SNP6 Copy number analysis (GISTIC2)
Thymoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1QF8RTZ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1QF8RTZ
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 123 tumor samples used in this analysis: 19 significant arm-level results, 0 significant focal amplifications, and 12 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.

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 1. Get Full Table Deletions Table - 12 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 4.4308e-07 | 4.4308e-07 | chr9:21626574-22448737 | 5
22q12.1 | 0.003837 | 0.0053635 | chr22:27070807-31323899 | 53
6p25.2 | 0.019861 | 0.019861 | chr6:1-10745081 | 71
3p22.2 | 0.038116 | 0.038116 | chr3:1-85435613 | 630
2q37.1 | 0.1088 | 0.1088 | chr2:219258895-237491936 | 181
6q21 | 0.1088 | 0.1088 | chr6:101844516-171115067 | 404
10q26.3 | 0.10874 | 0.1088 | chr10:87808738-135534747 | 428
19p13.11 | 0.1088 | 0.1088 | chr19:16800553-21268054 | 115
22q13.32 | 0.065503 | 0.1088 | chr22:33832149-51304566 | 263
7q36.3 | 0.20585 | 0.19639 | chr7:154685874-159138663 | 25
11q22.1 | 0.18913 | 0.19639 | chr11:100864426-101327187 | 1
9q22.33 | 0.23403 | 0.25655 | chr9:1-141213431 | 1001

Genes in Wide Peak

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

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

Genes
RN7SL151P
CDKN2A
CDKN2B
MTAP
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.1.

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

Genes
EWSR1
MN1
NF2
CHEK2
MIR3200
SEC14L6
KIAA1658
MGC20647
RFPL1S
SNORD125
RN7SL162P
SNORD42|ENSG00000201209.1
RN7SL757P
AP1B1
LIF
NEFH
OSM
RFPL1
TCN2
XBP1
NIPSNAP1
THOC5
MTMR3
GAL3ST1
SF3A1
RASL10A
GAS2L1
TTC28
PES1
SEC14L2
PITPNB
OSBP2
C22orf31
RHBDD3
UQCR10
MTFP1
ZMAT5
TBC1D10A
KREMEN1
ZNRF3
ASCC2
EMID1
HSCB
CCDC117
HORMAD2
DUSP18
CABP7
RNF215
SEC14L3
SEC14L4
SLC35E4
CCDC157
GATSL3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.2.

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

Genes
IRF4
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
CDYL
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
NRN1
TMEM14C
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
TXNDC5
RIOK1
FOXQ1
HUS1B
SNRNP48
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
PSMG4
C6orf201
PPP1R3G
MIR4645
MIR5689
MIR5683

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p22.2.

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

Genes
VHL
CTNNB1
FANCD2
FHIT
MITF
MLH1
MYD88
PPARG
RAF1
XPC
BAP1
SRGAP3
FOXP1
SETD2
PBRM1
MIR5688
LINC00971
RN7SL751P
RN7SKP61
RN7SL647P
RN7SL92P
ZNF717
LINC00960
FAM86DP
RN7SL294P
snoU13|ENSG00000238416.1
GXYLT2
RNA5SP136
snoU13|ENSG00000238568.1
RYBP
LINC00870
LINC00877
RN7SL271P
GPR27
RN7SL418P
MIR3136
RNA5SP135
RN7SL482P
U3|ENSG00000200222.1
SNTN
RNA5SP134
LINC00698
RN7SL863P
PTPRG
U3|ENSG00000212211.1
NPCDR1
RPP14
RNU6ATAC26P
PDE12
snoU13|ENSG00000238905.1
HESX1
RNA5SP133
RN7SKP45
MIR3938
ESRG
CHDH
SNORD63|ENSG00000251987.1
SNORA26|ENSG00000212608.1
SNORD38|ENSG00000207109.1
RN7SL821P
snoU13|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19|ENSG00000222345.1
SNORD19B|ENSG00000238862.1
SNORD19|ENSG00000212493.1
SNORD19B|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13|ENSG00000238350.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000251938.1
PRSS44
PRSS45
SNORD77|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
U8|ENSG00000212145.2
RN7SKP58
SCARNA21|ENSG00000252409.1
ZNF621
SNORA64|ENSG00000202517.1
RN7SL411P
SNORA62|ENSG00000202363.1
SNORA6
MIR26A1
ITGA9
RNA5SP129
snoU13|ENSG00000238929.1
RNU6ATAC4P
TRANK1
HSPD1P6
RN7SKP227
RNA5SP128
RN7SL296P
TMPPE
CCR4
TRIM71
snoU13|ENSG00000238646.1
SNORA25|ENSG00000201701.1
OSBPL10
STT3B
RNA5SP127
U3|ENSG00000199927.1
LINC00693
CMC1
RN7SL859P
SNORD5|ENSG00000272166.1
RNA5SP126
RNA5SP125
RN7SL216P
LINC00691
UBE2E2
HMGB1P5
RNY4P22
MIR3135A
U7|ENSG00000271841.1
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13|ENSG00000238345.1
snoU13|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13|ENSG00000239126.1
EGOT
SNORA43|ENSG00000253049.1
RN7SKP144
RN7SL120P
ACAA1
ACVR2B
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR5
CCR8
ACKR2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FBLN2
FLNB
GBE1
GNAI2
GOLGA4
XCR1
GPX1
GRM2
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RAB5A
RARB
ROBO1
ROBO2
RPL15
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
TMF1
CLEC3B
TNNC1
TOP2B
UBA7
UBE2E1
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
BHLHE40
CADPS
HYAL2
SUCLG2
KAT2B
BSN
ACKR5
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
CXCR6
CHL1
ARPP21
CCR9
USP19
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
EXOSC7
PDZRN3
CAND2
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
THUMPD3
MYRIP
PTPN23
DNAH1
LRIG1
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LMCD1
ARHGEF3
VILL
SSUH2
TRNT1
DYNC1LI1
C3orf18
CRBN
SS18L2
CCDC174
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
ELP6
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ARL8B
SETD5
TMEM40
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
BRK1
ZKSCAN7
LMOD3
RAD18
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
LRRN1
SELK
PROK2
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
THOC7
WDR82
TSEN2
C3orf20
ATRIP
NICN1
MON1A
JAGN1
KBTBD8
IL17RC
ABHD14B
GTDC2
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ACTR8
CMTM7
SLC25A26
ZNF501
FANCD2OS
LRRC3B
GALNT15
GPR62
KCNH8
FAM3D
LYZL4
KLHL40
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SYNPR
LSMEM2
ASB14
FAM19A4
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
PPP4R2
ZCWPW2
NEK10
CMTM8
CCDC13
FGD5
CNTN4
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
DNAH12
DENND6A
ZNF620
ALS2CL
TMIE
EOGT
FBXW12
ZNF619
LINC00692
CCDC66
TCAIM
SUMF1
RPUSD3
PRRT3
EIF4E3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
TPRXL
ZNF445
SPATA12
TOPAZ1
TMEM110
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
FAM19A1
MIR425
GLB1
SPINK8
ARIH2OS
C3orf84
MIR563
FAM198A
CCR2
PRSS46
FRG2C
MIR1284
MIR1324
MIR378B
MIR4271
MIR4273
MIR3923
MIR3714
KRBOX1
MIR4787
MIR4791
MIR4790
MIR4443
MIR4792
MIR4442

Genes in Wide Peak

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

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

Genes
ACSL3
PAX3
FEV
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
ALPI
ALPP
ALPPL2
BCS1L
CHRNG
COL4A3
COL4A4
CRYBA2
CYP27A1
DES
EPHA4
GBX2
AGFG1
DNAJB2
HTR2B
SP110
IHH
INHA
INPP5D
IRS1
KCNJ13
NEU2
PDE6D
SERPINE2
PSMD1
PTMA
PTPRN
SAG
CCL20
SLC4A3
SP100
SPP2
TUBA4A
WNT6
ZNF142
SCG2
CUL3
DGKD
STK16
CDK5R2
RQCD1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
FARSB
ABCB6
ARL4C
SPEG
NMUR1
SP140
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
GIGYF2
CNPPD1
STK36
GMPPA
CAB39
PRKAG3
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
PID1
ATG16L1
ANKZF1
USP40
HJURP
ASIC4
DOCK10
C2orf83
MFF
ACKR3
WDFY1
NYAP2
USP37
CTDSP1
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ITM2C
RHBDD1
PLCD4
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
DIS3L2
AP1S3
SPATA3
TMEM198
ZFAND2B
FBXO36
CCDC140
SLC23A3
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
CCDC108
C2orf72
MROH2A
RESP18
C2orf82
ASB18
MIR375
PRSS56
MIR1471
MIR4268
MIR3132
MIR5001
MIR5702
MIR5703

Genes in Wide Peak

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

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

Genes
FGFR1OP
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
GOPC
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13|ENSG00000239136.1
AIRN
SNORA29
SNORA20|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13|ENSG00000252609.1
SNORD28|ENSG00000212295.1
TFB1M
U8|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
ACAT2
AIM1
AMD1
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FUCA2
FYN
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PREP
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
TBP
TCF21
TCP1
TCTE3
DYNLT1
THBS2
NR2E1
TPD52L1
UTRN
EZR
VIP
EPM2A
DDO
RNASET2
SNX3
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
MED23
QKI
AKAP7
ATG5
WTAP
AKAP12
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
BVES
SEC63
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
OSTM1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
MPC1
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
SOBP
PHF10
QRSL1
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
PDSS2
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
HACE1
TMEM181
ZBTB2
BEND3
ABRACL
PBOV1
TRMT11
PERP
SMOC2
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
ARMC2
L3MBTL3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
ARHGAP18
SYTL3
GTF3C6
MTFR2
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAGAP
TAAR9
TAAR1
NCOA7
HINT3
PACRG
RAET1E
ZC2HC1B
RAET1L
SAMD3
PNLDC1
RNF217
NKAIN2
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
WDR27
MCM9
SHPRH
CEP57L1
PPIL6
DCBLD1
PRR18
TAAR6
SLC35D3
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
SUMO4
CENPW
SOGA3
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
TCP10L2
LINC00242
GTF2H5
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR587
MIR588
METTL24
TMEM242
TRAPPC3L
MIR1202
MIR1273C
MIR3144
MIR3918
MIR3939
MIR3668
SMLR1
MIR4466
MIR4465
MIR548AJ1
MIR548H5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
PTEN
BMPR1A
FGFR2
TLX1
NFKB2
SUFU
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19|ENSG00000222588.1
SNORA19|ENSG00000207468.1
U3|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13|ENSG00000239125.1
SMNDC1
RN7SL450P
U4|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112|ENSG00000253068.1
FGF8
snoU13|ENSG00000239091.1
SNORD112|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12|ENSG00000212464.1
ERLIN1
snoU13|ENSG00000238472.1
COX15
ENTPD7
snoU13|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13|ENSG00000238991.1
ANKRD22
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
AGAP11
U3|ENSG00000252189.1
MIR346
RNA5SP322
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
FAS
ARL3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
CPN1
CTBP2
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
GLUD1
GOT1
PRLHR
GRK5
HABP2
HELLS
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT3
INPP5A
KIF11
ABLIM1
LIPA
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
DCLRE1A
FRAT1
ACTR1A
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
MGEA5
PRDX3
ADIRF
VAX1
ATE1
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
PDCD4
VENTX
R3HCC1L
POLL
BLNK
KCNIP2
CUZD1
CALY
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
EXOC6
FAM35A
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
WBP1L
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
WDR11
FAM178A
DHX32
TDRD1
BCCIP
C10orf2
TM9SF3
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
MCMBP
C10orf95
PLEKHS1
PDZD7
C10orf88
UBTD1
WDR96
LRRC27
TNKS2
TRIM8
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
GPR123
LZTS2
LCOR
MRPL43
AFAP1L2
PYROXD2
USMG5
ATAD1
ARHGAP19
KNDC1
MTG1
BBIP1
FANK1
OPALIN
SYCE1
OPN4
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
C10orf32
GSTO2
SFR1
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
TRUB1
VTI1A
HECTD2
FGFBP3
C10orf82
CACUL1
SLC35G1
CCDC147
PWWP2B
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
FUOM
JAKMIP3
STK32C
RBM20
FFAR4
KCNK18
LIPM
CYP26C1
NANOS1
HMX3
CCDC172
SLC16A12
CC2D2B
ARMS2
TEX36
C10orf120
FOXI2
GOLGA7B
C10orf85
C10orf62
IFIT1B
FRG2B
SPRN
MIR146B
MIR202
FAM196A
FAM25A
LIPK
LIPN
MIR607
NUTM2A
NUTM2D
TLX1NB
C10orf131
KLLN
MIR1307
MIR2110
MIR378C
MIR3157
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.11.

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

Genes
JAK3
ELL
ZNF66
ZNF737
ZNF826P
ZNF90
ZNF253
ZNF506
LINC00663
ZNF101
NDUFA13
MIR640
MEF2BNB
MEF2B
RN7SL70P
RN7SL155P
MIR3189
RN7SL513P
PIK3R2
RNA5SP468
SNORA68|ENSG00000207166.1
RN7SL823P
RN7SL835P
F2RL3
BST2
COMP
NCAN
NR2F6
GDF1
IL12RB1
INSL3
JUND
MYO9B
PDE4C
PIK3R2
RAB3A
UPF1
RPL18A
SLC5A5
UBA52
ZNF14
ZNF85
RFXANK
LPAR2
CRLF1
HOMER3
GDF15
SUGP2
B3GNT3
IFI30
CERS1
COPE
UNC13A
MAST3
FCHO1
SIN3B
CRTC1
MAU2
FKBP8
TMEM59L
PGLS
LSM4
ARRDC2
CPAMD8
BABAM1
GMIP
ISYNA1
TM6SF2
DDX49
GATAD2A
PGPEP1
TMEM161A
C19orf60
MAP1S
KLHL26
USE1
ATP13A1
ANO8
SUGP1
MRPL34
DDA1
KXD1
ABHD8
OCEL1
COLGALT1
ZNF430
PBX4
KIAA1683
ZNF93
PLVAP
USHBP1
TSSK6
GTPBP3
MPV17L2
ZNF486
ZNF682
HAUS8
MVB12A
ARMC6
CCDC124
NXNL1
LRRC25
NR2C2AP
ANKLE1
CILP2
SSBP4
ZNF626
FAM129C
NWD1
SLC25A42
YJEFN3
SLC27A1
HAPLN4
TMEM221
MIR3188

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

Table S9. 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
MIR3909
SNORA76|ENSG00000253007.2
MIR4764
ACR
ACO2
ADSL
ATF4
BIK
TSPO
MPPED1
CHKB
CPT1B
CSF2RB
CSNK1E
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
MCHR1
H1F0
HMOX1
IL2RB
KCNJ4
LGALS1
LGALS2
MB
MCM5
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
HMGXB4
TOM1
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
RASD2
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
ISX
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 7q36.3.

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

Genes
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
EN2
MNX1
INSIG1
PTPRN2
VIPR2
UBE3C
DNAJB6
PAXIP1
NCAPG2
WDR60
ESYT2
LMBR1
NOM1
C7orf13
RNF32
RBM33
CNPY1
BLACE
MIR5707

Genes in Wide Peak

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

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

Genes
PGR

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.33.

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

Genes
GNAQ
ABL1
FANCC
FANCG
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13|ENSG00000238530.1
MIR455
COL27A1
FKBP15
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
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
SNX18P3
IGFBPL1
snoU13|ENSG00000238313.1
U8|ENSG00000200026.1
SHB
RN7SKP171
RN7SL463P
MIR4476
MIR4540
LINC00961
RGP1
RN7SL22P
RMRP
MIR4667
RN7SL338P
FLJ00273
FAM205CP
FAM205B
GALT
RN7SKP24
KIAA1161
RNA5SP282
RN7SKP114
SNORD121A
SNORD121B
RNU4ATAC11P
PTENP1
RNU4ATAC15P
TMEM215
GVQW1
RNA5SP281
snoU13|ENSG00000239155.1
LINC00032
RNA5SP280
RN7SL100P
SNORA31|ENSG00000252580.1
RN7SKP120
RMRPP5
DMRTA1
RN7SL151P
SNORD39|ENSG00000264379.1
MIR31HG
IFNA6
KLHL9
PTPLAD2
SNORA30|ENSG00000202189.1
MIR491
MIR4474
MIR4473
ACER2
snoU13|ENSG00000238348.1
RN7SL158P
SCARNA8
RN7SKP258
MIR3152
RN7SL720P
RN7SL98P
RN7SL157P
LINC00583
LURAP1L
RN7SL849P
RN7SL5P
SNORD27|ENSG00000251699.1
RN7SL123P
snoU13|ENSG00000252110.1
RN7SL25P
C9orf38
MLANA
snoU13|ENSG00000238654.1
INSL4
AK3
CDC37L1
CARM1P1
RN7SL592P
RNA5SP279
RN7SL412P
FAM138C
ABCA1
ABCA2
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNB1
IFNW1
IL11RA
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RORB
RPL7A
RPL12
RPS6
CCL19
CCL21
SH3GL2
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
PRPF4
KLF4
GTF3C5
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
TRIM14
MELK
RUSC2
PPP1R26
SEC16A
ZBTB5
KIAA0020
TNFSF15
PTBP3
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
CACFD1
PSIP1
INSL6
SLC2A6
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
KIAA1045
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
DDX58
RABGAP1
TMEM2
TMEM245
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
NELFB
NIPSNAP3A
NSMF
GPSM1
GAPVD1
PHF19
ZNF658
SPATA31A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
EXOSC3
ABHD17B
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
EQTN
TBC1D13
NUTM2F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
TOR4A
CNTLN
TEX10
FOCAD
UBE2R2
EXD3
FAM206A
NMRK1
NOL8
SPATA6L
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
DENND4C
RABL6
CDK5RAP2
UBAP2
PLGRKT
CBWD1
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KCNT1
KIAA1432
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
ZNF462
DMRT3
PRDM12
NAA35
SLC28A3
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOB3B
CAAP1
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
FAM214B
GKAP1
PDCD1LG2
AKNA
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
NTNG2
HIATL1
HINT2
C9orf24
PIGO
PPAPDC3
ZDHHC12
FAM73B
ARHGEF39
C9orf3
FIBCD1
KIAA1984
TMEM141
C9orf37
FGD3
MVB12B
TPD52L3
WDR34
SAPCD2
C9orf69
LRSAM1
IL33
C9orf123
UAP1L1
SLC25A51
MRRF
ARRDC1
DPH7
ADAMTSL1
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19P
ARID3C
RPP25L
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf62
C9orf66
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC39B
TRMT10B
TTC16
FAM120AOS
FAM154A
FREM1
KIAA2026
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
PRUNE2
C9orf96
KCNV2
OLFML2A
TMEM252
QSOX2
GLIS3
ZNF367
C9orf91
C9orf72
CCDC171
NAIF1
FAM219A
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
FAM205A
CRB2
SCAI
C9orf117
C9orf47
SPATA31E1
LCN12
C9orf142
TPRN
TUSC1
FAM78A
OR13C9
OR13D1
FOXD4L3
IFNE
ZDHHC21
GPR144
QRFP
OR1J1
OR1B1
KIF24
MURC
FOXD4L4
GLT6D1
ENHO
PTAR1
ERCC6L2
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
SPATA31A6
SPATA31D1
C9orf153
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
FAM221B
OR13J1
CTSL3P
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
TOMM5
FAM74A4
C9orf170
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR31
ANKRD20A3
ANKRD20A2
NUTM2G
ANKRD18B
C9orf173
NRARP
FOXB2
C9orf129
FAM27A
DNAJC25
SPATA31A2
SPATA31A4
CBWD6
HRCT1
SPATA31A1
FOXD4L6
FOXD4L5
MSMP
MIR600HG
MIR602
FAM27D1
RNF208
SPATA31A3
SPATA31A5
CBWD7
CARD9
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
MIR876
MIR873
C9orf92
IZUMO3
FAM27E3
FAM27C
FAM27B
MIR1299
MIR3074
MIR3154
MIR4291
MIR4290
MIR4289
CCDC180
MIR3689A
MIR3911
MIR3927
MIR3689B
MIR3689D1
MIR4477A
MIR3689F
MIR3960
MIR4665
MIR4475
MIR4674
MIR4478
MIR3689C
MIR3689D2
MIR4670
MIR3689E
MIR548AW

Arm-level results

Table 2. 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 | 0.04 | -0.317 | 0.994 | 0.06 | 0.492 | 0.778
1q | 1195 | 0.17 | 5.93 | 6.05e-08 | 0.03 | -0.949 | 0.981
2p | 624 | 0.01 | -2.08 | 0.994 | 0.01 | -2.08 | 0.981
2q | 967 | 0.00 | -2.5 | 0.994 | 0.02 | -1.69 | 0.981
3p | 644 | 0.01 | -1.94 | 0.994 | 0.10 | 2.54 | 0.0314
3q | 733 | 0.04 | -0.288 | 0.994 | 0.06 | 0.527 | 0.778
4p | 289 | 0.02 | -1.59 | 0.994 | 0.04 | -0.362 | 0.981
4q | 670 | 0.02 | -1.62 | 0.994 | 0.03 | -0.804 | 0.981
5p | 183 | 0.09 | 2.16 | 0.0635 | 0.01 | -1.94 | 0.981
5q | 905 | 0.07 | 1.26 | 0.317 | 0.01 | -1.99 | 0.981
6p | 710 | 0.00 | -2.3 | 0.994 | 0.16 | 5.85 | 9.63e-08
6q | 556 | 0.00 | -2.31 | 0.994 | 0.15 | 5.45 | 4.95e-07
7p | 389 | 0.12 | 3.9 | 0.000636 | 0.03 | -1 | 0.981
7q | 783 | 0.13 | 4.25 | 0.000215 | 0.02 | -1.45 | 0.981
8p | 338 | 0.10 | 2.57 | 0.0349 | 0.01 | -1.93 | 0.981
8q | 551 | 0.09 | 2.16 | 0.0635 | 0.02 | -1.52 | 0.981
9p | 301 | 0.09 | 2.24 | 0.0635 | 0.04 | -0.625 | 0.981
9q | 700 | 0.09 | 2.15 | 0.0635 | 0.02 | -1.52 | 0.981
10p | 253 | 0.02 | -1.62 | 0.994 | 0.02 | -1.21 | 0.981
10q | 738 | 0.02 | -1.65 | 0.994 | 0.02 | -1.65 | 0.981
11p | 509 | 0.01 | -1.98 | 0.994 | 0.07 | 1.29 | 0.437
11q | 975 | 0.01 | -2.02 | 0.994 | 0.06 | 0.421 | 0.793
12p | 339 | 0.03 | -0.682 | 0.994 | 0.07 | 0.955 | 0.679
12q | 904 | 0.03 | -0.727 | 0.994 | 0.06 | 0.493 | 0.778
13q | 560 | 0.01 | -1.92 | 0.994 | 0.11 | 3.39 | 0.00347
14q | 938 | 0.11 | 2.97 | 0.0149 | 0.02 | -1.5 | 0.981
15q | 810 | 0.10 | 2.56 | 0.0349 | 0.02 | -1.51 | 0.981
16p | 559 | 0.02 | -1.6 | 0.994 | 0.04 | -0.376 | 0.981
16q | 455 | 0.02 | -1.48 | 0.994 | 0.11 | 3.01 | 0.00862
17p | 415 | 0.02 | -1.47 | 0.994 | 0.12 | 3.44 | 0.00347
17q | 972 | 0.05 | 0.129 | 0.994 | 0.06 | 0.535 | 0.778
18p | 104 | 0.03 | -1.12 | 0.994 | 0.06 | 0.52 | 0.778
18q | 275 | 0.03 | -1.13 | 0.994 | 0.06 | 0.509 | 0.778
19p | 681 | 0.03 | -1.21 | 0.994 | 0.03 | -1.21 | 0.981
19q | 935 | 0.03 | -1.22 | 0.994 | 0.03 | -1.22 | 0.981
20p | 234 | 0.08 | 1.73 | 0.143 | 0.01 | -1.96 | 0.981
20q | 448 | 0.08 | 1.72 | 0.143 | 0.01 | -1.96 | 0.981
21q | 258 | 0.03 | -1.1 | 0.994 | 0.07 | 1.36 | 0.433
22q | 564 | 0.05 | -0.157 | 0.994 | 0.11 | 3.1 | 0.00764
Xq | 668 | 0.03 | -1.16 | 0.994 | 0.05 | 0.0612 | 0.981

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/THYM-TP/11449627/GDAC_MergeDataFiles_11452101/THYM-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 3. Get Full Table First 10 out of 123 Input Tumor Samples.

Tumor Sample Names
TCGA-3G-AB0O-01A-22D-A422-01
TCGA-3G-AB0Q-01A-11D-A422-01
TCGA-3G-AB0T-01A-11D-A422-01
TCGA-3G-AB14-01A-11D-A422-01
TCGA-3G-AB19-01A-21D-A422-01
TCGA-3Q-A9WF-01A-11D-A422-01
TCGA-3S-A8YW-01A-11D-A422-01
TCGA-3S-AAYX-01A-11D-A422-01
TCGA-3T-AA9L-01A-11D-A422-01
TCGA-4V-A9QI-01A-11D-A422-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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