GTF2A1L
STON1
AAK1
CEP68
PSME4
EXOC6B
EHBP1
RHOQ
HAAO
WBP1
PRKD3
RASGRP3
QPCT
VAX2
CNRIP1
FAM98A
RAB11FIP5
NFU1
ERLEC1
BMP10
ZNF638
HTRA2
LGALSL
EHD3
CD207
TPRKB
WDPCP
MEMO1
ASB3
CRIM1
PCYOX1
NAT8B
VPS54
DYNC2LI1
ETAA1
HEATR5B
AFTPH
C2orf42
FANCL
SRBD1
MOB1A
C2orf56
NAGK
TTC27
SLC30A6
CCDC88A
GKN1
CYP26B1
POLE4
KCNK12
PNO1
RPL23AP32
RTN4
PELI1
TTC7A
SMEK2
BIRC6
MTA3
SLC4A5
NLRC4
THADA
ATL2
ABCG5
ABCG8
GMCL1
TTC31
PAPOLG
OR7E91P
GALNT14
CAMKMT
GEMIN6
ANKRD53
LRRTM4
FBXO11
THUMPD2
INO80B
WDR54
FAM161A
FAM176A
ANTXR1
YIPF4
PRADC1
KIAA1841
DPY30
MCEE
LOXL3
PCGF1
CCDC142
FAM136A
LBX2
PNPT1
MCFD2
ATP6V1E2
DHX57
PKDCC
CAPN13
HNRPLL
SFXN5
CCDC104
TEX261
CCDC85A
WDR92
MRPL53
PPP1R21
C2orf73
REG3G
C2orf63
PLEKHH2
GALM
TMEM178
AHSA2
C2orf65
COMMD1
FBXO41
PUS10
LINC00309
MYADML
FAM82A1
ASPRV1
LOC151534
OXER1
CLEC4F
DQX1
KCNG3
ALMS1P
TET3
GKN2
APLF
TMEM17
SPRED2
LCLAT1
CCDC75
LINC00486
C2orf61
CYP1B1-AS1
STON1-GTF2A1L
LOC339803
C2orf74
LOC339807
FIGLA
NOTO
CDKL4
PRORSD1P
LRRTM1
LOC375196
LOC388942
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
SULT6B1
LOC400950
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
MIR216A
MIR217
CAPN14
CHAC2
FBXO48
LOC644838
MIR558
MIR559
LOC728730
LOC728819
MORN2
SNORA36C
SNORA70B
MIR216B
LOC100128590
LOC100129726
LOC100132215
LOC100133985
LOC100134259
DBIL5P2
SNAR-H
LOC100189589
ARHGEF33
LOC100271832
LOC100288911
GPR75-ASB3
MIR4264
MIR3126
MIR3682
LOC100505876
BOLA3-AS1
INO80B-WBP1
MIR4765
MIR4426
MIR4434
MIR4778
MIR4432
MIR548AD
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 22 significant results found. The significance cutoff is at Q value=0.25.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 2121 0.02 0.0501 1 0.04 3.01 0.00478
1q 1955 0.04 1.99 0.117 0.01 -1.36 1
2p 924 0.02 -2.71 1 0.02 -2.48 1
2q 1556 0.01 -2.72 1 0.03 -0.609 1
3p 1062 0.08 3.19 0.00413 0.02 -2.56 1
3q 1139 0.11 6.5 4.08e-10 0.01 -3.11 1
4p 489 0.02 -3.46 1 0.04 -1.63 1
4q 1049 0.02 -2.75 1 0.02 -2.06 1
5p 270 0.04 -1.97 1 0.02 -3.73 1
5q 1427 0.03 -0.802 1 0.03 -0.295 1
6p 1173 0.01 -2.97 1 0.05 1.05 0.344
6q 839 0.01 -3.81 1 0.08 2.53 0.0192
7p 641 0.20 12.8 0 0.00 -4.16 1
7q 1277 0.19 15.2 0 0.00 -3.52 1
8p 580 0.12 4.82 5.64e-06 0.42 31.2 0
8q 859 0.23 16.4 0 0.08 2.47 0.0209
9p 422 0.05 -0.742 1 0.05 -0.541 1
9q 1113 0.09 4.53 1.92e-05 0.02 -2.45 1
10p 409 0.03 -2.8 1 0.08 1.41 0.197
10q 1268 0.03 -1.19 1 0.09 4.62 1.09e-05
11p 862 0.04 -0.994 1 0.02 -2.97 1
11q 1515 0.05 1.16 0.544 0.01 -2.74 1
12p 575 0.03 -2.48 1 0.10 3.93 0.000213
12q 1447 0.03 -0.733 1 0.04 0.541 0.62
13q 654 0.01 -3.34 1 0.15 8.63 0
14q 1341 0.02 -2.22 1 0.05 0.742 0.509
15q 1355 0.01 -2.69 1 0.06 2.03 0.0566
16p 872 0.06 0.668 1 0.08 2.43 0.0218
16q 702 0.02 -2.83 1 0.21 14.5 0
17p 683 0.01 -3.32 1 0.14 8.29 0
17q 1592 0.02 -1.81 1 0.04 0.319 0.714
18p 143 0.04 -2.27 1 0.14 5.75 2.98e-08
18q 446 0.02 -2.95 1 0.20 12.2 0
19p 995 0.02 -2.8 1 0.03 -1.21 1
19q 1709 0.02 -1.31 1 0.03 0.354 0.714
20p 355 0.04 -1.55 1 0.04 -1.95 1
20q 753 0.04 -0.734 1 0.02 -2.88 1
21q 509 0.04 -1.51 1 0.04 -1.51 1
22q 921 0.01 -3.92 1 0.09 3.87 0.000243
Xq 1312 0.01 -3.49 1 0.07 3.13 0.00354
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

  • Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

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

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PRAD-TP/9826610/GDAC_MergeDataFiles_9828755/PRAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 419 Input Tumor Samples.

Tumor Sample Names
TCGA-2A-A8VL-01A-21D-A376-01
TCGA-2A-A8VO-01A-11D-A376-01
TCGA-2A-A8VT-01A-11D-A376-01
TCGA-2A-A8VV-01A-11D-A376-01
TCGA-2A-A8VX-01A-11D-A376-01
TCGA-2A-A8W1-01A-11D-A376-01
TCGA-2A-A8W3-01A-11D-A376-01
TCGA-CH-5737-01A-11D-1574-01
TCGA-CH-5738-01A-11D-1574-01
TCGA-CH-5739-01A-11D-1574-01

Figure 3.  Segmented copy number profiles in the input data

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

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

Region Data

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

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

  2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

  1. Cytoband

  2. Q value

  3. Residual Q value

  4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)