SNP6 Copy number analysis (GISTIC2)
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C17943KQ
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 579 tumor samples used in this analysis: 31 significant arm-level results, 33 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 - 33 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
8q24.21 3.5144e-156 3.5144e-156 chr8:128494482-129683450 7
3q26.2 9.4353e-120 9.4353e-120 chr3:168670994-168780606 0 [MECOM]
19q12 1.221e-94 1.2406e-69 chr19:30306758-30331242 1
19p13.12 6.6681e-40 1.8338e-39 chr19:15333311-15422141 2
11q14.1 1.0269e-31 1.0269e-31 chr11:77620713-78035831 9
1p34.3 5.3404e-27 5.3404e-27 chr1:39887948-40168864 8
1q21.3 7.1258e-29 4.9736e-20 chr1:150483517-150739128 13
6p22.3 9.1836e-16 9.1836e-16 chr6:18466469-18508269 1
7q36.3 4.456e-13 4.456e-13 chr7:146325573-159138663 109
5p15.33 4.6468e-11 4.6468e-11 chr5:1-1428010 25
20q13.33 3.5649e-10 1.5394e-09 chr20:62137482-63025520 33
1q42.2 6.9016e-14 2.2482e-09 chr1:234417530-235727932 18
Xp11.23 1.3189e-08 1.3189e-08 chrX:48680692-49578093 44
12p12.1 2.5049e-12 2.5043e-07 chr12:24880663-25807307 7
2q31.2 6.0134e-07 6.0134e-07 chr2:178462915-178609187 2
15q26.3 1.5847e-06 1.5847e-06 chr15:97998762-102531392 39
Xq28 3.3445e-06 3.3445e-06 chrX:152900017-154883511 72
17q25.3 2.0291e-05 2.0291e-05 chr17:77611030-78331244 15
4p16.3 2.0764e-05 2.0764e-05 chr4:1653353-1991609 11
10p15.3 0.00020684 0.00020684 chr10:749239-1314547 7
8p11.21 0.00049422 0.00049422 chr8:41567872-42008185 4
12p13.33 1.374e-06 0.00067154 chr12:1-3550659 33
14q11.2 9.6311e-06 0.00086296 chr14:21338460-21606746 13
19q13.2 7.5273e-28 0.0018704 chr19:39311557-40342966 42
10q22.3 0.0066954 0.0066954 chr10:79307111-79800033 6
4q13.3 0.0081748 0.0081748 chr4:73122319-74289961 7
18q11.2 0.0084374 0.0084374 chr18:23773718-24293308 4
2p23.2 0.016102 0.016102 chr2:28811078-28966789 2
20p13 0.067285 0.067285 chr20:1-4110252 88
12q15 0.12926 0.12926 chr12:69687666-70259497 9
22q12.2 0.13558 0.13558 chr22:30113489-30703254 11
20q11.21 0.027231 0.16894 chr20:30061713-30332464 9
14q32.33 0.0058637 0.19733 chr14:105140737-107349540 45
Genes in Wide Peak

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

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

Genes
MYC
RN7SKP226
TMEM75
MIR1205
MIR1207
PVT1
MIR1208
Genes in Wide Peak

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

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

Genes
CCNE1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
BRD4
EPHX3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q14.1.

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

Genes
NDUFC2
THRSP
GAB2
AAMDC
USP35
KCTD14
ALG8
INTS4
KCTD21
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.3.

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

Genes
SNORA55
BMP8A
PABPC4
PPIE
MACF1
HEYL
HPCAL4
NT5C1A
Genes in Wide Peak

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

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

Genes
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
CTSS
ECM1
ENSA
MCL1
ADAMTSL4
GOLPH3L
HORMAD1
MIR4257
Genes in Wide Peak

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

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

Genes
RNF144B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q36.3.

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

Genes
EZH2
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
AOC1
DPP6
EN2
GBX1
MNX1
INSIG1
KCNH2
NOS3
PTPRN2
RARRES2
RHEB
SLC4A2
SMARCD3
VIPR2
XRCC2
ZNF212
ZNF282
CUL1
ASIC3
PDIA4
UBE3C
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
CNTNAP2
GIMAP2
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ESYT2
ZNF398
KMT2C
GALNT11
LMBR1
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
ZBED6CL
AGAP3
C7orf13
ZNF786
ASB10
RNF32
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
C7orf33
CNPY1
ZNF775
ATG9B
BLACE
WDR86
GIMAP6
ZNF862
ACTR3C
ZNF783
MIR548F4
MIR5707
Genes in Wide Peak

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

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

Genes
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
SLC6A19
SLC6A18
MIR4457
MIR4456
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
NPBWR2
MIR647
MIR1914
C20ORF135
SLC2A4RG
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
PCMTD2
ZNF512B
C20orf195
PPDPF
DNAJC5
ZGPAT
HELZ2
ZBTB46
SAMD10
ABHD16B
C20orf201
LINC00176
Genes in Wide Peak

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

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

Genes
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
GNG4
TARBP1
TBCE
GGPS1
TOMM20
RBM34
ARID4B
SLC35F3
B3GALNT2
IRF2BP2
COA6
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.23.

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

Genes
TFE3
GAGE1
MAGIX
RN7SL262P
GPKOW
WDR45
RN7SL139P
ERAS
CACNA1F
GAGE2C
KCND1
PRICKLE3
PLP2
SYP
SLC35A2
PAGE1
HDAC6
PQBP1
TIMM17B
PIM2
WDR45
PRAF2
GAGE12I
GAGE2E
PCSK1N
CCDC22
FOXP3
OTUD5
GRIPAP1
PPP1R3F
CCDC120
GAGE10
GAGE2B
GAGE13
GAGE12G
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
GAGE12F
GAGE12D
Genes in Wide Peak

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

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
IFLTD1
C12orf77
Genes in Wide Peak

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

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

Genes
TTC30A
PDE11A
Genes in Wide Peak

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

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

Genes
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
VIMP
TTC23
LRRK1
TM2D3
ARRDC4
LINC00923
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
ADAMTS17
DNM1P46
CERS3
FAM169B
SPATA41
OR4F6
OR4F15
Genes in Wide Peak

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

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

Genes
MTCP1
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36|ENSG00000251846.1
RN7SL687P
ABCD1
ARHGAP4
ATP6AP1
AVPR2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
GDI1
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
TAZ
VBP1
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SRPK3
CTAG2
TMLHE
PLXNA3
PDZD4
FAM3A
BRCC3
H2AFB3
RAB39B
GAB3
PNCK
CTAG1A
H2AFB2
H2AFB1
OPN1MW2
SMIM9
CMC4
MIR718
Genes in Wide Peak

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

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

Genes
CBX8
snoU13|ENSG00000239173.1
GAA
SGSH
CBX4
EIF4A3
CCDC40
RNF213
CARD14
CBX2
TBC1D16
RBFOX3
SLC26A11
ENPP7
MIR4739
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

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

Genes
FGFR3
WHSC1
MIR943
SCARNA22
RN7SL671P
LETM1
NELFA
SLBP
TACC3
TMEM129
FAM53A
Genes in Wide Peak

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

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

Genes
ADARB2
IDI1
WDR37
LARP4B
GTPBP4
IDI2
LINC00200
Genes in Wide Peak

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

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

Genes
SNORD112|ENSG00000238966.1
RN7SL149P
ANK1
KAT6A
Genes in Wide Peak

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

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

Genes
KDM5A
FKBP4
CBX3P4
CACNA1C
LINC00940
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
WNK1
ADIPOR2
WNT5B
RHNO1
NRIP2
CCDC77
CACNA2D4
FBXL14
DCP1B
B4GALNT3
IQSEC3
LRTM2
MIR3649
Genes in Wide Peak

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

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

Genes
RNASE8
RN7SL189P
RNASE2
RNASE3
SLC39A2
ZNF219
ARHGEF40
NDRG2
METTL17
RNASE7
TPPP2
RNASE13
TMEM253
Genes in Wide Peak

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

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

Genes
LGALS17A
EID2
RN7SL566P
IFNL4
snoU13|ENSG00000251709.1
CLC
ECH1
FBL
HNRNPL
NFKBIB
MRPS12
RPS16
SUPT5H
ZFP36
DYRK1B
GMFG
PAK4
DLL3
SIRT2
LGALS13
PAF1
SARS2
SAMD4B
MED29
LGALS14
LRFN1
PLEKHG2
TIMM50
FBXO17
EID2B
RINL
FBXO27
LGALS16
IFNL2
IFNL3
IFNL1
NCCRP1
SYCN
LEUTX
SELV
PAPL
MIR4530
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.3.

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

Genes
RN7SL284P
RNA5SP321
KCNMA1
RPS24
DLG5
POLR3A
Genes in Wide Peak

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

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

Genes
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
ALB
ADAMTS3
ANKRD17
COX18
Genes in Wide Peak

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

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

Genes
U3|ENSG00000265369.2
U3|ENSG00000252921.1
TAF4B
KCTD1
Genes in Wide Peak

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

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

Genes
RNA5SP89
PLB1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p13.

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

Genes
MIR103A2
MAVS
U3|ENSG00000201346.1
RN7SL839P
RN7SL555P
TMEM239
SNORD57
SNORD56|ENSG00000229686.1
SNORD86
SNORA51|ENSG00000271798.1
SNORD110
MIR1292
SNORD119
RN7SL561P
TCF15
CSNK2A1
DEFB128
DEFB127
DEFB126
DEFB125
AVP
CDC25B
CENPB
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PDYN
PTPRA
SIGLEC1
SNRPB
SOX12
TGM3
ATRN
PSMF1
SNPH
LZTS3
SIRPB1
NOP56
RBCK1
RNF24
UBOX5
SPEF1
C20orf194
SDCBP2
ANGPT4
SMOX
C20orf27
AP5S1
TMEM74B
SIRPG
NSFL1C
CPXM1
EBF4
TRIB3
FASTKD5
GFRA4
VPS16
PCED1A
MRPS26
DDRGK1
ZNF343
NRSN2
PANK2
ADAM33
FAM110A
SLC4A11
ZCCHC3
SCRT2
SLC52A3
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
C20orf96
SRXN1
DEFB129
SIRPA
STK35
SIRPB2
RSPO4
TGM6
DEFB132
C20orf202
RAD21L1
TMEM239
Genes in Wide Peak

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

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

Genes
MYRFL
RN7SL804P
LYZ
YEATS4
CCT2
FRS2
RAB3IP
BEST3
LRRC10
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q12.2.

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

Genes
MGC20647
LIF
OSM
MTMR3
UQCR10
ZMAT5
TBC1D10A
ASCC2
HORMAD2
CABP7
GATSL3
Genes in Wide Peak

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

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

Genes
LINC00028
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
DEFB124
MIR3193
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.33.

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

Genes
AKT1
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
CRIP1
CRIP2
BRF1
JAG2
MTA1
SIVA1
PACS2
GPR132
CDCA4
INF2
TMEM121
BTBD6
AHNAK2
PLD4
ADSSL1
NUDT14
CEP170B
C14orf80
TEX22
MIR4710

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
19p13.3 3.6225e-145 3.6225e-145 chr19:1272041-1882761 24
22q13.32 9.0969e-69 9.0969e-69 chr22:48668761-51304566 42
11p15.5 1.2745e-41 1.2745e-41 chr11:502218-772981 15
6q27 1.8796e-36 1.8796e-36 chr6:167455614-171115067 26
1p36.11 6.4963e-35 6.4963e-35 chr1:26963410-27570286 15
13q14.2 3.7837e-34 3.7837e-34 chr13:48875329-49064807 2
5q13.2 4.3582e-89 3.0919e-30 chr5:66492413-80256908 107
18q23 1.4586e-29 1.4998e-29 chr18:68317374-78077248 38
5q12.1 1.898e-76 6.1055e-28 chr5:58151172-59818245 3
7p22.1 6.4794e-26 6.3993e-26 chr7:1-7154812 86
4q34.3 7.1796e-32 8.8342e-24 chr4:179280062-182757119 4
8p23.3 2.4363e-44 5.8143e-21 chr8:1-1459231 6
17q11.2 1.2606e-18 1.874e-18 chr17:29326736-29722618 5
10q24.2 4.6842e-17 4.6842e-17 chr10:88859357-110701986 234
8p21.2 1.2794e-37 1.1048e-15 chr8:25994239-26250295 3
Xp21.1 1.9393e-14 1.8872e-14 chrX:30865118-34644819 7
16q23.1 4.0133e-23 3.8631e-13 chr16:78098006-79299841 3
15q15.1 5.3594e-23 1.1436e-12 chr15:41795901-42121792 5
12q24.33 8.8294e-12 8.8294e-12 chr12:131625061-133851895 33
3q13.31 1.2256e-11 1.2256e-11 chr3:116297365-118620828 4
2q22.1 1.0428e-11 3.6035e-09 chr2:140708948-143637838 2
16p13.3 5.0503e-09 5.0503e-09 chr16:3764793-4004422 1
14q23.3 3.6509e-08 3.6331e-08 chr14:59114448-73526147 115
3p26.2 5.6373e-08 5.6571e-08 chr3:1-4535479 12
9q34.13 2.484e-06 2.5126e-06 chr9:132130994-140151408 183
4q22.1 8.3817e-12 4.0862e-06 chr4:90844993-93240505 2
19q13.43 3.3841e-18 1.0991e-05 chr19:58119765-59128983 46
2q37.3 4.8627e-09 7.3424e-05 chr2:234985548-243199373 73
19q13.33 2.0274e-17 0.00024287 chr19:46376619-49564123 109
9p24.3 0.00025759 0.00026046 chr9:1-2018113 11
11q25 0.00097573 0.00099341 chr11:121168179-135006516 122
16q22.1 2.3615e-16 0.0024686 chr16:67736926-69141977 33
17p12 0.0056738 0.007831 chr17:11888973-12456081 3
21q22.3 0.025317 0.025482 chr21:42519390-48129895 94
10p15.3 0.069068 0.069551 chr10:1-1040137 9
2p25.3 0.092953 0.092953 chr2:1-24426250 130
1q41 0.18366 0.18417 chr1:207316102-220705691 80
15q11.2 6.9462e-12 0.19006 chr15:25219196-25922484 7
Genes in Wide Peak

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

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

Genes
TCF3
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
EFNA2
GAMT
RPS15
APC2
UQCR11
DAZAP1
MBD3
PCSK4
REXO1
KLF16
MUM1
REEP6
PLK5
C19orf25
ATP8B3
ADAMTSL5
MEX3D
Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
ACR
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
IL17REL
PIM3
ODF3B
SYCE3
MIR3201
MIR3667
MIR4535
Genes in Wide Peak

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

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

Genes
HRAS
TMEM80
SCT
MIR210HG
DRD4
IRF7
TALDO1
RASSF7
DEAF1
CDHR5
PHRF1
EPS8L2
LRRC56
C11orf35
MIR210
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MLLT4
MIR4644
TCP10
TTLL2
GPR31
CCR6
KIF25
PDCD2
PSMB1
TBP
TCTE3
THBS2
C6orf123
DLL1
UNC93A
PHF10
C6orf70
SMOC2
FRMD1
LINC00574
FAM120B
DACT2
WDR27
C6orf120
TCP10L2
LINC00242
Genes in Wide Peak

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

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

Genes
ARID1A
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
SFN
SLC9A1
NR0B2
NUDC
PIGV
GPATCH3
FAM46B
C1orf172
TRNP1
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: Cancer Gene Census[7].

Genes
RB1
LPAR6
Genes in Wide Peak

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

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

Genes
PIK3R1
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
MIR4804
RN7SL153P
MIR4803
snoU13|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13|ENSG00000238334.1
SNORA50|ENSG00000220986.1
RN7SL103P
7SK|ENSG00000249352.3
U8|ENSG00000212249.2
ARSB
BHMT
BTF3
CCNB1
CDK7
CRHBP
DHFR
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
TNPO1
MAP1B
MSH3
NAIP
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
THBS4
SERF1A
ENC1
AP3B1
PDE8B
SCAMP1
CARTPT
ZFYVE16
COL4A3BP
LHFPL2
NSA2
IQGAP2
SV2C
MRPS27
FAM169A
DMGDH
GCNT4
AGGF1
BDP1
ANKRA2
MCCC2
ARHGEF28
SLC30A5
CENPH
PTCD2
UTP15
GFM2
SPZ1
MRPS36
FCHO2
JMY
TMEM171
TMEM174
POC5
MARVELD2
PAPD4
ZNF366
FAM151B
CCDC125
CMYA5
ANKRD31
SERINC5
ANKRD34B
GTF2H2C
SERF1B
ANKDD1B
MTRNR2L2
OCLN
Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
CYB5A
MBP
NFATC1
ZNF236
CTDP1
TSHZ1
TXNL4A
ADNP2
KCNG2
TIMM21
ZNF407
CNDP2
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
LINC00908
ATP9B
LINC00909
HSBP1L1
C18orf63
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

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

Genes
FKSG52
MIR582
PDE4D
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.1.

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

Genes
PMS2
CARD11
PMS2CL
GRID2IP
FLJ20306
RN7SL851P
SNORA42|ENSG00000207217.1
RN7SL556P
ZNF815P
MIR589
snoU13|ENSG00000238394.1
ZNF890P
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
ACTB
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
RAC1
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KDELR2
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
GET4
CCZ1
RNF216
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM220A
ZFAND2A
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
SLC29A4
RSPH10B
OCM
RSPH10B2
ANKRD61
MIR3683
MIR4656
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

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

Genes
RPL23AP53
OR4F21
FBXO25
TDRP
ERICH1
ZNF596
Genes in Wide Peak

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

Table S45.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 10q24.2.

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

Genes
PTEN
TLX1
NFKB2
SUFU
RN7SKP278
RNA5SP326
RNA5SP325
snoU13|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112|ENSG00000253068.1
FGF8
snoU13|ENSG00000239091.1
SNORD112|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12|ENSG00000212464.1
ERLIN1
snoU13|ENSG00000238472.1
COX15
ENTPD7
snoU13|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13|ENSG00000238991.1
ANKRD22
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
ACTA2
FAS
ARL3
ENTPD1
CHUK
ABCC2
COL17A1
CPN1
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DNTT
GOT1
HELLS
HPS1
HTR7
IDE
IFIT2
IFIT3
KIF11
LIPA
NDUFB8
PAX2
PDE6C
PGAM1
PITX3
PPP1R3C
PSD
ALDH18A1
RBP4
SCD
SFRP5
FBXW4
SLIT1
TAF5
TLL2
WNT8B
LIPF
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
NEURL
LGI1
NOLC1
GSTO1
MINPP1
KIF20B
SH3PXD2A
SLK
FRAT1
ACTR1A
NPM3
RPP30
SORBS1
MGEA5
CPEB3
NT5C2
PDCD11
SORCS3
PPRC1
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
R3HCC1L
POLL
BLNK
KCNIP2
CALHM2
CUTC
PLCE1
PANK1
EXOC6
CCNJ
MARCH5
CNNM2
WBP1L
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
FAM178A
C10orf2
TM9SF3
AS3MT
STAMBPL1
SEMA4G
AVPI1
MMS19
NOC3L
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
C10orf95
PDZD7
UBTD1
WDR96
TNKS2
TRIM8
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
LZTS2
LCOR
MRPL43
PYROXD2
USMG5
ATAD1
ARHGAP19
OPALIN
HOGA1
SORCS1
PIK3AP1
MORN4
ZFYVE27
FRA10AC1
C10orf32
GSTO2
SFR1
CALHM3
C10orf129
LIPJ
HECTD2
FGFBP3
SLC35G1
CCDC147
CALHM1
FFAR4
LIPM
CYP26C1
SLC16A12
CC2D2B
GOLGA7B
C10orf62
IFIT1B
MIR146B
LIPK
LIPN
MIR607
NUTM2A
NUTM2D
TLX1NB
C10orf131
KLLN
MIR1307
MIR3157
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

Genes
SDAD1P1
RNA5SP258
PPP2R2A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
snoU13|ENSG00000238969.1
MIR548F5
MIR3915
RNA5SP501
DMD
FTHL17
FAM47A
Genes in Wide Peak

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

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

Genes
RNA5SP431
PIH1
WWOX
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
MIR626
TYRO3
MAPKBP1
MGA
RPAP1
Genes in Wide Peak

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

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

Genes
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
GOLGA3
MMP17
POLE
PXMP2
SFSWAP
ZNF10
ZNF26
ZNF84
ULK1
ZNF268
P2RX2
ANKLE2
GALNT9
CHFR
EP400
FBRSL1
NOC4L
PUS1
PGAM5
DDX51
EP400NL
ZNF605
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
LINC00901
TUSC7
RN7SL582P
MIR4447
Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B
Genes in Wide Peak

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

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

Genes
CREBBP
Genes in Wide Peak

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

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

Genes
GPHN
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3|ENSG00000200693.1
WDR89
SCARNA20|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112|ENSG00000252380.1
SIX1
U3|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTN1
ARG2
ZFP36L1
EIF2S1
ESR2
FUT8
GPX2
HIF1A
HSPA2
MAX
MAP3K9
MNAT1
MTHFD1
PIGH
PPM1A
PRKCH
RAD51B
RTN1
SRSF5
SLC8A3
SNAPC1
SPTB
DPF3
ADAM21
ADAM20
DCAF5
AKAP5
RGS6
KIAA0247
MED6
VTI1B
ZBTB1
PCNX
DAAM1
SYNE2
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
KCNH5
RDH11
COX16
DHRS7
SIX4
ZFYVE1
EXD2
SLC39A9
RHOJ
GALNT16
PLEKHH1
TRMT5
SMOC1
MPP5
PCNXL4
SGPP1
SYT16
CHURC1
L3HYPDH
RDH12
PPP1R36
SLC38A6
FAM71D
TMEM229B
TMEM30B
C14orf39
LRRC9
RAB15
PLEKHD1
LINC00238
MIR625
CCDC175
MIR548H1
MIR4708
MIR5694
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.2.

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

Genes
SNORA43|ENSG00000253049.1
RN7SKP144
RN7SL120P
IL5RA
SETMAR
CHL1
CNTN6
TRNT1
CRBN
LRRN1
CNTN4
SUMF1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.13.

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

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
FNBP1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
ABCA2
ASS1
C8G
ENTPD2
CEL
COL5A1
DBH
SARDH
TOR1A
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PTGDS
RPL7A
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
FUBP3
GTF3C5
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
USP20
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
MAN1B1
SETX
PMPCA
EXOSC2
NCS1
GPSM1
GBGT1
NDOR1
TOR1B
NTMT1
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
PRRX2
C9orf78
FBXW5
RABL6
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
GPR107
PRDM12
DDX31
AIF1L
UCK1
NTNG2
PPAPDC3
FIBCD1
KIAA1984
TMEM141
SAPCD2
C9orf69
UAP1L1
TMEM203
NACC2
C9orf116
LCN8
SLC34A3
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
C9orf50
C9orf169
C9orf171
LCN15
LRRC26
TMEM8C
LCN9
LCNL1
C9orf139
FAM166A
SOHLH1
C9orf173
RNF208
CARD9
MIR3689A
MIR3689B
MIR3689D1
MIR3689F
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR548AW
Genes in Wide Peak

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

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

Genes
RN7SKP248
CCSER1
Genes in Wide Peak

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

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

Genes
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
ZNF134
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
ZNF154
UBE2M
TRIM28
ZNF256
ZNF211
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF586
ZNF446
ZSCAN18
RPL23AP79
ZNF329
ZNF552
ZNF671
ZNF606
ZBTB45
ZNF587
ZNF551
ZNF837
C19orf18
ZNF418
ZNF497
ZNF584
ZSCAN4
ZNF776
ZSCAN1
ZSCAN22
ZNF324B
ZNF587B
MIR4754
Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
ACKR3
GAL3ST2
RAB17
MLPH
IQCA1
C2orf54
ILKAP
ING5
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
DUSP28
ESPNL
AQP12A
KLHL30
OR6B2
ASB18
PRR21
AQP12B
D2HGDH
MIR4269
MIR4786
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
RN7SL345P
SEC1P
DBP
GRWD1
C19orf68
CABP5
TPRX2P
SNORD23|ENSG00000221803.1
RN7SL322P
RN7SL533P
snoU13|ENSG00000252071.1
MIR320E
RN7SL364P
PGLYRP1
NOVA2
BAX
BCAT2
C5AR1
CA11
CALM3
CGB
AP2S1
CRX
EMP3
FTL
FUT1
FUT2
GRIN2D
ARHGAP35
GYS1
KCNJ14
LHB
LIG1
NPAS1
NUCB1
PPP5C
PTGIR
RPL18
SEPW1
SLC1A5
SLC8A2
SULT2B1
SULT2A1
TULP2
PLA2G4C
NAPA
CYTH2
DHX34
SAE1
RUVBL2
KDELR1
KPTN
CARD8
ZC3H4
SYNGR4
PPP1R15A
PRKD2
CCDC9
IRF2BP1
FGF21
BBC3
C5AR2
DHDH
STRN4
GLTSCR2
GLTSCR1
EHD2
HSD17B14
FAM83E
RASIP1
TMEM160
PNMAL1
TMEM143
SPHK2
MEIS3
PNMAL2
PLEKHA4
ELSPBP1
HIF3A
FKRP
CCDC8
ZNF541
CCDC114
CGB5
CGB7
CGB8
GNG8
CGB1
CGB2
LMTK3
NTN5
DACT3
IGFL2
ZNF114
SPACA4
PRR24
TPRX1
MAMSTR
IZUMO1
MYPOP
NANOS2
IGFL1
IGFL3
IGFL4
CCDC61
MIR769
BSPH1
MIR3191
PPP5D1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.3.

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

Genes
RNA5SP279
RN7SL412P
FAM138C
DMRT1
FOXD4
DMRT2
KANK1
CBWD1
DMRT3
DOCK8
C9orf66
Genes in Wide Peak

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

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

Genes
FLI1
snoU13|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
ACRV1
APLP2
CHEK1
ETS1
HSPA8
STT3A
KCNJ1
VWA5A
NFRKB
NRGN
OPCML
ST3GAL4
SORL1
SRPR
ST14
ZNF202
BARX2
EI24
FEZ1
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
VSIG2
OR8B8
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
CRTAM
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ROBO3
FAM118B
MSANTD2
CLMP
C11orf63
CCDC15
PUS3
JAM3
KIRREL3
RPUSD4
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
PANX3
TMEM45B
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
SPATA19
HEPACAM
OR8D1
OR8D2
OR8B4
C11orf44
TMEM225
OR8D4
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
HEPN1
PATE3
MIR4697
MIR4493
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.1.

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

Genes
CDH1
RPS2P45
RNA5SP429
snoU109|ENSG00000252640.1
snoU109|ENSG00000252040.1
snoU13|ENSG00000238343.1
SLC7A6OS
SNORA48|ENSG00000212445.1
CTRL
NUTF2
CDH3
LCAT
NFATC3
PSKH1
PSMB10
SLC12A4
SLC7A6
EDC4
PLA2G15
PRMT7
DUS2L
SMPD3
DDX28
TSNAXIP1
THAP11
RANBP10
DPEP2
DPEP3
TANGO6
ESRP2
CENPT
NRN1L
ZFP90
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

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

Genes
MAP2K4
MIR744
RPL21P122
Genes in Wide Peak

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

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

Genes
TMPRSS2
S100B
PRED62
PRED60
LINC00316
LINC00315
LINC00205
LINC00334
PRED58
PRED57
SSR4P1
LINC00162
LINC00163
C21orf90
LRRC3DN
snoZ6|ENSG00000264452.1
snoZ6|ENSG00000266692.1
RRP1
CSTB
LINC00322
MIR5692B
NDUFV3
RNA5SP492
SNORA3|ENSG00000251778.1
LINC00112
LINC00111
snoU13|ENSG00000252771.1
SNORA32|ENSG00000207503.1
FAM3B
ADARB1
AIRE
PTTG1IP
C21orf2
CBS
COL6A1
COL6A2
CRYAA
PRMT2
ITGB2
LSS
MX1
MX2
PCNT
PDE9A
PFKL
PKNOX1
PWP2
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
U2AF1
UBE2G2
C21orf33
PDXK
MCM3AP
ABCG1
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
BACE2
C2CD2
DNMT3L
ZBTB21
UBASH3A
SLC37A1
PCBP3
C21orf58
YBEY
TSPEAR
RIPK4
AGPAT3
PRDM15
TMPRSS3
COL18A1
LRRC3
SPATC1L
C21orf67
FAM207A
RSPH1
UMODL1
LINC00313
SIK1
LINC00479
C21orf128
LINC00319
MIR3197
Genes in Wide Peak

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

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

Genes
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ZMYND11
DIP2C
LARP4B
PRR26
Genes in Wide Peak

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

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

Genes
MYCN
PFN4
RN7SL610P
UBXN2A
RN7SKP27
RNA5SP87
RN7SL117P
TDRD15
GDF7
RNA5SP86
RN7SL140P
LINC00954
SNORA40|ENSG00000212455.1
RN7SKP168
SNORA40|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13|ENSG00000238371.1
LINC00276
MIR3125
SNORD18|ENSG00000238503.1
MIR548S
RN7SL674P
RNA5SP85
RNA5SP84
LINC00570
RN7SL832P
SNORA80B
SNORA51|ENSG00000206898.1
RN7SL66P
SNORA2|ENSG00000206647.1
SNORA26|ENSG00000212558.1
snoU13|ENSG00000238462.1
IAH1
snoU13|ENSG00000238888.1
MBOAT2
RNU6ATAC37P
RN7SKP112
FLJ30594
SNORA31|ENSG00000252238.1
RN7SL531P
DCDC2C
SNORA73|ENSG00000252531.1
snoU13|ENSG00000238722.1
TMEM18
FAM110C
ACP1
APOB
RHOB
DDX1
E2F6
FKBP1B
HPCAL1
ID2
KCNF1
KCNS3
MATN3
ODC1
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
PDIA6
YWHAQ
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
TRAPPC12
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
ADI1
ALLC
KIDINS220
WDR35
RDH14
C2orf43
HS1BP3
COLEC11
SMC6
NOL10
C2orf44
FAM49A
RSAD2
NT5C1B
KLHL29
CMPK2
OSR1
TTC32
C2orf50
PQLC3
FAM84A
CYS1
ATP6V1C2
RNASEH1
FAM150B
LINC00299
MSGN1
GEN1
C2orf48
FAM228B
MFSD2B
LINC00487
FAM228A
RAD51AP2
MIR4261
MIR4262
MIR3681
MIR4757
MIR4429
Genes in Wide Peak

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

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

Genes
SNORA36B
snoU13|ENSG00000238576.1
snoU13|ENSG00000238798.1
U3|ENSG00000221673.1
RNA5SP76
SLC30A10
U3|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
SERTAD4
MIR4260
MIR205HG
MIR29B2
MIR29C
ATF3
CD34
CENPF
CR1
CR1L
CR2
CD55
EPRS
ESRRG
HSD11B1
IRF6
KCNK2
LAMB3
CD46
NEK2
PLXNA2
PPP2R5A
PROX1
PTPN14
TGFB2
TRAF5
USH2A
LPGAT1
BPNT1
RAB3GAP2
INTS7
NSL1
RPS6KC1
DIEXF
FLVCR1
NENF
G0S2
RRP15
KCTD3
DTL
GPATCH2
TMEM206
BATF3
IARS2
HHAT
RCOR3
SMYD2
CAMK1G
VASH2
TRAF3IP3
LINC00467
ANGEL2
LYPLAL1
TATDN3
C1orf74
C1orf227
FAM71A
SYT14
RD3
MIR215
C1orf132
Genes in Wide Peak

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

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

Genes
SNORD109B
SNORD115|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64|ENSG00000270704.2
SNHG14
UBE3A
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 31 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 0.32 2.36 0.0453 0.17 -4.82 1
1q 1195 0.40 5.65 8.24e-08 0.15 -5.89 1
2p 624 0.34 -1.16 1 0.16 -8.36 1
2q 967 0.28 -1.59 1 0.16 -7.08 1
3p 644 0.31 -2.39 1 0.26 -4.46 1
3q 733 0.50 7.2 5.88e-12 0.18 -6.13 1
4p 289 0.20 -6.56 1 0.61 9.78 0
4q 670 0.14 -6.52 1 0.66 15 0
5p 183 0.38 -1.56 1 0.42 0.0844 0.746
5q 905 0.15 -7 1 0.44 5.55 3.44e-08
6p 710 0.39 1.52 0.215 0.43 3.25 0.0011
6q 556 0.27 -3.77 1 0.51 6.39 2.22e-10
7p 389 0.38 -0.473 1 0.32 -2.96 1
7q 783 0.40 2.83 0.0131 0.23 -4.75 1
8p 338 0.31 -2.86 1 0.63 10.6 0
8q 551 0.48 4.68 1.16e-05 0.30 -2.62 1
9p 301 0.24 -5.68 1 0.56 6.98 4.24e-12
9q 700 0.14 -7.39 1 0.54 9.04 0
10p 253 0.36 -2.28 1 0.29 -4.92 1
10q 738 0.24 -4.97 1 0.27 -3.39 1
11p 509 0.18 -7.88 1 0.41 1.42 0.14
11q 975 0.25 -2.86 1 0.33 0.744 0.397
12p 339 0.49 4.2 8.86e-05 0.28 -4.44 1
12q 904 0.36 1.72 0.155 0.28 -2.15 1
13q 560 0.22 -5.18 1 0.60 10.8 0
14q 938 0.16 -6.66 1 0.42 4.64 3.62e-06
15q 810 0.13 -7.55 1 0.52 8.98 0
16p 559 0.21 -5.04 1 0.65 13.2 0
16q 455 0.18 -5.34 1 0.75 17.8 0
17p 415 0.18 -4.2 1 0.86 22.9 0
17q 972 0.22 -2.87 1 0.72 20.2 0
18p 104 0.31 -4.41 1 0.53 4.53 5.85e-06
18q 275 0.24 -5.85 1 0.58 8.08 1.02e-15
19p 681 0.41 2.06 0.0788 0.48 5.33 1.11e-07
19q 935 0.38 2.26 0.0535 0.45 5.67 1.74e-08
20p 234 0.54 5.86 3.02e-08 0.19 -7.65 1
20q 448 0.59 10 0 0.15 -7.72 1
21q 258 0.28 -5.01 1 0.43 0.712 0.397
22q 564 0.16 -5.28 1 0.77 19.8 0
Xq 668 0.30 -2.05 1 0.60 11.6 0
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/OV-TP/11448369/GDAC_MergeDataFiles_11450986/OV-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_GENCODE_v18_20140127.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 579 Input Tumor Samples.

Tumor Sample Names
TCGA-04-1331-01A-01D-0428-01
TCGA-04-1332-01A-01D-0428-01
TCGA-04-1335-01A-01D-0428-01
TCGA-04-1336-01A-01D-0428-01
TCGA-04-1337-01A-01D-0428-01
TCGA-04-1338-01A-01D-0428-01
TCGA-04-1341-01A-01D-0428-01
TCGA-04-1342-01A-01D-0428-01
TCGA-04-1343-01A-01D-0428-01
TCGA-04-1346-01A-01D-0428-01

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)