SNP6 Copy number analysis (GISTIC2)
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
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 (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1K35T1N
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 1090 tumor samples used in this analysis: 27 significant arm-level results, 30 significant focal amplifications, and 45 significant focal deletions were found.

Results
Focal results

Figure 1.  Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1.  Get Full Table Amplifications Table - 30 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
7p11.2 0 0 chr7:54964317-54973195 1
12q14.1 3.5024e-192 8.2598e-167 chr12:58135797-58152580 4
4q12 2.2587e-126 2.2587e-126 chr4:55139083-55158044 2
1q32.1 1.0232e-94 1.0873e-93 chr1:204443069-204529807 2
12q15 7.2016e-75 1.7848e-26 chr12:69178021-69265277 3
12p13.32 1.88e-24 1.88e-24 chr12:4277010-4432075 2
3q26.33 3.4238e-23 3.4238e-23 chr3:181256574-181508514 1
8q24.21 1.9283e-12 1.9283e-12 chr8:127927022-131296766 22
7q31.2 3.0786e-14 2.4366e-11 chr7:116318088-116493406 2
2p24.3 2.0395e-09 2.0395e-09 chr2:16015911-16358714 4
17q25.1 3.483e-07 3.483e-07 chr17:73270907-73596428 8
1q44 1.8403e-07 7.5268e-07 chr1:243003523-244858016 10
17p13.2 5.0804e-06 5.0804e-06 chr17:5120021-5142747 1
19p13.3 6.5163e-06 6.5163e-06 chr19:713557-827048 7
13q34 1.552e-05 1.552e-05 chr13:109765147-110444337 3
7q21.2 4.0153e-09 4.8822e-05 chr7:92179103-92530348 2
1p36.21 5.1944e-05 5.1944e-05 chr1:13862648-14377937 4
4p16.3 0.00010315 0.00010315 chr4:1778797-1816689 2
7q32.3 4.6764e-09 0.0019694 chr7:129605835-131642364 22
11q24.1 0.0036642 0.0036642 chr11:118074060-123443121 79
10p15.1 0.0041195 0.0041195 chr10:1-6398978 55
Xp11.21 0.0048849 0.0048849 chrX:53647932-56536223 29
7q11.21 6.4539e-11 0.016504 chr7:57925000-63128930 2
1q22 0.0015739 0.039876 chr1:156119131-156752580 29
19q13.2 0.024565 0.065617 chr19:39363864-39953130 27
5p15.33 0.073651 0.073651 chr5:1019815-1314315 7
11p13 0.083141 0.083141 chr11:31372873-32350255 7
14q32.33 0.086431 0.086431 chr14:104982904-105333748 10
9q34.3 0.13918 0.13918 chr9:140012419-141213431 36
19q12 0.025734 0.17887 chr19:30036025-30321189 5
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 12p13.32.

Table S6.  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 3q26.33.

Table S7.  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 8q24.21.

Table S8.  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
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 7q31.2.

Table S9.  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 2p24.3.

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

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

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

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

Genes
MYO15B
GRB2
LLGL2
KIAA0195
CASKIN2
SLC25A19
TSEN54
MIR3678
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 17p13.2.

Table S13.  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 19p13.3.

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

Genes
MIR4745
AZU1
PALM
PTBP1
LPPR3
MISP
MIR3187
Genes in Wide Peak

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

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

Genes
LINC00676
IRS2
MYO16
Genes in Wide Peak

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

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

Genes
CDK6
FAM133B
Genes in Wide Peak

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

Table S17.  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 4p16.3.

Table S18.  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 7q32.3.

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

Genes
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
CPA1
CPA2
MEST
MKLN1
PODXL
KLHDC10
CPA4
ZC3HC1
TMEM209
CPA5
CEP41
TSGA13
KLF14
SSMEM1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q24.1.

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

Genes
DDX6
CBL
ARHGEF12
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
ARCN1
CD3D
CD3E
DPAGT1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
MCAM
KMT2A
PVRL1
SORL1
TECTA
UPK2
USP2
UBE4A
MPZL2
HYOU1
ATP5L
TREH
PHLDB1
TRIM29
POU2F3
TRAPPC4
VPS11
CRTAM
IFT46
GRAMD1B
ABCG4
RNF26
NLRX1
CLMP
PDZD3
C11orf63
MFRP
TMEM25
UBASH3B
C1QTNF5
AMICA1
TMEM136
FOXR1
CCDC153
CCDC84
BSX
MIRLET7A2
MIR100
MIR125B1
BLID
MIR4493
MIR4492
Genes in Wide Peak

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

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

Genes
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
CALML3
AKR1C4
KLF6
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
PFKFB3
PFKP
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
ASB13
TUBAL3
AKR1E2
FBXO18
RBM17
IDI2
UCN3
LINC00200
PRR26
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.21.

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

Genes
SNORD112|ENSG00000252961.1
APEX2
SNORA11|ENSG00000221750.1
SNORA11|ENSG00000221716.1
GNL3L
U3|ENSG00000252175.1
RNA5SP505
ALAS2
FGD1
PFKFB1
TRO
HUWE1
RRAGB
MAGED2
KLF8
PHF8
MAGEH1
FAM120C
WNK3
TSR2
FAM104B
PAGE5
FOXR2
PAGE3
USP51
PAGE2
ITIH6
PAGE2B
MTRNR2L10
Genes in Wide Peak

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

Table S23.  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 1q22.

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

Genes
PRCC
snoU13|ENSG00000238843.1
BGLAP
SNORA26|ENSG00000252236.1
CRABP2
HDGF
MEF2D
CCT3
SLC25A44
C1orf61
NES
PMF1
SMG5
RRNAD1
GPATCH4
RHBG
HAPLN2
BCAN
SEMA4A
MRPL24
PAQR6
ISG20L2
TMEM79
C1orf85
TSACC
IQGAP3
APOA1BP
TTC24
VHLL
Genes in Wide Peak

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

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

Genes
RN7SL566P
IFNL4
snoU13|ENSG00000251709.1
NFKBIB
MRPS12
RPS16
SUPT5H
ZFP36
GMFG
PAK4
SIRT2
PAF1
SARS2
SAMD4B
MED29
LRFN1
PLEKHG2
FBXO17
RINL
FBXO27
IFNL2
IFNL3
IFNL1
NCCRP1
SYCN
PAPL
MIR4530
Genes in Wide Peak

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

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

Genes
MIR4635
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
MIR4457
Genes in Wide Peak

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

Table S27.  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 S28.  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 9q34.3.

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

Genes
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
CACNA1B
GRIN1
SSNA1
TUBB4B
NOXA1
NELFB
NSMF
NDOR1
ANAPC2
TOR4A
EXD3
EHMT1
C9orf37
ARRDC1
DPH7
TMEM203
ZMYND19
SLC34A3
TPRN
PNPLA7
C9orf169
ENTPD8
LRRC26
FAM166A
C9orf173
NRARP
MIR602
RNF208
Genes in Wide Peak

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

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

Genes
C19orf12
POP4
CCNE1
PLEKHF1
VSTM2B

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 - 45 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 chr9:21141750-23690570 24
10q23.31 3.5011e-65 2.8255e-58 chr10:89617158-89755074 3
11p15.1 3.2059e-49 3.7874e-38 chr11:16623557-16799846 1
1p36.23 2.8133e-59 5.6823e-35 chr1:7908902-8336254 4
6q26 1.1187e-34 5.2953e-29 chr6:163736503-164264583 3
10q26.3 3.8214e-42 1.0861e-28 chr10:135190263-135214343 1
4q34.3 2.4436e-25 2.4436e-25 chr4:179280062-182757119 4
19q13.41 1.7885e-35 1.2507e-24 chr19:51323233-53037389 68
13q14.2 1.7867e-30 5.1266e-20 chr13:48875329-49064807 2
1p32.3 2.2461e-20 4.0844e-16 chr1:50879767-51529064 4
2q37.1 5.8558e-14 8.5809e-14 chr2:233547367-233727481 2
22q13.32 6.3081e-11 5.9424e-11 chr22:48026910-51304566 42
15q14 1.3527e-10 1.3204e-10 chr15:33485762-47478056 169
5q34 8.5822e-10 8.5822e-10 chr5:161581324-166712758 5
14q13.1 1.4385e-10 3.619e-09 chr14:33297556-34394000 1
11p15.5 2.673e-13 4.1148e-08 chr11:1-3819266 100
3q29 1.5626e-09 1.1445e-07 chr3:190596953-197066709 64
13q22.1 1.9552e-16 9.1993e-07 chr13:67772598-75859094 24
14q24.2 1.0951e-16 3.8219e-06 chr14:69196549-77583215 102
8p23.2 1.038e-05 1.017e-05 chr8:2112968-4251283 2
1p36.32 2.7779e-35 2.0626e-05 chr1:3814904-6475685 13
12q12 1.3585e-07 2.5305e-05 chr12:42028480-46578647 21
17q11.2 2.8056e-05 2.8238e-05 chr17:29326736-29722618 5
17p13.1 9.4379e-05 9.4637e-05 chr17:7528230-7591760 3
3p21.31 0.00016309 0.00015774 chr3:47049863-47272884 2
3q13.31 3.4893e-05 0.0002898 chr3:115440285-118620828 7
19q13.43 6.9341e-31 0.00030828 chr19:55426781-59128983 141
12p13.1 0.00043096 0.00043856 chr12:12710990-13338025 14
2q22.1 0.0017068 0.002111 chr2:140708948-143637838 2
5p15.33 0.0041237 0.0042285 chr5:1-7048226 44
18q23 0.0043619 0.0042815 chr18:65181982-78077248 46
6q22.31 4.8365e-08 0.015401 chr6:111216911-147834826 202
16p12.2 0.03549 0.03549 chr16:20579968-27090703 64
10p15.3 0.0041397 0.040277 chr10:1048399-2048902 5
Xq21.1 0.046153 0.046153 chrX:76710176-77102528 1
1q42.11 0.0013326 0.046941 chr1:212280115-227085461 99
1q44 0.0030753 0.052248 chr1:245868364-247355463 12
10p13 0.023139 0.065031 chr10:12616863-12768978 2
8q24.3 0.081942 0.081942 chr8:144486368-146364022 75
16q23.1 0.092802 0.091922 chr16:73093053-90354753 166
11p11.2 0.014706 0.098302 chr11:45945772-46626256 7
1p22.1 0.0022649 0.10397 chr1:92706523-94028812 19
14q31.3 5.9729e-10 0.11807 chr14:69196549-107349540 417
12q15 0.002277 0.15799 chr12:67711731-69082595 7
6p25.3 0.16831 0.16831 chr6:1-13548164 89
Genes in Wide Peak

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

Table S31.  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
IFNA4
IFNA5
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
MTAP
C9orf53
IFNE
MIR31
Genes in Wide Peak

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

Table S32.  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 11p15.1.

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

Genes
C11orf58
Genes in Wide Peak

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

Table S34.  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 S35.  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 10q26.3.

Table S36.  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 4q34.3.

Table S37.  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 19q13.41.

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

Genes
PPP2R1A
KLK2
MIR643
snoU13|ENSG00000238630.1
HCCAT3
FPR1
snoU13|ENSG00000238486.1
SIGLEC5
CEACAM18
SIGLEC22P
SIGLEC17P
KLK13
KLK9
KLKP1
KLK3
CD33
SIGLEC6
ETFB
FPR2
FPR3
HAS1
LIM2
NKG7
KLK7
KLK6
KLK10
ZNF175
SIGLEC5
KLK4
ZNF432
KLK11
KLK8
KLK5
SIGLEC7
SIGLEC9
SIGLEC8
KLK14
KLK12
KLK15
ZNF350
ZNF649
ZNF613
ZNF614
ZNF528
ZNF577
SIGLEC10
SIGLEC12
ZNF616
ZNF766
CTU1
CLDND2
VSIG10L
LINC00085
ZNF480
ZNF534
ZNF578
ZNF836
ZNF610
KLK9
SIGLECL1
ZNF615
ZNF841
ZNF880
IGLON5
MIRLET7E
MIR125A
MIR99B
SIGLEC14
Genes in Wide Peak

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

Table S39.  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 1p32.3.

Table S40.  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 2q37.1.

Table S41.  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 22q13.32.

Table S42.  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 15q14.

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

Genes
BUB1B
FKSG62
RN7SKP101
SNORD11|ENSG00000238819.1
SNORA41|ENSG00000207516.1
HMGN2P46
snoU13|ENSG00000238583.1
SLC30A4
SNORA11|ENSG00000261709.2
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
GATM
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
RYR3
SPINT1
SRP14
TP53BP1
TYRO3
EIF3J
SNAP23
SLC28A2
TGM5
PPIP5K1
AQR
LCMT2
RASGRP1
GPR176
CHP1
OIP5
BAHD1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
SERF2
TMEM87A
RPAP1
BLOC1S6
RPUSD2
TUBGCP4
EHD4
DUOX2
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
PPP1R14D
ZNF770
HAUS2
RMDN3
DNAJC17
NOP10
EMC7
PAK6
CASC5
AVEN
STARD9
VPS18
SQRDL
ZNF106
SPATA5L1
CHAC1
KATNBL1
WDR76
TMEM62
SPG11
ELL3
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
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
DUOXA2
GOLGA8B
EIF2AK4
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4510
Genes in Wide Peak

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

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

Genes
RN7SKP60
NUDCD2
CCNG1
HMMR
MAT2B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q13.1.

Table S45.  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 11p15.5.

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

Genes
CARS
HRAS
NUP98
snoU13|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
ART1
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
RNH1
MRPL23
TALDO1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
TRPM5
BET1L
CEND1
CDHR5
TOLLIP
PIDD
KCNQ1DN
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
SYT8
OSBPL5
LRRC56
MRGPRE
ART5
SCGB1C1
NLRP6
C11orf35
EFCAB4A
ANO9
B4GALNT4
PDDC1
MRGPRG
IFITM5
FAM99A
IFITM10
MIR210
MUC5B
MIR4298
MIR4686
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

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

Genes
TFRC
snoU13|ENSG00000238491.1
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
MIR570
Genes in Wide Peak

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

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

Genes
LINC00347
LINC00381
RNY1P5
LINC00402
LINC00392
LINC00393
RNY1P8
SNORA9|ENSG00000199282.1
SNORA68|ENSG00000251715.1
SNORD37|ENSG00000212377.1
RNA5SP32
LINC00348
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
KLF5
DACH1
PIBF1
KLF12
DIS3
KLHL1
BORA
MZT1
Genes in Wide Peak

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

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

Genes
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
ACTN1
ACYP1
ZFP36L1
DLST
ESRRB
FOS
LTBP2
MAP3K9
ALDH6A1
PGF
PSEN1
ABCD4
SRSF5
SLC8A3
DPF3
NUMB
ADAM21
ADAM20
DCAF5
EIF2B2
PNMA1
RGS6
KIAA0247
AREL1
MED6
BATF
NPC2
ACOT2
TMED10
VASH1
PCNX
TTLL5
ANGEL1
TTC9
SIPA1L1
DCAF4
MLH3
COQ6
FCF1
COX16
ZFYVE1
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
YLPM1
GALNT16
ZNF410
RBM25
SMOC1
IRF2BPL
ZC2HC1C
CCDC176
DNAL1
RPS6KL1
PAPLN
ELMSAN1
NEK9
IFT43
JDP2
PTGR2
FAM161B
C14orf166B
PROX2
VSX2
HEATR4
PLEKHD1
ACOT1
ACOT6
SYNDIG1L
MIR4505
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 1p36.32.

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

Genes
RPL22
LINC00337
KCNAB2
ACOT7
ICMT
CHD5
AJAP1
NPHP4
GPR153
RNF207
HES3
MIR4689
MIR4417
Genes in Wide Peak

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

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

Genes
SCAF11
RN7SL246P
RNA5SP361
SNORA74|ENSG00000252917.1
RN7SL10P
RNA5SP360
NELL2
TWF1
YAF2
PLEKHA8P1
IRAK4
PPHLN1
ADAMTS20
PUS7L
TMEM117
ZCRB1
PRICKLE1
ANO6
ARID2
GXYLT1
DBX2
Genes in Wide Peak

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

Table S53.  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 17p13.1.

Table S54.  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 3p21.31.

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

Genes
SETD2
snoU13|ENSG00000251938.1
Genes in Wide Peak

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

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

Genes
LINC00901
TUSC7
RN7SL582P
LINC00903
RN7SL815P
LSAMP
MIR4447
Genes in Wide Peak

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

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

Genes
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13|ENSG00000239137.1
A1BG
IL11
PEG3
PTPRH
RPL28
RPS5
AURKC
TNNI3
TNNT1
ZNF8
ZNF17
MZF1
ZNF132
ZNF135
ZNF154
UBE2M
TRIM28
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
SLC27A5
U2AF2
PPP6R1
ZIM2
HSPBP1
ZNF324
CHMP2A
ZNF544
UBE2S
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
NLRP2
ZNF416
ZNF446
NAT14
VN1R1
ZNF304
ZNF471
USP29
ZNF667
ZSCAN18
RPL23AP79
ZSCAN5A
ZNF329
ZNF419
ISOC2
ZNF552
ZNF671
ZNF606
BRSK1
SUV420H2
ZBTB45
ZNF587
FIZ1
GALP
ZNF628
ZNF551
ZNF835
RDH13
ZIM3
ZNF837
ZNF543
COX6B2
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
C19orf18
ZNF418
TMEM190
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
ZNF497
ZNF550
ZNF579
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
DNAAF3
ZNF773
ZNF470
ZNF749
ZNF324B
ZNF772
SBK2
SHISA7
SGK110
ZNF587B
ZNF865
MIR4754
Genes in Wide Peak

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

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

Genes
HTR7P1
SNORD88
GPRC5A
MIR613
CDKN1B
CREBL2
GPR19
HEBP1
DDX47
GPRC5D
KIAA1467
APOLD1
GSG1
MIR614
Genes in Wide Peak

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

Table S59.  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 5p15.33.

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

Genes
RNA5SP176
RN7SKP79
UBE2QL1
RN7SKP73
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIP13
PDCD6
SLC12A7
PAPD7
TPPP
EXOC3
KIAA0947
IRX4
NSUN2
CEP72
AHRR
MRPL36
BRD9
IRX1
ZDHHC11
LPCAT1
CLPTM1L
MED10
NKD2
C5orf55
C5orf38
IRX2
ADAMTS16
SLC6A19
SLC6A18
MIR4277
MIR4457
MIR4456
Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
CYB5A
MBP
NFATC1
ZNF236
CTDP1
SOCS6
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
GTSCR1
DOK6
LINC00908
ATP9B
LINC00909
HSBP1L1
C18orf63
Genes in Wide Peak

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

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

Genes
MYB
ROS1
TNFAIP3
GOPC
STXBP5
RNA5SP222
FBXO30
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
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
MAP3K5
NMBR
ENPP1
ENPP3
PEX7
PLAGL1
PLN
PKIB
PTPRK
REV3L
SGK1
TCF21
TPD52L1
UTRN
EPM2A
WISP3
VNN2
VNN1
TAAR5
MAP7
TAAR2
MED23
AKAP7
PHACTR2
BCLAF1
TRDN
CITED2
TRAF3IP2
HBS1L
SMPDL3A
RAB32
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
ADGB
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
SHPRH
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 16p12.2.

Table S63.  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 10p15.3.

Table S64.  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 Xq21.1.

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

Genes
ATRX
Genes in Wide Peak

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

Table S66.  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
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
NSL1
RPS6KC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
KCTD3
MARC2
SUSD4
GPATCH2
TMEM206
BATF3
IARS2
ENAH
SMYD2
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 1q44.

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

Genes
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
ZNF124
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 10p13.

Table S68.  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 8q24.3.

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

Genes
RECQL4
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
CYC1
EEF1D
GPT
GRINA
HSF1
TONSL
PLEC
RPL8
TSTA3
ZNF7
ZNF16
GPAA1
FOXH1
LRRC14
ZNF623
PUF60
ZC3H3
BOP1
SCRIB
FBXL6
OPLAH
COMMD5
CPSF1
CYHR1
VPS28
FAM203A
EXOSC4
SLC39A4
ZNF250
PYCRL
C8orf33
SLC52A2
GSDMD
ARHGAP39
ZNF34
SHARPIN
SCRT1
MAF1
PARP10
TIGD5
PPP1R16A
ZNF251
KIFC2
NAPRT1
MFSD3
ADCK5
MAPK15
ZNF707
FAM83H
NRBP2
ZNF517
KIAA1875
TMEM249
SPATC1
MAFA
LRRC24
MROH6
MROH1
FAM203B
MIR4664
Genes in Wide Peak

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

Table S70.  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
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
KARS
MC1R
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
VPS9D1
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
CFDP1
PRDM7
GABARAPL2
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
BANP
RFWD3
ZDHHC7
CENPN
JPH3
VAT1L
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNRF1
CNTNAP4
CENPBD1
ZNF276
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
TMEM170A
SLC38A8
ADAD2
ZFP1
ADAMTS18
LDHD
MLKL
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
FAM92B
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 11p11.2.

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

Genes
CREB3L1
MIR4688
PHF21A
CHRM4
MDK
DGKZ
AMBRA1
Genes in Wide Peak

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

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

Genes
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
GFI1
RPL5
EVI5
GLMN
MTF2
TMED5
FNBP1L
CCDC18
FAM69A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.3.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
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
SERPINA3
ACTN1
ACYP1
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF5
EML1
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
ATXN3
MAP3K9
ALDH6A1
SERPINA5
PGF
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSEN1
PSMC1
ABCD4
MOK
SEL1L
SRSF5
SLC8A3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
AREL1
TECPR2
MED6
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
SNW1
PCNX
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
TTC9
FLRT2
SIPA1L1
DCAF4
KIF26A
TMEM251
MLH3
GPR132
POMT2
COQ6
FCF1
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
GALNT16
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
SMOC1
MOAP1
IRF2BPL
INF2
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
AMN
SLIRP
DNAL1
RPS6KL1
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
ELMSAN1
NEK9
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
GSC
SERPINA12
PRIMA1
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
SYNE3
EML5
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
SERPINA9
VSX2
COX8C
ASPG
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
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
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
MIR4505
MIR151B
MIR4710
MIR2392
Genes in Wide Peak

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

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

Genes
SNORA70G
DYRK2
IFNG
RAP1B
IL22
IL26
MDM1
Genes in Wide Peak

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

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

Genes
IRF4
PHACTR1
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CDYL
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
TBC1D7
NRN1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
SMIM13
SYCP2L
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
PSMG4
C6orf201
PPP1R3G
TMEM170B
MIR4645
MIR5689
MIR5683
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 27 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 0.11 2.03 0.109 0.20 12.7 0
1q 1195 0.11 2.08 0.109 0.05 -4.61 1
2p 624 0.05 -5.38 1 0.05 -4.7 1
2q 967 0.04 -5.41 1 0.05 -4.42 1
3p 644 0.07 -3.34 1 0.07 -2.95 1
3q 733 0.07 -2.77 1 0.06 -3.75 1
4p 289 0.05 -5.51 1 0.12 2.35 0.0225
4q 670 0.04 -5.88 1 0.15 5.6 3.11e-08
5p 183 0.06 -4.75 1 0.08 -2.49 1
5q 905 0.05 -4.86 1 0.08 -1.69 1
6p 710 0.03 -6.54 1 0.11 1.86 0.061
6q 556 0.03 -6.75 1 0.18 8.79 0
7p 389 0.55 49.1 0 0.02 -5.66 1
7q 783 0.58 54.9 0 0.02 -5.5 1
8p 338 0.10 -0.24 1 0.08 -2.52 1
8q 551 0.11 1.42 0.322 0.06 -4.47 1
9p 301 0.08 -2.34 1 0.31 22.7 0
9q 700 0.10 -0.0441 1 0.15 5.49 5.41e-08
10p 253 0.13 1.95 0.117 0.55 47.7 0
10q 738 0.01 -6.43 1 0.55 51.1 0
11p 509 0.05 -4.67 1 0.16 6.18 1.08e-09
11q 975 0.07 -2.08 1 0.11 2.3 0.0246
12p 339 0.09 -1.36 1 0.09 -1.27 1
12q 904 0.06 -3.5 1 0.11 1.94 0.0538
13q 560 0.02 -7.57 1 0.28 20.1 0
14q 938 0.03 -6.44 1 0.21 13.7 0
15q 810 0.04 -5.84 1 0.15 5.86 7.48e-09
16p 559 0.05 -4.96 1 0.08 -2.25 1
16q 455 0.05 -4.65 1 0.10 0.432 0.62
17p 415 0.07 -3.52 1 0.08 -1.89 1
17q 972 0.08 -1.03 1 0.05 -4.42 1
18p 104 0.08 -2.64 1 0.14 3.61 0.000385
18q 275 0.08 -2.59 1 0.12 2.14 0.0351
19p 681 0.31 23.3 0 0.08 -1.48 1
19q 935 0.26 16.9 0 0.28 19.5 0
20p 234 0.25 15.8 0 0.03 -6.6 1
20q 448 0.25 15.9 0 0.03 -7 1
21q 258 0.09 -1.58 1 0.08 -2.53 1
22q 564 0.07 -3.12 1 0.23 14.7 0
Xp 418 0.03 -6.77 1 0.21 11.7 0
Xq 668 0.06 -3.9 1 0.17 8.33 0
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

  • Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBMLGG-TP/22217773/GDAC_MergeDataFiles_12184422/GBMLGG-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/gistic/CNV/SNP6.merged.151117.hg19.CNV.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 1090 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)