SNP6 Copy number analysis (GISTIC2)
Uveal Melanoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C14F1PVN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C14F1PVN
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.22 (Firehose task version: 140).

Summary

There were 80 tumor samples used in this analysis: 24 significant arm-level results, 3 significant focal amplifications, and 19 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 - 3 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
--- | --- | --- | --- | ---
8q24.22 | 1.7325e-19 | 1.7325e-19 | chr8:107863152-146364022 | 247
6p24.3 | 1.925e-05 | 1.925e-05 | chr6:1-18226822 | 115
17q25.3 | 0.17637 | 0.17637 | chr17:52926827-81195210 | 411

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.22.

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

Genes
EXT1
MYC
RECQL4
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25|ENSG00000251744.1
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
SNORD112|ENSG00000252559.1
TMEM74
RNA5SP275
ADCY8
ANGPT1
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HSF1
EIF3E
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
PTK2
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRHR
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
GPAA1
FOXH1
EBAG9
LRRC14
EMC2
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
KHDRBS3
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
KCNV1
MTBP
AGO2
COMMD5
MRPL13
ATAD2
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
THEM6
FAM49B
CHRAC1
EXOSC4
TRMT12
WDYHV1
SLC39A4
SYBU
GSDMC
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
DSCC1
DERL1
SLC52A2
GSDMD
ARHGAP39
ZNF34
SHARPIN
SCRT1
TRAPPC9
TATDN1
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
PKHD1L1
NAPRT1
TBC1D31
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
FAM84B
FAM91A1
SLC30A8
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
MROH5
MAFA
SAMD12
MIR30B
MIR30D
LRRC24
MROH6
FER1L6
MROH1
FAM203B
OC90
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3610
MIR4662B
MIR4663
MIR4664
MIR5194

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.3.

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

Genes
IRF4
DEK
RNA5SP204
STMND1
U3|ENSG00000251793.1
MIR4639
RN7SL332P
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
FAM8A1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
MCUR1
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
KDM1B
RBM24
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
NHLRC1
PSMG4
C6orf201
PPP1R3G
TMEM170B
MIR4645
MIR5689
MIR5683

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

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

Genes
BRIP1
CD79B
CLTC
DDX5
HLF
PRKAR1A
ASPSCR1
MSI2
CANT1
MIR4525
RAB40B
snoU13|ENSG00000238403.1
snoU13|ENSG00000238947.1
DUS1L
PCYT2
SLC25A10
LINC00482
MIR1250
MIR657
MIR4730
CBX8
snoU13|ENSG00000239173.1
ENGASE
DDC8
RN7SL454P
SNORA30|ENSG00000200063.1
RN7SL236P
FLJ45079
LINC00338
LINC00868
MIR636
SNORD1B
SNHG16
PRCD
snoU13|ENSG00000238418.1
MYO15B
RN7SL573P
MIR3615
CD300LD
GPRC5C
RNA5SP448
LINC00469
SSTR2
SCARNA24|ENSG00000252274.1
RN7SKP180
LINC00511
MAP2K6
SNORA40|ENSG00000252352.1
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
RN7SL622P
SNORA38B
MIR548D2
RN7SL756P
snoU13|ENSG00000238612.1
PSMD12
SNORA8|ENSG00000207410.1
RNA5SP447
RNA5SP446
MIR634
RNA5SP445
RN7SL735P
RNA5SP444
SLC16A6P1
RN7SL404P
RN7SL409P
PLEKHM1P
SMURF2
MIR5047
MIR3064
SNORD104
SNORA76|ENSG00000266402.2
TCAM1P
RN7SL805P
ACE
TLK2
TBC1D3P2
RN7SL800P
snoU13|ENSG00000238799.1
RN7SL448P
RN7SL606P
PPM1D
RPL12P38
SCARNA20|ENSG00000252577.1
USP32
MIR4729
PRR11
MIR301A
MIR454
RN7SL716P
PPM1E
U3|ENSG00000212195.1
DYNLL2
SRSF1
VEZF1
MRPS23
RN7SKP94
RN7SL449P
RN7SL437P
RNF126P1
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NPTX1
P4HB
PDE6G
SEPT4
PRKCA
PRPSAP1
PSMC5
PYCR1
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
COIL
AKAP1
EPX
AXIN2
DGKE
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
POLG2
CD300A
TMC6
DDX42
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
PTRH2
SDK2
BCAS3
TMEM104
RNF43
MKS1
C17orf80
CCDC40
WIPI1
SMG8
TMEM100
NPLOC4
ST6GALNAC1
TEX2
TEX14
WDR45B
CCDC47
MIF4GD
INTS2
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
FN3K
DNAI2
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
OGFOD3
ZNF750
NUP85
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
CBX2
FAM104A
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
MGAT5B
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
EFCAB3
NOTUM
TMC8
ANKFN1
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
STXBP4
MYADML2
NPB
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
OXLD1
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
LRRC37A3
YPEL2
C17orf82
BTBD17
TEX19
CUEDC1
MIR142
MIR21
MXRA7
CPSF4L
SMIM5
MIR633
SMIM6
TEN1
C17orf99
MIR4316
MIR338
MIR3186
MIR3614
MIR3678
MIR3615
MIR4739
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524B

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 - 19 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
--- | --- | --- | --- | ---
11p15.1 | 1.1184e-22 | 1.1184e-22 | chr11:16623557-16799846 | 1
1p36.21 | 0.00037508 | 0.00037508 | chr1:1-48649489 | 789
3q24 | 0.0051924 | 0.0051924 | chr3:142896601-143694372 | 1
3p22.2 | 0.0054434 | 0.0052458 | chr3:38314751-38389497 | 1
3p25.1 | 0.014594 | 0.014594 | chr3:13545239-13692618 | 1
6q27 | 0.0051924 | 0.014594 | chr6:166922042-167347293 | 1
11q24.3 | 0.024263 | 0.024263 | chr11:114997555-133313263 | 198
3q29 | 0.024263 | 0.024263 | chr3:194238890-194369918 | 1
16q12.1 | 0.017634 | 0.024808 | chr16:47735031-48202502 | 1
2q37.2 | 0.027043 | 0.028814 | chr2:225871674-243199373 | 173
8p11.22 | 0.047308 | 0.047308 | chr8:38312793-38587017 | 1
6q22.31 | 0.0051924 | 0.073367 | chr6:123955968-125285408 | 1
3p25.2 | 0.088845 | 0.088845 | chr3:12809221-12884390 | 2
16q23.3 | 0.073367 | 0.091983 | chr16:82873004-83542835 | 2
3p14.2 | 0.097659 | 0.098011 | chr3:58619023-67065663 | 26
16q24.3 | 0.10472 | 0.11648 | chr16:89378665-90354753 | 27
5q23.1 | 0.22404 | 0.22603 | chr5:113695143-158639879 | 407
17q12 | 0.22603 | 0.22603 | chr17:27397975-51318309 | 506
8q11.21 | 0.24065 | 0.24412 | chr8:1-146364022 | 889

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.1.

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

Genes
C11orf58

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.21.

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

Genes
LCK
MPL
MUTYH
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
SKINTL
TRABD2B
LINC00853
CYP4A22
CYP4Z2P
KNCN
LINC00505
NSUN4
TMEM69
snoU13|ENSG00000238945.1
RNA5SP47
BTBD19
SNORD38B
SNORD38A
SNORD46|ENSG00000200913.1
SNORD55
MIR5584
RN7SL479P
RNA5SP46
RNA5SP45
RN7SL326P
MIR30C1
MIR30E
BMP8B
SNORA55
BMP8A
RNA5SP44
MYCBP
SNORA63|ENSG00000252448.1
snoU13|ENSG00000238871.1
MIR5581
MEAF6
RNA5SP43
SNORA63|ENSG00000201448.1
RN7SL131P
RN7SL281P
PSMB2
RNY5P1
SNORA62|ENSG00000201542.1
RN7SL503P
RN7SL136P
ZMYM6
SNORD112|ENSG00000252728.1
SMIM12
RNA5SP42
RN7SKP16
MIR3605
FKSG48
ZBTB8OS
ZBTB8B
RN7SL122P
MTMR9LP
MIR5585
MIR4254
FABP3
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18|ENSG00000252691.1
SCARNA17|ENSG00000252190.1
MAN1C1
snoU13|ENSG00000238889.1
SYF2
snoU13|ENSG00000238986.1
RN7SL857P
snoU13|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16|ENSG00000252404.1
RN7SL451P
SNORA77|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
AK2
ALPL
RERE
ATP6V0B
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
PLK3
CNR2
COL8A2
COL9A2
COL16A1
CORT
CSF3R
CTPS1
CYP4A11
CYP4B1
DDOST
DFFB
DPH2
DVL1
E2F2
ECE1
EDN2
PHC2
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FAAH
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
INPP5B
IPP
STMN1
MATN1
MFAP2
MTF1
MTHFR
MYCL
NASP
NBL1
NDUFS5
NFYC
NPPA
NPPB
YBX1
OPRD1
PAFAH2
PRDX1
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKCZ
PTAFR
PTPRF
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RPS8
RSC1A1
SCNN1D
SRSF4
ST3GAL3
STIL
SKI
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TIE1
TNFRSF1B
TP73
TNFRSF4
UQCRH
UROD
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LAPTM5
PTP4A2
SNHG3
NR0B2
RAD54L
PIK3R3
MMP23B
KCNAB2
FCN3
YARS
MKNK1
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
PER3
EIF2B3
ARTN
MAP3K6
KCNQ4
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
THEMIS2
H6PD
ISG15
PLCH2
IPO13
KDM4A
CROCC
PUM1
CEP104
RIMS3
EFCAB14
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
TSPAN1
CELA3A
PDZK1IP1
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
AKR1A1
TESK2
PPIE
MAD2L2
PPIH
CAP1
LRRC41
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
EBNA1BP2
KIF2C
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
FOXJ3
SCMH1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
MAST2
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
SZT2
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
STX12
CLIC4
MMACHC
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HEYL
AGO1
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
SSU72
GNL2
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF691
MECR
UTP11L
SDF4
MRTO4
HPCAL4
YTHDF2
ZCCHC17
PADI3
CMPK1
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
RNF220
VPS13D
EVA1B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
POMGNT1
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
DMAP1
AJAP1
TMEM234
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
ZSWIM5
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
PLA2G2F
SMAP2
ATPAF1
S100PBP
EXO5
CEP85
NMNAT1
ELOVL1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZFP69B
PHACTR4
AUNIP
ERI3
C1orf50
CCDC28B
EFHD2
MMEL1
RSG1
NKAIN1
MUL1
TMEM53
AKIRIN1
HECTD3
YRDC
NOL9
PPCS
LIN28A
SH3D21
SNIP1
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
HYI
SESN2
ESPN
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
ZMYND12
NBPF3
LZIC
NT5C1A
TRIM63
FAM167B
C1orf170
HPDL
MFSD2A
SYTL1
IGSF21
LSM10
C1orf94
KIAA2013
THAP3
STPG1
SPOCD1
UBXN11
FBXO44
ATPIF1
MED8
ADC
TMEM54
TOE1
ERMAP
CSMD2
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
GJB4
HMGB4
RNF19B
A3GALT2
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
KLF17
TMEM125
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
MOB3C
DCDC2B
ZNF362
MANEAL
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
CCDC17
SLC2A7
CALML6
IFNLR1
CITED4
FAM43B
PAQR7
AGO3
AGO4
FAM76A
TMEM201
CYP4Z1
C1orf86
TXLNA
SLFNL1
ATAD3C
AKR7L
FNDC5
TTLL10
TMCO4
ZNF683
CYP4X1
NPHP4
BEST4
RSPO1
EPHA10
RIMKLA
SLC25A34
C1orf174
KLHL17
TMEM52
TFAP2E
C1orf228
ZFP69
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
TCTEX1D4
SERINC2
FAM131C
SPATA21
CCDC23
TEX38
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
FAM183A
ANKRD65
PRAMEF7
LURAP1
PEF1
MIR429
KIAA0754
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
ZBTB8A
PRAMEF22
PRAMEF15
PRAMEF16
MIR552
CCDC30
CDK11A
SLC35E2B
C1orf234
OR4F29
FAM229A
FOXO6
MIR4255
MIR4253
MIR1273D
MIR4252
MIR3659
MIR3917
MIR3675
ZMYM6NB
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

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

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

Genes
SLC9A9

Genes in Wide Peak

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

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

Genes
SLC22A14

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.1.

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

Genes
FBLN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MIR1913

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

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

Genes
DDX6
PCSK7
CBL
FLI1
PAFAH1B2
ARHGEF12
snoU13|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CD3D
CD3E
CHEK1
DPAGT1
ETS1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
IL10RA
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NFRKB
NRGN
PVRL1
SCN2B
SCN4B
ST3GAL4
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZNF202
BARX2
USP2
UBE4A
EI24
FEZ1
ARHGAP32
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
OR8B8
OR8B2
DCPS
ZBTB44
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
TMPRSS13
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
ESAM
TIRAP
C1QTNF5
PANX3
APOA5
TMEM45B
AMICA1
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
HEPN1
PATE3
MIR4493
MIR4492

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

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

Genes
TMEM44

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q12.1.

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

Genes
ABCC12

Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SAG
CCL20
SP100
SPP2
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
CAPN10
SP140
PASK
ATG4B
SH3BP4
NGEF
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
PID1
ATG16L1
USP40
HJURP
HES6
C2orf83
MFF
ACKR3
NYAP2
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
DNER
B3GNT7
SP140L
AGAP1
TWIST2
DIS3L2
NEU4
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
C2orf72
DUSP28
MROH2A
ESPNL
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4269
MIR4786
MIR5001
MIR5702
MIR5703

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.22.

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

Genes
C8orf86

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
NKAIN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p25.2.

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

Genes
SNORA7A
RPL32

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
MIR3182
RN7SL134P

Genes in Wide Peak

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

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

Genes
FHIT
RN7SL482P
U3|ENSG00000200222.1
SNTN
RNA5SP134
LINC00698
RN7SL863P
PTPRG
U3|ENSG00000212211.1
NPCDR1
ATXN7
CADPS
MAGI1
PSMD6
LRIG1
FEZF2
ADAMTS9
C3orf14
THOC7
KBTBD8
SLC25A26
FAM3D
C3orf49
SYNPR
PRICKLE2
C3orf67

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

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

Genes
FANCA
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
AFG3L1P
C16orf3
DPEP1
GAS8
MC1R
CHMP1A
RPL13
SPG7
CDK10
VPS9D1
TUBB3
PRDM7
TCF25
CPNE7
DEF8
DBNDD1
SPIRE2
CENPBD1
ZNF276
SPATA2L
SPATA33

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q23.1.

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

Genes
CD74
EBF1
ITK
PDGFRB
LSM11
THG1L
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
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
SGCD
SLC6A7
SLC12A2
SLC22A4
SLC22A5
SNX2
SPARC
SPINK1
SPOCK1
TAF7
TCF7
TCOF1
TGFBI
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
P4HA2
ATG12
CNOT8
HAND1
MED7
MYOT
NRG2
CXCL14
H2AFY
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
SEC24A
FAXDC2
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
KIF3A
SYNPO
ABLIM3
HMGXB3
ARHGAP26
FSTL4
SEPT8
ACSL6
PHF15
LARP1
HARS2
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
HAVCR1
CYFIP2
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
GRAMD3
PCYOX1L
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PSD2
MEGF10
SPINK7
HAVCR2
SMIM3
FCHSD1
LYRM7
CDKN2AIPNL
TIMD4
ZNF300
MYOZ3
PRDM6
FTMT
FNIP1
SLC35A4
MARCH3
SCGB3A2
PPARGC1B
PRRC1
ZNF474
AFAP1L1
GRPEL2
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
CEP120
SLC25A48
SRFBP1
ZMAT2
CCDC112
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
ADAMTS19
SPATA24
DNAJC18
STK32A
AQPEP
SLC36A1
RELL2
SLC36A3
KIF4B
CHSY3
FAM170A
ARSI
IRGM
CATSPER3
NIPAL4
DND1
C5orf48
PROB1
C5orf46
ARHGEF37
SPINK6
ANKHD1
MIR143
MIR145
SPINK14
FNDC9
C5orf56
IGIP
CTXN3
GRXCR2
SPINK9
CCNI2
C5orf52
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 17q12.

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

Genes
RARA
BRCA1
COL1A1
ERBB2
ETV4
LASP1
MLLT6
NF1
TAF15
SUZ12
snoZ178
RN7SL699P
snoU13|ENSG00000238815.1
snoU13|ENSG00000239135.1
HILS1
NXPH3
ZNF652
snoU13|ENSG00000238804.1
SNF8
SNORA68|ENSG00000212565.1
RN7SL125P
HOXB4
HOXB3
HOXB2
HOXB1
U3|ENSG00000200538.1
MIR1203
MIR152
PNPO
KPNB1
MRPL45P2
ITGB3
snoU13|ENSG00000252088.1
RN7SL270P
LRRC37A17P
RNU6ATAC3P
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
ZNF385C
TTC25
RN7SL871P
RN7SL399P
RNA5SP442
EIF1
KRT42P
LINC00974
KRT223P
KRT222
KRT222
RNA5SP441
GJD3
RNY4P8
SNORD124
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
ARL5C
LINC00672
SNORA21|ENSG00000199293.1
SNORA21|ENSG00000252699.1
RPL23
RNA5SP440
CISD3
MIR4726
RN7SL102P
RN7SL458P
SOCS7
HMGB1P24
MIR2909
RNA5SP439
CCL4L2
RN7SL301P
CCL4
CCL18
RN7SKP274
SNORD7
SLFN12L
SLFN5
Vault|ENSG00000252328.1
snoU13|ENSG00000238858.1
RNA5SP438
C17orf75
SH3GL1P1
RNA5SP437
UTP6
RNU6ATAC7P
RN7SL45P
RN7SL79P
EVI2A
RN7SL138P
TEFM
SUZ12P
RN7SL316P
LRRC37BP1
SMURF2P1
SNORD63|ENSG00000252112.1
MIR423
MIR3184
RNY4P13
RNY4P13
snoU13|ENSG00000239129.1
SNORA70|ENSG00000252657.1
MIR4523
TIAF1
ACACA
ASIC2
ACLY
AP2B1
AOC2
ARL4D
ATP5G1
ATP6V0A1
BLMH
FMNL1
CACNB1
CDC6
CDC27
CHAD
CCR7
CNP
CPD
CRHR1
CRYBA1
CSF3
DHX8
DLX3
DLX4
DUSP3
EVI2B
EZH1
GAST
KAT2A
GFAP
GIP
GNGT2
GRB7
GRN
HCRT
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
IFI35
IGFBP4
ITGA2B
ITGA3
ITGB3
JUP
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LHX1
LIG3
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
MYO1D
NAGLU
NFE2L1
NGFR
NME1
NMT1
NSF
OMG
PDK2
PEX12
PHB
MED1
PPY
PSMB3
PYY
PSMD3
PSMD11
RAB5C
RAD51D
RPL19
RPL27
CCL1
CCL2
CCL3
CCL3L1
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL23
SGCA
SLC4A1
SLC6A4
SMARCE1
SP2
STAT3
STAT5A
STAT5B
TADA2A
HNF1B
MLX
THRA
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
PCGF2
ZNF207
RND2
PIP4K2B
SPOP
CNTNAP1
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
ABCC3
CDK5R1
CACNA1G
HAP1
SPAG9
ZNHIT3
EFTUD2
NPEPPS
GOSR1
CCL4L1
GOSR2
NR1D1
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
GJC1
TOB1
PSME3
NBR2
SLC35B1
CALCOCO2
RAMP2
HOXB13
VAT1
LEPREL4
HEXIM1
IGF2BP1
CCT6B
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
KAT7
SYNRG
CASC3
KCNH4
FAM215A
KRT23
TMEM98
TBC1D29
AATF
TUBG2
NKIRAS2
COA3
GIT1
PSMC3IP
SNX11
TBX21
SOST
UTP18
RAPGEFL1
ABI3
COPZ2
MRPL27
ARL17A
CRLF3
SLC25A39
LUC7L3
HIGD1B
CDK12
KRT20
NLE1
FNDC8
MBTD1
CWC25
LINC00483
EPN3
SLFN12
KLHL11
RHOT1
RSAD1
COPRS
LRRC59
ADAP2
GSDMB
CA10
ATXN7L3
PLXDC1
LYZL6
NUFIP2
TAOK1
ARHGAP23
FKBP10
XYLT2
SPATA20
UBE2Z
WNK4
C17orf53
TMUB2
DHX58
MMP28
DHRS11
PRR15L
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
FAM117A
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
RNF135
MIEN1
MRPL45
VPS25
TMEM101
PRAC
RAB11FIP4
GHDC
PPP1R9B
CORO6
TNS4
FBXL20
SSH2
TP53I13
LRRC46
SCRN2
ANKRD40
ZNF830
SLFN11
RASL10B
G6PC3
ASB16
PGAP3
HSPB9
ORMDL3
PLCD3
TMEM106A
LRRC37B
OSBPL7
NT5C3B
ABHD15
RFFL
ZPBP2
SPATA32
HEXIM2
LSM12
CCDC43
TMEM132E
WFIKKN2
B4GALNT2
SPACA3
ANKRD13B
EFCAB13
MRPL10
KRT40
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
WIPF2
KRT25
TMEM99
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
SPPL2C
KRT28
KRT24
ARHGAP27
SAMD14
RDM1
GAS2L2
STH
TAC4
C17orf66
KANSL1
FAM171A2
C17orf104
TTLL6
PIGW
C17orf78
GSDMA
PTRF
KLHL10
MSL1
KRT27
SLFN14
LRRC37A11P
STAC2
KRT26
EFCAB5
TMIGD1
C17orf98
LINC00671
RPRML
KRT39
MYO18A
C17orf102
MIR10A
MIR193A
MIR196A1
TBC1D3B
TBC1D3C
CCL3L3
GPR179
LRRC37A2
FBXO47
TBC1D3G
NME2
MIR632
TBC1D3
TBC1D3H
MIR365B
C17orf96
MIR2117
MIR3185
LRRC3C
ARL17B
C17orf112
MIR4523
MIR4734
MIR4724
MIR4733
MIR4727
MIR4725
MIR5089
PTGES3L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q11.21.

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

Genes
EXT1
COX6C
FGFR1
MYC
PCM1
PLAG1
TCEA1
WRN
RECQL4
NCOA2
WHSC1L1
CHCHD7
HOOK3
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25|ENSG00000251744.1
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
SNORD112|ENSG00000252559.1
TMEM74
RNA5SP275
snoU13|ENSG00000238687.1
RIMS2
MIR3151
RNU6ATAC8P
snoU13|ENSG00000238533.1
snoU13|ENSG00000238372.1
RN7SL563P
NACAP1
RN7SKP249
RN7SL685P
RNU6ATAC41P
MIR1273A
SNORD77|ENSG00000212414.1
RN7SL350P
RN7SKP85
KCNS2
NIPAL2
SNORA72|ENSG00000207067.1
LAPTM4B
U3|ENSG00000207215.1
PTDSS1
snoU13|ENSG00000238791.1
FSBP
RNA5SP274
LINC00535
RN7SKP231
snoU13|ENSG00000239134.1
MIR4661
RN7SL777P
RNA5SP273
LINC00534
RNA5SP272
MMP16
REXO1L10P|ENSG00000255940.1
REXO1L11P
REXO1L10P|ENSG00000270416.1
snoU13|ENSG00000238566.1
SLC10A5
IMPA1P
RN7SL308P
RN7SL107P
SNORA20|ENSG00000206649.1
RN7SL41P
snoU13|ENSG00000238595.1
CASC9
RNA5SP271
U8|ENSG00000200191.1
RN7SL19P
snoU13|ENSG00000238450.1
RNA5SP270
RN7SL675P
RN7SKP29
RNA5SP269
PREX2
RNA5SP268
SNORD87
LINC00967
PDE7A
LINC00966
RN7SKP135
RN7SL135P
NKAIN3
RN7SKP97
CA8
RNA5SP267
SNORA51|ENSG00000206853.1
snoU13|ENSG00000238433.1
LINC00588
RNA5SP266
LINC00968
SDR16C6P
SNORA3|ENSG00000221093.1
SNORD54
RPS20
RN7SL323P
RN7SL798P
SNORA1|ENSG00000199405.1
RNA5SP265
XKR4
RN7SL250P
RNU105C
RNU6ATAC32P
MRPL15
NPBWR1
SNORA7|ENSG00000201316.1
RN7SKP294
UBE2V2
CEBPD
RN7SKP32
LINC00293
RN7SKP41
U3|ENSG00000201329.1
POTEA
RN7SL806P
snoU13|ENSG00000238714.1
SNORD112|ENSG00000238966.1
RN7SL149P
MIR486
SNORD65|ENSG00000238936.1
MIR548AO
IDO1
ADAM3A
ADAM5
SNORD38|ENSG00000207199.1
PLEKHA2
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
RNA5SP264
RN7SKP201
RN7SL457P
RN7SL621P
SNORA70|ENSG00000252505.1
SNORD13
RNA5SP263
RNA5SP262
RNA5SP261
UBXN8
TUBBP1
FAM183CP
LINC00589
RN7SL781P
RNA5SP260
RNA5SP259
MIR4287
snoU13|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13|ENSG00000238466.1
U3|ENSG00000251944.1
SNORA62|ENSG00000201157.1
RNA5SP256
MIR548V
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
LINC00529
MIR598
SNORD112|ENSG00000252565.1
SOX7
RNA5SP252
PRSS51
snoU13|ENSG00000238496.1
snoU13|ENSG00000239065.1
MIR597
U3|ENSG00000252543.1
SNORA70|ENSG00000207244.1
RN7SL178P
SGK223
ALG1L13P
FAM86B3P
LRLE1
FAM85B
FAM90A24P
FAM66E
DEFB105A
DEFB105B
DEFB103B
ZNF705G
FAM66B
XKR5
MIR4659A
AGPAT5
RN7SKP159
RN7SL318P
SNORA70|ENSG00000206661.1
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
NAT1
NAT2
ADCY8
ADRA1A
ADRB3
ANGPT1
ANGPT2
ANK1
ANXA13
ASAH1
ASPH
ATP6V1B2
ATP6V1C1
BAI1
BLK
BMP1
POLR3D
BNIP3L
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CHRNA2
CHRNB3
CLU
CRH
CTSB
CYC1
CYP7A1
CYP11B1
CYP11B2
DECR1
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYS
DPYSL2
DUSP4
E2F5
EEF1D
EGR3
EIF4EBP1
DMTN
EPHX2
CLN8
EXTL3
EYA1
FABP4
FABP5
PTK2B
FDFT1
FGL1
FNTA
ADAM2
GATA4
GEM
GFRA2
GLI4
GML
GNRH1
GPR20
GPT
GRINA
GSR
GTF2E2
NRG1
HNF4G
HSF1
IKBKB
IL7
IMPA1
EIF3E
KCNQ3
LOXL2
LPL
LY6E
LY6H
LYN
MATN2
MCM4
MOS
MSR1
MSRA
MYBL1
NBN
NDUFB9
NEFM
TONSL
NOV
ODF1
TNFRSF11B
OPRK1
PDGFRL
ENPP2
PENK
PLAT
PLEC
PNOC
PMP2
POLB
POLR2K
PPP2CB
PPP2R2A
PPP3CC
PKIA
PRKDC
PTK2
PEX2
RAB2A
RAD21
RP1
RPL7
RPL8
RPL30
SDC2
SDCBP
SFRP1
SFTPC
ST3GAL1
SLA
SLC7A2
SLC18A1
SLC20A2
SNAI2
SNTB1
SPAG1
SQLE
STC1
STK3
TACC1
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
COL14A1
UQCRB
VDAC3
YWHAZ
ZNF7
ZNF16
FZD3
TUSC3
KAT6A
PSCA
FZD6
NSMAF
LY6D
RGS20
TNKS
GPAA1
ADAM18
ADAM9
ADAM7
RIPK2
TNFRSF10D
TNFRSF10C
TNFRSF10B
GGH
CPNE3
FOXH1
CHRNA6
TRPA1
DOK2
ASH2L
CCNE2
EBAG9
MYOM2
DLGAP2
MSC
MFHAS1
KCNB2
CYP7B1
BAG4
ENTPD4
ARHGEF10
MTFR1
LRRC14
EMC2
ST18
TOX
MTSS1
PHYHIP
RB1CC1
ZNF623
KIAA0196
KBTBD11
HHLA1
SORBS3
TRIB1
HRSP12
NPM2
DLC1
NDRG1
CPQ
SPAG11B
LYPLA1
ARFGEF1
KHDRBS3
DCTN6
PNMA2
ADAM28
POP1
AP3M2
COPS5
RBPMS
WWP1
STMN2
ERLIN2
LZTS1
PROSC
ZHX1
PUF60
ZHX2
DENND3
XPO7
TRIM35
ZC3H3
EFR3A
RRS1
SULF1
RHOBTB2
BOP1
DDHD2
KIF13B
PSD3
ZFPM2
HEY1
TRAM1
LEPROTL1
SCRIB
SPIDR
SLC39A14
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
GPR124
KIAA1429
RGS22
FBXL6
FBXO25
OPLAH
PABPC1
KCNV1
STAU2
MTBP
DKK4
AGO2
LSM1
ADAMDEC1
BHLHE22
MRPS28
COMMD5
MRPL13
ATAD2
CNOT7
CPSF1
PURG
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
RMDN1
ZNF706
GOLGA7
VPS28
FAM203A
KCNK9
THEM6
UBR5
SCARA3
FAM49B
AZIN1
ATP6V1H
OTUD6B
TMEM66
CHRAC1
SNTG1
GDAP1
EXOSC4
PDP1
CNGB3
KCTD9
ESRP1
IMPAD1
TMEM70
PINX1
TRMT12
OXR1
WDYHV1
PIWIL2
ELP3
THAP1
ARMC1
INTS10
CCDC25
UBE2W
TMEM55A
SLC39A4
CHD7
SYBU
INTS8
INTS9
CSGALNACT1
HR
PAG1
PBK
ZNF395
BIN3
TEX15
GSDMC
C8orf44
JPH1
C8orf4
ENY2
CPA6
SLURP1
SLC45A4
MTUS1
KIAA1456
ZFAT
KIAA1967
ZNF250
SH2D4A
PRDM14
SNX16
NECAB1
PDLIM2
SOX17
CSMD1
EBF2
FAM160B2
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
MTMR9
DUSP26
DSCC1
DERL1
SLC52A2
HMBOX1
EFCAB1
MCPH1
PPP1R3B
PLEKHF2
ZMAT4
ZFAND1
ZFHX4
GSDMD
RNF122
CSPP1
BAALC
GRHL2
DOCK5
VCPIP1
TTI2
RAB11FIP1
REEP4
ARHGAP39
ZNF34
SLC25A32
DCSTAMP
STMN4
RNF170
SLCO5A1
SHARPIN
SCRT1
SOX7
FAM167A
SLC35G5
CRISPLD1
TRAPPC9
TM2D2
TATDN1
NCALD
SGK196
MAF1
UTP23
GINS4
PPAPDC1B
MAK16
TRIM55
FUT10
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
FAM86B1
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
ERI1
ZNF251
KIFC2
TMEM67
LONRF1
CHMP7
MTDH
CHMP4C
PKHD1L1
NAPRT1
TBC1D31
RP1L1
TP53INP1
TGS1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SMIM19
SLC26A7
PCMTD1
CTHRC1
OSR2
C8orf34
TOP1MT
CLDN23
ZNF572
GOT1L1
FAM92A1
VPS37A
NDUFAF6
TMEM68
ABRA
LYPD2
TMEM71
SGCZ
ADHFE1
UBXN2B
PXDNL
AGPAT6
UNC5D
LETM2
DCAF4L2
RALYL
HGSNAT
DEFB104A
PEBP4
CDCA2
RDH10
C8orf56
ANKRD46
ESCO2
FBXO16
FAM84B
C8orf37
VPS13B
TDRP
ERICH1
SLC7A13
TDH
FAM91A1
C8orf48
MCMDC2
CLVS1
KCNU1
SBSPON
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
ZNF596
IDO2
SDR16C5
ADCK5
TSNARE1
R3HCC1
PRSS55
C8orf74
HTRA4
ADAM32
C8orf47
LGI3
MAPK15
DEFB106A
DEFB107A
DEFB130|ENSG00000232948.1
ATP6V0D2
NEIL2
YTHDF3
C8orf46
REXO1L1
XKR6
NSMCE2
ZNF707
FAM83H
MICU3
C8orf31
ZFP41
SCARA5
TRIQK
DPY19L4
FBXO43
PPP1R42
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
USP17L2
CA13
NUGGC
C8orf86
FAM150A
XKR9
C8orf87
RBM12B
MROH5
MAFA
GDF6
C8orf59
SAMD12
LINC00599
MIR30B
MIR30D
MIR320A
DEFB103A
LRRC24
C8orf22
DEFB107B
DEFB104B
DEFB106B
C8orf58
DEFB135
DEFB136
ZNF704
MBOAT4
SNHG6
MROH6
FABP9
FABP12
SPAG11A
FER1L6
MIR548A3
MIR596
MIR599
MROH1
FAM203B
DEFA1B
ZNF705D
OC90
MIR875
TCF24
LRRC69
ZNF705B
DEFB4B
MIR1205
MIR1207
PVT1
MIR548I3
MIR2053
MIR1208
MIR548H4
MIR3148
MIR4288
MIR4286
MIR3686
MIR548AA1
MIR3622B
MIR3150B
MIR3610
SMIM18
MIR4469
MIR378D2
MIR4662B
MIR4663
MIR4664
MIR4660
MIR4471
MIR4470
MIR5680
MIR5692A2
MIR5194
MIR5708
MIR5681A

Arm-level results

Table 3. Get Full Table Arm-level significance table - 24 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 | -1.53 | 0.986 | 0.25 | 6.72 | 7.33e-11
1q | 1195 | 0.10 | 1.42 | 0.167 | 0.04 | -0.779 | 0.985
2p | 624 | 0.12 | 2.71 | 0.0171 | 0.00 | -2.03 | 0.985
2q | 967 | 0.10 | 1.47 | 0.161 | 0.00 | -2.16 | 0.985
3p | 644 | 0.00 | -1.48 | 0.986 | 0.54 | 18.8 | 0
3q | 733 | 0.00 | -1.5 | 0.986 | 0.54 | 18.5 | 0
4p | 289 | 0.09 | 1.58 | 0.136 | 0.03 | -0.901 | 0.985
4q | 670 | 0.04 | -0.634 | 0.986 | 0.05 | -0.163 | 0.985
5p | 183 | 0.04 | -0.449 | 0.986 | 0.01 | -1.46 | 0.985
5q | 905 | 0.04 | -0.77 | 0.986 | 0.04 | -0.77 | 0.985
6p | 710 | 0.47 | 15.9 | 0 | 0.05 | -0.292 | 0.985
6q | 556 | 0.19 | 4.53 | 2.37e-05 | 0.32 | 9.67 | 0
7p | 389 | 0.11 | 2.44 | 0.0275 | 0.00 | -1.97 | 0.985
7q | 783 | 0.10 | 1.61 | 0.136 | 0.00 | -2.1 | 0.985
8p | 338 | 0.38 | 11.5 | 0 | 0.33 | 9.66 | 0
8q | 551 | 0.68 | 23.9 | 0 | 0.17 | 2.8 | 0.0116
9p | 301 | 0.08 | 1.26 | 0.211 | 0.11 | 2.25 | 0.0497
9q | 700 | 0.07 | 0.437 | 0.59 | 0.09 | 1.37 | 0.316
10p | 253 | 0.00 | -2.04 | 0.986 | 0.01 | -1.54 | 0.985
10q | 738 | 0.00 | -2.19 | 0.986 | 0.01 | -1.72 | 0.985
11p | 509 | 0.12 | 2.45 | 0.0275 | 0.04 | -0.431 | 0.985
11q | 975 | 0.13 | 2.49 | 0.0275 | 0.03 | -1.13 | 0.985
12p | 339 | 0.04 | -0.488 | 0.986 | 0.04 | -0.488 | 0.985
12q | 904 | 0.04 | -0.793 | 0.986 | 0.03 | -1.25 | 0.985
13q | 560 | 0.08 | 0.902 | 0.358 | 0.04 | -0.531 | 0.985
14q | 938 | 0.04 | -0.833 | 0.986 | 0.01 | -1.74 | 0.985
15q | 810 | 0.03 | -1.19 | 0.986 | 0.05 | -0.266 | 0.985
16p | 559 | 0.05 | -0.101 | 0.923 | 0.04 | -0.579 | 0.985
16q | 455 | 0.02 | -1.33 | 0.986 | 0.20 | 5.93 | 1.01e-08
17p | 415 | 0.10 | 1.99 | 0.0657 | 0.03 | -0.937 | 0.985
17q | 972 | 0.11 | 1.98 | 0.0657 | 0.01 | -1.65 | 0.985
18p | 104 | 0.01 | -1.46 | 0.986 | 0.01 | -1.46 | 0.985
18q | 275 | 0.01 | -1.53 | 0.986 | 0.01 | -1.53 | 0.985
19p | 681 | 0.03 | -1.16 | 0.986 | 0.04 | -0.687 | 0.985
19q | 935 | 0.03 | -1.26 | 0.986 | 0.04 | -0.808 | 0.985
20p | 234 | 0.10 | 2.11 | 0.0547 | 0.01 | -1.4 | 0.985
20q | 448 | 0.11 | 2.38 | 0.0293 | 0.00 | -1.99 | 0.985
21q | 258 | 0.18 | 5.25 | 7.95e-07 | 0.03 | -0.734 | 0.985
22q | 564 | 0.07 | 0.802 | 0.394 | 0.00 | -2.07 | 0.985
Xp | 418 | 0.15 | 3.5 | 0.00158 | 0.17 | 4.47 | 2.03e-05
Xq | 668 | 0.13 | 2.78 | 0.0161 | 0.18 | 4.64 | 1.01e-05

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/UVM-TP/14521642/GDAC_MergeDataFiles_12187690/UVM-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 80 Input Tumor Samples.

Tumor Sample Names
TCGA-RZ-AB0B-01A-11D-A39V-01
TCGA-V3-A9ZX-01A-11D-A39V-01
TCGA-V3-A9ZY-01A-11D-A39V-01
TCGA-V4-A9E5-01A-11D-A39V-01
TCGA-V4-A9E7-01A-11D-A39V-01
TCGA-V4-A9E8-01A-11D-A39V-01
TCGA-V4-A9E9-01A-11D-A39V-01
TCGA-V4-A9EA-01A-11D-A39V-01
TCGA-V4-A9EC-01A-11D-A39V-01
TCGA-V4-A9ED-01A-11D-A39V-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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