Glioblastoma Multiforme: Copy number analysis (GISTIC2)
(primary solid tumor cohort)
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: 23 significant arm-level results, 24 significant focal amplifications, and 46 significant focal deletions were found.

Results
Focal results

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

Table 1. Get Full Table Amplifications Table - 24 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 | 1.9648e-144 | 4.0464e-118 | chr12:58135797-58152580 | 4
4q12 | 3.0098e-103 | 3.0098e-103 | chr4:55139083-55159166 | 1
1q32.1 | 6.8424e-72 | 1.0227e-71 | chr1:204443069-204529807 | 2
12q15 | 1.3225e-73 | 5.5795e-32 | chr12:69178021-69265277 | 2
3q26.33 | 5.8115e-21 | 5.8115e-21 | chr3:181256574-181508514 | 2
19p13.2 | 8.6705e-13 | 8.6705e-13 | chr19:7300056-7398264 | 0 [INSR]
12p13.32 | 1.4577e-10 | 1.4577e-10 | chr12:4325317-4436676 | 2
7q31.2 | 1.6065e-08 | 4.4237e-08 | chr7:116318088-116480275 | 1
17p13.2 | 7.8145e-08 | 7.8145e-08 | chr17:5120021-5142747 | 2
1p36.21 | 5.7591e-07 | 5.7591e-07 | chr1:13862648-14377937 | 2
1q44 | 1.9293e-07 | 1.0411e-06 | chr1:243042268-244858016 | 11
2p24.3 | 1.9683e-06 | 1.9683e-06 | chr2:16015911-16440790 | 2
7q21.2 | 4.1597e-08 | 9.6362e-06 | chr7:92179103-92530348 | 3
4p16.3 | 0.00055266 | 0.00055266 | chr4:1778797-1816689 | 2
7q11.21 | 2.7048e-12 | 0.0014598 | chr7:57925000-63128930 | 6
17q25.1 | 0.0025755 | 0.0025755 | chr17:73169833-73641051 | 16
14q32.33 | 0.0081227 | 0.0081227 | chr14:104982904-105333748 | 10
13q34 | 0.01894 | 0.01894 | chr13:109765147-110884637 | 3
11p13 | 0.053492 | 0.053492 | chr11:31382963-32068175 | 6
19q12 | 0.056751 | 0.056751 | chr19:30211822-30321189 | 1
8q24.21 | 0.087726 | 0.087726 | chr8:127927022-131800277 | 21
21q21.1 | 0.12748 | 0.12748 | chr21:17519797-17649826 | 1
7q36.1 | 0.02544 | 0.24401 | chr7:123349925-159138663 | 317

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 12p13.32.

Table S6. 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 S7. 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 17p13.2.

Table S8. 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 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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q36.1.

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

Genes
BRAF
EZH2
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
CPA4
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 46 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 0 | 0 | chr9:21238609-22646396 | 19
10q23.31 | 6.5702e-59 | 4.0791e-56 | chr10:89617158-90034038 | 2
1p36.23 | 7.086e-55 | 1.0335e-38 | chr1:7829287-8423509 | 7
6q26 | 4.5371e-34 | 1.3754e-29 | chr6:163767962-165698161 | 2
13q14.2 | 7.9711e-28 | 7.9711e-28 | chr13:48833767-49064807 | 2
10q26.3 | 4.9031e-24 | 5.6422e-17 | chr10:135190263-135214343 | 1
19q13.41 | 8.5135e-16 | 8.5135e-16 | chr19:51500335-51915080 | 19
15q14 | 1.3917e-13 | 1.3719e-13 | chr15:33357233-44170698 | 141
1p32.3 | 7.373e-16 | 1.4673e-12 | chr1:50879767-51569162 | 3
14q13.1 | 2.5011e-12 | 1.3359e-11 | chr14:33301849-34394000 | 1
22q13.32 | 1.5587e-10 | 1.5048e-10 | chr22:48026910-49176545 | 5
4q34.3 | 3.7489e-09 | 3.7489e-09 | chr4:178911874-183060693 | 1
17q11.2 | 3.311e-07 | 3.3223e-07 | chr17:29326736-29722618 | 5
3q29 | 9.3013e-07 | 6.4845e-06 | chr3:190373502-197029425 | 63
17p13.1 | 6.5477e-08 | 2.6899e-05 | chr17:7526963-7591760 | 4
8p23.2 | 7.2776e-05 | 7.4667e-05 | chr8:2079140-6262191 | 1
1p36.32 | 3.9175e-26 | 0.00020871 | chr1:3394251-6475685 | 28
10p13 | 0.00012949 | 0.001011 | chr10:12616863-12768978 | 2
18q22.3 | 0.0019013 | 0.0018819 | chr18:67995567-73836684 | 17
1p22.1 | 1.0386e-05 | 0.0024023 | chr1:92759774-93924485 | 12
6q22.31 | 7.0467e-08 | 0.0028583 | chr6:111216911-147138228 | 194
10p11.23 | 0.00044158 | 0.0028583 | chr10:29830429-29892002 | 4
12p13.1 | 0.0029605 | 0.0030183 | chr12:9851683-18838946 | 105
12q12 | 0.00017465 | 0.0040455 | chr12:42982652-46578647 | 14
10p15.3 | 0.00078094 | 0.0044115 | chr10:1050841-2048902 | 7
11p15.5 | 0.003861 | 0.0047945 | chr11:1-6417816 | 198
16p12.2 | 0.004977 | 0.0047945 | chr16:20751348-27090703 | 61
2q37.1 | 0.0049419 | 0.0063679 | chr2:233432884-233736132 | 3
1q42.11 | 0.00093216 | 0.019738 | chr1:210847515-231667237 | 158
Xp22.2 | 0.023248 | 0.023334 | chrX:11792056-12870927 | 2
3q22.1 | 6.975e-05 | 0.023605 | chr3:129625562-129871534 | 3
2q22.1 | 0.030455 | 0.033853 | chr2:139655617-143637838 | 1
17p13.2 | 5.8234e-06 | 0.037001 | chr17:3851656-4048080 | 1
16q23.3 | 0.042478 | 0.042157 | chr16:70833950-90354753 | 178
1q44 | 0.0061226 | 0.042947 | chr1:245864790-247265054 | 10
4p16.3 | 0.05494 | 0.053602 | chr4:1197147-1284820 | 2
11p11.2 | 0.031131 | 0.056478 | chr11:36679363-49580689 | 85
12q15 | 0.0021194 | 0.065082 | chr12:58350632-69140499 | 44
3p21.1 | 0.083502 | 0.08181 | chr3:28358955-93777876 | 443
5q35.3 | 0.095756 | 0.09355 | chr5:149937740-180915260 | 252
3q13.31 | 0.00039855 | 0.10732 | chr3:115440285-116429324 | 1
14q31.3 | 0.0011123 | 0.12925 | chr14:69062324-107349540 | 403
21q22.3 | 0.14164 | 0.14227 | chr21:46230687-46306160 | 1
9q34.2 | 0.14464 | 0.14427 | chr9:136602059-136892308 | 1
11q14.1 | 0.13982 | 0.15697 | chr11:78285273-81604120 | 5
14q24.2 | 5.8011e-07 | 0.16658 | chr14:58888403-107349540 | 475

Genes in Wide Peak

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

Table S23. 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 S24. 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 S25. 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 S26. 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 S27. 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 S28. 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 S29. 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 S30. 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
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
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 S31. 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 S32. 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 22q13.32.

Table S33. 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 4q34.3.

Table S34. 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 S35. 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 S36. 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 S37. 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 S38. 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 S39. 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 10p13.

Table S40. 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 18q22.3.

Table S41. 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 S42. 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 6q22.31.

Table S43. 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
ARG1
COL10A1
CTGF
EPB41L2
EYA4
FABP7
FRK
FUCA2
FYN
GJA1
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
MAP3K5
NMBR
ENPP1
ENPP3
PEX7
PLAGL1
PLN
PKIB
PTPRK
REV3L
RPS12
SGK1
TCF21
TPD52L1
TSPYL1
UTRN
EPM2A
STX7
PEX3
STX11
WISP3
VNN2
VNN1
TAAR5
MAP7
TAAR2
TAAR3
MED23
AKAP7
TBPL1
KIAA0408
PHACTR2
BCLAF1
TRDN
CITED2
TRAF3IP2
HBS1L
SMPDL3A
RAB32
TSPYL4
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MOXD1
PDE7B
DSE
HDDC2
TUBE1
RWDD1
AIG1
VTA1
HECA
IL20RA
AHI1
VNN3
ECHDC1
HYMAI
GPR126
KIAA1244
NHSL1
SERINC1
C6orf115
PBOV1
TRMT11
PERP
ALDH8A1
OR2A4
FAM184A
ADGB
RNF146
SF3B5
TAAR8
FBXO30
RPF2
L3MBTL3
RSPO3
LTV1
REPS1
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
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
C6orf191
FAM26E
MCM9
SHPRH
LINC00326
LOC285740
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
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 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 12p13.1.

Table S45. 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
CLECL1
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 S46. 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 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 11p15.5.

Table S48. 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 16p12.2.

Table S49. 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 S50. 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 1q42.11.

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

Genes
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
ACTA1
PARP1
AGT
ARF1
ATF3
CAPN2
CENPF
EPHX1
EPRS
ESRRG
GALNT2
GUK1
H3F3A
HLX
ITPKB
KCNH1
KCNK2
LBR
MARK1
NEK2
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
SRP9
AURKAPS1
TGFB2
LEFTY2
TLR5
TP53BP2
TRAF5
USH2A
WNT9A
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
TAF1A
TMEM63A
URB2
LPGAT1
BPNT1
LEFTY1
SPHAR
CAPN9
DUSP10
COG2
FBXO28
ABCB10
RAB3GAP2
INTS7
NSL1
RPS6KC1
RNU5F-1
TAF5L
FLVCR1
CNIH4
PYCR2
NENF
RRP15
TRIM17
KCTD3
DTL
EGLN1
MARC2
SUSD4
GPATCH2
TMEM206
BATF3
SLC30A10
IARS2
ENAH
NUP133
RCOR3
SMYD2
ADCK3
GJC2
RHOU
ACBD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
WDR26
TRIM11
MIXL1
C1orf124
OBSCN
LINC00467
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
SNAP47
C1orf96
LYPLAL1
DNAH14
C1orf131
SPATA17
MRPL55
HIST3H2BB
TATDN3
BROX
CNIH3
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
C1orf65
IBA57
LIN9
ZNF678
PRSS38
RD3
MIA3
C1orf95
FAM89A
CAPN8
C1orf140
FAM177B
ZNF847P
MIR194-1
MIR215
TRIM67
H3F3AP4
DUSP5P
FLVCR1-AS1
LOC643723
SNRPD2P2
SNORA36B
SNORA16B
LOC728463
LOC100130093
MIR1182
MIR664
MIR320B2
MIR3122
MIR3620
PROX1-AS1
MIR4666A
MIR4742
LINC00538

Genes in Wide Peak

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

Table S52. 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 3q22.1.

Table S53. 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 2q22.1.

Table S54. 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 S55. 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 16q23.3.

Table S56. 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 S57. 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 4p16.3.

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

Genes
CTBP1
C4orf42

Genes in Wide Peak

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

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

Genes
DDB2
EXT2
CREB3L1
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
ACP2
ARHGAP1
CHRM4
CRY2
F2
FOLH1
CD82
LRP4
MDK
MYBPC3
NDUFS3
PSMC3
PTPRJ
RAPSN
SPI1
DGKZ
CHST1
API5
MADD
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
NR1H3
CELF1
NUP160
FNBP4
MTCH2
PACSIN3
HSD17B12
PHF21A
SLC35C1
AMBRA1
KBTBD4
TTC17
PRDM11
SYT13
LRRC4C
ALX4
C11orf49
ZNF408
AGBL2
ARFGAP2
ACCS
TSPAN18
SLC39A13
C1QTNF4
PTPMT1
OR4X2
OR4B1
GYLTL1B
LOC120824
C11orf94
ALKBH3
LOC221122
OR4C3
OR4S1
LOC283116
HARBI1
DKFZp779M0652
C11orf96
ACCSL
OR4X1
HNRNPKP3
FAM180B
OR4A47
OR4C45
MIR129-2
TRIM64C
SNORD67
LOC729799
MIR670
MIR3160-2
MIR3160-1
LOC100507205
LOC100507300
LOC100507401
MIR4688

Genes in Wide Peak

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

Table S60. 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 3p21.1.

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

Genes
CTNNB1
FHIT
MITF
MLH1
MYD88
BAP1
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
EPHA3
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
HTR1F
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
POU1F1
PRKAR2A
PRKCD
PROS1
PTH1R
PTPRG
QARS
SNORA62
ROBO1
ROBO2
RPL29
ATXN7
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
TKT
TMF1
CLEC3B
TNNC1
UBA7
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CGGBP1
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
VPRBP
IP6K1
EPM2AIP1
PSMD6
TRANK1
DLEC1
EXOG
XYLB
OXSR1
PDCD6IP
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
CRTAP
ARL6IP5
NPRL2
CXCR6
CSPG5
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
GNL3
RBMS3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
VILL
ABHD5
DYNC1LI1
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ZNF654
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
KIF9
AZI2
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
GPR62
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
ZCWPW2
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
ARL13B
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
C3orf38
ENTPD3-AS1
ZNF619
ZNF621
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
STX19
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
SNORA6
TMPPE
LOC644714
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
LOC100128640
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4444-1
MIR4443
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.3.

Table S62. 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
SYNPO
RNF44
TBC1D9B
ATP10B
N4BP3
FAF2
WWC1
FBXW11
LARP1
ZNF346
GEMIN5
CCDC69
TSPAN17
OR4F3
HAVCR1
CYFIP2
PRELID1
MAT2B
MRPL22
KCNIP1
ZNF354C
RPL26L1
C5orf45
DCTN4
DDX41
NOP16
HMP19
UIMC1
RAB24
NEURL1B
FAM193B
TMED9
CDHR2
CCDC99
THG1L
GALNT10
NHP2
RBM22
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
C5orf62
UNC5A
TRIM41
BOD1
COL23A1
TIMD4
ZNF300
MYOZ3
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 3q13.31.

Table S63. 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 14q31.3.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
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
SERPINA3
ACTN1
ACYP1
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF5
ELK2AP
EML1
ERH
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
ATXN3
MAP3K9
ALDH6A1
NDUFB1
SERPINA5
PGF
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSEN1
PSMC1
ABCD4
MOK
SEL1L
SRSF5
SLC8A3
SLC10A1
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0125
KIAA0317
TECPR2
MED6
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
SNW1
PCNX
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
TTC9
FLRT2
SIPA1L1
DCAF4
KIF26A
C14orf109
MLH3
PRO1768
GPR132
POMT2
COQ6
FCF1
SERPINA10
GLRX5
COX16
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
GALNTL1
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
AMN
SLIRP
DNAL1
RPS6KL1
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
ADAM21P1
GSC
SERPINA12
PRIMA1
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
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
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
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
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
LOC100507043
SYNJ2BP-COX16
MIR4505
MIR3545
MIR4709
MIR4710
MIR2392
LOC100628307

Genes in Wide Peak

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

Table S65. 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 9q34.2.

Table S66. 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 S67. 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 14q24.2.

Table S68. 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
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
NDUFB1
SIX6
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMC1
ABCD4
RAD51B
MOK
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
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
KIAA0586
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
DHRS7
ASB2
SIX4
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
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
C14orf149
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
SLC38A6
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
COX8C
ASPG
RAB15
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
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
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
C14orf38
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
HIF1A-AS2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 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 | 4.11 | 9.91e-05 | 0.03 | -4.57 | 1
1q | 1955 | 0.15 | 4.86 | 3.4e-06 | 0.03 | -4.8 | 1
2p | 924 | 0.06 | -3.74 | 1 | 0.06 | -3.49 | 1
2q | 1556 | 0.06 | -3.28 | 1 | 0.06 | -2.88 | 1
3p | 1062 | 0.10 | -0.574 | 1 | 0.08 | -2.24 | 1
3q | 1139 | 0.11 | 0.4 | 1 | 0.06 | -3.09 | 1
4p | 489 | 0.07 | -3.44 | 1 | 0.11 | -0.733 | 1
4q | 1049 | 0.06 | -3.47 | 1 | 0.11 | 0.121 | 0.786
5p | 270 | 0.09 | -2.29 | 1 | 0.09 | -2.29 | 1
5q | 1427 | 0.08 | -1.97 | 1 | 0.08 | -1.31 | 1
6p | 1173 | 0.04 | -4.37 | 1 | 0.16 | 3.91 | 0.000139
6q | 839 | 0.05 | -4.22 | 1 | 0.22 | 8.37 | 0
7p | 641 | 0.82 | 52.5 | 0 | 0.07 | -1.27 | 1
7q | 1277 | 0.83 | 56.1 | 0 | 0.06 | -1.48 | 1
8p | 580 | 0.09 | -1.48 | 1 | 0.12 | 0.256 | 0.76
8q | 859 | 0.10 | -0.543 | 1 | 0.09 | -1.3 | 1
9p | 422 | 0.11 | -0.16 | 1 | 0.38 | 18.4 | 0
9q | 1113 | 0.14 | 2.75 | 0.0134 | 0.18 | 5.05 | 7.54e-07
10p | 409 | 0.15 | 0.952 | 0.682 | 0.85 | 53.7 | 0
10q | 1268 | 0.05 | -1.6 | 1 | 0.86 | 58.8 | 0
11p | 862 | 0.02 | -6.1 | 1 | 0.18 | 5.17 | 4.19e-07
11q | 1515 | 0.02 | -5.82 | 1 | 0.17 | 5.63 | 3.66e-08
12p | 575 | 0.11 | -0.314 | 1 | 0.13 | 0.798 | 0.472
12q | 1447 | 0.09 | -0.717 | 1 | 0.11 | 0.999 | 0.374
13q | 654 | 0.03 | -5.39 | 1 | 0.33 | 15.7 | 0
14q | 1341 | 0.05 | -3.84 | 1 | 0.27 | 12.7 | 0
15q | 1355 | 0.05 | -3.76 | 1 | 0.18 | 6.07 | 2.9e-09
16p | 872 | 0.07 | -2.57 | 1 | 0.12 | 0.717 | 0.499
16q | 702 | 0.08 | -2.49 | 1 | 0.15 | 3 | 0.00391
17p | 683 | 0.08 | -2.39 | 1 | 0.13 | 1.35 | 0.235
17q | 1592 | 0.10 | 0.284 | 1 | 0.09 | -0.785 | 1
18p | 143 | 0.10 | -1.37 | 1 | 0.14 | 1.03 | 0.374
18q | 446 | 0.10 | -1.06 | 1 | 0.12 | 0.169 | 0.786
19p | 995 | 0.40 | 21.3 | 0 | 0.09 | -1.05 | 1
19q | 1709 | 0.35 | 19.4 | 0 | 0.10 | 0.544 | 0.586
20p | 355 | 0.39 | 19.7 | 0 | 0.05 | -3.87 | 1
20q | 753 | 0.39 | 20.4 | 0 | 0.05 | -3.78 | 1
21q | 509 | 0.12 | 0.0636 | 1 | 0.08 | -2.53 | 1
22q | 921 | 0.08 | -1.66 | 1 | 0.33 | 16.6 | 0
Xq | 1312 | 0.04 | -4.24 | 1 | 0.21 | 8.03 | 2.22e-15

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-TP/2328062/2.GDAC_MergeDataFiles.Finished/GBM-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

- Reference Genome = /xchip/cga/reference/gistic2/hg19_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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