LowPass Copy number analysis (GISTIC2)
Lung Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
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/C1ZC81S9
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 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 3
14q13.2 8.5605e-10 8.5605e-10 chr14:36253855-36359486 3
10p11.1 7.7606e-09 1.5236e-07 chr10:38777087-38901643 0 [SEPT7P9]
1q21.3 2.6308e-06 6.9013e-06 chr1:120505236-152317480 156
20q13.2 3.5257e-05 3.5257e-05 chr20:52182686-52325184 1
12p12.1 4.7229e-05 0.00079415 chr12:24845424-25500272 7
8p11.21 0.0014306 0.0014306 chr8:42018595-47462777 22
7p11.2 0.0015585 0.0024294 chr7:54612077-56175489 21
5p13.2 0.0025739 0.0054039 chr5:36847490-37655105 5
5q31.3 0.0058727 0.0058727 chr5:140693187-140828596 20
8q24.21 6.5201e-05 0.006894 chr8:128528311-129213692 6
19q13.11 0.0081957 0.0081957 chr19:34266780-34998944 9
2q31.1 0.0098941 0.0098941 chr2:170614261-170755876 5
1p31.1 0.017912 0.017912 chr1:84313530-84342583 1
8q22.3 0.0010673 0.022831 chr8:101933474-101989217 2
9p21.3 0.030929 0.030929 chr9:21952539-22024723 3
4p16.1 0.021654 0.031711 chr4:10174189-10452816 1
Xq28 0.04317 0.04317 chrX:151610247-155270560 108
4p15.2 0.048851 0.049678 chr4:26240748-26375976 1
7p21.1 0.030929 0.054307 chr7:16987241-20665079 15
2p25.1 0.056876 0.056876 chr2:11396355-11470704 1
20p11.21 0.058367 0.058367 chr20:23329302-23633577 11
11q24.3 0.081231 0.081231 chr11:129844642-129931406 2
5p15.33 0.0032657 0.091765 chr5:1-3284727 33
10p12.2 0.090916 0.096435 chr10:22551974-22640334 3
Xp22.11 0.055688 0.096435 chrX:23656157-24251235 9
7q22.1 0.030929 0.10321 chr7:97118157-103703617 151
3q26.2 0.12077 0.12077 chr3:169726147-170140845 5
13q31.1 0.12338 0.12338 chr13:81658077-81682427 0 [LINC00564]
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 6
7q31.1 0.024592 0.14685 chr7:112490136-112649803 1
12p11.21 0.017912 0.14685 chr12:30796994-39233501 28
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 79
8q21.11 0.00018082 0.87357 chr8:1-146364022 889
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: Cancer Gene Census[7].

Genes
MDM2
SLC35E3
CPM
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: Cancer Gene Census[7].

Genes
snoU13|ENSG00000238718.1
BRMS1L
RALGAPA1
Genes in Wide Peak

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

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

Genes
ARNT
BCL9
NOTCH2
PDE4DIP
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
CTSK
CTSS
ECM1
ENSA
FCGR1A
FLG
FMO5
GJA5
GJA8
MCL1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A10
S100A11
VPS72
TCHH
TUFT1
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
CHD1L
SETDB1
SV2A
RBM8A
SF3B4
PIAS3
SEMA6C
POLR3C
TXNIP
MTMR11
TDRKH
CD160
VPS45
POGZ
RPRD2
CA14
NBPF14
TMOD4
CERS2
BOLA1
APH1A
PLEKHO1
GPR89B
OAZ3
MRPS21
ADAMTSL4
C1orf56
GOLPH3L
FAM63A
CDC42SE1
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
GABPB2
TCHHL1
RPTN
LIX1L
C1orf51
HFE2
ANKRD35
NBPF12
BNIPL
PPIAL4A
NBPF11
RIIAD1
THEM5
NBPF16
ANKRD34A
HIST2H2AB
NOTCH2NL
LYSMD1
HRNR
NBPF9
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
C2CD4D
NBPF20
MIR4257
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: 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: Cancer Gene Census[7].

Genes
KRAS
RN7SL38P
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: Cancer Gene Census[7].

Genes
HOOK3
RN7SKP41
U3|ENSG00000201329.1
POTEA
RN7SL806P
snoU13|ENSG00000238714.1
CHRNB3
FNTA
IKBKB
PLAT
POLB
SLC20A2
VDAC3
CHRNA6
AP3M2
DKK4
THAP1
RNF170
SGK196
SMIM19
HGSNAT
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: Cancer Gene Census[7].

Genes
EGFR
snoU13|ENSG00000238673.1
PHKG1
SNORA15|ENSG00000207168.1
SNORA22|ENSG00000206603.1
RN7SL64P
ZNF713
MRPS17
SNORA73|ENSG00000252054.1
VSTM2A
CCT6A
GBAS
PSPH
SEC61G
SUMF2
CHCHD2
MRPS17
LANCL2
VOPP1
SEPT14
FKBP9L
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: Cancer Gene Census[7].

Genes
WDR70
RN7SL37P
NUP155
NIPBL
C5orf42
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: Cancer Gene Census[7].

Genes
PCDHGB8P
TAF7
PCDHGB4
PCDHGA8
PCDHGA12
PCDHGB7
PCDHGB6
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
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: Cancer Gene Census[7].

Genes
MYC
TMEM75
MIR1205
MIR1207
PVT1
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: Cancer Gene Census[7].

Genes
WTIP
RN7SL154P
RN7SL150P
GPI
KIAA0355
UBA2
LSM14A
KCTD15
PDCD2L
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: Cancer Gene Census[7].

Genes
U3|ENSG00000252981.1
SSB
METTL5
UBR3
KLHL23
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: 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: Cancer Gene Census[7].

Genes
RN7SL685P
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: Cancer Gene Census[7].

Genes
CDKN2A
CDKN2B
C9orf53
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: 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: Cancer Gene Census[7].

Genes
MTCP1
WASH6P|ENSG00000182484.10
WASIR1|ENSG00000185203.7
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36|ENSG00000251846.1
RN7SL687P
RN7SL667P
snoU13|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
GABRA3
GDI1
HCFC1
IDH3G
IL9R|ENSG00000124334.12
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7|ENSG00000124333.10
TAZ
VBP1
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SPRY3|ENSG00000168939.6
ZNF275
TREX2
SRPK3
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
PDZD4
FAM3A
BRCC3
H2AFB3
FAM58A
PNMA5
RAB39B
GAB3
PNCK
ZFP92
CSAG1
CTAG1A
H2AFB2
H2AFB1
OPN1MW2
SMIM9
CMC4
PNMA6C
MIR718
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: 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: Cancer Gene Census[7].

Genes
SNORD56|ENSG00000200753.1
MIR3146
RN7SKP266
SNORA63|ENSG00000199473.1
AHR
ITGB8
TWIST1
HDAC9
SNX13
PRPS1L1
TWISTNB
FERD3L
TMEM196
ABCB5
MACC1
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: 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: Cancer Gene Census[7].

Genes
CST13P
RNA5SP479
CST3
CST8
NXT1
NAPB
GZF1
CSTL1
CST9L
CST9
CST11
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: Cancer Gene Census[7].

Genes
LINC00167
PRDM10
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: Cancer Gene Census[7].

Genes
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
IRX4
CEP72
AHRR
MRPL36
BRD9
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
C5orf38
IRX2
SLC6A19
SLC6A18
MIR4277
MIR4457
MIR4456
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: Cancer Gene Census[7].

Genes
BMI1
SPAG6
COMMD3
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: Cancer Gene Census[7].

Genes
SNORA68|ENSG00000201407.1
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: Cancer Gene Census[7].

Genes
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
MIR4658
MIR106B
MIR93
MIR25
AZGP1P1
SNORA40|ENSG00000222966.1
CYP3A4
snoU13|ENSG00000239133.1
MYH16
snoU13|ENSG00000238459.1
MIR3609
RN7SL13P
RN7SL478P
RN7SKP104
ACHE
ASNS
AZGP1
AP1S1
CUX1
CYP3A7
CYP3A5
EPHB4
EPO
GNB2
AGFG2
LRCH4
MCM7
NPTX2
OCM2
SERPINE1
PCOLCE
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
STAG3
CPSF4
COPS6
PDAP1
LMTK2
ZKSCAN5
CLDN15
BRI3
TECPR1
PTCD1
FBXO24
DNAJC2
PILRA
FIS1
ACTL6B
SRRT
ALKBH4
ZCWPW1
C7orf43
BAIAP2L1
MEPCE
SLC12A9
SMURF1
MOSPD3
GIGYF1
CYP3A43
ZNF655
PVRIG
GAL3ST4
PRKRIP1
ORAI2
OR2AE1
TSC22D4
TRIM56
ARMC10
ZNF394
TRIM4
MYL10
COL26A1
MUC17
BHLHA15
ZSCAN25
FAM200A
PPP1R35
GPC2
LRWD1
FBXL13
NAPEPLD
TMEM130
NYAP1
CNPY4
POLR2J2
MBLAC1
ZNF789
MOGAT3
GJC3
DPY19L2P2
GATS
NAT16
SLC26A5
LAMTOR4
KPNA7
C7orf61
UFSP1
SPDYE3
SPDYE2
POLR2J3
UPK3BL
RASA4B
SPDYE2B
MIR548O
MIR5692C2
MIR5692A1
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: 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: Cancer Gene Census[7].

Genes
LINC00340
SOX4
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: 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: 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: Cancer Gene Census[7].

Genes
LINC00515
ATP5J
GABPA
MRPL39
JAM2
MIR155HG
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: 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: Cancer Gene Census[7].

Genes
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112|ENSG00000251863.1
SNORA25|ENSG00000252204.1
STMN1P1
snoU13|ENSG00000239033.1
snoU13|ENSG00000238661.1
SNORA75|ENSG00000212533.1
LINC00941
BICD1
DDX11
PKP2
DNM1L
IPO8
YARS2
KIAA1551
FAM60A
CAPRIN2
FGD4
CPNE8
DENND5B
AMN1
METTL20
H3F3C
TSPAN11
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: 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: Cancer Gene Census[7].

Genes
LAMA4
WISP3
TUBE1
FAM229B
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: Cancer Gene Census[7].

Genes
RNA5SP179
RNA5SP178
MIR887
U8|ENSG00000202269.1
MIR4637
FAM105A
CT49
ANKRD33B
CMBL
FAM173B
RNA5SP177
SNORD123
MIR4636
RNA5SP176
RN7SKP79
UBE2QL1
RN7SKP73
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
ADCY2
CTNND2
DAP
DNAH5
MTRR
MYO10
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
BASP1
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
IRX4
TAS2R1
FAM134B
NSUN2
CEP72
ANKH
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
C5orf49
C5orf38
IRX2
ADAMTS16
SLC6A19
SLC6A18
MARCH11
MIR4277
MIR4458
MIR4457
MIR4456
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: Cancer Gene Census[7].

Genes
EXT1
COX6C
FGFR1
MYC
PCM1
PLAG1
TCEA1
WRN
RECQL4
NCOA2
WHSC1L1
CHCHD7
HOOK3
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25|ENSG00000251744.1
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
SNORD112|ENSG00000252559.1
TMEM74
RNA5SP275
snoU13|ENSG00000238687.1
RIMS2
MIR3151
RNU6ATAC8P
snoU13|ENSG00000238533.1
snoU13|ENSG00000238372.1
RN7SL563P
NACAP1
RN7SKP249
RN7SL685P
RNU6ATAC41P
MIR1273A
SNORD77|ENSG00000212414.1
RN7SL350P
RN7SKP85
KCNS2
NIPAL2
SNORA72|ENSG00000207067.1
LAPTM4B
U3|ENSG00000207215.1
PTDSS1
snoU13|ENSG00000238791.1
FSBP
RNA5SP274
LINC00535
RN7SKP231
snoU13|ENSG00000239134.1
MIR4661
RN7SL777P
RNA5SP273
LINC00534
RNA5SP272
MMP16
REXO1L10P|ENSG00000255940.1
REXO1L11P
REXO1L10P|ENSG00000270416.1
snoU13|ENSG00000238566.1
SLC10A5
IMPA1P
RN7SL308P
RN7SL107P
SNORA20|ENSG00000206649.1
RN7SL41P
snoU13|ENSG00000238595.1
CASC9
RNA5SP271
U8|ENSG00000200191.1
RN7SL19P
snoU13|ENSG00000238450.1
RNA5SP270
RN7SL675P
RN7SKP29
RNA5SP269
PREX2
RNA5SP268
SNORD87
LINC00967
PDE7A
LINC00966
RN7SKP135
RN7SL135P
NKAIN3
RN7SKP97
CA8
RNA5SP267
SNORA51|ENSG00000206853.1
snoU13|ENSG00000238433.1
LINC00588
RNA5SP266
LINC00968
SDR16C6P
SNORA3|ENSG00000221093.1
SNORD54
RPS20
RN7SL323P
RN7SL798P
SNORA1|ENSG00000199405.1
RNA5SP265
XKR4
RN7SL250P
RNU105C
RNU6ATAC32P
MRPL15
NPBWR1
SNORA7|ENSG00000201316.1
RN7SKP294
UBE2V2
CEBPD
RN7SKP32
LINC00293
RN7SKP41
U3|ENSG00000201329.1
POTEA
RN7SL806P
snoU13|ENSG00000238714.1
SNORD112|ENSG00000238966.1
RN7SL149P
MIR486
SNORD65|ENSG00000238936.1
MIR548AO
IDO1
ADAM3A
ADAM5
SNORD38|ENSG00000207199.1
PLEKHA2
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
RNA5SP264
RN7SKP201
RN7SL457P
RN7SL621P
SNORA70|ENSG00000252505.1
SNORD13
RNA5SP263
RNA5SP262
RNA5SP261
UBXN8
TUBBP1
FAM183CP
LINC00589
RN7SL781P
RNA5SP260
RNA5SP259
MIR4287
snoU13|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13|ENSG00000238466.1
U3|ENSG00000251944.1
SNORA62|ENSG00000201157.1
RNA5SP256
MIR548V
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
LINC00529
MIR598
SNORD112|ENSG00000252565.1
SOX7
RNA5SP252
PRSS51
snoU13|ENSG00000238496.1
snoU13|ENSG00000239065.1
MIR597
U3|ENSG00000252543.1
SNORA70|ENSG00000207244.1
RN7SL178P
SGK223
ALG1L13P
FAM86B3P
LRLE1
FAM85B
FAM90A24P
FAM66E
DEFB105A
DEFB105B
DEFB103B
ZNF705G
FAM66B
XKR5
MIR4659A
AGPAT5
RN7SKP159
RN7SL318P
SNORA70|ENSG00000206661.1
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
NAT1
NAT2
ADCY8
ADRA1A
ADRB3
ANGPT1
ANGPT2
ANK1
ANXA13
ASAH1
ASPH
ATP6V1B2
ATP6V1C1
BAI1
BLK
BMP1
POLR3D
BNIP3L
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CHRNA2
CHRNB3
CLU
CRH
CTSB
CYC1
CYP7A1
CYP11B1
CYP11B2
DECR1
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYS
DPYSL2
DUSP4
E2F5
EEF1D
EGR3
EIF4EBP1
DMTN
EPHX2
CLN8
EXTL3
EYA1
FABP4
FABP5
PTK2B
FDFT1
FGL1
FNTA
ADAM2
GATA4
GEM
GFRA2
GLI4
GML
GNRH1
GPR20
GPT
GRINA
GSR
GTF2E2
NRG1
HNF4G
HSF1
IKBKB
IL7
IMPA1
EIF3E
KCNQ3
LOXL2
LPL
LY6E
LY6H
LYN
MATN2
MCM4
MOS
MSR1
MSRA
MYBL1
NBN
NDUFB9
NEFM
TONSL
NOV
ODF1
TNFRSF11B
OPRK1
PDGFRL
ENPP2
PENK
PLAT
PLEC
PNOC
PMP2
POLB
POLR2K
PPP2CB
PPP2R2A
PPP3CC
PKIA
PRKDC
PTK2
PEX2
RAB2A
RAD21
RP1
RPL7
RPL8
RPL30
SDC2
SDCBP
SFRP1
SFTPC
ST3GAL1
SLA
SLC7A2
SLC18A1
SLC20A2
SNAI2
SNTB1
SPAG1
SQLE
STC1
STK3
TACC1
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
COL14A1
UQCRB
VDAC3
YWHAZ
ZNF7
ZNF16
FZD3
TUSC3
KAT6A
PSCA
FZD6
NSMAF
LY6D
RGS20
TNKS
GPAA1
ADAM18
ADAM9
ADAM7
RIPK2
TNFRSF10D
TNFRSF10C
TNFRSF10B
GGH
CPNE3
FOXH1
CHRNA6
TRPA1
DOK2
ASH2L
CCNE2
EBAG9
MYOM2
DLGAP2
MSC
MFHAS1
KCNB2
CYP7B1
BAG4
ENTPD4
ARHGEF10
MTFR1
LRRC14
EMC2
ST18
TOX
MTSS1
PHYHIP
RB1CC1
ZNF623
KIAA0196
KBTBD11
HHLA1
SORBS3
TRIB1
HRSP12
NPM2
DLC1
NDRG1
CPQ
SPAG11B
LYPLA1
ARFGEF1
KHDRBS3
DCTN6
PNMA2
ADAM28
POP1
AP3M2
COPS5
RBPMS
WWP1
STMN2
ERLIN2
LZTS1
PROSC
ZHX1
PUF60
ZHX2
DENND3
XPO7
TRIM35
ZC3H3
EFR3A
RRS1
SULF1
RHOBTB2
BOP1
DDHD2
KIF13B
PSD3
ZFPM2
HEY1
TRAM1
LEPROTL1
SCRIB
SPIDR
SLC39A14
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
GPR124
KIAA1429
RGS22
FBXL6
FBXO25
OPLAH
PABPC1
KCNV1
STAU2
MTBP
DKK4
AGO2
LSM1
ADAMDEC1
BHLHE22
MRPS28
COMMD5
MRPL13
ATAD2
CNOT7
CPSF1
PURG
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
RMDN1
ZNF706
GOLGA7
VPS28
FAM203A
KCNK9
THEM6
UBR5
SCARA3
FAM49B
AZIN1
ATP6V1H
OTUD6B
TMEM66
CHRAC1
SNTG1
GDAP1
EXOSC4
PDP1
CNGB3
KCTD9
ESRP1
IMPAD1
TMEM70
PINX1
TRMT12
OXR1
WDYHV1
PIWIL2
ELP3
THAP1
ARMC1
INTS10
CCDC25
UBE2W
TMEM55A
SLC39A4
CHD7
SYBU
INTS8
INTS9
CSGALNACT1
HR
PAG1
PBK
ZNF395
BIN3
TEX15
GSDMC
C8orf44
JPH1
C8orf4
ENY2
CPA6
SLURP1
SLC45A4
MTUS1
KIAA1456
ZFAT
KIAA1967
ZNF250
SH2D4A
PRDM14
SNX16
NECAB1
PDLIM2
SOX17
CSMD1
EBF2
FAM160B2
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
MTMR9
DUSP26
DSCC1
DERL1
SLC52A2
HMBOX1
EFCAB1
MCPH1
PPP1R3B
PLEKHF2
ZMAT4
ZFAND1
ZFHX4
GSDMD
RNF122
CSPP1
BAALC
GRHL2
DOCK5
VCPIP1
TTI2
RAB11FIP1
REEP4
ARHGAP39
ZNF34
SLC25A32
DCSTAMP
STMN4
RNF170
SLCO5A1
SHARPIN
SCRT1
SOX7
FAM167A
SLC35G5
CRISPLD1
TRAPPC9
TM2D2
TATDN1
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
TBC1D31
RP1L1
TP53INP1
TGS1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SMIM19
SLC26A7
PCMTD1
CTHRC1
OSR2
C8orf34
TOP1MT
CLDN23
ZNF572
GOT1L1
FAM92A1
VPS37A
NDUFAF6
TMEM68
ABRA
LYPD2
TMEM71
SGCZ
ADHFE1
UBXN2B
PXDNL
AGPAT6
UNC5D
LETM2
DCAF4L2
RALYL
HGSNAT
DEFB104A
PEBP4
CDCA2
RDH10
C8orf56
ANKRD46
ESCO2
FBXO16
FAM84B
C8orf37
VPS13B
TDRP
ERICH1
SLC7A13
TDH
FAM91A1
C8orf48
MCMDC2
CLVS1
KCNU1
SBSPON
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ZNF596
IDO2
SDR16C5
ADCK5
TSNARE1
R3HCC1
PRSS55
C8orf74
HTRA4
ADAM32
C8orf47
LGI3
MAPK15
DEFB106A
DEFB107A
DEFB130|ENSG00000232948.1
ATP6V0D2
NEIL2
YTHDF3
C8orf46
REXO1L1
XKR6
NSMCE2
ZNF707
FAM83H
MICU3
C8orf31
ZFP41
SCARA5
TRIQK
DPY19L4
FBXO43
PPP1R42
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
USP17L2
CA13
NUGGC
C8orf86
FAM150A
XKR9
C8orf87
RBM12B
MROH5
MAFA
GDF6
C8orf59
SAMD12
LINC00599
MIR30B
MIR30D
MIR320A
DEFB103A
LRRC24
C8orf22
DEFB107B
DEFB104B
DEFB106B
C8orf58
DEFB135
DEFB136
ZNF704
MBOAT4
SNHG6
MROH6
FABP9
FABP12
SPAG11A
FER1L6
MIR548A3
MIR596
MIR599
MROH1
FAM203B
DEFA1B
ZNF705D
OC90
MIR875
TCF24
LRRC69
ZNF705B
DEFB4B
MIR1205
MIR1207
PVT1
MIR548I3
MIR2053
MIR1208
MIR548H4
MIR3148
MIR4288
MIR4286
MIR3686
MIR548AA1
MIR3622B
MIR3150B
MIR3610
SMIM18
MIR4469
MIR378D2
MIR4662B
MIR4663
MIR4664
MIR4660
MIR4471
MIR4470
MIR5680
MIR5692A2
MIR5194
MIR5708
MIR5681A

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 3
Xp11.1 1.6201e-07 3.1788e-05 chrX:58103757-62195567 0 [ZXDA]
15q11.2 7.4165e-05 9.535e-05 chr15:25294598-25486359 2
19p13.2 8.2295e-05 0.00011247 chr19:8996097-9090978 1
10p11.1 0.00017281 0.00017281 chr10:38773386-38901643 0 [SEPT7P9]
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 1
13q14.2 0.00041466 0.0031399 chr13:49116366-49265161 1
1p36.11 0.0019828 0.0068152 chr1:24150579-24412338 9
3p12.3 0.0068152 0.0068152 chr3:79630681-79764849 1
19p13.3 0.012447 0.021231 chr19:1168036-1282863 7
3q13.11 0.024806 0.024806 chr3:103347409-103441522 0 [MIR548AB]
21q21.1 0.024806 0.024806 chr21:18002996-18655465 0 [LINC00478]
9p21.2 7.4165e-05 0.03399 chr9:22431064-26112691 6
12p13.1 0.03399 0.03399 chr12:13024182-14127042 13
22q13.32 0.036197 0.036197 chr22:47837821-49147869 3
6q16.2 0.0021798 0.043939 chr6:99463965-99569838 0 [MIR548AI]
1p22.2 0.019509 0.074656 chr1:90813753-91029702 1
1p13.2 0.0021798 0.080089 chr1:102275933-149895119 243
5q14.3 0.050524 0.083934 chr5:73168188-88883185 87
11q22.3 0.021182 0.1224 chr11:104219145-124046166 211
8p23.1 0.12995 0.12995 chr8:9586974-9696474 2
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 21
16q24.2 0.19997 0.19997 chr16:87345556-90354753 62
19q13.2 0.19997 0.19997 chr19:39990221-40279182 10
5q21.2 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 [LINC00364]
13q12.11 0.012447 0.2397 chr13:1-41929239 192
7q36.2 0.24671 0.24671 chr7:119737203-159138663 346
11q12.1 0.0016279 0.34227 chr11:49916017-59443398 115
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: Cancer Gene Census[7].

Genes
CDKN2A
CDKN2B
C9orf53
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: Cancer Gene Census[7].

Genes
SNORD115|ENSG00000212428.1
SNHG14
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: Cancer Gene Census[7].

Genes
MUC16
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.1.

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

Genes
CCNG2
Genes in Wide Peak

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

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

Genes
LINC00462
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238538.1
RN7SL24P
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 S44.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 S45.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

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

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

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

Genes
RN7SKP120
RMRPP5
DMRTA1
ELAVL2
TUSC1
IZUMO3
Genes in Wide Peak

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

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

Genes
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
EMP1
HEBP1
GPRC5D
KIAA1467
GSG1
C12orf36
MIR614
Genes in Wide Peak

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

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

Genes
FAM19A5
LINC00898
MIR3201
Genes in Wide Peak

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

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

Genes
[U3|ENSG00000199666.1]
Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
LINC00622
snoU13|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
ADORA3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
CELSR2
FCGR1A
FMO5
GJA5
GJA8
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
TBX15
TSHB
CSDE1
HIST2H2AC
HIST2H2BE
HIST2H4A
ITGA10
PEX11B
SLC16A4
CD101
CHD1L
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
LAMTOR5
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
ADAM30
CD160
DDX20
NTNG1
WDR47
CLCC1
NBPF14
PTPN22
PHGDH
CHIA
GPSM2
SLC25A24
BOLA1
HAO2
GPR89B
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
OLFML3
AMIGO1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
STRIP1
ZNF697
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
LIX1L
DRAM2
PIFO
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
NBPF12
CHIAP2
FNDC7
PPIAL4A
UBL4B
NBPF11
SPAG17
HIPK1
AKNAD1
MAGI3
FAM19A3
NBPF16
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
MYBPHL
SLC6A17
C1orf137
NOTCH2NL
NBPF9
MIR197
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
NBPF6
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
NBPF20
MIR320B1
Genes in Wide Peak

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

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

Genes
SNORA70|ENSG00000206958.1
RNA5SP187
RN7SL629P
RN7SKP34
MIR3607
COX7C
NBPF22P
RN7SKP295
SCARNA18|ENSG00000238835.1
RN7SL378P
SSBP2
SNORA31|ENSG00000251828.1
snoU13|ENSG00000239159.1
MTX3
HOMER1
SNORA18|ENSG00000206592.1
RNY3P1
BHMT2
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13|ENSG00000238688.1
RNA5SP186
POLK
SNORA40|ENSG00000212363.1
RN7SL814P
ARSB
BHMT
CCNH
CKMT2
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
HEXB
HMGCR
MEF2C
MSH3
RASA1
RASGRF2
RPS23
TBCA
THBS4
XRCC4
ENC1
AP3B1
PDE8B
SCAMP1
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
NSA2
IQGAP2
SV2C
FAM169A
DMGDH
GCNT4
AGGF1
ARHGEF28
ATG10
ZCCHC9
GFM2
SPZ1
ATP6AP1L
JMY
POC5
ACOT12
TMEM167A
TMEM161B
PAPD4
FAM151B
CMYA5
ANKRD31
SERINC5
ANKRD34B
LINC00461
ANKDD1B
MIR4280
MTRNR2L2
Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
ACAT1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
VWA5A
MCAM
KMT2A
NCAM1
NNMT
NPAT
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
SLN
SORL1
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
USP2
HTR3B
ZW10
UBE4A
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK3
BACE1
TRIM29
CADM1
POU2F3
REXO2
TIMM8B
SIDT2
TRAPPC4
FXYD6
C11orf71
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
SCN3B
VPS11
TEX12
CRTAM
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
ABCG4
C11orf1
RNF26
NLRX1
CLMP
PDZD3
C11orf63
TMPRSS5
MFRP
BCO2
TMPRSS13
MSANTD4
BUD13
TMEM25
UBASH3B
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
APOA5
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
ANKK1
RNF214
FOXR1
CCDC153
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
C11orf87
C11orf92
C11orf88
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
CARD17
CLDN25
MIR4301
CASP12
MIR4493
MIR4491
MIR4492
Genes in Wide Peak

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

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

Genes
MIR597
TNKS
Genes in Wide Peak

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

Table S54.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 S55.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 S56.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL428P
CSPG4P12
SNORA25|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
NMB
PDE8A
SLC28A1
ZNF592
AKAP13
SEC11A
SCAND2P
ZSCAN2
ALPK3
WDR73
UBE2Q2P1
Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13|ENSG00000239186.1
AFG3L1P
APRT
C16orf3
CA5A
CDH15
CYBA
DPEP1
GALNS
GAS8
MC1R
MVD
CHMP1A
RPL13
SPG7
SLC7A5
CDK10
VPS9D1
PIEZO1
TUBB3
PRDM7
TCF25
ZCCHC14
CPNE7
IL17C
ANKRD11
TRAPPC2L
KLHDC4
DEF8
BANP
JPH3
DBNDD1
CDT1
MAP1LC3B
SPIRE2
CENPBD1
ZNF276
RNF166
SPATA2L
SPATA33
ZC3H18
ZNF778
ACSF3
LINC00304
SNAI3
CTU2
PABPN1L
C16orf95
Genes in Wide Peak

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

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

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

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

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

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

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

Table S60.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CDX2
BRCA2
FLT3
LHFP
KBTBD7
snoU13|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116|ENSG00000212553.1
RNY4P14
snoU13|ENSG00000238408.1
LINC00366
LINC00571
RNA5SP26
RN7SKP1
ARL2BPP3
DCLK1
LINC00445
LINC00457
SNORA25|ENSG00000199196.1
LINC00423
RNY1P4
SNORA16|ENSG00000212293.1
ZAR1L
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
LINC00365
LINC00544
LINC00572
LINC00297
MTUS2
RN7SL272P
URAD
LINC00543
GSX1
RNY1P1
SNORA27|ENSG00000207051.1
SNORD102
LINC00415
RNY1P3
RN7SL741P
RN7SL289P
PABPC3
LSP1|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
MIR2276
ANKRD20A19P
LINC00352
LINC00327
LINC00362
RNY3P4
LINC00621
SNORD36|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27|ENSG00000252128.1
snoU13|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
PARP4
ALOX5AP
ATP12A
CDK8
ELF1
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
GTF3A
HMGB1
PDX1
MAB21L1
SMAD9
MIPEP
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TRPC4
ZMYM2
IFT88
CCNA1
MTMR6
ZMYM5
KL
MTRF1
NUPL1
FRY
USPL1
MRPS31
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
WBP4
EXOSC8
PDS5B
SPG20
SACS
LATS2
NBEA
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
TNFRSF19
SUPT20H
CENPJ
RNF17
COG6
XPO4
MRP63
NAA16
PROSER1
KATNAL1
MEDAG
KBTBD6
STARD13
N4BP2L1
TPTE2
CSNK1A1L
RXFP2
TEX26
B3GALTL
STOML3
AMER2
USP12
MTIF3
N6AMT2
SKA3
MICU2
SPATA13
LNX2
PAN3
SLC46A3
C1QTNF9
FREM2
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERTM1
ATP5EP2
MIR621
CCDC169
MIR320D1
MIR3168
MIR4305
SPG20OS
SOHLH2
Genes in Wide Peak

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

Table S61.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BRAF
EZH2
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
CPED1
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707
Genes in Wide Peak

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

Table S62.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MIR3162
RN7SL435P
RN7SL42P
GLYATL1P2
BTBD18
C11orf31
RTN4RL2
RN7SKP259
RNA5SP341
PRG2
P2RX3
snoU13|ENSG00000238692.1
OR5G5P
TRIM51HP
APLNR
SERPING1
CNTF
CTNND1
OSBP
SSRP1
SLC43A1
UBE2L6
LPXN
GLYAT
PRG3
OR5I1
CLP1
DTX4
ZDHHC5
OR5L2
TIMM10
SLC43A3
TMX2
FAM111A
TRIM48
ZFP91
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
TRIM51
TNKS1BP1
GLYATL1
OR4C46
OR8I2
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
OR10AG1
OR5J2
OR4C13
OR4C12
OR9G4
OR5F1
OR5AP2
FAM111B
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
MIR130A
OR5B3
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 1300 0.15 1.61 0.31 0.15 1.61 0.162
1q 1195 0.42 10.2 0 0.11 -0.0989 0.981
2p 624 0.12 -1.17 1 0.00 -4.42 1
2q 967 0.07 -2.07 1 0.00 -4.09 1
3p 644 0.04 -3.02 1 0.22 1.83 0.119
3q 733 0.12 -0.758 1 0.12 -0.758 1
4p 289 0.09 -2.3 1 0.13 -1.45 1
4q 670 0.04 -3.23 1 0.14 -0.426 1
5p 183 0.43 6.77 8.86e-11 0.07 -2.5 1
5q 905 0.13 -0.215 1 0.17 1.01 0.371
6p 710 0.16 0.199 1 0.11 -1.21 1
6q 556 0.09 -1.96 1 0.24 2.32 0.0406
7p 389 0.43 7.28 3.43e-12 0.04 -2.88 1
7q 783 0.29 4.67 1.18e-05 0.01 -3.47 1
8p 338 0.14 -0.779 1 0.39 5.96 2.51e-08
8q 551 0.38 6.16 3.53e-09 0.10 -1.4 1
9p 301 0.07 -2.62 1 0.31 3.55 0.00129
9q 700 0.03 -3.15 1 0.24 2.71 0.015
10p 253 0.10 -2.15 1 0.12 -1.72 1
10q 738 0.06 -2.41 1 0.11 -1.23 1
11p 509 0.08 -2.36 1 0.08 -2.36 1
11q 975 0.13 -0.0711 1 0.09 -1.08 1
12p 339 0.19 0.35 1 0.20 0.563 0.57
12q 904 0.14 0.0859 1 0.10 -0.901 1
13q 560 0.07 -2.29 1 0.30 4.02 0.000396
14q 938 0.12 -0.219 1 0.15 0.527 0.57
15q 810 0.07 -2.07 1 0.25 3.45 0.00162
16p 559 0.15 -0.181 1 0.15 -0.181 0.994
16q 455 0.11 -1.52 1 0.19 0.687 0.518
17p 415 0.12 -1.35 1 0.31 3.85 0.0006
17q 972 0.24 3.63 0.00095 0.05 -2.15 1
18p 104 0.15 -1.15 1 0.24 1.09 0.369
18q 275 0.06 -3 1 0.29 2.94 0.00825
19p 681 0.04 -2.81 1 0.35 6.01 2.51e-08
19q 935 0.11 -0.674 1 0.25 3.78 0.00064
20p 234 0.16 -0.494 1 0.22 0.966 0.371
20q 448 0.21 1.07 0.709 0.14 -0.68 1
21q 258 0.15 -0.714 1 0.22 0.966 0.371
22q 564 0.03 -3.41 1 0.21 1.58 0.162
Xq 668 0.13 -0.501 1 0.21 1.8 0.119
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/11541947/segmentationfile.txt

  • Markers File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/LUAD-TP/11541947/markersfile.txt

  • Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.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)