SNP6 Copy number analysis (GISTIC2)
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C12J69HX
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C12J69HX
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 2.0.21 (Firehose task version: 127).

Summary

There were 569 tumor samples used in this analysis: 32 significant arm-level results, 32 significant focal amplifications, and 36 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 - 32 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
--- | --- | --- | --- | ---
8q24.21 | 6.8764e-153 | 6.8764e-153 | chr8:128494482-129683450 | 11
3q26.2 | 6.1982e-119 | 6.1982e-119 | chr3:168670994-168783199 | 0 [MECOM]
19q12 | 2.063e-93 | 3.53e-69 | chr19:30306758-30331242 | 1
19p13.12 | 2.9546e-38 | 4.4985e-38 | chr19:15333311-15422141 | 2
11q14.1 | 1.1081e-31 | 1.1081e-31 | chr11:77620713-78035831 | 9
1p34.3 | 6.4195e-27 | 6.4195e-27 | chr1:39887948-40168864 | 8
1q21.3 | 3.679e-26 | 4.0231e-18 | chr1:150483517-150739128 | 9
6p22.3 | 9.9439e-16 | 9.9439e-16 | chr6:18423406-18698180 | 3
7q36.3 | 6.2858e-13 | 6.2858e-13 | chr7:145626981-159138663 | 110
5p15.33 | 6.3359e-11 | 6.3359e-11 | chr5:1-1428010 | 26
20q13.33 | 2.1372e-10 | 9.7995e-10 | chr20:62137482-63025520 | 41
1q42.2 | 1.2932e-13 | 3.8729e-09 | chr1:234417530-235727932 | 17
Xp11.23 | 1.2878e-07 | 1.2878e-07 | chrX:48532582-49592201 | 50
2q31.2 | 2.5197e-07 | 2.5197e-07 | chr2:178462915-178609187 | 2
15q26.3 | 7.8057e-07 | 7.8057e-07 | chr15:97998762-102531392 | 35
12p12.1 | 2.6134e-11 | 1.6879e-06 | chr12:24880663-25881603 | 7
Xq28 | 1.6879e-06 | 1.6879e-06 | chrX:152900017-154883511 | 77
4p16.3 | 1.2475e-05 | 1.2475e-05 | chr4:1653353-1991609 | 11
17q25.3 | 1.2757e-05 | 1.2757e-05 | chr17:77641568-78054101 | 7
10p15.3 | 0.00018411 | 0.00018411 | chr10:749239-1314547 | 8
14q11.2 | 6.4202e-06 | 0.00061977 | chr14:21338460-21606746 | 13
8p11.21 | 0.00068231 | 0.00068231 | chr8:41567872-42008185 | 2
12p13.33 | 1.9938e-06 | 0.00072368 | chr12:1-3556349 | 35
19q13.2 | 7.2612e-27 | 0.0045813 | chr19:39311157-40342966 | 41
10q22.3 | 0.0050822 | 0.0050822 | chr10:79307097-79800033 | 5
18q11.2 | 0.0071339 | 0.0071339 | chr18:23773718-24293308 | 3
4q13.3 | 0.0072495 | 0.0072495 | chr4:73122319-74300609 | 4
2p23.2 | 0.011986 | 0.011986 | chr2:28811078-28966789 | 1
20p13 | 0.082808 | 0.082808 | chr20:1-4110252 | 89
22q12.2 | 0.12105 | 0.12105 | chr22:30113489-30813423 | 15
20q11.21 | 0.027771 | 0.17383 | chr20:30061713-30332464 | 10
14q32.33 | 0.0051711 | 0.18806 | chr14:105216303-107349540 | 26

Genes in Wide Peak

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

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

Genes
MYC
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
PVT1
MIR1205
MIR1206
MIR1207
MIR1204
MIR1208

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
BRD4
EPHX3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q14.1.

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

Genes
NDUFC2
THRSP
GAB2
USP35
KCTD14
ALG8
INTS4
KCTD21
NDUFC2-KCTD14

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.3.

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

Genes
PABPC4
MACF1
HEYL
HPCAL4
NT5C1A
BMP8A
SNORA55
PPIEL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
hsa-mir-4257
CTSS
ECM1
ENSA
MCL1
ADAMTSL4
GOLPH3L
HORMAD1
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

Table S7. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-548a-1
RNF144B
MIR548A1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q36.3.

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

Genes
EZH2
MLL3
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
ABP1
CDK5
DPP6
EN2
GBX1
MNX1
HTR5A
INSIG1
KCNH2
NOS3
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
VIPR2
XRCC2
ZNF212
ZNF282
CUL1
ACCN3
PDIA4
UBE3C
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
CNTNAP2
GIMAP2
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ESYT2
ZNF398
GALNT11
LMBR1
LINC00244
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
C7orf29
AGAP3
C7orf13
ZNF786
ASB10
RNF32
LOC154822
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5P3
CNPY1
LOC285889
ZNF775
LOC285972
ATG9B
WDR86
LOC401431
MIR153-2
GIMAP6
ZNF862
LOC645249
ACTR3C
MIR595
LOC728743
MIR671
LOC100128264
LOC100128822
LOC100131176
LOC100132707
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MIR3907
LOC100505483
LOC100506585
GIMAP1-GIMAP5

Genes in Wide Peak

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

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

Genes
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4457
MIR4456
MIR4635

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
hsa-mir-647
NPBWR2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
PCMTD2
SLC2A4RG
ZNF512B
C20orf195
PPDPF
DNAJC5
ZGPAT
PRIC285
ZBTB46
SAMD10
ABHD16B
LINC00266-1
C20orf201
LINC00176
MIR647
UCKL1-AS1
MIR941-1
MIR941-4
MIR941-2
MIR941-3
MIR1914
LOC100505815
RTEL1-TNFRSF6B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.2.

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

Genes
GNG4
TARBP1
TBCE
GGPS1
TOMM20
RBM34
ARID4B
SLC35F3
B3GALNT2
IRF2BP2
C1orf31
SNORA14B
LINC00184
LOC100506795
LOC100506810
MIR4753
MIR4671

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.23.

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

Genes
GATA1
TFE3
WAS
CACNA1F
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
ERAS
KCND1
PRICKLE3
PLP2
SUV39H1
SYP
SLC35A2
PAGE1
HDAC6
PQBP1
TIMM17B
PIM2
WDR45
PRAF2
GAGE12I
GAGE2E
GPKOW
PCSK1N
CCDC22
FOXP3
OTUD5
GRIPAP1
MAGIX
PPP1R3F
CCDC120
GLOD5
GAGE10
GAGE2B
GAGE13
GAGE12G
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
GAGE12F
GAGE8
GAGE12D

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q31.2.

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

Genes
PDE11A
TTC30A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
hsa-mir-1302-10
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
LINS
SELS
TTC23
LRRK1
TM2D3
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
ADAMTS17
DNM1P46
CERS3
FAM169B
WASH3P
FLJ42289
OR4F6
OR4F15
FAM138E
GPCRLTM7
DDX11L1
DDX11L9
LOC100507472
MIR4714

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

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

Genes
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
ABCD1
ARHGAP4
ATP6AP1
AVPR2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
OPN1MW
GDI1
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
TAZ
VBP1
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SRPK3
SNORA70
CTAG2
TMLHE
PLXNA3
PDZD4
FAM3A
FUNDC2
BRCC3
H2AFB3
RAB39B
GAB3
PNCK
CTAG1A
LINC00204B
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CXorf68
LINC00204A
MTCP1NB
MIR1184-1
MIR718
MIR3202-2
MIR1184-3
MIR1184-2
MIR3202-1
LOC100507404

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
hsa-mir-943
LETM1
WHSC2
SLBP
TACC3
TMEM129
FAM53A
SCARNA22
MIR943

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

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

Genes
CBX4
CCDC40
CBX8
CBX2
TBC1D16
ENPP7
MIR4739

Genes in Wide Peak

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

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

Genes
ADARB2
IDI1
WDR37
LARP4B
GTPBP4
IDI2-AS1
IDI2
LINC00200

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q11.2.

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

Genes
RNASE2
RNASE3
SLC39A2
ZNF219
ARHGEF40
NDRG2
METTL17
RNASE7
TPPP2
RNASE8
RNASE13
ECRP
C14orf176

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
ANK1
KAT6A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
KDM5A
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
CACNA2D4
FBXL14
DCP1B
B4GALNT3
LOC283440
IQSEC3
LOC574538
LRTM2
FAM138D
LOC100271702
LOC100288778
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

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

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

Genes
CLC
ECH1
FBL
HNRNPL
NFKBIB
MRPS12
RPS16
SUPT5H
ZFP36
DYRK1B
GMFG
PAK4
DLL3
SIRT2
LGALS13
PAF1
SARS2
SAMD4B
MED29
LGALS14
LRFN1
PLEKHG2
TIMM50
FBXO17
EID2B
RINL
FBXO27
LGALS16
EID2
IL28A
IL28B
IL29
NCCRP1
SYCN
LEUTX
SELV
PAPL
LGALS17A
LOC643669
LOC100129935
MIR4530

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.3.

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

Genes
KCNMA1
RPS24
DLG5
POLR3A
LOC100128292

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
TAF4B
KCTD1
LOC728606

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
ALB
ADAMTS3
ANKRD17
COX18

Genes in Wide Peak

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

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

Genes
PLB1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p13.

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

Genes
hsa-mir-103-2-as
hsa-mir-1292
AVP
CDC25B
CENPB
CSNK2A1
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PDYN
PTPRA
SIGLEC1
SNRPB
SOX12
TCF15
TGM3
ATRN
PSMF1
SNPH
ProSAPiP1
SIRPB1
NOP56
RBCK1
RNF24
UBOX5
SPEF1
C20orf194
SNORD57
SNORD56
SDCBP2
ANGPT4
C20orf27
C20orf29
TMEM74B
SIRPG
NSFL1C
CPXM1
MAVS
EBF4
TRIB3
FASTKD5
GFRA4
VPS16
FAM113A
MRPS26
DDRGK1
ZNF343
NRSN2
PANK2
ADAM33
DEFB126
FAM110A
SLC4A11
ZCCHC3
SCRT2
C20orf54
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
C20orf96
SRXN1
DEFB127
DEFB129
SIRPA
STK35
DEFB125
DEFB128
SIRPB2
RSPO4
TGM6
DEFB132
C20orf202
MIR103A2
RAD21L1
SNORA51
SNORD86
SNORD110
SNORD119
LOC100134015
TMEM239
LOC100289473
MIR1292
MIR103B2
LOC100507495
FKBP1A-SDCBP2

Genes in Wide Peak

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

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

Genes
LIF
OSM
MTMR3
SF3A1
SEC14L2
UQCR10
ZMAT5
TBC1D10A
ASCC2
KIAA1656
HORMAD2
CABP7
RNF215
CCDC157
GATSL3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-3193
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
LINC00028
PSIMCT-1
MIR3193

Genes in Wide Peak

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

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

Genes
AKT1
CRIP1
CRIP2
ELK2AP
BRF1
JAG2
ADAM6
MTA1
KIAA0125
SIVA1
PACS2
GPR132
CDCA4
TMEM121
BTBD6
AHNAK2
C14orf79
PLD4
MGC23270
NUDT14
KIAA0284
C14orf80
LINC00226
LINC00221
TEX22
ZBTB42

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 - 36 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
--- | --- | --- | --- | ---
19p13.3 | 2.9235e-140 | 2.9235e-140 | chr19:1272041-1882761 | 24
22q13.32 | 8.8866e-64 | 8.8866e-64 | chr22:49146971-51304566 | 42
11p15.5 | 1.3243e-41 | 1.3541e-41 | chr11:502218-772981 | 17
6q27 | 2.5611e-36 | 2.5671e-36 | chr6:156266097-171115067 | 92
13q14.2 | 2.4157e-35 | 2.4106e-35 | chr13:48833767-49064807 | 2
1p36.11 | 8.5799e-35 | 8.5799e-35 | chr1:26795113-27570286 | 16
5q13.2 | 4.7787e-89 | 4.026e-31 | chr5:66492413-80256908 | 96
18q23 | 2.175e-29 | 2.1623e-29 | chr18:67995567-78077248 | 36
5q11.2 | 2.4885e-75 | 1.4221e-26 | chr5:58145167-59787985 | 3
7p22.1 | 3.069e-25 | 3.069e-25 | chr7:1-6733205 | 81
4q34.3 | 5.6969e-33 | 8.3475e-25 | chr4:178911874-183060693 | 1
15q15.1 | 6.945e-23 | 6.945e-23 | chr15:41795901-42068054 | 5
8p23.3 | 1.4447e-41 | 2.3276e-19 | chr8:1-1244373 | 6
17q11.2 | 3.7956e-18 | 5.6793e-18 | chr17:29326736-29722618 | 5
10q24.2 | 5.0906e-17 | 5.0997e-17 | chr10:88859357-111624768 | 239
8p21.2 | 5.3517e-36 | 9.5306e-15 | chr8:25896447-26250295 | 1
Xp21.1 | 1.0638e-13 | 1.0638e-13 | chrX:30865118-34644819 | 4
16q23.1 | 8.9636e-23 | 1.2204e-12 | chr16:78016120-79627770 | 2
12q24.33 | 1.0568e-11 | 1.0281e-11 | chr12:131692956-133851895 | 27
2q22.1 | 4.0675e-12 | 1.4488e-09 | chr2:139655617-143637838 | 1
16p13.3 | 4.2148e-09 | 4.1204e-09 | chr16:3764793-4013466 | 1
14q23.3 | 2.6714e-08 | 2.6714e-08 | chr14:59114448-73705982 | 105
3p26.2 | 6.1181e-08 | 6.1138e-08 | chr3:1-4396118 | 8
9q34.13 | 1.9449e-06 | 1.9721e-06 | chr9:131933735-140151408 | 181
4q22.1 | 8.6219e-12 | 4.7702e-06 | chr4:90844993-93240505 | 1
19q13.43 | 4.2607e-17 | 3.4147e-05 | chr19:58368882-59128983 | 35
2q37.3 | 8.1082e-09 | 0.0001243 | chr2:234985548-243199373 | 82
19q13.33 | 6.0419e-17 | 0.00023297 | chr19:46080683-49564123 | 151
9p24.3 | 0.00034178 | 0.00034501 | chr9:1-12693402 | 48
16q22.1 | 5.695e-17 | 0.00087639 | chr16:68383494-68879824 | 4
11q25 | 0.0019841 | 0.0019797 | chr11:120006706-135006516 | 126
17p12 | 0.00397 | 0.0054218 | chr17:11896630-12456081 | 3
21q22.3 | 0.018397 | 0.018561 | chr21:42519390-48129895 | 103
10p15.3 | 0.076817 | 0.076711 | chr10:1-1040137 | 5
2p25.3 | 0.098506 | 0.098506 | chr2:1-25969186 | 126
1q41 | 0.14714 | 0.14644 | chr1:207316102-220440260 | 83

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.3.

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

Genes
TCF3
hsa-mir-1909
EFNA2
GAMT
RPS15
APC2
UQCR11
DAZAP1
MBD3
PCSK4
C19orf24
REXO1
KLF16
MUM1
REEP6
PLK5
C19orf25
ATP8B3
ADAMTSL5
NDUFS7
ONECUT3
MEX3D
LOC100288123
MIR1909

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: Cancer Gene Census[7].

Genes
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
NCAPH2
MOV10L1
MIOX
PANX2
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR4535

Genes in Wide Peak

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

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

Genes
HRAS
hsa-mir-210
DRD4
IRF7
SCT
TALDO1
RASSF7
DEAF1
CDHR5
PHRF1
EPS8L2
LRRC56
LOC143666
C11orf35
TMEM80
MIR210
MIR210HG

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
hsa-mir-1202
ACAT2
CCR6
GPR31
IGF2R
KIF25
LPA
MAS1
MAP3K4
PARK2
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
EZR
RNASET2
SYNJ2
QKI
WTAP
PDE10A
C6orf123
DLL1
MRPL18
SNX9
BRP44L
UNC93A
PHF10
C6orf70
AGPAT4
TULP4
ARID1B
TMEM181
SMOC2
ZDHHC14
FRMD1
AGPAT4-IT1
C6orf208
LPAL2
RSPH3
TTLL2
FAM120B
FNDC1
SERAC1
LINC00473
SYTL3
SFT2D1
TAGAP
PACRG
PNLDC1
LOC154449
DACT2
C6orf118
OSTCP1
WDR27
LOC285796
PRR18
C6orf120
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
LOC441177
MLLT4-AS1
SNORA20
SNORA29
TMEM242
LOC729603
HGC6.3
LOC100129518
C6orf99
LOC100289495
MIR1913
MIR3918
MIR3939
MIR3692
CAHM
MIR4466
MIR4644

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
ARID1A
hsa-mir-1976
SFN
HMGN2
RPS6KA1
SLC9A1
NR0B2
NUDC
GPN2
PIGV
GPATCH3
ZDHHC18
FAM46B
C1orf172
TRNP1
MIR1976

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.2.

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

Genes
PIK3R1
ARSB
BHMT
BTF3
CCNB1
CDK7
CRHBP
DHFR
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
TNPO1
MAP1B
MSH3
NAIP
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
THBS4
SERF1A
ENC1
AP3B1
PDE8B
HOMER1
SCAMP1
CARTPT
ZFYVE16
COL4A3BP
LHFPL2
NSA2
IQGAP2
SMA4
SMA5
SV2C
MRPS27
OTP
BHMT2
FAM169A
DMGDH
GCNT4
POLK
AGGF1
WDR41
BDP1
ANKRA2
MCCC2
RGNEF
SLC30A5
CENPH
PTCD2
UTP15
ZBED3
GFM2
SPZ1
MRPS36
FCHO2
JMY
TMEM171
TMEM174
POC5
MARVELD2
PAPD4
ZNF366
FAM151B
S100Z
CCDC125
CMYA5
ANKRD31
SERINC5
ANKRD34B
MTX3
CRSP8P
LOC644936
LOC647859
GUSBP3
GTF2H2B
SNORA47
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100170939
LOC100272216
NCRUPAR
MTRNR2L2
OCLN
MIR4804
MIR4803

Genes in Wide Peak

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

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

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TSHZ1
TXNL4A
ADNP2
KCNG2
SALL3
TIMM21
ZNF407
CNDP2
RBFA
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.1.

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

Genes
PMS2
CARD11
hsa-mir-589
hsa-mir-339
ACTB
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
RAC1
FSCN1
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KIAA0415
KDELR2
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
GET4
CCZ1
RNF216
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
FAM20C
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
C7orf70
ZFAND2A
COX19
KIAA1908
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
DAGLB
SLC29A4
RSPH10B
TFAMP1
UNCX
LOC389458
ELFN1
GRID2IP
ZNF815
RNF216P1
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
MIR589
RSPH10B2
LOC100288524
RBAK-LOC389458
MIR4648
MIR4655
MIR4656

Genes in Wide Peak

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

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

Genes
LINC00290

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
hsa-mir-626
TYRO3
MGA
RPAP1
MIR626

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

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

Genes
FBXO25
C8orf42
ERICH1
ZNF596
OR4F21
RPL23AP53

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q24.2.

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

Genes
TLX1
NFKB2
PTEN
SUFU
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
ACTA2
FAS
ARL3
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DNTT
FGF8
GOT1
HELLS
HHEX
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
KIF11
LIPA
NDUFB8
PAX2
PDE6C
PGAM1
PITX3
PPP1R3C
PSD
ALDH18A1
RBP4
SCD
SFRP5
FBXW4
SLIT1
TAF5
TLL2
WNT8B
LIPF
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
NEURL
LGI1
NOLC1
GSTO1
MINPP1
KIF20B
SH3PXD2A
SLK
ZNF518A
FRAT1
ACTR1A
NPM3
RPP30
SORBS1
ERLIN1
LBX1
MGEA5
CPEB3
NT5C2
PDCD11
SORCS3
PPRC1
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
C10orf28
POLL
BLNK
KCNIP2
EXOSC1
CALHM2
CUTC
PLCE1
PANK1
EXOC6
CCNJ
MARCH5
CNNM2
C10orf26
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
FAM178A
C10orf2
TM9SF3
ENTPD7
AS3MT
STAMBPL1
SEMA4G
AVPI1
HPSE2
MMS19
NOC3L
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
C10orf95
PDZD7
OBFC1
UBTD1
WDR96
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
LZTS2
LCOR
MRPL43
PYROXD2
USMG5
ATAD1
ARHGAP19
ITPRIP
LINC00263
OPALIN
HOGA1
SORCS1
PIK3AP1
MORN4
ZFYVE27
FRA10AC1
ANKRD22
SFXN2
C10orf32
NUDT9P1
GSTO2
SFR1
CALHM3
C10orf129
LIPJ
CFL1P1
HECTD2
FGFBP3
NKX2-3
SLC35G1
CCDC147
CALHM1
PIPSL
BLOC1S2
FLJ37201
O3FAR1
LIPM
CYP26C1
SLC16A12
CC2D2B
FLJ41350
GOLGA7B
MIR107
C10orf62
LOC439994
IFIT1B
MIR146B
LIPK
LIPN
LOC643529
SNORA12
MIR608
MIR609
FAM22A
FAM22D
LOC728190
LOC728218
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
KLLN
LOC100188947
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
FAS-AS1
MIR3157
MIR3158-1
MIR3158-2
LOC100505540
LOC100505761
LOC100505839
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
MIR4679-1
MIR4679-2
MIR4678
MIR4482-1
MIR4685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

Genes
PPP2R2A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
hsa-mir-548f-5
DMD
FTHL17
FAM47A

Genes in Wide Peak

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

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

Genes
CLEC3A
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.33.

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

Genes
GOLGA3
MMP17
POLE
PXMP2
SFSWAP
ZNF10
ZNF26
ZNF84
ZNF140
ULK1
ZNF268
P2RX2
ANKLE2
GALNT9
CHFR
EP400
FBRSL1
NOC4L
PUS1
PGAM5
DDX51
EP400NL
LOC647589
SNORA49
LOC100130238
ZNF605
LOC100507055

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
CREBBP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
GPHN
hsa-mir-625
hsa-mir-548h-1
ACTN1
ARG2
ZFP36L1
EIF2S1
ERH
ESR2
FNTB
FUT8
GPX2
HIF1A
HSPA2
MAX
MAP3K9
MNAT1
MTHFD1
SIX6
PIGH
PPM1A
PPP2R5E
PRKCH
PSEN1
RAD51B
RTN1
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
ZBTB25
DPF3
ADAM21
ADAM20
DCAF5
AKAP5
RGS6
KIAA0247
MED6
VTI1B
ZBTB1
PCNX
DAAM1
SYNE2
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
KCNH5
RDH11
COX16
ATP6V1D
JKAMP
DHRS7
SIX4
ZFYVE1
EXD2
SYNJ2BP
SLC39A9
C14orf162
RHOJ
GALNTL1
PLEKHH1
TRMT5
RBM25
SMOC1
MPP5
C14orf135
GPR135
SGPP1
SYT16
CHURC1
WDR89
C14orf149
GPHB5
RDH12
ADAM21P1
PPP1R36
SLC38A6
LOC145474
FAM71D
TMEM229B
TMEM30B
C14orf55
C14orf39
SNORD56B
RAB15
FLJ22447
PLEKHD1
LINC00238
TEX21P
LOC645431
FLJ43390
C14orf38
LOC100289511
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4708
MIR4706
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.2.

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

Genes
IL5RA
SETMAR
CHL1
CNTN6
TRNT1
CRBN
LRRN1
CNTN4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.13.

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

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
FNBP1
hsa-mir-4292
hsa-mir-126
ABCA2
ABO
ASS1
C8G
ENTPD2
CEL
CELP
COL5A1
DBH
SARDH
TOR1A
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
FUBP3
CLIC3
GTF3C5
GTF3C4
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
USP20
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
SETX
PMPCA
EXOSC2
NCS1
GPSM1
DKFZP434A062
GBGT1
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
TOR1B
METTL11A
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
PRRX2
C9orf78
FBXW5
C9orf86
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
GPR107
PRDM12
CARD9
DDX31
AIF1L
UCK1
NTNG2
PRRC2B
PPAPDC3
FIBCD1
KIAA1984
SNHG7
TMEM141
SAPCD2
C9orf69
UAP1L1
TMEM203
NACC2
C9orf116
LCN8
FAM69B
ASB6
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LINC00094
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
C9orf50
C9orf169
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
C9orf106
LCN10
C9orf173
FAM163B
RNF224
SNORA17
SNORA43
SNORD62B
RNF208
DNLZ
LOC100128593
LOC100129722
LOC100130954
LOC100131193
RNU6ATAC
LOC100272217
LOC100289341
MIR4292
MIR3621
MIR3689A
MIR3689B
LOC100506190
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF256
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
ZSCAN18
MGC2752
ZNF329
ZNF606
ZBTB45
ZNF837
C19orf18
ZNF418
ZNF417
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
A1BG-AS1
LOC646862
ZNF814
LOC100128398
LOC100131691
MIR4754

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
FLJ43879
MIR149
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

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

Genes
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
BAX
BCAT2
C5AR1
CA11
CALM3
CGB
AP2S1
CRX
DBP
DMPK
DMWD
EMP3
FTL
FUT1
FUT2
GIPR
GPR4
GRIN2D
ARHGAP35
GYS1
FOXA3
KCNJ14
LHB
LIG1
NOVA2
NPAS1
NUCB1
PPP5C
PTGIR
RPL18
SEPW1
SLC1A5
SLC8A2
SNRPD2
SULT2B1
SULT2A1
TULP2
SYMPK
PLA2G4C
NAPA
PGLYRP1
CYTH2
DHX34
SAE1
RUVBL2
KDELR1
KPTN
CARD8
ZC3H4
FBXO46
SYNGR4
PPP1R15A
EML2
PRKD2
CCDC9
IRF2BP1
FGF21
BBC3
GPR77
DHDH
STRN4
GLTSCR2
GLTSCR1
EHD2
HSD17B14
QPCTL
FAM83E
RASIP1
TMEM160
PNMAL1
TMEM143
CABP5
SPHK2
MEIS3
PNMAL2
PLEKHA4
ELSPBP1
HIF3A
FKRP
RSPH6A
GRWD1
CCDC8
ZNF541
CCDC114
DKFZp434J0226
CGB5
CGB7
CGB8
GNG8
CGB1
CGB2
LMTK3
NTN5
DACT3
SIX5
IGFL2
ZNF114
SPACA4
PRR24
TPRX1
MAMSTR
IZUMO1
MYPOP
NANOS2
IGFL1
LOC388553
IGFL3
MIR330
IGFL4
SEC1
SNORD23
MIR642A
CCDC61
MIR769
SNAR-G1
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-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-C1
SNAR-C3
SNAR-G2
SNAR-A14
LOC100287177
MIR3191
MIR3190
MIR320E
MIR642B
LOC100505681
LOC100505812
LOC100506012
LOC100506068

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.3.

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

Genes
JAK2
CD274
hsa-mir-101-2
hsa-mir-1302-9
DMRT1
FOXD4
MLANA
GLDC
INSL4
PTPRD
RFX3
RLN1
RLN2
SLC1A1
SMARCA2
VLDLR
KIAA0020
RCL1
DMRT2
INSL6
KDM4C
KANK1
RANBP6
AK3
C9orf68
CDC37L1
C9orf46
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
UHRF2
C9orf66
KIAA2026
KCNV2
GLIS3
FLJ35024
PPAPDC2
MIR101-2
FAM138C
WASH1
MIR4665

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.1.

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

Genes
CDH1
CDH3
SMPD3
ZFP90

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

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

Genes
FLI1
ARHGEF12
hsa-mir-3167
hsa-mir-100
ACRV1
APLP2
CHEK1
ETS1
GRIK4
HSPA8
STT3A
KCNJ1
KCNJ5
VWA5A
NFRKB
NRGN
OPCML
SC5DL
ST3GAL4
SORL1
SRPR
ST14
TECTA
ZNF202
BARX2
EI24
FEZ1
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
VSIG2
POU2F3
OR8G2
OR8B8
OR8G1
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
CRTAM
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ROBO3
FAM118B
C11orf61
CLMP
C11orf63
CCDC15
PUS3
JAM3
KIRREL3
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
PANX3
TMEM45B
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
LINC00167
HEPN1
LOC649133
LOC100128239
PATE3
MIR3167
LOC100507392
MIR4697
MIR4493

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
MIR744

Genes in Wide Peak

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

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

Genes
TMPRSS2
hsa-mir-3197
ADARB1
AIRE
PTTG1IP
C21orf2
CBS
COL6A1
COL6A2
CRYAA
CSTB
PRMT2
ITGB2
LSS
MX1
MX2
NDUFV3
PCNT
PDE9A
PFKL
PKNOX1
PWP2
S100B
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
U2AF1
UBE2G2
C21orf33
PDXK
RRP1
MCM3AP
ABCG1
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
BACE2
C2CD2
DNMT3L
ZNF295
UBASH3A
SLC37A1
PCBP3
C21orf58
YBEY
TSPEAR
LINC00112
LINC00111
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
COL18A1
LRRC3
C21orf56
C21orf67
FAM207A
RSPH1
UMODL1
LINC00313
C21orf90
MCM3AP-AS1
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00315
LINC00319
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LOC642852
LINC00163
SSR4P1
LOC100129027
MIR3197
LOC100505746

Genes in Wide Peak

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

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

Genes
ZMYND11
DIP2C
LARP4B
TUBB8
C10orf108

Genes in Wide Peak

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

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ADCY3
APOB
RHOB
DDX1
DTNB
E2F6
FKBP1B
HPCAL1
ID2
KCNF1
KCNS3
MATN3
ODC1
POMC
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
PDIA6
MYCNOS
YWHAQ
EFR3B
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
ITSN2
TRAPPC12
DNAJC27
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
ADI1
ALLC
KIDINS220
WDR35
RDH14
C2orf43
HS1BP3
COLEC11
CENPO
SMC6
NOL10
C2orf44
FAM49A
RSAD2
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
OSR1
TTC32
C2orf50
PQLC3
LOC150622
FAM84A
GDF7
UBXN2A
CYS1
ATP6V1C2
RNASEH1
FAM150B
IAH1
FLJ33534
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
PFN4
LOC375190
LOC386597
MFSD2B
PTRHD1
LOC400940
LINC00487
FLJ12334
FAM110C
LOC645949
C2orf84
LOC727982
RAD51AP2
DNAJC27-AS1
LOC730811
MIR1301
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

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

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

Genes
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
ATF3
CD34
CENPF
CR1
CR1L
CR2
CD55
EPRS
ESRRG
HSD11B1
IRF6
KCNH1
KCNK2
LAMB3
CD46
NEK2
PLXNA2
PPP2R5A
PROX1
PTPN14
TGFB2
TRAF5
USH2A
SLC30A1
LPGAT1
BPNT1
INTS7
NSL1
RPS6KC1
RNU5F-1
DIEXF
FLVCR1
NENF
G0S2
RRP15
KCTD3
DTL
GPATCH2
TMEM206
BATF3
SLC30A10
IARS2
HHAT
RCOR3
SERTAD4
SMYD2
CAMK1G
VASH2
TRAF3IP3
LINC00467
ANGEL2
LYPLAL1
SPATA17
TATDN3
C1orf74
LOC148696
C1orf227
FAM71A
SYT14
RD3
MIR194-1
MIR205
MIR215
MIR29B2
MIR29C
C1orf133
MIR205HG
FLVCR1-AS1
LOC643723
SNORA36B
SNORA16B
LOC728463
MIR664
MIR4260
MIR3122
PROX1-AS1
LINC00538

Arm-level results

Table 3. Get Full Table Arm-level significance table - 32 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.32 | 2.38 | 0.0387 | 0.16 | -5.04 | 1
1q | 1955 | 0.40 | 5.63 | 8.88e-08 | 0.14 | -6.13 | 1
2p | 924 | 0.33 | -1.74 | 1 | 0.16 | -8.56 | 1
2q | 1556 | 0.28 | -1.78 | 1 | 0.16 | -6.96 | 1
3p | 1062 | 0.30 | -2.44 | 1 | 0.26 | -4.26 | 1
3q | 1139 | 0.49 | 6.76 | 1.42e-10 | 0.18 | -6.35 | 1
4p | 489 | 0.20 | -6.57 | 1 | 0.62 | 9.99 | 0
4q | 1049 | 0.15 | -6.44 | 1 | 0.66 | 14.8 | 0
5p | 270 | 0.38 | -1.5 | 1 | 0.42 | -0.00973 | 0.806
5q | 1427 | 0.15 | -6.93 | 1 | 0.44 | 5.33 | 1.18e-07
6p | 1173 | 0.39 | 1.59 | 0.185 | 0.43 | 3.55 | 0.000373
6q | 839 | 0.27 | -3.71 | 1 | 0.51 | 6.36 | 2.74e-10
7p | 641 | 0.39 | -0.106 | 1 | 0.32 | -2.68 | 1
7q | 1277 | 0.40 | 2.93 | 0.00836 | 0.22 | -4.67 | 1
8p | 580 | 0.31 | -2.75 | 1 | 0.63 | 10.7 | 0
8q | 859 | 0.48 | 4.66 | 1.26e-05 | 0.30 | -2.7 | 1
9p | 422 | 0.24 | -5.74 | 1 | 0.55 | 6.64 | 4.34e-11
9q | 1113 | 0.15 | -7.26 | 1 | 0.54 | 8.9 | 0
10p | 409 | 0.35 | -2.26 | 1 | 0.29 | -4.88 | 1
10q | 1268 | 0.23 | -4.73 | 1 | 0.27 | -3.06 | 1
11p | 862 | 0.18 | -7.57 | 1 | 0.40 | 1.49 | 0.124
11q | 1515 | 0.25 | -2.97 | 1 | 0.33 | 0.434 | 0.554
12p | 575 | 0.49 | 4.35 | 4.6e-05 | 0.28 | -4.17 | 1
12q | 1447 | 0.36 | 1.78 | 0.15 | 0.28 | -2.12 | 1
13q | 654 | 0.22 | -5.61 | 1 | 0.60 | 9.7 | 0
14q | 1341 | 0.16 | -7.15 | 1 | 0.41 | 3.62 | 0.000295
15q | 1355 | 0.13 | -7.35 | 1 | 0.52 | 9.23 | 0
16p | 872 | 0.21 | -5.15 | 1 | 0.64 | 12.8 | 0
16q | 702 | 0.18 | -5.46 | 1 | 0.75 | 17.5 | 0
17p | 683 | 0.18 | -3.96 | 1 | 0.86 | 23.1 | 0
17q | 1592 | 0.23 | -2.37 | 1 | 0.73 | 20.3 | 0
18p | 143 | 0.31 | -4.23 | 1 | 0.54 | 4.79 | 1.71e-06
18q | 446 | 0.24 | -5.51 | 1 | 0.59 | 8.34 | 0
19p | 995 | 0.40 | 1.67 | 0.174 | 0.47 | 4.81 | 1.68e-06
19q | 1709 | 0.38 | 3.01 | 0.00739 | 0.44 | 6.21 | 6.67e-10
20p | 355 | 0.54 | 5.79 | 4.61e-08 | 0.19 | -7.78 | 1
20q | 753 | 0.59 | 9.94 | 0 | 0.15 | -7.63 | 1
21q | 509 | 0.29 | -4.39 | 1 | 0.43 | 1.2 | 0.202
22q | 921 | 0.17 | -5 | 1 | 0.77 | 19.7 | 0
Xq | 1312 | 0.30 | -1.3 | 1 | 0.61 | 12.6 | 0

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV-TP/8017716/GDAC_MergeDataFiles_3126532/OV-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

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 569 Input Tumor Samples.

Tumor Sample Names
TCGA-04-1331-01A-01D-0428-01
TCGA-04-1332-01A-01D-0428-01
TCGA-04-1335-01A-01D-0428-01
TCGA-04-1336-01A-01D-0428-01
TCGA-04-1337-01A-01D-0428-01
TCGA-04-1338-01A-01D-0428-01
TCGA-04-1341-01A-01D-0428-01
TCGA-04-1342-01A-01D-0428-01
TCGA-04-1343-01A-01D-0428-01
TCGA-04-1346-01A-01D-0428-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- 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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