Stomach Adenocarcinoma: 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 2.0.16a (cga svn revision 43808).

Summary

There were 161 tumor samples used in this analysis: 21 significant arm-level results, 29 significant focal amplifications, and 39 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 - 29 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
--- | --- | --- | --- | ---
17q12 | 1.849e-23 | 1.849e-23 | chr17:37836582-37920967 | 5
19q12 | 1.5548e-22 | 1.5548e-22 | chr19:30183172-30400157 | 2
8q24.21 | 6.6214e-13 | 6.6214e-13 | chr8:128627168-128754688 | 1
20q13.2 | 2.5458e-10 | 2.5458e-10 | chr20:51919706-52644190 | 4
7q21.2 | 4.4516e-10 | 5.1801e-10 | chr7:91785971-92678901 | 11
12p12.1 | 2.2011e-08 | 2.2011e-08 | chr12:25348817-25514596 | 2
12q15 | 6.0808e-08 | 6.0808e-08 | chr12:68272086-70036889 | 21
6p21.1 | 1.3341e-07 | 2.0086e-07 | chr6:43593968-43712957 | 4
18q11.2 | 1.089e-06 | 1.089e-06 | chr18:19552852-19790248 | 1
10q26.13 | 1.4278e-05 | 1.4278e-05 | chr10:123240288-123399846 | 1
8p23.1 | 2.1838e-05 | 2.1838e-05 | chr8:11365904-12562991 | 21
1q42.3 | 2.125e-06 | 5.2826e-05 | chr1:234915915-235099546 | 0 [LOC100506810]
11q13.3 | 5.6183e-05 | 5.6183e-05 | chr11:68946859-69806269 | 6
15q26.1 | 0.00011758 | 0.00011758 | chr15:91063142-91404476 | 2
7p11.2 | 0.00024351 | 0.00034178 | chr7:55076540-55593561 | 3
13q22.1 | 0.00019657 | 0.00055076 | chr13:73664648-73917853 | 0 [KLF5]
3q26.2 | 0.00080397 | 0.00080397 | chr3:165943544-172140317 | 35
1p36.22 | 0.0032738 | 0.0032738 | chr1:10694126-11093740 | 4
11p13 | 0.013254 | 0.013254 | chr11:34638389-35493919 | 7
6q12 | 0.0041613 | 0.016012 | chr6:63903355-64323832 | 2
9p24.1 | 0.014691 | 0.018151 | chr9:4764022-5566129 | 11
13q12.3 | 0.012408 | 0.019858 | chr13:31502987-34013457 | 15
5p13.1 | 0.00122 | 0.042444 | chr5:35850976-50133343 | 61
9p13.3 | 0.053217 | 0.075096 | chr9:32137009-36856267 | 94
1q21.3 | 0.0040329 | 0.079031 | chr1:120156421-174126741 | 587
Xq27.3 | 0.094487 | 0.094487 | chrX:141545065-144594702 | 6
9q34.3 | 0.11197 | 0.11197 | chr9:139857913-140151408 | 31
6q23.3 | 0.094487 | 0.13673 | chr6:133942075-157232936 | 126
5p15.33 | 0.079031 | 0.21179 | chr5:1-26103920 | 97

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
GRB7
MIEN1
PGAP3
MIR4728

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
C19orf12

Genes in Wide Peak

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

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

Genes
MYC

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
ZNF217
BCAS1
TSHZ2
SUMO1P1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
hsa-mir-1285-1
KRIT1
PEX1
ANKIB1
GATAD1
RBM48
MGC16142
FAM133B
LRRD1
LOC728066

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
LYRM5

Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
IFNG
LYZ
RAP1B
YEATS4
CCT2
FRS2
CPSF6
IL22
SLC35E3
IL26
MDM1
NUP107
LRRC10
MIR1279
SNORA70G
MIR3913-2
MIR3913-1
LOC100507250

Genes in Wide Peak

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

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

Genes
MAD2L1BP
GTPBP2
MRPS18A
RSPH9

Genes in Wide Peak

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

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

Genes
GATA6

Genes in Wide Peak

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

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

Genes
FGFR2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p23.1.

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

Genes
BLK
CTSB
FDFT1
GATA4
LINC00208
FAM86B1
DEFB109P1
DEFB130
NEIL2
USP17L2
FAM90A25P
LOC392196
DEFB135
DEFB136
DEFB134
FAM86B2
ZNF705D
FAM66D
FAM66A
LOC100133267
LOC100506990

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CCND1
FGF3
FGF4
FGF19
MYEOV
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
CRTC3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR
LANCL2
VOPP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
hsa-mir-569
hsa-mir-551b
MECOM
CLDN11
SERPINI1
SERPINI2
PLD1
PRKCI
SKIL
SLC2A2
TERC
SEC62
PDCD10
TNIK
GPR160
GOLIM4
MYNN
EIF5A2
SLC7A14
FNDC3B
ZBBX
LRRC31
PHC3
ARPM1
EGFEM1P
WDR49
LRRC34
RPL22L1
LRRIQ4
SAMD7
TMEM212
LOC646168
MIR551B
MIR569
LOC100128164

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.22.

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

Genes
MASP2
TARDBP
CASZ1
C1orf127

Genes in Wide Peak

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

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

Genes
CD44
SLC1A2
PDHX
PAMR1
EHF
APIP
MIR1343

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
PTP4A1
LGSN

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.1.

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

Genes
JAK2
CD274
hsa-mir-101-2
INSL4
RLN1
RLN2
RCL1
INSL6
C9orf46
PDCD1LG2
MIR101-2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.3.

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

Genes
BRCA2
KL
FRY
N4BP2L2
HSPH1
PDS5B
STARD13
N4BP2L1
CG030
RXFP2
TEX26
B3GALTL
EEF1DP3
ZAR1L
TEX26-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.1.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
C6
C7
C9
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
OXCT1
PRKAA1
PTGER4
RPL37
SEPP1
SKP2
SLC1A3
ZNF131
OSMR
NUP155
PAIP1
MRPS30
NNT
TTC33
NIPBL
FBXO4
WDR70
CCL28
C5orf28
C5orf42
PARP8
CARD6
LMBRD2
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR3650
LOC100506548
EGFLAM-AS4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
FANCG
PAX5
ACO1
ANXA2P2
NUDT2
AQP3
AQP7
BAG1
CA9
CCIN
CD72
CLTA
CNTFR
GALT
B4GALT1
DNAJA1
IL11RA
NDUFB6
NFX1
NPR2
PRSS3
RMRP
CCL19
CCL21
TESK1
TLN1
TPM2
VCP
RECK
RGP1
MELK
RUSC2
GNE
TOPORS
SIGMAR1
CREB3
UNC13B
CCL27
PTENP1
DCTN3
KIAA1045
DDX58
DNAJB5
DCAF12
SPAG8
DNAI1
SIT1
SPINK4
STOML2
UBAP1
CHMP5
TMEM8B
APTX
UBE2R2
SMU1
UBAP2
OR2S2
KIAA1161
GBA2
NOL6
FAM214B
HINT2
C9orf24
PIGO
C9orf100
FP588
TAF1L
ARID3C
C9orf23
C9orf131
RNF38
GLIPR2
LOC158376
ATP8B5P
C9orf25
CCDC107
FAM205A
KIF24
ENHO
FAM205B
C9orf128
OR13J1
TMEM215
LOC415056
SUGT1P1
ANKRD18B
HRCT1
MSMP
FAM166B
SNORD121A
SNORD121B
LOC100129250
MIR4667
MIR4475

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
PDE4DIP
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
ALDH9A1
APCS
APOA2
FASLG
SERPINC1
ATP1A2
ATP1A4
ATP1B1
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
DPT
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
F5
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
DARC
GBA
GBAP1
GJA5
GJA8
HDGF
HMGCS2
HSPA6
HSPA7
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LMNA
LMX1A
LOR
LY9
MCL1
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYOC
NDUFS2
NHLH1
NIT1
NPR1
DDR2
PDZK1
PFDN2
PIGC
PI4KB
PKLR
PRRX1
POU2F1
PPOX
PRKAB2
PSMB4
PSMD4
PEX19
RAB13
RFX5
RGS4
RIT1
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
XCL2
VPS72
THBS3
TCHH
TOP1P1
CCT3
TUFT1
TNFSF4
UCK2
USF1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
RGS5
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
ADAM15
PEX11B
CREG1
CD84
SELENBP1
TNFSF18
MPZL1
SH2D2A
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
AIM2
ADAMTS4
SEC22B
CHD1L
PRDX6
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
GPA33
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
TXNIP
PMVK
FAM189B
NES
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
CELF3
PMF1
DUSP12
VPS45
KIAA0907
KIFAP3
ATF6
POGZ
SYT11
PRRC2C
RPRD2
SMG5
NCSTN
GPR161
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
BRP44
OLFML2B
C1orf43
DNM3
CHTOP
PHGDH
LCE2B
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
USP21
SLC39A1
RNF115
KLHL20
LAMTOR2
TMOD4
NME7
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
ACP6
C1orf9
GPR89B
HSD17B7
UFC1
METTL13
OAZ3
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
DARS2
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
C1orf112
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
C1orf114
SLAMF7
CADM3
PRUNE
HAPLN2
GAS5
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
MGC4473
FCRL2
MRPL24
TNFAIP8L2
C1orf54
PAQR6
TRIM46
C1orf129
TARS2
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
NUF2
REG4
HORMAD1
TOMM40L
POLR3GL
TMEM79
ZBTB37
LCE3D
FCRLA
ANKRD36BP1
MAEL
AQP10
SLAMF9
PYGO2
ZNF697
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
FMO9P
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
HIST2H3C
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
RC3H1
DCST1
METTL11B
FAM78B
BNIPL
LRRC71
PYHIN1
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
TIPRL
RIIAD1
THEM5
SLC9A11
NBPF15
ANKRD34A
RUSC1-AS1
C1orf204
C1orf111
LOC284688
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
ANKRD45
C1orf110
OR10R2
FCRL6
NBPF7
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
LOC375010
PEAR1
SFT2D2
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
NBPF9
MIR199A2
MIR214
MIR9-1
HIST2H2BF
ETV3L
LRRC52
LOC440700
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
PRR9
SNORD74
RPL31P11
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA4
SNORA42
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
LOC730159
PPIAL4E
PFN1P2
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR1295A
MIR3119-1
MIR3120
MIR4257
MIR3119-2
MIR4258
MIR3658
LOC100505633
LOC100505666
LOC100505795
LOC100505918
LOC100506023
LOC100506046
PMF1-BGLAP
TNFAIP8L2-SCNM1
MIR4654
DNM3OS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq27.3.

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

Genes
SLITRK4
SPANXN3
UBE2NL
SPANXN4
SPANXN1
SPANXN2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
ABCA2
ENTPD2
FUT7
GRIN1
PTGDS
SSNA1
CLIC3
TUBB4B
MAN1B1
COBRA1
NDOR1
ANAPC2
DPP7
NPDC1
SAPCD2
UAP1L1
TMEM203
SLC34A3
C9orf142
TPRN
C9orf169
LRRC26
LCNL1
C9orf139
FAM166A
C9orf173
RNF224
RNF208
LOC100129722
LOC100289341
MIR3621

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q23.3.

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

Genes
MYB
TNFAIP3
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
ESR1
FUCA2
GRM1
HIVEP2
IFNGR1
MAP3K5
NMBR
OPRM1
PCMT1
PEX7
PLAGL1
SGK1
TCF21
UTRN
VIP
EPM2A
PEX3
STX11
MAP7
LATS1
TBPL1
AKAP12
PHACTR2
BCLAF1
UST
CITED2
HBS1L
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
HEBP2
CCDC28A
MTHFD1L
IPCEF1
TIAM2
FBXO5
RGS17
PDE7B
CLDN20
NOX3
TFB1M
AIG1
VTA1
HECA
IL20RA
MTRF1L
AHI1
RMND1
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
ZBTB2
C6orf115
PBOV1
PERP
ALDH8A1
ULBP3
C6orf211
ADGB
C6orf97
MYCT1
ULBP2
ULBP1
PPP1R14C
SF3B5
FBXO30
LRP11
LTV1
REPS1
PPIL4
FAM54A
C6orf72
IL22RA2
ADAT2
STXBP5
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
MGC34034
SLC2A12
LOC154092
OLIG3
TXLNB
SHPRH
LOC285740
SLC35D3
ZC3H12D
ECT2L
NUP43
RAET1G
HMGA1P7
SUMO4
SAMD5
IYD
FLJ46906
LOC645434
RAET1K
LOC729176
LOC729178
LOC100128176
LINC00271
LOC100132735
NHEG1
MIR3145
MIR3668
MIR3662
LOC100507462
LOC100507489
LOC100507557
MIR4466
MIR4465
LOC100652739

Genes in Wide Peak

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

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

Genes
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
CDH10
CDH12
CDH18
CTNND2
DAP
DNAH5
MTRR
MYO10
NDUFS6
PMCHL1
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
BASP1
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
PP7080
IRX4
TAS2R1
FAM134B
FAM105A
NSUN2
CEP72
ANKH
PRDM9
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
CCDC127
UBE2QL1
C5orf49
FAM173B
CMBL
PLEKHG4B
C5orf38
IRX2
ADAMTS16
LOC255167
LOC285577
LOC285692
LOC285696
SLC6A19
LOC340094
LOC340107
SLC6A18
LRRC14B
FLJ33360
LOC401177
TAG
MARCH11
LOC442132
ANKRD33B
GUSBP1
SDHAP3
LOC728613
LOC729506
SNORD123
LOC100130744
MIR4277
MIR4278
LOC100505738
LOC100505806
LOC100506688
MIR4458
MIR4454
MIR4457
MIR4637
MIR4636
MIR4456
MIR4635

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 - 39 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
--- | --- | --- | --- | ---
16q23.1 | 1.4145e-45 | 1.4145e-45 | chr16:78129058-79627770 | 1
5q11.2 | 1.3422e-24 | 1.3422e-24 | chr5:58260298-59787985 | 3
9p24.1 | 3.326e-23 | 3.811e-19 | chr9:8310705-12693402 | 1
4q22.1 | 6.7269e-20 | 8.3702e-17 | chr4:91148280-93240505 | 1
6p25.3 | 1.1835e-13 | 1.1835e-13 | chr6:1608837-2252425 | 2
20p12.1 | 1.5156e-13 | 1.5156e-13 | chr20:14690293-15165995 | 1
9p21.3 | 6.8002e-25 | 5.572e-12 | chr9:21865498-21997722 | 2
3p14.2 | 2.1891e-14 | 7.1594e-12 | chr3:59034763-61547330 | 1
7q31.1 | 6.3432e-12 | 1.4823e-09 | chr7:110725672-111366370 | 1
18q21.2 | 4.9405e-09 | 4.9405e-09 | chr18:48472083-48705371 | 2
6q26 | 1.2647e-08 | 1.2647e-08 | chr6:161693099-163153207 | 1
Xp21.2 | 3.3064e-08 | 7.5286e-08 | chrX:30870233-32661893 | 3
4q34.3 | 1.8856e-11 | 2.5576e-07 | chr4:178911874-186321446 | 34
1p36.11 | 1.6583e-06 | 1.6583e-06 | chr1:26900639-27322419 | 9
19p13.3 | 1.7983e-05 | 1.7983e-05 | chr19:2473582-4675277 | 68
3q26.31 | 3.2591e-05 | 3.2591e-05 | chr3:173999806-175760559 | 2
10q23.31 | 0.00028437 | 0.00027995 | chr10:89506488-90034038 | 4
11p15.5 | 0.00098046 | 0.0010145 | chr11:2441018-3115942 | 10
22q13.31 | 0.0011946 | 0.0011946 | chr22:46241129-51304566 | 70
17p12 | 0.0015918 | 0.0015974 | chr17:10740609-13975082 | 13
15q11.2 | 0.0020244 | 0.0020077 | chr15:1-54308486 | 391
7q36.3 | 1.0118e-05 | 0.0025408 | chr7:157210222-159138663 | 11
8p23.2 | 0.0029367 | 0.0029587 | chr8:2079140-6262191 | 1
12p13.31 | 0.0033931 | 0.0034054 | chr12:7307243-12267067 | 99
2q37.2 | 0.0010644 | 0.0084283 | chr2:235913227-237079324 | 2
16p13.3 | 0.0082753 | 0.0084283 | chr16:5144019-7771745 | 1
11q23.2 | 0.016157 | 0.015889 | chr11:101953812-135006516 | 307
17q24.3 | 0.015326 | 0.021741 | chr17:70116519-70595192 | 2
3p26.1 | 0.004033 | 0.026241 | chr3:1-8263567 | 17
2q33.3 | 0.00048073 | 0.027067 | chr2:204826225-206558638 | 1
Xq21.33 | 0.042035 | 0.041483 | chrX:94288568-98718611 | 4
1q44 | 0.054819 | 0.054805 | chr1:245282267-245913707 | 1
Xp22.2 | 0.027853 | 0.061617 | chrX:9891764-11137490 | 4
14q23.3 | 0.084078 | 0.10644 | chr14:1-77739344 | 482
2q32.1 | 0.0064619 | 0.17503 | chr2:121553966-201663622 | 365
17q21.2 | 0.12391 | 0.17503 | chr17:38906154-39581297 | 45
21q11.2 | 0.18248 | 0.1856 | chr21:1-33947779 | 122
14q32.33 | 0.13497 | 0.22044 | chr14:92629600-107349540 | 248
13q33.1 | 0.24307 | 0.24307 | chr13:1-115169878 | 414

Genes in Wide Peak

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

Table S28. 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 5q11.2.

Table S29. 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 9p24.1.

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

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

Genes
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
LRRN3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
SMAD4
ELAC1

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
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.2.

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

Genes
hsa-mir-548f-5
DMD
FTHL17

Genes in Wide Peak

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

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

Genes
hsa-mir-1305
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ENPP6
C4orf38
RWDD4
CCDC111
ANKRD37
LOC389247
HELT
FAM92A3
SLED1
LINC00290
LOC728175
LOC731424
CLDN24
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

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

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

Genes
ARID1A
SFN
NR0B2
NUDC
GPN2
PIGV
GPATCH3
ZDHHC18
C1orf172

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
hsa-mir-637
AES
DAPK3
EEF2
GNA15
GNG7
MATK
GADD45B
NFIC
MAP2K2
SGTA
TBXA2R
THOP1
TLE2
S1PR4
APBA3
CHAF1A
EBI3
HMG20B
SEMA6B
ZFR2
PIP5K1C
SNORD37
TJP3
ITGB1BP3
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
STAP2
CCDC94
C19orf10
NCLN
SHD
ZNF77
C19orf29
CELF5
FSD1
TLE6
ZNF556
UBXN6
DOHH
CREB3L3
HDGFRP2
RAX2
MPND
ATCAY
ZNF554
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
MFSD12
GIPC3
DIRAS1
ZNF555
ANKRD24
C19orf77
C19orf29-AS1
PLIN5
MIR637
PLIN4
C19orf71
MIR4746

Genes in Wide Peak

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

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

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

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

Genes
PTEN
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

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

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

Genes
CARS
CDKN1C
KCNQ1
NAP1L4
SLC22A18
SLC22A18AS
PHLDA2
KCNQ1OT1
KCNQ1DN
SNORA54

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-548h-3
hsa-mir-744
DNAH9
ZNF18
ARHGAP44
HS3ST3A1
ELAC2
MYOCD
CDRT15P1
FLJ34690
SHISA6
MIR744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

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

Genes
BUB1B
C15orf55
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
OCA2
PLCB2
MAPK6
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
USP50
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1266
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B

Genes in Wide Peak

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

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

Genes
hsa-mir-595
hsa-mir-153-2
PTPRN2
VIPR2
NCAPG2
WDR60
ESYT2
LOC154822
MIR153-2
MIR595
LOC100506585

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.31.

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

Genes
ETV6
hsa-mir-1244-3
A2M
A2MP1
APOBEC1
C3AR1
CD69
PHC1
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
M6PR
OLR1
PRB1
PRB3
PRB4
PRH1
PRH2
PEX5
PZP
SLC2A3
MFAP5
KLRC4
CSDA
CD163
GDF3
CLEC2B
KLRG1
KLRAP1
PRR4
KLRK1
GABARAPL1
NECAP1
CLEC4E
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
CLEC1B
CLEC1A
KLRF1
MAGOHB
FAM90A1
STYK1
FOXJ2
AICDA
RIMKLB
CLEC7A
BCL2L14
NANOG
CLEC6A
C12orf59
SLC2A14
A2ML1
LOC144571
CLEC12A
CLECL1
CLEC4C
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
CD163L1
CLEC9A
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
LOC389634
ZNF705A
FAM66C
DDX12P
POU5F1P3
LOC642846
FAM86FP
PRB2
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
KLRC4-KLRK1
PRH1-PRR4

Genes in Wide Peak

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

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

Genes
GBX2
AGAP1

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
MMP20
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
YAP1
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100128239
LOC100132078
PATE3
LOC100288077
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

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

Genes
SOX9
LOC100499467

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.1.

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

Genes
GRM7
IL5RA
ITPR1
SETMAR
BHLHE40
EDEM1
CHL1
CNTN6
TRNT1
CRBN
ARL8B
LRRN1
CNTN4
SUMF1
EGOT
LOC100507582
MIR4790

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q33.3.

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

Genes
PARD3B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
hsa-mir-548m
DIAPH2
RPA4
LOC643486

Genes in Wide Peak

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

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

Genes
KIF26B

Genes in Wide Peak

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

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

Genes
CLCN4
MID1
WWC3
LOC100288814

Genes in Wide Peak

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

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

Genes
KTN1
NKX2-1
GPHN
NIN
CCNB1IP1
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ACTN1
ACYP1
ANG
APEX1
ARF6
ARG2
ARHGAP5
BCL2L2
BMP4
ZFP36L1
ENTPD5
CDKN3
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
DLST
EIF2S1
ERH
ESR2
ESRRB
FKBP3
FOXG1
FNTB
FOS
FUT8
GCH1
GMFB
GPR33
GPX2
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
LGALS3
LTBP2
MAX
MGAT2
CTAGE5
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
PNP
NRL
SIX6
OTX2
OXA1L
PAX9
PCK2
PGF
PIGH
PNN
POLE2
PPM1A
PPP2R5E
PRKCH
PRKD1
PSEN1
PSMA3
PSMA6
PSMB5
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPL36AL
RPS29
RTN1
SALL2
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGFB3
TGM1
ZBTB25
PABPN1
DPF3
GEMIN2
NUMB
ADAM21
ADAM20
CDKL1
DCAF5
EIF2B2
AP1G2
SLC7A7
NEMF
PNMA1
CPNE6
AKAP6
AKAP5
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
KIAA0317
TOX4
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
BATF
TM9SF1
NPC2
EXOC5
CGRRF1
EDDM3A
DHRS4
ACOT2
TMED10
FERMT2
RIPK3
AP4S1
C14orf1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
VASH1
ATG14
ZBTB1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
SYNE2
SCFD1
KHNYN
ANGEL1
SLC7A8
ZFYVE26
TTC9
KLHDC2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
NKX2-8
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
ERO1L
COQ6
FAM158A
ATL1
FCF1
RDH11
ZNF219
COX16
GMPR2
SLC22A17
DACT1
ATP6V1D
JKAMP
MBIP
DHRS7
C14orf166
SIX4
ZFYVE1
GNG2
KLHL28
C14orf101
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
RNF31
RBM23
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SYNJ2BP
SLC39A9
C14orf167
G2E3
FLVCR2
OSGEP
C14orf118
ARHGEF40
MUDENG
EAPP
ACTR10
YLPM1
METTL3
LTB4R2
C14orf162
SDR39U1
RPGRIP1
TMEM63C
PELI2
RHOJ
NDRG2
GALNTL1
PLEKHH1
NYNRIN
TXNDC16
TRMT5
HOMEZ
CHD8
FANCM
ZNF410
NGB
RBM25
SNX6
SAV1
C14orf93
ABHD4
NPAS3
SMOC1
EDDM3B
IRF2BPL
MPP5
CDH24
C14orf135
GPR135
METTL17
IL25
GNPNAT1
THTPA
OR4K5
OR11H2
OR4K1
METTL21D
ZC2HC1C
C14orf169
IPO4
L2HGDH
C14orf45
NUBPL
DCAF11
DDHD1
OR4K15
SGPP1
TMX1
DNAL1
RPS6KL1
SYT16
FSCB
BRMS1L
JPH4
RNASE7
INSM2
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
KIAA1737
RPPH1
SLC25A21
PAPLN
LRRC16B
PPP1R3E
TMEM55B
CHURC1
C14orf43
LIN52
NEK9
TTC5
MAPK1IP1L
EGLN3
C14orf126
IFT43
WDR89
C14orf149
TRIM9
DHRS1
CMTM5
MIA2
C14orf28
TRAPPC6B
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
NAA30
GPHB5
JDP2
ISCA2
ACOT4
KLHL33
RPL10L
RDH12
ADAM21P1
MIPOL1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
MDP1
LRFN5
FAM71D
TMEM229B
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
C14orf21
SPTSSA
ADCY4
C14orf183
RALGAPA1
SFTA3
FBXO33
IGBP1P1
LOC283547
C14orf182
LOC283553
GPR137C
PROX2
ZDHHC22
LOC283624
TSSK4
FAM177A1
DHRS4L2
C14orf55
C14orf39
SNORD8
SNORD56B
RNASE10
VSX2
OR6S1
SLC35F4
RAB15
FLJ31306
TBPL2
C14orf23
TOMM20L
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
FLJ22447
PLEKHD1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
LINC00238
OR4Q3
OR4M1
TEX21P
RNASE12
ACOT1
ACOT6
POTEM
LOC642426
ECRP
C14orf176
CBLN3
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
SNORD9
MIR624
DHRS4L1
C14orf38
LOC731223
SNORD127
SNORD126
MIR208B
KTN1-AS1
LOC100129794
LOC100288846
LOC100289511
MIR1260A
OTX2OS1
MIR4308
MIR4307
MIR548Y
LOC100505967
LOC100506071
LOC100506321
LOC100506433
NEDD8-MDP1
BCL2L2-PABPN1
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4503
MIR548AI
MIR4707
MIR4706
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q32.1.

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

Genes
CHN1
ERCC3
HOXD11
HOXD13
NFE2L2
PMS1
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-128-1
hsa-mir-663b
ACVR1
ACVR2A
BIN1
AOX1
RND3
ATP5G3
CACNB4
CCNT2
CHRNA1
COL3A1
COL5A2
ATF2
DARS
DLX1
DLX2
DYNC1I2
DPP4
FAP
FRZB
GAD1
GALNT3
GCG
MSTN
GLI2
GLS
GPD2
GPR17
GPR39
GRB14
GYPC
HNMT
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HSPD1
HSPE1
INPP1
ITGA6
ITGA4
ITGAV
ITGB6
KCNJ3
KIF5C
LCT
LRP2
LY75
MCM6
MGAT5
MYO1B
MYO7B
NAB1
NEB
NEUROD1
NR4A2
ORC4
PDE1A
PDK1
PLCL1
POLR2D
PROC
RBMS1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SP3
SSB
SSFA2
STAT1
STAT4
TFPI
TNFAIP6
TSN
TTN
WIPF1
CXCR4
SDPR
PKP4
HAT1
AGPS
PRKRA
SLC25A12
ABCB11
B3GALT1
KYNU
NMI
STK17B
GTF3C3
PPIG
HS6ST1
CIR1
CYTIP
ZEB2
TLK1
CD302
TANK
DHRS9
CALCRL
PSMD14
STAM2
KBTBD10
UBE2E3
MTX2
TBR1
MAP3K2
NCKAP1
RAPGEF4
GALNT5
NXPH2
COBLL1
PLA2R1
RAB3GAP1
UBXN4
SATB2
CLASP1
SF3B1
R3HDM1
TMEFF2
GCA
MOB4
GORASP2
SPATS2L
EPC2
ARL5A
HIBCH
PTPN18
MMADHC
STK39
METTL5
OLA1
C2orf27A
TFCP2L1
BAZ2B
SLC40A1
ARHGEF4
PDE11A
GULP1
FKBP7
ZAK
LRP1B
DNAJC10
ASNSD1
MFSD6
PLEKHB2
FIGN
RIF1
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
ZC3H15
CFC1
DNAH7
RPRM
UGGT1
SLC39A10
SLC4A10
SPC25
ERMN
HECW2
CWC22
G6PC2
PCGEM1
IFIH1
OSGEPL1
MARCH7
OBFC2A
PLEKHA3
BOLL
C2orf47
SAP130
SCRN3
FASTKD1
GTDC1
TTC21B
METTL8
CYBRD1
CSRNP3
PGAP1
DCAF17
MZT2B
YSK4
COQ10B
THSD7B
KIAA1715
TMEM163
AMMECR1L
CDCA7
ZRANB3
RAB6C
WDR75
C2orf88
CCDC115
MKI67IP
SFT2D3
TANC1
KCNH7
CCDC74A
LOC91149
SESTD1
CCDC74B
ANKRD44
ZNF804A
TTC30A
DAPL1
IMP4
MARS2
ORMDL1
TUBA3E
TUBA3D
FMNL2
GALNT13
OSBPL6
NOSTRIN
DIRC1
LYPD1
NUP35
XIRP2
TYW5
CNTNAP5
RBM45
BBS5
C2orf77
ACMSD
FAM168B
RFTN2
ACVR1C
UBR3
KCTD18
LYPD6
LYPD6B
CCDC148
MYO3B
DUSP19
LOC150527
FLJ32063
ANKAR
TTC30B
LOC150776
WTH3DI
ZSWIM2
ZNF385B
ARL6IP6
KLHL23
PPP1R1C
SGOL2
SLC38A11
WDSUB1
UPP2
GPR155
FAM171B
FAM123C
C2orf69
HNRNPA3
CERS6
METAP1D
LOC254128
CCDC150
CCDC141
LOC285084
LOC285103
SPOPL
MLK7-AS1
CYP27C1
NCKAP5
EVX2
AOX2P
GPR148
FONG
RBM43
LOC375295
CERKL
LOC389033
LOC389043
SP5
LOC401010
DKFZp686O1327
LOC401022
FSIP2
C2orf66
MIR10B
MIR128-1
C2orf27B
LOC440905
LOC440910
POTEKP
LOC440925
POTEE
PHOSPHO2
DFNB59
LOC554201
ANKRD30BL
LOC646743
LOC647012
CFC1B
MZT2A
MIR561
POTEF
PABPC1P2
MIR933
LOC100129961
LOC100130452
LOC100130691
TMEM194B
LOC100131320
SP9
CYP4F30P
LOC100144595
RNU4ATAC
LOC100216479
MIR1246
MIR548N
MIR1258
MIR1245A
ZEB2-AS1
MIR663B
SNORA70F
MIR3128
MIR3129
MIR3606
MIR3679
LOC100505695
LOC100506124
LOC100506134
LOC100506783
LOC100506866
LOC100507140
LOC100507600
LY75-CD302
PHOSPHO2-KLHL23
HSPE1-MOB4
MIR4783
MIR4437
MIR1245B
MIR4774
MIR4785
MIR4784
MIR4773-1
MIR4444-1
MIR4773-2
LOC100861402

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.2.

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

Genes
KRT10
KRT12
KRT31
KRT33A
KRT33B
KRT34
KRT37
KRT23
KRT20
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
KRTAP4-12
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
KRTAP4-4
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
KRT40
TMEM99
KRT28
KRT27
KRT26
KRT39
KRTAP4-11
KRTAP4-8
KRTAP2-2
KRTAP9-1
LOC730755
KRTAP4-9
KRTAP4-7
KRTAP16-1
LOC100505782

Genes in Wide Peak

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

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

Genes
hsa-mir-4327
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
APP
ATP5J
BACH1
BAGE
CXADR
GABPA
GRIK1
NCAM2
TMPRSS15
SOD1
HSPA13
TIAM1
TPTE
NRIP1
CLDN8
ADAMTS1
URB1
RWDD2B
USP16
CCT8
BTG3
ADAMTS5
LTN1
CLDN17
N6AMT1
USP25
HUNK
RBM11
MIS18A
LINC00158
CHODL-AS1
LINC00113
C21orf15
LINC00308
MRPL39
C21orf91
MRAP
C21orf7
SCAF4
JAM2
C21orf63
SAMSN1
C21orf119
BAGE5
BAGE4
BAGE3
BAGE2
MIR155HG
CYYR1
LINC00161
KRTAP13-1
CHODL
ANKRD30BP2
LIPI
ABCC13
LINC00189
C21orf91-OT1
LINC00314
KRTAP15-1
D21S2088E
LINC00307
LINC00515
KRTAP13-4
POTED
KRTAP7-1
KRTAP8-1
KRTAP11-1
KRTAP19-1
KRTAP13-2
KRTAP13-3
KRTAP23-1
KRTAP6-1
KRTAP6-2
KRTAP6-3
KRTAP19-2
KRTAP19-3
KRTAP19-4
KRTAP19-5
KRTAP19-6
KRTAP19-7
KRTAP20-1
KRTAP20-2
KRTAP21-1
KRTAP21-2
KRTAP22-1
KRTAP20-3
LOC339622
LINC00317
LINC00320
LOC388813
LINC00478
KRTAP26-1
ANKRD20A11P
MIRLET7C
MIR125B2
MIR155
MIR99A
GRIK1-AS1
KRTAP24-1
KRTAP27-1
SNORA80
KRTAP19-8
KRTAP25-1
TEKT4P2
KRTAP20-4
KRTAP22-2
KRTAP21-3
GRIK1-AS2
MIR4327
MIR3156-3
MIR3687
MIR3648
C21orf37
LINC00159
MIR4759

Genes in Wide Peak

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

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

Genes
AKT1
TCL1A
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
SERPINA3
BDKRB1
BDKRB2
SERPINA6
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ADAM6
DLK1
CCNK
MTA1
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
C14orf109
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CDCA4
ATG2B
UBR7
MEG3
BTBD7
ZNF839
C14orf132
DDX24
UNC79
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
RIN3
TMEM121
AMN
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
FAM181A
BTBD6
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
C14orf49
MGC23270
NUDT14
LINC00521
SERPINA11
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
CCDC85C
ITPK1-AS1
SERPINA9
LINC00226
LINC00221
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
MIR1247
MIR1185-1
MIR1185-2
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q33.1.

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Arm-level results

Table 3. Get Full Table Arm-level significance table - 21 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.07 | -1.65 | 1 | 0.16 | 1.54 | 0.177
1q | 1955 | 0.21 | 2.75 | 0.0148 | 0.13 | -0.0405 | 0.938
2p | 924 | 0.16 | -1.53 | 1 | 0.07 | -4.11 | 1
2q | 1556 | 0.14 | -0.698 | 1 | 0.08 | -2.65 | 1
3p | 1062 | 0.11 | -2.48 | 1 | 0.23 | 1.01 | 0.415
3q | 1139 | 0.23 | 1.12 | 0.522 | 0.13 | -1.71 | 1
4p | 489 | 0.07 | -4.21 | 1 | 0.36 | 3.37 | 0.00231
4q | 1049 | 0.05 | -4 | 1 | 0.33 | 4.2 | 0.000176
5p | 270 | 0.24 | -0.592 | 1 | 0.19 | -1.65 | 1
5q | 1427 | 0.07 | -2.93 | 1 | 0.24 | 2.17 | 0.0499
6p | 1173 | 0.22 | 0.87 | 0.699 | 0.15 | -1.27 | 1
6q | 839 | 0.19 | -0.837 | 1 | 0.19 | -0.67 | 1
7p | 641 | 0.47 | 7.1 | 4.28e-12 | 0.12 | -2.42 | 1
7q | 1277 | 0.43 | 7.98 | 6.66e-15 | 0.11 | -1.71 | 1
8p | 580 | 0.51 | 7.2 | 2.41e-12 | 0.38 | 3.35 | 0.00231
8q | 859 | 0.62 | 12 | 0 | 0.17 | -0.798 | 1
9p | 422 | 0.17 | -1.83 | 1 | 0.35 | 2.93 | 0.0074
9q | 1113 | 0.21 | 0.345 | 1 | 0.26 | 1.91 | 0.0862
10p | 409 | 0.24 | -0.27 | 1 | 0.20 | -1.2 | 1
10q | 1268 | 0.16 | -0.551 | 1 | 0.19 | 0.357 | 0.721
11p | 862 | 0.11 | -2.96 | 1 | 0.16 | -1.44 | 1
11q | 1515 | 0.13 | -1.1 | 1 | 0.15 | -0.328 | 1
12p | 575 | 0.21 | -0.746 | 1 | 0.20 | -1.06 | 1
12q | 1447 | 0.18 | 0.299 | 1 | 0.15 | -0.457 | 1
13q | 654 | 0.39 | 4.58 | 1.34e-05 | 0.16 | -1.63 | 1
14q | 1341 | 0.07 | -3.25 | 1 | 0.25 | 2.31 | 0.038
15q | 1355 | 0.14 | -1.04 | 1 | 0.19 | 0.442 | 0.721
16p | 872 | 0.19 | -0.56 | 1 | 0.19 | -0.56 | 1
16q | 702 | 0.13 | -2.42 | 1 | 0.24 | 0.517 | 0.712
17p | 683 | 0.12 | -2.63 | 1 | 0.40 | 4.94 | 1.54e-05
17q | 1592 | 0.15 | -0.393 | 1 | 0.17 | 0.39 | 0.721
18p | 143 | 0.24 | -0.681 | 1 | 0.30 | 0.935 | 0.438
18q | 446 | 0.17 | -1.87 | 1 | 0.40 | 4.43 | 9.58e-05
19p | 995 | 0.15 | -1.36 | 1 | 0.30 | 2.9 | 0.0074
19q | 1709 | 0.20 | 1.7 | 0.197 | 0.24 | 3.1 | 0.0049
20p | 355 | 0.56 | 8.72 | 0 | 0.14 | -2.19 | 1
20q | 753 | 0.64 | 12.7 | 0 | 0.05 | -3.2 | 1
21q | 509 | 0.11 | -3.2 | 1 | 0.38 | 4.03 | 0.000279
22q | 921 | 0.12 | -2.41 | 1 | 0.33 | 3.67 | 0.000983
Xq | 1312 | 0.15 | -0.755 | 1 | 0.18 | -0.021 | 0.938

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/STAD/1669650/2.GDAC_MergeDataFiles.Finished/STAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 161 Input Tumor Samples.

Tumor Sample Names
TCGA-B7-5816-01A-21D-1599-01
TCGA-B7-5818-01A-11D-1599-01
TCGA-BR-4183-01A-02D-1130-01
TCGA-BR-4184-01A-01D-1130-01
TCGA-BR-4187-01A-01D-1130-01
TCGA-BR-4188-01A-01D-1130-01
TCGA-BR-4190-01A-01D-1130-01
TCGA-BR-4191-01A-02D-1130-01
TCGA-BR-4194-01A-02D-1130-01
TCGA-BR-4195-01A-01D-1130-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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