SNP6 Copy number analysis (GISTIC2)
Glioblastoma Multiforme (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
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/C1VQ31W8
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 577 tumor samples used in this analysis: 25 significant arm-level results, 25 significant focal amplifications, and 46 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 - 25 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
7p11.2 0 0 chr7:54964317-54973195 1
12q14.1 1.9251e-150 8.9579e-124 chr12:58135797-58152580 4
4q12 4.6936e-106 4.6936e-106 chr4:55139083-55159166 2
1q32.1 5.0601e-76 7.513e-76 chr1:204443069-204529807 2
12q15 8.296e-75 1.3168e-31 chr12:69178021-69260755 3
3q26.33 1.5076e-20 1.5076e-20 chr3:181256574-181508514 1
12p13.32 5.0468e-11 5.0468e-11 chr12:4325317-4436676 2
19p13.2 1.0528e-11 3.8819e-10 chr19:7300056-7398264 0 [INSR]
7q31.2 3.2182e-08 5.8541e-08 chr7:116318088-116493406 2
17p13.2 1.5137e-07 1.5137e-07 chr17:5120021-5142747 1
2p24.3 2.0133e-07 2.0133e-07 chr2:16015911-16440790 5
1p36.21 1.156e-06 1.156e-06 chr1:13862648-14377937 4
1q44 3.6883e-07 1.9876e-06 chr1:243042268-244858016 10
7q21.2 5.0451e-08 3.1843e-06 chr7:92179103-92530348 2
4p16.3 0.00047406 0.00047406 chr4:1778797-1816689 2
7q11.21 5.7574e-12 0.0023197 chr7:57925000-63128930 2
17q25.1 0.0028237 0.0028237 chr17:73242158-73641051 13
19q12 0.0098935 0.0098935 chr19:30211822-30321189 1
11p13 0.026814 0.026814 chr11:31372873-32350255 7
14q32.33 0.070543 0.070543 chr14:104982904-105333748 10
8q24.21 0.10689 0.10689 chr8:127927022-131800277 23
21q21.1 0.17192 0.17192 chr21:17519797-17649826 1
19p13.3 0.04476 0.17648 chr19:1-1064484 40
13q34 0.015631 0.18465 chr13:103076946-114304134 69
13q34 0.011133 0.43029 chr13:113916990-114583289 12
Genes in Wide Peak

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

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

Genes
[SNORA73|ENSG00000252054.1]
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
TSPAN31
MARCH9
AGAP2
Genes in Wide Peak

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

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

Genes
PDGFRA
FIP1L1
Genes in Wide Peak

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

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

Genes
MDM4
PIK3C2B
Genes in Wide Peak

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

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

Genes
MDM2
SLC35E3
CPM
Genes in Wide Peak

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

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

Genes
SOX2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
CCND2
C12orf5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.2.

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

Genes
MET
CAPZA2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p13.2.

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

Genes
SCIMP
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.3.

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

Genes
MYCN
SNORA40|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13|ENSG00000238371.1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.21.

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

Genes
SCARNA11|ENSG00000253085.1
RNA5SP41
PRDM2
PDPN
Genes in Wide Peak

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

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

Genes
RN7SL148P
MIR4677
ADSS
CEP170
AKT3
ZBTB18
SDCCAG8
DESI2
C1orf100
C1orf101
Genes in Wide Peak

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

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

Genes
CDK6
FAM133B
Genes in Wide Peak

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

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

Genes
FGFR3
LETM1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q11.21.

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

Genes
RN7SL855P
ZNF733P
Genes in Wide Peak

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

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

Genes
MYO15B
GRB2
LLGL2
RECQL5
KIAA0195
GGA3
MRPS7
MIF4GD
CASKIN2
SLC25A19
TSEN54
SMIM5
MIR3678
Genes in Wide Peak

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

Table S17.  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 11p13.

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

Genes
U3|ENSG00000212551.1
DNAJC24
PAX6
RCN1
ELP4
IMMP1L
DCDC1
Genes in Wide Peak

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

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

Genes
AKT1
LINC00638
ZBTB42
SIVA1
INF2
ADSSL1
CEP170B
TMEM179
C14orf180
MIR4710
Genes in Wide Peak

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

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

Genes
MYC
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
ADCY8
ASAP1
FAM49B
GSDMC
MIR1205
MIR1207
PVT1
MIR1208
MIR3686
MIR5194
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q21.1.

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

Genes
LINC00478
Genes in Wide Peak

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

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

Genes
FSTL3
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
AZU1
HCN2
BSG
CDC34
CNN2
ELANE
GZMM
PALM
POLRMT
PRTN3
PTBP1
MADCAM1
PPAP2C
MED16
ABCA7
SHC2
FGF22
THEG
MIER2
RNF126
WDR18
LPPR3
KISS1R
R3HDM4
TMEM259
TPGS1
GRIN3B
MISP
C2CD4C
ODF3L2
PRSS57
MIR3187
Genes in Wide Peak

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

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

Genes
ERCC5
DCUN1D2
LINC00403
LINC00404
SNORD44
LINC00354
LINC00346
LINC00567
snoU13|ENSG00000238629.1
RN7SL783P
RN7SKP10
LINC00676
RNA5SP39
MIR1267
SNORD31
LINC00443
LINC00551
ARGLU1
LINC00460
RNA5SP38
SNORA25|ENSG00000252550.1
LINC00344
LINC00343
METTL21EP
RNY5P8
LINC00283
CCDC168
snoU13|ENSG00000238869.1
LINC00555
ATP4B
COL4A1
COL4A2
EFNB2
F7
F10
ING1
LAMP1
LIG4
SLC10A2
SOX1
TFDP1
TPP2
CUL4A
IRS2
PROZ
ARHGEF7
TUBGCP3
TNFSF13B
MYO16
ATP11A
MCF2L
BIVM
TMCO3
ANKRD10
RAB20
CARKD
PCID2
KDELC1
CARS2
GRTP1
ABHD13
TEX30
ADPRHL1
TEX29
SPACA7
METTL21C
DAOA
C13orf35
FAM155A
Genes in Wide Peak

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

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

Genes
LINC00454
GRK1
DCUN1D2
ATP4B
GAS6
LAMP1
TFDP1
CUL4A
TMCO3
GRTP1
ADPRHL1
TMEM255B

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 - 46 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
9p21.3 0 0 chr9:21227468-23690570 18
10q23.31 6.5075e-64 1.1173e-60 chr10:89617158-89755074 3
1p36.23 2.112e-58 2.9977e-43 chr1:7908902-8336254 4
6q26 1.1419e-34 3.0061e-30 chr6:163736503-164264583 3
13q14.2 1.5865e-26 7.5581e-20 chr13:48875329-49064807 2
10q26.3 1.3777e-26 2.0282e-18 chr10:135190263-135214343 1
19q13.41 2.3326e-15 2.4075e-15 chr19:51485195-51915080 21
1p32.3 2.2509e-15 2.0343e-12 chr1:50879767-51529064 4
15q14 4.1062e-12 4.1062e-12 chr15:33485762-45387898 149
22q13.32 7.681e-12 7.708e-12 chr22:48668761-51304566 42
14q13.1 4.5717e-13 9.0946e-12 chr14:33297556-34394000 1
4q34.3 1.4106e-09 1.4106e-09 chr4:179280062-182757119 4
8p23.2 5.3602e-06 5.4067e-06 chr8:3548028-4251283 2
17q11.2 6.061e-06 6.0544e-06 chr17:29326736-29722618 5
3q29 1.2778e-06 1.0171e-05 chr3:190375525-197029425 64
17p13.1 8.3636e-08 1.8159e-05 chr17:7528230-7591760 3
5q34 0.00011797 0.00011797 chr5:161581324-167461839 6
14q24.2 1.7751e-07 0.00042775 chr14:63563582-107349540 467
13q22.1 3.1605e-12 0.00065317 chr13:50260906-77685049 111
1p36.32 1.9107e-26 0.00073911 chr1:3394251-6475685 25
18q22.3 0.0012434 0.0012522 chr18:67995567-74327801 22
10p13 0.00018022 0.0013541 chr10:12616863-12768978 2
1p22.1 5.4067e-06 0.001372 chr1:92759774-93924485 16
6q22.31 1.1517e-07 0.0035699 chr6:111216911-145822991 194
12q12 0.00027855 0.0043565 chr12:42982652-46578647 13
11p15.5 0.0034885 0.0048153 chr11:1-6616814 192
10p15.3 0.00089427 0.0049686 chr10:1048399-2048902 5
16p12.2 0.0056968 0.0056968 chr16:20579968-27090703 64
12p13.1 0.0061918 0.0062776 chr12:8674063-19587581 125
10p11.23 0.0012397 0.0067858 chr10:29862242-30302313 2
2q37.1 0.0056321 0.0074476 chr2:233547367-233727481 2
2q22.1 0.0066412 0.0074476 chr2:140708948-143637838 2
Xp22.2 0.011821 0.011619 chrX:11792056-12637668 1
1q42.11 0.00054159 0.012508 chr1:211999806-227178961 105
16q23.1 0.023518 0.023162 chr16:70833950-90354753 191
17p13.2 3.4239e-06 0.027412 chr17:3851656-4048080 3
1q44 0.0067699 0.052883 chr1:245868364-247276929 11
3p21.1 0.057562 0.057562 chr3:41280645-56593629 279
11p11.2 0.030569 0.063887 chr11:37721288-56013797 116
9q34.2 0.070978 0.070491 chr9:136602059-136892308 1
12q15 0.0040275 0.070491 chr12:58369934-69140499 53
3q13.31 0.0014696 0.075256 chr3:114035080-123801471 73
4p16.3 0.084987 0.083726 chr4:1197147-1284820 1
21q21.1 0.11399 0.11313 chr21:1-26575481 41
3q22.1 4.0076e-05 0.14722 chr3:129610672-129871534 3
11q14.1 0.15631 0.17201 chr11:78285273-81604120 4
Genes in Wide Peak

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

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

Genes
DMRTA1
RN7SL151P
SNORD39|ENSG00000264379.1
MIR31HG
IFNA6
KLHL9
CDKN2A
CDKN2B
IFNA1
IFNA2
IFNA5
IFNA8
IFNA13
IFNA14
MTAP
C9orf53
IFNE
MIR31
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
RN7SL729P
TNFRSF9
PARK7
ERRFI1
Genes in Wide Peak

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

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

Genes
RN7SL366P
CAHM
QKI
Genes in Wide Peak

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

Table S29.  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 10q26.3.

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

Genes
PAOX
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.41.

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

Genes
SIGLEC22P
SIGLEC17P
KLK13
KLK9
CD33
ETFB
LIM2
NKG7
KLK10
KLK11
KLK8
SIGLEC7
SIGLEC9
KLK14
KLK12
CTU1
CLDND2
VSIG10L
KLK9
SIGLECL1
IGLON5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p32.3.

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

Genes
CDKN2C
MIR4421
FAF1
DMRTA2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q14.

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

Genes
BUB1B
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13|ENSG00000238494.1
snoU13|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13|ENSG00000238564.1
THBS1
FAM98B
U3|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18|ENSG00000252425.1
SLC12A6
TMCO5B
ACTC1
CAPN3
CHRM5
CKMT1B
EPB42
GANC
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
RYR3
SPINT1
SRP14
TP53BP1
TYRO3
EIF3J
SNAP23
TGM5
PPIP5K1
AQR
LCMT2
RASGRP1
GPR176
CHP1
OIP5
BAHD1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
SERF2
TMEM87A
RPAP1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
DLL4
INO80
PPP1R14D
ZNF770
HAUS2
RMDN3
DNAJC17
NOP10
EMC7
PAK6
CASC5
AVEN
STARD9
VPS18
ZNF106
CHAC1
KATNBL1
WDR76
TMEM62
SPG11
ELL3
C15orf41
ZFYVE19
FRMD5
DISP2
DPH6
C15orf57
KNSTRN
BMF
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
NUTM1
PLA2G4D
C15orf52
C15orf53
C15orf54
GOLGA8B
EIF2AK4
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4510
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 14q13.1.

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

Genes
NPAS3
Genes in Wide Peak

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

Table S36.  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 8p23.2.

Table S37.  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 17q11.2.

Table S38.  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 3q29.

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

Genes
TFRC
MIR4797
U4|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
RN7SL36P
MIR3137
LINC00884
LINC00887
RN7SL215P
RN7SL447P
snoU13|ENSG00000238902.1
RN7SKP222
APOD
CPN2
DLG1
FGF12
GP5
HES1
MFI2
MUC4
OPA1
PAK2
PCYT1A
PPP1R2
TNK2
NCBP2
ACAP2
PIGX
LSG1
HRASLS
ATP13A3
PIGZ
ATP13A4
CEP19
TMEM44
TM4SF19
ZDHHC19
LRRC15
FAM43A
MB21D2
XXYLT1
CCDC50
PYDC2
RNF168
SLC51A
FBXO45
MUC20
SENP5
TCTEX1D2
SMCO1
UTS2B
OSTN
ATP13A5
WDR53
NRROS
LINC00885
GMNC
MIR570
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

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

Genes
TP53
ATP1B2
SAT2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q34.

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

Genes
SNORA40|ENSG00000253065.1
RN7SKP60
NUDCD2
CCNG1
HMMR
MAT2B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.2.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
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
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
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
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5C
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
SEL1L
SRSF5
SLC8A3
SPTB
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
AREL1
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
MLH3
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
EVL
GSKIP
CINP
ASB2
ZFYVE1
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
RHOJ
GALNT16
PLEKHH1
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
SMOC1
MOAP1
IRF2BPL
MPP5
INF2
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
RDH12
GSC
SERPINA12
PRIMA1
PPP1R36
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SYNE3
EML5
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
SERPINA9
VSX2
COX8C
ASPG
RAB15
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
LINC00238
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4505
MIR4708
MIR151B
MIR4710
MIR2392
MIR5694
Genes in Wide Peak

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

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

Genes
CLN5
RN7SL571P
LINC00561
C13orf45
LINC00347
LINC00381
RNY1P5
LINC00402
LINC00392
LINC00393
RNY1P8
SNORA9|ENSG00000199282.1
SNORA68|ENSG00000251715.1
SNORD37|ENSG00000212377.1
RNA5SP32
LINC00348
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
ATP7B
KLF5
DACH1
GUCY1B2
KPNA3
LMO7
NEK3
PCDH8
PCDH9
UCHL3
UTP14C
TBC1D4
TRIM13
DLEU1
PIBF1
OLFM4
LECT1
KLF12
DIS3
FBXL3
INTS6
CKAP2
PCDH17
VPS36
THSD1
SPRYD7
KLHL1
PCDH20
RNASEH2B
DHRS12
BORA
TDRD3
DIAPH3
CCDC70
KCTD12
WDFY2
PRR20A
HNRNPA1L2
COMMD6
FAM124A
KCNRG
NEK5
DLEU2
ALG11
MZT1
SERPINE3
PRR20B
PRR20C
PRR20D
PRR20E
IRG1
MIR759
MIR3169
MIR3613
MIR4704
MIR548X2
MIR4703
MIR5007
MIR5693
Genes in Wide Peak

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

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

Genes
RPL22
LINC00337
RN7SL574P
MIR551A
MEGF6
DFFB
TP73
KCNAB2
CEP104
ACOT7
ICMT
CHD5
WRAP73
AJAP1
LRRC47
TPRG1L
CCDC27
NPHP4
C1orf174
GPR153
SMIM1
RNF207
HES3
MIR4689
MIR4417
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.3.

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

Genes
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
CYB5A
TSHZ1
TIMM21
ZNF407
CNDP2
NETO1
CNDP1
FAM69C
CBLN2
FBXO15
GTSCR1
LINC00908
LINC00909
C18orf63
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p13.

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

Genes
MIR4480
MIR548Q
Genes in Wide Peak

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

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

Genes
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
GFI1
RPL5
EVI5
MTF2
TMED5
CCDC18
FAM69A
Genes in Wide Peak

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

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

Genes
MYB
ROS1
TNFAIP3
GOPC
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
ARG1
COL10A1
CTGF
EPB41L2
EYA4
FABP7
FUCA2
FYN
GJA1
HDAC2
HIVEP2
HSF2
IFNGR1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
MAP3K5
NMBR
ENPP1
ENPP3
PEX7
PLAGL1
PLN
PKIB
PTPRK
REV3L
SGK1
TCF21
TPD52L1
UTRN
WISP3
VNN2
VNN1
TAAR5
MAP7
TAAR2
MED23
AKAP7
PHACTR2
BCLAF1
TRDN
CITED2
TRAF3IP2
HBS1L
SMPDL3A
TSPYL4
HEY2
ASF1A
CCDC28A
MOXD1
PDE7B
DSE
HDDC2
TUBE1
RWDD1
AIG1
HECA
IL20RA
AHI1
VNN3
ECHDC1
GPR126
KIAA1244
NHSL1
SERINC1
ABRACL
PBOV1
TRMT11
PERP
ALDH8A1
OR2A4
FAM184A
RNF146
SF3B5
TAAR8
L3MBTL3
LTV1
REPS1
ARHGAP18
GTF3C6
MTFR2
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAAR9
TAAR1
NCOA7
HINT3
ZC2HC1B
SAMD3
RNF217
NKAIN2
OLIG3
TXLNB
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
TMEM244
MCM9
DCBLD1
TAAR6
SLC35D3
RSPH4A
ECT2L
C6orf58
CENPW
SOGA3
CEP85L
THEMIS
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR588
TRAPPC3L
MIR3144
MIR3668
SMLR1
MIR4465
MIR548AJ1
MIR548H5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q12.

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

Genes
SCAF11
RN7SL246P
RNA5SP361
NELL2
TWF1
PLEKHA8P1
IRAK4
ADAMTS20
PUS7L
TMEM117
ANO6
ARID2
DBX2
Genes in Wide Peak

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

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

Genes
CARS
HRAS
NUP98
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62|ENSG00000201980.1
OR51C1P
SNORA7|ENSG00000206976.1
snoU13|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
CNGA4
CTSD
DRD4
DUSP8
HBB
HBD
HBE1
HBG2
HPX
IGF2
INS
IRF7
KCNQ1
LSP1|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
RNH1
MRPL23
RRM1
SMPD1
TRIM21
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IFITM2
TRIM3
PKP3
SIRT3
OR52A1
ARFIP2
TIMM10B
PGAP2
TRPM5
UBQLN3
BET1L
CEND1
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
FAM160A2
TRIM5
SYT8
PRKCDBP
OSBPL5
LRRC56
MRGPRE
ART5
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR52W1
OR56A4
OR56A1
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
DNHD1
SCGB1C1
C11orf42
NLRP6
OR56B4
OR52B2
C11orf35
OR51F1
OR51V1
EFCAB4A
ANO9
B4GALNT4
OR52L1
OR52B6
PDDC1
MRGPRG
IFITM5
FAM99A
OR56B1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
MUC5B
MIR4298
MIR4686
MIR4687
Genes in Wide Peak

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

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

Genes
ADARB2
IDI1
WDR37
IDI2
LINC00200
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p12.2.

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

Genes
PALB2
C16orf82
RNA5SP405
MIR548W
RN7SL557P
SNORA1|ENSG00000201541.1
DCTN5
SNORA75|ENSG00000212593.1
RN7SKP23
RN7SL245P
snoU13|ENSG00000239172.1
SMG1P1
RRN3P3
EEF2K
SDR42E2
snoU13|ENSG00000238712.1
NPIPB4
RRN3P1
SCARNA6|ENSG00000252798.1
snoU13|ENSG00000238954.1
NPIPB3
DCUN1D3
AQP8
CDR2
CRYM
NDUFAB1
PLK1
PRKCB
RBBP6
ACSM3
SCNN1B
SCNN1G
UQCRC2
ZP2
HS3ST4
HS3ST2
IGSF6
CACNG3
ERN2
GGA2
TNRC6A
METTL9
LCMT1
ARHGAP17
DNAH3
THUMPD1
POLR3E
UBFD1
TMEM159
LYRM1
USP31
CHP2
COG7
ERI2
SLC5A11
ACSM1
EARS2
VWA3A
OTOA
PDZD9
ANKS4B
ZKSCAN2
C16orf52
NPIPB5
Genes in Wide Peak

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

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

Genes
ETV6
RN7SL67P
RN7SL459P
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
A2M
ARHGDIB
CD69
CDKN1B
CREBL2
PHC1
EMP1
EPS8
GPR19
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PTPRO
PZP
MFAP5
KLRC4
YBX3
KLRG1
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
CLEC4E
TAS2R9
TAS2R7
TAS2R13
TAS2R10
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
PLEKHA5
MANSC1
STYK1
GPRC5D
ATF7IP
H2AFJ
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
RERGL
APOLD1
GSG1
RERG
PLCZ1
CAPZA3
LOH12CR1
TMEM52B
HIST4H4
A2ML1
CLEC12A
CLECL1
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CLEC9A
C12orf36
TAS2R42
CLEC2A
CLEC12B
SMCO3
PRB2
MIR614
SLC15A5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.23.

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

Genes
SNORD115|ENSG00000212411.1
MIR938
Genes in Wide Peak

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

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

Genes
KCNJ13
GIGYF2
Genes in Wide Peak

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

Table S56.  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 Xp22.2.

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

Genes
7SK|ENSG00000271814.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.11.

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

Genes
RN7SKP165
snoU13|ENSG00000239094.1
snoU13|ENSG00000238545.1
MIR4742
snoU13|ENSG00000238856.1
MIR320B2
SNORA72|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
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
PARP1
ATF3
CAPN2
CENPF
EPHX1
EPRS
ESRRG
H3F3A
ITPKB
KCNK2
LBR
MARK1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
SRP9
TGFB2
LEFTY2
TLR5
TP53BP2
USH2A
DEGS1
TAF1A
TMEM63A
BPNT1
LEFTY1
DUSP10
FBXO28
RAB3GAP2
INTS7
NSL1
RPS6KC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
KCTD3
DTL
MARC2
SUSD4
GPATCH2
TMEM206
BATF3
IARS2
ENAH
SMYD2
ADCK3
ACBD3
MARC1
AIDA
C1orf115
HHIPL2
VASH2
WDR26
MIXL1
DISP1
ANGEL2
LYPLAL1
DNAH14
TATDN3
BROX
CNIH3
C1orf227
FAM71A
SDE2
C1orf65
LIN9
MIA3
C1orf95
FAM177B
MIR215
Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13|ENSG00000239186.1
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
MIR3182
RN7SL134P
snoU13|ENSG00000238321.1
RN7SKP190
7SK|ENSG00000260682.2
MIR4720
GAN
PKD1L2
CMC2
RNA5SP431
PIH1
MON1B
SNORD33|ENSG00000252022.1
RN7SKP233
RNA5SP430
RN7SL520P
ADAT1
CHST6
SNORA76|ENSG00000252122.1
GLG1
NPIPB15
HCCAT5
PKD1L3
IST1
SNORD71
SNORA70D
TAT
SNORD112|ENSG00000251700.1
RNU6ATAC25P
AP1G1
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
ZNF19
ZNF23
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
VPS9D1
KIAA0513
PIEZO1
DHX38
ATP2C2
CLEC3A
CHST4
MPHOSPH6
EMC8
TUBB3
CFDP1
PRDM7
GABARAPL2
TCF25
PHLPP2
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
TXNL4B
BANP
RFWD3
ZNF821
ZDHHC7
FTSJD1
CENPN
JPH3
VAT1L
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNRF1
CNTNAP4
MARVELD3
CENPBD1
ZNF276
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
TMEM170A
SLC38A8
ADAD2
ZFP1
ADAMTS18
LDHD
MLKL
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
FAM92B
ATXN1L
CTU2
C16orf47
PABPN1L
C16orf74
CTRB2
CLEC18B
SYCE1L
MIR1910
C16orf95
MIR4719
MIR5093
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.2.

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

Genes
snoU13|ENSG00000238807.1
RNA5SP434
ZZEF1
Genes in Wide Peak

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

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

Genes
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
AHCTF1
SCCPDH
ZNF695
TFB2M
SMYD3
ZNF669
CNST
C1orf229
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.1.

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

Genes
BAP1
SETD2
PBRM1
RNA5SP133
RN7SKP45
MIR3938
ESRG
CHDH
SNORD63|ENSG00000251987.1
SNORA26|ENSG00000212608.1
SNORD38|ENSG00000207109.1
RN7SL821P
snoU13|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19|ENSG00000222345.1
SNORD19B|ENSG00000238862.1
SNORD19|ENSG00000212493.1
SNORD19B|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13|ENSG00000238350.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000251938.1
PRSS44
PRSS45
SNORD77|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
U8|ENSG00000212145.2
RN7SKP58
SCARNA21|ENSG00000252409.1
ALAS1
AMT
APEH
RHOA
CACNA1D
SLC25A20
CAMP
CCK
CDC25A
CISH
CCR1
CCR3
CCR5
ACKR2
COL7A1
CYP8B1
DAG1
DOCK3
DUSP7
CELSR3
GNAI2
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
NKTR
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
MANF
HYAL3
HYAL2
BSN
ACKR5
SEC22C
RRP9
CACNA2D2
IP6K1
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CCR9
USP19
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
EXOSC7
RAD54L2
STAB1
NBEAL2
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
PTPN23
DNAH1
ERC2
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
C3orf18
SS18L2
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
ELP6
SNRK
QRICH1
ULK4
ANO10
DALRD3
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZKSCAN7
SEMA3G
KIF15
PCBP4
LRTM1
KIAA1143
HHATL
SELK
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
WDR82
ATRIP
NICN1
MON1A
ABHD14B
GTDC2
UCN2
ZNF502
RFT1
ACTR8
ZNF501
GPR62
LYZL4
KLHL40
TMEM42
IQCF1
GLYCTK
PPM1M
LSMEM2
CCDC12
CCDC13
KLHDC8B
ALS2CL
TMIE
FBXW12
TCAIM
CCDC36
PRSS42
ZNF445
TOPAZ1
TMEM110
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
MIR425
SPINK8
ARIH2OS
C3orf84
FAM198A
CCR2
PRSS46
MIR4271
KRBOX1
MIR4787
MIR4443
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p11.2.

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

Genes
DDB2
EXT2
CREB3L1
TRIM51HP
TRIM49B
OR4C5
MIR3161
RNA5SP340
snoU13|ENSG00000252447.1
KBTBD4
PTPMT1
RN7SL652P
RN7SL772P
SNORD67|ENSG00000212135.1
SNORD67|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
PHF21A
CHST1
CD82
C11orf96
RN7SKP287
HNRNPKP3
SNORA31|ENSG00000251838.1
ACP2
ARHGAP1
CHRM4
CRY2
F2
FOLH1
LRP4
MDK
MYBPC3
NDUFS3
PSMC3
PTPRJ
RAPSN
SPI1
DGKZ
API5
MADD
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
NR1H3
CELF1
OR5I1
NUP160
FNBP4
MTCH2
OR5L2
PACSIN3
HSD17B12
SLC35C1
AMBRA1
KBTBD4
TTC17
PRDM11
SYT13
LRRC4C
ALX4
C11orf49
TRIM48
ZNF408
AGBL2
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
ARFGAP2
ACCS
TRIM51
TSPAN18
SLC39A13
C1QTNF4
OR4C46
OR4X2
OR4B1
GYLTL1B
OR8I2
C11orf94
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR5AS1
OR8K5
OR5T2
ALKBH3
OR4C3
OR4S1
OR10AG1
OR5J2
OR4C13
OR4C12
OR5F1
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
FAM180B
OR4A47
TRIM64C
MIR670
MIR4487
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.2.

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

Genes
VAV2
Genes in Wide Peak

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

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

Genes
HMGA2
WIF1
SNORA70G
DYRK2
CAND1
snoU13|ENSG00000238528.1
RN7SKP166
TMBIM4
RNA5SP362
RPSAP52
RNU6ATAC42P
snoU13|ENSG00000238592.1
MIR548C
SNORD83
XPOT
snoU13|ENSG00000238440.1
RPS11P6
AVPR1A
LDHAL6CP
snoU13|ENSG00000238475.1
SNORD112|ENSG00000252883.1
SNORA19|ENSG00000251822.1
RN7SKP65
GNS
IFNG
RAP1B
SLC16A7
USP15
TMEM5
IRAK3
MON2
TBC1D30
GRIP1
LEMD3
TBK1
IL22
TMBIM4
IL26
MDM1
NUP107
PPM1H
SRGAP1
LLPH
HELB
C12orf56
LRIG3
C12orf66
MSRB3
RASSF3
C12orf61
DPY19L2
FAM19A2
MIRLET7I
Genes in Wide Peak

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

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

Genes
SNORA5
PTPLB
SEC22A
snoU13|ENSG00000238480.1
SNORD112|ENSG00000252170.1
RN7SL172P
snoU13|ENSG00000238670.1
ARGFX
MIR5682
FSTL1
RN7SL397P
RN7SL762P
COX17
TIMMDC1
LINC00901
TUSC7
RN7SL582P
LINC00903
RN7SL815P
ADCY5
ADPRH
CASR
CD80
CD86
CSTA
GAP43
GOLGB1
GSK3B
GTF2E1
HCLS1
HGD
KPNA1
LSAMP
MYLK
NDUFB4
SLC15A2
UPK1B
B4GALT4
NR1I2
STXBP5L
IQCB1
POLQ
PDIA5
ZBTB20
FAM162A
PLA1A
FBXO40
SEMA5B
WDR5B
PARP14
ROPN1
TMEM39A
EAF2
POGLUT1
ARHGAP31
POPDC2
CCDC14
HSPBAP1
PARP9
DIRC2
MAATS1
LRRC58
CCDC58
DTX3L
IGSF11
C3orf30
PARP15
GPR156
RABL3
ILDR1
MIR568
MIR4796
MIR4447
Genes in Wide Peak

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

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

Genes
CTBP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

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

Genes
RNA5SP489
7SK|ENSG00000232512.2
RN7SL609P
LINC00308
LINC00317
LINC00320
RN7SKP147
RN7SL163P
SNORD74|ENSG00000201025.1
snoU13|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
C21orf91
SAMSN1
CHODL
LIPI
ABCC13
POTED
LINC00478
MIRLET7C
MIR125B2
MIR99A
MIR548X
MIR3687
C21orf37
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q22.1.

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

Genes
FAM86HP
ALG1L2
TRH
Genes in Wide Peak

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

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

Genes
TENM4
MIR708
MIR4300
MIR5579
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 25 significant results found. The significance cutoff is at Q value=0.25.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 1300 0.15 4.27 4.98e-05 0.03 -4.68 1
1q 1195 0.16 5.06 1.24e-06 0.03 -4.87 1
2p 624 0.07 -3.04 1 0.06 -3.42 1
2q 967 0.06 -2.9 1 0.06 -2.9 1
3p 644 0.11 0.0245 1 0.08 -2.01 1
3q 733 0.12 1.03 0.62 0.07 -2.82 1
4p 289 0.07 -3.29 1 0.10 -0.692 1
4q 670 0.06 -3.53 1 0.11 0.178 0.8
5p 183 0.09 -1.91 1 0.08 -2.15 1
5q 905 0.08 -1.85 1 0.08 -1.46 1
6p 710 0.05 -4.18 1 0.16 4.02 8.63e-05
6q 556 0.05 -3.9 1 0.23 8.96 0
7p 389 0.82 54.1 0 0.07 -1.25 1
7q 783 0.83 57 0 0.06 -1.5 1
8p 338 0.10 -0.963 1 0.11 0.0272 0.872
8q 551 0.11 -0.0619 1 0.08 -1.7 1
9p 301 0.12 0.353 1 0.38 19.9 0
9q 700 0.14 2.62 0.0198 0.19 6.3 5.49e-10
10p 253 0.14 0.761 0.763 0.86 55.6 0
10q 738 0.02 -2.37 1 0.86 59.4 0
11p 509 0.03 -5.27 1 0.18 5.31 1.77e-07
11q 975 0.02 -5.48 1 0.17 5.42 1e-07
12p 339 0.11 -0.219 1 0.12 0.524 0.616
12q 904 0.09 -0.915 1 0.11 0.908 0.392
13q 560 0.02 -5.39 1 0.33 17 0
14q 938 0.05 -3.41 1 0.26 12.7 0
15q 810 0.05 -3.71 1 0.19 6.87 1.43e-11
16p 559 0.07 -2.72 1 0.12 0.94 0.392
16q 455 0.07 -2.6 1 0.16 3.4 0.000916
17p 415 0.09 -1.71 1 0.13 1.41 0.192
17q 972 0.11 0.807 0.763 0.08 -1.42 1
18p 104 0.11 -0.357 1 0.14 1.7 0.114
18q 275 0.11 -0.0259 1 0.12 0.466 0.626
19p 681 0.41 23 0 0.08 -1.26 1
19q 935 0.36 20.3 0 0.10 -0.051 0.889
20p 234 0.40 21.1 0 0.05 -3.57 1
20q 448 0.39 21.4 0 0.05 -3.75 1
21q 258 0.12 0.461 1 0.08 -2.25 1
22q 564 0.08 -1.54 1 0.33 17.1 0
Xp 418 0.03 -5.49 1 0.20 7.12 2.79e-12
Xq 668 0.03 -5.06 1 0.19 6.43 2.66e-10
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/GBM-TP/19076722/GDAC_MergeDataFiles_12184181/GBM-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 577 Input Tumor Samples.

Tumor Sample Names
TCGA-02-0001-01C-01D-0182-01
TCGA-02-0003-01A-01D-0182-01
TCGA-02-0006-01B-01D-0182-01
TCGA-02-0007-01A-01D-0182-01
TCGA-02-0009-01A-01D-0182-01
TCGA-02-0010-01A-01D-0182-01
TCGA-02-0011-01B-01D-0182-01
TCGA-02-0014-01A-01D-0182-01
TCGA-02-0015-01A-01G-0293-01
TCGA-02-0016-01A-01G-0293-01

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)