SNP6 Copy number analysis (GISTIC2)
Stomach and Esophageal carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
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 (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C17D2T76
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 2.0.22 (Firehose task version: 140).

Summary

There were 625 tumor samples used in this analysis: 28 significant arm-level results, 39 significant focal amplifications, and 60 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 - 39 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
11q13.3 3.0543e-104 3.1345e-104 chr11:69412882-69595013 4
17q12 6.758e-96 6.758e-96 chr17:37854508-37876018 1
8q24.21 1.0136e-68 1.0136e-68 chr8:128714098-128724664 0 [MYC]
19q12 9.6864e-60 3.1171e-57 chr19:30287570-30316875 1
12p12.1 3.6657e-44 5.5757e-44 chr12:25339898-25514596 3
7q21.2 1.4721e-40 2.8746e-40 chr7:91837002-92616517 8
18q11.2 4.1891e-32 4.1891e-32 chr18:19613596-19677022 0 [RNU6ATAC20P]
6p21.1 5.337e-32 1.4871e-31 chr6:43845008-43936728 0 [C6orf223]
3q26.2 3.5525e-30 3.5525e-30 chr3:169485640-169498441 2
12q15 1.2003e-24 1.6049e-24 chr12:69541270-69978625 5
8p23.1 6.154e-25 2.4453e-24 chr8:11547791-11638987 3
7p11.2 9.2231e-25 1.2439e-20 chr7:55037806-55372336 1
20q13.2 2.2851e-15 2.2851e-15 chr20:52172596-52427475 1
1q42.3 4.6764e-17 1.0521e-14 chr1:235078939-235098068 0 [RN7SL668P]
15q26.1 1.1628e-12 1.1628e-12 chr15:90663892-90703835 1
11p13 3.1904e-10 3.7097e-10 chr11:35244045-35263023 1
13q22.1 1.4227e-08 1.0057e-07 chr13:73725494-73872751 1
19p13.2 1.3991e-05 1.3991e-05 chr19:7300056-7397014 0 [INSR]
5p15.33 2.1894e-07 5.3574e-05 chr5:1-1287702 22
9p13.3 4.0506e-05 0.00011847 chr9:35533693-35696801 12
6q21 0.00014255 0.00034044 chr6:107114362-107221941 1
Xq28 0.00045173 0.00045173 chrX:151841230-154883300 101
8p11.21 0.00034947 0.0012208 chr8:41600998-42701687 16
10q26.13 9.2953e-05 0.0023564 chr10:122750155-123425303 2
7p22.3 0.00012504 0.0024097 chr7:1-7921611 90
9q34.3 0.0024097 0.0024097 chr9:139857644-140290845 36
1q21.3 3.2688e-07 0.0030329 chr1:149890534-152178704 78
5p13.1 2.4266e-05 0.0041468 chr5:38167585-44523118 38
1p36.22 0.0027067 0.010826 chr1:10686864-11068052 3
6q12 0.0033126 0.038092 chr6:64038067-64323832 1
14q13.3 0.04399 0.04399 chr14:35795996-38931445 23
2q12.2 0.06236 0.06236 chr2:105734605-106853661 7
9p24.1 0.040829 0.064449 chr9:4764022-5742427 10
10p11.22 0.065629 0.065629 chr10:31856589-34276486 11
18p11.32 0.07148 0.07148 chr18:983189-1566925 2
1p34.2 0.040829 0.10878 chr1:40264205-40874003 10
10q22.2 0.019903 0.11757 chr10:76480910-77572076 9
19q13.43 0.0036227 0.17266 chr19:58675418-59128983 24
13q12.3 0.065629 0.18547 chr13:30751053-35810395 29
Genes in Wide Peak

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

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

Genes
CCND1
FGF4
FGF19
ORAOV1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
Genes in Wide Peak

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

Table S3.  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 12p12.1.

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

Genes
KRAS
CASC1
LYRM5
Genes in Wide Peak

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

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

Genes
CDK6
RN7SL7P
GATAD1
KRIT1
PEX1
ANKIB1
RBM48
FAM133B
Genes in Wide Peak

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

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

Genes
MYNN
ACTRT3
Genes in Wide Peak

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

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

Genes
RN7SL804P
LYZ
YEATS4
FRS2
CPSF6
Genes in Wide Peak

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

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

Genes
C8orf49
GATA4
NEIL2
Genes in Wide Peak

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

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

Genes
EGFR
Genes in Wide Peak

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

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

Genes
ZNF217
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
RN7SL755P
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
CD44
Genes in Wide Peak

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

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

Genes
RNY1P8
Genes in Wide Peak

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

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

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

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

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

Genes
RN7SL22P
RMRP
MIR4667
CA9
CD72
TESK1
TPM2
RUSC2
SIT1
ARHGEF39
CCDC107
FAM166B
Genes in Wide Peak

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

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

Genes
QRSL1
Genes in Wide Peak

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

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

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

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

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

Genes
snoU13|ENSG00000238714.1
SNORD112|ENSG00000238966.1
RN7SL149P
ANK1
CHRNB3
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
CHRNA6
AP3M2
DKK4
THAP1
SMIM19
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q26.13.

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

Genes
FGFR2
RN7SKP167
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.3.

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

Genes
PMS2
CARD11
RPA3
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
MIOS
RNF216
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
C1GALT1
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM220A
ZFAND2A
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
SLC29A4
RSPH10B
COL28A1
OCM
RSPH10B2
ANKRD61
MIR3683
MIR4656
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
ABCA2
ENTPD2
FUT7
GRIN1
PTGDS
SSNA1
TUBB4B
MAN1B1
NELFB
NDOR1
ANAPC2
DPP7
TOR4A
EXD3
NPDC1
SAPCD2
UAP1L1
TMEM203
SLC34A3
C9orf142
TPRN
C9orf169
LRRC26
LCNL1
C9orf139
FAM166A
C9orf173
NRARP
RNF208
Genes in Wide Peak

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

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

Genes
ARNT
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
CTSK
CTSS
ECM1
ENSA
MCL1
PI4KB
PSMB4
PSMD4
RFX5
RORC
S100A10
S100A11
VPS72
TCHH
TUFT1
PIP5K1A
ANXA9
SELENBP1
PRPF3
SETDB1
SF3B4
SEMA6C
MTMR11
TDRKH
VPS45
POGZ
RPRD2
CA14
TMOD4
CERS2
APH1A
PLEKHO1
OAZ3
MRPS21
ADAMTSL4
C1orf56
GOLPH3L
FAM63A
CDC42SE1
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
GABPB2
TCHHL1
RPTN
C1orf51
BNIPL
RIIAD1
THEM5
LYSMD1
C2CD4D
MIR4257
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.1.

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

Genes
LIFR
FGF10
CCL28
ANXA2R
SNORD72
RPL37
SNORA57|ENSG00000212567.1
SNORA63|ENSG00000199552.1
LINC00604
LINC00603
C6
C7
C9
DAB2
FYB
GHR
HMGCS1
OXCT1
PRKAA1
PTGER4
SEPP1
ZNF131
OSMR
PAIP1
NNT
TTC33
FBXO4
C5orf28
CARD6
MROH2B
EGFLAM
NIM1
RICTOR
C5orf51
PLCXD3
C5orf34
CCDC152
MIR3650
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.22.

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

Genes
PEX14
CASZ1
C1orf127
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: Cancer Gene Census[7].

Genes
PTP4A1
Genes in Wide Peak

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

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

Genes
LINC00517
SNORA42|ENSG00000200385.1
TTC6
MIR4503
SLC25A21
RN7SKP257
DPPA3P2
RN7SKP21
PTCSC3
snoU13|ENSG00000238718.1
SNORA31|ENSG00000253059.1
FOXA1
NFKBIA
PAX9
SSTR1
MBIP
BRMS1L
INSM2
MIPOL1
CLEC14A
RALGAPA1
SFTA3
LINC00609
Genes in Wide Peak

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

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

Genes
C2orf49
FHL2
NCK2
TGFBRAP1
GPR45
UXS1
C2orf40
Genes in Wide Peak

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

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

Genes
JAK2
CD274
INSL4
RLN1
RLN2
RCL1
INSL6
PLGRKT
KIAA1432
PDCD1LG2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p11.22.

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

Genes
LINC00838
RN7SL398P
RN7SL847P
CCDC7
RN7SL825P
ITGB1
KIF5B
NRP1
C10orf68
EPC1
ARHGAP12
Genes in Wide Peak

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

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

Genes
RN7SKP72
LINC00470
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
COL9A2
MYCL
PPT1
RLF
ZMPSTE24
CAP1
TRIT1
SMAP2
MFSD2A
TMCO2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.2.

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

Genes
MIR606
VDAC2
KAT6B
DUSP13
C10orf11
ZNF503
COMTD1
SAMD8
DUPD1
Genes in Wide Peak

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

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

Genes
RN7SL525P
RN7SL693P
RNA5SP473
A1BG
RPS5
ZNF8
MZF1
ZNF132
UBE2M
TRIM28
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
RPL23AP79
ZBTB45
ZNF837
ZNF497
ZNF584
ZSCAN22
ZNF324B
MIR4754
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.3.

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

Genes
BRCA2
LINC00457
SNORA25|ENSG00000199196.1
LINC00423
RNY1P4
SNORA16|ENSG00000212293.1
ZAR1L
EEF1DP3
LINC00545
LINC00398
LINC00426
LINC00427
ALOX5AP
HMGB1
RFC3
KL
FRY
USPL1
N4BP2L2
HSPH1
PDS5B
NBEA
KATNAL1
MEDAG
STARD13
N4BP2L1
RXFP2
TEX26
B3GALTL

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 - 60 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
16q23.1 4.6213e-224 4.6213e-224 chr16:78098006-79031486 1
9p21.3 1.3142e-183 5.0957e-145 chr9:21931610-22003135 2
4q22.1 1.1834e-129 2.4469e-123 chr4:91271445-93240505 1
5q12.1 1.5087e-119 1.5087e-119 chr5:58998410-59780946 2
6p25.3 1.2935e-67 1.2935e-67 chr6:1608837-2624052 2
3p14.2 1.4613e-66 4.3887e-59 chr3:59701447-61026498 2
Xp21.1 1.6746e-61 1.7847e-57 chrX:32117084-32611359 2
7q31.1 3.514e-66 8.5889e-51 chr7:110746146-111366370 1
20p12.1 1.5218e-43 1.5218e-43 chr20:14301156-15274325 2
18q21.2 9.5122e-46 1.2363e-38 chr18:48472083-48650073 3
9p23 1.0436e-58 1.9357e-37 chr9:8885227-12687261 2
6q26 7.3969e-27 5.5863e-24 chr6:161693099-163153207 1
3q26.31 2.7783e-22 5.1413e-22 chr3:174345545-175760559 3
2q22.1 7.3719e-27 1.3676e-20 chr2:140708948-143637838 2
1p36.11 2.3847e-20 2.8844e-18 chr1:26963410-27127934 4
8p23.2 4.8219e-13 4.7153e-13 chr8:2112968-4251283 2
10q23.31 4.8192e-17 1.1201e-10 chr10:89506488-90034038 6
19p13.3 2.361e-10 2.3337e-10 chr19:2697647-3363200 17
21q11.2 9.5108e-12 6.1573e-10 chr21:1-15609812 14
11q25 2.5401e-09 2.5401e-09 chr11:133400280-135006516 11
7q36.3 8.0904e-25 1.1102e-08 chr7:157210222-158385117 3
4q34.3 8.6808e-26 2.3909e-08 chr4:179280062-186321446 36
11p15.5 4.3307e-07 4.3299e-07 chr11:2441018-2892511 2
15q11.2 1.1671e-06 1.1848e-06 chr15:1-27218028 56
3p26.2 1.4507e-14 1.5603e-06 chr3:3220635-4535479 3
2q33.3 2.4322e-14 2.0364e-06 chr2:204826225-206558638 1
17p12 5.0764e-06 5.2535e-06 chr17:11866892-12456081 4
Xq21.33 1.4808e-06 6.6313e-06 chrX:96134519-99356556 3
1p13.2 5.3792e-07 8.6283e-05 chr1:112530734-119426205 65
18q12.2 4.5297e-13 0.00016298 chr18:36593175-39537209 2
17q24.3 0.00025002 0.00025318 chr17:70116519-70642789 2
10q22.3 1.3263e-08 0.00029052 chr10:77312101-78597839 4
14q23.3 6.8752e-05 0.00062472 chr14:66963153-67658112 1
2q37.2 2.7321e-11 0.0014369 chr2:235913227-237102098 3
21q22.13 1.9584e-05 0.0020022 chr21:38638578-38997673 1
12p13.1 0.0030457 0.003101 chr12:7033593-19287837 160
16p13.3 4.0807e-05 0.0044419 chr16:5144019-7780235 2
1q44 5.024e-06 0.0051042 chr1:245290228-245913707 1
6q16.3 5.3634e-05 0.0051042 chr6:76782316-116787016 188
1q44 8.6571e-07 0.0080733 chr1:245868364-247052144 6
2q32.1 5.9295e-12 0.010041 chr2:187373995-187560595 1
10p15.3 0.0059629 0.014948 chr10:1-857150 8
3q11.1 1.2548e-06 0.026146 chr3:90078624-93767487 3
9q21.11 0.00062217 0.026146 chr9:38619152-71322791 58
16p13.3 2.5925e-05 0.034602 chr16:1-766484 42
12q23.1 0.038071 0.037261 chr12:99119269-100424312 3
Xp22.2 2.5567e-07 0.045073 chrX:9891764-11137490 3
4p15.2 0.010947 0.051583 chr4:20726855-22351071 1
Xp11.3 1.9264e-05 0.052787 chrX:44702452-45008304 2
4p16.3 0.011116 0.06192 chr4:1-5053961 75
22q11.1 0.047688 0.086496 chr22:1-18218209 21
10p11.21 0.054447 0.11785 chr10:34059131-35328087 1
Xq11.2 0.010614 0.11785 chrX:63002762-64136373 5
13q14.2 0.00026302 0.17401 chr13:48875329-49064807 2
13q12.11 0.00024975 0.18557 chr13:1-23727991 46
10q21.1 0.0035782 0.19585 chr10:52644085-54077929 4
13q21.31 0.0035991 0.19585 chr13:55747586-70276983 32
19q13.11 0.19585 0.19585 chr19:31198022-36216055 77
14q32.32 0.0089633 0.20521 chr14:96009749-107349540 200
22q13.31 0.14318 0.24114 chr22:45402127-51304566 71
Genes in Wide Peak

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

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

Genes
PIH1
Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53
Genes in Wide Peak

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

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

Genes
RN7SKP248
Genes in Wide Peak

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

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

Genes
FKSG52
MIR582
Genes in Wide Peak

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

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

Genes
FOXC1
GMDS
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
U3|ENSG00000212211.1
NPCDR1
Genes in Wide Peak

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

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

Genes
MIR3915
RNA5SP501
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238922.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
RNA5SP475
FLRT3
Genes in Wide Peak

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

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

Genes
RN7SL695P
SMAD4
ELAC1
Genes in Wide Peak

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

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

Genes
RN7SL5P
SNORD27|ENSG00000251699.1
Genes in Wide Peak

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

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

Genes
PARK2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

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

Genes
snoU13|ENSG00000271842.1
MIR4789
RN7SKP40
Genes in Wide Peak

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

Table S48.  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 1p36.11.

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

Genes
ARID1A
RN7SL501P
snoU13|ENSG00000238316.1
PIGV
Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
ATAD1
KLLN
Genes in Wide Peak

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

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

Genes
GNA11
ZNF554
AES
GNA15
SGTA
THOP1
TLE2
S1PR4
SLC39A3
NCLN
ZNF77
CELF5
TLE6
ZNF556
ZNF57
DIRAS1
ZNF555
Genes in Wide Peak

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

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

Genes
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
TPTE
RBM11
LIPI
POTED
MIR3687
Genes in Wide Peak

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

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

Genes
IGSF9B
NCAPD3
ACAD8
B3GAT1
THYN1
JAM3
GLB1L2
VPS26B
GLB1L3
SPATA19
MIR4697
Genes in Wide Peak

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

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

Genes
MIR595
PTPRN2
MIR5707
Genes in Wide Peak

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

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

Genes
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
ENPP6
RWDD4
CCDC111
HELT
CLDN24
MIR1305
MIR3945
MIR4455
Genes in Wide Peak

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

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

Genes
KCNQ1OT1
KCNQ1
Genes in Wide Peak

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

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

Genes
LINC00929
SNORA48|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64|ENSG00000270704.2
SNHG14
SNURF
snoU13|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13|ENSG00000239083.1
CHEK2P2
RN7SL584P
GABRA5
GABRB3
NDN
SNRPN
UBE3A
MKRN3
CYFIP1
NPAP1
NIPA2
TUBGCP5
NIPA1
GOLGA6L2
HERC2P3
GOLGA6L1
GOLGA8I
GOLGA8EP
OR4M2
POTEB2
MIR4508
POTEB
Genes in Wide Peak

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

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

Genes
SETMAR
LRRN1
SUMF1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q33.3.

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

Genes
PARD3B
Genes in Wide Peak

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

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

Genes
MAP2K4
MIR744
RPL21P122
ZNF18
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
SNORA25|ENSG00000252296.1
RN7SL74P
RPA4
Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
AMPD1
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD58
IGSF3
MOV10
NGF
NHLH2
PTGFRN
SLC16A1
SYCP1
TSHB
CSDE1
CD101
TSPAN2
BCAS2
AP4B1
PHTF1
PTPN22
RSBN1
GDAP2
FAM46C
ST7L
SLC22A15
CTTNBP2NL
OLFML3
DCLRE1B
VTCN1
SIKE1
TRIM45
VANGL1
MAB21L3
SYT6
SPAG17
HIPK1
MAGI3
FAM19A3
PPM1J
C1orf137
MIR320B1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

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

Genes
LINC00669
RN7SKP182
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

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

Genes
LINC00511
SOX9
Genes in Wide Peak

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

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

Genes
SNORA31|ENSG00000252888.1
RN7SL518P
MIR606
C10orf11
Genes in Wide Peak

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

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

Genes
GPHN
Genes in Wide Peak

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

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

Genes
RN7SL204P
GBX2
AGAP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.13.

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

Genes
DYRK1A
Genes in Wide Peak

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

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

Genes
ETV6
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
C1R
SCARNA12
A2M
APOBEC1
ARHGDIB
C1S
C3AR1
CD69
CDKN1B
CREBL2
ATN1
PHC1
EMP1
EPS8
GPR19
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PTPN6
PTPRO
PEX5
PZP
SLC2A3
MFAP5
KLRC4
YBX3
CD163
GDF3
CLSTN3
LPCAT3
KLRG1
EMG1
KLRAP1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
NECAP1
CLEC4E
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
NANOG
APOLD1
GSG1
RBP5
RERG
PLCZ1
CAPZA3
CLEC6A
C12orf57
LOH12CR1
TMEM52B
HIST4H4
SLC2A14
A2ML1
CLEC12A
CLECL1
CLEC4C
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CD163L1
CLEC9A
C12orf36
CLEC4D
ACSM4
TAS2R42
DPPA3
NANOGNB
CLEC2A
CLEC12B
LINC00937
MIR141
MIR200C
ZNF705A
SMCO3
PRB2
MIR614
SLC15A5
Genes in Wide Peak

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

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

Genes
SNORA40|ENSG00000252138.1
RBFOX1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q44.

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

Genes
KIF26B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.3.

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

Genes
PRDM1
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
snoU13|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18|ENSG00000252249.1
U3|ENSG00000221455.1
U3|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73|ENSG00000222145.1
RN7SL183P
snoU13|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70|ENSG00000206886.1
RNA5SP210
SNORD112|ENSG00000252932.1
HTR1B
U6|ENSG00000272445.1
AIM1
AMD1
BCKDHB
CCNC
CGA
CNR1
COL10A1
EPHA7
FOXO3
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1E
LAMA4
MARCKS
ME1
NT5E
PGM3
POU3F2
PREP
REV3L
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
PNISR
IBTK
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
FAM46A
RARS2
PDSS2
SMIM8
LYRM2
SNX14
HACE1
BEND3
RRAGD
BACH2
C6orf164
MICAL1
MANEA
GPR63
SPACA1
SH3BGRL2
ARMC2
MCHR2
FAXC
GJA10
USP45
SLC22A16
UBE3D
GTF3C6
MRAP2
KLHL32
SLC16A10
RIPPLY2
IRAK1BP1
PM20D2
SRSF12
C6orf165
PRSS35
LCA5
C6orf163
AK9
HS3ST5
LACE1
MMS22L
CEP57L1
PPIL6
GJB7
LIN28B
FAM26F
RFPL4B
FAM229B
MIR587
METTL24
MIR2113
MIR4464
MIR4643
MIR548AI
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q44.

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

Genes
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
SCCPDH
TFB2M
SMYD3
CNST
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q32.1.

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

Genes
ITGAV
Genes in Wide Peak

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

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

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

This is the comprehensive list of deleted genes in the wide peak for 3q11.1.

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

Genes
U3|ENSG00000212598.1
PROS1
STX19
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.11.

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

Genes
CBWD3
PGM5P2
RNA5SP284
SNORA70|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
PGM5
ZNF658
SPATA31A7
CNTNAP3
ANKRD20A1
TMEM252
CBWD5
FOXD4L3
FOXD4L4
SPATA31A6
FAM74A4
ANKRD20A3
ANKRD20A2
FAM27A
SPATA31A2
SPATA31A4
CBWD6
SPATA31A1
FOXD4L6
FOXD4L5
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR4477A
Genes in Wide Peak

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

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

Genes
MIR3176
MIR5587
ITFG3
HBZ
SNRNP25
POLR3K
WASIR2
WASH4P
DDX11L10
ARHGDIG
HBA1
HBA2
HBM
HBQ1
MPG
NME4
CAPN15
NPRL3
AXIN1
RGS11
RHBDL1
PIGQ
RAB11FIP3
STUB1
MRPL28
DECR2
LUC7L
RAB40C
TMEM8A
RHBDF1
PDIA2
ITFG3
WDR24
C16orf13
FAM195A
RHOT2
WFIKKN1
C16orf11
FBXL16
WDR90
NHLRC4
JMJD8
Genes in Wide Peak

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

Table S80.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RNA5SP366
ANKS1B
FAM71C
Genes in Wide Peak

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

Table S81.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CLCN4
MID1
WWC3
Genes in Wide Peak

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

Table S82.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
KCNIP4
Genes in Wide Peak

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

Table S83.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
KDM6A
DUSP21
Genes in Wide Peak

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

Table S84.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR3
WHSC1
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
CTBP1
DGKQ
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
MSX1
MYL5
PDE6B
RGS12
RNF4
SH3BP2
NELFA
SLBP
NOP14
FAM193A
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
NSG1
STX18
FGFRL1
CYTL1
PIGG
LYAR
UVSSA
ZFYVE28
TNIP2
HAUS3
MFSD7
TMEM175
TMEM128
TMEM129
OTOP1
FAM53A
ZBTB49
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
MIR4800
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.1.

Table S85.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13|ENSG00000251737.1
RN7SL843P
CECR9
CECR3
CECR7
HSFY1P1
TPTEP1
KCNMB3P1
OR11H1
POTEH
ATP6V1E1
IL17RA
BCL2L13
CECR6
CECR5
CECR2
CECR1
SLC25A18
GAB4
CCT8L2
XKR3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

Table S86.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PARD3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq11.2.

Table S87.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL799P
MTMR8
AMER1
ASB12
MIR1468
Genes in Wide Peak

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

Table S88.  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 13q12.11.

Table S89.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RNY3P4
LINC00621
SNORD36|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27|ENSG00000252128.1
snoU13|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
FGF9
GJA3
GJB2
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
LATS2
CRYL1
IL17D
MPHOSPH8
XPO4
MRP63
TPTE2
N6AMT2
SKA3
MICU2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.1.

Table S90.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MIR605
PRKG1
DKK1
CSTF2T
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.31.

Table S91.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13|ENSG00000238455.1
PCDH9
PCDH17
PCDH20
TDRD3
DIAPH3
PRR20A
PRR20B
PRR20C
PRR20D
PRR20E
MIR3169
MIR4704
MIR548X2
MIR5007
Genes in Wide Peak

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

Table S92.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CEBPA
RN7SL765P
RN7SL491P
GPR42
MIR5196
HAMP
LINC00904
SNORD111|ENSG00000252230.1
SCGB1B2P
WTIP
RN7SL154P
RN7SL150P
LRP3
C19orf40
RN7SKP22
RN7SL789P
SNORA68|ENSG00000201388.1
RNA5SP472
RNA5SP471
THEG5
ATP4A
CD22
CEBPG
COX6B1
ETV2
GPI
FFAR1
FFAR3
FFAR2
HPN
MAG
PEPD
FXYD1
FXYD3
SCN1B
USF2
PDCD5
KIAA0355
UBA2
TMEM147
UPK1A
SLC7A9
ZNF507
HAUS5
LSM14A
GAPDHS
ZBTB32
LSR
FXYD7
FXYD5
GPATCH1
ZNF302
SLC7A10
TSHZ3
GRAMD1A
CHST8
KCTD15
RBM42
ANKRD27
PDCD2L
CEP89
RHPN2
ZNF30
TDRD12
DMKN
WDR88
ZNF792
DPY19L3
ZNF599
FAM187B
LGI4
SCGB2B2
ZNF181
SBSN
RGS9BP
KRTDAP
NUDT19
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.32.

Table S93.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
AKT1
TCL1A
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
BDKRB1
BDKRB2
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
BRF1
HSP90AA1
JAG2
KLC1
MARK3
PPP2R5C
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DLK1
MTA1
BAG5
C14orf2
CDC42BPB
TCL1B
TECPR2
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
GPR132
EVL
GSKIP
CINP
CDCA4
ATG2B
ZNF839
BEGAIN
INF2
ZFYVE21
WDR25
TMEM121
AMN
SETD3
HHIPL1
BTBD6
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
PLD4
ADSSL1
SLC25A29
NUDT14
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
ASPG
C14orf64
RTL1
TMEM179
C14orf180
MIR127
MIR136
MIR154
MIR203
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1197
MIR1193
MIR4309
MIR151B
MIR4710
MIR2392
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

Table S94.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
ACR
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
MIOX
TRMU
PANX2
CERK
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 28 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 0.14 -1.57 1 0.19 2.07 0.0392
1q 1195 0.27 6.04 3.94e-09 0.13 -2.6 1
2p 624 0.23 -1.4 1 0.09 -8.42 1
2q 967 0.19 -0.886 1 0.10 -5.78 1
3p 644 0.14 -4.93 1 0.37 6.73 3.48e-11
3q 733 0.30 3.11 0.00421 0.23 -0.535 1
4p 289 0.10 -7.98 1 0.47 8.92 0
4q 670 0.08 -7.58 1 0.43 10.4 0
5p 183 0.29 -1.17 1 0.31 0.131 0.875
5q 905 0.10 -5.38 1 0.37 9.15 0
6p 710 0.21 -1.57 1 0.19 -2.53 1
6q 556 0.19 -3.85 1 0.22 -2.31 1
7p 389 0.50 11.8 0 0.14 -5.68 1
7q 783 0.44 12 0 0.15 -3.68 1
8p 338 0.49 9 0 0.46 7.48 1.96e-13
8q 551 0.58 17.2 0 0.24 -0.826 1
9p 301 0.19 -4.52 1 0.46 8.7 0
9q 700 0.23 -0.815 1 0.35 5.9 6.31e-09
10p 253 0.25 -2.55 1 0.26 -2.27 1
10q 738 0.18 -2.89 1 0.23 -0.233 1
11p 509 0.18 -4.45 1 0.24 -1.5 1
11q 975 0.19 -0.713 1 0.24 2.22 0.0283
12p 339 0.27 -1.26 1 0.22 -3.64 1
12q 904 0.20 -0.542 1 0.17 -2.5 1
13q 560 0.38 6.05 3.94e-09 0.24 -1.05 1
14q 938 0.16 -2.59 1 0.29 4.49 1.15e-05
15q 810 0.14 -4.66 1 0.27 2.42 0.0175
16p 559 0.19 -3.42 1 0.31 2.72 0.00826
16q 455 0.17 -4.88 1 0.32 2.53 0.0138
17p 415 0.13 -6.29 1 0.43 8.01 3.25e-15
17q 972 0.19 -0.622 1 0.20 -0.362 1
18p 104 0.29 -1.56 1 0.40 3.87 0.000149
18q 275 0.18 -4.69 1 0.49 9.74 0
19p 681 0.14 -4.94 1 0.35 6.07 2.33e-09
19q 935 0.22 0.285 1 0.29 4.43 1.39e-05
20p 234 0.59 14.9 0 0.18 -4.74 1
20q 448 0.63 19.7 0 0.08 -6.72 1
21q 258 0.11 -7.76 1 0.49 10 0
22q 564 0.16 -4.73 1 0.39 6.94 8.82e-12
Xp 418 0.11 -8.28 1 0.24 -1.93 1
Xq 668 0.16 -4.51 1 0.19 -3 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/STES-TP/14521231/GDAC_MergeDataFiles_14524132/STES-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 625 Input Tumor Samples.

Tumor Sample Names
TCGA-2H-A9GF-01A-11D-A37B-01
TCGA-2H-A9GH-01A-11D-A37B-01
TCGA-2H-A9GI-01A-11D-A37B-01
TCGA-2H-A9GJ-01A-11D-A37B-01
TCGA-2H-A9GK-01A-11D-A37B-01
TCGA-2H-A9GL-01A-12D-A37B-01
TCGA-2H-A9GM-01A-11D-A37B-01
TCGA-2H-A9GN-01A-11D-A37B-01
TCGA-2H-A9GO-01A-11D-A37B-01
TCGA-2H-A9GQ-01A-11D-A37B-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)