SNP6 Copy number analysis (GISTIC2)
Pheochromocytoma and Paraganglioma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C13X85QT
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C13X85QT
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 2.0.22 (Firehose task version: 140).

Summary

There were 162 tumor samples used in this analysis: 19 significant arm-level results, 7 significant focal amplifications, and 21 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 - 7 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
--- | --- | --- | --- | ---
1q21.3 | 0.00036807 | 0.00036807 | chr1:120523956-154950221 | 257
4q31.1 | 0.00065478 | 0.00065478 | chr4:140946021-140992630 | 1
17q21.31 | 0.0010946 | 0.0010946 | chr17:42282074-42389627 | 5
12q13.3 | 0.032245 | 0.032245 | chr12:55017371-58374945 | 121
14q24.3 | 0.05856 | 0.05856 | chr14:77411889-77529068 | 2
4q25 | 0.218 | 0.24153 | chr4:55115761-118191881 | 347
11p15.2 | 0.24234 | 0.24234 | chr11:12145534-25296454 | 89

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
NOTCH2
TPM3
PDE4DIP
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
CHRNB2
CKS1B|ENSG00000173207.8
CTSK
CTSS
ECM1
ENSA
FCGR1A
FLG
FMO5
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
NPR1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
TCHH
TUFT1
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
JTB
MTMR11
SLC27A3
TDRKH
CD160
VPS45
POGZ
RPRD2
SNAPIN
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
TMOD4
CERS2
CRNN
BOLA1
APH1A
PLEKHO1
GPR89B
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
CDC42SE1
PGLYRP4
ATP8B2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GABPB2
TCHHL1
RPTN
TDRD10
SHE
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
NBPF12
LELP1
BNIPL
SPRR4
PPIAL4A
LCE4A
NBPF11
CRTC2
LCE5A
RIIAD1
THEM5
NBPF16
ANKRD34A
HIST2H2AB
S100A7A
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
NOTCH2NL
LYSMD1
HRNR
FLG2
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
C2CD4D
NBPF20
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q31.1.

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

Genes
MAML3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q21.31.

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

Genes
U3|ENSG00000221496.1
RN7SL507P
SLC4A1
UBTF
RUNDC3A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.3.

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

Genes
CDK4
DDIT3
NACA
RN7SKP65
MIR26A2
snoU13|ENSG00000238436.1
RN7SL312P
MIR1228
HBCBP
RDH16
SNORA48|ENSG00000212383.1
RN7SL809P
SNORD59A
RBMS2
RNF41
RN7SL770P
MMP19
TMEM198B
ORMDL2
APOF
ATP5B
CD63
CDK2
CS
CYP27B1
DGKA
ERBB3
B4GALNT1
BLOC1S1
GLI1
INHBC
ITGA7
KIF5A
LRP1
MARS
METTL1
MIP
MYL6
MYO1A
NAB2
PA2G4
PRIM1
RAB5B
RDH5
RPL41
RPS26
TSPAN31
SHMT2
PMEL
SMARCC2
STAT2
STAT6
SUOX
TAC3
HSD17B6
TIMELESS
TESPA1
ZBTB39
PAN2
TSFM
CTDSP2
GDF11
CNPY2
DCTN2
AVIL
PTGES3
OS9
BAZ2A
NXPH4
GPR182
R3HDM2
TMEM194A
ESYT1
METTL21B
GLS2
IL23A
NDUFA4L2
NEUROD4
ARHGAP9
IKZF4
SLC26A10
NABP2
PIP4K2C
INHBE
WIBG
SARNP
ZC3H10
DNAJC14
LACRT
XRCC6BP1
MARCH9
COQ10A
MBD6
ARHGEF25
AGAP2
DCD
MUCL1
OR2AP1
OR10P1
SDR9C7
OR10A7
MYL6B
DTX3
METTL7B
STAC3
OR6C74
OR6C3
OR6C6
ANKRD52
SLC39A5
SPRYD4
OR6C2
OR6C4
OR6C1
OR6C75
OR6C76
OR6C70
OR6C65
OR6C68
OR9K2
MIR616

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q24.3.

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

Genes
RN7SL356P
IRF2BPL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q25.

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

Genes
KDR
KIT
PDGFRA
RAP1GDS1
TET2
FIP1L1
MTRNR2L13
RN7SL808P
MIR577
RN7SL184P
TIFA
C4orf32
ENPEP
RN7SL275P
CCDC109B
MIR576
RN7SL55P
SNORD112|ENSG00000252566.1
GIMD1
RN7SL89P
SNORA31|ENSG00000252136.1
TACR3
BDH2
CISD2
snoU13|ENSG00000238948.1
RN7SL728P
MIR1255A
ADH1B
PCNAP1
MIR3684
EIF4E
RN7SKP28
RNA5SP164
RN7SKP248
GPRIN3
RN7SKP244
RNU6ATAC31P
IBSP
snoU13|ENSG00000238652.1
RN7SL681P
RN7SKP96
MIR4451
RN7SKP48
RN7SL552P
MRPS18C
snoR442|ENSG00000252834.1
MIR575
LINC00575
SNORD42|ENSG00000202440.1
HNRNPD
SNORA31|ENSG00000252762.1
SNORA75|ENSG00000212620.1
OR7E94P
LINC00989
NAA11
RN7SL127P
MIR5096
snoU13|ENSG00000238816.1
SNORD75|ENSG00000221711.1
MIR548AH
MIR4450
SNORD50|ENSG00000199857.1
CDKL2
BTC
PPBPP2
RN7SL218P
PPBP
PF4
PF4V1
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
RNA5SP163
snoU13|ENSG00000238318.1
CSN1S2AP
SULT1B1
UGT2A1
UGT2A2
UGT2B10
TMPRSS11BNL
FTLP10
TMPRSS11GP
SNORA62|ENSG00000202374.1
GNRHR
UBA6
TECRL
snoU13|ENSG00000238925.1
snoU13|ENSG00000238541.1
snoU13|ENSG00000238579.1
NOA1
RN7SL357P
RN7SL492P
ARL9
SRP72
RNA5SP162
KIAA1211
RNA5SP161
RN7SKP30
RN7SL822P
RN7SL424P
ADH1A
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
ALB
AMBN
ANK2
ANXA3
AREG
ART3
ATOH1
BMP3
BMPR1B
CAMK2D
CASP6
CCNG2
SCARB2
CDS1
CENPC
CENPE
CSN1S1
CSN2
CSN3
DCK
DMP1
DSPP
EGF
EPHA5
EREG
FGF5
GC
GK2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
H2AFZ
HADH
HTN1
HTN3
CFI
IGFBP7
IGJ
IL8
CXCL10
MANBA
CXCL9
AFF1
MTTP
MUC7
NFKB1
PDHA2
PITX2
PKD2
POLR2B
PPEF2
PPAT
PPP3CA
PRKG2
MAPK10
PTPN13
REST
RPL34
CXCL6
CXCL11
CXCL5
SNCA
SPINK2
SPP1
STATH
SULT1E1
UBE2D3
UGT2B4
UGT2B7
UGT2B15
UGT2B17
UGT8
SPARCL1
USO1
UNC5C
LAMTOR3
SLC4A4
HERC3
PAPSS1
AIMP1
TMPRSS11D
ABCG2
ADAMTS3
CLOCK
CEP135
G3BP2
HNRNPDL
TSPAN5
ENAM
FAM13A
SEC24B
CXCL13
PAICS
PDLIM5
RRH
UGT2B11
HPSE
NMU
SMR3B
NPFFR2
UGT2A1
CCNI
SEC31A
RUFY3
MMRN1
WDFY3
METAP1
LPHN3
PARM1
RCHY1
ANKRD17
STAP1
SMR3A
PPA2
DAPP1
DKK2
NAAA
COQ2
HPGDS
TMPRSS11E
COPS4
HSD17B11
LEF1
HERC5
PLAC8
LARP7
EMCN
NUDT9
NUP54
GAR1
UGT2B28
ARHGEF38
ODAM
HERC6
BANK1
SDAD1
C4orf21
AP1AR
BMP2K
SEPT11
EXOC1
TMEM165
SMARCAD1
MEPE
PRDM8
UTP3
INTS12
KLHL8
SHROOM3
ENOPH1
PROL1
OSTC
NEUROG2
SLC39A8
NDST4
ETNPPL
MRPL1
ELOVL6
ARSJ
SRD5A3
THAP9
UGT2A3
GSTCD
SCD5
DNAJB14
FRAS1
ALPK1
CXXC4
PLA2G12A
ARHGAP24
C4orf17
FAM175A
HOPX
COL25A1
AGPAT9
PIGY
CABS1
YTHDC1
MOB1B
TRMT10A
TBCK
HELQ
CYP2U1
DDIT4L
PCAT4
ANTXR2
LIN54
TMPRSS11B
AASDH
PDCL2
C4orf36
TRAM1L1
SLC9B2
SLC9B1
PAQR3
THAP6
C4orf26
PPM1K
RASGEF1B
TIGD2
RASSF6
SGMS2
CNOT6L
C4orf22
EPGN
NPNT
FDCSP
NAP1L5
COX18
STPG2
CCDC158
TMPRSS11A
SOWAHB
LRIT3
SLC10A6
HSD17B13
TMPRSS11F
C4orf40
AMTN
CCSER1
MIR302A
MTHFD2L
TMEM150C
MIR302B
MIR302C
MIR302D
MIR367
AREGB
MIR297
FAM47E
MIR1269A
THEGL
MIR548AG1
MIR4452
FAM47E
MIR5705
PYURF

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p15.2.

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

Genes
FANCF
SVIP
RNA5SP338
RNA5SP337
RNA5SP336
SLC6A5
SNORA1|ENSG00000207407.1
MIR4486
RNA5SP335
RNA5SP334
RNA5SP333
SAA3P
TPH1
SNORD14B
SNORD14A
OR7E14P
RN7SKP90
C11orf58
RN7SL188P
PSMA1
RNA5SP332
SPON1
RNA5SP331
RN7SKP151
LINC00958
SCARNA16|ENSG00000252329.1
PARVA
ARNTL
CALCA
CALCB
COPB1
GAS2
GTF2H1
KCNC1
KCNJ11
LDHA
LDHC
MYOD1
NELL1
NUCB2
PDE3B
PIK3C2A
PSMA1
PTH
RPS13
SAA1
SAA2
SAA4
ABCC8
TEAD1
TSG101
CSRP3
MICAL2
USH1C
PRMT3
HTATIP2
HPS5
RRAS2
SERGEF
ZDHHC13
UEVLD
SOX6
SLC17A6
E2F8
FAR1
BTBD10
PTPN5
MICALCL
NAV2
SAAL1
MRGPRX2
MRGPRX3
MRGPRX4
CYP2R1
DBX1
PLEKHA7
SPTY2D1
TMEM86A
LDHAL6A
ANO5
MRGPRX1
IGSF22
LUZP2
OTOG
NCR3LG1
INSC
MIR3159
CCDC179
MIR4694

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 - 21 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
--- | --- | --- | --- | ---
1p12 | 5.9693e-19 | 5.9693e-19 | chr1:117751737-118152240 | 1
17q11.2 | 1.6136e-09 | 1.6136e-09 | chr17:28433783-29601307 | 21
3p24.1 | 8.8072e-07 | 8.8072e-07 | chr3:27762089-28619698 | 3
3q26.1 | 5.3979e-06 | 5.2481e-06 | chr3:162886928-163894013 | 2
11q22.1 | 0.00013401 | 0.00014492 | chr11:98990382-100513772 | 2
11p15.4 | 0.0005745 | 0.00053173 | chr11:1-10330781 | 254
6p12.3 | 0.00084406 | 0.00085808 | chr6:49915604-49978544 | 2
9p24.2 | 0.0010529 | 0.001077 | chr9:3050941-3826080 | 1
5q15 | 0.0026275 | 0.0027578 | chr5:93948531-94087183 | 1
4q28.3 | 0.0038918 | 0.0036687 | chr4:90644509-191154276 | 420
16q21 | 0.0036933 | 0.0036687 | chr16:61773081-62438663 | 2
6q16.1 | 0.0070166 | 0.0074664 | chr6:93500378-95273663 | 2
12q21.33 | 0.010999 | 0.01074 | chr12:91383361-91498710 | 1
17p13.2 | 0.033855 | 0.033855 | chr17:6344536-6547775 | 4
8p22 | 0.037391 | 0.038192 | chr8:11189489-17434338 | 43
22q13.31 | 0.040712 | 0.040712 | chr22:35962587-51304566 | 254
8q23.3 | 0.060878 | 0.058778 | chr8:113652366-116964867 | 2
9q21.12 | 0.12416 | 0.12297 | chr9:38619152-101052796 | 242
1q42.13 | 0.15679 | 0.15382 | chr1:216596596-249250621 | 304
13q22.3 | 0.17067 | 0.17975 | chr13:78338017-78522426 | 2
Xp21.1 | 0.22796 | 0.22796 | chrX:30865118-34644819 | 7

Genes in Wide Peak

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

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

Genes
MAN1A2

Genes in Wide Peak

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

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

Genes
RN7SL138P
TEFM
SUZ12P
RN7SL316P
LRRC37BP1
SMURF2P1
SNORD63|ENSG00000252112.1
MIR423
MIR3184
BLMH
CPD
SLC6A4
GOSR1
TBC1D29
CRLF3
ADAP2
ATAD5
NSRP1
RNF135
TMIGD1
MIR4733

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p24.1.

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

Genes
CMC1
AZI2
ZCWPW2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.1.

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

Genes
snoU13|ENSG00000238398.1
MIR1263

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.1.

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

Genes
RN7SL222P
RN7SKP53

Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
ADM
RN7SKP50
RN7SL56P
snoU13|ENSG00000238387.1
SNORA23
MIR5691
RNA5SP330
SNORA45
SNORA3|ENSG00000200983.1
SCARNA20|ENSG00000252778.1
OR10AB1P
GVINP1
TAF10
RRP8
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62|ENSG00000201980.1
OR51C1P
SNORA7|ENSG00000206976.1
snoU13|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
HBB
HBD
HBE1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
RNH1
MRPL23
RPL27A
RRM1
SMPD1
TRIM21
ST5
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
TRIM66
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
PKP3
SWAP70
DENND5A
SIRT3
OR52A1
ARFIP2
OR10A3
TIMM10B
RBMXL2
PGAP2
TRPM5
UBQLN3
BET1L
CEND1
CYB5R2
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
SBF2
FAM160A2
TRIM5
SYT8
PRKCDBP
OSBPL5
LRRC56
MRGPRE
ART5
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
OR56B4
OR52B2
C11orf35
OR51F1
OR51V1
EFCAB4A
OR10A4
OLFML1
NLRP10
NLRP14
ANO9
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
MRGPRG
IFITM5
FAM99A
OR56B1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
TMEM41B
MUC5B
MIR302E
MIR4298
MIR4686
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p12.3.

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

Genes
DEFB113
DEFB114

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.2.

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

Genes
RFX3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
ANKRD32

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q28.3.

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

Genes
IL2
RAP1GDS1
DUX4
TET2
FBXW7
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
C4orf45
U3|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
SNORD73A
SNORD73
RNA5SP168
RNA5SP167
RNA5SP166
RN7SL254P
MIR4799
RNA5SP165
TMEM184C
RN7SKP235
ANAPC10
HHIP
MIR3139
USP38
snoU13|ENSG00000238695.1
RN7SL152P
UCP1
SNORD112|ENSG00000252300.1
RN7SKP253
RN7SKP237
ACA64|ENSG00000239005.1
RN7SL311P
RN7SL382P
LINC00500
LINC00499
LINC00498
LINC00616
LINC00613
PCDH10
SNORA70|ENSG00000252014.1
RN7SL205P
RNY5P4
snoU13|ENSG00000238802.1
HSPA4L
INTU
RN7SL335P
QRFPR
RN7SKP137
MAD2L1
SNORA11|ENSG00000221245.1
C4orf3
CEP170P1
SNHG8
NT5C3AP1
MTRNR2L13
RN7SL808P
MIR577
RN7SL184P
TIFA
C4orf32
ENPEP
RN7SL275P
CCDC109B
MIR576
RN7SL55P
SNORD112|ENSG00000252566.1
GIMD1
RN7SL89P
SNORA31|ENSG00000252136.1
TACR3
BDH2
CISD2
snoU13|ENSG00000238948.1
RN7SL728P
MIR1255A
ADH1B
PCNAP1
MIR3684
EIF4E
RN7SKP28
RNA5SP164
RN7SKP248
ADH1A
ADH1C
ADH4
ADH5
ADH6
ADH7
AGA
ANK2
SLC25A4
ANXA5
ATOH1
BMPR1B
CAMK2D
CASP3
CASP6
CCNA2
LRBA
CLGN
CENPE
CLCN3
CPE
CTSO
DCTD
EDNRA
EGF
ELF2
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGF2
FGG
FRG1
GAB1
GLRB
GPM6A
GRIA2
GRID2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HPGD
CFI
IL15
ING2
IRF2
KLKB1
SMAD1
MANBA
MGST2
NR3C2
MTNR1A
MTTP
NDUFC1
NEK1
NFKB1
NPY1R
NPY2R
NPY5R
PDHA2
PET112
PITX2
PLRG1
EXOSC9
POU4F2
PPID
PPP3CA
ABCE1
RPL34
RPS3A
MSMO1
SFRP2
SNCA
TDO2
TLL1
TRPC3
UBE2D3
UGT8
VEGFC
GLRA3
SMARCA5
SORBS2
PRSS12
UNC5C
LAMTOR3
PDE5A
SAP30
INPP4B
PAPSS1
LRAT
AIMP1
NDST3
HAND2
RAPGEF2
MFAP3L
SEC24D
TSPAN5
SPRY1
PGRMC2
SEC24B
MAB21L2
PDLIM5
RRH
PLK4
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
MMRN1
PALLD
TBC1D9
METAP1
KIAA0922
TRIM2
SLC7A11
CCRN4L
FAM149A
FBXO8
PPA2
DAPP1
DKK2
ARFIP1
HPGDS
ZNF330
SPOCK3
AADAT
LEF1
FAM198B
LARP7
EMCN
MYOZ2
ASIC5
GALNT7
CLDN22
GAR1
PCDH18
USP53
OTUD4
DCHS2
ARHGEF38
C4orf27
MARCH1
BANK1
LARP1B
BBS7
NEIL3
TMEM144
TMA16
C4orf21
AP1AR
MAML3
DDX60
CDKN2AIP
TENM3
LRP2BP
FSTL5
SMARCAD1
STOX2
INTS12
ANKRD50
RNF150
KIAA1430
FNIP2
SH3RF1
METTL14
OSTC
IL21
RXFP1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
NDST4
ETNPPL
ELOVL6
NDNF
FAT4
ARSJ
ARHGAP10
MLF1IP
GSTCD
MAP9
TNIP3
PHF17
DNAJB14
WWC2
NAA15
C4orf29
ALPK1
CXXC4
CEP44
SETD7
PLA2G12A
SLC25A31
RAB33B
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
KIAA1109
COL25A1
MGARP
CBR4
FHDC1
PRMT10
DDX60L
NAF1
TRMT10A
TBCK
CYP2U1
DDIT4L
WDR17
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
SPATA4
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
FAM218A
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
RBM46
SGMS2
SYNPO2
C4orf46
TIGD4
RWDD4
CCDC111
TRIML2
ELMOD2
NPNT
CCDC110
MFSD8
RNF175
STPG2
TRIML1
PRSS48
LRIT3
ANKRD37
TRIM61
HELT
CCSER1
MIR302A
GUSBP5
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
C4orf51
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
FAM160A1
MIR297
CLDN24
MIR1305
MIR548G
MIR3140
MIR4276
MIR3945
MIR4455
MIR4453

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q21.

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

Genes
snoU13|ENSG00000238507.1
RN7SKP76

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.1.

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

Genes
SNORA18|ENSG00000252249.1
EPHA7

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.33.

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

Genes
KERA

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.2.

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

Genes
RNA5SP435
KIAA0753
FAM64A
ACKR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p22.

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

Genes
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
BLK
CTSB
FDFT1
GATA4
MSR1
SLC7A2
TUSC3
DLC1
CNOT7
KIAA1456
FAM167A
FAM86B1
LONRF1
VPS37A
SGCZ
TDH
C8orf48
DEFB130|ENSG00000232948.1
NEIL2
MICU3
USP17L2
DEFB135
DEFB136
ZNF705D
MIR5692A2

Genes in Wide Peak

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

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

Genes
EP300
MYH9
PDGFB
MKL1
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
LINC00229
SCUBE1
RNU12
RN7SKP80
RRP7B
RRP7A
snoU13|ENSG00000238498.1
LINC00634
SHISA8
MIR33A
RNU6ATAC22P
RBX1
snoU13|ENSG00000238887.1
MIR4766
FAM83F
RN7SKP210
SNORD43|ENSG00000263764.1
SNORD83A
SNORD83B
APOBEC3F
APOBEC3C
FAM227A
RN7SL704P
snoU13|ENSG00000238569.1
NOL12
RN7SL385P
RN7SKP214
snoU13|ENSG00000239056.1
CACNG2
RN7SL349P
APOL4
ACR
ACO2
ADSL
ATF4
BIK
TSPO
MPPED1
CHKB
CPT1B
CSF2RB
CSNK1E
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
MCHR1
H1F0
IL2RB
KCNJ4
LGALS1
LGALS2
MB
MFNG
MGAT3
MPST
NAGA
NCF4
NDUFA6
NHP2L1
PMM1
POLR2F
PPARA
MAPK11
PVALB
RAC2
RANGAP1
RPL3
MAPK12
SBF1
SOX10
SREBF2
SSTR3
ST13
TCF20
TEF
TST
UPK3A
WNT7B
PLA2G6
GALR3
APOL1
EIF3D
CACNA1I
SYNGR1
GRAP2
PICK1
GTPBP1
APOBEC3B
CELSR1
PPP6R2
ZBED4
JOSD1
SCO2
DNAL4
PKDREJ
TAB1
SLC25A17
DDX17
NUP50
TOB2
KDELR3
IFT27
TRIOBP
CDC42EP1
DMC1
RABL2B
PACSIN2
TNRC6B
GRAMD4
TTLL12
MLC1
ZC3H7B
KIAA0930
GCAT
CBX6
NPTXR
CBX7
SLC16A8
MAPK8IP2
RBFOX2
SH3BP1
PLXNB2
MAFF
BRD1
APOL2
TBC1D22A
CBY1
SUN2
TTLL1
SAMM50
ATXN10
FAM19A5
TXN2
TMEM184B
SULT4A1
GGA1
RIBC2
ARFGAP3
SMC1B
CYTH4
CSDC2
MCAT
DESI1
SGSM3
CARD10
PARVB
NCAPH2
EIF3L
GTSE1
A4GALT
MOV10L1
SMCR7L
FAM118A
TTC38
MIOX
PRR5
TRMU
SEPT3
PANX2
TOMM22
PDXP
APOBEC3G
XPNPEP3
PARVG
CERK
EFCAB6
CENPM
CRELD2
C22orf46
KCTD17
CCDC134
ADM2
FOXRED2
BAIAP2L2
TRABD
PNPLA3
APOL6
APOL5
APOL3
L3MBTL2
HDAC10
LDOC1L
POLDIP3
C22orf23
PHF5A
KIAA1644
SHANK3
MICALL1
TUBGCP6
LMF2
RPS19BP1
SMDT1
SERHL
PHF21B
KLHDC7B
ELFN2
C1QTNF6
TNFRSF13C
ANKRD54
APOBEC3D
ENTHD1
DNAJB7
CHADL
MEI1
FAM109B
NFAM1
PNPLA5
TMPRSS6
APOBEC3H
WBP2NL
POLR3H
APOBEC3A
SERHL2
ATP5L2
TEX33
C22orf34
LINC00207
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR658
MIR659
MIR1281
MIR3201
MIR3619
MIR3667
MIR4763
MIR4534
MIR378I
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q23.3.

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

Genes
TRPS1
MIR2053

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.12.

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

Genes
GNAQ
FANCC
OMD
SYK
XPA
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
snoU13|ENSG00000238746.1
RNA5SP288
MIR27B
MIR23B
MIR2278
PCAT7
ZNF169
snoU13|ENSG00000238792.1
MIRLET7DHG
CENPP
SNORA84
snoU13|ENSG00000238996.1
LINC00475
LINC00484
MIR3153
SHC3
U3|ENSG00000252299.1
U6|ENSG00000271923.1
SPATA31C1
SNORA26|ENSG00000212421.1
RN7SKP264
IDNK
SNORD112|ENSG00000252256.1
snoU13|ENSG00000238608.1
RN7SKP242
SPATA31D3
SPATA31D4
SPATA31D5P
SNORD95|ENSG00000200969.1
RNA5SP287
TLE4
RN7SKP59
PCA3
snoU13|ENSG00000238598.1
RNY4P1
RN7SKP47
RNA5SP286
snoU13|ENSG00000238402.1
RNA5SP285
MIR204
RN7SL570P
CBWD3
PGM5P2
RNA5SP284
SNORA70|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
ALDH1A1
ANXA1
APBA1
AUH
KLF9
CKS2
CTSL
DAPK1
ECM2
S1PR3
FBP1
FOXE1
FXN
GAS1
GCNT1
HNRNPK
HSD17B3
IARS
NCBP1
NFIL3
NINJ1
NTRK2
ROR2
OGN
PCSK5
PGM5
PHF2
PRKACG
PTCH1
RORB
TLE1
TMOD1
CORO2A
ZFAND5
PIP5K1B
CDC14B
FBP2
FAM189A2
TJP2
GDA
GNA14
TRIM14
SEMA4D
ANP32B
SPTLC1
GADD45G
SPIN1
SLC35D2
ZNF510
HABP4
SMC5
FAM120A
VPS13A
AGTPBP1
BICD2
TDRD7
CDK20
TMEM2
ZNF658
SPATA31A7
OSTF1
PSAT1
UBQLN1
ABHD17B
GOLM1
C9orf156
NANS
NUTM2F
DIRAS2
ASPN
NMRK1
NOL8
C9orf40
RFK
TBC1D2
HEMGN
KIF27
BARX1
NAA35
SLC28A3
IPPK
WNK2
SECISBP2
ZCCHC6
CNTNAP3
RMI1
TRPM3
GKAP1
ISCA1
ZNF484
CEP78
ANKRD20A1
C9orf64
C9orf89
HIATL2
HIATL1
C9orf3
FGD3
FAM122A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
PTPDC1
ANKRD19P
TRPM6
NXNL2
RASEF
FAM120AOS
TSTD2
ZNF782
PRUNE2
TMEM252
ZNF367
SUSD3
CBWD5
MAMDC2
FRMD3
C9orf47
SPATA31E1
FOXD4L3
FOXD4L4
PTAR1
ERCC6L2
SPATA31A6
SPATA31D1
C9orf153
CTSL3P
FAM74A4
C9orf170
MIRLET7A1
MIRLET7D
MIRLET7F1
ANKRD20A3
ANKRD20A2
NUTM2G
FOXB2
C9orf129
FAM27A
SPATA31A2
SPATA31A4
CBWD6
SPATA31A1
FOXD4L6
FOXD4L5
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR3074
MIR4291
MIR4290
MIR4289
CCDC180
MIR4477A
MIR4670

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.13.

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

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13|ENSG00000239094.1
snoU13|ENSG00000238545.1
MIR4742
snoU13|ENSG00000238856.1
MIR320B2
SNORA72|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13|ENSG00000238576.1
snoU13|ENSG00000238798.1
U3|ENSG00000221673.1
RNA5SP76
SLC30A10
U3|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
CAPN2
CHML
LYST
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
LBR
LGALS8
MARK1
MTR
NID1
NVL
PSEN2
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TSNAX
ZNF124
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
AKT3
BPNT1
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
AHCTF1
OR2M4
OR2L2
OR2T1
TAF5L
DISC1
CNIH4
PYCR2
RRP15
DESI2
SCCPDH
TRIM17
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
ZNF692
IARS2
ENAH
NUP133
ERO1LB
FMN2
ADCK3
ZNF695
GJC2
SIPA1L2
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
SPRTN
OBSCN
EFCAB2
MLK4
ZNF496
C1orf198
DISP1
WNT3A
HIST3H2A
NLRP3
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
BROX
SLC35F3
B3GALNT2
GCSAML
CNIH3
EXOC8
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
TRIM67
MAP1LC3C
OR13G1
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q22.3.

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

Genes
RN7SL810P
EDNRB

Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238969.1
MIR548F5
MIR3915
RNA5SP501
DMD
FTHL17
FAM47A

Arm-level results

Table 3. Get Full Table Arm-level significance table - 19 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1300 | 0.07 | -0.612 | 0.999 | 0.64 | 24.5 | 0
1q | 1195 | 0.13 | 1.72 | 0.435 | 0.20 | 4.9 | 1.78e-06
2p | 624 | 0.04 | -1.7 | 0.999 | 0.06 | -0.563 | 1
2q | 967 | 0.01 | -3.05 | 0.999 | 0.08 | -0.0344 | 1
3p | 644 | 0.01 | -2.5 | 0.999 | 0.39 | 14.7 | 0
3q | 733 | 0.00 | -2.5 | 0.999 | 0.54 | 22.1 | 0
4p | 289 | 0.03 | -2.1 | 0.999 | 0.07 | -0.0317 | 1
4q | 670 | 0.02 | -2.64 | 0.999 | 0.06 | -0.661 | 1
5p | 183 | 0.07 | 0.081 | 0.999 | 0.03 | -1.72 | 1
5q | 905 | 0.05 | -1.63 | 0.999 | 0.05 | -1.63 | 1
6p | 710 | 0.08 | 0.222 | 0.999 | 0.03 | -2.31 | 1
6q | 556 | 0.06 | -0.861 | 0.999 | 0.12 | 2.29 | 0.0351
7p | 389 | 0.17 | 4.7 | 5.38e-05 | 0.01 | -2.9 | 1
7q | 783 | 0.14 | 2.62 | 0.0905 | 0.05 | -1.29 | 1
8p | 338 | 0.07 | -0.032 | 0.999 | 0.13 | 2.9 | 0.00636
8q | 551 | 0.09 | 0.553 | 0.999 | 0.08 | 0.266 | 0.953
9p | 301 | 0.03 | -2.11 | 0.999 | 0.07 | -0.0419 | 1
9q | 700 | 0.02 | -2.64 | 0.999 | 0.07 | -0.387 | 1
10p | 253 | 0.07 | 0.244 | 0.999 | 0.01 | -3.03 | 1
10q | 738 | 0.06 | -0.753 | 0.999 | 0.01 | -3.28 | 1
11p | 509 | 0.04 | -1.45 | 0.999 | 0.35 | 13.2 | 0
11q | 975 | 0.02 | -2.64 | 0.999 | 0.25 | 7.73 | 2.14e-14
12p | 339 | 0.07 | -0.117 | 0.999 | 0.01 | -2.77 | 1
12q | 904 | 0.09 | 0.257 | 0.999 | 0.00 | -3.61 | 1
13q | 560 | 0.06 | -0.778 | 0.999 | 0.05 | -1.06 | 1
14q | 938 | 0.03 | -2.32 | 0.999 | 0.13 | 2.07 | 0.0561
15q | 810 | 0.08 | 0.14 | 0.999 | 0.03 | -2.37 | 1
16p | 559 | 0.04 | -1.68 | 0.999 | 0.06 | -0.818 | 1
16q | 455 | 0.04 | -1.68 | 0.999 | 0.03 | -1.97 | 1
17p | 415 | 0.00 | -2.79 | 0.999 | 0.38 | 15.2 | 0
17q | 972 | 0.03 | -2.34 | 0.999 | 0.13 | 2.04 | 0.0568
18p | 104 | 0.05 | -0.593 | 0.999 | 0.10 | 1.83 | 0.0867
18q | 275 | 0.06 | -0.29 | 0.999 | 0.04 | -1.48 | 1
19p | 681 | 0.12 | 2.24 | 0.169 | 0.01 | -3.13 | 1
19q | 935 | 0.09 | 0.379 | 0.999 | 0.04 | -1.82 | 1
20p | 234 | 0.07 | 0.283 | 0.999 | 0.01 | -2.7 | 1
20q | 448 | 0.06 | -0.491 | 0.999 | 0.02 | -2.52 | 1
21q | 258 | 0.02 | -2.02 | 0.999 | 0.23 | 7.76 | 1.97e-14
22q | 564 | 0.03 | -1.79 | 0.999 | 0.36 | 13.9 | 0
Xp | 418 | 0.05 | -0.818 | 0.999 | 0.31 | 11.3 | 0
Xq | 668 | 0.04 | -1.3 | 0.999 | 0.31 | 11.1 | 0

Methods & Data
Input
Description

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PCPG-TP/14520655/GDAC_MergeDataFiles_12186300/PCPG-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

- Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 162 Input Tumor Samples.

Tumor Sample Names
TCGA-P7-A5NY-01A-12D-A35C-01
TCGA-P8-A5KC-01A-11D-A35C-01
TCGA-P8-A5KD-01A-11D-A35C-01
TCGA-P8-A6RX-01A-11D-A35C-01
TCGA-P8-A6RY-01A-12D-A35C-01
TCGA-PR-A5PF-01A-11D-A35C-01
TCGA-PR-A5PG-01A-11D-A35C-01
TCGA-PR-A5PH-01A-11D-A35C-01
TCGA-QR-A6GO-01A-11D-A35C-01
TCGA-QR-A6GR-01A-11D-A35C-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle