SNP6 Copy number analysis (GISTIC2)
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1BC3WV2
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1BC3WV2
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 2.0.19 (Firehose task version: 125).

Summary

There were 18 tumor samples used in this analysis: 8 significant arm-level results, 1 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.

Table 1. Get Full Table Amplifications Table - 1 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
--- | --- | --- | --- | ---
2p16.1 | 1.6012e-07 | 1.6012e-07 | chr2:60700794-61776974 | 13

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p16.1.

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

Genes
REL
BCL11A
PEX13
XPO1
USP34
PAPOLG
KIAA1841
AHSA2
PUS10
LOC339803
C2orf74
FLJ16341
SNORA70B

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 - 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 | 0.049975 | 0.049975 | chr9:21555227-22448737 | 5
1q43 | 0.14805 | 0.14805 | chr1:15569713-249250621 | 2170
1p22.1 | 0.14805 | 0.14805 | chr1:86114902-119946150 | 261
2q22.3 | 0.14805 | 0.14805 | chr2:115916647-168118431 | 195
6q23.3 | 0.14805 | 0.14805 | chr6:137814087-138410514 | 1
10q23.31 | 0.14805 | 0.14805 | chr10:83636583-115949820 | 300
13q33.3 | 0.14805 | 0.14805 | chr13:26781529-115169878 | 363
15q15.1 | 0.14805 | 0.14805 | chr15:40395404-45299932 | 107
6q14.1 | 0.15709 | 0.22397 | chr6:74403249-119259018 | 194
8q12.1 | 0.24596 | 0.24596 | chr8:49829161-71591743 | 98
16p13.13 | 0.24596 | 0.24596 | chr16:8886383-12754094 | 31
17q24.1 | 0.24621 | 0.24596 | chr17:1-81195210 | 1386

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
MTAP
C9orf53
CDKN2B-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

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

Genes
ABL2
ARNT
BCL9
CDKN2C
ELK4
EPS15
FCGR2B
FH
JAK1
JUN
LCK
MDM4
MPL
MUC1
MUTYH
MYCL1
NOTCH2
NRAS
NTRK1
PAX7
PBX1
PRCC
SDHB
SDHC
SFPQ
TAL1
TPM3
TPR
ARID1A
BCL10
PDE4DIP
THRAP3
TRIM33
RBM15
SLC45A3
MDS2
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
ABCA4
ACADM
ACTA1
ACTN2
ADAR
ADORA1
ADORA3
PARP1
ADSS
AGL
AGT
AK2
AK4
ALDH9A1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
ARF1
RHOC
ASTN1
SERPINC1
ATF3
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
ATP5F1
ATP6V0B
AVPR1B
BAI2
BGLAP
BMP8B
BRDT
C1QA
C1QB
C1QC
C4BPA
C4BPB
C8A
C8B
CACNA1E
CACNA1S
CAPN2
CAPZA1
CAPZB
CASP9
CASQ1
CASQ2
RUNX3
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
CD34
CD48
CD53
CD58
CDA
CDC20
CDC42
CD52
CENPF
RCC1
CHI3L1
CHI3L2
CHIT1
CHML
LYST
CHRM3
CHRNB2
CKS1B
CLCA1
CLCNKA
CLCNKB
CLK2
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
COPA
CPT2
CR1
CR1L
CR2
CRABP2
CRP
CRYZ
CSF1
CSF3R
CSRP1
CTBS
CTH
CTPS
CTSE
CTSK
CTSS
CYP2J2
CYP4A11
CYP4B1
DAB1
CD55
DBT
GADD45A
DDOST
DHX9
DHCR24
DIO1
DPH2
DPT
DPYD
DR1
E2F2
ECE1
ECM1
S1PR1
EDN2
PHC2
EIF2D
EFNA1
EFNA3
EFNA4
CELSR2
EPHA2
ELAVL4
ELF3
ENSA
EPB41
EPHA8
EPHB2
EPHX1
EPRS
ESRRG
ETV3
EXTL1
EXTL2
EYA3
F3
F5
F13B
FAAH
FABP3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FGR
FHL3
FOXE3
FOXD2
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
FUCA1
DARC
IFI6
GALE
GALNT2
GBA
GBAP1
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GLUL
GNAI3
GNAT2
GNG4
GNG5
SFN
GPR3
GPR25
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
GUK1
H3F3A
HCRTR1
HDAC1
HDGF
CFH
CFHR1
CFHR2
MR1
HLX
HMGN2
HMGCL
HMGCS2
HNRNPU
HPCA
HSD3B1
HSD3B2
HSD11B1
HSPA6
HSPA7
IGSF3
HSPG2
HTR1D
HTR6
ID3
IFI16
CYR61
IL6R
IL10
IL12RB2
ILF2
INPP5B
INSRR
IPP
IRF6
ITPKB
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNH1
KCNJ9
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
STMN1
LBR
LEPR
LGALS8
LMNA
LMX1A
LOR
LY9
TACSTD2
MAGOH
MARK1
MATN1
MCL1
CD46
SMCP
MEF2D
MFAP2
MGST3
MNDA
MOV10
MPZ
MSH4
MTF1
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NASP
NBL1
NCF2
NDUFS2
NDUFS5
NEK2
NFIA
NFYC
NGF
NHLH1
NHLH2
NID1
NIT1
NPR1
NRD1
YBX1
ROR1
DDR2
NVL
OPRD1
ORC1
OVGP1
PAFAH2
PRDX1
CDK18
PDC
PDE4B
PDZK1
PFDN2
PFKFB2
PGM1
PIGC
PIGR
PIK3C2B
PI4KB
PIN1P1
PKLR
PKP1
PLA2G2A
PLA2G4A
PLA2G5
PLXNA2
PRRX1
POU2F1
POU3F1
PPOX
PPP1R8
PPP2R5A
PPT1
PRELP
PRKAA2
PRKAB2
PRKACB
PKN2
PROX1
PSEN2
PSMA5
PSMB2
PSMB4
PSMD4
PTAFR
PTGER3
PTGFR
PTGFRN
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PTPRF
PEX19
ABCD3
RAB3B
RAB4A
RAB13
RABGGTB
RABIF
RAP1A
RAP1GAP
RBBP4
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RHCE
RHD
RIT1
RLF
RNASEL
RNF2
RNPEP
SNORD21
RORC
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RPS27
RSC1A1
RXRG
RYR2
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
SCP2
XCL1
SELE
SELL
SELP
SRSF4
SHC1
ST3GAL3
STIL
SLAMF1
SLC1A7
SLC2A1
SLC6A9
SLC9A1
SLC16A1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRP9
TROVE2
SSR2
AURKAPS1
STXBP3
XCL2
SYCP1
TAF12
TAF13
TARBP1
CNTN2
TBCE
TBX15
TCEA3
TCEB3
VPS72
TGFB2
LEFTY2
TGFBR3
THBS3
TCHH
TIE1
TLR5
GPR137B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TRAF5
CCT3
TSHB
TSNAX
TTC4
TUFT1
TNFSF4
UCK2
UQCRH
UROD
USF1
USP1
USH2A
VCAM1
WNT2B
WNT9A
ZSCAN20
ZNF124
ZBTB17
SLC30A1
SLC30A2
LUZP1
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
DAP3
NPHS2
BTG2
PTP4A2
HIST3H3
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
SNHG3
NR0B2
RAD54L
GNPAT
DYRK3
TTF2
CDC42BPA
RGS5
PPFIA4
PIK3R3
ITGA10
LMO4
FCN3
BLZF1
CDC14A
DEGS1
KMO
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
VAMP4
PEA15
B4GALT3
B4GALT2
B3GALT2
ADAM15
PABPC4
FPGT
PEX11B
CREG1
CD84
FUBP1
EIF2B3
RAB7L1
SELENBP1
TNFSF18
TAF1A
MPZL1
SH2D2A
ARTN
MAP3K6
ANGPTL1
DIRAS3
TBX19
FCGR2C
SLC16A4
PRPF3
KCNQ4
EXO1
ARHGEF2
DEDD
ZMYM4
ZMYM6
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
SRSF11
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
AIM2
GGPS1
RASAL2
C1orf38
ADAMTS4
TMEM59
SEC22B
CHD1L
SOX13
PRDX6
CLCA3P
CLCA2
IKBKE
HS2ST1
IPO13
SDC3
SLC25A44
KIAA0040
KDM4A
CROCC
PUM1
NOS1AP
TMEM63A
RIMS3
TOMM20
KIAA0494
URB2
ARHGEF11
DNAJC6
CEP350
CEP170
LRIG2
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
ZBTB40
LPGAT1
KIF14
RBM8A
NR1I3
AKT3
INSL5
PIGK
SCAMP3
PTPRU
ARPC5
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
PRG4
GPA33
STX6
HNRNPR
SRRM1
CNKSR1
SF3B4
ZMPSTE24
BCAS2
AKR1A1
WARS2
BPNT1
CEPT1
PIAS3
TESK2
TIMM17A
LRRN2
PPIE
VAV3
HAX1
PPIH
ZNF238
C1orf61
CAP1
LRRC41
SEMA6C
HBXIP
SLC19A2
IFI44
POLR3C
IVNS1ABP
TXNIP
LEFTY1
SPHAR
PMVK
KHDRBS1
GMEB1
FAM189B
AP4B1
NUDC
PHTF1
CAPN9
NES
KDM5B
AHCYL1
SRSF10
SDCCAG8
CFHR4
CFHR3
WDR3
OCLM
JTB
MTMR11
MAN1A2
SF3A3
MLLT11
IFI44L
EBNA1BP2
SLC27A3
KIF2C
IL24
TDRKH
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
CELF3
MST1P2
DDX20
DUSP10
MST1P9
PADI2
PMF1
DUSP12
VPS45
LYPLA2
CTRC
COG2
CLCA4
MTF2
DNAJC8
NTNG1
PLEKHA6
FOXJ3
KIAA0907
WDR47
KIFAP3
ATF6
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
RBM34
USP33
WDTC1
KIF21B
NMNAT2
KIAA0090
NFASC
POGZ
GLT25D2
MAST2
NCDN
CLCC1
SLC35D1
RGL1
PLEKHM2
SYT11
PRRC2C
FBXO28
RPRD2
OTUD3
LPHN2
CAMSAP2
KIAA1107
ZCCHC11
SZT2
DNAJC16
UBR4
USP24
SRGAP2
SMG5
NCSTN
ATP13A2
CRB1
ITGB3BP
GPR161
CELA3B
SLC35A3
ABCB10
MACF1
LRRC8B
ZNF281
SNAPIN
LPAR3
PADI4
DDAH1
TMEM50A
OPN3
PHLDA3
RUSC1
CA14
KPNA6
SSBP3
STX12
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
TRIM58
INTS7
OLFML2B
AHCTF1
C1orf43
CLIC4
NSL1
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
DNM3
TOR1AIP1
CHTOP
C1orf144
LDLRAP1
SERBP1
OR1C1
PTPN22
PHGDH
LCE2B
OR2M4
OR2L2
OR2L1P
OPTC
PLA2G2D
AK5
MYCBP
OR10J1
HEYL
EIF2C1
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORA66
SNORD47
SNORD45B
SNORD45A
SNORD44
SNORD55
RNU11
RNU5F-1
RNF11
USP21
FOXD3
DIEXF
TRAPPC3
TAF5L
CACYBP
HSPB7
CHIA
SLC39A1
DISC2
DISC1
AHDC1
RNF115
KLHL20
TEKT2
SMPDL3B
ANGPTL3
LAMTOR2
FLVCR1
PRO0611
UBE2T
LINC00339
CNIH4
TMOD4
GNL2
GPSM2
PYCR2
NME7
ALG6
NENF
PADI1
IL19
CERS2
SLC25A24
PLA2G2E
DNTTIP2
CRNN
G0S2
IL20
DCAF8
HP1BP3
F11R
TMED5
RRP15
GLRX2
BOLA1
PPPDE1
CELA2B
ZNF593
ZBTB7B
ZNF691
TXNDC12
TNNI3K
RRNAD1
ADIPOR1
SCCPDH
SH3GLB1
MECR
APH1A
UTP11L
TRIM17
KCTD3
MRTO4
PLEKHO1
HAO2
ACP6
TMEM69
MRPL37
IER5
HOOK1
SNX7
UCHL5
C1orf9
HPCAL4
YTHDF2
GPR89B
HSD17B7
UFC1
DTL
ZCCHC17
METTL13
DPH5
HSPB11
OAZ3
PADI3
CYB5R1
CMPK1
ARID4B
CD244
GPR88
DPM3
WNT4
YIPF1
FBXO42
MRPS21
CCDC76
TMCO1
ADAMTSL4
CRCT1
RNF186
SPATA6
EGLN1
L1TD1
KIAA1383
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
SWT1
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
PQLC2
LAX1
RHBDL2
DUSP23
ADPRHL2
TRNAU1AP
C1orf27
C1orf109
C1orf56
C1orf123
MARC2
TTC22
AIM1L
SUSD4
KIF26B
RALGPS2
GPATCH2
BSDC1
XKR8
TMEM39B
PRPF38B
HEATR1
CDCA8
LRRC8D
MSTO1
DARS2
ARHGEF10L
PRMT6
RNF220
FAM176B
GOLPH3L
TMEM57
KLHDC8A
TRIM62
ETNK2
RAVER2
KIRREL
TMEM206
YY1AP1
ECHDC2
FGGY
MCOLN3
SLC22A15
YOD1
CAMK2N1
BATF3
SLC30A10
UBE2Q1
RNPC3
ITLN1
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
ZNF692
NBPF1
IARS2
MAP7D1
IPO9
TMEM48
NECAP2
IQCC
C1orf112
HHAT
ENAH
NUP133
RCOR3
C1orf106
LRIF1
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
RCC2
FAM212B
DMAP1
GNG12
SLC50A1
TMEM234
FAM54B
SERTAD4
CCBL2
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
TMEM167B
OLFML3
SMYD2
LHX9
OTUD7B
ADCK3
C1orf63
PITHD1
RAB25
PGLYRP4
ZNF695
RHBG
MAN1C1
SCYL3
GJC2
CAMK1G
NIPAL3
SEPN1
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
AMIGO1
ODF2L
CGN
KIAA1324
IGSF9
LRRC7
SIPA1L2
KIF17
ZNF687
ZSWIM5
POGK
KIAA1522
HCN3
CACHD1
MIER1
KIAA1614
FAM5B
C1orf114
GRHL3
SLAMF7
ZP4
CADM3
PTBP2
RHOU
PRUNE
DNASE2B
DLGAP3
IL22RA1
HIVEP3
KLHL12
LGR6
GPBP1L1
HAPLN2
GAS5
PAPPA2
CELA2A
BCAN
GPATCH3
TNN
MRPS14
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
TINAGL1
LEPRE1
TFB2M
SEMA4A
TOR3A
RFWD2
GREM2
RGS18
PLA2G2F
HIAT1
NUCKS1
SMAP2
ACBD3
SMYD3
ATPAF1
MARC1
S100PBP
MEAF6
DEM1
CEP85
ARV1
ELOVL1
AIDA
DCLRE1B
MRPS15
MRPL9
PINK1
JMJD4
MARCKSL1
INTS3
ZNF643
SELRC1
PHACTR4
C1orf135
SCNM1
ERI3
C1orf50
WDR77
C1orf116
MGC4473
CCDC28B
C1orf35
EFHD2
RSG1
FCRL2
DLEU2L
NKAIN1
TTC13
EPS8L3
CDC73
MRPL24
MUL1
PGBD5
TNFAIP8L2
C1orf54
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
PPCS
LIN28A
SH3D21
TTLL7
SNIP1
C1orf115
HHIPL2
VASH2
AGMAT
WDR78
ZMYM1
ZNF669
RPAP2
ZNF672
FAM110D
KIAA0319L
DHDDS
PAQR6
DENND2D
WLS
PCNXL2
TRIM46
C1orf129
RPF1
SIKE1
ZC3H12A
TARS2
WDR26
TRIM45
EDEM3
FLAD1
TRAF3IP3
ZNF436
TAS1R2
SH3BP5L
NPL
GJA9
OR6N2
OR6K2
OR2G3
OR2G2
OR2C3
SYNC
CFHR5
TRIM11
C1orf21
ACTL8
ANKRD13C
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
TSSK3
NUAK2
VANGL1
ST6GALNAC5
ISG20L2
HYI
FCRL5
FCRL4
SH3BGRL3
DDX59
NUF2
RASSF5
SESN2
HMCN1
GPR61
MIXL1
STK40
C1orf124
TM2D1
FCAMR
REG4
OBSCN
TMEM222
C1orf49
HORMAD1
TOMM40L
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
TMEM79
NTPCR
EFCAB2
DDI2
ACBD6
PROK1
KIAA1804
EFCAB7
ZBTB37
NT5C1A
LCE3D
TRIM63
LINC00260
PSRC1
FAM167B
LINC00467
MGC12982
CROCCP2
FCRLA
ANKRD36BP1
ZNF496
HPDL
ATP1A1OS
AGBL4
MFSD2A
C1orf198
PPP1R15B
ATG4C
MAEL
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
DISP1
SNHG12
FAM40A
RGS8
DOCK7
WNT3A
NAV1
SEC16B
AQP10
LHX4
SLAMF9
C1orf201
PYGO2
ANGEL2
SPOCD1
ZNF697
IGFN1
NUP210L
BTF3L4
UBXN11
NEXN
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
LEMD1
ZNF670
ATPIF1
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
C1orf85
MED8
KTI12
C1orf212
ADC
TMEM54
HENMT1
TOE1
NLRP3
ERMAP
PGLYRP3
CSMD2
MYSM1
GNRHR2
CROCCP3
FHAD1
SLAMF6
OSBPL9
SLC26A9
OMA1
RAB42
FCRL1
FCRL3
LRRC42
GBP4
GBP5
FAM46B
FMO9P
FAM36A
TSEN15
FAM129A
SNAP47
TADA1
THEM4
SH2D1B
SSX2IP
OLFM3
GABPB2
TCHHL1
RPTN
CCDC163P
TDRD10
SHE
C1orf172
C1orf96
WDR63
KLHDC9
AXDND1
MAB21L3
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
ASB17
TYW3
C1orf173
LRRIQ3
MYOM3
DMBX1
OR10J5
TMCO2
ZNF684
TCEANC2
PODN
LRRC39
GJB4
HMGB4
RNF19B
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
HSD3BP4
SPATA17
EDARADD
KLF17
TMEM125
C1orf182
IQGAP3
APOA1BP
ARHGEF19
MRPL55
HIST3H2BB
DRAM2
C1orf88
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ITLN2
SYT6
C1orf74
CREB3L4
BROX
SAMD13
C1orf52
C1orf51
TMEM56
NBPF4
UBE2U
SLC35F3
LOC148696
LOC148709
PTPRVP
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
SLC30A7
C1orf213
KNCN
MOB3C
GLIS1
LELP1
RC3H1
MGC27382
DCDC2B
ZNF362
LOC149086
DCST1
CNIH3
LOC149134
MANEAL
IL23R
METTL11B
FAM78B
SHISA4
EXOC8
PDIK1L
BNIPL
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
LRRC71
C1orf64
RNF187
RP11-165H20.1
PYHIN1
C1orf227
FAM71A
DENND2C
GBP6
LPPR5
FNDC7
DENND1B
TDRD5
TOR1AIP2
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
SPRR4
KANK4
SASS6
C1orf55
CNST
FAM43B
PPIAL4A
HFM1
PAQR7
TTC24
C1orf65
UBL4B
PDIA3P
EIF2C3
EIF2C4
LCE4A
ALG14
FAM76A
LINC00466
C1orf168
TMEM61
CYP4Z1
CDCP2
SLC5A9
CC2D1B
NBPF11
NUDT17
FLJ23867
TXLNA
TCTEX1D1
PLD5
C1orf100
SPAG17
SLFNL1
KRTCAP2
CRTC2
IBA57
HIPK1
SLC44A5
AKR7L
AKR7A2P1
TMEM9
FNDC5
EPHX4
AKNAD1
SLC41A1
OR2T6
LCE5A
TMCO4
MCOLN2
COL24A1
LOC255654
PCSK9
SYT14
ST6GALNAC3
C1orf101
ZNF683
ARHGAP30
C1orf192
NEGR1
ASPM
CYP4X1
MAGI3
TIPRL
BEST4
PGBD2
FAM19A3
RIIAD1
THEM5
OR2L13
SLC9A11
OR14A16
CYP4A22
C1orf185
LOC284551
NBPF15
LINC00303
LOC284576
LOC284578
LOC284581
FAM102B
SYPL2
CYB561D1
ANKRD34A
RUSC1-AS1
LOC284632
LOC284648
DKFZP564C196
RSPO1
EPHA10
C1orf204
C1orf111
LOC284688
ZNF326
BTBD8
HNRNPU-AS1
RIMKLA
SLC25A34
ESPNP
LIN9
VN1R5
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
FAM151A
S100A7A
LINGO4
RXFP4
ANKRD45
LOC339442
FAM5C
MTMR9LP
ZBTB8OS
TFAP2E
ZNF678
PRSS38
LOC339505
C1orf110
FAM58BP
LOC339524
LOC339529
LOC339535
C1orf228
ZNF642
RD3
CCDC18
OR6F1
OR2W3
OR2T8
OR2T3
MYBPHL
OR10R2
FCRL6
KCNT2
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
OR2T29
SERINC2
FAM159A
FAM131C
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PADI6
RGSL1
BMP8A
IRF2BP2
ZBTB41
CYCSP52
SPATA21
CCDC23
ATPAF1-AS1
HEATR8
FAM73A
LOC375010
PEAR1
SFT2D2
MIA3
C1orf95
FAM89A
RPS10P7
CATSPER4
NSUN4
ILDR2
TMEM82
TRNP1
CD164L2
LOC388630
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
PLA2G2C
SKINTL
UOX
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
TMEM200B
SH2D5
C1orf130
LOC400752
C1orf141
GBP1P1
FLJ27354
MIR137HG
C1orf226
LOC400794
C1orf220
C1orf140
NBPF9
FAM177B
LDLRAD2
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
LOC402779
OR2T27
OR2T35
APOBEC4
MIR101-1
MIR137
MIR181B1
MIR186
MIR194-1
MIR197
MIR199A2
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
MIR30C1
MIR30E
MIR9-1
RGS21
LHX8
C1orf180
UQCRHL
MINOS1
FLJ32224
FAM183A
ZYG11A
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
PGCP1
OR10J3
OR2W5
OR13G1
MIR135B
KPRP
LCE6A
SUMO1P3
GEMIN8P4
RBMXL1
LURAP1
PEF1
C1orf98
HIST2H4B
DUSP5P
C1orf133
PRR9
MIR488
CYB5RL
SNORD74
RPL31P11
LOC641515
MIR205HG
SRG7
FLVCR1-AS1
CYMP
KIAA0754
LOC643441
LOC643723
LOC644242
PPIAL4G
LOC644961
PPIAL4D
LOC645166
SNRPD2P2
LOC645676
POU5F1P4
RPS7P5
S100A7L2
LOC646268
LOC646471
LOC646626
LOC646627
EMBP1
SRGAP2P2
LOC648740
ZBTB8A
NBPF6
LOC653160
PPIAL4B
LOC653513
GPR89A
LOC653566
PPIAL4C
HIST2H3D
TMEM183B
FAM72B
PCP4L1
SCARNA3
SCARNA2
SCARNA4
SCARNA1
SNORA14B
SNORA36B
SNORA42
SNORA44
SNORA55
SNORA61
SNORA77
SNORA16A
SNORD45C
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR548D1
MIR553
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
ZBTB8B
LOC728431
PPIEL
LOC728463
CCDC30
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729041
LOC729059
HSD52
FAM72A
FLJ37453
LOC729970
LOC729987
LOC730102
LOC730159
LOC730227
PPIAL4E
LOC731275
PFN1P2
MIR765
MIR942
MIR190B
MIR760
MIR921
LOC100128071
LOC100128787
LOC100129046
LOC100129138
LOC100129196
LOC100129269
C1orf68
MSTO2P
LOC100129620
LOC100129924
LOC100130000
LOC100130093
LOC100130197
LOC100130331
LOC100130557
LOC100131060
TSTD1
LOC100131234
LOC100131564
LOC100131825
LOC100132111
NBPF10
FCGR1C
ZRANB2-AS1
LOC100132774
C2CD4D
LOC100286793
LOC100287722
LOC100287814
LGALS8-AS1
GM140
LOC100288079
LOC100289178
LOC100289211
MIR320B1
MIR1182
MIR1537
MIR1231
MIR1278
MIR1295A
MIR1976
MIR548F1
MIR664
MIR1262
LOC100302401
LINC00184
TSNAX-DISC1
MIR320B2
MIR761
ZBED6
MIR3119-1
MIR3123
MIR3115
MIR3117
MIR3124
MIR3120
MIR4260
MIR4255
MIR4253
MIR3122
MIR4256
MIR4257
MIR3119-2
MIR4258
MIR4254
MIR3121
MIR3659
MIR3917
MIR3620
MIR3658
MIR3916
MIR3605
MIR3671
MIR548AA1
MIR3675
LOC100505633
LOC100505666
LOC100505768
LOC100505795
PROX1-AS1
LOC100505918
LOC100506023
LOC100506046
ZMYM6NB
LOC100506343
KDM5B-AS1
LOC100506730
LOC100506795
LOC100506801
LOC100506810
LOC100506963
LOC100507178
LOC100507423
LOC100507564
LOC100507634
FPGT-TNNI3K
GJA9-MYCBP
HEATR8-TTC4
PMF1-BGLAP
LOC100527964
TMEM56-RWDD3
C1orf151-NBL1
ZNF670-ZNF695
TNFAIP8L2-SCNM1
MIR4695
MIR4420
MIR4753
MIR4422
MIR4666A
MIR4781
MIR4424
MIR4794
MIR4677
MIR4735
MIR4671
MIR4654
MIR4427
MIR4684
MIR4711
MIR2682
MIR4742
MIR4423
MIR378F
DNM3OS
RCAN3AS
NEGR1-IT1
ZRANB2-AS2
LINC00538

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PKN2
PSMA5
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
KIAA1107
SLC35A3
LRRC8B
RWDD3
PTPN22
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
HAO2
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
RPAP2
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
DNAJA1P5
HENMT1
GBP4
GBP5
OLFM3
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
TMEM56
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AKR7A2P1
EPHX4
AKNAD1
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
GBP7
C1orf146
FAM69A
SLC6A17
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.3.

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

Genes
ERCC3
hsa-mir-128-1
hsa-mir-663b
ACVR1
ACVR2A
BIN1
RND3
CACNB4
CCNT2
DARS
DBI
DPP4
EN1
FAP
GALNT3
GCG
GLI2
GPD2
GPR17
GPR39
GRB14
GYPC
HNMT
INHBB
ITGB6
KCNJ3
KIF5C
LCT
LY75
MCM6
MGAT5
MYO7B
NEB
NR4A2
ORC4
POLR2D
PROC
PTPN4
RALB
RBMS1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
TNFAIP6
TSN
CXCR4
PKP4
MARCO
DDX18
KYNU
NMI
HS6ST1
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
TBR1
MAP3K2
GALNT5
NXPH2
COBLL1
PLA2R1
RAB3GAP1
UBXN4
CLASP1
R3HDM1
GCA
EPC2
ARL5A
PTPN18
MMADHC
C2orf27A
TFCP2L1
BAZ2B
ARHGEF4
INSIG2
LRP1B
CCDC93
PLEKHB2
FIGN
RIF1
STEAP3
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
CFC1
RPRM
UGGT1
SLC4A10
ERMN
DPP10
EPB41L5
IFIH1
MARCH7
TMEM185B
SAP130
GTDC1
TTC21B
CSRNP3
MZT2B
YSK4
THSD7B
TMEM177
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
MKI67IP
SFT2D3
LOC84931
TANC1
KCNH7
CCDC74A
CCDC74B
DAPL1
IMP4
TUBA3E
TUBA3D
FMNL2
GALNT13
LYPD1
XIRP2
CNTNAP5
ACMSD
FAM168B
C2orf76
ACVR1C
LYPD6
LYPD6B
CCDC148
TMEM37
LOC150527
LOC150776
WTH3DI
ARL6IP6
SLC38A11
WDSUB1
UPP2
C1QL2
PCDP1
FAM123C
LOC254128
LOC285103
SPOPL
CYP27C1
NCKAP5
GPR148
RBM43
LOC389033
LOC389043
LOC401010
DKFZp686O1327
MIR128-1
C2orf27B
LOC440905
LOC440910
POTEKP
POTEE
LOC554201
ANKRD30BL
LOC646743
LOC647012
CFC1B
MZT2A
POTEF
PABPC1P2
LOC100129961
LOC100131320
CYP4F30P
LOC100144595
RNU4ATAC
LOC100216479
ZEB2-AS1
MIR663B
SNORA70F
MIR3679
LOC100506124
LOC100506134
LOC100507600
LY75-CD302
MIR4783
MIR4785
MIR4784
MIR4773-1
MIR4773-2

Genes in Wide Peak

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

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

Genes
TNFAIP3

Genes in Wide Peak

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

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

Genes
BMPR1A
TLX1
NFKB2
PTEN
SUFU
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
ACTA2
ADD3
ADRA2A
ADRB1
FAS
ARL3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DNTT
DUSP5
FGF8
GLUD1
GOT1
GRID1
HABP2
HELLS
HHEX
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
KIF11
LIPA
MXI1
NDUFB8
NRAP
PAX2
PDE6C
PGAM1
PITX3
PPP1R3C
PSD
ALDH18A1
RBP4
RGR
SCD
SFRP5
FBXW4
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TLL2
WNT8B
XPNPEP1
SHOC2
LIPF
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
LGI1
NOLC1
GSTO1
MINPP1
KIF20B
SH3PXD2A
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
RPP30
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
C10orf116
LDB3
CPEB3
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
LRIT1
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
GHITM
PDCD4
C10orf28
POLL
BLNK
KCNIP2
EXOSC1
CALHM2
CUTC
PLCE1
ACSL5
PANK1
FAM190B
EXOC6
FAM35A
CCNJ
MARCH5
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
FAM178A
C10orf2
TM9SF3
ENTPD7
AS3MT
STAMBPL1
GPAM
SEMA4G
AVPI1
HPSE2
MMS19
NOC3L
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
C10orf95
C10orf81
PDZD7
OBFC1
UBTD1
WDR96
TNKS2
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
PCGF5
LZTS2
LCOR
MRPL43
PYROXD2
USMG5
ATAD1
ARHGAP19
ITPRIP
LINC00263
CDHR1
BBIP1
OPALIN
OPN4
HOGA1
SORCS1
PIK3AP1
MORN4
ZFYVE27
FRA10AC1
ANKRD22
SFXN2
C10orf32
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
C10orf129
LIPJ
CFL1P1
VTI1A
LOC143188
HECTD2
FGFBP3
NKX2-3
SLC35G1
CCDC147
LOC170425
CALHM1
PIPSL
BLOC1S2
RBM20
LOC282997
FLJ37201
O3FAR1
LIPM
CYP26C1
LRIT2
NHLRC2
C10orf99
SLC16A12
CC2D2B
GUCY2GP
FLJ41350
GOLGA7B
MIR107
C10orf62
LOC439994
IFIT1B
MIR346
MIR146B
FAM25A
LIPK
LIPN
LOC643529
RPL13AP6
SNORA12
MIR608
MIR609
FAM22A
FAM22D
LOC728190
LOC728218
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
KLLN
LOC100188947
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
FAS-AS1
MIR3157
MIR3158-1
MIR4295
MIR3158-2
LOC100505540
LOC100505761
LOC100505839
LOC100505933
LOC100507470
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4678
MIR4482-1
MIR4685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q33.3.

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

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

Genes in Wide Peak

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

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

Genes
BUB1B
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
B2M
CAPN3
CKMT1B
EPB42
GANC
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MFAP1
PLCB2
RAD51
SPINT1
TP53BP1
TYRO3
EIF3J
JMJD7-PLA2G4B
SNAP23
TGM5
PPIP5K1
LCMT2
SERF2
CHP
OIP5
BAHD1
MAPKBP1
RTF1
MGA
VPS39
CCNDBP1
C15orf63
TMEM87A
RPAP1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
SPTBN5
CTDSPL2
DLL4
INO80
PPP1R14D
HAUS2
FAM82A2
DNAJC17
PAK6
CASC5
STARD9
VPS18
ZFP106
CHAC1
WDR76
TMEM62
SPG11
ELL3
ZFYVE19
FRMD5
DISP2
C15orf57
C15orf23
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
ZSCAN29
TTBK2
CDAN1
STRC
ADAL
EXD1
RHOV
UBR1
PATL2
PLA2G4F
LRRC57
PLA2G4D
MRPL42P5
C15orf52
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
MIR626
MIR627
LOC728758
OIP5-AS1
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4310
LOC100505648
SERF2-C15ORF63

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.1.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
BCKDHB
CCNC
CGA
CNR1
COL10A1
COL12A1
COX7A2
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
BRD7P3
ASF1A
PNISR
IBTK
SENP6
FBXL4
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
FAM46A
TMEM30A
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
CD109
PM20D2
SRSF12
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
MCM9
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
RSPH4A
GJB7
SNHG5
LINC00222
CEP85L
LIN28B
FAM26F
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
TPI1P3
C6orf186
BET3L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q12.1.

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

Genes
PLAG1
TCEA1
NCOA2
CHCHD7
hsa-mir-124-2
ASPH
CA8
CRH
CYP7A1
NPBWR1
LYN
MOS
MYBL1
OPRK1
PDE7A
PENK
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SULF1
TRAM1
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
LACTB2
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
PRDM14
SOX17
CSPP1
VCPIP1
PREX2
SLCO5A1
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.13.

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

Genes
TNFRSF17
CIITA
SOCS1
hsa-mir-548h-2
EMP2
GRIN2A
GSPT1
NUBP1
PMM2
PRM1
PRM2
TNP2
USP7
SNN
LITAF
CLEC16A
CARHSP1
TMEM186
RSL1D1
DEXI
C16orf72
ZC3H7A
TXNDC11
PRM3
ATF7IP2
SNX29
RMI2
TEKT5
BCAR4
FAM18A
MIR548X

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.1.

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

Genes
BRCA1
CD79B
CLTC
COL1A1
DDX5
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
PER1
PRKAR1A
RARA
MAP2K4
TP53
TAF15
GAS7
USP6
SUZ12
ASPSCR1
BRIP1
MSI2
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
hsa-mir-3185
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
hsa-mir-4315-1
hsa-mir-2117
hsa-mir-2909
hsa-mir-632
hsa-mir-365-2
hsa-mir-3184
hsa-mir-144
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
hsa-mir-4314
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
AANAT
ABR
ACACA
ACADVL
ACCN1
ACLY
ACOX1
ACTG1
ADORA2B
AP2B1
ALDH3A1
ALDH3A2
ALDOC
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
AOC2
BIRC5
APOH
ARL4D
ARHGDIA
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
ATP5G1
ATP6V0A1
BLMH
C1QBP
FMNL1
CA4
CACNB1
CACNG1
CD7
CD68
CDC6
CDC27
CDK3
CHAD
CHD3
CHRNB1
CHRNE
CCR7
CNP
COX10
COX11
CPD
CLDN7
CRHR1
CRK
CRYBA1
CSF3
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CTNS
CYB561
ACE
DHX8
DLG4
DLX3
DLX4
DNAH9
DPH1
DRG2
DUSP3
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
ERN1
EVI2A
EVI2B
EVPL
EZH1
BPTF
FASN
FDXR
FGF11
FOXJ1
FOXO3B
FLII
FLOT2
GAST
FZD2
G6PC
GAA
GALK1
GCGR
KAT2A
GFAP
GH1
GH2
GIP
GNGT2
GP1BA
CCR10
UTS2R
GPS1
GPS2
GRB2
GRB7
GRN
GRIN2C
GUCY2D
H3F3B
HCRT
HIC1
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HSD17B1
ICAM2
ICT1
IFI35
IGFBP4
FOXK2
ITGA2B
ITGA3
ITGAE
ITGB3
ITGB4
JUP
KCNJ2
KCNJ12
KCNJ16
KPNB1
KPNA2
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS3BP
LGALS9
LHX1
LIG3
LLGL2
LLGL1
LPO
NBR1
MAFG
MAPT
ADAM11
MEIS3P1
MAP3K3
MEOX1
MFAP4
MNT
MPO
MPP2
MPP3
TRIM37
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYL4
MYO1C
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NOS2
NPTX1
NSF
NUP88
OMG
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
P4HB
PAFAH1B1
PDE6G
PDK2
PECAM1
SERPINF1
PEX12
PFAS
PFN1
PHB
PITPNA
PLD2
SERPINF2
PMP22
PNMT
SEPT4
POLR2A
MED1
PPY
PRKCA
MAPK7
MAP2K3
MAP2K6
PRPSAP1
PRPSAP2
PSMB3
PSMB6
PYY
PSMC5
PSMD3
PSMD11
PSMD12
PYCR1
PCYT2
RAB5C
RAC3
RAD51C
RAD51D
RCVRN
RFNG
RPA1
RPL19
RPL23A
RPL26
RPL27
RPL38
MRPL12
RPS6KB1
SCN4A
SCO1
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SEC14L1
SECTM1
SRSF1
SRSF2
SGCA
SGSH
SH3GL1P1
SH3GL1P2
SHBG
SHMT1
SLC2A4
SLC4A1
SLC6A4
SMARCD2
SMARCE1
SUMO2
SOX9
SOX15
SP2
SREBF1
SRP68
SSTR2
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
VAMP2
TADA2A
TBCD
TBX2
HNF1B
MLX
THRA
TIMP2
TK1
TNFAIP1
TOP2A
TOP3A
DNAJC7
TUBG1
UBB
UBE2G1
UBTF
TRPV1
VTN
WNT3
WNT9B
YWHAE
ZNF18
PCGF2
TRIM25
VEZF1
RNF112
ZNF207
ZNF232
RND2
COIL
AKAP1
EPX
AXIN2
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
PIP4K2B
SLC25A11
SPOP
DOC2B
FOXN1
PPM1D
CNTNAP1
DGKE
COPS3
CBX4
TCAP
SCARF1
SKAP1
DNAH17
AOC3
BECN1
KRT38
KRT37
KRT36
TNK1
ABCC3
MYH13
TNFSF13
TNFSF12
RGS9
GALR2
TMEM11
KSR1
CDK5R1
SPHK1
CACNA1G
HAP1
MAP3K14
SOCS3
TM4SF5
SPAG9
SLC13A2
UNC119
MTMR4
SLC16A6
SLC16A5
SLC16A3
RABEP1
SYNGR2
HGS
KCNAB3
AURKB
TIAF1
NOG
BZRAP1
CYTH1
ZNHIT3
GLP2R
EFTUD2
RPL23
SLC9A3R1
COG1
RECQL5
NTN1
STX8
PIGL
PGS1
TBX4
RPH3AL
FXR2
NPEPPS
MPDU1
GOSR1
SPAG7
CCL4L1
GOSR2
NR1D1
NCOR1
TRAF4
AATK
KIAA0100
ULK2
CCDC144A
ACAP1
TBKBP1
KIAA0195
EIF4A3
PLEKHM1
KIAA0753
MED24
LRRC37A
MRC2
SGSM2
ARHGAP44
HELZ
HS3ST3B1
HS3ST3A1
MED13
HDAC5
TOM1L1
GJC1
TOB1
ALYREF
PSME3
EIF1
NBR2
SLC35B1
DCAF7
CALCOCO2
RAMP2
ABCA10
ABCA9
ABCA8
PEMT
BAIAP2
CLEC10A
ATP5H
HOXB13
VAT1
APPBP2
MYBBP1A
FBXW10
PRPF8
LEPREL4
ST6GALNAC2
HEXIM1
SPAG5
TRIM16
IGF2BP1
GNA13
CCT6B
RAI1
KIF1C
GRAP
SEPT9
CD300C
C1QL1
RUNDC3A
STARD3
CBX1
RAB40B
TLK2
DDX52
DUSP14
KAT7
AKAP10
POLG2
NXPH3
SNF8
SYNRG
CD300A
TMC6
DDX42
GABARAP
CASC3
IKZF3
ZNF652
PPM1E
NLRP1
ARHGEF15
ARSG
EPN2
AZI1
SARM1
RAP1GAP2
CAMTA2
GPATCH8
KDM6B
ZZEF1
GGA3
MPRIP
JMJD6
EXOC7
KIAA0664
SMG6
WSCD1
USP22
CTDNEP1
KCNH4
ABCA6
ABCA5
TNFRSF13B
KCTD2
MMD
PIK3R5
WBP2
CDC42EP4
C17orf81
FAM215A
PPY2
PYY2
SHPK
AIPL1
FSCN2
NOL11
DHRS7B
KRT23
RNF167
TMEM98
POLDIP2
TBC1D29
TANC2
WSB1
NAT9
SENP3
OR1A2
PITPNC1
ERAL1
NARF
AATF
OR4D1
SNORD4B
SNORD4A
SNORA67
SNORD49A
SNORD42B
SNORD42A
PELP1
B9D1
CACNG5
CACNG4
TUBG2
TMEM97
NKIRAS2
CCDC56
GIT1
RANGRF
SAP30BP
PSMC3IP
SNX11
TIMM22
TBX21
NT5C
SOCS7
CDR2L
TAX1BP3
MINK1
GEMIN4
SOST
MED31
DERL2
FAM18B1
GLOD4
MRPS7
YBX2
UTP18
RNFT1
HN1
MYO15A
TUBD1
DCXR
RAPGEFL1
TACO1
ABI3
COPZ2
MRPL27
PIPOX
AMZ2
ARL17A
CRLF3
TRPV2
ANKFY1
ANAPC11
SIRT7
SLC25A39
MRPS23
PTRH2
RASD1
NLK
LUC7L3
HIGD1B
CDK12
INPP5K
KRT20
NLE1
FAM64A
SDK2
XAF1
FNDC8
FAM20A
C17orf59
MBTD1
BCAS3
TMEM104
CWC25
ALKBH5
RNF43
TTC19
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
GPR172B
LRRC37A4
MED9
SLFN12
WRAP53
PNPO
KLHL11
RNMTL1
SMG8
SLC47A1
TMEM100
VPS53
RHOT1
RSAD1
C17orf79
LRRC59
C17orf85
MSX2P1
NPLOC4
TSR1
C17orf63
PRR11
ADAP2
ST6GALNAC1
UTP6
TEX2
GSDMB
GPRC5C
TEX14
WDR45L
DHX33
CA10
NT5M
ATXN7L3
C17orf48
CCDC47
PLSCR3
PLXDC1
LYZL6
CBX8
ZNF286A
ZNF287
MIF4GD
INTS2
CASKIN2
RPTOR
NUFIP2
ZNF624
TAOK1
NLGN2
BAHCC1
USP36
ARHGAP23
PHF12
ZBTB4
RNF213
TNRC6C
CXCL16
TRAPPC1
PCTP
SCPEP1
ALOXE3
SLC25A19
ELAC2
FKBP10
SRR
UBE2O
HEATR6
DUS1L
FN3K
XYLT2
C17orf75
NXN
DNAI2
TEKT3
SMURF2
ENGASE
SPATA20
MRPL38
UBE2Z
WNK4
C17orf53
MIS12
C17orf39
METTL16
TMUB2
CARD14
DHX58
PHF23
MMP28
DHRS11
MFSD11
PRR15L
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
TEFM
ZNF750
ACBD4
FAM57A
DCAKD
GGNBP2
NUP85
ATAD5
MRM1
PLEKHH3
MYO15B
FAM106A
CTC1
DBF4B
MYO19
ACSF2
C17orf70
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
LIMD2
KCNH6
FAM117A
NDEL1
VMP1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
PITPNM3
LRRC48
TMEM93
TTC25
RILP
TEKT1
KRTAP4-12
RAB34
TSPAN10
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
GSG2
MYCBPAP
QRICH2
NSRP1
PPP1R1B
TBC1D3F
ZMYND15
CAMKK1
RPAIN
RNF135
MIEN1
MRPL45
VPS25
TMEM107
LSMD1
TMEM101
PRAC
RAB11FIP4
NEURL4
GHDC
KRTAP4-4
ZNF594
KIF2B
HES7
USP32
PPP1R9B
SPATA22
CBX2
MGC12916
TXNDC17
FAM104A
CORO6
TNS4
FBXL20
MIR22HG
MGC16275
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
FBF1
UNK
SSH2
TP53I13
IFT20
LRRC46
SCRN2
AOC4
CEP95
TRIM47
ANKRD40
ZNF830
SLFN11
RASL10B
ATPAF2
TMEM88
STRADA
C17orf72
SPECC1
G6PC3
ASB16
MAFG-AS1
OTOP2
PGAP3
MYOCD
PIGS
TTYH2
HSPB9
ORMDL3
CDRT7
CDRT15P1
SAT2
PLCD3
SLC46A1
TMEM106A
LRRC37B
CYGB
RNF157
SMYD4
OSBPL7
C1QTNF1
NT5C3L
ABHD15
TLCD1
PPP1R27
CNTROB
FTSJ3
RFFL
RPL29P2
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
ZPBP2
CYB5D1
OVCA2
USP43
KRBA2
C17orf64
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
FLJ40194
B4GALNT2
SPACA3
SGK494
SEZ6
ANKRD13B
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
C17orf57
MRPL10
WDR81
TBC1D16
AFMID
GJD3
KRT222
KRT40
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
DYNLL2
SMCR5
SMCR8
SMCR9
MGAT5B
TOM1L2
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
DNAH2
RTN4RL1
TCAM1P
EFCAB3
SLC47A2
CDRT15
WDR16
CCDC42
PIK3R6
ODF4
C17orf50
SLFN13
SLC35G3
UNC45B
LOC146880
CD300LG
KIF18B
RUNDC1
EME1
TMEM199
PROCA1
DHRS13
KCTD11
C17orf69
LOC147093
NOTUM
TMC8
TRIM16L
LRRC37BP1
WIPF2
KRT25
TMEM99
ANKFN1
MARCH10
MFSD6L
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
TRPV3
SLC16A11
FBXO39
IMP5
KRT28
USP32P1
KRT24
CEP112
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
ARHGAP27
ZNF385C
SAMD14
C17orf108
SLC16A13
C17orf74
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
RDM1
SPNS3
USP32P2
GAS2L2
STH
MTVR2
STXBP4
LOC253962
TBC1D28
C17orf61
TAC4
MYADML2
BCL6B
CDRT15L2
C17orf103
NPB
C17orf66
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
LOC284009
VMO1
C17orf58
MILR1
LOC284023
LINC00324
FLJ34690
CDRT4
CCDC144B
KIAA1267
C17orf105
FAM171A2
C17orf104
TTLL6
LOC284080
C17orf47
KRT18P55
NEK8
PIGW
C17orf78
LOC284100
CISD3
GSDMA
SLC13A5
TMEM102
KRT42P
PTRF
FAM27L
FLJ36000
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
LGALS9B
METRNL
TUSC5
KLHL10
RAB37
LOC339166
TMEM95
METTL2A
CCDC144NL
C17orf65
C17orf67
ENPP7
C17orf90
CCDC137
ARL16
LOC339240
C17orf51
MSL1
CD300E
SMTNL2
ALOX15P1
NACA2
KRT27
SLFN14
FLJ43826
STAC2
OTOP3
SKA2
CCL14-CCL15
CCDC144C
FAM195B
GPR142
TBC1D26
ZACN
KRT26
FAM101B
HOXB13-AS1
HILS1
CDRT1
SPEM1
EFCAB5
LRRC37A3
RNF126P1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
TMEM220
SHISA6
FAM211A
TMIGD1
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
OR3A4P
ARL5C
KRT39
SLC25A35
MYO18A
C17orf97
MED11
KRT16P2
GRAPL
C17orf102
LOC400604
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
MGC57346
CUEDC1
LOC404266
MIR10A
MIR132
MIR142
MIR144
MIR152
MIR193A
MIR195
MIR196A1
MIR21
MIR212
MIR22
MIR301A
TNFSF12-TNFSF13
TBC1D3B
TBC1D3C
CCL3L3
MXRA7
RNASEK
TBC1D3P5
SUZ12P
LOC440434
GPR179
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR324
MIR338
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451A
MIR497
SNORA21
CPSF4L
C17orf109
SLC35G6
RNF222
PIRT
LOC644172
LOC644246
CDRT15P2
FAM83G
KRT16P3
EVPLL
LOC645638
SEBOX
SNORA48
SNORD10
OR1D4
KRTAP4-11
MRPL45P2
TBC1D3P1-DHX40P1
LOC653653
TBC1D3G
LGALS9C
NME1-NME2
LINC00338
SCARNA20
SCARNA21
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORA59B
SNORA59A
SNORD7
SNORD49B
SNORD65
SNORD91A
SNORD91B
SNORD104
MIR33B
MIR632
MIR634
MIR635
MIR636
MIR657
BHLHA9
TLCD2
KRTAP4-8
KRTAP2-2
KRTAP9-1
LOC728392
NSFP1
FLJ45513
ZNF286B
LOC729683
TBC1D3
TBC1D3H
LOC730755
PRCD
MIR454
SNORD124
SNORA38B
MIR744
MIR365B
LOC100128288
LOC100128977
FAM106CP
LOC100130148
C17orf107
LOC100130581
C17orf110
LOC100130950
LOC100131096
LOC100131347
CD300LD
DBIL5P
KRTAP4-9
KRTAP4-7
LOC100133991
KCNJ18
TEN1
C17orf99
C17orf96
LOC100190938
LOC100287042
LOC100289255
LOC100294362
MIR1288
MIR1253
MIR1203
MIR1250
MIR1180
LOC100306951
MIR2117
MIR3183
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR2909
MIR3185
MIR4314
MIR3184
MIR4315-1
MTRNR2L1
LOC100499466
LOC100499467
MIR3614
MIR3678
MIR3615
MIR3676
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
LOC100506388
SPAG5-AS1
LOC100506650
AA06
LOC100506713
SLFN12L
MIR497HG
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
RAD51L3-RFFL
RNASEK-C17ORF49
C17orf61-PLSCR3
FAM18B2-CDRT4
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4523
MIR4731
MIR4728
MIR4726
MIR4739
MIR4734
MIR4729
MIR4737
MIR4736
MIR4724
MIR4733
MIR451B
MIR4522
MIR4738
MIR4740
MIR4524A
MIR4730
MIR4732
MIR3064
MIR4723
MIR4520A
MIR4521
MIR5047
MIR4727
MIR4725
MIR4520B
LOC100653515
RAB34

Arm-level results

Table 3. Get Full Table Arm-level significance table - 8 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.06 | 0.24 | 0.635 | 0.06 | 0.24 | 0.868
1q | 1955 | 0.17 | 2.34 | 0.0969 | 0.00 | -0.873 | 0.868
2p | 924 | 0.06 | -0.0167 | 0.635 | 0.06 | -0.0167 | 0.868
2q | 1556 | 0.06 | 0.0522 | 0.635 | 0.00 | -0.973 | 0.868
3p | 1062 | 0.11 | 0.957 | 0.49 | 0.00 | -0.995 | 0.868
3q | 1139 | 0.17 | 1.99 | 0.154 | 0.00 | -0.956 | 0.868
4p | 489 | 0.00 | -1.11 | 0.868 | 0.00 | -1.11 | 0.868
4q | 1049 | 0.00 | -0.996 | 0.868 | 0.11 | 0.954 | 0.868
5p | 270 | 0.11 | 0.748 | 0.534 | 0.00 | -1.07 | 0.868
5q | 1427 | 0.06 | 0.0249 | 0.635 | 0.00 | -0.987 | 0.868
6p | 1173 | 0.11 | 0.989 | 0.49 | 0.00 | -0.984 | 0.868
6q | 839 | 0.06 | -0.0328 | 0.635 | 0.06 | -0.0328 | 0.868
7p | 641 | 0.22 | 2.78 | 0.0358 | 0.00 | -0.969 | 0.868
7q | 1277 | 0.17 | 2.05 | 0.154 | 0.00 | -0.942 | 0.868
8p | 580 | 0.12 | 0.913 | 0.49 | 0.06 | -0.0178 | 0.868
8q | 859 | 0.11 | 0.901 | 0.49 | 0.00 | -1.02 | 0.868
9p | 422 | 0.06 | -0.109 | 0.635 | 0.06 | -0.109 | 0.868
9q | 1113 | 0.06 | -0.039 | 0.635 | 0.00 | -1.02 | 0.868
10p | 409 | 0.06 | -0.111 | 0.635 | 0.06 | -0.111 | 0.868
10q | 1268 | 0.06 | 0.0509 | 0.635 | 0.06 | 0.0509 | 0.868
11p | 862 | 0.06 | -0.0875 | 0.635 | 0.00 | -1.05 | 0.868
11q | 1515 | 0.22 | 3.19 | 0.0141 | 0.00 | -0.887 | 0.868
12p | 575 | 0.06 | -0.141 | 0.635 | 0.00 | -1.07 | 0.868
12q | 1447 | 0.06 | 0.0291 | 0.635 | 0.00 | -0.985 | 0.868
13q | 654 | 0.06 | -0.126 | 0.635 | 0.00 | -1.07 | 0.868
14q | 1341 | 0.11 | 1.04 | 0.49 | 0.00 | -0.967 | 0.868
15q | 1355 | 0.12 | 1.23 | 0.488 | 0.12 | 1.23 | 0.868
16p | 872 | 0.06 | -0.0266 | 0.635 | 0.06 | -0.0266 | 0.868
16q | 702 | 0.12 | 1.04 | 0.49 | 0.12 | 1.04 | 0.868
17p | 683 | 0.06 | -0.121 | 0.635 | 0.00 | -1.06 | 0.868
17q | 1592 | 0.06 | 0.06 | 0.635 | 0.00 | -0.97 | 0.868
18p | 143 | 0.18 | 1.76 | 0.194 | 0.07 | -0.0268 | 0.868
18q | 446 | 0.18 | 1.86 | 0.179 | 0.07 | 0.0251 | 0.868
19p | 995 | 0.00 | -1.06 | 0.868 | 0.00 | -1.06 | 0.868
19q | 1709 | 0.00 | -0.985 | 0.868 | 0.00 | -0.985 | 0.868
20p | 355 | 0.11 | 0.769 | 0.534 | 0.00 | -1.06 | 0.868
20q | 753 | 0.06 | -0.108 | 0.635 | 0.00 | -1.06 | 0.868
21q | 509 | 0.28 | 3.69 | 0.0045 | 0.00 | -0.946 | 0.868
22q | 921 | 0.00 | -1.04 | 0.868 | 0.06 | -0.0763 | 0.868
Xq | 1312 | 0.07 | 0.189 | 0.635 | 0.18 | 2.18 | 0.587

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/DLBC-TP/4433099/GDAC_MergeDataFiles_3124885/DLBC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 18 Input Tumor Samples.

Tumor Sample Names
TCGA-FA-8693-01A-11D-2389-01
TCGA-FF-8041-01A-11D-2209-01
TCGA-FF-8042-01A-11D-2209-01
TCGA-FF-8043-01A-11D-2209-01
TCGA-FF-8046-01A-11D-2209-01
TCGA-FF-8047-01A-11D-2209-01
TCGA-FF-8061-01A-11D-2209-01
TCGA-FF-8062-01A-11D-2209-01
TCGA-FM-8000-01A-11D-2209-01
TCGA-G8-6324-01A-11D-2209-01

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 © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle