SNP6 Copy number analysis (GISTIC2)
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1SF2TNW
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 490 tumor samples used in this analysis: 30 significant arm-level results, 30 significant focal amplifications, and 50 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 - 30 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
3q26.33 6.7427e-195 6.7427e-195 chr3:181401404-182481981 3
8p11.23 3.7653e-83 3.7653e-83 chr8:38170522-38247105 2
11q13.3 4.3039e-77 4.3039e-77 chr11:69699947-70248899 6
8q24.21 9.3281e-27 9.3281e-27 chr8:128297257-128452765 1
2p16.1 1.4693e-17 1.4693e-17 chr2:60450758-61267829 7
7p11.2 4.484e-17 4.9931e-17 chr7:54781785-55694877 4
4q12 4.7023e-16 4.7023e-16 chr4:56190345-56532615 6
5p15.33 1.7858e-18 4.6654e-13 chr5:1-1428010 26
9p13.3 1.6704e-10 1.6704e-10 chr9:35109573-36060450 30
19q13.2 3.9815e-24 7.9852e-10 chr19:38271451-39311155 25
19q12 2.8866e-16 1.271e-07 chr19:30287570-30465652 2
1q21.2 6.9006e-06 6.9006e-06 chr1:120523956-154693180 244
22q11.21 1.4878e-05 1.4878e-05 chr22:18613558-22141228 90
20q11.21 4.9395e-05 4.9395e-05 chr20:26196264-30564096 26
2q31.2 6.4766e-05 6.4766e-05 chr2:178083264-178154838 5
7q21.2 0.00010731 0.00011296 chr7:91474555-93654751 27
15q26.3 0.00022287 0.00022287 chr15:94031960-102531392 42
12q15 0.00063339 0.00063339 chr12:67813808-71115184 28
17q25.1 0.00071117 0.00071117 chr17:70512321-76301198 129
5p12 3.5178e-09 0.0019987 chr5:30913798-50133343 89
14q13.3 0.0060425 0.0060425 chr14:36664829-38235870 10
18q11.2 0.0067033 0.0067033 chr18:23753292-24419705 4
12p13.33 0.010428 0.010428 chr12:1-3480534 34
13q34 0.0157 0.0157 chr13:113773700-114847012 20
6q12 0.0032741 0.044845 chr6:63667925-66113677 4
6p12.1 0.0018249 0.053755 chr6:54288464-56484757 7
Xq28 0.055035 0.055035 chrX:147462113-155270560 145
18p11.32 0.17112 0.17112 chr18:1-923766 11
20p12.2 0.18243 0.18243 chr20:11194380-11393881 1
3p11.1 0.20924 0.20924 chr3:90015494-90236050 0 [EPHA3]
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
SOX2
SOX2-OT
FLJ46066
Genes in Wide Peak

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

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

Genes
WHSC1L1
LETM2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
hsa-mir-548k
CTTN
PPFIA1
FADD
ANO1
MIR548K
Genes in Wide Peak

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

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

Genes
POU5F1B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p16.1.

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

Genes
REL
BCL11A
PEX13
PAPOLG
PUS10
FLJ16341
MIR4432
Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2
VOPP1
Genes in Wide Peak

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

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

Genes
CLOCK
NMU
TMEM165
SRD5A3
PDCL2
LOC100506462
Genes in Wide Peak

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

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

Genes
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4457
MIR4456
MIR4635
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
CA9
CD72
NPR2
RMRP
TESK1
TLN1
TPM2
RECK
RGP1
RUSC2
CREB3
UNC13B
SPAG8
SIT1
TMEM8B
OR2S2
GBA2
FAM214B
HINT2
C9orf100
FP588
LOC158376
ATP8B5P
CCDC107
C9orf128
OR13J1
HRCT1
MSMP
FAM166B
MIR4667
Genes in Wide Peak

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

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

Genes
ACTN4
ECH1
LGALS4
LGALS7
PSMD8
RYR1
DPF1
KCNK6
SPINT2
MAP4K1
SIPA1L3
EIF3K
CATSPERG
C19orf33
WDR87
YIF1B
PPP1R14A
RASGRP4
FAM98C
CAPN12
GGN
SPRED3
LOC644554
LGALS7B
LOC100631378
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q12.

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

Genes
CCNE1
URI1
Genes in Wide Peak

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

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

Genes
ARNT
BCL9
NOTCH2
TPM3
PDE4DIP
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
CHRNB2
CTSK
CTSS
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
NPR1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
SNAPIN
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
FAM91A2
S100A14
GATAD2B
CGN
ZNF687
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
S100A7L2
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR190B
C1orf68
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 22q11.21.

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

Genes
CLTCL1
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
ARVCF
COMT
CRKL
GGT3P
GP1BB
GSC2
SERPIND1
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
P2RX6
SNAP29
DGCR2
TXNRD2
USP18
HIC2
TSSK2
SDF2L1
PPIL2
DGCR11
DGCR9
DGCR5
DGCR10
TRMT2A
POM121L8P
YPEL1
ZDHHC8
MED15
TUBA8
DGCR8
GNB1L
MRPL40
RTN4R
C22orf29
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
MGC16703
C22orf39
C22orf25
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
CCDC116
POM121L4P
LOC284865
PI4KAP2
LOC388849
LOC400891
BCRP2
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
TMEM191C
TMEM191B
PI4KAP1
LOC729444
MIR301B
MIR1286
MIR1306
MIR3618
SEPT5-GP1BB
MIR4761
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-3193
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
MLLT10P1
LINC00028
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
PSIMCT-1
MIR3193
Genes in Wide Peak

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

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

Genes
NFE2L2
hsa-mir-3128
HNRNPA3
LOC100130691
MIR3128
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
hsa-mir-489
hsa-mir-1285-1
CALCR
KRIT1
CYP51A1
GNG11
GNGT1
PEX1
MTERF
TFPI2
BET1
ANKIB1
SAMD9
CCDC132
GATAD1
RBM48
MGC16142
SAMD9L
HEPACAM2
FAM133B
LRRD1
MIR489
MIR653
LOC728066
MIR4652
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
hsa-mir-1302-10
hsa-mir-1469
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
NR2F2
CHSY1
SYNM
OR4F4
LINS
MCTP2
SELS
TTC23
LRRK1
TM2D3
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
LOC145820
SPATA8
ADAMTS17
DNM1P46
CERS3
FAM169B
WASH3P
FLJ42289
OR4F6
OR4F15
LOC400456
FAM138E
GPCRLTM7
DDX11L1
DDX11L9
MIR1469
LOC100507472
MIR4714
Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
YEATS4
DYRK2
CCT2
FRS2
CPSF6
KCNMB4
IL22
SLC35E3
IL26
MDM1
NUP107
RAB3IP
BEST3
LRRC10
MIR1279
SNORA70G
MIR3913-2
MIR3913-1
LOC100507250
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
hsa-mir-4316
hsa-mir-636
AANAT
ACOX1
BIRC5
CDK3
EVPL
FDXR
FOXJ1
GALK1
GRB2
GRIN2C
H3F3B
ICT1
ITGB4
LLGL2
PRPSAP1
RPL38
SEC14L1
SRSF2
SUMO2
SRP68
SSTR2
TK1
GALR2
SPHK1
SLC16A5
SYNGR2
SLC9A3R1
COG1
RECQL5
KIAA0195
ATP5H
ST6GALNAC2
SEPT9
CD300C
CD300A
TMC6
GGA3
JMJD6
EXOC7
KCTD2
WBP2
CDC42EP4
NAT9
SAP30BP
NT5C
CDR2L
MRPS7
HN1
SDK2
TMEM104
C17orf80
ST6GALNAC1
GPRC5C
MIF4GD
CASKIN2
TNRC6C
SLC25A19
UBE2O
DNAI2
MRPL38
MFSD11
ARMC7
RHBDF2
NUP85
MYO15B
QRICH2
FAM104A
MGC16275
FBF1
UNK
TRIM47
OTOP2
TTYH2
CYGB
RNF157
METTL23
USH1G
CD300LB
KIF19
AFMID
MGAT5B
CD300LF
C17orf77
TMC8
SLC39A11
TRIM65
UNC13D
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
RAB37
CD300E
OTOP3
GPR142
ZACN
BTBD17
LINC00511
LOC400620
FLJ45079
MXRA7
CPSF4L
C17orf109
LINC00338
SCARNA16
SNORD1A
SNORD1B
SNORD1C
MIR636
PRCD
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
MIR4316
LOC100499467
MIR3678
MIR3615
LOC100507218
LOC100507246
LOC100507351
TEN1-CDK3
MIR4738
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p12.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
C6
C7
C9
CDH6
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
WDR70
BRIX1
C5orf22
CCL28
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
LOC340113
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR4279
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.3.

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

Genes
NKX2-1
FOXA1
PAX9
NKX2-8
MBIP
SLC25A21
MIPOL1
SFTA3
LOC100129794
MIR4503
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
TAF4B
PSMA8
KCTD1
LOC728606
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
KDM5A
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
CACNA2D4
FBXL14
DCP1B
B4GALNT3
LOC283440
IQSEC3
LOC574538
LRTM2
FAM138D
LOC100271702
LOC100288778
LOC100292680
MIR3649
LOC100507424
LOC100652846
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q34.

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

Genes
ATP4B
F7
F10
GAS6
LAMP1
GRK1
TFDP1
CUL4A
PROZ
RASA3
TMCO3
DCUN1D2
PCID2
GRTP1
ADPRHL1
FAM70B
FLJ44054
FLJ41484
LINC00552
LOC100506394
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
PTP4A1
PHF3
LGSN
EYS
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p12.1.

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

Genes
BMP5
DST
HCRTR2
HMGCLL1
COL21A1
FAM83B
GFRAL
Genes in Wide Peak

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

Table S27.  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
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
HCFC1
HMGB3
IDH3G
IDS
IL9R
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MECP2
MPP1
MTM1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
FAM50A
GPR50
MAMLD1
BCAP31
SPRY3
ZNF275
TREX2
SRPK3
SNORA70
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
GABRQ
PDZD4
FAM3A
FUNDC2
PRRG3
BRCC3
CD99L2
H2AFB3
TMEM185A
PNMA6A
FATE1
CXorf40A
FAM58A
PNMA5
RAB39B
PASD1
GAB3
PNCK
ZFP92
CSAG1
VMA21
CTAG1A
MAGEA2B
LINC00204B
CSAG3
MIR105-1
MIR105-2
H2AFB2
H2AFB1
F8A2
F8A3
CXorf40B
MIR452
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
CSAG2
MIR767
HSFX2
LOC100131434
CXorf68
LINC00204A
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR718
MIR2114
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
LOC100507404
MAGEA10-MAGEA5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.32.

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

Genes
ADCYAP1
CETN1
TYMS
YES1
USP14
THOC1
CLUL1
ENOSF1
COLEC12
C18orf56
ROCK1P1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p12.2.

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

Genes
LOC339593

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 - 50 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 1.1556e-187 3.1306e-173 chr9:21865498-21997722 2
8p23.2 2.0716e-72 2.0716e-72 chr8:2079140-6262191 1
2q22.1 1.3573e-57 1.3444e-51 chr2:139655617-143637838 1
10q23.31 6.3677e-31 6.3677e-31 chr10:89617158-90034038 2
5q11.2 1.2925e-22 1.338e-22 chr5:58260298-59787985 3
1p13.1 3.6762e-17 4.8908e-13 chr1:114227160-119426205 45
19p13.3 6.4139e-13 6.4575e-13 chr19:1-987570 38
11p15.5 9.3479e-13 9.3479e-13 chr11:1-4406284 123
13q14.2 1.1857e-15 1.56e-10 chr13:48833767-49064807 2
3p13 6.9832e-23 6.3297e-10 chr3:70016017-71729299 3
4q22.1 9.2779e-13 6.9652e-10 chr4:90844993-93240505 1
4q35.2 4.6528e-22 4.2066e-09 chr4:187475875-188227950 1
18q23 4.9102e-09 4.9208e-09 chr18:73139336-78077248 19
3p25.3 7.0828e-13 7.1063e-09 chr3:11593014-11833472 1
Xq22.3 1.6356e-08 1.663e-08 chrX:107395766-108023686 3
2q37.1 8.1511e-19 6.21e-08 chr2:213401694-243199373 285
16q23.1 1.4206e-06 1.3742e-06 chr16:78016120-79627770 2
16p13.3 1.7557e-06 1.7322e-06 chr16:3764793-4013466 1
19q13.32 3.5569e-06 3.5569e-06 chr19:46890223-54375825 364
3p12.3 3.0451e-20 5.6815e-06 chr3:77699023-81540112 1
7q36.3 1.6363e-06 9.8531e-06 chr7:151211607-159138663 41
11q25 1.9967e-09 1.0463e-05 chr11:126875846-135006516 35
1p36.32 1.8059e-08 3.4734e-05 chr1:1-27864255 451
4q32.2 7.4991e-12 4.0737e-05 chr4:164439857-165912961 6
6p25.3 0.00022319 0.00021794 chr6:1-10745065 67
13q12.11 8.4943e-09 0.00025061 chr13:1-23903159 29
17q25.3 0.00026481 0.00066538 chr17:80031841-81195210 22
10p15.3 4.4e-08 0.00084366 chr10:1-1040137 5
15q21.1 1.8539e-06 0.00088073 chr15:44964334-45036916 1
Xp21.2 1.9322e-05 0.00098715 chrX:30865118-34644819 4
9p13.1 6.153e-08 0.0012044 chr9:38619152-71152237 50
4p15.31 0.0014421 0.0014421 chr4:20726855-22330985 2
10p15.1 2.4508e-07 0.001692 chr10:5018825-5136914 1
7q11.22 0.00089096 0.0034764 chr7:66780207-70601215 1
9p24.1 1.1643e-13 0.0041189 chr9:7799607-12693402 1
21q11.2 0.0013242 0.0041189 chr21:1-22117102 39
17q11.2 0.0026397 0.0059451 chr17:29326736-29722618 5
11q22.1 9.3725e-05 0.0083186 chr11:90601742-100558999 48
14q11.2 0.0085454 0.0088213 chr14:1-27379462 160
Xp11.3 0.00036056 0.0088856 chrX:44702452-45008304 2
21q22.3 0.0040311 0.011843 chr21:42217276-44075429 27
22q11.21 0.0097261 0.019668 chr22:1-18562887 26
6q26 0.0027291 0.023792 chr6:161693099-163761254 3
12q24.31 0.035081 0.03442 chr12:94654455-133851895 365
15q12 0.0001136 0.037165 chr15:1-40986113 231
22q13.32 0.01373 0.046057 chr22:45402127-51304566 82
6q22.31 0.0061567 0.052151 chr6:123955968-125232805 1
2p25.3 0.15659 0.15758 chr2:1-21910610 101
Xp22.2 0.0053397 0.16646 chrX:3474210-11137490 24
3p11.1 2.3393e-08 0.21283 chr3:79814918-93777876 15
Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

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

Genes
CSMD1
Genes in Wide Peak

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

Table S32.  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 10q23.31.

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

Genes
PTEN
KLLN
Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1
Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
hsa-mir-942
hsa-mir-320b-1
AMPD1
ATP1A1
CASQ2
CD2
CD58
IGSF3
NGF
NHLH2
PTGFRN
SYCP1
TSHB
CSDE1
TTF2
CD101
TSPAN2
BCAS2
AP4B1
PHTF1
WDR3
MAN1A2
PTPN22
RSBN1
GDAP2
FAM46C
SLC22A15
OLFML3
DCLRE1B
VTCN1
SIKE1
TRIM45
VANGL1
ATP1A1OS
MAB21L3
SYT6
DENND2C
SPAG17
HIPK1
BCL2L15
MIR942
LOC100287722
MIR320B1
Genes in Wide Peak

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

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

Genes
FSTL3
hsa-mir-3187
hsa-mir-1302-11
AZU1
HCN2
BSG
CDC34
CFD
ARID3A
ELANE
GZMM
PALM
POLRMT
PRTN3
PTBP1
MADCAM1
PPAP2C
MED16
SHC2
FGF22
THEG
MIER2
RNF126
LPPR3
OR4F17
KISS1R
R3HDM4
TPGS1
C19orf21
C2CD4C
ODF3L2
WASH5P
FLJ45445
PRSS57
FAM138F
FAM138A
MIR3187
MIR4745
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

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

Genes
CARS
HRAS
NUP98
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
RHOG
ART1
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
OR7E12P
KCNQ1OT1
PKP3
SIRT3
PGAP2
C11orf21
TRPM5
IGF2-AS1
BET1L
CEND1
CDHR5
TOLLIP
PIDD
KCNQ1DN
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
MOB2
SYT8
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
OR52B4
LOC143666
SCGB1C1
NLRP6
NS3BP
LOC255512
C11orf35
H19
EFCAB4A
TMEM80
C11orf36
ANO9
LOC338651
B4GALNT4
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
MIR483
SNORA52
LOC650368
LOC653486
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686
MIR4687
Genes in Wide Peak

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

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

Genes
RB1
LPAR6
Genes in Wide Peak

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

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

Genes
FOXP1
hsa-mir-1284
MIR1284
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
FAM190A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

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

Genes
FAT1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TXNL4A
ADNP2
KCNG2
SALL3
RBFA
PQLC1
PARD6G
LOC284276
LOC339298
ATP9B
HSBP1L1
LOC100130522
LOC100131655
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.3.

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

Genes
VGLL4
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
COL4A5
COL4A6
IRS4
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.1.

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
CLEC3A
WWOX
Genes in Wide Peak

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

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

Genes
CREBBP
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

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

Genes
KLK2
PPP2R1A
ZNF331
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
DBP
EMP3
ETFB
FCGRT
FLT3LG
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
HRC
PRMT1
IRF3
KCNA7
KCNC3
KCNJ14
KLK1
LHB
LIG1
LIM2
MYBPC2
NKG7
NPAS1
NTF4
NUCB1
POLD1
PRRG2
KLK7
KLK6
KLK10
PTGIR
RPL18
RPS11
RRAS
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SPIB
SULT2B1
SULT2A1
TULP2
NR1H2
ZNF28
ZNF137P
ZNF175
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
CYTH2
NAPSA
KLK4
ZNF432
DHX34
SAE1
RUVBL2
KDELR1
KLK11
KPTN
KLK8
PNKP
ATF5
CARD8
ZC3H4
RPL13A
SYNGR4
NUP62
PPP1R15A
KLK5
PRKD2
ZNF473
KLK13
CCDC9
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
DHDH
SLC6A16
STRN4
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
HSD17B14
VRK3
PTOV1
TRPM4
FAM83E
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
KLK15
ZNF701
ZNF83
ZNF415
CABP5
SPHK2
MEIS3
SLC17A7
RCN3
PNMAL2
PRR12
PLEKHA4
SCAF1
ZNF350
TSKS
ELSPBP1
LIN7B
ZNF649
FKRP
TBC1D17
MYH14
ZNF665
ZNF613
ZNF702P
ZNF614
FUZ
ZNF611
MED25
BCL2L12
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
SNORD35B
ZNF347
ZNF577
C19orf48
SIGLEC10
SIGLEC12
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF765
NLRP12
ZNF845
CCDC114
ACPT
CGB5
CGB7
LRRC4B
CGB8
GNG8
BIRC8
FAM71E1
PTH2
SIGLEC11
CGB1
CGB2
LMTK3
CLDND2
ZNF816
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147804
CCDC155
DACT3
ZNF836
ZNF610
ZNF600
ZNF320
ZNF114
ZNF525
SPACA4
C19orf76
PRR24
NAPSB
IL4I1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VN1R2
VN1R4
C19orf81
ZNF677
ZNF808
ZNF761
ZNF321P
SIGLEC16
FLJ26850
ZNF880
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
MIR371A
MIR372
MIR373
DPRX
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC646508
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR643
RPL13AP5
CEACAM18
FLJ30403
SIGLEC14
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100129083
BSPH1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SNAR-A14
ERVV-2
MIR1283-2
MIR1323
MIR1283-1
MIR3191
MIR3190
MIR320E
MIR4324
LOC100505681
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF816-ZNF321P
MIR371B
MIR4749
MIR4750
MIR4751
Genes in Wide Peak

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

Table S49.  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 7q36.3.

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

Genes
MLL3
hsa-mir-595
hsa-mir-153-2
DPP6
EN2
MNX1
HTR5A
INSIG1
PTPRN2
SHH
VIPR2
XRCC2
UBE3C
DNAJB6
PAXIP1
PRKAG2
NCAPG2
WDR60
ACTR3B
ESYT2
GALNT11
LMBR1
LINC00244
NOM1
C7orf13
RNF32
LOC154822
RBM33
GALNTL5
LOC202781
FABP5P3
CNPY1
LOC285889
MIR153-2
LOC645249
MIR595
LOC100128264
LOC100128822
LOC100132707
LOC100505483
LOC100506585
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

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

Genes
FLI1
APLP2
ETS1
KCNJ1
KCNJ5
NFRKB
OPCML
ST14
BARX2
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
PRDM10
TP53AIP1
JAM3
GLB1L2
VPS26B
GLB1L3
TMEM45B
ADAMTS15
C11orf45
SPATA19
LOC283174
LOC283177
SNX19
LINC00167
LOC100128239
LOC100507392
MIR4697
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
MTOR
FUCA1
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RHCE
RHD
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
CROCCP3
FHAD1
LOC115110
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.2.

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

Genes
ANP32C
MARCH1
C4orf39
TRIM61
LOC100505989
LOC100506013
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

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

Genes
IRF4
BMP6
BPHL
DSP
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
CDYL
LY86
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
NRN1
TMEM14C
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
TXNDC5
RIOK1
FOXQ1
HUS1B
SNRNP48
C6orf195
PIP5K1P1
LINC00518
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
PSMG4
DKFZP686I15217
C6orf201
PPP1R3G
HULC
SCARNA27
LOC100130275
MIR3691
LOC100506207
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4645
Genes in Wide Peak

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

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

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

This is the comprehensive list of deleted genes in the wide peak for 17q25.3.

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

Genes
CD7
CSNK1D
FASN
UTS2R
FOXK2
SECTM1
TBCD
SLC16A3
RAB40B
NARF
WDR45L
FN3K
C17orf62
FN3KRP
C17orf101
ZNF750
B3GNTL1
CCDC57
HEXDC
METRNL
FLJ43681
TEX19
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

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

Genes
ZMYND11
DIP2C
LARP4B
TUBB8
C10orf108
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

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

Genes
B2M
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.2.

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

Genes
hsa-mir-548f-5
DMD
FTHL17
FAM47A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p13.1.

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

Genes
hsa-mir-1299
PGM5
ZNF658
FAM75A7
CNTNAP3
ANKRD20A1
FAM201A
CBWD5
LOC286297
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
FAM74A1
FAM74A4
ZNF658B
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920
Genes in Wide Peak

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

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

Genes
KCNIP4
KCNIP4-IT1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.1.

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

Genes
AKR1C2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.22.

Table S63.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
AUTS2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.1.

Table S64.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PTPRD
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

Table S65.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
POTED
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

Table S66.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.1.

Table S67.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MAML2
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
FUT4
MRE11A
MTNR1B
JRKL
MTMR2
MED17
CEP57
GPR83
SRSF8
ENDOD1
PANX1
C11orf54
CWC15
CNTN5
ANKRD49
KDM4D
C11orf75
TAF1D
CCDC82
KIAA1731
SLC36A4
FAT3
FAM76B
SESN3
PIWIL4
AMOTL1
CCDC67
HEPHL1
VSTM5
FOLR4
KDM4DL
SCARNA9
LOC643037
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
MIR1304
MIR1260B
Genes in Wide Peak

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

Table S68.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

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

This is the comprehensive list of deleted genes in the wide peak for Xp11.3.

Table S69.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
KDM6A
DUSP21
Genes in Wide Peak

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

Table S70.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TMPRSS2
hsa-mir-3197
MX1
MX2
TFF1
TFF2
TFF3
ABCG1
BACE2
C2CD2
ZNF295
UBASH3A
SLC37A1
LINC00112
LINC00111
FAM3B
RIPK4
PRDM15
TMPRSS3
RSPH1
UMODL1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00323
MIR3197
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.21.

Table S71.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-648
hsa-mir-3198
ATP6V1E1
BID
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
HSFY1P1
CECR6
CECR5
CECR3
CECR2
CECR1
MICAL3
OR11H1
SLC25A18
GAB4
CCT8L2
XKR3
TPTEP1
MIR648
CECR7
CECR5-AS1
FLJ41941
MIR3198-1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

Table S72.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PARK2
PACRG
LOC285796
Genes in Wide Peak

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

Table S73.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ALDH2
BCL7A
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DTX1
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
LTA4H
MMP17
MSI1
MVK
MYBPC1
MYL2
NFYB
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
BRAP
ULK1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
HRK
ADAM1
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
SNRNP35
PRDM4
CIT
PWP1
FICD
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
FBXW8
HSPB8
HCAR1
UTP20
IFT81
FAM216A
HCFC2
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
GPR133
MORN3
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
TMEM119
LOC338799
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
C12orf76
LOC400084
FLJ37505
MIR135A2
LOC440117
FLJ31485
MIR331
EID3
MIR492
MAP1LC3B2
LOC643770
LOC647589
SNORA49
SNORA53
MIR620
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4498
MIR4472-2
MIR4700
MIR4497
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

Table S74.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BUB1B
C15orf55
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
NBEAP1
CHRM5
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
IVD
MEIS2
TRPM1
NDN
OCA2
PLCB2
RYR3
SCG5
SNRPN
SRP14
THBS1
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
AQR
ARHGAP11A
SLC12A6
RASGRP1
GPR176
BAHD1
FAN1
GOLGA8A
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
GREM1
RPUSD2
TMEM85
KLF13
MAGEL2
MTMR10
ZNF770
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
C15orf29
NIPA2
C15orf41
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
TUBGCP5
NIPA1
PAR1
LOC145845
TMCO5A
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
FSIP1
LPCAT4
LOC283683
OR4N4
LOC283710
FAM98B
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
LOC503519
C15orf56
PHGR1
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1233-2
MIR3942
LOC100507466
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4509-3
MIR4715
TMCO5B
Genes in Wide Peak

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

Table S75.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535
Genes in Wide Peak

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

Table S76.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NKAIN2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.3.

Table S77.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MYCN
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
APOB
RHOB
DDX1
E2F6
HPCAL1
ID2
KCNF1
KCNS3
MATN3
ODC1
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
ROCK2
GREB1
LAPTM4A
RNF144A
PDIA6
MYCNOS
YWHAQ
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
TRAPPC12
NBAS
CPSF3
SNTG2
ADI1
ALLC
KIDINS220
WDR35
RDH14
C2orf43
HS1BP3
COLEC11
SMC6
NOL10
FAM49A
RSAD2
NT5C1B
CMPK2
MBOAT2
TMEM18
OSR1
TTC32
C2orf50
PQLC3
LOC150622
FAM84A
GDF7
CYS1
ATP6V1C2
RNASEH1
FAM150B
IAH1
FLJ33534
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
LOC386597
LOC400940
LINC00487
FLJ12334
FAM110C
LOC727982
RAD51AP2
LOC730811
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429
Genes in Wide Peak

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

Table S78.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-651
SHROOM2
STS
CLCN4
KAL1
MID1
GPR143
PRKX
TBL1X
HDHD1
PNPLA4
VCX
VCX2
VCX3A
WWC3
NLGN4X
FAM9A
FAM9B
LOC389906
VCX3B
MIR651
LOC100288814
MIR4770
MIR4767
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

Table S79.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
EPHA3
GBE1
HTR1F
POU1F1
PROS1
CGGBP1
CHMP2B
ZNF654
ARL13B
CADM2
C3orf38
VGLL3
STX19
LOC440970
MIR4795
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 30 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 0.21 -3 1 0.40 4.99 8.62e-07
1q 1955 0.41 5.07 8.82e-07 0.28 -0.832 1
2p 924 0.45 3.14 0.00308 0.12 -9.14 1
2q 1556 0.29 -1.64 1 0.13 -8.05 1
3p 1062 0.26 -2.36 1 0.83 20.4 0
3q 1139 0.67 11.9 0 0.58 7.19 1.16e-12
4p 489 0.15 -7.29 1 0.67 11.2 0
4q 1049 0.10 -7.83 1 0.62 11.3 0
5p 270 0.66 8.15 4.44e-15 0.61 5.97 3.74e-09
5q 1427 0.18 -3.94 1 0.76 19 0
6p 1173 0.27 -3.77 1 0.29 -2.68 1
6q 839 0.22 -6.42 1 0.29 -4.16 1
7p 641 0.53 5.25 3.71e-07 0.26 -4.61 1
7q 1277 0.47 5.3 3.28e-07 0.22 -4.82 1
8p 580 0.34 -2.02 1 0.70 12.2 0
8q 859 0.53 6.19 2.45e-09 0.29 -3.36 1
9p 422 0.29 -3.52 1 0.71 12.5 0
9q 1113 0.34 -0.923 1 0.61 10.3 0
10p 409 0.25 -5.75 1 0.52 4.08 5.54e-05
10q 1268 0.14 -7.23 1 0.51 6.87 1.09e-11
11p 862 0.21 -6.41 1 0.41 1.1 0.258
11q 1515 0.24 -3.74 1 0.36 1.05 0.267
12p 575 0.48 3.26 0.00224 0.18 -7.79 1
12q 1447 0.34 -0.133 1 0.15 -7.32 1
13q 654 0.21 -5.37 1 0.68 12 0
14q 1341 0.38 1.31 0.271 0.45 4.18 3.95e-05
15q 1355 0.29 -2.14 1 0.36 0.621 0.465
16p 872 0.24 -5.24 1 0.39 0.38 0.587
16q 702 0.25 -5.15 1 0.45 2.12 0.0356
17p 683 0.26 -4.01 1 0.68 12.2 0
17q 1592 0.36 1.52 0.196 0.31 -0.783 1
18p 143 0.39 -1.89 1 0.43 -0.275 0.973
18q 446 0.32 -3.29 1 0.48 2.68 0.00822
19p 995 0.31 -2.31 1 0.45 2.97 0.00355
19q 1709 0.38 2.61 0.0151 0.36 1.64 0.101
20p 355 0.55 5.49 1.33e-07 0.21 -6.7 1
20q 753 0.54 6.3 1.49e-09 0.21 -6.01 1
21q 509 0.24 -5.28 1 0.60 7.97 3.11e-15
22q 921 0.55 6.94 2.62e-11 0.35 -0.877 1
Xq 1312 0.17 -7.02 1 0.29 -2.62 1
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC-TP/5950500/GDAC_MergeDataFiles_4580465/LUSC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 490 Input Tumor Samples.

Tumor Sample Names
TCGA-18-3406-01A-01D-0978-01
TCGA-18-3407-01A-01D-1969-01
TCGA-18-3408-01A-01D-0978-01
TCGA-18-3409-01A-01D-0978-01
TCGA-18-3410-01A-01D-1969-01
TCGA-18-3411-01A-01D-1969-01
TCGA-18-3412-01A-01D-0978-01
TCGA-18-3414-01A-01D-0978-01
TCGA-18-3415-01A-01D-0978-01
TCGA-18-3416-01A-01D-0978-01

Figure 3.  Segmented copy number profiles in the input data

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

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

Region Data

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

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

  2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

  1. Cytoband

  2. Q value

  3. Residual Q value

  4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

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