Glioblastoma Multiforme: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16a (cga svn revision 43808).

Summary

There were 563 tumor samples used in this analysis: 22 significant arm-level results, 23 significant focal amplifications, and 51 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 - 23 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 | 0 [EGFR]
12q14.1 | 2.6822e-146 | 3.4837e-119 | chr12:58135797-58152580 | 4
4q12 | 3.8415e-103 | 3.8415e-103 | chr4:55139083-55159166 | 1
1q32.1 | 3.2661e-70 | 4.208e-70 | chr1:204443069-204529807 | 2
12q15 | 2.3945e-75 | 2.1128e-32 | chr12:69178021-69265277 | 2
3q26.33 | 7.6889e-21 | 7.6889e-21 | chr3:181256574-181508514 | 2
19p13.2 | 1.0258e-12 | 1.0258e-12 | chr19:7300056-7398264 | 0 [INSR]
17p13.2 | 5.5938e-12 | 5.5938e-12 | chr17:5120021-5142747 | 2
12p13.32 | 1.8448e-10 | 1.8448e-10 | chr12:4325317-4436676 | 2
7q31.2 | 1.7801e-08 | 3.2625e-08 | chr7:116318088-116480275 | 1
1p36.21 | 1.0782e-06 | 1.0782e-06 | chr1:13862648-14377937 | 2
1q44 | 3.6848e-07 | 1.1884e-06 | chr1:243042268-244858016 | 11
2p24.3 | 2.1148e-06 | 2.1148e-06 | chr2:16015911-16440790 | 2
7q21.2 | 4.7227e-08 | 3.2157e-06 | chr7:92179103-92530348 | 3
4p16.3 | 0.00062853 | 0.00062853 | chr4:1778797-1816689 | 2
7q11.21 | 2.7781e-12 | 0.0013085 | chr7:57925000-63128930 | 6
17q25.1 | 0.0026165 | 0.0026165 | chr17:73169833-73641051 | 16
14q32.33 | 0.0082055 | 0.0082055 | chr14:104982904-105333748 | 10
13q34 | 0.025942 | 0.025942 | chr13:109765147-110884637 | 3
11p13 | 0.050059 | 0.050059 | chr11:31382963-32068175 | 6
19q12 | 0.057903 | 0.057903 | chr19:30211822-30321189 | 1
8q24.21 | 0.090978 | 0.090978 | chr8:127927022-131800277 | 21
21q21.1 | 0.13143 | 0.13143 | chr21:17519797-17649826 | 1

Genes in Wide Peak

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

Table S1. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S2. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PDGFRA

Genes in Wide Peak

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

Table S3. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S4. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MDM2
CPM

Genes in Wide Peak

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

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

Genes
SOX2
SOX2-OT

Genes in Wide Peak

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

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

Genes
SCIMP
LOC100130950

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's 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's Cancer Gene Census [7].

Genes
MET

Genes in Wide Peak

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

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

Genes
PRDM2
PDPN

Genes in Wide Peak

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

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

Genes
ADSS
CEP170
AKT3
ZNF238
SDCCAG8
PPPDE1
C1orf100
C1orf101
LOC339529
LOC731275
MIR4677

Genes in Wide Peak

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

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

Genes
MYCN
MYCNOS

Genes in Wide Peak

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

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

Genes
CDK6
FAM133B
LOC728066

Genes in Wide Peak

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

Table S13. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S14. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-4283-2
LOC643955
LOC100287704
LOC100287834
MIR4283-2
MIR4283-1

Genes in Wide Peak

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

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

Genes
GRB2
LLGL2
SUMO2
RECQL5
KIAA0195
GGA3
MRPS7
MIF4GD
CASKIN2
SLC25A19
NUP85
MYO15B
TSEN54
C17orf109
LOC100287042
MIR3678

Genes in Wide Peak

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

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

Genes
AKT1
SIVA1
INF2
ADSSL1
MGC23270
KIAA0284
TMEM179
C14orf180
ZBTB42
MIR4710

Genes in Wide Peak

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

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

Genes
COL4A1
IRS2
MYO16

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's Cancer Gene Census [7].

Genes
PAX6
ELP4
DNAJC24
IMMP1L
DCDC1
DKFZp686K1684

Genes in Wide Peak

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

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

Genes
CCNE1

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's Cancer Gene Census [7].

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
ADCY8
POU5F1B
PVT1
ASAP1-IT1
ASAP1
FAM49B
GSDMC
LOC727677
LOC728724
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
LOC100507117
PCAT1

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's Cancer Gene Census [7].

Genes
LINC00478

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 - 51 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 | chr9:21238609-22646396 | 19
10q23.31 | 7.02e-58 | 8.864e-55 | chr10:89617158-90034038 | 2
1p36.23 | 4.977e-54 | 8.6983e-38 | chr1:7829287-8423509 | 7
6q26 | 2.1079e-33 | 3.4949e-29 | chr6:163767962-165698161 | 2
13q14.2 | 1.5395e-27 | 7.3019e-25 | chr13:48833767-49064807 | 2
10q26.3 | 3.4643e-25 | 5.3663e-18 | chr10:135190263-135214343 | 1
19q13.41 | 4.4028e-16 | 4.4028e-16 | chr19:51500335-51915080 | 19
15q14 | 2.0701e-13 | 2.0501e-13 | chr15:32987127-44170698 | 143
1p32.3 | 1.1252e-15 | 1.8498e-12 | chr1:50879767-51569162 | 3
14q13.1 | 5.2006e-12 | 6.5032e-11 | chr14:33301849-34394000 | 1
4q34.3 | 1.2965e-08 | 1.2965e-08 | chr4:178911874-183060693 | 1
17q11.2 | 4.2919e-07 | 4.3914e-07 | chr17:29326736-29722618 | 5
3q29 | 1.0786e-06 | 7.3159e-06 | chr3:190373502-197029425 | 63
17p13.1 | 7.7542e-08 | 3.045e-05 | chr17:7526963-7591760 | 4
8p23.2 | 4.6342e-05 | 4.7759e-05 | chr8:2079140-6262191 | 1
1p36.32 | 6.6821e-26 | 0.00017177 | chr1:3394251-6475685 | 28
14q24.2 | 6.8303e-07 | 0.00053522 | chr14:63563582-107349540 | 448
10p13 | 0.00015766 | 0.0011492 | chr10:12616863-12768978 | 2
12p13.1 | 0.001298 | 0.0013144 | chr12:9880268-18838946 | 104
12q12 | 3.2304e-05 | 0.0019131 | chr12:42982652-46578647 | 14
18q22.3 | 0.0020727 | 0.0020773 | chr18:67995567-73836684 | 17
1p22.1 | 1.2491e-05 | 0.0027648 | chr1:92759774-93924485 | 12
10p11.23 | 0.00050416 | 0.00327 | chr10:29830429-29892002 | 4
11p15.5 | 0.0026618 | 0.0033272 | chr11:1-6417816 | 198
22q13.31 | 2.3416e-09 | 0.00348 | chr22:46657955-46695317 | 2
10p15.3 | 0.00090941 | 0.0051234 | chr10:1050841-2048902 | 7
16p12.2 | 0.0054096 | 0.005204 | chr16:20751348-27090703 | 61
2q37.1 | 0.0054119 | 0.0068949 | chr2:233432884-233736132 | 3
21q22.3 | 0.0090836 | 0.0091965 | chr21:46230687-46306160 | 1
6q22.31 | 1.628e-06 | 0.011868 | chr6:109483624-147162754 | 210
3p21.1 | 0.017923 | 0.017923 | chr3:52804560-52849056 | 2
1q42.11 | 0.0011377 | 0.021391 | chr1:210847515-227129582 | 105
4p16.3 | 0.022168 | 0.022168 | chr4:1197147-1244266 | 1
3q22.1 | 7.7881e-05 | 0.023249 | chr3:129625562-129871534 | 3
11p11.2 | 0.015408 | 0.030302 | chr11:36679363-46868487 | 48
2q22.1 | 0.034764 | 0.039384 | chr2:139655617-143637838 | 1
17p13.2 | 6.7998e-06 | 0.040502 | chr17:3851656-4048080 | 1
12q15 | 0.00055768 | 0.042447 | chr12:58350632-69140499 | 44
16q23.3 | 0.046334 | 0.047553 | chr16:70833950-90354753 | 178
1q44 | 0.0068949 | 0.048386 | chr1:245864790-247265054 | 10
22q13.31 | 1.9996e-10 | 0.079654 | chr22:47571204-48018269 | 1
8q24.3 | 0.081261 | 0.081939 | chr8:144645461-144730331 | 6
5q35.2 | 0.089557 | 0.08866 | chr5:150224096-180915260 | 247
Xq23 | 0.10758 | 0.10677 | chrX:110037863-110489519 | 1
3q13.31 | 0.00045988 | 0.12393 | chr3:115440285-116429324 | 1
Xp22.2 | 0.12384 | 0.12393 | chrX:11792056-12870927 | 2
13q12.11 | 0.00019568 | 0.14346 | chr13:1-19748348 | 3
9q34.2 | 0.15286 | 0.15197 | chr9:136602059-136892308 | 1
11q14.1 | 0.15334 | 0.17399 | chr11:78285273-81604120 | 5
22q13.32 | 2.3459e-10 | 0.34245 | chr22:48668761-49176545 | 5
22q12.2 | 0.074893 | 0.49049 | chr22:1-36958275 | 308

Genes in Wide Peak

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

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

Genes
hsa-mir-31
CDKN2A
CDKN2B
IFNA1
IFNA2
IFNA5
IFNA6
IFNA8
IFNA13
IFNA14
IFNA22P
MTAP
C9orf53
KLHL9
DMRTA1
IFNE
MIR31
MIR31HG
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
TNFRSF9
PER3
VAMP3
UTS2
PARK7
SLC45A1
ERRFI1

Genes in Wide Peak

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

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

Genes
QKI
CAHM

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

Table S27. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S28. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CD33
ETFB
LIM2
NKG7
KLK10
KLK11
KLK13
SIGLEC7
SIGLEC9
KLK14
KLK12
CTU1
CLDND2
VSIG10L
LOC147646
KLK9
SIGLECP3
C19orf75
IGLON5

Genes in Wide Peak

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

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

Genes
BUB1B
C15orf55
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
ACTC1
CAPN3
CHRM5
CKMT1B
EPB42
GANC
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
RYR3
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
JMJD7-PLA2G4B
SNAP23
TGM5
PPIP5K1
AQR
LCMT2
SLC12A6
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
CCNDBP1
C15orf63
TMEM87A
RPAP1
GREM1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
DLL4
INO80
PPP1R14D
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
C15orf24
PAK6
CASC5
AVEN
GJD2
STARD9
VPS18
ZFP106
CHAC1
C15orf29
WDR76
TMEM62
ELL3
C15orf41
ZFYVE19
DISP2
ATPBD4
C15orf57
C15orf23
BMF
CHST14
TGM7
CATSPER2
PLA2G4E
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
LPCAT4
PLA2G4F
LRRC57
FAM98B
PLA2G4D
FMN1
MRPL42P5
C15orf52
C15orf53
C15orf54
GOLGA8B
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
MIR626
MIR627
ANP32AP1
LOC728758
OIP5-AS1
LOC100131089
ANKRD63
JMJD7
PLA2G4B
MIR1233-1
MIR1282
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4510
TMCO5B

Genes in Wide Peak

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

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

Genes
CDKN2C
FAF1
DMRTA2

Genes in Wide Peak

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

Table S31. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S32. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LINC00290

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

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

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

Genes
TFRC
hsa-mir-570
hsa-mir-3137
APOD
CPN2
DLG1
FGF12
GP5
HES1
MFI2
MUC4
OPA1
PAK2
PCYT1A
PPP1R2
TNK2
NCBP2
ACAP2
UBXN7
PIGX
LSG1
HRASLS
ATP13A3
PIGZ
ATP13A4
MGC2889
CEP19
TMEM44
TM4SF19
ZDHHC19
LRRC15
FAM43A
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
OSTalpha
FBXO45
MUC20
SENP5
TCTEX1D2
C3orf43
SDHAP1
UTS2D
OSTN
ATP13A5
WDR53
LRRC33
FLJ34208
LOC401109
GMNC
LOC647323
MIR570
SDHAP2
LOC100128023
LOC100131551
SNAR-I
MFI2-AS1
LOC100507391
TM4SF19-TCTEX1D2
MIR4797

Genes in Wide Peak

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

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

Genes
TP53
ATP1B2
SHBG
SAT2

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
RPL22
hsa-mir-551a
DFFB
MEGF6
TP73
KCNAB2
CEP104
ACOT7
ICMT
CHD5
WRAP73
AJAP1
TP73-AS1
LRRC47
TPRG1L
CCDC27
NPHP4
LOC284661
C1orf174
GPR153
LOC388588
RNF207
HES3
MIR551A
LOC728716
LOC100133612
MIR4689
MIR4417

Genes in Wide Peak

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

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MTHFD1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPP2R5C
PPP2R5E
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
SEL1L
SRSF5
SLC8A3
SLC10A1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
MLH3
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
ATP6V1D
EVL
C14orf129
CINP
ASB2
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
COX8C
ASPG
RAB15
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307

Genes in Wide Peak

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

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

Genes
hsa-mir-548q
MIR4480

Genes in Wide Peak

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

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
ARHGDIB
ART4
CD69
CDKN1B
CREBL2
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
MGP
MGST1
OLR1
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
KLRC4
CSDA
GPRC5A
CLEC2B
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
MANSC1
MAGOHB
STYK1
GPRC5D
ATF7IP
H2AFJ
LMO3
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
DUSP16
APOLD1
GSG1
RERG
HTR7P1
LOH12CR1
C12orf59
HIST4H4
ERP27
C12orf60
CLEC12A
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
CLEC9A
C12orf36
LOC338817
TAS2R42
CLEC2A
CLEC12B
RPL13AP20
C12orf69
LOH12CR2
PRB2
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100506314
KLRC4-KLRK1
PRH1-PRR4
MIR3974

Genes in Wide Peak

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

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

Genes
NELL2
TWF1
RNY5
SCAF11
PLEKHA8P1
IRAK4
ADAMTS20
PUS7L
RACGAP1P
TMEM117
ANO6
ARID2
LOC400027
DBX2

Genes in Wide Peak

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

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

Genes
CYB5A
TSHZ1
TIMM21
ZNF407
CNDP2
NETO1
CNDP1
FAM69C
CBLN2
FBXO15
ZADH2
C18orf62
LOC400655
LOC400657
C18orf63
LOC100505776
LOC100505817

Genes in Wide Peak

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

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

Genes
DR1
GFI1
SNORD21
RPL5
EVI5
MTF2
SNORA66
TMED5
RPAP2
CCDC18
FAM69A
LOC100131564

Genes in Wide Peak

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

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

Genes
hsa-mir-938
hsa-mir-604
MIR604
MIR938

Genes in Wide Peak

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

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

Genes
CARS
HRAS
NUP98
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
CNGA4
CTSD
DRD4
DUSP8
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
IGF2
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
SMPD1
TRIM21
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IFITM2
OR7E12P
KCNQ1OT1
PKP3
SIRT3
OR52A1
PGAP2
C11orf21
TRPM5
UBQLN3
IGF2-AS1
BET1L
CEND1
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
FAM160A2
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR52W1
OR56A4
OR56A1
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
SCGB1C1
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
OR51V1
H19
EFCAB4A
TMEM80
C11orf36
ANO9
LOC338651
B4GALNT4
OR52L1
OR52B6
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TRIM6-TRIM34
MIR483
SNORA52
LOC650368
LOC653486
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686
MIR4687

Genes in Wide Peak

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

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

Genes
TTC38
CN5H6.4

Genes in Wide Peak

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

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

Genes
ADARB2
IDI1
WDR37
IDI2-AS1
IDI2
LINC00200
ADARB2-AS1

Genes in Wide Peak

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

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

Genes
PALB2
hsa-mir-548w
AQP8
CDR2
CRYM
NDUFAB1
PLK1
PRKCB
RBBP6
ACSM3
SCNN1B
SCNN1G
UQCRC2
ZP2
HS3ST4
HS3ST2
IGSF6
CACNG3
ERN2
GGA2
NPIPL3
TNRC6A
EEF2K
METTL9
LCMT1
ARHGAP17
DNAH3
POLR3E
UBFD1
TMEM159
LYRM1
USP31
CHP2
LOC81691
DCTN5
COG7
ERI2
SLC5A11
DCUN1D3
EARS2
VWA3A
OTOA
C16orf82
PDZD9
ANKS4B
ZKSCAN2
SLC7A5P2
CRYM-AS1
LOC554206
LOC641298
LOC653786
MIR548D2
RRN3P1
C16orf52
RRN3P3
LOC100132247
LOC100190986
LOC100271836
MIR548AA2
LOC100506655
SNX29P1

Genes in Wide Peak

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

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

Genes
KCNJ13
GIGYF2
EFHD1

Genes in Wide Peak

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

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

Genes
PTTG1IP

Genes in Wide Peak

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

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

Genes
MYB
ROS1
TNFAIP3
STL
GOPC
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
AMD1
ARG1
COL10A1
CTGF
EPB41L2
EYA4
FABP7
FRK
FUCA2
FYN
GJA1
GPR6
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
MAP3K5
NMBR
ENPP1
ENPP3
PEX7
PLAGL1
PLN
PKIB
PTPRK
REV3L
RPS12
SGK1
SMPD2
TCF21
TPD52L1
TSPYL1
UTRN
EPM2A
STX7
PEX3
DDO
STX11
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
MAP7
TAAR2
TAAR3
MED23
AKAP7
TBPL1
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
TRDN
CITED2
TRAF3IP2
HBS1L
SMPDL3A
RAB32
CDK19
TSPYL4
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MOXD1
PDE7B
DSE
HDDC2
TUBE1
CDC40
RWDD1
AIG1
VTA1
HECA
IL20RA
AHI1
VNN3
ECHDC1
HYMAI
GPR126
KIAA1244
NHSL1
SERINC1
C6orf115
PBOV1
TRMT11
PERP
ALDH8A1
MICAL1
OR2A4
FAM184A
ADGB
RNF146
SF3B5
TAAR8
FBXO30
RPF2
L3MBTL3
RSPO3
LTV1
REPS1
SLC22A16
KIAA1919
ARHGAP18
GTF3C6
FAM54A
TMEM200A
NUS1
IL22RA2
C6orf192
SLC16A10
ADAT2
CLVS2
TAAR9
TAAR1
NCOA7
HINT3
LOC153910
ZC2HC1B
SAMD3
MGC34034
SLC2A12
LOC154092
RNF217
NKAIN2
OLIG3
TXLNB
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
C6orf191
FAM26E
MCM9
SHPRH
LINC00326
LOC285740
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
TAAR6
SLC35D3
RSPH4A
ECT2L
C6orf58
HMGA1P7
CENPW
C6orf174
CEP85L
THEMIS
FAM26F
FLJ46906
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
MIR548B
TPI1P3
C6orf186
LOC729176
BET3L
LINC00271
LOC100132735
LOC100287632
NHEG1
MIR3145
MIR3668
MIR3662
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
MIR4465

Genes in Wide Peak

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

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

Genes
ITIH1
ITIH3

Genes in Wide Peak

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

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

Genes
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
PARP1
ATF3
CAPN2
CENPF
EPHX1
EPRS
ESRRG
H3F3A
HLX
ITPKB
KCNH1
KCNK2
LBR
MARK1
NEK2
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
SRP9
AURKAPS1
TGFB2
LEFTY2
TLR5
TP53BP2
TRAF5
USH2A
SLC30A1
DEGS1
TAF1A
TMEM63A
LPGAT1
BPNT1
LEFTY1
DUSP10
FBXO28
RAB3GAP2
INTS7
NSL1
RPS6KC1
RNU5F-1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
KCTD3
DTL
MARC2
SUSD4
GPATCH2
TMEM206
BATF3
SLC30A10
IARS2
ENAH
RCOR3
SMYD2
ACBD3
MARC1
AIDA
C1orf115
HHIPL2
VASH2
WDR26
MIXL1
LINC00467
DISP1
ANGEL2
LYPLAL1
DNAH14
SPATA17
TATDN3
BROX
CNIH3
C1orf227
FAM71A
C1orf55
C1orf65
LIN9
RD3
MIA3
C1orf95
CAPN8
C1orf140
FAM177B
MIR194-1
MIR215
H3F3AP4
FLVCR1-AS1
LOC643723
SNORA36B
SNORA16B
LOC728463
MIR664
MIR320B2
MIR3122
PROX1-AS1
MIR4742
LINC00538

Genes in Wide Peak

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

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

Genes
CTBP1

Genes in Wide Peak

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

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

Genes
TRH
ALG1L2
FAM86HP

Genes in Wide Peak

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

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

Genes
EXT2
CREB3L1
hsa-mir-3160-2
hsa-mir-129-2
ARHGAP1
CHRM4
CRY2
F2
CD82
MDK
DGKZ
CHST1
API5
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
HSD17B12
PHF21A
SLC35C1
AMBRA1
TTC17
PRDM11
SYT13
LRRC4C
ALX4
ZNF408
ACCS
TSPAN18
GYLTL1B
C11orf94
ALKBH3
LOC221122
HARBI1
DKFZp779M0652
C11orf96
ACCSL
HNRNPKP3
MIR129-2
SNORD67
LOC729799
MIR670
MIR3160-2
MIR3160-1
LOC100507205
LOC100507300
MIR4688

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
ZZEF1

Genes in Wide Peak

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

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

Genes
HMGA2
WIF1
hsa-mir-548c
hsa-let-7i
AVPR1A
GNS
IFNG
RAP1B
DYRK2
SLC16A7
USP15
TMEM5
IRAK3
XPOT
MON2
TBC1D30
GRIP1
LEMD3
TBK1
IL22
TMBIM4
IL26
CAND1
MDM1
NUP107
PPM1H
SRGAP1
LLPH
HELB
C12orf56
LRIG3
C12orf66
RPSAP52
MSRB3
RASSF3
C12orf61
DPY19L2
FAM19A2
FLJ41278
MIRLET7I
MIR548C
SNORA70G
MIR548Z
LOC100507250

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AP1G1
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
TAT
ZNF19
ZNF23
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
TXNL4B
BANP
RFWD3
ZNF821
ZDHHC7
FTSJD1
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
MARVELD3
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
SNAI3
FAM92B
ATXN1L
PKD1L3
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
CTRB2
CLEC18B
SNORD68
SNORD71
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
SYCE1L
LOC100287036
MIR1910
SNORA70D
MIR3182
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

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's Cancer Gene Census [7].

Genes
AHCTF1
SCCPDH
ZNF695
TFB2M
SMYD3
ZNF670
LOC149134
CNST
LOC255654
ZNF670-ZNF695

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q24.3.

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

Genes
EEF1D
TSTA3
PYCRL
TIGD5
NAPRT1
C8orf73

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

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

Genes
EBF1
ITK
NPM1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
ADRA1B
ANXA6
ATOX1
BNIP1
CANX
CCNG1
CLTB
NKX2-5
DBN1
DOCK2
DRD1
DUSP1
F12
FABP6
FAT2
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GLRA1
GM2A
GRK6
GPX3
GRIA1
GRM6
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
IL12B
KCNMB1
LCP2
LTC4S
MFAP3
MGAT1
MSX2
MAPK9
PROP1
RARS
SGCD
SLC34A1
SLIT3
SNCB
SPARC
STK10
ZNF354A
TTC1
STC2
ADAM19
FGF18
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
ADAMTS2
CLINT1
MAML1
GFPT2
G3BP1
TNIP1
GNB2L1
SLU7
RGS14
CPLX2
C5orf4
FAM114A2
BTNL3
LMAN2
SOX30
MGAT4B
B4GALT7
RNF44
TBC1D9B
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
ZNF346
GEMIN5
CCDC69
TSPAN17
OR4F3
HAVCR1
CYFIP2
PRELID1
MAT2B
MRPL22
KCNIP1
ZNF354C
RPL26L1
C5orf45
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
CCDC99
THG1L
GALNT10
NHP2
RNF130
NMUR2
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
C5orf54
GMCL1P1
RMND5B
CCNJL
PANK3
SAP30L
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
HAVCR2
AGXT2L2
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
ZNF300
UBTD2
SCGB3A1
SFXN1
GPRIN1
PWWP2A
C1QTNF2
ZNF354B
C5orf47
C5orf58
OR2Y1
LSM11
ZNF300P1
NUDCD2
UBLCP1
SLC36A2
C5orf41
BTNL9
PPP1R2P3
FAM71B
RNF145
HIGD2A
FAM153B
LOC202181
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
LOC340037
PFN3
ZNF879
IRGM
FBLL1
NIPAL4
C5orf25
FLJ38109
MIR103A1
MIR146A
MIR218-2
FNDC9
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
LOC728554
AACSP1
LOC729678
OR4F29
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3912
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq23.

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

Genes
PAK3

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's Cancer Gene Census [7].

Genes
LSAMP

Genes in Wide Peak

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

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

Genes
PRPS2
FRMPD4

Genes in Wide Peak

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

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

Genes
PHF2P1
ANKRD20A9P
LINC00442

Genes in Wide Peak

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

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

Genes
VAV2

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's Cancer Gene Census [7].

Genes
hsa-mir-4300
hsa-mir-708
ODZ4
MIR708
MIR4300

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
FAM19A5
LOC284933
MIR3201
MIR4535

Genes in Wide Peak

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

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

Genes
BCR
EWSR1
MN1
MYH9
NF2
SMARCB1
CLTCL1
CHEK2
hsa-mir-3200
hsa-mir-3199-2
hsa-mir-548j
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ADORA2A
ADRBK2
AP1B1
ARVCF
ATP6V1E1
BID
COMT
CRKL
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
DDT
GGT1
GGT3P
GGT5
GNAZ
GP1BB
GSC2
GSTT1
GSTT2
SERPIND1
HMOX1
IGLL1
LIF
LIMK2
MB
MCM5
MIF
MMP11
DRG1
NEFH
OSM
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
RFPL1
SLC5A1
SMTN
SLC5A4
SLC7A4
SLC25A1
SNRPD3
TBX1
TCN2
TIMP3
CLDN5
TOP1P2
HIRA
UBE2L3
UFD1L
VPREB1
XBP1
YWHAH
ZNF70
ZNF74
DGCR6
LZTR1
DGCR14
SYN3
CDC45
TPST2
NIPSNAP1
APOL1
THOC5
EIF3D
MTMR3
TOP3B
P2RX6
LARGE
SNAP29
GAL3ST1
RAB36
PPM1F
DEPDC5
SFI1
DGCR2
HMGXB4
TOM1
SF3A1
TXNRD2
RASL10A
GAS2L1
RFPL3-AS1
RFPL3
RFPL2
RFPL1-AS1
USP18
MORC2
HIC2
TTC28
SPECC1L
PES1
CABIN1
PRAME
SEC14L2
RBFOX2
SEZ6L
RASD2
PATZ1
TSSK2
SDF2L1
PPIL2
PITPNB
PISD
OSBP2
IL17RA
APOL2
AP1B1P1
ANKRD62P1-PARP4P3
POTEH
BCL2L13
TFIP11
C22orf31
GSTTP1
C22orf24
DGCR11
DGCR9
FBXO7
RHBDD3
POM121L1P
TXN2
DGCR5
DGCR10
FBXW4P1
TRMT2A
INPP5J
RTDR1
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L9P
UQCR10
POM121L8P
YPEL1
ZDHHC8
VPREB3
PLA2G3
C22orf43
C22orf28
MTFP1
MED15
UPB1
TUBA8
CECR1
DGCR8
GNB1L
TUG1
PEX26
ZMAT5
SUSD2
EIF4ENIF1
ASPHD2
MICAL3
MRPL40
RTN4R
SLC2A11
C22orf29
FOXRED2
THAP7
APOL6
APOL5
APOL4
APOL3
OR11H1
C22orf13
SLC25A18
TBC1D10A
KREMEN1
ZNRF3
ASCC2
TMEM191A
MYO18B
KLHL22
DGCR6L
KIAA1656
RIMBP3
KIAA1671
HPS4
SCARF2
GGTLC2
GUSBP11
DERL3
IGLL3P
LRP5L
RNF185
ISX
LOC96610
MGC16703
PIK3IP1
GAB4
C22orf39
C22orf25
ZNF280A
SGSM1
EMID1
SELM
ZNF280B
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
C22orf15
HSCB
CCDC117
HORMAD2
DUSP18
MORC2-AS1
C22orf42
CCDC116
CABP7
RNF215
PRR14L
BPIFC
TMEM211
SEC14L3
POM121L4P
RGL4
LOC284865
LOC284889
TTC28-AS1
SEC14L4
SLC35E4
LOC339666
PI4KAP2
SDC4P
TPTEP1
LOC388849
FAM211B
LOC391322
LOC400891
BCRP2
CHCHD10
SRRD
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
PIWIL3
MIAT
CCDC157
BCRP3
TMEM191C
C22orf45
POM121L10P
LOC648691
CES5AP1
GATSL3
GSTTP2
GSTT2B
MIR648
MIR650
TMEM191B
PI4KAP1
LOC729444
SEC14L6
DDTL
SNORD125
MIR301B
LOC100128531
CECR7
CECR5-AS1
FLJ41941
MIR1286
MIR1306
MIR548J
MIR3200
MIR3199-2
MIR3198-1
MIR3199-1
IGLL5
MIR3909
MIR3653
MIR3618
MIR3928
LOC100506195
SEPT5-GP1BB
MIR4764
MIR4761

Arm-level results

Table 3. Get Full Table Arm-level significance table - 22 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.14 | 4.07 | 0.00012 | 0.03 | -4.59 | 1
1q | 1955 | 0.15 | 4.79 | 4.71e-06 | 0.03 | -4.68 | 1
2p | 924 | 0.06 | -3.92 | 1 | 0.06 | -3.67 | 1
2q | 1556 | 0.05 | -3.53 | 1 | 0.06 | -3 | 1
3p | 1062 | 0.10 | -0.77 | 1 | 0.08 | -2.42 | 1
3q | 1139 | 0.11 | 0.204 | 1 | 0.06 | -3.24 | 1
4p | 489 | 0.07 | -3.81 | 1 | 0.11 | -1.02 | 1
4q | 1049 | 0.06 | -3.63 | 1 | 0.11 | -0.086 | 0.929
5p | 270 | 0.09 | -2.57 | 1 | 0.09 | -2.57 | 1
5q | 1427 | 0.08 | -2.1 | 1 | 0.08 | -1.44 | 1
6p | 1173 | 0.04 | -4.5 | 1 | 0.16 | 3.69 | 0.000352
6q | 839 | 0.05 | -4.37 | 1 | 0.23 | 8.16 | 5.55e-16
7p | 641 | 0.82 | 51.4 | 0 | 0.07 | -1.4 | 1
7q | 1277 | 0.83 | 55.4 | 0 | 0.06 | -1.54 | 1
8p | 580 | 0.09 | -1.98 | 1 | 0.12 | 0.088 | 0.885
8q | 859 | 0.10 | -1.01 | 1 | 0.10 | -1.26 | 1
9p | 422 | 0.12 | -0.28 | 1 | 0.37 | 17.6 | 0
9q | 1113 | 0.15 | 2.66 | 0.0174 | 0.17 | 4.68 | 4.83e-06
10p | 409 | 0.14 | 0.687 | 0.984 | 0.85 | 52.2 | 0
10q | 1268 | 0.05 | -1.68 | 1 | 0.86 | 57.9 | 0
11p | 862 | 0.02 | -6.23 | 1 | 0.18 | 5.01 | 1.01e-06
11q | 1515 | 0.02 | -5.89 | 1 | 0.17 | 5.59 | 4.62e-08
12p | 575 | 0.11 | -0.574 | 1 | 0.13 | 0.52 | 0.625
12q | 1447 | 0.09 | -0.999 | 1 | 0.11 | 0.831 | 0.477
13q | 654 | 0.03 | -5.54 | 1 | 0.33 | 15.2 | 0
14q | 1341 | 0.05 | -3.93 | 1 | 0.27 | 12.6 | 0
15q | 1355 | 0.05 | -3.71 | 1 | 0.18 | 6.01 | 4.06e-09
16p | 872 | 0.07 | -3.03 | 1 | 0.12 | 0.583 | 0.622
16q | 702 | 0.07 | -2.96 | 1 | 0.16 | 2.94 | 0.00475
17p | 683 | 0.08 | -2.47 | 1 | 0.13 | 1.09 | 0.365
17q | 1592 | 0.11 | 0.57 | 1 | 0.08 | -1.15 | 1
18p | 143 | 0.10 | -1.51 | 1 | 0.14 | 0.841 | 0.477
18q | 446 | 0.10 | -1.17 | 1 | 0.12 | 0.0327 | 0.885
19p | 995 | 0.40 | 21 | 0 | 0.09 | -1.37 | 1
19q | 1709 | 0.35 | 19.5 | 0 | 0.11 | 0.488 | 0.625
20p | 355 | 0.39 | 19 | 0 | 0.05 | -4.07 | 1
20q | 753 | 0.38 | 19.6 | 0 | 0.05 | -3.96 | 1
21q | 509 | 0.12 | -0.202 | 1 | 0.08 | -2.63 | 1
22q | 921 | 0.08 | -1.8 | 1 | 0.34 | 16.4 | 0
Xq | 1312 | 0.04 | -4.31 | 1 | 0.22 | 8.35 | 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.

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/1668887/2.GDAC_MergeDataFiles.Finished/GBM.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 563 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
[2] GISTIC version 1
[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)
[4] GISTIC version 2
[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)
[7] The Sanger Institute: Cancer Gene Census
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