SNP6 Copy number analysis (GISTIC2)
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1X34WCP
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/C1X34WCP
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 191 tumor samples used in this analysis: 14 significant arm-level results, 7 significant focal amplifications, and 16 significant focal deletions were found.

Results
Focal results

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

Table 1. Get Full Table Amplifications Table - 7 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
11q23.3 | 3.1249e-09 | 3.1249e-09 | chr11:118341650-118354357 | 1
21q22.2 | 1.4239e-06 | 1.4239e-06 | chr21:39579187-42282190 | 20
1q43 | 0.0019328 | 0.0019328 | chr1:236900019-236902363 | 1
1p33 | 0.019516 | 0.019516 | chr1:47516423-47533836 | 2
20q11.21 | 0.14404 | 0.14404 | chr20:26197900-30867110 | 36
13q31.3 | 0.21138 | 0.21138 | chr13:90236534-92243193 | 8
19p13.2 | 0.21138 | 0.21138 | chr19:7325274-21666209 | 431

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q23.3.

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

Genes
KMT2A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q22.2.

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

Genes
ERG
SNORA51|ENSG00000207147.1
MIR4760
snoU13|ENSG00000238556.1
SNORA62|ENSG00000272015.1
DSCAM
ETS2
HMGN1
KCNJ15
PCP4
SH3BGR
WRB
PSMG1
B3GALT5
BRWD1
C21orf88
LCA5L
IGSF5
DSCR10
LINC00114

Genes in Wide Peak

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

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

Genes
ACTN2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p33.

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

Genes
CYP4Z1
CYP4X1

Genes in Wide Peak

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

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

Genes
RNA5SP482
RNA5SP481
XKR7
LINC00028
DEFB122
SNORA40|ENSG00000212134.1
RNA5SP480
BCL2L1
FOXS1
HCK
ID1
PLAGL2
KIF3B
TM9SF4
TPX2
POFUT1
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TSPY26P
CCM2L
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB123
DEFB124
FRG1B
MIR663A
MIR1825
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q31.3.

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

Genes
LINC00379
LINC00410
RNA5SP34
LINC00559
SNORD38|ENSG00000200733.1
GPC5
MIR17HG
MIR622

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.2.

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

Genes
JAK3
LYL1
SMARCA4
TPM4
ELL
BRD4
LINC00664
ZNF738
RNA5SP469
ZNF66
ZNF737
ZNF826P
ZNF90
ZNF253
ZNF506
LINC00663
ZNF101
NDUFA13
MIR640
MEF2BNB
MEF2B
RN7SL70P
RN7SL155P
MIR3189
RN7SL513P
PIK3R2
RNA5SP468
SNORA68|ENSG00000207166.1
RN7SL823P
RN7SL835P
F2RL3
TMEM38A
RN7SL146P
RN7SL844P
RAB8A
LINC00661
UCA1
CYP4F24P
CYP4F8
CYP4F23P
OR7A5
RN7SL842P
RN7SL337P
RN7SL231P
LPHN1
SAMD1
RLN3
NANOS3
RN7SL619P
C19orf53
SYCE2
SNORD41|ENSG00000209702.1
WDR83OS
ZNF490
ZNF709
ZNF625
RNA5SP467
ZNF788
RNA5SP466
ZNF844
RNA5SP465
RNA5SP464
ZNF763
ZNF833P
RN7SL833P
RN7SL669P
snoU13|ENSG00000238349.1
DKFZP761J1410
CCDC159
RN7SL298P
SPC24
RN7SL192P
TMED1
MIR4748
MIR638
MIR1238
MIR1181
S1PR2
SNORD105B
SNORD105
RN7SL94P
SNORA70|ENSG00000200237.1
ZNF177
ZNF699
OR7E19P
RPS28
NDUFA7
RN7SL115P
RNA5SP463
C19orf59
PET100
ACP5
ASNA1
BST2
CACNA1A
CALR
CD97
CDKN2D
CNN1
COMP
NCAN
DHPS
DNASE2
DNM2
DNMT1
ELAVL1
ELAVL3
EPOR
NR2F6
FARSA
FCER2
GCDH
GDF1
DNAJB1
ICAM1
ICAM3
ICAM4
IL12RB1
ILF3
INSL3
JUNB
JUND
LDLR
CYP4F3
MAN2B1
MYO1F
MYO9B
HNRNPM
NDUFA7
NDUFB7
NFIX
NOTCH3
P2RY11
PDE4A
PDE4C
PIK3R2
PIN1
PRKACA
PKN1
PRKCSH
MAP2K7
PTGER1
RAB3A
RAD23A
UPF1
RFX1
RPL18A
CCL25
SLC1A6
SLC5A5
SNAPC2
STXBP2
PRDX2
ICAM5
TYK2
UBA52
ZNF14
ZNF708
ZNF20
ZNF69
ZNF85
ZNF121
ZNF136
CYP4F2
RFXANK
EIF3G
STX10
AP1M1
LPAR2
RAB11B
CRLF1
MED26
HOMER3
IL27RA
GDF15
TECR
RAB3D
IER2
KEAP1
AP1M2
SUGP2
DDX39A
ZNF443
AKAP8
B3GNT3
CLEC4M
KLF2
IFI30
TIMM44
CARM1
CHERP
RNASEH2A
KLF1
CERS1
GIPC1
ZNF266
PNPLA6
ILVBL
CDC37
COPE
MAST1
UNC13A
MAST3
FCHO1
SIN3B
ARHGEF18
CRTC1
MAU2
CASP14
FKBP8
TMEM59L
PGLS
LSM4
KANK2
FAM32A
OR7A17
TSPAN16
OR10H3
OR10H2
OR10H1
OR7E24
OR7C2
OR7C1
AKAP8L
ARRDC2
CPAMD8
BABAM1
HOOK2
TNPO2
EMR2
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
GMIP
CD320
ECSIT
ISYNA1
ZNF44
TM6SF2
S1PR5
DDX49
ZNF562
GATAD2A
BEST2
FBXL12
PGPEP1
CC2D1A
TMEM161A
C19orf60
MAP1S
KLHL26
C19orf66
ZNF823
TRMT1
ASF1B
USE1
C19orf80
PPAN
RETN
XAB2
ATP13A1
RGL3
SLC44A2
MCOLN1
DOCK6
CAMSAP3
ZNF317
ANO8
SUGP1
CYP4F11
EPS15L1
WIZ
UBL5
RASAL3
MRPL34
KRI1
ZSWIM4
CYP4F12
YIPF2
C19orf43
DDA1
KXD1
SMIM7
ZNF426
C19orf57
ABHD8
CERS4
OCEL1
COLGALT1
EPHX3
PODNL1
SLC35E1
ZNF442
LRRC8E
ZNF430
PBX4
KIAA1683
CCDC130
ADAMTS10
QTRT1
ZNF93
PLVAP
RTBDN
ANGPTL6
USHBP1
TSSK6
PRAM1
C19orf44
MRI1
FBXW9
WDR83
ZNF414
ELOF1
ZNF333
FBN3
ZNF559
EMR3
GTPBP3
MPV17L2
HSH2D
ATG4D
SYDE1
MBD3L1
DCAF15
GADD45GIP1
ZNF799
C19orf52
ZNF700
ZNF439
ZNF486
ZNF682
PEX11G
ZNF561
OLFM2
HAUS8
MVB12A
ARMC6
MUC16
FDX1L
NACC1
PGLYRP2
CCDC124
EVI5L
NXNL1
CCDC151
ZNF653
CIB3
RAVER1
OR7D4
OR7G1
OR1M1
CALR3
TRAPPC5
PCP2
ZNF441
ZNF491
ZNF440
SWSAP1
LRRC25
OR1I1
NR2C2AP
CCDC105
CYP4F22
OR10H4
ANKLE1
ZNF358
ZNF560
ZNF563
CILP2
ZNF558
ZNF714
LINC00905
ZNF846
OR7D2
ZNF791
ZNF564
ZNF709
ZNF433
SSBP4
ZNF431
ZNF627
DAND5
ZNF626
FAM129C
C19orf38
KANK3
ACTL9
OR2Z1
C19orf82
ZNF763
OR10H5
NWD1
SLC25A42
ZNF493
CLEC4G
PALM3
C19orf45
TMEM205
YJEFN3
SLC27A1
C3P1
ZNF788
CLEC17A
OR7G2
OR7G3
OR7A10
HAPLN4
CTXN1
MIR181C
MIR199A1
MIR23A
MIR27A
MIR181D
C19orf67
MIR639
ZNF812
ZNF878
ZGLP1
TMEM221
MIR1470
MIR3188
MIR4322
TGFBR3L
ZNF177
MIR5695
MIR4999
MIR5684
MIR5589

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 - 16 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
--- | --- | --- | --- | ---
5q31.2 | 1.0079e-07 | 1.0079e-07 | chr5:112819861-155310974 | 392
1q43 | 8.5631e-07 | 8.5631e-07 | chr1:236767073-236961354 | 1
10p12.31 | 0.00016265 | 0.00016751 | chr10:18970028-19889093 | 1
17q11.2 | 0.00029597 | 0.00029745 | chr17:28936804-29722618 | 14
16q23.1 | 0.00049839 | 0.00049538 | chr16:66780177-82663437 | 206
7p12.1 | 0.00087009 | 0.00087439 | chr7:50632522-51004541 | 2
7q34 | 4.775e-05 | 0.00099401 | chr7:122809112-159138663 | 329
12p13.2 | 0.0021964 | 0.002234 | chr12:11415451-13714180 | 28
3p13 | 0.019183 | 0.019183 | chr3:64670406-75234217 | 37
18p11.21 | 0.019349 | 0.01975 | chr18:12273033-18689746 | 25
7q34 | 6.3463e-05 | 0.046666 | chr7:122809112-159138663 | 329
9p23 | 0.048727 | 0.046666 | chr9:9437437-12687261 | 1
12q21.33 | 0.091515 | 0.090757 | chr12:88430194-96043393 | 51
17p13.2 | 0.12151 | 0.1217 | chr17:1-8378457 | 244
20q13.13 | 0.14909 | 0.14386 | chr20:30824728-55265542 | 300
9q21.32 | 0.2286 | 0.24284 | chr9:1-141213431 | 1001

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q31.2.

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

Genes
CD74
PDGFRB
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
RNA5SP198
RN7SKP232
RNA5SP197
ZNF300P1
snoU13|ENSG00000239191.1
snoU13|ENSG00000238369.1
MIR378A
RN7SL868P
U3|ENSG00000221043.1
MIR143HG
RN7SKP145
MIR584
SH3TC2
SPINK13
RN7SL791P
RNA5SP196
GPR151
RN7SKP246
KCTD16
RN7SL87P
RN7SL68P
PCDHGB8P
PCDHB18
PCDHB17
PCDHA14
WDR55
MIR3655
SNORA27|ENSG00000200235.1
SNORD45|ENSG00000200051.1
CYSTM1
PURA
TMEM173
ECSCR
RN7SKP64
RNA5SP195
SNORA74A
SNORA74|ENSG00000252213.1
RNA5SP194
RN7SL867P
snoU13|ENSG00000238745.1
SNORD63|ENSG00000206989.1
SNORD63|ENSG00000222937.1
RN7SL682P
snoU13|ENSG00000238605.1
NPY6R
MIR874
RNA5SP193
FBXL21
TIFAB
MIR4461
MIR4461
PCBD2
RN7SL541P
PPP2CA
SKP1
snoU13|ENSG00000238796.1
HSPA4
LEAP2
UQCRQ
RNA5SP192
snoZ6|ENSG00000253067.1
HINT1
RNA5SP191
RNU6ATAC10P
KIAA1024L
MIR4633
C5orf63
RN7SKP117
RN7SL711P
RN7SL689P
snoU13|ENSG00000239103.1
snoU13|ENSG00000252295.1
snoU13|ENSG00000239067.1
snoU13|ENSG00000239084.1
RNA5SP190
RN7SL174P
TNFAIP8
MIR5706
snoU13|ENSG00000239011.1
DTWD2
ARL14EPL
AP3S1
RN7SKP89
RNU4ATAC13P
ADRB2
ANXA6
ATOX1
ALDH7A1
CAMK2A
CAMLG
CD14
CDC25C
CDO1
CDX1
CSF1R
CSF2
CSNK1A1
CSNK1G3
CTNNA1
DMXL1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EGR1
ETF1
FAT2
FBN2
FGF1
GDF9
GFRA3
GLRA1
GM2A
GPX3
GRIA1
NR3C1
HARS
HSD17B4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL13
IRF1
KCNN2
LECT2
LMNB1
LOX
SMAD5
MFAP3
NDUFA2
NEUROG1
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2R2B
RPS14
SLC6A7
SLC12A2
SLC22A4
SLC22A5
SNX2
SPARC
SPINK1
SPOCK1
TAF7
TCF7
TCOF1
TGFBI
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
EIF4EBP3
PCDHGB4
CDC23
HDAC3
P4HA2
ATG12
CNOT8
HAND1
MYOT
NRG2
CXCL14
H2AFY
RNF14
SNCAIP
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
SEC24A
FAXDC2
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
KIF3A
SYNPO
ABLIM3
HMGXB3
ARHGAP26
FSTL4
SEPT8
ACSL6
PHF15
LARP1
HARS2
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
PKD2L2
AFF4
IL17B
SLC27A6
SNX24
MRPL22
PCDHB1
TMED7
ISOC1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
LARS
CXXC5
RAPGEF6
KDM3B
PHAX
RBM27
ZCCHC10
TMCO6
TRIM36
GALNT10
RBM22
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
ZNF608
SEMA6A
PCDHB16
HMHB1
SIL1
ARAP3
YTHDC2
GRAMD3
PCYOX1L
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PSD2
MEGF10
SPINK7
SMIM3
FCHSD1
LYRM7
CDKN2AIPNL
ZNF300
MYOZ3
PRDM6
FTMT
FNIP1
SLC35A4
MARCH3
SCGB3A2
PPARGC1B
PRRC1
ZNF474
AFAP1L1
GRPEL2
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
CEP120
SLC25A48
SRFBP1
ZMAT2
CCDC112
PRELID2
SH3RF2
PLAC8L1
ADAMTS19
SPATA24
DNAJC18
STK32A
AQPEP
SLC36A1
RELL2
SLC36A3
KIF4B
CHSY3
FAM170A
ARSI
IRGM
CATSPER3
DND1
C5orf48
PROB1
C5orf46
ARHGEF37
SPINK6
ANKHD1
MIR143
MIR145
SPINK14
C5orf56
IGIP
CTXN3
GRXCR2
SPINK9
CCNI2
MIR1303
TICAM2
MIR3141
MIR3936
MIR3661
MIR378H
MIR4460
MIR5197
MIR5692C1

Genes in Wide Peak

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

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

Genes
ACTN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p12.31.

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

Genes
U3|ENSG00000200545.1

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
RN7SL138P
TEFM
SUZ12P
RN7SL316P
LRRC37BP1
EVI2B
OMG
CRLF3
ADAP2
ATAD5
RNF135
MIR4733

Genes in Wide Peak

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

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

Genes
CBFB
CDH1
MAF
snoU13|ENSG00000238321.1
RN7SKP190
7SK|ENSG00000260682.2
MIR4720
GAN
PKD1L2
CMC2
RNA5SP431
PIH1
MON1B
SNORD33|ENSG00000252022.1
RN7SKP233
RNA5SP430
RN7SL520P
ADAT1
CHST6
SNORA76|ENSG00000252122.1
GLG1
NPIPB15
HCCAT5
PKD1L3
IST1
SNORD71
SNORA70D
TAT
SNORD112|ENSG00000251700.1
RNU6ATAC25P
FLJ00418
SNORD111|ENSG00000221066.1
SNORD111B
SF3B3
RN7SL279P
RN7SL407P
snoU13|ENSG00000238734.1
FKSG63
PDXDC2P
MIR140
SNORA62|ENSG00000252443.1
snoU13|ENSG00000238683.1
COG8
CHTF8
RPS2P45
RNA5SP429
snoU109|ENSG00000252640.1
snoU109|ENSG00000252040.1
snoU13|ENSG00000238343.1
SLC7A6OS
SNORA48|ENSG00000212445.1
CTRL
NUTF2
RN7SKP118
TRADD
RN7SL543P
AARS
AP1G1
AGRP
ZFHX3
CA7
CALB2
CDH3
CDH16
CTRB1
DHODH
NQO1
E2F4
GCSH
HAS3
HP
HPR
HSD11B2
HSD17B2
HSF4
KARS
LCAT
NFATC3
PLCG2
PSKH1
PSMB10
PSMD7
RRAD
ST3GAL2
SLC9A5
SLC12A4
SNTB2
TERF2
ZNF19
ZNF23
CES2
NAE1
NOL3
SLC7A6
ATP6V0D1
BCAR1
DHX38
CLEC3A
CHST4
MPHOSPH6
CFDP1
CTCF
NFAT5
WWP2
DDX19B
GABARAPL2
PHLPP2
ATMIN
CES3
CHST5
EDC4
PLA2G15
COG4
PLEKHG4
LRRC29
VPS4A
NOB1
TMEM208
FHOD1
ZDHHC1
PARD6A
NIP7
FAM96B
TPPP3
WWOX
BCMO1
TERF2IP
PRMT7
HYDIN
DUS2L
CHTF8
TXNL4B
PDPR
RFWD3
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
VAC14
FTSJD1
DDX28
TSNAXIP1
CENPN
THAP11
PDP2
RANBP10
VAT1L
PDF
DPEP2
DPEP3
ACD
FA2H
FAM65A
TMEM231
TANGO6
WDR59
ELMO3
ESRP2
CENPT
C16orf70
CYB5B
CMIP
GFOD2
PMFBP1
DYNLRB2
ENKD1
B3GNT9
CIRH1A
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
SDR42E1
PKD1L2
EXOSC6
C16orf46
NRN1L
CDYL2
TMEM170A
ZFP90
RLTPR
KCTD19
IL34
TMED6
ZFP1
ADAMTS18
LDHD
FUK
MLKL
CCDC79
CES4A
EXOC3L1
NUDT7
CLEC18C
ATXN1L
CLEC18A
C16orf86
C16orf47
CTRB2
MIR328
CLEC18B
KIAA0895L
SYCE1L
MIR1538
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p12.1.

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

Genes
SNORA4|ENSG00000201133.1
GRB10

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q34.

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

Genes
BRAF
EZH2
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
RARRES2
RHEB
SLC4A2
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
CLEC5A
MKRN1
POT1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
CPA4
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

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

Genes
ETV6
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
CDKN1B
CREBL2
EMP1
GPR19
LRP6
PRB1
PRB3
PRB4
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
APOLD1
GSG1
LOH12CR1
C12orf36
PRB2
MIR614

Genes in Wide Peak

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

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

Genes
MITF
FOXP1
RN7SL294P
snoU13|ENSG00000238416.1
GXYLT2
RNA5SP136
snoU13|ENSG00000238568.1
RYBP
LINC00870
LINC00877
RN7SL271P
GPR27
RN7SL418P
MIR3136
RNA5SP135
RN7SL482P
CNTN3
TMF1
SUCLG2
UBA3
MAGI1
ARL6IP5
PDZRN3
FRMD4B
LRIG1
EBLN2
SHQ1
LMOD3
PROK2
KBTBD8
SLC25A26
FAM19A4
PPP4R2
EOGT
EIF4E3
FAM19A1
MIR1284

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.21.

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

Genes
RN7SL662P
POTEC
CXADRP3
CYP4F35P
ANKRD20A5P
ZNF519
RN7SL362P
MIR4526
MIR5190
snoU13|ENSG00000238309.1
LDLRAD4
MC2R
MC5R
PTPN2
RNMT
SLMO1
AFG3L2
CEP192
SPIRE1
PSMG2
CEP76
SEH1L
TUBB6
FAM210A
ANKRD30B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q34.

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

Genes
BRAF
EZH2
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
RARRES2
RHEB
SLC4A2
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
CLEC5A
MKRN1
POT1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
CPA4
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
RN7SL5P

Genes in Wide Peak

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

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

Genes
BTG1
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13|ENSG00000239073.1
SNORD74|ENSG00000201502.1
snoU13|ENSG00000238361.1
snoU13|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
ATP2B1
DCN
EPYC
DUSP6
NR2C1
EEA1
GALNT4
CRADD
SOCS2
PLXNC1
METAP2
KERA
NUDT4
MRPL42
CCDC41
VEZT
FGD6
NDUFA12
TMCC3
CEP290
USP44
TMTC3
CCER1
C12orf79
POC1B
C12orf74
PLEKHG7
MIR331
CLLU1OS
CLLU1
MIR492
MIR3685
MIR5700

Genes in Wide Peak

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

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

Genes
PER1
TP53
USP6
SNORA69|ENSG00000212206.1
CTC1
MIR3676
SNORD118
TMEM107
snoU13|ENSG00000238676.1
SCARNA21|ENSG00000252835.1
RPL29P2
snoU13|ENSG00000251860.1
SNORD10
SNORA48|ENSG00000209582.1
SNORA67|ENSG00000264772.2
SLC35G6
GABARAP
ALOX12P2
TEKT1
C17orf100
RNA5SP435
DERL2
RN7SL784P
RN7SL171P
SPNS2
RN7SL774P
snoU13|ENSG00000238807.1
RNA5SP434
C17orf85
SHPK
ASPA
OR1E1
OR1D4
RN7SL605P
MIR1253
RN7SL608P
snoU13|ENSG00000239024.1
RN7SL33P
SNORD91A
SNORD91B
RN7SL624P
TLCD2
snoU13|ENSG00000238946.1
RN7SL105P
BHLHA9
MIR3183
TIMM22
DBIL5P
DOC2B
ABR
ACADVL
ALOX12
ALOX12B
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MNT
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RPA1
RPL26
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E2
OR1G1
OR3A3
SLC25A11
SCARF1
TNK1
TNFSF13
TM4SF5
RABEP1
KCNAB3
AURKB
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
CLUH
SMG6
WSCD1
CTDNEP1
ELP5
SHPK
AIPL1
RNF167
SENP3
OR1A2
PELP1
RANGRF
TAX1BP3
MINK1
GEMIN4
MED31
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
C17orf59
SLC52A1
WRAP53
RNMTL1
VPS53
TSR1
DHX33
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
ACKR6
EMC6
RILP
GSG2
ZMYND15
CAMKK1
RPAIN
LSMD1
NEURL4
ZNF594
HES7
SPATA22
TXNDC17
TMEM88
SAT2
SMYD4
CNTROB
CYB5D1
OVCA2
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
WDR81
DNAH2
RTN4RL1
ODF4
KCTD11
TRPV3
SLC16A11
FBXO39
SLC16A13
C17orf74
SPNS3
TMEM256
BCL6B
VMO1
LINC00324
SLC13A5
TMEM102
TUSC5
TMEM95
SMTNL2
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR212
MIR22HG
TNFSF12
RNASEK
MIR324
MIR497HG
RNF222
C17orf107
MIR4314
MIR4520B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20q13.13.

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

Genes
TOP1
MAFB
ASXL1
RN7SL170P
U3|ENSG00000252536.1
FAM209A
GCNT7
snoU13|ENSG00000238294.1
RNA5SP487
RNU4ATAC7P
RN7SKP184
RN7SL603P
MIR3194
RN7SL672P
RN7SL636P
LINC00651
snoU13|ENSG00000239157.1
RN7SL197P
KCNB1
SNORD12
SNORD12B
SNORD12C
ZFAS1
LINC00494
SNORD36|ENSG00000252227.1
RNA5SP486
RN7SL243P
MIR3616
RN7SKP33
SNX21
RNU6ATAC38P
SPINT4
WFDC10A
RNA5SP485
RBPJL
RN7SL31P
KCNK15
MIR3646
R3HDML
FITM2
RN7SL443P
SCARNA15|ENSG00000252193.1
RN7SL666P
RN7SKP100
SNORA26|ENSG00000212224.1
RN7SL615P
RNA5SP484
SNORD112|ENSG00000252434.1
RN7SL194P
RN7SL680P
RN7SL116P
RN7SKP173
ARHGAP40
MIR548O2
SNORA60
SNORA71|ENSG00000201811.1
SNORA71D
SNORA71C
SNORA71A
SNORA71B
SNHG17
RN7SL237P
RN7SKP185
LINC00489
RBL1
RN7SL156P
snoU13|ENSG00000239089.1
LINC00657
SCAND1
snoU13|ENSG00000238549.1
RN7SKP271
FER1L4
GDF5OS
RNA5SP483
SNORD56|ENSG00000201151.1
MIR499A
MIR644A
RN7SL511P
EFCAB8
C20orf203
ADA
AHCY
ASIP
BPI
CD40
CEBPB
CSE1L
CSTF1
CYP24A1
DNMT3B
E2F1
EPB41L1
EYA2
GGT7
GHRH
GSS
HNF4A
EIF6
KCNG1
KCNS1
LBP
MC3R
MMP9
MYBL2
NFATC2
NNAT
PFDN4
PI3
PLCG1
PLTP
CTSA
PTGIS
PTPN1
RBL1
RPN2
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SNTA1
SPAG4
SRC
STAU1
STK4
AURKA
TFAP2C
TGM2
TNNC2
UBE2V1
YWHAB
ZNF217
GDF5
NCOA3
BCAS1
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
B4GALT5
KIF3B
RBM39
TTI1
SPATA2
ACOT8
ATP9A
SGK2
RBM12
MYL9
WFDC2
PROCR
ARFGEF2
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
UBE2C
PTPRT
PKIG
CEP250
PXMP4
DLGAP4
RALY
MAPRE1
ZHX3
NCOA6
SLC9A8
ADNP
ZMYND8
SAMHD1
AAR2
L3MBTL1
PPP1R16B
TRPC4AP
TP53TG5
MOCS3
SLC35C2
IFT52
PHF20
BPIFA1
RTFDC1
OSER1
PIGT
ERGIC3
CDK5RAP1
UQCC
BCAS4
DDX27
ZNF334
ZFP64
EDEM2
DOK5
DBNDD2
ACSS2
RNF114
SULF2
C20orf24
CTNNBL1
CASS4
EPPIN
RALGAPB
JPH2
SALL4
ZNFX1
NDRG3
SLC12A5
PREX1
MYH7B
NCOA5
TP53INP2
RPRD1B
TGIF2
DHX35
MANBAL
ELMO2
ZNF335
PCIF1
NECAB3
CDH22
SLC13A3
LPIN3
GDAP1L1
TTPAL
ACTR5
DSN1
PABPC1L
BPIFB2
SLC2A10
FAM83D
DYNLRB1
ITCH
SLA2
CHD6
MAP1LC3A
PARD6B
ZNF341
TOX2
KIAA1755
EMILIN3
SYS1
WFDC8
ZSWIM1
BPIFB1
TP53RK
DNTTIP1
FAM210B
VSTM2L
SNHG11
WFDC12
SPATA25
OCSTAMP
TSHZ2
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
FAM83C
SLC32A1
BPIFA2
WFDC3
C20orf112
CBLN4
MROH8
SOGA1
TLDC2
RIMS4
SUN5
ROMO1
NEURL2
ZSWIM3
C20orf62
WFDC6
C20orf173
FAM65C
CNBD2
ADIG
GTSF1L
WFDC5
COMMD7
BPIFB4
WFDC13
ACTL10
WFDC11
WFDC9
WFDC10B
BPIFA4P
BPIFB3
TMEM189
FAM209B
MIR645
MIR1825
MIR3617
MIR4756
MIR4755

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.32.

Table S23. 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 3. Get Full Table Arm-level significance table - 14 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 | 0.02 | 0.595 | 0.882 | 0.00 | -1.46 | 0.944
1q | 1195 | 0.01 | -0.119 | 0.945 | 0.00 | -1.48 | 0.944
2p | 624 | 0.01 | -0.252 | 0.945 | 0.00 | -1.55 | 0.944
2q | 967 | 0.01 | -0.843 | 0.945 | 0.00 | -1.51 | 0.944
3p | 644 | 0.01 | -0.882 | 0.945 | 0.02 | 0.414 | 0.905
3q | 733 | 0.01 | -0.867 | 0.945 | 0.02 | 0.439 | 0.905
4p | 289 | 0.02 | 0.968 | 0.606 | 0.01 | -0.294 | 0.944
4q | 670 | 0.02 | 1.09 | 0.6 | 0.01 | -0.211 | 0.944
5p | 183 | 0.01 | -0.966 | 0.945 | 0.01 | -0.34 | 0.944
5q | 905 | 0.00 | -1.5 | 0.945 | 0.03 | 2.48 | 0.0531
6p | 710 | 0.01 | -0.888 | 0.945 | 0.00 | -1.54 | 0.944
6q | 556 | 0.01 | -0.915 | 0.945 | 0.00 | -1.56 | 0.944
7p | 389 | 0.01 | -0.841 | 0.945 | 0.09 | 9.33 | 0
7q | 783 | 0.00 | -1.45 | 0.945 | 0.10 | 11.7 | 0
8p | 338 | 0.12 | 12.5 | 0 | 0.01 | -0.817 | 0.944
8q | 551 | 0.12 | 13.3 | 0 | 0.00 | -1.47 | 0.944
9p | 301 | 0.01 | -0.946 | 0.945 | 0.01 | -0.315 | 0.944
9q | 700 | 0.01 | -0.878 | 0.945 | 0.01 | -0.227 | 0.944
10p | 253 | 0.01 | -0.325 | 0.945 | 0.01 | -0.954 | 0.944
10q | 738 | 0.02 | 0.44 | 0.943 | 0.01 | -0.866 | 0.944
11p | 509 | 0.02 | 1.04 | 0.6 | 0.01 | -0.247 | 0.944
11q | 975 | 0.03 | 2.52 | 0.0467 | 0.01 | -0.807 | 0.944
12p | 339 | 0.00 | -1.57 | 0.945 | 0.02 | 0.961 | 0.533
12q | 904 | 0.00 | -1.52 | 0.945 | 0.01 | -0.854 | 0.944
13q | 560 | 0.03 | 2.34 | 0.0641 | 0.01 | -0.879 | 0.944
14q | 938 | 0.01 | -0.18 | 0.945 | 0.00 | -1.51 | 0.944
15q | 810 | 0.00 | -1.52 | 0.945 | 0.02 | 1.11 | 0.532
16p | 559 | 0.00 | -1.55 | 0.945 | 0.01 | -0.266 | 0.944
16q | 455 | 0.00 | -1.56 | 0.945 | 0.02 | 0.997 | 0.533
17p | 415 | 0.00 | -1.53 | 0.945 | 0.07 | 6.76 | 9.51e-11
17q | 972 | 0.02 | 0.563 | 0.882 | 0.04 | 3.22 | 0.0063
18p | 104 | 0.00 | -1.6 | 0.945 | 0.03 | 1.52 | 0.369
18q | 275 | 0.00 | -1.58 | 0.945 | 0.02 | 0.942 | 0.533
19p | 681 | 0.03 | 1.77 | 0.19 | 0.02 | 1.12 | 0.532
19q | 935 | 0.03 | 1.87 | 0.174 | 0.02 | 1.21 | 0.532
20p | 234 | 0.01 | -0.336 | 0.945 | 0.00 | -1.59 | 0.944
20q | 448 | 0.01 | -0.927 | 0.945 | 0.01 | -0.927 | 0.944
21q | 258 | 0.04 | 3.51 | 0.00227 | 0.01 | -0.27 | 0.944
22q | 564 | 0.05 | 4.31 | 0.000107 | 0.01 | -0.196 | 0.944
Xq | 668 | 0.01 | -0.196 | 0.945 | 0.03 | 2.4 | 0.0545

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/LAML-TB/11447784/GDAC_MergeDataFiles_5132078/LAML-TB.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 191 Input Tumor Samples.

Tumor Sample Names
TCGA-AB-2803-03A-01D-0756-21
TCGA-AB-2804-03A-01D-0756-21
TCGA-AB-2805-03A-01D-0756-21
TCGA-AB-2806-03A-01D-0756-21
TCGA-AB-2807-03A-01D-0756-21
TCGA-AB-2808-03A-01D-0756-21
TCGA-AB-2809-03A-01D-0756-21
TCGA-AB-2810-03A-01D-0756-21
TCGA-AB-2811-03A-01D-0756-21
TCGA-AB-2812-03A-01D-0756-21

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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