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 2.0.16 (cga svn revision 38839).

Summary

There were 560 tumor samples used in this analysis: 22 significant arm-level results, 17 significant focal amplifications, and 40 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 - 17 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 | chr7:54964317-55090624 | 1
12q14.1 | 1.8194e-140 | 4.4124e-108 | chr12:58125396-58152580 | 4
4q12 | 3.6442e-90 | 3.6442e-90 | chr4:55032249-55115704 | 1
1q32.1 | 1.6314e-61 | 1.7658e-61 | chr1:204389315-204539784 | 2
12q15 | 1.2932e-77 | 1.0869e-39 | chr12:69178021-69260755 | 2
3q26.33 | 2.0967e-13 | 2.0967e-13 | chr3:181101393-181732176 | 2
12p13.32 | 3.5648e-09 | 3.5648e-09 | chr12:4374374-4432075 | 2
7q31.2 | 3.261e-08 | 4.5448e-08 | chr7:116318088-116493406 | 1
2p24.3 | 4.1978e-07 | 4.1978e-07 | chr2:16015911-16422098 | 2
1q44 | 6.7766e-07 | 9.1999e-07 | chr1:243431718-244855072 | 9
1p36.21 | 2.7245e-06 | 2.7245e-06 | chr1:13862648-14377937 | 2
7q21.2 | 3.1818e-05 | 6.7981e-05 | chr7:92179103-92530348 | 3
14q32.33 | 0.0092519 | 0.0092519 | chr14:104982904-105333748 | 10
4p16.3 | 0.011142 | 0.011142 | chr4:1778797-1817427 | 2
13q34 | 0.03945 | 0.03945 | chr13:109765147-110818101 | 3
8q24.21 | 0.11293 | 0.11293 | chr8:127927022-130347325 | 15
7q32.1 | 0.03043 | 0.11415 | chr7:128086513-130114226 | 36

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's Cancer Gene Census [7].

Genes
EGFR

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'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 S3. 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 S4. 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 S5. 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 S6. 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 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 2p24.3.

Table S9. 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 1q44.

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

Genes
ADSS
AKT3
ZNF238
SDCCAG8
PPPDE1
C1orf100
C1orf101
LOC339529
MIR4677

Genes in Wide Peak

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

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute'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 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 14q32.33.

Table S13. 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 4p16.3.

Table S14. 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 13q34.

Table S15. 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 8q24.21.

Table S16. 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
POU5F1B
PVT1
LOC727677
LOC728724
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208
PCAT1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q32.1.

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

Genes
SMO
hsa-mir-183
OPN1SW
CALU
CPA1
CPA2
FLNC
IRF5
NRF1
UBE2H
ATP6V1F
KLHDC10
AHCYL2
TNPO3
HILPDA
CPA4
ZC3HC1
METTL2B
FAM40B
CCDC136
FAM71F1
TMEM209
CPA5
CEP41
C7orf45
TPI1P2
TSPAN33
FAM71F2
KCP
FLJ45340
MIR182
MIR183
MIR96
LOC407835
LOC100130705
LOC100287482

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 - 40 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 | chr9:21238609-23690570 | 20
10q23.31 | 2.4096e-60 | 1.77e-59 | chr10:89617158-90034038 | 2
1p36.23 | 4.5123e-56 | 3.0129e-30 | chr1:7829287-8423509 | 7
6q26 | 5.5567e-22 | 2.7188e-21 | chr6:163767962-165698161 | 2
13q14.2 | 6.3785e-23 | 2.0532e-18 | chr13:48833767-49064807 | 2
1p32.3 | 2.7659e-19 | 1.7531e-16 | chr1:50879767-51569162 | 3
1p36.31 | 1.7849e-48 | 1.1766e-10 | chr1:4841981-6475685 | 11
14q13.1 | 4.2789e-08 | 4.351e-08 | chr14:33301849-34394000 | 1
19q13.41 | 1.7777e-09 | 4.9987e-08 | chr19:50978394-53037389 | 84
3q29 | 2.0114e-08 | 1.015e-07 | chr3:190595782-196020883 | 41
17q11.2 | 1.4779e-07 | 1.5136e-07 | chr17:29326736-29722618 | 5
15q14 | 1.8579e-11 | 2.8544e-07 | chr15:31669937-42567241 | 113
4q34.3 | 3.0091e-07 | 3.0181e-07 | chr4:178911874-183060693 | 1
17p13.1 | 2.2131e-05 | 2.2131e-05 | chr17:7535461-7591760 | 2
1p22.1 | 2.2646e-07 | 6.3585e-05 | chr1:92851928-93924485 | 11
2q37.1 | 4.3206e-05 | 6.8005e-05 | chr2:233547367-233736132 | 2
22q13.32 | 8.0486e-05 | 8.2339e-05 | chr22:45246472-51304566 | 83
2q22.1 | 0.00011675 | 0.00014467 | chr2:139655617-143637838 | 1
1q44 | 0.00013125 | 0.00070874 | chr1:245864790-247110824 | 7
16p12.2 | 0.001254 | 0.0012333 | chr16:20936251-27090703 | 56
13q21.2 | 1.0578e-08 | 0.0038627 | chr13:49867546-77454480 | 77
11p15.5 | 0.0044114 | 0.0062359 | chr11:1-7277774 | 224
12p13.1 | 0.0078283 | 0.0079247 | chr12:9880268-20169548 | 108
1q42.11 | 0.00082335 | 0.0085429 | chr1:211999806-227178961 | 98
18q22.3 | 0.0085429 | 0.0085429 | chr18:67995567-73836684 | 17
3q13.31 | 0.0023156 | 0.0122 | chr3:112218119-131181443 | 171
12q12 | 0.0083526 | 0.0122 | chr12:41830374-46578647 | 20
15q21.1 | 7.1899e-08 | 0.0122 | chr15:41403242-51741000 | 129
6q22.31 | 0.0031797 | 0.022757 | chr6:109483624-147138228 | 210
10q11.23 | 0.0027834 | 0.048258 | chr10:52644085-54061437 | 4
11p11.2 | 0.03354 | 0.048258 | chr11:36679363-46868487 | 48
16q12.1 | 0.050463 | 0.082676 | chr16:47735031-64981096 | 111
12q21.31 | 0.053698 | 0.088361 | chr12:74674746-93402674 | 69
5q34 | 0.11826 | 0.11769 | chr5:140096976-180915260 | 388
5q13.1 | 0.13254 | 0.1346 | chr5:65475684-70752389 | 30
21q21.1 | 0.14407 | 0.14093 | chr21:1-29097845 | 59
2p14 | 0.13539 | 0.16628 | chr2:64341526-70905098 | 51
19q13.43 | 6.1964e-07 | 0.16628 | chr19:54876653-59128983 | 160
2p25.3 | 0.091408 | 0.21073 | chr2:1-8063458 | 30
16q23.1 | 0.12994 | 0.23997 | chr16:70806675-90354753 | 178

Genes in Wide Peak

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

Table S18. 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
FLJ35282
MIR31HG
CDKN2B-AS1

Genes in Wide Peak

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

Table S19. 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 S20. 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 S21. 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 S22. 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 1p32.3.

Table S23. 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 1p36.31.

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

Genes
RPL22
KCNAB2
ACOT7
ICMT
CHD5
NPHP4
GPR153
RNF207
HES3
MIR4689
MIR4417

Genes in Wide Peak

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

Table S25. 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 19q13.41.

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

Genes
KLK2
PPP2R1A
hsa-mir-643
hsa-mir-125a
KLK3
CD33
SIGLEC6
ETFB
FPR1
FPR2
FPR3
GPR32
HAS1
KLK1
LIM2
NKG7
KLK7
KLK6
KLK10
CLEC11A
ZNF175
SIGLEC5
KLK4
ZNF432
KLK11
KLK8
KLK5
KLK13
SIGLEC7
SIGLEC9
SIGLEC8
KLK14
KLK12
SHANK1
KLK15
ZNF350
ZNF649
ZNF613
ZNF614
SYT3
ZNF528
ZNF577
C19orf48
SIGLEC10
SIGLEC12
ZNF616
ZNF766
CTU1
ACPT
LRRC4B
CLDND2
JOSD2
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ZNF836
ZNF610
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
C19orf81
ZNF880
IGLON5
MIRLET7E
MIR125A
MIR99B
ASPDH
KLKP1
SNORD88A
SNORD88B
SNORD88C
MIR643
CEACAM18
FLJ30403
SIGLEC14
SNAR-F
LOC100129083

Genes in Wide Peak

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

Table S27. 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
FGF12
GP5
HES1
MUC4
OPA1
PCYT1A
PPP1R2
TNK2
ACAP2
LSG1
HRASLS
ATP13A3
ATP13A4
MGC2889
TMEM44
ZDHHC19
LRRC15
FAM43A
MB21D2
XXYLT1
CCDC50
PYDC2
OSTalpha
MUC20
SDHAP1
UTS2D
OSTN
ATP13A5
FLJ34208
LOC401109
LOC647323
MIR570
SDHAP2
LOC100128023
LOC100131551
LOC100507391

Genes in Wide Peak

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

Table S28. 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 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-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
ACTC1
CHRM5
CHRNA7
GCHFR
ITPKA
IVD
LTK
MEIS2
PLCB2
RAD51
RYR3
SCG5
SPINT1
SRP14
THBS1
TYRO3
JMJD7-PLA2G4B
AQR
ARHGAP11A
SLC12A6
RASGRP1
GPR176
CHP
OIP5
BAHD1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
TMEM87A
RPAP1
GREM1
RPUSD2
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
DLL4
INO80
PPP1R14D
ZNF770
FAM82A2
DNAJC17
NOP10
C15orf24
PAK6
CASC5
AVEN
GJD2
VPS18
CHAC1
C15orf29
C15orf41
ZFYVE19
DISP2
ULK4P3
ULK4P1
ATPBD4
C15orf57
C15orf23
BMF
CHST14
PLA2G4E
LOC145845
TMCO5A
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
EXD1
FSIP1
RHOV
LPCAT4
PLA2G4F
FAM98B
PLA2G4D
FMN1
MRPL42P5
C15orf52
C15orf53
C15orf54
GOLGA8B
EIF2AK4
C15orf62
C15orf56
PHGR1
MIR626
MIR627
ANP32AP1
OIP5-AS1
LOC100131089
ANKRD63
JMJD7
PLA2G4B
ULK4P2
LOC100288615
MIR1233-1
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
MIR4510
TMCO5B

Genes in Wide Peak

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

Table S30. 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 17p13.1.

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

Genes
TP53
ATP1B2

Genes in Wide Peak

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

Table S32. 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
CCDC18
FAM69A
LOC100131564

Genes in Wide Peak

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

Table S33. Genes in bold are cancer genes as defined by The Sanger Institute's 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 S34. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

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

Table S35. 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 1q44.

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

Genes
AHCTF1
SCCPDH
TFB2M
SMYD3
LOC149134
CNST
LOC255654

Genes in Wide Peak

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

Table S37. 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
SCNN1B
SCNN1G
UQCRC2
ZP2
HS3ST4
HS3ST2
IGSF6
CACNG3
ERN2
GGA2
NPIPL3
TNRC6A
EEF2K
METTL9
LCMT1
ARHGAP17
DNAH3
POLR3E
UBFD1
TMEM159
USP31
CHP2
DCTN5
COG7
SLC5A11
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 13q21.2.

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

Genes
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
ATP7B
KLF5
DACH1
GUCY1B2
KPNA3
LMO7
NEK3
PCDH8
PCDH9
ATXN8OS
UCHL3
DLEU2
UTP14C
TBC1D4
TRIM13
DLEU1
PIBF1
OLFM4
SUGT1
LECT1
KLF12
DIS3
INTS6
CKAP2
PCDH17
VPS36
PHF11
RCBTB1
THSD1
SPRYD7
KLHL1
PCDH20
RNASEH2B
DHRS12
BORA
TDRD3
CAB39L
DIAPH3
CCDC70
SETDB2
EBPL
ARL11
WDFY2
PRR20A
HNRNPA1L2
ST13P4
COMMD6
DLEU7
FAM124A
TPTE2P3
CTAGE10P
OR7E156P
KCNRG
LINC00282
LINC00550
LINC00347
NEK5
THSD1P1
MIR15A
MIR16-1
ALG11
MZT1
SERPINE3
CTAGE11P
PRR20B
PRR20C
PRR20D
PRR20E
MIR1297
MIR759
MIR3169
MIR3613
MIR4703

Genes in Wide Peak

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

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

Genes
CARS
HRAS
NUP98
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
SMPD1
TRIM21
STIM1
TAF10
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
ZNF214
ZNF215
RASSF7
IFITM1
OR6A2
DCHS1
BRSK2
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IFITM2
TRIM3
OR7E12P
KCNQ1OT1
PKP3
RRP8
SIRT3
OR52A1
ARFIP2
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
IGF2-AS1
BET1L
CEND1
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
MRPL17
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
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
C11orf36
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
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 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
PLEKHA5
MANSC1
MAGOHB
STYK1
GPRC5D
ATF7IP
H2AFJ
LMO3
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
DUSP16
APOLD1
GSG1
RERG
PLCZ1
HTR7P1
CAPZA3
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
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 1q42.11.

Table S41. 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
KCNK2
LBR
MARK1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
SRP9
AURKAPS1
TGFB2
LEFTY2
TLR5
TP53BP2
USH2A
DEGS1
TAF1A
TMEM63A
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
SMYD2
ADCK3
ACBD3
MARC1
AIDA
C1orf115
HHIPL2
VASH2
WDR26
MIXL1
DISP1
ANGEL2
LYPLAL1
DNAH14
SPATA17
TATDN3
BROX
CNIH3
C1orf227
FAM71A
C1orf55
C1orf65
LIN9
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 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 3q13.31.

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

Genes
GATA2
RPN1
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
ADCY5
ADPRH
ATP6V1A
CASR
CD80
CD86
CSTA
DRD3
GAP43
GOLGB1
GP9
GSK3B
GTF2E1
HCLS1
HGD
ITGB5
KPNA1
LSAMP
MCM2
MYLK
NDUFB4
PLXNA1
RHO
SLC15A2
TRH
UPK1B
UMPS
CNBP
ZNF80
ZNF148
RAB7A
RUVBL1
B4GALT4
SNX4
NR1I2
MBD4
H1FX
KALRN
STXBP5L
IQCB1
COX17
POLQ
ALDH1L1
PDIA5
FSTL1
MGLL
COPG
TMCC1
PLXND1
C3orf27
C3orf17
ZBTB20
FAM162A
SEC22A
ATP2C1
ACAD9
ASTE1
KLF15
GTPBP8
SEC61A1
PIK3R4
PODXL2
TIMMDC1
PLA1A
FBXO40
SEMA5B
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
SLC41A3
SLC35A5
TMEM39A
IFT122
WDR52
EAF2
MUC13
C3orf37
POGLUT1
ISY1
HEG1
KIAA1257
ARHGAP31
KIAA1407
EEFSEC
POPDC2
ATG3
CCDC14
ZXDC
HSPBAP1
QTRTD1
CCDC48
NEK11
NAA50
ABTB1
PARP9
CHCHD6
SLC12A8
DIRC2
C3orf15
LOC90246
C3orf25
BOC
TXNRD3
OSBPL11
LRRC58
CCDC58
CD200R1
TPRA1
UROC1
NUDT16
COL6A6
RPL32P3
H1FOO
DTX3L
CCDC80
ROPN1B
C3orf22
SPICE1
NUDT16P1
IGSF11
C3orf30
PARP15
DNAJB8
GPR156
CHST13
KBTBD12
ALG1L
PTPLB
TIGIT
KIAA2018
ZDHHC23
NUP210P1
COL6A5
LSAMP-AS3
DNAJB8-AS1
RABL3
ILDR1
RAB43
LOC339874
H1FX-AS1
CD200R1L
CCDC37
MIR198
ARGFX
ALG1L2
TXNRD3NB
COL6A4P2
LOC653712
SNORA7B
MIR568
FAM86HP
LOC100125556
LOC100129550
ZBTB20-AS1
MIR1280
MIR548I1
IGSF11-AS1
MYLK-AS1
LOC100507032
ISY1-RAB43
MIR4796
MIR4446

Genes in Wide Peak

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

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

Genes
NELL2
TWF1
RNY5
SCAF11
YAF2
PDZRN4
PLEKHA8P1
IRAK4
PPHLN1
ADAMTS20
PUS7L
RACGAP1P
TMEM117
ZCRB1
PRICKLE1
ANO6
ARID2
GXYLT1
LOC400027
DBX2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

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

Genes
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
B2M
CAPN3
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
PDIA3
HDC
ITPKA
LTK
MAP1A
MFAP1
SLC12A1
SORD
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
SECISBP2L
LCMT2
SERF2
SLC27A2
CHP
OIP5
CEP152
MAPKBP1
RTF1
MGA
VPS39
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PLDN
TUBGCP4
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
SPTBN5
CTDSPL2
DUOX1
TRPM7
FLJ10038
HAUS2
DTWD1
STARD9
SQRDL
ZFP106
SPATA5L1
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
SPPL2A
FRMD5
SHF
DUOXA1
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
LOC145663
ZSCAN29
TTBK2
CDAN1
STRC
ADAL
EXD1
C15orf33
UBR1
PATL2
PLA2G4F
LRRC57
HMGN2P46
SLC24A5
PLA2G4D
GLDN
USP50
TNFAIP8L3
SHC4
CTXN2
DUOXA2
CATSPER2P1
CKMT1A
SERINC4
LOC645212
MIR626
MIR627
LOC728758
OIP5-AS1
MIR147B
LOC100129387
LOC100132724
JMJD7
PLA2G4B
MIR1282
LOC100306975
MIR4310
SERF2-C15ORF63
MIR4716
MIR4713
MIR4712

Genes in Wide Peak

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

Table S46. 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 10q11.23.

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

Genes
hsa-mir-605
PRKG1
CSTF2T
MIR605

Genes in Wide Peak

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

Table S48. 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 16q12.1.

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

Genes
CYLD
HERPUD1
hsa-mir-138-2
hsa-mir-3181
ADCY7
AMFR
BBS2
CBLN1
CDH8
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
POLR2C
RBL2
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC12A3
GPR56
N4BP1
NUP93
IRX5
KATNB1
NUDT21
CNOT1
ZNF423
RPGRIP1L
ARL2BP
DKFZP434H168
TOX3
CCDC113
C16orf80
BRD7
PLLP
CES1P1
LPCAT2
HEATR3
SLC38A7
OGFOD1
DOK4
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
FTO
IRX6
IRX3
C16orf57
SETD6
FAM192A
CHD9
LONP2
NLRC5
CCDC135
CAPNS2
MT4
ABCC11
NKD1
RSPRY1
CCDC102A
ABCC12
C16orf78
SNX20
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
LOC283856
MT1DP
TEPP
LOC388276
CES1P2
MIR138-2
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
SNORA46
SNORA50
MIR3935
LOC100505619
LOC100507577
MIR548AE2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.31.

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

Genes
BTG1
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ATP2B1
CSRP2
DCN
EPYC
DUSP6
KCNC2
LUM
KITLG
MYF5
MYF6
PPP1R12A
NAP1L1
NTS
PAWR
SYT1
ALX1
EEA1
PPFIA2
GALNT4
LIN7A
RASSF9
GLIPR1
KERA
KRR1
PHLDA1
ZDHHC17
MGAT4C
CCDC59
SLC6A15
ACSS3
BBS10
CEP290
LRRIQ1
C12orf26
CAPS2
NAV3
C12orf29
OSBPL8
GLIPR1L2
TSPAN19
E2F7
TMTC2
TMTC3
C12orf50
C12orf12
LOC256021
GLIPR1L1
POC1B
OTOGL
LOC338758
C12orf74
PTPRQ
MKRN9P
C12orf37
PLEKHG7
ATXN7L3B
CLLU1OS
CLLU1
MIR617
MIR618
LOC728084
MIR1252
POC1B-GALNT4
MIR4699
MIR548AL

Genes in Wide Peak

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

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
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
hsa-mir-378
hsa-mir-145
hsa-mir-584
ADRA1B
ADRB2
ANXA6
ATOX1
BNIP1
CAMK2A
CANX
CCNG1
CDX1
CLTB
CSF1R
CSNK1A1
NKX2-5
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
DUSP1
F12
FABP6
FAT2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
NDST1
HTR4
IL12B
KCNMB1
LCP2
LTC4S
MFAP3
MGAT1
MSX2
PCDH1
PCDHGC3
PDE6A
POU4F3
PPP2R2B
MAPK9
PROP1
RARS
RPS14
SGCD
SLC6A7
SLC34A1
SLIT3
SNCB
SPARC
SPINK1
STK10
TAF7
ZNF354A
TCOF1
TTC1
STC2
PCDHGB4
ADAM19
FGF18
HDAC3
SQSTM1
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
ADAMTS2
RNF14
CLINT1
PCDHGA8
PCDHA9
MAML1
KIAA0141
JAKMIP2
GFPT2
GNPDA1
G3BP1
TNIP1
GNB2L1
SLU7
RGS14
CPLX2
C5orf4
FAM114A2
TCERG1
BTNL3
LMAN2
SPINK5
SOX30
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
ZNF346
GEMIN5
PCDHGA12
CCDC69
PCDHB5
TSPAN17
OR4F3
HAVCR1
CYFIP2
PRELID1
IL17B
MAT2B
MRPL22
PCDHB1
KCNIP1
ZNF354C
RPL26L1
C5orf45
DCTN4
PCDH12
DDX41
NOP16
LARS
HMP19
UIMC1
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
CDHR2
CCDC99
THG1L
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
NMUR2
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
KCTD16
PCDHB16
HMHB1
C5orf54
GMCL1P1
ARAP3
RMND5B
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC25A2
PCDHB19P
THOC3
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
SFXN1
GPRIN1
PWWP2A
C1QTNF2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
C5orf58
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SLC36A2
SPINK13
C5orf41
LOC153469
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
HIGD2A
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
LOC340037
ARSI
PFN3
ZNF879
IRGM
FBLL1
NIPAL4
C5orf25
FLJ38109
C5orf46
ARHGEF37
SPINK6
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
FLJ16171
MIR340
SNORD95
SNORD96A
LOC643201
GRXCR2
SPINK9
ZFP62
CBY3
FAM153C
SNORA74B
MIR585
MIR143HG
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3912
LOC100505658
LOC100507387
MIR4634
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.1.

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

Genes
PIK3R1
CCNB1
CDK7
GTF2H2
CD180
NAIP
PMCHL2
RAD17
SMN1
SMN2
TAF9
SERF1A
SMA4
SMA5
SLC30A5
CENPH
MRPS36
MARVELD2
CCDC125
MAST4
LOC647859
GUSBP3
GTF2H2B
GTF2H2C
SERF1B
GTF2H2D
GUSBP9
LOC100170939
LOC100272216
OCLN

Genes in Wide Peak

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

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

Genes
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
APP
ATP5J
BAGE
CXADR
GABPA
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
ADAMTS1
BTG3
ADAMTS5
USP25
RBM11
LINC00158
CHODL-AS1
C21orf15
LINC00308
MRPL39
C21orf91
JAM2
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
MIR155HG
CYYR1
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
D21S2088E
LINC00515
POTED
LOC339622
LINC00317
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR155
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37
MIR4759

Genes in Wide Peak

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

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

Genes
hsa-mir-1285-2
hsa-mir-3126
ANXA4
GFPT1
MXD1
MEIS1
PCBP1
PLEK
PPP3R1
RAB1A
SLC1A4
SNRPG
TGFA
TIA1
SERTAD2
ARHGAP25
ACTR2
C1D
PROKR1
SNRNP27
AAK1
CEP68
CNRIP1
NFU1
BMP10
LGALSL
PCYOX1
ETAA1
AFTPH
C2orf42
GKN1
PNO1
GMCL1
ANTXR1
FAM136A
WDR92
LINC00309
ASPRV1
GKN2
APLF
SPRED2
LOC339807
LOC400958
PCBP1-AS1
FBXO48
LOC644838
SNORA36C
LOC100133985
MIR3126
MIR4434
MIR4778

Genes in Wide Peak

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

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

Genes
hsa-mir-1274b
A1BG
FCAR
FKBP1AP1
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR2
PEG3
PTPRH
RPL28
RPS5
AURKC
SYT5
TNNI3
TNNT1
ZNF8
ZNF17
MZF1
ZNF132
ZNF134
ZNF135
ZNF154
UBE2M
ZNF264
NCR1
TRIM28
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
LILRB1
SLC27A5
LILRB4
LILRA1
LILRA2
U2AF2
PPP6R1
ZIM2
HSPBP1
ZNF324
CHMP2A
ZNF544
UBE2S
CCDC106
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
NLRP2
ZNF416
ZNF446
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
ZNF71
ZNF667
ZSCAN18
MGC2752
ZSCAN5A
LILRP2
ZNF329
ZNF419
ISOC2
ZNF552
ZNF671
ZNF606
BRSK1
SUV420H2
ZBTB45
ZNF587
FIZ1
GALP
ZNF628
KIR3DX1
ZNF551
ZNF835
LENG9
RDH13
ZIM3
LENG8
KIR3DL3
ZNF837
ZNF543
COX6B2
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF497
ZNF550
ZNF579
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
ZNF773
LOC386758
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF772
A1BG-AS1
DUXA
SBK2
LOC646862
SHISA7
ZNF814
MIMT1
LOC100128252
LOC100128398
SGK110
LOC100131691
PEG3-AS1
ZNF587B
ZNF865
MIR4754

Genes in Wide Peak

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

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

Genes
ACP1
RPS7
SOX11
TPO
TSSC1
PXDN
RNF144A
MYT1L
SH3YL1
TRAPPC12
SNTG2
ADI1
ALLC
COLEC11
RSAD2
CMPK2
TMEM18
LOC150622
RNASEH1
FAM150B
LOC339822
LOC386597
LOC400940
LINC00487
FAM110C
LOC727982
LOC730811
LOC100505964
LOC100506054
LOC100506274

Genes in Wide Peak

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

Table S57. 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

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 | 0.07 | 2.41 | 0.0386 | 0.02 | -3.53 | 1
1q | 1955 | 0.08 | 2.95 | 0.00874 | 0.01 | -4.11 | 1
2p | 924 | 0.04 | -3.14 | 1 | 0.02 | -4.73 | 1
2q | 1556 | 0.03 | -2.81 | 1 | 0.02 | -4.2 | 1
3p | 1062 | 0.05 | -1.39 | 1 | 0.06 | -0.905 | 1
3q | 1139 | 0.06 | -0.631 | 1 | 0.05 | -1.61 | 1
4p | 489 | 0.02 | -4.78 | 1 | 0.06 | -1.77 | 1
4q | 1049 | 0.02 | -4.2 | 1 | 0.05 | -1.94 | 1
5p | 270 | 0.05 | -2.61 | 1 | 0.04 | -3.78 | 1
5q | 1427 | 0.04 | -1.84 | 1 | 0.03 | -2.69 | 1
6p | 1173 | 0.02 | -4.02 | 1 | 0.10 | 3.04 | 0.00383
6q | 839 | 0.02 | -4.06 | 1 | 0.17 | 8.95 | 0
7p | 641 | 0.78 | 62.6 | 0 | 0.03 | -1.89 | 1
7q | 1277 | 0.79 | 69.8 | 0 | 0.03 | -1.4 | 1
8p | 580 | 0.05 | -2.36 | 1 | 0.07 | -0.837 | 1
8q | 859 | 0.06 | -0.783 | 1 | 0.04 | -2.67 | 1
9p | 422 | 0.04 | -2.4 | 1 | 0.41 | 28.3 | 0
9q | 1113 | 0.08 | 1.07 | 0.615 | 0.16 | 8.2 | 5.41e-16
10p | 409 | 0.08 | -0.105 | 1 | 0.81 | 62.7 | 0
10q | 1268 | 0.02 | -1.86 | 1 | 0.82 | 72.6 | 0
11p | 862 | 0.01 | -5.15 | 1 | 0.12 | 3.98 | 0.000135
11q | 1515 | 0.01 | -4.38 | 1 | 0.09 | 3.22 | 0.00229
12p | 575 | 0.08 | 0.197 | 1 | 0.11 | 2.77 | 0.00835
12q | 1447 | 0.06 | -0.243 | 1 | 0.09 | 2.66 | 0.011
13q | 654 | 0.01 | -5.2 | 1 | 0.28 | 17.9 | 0
14q | 1341 | 0.02 | -3.53 | 1 | 0.25 | 17.9 | 0
15q | 1355 | 0.02 | -4.29 | 1 | 0.11 | 4.98 | 1.39e-06
16p | 872 | 0.04 | -3.19 | 1 | 0.06 | -1.3 | 1
16q | 702 | 0.04 | -3.42 | 1 | 0.09 | 1.05 | 0.357
17p | 683 | 0.03 | -4.16 | 1 | 0.08 | -0.00741 | 1
17q | 1592 | 0.05 | -1.22 | 1 | 0.03 | -2.62 | 1
18p | 143 | 0.06 | -2.3 | 1 | 0.09 | 0.587 | 0.639
18q | 446 | 0.06 | -1.66 | 1 | 0.08 | -0.0139 | 1
19p | 995 | 0.33 | 23.6 | 0 | 0.05 | -1.52 | 1
19q | 1709 | 0.29 | 23.5 | 0 | 0.08 | 1.98 | 0.0621
20p | 355 | 0.31 | 19.7 | 0 | 0.03 | -4.01 | 1
20q | 753 | 0.31 | 20.9 | 0 | 0.03 | -3.65 | 1
21q | 509 | 0.06 | -1.4 | 1 | 0.05 | -2.16 | 1
22q | 921 | 0.03 | -3.52 | 1 | 0.26 | 17.7 | 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.

- 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/1444477/2.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 = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 560 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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