Ovarian Serous Cystadenocarcinoma: 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 2.0.15 (cga svn revision 34144).

Summary

There were 547 tumor samples used in this analysis: 29 significant arm-level results, 35 significant focal amplifications, and 46 significant focal deletions were found.

Results
Focal results

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

Table 1. Get Full Table Amplifications Table - 35 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 | 2.645e-77 | 2.645e-77 | chr8:128574848-129810279 | 5
19q12 | 1.8147e-87 | 8.4949e-76 | chr19:34947990-35023082 | 1
3q26.2 | 1.0722e-60 | 1.0722e-60 | chr3:170905217-170923258 | 0 [MECOM]
11q14.1 | 1.8202e-27 | 1.8202e-27 | chr11:77380133-77677802 | 8
19p13.12 | 9.5462e-26 | 9.5462e-26 | chr19:15170840-15307576 | 3
1p34.2 | 2.8098e-22 | 2.8098e-22 | chr1:39202850-41086944 | 35
12p12.1 | 1.8789e-23 | 1.6579e-18 | chr12:25170627-25614145 | 4
1q21.2 | 6.8869e-19 | 3.7688e-17 | chr1:148865181-148945656 | 3
19q13.2 | 1.5839e-30 | 7.4956e-12 | chr19:44826753-45144839 | 7
14q11.2 | 5.7865e-11 | 7.9832e-10 | chr14:20410492-20676586 | 12
4q13.3 | 1.5475e-06 | 1.5475e-06 | chr4:74125200-74354544 | 2
15q26.3 | 3.2593e-06 | 3.2593e-06 | chr15:95132799-100338915 | 31
18q11.2 | 8.2233e-06 | 8.2233e-06 | chr18:22027716-22651382 | 3
1q42.3 | 3.0555e-07 | 4.7381e-05 | chr1:232170286-246035122 | 76
2q32.2 | 6.5433e-05 | 6.5433e-05 | chr2:189140907-191904323 | 23
8p11.21 | 8.2311e-05 | 8.2311e-05 | chr8:41547476-42127342 | 6
12p13.33 | 1.2509e-06 | 0.00010553 | chr12:1-3427580 | 28
7q36.1 | 0.00015244 | 0.00015244 | chr7:140970066-158821424 | 160
5p15.33 | 0.00021543 | 0.00021543 | chr5:1-1378802 | 22
20q11.21 | 6.8185e-05 | 0.00025249 | chr20:29667144-29796125 | 3
10q22.3 | 0.00026264 | 0.00026264 | chr10:78865906-79558000 | 5
6p22.3 | 0.00011438 | 0.00026785 | chr6:18346548-19527820 | 4
4p16.3 | 0.00070192 | 0.00070192 | chr4:740666-2117746 | 30
20q13.33 | 0.00019457 | 0.0010094 | chr20:61541411-62311460 | 37
12q15 | 0.00010553 | 0.0016619 | chr12:67973933-69429474 | 11
17q25.3 | 0.0028609 | 0.0028609 | chr17:76596751-78036719 | 59
10p15.3 | 0.0093974 | 0.0093974 | chr10:1-1527450 | 12
11p13 | 0.028659 | 0.028659 | chr11:32127196-32691194 | 4
6p21.1 | 0.017132 | 0.035867 | chr6:42634743-44107345 | 40
6q21 | 0.039051 | 0.039051 | chr6:107040710-107666415 | 8
12q13.11 | 0.0063755 | 0.06249 | chr12:44142721-45353311 | 5
20p13 | 0.095219 | 0.095219 | chr20:1-1089326 | 22
14q32.33 | 0.042123 | 0.16536 | chr14:101547570-106368585 | 58
17p13.3 | 0.2035 | 0.2035 | chr17:1086707-1354646 | 6
2p23.2 | 0.24476 | 0.24476 | chr2:28661441-28851580 | 2

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's Cancer Gene Census [7].

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

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's Cancer Gene Census [7].

Genes
CCNE1

Genes in Wide Peak

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

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

Genes
NDUFC2
THRSP
GAB2
USP35
KCTD14
ALG8
INTS4
KCTD21

Genes in Wide Peak

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

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

Genes
BRD4
NOTCH3
EPHX3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MYCL1
hsa-mir-30c-1
BMP8B
COL9A2
NDUFS5
NFYC
PPT1
RLF
PABPC4
KCNQ4
RIMS3
ZMPSTE24
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
OXCT2
SMAP2
DEM1
ZNF643
AKIRIN1
NT5C1A
MFSD2A
TMCO2
ZNF684
ZNF642
BMP8A
MIR30C1
MIR30E
KIAA0754
SNORA55
LOC728448
LOC100130557

Genes in Wide Peak

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

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

Genes
KRAS
CASC1
LYRM5
IFLTD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
ENSA
GOLPH3L
HORMAD1

Genes in Wide Peak

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

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

Genes
CLC
FBL
FCGBP
DYRK1B
LGALS14
LEUTX
LOC400696

Genes in Wide Peak

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

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

Genes
RNASE2
RNASE3
SLC39A2
ZNF219
FLJ10357
NDRG2
METT11D1
RNASE7
TPPP2
RNASE8
RNASE13
C14orf176

Genes in Wide Peak

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

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

Genes
ANKRD17
COX18

Genes in Wide Peak

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

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

Genes
hsa-mir-1302-2
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
LINS1
SELS
TTC23
LRRK1
TM2D3
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
LOC145814
ADAMTS17
C15orf51
LASS3
FAM169B
WASH3P
FLJ42289
OR4F6
OR4F15
FAM138E
LOC100288778

Genes in Wide Peak

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

Table S12. Genes in bold are cancer genes as defined by The Sanger Institute's 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 1q42.3.

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

Genes
FH
hsa-mir-1537
ACTN2
ADSS
CHML
LYST
CHRM3
GNG4
HNRNPU
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
ZNF124
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZNF238
SDCCAG8
RBM34
OPN3
AHCTF1
OR1C1
PPPDE1
SCCPDH
ARID4B
KIF26B
HEATR1
ERO1LB
FMN2
ZNF695
ZP4
TFB2M
GREM2
SMYD3
ZNF669
OR2G3
OR2G2
OR2C3
EFCAB2
ZNF496
ZNF670
NLRP3
FAM36A
OR2B11
WDR64
EDARADD
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
C1orf101
NCRNA00201
VN1R5
LOC339535
OR6F1
IRF2BP2
C1orf31
C1orf229
MAP1LC3C
OR2W5
OR13G1
SNORA14B
LOC731275
LOC100130331

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q32.2.

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

Genes
PMS1
hsa-mir-1245
COL3A1
COL5A2
MSTN
GLS
INPP1
MYO1B
NAB1
STAT1
STAT4
HIBCH
SLC40A1
GULP1
ASNSD1
MFSD6
OSGEPL1
WDR75
C2orf88
ORMDL1
DIRC1
ANKAR
TMEM194B

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
MYST3
AGPAT6
NKX6-3
MIR486

Genes in Wide Peak

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

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

Genes
KDM5A
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
CACNA2D4
FBXL14
DCP1B
B4GALNT3
HSN2
IQSEC3
LRTM2
FAM138D
LOC100292680

Genes in Wide Peak

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

Table S17. Genes in bold are cancer genes as defined by The Sanger Institute's 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
CASP2
CDK5
CLCN1
DPP6
EN2
EPHA1
EPHB6
GBX1
MNX1
HTR5A
INSIG1
KCNH2
KEL
NOS3
PIP
PRSS1
PRSS2
TAS2R38
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
SSBP1
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
MGAM
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
CLEC5A
CNTNAP2
GIMAP2
OR2F1
TPK1
ZNF777
TMEM176B
REPIN1
TAS2R3
TAS2R4
PRKAG2
NUB1
TAS2R5
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
TRPV5
ACTR3B
KIAA1147
ESYT2
ZNF398
GALNT11
LMBR1
C7orf4
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
OR6W1P
LOC93432
C7orf29
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
ASB10
TRYX3
MOXD2
RNF32
TRY6
LOC154761
LOC154822
GIMAP8
CRYGN
ZNF425
ZNF783
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5L3
TAS2R39
TAS2R40
TAS2R41
CNPY1
FLJ40852
FAM115C
ZNF775
ATG9B
TAS2R60
CTAGE6
OR6V1
OR2A12
OR2A1
WDR86
GSTK1
OR2A25
OR2A5
OR2A7
OR2A20P
LOC401431
OR2A42
MIR153-2
LOC441294
OR2A9P
OR2A2
ARHGEF5L
GIMAP6
WEE2
ZNF862
ACTR3C
MIR595
LOC728743
MIR671
LOC100124692
LOC100128542
CTAGE4
LOC100128822
LOC100132707

Genes in Wide Peak

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

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

Genes
SDHA
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
LOC25845
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100310782

Genes in Wide Peak

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

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

Genes
BCL2L1
TPX2
COX4I2

Genes in Wide Peak

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

Table S20. Genes in bold are cancer genes as defined by The Sanger Institute's 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 6p22.3.

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

Genes
DEK
hsa-mir-548a-1
RNF144B
MIR548A1

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
hsa-mir-943
CTBP1
DGKQ
GAK
IDUA
LETM1
WHSC2
SLBP
MAEA
PCGF3
SPON2
TACC3
CPLX1
SLC26A1
FGFRL1
KIAA1530
TMEM175
C4orf42
TMEM129
FAM53A
CRIPAK
RNF212
NAT8L
POLN
C4orf48
SCARNA22
MIR943
LOC100130872

Genes in Wide Peak

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

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

Genes
hsa-mir-647
EEF1A2
NPBWR2
KCNQ2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
SLC2A4RG
ZNF512B
C20orf195
PPDPF
DNAJC5
ZGPAT
PRIC285
ZBTB46
SAMD10
C20orf135
C20orf201
NCRNA00176
MIR647
UCKL1AS
MIR941-1
MIR941-2
MIR941-3

Genes in Wide Peak

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

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

Genes
LYZ
CNOT2
PTPRB
PTPRR
YEATS4
CCT2
FRS2
KCNMB4
RAB3IP
BEST3
LRRC10

Genes in Wide Peak

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

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

Genes
ASPSCR1
hsa-mir-1250
ACTG1
ARHGDIA
CD7
CSNK1D
SLC25A10
FASN
UTS2R
GPS1
MAFG
P4HB
PDE6G
PYCR1
PCYT2
RAC3
RFNG
MRPL12
SECTM1
SLC16A3
HGS
AATK
THOC4
BAIAP2
AZI1
FSCN2
NARF
DCXR
ANAPC11
SIRT7
NPLOC4
BAHCC1
DUS1L
C17orf62
C17orf101
C17orf70
TSPAN10
LOC92659
DYSFIP1
SLC38A10
C17orf56
NOTUM
STRA13
LRRC45
MYADML2
NPB
CCDC57
HEXDC
C17orf89
C17orf55
TMEM105
C17orf90
CCDC137
ARL16
LOC388428
TEX19
FLJ90757
MIR338
MIR657

Genes in Wide Peak

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

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

Genes
ADARB2
IDI1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
C10orf110
IDI2
TUBB8
NCRNA00200
C10orf108

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
WT1
EIF3M
WIT1
CCDC73

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
MEA1
PEX6
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
POLR1C
MAD2L1BP
CUL7
C6orf108
CNPY3
SLC22A7
CUL9
UBR2
KIAA0240
ZNF318
YIPF3
GNMT
MRPL2
GTPBP2
MRPS18A
XPO5
DLK2
TTBK1
C6orf153
ABCC10
KLC4
TJAP1
KLHDC3
PTCRA
C6orf223
RSPH9
C6orf154
RPL7L1
CRIP3
C6orf226
LOC100132354

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

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

Genes
hsa-mir-587
AIM1
C6orf203
QRSL1
PDSS2
BEND3
RTN4IP1
LOC553137

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.11.

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

Genes
SFRS2IP
SLC38A2
SLC38A1
ARID2
LOC400027

Genes in Wide Peak

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

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

Genes
CSNK2A1
SOX12
TCF15
PSMF1
RBCK1
ANGPT4
TRIB3
NRSN2
DEFB126
FAM110A
ZCCHC3
SCRT2
C20orf54
TBC1D20
C20orf96
SRXN1
DEFB127
DEFB129
DEFB125
DEFB128
RSPO4
DEFB132

Genes in Wide Peak

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

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

Genes
AKT1
hsa-mir-203
CKB
CRIP1
CRIP2
DYNC1H1
EIF5
BRF1
HSP90AA1
JAG2
KLC1
MARK3
RAGE
TNFAIP2
TRAF3
XRCC3
ADAM6
MTA1
BAG5
C14orf2
CDC42BPB
KIAA0125
TECPR2
SIVA1
RCOR1
PACS2
PPP1R13B
KIF26A
GPR132
CINP
CDCA4
ZNF839
INF2
ZFYVE21
TMEM121
AMN
C14orf153
BTBD6
C14orf73
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
C14orf79
PLD4
ADSSL1
MGC23270
NUDT14
KIAA0284
C14orf80
ASPG
TMEM179
C14orf180
MIR203
SNORA28
ZBTB42
LOC100133469

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p13.3.

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

Genes
CRK
MYO1C
YWHAE
INPP5K
TUSC5
BHLHA9

Genes in Wide Peak

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

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

Genes
PPP1CB
PLB1

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

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
19p13.3 | 6.0563e-118 | 6.0563e-118 | chr19:1-3178101 | 114
22q13.31 | 7.9874e-48 | 7.9874e-48 | chr22:45036619-49691432 | 50
1p36.11 | 1.2113e-40 | 1.2113e-40 | chr1:26625580-27556982 | 19
6q26 | 4.7118e-30 | 5.0247e-30 | chr6:156307789-170899992 | 80
11p15.5 | 1.0312e-29 | 1.0312e-29 | chr11:1-699860 | 33
13q14.2 | 1.5036e-34 | 3.1575e-28 | chr13:47731768-47890810 | 1
5q11.2 | 6.4551e-55 | 2.92e-25 | chr5:58180924-59823742 | 3
15q15.1 | 2.92e-25 | 2.92e-25 | chr15:39578280-40233689 | 14
7p22.3 | 5.6305e-21 | 5.6305e-21 | chr7:1-7196158 | 76
17q11.2 | 4.2139e-19 | 6.5715e-19 | chr17:26350862-26746744 | 4
10q23.31 | 2.2786e-18 | 1.6435e-16 | chr10:89607138-90024018 | 2
4q35.2 | 9.9007e-22 | 4.4498e-16 | chr4:179148868-191273063 | 50
2q37.3 | 1.0601e-18 | 7.9859e-14 | chr2:239024320-242951149 | 42
5q13.2 | 1.5466e-66 | 1.0047e-13 | chr5:66528169-75006657 | 52
18q23 | 1.6284e-12 | 1.6976e-12 | chr18:66146547-76117153 | 30
4q22.1 | 2.2603e-15 | 4.9687e-12 | chr4:91092757-93459528 | 2
8p23.3 | 5.5843e-19 | 1.5826e-11 | chr8:1-6255647 | 14
2q22.1 | 6.6639e-14 | 2.3109e-10 | chr2:139248662-143354308 | 1
9q34.2 | 5.7008e-10 | 5.7008e-10 | chr9:132698183-139566626 | 149
8p21.2 | 1.2358e-13 | 4.76e-08 | chr8:25952364-26306212 | 1
16q23.1 | 5.897e-12 | 5.8479e-07 | chr16:76686559-78185271 | 1
17p12 | 4.6663e-07 | 7.439e-07 | chr17:15405082-15555845 | 2
12q24.33 | 5.2845e-11 | 7.8286e-06 | chr12:131118137-132349534 | 19
14q23.3 | 1.344e-05 | 1.344e-05 | chr14:61332279-72207941 | 72
11q25 | 2.3584e-05 | 2.3329e-05 | chr11:121006002-134452384 | 109
12q23.1 | 2.5868e-08 | 3.9223e-05 | chr12:97648132-98955403 | 2
16p13.3 | 6.7213e-05 | 6.7159e-05 | chr16:3704794-3953467 | 1
21q11.2 | 0.00011851 | 0.00041515 | chr21:1-25682320 | 30
21q22.3 | 8.2974e-05 | 0.00043379 | chr21:43399738-46944323 | 67
2p25.3 | 0.00067208 | 0.00067208 | chr2:1-20731591 | 78
10q26.13 | 1.1412e-05 | 0.0010714 | chr10:100016009-135374737 | 268
5q14.3 | 3.9486e-43 | 0.0023228 | chr5:70717447-108113641 | 137
13q13.1 | 1.7242e-07 | 0.0047955 | chr13:31781908-31880005 | 1
19q13.32 | 1.0452e-07 | 0.0050416 | chr19:53093308-53193111 | 20
3p26.3 | 0.00080214 | 0.0058448 | chr3:1-16904112 | 109
19q13.43 | 7.0225e-07 | 0.0063478 | chr19:63068201-63811651 | 32
1q32.3 | 0.0064595 | 0.0064595 | chr1:205382725-218506883 | 73
3p14.2 | 0.0011587 | 0.0064595 | chr3:51839890-61522370 | 87
6p25.3 | 0.015565 | 0.015565 | chr6:1-2712339 | 11
9p21.3 | 0.017234 | 0.017441 | chr9:21177335-26831183 | 24
16q24.3 | 2.1039e-08 | 0.021336 | chr16:87821235-88104546 | 1
10p15.3 | 0.034665 | 0.033991 | chr10:1-1219490 | 11
16q22.1 | 0.00030396 | 0.049229 | chr16:67037158-67437325 | 3
20p12.1 | 0.12365 | 0.12365 | chr20:13912029-15984135 | 2
4p15.31 | 0.19564 | 0.19316 | chr4:20335953-21999843 | 2
3q13.31 | 0.20511 | 0.207 | chr3:117644353-120103518 | 1

Genes in Wide Peak

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

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

Genes
GNA11
STK11
TCF3
FSTL3
hsa-mir-1227
hsa-mir-1909
hsa-mir-1302-2
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
GADD45B
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
SGTA
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
MED16
APC2
ABCA7
UQCR
SBNO2
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
SLC39A3
THEG
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
NCLN
SPPL2B
WDR18
REXO1
ZNF77
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
KLF16
DOT1L
KISS1R
LMNB2
MUM1
MIDN
C19orf22
C19orf6
C19orf20
REEP6
C19orf36
SCAMP4
ADAT3
ZNF554
GRIN3B
ZNF57
JSRP1
MOBKL2A
C19orf21
PLK5P
C2CD4C
C19orf23
C19orf25
ATP8B3
DIRAS1
ZNF555
C19orf26
C19orf34
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
ONECUT3
MEX3D
FLJ45445
PRSSL1
FAM138F
LINGO3
FAM138A
FAM138C

Genes in Wide Peak

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

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

Genes
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
CELSR1
SAPS2
ZBED4
SCO2
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
FAM19A5
NCAPH2
GTSE1
MOV10L1
TTC38
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
CN5H6.4
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
C22orf41
LOC100144603

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's Cancer Gene Census [7].

Genes
ARID1A
hsa-mir-1976
SFN
HMGN2
RPS6KA1
SLC9A1
NR0B2
NUDC
WDTC1
GPN2
PIGV
GPATCH3
DHDDS
TMEM222
ZDHHC18
SYTL1
FAM46B
C1orf172
TRNP1

Genes in Wide Peak

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

Table S38. Genes in bold are cancer genes as defined by The Sanger Institute's 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
C6orf59
C6orf208
LPAL2
RSPH3
TTLL2
FAM120B
FNDC1
SERAC1
C6orf176
SYTL3
SFT2D1
TAGAP
PACRG
PNLDC1
LOC154449
DACT2
C6orf118
OSTCL
WDR27
LOC285796
PRR18
C6orf120
TCP10L2
C6orf122
GTF2H5
LOC441177
C6orf124
SNORA20
SNORA29
LOC729603
HGC6.3

Genes in Wide Peak

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

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

Genes
HRAS
hsa-mir-210
DRD4
IRF7
PSMD13
RNH1
SCT
RASSF7
IFITM1
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
BET1L
MUPCDH
PHRF1
SIGIRR
RIC8A
ATHL1
PTDSS2
ODF3
LRRC56
LOC143666
SCGB1C1
NLRP6
C11orf35
TMEM80
ANO9
B4GALNT4
IFITM5
MIR210
LOC100133161

Genes in Wide Peak

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

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

Genes
LPAR6

Genes in Wide Peak

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

Table S41. Genes in bold are cancer genes as defined by The Sanger Institute's 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 15q15.1.

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

Genes
hsa-mir-626
LTK
TYRO3
JMJD7-PLA2G4B
MAPKBP1
MGA
RPAP1
EHD4
SPTBN5
PLA2G4E
PLA2G4D
MIR626
JMJD7
PLA2G4B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.3.

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

Genes
PMS2
CARD11
hsa-mir-589
hsa-mir-339
ACTB
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
RAC1
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KIAA0415
KDELR2
ADAP1
IQCE
UNC84A
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
C7orf20
C7orf28A
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
C7orf27
SDK1
FOXK1
MMD2
DAGLB
C7orf28B
SLC29A4
RSPH10B
TFAMP1
UNCX
LOC389458
ELFN1
GRID2IP
ZNF815
RNF216L
PMS2CL
MIR339
OCM
MIR589
RSPH10B2

Genes in Wide Peak

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

Table S44. 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 10q23.31.

Table S45. 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 4q35.2.

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

Genes
DUX4
hsa-mir-1305
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
TUBB4Q
STOX2
KIAA1430
C4orf41
MLF1IP
WWC2
SNX25
MGC45800
ZFP42
ENPP6
C4orf38
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
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 2q37.3.

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

Genes
hsa-mir-149
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
HDAC4
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
RNPEPL1
GAL3ST2
C2orf54
ING5
MGC16025
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
C2orf85
DUSP28
AQP12A
OR6B2
MIR149
PRR21
AQP12B
D2HGDH
LOC728323
PP14571

Genes in Wide Peak

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

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

Genes
PIK3R1
BTF3
CCNB1
CDK7
FOXD1
GTF2H2
HEXB
HMGCR
TNPO1
MAP1B
NAIP
OCLN
PMCHL2
RAD17
SMN1
SMN2
TAF9
SERF1A
ENC1
CARTPT
COL4A3BP
NSA2
MRPS27
FAM169A
GCNT4
POLK
BDP1
ANKRA2
MCCC2
RGNEF
SLC30A5
CENPH
PTCD2
UTP15
GFM2
MRPS36
FCHO2
TMEM171
TMEM174
MARVELD2
ZNF366
CCDC125
ANKRD31
LOC647859
GUSBP3
GTF2H2B
LOC653391
GTF2H2C
SERF1B
GTF2H2D
LOC100170939
LOC100272216

Genes in Wide Peak

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

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

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TSHZ1
TXNL4A
ADNP2
KCNG2
SALL3
C18orf55
ZNF407
CNDP2
C18orf22
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
ZADH2
C18orf62
LOC284276
ATP9B
LOC400657
HSBP1L1
LOC100130522

Genes in Wide Peak

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

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

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

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

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
C8orf42
ERICH1
ZNF596
OR4F21
RPL23AP53
MIR596

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 9q34.2.

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

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
hsa-mir-126
ABCA2
ABO
C8G
ENTPD2
CEL
CELP
COL5A1
DBH
SARDH
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
CLIC3
GTF3C5
GTF3C4
MED27
ADAMTSL2
KIAA0649
SEC16A
LAMC3
TUBB2C
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
NOXA1
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
SETX
PMPCA
COBRA1
NELF
GPSM1
LOC26102
GBGT1
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
FBXW5
C9orf167
EXD3
C9orf86
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
CARD9
DDX31
AIF1L
UCK1
NTNG2
BAT2L
PPAPDC3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf140
C9orf69
UAP1L1
TMEM203
NACC2
C9orf116
LCN8
FAM69B
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
C9orf98
C9orf96
QSOX2
NCRNA00094
LCN12
C9orf142
C9orf75
FAM78A
QRFP
GLT6D1
PNPLA7
C9orf169
ENTPD8
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
LCN10
C9orf173
NRARP
FAM163B
SNORA17
SNORA43
SNORD62B
RNF208
DNLZ
LOC100131193
RNU6ATAC
LOC100289341

Genes in Wide Peak

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

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

Genes
PPP2R2A

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

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

Table S56. 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 12q24.33.

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

Genes
GOLGA3
POLE
PXMP2
ZNF10
ZNF26
ZNF84
ZNF140
ZNF268
P2RX2
ANKLE2
GALNT9
CHFR
FBRSL1
NOC4L
PGAM5
DDX51
EP400NL
LOC100130238
ZNF605

Genes in Wide Peak

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

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

Genes
RAD51L1
GPHN
hsa-mir-625
hsa-mir-548h-1
ACTN1
ARG2
ZFP36L1
EIF2S1
ERH
ESR2
FNTB
FUT8
GPX2
HSPA2
MAX
MAP3K9
MTHFD1
PIGH
PPP2R5E
SFRS5
SLC8A3
SLC10A1
SPTB
ZBTB25
ADAM21
ADAM20
DCAF5
AKAP5
RGS6
KIAA0247
MED6
VTI1B
ZBTB1
PCNX
SYNE2
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
PLEK2
KCNH5
RDH11
COX16
ATP6V1D
EXD2
SYNJ2BP
SLC39A9
C14orf162
RHOJ
GALNTL1
PLEKHH1
SMOC1
MPP5
SGPP1
SYT16
CHURC1
WDR89
GPHB5
RDH12
ADAM21P
C14orf50
LOC145474
FAM71D
TMEM229B
SNORD56B
RAB15
C14orf181
FLJ44817
C14orf53
LOC645431
FLJ43390
LOC100289511

Genes in Wide Peak

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

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

Genes
FLI1
hsa-mir-100
hsa-mir-125b-1
ACRV1
APLP2
CHEK1
ETS1
HSPA8
STT3A
KCNJ1
KCNJ5
VWA5A
NFRKB
NRGN
OPCML
ST3GAL4
SRPR
ST14
ZNF202
BARX2
EI24
FEZ1
RICS
ADAMTS8
IGSF9B
NCAPD3
VSIG2
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
ASAM
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
SPATA19
HEPACAM
OR8D1
OR8D2
OR8B4
LOC283174
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
LOC399959
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
NCRNA00167
HEPN1
LOC100128239
PATE3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

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

Genes
ANKS1B
FAM71C

Genes in Wide Peak

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

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

Genes
CREBBP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

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

Genes
hsa-mir-125b-2
BAGE
CXADR
NCAM2
PRSS7
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
NCRNA00157
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
C21orf99
LIPI
ABCC13
POTED
C21orf131
C21orf34
C21orf81
MIRLET7C
MIR125B2
MIR99A

Genes in Wide Peak

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

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

Genes
ADARB1
AIRE
PTTG1IP
C21orf2
COL6A1
COL6A2
CRYAA
CSTB
PRMT2
ITGB2
LSS
PCNT
PFKL
PWP2
S100B
SLC19A1
SUMO3
TRAPPC10
TRPM2
UBE2G2
C21orf33
PDXK
RRP1
MCM3AP
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
DNMT3L
PCBP3
C21orf58
C21orf57
C21orf29
AGPAT3
COL18A1
LRRC3
C21orf56
C21orf67
C21orf70
C21orf84
C21orf90
MCM3APAS
SIK1
C21orf125
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
NCRNA00162
NCRNA00175
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
C21orf122

Genes in Wide Peak

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

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

Genes
MYCN
ACP1
RHOB
DDX1
E2F6
HPCAL1
ID2
KCNF1
KCNS3
MATN3
ODC1
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
ROCK2
GREB1
LAPTM4A
RNF144A
PDIA6
MYCNOS
YWHAQ
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
TTC15
NBAS
CPSF3
SNTG2
ADI1
ALLC
KIDINS220
WDR35
RDH14
HS1BP3
COLEC11
SMC6
NOL10
FAM49A
RSAD2
NT5C1B
CMPK2
MBOAT2
TMEM18
OSR1
TTC32
C2orf50
PQLC3
LOC150622
FAM84A
CYS1
ATP6V1C2
RNASEH1
FAM150B
IAH1
LOC339788
MSGN1
GEN1
C2orf48
C2orf90
LOC400940
FAM110C
RAD51AP2
LOC730811
SNORA80B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.13.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-2110
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-608
hsa-mir-1287
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2E1
CYP17A1
DMBT1
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HMX2
HPS1
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
RGS10
SCD
FBXW4
SLC18A2
TAF5
TCF7L2
TECTB
TIAL1
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
DCLRE1A
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
DNMBP
RP11-529I10.4
SEC31B
ATRNL1
C10orf137
CNNM1
PDCD4
VENTX
POLL
KCNIP2
CUZD1
CALY
CALHM2
CUTC
CHST15
ACSL5
ZRANB1
NSMCE4A
CNNM2
C10orf26
C10orf118
CWF19L1
HIF1AN
BRWD2
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
HPSE2
C10orf84
LHPP
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
C10orf119
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
C10orf79
LRRC27
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
PCGF6
GPR123
LZTS2
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
KNDC1
ITPRIP
C10orf75
MTG1
NCRNA00081
FANK1
SYCE1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
SFXN2
PDZD8
C10orf32
GSTO2
C10orf78
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
NKX2-3
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
C10orf93
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
ARMS2
C10orf122
GUCY2G
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FOXI2
FAM45A
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
LOC653543
LOC653544
LOC653545
LOC653548
SNORA12
MIR608
MIR609
LOC728410
LOC729020
TLX1NB
LOC100169752
NCRNA00093

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q14.3.

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

Genes
hsa-mir-548p
hsa-mir-583
hsa-mir-1974
hsa-mir-9-2
ARSB
BHMT
BTF3
CAST
CCNH
CETN3
CHD1
CKMT2
COX7C
CRHBP
HAPLN1
VCAN
DHFR
EFNA5
F2R
F2RL1
F2RL2
FOXD1
GLRX
HEXB
HMGCR
TNPO1
LNPEP
MAP1B
MEF2C
MSH3
PAM
PCSK1
RASA1
RASGRF2
RPS23
TBCA
NR2F1
THBS4
XRCC4
ST8SIA4
ENC1
AP3B1
PDE8B
RAB9P1
HOMER1
SCAMP1
CARTPT
TTC37
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
NSA2
POLR3G
IQGAP2
RHOBTB3
ELL2
SV2C
MRPS27
HISPPD1
OTP
SSBP2
BHMT2
FAM169A
DMGDH
GCNT4
POLK
ERAP1
GIN1
AGGF1
WDR41
RIOK2
BDP1
ARRDC3
ANKRA2
MCCC2
ERAP2
RGNEF
FBXL17
MCTP1
PTCD2
NUDT12
ATG10
SPATA9
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
SPZ1
C5orf30
ATP6AP1L
FCHO2
LYSMD3
SLCO6A1
JMY
POU5F2
TMEM171
TMEM174
C5orf37
ACOT12
TMEM167A
MBLAC2
TMEM161B
ARSK
FAM81B
PAPD4
LIX1
ZNF366
FAM151B
S100Z
C5orf27
CMYA5
ANKRD31
SERINC5
C5orf36
GPR150
NBPF22P
RGMB
RFESD
ANKRD34B
FAM174A
MTX3
SLCO4C1
LOC441089
FLJ42709
LOC644936
LOC645323
SCARNA18
SNORA47
MIR583
LOC728723
LOC100129716
LOC100133050
NCRUPAR

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q13.1.

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

Genes
BRCA2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

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

Genes
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-C5
SNAR-C1
SNAR-C3
SNAR-A14

Genes in Wide Peak

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

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

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-563
hsa-mir-885
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RPL32
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
TIMP4
NR2C2
WNT7A
BRPF1
COLQ
CAMK1
BHLHE40
SH3BP5
VGLL4
EDEM1
TATDN2
IQSEC1
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LSM3
LOH3CR2A
LMCD1
C3orf32
TRNT1
CRBN
C3orf19
GHRL
ARL8B
SETD5
TMEM40
TMEM111
C3orf10
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
HDAC11
TSEN2
GRIP2
C3orf20
JAGN1
C3orf42
IL17RC
EAF1
OXNAD1
C3orf24
GALNTL2
CHCHD4
METTL6
C3orf31
IL17RE
CPNE9
FGD5
CIDECP
CNTN4
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
DVWA
TPRXL
LHFPL4
LOC401052
LOC440944
SNORA7A
MIR563
MIR885
EGOT
GHRLOS

Genes in Wide Peak

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

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute's 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
NCRNA00181
ZNF814
LOC100131691

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q32.3.

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

Genes
hsa-mir-664
hsa-mir-194-1
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
C1orf107
FLVCR1
NENF
G0S2
RRP15
KCTD3
DTL
GPATCH2
TMEM206
BATF3
SLC30A10
IARS2
HHAT
RCOR3
SERTAD4
SMYD2
CAMK1G
VASH2
TRAF3IP3
C1orf97
ANGEL2
LYPLAL1
SPATA17
TATDN3
C1orf74
LOC148696
C1orf227
FAM71A
SYT14
RD3
MIR194-1
MIR205
MIR215
MIR29B2
MIR29C
C1orf133
LOC642587
LQK1
SNORA36B
SNORA16B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
FHIT
BAP1
PBRM1
hsa-mir-135a-1
hsa-let-7g
ACY1
ALAS1
ARF4
C3orf51
CACNA1D
DNASE1L3
DUSP7
FLNB
ITIH1
ITIH3
ITIH4
PDHB
PRKCD
RPL29
NEK4
TKT
TNNC1
WNT5A
SLMAP
ACOX2
HESX1
RRP9
PARP3
RPP14
FAM107A
NISCH
TWF2
STAB1
C3orf63
ABHD14A
WDR51A
DNAH1
ERC2
APPL1
GNL3
SPCS1
ARHGEF3
SFMBT1
PHF7
TLR9
IL17RD
PXK
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
SEMA3G
PCBP4
ABHD6
LRTM1
SELK
NT5DC2
WDR82
ABHD14B
RFT1
ACTR8
GPR62
FAM3D
IQCF1
GLYCTK
PPM1M
ASB14
C3orf67
KCTD6
DNAH12
PDE12
FAM116A
CCDC66
SPATA12
TMEM110
IQCF2
IQCF5
MUSTN1
MIRLET7G
MIR135A1
LOC440957
SNORD19
SNORD69
HESRG
SNORD19B
C3orf74

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

Table S73. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IRF4
FOXF2
FOXC1
GMDS
EXOC2
DUSP22
FOXQ1
HUS1B
C6orf195
LOC285768
MYLK4

Genes in Wide Peak

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

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-31
CDKN2A
CDKN2B
ELAVL2
IFNA1
IFNA2
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
MTAP
C9orf53
KLHL9
DMRTA1
TUSC1
IFNE
MIR31
LOC554202
CDKN2BAS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

Table S75. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ANKRD11

Genes in Wide Peak

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

Table S76. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IDI1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
C10orf110
IDI2
TUBB8
NCRNA00200
C10orf108

Genes in Wide Peak

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

Table S77. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CDH1
CDH3
ZFP90

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

Table S78. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FLRT3
MACROD2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

Table S79. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
KCNIP4
NCRNA00099

Genes in Wide Peak

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

Table S80. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LOC285194

Arm-level results

Table 3. Get Full Table Arm-level significance table - 29 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.25 | 1.57 | 0.229 | 0.10 | -6.02 | 1
1q | 1572 | 0.36 | 6.8 | 5.23e-11 | 0.06 | -7.58 | 1
2p | 753 | 0.26 | -2.41 | 1 | 0.06 | -11.1 | 1
2q | 1235 | 0.22 | -2.14 | 1 | 0.06 | -9.41 | 1
3p | 853 | 0.25 | -2.48 | 1 | 0.20 | -4.53 | 1
3q | 917 | 0.53 | 11.6 | 0 | 0.09 | -7.47 | 1
4p | 366 | 0.15 | -6.97 | 1 | 0.51 | 7.75 | 1.52e-14
4q | 865 | 0.10 | -7.08 | 1 | 0.56 | 13.2 | 0
5p | 207 | 0.36 | 0.0843 | 1 | 0.29 | -2.74 | 1
5q | 1246 | 0.15 | -4.72 | 1 | 0.40 | 7.01 | 2.93e-12
6p | 937 | 0.39 | 4.54 | 1.8e-05 | 0.26 | -1.44 | 1
6q | 692 | 0.23 | -3.3 | 1 | 0.47 | 7.22 | 6.9e-13
7p | 508 | 0.32 | -0.703 | 1 | 0.27 | -2.83 | 1
7q | 1071 | 0.38 | 5.13 | 1.12e-06 | 0.11 | -6.99 | 1
8p | 495 | 0.28 | -1.78 | 1 | 0.68 | 16.4 | 0
8q | 697 | 0.55 | 10.8 | 0 | 0.35 | 1.41 | 0.154
9p | 343 | 0.23 | -4.23 | 1 | 0.52 | 7.65 | 2.9e-14
9q | 916 | 0.16 | -5.04 | 1 | 0.52 | 11.3 | 0
10p | 312 | 0.29 | -2.8 | 1 | 0.20 | -6.59 | 1
10q | 1050 | 0.16 | -5.59 | 1 | 0.23 | -2.58 | 1
11p | 731 | 0.10 | -8.68 | 1 | 0.34 | 1.38 | 0.157
11q | 1279 | 0.20 | -2.79 | 1 | 0.26 | -0.022 | 0.902
12p | 484 | 0.43 | 4.35 | 3.34e-05 | 0.20 | -5.44 | 1
12q | 1162 | 0.29 | 0.817 | 0.672 | 0.23 | -1.8 | 1
13q | 554 | 0.20 | -4.6 | 1 | 0.54 | 9.79 | 0
14q | 1144 | 0.09 | -7.66 | 1 | 0.36 | 4.43 | 9.66e-06
15q | 1132 | 0.09 | -7.48 | 1 | 0.42 | 7.4 | 1.96e-13
16p | 719 | 0.13 | -6.47 | 1 | 0.57 | 12.4 | 0
16q | 562 | 0.11 | -6.12 | 1 | 0.71 | 18.6 | 0
17p | 575 | 0.11 | -5.23 | 1 | 0.79 | 23 | 0
17q | 1321 | 0.19 | -2.49 | 1 | 0.58 | 16.4 | 0
18p | 117 | 0.21 | -5.6 | 1 | 0.52 | 6.77 | 1.43e-11
18q | 340 | 0.15 | -6.86 | 1 | 0.56 | 10.2 | 0
19p | 870 | 0.34 | 1.66 | 0.212 | 0.43 | 5.78 | 8.03e-09
19q | 1452 | 0.27 | 1.13 | 0.456 | 0.42 | 8.55 | 0
20p | 295 | 0.45 | 4.4 | 3.05e-05 | 0.16 | -7.4 | 1
20q | 627 | 0.51 | 9.16 | 0 | 0.11 | -7.55 | 1
21q | 422 | 0.19 | -6.42 | 1 | 0.32 | -0.817 | 1
22q | 764 | 0.10 | -5.62 | 1 | 0.73 | 20.8 | 0

Methods & Data
Input

Table 4. Get Full Table First 10 out of 547 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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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- Maintainer = Dan DiCara

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