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 537 tumor samples used in this analysis: 25 significant arm-level results, 14 significant focal amplifications, and 51 significant focal deletions were found.

Results
Focal results

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

Table 1. Get Full Table Amplifications Table - 14 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 | chr7:54931889-54940689 | 0 [EGFR]
4q12 | 1.9161e-85 | 1.9161e-85 | chr4:54727006-54861623 | 1
12q14.1 | 4.4294e-117 | 2.3639e-84 | chr12:56370368-56455799 | 9
1q32.1 | 1.1746e-62 | 1.3349e-62 | chr1:202664385-202815140 | 2
12q15 | 7.1631e-77 | 2.0869e-53 | chr12:67458319-67547022 | 2
3q26.33 | 3.3041e-11 | 3.3041e-11 | chr3:182584087-183214870 | 2
12p13.32 | 9.7872e-09 | 9.7872e-09 | chr12:4066737-4302336 | 2
7q31.2 | 1.7517e-08 | 3.0092e-08 | chr7:116105324-116267511 | 1
1q44 | 3.086e-07 | 6.0698e-07 | chr1:241495233-242804011 | 6
1p36.21 | 1.2539e-06 | 1.2539e-06 | chr1:13735235-14250524 | 2
7q21.2 | 1.0958e-06 | 2.4105e-06 | chr7:91966270-92368284 | 5
2p24.3 | 3.2222e-06 | 3.2222e-06 | chr2:15933362-16304271 | 2
13q34 | 0.042782 | 0.042782 | chr13:103769050-110973523 | 20
8q24.21 | 0.094211 | 0.094211 | chr8:127996204-130415992 | 7

Genes in Wide Peak

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

Table S1. 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 12q14.1.

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
OS9
FAM119B
MARCH9
AGAP2
LOC100130776

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
SOX2OT

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 1q44.

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

Genes
ADSS
AKT3
ZNF238
SDCCAG8
C1orf100
C1orf101

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 7q21.2.

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

Genes
CDK6
PEX1
C7orf64
MGC16142
FAM133B

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 13q34.

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

Genes
hsa-mir-1267
COL4A1
COL4A2
EFNB2
ING1
LIG4
IRS2
ARHGEF7
TNFSF13B
MYO16
ARGLU1
ANKRD10
RAB20
CARKD
CARS2
ABHD13
C13orf16
DAOA
C13orf29
FAM155A

Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1208
hsa-mir-1206
hsa-mir-1204
POU5F1B
PVT1
LOC727677

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

Table 2. Get Full Table Deletions Table - 51 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 0 | 0 | chr9:21337238-23680570 | 15
10q23.31 | 6.6264e-55 | 1.9145e-52 | chr10:89607138-90024018 | 2
1p36.23 | 5.6379e-51 | 3.0181e-48 | chr1:7751874-8309316 | 6
10q23.1 | 2.1447e-20 | 3.8865e-18 | chr10:82379735-85894629 | 1
6q26 | 2.5539e-19 | 1.9954e-17 | chr6:163662302-165618151 | 1
1p33 | 1.6258e-19 | 2.0823e-16 | chr1:50652354-51341750 | 3
13q14.2 | 8.0644e-19 | 1.0478e-15 | chr13:47731768-47962808 | 2
14q13.1 | 4.2884e-12 | 4.2884e-12 | chr14:32371600-33463751 | 1
15q14 | 4.2884e-12 | 4.2884e-12 | chr15:31935411-38816958 | 52
3p21.31 | 4.074e-10 | 4.074e-10 | chr3:46424169-46515615 | 1
8p23.2 | 5.4328e-10 | 5.4328e-10 | chr8:2080589-6255647 | 1
4q35.1 | 1.349e-07 | 1.5604e-07 | chr4:176134071-191273063 | 59
10p13 | 1.1038e-08 | 3.8706e-07 | chr10:16598992-16909230 | 1
3q29 | 8.1702e-08 | 6.2164e-07 | chr3:192078476-197505280 | 36
17p13.1 | 7.3605e-07 | 9.5451e-07 | chr17:7476186-7534290 | 2
22q13.31 | 3.0401e-06 | 3.1485e-06 | chr22:44619793-49691432 | 62
10p13 | 6.9023e-07 | 3.7594e-05 | chr10:12332572-12915213 | 1
19q13.33 | 7.4786e-05 | 7.2827e-05 | chr19:50971881-59162546 | 357
11p15.4 | 0.00013186 | 0.00012913 | chr11:4617298-4658488 | 2
17q22 | 0.0001098 | 0.00016367 | chr17:52553420-53272917 | 1
17q11.2 | 0.00011676 | 0.00016367 | chr17:26350862-26746744 | 4
1q44 | 8.987e-05 | 0.00016685 | chr1:243931413-244771113 | 1
2q37.1 | 0.00023185 | 0.00023185 | chr2:233255611-233467000 | 3
4q24 | 0.00016367 | 0.00027045 | chr4:103212807-103643260 | 1
10q11.21 | 2.7537e-09 | 0.0002799 | chr10:44190049-44775968 | 2
12q15 | 0.00085757 | 0.00085132 | chr12:64145677-67368862 | 14
3q13.31 | 0.00031488 | 0.00088614 | chr3:116922975-117912014 | 1
1p22.1 | 1.83e-05 | 0.002181 | chr1:92532362-94407394 | 18
10p15.3 | 4.6351e-06 | 0.0040988 | chr10:1198827-3169967 | 2
10q11.23 | 3.2339e-05 | 0.0050659 | chr10:52314091-53747935 | 5
16p12.1 | 0.0022498 | 0.0059653 | chr16:20270894-26988410 | 61
10q11.23 | 0.00022435 | 0.0063228 | chr10:50469025-50565460 | 2
13q21.2 | 1.0761e-06 | 0.0079708 | chr13:48765547-92681733 | 96
11p11.2 | 0.016283 | 0.016654 | chr11:46097348-46582832 | 5
1q41 | 0.00377 | 0.018921 | chr1:206482777-229733860 | 158
8q24.3 | 0.027461 | 0.028102 | chr8:144487985-146274826 | 76
12p13.1 | 0.060812 | 0.060363 | chr12:9281636-21580636 | 115
6q16.3 | 0.0079603 | 0.069683 | chr6:70978855-118338364 | 196
2q22.1 | 0.071912 | 0.070962 | chr2:139248662-143354308 | 1
9q34.3 | 0.074877 | 0.076269 | chr9:136313587-136912612 | 2
5q35.3 | 0.10043 | 0.10054 | chr5:140071300-180857866 | 367
18q22.3 | 0.11523 | 0.11533 | chr18:59134918-76117153 | 54
6q24.2 | 1.9733e-05 | 0.12917 | chr6:125183614-148709593 | 116
21q21.1 | 0.13231 | 0.12917 | chr21:1-27135300 | 40
16q12.1 | 0.13293 | 0.13568 | chr16:46942223-63538597 | 97
16p13.3 | 0.066818 | 0.14324 | chr16:5085718-8560695 | 1
2p25.3 | 0.15543 | 0.1499 | chr2:1-6907089 | 21
17p12 | 0.12538 | 0.16292 | chr17:15405082-15555845 | 2
3q26.31 | 0.083909 | 0.189 | chr3:173057484-173646142 | 1
5p15.33 | 0.18825 | 0.189 | chr5:1-10408133 | 53
6q22.31 | 0.00098273 | 0.80377 | chr6:1-170899992 | 1120

Genes in Wide Peak

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

Table S14. 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
IFNA6
IFNA8
IFNA13
MTAP
C9orf53
DMRTA1
IFNE
MIR31
LOC554202
CDKN2BAS

Genes in Wide Peak

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

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

Genes
PTEN
KILLIN

Genes in Wide Peak

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

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

Genes
TNFRSF9
PER3
VAMP3
UTS2
PARK7
ERRFI1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.1.

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

Genes
NRG3

Genes in Wide Peak

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

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

Genes
QKI

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p33.

Table S19. 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 13q14.2.

Table S20. 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 14q13.1.

Table S21. 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 15q14.

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

Genes
BUB1B
C15orf55
hsa-mir-1233
hsa-mir-1233
ACTC1
CHRM5
IVD
MEIS2
PLCB2
RAD51
SRP14
THBS1
AQR
SLC12A6
RASGRP1
GPR176
BAHD1
GOLGA8A
RPUSD2
TMEM85
ZNF770
NOP10
C15orf24
PAK6
CASC5
AVEN
GJD2
C15orf29
C15orf41
DISP2
ATPBD4
C15orf57
C15orf23
BMF
CHST14
LOC145845
TMCO5A
CSNK1A1P
SPRED1
PGBD4
FSIP1
LPCAT4
FAM98B
MRPL42P5
C15orf52
C15orf53
C15orf54
GOLGA8B
EIF2AK4
C15orf56
PHGR1
LOC723972

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.31.

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

Genes
LTF

Genes in Wide Peak

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

Table S24. 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 4q35.1.

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

Genes
DUX4
hsa-mir-1305
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
SORBS2
FAM149A
PDLIM3
CLDN22
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
TUBB4Q
STOX2
KIAA1430
SPCS3
C4orf41
MLF1IP
WWC2
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
TRIML1
ANKRD37
HELT
FAM92A3
C4orf47
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

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

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

Genes
RSU1

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
APOD
CPN2
FGF12
GP5
HES1
MUC4
OPA1
PCYT1A
PPP1R2
TNK2
ACAP2
LSG1
HRASLS
ATP13A3
ATP13A4
MGC2889
TMEM44
ZDHHC19
LRRC15
FAM43A
C3orf59
C3orf21
CCDC50
PYDC2
OSTalpha
MUC20
SDHALP1
UTS2D
OSTN
ATP13A5
MIR570
SDHALP2
LOC100128023
LOC100131551

Genes in Wide Peak

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

Table S28. 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 22q13.31.

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

Genes
hsa-let-7b
ACR
ARSA
CHKB
CPT1B
TYMP
PPARA
MAPK11
MAPK12
SBF1
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
FAM19A5
NCAPH2
GTSE1
MOV10L1
TTC38
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC150381
C22orf40
CN5H6.4
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

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

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

Genes
CAMK1D

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
KLK2
PPP2R1A
ZNF331
hsa-mir-373
hsa-mir-519a-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-220c
hsa-mir-769
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
DBP
DMWD
EMP3
ETFB
FCGRT
FLT3LG
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GPR32
GRIN2D
GRLF1
GYS1
HAS1
FOXA3
HRC
PRMT1
IRF3
KCNA7
KCNC3
KCNJ14
KLK1
LHB
LIG1
LIM2
MYBPC2
NKG7
NOVA2
NPAS1
NTF4
NUCB1
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTGIR
RPL18
RPS11
RRAS
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SPIB
SULT2B1
SULT2A1
TULP2
NR1H2
ZNF28
ZNF137
ZNF175
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
CYTH2
NAPSA
KLK4
ZNF432
DHX34
SAE1
RUVBL2
KDELR1
KLK11
KPTN
KLK8
PNKP
ATF5
CARD8
ZC3H4
RPL13A
SYNGR4
NUP62
PPP1R15A
KLK5
PRKD2
ZNF473
KLK13
CCDC9
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
DHDH
SLC6A16
STRN4
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
HSD17B14
VRK3
PTOV1
TRPM4
FAM83E
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
KLK15
ZNF701
ZNF83
ZNF415
CABP5
SPHK2
MEIS3
SLC17A7
RCN3
PNMAL2
PRR12
PLEKHA4
SCAF1
CACNG7
ZNF350
TSKS
ELSPBP1
LIN7B
HIF3A
ZNF649
FKRP
TBC1D17
MYH14
ZNF665
ZNF613
ZNF702P
ZNF614
FUZ
RSHL1
ZNF611
MED25
BCL2L12
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
SNORD35B
ZNF347
ZNF577
C19orf48
SIGLEC10
SIGLEC12
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
CGB8
GNG8
BIRC8
FAM71E1
PTH2
SIGLEC11
CGB1
CGB2
LMTK3
CLDND2
ZNF816A
ZNF813
JOSD2
C19orf41
CPT1C
ALDH16A1
NTN5
VSIG10L
NCRNA00085
ZNF480
ZNF534
ZNF578
LOC147804
CCDC155
DACT3
IGFL2
ZNF836
ZNF610
ZNF600
ZNF320
ZNF114
ZNF525
SPACA4
C19orf76
PRR24
NAPSB
IL4I1
TPRX1
MAMSTR
IZUMO1
C19orf63
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VN1R2
VN1R4
MYPOP
NANOS2
ZNF677
IGFL1
IGFL3
ZNF808
ZNF761
ZNF321
SIGLEC16
FLJ26850
ZNF880
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
MIR371
MIR372
MIR373
IGFL4
DPRX
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR643
RPL13AP5
CCDC61
CEACAM18
MIR769
SIGLEC14
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
BSPH1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SNAR-A14

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
OR51E1
OR51D1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q22.

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

Genes
MSI2

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG

Genes in Wide Peak

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

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

Genes
SMYD3

Genes in Wide Peak

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

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

Genes
KCNJ13
GIGYF2
C2orf82

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q24.

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

Genes
SLC39A8

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.21.

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

Genes
CXCL12
TMEM72

Genes in Wide Peak

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

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

Genes
HMGA2
IFNG
RAP1B
DYRK2
IRAK3
GRIP1
IL22
TMBIM4
IL26
CAND1
MDM1
LLPH
HELB
RPSAP52

Genes in Wide Peak

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

Table S40. 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 1p22.1.

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

Genes
hsa-mir-760
ABCA4
DR1
GFI1
GCLM
SNORD21
RPL5
EVI5
BCAR3
MTF2
SNORA66
DNTTIP2
TMED5
FNBP1L
RPAP2
CCDC18
FAM69A
MIR760

Genes in Wide Peak

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

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

Genes
ADARB2
PFKP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.23.

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

Genes
hsa-mir-605
PRKG1
DKK1
CSTF2T
MIR605

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p12.1.

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

Genes
PALB2
AQP8
CDR2
CRYM
NDUFAB1
PLK1
PRKCB
RBBP6
ACSM3
SCNN1B
SCNN1G
UQCRC2
ZP2
HS3ST4
HS3ST2
IGSF6
CACNG3
ERN2
GGA2
NPIPL3
TNRC6A
EEF2K
METTL9
LCMT1
ACSM5
ARHGAP17
DNAH3
THUMPD1
POLR3E
UBFD1
TMEM159
LYRM1
USP31
CHP2
LOC81691
DCTN5
COG7
ERI2
SLC5A11
ACSM1
ACSM2A
DCUN1D3
EARS2
VWA3A
OTOA
C16orf82
PDILT
C16orf65
ANKS4B
ZKSCAN2
ACSM2B
IMAA
NCRNA00169
LOC641298
LOC653786
LOC730092
C16orf52
LOC100131998
LOC100132247
LOC100190986
LOC100271836

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.23.

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

Genes
CHAT
SLC18A3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.2.

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

Genes
hsa-mir-92a-1
hsa-mir-622
hsa-mir-1297
hsa-mir-15a
ATP7B
KLF5
BTF3L1
CLN5
DACH1
EDNRB
GPC5
GUCY1B2
KPNA3
LMO7
NEK3
PCDH8
PCDH9
POU4F1
ATXN8OS
UCHL3
SCEL
DLEU2
UTP14C
TBC1D4
TRIM13
SPRY2
DLEU1
PIBF1
OLFM4
SUGT1
LECT1
KLF12
DIS3
MYCBP2
SLITRK5
FBXL3
INTS6
CKAP2
PCDH17
VPS36
PHF11
NDFIP2
RCBTB1
THSD1
C13orf1
KLHL1
RBM26
PCDH20
RNF219
RNASEH2B
DHRS12
C13orf34
TDRD3
CAB39L
DIAPH3
CCDC70
SETDB2
SLITRK6
EBPL
SLITRK1
KCTD12
ARL11
WDFY2
SLAIN1
PRR20A
LOC144776
HNRNPA1L2
FAM10A4
COMMD6
DLEU7
FAM124A
LOC220115
LOC220429
OR7E156P
KCNRG
FLJ37307
NEK5
THSD1P
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ALG11
C13orf37
SERPINE3
LOC647288
MIR548A2
PRR20B
PRR20C
PRR20D
PRR20E

Genes in Wide Peak

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

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

Genes
CREB3L1
CHRM4
MDK
DGKZ
AMBRA1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q41.

Table S48. 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-205
ACTA1
PARP1
AGT
ARF1
ATF3
CAPN2
CENPF
EPHX1
EPRS
ESRRG
GALNT2
GUK1
H3F3A
HLX
HSD11B1
IRF6
ITPKB
KCNH1
KCNK2
LAMB3
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
C1orf107
TAF5L
FLVCR1
CNIH4
PYCR2
NENF
G0S2
RRP15
TRIM17
KCTD3
DTL
EGLN1
MOSC2
SUSD4
GPATCH2
TMEM206
BATF3
SLC30A10
IARS2
HHAT
ENAH
NUP133
RCOR3
SERTAD4
SMYD2
CABC1
GJC2
CAMK1G
RHOU
ACBD3
MOSC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
WDR26
TRAF3IP3
TRIM11
MIXL1
C1orf124
OBSCN
C1orf97
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
SNAP47
C1orf96
LYPLAL1
DNAH14
C1orf131
SPATA17
MRPL55
HIST3H2BB
TATDN3
C1orf74
C1orf58
CNIH3
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
C1orf65
C1orf69
SYT14
LIN9
ZNF678
PRSS38
RD3
MIA3
C1orf95
FAM89A
CAPN8
LOC400804
FAM177B
MIR194-1
MIR205
MIR215
TRIM67
LOC440926
DUSP5P
C1orf133
LOC642587
LQK1
SNORA36B
SNORA16B
LOC100130093

Genes in Wide Peak

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

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

Genes
RECQL4
hsa-mir-1234
hsa-mir-661
CYC1
EEF1D
GPT
GRINA
HSF1
NFKBIL2
PLEC1
RPL8
TSTA3
ZNF7
ZNF16
DGAT1
GPAA1
FOXH1
LRRC14
ZNF623
PUF60
ZC3H3
BOP1
SCRIB
FBXL6
OPLAH
COMMD5
CPSF1
CYHR1
VPS28
C8orf30A
EXOSC4
SLC39A4
ZNF250
PYCRL
C8orf33
C8orf51
GPR172A
GSDMD
KIAA1688
ZNF34
SHARPIN
EPPK1
SCRT1
MAF1
PARP10
TIGD5
PPP1R16A
ZNF251
KIFC2
NAPRT1
MFSD3
RHPN1
ADCK5
MAPK15
ZNF707
BREA2
FAM83H
ZNF252
TMED10P
C8orf77
NRBP2
ZNF517
KIAA1875
C8ORFK29
SPATC1
MAFA
MGC70857
LRRC24
C8orf73
SCXB
MIR661
HEATR7A
MIR937
MIR939
SCXA
LOC100130274

Genes in Wide Peak

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

Table S50. 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
hsa-mir-1244
hsa-mir-1244
ARHGDIB
ART4
CD69
CDKN1B
CREBL2
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
IAPP
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
MGP
MGST1
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
RECQL
SLCO1A2
KLRC4
CSDA
GPRC5A
CLEC2B
SLCO1B1
KLRA1
STRAP
PRR4
KLRK1
GABARAPL1
SLCO1B3
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
HEBP1
GOLT1B
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
SLCO1C1
PLEKHA5
MANSC1
MAGOHB
STYK1
GPRC5D
ATF7IP
H2AFJ
LMO3
KIAA1467
CLEC7A
BCL2L14
RERGL
PLBD1
PYROXD1
C12orf39
DUSP16
APOLD1
GSG1
RERG
PLCZ1
HTR7P
CAPZA3
LOH12CR1
C12orf59
HIST4H4
ERP27
AEBP2
C12orf60
CLEC12A
CLECL1
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
CLEC9A
C12orf36
LST-3TM12
TAS2R42
LOC374443
CLEC2A
CLEC12B
RPL13AP20
DDX12
C12orf69
LOH12CR2
LOC642846
PRB2
MIR613
MIR614

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.3.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-587
hsa-mir-2113
hsa-mir-30a
AIM1
AMD1
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COX7A2
EEF1A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
REV3L
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDC2L6
MDN1
TSPYL4
KIAA0776
ORC3L
MTO1
SFRS18
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
NCRNA00120
DDX43
FAM46A
TMEM30A
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
MANEA
C6orf155
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
C6orf168
GJA10
RTN4IP1
USP45
SLC22A16
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
C6orf150
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SFRS13B
C6orf221
C6orf165
PRSS35
LCA5
C6orf163
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
VGLL2
LACE1
C6orf167
FAM26E
SCML4
C6orf182
PPIL6
FLJ34503
DCBLD1
DPPA5
RSPH4A
GJB7
SNHG5
C6orf147
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
LOC442245
RFPL4B
LOC553137
C6orf225
TSG1
SNORD50B
LOC728402
C6orf186
BET3L
KHDC1L

Genes in Wide Peak

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

Table S52. 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 9q34.3.

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

Genes
COL5A1
RXRA

Genes in Wide Peak

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

Table S54. 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-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-1303
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
PCDH24
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
GMCL1L
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
LOC134466
NUDCD2
UBLCP1
SLC36A2
SPINK5L3
C5orf41
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
HIGD2A
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
ARSI
PFN3
ZNF879
IRGM
FBLL1
NIPAL4
C5orf25
C5orf46
FLJ41603
SPINK6
MIR103-1
MIR143
MIR145
MIR146A
MIR218-2
SPINK5L2
C5orf40
MIR340
SNORD95
SNORD96A
GRXCR2
SPINK9
ZFP62
CBY3
FAM153C
SNORA74B
MIR548D2
MIR585
LOC728264
LOC728554
AACSL
LOC729678
OR4F29
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
LOC100286948

Genes in Wide Peak

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

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

Genes
BCL2
CDH7
CYB5A
KDSR
GALR1
MBP
NFATC1
SERPINB2
SERPINB5
SERPINB8
SERPINB10
SERPINB13
SERPINB3
SERPINB4
ZNF236
SERPINB7
CTDP1
SOCS6
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
SALL3
CDH19
C18orf55
TMX3
ZNF407
CNDP2
CCDC102B
C18orf22
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
DSEL
FAM69C
CBLN2
FBXO15
DOK6
C18orf20
ZADH2
C18orf62
LOC284276
HMSD
ATP9B
LOC400657
HSBP1L1
LOC100130522

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q24.2.

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

Genes
MYB
TNFAIP3
STL
hsa-mir-548a-2
hsa-mir-588
ARG1
CTGF
EPB41L2
EYA4
FUCA2
GRM1
HIVEP2
IFNGR1
LAMA2
MAP3K5
NMBR
ENPP1
ENPP3
PEX7
PLAGL1
PTPRK
RPS12
SGK1
TCF21
TPD52L1
UTRN
EPM2A
STX7
PEX3
STX11
VNN2
VNN1
TAAR5
MAP7
TAAR2
TAAR3
MED23
AKAP7
TBPL1
KIAA0408
PHACTR2
BCLAF1
CITED2
HBS1L
RAB32
HEY2
HEBP2
CCDC28A
MOXD1
PDE7B
HDDC2
AIG1
VTA1
HECA
IL20RA
AHI1
VNN3
ECHDC1
HYMAI
GPR126
KIAA1244
NHSL1
C6orf115
PBOV1
TRMT11
PERP
ALDH8A1
OR2A4
C6orf103
RNF146
SF3B5
TAAR8
FBXO30
L3MBTL3
RSPO3
LTV1
REPS1
ARHGAP18
FAM54A
TMEM200A
IL22RA2
C6orf192
ADAT2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
LOC153910
C6orf94
SAMD3
MGC34034
SLC2A12
RNF217
OLIG3
TXLNB
C6orf191
SHPRH
LOC285733
LOC285735
LOC285740
TAAR6
SLC35D3
ECT2L
C6orf58
C6orf173
C6orf174
THEMIS
SAMD5
SNORD101
SNORD100
SNORA33
CTAGE9
LOC729176
C6orf217
NHEG1

Genes in Wide Peak

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

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

Genes
hsa-mir-155
hsa-mir-125b-2
APP
ATP5J
BAGE
CXADR
GABPA
NCAM2
PRSS7
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
NCRNA00158
NCRNA00157
C21orf15
MRPL39
C21orf91
JAM2
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
MIR155HG
CYYR1
CHODL
C21orf99
LIPI
ABCC13
C21orf71
POTED
C21orf131
C21orf34
C21orf81
MIRLET7C
MIR125B2
MIR99A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q12.1.

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

Genes
CYLD
HERPUD1
hsa-mir-138-2
ADCY7
AMFR
BBS2
CBLN1
CDH8
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
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
CES4
LPCAT2
HEATR3
SLC38A7
OGFOD1
DOK4
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
FTO
IRX6
IRX3
C16orf57
SETD6
FAM192A
CHD9
NLRC5
CCDC135
CAPNS2
MT4
NKD1
RSPRY1
CCDC102A
C16orf78
SNX20
CPNE2
GPR114
KLKBL4
CES7
GPR97
TMEM188
LOC283856
MT1DP
TEPP
MIR138-2
MT1IP
LOC644649
SNORA46
SNORA50

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

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

Genes
A2BP1

Genes in Wide Peak

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

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

Genes
ACP1
RPS7
SOX11
TPO
TSSC1
PXDN
MYT1L
SH3YL1
TTC15
SNTG2
ADI1
ALLC
COLEC11
TMEM18
LOC150622
RNASEH1
FAM150B
C2orf90
LOC400940
FAM110C
LOC730811

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

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

Genes
TRIM16
CDRT1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

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

Genes
FNDC3B

Genes in Wide Peak

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

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

Genes
ADCY2
MTRR
NDUFS6
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
SEMA5A
TRIP13
PDCD6
SLC12A7
POLS
TPPP
EXOC3
CCT5
KIAA0947
LOC25845
IRX4
TAS2R1
NSUN2
CEP72
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
MED10
NKD2
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285692
SLC6A19
LOC340094
SLC6A18
LRRC14B
FLJ33360
SDHAP3
LOC728613
SNORD123
LOC100310782

Genes in Wide Peak

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

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

Genes
PRDM1
CCND3
DAXX
FANCE
HMGA1
IRF4
MLLT4
MYB
PIM1
POU5F1
TRIM27
ROS1
SFRS3
TNFAIP3
DEK
TFEB
STL
HIST1H4I
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-548a-2
hsa-mir-588
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-30a
hsa-mir-133b
hsa-mir-586
hsa-mir-1275
hsa-mir-219-1
hsa-mir-1236
hsa-mir-877
hsa-mir-548a-1
ABCF1
ACAT2
CRISP1
AGER
AIF1
AIM1
AMD1
ARG1
ATP6V1G2
BAI3
BAK1
BCKDHB
CFB
BMP5
BMP6
DST
BPHL
BTN1A1
BYSL
C2
C4A
C4B
DDR1
RUNX2
CCNC
CDC5L
CDKN1A
CDSN
CGA
CLIC1
CLPS
CCR6
CNR1
COL9A1
COL10A1
COL11A2
COL12A1
COL19A1
COX7A2
ATF6B
MAPK14
CSNK2B
CTGF
CYP21A2
DNAH8
DOM3Z
DSP
E2F3
EDN1
EEF1A1
SERPINB1
SLC29A1
EPB41L2
EPHA7
EYA4
ESR1
F13A1
FABP7
FKBP5
FOXF2
FOXC1
FOXO3
FRK
FUCA2
FYN
GABBR1
GABRR1
GABRR2
GCNT2
GJA1
GCLC
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPR6
GPR31
GPX5
GRIK2
GRM1
GRM4
GSTA1
GSTA2
GSTA3
GSTA4
GTF2H4
GUCA1A
GUCA1B
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HCRTR2
HDAC2
HFE
HIVEP1
HIVEP2
HLA-A
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSF2
HSPA1A
HSPA1B
HSPA1L
HSP90AB1
HTR1B
HTR1E
ID4
IFNGR1
IGF2R
IL17A
IMPG1
ITPR3
JARID2
KIFC1
KIF25
KPNA5
LAMA2
LAMA4
LPA
LTA
LTB
MARCKS
MAK
MAN1A1
MAS1
MCM3
MDFI
ME1
MEA1
MAP3K4
MAP3K5
MEP1A
MICA
MICB
MLN
MOCS1
MOG
MSH5
MUT
MYO6
RPL10A
NEDD9
NEU1
NFKBIE
NFKBIL1
NFYA
NMBR
NQO2
NOTCH4
NT5E
OPRM1
PARK2
PBX2
PCMT1
PDCD2
ENPP1
ENPP3
PEX6
PEX7
PGC
PGK2
PGM3
PHF1
SERPINB6
SERPINB9
PKHD1
PLAGL1
PLG
PLN
POLH
POU3F2
PPARD
PPP1R2P1
PPP1R10
PPP2R5D
PREP
PRIM2
PKIB
MAPK13
PRL
PSMB1
PSMB8
PSMB9
PTK7
PTPRK
RGL2
PRPH2
REV3L
RHAG
RING1
BRD2
RNF5
RPS6KA2
RPS10
RPS12
RPS18
RREB1
RXRB
VPS52
ATXN1
SGK1
SIM1
SKIV2L
SLC17A1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SNRPC
SOD2
SOX4
SRF
SRPK1
SSR1
ELOVL4
T
TAF11
MAP3K7
TAP1
TAP2
TAPBP
TBCC
TBP
TCF19
TCF21
TCP1
TCP10
TCP11
TCTE3
PPP1R11
DYNLT1
TEAD3
TFAP2A
TFAP2B
THBS2
NR2E1
TNF
TNXA
TNXB
TPBG
TPD52L1
TPMT
CRISP2
TSPYL1
TTK
TUBB2A
TULP1
UTRN
VARS
VEGFA
EZR
VIP
ZNF76
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204
PTP4A1
ALDH5A1
BAT2
BAT3
BAT4
BAT1
BAT5
SLC39A7
HSD17B8
OR2H2
RDBP
LST1
PLA2G7
EPM2A
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
STX7
CMAH
DHX16
SUPT3H
PEX3
GCM1
DDO
RNASET2
KCNK5
STX11
B3GALT4
SNX3
RNGTT
RIPK1
CD164
SYNGAP1
WISP3
STK19
IER3
SYNJ2
VNN2
VNN1
PRPF4B
WASF1
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
TAAR5
MAP7
TBX18
LATS1
GCM2
WDR46
ZBTB22
TAAR2
TAAR3
CD83
HMGN3
PPT2
CDYL
NCR2
MED23
QKI
LY86
FHL5
AKAP7
ATG5
MED20
SLC25A27
TBPL1
EEF1E1
BAG2
POLR1C
MAD2L1BP
WTAP
AKAP12
MDC1
TRAM2
KIAA0408
PHACTR2
FAM65B
ZSCAN12
BCLAF1
CUL7
ZBTB24
KIAA0319
SNAP91
FIG4
NUP153
CASP8AP2
RANBP9
SLC17A4
UST
TRIM10
FLOT1
RCAN2
SLC17A2
HCG9
PRSS16
CRISP3
TRDN
CITED2
BTN3A3
BTN2A2
PECI
PFDN6
HMGN4
TRIM38
CAP2
SYNCRIP
UBD
AGPAT1
SLC35A1
SCGN
C6orf108
C6orf10
FARS2
FUT9
CNPY3
TRAF3IP2
HBS1L
SLC17A3
RPP40
FRS3
PDE10A
SLC22A7
HCP5
EHMT2
SMPDL3A
APOBEC2
PNRC1
ASCC3
RAB32
TRIM31
KATNA1
BTN3A2
BTN3A1
BTN2A1
CAPN11
BVES
NUDT3
SEC63
NRM
STK38
RBM16
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
FTSJD2
CDC2L6
CUL9
MAP3K7IP2
MDN1
TSPYL4
ANKS1A
UBR2
SASH1
SYNE1
KIAA0776
SIRT5
PHF3
HEY2
DAAM2
KIAA0240
DDAH2
HEBP2
ORC3L
CD2AP
BRD7P3
MTCH1
ZNF318
SPDEF
MTO1
ASF1A
YIPF3
USP49
CCDC28A
MTHFD1L
SFRS18
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
OR2B6
TIAM2
FBXL4
C6orf123
FAM50B
FBXO9
FBXO5
SLC17A5
OR12D2
OR11A1
RGS17
OR2W1
OR2J2
OR2H1
SNORD52
SNORD50A
SNORD48
PDE7B
FILIP1
BRPF3
GNMT
TNFRSF21
SESN1
TINAG
DLL1
OSTM1
MRPS18B
TMEM14A
MRPL18
NDUFAF4
C6orf15
MYLIP
ABT1
DSE
PRICKLE4
PACSIN1
ZNRD1
CLDN20
NOX3
DEF6
C6orf48
SLC35B3
HDDC2
GMNN
MRPL2
TFB1M
CYB5R4
TUBE1
C6orf203
TBC1D7
NRN1
CYP39A1
CDC40
RWDD1
AIG1
NOL7
SNX9
FAM8A1
UBE2J1
DCDC2
ETV7
TMEM14C
VTA1
LGSN
TTRAP
CUTA
PPIL1
BRP44L
HECA
RAB23
COQ3
CLIC5
IL20RA
TREM2
TREM1
UNC93A
HCG4
GFOD1
HMGCLL1
MTRF1L
CCHCR1
GTPBP2
BTN2A3
AHI1
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
MRPS18A
MRPS10
LRRC1
PHF10
QRSL1
VNN3
TMEM63B
NCRNA00120
DDX43
FAM46A
LRRC16A
TBC1D22B
TMEM30A
EXOC2
C6orf64
C6orf70
LMBRD1
TRERF1
ACOT13
ECHDC1
APOM
BTNL2
KCNQ5
TRIM39
AGPAT4
WRNIP1
DUSP22
TULP4
RARS2
HYMAI
PDSS2
LYRM4
C6orf162
VARS2
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
MRS2
PLEKHG1
ARID1B
LRFN2
AARS2
XPO5
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
CPNE5
LSM2
C6orf47
LY6G5B
C6orf115
RRAGD
LY6G6D
ENPP5
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
ZFAND3
SLC22A23
C6orf164
MUTED
CCDC90A
GPSM3
FKBPL
KIF13A
PERP
SMOC2
POPDC3
ZNF323
ALDH8A1
C6orf106
MICAL1
MRPL14
DLK2
LY6G6E
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
ZNF322A
MANEA
C6orf103
TREML2
RPP21
C6orf155
C6orf134
FRMD1
C6orf59
C6orf208
C6orf97
MYCT1
ZKSCAN3
ULBP2
ULBP1
ZSCAN16
LPAL2
RNF39
SLC44A4
C6orf27
C6orf25
LY6G6C
LY6G5C
PRR3
KHDC1
NCRNA00171
PRRT1
EGFL8
HCG2P7
HCG4P6
GPR63
TXNDC5
COL21A1
C6orf62
OR5V1
OR2B2
PPP1R14C
OR12D3
SPACA1
RNF146
TMEM14B
SF3B5
TAAR8
SH3BGRL2
RIOK1
TFAP2D
KCNK16
RSPH3
TTLL2
FKSG83
DTNBP1
ARMC2
FBXO30
RPF2
C6orf125
L3MBTL3
FAM120B
MCHR2
PGBD1
C6orf168
FNDC1
TTBK1
GJA10
RTN4IP1
C6orf105
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
HIST1H2AH
HIST1H2BK
PPIL4
PAQR8
C6orf114
SLC22A16
C6orf153
KCNK17
ABCC10
TRIM15
KLC4
UBE2CBP
C6orf142
C6orf176
KIAA1919
TJAP1
ARHGAP18
POM121L2
SYTL3
FOXQ1
GTF3C6
MRAP2
RWDD2A
IL17F
FAM54A
SFT2D1
EFHC1
BTBD9
KLHL32
TMEM200A
SCAND3
C6orf150
FOXP4
KLHDC3
NUS1
C6orf72
SLC26A8
IL22RA2
MAS1L
C6orf192
SLC16A10
IP6K3
TAGAP
TAF8
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SFRS13B
C6orf141
HUS1B
TRIM40
DPCR1
NRSN1
LOC153910
C6orf94
SNRNP48
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
MBOAT1
HDGFL1
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
C6orf195
LOC154449
C6orf129
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
PSORS1C1
PSORS1C2
KIAA1949
PTCRA
OSTCL
TCTE1
KHDRBS2
TUBB
C6orf163
MGC26597
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
RSPH9
C6orf154
TREML2P
LOC221442
C6orf130
KIF6
TMEM217
FGD2
PI16
C6orf89
C6orf81
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12L1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
LOC221710
SYCP2L
C6orf218
C6orf145
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
GPR111
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
LOC222699
C6orf146
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
HCG27
C6orf191
C6orf167
WDR27
FAM26E
MCM9
RNF144B
HIST1H2BA
SCML4
GPX6
SHPRH
NCR3
LY6G6F
MDGA1
GPR110
ZNF311
LOC285733
LOC285735
LOC285740
C6orf182
PPIL6
FLJ34503
DCBLD1
LOC285768
LOC285780
CAGE1
LOC285796
PRR18
LOC285830
HCG22
LOC285847
PNPLA1
TREML4
RPL7L1
RNF5P1
TAAR6
SLC35D3
ZC3H12D
MYLK4
DPPA5
IFITM4P
C6orf127
TREML1
TREML3
RSPH4A
ECT2L
EYS
ZNF391
ZFP57
TUBB2B
SLC35B2
C6orf52
NUP43
HCG26
C6orf58
RAET1G
KAAG1
GUSBL2
GJB7
NHLRC1
ZKSCAN4
GUSBL1
SNHG5
FAM136B
SUMO4
C6orf147
C6orf173
C6orf174
C6orf204
C6orf120
THEMIS
PSMG4
SFTA2
C6orf126
C6orf222
C6orf140
GFRAL
LIN28B
SAMD5
IYD
MUC21
DKFZP686I15217
FLJ22536
MCCD1
C6orf26
C6orf227
CRIP3
KLHL31
TCP10L2
C6orf122
DEFB133
C6orf201
GTF2H5
HERV-FRD
MIR206
MIR219-1
MIR30A
MIR30C2
HCG18
C6orf226
TMEM151B
OOEP
FAM26F
LOC441177
OR2B3
OR2J3
OR14J1
OR10C1
C6orf138
MCART3P
LOC442245
RFPL4B
MIR133B
GGNBP1
HCG11
LOC553137
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
CTAGE9
RAET1K
C6orf132
PPP1R3G
ZNF389
C6orf124
LYPLA2P1
SNORA20
SNORA29
SNORA38
SNORD50B
SNORD32B
SNORD84
SNORD117
MIR548A1
MIR548B
MIR586
LOC728402
C6orf186
HULC
LOC729176
LOC729603
LOC730101
TDRG1
TMEM170B
SCARNA27
MIR877
HGC6.3
BET3L
KHDC1L
PSORS1C3
C6orf217
LOC100132354
C6orf41
TOMM6
LOC100270746
LOC100287718
NHEG1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 25 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.08 | 4.4 | 3.01e-05 | 0.01 | -4.15 | 1
1q | 1572 | 0.09 | 4.33 | 3.6e-05 | 0.01 | -4.26 | 1
2p | 753 | 0.04 | -1.97 | 1 | 0.02 | -3.61 | 1
2q | 1235 | 0.03 | -1.71 | 1 | 0.02 | -3.44 | 1
3p | 853 | 0.05 | -0.166 | 1 | 0.05 | -0.166 | 0.959
3q | 917 | 0.06 | 0.828 | 0.662 | 0.04 | -1.03 | 1
4p | 366 | 0.02 | -3.86 | 1 | 0.05 | -1.22 | 1
4q | 865 | 0.02 | -3.71 | 1 | 0.04 | -1.49 | 1
5p | 207 | 0.06 | -0.012 | 1 | 0.04 | -2.44 | 1
5q | 1246 | 0.06 | 0.566 | 0.857 | 0.03 | -1.93 | 1
6p | 937 | 0.02 | -3.51 | 1 | 0.08 | 2.44 | 0.0189
6q | 692 | 0.02 | -3.17 | 1 | 0.16 | 10.1 | 0
7p | 508 | 0.79 | 72.1 | 0 | 0.03 | -1.48 | 1
7q | 1071 | 0.79 | 76.7 | 0 | 0.03 | -1.26 | 1
8p | 495 | 0.04 | -1.65 | 1 | 0.06 | -0.043 | 0.917
8q | 697 | 0.06 | 0.145 | 1 | 0.04 | -2.03 | 1
9p | 343 | 0.06 | 0.102 | 1 | 0.38 | 30.5 | 0
9q | 916 | 0.07 | 1.97 | 0.107 | 0.16 | 10.8 | 0
10p | 312 | 0.10 | 1.67 | 0.186 | 0.81 | 71.8 | 0
10q | 1050 | 0.03 | -0.931 | 1 | 0.83 | 80.2 | 0
11p | 731 | 0.01 | -4.52 | 1 | 0.11 | 5.69 | 2.54e-08
11q | 1279 | 0.01 | -3.82 | 1 | 0.09 | 4.29 | 2.91e-05
12p | 484 | 0.07 | 1.11 | 0.472 | 0.08 | 2 | 0.0494
12q | 1162 | 0.05 | 0.297 | 0.996 | 0.07 | 2.39 | 0.0205
13q | 554 | 0.00 | -4.67 | 1 | 0.28 | 21.6 | 0
14q | 1144 | 0.01 | -3.81 | 1 | 0.24 | 19.7 | 0
15q | 1132 | 0.01 | -3.63 | 1 | 0.12 | 6.62 | 7.63e-11
16p | 719 | 0.03 | -2.75 | 1 | 0.07 | 1.08 | 0.275
16q | 562 | 0.03 | -2.97 | 1 | 0.09 | 3.12 | 0.00249
17p | 575 | 0.02 | -3.76 | 1 | 0.08 | 2.34 | 0.0221
17q | 1321 | 0.04 | -1.15 | 1 | 0.03 | -1.73 | 1
18p | 117 | 0.05 | -1.01 | 1 | 0.10 | 3.8 | 0.000217
18q | 340 | 0.05 | -0.592 | 1 | 0.07 | 1.16 | 0.252
19p | 870 | 0.33 | 27.9 | 0 | 0.06 | 0.262 | 0.736
19q | 1452 | 0.31 | 26.9 | 0 | 0.10 | 4.9 | 1.71e-06
20p | 295 | 0.31 | 24.4 | 0 | 0.02 | -2.95 | 1
20q | 627 | 0.32 | 25.7 | 0 | 0.03 | -2.49 | 1
21q | 422 | 0.06 | 0.496 | 0.864 | 0.05 | -0.742 | 1
22q | 764 | 0.03 | -2.44 | 1 | 0.26 | 20.7 | 0

Methods & Data
Input

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/1216763/2.GDAC_MergeDataFiles.Finished/GBM.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

- Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

- CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.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 537 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-02-0021-01A-01D-0182-01
TCGA-02-0024-01B-01D-0182-01

Figure 3. Segmented copy number profiles in the input data

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
Meta

- Maintainer = Dan DiCara

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