LowPass Copy number analysis (GISTIC2)
Lung Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Spring Yingchun Liu (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): LowPass Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1Z899VV
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 2.0.20 (Firehose task version: 126).

Summary

There were 120 tumor samples used in this analysis: 20 significant arm-level results, 41 significant focal amplifications, and 38 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 - 41 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
12q15 1.6831e-13 1.6831e-13 chr12:69160306-69242895 1
14q13.2 8.5605e-10 8.5605e-10 chr14:36253855-36359486 2
10p11.1 7.7606e-09 1.5236e-07 chr10:38777087-38901643 0 [LOC399744]
1q21.2 2.6308e-06 6.9013e-06 chr1:120505236-152317480 157
20q13.2 3.5257e-05 3.5257e-05 chr20:52182686-52325184 1
12p12.1 4.7229e-05 0.00079415 chr12:24845424-25500272 6
8p11.21 0.0014306 0.0014306 chr8:42018595-47462777 18
7p11.2 0.0015585 0.0024294 chr7:54612077-56175489 17
5p13.2 0.0025739 0.0054039 chr5:36847490-37655105 5
5q31.3 0.0058727 0.0058727 chr5:140693187-140828596 21
8q24.21 6.5201e-05 0.006894 chr8:128528311-129213692 11
19q13.11 0.0081957 0.0081957 chr19:34266780-34998944 7
2q31.1 0.0098941 0.0098941 chr2:170614261-170755876 3
1p31.1 0.017912 0.017912 chr1:84313530-84342583 1
8q22.3 0.0010673 0.022831 chr8:101933474-101989217 1
9p21.3 0.030929 0.030929 chr9:21952539-22024723 4
4p16.1 0.021654 0.031711 chr4:10174189-10452816 1
Xq28 0.04317 0.04317 chrX:151610247-155270560 106
4p15.2 0.048851 0.049678 chr4:26240748-26375976 1
7p21.1 0.030929 0.054307 chr7:16987241-20665079 14
2p25.1 0.056876 0.056876 chr2:11396355-11470704 1
20p11.21 0.058367 0.058367 chr20:23329302-23633577 10
11q24.3 0.081231 0.081231 chr11:129844642-129931406 2
5p15.33 0.0032657 0.091765 chr5:1-3284727 36
10p12.2 0.090916 0.096435 chr10:22551974-22640334 4
Xp22.11 0.055688 0.096435 chrX:23656157-24251235 8
7q22.1 0.030929 0.10321 chr7:97118157-103703617 140
3q26.2 0.12077 0.12077 chr3:169726147-170140845 5
13q31.1 0.12338 0.12338 chr13:81658077-81682427 0 [SPRY2]
6p22.3 0.1277 0.1277 chr6:21544807-21859971 2
Xp11.1 0.0776 0.13057 chrX:58103757-62195567 0 [ZXDA]
18q21.2 0.1338 0.1338 chr18:51864887-51896376 2
4q12 0.14211 0.14211 chr4:56411776-56520547 3
21q21.3 0.14522 0.14522 chr21:26928178-27147344 8
7q31.1 0.024592 0.14685 chr7:112490136-112649803 1
12p11.21 0.017912 0.14685 chr12:30796994-39233501 22
1q41 0.017513 0.15834 chr1:221027121-221073250 1
6q21 0.20368 0.20368 chr6:112359829-112553049 4
11p14.1 0.24453 0.24453 chr11:28520760-28561858 0 [METTL15]
5p15.2 0.02701 0.54237 chr5:1-17112064 87
8q21.11 0.00018082 0.87357 chr8:1-146364022 853
Genes in Wide Peak

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

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

Genes
MDM2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.2.

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

Genes
BRMS1L
RALGAPA1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
ARNT
BCL9
NOTCH2
PDE4DIP
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
CTSK
CTSS
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
MCL1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A10
S100A11
VPS72
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
SV2A
RBM8A
SF3B4
PIAS3
SEMA6C
POLR3C
TXNIP
MTMR11
MLLT11
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
CA14
NBPF14
RNF115
TMOD4
CERS2
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
C1orf56
GOLPH3L
FAM63A
CDC42SE1
OTUD7B
FAM91A2
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
HIST2H3C
LIX1L
C1orf51
HFE2
ANKRD35
BNIPL
PPIAL4A
PDIA3P
NBPF11
NUDT17
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
LINGO4
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
NBPF9
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
TNFAIP8L2-SCNM1
Genes in Wide Peak

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

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

Genes
ZNF217
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
C12orf77
Genes in Wide Peak

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

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

Genes
HOOK3
CHRNB3
FNTA
IKBKB
PLAT
POLB
SLC20A2
VDAC3
CHRNA6
AP3M2
DKK4
THAP1
RNF170
SGK196
C8orf40
HGSNAT
POTEA
MIR4469
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR
CCT6A
GBAS
PHKG1
PSPH
SEC61G
SUMF2
CHCHD2
MRPS17
LANCL2
VOPP1
VSTM2A
LOC285878
SEPT14
ZNF713
FKBP9L
SNORA15
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.2.

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

Genes
NUP155
NIPBL
WDR70
C5orf42
LOC646719
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q31.3.

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

Genes
TAF7
PCDHGB4
PCDHGA8
PCDHGA12
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
PVT1
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
GPI
KIAA0355
UBA2
LSM14A
KCTD15
PDCD2L
WTIP
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q31.1.

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

Genes
SSB
METTL5
UBR3
Genes in Wide Peak

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

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

Genes
TTLL7
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q22.3.

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

Genes
YWHAZ
Genes in Wide Peak

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

Table S15.  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 amplified genes in the wide peak for 4p16.1.

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

Genes
ZNF518B
Genes in Wide Peak

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

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

Genes
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CETN2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
GABRA3
OPN1MW
GDI1
HCFC1
IDH3G
IL9R
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SPRY3
ZNF275
TREX2
SRPK3
SNORA70
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
GABRQ
PDZD4
FAM3A
FUNDC2
BRCC3
H2AFB3
PNMA6A
FAM58A
PNMA5
RAB39B
GAB3
PNCK
ZFP92
CSAG1
CTAG1A
MAGEA2B
LINC00204B
CSAG3
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CSAG2
CXorf68
LINC00204A
MTCP1NB
PNMA6C
PNMA6D
MIR1184-1
MIR718
MIR3202-2
MIR1184-3
MIR1184-2
MIR3202-1
LOC100507404
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p15.2.

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

Genes
RBPJ
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p21.1.

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

Genes
hsa-mir-3146
hsa-mir-1302-6
AHR
ITGB8
TWIST1
HDAC9
SNX13
PRPS1L1
TWISTNB
FERD3L
TMEM196
ABCB5
MACC1
MIR3146
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p25.1.

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

Genes
ROCK2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.21.

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

Genes
CST3
CST8
NXT1
NAPB
GZF1
CSTL1
CST9L
CST9
CST11
CSTT
Genes in Wide Peak

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

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

Genes
PRDM10
LINC00167
Genes in Wide Peak

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

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

Genes
hsa-mir-4277
NDUFS6
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
IRX4
CEP72
AHRR
MRPL36
BRD9
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
C5orf38
IRX2
SLC6A19
SLC6A18
LRRC14B
SDHAP3
LOC728613
MIR4277
LOC100506688
MIR4457
MIR4456
MIR4635
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p12.2.

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

Genes
BMI1
SPAG6
COMMD3
COMMD3-BMI1
Genes in Wide Peak

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

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

Genes
EIF2S3
SAT1
ZFX
PRDX4
ACOT9
APOO
KLHL15
CXorf58
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
ACHE
ASNS
AZGP1
AP1S1
CUX1
CYP3A7
CYP3A4
CYP3A5
EPHB4
EPO
GNB2
AGFG2
LRCH4
MCM7
NPTX2
OCM2
SERPINE1
PCOLCE
PMS2P1
POLR2J
RELN
PSMC2
TAC1
TAF6
TFR2
TRIP6
VGF
ZAN
ZNF3
ZKSCAN1
ZSCAN21
TRRAP
BUD31
PLOD3
AP4M1
PMPCB
ATP5J2
MUC12
ARPC1B
RASA4
LRRC17
POP7
ZNHIT1
ARPC1A
SH2B2
STAG3
CPSF4
COPS6
PDAP1
LMTK2
ZKSCAN5
CLDN15
BRI3
TECPR1
PTCD1
FBXO24
DNAJC2
PILRB
PILRA
FIS1
ACTL6B
SRRT
ALKBH4
ZCWPW1
C7orf43
BAIAP2L1
MEPCE
SLC12A9
SMURF1
MOSPD3
GIGYF1
RABL5
CYP3A43
ZNF655
PVRIG
GAL3ST4
PRKRIP1
ORAI2
OR2AE1
TSC22D4
TRIM56
ARMC10
ZNF394
MYH16
TRIM4
MYL10
EMID2
MUC17
BHLHA15
ZNF498
FAM200A
PPP1R35
GPC2
LRWD1
FAM185A
FBXL13
NAPEPLD
TMEM130
NYAP1
CNPY4
POLR2J2
MBLAC1
ZNF789
MOGAT3
GJC3
DPY19L2P2
GATS
NAT16
SLC26A5
MGC72080
C7orf59
KPNA7
C7orf61
UFSP1
MIR106B
MIR25
MIR93
SPDYE3
SPDYE2
POLR2J3
AZGP1P1
SPDYE6
RPL19P12
LOC100129845
UPK3BL
LOC100289187
LOC100289561
SPDYE2L
SAP25
MIR4285
MIR3609
ATP5J2-PTCD1
MIR4653
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1
Genes in Wide Peak

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

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

Genes
CLDN11
PRKCI
SKIL
GPR160
PHC3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

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

Genes
SOX4
LINC00340
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q21.2.

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

Genes
STARD6
C18orf54
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
CLOCK
NMU
PDCL2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q21.3.

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

Genes
hsa-mir-155
ATP5J
GABPA
MRPL39
JAM2
MIR155HG
LINC00515
MIR155
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.1.

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

Genes
C7orf60
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p11.21.

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

Genes
BICD1
DDX11
PKP2
DNM1L
IPO8
YARS2
C12orf35
FAM60A
CAPRIN2
FLJ13224
ALG10
FGD4
ALG10B
CPNE8
DENND5B
AMN1
METTL20
SYT10
H3F3C
TSPAN11
LOC100287314
LOC100506660
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q41.

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

Genes
HLX
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

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

Genes
LAMA4
WISP3
TUBE1
C6orf225
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.2.

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

Genes
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
CTNND2
DAP
DNAH5
MTRR
MYO10
NDUFS6
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
PP7080
IRX4
TAS2R1
FAM134B
FAM105A
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285577
LOC285692
SLC6A19
LOC340094
SLC6A18
LRRC14B
FLJ33360
TAG
MARCH11
LOC442132
ANKRD33B
SDHAP3
LOC728613
LOC729506
SNORD123
LOC100130744
MIR4277
MIR4278
LOC100505738
LOC100505806
LOC100506688
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q21.11.

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

Genes
COX6C
EXT1
FGFR1
MYC
PCM1
PLAG1
TCEA1
WRN
RECQL4
NCOA2
WHSC1L1
CHCHD7
HOOK3
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
hsa-mir-1273
hsa-mir-875
hsa-mir-3150
hsa-mir-3149
hsa-mir-2052
hsa-mir-124-2
hsa-mir-486
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ADCY8
ADRA1A
ADRB3
ANGPT1
ANGPT2
ANK1
ANXA13
ASAH1
ASPH
ATP6V1B2
ATP6V1C1
BAI1
BLK
BMP1
POLR3D
BNIP3L
OSGIN2
CA1
CA2
CA3
CA8
CALB1
RUNX1T1
CDH17
CEBPD
CHRNA2
CHRNB3
CLU
CRH
CTSB
CYC1
CYP7A1
CYP11B1
CYP11B2
ADAM3A
DECR1
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYS
DPYSL2
DUSP4
E2F5
EEF1D
EGR3
EIF4EBP1
EPB49
EPHX2
CLN8
EXTL3
EYA1
FABP4
FABP5
PTK2B
FDFT1
FGL1
FNTA
ADAM2
GATA4
GEM
GFRA2
GLI4
GML
GNRH1
NPBWR1
GPR20
GPT
GRINA
GSR
GTF2E2
HAS2
NRG1
HNF4G
HSF1
IKBKB
IL7
IMPA1
IDO1
EIF3E
KCNQ3
KCNS2
LOXL2
LPL
LY6E
LY6H
LYN
MATN2
MCM4
MMP16
MOS
MSR1
MSRA
MYBL1
NBN
NDUFB9
NEFM
NEFL
TONSL
NKX3-1
NOV
ODF1
TNFRSF11B
OPRK1
PDE7A
PDGFRL
ENPP2
PENK
PLAT
PLEC
PNOC
PMP2
POLB
POLR2K
POU5F1B
PPP2CB
PPP2R2A
PPP3CC
PKIA
PRKDC
PTK2
PVT1
PEX2
RAB2A
RAD21
RP1
RPL7
RPL8
RPL30
RPS20
SDC2
SDCBP
SFRP1
SFTPC
ST3GAL1
SLA
SLC7A2
SLC18A1
SLC20A2
SNAI2
SNTB1
SPAG1
SQLE
STAR
STC1
STK3
TACC1
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
UBE2V2
COL14A1
UQCRB
VDAC3
YWHAZ
ZNF7
ZNF16
FZD3
TUSC3
UBXN8
KAT6A
PSCA
FZD6
NSMAF
LY6D
RGS20
JRK
TNKS
EIF3H
DGAT1
GPAA1
ADAM18
ADAM9
ADAM7
RIPK2
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
GGH
WISP1
CPNE3
FOXH1
CHRNA6
TRPA1
DOK2
ASH2L
MTMR7
CCNE2
EBAG9
MYOM2
DLGAP2
MSC
MFHAS1
KCNB2
CYP7B1
BAG4
ENTPD4
ARHGEF10
MTFR1
LRRC14
TTC35
RIMS2
ST18
TOX
MTSS1
PTDSS1
PHYHIP
RB1CC1
ZNF623
KIAA0196
KBTBD11
HHLA1
SORBS3
TRIB1
HRSP12
NPM2
DLC1
NDRG1
PGCP
SPAG11B
LYPLA1
ARFGEF1
COLEC10
KHDRBS3
DCTN6
PNMA2
ADAM28
POP1
AP3M2
COPS5
RBPMS
WWP1
STMN2
PTP4A3
ERLIN2
LZTS1
PROSC
RNF139
ZHX1
PUF60
ZHX2
DENND3
XPO7
TRIM35
ZC3H3
EFR3A
RRS1
SULF1
RHOBTB2
ARC
BOP1
DDHD2
KIF13B
PSD3
ZFPM2
HEY1
TRAM1
LEPROTL1
SCRIB
KIAA0146
SLC39A14
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
GPR124
KIAA1429
C8orf71
RGS22
FBXL6
PTTG3P
FBXO25
FGF20
SNORA72
SNORD54
OPLAH
PABPC1
KCNV1
STAU2
MTBP
DKK4
EIF2C2
LSM1
ADAMDEC1
BHLHE22
MRPS28
COMMD5
MRPL13
ATAD2
ASAP1-IT1
MRPL15
CNOT7
CPSF1
PURG
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
FAM82B
ZNF706
GOLGA7
VPS28
ZDHHC2
FAM203A
KCNK9
SLC25A37
C8orf55
UBR5
SCARA3
FAM49B
AZIN1
ATP6V1H
OTUD6B
TMEM66
CHRAC1
SNTG1
GDAP1
EXOSC4
PDP1
CNGB3
LY6K
KCTD9
ESRP1
IMPAD1
TMEM70
PINX1
TRMT12
OXR1
WDYHV1
PIWIL2
ELP3
THAP1
ARMC1
INTS10
CCDC25
UBE2W
BRF2
AGPAT5
LAPTM4B
C8orf39
TMEM55A
SLC39A4
CHD7
SYBU
INTS8
INTS9
CSGALNACT1
HR
PAG1
PBK
ZNF395
DEFB103B
BIN3
TEX15
GSDMC
C8orf44
JPH1
C8orf4
ENY2
CPA6
SLURP1
SLC45A4
MTUS1
KIAA1456
ZFAT
KIAA1967
ZNF250
PLEKHA2
SH2D4A
PRDM14
SNX16
NECAB1
PDLIM2
SOX17
CSMD1
EBF2
FAM160B2
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
MTMR9
DUSP26
C8orf51
DSCC1
DERL1
GPR172A
HMBOX1
EFCAB1
MCPH1
PPP1R3B
PLEKHF2
ZMAT4
ZFAND1
ZFHX4
GSDMD
NIPAL2
RNF122
CSPP1
BAALC
NUDT18
ZNF696
GRHL2
DOCK5
FLJ14107
VCPIP1
ZNF703
TTI2
RAB11FIP1
PREX2
REEP4
ARHGAP39
ZNF34
SLC25A32
TM7SF4
STMN4
RNF170
SLCO5A1
SHARPIN
EPPK1
SCRT1
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
CRISPLD1
TRAPPC9
TM2D2
TATDN1
NACAP1
NCALD
SGK196
MAF1
UTP23
GINS4
PPAPDC1B
MAK16
TRIM55
FUT10
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
FAM86B1
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
ERI1
ZNF251
KIFC2
TMEM67
LONRF1
CHMP7
MTDH
CHMP4C
PKHD1L1
NAPRT1
WDR67
HPYR1
RP1L1
TP53INP1
TGS1
MFSD3
MAL2
XKR4
CSMD3
RHPN1
FBXO32
C8orf40
SLC26A7
PCMTD1
CTHRC1
OSR2
C8orf34
TOP1MT
CLDN23
ZNF572
GOT1L1
FAM92A1
VPS37A
C8orf38
TMEM68
ABRA
LYPD2
NKX2-6
TMEM71
SGCZ
ADHFE1
UBXN2B
PXDNL
AGPAT6
UNC5D
LETM2
DCAF4L2
RALYL
HGSNAT
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
ESCO2
FBXO16
LOC157627
FAM84B
C8orf37
VPS13B
C8orf42
ERICH1
SLC7A13
TDH
TMEM74
FAM91A1
C8orf48
C8orf45
CLVS1
NKX6-3
KCNU1
C8orf84
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ZNF596
IDO2
DEFT1P
SDR16C5
ADCK5
TSNARE1
R3HCC1
PRSS55
C8orf74
HTRA4
ADAM32
C8orf47
LGI3
MAPK15
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
ATP6V0D2
NEIL2
YTHDF3
C8orf46
LOC254896
REXO1L1
ADAM5P
FLJ10661
XKR6
NSMCE2
LOC286059
ZNF707
BREA2
FAM83H
LOC286083
LOC286094
EFHA2
ZNF252
TMED10P1
C8orf77
LOC286114
C8orf31
ZFP41
SCARA5
LOC286135
RNF5P1
C8orf83
DPY19L4
FBXO43
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
GPIHBP1
LOC340357
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
POTEA
SLC10A5
LOC349196
SPATC1
USP17L2
CA13
XKR5
FAM90A25P
LOC389641
C8orf80
C8orf86
FAM150A
XKR9
LOC389676
RBM12B
FLJ43860
MAFA
LOC392196
LOC392232
GDF6
LOC401463
C8orf59
SAMD12
MIR124-1
MIR124-2
MIR30B
MIR30D
MIR320A
DEFB103A
C8orf82
FER1L6-AS1
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
FLJ39080
FLJ46284
FLJ42969
C8orf85
LRRC24
DEFA10P
C8orf22
MIR383
LINC00293
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
LINC00251
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
DEFB135
DEFB136
DEFB134
ZNF704
C8orf69
C8orf75
MBOAT4
LINC00051
MIR486
DEFB109P1B
SNHG6
SNORD87
C8orf73
SCXB
LINC00535
UG0898H09
RPL23AP53
RAD21-AS1
FAM90A14
FABP9
FABP12
FAM86B2
SPAG11A
FER1L6
MIR596
MIR597
MIR598
MIR599
MIR661
LOC727677
HEATR7A
LOC728024
DEFA1B
FAM90A20
LOC728724
FAM90A19
ZNF705D
OC90
LOC731779
MIR875
MIR937
MIR939
LOC100127983
LOC100128126
LOC100128338
LOC100128750
FAM66B
LOC100128993
TCF24
SCXA
LOC100130155
LOC100130231
CCDC166
LOC100130298
LOC100130301
LRRC69
LOC100130964
LOC100131726
ZNF705G
FAM66E
LOC100132396
LOC100132891
FAM66D
FAM66A
SBF1P1
LOC100133267
LOC100133669
LOC100192378
LOC100287015
DEFT1P2
LOC100287846
LOC100288181
REXO1L2P
LOC100288748
DEFB4B
MIR1205
MIR1322
MIR1206
MIR1207
MIR1204
MIR548I3
MIR1234
MIR2053
MIR2052
MIR1208
MIR4287
MIR3148
MIR4288
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
MIR3150B
MIR3610
LOC100505659
LOC100505676
LOC100505718
LOC100506990
LOC100507117
LOC100507156
LOC100507341
LOC100507632
LOC100507651
C8orf44-SGK3
ZHX1-C8ORF76
MIR4469
MIR378D2
MIR548O2
MIR4661
MIR4663
MIR4472-1
MIR4664
MIR4659A
MIR4660
MIR4659B
MIR4471
MIR4470
LOC100616530
LOC100652791
PCAT1
LINC00536
FSBP

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 - 38 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 2.623e-34 6.9768e-32 chr9:21966776-22008600 4
Xp11.1 1.6201e-07 3.1788e-05 chrX:58103757-62195567 0 [ZXDA]
15q11.2 7.4165e-05 9.535e-05 chr15:25294598-25486359 71
19p13.2 8.2295e-05 0.00011247 chr19:8996097-9090978 1
10p11.1 0.00017281 0.00017281 chr10:38773386-38901643 0 [LOC399744]
4p16.1 0.00029924 0.00029924 chr4:10187381-10282417 0 [WDR1]
Xp21.1 9.0401e-05 0.0011161 chrX:36707139-36813689 0 [FAM47C]
4q21.1 0.0031399 0.0031399 chr4:78125768-78413734 0 [CXCL13]
13q14.2 0.00041466 0.0031399 chr13:49116366-49265161 0 [RCBTB2]
1p36.11 0.0019828 0.0068152 chr1:24150579-24412338 7
3p12.3 0.0068152 0.0068152 chr3:79630681-79764849 1
19p13.3 0.012447 0.021231 chr19:1168036-1282863 8
3q13.11 0.024806 0.024806 chr3:103347409-103441522 0 [MIR548A3]
21q21.1 0.024806 0.024806 chr21:18002996-18655465 0 [LINC00478]
9p21.2 7.4165e-05 0.03399 chr9:22431064-26112691 5
12p13.1 0.03399 0.03399 chr12:13024182-14127042 13
22q13.32 0.036197 0.036197 chr22:47837821-49147869 5
6q16.1 0.0021798 0.043939 chr6:99463965-99569838 0 [FBXL4]
1p22.2 0.019509 0.074656 chr1:90813753-91029702 0 [BARHL2]
1p13.2 0.0021798 0.080089 chr1:102275933-149895119 248
5q14.3 0.050524 0.083934 chr5:73168188-88883185 82
11q22.3 0.021182 0.1224 chr11:104219145-124046166 201
8p23.1 0.12995 0.12995 chr8:9586974-9696474 3
2q22.1 0.13694 0.13694 chr2:141620779-142111538 1
6q24.1 0.0031399 0.13694 chr6:140637478-140681819 0 [MIR3668]
12q24.21 0.1578 0.1578 chr12:114235967-114823870 2
15q25.2 0.055667 0.19997 chr15:84739057-86121490 18
16q24.2 0.19997 0.19997 chr16:87345556-90354753 60
19q13.2 0.19997 0.19997 chr19:39990221-40279182 11
5q21.1 0.19997 0.20816 chr5:102635548-102877757 0 [NUDT12]
6p21.2 0.20816 0.20816 chr6:39913115-40167965 0 [MOCS1]
11p14.1 0.20816 0.20816 chr11:27853438-28038089 0 [KIF18A]
8q23.1 0.22552 0.22552 chr8:108575719-108623527 0 [ANGPT1]
18q21.32 0.22552 0.22552 chr18:57965327-60210027 7
13q21.32 0.03399 0.22799 chr13:68493404-68551231 0 [PCDH9]
13q11 0.012447 0.2397 chr13:1-41929239 148
7q36.2 0.24671 0.24671 chr7:119737203-159138663 336
11q12.1 0.0016279 0.34227 chr11:49916017-59443398 119
Genes in Wide Peak

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

Table S38.  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 15q11.2.

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

Genes
IPW
PAR1
SNORD115-1
PAR4
SNORD116-19
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
SNORD115-43
SNORD116-28
SNORD116-29
SNORD115-24
SNORD115-27
SNORD115-28
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

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

Genes
MUC16
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
CNR2
FUCA1
HMGCL
SRSF10
PNRC2
MYOM3
MIR378F
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.3.

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

Genes
ROBO1
Genes in Wide Peak

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

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

Genes
STK11
ATP5D
CIRBP
SBNO2
C19orf24
MIDN
CIRBP-AS1
C19orf26
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.2.

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

Genes
ELAVL2
DMRTA1
TUSC1
FLJ35282
LOC100506422
Genes in Wide Peak

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

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

Genes
hsa-mir-614
EMP1
GRIN2B
GPRC5A
HEBP1
GPRC5D
KIAA1467
GSG1
HTR7P1
C12orf36
RPL13AP20
MIR614
LOC100506314
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

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

Genes
hsa-mir-3201
FAM19A5
LOC284933
FLJ46257
MIR3201
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
ADORA3
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
CELSR2
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
TTF2
ITGA10
PEX11B
SLC16A4
CD101
SEC22B
CHD1L
LRIG2
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
CD160
DDX20
NTNG1
WDR47
CLCC1
NBPF14
PTPN22
PHGDH
CHIA
RNF115
GPSM2
SLC25A24
BOLA1
HAO2
ACP6
GPR89B
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
FAM91A2
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
DNAJA1P5
HENMT1
GNRHR2
OLFM3
MAB21L3
HIST2H3C
ATXN7L2
C1orf194
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
RP11-165H20.1
DENND2C
FNDC7
PPIAL4A
UBL4B
PDIA3P
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
MYBPHL
NBPF7
LOC375010
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
NBPF9
MIR197
LOC440600
BCL2L15
HIST2H2BF
PGCP1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
LOC648740
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR942
LOC100129138
LOC100129269
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
LOC100506343
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q14.3.

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

Genes
hsa-mir-9-2
hsa-mir-4280
ARSB
BHMT
CCNH
CKMT2
COX7C
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
HEXB
HMGCR
MEF2C
MSH3
RASA1
RASGRF2
RPS23
TBCA
THBS4
XRCC4
ENC1
AP3B1
PDE8B
HOMER1
SCAMP1
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
NSA2
IQGAP2
SV2C
OTP
SSBP2
BHMT2
FAM169A
RNU5E-1
RNU5D-1
DMGDH
GCNT4
POLK
AGGF1
WDR41
RGNEF
ATG10
ZCCHC9
ZBED3
GFM2
SPZ1
ATP6AP1L
JMY
POC5
ACOT12
TMEM167A
TMEM161B
PAPD4
FAM151B
S100Z
CMYA5
ANKRD31
SERINC5
NBPF22P
ANKRD34B
MTX3
MIR9-2
CRSP8P
LOC644936
LINC00461
SCARNA18
SNORA47
LOC728723
LOC100131067
NCRUPAR
MIR4280
MTRNR2L2
MIR3607
LOC100505894
MIR3977
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
VWA5A
MCAM
NCAM1
NNMT
NPAT
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
SLN
SORL1
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
ZNF259
USP2
HTR3B
ZW10
UBE4A
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
TIMM8B
SIDT2
TRAPPC4
FXYD6
C11orf71
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
ABCG4
C11orf1
RNF26
NLRX1
ALG9
CLMP
PDZD3
C11orf63
TMPRSS5
MFRP
BCO2
TMPRSS13
KIAA1826
BUD13
TMEM25
UBASH3B
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf65
MPZL3
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
C11orf87
C11orf92
C11orf88
MIR100HG
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
CARD17
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
LOC100288346
BACE1-AS
MIR4301
LOC100499227
MIR3656
CASP12
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
LOC100652768
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.1.

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

Genes
hsa-mir-597
TNKS
MIR597
Genes in Wide Peak

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

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

Genes
LRP1B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.21.

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

Genes
TBX5
RBM19
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q25.2.

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

Genes
NMB
PDE8A
SLC28A1
ZNF592
AKAP13
SEC11A
SCAND2
ZSCAN2
ALPK3
WDR73
GOLGA6L5
LOC388152
UBE2Q2P1
DNM1P41
LOC440300
LOC648809
LOC100505679
LOC100506874
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.2.

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

Genes
CBFA2T3
FANCA
AFG3L1P
APRT
C16orf3
CA5A
CDH15
CYBA
DPEP1
GALNS
GAS8
MC1R
MVD
CHMP1A
RPL13
SPG7
SLC7A5
CDK10
C16orf7
PIEZO1
TUBB3
PRDM7
TCF25
ZCCHC14
CPNE7
IL17C
ANKRD11
TRAPPC2L
KLHDC4
DEF8
BANP
JPH3
DBNDD1
FBXO31
CDT1
MAP1LC3B
SPIRE2
ZNF469
CENPBD1
ZNF276
RNF166
SPATA2L
C16orf55
ZC3H18
SLC22A31
ZFPM1
MGC23284
ZNF778
ACSF3
LINC00304
SNAI3
CTU2
PABPN1L
LOC400558
SNORD68
LOC100128881
LOC100130015
LOC100287036
C16orf95
MIR4722
Genes in Wide Peak

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

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

Genes
CLC
DLL3
LGALS13
LGALS14
EID2B
LGALS16
EID2
LEUTX
SELV
LGALS17A
LOC100129935
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.32.

Table S56.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MC4R
TNFRSF11A
PIGN
CDH20
ZCCHC2
KIAA1468
RNF152
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q11.

Table S57.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BRCA2
CDX2
FLT3
LHFP
TTL
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
CDK8
ELF1
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
GTF3A
HMGB1
PDX1
MAB21L1
SMAD9
MIPEP
PABPC3
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TRPC4
TUBA3C
ZMYM2
IFT88
CCNA1
MTMR6
DCLK1
ZMYM5
KL
MTRF1
NUPL1
FRY
SLC25A15
USPL1
MRPS31
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
WBP4
EXOSC8
PDS5B
SPG20
MTUS2
SACS
LATS2
SNORD102
NBEA
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
PSPC1
TNFRSF19
FAM48A
CENPJ
RNF17
COG6
XPO4
MRP63
NAA16
PROSER1
KATNAL1
KBTBD7
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
CG030
CSNK1A1L
RXFP2
TEX26
B3GALTL
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
ZDHHC20
PAN3
PHF2P1
SUGT1P3
SLC46A3
ANKRD20A9P
C1QTNF9
FREM2
LINC00442
TPTE2P6
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERTM1
LINC00547
LINC00548
ATP5EP2
LOC440131
C1QTNF9B-AS1
SNORA27
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
MIR621
CCDC169
ANKRD26P3
RPL21P28
LINC00426
LINC00421
PAN3-AS1
MIR548F5
MIR2276
MIR320D1
MIR4305
LINC00327
TEX26-AS1
SPG20OS
CCDC169-SOHLH2
MIR4499
LOC100616668
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.2.

Table S58.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BRAF
EZH2
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CADPS2
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q12.1.

Table S59.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3162
hsa-mir-130a
APLNR
SERPING1
CNTF
CTNND1
OSBP
P2RX3
PRG2
SSRP1
SLC43A1
UBE2L6
LPXN
GLYAT
PRG3
OR5I1
CLP1
DTX4
ZDHHC5
OR5L2
TIMM10
SLC43A3
TMX2
FAM111A
TRIM48
ZFP91
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
SPRYD5
TNKS1BP1
GLYATL1
OR4C46
OR8I2
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
C11orf31
OR10AG1
OR5J2
OR4C13
OR4C12
OR9G4
LOC283194
OR5F1
OR5AP2
RTN4RL2
FAM111B
ZFP91-CNTF
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
MIR130A
LOC440041
LOC441601
OR5B3
OR8U8
OR9G9
BTBD18
LOC646813
MIR3162
TMX2-CTNND1
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 20 significant results found. The significance cutoff is at Q value=0.25.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 2121 0.15 1.54 0.353 0.15 1.54 0.176
1q 1955 0.42 10.2 0 0.11 -0.126 1
2p 924 0.12 -1.26 1 0.00 -4.47 1
2q 1556 0.07 -2.1 1 0.00 -4.12 1
3p 1062 0.04 -3 1 0.22 1.88 0.101
3q 1139 0.12 -0.812 1 0.12 -0.812 1
4p 489 0.09 -2.24 1 0.13 -1.38 1
4q 1049 0.04 -3.25 1 0.14 -0.461 1
5p 270 0.43 6.82 6.2e-11 0.07 -2.48 1
5q 1427 0.13 -0.282 1 0.17 0.938 0.387
6p 1173 0.16 0.234 1 0.11 -1.18 1
6q 839 0.09 -2 1 0.24 2.26 0.048
7p 641 0.43 7.37 1.75e-12 0.04 -2.85 1
7q 1277 0.29 4.69 1.12e-05 0.01 -3.46 1
8p 580 0.14 -0.712 1 0.39 6.09 2.26e-08
8q 859 0.38 6.14 4.18e-09 0.10 -1.42 1
9p 422 0.07 -2.63 1 0.31 3.52 0.00126
9q 1113 0.03 -3.16 1 0.24 2.68 0.0162
10p 409 0.10 -2.1 1 0.12 -1.67 1
10q 1268 0.06 -2.34 1 0.11 -1.14 1
11p 862 0.08 -2.3 1 0.08 -2.3 1
11q 1515 0.13 -0.185 1 0.09 -1.18 1
12p 575 0.19 0.428 1 0.20 0.642 0.521
12q 1447 0.14 0.0434 1 0.10 -0.939 1
13q 654 0.07 -2.48 1 0.30 3.63 0.00113
14q 1341 0.12 -0.462 1 0.15 0.261 0.756
15q 1355 0.07 -2.04 1 0.25 3.51 0.00126
16p 872 0.15 -0.198 1 0.15 -0.198 1
16q 702 0.11 -1.52 1 0.19 0.679 0.521
17p 683 0.12 -1.31 1 0.31 3.92 0.000451
17q 1592 0.24 3.62 0.000977 0.05 -2.16 1
18p 143 0.15 -1.11 1 0.24 1.13 0.321
18q 446 0.06 -2.96 1 0.29 3.01 0.00658
19p 995 0.04 -2.89 1 0.35 5.81 6.24e-08
19q 1709 0.11 -0.47 1 0.25 4.11 0.00026
20p 355 0.16 -0.467 1 0.22 0.998 0.374
20q 753 0.21 1.15 0.629 0.14 -0.619 1
21q 509 0.15 -0.568 1 0.22 1.14 0.321
22q 921 0.03 -3.39 1 0.21 1.62 0.161
Xq 1312 0.13 -0.225 1 0.21 2.16 0.0557
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/PrepareGisticDNASeq/LUAD-TP/6154863/segmentationfile.txt

  • Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/LUAD-TP/6154863/markersfile.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 = 0.3

  • Deletion Threshold = 0.3

  • Cap Values = 2

  • Broad Length Cutoff = 0.5

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 10

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 10000

  • Gene GISTIC = 0

Table 4.  Get Full Table First 10 out of 120 Input Tumor Samples.

Tumor Sample Names
TCGA-05-4249-01A-01D-1103-02
TCGA-05-4250-01A-01D-1103-02
TCGA-05-4382-01A-01D-1203-02
TCGA-05-4384-01A-01D-1751-02
TCGA-05-4389-01A-01D-1203-02
TCGA-05-4390-01A-02D-1751-02
TCGA-05-4395-01A-01D-1203-02
TCGA-05-4396-01A-21D-1853-02
TCGA-05-4397-01A-01D-1203-02
TCGA-05-4398-01A-01D-1203-02

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)